Molecular Dynamics Simulations of Rhodopsin Point Mutants at the Cytoplasmic Side of Helices 3 and 6

Abstract

The present work reports on a structural analysis carried out through different computer simulations of a set of rhodopsin mutants with differential functional features in regard to the wild type. Most of these mutants, whose experimental features had previously been reported [Ramon et al. J Biol Chem 282, 14272–14282 (2007)], were designed to perturb a network of electrostatic interactions located at the cytoplasmic sides of transmembrane helices 3 and 6. Geometric and energetic features derived from the detailed analysis of a series of molecular dynamics simulations of the different rhodopsin mutants, involving positions 134(3.49), 247(6.30), and 251(6.34), suggest that the protein structure is sensitive to these mutations through the local changes induced that extend further to the secondary structure of neighboring helices and, ultimately, to the packing of the helical bundle. Overall, the results obtained highlight the complexity of the analyzed network of electrostatic interactions where the effect of each mutation on protein structure can produce rather specific features.     

How does the metabolism of tumour cells differ from that of normal cells

Tumour cells thrive in environments that would be hostile to their normal cell counterparts. Survival depends on the selection of cell lines that harbour modifications of both, gene regulation that shifts the balance between the cell cycle and apoptosis and those that involve the plasticity of the metabolic machinery. With regards to metabolism, the selected phenotypes usually display enhanced anaerobic glycolysis even in the presence of oxygen, the so-called Warburg effect, and anabolic pathways that provide precursors for the synthesis of lipids, proteins and DNA. The review will discuss the original ideas of Otto Warburg and how they initially led to the notion that mitochondria of tumour cells were dysfunctional. Data will be presented to show that not only the organelles are viable and respiring, but that they are key players in tumorigenesis and metastasis. Likewise, interconnecting pathways that stand out in the tumour phenotype and that require intact mitochondria such as glutaminolysis will be addressed. Furthermore, comments will be made as to how the peculiarities of the biochemistry of tumour cells renders them amenable to new forms of treatment by highlighting possible targets for inhibitors. In this respect, a case study describing the effect of a metabolite analogue, the alkylating agent 3BP (3-bromopyruvate), on glycolytic enzyme targets will be presented.     

Prediction of Antimicrobial Activity of Synthetic Peptides by a Decision Tree Model

Antimicrobial resistance is a persistent problem in the public health sphere. However, recent attempts to find effective substitutes to combat infections have been directed at identifying natural antimicrobial peptides in order to circumvent resistance to commercial antibiotics. This study describes the development of synthetic peptides with antimicrobial activity, created in silico by site-directed mutation modeling using wild-type peptides as scaffolds for these mutations. Fragments of antimicrobial peptides were used for modeling with molecular modeling computational tools. To analyze these peptides, a decision tree model, which indicated the action range of peptides on the types of microorganisms on which they can exercise biological activity, was created. The decision tree model was processed using physicochemistry properties from known antimicrobial peptides available at the Antimicrobial Peptide Database (APD). The two most promising peptides were synthesized, and antimicrobial assays showed inhibitory activity against Gram-positive and Gram-negative bacteria. Colossomin C and colossomin D were the most inhibitory peptides at 5 μg/ml against Staphylococcus aureus and Escherichia coli. The methods described in this work and the results obtained are useful for the identification and development of new compounds with antimicrobial activity through the use of computational tools.     

The Himalayas: Barrier and conduit for gene flow

The Himalayan mountain range is strategically located at the crossroads of the major cultural centers in Asia, the Middle East and Europe. Although previous Y‐chromosome studies indicate that the Himalayas served as a natural barrier for gene flow from the south to the Tibetan plateau, this region is believed to have played an important role as a corridor for human migrations between East and West Eurasia along the ancient Silk Road. To evaluate the effects of the Himalayan mountain range in shaping the maternal lineages of populations residing on either side of the cordillera, we analyzed mitochondrial DNA variation in 344 samples from three Nepalese collections (Newar, Kathmandu and Tamang) and a general population of Tibet. Our results revealed a predominantly East Asian‐specific component in Tibet and Tamang, whereas Newar and Kathmandu are both characterized by a combination of East and South Central Asian lineages. Interestingly, Newar and Kathmandu harbor several deep‐rooted Indian lineages, including M2, R5, and U2, whose coalescent times from this study (U2, >40 kya) and previous reports (M2 and R5, >50 kya) suggest that Nepal was inhabited during the initial peopling of South Central Asia. Comparisons with our previous Y‐chromosome data indicate sex‐biased migrations in Tamang and a founder effect and/or genetic drift in Tamang and Newar. Altogether, our results confirm that while the Himalayas acted as a geographic barrier for human movement from the Indian subcontinent to the Tibetan highland, it also served as a conduit for gene flow between Central and East Asia. Am J Phys Anthropol 151:169–182, 2013. © 2013 Wiley Periodicals, Inc.     

黄土高原沟壑区森林带不同植物群落土壤氮素含量及其转化

为了探讨在黄土高原退耕还林还草过程中植物群落对土壤氮素含量及形态分布的影响,本文选择退耕历史较长的黄土高原沟壑区——安塞县洞子沟流域8种典型植物群落下0-10cm和10-20cm的土壤为对象,测定了土壤中有机氮、矿化氮、微生物量氮、硝态氮和铵态氮的含量。结果表明,从草本群落到乔灌草群落,土壤各形态氮素含量均增加,整体表现为乔灌草群落>灌草群落>草本群落。然而人工刺槐林的土壤氮素水平远低于自然恢复的乔灌草群落,甚至低于灌草群落。0-10cm 土层各形态氮素均高于10-20cm 土层。硝态氮对植物群落的变化最为敏感,可作为土壤氮素水平的敏感指标。土壤有机质、pH、容重与氮素含量极显著相关,各种氮素间极显著正相关。各种氮素占总氮的比例对总氮的变化有着不同的响应,有机氮、可矿化氮和微生物量氮占总氮的比例相对稳定,硝态氮占总氮的比例随总氮含量的增加而增加,铵态氮占总氮的比例随总氮含量的增加而降低。     

黄土丘陵区不同植被土壤氮素转化微生物生理群特征及差异

采用最大或然计数法(most probable number, MPN)对黄土高原洞子沟流域不同植被恢复阶段土壤氮素微生物生理群(氨化细菌、亚硝化细菌、反硝化细菌)数量分布特征进行了测定,结果表明:1)土壤氨化细菌、亚硝化细菌和反硝化细菌数量随植被恢复而增加,三者最大值分别为最小值的74、4和31倍,其中氨化细菌和反硝化细菌的数量在铁杆蒿群落最低,辽东栎群落最高,亚硝化细菌数量在丁香群落最低,辽东栎群落最高;2)植被恢复对各氮素生理群影响不同,对氨化细菌影响最大,其次分别为反硝化细菌和亚硝化细菌;3)各氮素生理群数量差异较大,氨化细菌>反硝化细菌>亚硝化细菌。研究区氨化细菌占总数的75%-80%,反硝化细菌占20%-25%时,生态系统最为稳定;4)土壤理化性质与各功能菌关系紧密,其中,土壤容重和硝态氮含量与微生物数量相关性最大,全钾、矿化氮和微生物量氮也表现出很大的相关性。     

黄土丘陵沟壑区不同植被区土壤生态化学计量特征

以黄土丘陵沟壑区3个植被区(森林区、森林草原区、草原区)不同坡向土壤作为研究对象,对土壤有机C、全N、全P、全K含量及其化学计量特征进行了研究.结果表明,不同植被区、坡向和土层土壤养分含量及其化学计量特征均有明显不同.土壤有机C、全N变异性较大,全P、全K变异性较小.表层土壤养分含量显著高于底层土壤;同一土层之间有机C、全N含量变异性较大,全P、全K含量变异性较小.不同坡向之间养分含量不同,阴坡最大,阳坡最小.土壤养分含量受植被类型及植被盖度的影响,森林区＞草原区＞森林草原区.土壤C/N、C/P、C/K、N/P、N/K比都较稳定,C/N比的变化范围为5.65-12.57,平均值为9.44; C/P比的变化范围为3.62-17.32,平均值为8.15;C/K比的变化范围为0.10-0.55,平均值为0.26;N/P比的变化范围为0.43-1.38,平均值为0.86; N/K比的变化范围为0.01-0.05,平均值为0.03;P/K比值较稳定,为0.03.土壤有机C和全N极显著正相关,全N和全P极显著正相关.     

太子参红外指纹图谱的双指标序列分析

本文采用傅里叶变换红外光谱仪测定了四大种植主产区(安徽、江苏、福建、贵州)的栽培品及河南的野生品,共13个批次太子参甲醇提取物,获得不同产地太子参栽培品的FTIR指纹图谱,并对指纹图谱进行了相似度的计算,同时结合(共有峰率,变异峰率)双指标序列分析方法,对不同产地太子参的FTIR光谱进行了研究。结果表明,该方法所建立的太子参FTIR指纹图谱能够区分栽培品和野生品的差异,双指标序列分析法能够为产区间和产区内太子参品质差异提供参考,两种分析方法结合可为该药材的质量分析、评价与控制提供依据。     

单纯疱疹病毒1型引起的发热出疹性疾病需要与手足口病进行鉴别

对2008年在甘肃省发生的一起疑似手足口病(HFMD)的发热出疹性疾病的流行进行病原体的实验室检测,明确引起这起传染病流行的病原体。从4名发热出疹患者采集的8份临床标本中(每个患者采集咽拭子和疱疹液标本),首先将临床标本接种到RD和HEp-2细胞上进行病毒分离,对病毒分离阳性的标本提取病毒核酸,然后使用荧光定量-逆转录-聚合酶链式反应(RT-PCR)进行人肠道病毒(HEV)核酸的检测。对HEV检测结果阴性的标本采用序列非依赖的单引物扩增技术(SISPA)进行"未知病原体"的鉴定。分离到的6株病毒均鉴定为单纯疱疹病毒I型(HSV-1),结合分析这起流行中患者的临床表现、流行病学调查结果以及实验室检测结果,表明HSV-1是引起这起发热出疹性疾病流行的病原体。6株HSV-1的gG区核苷酸和氨基酸水平上差异都较小,同源性分别高达98.8%和97.9%,说明这起疫情是由同一个病毒传播链引起的。HSV-1等病毒引起的发热出疹性疾病需要与HFMD进行鉴别诊断,由于仅从临床症状和流行病学资料上判断引起发热出疹性疾病的病原体是非常困难的,因此,必须依赖于实验室的诊断。     

Mammary tumor development is directly inhibited by lifelong n-3 polyunsaturated fatty acids

IntroductionDespite the advocacy that diet may be a significant contributor to cancer prevention, there is a lack of direct evidence from epidemiological and experimental studies to substantiate such claims. Experimental studies suggest that n-3 polyunsaturated fatty acids (n-3 PUFA) from marine oils may reduce breast cancer risk, however, findings are equivocal. Thus, in this study, novel transgenic mouse models were employed to provide, for the first time, direct evidence for an anti-cancer role of n-3 PUFA in mammary tumorigenesis.Methodsfat-1 Mice, which are capable of endogenous n-3 PUFA synthesis, were bred with mouse mammary tumor virus (MMTV)-neu(ndl)-YD5 mice, an aggressive breast cancer model. The resultant offspring, including novel hybrid progeny, were assessed for tumor onset, size and multiplicity as well as n-3 PUFA composition in mammary gland and tumor tissue. A complementary group of MMTV-neu(ndl)-YD5 mice were fed n-3 PUFA in the diet.ResultsMice expressing MMTV-neu(ndl)-YD5 and fat-1 displayed significant (P<.05) reductions in tumor volume (~30%) and multiplicity (~33%), as well as reduced n-6 PUFA and enriched n-3 PUFA in tumor phospholipids relative to MMTV-neu(ndl)-YD5 control mice. The effect observed in hybrid progeny was similarly observed in n-3 PUFA diet fed mice.ConclusionUsing complementary genetic and conventional dietary approaches we provide, for the first time, unequivocal experimental evidence that n-3 PUFA is causally linked to tumor prevention.