Silver‐induced conformational changes of polypeptides: a CD study

The role of silver ions in various pathologies, as well as their effect on peptide conformation and properties are less understood. Consequently, we synthesized several peptides with various residues in their sequence to investigate silver‐induced conformational changes at various pH values by Circular Dichroism spectroscopy. Uniquely, the glycine‐based, histidine‐containing peptide showed a severe change from a random coil and β‐turn conformation to large α‐helices during silver binding. When comparing the effect of silver ions on the conformation of bradykinin a similar tendency was found. Besides, silver ions reduced the amyloid‐β peptide tendency to aggregation. Our results suggest a specific and protective role for silver ions in brain pathologies, which is related to their high affinity toward physiologically and pharmacologically active peptides. Fourier transform infrared spectroscopy studies as well as the mass spectrometric ones support our conclusions. Copyright © 2011 European Peptide Society and John Wiley & Sons, Ltd.     

HomeRange: A global database of mammalian home ranges

Motivation

Home range is a common measure of use of space by animals because it provides ecological information that is useful for conservation applications. In macroecological studies, values are typically aggregated to species means to examine general patterns of use of space by animals. However, this ignores the environmental context in which the home range was estimated and does not account for intraspecific variation in home range size. In addition, the focus of macroecological studies on home ranges has historically been biased towards terrestrial mammals. The use of aggregated numbers and the terrestrial focus limit our ability to examine home-range patterns across different environments, their variation in time and variation between different levels of organization. Here, we introduce HomeRange, a global database with 75,611 home-range values across 960 different species of mammals, including terrestrial, aquatic and aerial species.

Main types of variables contained

The dataset contains estimates of home ranges of mammals, species names, methodological information on data collection, method of home-range estimation, period of data collection, study coordinates and name of location, in addition to species traits derived from the studies, such as body mass, life stage, reproductive status and locomotor habit.

Spatial location and grain

The collected data are distributed globally. Across studies, the spatial accuracy varies, with the coarsest resolution being 1°.

Time period and grain

The data represent information published between 1939 and 2022. Across studies, the temporal accuracy varies; some studies report start and end dates specific to the day, whereas for other studies only the month or year is reported.

Major taxa and level of measurement

Mammalian species from 24 of the 27 different taxonomic orders. Home-range estimates range from individual-level values to population-level averages.

Software format

Data are supplied as a comma-delimited text file (.csv) and can be loaded directly into R using the “HomeRange” R package ( https://github.com/SHoeks/HomeRange ).     

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate

Nonsyndromic or isolated cleft lip with or without cleft palate (CL/P) occurs in wide geographic distribution with an average birth prevalence of 1/700. We used direct sequencing as an approach to study candidate genes for CL/P. We report here the results of sequencing on 20 candidate genes for clefts in 184 cases with CL/P selected with an emphasis on severity and positive family history. Genes were selected based on expression patterns, animal models, and/or role in known human clefting syndromes. For seven genes with identified coding mutations that are potentially etiologic, we performed linkage disequilibrium studies as well in 501 family triads (affected child/mother/father). The recently reported MSX1 P147Q mutation was also studied in an additional 1,098 cleft cases. Selected missense mutations were screened in 1,064 controls from unrelated individuals on the Centre d'Étude du Polymorphisme Humain (CEPH) diversity cell line panel. Our aggregate data suggest that point mutations in these candidate genes are likely to contribute to 6% of isolated clefts, particularly those with more severe phenotypes (bilateral cleft of the lip with cleft palate). Additional cases, possibly due to microdeletions or isodisomy, were also detected and may contribute to clefts as well. Sequence analysis alone suggests that point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated cleft lip with or without cleft palate, and the linkage disequilibrium data support a larger, as yet unspecified, role for variants in or near MSX2, JAG2, and SKI. This study also illustrates the need to test large numbers of controls to distinguish rare polymorphic variants and prioritize functional studies for rare point mutations.     

Arabinogalactans and arabinogalactan-proteins induce embryogenesis in wheat (Triticum aestivum L.) microspore culture

The objective of this study was to improve induction of embryogenesis in wheat microspore culture in order to obtain a high number of regenerable embryos. The arabinogalactan (AG) Larcoll and the arabinogalactan-protein (AGP) from gum arabic were tested on two spring genotypes to see if they could increase microspore viability and induce embryogenesis in the microspore culture. Adding Larcoll significantly decreased microspore mortality in both genotypes regardless of the presence or absence of ovaries in the culture. Similarly, gum arabic had a strong effect on the number of embryos produced and regenerated green plants. In fact, by using only gum arabic we were able to obtain green plants from wheat microspore cultures without the presence of ovaries. In addition to preventing a high mortality rate of the cells, our results show that the induction of embryogenesis in wheat microspore cultures is strongly affected by the use of both AG or AGP.An erratum to this article can be found at     

Effect of copper sulfate on experimental atherosclerosis

Serum copper concentration increases significantly (p<0.01) in rats with experimental atherosclerosis compared to a control group. The serum zinc, the zinc, and copper concentration in abdominal aorta and in liver decreases significantly (p<0.05) compared to the control group. Administration of copper sulfate for 100 d in these animals induces a significant increase of serum copper (p<0.01), decrease of serum cholesterol (p<0.05) and increase of liver copper concentration as compared with the group fed only a high cholesterol diet. In the aorta of these animals the copper concentration increases and edema and lipid infiltration are considerably less than in the group of animals fed only a high lipid diet.     

Detection of Low-Level Mixed-Population Drug Resistance in Mycobacterium tuberculosis Using High Fidelity Amplicon Sequencing

Undetected and untreated, low-levels of drug resistant (DR) subpopulations in clinical Mycobacterium tuberculosis (Mtb) infections may lead to development of DR-tuberculosis, potentially resulting in treatment failure. Current phenotypic DR susceptibility testing has a theoretical potential for 1% sensitivity, is not quantitative, and requires several weeks to complete. The use of “single molecule-overlapping reads” (SMOR) analysis with next generation DNA sequencing for determination of ultra-rare target alleles in complex mixtures provides increased sensitivity over standard DNA sequencing. Ligation free amplicon sequencing with SMOR analysis enables the detection of resistant allele subpopulations at ≥0.1% of the total Mtb population in near real-time analysis. We describe the method using standardized mixtures of DNA from resistant and susceptible Mtb isolates and the assay’s performance for detecting ultra-rare DR subpopulations in DNA extracted directly from clinical sputum samples. SMOR analysis enables rapid near real-time detection and tracking of previously undetectable DR sub-populations in clinical samples allowing for the evaluation of the clinical relevance of low-level DR subpopulations. This will provide insights into interventions aimed at suppressing minor DR subpopulations before they become clinically significant.     

Leaf herbivory and fluctuating asymmetry as indicators of mangrove stress

Wetlands Ecology and Management - Fluctuating asymmetry (FA), a widely used measure of developmental instability in plants and animals, which describes random differences in size and/or shape...     

Physiological properties of some yeast strains

Twenty yeast strains have recently been isolated in pure cultures from natural and industrial sources and identified based mainly on physiological properties. The majority of the strains (15) are alcohologenic belonging to the genus Saccharomyces and comprise two brewer's (beer) yeast strains (S. carlsbergensis= S. uvarum A and B), two baker's yeast strains (S. cerevisiae CA and CP), one spirit yeast strain (S. cerevisiae CF) and ten wine yeast strains (S. cerevisiae var. ellipsoideus = S. ellipsoideus 1, 3, 4, 6, 8 and 9; S. oviformis 2, 5 and 7; and S. uvarum 10). The other 5 yeast strains belong to different species: Kloeckera apiculate, Candida mycoderma (Mycoderma vini), Pichia membranaefaciens, Rhodotorula glutinis and Torulopsis holmii, respectively.     

Biochemical differences in Cannabis sativa L. depending on sexual phenotype

Hemp (Cannabis sativa L.) is a species considered as having one of the most complicated mechanisms of sex determination. Peroxidase and esterase isoenzymes in leaves of the two sexual phenotypes of hemp were studied. Significant differences in isoperoxidase and isoesterase patterns were found between male and female plants, both in the number and stain intensity of bands. For both esterase and peroxidase, the isoenzymatic spectrum is richer for staminate plants. Also, some differences are obvious between the two sexes concerning catalase and peroxidase activities, as well as the level of soluble protein. The quantitative analysis of flavones, polyholozides and polyphenols emphasized differences depending not only on sex, but also on tested organ.