Peptide Finder: mapping measured molecular masses to peptides and proteins

The identification of unknown amino acid sequences of peptides as well as protein identification is of great significance in proteomics. Here, we present a publicly available web application that facilitates a high resolution mapping of measured molecular masses to peptides and proteins, irrespectively of the enzyme/digestion method used. Furthermore, multi-filtering may be applied in terms of measured mass tolerance, molecular mass and isoelectric point range as well as pattern matching to refine the results. This approach serves complementary to the existing solutions for protein identification and gives insights in novel peptides discovery and protein identification at the cases where the identification scores from the other approaches may be below significance threshold. Peptide Finder has been proven useful in proteomics procedures with experimental data from MALDI-TOF. AVAILABILITY: Peptide Finder web-application is available at http://bioserver-1.bioacademy.gr/Bioserver/PeptideFinder/.     

Endocytic recycling proteins EHD1 and EHD2 interact with fer-1-like-5 (Fer1L5) and mediate myoblast fusion

The mammalian ferlins are calcium-sensing, C2 domain-containing proteins involved in vesicle trafficking. Myoferlin and dysferlin regulate myoblast fusion and muscle membrane resealing, respectively. Correspondingly, myoferlin is most highly expressed in singly nucleated myoblasts, whereas dysferlin expression is increased in mature, multinucleated myotubes. Myoferlin also mediates endocytic recycling and participates in trafficking the insulin-like growth factor receptor. We have now characterized a novel member of the ferlin family, Fer1L5, because of its high homology to dysferlin and myoferlin. We found that Fer1L5 protein is expressed in small myotubes that contain only two to four nuclei. We also found that Fer1L5 protein binds directly to the endocytic recycling proteins EHD1 and EHD2 and that the second C2 domain in Fer1L5 mediates this interaction. Reduction of EHD1 and/or EHD2 inhibits myoblast fusion, and EHD2 is required for normal translocation of Fer1L5 to the plasma membrane. The characterization of Fer1L5 and its interaction with EHD1 and EHD2 underscores the complex requirement of ferlin proteins and mediators of endocytic recycling for membrane trafficking events during myotube formation.     

Physiological and anatomical responses of wheat to induced dehydration and rehydration

Hydroponically grown wheat seedlings of two prominent Bulgarian cultivars (Katya and Prelom) were subjected to 48 h osmotic stress with PEG 8000 and were then rehydrated. The degree of stress was evaluated by monitoring relative water content, lipid peroxidation level, and accumulation of free proline and hydrogen peroxide in the leaves. Anatomy and ultrastructure of leaf tissue were observed under light microscopy. After imposition of stress, drought tolerant cultivar Katya displayed higher free proline content and significantly lower malondialdehyde and peroxide concentration in leaves than in the leaves of susceptible cultivar Prelom. After 24 h of rehydration Katya showed better ability to restore leaf water status and an apparent tendency towards recovery, whereas Prelom sustained higher levels of hydrogen peroxide, lipid peroxidation products and free proline and markedly low relative water content. Here, we have uncovered some of the characteristics displayed by cultivar Katya that enable it to survive and recover from severe osmotic stress. Interestingly, there was congruence between our results and the high level of cultivar Katya drought tolerance observed in the field.     

Synthesis,biological evaluation and molecular modeling of a novel series of fused 1,2,3-triazoles as potential anti-coronavirus agents

Synthesis and biological evaluation of a novel library of fused 1,2,3-triazole derivatives are described. The in-house developed multicomponent reaction based on commercially available starting materials was applied and broad biological screening against various viruses was performed, showing promising antiviral properties for compounds 14d, 14n, 14q, 18f and 18i against human coronavirus 229E. Further in silico studies identified the key molecular interactions between those compounds and the 3-chymotrypsin-like protease, which is essential to the intracellular replication of the virus, supporting the hypothesis that the protease is the target molecule of the potential antiviral derivatives.     

Diet‐induced Changes in Intra‐abdominal Adipose Tissue and CVD Risk in American Women

The aim of the study was to determine what effect weight loss had on intra‐abdominal adipose tissue (IAAT) and cardiovascular disease (CVD) risk in 135 premenopausal overweight African‐American (AA) and European‐American (EA) women matched for BMI. Blood lipids, systolic blood pressure (SBP), diastolic BP (DBP), and IAAT (computed tomography determined) were examined prior to and after an 800 kcal/day diet producing 12 kg‐weight loss. Significant decreases in IAAT (～38%), total cholesterol (TC; 3%), low‐density lipoproteins (LDLs: 6%), triglycerides (TGs: 27%), cholesterol/high‐density lipoprotein ratio (C/HDL ratio: 18%), SBP (3%), and DBP (3%) occurred while HDL increased (16%), following weight loss and 1 month energy balance. Significant interactions between time and race showed that AA women decreased TG and increased HDL proportionately less than EA women. After adjusting for ΔIAAT, none of the CVD variables significantly changed after weight loss with the exception of HDL and C/HDL ratio. After adjusting for ΔLF (leg fat), ΔTC, ΔTG, ΔLDL, and ΔC/HDL ratio were significantly different. Multiple regression showed that independent of each other, ΔIAAT was significantly and positively related to ΔTC (adjusted β = 0.24) and ΔTG (adjusted β = 0.47), and ΔLF was negatively related to ΔTC (adjusted β = ?0.19) and ΔTG (adjusted β = ?0.18). Overweight and premenopausal AA and EA women benefitted from weight loss by decreasing IAAT and improving CVD risk. The changes in IAAT were significantly related to blood lipids, but loss of LF seems to be related to reduced improvement in TC and TG. Based on these results, interventions should focus on changes on IAAT.     

Activation of TRAIL‐DR5 pathway promotes sensorineural degeneration in the inner ear

Tumor necrosis factor (TNF) family cytokines are important mediators of inflammation. Elevated levels of serum TNF‐α are associated with human sensorineural hearing loss via poorly understood mechanisms. We demonstrate, for the first time, expression of TNF‐related apoptosis‐inducing ligand (TRAIL) and its signaling death receptor 5 (DR5) in the murine inner ear and show that exogenous TRAIL can trigger hair cell and neuronal degeneration, which can be partly prevented with DR5‐blocking antibodies.     

Physiological responses of two wheat cultivars to soil drought

Young plants of the two wheat cultivars Katya and Prelom, differing in their reaction to drought in the field, were grown in soil in pots, and their water status was assessed as well as the intensity of gas exchange, chlorophyll fluorescence, and accumulation of compatible solutes and hydrogen peroxide after 7 days of dehydration. It was established that cv. Katya displayed markedly better tolerance to soil drying in comparison with cv. Prelom. This was partly due to the more effective control of water balance, activity of the photosynthetic apparatus, and metabolic activity of leaves under stress. Consequently, lower amounts of hydrogen peroxide were accumulated and a lower membrane injury index was determined.