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51.
[目的] 比较持续母乳喂养条件下不同分娩方式的34周龄婴儿肠道菌群差异,探讨分娩方式对较大婴儿肠道菌群发育的影响。[方法] 在北京地区招募健康足月分娩母乳喂养婴儿,在34周仍然参与随访的持续母乳喂养婴儿共21例,其中剖宫产婴儿16例、阴道分娩婴儿5例,进行肠道菌群的16S rRNA检测。[结果] 两组共21个粪便样本中,共注释到6个门,分别为:疣微菌门、变形菌门、梭杆菌门、厚壁菌门、放线菌门和拟杆菌门;两组共21个样本中共有57个OTU注释到属水平,其中,26个属水平OTU被注释到厚壁菌门,18个属水平OTU被注释到变形菌门,6个属水平OTU被注释到放线菌门,5个属水平OTU被注释到拟杆菌门,梭杆菌门、疣微菌门各有1个属水平OTU被注释。其中变形菌门在阴道分娩组(44.17%)肠道菌群中的含量高于剖宫产组(16.10%);而放线菌门在阴道分娩婴儿(0.00%)肠道菌群中的含量低于剖宫产婴儿(0.09%)。阴道分娩组与剖宫产组相比,共有7个菌属的丰度发生了显著降低(P<0.05),分别为副杆菌属、葡萄球菌属、嗜血杆菌属、乳杆菌属、肠球菌属、双歧杆菌属及一注释到科水平的毛螺旋菌科OTU。[结论] 分娩方式对持续母乳喂养的婴儿肠道菌群结构存在影响,且这种影响在出生后34周仍然存在。 相似文献
52.
53.
Barry J. Grant Lars Skjrven Xin‐Qiu Yao 《Protein science : a publication of the Protein Society》2021,30(1):20-30
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and dynamics. Major functionality includes biomolecular database searching and retrieval, sequence and structure conservation analysis, ensemble normal mode analysis, protein structure and correlation network analysis, principal component, and related multivariate analysis methods. Here, we review recent package developments, including a new underlying segregation into separate packages for distinct analysis, and introduce a new method for structure analysis named ensemble difference distance matrix analysis (eDDM). The eDDM approach calculates and compares atomic distance matrices across large sets of homologous atomic structures to help identify the residue wise determinants underlying specific functional processes. An eDDM workflow is detailed along with an example application to a large protein family. As a new member of the Bio3D family, the Bio3D‐eddm package supports both experimental and theoretical simulation‐generated structures, is integrated with other methods for dissecting sequence‐structure–function relationships, and can be used in a highly automated and reproducible manner. Bio3D is distributed as an integrated set of platform independent open source R packages available from: http://thegrantlab.org/bio3d/ . 相似文献
54.
关中平原麦玉轮作体系作物秸秆不同还田模式下土壤有机碳和无机碳库变化特征 总被引:1,自引:0,他引:1
为探究不同秸秆还田模式对土壤碳库的影响,以陕西关中平原连续11年麦玉秸秆还田定位试验为基础,选择5种还田模式,即秸秆均不还田(CK)、小麦高留茬-玉米秸秆粉碎还田(WH-MC)、小麦玉米秸秆均粉碎还田(WC-MC)、小麦高留茬-玉米秸秆不还田(WH-MN)和小麦秸秆粉碎还田-玉米秸秆不还田(WC-MN),测定不同模式土壤有机碳(SOC)、活性碳组分和无机碳(SIC)在0~40 cm土层的分布。结果表明: 与CK相比,WH-MC和WC-MC的SOC储量分别增加28.1%和22.2%,SIC储量分别增加20.4%和17.3%;与试验初始土壤碳储量相比,各还田模式SOC固持量变化为-0.84~6.55 t·hm-2,SIC固持量为-0.26~8.61 t·hm-2;土壤总固碳效率为7.5%,维持土壤初始碳储量水平的最小碳投入量为4.65 t·hm-2·a-1;与CK相比,WH-MC和WC-MC显著提升0~20 cm土层活性碳组分含量。主成分分析表明,不同还田模式下土壤碳库变化主要受秸秆投入量的影响。来源于灌溉水和植物残体的Ca2+、Mg2+与SOC矿化产生的CO2可共沉淀形成CaCO3,可能是本研究SIC增加的主要机制。从提高土壤碳固持角度来看,小麦高留茬-玉米秸秆粉碎还田模式为最佳还田模式。 相似文献
55.
目的探讨不同分娩方式对婴儿出生后1年内肠道菌群定植的影响。方法选取45例新生儿为研究对象,根据分娩方式分为自然分娩组(n=27)和剖宫产组(n=18)。收集婴儿出生后0(胎粪)、3、6和12个月的粪便标本,应用高通量测序技术分析肠道菌群多样性及组成。结果与自然分娩组比较,在0个月时剖宫产组婴儿粪便标本拟杆菌门的相对丰度显著降低(Z=-2.374 1,P=0.017 6)。2组研究对象中,除自然分娩组和剖宫产组0个月时婴儿粪便标本分别以埃希菌-志贺菌属和克雷伯菌属为优势菌属外,余下均以双歧杆菌属为优势菌属。相比于自然分娩组,在0个月时剖宫产组婴儿粪便标本埃希菌-志贺菌属和肠杆菌属所占比例显著降低(Z=-2.136 4,P=0.032 7;Z=-2.940 8,P=0.003 3),克雷伯菌属和罗氏菌属所占比例显著升高(Z=-2.642 4,P=0.008 2;Z=-2.299 4,P=0.021 5);6个月时罗氏菌属所占比例显著降低(Z=-2.045 0,P=0.040 9),肠球菌属所占比例显著升高(Z=-2.109 2,P=0.034 9)。结论不同分娩方式下的婴儿肠道菌群的构成存在显著差异。 相似文献
56.
Velmurugan Karthikraja Abishek Suresh Sajitha Lulu Uma Kangueane Pandjassarame Kangueane 《Bioinformation》2009,4(3):101-111
Homodimers have a role in catalysis and regulation through the formation of stable interfaces. These interfaces are formed through different
folding mechanisms such as 2-state without stable intermediate (2S), 3-state with monomer intermediate (3SMI) and 3-state with dimer
intermediate (3SDI). Therefore, it is of interest to understand folding mechanism using structural features at the interfaces. Several studies have
documented the significance of structural features for the understanding of homodimer folding mechanisms. However, the known features
provide limited information for understanding homodimer folding mechanisms. Hence, we created an extended dataset of 47 homodimers (twenty
eight 2S, twelve 3SMI and seven 3SDI) to examine the types of interfaces in protein homodimers. 2S are usually small sized, 3SMI are often
medium sized and 3SDI often exist as large sized proteins. The ratio of interface to total (I/T) residue is large in 2S and small in 3SMI and 3SDI.
Hence, we used I/T measure to group 2S, 3SMI and 3SDI into categories with large I/T (≫ 50%), moderate I/T (50 - 25%) and small I/T (≪ 25%)
interfaces. The grouping is further sub-grouped based on the type of physical interaction visualized at the interface using representations in two
dimensions (2D). 2D representation of the interface shows eight different forms of interactions in these homodimers. 2S homodimers frequently
have large I/T and thus, utilize the entire protein structure in the formation of the interface where the individual subunits are heavily inter
communicated with each other. This is not true in the case of 3SMI and 3SDI. 3SMI subunits usually interact with each other at the interface with
a gentle touch-like contact and hence, they have low I/T ratio. 3SDI are often quite different in interaction compared to 3SMI and their subunits
do deeply interact at the interface with only one part of the surface and hence also having low I/T ratio. 相似文献
57.
Pesticide ecotoxicological effect factors and their uncertainties for freshwater ecosystems 总被引:1,自引:1,他引:0
Rosalie van Zelm Mark A. J. Huijbregts Leo Posthuma Arjen Wintersen Dik van de Meent 《The International Journal of Life Cycle Assessment》2009,14(1):43-51
Background, aim, and scope Characterization factors for ecotoxicity in the Life Cycle Impact Assessment (LCIA) are used to convert emissions into ecotoxicological
impacts. Deriving them involves a fate and an effect analysis step. The fate factor quantifies the change in environmental
concentration per unit of emission, while the effect factor quantifies the change in impact on the ecosystem per unit of environmental
concentration. This paper calculates freshwater ecotoxicological effect factors for 397 pesticides belonging to 11 pesticide-specific
toxic modes of action (TMoA), such as acetylcholinesterase inhibition and photosynthesis inhibition. Moreover, uncertainties
in the effect factors due to uncertain background concentrations and due to limited toxicity data are quantified.
Methods To calculate median ecotoxicological effect factors (EEFs), toxic pressure assessments were made, based on the species sensitivity
distribution—and the multisubstance potentially affected fraction—concept. The EEF quantifies an estimate of the fraction
of species that is probably affected due to a marginal change in concentration of a pesticide. EEFs were divided into a TMoA-specific
and a chemical-specific part, which were calculated on the basis of physicochemical properties, emissions, and toxicity data.
Propagation of parameter uncertainty in the EEFs and the TMoA- and chemical-specific parts was quantified by Monte Carlo simulation
and results were reported as 90% confidence intervals.
Results Median EEFs range from 2·10−3 to 7·106 l/g. Uncertainty in the TMoA-specific part is dominated by uncertainty in the TMoA-specific spread in species sensitivity
and by uncertainty in the effective toxicity of a TMoA. Uncertainty in the chemical-specific part of the EEFs depends on the
number of species for which toxicity data are available to calculate average toxicity (n
s) and ranges from a median uncertainty of 2.6 orders of magnitude for n
s = 2 to one order of magnitude for n
s ≥ 4. The TMoA-specific effect factor for systemic fungicides shows the largest uncertainty range. For seven TMoAs, uncertainty
ranges of the TMoA-specific effect factor are less than two orders of magnitude. For the other four TMoAs, the EEF uncertainty
range is between two and eight orders of magnitude. For the chemical-specific part of the EEFs, we found that variation in
uncertainty readily decreases for pesticides for which toxicity data are available for at least three species.
Discussion The same parameters that contributed most to uncertainty were found for pesticides as were found before for high-production-volume
chemicals. However, uncertainty in concentrations of pesticides was lower. TMoA-specific factors obtained with the applied
nonlinear method differ up to nine orders of magnitude from the factor of 0.5, which is used in the linear method. With the
applied method, a distinction in EEFs can be made among different TMoAs.
Conclusions Ecotoxicological effect factors are presented, including overviews of their uncertainty ranges and the main contributors to
uncertainty. The applied nonlinear method provides the possibility to quantify parameter uncertainty in the TMoA-specific
part of the ecotoxicological effect factor, which is helpful to get more insight in how uncertainty in ecotoxicological characterization
factors can be reduced.
Recommendations and perspectives The calculated uncertainty ranges can be included in life cycle assessment (LCA) case studies, which allows for better interpretation
of LCA results obtained with the EEFs. To put the uncertainty in effect factors into perspective within LCIA, more information
on the uncertainty in fate factors should be derived.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. 相似文献
58.
Wenjun Zheng 《Proteins》2009,76(3):747-762
F1 ATPase, a rotary motor comprised of a central stalk ( γ subunit) enclosed by three α and β subunits alternately arranged in a hexamer, features highly cooperative binding and hydrolysis of ATP. Despite steady progress in biophysical, biochemical, and computational studies of this fascinating motor, the structural basis for cooperative ATPase involving its three catalytic sites remains not fully understood. To illuminate this key mechanistic puzzle, we have employed a coarse‐grained elastic network model to probe the allosteric couplings underlying the cyclic conformational transition in F1 ATPase at a residue level of detail. We will elucidate how ATP binding and product (ADP and phosphate) release at two catalytic sites are coupled with the rotation of γ subunit via various domain motions in α 3 β 3 hexamer (including intrasubunit hinge‐bending motions in β subunits and intersubunit rigid‐body rotations between adjacent α and β subunits). To this end, we have used a normal‐mode‐based correlation analysis to quantify the allosteric couplings of these domain motions to local motions at catalytic sites and the rotation of γ subunit. We have then identified key amino acid residues involved in the above couplings, some of which have been validated against past studies of mutated and γ ‐truncated F1 ATPase. Our finding strongly supports a binding change mechanism where ATP binding to the empty catalytic site triggers a series of intra‐ and intersubunit domain motions leading to ATP hydrolysis and product release at the other two closed catalytic sites. Proteins 2009. © 2009 Wiley‐Liss, Inc. 相似文献
59.
Neuronal growth cones are motile structures located at the end of axons that translate extracellular guidance information into directional movements. Despite the important role of growth cones in neuronal development and regeneration, relatively little is known about the topography and mechanical properties of distinct subcellular growth cone regions under live conditions. In this study, we used the AFM to study the P domain, T zone, and C domain of live Aplysia growth cones. The average height of these regions was calculated from contact mode AFM images to be 183 ± 33, 690 ± 274, and 1322 ± 164 nm, respectively. These findings are consistent with data derived from dynamic mode images of live and contact mode images of fixed growth cones. Nano-indentation measurements indicate that the elastic moduli of the C domain and T zone ruffling region ranged between 3-7 and 7-23 kPa, respectively. The range of the measured elastic modulus of the P domain was 10-40 kPa. High resolution images of the P domain suggest its relatively high elastic modulus results from a dense meshwork of actin filaments in lamellipodia and from actin bundles in the filopodia. The increased mechanical stiffness of the P and T domains is likely important to support and transduce tension that develops during growth cone steering. 相似文献
60.
Using different endothelial/smooth muscle cell co-culture modes to simulate the intimal structure of blood vessels, the water filtration rate and the infiltration/accumulation of LDL of the cultured cell layers were studied. The three cell culture modes of the study were: (i) The endothelial cell monolayer (EC/Φ); (ii) endothelial cells directly co-cultured on the smooth muscle cell monolayer (EC-SMC); (iii) endothelial cells and smooth muscle cells cultured on different sides of a Millicell-CM membrane (EC/SMC). It was found that under the same condition, the water filtration rate was the lowest for the EC/SMC mode and the highest for the EC/Φ mode, while the infiltration/accumulation of DiI-LDLs was the lowest in the EC/Φ mode and the highest in the EC-SMC mode. It was also found that DiI-LDL infiltration/accumulation in the cultured cell layers increased with the increasing water filtration rate. The results from the in vitro model study therefore suggest that the infiltration/accumulation of the lipids within the arterial wall is positively correlated with concentration polarization of atherogenic lipids, and the integrity of the endothelium plays an important role in the penetration and accumulation of atherogenic lipids in blood vessel walls. 相似文献