Allelopathic invasive tree (<Emphasis Type="Italic">Rhamnus cathartica</Emphasis>) alters native plant communities

Many plants release allelopathic chemicals that can inhibit germination, growth, and/or survival in neighboring plants. These impacts appear magnified with the invasion of some non-native plants which may produce allelochemicals against which native fauna have not co-evolved resistance. Our objective was to examine the potential allelopathic impact of an invasive non-native shrub/tree on multiple plant species using field observation and experimental allelopathy studies. We surveyed and collected an invasive, non-native tree/shrub (Rhamnus cathartica) at Tifft Nature Preserve (a 107-ha urban natural area near Lake Erie in Buffalo, NY). We also surveyed understory plant communities in the urban forest to examine correlations between R. cathartica abundance and local plant community abundance and richness. We then used experimental mesocosms to test if patterns observed in the field could be explained by adding increased dosages of R. cathartica to soils containing five plant species, including native and non-native woody and herbaceous species. In the highly invaded urban forest, we found that herbaceous cover, shrubs and woody seedlings negatively covaried with R. cathartica basal area and seedlings density. In the mesocosm experiments, R. cathartica resulted in significant decreases in plant community species richness, abundance, and shifted biomass allocation from roots. Our results provide evidence that R. cathartica is highly allelopathic in its invaded range, that R. cathartica roots have an allelopathic effect and that some plant species appear immune. We suggest that these effects may explain the plant’s ability to form dense monocultures and resist competitors, as well as shift community composition with species-specific impacts.     

Flow cytometric detection of proteolysis in peptide libraries synthesised on optically encoded supports

The concept of optically encoding particles for solid phase organic synthesis has existed in the literature for several years. However, there remains a significant challenge to producing particles that are capable of withstanding harsh solvents and reagents whilst maintaining the integrity and range of the optical encoding. In this study, a new generation of fluorescently encoded support particles was used for both solid phase peptide synthesis and on-particle analysis of proteolysis in a multiplexed, flow cytometric assay. The success of the assay was demonstrated through the use of a model protease, trypsin. Our results show that the use of solid supports with high peptide yield, high swellability in water and high penetration of the enzyme into the interior of the particle is not absolutely necessary for proteolysis assays.     

ProteoWizard: open source software for rapid proteomics tools development

SUMMARY: The ProteoWizard software project provides a modular and extensible set of open-source, cross-platform tools and libraries. The tools perform proteomics data analyses; the libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard proteomics and LCMS dataset computations. The library contains readers and writers of the mzML data format, which has been written using modern C++ techniques and design principles and supports a variety of platforms with native compilers. The software has been specifically released under the Apache v2 license to ensure it can be used in both academic and commercial projects. In addition to the library, we also introduce a rapidly growing set of companion tools whose implementation helps to illustrate the simplicity of developing applications on top of the ProteoWizard library. AVAILABILITY: Cross-platform software that compiles using native compilers (i.e. GCC on Linux, MSVC on Windows and XCode on OSX) is available for download free of charge, at http://proteowizard.sourceforge.net. This website also provides code examples, and documentation. It is our hope the ProteoWizard project will become a standard platform for proteomics development; consequently, code use, contribution and further development are strongly encouraged.     

The effect of traditional management burning on lichen diversity

Question: How does regular management burning of a northern, Calluna vulgaris‐dominated heathland affect the lichen diversity at the patch and landscape scale? Location: Mar Lodge Estate, Scottish Highlands, United Kingdom. Methods: 26 fire sites of different ages and 11 long‐term unburnt stands were surveyed to create a chronosequence of changing lichen diversity following burning. Data were analysed graphically, with a GLM and using a CCA. Results: Though the immediate effect of fire was to significantly reduce lichen diversity, it generally recovered within 20 years. There was a significant difference in the population dynamics between wet and dry moorland areas with terricolous lichens in the former site being replaced by pleurocarpous mosses. Older stands, unburnt for 25 years or more, generally had lower diversity than stands 10 to 15 years old. Changes in lichen diversity and community composition can be attributed to the development of Calluna stand structure following burning. Conclusions: Fire can be seen to play an important role in maintaining the diversity of lichens in heathland areas by providing a variety of stand‐structures and ages across the landscape that favours the development of greater beta‐diversity.     

A mouse to human search for plasma proteome changes associated with pancreatic tumor development

Background

The complexity and heterogeneity of the human plasma proteome have presented significant challenges in the identification of protein changes associated with tumor development. Refined genetically engineered mouse (GEM) models of human cancer have been shown to faithfully recapitulate the molecular, biological, and clinical features of human disease. Here, we sought to exploit the merits of a well-characterized GEM model of pancreatic cancer to determine whether proteomics technologies allow identification of protein changes associated with tumor development and whether such changes are relevant to human pancreatic cancer.

Methods and Findings

Plasma was sampled from mice at early and advanced stages of tumor development and from matched controls. Using a proteomic approach based on extensive protein fractionation, we confidently identified 1,442 proteins that were distributed across seven orders of magnitude of abundance in plasma. Analysis of proteins chosen on the basis of increased levels in plasma from tumor-bearing mice and corroborating protein or RNA expression in tissue documented concordance in the blood from 30 newly diagnosed patients with pancreatic cancer relative to 30 control specimens. A panel of five proteins selected on the basis of their increased level at an early stage of tumor development in the mouse was tested in a blinded study in 26 humans from the CARET (Carotene and Retinol Efficacy Trial) cohort. The panel discriminated pancreatic cancer cases from matched controls in blood specimens obtained between 7 and 13 mo prior to the development of symptoms and clinical diagnosis of pancreatic cancer.

Conclusions

Our findings indicate that GEM models of cancer, in combination with in-depth proteomic analysis, provide a useful strategy to identify candidate markers applicable to human cancer with potential utility for early detection.     

哺乳动物阴茎骨长度与延长性插入模式之间存在正相关的关系

阴茎骨长度增加的进化 ,部分原因与交配模式有关 ,后者涉及到延长性插入持续时间。但是 ,对于北美的食肉动物来说 ,这个假说一直有争议。为了检验这个假说 ,我们收集了来自食肉动物、蝙蝠和灵长类的 1 4 4个属 31 5种哺乳动物阴茎骨长度和体重的数据 ,除了阴茎骨长度和体重以外 ,对已知的 39个属的插入持续时间进行了线形多次回归分析。结果表明 :阴茎骨长度与插入持续时间之间存在极显著的正相关关系 (r2 =0 6 5 ,F=4 0 4 8,P <0 0 0 0 1 )。然后 ,使用了独立对比的比较分析以控制数据系统发育的偏差 ,在物种水平上对数据进行了分析 ,结果证实 :阴茎骨长度与插入持续时间之间有显著的相关关系 (r2 =0 6 9,F =34 2 3,P <0 0 0 1 )。本研究支持阴茎骨长度进化的延长性插入假说