Biology subjects

V, V.

Publications and source records attributed to V, V..

9 recordsLinked to original sources

bioRxiv2026

Production of a resilient biosurfactant using agro-wastes and Paenibacillus dendritiformis isolated from petroleum-contaminated soil: a break-even analysis at pilot scale

Wastes from mustard oil mills and dairy were used as partial replacement of pure reagents in modified Bushnell and Haas broth media for production of biosurfactant by Paenibacillus dendritiformis isolated from petroleum-contaminated soil. The process was optimised by construction of a response model using Taguchi experimental design, leading to a 28.23% increase in performance characteristics and a 13.23 % increase in yield of biosurfactant. The optimized production medium consisted of carbon @7.9 %, nitrogen @ 1.1% and agitation rate 180 r.p.m. This was provided by adding glucose @ 2%, ammonium nitrate @0.2%, mustard oil seed meal @10% and whey@ 10% in modified Bushnell Haas broth. The biosurfactant produced retained its properties during exposure to a wide range of pH values (5-11), high temperatures (up to 121C), high salinities of up to 5% and also five -fold concentration. Approximately three- fold increase in yield of the biosurfactant (25g/L to 68.5g/L) was obtained upon scaling-up the production from 100ml to 1500 ml in a lab scale fermenter with agitation @ 150r.p.m. and D.O. levels maintained at 6mg/L. Power calculations and the cost thereof was calculated (Rs 10.24 /L) and summed up with the cost of raw materials Rs 8.40/L and found to be Rs 18.64/L of product .Since 68.5g product is present in 1L, the cost is calculated to be Rs 271/- per kg. Comparison with selling price of currently used chemical surfactants like Linear Alkyl Benzene sulphonic acid (LAB) and sodium Lauryl sulphate and Sodium Lauryl ether sulphate (SLS and SLES) reveals that prices of these products varies from Rs 120 to 600 per kg depending on manufacturer and quality, order quantity. From the above studies it can be seen that production and use of this multiutility biosurfactant has, besides a clear advantage over chemically produced surfactants in terms of sustainability, a fairly good comparison with selling price of currently used chemical surfactants. The present study on the production costs (excluding capital costs) successfully demonstrates a break even analysis into the production of biosurfactants.

microbiology↗

bioRxiv2026

Diversified Portfolios of Bacterial Communities in Peri-urban Miyawaki Forests and Grassland Shaping Ecosystem Functions and Services

Soil microflora is fundamental to ecosystem functioning, yet their contribution in Miyawaki afforestation, a globally implemented ecological engineering approach, remains poorly characterized. In the present study, we examined the bacterial taxonomic diversity and their functional potential in a peri-urban Miyawaki mini-forest and compared with a nearby grassland the pre-existing ecosystem across dry and wet seasons. The Miyawaki plantation comprised of highly diverse native trees, sub-trees and shrubs spanning evergreen and deciduous varieties, potentiating nitrogen-fixation, diverse litter generation and rooting strategies resulting in pronounced functional heterogeneity. Notably relative to grassland, the Miyawaki forest was intensively managed and supplemented with organic amendments, and supportive irrigation, buffering the seasonal moisture stress. Using 16S rRNA amplicon sequencing of soil eDNA, we characterized seasonal variation in soil bacterial communities in both the systems. The observed soil bacterial community organization in forest as compared to the unmanaged grassland indicates combined influence of vegetation structure, dense canopy cover, continuous litter generation and root exudates. Microbial assemblages in the forest specialised in heterotrophic complex carbon degradation, biofilm formation, exopolysaccharide production and sporulation pathways which suggests adaptive abilities to anoxic microsites and other stressful conditions. In contrast, grassland soils harboured less diversified bacterial communities dominated by phototrophic and oxidative stress adaptation pathways consistent with sun lit, non-irrigated and moisture-variable conditions. Nonetheless, functional divergence in dry season reflects temporal reorganization of microbial communities marking a gradual trend towards soil ecosystem development. Together, these findings establish microbial baseline for Miyawaki forests revealing how tree-dense mini-forests restructure soil bacterial communities relative to grasslands highlighting the value of identifying soil microbial indicators for critically evaluating urban afforestation outcomes over extended time scales to inform sustainable design and policy. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/704982v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@15e1bb1org.highwire.dtl.DTLVardef@16c1dddorg.highwire.dtl.DTLVardef@11c99ecorg.highwire.dtl.DTLVardef@bd6d1d_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic representation of the study depicting the Miyawaki forest and nearby grassland.

ecology↗

bioRxiv2023

Genetic diversity and evidence of recombination of Horsegram yellow mosaic virus infecting pole bean (Phaseolus vulgaris L.) from South India

The yellow mosaic disease (YMD) caused by begomoviruses is a major constraint for the production of pole bean (Phaseolus vulgaris L.) in India. Survey was carried out in the eastern dry zone of Karnataka during 2019-20 to record the incidence of yellow mosaic disease in pole bean which revealed the ubiquitous prevalence of YMD in pole bean ranging from 6.02 to 80.74 per cent. Leaf samples collected (symptomatic and asymptomatic) were subjected for begomovirus detection using specific primers. Twelve samples, representing all the 12 taluks in the surveyed region were considered for full genome amplification by RCA, cloned and sequenced. Genome length of 12 current isolates ranged from 2718 - 2744 and 2668 - 2671 nucleotides for DNA-A and DNA-B, respectively. Sequence analysis using Sequence Demarcation Tool (SDT) showed >91 per cent nucleotide identity of current isolates (DNA-A) with other horsegram yellow mosaic virus (HgYMV) isolates available in the GenBank. As per existing ICTV criteria, all the current isolates can be considered as strains of HgYMV. Further, DNA-B associated with all the 12 isolates also shared >91 per cent nucleotide identity with DNA-B of HgYMV isolates, indicating absence of component re-assortment in HgYMV. Variation in the pairwise nucleotide identity and phylogenetic analysis confirmed the existence of new strains within the current HgYMV isolates. GC plot analysis reveals potential recombination in the low GC rich regions. Further, recombination breakpoint analysis indicated intra-species recombination in both DNA-A and DNA-B, which might have driven the origin of new strains in HgYMV. This is the first comprehensive study on begomoviruses ioslates associated with the yellow mosaic disease of pole bean based on complete genome sequencing in the world.

molecular biology↗

bioRxiv2023

Virome analyses by next-generation sequencing (NGS) in chilli (Capsicum anuum L.) presented with diverse symptoms phenotype revealed the association of seven plant viruses

Chilli is an important vegetable and spice crop, is known to be infected by several viruses. Techniques used in diagnosis of plant viral diseases before Next-generation sequencing (NGS) are having limitation of identifying the only known viruses. In the present study, virome analyses in infected chilli leaf samples was carried out using NGS to know the diversity of both known and unknown viruses associated with diseased symptoms. For virome profiling, samples from 19 fields were collected from chilli plants showing leaf curling, vein banding, mosaic, mottling, shoestring/rat tail/filiform/leathery and dull coloured leaves. Viral disease incidence in the surveyed fields varied from 26.66% to 47.50%. Total RNA was extracted from the 19 chilli leaf samples collected from fields and were pooled at equimolar concentration for virome profiling. From the rRNA-depleted pooled total RNA, mRNA and sRNA libraries were prepared and sequenced using Illumina NOVASEQ 6000 platform. Raw sequence data obtained was de novo assembled using three approaches; mRNAome with Trinity, sRNAome with Velvet and whole transcriptome (WT) with SPAdes assembly. Chilli virome, pairwise sequence identity and phylogenetic analyses revealed the presence of seven different viruses; chilli leaf curl virus (ChiLCV) along with its associated alpha and betasatellites, cucumber mosaic virus (CMV), groundnut bud necrosis orthotospovirus (GBNV), pepper cryptic virus-2 (PCV-2), pepper vein yellows virus (PeVYV), bell pepper alphaendornavirus (BPEV) and tobacco vein clearing virus (TVCV). From the virus associated contigs, complete/near-complete genomes for ChiLCV, CMV, PCV-2, PeVYV and BPEV and, partial genomes for GBNV and TVCV were reconstructed from the RNAome. Recombination breakpoint analyses revealed presence of recombination breakpoints in ChiLCV (coat protein and AC4 regions), CMV RNA2 (2a protein region) and P0, P3 and P5 protein regions of PeVYV. viruses identified in the current study are known to be originated from intra and interspecific recombination. Further, all the viruses detected in the pooled RNA sample were validated by PCR and loop mediated isothermal amplification (LAMP) using specific primers designed. Among the seven viruses identified in the study in chilli, PeVYV and BPEV are the first reports from India.

molecular biology↗

bioRxiv2022

Detection and molecular characterization of a phytoplasma associated with Cucumber (Cucumis sativus) and its first report from India

Cucumber (Cucumis sativus) plants exhibiting typical phyllody symptoms were collected from farmers field of Chintamani, Chickballapur districts of Karnataka (India). Disease incidence of phyllody was 2-3%. The etiology of the cucumber phyllody phytoplasma (CuPP) was confirmed by amplifying 16S rRNA gene from symptomatic plants using PCR followed by nested PCR using universal primers pairs P1/P7 and R16F2n/R16R2. After general detection the non-ribosomal SecY and rp (ribosomal protein) genes was amplified using specific primers. The PCR amplified products 16SrRNA (1.2 kb), SecY (1.6 kb) rp gene (1.2 kb) was cloned and sequenced. Sequence and phylogenetic analyses of 16S rRNA, secY and rp genes revealed that the detected phytoplasma is a member of the 16SrI group (Candidatus Phytoplasma asteris). Further on the basis of computer-simulated RFLP (= in silico RFLP) analysis of amplified F2n/R2 region of 16S rRNA gene indicates that, the detected phytoplasma was belongs to the subgroup X (16SrII-X). This is the first report on phytoplasma associated with phyllody disease of cucumber in India.

molecular biology↗

bioRxiv2020

In-vitro and Insilico screening platform for the identification of aldose reductase inhibitors for antidiabetic lead compounds from Abutilon Indicum (L.)

IntroductionType 2 Diabetes Mellitus (T2DM) is a long-term metabolic disorder that primarily characterized by impaired insulin resistance to become hyperglycemia. People suffering from T2DM have a higher risk of developing various diseases but, on top of that, some diabetic drugs are also suspected of increasing the risk in some cases. Aldose reductase is a key target enzyme to catalyze the reduction of glucose to sorbitol and does not readily diffuse across cell membranes and cause retinopathy and neuropathy. The aldolase reductase inhibitors prevent the conversion of glucose to sorbitol and may have the capacity of preventing and / or treating several diabetic complications. It will be expected to be twofold in the subsequent decade due to intensification in the senile population with the number of people affected, thus adding to the liability on medical providers in poor developed countries using herbal medicine to control the diabetes. In recent investigation, the antidiabetic property of phytochemicals extracted from leafs of Abutilon indicum (L.) is elucidated using animal models. Materials and MethodsIn the current study using aldose reductase enzyme assay inhibitor of Rat lens Aldose reductase were treated with A. indicum methanolic leaf extract at different concentrations (6.25, 12.5, 25, 50, 100, and 200g/mL). Copper sulphate was used as reference drug and docking studies to predict the screen the best aldose reductase inhibitor. Results and DiscussionThe crude extract exhibited cytotoxicity against rat lens aldose reductase (IC50 = 135.8 g/L vs ref 13.60 g/L) using In Vitro. The docking is performed with 11 compounds shows Ertugliflozin, 9H-Cycloisolongifolene, 8-oxo and 7-hydroxy cadalene showed a good binding interaction with aldose reductase. ConclusionWe are concluding that the invitro and in silico analysis helps researchers to utilize these compound for aldose reductase inhibitors and further can be used for clinical applications.

biochemistry↗

bioRxiv2020

A velocity plan with internal feedback control best explains modulation of saccade kinematics during eye-hand coordination.

Fast movements like saccadic eye movements that occur in the absence of sensory feedback are often thought to be under internal feedback control. In this framework, a desired input in the form of desired displacement signal is widely believed to be encoded in a spatial map of the superior colliculus (SC). This is then converted into a dynamic velocity signal that drives the oculomotor neurons. However, recent evidence has shown the presence of a dynamic signal within SC neurons, which correlates with saccade velocity. Hence, we used models based on optimal control theory to test whether saccadic execution could be achieved by a velocity based internal feedback controller. We compared the ability of a trajectory control model based on velocity to that of an endpoint control model based on final displacement to capture saccade behavior of modulation of peak saccade velocity by the hand movement, independent of the saccade amplitude. The trajectory control model tracking the desired velocity in optimal feedback control framework predicted this saccade velocity modulation better than an endpoint control model. These results suggest that the saccadic system has the flexibility to incorporate a velocity plan based internal feedback control that is imposed by task context. NEW & NOTEWORTHYWe show that the saccade generation system may use an explicit velocity tracking controller when demand arises. Modulation of peak saccade velocity due to modulation of the velocity of the accompanying hand movement was better captured using a velocity tracking stochastic optimal control model compared to an endpoint model of saccade control. This is the first evidence of trajectory planning and control for the saccadic system based on optimal control theory.

neuroscience↗

bioRxiv2020

Secondary structural characterization of the nucleic acids from circular dichroism spectra using extreme gradient boosting decision-tree algorithm

Nucleic acids exhibit a repertoire of conformational preference depending on the sequence and environment. Circular dichroism (CD) is an important and valuable tool for monitoring such secondary structural conformations of nucleic acids. Nonetheless, the CD spectral diversity associated with these structures poses a challenge in obtaining the quantitative information about the secondary structural content of a given CD spectrum. To this end, the competence of extreme gradient boosting decision-tree algorithm has been exploited here to predict the diverse secondary structures of nucleic acids. A curated library of 610 CD spectra corresponding to 16 different secondary structures of nucleic acids has been developed and used as a training dataset. For a test dataset of 242 CD spectra, the algorithm exhibited the prediction accuracy of 99%. For the sake of accessibility, the entire process is automated and implemented as a webserver, called CD-NuSS (CD to nucleic acids secondary structure) and is freely accessible at https://www.iith.ac.in/cdnuss/. The XGBoost algorithm presented here may also be extended to identify the hybrid nucleic acid topologies in future.

bioinformatics↗

bioRxiv2018

INDEX-db: The Indian Exome Reference database (Phase-I)

Deep sequencing based genetic mapping has greatly enhanced the ability to catalog variants with plausible disease association. The bigger challenge now is to ascertain pathological significance to the array of identified variants to specific disease conditions. Differential selection pressure may impact frequency of genetic variations, and thus the detection of association with disease conditions, across populations. To understand the genotype to phenotype correlations, it thus becomes important to first understand the genetic variation spectrum of a population by creating a reference map. In this study, we report the development of phase I of a new database of coding variations, from the Indian population, with an aim to establish a centralized database of integrated information. This could be useful for researchers involved in studying disease mechanism at the clinical, genetic and cellular level.\n\nDatabase URL: http://indexdb.ncbs.res.in

genomics↗