Is there a connection between weather at departure sites,onset of migration and timing of soaring‐bird autumn migration in Israel?

Aims Different aspects of soaring‐bird migration are influenced by weather. However, the relationship between weather and the onset of soaring‐bird migration, particularly in autumn, is not clear. Although long‐term migration counts are often unavailable near the breeding areas of many soaring birds in the western Palaearctic, soaring‐bird migration has been systematically monitored in Israel, a region where populations from large geographical areas converge. This study tests several fundamental hypotheses regarding the onset of migration and explores the connection between weather, migration onset and arrival at a distant site. Location Globally gridded meteorological data from the breeding areas in north‐eastern Europe were used as predictive variables in relation to the arrival of soaring migrants in Israel. Methods Inverse modelling was used to study the temporal and spatial influence of weather on initiation of migration based on autumn soaring‐bird migration counts in Israel. Numerous combinations of migration duration and temporal influence of meteorological variables (temperature, sea‐level pressure and precipitable water) were tested with different models for meteorological sensitivity. Results The day of arrival in Israel of white storks, honey buzzards, Levant sparrowhawks and lesser spotted eagles was significantly and strongly related to meteorological conditions in the breeding area days or even weeks before arrival in Israel. The cumulative number of days or cumulative value above or below a meteorological threshold performed significantly better than other models tested. Models provided reliable estimates of migration duration for each species. Main conclusions The meteorological triggers of migration at the breeding grounds differed between species and were related to deteriorating living conditions and deteriorating migratory flight conditions. Soaring birds are sensitive to meteorological triggers at the same period every year and their temporal response to weather appears to be constrained by their annual routine.     

Extinction‐driven changes in frugivore communities on oceanic islands

Global change and human expansion have resulted in many species extinctions worldwide, but the geographic variation and determinants of extinction risk in particular guilds still remain little explored. Here, we quantified insular extinctions of frugivorous vertebrates (including birds, mammals and reptiles) across 74 tropical and subtropical oceanic islands within 20 archipelagos worldwide and investigated extinction in relation to island characteristics (island area, isolation, elevation and climate) and species’ functional traits (body mass, diet and ability to fly). Out of the 74 islands, 33 islands (45%) have records of frugivore extinctions, with one third (mean: 34%, range: 2–100%) of the pre‐extinction frugivore community being lost. Geographic areas with more than 50% loss of pre‐extinction species richness include islands in the Pacific (within Hawaii, Cook Islands and Tonga Islands) and the Indian Ocean (Mascarenes, Seychelles). The proportion of species richness lost from original pre‐extinction communities is highest on small and isolated islands, increases with island elevation, but is unrelated to temperature or precipitation. Large and flightless species had higher extinction probability than small or volant species. Across islands with extinction events, a pronounced downsizing of the frugivore community is observed, with a strong extinction‐driven reduction of mean body mass (mean: 37%, range: –18–100%) and maximum body mass (mean: 51%, range: 0–100%). The results document a substantial trophic downgrading of frugivore communities on oceanic islands worldwide, with a non‐random pattern in relation to geography, island characteristics and species’ functional traits. This implies severe consequences for ecosystem processes that depend on mutualistic plant–animal interactions, including ecosystem dynamics that result from the dispersal of large‐seeded plants by large‐bodied frugivores. We suggest that targeted conservation and rewilding efforts on islands are needed to halt the defaunation of large and non‐volant seed dispersers and to restore frugivore communities and key ecological interactions.     

miRNA normalization enables joint analysis of several datasets to increase sensitivity and to reveal novel miRNAs differentially expressed in breast cancer

Different miRNA profiling protocols and technologies introduce differences in the resulting quantitative expression profiles. These include differences in the presence (and measurability) of certain miRNAs. We present and examine a method based on quantile normalization, Adjusted Quantile Normalization (AQuN), to combine miRNA expression data from multiple studies in breast cancer into a single joint dataset for integrative analysis. By pooling multiple datasets, we obtain increased statistical power, surfacing patterns that do not emerge as statistically significant when separately analyzing these datasets. To merge several datasets, as we do here, one needs to overcome both technical and batch differences between these datasets. We compare several approaches for merging and jointly analyzing miRNA datasets. We investigate the statistical confidence for known results and highlight potential new findings that resulted from the joint analysis using AQuN. In particular, we detect several miRNAs to be differentially expressed in estrogen receptor (ER) positive versus ER negative samples. In addition, we identify new potential biomarkers and therapeutic targets for both clinical groups. As a specific example, using the AQuN-derived dataset we detect hsa-miR-193b-5p to have a statistically significant over-expression in the ER positive group, a phenomenon that was not previously reported. Furthermore, as demonstrated by functional assays in breast cancer cell lines, overexpression of hsa-miR-193b-5p in breast cancer cell lines resulted in decreased cell viability in addition to inducing apoptosis. Together, these observations suggest a novel functional role for this miRNA in breast cancer. Packages implementing AQuN are provided for Python and Matlab: https://github.com/YakhiniGroup/PyAQN.     

The role of emergent vegetation in structuring aquatic insect communities in peatland drainage ditches

Availability of macrophyte habitat is recognized as an important driver of aquatic insect communities in peatland drainage ditches; however, eutrophication can lead to the decline of submerged vegetation. While emergent vegetation is able to persist in eutrophicated ditches, vegetation removal, carried out during ditch maintenance, can reduce the availability of this habitat. In this study, we applied the landscape filtering approach to determine whether the absence of emergent vegetation is a habitat filter which structures aquatic insect communities in peatland drainage ditches under different trophic conditions. To this end, a field study was carried out in one mesotrophic (Naardermeer) and one eutrophic (Wormer and Jisperveld) peatland in the province of North Holland, The Netherlands. We assigned life history strategies to insect species and applied linear mixed models and redundancy analyses to taxonomic and functional aquatic insect community data. Our results indicate that while differences between peatlands primarily determine the species pool within each wetland, emergent vegetation acted as a secondary filter by structuring functional community composition within ditches. The eutrophic peatland was dominated by insects adapted to abiotic extremes, while species with good dispersal abilities were strongly related to emergent vegetation cover. This study demonstrates the applicability of life history strategies to provide insight into the filtering of species due to availability of emergent macrophyte habitat. To ensure greater diversity of insect communities in ditch habitats, it is recommended that some vegetation be spared during maintenance to leave patches from which insect recolonization can occur.     

Macrolide resistance determination and molecular typing of Mycoplasma pneumoniae by pyrosequencing

The first choice antibiotics for treatment of Mycoplasma pneumoniae infections are macrolides. Several recent studies, however, have indicated that the prevalence of macrolide (ML)-resistance, which is determined by mutations in the bacterial 23S rRNA, is increasing among M. pneumoniae isolates. Consequently, it is imperative that ML-resistance in M. pneumoniae is rapidly detected to allow appropriate and timely treatment of patients. We therefore set out to determine the utility of pyrosequencing as a convenient technique to assess ML-resistance. In addition, we studied whether pyrosequencing could be useful for molecular typing of M. pneumoniae isolates. To this end, a total of four separate pyrosequencing assays were developed. These assays were designed such as to determine a short genomic sequence from four different sites, i.e. two locations within the 23S rRNA gene, one within the MPN141 (or P1) gene and one within the MPN528a gene. While the 23S rRNA regions were employed to determine ML-resistance, the latter two were used for molecular typing. The pyrosequencing assays were performed on a collection of 108 M. pneumoniae isolates. The ML-resistant isolates within the collection (n = 4) were readily identified by pyrosequencing. Moreover, each strain was correctly typed as either a subtype 1 or subtype 2 strain by both the MPN141 and MPN528a pyrosequencing test. Interestingly, two recent isolates from our collection, which were identified as subtype 2 strains by the pyrosequencing assays, were found to carry novel variants of the MPN141 gene, having rearrangements in each of the two repetitive elements (RepMP4 and RepMP2/3) within the gene. In conclusion, pyrosequencing is a convenient technique for ML-resistance determination as well as molecular typing of M. pneumoniae isolates.     

In situ detection of S-glutathionylated proteins following glutaredoxin-1 catalyzed cysteine derivatization

S-glutathionylation is rapidly emerging as an important post-translational modification, responsible for transducing oxidant signals. However, few approaches are available that allow visualization of glutathione mixed disulfides in intact cells. We describe here a glutaredoxin1-dependent cysteine derivatization and labeling approach, in order to visualize S-glutathionylation patterns in situ. Using this new method, marked S-glutathionylation was observed in epithelial cells, which was predominant at membrane ruffles. As expected, the labeling intensity was further enhanced in response to bolus oxidant treatments, or in cells overexpressing Nox1 plus its coactivators. In addition, manipulation of endogenous levels of glutaredoxin-1 via RNAi, or overexpression resulted in altered sensitivity to H2O2 induced formation of glutathione mixed disulfides. Overall, the derivatization approach described here preferentially detects S-glutathionylation and provides an important means to visualize this post-translational modification in sub-cellular compartments and to investigate its relation to normal physiology as well as pathology.     

Exercise training restores uncoupling protein-3 content in limb muscles of patients with chronic obstructive pulmonary disease

Oxidative capacity and uncoupling protein-3 (UCP3) content are reduced in limb muscles of patients with chronic obstructive pulmonary disease (COPD). It has been hypothesized that the physiological role of UCP3 is to protect mitochondria against lipotoxicity in cases where fatty acid influx exceeds the capacity to oxidize them. Exercise training improves oxidative capacity and reduces UCP3 protein content in healthy subjects, but the response of UCP3 to training in COPD is unknown. We studied the effect of exercise training on UCP3 content in limb muscles of COPD patients. For this, seven healthy age-matched subjects and thirteen patients with COPD were studied. All patients were admitted to an 8-wk exercise training intervention. Exercise capacity was assessed by means of an incremental cycle ergometry test. Biopsies were taken from the vastus lateralis in which UCP3 and lipid peroxidation levels were determined by Western blotting. Citrate synthase and 3-hydroxyacyl-CoA dehydrogenase (HAD; an enzyme involved in fatty acid oxidation) were measured as indexes of muscle oxidative capacity. UCP3 in COPD was approximately 50% lower compared with healthy age-matched controls. In COPD, training induced upregulation of UCP3 [from 67.7 (SD 41.8) to 113.8 (SD 104.2) arbitrary units (AU), P = 0.062], especially in the patients who showed no increase in HAD activity [from 80.9 (SD 52.6) to 167.9 (SD 109.1) AU, P = 0.028], whereas lipid peroxidation levels remained unaltered. We conclude that exercise-training can restore muscle UCP3 protein level in COPD, and the nature of this response complies with the hypothesis that UCP3 may protect against lipotoxicity.     

A cell wall-associated polysaccharide is required for bacteriophage adsorption to the Streptococcus thermophilus cell surface

Streptococcus thermophilus strain ST64987 was exposed to a member of a recently discovered group of S. thermophilus phages (the 987 phage group), generating phage-insensitive mutants, which were then characterized phenotypically and genomically. Decreased phage adsorption was observed in selected bacteriophage-insensitive mutants, and was partnered with a sedimenting phenotype and increased cell chain length or aggregation. Whole genome sequencing of several bacteriophage-insensitive mutants identified mutations located in a gene cluster presumed to be responsible for cell wall polysaccharide production in this strain. Analysis of cell surface-associated glycans by methylation and NMR spectroscopy revealed a complex branched rhamno-polysaccharide in both ST64987 and phage-insensitive mutant BIM3. In addition, a second cell wall-associated polysaccharide of ST64987, composed of hexasaccharide branched repeating units containing galactose and glucose, was absent in the cell wall of mutant BIM3. Genetic complementation of three phage-resistant mutants was shown to restore the carbohydrate and phage resistance profiles of the wild-type strain, establishing the role of this gene cluster in cell wall polysaccharide production and phage adsorption and, thus, infection.