Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs

In this study, data genotyping by sequence (GBS) was used to perform single step GWAS (ssGWAS) to identify SNPs associated with the litter traits in domestic pigs and search for candidate genes in the region of significant SNPs. After quality control, 167,355 high-quality SNPs from 532 pigs were obtained. Phenotypic traits on 2112 gilt litters from 532 pigs were recorded including total number born (TNB), number born alive (NBA), and litter weight born alive (LWB). A single-step genomic BLUP approach (ssGBLUP) was used to implement the genome-wide association analysis at a 5% genome-wide significance level. A total of 8, 23 and 20 significant SNPs were associated with TNB, NBA, and LWB, respectively, and these significant SNPs accounted for 62.78%, 79.75%, and 58.79% of genetic variance. Furthermore, 1 (SSC14: 16314857), 4 (SSC1: 81986236, SSC1: 66599775, SSC1: 161999013, and SSC1: 267883107), and 5 (SSC9: 29030061, SSC2: 32368561, SSC5: 110375350, SSC13: 45619882 and SSC13: 45647829) significant SNPs for TNB, NBA, and LWB were inferred to be novel loci. At SSC1, the AIM1 and FOXO3 genes were found to be associated with NBA; these genes increase ovarian reproductive capacity and follicle number and decrease gonadotropin levels. The genes SLC36A4 and INTU are involved in cell growth, cytogenesis and development were found to be associated with LWB. These significant SNPs can be used as an indication for regions in the Sus scrofa genome for variability in litter traits, but further studies are expected to confirm causative mutations.     

Expression and prognostic relevance of PRAME in primary osteosarcoma

The preferentially expressed antigen of melanoma (PRAME), a cancer-testis antigen with unknown function, is expressed in many human malignancies and is considered an attractive potential target for tumor immunotherapy. However, studies of its expression and function in osteosarcoma have rarely been reported. In this study, we found that PRAME is expressed in five osteosarcoma cell lines and in more than 70% of osteosarcoma patient specimens. In addition, an immunohistochemical analysis showed that high PRAME expression was associated with poor prognosis and lung metastasis. Furthermore, PRAME siRNA knockdown significantly suppressed the proliferation, colony formation, and G1 cell cycle arrest in U-2OS cells. Our results suggest that PRAME plays an important role in cell proliferation and disease progression in osteosarcoma. However, the detail mechanisms of PRAME function in osteosarcoma require further investigation.     

Plant synthetic epigenomic engineering for crop improvement

Efforts have been directed to redesign crops with increased yield, stress adaptability, and nutritional value through synthetic biology—the application of engineering principles to biology. A recent expansion in our understanding of how epigenetic mechanisms regulate plant development and stress responses has unveiled a new set of resources that can be harnessed to develop improved crops, thus heralding the promise of “synthetic epigenetics.” In this review, we summarize the latest advances in e...     

Discovery of novel anti-tuberculosis agents with pyrrolo[1,2-a]quinoxaline-based scaffold

A series of small molecules with novel pyrrolo[1,2-a]quinoxaline-based scaffold was designed via molecular hybridization of privileged agents active against Mycobacterium tuberculosis. Twenty-three compounds were synthesized and investigated for their antitubercular activities in vitro where ten compounds showed appreciable activities and moderate cytotoxicity. Compound 12g with MIC values of 5?μg/ml as a representative may possess better oral bioavailability and indicated high permeability by the parallel artificial membrane permeation assay of the blood-brain barrier (PAMPA-BBB). Further, the determination of enzyme inhibition and molecular docking study indicated that InhA may be the biological target of the active compounds. The results suggest the pyrrolo[1,2-a]quinoxaline hybrids as potential antitubercular leads for the development of new antitubercular agents.     

High serum alkaline phosphatase cooperating with MMP-9 predicts metastasis and poor prognosis in patients with primary osteosarcoma in Southern China

Background

A malignant fibrous histiocytoma is a soft tissue tumor that most commonly occurs in the extremities, but rarely involves the liver. The clinical characteristics and therapeutic experiences of primary hepatic malignant fibrous histiocytoma are still limited.

Methods

Two cases of primary hepatic malignant fibrous histiocytoma were analyzed retrospectively, and all the literature concerning primary hepatic malignant fibrous histiocytoma was analyzed.

Results

In China, a total of 76 cases had been reported, among which 50 were men, with a male to female ratio of 1.9:1. Mean age of the patients was 51.0 years old, and more than 85 percent were older than 40 years. 82.9 percent (63/76) of hepatic MFH were solitary lesions, with tumor size ranging from 2.5 to 23.5 cm (average 10.3 cm). Major clinical presentation (78.4%) was abdominal pain or discomfort, accompanied with some other non-specific symptoms such as malaise, anorexia, weight loss, jaundice and fever, and small cases (14.9%) were asymptomatic. Computed tomography and ultrasound usually revealed the location of lesions. The rate of pre-operative misdiagnosis was extremely high, and 14.9 percent of patients were even misdiagnosed as a benign liver cyst, liver abscess or hematoma. Integrated resection was performed among the most cases (49/68), among which only a few ones (12 cases) were introduced to have no recurrence or metastasis or be still alive with no detail information provided, while among the cases with palliative operation or only a biopsy, the cases that were followed-up all died.

Conclusions

Hepatic malignant fibrous histiocytoma is a rare malignant mesenchymal tumor. The variable features of clinical presentations and images make the diagnosis difficult. Though the prognosis of primary hepatic malignant fibrous histiocytoma was rather poor, integrated resection might provide a few cases a good opportunity for surviving, suggesting that surgery might be an effective treatment.     

Rice and Arabidopsis homologs of yeast CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4 commonly interact with Polycomb complexes but exert divergent regulatory functions

Both genetic and epigenetic information must be transferred from mother to daughter cells during cell division. The mechanisms through which information about chromatin states and epigenetic marks like histone 3 lysine 27 trimethylation (H3K27me3) are transferred have been characterized in animals; these processes are less well understood in plants. Here, based on characterization of a dwarf rice (Oryza sativa) mutant (dwarf-related wd40 protein 1, drw1) deficient for yeast CTF4 (CHROMOSOME TRANSMISSION FIDELITY PROTEIN 4), we discovered that CTF4 orthologs in plants use common cellular machinery yet accomplish divergent functional outcomes. Specifically, drw1 exhibited no flowering-related phenotypes (as in the putatively orthologous Arabidopsis thaliana eol1 mutant), but displayed cell cycle arrest and DNA damage responses. Mechanistically, we demonstrate that DRW1 sustains normal cell cycle progression by modulating the expression of cell cycle inhibitors KIP-RELATED PROTEIN 1 (KRP1) and KRP5, and show that these effects are mediated by DRW1 binding their promoters and increasing H3K27me3 levels. Thus, although CTF4 orthologs ENHANCER OF LHP1 1 (EOL1) in Arabidopsis and DRW1 in rice are both expressed uniquely in dividing cells, commonly interact with several Polycomb complex subunits, and promote H3K27me3 deposition, we now know that their regulatory functions diverged substantially during plant evolution. Moreover, our work experimentally illustrates specific targets of CTF4/EOL1/DRW1, their protein–proteininteraction partners, and their chromatin/epigenetic effects in plants.

Dwarf-related wd40 protein 1 associates with Polycomb complexes to deposit histone 3 lysine 27 trimethylation marks and promotes cell cycle progression in rice.     

Detecting the selection signatures in Chinese Duroc,Landrace, Yorkshire,Liangshan, and Qingyu pigs

Functional & Integrative Genomics - Here we used two kinds of chips data from 5 pig breeds, Chinese Duroc (DD), Landrace (LL), Yorkshire (YY), Liangshan (LS), and Qingyu pigs (QY) in China to...     

光照强度对葡萄愈伤组织形成过程中相关酶活性和基因表达的影响

文中分析了葡萄愈伤组织诱导和继代培养的最佳光照强度并探索葡萄愈伤组织褐变的机理。以金手指葡萄的幼嫩茎段为材料,设置0、500、1 000、1 500、2 000、2 500、3 000和4 000 Lx等8个光照强度,研究不同光照强度对葡萄愈伤组织的诱导率、褐化率及相关酶活性和基因表达的影响。结果表明,在0、500、1 000和1 500 Lx光照强度处理下,愈伤组织的诱导率均达到92%以上,显著高于其他处理(P0.05),其中1 000和1 500 Lx光照强度处理愈伤组织及其继代培养的生长势良好且褐化程度较轻;绿原酸、咖啡酸、对羟基苯甲酸和香豆酸与葡萄愈伤组织褐变关系密切,其中绿原酸的含量与褐化程度呈显著正相关(P0.05);POD和PPO酶活性与褐化率呈极显著负相关(P0.01);POD、PPO和PAL酶基因的表达量与褐化率呈显著(P0.05)或极显著(P0.01)正相关。因此,葡萄愈伤组织诱导和继代培养适宜的光照强度为1 000-1 500 Lx,光照强度过高或过低对其正常的生理生长都有较大负面影响。