novoBreak: local assembly for breakpoint detection in cancer genomes.

We present novoBreak, a genome-wide local assembly algorithm that discovers somatic and germline structural variation breakpoints in whole-genome sequencing data. novoBreak consistently outperformed existing algorithms on real cancer genome data and on synthetic tumors in the ICGC-TCGA DREAM 8.5 Somatic Mutation Calling Challenge primarily because it more effectively utilized reads spanning breakpoints. novoBreak also demonstrated great sensitivity in identifying short insertions and deletions

The role of patient volunteers in Fangcang Shelter Hospital during the Omicron wave of COVID-19 pandemic in Shanghai, China: a qualitative study

ObjectiveDuring the Omicron wave of the COVID-19 pandemic in Shanghai, Fangcang Shelter Hospital (FSH) served as the major way in patient quarantine. Many COVID patients served as volunteers in FSH providing a lot of assistance for the medical workers and other COVID patients. The aim of this study was to explore the experiences of patient volunteers in FSH. It helps health professionals better understand their motivational incentives and barriers in their volunteer work, and improves recruiting and managing volunteers in subsequent public health emergencies.MethodsThis is a qualitative study using semi-structured interviews. Thirteen patient volunteers working in an FSH in Shanghai were included. Thematic analysis was applied to data analysis.ResultsFour themes and nine subthemes were identified. The wishes to give back to society and the responsibility of politics and religion were the main reasons for the patients to serve as volunteers in FSH. The patient volunteers served as the bridge to reduce the communication barriers between other patients and healthcare professionals. They also provided support in supply distribution and psychological counseling. They viewed voluntary work as a usual task and tried to solve the barriers in their work. In turn, the voluntary work brought them benefits in mental and physical health, as well as another chance for growth.ConclusionWorking as volunteers in FSHs not only brought personal benefits to the COVID patients but also fulfilled the needs of the healthcare system during public health emergencies. The mode of mutual help between patients could be taken as an example in other public health emergencies

Anti-endometriotic effect of Angelica sinensis (Oliv.) Diels extract in human endometriotic cells and rats

Purpose: To study the anti-endometriotic effect of Angelica sinensis (Oliv.) Diels extract (ASDE) in human endometriotic cells and rats.Method: Forty female rats were randomly divided into four groups (10 rats/group): control, endometriosis+danazol, endometriosis+high dose of ASDE and low dose of ASDE. The rats were orally administered either vehicle (200 μL of PBS) alone or ASDE (140, 280 and 560 mg/kg/day) for 5 weeks. Danazol was used as the control drug. After induction of endometriosis for 4 weeks, the rats were sacrificed by cervical dislocation and the peritoneum and visceral organs examined visually to measure the number of endometriotic lesions. Serum levels of cancer antigen 125 (CA-125) and interleukin 13 (IL-13), interleukin 18 (IL-18) and tumor necrosis factor-alpha (TNF-α) of peritoneal fluids of rats were measured using ELISA kits. Western blot assay was performed to measure the levels of matrix metalloproteinase-2 (MMP-2) and matrix metalloproteinase-9 (MMP-9)  expressions after 24 h of treatment with ASDE (30, 60, and 120 μg/mL).Results: ASDE-treated rats displayed reduced numbers of total endometriotic lesions when compared with vehicle-treated controls (p < 0.01). When the rats were treated with high dose of ASDE, serum CA-125 level, as well as IL-18 and TNF-α levels in peritoneal fluids were significantly lower than that of the control group (p < 0.01); however, IL-13 level in peritoneal fluids was significantly higher than that of the control group (p < 0.01). ASDE treatment significantly suppressed the levels of MMP-2 and MMP-9 protein in 11Z cell (p < 0.01).Conclusion: The results reveal that ASDE exhibits significant anti-endometriotic effect by inhibiting inflammatory factors in rats. Thus, the plant extract can potentially be developed for the clinical management of endometriosis. Keywords: Angelica sinensis, Endometriosis, Cancer antigen, Endometriotic lesions, Matrix metalloproteinas

PigGIS: Pig Genomic Informatics System

Pig Genomic Information System (PigGIS) is a web-based depository of pig (Sus scrofa) genomic learning mainly engineered for biomedical research to locate pig genes from their human homologs and position single nucleotide polymorphisms (SNPs) in different pig populations. It utilizes a variety of sequence data, including whole genome shotgun (WGS) reads and expressed sequence tags (ESTs), and achieves a successful mapping solution to the low-coverage genome problem. With the data presently available, we have identified a total of 15 700 pig consensus sequences covering 18.5 Mb of the homologous human exons. We have also recovered 18 700 SNPs and 20 800 unique 60mer oligonucleotide probes for future pig genome analyses. PigGIS can be freely accessed via the web at and

Serum metabolomics profiles in response to n-3 fatty acids in Chinese patients with type 2 diabetes: a double-blind randomised controlled trial.

We aimed to investigate the change of serum metabolomics in response to n-3 fatty acid supplements in Chinese patients with type 2 diabetes (T2D). In a double-blind parallel randomised controlled trial, 59 Chinese T2D patients were randomised to receive either fish oil (FO), flaxseed oil (FSO) or corn oil capsules (CO, served as a control group) and followed up for 180 days. An additional 17 healthy non-T2D participants were recruited at baseline for cross-sectional comparison between cases and non-cases. A total of 296 serum metabolites were measured among healthy controls and T2D patients before and after the intervention. Serum 3-carboxy-4-methyl-5-propyl-2-furanpropanoate (CMPF) (P-interaction = 1.8 × 10(-7)) was the most significant metabolite identified by repeated-measures ANOVA, followed by eicosapentaenoate (P-interaction = 4.6 × 10(-6)), 1-eicosapentaenoylglycerophosphocholine (P-interaction = 3.4 × 10(-4)), docosahexaenoate (P-interaction = 0.001), linolenate (n-3 or n-6, P-interaction = 0.005) and docosapentaenoate (n-3, P-interaction = 0.021). CMPF level was lower in T2D patients than in the healthy controls (P = 0.014) and it was significantly increased in the FO compared with CO group (P = 1.17 × 10(-7)). Furthermore, change of CMPF during the intervention was negatively correlated with change of serum triglycerides (P = 0.016). In conclusion, furan fatty acid metabolite CMPF was the strongest biomarker of fish oil intake. The association of CMPF with metabolic markers warrants further investigation.This study was funded by the National Basic Research Program of China (973 Program: 2015CB553604); by National Natural Science Foundation of China (NSFC: 81273054); and by the Ph.D. Programs Foundation of Ministry of Education of China (20120101110107). J.-S.Z. acknowledges support from MRC Epidemiology Unit (MC_UU_12015/5) and the Cambridge Initiative – Nutrition (RG71466, SJAH/004). F.I. acknowledges support from the MRC Epidemiology Unit (MC_UU_12015/5).This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/srep2952

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture

TreeFam: a curated database of phylogenetic trees of animal gene families

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at and

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