Mitochondrial DNA insertions in the nuclear Capra hircus genome.

Nuclear mitochondrial pseudogenes (numts), originating from mtDNA insertions into the nuclear genome, have been detected in many species. However, the distribution of numts in the newly published nuclear genome of domestic goat (Capra hircus) has not yet been explored. We used the entire goat mtDNA sequence and nuclear genome, to identify 118 numts using BLAST. Of these, 79 were able to map sequences to the genome. Further analysis showed that the size of the numts ranged from 318 to 9608 bp, and the homologous identity between numts and their respective corresponding mtDNA fragments varied between 65 and 99%. The identified Yunnan black goat numts covered nearly all the mitochondrial genes including mtDNA control region, and were distributed over all chromosomes with the exception of chromosomes 18, 21, and 25. The Y chromosome was excluded from our analysis, as sequence data are currently not available. Among the discovered 79 numts that we were able to map to the genome, 26 relatively complete mitochondrial genes were detected. Our results constitute valuable information for subsequent studies related to mitochondrial genes and goat evolution.

Management of clinically negative nodes (N0) in supraglottic laryngeal carcinoma: A systematic review.

The purpose of this study was to evaluate the treatment of clinically negative cervical lymph nodes in supraglottic carcinoma by a meta-analysis. The search words were "supraglottic carcinoma", "cervical lymph nodes negative/cN0", "radical neck dissection", and "radiotherapy". The databases included the Chinese biomedical literature database, Medline, Cochrane library, EMBASE database, journals, and theses, etc. from 1989 onwards. Using the 5-year overall survival, disease-free survival, and disease-specific survival rates, and the recurrence and distant metastasis rates as observation indexes, the proper model and method were selected after a heterogeneity test to allow combined statistic tests, sensitivity analysis, and publication bias analysis to be conducted. Four studies (807 cases) were included in the analysis. Comparisons of the 5-year overall survival, disease-free survival, and disease-specific survival rates as well as lymph node metastasis and the recurrence rate for radical neck dissection and radiotherapy showed no significant differences. There was no advantage of radical neck dissection in supraglottic carcinoma with clinically negative cervical lymph nodes compared to radiotherapy. However, owing to the lack of a prospective study and large number of cases, selection bias and measurement bias may still exist.

Comparative transcriptome analysis reveals three potential antiviral signaling pathways in lymph organ tissue of the red swamp crayfish, Procambarus clarkii.

The red swamp crayfish (Procambarus clarkii) is one of the most economically important farmed aquatic species in China. Compared with its relatively well-known antibacterial and antifungal mechanisms, the antiviral mechanism is still unclear. We used Illumina-based RNA sequencing and bioinformatic technology to obtain high-quality sequence reads from the crayfish lymph organ. A total of 5933 differentially expressed genes (DEGs) were identified between normal and white spot syndrome virus-challenged samples. Of these, 4638 genes were differentially upregulated and 1295 differentially downregulated by more than two-fold. The DEGs were then mapped to different signaling pathways; the Janus kinase/signal transducers and activators of transcription, insulin, and Wnt signaling pathways were predicted to be involved in crayfish antiviral innate immunity. These results provide new insights into crayfish antiviral immunity mechanisms.

Evaluation of the stability of reference genes in bone mesenchymal stem cells from patients with avascular necrosis of the femoral head.

This study aimed to evaluate 12 genes (18S, GAPDH, B2M, ACTB, ALAS1, GUSB, HPRT1, PBGD, PPIA, PUM1, RPL29, and TBP) for their reliability and stability as reference sequences for real-time quantitative PCR (RT-qPCR) in bone marrow-derived mesenchymal stem cells (BMSCs) isolated from patients with avascular necrosis of the femoral head (ANFH). BMSCs were isolated from 20 ANFH patients divided into four groups according to etiology, and four donors with femoral neck fractures. Total RNA was isolated from BMSCs and reverse transcribed into complementary DNA, which served as a template for RT-qPCR. Three commonly used programs were then used to analyze the results. Reference gene expression varied within each group, between specific groups, and among all five groups. Based on comparisons of all five groups, two of the programs used suggested that HPRT1 was the most stable reference gene, while 18S and ACTB were the most variable. Among the 12 candidate reference genes, HPRT1 exhibited the greatest reliability, followed by PPIA. Thus, these sequences could be used as references for the normalization of RT-qPCR results.

A novel lumazine synthase molecule from Brucella significantly promotes the immune-stimulation effects of antigenic protein.

Brucella, an intracellular parasite that infects some livestock and humans, can damage or destroy the reproductive system of livestock. The syndrome is referred to as brucellosis and often occurs in pastoral areas; it is contagious from livestock to humans. In this study, the intact Brucella suis outer membrane protein 31 (omp31) gene was cloned, recombinantly expressed, and examined as a subunit vaccine candidate. The intact Brucella lumazine synthase (bls) gene was cloned and recombinantly expressed to study polymerization function in vitro. Non-reducing gel electrophoresis showed that rBs-BLS existed in different forms in vitro, including as a dimer and a pentamer. An enzyme-linked immunosorbent assay result showed that rOmp31 protein could induce production of an antibody in rabbits. However, the rOmp31-BLS fusion protein could elicit a much higher antibody titer in rabbits; this construct involved fusion of the Omp31 molecule with the BLS molecule. Our results indicate that Omp31 is involved in immune stimulation, while BLS has a polymerizing function based on rOmp31-BLS fusion protein immunogenicity. These data suggest that Omp31 is an ideal subunit vaccine candidate and that the BLS molecule is a favorable transport vector for antigenic proteins.

Effectiveness of olfactory ensheathing cell transplantation for treatment of spinal cord injury.

The aim of this study was to determine the effectiveness and safety of transplantation of olfactory ensheathing cells for functional repair of the spinal cord. An olfactory bulb was obtained from a 4- to 5-month-old aborted fetus, and it was digested into single olfactory ensheathing cells and then cultured and purified for 1 to 2 weeks. Under general anesthesia, these single-cell suspensions of olfactory ensheathing cells were injected into the corresponding spinal injury site with 0.45-mm-diameter injections. The American Spinal Injury Association (ASIA) Impairment Scale was used to evaluate spinal function. A total of 15 patients (12 men, 3 women; age range, 18-56 years; mean age, 40) were admitted for obsolete spinal injuries. Spinal functions of the 15 patients were observed and followed postoperatively for a period ranging from 2 weeks to 1 month. All the 15 patients exhibited improvements in spinal function, and the improvement tendencies continued. Twelve patients had obvious spinal function improvement, and three had slight improvement according to the ASIA scale, with an obvious difference between preoperation and postoperation measures (P < 0.05). No fevers, infections, functional deteriorations, or deaths were seen. Thus, transplantation of olfactory ensheathing cells promoted spinal and neurofunctional recovery in patients with malignant spinal injuries, and this therapeutic method was safe.

Whole exome sequencing implicates PTCH1 and COL17A1 genes in ossification of the posterior longitudinal ligament of the cervical spine in Chinese patients.

Ossification of the posterior longitudinal ligament (OPLL) of the cervical spine is a complex multifactorial disease. Patients with OPLL commonly present with symptoms in their 40s or 50s. The genetic basis of OPLL remains poorly understood. Exome capture combined with massively parallel DNA sequencing has been proposed as an efficient strategy to search for disease-causing genes of both monogenic and multigenic disorders. To identify candidate pathogenic genes associated with OPLL, we performed whole exome sequencing (WES) on two unrelated southern Chinese OPLL patients. The entire DNA coding region of the candidate genes was amplified by PCR and Sanger sequenced. The common single nucleotide polymorphisms were analyzed by association studies. WES revealed p.T265S/PTCH1, p.P1232L/PTCH1, and p.T902S/COL17A1 mutants in the two female cases with mixed OPLL. These were confirmed by Sanger sequencing. p.P1232L/PTCH1, p.N1374D/COL17A1 and p.T902S/COL17A1 were subsequently identified in three males with continuous OPLL and one female with mixed OPLL. The association studies indicated that the SNPs rs805698 and rs4918079 in COL17A1 were significantly associated with OPLL. This study suggests that WES may be a practical approach to revealing significant genetic involvement in OPLL. Variants of the PTCH1 and COL17A1 genes may contribute to the development of OPLL.

Genetic diversity analysis of barley landraces and cultivars in the Shanghai region of China.

We analyzed the genetic diversity of 115 barley germplasms, including 112 landraces and three new barley cultivars grown in the Shanghai region, using a set of 11 SSR markers. Sixty-six alleles were observed at the 11 SSR loci, ranged from three to ten, with a mean of six alleles per locus. The polymorphism information content ranged from 0.568 to 0.853, with a mean of 0.732, indicating considerable genetic variation in barley in the Shanghai area. Clustering analysis indicated that these barley accessions could be divided into two categories (A and B). Ninety-seven six-rowed barley cultivars were classified in the A category; sixteen two-rowed and two six-rowed barley cultivars were classified in the B category. This demonstrated genetic differences between two-rowed and six-rowed barley varieties. In addition, we found that the three new barley cultivars are closely related.