A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Digital Image Processing of Electron Micrographs: The PIC System II

The PIC system, an integrated package of Fortran programs and subroutines designed to run on the Digital Equipment Corporation VAX family of computers, has been developed for analysis of electron micrographs with emphasis on the particular requirements for structural analysis of biological macromolecules. The substantially improved VAX version of PIC reported here has been developed from an earlier PDP-11 version which was, in turn, developed from a set of IBM 370 programs called MDPP. PIC now encompasses over 150 commands or processing operations that afford a comprehensive range of image processing operations including image restoration, enhancement, Fourier analysis, correlation averaging, and multivariate statistical analysis including clustering and classification. In particular, we describe our software for correction of imperfect lattices, as well as programs for correlation alignment and averaging of single particle images

ANISOTROPIC, SORPTION AND FILTERING PROPERTIES OF THIN-LAYER POLYMER MATERIALS

The paper presents the results of studies on the production of thin-layer nanofiber non-woven materials based on silk fibroin and acrylonitrile copolymer by the electrospinning method. The dependence of anisotropy characterizing the structural states of the obtained thin-layer polymeric materials on deformation effects, their sorption and filtration properties has been studied. The broad possibility of using nanofiber nonwoven materials as nanofilters and the efficiency of the filtration process of nonwoven materials with an increase in the size of their nanopores are shown.Keywords: Polymer, Silk Fibroin, Acrylonitrile Copolymer, Electrospinning, Isotropic, Anisotropic, Orientation, Nanofiber, Nanomaterial, Formation, Structure, Deformation, Nanofilter

DNA Authentication of St John’s Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region

open access articleThere is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 103 ITS copies µL−1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected

Methods for Joint Normalization and Comparison of Hi-C data

The development of chromatin conformation capture technology has opened new avenues of study into the 3D structure and function of the genome. Chromatin structure is known to influence gene regulation, and differences in structure are now emerging as a mechanism of regulation between, e.g., cell differentiation and disease vs. normal states. Hi-C sequencing technology now provides a way to study the 3D interactions of the chromatin over the whole genome. However, like all sequencing technologies, Hi-C suffers from several forms of bias stemming from both the technology and the DNA sequence itself. Several normalization methods have been developed for normalizing individual Hi-C datasets, but little work has been done on developing joint normalization methods for comparing two or more Hi-C datasets. To make full use of Hi-C data, joint normalization and statistical comparison techniques are needed to carry out experiments to identify regions where chromatin structure differs between conditions. We develop methods for the joint normalization and comparison of two Hi-C datasets, which we then extended to more complex experimental designs. Our normalization method is novel in that it makes use of the distance-dependent nature of chromatin interactions. Our modification of the Minus vs. Average (MA) plot to the Minus vs. Distance (MD) plot allows for a nonparametric data-driven normalization technique using loess smoothing. Additionally, we present a simple statistical method using Z-scores for detecting differentially interacting regions between two datasets. Our initial method was published as the Bioconductor R package HiCcompare [http://bioconductor.org/packages/HiCcompare/](http://bioconductor.org/packages/HiCcompare/). We then further extended our normalization and comparison method for use in complex Hi-C experiments with more than two datasets and optional covariates. We extended the normalization method to jointly normalize any number of Hi-C datasets by using a cyclic loess procedure on the MD plot. The cyclic loess normalization technique can remove between dataset biases efficiently and effectively even when several datasets are analyzed at one time. Our comparison method implements a generalized linear model-based approach for comparing complex Hi-C experiments, which may have more than two groups and additional covariates. The extended methods are also available as a Bioconductor R package [http://bioconductor.org/packages/multiHiCcompare/](http://bioconductor.org/packages/multiHiCcompare/). Finally, we demonstrate the use of HiCcompare and multiHiCcompare in several test cases on real data in addition to comparing them to other similar methods (https://doi.org/10.1002/cpbi.76)

THE INFLUENCE OF FULVIC ACID ON COPPER(II), CADMIUM(II) AND ZINC(II) REMOVAL FROM DRINKING WATER BY ALUM COAGULATION AND COPPER(II) AND CADMIUM(II) COMPLEXING CAPACITY MEASUREMENTS OF FULVIC ACID AND NATURAL FRESHWATER SAMPLES BY DIALYSIS TITRATION

The metal ion complexing chemistry of organic ligands commonly found in drinking water sources is the object of the studies in this dissertation. These ligands, called humics as a class, were modelled in some cases by a soil-derived humic material called fulvic acid. The role of natural humics in the transport and speciation of dissolved metal ions in drinking water sources, particularly health hazards like Cd(\u272+), is investigated. Some properties of soil-derived fulvic acid (SFA) were also elucidated. One study modelled a drinking water clarification and decolorizing process using aluminum hydroxide coagulation to measure Cd(\u272+), Zn(\u272+) and Cu(\u272+) removal from solution by the coagulation treatment. The effect of SFA on these metal ion removals was determined in a statistically designed experiment where the relative effects of changing metal ion concentration, Al(\u273+) concentration, solution pH, and SFA concentration on metal ion removal were revealed. Over the variable levels used in the experiment, increasing pH from 5 to 7, and increasing Al(\u273+) dosage caused the greatest overall increase in Cu(\u272+), Cd(\u272+) and Zn(\u272+) removal. Fulvic acid, representing naturally-occurring humics, aided metal ion removal when enough aluminum coagulant was used to remove all dissolved fulvic acid. When insufficient coagulant was used and some fulvic acid remained in solution, the humic material stabilized dissolved metal ions by formation of a soluble metal ion complex and resolubilized metal ions ordinarily coprecipitated with the aluminum hydroxide floc. Cu(\u272+) is very effectively removed on average (\u3e 90%) under the experimental conditions, but Cd(\u272+) and Zn(\u272+) are not (\u3c 20%). To perform the metal ion removal experiment, and to filter natural water samples with no substantial metal ion losses due to wall effects or contaminations, a microfilter apparatus was assembled and evaluated. The apparatus has all plastic surfaces for solution contact and allows vacuum filtration directly into a polypropylene receiving vessel, thereby eliminating the need for a filter flask. Cu(\u272+) losses and contaminations during filtration of standard Cu(\u272+) solutions through the plastic filter apparatus or a glass filter support, with cellulose acetate or polycarbonate filter membranes, were measured in a statistically designed experiment. The results show small Cu(\u272+) losses with the plastic filter support and either membrane (0-13% losses) compared to the glass support with either membrane (25-79% losses). The use of an all plastic filter apparatus for the filtration of natural water samples is recommended to minimize changes to the native levels of dissolved metal ions. A dialysis separation technique, where complexed and unbound metal ions are distinguished in the determination of natural freshwater metal ion binding capacities, was evaluated in another study. The dialysis technique metal ion binding results could not be distinguished from potentiometric titration results in a statistical comparison of the two methods. Nomenclature to describe metal ion binding in natural water systems was suggested. A brief literature survey of metal ion binding studies was described. The dialysis technique was applied to the measurement of 6.25 (mu)M EDTA, 15.5 (mu)M SFA and seven natural water sample capacities of Cu(\u272+) and Cd(\u272+) complexation. The metal ion binding capacities of SFA increased with pH and Cu(\u272+)-SFA capacities were greater than Cd(\u272+)-SFA capacities at the same pH. The Cu(\u272+) binding ability of the natural water samples correlates negatively with their alkalinity, pH, hardness and conductance. Cd(\u272+) binding capacities did not correlate well with any water sample characteristic

Specialized prefrontal “auditory fields”: organization of primate prefrontal-temporal pathways

No other modality is more frequently represented in the prefrontal cortex than the auditory, but the role of auditory information in prefrontal functions is not well understood. Pathways from auditory association cortices reach distinct sites in the lateral, orbital, and medial surfaces of the prefrontal cortex in rhesus monkeys. Among prefrontal areas, frontopolar area 10 has the densest interconnections with auditory association areas, spanning a large antero-posterior extent of the superior temporal gyrus from the temporal pole to auditory parabelt and belt regions. Moreover, auditory pathways make up the largest component of the extrinsic connections of area 10, suggesting a special relationship with the auditory modality. Here we review anatomic evidence showing that frontopolar area 10 is indeed the main frontal “auditory field” as the major recipient of auditory input in the frontal lobe and chief source of output to auditory cortices. Area 10 is thought to be the functional node for the most complex cognitive tasks of multitasking and keeping track of information for future decisions. These patterns suggest that the auditory association links of area 10 are critical for complex cognition. The first part of this review focuses on the organization of prefrontal-auditory pathways at the level of the system and the synapse, with a particular emphasis on area 10. Then we explore ideas on how the elusive role of area 10 in complex cognition may be related to the specialized relationship with auditory association cortices