Phosphorelays Provide Tunable Signal Processing Capabilities for the Cell

Achieving a complete understanding of cellular signal transduction requires deciphering the relation between structural and biochemical features of a signaling system and the shape of the signal-response relationship it embeds. Using explicit analytical expressions and numerical simulations, we present here this relation for four-layered phosphorelays, which are signaling systems that are ubiquitous in prokaryotes and also found in lower eukaryotes and plants. We derive an analytical expression that relates the shape of the signal-response relationship in a relay to the kinetic rates of forward, reverse phosphorylation and hydrolysis reactions. This reveals a set of mathematical conditions which, when satisfied, dictate the shape of the signal-response relationship. We find that a specific topology also observed in nature can satisfy these conditions in such a way to allow plasticity among hyperbolic and sigmoidal signal-response relationships. Particularly, the shape of the signal-response relationship of this relay topology can be tuned by altering kinetic rates and total protein levels at different parts of the relay. These findings provide an important step towards predicting response dynamics of phosphorelays, and the nature of subsequent physiological responses that they mediate, solely from topological features and few composite measurements; measuring the ratio of reverse and forward phosphorylation rate constants could be sufficient to determine the shape of the signal-response relationship the relay exhibits. Furthermore, they highlight the potential ways in which selective pressures on signal processing could have played a role in the evolution of the observed structural and biochemical characteristic in phosphorelays.     

IL-6/IFN-beta 2 in synovial effusions of patients with rheumatoid arthritis and other arthritides. Identification of several isoforms and studies of cellular sources

We have looked for IL-6, a cytokine that has immunomodulating and inflammation-associated activities, in joint exudates (fluid and mononuclear cells) from patients with rheumatoid arthritis and other arthritides using both biologic and biochemical assays. IL-6 was assessed by its ability to stimulate alpha 1-antichymotrypsin secretion from the human hepatoma cell line Hep3B clone 2, an activity which is blocked by an antiserum to Escherichia coli derived IL-6, and by the growth of the IL-6-dependent murine hybridoma 7TD1 cell line. IL-6 isoforms in synovial fluid were characterized by immunoaffinity chromatography followed by Western blotting. The presence of IL-1 in synovial fluids and its production by synovial fluid mononuclear cells was monitored by Western blotting and indirect immunofluorescence with polyclonal anti-IL-1 beta antisera. In an analysis of 30 effusions from 27 rheumatoid patients with acutely inflamed joints, abundant quantities of IL-6 (greater than 2 ng/ml) were detected in 23 by the alpha 1-antichymotrypsin bioassay. Several rheumatoid synovial fluids also had elevated IL-6 levels in the 7TD1 bioassay. Seven of nine nonrheumatoid effusions also contained high levels of IL-6 (greater than 2 ng/ml). No IL-1 (less than 0.25 ng/ml) could be detected by Western blotting in 10 rheumatoid effusions even though eight of these contained high levels of IL-6. The IL-6 activity could be neutralized with a rabbit antiserum to rIL-6. Multiple IL-6 isoforms (25, 30, 45 kDa) were present in two rheumatoid and one traumatic effusion studied. Fresh mononuclear cells isolated from various synovial effusions did not appear to make IL-6 constitutively, as no IL-6 could be detected in the media of cells cultured for 12 to 18 h after isolation. Similarly, there was no constitutive production of IL-1 by these cells. However, synovial fluid mononuclear cells could be induced to secrete both IL-6 and IL-1 after stimulation with LPS. The LPS-responsive cells were monocytes and not lymphocytes or dendritic cells. These findings suggest that IL-6 is involved in inflammatory joint disease. However, the primary cells synthesizing it may be located in the synovial lining instead of the joint exudate.     

Comparative Analysis of the Orphan CRISPR2 Locus in 242 Enterococcus faecalis Strains

Clustered, Regularly Interspaced Short Palindromic Repeats and their associated Cas proteins (CRISPR-Cas) provide prokaryotes with a mechanism for defense against mobile genetic elements (MGEs). A CRISPR locus is a molecular memory of MGE encounters. It contains an array of short sequences, called spacers, that generally have sequence identity to MGEs. Three different CRISPR loci have been identified among strains of the opportunistic pathogen Enterococcus faecalis. CRISPR1 and CRISPR3 are associated with the cas genes necessary for blocking MGEs, but these loci are present in only a subset of E. faecalis strains. The orphan CRISPR2 lacks cas genes and is ubiquitous in E. faecalis, although its spacer content varies from strain to strain. Because CRISPR2 is a variable locus occurring in all E. faecalis, comparative analysis of CRISPR2 sequences may provide information about the clonality of E. faecalis strains. We examined CRISPR2 sequences from 228 E. faecalis genomes in relationship to subspecies phylogenetic lineages (sequence types; STs) determined by multilocus sequence typing (MLST), and to a genome phylogeny generated for a representative 71 genomes. We found that specific CRISPR2 sequences are associated with specific STs and with specific branches on the genome tree. To explore possible applications of CRISPR2 analysis, we evaluated 14 E. faecalis bloodstream isolates using CRISPR2 analysis and MLST. CRISPR2 analysis identified two groups of clonal strains among the 14 isolates, an assessment that was confirmed by MLST. CRISPR2 analysis was also used to accurately predict the ST of a subset of isolates. We conclude that CRISPR2 analysis, while not a replacement for MLST, is an inexpensive method to assess clonality among E. faecalis isolates, and can be used in conjunction with MLST to identify recombination events occurring between STs.     

Exogenous application of calcium chloride in wheat genotypes alleviates negative effect of drought stress by modulating antioxidant machinery and enhanced osmolyte accumulation

Plants use various mechanisms to cope with drought constraints at morphological, physiological, and biochemical level by means of different adaptive mechanisms. All organisms use a network of signal transduction pathways to control their metabolism and to adapt to the environment. Among these pathways, calcium (Ca²⁺) ions play an important role as a universal second messenger. Calcium has unique properties and universal ability to transmit diverse signals that trigger primary physiological actions in the cell in response to hormones, pathogens, and stress factors. Calcium plays a fundamental role in regulating the polar growth of cells and tissues and participates in plant adaptation to various stress factors. This study was conducted to examine the role of Ca²⁺ in ameliorating the adverse effect of drought stress responses in two contrasting wheat genotypes, HD 2733 (drought sensitive) and HD 2987 (drought tolerant), differing in their drought tolerance. The plants were treated with mannitol or Hoagland solution and then supplemented with CaCl₂ (10 mM). Measurements of seed germination, shoot growth, and chlorophyll content showed that calcium treatment increased all these factors in tolerant genotype (HD 2987) under induced stress condition. Drought stress reduced relative water content, osmolyte, and soluble sugar accumulation in both the genotypes, but CaCl₂ supplementation increased all the components under stress condition in HD 2987 as compared to HD 2733. The oxidative damage caused by induced stress was lower in HD 2987 compared to HD 2733 genotypes as assessed by their higher photosynthetic capacity and lower electrolyte leakage, malondialdehyde (MDA) content as well as H₂O₂ accumulation. Less accumulation of superoxide and H₂O₂ was also observed in HD 2987 genotype after CaCl₂ supplementation combined with mannitol treatment. In addition, the enhanced accumulation of calcium in the HD 2987 genotype is correlated with the higher activities of antioxidant enzymes than HD 2733 genotype under similar stress conditions. Our findings provide evidence of the protective role of exogenous calcium in conferring better tolerance against mannitol-induced drought stress in wheat genotypes, which could be useful as genetic stock to develop wheat tolerant varieties in breeding programs.     

Nitrogen fixation ability explains leaf chemistry and arbuscular mycorrhizal responses to fertilization

Atmospheric nitrogen (N) and phosphorus (P) deposition rates are predicted to drastically increase in the coming decades. The ecosystem level consequences of these increases will depend on how plant tissue nutrient concentrations, stoichiometry and investment in nutrient uptake mechanisms such as arbuscular mycorrhizal fungi (AMF) change in response to increased nutrient availability, and how responses differ between plant functional types. Using a factorial nutrient addition experiment with seedlings of multiple N-fixing and non-N-fixing tree species, we examined whether leaf chemistry and AMF responses differ between these dominant woody plant functional groups of tropical savanna and dry forest ecosystems. We found that N-fixers have remarkably stable foliar chemistry that stays constant with external input of nutrients. Non-N-fixers responded to N and N + P addition by increasing both concentrations and total amounts of foliar N, but showed a corresponding decrease in P concentrations while total amounts of foliar P stayed constant, suggesting a ‘dilution’ of tissue P with increased N availability. Non-N-fixers also showed an increase in N:P ratios with N and N + P addition, probably driven by both an increase in N and a decrease in P concentrations. AMF colonization decreased with N + P addition in non-N-fixers and increased with N and N + P addition in N-fixers, suggesting differences in their nutrient acquisition roles in the two plant functional groups. Our results suggest that N-fixers and non-N-fixers can differ significantly in their responses to N and P deposition, with potential consequences for future nutrient and carbon cycling in savanna and dry forest ecosystems.     

Lyotropic Liquid Crystalline Nanoparticles of Amphotericin B: Implication of Phytantriol and Glyceryl Monooleate on Bioavailability Enhancement

Implication of different dietary specific lipids such as phytantriol (PT) and glyceryl monooleate (GMO) on enhancing the oral bioavailability of amphotericin B (AmB) was examined. Liquid crystalline nanoparticles (LCNPs) were prepared using hydrotrope method, followed by in vitro characterization, Caco-2 cell monolayer uptake, and in vivo pharmacokinetic and toxicity evaluation. Optimized AmB-LCNPs displayed small particle size (<?210 nm) with a narrow distribution (~?0.2), sustained drug release and high gastrointestinal stability, and reduced hemolytic toxicity. PLCNPs presented slower release, i.e., ~?80% as compared to ~?90% release in case of GLCNPs after 120 h. Significantly higher uptake in Caco-2 monolayer substantiated the role of LCNPs in increasing the intestinal permeability followed by increased drug titer in plasma. Pharmacokinetic studies demonstrated potential of PT in enhancing the bioavailability (approximately sixfold) w.r.t. of its native counterpart with reduced nephrotoxicity as presented by reduced nephrotoxicity biomarkers and histology studies. These studies established usefulness of PLCNPs over GLCNPs and plain drug. It can be concluded that acid-resistant lipid, PT, can be utilized efficiently as an alternate lipid for the preparation of LCNPs to enhance bioavailability and to reduce nephrotoxicity of the drug as compared to other frequently used lipid, i.e., GMO.     

GH10 XynF1 and Xyn11A: the predominant xylanase identified in the profiling of extracellular proteome of <Emphasis Type="Italic">Aspergillus oryzae</Emphasis> LC1

Advanced techniques of enzyme production and purification have become prerequisite due to their diverse industrial applications. There is an utmost requirement for screening of new strains capable of synthesising industrially useful enzymes. The present study reports the production and profiling of extracellular proteins expressed by the newly isolated strain of a filamentous fungus, Aspergillus oryzae LC1. The extracellular enzyme production was done by submerged fermentation using Mendel’s and Sternberg’s medium (MSM), and its optimisation was done using one factor at a time (OFAT). The presence of xylanase was confirmed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymography. In addition, the profiling of extracellular proteome of Aspergillus oryzae LC1 was carried out by liquid chromatography coupled tandem mass spectrometry (LC-MS/MS). In this study, media optimisation showed 5.7-fold increase in xylanase activity. The multiple bands observed in zymography revealed the presence of various forms of xylanase. A total of 73 proteins were identified in LC-MS/MS analysis. Functional classification showed that the hydrolytic enzymes consisted of 48% glycoside hydrolase, 11% proteases, 1% polysaccharide lyase and esterase’s, 9% oxidoreductases and 30% other proteins. A total of 26 families of glycosidic hydrolase were detected with other protein families such as serine peptidase, S, LysM, G-D-S-L, M35, carboxyl esterase (CE1), pectate lyase (PL) and oxidoreductases. Among the huge diversity of synergistically acting biomass cleaving enzymes, endo-1, 4-β xylanase with isoforms: xyn F1, xyn B, β xylanase and xyn 11A belonging to GH10 family covered the major portion of the total percentage of identified proteins. As per our knowledge, this is the first report of extracellular proteome analysis of Aspergillus oryzae LC1 suggesting its capability for recombinant expression and evaluation in hemicellulose deconstruction applications.     

Antiapoptotic effects of vitamins C and E against cypermethrin‐induced oxidative stress and spermatogonial germ cell apoptosis

Toxicological studies have demonstrated the relation between use of agrochemicals and fertility issues within males. Thus, the present study aimed to elucidate the propensity of cypermethrin (CYP) in bringing testicular germ cell apoptosis and effective attenuation by vitamins C and E in caprines. Reproductive toxicity of CYP was evaluated using histomorphological, cytological, and biochemical changes in the testicular germ cells in dose‐dependent (1, 5, 10 μg/mL) and time‐dependent (4, 6, 8 h) manner. Histological and ethidium bromide/acridine orange fluorescence staining exhibited that vitamins C and E (0.5 and 1.0 mM) successfully diminished the CYP‐induced testicular germ cells apoptosis. CYP exposure along with vitamins C and E supplementation also resulted in significantly increased ferric reducing antioxidant power activity along with the antioxidant enzymes, namely catalase, superoxide dismutase, and glutathione‐s‐transferase, and decreased lipid peroxidation in testicular germ cells. Thus, vitamins C and E ameliorated CYP‐induced testicular germ cell apoptosis, thereby preventing spermatogonial cells degeneration and male infertility.     

An efficient algorithm after ungapped analysis in BLAST.

Basic Local Alignment Search Tool (BLAST) is a popular tool used for determining the patterns in genomic sequences. The algorithm of BLAST has gone for various changes from time to time. One third of the time is taken by BLAST to perform the gapped analysis on the sequences. An efficient algorithm has been presented that employs a new approach for curtailing the amount of sequences that proceed for gapped alignment. So this method will work after the ungapped alignment process is over. This works because of the fact that it is not necessary to perform gapped alignment for all the sequences that are coming from ungapped analysis. There is a significant increase in speed of the alignment process without compromising on the sensitivity of the result.     

Application of photographic capture–recapture modelling to estimate demographic parameters for male Asian elephants

In addition to the threats of habitat loss and degradation, adult males of the Asian elephant Elephas maximus also face greater threats from ivory poaching and conflict with humans. To understand the impact of these threats, conservationists need robust estimates of abundance and vital rates specifically for the adult male segment of elephant populations. By integrating the identification of individual male elephants in a population from distinct morphology and natural markings, with modern capture–recapture (CR) sampling designs, it is possible to estimate various demographic parameters that are otherwise difficult to obtain from this long-lived and wide-ranging megaherbivore. In this study, we developed systematic individual identification protocols and integrated them into CR sampling designs to obtain capture histories and thereby estimate the abundance of adult bull elephants in a globally important population in southern India. We validated these estimates against those obtained from an independent method combining line-transect density estimates with age–sex composition data for elephants. The sampled population was open to gains and losses between sampling occasions. The abundance of adult males in the 176 km² study area was (SÊ ) = 134(14.20) and they comprised 14% (±1%) of the total elephant population. Time-specific abundance estimates for each sampling occasion showed a distinct increase in adult male numbers over the sampling period, explained by seasonal patterns of local migration. CR-based estimates for adult male abundance closely matched estimates from distance-based methods. Thus, while providing abundance data of comparable rigour and precision, photographic CR methods permit estimation of demographic parameters for the Asian elephant that are both urgently needed and difficult to obtain.