The Deuterator: software for the determination of backbone amide deuterium levels from H/D exchange MS data

Background  

The combination of mass spectrometry and solution phase amide hydrogen/deuterium exchange (H/D exchange) experiments is an effective method for characterizing protein dynamics, and protein-protein or protein-ligand interactions. Despite methodological advancements and improvements in instrumentation and automation, data analysis and display remains a tedious process. The factors that contribute to this bottleneck are the large number of data points produced in a typical experiment, each requiring manual curation and validation, and then calculation of the level of backbone amide exchange. Tools have become available that address some of these issues, but lack sufficient integration, functionality, and accessibility required to address the needs of the H/D exchange community. To date there is no software for the analysis of H/D exchange data that comprehensively addresses these issues.     

TC10 Is Regulated by Caveolin in 3T3-L1 Adipocytes

Background

TC10 is a small GTPase found in lipid raft microdomains of adipocytes. The protein undergoes activation in response to insulin, and plays a key role in the regulation of glucose uptake by the hormone.

Methodology/Principal Findings

TC10 requires high concentrations of magnesium in order to stabilize guanine nucleotide binding. Kinetic analysis of this process revealed that magnesium acutely decreased the nucleotide release and exchange rates of TC10, suggesting that the G protein may behave as a rapidly exchanging, and therefore active protein in vivo. However, in adipocytes, the activity of TC10 is not constitutive, indicating that mechanisms must exist to maintain the G protein in a low activity state in untreated cells. Thus, we searched for proteins that might bind to and stabilize TC10 in the inactive state. We found that Caveolin interacts with TC10 only when GDP-bound and stabilizes GDP binding. Moreover, knockdown of Caveolin 1 in 3T3-L1 adipocytes increased the basal activity state of TC10.

Conclusions/Significance

Together these data suggest that TC10 is intrinsically active in vivo, but is maintained in the inactive state by binding to Caveolin 1 in 3T3-L1 adipocytes under basal conditions, permitting its activation by insulin.     

Serum trace mineral variations in Nili-Ravi buffaloes suffering with prepartum vaginal prolapse in two different agro-ecological zones of Punjab, Pakistan

The present study was conducted during 2005 and 2006 on 200 Nili-Ravi buffaloes kept in two agroecological zones (irrigated [zone 1] and rain-fed [zone-2]) of Punjab, Pakistan, with the objective to determine the level of trace minerals (Cu, Fe, Zn, Se) in serum of the buffaloes suffering from vaginal prolapse and to compare them with their healthy counterparts. In each zone 50 buffaloes suffering from prepartum vaginal prolapse during their seventh month of gestation were identified through survey. Vaginal prolapse-affected buffaloes belonging to zone 1 were identified as group VPB1 (N = 50), whereas buffaloes belonging to zone 2 were recognized as VPB2 (N = 50). The buffaloes of control group in zone 1 and zone 2 were identified as NCB1 and NCB2, respectively. The blood samples in all four groups of buffaloes were collected three times, i.e., first when these animals were in the eighth month of gestation, second during the eighth to ninth month of gestation, and finally when these animals were in the ninth or later month of gestation. The mean serum copper concentrations in buffaloes of group VPB1 were significantly lower (P < 0.05) in comparison with NCB1 and NCB2, whereas there were nonsignificant differences (P > 0.05) in copper concentrations between VPB1 and VPB2. There was a significant difference (P < 0.05) of iron concentration in VPB1 compared with NCB1 and NCB2. Similarly, VPB2 also had significantly lower (P < 0.05) iron concentrations compared with NCB1 and NCB2. Serum zinc concentrations were significantly lower (P < 0.05) in animals of the VPB1 group when compared with NCB1 and NCB2. Similarly, lower zinc concentrations were observed in VPB2 in comparison with NCB1 and NCB2. There was significantly lower (P < 0.05) zinc concentration in affected buffaloes (VPB1 and VPB2) from the ninth month of gestation to term when compared with those in the eighth to ninth mo of gestation, and with those not yet in the eighth month of gestation. Serum selenium concentration were significantly higher (P < 0.05) in control group buffaloes (NCB1 and NCB2) in comparison with vaginal prolapse-affected buffaloes (VPB1 and VPB2). During different stages of gestation, mean serum selenium concentrations varied nonsignificantly (P > 0.05) within each group of buffalo. Based on information obtained from this study, it was concluded that the low serum concentration of copper and selenium are linked to increased incidence of vaginal prolapse in buffaloes during the last trimester of gestation.     

四种独立通风笼具（IVC）的检测

目的比较4种独立通风笼具（individually ventilated cages,IVC）的环境参数。方法参考GB14925-2001的检测方法对分别来自4个厂家生产的4种不同的IVC进行环境检测。结果4种IVC在空气洁净度、落下菌、噪声和照度等4个指标检测数据较为一致;在梯度压差、换气次数、气流速度等3个指标存在较大的差别;而温湿度等指标取决于IVC所处的外部环境。结论目前缺乏国家标准对IVC环境指标进行限定,各厂家所生产的IVC存在差异,需要在此方面加强研究,以促进IVC的标准化,更好的服务于实验动物行业。     

日光温室栽培对杏花及果实生长发育的影响

对日光温室内与露地栽培的金太阳杏的花期物候、花型及果实生长发育进行了系统观察与分析,结果表明,日光温室栽培比露地栽培的始花期提前33d,花期延长4d,不完全花比例上升33.25%;果枝上花的有效性顺序由露地时的中果枝>长果枝>短果枝>花束状果枝变为温室栽培的短果枝>花束状果枝>中果枝>长果枝;日光温室栽培使杏果实发育的第 、 阶段延长,第 阶段缩短,整个生育期延长15d。统计分析认为:日光温室栽培的第 阶段生长速率显著低于露地,第 阶段的累积生长量显著高于露地。较低的夜间温度是造成温室内杏果实第 阶段较长、生长较慢以及果个变大的原因。     

Synthesis and urease enzyme inhibitory effects of some dicoumarols

Dicoumarols 1-10 with substituted phenyl residues at C-11 were synthesized and screened for their urease inhibition effects. All synthesized compounds showed varying degree of urease inhibitory activity ranging from IC50 = 74.30-91.35 microM.     

Juliflorine: A potent natural peripheral anionic-site-binding inhibitor of acetylcholinesterase with calcium-channel blocking potential, a leading candidate for Alzheimer’s disease therapy

The alkaloid juliflorine (1) from Prosopis juliflora inhibited acetylcholinesterase (AChE, EC 3.1.1.7) and butyrylcholinesterase (BChE, EC 3.1.1.8) enzymes in a concentration-dependent fashion with IC₅₀ values 0.42 and 0.12 μM, respectively. Lineweaver-Burk as well as Dixon plots and their secondary replots indicated that the nature of inhibition was purely of non-competitive type with K_i values 0.4 and 0.1 μM, against AChE and BChE, respectively. By molecular docking studies compound 1 was found to be ideally spaced inside the aromatic gorge of AChE with rings A/B remaining at the top and rings C/D penetrating deep into the gorge, that might be due to the greater hydrophobicity of rings C/D as compared to rings A/B, allowing their simultaneous interaction with the peripheral anionic and quaternary ammonium-binding sites. The 1-AChE complex was found to be stabilized by hydrophobic contacts, hydrogen bonding, and π-π stacking between the compound 1 and amino acid residues of the aromatic gorge of AChE. Amino acid residues Tyr70, Asp72, Tyr121, Trp279, and Tyr334 of the peripheral anionic site (PAS) of AChE were found to be exclusively involved in the hydrophobic contacts with compound 1 that might be responsible for the competitive mode of inhibition. Compound 1 also showed dose-dependent (30-500 μg/mL) spasmolytic and Ca²⁺-channel blocking activities in isolated rabbit jejunum preparations. The cholinesterase inhibitory potential along with calcium-channel blocking activity of compound 1 and safe profile in human neutrophils viable assay could make it a possible drug candidate for Alzheimer’s disease.     

Genomic affinities in Arachis section Arachis (Fabaceae): molecular and cytogenetic evidence

Section Arachis is the largest of nine sections in the genus Arachis and includes domesticated peanut, A. hypogaea L. Most species are diploids (x=10) with two tetraploids and a few aneuploids. Three genome types have been recognized in this section (A, B and D), but the genomes are not well characterized and relationships of several newly described species are uncertain. To clarify genomic relationships in section Arachis, cytogenetic information and molecular data from amplified fragment length polymorphism (AFLP) and the trnT-F plastid region were used to provide an additional insight into genome composition and species relationships. Cytogenetic information supports earlier observations on genome types of A. cruziana, A. herzogii, A. kempff-mercadoi and A. kuhlmannii but was inconclusive about the genome composition of A. benensis, A. hoehnei, A. ipaensis, A. palustris, A. praecox and A. williamsii. An AFLP dendrogram resolved species into four major clusters and showed A. hypogaea grouping closely with A. ipaensis and A. williamsii. Sequence data of the trnT-F region provided genome-specific information and showed for the first time that the B and D genomes are more closely related to each other than to the A genome. Integration of information from cytogenetics and biparentally and maternally inherited genomic regions show promise in understanding genome types and relationships in Arachis.