Cleavage of natural rubber by rubber oxygenases in Gram-negative bacteria

Bacterial degradation of natural rubber (NR) in an oxic environment is initiated by oxidative cleavage of double bonds in the NR-carbon backbone and is catalyzed by extracellular haem-containing rubber oxygenases. NR-cleavage products of sufficiently low molecular mass are taken up by the cells and metabolized for energy and biomass formation. Gram-negative and Gram-positive NR-degrading bacteria (usually) employ different types of rubber oxygenases such as RoxA and/or RoxB (most Gram-negative NR-degraders) or latex clearing protein Lcp (most Gram-positive NR-degraders). In order to find novel orthologues of Rox proteins, we have revisited databases and provide an update of Rox-like proteins. We describe the putative evolution of rubber oxygenases and confirm the presence of a third subgroup of Rox-related proteins (RoxCs), the biological function of which remains, however, unclear. We summarize the knowledge on the taxonomic position of Steroidobacter cummioxidans 35Y and related species. Comparison of genomic and biochemical features of strain 35Y with other species of the genus Steroidobacter suggests that strain 35Y represents a species of a novel genus for which the designation Aurantibaculum gen. nov. is proposed. A short summary on the capabilities of NR-degrading consortia, that could be superior in biotechnological applications compared to pure cultures, is also provided. KEY POINTS: • Three types of rubber oxygenases exist predominantly in Gram-negative microbes • S. cummioxidans 35Y contains RoxA and RoxB which are superior in activity • S. cummioxidans 35Y represents a species of a novel genus.

Theoretical insight on the optical centred electrical properties of guanidinium isophthalate NLO crystal for electro-optic Q switches

Guanidinium isophthalate single crystals with dimensions 16 × 4 x 2 mm3 were prepared by the low temperature solvent evaporation method and growth kinetics with interfacial tension was discussed to bring out the growth parameters of guanidinium isophthalate single crystals. The harvested single crystals were utilized for various characterization studies like powder X-ray diffraction, optical transmission, photoluminescence, laser damage study and optical limiting studies. The visualization of varying potential regions on the surfaces to quantify short contacts were generated by Hirshfeld surface analysis. 2D fingerprint plots were analyzed, in which H ….H contact was found to be the most significant with 54.1%. Growth kinetics of the crystalline material was studied to reveal the nucleation process. Crystal samples prepared with reference to the solubility data were found to be free of inclusions and cracks and had maximum transmittance in the complete visible region. The electronic disorder of the crystal sample was reported in the form of Urbach energy. The PL spectra with the emission intensity provide the emission characteristic of the title compound. The major fundamental optical limit for a crystal material is experimentally measured and presented in the picosecond regime. Thus the present work contributes to the understanding of growth, structural, optical and electronic characteristics of the title guanidinium isophthalate single crystals for the fabrication of electro-optic devices in photonic industry.

Identification of conserved genomic signatures specific to Bifidobacterium species colonising the human gut

Bifidobacterium species are known for their ability to inhabit various habitats and are often regarded as the first colonisers of the human gut. In the present work, we have used comparative genomics to identify conserved genomic signatures specific to Bifidobacterium species associated with the human gut. Our approach discovered five genomic signatures with varying lengths and confidence. Among the predicted five signatures, a 1790 bp multi-drug resistance (MDR) signature was found to be remarkably specific to only those species that can colonise the human gut. The signature codes for a membrane transport protein belonging to the major facilitator superfamily (MFS) generally involved in MDR. Phylogenetic analyses of the MDR signature suggest a lineage-specific evolution of the MDR signature in bifidobacteria colonising the human gut. Functional annotation led to the discovery of two conserved domains in the protein; a catalytic MFS domain involved in the efflux of drugs and toxins, and a regulatory cystathionine-β-synthase (CBS) domain that can interact with adenosyl-carriers. Molecular docking simulation performed with the modelled tertiary structure of the MDR signature revealed the putative functional role of the covalently linked domains. The MFS domain displayed a high affinity towards various protein synthesis inhibitor antibiotics and human bile acids, whereas the C-terminally linked CBS domain exhibited favourable binding with molecular structures of ATP and AMP. Therefore, we believe that the predicted signature represents a niche-specific survival trait involved in bile and antibiotic resistance, imparting an adaptive advantage to the Bifidobacterium species colonising the human gut.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03492-4.

A Review on Microalgae Biofuel Production and use in CI Engine Applications

Alternative fuel technology of third-generation biofuels in place of conventional fossil fuels is currently being witnessed at a global level. Due to its sustainability and environmental friendliness, in recent years more importance is being given to biodiesel in CI engine applications. Recent trends show that microalgae are promoted as a bio-fuel due to their inherent advantages of abundant availability of oil sources and faster growth rate with ease of cultivation. Particular species of algae such as Chlorella, Botryococcus braunii, and Scenedesmus obliquus are conventionally favored for biodiesel production as they have a prominent amount of lipids content. This review outlines the current state of experimental investigations on the use of different algae biodiesel blends with diesel for CI engines. Amongst the different algae-based biodiesel, the dual Calophyllum Inophyllum methyl ester blend (CIME20) with DEE demonstrated the maximum brake thermal efficiency (BTE) and better brake-specific fuel consumption (BSFC) of CI engines. In terms of emissions, the CO, UBHC, and smoke levels are significantly lower for algae blends in contrast to neat diesel.

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties.

Use of diamond sensors for a high-flux, high-rate X-ray pass-through diagnostic

X-ray free-electron lasers (XFELs) deliver pulses of coherent X-rays on the femtosecond time scale, with potentially high repetition rates. While XFELs provide high peak intensities, both the intensity and the centroid of the beam fluctuate strongly on a pulse-to-pulse basis, motivating high-rate beam diagnostics that operate over a large dynamic range. The fast drift velocity, low X-ray absorption and high radiation tolerance properties of chemical vapour deposition diamonds make these crystals a promising candidate material for developing a fast (multi-GHz) pass-through diagnostic for the next generation of XFELs. A new approach to the design of a diamond sensor signal path is presented, along with associated characterization studies performed in the XPP endstation of the LINAC Coherent Light Source (LCLS) at SLAC. Qualitative charge collection profiles (collected charge versus time) are presented and compared with those from a commercially available detector. Quantitative results on the charge collection efficiency and signal collection times are presented over a range of approximately four orders of magnitude in the generated electron-hole plasma density.

Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice

In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.

Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future

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The inaccessible extreme environments harbor a large majority of anaerobic microbes which remain unknown.

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Anaerobic microbes are used in a variety of industrial applications.

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In the future, metagenomic-assisted techniques can be used to identify novel anaerobic microbes from the unexplored extreme environments.

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Genetic engineering can be used to enhance the efficiency of anaerobic microbes for various processes.

The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.

Characterisation and Assessment of Physicochemical Properties of Grapeseed Methyl Ester Using Predictive Correlations and ASTM Standards For CI Engine Application

In the present work, a detailed investigation of the physio-chemical characteristics of grapeseed methyl ester (GSME) obtained from winery biomass waste has been carried out to evaluate its suitability as an energy alternate, for CI engines. GSME was subjected to Gas chromatography and mass spectrometry analysis from which fatty acids compositions were determined followed by other interpretations such as carbon number, number of double bonds, etc. Two different predictive correlations were identified from the literature for predicting the properties that are considered important, for using GSME as a fuel. The predicted properties of GSME are compared with the experimental results obtained through standard ASTM procedures, for diesel, neat grapeseed oil (GSO) and GSME, respectively. Further, the influence of the structural and compositional characteristics of GSME on the physicochemical properties like density, kinematic viscosity, lower calorific value, etc. has been evaluated and found to be closer to diesel.

Prospects for beyond the Standard Model physics searches at the Deep Underground Neutrino Experiment: DUNE Collaboration

The Deep Underground Neutrino Experiment (DUNE) will be a powerful tool for a variety of physics topics. The high-intensity proton beams provide a large neutrino flux, sampled by a near detector system consisting of a combination of capable precision detectors, and by the massive far detector system located deep underground. This configuration sets up DUNE as a machine for discovery, as it enables opportunities not only to perform precision neutrino measurements that may uncover deviations from the present three-flavor mixing paradigm, but also to discover new particles and unveil new interactions and symmetries beyond those predicted in the Standard Model (SM). Of the many potential beyond the Standard Model (BSM) topics DUNE will probe, this paper presents a selection of studies quantifying DUNE's sensitivities to sterile neutrino mixing, heavy neutral leptons, non-standard interactions, CPT symmetry violation, Lorentz invariance violation, neutrino trident production, dark matter from both beam induced and cosmogenic sources, baryon number violation, and other new physics topics that complement those at high-energy colliders and significantly extend the present reach.

Distal Transradial Access for Diagnostic Cerebral Angiography and Neurointervention: Systematic Review and Meta-analysis

BACKGROUND

Radial artery access for cerebral angiography is traditionally performed in the wrist. Distal transradial access in the anatomic snuffbox is an alternative with several advantages.

PURPOSE

Our aim was to review the safety and efficacy of distal transradial access for diagnostic cerebral angiography and neurointerventions.

DATA SOURCES

We performed a comprehensive search of the literature using PubMed, Scopus, and EMBASE.

STUDY SELECTION

The study included all case series of at least 10 patients describing outcomes associated with distal transradial access for diagnostic cerebral angiography or a neurointervention.

DATA ANALYSIS

Random-effects models were used to obtain pooled rates of procedural success and complications.

DATA SYNTHESIS

A total of 7 studies comprising 348 (75.8%) diagnostic cerebral angiograms and 111 (24.2%) interventions met the inclusion criteria. The pooled success rate was 95% (95% CI, 91%-98%; I² = 74.33). The pooled minor complication rate was 2% (95% CI, 1%-4%; I² = 0. No major complications were reported. For diagnostic procedures, the combined mean fluoroscopy time was 13.53 [SD, 8.82] minutes and the mean contrast dose was 74.9 [SD, 35.6] mL.

LIMITATIONS

A small number of studies met the inclusion criteria, all of them were retrospective, and none compared outcomes with proximal transradial or femoral access.

CONCLUSIONS

Early experience with distal transradial access suggests that it is a safe and effective alternative to proximal radial and femoral access for performing diagnostic cerebral angiography and interventions. Additional studies are needed to establish its efficacy and compare it with other access sites.

Pharmacokinetic and pharmacodynamic evaluation of Solid self-nanoemulsifying delivery system (SSNEDDS) loaded with curcumin and duloxetine in attenuation of neuropathic pain in rats

The present investigation is focused on improving oral bioavailability of poorly soluble and lipophilic drugs, curcumin (CRM) and duloxetine (DXH), through the solid self-nanoemulsifying drug delivery system (S-SNEDDS) and identifying their potential against attenuation of NP in chronic constriction injury (CCI)-induced rats through the solid self-nanoemulsifying drug delivery system (S-SNEDDS). The optimized batch of S-SNEDDS reported was containing CRM and DXH (30 mg each), castor oil (20% w/w), tween-80 (40% w/w), transcutol-P (40% w/w), and syloid 244 FP (1 g). The high dose of each of naïve CRM (NCH), naïve DXH (NDH), physical mixture of DXH and CRM (C-NCM-DXH), S-SNEDDS-CRM (SCH), S-SNEDDS-DXH (SDH), and S-SNEDDS-CRM-DXH (C-SCH-SDH) was subjected for MTT assay. The developed formulations were subjected to pharmacokinetic studies and results showed about 8 to 11.06 and 2-fold improvement in oral bioavailability of CRM and DXH through S-SNEDDS. Furthermore, CCI-induced male Wistar rats were treated with SSNEDDS containing CRM and DXH, S-SNEDDS containing individual drug, individual naïve forms, and their combination from the day of surgery for 14 days and evaluated for behavioral at pre-determined time intervals. On the terminal day, animals were sacrificed to assess tissue myeloperoxidase, superoxide anion, protein, tumor necrosis factor-α, total calcium levels, and histopathological changes. Pronounced effect was observed in rats treated with S-SNEDDS containing both drugs with respect to rats receiving any of other treatments owing to enhanced oral bioavailability through S-SNEDDS. Therefore, it can be concluded that S-SNEDDS of both drugs and their coadministration can accelerate the prevention of NP.

Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes

The traditional medicinal systems (TMS) of India (Prakriti) and Korea (Sasang) classify human individuals based on their constitution determined by the physiological and psychological traits of individuals. Similarities in the constitutions are already found between the classes of Prakriti (Vata, Pitta, and Kapha) and Sasang (TE: Taeeumin, SE: Soeumin, and SY: Soyangin) systems. Gut health is an important aspect of this constitution based classification in TMS. To determine the role of gut microbes in such classifications, we have analyzed the gut microbiome (taxa and imputed functions) in the constitutionally similar Prakriti and Sasang classes. An enrichment of Bacteroides and Prevotella enterotypes is observed in the Sasang and Prakriti samples, respectively. The impact of the constitution is found to be more prominent with respect to the taxa and predicted-functions within the Prakriti classes. Gut microbiome functional-level similarities are found to correlate well with the host phenotypes of the constitutionally similar Prakriti and Sasang classes. An enrichment of carbohydrate and amino-acid metabolism is observed in the Vata and SE classes which may be responsible for meeting with their high energy demands and lean phenotype. The Pitta and SY classes exhibit the high capacity to metabolize toxins. An enrichment of functions responsible for predisposition to obesity and high drug metabolism is observed in the Kapha and TE classes. The contribution of gut adaptive functions is found to correlate with the constitution-based classification in both Prakriti and Sasang systems. The TE class harboured the highest number of biofilm-forming and stress-tolerant microbes thus exhibiting the maximum tolerance of environmental stress. Similarities in the gut microbiota and the resulting disease predisposition patterns are found to exist between the constitutionally matching Prakriti and Sasang classes.

In silico functional and evolutionary analyses of rubber oxygenases (RoxA and RoxB)

The study presents an in silico identification of poly (cis-1,4-isoprene) cleaving enzymes, viz., RoxA and RoxB in bacteria, followed by their functional and evolutionary exploration using comparative genomics. The orthologs of these proteins were found to be restricted to Gram-negative beta-, gamma-, and delta-proteobacteria. Toward the evolutionary propagation, the RoxA and RoxB genes were predicted to have evolved via a common interclass route of horizontal gene transfer in the phylum Proteobacteria (delta → gamma → beta). Besides, recombination, mutation, and gene conversion were also detected in both the genes leading to their diversification. Further, the differential selective pressure is predicted to be operating on entire RoxA and RoxB genes such that the former is diversifying further, whereas the latter is evolving to reduce its genetic diversity. However, the structurally and functionally important sites/residues of these genes were found to be preventing changes implying their evolutionary conservation. Further, the phylogenetic analysis demonstrated a sharp split between the RoxA and RoxB orthologs and indicated the emergence of their variant as another type of putative rubber oxygenase (RoxC) in the class Gammaproteobacteria. A detailed in silico analysis of the signature motifs and residues of Rox sequences exhibited important differences as well as similarities among the RoxA, RoxB, and putative RoxC sequences. Although RoxC appears to be a hybrid of RoxA and RoxB, the signature motifs and residues of RoxC are more similar to RoxB.

Functional signature analysis of extreme Prakriti endophenotypes in gut microbiome of western Indian rural population

Ayurveda is practiced in India from ancient times and stratifies the individuals based on their Prakriti constitution. Advancements in modern science have led to the association of Prakriti with molecular, biochemical, genomic and other entities. We have recently explored the gut microbiome composition and microbial signatures in healthy extreme Prakriti endo-phenotypes. However, their functional potentials are still lacking. The present study includes 63 females (29 Vata, 11 Pitta, and 23 Kapha) and 50 males (13 Vata, 18 Pitta, and 19 Kapha) samples. The predictive functional profiling and organism level functional traits of the human gut microbiome have been carried out in Prakriti groups using imputed metagenomic approach. A higher functional level redundancy is found than the taxonomy across the Prakriti groups, however the dominant taxa contributing to the functional profiles are found to be different. A high number of functional signatures specific to the Prakriti groups were identified in female datasets. Some of the functional signatures were found to be gender specific. For example, a higher abundance of microbes contributing potential pathogenic and stress tolerance related functions was found in Kapha in female and Pitta in male. The functional signatures correlated well with phenotypes and disease predisposition of Prakriti groups.

Exploration of Survival Traits, Probiotic Determinants, Host Interactions, and Functional Evolution of Bifidobacterial Genomes Using Comparative Genomics

Members of the genus Bifidobacterium are found in a wide-range of habitats and are used as important probiotics. Thus, exploration of their functional traits at the genus level is of utmost significance. Besides, this genus has been demonstrated to exhibit an open pan-genome based on the limited number of genomes used in earlier studies. However, the number of genomes is a crucial factor for pan-genome calculations. We have analyzed the pan-genome of a comparatively larger dataset of 215 members of the genus Bifidobacterium belonging to different habitats, which revealed an open nature. The pan-genome for the 56 probiotic and human-gut strains of this genus, was also found to be open. The accessory- and unique-components of this pan-genome were found to be under the operation of Darwinian selection pressure. Further, their genome-size variation was predicted to be attributed to the abundance of certain functions carried by genomic islands, which are facilitated by insertion elements and prophages. In silico functional and host-microbe interaction analyses of their core-genome revealed significant genomic factors for niche-specific adaptations and probiotic traits. The core survival traits include stress tolerance, biofilm formation, nutrient transport, and Sec-secretion system, whereas the core probiotic traits are imparted by the factors involved in carbohydrate- and protein-metabolism and host-immunomodulations.

Evaluation of neuroprotective effects of wedelolactone and gallic acid on aluminium-induced neurodegeneration: Relevance to sporadic amyotrophic lateral sclerosis

Al exposure causes an alteration in the several ions in the body and causes toxicity. Such as apoptosis, oxidative stress, disruption in neuronal transport, mitochondrial damage, excitotoxicity, generation of inflammatory mediators, and microglial activation. These multiple mechanisms lead to the several neurodegenerative diseases, including sporadic amyotrophic lateral sclerosis (sALS). The study aims to unravel the mechanisms behind the neuroprotective effects of wedelolactone (WL) and gallic acid (GA) against aluminium-induced neurodegeneration and thereby to unlock a platform to find a cure for sALS. We studied the neuroprotective effects of WL (100 & 200 mg/kg) and GA (100 & 200 mg/kg) using aluminium chloride (AlCl₃)-induced neurodegeneration model. The study was conducted using male Wistar rats. We assessed the effects of WL and GA on motor learning ability, motor coordination, locomotor activity, cytokine production, BDNF, glutathione peroxidase (GPx), m-calpain, caspase-3 inhibition and L-glutamate level. The study suggests that the treatment with WL and GA could protect the motor neurons from the toxicity that caused by Al via improving the antioxidant status, BDNF, and by preventing glutamate excitotoxicity. Also, WL and GA are found to be effective in inhibiting caspase-3 activation and downregulating inflammatory cytokines. WL and GA also found effective in improving the motor learning abilities and motor coordination in rats. The protective effects of the WL and GA were further confirmed from histopathological results. WL and GA prevent the neurofibrillary tangle formation and neuronal damage. The study concluded that the WL and GA were dose-dependently effective in managing the AlCl₃-induced neurodegeneration.

Metabolic and taxonomic insights into the Gram-negative natural rubber degrading bacterium Steroidobacter cummioxidans sp. nov., strain 35Y

The pathway of rubber (poly [cis-1,4-isoprene]) catabolism is well documented for Gram-positive rubber degraders but only little information exists for Gram-negative species. The first documented potent rubber degrading Gram-negative strain is Xanthomonas sp. strain 35Y that uses extracellular rubber oxygenases for the initial cleavage of the polyisoprene molecule. However, neither the exact phylogenetic position of Xanthomonas sp. strain 35Y nor the catabolic pathway of the primary polyisoprene cleavage products have been investigated. In this contribution, we started to address both these issues by a comprehensive taxonomic characterization and by the analysis of the draft genome sequence of strain 35Y. Evaluation of the 16S rRNA gene sequence pointed to a borderline taxonomic position of strain 35Y as a novel species of the genus Steroidobacter. Further, substantial differences in the genotypic properties of strain 35Y and the members of the genus Steroidobacter, including average nucleotide identity (ANI) and in silico DNA-DNA hybridization (DDH), resolved the taxonomic position of strain 35Y and suggested its positioning as a novel species of the genus Steroidobacter. This was further confirmed by comparative analysis of physiological and biochemical features of strain 35Y with other members of the genus Steroidobacter. Thus, we conclude that strain 35Y represents a novel species of the genus Steroidobacter, for which we propose the designation Steroidobacter cummioxidans sp. nov., strain 35YT. A comprehensive analysis of the draft genome of S. cummioxidans strain 35Y revealed similarities but also substantial differences to rubber degrading Gram-positive counterparts. In particular, the putative transporters for the uptake of polyisoprene cleavage products differ from Gram-positive rubber degrading species. The draft genome sequence of S. cummioxidans strain 35Y will be useful for researchers to experimentally verify the predicted similarities and differences in the pathways of polyisoprene catabolism in Gram-positive and Gram-negative rubber degrading species.

Lactobacillus fermentum FTDC 8312 combats hypercholesterolemia via alteration of gut microbiota

In this study, hypercholesterolemic mice fed with Lactobacillus fermentum FTDC 8312 after a seven-week feeding trial showed a reduction in serum total cholesterol (TC) levels, accompanied by a decrease in serum low-density lipoprotein cholesterol (LDL-C) levels, an increase in serum high-density lipoprotein cholesterol (HDL-C) levels, and a decreased ratio of apoB100:apoA1 when compared to those fed with control or a type strain, L. fermentum JCM 1173. These have contributed to a decrease in atherogenic indices (TC/HDL-C) of mice on the FTDC 8312 diet. Serum triglyceride (TG) levels of mice fed with FTDC 8312 and JCM 1173 were comparable to those of the controls. A decreased ratio of cholesterol and phospholipids (C/P) was also observed for mice fed with FTDC 8312, leading to a decreased number of spur red blood cells (RBC) formation in mice. Additionally, there was an increase in fecal TC, TG, and total bile acid levels in mice on FTDC 8312 diet compared to those with JCM 1173 and controls. The administration of FTDC 8312 also altered the gut microbiota population such as an increase in the members of genera Akkermansia and Oscillospira, affecting lipid metabolism and fecal bile excretion in the mice. Overall, we demonstrated that FTDC 8312 exerted a cholesterol lowering effect that may be attributed to gut microbiota modulation.

Protective effect of co-administration of curcumin and sildenafil in alcohol induced neuropathy in rats

Neuropathic pain associated with chronic alcohol consumption is a medico-socioeconomical problem that affects both central and peripheral nervous system and has no satisfactory treatment till date. The present study was designed to investigate the protective effect of co-administration of curcumin and sildenafil on alcohol induced neuropathic pain in rats. In order to carry out this, ethanol (35% v/v, 10g/kg, p.o.) was administered for 10 weeks to induce neuropathic pain. Curcumin (30 and 60mg/kg, i.p.) and sildenafil (5 and 10mg/kg, i.p.) were given alone and in combination at their lower doses (30mg/kg curcumin and 5mg/kg, sildenafil, i.p.) to investigate the changes in thermal and mechanical hyperalgesia, allodynia and histopathological parameters. Biochemical estimations of thiobarbituric acid reactive species, glutathione and protein was also carried out to evaluate oxidative stress. The results revealed that chronic alcohol consumption for 10 weeks caused significant thermal and mechanical hyperalgesia, allodynia and increased oxidative stress. Individual administration of both the drugs at their low as well as high doses were able to improve the symptoms of alcohol induced neuropathic pain. Whereas co-administration of curcumin and sildenafil at their lower doses itself were found to significantly improve nerve functions, biochemical and histopathological parameters as compared to their individual administration. It is therefore proposed that co-administration of curcumin and sildenafil may bring new dimension towards attenuation of alcohol induced neuropathic pain affecting central as well as peripheral nervous system.

Redox responsive albumin autogenic nanoparticles for the delivery of cancer drugs

The present study explores preparation and characterization of redox sensitive albumin autogenic nanoparticles (ANPs) for drug delivery applications. Human serum albumin nanoparticles are prepared by desolvation method. The particles are stabilized through self-crosslinking and no external stabilizers are involved in the preparation. ANPs are then subjected to Camptothecin (CPT) drug loading. Experiments on in vitro and in vivo release profile, cytotoxic and cytocompatability, hemocompatability, blood clearance, tracking and bio imaging are studied in detail. The redox sensitive and drug release properties of ANPs studied in the presence of glutathione. Results on the physical, chemical and instrumental characterization warrant the property of the nanoparticles. ANPs obtained in the present study is biocompatible, biodegradable, effectively entangle the chosen drug, release the drug in the controlled manner, sensitive to reducing environment, nil toxicity and appreciable uptake by cells. In the current scenario on the requirement of a drug carrier with redox sensitive property to encounter cancer cells, the results of the present study on albumin nanoparticles with redox sensitivity is smart and pave the way in the cancer therapeutics.

Multifaceted effects of aluminium in neurodegenerative diseases: A review

Aluminium (Al) is the most common metal and widely distributed in our environment. Al was first isolated as an element in 1827, and its use began only after 1886. Al is widely used for industrial applications and consumer products. Apart from these it is also used in cooking utensils and in pharmacological agents, including antacids and antiperspirants from which the element usually enters into the human body. Evidence for the neurotoxicity of Al is described in various studies, but still the exact mechanism of Al toxicity is not known. However, the evidence suggests that the Al can potentiate oxidative stress and inflammatory events and finally leads to cell death. Al is considered as a well-established neurotoxin and have a link between the exposure and development of neurodegenerative diseases, including Amyotrophic Lateral Sclerosis (ALS), Alzheimer's disease (AD), dementia, Gulf war syndrome and Parkinsonism. Here, we review the detailed possible pathogenesis of Al neurotoxicity. This review summarizes Al induced events likewise oxidative stress, cell mediated toxicity, apoptosis, inflammatory events in the brain, glutamate toxicity, effects on calcium homeostasis, gene expression and Al induced Neurofibrillary tangle (NFT) formation. Apart from these we also discussed animal models that are commonly used for Al induced neurotoxicity and neurodegeneration studies. These models help to find out a better way to treat and prevent the progression in Al induced neurodegenerative diseases.

Study on cerebroprotective actions of Clerodendron glandulosumleaves extract against long term bilateral common carotid artery occlusion in rats

Stroke is a major cause of death and disability worldwide. The resulting burden on the society continues to grow, with increase in the incidence of stroke. Oxidative stress has been involved in the pathogenesis of several neurological diseases including acute stroke.Focal and global cerebral ischemia represents diseases that are common in the human population.In recent years much attention is being paid towards the exploration of herbal preparation, antioxidant agents and combination therapies including COX-2 inhibitors in experimental model of stroke.Possible effect of a hydroalcoholic leaf extract of Clerodendron glandulosumColeb (C. glandulosum)on oxidant-antioxidant status in ischemia-hypoperfusion injury in the rat forebrain has been investigated.Healthy adult male Wistar albino rats were divided into five groups (n=8). Group I was served as Sham control (normal saline 1ml/kg, orally), group II was served hypoperfusion control (normal saline 1ml/kg, orally), group III, group IV were served as hydroalcoholic extract treated (200 and 400mg/kg, orally) and group V was treated with Quercetin (10mg/kg, orally) for 14days to assess preventive and curative effects of C. glandulosum. Flavonoid and phenolic compounds exhibit a broad spectrum of biological activity, including antioxidant. C. glandulosum extract (200 and 400mg/kg, p.o) was administered orally, once daily for a period of 2 weeks after the occlusion of BCCA. After 14th days rats were subjected to behavioral studies. After behavioral studies animals were sacrificed and brain was removed and homogenized. Estimation of Lipid peroxidation (LPO) Myeloperoxidase (MPO), estimation of protein levels and the activities of Superoxide dismutase (SOD), Catalase (CAT), were performed. Infarct size and histopathological changes were observed in treated groups.

Synthesis and Compositional Analysis of Permalloy Powder Prepared by Arc-Discharge

We report the synthesis, compositional, structural and magnetic properties of permalloy powders prepared using an arc-discharge method under different atmospheres. Ion beam analysis results showed that powder prepared in air had a higher concentration of oxygen than those prepared under nitrogen or argon atmospheres. X-ray diffraction measurements showed that powders prepared in air contained magnetite (Fe3O4) and other phases, while powders prepared under nitrogen or argon predominately contained permalloy. The permalloy powders contained a broad range of particle sizes, and nanoparticles as small as 10 nm were evident from transmission electron microscopy data. The saturation magnetizations were significantly lower for the powders prepared in air than those prepared under nitrogen or argon. This can be attributed to oxidation, where the saturation magnetization is predominately from Fe3O4 for powders made in air. The coercive fields were also significantly larger for powders prepared in air, which is consistent with the powders containing different phases when compared with the permalloy powders. Our results show that permalloy powders can be made in nitrogen and argon, allowing for the production of low oxygen content permalloy powders for device applications. Our results also suggest that the use of an iron anode could result in Fe3O4 powders.

Interaction of sol-gel derived tiO2- and siO2-based bionanocomposites with erythrocytes and serum proteins

Nanoenabled drug carriers are emerging as alternatives to conventional small-molecule drugs and their in-vitro biocompatibility evaluation with blood components is a necessary part of early preclinical development. In the present study, Chitosan-based bionanocomposites of sol-gel derived TiO2 and SiO2 were synthesised by the ex situ process. Samples were characterised by X-ray diffraction, Fourier transformed infrared spectrophotometer, transmission electron microscopy and selected area electron diffraction techniques. The analysis reveals the formation of single-phase oxides and their bionanocomposites. Haemolysis (destruction of red blood cell) study was performed by spectrophotometer to assess the haemocompatibility nature as a function of different incubation time. Experimental results reveal the percentage of haemolysis increase with the increase of the incubation time, but it was found to be <2%. This confirms our bionanocomposites are more haemocompatible as compared with respective nanocrystalline ceramics. Also, the interaction of our bionanocomposites with serum proteins at various incubation periods (1-24 h) were investigated using sodium dodecyl sulphate-polyacrylamide gel experiment, the obtained results were discussed in details.

Functional assignment of metagenomic data: challenges and applications

Metagenomic sequencing provides a unique opportunity to explore earth's limitless environments harboring scores of yet unknown and mostly unculturable microbes and other organisms. Functional analysis of the metagenomic data plays a central role in projects aiming to explore the most essential questions in microbiology, namely 'In a given environment, among the microbes present, what are they doing, and how are they doing it?' Toward this goal, several large-scale metagenomic projects have recently been conducted or are currently underway. Functional analysis of metagenomic data mainly suffers from the vast amount of data generated in these projects. The shear amount of data requires much computational time and storage space. These problems are compounded by other factors potentially affecting the functional analysis, including, sample preparation, sequencing method and average genome size of the metagenomic samples. In addition, the read-lengths generated during sequencing influence sequence assembly, gene prediction and subsequently the functional analysis. The level of confidence for functional predictions increases with increasing read-length. Usually, the most reliable functional annotations for metagenomic sequences are achieved using homology-based approaches against publicly available reference sequence databases. Here, we present an overview of the current state of functional analysis of metagenomic sequence data, bottlenecks frequently encountered and possible solutions in light of currently available resources and tools. Finally, we provide some examples of applications from recent metagenomic studies which have been successfully conducted in spite of the known difficulties.

Cerebroprotective effect of Eclipta alba against global model of cerebral ischemia induced oxidative stress in rats

Oxidative stress is believed to contribute to neuronal damage induced by cerebral ischemia/reperfusion (I/R) injury. The present study was undertaken to evaluate the possible cerebroprotective and antioxidant effect of hydroalcoholic extract of Eclipta alba against global cerebral ischemia in the rat. Adult Wistar albino rats were treated with extract of Eclipta alba (250 and 500mg/kg/day, p.o.) for 10 days. The global cerebral ischemia-reperfusion injury was induced by occluding bilateral common carotid arteries (BCCA) for 30min, followed by 4h reperfusion. Quercetin (20mg/kg, i.p.) was used for the reference compound. After that, animals were sacrificed by decapitation, brain was removed, various biochemical estimations, cerebral edema, assessment of cerebral infarct size, and histopathological examinations were carried out. BCCA caused significant depletion in superoxide dismutase (SOD), glutathione peroxidase (GPx), reduced glutathione (GSH), catalase (CAT), glutahione-S-transferase (GST), glutathione ruductase (GR) and significant increase in malondialdehyde (MDA) in brain. Pretreatment with hydroalcoholic extract of Eclipta alba significantly reversed the levels of biochemical parameters and significantly reduced the edema and cerebral infarct size as compared to the ischemic control group. Eclipta alba at higher dose markedly reduced ischemia-induced neuronal loss of the brain. Reduction of cerebral edema, an early symptom of ischemia, is one of the most important remedies for reducing subsequent chronic neural damage in stroke. The results of the study show that Eclipta alba pretreatment ameliorates cerebral ischemia/reperfusion injury and enhances the antioxidant defense against BCCA occlusion induced I/R in rats; so it exhibits cerebroprotective property. HPLC fingerprint of hydroalcoholic extract of Eclipta alba was performed for conforming the coumestan present in the plant extract.

Anti-obese activity of Butea monosperma (Lam) bark extract in experimentally induced obese rats

To study the efficacy of ethanolic extract of B. monosperma bark in cafeteria and atherogenic diet fed rats and monosodium glutamate (MSG) obese rats, different doses (200, 400 and 800 mg/kg) of ethanolic extract of B. monosperma bark showed dose dependent decrease in body weight, daily food intake, glucose, lipids, internal organs' weight and fat pad weight in cafeteria and atherogenic diet fed rats and monosodium glutamate obese rats. The results suggested that B. monosperma has significant anti-obese activity.

Cerebroprotective activity of Wedelia calendulacea on global cerebral ischemia in rats

The present study was to investigate the effect of W. calendulacea on ischemia and reperfusion-induced cerebral injury. Cerebral ischemia was induced by occluding right and left common carotid arteries (global cerebral ischemia) for 30 min followed by reperfusion for 1 h and 4 h individually. Various biochemical alterations, produced subsequent to the application of bilateral carotid artery occlusion (BCAO) followed by reperfusion viz. increase in lipid peroxidation (LPO), hydrogen peroxide (H2O2), and decrease in reduced glutathione (GSH), catalase (CAT) and superoxide dismutase (SOD), level in the brain tissue, Western blot analysis (Cu-Zn-SOD and CAT) and assessment of cerebral infarct size were measured. All those enzymes are markedly reversed and restored to near normal level in the groups pretreated with W. calendulacea (250 and 500 mg/kg given orally in single and double dose/day for 10 days) in dose-dependent way. The effect of W. calendulacea had increased significantly the protein expression of copper/zinc superoxide dismutase (Cu-Zn-SOD) and CAT in cerebral ischemia. W. claendulacea was markedly decrease cerebral infarct damages but results are not statistically significant. It can be concluded that W. calendulacea possesses a neuroprotective activity against cerebral ischemia in rat.

Antihyperlipidemic potential of Cedrus deodara extracts in monosodium glutamate induced obesity in neonatal rats

OBJECTIVE

To study the antihyperlipidemic effect of Cedrus deodara (C. deodara) against monosodium glutamate (MSG) induced obesity in neonatal rats.

MATERIALS AND METHODS

The studies were carried out on newborn neonatal rats and were injected intraperitoneally with 2 mg/g of MSG on the 2(nd) and 4(th) postnatal days and 4 mg/g on 6(th), 8(th) and 10(th) postnatal days. Ethanolic extract (EE) and acetone extract (AE) of C. deodara was administered in a dose of 100 and 200 mg/kg, p.o./day at the age of 65 days. On day 60 of treatment, body weight, locomotor activity, body temperature, and various biochemical parameters like serum glucose, total cholesterol, triglyceride, and organs weights were recorded.

RESULTS

There was a significant reduction in body weight, organs and increased body temperature, locomotor activity after treatment with extracts. C. deodara decreased serum glucose, total cholesterol and triglyceride, low density lipoprotein (LDL) and very low density lipoprotein (VLDL) levels and increased high density lipoprotein (HDL) significantly has compared to MSG-control rats.

CONCLUSION

C. deodara extracts exhibited antihyperlipidemic effect and it possesses anti-obesity properties in MSG induced obese rats.

CdO-based nanostructures as novel CO(2) gas sensors

Crystalline Cd(OH)(2)/CdCO(3) nanowires, having lengths in the range from 0.3 up to several microns and 5-30 nm in diameter, were synthesized by a microwave-assisted wet chemical route and used as a precursor to obtain CdO nanostructures after a suitable thermal treatment in air. The morphology and microstructure of the as-synthesized and annealed materials have been investigated by scanning electron microscopy, transmission electron microscopy, x-ray diffraction and thermogravimetry-differential scanning calorimetry. The change in morphology and electrical properties with temperature has revealed a wire-to-rod transformation along with a decreases of electrical resistance. Annealed samples were printed on a ceramic substrate with interdigitated contacts to fabricate resistive solid state sensors. Gas sensing properties were explored by monitoring CO(2) in synthetic air in the concentration range 0.2-5 v/v% (2000-50 000 ppm). The effect of annealing temperature, working temperature and CO(2) concentration on sensing properties (sensitivity, response/recovery time and stability) were investigated. The results obtained demonstrate that CdO-based thick films have good potential as novel CO(2) sensors for practical applications.

Antiulcerogenic activity of Terminalia chebula fruit in experimentally induced ulcer in rats

CONTEXT

Terminalia chebula Retz. (Combretaceae) is a medium-sized tree that grows in the wild throughout India. T. chebula has been extensively used in Ayurveda, Unani, and homoeopathic medicine. The fruit has been used as a traditional medicine for a household remedy against various human ailments. Traditionally T. chebula is used to cure chronic ulcer, gastritis, and stomach cancers.

OBJECTIVE

The present study is to evaluate the antiulcer effect of hydroalcoholic (70%) extract of Terminalia chebula fruit.

MATERIALS AND METHODS

Aspirin, ethanol and cold restraint stress-induced ulcer methods in rats were used for the study. The effects of the extract on gastric secretions, pH, total and free acidity using pylorus ligated methods were also evaluated.

RESULTS

Animals pretreated with doses of 200 and 500 mg/kg hydroalcoholic extract showed significant reduction in lesion index, total affected area and percentage of lesion in comparison with control group (P < 0.05 and P < 0.01) in the aspirin, ethanol and cold restraint stress-induced ulcer models. Similarly extracts increased mucus production in aspirin and ethanol-induced ulcer models. At doses of 200 and 500 mg/kg of T. chebula extract showed antisecretory activity in pylorus ligated model, which lead to a reduction in the gastric juice volume, free acidity, total acidity, and significantly increased gastric pH.

DISCUSSION AND CONCLUSION

These findings indicate that hydroalcoholic extract of the fruit T. chebula displays potential antiulcerogenic activity. This activity thus lends pharmacological credence to the suggested use of the plant as a natural remedy in the treatment or management of ulcer.

Expression of conjoined genes: another mechanism for gene regulation in eukaryotes

From the ENCODE project, it is realized that almost every base of the entire human genome is transcribed. One class of transcripts resulting from this arises from the conjoined gene, which is formed by combining the exons of two or more distinct (parent) genes lying on the same strand of a chromosome. Only a very limited number of such genes are known, and the definition and terminologies used for them are highly variable in the public databases. In this work, we have computationally identified and manually curated 751 conjoined genes (CGs) in the human genome that are supported by at least one mRNA or EST sequence available in the NCBI database. 353 representative CGs, of which 291 (82%) could be confirmed, were subjected to experimental validation using RT-PCR and sequencing methods. We speculate that these genes are arising out of novel functional requirements and are not merely artifacts of transcription, since more than 70% of them are conserved in other vertebrate genomes. The unique splicing patterns exhibited by CGs reveal their possible roles in protein evolution or gene regulation. Novel CGs, for which no transcript is available, could be identified in 80% of randomly selected potential CG forming regions, indicating that their formation is a routine process. Formation of CGs is not only limited to human, as we have also identified 270 CGs in mouse and 227 in drosophila using our approach. Additionally, we propose a novel mechanism for the formation of CGs. Finally, we developed a database, ConjoinG, which contains detailed information about all the CGs (800 in total) identified in the human genome. In summary, our findings reveal new insights about the functionality of CGs in terms of another possible mechanism for gene regulation and genomic evolution and the mechanism leading to their formation.

MetaBioME: a database to explore commercially useful enzymes in metagenomic datasets

Microbial enzymes have many known applications as biocatalysts in biotechnology, agriculture, medical and other industries. However, only a few enzymes are currently employed for such commercial applications. In this scenario, the current onslaught of metagenomic data provides a new unexplored treasure trove of genomic wealth that can not only enhance the enzyme repertoire by the discovery of novel commercially useful enzymes (CUEs) but can also reveal better functional variants for existing CUEs. We prepared a catalogue of CUEs using text mining of PubMed abstracts and other publicly available information, and manually curated the data to identify 510 CUEs. Further, in order to identify novel homologues of these CUEs, we identified potential ORFs in publicly available metagenomic datasets from 10 diverse sources. Using this strategy, we have developed a resource called MetaBioME (http://metasystems.riken.jp/metabiome/) that comprises (i) a database of CUEs and (ii) a comprehensive platform to facilitate homology-based computational identification of novel homologous CUEs from metagenomic and bacterial genomic datasets. Using MetaBioME, we have identified several novel homologues to known CUEs that can potentially serve as leads for further experimental verification.

Grain boundary effect on the dielectric properties of nanocrystalline beta-CuSCN

The physics of grain boundaries in semiconductors is of interest both from a fundamental as well as technical point of view because they play crucial role in controlling properties. The grain boundary effect in the nanocrystalline materials are more because the volume fraction of atoms lying at the grain boundaries of the nanocrystalline materials are more as compared with conventional coarse-grained polycrystalline materials. The most attractive hole transporting electrolyte material of dye sensitized solar cell is CuSCN because of its band gap, valence band edge position and p-type semiconducting nature. We have synthesised nanocrystalline beta phase of CuSCN using co-precipitation technique. The grain boundary effect on the dielectric behaviour has been investigated using impedance spectroscopy in a wide frequency range 1 Hz to 1 MHz under dc bias voltages 0 V to -4.2 V. The results are analyzed with double (or back-to-back) Schottky grain boundary barrier model and discussed in detail.

Genome of an endosymbiont coupling N2 fixation to cellulolysis within protist cells in termite gut

Termites harbor diverse symbiotic gut microorganisms, the majority of which are as yet uncultivable and their interrelationships unclear. Here, we present the complete genome sequence of the uncultured Bacteroidales endosymbiont of the cellulolytic protist Pseudotrichonympha grassii, which accounts for 70% of the bacterial cells in the gut of the termite Coptotermes formosanus. Functional annotation of the chromosome (1,114,206 base pairs) unveiled its ability to fix dinitrogen and recycle putative host nitrogen wastes for biosynthesis of diverse amino acids and cofactors, and import glucose and xylose as energy and carbon sources. Thus, nitrogen fixation and cellulolysis are coupled within the protist's cells. This highly evolved symbiotic system probably underlies the ability of the worldwide pest termites Coptotermes to use wood as their sole food.