# pos

id: cord-013784-zhgjmt2j
pos: NNP
token:
  https://media.addgene.org/cms/filer_public/61/16/611619f4-0926-4a07-b5c7-e286a8ecf7f5/broadgpp-sequencing-protocol

lemma:
  https://media.addgene.org/cms/filer_public/61/16/611619f4-0926-4a07-b5c7-e286a8ecf7f5/broadgpp-sequencing-protocol


# ent

id: cord-001270-l8aa9cl3
type: PROTEIN
entity:
  GFP JL8 1 5000 Clontech α tubulin mouse monoclonal antibody 1 8 000 Sigma HA high affinity anti HA antibody rat monoclonal 1 1 000 Roche cat 11867423001


id: cord-103683-xcsal8vk
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 07 01 181735 sha 91b92522bd71deff13dfd6000f6a173bf74eda54 doc_id 103683 cord_uid xcsal8vk


id: cord-198395-v15queyh
type: WORK_OF_ART
entity:
  Incentives And Disincentives For Ridesharing A Behavioral Study Department of Transportation Federal Highway Administration


id: cord-265418-yqe9vdj1
type: CHEMICAL
entity:
  D 1 9 p a t i e n t s E m e r g M i c r o b e s I n f e c t 9 7 6 1 7 7 0 2 0 2 0 a r u y a m a T N a r a K Y o s h i k a w a H S u z u k i N T x k a m e m b e r o f t h e n o n r e c e p t o r t y r o s i n e k i n a s e o f t h e T e c f a m i l y f o r m s a c o m p l e x w i t h p o l y A D P r i b o s e p o l y m e r a s e 1 a n d e l o n g a t i o n f a c t o r 1 a l p


id: cord-288824-sygnmiun
type: WORK_OF_ART
entity:
  Has Implications for the Ancestor of Isolation and Characterization of a Novel Betacoronavirus Subgroup A Coronavirus Rabbit Coronavirus


id: cord-288824-sygnmiun
type: PRODUCT
entity:
  Ecoepidemiology and Complete Genome Comparison of Different Strains of Severe Acute Respiratory Syndrome Related Rhinolophus


id: cord-315483-l6dm82pp
type: DNA
entity:
  SCIentIFIC REPORtS 2018 8 6794 DOI 10 1038 s41598 018 24905 y duck and human IFIT5 Fig 1C One of the structural hallmarks


id: cord-315483-l6dm82pp
type: CELL_LINE
entity:
  42 Immortalized chicken fibroblasts DF 1 human embryonic kidney cells 293T HEK 293T and Madin Darby canine kidney MDCK cells


id: cord-342047-pm3i54mb
type: DNA
entity:
  interleukin IL 1β IL2 IL4 IL6 IL10 IL12 C reactive protein vascular endothelial growth factor VEGF insulin


id: cord-322129-uyswj4ow
type: CARDINAL
entity:
  10 m of great apes ensuring that individuals needing to cough or sneeze ideally leave the area or at least cough sneeze into the crux of their elbows imposing a


id: cord-103638-n5kpvsvg
type: WORK_OF_ART
entity:
  RNA Synthetic Oligonucleotides Inhibit CRISPR Cpf1 Mediated Genome Editing Crystal Structure of Cpf1


id: cord-103892-v6gkubd4
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 06 30 179606 sha 0701f8c95746cc75574183cac58ac451ad3871e4 doc_id 103892 cord_uid v6gkubd4 RNA polymerases RNAPs


id: cord-006034-xfyavk3m
type: DNA
entity:
  reverse fusion primer 5 CCTCTCTATGGG CAGTCGGTGATACGAGCTGACGACARCCATG 3 The PCR amplified 16S V5 V6 amplicons


id: cord-350286-n7ylgqfu
type: GGP
entity:
  bioRxiv DOI 10 1101 2020 03 13 990598 sha 7b1d3cd2210cdb4bb41a1af294cf02bd04f58525 doc_id 350286 cord_uid n7ylgqfu Recently emerged coronavirus designated


id: cord-350286-n7ylgqfu
type: GGP
entity:
  Human SARS CoV 72 99 Graphs in Figures 7A 7B and 7C depict the propensity for disorder in ORF3a proteins


id: cord-350286-n7ylgqfu
type: ORG
entity:
  Noncanonical Transcription Initiation Signals of Severe Acute Respiratory Syndrome Coronavirus Ultrastructure and Origin of Membrane Vesicles Associated


id: cord-350286-n7ylgqfu
type: ORG
entity:
  the Severe Acute Respiratory Syndrome Coronavirus Are Required for Efficient Assembly Trafficking and Release of Virus Like Particles Multiple Nucleic Acid Binding Sites


id: cord-350286-n7ylgqfu
type: ORG
entity:
  Animal Severe Acute Respiratory Syndrome Coronaviruses Disrupts the Functional Expression of Open Reading Frame 8


id: cord-343107-oj1re34k
type: PROTEIN
entity:
  MERS CoV spike glycoprotein date 2019 07 11 journal Nat Commun DOI 10 1038 s41467 019 10897 4 sha 1fb860b35fac03bc319a2d12de832b65ca392c55 doc_id 343107


id: cord-343107-oj1re34k
type: DNA
entity:
  Trp18 Asp20 Pro23 Asp24 Val26 Ser28 Glu188 Ser191 Asn222 Asn226 Lue234 Arg235 and Asn236 We first examined the effects of these NTD mutations


id: cord-343107-oj1re34k
type: ORG
entity:
  Dr Changfa Fan Division of Animal Model Research Institute for Laboratory Animal Resources National Institutes for Food and Drug Control


id: cord-004126-u6ts87ur
type: ORG
entity:
  the Integrated Research Facility Rocky Mountain Laboratories RML Division of Intramural Research DIR


id: cord-004126-u6ts87ur
type: ORG
entity:
  National Institute of Allergy and Infectious Disease NIAID National Institutes of Health NIH Vaccinations


id: cord-342012-1w3x0g42
type: ORG
entity:
  The State Council of The People s Republic of China National Health Commission of People s Republic of China Notice of the General Office of the National Health Commission


id: cord-003318-abs9rvjk
type: DNA
entity:
  Elaeis guineensis XP_010933168 1 85 Musa acuminata subsp Malaccensis XP_009397543 1 83 and Anthurium amnicola JAT62313 1 81


id: cord-003318-abs9rvjk
type: CELL_LINE
entity:
  human cancer cell lines HCT 116 human colon cancer cell line Bel7402 human hepatocellular carcinoma cell line MGC803 human gastric carcinoma cell line


id: cord-288916-i8ukefp8
type: PROTEIN
entity:
  rabbit monoclonal anti STAT1 Cell Signalling mouse monoclonal anti IRF1 BD Transduction Laboratories rabbit polyclonal anti HLA B Thermo Fisher rabbit polyclonal antibody anti ISG15 Cell Signalling mouse monoclonal anti SBP tag


id: cord-103081-k7ev5qkn
type: GGP
entity:
  Macrophage A and Macrophage B Mϕ A Mϕ B Both of 98 these clusters expressed classical macrophage markers


id: cord-103081-k7ev5qkn
type: WORK_OF_ART
entity:
  RNA Sequencing of Adult Kidney Rare Cell Types and Novel Cell States Revealed in Fibrosis Representation


id: cord-103081-k7ev5qkn
type: LAW
entity:
  Comprehensive Integration of Single Cell Data A Transcriptional Map of the Renal Tubule Linking Structure to Function Single Cell Transcriptomics


id: cord-263868-ewnf96cz
type: CHEMICAL
entity:
  DMF 162 8 158 2 158 0 134 5 117 4 115 1 112 7 69 8 69 6 68 1 68 1 61 1 59 3 The pure maleimide biotin


id: cord-013614-j6h338qa
type: GGP
entity:
  c d e p 0 0001 p 0 001 p 0 01 p 0 05 ns p 0 05 although we cannot conclude whether it is a direct or indirect interaction Interestingly consistent with IP MS analysis and genome


id: cord-333145-a20dlaxn
type: DNA
entity:
  paired human immunoglobulin heavy and light chain repertoire 23 Taesung Park 24 Korean Kawasaki Disease Genetics Consortium Taiwan Kawasaki Disease Genetics Consortium Acknowledgements


id: cord-333145-a20dlaxn
type: GGP
entity:
  NC_000006 11 25 5 32 78 Mb and one in the immunoglobulin heavy variable gene IGHV region on chromosome 14q32


id: cord-282566-rgo5sj5i
type: PROTEIN
entity:
  rabbit polyclonal serum anti Nm2C4 3 strain 1 3 000 Alexa Fluor conjugated phalloidin 1 300 and DAPI 0 5 mg ml 1


id: cord-262470-nkql7h9x
type: CELL_TYPE
entity:
  enterocytes pancreatic ductal cells prostate luminal epithelial cells cholangiocytes 51 oligodendrocytes


id: cord-262470-nkql7h9x
type: PROTEIN
entity:
  LID20728 LID20729 LID47030 LID47031 LID47036 LID47037 LID21040 LID21041 LID47032 LID47033 LID20870 LID20871 LID20872 LID20873 LID21183 LID21184 LID21042 LID21043 LID20920 LID20921 LID20924 LID20925 LID20821 LID20822 LID46983 LID46984 LID20819 LID20820 LID21038 LID21039 LID20732 LID20733 LID20868 LID20869


id: cord-262470-nkql7h9x
type: ORG
entity:
  Biogen Idec Boehringer Ingelheim Third Rock Pliant Samumed NuMedii Indaloo Theravance LifeMax Three Lake Partners Optikira


id: cord-262470-nkql7h9x
type: WORK_OF_ART
entity:
  Cardiac Involvement in a Patient With Coronavirus Disease 2019 COVID 19 Association of Coronavirus Disease 2019 COVID 19 With


id: cord-262470-nkql7h9x
type: DISEASE
entity:
  herpes simplex virus type 1 infects enteric neuron and mucosal nerve fibers within the gastrointestinal tract


id: cord-102481-obig3mu1
type: GGP
entity:
  4a c 5 euploid sporadic AD subjects example in Supplementary Fig 14a for complete list of brain samples see Supplementary Table 1


id: cord-346054-k84rcpav
type: PROTEIN
entity:
  monoclonal mouse anti His tag antibody 1 1000 diluted Cat DIA 900 Dianova Hamburg Germany Bound antibodies


id: cord-103915-rzy7mejb
type: DNA
entity:
  anterioposterior AP mediolateral ML 1 AP 1 mm ML 1 5 mm 2 AP 0 5 mm ML 2 5 mm 3 AP 1 5 mm ML 2 5 mm 4 AP 0 5 mm ML 3 5 mm 5 AP 2 0 mm ML 3 5 mm 6 AP 0 5 mm ML 3 5


id: cord-286217-3uklf2u2
type: PROTEIN
entity:
  anti His antibody Merck Millipore USA Cat 05 949 and Coomassie brilliant blue staining Recombinant SARS CoV 2 proteins


id: cord-286217-3uklf2u2
type: GGP
entity:
  coronaviruses i e SARS CoV 12 45 46 and MERS CoV 45 as well as the four known mild human coronaviruses 47 48 i e CoV 229E CoV OC43 CoV HKU 1 and CoV NL63


id: cord-252597-ea78sjcs
type: GGP
entity:
  SARS CoV 2 spike gene S see Table 6 of the Supplementary Material Interestingly 2 out of 3 namely g 24552T C p 997I T


id: cord-013784-zhgjmt2j
type: PROTEIN
entity:
  goat anti mouse secondary antibodies 1 200 Biotium and Hoechst 33342 1 1000 Life Technologies counterstain


id: cord-292862-ezrkg0dc
type: ORG
entity:
  National Heart Lung and Blood Institute Acute Respiratory Distress Syndrome ARDS Clinical Trials Network Randomized


id: cord-284015-vvtv492b
type: DNA
entity:
  14 mammals cat dog horse cow hedgehog human macaque mouse rat Black flying fox Little brown bat Brandt s bat David s myotis and Large flying fox Supplementary Table S2


id: cord-284015-vvtv492b
type: CL
entity:
  stem and crown megabat branches The species tree shown in Fig 1 was used as a guide tree in the analysis Likelihood ratio tests and inspections of the P value were used to compare likelihoods between two models i that assumed the megabat lineages as foreground branches and ii that assumed the dN dS


id: cord-271693-7tg21up3
type: LAW
entity:
  Systematic Evaluation of Molecular Networks for Discovery of Disease Genes Assessment of network module


# url

id: cord-013784-zhgjmt2j
domain: media.addgene.org
url:
  http://media.addgene.org/cms/filer_public/61/16/611619f4-0926-4a07-b5c7-e286a8ecf7f5/broadgpp-sequencing-protocol


# bib

id: cord-001270-l8aa9cl3
title: Antiviral restriction factor transgenesis in the domestic cat
author: Wongsrikeao, Pimprapar
date: 2011-09-11
txt: ./txt/cord-001270-l8aa9cl3.txt
cache: ./cache/cord-001270-l8aa9cl3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006694/
doi: 10.1038/nmeth.1703
summary:
  In contrast to primates, feline species lack antiviral TRIM5α genes 11 but have potently restrictive APOBEC3 proteins 9, 10 , which sets up intriguing possibilities for testing such genes at the whole-animal level, for conferring gene-based immunity with them or engineered variants 12, 13 , and potentially for HIV-1 disease model development 10 . In experiments summarized in Supplementary Table 1 , we subjected 195 in vitro-matured grade I and II domestic cat oocytes to perivitelline space microinjection (PVSMI) with lentiviral vector TSinG 5 ; we performed injection 10-12 h before or 10-12 h after in vitro fertilization (IVF) (Supplementary Fig. 1 ). We consistently observed embryo-pervasive, abundant expression of both proteins encoded by dual gene vectors in cat blastocysts when we injected lentiviral vector before IVF ( Fig. 1b and Supplementary Table 2 ).

abstract:
  Studies of the domestic cat have contributed to many scientific advances, including the present understanding of the mammalian cerebral cortex. A practical capability for cat transgenesis is needed to realize the distinctive potential of research on this neurobehaviorally complex, accessible species for advancing human and feline health. For example, humans and cats are afflicted with pandemic AIDS lentiviruses that are susceptible to species-specific restriction factors. Here we introduced genes encoding such a factor, rhesus macaque TRIMCyp, and eGFP, into the cat germline. The method establishes gamete-targeted transgenesis for the first time in a carnivore. We observed uniformly transgenic outcomes, widespread expression, no mosaicism and no F1 silencing. TRIMCyp transgenic cat lymphocytes resisted feline immunodeficiency virus replication. This capability to experimentally manipulate the genome of an AIDS-susceptible species can be used to test the potential of restriction factors for HIV gene therapy and to build models of other infectious and noninfectious diseases. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nmeth.1703) contains supplementary material, which is available to authorized users.


id: cord-003318-abs9rvjk
title: The enzymatic biosynthesis of acylated steroidal glycosides and their cytotoxic activity
author: Liu, Ming
date: 2018-05-01
txt: ./txt/cord-003318-abs9rvjk.txt
cache: ./cache/cord-003318-abs9rvjk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251810/
doi: 10.1016/j.apsb.2018.04.006
summary:
  Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. We therefore inferred that testosterone (8) was first glycosylated at the 17β-hydroxyl group by OsSGT1 to form T-17β-G (8a), which was then selectively acetylated at C-6 0 of sugar moiety to yield the 6 0 -AT-17β-G (8b) by a soluble bacterial acetyltransferase ( Supplementary Information Fig. S52) . The optimal pH and temperature of OsSGT1-catalyzed reaction using the cell-free extract of BL21(DE3)[pET28a-OsSGT1þp-Gro7] as the biocatalyst were first determined to be alkaline pH value of 11 and 50 1C, respectively (Supplementary Information Fig. S62 ).

abstract:
  Herein we describe the discovery and functional characterization of a steroidal glycosyltransferase (SGT) from Ornithogalum saundersiae and a steroidal glycoside acyltransferase (SGA) from Escherichia coli and their application in the biosynthesis of acylated steroidal glycosides (ASGs). Initially, an SGT gene, designated as OsSGT1, was isolated from O. saundersiae. OsSGT1-containing cell free extract was then used as the biocatalyst to react with 49 structurally diverse drug-like compounds. The recombinant OsSGT1 was shown to be active against both 3β- and 17β-hydroxyl steroids. Unexpectedly, in an effort to identify OsSGT1, we found the bacteria lacA gene in lac operon actually encoded an SGA, specifically catalyzing the acetylations of sugar moieties of steroid 17β-glucosides. Finally, a novel enzymatic two-step synthesis of two ASGs, acetylated testosterone-17-O-β-glucosides (AT-17β-Gs) and acetylated estradiol-17-O-β-glucosides (AE-17β-Gs), from the abundantly available free steroids using OsSGT1 and EcSGA1 as the biocatalysts was developed. The two-step process is characterized by EcSGA1-catalyzed regioselective acylations of all hydroxyl groups on the sugar unit of unprotected steroidal glycosides (SGs) in the late stage, thereby significantly streamlining the synthetic route towards ASGs and thus forming four monoacylates. The improved cytotoxic activities of 3′-acetylated testosterone17-O-β-glucoside towards seven human tumor cell lines were thus observable.


id: cord-004126-u6ts87ur
author: Furuyama, Wakako
date: 2020-01-10
txt: ./txt/cord-004126-u6ts87ur.txt
cache: ./cache/cord-004126-u6ts87ur.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954110/
doi: 10.1038/s41541-019-0155-z
summary:
  Moreover, single vaccination induced cross-protective H5-specific antibodies and protected mice against lethal challenge with various H5 clade 2 viruses, highlighting the potential of the VSV-based HAfl as a pan-H5 influenza virus emergency vaccine. We found that a single vaccination with VSV-vectors expressing the full-length HA (HAfl) induced crossreactive H5-specific antibodies and conferred complete protection against lethal challenge with various H5 clade 2 viruses. In contrast to all the sHA-based vaccines, single doses of the VSV-EBOV-HAfl or VSV-HAfl vectors were sufficient to provide complete protection from lethal homologous H5N1 challenge in mice (Fig. 2) . However, this study did not provide any data supporting an advantage of including VSV-EBOV as part of the vector design over just expressing VSV-HAfl as both vectors performed similarly well with no statistically significant difference in efficacy following single-dose or prime/boost administration (Fig. 2 ) nor in antibody responses (Fig. 3, Table 1 ).

title:
  A single dose of a vesicular stomatitis virus-based influenza vaccine confers rapid protection against H5 viruses from different clades

abstract:
  The avian influenza virus outbreak in 1997 highlighted the potential of the highly pathogenic H5N1 virus to cause severe disease in humans. Therefore, effective vaccines against H5N1 viruses are needed to counter the potential threat of a global pandemic. We have previously developed a fast-acting and efficacious vaccine against Ebola virus (EBOV) using the vesicular stomatitis virus (VSV) platform. In this study, we generated recombinant VSV-based H5N1 influenza virus vectors to demonstrate the feasibility of this platform for a fast-acting pan-H5 influenza virus vaccine. We chose multiple approaches regarding antigen design and genome location to define a more optimized vaccine approach. After the VSV-based H5N1 influenza virus constructs were recovered and characterized in vitro, mice were vaccinated by a single dose or prime/boost regimen followed by challenge with a lethal dose of the homologous H5 clade 1 virus. We found that a single dose of VSV vectors expressing full-length hemagglutinin (HAfl) were sufficient to provide 100% protection. The vaccine vectors were fast-acting as demonstrated by uniform protection when administered 3 days prior to lethal challenge. Moreover, single vaccination induced cross-protective H5-specific antibodies and protected mice against lethal challenge with various H5 clade 2 viruses, highlighting the potential of the VSV-based HAfl as a pan-H5 influenza virus emergency vaccine.


id: cord-006034-xfyavk3m
author: Gil-Cruz, Cristina
date: 2016-10-31
txt: ./txt/cord-006034-xfyavk3m.txt
cache: ./cache/cord-006034-xfyavk3m.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7097164/
doi: 10.1038/ni.3566
summary:
  Moreover, we found that the lack of innate immunological sensing in Myd88-cKO mice did not affect expression of the Ccl19-Cre transgene in CD31 − PDPN + stromal cells of PPs or mLNs (Fig. 1c,d) . Likewise, the expression of other canonical FRC markers was not altered by the absence of MyD88 in EYFP + cells of PPs or mLNs (Fig. 1g) MyD88 signaling in FRCs controls antiviral ILC1 responses To assess whether an invasive enteric pathogen would substantially alter the activity of FRCs, we infected MyD88-sufficient mice and mice with FRC-specific MyD88 deficiency with mouse hepatitis virus (MHV). The accelerated viral control in Myd88-cKO mice as early as on day 3 after infection suggested that innate antiviral immune cells had been activated by the FRC-specific MyD88 deficiency.

title:
  Fibroblastic reticular cells regulate intestinal inflammation via IL-15-mediated control of group 1 ILCs

abstract:
  Fibroblastic reticular cells (FRCs) of secondary lymphoid organs form distinct niches for interaction with hematopoietic cells. We found here that production of the cytokine IL-15 by FRCs was essential for the maintenance of group 1 innate lymphoid cells (ILCs) in Peyer's patches and mesenteric lymph nodes. Moreover, FRC-specific ablation of the innate immunological sensing adaptor MyD88 unleashed IL-15 production by FRCs during infection with an enteropathogenic virus, which led to hyperactivation of group 1 ILCs and substantially altered the differentiation of helper T cells. Accelerated clearance of virus by group 1 ILCs precipitated severe intestinal inflammatory disease with commensal dysbiosis, loss of intestinal barrier function and diminished resistance to colonization. In sum, FRCs act as an 'on-demand' immunological 'rheostat' by restraining activation of group 1 ILCs and thereby preventing immunopathological damage in the intestine. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/ni.3566) contains supplementary material, which is available to authorized users.


id: cord-007073-soov8q3q
author: Wang, Claire Y T
date: 2019-08-13
txt: ./txt/cord-007073-soov8q3q.txt
cache: ./cache/cord-007073-soov8q3q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108192/
doi: 10.1093/cid/ciz761
summary:
  A similar pattern of PeV infection, but with lower incidence rates, was observed in 200 Finnish children enrolled between 1996 and 2007 where by age 12 months 22% had PeV detected in their stools on at least 1 occasion, which increased to 48% approaching their second birthday [15] . We therefore aimed to describe the epidemiology of PeV in the first 2 years of life by the means of an unselected communitybased birth cohort whose recruitment coincided with the first reported outbreak of severe PeV-A3 disease in Australia [5, 19] , and to investigate the risk factors and symptoms associated with acquiring PeV in these young children. The Observational Research in Childhood Infectious Diseases (ORChID) project (ClinicalTrials.gov identifier NCT01304914) is a community-based, longitudinal, birth cohort study of acute respiratory infections (ARIs) and acute gastroenteritis (AGE) in unselected, healthy Australian children in their first 2 years of life [20] [21] [22] [23] .

title:
  Parechovirus A Infections in Healthy Australian Children During the First 2 Years of Life: A Community-based Longitudinal Birth Cohort Study

abstract:
  BACKGROUND: Hospital-based studies identify parechovirus (PeV), primarily PeV-A3, as an important cause of severe infections in young children. However, few community-based studies have been published and the true PeV infection burden is unknown. We investigated PeV epidemiology in healthy children participating in a community-based, longitudinal birth cohort study. METHODS: Australian children (n = 158) enrolled in the Observational Research in Childhood Infectious Diseases (ORChID) study were followed from birth until their second birthday. Weekly stool and nasal swabs and daily symptom diaries were collected. Swabs were tested for PeV by reverse-transcription polymerase chain reaction and genotypes determined by subgenomic sequencing. Incidence rate, infection characteristics, clinical associations, and virus codetections were investigated. RESULTS: PeV was detected in 1423 of 11 124 (12.8%) and 17 of 8100 (0.2%) stool and nasal swabs, respectively. Major genotypes among the 306 infection episodes identified were PeV-A1 (47.9%), PeV-A6 (20.1%), and PeV-A3 (18.3%). The incidence rate was 144 episodes (95% confidence interval, 128–160) per 100 child-years. First infections appeared at a median age of 8 (interquartile range, 6.0–11.7) months. Annual seasonal peaks changing from PeV-A1 to PeV-A3 were observed. Infection was positively associated with age ≥6 months, summer season, nonexclusive breastfeeding at age <3 months, and formal childcare attendance before age 12 months. Sole PeV infections were either asymptomatic (38.4%) or mild (32.7%), while codetection with other viruses in stool swabs was common (64.4%). CONCLUSIONS: In contrast with hospital-based studies, this study showed that diverse and dynamically changing PeV genotypes circulate in the community causing mild or subclinical infections in children. Parechovirus can cause severe illnesses in children. However, studies focus mainly on hospitalized populations. True disease burden in the community remains largely unknown. From our community-based cohort, we found diverse parechovirus genotypes in the community, causing mild or subclinical infections in children.


id: cord-013614-j6h338qa
title: ERCC6L2 promotes DNA orientation-specific recombination in mammalian cells
author: Liu, Xiaojing
date: 2020-04-30
txt: ./txt/cord-013614-j6h338qa.txt
cache: ./cache/cord-013614-j6h338qa.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608219/
doi: 10.1038/s41422-020-0328-3
summary:
  To identify potentially new NHEJ factors, we combined chemical perturbation screens on 36 compounds with focused CRISPRknockout screens on 414 genes in the CH12 B cell line ( Fig. 1a ; Supplementary information, Table S1 , see Materials and Methods for details). ERCC6L2 clusters with other NHEJ factors Next, we clustered all 414 DNA repair genes by their z-scores across the 36 chemicals used, which categorized genes into three major groups depending on their impact on cell growth (Supplementary information, Fig. S1a ). Furthermore, the helicase catalytic-dead (DEAH > AAAH) mutant did not promote CSR ( Fig. 3a ; Supplementary information, Fig. S4b ), indicating that ERCC6L2''s predicted catalytic activity is required for DNA end-joining. To bypass the B cell development defect of core-NHEJ factor deficiencies and quickly access the directional CSR, we deleted the non-productive IgH allele in CH12F3 cells as previous described 18 (Supplementary information, Fig. S8c , named CH12-NCDel cells) and perform HTGTS assay with endogenous AID Sμ baits.

abstract:
  Programmed DNA recombination in mammalian cells occurs predominantly in a directional manner. While random DNA breaks are typically repaired both by deletion and by inversion at approximately equal proportions, V(D)J and class switch recombination (CSR) of immunoglobulin heavy chain gene overwhelmingly delete intervening sequences to yield productive rearrangement. What factors channel chromatin breaks to deletional CSR in lymphocytes is unknown. Integrating CRISPR knockout and chemical perturbation screening we here identify the Snf2-family helicase-like ERCC6L2 as one such factor. We show that ERCC6L2 promotes double-strand break end-joining and facilitates optimal CSR in mice. At the cellular levels, ERCC6L2 rapidly engages in DNA repair through its C-terminal domains. Mechanistically, ERCC6L2 interacts with other end-joining factors and plays a functionally redundant role with the XLF end-joining factor in V(D)J recombination. Strikingly, ERCC6L2 controls orientation-specific joining of broken ends during CSR, which relies on its helicase activity. Thus, ERCC6L2 facilitates programmed recombination through directional repair of distant breaks.


id: cord-013658-vygiate7
author: Yang, Jian
date: 2020-06-01
txt: ./txt/cord-013658-vygiate7.txt
cache: ./cache/cord-013658-vygiate7.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608266/
doi: 10.1038/s41396-020-0689-0
summary:
  Within saline lakes, a considerable amount of DOC is originated from terrestrially derived dissolved organic matter (tDOM) from surrounding soils [5] , and may undergo extensive transformations by lacustrine microbial communities [6] . To address these knowledge gaps, the linkage between aquatic microbial communities and the degradation potentials of tDOM in the QTP lakes of different salinity was investigated in this study by performing microcosm experiments and using a suite of analytical techniques. In the meanwhile, distinct microbial taxa appeared to be responsible for the transformation of tDOM among different lakes, as evidenced by abundance increases of lake-specific OTUs after microcosm incubations (Supplementary Table S2 ). In this study, the relative abundances of certain copiotrophic OTUs showed a dramatic increase (>10 times) in response to the addition of tDOM during microcosm incubations of two saline lake (TSL and XCDL) samples (Supplementary Table S2 ).

title:
  Potential utilization of terrestrially derived dissolved organic matter by aquatic microbial communities in saline lakes

abstract:
  Lakes receive large amounts of terrestrially derived dissolved organic matter (tDOM). However, little is known about how aquatic microbial communities interact with tDOM in lakes. Here, by performing microcosm experiments we investigated how microbial community responded to tDOM influx in six Tibetan lakes of different salinities (ranging from 1 to 358 g/l). In response to tDOM addition, microbial biomass increased while dissolved organic carbon (DOC) decreased. The amount of DOC decrease did not show any significant correlation with salinity. However, salinity influenced tDOM transformation, i.e., microbial communities from higher salinity lakes exhibited a stronger ability to utilize tDOM of high carbon numbers than those from lower salinity. Abundant taxa and copiotrophs were actively involved in tDOM transformation, suggesting their vital roles in lacustrine carbon cycle. Network analysis indicated that 66 operational taxonomic units (OTUs, affiliated with Alphaproteobacteria, Actinobacteria, Bacteroidia, Bacilli, Gammaproteobacteria, Halobacteria, Planctomycetacia, Rhodothermia, and Verrucomicrobiae) were associated with degradation of CHO compounds, while four bacterial OTUs (affiliated with Actinobacteria, Alphaproteobacteria, Bacteroidia and Gammaproteobacteria) were highly associated with the degradation of CHOS compounds. Network analysis further revealed that tDOM transformation may be a synergestic process, involving cooperation among multiple species. In summary, our study provides new insights into a microbial role in transforming tDOM in saline lakes and has important implications for understanding the carbon cycle in aquatic environments.


id: cord-013784-zhgjmt2j
author: Tang, Min
date: 2020-06-04
txt: ./txt/cord-013784-zhgjmt2j.txt
cache: ./cache/cord-013784-zhgjmt2j.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7608409/
doi: 10.1038/s41422-020-0338-1
summary:
  To move beyond serum-free sphere culture-based models, we utilized a DLP-based rapid 3D bioprinting system to generate 3D tri-culture or tetra-culture glioblastoma tissue models, with a background "normal brain" made up of NPCs and astrocytes and a tumor mass generated by GSCs, with or without macrophage, using brain-specific extracellular matrix (ECM) materials (Fig. 1a ). 35 While patient-derived glioblastoma cells grown under serum-free conditions enrich for stem-like tumor cells (GSCs) that form spheres and more closely replicate transcriptional profiles and invasive potential than standard culture conditions, we previously demonstrated that spheres display differential transcriptional profiles and cellular dependencies in an RNA interference screen compared to in vivo xenografts. [49] [50] [51] g Therapeutic efficacy prediction of drugs in all cancer cells in the CTRP dataset based on differentially expressed genes between the 3D tetra-culture model and GSCs grown in sphere culture as defined by RNA-seq.

title:
  Three-dimensional bioprinted glioblastoma microenvironments model cellular dependencies and immune interactions

abstract:
  Brain tumors are dynamic complex ecosystems with multiple cell types. To model the brain tumor microenvironment in a reproducible and scalable system, we developed a rapid three-dimensional (3D) bioprinting method to construct clinically relevant biomimetic tissue models. In recurrent glioblastoma, macrophages/microglia prominently contribute to the tumor mass. To parse the function of macrophages in 3D, we compared the growth of glioblastoma stem cells (GSCs) alone or with astrocytes and neural precursor cells in a hyaluronic acid-rich hydrogel, with or without macrophage. Bioprinted constructs integrating macrophage recapitulate patient-derived transcriptional profiles predictive of patient survival, maintenance of stemness, invasion, and drug resistance. Whole-genome CRISPR screening with bioprinted complex systems identified unique molecular dependencies in GSCs, relative to sphere culture. Multicellular bioprinted models serve as a scalable and physiologic platform to interrogate drug sensitivity, cellular crosstalk, invasion, context-specific functional dependencies, as well as immunologic interactions in a species-matched neural environment.


id: cord-015527-ph576eji
author: Mostajo, Nelly F
date: 2019-09-30
txt: ./txt/cord-015527-ph576eji.txt
cache: ./cache/cord-015527-ph576eji.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108008/
doi: 10.1093/nargab/lqz006
summary:
  Although we performed mappings, read countings, and normalization for all samples, bat genome assemblies and all six data sets ( Table 2 ; overall 1568 mappings), we only selected one comparison per data set to exemplarily show novel and significantly differential expressed ncRNAs (Supplementary Files S2.1-S2.15; divided by data set and input annotation). To give a better estimation of transcribed and potentially functional ncRNAs, we used six Illumina short-read RNA-Seq data sets derived from four bat species (Table 2) to estimate the expression levels of our novel annotations. To this end, we used the RNA-Seq data sets Field-2015 , Field-2018 , Hölzer-2019 and Weber-2019 (Table 2 ) as a basis to identify DE ncRNAs that were newly discovered in this study and were not part of the current NCBI or Ensembl genome annotations for this bat species.

title:
  A comprehensive annotation and differential expression analysis of short and long non-coding RNAs in 16 bat genomes

abstract:
  Although bats are increasingly becoming the focus of scientific studies due to their unique properties, these exceptional animals are still among the least studied mammals. Assembly quality and completeness of bat genomes vary a lot and especially non-coding RNA (ncRNA) annotations are incomplete or simply missing. Accordingly, standard bioinformatics pipelines for gene expression analysis often ignore ncRNAs such as microRNAs or long antisense RNAs. The main cause of this problem is the use of incomplete genome annotations. We present a complete screening for ncRNAs within 16 bat genomes. NcRNAs affect a remarkable variety of vital biological functions, including gene expression regulation, RNA processing, RNA interference and, as recently described, regulatory processes in viral infections. Within all investigated bat assemblies, we annotated 667 ncRNA families including 162 snoRNAs and 193 miRNAs as well as rRNAs, tRNAs, several snRNAs and lncRNAs, and other structural ncRNA elements. We validated our ncRNA candidates by six RNA-Seq data sets and show significant expression patterns that have never been described before in a bat species on such a large scale. Our annotations will be usable as a resource (rna.uni-jena.de/supplements/bats) for deeper studying of bat evolution, ncRNAs repertoire, gene expression and regulation, ecology and important host–virus interactions.


id: cord-024810-z323cl40
author: Wicaksono, Irmandy
date: 2020-04-23
txt: ./txt/cord-024810-z323cl40.txt
cache: ./cache/cord-024810-z323cl40.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222957/
doi: 10.1038/s41528-020-0068-y
summary:
  Here, we have developed a tailored, electronic textile conformable suit (E-TeCS) to perform large-scale, multimodal physiological (temperature, heart rate, and respiration) sensing in vivo. Similar to a compression shirt, the soft and stretchable nature of the tailored E-TeCS allows intimate contact between electronics and the skin with a pressure value of around ~25 mmHg, allowing for physical comfort and improved precision of sensor readings on skin. Through this work, we have developed a technique of combining thin, customizable conformable electronic devices, including interconnect lines and off-the-shelf integrated circuits, with plastic substrates that can be woven into knitted textile using an accessible and high-throughput manufacturing approach. We demonstrate the capability of our electronic textile conformable suit (E-TeCS) for distributed, wireless physiological sensing, such as temperature, respiration and heart-rate detection, and physical activity monitoring around the human body during a physical exercise.

title:
  A tailored, electronic textile conformable suit for large-scale spatiotemporal physiological sensing in vivo

abstract:
  The rapid advancement of electronic devices and fabrication technologies has further promoted the field of wearables and smart textiles. However, most of the current efforts in textile electronics focus on a single modality and cover a small area. Here, we have developed a tailored, electronic textile conformable suit (E-TeCS) to perform large-scale, multimodal physiological (temperature, heart rate, and respiration) sensing in vivo. This platform can be customized for various forms, sizes and functions using standard, accessible and high-throughput textile manufacturing and garment patterning techniques. Similar to a compression shirt, the soft and stretchable nature of the tailored E-TeCS allows intimate contact between electronics and the skin with a pressure value of around ~25 mmHg, allowing for physical comfort and improved precision of sensor readings on skin. The E-TeCS can detect skin temperature with an accuracy of 0.1 °C and a precision of 0.01 °C, as well as heart rate and respiration with a precision of 0.0012 m/s(2) through mechano-acoustic inertial sensing. The knit textile electronics can be stretched up to 30% under 1000 cycles of stretching without significant degradation in mechanical and electrical performance. Experimental and theoretical investigations are conducted for each sensor modality along with performing the robustness of sensor-interconnects, washability, and breathability of the suit. Collective results suggest that our E-TeCS can simultaneously and wirelessly monitor 30 skin temperature nodes across the human body over an area of 1500 cm(2), during seismocardiac events and respiration, as well as physical activity through inertial dynamics.


id: cord-102481-obig3mu1
author: Alić, Ivan
date: 2020-01-31
txt: ./txt/cord-102481-obig3mu1.txt
cache: ./cache/cord-102481-obig3mu1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.01.29.918037
doi: 10.1101/2020.01.29.918037
summary:
  The validity of this prediction was tested by an independent biochemical method (ELISA), by measuring the Aβ-peptide concentrations within the isogenic T21:D21 organoid CM comparison, which showed an increase in absolute concentrations caused by T21 for each Aβ 1-38, 1-40 and 1-42, with no difference in the Aβ 1-42/1-40 ratio between T21 and isogenic D21 lines, mirroring the readout in the absolute levels of IP-MS peaks ( Supplementary Fig. 6 ). Pearson''s coefficient showed a high level of colocalisation (>0.55) of both the main substrate (Aβx-40) and its putative degradation product (Aβx-34) with BACE2 in neurons of cerebral organoids, in LAMP2+ compartment (known to be a subset of lyzosomes, therefore low pH vesicles) ( Fig. 3 & Supplementary Fig. 8 ). Our data in Figs.1 and Supplementary Fig. 7 suggest that anti-amyloidogenic activity of BACE2 is gene-dose dependent, and its level varies between individuals, with SNP allelic differences in BACE2 correlating with age of dementia onset.

title:
  “Patient-specific Alzheimer-like pathology in trisomy 21 cerebral organoids reveals BACE2 as a gene-dose-sensitive AD-suppressor in human brain”

abstract:
  A population of >6 million people worldwide at high risk of Alzheimer’s disease (AD) are those with Down Syndrome (DS, caused by trisomy 21 (T21)), 70% of whom develop dementia during lifetime, caused by an extra copy of β-amyloid-(Aβ)-precursor-protein gene. We report AD-like pathology in cerebral organoids grown in vitro from non-invasively sampled strands of hair from 71% of DS donors. The pathology consisted of extracellular diffuse and fibrillar Aβ deposits, hyperphosphorylated/pathologically conformed Tau, and premature neuronal loss. Presence/absence of AD-like pathology was donor-specific (reproducible between individual organoids/iPSC lines/experiments). Pathology could be triggered in pathology-negative T21 organoids by CRISPR/Cas9-mediated elimination of the third copy of chromosome-21-gene BACE2, but prevented by combined chemical β and γ-secretase inhibition. We found that T21-organoids secrete increased proportions of Aβ-preventing (Aβ1-19) and Aβ-degradation products (Aβ1-20 and Aβ1-34). We show these profiles mirror in cerebrospinal fluid of people with DS. We demonstrate that this protective mechanism is mediated by BACE2-trisomy and cross-inhibited by clinically trialled BACE1-inhibitors. Combined, our data prove the physiological role of BACE2 as a dose-sensitive AD-suppressor gene, potentially explaining the dementia delay in ∼30% of people with DS. We also show that DS cerebral organoids could be explored as pre-morbid AD-risk population detector and a system for hypothesis-free drug screens as well as identification of natural suppressor genes for neurodegenerative diseases.


id: cord-103081-k7ev5qkn
author: Janosevic, Danielle
date: 2020-05-30
txt: ./txt/cord-103081-k7ev5qkn.txt
cache: ./cache/cord-103081-k7ev5qkn.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.05.27.118620
doi: 10.1101/2020.05.27.118620
summary:
  Note that the expression of cluster-defining markers varied significantly during the injury and 63 recovery phases of sepsis ( Fig. S1b; Supplementary Table 1 ). One of the subclusters showed 112 increased expression of alternatively activated macrophages (M2) markers such as Arg1 113 (Arginase 1) and Mrc1 (Cd206) 27 at later time points (36 hours, Supplementary Fig. 4b) . Such 181 communication patterns among these four cell types may also explain macrophage clustering 182 around S1 tubules at later time points in sepsis as we previously reported 13 . To this end, we selected the differentially expressed genes from all cells combined (pseudo 203 bulk) for each time point across the mouse sepsis timeline (Supplementary Table 4) . Our data 215 cover nearly all renal cell types and are time-anchored, thus providing a detailed and precise 216 view of the evolution of sepsis in the kidney at the cellular and molecular level.

title:
  The orchestrated cellular and molecular responses of the kidney to endotoxin define the sepsis timeline

abstract:
  Clinical sepsis is a highly dynamic state that progresses at variable rates and has life-threatening consequences. Staging patients along the sepsis timeline requires a thorough knowledge of the evolution of cellular and molecular events at the tissue level. Here, we investigated the kidney, an organ central to the pathophysiology of sepsis. Single cell RNA sequencing revealed the involvement of various cell populations in injury and repair to be temporally organized and highly orchestrated. We identified key changes in gene expression that altered cellular functions and can explain features of clinical sepsis. These changes converged towards a remarkable global cell-cell communication failure and organ shutdown at a well-defined point in the sepsis timeline. Importantly, this time point was also a transition towards the emergence of recovery pathways. This rigorous spatial and temporal definition of murine sepsis will uncover precise biomarkers and targets that can help stage and treat human sepsis.


id: cord-103638-n5kpvsvg
author: Nguyen, Long T.
date: 2020-04-14
txt: ./txt/cord-103638-n5kpvsvg.txt
cache: ./cache/cord-103638-n5kpvsvg.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.13.036079
doi: 10.1101/2020.04.13.036079
summary:
  By extending the 3''or 5''-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes. However, the ENHANCE showed 5.4-fold and 3.4-fold and higher trans-cleavage activity compared to the wild-type crRNA for targeting the methylated dsDNA and ssDNA, respectively (Fig. 3e, Supplementary Fig. 20a) . While no clinical samples were tested, the results indicated the 3''DNA7-modified crRNA consistently demonstrated higher sensitivity for detecting CoV-2 dsDNA within 30 minutes as compared to the wild-type crCoV-2 ( Supplementary Figs.

title:
  Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection

abstract:
  The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3’- or 5’-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes.


id: cord-103683-xcsal8vk
title: The structure of enteric human adenovirus 41 - a leading cause of diarrhea in children
author: Rafie, K.
date: 2020-10-16
txt: ./txt/cord-103683-xcsal8vk.txt
cache: ./cache/cord-103683-xcsal8vk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.07.01.181735
doi: 10.1101/2020.07.01.181735
summary:
  The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Compared to the two other reported structures of human adenoviruses, HAdV-C5 (PDB: 6B1T (20) ) and HAdV-D26 (PDB: 5TX1(21)), the sequence identity of the capsid proteins ranges from 30-80% (Supplementary Table 3 ). The HAdV-F41 penton base undergoes assembly-induced conformational changes Located on the five-fold symmetry axes of adenovirus capsids, the penton base (PB) protein forms a homopentamer that contains integrin-binding motifs and serves as an assembly hub connecting the icosahedral capsid to the fibers (Fig. 1A) . The DNA-binding protein V is located at a conserved position at the inner face of the capsid After initial model building of the virion at pH=7.4, the asymmetric unit contained five peptide chains that still had not been assigned an identity.

abstract:
  Human adenovirus (HAdV) types F40 and F41 are a prominent cause of diarrhea and diarrhea-associated mortality in young children worldwide. These enteric HAdVs differ strikingly in tissue tropism and pathogenicity from respiratory and ocular adenoviruses, but the structural basis for this divergence has been unknown. Here we present the first structure of an enteric HAdV - HAdV-F41 - determined by cryo-EM to a resolution of 3.8Å. The structure reveals extensive alterations to the virion exterior as compared to non-enteric HAdVs, including a unique arrangement of capsid protein IX. The structure also provides new insights into conserved aspects of HAdV architecture such as a proposed location of protein V, which links the viral DNA to the capsid, and assembly-induced conformational changes in the penton base protein. Our findings provide the structural basis for adaptation to a fundamentally different tissue tropism of enteric HAdVs.


id: cord-103892-v6gkubd4
title: The mechanism of the nucleo-sugar selection by multi-subunit RNA polymerases
author: Mäkinen, Janne J.
date: 2020-07-01
txt: ./txt/cord-103892-v6gkubd4.txt
cache: ./cache/cord-103892-v6gkubd4.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.06.30.179606
doi: 10.1101/2020.06.30.179606
summary:
  Overall, these data demonstrated that the enhanced or diminished capabilities of the variant RNAPs to utilize 2''dGTP in the SNA assays reflected, in qualitative terms, their capabilities to utilize all four 2''dNTPs. The role of the β''Arg425 in selectively promoting the binding of NTPs was easy to explain because the β''Arg425 interacts with the 2''OH of the NTP analogues in several RNAP structures (Supplementary Table 5 , Fig. 1c, 4a, b) . We further hypothesized and demonstrated by in silico docking experiments that the 3''OH could move to within the hydrogen bond distance of the β''Arg425 if the deoxyribose moiety adopted a 2''-endo conformation (Supplementary Fig. 8 To test this hypothesis in crystallo, we solved the X-ray crystal structure of the initially transcribing complexes containing T. Overall, the comparative analysis of RNAP structures with CMPCPP, 2''dCTP and 3''dCTP suggested that the β''Arg425 inhibited the incorporation of 2''dNTPs by interacting with their 3''OH group and favoring the 2''-endo conformation of the deoxyribose moiety.

abstract:
  RNA polymerases (RNAPs) synthesize RNA from NTPs, whereas DNA polymerases synthesize DNA from 2’dNTPs. DNA polymerases select against NTPs by using steric gates to exclude the 2’ OH, but RNAPs have to employ alternative selection strategies. In single-subunit RNAPs, a conserved Tyr residue discriminates against 2’dNTPs, whereas selectivity mechanisms of multi-subunit RNAPs remain hitherto unknown. Here we show that a conserved Arg residue uses a two-pronged strategy to select against 2’dNTPs in multi-subunit RNAPs. The conserved Arg interacts with the 2’OH group to promote NTP binding, but selectively inhibits incorporation of 2’dNTPs by interacting with their 3’OH group to favor the catalytically-inert 2’-endo conformation of the deoxyribose moiety. This deformative action is an elegant example of an active selection against a substrate that is a substructure of the correct substrate. Our findings provide important insights into the evolutionary origins of biopolymers and the design of selective inhibitors of viral RNAPs.


id: cord-103915-rzy7mejb
author: Duricki, Denise A.
date: 2018-07-11
txt: ./txt/cord-103915-rzy7mejb.txt
cache: ./cache/cord-103915-rzy7mejb.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/367573
doi: 10.1101/367573
summary:
  We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. We also recently showed that injection of an adeno-associated viral vector (AAV) encoding full-length human NT3 (preproNT3, 30kDa) into forelimb muscles 24 hours after stroke in adult or elderly rats improved sensorimotor recovery 19 . We examined anatomical neuroplasticity in the C7 cervical spinal cord because we knew from experiments using adult and elderly rats that the less-affected corticospinal tract sprouts at this level (as well as other levels) after injection of AAV-NT3 into muscles including triceps brachii 19 . fMRI performed one week after stroke confirmed that somatosensory cortex was not active when the affected paw was stimulated in either vehicle or NT3 treated rats (p>0.05, Supplementary Fig. 6b ). Treatment of disabled arm muscles with NT3 protein, initiated 24 hours after stroke, caused changes in multiple locomotor circuits, and promoted a progressive recovery of sensory and motor function in rats.

title:
  Corticospinal neuroplasticity and sensorimotor recovery in rats treated by infusion of neurotrophin-3 into disabled forelimb muscles started 24 h after stroke

abstract:
  Stroke often leads to arm disability and reduced responsiveness to stimuli on the other side of the body. Neurotrophin-3 (NT3) is made by skeletal muscle during infancy but levels drop postnatally and into adulthood. It is essential for the survival and wiring-up of sensory afferents from muscle. We have previously shown that gene therapy delivery of human NT3 into the affected triceps brachii forelimb muscle improves sensorimotor recovery after ischemic stroke in adult and elderly rats. Here, to move this therapy one step nearer to the clinic, we set out to test the hypothesis that intramuscular infusion of NT3 protein could improve sensorimotor recovery after ischemic cortical stroke in adult rats. To simulate a clinically-feasible time-to-treat, twenty-four hours later rats were randomized to receive NT3 or vehicle by infusion into triceps brachii for four weeks using implanted minipumps. NT3 increased the accuracy of forelimb placement during walking on a horizontal ladder and increased use of the affected arm for lateral support during rearing. NT3 also reversed sensory deficits on the affected forearm. There was no evidence of forepaw sensitivity to cold stimuli after stroke or NT3 treatment. MRI confirmed that treatment did not induce neuroprotection. Functional MRI during low threshold electrical stimulation of the affected forearm showed an increase in peri-infarct BOLD signal with time in both stroke groups and indicated that neurotrophin-3 did not further increase peri-infarct BOLD signal. Rather, NT3 induced spinal neuroplasticity including sprouting of the spared corticospinal and serotonergic pathways. Neurophysiology showed that NT3 treatment increased functional connectivity between the corticospinal tracts and spinal circuits controlling muscles on the treated side. After intravenous injection, radiolabelled NT3 crossed from bloodstream into the brain and spinal cord in adult mice with or without strokes. Our results show that delayed, peripheral infusion of neurotrophin-3 can improve sensorimotor function after ischemic stroke. Phase I and II clinical trials of NT3 (for constipation and neuropathy) have shown that peripheral, high doses are safe and well tolerated, which paves the way for NT3 as a therapy for stroke.


id: cord-198395-v15queyh
title: Incentive-driven discontinuous transition to high ride-sharing adoption
author: Storch, David-Maximilian
date: 2020-08-25
txt: ./txt/cord-198395-v15queyh.txt
cache: ./cache/cord-198395-v15queyh.txt
extension: .txt
mime: text/plain
url: https://arxiv.org/pdf/2008.11079v1.pdf
doi: nan
summary:
  Fraction of shared ride requests from different origins (red) served by the four major for-hire vehicle transportation service providers in New York City by destination zone (January -December 2019) [27] . To understand how these incentives determine the adoption of ride-sharing, we study sharing decisions in a stylized city network [30] with a common origin o (e.g., from a central downtown location) in the center and multiple destinations d (illustrated in Fig. 3 ). a,b Sharing decisions for New York City and Chicago (blue dots) accumulate on two branches corresponding to the predicted high-and low-sharing regime as a function of request rate (compare Fig. 4) . The data is provided by New York City''s Taxi & Limousine Commission (TLC) [27] and consists of origin and destination zone per request, pickup and dropoff times, as well as a shared request tag, denoting a request for a single or shared ride.

abstract:
  Ride-sharing - the combination of multiple trips into one - may substantially contribute towards sustainable urban mobility. It is most efficient at high demand locations with many similar trip requests. However, here we reveal that people's willingness to share rides does not follow this trend. Modeling the fundamental incentives underlying individual ride-sharing decisions, we find two opposing adoption regimes, one with constant and one with decreasing adoption as demand increases. In the high demand limit, the transition between these regimes becomes discontinuous, switching abruptly from low to high ride-sharing adoption. Analyzing over 360 million ride requests in New York City and Chicago illustrates that both regimes coexist across the cities, consistent with our model predictions. These results suggest that current incentives for ride-sharing may be near the boundary to the high-sharing regime such that even a moderate increase in the financial incentives may significantly increase ride-sharing adoption.


id: cord-252597-ea78sjcs
author: Ramazzotti, Daniele
date: 2020-10-19
txt: ./txt/cord-252597-ea78sjcs.txt
cache: ./cache/cord-252597-ea78sjcs.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.22.044404
doi: 10.1101/2020.04.22.044404
summary:
  Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. The outbreak of coronavirus disease 2019 (COVID19) , which started in late 2019 in Wuhan (China) [1, 2] and was declared pandemic by the World Health Organization, is fueling the publication of an increasing number of studies aimed at exploiting the information provided by the viral genome of SARS-CoV-2 virus to identify its proximal origin, characterize the mode and timing of its evolution, as well as to define descriptive and predictive models of geographical spread and evaluate the related clinical impact [3, 4, 5] .

title:
  VERSO: a comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples

abstract:
  A global cross-discipline effort is ongoing to characterize the evolution of SARS-CoV-2 virus and generate reliable epidemiological models of its diffusion. To this end, phylogenomic approaches leverage accumulating genomic mutations to track the evolutionary history of the virus and benefit from the surge of sequences deposited in public databases. Yet, such methods typically rely on consensus sequences representing the dominant virus lineage, whereas a complex intra-host genomic composition is often observed within single hosts. Furthermore, most approaches might produce inaccurate results with noisy data and sampling limitations, as witnessed in most countries affected by the epidemics. We introduce VERSO (Viral Evolution ReconStructiOn), a new comprehensive framework for the characterization of viral evolution and transmission from sequencing data of viral genomes. Our probabilistic approach first delivers robust phylogenetic models from clonal variant profiles and then exploits variant frequency patterns to characterize and visualize the intra-host genomic diversity of samples, which may reveal uncovered infection events. We prove via extensive simulations that VERSO outperforms the state-of-the-art tools for phylogenetic inference, also in condition of noisy observations and sampling limitations. The application of our approach to 3960 SARS-CoV-2 samples from Amplicon sequencing and to 2766 samples from RNA-sequencing unravels robust phylogenomic models, improving the current knowledge on SARS-CoV-2 evolution and spread. Importantly, by exploiting co-occurrence patterns of minor variants, VERSO allows us to reveal uncovered infection paths, which are validated with contact tracing data. Moreover, the in-depth analysis of the mutational landscape of SARS-CoV-2 confirms a statistically significant increase of genomic diversity in time and allows us to identify a number of variants that are transiting from minor to clonal state in the population, as well as several homoplasies, some of which might indicate ongoing positive selection processes. Overall, the results show that the joint application of our framework and data-driven epidemiological models might improve currently available strategies for pathogen surveillance and analysis. VERSO is released as an open source tool at https://github.com/BIMIB-DISCo/VERSO.


id: cord-256652-ent4vu3z
author: Tan, Joshua
date: 2018-03-19
txt: ./txt/cord-256652-ent4vu3z.txt
cache: ./cache/cord-256652-ent4vu3z.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/nm.4513
doi: 10.1038/nm.4513
summary:
  investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. These findings, combined with data from peptide array experiments ( Supplementary Fig. 7) , identify the N-terminal junction binding site of the most potent neutralizing antibodies as including the first unit of the NANP repeat region and flanking non-repeat sequences, providing a molecular basis for the dual specificity of these antibodies.

title:
  A public antibody lineage that potently inhibits malaria infection by dual binding to the circumsporozoite protein

abstract:
  Immunization with attenuated Plasmodium falciparum sporozoites (PfSPZ) has been shown to be protective, but the features of the antibody response induced by this treatment remain unclear. To investigate this response at high resolution, we isolated IgM and IgG monoclonal antibodies from Tanzanian volunteers who were immunized by repeated injection of irradiated PfSPZ and who were found to be protected from controlled human malaria infection (CHMI) with infectious homologous PfSPZ. All IgG monoclonals isolated bound to P. falciparum circumsporozoite protein (PfCSP) and recognized distinct epitopes in the N-terminus, NANP repeat region, and C-terminus. Strikingly, the most effective antibodies, as assessed in a humanized mouse model, bound not only to the repeat region, but also to a minimal peptide at the PfCSP N-terminal junction that is not in the RTS,S vaccine. These dual-specific antibodies were isolated from different donors and used VH3-30 or VH3-33 alleles carrying tryptophan or arginine at position 52. Using structural and mutational data, we describe the elements required for germline recognition and affinity maturation. Our study provides potent neutralizing antibodies and relevant information for lineage-targeted vaccine design and immunization strategies.


id: cord-262470-nkql7h9x
author: Muus, Christoph
date: 2020-04-20
txt: ./txt/cord-262470-nkql7h9x.txt
cache: ./cache/cord-262470-nkql7h9x.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.19.049254
doi: 10.1101/2020.04.19.049254
summary:
  title: Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. To assess the association of age, sex, and smoking status with the expression of ACE2, TMPRSS2, and CTSL, we aggregated 22 scRNA-seq datasets of healthy human nasal and lung cells, as well as fetal samples.

title:
  Integrated analyses of single-cell atlases reveal age, gender, and smoking status associations with cell type-specific expression of mediators of SARS-CoV-2 viral entry and highlights inflammatory programs in putative target cells

abstract:
  The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, creates an urgent need for identifying molecular mechanisms that mediate viral entry, propagation, and tissue pathology. Cell membrane bound angiotensin-converting enzyme 2 (ACE2) and associated proteases, transmembrane protease serine 2 (TMPRSS2) and Cathepsin L (CTSL), were previously identified as mediators of SARS-CoV2 cellular entry. Here, we assess the cell type-specific RNA expression of ACE2, TMPRSS2, and CTSL through an integrated analysis of 107 single-cell and single-nucleus RNA-Seq studies, including 22 lung and airways datasets (16 unpublished), and 85 datasets from other diverse organs. Joint expression of ACE2 and the accessory proteases identifies specific subsets of respiratory epithelial cells as putative targets of viral infection in the nasal passages, airways, and alveoli. Cells that co-express ACE2 and proteases are also identified in cells from other organs, some of which have been associated with COVID-19 transmission or pathology, including gut enterocytes, corneal epithelial cells, cardiomyocytes, heart pericytes, olfactory sustentacular cells, and renal epithelial cells. Performing the first meta-analyses of scRNA-seq studies, we analyzed 1,176,683 cells from 282 nasal, airway, and lung parenchyma samples from 164 donors spanning fetal, childhood, adult, and elderly age groups, associate increased levels of ACE2, TMPRSS2, and CTSL in specific cell types with increasing age, male gender, and smoking, all of which are epidemiologically linked to COVID-19 susceptibility and outcomes. Notably, there was a particularly low expression of ACE2 in the few young pediatric samples in the analysis. Further analysis reveals a gene expression program shared by ACE2+TMPRSS2+ cells in nasal, lung and gut tissues, including genes that may mediate viral entry, subtend key immune functions, and mediate epithelial-macrophage cross-talk. Amongst these are IL6, its receptor and co-receptor, IL1R, TNF response pathways, and complement genes. Cell type specificity in the lung and airways and smoking effects were conserved in mice. Our analyses suggest that differences in the cell type-specific expression of mediators of SARS-CoV-2 viral entry may be responsible for aspects of COVID-19 epidemiology and clinical course, and point to putative molecular pathways involved in disease susceptibility and pathogenesis.


id: cord-263868-ewnf96cz
title: Chemical proteomics tracks virus entry and uncovers NCAM1 as Zika virus receptor
author: Srivastava, Mayank
date: 2020-08-04
txt: ./txt/cord-263868-ewnf96cz.txt
cache: ./cache/cord-263868-ewnf96cz.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41467-020-17638-y
doi: 10.1038/s41467-020-17638-y
summary:
  ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We used the labeled ZIKV to infect Vero cells and interacting proteins were crosslinked at fixed time points to identify the virus-host factors and elucidate the virus entry mechanism (Fig. 1c) . To further investigate whether the strategy was also capable of correlating spatial information with the virus crosslinked proteins, we performed the STRING analysis to determine whether there is statistical overrepresentation of specific genes or proteins in the sample at specific time points and identify proteins specific at the attachment or cellular entry stages ( Supplementary Fig. 6 ).

abstract:
  The outbreak of Zika virus (ZIKV) in 2016 created worldwide health emergency which demand urgent research efforts on understanding the virus biology and developing therapeutic strategies. Here, we present a time-resolved chemical proteomic strategy to track the early-stage entry of ZIKV into host cells. ZIKV was labeled on its surface with a chemical probe, which carries a photocrosslinker to covalently link virus-interacting proteins in living cells on UV exposure at different time points, and a biotin tag for subsequent enrichment and mass spectrometric identification of the receptor or other host proteins critical for virus internalization. We identified Neural Cell Adhesion Molecule (NCAM1) as a potential ZIKV receptor and further validated it through overexpression, knockout, and inhibition of NCAM1 in Vero cells and human glioblastoma cells U-251 MG. Collectively, the strategy can serve as a universal tool to map virus entry pathways and uncover key interacting proteins.


id: cord-265418-yqe9vdj1
title: Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis
author: Kumar, Nilesh
date: 2020-04-11
txt: ./txt/cord-265418-yqe9vdj1.txt
cache: ./cache/cord-265418-yqe9vdj1.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.09.033910
doi: 10.1101/2020.04.09.033910
summary:
  Integrated interactome-transcriptome analysis to generate Calu-3-specific humanIt is likely that the outcome of SARS-CoV-2 infection can largely be determined by the interaction patterns of host proteins and viral factors. By integrating this Calu-3 co-expression network with SIPs-derived PPI subnetwork, we generated Calu-3-specific human-SARS-CoV-2 Interactome (CSI) that contains 214 SIPs interacting with their first and second neighbors make a network of 4,123 nodes and 14,650 edges (Fig. 1c, Supplementary Data 1) . We showed that CSI follows a power law degree distribution with a few nodes harboring increased connectivity, and thus exhibits properties of a scale-free network (r 2 = 0.91; (Fig. 1d , Supplementary Data 1), similar to the previously generated other human-viral interactomes 12, 13, 14, 15, 16, 17, 18, 19, 20, 24, 25, 26, 27, 28 . In conclusion, we generated a human-SARS-CoV-2 interactome, integrated virusrelated transcriptome to interactome, discover COVID-19 pertinent structural and functional modules, identify high-value viral targets, and perform dynamic transcriptional modeling.

abstract:
  COVID-19 (Coronavirus disease 2019) is a respiratory illness caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). While the pathophysiology of this deadly virus is complex and largely unknown, we employ a network biology-fueled approach and integrated multiomics data pertaining to lung epithelial cells-specific coexpression network and human interactome to generate Calu-3-specific human-SARS-CoV-2 Interactome (CSI). Topological clustering and pathway enrichment analysis show that SARS-CoV-2 target central nodes of host-viral network that participate in core functional pathways. Network centrality analyses discover 28 high-value SARS-CoV-2 targets, which are possibly involved in viral entry, proliferation and survival to establish infection and facilitate disease progression. Our probabilistic modeling framework elucidates critical regulatory circuitry and molecular events pertinent to COVID-19, particularly the host modifying responses and cytokine storm. Overall, our network centric analyses reveal novel molecular components, uncover structural and functional modules, and provide molecular insights into SARS-CoV-2 pathogenicity.


id: cord-268645-5op2m7pu
author: Wu, Zhiqiang
date: 2015-08-11
txt: ./txt/cord-268645-5op2m7pu.txt
cache: ./cache/cord-268645-5op2m7pu.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/26262818/
doi: 10.1038/ismej.2015.138
summary:
  However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. Based on the partial genomic sequences of the viruses obtained by the assembly, we designed specific nested primers for PCR or reverse trancriptase-PCR to screen for each virus in individual samples from each bat species (the primer sequences for each virus are available in Supplementary Table S2 ). The diverse BtCoVs were grouped into several novel evolutionary clades that significantly differed from those of all known αand β-CoVs, providing additional evidence to support investigations of the evolution of bat-originated CoVs. With regard to BtParaVs, a previous study has revealed that bats host major mammalian ParaVs in the genera Rubulavirus, Morbillivirus, Henipavirus and the subfamily Pneumovirinae (Drexler et al., 2012) .

title:
  Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases

abstract:
  Studies have demonstrated that ~60%–80% of emerging infectious diseases (EIDs) in humans originated from wild life. Bats are natural reservoirs of a large variety of viruses, including many important zoonotic viruses that cause severe diseases in humans and domestic animals. However, the understanding of the viral population and the ecological diversity residing in bat populations is unclear, which complicates the determination of the origins of certain EIDs. Here, using bats as a typical wildlife reservoir model, virome analysis was conducted based on pharyngeal and anal swab samples of 4440 bat individuals of 40 major bat species throughout China. The purpose of this study was to survey the ecological and biological diversities of viruses residing in these bat species, to investigate the presence of potential bat-borne zoonotic viruses and to evaluate the impacts of these viruses on public health. The data obtained in this study revealed an overview of the viral community present in these bat samples. Many novel bat viruses were reported for the first time and some bat viruses closely related to known human or animal pathogens were identified. This genetic evidence provides new clues in the search for the origin or evolution pattern of certain viruses, such as coronaviruses and noroviruses. These data offer meaningful ecological information for predicting and tracing wildlife-originated EIDs.


id: cord-271693-7tg21up3
title: Identifying persistent structures in multiscale ‘omics data
author: Zheng, Fan
date: 2020-10-03
txt: ./txt/cord-271693-7tg21up3.txt
cache: ./cache/cord-271693-7tg21up3.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32587977/
doi: 10.1101/2020.06.16.151555
summary:
  Many different approaches have been devised or applied to detect structures in biological data, including standard clustering, network community detection, and low-dimensional data projection [5] [6] [7] , some of which can be tuned for sensitivity to objects of a certain size or scale (so-called ''resolution parameters'') [8, 9] . We first explored the idea of measuring community persistence via analysis of synthetic datasets [15] in which communities were simulated and embedded in the similarity network at two different scales (Supplementary Fig. 1a; Methods) . Application to protein-protein interaction networks from budding yeast and human found that HiDeF captured knowledge in GO more significantly than previous pipelines proposed for this task, including the NeXO approach to hierarchical community detection [23] and standard hierarchical clustering of pairwise protein distances calculated by three recent network embedding approaches [24] [25] [26] (Fig. 3a, Fig. 7) .

abstract:
  In any ‘omics study, the scale of analysis can dramatically affect the outcome. For instance, when clustering single-cell transcriptomes, is the analysis tuned to discover broad or specific cell types? Likewise, protein communities revealed from protein networks can vary widely in sizes depending on the method. Here we use the concept of “persistent homology”, drawn from mathematical topology, to identify robust structures in data at all scales simultaneously. Application to mouse single-cell transcriptomes significantly expands the catalog of identified cell types, while analysis of SARS-COV-2 protein interactions suggests hijacking of WNT. The method, HiDeF, is available via Python and Cytoscape.


id: cord-282566-rgo5sj5i
title: Pathogenic Neisseria meningitidis utilizes CD147 for vascular colonization
author: Bernard, Sandra C
date: 2014-06-01
txt: ./txt/cord-282566-rgo5sj5i.txt
cache: ./cache/cord-282566-rgo5sj5i.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/24880614/
doi: 10.1038/nm.3563
summary:
  However, β 2 -AR-depleted endothelial cells, although unable to promote signaling events, still support pilus-mediated bacterial adhesion, thus indicating that the primary meningococcal attachment requires another, yet unidentified, host receptor for type IV pili. Here, we report that CD147, a member of the immunoglobulin (Ig) superfamily, is a receptor for type IV pilus-mediated adhesion of pathogenic meningococci to human brain or peripheral endothelial cells through interaction with both major and minor pilins-PilE and PilV-and we establish the central role of CD147 for vascular colonization by meningococci in vivo. This study demonstrates that the specific interaction between the meningococcal ligands PilE and PilV and the cellular host receptor CD147 is essential for meningococcal adhesion to human endothelial cells and colonization of human blood vessels, a prerequisite to the major vascular alterations that are the hallmark of invasive meningococcal infections.

abstract:
  Neisseria meningitidis is a cause of meningitis epidemics worldwide and of rapidly progressing fatal septic shock. A crucial step in the pathogenesis of invasive meningococcal infections is the adhesion of bloodborne meningococci to both peripheral and brain endothelia, leading to major vascular dysfunction. Initial adhesion of pathogenic strains to endothelial cells relies on meningococcal type IV pili, but the endothelial receptor for bacterial adhesion remains unknown. Here, we report that the immunoglobulin superfamily member CD147 (also called extracellular matrix metalloproteinase inducer (EMMPRIN) or Basigin) is a critical host receptor for the meningococcal pilus components PilE and PilV. Interfering with this interaction potently inhibited the primary attachment of meningococci to human endothelial cells in vitro and prevented colonization of vessels in human brain tissue explants ex vivo and in humanized mice in vivo. These findings establish the molecular events by which meningococci target human endothelia, and they open new perspectives for treatment and prevention of meningococcus-induced vascular dysfunctions. SUPPLEMENTARY INFORMATION: The online version of this article (doi:10.1038/nm.3563) contains supplementary material, which is available to authorized users.


id: cord-284015-vvtv492b
title: Comparative genomic analyses illuminate the distinct evolution of megabats within Chiroptera
author: Nikaido, Masato
date: 2020-09-23
txt: ./txt/cord-284015-vvtv492b.txt
cache: ./cache/cord-284015-vvtv492b.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32966557/
doi: 10.1093/dnares/dsaa021
summary:
  We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The protein-coding genes in the genomes of Egyptian fruit bat and Leschenault''s rousette were identified based on the alignment with annotated gene sequences of 14 mammals (cat, dog, horse, cow, hedgehog, human, macaque, mouse, rat, Black flying fox, Little brown bat, Brandt''s bat, David''s myotis, and Large flying fox; Supplementary Table S2 ) that are available in the database. 71 Suggesting that FPR-mediated chemodetection is not directly linked with the difference in their habitats, mega-and microbats both possess two to eight FPRs. However, a previous study, by comparing the orthologous sequences among a broad range of mammals, found the signatures for the operation of positive selection in FPRs. 72 Therefore, to examine the possible contribution of FPRs to the adaptive evolution of megabats, more detailed investigation is necessary by focussing on the dN/dS values among orthologous FPR sequences of many bat species, which are lacking at present.

abstract:
  The revision of the sub-order Microchiroptera is one of the most intriguing outcomes in recent mammalian molecular phylogeny. The unexpected sister–taxon relationship between rhinolophoid microbats and megabats, with the exclusion of other microbats, suggests that megabats arose in a relatively short period of time from a microbat-like ancestor. In order to understand the genetic mechanism underlying adaptive evolution in megabats, we determined the whole-genome sequences of two rousette megabats, Leschenault’s rousette (Rousettus leschenaultia) and the Egyptian fruit bat (R. aegyptiacus). The sequences were compared with those of 22 other mammals, including nine bats, available in the database. We identified that megabat genomes are distinct in that they have extremely low activity of SINE retrotranspositions, expansion of two chemosensory gene families, including the trace amine receptor (TAAR) and olfactory receptor (OR), and elevation of the dN/dS ratio in genes for immunity and protein catabolism. The adaptive signatures discovered in the genomes of megabats may provide crucial insight into their distinct evolution, including key processes such as virus resistance, loss of echolocation, and frugivorous feeding.


id: cord-286217-3uklf2u2
title: SARS-CoV-2 proteome microarray for global profiling of COVID-19 specific IgG and IgM responses
author: Jiang, He-wei
date: 2020-07-14
txt: ./txt/cord-286217-3uklf2u2.txt
cache: ./cache/cord-286217-3uklf2u2.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32665645/
doi: 10.1038/s41467-020-17488-8
summary:
  Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We detected the SARS-CoV-2-specific IgG and IgM proteins bound to the array using fluorescent-labeled anti-human antibodies, thereby generating a global assessment of each patient''s humoral antibody response. All of the samples and the controls were probed on the proteome microarray, and after data filtering and normalization, we constructed the IgG and IgM profile for each serum and performed clustering analysis to generate heatmaps (Figs. To statistically analyze the IgG responses against SARS-CoV-2 proteins, we calculated the p-values followed by multiple testing correction (or q-values), and applied significant analysis of microarray (SAM) to identify significant positive proteins (Supplementary Fig. 7 and Data 2).

abstract:
  We still know very little about how the human immune system responds to SARS-CoV-2. Here we construct a SARS-CoV-2 proteome microarray containing 18 out of the 28 predicted proteins and apply it to the characterization of the IgG and IgM antibodies responses in the sera from 29 convalescent patients. We find that all these patients had IgG and IgM antibodies that specifically bind SARS-CoV-2 proteins, particularly the N protein and S1 protein. Besides these proteins, significant antibody responses to ORF9b and NSP5 are also identified. We show that the S1 specific IgG signal positively correlates with age and the level of lactate dehydrogenase (LDH) and negatively correlates with lymphocyte percentage. Overall, this study presents a systemic view of the SARS-CoV-2 specific IgG and IgM responses and provides insights to aid the development of effective diagnostic, therapeutic and vaccination strategies.


id: cord-288824-sygnmiun
author: Lam, SD
date: 2020-08-19
txt: ./txt/cord-288824-sygnmiun.txt
cache: ./cache/cord-288824-sygnmiun.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.05.01.072371
doi: 10.1101/2020.05.01.072371
summary:
  To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We correlated changes in the energy of the complex with changes in the structure of ACE2, chemical properties of residues in the binding interface, and experimental COVID-19 infection phenotypes from in vivo and in vitro animal studies. We used multiple methods to assess the relative change in binding energy (ΔΔG) of the SARS-CoV-2 S-protein:ACE2 complex following mutations in DC residues and DCEX residues that are likely to influence binding. Irrespective of host, the SARS-CoV-2 spike receptor binding domain is conserved (Fig. 4b) across tested human and animal associated SARS-CoV-2, suggesting mutations in the RBD are not required for infections observed in non-human species to date.

title:
  SARS-CoV-2 spike protein predicted to form complexes with host receptor protein orthologues from a broad range of mammals

abstract:
  SARS-CoV-2 has a zoonotic origin and was transmitted to humans via an undetermined intermediate host, leading to infections in humans and other mammals. To enter host cells, the viral spike protein (S-protein) binds to its receptor, ACE2, and is then processed by TMPRSS2. Whilst receptor binding contributes to the viral host range, S-protein:ACE2 complexes from other animals have not been investigated widely. To predict infection risks, we modelled S-protein:ACE2 complexes from 215 vertebrate species, calculated changes in the energy of the complex caused by mutations in each species, relative to human ACE2, and correlated these changes with COVID-19 infection data. We also analysed structural interactions to better understand the key residues contributing to affinity. We predict that mutations are more detrimental in ACE2 than TMPRSS2. Finally, we demonstrate phylogenetically that human SARS-CoV-2 strains have been isolated in animals. Our results suggest that SARS-CoV-2 can infect a broad range of mammals, but few fish, birds or reptiles. Susceptible animals could serve as reservoirs of the virus, necessitating careful ongoing animal management and surveillance.


id: cord-288916-i8ukefp8
title: The effects of IFITM1 and IFITM3 gene deletion on IFNγ stimulated protein synthesis
author: Gómez-Herranz, Maria
date: 2019-04-02
txt: ./txt/cord-288916-i8ukefp8.txt
cache: ./cache/cord-288916-i8ukefp8.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1016/j.cellsig.2019.03.024
doi: 10.1016/j.cellsig.2019.03.024
summary:
  A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The HPV16+ and IFITM1/3 positive cervical cancer cell line SiHa [38] [39] exhibit IFNγ inducible STAT1, IRF1, and IFITM1/3 proteins (Fig. 1G ). Also of note is attenuation of HLA-A, HLA-B, HLA-C, and ISG15 protein synthesis 24 h post-IFNγ treatment in the IFITM1/IFITM3 double null cells compared to parental SiHa (Fig. 5F vs 5B). By contrast, basal HLA-B protein expression was attenuated in the IFITM1/IFITM3 double null cells after IFNγ treatment (Fig. 6F vs 6E) .

abstract:
  Interferon-induced transmembrane proteins IFITM1 and IFITM3 (IFITM1/3) play a role in both RNA viral restriction and in human cancer progression. Using immunohistochemical staining of FFPE tissue, we identified subgroups of cervical cancer patients where IFITM1/3 protein expression is inversely related to metastasis. Guide RNA-CAS9 methods were used to develop an isogenic IFITM1/IFITM3 double null cervical cancer model in order to define dominant pathways triggered by presence or absence of IFITM1/3 signalling. A pulse SILAC methodology identified IRF1, HLA-B, and ISG15 as the most dominating IFNγ inducible proteins whose synthesis was attenuated in the IFITM1/IFITM3 double-null cells. Conversely, SWATH-IP mass spectrometry of ectopically expressed SBP-tagged IFITM1 identified ISG15 and HLA-B as dominant co-associated proteins. ISG15ylation was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. Proximity ligation assays indicated that HLA-B can interact with IFITM1/3 proteins in parental SiHa cells. Cell surface expression of HLA-B was attenuated in IFNγ treated IFITM1/IFITM3 double-null cells. SWATH-MS proteomic screens in cells treated with IFITM1-targeted siRNA cells resulted in the attenuation of an interferon regulated protein subpopulation including MHC Class I molecules as well as IFITM3, STAT1, B2M, and ISG15. These data have implications for the function of IFITM1/3 in mediating IFNγ stimulated protein synthesis including ISG15ylation and MHC Class I production in cancer cells. The data together suggest that pro-metastatic growth associated with IFITM1/3 negative cervical cancers relates to attenuated expression of MHC Class I molecules that would support tumor immune escape.


id: cord-292862-ezrkg0dc
author: Myerson, Jacob W.
date: 2020-04-18
txt: ./txt/cord-292862-ezrkg0dc.txt
cache: ./cache/cord-292862-ezrkg0dc.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.04.15.037564
doi: 10.1101/2020.04.15.037564
summary:
  We show that polystyrene nanoparticles and five liposome formulations do not accumulate in injured lungs, indicating that nanostructures that are not based on protein are not intrinsically drawn to marginated neutrophils in acute inflammation. 6, 10, 14, 18 Single cell suspensions prepared from mouse lungs were probed by flow cytometry to further characterize pulmonary neutrophils in naïve mice and in mice following LPS-induced inflammation. The protein component of each particle was labeled with 125 I for tracing in biodistributions, and assessed 30 minutes after IV administration of NPs. Both absolute LDNG lung uptake and ratio of lung uptake to liver uptake registered a ~25-fold increase between naïve control and LPS-injured animals (Figure 2A , Supplementary Table 1) . As with LDNGs and albumin NPs in Figure 2C -H, single cell suspensions were prepared from LPS-inflamed and naïve control lungs after circulation of fluorescent DBCO-IgG liposomes.

title:
  Supramolecular Organization Predicts Protein Nanoparticle Delivery to Neutrophils for Acute Lung Inflammation Diagnosis and Treatment

abstract:
  Acute lung inflammation has severe morbidity, as seen in COVID-19 patients. Lung inflammation is accompanied or led by massive accumulation of neutrophils in pulmonary capillaries (“margination”). We sought to identify nanostructural properties that predispose nanoparticles to accumulate in pulmonary marginated neutrophils, and therefore to target severely inflamed lungs. We designed a library of nanoparticles and conducted an in vivo screen of biodistributions in naive mice and mice treated with lipopolysaccharides. We found that supramolecular organization of protein in nanoparticles predicts uptake in inflamed lungs. Specifically, nanoparticles with agglutinated protein (NAPs) efficiently home to pulmonary neutrophils, while protein nanoparticles with symmetric structure (e.g. viral capsids) are ignored by pulmonary neutrophils. We validated this finding by engineering protein-conjugated liposomes that recapitulate NAP targeting to neutrophils in inflamed lungs. We show that NAPs can diagnose acute lung injury in SPECT imaging and that NAP-like liposomes can mitigate neutrophil extravasation and pulmonary edema arising in lung inflammation. Finally, we demonstrate that ischemic ex vivo human lungs selectively take up NAPs, illustrating translational potential. This work demonstrates that structure-dependent interactions with neutrophils can dramatically alter the biodistribution of nanoparticles, and NAPs have significant potential in detecting and treating respiratory conditions arising from injury or infections.


id: cord-295482-qffg6r91
title: Receptor-binding loops in alphacoronavirus adaptation and evolution
author: Wong, Alan H. M.
date: 2017-11-23
txt: ./txt/cord-295482-qffg6r91.txt
cache: ./cache/cord-295482-qffg6r91.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41467-017-01706-x
doi: 10.1038/s41467-017-01706-x
summary:
  Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. The structure shows that receptor binding is mediated solely by three extended loops, a feature shared by HCoV-NL63 and the closely related porcine respiratory coronavirus, PRCoV. The six RBDs differ in their receptor-binding affinity and their ability to be bound by a neutralizing antibody (9.8E12) and taken together, our findings suggest that the HCoV-229E sequence variation observed arose through adaptation and selection. HCoV-229E infection in humans does not provide protection against different isolates 37 , and viruses that contain a new RBD class that cannot be bound by the existing repertoire of loop-binding neutralizing antibodies provide an explanation for this observation.

abstract:
  RNA viruses are characterized by a high mutation rate, a buffer against environmental change. Nevertheless, the means by which random mutation improves viral fitness is not well characterized. Here we report the X-ray crystal structure of the receptor-binding domain (RBD) of the human coronavirus, HCoV-229E, in complex with the ectodomain of its receptor, aminopeptidase N (APN). Three extended loops are solely responsible for receptor binding and the evolution of HCoV-229E and its close relatives is accompanied by changing loop–receptor interactions. Phylogenetic analysis shows that the natural HCoV-229E receptor-binding loop variation observed defines six RBD classes whose viruses have successively replaced each other in the human population over the past 50 years. These RBD classes differ in their affinity for APN and their ability to bind an HCoV-229E neutralizing antibody. Together, our results provide a model for alphacoronavirus adaptation and evolution based on the use of extended loops for receptor binding.


id: cord-299605-j1ewxk4q
author: Lin, Jing-wen
date: 2017-02-03
txt: ./txt/cord-299605-j1ewxk4q.txt
cache: ./cache/cord-299605-j1ewxk4q.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/28155887/
doi: 10.1038/srep41722
summary:
  c. chabaudi, AS and CB, that differ in virulence in C57BL/6 mice, we performed high-resolution comparative whole-blood transcriptomic analysis throughout the acute phase of the blood-stage infection, and identified several transcriptomic signatures associated with severe malarial pathology before the onset of pathology or disease. Spearman''s rank correlation coefficient (r s ) analysis of unfiltered transcripts normalised across the median of all samples, revealed high levels of similarity amongst naïve and 2, 4 dpi samples in both AS and CB infections (Fig. 2ai ,ii, r s ranging from 0.73 to 0.88), while from 6 dpi onwards the whole blood transcriptomes diverge significantly from the earlier time points (r s ranging from 0.08 to − 0.59 compared to naïve controls). Importantly, in 4 of the CB infected mice that had reached humane end points at 9 dpi, these 5 genes showed an even higher level of up-regulation compared to naïve controls (Fig. 3c) , indicating possible lung pathology in these 4 CB infected mice.

title:
  Signatures of malaria-associated pathology revealed by high-resolution whole-blood transcriptomics in a rodent model of malaria

abstract:
  The influence of parasite genetic factors on immune responses and development of severe pathology of malaria is largely unknown. In this study, we performed genome-wide transcriptomic profiling of mouse whole blood during blood-stage infections of two strains of the rodent malaria parasite Plasmodium chabaudi that differ in virulence. We identified several transcriptomic signatures associated with the virulent infection, including signatures for platelet aggregation, stronger and prolonged anemia and lung inflammation. The first two signatures were detected prior to pathology. The anemia signature indicated deregulation of host erythropoiesis, and the lung inflammation signature was linked to increased neutrophil infiltration, more cell death and greater parasite sequestration in the lungs. This comparative whole-blood transcriptomics profiling of virulent and avirulent malaria shows the validity of this approach to inform severity of the infection and provide insight into pathogenic mechanisms.


id: cord-315483-l6dm82pp
author: Santhakumar, Diwakar
date: 2018-05-01
txt: ./txt/cord-315483-l6dm82pp.txt
cache: ./cache/cord-315483-l6dm82pp.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29717152/
doi: 10.1038/s41598-018-24905-y
summary:
  To confirm the sequence of the cDNA and to identify the genomic structure of the identified IFIT gene, the transcript was amplified from RNA extracted from NDV-infected CEFs. Complete sequence analysis of the gene revealed an open reading frame (ORF) of 1440 bps (479 amino acids excluding stop codon) with high sequence identity (48% and 67%) with the human and duck IFIT5 proteins, respectively ( Supplementary Fig. 1B) . The levels of chIFN-β gene induction was proportional to the NDV replication (Fig. 2D) , therefore, it can be inferred that the virus-induced expression of chicken IFIT5 is IFN-dependent and that chIFIT5 is an early-ISG with capacity to modulate initial steps of virus life cycle. To compare anti-viral effects of chIFIT5 (only IFIT gene identified in chickens so far) with its orthologous and homologous human proteins, huIFIT1, huIFIT2, huIFIT3 and huIFIT5 were expressed in chicken cells and antiviral affect was monitored (Fig. 5A ).

title:
  Chicken Interferon-induced Protein with Tetratricopeptide Repeats 5 Antagonizes Replication of RNA Viruses

abstract:
  The intracellular actions of interferon (IFN)-regulated proteins, including IFN-induced proteins with tetratricopeptide repeats (IFITs), attribute a major component of the protective antiviral host defense. Here we applied genomics approaches to annotate the chicken IFIT locus and currently identified a single IFIT (chIFIT5) gene. The profound transcriptional level of this effector of innate immunity was mapped within its unique cis-acting elements. This highly virus- and IFN-responsive chIFIT5 protein interacted with negative sense viral RNA structures that carried a triphosphate group on its 5′ terminus (ppp-RNA). This interaction reduced the replication of RNA viruses in lentivirus-mediated IFIT5-stable chicken fibroblasts whereas CRISPR/Cas9-edited chIFIT5 gene knockout fibroblasts supported the replication of RNA viruses. Finally, we generated mosaic transgenic chicken embryos stably expressing chIFIT5 protein or knocked-down for endogenous chIFIT5 gene. Replication kinetics of RNA viruses in these transgenic chicken embryos demonstrated the antiviral potential of chIFIT5 in ovo. Taken together, these findings propose that IFIT5 specifically antagonize RNA viruses by sequestering viral nucleic acids in chickens, which are unique in innate immune sensing and responses to viruses of both poultry and human health significance.


id: cord-318079-jvx1rh7g
author: Hinch, R.
date: 2020-09-22
txt: ./txt/cord-318079-jvx1rh7g.txt
cache: ./cache/cord-318079-jvx1rh7g.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.09.16.20195925
doi: 10.1101/2020.09.16.20195925
summary:
  The ABM was developed to simulate different non-pharmaceutical interventions including lockdown, physical distancing, self-isolation on symptoms, testing and contact tracing. A previous study of social contacts for infectious disease modelling, based on participants being asked to recall their interactions over the past day, has estimated the mean number of interactions that individuals have by age group [12] . We present OpenABM-Covid19, a COVID-19-specific agent-based model suitable for simulating the epidemic in different settings and assessing non-pharmaceutical interventions, including contact tracing using a mobile phone app. Further, on developing symptoms or during interventions such as contact tracing, the interaction pattern of individuals change to only include those in the household. One of the key aims of OpenABM-Covid19 was to model non-pharmaceutical interventions and, in particular, different forms of contact tracing. OpenABM-Covid19 is a versatile tool to model the COVID-19 epidemic in different settings and simulate different non-pharmaceutical interventions including contact tracing.

title:
  OpenABM-Covid19 - an agent-based model for non-pharmaceutical interventions against COVID-19 including contact tracing

abstract:
  SARS-CoV-2 has spread across the world, causing high mortality and unprecedented restrictions on social and economic activity. Policymakers are assessing how best to navigate through the ongoing epidemic, with models being used to predict the spread of infection and assess the impact of public health measures. Here, we present OpenABM-Covid19: an agent-based simulation of the epidemic including detailed age-stratification and realistic social networks. By default the model is parameterised to UK demographics and calibrated to the UK epidemic, however, it can easily be re-parameterised for other countries. OpenABM-Covid19 can evaluate non-pharmaceutical interventions, including both manual and digital contact tracing. It can simulate a population of 1 million people in seconds per day allowing parameter sweeps and formal statistical model-based inference. The code is open-source and has been developed by teams both inside and outside academia, with an emphasis on formal testing, documentation, modularity and transparency. A key feature of OpenABM-Covid19 is its Python interface, which has allowed scientists and policymakers to simulate dynamic packages of interventions and help compare options to suppress the COVID-19 epidemic.


id: cord-320325-sjab8zsk
author: Mendez, Aaron S
date: 2018-12-14
txt: ./txt/cord-320325-sjab8zsk.txt
cache: ./cache/cord-320325-sjab8zsk.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/nar/gky932
doi: 10.1093/nar/gky932
summary:
  Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. Using an RNA substrate that is efficiently cleaved by SOX in cells, we revealed that specific RNA sequences within and outside of the cleavage site significantly contribute to SOX binding efficiency and target processing. Given that both substrates contain the requisite unpaired bulge at the predicted cleavage site (see Figure 2A and Supplementary Figure S2 ), these observations suggest that additional sequence or structural features impact SOX targeting efficiency on individual RNAs. Two SOX point mutants, P176S and F179A, located in an unstructured region of the protein that bridges domains I and II have been shown to be selectively required for its endonucleolytic processing of RNA substrates (Supplementary Figure S3A and S3B) (8, 21) .

title:
  Site specific target binding controls RNA cleavage efficiency by the Kaposi''s sarcoma-associated herpesvirus endonuclease SOX

abstract:
  A number of viruses remodel the cellular gene expression landscape by globally accelerating messenger RNA (mRNA) degradation. Unlike the mammalian basal mRNA decay enzymes, which largely target mRNA from the 5′ and 3′ end, viruses instead use endonucleases that cleave their targets internally. This is hypothesized to more rapidly inactivate mRNA while maintaining selective power, potentially though the use of a targeting motif(s). Yet, how mRNA endonuclease specificity is achieved in mammalian cells remains largely unresolved. Here, we reveal key features underlying the biochemical mechanism of target recognition and cleavage by the SOX endonuclease encoded by Kaposi's sarcoma-associated herpesvirus (KSHV). Using purified KSHV SOX protein, we reconstituted the cleavage reaction in vitro and reveal that SOX displays robust, sequence-specific RNA binding to residues proximal to the cleavage site, which must be presented in a particular structural context. The strength of SOX binding dictates cleavage efficiency, providing an explanation for the breadth of mRNA susceptibility observed in cells. Importantly, we establish that cleavage site specificity does not require additional cellular cofactors, as had been previously proposed. Thus, viral endonucleases may use a combination of RNA sequence and structure to capture a broad set of mRNA targets while still preserving selectivity.


id: cord-322129-uyswj4ow
title: Comparative ACE2 variation and primate COVID-19 risk
author: Melin, Amanda D.
date: 2020-10-27
txt: ./txt/cord-322129-uyswj4ow.txt
cache: ./cache/cord-322129-uyswj4ow.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33110195/
doi: 10.1038/s42003-020-01370-w
summary:
  Infection studies of rhesus monkeys, long-tailed macaques, and vervets as biomedical models have made it clear that at least some nonhuman primate species are permissive to SARS-CoV-2 infection and develop symptoms in response to infection that resemble those of humans following the development of COVID-19, including similar age-related effects [11] [12] [13] [14] [15] [16] . We assessed the variation at amino acid residues identified as critical for ACE2 recognition by the SARS-CoV-2 RBD and undertook an analysis of positive selection and protein modeling to gauge the potential for adaptive differences and the likely effects of protein variation. In particular, the twelve sites in the ACE2 protein that are critical for binding of the SARS-CoV-2 virus are invariant across the Catarrhini, which includes great apes, gibbons, and monkeys of Africa and Asia (Fig. 1) .

abstract:
  The emergence of SARS-CoV-2 has caused over a million human deaths and massive global disruption. The viral infection may also represent a threat to our closest living relatives, nonhuman primates. The contact surface of the host cell receptor, ACE2, displays amino acid residues that are critical for virus recognition, and variations at these critical residues modulate infection susceptibility. Infection studies have shown that some primate species develop COVID-19-like symptoms; however, the susceptibility of most primates is unknown. Here, we show that all apes and African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at critical contact residues, and protein modeling predicts that these differences should greatly reduce SARS-CoV-2 binding affinity. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, and some lemurs, are likely to be highly susceptible to SARS-CoV-2. Urgent actions have been undertaken to limit the exposure of great apes to humans, and similar efforts may be necessary for many other primate species.


id: cord-322286-2de6r1h6
author: Vandewege, Michael W
date: 2020-07-22
txt: ./txt/cord-322286-2de6r1h6.txt
cache: ./cache/cord-322286-2de6r1h6.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/gbe/evaa151
doi: 10.1093/gbe/evaa151
summary:
  title: Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae We sequenced expressed transcripts from phyllostomid salivary glands and found strong signals of selection among immune-related genes. We sequenced the SMG transcriptomes of nine phyllostomid bats representing different subfamilies and different diets, and through analysis of orthologs characterized how selection on coding sequence and expression differences have shaped SMGs. Nine species from seven out of the 11 recognized subfamilies were chosen to maximize representation of the phylogenetic and dietary diversity of Phyllostomidae ( fig. After correcting for FDR, we found 53 genes where models of evolution allowing positive selection were significantly better fit to the data than neutrality in both M2a and M8 tests (supplementary table S2, Supplementary Material online). Moreover, given that some Golgi body-related genes appeared under selection in all branch-site tests, this organelle played some role in the adaptive radiation of phyllostomids.

title:
  Positive Selection and Gene Expression Analyses from Salivary Glands Reveal Discrete Adaptations within the Ecologically Diverse Bat Family Phyllostomidae

abstract:
  The leaf-nosed bats (Phyllostomidae) are outliers among chiropterans with respect to the unusually high diversity of dietary strategies within the family. Salivary glands, owing to their functions and high ultrastructural variability among lineages, are proposed to have played an important role during the phyllostomid radiation. To identify genes underlying salivary gland functional diversification, we sequenced submandibular gland transcriptomes from phyllostomid species representative of divergent dietary strategies. From the assembled transcriptomes, we performed an array of selection tests and gene expression analyses to identify signatures of adaptation. Overall, we identified an enrichment of immunity-related gene ontology terms among 53 genes evolving under positive selection. Lineage-specific selection tests revealed several endomembrane system genes under selection in the vampire bat. Many genes that respond to insulin were under selection and differentially expressed genes pointed to modifications of amino acid synthesis pathways in plant-visitors. Results indicate salivary glands have diversified in various ways across a functional diverse clade of mammals in response to niche specializations.


id: cord-323307-nu9ib62h
title: The genomes of two bat species with long constant frequency echolocation calls
author: Dong, Dong
date: 2016-10-26
txt: ./txt/cord-323307-nu9ib62h.txt
cache: ./cache/cord-323307-nu9ib62h.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1093/molbev/msw231
doi: 10.1093/molbev/msw231
summary:
  For homology-based gene prediction, the protein sequences of human, mouse, dog, cow, little brown bat and large flying fox were downloaded from Ensembl Release 72 and mapped onto the repeat-masked genome using GenBlastA (She, et al. Moreover, we identified 577, 453 and 182 positively selected genes in the great leaf-nosed bat, the Chinese rufous horseshoe bat and the large flying fox, (Supplementary Tables S10, 11, 12), respectively. Clade model C implemented in PAML was employed (Weadick and Chang 2012) , and the result also persisted that more positively selected genes were detected in the branches leading to echolocating bats (Supplementary Table S20 ). The genome re-sequencing analysis has been performed based generally on the following considerations: 1) to characterize the genetic diversity and patterns of evolution; 2) to understand the genetic bases of adaptation to high altitude in the great leaf-nosed bats.

abstract:
  Bats can perceive the world by using a wide range of sensory systems, and some of the systems have become highly specialized, such as auditory sensory perception. Among bat species, the Old World leaf-nosed bats and horseshoe bats (rhinolophoid bats) possess the most sophisticated echolocation systems. Here, we reported the whole-genome sequencing and de novo assembles of two rhinolophoid bats – the great leaf-nosed bat (Hipposideros armiger) and the Chinese rufous horseshoe bat (Rhinolophus sinicus). Comparative genomic analyses revealed the adaptation of auditory sensory perception in the rhinolophoid bat lineages, probably resulting from the extreme selectivity used in the auditory processing by these bats. Pseudogenization of some vision-related genes in rhinolophoid bats was observed, suggesting that these genes have undergone relaxed natural selection. An extensive contraction of olfactory receptor gene repertoires was observed in the lineage leading to the common ancestor of bats. Further extensive gene contractions can be observed in the branch leading to the rhinolophoid bats. Such concordance suggested that molecular changes at one sensory gene might have direct consequences for genes controlling for other sensory modalities. To characterize the population genetic structure and patterns of evolution, we re-sequenced the genome of 20 great leaf-nosed bats from four different geographical locations of China. The result showed similar sequence diversity values and little differentiation among populations. Moreover, evidence of genetic adaptations to high altitudes in the great leaf-nosed bats was observed. Taken together, our work provided a useful resource for future research on the evolution of bats.


id: cord-325155-lqzgz6p3
title: Hypertension and the roles of the 9p21.3 risk locus: classic findings and new association data
author: Gallo, Juan E.
date: 2020-09-15
txt: ./txt/cord-325155-lqzgz6p3.txt
cache: ./cache/cord-325155-lqzgz6p3.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S2590086220300276
doi: 10.1016/j.ijchy.2020.100050
summary:
  Two adjacent haplotype blocks characterize the 9p21.3 cardiovascular risk locus: left, the block or island containing the first part of the p15 gene and its wellcharacterized promoter, in which we observed clearly elevated associations (red) with blood pressure (DBP, SBP) and/or hypertension in a Colombian and a European study sample, and right, the block hypertension and BP association ''Hypertension island'' * (haplotype block < 60 kb) Lead CVD risk SNPs (haplotype block < 60 kb) Furthermore, in the European blood pressure studies [15, 16] genome-wide significance of DBP associations was attained, outside of the classic 9p21.3 CVD risk locus and its flanking regions, in the next gene MTAP (see Figure 2 and Theory), with a lowest p-value of 1.3 × 10 −10 for the sentinel SNP rs4364717 (red asterisk and red horizontal bar at left in Figure 2 ; see also the LocusZoom plot in Supplementary Material S3.2) .

abstract:
  Background The band 9p21.3 contains an established genomic risk zone for cardiovascular disease (CVD). Since the initial 2007 Wellcome Trust Case Control Consortium study (WTCCC), the increased CVD risk associated with 9p21.3 has been confirmed by multiple studies in different continents. However, many years later there was still no confirmed report of a corresponding association of 9p21.3 with hypertension, a major CV risk factor, nor with blood pressure (BP). Theory In this contribution, we review the bipartite haplotype structure of the 9p21.3 risk locus: one block is devoid of protein-coding genes but contains the lead CVD risk SNPs, while the other block contains the first exon and regulatory DNA of the gene for the cell cycle inhibitor p15. We consider how findings from molecular biology offer possibilities of an involvement of p15 in hypertension etiology, with expression of the p15 gene modulated by genetic variation from within the 9p21.3 risk locus. Results We present original results from a Colombian study revealing moderate but persistent association signals for BP and hypertension within the classic 9p21.3 CVD risk locus. These SNPs are mostly confined to a ‘hypertension island’ that spans less than 60 kb and coincides with the p15 haplotype block. We find confirmation in data originating from much larger, recent European BP studies, albeit with opposite effect directions. Conclusion Although more work will be needed to elucidate possible mechanisms, previous findings and new data prompt reconsidering the question of how variation in 9p21.3 might influence hypertension components of cardiovascular risk.


id: cord-333145-a20dlaxn
title: Association of an IGHV3-66 gene variant with Kawasaki disease
author: Johnson, Todd A.
date: 2020-10-26
txt: ./txt/cord-333145-a20dlaxn.txt
cache: ./cache/cord-333145-a20dlaxn.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33106546/
doi: 10.1038/s10038-020-00864-z
summary:
  In a meta-analysis of three GWAS for susceptibility to Kawasaki disease (KD) conducted in Japan, Korea, and Taiwan and follow-up studies with a total of 11,265 subjects (3428 cases and 7837 controls), a significantly associated SNV in the immunoglobulin heavy variable gene (IGHV) cluster in 14q33.32 was identified (rs4774175; OR = 1.20, P = 6.0 × 10(−9)). Considering that significant association of SNVs in the IGHV region with disease susceptibility was previously known only for rheumatic heart disease (RHD), a complication of acute rheumatic fever (ARF), these observations suggest that common B-cell related mechanisms may mediate the symptomology of KD and ARF as well as RHD. Instead, 7 out of 12 groups of SNVs in the 6p21 region examined in the Stage 2 analyses showed significant association in the metaanalyses of the data sets in the three GWAS as well as in the follow-up studies ( Table 1 and Supplementary Fig. 3A ).

abstract:
  In a meta-analysis of three GWAS for susceptibility to Kawasaki disease (KD) conducted in Japan, Korea, and Taiwan and follow-up studies with a total of 11,265 subjects (3428 cases and 7837 controls), a significantly associated SNV in the immunoglobulin heavy variable gene (IGHV) cluster in 14q33.32 was identified (rs4774175; OR = 1.20, P = 6.0 × 10(−9)). Investigation of nonsynonymous SNVs of the IGHV cluster in 9335 Japanese subjects identified the C allele of rs6423677, located in IGHV3-66, as the most significant reproducible association (OR = 1.25, P = 6.8 × 10(−10) in 3603 cases and 5731 controls). We observed highly skewed allelic usage of IGHV3-66, wherein the rs6423677 A allele was nearly abolished in the transcripts in peripheral blood mononuclear cells of both KD patients and healthy adults. Association of the high-expression allele with KD strongly indicates some active roles of B-cells or endogenous immunoglobulins in the disease pathogenesis. Considering that significant association of SNVs in the IGHV region with disease susceptibility was previously known only for rheumatic heart disease (RHD), a complication of acute rheumatic fever (ARF), these observations suggest that common B-cell related mechanisms may mediate the symptomology of KD and ARF as well as RHD.


id: cord-336209-grpi7gnc
author: Allen, Cameron
date: 2020-08-12
txt: ./txt/cord-336209-grpi7gnc.txt
cache: ./cache/cord-336209-grpi7gnc.txt
extension: .txt
mime: text/plain
url: https://api.elsevier.com/content/article/pii/S1462901120300654
doi: 10.1016/j.envsci.2020.07.029
summary:
  Finally, an effective science policy interface includes the establishment of a scientifically sound monitoring system and data infrastructure, technical capacities and tools to support assessment of land degradation as well as progress in LDN implementation, the evaluation of economic, social and environmental benefits and trade-offs associated with achieving LDN, and the effective collation and translation of scientific knowledge to policy-makers, planners and other relevant stakeholders (Akhtar-Schuster et al., 2011; Chasek et al., 2019; Cowie et al., 2018; Orr et al., 2017) . Enablers lagging furthest behind in terms of individual country progress correspond to the financial dimension (2.1 and 2.2), some elements of the policy/regulatory environment (3.1 land tenure, 3.2 integrated land-use planning, and 3.3 neutrality mechanism), as well as national technical capacities for LDN assessments and implementation (4.2).

title:
  Delivering an enabling environment and multiple benefits for land degradation neutrality: Stakeholder perceptions and progress

abstract:
  Achieving land degradation neutrality (LDN) was adopted by countries in 2015 as one of the targets of the global Sustainable Development Goals (SDGs). As LDN is a relatively new concept there is an increasing need for evidence on the potential socio-economic and environmental benefits of LDN as well as how an enabling environment for implementing LDN measures can be developed. This paper summarises the results from a global survey of LDN stakeholders, and a review of national progress in target setting that was commissioned by the United Nations Convention to Combat Desertification (UNCCD) in 2018. The study presents the perceptions of relevant stakeholders on the key components of an enabling environment for achieving and maintaining LDN (institutional, financial, policy/regulatory, and science-policy) as well as expectations of multiple benefits from its implementation. We also highlight key challenges and gaps in progress to date that are emerging from ongoing national target setting programs to implement LDN. The study finds that progress in implementing LDN has been widespread across countries. However there remains a lack of awareness of LDN and its key concepts along with high-level political buy-in. This may be impeding the integration of LDN into national development planning and budgeting processes where progress was assessed as limited. National capacities for securing land tenure and governance arrangements and integrated land use planning were perceived as comparatively low, further hampering the implementation of LDN. Despite these gaps, most stakeholders (>90 %) who participated in the global survey expected LDN to deliver a broad range of multiple benefits for human wellbeing, livelihoods and the natural environment. We argue that greater efforts are needed to raise awareness of LDN, educate core stakeholders in its concepts, enablers and benefits, raise its political profile, and provide evidence on national measures that will support implementation of LDN.


id: cord-340907-j9i1wlak
title: Evolutionary selection against short nucleotide sequences in viruses and their related hosts
author: Zarai, Yoram
date: 2020-04-27
txt: ./txt/cord-340907-j9i1wlak.txt
cache: ./cache/cord-340907-j9i1wlak.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32339222/
doi: 10.1093/dnares/dsaa008
summary:
  Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. Figure 3A and B depicts the average number of under-represented sequences of size m ¼ 3, 4, and 5 nucleotides, identified in few subsets of viruses in both the original and random variants of the virus. A sampling analysis that we performed (see Supplementary document, Section 2.8) suggests that the number of under-represented sequences identified in dsDNA viruses matches their genomic size, when compared with RNA viruses. To show that the correspondence between selection against short palindromic sequences in viruses and restriction sites cannot be explained by basic coding region features such as amino-acid content and order, codon usage bias and dinucleotide distribution, we also evaluated the overlap between restriction sites and common under-represented sequences of random variants of viruses.

abstract:
  Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.


id: cord-342012-1w3x0g42
title: Estimating clinical severity of COVID-19 from the transmission dynamics in Wuhan, China
author: Wu, Joseph T.
date: 2020-03-19
txt: ./txt/cord-342012-1w3x0g42.txt
cache: ./cache/cord-342012-1w3x0g42.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1038/s41591-020-0822-7
doi: 10.1038/s41591-020-0822-7
summary:
  For a completely novel pathogen, especially one with a high (say, >2) basic reproductive number (the expected number of secondary cases generated by a primary case in a completely susceptible population) relative to other recently emergent and seasonal directly transmissible respiratory pathogens 4 , assuming homogeneous mixing and mass action dynamics, the majority of the population will be infected eventually unless drastic public health interventions are applied over prolonged periods and/or vaccines become available sufficiently quickly. We therefore extended our previously published transmission dynamics model 4 , updated with real-time input data and enriched with additional new data sources, to infer a preliminary set of clinical severity estimates that could guide clinical and public health decision-making as the epidemic continues to spread globally. Given that we have parameterized the model using death rates inferred from projected case numbers (from traveler data) and observed death numbers in Wuhan, the precise fatality risk estimates may not be generalizable to those outside the original epicenter, especially during subsequent phases of the epidemic.

abstract:
  As of 29 February 2020 there were 79,394 confirmed cases and 2,838 deaths from COVID-19 in mainland China. Of these, 48,557 cases and 2,169 deaths occurred in the epicenter, Wuhan. A key public health priority during the emergence of a novel pathogen is estimating clinical severity, which requires properly adjusting for the case ascertainment rate and the delay between symptoms onset and death. Using public and published information, we estimate that the overall symptomatic case fatality risk (the probability of dying after developing symptoms) of COVID-19 in Wuhan was 1.4% (0.9–2.1%), which is substantially lower than both the corresponding crude or naïve confirmed case fatality risk (2,169/48,557 = 4.5%) and the approximator(1) of deaths/deaths + recoveries (2,169/2,169 + 17,572 = 11%) as of 29 February 2020. Compared to those aged 30–59 years, those aged below 30 and above 59 years were 0.6 (0.3–1.1) and 5.1 (4.2–6.1) times more likely to die after developing symptoms. The risk of symptomatic infection increased with age (for example, at ~4% per year among adults aged 30–60 years).


id: cord-342047-pm3i54mb
author: Du Preez, Andrea
date: 2020-09-21
txt: ./txt/cord-342047-pm3i54mb.txt
cache: ./cache/cord-342047-pm3i54mb.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32958745/
doi: 10.1038/s41398-020-01000-3
summary:
  Interestingly, combining the two distinct stress paradigms did not have an additive effect on behavioural and biological outcomes, but resulted in yet a different phenotype, characterized by increased anxiety-like behaviour, decreased plasma levels of IL1β, IL4 and VEGF, and decreased hippocampal neuronal differentiation, without altered neuroinflammation or corticosterone reactivity. Each treatment comprised one or two distinct stressors that was either in the form of repeated injection, which has been previously shown to differentially alter stress responses in BALB/C mice 20 and affective outcomes in outbred rats with high and low emotional reactivity 21 , or permanent social isolation, which has consistently been associated with depressivelike phenotypes 8, 9, 11 . Based on our data, we believe that the neurogenic profiles observed are a functional consequence of the neuroinflammatory changes associated with each stress exposure, given that microglia and astrocytes play an important role b Representative photomicrographs of the ventral (i) and dorsal (ii) dentate gyrus stained for Iba1 for repeatedly injected and socially isolated mice, respectively, all relative to controls.

title:
  The type of stress matters: repeated injection and permanent social isolation stress in male mice have a differential effect on anxiety- and depressive-like behaviours, and associated biological alterations

abstract:
  Chronic stress can alter the immune system, adult hippocampal neurogenesis and induce anxiety- and depressive-like behaviour in rodents. However, previous studies have not discriminated between the effect(s) of different types of stress on these behavioural and biological outcomes. We investigated the effect(s) of repeated injection vs. permanent social isolation on behaviour, stress responsivity, immune system functioning and hippocampal neurogenesis, in young adult male mice, and found that the type of stress exposure does indeed matter. Exposure to 6 weeks of repeated injection resulted in an anxiety-like phenotype, decreased systemic inflammation (i.e., reduced plasma levels of TNFα and IL4), increased corticosterone reactivity, increased microglial activation and decreased neuronal differentiation in the dentate gyrus (DG). In contrast, exposure to 6 weeks of permanent social isolation resulted in a depressive-like phenotype, increased plasma levels of TNFα, decreased plasma levels of IL10 and VEGF, decreased corticosterone reactivity, decreased microglial cell density and increased cell density for radial glia, s100β-positive cells and mature neuroblasts—all in the DG. Interestingly, combining the two distinct stress paradigms did not have an additive effect on behavioural and biological outcomes, but resulted in yet a different phenotype, characterized by increased anxiety-like behaviour, decreased plasma levels of IL1β, IL4 and VEGF, and decreased hippocampal neuronal differentiation, without altered neuroinflammation or corticosterone reactivity. These findings demonstrate that different forms of chronic stress can differentially alter both behavioural and biological outcomes in young adult male mice, and that combining multiple stressors may not necessarily cause more severe pathological outcomes.


id: cord-343107-oj1re34k
author: Zhou, Haixia
date: 2019-07-11
txt: ./txt/cord-343107-oj1re34k.txt
cache: ./cache/cord-343107-oj1re34k.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/31296843/
doi: 10.1038/s41467-019-10897-4
summary:
  Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. The 7D10 antibody recognizes the NTD of MERS-CoV S glycoprotein and neutralizes the infectivity of pseudotyped and live virus with a potency comparable to those of the most active RBD-targeting antibodies. The NTD N222Q mutation also dramatically reduced the binding and neutralization by 7D10, but did not dramatically affect the cell infection of pseudotyped MERS-CoV ( Supplementary Fig. 11) . A conformation-dependent neutralizing monoclonal antibody specifically targeting receptor-binding domain in Middle East respiratory syndrome coronavirus spike protein A humanized neutralizing antibody against MERS-CoV targeting the receptor-binding domain of the spike protein

title:
  Structural definition of a neutralization epitope on the N-terminal domain of MERS-CoV spike glycoprotein

abstract:
  Most neutralizing antibodies against Middle East respiratory syndrome coronavirus (MERS-CoV) target the receptor-binding domain (RBD) of the spike glycoprotein and block its binding to the cellular receptor dipeptidyl peptidase 4 (DPP4). The epitopes and mechanisms of mAbs targeting non-RBD regions have not been well characterized yet. Here we report the monoclonal antibody 7D10 that binds to the N-terminal domain (NTD) of the spike glycoprotein and inhibits the cell entry of MERS-CoV with high potency. Structure determination and mutagenesis experiments reveal the epitope and critical residues on the NTD for 7D10 binding and neutralization. Further experiments indicate that the neutralization by 7D10 is not solely dependent on the inhibition of DPP4 binding, but also acts after viral cell attachment, inhibiting the pre-fusion to post-fusion conformational change of the spike. These properties give 7D10 a wide neutralization breadth and help explain its synergistic effects with several RBD-targeting antibodies.


id: cord-346054-k84rcpav
title: PreDicta chip-based high resolution diagnosis of rhinovirus-induced wheeze
author: Niespodziana, Katarzyna
date: 2018-06-18
txt: ./txt/cord-346054-k84rcpav.txt
cache: ./cache/cord-346054-k84rcpav.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/29915220/
doi: 10.1038/s41467-018-04591-0
summary:
  Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. The analysis of IgG reactivity to structural and non-structural proteins and to recombinant fragments and synthetic peptides spanning VP1, VP2, and VP3 from RV89 is shown in Supplementary Fig. 2a for all 120 children and in Supplementary Fig. 2b for those children (n = 41) who had shown increases of RV89-specific antibody responses in follow-up serum samples taken after recovery. Based on our previous observations that antibody increases specific for the N-terminal portion of VP1 can be detected in serum samples obtained from subjects after RV infection 36 , the PreDicta chip was equipped with a VP1 peptide set which should allow detecting species-specific immune responses at high resolution ( Fig. 1 ).

abstract:
  Rhinovirus (RV) infections are major triggers of acute exacerbations of severe respiratory diseases such as pre-school wheeze, asthma and chronic obstructive pulmonary disease (COPD). The occurrence of numerous RV types is a major challenge for the identification of the culprit virus types and for the improvement of virus type-specific treatment strategies. Here, we develop a chip containing 130 different micro-arrayed RV proteins and peptides and demonstrate in a cohort of 120 pre-school children, most of whom had been hospitalized due to acute wheeze, that it is possible to determine the culprit RV species with a minute blood sample by serology. Importantly, we identify RV-A and RV-C species as giving rise to most severe respiratory symptoms. Thus, we have generated a chip for the serological identification of RV-induced respiratory illness which should be useful for the rational development of preventive and therapeutic strategies targeting the most important RV types.


id: cord-348972-r94fhpe0
title: Machine-learning approach expands the repertoire of anti-CRISPR protein families
author: Gussow, Ayal B.
date: 2020-07-29
txt: ./txt/cord-348972-r94fhpe0.txt
cache: ./cache/cord-348972-r94fhpe0.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32728052/
doi: 10.1038/s41467-020-17652-0
summary:
  The most striking and obvious common feature of the Acrs is their small size (weighted mean Acr length: 104 aa, Table 1 ), and the tendency to form sets of small proteins that are encoded by co-directional and closely spaced genes in (pro)virus genomes (hereafter directons; Fig. 1 , Table 1 ). As genes encoding Acrs tend to form small directons, we sought to estimate a heuristic maximum threshold for the mean directon size in a candidate family that would enrich our protein set for true Acrs. The initial set consisted of 232,616 clusters and was first filtered for clusters that included at least one member with an HTH-domain-containing protein encoded downstream, and at least one member from a self-targeting genome, two hallmark Acr characteristics 20 .

abstract:
  The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including diverse anti-CRISPR proteins (Acrs) that specifically inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small and highly variable proteins which makes their bioinformatic prediction a formidable task. We present a machine-learning approach for comprehensive Acr prediction. The model shows high predictive power when tested against an unseen test set and was employed to predict 2,500 candidate Acr families. Experimental validation of top candidates revealed two unknown Acrs (AcrIC9, IC10) and three other top candidates were coincidentally identified and found to possess anti-CRISPR activity. These results substantially expand the repertoire of predicted Acrs and provide a resource for experimental Acr discovery.


id: cord-350286-n7ylgqfu
author: Giri, Rajanish
date: 2020-04-03
txt: ./txt/cord-350286-n7ylgqfu.txt
cache: ./cache/cord-350286-n7ylgqfu.txt
extension: .txt
mime: text/plain
url: https://doi.org/10.1101/2020.03.13.990598
doi: 10.1101/2020.03.13.990598
summary:
  The results of this analysis are summarized in Table 2 , which clearly shows that most of the SARS-CoV-2 proteins contain at least one MoRF, indicating that disorder does play an important role in the functionality of these viral proteins. As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Global analysis of intrinsic disorder in the replicase polyprotein 1ab Table 3 represents the PPID mean scores of 15 non-structural proteins (Nsps) derived from the Replicase polyprotein 1ab in SARS-CoV-2, Human SARS CoV, and Bat CoV. Similar to many other non-structural proteins of coronaviruses, Nsp15s from SARS-CoV-2, Human SARS, and Bat CoV are predicted to possess multiple flexible regions but contain virtually no IDPRs (see Figures 32A, 32B, and 32C) .

title:
  When Darkness Becomes a Ray of Light in the Dark Times: Understanding the COVID-19 via the Comparative Analysis of the Dark Proteomes of SARS-CoV-2, Human SARS and Bat SARS-Like Coronaviruses

abstract:
  Recently emerged coronavirus designated as SARS-CoV-2 (also known as 2019 novel coronavirus (2019-nCoV) or Wuhan coronavirus) is a causative agent of coronavirus disease 2019 (COVID-19), which is rapidly spreading throughout the world now. More than 9,00,000 cases of SARS-CoV-2 infection and more than 47,000 COVID-19-associated mortalities have been reported worldwide till the writing of this article, and these numbers are increasing every passing hour. World Health Organization (WHO) has declared the SARS-CoV-2 spread as a global public health emergency and admitted that the COVID-19 is a pandemic now. The multiple sequence alignment data correlated with the already published reports on the SARS-CoV-2 evolution and indicated that this virus is closely related to the bat Severe Acute Respiratory Syndrome-like coronavirus (bat SARS-like CoV) and the well-studied Human SARS coronavirus (SARS CoV). The disordered regions in viral proteins are associated with the viral infectivity and pathogenicity. Therefore, in this study, we have exploited a set of complementary computational approaches to examine the dark proteomes of SARS-CoV-2, bat SARS-like, and human SARS CoVs by analysing the prevalence of intrinsic disorder in their proteins. According to our findings, SARS-CoV-2 proteome contains very significant levels of structural order. In fact, except for Nucleocapsid, Nsp8, and ORF6, the vast majority of SARS-CoV-2 proteins are mostly ordered proteins containing less intrinsically disordered protein regions (IDPRs). However, IDPRs found in SARS-CoV-2 proteins are functionally important. For example, cleavage sites in its replicase 1ab polyprotein are found to be highly disordered, and almost all SARS-CoV-2 proteins were shown to contain molecular recognition features (MoRFs), which are intrinsic disorder-based protein-protein interaction sites that are commonly utilized by proteins for interaction with specific partners. The results of our extensive investigation of the dark side of the SARS-CoV-2 proteome will have important implications for the structural and non-structural biology of SARS or SARS-like coronaviruses. Significance The infection caused by a novel coronavirus (SARS-CoV-2) that causes severe respiratory disease with pneumonia-like symptoms in humans is responsible for the current COVID-19 pandemic. No in-depth information on structures and functions of SARS-CoV-2 proteins is currently available in the public domain, and no effective anti-viral drugs and/or vaccines are designed for the treatment of this infection. Our study provides the first comparative analysis of the order- and disorder-based features of the SARS-CoV-2 proteome relative to human SARS and bat CoV that may be useful for structure-based drug discovery.


id: cord-351837-vasuu70k
author: Shannon, Ashleigh
date: 2020-09-17
txt: ./txt/cord-351837-vasuu70k.txt
cache: ./cache/cord-351837-vasuu70k.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/32943628/
doi: 10.1038/s41467-020-18463-z
summary:
  title: Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. This enzyme readily incorporates T-705-ribose-5′-phosphate into viral RNA in vitro, and cell culture based infectious virus studies show an increase in mutations in the presence of Favipiravir. To determine the efficacy and MoA of T-705 against SARS-CoV we first characterised nsp12 primerdependent activity using traditional annealed primer-template (PT) and self-priming hairpin (HP) RNAs that may confer additional stability on the elongation complex ( Supplementary Fig. 1c) . These data reveal that the SARS-CoV nsp12 is the fastest viral RdRp known, with rates significantly faster than the 5-20 s −1 observed for picornaviral polymerases at room temperature [33] [34] [35] and 4-18 s −1 for hepatitis C and dengue virus polymerases at 30 and 37°C 36, 37 .

title:
  Rapid incorporation of Favipiravir by the fast and permissive viral RNA polymerase complex results in SARS-CoV-2 lethal mutagenesis

abstract:
  The ongoing Corona Virus Disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has emphasized the urgent need for antiviral therapeutics. The viral RNA-dependent-RNA-polymerase (RdRp) is a promising target with polymerase inhibitors successfully used for the treatment of several viral diseases. We demonstrate here that Favipiravir predominantly exerts an antiviral effect through lethal mutagenesis. The SARS-CoV RdRp complex is at least 10-fold more active than any other viral RdRp known. It possesses both unusually high nucleotide incorporation rates and high-error rates allowing facile insertion of Favipiravir into viral RNA, provoking C-to-U and G-to-A transitions in the already low cytosine content SARS-CoV-2 genome. The coronavirus RdRp complex represents an Achilles heel for SARS-CoV, supporting nucleoside analogues as promising candidates for the treatment of COVID-19.


id: cord-354003-ko45l1qv
title: Parallel global profiling of plant TOR dynamics reveals a conserved role for LARP1 in translation
author: Scarpin, M Regina
date: 2020-10-15
txt: ./txt/cord-354003-ko45l1qv.txt
cache: ./cache/cord-354003-ko45l1qv.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/33054972/
doi: 10.7554/elife.58795
summary:
  Pioneering efforts to identify the mechanisms regulating translation of 5 0 TOP mRNAs, however, did show that wheat germ extracts contain a repressor that specifically limits translation of 5 0 TOP mRNAs in cell-free translation assays (Biberman and Meyuhas, 1999; Shama and Meyuhas, 1996) , suggesting that plants also discriminately regulate translation of 5 0 TOP mRNAs. Here, we show that the TOR-LARP1-5 0 TOP signaling axis regulates translation in Arabidopsis, impacting expression of a set of deeply conserved 5 0 TOP genes, including translation elongation factors, polyA-binding proteins, karyopherins/importins, and the translationally-controlled tumor protein. TOR-LARP1-5 0 TOP signaling in Arabidopsis seedlings regulates translation of mRNAs that encode deeply conserved eukaryotic proteins, plant lineage-specific proteins, and diverse proteins involved in ribosome biogenesis.

abstract:
  Target of rapamycin (TOR) is a protein kinase that coordinates eukaryotic metabolism. In mammals, TOR specifically promotes translation of ribosomal protein (RP) mRNAs when amino acids are available to support protein synthesis. The mechanisms controlling translation downstream from TOR remain contested, however, and are largely unexplored in plants. To define these mechanisms in plants, we globally profiled the plant TOR-regulated transcriptome, translatome, proteome, and phosphoproteome. We found that TOR regulates ribosome biogenesis in plants at multiple levels, but through mechanisms that do not directly depend on 5′ oligopyrimidine tract motifs (5′TOPs) found in mammalian RP mRNAs. We then show that the TOR-LARP1-5′TOP signaling axis is conserved in plants and regulates expression of a core set of eukaryotic 5′TOP mRNAs, as well as new, plant-specific 5′TOP mRNAs. Our study illuminates ancestral roles of the TOR-LARP1-5′TOP metabolic regulatory network and provides evolutionary context for ongoing debates about the molecular function of LARP1.


id: cord-354743-mjaqt6wk
title: Viruses are a dominant driver of protein adaptation in mammals
author: Enard, David
date: 2016-05-17
txt: ./txt/cord-354743-mjaqt6wk.txt
cache: ./cache/cord-354743-mjaqt6wk.txt
extension: .txt
mime: text/plain
url: https://www.ncbi.nlm.nih.gov/pubmed/27187613/
doi: 10.7554/elife.12469
summary:
  Intriguingly, unlike for non-immune VIPs or all VIPs considered together (top of Figure 4B ), immune VIPs, including antiviral VIPs (Supplementary file 1D), do not show any increase of adaptation compared to immune non-VIPs. The lack of a signal is unlikely to be due to reduced statistical power of the comparison in a smaller set of immune proteins, given that 1000 random samples of non-immune VIPs with the same size as the immune VIPs sample (241) always exhibited a significantly (p<0.05) increased rate of adaptation compared to non-immune non-VIPs. The classic MK test is known to be biased downward by the presence of slightly deleterious non-synonymous variants (Charlesworth and Eyre-Walker, 2008b) and this bias is difficult to eliminate fully even by excluding low frequency variants (Messer and Petrov, 2013) .

abstract:
  Viruses interact with hundreds to thousands of proteins in mammals, yet adaptation against viruses has only been studied in a few proteins specialized in antiviral defense. Whether adaptation to viruses typically involves only specialized antiviral proteins or affects a broad array of virus-interacting proteins is unknown. Here, we analyze adaptation in ~1300 virus-interacting proteins manually curated from a set of 9900 proteins conserved in all sequenced mammalian genomes. We show that viruses (i) use the more evolutionarily constrained proteins within the cellular functions they interact with and that (ii) despite this high constraint, virus-interacting proteins account for a high proportion of all protein adaptation in humans and other mammals. Adaptation is elevated in virus-interacting proteins across all functional categories, including both immune and non-immune functions. We conservatively estimate that viruses have driven close to 30% of all adaptive amino acid changes in the part of the human proteome conserved within mammals. Our results suggest that viruses are one of the most dominant drivers of evolutionary change across mammalian and human proteomes. DOI: http://dx.doi.org/10.7554/eLife.12469.001


