Is vegetation inside Carex sempervirens tussocks highly specific or an image of the surrounding vegetation?

Questions : How do species diversity, frequency and composition in tussocks differ from those in similar sized plots outside tussocks? Does the extent of the differences depend on community types or environmental conditions? Location : A sub‐alpine grassland in the Swiss National Park. Methods : In each of the two communities (short grass and tall graminoid) differing in species composition, grazing intensity and soil nutrient availability, relevés were made in 40 pairs of small circular plots, with one plot located inside a randomly selected Carex sempervirens tussock and the other outside. Results : We found 92 vascular species, of which 46 had a frequency higher than 5%. Species richness (S), pooled cover, Shannon's diversity (H) and cumulative species number (CS) were higher outside than inside the C. sempervirens tussocks, but evenness (J) was lower. S, H and CS differed more in the tall graminoid community than in the short grass community. However, dissimilarity between the paired relevés inside and outside tussocks did not differ between the two communities. Of the 46 most frequent species, 12 were statistically more and only one less frequent outside than inside the tussocks. Vegetation inside and outside tussocks could be clearly distinguished in the ordination space. Conclusion : Vegetation inside C. sempervirens tussocks is different from that in the surrounding area and represents an impoverished but homogenized version of the surrounding vegetation. Although tussocks of C. sempervirens were systematically avoided by grazers, there is little evidence that tussocks facilitate the species growing inside them.     

A glance at the emerging diagnostic biomarkers in the most prevalent genitourinary cancers

Genitourinary cancers comprise of a heterogenous group of cancers of which renal cell carcinoma, urothelial bladder carcinoma, and prostate adenocarcinoma are the most commonly encountered subtypes. A lot of research is ongoing using various strategies for exploration of novel biomarkers for genitourinary cancers. These biomarkers would not reduce the need for invasive diagnostic techniques but also could be used for early and accurate diagnosis to improve the clinical management required for the disease. Moreover, selecting the appropriate treatment regimen for the responsive patients based on these biomarkers would reduce the treatment toxicity as well as cost. Biomarkers identified using various advanced techniques like next generation sequencing and proteomics, which have been classified as immunological biomarkers, tissue-specific biomarkers and liquid biomarkers. Immunological biomarkers include markers of immunological pathways such as CTLA4, PD-1/PDl-1, tissue biomarkers include tissue specific molecules such as PSA antigen and liquid biomarkers include biomarkers detectable in urine, circulating cells etc.The purpose of this review is to provide a brief introduction to the most prevalent genitourinary malignancies, including bladder, kidney, and prostate cancers along with a major focus on the novel diagnostic biomarkers and the importance of targeting them prior to genitourinary cancers treatment. Understanding these biomarkers and their potential in diagnosis of genitourinary cancer would not help in early and accurate diagnosis as mentioned above but may also lead towards a personalized approach for better diagnosis, prognosis and specified treatment approach for an individual.     

Actin assembly controlled by GDP-Rab27a is essential for endocytosis of the insulin secretory membrane

We have recently reported that GDP-bound Rab27a regulates endocytosis of the insulin secretory membrane via its binding to coronin 3, an actin-binding protein. The aim of this study was to examine the participation of actin assembly in the Rab27a-dependent regulation of endocytosis using a pancreatic beta cell line, MIN6. Coronin 3 promoted F-actin bundling only in the presence of GDP-Rab27a. This effect was independent of coronin-3-binding to the actin-related proteins 2 and 3 (Arp2/3). Uptake of anti-phogrin-lumen antibody into MIN6 was inhibited by anti-coronin-3-C antibody which recognizes the actin-binding site. This inhibition was also observed with coronin-3-R28D, which lacks in actin binding. These results suggest that coronin 3 is a genuine GDP-Rab27a effector, and that controls endocytosis of the secretory membrane via modulating actin assembly in pancreatic β-cells.     

Synchro-PASEF Allows Precursor-Specific Fragment Ion Extraction and Interference Removal in Data-Independent Acquisition

Data-independent acquisition (DIA) methods have become increasingly popular in mass spectrometry–based proteomics because they enable continuous acquisition of fragment spectra for all precursors simultaneously. However, these advantages come with the challenge of correctly reconstructing the precursor–fragment relationships in these highly convoluted spectra for reliable identification and quantification. Here, we introduce a scan mode for the combination of trapped ion mobility spectrometry with parallel accumulation—serial fragmentation (PASEF) that seamlessly and continuously follows the natural shape of the ion cloud in ion mobility and peptide precursor mass dimensions. Termed synchro-PASEF, it increases the detected fragment ion current several-fold at sub-second cycle times. Consecutive quadrupole selection windows move synchronously through the mass and ion mobility range. In this process, the quadrupole slices through the peptide precursors, which separates fragment ion signals of each precursor into adjacent synchro-PASEF scans. This precisely defines precursor–fragment relationships in ion mobility and mass dimensions and effectively deconvolutes the DIA fragment space. Importantly, the partitioned parts of the fragment ion transitions provide a further dimension of specificity via a lock-and-key mechanism. This is also advantageous for quantification, where signals from interfering precursors in the DIA selection window do not affect all partitions of the fragment ion, allowing to retain only the specific parts for quantification. Overall, we establish the defining features of synchro-PASEF and explore its potential for proteomic analyses.     

High Throughput Sequential ELISA for Validation of Biomarkers of Acute Graft-Versus-Host Disease

Unbiased discovery proteomics strategies have the potential to identify large numbers of novel biomarkers that can improve diagnostic and prognostic testing in a clinical setting and may help guide therapeutic interventions. When large numbers of candidate proteins are identified, it may be difficult to validate candidate biomarkers in a timely and efficient fashion from patient plasma samples that are event-driven, of finite volume and irreplaceable, such as at the onset of acute graft-versus-host disease (GVHD), a potentially life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT).Here we describe the process of performing commercially available ELISAs for six validated GVHD proteins: IL-2Rα⁵, TNFR1⁶, HGF⁷, IL-8⁸, elafin², and REG3α³ (also known as PAP1) in a sequential fashion to minimize freeze-thaw cycles, thawed plasma time and plasma usage. For this procedure we perform the ELISAs in sequential order as determined by sample dilution factor as established in our laboratory using manufacturer ELISA kits and protocols with minor adjustments to facilitate optimal sequential ELISA performance. The resulting plasma biomarker concentrations can then be compiled and analyzed for significant findings within a patient cohort. While these biomarkers are currently for research purposes only, their incorporation into clinical care is currently being investigated in clinical trials.This technique can be applied to perform ELISAs for multiple proteins/cytokines of interest on the same sample(s) provided the samples do not need to be mixed with other reagents. If ELISA kits do not come with pre-coated plates, 96-well half-well plates or 384-well plates can be used to further minimize use of samples/reagents.     

Structure and expression of a novel compact myelin protein – Small VCP-interacting protein (SVIP)

SVIP (small p97/VCP-interacting protein) was initially identified as one of many cofactors regulating the valosin containing protein (VCP), an AAA+ ATPase involved in endoplasmic-reticulum-associated protein degradation (ERAD). Our previous study showed that SVIP is expressed exclusively in the nervous system. In the present study, SVIP and VCP were seen to be co-localized in neuronal cell bodies. Interestingly, we also observed that SVIP co-localizes with myelin basic protein (MBP) in compact myelin, where VCP was absent. Furthermore, using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopic measurements, we determined that SVIP is an intrinsically disordered protein (IDP). However, upon binding to the surface of membranes containing a net negative charge, the helical content of SVIP increases dramatically. These findings provide structural insight into interactions between SVIP and myelin membranes.     

Molecular simulation of realistic membrane models of alkylated PEEK membranes

Atomistic molecular modelling has proven to be a useful tool for the investigation of transport properties of small gas molecules in polymer membrane matrices. The quality of the predictions of these properties based on molecular simulation depends principally on the quality of the membrane model. The predicted gas transport properties of small gas molecules in the same glassy polymer membrane show often a large scatter in gas diffusion and solubility simulated values. In order to reduce the scatter in predicted gas transport properties in glassy polymer membranes, numerical analysis of structural features of the membrane model is used for pre-selecting only the realistic ones for further simulations using transition-state theory (TST) approach. Simulation results of gas solubility and diffusion in alkylated poly-ether–ether–ketone (PEEK) membranes will illustrate the approach.     

Therapeutic options for triple-negative breast cancers with defective homologous recombination

Breast cancer is the most common malignancy among women in developed countries, affecting more than a million women per year worldwide. Over the last decades, our increasing understanding of breast cancer biology has led to the development of endocrine agents against hormone receptor-positive tumors and targeted therapeutics against HER2-expressing tumors. However, no targeted therapy is available for patients with triple-negative breast cancer, lacking expression of hormone receptors and HER2. Overlap between BRCA1-mutated breast cancers and triple-negative tumors suggests that an important part of the triple-negative tumors may respond to therapeutics targeting BRCA1-deficient cells. Here, we review the features shared between triple-negative, basal-like and BRCA1-related breast cancers. We also discuss the development of novel therapeutic strategies to target BRCA1-mutated tumors and triple-negative tumors with BRCA1-like features. Finally, we highlight the utility of mouse models for BRCA1-mutated breast cancer to optimize (combination) therapy and to understand drug resistance.     

Inter‐laboratory validation of a rapid assay for the detection and quantification of Legionella spp. in water samples

Aims: To compare the standard culture method with a new, rapid test (ScanVIT‐Legionella?) using fluorescently labelled gene probes for the detection and enumeration of Legionella spp. The new technique was validated through experiments conducted on both artificially and naturally contaminated water and through an inter‐laboratory comparison. Methods and Results: All samples were processed by the ScanVIT test according to the manufacturer’s instructions and by a culture method (ISO 11731). ScanVIT detected significantly more positive samples, although concentrations were similar and a strong positive correlation between the two methods was observed (r = 0·888, P < 0·001). The new test was more accurate in identifying the co‐presence of Legionella pneumophila and Leg. non‐pneumophila. ScanVIT showed a slightly higher Legionella recovery from water samples artificially contaminated with Leg. pneumophila alone or together with Pseudomonas aeruginosa. Lastly, the inter‐laboratory comparison revealed that the ScanVIT test exhibits a lower variability than the traditional culture test (mean coefficient of variation 8·7 vs 16·1%). Conclusions: The results confirmed that the ScanVIT largely overlaps the reference method and offers advantages in terms of sensitivity, quantitative reliability and reduced assay time. Significance and Impact of the Study: The proposed method may represent a useful validated alternative to traditional culture for the rapid detection and quantification of Legionella spp. in water.     

A Nonparametric Test for Differences in the Dispersion of Dependent Samples

A new statistic Δ to test the hypothesis of a difference in the dispersion of two dependent samples of ordinal data quality is proposed. It draws on the idea of rank assignment originally forwarded by Siegel and Tukey (1960). No exact probability levels can be given for this statistic for the time being, but it is shown that the statistic is linearly related to the so-called Hotelling-Pabst statistic D, and that one can use exact tables of the latter as a substitute in the statistical decision process with small samples. For larger samples, an approximation of Δ to the standard normal distribution is given. The problem of tied observations is not sufficiently solved yet. A conservative procedure of rank assignment is proposed as long as the exact distribution of Δ in the presence of ties is unknown.