Expression, Prognostic Value, and Functional Mechanism of Polarity-Related Genes in Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is a common malignant tumor with high mortality and poor prognoses around the world. Within-cell polarity is crucial to cell development and function maintenance, and some studies have found that it is closely related to cancer initiation, metastasis, and prognosis. The aim of our research was to find polarity-related biomarkers which improve the treatment and prognosis of HCC. For the knowledge-driven analysis, 189 polarity-related genes (PRGs) were retrieved and curated manually from the molecular signatures database and reviews. Meanwhile, in the data-driven part, genomic datasets and clinical records of HCC was obtained from the cancer genome atlas database. The potential candidates were considered in the respect to differential expression, mutation rate, and prognostic value. Sixty-one PRGs that passed the knowledge and data-driven screening were applied for function analysis and mechanism deduction. Elastic net model combing least absolute shrinkage and selection operator and ridge regression analysis refined the input into a 12-PRG risk model, and its pharmaceutical potency was evaluated. These findings demonstrated that the integration of multi-omics of PRGs can help us in untangling the liver cancer pathogenesis as well as illustrate the underlying mechanisms and therapeutic targets.

Effect of alprostadil in the treatment of intensive care unit patients with acute renal injury.

BACKGROUND: Acute kidney injury (AKI) is a sudden or rapid decline in the filtration function of the kidneys which is marked by increased serum creatinine or blood urea nitrogen. AIM: To examine the value of alprostadil-assisted continuous venous-venous hemofiltration (CVVH) in the treatment of severe AKI in severely ill patients. METHODS: This was a retrospective study and the inclusion criteria were as follows: (1) Age of patients (≥ 18 years); (2) Admission to intensive care unit due to non-renal primary disease, APACHE II score (≥ 18 points); (3) The diagnostic criteria of AKI guidelines were formulated with reference to the Global Organization for the Improvement of Prognosis in Kidney Diseases, with AKI grades of II-III; (4) All patients were treated with CVVH; and (5) Complete basic data were obtained for all patients. RESULTS: The clinical effect of alprostadil administered in the treatment group was better than that observed in the control group (P < 0.05). The urine output of patients in the alprostadil group returned to normal time (9.1 ± 2.0 d) and was lower than that in the control group (10.6 ± 2.5 d), the difference was statistically significant (P < 0.05); adverse reactions occurred in the alprostadil group compared with the control group, but the difference was not statistically significant (P > 0.05). CONCLUSION: Alprostadil-assisted CVVH in the treatment of severely ill patients with AKI can effectively improve the renal resistance index and partial pressure of urine oxygen, and has a positive effect on improving renal function.

Draft Genome Sequence of Carbapenem-Resistant Klebsiella pneumoniae XPY20 Collected from a Bloodstream Infection Patient.

Bloodstream infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been a severe problem with high clinical costs and high mortality rates. The blaKPC-2-producing CRKP strain XPY20 was collected from the blood of a patient. The genome characteristics and antimicrobial resistance mechanisms were determined using next-generation sequencing.

First report of HGD mutations in a Chinese with alkaptonuria.

Alkaptonuria (AKU) is one of the first prototypic inborn errors in metabolism and the first human disease found to be transmitted via Mendelian autosomal recessive inheritance. It is caused by HGD mutations, which leads to a deficiency in homogentisate 1,2-dioxygenase (HGD) activity. To date, several HGD mutations have been identified as the cause of the prototypic disease across different ethnic populations worldwide. However, in Asia, the HGD mutation is very rarely reported. For the Chinese population, no literature on HGD mutation screening is available to date. In this paper, we describe two novel HGD mutations in a Chinese AKU family, the splicing mutation of IVS7+1G>C, a donor splice site of exon 7, and a missense mutation of F329C in exon 12. The predicted new splicing site of the mutated exon 7 sequence demonstrated a 303bp extension after the mutation site. The F329C mutation most probably disturbed the stability of the conformation of the two loops critical to the Fe(2+) active site of the HGD enzyme.

Transcriptome analysis of Nicotiana tabacum infected by Cucumber mosaic virus during systemic symptom development.

Virus infection of plants may induce a variety of disease symptoms. However, little is known about the molecular mechanism of systemic symptom development in infected plants. Here we performed the first next-generation sequencing study to identify gene expression changes associated with disease development in tobacco plants (Nicotiana tabacum cv. Xanthi nc) induced by infection with the M strain of Cucumber mosaic virus (M-CMV). Analysis of the tobacco transcriptome by RNA-Seq identified 95,916 unigenes, 34,408 of which were new transcripts by database searches. Deep sequencing was subsequently used to compare the digital gene expression (DGE) profiles of the healthy plants with the infected plants at six sequential disease development stages, including vein clearing, mosaic, severe chlorosis, partial and complete recovery, and secondary mosaic. Thousands of differentially expressed genes were identified, and KEGG pathway analysis of these genes suggested that many biological processes, such as photosynthesis, pigment metabolism and plant-pathogen interaction, were involved in systemic symptom development. Our systematic analysis provides comprehensive transcriptomic information regarding systemic symptom development in virus-infected plants. This information will help further our understanding of the detailed mechanisms of plant responses to viral infection.

LXtoo: an integrated live Linux distribution for the bioinformatics community.

BACKGROUND: Recent advances in high-throughput technologies dramatically increase biological data generation. However, many research groups lack computing facilities and specialists. This is an obstacle that remains to be addressed. Here, we present a Linux distribution, LXtoo, to provide a flexible computing platform for bioinformatics analysis. FINDINGS: Unlike most of the existing live Linux distributions for bioinformatics limiting their usage to sequence analysis and protein structure prediction, LXtoo incorporates a comprehensive collection of bioinformatics software, including data mining tools for microarray and proteomics, protein-protein interaction analysis, and computationally complex tasks like molecular dynamics. Moreover, most of the programs have been configured and optimized for high performance computing. CONCLUSIONS: LXtoo aims to provide well-supported computing environment tailored for bioinformatics research, reducing duplication of efforts in building computing infrastructure. LXtoo is distributed as a Live DVD and freely available at http://bioinformatics.jnu.edu.cn/LXtoo.

[Effect of salpingectomy on ovarian function].

OBJECTIVE: To investigate the effects of salpingectomy on ovarian function. METHODS: Fifty-four women with previous unilateral salpingectomy and 64 with bilateral salpingectomy (study groups) and 59 infertile patients with obstruction of fallopian tube (control group) received in vitro fertilization-embryo transfer (IVF-ET) treatment. The baseline levels of serum FSH, LH, E2, PRL, ovarian response to superovulation and outcome of IVF-ET among the three groups were compared. RESULT: There were no significant differences in the baseline endocrine levels among three groups. There were more ampules and days of gonadotropin (Gn) administration, fewer oocytes retrieved in bilateral salpingectomy group than in control group (P <0.05). The duration of Gn administration of unilateral salpingectomy group was significantly longer than that of control group (P <0.05). The number of oocytes retrieved and the total ampules of Gn administration in unilateral salpingectomy group were not different with those of bilateral salpingectomy group and control group (P >0.05). Among the patients with the history of unilateral salpingectomy, significantly fewer oocytes were retrieved from the ovary on the operated side (P <0.05). There were no significant difference in the fertilization rates, cleavage rates, good-embryo rate, implantation rate, clinical pregnancy rates and good-embryo number among the three groups. CONCLUSION: Salpingectomy has no obvious effect on the outcome of IVF-ET and baseline endocrine within a period of time, but it reduces the ovarian response to superovulation on ipsilateral ovary in IVF-ET.