ATP and its N<Superscript>6</Superscript>-substituted analogues: parameterization,molecular dynamics simulation and conformational analysis

In this work we used a combination of classical molecular dynamics and simulated annealing techniques to shed more light on the conformational flexibility of 12 adenosine triphosphate (ATP) analogues in a water environment. We present simulations in AMBER force field for ATP and 12 published analogues [Shah et al. (1997) Proc Natl Acad Sci USA 94: 3565–3570]. The calculations were carried out using the generalized Born (GB) solvation model in the presence of the cation Mg²⁺. The ion was placed at a close distance (2 Å) from the charged oxygen atoms of the beta and gamma phosphate groups of the ?3 negatively charged ATP analogue molecules. Analysis of the results revealed the distribution of inter-proton distances H8–H1′ and H8–H2′ versus the torsion angle ψ (C4–N9-C1′–O4′) for all conformations of ATP analogues. There are two gaps in the distribution of torsion angle ψ values: the first is between ?30 and 30 degrees and is described by cis-conformation; and the second is between 90 and 175 degrees, which mostly covers a region of anti conformation. Our results compare favorably with results obtained in experimental assays [Jiang and Mao (2002) Polyhedron 21:435–438].

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Figure Dihedral O4′–C1′–N9–C4 angle dependence on inter-proton distances H8–H1′ (crosses) and H8–H2′ (dots) measured for ATP

     

Microbial community analysis and identification of alternative host-specific fecal indicators in fecal and river water samples using pyrosequencing

It is important to know the comprehensive microbial communities of fecal pollution sources and receiving water bodies for microbial source tracking. Pyrosequencing targeting the V1-V3 hypervariable regions of the 16S rRNA gene was used to investigate the characteristics of bacterial and Bacteroidales communities in major fecal sources and river waters. Diversity analysis indicated that cow feces had the highest diversities in the bacterial and Bacteroidales group followed by the pig sample, with human feces having the lowest value. The Bacteroidales, one of the potential fecal indicators, totally dominated in the fecal samples accounting for 31%-52% of bacterial sequences, but much less (0.6%) in the river water. Clustering and Venn diagram analyses showed that the human sample had a greater similarity to the pig sample in the bacterial and Bacteroidales communities than to samples from other hosts. Traditional fecal indicators, i.e., Escherichia coli, were detected in the human and river water samples at very low rates and Clostridium perfringens and enterococci were not detected in any samples. Besides the Bacteroidales group, some microorganisms detected in the specific hosts, i.e., Parasutterella excrementihominis, Veillonella sp., Dialister invisus, Megamonas funiformis, and Ruminococcus lactaris for the human and Lactobacillus amylovorus and Atopostipes sp. for the pig, could be used as potential host-specific fecal indicators. These microorganisms could be used as multiple fecal indicators that are not dependent on the absence or presence of a single indicator. Monitoring for multiple indicators that are highly abundant and host-specific would greatly enhance the effectiveness of fecal pollution source tracking.     

Cleavage of von Willebrand factor by granzyme M destroys its factor VIII binding capacity

Von Willebrand factor (VWF) is a pro-hemostatic multimeric plasma protein that promotes platelet aggregation and stabilizes coagulation factor VIII (FVIII) in plasma. The metalloproteinase ADAMTS13 regulates the platelet aggregation function of VWF via proteolysis. Severe deficiency of ADAMTS13 is associated with thrombotic thrombocytopenic purpura, but does not always correlate with its clinical course. Therefore, other proteases could also be important in regulating VWF activity. In the present study, we demonstrate that VWF is cleaved by the cytotoxic lymphocyte granule component granzyme M (GrM). GrM cleaved both denaturated and soluble plasma-derived VWF after Leu at position 276 in the D3 domain. GrM is unique in that it did not affect the multimeric size and pro-hemostatic platelet aggregation ability of VWF, but instead destroyed the binding of VWF to FVIII in vitro. In meningococcal sepsis patients, we found increased plasma GrM levels that positively correlated with an increased plasma VWF/FVIII ratio in vivo. We conclude that, next to its intracellular role in triggering apoptosis, GrM also exists extracellularly in plasma where it could play a physiological role in controlling blood coagulation by determining plasma FVIII levels via proteolytic processing of its carrier VWF.     

Experimental and theoretical study on high temperature induced changes in chlorophyll <Emphasis Type="Italic">a</Emphasis> fluorescence oscillations in barley leaves upon 2 % CO<Subscript>2</Subscript>

Oscillations in many of photosynthetic quantities with a period of about 1 min can be routinely measured with higher plant leaves after perturbation of the steady state by sudden change in gas phase. Among all hypotheses suggested so far to explain the oscillations, an effect of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPCO) activation status to control the oscillations is highly probable, at least upon high temperature (HT) treatment when in vivo RuBPCO activity controlled by RuBPCO activase (RuBPCO-A) decreases. Therefore, we measured the oscillations in fluorescence signal coming from barley leaves (Hordeum vulgare L. cv. Akcent) after their exposure for various time intervals to different HTs in darkness. We also evaluated steady state fluorescence and CO₂ exchange parameters to have an insight to functions of electron transport chain within thylakoid membrane and Calvin cycle before initiation of the oscillations. The changes in period of the oscillations induced by moderate HT (up to 43 °C) best correlated with changes in non-photochemical fluorescence quenching (q_N) that in turn correlated with changes in gross photosynthetic rate (P _G) and rate of RuBPCO activation (k_act). Therefore, we suggest that changes in period of the oscillations caused by moderate HT are mainly controlled by RuBPCO activation status. For more severe HT (45 °C), the oscillations disappeared which was probably caused by an insufficient formation of NADPH by electron transport chain within thylakoid membrane as judged from a decrease in photochemical fluorescence quenching (q_P). Suggestions made on the basis of experimental data were verified by theoretical simulations of the oscillations based on a model of Calvin cycle and by means of a control analysis of the model.     

Tumor necrosis factor-alpha stimulates gastric epithelial cell proliferation

TNF-alpha is a cytokine produced during gastric mucosal injury. We examined whether TNF-alpha could promote mucosal repair by stimulation of epithelial cell proliferation and explored further the underlying mechanisms in a rat gastric mucosal epithelial cell line (RGM-1). TNF-alpha treatment (1-10 ng/ml) for 12 or 24 h significantly increased cell proliferation but did not induce apoptosis in RGM-1 cells. TNF-alpha treatment significantly increased cytosolic phospholipase A(2) and cyclooxygenase-2 (COX-2) protein expression and PGE(2) level but did not affect the protein levels of EGF, basic fibroblast growth factor, and COX-1 in RGM-1 cells. The mRNA of TNF receptor (TNF-R) 2 but not of TNF-R1 was also increased. Dexamethasone dose dependently inhibited the stimulatory effect of TNF-alpha on cell proliferation, which was associated with a significant decrease in cellular COX-2 expression and PGE(2) level. A selective COX-2 inhibitor 3-(3-fluorophenyl)-4-[4-(methylsulfonyl)phenyl]-5,5-dimethyl-(5)H-furan-2-one (DFU) by itself had no effect on basal cell proliferation but significantly reduced the stimulatory effect of TNF-alpha on RMG-1 cells. Combination of dexamethasone and DFU did not produce an additive effect. PGE(2) significantly reversed the depressive action of dexamethasone on cell proliferation. These results suggest that TNF-alpha plays a regulatory role in epithelial cell repair in the gastric mucosa via the TNF-alpha receptor and activation of the arachidonic acid/PG pathway.     

A Study of Glutathione <Emphasis Type="Italic">S</Emphasis>-transferase pi Expression in Central Nervous System of Subjects with Amyotrophic Lateral Sclerosis Using RNA Extraction from Formalin-Fixed,Paraffin-Embedded Material

The expression of glutathione S-transferase pi (GST pi), an enzyme responsible for inactivation of a large variety of toxic compounds was studied in spinal cord, motor and sensory brain cortex obtained from patients who died in the course of amyotrophic lateral sclerosis (ALS). The studies were performed on formalin-fixed, paraffin-embedded (FFPE) and freshly frozen tissues. The method of RNA isolation from FFPE was modified. A significant decrease of GST pi-mRNA expression was found in cervical spinal cord and motor brain cortex of ALS subjects comparing to analogue control tissues (P < 0.01), as well as in motor cortex of ALS subjects comparing to their sensory cortex (P < 0.05). In spinal cords the decrease in GST pi-mRNA expression was accompanied by a decrease of GST pi protein level. Results indicated lowered GST pi expression on both mRNA and protein levels in the regions of nervous system affected by ALS. The non-properly inactivated by GST toxic electrophiles and organic peroxides may thus contribute to motor neurons damage.     

Polymorphism of the angiotensin II type 1 receptor in patients with essential hypertension in Ukrainian population

The distribution of polymorphism of the angiotensin II type 1 receptor in Ukrainian population was investigated. Healthy persons had genotypes AA (51%), AC (34%), CC (15%) and alleles A (68%), C (32%). We suppose the prevalence of allele C and genotypes CC in health persons in Ukrainian population. The frequencies of genotypes and alleles in patients with essential hypertension were AA (22,85%), AC (51,9%), CC (25,3%) and A (48,7%), C (51,3%). Thus the development of essential hypertension was associated with the presence of allele C and its homozygote variant. Moreover the severity and complications of hypertension depended on the presence of this allele and genotype. We concluded that Ukrainian population has specific distribution of polymorphism of the angiotensin II type 1 receptor with prevalence of allele C1166 and genotype CC. The presence of these genetic variants is a risk factor for essential hypertension.     

Changes in serum leptin levels in strenuous exercise and its relation to zinc deficiency in rats

This study aimed to investigate the possible changes in serum leptin concentration caused by acute exercise and the effects of zinc deficiency on these changes. Forty male rats were divided into control-control, control-elercise, zinc-deficient-control, and zinc-deficient-exercise groups (10 rats in each). Control-exercise and zinc-deficient-exercise groups performed exercisse at 6 m/min speed on a rodent treadmill for 60 min or until exhaustion. All rats were decapitated 48h after the exercise, and blood samples were collected to determine serum leptin and zinc levels. Serum leptin levels in the zinc-deficient-control group were lower than in the control-control group. The mean exercise time of control-exercise group was significantly longer than the zinc-deficient-exercise group. We conclude that serum leptin levels significantly decrease both 48 h after strenuous exercise and in the zinc-deficient rats, and there is a further decrease in leptin levels when rats fed on a zinc-deficient diet performed exercise.     

Virulotypes of Bacillus anthracis strains isolated in Poland

Bacillus anthracis--the causative agent of anthrax--possesses several virulence genes located in the chromosome as well as in two B. anthracis virulence plasmids: pXO1 and pXO2. In the presented study, we determined occurrence of six virulence markers located in the virulence plasmids (capA, capB, capC, pagA, lef and cya) for capsule and toxin production together with virulence-associated gene gerXA and chromosomal gene sap, which are responsible for germination and S-layer biosynthesis respectively. Fourteen strains of B. anthracis isolated in Poland and belonging to five different MLVA genotypes were analyzed by PCR for presence of the aforementioned genes. Two virulotypes were found in tested strains. The only variation was absence of capA, capB and capC due to a lack of pXO2.     

Donuts, scratches and blanks: robust model-based segmentation of microarray images

MOTIVATION: Inner holes, artifacts and blank spots are common in microarray images, but current image analysis methods do not pay them enough attention. We propose a new robust model-based method for processing microarray images so as to estimate foreground and background intensities. The method starts with a very simple but effective automatic gridding method, and then proceeds in two steps. The first step applies model-based clustering to the distribution of pixel intensities, using the Bayesian Information Criterion (BIC) to choose the number of groups up to a maximum of three. The second step is spatial, finding the large spatially connected components in each cluster of pixels. The method thus combines the strengths of the histogram-based and spatial approaches. It deals effectively with inner holes in spots and with artifacts. It also provides a formal inferential basis for deciding when the spot is blank, namely when the BIC favors one group over two or three. RESULTS: We apply our methods for gridding and segmentation to cDNA microarray images from an HIV infection experiment. In these experiments, our method had better stability across replicates than a fixed-circle segmentation method or the seeded region growing method in the SPOT software, without introducing noticeable bias when estimating the intensities of differentially expressed genes. AVAILABILITY: spotSegmentation, an R language package implementing both the gridding and segmentation methods is available through the Bioconductor project (http://www.bioconductor.org). The segmentation method requires the contributed R package MCLUST for model-based clustering (http://cran.us.r-project.org). CONTACT: fraley@stat.washington.edu.