Summary of your 'study carrel' ============================== This is a summary of your Distant Reader 'study carrel'. The Distant Reader harvested & cached your content into a collection/corpus. It then applied sets of natural language processing and text mining against the collection. The results of this process was reduced to a database file -- a 'study carrel'. The study carrel can then be queried, thus bringing light specific characteristics for your collection. These characteristics can help you summarize the collection as well as enumerate things you might want to investigate more closely. This report is a terse narrative report, and when processing is complete you will be linked to a more complete narrative report. Eric Lease Morgan Number of items in the collection; 'How big is my corpus?' ---------------------------------------------------------- 41 Average length of all items measured in words; "More or less, how big is each item?" ------------------------------------------------------------------------------------ 6237 Average readability score of all items (0 = difficult; 100 = easy) ------------------------------------------------------------------ 5 Top 50 statistically significant keywords; "What is my collection about?" ------------------------------------------------------------------------- 7 Fig 5 TGEV 4 PCR 2 protein 2 cell 2 S12 2 PEDV 2 AOB 2 AOA 1 wood 1 transfer 1 target 1 sulfate 1 substrate 1 strain 1 sob 1 siRNA 1 response 1 protease 1 plant 1 phase 1 perchlorate 1 pep 1 nitrile 1 nitrate 1 mutan 1 microbial 1 method 1 mass 1 lactobacillus 1 lactic 1 inhibitor 1 group 1 gold 1 gas 1 formaldehyde 1 fgf23 1 family 1 enzyme 1 dna 1 dextransucrase 1 degradation 1 cysteine 1 coli 1 antigen 1 antibody 1 animal 1 acid 1 WWTP 1 VLP Top 50 lemmatized nouns; "What is discussed?" --------------------------------------------- 1221 cell 745 protein 664 % 616 gene 556 virus 465 c 445 protease 443 strain 419 production 418 study 415 ° 387 inhibitor 387 group 384 enzyme 383 activity 378 sample 375 acid 361 method 351 time 351 response 345 culture 344 concentration 343 expression 336 system 331 substrate 328 sequence 326 bacteria 304 result 294 growth 293 vaccine 281 antibody 281 analysis 276 phase 268 ml 256 primer 256 g 248 h 246 medium 244 condition 240 biofilm 238 assay 232 infection 231 family 228 reaction 228 product 228 formation 225 control 224 effect 220 detection 216 process Top 50 proper nouns; "What are the names of persons or places?" -------------------------------------------------------------- 2091 al 1585 et 1052 . 541 Fig 353 PCR 205 pH 199 TGEV 187 RT 185 −1 174 RNA 148 E. 143 P. 134 S 133 IL 121 AOB 117 USA 113 M 112 M. 106 PEDV 102 SUMO 101 S. 98 PBS 97 L 96 China 92 putida 92 IBV 92 ELISA 89 Table 88 VLP 86 Fubc 86 AOA 86 16S 84 II 84 C 82 SIBA 82 Escherichia 81 niger 81 NC8-pSIP409-pgsA 73 T 72 mg 71 B 71 Aspergillus 70 B. 69 CotC 69 B.s 68 C. 67 DCpep 65 MVA 64 Pseudomonas 63 L. Top 50 personal pronouns nouns; "To whom are things referred?" ------------------------------------------------------------- 323 it 248 we 132 they 89 i 43 them 8 itself 5 us 4 one 4 hipb 4 he 2 you 1 tv005 1 themselves 1 rosetta(de3)/pet22b 1 iga1 1 ch/ 1 biocatalysis 1 3times Top 50 lemmatized verbs; "What do things do?" --------------------------------------------- 7507 be 1105 use 816 have 558 show 307 contain 290 base 270 increase 222 obtain 219 compare 206 perform 193 determine 190 indicate 187 include 186 find 185 observe 183 detect 177 describe 171 produce 167 result 167 grow 159 reduce 156 do 151 express 138 induce 136 follow 134 cause 132 develop 130 target 126 add 125 apply 118 involve 117 suggest 117 purify 117 provide 117 demonstrate 116 require 116 report 110 form 108 inhibit 108 analyze 107 bind 103 improve 100 incubate 99 test 99 isolate 95 treat 95 take 94 oxidize 94 enhance 91 measure Top 50 lemmatized adjectives and adverbs; "How are things described?" --------------------------------------------------------------------- 555 high 479 not 415 different 391 also 332 - 284 specific 280 other 271 low 253 bacterial 211 recombinant 211 however 210 only 196 well 190 more 190 immune 181 such 155 most 154 same 146 therefore 143 respectively 141 porcine 139 microbial 139 important 139 first 134 several 133 further 124 real 118 as 117 total 117 then 115 significantly 115 mass 114 present 113 molecular 112 small 110 previously 109 similar 109 new 108 large 106 non 106 human 101 significant 97 novel 94 biological 93 intestinal 92 fungal 92 enteric 92 efficient 90 thus 90 single Top 50 lemmatized superlative adjectives; "How are things described to the extreme?" ------------------------------------------------------------------------- 59 most 40 high 28 good 23 least 12 Most 8 low 8 close 5 large 3 short 3 late 3 great 3 early 2 long 2 big 2 bad 1 postsurgery 1 near 1 hexose Top 50 lemmatized superlative adverbs; "How do things do to the extreme?" ------------------------------------------------------------------------ 96 most 16 least 6 well 1 near Top 50 Internet domains; "What Webbed places are alluded to in this corpus?" ---------------------------------------------------------------------------- 5 www.ncbi.nlm.nih.gov 4 doi.org 1 www.softberry.com 1 www.proteolysis.org 1 www.phylip.com 1 www.ncbi 1 www.jalview.org 1 www.fludb.org 1 www.cazy 1 www.b-basic.nl 1 www.arb-home.de 1 www 1 viceroy.eeb 1 pyro.cme.msu.edu 1 merops.sanger.ac.uk 1 merops.sanger 1 i.cs.hku.hk 1 genome.jgi-psf.org 1 ec.europa.eu 1 crispr.dbcls.jp 1 bp.nuap.nagoya-u.ac.jp 1 avermitilis.ls.kitasato-u.ac 1 archaea.u-psud.fr 1 202.120.12.133 Top 50 URLs; "What is hyperlinked from this corpus?" ---------------------------------------------------- 2 http://www.ncbi.nlm.nih.gov/BLAST 1 http://www.softberry.com/ 1 http://www.proteolysis.org/ 1 http://www.phylip.com/ 1 http://www.ncbi.nlm.nih.gov/sra/ 1 http://www.ncbi.nlm.nih.gov/GenBank/ 1 http://www.ncbi.nlm.nih.gov/BLAST/ 1 http://www.ncbi 1 http://www.jalview.org 1 http://www.fludb.org 1 http://www.cazy 1 http://www.b-basic.nl 1 http://www.arb-home.de 1 http://www 1 http://viceroy.eeb 1 http://pyro.cme.msu.edu/pyro/help.jsp 1 http://merops.sanger.ac.uk/ 1 http://merops.sanger 1 http://i.cs.hku.hk/~sirna/ 1 http://genome.jgi-psf.org/finished_microbes/ 1 http://ec.europa.eu/ 1 http://doi.org/10.1007/s00253-020-10733-6 1 http://doi.org/10.1007/s00253-020-10541-y 1 http://doi.org/10.1007/s00253-019-10319-x 1 http://doi.org/10.1007/s00253-019-09835-7 1 http://crispr.dbcls.jp/ 1 http://bp.nuap.nagoya-u.ac.jp/ 1 http://avermitilis.ls.kitasato-u.ac 1 http://archaea.u-psud.fr/ 1 http://202.120.12.133/TAfinder/ Top 50 email addresses; "Who are you gonna call?" ------------------------------------------------- 1 wangxiaomei@caas.cn Top 50 positive assertions; "What sentences are in the shape of noun-verb-noun?" ------------------------------------------------------------------------------- 4 cells did not 4 group were significantly 4 proteases are important 3 group was comparison 3 production was higher 3 studies have also 2 cells were surface 2 cells were then 2 enzymes is very 2 gene was further 2 genes were quite 2 group was dramatically 2 inhibitors have not 2 inhibitors targeting different 2 method is urgently 2 pcr using primers 2 production did not 2 proteases are also 2 response following oral 2 response was also 2 response was stronger 2 samples were eventually 2 samples were then 2 study showed considerable 2 virus was also 1 . were rarely 1 acid is responsible 1 acid was easily 1 acid was low 1 acid was most 1 acids are phosphoenolpyruvate 1 acids are substrates 1 activities are different 1 activities are difficult 1 activities are putatively 1 activities including β 1 activities were too 1 activity has not 1 activity is comparable 1 activity was always 1 activity was detectable 1 activity was highest 1 activity was not 1 activity was strongly 1 activity was then 1 activity were comparable 1 c using supertaq 1 c were also 1 cell is about 1 cells are able Top 50 negative assertions; "What sentences are in the shape of noun-verb-no|not-noun?" --------------------------------------------------------------------------------------- 2 inhibitors have not yet 1 activity has not yet 1 cells contained no activity 1 culture was not fully 1 enzyme has not yet 1 expression is not constitutive 1 genes are not as 1 method is not applicable 1 methods are not suitable 1 pcr was not completely 1 production did not always 1 production is not very 1 responses is not clear 1 responses were not well 1 strain was not pathogenic 1 viruses are not suitable A rudimentary bibliography -------------------------- id = cord-276575-jfug80yu author = Aigner, Achim title = Applications of RNA interference: current state and prospects for siRNA-based strategies in vivo date = 2007-04-25 keywords = PEI; RNA; siRNA summary = doi = 10.1007/s00253-007-0984-y id = cord-012089-haqqrwad author = Baez, Antonino title = High-flux isobutanol production using engineered Escherichia coli: a bioreactor study with in situ product removal date = 2011-03-10 keywords = Fig; JCL260 summary = Since the feasibility of a bioprocess depends critically on the final product titer (Stephanopoulos 2007) , a synthetic approach to produce higher alcohols from nonfermentative pathways in Escherichia coli was previously devised (Atsumi et al. 2008) , in the present work, gas stripping integrated with fermentation was used to compare the isobutanol production by the high producer (JCL260), isobutanol-tolerant (SA481), and the parental (JCL16) strains carrying pSA65 and pSA69 plasmids. Error bars represent the difference between duplicate cultures Fig. 4 Time profile of acetate production by JCL260 PoxB − mutant and high isobutanol producer (JCL260) strains harboring pSA65/pSA69 plasmids cultivated in shake flasks containing 25 mL of medium. (2010b) found that isobutanol production, cell growth, and glucose consumption rate of SA481 tested in flask cultures were similar to those of JCL260 and that improved tolerance of SA481 did not increase the final titer. doi = 10.1007/s00253-011-3173-y id = cord-012099-fveq5c9w author = Chao, Yuanqing title = Optimization of fixation methods for observation of bacterial cell morphology and surface ultrastructures by atomic force microscopy date = 2011-09-01 keywords = AFM summary = doi = 10.1007/s00253-011-3551-5 id = cord-012432-te3sysra author = Chmura, A. title = Utilization of arylaliphatic nitriles by haloalkaliphilic Halomonas nitrilicus sp. nov. isolated from soda soils date = 2008-11-01 keywords = Halomonas; PAN; PPN; nitrile summary = doi = 10.1007/s00253-008-1685-x id = cord-282321-svoshzz8 author = Eboigbodin, Kevin title = Reverse transcription strand invasion based amplification (RT-SIBA): a method for rapid detection of influenza A and B date = 2016-04-11 keywords = PCR; SIBA summary = doi = 10.1007/s00253-016-7491-y id = cord-012054-bpgb7tgo author = Ferreira, Maria Isabel M. title = Degradation of 4-fluorophenol by Arthrobacter sp. strain IF1 date = 2008-03-01 keywords = Arthrobacter; IF1; degradation; strain summary = doi = 10.1007/s00253-008-1343-3 id = cord-302503-7s9f8wje author = Fu, Yuguang title = Rapid and efficient detection methods of pathogenic swine enteric coronaviruses date = 2020-05-19 keywords = PCR; PEDV; TGEV summary = In October 2010, a severe PED outbreak caused by a highly virulent PEDV variant emerged in southern China with high mortality ranging from 70 to 100%; the result was devastating damage to the pig farm industry and tremendous economic losses, and later, the PEDV variant spreads to other countries, e.g., USA, Canada, and Mexico ( For the early and rapid detection of PEDV, different types of PCR methods have been developed. A TaqMan probe-based real-time PCR to differentiate porcine epidemic diarrhea virus virulent strains from attenuated vaccine strains Development and evaluation of a duplex real-time RT-PCR for detection and differentiation of virulent and variant strains of porcine epidemic diarrhea viruses from the United States Development of a TaqMan-based real-time RT-PCR assay for the detection of SADS-CoV associated with severe diarrhea disease in pigs doi = 10.1007/s00253-020-10645-5 id = cord-257136-zpeh8pmc author = Huang, Xin title = A TaqMan-probe-based multiplex real-time RT-qPCR for simultaneous detection of porcine enteric coronaviruses date = 2019-04-26 keywords = PEDV; TGEV summary = To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, specific primers and probes were designed based on the highly conserved regions of transmissible gastroenteritis virus (TGEV) N, porcine epidemic diarrhea virus (PEDV) M, porcine deltacoronavirus (PDCoV) M, and porcine enteric alphacoronavirus (PEAV) N genes respectively. To develop a simple, rapid, accurate, and high-throughput detection method for diagnosis and differential diagnosis on swine enteric coronaviruses, a TaqMan-probe-based multiplex real-time RT-qPCR assay was established to simultaneously detect TGEV, PEDV, PEAV, and PDCoV from the same reaction vial. To establish a high-specific multiplex real-time RT-qPCR for the detection and differential diagnosis of swine enteric coronaviruses, primer sets, and TaqMan probes were designed targeting the highly conserved regions of PEDV or PDCoV M genes and TGEV or PEAV N genes, based on bioinformatics analysis of each virus. doi = 10.1007/s00253-019-09835-7 id = cord-012062-xlw92xoe author = Ichinose, Hitomi title = Characterization of a modular enzyme of exo-1,5-α-l-arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893 date = 2008-09-01 keywords = PNP summary = doi = 10.1007/s00253-008-1551-x id = cord-339694-sp212tai author = Jiang, Xinpeng title = A phase trial of the oral Lactobacillus casei vaccine polarizes Th2 cell immunity against transmissible gastroenteritis coronavirus infection date = 2016-03-28 keywords = PBS; TGEV; lactobacillus; response summary = doi = 10.1007/s00253-016-7424-9 id = cord-012085-ubdzhkfq author = Jin, Tao title = Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China date = 2011-02-01 keywords = AOA; AOB; PCR summary = The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for amoA gene. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition. Overall, AOB amoA gene copy number was 100 times lower than that of AOA, suggesting that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. doi = 10.1007/s00253-011-3107-8 id = cord-287602-vda01gj6 author = Jin, Yu-Bei title = Immune responses induced by recombinant Lactobacillus plantarum expressing the spike protein derived from transmissible gastroenteritis virus in piglets date = 2018-07-18 keywords = TGEV summary = doi = 10.1007/s00253-018-9205-0 id = cord-012064-egzl6zk9 author = Koopman, Frank W. title = C(1) compounds as auxiliary substrate for engineered Pseudomonas putida S12 date = 2009-06-01 keywords = S12; formaldehyde summary = The hps and phi genes of Bacillus brevis, encoding two key steps of the ribulose monophosphate (RuMP) pathway, were introduced to construct a pathway for the metabolism of the toxic methanol oxidation intermediate formaldehyde. Black arrows indicate the assimilatory RuMP pathway, dashed arrows indicate the dissimilatory RuMP pathway, gray arrows indicate the linear oxidation of formaldehyde to carbon dioxide formate dehydrogenase (Fmd) from the methylotrophic yeast Hansenula polymorpha in Saccharomyces cerevisiae resulted in an increased biomass yield with formaldehyde as auxiliary substrate (Baerends et al. The RuMP pathway strain showed significantly improved performance over the control strain, achieving a biomass yield-on-glucose of 91% when using formaldehyde as auxiliary substrate. putida S12pJNNhp(t) and an empty vector control strain were cultured in a C-limited chemostat with glucose as the primary carbon source and formaldehyde as auxiliary substrate. b Biomass yield increase (on glucose) as function of relative formaldehyde concentration in chemostat cultures of strains S12pJNNhp(t) (triangles) and S12pJNN (t) (squares). doi = 10.1007/s00253-009-1922-y id = cord-012095-vzk2m91v author = Kraakman, Norbertus J. R. title = Review of mass transfer aspects for biological gas treatment date = 2011-06-24 keywords = gas; mass; phase; transfer summary = doi = 10.1007/s00253-011-3365-5 id = cord-004592-a3k56ulv author = Liu, Xiaoju title = SUMO fusion system facilitates soluble expression and high production of bioactive human fibroblast growth factor 23 (FGF23) date = 2012-01-17 keywords = Fig; SUMO; fgf23 summary = To prepare soluble and bioactive recombinant human FGF23 to meet the increasing demand in its pharmacological application, small ubiquitin-related modifier (SUMO)-FGF23 fusion gene and FGF23 non-fusion gene were amplified by standard PCR methods and cloned into vector pET-22b and pET-3c, then transformed into Escherichia coli Rosetta (DE3) and BL21 (DE3). An analysis was performed to determine the effects of the three factors (IPTG concentration, temperature, and time after induction) on the expression yield and productivity of soluble FGF23 in Rosetta(DE3)/pET22b-SUMO-FGF23. The results showed that, except for the combination of pET22b-SUMO-FGF23 and pET3c-SUMO-FGF23, the two kinds of plasmid, and the Rosetta(DE3) host strain (Fig. 3a) , all other combinations had no target protein expressed. Concerning optimal cell growth conditions for protein production, we screened for suitable IPTG concentration, temperature, and time after induction for the expression yield and productivity of soluble FGF23 in Rosetta(DE3)/ pET22b/SUMO-FGF23. High-level expression and purification of soluble recombinant FGF21 protein by SUMO fusion in Escherichia coli doi = 10.1007/s00253-011-3864-4 id = cord-012101-mfgca1ou author = Luesken, Francisca A. title = Diversity and enrichment of nitrite-dependent anaerobic methane oxidizing bacteria from wastewater sludge date = 2011-06-11 keywords = Lieshout; NC10; WWTP summary = doi = 10.1007/s00253-011-3361-9 id = cord-321602-88b2h06y author = Lv, Chenfei title = Construction of an infectious bronchitis virus vaccine strain carrying chimeric S1 gene of a virulent isolate and its pathogenicity analysis date = 2020-08-19 keywords = Fig; H120; IBV; SCS1 summary = doi = 10.1007/s00253-020-10834-2 id = cord-012056-8b3xffsh author = Maas, Ronald H. W. title = Lactic acid production from lime-treated wheat straw by Bacillus coagulans: neutralization of acid by fed-batch addition of alkaline substrate date = 2008-04-01 keywords = LTWS; acid; lactic summary = doi = 10.1007/s00253-008-1361-1 id = cord-012090-pnt4y7zd author = Marasabessy, Ahmad title = Enhancing Jatropha oil extraction yield from the kernels assisted by a xylan-degrading bacterium to preserve protein structure date = 2011-05-10 keywords = Jatropha; MB4 summary = doi = 10.1007/s00253-011-3312-5 id = cord-012086-sqv56mmq author = Meijnen, Jean-Paul title = Improved p-hydroxybenzoate production by engineered Pseudomonas putida S12 by using a mixed-substrate feeding strategy date = 2011-02-02 keywords = S12; pep summary = The key precursors for p-hydroxybenzoate production by engineered Pseudomonas putida S12 are phosphoenolpyruvate (PEP) and erythrose-4-phosphate (E4P), for which the pentose phosphate (PP) pathway is an important source. Even without xylose-co-feeding, p-hydroxybenzoate production was improved in the evolved xylose-utilizing strain, which may indicate an intrinsically elevated PP pathway activity. Pseudomonas putida S12 is a solvent-tolerant bacterium that has been developed as a platform host for the production of a range of substituted aromatic compounds such as phenol, tcinnamate, p-coumarate, p-hydroxybenzoate, and p-hydroxystyrene (Nijkamp et al. putida S12pal_xylB7 on glucose as single carbon source showed a product-tosubstrate yield of 4.9 Cmol%, with a specific production (Fig. 3b) . Because of the improved biomass yield, the effect of the primary substrate on the specific phydroxybenzoate production rate q p was limited: the q p on glycerol (8.57 μmol C (g CDW) −1 h −1 ) was only slightly higher than on glucose (7.96 μmol C (g CDW) −1 h −1 ). doi = 10.1007/s00253-011-3089-6 id = cord-010914-08omkszy author = Morinaga, Kana title = Peculiarities of biofilm formation by Paracoccus denitrificans date = 2020-01-30 keywords = GMP; Paracoccus summary = doi = 10.1007/s00253-020-10400-w id = cord-011212-ovjdzyxv author = Pan, Qing title = Development and application of a novel ELISA for detecting antibodies against group I fowl adenoviruses date = 2019-12-14 keywords = China; ELISA summary = doi = 10.1007/s00253-019-10208-3 id = cord-011320-cwvkox29 author = Puente-Massaguer, Eduard title = Integrating nanoparticle quantification and statistical design of experiments for efficient HIV-1 virus-like particle production in High Five cells date = 2020-01-06 keywords = CCI; High; MOI; VLP; cell summary = doi = 10.1007/s00253-019-10319-x id = cord-010991-fp8hljbq author = Rather, Shabeer Ahmad title = Antibodies generated against dextransucrase exhibit potential anticariostatic properties in Streptococcus mutans date = 2020-01-03 keywords = antibody; dextransucrase; mutan summary = For vaccine development, attention was paid on the purified antigens involved in the pathogenesis of dental caries for the development of potentially safer vaccines, which may reduce the viability of bacteria in the saliva, impairing the surface adhesion and inhibiting the metabolically active enzymes involved in caries formation (Chen and Wang 2010) . mutans have shown encouraging results related to dental caries protection, but were limited by the cross-reactive epitopes against human heart and skeleton muscle tissues as detected by indirect immunofluorescence and crossed immunoelectrophoresis (Kt et al. In the present study, we have tried to evaluate the effect of anti-dextransucrase antibodies on caries formation by using purified dextransucrase as the antigen from S. Protein samples of the liver, heart, spleen, kidney of mice, rat and liver, kidney of rabbit were analysed by western blot analysis to evaluate the cross reactivity of purified antibody with mammalian tissues Fig. 5a . doi = 10.1007/s00253-019-10327-x id = cord-011012-5mev3otu author = Rathore, Abhishek Singh title = Production and immunogenicity of Fubc subunit protein redesigned from DENV envelope protein date = 2020-03-30 keywords = DENV; Fubc; protein summary = It was observed by ELISA that Fubc fusion protein elicited higher serum IgG antibody response either in the presence or in absence of Freund''s adjuvant in comparison to the immune response of Fu and bc peptides separately. Herein, we have expressed the recombinant Fubc antigenic protein, optimised its large-scale purification protocol and finally evaluated its protein-specific immune response in BALB/c mice. Therefore, these two conserved Fu and bc loops have been selected to design a recombinant Fubc antigenic protein for the development of dengue subunit vaccine. Immune response to the purified Fubc protein in BALB/c mice From indirect ELISA, it was observed that the serum IgG levels in both male and female groups treated with Fubc proteins were significantly higher than those treated with only adjuvant and PBS control (Fig. 4a, b) . Antibodies to envelope glycoprotein of dengue virus during the natural course of infection are predominantly cross-reactive and recognize epitopes containing highly conserved residues at the fusion loop of domain II doi = 10.1007/s00253-020-10541-y id = cord-012448-9cuq0jqg author = Roosen, Christoph title = Ionic liquids in biotechnology: applications and perspectives for biotransformations date = 2008-12-01 keywords = CALB summary = doi = 10.1007/s00253-008-1730-9 id = cord-288673-ku3tmjd3 author = Sabotič, Jerica title = Microbial and fungal protease inhibitors—current and potential applications date = 2012-01-05 keywords = Barrett; Rawlings; Staphylococcus; cysteine; family; inhibitor; plant; protease; protein; target summary = Because proteases play essential roles in life and death processes in all living organisms and because peptide bond hydrolysis is irreversible, anomalies in proteolytic activities lead to numerous pathological conditions, including cancer, neurodegenerative disorders and inflammatory and cardiovascular diseases, as well as bacterial, viral and parasitic diseases (Lopez-Otin and Bond 2008; Turk 2006) . Another important oral cavity pathogen involved in periodontal disease, Porphyromonas gingivalis, in addition to a few cysteine proteases (discussed further in the following), produces a serine protease, a prolyl tripeptidyl peptidase PtpA (family S9), which is involved in degrading host connective tissue, providing nutrients for bacterial growth (Banbula et al. Several proteases of the serine catalytic type have also been targeted for the design of specific protease inhibitors for use in cancer treatment, including the urokinase plasminogen activator and matriptase (Abbenante and Fairlie 2005; Bialas and Kafarski 2009; Ulisse et al. doi = 10.1007/s00253-011-3834-x id = cord-012430-3uvhoca9 author = Sanchis, Joaquin title = Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates date = 2008-11-01 keywords = PCR; method summary = doi = 10.1007/s00253-008-1678-9 id = cord-012431-l2i5utne author = Sorokin, D. Y. title = Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors date = 2008-10-01 keywords = Sorokin; Thioalkalivibrio; sob summary = title: Microbiological analysis of the population of extremely haloalkaliphilic sulfur-oxidizing bacteria dominating in lab-scale sulfide-removing bioreactors Therefore, the feasibility of sulfide oxidation into elemental sulfur under oxygen limitation was tested at extremely haloalkaline conditions in lab-scale bioreactors using mix sediments from hypersaline soda lakes as inoculum. The microbiological analysis, both culture dependent and independent, of the successfully operating bioreactors revealed a domination of obligately chemolithoautotrophic and extremely haloalkaliphilic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio. Molecular analysis of the biomass from two SL-BR and two FBR bioreactors based on 16S rRNA gene DGGE showed low genetic diversity, typical for autotrophic mix cultures with domination of one to two SOB genotypes and some side heterotrophic populations (Fig. 4) . In the natural soda lake sediments, often another genus of low salt-tolerant alkaliphilic SOB (Thioalkalimicrobium) can be found, which is characterized by extremely high rates of sulfide oxidation (Sorokin and Kuenen 2005; Sorokin et al. doi = 10.1007/s00253-008-1598-8 id = cord-012066-8anhcyia author = Stams, Alfons J. M. title = Citric acid wastewater as electron donor for biological sulfate reduction date = 2009-07-01 keywords = S101; sulfate summary = doi = 10.1007/s00253-009-1995-7 id = cord-354904-7gq2e6f0 author = Staroverov, Sergey A. title = Prospects for the use of spherical gold nanoparticles in immunization date = 2018-11-06 keywords = GNP; TGEV; animal; antigen; gold summary = doi = 10.1007/s00253-018-9476-5 id = cord-011147-55whf8md author = Sun, Hengchang title = Oral delivery of Bacillus subtilis spores expressing Clonorchis sinensis paramyosin protects grass carp from cercaria infection date = 2020-01-07 keywords = CFU; Fig; group summary = title: Oral delivery of Bacillus subtilis spores expressing Clonorchis sinensis paramyosin protects grass carp from cercaria infection Potential pathogenetic bacteria with lower abundance and higher abundances of candidate probiotics and bacteria associated with digestion in 1 × 10(11) CFU/g B.s-CotC-CsPmy spores administrated fishes could be detected compared with control group. In the present study, the specific IgM antibody levels in serum, bile, intestinal mucus, and skin mucus of grass carp orally administrated with different dosages of spores (B.s-CotC-CsPmy) were significantly increased with dosedependent from the 2nd week after the beginning of the immunization till to 6 weeks (Fig. 2) . Immune response induced by oral delivery of Bacillus subtilis spores expressing enolase of Clonorchis sinensis in grass carps (Ctenopharyngodon idellus) doi = 10.1007/s00253-019-10316-0 id = cord-012072-98wuq5ri author = Sun, Yvonne title = Behavioral response of dissimilatory perchlorate-reducing bacteria to different electron acceptors date = 2009-06-17 keywords = nitrate; perchlorate summary = doi = 10.1007/s00253-009-2051-3 id = cord-012435-tt44dkqd author = Temudo, Margarida F. title = Diversity of microbial communities in open mixed culture fermentations: impact of the pH and carbon source date = 2008-10-01 keywords = Fig; microbial; substrate summary = doi = 10.1007/s00253-008-1669-x id = cord-012058-ds7u3ke9 author = Verma, Pradeep title = Determination of fungal activity in modified wood by means of micro-calorimetry and determination of total esterase activity date = 2008-08-01 keywords = DMDHEU; wood summary = doi = 10.1007/s00253-008-1525-z id = cord-348310-nc1tq5af author = Vázquez-Ramírez, Daniel title = High titer MVA and influenza A virus production using a hybrid fed-batch/perfusion strategy with an ATF system date = 2019-02-23 keywords = Fig; Hybrid; MVA; cell summary = doi = 10.1007/s00253-019-09694-2 id = cord-026729-hn0q0sbv author = Xu, Jun title = Functional investigation of the chromosomal ccdAB and hipAB operon in Escherichia coli Nissle 1917 date = 2020-06-13 keywords = Escherichia; Fig; coli; dna summary = doi = 10.1007/s00253-020-10733-6 id = cord-012096-d7e89x03 author = Zhang, Tong title = Ammonia-oxidizing archaea and ammonia-oxidizing bacteria in six full-scale wastewater treatment bioreactors date = 2011-06-25 keywords = 16S; AOA; AOB summary = doi = 10.1007/s00253-011-3408-y id = cord-012098-1nxws0dk author = van den Brink, Joost title = Fungal enzyme sets for plant polysaccharide degradation date = 2011-07-23 keywords = Aspergillus; enzyme summary = doi = 10.1007/s00253-011-3473-2