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The polled phenotype of cattle is increasingly becoming favourable mainly because of the enhanced emphasis on animal welfare, for which the causative mutations have been reported during the past years. The Shuxuan cattle are a new synthetic breed by crossing the indigenous cattle with both Simmental and Holstein semen in Sichuan of Southwest China, in which about 15% of polled individuals have newly emerged. Because official record about POLLED genotypes for the historically imported sires is unavailable, we therefore genotyped the proposed POLLED variants of P202ID, P80kbID and P219ID among 48 polled and 16 horned Shuxuan cattle. It was first revealed that all three candidate mutations have been simultaneously introgressed into Shuxuan cattle, whereas the P202ID mutation is dominant. Furthermore, one polled animal still remains to carry none of the three candidate mutations, which suggests that further mutation(s) would also exist. Additionally, we sequenced mitochondrial DNA and found that Shuxuan cattle are composed of two matrilineal origins of Bos taurus (65.6%) and B. indicus (34.4%); and there is no origin-biased distribution of polled phenotype. In conclusion, our study first supports the recently reported novel candidate mutation of P219ID and detects simultaneous presences of all three known POLLED mutations within a cattle breed.

Although various computer tools have been elaborately developed to calculate a series of statistics in molecular population genetics for both small- and large-scale DNA data, there is no efficient and easy-to-use toolkit available yet for exclusively focusing on the steps of mathematical calculation. Here, we present PopSc, a bioinformatic toolkit for calculating 45 basic statistics in molecular population genetics, which could be categorized into three classes, including (i) genetic diversity of DNA sequences, (ii) statistical tests for neutral evolution, and (iii) measures of genetic differentiation among populations. In contrast to the existing computer tools, PopSc was designed to directly accept the intermediate metadata, such as allele frequencies, rather than the raw DNA sequences or genotyping results. PopSc is first implemented as the web-based calculator with user-friendly interface, which greatly facilitates the teaching of population genetics in class and also promotes the convenient and straightforward calculation of statistics in research. Additionally, we also provide the Python library and R package of PopSc, which can be flexibly integrated into other advanced bioinformatic packages of population genetics analysis.

Verticillium dahliae Kleb. is a phytopathogenic fungus that causes wilt disease in a wide range of crops, including cotton. The life cycle of V. dahliae includes three vegetative phases: parasitic, saprophytic and dormant. The dormant microsclerotia are the primary infectious propagules, which germinate when they are stimulated by root exudates. In this study, we report the first application of Agrobacterium tumefaciens-mediated transformation (ATMT) for construction of insertional mutants from a virulent defoliating isolate of V. dahliae (V592). Changes in morphology, especially a lack of melanized microsclerotia or pigmentation traits, were observed in mutants. Together with the established laboratory unimpaired root dip-inoculation approach, we found insertional mutants to be affected in their pathogenicities in cotton. One of the genes tagged in a pathogenicity mutant encoded a glutamic acid-rich protein (VdGARP1), which shared no significant similarity to any known annotated gene. The vdgarp1 mutant showed vigorous mycelium growth with a significant delay in melanized microsclerotial formation. The expression of VdGARP1 in the wild type V529 was organ-specific and differentially regulated by different stress agencies and conditions, in addition to being stimulated by cotton root extract in liquid culture medium. Under extreme infertile nutrient conditions, VdGARP1 was not necessary for melanized microsclerotial formation. Taken together, our data suggest that VdGARP1 plays an important role in sensing infertile nutrient conditions in infected cells to promote a transfer from saprophytic to dormant microsclerotia for long-term survival. Overall, our findings indicate that insertional mutagenesis by ATMT is a valuable tool for the genome-wide analysis of gene function and identification of pathogenicity genes in this important cotton pathogen.

Background: Two polymorphisms, -260C/T and -651C/T, in the CD14 gene have been implicated in susceptibility to cancer. However, the results remain inconclusive. This meta-analysis aimed to investigate the association between the two polymorphisms and risk of cancer. Methods: All eligible case-control studies published up to March 2014 were identified by searching PubMed, Web of Science, CNKI and WanFang database. Pooled odds ratio (OR) with 95% confidence interval (CI) were used to access the strength of this association in fixed- or random-effects model. Results: 17 case-control studies from fourteen articles were included. Of those, there were 17 studies (4198 cases and 4194 controls) for -260C/T polymorphism and three studies (832 cases and 1190 controls) for -651C/T polymorphism. Overall, no significant associations between the two polymorphisms of CD14 gene and cancer risk were found. When stratified by ethnicity, cancer type and source of control, similar results were observed among them. In addition, in further subgroups analysis by Helicobacter pylori (H. pylori) infection status and tumor location in gastric cancer subgroup, we found that the CD14 -260C/T polymorphism may increase the risk of gastric cancer in H. pylori-infected individuals. Conclusions: This meta-analysis suggests that the CD14 -260C/T polymorphism may increase the risk of gastric cancer in H. pylori-infected individuals. However, large and well-designed studies are warranted to validate our findings. [ABSTRACT FROM AUTHOR]

Depression is associated with poorer outcomes in a wide spectrum of surgeries but the specific effects of depression in patients undergoing cervical spine surgery are unknown. This study aimed to evaluate the prevalence and impact of pre-surgical clinical depression on pain and other outcomes after surgery for cervical degenerative disc disease using a national representative database. Data of patients with cervical myelopathy and radiculopathy were extracted from the 2005–2014 US Nationwide Inpatient Sample (NIS) database. Included patients underwent anterior discectomy and fusion (ACDF). Acute or chronic post-surgical pain, postoperative complications, unfavorable discharge, length of stay (LOS) and hospital costs were evaluated. Totally 215,684 patients were included. Pre-surgical depression was found in 29,889 (13.86%) patients, with a prevalence nearly doubled during 2005–2014 in the US. Depression was independently associated with acute or chronic post-surgical pain (aOR: 1.432), unfavorable discharge (aOR: 1.311), prolonged LOS (aOR: 1.152), any complication (aOR: 1.232), respiratory complications/pneumonia (aOR: 1.153), dysphagia (aOR: 1.105), bleeding (aOR: 1.085), infection/sepsis (aOR: 1.529), and higher hospital costs (beta: 1080.640) compared to non-depression. No significant risk of delirium or venous thrombotic events was observed in patients with depression as compared to non-depression. Among patients receiving primary surgery, depression was independently associated with prolonged LOS (aOR: 1.150), any complication (aOR:1.233) and postoperative pain (aOR:1.927). In revision surgery, no significant associations were found for prolonged LOS, any complication or pain. In conclusion, in the US patients undergoing ACDF, pre-surgical clinical depression predicts post-surgical acute or chronic pain, a slightly prolonged LOS and the presence of any complication. Awareness of these associations may help clinicians stratify risk preoperatively and optimize patient care.

There are a few well-known indigenous breeds of Chinese rabbits in Sichuan and Fujian provinces, for which the genetic diversity and population structure have been poorly investigated. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) approach to comprehensively discover genome-wide SNPs of 104 rabbits from four Chinese indigenous breeds: 30 Sichuan White, 34 Tianfu Black, 32 Fujian Yellow and eight Fujian Black. A total of 7,055,440 SNPs were initially obtained, from which 113,973 high-confidence SNPs (read depth ≥ 3, calling rate = 100% and biallelic SNPs) were selected to study the genetic diversity and population structure. The mean polymorphism information content (PIC) and nucleotide diversity (π) of each breed slightly varied with ranging from 0.2000 to 0.2281 and from 0.2678 to 0.2902, respectively. On the whole, Fujian Yellow rabbits showed the highest genetic diversity, which was followed by Tianfu Black and Sichuan White rabbits. The principal component analysis (PCA) revealed that the four breeds were clearly distinguishable. Our results first reveal the genetic differences among these four rabbit breeds in the Sichuan and Fujian provinces and also provide a high-confidence set of genome-wide SNPs for Chinese indigenous rabbits that could be employed for gene linkage and association analyses in the future.