B7-H1-induced apoptosis as a mechanism of immune privilege of corneal allografts

The programmed death-1 (PD-1) costimulatory pathway has been demonstrated to play a role in the regulation of immune responses and peripheral tolerance. We investigated the role of this pathway in establishing an immune privilege status of corneal allografts in mice. B7-H1, but not B7-DC or PD-1, was expressed constitutively in the eye, i.e., cornea, iris-ciliary body, and retina. After corneal allografting, PD-1(+)CD4(+) T cells infiltrated and adhered with B7-H1(+) corneal endothelium. Blockade of PD-1 or B7-H1, but not B7-DC, led to accelerated corneal allograft rejection. In B7-H1-expressing corneal allografts, apoptosis of the infiltrating PD-1(+)CD4(+) or CD8(+) T cells was observed, after which there was allograft acceptance. In contrast, B7-H1 blockade suppressed apoptosis of infiltrating PD-1(+) T cells, which led to allograft rejection. In vitro, destruction of corneal endothelial cells by alloreactive T cells was enhanced when the cornea was pretreated with anti-B7-H1 Ab. This is the first demonstration that the constitutive expression of B7-H1 plays a critical role in corneal allograft survival. B7-H1 expressed on corneal endothelial cells maintains long-term acceptance of the corneal allografts by inducing apoptosis of effector T cells within the cornea.     

Genetic Variants in RKIP Are Associated with Clear Cell Renal Cell Carcinoma Risk in a Chinese Population

Background

Raf-1 kinase inhibitor protein (RKIP) plays a critical role in tumor development by regulating cell functions such as invasion, apoptosis and differentiation. Down-regulation of RKIP expression has been implicated in the development and progression of renal cell carcinoma (RCC). Herein, we hypothesized that genetic polymorphisms in RKIP might be associated with susceptibility and progression of RCC.

Methods

A total of 5 tagging single-nucleotide polymorphisms (tSNPs) in RKIP were selected and genotyped by SNapShot method in a case-control study of 859 RCC patients and 1004 controls. The logistic regression was used to evaluate the genetic association with occurrence and progression of RCC. The functionality of the important SNP was preliminary examined by qRT-PCR.

Result

We found that the rs17512051 in the promoter region of RKIP was significantly associated with decreased clear cell RCC (ccRCC) risk (TA/AA vs. TT: P = 0.039, OR = 0.78, 95%CI = 0.62–0.99). Another SNP (rs1051470) in the 3′UTR region of RKIP was marginally associated with increased ccRCC risk (TT vs. CC+CT: OR = 1.45, 95%CI = 1.01–2.09). In the stratified analysis, the protective effect of rs17512051 was more predominant in the subgroups of male, non-smokers, non-drinkers as well as subjects without history of diabetes. Furthermore, we observed higher RKIP mRNA levels in the presence of the rs17512051A allele in normal renal tissues.

Conclusion

Our results suggest that the potentially functional RKIP rs17512051 polymorphism may affect ccRCC susceptibility through altering the endogenous RKIP expression level. Risk effects and the functional impact of this polymorphism need further validation.     

Distinct distribution patterns of prokaryotes between sediment and water in the Yellow River estuary

Applied Microbiology and Biotechnology - There are close exchanges between sediment and water in estuaries; however, the patterns of prokaryotic community assembly in these two habitat types are...     

A Bayesian Framework to Identify Methylcytosines from High-Throughput Bisulfite Sequencing Data

High-throughput bisulfite sequencing technologies have provided a comprehensive and well-fitted way to investigate DNA methylation at single-base resolution. However, there are substantial bioinformatic challenges to distinguish precisely methylcytosines from unconverted cytosines based on bisulfite sequencing data. The challenges arise, at least in part, from cell heterozygosis caused by multicellular sequencing and the still limited number of statistical methods that are available for methylcytosine calling based on bisulfite sequencing data. Here, we present an algorithm, termed Bycom, a new Bayesian model that can perform methylcytosine calling with high accuracy. Bycom considers cell heterozygosis along with sequencing errors and bisulfite conversion efficiency to improve calling accuracy. Bycom performance was compared with the performance of Lister, the method most widely used to identify methylcytosines from bisulfite sequencing data. The results showed that the performance of Bycom was better than that of Lister for data with high methylation levels. Bycom also showed higher sensitivity and specificity for low methylation level samples (<1%) than Lister. A validation experiment based on reduced representation bisulfite sequencing data suggested that Bycom had a false positive rate of about 4% while maintaining an accuracy of close to 94%. This study demonstrated that Bycom had a low false calling rate at any methylation level and accurate methylcytosine calling at high methylation levels. Bycom will contribute significantly to studies aimed at recalibrating the methylation level of genomic regions based on the presence of methylcytosines.     

Molecular Fingerprint and Dominant Environmental Factors of Nitrite-Dependent Anaerobic Methane-Oxidizing Bacteria in Sediments from the Yellow River Estuary,China

Nitrite-dependent anaerobic methane oxidation (n-damo) is performed by “Candidatus Methylomirabilis oxyfera” (M. oxyfera), which connects the carbon and nitrogen global nutrient cycles. In the present study, M. oxyfera-like bacteria sequences were successfully recovered from Yellow River Estuary sediments using specific primers for 16S rRNA and pmoA genes. A M. oxyfera-like sequences analysis based on the 16S rRNA gene revealed greater diversity compared with the pmoA gene; the 16S rRNA gene sequences retrieved from the Yellow River Estuary sediments belong to groups A as well as B and were mainly found in freshwater habitats. Quantitative PCR showed that 16S rRNA gene abundance varied from 9.28±0.11×10³ to 2.10±0.13×10⁵ copies g^-1 (dry weight), and the pmoA gene abundance ranged from 8.63±0.50×10³ to 1.83±0.18×10⁵ copies g^-1 (dry weight). A correlation analysis showed that the total organic carbon (TOC) and ammonium (NH₄ ⁺) as well as the ratio of total phosphorus to total nitrogen (TP/TN) influenced the M. oxyfera-like bacteria distribution in the Yellow River Estuary sediments. These findings will aid in understanding the n-damo bacterial distribution pattern as well as their correlation with surrounding environmental factors in temperate estuarine ecosystems.     

西北印度洋卡尔斯伯格脊卧蚕热液羽流影响区细菌群落结构特征及其演化

【目的】热液羽流影响区包括热液羽流流经区域和羽流中性浮力层下方受热液颗粒物影响的区域。随着热液羽流的演化,热液羽流影响区内微生物群落的结构组成也会发生相应的变化,但是,由于观测和取样困难等原因,迄今热液羽流影响区不同空间位置微生物的群落结构特征及其在月际尺度上的演化尚不清楚。【方法】中国大洋49航次在卧蚕1号热液喷口东南侧300 m处投放了沉积物捕获器锚系,在不同离底高度开展了为期18个月的观测和时序采水。本文采用Illumina MiSeq高通量测序技术对水样中的微生物类群进行测序分析,结合现场实时探测的浊度异常资料,研究卧蚕热液区附近中性浮力羽流和热液颗粒沉降区细菌群落结构的特征和演化及其影响因素。【结果】结果表明,样品中细菌群落以γ-变形菌纲(Gammaproteobacteria)、弯曲菌纲(Camplylobacteria)、α-变形菌纲(Alphaproteobacteria)、拟杆菌纲(Bacteroidia)、梭菌纲(Clostridia)和脱硫叶菌纲(Desulfobulbia)为主。在时间上,优势类群的相对丰度随浊度起伏发生变化,当浊度异常值升高时,弯曲菌纲相对丰度...     

一株产嗜铁素耐镉菌的分离及其对黑麦草种子萌发的作用

【背景】产嗜铁素细菌(Siderophore-ProducingBacteria,SPB)是一类耐重金属性能较好的促生微生物,将其应用于土壤重金属污染修复方面的研究已成为该领域的研究热点。【目标】为重金属镉污染土壤修复提供种质资源,并探究产嗜铁素细菌对Cd~(2+)胁迫下黑麦草种子萌发的影响。【方法】采用微生物分离纯化技术,从甘肃省临泽县宏鑫矿业尾矿区采集土壤样品,分离筛选出一株能够产嗜铁素且耐镉胁迫的菌株,采用16SrRNA基因序列鉴定该菌株,并测定其嗜铁素螯合基团结构类型及生长和产嗜铁素曲线,对菌株嗜铁素分离纯化后测定其荧光强度并进行紫外光谱扫描,最后探究嗜铁素及其产生菌对Cd~(2+)胁迫下黑麦草种子萌发的影响。【结果】经鉴定该菌为假单胞菌属(Pseudomonassp.W-STS-8),能产生一种黄绿色嗜铁素——脓菌素(Pyoverdine),该嗜铁素同时具有异羟肟酸型和儿茶酚型2种螯合结构;其嗜铁素产量在菌株生长稳定期的后期达到最大值(68%),而且嗜铁素产量与菌株生物量呈正相关。嗜铁素经分离纯化后,在紫外灯(254 nm)下可见荧光,在400 nm处具有紫外光谱特征吸收峰。该菌及其嗜铁素对Cd~(2+)胁迫下黑麦草种子萌发实验结果表明,与对照相比,经W-STS-8菌悬液和嗜铁素处理后黑麦草种子发芽率显著上升,分别提高了73.14%和150.92%。【结论】对该菌株的深入研究,可为重金属镉污染土壤的微生物-植物联合修复的生态修复工程提供种质资源和科学基础。     

西北印度洋卡尔斯伯格脊卧蚕热液羽流影响区古菌群落动态变化特征

【目的】热液羽流在浮力上升和非浮力侧向迁移过程中与背景海水不断进行物质和能量的交换。因海底热液活动和洋流的流速流向均存在动态变化性,热液羽流的高度、物理化学参数和微生物群落也随时空发生演化。然而,由于缺乏热液羽流的长期监测和时序取样,微生物群落(尤其是古菌)的多样性及其时空演化尚不清楚。【方法】2018年7月-2019年6月,在卧蚕1号热液喷口东南300 m处放置了一套带有2个沉积物捕获器(分别距海底300 m和40 m)和一个浊度仪(距海底150 m)的锚系潜标,对热液羽流和热液羽流下方颗粒物沉降区的近底水样进行了为期18个月的观测和时序采样。本研究采用16S rRNA基因高通量测序技术研究了水样中古菌群落的多样性,以了解羽流层和近底沉降层古菌群落结构的特征与时空演化。【结果】热原体纲(Thermoplasmata)、甲烷八叠球菌纲(Methanosarcinia)和甲烷杆菌纲(Methanobacteria)等热液来源古菌,当浊度异常值较高时,它们的丰度也增加。从空间上看,热液羽流区和近底沉降区古菌群落结构在门和纲水平上具有相似性,但在目水平上表现出差异性,而且各主要类群的相对丰度也存在差异,其中热原体纲在羽流层中的丰度普遍高于近底沉降层,而氨氧化古菌和甲烷八叠球菌纲在沉降层的丰度较高。【结论】卧蚕热液区东南300 m热液羽流层和近底沉降层均受到了热液的影响,羽流层受热液影响的程度相对更显著,而近底沉降层除了受到一定程度的热液影响外,还可能受到了再悬浮沉积物的影响。热液贡献大小的动态变化和底层沉积物再悬浮可能是造成热液区近端水体古菌群落时空异质性的主要因素。本研究深化了对热液影响区古生菌群落结构及其月际尺度时空分布特征的认识。     

MALDITOF MS快速检测病原菌耐药性的应用进展

基质辅助激光解析电离飞行时间质谱(MALDITOF MS)技术已经在病原菌鉴定上取得了非常理想的效果,具有流程简单、准确快速、高通量等优点,被越来越广泛地应用于临床微生物实验室中。作为一种快速、简便且经济的方法,MALDITOF MS在病原菌耐药性的临床检测方面也展现出巨大的潜力,是目前临床微生物学领域的一大研究热点。国内外已有许多基于MALDITOF MS检测病原菌耐药性的相关研究,并提出了多种不同的方法,本文将对病原菌耐药性的主要检测方法和原理进行综述。