Controls of Soil Spatial Variability in a Dry Tropical Forest

We examined the roles of lithology, topography, vegetation and fire in generating local-scale (<1 km²) soil spatial variability in a seasonally dry tropical forest (SDTF) in southern India. For this, we mapped soil (available nutrients, Al, total C, pH, moisture and texture in the top 10cm), rock outcrops, topography, all native woody plants ≥1 cm diameter at breast height (DBH), and spatial variation in fire frequency (times burnt during the 17 years preceding soil sampling) in a permanent 50-ha plot. Unlike classic catenas, lower elevation soils had lesser moisture, plant-available Ca, Cu, Mn, Mg, Zn, B, clay and total C. The distribution of plant-available Ca, Cu, Mn and Mg appeared to largely be determined by the whole-rock chemical composition differences between amphibolites and hornblende-biotite gneisses. Amphibolites were associated with summit positions, while gneisses dominated lower elevations, an observation that concurs with other studies in the region which suggest that hillslope-scale topography has been shaped by differential weathering of lithologies. Neither NO₃⁻-N nor NH₄⁺-N was explained by the basal area of trees belonging to Fabaceae, a family associated with N-fixing species, and no long-term effects of fire on soil parameters were detected. Local-scale lithological variation is an important first-order control over soil variability at the hillslope scale in this SDTF, by both direct influence on nutrient stocks and indirect influence via control of local relief.     

A novel catalytic mechanism for ATP hydrolysis employed by the N-terminal nucleotide-binding domain of Cdr1p, a multidrug ABC transporter of Candida albicans

Although essentially conserved, the N-terminal nucleotide-binding domain (NBD) of Cdr1p and other fungal transporters has some unique substitutions of amino acids which appear to have functional significance for the drug transporters. We have previously shown that the typical Cys193 in Walker A as well as Trp326 and Asp327 in the Walker B of N-terminal NBD (NBD-512) of Cdr1p has acquired unique roles in ATP binding and hydrolysis. In the present study, we show that due to spatial proximity, fluorescence resonance energy transfer (FRET) takes place between Trp326 of Walker B and MIANS [2-(4-maleimidoanilino) naphthalene-6-sulfonic acid] on Cys193 of Walker A motif. By exploiting FRET, we demonstrate how these critical amino acids are positioned within the nucleotide-binding pocket of NBD-512 to bind and hydrolyze ATP. Our results show that both Mg²⁺ coordination and nucleotide binding contribute to the formation of the active site. The entry of Mg²⁺ into the active site causes the first large conformational change that brings Trp326 and Cys193 in close proximity to each other. We also show that besides Trp326, typical Glu238 in the Q-loop also participates in coordination of Mg²⁺ by NBD-512. A second conformational change is induced when ATP, but not ADP, docks into the pocket. Asn328 does sensing of the γ-phosphate of the substrate in the extended Walker B motif, which is essential for the second conformational change that must necessarily precede ATP hydrolysis. Taken together our results imply that the uniquely placed residues in NBD-512 have acquired critical roles in ATP catalysis, which drives drug extrusion.     

Biogenic Synthesis, Purification, and Chemical Characterization of Anti-inflammatory Resolvins Derived from Docosapentaenoic Acid (DPAn-6)

Enzymatically oxygenated derivatives of the ω-3 fatty acids cis-4,7,10,13,16,19-docosahexaenoic acid (DHA) and cis-5,8,11,14,17-eicosapentaenoic acid, known as resolvins, have potent inflammation resolution activity (Serhan, C. N., Clish, C. B., Brannon, J., Colgan, S. P., Chiang, N., and Gronert, K. (2000) J. Exp. Med. 192, 1197–1204; Hong, S., Gronert, K., Devchand, P. R., Moussignac, R., and Serhan, C. N. (2003) J. Biol. Chem. 278, 14677–14687). Our objective was to determine whether similar derivatives are enzymatically synthesized from other C-22 fatty acids and whether these molecules possess inflammation resolution properties. The reaction of DHA, DPAn-3, and DPAn-6 with 5-, 12-, and 15-lipoxygenases produced oxylipins, which were identified and characterized by liquid chromatography coupled with tandem mass-spectrometry. DPAn-6 and DPAn-3 proved to be good substrates for 15-lipoxygenase. 15-Lipoxygenase proved to be the most efficient enzyme of the three tested for conversion of long chain polyunsaturated fatty acids to corresponding oxylipins. Since DPAn-6 is a major component of Martek DHA-S™ oil, we focused our attention on reaction products obtained from the DPAn-6 and 15-lipoxygenase reaction. (17S)-hydroxy-DPAn-6 and (10,17S)-dihydroxy-DPAn-6 were the main products of this reaction. These compounds were purified by preparatory high performance liquid chromatography techniques and further characterized by NMR, UV spectrophotometry, and tandem mass spectrometry. We tested both compounds in two animal models of acute inflammation and demonstrated that both compounds are potent anti-inflammatory agents that are active on local intravenous as well as oral administration. These oxygenated DPAn-6 compounds can thus be categorized as a new class of DPAn-6-derived resolvins.Enzymatically formed oxygenation products of C-20 and C-22 long chain polyunsaturated fatty acids (LC-PUFAs),⁴ have important biological roles in inflammation, allergies, and blood clotting and are thus believed to have therapeutic potential in several chronic immune diseases (1–10) Several biologically important products of cis-5,8,11,14-eicosatetraenoic acid/arachidonic acid (ARA), cis-5,8,11,14,17-eicosapentaenoic acid (EPA), and cis-4,7,10,13,16,19-docosahexaenoic acid (DHA) have been described (4, 11, 12). Proinflammatory oxylipins, such as leukotrienes and some prostaglandins, are derived from ARA, an ω-6 fatty acid. Interestingly, the same fatty acid also serves as a precursor to anti-inflammatory or proresolution molecules like lipoxins (13, 14). Stable analogues of lipoxins are being developed as drugs for asthma and other inflammatory airway diseases (15, 16). Oxylipins derived from ω-3 fatty acids, such as DHA and EPA, known as resolvins, are primarily anti-inflammatory in nature (17). EPA acts as a precursor to the E-series resolvins that have shown potential in the treatment of colitis, arthritis, and periodontitis (18–20). The resolvins of the D-series derived from DHA are useful as neuroprotective agents. 10,17-Dihydroxy-4,7,11,13,15,19-docosahexaenoic acid (10,17-HDHA) or neuroprotectin D1 is a resolvin that is formed endogenously in the human brain and eye and is believed to exert its protective effect against cell injury-induced oxidative stress (21–23).The main enzymes responsible for the production of these oxygenated LC-PUFA products are primarily lipoxygenases and, in addition, cyclo-oxygenases and cytochromes P450. These enzymes produce oxylipins via transcellular activity, often involving multiple cell types (24). This activity mainly results in mono-, di-, and tri-hydroxylation products of fatty acids that have varying potencies, depending on the exact structure of the compound. Lipoxygenases are non-heme, iron-containing dioxygenases that catalyze the regioselective and enantioselective oxidation of polyunsaturated fatty acids containing one or more cis,cis-1,4-pentadienoic moieties to give the corresponding hydroperoxy derivatives (25, 26). We thus considered that, in addition to DHA and EPA, other C-22 PUFAs containing such methylene interrupted double bonds may also be substrates for lipoxygenases and that resulting products may have anti-inflammatory activity similar to DHA-derived resolvins. DPAn-6 (cis-4,7,10,13,16-docosapentaenoic acid) is present in algal oils, and recent studies have demonstrated that this fatty acid has anti-inflammatory activities in vitro and, in conjunction with DHA, also has anti-inflammatory activity in vivo.⁵ Also, it has been suggested that a combination of DHA and DPAn-6 could be a beneficial natural therapy in neuroinflammatory conditions like Alzheimer disease. Specifically, in a 3×Tg-AD mouse model of Alzheimer disease, DPAn-6 was shown to reduce levels of early stage phospho-Tau epitopes, which in turn correlated with a reduction in phosphorylated c-Jun N-terminal kinase, a putative Tau kinase (27). Although the precise mechanism of action of DPAn-6 in these inflammatory milieus is not known, it suggests a possible role for oxylipin products of DPAn-6 in resolution of inflammation. Also, another LC-PUFA, DPAn-3 (cis-7,10,13,16,19-docosapentaenoic acid) usually present along with DHA and EPA in marine oils is known to be a potent inhibitor of platelet aggregation (28–30). In addition, this LC-PUFA has a potent inhibitory effect on angiogenesis through the suppression of VEGFR-2 (vascular endothelial-cell growth factor receptor 2) expression. Angiogenesis is known to contribute to tumor growth, inflammation, and microangiopathy, again pointing to the possibility that anti-inflammatory activity of DPAn-3 might be mediated through resolvin-like products as in the case of DHA and EPA (31).The purpose of this research was to determine whether oxylipins are formed from the C-22 LC-PUFAs, DPAn-6 and DPAn-3, by lipoxygenase activity; to compare them to products formed from DHA; to chemically characterize products; to purify key oxylipin products from the DPAn-6/15-lipoxygenase reaction; and to test whether these compounds have resolvin-like anti-inflammatory activity. This research also sets the stage for preparation and isolation of a wide range of other C-22 oxylipins that could be evaluated as potential anti-inflammatory compounds.     

A spectrophotometric method for calmodulin assay

The activity of calmodulin as an activator of cAMP phosphodiesterase was assayed. AMP was hydrolyzed by 5'-nucleotidase, and the adenosine formed was measured by both liquid scintillation counting and spectrophotometry at 265 nm. Calmodulin activities measured by the two methods were equivalent, indicating that spectrophotometric assay of calmodulin can be used in place of the isotopic method.     

TiD: Standalone software for mining putative drug targets from bacterial proteome

TiD is a standalone application, which relies on basic assumption that a protein must be essential for pathogens survival and non-homologous with host to qualify as putative target. With an input bacterial proteome, TiD removes paralogous proteins, picks essential ones, and excludes proteins homologous with host organisms. The targets illustrate non-homology with at least 40 out of 84 gut microbes, considered safe for human. TiD classifies proposed targets as known, novel and virulent. Users can perform pathway analysis, choke point analysis, interactome analysis, subcellular localization and functional annotations through web servers cross-referenced with the application. Drug targets identified by TiD for Listeria monocytogenes, Bacillus anthracis and Pseudomonas aeruginosa have revealed significant overlaps with previous studies. TiD takes < 2 h to scan putative targets from a bacterial proteome with ~ 5000 proteins; hence, we propose it as a useful tool for rational drug design. TiD is available at http://bmicnip.in/TiD/.     

Oligomeric Hsp33 with enhanced chaperone activity: gel filtration, cross-linking, and small angle x-ray scattering (SAXS) analysis

Hsp33, an Escherichia coli cytosolic chaperone, is inactive under normal conditions but becomes active upon oxidative stress. It was previously shown to dimerize upon activation in a concentration- and temperature-dependent manner. This dimer was thought to bind to aggregation-prone target proteins, preventing their aggregation. In the present study, we report small angle x-ray scattering (SAXS), steady state and time-resolved fluorescence, gel filtration, and glutaraldehyde cross-linking analysis of full-length Hsp33. Our circular dichroism and fluorescence results show that there are significant structural changes in oxidized Hsp33 at different temperatures. SAXS, gel filtration, and glutaraldehyde cross-linking results indicate, in addition to the dimers, the presence of oligomeric species. Oxidation in the presence of physiological salt concentration leads to significant increases in the oligomer population. Our results further show that under conditions that mimic the crowded milieu of the cytosol, oxidized Hsp33 exists predominantly as an oligomeric species. Interestingly, chaperone activity studies show that the oligomeric species is much more efficient compared with the dimers in preventing aggregation of target proteins. Taken together, these results indicate that in the cell, Hsp33 undergoes conformational and quaternary structural changes leading to the formation of oligomeric species in response to oxidative stress. Oligomeric Hsp33 thus might be physiologically relevant under oxidative stress.     

Human MICAL1: Activation by the small GTPase Rab8 and small‐angle X‐ray scattering studies on the oligomerization state of MICAL1 and its complex with Rab8

Human MICAL1 is a member of a recently discovered family of multidomain proteins that couple a FAD‐containing monooxygenase‐like domain to typical protein interaction domains. Growing evidence implicates the NADPH oxidase reaction catalyzed by the flavoprotein domain in generation of hydrogen peroxide as a second messenger in an increasing number of cell types and as a specific modulator of actin filaments stability. Several proteins of the Rab families of small GTPases are emerging as regulators of MICAL activity by binding to its C‐terminal helical domain presumably shifting the equilibrium from the free – auto‐inhibited – conformation to the active one. We here extend the characterization of the MICAL1–Rab8 interaction and show that indeed Rab8, in the active GTP‐bound state, stabilizes the active MICAL1 conformation causing a specific four‐fold increase of k_cat of the NADPH oxidase reaction. Kinetic data and small‐angle X‐ray scattering (SAXS) measurements support the formation of a 1:1 complex between full‐length MICAL1 and Rab8 with an apparent dissociation constant of approximately 8 μM. This finding supports the hypothesis that Rab8 is a physiological regulator of MICAL1 activity and shows how the protein region preceding the C‐terminal Rab‐binding domain may mask one of the Rab‐binding sites detected with the isolated C‐terminal fragment. SAXS‐based modeling allowed us to propose the first model of the free full‐length MICAL1, which is consistent with an auto‐inhibited conformation in which the C‐terminal region prevents catalysis by interfering with the conformational changes that are predicted to occur during the catalytic cycle.