Approaches to modeling intramammary infections in dairy cattle

In this paper, three approaches (Markov processes, discrete-event simulation, and differential equations) to modeling intramammary infections (IMI; focusing on the dynamic changes between uninfected, subclinical, and clinical udder-health states) are described. The objectives were to describe the various approaches to modeling intramammary infections, determine if simulations of the examples of the three approaches yield stable prevalences, and discuss the approaches' limitations. The literature review showed that there is no agreement on the proportion of animals that change health states. The approach of discrete-event simulation modeling included the most cow-level risk factors and udder-health states (hence, was judged to replicated best the dynamics of the infection process) and yielded stable prevalences for all udder-health states. However, there remain parts of the dynamics that need further research. These include the pathogen-specific probabilities and times of occurrence for: regression of clinical IMI to subclinical IMI, flare-up of subclinical IMI to clinical IMI, and incidence of subclinical IMI. Also, the assumption in all current approaches of homogenous mixing is violated because the primary contact structure for contagious pathogens during milking is either between cows through residual infectious milk in the milking machine or within a cow by vacuum fluctuations or teat-cup liner slips. Better contact structures should be incorporated so that the effects of control strategies can be better-estimated. Moreover, the three modeling approaches discussed assumed that all non-infected quarters are susceptible to infection—which might be denied by work in genetic resistance.     

草鱼鳃组织蛋白双向电泳技术的建立及优化

为建立并优化草鱼鳃蛋白质组双向电泳的技术体系,实验将草鱼鳃经裂解处理后,通过固相p H梯度胶条进行一向等电聚焦和SDS聚丙烯酰胺凝胶垂直电泳进行蛋白分离,对不同的裂解液配方、蛋白纯化方法、IPG胶条的分离范围、上样量和染色方法等进行了探索和优化,并应用lmage Master 2D Platinum 7.0软件对电泳图谱进行了分析。结果表明:采用裂解液中添加DTT来取代Tris和TBP、选择分离范围为pH4-7的IPG胶条和150μg的主动水化上样,电泳结束后对凝胶进行硝酸银染色,获得了覆盖范围广、低背景、高分辨率、适合差异蛋白分析的双向电泳参考图谱。     

基于RNA-seq数据筛选鸡睾丸附睾间差异表达基因及其功能分析

本文旨在通过对种公鸡睾丸和附睾进行转录组测序和生物信息学分析,筛选出2种组织中的差异表达基因并分析其生物学功能,探究睾丸和附睾在鸡精子发生和成熟过程中的作用.本研究共以8只公鸡的睾丸和附睾组织为对象,采用RNA-seq技术分析2种组织中的基因表达情况,筛选出差异表达基因并对差异表达基因进行GO和KEGG通路富集分析.结...     

Differential evolution algorithm for solving multi-objective crop planning model

This study presents four strategies of a novel evolutionary algorithm, multi-objective differential evolution algorithm (MDEA). The four strategies namely, MDEA1, MDEA2, MDEA3 and MDEA4 are adapted to solve the multi-objective crop planning model with multiple constraints in a farmland in the Vaalharts irrigation scheme (VIS) in South Africa. The three objectives of the model are to minimize the total irrigation water (m²) and to maximize both the total net income in South African Rand (ZAR) from farming and the total agricultural output in tons. The total area of the farm is 771,000 m² and supplied with 704,694 m² of irrigation water annually. Numerical results produce non-dominated solutions which converge to Pareto optimal fronts. MDEA1 and MDEA2 strategies with binomial crossover method are better for solving the crop planning problem presented than MDEA3 and MDEA4 strategies with exponential crossover method. MDEA1 found a solution with the highest total net income of ZAR 1,304,600 with the corresponding total agricultural output, total irrigation water and total planting areas of 316.26 tons, 702,000 m³ and 725,000 m², respectively. The planting areas for the crops in the solution are 73,463 m² for maize, 551,660 m² for groundnut, 50,000 m² for Lucerne and 50,000 m² for Peacan nut. It can be concluded that MDEA is a good algorithm for solving crop planning problem especially in water deficient areas like South Africa.     

分离基因的有效手段-mRNA差异显示技术

mRNA差异显示技术从开始应用至今已经有10年了。在此期间,此项技术也在不断发展完善。简要综述了差异显示技术的基本原理、优越性、存在的主要缺陷及其技术改进等方面的研究进展。     

差异演化算法改进与应用

提出了一种改进的差异演化算法MDE(modified differential evolution algorithm),该算法首先对差异演化算法的缩放因子进行混沌计算,减少了用户参与程度,平衡了算法的收敛速度与全局搜索能力;其次引入灾变因子,对群体中的个体进行小概率淘汰,同时又有新的个体加入,从而提高了群体多样性,提高了算法的全局搜索能力.仿真实验与工程实例表明,该算法具有较好的全局搜索能力.     

日本血吸虫蛋白质组学研究进展

随着日本血吸虫(Schistosoma japonicum)基因组学的发展,应用双向电泳、质谱分析及生物信息学分析开展的蛋白质组学研究正成为日本血吸虫研究的前沿领域。生物体中的基因是相对稳定,但是蛋白质的活动随着生命活动的进行表现出动态的变化,并具有对外界环境发生反应的能力。对日本血吸虫进行蛋白质组学方面的研究,能直接地反映其生理功能的过程。这些研究为研制开发抗日本血吸虫病疫苗、新型治疗药物提供了新的途径。论文从日本血吸虫童虫部分差异表达蛋白、成虫蛋白质的性别差异性、药物相关蛋白组学、免疫蛋白组学等方面,对日本血吸虫蛋白质组学研究做了概述。     

脊尾白虾对低氧响应的转录组学分析

本研究通过高通量测序,分析低氧胁迫下脊尾白虾(Palaemon carincauda)某些基因的差异表达,获得10.62 Gb高质量测序数据,组装得到155113条转录本和118953条Unigene。注释Unigene 37580条。其中,33659条Unigene与Nr蛋白数据库基因同源;11275条Unigene注释到KEGG数据库,归类到223个代谢通路。低氧胁迫产生1392条差异表达基因,包括311条上调基因和1081条下调基因,784条差异基因得到注释,并富集到抗氧化活性、细胞连接、蛋白结合转录因子活性、多细胞生物过程、复制和生殖等过程,表明低氧胁迫激活了虾体适应缺氧的一系列生理活动。其中,低氧胁迫下,低氧诱导因子1(HIF1) 2个亚基HIF1α和HIF1β表达量上调;实时定量测定证实,在胁迫的后期,脊尾白虾肝胰脏和鳃HIF1α和HIF1β明显上调,推测脊尾白虾细胞在低溶氧环境下诱导HIF产生,刺激机体增加血液氧的供应能力。同时,低氧胁迫下,脊尾白虾差异基因富集到糖酵解/葡萄糖生成、精氨酸和脯氨酸代谢和丙酮酸代谢等通路,表明虾体缺氧使糖酵解等无氧代谢途径增强,同时促进了部分糖类和氨基酸的代谢。另外,低氧胁迫下,脊尾白虾溶酶体通路、吞噬通路、过氧化物酶体通路和内吞作用通路的差异基因较多,推测低氧诱导因子可能通过抑制线粒体生物合成和活化线粒体自噬来降低线粒体氧耗。     

弓形虫卵囊感染小鼠的急性期与慢性期的脑组织蛋白质组变化

弓形虫是一种呈世界性分布的机会性致病原虫,可引起致命性脑炎.人弓形虫病急性感染往往与弓形虫卵囊污染密切相关.探究弓形虫卵囊感染对宿主的致病机制和防控弓形虫病具有重要意义.因此,本研究利用iTRAQ技术,结合2D-LC-MS/MS分析弓形虫PRU虫株卵囊急、慢性感染小鼠后,其脑组织蛋白质的差异表达情况.结果 表明,在急性...     

Anabolism,catabolism and proteomic analysis in the slow‐twitch muscle of pacu (Piaractus mesopotamicus) submitted to prolonged fasting followed by refeeding

Here, we aimed to study the slow muscle of the fish Piaractus mesopotamicus submitted to 30 days of fasting (D30) followed by 1 day (D31) or 30 days of refeeding (D60). Histological analysis of fibre diameter was performed in D30 and D60. The gene expression of parvalbumin (pvalb), atrogenes (murf1a, murf1b, mafbx) and anabolic genes (igf‐1, mtor) was analysed using RT‐qPCR in D30, D31 and D60. The proteome was obtained by shotgun proteomics at D30 and D60, and the set of differentially expressed proteins was analysed by bioinformatics. In all experiments, the control was regularly fed fish. The histological analysis showed no changes in muscle fibre diameter. The expression of catabolic and anabolic genes was not changed, except for the downregulation of igf‐1 in D30 and of mafbx in D31. The expression of pvalb was not changed in D30 and D60 but was decreased in D31. The proteomic analysis identified 169 proteins in D30 (24 upregulated and 18 downregulated) and 170 proteins in D60 (17 upregulated and 21 downregulated); many of them were related to energetic metabolism and intracellular Ca²⁺ homoeostasis. Overall, our results indicate that the slow‐twitch muscle presented few changes upon prolonged fasting and refeeding condition.