Localized primary gastrointestinal diffuse large B cell lymphoma received a surgical approach: an analysis of prognostic factors and comparison of staging systems in 101 patients from a single institution

Clinical characteristics and survival rate of patients with localized PG-DLBCL. It shows the clinical characteristics and Rituximab treatment between localized PG-DLBCL patients with surgery and those with chemotherapy alone. (PDF 276 kb

Comparison of Gene Expression and Genome-Wide DNA Methylation Profiling between Phenotypically Normal Cloned Pigs and Conventionally Bred Controls

Animal breeding via Somatic Cell Nuclear Transfer (SCNT) has enormous potential in agriculture and biomedicine. However, concerns about whether SCNT animals are as healthy or epigenetically normal as conventionally bred ones are raised as the efficiency of cloning by SCNT is much lower than natural breeding or In-vitro fertilization (IVF). Thus, we have conducted a genome-wide gene expression and DNA methylation profiling between phenotypically normal cloned pigs and control pigs in two tissues (muscle and liver), using Affymetrix Porcine expression array as well as modified methylation-specific digital karyotyping (MMSDK) and Solexa sequencing technology. Typical tissue-specific differences with respect to both gene expression and DNA methylation were observed in muscle and liver from cloned as well as control pigs. Gene expression profiles were highly similar between cloned pigs and controls, though a small set of genes showed altered expression. Cloned pigs presented a more different pattern of DNA methylation in unique sequences in both tissues. Especially a small set of genomic sites had different DNA methylation status with a trend towards slightly increased methylation levels in cloned pigs. Molecular network analysis of the genes that contained such differential methylation loci revealed a significant network related to tissue development. In conclusion, our study showed that phenotypically normal cloned pigs were highly similar with normal breeding pigs in their gene expression, but moderate alteration in DNA methylation aspects still exists, especially in certain unique genomic regions

ChickVD: a sequence variation database for the chicken genome

Working in parallel with the efforts to sequence the chicken (Gallus gallus) genome, the Beijing Genomics Institute led an international team of scientists from China, USA, UK, Sweden, The Netherlands and Germany to map extensive DNA sequence variation throughout the chicken genome by sampling DNA from domestic breeds. Using the Red Jungle Fowl genome sequence as a reference, we identified 3.1 million non-redundant DNA sequence variants. To facilitate the application of our data to avian genetics and to provide a foundation for functional and evolutionary studies, we created the ‘Chicken Variation Database’ (ChickVD). A graphical MapView shows variants mapped onto the chicken genome in the context of gene annotations and other features, including genetic markers, trait loci, cDNAs, chicken orthologs of human disease genes and raw sequence traces. ChickVD also stores information on quantitative trait loci using data from collaborating institutions and public resources. Our data can be queried by search engine and homology-based BLAST searches. ChickVD is publicly accessible at http://chicken.genomics.org.cn

Influence of radiation on Hemarthria compressa's genetic variations

Using the material of Hemarthria compressa (L.F.) R.Br. cv. YA’AN, we carried out this research to study the influence of radiation on the genetic variation of plants. Genetic difference was analyzed with expressed sequence tag-simple sequence repeat (EST-SSR) molecular marker through the comparison of 60Co-γ radiation on H. compressa seed stems and original variety. By using 20 primer pairs, 176 polymerase chain reaction (PCR)-amplifications with clear and consistent bands were obtained. The results showed that 155 of 176 bands were polymorphic, which indicating an 88.07% polymorphism rate, and each pair of primers had 8.8 amplified bands on average; the amplitude of polymorphism information content was 0.4709–0.6952 with an average value 0.6081. The genetic similarity coefficient of H. compressa and its mutants ranged from 0.4318 to 0.8239 with an average of 0.6671. As a consequence, existence of genetic differences between the mutants and the basic material was proved.We gratefully acknowledge financial support from the Modern Agro-industry Technology Research System (CARS-34) and the Sichuan Province Breeding Research grant (2016NZ0098-11).Peer reviewe

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Productive Performance, Serum Antioxidant Status, Tissue Selenium Deposition, and Gut Health Analysis of Broiler Chickens Supplemented with Selenium and Probiotics—A Pilot Study

The effect and interaction of dietary selenium (Se) and probiotics on three yellow chicken growth performance, tissue Se content, antioxidant capacity, and gut health were studied from 0 to 70 days of age. A total of 400 one-day-old broilers were distributed into four groups (I-Se, O-Se, I-Se + pros, and O-Se + pros groups) consisting of a 2 × 2 factorial design. The main factors were the source of Se (I-Se = inorganic Se: 0.2 mg/kg sodium selenite; O-Se = organic Se: 0.2 mg/kg Selenium yeast) and the level of probiotics (0.5% EM or 0% EM, the component of EM mainly includes Lactobacillus and Yeast at the dose of 2 × 108 cfu/kg and 3 × 107 cfu/kg, respectively). Each treatment had 5 duplicates consisting of 20 broilers. The results showed that the I-Se group had a greater (p < 0.05) ratio of feed: weight gain (F/G) of broilers at Starter (0–35 d) than the other treatments. Compared to the I-Se group, the O-Se group increased (p < 0.05) Se concentrations in the liver, pancreas, breast muscles, thigh muscle, and the activity of total antioxidative capacity (T-AOC) in serum, as well as the relative abundance of Barnesiella and Lactobacillus in cecum. Meanwhile, probiotics enhanced (p < 0.05) Se concentrations in the pancreas, thigh muscle, serum, and the activity of T-AOC and glutathione peroxidase (GSH-Px), the duodenum’s ratio of villi height to crypt depth (V/C), the jejunum villus height and V/C, and the ileum’s villus height. Furthermore, the significant interactions (p < 0.05) between Se sources and the level of probiotics were observed in Se concentrations in the pancreas, thigh muscle, serum, crypt depth of duodenum, and villus height of jejunum of birds, and Barnesiella abundance in the cecal. In conclusion, our results demonstrate that the combination of O-Se + pros can improve broiler early growth performance, tissue Se content in the pancreas, thigh muscle, and serum, promote intestinal development, and regulate the composition of intestinal flora, suggesting a better combination. These findings provide an effective method of nutrient combination addition to improving the performance of three yellow chickens