AnthropMMD: An R package with a graphical user interface for the mean measure of divergence

The mean measure of divergence is a dissimilarity measure between groups of individuals described by dichotomous variables. It is well suited to datasets with many missing values, and it is generally used to compute distance matrices and represent phenograms. Although often used in biological anthropology and archaeozoology, this method suffers from a lack of implementation in common statistical software. A package for the R statistical software, AnthropMMD, is presented here. Offering a dynamic graphical user interface, it is the first one dedicated to Smith's mean measure of divergence. The package also provides facilities for graphical representations and the crucial step of trait selection, so that the entire analysis can be performed through the graphical user interface. Its use is demonstrated using an artificial dataset, and the impact of trait selection is discussed. Finally, AnthropMMD is compared to three other free tools available for calculating the mean measure of divergence, and is proven to be consistent with them.     

获取生物物种名录信息的R程序包SP2000

物种名录为衡量区域和全球生物多样性提供了数据基础。随着互联网的兴起与发展, 人们将地球上已知的动物、植物、微生物等类群的物种名录信息存储到公共数据平台中, 并对物种名录进行快速及时地更新, 这极大地促进了分类学、保护生物学和宏观生态学等学科的发展, 成为政府或国际组织开展物种保育现状评估、红色名录编撰和生物多样性保护的重要依据。物种2000中国节点(http://www.sp2000.org.cn)和Catalogue of Life网站(http://www.catalogueoflife.org)分别是中国和全球最大的生物物种名录数据平台, 截至2020年6月4日, 其收录的物种数分别为122,280种和1,829,672种。然而这些数据平台仅提供物种查询、检索、下载等基本功能, 难以满足使用者准确、快速地批量获取所需生物物种名录数据信息的需求, 制约了这些大数据平台在生物多样性研究和保护中的作用。因此, 我们选取R语言开发了程序包SP2000, 旨在帮助用户批量获取中国或全球生物物种名录信息。该程序包具有跨Windows、MacOS、Linux等多个系统运行、操作便捷、代码开源等特点。为了方便用户使用, 本文详细介绍了SP2000的基本原理、特点及使用指南, 包括程序包的下载、安装、运行和参数设置等。     

BioFTF: An R package for biodiversity assessment with the functional data analysis approach

This paper presents the R package BioFTF, which is a tool for statistical biodiversity assessment in the functional data analysis framework. Diversity is a key topic in many research fields; however, in the literature, it is demonstrated that the existing indices do not capture the different aspects of this concept. Thus, a main drawback is that different indicators may lead to different orderings among communities according to their biodiversity. A possible method to evaluate biodiversity consists in using diversity profiles that are curves depending on a specific parameter. In this setting, it is possible to adopt some functional instruments proposed in the literature, such as the first and second derivatives, the curvature, the radius of curvature and the arc length. Specifically, the derivatives and the curvature (or the radius of curvature) highlight any peculiar behaviour of the profiles, whereas the arc length helps in ranking curves, given the richness. Because these instruments do not solve the issue of ranking communities with different numbers of species, we propose an important methodological contribution that introduces the surface area. Indeed, this tool is a scalar measure that reflects the information provided by the biodiversity profile and allows for ordering communities with different richness. However, this approach requires mathematical skills that the average user may not have; thus, our idea is to provide a user-friendly tool for both non-statistician and statistician practitioners to measure biodiversity in a functional context.     

EcoGenetics: An R package for the management and exploratory analysis of spatial data in landscape genetics

The integration of ecology and genetics has become established in recent decades, in hand with the development of new technologies, whose implementation is allowing an improvement of the tools used for data analysis. In a landscape genetics context, integrative management of population information from different sources can make spatial studies involving phenotypic, genotypic and environmental data simpler, more accessible and faster. Tools for exploratory analysis of autocorrelation can help to uncover the spatial genetic structure of populations and generate appropriate hypotheses in searching for possible causes and consequences of their spatial processes. This study presents EcoGenetics, an R package with tools for multisource management and exploratory analysis in landscape genetics.     

shinyChromosome:An R/Shiny Application for Interactive Creation of Non-circular Plots of Whole Genomes

Non-circular plots of whole genomes are natural representations of genomic data aligned along all chromosomes.Currently,there is no specialized graphical user interface(GUI) designed to produce non-circular whole genome diagrams,and the use of existing tools requires considerable coding effort from users.Moreover,such tools also require improvement,including the addition of new functionalities.To address these issues,we developed a new R/Shiny application,named shiny Chromosome,as a GUI for the interactive creation of non-circular whole genome diagrams.shiny Chromosome can be easily installed on personal computers for own use as well as on local or public servers for community use.Publication-quality images can be readily generated and annotated from user input using diverse widgets.shiny Chromosome is deployed at http://150.109.59.144:3838/shiny Chromosome/,http://shiny Chromosome.ncpgr.cn,and https://yimingyu.shinyapps.io/shiny Chromosome for online use.The source code and manual of shiny Chromosome are freely available at https://github.com/venyao/shiny Chromosome.     

Ratio of ellipticities between 192 and 208 nm (R1): An effective electronic circular dichroism parameter for characterization of the helical components of proteins and peptides

Circular dichroism (CD) spectroscopy represents an important tool for characterization of the peptide and protein secondary structures that mainly arise from the conformational disposition of the peptide backbone in solution. In 1991 Manning and Woody proposed that, in addition to the signal intensity, the ratio between and ((R₂ ) ? [θ]₂₂₂/[θ]₂₀₈), along with and ((R₁ ) ? [θ]₁₉₂/[θ]₂₀₈), may be utilized towards identifying the peptide/protein conformation (especially 3₁₀‐ and α‐helices). However, till date the use of the ratiometric ellipticity component for helical structure analysis of peptides and proteins has not been reported. We studied a series of temperature dependent CD spectra of a thermally stable, model helical peptide and its related analogs in water as a function of added 2,2,2‐trifluoroethanol (TFE) in order to explore their landscape of helicity. For the first time, we have experimentally shown here that the R₁ parameter can characterize better the individual helices, while the other parameter R₂ and the signal intensity do not always converge. We emphasize the use of the R₁ ratio of ellipticities for helical characterization because of the common origin of these two bands (exciton splitting of the amide π→ π* transition in a helical polypeptide). This approach may become worthwhile and timely with the increasing accessibility of CD synchrotron sources.     

The effect of ring size on vibrational spectroscopy and hydrogen bonding properties for the complexes between small ring carbonyl compounds with HF and HCl: Theoretical analysis

The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom.     

A field portable system for the measurement of gas exchange of leaves under natural and controlled conditions: examples with field-grown Eucalyptus pauciflora Sieb. ex Spreng. ssp. pauciflora, E. behriana F. Muell. and Pinus radiata R. Don.

Abstract A field portable system is described which measures the response of gas exchange of one leaf to changes in environmental parameters under controlled conditions, and which simultaneously measures the gas exchange of another leaf as the climatic parameters vary naturally. The system consists of two independently operating cuvettes. It enables detailed studies of photosynthesis and stomata/transpiration of leaves attached to the plant in their natural position. It provides control of temperature, humidity, CO₂ and oxygen concentration (or, alternatively, of other gases) as well as of light. Infrared gas analyzers for CO₂ and H₂O are used which allow similar time constants for the measurement of the two gases. Examples of a diurnal course of gas exchange of a leaf in its natural exposition and of experiments with steady-state responses of gas exchange are presented. In Eucalyptus pauciflora Sieb. ex Spreng. ssp. pauciflora, a set of response curves of CO, assimilation (A) to CO₂, as measured at various leaf temperatures and light levels, shows carboxylation efficiency to be light saturated at the lower photon irradiances the lower the leaf temperature is. Carboxylation efficiency is maximal at 25°C. At ambient CO, partial pressure stomata open in a way that CO₂ assimilation occurs at a rate found within the curvature region of the CO₂ response function of A. The light-independent CO² compensation point as a function of temperature is presented. Applying a combined heat/low humidity pulse (15 or 60 min) on leaves of Eucalyptus behriana F. Muell. or Pinus radiata R. Don, respectively, leads to a lower level of intercellular carbon dioxide partial pressure (C_i) during the decline in A and leaf conductance to water vapour (g). A lower C_i level is maintained during recovery of A and g, A almost reaching the pre-pulse level but not g. The existence of an after-effect indicates that the response to the combined high temperature/low humidity pulse is a multi-step process.     

N-terminal extended conjugates of the agonists and antagonists of both bradykinin receptor subtypes: structure-activity relationship, cell imaging using ligands conjugated with fluorophores and prospect for functionally active cargoes

Peptide agonists and antagonists of both bradykinin (BK) B(1) and B(2) receptors (B(1)R, B(2)R) are known to tolerate to a certain level N-terminal sequence extensions. Using this strategy, we produced and characterized the full set of fluorescent ligands by extending both agonists and antagonist peptides at both receptor subtypes with 5(6)-carboxyfluorescein (CF) and the ε-aminocaproyl (ε-ACA) optional spacer. Alternatively, kinin receptor ligands were extended with another carboxylic acid cargo (chlorambucil, biotinyl, pentafluorocinnamoyl, AlexaFluor-350 (AF350), ferrocenoyl, cetirizine) or with fluorescein isothiocyanate. N-terminal extension always reduced receptor affinity, more importantly for bulkier substituents and more so for the agonist version compared to the antagonist. This loss was generally alleviated by the presence of the spacer and modulated by the species of origin for the receptor. We report and review the pharmacological properties of these N-terminally extended peptides and the use of fluorophore-conjugated ligands in imaging of cell receptors and of angiotensin converting enzyme (ACE) in intact cells. Antagonists (B(1)R: B-10376: CF-ε-ACA-Lys-Lys-[Hyp(3), CpG(5), D-Tic(7), CpG(8)]des-Arg(9)-BK; B(2)R: B-10380: CF-ε-ACA-D-Arg-[Hyp(3), Igl(5), D-Igl(7), Oic(8)]-BK and fluorescein-5-thiocarbamoyl (FTC)-B-9430) label the plasma membrane of cells expressing the cognate receptors. The B(2)R agonists CF-ε-ACA-BK, AF350-ε-ACA-BK and FTC-B-9972 are found in endosomes and model the endosomal degradation of BK in a complementary manner. The uneven surface fluorescence associated to the B(1)R agonist B-10378 (CF-ε-ACA-Lys-des-Arg(9)-BK) is compatible with a particular form of agonist-induced receptor translocation. CF-ε-ACA-BK binds to the carboxydipeptidase ACE with an affinity identical to that of BK. Metal- or drug-containing cargoes further show the prospect of ligands that confer special signaling to kinin receptors.