DPHL:A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery

To address the increasing need for detecting and validating protein biomarkers in clinical specimens, mass spectrometry (MS)-based targeted proteomic techniques, including the selected reaction monitoring (SRM), parallel reaction monitoring (PRM), and massively parallel data-independent acquisition (DIA), have been developed. For optimal performance, they require the fragment ion spectra of targeted peptides as prior knowledge. In this report, we describe a MS pipeline and spectral resource to support targeted proteomics studies for human tissue samples. To build the spectral resource, we integrated common open-source MS computational tools to assemble a freely accessible computational workflow based on Docker. We then applied the workflow to generate DPHL, a comprehensive DIA pan-human library, from 1096 data-dependent acquisition (DDA) MS raw files for 16 types of cancer samples. This extensive spectral resource was then applied to a proteomic study of 17 prostate cancer (PCa) patients. Thereafter, PRM validation was applied to a larger study of 57 PCa patients and the differential expression of three proteins in prostate tumor was validated. As a second application, the DPHL spectral resource was applied to a study consisting of plasma samples from 19 diffuse large B cell lymphoma (DLBCL) patients and 18 healthy control subjects. Differentially expressed proteins between DLBCL patients and healthy control subjects were detected by DIA-MS and confirmed by PRM. These data demonstrate that the DPHL supports DIA and PRM MS pipelines for robust protein biomarker discovery. DPHL is freely accessible at https://www.iprox.org/page/project.html?id=IPX0001400000.     

海南坡鹿围栏种群动态与食物资源关系的初步分析

1986年海南省大田国家级自然保护区在境内设立面积为95公顷的围栏,将86只海南坡鹿分隔成一个孤立的种群。经过3个繁殖年度,种群发展到158只。随着种群数量的增加,坡鹿采食植物的种类密度、高度和频率均明显减少,而坡鹿不食的植物种类则明显增加。种群出生率和年度增长率随种群数量增加而逐年降低,而种群死亡率却有增加趋势。种群密度过高产生的拥挤效应和食物资源不足是造成种群出生率和年度增长率下降的主要原因。本文还就保护区应采取的管理措施,提出了相应的建议。     

渤海水母体细菌的微生态分布及弧菌生物学特性

采用稀平板法对我国辽宁渤海海域水母体中细菌的微生态分布进行了考察,结果表明,在渤海水母体中各部位均有腐生性细菌及弧菌生长,其中腐生性细菌主要存在于水母体现,而弧菌除存在于水母体表外,有的则能在水母体内深层生长,水母体细菌微生态研究结果表明,弧菌的占细菌总数的90％以上,通过改进TCBAS培养基,从水母体中分离得到6株优势类群的细菌,对其菌落特征、菌体形态、生理生化特性进行了研究,它们都具备弧菌属的共同特点：革兰氏阴性,氧化酶阳性,兼性厌氧,TCBS培养基上能生长,对O／129敏感,初步鉴定为弧菌属,研究还发现,这几株菌都能产蛋白酶,其中JF2、JF4、JF5、JF6产蛋白酶的能力明显较强,它们极有可能是导致水母捕捞后快速解体腐败的主要原因。     

Insect pest damage increases faba bean (Vicia faba) yield components but only in the absence of insect pollination

Identifying and quantifying crop stressors interactions in agroecosystems is necessary to guide sustainable crop management strategies. Over the last 50 years, faba bean cropping area has been declining, partly due to yield instabilities associated with uneven insect pollination and herbivory. Yet, the effect of interactions between pollinators and a key pest, the broad bean beetle Bruchus rufimanus (florivorous and seed predating herbivore) on faba bean yield has not been investigated. Using a factorial cage experiment in the field, we investigated how interactions between two hypothesized stressors, lack of insect pollination by bumblebees and herbivory by the broad bean beetle, affect faba bean yield. Lack of bumblebee pollination reduced bean weight per plant by 15%. Effects of the broad bean beetle differed between the individual plant and the plant‐stand level (i.e., when averaging individual plant level responses at the cage level), likely due to high variation in the level of herbivory among individual plants. At the individual plant level, herbivory increased several yield components but only in the absence of pollinators, possibly due to plant overcompensation and/or pollination by the broad bean beetle. At the plant‐stand level, we found no effect of the broad bean beetle on yield. However, there was a tendency for heavier individual bean weight with bumblebee pollination, but only in the absence of broad bean beetle herbivory, possibly due to a negative effect of the broad bean beetle on the proportion of legitimate flower visits by bumblebees. This is the first experimental evidence of interactive effects between bumblebees and the broad bean beetle on faba bean yield. Our preliminary findings of negative and indirect associations between the broad bean beetle and individual bean weight call for a better acknowledgment of these interactions in the field in order to understand drivers of crop yield variability in faba bean.     

基于扎根理论的社区参与国家公园建设与管理的机制研究

大量研究表明自然保护地周边社区居民对保护地的态度是影响社区参与保护,实现保护地管理目标的主要因素,由此建立了"认知-态度-参与"的行为逻辑。中国国家公园体制建设希望进一步推进社区与保护地的关系,全面提升自然保护管理效率,也建立在对这一行为逻辑的认同之上。为验证社区认知与行为的关系,并为促进不同利益相关者参与国家公园建设与管理提供科学支持,研究试图分析武夷山国家公园体制试点区社区居民的国家公园的"认知-态度-参与"的行为逻辑以揭示社区参与国家公园建设与管理的深层机制。与一般研究不同在于,本研究是针对正在建设中的国家公园,使得本地利益相关方的态度有机会影响国家公园建设进程。为获得社区"认知-态度-参与"核心观念,探索社区参与的过程和方式,提出促进社区参与的方法,研究采用扎根理论这一质性研究方法,基于对本地利益相关者采用半结构化开放问题的深度访谈,归纳出概念与范畴,形成社区参与国家公园建设与管理的理论。研究首先形成45个概念与13个范畴,通过范式模型研究发现,稳定资源使用权利、引导社区参与决策、保障社区发展权利、创新社区产业模式、提高个体适应能力、降低政策风险影响等六个主范畴能够解释社区居民对国家公园的认知-态度-参与这一行为逻辑。通过归纳主范畴,研究进一步提炼出社区参与国家公园建设与管理的理论核心在于社区自然资源管理的自主性、创新性与适应性,其内在机制在于社区参与是一个自主性提高的动态过程,需要通过保障社区生计资源禀赋来实现长期的价值转化,最终使其成为社会-生态系统适应性治理的组成部分。在理论阐释基础上,研究提出从改善社区认知、提升社区参与角度推进国家公园建设的路径。研究也指出,所提出的社区参与机制理论能够提炼量化指标评价社区参与,追踪武夷山国家公园体制试点进程。     

Evidence for diet partitioning among three coexisting native freshwater fishes in South Africa's Cape Fold Ecoregion

The partitioning of limited resources commonly explains how different species can coexist within the same ecological community. In this 2010 study, the diets of three coexisting freshwater fishes (Cape galaxias Galaxias zebratus, n = 27; Cape kurper Sandelia capensis, n = 60; Breede River redfin Pseudobarbus burchelli, n = 77) were characterised and compared in three headwater streams in South Africa's Cape Fold Ecoregion using gut contents and stable isotope analyses. These data were analysed to ascertain whether the three species exploit distinct trophic niches. Both approaches provided evidence that these species occupy different trophic niches, though with some overlap. However, dietary differences among sites were not consistent and were probably influenced by site-specific factors like resource availability. Pseudobarbus burchelli had a broader niche breadth at Tierkloof Stream than the other two species, but not at Waaihoek or Tierstel Streams. Our results also suggest that P. burchelli consumed a more omnivorous diet than do the other two species, whereas S. capensis occupied a higher trophic position than the other two species and consumed vertebrates. Our findings suggest that these species occupy non-equivalent feeding niches in Cape Fold Ecoregion headwater streams, and that diet partitioning might facilitate their coexistence in these systems.     

A structured analysis of risk to important wildlife elements in three Australian Wildlife Conservancy sanctuaries

Where data and information are lacking, structured expert risk assessments can provide a powerful tool to progress natural resource planning. In many situations, practitioners make informal assessments of risk within small groups that typically constitute employees. In this study, we report on three small (in terms of experts) structured expert‐based risk assessment case studies conducted by expert employees of a not‐for‐profit organisation (Australian Wildlife Conservancy) to demonstrate the utility of the approach. The case studies were carried out for three wildlife sanctuaries managed by AWC: Faure Island, Karakamia and Paruna. The likelihood that a set of direct risk factors would cause management failure for sets of important wildlife elements in the three sanctuaries was elicited from the small group of ecological experts. The analysis was couched in terms of a management aim to not lose species from each wildlife element over the management period of 25 years with current management. The experts believed, in particular, that increasing temperature and decreasing water availability associated with climate change were likely to impact significantly upon the vegetation elements and water‐reliant fauna associated with the sanctuaries. Some vegetation elements were also thought likely to be at risk of over‐grazing, unsuitable fire regimes and, in some cases, disease. In addition to predation by exotic predators at one sanctuary, the experts identified additional direct risk factors for various fauna elements associated with expected changes to the vegetation elements, including reduction in food availability, nesting habitat, and generally important life media. From the risk analyses, a preliminary conceptual model was developed to underpin monitoring and to indicate areas for possible management intervention and research. The case studies demonstrate that even in a small workplace team, structured risk assessments can be efficiently accomplished and can provide expedient and transparent information that effectively captures and aggregates the views of the experts.     

DIAlignR Provides Precise Retention Time Alignment Across Distant Runs in DIA and Targeted Proteomics

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Highlights

• •Retention time shift can lead to inversion of elution order of peptides.
• •Global alignment methods are suboptimal for alignment of distant runs.
• •DIAlignR employs hybrid (global + local) RT alignment approach.
• •DIAlignR can align swapped peaks accurately across distant runs.