Search

Despite the ubiquity of the genus Citrobacter in clinical, industrial, and environmental scenarios, a large number of Citrobacter strains have not been explored at the genome-scale level. In this study, accurate taxonomic assignment of strain AAK_AS5 isolated from activated sludge was achieved by in-silico genomic comparison using Overall Genome-based Relatedness Indices (ANI(OAT): 97.55%, ANIb:97.28%, and ANIm: 97.83%) that indicated its closest identity to the related strain Citrobacter portucalensis A60

Podocytes, a vital component of the glomerular filtration barrier, are vulnerable to various noxious stimuli, including Hypoxic. HIF1α that transduces hypoxic adaptations induces Transglutaminase 2 (TG2), which catalyses cross-linking of extracellular matrix proteins. In this study, we investigated the mechanism of regulation of TG2 by HIF1α.HIF1α was induced in podocytes by treating with FG4592 (Roxadustat) or hypoxia (1% oxygen) and in mice by treating with FG4592. Gene expression and protein analysis of ZEB2, TRPC6 and TG2 were performed in both experimental models. Histological and kidney function analyses were performed in mice.Data mining revealed co-expression of HIF1α, ZEB2, TRPC6 and TG2 in the chronic kidney diseases (CKD)-validated dataset. We observed elevated expression of ZEB2, TRPC6 and TG2 in FG4592-treated podocytes. Ectopic expression of ZEB2 resulted in high TRPC6 expression, elevated intracellular calcium levels and increased TG2 activity. Blocking the TRPC6 channel or inhibiting its expression partially attenuated FG4592-induced TG2 activity, whereas suppression of ZEB2 expression significantly abolished TG2 activity. Furthermore, we noticed the induction of the ZEB2/TRPC6/TG2 axis in podocytes in mice administered with FG-4592. Metformin ameliorated the HIF1α-induced podocyte injury and proteinuria in mice administered with FG-4592.This study demonstrates that HIF1α stimulates both TG2 expression and activity via ZEB2/TRPC6 axis, whereas abrogation of HIF1α by metformin prevented hypoxia-induced glomerular injury. Metformin could be explored to treat proteinuric diseases such as CKD, sleep apnea and renal Ischemia-reperfusion-injury, where hypoxia is considered a risk factor.

Cross-reactive and broadly neutralizing antibodies against surface proteins of diverse strains of rapidly evolving viral pathogens like SARS-CoV-2 can prevent infection and therefore are crucial for the development of effective universal vaccines. While antibodies typically incorporate mutations in their complementarity determining regions during affinity maturation, mutations in the framework regions have been reported as players in determining properties of broadly neutralizing antibodies against HIV and the Influenza virus. We propose an increase in the cross-reactive potential of CR3022 against the emerging SARS- CoV-2 variants of concern through enhanced conformational flexibility. In this study, we use molecular dynamics simulations, in silico mutagenesis, structural modeling, and docking to explore the role of light chain FWR mutations in CR3022, a SARS-CoV anti-spike (S)-protein antibody cross-reactive to the S-protein receptor binding domain of SARS-CoV-2. Our study shows that single substitutions in the light chain framework region of CR3022 with conserved epitopes across SARS-CoV strains allow targeting of diverse antibody epitope footprints that align with the epitopes of recently-categorized neutralizing antibody classes while enabling binding to more than one strain of SARS-CoV-2. Our study has implications for rapid and evolution-based engineering of broadly neutralizing antibodies and reaffirms the role of framework mutations in effective change of antibody orientation and conformation via improved flexibility. Communicated by Ramaswamy H. Sarma

In this article, a study of wideband substrate integrated waveguide (SIW) cavity based slot antenna is presented. The proposed antenna consists of a U-shaped slot etched in the ground plane which helps in achieving the wideband behaviour. A detailed analysis of the SIW cavity and prediction of various modes propagating inside it using accurate design equations are discussed. An equivalent circuit modeling of the proposed antenna along with surface current distributions at various resonating frequencies is also performed. Parametric study on various parameters to improve the performance in terms of wide impedance bandwidth, gain and efficiency levels are also discussed in detail. The fabricated prototype of the proposed SIW antenna shows the reflection coefficient S11

Hypoxia-inducible factor1 (HIF1) plays a pivotal role in ensuring cells adapt to low-oxygen conditions. Depletion of oxygen, a co-substrate during hydroxylation of prolyl (P402 and P564) residues of HIF1⍺, evades HIF1⍺ ubiquitination and enables its dimerization with HIF1β to mediate global transcriptional response to hypoxia. Though HIF1 is largely considered eliciting a protective role during physiological or pathological hypoxia or ischemia, elevated HIF1 during chronic hypoxia contributes to glomerular diseases’ pathology and proteinuria. The glomerulus is responsible for renal permselectivity and excretion of ultra-filtrated urine. Podocytes are the glomerulus’ major cell types and are instrumental for glomerular filtration, permselectivity, and glomerular basement membrane maintenance. Podocyte injury is expected to impair the efficiency of glomerular filtration and manifestation of glomerulosclerosis and proteinuria. Accumulated evidence suggests that podocytes are susceptible to various insults during chronic hypoxia, including podocyte EMT, slit-diaphragm dysfunction, foot process effacement, and cytoskeletal derangement due to accumulation of HIF1. This review discusses how hypoxia/HIF1 signaling regulates various features and function of podocytes during exposure to chronic hypoxia or inducing HIF1 by various chemical modulators.

An effective tunnelling recombination junction (TRJ) is the most important part in a series connected tandem solar cell, and it always plays a significant role to match the current densities of individual solar cells. The aim of this paper is to find a TRJ that shows more efficient ohmic behavior compared to that used in typical thin film tandem solar cells, due to high current nature. Silicon heterojunction (SHJ) based tandem solar cell structure (a-Si:H/SHJ) was studied in detail with simulations using Advanced Semiconductor Analysis (ASA) software. Trap assisted recombination tunnelling and field enhanced mobility mechanisms have been included in our model analysis. Moreover, we also have simulated individual device characteristics of each a-Si:H (n-i-p), SHJ cell (top and bottom subcells of an a-Si:H/SHJ tandem cell), and correlated with the performance of the a-Si:H/SHJ tandem solar cell. The tandem device with a TRJ, the type which used in a thin film silicon tandem cell, shows low open circuit voltage (Voc) = 1.12 V and poor fill factor (FF) = 0.29 with S-shape in light current density–voltage (J-V) characteristics due to charge transport issue at the interface of top and bottom cells. An appropriate TRJ gives efficient recombination and an excellent ohmic contact at the interface between the subcells to match the current of each device. With the implementation of the optimum TRJ at the junction of two cells, Voc and FF have improved significantly to 1.35 V and 0.79 respectively. Also, we observed that the Voc of the tandem solar cell is nearly equal to the sum of the corresponding individual subcells, confirming no trapping related field loss at the junction.

Renal synovial sarcoma is a rare disease with less than 200 cases reported in the literature. A 36-year-old lady presented with hematuria and underwent radical nephrectomy for a left-sided renal synovial sarcoma. She developed lung metastasis and the disease progressed further despite of chemotherapy. Renal synovial sarcoma can be diagnosed by studying morphology and performing an Immuno-histochemistry (IHC) panel (Transducin-like enhancer of split (TLE); B Cell Lymphoma (BCL)-2; CD99) on resected tumor tissue. Molecular testing for t(x; 18)(p11.2;q11.2) translocation is considered the gold standard diagnostic test. The common presenting symptoms include hematuria, pain, or a palpable lump. The imaging modalities are not diagnostic and surgical resection is the treatment of choice at present. Due to the rarity of the disease, the treatment guidelines are not well-defined. Anthracyclines alone or in combination with Ifosfamide has been reported to be used in the literature in the adjuvant as well as metastatic settings. The overall prognosis is poor with a short median survival ranging from 6 to 24 months.

Reactive oxygen species (ROS) generated by NADPH oxidases (NOX/DUOX) provide antimicrobial defense, redox signaling, and gut barrier maintenance. Inactivating NOX variants are associated with comorbid intestinal inflammation in chronic granulomatous disease (CGD; NOX2) and pediatric inflammatory bowel disease (IBD; NOX1); however Nox-deficient mice do not reflect human disease susceptibility. Here we assessed if a hypomorphic patient-relevant CGD mutation will increase the risk for intestinal inflammation in mice. Cyba (p22phox) mutant mice generated low intestinal ROS, while maintaining Nox4 function. The Cyba variant caused profound mucus layer disruption with bacterial penetration into crypts, dysbiosis, and a compromised innate immune response to invading microbes, leading to mortality. Approaches used in treatment-resistant CGD or pediatric IBD such as bone marrow transplantation or oral antibiotic treatment ameliorated or prevented disease in mice. The Cyba mutant mouse phenotype implicates loss of both mucus barrier and efficient innate immune defense in the pathogenesis of intestinal inflammation due to ROS deficiency, supporting a combined-hit model where a single disease variant compromises different cellular functions in interdependent compartments.

Glomerular podocytes are instrumental in ensuring glomerular permselectivity and regulating the integrity of glomerular biology. However, podocytes are vulnerable to various noxious stimuli such as hypoxia, and podocyte injury presented with glomerulosclerosis and impaired kidney function. The mechanism of hypoxia-induced podocyte injury vis-a-vis glomerulosclerosis has remained enigmatic. Hypoxia inducible factor 1α (HIF1α) that transduces hypoxic adaptations, induces Transglutaminase 2 (TG2), a calcium dependent enzyme that catalyzes intramolecular ε-(γ-glutamyl) lysine cross-links of extracellular matrix (ECM) proteins. In this study, we investigated the mechanism of regulation of TG2 by HIF1α. Stabilization of HIF1α by FG4592 (Roxadustat) and physiological hypoxia, resulted in elevated expression of ZEB2 (zinc-finger E-box-homeobox 2) and its downstream target TRPC6 (transient receptor potential channel 6). ZEB2 transcriptionally activates TG2 expression, whereas, via TRPC6, it induces calcium influx, inturn it increases the TG2 activity. Blocking the TRPC6 action or suppressing its expression only partially attenuated FG4592 induced TG2 activity, whereas suppression of ZEB2 expression significantly abolished TG2 activity. This study demonstrates that stabilization of HIF1α stimulates both TG2 expression and activity, whereas abrogation of HIF1α by metformin prevented HIF1α regulated TG2 and consequent glomerular injury.

The prevalence of diabetes reaches epidemic proportions. Diabetes is the leading cause of end-stage kidney disease (ESKD) since 30–40% of diabetic patients develop diabetic nephropathy. Albuminuria and glomerular filtration rate used to assess kidney function are considered surrogate outcomes of chronic kidney disease. The search for a biomarker that predicts progression to diabetic kidney disease is intense. We analyzed the association of serum advanced glycation end-products (AGEs) index (AGI) with impaired kidney function in poorly controlled type II diabetic patients. We observed an association between AGI and impaired kidney function in microalbuminuria patients with hyperglycemia. A significant association between AGEs, particularly carboxymethyl lysine (CML), and impaired kidney function were observed. Administration of AGEs to mice showed heavy proteinuria and glomerular abnormalities. Reduced podocyte number in mice administered with AGEs could be attributed to the epithelial-mesenchymal transition of podocytes. Our study suggests CML could be independently related to the podocyte injury and the risk of DN progression to ESKD in patients with microalbuminuria. AGEs in general or CML could be considered a prognostic marker to assess diabetic kidney disease.

Dysregulated redox signaling can exaggerate inflammation, but it is now recognized that reactive species are central mediators to both pro-inflammatory and anti-inflammatory processes. Signal regulation can occur by direct modification of proteins or lipids, or via the coordinated transfer of electrons between proteins forming a redox relay. Recently the focus shifted from reactive oxygen and nitrogen species to sulfur and carbonyl species in inflammatory signaling. Extensive interplay exists between distinct species, either within individual cells, between distinct cells, or between host cells and microbes. Reactive species act as one highly regulated network regulating inflammatory decision making of the host. Selected examples, mainly in innate immune cells, will be presented, emphasizing the interconnected nature of reactive species during inflammatory signaling.

Introduction: Computational antibody engineering, affinity maturation, and screening greatly aid in vaccine and therapeutic antibody development by increasing the speed and accuracy of predictions. This study presents a protocol for designing affinity enhancing mutants of antibodies through in silico mutagenesis. A SARS-CoV-2 cross-reactive neutralizing antibody, CR3022, is considered as a case study.Methods: Our study aimed at generating antibody candidates from the human antibody CR3022 (derived from convalescent SARS patient) against the RBD of SARS-CoV-2 via in silico affinity maturation using site-directed mutagenesis in mutation hotspots. We optimized the paratope of the CR3022 antibody towards the RBD of SARS-CoV-2 for better binding affinity and stability, employing molecular modeling, docking, dynamics simulations, and molecular mechanics energies combined with generalized Born and surface area (MM-GBSA). Results: Nine antibody candidates were generated post in silico site-directed mutagenesis followed by preliminary screening. Molecular dynamics simulation of 100 nanoseconds and MM-GBSA analysis confirmed L-K45S as a lead antibody with the highest binding affinity against the RBD compared to wild-type and mutant counterparts. Three out of the remaining mutants were also found to have distinct epitopes and binding, possessing a potential to be developed against emerging SARS-CoV-2 variants of concern. Conclusion: The study demonstrates the use of an integrative antibody engineering protocol for enhancing affinity and neutralization potential through mutagenesis using robust open-source computational tools and predictors. This study highlights unique scoring and ranking methods for evaluating docking efficiency. It also underscores the importance of framework mutations for developing broadly neutralizing antibodies.

Glomerular podocytes are integral members of the glomerular filtration barrier in the kidney and are crucial for glomerular permselectivity. These highly differentiated cells are vulnerable to an array of noxious stimuli that prevail in several glomerular diseases. Elevated circulating growth hormone (GH) levels are associated with podocyte injury and proteinuria in diabetes. However, the precise mechanism(s) by which excess GH elicits podocytopathy remains to be elucidated. Previous studies have shown that podocytes express GH receptor (GHR) and induce Notch signaling when exposed to GH. In the present study, we demonstrated that GH induces TGF-β1 signaling and provokes cell cycle reentry of otherwise quiescent podocytes. Though differentiated podocytes reenter the cell cycle in response to GH and TGF-β1, they cannot accomplish cytokinesis, despite karyokinesis. Owing to this aberrant cell cycle event, GH- or TGF-β1-treated cells remain binucleated and undergo mitotic catastrophe. Importantly, inhibition of JAK2, TGFBR1 (TGF-β receptor 1), or Notch prevented cell cycle reentry of podocytes and protected them from mitotic catastrophe associated with cell death. Inhibition of Notch activation prevents GH-dependent podocyte injury and proteinuria. Similarly, attenuation of GHR expression abated Notch activation in podocytes. Kidney biopsy sections from patients with diabetic nephropathy (DN) show activation of Notch signaling and binucleated podocytes. These data indicate that excess GH induced TGF-β1-dependent Notch1 signaling contributes to the mitotic catastrophe of podocytes. This study highlights the role of aberrant GH signaling in podocytopathy and the potential application of TGF-β1 or Notch inhibitors, as a therapeutic agent for DN.

Hypoxia-inducible factor1 (HIF1) plays a pivotal role in ensuring cells adapt to low-oxygen conditions. Depletion of oxygen, a co-substrate during hydroxylation of prolyl (P402 and P564) residues of HIF1⍺, evades HIF1⍺ ubiquitination and enables its dimerization with HIF1β to mediate global transcriptional response to hypoxia. Though HIF1 is largely considered eliciting a protective role during physiological or pathological hypoxia or ischemia, elevated HIF1 during chronic hypoxia contributes to glomerular diseases' pathology and proteinuria. The glomerulus is responsible for renal permselectivity and excretion of ultra-filtrated urine. Podocytes are the glomerulus' major cell types and are instrumental for glomerular filtration, permselectivity, and glomerular basement membrane maintenance. Podocyte injury is expected to impair the efficiency of glomerular filtration and manifestation of glomerulosclerosis and proteinuria. Accumulated evidence suggests that podocytes are susceptible to various insults during chronic hypoxia, including podocyte EMT, slit-diaphragm dysfunction, foot process effacement, and cytoskeletal derangement due to accumulation of HIF1. This review discusses how hypoxia/HIF1 signaling regulates various features and function of podocytes during exposure to chronic hypoxia or inducing HIF1 by various chemical modulators.

Dysregulated redox signaling and oxidative injury are associated with inflammatory processes and fibrosis. H2O2 generation by NOX4 has been suggested as a key driver in the development of fibrosis and a small molecule drug is under evaluation in clinical trials for idiopathic pulmonary fibrosis and primary biliary cholangitis. Fibrosis is a common complication in Crohn's disease (CD) leading to stricture formation in 35–40% of patients, who require surgical interventions in the absence of therapeutic options. Here we assess NOX4 expression in CD patients with inflammatory or stricturing disease and examine whether loss of NOX4 is beneficial in acute and fibrotic intestinal disease. NOX4 was upregulated in inflamed mucosal tissue of CD and ulcerative colitis (UC) patients, in CD ileal strictures, and in mice with intestinal inflammation. Nox4 deficiency in mice promoted pathogen colonization and exacerbated tissue injury in acute bacterial and chemical colitis. In contrast, in two chronic injury models aberrant tissue remodeling and fibrosis-related gene expression did not differ substantially between Nox4−/− mice and wildtype mice, suggesting that Nox4 is dispensable in TGF-β1-driven intestinal fibrogenesis. While animal models do not recapitulate all the hallmarks of CD fibrosis, the tissue-protective role of Nox4 warrants a cautious approach to pharmacological inhibitors., Graphical abstract Image 1, Highlights • NOX4 is elevated in inflammatory bowel disease strictures and inflamed biopsies. • Murine intestinal fibrogenesis is not dependent on Nox4. • Nox4 is protective in acute murine colitis.

A chemometric data analysis challenge has been arranged during the first edition of the "International Workshop on Spectroscopy and Chemometrics", organized by the Vistamilk SFI Research Centre and held online in April 2021. The aim of the competition was to build a calibration model in order to predict milk quality traits exploiting the information contained in mid-infrared spectra only. Three different traits have been provided, presenting heterogeneous degrees of prediction complexity thus possibly requiring trait-specific modelling choices. In this paper the different approaches adopted by the participants are outlined and the insights obtained from the analyses are critically discussed., Comment: 17 pages, 6 figures, 6 tables

Food items that are unprocessed and do not contain preservatives, artifi cial colours, chemicals, fi llers, artifi cial fl avours etc are called as Natural foods.

The demand of tomato (Solanum lycopersicum L.) and its products continue to rise due to its excellent source of antioxidants including lycopene, total carotenoids, ascorbic acid and total soluble solids. The present experiment was carried out during the autumn-winter season of 2014–2016. The seven parents were crossed in half diallel fashion and the resultant 21 F1 hybrids along with their parents and one hybrid check (BSS - 488) were evaluated in randomized complete block design with three replications for eight morpho-chemical quality component traits in tomato. The highest standard heterosis were observed in the cross Selection-12 × Pusa-120 (12.16%) for pericarp thickness, Pusa Rohini × Selection-12 (25.95%) for total soluble solids, H-86 × Pusa Rohini (23.53) for ascorbic acid, Selection-12 × CLNB (38.79) for total phenolics, Arka Alok × CLNB (46.49) for total antioxidant capacity, Pusa Rohini × Arka Alok (25.95) for lycopene and total carotenoids (29.53). Among the crosses Pusa Rohini × CLNR, Arka Alok × CLNB, H-86 × Pusa-120 and H-86 × CLNR were found to be better for most of the quality traits and these crosses could be considered as most promising specific combiners. Among the parents, Selection-12, CLNB, Pusa Rohini and Arka Alok were identified as most promising general combiners for quality traits and these may be used as valuable donors in the hybridization programme for producing promising varieties.

The nature and coordination sites of the Schiff base 3,3'-(1E,1'E)-(1,3-phenylenebis(azan-1-yl-1-ylidene))bis(methan-1-yl-1-ylidene)dinaphthalen-2-ol (APHN) were tuned by its selective reduction to design a highly efficient fluorescent probe, 3,3'-(pyridine-2,6-diylbis(azanediyl))bis(methylene)dinaphthalen-2-ol (RAPHN). The structures of APHN, RAPHN, and the RAPHN-Fe

Reactive oxygen species (ROS) generated by NADPH oxidases (NOX/DUOX) provide antimicrobial defense, redox signaling, and gut barrier maintenance. Inactivating NOX variants are associated with comorbid intestinal inflammation in chronic granulomatous disease (CGD; NOX2) and pediatric inflammatory bowel disease (IBD; NOX1); however Nox-deficient mice do not reflect human disease susceptibility. Here we assessed if a hypomorphic patient-relevant CGD mutation will increase the risk for intestinal inflammation in mice. Cyba (p22

Podocytes are integral members of the filtration barrier in the kidney and are crucial for glomerular permselectivity. Podocytes are highly differentiated and vulnerable to an array of noxious stimuli during various clinical conditions whereas podocyte loss plays a key role in progressive glomerular diseases. Elevated circulating growth hormone (GH) levels are associated with podocyte injury and proteinuria in diabetics. Previous studies have shown that podocytes express GH receptors (GHR), and induce Notch signaling when exposed to GH. However, the precise mechanism(s) by which excess GH elicits podocytopathy remains to be elucidated. In the present study, we demonstrate that GH induces cognate TGF-β1 signaling and provokes cell cycle re-entry of otherwise quiescent podocytes. Though, differentiated podocytes re-enter the cell cycle in response to GH and TGF-β1 unable to accomplish cytokinesis, despite nuclear division. Owing to this aberrant cell-cycle events significant amount of GH or TGF-β1 treated cells remain binucleated and undergo mitotic catastrophe. Importantly, inhibition of GHR, TGFBR1, or Notch signaling prevented cell cycle re-entry and protects podocyte from cell death. Furthermore, inhibition of Notch activation prevents GH-dependent podocyte injury and proteinuria. Kidney biopsy sections from patients with diabetic nephropathy show activation of Notch signaling and bi-nucleated podocytes. All these data confirm that excess GH induces Notch1 signaling via TGF-β1 and contributes to the mitotic catastrophe of podocytes. This study highlights the role of aberrant GH signaling in the podocytopathy and the potential application of inhibitors of TGF-β1 or Notch inhibitors as a therapeutic agent for diabetic nephropathy.Significance StatementElevated circulating levels of growth hormone (GH) associated with glomerular hypertrophy and proteinuria. Whereas decreased GH action protected against proteinuria. Podocytes are highly differentiated cells that play a vital role in glomerular filtration and curb protein loss. The direct role of GH in podocytes is the focus of our study. We found that GH induces TGF-β1 and both provoke cell cycle re-entry of podocytes in Notch1 dependent manner. Notch activation enables the podocytes to accomplish karyokinesis, but not cytokinesis owing to which podocytes remain binucleated. Binucleated podocytes that were observed during GH/TGF-β1 treatment are susceptible to cell death. Our study highlighted the fact that enforcing the differentiated podocytes to re-enter the cell cycle results in mitotic catastrophe and permanent loss.

Over the last decade, seismic inversion has acquired the status of being a routine interpretation step during exploration as well as development of fields. For detailed reservoir characterization, prestack inversion is desirable; however, poststack inversion is a reasonably effective tool. The inversion starts with calibration of the well with seismic data. The synthetic seismogram is tied with stacked seismic data on the basic premise that the seismic data (full stack) mimics the zero-offset data and therefore should match with the zero-offset synthetic seismogram. Generally, a good match is obtained. However, during the course of many inversion exercises, it is observed that the synthetic-to-seismic match is not good in parts of the drilled interval. There could be many reasons for this partial mismatch. One of the important reasons is that the well data represent one-dimensional data, whereas the seismic data are stacked over an angle range. In other words, the well data are equivalent to zero-offset data, whereas seismic is not. The poor calibration at the well location leads to lack of confidence in inversion results. The possible solution, such as simultaneous or full-waveform inversion, involves a lot of computation time and hardware requirements. An alternative approach is introduced which uses elastic impedance instead of normal P-impedance for synthetic match and inversion of stacked data. The synthetic seismic generated from elastic impedance shows an improved match with seismic data. The approach is quick, reliable, easy, and not heavy on computational resources. The result is inverted volumes with better hydrocarbon delineation and characterization ability.

Psychrophilic micro-organisms are the most dominant flora in cold habitats. Their unique ability to survive and multiply at low temperatures (

An investigation of laser dressing of metal-bonded diamond blades is reported. The influence of laser irradiation on the diamond particles and bond material was reported, and the bonding material w...

Three 16S rRNA gene clone libraries (P1L, P4L and P8L) were constructed using three soil samples (P1S, P4S and P8S) collected near Pindari glacier, Himalayas. The three libraries yielded a total of 703 clones. Actinobacteria, Firmicutes and Proteobacteria were common to the three libraries. In addition to the above P1L and P8L shared the phyla Acidobacteria, Bacteroidetes, Gemmatimonadetes and Planctomycetes. Phyla Chlamydiae, Chlorobi, Chloroflexi, Dictyoglomi, Fibrobacteres, Nitrospirae, Verrucomicrobia, candidate division SPAM and candidate TM7s TM7a phylum were present only in P1L. Rarefaction analysis indicated that the bacterial diversity in P4S and P8S soil samples was representative of the sample. Principal component analysis (PCA) revealed that P1S and P8S were different from P4S soil sample. PCA also indicated that arsenic content, pH, Cr and altitude influence the observed differences in the percentage of specific OTUs in the three 16S rRNA gene clone libraries. The observed bacterial diversity was similar to that observed for other Himalayan and non-polar cold habitats. A total of 40 strains of bacteria were isolated from the above three soil samples and based on the morphology 20 bacterial strains were selected for further characterization. The 20 bacteria belonged to 12 different genera. All the isolates were psychro-, halo- and alkalitolerant. Amylase and urease activities were detected in majority of the strains but lipase and protease activities were not detected. Long chain, saturated, unsaturated and branched fatty acids were predominant in the psychrotolerant bacteria.

CSM2, a cold-sensitive mutant of psychrophilic Pseudomonas syringae, grows like wild-type cells when cultured at 22 and 28 degrees C; but at 4 degrees C, the growth is retarded. In CSM2, AAT (coding for aspartate aminotransferase) is identified as the mutated gene. The expression of AAT in Pseudomonas syringae was transiently enhanced when cells were shifted from 22 to 4 degrees C indicating that AAT is cold-inducible. Complementation of the mutated AAT transformed CSM2 from a cold-sensitive phenotype to a cold-resistant phenotype like the wild-type cells, thus providing evidence for the first time that AAT is required for low-temperature growth.

A cold-active heat-labile t-RNA modification GTPase (TrmE) from psychrophilic bacterium Pseudomonas syringae (Lz4W) has been purified and characterized. The purified TrmE is a 53 kDa protein, has GTPase activity and hydrolyses only the oxy and deoxy forms of GTP but not the other nucleotide triphosphates. The enzyme exhibits optimal activity at 12-18 degrees C and retains 65% of its optimal activity at 4 degrees C, indicating that it is a cold-active enzyme. The enzyme is also heat-labile and loses 60% of its activity at 30 degrees C. This is the first report on the purification and characterization of a TrmE from a psychrophilic bacterium.

Calcium ions (Ca(2+)) are important in numerous signal transduction processes, including the development and differentiation of T cells in the thymus. We report that thymocytes have multiple types of pore-forming α subunits and regulatory β subunits that constitute voltage-gated Ca(2+) (Cav) channels. In mice, T cell-specific deletion of the gene encoding the β2 regulatory subunit of Cav channels (Cacnb2) reduced the abundances of the channels Cav1.2 and Cav1.3 (both of which contain pore-forming α1 subunits) and impaired T cell development, which led to a substantial decrease in the numbers of thymocytes and peripheral T cells. Similar to the effect of Cacnb2 deficiency, pharmacological blockade of pore-forming Cav1α subunits reduced the sustained Ca(2+) influx in thymocytes upon stimulation of the T cell receptor, decreased the abundance of the transcription factor NFATc3, inhibited the proliferation of thymocytes in vitro, and led to lymphopenia in mice. Together, our data suggest that Cav1 channels are conduits for the sustained Ca(2+) influx that is required for the development of T cells.