Competitive asymmetry, foraging area size and coexistence of annuals

Individuals allocate resources to the expansion of their foraging area and those resources are no longer available for the traits that determine how well those individuals are able to protect their foraging area against competitors. The resulting trade‐off between foraging area size and the traits associated with the ability to compete for the resources within the foraging area applies to ecological scenarios as different as territorial defence by individuals and colonies, and light competition in plants. Whether the trade‐off affects species performance in competition for resources at the area of overlap between foraging areas depends on the symmetry of resource division. In symmetric competition resources are divided equally between the competitors, while in asymmetric competition the individual with the smallest foraging area, and consequently the greatest competitive ability, gains all the resources. Competition may also be a combination of the symmetric and asymmetric processes. I studied the effects of competitive asymmetry on population dynamics and coexistence of two annual species with different sized foraging areas using an individual‐based spatially explicit simulation model. Symmetric competition favoured the species with the larger foraging area and did not allow coexistence. Competitive asymmetry favoured the species with smaller foraging area and allowed coexistence, which was due to the consequences of losing an asymmetric competition being more severe than losing a symmetric competition. The mechanism of coexistence is the larger foraging area's superiority in low population densities (little competition) and the smaller foraging area's ability to win a large foraging area when competition was intense. Competitive asymmetry and small size of both foraging areas led to population dynamics dominated by long‐term fluctuations of small intensity. Symmetric competition and large size of the foraging areas led to large short‐term fluctuations, which often resulted in the extinction of one or both of the species due to demographic stochasticity.     

Predictive value of the ear-crease sign in coronary artery disease.

The value of the ear-crease sign in predicting the presence of coronary artery disease was studied in 340 consecutive patients who underwent coronary arteriography. In this selected population, 75.6% of whom had coronary artery disease, the sensitivity of the sign was 59.5%, the specificity 81.9% and the positive predictive value 91.1%. The sign was associated with increasing age but was also independently associated with obstructive coronary artery disease. No significant correlation was found between the sign and the presence of risk factors or other signs of such disease, except for corneal arcus. In symptomatic patients the sign suggested the presence of more extensive coronary artery disease. In an asymptomatic population with a low prevalence of coronary artery disease it appears to be of limited value in predicting obstructive coronary artery disease. However, it may identify a subset of patients prone to early ageing and to the early development of coronary artery disease, whose prognosis might be improved by early preventive measures.     

Regulation of amino acid transport in growing cells of Streptomyces hydrogenans

The uptake of various amino acids into Streptomyces hydrogenans grown in chemostatically and turbidostatically controlled steady state cultures has been investigated. A close correlation between transport capacity and the growth rates of the cells was found. As shown by kinetic analysis, the increased transport is due to elevated maximum uptake rates, the apparent Michaelis constants remaining unchanged. Analysis of the unidirectional fluxes of cycloleucine revealed that not only the influx is raised as the growth rate is increased but also the efflux. Hence, the conclusion is drawn that the growth-rate dependent modulation of transport capacity is, at least, partially due to the variation of the concentration of active transport components. Since the cells were grown in the absence of external amino acids the results suggest that amino acid transport into S. hydrogenans is under the control of endogenous effectors.List of Abbreviations AIB 2-aminoisobutyric acid - Cycloleucine 1-aminocyclopentane-1-carboxylic acid     

Molecular docking analysis and dynamics simulation of salbutamol with the monoamine oxidase B (MAO-B) enzyme

The monoamine oxidase B (MAO-B) enzyme is linked with Parkinson''s disease. Therefore, it is of interest to document the molecular docking analysis and dynamics simulation of salbutamol, a well-known β2-adrenoceptor agonist, with the monoamine oxidase B (MAO-B) enzyme for further consideration in drug design and development.     

TMBIM5 is the Ca2+/H+ antiporter of mammalian mitochondria

Mitochondrial Ca²⁺ ions are crucial regulators of bioenergetics and cell death pathways. Mitochondrial Ca²⁺ content and cytosolic Ca²⁺ homeostasis strictly depend on Ca²⁺ transporters. In recent decades, the major players responsible for mitochondrial Ca²⁺ uptake and release have been identified, except the mitochondrial Ca²⁺/H⁺ exchanger (CHE). Originally identified as the mitochondrial K⁺/H⁺ exchanger, LETM1 was also considered as a candidate for the mitochondrial CHE. Defining the mitochondrial interactome of LETM1, we identify TMBIM5/MICS1, the only mitochondrial member of the TMBIM family, and validate the physical interaction of TMBIM5 and LETM1. Cell‐based and cell‐free biochemical assays demonstrate the absence or greatly reduced Na⁺‐independent mitochondrial Ca²⁺ release in TMBIM5 knockout or pH‐sensing site mutants, respectively, and pH‐dependent Ca²⁺ transport by recombinant TMBIM5. Taken together, we demonstrate that TMBIM5, but not LETM1, is the long‐sought mitochondrial CHE, involved in setting and regulating the mitochondrial proton gradient. This finding provides the final piece of the puzzle of mitochondrial Ca²⁺ transporters and opens the door to exploring its importance in health and disease, and to developing drugs modulating Ca²⁺ exchange.     

Fast-HBR: Fast hash based duplicate read remover

The Next-Generation Sequencing (NGS) platforms produce massive amounts of data to analyze various features in environmental samples. These data contain multiple duplicate reads which impact the analyzing process efficiency and accuracy. We describe Fast-HBR, a fast and memory-efficient duplicate reads removing tool without a reference genome using de-novo principles. It uses hash tables to represent reads in integer value to minimize memory usage for faster manipulation. Fast-HBR is faster and has less memory footprint when compared with the state of the art De-novo duplicate removing tools. Fast-HBR implemented in Python 3 is available at https://github.com/Sami-Altayyar/Fast-HBR.     

Potential effects and relevant lead compounds of Vigna mungo (L.) Hepper seeds against bacterial infection,helminthiasis, thrombosis and neuropharmacological disorders

Multidrug-resistant bacterial infections, helminthiasis, thrombosis, anxiety and insomnia are some of the major global health concerns. Vigna mungo (L.) Hepper (VM) has been used traditionally to treat microbial infection, helminthic disorder, schizophrenia, memory loss, and blood circulatory problem. This research aims to discover antibacterial, anthelmintic, thrombolytic and neuropharmacological effects of the methanol extract of Vigna mungo seeds (MESVM), and also in-silico prediction of relevant lead compounds by molecular docking and ADME/T analysis. The crude extracts and subsequent fractions of MESVM were investigated for antibacterial activity by disc diffusion method, anthelmintic activity by paralysis and death test on earthworms, and thrombolytic activity by in vitro blood clot dissolution test. Open-field test and elevated plus maze test were performed for evaluating anxiolytic activity of the extracts. Using molecular docking, ligand poses of selected VM seeds’ phytoconstituents were predicted targeting tubulin, GlcN-6-P synthase, and human tissue plasminogen activator proteins for anthelmintic, antibacterial, and thrombolytic activity, respectively. In the antibacterial activity test, the MESVM at 10000 μg/mL concentration created highest and significant (P < 0.001) zone of inhibition against Staphylococcus aureus (15.42 mm) and Escherichia coli (12 mm) compared with tetracycline. The MESVM exhibited remarkable anthelmintic activity at 50 mg/mL concentration with 35.4 min paralysis time, 75.2 min death time and were closer to the durations of standard drug albendazole. No test extract showed anxiolytic activity. In thrombolytic activity test, all concentrations of MESVM produced clot lytic activity with high significance (P < 0.001) in comparison with the blank. In docking, 2′-hydroxygenistein, cyclokievitone hydrate, and aureol displayed maximum affinity to the target proteins for anthelmintic, antibacterial, and thrombolytic activity, respectively. This research revealed that the MESVM demonstrated potential anthelmintic, antibacterial and thrombolytic effects that confirmed the folkloric uses of VM and the found relevant lead compounds might be further optimized in future drug development.     

Enzymatic hydrolysis of olive wastewater for hydroxytyrosol enrichment

Aspergillus niger broth culture on wheat bran was assessed for olive wastewater (OW) hydrolysis in order to release hydroxytyrosol (HT). The enzyme profiles of this culture broth gave essentially (IU/L): 3000 β-glucosidase and 100 esterase. Hydrolysis activity of A. niger enzyme preparation was evaluated by using three substrates: raw OW, phenolic fraction extracted from OW by ethyl acetate and its corresponding exhausted fraction. Large amounts of free simple phenolics were released from exhausted fraction and raw OW after enzymatic treatment. HPLC analyses show that HT was the main phenolic compound. One step of ethyl acetate extraction of hydrolysed OW allowed the recovery of 0.8 g of HT per litre of OW. The antioxidant activity of extracts from OW and exhausted fraction, measured by DPPH method, was drastically enhanced after hydrolysis treatment. This study demonstrates that hydrolysed OW is a potential source of bioactive phenolic compounds with promising applications in food and pharmaceutical industries.     

Implications of biofuel policy‐driven land cover change for rainfall erosivity and soil erosion in the United States

Large‐scale conversion of traditional agricultural cropping systems to biofuel cropping systems is predicted to have significant impact on the hydrologic cycle. Changes in the hydrologic cycle lead to changes in rainfall and its erosive power, and consequently soil erosion that will have onsite impacts on soil quality and crop productivity, and offsite impacts on water quality and quantity. We examine regional change in rainfall erosivity and soil erosion resulting from biofuel policy‐induced land use/land cover (LULC) change. Regional climate is simulated under current and biofuel LULC scenarios for the period 1979–2004 using the Weather Research Forecast (WRF) model coupled to the NOAH land surface model. The magnitude of change in rainfall erosivity under the biofuel scenario is 1.5–3 times higher than the change in total annual rainfall. Over most of the conterminous United States (~56%), the magnitude of the change in erosivity is between ?2.5% and +2.5%. A decrease in erosivity of magnitude 2.5–10% is predicted over 23% of the area, whereas an increase of the same magnitude is predicted over 14% of the area. Corresponding to the changes in rainfall erosivity and crop cover, a decrease in soil loss is predicted over 60% of the area under the biofuel scenario. In Kansas and Oklahoma, the states in which a large fraction of land area is planted with switchgrass under the biofuel scenario, soil loss is estimated to decrease 12% relative to the baseline. This reduction in soil loss is due more to changes in the crop cover factor than changes in rainfall or rainfall erosivity. This indicates that the changes in LULC, due to future cellulosic biofuel feedstock production, can have significant implications for regional soil and water resources in the United States and we recommend detailed investigation of the trade‐offs between land use and management options.     

Determination of plasma microRNA for early detection of gastric cancer

Gastric cancer is the fourth most prevalent malignancy worldwide and remains the second most common cause of cancer-related death globally. Understanding the molecular structure of gastric carcinogenesis might identify new diagnostic and therapeutic strategies for this disease. Thus, early detection of gastric cancer is a key measure to reduce the mortality and improve the prognosis of gastric cancer. There have recently been several reports that microRNAs (miRNAs) circulate in highly stable, cell-free forms in blood. Because serum and plasma miRNAs are relatively easy to access, circulating miRNAs also have great potential to serve as non-invasive biomarkers. Although a number of miRNAs associated with gastric cancer have been identified, the underlying mechanism of these miRNAs in tumorigenesis and tumor progression remains to be investigated. The purpose of this study is to identify the potential of serum miRNAs as biomarkers for early detection of gastric cancer patients. RNA was isolated using the High Pure miRNA Isolation Kit (Roche) following the manufacturer’s protocol. cDNA and preamplification protocols were obtained from the isolated plasma miRNAs. The BioMark? 96.96 Dynamic Array (Fluidigm Corporation) for real-time qPCR was used to simultaneously quantite the expression of 740 miRNAs. All statistical analyses were performed using the Biogazelle’s qbase PLUS 2.0 software. In this study, among 740 miRNAs that we analyzed only miR-195-5p was significantly (p < 0.05, fold changes = 13, 3) down-regulated in gastric cancer patients compared with control. We demonstrated that miR-195-5p is a novel tumor suppressor miRNA and may contribute to gastric carcinogenesis. The miRNA expression profile described in this study should contribute to future studies on the role of miRNAs in gastric cancer.