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1.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Phylum Euryarchaeota
- Halococcus hamelinensis, sequence accession PRJNA80845 [1]
- “Methanocella conradii” HZ254, sequence accession CP003243 [2]
- Thermococcus litoralis NS-C, sequence accession AHVB00000000 [3]
Phylum Crenarchaeota
- Candidatus Nitrosopumilus salaria” BD31, sequence accession AEXL00000000 [4]
- Candidatus Nitrosoarchaeum limnia, sequence accession AHJG00000000 [5]
Phylum Deinococcus-Thermus
Phylum Proteobacteria
- Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession CP003099 [7]
- Alishewanella jeotgali, sequence accession AHTH00000000 [8]
- Enterobacter aerogenes KCTC 2190, sequence accession CP002824 [9]
- Escherichia coli O104:H4, sequence accession AFOB02000092 [10]
- Helicobacter pylori strains 17874, sequence accession PRJNA76569 [11]
- Helicobacter pylori strains P79, sequence accession PRJNA76567 [11]
- Janthinobacterium sp. Strain PAMC 25724, sequence accession AHHB00000000 [12]
- Klebsiella oxytoca KCTC 1686, sequence accession CP003218 [13]
- Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession CP003200 (chromosome), CP003223 (plasmid pKPHS1), CP003224 (plasmid pKPHS2), CP003225 (plasmid pKPHS3), CP003226 (plasmid pKPHS4), CP003227 (plasmid pKPHS5), CP003228 (plasmid pKPHS6) [14]
- Oceanimonas sp. GK1, sequence accession CP003171 [15]
- “Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession NZ_ACIS01000000 [16]
- Pseudomonas extremaustralis 14-3b, sequence accession AHIP00000000 [17]
- Pseudomonas sp. Strain PAMC 25886, sequence accession AHHC00000000 [18]
- Psychrobacter, sequence accession AHVZ00000000 [19]
- Rahnella sp. Strain Y9602, sequence accession CP002505 [20]
- Rhizobium sp. Strain PDO1-076, sequence accession AHZC00000000 [21]
- Rhodospirillum photometricum DSM122, sequence accession HE663493 [22]
- “Rickettsia sibirica sibirica”, sequence accession AHIZ00000000 [23]
- Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession AHZB00000000 [24]
- Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
- Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession CAGQ00000000 [26]
- Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession CP003278 (chromosome) and CP003279 (plasmid) [27]
- Sphingomonas echinoides ATCC 14820, sequence accession AHIR00000000 [28]
- Strain HIMB55, sequence accession AGIF00000000 [29]
- Vibrio harveyi CAIM 1792, sequence accession AHHQ00000000 [30]
- Wolbachia Strain wAlbB, sequence accession CAGB01000001 to CAGB01000165 [31]
- Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession CAGJ01000001 to CAGJ01000217 [32]
Phylum Tenericutes
Phylum Firmicutes
- Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
- Clostridium difficile Strain CD37, sequence accession AHJJ00000000 [35]
- Clostridium perfringens, sequence accession AFES00000000 [36]
- Lactobacillus fructivorans KCTC 3543, sequence accession AEQY00000000 [37]
- Lactococcus lactis IO-1, sequence accession AP012281 [38]
- Lactobacillus plantarum strain NC8, sequence accession AGRI00000000 [39]
- Paenibacillus dendritiformis C454, sequence accession AHKH00000000 [40]
- Paenibacillus sp. Strain Aloe-11, sequence accession AGFI00000000 [41]
- “Peptoniphilus rhinitidis” 1-13T, sequence accession BAEW01000001 to BAEW01000056 [42]
- Streptococcus macedonicus ACA-DC 198, sequence accession HE613569 and HE613570 [43]
- Staphylococcus aureus VC40, sequence accession CP003033 [44]
- Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession CP003295 (chromosome), CP003296 (plasmid) [45]
- Streptococcus macedonicus ACA-DC 198, sequence accession HE613569 (chromosome), HE613570 (plasmid pSMA198) [46]
Phylum Actinobacteria
- Actinoplanes sp. SE50/110, sequence accession CP003170 [47]
- Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
- Nocardia cyriacigeorgica GUH-2, sequence accession FO082843 [49]
- Salinibacterium sp., sequence accession AHWA00000000 [50]
- Streptomyces acidiscabies 84-104, sequence accession AHBF00000000 [51]
Non-Bacterial genomes
- Bluetongue Virus Serotype 2, sequence accession AJ783905 (Seg-6) and JQ681257 (Seg-1), JQ681257 (Seg-1), JQ681258 (Seg-2), JQ681259 (Seg-3), JQ681260 (Seg-4), JQ681261 (Seg-5), JQ681262 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to JQ681265 (Seg-10) [52]
- Virus Serotype 1, sequence accession AJ585111 (Seg-2), AJ586659 (Seg-6), JQ282770 (Seg-1), JQ282771 (Seg-3), JQ282772 (Seg-4), JQ282773 (Seg-5), JQ282774 (Seg-7), JQ282775 (Seg-8), JQ282776 (Seg-9), and JQ282777 (Seg-10) [52]
- Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
- Danio rerio, sequence accession JQ434101 [54]
- Enterococcal Bacteriophage SAP6, sequence accession JF731128 [55]
- Eubenangee virus, sequence accession JQ070376 through JQ070385 [56]
- Fujian/411-like viruses, sequence accession CY087969 to CY088568 [57]
- Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession JQ611712 (segment S), JQ611713 (segment M), and JQ611714 (segment L) [58]
- Pata virus, sequence accession JQ070386 through JQ070395 [59]
- Porcine Circovirus 2, sequence accession JQ413808 [60]
- Porcine Reproductive and Respiratory Syndrome Virus, sequence accession JQ326271 [61]
- Streptococcus mutans Phage M102AD, sequence accession DQ386162 [62]
- Tilligery virus, sequence accession JQ070366 through JQ070375 [63]
2.
Lavanya Rishishwar Lee S. Katz Nitya V. Sharma Lori Rowe Michael Frace Jennifer Dolan Thomas Brian H. Harcourt Leonard W. Mayer I. King Jordan 《Journal of bacteriology》2012,194(20):5649-5656
Containment strategies for outbreaks of invasive Neisseria meningitidis disease are informed by serogroup assays that characterize the polysaccharide capsule. We sought to uncover the genomic basis of conflicting serogroup assay results for an isolate (M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the M16917 isolate and performed a variety of comparative sequence analyses against N. meningitidis reference genome sequences of known serogroups. Multilocus sequence typing and whole-genome sequence comparison revealed that M16917 is a member of the ST-11 sequence group, which is most often associated with serogroup C. However, sequence similarity comparisons and phylogenetic analysis showed that the serogroup diagnostic capsule polymerase gene (synD) of M16917 belongs to serogroup B. These results suggest that a capsule-switching event occurred based on homologous recombination at or around the capsule locus of M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the M16917 genome sequence, which led to the introduction of an ∼2-kb serogroup B sequence cassette into the serogroup C genomic background. Since there is no currently available vaccine for serogroup B strains of N. meningitidis, this kind capsule-switching event could have public health relevance as a vaccine escape mutant. 相似文献
3.
4.
damo Davi Digenes Siena Isabela Ichihara de Barros Camila Baldin Storti Carlos Alberto Oliveira de Biagi Júnior Larissa Anastacio da Costa Carvalho Silvya Stuchi Maria&#x;Engler Josane de Freitas Sousa Wilson Araújo Silva Jr 《Journal of cellular and molecular medicine》2022,26(3):671
Our previous work using a melanoma progression model composed of melanocytic cells (melanocytes, primary and metastatic melanoma samples) demonstrated various deregulated genes, including a few known lncRNAs. Further analysis was conducted to discover novel lncRNAs associated with melanoma, and candidates were prioritized for their potential association with invasiveness or other metastasis‐related processes. In this sense, we found the intergenic lncRNA U73166 (ENSG00000230454) and decided to explore its effects in melanoma. For that, we silenced the lncRNA U73166 expression using shRNAs in a melanoma cell line. Next, we experimentally investigated its functions and found that migration and invasion had significantly decreased in knockdown cells, indicating an essential association of lncRNA U73166 for cancer processes. Additionally, using naïve and vemurafenib‐resistant cell lines and data from a patient before and after resistance, we found that vemurafenib‐resistant samples had a higher expression of lncRNA U73166. Also, we retrieved data from the literature that indicates lncRNA U73166 may act as a mediator of RNA processing and cell invasion, probably inducing a more aggressive phenotype. Therefore, our results suggest a relevant role of lncRNA U73166 in metastasis development. We also pointed herein the lncRNA U73166 as a new possible biomarker or target to help overcome clinical vemurafenib resistance. 相似文献
5.
In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain AF407339. We challenged a previous study which suggested only one recombination event in AF407339 based on 25 CSFV genomes. Through our re-analysis on the 25 genomes in the previous study and the 41 genomes used in the present study, we argued that there should be possibly at least two clear recombination events happening in AF407339 through genome-wide scanning. The reasons for identifying only one recombination event in the previous study might be due to the limited number of available CSFV genome sequences at that time and the limited usage of detection methods. In contrast, as identified by most detection methods using all available CSFV genome sequences, two major recombination events were found at the starting and ending zones of the genome AF407339, respectively. The first one has two parents AF333000 (minor) and AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents AF531433 (minor) and GQ902941 (major) with beginning and ending breakpoints at 8397 and 11,078 nt of the genome respectively. Phylogenetic incongruence analysis using neighbor-joining algorithm with 1000 bootstrapping replicates further supported the existence of these two recombination events. In addition, we also identified additional 18 recombination events on the available CSFV strains. Some of them may be trivial and can be ignored. In conclusion, CSFV might have relatively high frequency of homologous recombination events. Genome-wide scanning of identifying recombination events should utilize multiple detection methods so as to reduce the risk of misidentification. 相似文献
6.
The small chaperone protein Hsp27 confers resistance to apoptosis, and therefore is an attractive anticancer drug target. We report here a novel mechanism underlying the tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) sensitizing activity of the small molecule LY303511, an inactive analog of the phosphoinositide 3-kinase inhibitor inhibitor LY294002, in HeLa cells that are refractory to TRAIL-induced apoptosis. On the basis of the fact that LY303511 is derived from LY294002, itself derived from quercetin, and earlier findings indicating that quercetin and LY294002 affected Hsp27 expression, we investigated whether LY303511 sensitized cancer cells to TRAIL via a conserved inhibitory effect on Hsp27. We provide evidence that upon treatment with LY303511, Hsp27 is progressively sequestered in the nucleus, thus reducing its protective effect in the cytosol during the apoptotic process. LY303511-induced nuclear translocation of Hsp27 is linked to its sustained phosphorylation via activation of p38 kinase and MAPKAP kinase 2 and the inhibition of PP2A. Furthermore, Hsp27 phosphorylation leads to the subsequent dissociation of its large oligomers and a decrease in its chaperone activity, thereby further compromising the death inhibitory activity of Hsp27. Furthermore, genetic manipulation of Hsp27 expression significantly affected the TRAIL sensitizing activity of LY303511, which corroborated the Hsp27 targeting activity of LY303511. Taken together, these data indicate a novel mechanism of small molecule sensitization to TRAIL through targeting of Hsp27 functions, rather than its overall expression, leading to decreased cellular protection, which could have therapeutic implications for overcoming chemotherapy resistance in tumor cells. 相似文献
7.
Anusri Tripathi Sudip Kumar Dutta Monalisa Majumdar Lena Dhara Debolina Banerjee Krishnangshu Roy 《Indian journal of microbiology》2012,52(4):557-564
Pathogenic Klebsiella pneumoniae, resistant to beta-lactam and quinolone drugs, is widely recognized as important bacteria causing array of diseases. The resistance property is obtained by acquisition of plasmid encoded blaTEM, blaSHV, blaCTX-M, QNRA, QNRB and QNRS genes. The aim of this study was to document the prevalence and association of these resistant genes in K. pneumoniae infecting patients in India. Approximately 97 and 76.7 % of the 73 K. pneumoniae isolates showed resistance towards beta-lactam and quinolone drugs respectively. Bla genes were detected in 74 % of K. pneumoniae isolates; with prevalence in the following order: blaTEM > blaSHV > blaCTXM. QNR genes were detected in 67 % samples. Chi-square analysis revealed significant association between presence of bla and qnr genes in our study (P value = 0.000125). Sequence analysis of some blaTEM, blaSHV, blaCTX-M and QNRB PCR products revealed presence of blaTEM1 (GenBank accession: JN193522), blaTEM116 (JN193523 and JN193524), blaSHV11, blaCTXM72 variants (JF523199) and QNRB1 (JN193526 and JN193527) in our samples. 相似文献
8.
9.
10.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
- Phylum Crenarchaeota
- Thermoproteus tenax, strain Kra1, DSM 2078T sequence accession FN869859 [1]
- Phylum Euryarchaeota
- Haloarcula hispanica CGMCC 1.2049, sequence accession CP002921 (chromosome I), CP002922 (chromosome II), and CP002923 (plasmid pHH400) [2]
- Methanococcus maripaludis, strain X1 (unculturable) sequence accession CP002913 [3]
- Phylum Proteobacteria
- Acinetobacter baumannii strain 1656-2, sequence accession CP001921 [4]
- Arcobacter butzleri strain ED-1, sequence accession AP012047, AP012048, and AP012049 [5]
- Brucella suis strain 1330, sequence accession CP002997 and CP002998 [6]
- Campylobacter fetus subsp. venerealis NCTC 10354, sequence accession AFGH01000000 [7]
- “Chromobacterium sp.” strain C-61, sequence accession CAEE01000001 to CAEE01001118 [8]
- Cronobacter sakazakii strain E899, sequence accession AFMO00000000 [9]
- “Desulfovibrio sp.” strain A2, sequence accession AGFG01000000 [10]
- “Erythrobacter sp.” strain NAP1, sequence accession NZ_AAMW00000000 [11]
- Escherichia coli strain XH140A, sequence accession AFVX01000000 [12]
- Escherichia coli strain XH001, sequence accession AFYG01000000 [13]
- Haemophilus haemolyticus strain M19107, sequence accession AFQN00000000 [14]
- Haemophilus haemolyticus strain M19501, sequence accession AFQO00000000 [14]
- Haemophilus haemolyticus strain M21127, sequence accession AFQP00000000 [14]
- Haemophilus haemolyticus strain M21621, sequence accession AFQQ00000000 [14]
- Haemophilus haemolyticus strain M21639, sequence accession AFQR00000000 [14]
- Idiomarina sp.” strain A28L, sequence accession AFPO01000001 to AFPO01000028 [15]
- Ketogulonicigenium vulgare” strain WSH-001, sequence accession CP002018 (chromosome), CP002019 (plasmid pKVU_100), and CP002020 (plasmid pKVU_200) [16]
- Methylobacter tundripaludum strain SV96, sequence accession AEGW00000000 [17]
- Pseudogulbenkiania sp.” strain NH8B, sequence accession AP012224 [18]
- Pseudomonas aeruginosa NCGM1179, sequence accession DF126593 through DF126613 [19]
- Pseudomonas putida strain B001, sequence accession CAED01000001 to CAEE01000262 [20]
- Pseudomonas putida strain B6-2, sequence accession AGCS01000000 [21]
- Pseudomonas stutzeri CGMCC 1.1803, sequence accession CP002881 [22]
- Ralstonia solanacearum phylotype IB, strain Y45, sequence accession AFWL01000000 [23]
- Rheinheimera sp.” strain A13L, sequence accession AFHI01000001 through AFHI01000072 [24]
- Sphingobium yanoikuyae strain XLDN2-5, sequence accession AFXE01000000 [25]
- Vibrio cholerae strain Amazonia, sequence accession AFSV01000000 [26]
- Phylum Firmicutes
- Bacillus coagulans strain XZL4, sequence accession AFWM01000000 [27]
- Bacillus megaterium strain WSH-002, sequence accession CP003017 (chromosome), plasmids CP003018 (plasmid pBME_100), CP003019 (plasmid pBME_200), and CP003020 (plasmid pBME_300) [28]
- Bacillus pumilus strain S-1, sequence accession AGBY00000000 [29]
- “Desulfosporosinus sp.” strain OT, sequence accession AGAF01000000 [30]
- Lentibacillus jeotgali strain Grbi, sequence accession AGAV01000000 [31]
- Leuconostoc carnosum KCTC 3525, sequence accession BACM01000000 [32]
- Listeria ivanovii subsp. ivanovii strain PAM 55, sequence accession FR687253 [33]
- Paenibacillus riograndensis strain SBR5, sequence accession AGBD01000000 [34]
- Sporolactobacillus inulinus strain CASD, sequence accession AFVQ00000000 [35]
- Streptococcus pseudopneumoniae strain IS7493, sequence accession CP002925 and CP002926 [36]
- Streptococcus salivarius strain 57.I, sequence accession CP002888 and CP002889 [37]
- Streptococcus salivarius strain M18, sequence accession AGBV01000000 [38]
- Streptococcus suis SS12, sequence accession CP002640 [39]
- Streptococcus suis D9, sequence accession CP002641 [39]
- Streptococcus suis D12, sequence accession CP002644 [39]
- Streptococcus suis ST1, sequence accession CP002651 [39]
- Weissella thailandensis strain fsh4-2, sequence accession HE575133 through HE575182 [40]
- Phylum Tenericutes
- Mycoplasma anatis strain 1340, sequence accession AFVJ00000000 [41]
- Mycoplasma capricolum subsp. capripneumoniae strain M1601, sequence accession AENG01000000 [42]
- Mycoplasma putrefaciens Type strain KS1, sequence accession CP003021 [43]
- Corynebacterium pseudotuberculosis strain PAT10, sequence accession CP002924 [44]
- Phylum Actinobacteria
- Bifidobacterium animalis subsp. lactis strain BLC1, sequence accession CP003039 [45]
- Bifidobacterium breve strain DPC 6330, sequence accession AFXX01000000 [46]
- Brachybacterium squillarum strain M-6-3, sequence accession AGBX01000000 [47]
- “Citricoccus sp.” strain CH26A, sequence accession AFXQ01000000 [48]
- Corynebacterium glutamicum strain S9114, sequence accession AFYA01000000 [49]
- Dietzia alimentaria strain 72, sequence accession AGFF01000000 [50]
- Mycobacterium colombiense CECT 3035, sequence accession AFVW00000000 [51]
- Mycobacterium tuberculosis NCGM2209, sequence accession DF126614 and DF126615 [52]
- Rhodococcus erythropolis strain XP, sequence accession AGCF01000000 [53]
- Serinicoccus profundi MCCC 1A05965T, sequence accession AFYF00000000 [54]
- Phylum Spirochaetes
- Leptospira interrogans, sequence accession CP001221 (CI), CP001222 (CII) [55]
- Phylum Bacteroidetes
- Bacteroides faecis Type strain MAJ27T, sequence accession AGDG01000000 [56]
- Bizionia argentinensis, Type strain JUB59T sequence accession AFXZ01000000 [57]
- Flavobacterium branchiophilum strain FL-15, sequence accession FQ859183 [58]
- “Flavobacteriaceae” strain S85, sequence accession AFPK00000000 [59]
- Phylum Thermotogae
- “Thermotoga sp.” strain RQ2, sequence accession CP000969 [60]
Non-Bacterial genomes
- Aspergillus kawachii IFO 4308, sequence accession DF126447 through DF126592, BACL01000001 through BACL01001641, AP012272 [61]
- Cajanus cajan pigeonpea, sequence accession PRJNA72815 [62]
- Coxsackievirus A22, sequence accession JN542510 [63]
- Gordonia phage GRU1, sequence accession JF923797 [64]
- Gordonia phage GTE5, sequence accession JF923796 [64]
- Heterocephalus glaber naked mole rat, sequence accession AFSB00000000, AFSB01000000 [65]
- Human Adenovirus Prototype 17, sequence accession HQ910407 [66]
- Macaca mulatta lasiota rhesus macaque, sequence accession AEHL00000000 [67]
- Macaca mulatta mulatta rhesus macaque, sequence accession AEHK00000000 [67]
- Porcine epidemic diarrhea virus, sequence accession JN547228 [68]
11.
12.
Bryony N. Parsons Suzanne Humphrey Anne Marie Salisbury Julia Mikoleit Jay C. D. Hinton Melita A. Gordon Paul Wigley 《PLoS neglected tropical diseases》2013,7(10)
Salmonella enterica serovar Typhimurium Sequence Type (ST) 313 is a major cause of invasive non-Typhoidal salmonellosis in sub-Saharan Africa. No animal reservoir has been identified, and it has been suggested that ST313 is adapted to humans and transmission may occur via person-to-person spread. Here, we show that ST313 cause severe invasive infection in chickens as well as humans. Oral infection of chickens with ST313 isolates D23580 and Q456 resulted in rapid infection of spleen and liver with all birds infected at these sites by 3 days post-infection. In contrast, the well-defined ST19 S. Typhimurium isolates F98 and 4/74 were slower to cause invasive disease. Both ST19 and ST313 caused hepatosplenomegaly, and this was most pronounced in the ST313-infected animals. At 3 and 7 days post-infection, colonization of the gastrointestinal tract was lower in birds infected with the ST313 isolates compared with ST19. Histological examination and expression of CXCL chemokines in the ileum showed that both D23580 (ST313) and 4/74 (ST19) strains caused increased CXCL expression at 3 days post-infection, and this was significantly higher in the ileum of D23580 vs 4/74 infected birds. At 7 days post-infection, reduced chemokine expression occurred in the ileum of the D23580 but not 4/74-infected birds. Histological analysis showed that D23580 infection resulted in rapid inflammation and pathology including villous flattening and fusion at 3 days post-infection, and subsequent resolution by 7 days. In contrast, 4/74 induced less inflammation and pathology at 3 days post-infection. The data presented demonstrate that ST313 is capable of causing invasive disease in a non-human host. The rapid invasive nature of infection in the chicken, coupled with lower gastrointestinal colonization, supports the hypothesis that ST313 is a distinct pathovariant of S. Typhimurium that has evolved to become a systemic pathogen that can cause disease in several hosts. 相似文献
13.
Zihao Pan Jiale Ma Wenyang Dong Wenchao Song Kaicheng Wang Chengping Lu Huochun Yao 《Applied and environmental microbiology》2015,81(3):976-985
Streptococcus suis is an emerging zoonotic pathogen causing severe infections in pigs and humans. In previous studies, 33 serotypes of S. suis have been identified using serum agglutination. Here, we describe a novel S. suis strain, CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain CZ130302 was reproduced in the BALB/c mouse model. The strain showed a high fatality rate (8/10), higher than those for known virulent serotype 2 strains P1/7 (1/10) and 9801 (2/10). Cell adhesion assay results with bEnd.3 and HEp2 cells showed that CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain CZ130302 had no strong cross-reaction with the other 33 S. suis serotypes. The multiplex PCR assays revealed no specified bands for all four sets used to detect the other 33 serotypes. In addition, genetic analysis of the whole cps gene clusters of all serotypes was performed in this study. The results of comparative genomics showed that the cps gene cluster of CZ130302, which was not previously reported, showed no homology to the gene sequences of the other strains. Especially, the wzy, wzx, and acetyltransferase genes of strain CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain CZ130302 represents a novel variant serotype of S. suis (designated serotype Chz) which has a high potential to be virulent and associated with meningitis in animals. 相似文献
14.
The purpose of this table is to provide the community with a citable record of publications of ongoing genome sequencing projects that have led to a publication in the scientific literature. While our goal is to make the list complete, there is no guarantee that we may have omitted one or more publications appearing in this time frame. Readers and authors who wish to have publications added to subsequent versions of this list are invited to provide the bibliographic data for such references to the SIGS editorial office.
Phylum Crenarchaeota
Phylum Deinococcus-Thermus
Phylum Proteobacteria
- “Achromobacter arsenitoxydans” SY8, sequence accession AGUF00000000 [3]
- Acidovorax sp. Strain NO1, sequence accession AGTS00000000 [4]
- Acinetobacter baumannii AB4857, sequence accession AHAG00000000 [5]
- Acinetobacter baumannii AB5075, sequence accession AHAH00000000 [5]
- Acinetobacter baumannii AB5256, sequence accession AHAI00000000 [5]
- Acinetobacter baumannii AB5711, sequence accession AHAJ00000000 [5]
- Aeromonas salmonicida, sequence accession AGVO00000000 [6]
- Aggregatibacter actinomycetemcomitans RHAA1, sequence accession AHGR00000000 [7]
- Agrobacterium tumefaciens 5A, sequence accession AGVZ00000000 [8]
- Azoarcus sp. Strain KH32C, sequence accession AP012304, AP012305 [9]
- Burkholderia sp. Strain YI23, sequence accession CP003087 (Chromosome 1), CP003088 (Chromosome 2), CP003089 (Chromosome 3), CP003090 (plasmid BYI23_D), CP003091 (plasmid BYI23_E) CP003092 (plasmid BYI23_F) [10]
- Brucella suis VBI22, sequence accession CP003128, CP003129 [11]
- Comamonas testosteroni ATCC 11996, sequence accession AHIL00000000 [12]
- “Commensalibacter intestini” A911T, sequence accession AGFR00000000 [13]
- Edwardsiella ictaluri, sequence accession CP001600.1 [14]
- Enterobacter cloacae subsp. dissolvens SDM, sequence accession AGSY00000000 [15]
- “Gluconobacter morbifer” G707T, sequence accession AGQV00000000 [16]
- Legionella dumoffii TEX-KL, sequence accession AGVT00000000 [17]
- Legionella dumoffii NY-23, sequence accession AGVU00000000 [17]
- Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession CP003192 [18]
- Marinobacterium stanieri S30, sequence accession AFPL00000000 [19]
- “Marinobacter manganoxydans” MnI7-9, sequence accession CP001978 to CP001980 [20]
- Mesorhizobium alhagi CCNWXJ12-2T, sequence accession AHAM00000000 [21]
- Mesorhizobium amorphae, sequence accession AGSN00000000 [22]
- Methylomicrobium alcaliphilum 20Z, sequence accession FO082060 and FO082061 [23]
- Mitsuaria sp. Strain H24L5A, sequence accession CAFG01000001 to CAFG01000607 [24]
- Novosphingobium pentaromativorans US6-1, sequence accession AGFM00000000 [25]
- Pantoea ananatis B1-9, sequence accession CAEI01000001 to CAEI01000169 [26]
- Pantoea ananatis LMG 5342, sequence accession HE617160 (chromosome), HE617161 (pPANA10) [27]
- Pantoea ananatis Strain PA13, sequence accession CP003085 and CP003086 [28]
- Pseudomonas aeruginosa, sequence accession AFXI00000000 [29]
- Pseudomonas aeruginosa, sequence accession AFXJ00000000 [29]
- Pseudomonas aeruginosa, sequence accession AFXK00000000 [29]
- Pseudomonas chlororaphis GP72, sequence accession AHAY01000000 [30]
- Pseudomonas fluorescens F113, sequence accession CP003150 [31]
- Pseudomonas fluorescens Wayne 1R, sequence accession CADX01000001 to CADX01000090 [32]
- Pseudomonas fluorescens Wood1R, sequence accession CAFF01000001 to CAFF01001437 [32]
- Pseudomonas psychrotolerans L19, sequence accession AHBD00000000 [33]
- Pseudoalteromonas rubra ATCC 29570T, sequence accession AHCD00000000 [34]
- Pseudomonas stutzeri SDM-LAC, sequence accession AGSX00000000 [35]
- Pseudoxanthomonas spadix BD-a59, sequence accession CP003093 [36]
- Rickettsia slovaca, sequence accession CP002428 [37]
- Salmonella enterica serovar Pullorum RKS5078, sequence accession CP003047 [38]
- Sinorhizobium meliloti CCNWSX0020, sequence accession AGVV00000000 [39]
- Sphingobium sp. Strain SYK-6, sequence accession AP012222 and AP012223 [40]
- Sphingomonas sp. Strain PAMC 26605, sequence accession AHIS00000000 [41]
- Stenotrophomonas maltophilia RR-10, sequence accession AGRB00000000 [42]
- Strain HIMB30, sequence accession AGIG00000000 [43]
- Taylorella equigenitalis, sequence accession CP003059 [44]
- Vibrio campbellii DS40M4, sequence accession AGIE00000000 [45]
- Vibrio fischeri SR5, sequence accession AHIH00000000 [46]
- Yersinia enterocolitica, sequence accession AGQO00000000 [47]
Phylum Tenericutes
- Candidatus Mycoplasma haemominutum, sequence accession HE613254 [48]
- Mycoplasma haemocanis strain Illinois, sequence accession CP003199 [49]
- Mycoplasma iowae, sequence accession AGFP00000000 [50]
- Mycoplasma pneumoniae Type 2a Strain 309, sequence accession AP012303 [51]
Phylum Firmicutes
- Bacillus cereus F837/76, sequence accession CP003187 (chromosome) CP003188 (pF837_55kb), CP003189 (pF837_10kb) [52]
- Brevibacillus laterosporus Strain GI-9, sequence accession CAGD01000001 to CAGD01000061 [53]
- Clostridium sporogenes PA 3679, sequence accession AGAH00000000 [54]
- Enterococcus mundtii CRL1656, sequence accession AFWZ00000000.1 [55]
- Geobacillus thermoleovorans CCB_US3_UF5, sequence accession CP003125 [56]
- Lactobacillus curvatus Strain CRL705, sequence accession AGBU01000000 [57]
- Lactobacillus rhamnosus ATCC 8530, sequence accession CP003094 [58]
- Lactobacillus rhamnosus R0011, sequence accession AGKC00000000 [59]
- Lactococcus garvieae TB25, sequence accession AGQX01000000 [60]
- Lactococcus garvieae LG9, sequence accession AGQY01000000 [60]
- Lactococcus lactis subsp. cremoris A76, sequence accession CP003132 (chromosome), CP003136 (pQA505), CP003135 (PQA518), CP003134 (pQA549), CP003133 (pQA554) [61]
- Leuconostoc citreum LBAE C10, sequence accession CAGE00000000 [62]
- Leuconostoc citreum LBAE C11, sequence accession CAGF00000000 [62]
- Leuconostoc citreum LBAE E16, sequence accession CAGG00000000 [62]
- Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession CP003101 [63]
- Paenibacillus peoriae Strain KCTC 3763T, sequence accession AGFX00000000 [64]
- Pediococcus acidilactici MA18/5M, sequence accession AGKB00000000 [65]
- Pediococcus claussenii ATCC BAA-344T, sequence accession CP003137 (chromosome), CP003138 (pPECL-1), CP003139 (pPECL-2), CP003140 (pPECL-3), CP003141 (pPECL-4), CP003142 (pPECL-5), CP003143 (pPECL-6), CP003144 (pPECL-7), CP003145 (pPECL-8) [66]
- Staphylococcus aureus M013, sequence accession CP003166 [67]
- Staphylococcus aureus subsp. aureus TW20, sequence accession FN433596 [68]
- Weissella confusa LBAE C39-2, sequence accession CAGH00000000 [69]
Phylum Actinobacteria
- Corynebacterium casei, sequence accession CAFW01000001 to CAFW01000106 [70]
- Corynebacterium glutamicum, sequence accession AGQQ00000000 [71]
- Leucobacter chromiiresistens, sequence accession AGCW00000000 [72]
- Mycobacterium abscessus, sequence accession AGQU00000000 [73]
- Propionibacterium acnes ST9, sequence accession CP003195 [74]
- Propionibacterium acnes ST22, sequence accession CP003196 [74]
- Propionibacterium acnes ST27, sequence accession CP003197 [74]
- Saccharomonospora azurea SZMC 14600, sequence accession AHBX00000000 [75]
- Streptomyces sp. Strain TOR3209, sequence accession AGNH00000000 [76]
- Streptomyces sp. Strain W007, sequence accession AGSW00000000 [77]
Phylum Spirochaetes
- Borrelia valaisiana VS116, sequence accession ABCY02000001 (chromosome), CP001439 (plasmid Ip17), CP001437 (Ip25), CP001440 (plasmid Ip 28-3), CP001442 (plasmid Ip28-8), CP001436 (Ip 36), CP001433 (plasmid Ip 54), CP001438 (plasmid cp9), CP001432 (plasmid cp26), CP001441 (plasmid cp32-5), CP001434 (plasmid cp32-7), CP001435 (plasmid cp32-10) [78]
- “Borrelia bissettii” DN127, sequence accession CP002746 (chromosome), CP002756 (plasmid Ip12), CP002757 (plasmid Ip25), CP002758 (plasmid 28-3), CP002759 (plasmid Ip 28-4), CP002760 (Ip28-7), CP002761 (plasmid Ip54), CP002762 (plasmid Ip56), CP002755 (plasmid cp9), CP002747 (plasmid cp26), CP002749 (plasmid cp32-3), CP002750 (plasmid cp32-4), CP002751 (plasmid 32-5), CP002752 (plasmid cp32-6), CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), CP002748 (plasmid cp32-11) [78]
- Borrelia spielmanii A14S, sequence accession ABKB02000001 (chromosome), CP001468 (plasmid Ip17), CP001471 (Ip28-3), CP001470 (plasmid Ip28-4), CP001465 (plasmid Ip28-2), CP001466 (plasmid Ip36), CP001464 (plasmid Ip38), CP001469 (plasmid Ip54), ABKB02000016, ABKB02000020 (plasmid cp9), CP001467 (plasmid cp26), ABKB02000026 (plasmid cp32-3), ABKB02000031 (plasmid 32-5), ABKB02000021 (plasmid cp32-12), ABKB02000014 (unidentified) [78]
Non-Bacterial genomes
- Aspergillus flavus, sequence accession GSE32177 [79]
- Bacteriophage SPN3UB, sequence accession JQ288021 [80]
- Bamboo mitochondria, sequence accession JQ235166 to JQ235179 [81]
- Boea hygrometrica chloroplast, sequence accession JN107811 [82]
- Boea hygrometrica mitochondrial, sequence accession JN107812 [82]
- Canine Picornavirus, sequence accession JN831356 [83]
- Chandipura virus (CHPV) CIN0327, sequence accession GU212856.1 [84]
- Chandipura virus (CHPV) CIN0451, sequence accession GU212857.1 [84]
- Chandipura virus (CHPV) CIN0751, sequence accession GU212858.1 [84]
- Chandipura virus (CHPV) CIN0755, sequence accession GU190711.1 [84]
- Chinese Porcine Parvovirus Strain PPV2010, sequence accession JN872448 [85]
- Common midwife toad megavirus, sequence accession JQ231222 [86]
- Dengue Virus Serotype 4, sequence accession JN983813 [87]
- Duck Tembusu Virus, sequence accession JF270480 [88]
- Duck Tembusu Virus, sequence accession JQ314464 [88]
- Duck Tembusu Virus, sequence accession JQ314465 [88]
- Emiliania huxleyi Virus 202, sequence accession HQ634145 [89]
- Emiliania huxleyi Virus EhV-88, sequence accession JF974310 [89]
- Emiliania huxleyi EhV-201, sequence accession JF974311 [89]
- Emiliania huxleyi EhV-207, sequence accession JF974317 [89]
- Emiliania huxleyi EhV-208, sequence accession JF974318 [89]
- Glarea lozoyensis, sequence accession GUE00000000 [90]
- Nannochloropis gaditana, sequence accession AGNI00000000 [91]
- Oryza sativa cv., sequence accession DRA000499 [92]
- Partetravirus, sequence accession JN990269 [93]
- Porcine Bocavirus PBoV5, sequence accession JN831651 [94]
- Porcine epidemic diarrhea virus, sequence accession JQ282909 [95]
- Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession HM624080 [96]
- Pseudomonas fluorescens phage OBP, sequence accesssion JN627160 [97]
- RNA Virus from Avocado, sequence accession JN880414 [98]
- Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession JN391180 [99]
- Schistosoma haematobium, sequence accession PRJNA78265 [100]
- Schistosoma mansoni, sequence accession ERP00038 [101]
- Stenopirates sp., sequence accession JN100019 [102]
- T7-Like Virus, sequence accession JN651747 [103]
- Vibrio harveyi siphophage VHS1, sequence accession JF713456 [104]
- Tyrolean ice man, sequence accession ERP001144 [105]
15.
Xiang Li Xiao-Yan Jiang Jin Ge Jing Wang Guo-Jun Chen Liang Xu Duan-Yang Xie Tian-You Yuan Da-Sheng Zhang Hong Zhang Yi-Han Chen 《PloS one》2014,9(1)
Long non-coding RNAs (lncRNAs) are key regulatory molecules involved in a variety of biological processes and human diseases. However, the pathological effects of lncRNAs on primary varicose great saphenous veins (GSVs) remain unclear. The purpose of the present study was to identify aberrantly expressed lncRNAs involved in the prevalence of GSV varicosities and predict their potential functions. Using microarray with 33,045 lncRNA and 30,215 mRNA probes, 557 lncRNAs and 980 mRNAs that differed significantly in expression between the varicose great saphenous veins and control veins were identified in six pairs of samples. These lncRNAs were sub-grouped and mRNAs expressed at different levels were clustered into several pathways with six focused on metabolic pathways. Quantitative real-time PCR replication of nine lncRNAs was performed in 32 subjects, validating six lncRNAs (AF119885, AK021444, NR_027830, G36810, NR_027927, uc.345-). A coding-non-coding gene co-expression network revealed that four of these six lncRNAs may be correlated with 11 mRNAs and pathway analysis revealed that they may be correlated with another 8 mRNAs associated with metabolic pathways. In conclusion, aberrantly expressed lncRNAs for GSV varicosities were here systematically screened and validated and their functions were predicted. These findings provide novel insight into the physiology of lncRNAs and the pathogenesis of varicose veins for further investigation. These aberrantly expressed lncRNAs may serve as new therapeutic targets for varicose veins. The Human Ethnics Committee of Shanghai East Hospital, Tongji University School of Medicine approved the study (NO.: 2011-DF-53). 相似文献
16.
The primary objective of this study was to construct an immune-related long noncoding RNAs (IRLs) classifier to precisely predict the prognosis and immunotherapy response of patients with thymic epithelial tumors (TET). Based on univariable Cox regression analysis and Lasso regression, six prognosis-related IRLs (AC004466.3, AC138207.2, AC148477.2, AL450270.1, HOXB-AS1 and SNHG8) were selected to build an IRL classifier. Importantly, results of qRT-PCR validated that higher expression levels of AC138207.2, AC148477.2, AL450270.1 and SNHG8 as well as lower expression levels of AC004466.3, and HOXB-AS1 in TETs samples compared with normal controls. The IRL classifier could effectively classify patients into the low-risk and high-risk groups based on the different survival parameters. In terms of predictive ability and clinical utility, the IRL classifier was superior to Masaoka staging system. Additionally, IRL classifier is significantly associated with immune cells infiltration (dendritic cells, activated CD4 memory T cells and tumor-infiltrating lymphocyte (TIL), T cell subsets in particular), immune microenvironment (immune score and immune checkpoint inhibitors) and immunogenicity (TMB) in TETs, which hints that IRL classifier is tightly correlated with immune characteristics and might guide more effective immunotherapy strategies for TETs patients. Encouragingly, according to TIDE algorithm, there were more immunotherapy responders in the low-risk IRL subgroup and the IRL score was robustly negatively linked to the immunotherapeutic response. To sum up, the IRL classifier was established, which can be used to predict the prognosis, immune infiltration status, immunotherapy response in TETs patients, and may facilitate personalized counseling for immunotherapy. 相似文献
17.
Marius R. Robciuc Paulina Skrobuk Andrey Anisimov Vesa M. Olkkonen Kari Alitalo Robert H. Eckel Heikki A. Koistinen Matti Jauhiainen Christian Ehnholm 《PloS one》2012,7(10)
Peroxisome proliferator-activated receptor (PPAR) delta is an important regulator of fatty acid (FA) metabolism. Angiopoietin-like 4 (Angptl4), a multifunctional protein, is one of the major targets of PPAR delta in skeletal muscle cells. Here we investigated the regulation of Angptl4 and its role in mediating PPAR delta functions using human, rat and mouse myotubes. Expression of Angptl4 was upregulated during myotubes differentiation and by oleic acid, insulin and PPAR delta agonist GW501516. Treatment with GW501516 or Angptl4 overexpression inhibited both lipoprotein lipase (LPL) activity and LPL-dependent uptake of FAs whereas uptake of BSA-bound FAs was not affected by either treatment. Activation of retinoic X receptor (RXR), PPAR delta functional partner, using bexarotene upregulated Angptl4 expression and inhibited LPL activity in a PPAR delta dependent fashion. Silencing of Angptl4 blocked the effect of GW501516 and bexarotene on LPL activity. Treatment with GW501516 but not Angptl4 overexpression significantly increased palmitate oxidation. Furthermore, Angptl4 overexpression did not affect the capacity of GW501516 to increase palmitate oxidation. Basal and insulin stimulated glucose uptake, glycogen synthesis and glucose oxidation were not significantly modulated by Angptl4 overexpression. Our findings suggest that FAs-PPARdelta/RXR-Angptl4 axis controls the LPL-dependent uptake of FAs in myotubes, whereas the effect of PPAR delta activation on beta-oxidation is independent of Angptl4. 相似文献
18.
Senbagam Duraisamy Fazal Husain Senthilkumar Balakrishnan Aswathy Sathyan Prabhu Subramani Prahalathan Chidambaram Selvaraj Arokiyaraj Wahidah H. Al-Qahtani Jothiramalingam Rajabathar Anbarasu Kumarasamy 《Current issues in molecular biology》2022,44(2):731
Breast milk is the combination of bioactive compounds and microflora that promote newborn’s proper growth, gut flora, and immunity. Thus, it is always considered the perfect food for newborns. Amongst their bioactives, probiotic communities—especially lactic acid bacteria (LAB)—are characterized from breast milk over the first month of parturition. In this study, seven LAB were characterized phenotypically and genotypically as Levilactobacillus brevis BDUMBT08 (MT673657), L. gastricus BDUMBT09 (MT774596), L. paracasei BDUMBT10 (MT775430), L. brevis BDUMBT11 (MW785062), L. casei BDUMBT12 (MW785063), L. casei BDUMBT13 (MW785178), and Brevibacillus brevis M2403 (MK371781) from human breast milk. Their tolerance to lysozyme, acid, bile, gastric juice, pancreatic juice, and NaCl and potential for mucoadhesion, auto-aggregation, and co-aggregation with pathogens are of great prominence in forecasting their gut colonizing ability. They proved their safety aspects as they were negative for virulence determinants such as hemolysis and biofilm production. Antibiogram of LAB showed their sensitivity to more than 90% of the antibiotics tested. Amongst seven LAB, three isolates (L. brevis BDUMBT08 and BDUMBT11, and L. gatricus BDUMBT09) proved their bacteriocin producing propensity. Although the seven LAB isolates differed in their behavior, their substantial probiotic properties with safety could be taken as promising probiotics for further studies to prove their in vivo effects, such as health benefits, in humans. 相似文献
19.
The combination of docetaxel, cisplatin, and S-1 (DCS) is a common chemotherapy regimen for patients with gastric cancer (GC). However, studies on long noncoding RNAs (lncRNAs) associated with the chemotherapeutic response to and prognosis after DCS remain lacking. The aim of the present study was to identify DCS mRNAs-lncRNAs associated with chemotherapy response and prognosis in GC patients. In the present study, we identified 548 lncRNAs associated with these 16 mRNAs in the TCGA and GSE31811 datasets. Eleven lncRNAs were used to construct a prognostic signature by least absolute shrinkage and selection operator (LASSO) regression. A model including the 11 lncRNAs (LINC02532, AC007277.1, AC005324.4, AL512506.1, AC068790.7, AC022509.2, AC113139.1, LINC00106, AC005165.1, MIR100HG, and UBE2R2-AS1) associated with the prognosis of GC was constructed. The signature was validated in the TCGA database, model comparison, and qRT-PCR experiments. The results showed that the risk signature was a more effective prognostic factor for GC patients. Furthermore, the results showed that this model can well predicting chemotherapy drug response and immune infiltration of GC patients. In addition, our experimental results indicated that lower expression levels of LINC00106 and UBE2R2-AS1 predicted worse drug resistance in AGS/DDP cells. The experimental results agreed with the predictions. Furthermore, knockdown of LINC00106 or UBE2R2-AS1 can significantly enhanced the proliferation and migration of GC AGS cells in vitro. In conclusion, a novel DCS therapy-related lncRNA signature may become a new strategy to predict chemotherapy response and prognosis in GC patients. LINC00106 and UBE2R2-AS1 may exhibit a tumor suppressive function in GC. 相似文献
20.
Qing Li Ting-Ting Liu Wen-Long Qiao Jia-Wei Hao Qing-Rui Qin Shuang Wei Xue-Mei Li Chun-Yu Qiu Wang-Ping Hu 《The Journal of biological chemistry》2023,299(3)
Acid-sensing ion channels (ASICs) play an important role in pain associated with tissue acidification. Peripheral inhibitory group II metabotropic glutamate receptors (mGluRs) have analgesic effects in a variety of pain conditions. Whether there is a link between ASICs and mGluRs in pain processes is still unclear. Herein, we show that the group II mGluR agonist LY354740 inhibited acid-evoked ASIC currents and action potentials in rat dorsal root ganglia neurons. LY354740 reduced the maximum current response to protons, but it did not change the sensitivity of ASICs to protons. LY354740 inhibited ASIC currents by activating group II mGluRs. We found that the inhibitory effect of LY354740 was blocked by intracellular application of the Gi/o protein inhibitor pertussis toxin and the cAMP analogue 8-Br-cAMP and mimicked by the protein kinase A (PKA) inhibitor H-89. LY354740 also inhibited ASIC3 currents in CHO cells coexpressing mGluR2 and ASIC3 but not in cells expressing ASIC3 alone. In addition, intraplantar injection of LY354740 dose-dependently alleviated acid-induced nociceptive behavior in rats through local group II mGluRs. Together, these results suggested that activation of peripheral group II mGluRs inhibited the functional activity of ASICs through a mechanism that depended on Gi/o proteins and the intracellular cAMP/PKA signaling pathway in rat dorsal root ganglia neurons. We propose that peripheral group II mGluRs are an important therapeutic target for ASIC-mediated pain. 相似文献