DeltAMT: a statistical algorithm for fast detection of protein modifications from LC-MS/MS data

Identification of proteins and their modifications via liquid chromatography-tandem mass spectrometry is an important task for the field of proteomics. However, because of the complexity of tandem mass spectra, the majority of the spectra cannot be identified. The presence of unanticipated protein modifications is among the major reasons for the low spectral identification rate. The conventional database search approach to protein identification has inherent difficulties in comprehensive detection of protein modifications. In recent years, increasing efforts have been devoted to developing unrestrictive approaches to modification identification, but they often suffer from their lack of speed. This paper presents a statistical algorithm named DeltAMT (Delta Accurate Mass and Time) for fast detection of abundant protein modifications from tandem mass spectra with high-accuracy precursor masses. The algorithm is based on the fact that the modified and unmodified versions of a peptide are usually present simultaneously in a sample and their spectra are correlated with each other in precursor masses and retention times. By representing each pair of spectra as a delta mass and time vector, bivariate Gaussian mixture models are used to detect modification-related spectral pairs. Unlike previous approaches to unrestrictive modification identification that mainly rely upon the fragment information and the mass dimension in liquid chromatography-tandem mass spectrometry, the proposed algorithm makes the most of precursor information. Thus, it is highly efficient while being accurate and sensitive. On two published data sets, the algorithm effectively detected various modifications and other interesting events, yielding deep insights into the data. Based on these discoveries, the spectral identification rates were significantly increased and many modified peptides were identified.     

A complete solution for dissecting pure main and epistatic effects of QTL in triple testcross design

Epistasis plays an important role in genetics, evolution and crop breeding. To detect the epistasis, triple test cross (TTC) design had been developed several decades ago. Classical procedures for the TTC design use only linear transformations Z(1), Z(2) and Z(3), calculated from the TTC family means of quantitative trait, to infer the nature of the collective additive, dominance and epistatic effects of all the genes. Although several quantitative trait loci (QTL) mapping approaches in the TTC design have been developed, these approaches do not provide a complete solution for dissecting pure main and epistatic effects. In this study, therefore, we developed a two-step approach to estimate all pure main and epistatic effects in the F(2)-based TTC design under the F(2) and F(∞) metric models. In the first step, with Z(1) and Z(2) the augmented main and epistatic effects in the full genetic model that simultaneously considered all putative QTL on the whole genome were estimated using empirical Bayes approach, and with Z(3) three pure epistatic effects were obtained using two-dimensional genome scans. In the second step, the three pure epistatic effects obtained in the first step were integrated with the augmented epistatic and main effects for the further estimation of all other pure effects. A series of Monte Carlo simulation experiments has been carried out to confirm the proposed method. The results from simulation experiments show that: 1) the newly defined genetic parameters could be rightly identified with satisfactory statistical power and precision; 2) the F(2)-based TTC design was superior to the F(2) and F(2:3) designs; 3) with Z(1) and Z(2) the statistical powers for the detection of augmented epistatic effects were substantively affected by the signs of pure epistatic effects; and 4) with Z(3) the estimation of pure epistatic effects required large sample size and family replication number. The extension of the proposed method in this study to other base populations was further discussed.     

光强在低温弱光胁迫后番茄叶片光合作用恢复中的作用

为了研究光强在低温弱光胁迫后番茄叶片光合作用恢复中的作用,以番茄品种浙粉202为材料,研究了低温弱光后恢复期全光照与遮荫对光合作用和叶绿素荧光参数的影响。结果表明：低温弱光（8℃/12℃,PFD 80 μmol·m^-2·s^-1）导致番茄叶片P_n、Φ_PSⅡ、qP和F_v′/F_m′的下降,但诱导了NPQ的上升,未引起F_v/F_m的变化;全光照（100%光照）下恢复1 使得植株叶片P_n、F_v/F_m、Φ_PSⅡ、qP、NPQ和F_v′/F_m′均大幅下降,随后光合和荧光参数可缓慢恢复至对照水平;遮荫（40%光照）恢复植株F_v/F_m、Φ_PSⅡ和F_v′/F_m′仅在第一天稍有下降,而P_n和qP还略有上升,NPQ虽有所降低但仍显著高于对照水平,随后光合和荧光参数均可迅速恢复到对照水平。说明低温弱光虽抑制了光合作用的进行,但并未引起光抑制的发生;全光照恢复加剧了叶片光抑制的发生,而遮荫恢复可通过叶片PSⅡ光化学活性的快速恢复和天线色素热耗散能力的增强以保护光合机构免受伤害,有利于光合作用的迅速恢复。     

一次性可调压限压式灌肠器的实验研究

目的:研究一次性可调压限压式灌肠器的性能。方法:建立模型,测定模拟体内环境下灌肠治疗时肠管各点的压力和灌肠器可调压限压阀开启时的压力是否一致。结果:测定模拟肠管各点压力与灌肠器的可调压限压阀开启时压力一致。结论:一次性可调压限压式灌肠器的性能达到设计要求,操作简便,具有科学性、稳定性、安全性,值得推广。     

黄麻两个栽培种及其野生类型与三个近缘种的核型分析

本研究选取黄麻属（Corchorus）2个栽培品种及其4个野生类型和3个野生近缘种为材料,采用常规根尖压片法对黄麻属供试材料的染色体数目和核型进行研究。结果表明：染色体数目均为2n=14。核型公式分别为：宽叶长果（长果黄麻栽培种）2n=2x=14=14m(4SAT);南阳野生长果（长果黄麻野生类型）2n=2x=14=14m(2SAT);坦桑尼亚野生长果（长果黄麻野生类型）2n=2x=14=2M+12m;闽麻5号（圆果黄麻栽培种）2n=2x=14=12m+2sm;爱店野生圆果（圆果黄麻野生类型）2n=2x=14=14m ;廉江野生圆果（圆果黄麻野生类型） 2n=2x=14=4M+10m;假黄麻（黄麻属野生近缘种）2n=2x=14=2M+12m;假长果（黄麻属野生近缘种）2n=2x=14=2M+12m;甜麻（黄麻属野生近缘种）2n=2x=14=14m。其中除了宽叶长果核型分类为1B外,其他的都为1A型。本文还讨论了黄麻野生近缘种甜麻的分类学地位。     

克拉维酸生产中废乙酸乙酯的紫外扫描评价方法及树脂处理

建立克拉维酸生产中废乙酸乙酯的快捷评价方法。采用紫外吸收扫描,以吸收面积作为评价指标,全面评价废乙酸乙酯中的杂质残留。选用不同的树脂吸附处理废乙酸乙酯。结果表明:废乙酸乙酯经FPA90Cl树脂吸附处理后,紫外吸收面积最小,仅有225.601±5.499,残留的杂质最少。经条件优化后,批处理量为60 m3废乙酸乙酯的树脂用于克拉维酸生产,产品质量与新乙酸乙酯生产的产品质量相近。使用树脂处理废乙酸乙酯可减轻乙酸乙酯蒸馏回收和环保的压力,降低生产成本,具有良好的经济效益和环境效益。     

绝经后女性心血管危险因素与骨密度的相关关系

目的:本研究的目的是评估绝经后女性冠心病患者心血管危险因素与骨密度的相关关系。方法:评估216例拟行冠脉造影的绝经后女性冠心病患者的危险因素,并于冠脉造影检查前日或次日行骨密度检测,依据T值将受试者分为2组:骨量正常组(T值大于-1SD)、低骨量组(T值小于-1SD)。结果:2组患者在BMI、糖尿病、高血压及吸烟等均无显著性差异。低骨量组冠心病的发生率及年龄显著高于骨量正常组。Logistic回归分析显示绝经后女性冠心病患者年龄与骨密度独立相关(OR=1.072 CI:1.036～1.11p=0.001)。结论:年龄与绝经后女性冠心病患者骨密度负相关,心血管病危险因素或冠心病与骨量不相关。     

Biodiesel production using Aspergillus niger as a whole‐cell biocatalyst in a packed‐bed reactor

Enzymatic lipase transesterification of palm oil to biodiesel in a packed‐bed reactor (PBR) using a novel strain of the fungus Aspergillus niger, immobilized within polyurethane biomass support particles (BSPs), was investigated. A three‐step addition of methanol was used to reduce lipase inhibition by immiscible methanol. The influence of water content and PBR flow rate was investigated. FAME yield was enhanced with an increase of PBR flow rate in the range of 0.15–30 L h^?1, where inefficient mixing of the reaction mixture at lower flow rates resulted in low conversion rates i.e. 69% after 72‐h reaction. Adding the third mole equivalent of methanol resulted in lipase inhibition due to methanol migration into the accumulated glycerol layer. Glutaraldehyde (GA) solution (0.5 vol.%) was used to stabilize lipase activity, which led to a high FAME yield (>90%) in the PBR after 72‐h of reaction time at a flow rate of 15 L h^?1, and a water content of 15%. Moreover, a high conversion rate (>85%) was maintained after four palm oil batch conversion cycles in the PBR. In contrast, lipase activity of non‐GA‐treated cells decreased with each PBR batch cycle, where only 70% FAME was produced after the forth PBR cycle. Transesterification of palm oil in a PBR system using BSPs‐immobilized A. niger as a whole‐cell biocatalyst is a viable process for enzymatic biodiesel production.     

Human anti-V3 HIV-1 monoclonal antibodies encoded by the VH5-51/VL lambda genes define a conserved antigenic structure

Preferential usage of immunoglobulin (Ig) genes that encode antibodies (Abs) against various pathogens is rarely observed and the nature of their dominance is unclear in the context of stochastic recombination of Ig genes. The hypothesis that restricted usage of Ig genes predetermines the antibody specificity was tested in this study of 18 human anti-V3 monoclonal Abs (mAbs) generated from unrelated individuals infected with various subtypes of HIV-1, all of which preferentially used pairing of the VH5-51 and VL lambda genes. Crystallographic analysis of five VH5-51/VL lambda-encoded Fabs complexed with various V3 peptides revealed a common three dimensional (3D) shape of the antigen-binding sites primarily determined by the four complementarity determining regions (CDR) for the heavy (H) and light (L) chains: specifically, the H1, H2, L1 and L2 domains. The CDR H3 domain did not contribute to the shape of the binding pocket, as it had different lengths, sequences and conformations for each mAb. The same shape of the binding site was further confirmed by the identical backbone conformation exhibited by V3 peptides in complex with Fabs which fully adapted to the binding pocket and the same key contact residues, mainly germline-encoded in the heavy and light chains of five Fabs. Finally, the VH5-51 anti-V3 mAbs recognized an epitope with an identical 3D structure which is mimicked by a single mimotope recognized by the majority of VH5-51-derived mAbs but not by other V3 mAbs. These data suggest that the identification of preferentially used Ig genes by neutralizing mAbs may define conserved epitopes in the diverse virus envelopes. This will be useful information for designing vaccine immunogen inducing cross-neutralizing Abs.