In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity

Worldwide gastric carcinoma has marked geographical variations and worse outcome in patients from the West compared to the East. Although these differences has been explained by better diagnostic criteria, improved staging methods and more radical surgery, emerging evidence supports the concept that gene expression differences associated to ethnicity might contribute to this disparate outcome. Here, we collected datasets from 4 normal and 11 gastric carcinoma Serial Gene Expression Analysis (SAGE) libraries from two different ethnicities. All normal SAGE libraries as well as 7 tumor libraries were from the West and 4 tumor libraries were from the East. These datasets we compare by Correspondence Analysis and Support Tree analysis and specific differences in tags expression were identified by Significance Analysis for Microarray. Tags to gene assignments were performed by CGAP-SAGE Genie or TAGmapper. The analysis of global transcriptome shows a clear separation between normal and tumor libraries with 90 tags differentially expressed. A clear separation was also found between the West and the East tumor libraries with 54 tags differentially expressed. Tags to gene assignments identified 15 genes, 5 of them with significant higher expression in the West libraries in comparison to the East libraries. qRT-PCR in cell lines from west and east origin confirmed these differences. Interestingly, two of these genes have been associated to aggressiveness (COL1A1 and KLK10). In conclusion we found that in silico analysis of SAGE libraries from two different ethnicities reveal differences in gene expression profile. These expression differences might contribute to explain the disparate outcome between the West and the East

Draft genome sequence of chloride-tolerant Leptospirillum ferriphilum Sp-Cl from industrial bioleaching operations in northern Chile

Indexación: Web of Science; PubMedLeptospirillum ferriphilum Sp-Cl is a Gram negative, thermotolerant, curved, rod- shaped bacterium, isolated from an industrial bioleaching operation in northern Chile, where chalcocite is the major copper mineral and copper hydroxychloride atacamite is present in variable proportions in the ore. This strain has unique features as compared to the other members of the species, namely resistance to elevated concentrations of chloride, sulfate and metals. Basic microbiological features and genomic properties of this biotechnologically relevant strain are described in this work. The 2,475,669 bp draft genome is arranged into 74 scaffolds of 74 contigs. A total of 48 RNA genes and 2,834 protein coding genes were predicted from its annotation; 55 % of these were assigned a putative function. Release of the genome sequence of this strain will provide further understanding of the mechanisms used by acidophilic bacteria to endure high osmotic stress and high chloride levels and of the role of chloride-tolerant iron-oxidizers in industrial bioleaching operations.https://standardsingenomics.biomedcentral.com/articles/10.1186/s40793-016-0142-

The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes : sequences, taxa and classifications reconsidered

Acknowledgements We acknowledge Marie Zirk for her work in designing the UNITE logotype and creating the visual abstract for this article. Funding UNITE database development is financed by the Estonian Research Council [PRG1170]; European Union's Horizon 2020 project BGE [101059492]. The PlutoF digital infrastructure is supported by the European Union's Horizon 2020 project BiCIKL [101007492]; Estonian Research Infrastructure roadmap project DiSSCo Estonia. Funding for open access charge: UNITE Community. Conflict of interest statement. None declared.Peer reviewedPublisher PD

Reprimo as a potential biomarker for early detection in gastric cancer

Purpose: Gastric cancer is a curable disease if diagnosed at early stage. However, most cases are diagnosed at advanced stage because of the lack of screening programs. Therefore, the identification of plasma biomarkers for early detection is necessary. Experimental Design: To search for these biomarkers, we evaluated the DNA methylation patterns of 24 genes by Methylation-specific PCR in primary tissues from 32 retrospectively collected gastric cancer cases (testing group). Correlation between methylation and gene expression was evaluated in the MKN-45 cell line after treatment with 5-aza-2′- deoxycytidine. The most frequently hypermethylated genes were next evaluated in primary tissues and plasma samples from 43 prospectively collected gastric cancer cases as well as plasma samples from 31 asymptomatic age- and gender-matched controls (validation group). Results: In the testing group, 11 genes were hypermethylated in at least 50% of cases (APC, SHP1, E-cadherin, ER, Reprimo, SEMA3B

Serial Analysis for Microarray of East and West gastric carcinoma SAGE libraries

To the left and shown in orange color, the significant tags with higher expression in the West tumor libraries; to the right and shown in blue color, the significant tags with higher expression in the East tumor libraries.<p><b>Copyright information:</b></p><p>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"</p><p>http://www.molecular-cancer.com/content/7/1/22</p><p>Molecular Cancer 2008;7():22-22.</p><p>Published online 27 Feb 2008</p><p>PMCID:PMC2323622.</p><p></p

Correspondence Analysis of normal and tumor SAGE libraries of the stomach

A two-dimensional plot is shown where the green dots represent all the normal libraries, the blue dots are the East tumor libraries, and the red, orange and yellow dots are West tumor libraries, microdissected, xenograft and bulk respectively.<p><b>Copyright information:</b></p><p>Taken from "In Silico analysis of Gastric carcinoma Serial Analysis of Gene Expression libraries reveals different profiles associated with ethnicity"</p><p>http://www.molecular-cancer.com/content/7/1/22</p><p>Molecular Cancer 2008;7():22-22.</p><p>Published online 27 Feb 2008</p><p>PMCID:PMC2323622.</p><p></p

16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome

<div><p>Changes in the relative abundances of many intestinal microorganisms, both those that naturally occur in the human gut microbiome and those that are considered pathogens, have been associated with a range of diseases. To more accurately diagnose health conditions, medical practitioners could benefit from a molecular, culture-independent assay for the quantification of these microorganisms in the context of a healthy reference range. Here we present the targeted sequencing of the microbial 16S rRNA gene of clinically relevant gut microorganisms as a method to provide a gut screening test that could assist in the clinical diagnosis of certain health conditions. We evaluated the possibility of detecting 46 clinical prokaryotic targets in the human gut, 28 of which could be identified with high precision and sensitivity by a bioinformatics pipeline that includes sequence analysis and taxonomic annotation. These targets included 20 commensal, 3 beneficial (probiotic), and 5 pathogenic intestinal microbial taxa. Using stool microbiome samples from a cohort of 897 healthy individuals, we established a reference range defining clinically relevant relative levels for each of the 28 targets. Our assay quantifies 28 targets in the context of a healthy reference range and correctly reflected 38/38 verification samples of real and synthetic stool material containing known gut pathogens. Thus, we have established a method to determine microbiome composition with a focus on clinically relevant taxa, which has the potential to contribute to patient diagnosis, treatment, and monitoring. More broadly, our method can facilitate epidemiological studies of the microbiome as it relates to overall human health and disease.</p></div

Predicted nutrient assimilation pathways of carbon, nitrogen, phosphorous and sulfur in “<i>Ferrovum</i>” strain JA12.

<p>Inorganic phosphate is predicted to be taken up by the phosphate specific transport system (PST) and made available to the metabolism or stored as polyphosphate (P_n). A sulfate permease (SulP) is predicted to be responsible for the uptake of sulfate which then is activated by a sulfate adenylyltransferase to adenosine-phosphosulfate (APS) and subsequently reduced to sulfide. Carbon dioxide appears to be reduced to 3-phosphoglycerate in the Calvin-Benson-Bassham cycle indicated by its key enzyme RuBisCO. Bicarbonate may be fixed in the carboxysome using a carbonic anhydrase (CA) and a RuBisCO. “<i>Ferrovum</i>” strain JA12 is predicted to either take up ammonium directly by the ammonium transporter (AmtB) or reduce nitrate or nitrite to ammonium. No names for the nitrate and nitrite transporters and reductases are indicated due to contradicting nomenclature in the databases. Apparently, urea is taken up <i>via</i> an ABC transporter (Urt) and hydrolysed to ammonia and bicarbonate by the urease (UreABC). The subsequent spontaneous protonation of ammonia to ammonium at circum neutral pH reduces the proton concentration within the cytoplasm. The energy for all metabolic processes seems to be derived from the oxidation of ferrous iron.</p

Predicted electron transfer from ferrous iron to the terminal electron acceptors in “<i>Ferrovum</i>” strain JA12.

<p>Ferrous iron is probably oxidised at the cell surface by a high molecular mass cytochrome (Cyc2-like). The relevance of the identified high potential iron-sulfur protein (HiPIP) in this process remains unknown. The electrons appear to be further transferred <i>via</i> soluble <i>c</i>-type cytochromes in the periplasm either uphill driven by the proton motive force to the <i>bc</i>₁ complex and NADH dehydrogenase to produce reduction equivalents (NAD(P)H), or downhill <i>via</i> the <i>cbb</i>₃-type cytochrome <i>c</i> oxidase or alternatively <i>via</i> one of the quinol oxidases (cytochrome <i>bd</i> complex, cytochrome <i>bo</i>₃ ubiquinol oxidase) to the terminal acceptor oxygen. The reduction of oxygen to water at the terminal oxidases neutralises protons entering the cell during ATP synthesis <i>via</i> the ATP synthase (F₀F₁). The terminal oxidases <i>bo</i>₃ and <i>cbb</i>₃ pump protons into the periplasm driven by the downhill electron transfer to oxygen. Since the identity of the quinol derivates produced by “<i>Ferrovum</i>” strain JA12 was not investigated QH₂ represents the reduced form and Q the oxidised form of the quinol derivative, respectively. The genome also encodes other potential oxidoreductases which could channel electrons into the quinol pool (e.g. sulfide quinone oxidoreductase (SQR), electron transfer flavoprotein oxidoreductase (ETF), succinate dehydrogenase (SDH) of the citrate cycle).</p