Estimating sampling error of evolutionary statistics based on genetic covariance matrices using maximum likelihood

We explore the estimation of uncertainty in evolutionary parameters using a recently devised approach for resampling entire additive genetic variance–covariance matrices ( G ). Large‐sample theory shows that maximum‐likelihood estimates (including restricted maximum likelihood, REML) asymptotically have a multivariate normal distribution, with covariance matrix derived from the inverse of the information matrix, and mean equal to the estimated G . This suggests that sampling estimates of G from this distribution can be used to assess the variability of estimates of G , and of functions of G . We refer to this as the REML‐MVN method. This has been implemented in the mixed‐model program WOMBAT. Estimates of sampling variances from REML‐MVN were compared to those from the parametric bootstrap and from a Bayesian Markov chain Monte Carlo (MCMC) approach (implemented in the R package MCMCglmm). We apply each approach to evolvability statistics previously estimated for a large, 20‐dimensional data set for Drosophila wings. REML‐MVN and MCMC sampling variances are close to those estimated with the parametric bootstrap. Both slightly underestimate the error in the best‐estimated aspects of the G matrix. REML analysis supports the previous conclusion that the G matrix for this population is full rank. REML‐MVN is computationally very efficient, making it an attractive alternative to both data resampling and MCMC approaches to assessing confidence in parameters of evolutionary interest.     

Optimizing resolution in multidimensional NMR by three-way decomposition

Resolution depends on the number of points sampled in a FID; in indirectly detected dimensions it is an important determinant of the total experiment time. Based on the high redundancy present in NMR data, we propose the following timesaving scheme for three-dimensional spectra. An extensive grid of discrete t1- and t2-values is used, which increases resolution while preserving the spectral width. Total experiment time is reduced by avoiding the recording of t3-FIDs for selected pairs of t1 and t2; typically the recording is omitted for about 75% of the (t1,t2) combinations. These data sets are referred to as sparse, and post-experimental processing making optimal use of spectral redundancy provides the missing, non-recorded data. We have previously shown that three-way decomposition (TWD) within the MUNIN approach provides a practical way to process dense NMR data sets. Here, a novel TWD algorithm [Ibraghimov, (2002) Numer. Linear Algebra Appl. 9, 551–565] is used to complement a sparselyrecorded time-domain data set by providing the missing FIDs for all (t1,t2) combinations omitted in the experiment. A necessary condition is that for each t1-value at least a few FIDs are recorded, and similar for each t2-value. The method is demonstrated on non-uniformly sampled ¹⁵N-NOESY-HSQC data sets recorded for the 14 kD protein azurin. The spectra obtained by TWD, reconstruction and ordinary transform to frequency-domain are, in spite of the large number of signals and the high dynamic range typical for NOESYs, highly similar to a corresponding reference spectrum, for which all (t1,t2) combinations were recorded.     

Comparison of redox and ligand binding behaviour of yeast and bovine cytochrome c oxidases using FTIR spectroscopy

Redox and CO photolysis FTIR spectra of yeast cytochrome c oxidase WT and mutants are compared to those from bovine and P. denitrificans CcOs in order to establish common functional features. All display changes that can be assigned to their E242 (bovine numbering) equivalent and to weakly H-bonded water molecules. The additional redox-sensitive band reported at 1736?cm^?1 in bovine CcO and previously assigned to D51 is absent from yeast CcO and couldn't be restored by introduction of a D residue at the equivalent position of the yeast protein. Redox spectra of yeast CcO also show much smaller changes in the amide I region, which may relate to structural differences in the region around D51 and the subunit I/II interface.     

基于Nextflow构建的宏条形码自动化分析流程EPPS

基于宏条形码技术的物种快速检测有助于生物多样性的评估、预测和保护。本文介绍了常用宏条形码分析的步骤和参数设定方法。我们利用Nextflow搭建了一款宏条形码分析流程EPPS, 可以自动化地运行从原始数据的质量控制到环境多样性的比较。Nextflow软件还拥有流程监控的功能, 可视化输出每个进程所消耗的时间与内存。本文还使用测试数据和已发表数据证明该平台能够有效地分析宏条形码数据并可靠地分析环境生物多样性的相似性。     

Local cryostimulation acutely preserves maximum isometric handgrip strength following fatigue in young women

Several types of cryostimulation have been recently proposed to rapidly lower skin temperature therefore gaining a possible neuro/muscular recovery after strenuous exercise or, more generally, in sports. Local cryostimulation may be a viable and relatively portable tool to obtain physiological benefits in previously-efforted muscular districts. However, cohesive and standardized cryo-exposure protocols are lacking as well as the righteous procedure to efficaciously combine duration, treatments and temperature in relation to desirable effects on muscular strength. In this randomized-controlled study, fifty young women were tested for maximum isometric handgrip strength, before and after exhausting contractions.Following the fatiguing protocol, the intervention group (cryo, n = 25, 24.7 ± 2.5 years, BMI 21.7 ± 1.8 kg/m²) underwent a 6-min local cryostimulation (−160 °C) on the extensor-flexor muscles of the dominant arm, while control-matched peers sat rested in a thermo-neutral room (22 ± 0.5 °C). Handgrip tests were repeated at baseline (T0), after cryostimulation (T1), and 15 min after T1 (T2). Throughout the protocol, the AUC of the strength performance was significantly higher in the cryo- compared to control group (P = 0.006). In particular, following fatigue and cryostimulation, the cryo group preserved higher strength at T1 with respect to controls (26.8 ± 2.8 vs 23.9 ± 2.8 kg, Bonferroni's post-hoc, P < 0.01). Likewise, ventral and dorsal temperature, recorded with a thermal camera, were lower in cryo- than control group (P < 0.0001).In conclusion, a brief session of local cryostimulation may acutely preserve maximal isometric force in young women following a fatiguing protocol. These findings may have implications in orchestrating strategies of district muscular recovery.     

Xenoestrogenic short ethoxy chain nonylphenol is oxidized by a flavoprotein alcohol dehydrogenase from <Emphasis Type="Italic">Ensifer</Emphasis> sp. strain AS08

The ethoxy chains of short ethoxy chain nonylphenol (NPEO_av2.0, containing average 2.0 ethoxy units) were dehydrogenated by cell-free extracts from Ensifer sp. strain AS08 grown on a basal medium supplemented with NPEO_av2.0. The reaction was coupled with the reduction in 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide and phenazine methosulfate. The enzyme (NPEO_av2.0 dehydrogenase; NPEO-DH) was purified to homogeneity with a yield of 20% and a 56-fold increase in specific activity. The molecular mass of the native enzyme was 120 kDa, consisting of two identical monomer units (60 kDa). The gene encoding NPEO-DH was cloned, which consisted of 1,659 bp, corresponding to a protein of 553 amino acid residues. The deduced amino acid sequence agreed with the N-terminal amino acid sequence of the purified NPEO-DH. The presence of a flavin adenine dinucleotide (FAD)-binding motif and glucose–methanol–choline (GMC) oxidoreductase signature motifs strongly suggested that the enzyme belongs to the GMC oxidoreductase family. The protein exhibited homology (40–45% identity) with several polyethylene glycol dehydrogenases (PEG-DHs) of this family, but the identity was lower than those (approximately 58%) among known PEG-DHs. The substrate-binding domain was more hydrophobic compared with those of glucose oxidase and PEG-DHs. The recombinant protein had the same molecular mass as the purified NPEO-DH and dehydrogenated PEG400-2000, NPEO_av2.0 and its components, and NPEOav10, but only slight or no activity was found using diethylene glycol, triethylene glycol, and PEG200. English edition: The paper was edited by a native speaker through American Journal Experts ().     

犬瘟热病毒XJ株的分离鉴定

应用犬肺原代巨噬细胞,从新疆阿克苏送检的一只病死犬肺脏中分离出1株犬瘟热病毒,并对其进行了形态学、理化学、血清学、动物感染试验、分子生物学鉴定。结果证明所分离的XJ株为1株CDV的强毒株。     

基于表型性状的孔雀草种质遗传多样性分析

为了了解孔雀草种质间的亲缘关系,提高孔雀草种质的利用效率,从18个形态特征对40份孔雀草种质进行了遗传变异分析、主成分分析及聚类分析。结果表明,孔雀草表型多样性丰富,种质间表型性状变异程度高,变异系数(CV值)范围3.92%~46.25%,以花朵数最大,其次是冠幅和株高;Shannon-Weaver多样性指数则以叶片性状及花性状较高,平均2.0以上。国内种质比国外种质多样性更丰富。通过主成分分析,筛选出对总体方差累计贡献率达78.949%的4个主成分,并筛选出综合性状表现良好的种质10份。参试的40份种质在欧氏距离阈值为7.29处可分为两大类,一类植株生长势较强包含2份种质(水星黄色和橙色);其余38份种质为一类,在欧氏距离阈值为6.0处,又以花色差异可进一步划分为2个类群,说明生长势及花色可作为孔雀草种质依据表型性状分类的重要指标。     

Limits of application of initiated chemiluminescence in monitoring of oncological process of mucous membrane of mouth and larynx

Investigation into the limits of application of chemiluminescence (CL) methods in oncology still attracts the attention of researchers. In the present work we analyze the screening and monitoring of oncological processes (OP) in the mucous membrane of the mouth and larynx by initiated CL (ICL). Chemiluminescence has already been used by stomatologists to define the start of OP, but methods that reflect the metabolic changes in organism under cancer diagnostics still have not found their place. This work presents results of ICL on blood serum (BS) of patients with oncological diseases at different stages of medical treatment compared with those of healthy people. We found an essential metabolic difference only in types of OP that are characterized by two maxima on chemiluminograms. These OP represent only 12.81% of groups of patients with oncological diseases. The possibility to apply ICL methods to monitor operation quality and control medical treatment at different stages when the two ICL maxima are present is established. At present, the chemiluminograms with the two maxima are mostly informative, but this does not exclude the quantitative analysis of other ICL kinetic methods and is encouraging for their investigation. Any OP introduces changes in organism function and these should be reflected in the ICL. Copyright © 2016 John Wiley & Sons, Ltd.     

Resonance Raman and FTIR spectroscopic characterization of the closed and open states of channelrhodopsin-1

Channelrhodopsin-1 from Chlamydomonas augustae (CaChR1) is a light-activated cation channel, which is a promising optogenetic tool. We show by resonance Raman spectroscopy and retinal extraction followed by high pressure liquid chromatography (HPLC) that the isomeric ratio of all-trans to 13-cis of solubilized channelrhodopsin-1 is with 70:30 identical to channelrhodopsin-2 from Chlamydomonas reinhardtii (CrChR2). Critical frequency shifts in the retinal vibrations are identified in the Raman spectrum upon transition to the open (conductive P₂³⁸⁰) state. Fourier transform infrared spectroscopy (FTIR) spectra indicate different structures of the open states in the two channelrhodopsins as reflected by the amide I bands and the protonation pattern of acidic amino acids.