Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations

Chemical modification or radiation can cause DNA damage, which plays a crucial role for mutagenesis of DNA, carcinogenesis, and aging. DNA damage can also alter the fine structure of DNA that may serve as a recognition signal for DNA repair enzymes. A new, advanced sampling replica-exchange method has been developed to specifically enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) simulations. The approach employs specific biasing potentials acting on pairs of pseudodihedral angles of the nucleic acid backbone that are added in the replica simulations to promote transitions of the most common substates of the DNA backbone. The sampled states can exchange with a reference simulation under the control of the original force field. The application to 7,8-dihydro-8oxo-guanosine, one of the most common oxidative damage in DNA indicated better convergence of sampled states during 10 ns simulations compared to 20 times longer standard MD simulations. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions, including explicit solvent and ions. The biasing potential-replica exchange MD simulations indicated significant differences in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine compared to a regular guanosine in the same sequence context. This concerns both the ratio of the B-DNA substates B_I and B_II associated with the backbone dihedral angles ε and ζ but also coupled changes in the backbone dihedral angles α and γ. Such differences may play a crucial role in the initial recognition of damaged DNA by repair enzymes.     

Differential protein input in the maternal diet alters the skeletal muscle transcriptome in fetal sheep

Mammalian Genome - Maternal nutrition during pregnancy is one of the major intrauterine environmental factors that influence fetal development by significantly altering the expression of genes that...     

环境因子对新疆鹅喉羚群体遗传多样性的影响

环境因素在物种进化和遗传变异过程中起着非常重要的作用。为探讨新疆鹅喉羚遗传多样性与环境因子的关系,本研究采用聚合酶链式反应（PCR）和直接测序的方法,测定了新疆鹅喉羚11个群体84份样本的线粒体DNA Cyt b基因（1140 bp）和D-loop区（1100 bp）序列,分析各群体遗传多样性及环境因子对遗传多样性的影响。结果显示新疆鹅喉羚具有较高的单倍型多样性,较低的核苷酸多样性,表明其遗传多样性处于较低水平。环境因子与群体遗传多样性的相关性分析结果表明,海拔、年均降水量、年均气温、人口数量是影响新疆鹅喉羚遗传多样性的主要环境因子,其中海拔是最关键的环境因子。本研究结论为新疆鹅喉羚群体有效合理的保护与管理提供理论依据。     

Spinach-based RNA mimicking GFP in plant cells

Functional & Integrative Genomics - Spinach RNA-mimicking GFP (S-RMG) has been successfully used to monitor cellular RNAs including microRNAs in bacterium, yeast, and human cells. However,...     

Rheological Behaviour of Instant Hot Chocolate Beverage: Part 1. Optimization of the Effect of Different Starches and Gums

In this study, effects of different starches (tapioca (TS), wheat (WS), corn (CS), potato (PS), modified corn (MCS) and modified potato (MPS)) and gums (xanthan gum (XG), guar gum (GG), alginate (A), salep (S), locust bean gum (LBG) and carrageen (C)) on the rheological properties of model hot chocolate beverage were studied. Swelling power (SP) of the starches and water absorption capacity (WAC) of the gums were determined. Hot chocolate beverages showed pseudoplastic behaviour. Ostwald de Waele model accurately described flow behaviour of each beverage sample. K, n, R ² values for Ostwald model were in the range of 4.8–160.3 mPa.sⁿ, 0.5117–0.9745, 0.9972–0.9998, respectively. The highest synergic effect in the model was observed between the interaction of MCS and XG. The XG-PS, XG-TS, XG-CS combinations showed the highest K and viscosity values, respectively.     

黑果枸杞不同组织内生细菌群落多样性

【目的】黑果枸杞是我国荒漠区特有的药用盐生植物,本研究分析了黑果枸杞不同组织中内生细菌群落多样性特征及分布规律。【方法】应用Illumina MiSeq高通量测序技术对黑果枸杞内生细菌的16S rRNAV5-V7区域序列进行测定,并分析群落组成、多样性及功能等生物学信息。【结果】黑果枸杞不同组织内生细菌群落多样性及功能均有较大的差异。花、叶、果、茎和根产生的OTUs分别是182、173、119、187和254,群落多样性表现为根花果、茎叶。从门水平上看,变形菌门是优势菌门,在不同组织中均有分布,花、叶、果、茎和根中的相对丰度分别为87.66%、41.51%、81.76%、97.67%和61.85%。在属水平上显示内生细菌的分布表现出器官差异性。花部能够准确分类的优势菌属为沙雷氏菌属和不动杆菌属,相对丰度分别为11.57%和8.55%。叶部为红球菌属和慢生根瘤菌属,相对丰度分别为29.68%和5.53%。果实中为泛菌属、红球菌属和沙雷氏菌属,相对丰度分别为23.12%、5.52%和4.29%。茎部为沙雷氏菌属和假单胞菌属,相对丰度分别为12.03%和17.71%。根部为盐单胞菌属、Fodinicurvata和Lipingzhangella,相对丰度分别为24.18%、5.16%和4.86%。在不同组织中分布较广的盐单胞菌、沙雷氏菌、不动杆菌、红球菌、泛菌等菌属均具有较高耐盐性和促生、生防、降解有机污染物及抗氧化等功能。PICRUSt功能预测分析显示,黑果枸杞组织中内生细菌功能中涉及丰富的多糖、萜类和酮类、酶及维他命等次生代谢产物的生物合成。【结论】黑果枸杞内生细菌具有丰富的群落和功能多样性,拥有多种益生功能性状,也含有多个与人和植物体代谢相关的功能信息。不同组织优势菌属和功能信息各有不同,其中根部的内生细菌物种最丰富,花部和茎部参与各种代谢调控的细菌丰度最高。此外,不同组织中还含有大量未知种属的微生物类群,这些都为内生细菌功能利用和挖掘新的有益微生物资源提供广阔的发展空间。