Biochemical investigation of multicorer sediment profile PS74/120-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/121-1

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/127-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/128-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Biochemical investigation of multicorer sediment profile PS74/107-2

To detect and track the impact of large-scale environmental changes in a the transition zone between the northern North Atlantic and the central Arctic Ocean, and to determine experimentally the factors controlling deep-sea biodiversity, the Alfred- Wegener-Institute for Polar and Marine Research (AWI) established the deep-sea long-term observatory HAUSGARTEN, which constitutes the first, and until now only open-ocean long-term station in a polar region. Virtually undisturbed sediment samples have been taken using a video-guided multiple corer (MUC) at 13 HAUSGARTEN stations along a bathymetric (1,000 - 4,000 m water depth) and a latitudinal transect in 2,500 m water depth as well as two stations at 230 and 1,200 m water depth within the framework of the KONGHAU project. Various biogenic sediment compounds were analyzed to estimate the input of organic matter from phytodetritus sedimentation, benthic activities (e.g. bacterial exoenzymatic activity), and the total biomass of the smallest sediment-inhabiting organisms (size range: bacteria to meiofauna).

Structural and Biochemical Dissection of the Trehalose Biosynthetic Complex in Pathogenic Fungi

Trehalose is a non-reducing disaccharide essential for pathogenic fungal survival and virulence. The biosynthesis of trehalose requires the trehalose-6-phosphate synthase, Tps1, and trehalose-6-phosphate phosphatase, Tps2. More importantly, the trehalose biosynthetic pathway is absent in mammals, conferring this pathway as an ideal target for antifungal drug design. However, lack of germane biochemical and structural information hinders antifungal drug design against these targets.

In this dissertation, macromolecular X-ray crystallography and biochemical assays were employed to understand the structures and functions of proteins involved in the trehalose biosynthetic pathway. I report here the first eukaryotic Tps1 structures from Candida albicans (C. albicans) and Aspergillus fumigatus (A. fumigatus) with substrates or substrate analogs. These structures reveal the key residues involved in substrate binding and catalysis. Subsequent enzymatic assays and cellular assays highlight the significance of these key Tps1 residues in enzyme function and fungal stress response. The Tps1 structure captured in its transition-state with a non-hydrolysable inhibitor demonstrates that Tps1 adopts an “internal return like” mechanism for catalysis. Furthermore, disruption of the trehalose biosynthetic complex formation through abolishing Tps1 dimerization reveals that complex formation has regulatory function in addition to trehalose production, providing additional targets for antifungal drug intervention.

I also present here the structure of the Tps2 N-terminal domain (Tps2NTD) from C. albicans, which may be involved in the proper formation of the trehalose biosynthetic complex. Deletion of the Tps2NTD results in a temperature sensitive phenotype. Further, I describe in this dissertation the structures of the Tps2 phosphatase domain (Tps2PD) from C. albicans, A. fumigatus and Cryptococcus neoformans (C. neoformans) in multiple conformational states. The structures of the C. albicans Tps2PD -BeF3-trehalose complex and C. neoformans Tps2PD(D24N)-T6P complex reveal extensive interactions between both glucose moieties of the trehalose involving all eight hydroxyl groups and multiple residues of both the cap and core domains of Tps2PD. These structures also reveal that steric hindrance is a key underlying factor for the exquisite substrate specificity of Tps2PD. In addition, the structures of Tps2PD in the open conformation provide direct visualization of the conformational changes of this domain that are effected by substrate binding and product release.

Last, I present the structure of the C. albicans trehalose synthase regulatory protein (Tps3) pseudo-phosphatase domain (Tps3PPD) structure. Tps3PPD adopts a haloacid dehydrogenase superfamily (HADSF) phosphatase fold with a core Rossmann-fold domain and a α/β fold cap domain. Despite lack of phosphatase activity, the cleft between the Tps3PPD core domain and cap domain presents a binding pocket for a yet uncharacterized ligand. Identification of this ligand could reveal the cellular function of Tps3 and any interconnection of the trehalose biosynthetic pathway with other cellular metabolic pathways.

Combined, these structures together with significant biochemical analyses advance our understanding of the proteins responsible for trehalose biosynthesis. These structures are ready to be exploited to rationally design or optimize inhibitors of the trehalose biosynthetic pathway enzymes. Hence, the work described in this thesis has laid the groundwork for the design of Tps1 and Tps2 specific inhibitors, which ultimately could lead to novel therapeutics to treat fungal infections.

The effect of Ligula intestinalis on blood sex steroid hormones, gonadal tissue and some other biological parameters changes of Chalcalburnus mossulensis in Vahdat dam of Kordestan-Iran

Chalcalburnus mossulensis from the cyprinidae family is one of the indigenous fish in Gheshlag Lake of Kordestan-Iran. Ligula intestinalis is one of the infective parasites of this fish. In this study, the effect of this parasite on some biological aspects of this fish like weight, length, PI, CF, GSR, blood sex steroid hormones and gonadal tissue, was investigated. During one year, by seasonal sampling, 144 fish sample from mentioned species were collected using trap net. By considering the scale sample, the fish with the same age were separated and tested as the point of infection with the parasite. By biochemical and histopathological investigation of fish blood and gonad tissue, it was clear that increase in infection rate of fish, caused decrease in biological parameters. There was a significant difference (p<0.05) between the means of sex steroid hormones (17-B Estradiol and Testostreone) of infected and non-infected fish and this parameter was significantly lower in infected ones. This significant difference also was seen between the means of male and female gonads maturation steps of infected and non-infected samples. The reason for lack of maturation of gonads tissue is infection by Ligula intestinalis. Also in gonads of infected fish, abnormal degenerative changes like MMC (Melano-Macrophage Center), hemorrhage and necrosis were seen that were not reported by other researchers. So the spread of this parasite in different water sources should be consider as the point of the maintenance of native species and cultivated fish.

Biochemical parameters response to weight loss in patients with non-alcoholic steatohepatitis.

Background: Non-alcoholic steatohepatitis (NASH) is a chronic liver disease that is capable of progressing to end-stage liver disease, but generally has a benign course. Non-alcoholic steatohepatitis (NASH) is a growing public health problem with no approved therapy. NASH projected to be the leading cause of liver transplantation in the United States by 2020. Obesity, non-insulin-dependent diabetes mellitus and hyperlipidaemia are the most common associations of the disease. Global prevalence of NASH is 10-24% amongst general population but increases to 25-75% in obese diabetic individuals. Objective: There is an urgent need for efficient therapeutic options as there is still no approved medication. The aim of this study was to detect changes in biochemical parameters including insulin resistance, cytokines, blood lipid profile and liver enzymes following weight loss in patients with non-alcoholic steatohepatitis. Materials and methods: One hundred obese patients with NASH, their age between 35-50 years, body mass index (BMI) from 30 to 35 Kg/m2 were included in the study in two subgroups; the first group (A) received moderate aerobic exercise training in addition to diet regimen , where the second group (B) received no treatment intervention. Results: The mean values of leptin, TNF-α, IL6, IL8, Alanine Aminotransferase (ALT), Aspartate Aminotransferase (AST), Homeostasis Model Assessment-Insulin Resistance- index (HOMA-IR), Total Cholesterol (TC), Low Density Lipoprotein Cholesterol (LDL-c) , Triglycerides (TG) and BMI were significantly decreased in group (A), where the mean value of Adiponectin and High Density Lipoprotein Cholesterol (HDL-c) were significantly increased, while there were no significant changes in group (B). Also, there was a significant difference between both groups at the end of the study. Conclusion: Weight loss modulates insulin resistance, adiponectin, leptin, inflammatory cytokine levels and markers of hepatic function in patients with nonalcoholic steatohepatitis.

Influence of magnesium on biochemical parameters of iron and oxidative stress in patients with type 2 diabetes

Introduction: Studies have shown that oxidative stress, found in patients with type 2 diabetes, may be due to changes in the metabolism of minerals, such as magnesium and iron. Data related to compartmentalization of these minerals in diabetes are scarce and controversial. Objective: This study assessed the influence of magnesium on biochemical parameters of iron and oxidative stress in patients with type 2 diabetes. Methods: A case-control study in male and female subjects aged 27-59 years, divided into two groups: type 2 diabetes (n=40) and control (n=48). Intake of magnesium and iron was assessed by three-day food record. Plasma, erythrocyte and urinary levels of magnesium, serum iron, ferritin, total iron binding capacity, fasting glucose, glycated hemoglobin, insulin, creatinine clearance and plasma thiobarbituric acid reactive substances (TBARS) were analyzed. Results and Discussion: Magnesium intake and plasma magnesium were lower in diabetic subjects. There was low urinary magnesium excretion, with no difference between groups. Although normal, the diabetic group had lower serum iron and ferritin concentrations compared to control subjects. Plasma TBARS in diabetic patients was higher than control while creatinine clearance was lower. An inverse correlation between erythrocyte magnesium and serum iron and ferritin was observed in the diabetes group. Conclusions: Diabetes induced hypomagnesemia and this, associated with chronic hyperglycemia, may have enhanced oxidative stress. Erythrocyte magnesium may have contributed to prevent iron overload and worsening of oxidative stress and hyperglycemic status.

Structural and Biochemical Characterization of Peroxiredoxin Q beta from Xylella fastidiosa CATALYTIC MECHANISM and HIGH REACTIVITY

The phytopathogenic bacterium Xylella fastidiosa is the etiological agent of various plant diseases. To survive under oxidative stress imposed by the host, microorganisms express antioxidant proteins, including cysteine-based peroxidases named peroxiredoxins. This work is a comprehensive analysis of the catalysis performed by PrxQ from X. fastidiosa (XfPrxQ) that belongs to a peroxiredoxin class still poorly characterized and previously considered as moderately reactive toward hydroperoxides. Contrary to these assumptions, our competitive kinetics studies have shown that the second-order rate constants of the peroxidase reactions of XfPrxQ with hydrogen peroxide and peroxynitrite are in the order of 107 and 106 M(-1) s(-1), respectively, which are as fast as the most efficient peroxidases. The XfPrxQ disulfides were only slightly reducible by dithiothreitol; therefore, the identification of a thioredoxin system as the probable biological reductant of XfPrxQ was a relevant finding. We also showed by site-specific mutagenesis and mass spectrometry that an intramolecular disulfide bond between Cys-47 and Cys-83 is generated during the catalytic cycle. Furthermore, we elucidated the crystal structure of XfPrxQ C47S in which Ser-47 and Cys-83 lie similar to 12.3 angstrom apart. Therefore, significant conformational changes are required for disulfide bond formation. In fact, circular dichroism data indicated that there was a significant redox-dependent unfolding of alpha-helices, which is probably triggered by the peroxidatic cysteine oxidation. Finally, we proposed a model that takes data from this work as well data as from the literature into account.

Pressure Induced Structural Changes and Gas Diffusion Pathways in Monomeric Fluorescent Proteins

Fluorescent proteins (FPs) are extremely valuable biochemical markers which have found a wide range of applications in cellular and molecular biology research. The monomeric variants of red fluorescent proteins (RFPs), known as mFruits, have been especially valuable for in vivo applications in mammalian cell imaging. Fluorescent proteins consist of a chromophore caged in the beta-barrel protein scaffold. The photophysical properties of an FP is determined by its chromophore structure and its interactions with the protein barrel. Application of hydrostatic pressure on FPs results in the modification of the chromophore environment which allows a systematic study of the role of the protein-chromophore interactions on photophysical properties of FPs. Using Molecular Dynamics (MD) computer simulations, I investigated the pressure induced structural changes in the monomeric variants mCherry, mStrawberry, and Citrine. The results explain the molecular basis for experimentally observed pressure responses among FP variants. It is found that the barrel flexibility, hydrogen bonding interactions and chromophore planarity of the FPs can be correlated to their contrasting photophysical properties at vaious pressures. I also investigated the oxygen diffusion pathways in mOrange and mOrange2 which exhibit marked differences in oxygen sensitivities as well as photostability. Such computational identifications of structural changes and oxygen diffusion pathways are important in guiding mutagenesis efforts to design fluorescent proteins with improved photophysical properties.

Changes In The Bacterial Community Of Soil From A Neutral Mine Drainage Channel.

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments.

Molecular And Biochemical Characterization Of Caffeine Synthase And Purine Alkaloid Concentration In Guarana Fruit.

Guarana seeds have the highest caffeine concentration among plants accumulating purine alkaloids, but in contrast with coffee and tea, practically nothing is known about caffeine metabolism in this Amazonian plant. In this study, the levels of purine alkaloids in tissues of five guarana cultivars were determined. Theobromine was the main alkaloid that accumulated in leaves, stems, inflorescences and pericarps of fruit, while caffeine accumulated in the seeds and reached levels from 3.3% to 5.8%. In all tissues analysed, the alkaloid concentration, whether theobromine or caffeine, was higher in young/immature tissues, then decreasing with plant development/maturation. Caffeine synthase activity was highest in seeds of immature fruit. A nucleotide sequence (PcCS) was assembled with sequences retrieved from the EST database REALGENE using sequences of caffeine synthase from coffee and tea, whose expression was also highest in seeds from immature fruit. The PcCS has 1083bp and the protein sequence has greater similarity and identity with the caffeine synthase from cocoa (BTS1) and tea (TCS1). A recombinant PcCS allowed functional characterization of the enzyme as a bifunctional CS, able to catalyse the methylation of 7-methylxanthine to theobromine (3,7-dimethylxanthine), and theobromine to caffeine (1,3,7-trimethylxanthine), respectively. Among several substrates tested, PcCS showed higher affinity for theobromine, differing from all other caffeine synthases described so far, which have higher affinity for paraxanthine. When compared to previous knowledge on the protein structure of coffee caffeine synthase, the unique substrate affinity of PcCS is probably explained by the amino acid residues found in the active site of the predicted protein.

Changes In Chromatin Structure In Nih 3t3 Cells Induced By Valproic Acid And Trichostatin A.

Valproic acid (VPA) and trichostatin A (TSA) are known histone deacetylase inhibitors (HDACIs) with epigenetic activity that affect chromatin supra-organization, nuclear architecture, and cellular proliferation, particularly in tumor cells. In this study, chromatin remodeling with effects extending to heterochromatic areas was investigated by image analysis in non-transformed NIH 3T3 cells treated for different periods with different doses of VPA and TSA under conditions that indicated no loss of cell viability. Image analysis revealed chromatin decondensation that affected not only euchromatin but also heterochromatin, concomitant with a decreased activity of histone deacetylases and a general increase in histone H3 acetylation. Heterochromatin protein 1-α (HP1-α), identified immunocytochemically, was depleted from the pericentromeric heterochromatin following exposure to both HDACIs. Drastic changes affecting cell proliferation and micronucleation but not alteration in CCND2 expression and in ratios of Bcl-2/Bax expression and cell death occurred following a 48-h exposure of the NIH 3T3 cells particularly in response to higher doses of VPA. Our results demonstrated that even low doses of VPA (0.05 mM) and TSA (10 ng/ml) treatments for 1 h can affect chromatin structure, including that of the heterochromatin areas, in non-transformed cells. HP1-α depletion, probably related to histone demethylation at H3K9me3, in addition to the effect of VPA and TSA on histone H3 acetylation, is induced on NIH 3T3 cells. Despite these facts, alterations in cell proliferation and micronucleation, possibly depending on mitotic spindle defects, require a longer exposure to higher doses of VPA and TSA.

Bleeding Complications In Dengue Are Not Associated With Significant Changes In The Modulators Of The Endothelial Barrier.

Bleeding complications in dengue may occur irrespective of the presence of plasma leakage. We compared plasma levels of modulators of the endothelial barrier among three dengue groups: bleedings without plasma leakage, dengue hemorrhagic fever, and non-complicated dengue. The aim was to evaluate whether the presence of subtle alterations in microvascular permeability could be detected in bleeding patients. Plasma levels of VEGF-A and its soluble receptors were not associated with the occurrence of bleeding in patients without plasma leakage. These results provide additional rationale for considering bleeding as a complication independent of endothelial barrier breakdown, as proposed by the 2009 WHO classification.