MyD88 plays a critical T cell-intrinsic role in supporting CD8 T cell expansion during acute lymphocytic choriomeningitis virus infection

During acute lymphocytic choriomeningitis virus (LCMV) infection, CD8 T cells rapidly expand and differentiate into effectors that are required for viral clearance. The accumulation of activated T cells is greatly reduced in mice lacking the adaptor molecule MyD88. Although MyD88 has generally been considered to indirectly regulate adaptive immune responses by controlling inflammatory cytokine production and Ag presentation in innate immune cells, in this study, we identify an unappreciated cell-intrinsic role for MyD88 in LCMV-specific CD8 T cells. Using reciprocal adoptive transfer models and bone marrow chimeras, we show that Myd88(-/-) CD8 T cells are defective in their clonal expansion in response to LCMV infection, independent of their environment. Furthermore, we show that while MyD88 is dispensable for initial activation and division of LCMV-specific CD8 T cells during the early stages of viral infection, MyD88-dependent signals are critical for supporting their survival and sustained accumulation.     

Mutations at Arginine 352 Alter the Pore Architecture of CFTR

Arginine 352 (R352) in the sixth transmembrane domain of the cystic fibrosis transmembrane conductance regulator (CFTR) previously was reported to form an anion/cation selectivity filter and to provide positive charge in the intracellular vestibule. However, mutations at this site have nonspecific effects, such as inducing susceptibility of endogenous cysteines to chemical modification. We hypothesized that R352 stabilizes channel structure and that charge-destroying mutations at this site disrupt pore architecture, with multiple consequences. We tested the effects of mutations at R352 on conductance, anion selectivity and block by the sulfonylurea drug glipizide, using recordings of wild-type and mutant channels. Charge-altering mutations at R352 destabilized the open state and altered both selectivity and block. In contrast, R352K-CFTR was similar to wild-type. Full conductance state amplitude was similar to that of wild-type CFTR in all mutants except R352E, suggesting that R352 does not itself form an anion coordination site. In an attempt to identify an acidic residue that may interact with R352, we found that permeation properties were similarly affected by charge-reversing mutations at D993. Wild-type-like properties were rescued in R352E/D993R-CFTR, suggesting that R352 and D993 in the wild-type channel may interact to stabilize pore architecture. Finally, R352A-CFTR was sensitive to modification by externally applied MTSEA⁺, while wild-type and R352E/D993R-CFTR were not. These data suggest that R352 plays an important structural role in CFTR, perhaps reflecting its involvement in forming a salt bridge with residue D993.     

Extensive conformational transitions are required to turn on ATP hydrolysis in myosin

Conventional myosin is representative of biomolecular motors in which the hydrolysis of adenosine triphosphate (ATP) is coupled to large-scale structural transitions both in and remote from the active site. The mechanism that underlies such “mechanochemical coupling,” especially the causal relationship between hydrolysis and allosteric structural changes, has remained elusive despite extensive experimental and computational analyses. In this study, using combined quantum mechanical and molecular mechanical simulations and different conformations of the myosin motor domain, we provide evidence to support that regulation of ATP hydrolysis activity is not limited to residues in the immediate environment of the phosphate. Specifically, we illustrate that efficient hydrolysis of ATP depends not only on the proper orientation of the lytic water but also on the structural stability of several nearby residues, especially the Arg238-Glu459 salt bridge (the numbering of residues follows myosin II in Dictyostelium discoideum) and the water molecule that spans this salt bridge and the lytic water. More importantly, by comparing the hydrolysis activities in two motor conformations with very similar active-site (i.e., Switches I and II) configurations, which distinguished this work from our previous study, the results clearly indicate that the ability of these residues to perform crucial electrostatic stabilization relies on the configuration of residues in the nearby N-terminus of the relay helix and the “wedge loop.” Without the structural support from those motifs, residues in a closed active site in the post-rigor motor domain undergo subtle structural variations that lead to consistently higher calculated ATP hydrolysis barriers than in the pre-powerstroke state. In other words, starting from the post-rigor state, turning on the ATPase activity requires not only displacement of Switch II to close the active site but also structural transitions in the N-terminus of the relay helix and the “wedge loop,” which have been proposed previously to be ultimately coupled to the rotation of the converter subdomain 40 Å away.     

An entropy-based approach for testing genetic epistasis underlying complex diseases

The genetic basis of complex diseases is expected to be highly heterogeneous, with complex interactions among multiple disease loci and environment factors. Due to the multi-dimensional property of interactions among large number of genetic loci, efficient statistical approach has not been well developed to handle the high-order epistatic complexity. In this article, we introduce a new approach for testing genetic epistasis in multiple loci using an entropy-based statistic for a case-only design. The entropy-based statistic asymptotically follows a χ² distribution. Computer simulations show that the entropy-based approach has better control of type I error and higher power compared to the standard χ² test. Motivated by a schizophrenia data set, we propose a method for measuring and testing the relative entropy of a clinical phenotype, through which one can test the contribution or interaction of multiple disease loci to a clinical phenotype. A sequential forward selection procedure is proposed to construct a genetic interaction network which is illustrated through a tree-based diagram. The network information clearly shows the relative importance of a set of genetic loci on a clinical phenotype. To show the utility of the new entropy-based approach, it is applied to analyze two real data sets, a schizophrenia data set and a published malaria data set. Our approach provides a fast and testable framework for genetic epistasis study in a case-only design.     

Social organization of black-and-white snub-nosed monkeys (Rhinopithecus bieti) at Deqin, China

Data on social organization of two bands of black-and-white snub-nosed monkeys (Rhinopithecus bieti) were collected when the monkeys were crossing an open spot at Nanren and Bamei (northwest of Yunnan, China) using a sampling rule where individuals within one social unit are spatially closer to each other than individuals between social units. The typical pattern of social organization in this sample was multiple adult females (AFs) and their offspring with one adult male (AM) in a one-male unit (OMU), similar to that of many other colobines. In such units, on average one male is associated with 4.0 AFs and 2.5 of their offspring. Moreover, there are multimale/multifemale units and monogamous units besides OMUs. All bisexual units traveled together with at least one all-male unit as a cohesive band. In two bands of monkeys, 87% of AMs in bisexual units were within OMUs, 7.8% within monogamous units and 5.2% within multimale, multifemale units. In the Bamei band, 6.7% of AMs were in the all-male unit. The size of OMUs in the Nanren band was larger than that of the Bamei band, with more AFs and juveniles, which may be related to better conservation in the Nanren band's habitat. For the Nanren band, the average number of AFs in OMUs varied across time, increasing from 4.3 in 1994 to 5.1 in 2001, and then decreasing to 3.8 in 2005. This article suggests three possible explanations for this variation, but more data are needed for these hypotheses to be tested.     

假单胞菌DLL-E4尿黑酸降解基因的克隆与功能的初步分析

通过接合转移将质粒pSC123上的转座子Tn5随机插入到DLL-E4基因组DNA中,从大约8,000个突变子中筛选到1株在LB培养基上积累红褐色物质的突变株M18,该突变株不能以L-苯丙氨酸(L-Phenylalanine, Phe)为唯一碳源生长。SEFA-PCR扩增转座子侧翼序列发现其与已报道的尿黑酸1,2-双加氧酶基因hmgA的同源性为92%。将hmgA定向克隆至表达载体pET-29a中,转化至Escherichia coli BL21,经IPTG诱导后可表达分子量约为48kD的蛋白;诱导后转化子粗酶液对尿黑酸有很好的降解效果。将hmgA连入自杀性载体pEX19Gm,通过同源重组整合至M18染色体中,使其恢复了DLL-E4利用Phe的能力,证实了HmgA是尿黑酸苯环裂解酶。     

黄芩甙对肝癌细胞BEL-7402形态学的影响

目的观察黄芩甙对肝癌细胞BEL-7402凋亡的影响,同时观察对肝癌细胞形态及超微结构、线粒体超微结构、线粒体膜电位和细胞内Ca^2＋的影响,探讨线粒体损伤在黄芩甙诱导肝癌细胞凋亡中的作用及可能的机制。方法应用细胞培养技术培养肝癌细胞BEL-7402,光镜、倒置显微镜、扫描电镜、透射电镜观察细胞形态及超微结构的变化尤其是线粒体的变化,应用流式细胞仪检测细胞凋亡百分率及线粒体膜电位、细胞内Ca^2＋的改变,免疫组化法检测细胞Bcl-2、Pax蛋白表达。结果黄芩甙诱导肝癌细胞BEL-7402凋亡呈剂量依赖关系,细胞形态、超微结构及线粒体超微结构出现明显改变,降低肝癌细胞线粒体膜电位,使细胞内Ca^2＋增加,细胞Pax表达增加,广泛分布于胞核和胞质中,Bcl-2表达减少。结论黄芩甙诱导肝癌细胞BEL-7402凋亡,线粒体损伤在黄芩甙诱导肝癌细胞凋亡中起重要作用,其机制可能为抑制肝癌细胞Bcl-2蛋白表达,促进Pax蛋白表达及细胞内Ca^2＋增加,激发线粒体膜通透性转运孔开放,线粒体跨膜电位降低,使肝癌细胞凋亡。     

Mitochondrial DNA analysis of human remains from the Yuansha site in Xinjiang,China

The Yuansha site is located in the center of the Taklimakan Desert of Xinjiang, in the southern Silk Road region. MtDNA was extracted from fifteen human remains excavated from the Yuansha site, dating back 2,000–2,500 years. Analysis of the phylogenetic tree and the multidimensional scaling (MDS) reveals that the Yuansha population has relatively close relationships with the modern populations of South Central Asia and Indus Valley, as well as with the ancient population of Chawuhu.     

Development of an enrichment culture growing at low temperature used for ensiling rice straw

To speed up the conversion of rice straw into feeds in a low-temperature region, a start culture used for ensiling rice straw at low temperature was selected by continuous enrichment cultivation. During the selection, the microbial source for enrichment was rice straw and soil from two places in Northeast China. Lab-scale rice straw fermentation at 10 degrees C verified, compared with the commercial inocculant, that the selected start culture lowered the pH of the fermented rice straw more rapidly and produced more lactic acid. The results from denatured gradient gel eletrophoresis showed that the selected start culture could colonize into the rice straw fermentation system. To analyze the composition of the culture, a 16S clone library was constructed. Sequencing results showed that the culture mainly consisted of two bacterial species. One (A) belonged to Lactobacillus and another (B) belonged to Leuconostoc. To make clear the roles of composition microbes in the fermented system, quantitative PCR was used. For species A, the DNA mass increased continuously until sixteen days of the fermentation, which occupied 65%. For species B, the DNA mass amounted to 5.5% at six days of the fermentation, which was the maximum relative value during the fermentation. To the authors' best knowledge, this is the first report on ensiling rice straw with a selected starter at low temperature and investigation of the fermented characteristics.