Panorama of neoplasms of upper GI tract: a 5 year research study

Background: The diseases of the gastrointestinal tract (GIT) are the most common and leading cause of morbidity and mortality than the disorders of any other systems of the body. Gastrointestinal (GI) tract tumors are one of the most common cancers accounting for 11% of all cancers. Among these tumors, upper gastrointestinal tract malignancies are quite aggressive with a dismal prognosis. Malignant tumors are most common than benign. The most common carcinoma of the esophagus is Squamous cell carcinoma (SCC). Incidence of SCC is less than 5 per 100,000 populations in males and 1 per 100,000 populations in females. Gastric cancer was the second most common cancer in the World and 60% of them occurred in developing countries. The most common carcinoma of the Stomach is Adenocarcinoma.Aim & Objectives: To study the spectrum of neoplastic lesions of the upper gastrointestinal tract by the examination of endoscopic biopsies and surgically resected specimens. To determine the degree of severity of the malignancies by assessing the depth of invasion, Lymph nodal & Omental spread.Methods: The present study is both retrospective & prospective study for a period of 5 years from January 2007 to December 2011. The sample size includes all the endoscopic biopsies & surgically resected specimens of gastrointestinal tract received at Department of Pathology, S.V. Medical College, Tirupati. The study also obtained clearance from the ethical committee of the institution. The biopsy specimens thus obtained were fixed in 10% buffered neutral formalin. The sections were stained routinely with H & E. Special stains and IHC done wherever necessary.Results: we have received 120 specimens regarding the upper gastrointestinal system. Among these 120 specimens, 71 specimens were endoscopic biopsies & 49 specimens were surgically resected specimens. Out of 71 Endoscopic biopsies 28 biopsies were malignant among which 2 was esophagus and 26 were stomach. Out of 49 surgically resected specimens 1 was benign and 32 were malignant tumors. Out of 59 neoplasms of stomach there were single cases each of Sub mucosal Lipoma, Malignant lymphoma, GIST & 56 cases of Adenocarcinoma & its variants were noted.Conclusion: Most of the neoplasms are of stomach (97%). All the neoplasms are malignant except one benign lesion sub mucous lipoma of stomach. Most of the neoplasms of stomach were Adenocarcinoma (96.5%). Both tumors of esophagus were squamous cell carcinoma occurred after 50 years of age.

Single Nucleotide Variants And Indels Identified From Whole-genome Re-sequencing Of Guzerat, Gyr, Girolando And Holstein Cattle Breeds

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Whole-genome re-sequencing, alignment and annotation analyses were undertaken for 12 sires representing four important cattle breeds in Brazil: Guzerat (multi-purpose), Gyr, Girolando and Holstein (dairy production). A total of approximately 4.3 billion reads from an Illumina HiSeq 2000 sequencer generated for each animal 10.7 to 16.4-fold genome coverage. A total of 27,441,279 single nucleotide variations (SNVs) and 3,828,041 insertions/deletions (InDels) were detected in the samples, of which 2,557,670 SNVs and 883,219 InDels were novel. The submission of these genetic variants to the dbSNP database significantly increased the number of known variants, particularly for the indicine genome. The concordance rate between genotypes obtained using the Bovine HD BeadChip array and the same variants identified by sequencing was about 99.05%. The annotation of variants identified numerous non-synonymous SNVs and frameshift InDels which could affect phenotypic variation. Functional enrichment analysis was performed and revealed that variants in the olfactory transduction pathway was over represented in all four cattle breeds, while the ECM-receptor interaction pathway was over represented in Girolando and Guzerat breeds, the ABC transporters pathway was over represented only in Holstein breed, and the metabolic pathways was over represented only in Gyr breed. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Gyr, Girolando, Guzerat and Holstein breeding programs. © 2017 Stafuzza et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.123Conselho Nacional de Desenvolvimento Científico e TecnológicoCAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível SuperiorFAPEMIG, Fundação de Amparo à Pesquisa do Estado de Minas GeraisConselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES

Study On The Introgression Of Beef Breeds In Canchim Cattle Using Single Nucleotide Polymorphism Markers

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)The aim of this study was to evaluate the level of introgression of breeds in the Canchim (CA: 62.5% Charolais-37.5% Zebu) and MA genetic group (MA: 65.6% Charolais-34.4% Zebu) cattle using genomic information on Charolais (CH), Nelore (NE), and Indubrasil (IB) breeds. The number of animals used was 395 (CA and MA), 763 (NE), 338 (CH), and 37 (IB). The Bovine 50SNP BeadChip from Illumina panel was used to estimate the levels of introgression of breeds considering the Maximum likelihood, Bayesian, and Single Regression method. After genotype quality control, 32,308 SNPs were considered in the analysis. Furthermore, three thresholds to prune out SNPs in linkage disequilibrium higher than 0.10, 0.05, and 0.01 were considered, resulting in 15,286, 7,652, and 1,582 SNPs, respectively. For k = 2, the proportion of taurine and indicine varied from the expected proportion based on pedigree for all methods studied. For k = 3, the Regression method was able to differentiate the animals in three main clusters assigned to each purebred breed, showing more reasonable according to its biological viewpoint. Analyzing the data considering k = 2 seems to be more appropriate for Canchim-MA animals due to its biological interpretation. The usage of 32,308 SNPs in the analyses resulted in similar findings between the estimated and expected breed proportions. Using the Regression approach, a contribution of Indubrasil was observed in Canchim-MA when k = 3 was considered. Genetic parameter estimation could account for this breed composition information as a source of variation in order to improve the accuracy of genetic models. Our findings may help assemble appropriate reference populations for genomic prediction for Canchim-MA in order to improve prediction accuracy. Using the information on the level of introgression in each individual could also be useful in breeding or crossing design to improve individual heterosis in crossbred cattle. © 2017 Buzanskas et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.12202663/09-0, CAPES, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior449564/2014-2, CNPq, Conselho Nacional de Desenvolvimento Científico e TecnológicoCoordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq

Building The Sugarcane Genome For Biotechnology And Identifying Evolutionary Trends

Background: Sugarcane is the source of sugar in all tropical and subtropical countries and is becoming increasingly important for bio-based fuels. However, its large (10 Gb), polyploid, complex genome has hindered genome based breeding efforts. Here we release the largest and most diverse set of sugarcane genome sequences to date, as part of an on-going initiative to provide a sugarcane genomic information resource, with the ultimate goal of producing a gold standard genome.Results: Three hundred and seventeen chiefly euchromatic BACs were sequenced. A reference set of one thousand four hundred manually-annotated protein-coding genes was generated. A small RNA collection and a RNA-seq library were used to explore expression patterns and the sRNA landscape. In the sucrose and starch metabolism pathway, 16 non-redundant enzyme-encoding genes were identified. 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