Analyses of Elaeocarpus sphaericus Extract for Antioxidant, Antiproliferative and Gene Repression Activities against HIF-1α and VEGF.

The study presents antioxidant, phytochemical, anti-proliferative, and gene repression activities against Hypoxia-inducible factor (HIF-1) alpha and Vascular endothelial growth factor (VEGF) of Elaeocarpus sphaericus extract. Elaeocarpus sphaericus dried and crushed plant leaves were extracted using water and methanol by ASE (Accelerated Solvent Extraction) method. Total phenolic content (TPC) and total flavonoid content (TFC) were used to measure the extracts' phytochemical activity (TFC). Antioxidant potential of the extracts was measured through DPPH, ABTS, FRAP, and TRP. Methanolic extract of the leaves of E. sphaericus has shown a higher amount of TPC (94.666±4.040 mg/gm GAE) and TFC value (172.33±3.21 mg/gm RE). The antioxidant properties of extracts in the yeast model (Drug Rescue assay) showed promising results. Ascorbic acid, gallic acid, hesperidin, and quercetin were found in the aqueous and methanolic extracts of E. sphaericus at varying amounts, according to a densiometric chromatogram generated by HPTLC analysis. Methanolic extract of E. sphaericus (10 mg/ml) has shown good antimicrobial potential against all bacterial strains used in the study except E. coli. The anticancer activity of the extract in HeLa cell lines ranged from 77.94±1.03 % to 66.85±1.95 %, while it ranged from 52.83±2.57 % to 5.44 % in Vero cell lines at varying concentration (1000 µg/ml-31.2 µg/ml). A promising effect of extract was observed on the expression activity of HIF-1 and VEGF gene through RT-PCR assay.

Transition metal dichalcogenides integrated waveguide modulator and attenuator in silicon nitride platform.

Embedding transition metal dichalcogenides (TMDs) into optical devices enhance the light-matter interaction, which holds a great promise for designing compact integrated photonic components. The chemical composition and thickness of TMDs affect their electronic and optical properties. The optical properties demonstrate stable and strong gate tunable optical response near the excitonic transitions. These materials are, therefore, promising candidates for designing electro-optic modulators and attenuators. Here, an electro-absorption modulator is investigated based on integrating different TMD monolayers on silicon nitride waveguides near the excitonic binding energy. A comparison of absorption changes due to electrostatically induced charges in MoS2, MoSe2, WS2, WSe2, and graphene has been presented for modulator design. The results show that with the confinement factor of about 0.10% in the monolayer TMDs, the modulation strength is 10x higher in WS2 as compared to the graphene-based modulator design. The WS2 based modulator shows the highest modulation strength with an improvement by a factor of 5 as compared to Mo based designs. Further, the change in the spectral response of these materials with thickness and chemical composition has been exploited for the design of attenuator. A micro-opto-mechanical system technology with TMD integrated supersubstrate above a Si3N4 waveguide affecting the optical response is investigated. By replacing the TMD in the supersubstrate with Se atom instead of S in the MX2 and WX2 compound, the attenuation is shifted from visible to near-infrared range allowing tuning from 620 to 750 nm. The tuning of the attenuation wavelength will help the designer choose the best material for visible light photonic applications.

Utilizing ethnic-specific differences in minor allele frequency to recategorize reported pathogenic deafness variants.

Ethnic-specific differences in minor allele frequency impact variant categorization for genetic screening of nonsyndromic hearing loss (NSHL) and other genetic disorders. We sought to evaluate all previously reported pathogenic NSHL variants in the context of a large number of controls from ethnically distinct populations sequenced with orthogonal massively parallel sequencing methods. We used HGMD, ClinVar, and dbSNP to generate a comprehensive list of reported pathogenic NSHL variants and re-evaluated these variants in the context of 8,595 individuals from 12 populations and 6 ethnically distinct major human evolutionary phylogenetic groups from three sources (Exome Variant Server, 1000 Genomes project, and a control set of individuals created for this study, the OtoDB). Of the 2,197 reported pathogenic deafness variants, 325 (14.8%) were present in at least one of the 8,595 controls, indicating a minor allele frequency (MAF) > 0.00006. MAFs ranged as high as 0.72, a level incompatible with pathogenicity for a fully penetrant disease like NSHL. Based on these data, we established MAF thresholds of 0.005 for autosomal-recessive variants (excluding specific variants in GJB2) and 0.0005 for autosomal-dominant variants. Using these thresholds, we recategorized 93 (4.2%) of reported pathogenic variants as benign. Our data show that evaluation of reported pathogenic deafness variants using variant MAFs from multiple distinct ethnicities and sequenced by orthogonal methods provides a powerful filter for determining pathogenicity. The proposed MAF thresholds will facilitate clinical interpretation of variants identified in genetic testing for NSHL. All data are publicly available to facilitate interpretation of genetic variants causing deafness.

An arsenate-reducing and alkane-metabolizing novel bacterium, Rhizobium arsenicireducens sp. nov., isolated from arsenic-rich groundwater.

A novel arsenic (As)-resistant, arsenate-respiring, alkane-metabolizing bacterium KAs 5-22T, isolated from As-rich groundwater of West Bengal was characterized by physiological and genomic properties. Cells of strain KAs 5-22T were Gram-stain-negative, rod-shaped, motile, and facultative anaerobic. Growth occurred at optimum of pH 6.0-7.0, temperature 30 °C. 16S rRNA gene affiliated the strain KAs 5-22T to the genus Rhizobium showing maximum similarity (98.4 %) with the type strain of Rhizobium naphthalenivorans TSY03bT followed by (98.0 % similarity) Rhizobium selenitireducens B1T. The genomic G + C content was 59.4 mol%, and DNA-DNA relatedness with its closest phylogenetic neighbors was 50.2 %. Chemotaxonomy indicated UQ-10 as the major quinone; phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as major polar lipids; C16:0, C17:0, 2-OH C10:0, 3-OH C16:0, and unresolved C18:1 É·7C/É·9C as predominant fatty acids. The cells were found to reduce O2, As5+, NO3-, SO42- and Fe3+ as alternate electron acceptors. The strain's ability to metabolize dodecane or other alkanes as sole carbon source using As5+ as terminal electron acceptor was supported by the presence of genes encoding benzyl succinate synthase (bssA like) and molybdopterin-binding site (mopB) of As5+ respiratory reductase (arrA). Differential phenotypic, chemotaxonomic, genotypic as well as physiological properties revealed that the strain KAs 5-22T is separated from its nearest recognized Rhizobium species. On the basis of the data presented, strain KAs 5-22T is considered to represent a novel species of the genus Rhizobium, for which the name Rhizobium arsenicireducens sp. nov. is proposed as type strain (=LMG 28795T=MTCC 12115T).

Bifunctional recombinant cellulase-xylanase (rBhcell-xyl) from the polyextremophilic bacterium Bacillus halodurans TSLV1 and its utility in valorization of renewable agro-residues.

The thermostable bifunctional CMCase and xylanase encoding gene (rBhcell-xyl) from Bacillus halodurans TSLV1 has been expressed in Escherichia coli. The recombinant E. coli produced rBhcell-xyl (CMCase 2272 and 910 U L-1 xylanase). The rBhcell-xyl is a ~62-kDa monomeric protein with temperature and pH optima of 60 °C and 6.0 with T1/2 of 7.0 and 3.5 h at 80 °C for CMCase and xylanase, respectively. The apparent K m values (CMC and Birchwood xylan) are 3.8 and 3.2 mg mL-1. The catalytic efficiency (k cat/K m ) values of xylanase and CMCase are 657 and 171 mL mg-1 min-1, respectively. End-product analysis confirmed that rBhcell-xyl is a unique endo-acting enzyme with exoglucanase activity. The rBhcell-xyl is a GH5 family enzyme possessing single catalytic module and carbohydrate binding module. The action of rBhcell-xyl on corn cobs and wheat bran liberated reducing sugars, which can be fermented to bioethanol and fine biochemicals.

Bioprocess for efficient production of recombinant Pichia anomala phytase and its applicability in dephytinizing chick feed and whole wheat flat Indian breads.

The phytase of the yeast Pichia anomala (PPHY) is a suitable biocatalyst as a food and feed additive because of its adequate thermostability, acid stability, protease insensitivity and broad substrate spectrum. The cell-bound nature and low phytase titres are the main bottlenecks for its utility in food and feed industries. In this investigation, we have overcome the problems by constitutive secretory expression of PPHY under glyceraldehyde phosphate dehydrogenase (GAP) promoter. A ~44-fold increase in rPPHY titre has been achieved after optimization of cultural variables by one-variable-at-a-time approach and two factorial statistical design. The use of GAP promoter makes the cultivation of the recombinant P. pastoris straight forward and eliminates the requirement of methanol for induction and hazards associated with its storage. Among metal-phytate complexes, Ca(2+) phytate is hydrolyzed more efficiently by rPPHY than Co(2+), Mn(2+), Mg(2+), Fe(3+) and Zn(2+) phytates. The enzyme is effective in dephytinizing whole wheat unleavened flat Indian breads (naan and tandoori) and different broiler feeds, thus mitigating anti-nutritional effects of phytates.

Advancing genetic testing for deafness with genomic technology.

BACKGROUND: Non-syndromic hearing loss (NSHL) is the most common sensory impairment in humans. Until recently its extreme genetic heterogeneity precluded comprehensive genetic testing. Using a platform that couples targeted genomic enrichment (TGE) and massively parallel sequencing (MPS) to sequence all exons of all genes implicated in NSHL, we tested 100 persons with presumed genetic NSHL and in so doing established sequencing requirements for maximum sensitivity and defined MPS quality score metrics that obviate Sanger validation of variants. METHODS: We examined DNA from 100 sequentially collected probands with presumed genetic NSHL without exclusions due to inheritance, previous genetic testing, or type of hearing loss. We performed TGE using post-capture multiplexing in variable pool sizes followed by Illumina sequencing. We developed a local Galaxy installation on a high performance computing cluster for bioinformatics analysis. RESULTS: To obtain maximum variant sensitivity with this platform 3.2-6.3 million total mapped sequencing reads per sample were required. Quality score analysis showed that Sanger validation was not required for 95% of variants. Our overall diagnostic rate was 42%, but this varied by clinical features from 0% for persons with asymmetric hearing loss to 56% for persons with bilateral autosomal recessive NSHL. CONCLUSIONS: These findings will direct the use of TGE and MPS strategies for genetic diagnosis for NSHL. Our diagnostic rate highlights the need for further research on genetic deafness focused on novel gene identification and an improved understanding of the role of non-exonic mutations. The unsolved families we have identified provide a valuable resource to address these areas.

Optimization of heterologous expression of the phytase (PPHY) of Pichia anomala in P. pastoris and its applicability in fractionating allergenic glycinin from soy protein.

The phytase (PPHY) of Pichia anomala has the requisite properties of thermostability and acidstability, broad substrate spectrum, and protease insensitivity, which make it a suitable candidate as a feed and food additive. The 1,389-bp PPHY gene was amplified from P. anomala genomic DNA, cloned in pPICZαA, and expressed extracellularly in P. pastoris X33. Three copies of PPHY have been detected integrated into the chromosomal DNA of the recombinant P. pastoris. The size exclusion chromatography followed by electrophoresis of the pure rPPHY confirmed that this is a homohexameric glycoprotein of ~420 kDa with a 24.3 % portion as N-linked glycans. The temperature and pH optima of rPPHY are 60 °C and 4.0, similar to the endogenous enzyme. The kinetic characteristics K(m), V(max), K(cat), and K(cat)/K(m) of rPPHY are 0.2 ± 0.03 mM, 78.2 ± 1.43 nmol mg(-1) s(-1), 65,655 ± 10.92 s(-1), and 328.3 ± 3.12 µM(-1) s(-1), respectively. The optimization of medium components led to a 21.8-fold improvement in rPPHY production over the endogenous yeast. The rPPHY titer attained in shake flasks could also be sustained in the laboratory fermenter. The rPPHY accounts for 57.1 % of the total secreted protein into the medium. The enzyme has been found useful in fractionating allergenic protein glycinin from soya protein besides dephytinization.

Antimycobacterial labdane diterpenes from Leucas stelligera.

Phytochemical investigation of the acetone extract of the aerial parts of Leucas stelligera afforded four new compounds (1-4) belonging to the labdane diterpene series as well as two known flavones, velutin (5) and chrysoeriol (6). Structure elucidation of the new compounds was carried out using 1D and 2D NMR spectroscopic data and single-crystal X-ray crystallography of compound 1. Compounds 1-4 exhibited selective antimycobacterial activity against Mycobacterium tuberculosis with IC50 values in the range 5.02-9.80 µg/mL.

Absent right superior vena cava and persistent left superior vena cava: An incidental finding.

A patient with Marfan syndrome undergoing Bentall operation was found to have an absent right superior vena cava and persistent left superior vena cava. The dilation of coronary sinus raised the suspicion of persistent left superior vena cava. The diagnosis was confirmed by agitated saline contrast echocardiography and computed tomography of the chest.

A Collaborative Metaverse based A-La-Carte Framework for Tertiary Education (CO-MATE).

The paper aims to propose a futuristic educational and learning framework called CO-MATE (Collaborative Metaverse-based A-La-Carte Framework for Tertiary Education). The architectural framework of CO-MATE was conceptualized in a four-layered approach which depicts various infrastructure and service layer functionalities. CO-MATE is a technologically driven educational metaverse environment involving loosely coupled building blocks to provide an a-la-carte model for platform designers. For this, the authors had undertaken a systematic mapping study of the pre/post-COVID period to review the application of various emerging technologies. Further, the paper also discusses the core attributes and component offerings of CO-MATE for a technology-driven and automated immersive-learning environment and exemplifies the same through various use cases.

Wintertime aerosol properties of urban desert region of western India: Implications in regional climate assessment.

This study assessed the inter-relation between physiochemical and optical characteristics of aerosols measured at a desert-urban region affected by anthropogenic sources and desert dust during October 2020 to January 2021. Based on horizontal visibility and measured PM2.5 concentration, clear (37 %), light (33 %) and high (31 %) pollution periods were identified. Elemental and organic carbon (50 ± 15 µgm-3; 31 %) and secondary inorganics (53 ± 21 µgm-3; 33 %) dominated the PM2.5 mass (160 ± 4 µgm-3) during high pollution period with low dust (14 ± 7 µgm-3; 8 %) content. Interestingly, the clear pollution period was also influenced by carbonaceous fraction (19 ± 8 µgm-3; 32 %) and secondary inorganics (19 ± 5 µgm-3; 32 %), but the PM2.5 concentrations (59 ± 9 µgm-3) were ∼ one-third as compared to high pollution period. High scattering coefficients were observed which were comparable to highly polluted Indian city like Delhi. An exponential increase in non-absorbing material was observed and showed clear influence on light absorption capacity of EC and dust due to coating/mixing. High absorption Ångström exponent (AAE) >0.6 was observed for the ratio of non-absorbing to light absorbing components (LAC) in the range of 1-2.5 and EC/PM2.5 fraction of 7-14 %. While further increase in non-absorbing to absorbing components ratio > 4 and low amount of EC (<4 %) tend to decrease AAE below 0.4. Higher mass absorption cross-section (>30 m2g-1 of EC) was observed when 4-10 % EC fraction of PM2.5 associated with 1.5-3.5 times non-absorbing components to total absorbing components. Likewise, absorption enhanced by three to five folds compared to uncoated EC for low EC fraction (3-6 %) in PM2.5, but high non-absorbing to absorbing component ratio (>2.5). Interestingly, absorption was minimally amplified for nominal coating fraction associated with significant core materials or vice-versa. These findings have implications not only in regional climate assessment but also for other regions with comparable geography and source-mixes.

Pre-capture multiplexing improves efficiency and cost-effectiveness of targeted genomic enrichment.

BACKGROUND: Targeted genomic enrichment (TGE) is a widely used method for isolating and enriching specific genomic regions prior to massively parallel sequencing. To make effective use of sequencer output, barcoding and sample pooling (multiplexing) after TGE and prior to sequencing (post-capture multiplexing) has become routine. While previous reports have indicated that multiplexing prior to capture (pre-capture multiplexing) is feasible, no thorough examination of the effect of this method has been completed on a large number of samples. Here we compare standard post-capture TGE to two levels of pre-capture multiplexing: 12 or 16 samples per pool. We evaluated these methods using standard TGE metrics and determined the ability to identify several classes of genetic mutations in three sets of 96 samples, including 48 controls. Our overall goal was to maximize cost reduction and minimize experimental time while maintaining a high percentage of reads on target and a high depth of coverage at thresholds required for variant detection. RESULTS: We adapted the standard post-capture TGE method for pre-capture TGE with several protocol modifications, including redesign of blocking oligonucleotides and optimization of enzymatic and amplification steps. Pre-capture multiplexing reduced costs for TGE by at least 38% and significantly reduced hands-on time during the TGE protocol. We found that pre-capture multiplexing reduced capture efficiency by 23 or 31% for pre-capture pools of 12 and 16, respectively. However efficiency losses at this step can be compensated by reducing the number of simultaneously sequenced samples. Pre-capture multiplexing and post-capture TGE performed similarly with respect to variant detection of positive control mutations. In addition, we detected no instances of sample switching due to aberrant barcode identification. CONCLUSIONS: Pre-capture multiplexing improves efficiency of TGE experiments with respect to hands-on time and reagent use compared to standard post-capture TGE. A decrease in capture efficiency is observed when using pre-capture multiplexing; however, it does not negatively impact variant detection and can be accommodated by the experimental design.

Phyllocladane diterpenes from Anisomeles heyneana.

New phyllocladane diterpene, phyllocladan-16α,17-dihydroxy-19-oic acid (1), together with known phyllocladane diterpene, phyllocladan-16α,19-diol (2), cembrane diterpene ovatodiolide (3), sitosteryl-3-O-ß-D-glucoside (4), and verbascoside (5), were isolated from aerial parts of Anisomeles heyneana. The structure of compound 1 was elucidated by 1D and 2D NMR analyses which included HSQC, HMBC, and nuclear overhauser effect spectroscopy (NOESY) experiments as well as X-ray crystallography. This is the first report of phyllocladane diterpenes from genus Anisomeles. Compounds 1, 3, 4, and 5 were evaluated for inhibition of Mycobacterium tuberculosis and 3 was found to exhibit anti-mycobacterial activity with IC90 6.53 µg/ml. Compounds 1, 3, and 5, at 100 µg/ml, were also evaluated for inhibition of Thp-1 cell lines, and compounds 1 and 3 showed 59.02% and 96.4% inhibitions, respectively.

Recent advances in biofuel production through metabolic engineering.

Rising global energy demands and climate crisis has created an unprecedented need for the bio-based circular economy to ensure sustainable development with the minimized carbon footprint. Along with conventional biofuels such as ethanol, microbes can be used to produce advanced biofuels which are equivalent to traditional fuels in their energy efficiencies and are compatible with already established infrastructure and hence can be directly blended in higher proportions without overhauling of the pre-existing setup. Metabolic engineering is at the frontiers to develop microbial chassis for biofuel bio-foundries to meet the industrial needs for clean energy. This review does a thorough inquiry of recent developments in metabolic engineering for increasing titers, rates, and yields (TRY) of biofuel production by engineered microorganisms.

An ML prediction model based on clinical parameters and automated CT scan features for COVID-19 patients.

Outcome prediction for individual patient groups is of paramount importance in terms of selection of appropriate therapeutic options, risk communication to patients and families, and allocating resource through optimum triage. This has become even more necessary in the context of the current COVID-19 pandemic. Widening the spectrum of predictor variables by including radiological parameters alongside the usually utilized demographic, clinical and biochemical ones can facilitate building a comprehensive prediction model. Automation has the potential to build such models with applications to time-critical environments so that a clinician will be able to utilize the model outcomes in real-time decision making at bedside. We show that amalgamation of computed tomogram (CT) data with clinical parameters (CP) in generating a Machine Learning model from 302 COVID-19 patients presenting to an acute care hospital in India could prognosticate the need for invasive mechanical ventilation. Models developed from CP alone, CP and radiologist derived CT severity score and CP with automated lesion-to-lung ratio had AUC of 0.87 (95% CI 0.85-0.88), 0.89 (95% CI 0.87-0.91), and 0.91 (95% CI 0.89-0.93), respectively. We show that an operating point on the ROC can be chosen to aid clinicians in risk characterization according to the resource availability and ethical considerations. This approach can be deployed in more general settings, with appropriate calibrations, to predict outcomes of severe COVID-19 patients effectively.

Automated Quantification of Inflamed Lung Regions in Chest CT by UNet++ and SegCaps: A Comparative Analysis in COVID-19 Cases.

During the current COVID-19 pandemic, a high volume of lung imaging has been generated in the aid of the treating clinician. Importantly, lung inflammation severity, associated with the disease outcome, needs to be precisely quantified. Producing consistent and accurate reporting in high-demand scenarios can be a challenge that can compromise patient care with significant inter- or intra-observer variability in quantifying lung inflammation in a chest CT scan. In this backdrop, automated segmentation has recently been attempted using UNet++, a convolutional neural network (CNN), and results comparable to manual methods have been reported. In this paper, we hypothesize that the desired task can be performed with comparable efficiency using capsule networks with fewer parameters that make use of an advanced vector representation of information and dynamic routing. In this paper, we validate this hypothesis using SegCaps, a capsule network, by direct comparison, individual comparison with CT severity score, and comparing the relative effect on a ML(machine learning)-based prognosis model developed elsewhere. We further provide a scenario, where a combination of UNet++ and SegCaps achieves improved performance compared to individual models.

Withania somnifera as an Adjunctive Treatment for Refractory Restless Legs Syndrome in Parkinson's Disease: A Case Report.

Non-motor symptoms of Parkinson's disease (PD), such as insomnia and restless legs syndrome (RLS), tend to worsen and become refractory as neurodegeneration progresses. We report the case of a 72-year-old female with a six-year history of PD and two-and-half-year history of insomnia and refractory RLS. We added a neuroprotective agent, Withania somnifera, to the existing treatment regimen for her insomnia. Besides the partial remission of her insomnia and motor symptoms of PD, there was a complete reversal of the RLS symptoms. Withania somnifera has been shown to improve PD symptoms by preventing oxidative damage of the nigrostriatal dopaminergic neurons and improving dopamine levels in the midbrain and corpus striatum. Our case provides the first-time evidence where Withania somnifera added for insomnia caused a complete remission of refractory RLS, possibly due to its anti-apoptotic and pro-dopaminergic actions. Withania somnifera could prove beneficial in cases where the disease advances but further addition of dopamine agonists for refractory RLS is not possible due to the risk of dopamine augmentation.