Microbulbifer hainanensis sp. nov., a moderately halopilic bacterium isolated from mangrove sediment

Antonie van Leeuwenhoek - A new bacterium was successfully isolated from a mangrove sediment sample in Haikou City, Hainan Province, China. The organism is a Gram-negative, rod-shaped, non-motile...     

Intra-Genomic Heterogeneity in 16S rRNA Genes in Strictly Anaerobic Clinical Isolates from Periodontal Abscesses

Background

Members of the genera Prevotella, Veillonella and Fusobacterium are the predominant culturable obligate anaerobic bacteria isolated from periodontal abscesses. When determining the cumulative number of clinical anaerobic isolates from periodontal abscesses, ambiguous or overlapping signals were frequently encountered in 16S rRNA gene sequencing chromatograms, resulting in ambiguous identifications. With the exception of the genus Veillonella, the high intra-chromosomal heterogeneity of rrs genes has not been reported.

Methods

The 16S rRNA genes of 138 clinical, strictly anaerobic isolates and one reference strain were directly sequenced, and the chromatograms were carefully examined. Gene cloning was performed for 22 typical isolates with doublet sequencing signals for the 16S rRNA genes, and four copies of the rrs-ITS genes of 9 Prevotella intermedia isolates were separately amplified by PCR, sequenced and compared. Five conserved housekeeping genes, hsp60, recA, dnaJ, gyrB1 and rpoB from 89 clinical isolates of Prevotella were also amplified by PCR and sequenced for identification and phylogenetic analysis along with 18 Prevotella reference strains.

Results

Heterogeneity of 16S rRNA genes was apparent in clinical, strictly anaerobic oral bacteria, particularly in the genera Prevotella and Veillonella. One hundred out of 138 anaerobic strains (72%) had intragenomic nucleotide polymorphisms (SNPs) in multiple locations, and 13 strains (9.4%) had intragenomic insertions or deletions in the 16S rRNA gene. In the genera Prevotella and Veillonella, 75% (67/89) and 100% (19/19) of the strains had SNPs in the 16S rRNA gene, respectively. Gene cloning and separate amplifications of four copies of the rrs-ITS genes confirmed that 2 to 4 heterogeneous 16S rRNA copies existed.

Conclusion

Sequence alignment of five housekeeping genes revealed that intra-species nucleotide similarities were very high in the genera Prevotella, ranging from 94.3–100%. However, the inter-species similarities were relatively low, ranging from 68.7–97.9%. The housekeeping genes rpoB and gyrB1 were demonstrated to be alternative classification markers to the species level based on intra- and inter-species comparisons, whereas based on phylogenetic tree rpoB proved to be reliable phylogenetic marker for the genus Prevotella.     

The potato amylase inhibitor gene SbAI regulates cold‐induced sweetening in potato tubers by modulating amylase activity

Potato cold‐induced sweetening (CIS) is critical for the postharvest quality of potato tubers. Starch degradation is considered to be one of the key pathways in the CIS process. However, the functions of the genes that encode enzymes related to starch degradation in CIS and the activity regulation of these enzymes have received less attention. A potato amylase inhibitor gene known as SbAI was cloned from the wild potato species Solanum berthaultii. This genetic transformation confirmed that in contrast to the SbAI suppression in CIS‐resistant potatoes, overexpressing SbAI in CIS‐sensitive potatoes resulted in less amylase activity and a lower rate of starch degradation accompanied by a lower reducing sugar (RS) content in cold‐stored tubers. This finding suggested that the SbAI gene may play crucial roles in potato CIS by modulating the amylase activity. Further investigations indicated that pairwise protein–protein interactions occurred between SbAI and α‐amylase StAmy23, β‐amylases StBAM1 and StBAM9. SbAI could inhibit the activities of both α‐amylase and β‐amylase in potato tubers primarily by repressing StAmy23 and StBAM1, respectively. These findings provide the first evidence that SbAI is a key regulator of the amylases that confer starch degradation and RS accumulation in cold‐stored potato tubers.     

Genetic Analysis of an Emerging GII.P2–GII.2 Norovirus Associated with a 2016 Outbreak of Acute Gastroenteritis in China

<正>Dear Editor,Noroviruses are positive-sense, single-stranded RNA viruses belonging to Caliciviridae and account for more than 50%of all acute gastroenteritis (AGE) outbreaks worldwide and cause an estimated 200,000 deaths per year among children\5 years of age, primarily in developing countries (Hall et al. 2012; Glass et al. 2009). The norovirus genome contains three open reading frames (ORFs).     

基于光合系统参数建立马铃薯耐荫性综合评价体系

为构建便捷的马铃薯(Solanum tuberosum)耐荫性综合评价体系并发掘耐荫种质, 以35个马铃薯品种(系)为实验材料, 测定块茎膨大期遮荫下植株叶片叶绿素含量、光合能力和叶绿素荧光等光合参数及收获后块茎单株产量和淀粉含量等指标。根据耐荫系数, 利用主成分分析法、隶属函数法、聚类分析法和逐步回归分析法进行综合评价。通过主成分分析将马铃薯耐荫性相关的13个单项光合指标转换为6个综合指标, 代表了全部信息的87.51%。以此计算各种质的隶属函数值, 并以主成分的贡献率进行加权, 最终获得所用材料耐荫性的综合评价值(D值)。根据D值聚类分析结果将35个马铃薯分为4类, 其中Eshu10和Lishu6分别为耐荫性最强和最弱的品种。通过逐步回归分析建立了马铃薯耐荫性评价数学模型: D=0.060+0.106G_s+0.214qP+0.143NPQ。同时, 用该评价体系鉴定为耐荫性强的品种(系)在遮荫后其产量和/或淀粉含量等指标减幅均低于耐荫性弱的种质, 表明该评价体系可用于快速评价和预测马铃薯种质的耐荫性。     

光照和温度对红花槭限制生长保存的影响

该文主要探讨了光照时间、光照强度、温度及昼夜温差等保存条件对卓越红花槭(Acer rubrum cv. ‘Somerset’)限制生长保存的影响。结果表明, 在为期182天的保存过程中, 离体材料前期以分化生长为主, 后期以营养生长为主, 并呈现一定的低温适应性。温度对离体材料生长的影响达极显著水平(P<0.01); 光照时间和光照强度影响持久, 二者交互作用达显著水平(P<0.05); 昼夜温差对平均出芽数和生根率都有显著影响。研究表明, 保存效果最好的条件是T3 (25°C, 12小时光照, 62.50 μmol·m ^-2·s ^-1)和T7 (25°C, 12小时光照, 31.25 μmol·m ^-2·s ^-1)处理组, 但最佳保存条件的选择标准并不唯一, 其核心是保证种质材料的分化能力。     

Overexpression of Aurora-A enhances invasion and matrix metalloproteinase-2 expression in esophageal squamous cell carcinoma cells

Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive cancers, and metastasis is the principal cause of death in ESCC patients. It has been shown that amplification and overexpression of mitotic serine/threonine kinase Aurora-A occur in several types of human tumors, including ESCC. Moreover, increase in expression levels of Aurora-A has been predicted to correlate with the grades of tumor differentiation and invasive capability. However, the mechanisms by which Aurora-A mediates its invasive effects still remain elusive. In this article, we showed that Aurora-A overexpression significantly increased cell migration and invasion as well as secretion and expression of matrix metalloproteinase-2 (MMP-2). Conversely, siRNA-mediated knockdown of Aurora-A expression in human ESCC cells led to inhibition of cell invasiveness as well as secretion and expression of MMP-2. In addition, Aurora-A overexpression increased phosphorylation levels of p38 mitogen-activated protein kinase (MAPK) and Akt, and the knockdown of Aurora-A by siRNA decreased the activity of p38 MAPK and Akt. Moreover, the blocking of the activity of above kinases using chemical inhibitors suppressed the ability of Aurora-A to induce MMP-2 secretion and expression as well as cell invasion. These data show that overexpression of Aurora-A contributes to the malignancy development of ESCC by enhancing tumor cell invasion as well as MMP-2 activity and expression, which can occur through signaling pathways involving p38 MAPK and Akt protein kinases. Taken together, these studies provide a molecular basis for promoting the role of Aurora-A in malignancy development of ESCC.     

Antimicrobial peptides from the skin of the Asian frog, Odorrana jingdongensis: De novo sequencing and analysis of tandem mass spectrometry data

Eight intact antimicrobial peptides were identified from the skin of Odorrana jingdongensis by de novo sequencing following low energy ESI CID Q-TOF MS/MS in positive-mode with the help of Edman degradation and structural similarity analysis. We devised exact mass measurements to discriminate the K/Q amino acid residue in the peptides between 2.0kDa to 3.8kDa. Moreover, the cleavage at the CS bond at the side chain of Met was observed in all the spectra of the peptides containing Met residue. And we found unusual cleavages within the intramolecular disulfide loop with high frequency. Our data revealed that the cleavage pathways are significantly different from those reported previously which are similar to the cycle peptide cleavage mode followed by the secondary cleavage at the CS bond on oxidized Cys. Thus, our results highly suggest that ion series generated from the cleavages within the intramolecular disulfide loop should be considered in both the top-down sequencing and the disulfide bridge location with the presence of a relatively high intensity of MH(+)-28 ion marker. Furthermore, our activity data implied that different AMPs may use different strategies to kill microbes.