Case report: Identification of a frameshift mutation in GC enrichment and the GCC repeat region of the androgen insensitivity receptor (AR) gene in a patient with complete androgen insensitivity syndrome by whole-exome sequencing (WES) combined with specific PCR and deep sequencing.

Background: Androgen insensitivity syndrome (AIS) is an X-linked recessive hereditary disease caused due to a reduced or absent function of the androgen receptor (AR) protein encoded by the AR gene (OMIM-Gene# 313,700). Genetic testing is important in the diagnosis, clinical management, and prevention of AIS (MIM# 300,068). The AR (HGNC: 644) pathogenic variant detection rate ranges from 65% to 95% for patients with complete AIS (CAIS) and 40%-45% for patients with partial androgen insensitivity syndrome (PAIS). Identification of a pathogenic mutation in the AR confirms the diagnosis of AIS, especially in the milder forms that may have a phenotypic overlap with other disorders of sex development. Improvement of the molecular diagnostic rate of AIS is urgently required in clinical practice. We reported the results of the molecular diagnosis of a patient with CAIS who failed previously in either the traditional Sanger sequencing or next-generation sequencing (NGS). Using whole-exome sequencing (WES) combined with a special polymerase chain reaction (PCR) and deep sequencing, we successfully identified a pathogenic variant, a hemizygous mutation (c.1395-1396insGA), in the GC-enriched and unstable GCC repeat regions of the AR gene of the proband. Conclusion: The results may be advantageous for the improvement of the detection rate of AIS, as well as other inherited disorders whose disease-causing genes contain GC-enriched and unstable GCC repeat regions.

Metagenomic sequencing reveals the relationship between microbiota composition and quality of Chinese Rice Wine.

Chinese Rice Wine (CRW) is a common alcoholic beverage in China. To investigate the influence of microbial composition on the quality of CRW, high throughput sequencing was performed for 110 wine samples on bacterial 16S rRNA gene and fungal Internal Transcribed Spacer II (ITS2). Bioinformatic analyses demonstrated that the quality of yeast starter and final wine correlated with microbial taxonomic composition, which was exemplified by our finding that wine spoilage resulted from a high proportion of genus Lactobacillus. Subsequently, based on Lactobacillus abundance of an early stage, a model was constructed to predict final wine quality. In addition, three batches of 20 representative wine samples selected from a pool of 110 samples were further analyzed in metagenomics. The results revealed that wine spoilage was due to rapid growth of Lactobacillus brevis at the early stage of fermentation. Gene functional analysis indicated the importance of some pathways such as synthesis of biotin, malolactic fermentation and production of short-chain fatty acid. These results led to a conclusion that metabolisms of microbes influence the wine quality. Thus, nurturing of beneficial microbes and inhibition of undesired ones are both important for the mechanized brewery.

Exploration on mechanism of a new type of melatonin receptor agonist Neu-p11 in hypoxia-reoxygenation injury of myocardial cells.

To explore the mechanism of a new type of melatonin receptor agonist Neu-p11 in hypoxia-reoxygenation injury of myocardial cells. Hypoxia/reoxygenation (H/R) model of H9c2 myocardial cells was established, and the cells were divided into control group, H/R group, and Neu-p11 group. Apoptosis rates of myocardial cells in different groups, the contents of creatinine kinase (CK), lactic dehydrogenase (LDH), superoxide dismutase (SOD), and malondialdehyde (MDA) in cell culture media were compared. Myocardial cells in control group showed diverse shape, and the refractivity of cells were high and the pulse was strong with synchronous rhythm of 60-80/min; The refractivity of myocardial cells in H/R group decreased, the pseudopodium was thinner, and the rhythm was reduced to 30-40/min; The morphology and refractivity of myocardial cells in Neu-p11 group were significantly improved with rhythm of 50-60/min. The apoptosis rates in the control group, the H/R group, and the Neu-p11 group were 2.48, 39.66, and 17.94 %, respectively. Levels of CK, LDH, and MDA were significantly decreased in Neu-p11 compared with H/R group, yet, both of which were significantly higher than that in control group. The SOD level was significantly lower in H/R group compared to that in control group, and Neu-p11 group with no statistical difference between the Neu-p11 group and the control group. Neu-p11 has protective effects on hypoxia-reoxygenation injury of myocardial cells. It inhibits cell apoptosis and improves the morphology and rhythm of myocardial cells; It alleviates injury of cell membrane by reducing its permeability, which can stabilize myocardial cell membrane; It also alleviates lipid peroxidation and protects mitochondria from myocardial ischemia/reperfusion injury.

[Detection of somatic mutations in deteriorated cell of peritoneal mesothelioma by whole genome sequencing].

OBJECTIVE: To detect the somatic mutations in peritoneal mesothelioma with whole genome sequencing technique. METHODS: Surgically resected cancer and pericancerous tissue samples from one patient with peritoneal mesothelioma were obtained. The whole genome sequences of tumor tissue and pericancerous tissue were examined by the second generation sequencing technique and compared with reference sequences from human genome database. RESULTS: There were 639 717 single nucleotide variations (Single Nucleotide Variation SNV) found in both tumor and pericancerous tissue cells; while 20 302 SNVs were unique for tumor cells and 2 185 SNVs unique for pericancerous tissue, but still 223 SNVs found in cancer and pericancerous tissue were differed from those in human genome database. CONCLUSION: The preliminary results indicate that merely comparing the gene sequences of cancer and pericancerous tissue samples in an individual with the human genome reference sequence can not accurately locate all somatic mutations in pathological cells. For those individualized diseases caused by random somatic mutations, it is suggested to sequence the whole genome at birth or at least to reserve a DNA sample at early age for both research and clinical needs.

Microbial community structure in fermentation process of Shaoxing rice wine by Illumina-based metagenomic sequencing.

BACKGROUND: To understand the role of the community structure of microbes in the environment in the fermentation of Shaoxing rice wine, samples collected from a wine factory were subjected to Illumina-based metagenomic sequencing. RESULTS: De novo assembly of the sequencing reads allowed the characterisation of more than 23 thousand microbial genes derived from 1.7 and 1.88 Gbp of sequences from two samples fermented for 5 and 30 days respectively. The microbial community structure at different fermentation times of Shaoxing rice wine was revealed, showing the different roles of the microbiota in the fermentation process of Shaoxing rice wine. The gene function of both samples was also studied in the COG database, with most genes belonging to category S (function unknown), category E (amino acid transport and metabolism) and unclassified group. CONCLUSION: The results show that both the microbial community structure and gene function composition change greatly at different time points of Shaoxing rice wine fermentation.

[Effects of wenhua juanbi recipe on the gene expression profile of the synovium in collagen-induced arthritic rats].

OBJECTIVE: To study the effects of Wenhua Juanbi recipe (WJR) on the gene expression profile of the synovium in collagen-induced arthritis (CIA) rats, and to explore its mechanisms for treating CIA. METHODS: The CIA model was induced by intradermal injection of bovine collagen type II emulsion from the tail of 40 healthy male Wistar rats. Selected 16 successfully modeled rats were randomly divided into the model group and the WJR-treated group, 8 in each group. WJR at the daily dose of 22.9 g/kg was given to rats in the WJR-treated group by gastrogavage, while normal saline was given to those in the model group. Both were performed once daily, for 30 successive days. By the end of medication, the total RNA was extracted from the synovium of rats in the two groups. The gene expression profile of each sample was analyzed using Illumina oligonucleotide microarray. RESULTS: Compared with the model group, after the intervention of WJR, 222 differentially expressed genes were identified in CIA rats, including 76 genes up-regulated (such as RatNP-3b and so on) and 146 downregulated (such as Angptl 2, Muc1, bcl-2, and so on). The differential genes were mainly involved with apoptosis, angiopoietin, defensin gene, cytokine, signal transduction, oncogene, etc. CONCLUSION: WJR played a role in treating CIA multi-target possibly through regulating and controlling multiple genes expressions. Wenhua Juanbi Recipe; collagen-induced arthritis; synovium; gene expression

Acute hepatic failure-derived bone marrow mesenchymal stem cells express hepatic progenitor cell genes.

Hepatic progenitor cell (HPC) transplantation is a promising alternative to liver transplantation for patients with end-stage liver disease. However, the precise origin of HPCs is unclear. This study aimed to determine whether bone marrow mesenchymal stem cells (BMSCs) isolated from rats in acute hepatic failure (AHF) possess hepatic potential and/or characteristics. BMSCs were isolated from normal rats as well as rats in which AHF was induced by D-galactosamine. HPCs and primary hepatocytes were isolated from normal rats for comparison. The Affymetrix GeneChip Rat Genome 230 2.0 Array was used to perform transcriptome profiling of the AHF-derived BMSCs and HPCs. The results showed that AHF-derived BMSCs had a gene expression profile significantly different from that of control BMSCs. More than 87.7% of the genes/probe sets that were upregulated more than 2-fold in AHF-derived BMSCs were expressed by HPCs, including 12 genes involved in liver development, early hepatocyte differentiation and hepatocyte metabolism. Confirmatory quantitative RT-PCR analysis yielded similar results. In addition, 940 probe sets/genes were expressed in both AHF-derived BMSCs and HPCs but were absent in control cells. Compared to the control cells, AHF-derived BMSCs shared more commonly expressed genes with HPCs. AHF-derived BMSCs have a hepatic transcriptional profile and express many of the same genes expressed by HPCs, strongly suggesting that BMSCs may be a resource for hepatocyte regeneration, and further confirming their potential as a strong source of hepatocyte regeneration during severe hepatic damage.

Hereditary gingival fibromatosis: a three-generation case and pathogenic mechanism research on progress of the disease.

BACKGROUND: Hereditary gingival fibromatosis (HGF) is a rare benign disorder characterized by progressive overgrowth of gingiva. Although the clinical and histopathologic characteristics of HGF are explicit, the pathogenic mechanism remains unclear. The goal of this article is to describe a three-generation HGF case and discuss the diagnosis, treatment, and inheritance of the disease. The known cellular and molecular features of HGF are also emphasized. METHODS: Family and medical histories of the patients were recorded, and a series of preliminary examinations, including clinical, histologic, radiographic, and gene examination, were performed to make a diagnosis and learn about the genetic characteristics. An all-quadrant flap surgery was performed to remove excess gingiva, and orthodontic treatment was undertaken to help tooth eruption. Recent advances were reviewed for further knowledge of genetic, cellular, and molecular features of HGF. RESULTS: The patient's manifestations and examinations showed a typical HGF characteristic. There was no recurrence after surgery, and the premolars and molars erupted to bite plane. Genetic studies have found several gene mutations involved in HGF. Only the son-of-sevenless-1 gene is identified. Multiple molecular factors, such as transforming growth factor-ß and matrix metalloproteinases, participate in HGF, regulating the extracellular matrix. CONCLUSIONS: Surgical intervention is the usual treatment of HGF, but patients still have to deal with the risk of recurrence. Once the correlations between gene mutations, molecular changes, histology, and clinical situation are clear, they can be applied to clinical application, providing novel methods for disease prognosis and diagnosis and targets for disease prevention and treatment.

Familial syndrome resembling Aarskog syndrome.

Aarskog(-Scott) syndrome (AAS) is characterized by short stature, and facial, limb, and genital anomalies. AAS can be an X-linked condition caused by mutations in the FGD1 gene, but there is evidence that an autosomal dominant or recessive form also exists. We report on a Chinese family in whom several members have manifestations of AAS, but differ in limb anomalies and show additional characteristics. FGD1 sequencing and linkage analysis excluded FGD1 as the cause in this family. A common known submicroscopic chromosome imbalance is less likely. Both autosomal dominant and recessive patterns of inheritance remain possible.

Transcriptional profiling and hepatogenic potential of acute hepatic failure-derived bone marrow mesenchymal stem cells.

UNLABELLED: Liver stem cell (LSC) transplantation is a promising alternate approach to liver transplantation for patients with end-stage liver disease. However, the precise origin of LSCs remains unclear. Herein we determine if bone marrow mesenchymal stem cells (BMSCs) isolated from rats in acute hepatic failure (AHF) possess hepatic characteristics and have differentiation potential. BMSCs were isolated from AHF and sham-operated rats, and primary hepatocytes were isolated from normal rats for comparison. The transcriptomic profile of BMSCs and primary hepatocytes was analyzed using the Affymetrix GeneChip Rat Genome 230 2.0 Array. BMSCs isolated from AHF and normal rats were induced to differentiate into hepatocytes in vitro and the degree of hepatic differentiation was assessed using quantitative real time RT-PCR, immunohistochemistry, and biochemical assays. AHF-derived BMSCs had a significantly different gene expression profile compared to control BMSCs. Thirty-four gene/probe sets were expressed in both AHF-derived BMSCs and primary hepatocytes, but were absent in control-derived BMSCs, including 3 hepatocyte-specific genes. Forty-four genes were up-regulated more than 2-fold in AHF-derived BMSCs compared to controls, including 3 genes involved in hepatocyte metabolism and development. Furthermore, AHF-derived BMSCs expressed more hepatocyte related genes than control BMSCs. Additional experiments to validate the differentiation of AHF-derived BMSCs, compared to control-derived BMSCs, showed that several hepatocyte-specific genes and proteins [such as albumin (ALB) and alpha fetoprotein (AFP)] were expressed earlier, and at higher levels, after 1 week of differentiation. Hepatocyte-specific metabolic functions were also significantly higher in the AHF group compared to control cells. CONCLUSION: AHF-derived BMSCs had a hepatic transcriptional profile and expressed hepatocyte specific genes early during differentiation, and possessed greater hepatogenic potency in vitro compared to cells isolated from control animals, further confirming their potential as a stem cell-based therapy for end-stage liver disease.

The immunostimulating effect of bacterial genomic DNA on the innate immune responses of bivalve mussel, Hyriopsis cumingii Lea.

The genomic DNA of Escherichia coli, which contains the unmethylated CpG motif, was used to evaluate the immunostimulating effect of bacterial DNA on innate immune responses in the bivalve mussel Hyriopsis cumingii Lea. The results showed that the E. coli DNA had no significant effect on the production of superoxide anion (O(2-)) or acid phosphatase (AP) by haemocytes in vitro. However, the bactericidal activity of the haemocytes was significantly increased when the cells were incubated with 50 or 100mug/ml bacterial DNA for 12 and 24h. Antibacterial activity, lysozyme activity, and prophenoloxidase (proPO) production of haemolymph were also increased, when the bivalve molluscs were injected with 50 or 100mug/ml of bacterial DNA for 12 and 24h. These activities returned to the control level after 48h. This work showed the bacterial DNA with unmethylated CpG motif could activate some parameters of the immune system of bivalve molluscs in vivo and in vitro.