Most of the existing in silico phosphorylation site prediction systems use machine learning approach that requires preparing a good set of classification data in order to build the classification ...knowledge. Furthermore, phosphorylation is catalyzed by kinase enzymes and hence the kinase information of the phosphorylated sites has been used as major classification data in most of the existing systems. Since the number of kinase annotations in protein sequences is far less than that of the proteins being sequenced to date, the prediction systems that use the information found from the small clique of kinase annotated proteins can not be considered as completely perfect for predicting outside the clique. Hence the systems are certainly not generalized. In this paper, a novel generalized prediction system, PPRED (Phosphorylation PREDictor) is proposed that ignores the kinase information and only uses the evolutionary information of proteins for classifying phosphorylation sites.
Experimental results based on cross validations and an independent benchmark reveal the significance of using the evolutionary information alone to classify phosphorylation sites from protein sequences. The prediction performance of the proposed system is better than those of the existing prediction systems that also do not incorporate kinase information. The system is also comparable to systems that incorporate kinase information in predicting such sites.
The approach presented in this paper provides an efficient way to identify phosphorylation sites in a given protein primary sequence that would be a valuable information for the molecular biologists working on protein phosphorylation sites and for bioinformaticians developing generalized prediction systems for the post translational modifications like phosphorylation or glycosylation. PPRED is publicly available at the URL http://www.cse.univdhaka.edu/~ashis/ppred/index.php.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Present investigation was conducted at the Research Farm of Indian Institute of Soil Science, Bhopal during 2017-18 and 2018-19 to study the performance of chickpea crop under various nutrient ...management modules in a Vertisol. The field experiment was set up in a randomized block design with three replications of twelve different INM modules. During the rabi seasons of 2017-18 and 2018-19, the chickpea (cv. JG-315) was grown with a set of treatments. The crop's performance was evaluated in terms of growth, yield (grain and straw), nutritional content, and nutrient uptake under different treatments. At crop harvest, the physic-chemical characteristics of the soil were also evaluated. Finally, the relationship between the numerous examined parameters was determined. The results showed that integrated nutrient management modules had a positive impact on chickpea crop performance and productivity when compared to using only inorganic fertilizer. The INM modules dramatically increased soil organic carbon and improved soil health in terms of physical and chemical qualities, in addition to higher crop performance. Among the various modules, (1) application of 75% STCR dose + FYM @ 5t ha-1to maize followed by 100% P only to chickpea and (2) application of FYM @ 20t ha-1to maize followed by FYM @ 5t ha-1 to chickpea increased the productivity and nutrient uptake in chickpea, improved soil physico-chemical properties and reflected as viable technique in improving soil nutrient availability on sustainable basis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Four novel dimeric bis-μ-imido bridged metal–metal bonded oxidomolybdenum(V) complexes MoV 2O2L′2 1–4 (1–4) (where L′1–4 are rearranged ligands formed in situ from H2L1–4) and a new mononuclear ...dioxidomolybdenum(VI) complex MoVIO2L5 (5) synthesized from salen type N2O2 ligands are reported. This rare series of imido-bridged complexes (1–4) have been furnished from rearranged H3L′1–4 ligands, containing an aromatic diimine (o-phenylenediamine) “linker”, where Mo assisted hydrolysis followed by −CN bond cleavage of one of the arms of the ligand H2L1–4 took place. A monomeric molybdenum(V) intermediate species MoVO(HL′1–4)(OEt) (I d 1–4 ) was generated in situ. The concomitant deprotonation and dimerization of two molybdenum(V) intermediate species (I d 1–4 ) ultimately resulted in the formation of a bis-μ-imido bridge between the two molybdenum centers of MoV 2O2L′2 1–4 (1–4). The mechanism of formation of 1–4 has been discussed, and one of the rare intermediate monomeric molybdenum(V) species I d 4 has been isolated in the solid state and characterized. The monomeric dioxidomolybdenum(VI) complex MoVIO2L5 (5) was prepared from the ligand H2L5 where the aromatic “linker” was replaced by an aliphatic diimine (1,2-diaminopropane). All the ligands and complexes have been characterized by elemental analysis, IR, UV–vis spectroscopy, NMR, ESI-MS, and cyclic voltammetry, and the structural features of 1, 2, 4, and 5 have been solved by X-ray crystallography. The DNA binding and cleavage activity of 1–5 have been explored. The complexes interact with CT-DNA by the groove binding mode, and the binding constants range between 103 and 104 M–1. Fairly good photoinduced cleavage of pUC19 supercoiled plasmid DNA was exhibited by all the complexes, with 4 showing the most promising photoinduced DNA cleavage activity of ∼93%. Moreover, in vitro cytotoxic activity of all the complexes was evaluated by MTT assay, which reveals that the complexes induce cell death in MCF-7 (human breast adenocarcinoma) and HCT-15 (colon cancer) cell lines.
Selenium (Se) reservoirs in coal waste rock from the Elk Valley, southeastern British Columbia, the location of Canada’s major steelmaking coal mines, were characterized and quantified by analyzing ...samples collected from the parent rock, freshly blasted waste rock (less than 10 days old), and aged waste rock (deposited between 1982 and 2012). Se is present throughout the waste rock dumps at a mean digestible (SeD) concentration of 3.12 mg/kg. Microprobe analyses show that Se is associated with the primary minerals sphalerite, pyrite, barite, and chalcopyrite and secondary Fe oxyhydroxides. Selenium K-edge X-ray absorption near-edge spectroscopy analyses indicate that, on average, 21% of Se is present as selenide (Se2–) in pyrite and sphalerite, 19% of Se is present as selenite (Se4+) in barite, 21% of Se is present as exchangeable Fe oxyhydroxide and clay-adsorbed Se4+, and 39% of Se is present as organoselenium associated with coaly matter. The dominant source minerals for aqueous-phase Se are pyrite and sphalerite. Secondary Fe oxyhydroxide sequesters, on average, 37% of Se released by pyrite oxidation. Measured long-term Se fluxes from a rock drain at the base of a waste dump suggest that at least 20% of Se2–-bearing sulfides were oxidized and released from that dump over the past 30 year period; however, the Se mass lost was not evident in SeD analyses.
The biogeochemical cycling of phosphorus (P) in South and Southeast Asian floodplain and delta aquifers has received insufficient attention in research studies, even though dissolved orthophosphate ...(PO43−) in this region is closely linked with the widespread contamination of groundwater with toxic arsenic (As). The overarching aim of this study was to characterize the enrichment of P in anoxic groundwater and to provide insight into the biogeochemical mechanisms underlying its mobilization, subsurface transport, and microbial cycling. Detailed groundwater analyses and in situ experiments were conducted that focused on three representative field sites located in the Red River Delta (RRD) of Vietnam and the Bengal Delta Plain (BDP) in West Bengal, India. The results showed that the total concentrations of dissolved P (TDP) ranged from 0.03 to 1.50 mg L−1 in groundwater, with PO43− being the dominant P species. The highest concentrations occurred in anoxic sandy Holocene aquifers where PO43− was released into groundwater through the microbial degradation of organic carbon and the concomitant reductive dissolution of Fe(III)-(hydr)oxides. The mobilization of PO43− may still constitute an active process within shallow Holocene sediments. Furthermore, a sudden supply of organic carbon may rapidly decrease the redox potential, which causes an increase in TDP concentrations in groundwater, as demonstrated by a field experiment. Considering the subsurface transport of PO43−, Pleistocene aquifer sediments represented effective sinks; however, the enduring contact between oxic Pleistocene sediments and anoxic groundwater also changed the sediments PO43−-sorption capacity over time. A stable isotope analysis of PO43−-bound oxygen indicated the influences of intracellular microbial cycling as well as a specific PO43− source with a distinct isotopically heavy signal. Consequently, porous aquifers in Asian floodplain and delta regions proved to be ideal natural laboratories to study the biogeochemical cycling of P and its behavior in groundwater environments.
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•Overall high PO43− conc. in groundwater of the Red River Delta and the Bengal Delta•PO43− represented the dominant P species in anoxic groundwater reaching 1.5 mg L−1.•PO43− release via reductive dissolution of Fe-oxides coupled with OM mineralization•PO43− is subject to microbial cycling, subsurface transport, and immobilization.•Stable O isotope analysis in PO43− as tool to unravel P cycling and its sources
Most pathogenic bacteria require iron for growth. However, this metal is not freely available in the mammalian host. Due to its poor solubility and propensity to catalyze the generation of reactive ...oxygen species, host iron is kept in solution bound to specialized iron binding proteins. Access to iron is an important factor in the outcome of bacterial infections; iron limitation frequently induces virulence and drives pathogenic interactions with host cells. Here, we review the response of
to changes in iron availability, the relevance of this response to TB pathogenesis, and its potential for the design of new therapeutic interventions.
This study investigates the risk of arsenic (As) exposure to the communities in rural Bengal, even when they have been supplied with As safe drinking water. The estimates of exposure via dietary and ...drinking water routes show that, when people are consuming water with an As concentration of less than 10 μg L–1, the total daily intake of inorganic As (TDI-iAs) exceeds the previous provisional tolerable daily intake (PTDI) value of 2.1 μg day–1 kg–1 BW, recommended by the World Health Organization (WHO) in 35% of the cases due to consumption of rice. When the level of As concentration in drinking water is above 10 μg L–1, the TDI-iAs exceeds the previous PTDI for all the participants. These results imply that, when rice consumption is a significant contributor to the TDI-iAs, supplying water with an As concentration at the current national drinking water standard for India and Bangladesh would place many people above the safety threshold of PTDI. We also found that the consumption of vegetables in rural Bengal does not pose a significant health threat to the population independently. This study suggests that any effort to mitigate the As exposure of the villagers in Bengal must consider the risk of As exposure from rice consumption together with drinking water.
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