Presence Of Various Genes Research Articles

Effect of salinity on genes involved in the stress response in mangrove soils.

Mangroves are a challenging ecosystem for the microorganisms that inhabit them, considering they are subjected to stressful conditions such as high and fluctuating salinity. Metagenomic analysis of mangrove soils under contrasting salinity conditions was performed at the mouth of the Ranchera River to the Caribbean Sea in La Guajira, Colombia, using shotgun sequencing and the Illumina Hiseq 2500 platform. Functional gene analysis demonstrated that salinity could influence the abundance of microbial genes involved in osmoprotectant transport, DNA repair, heat shock proteins (HSP), and Quorum Sensing, among others. In total, 135 genes were discovered to be linked to 12 pathways. Thirty-four genes out of 10 pathways had statistical differences for a p-value and FDR < 0.05. UvrA and uvrB (nucleotide excision repair), groEL (HSP), and secA (bacterial secretion system) genes were the most abundant and were enriched by high salinity. The results of this study showed the prevalence of diverse genetic mechanisms that bacteria use as a response to survive in the challenging mangrove, as well as the presence of various genes that are recruited in order to maintain bacterial homeostasis under conditions of high salinity.

De novo genome sequence of endophytic biocontrol strain Bacillus sp. ST24 isolated from rice seed.

In this study, we present the genome sequence of Bacillus sp. strain ST24, an endophytic bacterium isolated from rice seeds. The genome assembly comprises a total of 5,799,877 bp, with a GC content of 34.81%. Furthermore, our analysis revealed the presence of various genes associated with antibiotic production, as well as genes involved in polyketide biosynthesis and non-ribosomal polyketide-like clusters.

Metagenome-assembled genomes for biomarkers of bio-functionalities in Laal dahi, an Indian ethnic fermented milk product

Laal dahi is a sweetened and soft pudding-like fermented milk product of the Eastern regions of India, which has not been studied for its microbial community structures and health promoting functionality in terms of ‘omics’ approaches. We applied metagenomic and metagenomes-assembled genomes (MAGs) tools to decipher the biomarkers for genes encoding for different health promoting functionalities in laal dahi. Abundance of bacterial domains was observed with negligible presence of eukaryotes and viruses. Bacillota was the most abundant phylum with different bacterial species viz., Enterococcus italicus, Lactococcus raffinolactis, Lactobacillus helveticus, Bifidobacterium mongoliense, Hafnia alvei, Lactococcus lactis, Acetobacter okinawensis, Streptococcus thermophilus, Thermus thermophilus, Leuconostoc citreum, Leuconostoc pseudomesenteroides, Acetobacter orientalis, Lactobacillus gallinarum, Lactococcus chungangensis and Lactobacillus delbrueckii. Comparison of laal dahi microbiome with that of similar fermented milk products was also carried out after retrieving the metagenomic datasets from public databases. Significant abundance of Lb. helveticus, E. italicus, Lc. raffinolactis and Lc. lactis in laal dahi. Interestingly, Bifidobacterium mongoliense, Lb. gallinarum, Lc. chungangensis and Acetobacter okinawensis were only detected in laal dahi but Streptococcus infantarius, Lacticaseibacillus rhamnosus and Lb. johnsonii were absent. Reconstruction of putative single environment-specific genomes from metagenomes in addition to subsampling of the abundant species resulted in five high-quality MAGs identified as Lactobacillus delbrueckii, Lactobacillus helveticus, Lactococcus chungangensis, Lactococcus lactis and Streptococcus thermophilus. All MAGs showed the presence of various genes with several putative functions corresponding to different probiotic and prebiotic functions, short-chain fatty acids production, immunomodulation, antitumor genes, essential amino acid and vitamin biosynthesis. Genes for γ-Aminobutyric acid (GABA) production were only detected in MAG of Lactococcus lactis. Gene clusters for secondary metabolites (antimicrobial peptides) were detected in all MAGs except Lc. chungangensis. Additionally, detection of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) elements was observed only in Lactobacillus delbrueckii and Streptococcus thermophilus. Annotation of several genes with potential health beneficial properties in all five MAGs may support the need to explore the culturability of these MAGs for future use in controlled fermentation of functional dairy products.

Genomic characterization of endemic diarrheagenic Escherichia coli and Escherichia albertii from infants with diarrhea in Vietnam.

Diarrheagenic Escherichia coli (DEC) is a group of bacterial pathogens that causes life-threatening diarrhea in children in developing countries. However, there is limited information on the characteristics of DEC isolated from patients in these countries. A detailed genomic analysis of 61 DEC-like isolates from infants with diarrhea was performed to clarify and share the characteristics of DEC prevalent in Vietnam. DEC was classified into 57 strains, including 33 enteroaggregative E. coli (EAEC) (54.1%), 20 enteropathogenic E. coli (EPEC) (32.8%), two enteroinvasive E. coli (EIEC) (3.3%), one enterotoxigenic E. coli (ETEC), and one ETEC/EIEC hybrid (1.6% each), and surprisingly into four Escherichia albertii strains (6.6%). Furthermore, several epidemic DEC clones showed an uncommon combination of pathotypes and serotypes, such as EAEC Og130:Hg27, EAEC OgGp9:Hg18, EAEC OgX13:H27, EPEC OgGp7:Hg16, and E. albertii EAOg1:HgUT. Genomic analysis also revealed the presence of various genes and mutations associated with antibiotic resistance in many isolates. Strains that demonstrate potential resistance to ciprofloxacin and ceftriaxone, drugs recommended for treating childhood diarrhea, accounted for 65.6% and 41%, respectively. Our finding indicate that the routine use of these antibiotics has selected resistant DECs, resulting in a situation where these drugs do not provide in therapeutic effects for some patients. Bridging this gap requires continuous investigations and information sharing regarding the type and distribution of endemic DEC and E. albertii and their antibiotic resistance in different countries.

Performance of halotolerant bacteria associated with Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L. ameliorate tomato plant growth and tolerance to saline stress: from selective isolation to genomic analysis of potential determinants.

The use of halotolerant beneficial plant-growth-promoting (PGP) bacteria is considered as a promising eco-friendly approach to improve the salt tolerance of cash crops. One strategy to enhance the possibility of obtaining stress-alleviating bacteria is to screen salt impacted soils. In this study, amongst the 40 endophytic bacteria isolated from the roots of Sahara-inhabiting halophytes Atriplex halimus L. and Lygeum spartum L., 8 showed interesting NaCl tolerance in vitro. Their evaluation, through different tomato plant trials, permitted the isolate IS26 to be distinguished as the most effective seed inoculum for both plant growth promotion and mitigation of salt stress. On the basis of 16S rRNA gene sequence, the isolate was closely related to Stenotrophomonas rhizophila. It was then screened in vitro for multiple PGP traits and the strain-complete genome was sequenced and analysed to further decipher the genomic basis of the putative mechanisms underlying its osmoprotective and plant growth abilities. A remarkable number of genes putatively involved in mechanisms responsible for rhizosphere colonization, plant association, strong competition for nutrients, and the production of important plant growth regulator compounds, such as AIA and spermidine, were highlighted, as were substances protecting against stress, including different osmolytes like trehalose, glucosylglycerol, proline, and glycine betaine. By having genes related to complementary mechanisms of osmosensing, osmoregulation and osmoprotection, the strain confirmed its great capacity to adapt to highly saline environments. Moreover, the presence of various genes potentially related to multiple enzymatic antioxidant processes, able to reduce salt-induced overproduction of ROS, was also detected.

Detection of Various Beta-Lactamases in Escherichia coli and Klebsiella sp.: A Study from Tertiary Care Centre of North India

AbstractObjective: The emergence of carbapenem-resistant Escherichia coli and Klebsiella species is a global threat. We aimed to compare two phenotypic methods and evaluate the genotypic method for the detection of beta-lactamases produced by E. coli and Klebsiella spp. Materialsand Methods: One hundred and twenty-six E. coli and Klebsiella isolates were examined for phenotypic production of beta-lactamases by using disc diffusion, combined disc test (CDT) and modified carbapenem inactivation method (mCIM). All strains were also studied for the presence of various genes by polymerase chain reaction. Results: Out of 126 isolates, 96% of the isolates were extended-spectrum β-lactamase (ESBL) producers based on the presence of various ESBL genes. CDT method showed higher number of total (89%) carbapenemases in comparison to mCIM (81%). Among carbapenemases none of the isolates were Klebsiella pneumoniae carbapenemase producer by CDT, while 69% isolates were metallo-beta-lactamase (MBL) producers. Another method, mCIM/ethylene diamine tetraacetic acid mCIM showed 100% agreement for MBL detection. As regards, AmpC and class D carbapenemases; 0.04% and 16% positivity was detected, respectively, based on CDT method. Molecular analysis revealed 91% of the isolates harbouring carbapenemase genes. blaNDM was the most common gene detected followed byblaOXA-48. Nine of the blaNDM-positive isolates also possessed blaOXA-48 gene. Conclusion: Our finding shows high percentages of ESBL and carbapenemases in E. coli and Klebsiella spp. Among phenotypic methods, CDT seems to be a better choice as prevalence of carbapenemases shows lots of variation in our country. For Class B enzymes, both CDT and mCIM/eCIM can be used in the routine laboratories.

Identification and characterization of novel penta‐podded genotypes in the cultivated lentil

AbstractOur study reports the identification of two novel multi‐flowering (MF) genotypes, PMF‐1 and PMF‐2, in cultivated lentil (Lens culinaris Medik.), stably forming up to five flowers per peduncle (FPP) on I2 nodes at multiple flowering nodes (beyond the ninth node). These genotypes were identified from the ICARDA (International Centre for Agricultural Research in the Dry Areas) nursery received from Lebanon. Stable MF was observed under open field conditions at IARI (the Indian Agricultural Research Institute), New Delhi, India, during the year 2017–2018 and 2018–2019, and also in the partially controlled glasshouse conditions. In addition, we identified two more stable genotypes, namely, PMF‐3 and PMF‐4, producing four flowers and a genotype, ILL7663, producing only one to two flowers at multiple flowering nodes under normal growing conditions. It is speculated that the expression of the MF trait is the result of interaction between specific genetic loci with the environmental conditions during the bud formation stage in the identified lines. The possibility of the presence of various genes known in other crops like pea (Pisum sativum L.) and chickpea (Cicer arietinum L.), along with various environmental factors regulating the MF expression, is also worked out for lentil. Further, these novel resources can be used for genetic studies aimed to identify the locus regulating the MF trait in lentil.

Abundance of antibiotic resistance genes in environmental bacteriophages.

The ecosystem is continuously exposed to a wide variety of antimicrobials through waste effluents, agricultural run-offs and animal-related and anthropogenic activities, which contribute to the spread of antibiotic resistance genes (ARGs). The contamination of ecosystems with ARGs may create increased opportunities for their transfer to naive microbes and eventually lead to entry into the human food chain. Transduction is a significant mechanism of horizontal gene transfer in natural environments, which has traditionally been underestimated as compared to transformation. We explored the presence of ARGs in environmental bacteriophages in order to recognize their contribution in the spread of ARGs in environmental settings. Bacteriophages were isolated against environmental bacterial isolates, purified and bulk cultured. They were characterized, and detection of ARG and intI genes including blaTEM, blaOXA-2, intI1, intI2, intI3, tetA and tetW was carried out by PCR. This study revealed the presence of various genes [tetA (12.7 %), intI1 (10.9 %), intI2 (10.9 %), intI3 (9.1 %), tetW (9.1 %) and blaOXA-2 (3.6 %)] and blaTEM in a significantly higher proportion (30.9 %). blaSHV, blaOXA-1, tetO, tetB, tetG, tetM and tetS were not detected in any of the phages. Soil phages were the most versatile in terms of ARG carriage. Also, the relative abundance of tetA differed significantly vis-à-vis source. The phages from organized farms showed varied ARGs as compared to the unorganized sector, although blaTEM ARG incidences did not differ significantly. The study reflects on the role of phages in dissemination of ARGs in environmental reservoirs, which may provide an early warning system for future clinically relevant resistance mechanisms.

Evolution and Diversity of Listeria monocytogenes from Clinical and Food Samples in Shanghai, China.

Listeria monocytogenes is a significant foodborne pathogen causing severe systemic infections in humans with high mortality rates. The objectives of this work were to establish a phylogenetic framework of L. monocytogenes from China and to investigate sequence diversity among different serotypes. We selected 17 L. monocytogenes strains recovered from patients and foods in China representing serotypes 1/2a, 1/2b, and 1/2c. Draft genome sequences were determined using Illumina MiSeq technique and associated protocols. Open reading frames were assigned using prokaryotic genome annotation pipeline by NCBI. Twenty-four published genomes were included for comparative genomic and phylogenetic analysis. More than 154,000 single nucleotide polymorphisms (SNPs) were identified from multiple genome alignment and used to reconstruct maximum likelihood phylogenetic tree. The 41 genomes were differentiated into lineages I and II, which consisted of 4 and 11 subgroups, respectively. A clinical strain from China (SHL009) contained significant SNP differences compared to the rest genomes, whereas clinical strain SHL001 shared most recent common ancestor with strain SHL017 from food. Moreover, clinical strains SHL004 and SHL015 clustered together with two strains (08-5578 and 08-5923) recovered from an outbreak in Canada. Partial sequences of a plasmid found in the Canadian strain were also present in SHL004. We investigated the presence of various genes and gene clusters associated with virulence and subgroup-specific genes, including internalins, L. monocytogenes pathogenicity islands (LIPIs), L. monocytogenes genomic islands (LGIs), stress survival islet 1 (SSI-1), and clustered regularly interspaced short palindromic repeats (CRISPR)/cas system. A novel genomic island, denoted as LGI-2 was identified. Comparative sequence analysis revealed differences among the L. monocytogenes strains related to virulence, survival abilities, and attributes against foreign genetic elements. L. monocytogenes from China were genetically diverse. Strains from clinical specimens and food related closely suggesting foodborne transmission of human listeriosis.

Correction: Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.

Bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. Staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host's immune response and antibiotics. Commensal S. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm accumulation. We quantified the differences in biofilm formation in 98 S. epidermidis isolates from various sources, and investigated population structure based on ribosomal multilocus typing (rMLST) and the presence/absence of genes involved in adhesion and biofilm formation. All isolates were able to adhere and form biofilms in in vitro growth assays and confocal microscopy allowed classification into 5 biofilm morphotypes based on their thickness, biovolume and roughness. Phylogenetic reconstruction grouped isolates into three separate clades, with the isolates in the main disease associated clade displaying diversity in morphotype. Of the biofilm morphology characteristics, only biofilm thickness had a significant association with clade distribution. The distribution of some known adhesion-associated genes (aap and sesE) among isolates showed a significant association with the species clonal frame. These data challenge the assumption that biofilm-associated genes, such as those on the ica operon, are genetic markers for less invasive S. epidermidis isolates, and suggest that phenotypic characteristics, such as adhesion and biofilm formation, are not fixed by clonal descent but are influenced by the presence of various genes that are mobile among lineages.

Biofilm Morphotypes and Population Structure among Staphylococcus epidermidis from Commensal and Clinical Samples.

Bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. Staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host’s immune response and antibiotics. Commensal S. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm accumulation. We quantified the differences in biofilm formation in 98 S. epidermidis isolates from various sources, and investigated population structure based on ribosomal multilocus typing (rMLST) and the presence/absence of genes involved in adhesion and biofilm formation. All isolates were able to adhere and form biofilms in in vitro growth assays and confocal microscopy allowed classification into 5 biofilm morphotypes based on their thickness, biovolume and roughness. Phylogenetic reconstruction grouped isolates into three separate clades, with the isolates in the main disease associated clade displaying diversity in morphotype. Of the biofilm morphology characteristics, only biofilm thickness had a significant association with clade distribution. The distribution of some known adhesion-associated genes (aap and sesE) among isolates showed a significant association with the species clonal frame. These data challenge the assumption that biofilm-associated genes, such as those on the ica operon, are genetic markers for less invasive S. epidermidis isolates, and suggest that phenotypic characteristics, such as adhesion and biofilm formation, are not fixed by clonal descent but are influenced by the presence of various genes that are mobile among lineages.

Emergence of Tetracycline Resistant Vibrio cholerae O1 Biotype El Tor Serotype Ogawa with Classical ctxB Gene from a Cholera Outbreak in Odisha, Eastern India.

In September 2010, a cholera outbreak was reported from Odisha, Eastern India. V. cholerae isolated from the clinical samples were biochemically and serologically confirmed as serogroup O1, biotype El Tor, and serotype Ogawa. Multiplex PCR screening revealed the presence of various genes, namely, ompW, ctxB, zot, rfbO1, tcp, ace, hlyA, ompU, rtx, and toxR, in all of the isolates. The isolates were resistant to co-trimoxazole, nalidixic acid, polymyxin B, spectinomycin, streptomycin, sulfamethoxazole, tetracycline, trimethoprim, and vibriostatic agent 2,4-diamino-6,7-diisopropylpteridine (O/129). Minimum inhibitory concentration of tetracycline decreased in the presence of carbonyl cyanide m-chlorophenylhydrazone (CCCP), suggesting the involvement of efflux pumps. PCR analysis confirmed the presence of class I integrons as well as SXT elements harbouring antibiotic resistance genes in all isolates. Sequencing revealed the presence of ctxB gene of classical biotype in all the isolates. The isolates harboured an RS1-CTX prophage array with El Tor type rstR and classical ctxB on the large chromosome. The study indicated that the V. cholerae El Tor variants are evolving in the area with better antibiotic resistance and virulence potential.

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi.

Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.

In Silico Structural and Functional Annotation of Hypothetical Proteins of Vibrio cholerae O139.

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

Influence of isolate origin and presence of various genes on biofilm formation byEnterococcus faecium

Enterococcus faecium, a major cause of nosocomial infections, is often isolated from conditions where biofilm is considered to be important in the establishment of infections. We investigated biofilm formation among E. faecium isolates from diverse sources and found that the occurrence and amount of biofilm formation were significantly greater in clinical isolates than fecal isolates from community volunteers. We also found that the presence of the empfm (E. faecium pilus) operon was associated with the amount of biofilm formation. Furthermore, we analyzed the possible association between the distribution of 16 putative virulence genes and the occurrence of biofilm production. Even though the prevalence of these virulence genes was significantly higher in clinical isolates, we did not observe any correlation with the occurrence of biofilm formation.

The Majority of a Collection of U.S. Endocarditis Enterococcus faecalis Isolates Obtained from 1974 to 2004 Lack Capsular Genes and Belong to Diverse, Non-Hospital-Associated Lineages

ABSTRACT Eighty-one endocarditis-derived Enterococcus faecalis isolates that were collected from individual patients in the United States between 1974 and 2004 were sequence typed and analyzed for the presence of various genes, including some previously associated with virulence. Overall, using our previously described trilocus sequence typing (TLST), 44 different sequence types (STs) were found within this collection; 26 isolates were singletons (a unique TLST sequence type [ST T ]), some ST T s contained multiple isolates (up to 6 isolates), and 16% of the isolates (13 isolates) could be grouped by additional sequence typing into clonal cluster 21 (CC21). Of note, only four isolates (7%) of the 56 whose multilocus sequence types were determined were found to belong to one of the previously described hospital-associated clonal clusters CC2 and CC9, and only 15% and 37% of all isolates had high-level resistance to gentamicin and streptomycin, respectively, including 10% that were resistant to both. We also found that 64% of the isolates lacked the genes for production of capsule polysaccharide, which has been proposed to enhance the pathogenic potential of the hospital-associated clonal clusters. In summary, while our collection is not a random sample of cases of E. faecalis endocarditis, these results indicate that nonencapsulated strains belonging to non-hospital-associated lineages were predominant among endocarditis E. faecalis isolates recovered during this time period.

Abstract 2332: The new protein FAM110B regulates the expression of E-cadherin and is involved in cell migration and invasion

Abstract FAM110B was first identified in a functional screen using genetic suppressor elements to identify new genes involved in the sensitivity to topoisomerase II poisons (Gros et al. Cancer Res, 2003 63: 164-71). FAM110B is extremely conserved in vertebrates. It shares strong sequence homologies with the two other members of this new family (FAM110A &amp; C), but has no known functional domains. We generated a polyclonal antibody and showed that endogenous FAM110B had a MW of ≈40 kDa and was expressed in various cancer cell lines with a predominant cytoplasmic localization. To identify its biological function, we evaluate the different genes/pathways that it could modulate, using specific lentiviral shRNA to target FAM110B in HeLa cells. We found that transient downregulation of FAM110B induced a net decrease in cell proliferation and cell survival. It also induced a change in cell morphology which was accompanied by an increase in E-cadherin and a decrease in N-cadherin expression which are two markers of a reverse epithelial to mesenchymal (EMT) transition phenotype. We also measured the levels of SNAIL and SLUG protein levels, two known repressors of E-cadherin expression and found that only SLUG was decreased in shFAM110B-transfected cells, suggesting that regulation of E-cadherin expression by FAM110B involves, at least in part, its transcriptional repression by SLUG. Increased expression of E-cadherin was confirmed at the mRNA level by microarray analyses comparing control cells to shFAM110B-transfected cells. This analysis also revealed the presence of various genes involved in EMT among the 1000 most differentially expressed genes (adjusted t-value &amp;gt; 7 or &amp;lt; -7) such as Twist2, fibronectin 1, Collagen 1A1 &amp; 4, MMP2, PAI-1, claudin1 &amp; 4, integrin α4, Nestin, interleukin 8, MUC1, or MUC16. Our data were confirmed at the functional level by analyzing the effects of FAM110B repression on the motility/migratory behaviour of HeLa cells using the wound model. While cells expressing control shRNA were able to invade the wound within 7-10h, cells with reduced levels of FAM110B had barely started to move towards the wound. Similarly, shFAM110B-transfected cells displayed a 2-fold decrease in their capacity to invade and migrate through collagen gels as compared to control cells. Using the Cignal Finder Cancer 10-Pathway Reporter Assay, we assess whether other signalling pathways could be deregulated following FAM110B downregulation. We found that Wnt, TGF-β and the Notch pathways, which are all involved in EMT, were significantly downregulated in shFAM110B-transfected cells, which is in accordance with our previous observations. Together, our results provide new evidences on the potential role of FAM110B in the regulation of E-cadherin expression and more generally in crucial cellular processes such as cell motility, migration, invasion and metastasis which makes it a new potential target for cancer therapy. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 2332. doi:10.1158/1538-7445.AM2011-2332

Distribution of pathogenicity islands among Colombian isolates of Salmonella

Salmonella pathogenicity islands (SPIs) are regions scattered along the bacterial chromosome, with an acknowledged pivotal role during gastrointestinal and systemic infection. The distribution of SPIs has been investigated in reference strains. However, there is a lack of studies on their presence and/or assortment within the genomes of Salmonella enterica (S. enterica) serovars that circulate in different geographical regions. Therefore, in this study, we aimed to determine the presence of genes of the pathogenicity islands 1 to 5 (SPI-1 to 5), in Salmonella clinical isolates from Colombian patients with systemic and enteric outcomes. A total of 125 strains of S. enterica belonging to different serovars were isolated from various clinical samples. Strains were identified and screened for the presence of various genes located in pathogenicity islands. The genes tested were selected according to the attributed pathogenic function and detected by PCR for the SPI-1 hilA and invA; for SPI-2 spiC and ttrC; for SPI-3 misL and mgtC; for SPI-4 orfL and SPI-4R; and for SPI-5 pipD and sopB. Salmonella pathogenicity islands 1 to 5 were detected in isolates from patients with systemic and gastrointestinal infection. All the systemic isolates possessed all the genes tested; in contrast, 16 isolates from stool samples lacked one or more sequences encoded by the SPI-3 and SPI-4 (p < 0.000001). These results describe the heterogeneous distribution of SPIs-encoded sequences within the genomes of Colombian clinical isolates, and reveal important differences among systemic and stool sample isolates.

The Double Bromodomain Proteins Brd2 and Brd3 Couple Histone Acetylation to Transcription

Posttranslational histone modifications are crucial for the modulation of chromatin structure and regulation of transcription. Bromodomains present in many chromatin-associated proteins recognize acetylated lysines in the unstructured N-terminal regions of histones. Here, we report that the double bromodomain proteins Brd2 and Brd3 associate preferentially in vivo with hyperacetylated chromatin along the entire lengths of transcribed genes. Brd2- and Brd3-associated chromatin is significantly enriched in H4K5, H4K12, and H3K14 acetylation and contains relatively little dimethylated H3K9. Both Brd2 and Brd3 allowed RNA polymerase II to transcribe through nucleosomes in a defined transcription system. Such activity depended on specific histone H4 modifications known to be recognized by the Brd proteins. We also demonstrate that Brd2 has intrinsic histone chaperone activity and is required for transcription of the cyclin D1 gene in vivo. These data identify proteins that render nucleosomes marked by acetylation permissive to the passage of elongating RNA polymerase II.