Survey of environmental enhancement programs for laboratory primates

Animal welfare regulations in the United States require that nonhuman primate environmental enhancement plans be made in accordance with currently accepted professional standards; however, little information is available for quantifying common practice. Here we report the results of a 2003 survey that was sent to individuals overseeing enrichment programs at a variety of primate research institutions. The surveys requested information on program administration and management, implementation standards, procedures, and constraints pertaining to major categories of environmental enrichment, as well as intervention plans for animals exhibiting behavioral pathologies. Data were obtained on the management of 35,863 primates in 22 facilities. Behavioral scientists performed program oversight at the majority of facilities. Most programs reported recent changes, most commonly due to external site visits, and least commonly resulting from internal review. Most facilities' institutional animal care and use committees (IACUCs) included of individuals with behavioral expertise, and about two-thirds reported that enrichment issues could influence research protocol design. While most primates were reported to be housed socially (73%), social housing for indoor-housed primates appears to have changed little over the past 10 years. Research protocol issues and social incompatibility were commonly cited constraints. Implementation of feeding, manipulanda, and structural enrichment was relatively unconstrained, and contributions to these aspects of behavioral management generally included individuals in a wide variety of positions within a facility. In contrast, enrichment devices were used on a less widespread basis within facilities, and positive reinforcement programs that involved dedicated trainers were rare. We suggest that altering the role of the IACUC would be a productive avenue for increasing the implementation of social housing, and that an emphasis on prevention rather than intervention against behavioral pathology is warranted. The data from this survey may be useful for anticipating future program evaluations, establishing more effective internal evaluations, and assessing program progress and resource allocation.     

Comparison of four enrichment broths for the detection of non-O157 Shiga-toxin-producing Escherichia coli O91, O103, O111, O119, O121, O145 and O165 from pure culture and food samples

Aims: We compared the efficiency of universal pre‐enrichment broth (UPB), modified Escherichia coli broth containing novobiocin (mEC + n), modified Tryptic Soy Broth (mTSB) and mTSB with novobiocin (mTSB + n) for the enrichment of non‐O157 Shiga‐toxin‐producing E. coli (STEC). Methods and Results: Freeze‐injured and control non‐O157 STEC (O91, O103, O111, O119, O121, O145 and O165) strains were used to artificially contaminate beef and radish sprout samples, which were then cultivated in each of the four enrichment media. After incubation, STEC strains were detected by loop‐mediated isothermal amplification (LAMP) and plating assays. Enrichment in mEC + n was least effective for facilitating the detection of uninjured STEC strains in radish sprouts, while mTSB + n was least effective for enriching freeze‐injured non‐O157 STEC strains from beef samples for detection by LAMP assay. UPB and mTSB were superior to mEC + n and mTSB + n for the enrichment of non‐O157 STEC from food samples. Conclusions: The enrichment of non‐O157 STEC was negatively affected by the addition of novobiocin to enrichment broths. Significance and Impact of the study: Novobiocin should not be added to media used for the enrichment of non‐O157 STEC in food when cell injury is anticipated.     

Becoming a better swimmer: structural complexity enhances agility in a captive‐reared fish

To test whether swimming skills can be improved by exposure to structurally complex environments, juvenile rainbow trout Oncorhynchus mykiss were reared in either physically enriched or plain tanks for 2 months and were then screened to test their ability to swim along a channel while avoiding obstructions. The results show that even a relatively short exposure period to enrichment improves O. mykiss swimming agility.     

Integrative computational evaluation of genetic markers for Alzheimer’s disease

Recent studies have reported hundreds of genes linked to Alzheimer’s Disease (AD). However, many of these candidate genes may be not identified in different studies when analyses were replicated. Moreover, results could be controversial. Here, we proposed a computational workflow to curate and evaluate AD related genes. The method integrates large scale literature knowledge data and gene expression data that were acquired from postmortem human brain regions (AD case/control: 31/32 and 22/8). Pathway Enrichment, Sub-Network Enrichment, and Gene-Gene Interaction analysis were conducted to study the pathogenic profile of the candidate genes, with 4 metrics proposed and validated for each gene. By using our approach, a scalable AD genetic database was developed, including AD related genes, pathways, diseases and info of supporting references. The AD case/control classification supported the effectiveness of the 4 proposed metrics, which successfully identified 21 well-studied AD genes (i.g. TGFB1, CTNNB1, APP, IL1B, PSEN1, PTGS2, IL6, VEGFA, SOD1, AKT1, CDK5, TNF, GSK3B, TP53, CCL2, BDNF, NGF, IGF1, SIRT1, AGER and TLR) and highlighted one recently reported AD gene (i.g. ITGB1). The computational biology approach and the AD database developed in this study provide a valuable resource which may facilitate the understanding of the AD genetic profile.     

On‐plate‐selective enrichment of glycopeptides using boronic acid‐modified gold nanoparticles for direct MALDI‐QIT‐TOF MS analysis

In this study, an on‐plate‐selective enrichment method is developed for fast and efficient glycopeptide investigation. Gold nanoparticles were first spotted and sintered on a stainless‐steel plate, then modified with 4‐mercaptophenylboronic acid to provide porous substrate with large specific surface and dual functions. These spots were used to selectively capture glycopeptides from peptide mixtures and the captured target peptides could be analyzed by MALDI‐MS simply by deposition of 2,5‐dihydroxybenzoic acid matrix. Horseradish peroxidase was employed as a standard glycoprotein to investigate the enrichment efficiency. In this way, the enrichment, washing and detection steps can all be fulfilled on a single MALDI target plate. The relatively small sample amount needed, low detection limit and rapid selective enrichment have made this on‐plate strategy promising for online enrichment of glycopeptides, which could be applied in high‐throughput proteome research.     

Highly Efficient Identification of O‐GalNAc Glycosylation by an Acid‐Assisted Glycoform Simplification Approach

Compared with N‐linked glycosylation, the analysis of O‐GalNAc glycosylation is extremely challenging due to the high structure diversity of glycans and lack of glycosidases to release O‐GalNAc glycans. In this work, a glycoform simplification strategy by combining HILIC enrichment with chemical de‐sialylation to characterize O‐GalNAc glycosylation of human serum is presented. This method is first validated by using the bovine fetuin as the test sample. It is found that more than 90% of the sialic acid residues can be removed from bovine fetuin by the acid‐assisted de‐sialylation method, which significantly simplifies the glycan structure and improves identification sensitivity. Indeed, the number of identified peptide backbones increases nearly one fold when this strategy is used. This method is further applied to analyze the human serum sample, where 185 O‐GalNAc modified peptide sequences corresponding to 94 proteins with high confidence (FDR (false detection rate) <1%) are identified. This straight forward strategy can significantly reduce the variations of glycan structures, and is applicable to analysis of other biological samples with high complexity.     

Nematode Indicators of Organic Enrichment

The organisms of the soil food web, dependent on resources from plants or on amendment from other sources, respond characteristically to enrichment of their environment by organic matter. Primary consumers of the incoming substrate, including bacteria, fungi, plant-feeding nematodes, annelids, and some microarthropods, are entry-level indicators of enrichment. However, the quantification of abundance and biomass of this diverse group, as an indicator of resource status, requires a plethora of extraction and assessment techniques. Soluble organic compounds are absorbed by bacteria and fungi, while fungi also degrade more recalcitrant sources. These organisms are potential indicators of the nature of incoming substrate, but current methods of biomass determination do not reliably indicate their community composition. Guilds of nematodes that feed on bacteria (e.g., Rhabditidae, Panagrolaimidae) and fungi (e.g., Aphelenchidae, Aphelenchoididae) are responsive to changes in abundance of their food. Through direct herbivory, plant-feeding nematodes (e.g., many species of Tylenchina) also contribute to food web resources. Thus, analysis of the nematode community of a single sample provides indication of carbon flow through an important herbivore channel and through channels mediated by bacteria and fungi. Some nematode guilds are more responsive than others to resource enrichment. Generally, those bacterivores with short lifecycles and high reproductive potential (e.g., Rhabditidae) most closely mirror the bloom of bacteria or respond most rapidly to active plant growth. The feeding habits of some groups remain unclear. For example, nematodes of the Tylenchidae may constitute 30% or more of the individuals in a soil sample; further study is necessary to determine which resource channels they portray and the appropriate level of taxonomic resolution for this group. A graphic representation of the relative biomass of bacterivorous, fungivorous, and herbivorous nematodes provides a useful tool for assessing the importance of the bacterial, fungal, and plant resource channels in an extant food web.     

Soil GHG fluxes are altered by N deposition: New data indicate lower N stimulation of the N2O flux and greater stimulation of the calculated C pools

The effects of nitrogen (N) deposition on soil organic carbon (C) and greenhouse gas (GHG) emissions in terrestrial ecosystems are the main drivers affecting GHG budgets under global climate change. Although many studies have been conducted on this topic, we still have little understanding of how N deposition affects soil C pools and GHG budgets at the global scale. We synthesized a comprehensive dataset of 275 sites from multiple terrestrial ecosystems around the world and quantified the responses of the global soil C pool and GHG fluxes induced by N enrichment. The results showed that the soil organic C concentration and the soil CO₂, CH₄ and N₂O emissions increased by an average of 3.7%, 0.3%, 24.3% and 91.3% under N enrichment, respectively, and that the soil CH₄ uptake decreased by 6.0%. Furthermore, the percentage increase in N₂O emissions (91.3%) was two times lower than that (215%) reported by Liu and Greaver (Ecology Letters, 2009, 12:1103–1117). There was also greater stimulation of soil C pools (15.70 kg C ha^?1 year^?1 per kg N ha^?1 year^?1) than previously reported under N deposition globally. The global N deposition results showed that croplands were the largest GHG sources (calculated as CO₂ equivalents), followed by wetlands. However, forests and grasslands were two important GHG sinks. Globally, N deposition increased the terrestrial soil C sink by 6.34 Pg CO₂/year. It also increased net soil GHG emissions by 10.20 Pg CO₂‐Geq (CO₂ equivalents)/year. Therefore, N deposition not only increased the size of the soil C pool but also increased global GHG emissions, as calculated by the global warming potential approach.     

乳腺癌致病microRNA调控网络的识别与生物信息学分析

目的:构建并解析乳腺癌致病microRNA(miRNA)调控网络,探究其在乳腺癌发生发展中的调控机制。方法:整合TCGA、ENCODE、Fantom等公共数据库资源,得到miRNA、转录因子和基因候选调控关系数据,结合差异表达、变异系数与PCA,构建乳腺癌miRNA调控网络,解析调控网络的度中心性与聚类系数,使用DAVID进行功能富集分析,构建Cox回归模型作生存曲线。结果:共识别miRNA调控网络262个,其中包含5个显著差异表达miRNA,8个转录因子和130个基因。通过功能富集分析发现这些miRNA靶基因显著参与细胞周期、细胞分化、细胞生长、转移等转录后调控的肿瘤生物进程,并与FoxO信号通路、p53信号通路、基因监测通路等信号通路高度相关。通过分析生存曲线发现hsa-mir-144与hsa-mir-133a-2显著与乳腺癌患者生存相关。结论:识别的乳腺癌致病miRNA调控网络中miRNA之间有相互作用,且网络整体功能不仅受hub网络影响,也受元件自身特性影响,这些miRNA靶基因显著富集于肿瘤相关生物学进程与信号通路中。     

Experimental conditions improving in‐solution target enrichment for ancient DNA

High‐throughput sequencing has dramatically fostered ancient DNA research in recent years. Shotgun sequencing, however, does not necessarily appear as the best‐suited approach due to the extensive contamination of samples with exogenous environmental microbial DNA. DNA capture‐enrichment methods represent cost‐effective alternatives that increase the sequencing focus on the endogenous fraction, whether it is from mitochondrial or nuclear genomes, or parts thereof. Here, we explored experimental parameters that could impact the efficacy of MYbaits in‐solution capture assays of ~5000 nuclear loci or the whole genome. We found that varying quantities of the starting probes had only moderate effect on capture outcomes. Starting DNA, probe tiling, the hybridization temperature and the proportion of endogenous DNA all affected the assay, however. Additionally, probe features such as their GC content, number of CpG dinucleotides, sequence complexity and entropy and self‐annealing properties need to be carefully addressed during the design stage of the capture assay. The experimental conditions and probe molecular features identified in this study will improve the recovery of genetic information extracted from degraded and ancient remains.     

两个糙皮侧耳菌株的比较基因组学研究

随着糙皮侧耳基因组测序的完成,基因组数据的深入挖掘和利用成为研究重点。本研究基于较高质量的糙皮侧耳CCMSSC00389-1和CCMSSC03989-1基因组图谱,开展了种内比较基因组学分析。CCMSSC00389-1和CCMSSC03989-1的11条染色体序列表现出良好的共线性,且分别含有89.92%和91.68%的保守基因。对菌株特有基因的GO富集分析表明,两菌株各自分化出一些独特的调控方式或途径。CCMSSC00389-1和CCMSSC03989-1之间共存在931 542个单核苷酸多态性位点,231 654个插入/缺失和9 221个结构变异。对与遗传变异重叠基因的GO富集分析表明,碳水化合物降解、物质运输/催化和调控/蛋白活性相关的基因分别容易发生SNP、In/Del和SV变异。CCMSSC00389-1中50.326kb缺失序列的断点两侧含有双链断裂修复（DSB）信号,推测DSB介导50.326kb序列的缺失。     

Mining functional gene modules linked with rheumatoid arthritis using a SNP-SNP network

The identification of functional gene modules that are derived from integration of information from different types of networks is a powerful strategy for interpreting the etiology of complex diseases such as rheumatoid arthritis (RA). Genetic variants are known to increase the risk of developing RA. Here, a novel method, the construction of a genetic network, was used to mine functional gene modules linked with RA. A polymorphism interaction analy-sis (PIA) algorithm was used to obtain cooperating single nucleotide polymorphisms (SNPs) that contribute to RA disease. The acquired SNP pairs were used to construct a SNP-SNP network. Sub-networks defined by hub SNPs were then extracted and turned into gene modules by mapping SNPs to genes using dbSNP database. We per-formed Gene Ontology (GO) analysis on each gene module, and some GO terms enriched in the gene modules can be used to investigate clustered gene function for better understanding RA pathogenesis. This method was applied to the Genetic Analysis Workshop 15 (GAW 15) RA dataset. The results show that genes involved in func-tional gene modules, such as CD160 (rs744877) and RUNX1 (rs2051179), are especially relevant to RA, which is supported by previous reports. Furthermore, the 43 SNPs involved in the identified gene modules were found to be the best classifiers when used as variables for sample classification.     

基于基因表达变异性的通路富集方法研究

当前的通路富集方法主要是基于基因的表达差异,很少有方法从通路变异性(方差)角度对其富集分析．我们注意到用合适的统计量描述通路的变异性时,在疾病表型下一些通路的变异性有明显的上升或者下降．因此本研究假设：通路变异性程度在不同表型中存在差异．本文设计了14种描述通路变异性的统计量与检验方法,检测不同表型下变异性有差异的通路即富集通路,并将富集结果与文献检索结果进行比较,同时,分析不同芯片预处理方法对数据和结果的影响．研究结果表明：5种预处理方法中,多阵列对数健壮算法(RMA)是数据预处理的最优方法;不同表型下通路的变异性程度存在差异;根据文献检索的通路结果,14种基于变异性的通路富集方法中,以通路中各基因欧氏距离的方差做统计量进行permutation检验(方法11)能有效识别显著通路,其富集结果优于基因集富集分析(GSEA)．综上所述,基于通路变异性的通路富集策略具有可行性,不仅对通路富集分析有一定的理论指导意义,而且为人类疾病研究提供新的视角．