Combining fold recognition and exploratory data analysis for searching for glycosyltransferases in the genome of Mycobacterium tuberculosis

Fold recognition was applied to the systematic analysis of the all sequences encoded by the genome of Mycoplasma tuberculosis H37Rv in order to identify new putative glycosyltransferases. The search was conducted against a library composed of all known crystal structures of glycosyltransferases and some related proteins. A clear relationship appeared between some sequences and some folds. It appears necessary to complete the fold recognition approach with a statistical approach in order to identify the relevant data above the background noise. Exploratory data analysis was carried out using several methods. Analytical methods confirmed the validity of the approach, while predictive methods, although very preliminary in the present case, allowed for identifying a number of sequences of interest that should be further investigated. This new approach of combining bioinformatics and chemometrics appears to be a powerful tool for analysis of newly sequenced genomes. Its application to glycobiology is of great interest.     

Activation of the ATPase activity of hsp90 by the stress-regulated cochaperone aha1

Client protein activation by Hsp90 involves a plethora of cochaperones whose roles are poorly defined. A ubiquitous family of stress-regulated proteins have been identified (Aha1, activator of Hsp90 ATPase) that bind directly to Hsp90 and are required for the in vivo Hsp90-dependent activation of clients such as v-Src, implicating them as cochaperones of the Hsp90 system. In vitro, Aha1 and its shorter homolog, Hch1, stimulate the inherent ATPase activity of yeast and human Hsp90. The identification of these Hsp90 cochaperone activators adds to the complex roles of cochaperones in regulating the ATPase-coupled conformational changes of the Hsp90 chaperone cycle.     

Effects of T cell frequency and graft size on transplant outcome in mice

The features that determine whether graft-reactive T lymphocytes develop into effector cells capable of mediating organ destruction are not well understood. To investigate potential factors involved in this process, we first confirmed that female recipient mice acutely rejected minor Ag-disparate male skin, but not heart transplants. Despite this difference in outcome, heart and skin transplantation induced antidonor T cell responses of similar magnitude, specificity, and cytokine profile. The heart-graft-primed T cells transiently infiltrated the graft and ultimately induced the development of chronic transplant vasculopathy. Increasing the frequency of donor-reactive T cells by presensitization or by using TCR (CD8+ antimale)-transgenic recipients did not mediate acute rejection but accelerated the pace and severity of the vasculopathy. Surprisingly, decreasing the tissue mass of the donor heart by 50% resulted in acute rejection of these smaller grafts without increasing the frequency of antidonor effector T cells in the recipients. In complementary studies, placement of one or two male skin grafts on a single recipient did not affect the frequency or cytokine profile of the induced antimale T cell repertoire. Nonetheless, the recipients of single grafts acutely rejected the transplanted skin while the recipients of two skin grafts did not. These results provide new insight into the pathogenesis of transplant vasculopathy and provide an explanation for the difference in outcome between murine skin and heart transplants by highlighting the novel concept that the efficiency of transplant-reactive T cell immunity is heavily influenced by the tissue burden it encounters at the effector stage.     

Re-alimentation strategy to manoeuvre body condition and carcass characteristics in cull ewes

Improvement in body condition and carcass traits through nutritional intervention was studied in cull ewes. Sixty-eight adult non-productive Malpura ewes (average body weight 26.7 ± 0.33 kg) were randomly divided into four equal groups: G0 maintained on free grazing for 8 h on protected natural rangeland with ad libitum guar (Cyamopsis tetragonoloba) straw (GS) after grazing; G1, G2 and G3 fed with supplemental concentrate at the rate of 250 g, 2.5% of live weight (LW) and ad libitum, respectively. The experiment was continued for 90 days and daily feed intake, weekly LW and body condition score (BCS) were recorded. Intake and digestibility of nutrients were assessed by indicator method. Rumen fermentation attributes and blood biochemical profile were studied to assess the dietary effects and animals were slaughtered at the end of experiment for evaluation of carcass characteristics. Higher dry matter (DM) intake and improvement in plane of nutrition was observed in G2 and G3 with a higher LW gain (LWG) and improvement in BCS than in G0. The digestibility of DM, organic matter, CP, ADF and cellulose was higher (P < 0.05) in G2 and G3 than in G0. A lower ruminal pH and ammonia N but higher total N and trichloroacetic acid-precipitable N, an increase in holotrichs, spirotrichs and total protozoa population, increase in haemoglobin but decrease in serum total cholesterol and non-esterified fatty acids were observed in high-concentrate-fed groups. Carcass attributes revealed increase (P < 0.05) in empty LW, dressing yield, eye muscle area, subcutaneous and intramuscular fat, decrease in shear force value and higher (P < 0.05) protein content in Longissimus dorsi muscle in test groups than in the control. Above all, the G2 animals had better rumen environment and blood biochemical attributes and consumed more feed with enhanced digestibility that supported higher LWG at better feed conversion efficiency, improvement in BCS and carcass quality. Thus, re-alimentation of cull ewes with challenged feeding of concentrate at 2.5% of LW on a basal roughage diet for a period of 3 months may have promise for better economic return to the farmers with possibly meeting quality mutton for human consumption.     

The demographic effects of functional traits: an integral projection model approach reveals population‐level consequences of reproduction‐defence trade‐offs

Quantitatively linking individual variation in functional traits to demography is a necessary step to advance our understanding of trait‐based ecological processes. We constructed a population model for Asclepias syriaca to identify how functional traits affect vital rates and population growth and whether trade‐offs in chemical defence and demography alter population growth. Plants with higher foliar cardenolides had lower fibre, cellulose and lignin levels, as well as decreased sexual and clonal reproduction. Average cardenolide concentrations had the strongest effect on population growth. In both the sexual and clonal pathway, the trade‐off between reproduction and defence affected population growth. We found that both increasing the mean of the distribution of individual plant values for cardenolides and herbivory decreased population growth. However, increasing the variance in both defence and herbivory increased population growth. Functional traits can impact population growth and quantifying individual‐level variation in traits should be included in assessments of population‐level processes.     

Displacement of alpha-actinin from the NMDA receptor NR1 C0 domain By Ca2+/calmodulin promotes CaMKII binding

Ca2+ influx through the N-methyl-d-aspartate (NMDA)-type glutamate receptor triggers activation and postsynaptic accumulation of Ca2+/calmodulin-dependent kinase II (CaMKII). CaMKII, calmodulin, and alpha-actinin directly bind to the short membrane proximal C0 domain of the C-terminal region of the NMDA receptor NR1 subunit. In a negative feedback loop, calmodulin mediates Ca2+-dependent inactivation of the NMDA receptor by displacing alpha-actinin from NR1 C0 upon Ca2+ influx. We show that Ca2+-depleted calmodulin and alpha-actinin simultaneously bind to NR1 C0. Upon addition of Ca2+, calmodulin dislodges alpha-actinin. Either the N- or C-terminal half of calmodulin is sufficient for Ca2+-induced displacement of alpha-actinin. Whereas alpha-actinin directly antagonizes CaMKII binding to NR1 C0, the addition of Ca2+/calmodulin shifts binding of NR1 C0 toward CaMKII by displacing alpha-actinin. Displacement of alpha-actinin results in the simultaneous binding of calmodulin and CaMKII to NR1 C0. Our results reveal an intricate mechanism whereby Ca2+ functions to govern the complex interactions between the two most prevalent signaling molecules in synaptic plasticity, the NMDA receptor and CaMKII.     

Molecular Integrators of Neuropathy and Pain in Diabetes Mellitus

Glycation of nucleotides, proteins and phospholipids contributes to the development of late diabetic complications,including the most debilitating one——diabetic neuropathy. Reactive intermediates of AGE formation such as glyoxal, methylglyoxal(MG) and other dicarbonyls are detoxified by the glyoxalase-system. However little is known about the regulation and nature of the mechanisms underlying neuropathology. Therefore we decided to focus on the role of MG-glyoxalase 1(GLO-1) system in modulation of painful diabetic neuropathy.