Genetic diversity of natural populations of Arabidopsis thaliana (L.) Heynh. in Karelia

The genetic structure of ten natural populations of Arabidopsis thaliana (L.) Heynh. at eight isozyme loci was studied. The populations were located in the northern part of the species range, 200 km from the north to the south along the Onega Lake coast in Karelia. Considerable genetic diversity (P99% = 43.7, Hobs = 0.003) was revealed that is not typical of populations of self-pollinating plant species. A direct correlation between the proportion of polymorphic loci and geographical latitude was shown (r = 0.68; P < 0.05). It is suggested that a high polymorphism level in Karelian Arabidopsis thaliana (L.) populations increasing from the south to the north is due to extreme environmental conditions in the northern part of the species range. The distribution of genetic diversity within and between populations is typical of self-pollinating species: the larger part of the total diversity resides among populations (GST = 0.583).     

Collaborative study report: Evaluation of the ATCC experimental mycoplasma reference strains panel prepared for comparison of NAT-based and conventional mycoplasma detection methods

The main goal of this collaborative study was to evaluate the experimental panel of cryopreserved mycoplasma reference strains recently prepared by the American Type Culture Collection (ATCC^®) in order to assess the viability and dispersion of cells in the mycoplasma stocks by measuring the ratio between the number of genomic copies (GC) and the number of colony forming units (CFU) in the reference preparations. The employment of microbial reference cultures with low GC/CFU ratios is critical for unbiased and reliable comparison of mycoplasma testing methods based on different methodological approaches, i.e., Nucleic Acid Testing (NAT) and compendial culture-based techniques. The experimental panel included ten different mycoplasma species known to represent potential human and animal pathogens as well as common contaminants of mammalian and avian cell substrates used in research, development, and manufacture of biological products. Fifteen laboratories with expertise in field of mycoplasma titration and quantification of mycoplasmal genomic DNA participated in the study conducted from February to October of 2012. The results of this study demonstrated the feasibility of preparing highly viable and dispersed (possessing low GC/CFU ratios) frozen stocks of mycoplasma reference materials, required for reliable comparison of NAT-based and conventional mycoplasma detection methods.     

COPS5 (Jab1) Protein Increases β Site Processing of Amyloid Precursor Protein and Amyloid β Peptide Generation by Stabilizing RanBP9 Protein Levels

Increased processing of amyloid precursor protein (APP) and accumulation of neurotoxic amyloid β peptide (Aβ) in the brain is central to the pathogenesis of Alzheimer''s disease (AD). Therefore, the identification of molecules that regulate Aβ generation is crucial for future therapeutic approaches for AD. We demonstrated previously that RanBP9 regulates Aβ generation in a number of cell lines and primary neuronal cultures by forming tripartite protein complexes with APP, low-density lipoprotein-related protein, and BACE1, consequently leading to increased amyloid plaque burden in the brain. RanBP9 is a scaffold protein that exists and functions in multiprotein complexes. To identify other proteins that may bind RanBP9 and regulate Aβ levels, we used a two-hybrid analysis against a human brain cDNA library and identified COPS5 as a novel RanBP9-interacting protein. This interaction was confirmed by coimmunoprecipitation experiments in both neuronal and non-neuronal cells and mouse brain. Colocalization of COPS5 and RanBP9 in the same subcellular compartments further supported the interaction of both proteins. Furthermore, like RanBP9, COPS5 robustly increased Aβ generation, followed by increased soluble APP-β (sAPP-β) and decreased soluble-APP-α (sAPP-α) levels. Most importantly, down-regulation of COPS5 by siRNAs reduced Aβ generation, implying that endogenous COPS5 regulates Aβ generation. Finally, COPS5 levels were increased significantly in AD brains and APΔE9 transgenic mice, and overexpression of COPS5 strongly increased RanBP9 protein levels by increasing its half-life. Taken together, these results suggest that COPS5 increases Aβ generation by increasing RanBP9 levels. Thus, COPS5 is a novel RanBP9-binding protein that increases APP processing and Aβ generation by stabilizing RanBP9 protein levels.     

Automatic Prediction of Rheumatoid Arthritis Disease Activity from the Electronic Medical Records

Objective

We aimed to mine the data in the Electronic Medical Record to automatically discover patients'' Rheumatoid Arthritis disease activity at discrete rheumatology clinic visits. We cast the problem as a document classification task where the feature space includes concepts from the clinical narrative and lab values as stored in the Electronic Medical Record.

Materials and Methods

The Training Set consisted of 2792 clinical notes and associated lab values. Test Set 1 included 1749 clinical notes and associated lab values. Test Set 2 included 344 clinical notes for which there were no associated lab values. The Apache clinical Text Analysis and Knowledge Extraction System was used to analyze the text and transform it into informative features to be combined with relevant lab values.

Results

Experiments over a range of machine learning algorithms and features were conducted. The best performing combination was linear kernel Support Vector Machines with Unified Medical Language System Concept Unique Identifier features with feature selection and lab values. The Area Under the Receiver Operating Characteristic Curve (AUC) is 0.831 (σ = 0.0317), statistically significant as compared to two baselines (AUC = 0.758, σ = 0.0291). Algorithms demonstrated superior performance on cases clinically defined as extreme categories of disease activity (Remission and High) compared to those defined as intermediate categories (Moderate and Low) and included laboratory data on inflammatory markers.

Conclusion

Automatic Rheumatoid Arthritis disease activity discovery from Electronic Medical Record data is a learnable task approximating human performance. As a result, this approach might have several research applications, such as the identification of patients for genome-wide pharmacogenetic studies that require large sample sizes with precise definitions of disease activity and response to therapies.     

Streptomyces ghanaensis pleiotropic regulatory gene wblA(gh) influences morphogenesis and moenomycin production

The wblA _gh gene, encoding a homologue of the WhiB-family of proteins, was identified in the sequenced genome of moenomycin producer Streptomyces ghanaensis. Deletion of the gene blocked aerial mycelium sporulation and caused a 230% increase in moenomycins production. S. ghanaensis overexpressing SSFG-01620: a homologue of extracellular protease inhibitor SCO0762, whose expression in Streptomyces coelicolor is down-regulated by wblA: showed deficiencies in sporulation similar to that of wblA _gh knockout strain. The wblA _gh gene of S. ghanaensis appears to play a negative role in the control of moenomycin biosynthesis and is essential for sporulation.     

Comparative analysis of genetic structure in natural populations of two Arabidopsis species with different degree of panmixia

Comparative analysis of genetic structure of northern natural populations of two Arabidopsis species with different degrees of panmixia was performed. The variability of 121 RAPD loci in seven populations of model plant A. thaliana possessing high degree of self fertility was studied together with 93 RAPD loci in population of cross-pollinating species A. lyrata ssp. petraea. The population of A. l. petraea demonstrated higher level of genetic variability (P 99% = 62.50%; H(exp) = 0.169) than the populations of A. Thaliana, which is obviously connected with biological features of reproduction of the species. A significant level of genetic variability (P 99% = 42.27%; H(exp) = 0.126) was revealed in populations of A. thaliana, which is not typical for self-pollinating plant species. The high population polymorphism of A. thaliana in the northern part of its range may be connected with adverse environmental conditions. The genetic distances between populations of the species studied (average DN = 0.494) confirm close relatedness between A. thaliana and A. l. petraea.     

Studies on Zn(II) and Cd(II) heteroligand complexes with RC(S)NHP(O)(OiPr)2 (R = Ph, NH2, PhNH) and α-diimine (bpy and phen) ligands. C-Cl bond cleavage of CH2Cl2 by [Zn(phen){PhC(S)NP(O)(OiPr)2}2]

The reaction of [ZnL^I,II₂] (L^I = [NH₂C(S)NP(O)(OiPr)₂]⁻; L^II = [PhNHC(S)NP(O)(OiPr)₂]⁻) or [Cd₂L^IV₄] (L^IV = [PhC(S)NP(O)(OiPr)₂]⁻) with 2,2′-bipyridine (bpy) or 1,10-phenanthroline (phen) leads to the heteroligand complexes [Zn(bpy)L^I,II₂], [Zn(phen)L^I,II₂], [Cd(bpy)L^IV₂] or [Cd(phen)L^IV₂], respectively. The introduction of the diimine ligands into the coordination sphere of the metal cation provokes a change from 1,5-O,S- to 1,3-N,S-coordination of the anionic ligands for Zn but not for the Cd species. The reaction of [Zn(phen)L^IV₂] (L^IV = PhC(S)NP(O)(OiPr)₂⁻) with CH₂Cl₂ cleaves the chlorine atoms from CH₂Cl₂ and leads to the formation of [Zn(phen)L^IVCl] and S,S′-bis(benzimidothio-N-diisopropoxyphosphoryl)methane (L^IV-CH₂-L^IV) in high yields. Using CHCl₃ or CCl₄ instead of CH₂Cl₂ does not lead to the formation of chlorine substituted products even under reflux conditions. The new compounds were investigated by ¹H and ³¹P{¹H} NMR, IR spectroscopy and microanalysis. Crystal structures of [ZnL^II₂], [Cd(phen)L^IV₂]·CH₂Cl₂, [Zn(bpy)L^I₂] and [Zn(phen)L^IVCl] were elucidated by X-ray diffraction.     

A2B adenosine receptor blockade enhances macrophage-mediated bacterial phagocytosis and improves polymicrobial sepsis survival in mice

Antimicrobial treatment strategies must improve to reduce the high mortality rates in septic patients. In noninfectious models of acute inflammation, activation of A2B adenosine receptors (A2BR) in extracellular adenosine-rich microenvironments causes immunosuppression. We examined A2BR in antibacterial responses in the cecal ligation and puncture (CLP) model of sepsis. Antagonism of A2BR significantly increased survival, enhanced bacterial phagocytosis, and decreased IL-6 and MIP-2 (a CXC chemokine) levels after CLP in outbred (ICR/CD-1) mice. During the CLP-induced septic response in A2BR knockout mice, hemodynamic parameters were improved compared with wild-type mice in addition to better survival and decreased plasma IL-6 levels. A2BR deficiency resulted in a dramatic 4-log reduction in peritoneal bacteria. The mechanism of these improvements was due to enhanced macrophage phagocytic activity without augmenting neutrophil phagocytosis of bacteria. Following ex vivo LPS stimulation, septic macrophages from A2BR knockout mice had increased IL-6 and TNF-α secretion compared with wild-type mice. A therapeutic intervention with A2BR blockade was studied by using a plasma biomarker to direct therapy to those mice predicted to die. Pharmacological blockade of A2BR even 32 h after the onset of sepsis increased survival by 65% in those mice predicted to die. Thus, even the late treatment with an A2BR antagonist significantly improved survival of mice (ICR/CD-1) that were otherwise determined to die according to plasma IL-6 levels. Our findings of enhanced bacterial clearance and host survival suggest that antagonism of A2BRs offers a therapeutic target to improve macrophage function in a late treatment protocol that improves sepsis survival.