The BARD1 C-Terminal Domain Structure and Interactions with Polyadenylation Factor CstF-50†

The BARD1 N-terminal RING domain binds BRCA1 while the BARD1 C-terminal ankyrin and tandem BRCT repeat domains bind CstF-50 to modulate mRNA processing and RNAP II stability in response to DNA damage. Here we characterize the BARD1 structural biochemistry responsible for CstF- 50 binding. The crystal structure of the BARD1 BRCT domain uncovers a degenerate phosphopeptide binding pocket lacking the key arginine required for phosphopeptide interactions in other BRCT proteins.Small angle X-ray scattering together with limited proteolysis results indicates that ankyrin and BRCT domains are linked by a flexible tether and do not adopt a fixed orientation relative to one another. Protein pull-down experiments utilizing a series of purified BARD1 deletion mutants indicate that interactions between the CstF-50 WD-40 domain and BARD1 involve the ankyrin-BRCT linker but do not require ankyrin or BRCT domains. The structural plasticity imparted by the ANK-BRCT linker helps to explain the regulated assembly of different protein BARD1 complexes with distinct functions in DNA damage signaling including BARD1-dependent induction of apoptosis plus p53 stabilization and interactions. BARD1 architecture and plasticity imparted by the ANK-BRCT linker are suitable to allow the BARD1 C-terminus to act as a hub with multiple binding sites to integrate diverse DNA damage signals directly to RNA polymerase

CHARACTERIZATION OF MICRO FLORA FROM COAL MINES OF BALUCHISTAN, PAKISTAN

The coal sites of our country Pakistan especially Baluchistan and their micro flora have not been defined properly. However, it is thought to harbour a number of microbes including harmful, non-harmful gram positive, gram negative, acidophilic, alkaliphilic, halophiles, and thermophiles within itself. The proposed study aims to seek a cultural and diversified cataloguing of the entire micro flora present in the coal sites of Mach, Baluchistan. The study spreads to a timeline of 3 months and samples will be collected from Mach coal mine. Moreover, workers, who are suffering from lung diseases in particular were, will also be subjected to analysis to assess probable correlation with microbes. Total of 150 samples were collected in which 50 of coal dust samples were collected with sterilized swabs. 50 samples of airborne debris from mines sewerage water where collected in pre-sterilized Duran bottles. Moreover 50 sputum mine worker samples were collected in sterilized stomacher bag for isolation and correlation studies. Out of 150 samples we isolate different genera of kingdom monera which are related to coal mines and environment. Isolated microbes includes harmful, non-harmful gram positive, gram negative,acidophile, alkaliphilic, halophiles sulphur oxidising and thermophiles bacteria’s which perform different activities according to the atmosphere and offered nutrient’s .obligate acidophilic, heterotropic ,aerobic motile ,gram negative bacteria are generally found. Acidiothiobacillus species is major among them. Beside it, Pseudomonas, flavobacteriu species, shigella specie, vibrio parahaemolyticuc, Staphylococcal aureus and Escherichia coli colonies are also obtained. Microscopy performs for colony morphology. During microscopy we found different shapes of bacteria’s like rod, cocci, spring shape etc. Further more we perfume APi 20 kit test for some bacterial species and compile the results. The study concluded that coal mines are riche in microbial flora which is effective for coal miners and also for the GDP growth of the country. Somehow there are also harmful bacteria’s but they do not produce great impact on miner. Keywords: coal mine microbial flora , microscopy, biochemical test

Bio-techniques for improvement of qualitative and quantitative traits in walnut (Juglans regia)

Walnut, Juglans regia (L.) is an economically significant plant for its immense nutritive and economic value. The breeding character of walnut has lent it a wide diversity in genetic characteristics. The principal vegetative and common traditional agronomic traits together with biochemical characterization i.e., karyotyping and isoenzyme expression have been the early research methods. However, these techniques are time-consuming and susceptible to the environmental variations. Literature is meager in the distribution, applied applications in general and the use of agriculture biotechnology in particular in case of walnut plants. The bio-techniques like molecular markers are adequate in number and there is little or no diversity in the method employed for research on walnuts. Despite basic research method, the organization of information, its retrieval and presentation structures, form elaboration experienced immense advancement via molecular markers such as RFLP, ISSR, RAPD AFLP, SSR and SNP. This appraisal in its first part provides detailed information regarding the present scenario of data on biogeographical distribution, health benefits of walnut worldwide and current applications in the agroforestry management, biochemical evaluations and applied uses of a walnut tree which is relevant for both basic and applied research. The review in its second part sheds light on the application of sophisticated agricultural biotechnology techniques such as use of molecular markers to evaluate, realize the full potential of walnut for increasing its quality, quantity and for its sustainable production which cannot be obtained through usual breeding techniques to meet the demands of a projected world population

Metabolome-wide association study on ABCA7 indicates a role of ceramide metabolism in Alzheimer’s disease

Genome-wide association studies (GWASs) have identified genetic loci associated with the risk of Alzheimer’s disease (AD), but the molecular mechanisms by which they confer risk are largely unknown. We conducted a metabolome-wide association study (MWAS) of AD-associated loci from GWASs using untargeted metabolic profiling (metabolomics) by ultraperformance liquid chromatography–mass spectrometry (UPLC-MS). We identified an association of lactosylceramides (LacCer) with AD-related single-nucleotide polymorphisms (SNPs) in ABCA7 (P = 5.0 × 10−5 to 1.3 × 10−44). We showed that plasma LacCer concentrations are associated with cognitive performance and genetically modified levels of LacCer are associated with AD risk. We then showed that concentrations of sphingomyelins, ceramides, and hexosylceramides were altered in brain tissue from Abca7 knockout mice, compared with wild type (WT) (P = 0.049–1.4 × 10−5), but not in a mouse model of amyloidosis. Furthermore, activation of microglia increases intracellular concentrations of hexosylceramides in part through induction in the expression of sphingosine kinase, an enzyme with a high control coefficient for sphingolipid and ceramide synthesis. Our work suggests that the risk for AD arising from functional variations in ABCA7 is mediated at least in part through ceramides. Modulation of their metabolism or downstream signaling may offer new therapeutic opportunities for AD

Metabolome-wide association study on ABCA7 indicates a role of ceramide metabolism in Alzheimer's disease.

Genome-wide association studies (GWASs) have identified genetic loci associated with the risk of Alzheimer's disease (AD), but the molecular mechanisms by which they confer risk are largely unknown. We conducted a metabolome-wide association study (MWAS) of AD-associated loci from GWASs using untargeted metabolic profiling (metabolomics) by ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). We identified an association of lactosylceramides (LacCer) with AD-related single-nucleotide polymorphisms (SNPs) in ABCA7 (P = 5.0 × 10-5 to 1.3 × 10-44). We showed that plasma LacCer concentrations are associated with cognitive performance and genetically modified levels of LacCer are associated with AD risk. We then showed that concentrations of sphingomyelins, ceramides, and hexosylceramides were altered in brain tissue from Abca7 knockout mice, compared with wild type (WT) (P = 0.049-1.4 × 10-5), but not in a mouse model of amyloidosis. Furthermore, activation of microglia increases intracellular concentrations of hexosylceramides in part through induction in the expression of sphingosine kinase, an enzyme with a high control coefficient for sphingolipid and ceramide synthesis. Our work suggests that the risk for AD arising from functional variations in ABCA7 is mediated at least in part through ceramides. Modulation of their metabolism or downstream signaling may offer new therapeutic opportunities for AD

Blinding for precision scattering experiments: The MUSE approach as a case study

Human bias is capable of changing the analysis of measured data sufficiently to alter the results of an experiment. It is incumbent upon modern experiments, especially those investigating quantities considered contentious in the broader community, to blind their analysis in an effort to minimize bias. The choice of a blinding model is experiment specific, but should also aim to prevent accidental release of results before an analysis is finalized. In this paper, we discuss common threats to an unbiased analysis, as well as common quantities that can be blinded in different types of nuclear physics experiments. We use the Muon Scattering Experiment as an example, and detail the blinding scheme used therein.Comment: 6 pages, 3 figure

Low levels of cathepsin D are associated with a poor prognosis in endometrial cancer

Total cytosolic cathepsin D (Cat D) levels were estimated by an immunoradiometric assay in a series of 156 consecutive patients with surgical stages I–III primary endometrial adenocarcinoma. Simultaneously, the tissue content of both oestrogen (ER) and progesterone (PR) receptors, and p185HER-2/neu, DNA content (ploidy), and the fraction of S-phase cells (S-phase) were also estimated. Tumoral Cat D content ranged from 0 to 243 pmol mg−1 protein (median 44 pmol mg−1 protein) and was not associated with any of the established clinicopathological and biological prognostic variables, with the exception of a weak positive correlation with the tumoral p185HER-2/neu levels. Univariable analysis performed on a subset of 97 patients, followed for a minimum of 2 years or until death, showed that patient age at diagnosis, high histological grade, advanced surgical stage, vascular invasion, positive peritoneal cytology, low levels of Cat D, negative ER and PR status, aneuploidy, and high S-phase were predictive of the presence of persistent or recurrent disease. However, multivariable analysis revealed that only histological grade, surgical stage, Cat D and PR were significantly associated with the patient's outcome. From these findings, we conclude that Cat D is an independent prognostic factor in endometrial adenocarcinoma, its low levels being associated with a worse clinical outcome. © 1999 Cancer Research Campaig