Fluctuation in the number,type and activity of blood neutrophils in cows exhibiting successful and unsuccessful completion of gestation cycle

Neutrophils (first line of cellular defense) are capable of detecting presence of foreign genome in the mother’s womb. Role of neutrophils during full gestation cycle of ruminants and the difference in their number, type, and activity in successful and unsuccessful pregnancies is not known. To evaluate this, blood samples were collected at artificial insemination (0 day) and on days 10, 14, 16, 18, and 21 in non-pregnant (NP) cows. However in pregnant (P) cows, samples were collected as indicated above and every 30 days for the complete gestation. In aborted cows, samples were collected as above till abortion. Higher total leukocyte counts were observed in NP and aborted cows at abortion. Neutrophil: lymphocyte ratio increased significantly (p < 0.05) in NP and aborted cows. Phagocytic activity (PA) and myeloperoxidase concentrations were significantly higher (p < 0.05) on day 18 post insemination in NP cows. PA and myeloperoxidase also increased significantly (p < 0.05) at abortion in aborted cows. Neutrophils exhibited limited decrease in their number and activity in successful pregnancies during implantation. After that their number and activity were constantly maintained throughout the gestation cycle. Any increase in the number and inflammatory activity of neutrophils may lead to non-pregnancy or loss in pregnancy.     

Benchmarking AlphaFold‐enabled molecular docking predictions for antibiotic discovery

Efficient identification of drug mechanisms of action remains a challenge. Computational docking approaches have been widely used to predict drug binding targets; yet, such approaches depend on existing protein structures, and accurate structural predictions have only recently become available from AlphaFold2. Here, we combine AlphaFold2 with molecular docking simulations to predict protein‐ligand interactions between 296 proteins spanning Escherichia coli''s essential proteome, and 218 active antibacterial compounds and 100 inactive compounds, respectively, pointing to widespread compound and protein promiscuity. We benchmark model performance by measuring enzymatic activity for 12 essential proteins treated with each antibacterial compound. We confirm extensive promiscuity, but find that the average area under the receiver operating characteristic curve (auROC) is 0.48, indicating weak model performance. We demonstrate that rescoring of docking poses using machine learning‐based approaches improves model performance, resulting in average auROCs as large as 0.63, and that ensembles of rescoring functions improve prediction accuracy and the ratio of true‐positive rate to false‐positive rate. This work indicates that advances in modeling protein‐ligand interactions, particularly using machine learning‐based approaches, are needed to better harness AlphaFold2 for drug discovery.     

Generation of Zerovalent Metal Core Nanoparticles Using n-(2-aminoethyl)-3-aminosilanetriol

In this work, a facile one-pot reaction for the formation of metal nanoparticles in a water solution through the use of n-(2-aminoethyl)-3-aminosilanetriol is presented. This compound can be used to effectively reduce and complex metal salts into metal core nanoparticles coated with the compound. By controlling the concentrations of salt and silane one is able to control reaction rates, particle size, and nanoparticle coating. The effects of these changes were characterized through transmission electron microscopy (TEM), UV-Vis spectrometry (UV-Vis), Nuclear Magnetic Resonance spectroscopy (NMR) and Fourier Transform Infrared spectroscopy (FTIR). A unique aspect to this reaction is that usually silanes hydrolyze and cross-link in water; however, in this system the silane is water-soluble and stable. It is known that silicon and amino moieties can form complexes with metal salts. The silicon is known to extend its coordination sphere to form penta- or hexa-coordinated species. Furthermore, the silanol group can undergo hydrolysis to form a Si-O-Si silica network, thereby transforming the metal nanoparticles into a functionalized nanocomposites.     

The dependency of autophagy and ubiquitin proteasome system during skeletal muscle atrophy

Among the four proteolytic systems in the cell, autophagy and the ubiquitin-proteasome system (UPS) are the main proteolytic events that allow for the removal of cell debris and proteins to maintain cellular homeostasis. Previous studies have revealed that these systems perform their functions independently of each other. However, recent studies indicate the existence of regulatory interactions between these proteolytic systems via ubiquitinated tags and a reciprocal regulation mechanism with several crosstalk points. UPS plays an important role in the elimination of short-lived/soluble misfolded proteins, whereas autophagy eliminates defective organelles and persistent insoluble protein aggregates. Both of these systems seem to act independently; however, disruption of one pathway affects the activity of the other pathway and contributes to different pathological conditions. This review summarizes the recent findings on direct and indirect dependencies of autophagy and UPS and their execution at the molecular level along with the important drug targets in skeletal muscle atrophy.     

Proteome‐wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: a holistic approach

Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation of the intestine among ruminants and humans. Currently, there are no effective vaccines and sensitive diagnostic tests available for its control and detection. For this, it is of paramount importance to identify the MAP antigens, which may be immunologically recognized by the host immune system. To address this challenge, we performed identification of the immunogenic epitopes in the MAP outer membrane proteins (OMPs). We have previously identified 57 MAP proteins as OMPs [Rana A, Rub A, Akhter Y. 2014. Molecular BioSystems, 10:2329–2337] and have evaluated them for the epitope selection and analysis employing a computational approach. Thirty‐five MAP OMPs are reported with nine‐mer peptides showing high binding affinity to major histocompatibility complex (MHC) class I molecules and 28 MAP OMPs with 15‐mer peptides of high binding affinity for MHC class II molecules. The presence of MHC binding epitopes indicates the potential cell‐mediated immune response inducing capacity of these MAP OMPs in infected host. To further investigate the humoral response inducing properties of OMPs of MAP, we report potential B cell epitopes based on the sequences of peptide antigens and their molecular structures. We also report 10 proteins having epitopes for both B and T cells representing potential candidates which may invoke both humoral and cellular immune responses in the host. These findings will greatly accelerate and expedite the formulation of effective and cost‐efficient vaccines and diagnostic tests against MAP infection. Copyright © 2015 John Wiley & Sons, Ltd.     

Diurnal variation of milk somatic and differential leukocyte counts of Murrah buffaloes as influenced by different milk fractions,seasons and parities

Milk cell counts are good indicators of a mammary infection and milk quality. The present study was done to record diurnal rhythmicity in the milk somatic and differential cell counts during different seasons, milk strips and parity in Murrah buffaloes. Milk somatic cell counts (SCC) were measured by SCC counter and milk differential cell counts were measured microscopically after making a milk smear and staining it to identify neutrophils, lymphocytes and macrophages. Maximum milk SCC was observed in the summer season. Milk neutrophils were lowest during thermoneutral (TN), intermediate during the winter season and highest during the summer season. Milk lymphocytes were highest during the winter season, intermediate in the TN and lowest in the summer season. Diurnal rhythm in the milk SCC and neutrophil percentage is noticed in the summer season only. Maximum milk SCC values were observed in the late strip but neutrophils were highest in the early strip. Diurnal rhythm was observed in the late strip for neutrophils and in mid strip for the lymphocytes. Milk SCC and milk neutrophils were found to be the highest in the multiparous buffaloes and diurnal rhythm was observed only in the lymphocytes of primiparous buffaloes. Milk macrophages were higher in the morning samples of primiparous as compared to the multiparous buffaloes. In this pioneer study, diurnal rhythms in the milk cell counts of buffaloes have been studied extensively. This will help in maintaining low milk cell counts in buffalo and thus help in getting more milk per buffalo during stress periods.     

Case studies examining LCA streamlining techniques

Pressure is mounting for more streamlined Life Cycle Assessment (LCA) methods that allow for evaluations that are quick and simple, but accurate. As part of an overall research effort to develop and demonstrate streamlined LCA, the U.S. Environmental Protection Agency has funded studies to examine the validity of various streamlining methods. Ten streamlining methods were identified and tested for accuracy against full LCAs. The objective of this effort was to identify streamlining methods that produced conclusions similar to those reached through full LCAs. Results of this evaluation showed that many streamlining methods give incorrect conclusions at least half of the time as compared to full LCAs. Streamlining will always incur the risk of obtaining results that are different than a full LCA. However, if some level of risk is acceptable, there are some general rules that can be used to select a streamlining method that will reduce the risk of serious error.