Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs

BACKGROUND: As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations. RESULTS: We developed a novel method to combine comparative genomics with de novo motif discovery to identify human transcription factor binding motifs that are overrepresented and conserved in the upstream regions of a set of co-regulated genes. The method is validated by analyzing a well-characterized muscle specific gene set, and the results showed that our approach performed better than the existing programs in terms of sensitivity and prediction rate. CONCLUSION: The newly developed method can be used to extract regulatory signals in co-regulated genes, which can be derived from the microarray clustering analysis

Rewilding the wildlife in Sangjiangyuan National Park, Qinghai-Tibetan Plateau

The targets of China’s national park construction are to protect the authenticity and integrity of the ecosystems, and to achieve the harmonious development between humans and nature. Because of the high intensity of human activities, the authenticity of ecosystems has deviated over the past few decades. It is time to rewild the wildlife and restore the authenticity of these ecosystems. The status of rewilding wildlife in Sanjiangyuan National Park, indicating that the wildlife population, diversity and wildness have increased within the National Park. The wildlife population in the national park has been restored, with about 60,000 Tibetan antelope, 60,000 Tibetan gazelle, 36,000 Tibetan wild ass, 10,000 wild yak, and 10,000 white-lipped deer up to 2017. However, overgrazing existed on the alpine grassland with population increasing both of ungulates and livestock

Additional file 1: of Quantifying traditional Chinese medicine patterns using modern test theory: an example of functional constipation

S1. Longitudinal data used for the validation of the tool. With respect to variable names, T1, T2, and T3 prefix indicate baseline, 1st follow-up, and 2nd follow-up, respectively. I1 to I10 suffix indicate number of item. (XLSX 32 kb

Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China

In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples—the most abundant phyla were Firmicutes (34.58%), Bacteroidetes (33.96%) and Verrucomicrobia (11.70%). At the genus level, a total of 66 genera were obtained—Rikenellaceae_RC9_gut_group (7.24%), Akkermansia (6.32%) and Ruminococcaceae_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (p < 0.05). Bacteroidete were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals

Effects of winter barn feeding and grazing on growth performance, meat quality and rumen fungal community of Tibetan sheep

The grazing grassland ecosystem on the Qinghai-Tibetan Plateau is highly impacted by seasonal temperature variations. During the long cold season, the biomass and nutrient contents of forage grass do not meet the nutritional needs of grazing livestock and seriously affect growth performance and livestock products. This study investigated different feeding strategies on growth performance, meat quality and rumen fungal community of Tibetan sheep in the winter. Twelve one-year-old healthy castrated Tibetan sheep with similar initial body weights were randomly grouped into traditional grazing (TG) and barn feeding (BF) groups. The TG sheep were labelled and grazed on the local cool-season pasture without feed supplementing, while BF sheep were fed a mixed diet in feeding shed. Compared with the TG group, significantly increased body weight and average daily weight gain (ADG) were observed in the BF group (p < 0.001), which resulted in a significant increase in the hot carcase weight, net meat weight, carcase rate and net meat rate (p < 0.01). Moreover, the longissimus dorsi muscle of the BF group showed significantly increased muscle fibre diameter, perimeter, and area and increased crude protein and ether extract contents (p < 0.01), while the meat tenderness and amino acid content were reduced. ITS high-throughput sequencing showed that Ascomycota was the predominant fungal phylum in the rumen of Tibetan sheep. At the genus level, the rumen of TG sheep presented higher proportions of Preussia, Anaeromyces and Pilidium, while the most abundant genera in the BF sheep were Penicillium, Acaulium and Vishniacozyma. In summary, BF strategy enhanced the relative abundance of several dominant fungal genera related to the nutrient absorption and metabolism capacity, and effectively improves the growth and slaughter performance and affects meat quality of Tibetan sheep in the winter

Comparative Analysis of the Composition of Fatty Acids and Metabolites between Black Tibetan and Chaka Sheep on the Qinghai&mdash;Tibet Plateau

The objective of this study was to investigate and compare fatty acids and metabolites in the longissimus dorsi muscle between Black Tibetan and Chaka sheep grazing in a highly saline environment. A total of eight castrated sheep (14 months old) with similar body weights (25 &plusmn; 2.2 kg) were selected. The experimental treatments included Black Tibetan (BT) and Chaka sheep (CK) groups, and each group had four replications. The experiment lasted for 20 months. All sheep grazed in a highly saline environment for the whole experimental period and had free access to water. The results showed that the diameter (42.23 vs. 51.46 &mu;m), perimeter (131.78 vs. 166.14 &mu;m), and area of muscle fibers (1328.74 vs. 1998.64 &mu;m2) were smaller in Chaka sheep than in Black Tibetan sheep. The ash content in the longissimus dorsi was lower in Chaka sheep than in Black Tibetan sheep (p = 0.010), and the contents of dry matter (DM), ether extract (EE), and crude protein (CP) in the longissimus dorsi showed no differences (p &gt; 0.05). For fatty acids, the proportions of C10:0, C15:0, and tC18:1 in the longissimus dorsi were higher in Chaka sheep than in Black Tibetan sheep (p &lt; 0.05). However, all other individual fatty acids were similar among treatments, including saturated fatty acids (SFAs), unsaturated fatty acids (UFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), and the ratios of n-6 PUFAs to n-3 PUFAs and PUFAs to SFAs (p &gt; 0.05). A total of 65 biomarkers were identified between the two breeds of sheep. Among these metabolites, 40 metabolic biomarkers were upregulated in the CK group compared to the BT group, and 25 metabolites were downregulated. The main metabolites include 30 organic acids, 9 amino acids, 5 peptides, 4 amides, 3 adenosines, 2 amines, and other compounds. Based on KEGG analysis, eight pathways, namely, fatty acid biosynthesis, purine metabolism, the biosynthesis of unsaturated fatty acids, renin secretion, the regulation of lipolysis in adipocytes, neuroactive ligand&ndash;receptor interaction, the cGMP-PKG signaling pathway, and the cAMP signaling pathway, were identified as significantly different pathways. According to the results on fatty acids and metabolites, upregulated organic acid and fatty acid biosynthesis increased the meat quality of Chaka sheep

Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau

The rumen microbiota of ruminants plays a vital role in fiber digestion, and environmental factors affect its community structure. The yak (Bos grunniens) is the main livestock species that inhabits the Qinghai-Tibet Plateau (QTP) at regions located at high-altitude of 3,000–5,000 m. This work investigated the rumen bacterial community of yak that grazed on the QTP during the whole year to evaluate the relationship between the rumen bacterial community and the nutrient composition of forage plant at three stages. In this study, the diversity of the rumen prokaryotic community composition was monitored in 10 full-grazing yak in an alpine meadow of the QTP. The nutrient composition of three forage growth stages was determined: re-green stage (REGY), grassy stage (GY), and withered stage (WGY). High-throughput sequencing of bacterial 16S rRNA gene was used. The results showed that the nutritive composition of the alpine meadow changed with the seasons: crude protein (CP) (13.22%) was high in forage during REGY (spring), while neutral detergent fiber (NDF) (59.00%) was high during WGY (winter). Microbial diversity and richness were highest during REGY and the average number of operational taxonomic units from 30 samples was 4,470. The microbial composition was dominated by members of Bacteroidetes (51.82%), followed by Firmicutes (34.08%), and the relative microbial abundance changed in the three forage growth stages. Unweighted UniFrac distance PcoA showed that the bacterial community structure differed between REGY, GY, and WGY. Furthermore, taxonomic groups did not present differences regarding gender in these three stages. The rumen microbiota was enriched with functional potentials that were related to ABC transporters, the two-component system, Aminoacyl-tRNA biosynthesis, and metabolism of Purine, Pyrimidine, Starch and sucrose metabolism. Significant differences were found in the composition, diversity, and function of yak ruminal microorganisms during different forage growth stages. This indicates that microbial changes in the rumen depend on changes in the forage nutritional composition. These findings provide evidence on the rumen microbial diversity of yaks in the QTP

Comparative Transcriptome Profiling of mRNA and lncRNA Related to Tail Adipose Tissues of Sheep

The Lanzhou Fat-Tail sheep (LFTS, long fat-tailed sheep) is an endangered sheep breed in China with a fat tail compared to the traditional local varieties, Small Tail Han sheep (STHS, thin-tailed sheep) with a small tail, and Tibetan sheep (TS, short thin-tailed sheep) with a little tail. However, little is known regarding how tail fat deposition is regulated by long noncoding RNA (lncRNA). To evaluate the lncRNA and mRNA associated with tail fat deposition and development among these breeds, high-throughput RNA sequencing of three individuals each of LFTS, STHS, and TS were performed and analyzed in this study. RNA sequencing data from these three groups revealed 10 differentially expressed genes (DEGs) and 37 differentially expressed lncRNAs between the LFTS and STHS groups, 390 DEGs and 59 differentially expressed lncRNAs between the LFTS and TS groups, and 80 DEGs and 16 differentially expressed lncRNAs between the STHS and TS groups (p-value &lt; 0.05 and fold change ≥ 2), respectively. Gene Ontology and pathway analysis of DEGs and target genes of differentially expressed lncRNAs revealed enrichment in fatty acid metabolism and fatty acid elongation-related pathways that contribute to fat deposition. Subsequently, the expression of 14 DEGs and 6 differentially expressed lncRNAs was validated by quantitative real-time PCR. Finally, two co-expression networks of differentially expressed mRNA and lncRNAs were constructed. The results suggested that some differentially expressed lncRNAs (TCONS_00372767, TCONS_00171926, TCONS_00054953, and TCONS_00373007) may play crucial roles as core lncRNAs in tail fat deposition processes. In summary, the present study extends the sheep tail fat lncRNA database and these differentially expressed mRNA and lncRNAs may provide novel candidate regulators for future genetic and molecular studies on tail fat deposition of sheep

Comparison of long-term quality of life between Billroth-I and Roux-en-Y anastomosis after distal gastrectomy for gastric cancer: a randomized controlled trial

Abstract. Background:. The results of studies comparing Billroth-I (B-I) with Roux-en-Y (R-Y) reconstruction on the quality of life (QoL) are still inconsistent. The aim of this trial was to compare the long-term QoL of B-I with R-Y anastomosis after curative distal gastrectomy for gastric cancer. Methods:. A total of 140 patients undergoing curative distal gastrectomy with D2 lymphadenectomy in West China Hospital, Sichuan University from May 2011 to May 2014 were randomly assigned to the B-I group (N = 70) and R-Y group (N = 70). The follow-up time points were 1, 3, 6, 9, 12, 24, 36, 48, and 60 months after the operation. The final follow-up time was May 2019. The clinicopathological features, operative safety, postoperative recovery, long-term survival as well as QoL were compared, among which QoL score was the primary outcome. An intention-to-treat analysis was applied. Results:. The baseline characteristics were comparable between the two groups. There were no statistically significant differences in terms of postoperative morbidity and mortality rates, and postoperative recovery between the two groups. Less estimated blood loss and shorter surgical duration were found in the B-I group. There were no statistically significant differences in 5-year overall survival (79% [55/70] of the B-I group vs. 80% [56/70] of the R-Y group, P = 0.966) and recurrence-free survival rates (79% [55/70] of the B-I group vs. 78% [55/70] of the R-Y group, P = 0.979) between the two groups. The scores of the global health status of the R-Y group were higher than those of the B-I group with statistically significant differences (postoperative 1 year: 85.4 ± 13.1 vs. 88.8 ± 16.1, P = 0.033; postoperative 3 year: 87.3 ± 15.2 vs. 92.8 ± 11.3, P = 0.028; postoperative 5 year: 90.9 ± 13.7 vs. 96.4 ± 5.6, P = 0.010), and the reflux (postoperative 3 year: 8.8 ± 12.9 vs. 2.8 ± 5.3, P = 0.001; postoperative 5 year: 5.1 ± 9.8 vs. 1.8 ± 4.7, P = 0.033) and epigastric pain (postoperative 1 year: 11.8 ± 12.7 vs. 6.1 ± 8.8, P = 0.008; postoperative 3 year: 9.4 ± 10.6 vs. 4.6 ± 7.9, P = 0.006; postoperative 5 year: 6.0 ± 8.9 vs. 2.7 ± 4.6, P = 0.022) were milder in the R-Y group than those of the B-I group at the postoperative 1, 3, and 5-year time points. Conclusions:. Compared with B-I group, R-Y reconstruction was associated with better long-term QoL by reducing reflux and epigastric pain, without changing survival outcomes. Trial Registration:. ChiCTR.org.cn, ChiCTR-TRC-10001434

Clinical significance of tumor deposits in gastric cancer after radical gastrectomy: a propensity score matching study

Abstract Objective The value of tumor deposits (TDs) in the prognosis and staging of gastric cancer (GC) is still under debate. This study aims to evaluate the prognostic value of TDs and the best ways to incorporate TDs in the TNM classification of GC. Methods Patients (n = 3460) undergoing curative gastrectomy for GC in the West China Hospital from 2005 to 2017 were retrospectively reviewed and divided into two groups according to the TD status (positive vs. negative). Later, clinicopathological features and overall survival (OS) between the two groups were compared. Thereafter, the associations between the presence of TD and other clinicopathological factors were evaluated through logistic regression. In addition, univariate and multivariate Cox regression were conducted for determining prognostic factors. The possibility of selection bias was reduced through conducting the 1:1 propensity score matching (PSM) analysis. The modified classification systems proposed previously that incorporated TDs into the TNM staging system were assessed. Results There were 10.5% of patients (362/3460) diagnosed with TDs. TDs were significantly related to unfavorable factors such as advanced T stage and N stage and independently associated with poor prognosis. The 5-year OS of patients with TDs was significantly lower than that of patients without TDs (31.0% vs. 60.9%, P < 0.001), whereas higher than that of patients with peritoneal metastasis (31.0% vs. 5.0%, P < 0.001). In patients receiving chemotherapy, the 5-year OS of patients with TDs was also significantly lower than that of patients without TDs (42.0% vs. 50.9%, P = 0.026). Moreover, the system incorporating TDs in the TNM classification as metastatic lymph nodes outperformed others. Conclusions TDs are related to the aggressive characteristics and are an independent prognostic factor for GC. Incorporating TDs in the TNM classification as the metastatic lymph nodes increases the accuracy in predicting prognosis