Are Differences in Genomic Data Sets due to True Biological Variants or Errors in Genome Assembly: An Example from Two Chloroplast Genomes

DNA sequencing has been revolutionized by the development of high-throughput sequencing technologies. Plummeting costs and the massive throughput capacities of second and third generation sequencing platforms have transformed many fields of biological research. Concurrently, new data processing pipelines made rapid de novo genome assemblies possible. However, high quality data are critically important for all investigations in the genomic era. We used chloroplast genomes of one Oryza species (O. australiensis) to compare differences in sequence quality: one genome ({"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209) was obtained through Illumina sequencing and reference-guided assembly and the other genome ({"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774) was obtained via target enrichment libraries and shotgun sequencing. Based on the whole genome alignment, {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 was more similar to the reference genome (O. sativa: {"type":"entrez-nucleotide","attrs":{"text":"AY522330","term_id":"42795537","term_text":"AY522330"}}AY522330) with 99.2% sequence identity (SI value) compared with the 98.8% SI values in the {"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774 genome; whereas the opposite result was obtained when the SI values in coding and noncoding regions of {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 and {"type":"entrez-nucleotide","attrs":{"text":"KJ830774","term_id":"662117268","term_text":"KJ830774"}}KJ830774 were compared. Additionally, the junctions of two single copies and repeat copies in the chloroplast genome exhibited differences. Phylogenetic analyses were conducted using these sequences, and the different data sets yielded dissimilar topologies: phylogenetic replacements of the two individuals were remarkably different based on whole genome sequencing or SNP data and insertions and deletions (indels) data. Thus, we concluded that the genomic composition of {"type":"entrez-nucleotide","attrs":{"text":"GU592209","term_id":"290790694","term_text":"GU592209"}}GU592209 was heterogeneous in coding and non-coding regions. These findings should impel biologists to carefully consider the quality of sequencing and assembly when working with next-generation data.     

Novel Variant Serotype of Streptococcus suis Isolated from Piglets with Meningitis

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, {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}CZ130302, isolated from an outbreak of acute piglet meningitis in eastern China. Strong pathogenicity of meningitis caused by strain {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}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 {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}CZ130302 was significantly close to P1/7 and 9801. Both the agglutination test and its complementary test showed that strain {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}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 {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}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 {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}CZ130302 are phylogenetically distinct from strains of the other 33 serotypes. Therefore, this study suggested that strain {"type":"entrez-nucleotide","attrs":{"text":"CZ130302","term_id":"57728550","term_text":"CZ130302"}}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.     

Extensive homologous recombination in classical swine fever virus: A re-evaluation of homologous recombination events in the strain AF407339

In this short report, the genome-wide homologous recombination events were re-evaluated for classical swine fever virus (CSFV) strain {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339. We challenged a previous study which suggested only one recombination event in {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}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 {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}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 {"type":"entrez-nucleotide","attrs":{"text":"AF407339","term_id":"15488012","term_text":"AF407339"}}AF407339, respectively. The first one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF333000","term_id":"13383931","term_text":"AF333000"}}AF333000 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"AY554397","term_id":"49860681","term_text":"AY554397"}}AY554397 (major) with beginning and ending breakpoints located at 19 and 607 nt of the genome respectively. The second one has two parents {"type":"entrez-nucleotide","attrs":{"text":"AF531433","term_id":"22347661","term_text":"AF531433"}}AF531433 (minor) and {"type":"entrez-nucleotide","attrs":{"text":"GQ902941","term_id":"298113017","term_text":"GQ902941"}}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.     

Streptomyces antibioticalis, a Novel Species from a Sanitary Landfill Soil

A novel isolate belonging to the genus Streptomyces, strain SL-4^T, was isolated from soil sample collected from a sanitary landfill, New Delhi, India. The taxonomic status of this isolate was studied by polyphasic approach including morphological, physiological and chemo-taxonomic characterization. Spore chains of SL-4^T were open loops, hooks or extended spirals of wide diameter (retinaculiperti). The cell wall peptidoglycan of the isolate SL-4^T contained L,L-diaminopimelic acid, suggesting that the strain has a cell wall of chemotype-I. The polar lipid profile of the isolate was of Type II, with phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and phosphatidylinositol mannosides. The 16SrRNA gene sequence similarity between SL-4^T and its phylogenetic relatives Streptomyces atrovirens NRRLB 16357^T ({"type":"entrez-nucleotide","attrs":{"text":"DQ026672","term_id":"68137786","term_text":"DQ026672"}}DQ026672), S. albogriseolus NRRLB 1305^T ({"type":"entrez-nucleotide","attrs":{"text":"AJ494865","term_id":"21742835","term_text":"AJ494865"}}AJ494865), S viridodiastaticus NBRC 13106^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184317","term_id":"90960133","term_text":"AB184317"}}AB184317), S. caelestis NRRL 2418^T ({"type":"entrez-nucleotide","attrs":{"text":"X80824","term_id":"587528","term_text":"X80824"}}X80824), S. flavoviridis NBRC 12772^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184842","term_id":"90960663","term_text":"AB184842"}}AB184842), S. pilosus NBRC 12807^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184161","term_id":"90959977","term_text":"AB184161"}}AB184161) and S. longispororuber NBRC 13488^T ({"type":"entrez-nucleotide","attrs":{"text":"AB184440","term_id":"90960256","term_text":"AB184440"}}AB184440) was 99.65, 99.65, 99.64, 99.23, 99.15, 99.14 and 99.13 % respectively. Subsequent DNA–DNA hybridization experiments with the test strain and its clade members showed 55.27, 44.27, 36.86, and 15.65 % relatedness between SL-4^T and its relatives S. atrovirens,S. albogriseolus, S. viridodiastaticus and S. longispororuber respectively. The genotypic and phenotypic data was analyzed to verify possibility of the isolate SL-4^T representing novel member of the genus Streptomyces, for which the name S. antibioticalis is being proposed. The type strain is SL-4^T (=CCM 7434^T=MTCC 8588^T).     

Postnatal PPARδ Activation and Myostatin Inhibition Exert Distinct yet Complimentary Effects on the Metabolic Profile of Obese Insulin-Resistant Mice

Background

Interventions for T2DM have in part aimed to mimic exercise. Here, we have compared the independent and combined effects of a PPARδ agonist and endurance training mimetic ({"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516) and a myostatin antibody and resistance training mimetic (PF-879) on metabolic and performance outcomes in obese insulin resistant mice.

Methodology/Principal Findings

Male ob/ob mice were treated for 6 weeks with vehicle, {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516, PF-879, or {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 in combination with PF-879. The effects of the interventions on body composition, glucose homeostasis, glucose tolerance, energy expenditure, exercise capacity and metabolic gene expression were compared at the end of study. {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 attenuated body weight and fat mass accumulation and increased the expression of genes of oxidative metabolism. In contrast, PF-879 increased body weight by driving muscle growth and altered the expression of genes involved in insulin signaling and glucose metabolism. Despite their differences, both interventions alone improved glucose homeostasis. Moreover, {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 more effectively improved serum lipids, and PF-879 uniquely increased energy expenditure, exercise capacity and adiponectin levels. When combined the robust effects of {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516 and/or PF-879 on body weight, adiposity, muscle mass, glycemia, serum lipids, energy expenditure and exercise capacity were highly conserved.

Conclusions/Significance

The data, for the first time, demonstrate postnatal inhibition of myostatin not only promotes gains in muscle mass similar to resistance training,but improves metabolic homeostasis. In several instances, these effects were either distinct from or complimentary to those of {"type":"entrez-nucleotide","attrs":{"text":"GW501516","term_id":"289075981","term_text":"GW501516"}}GW501516. The data further suggest that strategies to increase muscle mass, and not necessarily oxidative capacity, may effectively counter insulin resistance and T2DM.     

Inhibition of the group I mGluRs reduces acute brain damage and improves long-term histological outcomes after photothrombosis-induced ischaemia

Group I mGluRs (metabotropic glutamate receptors), including mGluR1 and mGluR5, are GPCRs (G-protein coupled receptors) and play important roles in physiology and pathology. Studies on their role in cerebral ischaemia have provided controversial results. In this study, we used a PT (photothrombosis)-induced ischaemia model to investigate whether antagonists to the group I mGluRs may offer acute and long-term protective effects in adult mice. Our results demonstrated that administration with mGluR5 antagonist MPEP [2-methyl-6-(phenylethynyl)-pyridine] or mGluR1 antagonist {"type":"entrez-nucleotide","attrs":{"text":"LY367385","term_id":"1257996803","term_text":"LY367385"}}LY367385 by intraperitoneal injection at 3 h after PT decreased brain infarct volume evaluated one day after ischaemia. Additive effects on infarct volume were observed upon co-injection with MPEP and {"type":"entrez-nucleotide","attrs":{"text":"LY367385","term_id":"1257996803","term_text":"LY367385"}}LY367385. These antagonists also significantly alleviated neurodegeneration and apoptosis in the penumbra. In addition, when evaluated 2 weeks after PT, they reduced infarct volume and tissue loss, attenuated glial scar formation, and inhibited cell proliferation in the penumbra. Importantly, co-injection with MPEP and {"type":"entrez-nucleotide","attrs":{"text":"LY367385","term_id":"1257996803","term_text":"LY367385"}}LY367385 reduced the expression levels of calpain, a Ca²⁺-activated protease known to mediate ischaemia-induced neuronal death. Injection of calpeptin, a calpain inhibitor, could inhibit neuronal death and brain damage after PT but injection of calpeptin together with MPEP and {"type":"entrez-nucleotide","attrs":{"text":"LY367385","term_id":"1257996803","term_text":"LY367385"}}LY367385 did not further improve the protective effects mediated by MPEP and {"type":"entrez-nucleotide","attrs":{"text":"LY367385","term_id":"1257996803","term_text":"LY367385"}}LY367385. These results suggest that inhibition of group I mGluRs is sufficient to protect ischaemic damage through the calpain pathway. Taken together, our results demonstrate that inhibition of group I mGluRs can mitigate PT-induced brain damage through attenuating the effects of calpain, and improve long-term histological outcomes.     

Genome sequences published outside of Standards in Genomic Sciences, January-March 2012

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

• Pyrobaculum strain 1860, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003098","term_id":"356640791","term_text":"CP003098"}}CP003098 [1]

Phylum Deinococcus-Thermus

• “Thermus sp.” Strain CCB_US3_UF1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003126","term_id":"359289533","term_text":"CP003126"}}CP003126 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003127","term_id":"359291781","term_text":"CP003127"}}CP003127 (plasmid) [2]

Phylum Proteobacteria

• “Achromobacter arsenitoxydans” SY8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGUF00000000","term_id":"359366799","term_text":"AGUF00000000"}}AGUF00000000 [3]
• Acidovorax sp. Strain NO1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGTS00000000","term_id":"363417938","term_text":"AGTS00000000"}}AGTS00000000 [4]
• Acinetobacter baumannii AB4857, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAG00000000","term_id":"371492156","term_text":"AHAG00000000"}}AHAG00000000 [5]
• Acinetobacter baumannii AB5075, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAH00000000","term_id":"371492114","term_text":"AHAH00000000"}}AHAH00000000 [5]
• Acinetobacter baumannii AB5256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAI00000000","term_id":"371492153","term_text":"AHAI00000000"}}AHAI00000000 [5]
• Acinetobacter baumannii AB5711, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAJ00000000","term_id":"371492197","term_text":"AHAJ00000000"}}AHAJ00000000 [5]
• Aeromonas salmonicida, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVO00000000","term_id":"356689990","term_text":"AGVO00000000"}}AGVO00000000 [6]
• Aggregatibacter actinomycetemcomitans RHAA1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHGR00000000","term_id":"359757447","term_text":"AHGR00000000"}}AHGR00000000 [7]
• Agrobacterium tumefaciens 5A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVZ00000000","term_id":"358008163","term_text":"AGVZ00000000"}}AGVZ00000000 [8]
• Azoarcus sp. Strain KH32C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012304","term_id":"358635055","term_text":"AP012304"}}AP012304, {"type":"entrez-nucleotide","attrs":{"text":"AP012305","term_id":"358639587","term_text":"AP012305"}}AP012305 [9]
• Burkholderia sp. Strain YI23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003087","term_id":"357934279","term_text":"CP003087"}}CP003087 (Chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP003088","term_id":"357937049","term_text":"CP003088"}}CP003088 (Chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP003089","term_id":"357938589","term_text":"CP003089"}}CP003089 (Chromosome 3), {"type":"entrez-nucleotide","attrs":{"text":"CP003090","term_id":"357939954","term_text":"CP003090"}}CP003090 (plasmid BYI23_D), {"type":"entrez-nucleotide","attrs":{"text":"CP003091","term_id":"357941606","term_text":"CP003091"}}CP003091 (plasmid BYI23_E) {"type":"entrez-nucleotide","attrs":{"text":"CP003092","term_id":"357941997","term_text":"CP003092"}}CP003092 (plasmid BYI23_F) [10]
• Brucella suis VBI22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003128","term_id":"358257303","term_text":"CP003128"}}CP003128, {"type":"entrez-nucleotide","attrs":{"text":"CP003129","term_id":"358259429","term_text":"CP003129"}}CP003129 [11]
• Comamonas testosteroni ATCC 11996, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIL00000000","term_id":"371454882","term_text":"AHIL00000000"}}AHIL00000000 [12]
• “Commensalibacter intestini” A911^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFR00000000","term_id":"353673384","term_text":"AGFR00000000"}}AGFR00000000 [13]
• Edwardsiella ictaluri, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001600.1","term_id":"238867551","term_text":"CP001600.1"}}CP001600.1 [14]
• Enterobacter cloacae subsp. dissolvens SDM, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSY00000000","term_id":"357435944","term_text":"AGSY00000000"}}AGSY00000000 [15]
• “Gluconobacter morbifer” G707^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQV00000000","term_id":"356416073","term_text":"AGQV00000000"}}AGQV00000000 [16]
• Legionella dumoffii TEX-KL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVT00000000","term_id":"358009168","term_text":"AGVT00000000"}}AGVT00000000 [17]
• Legionella dumoffii NY-23, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVU00000000","term_id":"358009167","term_text":"AGVU00000000"}}AGVU00000000 [17]
• Legionella pneumophila serogroup 12 Strain 570-CO-H, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003192","term_id":"364506764","term_text":"CP003192"}}CP003192 [18]
• Marinobacterium stanieri S30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPL00000000","term_id":"339778849","term_text":"AFPL00000000"}}AFPL00000000 [19]
• “Marinobacter manganoxydans” MnI7-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP001978 to CP001980","start_term":"CP001978","end_term":"CP001980","start_term_id":"311692891","end_term_id":"311697125"}}CP001978 to CP001980 [20]
• Mesorhizobium alhagi CCNWXJ12-2T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAM00000000","term_id":"359256606","term_text":"AHAM00000000"}}AHAM00000000 [21]
• Mesorhizobium amorphae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSN00000000","term_id":"355545111","term_text":"AGSN00000000"}}AGSN00000000 [22]
• Methylomicrobium alcaliphilum 20Z, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082060","term_id":"351716053","term_text":"FO082060"}}FO082060 and {"type":"entrez-nucleotide","attrs":{"text":"FO082061","term_id":"351720036","term_text":"FO082061"}}FO082061 [23]
• Mitsuaria sp. Strain H24L5A, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFG01000001 to CAFG01000607","start_term":"CAFG01000001","end_term":"CAFG01000607","start_term_id":"354809229","end_term_id":"354808623"}}CAFG01000001 to CAFG01000607 [24]
• Novosphingobium pentaromativorans US6-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFM00000000","term_id":"357601355","term_text":"AGFM00000000"}}AGFM00000000 [25]
• Pantoea ananatis B1-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAEI01000001 to CAEI01000169","start_term":"CAEI01000001","end_term":"CAEI01000169","start_term_id":"344197887","end_term_id":"344197719"}}CAEI01000001 to CAEI01000169 [26]
• Pantoea ananatis LMG 5342, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE617160","term_id":"365184443","term_text":"HE617160"}}HE617160 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE617161","term_id":"365188784","term_text":"HE617161"}}HE617161 (pPANA10) [27]
• Pantoea ananatis Strain PA13, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003085","term_id":"354986417","term_text":"CP003085"}}CP003085 and {"type":"entrez-nucleotide","attrs":{"text":"CP003086","term_id":"354685304","term_text":"CP003086"}}CP003086 [28]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXI00000000","term_id":"343788111","term_text":"AFXI00000000"}}AFXI00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXJ00000000","term_id":"343788109","term_text":"AFXJ00000000"}}AFXJ00000000 [29]
• Pseudomonas aeruginosa, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFXK00000000","term_id":"343788110","term_text":"AFXK00000000"}}AFXK00000000 [29]
• Pseudomonas chlororaphis GP72, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHAY01000000","term_id":"359757954","term_text":"gb||AHAY01000000"}}AHAY01000000 [30]
• Pseudomonas fluorescens F113, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003150","term_id":"359757955","term_text":"CP003150"}}CP003150 [31]
• Pseudomonas fluorescens Wayne 1R, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CADX01000001 to CADX01000090","start_term":"CADX01000001","end_term":"CADX01000090","start_term_id":"354924103","end_term_id":"354924014"}}CADX01000001 to CADX01000090 [32]
• Pseudomonas fluorescens Wood1R, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAFF01000001","term_id":"354698772","term_text":"CAFF01000001"}}CAFF01000001 to {"type":"entrez-nucleotide","attrs":{"text":"CAFF01001437","term_id":"354697336","term_text":"CAFF01001437"}}CAFF01001437 [32]
• Pseudomonas psychrotolerans L19, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBD00000000","term_id":"359372666","term_text":"AHBD00000000"}}AHBD00000000 [33]
• Pseudoalteromonas rubra ATCC 29570^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHCD00000000","term_id":"540289291","term_text":"AHCD00000000"}}AHCD00000000 [34]
• Pseudomonas stutzeri SDM-LAC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSX00000000","term_id":"357435965","term_text":"AGSX00000000"}}AGSX00000000 [35]
• Pseudoxanthomonas spadix BD-a59, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003093","term_id":"357433120","term_text":"CP003093"}}CP003093 [36]
• Rickettsia slovaca, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002428","term_id":"360041315","term_text":"CP002428"}}CP002428 [37]
• Salmonella enterica serovar Pullorum RKS5078, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003047","term_id":"357204415","term_text":"CP003047"}}CP003047 [38]
• Sinorhizobium meliloti CCNWSX0020, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGVV00000000","term_id":"359507569","term_text":"AGVV00000000"}}AGVV00000000 [39]
• Sphingobium sp. Strain SYK-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012222","term_id":"345135066","term_text":"AP012222"}}AP012222 and {"type":"entrez-nucleotide","attrs":{"text":"AP012223","term_id":"345138980","term_text":"AP012223"}}AP012223 [40]
• Sphingomonas sp. Strain PAMC 26605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIS00000000","term_id":"366040305","term_text":"AHIS00000000"}}AHIS00000000 [41]
• Stenotrophomonas maltophilia RR-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRB00000000","term_id":"359757773","term_text":"AGRB00000000"}}AGRB00000000 [42]
• Strain HIMB30, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIG00000000","term_id":"349602640","term_text":"AGIG00000000"}}AGIG00000000 [43]
• Taylorella equigenitalis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003059","term_id":"347973256","term_text":"CP003059"}}CP003059 [44]
• Vibrio campbellii DS40M4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIE00000000","term_id":"358251732","term_text":"AGIE00000000"}}AGIE00000000 [45]
• Vibrio fischeri SR5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIH00000000","term_id":"371496097","term_text":"AHIH00000000"}}AHIH00000000 [46]
• Yersinia enterocolitica, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQO00000000","term_id":"351780838","term_text":"AGQO00000000"}}AGQO00000000 [47]

Phylum Tenericutes

• Candidatus Mycoplasma haemominutum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613254","term_id":"357978897","term_text":"HE613254"}}HE613254 [48]
• Mycoplasma haemocanis strain Illinois, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003199","term_id":"363988676","term_text":"CP003199"}}CP003199 [49]
• Mycoplasma iowae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFP00000000","term_id":"349504222","term_text":"AGFP00000000"}}AGFP00000000 [50]
• Mycoplasma pneumoniae Type 2a Strain 309, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012303","term_id":"358640274","term_text":"AP012303"}}AP012303 [51]

Phylum Firmicutes

• Bacillus cereus F837/76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003187","term_id":"364509831","term_text":"CP003187"}}CP003187 (chromosome) {"type":"entrez-nucleotide","attrs":{"text":"CP003188","term_id":"364515227","term_text":"CP003188"}}CP003188 (pF837_55kb), {"type":"entrez-nucleotide","attrs":{"text":"CP003189","term_id":"364515372","term_text":"CP003189"}}CP003189 (pF837_10kb) [52]
• Brevibacillus laterosporus Strain GI-9, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGD01000001 to CAGD01000061","start_term":"CAGD01000001","end_term":"CAGD01000061","start_term_id":"359745324","end_term_id":"359745264"}}CAGD01000001 to CAGD01000061 [53]
• Clostridium sporogenes PA 3679, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGAH00000000","term_id":"364889226","term_text":"AGAH00000000"}}AGAH00000000 [54]
• Enterococcus mundtii CRL1656, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFWZ00000000.1","term_id":"354620965","term_text":"AFWZ00000000.1"}}AFWZ00000000.1 [55]
• Geobacillus thermoleovorans CCB_US3_UF5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003125","term_id":"359285645","term_text":"CP003125"}}CP003125 [56]
• Lactobacillus curvatus Strain CRL705, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGBU01000000","term_id":"354514905","term_text":"gb||AGBU01000000"}}AGBU01000000 [57]
• Lactobacillus rhamnosus ATCC 8530, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003094","term_id":"355393429","term_text":"CP003094"}}CP003094 [58]
• Lactobacillus rhamnosus R0011, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKC00000000","term_id":"357540515","term_text":"AGKC00000000"}}AGKC00000000 [59]
• Lactococcus garvieae TB25, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQX01000000","term_id":"359031556","term_text":"gb||AGQX01000000"}}AGQX01000000 [60]
• Lactococcus garvieae LG9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQY01000000","term_id":"359031592","term_text":"gb||AGQY01000000"}}AGQY01000000 [60]
• Lactococcus lactis subsp. cremoris A76, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003132","term_id":"358748197","term_text":"CP003132"}}CP003132 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003136","term_id":"358750967","term_text":"CP003136"}}CP003136 (pQA505), {"type":"entrez-nucleotide","attrs":{"text":"CP003135","term_id":"358750954","term_text":"CP003135"}}CP003135 (PQA518), {"type":"entrez-nucleotide","attrs":{"text":"CP003134","term_id":"358750911","term_text":"CP003134"}}CP003134 (pQA549), {"type":"entrez-nucleotide","attrs":{"text":"CP003133","term_id":"358750841","term_text":"CP003133"}}CP003133 (pQA554) [61]
• Leuconostoc citreum LBAE C10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGE00000000","term_id":"365487970","term_text":"CAGE00000000"}}CAGE00000000 [62]
• Leuconostoc citreum LBAE C11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGF00000000","term_id":"365512054","term_text":"CAGF00000000"}}CAGF00000000 [62]
• Leuconostoc citreum LBAE E16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGG00000000","term_id":"365528100","term_text":"CAGG00000000"}}CAGG00000000 [62]
• Leuconostoc mesenteroides subsp. mesenteroides Strain J18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003101","term_id":"948298071","term_text":"CP003101"}}CP003101 [63]
• Paenibacillus peoriae Strain KCTC 3763^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFX00000000","term_id":"359367787","term_text":"AGFX00000000"}}AGFX00000000 [64]
• Pediococcus acidilactici MA18/5M, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGKB00000000","term_id":"357540603","term_text":"AGKB00000000"}}AGKB00000000 [65]
• Pediococcus claussenii ATCC BAA-344^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003137","term_id":"361055534","term_text":"CP003137"}}CP003137 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003138","term_id":"361057275","term_text":"CP003138"}}CP003138 (pPECL-1), {"type":"entrez-nucleotide","attrs":{"text":"CP003139","term_id":"361057278","term_text":"CP003139"}}CP003139 (pPECL-2), {"type":"entrez-nucleotide","attrs":{"text":"CP003140","term_id":"361057281","term_text":"CP003140"}}CP003140 (pPECL-3), {"type":"entrez-nucleotide","attrs":{"text":"CP003141","term_id":"361057302","term_text":"CP003141"}}CP003141 (pPECL-4), {"type":"entrez-nucleotide","attrs":{"text":"CP003142","term_id":"361057319","term_text":"CP003142"}}CP003142 (pPECL-5), {"type":"entrez-nucleotide","attrs":{"text":"CP003143","term_id":"361057355","term_text":"CP003143"}}CP003143 (pPECL-6), {"type":"entrez-nucleotide","attrs":{"text":"CP003144","term_id":"361057377","term_text":"CP003144"}}CP003144 (pPECL-7), {"type":"entrez-nucleotide","attrs":{"text":"CP003145","term_id":"380450589","term_text":"CP003145"}}CP003145 (pPECL-8) [66]
• Staphylococcus aureus M013, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003166","term_id":"359829121","term_text":"CP003166"}}CP003166 [67]
• Staphylococcus aureus subsp. aureus TW20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FN433596","term_id":"269939526","term_text":"FN433596"}}FN433596 [68]
• Weissella confusa LBAE C39-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGH00000000","term_id":"365549261","term_text":"CAGH00000000"}}CAGH00000000 [69]

Phylum Actinobacteria

• Corynebacterium casei, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAFW01000001 to CAFW01000106","start_term":"CAFW01000001","end_term":"CAFW01000106","start_term_id":"356609265","end_term_id":"356606462"}}CAFW01000001 to CAFW01000106 [70]
• Corynebacterium glutamicum, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQQ00000000","term_id":"658109743","term_text":"AGQQ00000000"}}AGQQ00000000 [71]
• Leucobacter chromiiresistens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGCW00000000","term_id":"353529976","term_text":"AGCW00000000"}}AGCW00000000 [72]
• Mycobacterium abscessus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGQU00000000","term_id":"353453148","term_text":"AGQU00000000"}}AGQU00000000 [73]
• Propionibacterium acnes ST9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003195","term_id":"365742920","term_text":"CP003195"}}CP003195 [74]
• Propionibacterium acnes ST22, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003196","term_id":"365740656","term_text":"CP003196"}}CP003196 [74]
• Propionibacterium acnes ST27, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003197","term_id":"365738411","term_text":"CP003197"}}CP003197 [74]
• Saccharomonospora azurea SZMC 14600, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBX00000000","term_id":"359740650","term_text":"AHBX00000000"}}AHBX00000000 [75]
• Streptomyces sp. Strain TOR3209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNH00000000","term_id":"359357427","term_text":"AGNH00000000"}}AGNH00000000 [76]
• Streptomyces sp. Strain W007, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGSW00000000","term_id":"364010697","term_text":"AGSW00000000"}}AGSW00000000 [77]

Phylum Spirochaetes

• Borrelia valaisiana VS116, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABCY02000001","term_id":"224510974","term_text":"ABCY02000001"}}ABCY02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001439","term_id":"224497263","term_text":"CP001439"}}CP001439 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001437","term_id":"224497187","term_text":"CP001437"}}CP001437 (Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP001440","term_id":"224497290","term_text":"CP001440"}}CP001440 (plasmid Ip 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001442","term_id":"224497476","term_text":"CP001442"}}CP001442 (plasmid Ip28-8), {"type":"entrez-nucleotide","attrs":{"text":"CP001436","term_id":"224497148","term_text":"CP001436"}}CP001436 (Ip 36), {"type":"entrez-nucleotide","attrs":{"text":"CP001433","term_id":"224496993","term_text":"CP001433"}}CP001433 (plasmid Ip 54), {"type":"entrez-nucleotide","attrs":{"text":"CP001438","term_id":"224497250","term_text":"CP001438"}}CP001438 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001432","term_id":"224496964","term_text":"CP001432"}}CP001432 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP001441","term_id":"224497433","term_text":"CP001441"}}CP001441 (plasmid cp32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP001434","term_id":"224497064","term_text":"CP001434"}}CP001434 (plasmid cp32-7), {"type":"entrez-nucleotide","attrs":{"text":"CP001435","term_id":"224497109","term_text":"CP001435"}}CP001435 (plasmid cp32-10) [78]
• “Borrelia bissettii” DN127, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002746","term_id":"342222012","term_text":"CP002746"}}CP002746 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002756","term_id":"342223236","term_text":"CP002756"}}CP002756 (plasmid Ip12), {"type":"entrez-nucleotide","attrs":{"text":"CP002757","term_id":"342223270","term_text":"CP002757"}}CP002757 (plasmid Ip25), {"type":"entrez-nucleotide","attrs":{"text":"CP002758","term_id":"342223295","term_text":"CP002758"}}CP002758 (plasmid 28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002759","term_id":"342223320","term_text":"CP002759"}}CP002759 (plasmid Ip 28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002760","term_id":"342223351","term_text":"CP002760"}}CP002760 (Ip28-7), {"type":"entrez-nucleotide","attrs":{"text":"CP002761","term_id":"342223388","term_text":"CP002761"}}CP002761 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"CP002762","term_id":"342223459","term_text":"CP002762"}}CP002762 (plasmid Ip56), {"type":"entrez-nucleotide","attrs":{"text":"CP002755","term_id":"342223223","term_text":"CP002755"}}CP002755 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP002747","term_id":"342222829","term_text":"CP002747"}}CP002747 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"CP002749","term_id":"342222904","term_text":"CP002749"}}CP002749 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"CP002750","term_id":"342222947","term_text":"CP002750"}}CP002750 (plasmid cp32-4), {"type":"entrez-nucleotide","attrs":{"text":"CP002751","term_id":"342222990","term_text":"CP002751"}}CP002751 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"CP002752","term_id":"342223034","term_text":"CP002752"}}CP002752 (plasmid cp32-6), {"type":"entrez-nucleotide","attrs":{"text":"CP002753","term_id":"342223077","term_text":"CP002753"}}CP002753 (plasmid cp32-7), CP0027554 (plasmid cp32-9), {"type":"entrez-nucleotide","attrs":{"text":"CP002748","term_id":"342222857","term_text":"CP002748"}}CP002748 (plasmid cp32-11) [78]
• Borrelia spielmanii A14S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000001","term_id":"224514548","term_text":"ABKB02000001"}}ABKB02000001 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001468","term_id":"224497637","term_text":"CP001468"}}CP001468 (plasmid Ip17), {"type":"entrez-nucleotide","attrs":{"text":"CP001471","term_id":"224497796","term_text":"CP001471"}}CP001471 (Ip28-3), {"type":"entrez-nucleotide","attrs":{"text":"CP001470","term_id":"224497745","term_text":"CP001470"}}CP001470 (plasmid Ip28-4), {"type":"entrez-nucleotide","attrs":{"text":"CP001465","term_id":"224497532","term_text":"CP001465"}}CP001465 (plasmid Ip28-2), {"type":"entrez-nucleotide","attrs":{"text":"CP001466","term_id":"224497566","term_text":"CP001466"}}CP001466 (plasmid Ip36), {"type":"entrez-nucleotide","attrs":{"text":"CP001464","term_id":"224497496","term_text":"CP001464"}}CP001464 (plasmid Ip38), {"type":"entrez-nucleotide","attrs":{"text":"CP001469","term_id":"224497671","term_text":"CP001469"}}CP001469 (plasmid Ip54), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000016","term_id":"224513758","term_text":"ABKB02000016"}}ABKB02000016, {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000020","term_id":"224513743","term_text":"ABKB02000020"}}ABKB02000020 (plasmid cp9), {"type":"entrez-nucleotide","attrs":{"text":"CP001467","term_id":"224497607","term_text":"CP001467"}}CP001467 (plasmid cp26), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000026","term_id":"224513697","term_text":"ABKB02000026"}}ABKB02000026 (plasmid cp32-3), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000031","term_id":"224513641","term_text":"ABKB02000031"}}ABKB02000031 (plasmid 32-5), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000021","term_id":"224513736","term_text":"ABKB02000021"}}ABKB02000021 (plasmid cp32-12), {"type":"entrez-nucleotide","attrs":{"text":"ABKB02000014","term_id":"224513768","term_text":"ABKB02000014"}}ABKB02000014 (unidentified) [78]

Non-Bacterial genomes

• Aspergillus flavus, sequence accession {"type":"entrez-geo","attrs":{"text":"GSE32177","term_id":"32177"}}GSE32177 [79]
• Bacteriophage SPN3UB, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ288021","term_id":"378408798","term_text":"JQ288021"}}JQ288021 [80]
• Bamboo mitochondria, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"JQ235166 to JQ235179","start_term":"JQ235166","end_term":"JQ235179","start_term_id":"372861916","end_term_id":"372861969"}}JQ235166 to JQ235179 [81]
• Boea hygrometrica chloroplast, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107811","term_id":"340549387","term_text":"JN107811"}}JN107811 [82]
• Boea hygrometrica mitochondrial, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN107812","term_id":"340549473","term_text":"JN107812"}}JN107812 [82]
• Canine Picornavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831356","term_id":"377826518","term_text":"JN831356"}}JN831356 [83]
• Chandipura virus (CHPV) CIN0327, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212856.1","term_id":"309261828","term_text":"GU212856.1"}}GU212856.1 [84]
• Chandipura virus (CHPV) CIN0451, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212857.1","term_id":"309261834","term_text":"GU212857.1"}}GU212857.1 [84]
• Chandipura virus (CHPV) CIN0751, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU212858.1","term_id":"309261840","term_text":"GU212858.1"}}GU212858.1 [84]
• Chandipura virus (CHPV) CIN0755, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GU190711.1","term_id":"309099431","term_text":"GU190711.1"}}GU190711.1 [84]
• Chinese Porcine Parvovirus Strain PPV2010, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN872448","term_id":"374676766","term_text":"JN872448"}}JN872448 [85]
• Common midwife toad megavirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ231222","term_id":"375281729","term_text":"JQ231222"}}JQ231222 [86]
• Dengue Virus Serotype 4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN983813","term_id":"372290533","term_text":"JN983813"}}JN983813 [87]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF270480","term_id":"367465451","term_text":"JF270480"}}JF270480 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314464","term_id":"377824036","term_text":"JQ314464"}}JQ314464 [88]
• Duck Tembusu Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ314465","term_id":"377824038","term_text":"JQ314465"}}JQ314465 [88]
• Emiliania huxleyi Virus 202, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ634145","term_id":"356927554","term_text":"HQ634145"}}HQ634145 [89]
• Emiliania huxleyi Virus EhV-88, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974310","term_id":"347600450","term_text":"JF974310"}}JF974310 [89]
• Emiliania huxleyi EhV-201, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974311","term_id":"357972615","term_text":"JF974311"}}JF974311 [89]
• Emiliania huxleyi EhV-207, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974317","term_id":"347600924","term_text":"JF974317"}}JF974317 [89]
• Emiliania huxleyi EhV-208, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF974318","term_id":"347601393","term_text":"JF974318"}}JF974318 [89]
• Glarea lozoyensis, sequence accession GUE00000000 [90]
• Nannochloropis gaditana, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGNI00000000","term_id":"366047505","term_text":"AGNI00000000"}}AGNI00000000 [91]
• Oryza sativa cv., sequence accession DRA000499 [92]
• Partetravirus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN990269","term_id":"374718987","term_text":"JN990269"}}JN990269 [93]
• Porcine Bocavirus PBoV5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN831651","term_id":"371449604","term_text":"JN831651"}}JN831651 [94]
• Porcine epidemic diarrhea virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ282909","term_id":"377824029","term_text":"JQ282909"}}JQ282909 [95]
• Pseudomonas aeruginosa lytic bacteriophage PA1Ø, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HM624080","term_id":"315418954","term_text":"HM624080"}}HM624080 [96]
• Pseudomonas fluorescens phage OBP, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"JN627160","term_id":"359842892","term_text":"JN627160"}}JN627160 [97]
• RNA Virus from Avocado, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN880414","term_id":"371444768","term_text":"JN880414"}}JN880414 [98]
• Salmonella enterica Serovar Typhimurium Bacteriophage SPN1S, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN391180","term_id":"370344404","term_text":"JN391180"}}JN391180 [99]
• Schistosoma haematobium, sequence accession PRJNA78265 [100]
• Schistosoma mansoni, sequence accession {"type":"entrez-protein","attrs":{"text":"ERP00038","term_id":"550209647","term_text":"ERP00038"}}ERP00038 [101]
• Stenopirates sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN100019","term_id":"340008214","term_text":"JN100019"}}JN100019 [102]
• T7-Like Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JN651747","term_id":"374713556","term_text":"JN651747"}}JN651747 [103]
• Vibrio harveyi siphophage VHS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF713456","term_id":"334898816","term_text":"JF713456"}}JF713456 [104]
• Tyrolean ice man, sequence accession ERP001144 [105]

     

Genomic Basis of a Polyagglutinating Isolate of Neisseria meningitidis

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 ({"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917) from a patient with acute meningococcal disease. To this end, we characterized the complete genome sequence of the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}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 {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}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 {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}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 {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}M16917. Detailed analysis of this locus uncovered the locations of recombination breakpoints in the {"type":"entrez-nucleotide","attrs":{"text":"M16917","term_id":"167250","term_text":"M16917"}}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.     

LncRNA DQ786243 affects Treg related CREB and Foxp3 expression in Crohn’s disease

Background

Long non-coding RNAs (lncRNAs) have different functions in cells. They work as signals, decoys, guides, and scaffolds. Altered lncRNA levels can affect the expression of gene products. There are seldom studies on the role of lncRNAs in inflammatory bowel disease (IBD).

Results

Quantitative RT-PCR showed that {"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 was significantly overexpressed in clinical active CD patients compared with clinical inactive CD patients (P = 0.0118) or healthy controls (P = 0.002). CREB was also more highly expressed in active CD than in inactive CD (P = 0.0034) or controls (P = 0.0241). Foxp3 was interestingly lower in inactive CD than in active CD (P = 0.0317) or controls (P = 0.0103), but there were no apparent differences between active CD and controls. CRP was well correlated with {"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 (r = 0.489, P = 0.034), CREB (r = 0.500, P = 0.029) and Foxp3 (r = 0.546, P = 0.016). At 48 hours after {"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 transfection, qRT-PCR showed both CREB (P = 0.017) and Foxp3 (P = 0.046) had an increased mRNA expression in Jurkat cells. Western blot showed the same pattern. After {"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 transfection, CREB phosphorylation ratio (p-CREB/t-CREB) was increased (P = 0.0043).

Conclusion

{"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 can be related with severity of CD. It can affect the expression of CREB and Foxp3 through which regulates the function of Treg. CREB itself seems not the mediator of {"type":"entrez-nucleotide","attrs":{"text":"DQ786243","term_id":"110631570","term_text":"DQ786243"}}DQ786243 to up-regulate Foxp3. The phosphorylation of CREB might play a more important role in the process.     

Genome sequences published outside of Standards in Genomic Sciences, March-April 2012

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 {"type":"entrez-nucleotide","attrs":{"text":"CP003243","term_id":"379319823","term_text":"CP003243"}}CP003243 [2]
• Thermococcus litoralis NS-C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVB00000000","term_id":"374743520","term_text":"AHVB00000000"}}AHVB00000000 [3]

Phylum Crenarchaeota

• Candidatus Nitrosopumilus salaria” BD31, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEXL00000000","term_id":"386807666","term_text":"AEXL00000000"}}AEXL00000000 [4]
• Candidatus Nitrosoarchaeum limnia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJG00000000","term_id":"367466343","term_text":"AHJG00000000"}}AHJG00000000 [5]

Phylum Deinococcus-Thermus

• Deinococcus gobiensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002536","term_id":"324314064","term_text":"CP002536"}}CP002536 [6]

Phylum Proteobacteria

• Aggregatibacter actinomycetemcomitans strain ANH9381, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003099","term_id":"365745154","term_text":"CP003099"}}CP003099 [7]
• Alishewanella jeotgali, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHTH00000000","term_id":"374571619","term_text":"AHTH00000000"}}AHTH00000000 [8]
• Enterobacter aerogenes KCTC 2190, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002824","term_id":"334732565","term_text":"CP002824"}}CP002824 [9]
• Escherichia coli O104:H4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOB02000092","term_id":"340739517","term_text":"AFOB02000092"}}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 {"type":"entrez-nucleotide","attrs":{"text":"AHHB00000000","term_id":"372292151","term_text":"AHHB00000000"}}AHHB00000000 [12]
• Klebsiella oxytoca KCTC 1686, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003218","term_id":"365906294","term_text":"CP003218"}}CP003218 [13]
• Klebsiella pneumoniae subsp. pneumoniae HS11286, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003200","term_id":"364515570","term_text":"CP003200"}}CP003200 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003223","term_id":"365803686","term_text":"CP003223"}}CP003223 (plasmid pKPHS1), {"type":"entrez-nucleotide","attrs":{"text":"CP003224","term_id":"365803828","term_text":"CP003224"}}CP003224 (plasmid pKPHS2), {"type":"entrez-nucleotide","attrs":{"text":"CP003225","term_id":"365803989","term_text":"CP003225"}}CP003225 (plasmid pKPHS3), {"type":"entrez-nucleotide","attrs":{"text":"CP003226","term_id":"365804142","term_text":"CP003226"}}CP003226 (plasmid pKPHS4), {"type":"entrez-nucleotide","attrs":{"text":"CP003227","term_id":"365804147","term_text":"CP003227"}}CP003227 (plasmid pKPHS5), {"type":"entrez-nucleotide","attrs":{"text":"CP003228","term_id":"365804153","term_text":"CP003228"}}CP003228 (plasmid pKPHS6) [14]
• Oceanimonas sp. GK1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003171","term_id":"372983507","term_text":"CP003171"}}CP003171 [15]
• “Pseudogulbenkiania ferrooxidans” Strain 2002, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NZ_ACIS01000000","term_id":"224827334","term_text":"ref||NZ_ACIS01000000"}}NZ_ACIS01000000 [16]
• Pseudomonas extremaustralis 14-3b, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIP00000000","term_id":"371721769","term_text":"AHIP00000000"}}AHIP00000000 [17]
• Pseudomonas sp. Strain PAMC 25886, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHC00000000","term_id":"372002201","term_text":"AHHC00000000"}}AHHC00000000 [18]
• Psychrobacter, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHVZ00000000","term_id":"375126956","term_text":"AHVZ00000000"}}AHVZ00000000 [19]
• Rahnella sp. Strain Y9602, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002505","term_id":"321165934","term_text":"CP002505"}}CP002505 [20]
• Rhizobium sp. Strain PDO1-076, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZC00000000","term_id":"375058045","term_text":"AHZC00000000"}}AHZC00000000 [21]
• Rhodospirillum photometricum DSM122, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE663493","term_id":"378401447","term_text":"HE663493"}}HE663493 [22]
• “Rickettsia sibirica sibirica”, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIZ00000000","term_id":"374669031","term_text":"AHIZ00000000"}}AHIZ00000000 [23]
• Rickettsia sibirica subsp. mongolitimonae strain HA-91, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHZB00000000","term_id":"375318263","term_text":"AHZB00000000"}}AHZB00000000 [24]
• Salmonella enterica subsp. enterica Serotype Enteritidis Strain LA5, sequence accession [25]
• Salmonella enterica subsp. enterica Serotype Senftenberg Strain SS209, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAGQ00000000","term_id":"379987603","term_text":"CAGQ00000000"}}CAGQ00000000 [26]
• Salmonella enterica subsp. enterica Serovar Typhi P-stx-12, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003278","term_id":"374352002","term_text":"CP003278"}}CP003278 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP003279","term_id":"374356693","term_text":"CP003279"}}CP003279 (plasmid) [27]
• Sphingomonas echinoides ATCC 14820, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHIR00000000","term_id":"366040205","term_text":"AHIR00000000"}}AHIR00000000 [28]
• Strain HIMB55, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGIF00000000","term_id":"374304583","term_text":"AGIF00000000"}}AGIF00000000 [29]
• Vibrio harveyi CAIM 1792, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHHQ00000000","term_id":"374671508","term_text":"AHHQ00000000"}}AHHQ00000000 [30]
• Wolbachia Strain wAlbB, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGB01000001 to CAGB01000165","start_term":"CAGB01000001","end_term":"CAGB01000165","start_term_id":"371933004","end_term_id":"371931774"}}CAGB01000001 to CAGB01000165 [31]
• Xanthomonas axonopodis pv. punicae Strain LMG 859, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CAGJ01000001 to CAGJ01000217","start_term":"CAGJ01000001","end_term":"CAGJ01000217","start_term_id":"372556075","end_term_id":"372551622"}}CAGJ01000001 to CAGJ01000217 [32]

Phylum Tenericutes

• Mycoplasma hyorhinis Strain GDL-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003231","term_id":"367460291","term_text":"CP003231"}}CP003231 [33]

Phylum Firmicutes

• Bacillus subtilis, sequence accession BGSCID 3A27 through BGSCID 28A4 [34]
• Clostridium difficile Strain CD37, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHJJ00000000","term_id":"371930118","term_text":"AHJJ00000000"}}AHJJ00000000 [35]
• Clostridium perfringens, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFES00000000","term_id":"380306484","term_text":"AFES00000000"}}AFES00000000 [36]
• Lactobacillus fructivorans KCTC 3543, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEQY00000000","term_id":"316986063","term_text":"AEQY00000000"}}AEQY00000000 [37]
• Lactococcus lactis IO-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012281","term_id":"374672113","term_text":"AP012281"}}AP012281 [38]
• Lactobacillus plantarum strain NC8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGRI00000000","term_id":"376011245","term_text":"AGRI00000000"}}AGRI00000000 [39]
• Paenibacillus dendritiformis C454, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHKH00000000","term_id":"374393106","term_text":"AHKH00000000"}}AHKH00000000 [40]
• Paenibacillus sp. Strain Aloe-11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AGFI00000000","term_id":"374477730","term_text":"AGFI00000000"}}AGFI00000000 [41]
• “Peptoniphilus rhinitidis” 1-13^T, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BAEW01000001 to BAEW01000056","start_term":"BAEW01000001","end_term":"BAEW01000056","start_term_id":"374722129","end_term_id":"374722074"}}BAEW01000001 to BAEW01000056 [42]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 and {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 [43]
• Staphylococcus aureus VC40, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003033","term_id":"374362062","term_text":"CP003033"}}CP003033 [44]
• Streptococcus infantarius subsp. infantarius Strain CJ18, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003295","term_id":"374681091","term_text":"CP003295"}}CP003295 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP003296","term_id":"374682963","term_text":"CP003296"}}CP003296 (plasmid) [45]
• Streptococcus macedonicus ACA-DC 198, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE613569","term_id":"372283141","term_text":"HE613569"}}HE613569 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"HE613570","term_id":"372285142","term_text":"HE613570"}}HE613570 (plasmid pSMA198) [46]

Phylum Actinobacteria

• Actinoplanes sp. SE50/110, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP003170","term_id":"359832573","term_text":"CP003170"}}CP003170 [47]
• Amycolatopsis sp. Strain ATCC 39116, sequence accession [48]
• Nocardia cyriacigeorgica GUH-2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FO082843","term_id":"374843763","term_text":"FO082843"}}FO082843 [49]
• Salinibacterium sp., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHWA00000000","term_id":"375323651","term_text":"AHWA00000000"}}AHWA00000000 [50]
• Streptomyces acidiscabies 84-104, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AHBF00000000","term_id":"372137622","term_text":"AHBF00000000"}}AHBF00000000 [51]

Non-Bacterial genomes

• Bluetongue Virus Serotype 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ783905","term_id":"70907482","term_text":"AJ783905"}}AJ783905 (Seg-6) and {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681257","term_id":"383932043","term_text":"JQ681257"}}JQ681257 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ681258","term_id":"383932045","term_text":"JQ681258"}}JQ681258 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"JQ681259","term_id":"383932047","term_text":"JQ681259"}}JQ681259 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ681260","term_id":"383932049","term_text":"JQ681260"}}JQ681260 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ681261","term_id":"383932051","term_text":"JQ681261"}}JQ681261 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ681262","term_id":"383932053","term_text":"JQ681262"}}JQ681262 (Seg-7), JQ6812563 (Seg-8), JQ6812564 (Seg-9), to {"type":"entrez-nucleotide","attrs":{"text":"JQ681265","term_id":"383932059","term_text":"JQ681265"}}JQ681265 (Seg-10) [52]
• Virus Serotype 1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AJ585111","term_id":"118420282","term_text":"AJ585111"}}AJ585111 (Seg-2), {"type":"entrez-nucleotide","attrs":{"text":"AJ586659","term_id":"47826214","term_text":"AJ586659"}}AJ586659 (Seg-6), {"type":"entrez-nucleotide","attrs":{"text":"JQ282770","term_id":"383215071","term_text":"JQ282770"}}JQ282770 (Seg-1), {"type":"entrez-nucleotide","attrs":{"text":"JQ282771","term_id":"383215073","term_text":"JQ282771"}}JQ282771 (Seg-3), {"type":"entrez-nucleotide","attrs":{"text":"JQ282772","term_id":"383215075","term_text":"JQ282772"}}JQ282772 (Seg-4), {"type":"entrez-nucleotide","attrs":{"text":"JQ282773","term_id":"383215077","term_text":"JQ282773"}}JQ282773 (Seg-5), {"type":"entrez-nucleotide","attrs":{"text":"JQ282774","term_id":"383215079","term_text":"JQ282774"}}JQ282774 (Seg-7), {"type":"entrez-nucleotide","attrs":{"text":"JQ282775","term_id":"383215081","term_text":"JQ282775"}}JQ282775 (Seg-8), {"type":"entrez-nucleotide","attrs":{"text":"JQ282776","term_id":"383215083","term_text":"JQ282776"}}JQ282776 (Seg-9), and {"type":"entrez-nucleotide","attrs":{"text":"JQ282777","term_id":"383215085","term_text":"JQ282777"}}JQ282777 (Seg-10) [52]
• Chloroplast genome of Erycina pusilla, sequence accession JF_746994 [53]
• Danio rerio, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ434101","term_id":"384872525","term_text":"JQ434101"}}JQ434101 [54]
• Enterococcal Bacteriophage SAP6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF731128","term_id":"343411857","term_text":"JF731128"}}JF731128 [55]
• Eubenangee virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070376","term_id":"383513837","term_text":"JQ070376"}}JQ070376 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070385","term_id":"383513855","term_text":"JQ070385"}}JQ070385 [56]
• Fujian/411-like viruses, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CY087969 to CY088568","start_term":"CY087969","end_term":"CY088568","start_term_id":"380506411","end_term_id":"380507803"}}CY087969 to CY088568 [57]
• Hantavirus Variant of Rio Mamoré Virus, Maripa Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ611712","term_id":"384382977","term_text":"JQ611712"}}JQ611712 (segment S), {"type":"entrez-nucleotide","attrs":{"text":"JQ611713","term_id":"384382979","term_text":"JQ611713"}}JQ611713 (segment M), and {"type":"entrez-nucleotide","attrs":{"text":"JQ611714","term_id":"384382981","term_text":"JQ611714"}}JQ611714 (segment L) [58]
• Pata virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070386","term_id":"383513857","term_text":"JQ070386"}}JQ070386 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070395","term_id":"383513875","term_text":"JQ070395"}}JQ070395 [59]
• Porcine Circovirus 2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ413808","term_id":"383215164","term_text":"JQ413808"}}JQ413808 [60]
• Porcine Reproductive and Respiratory Syndrome Virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ326271","term_id":"382929416","term_text":"JQ326271"}}JQ326271 [61]
• Streptococcus mutans Phage M102AD, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"DQ386162","term_id":"88698119","term_text":"DQ386162"}}DQ386162 [62]
• Tilligery virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JQ070366","term_id":"383513817","term_text":"JQ070366"}}JQ070366 through {"type":"entrez-nucleotide","attrs":{"text":"JQ070375","term_id":"383513835","term_text":"JQ070375"}}JQ070375 [63]

     

Genetic Diagnosis of Two Dopa-Responsive Dystonia Families by Exome Sequencing

Dopa-responsive dystonia, a rare disorder typically presenting in early childhood with lower limb dystonia and gait abnormality, responds well to levodopa. However, it is often misdiagnosed with the wide spectrum of phenotypes. By exome sequencing, we make a rapid genetic diagnosis for two atypical dopa-responsive dystonia pedigrees. One pedigree, presented with prominent parkinsonism, was misdiagnosed as Parkinson''s disease until a known mutation in GCH1 (GTP cyclohydrolase 1) gene ({"type":"entrez-nucleotide","attrs":{"text":"NM_000161.2","term_id":"66932966","term_text":"NM_000161.2"}}NM_000161.2: c.631_632delAT, p.Met211ValfsX38) was found. The other pedigree was detected with a new compound heterozygous mutation in TH (tyrosine hydroxylase) gene [({"type":"entrez-nucleotide","attrs":{"text":"NM_000360.3","term_id":"88900502","term_text":"NM_000360.3"}}NM_000360.3: c.911C>T, p.Ala304Val) and ({"type":"entrez-nucleotide","attrs":{"text":"NM_000360.3","term_id":"88900502","term_text":"NM_000360.3"}}NM_000360.3: c.1358G>A, p.Arg453His)], whose proband, a pregnant woman, required a rapid and less-biased genetic diagnosis. In conclusion, we demonstrated that exome sequencing could provide a precise and rapid genetic testing in the diagnosis of Mendelian diseases, especially for diseases with wide phenotypes.     

Characterization of the Invasive,Multidrug Resistant Non-typhoidal Salmonella Strain D23580 in a Murine Model of Infection

A distinct pathovar of Salmonella enterica serovar Typhimurium, ST313, has emerged in sub-Saharan Africa as a major cause of fatal bacteremia in young children and HIV-infected adults. {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580, a multidrug resistant clinical isolate of ST313, was previously shown to have undergone genome reduction in a manner that resembles that of the more human-restricted pathogen, Salmonella enterica serovar Typhi. It has since been shown through tissue distribution studies that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 is able to establish an invasive infection in chickens. However, it remains unclear whether ST313 can cause lethal disease in a non-human host following a natural course of infection. Herein we report that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 causes lethal and invasive disease in a murine model of infection following peroral challenge. The LD₅₀ of {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 in female BALB/c mice was 4.7 x 10⁵ CFU. Tissue distribution studies performed 3 and 5 days post-infection confirmed that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 was able to more rapidly colonize the spleen, mesenteric lymph nodes and gall bladder in mice when compared to the well-characterized S. Typhimurium strain SL1344. {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 exhibited enhanced resistance to acid stress relative to SL1344, which may lend towards increased capability to survive passage through the gastrointestinal tract as well as during its intracellular lifecycle. Interestingly, {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 also displayed higher swimming motility relative to SL1344, S. Typhi strain Ty2, and the ST313 strain A130. Biochemical tests revealed that {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580 shares many similar metabolic features with SL1344, with several notable differences in the Voges-Proskauer and catalase tests, as well alterations in melibiose, and inositol utilization. These results represent the first full duration infection study using an ST313 strain following the entire natural course of disease progression, and serve as a benchmark for ongoing and future studies into the pathogenesis of {"type":"entrez-nucleotide","attrs":{"text":"D23580","term_id":"427513","term_text":"D23580"}}D23580.     

Genome sequences of Bacteria and Archaea published outside of Standards in Genomic Sciences, June �C September 2011

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 this subsequent versions of this list are invited to provide the bibliometric data for such references to the SIGS editorial office.

• Phylum Crenarchaeota
• Phylum Euryarchaeota
• Pyrococcus yayanosii CH1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002779","term_id":"334899445","term_text":"CP002779"}}CP002779 [1]
• Methanocella paludicola, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP011532","term_id":"282154984","term_text":"AP011532"}}AP011532 [2]
• Halorhabdus tiamatea, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNT00000000","term_id":"543102264","term_text":"AFNT00000000"}}AFNT00000000 [3]
• Thermococcus sp. Strain 4557, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002920","term_id":"340808746","term_text":"CP002920"}}CP002920 [4]
• Phylum Chloroflexi
• Phylum Proteobacteria
• Ralstonia solanacearum strain Po82, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002819","term_id":"334194119","term_text":"CP002819"}}CP002819 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002820","term_id":"334197458","term_text":"CP002820"}}CP002820 (megaplasmid) [5
• Desulfovibrio alaskensis G20, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP000112","term_id":"78217452","term_text":"CP000112"}}CP000112 [6]
• Methylophaga aminisulfidivorans MP^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIG00000000","term_id":"333790299","term_text":"AFIG00000000"}}AFIG00000000 [7]
• Acinetobacter sp. P8-3-8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIE00000000","term_id":"333463740","term_text":"AFIE00000000"}}AFIE00000000 [8]
• Sphingomonas strain KC8, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFMP01000000","term_id":"333609216","term_text":"gb||AFMP01000000"}}AFMP01000000 [9]
• Brucella pinnipedialis B2/94, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002078","term_id":"340558088","term_text":"CP002078"}}CP002078 and {"type":"entrez-nucleotide","attrs":{"text":"CP002079","term_id":"340560226","term_text":"CP002079"}}CP002079 [10]
• Salmonella enterica Serovar Typhimurium UK-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002614","term_id":"332986951","term_text":"CP002614"}}CP002614 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002615","term_id":"332991407","term_text":"CP002615"}}CP002615 (plasmid) [11]
• Bordetella pertussis CS, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002695","term_id":"332380677","term_text":"CP002695"}}CP002695 [12]
• Alteromonas sp. Strain SN2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002339","term_id":"332991508","term_text":"CP002339"}}CP002339 [13]
• Escherichia coli O104:H4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOB00000000","term_id":"340742082","term_text":"AFOB00000000"}}AFOB00000000 ({"type":"entrez-nucleotide","attrs":{"text":"LB226692","term_id":"753016073","term_text":"LB226692"}}LB226692) and {"type":"entrez-nucleotide","attrs":{"text":"AFPS00000000","term_id":"340736249","term_text":"AFPS00000000"}}AFPS00000000 (01-09591) [14]
• Acidithiobacillus caldus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002573","term_id":"340554897","term_text":"CP002573"}}CP002573 (Chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002574","term_id":"340557778","term_text":"CP002574"}}CP002574 (pLAtcm), {"type":"entrez-nucleotide","attrs":{"text":"CP002575","term_id":"340558034","term_text":"CP002575"}}CP002575 (pLAtc1), {"type":"entrez-nucleotide","attrs":{"text":"CP002576","term_id":"340558045","term_text":"CP002576"}}CP002576 (pLAtc2), {"type":"entrez-nucleotide","attrs":{"text":"CP002577","term_id":"340558059","term_text":"CP002577"}}CP002577 (pLAtc3) [15]
• Cupriavidus necator N-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002877","term_id":"338164315","term_text":"CP002877"}}CP002877 (chromosome 1), {"type":"entrez-nucleotide","attrs":{"text":"CP002878","term_id":"338167938","term_text":"CP002878"}}CP002878 (chromosome 2), {"type":"entrez-nucleotide","attrs":{"text":"CP002879","term_id":"338170382","term_text":"CP002879"}}CP002879 (pBB1), and {"type":"entrez-nucleotide","attrs":{"text":"CP002880","term_id":"338171767","term_text":"CP002880"}}CP002880 (pBB2) [16]
• Oligotropha carboxidovorans OM4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002821","term_id":"336093334","term_text":"CP002821"}}CP002821 (OM4 chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002822","term_id":"336096622","term_text":"CP002822"}}CP002822 (pHCG3b), {"type":"entrez-nucleotide","attrs":{"text":"CP002823","term_id":"336096746","term_text":"CP002823"}}CP002823 (pOC167B) [17]
• Oligotropha carboxidovorans OM5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002826","term_id":"336096911","term_text":"CP002826"}}CP002826 (OM5 chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002827","term_id":"336100253","term_text":"CP002827"}}CP002827 (pHCG3), and {"type":"entrez-nucleotide","attrs":{"text":"CP002828","term_id":"336100378","term_text":"CP002828"}}CP002828 (pOC167) [17]
• Pantoea ananatis LMG20103, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001875","term_id":"326698716","term_text":"CP001875"}}CP001875 [18]
• Helicobacter bizzozeronii strain CIII-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR871757","term_id":"335332259","term_text":"FR871757"}}FR871757 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"FR871758","term_id":"335334154","term_text":"FR871758"}}FR871758 (HBZ-1) [19]
• Vibrio anguillarum 775, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP002284 to CP002285","start_term":"CP002284","end_term":"CP002285","start_term_id":"335340310","end_term_id":"335343122"}}CP002284 to CP002285 [20]
• Zymomonas mobilis subsp. pomaceae, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002865","term_id":"336293797","term_text":"CP002865"}}CP002865 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002866","term_id":"336295481","term_text":"CP002866"}}CP002866 (p29192_1), {"type":"entrez-nucleotide","attrs":{"text":"CP002867","term_id":"336295515","term_text":"CP002867"}}CP002867 (p29192_2) [21]
• Agrobacterium sp. strain ATCC 31749, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AECL01000000","term_id":"333795931","term_text":"gb||AECL01000000"}}AECL01000000 [22]
• Xanthomonas spp. strain Xrc, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"CP002789","term_id":"341934791","term_text":"CP002789"}}CP002789 [23]
• Xanthomonas spp. strain Xoc, sequence accesssion {"type":"entrez-nucleotide","attrs":{"text":"AAQN00000000","term_id":"94721237","term_text":"AAQN00000000"}}AAQN00000000 [23]
• Glaciecola sp. Strain 4H-3-7+YE-5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002526","term_id":"332171715","term_text":"CP002526"}}CP002526 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002527","term_id":"332175949","term_text":"CP002527"}}CP002527 (plasmid) [24]
• Escherichia coli Strain HM605, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CADZ01000001","term_id":"335324271","term_text":"CADZ01000001"}}CADZ01000001 through {"type":"entrez-nucleotide","attrs":{"text":"CADZ01000154","term_id":"335324105","term_text":"CADZ01000154"}}CADZ01000154 [25]
• Salinisphaera shabanensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNV00000000","term_id":"543113482","term_text":"AFNV00000000"}}AFNV00000000 [26]
• Methyloversatilis universalis FAM5^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHG00000000","term_id":"333445722","term_text":"AFHG00000000"}}AFHG00000000 [27]
• Alicycliphilus denitrificans Strain BC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002449","term_id":"317115299","term_text":"CP002449"}}CP002449 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002450","term_id":"317119630","term_text":"CP002450"}}CP002450 (megaplasmid), {"type":"entrez-nucleotide","attrs":{"text":"CP002451","term_id":"317119756","term_text":"CP002451"}}CP002451 (plasmid) [28].
• Alicycliphilus denitrificans K601^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002657","term_id":"329308025","term_text":"CP002657"}}CP002657 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002658","term_id":"329312633","term_text":"CP002658"}}CP002658 (plasmid) [28]
• Oligotropha carboxidovorans Strain OM4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002821","term_id":"336093334","term_text":"CP002821"}}CP002821 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002822","term_id":"336096622","term_text":"CP002822"}}CP002822 (pHCG3b), {"type":"entrez-nucleotide","attrs":{"text":"CP002823","term_id":"336096746","term_text":"CP002823"}}CP002823 (pOC167B) [29]
• Oligotropha carboxidovorans Strain OM5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002826","term_id":"336096911","term_text":"CP002826"}}CP002826 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002827","term_id":"336100253","term_text":"CP002827"}}CP002827 (pHCG3), and {"type":"entrez-nucleotide","attrs":{"text":"CP002828","term_id":"336100378","term_text":"CP002828"}}CP002828 (pOC167) [29]
• Bradyrhizobiaceae strain SG-6C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOF01000000","term_id":"338235257","term_text":"gb||AFOF01000000"}}AFOF01000000 [30]
• Hyphomicrobium sp. Strain MC1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FQ859181","term_id":"337757426","term_text":"FQ859181"}}FQ859181 [31]
• Shewanella sp. Strain HN-41, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOZ01000000","term_id":"335867028","term_text":"gb||AFOZ01000000"}}AFOZ01000000 [32]
• Myxococcus fulvus HW-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002830","term_id":"337255776","term_text":"CP002830"}}CP002830 [33]
• Nitrosomonas sp. Strain AL212, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_015222","term_id":"325980881","term_text":"NC_015222"}}NC_015222 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"NC_015223","term_id":"325983714","term_text":"NC_015223"}}NC_015223 pNAL21201), {"type":"entrez-nucleotide","attrs":{"text":"NC_015221","term_id":"325980815","term_text":"NC_015221"}}NC_015221 (pNAL21202) [34]
• Ruegeria sp. Strain KLH11, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ACCW00000000","term_id":"218703200","term_text":"ACCW00000000"}}ACCW00000000 [35]
• Acidovorax avenae subsp. avenae RS-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPT01000000","term_id":"336283372","term_text":"gb||AFPT01000000"}}AFPT01000000 [36]
• Escherichia coli (ExPEC), sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAT00000000","term_id":"338771881","term_text":"AFAT00000000"}}AFAT00000000 [37]
• Vibrio mimicus SX-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADOO01000000","term_id":"340396595","term_text":"gb||ADOO01000000"}}ADOO01000000 [38]
• Agrobacterium tumefaciens Strain F2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFSD00000000","term_id":"338825258","term_text":"AFSD00000000"}}AFSD00000000 [39]
• Pasteurella multocida subsp. gallicida {"type":"entrez-nucleotide-range","attrs":{"text":"AFRR01000001 to AFRR01000489","start_term":"AFRR01000001","end_term":"AFRR01000489","start_term_id":"338220663","end_term_id":"338215299"}}AFRR01000001 to AFRR01000489 [40]
• Pseudomonas aeruginosa 138244, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEVV00000000","term_id":"537462489","term_text":"AEVV00000000"}}AEVV00000000 [41]
• Pseudomonas aeruginosa 152504, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEVW00000000","term_id":"557220721","term_text":"AEVW00000000"}}AEVW00000000 [41]
• Campylobacter jejuni strain 305, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADHL00000000","term_id":"315930937","term_text":"ADHL00000000"}}ADHL00000000 [42]
• Campylobacter jejuni strain DFVF1099, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ADHK00000000","term_id":"315928465","term_text":"ADHK00000000"}}ADHK00000000 [42]
• Xanthomonas campestris pv. raphani strain 756C, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002789","term_id":"341934791","term_text":"CP002789"}}CP002789 [43]
• Xanthomonas campestris pv. raphani strain BLS256, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AAQN01000001","term_id":"94721236","term_text":"AAQN01000001"}}AAQN01000001 [43]
• Rickettsia heilongjiangensis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002912","term_id":"340807448","term_text":"CP002912"}}CP002912 [44]
• Acidiphilium sp. Strain PM (DSM 24941), sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPR00000000","term_id":"338209258","term_text":"AFPR00000000"}}AFPR00000000 [45]
• Pseudomonas putida Strain S16, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002870","term_id":"338835784","term_text":"CP002870"}}CP002870 [46]
• Acinetobacter lwoffii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFQY01000000","term_id":"337752636","term_text":"gb||AFQY01000000"}}AFQY01000000 [47]
• Phylum Firmicutes
• Caldalkalibacillus thermarum strain TA2.A1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFCE00000000","term_id":"334181820","term_text":"AFCE00000000"}}AFCE00000000 [48]
• Listeria monocytogenes Scott A, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFGI00000000","term_id":"332188986","term_text":"AFGI00000000"}}AFGI00000000 [49]
• Lactococcus garvieae 8831, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFCD00000000","term_id":"333218454","term_text":"AFCD00000000"}}AFCD00000000 [50]
• Natranaerobius thermophilus JW/NM-WN-LF, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001034","term_id":"179349329","term_text":"CP001034"}}CP001034 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP001035","term_id":"179352354","term_text":"CP001035"}}CP001035 (plasmid) [51]
• Melissococcus plutonius ATCC 35311, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012200","term_id":"332369543","term_text":"AP012200"}}AP012200 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"AP012201","term_id":"332371286","term_text":"AP012201"}}AP012201 (plasmid) [52]
• Lactobacillus buchneri NRRL B-30929, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002652","term_id":"329127738","term_text":"CP002652"}}CP002652 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002653","term_id":"329130053","term_text":"CP002653"}}CP002653 (plasmid pLBU01), {"type":"entrez-nucleotide","attrs":{"text":"CP002654","term_id":"329130100","term_text":"CP002654"}}CP002654 (plasmid pLBU02), and {"type":"entrez-nucleotide","attrs":{"text":"CP002655","term_id":"329130119","term_text":"CP002655"}}CP002655 (plasmid pLBU03) [53]
• Lactobacillus kefiranofaciens ZW3 , sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002764","term_id":"333956887","term_text":"CP002764"}}CP002764 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002765","term_id":"333958796","term_text":"CP002765"}}CP002765 (plasmid), and {"type":"entrez-nucleotide","attrs":{"text":"CP002766","term_id":"333958996","term_text":"CP002766"}}CP002766 (plasmid) [54]
• Bacillus megaterium strain QM B1551, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001983","term_id":"294346812","term_text":"CP001983"}}CP001983 (chromosome), {"type":"entrez-nucleotide-range","attrs":{"text":"CP001984 to CP001990","start_term":"CP001984","end_term":"CP001990","start_term_id":"294351929","end_term_id":"294352220"}}CP001984 to CP001990 (plasmids pBM100 through pBM700) [55]
• Bacillus megaterium strain DSM319, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001982","term_id":"294799901","term_text":"CP001982"}}CP001982 (chromosome) [55]
• Listeria monocytogenes serovar 4a strain M7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002816","term_id":"336021869","term_text":"CP002816"}}CP002816 [56]
• Bacillus coagulans 2-6, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002472","term_id":"335366109","term_text":"CP002472"}}CP002472 [57]
• Streptococcus salivarius strain CCHSS3, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR873481","term_id":"338741860","term_text":"FR873481"}}FR873481 [58]
• Paenibacillus elgii B69, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHW01000000","term_id":"332713477","term_text":"gb||AFHW01000000"}}AFHW01000000 [59]
• Lactobacillus pentosus MP-10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR871759","term_id":"334880280","term_text":"FR871759"}}FR871759 through {"type":"entrez-nucleotide","attrs":{"text":"FR871848","term_id":"334883124","term_text":"FR871848"}}FR871848 [60]
• Leuconostoc pseudomesenteroides KCTC 3652, sequence accession AEOQ00000001 through AEOQ00001160 [61]
• Lactobacillus mali KCTC 3596, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACP01000001","term_id":"338747920","term_text":"BACP01000001"}}BACP01000001 through {"type":"entrez-nucleotide","attrs":{"text":"BACP01000122","term_id":"338747799","term_text":"BACP01000122"}}BACP01000122 [62]
• Paenibacillus polymyxa Type Strain ATCC 842^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOX01000000","term_id":"335355762","term_text":"gb||AFOX01000000"}}AFOX01000000 [63]
• Streptococcus salivarius strain JIM8777, sequence accssion {"type":"entrez-nucleotide","attrs":{"text":"FR873482","term_id":"338744031","term_text":"FR873482"}}FR873482 [64]
• Lactobacillus cypricasei KCTC 13900, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACS01000001 to BACS01000487","start_term":"BACS01000001","end_term":"BACS01000487","start_term_id":"338748625","end_term_id":"338748139"}}BACS01000001 to BACS01000487 [65]
• Lactobacillus zeae KCTC 3804, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACQ01000001","term_id":"338748035","term_text":"BACQ01000001"}}BACQ01000001 to BACQ101000113 [66]
• Listeria monocytogenes Serovar 4a Strain M7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002816","term_id":"336021869","term_text":"CP002816"}}CP002816 [67]
• Lactobacillus salivarius GJ-24, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOI00000000","term_id":"335351482","term_text":"AFOI00000000"}}AFOI00000000 [68]
• Lactobacillus johnsonii PF01, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFQJ01000000","term_id":"338762788","term_text":"gb||AFQJ01000000"}}AFQJ01000000 [69]
• Clostridium acetobutylicum DSM 1731, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002660","term_id":"336289872","term_text":"CP002660"}}CP002660 through {"type":"entrez-nucleotide","attrs":{"text":"CP002662","term_id":"336293787","term_text":"CP002662"}}CP002662 [70]
• Lactobacillus suebicus KCTC 3549, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"BACO01000000","term_id":"338746125","term_text":"dbj||BACO01000000"}}BACO01000000 [71]
• Brevibacillus laterosporus LMG 15441, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRV00000000","term_id":"338776733","term_text":"AFRV00000000"}}AFRV00000000 [72]
• Lactobacillus salivarius NIAS840, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFMN00000000","term_id":"334308865","term_text":"AFMN00000000"}}AFMN00000000 [73]
• Bifidobacterium animalis subsp. lactis CNCM I-2494, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002915","term_id":"340364148","term_text":"CP002915"}}CP002915 [74]
• Megasphaera elsdenii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HE576794","term_id":"341821300","term_text":"HE576794"}}HE576794 [75]
• Lactobacillus versmoldensis KCTC 3814, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACR01000001 to BACR01000102","start_term":"BACR01000001","end_term":"BACR01000102","start_term_id":"338748138","end_term_id":"338748037"}}BACR01000001 to BACR01000102 [76]
• Lactobacillus pentosus IG1, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"FR874848 to FR874860","start_term":"FR874848","end_term":"FR874860","start_term_id":"339636574","end_term_id":"339639349"}}FR874848 to FR874860 [77]
• Alicyclobacillus acidocaldarius Strain Tc-4-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002902","term_id":"339287872","term_text":"CP002902"}}CP002902 [78]
• Streptococcus thermophilus Strain JIM8232, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FR875178","term_id":"339277069","term_text":"FR875178"}}FR875178 [79]
• Streptococcus equi subsp. zooepidemicus Strain ATCC 35246, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002904","term_id":"338846021","term_text":"CP002904"}}CP002904 [80]
• Bacillus amyloliquefaciens XH7, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002927","term_id":"341825903","term_text":"CP002927"}}CP002927 [81]
• Leuconostoc kimchii Strain C2, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002898","term_id":"338851854","term_text":"CP002898"}}CP002898 [82]
• Lactobacillus malefermentans KCTC 3548, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"BACN01000001 to BACN01000172","start_term":"BACN01000001","end_term":"BACN01000172","start_term_id":"338736862","end_term_id":"338736691"}}BACN01000001 to BACN01000172 [83]
• Weissella koreensis KACC 15510, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002900","term_id":"338855046","term_text":"CP002900"}}CP002900 [84]
• Phylum Tenericutes
• Mycoplasma bovis Strain Hubei-1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002513","term_id":"338226653","term_text":"CP002513"}}CP002513 [85]
• Mycoplasma fermentans Strain M64, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_014921","term_id":"319776738","term_text":"NC_014921"}}NC_014921 [86]
• Haloplasma contractile, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFNU00000000","term_id":"543107448","term_text":"AFNU00000000"}}AFNU00000000 [87]
• Mycoplasma ovipneumoniae Strain SC01, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHO01000000","term_id":"336091059","term_text":"gb||AFHO01000000"}}AFHO01000000 [88]
• Phylum Actinobacteria
• Kocuria rhizophila P7-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFID00000000","term_id":"333463600","term_text":"AFID00000000"}}AFID00000000 [89]
• Streptomyces S4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CADY01000000","term_id":"334306078","term_text":"emb||CADY01000000"}}CADY01000000 [90]
• Corynebacterium nuruki S6-4^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFIZ00000000","term_id":"333352007","term_text":"AFIZ00000000"}}AFIZ00000000 [91]
• Propionibacterium humerusii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAM00000000.1","term_id":"328908381","term_text":"AFAM00000000.1"}}AFAM00000000.1 [92]
• Strain JDM601, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002329","term_id":"333484608","term_text":"CP002329"}}CP002329 [93]
• Streptomyces sp. strain Tü6071, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHJ01000000","term_id":"332514755","term_text":"gb||AFHJ01000000"}}AFHJ01000000 [94]
• Bifidobacterium breve UCC2003, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP000303","term_id":"339478266","term_text":"CP000303"}}CP000303 [95]
• Propionibacterium acnes, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002815","term_id":"335276409","term_text":"CP002815"}}CP002815 [96]
• Amycolicicoccus subflavus DQS3-9A1^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002786","term_id":"333479900","term_text":"CP002786"}}CP002786 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002787","term_id":"333484458","term_text":"CP002787"}}CP002787 (plasmid pAS9A-1), and {"type":"entrez-nucleotide","attrs":{"text":"CP002788","term_id":"333484486","term_text":"CP002788"}}CP002788 (plasmid pAS9A-2). [97]
• Gordonia neofelifaecis NRRL B-59395, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEUD01000000","term_id":"326199990","term_text":"gb||AEUD01000000"}}AEUD01000000 [98]
• Pseudonocardia dioxanivorans strain CB1190, sequence accession NC_015312-4 and CP002595-7 [99]
• Bifidobacterium longum subsp. longum KACC 91563, sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"CP002794 to CP002796","start_term":"CP002794","end_term":"CP002796","start_term_id":"338753582","end_term_id":"338755560"}}CP002794 to CP002796 [100]
• Streptomyces cattleya NRRL 8057, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FQ859185","term_id":"337764029","term_text":"FQ859185"}}FQ859185 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"FQ859184","term_id":"337762320","term_text":"FQ859184"}}FQ859184 (megaplasmid) [101]
• Rhodococcus sp. Strain R04, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFAQ01000000","term_id":"338230982","term_text":"gb||AFAQ01000000"}}AFAQ01000000 [102]
• Mycobacterium bovis BCG Moreau, sequence accession [103]
• Saccharopolyspora spinosa NRRL 18395, sequence accession [104]
• Mycobacterium tuberculosis CCDC5079, sequence accession [105]
• Mycobacterium tuberculosis CCDC5180, sequence accession [105]
• Amycolatopsis mediterranei S699, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002896","term_id":"340523290","term_text":"CP002896"}}CP002896 [106]
• Nesterenkonia sp. Strain F, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRW01000000","term_id":"340539543","term_text":"gb||AFRW01000000"}}AFRW01000000 [107]
• Streptomyces xinghaiensis NRRL {"type":"entrez-nucleotide","attrs":{"text":"B24674","term_id":"2510184","term_text":"B24674"}}B24674^T, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFRP01000000","term_id":"339790456","term_text":"gb||AFRP01000000"}}AFRP01000000 [108]
• Phylum Chlamydiae
• Chlamydophila abortus variant strain LLG, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFHM01000000","term_id":"1154501422"}}AFHM01000000 [109]
• Chlamydia psittaci 6BC, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002586","term_id":"328914189","term_text":"CP002586"}}CP002586 (chromosome), {"type":"entrez-nucleotide","attrs":{"text":"CP002587","term_id":"328915192","term_text":"CP002587"}}CP002587 (plasmid) [110]
• Chlamydia psittaci Cal10, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AEZD00000000","term_id":"328815518","term_text":"AEZD00000000"}}AEZD00000000 (draft chromosome and plasmid) [110]
• Chlamydia trachomatis, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002024","term_id":"339460423","term_text":"CP002024"}}CP002024 [111]
• Phylum Spirochaetes
• Spirochaeta thermophila DSM 6192, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001698","term_id":"306531442","term_text":"CP001698"}}CP001698 [112]
• Brachyspira intermedia, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002874","term_id":"343385146","term_text":"CP002874"}}CP002874 (chromosome) and {"type":"entrez-nucleotide","attrs":{"text":"CP002875","term_id":"343388016","term_text":"CP002875"}}CP002875 (plasmid) [113]
• Phylum Fibrobacteres
• Phylum Bacteroidetes
• Porphyromonas gingivalis TDC60, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AP012203","term_id":"333802964","term_text":"AP012203"}}AP012203 [114]
• Krokinobacter sp. strain 4H-3-7-5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002528","term_id":"332168736","term_text":"CP002528"}}CP002528 [115]
• Lacinutrix sp. strain 5H-3-7-4, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002825","term_id":"334725715","term_text":"CP002825"}}CP002825 [115]
• Bacterium HQM9, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPB00000000","term_id":"336042206","term_text":"AFPB00000000"}}AFPB00000000 [116]
• Anaerophaga sp. Strain HS1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFSL00000000","term_id":"339506355","term_text":"AFSL00000000"}}AFSL00000000 [117]
• Capnocytophaga canimorsus Strain 5, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002113","term_id":"339901044","term_text":"CP002113"}}CP002113 [118]
• Mesoflavibacter zeaxanthinifaciens strain S86, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFOE00000000","term_id":"339831579","term_text":"AFOE00000000"}}AFOE00000000 [119]
• Phylum Verrucomicrobia
• Phylum Lentisphaerae
• Phylum Thermotogae
• Kosmotoga olearia Strain TBF 19.5.1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP001634","term_id":"239505242","term_text":"CP001634"}}CP001634 [120]
• Domain Archaea
• "Candidatus Nitrosoarchaeum koreensis" MY1, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"AFPU00000000","term_id":"339521013","term_text":"AFPU00000000"}}AFPU00000000 [121]

Non-Bacterial genomes

• North-European Cucumber Cucumis sativus L., sequence accession {"type":"entrez-nucleotide-range","attrs":{"text":"FI132140-FI136208","start_term":"FI132140","end_term":"FI136208","start_term_id":"192759773","end_term_id":"192763063"}}FI132140-FI136208, {"type":"entrez-nucleotide-range","attrs":{"text":"GS765762-GS766880","start_term":"GS765762","end_term":"GS766880","start_term_id":"269146953","end_term_id":"269148071"}}GS765762-GS766880, {"type":"entrez-nucleotide-range","attrs":{"text":"GS815969-GS874855","start_term":"GS815969","end_term":"GS874855","start_term_id":"282718378","end_term_id":"282698342"}}GS815969-GS874855 [122]
• Castor bean Ricinus communis organelle genome, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"JF937588","term_id":"339516144","term_text":"JF937588"}}JF937588(chloroplast), {"type":"entrez-nucleotide","attrs":{"text":"HQ874649","term_id":"322394252","term_text":"HQ874649"}}HQ874649 (mitochondria) [123]
• Stretch Lagoon Orbivirus Umatilla, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ842619","term_id":"332713884","term_text":"HQ842619"}}HQ842619 through {"type":"entrez-nucleotide","attrs":{"text":"HQ842628","term_id":"332713902","term_text":"HQ842628"}}HQ842628 [124]
• Atlantic cod Gadus morhua, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CAEA01000001","term_id":"344901723","term_text":"CAEA01000001"}}CAEA01000001 through {"type":"entrez-nucleotide","attrs":{"text":"CAEA01554869","term_id":"344345641","term_text":"CAEA01554869"}}CAEA01554869 [125]
• Potato Solanum tuberosum L., sequence accession {"type":"entrez-nucleotide","attrs":{"text":"GS025503","term_id":"255349557","term_text":"GS025503"}}GS025503 through {"type":"entrez-nucleotide","attrs":{"text":"GS026177","term_id":"255350231","term_text":"GS026177"}}GS026177 [126]
• ΦCA82, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"HQ264138","term_id":"311336635","term_text":"HQ264138"}}HQ264138 [127]
• Paramecium caudatumreveals mitochondria, sequence accession NC001324 [128]
• bacteriophage IME08, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"NC_014260","term_id":"299778956","term_text":"NC_014260"}}NC_014260 [129]
• virus (ILTV), sequence accession HQ_630064 [130]
• Australian kangaroo Macropus eugenii, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"ABQO000000000","term_id":"377520186","term_text":"ABQO000000000"}}ABQO000000000 [131]
• Aichi virus, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"FJ890523","term_id":"260176795","term_text":"FJ890523"}}FJ890523 [132]
• "Candidatus Tremblaya princeps" Strain PCVAL, sequence accession {"type":"entrez-nucleotide","attrs":{"text":"CP002918","term_id":"340536387","term_text":"CP002918"}}CP002918 [133]

     

Investigation of Encephalopathy Caused by Shiga Toxin 2c-Producing Escherichia coli Infection in Mice

A large outbreak of Shiga toxin (Stx)-producing enteroaggregative Escherichia coli (EAEC) O104:H4 occurred in northern Germany. From this outbreak, at least 900 patients developed hemolytic uremic syndrome (HUS), resulting in more than 50 deaths. Thirty percent of the HUS patients showed encephalopathy. We previously established a mouse model with encephalopathy associated with blood brain barrier (BBB) damage after oral infection with the Shiga toxin (Stx) 2c-producing Escherichia coli O157: H- strain {"type":"entrez-nucleotide","attrs":{"text":"E32511","term_id":"13026758","term_text":"E32511"}}E32511 ({"type":"entrez-nucleotide","attrs":{"text":"E32511","term_id":"13026758","term_text":"E32511"}}E32511). In this model, we detected high expression of the Stx receptor synthase enzyme, glycosphingolipid globotriaosylceramide (Gb3) synthase, in endothelial cells (ECs) and neurons in the reticular formation of the medulla oblongata by in situ hybridization. Caspase-3 was activated in neurons in the reticular formation of the medulla oblongata and the anterior horn of the spinal cord. Astrocytes (ASTs) were activated in the medulla oblongata and spinal cord, and a decrease in aquaporin 4 around the ECs suggested that BBB integrity was compromised directly by Stx2c or through the activation of ASTs. We also report the effectiveness of azithromycin (AZM) in our model. Moreover, AZM strongly inhibited the release of Stx2c from {"type":"entrez-nucleotide","attrs":{"text":"E32511","term_id":"13026758","term_text":"E32511"}}E32511 in vitro.     

High Prevalence and Significant Association of ESBL and QNR Genes in Pathogenic Klebsiella pneumoniae Isolates of Patients from Kolkata, India

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 bla_TEM, bla_SHV, bla_CTX-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: bla_TEM > bla_SHV > bla_CTXM. 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 bla_TEM, bla_SHV, bla_CTX-M and QNRB PCR products revealed presence of bla_TEM1 (GenBank accession: {"type":"entrez-nucleotide","attrs":{"text":"JN193522","term_id":"343796760","term_text":"JN193522"}}JN193522), bla_TEM116 ({"type":"entrez-nucleotide","attrs":{"text":"JN193523","term_id":"343796762","term_text":"JN193523"}}JN193523 and {"type":"entrez-nucleotide","attrs":{"text":"JN193524","term_id":"343796764","term_text":"JN193524"}}JN193524), bla_SHV11, bla_CTXM72 variants ({"type":"entrez-nucleotide","attrs":{"text":"JF523199","term_id":"329024835","term_text":"JF523199"}}JF523199) and QNRB1 ({"type":"entrez-nucleotide","attrs":{"text":"JN193526","term_id":"343796802","term_text":"JN193526"}}JN193526 and {"type":"entrez-nucleotide","attrs":{"text":"JN193527","term_id":"343796804","term_text":"JN193527"}}JN193527) in our samples.     

Hypoxic Conditioned Medium from Rat Cerebral Cortical Cells Enhances the Proliferation and Differentiation of Neural Stem Cells Mainly through PI3-K/Akt Pathways

Purpose

To investigate the effects of hypoxic conditioned media from rat cerebral cortical cells on the proliferation and differentiation of neural stem cells (NSCs) in vitro, and to study the roles of PI3-K/Akt and JNK signal transduction pathways in these processes.

Methods

Cerebral cortical cells from neonatal Sprague–Dawley rat were cultured under hypoxic and normoxic conditions; the supernatant was collected and named ‘hypoxic conditioned medium’ (HCM) and ‘normoxic conditioned medium’ (NCM), respectively. We detected the protein levels (by ELISA) of VEGF and BDNF in the conditioned media and mRNA levels (by RT-PCR) in cerebral cortical cells. The proliferation (number and size of neurospheres) and differentiation (proportion of neurons and astrocytes over total cells) of NSCs was assessed. {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 and SP600125, inhibitors of PI3-K/Akt and JNK, respectively, were applied, and the phosphorylation levels of PI3-K, Akt and JNK were measured by western blot.

Results

The protein levels and mRNA expressions of VEGF and BDNF in 4% HCM and 1% HCM were both higher than that of those in NCM. The efficiency and speed of NSCs proliferation was enhanced in 4% HCM compared with 1% HCM. The highest percentage of neurons and lowest percentage of astrocytes was found in 4% HCM. However, the enhancement of NSCs proliferation and differentiation into neurons accelerated by 4% HCM was inhibited by {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 and SP600125, with {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 having a stronger inhibitory effect. The increased phosphorylation levels of PI3-K, Akt and JNK in 4% HCM were blocked by {"type":"entrez-nucleotide","attrs":{"text":"LY294002","term_id":"1257998346","term_text":"LY294002"}}LY294002 and SP600125.

Conclusions

4%HCM could promote NSCs proliferation and differentiation into high percentage of neurons, these processes may be mainly through PI3-K/Akt pathways.     

Fosmidomycin uptake into Plasmodium and Babesia-infected erythrocytes is facilitated by parasite-induced new permeability pathways

Background

Highly charged compounds typically suffer from low membrane permeability and thus are generally regarded as sub-optimal drug candidates. Nonetheless, the highly charged drug fosmidomycin and its more active methyl-derivative {"type":"entrez-nucleotide","attrs":{"text":"FR900098","term_id":"525219861","term_text":"FR900098"}}FR900098 have proven parasiticidal activity against erythrocytic stages of the malaria parasite Plasmodium falciparum. Both compounds target the isoprenoid biosynthesis pathway present in bacteria and plastid-bearing organisms, like apicomplexan parasites. Surprisingly, the compounds are inactive against a range of apicomplexans replicating in nucleated cells, including Toxoplasma gondii.

Methodology/Principal Findings

Since non-infected erythrocytes are impermeable for FR90098, we hypothesized that these drugs are taken up only by erythrocytes infected with Plasmodium. We provide evidence that radiolabeled {"type":"entrez-nucleotide","attrs":{"text":"FR900098","term_id":"525219861","term_text":"FR900098"}}FR900098 accumulates in theses cells as a consequence of parasite-induced new properties of the host cell, which coincide with an increased permeability of the erythrocyte membrane. Babesia divergens, a related parasite that also infects human erythrocytes and is also known to induce an increase in membrane permeability, displays a similar susceptibility and uptake behavior with regard to the drug. In contrast, Toxoplasma gondii-infected cells do apparently not take up the compounds, and the drugs are inactive against the liver stages of Plasmodium berghei, a mouse malaria parasite.

Conclusions/Significance

Our findings provide an explanation for the observed differences in activity of fosmidomycin and {"type":"entrez-nucleotide","attrs":{"text":"FR900098","term_id":"525219861","term_text":"FR900098"}}FR900098 against different Apicomplexa. These results have important implications for future screens aimed at finding new and safe molecular entities active against P. falciparum and related parasites. Our data provide further evidence that parasite-induced new permeability pathways may be exploited as routes for drug delivery.     

Comparative High-Resolution Mapping of the Wax Inhibitors Iw1 and Iw2 in Hexaploid Wheat

The wax (glaucousness) on wheat leaves and stems is mainly controlled by two sets of genes: glaucousness loci (W1 and W2) and non-glaucousness loci (Iw1 and Iw2). The non-glaucousness (Iw) loci act as inhibitors of the glaucousness loci (W). High-resolution comparative genetic linkage maps of the wax inhibitors Iw1 originating from Triticum dicoccoides, and Iw2 from Aegilops tauschii were developed by comparative genomics analyses of Brachypodium, sorghum and rice genomic sequences corresponding to the syntenic regions of the Iw loci in wheat. Eleven Iw1 and eight Iw2 linked EST markers were developed and mapped to linkage maps on the distal regions of chromosomes 2BS and 2DS, respectively. The Iw1 locus mapped within a 0.96 cM interval flanked by the {"type":"entrez-nucleotide","attrs":{"text":"BE498358","term_id":"9696891","term_text":"BE498358"}}BE498358 and {"type":"entrez-nucleotide","attrs":{"text":"CA499581","term_id":"24990541","term_text":"CA499581"}}CA499581 EST markers that are collinear with 122 kb, 202 kb, and 466 kb genomic regions in the Brachypodium 5S chromosome, the sorghum 6S chromosome and the rice 4S chromosome, respectively. The Iw2 locus was located in a 4.1 to 5.4-cM interval in chromosome 2DS that is flanked by the {"type":"entrez-nucleotide","attrs":{"text":"CJ886319","term_id":"143584862","term_text":"CJ886319"}}CJ886319 and {"type":"entrez-nucleotide","attrs":{"text":"CJ519831","term_id":"93083902","term_text":"CJ519831"}}CJ519831 EST markers, and this region is collinear with a 2.3 cM region spanning the Iw1 locus on chromosome 2BS. Both Iw1 and Iw2 co-segregated with the {"type":"entrez-nucleotide","attrs":{"text":"BF474014","term_id":"11543196","term_text":"BF474014"}}BF474014 and {"type":"entrez-nucleotide","attrs":{"text":"CJ876545","term_id":"143556664","term_text":"CJ876545"}}CJ876545 EST markers, indicating they are most likely orthologs on 2BS and 2DS. These high-resolution maps can serve as a framework for chromosome landing, physical mapping and map-based cloning of the wax inhibitors in wheat.     

Design of tandem genes cluster and expression vector for biosynthesis of soybean isoflavones

A tandem gene cluster CHS-CHI-IFS (rIFS) for secondary metabolites of plant isoflavones was constructed by using the chalcone synthase (CHS), chalcone isomerase (CHI), and isoflavone synthase (IFS) (GenBank accession numbers {"type":"entrez-nucleotide","attrs":{"text":"EU526827","term_id":"170783761","term_text":"EU526827"}}EU526827, {"type":"entrez-nucleotide","attrs":{"text":"EU526829","term_id":"170783765","term_text":"EU526829"}}EU526829, {"type":"entrez-nucleotide","attrs":{"text":"EU526830","term_id":"170783767","term_text":"EU526830"}}EU526830) in a single recombination event with the pET22b vector. The resulting expression vector pET-rIFS was heterogeneously expressed. The highlights of the vector include ease of handling, high efficiency and universal application among diverse plant species. To the best of our knowledge, this is the first attempt at developing a novel method of constructing tandem gene cluster for future research involving secondary metabolism of isoflavones and isoflavones engineering.Key words: Isoflavones biosynthesis, Novel method, Secondary metabolism, Tandem gene cluster