Biology subjects

Upadhyay, M.

Publications and source records attributed to Upadhyay, M..

9 recordsLinked to original sources

bioRxiv2025

Comparative Assessment of Chlorella vulgaris Cultivation in Synthetic, Oligotrophic and Industrial Wastewater for Sustainable Biomass Production

This study evaluates the physiological and biochemical responses of Chlorella vulgaris cultivated in synthetic BG11 medium, oligotrophic water, and industrial wastewater under controlled laboratory conditions with optimized pH and nitrogen-to-phosphorus (N:P) ratios. The highest cell density, growth rate, and pigment accumulation were observed in BG11 at neutral pH and higher N:P ratios. Moderately adjusted N:P ratios in industrial wastewater produced comparable biomass yields and improved photosynthetic efficiency, demonstrating its potential as a cost-effective medium for integrated wastewater treatment and algal biomass production. In contrast, oligotrophic water severely limited growth due to nutrient deficiency. FTIR analyses indicated that C. vulgaris maintains essential biochemical components under nutrient stress through adaptive metabolism. This comparative study provides new insights for designing scalable, sustainable microalgal cultivation systems that link biomass production with wastewater management within a circular bioeconomy framework.

systems biology↗

bioRxiv2025

DJ-1 deficiency and aging: dual drivers of retinal mitochondrial dysfunction.

We have previously extensively characterized the role of DJ-1 in oxidative stress regulation in the retina and RPE during aging. However, the DJ-1 protein also plays a role in regulating mitochondrias response to oxidative stress by translocating to the mitochondria where it helps clear generated reactive oxygen species (ROS). To study the effects of aging and oxidative stress in the retina, the DJ-1 KO mouse was analyzed. Freshly dissected ex vivo retinal punches were analyzed for real-time live cell metabolism. Total DNA and protein were isolated from RPE, and retina of 3- and 15-month-old DJ-1 WT and DJ-1 KO mice. The mitochondrial DNA (mtDNA) genome was divided into four discrete regions (RI-RIV), and lesions/10kb were quantified using long-extension PCR. mtDNA content was analyzed using RT-qPCR. Protein levels of OXPHOS complexes, POLG, OGG1, SOD2, and PGC1 were measured by western blotting. Seahorse analysis detected significantly decreased basal and maximal OCR in 3- and 15-month-old DJ-1 KO compared to age-matched DJ-1 WT. In the RPE, a significant decrease in the protein levels of the NDUFB8 subunit of CI, the SDHB subunit of CII, and MTCO1 of CIV in 15-month-old DJ-1 KO mice compared to 15-month-old DJ-1 WT, while the ATP5A subunit of CV was significantly decreased in 3-month-old DJ-1 KO mice compared to 3-month-old DJ-1 WT. In the retina, significantly decreased levels of NDUFB8 subunit of CI and MTCO1 of CIV were detected in the in 3-month-old DJ-1 KO mice compared to 3-month-old DJ-1 WT. We observed a significant increase in mtDNA gene content in 15-month-old DJ-1 KO RPE and retina compared to age-matched DJ-1 WT. The PGC1 levels significantly decreased in 3- and 15-month-old RPE lysates compared to their age group DJ-1 WT. However, in the retina, there was only a decrease in DJ-1 WT with aging. The POLG levels increased when 15-month-old DJ-1 KO lysates were compared to 15-month-old DJ-1 WT. The mtDNA lesions in the RPE detected a trend of increase in 15-month-old DJ-1 WT and DJ-1 KO RPE in all regions compared to 3-month-old mice. In the retina, a significant increase in mtDNA lesions/10kb accumulation in the 15-month-old DJ-1 WT RIV was detected compared to 3-month-old DJ-1 WT. The OGG1 levels significantly increased in 3-month-old retinal lysates compared to the 3-month-old DJ-1 WT. Our findings suggest that DJ-1 is critical for mitochondrial regulation and function in RPE and retina. The observed changes reflect mitochondrial dysfunction related to absence of DJ-1.

neuroscience↗

bioRxiv2024

Back to the horns: a reconstruction of the ancestral horn state through distinct types of recombination events.

BackgroundBreeding of the genetically polled animals is the desirable approach in modern cattle husbandry. At least four different genetic variants associated with polledness in cattle have been identified, suggesting genetic heterogeneity. These dominant variants have been identified on chromosome 1 between the regions of approx. 2.42 to 2.73 Mb (reference: ARS-UCD1.2), also called the POLLED locus. Among these variants, Friesian (PF, 80 kbp duplication) and Celtic (PC, 212 bp complex InDel) are the most observed in the majority of breeds in the production systems globally, such as in Holstein-Friesian (HF) and Fleckvieh (FV). While a putative causal association of PC with polledness is proven, the presence of large duplication in PF makes it difficult to prove the causality. ResultsIn this study, we conduct whole-genome sequencing (WGS) analysis of two trios exhibiting unexpected inheritance patterns related to PC and PF variants. In both instances, horned offspring were produced from mating pairs where one parent was homozygous for the polled variant, and the other was homozygous for the ancestral horned variant. By analyzing the WGS data generated using long-read sequence technology, we show that de-novo generation of the ancestral horned variant in both the offspring was the result of distinct recombination events. Specifically, in case of the HF trio, it was the result of non-allelic homologous recombination in the gametes of the sire (PF/PF), while in case of the FV trio, it was the result of allelic homologous recombination in the gametes of the dam (PC/PF). The findings from the HF trio support the hypothesis that the 80-kbp duplication is the genetic variant responsible for the polled phenotype of Friesian origin. ConclusionHere we show that different genomic arrangements in POLLED locus can lead to the emergence of de-novo ancestral horn phenotypes. These kinds of arrangements can make a reliable gene test less reliable and the derivation of the phenotype difficult to predict. Therefore, it is important for the large POLLED-locus that any deviation from the expected result is critically analyzed. Possibly some of these cases can further narrow down the sequence motif that is essential for polledness in cattle.

genomics↗

bioRxiv2024

Combined Linkage Disequilibrium and Linkage Analysis (cLDLA): implementation of a powerful approach to identify the genetic basis of complex traits in a bioinformatics workflow.

Identifying the relationship between the polymorphism segregating in a population and phenotypic differences of a trait observed between the individuals of a population is of major biological interest and represents the basis of forward genetics. Much of the traits of interest are influenced by several polymorphic genes and environmental conditions. Often the loci associated with such measurable traits are referred to as Quantitative trait loci. These loci are identified using several statistical approaches. One of them is combined linkage disequilibrium and linkage analysis (cLDLA). This approach, first proposed by Meuwissen and colleagues in 2002, is shown to be robust against population stratification/family structure and requires a relatively lower sample size compared to a genome-wide association study design. Previously, we have successfully used this approach in mapping several important traits in livestock such as identifying the genetic basis of polled condition in cattle and tail length in sheep. A cLDLA requires several complex computation processing and intermediary file conversion steps; for some of these steps no open-source tools are available. Therefore, running this analysis, manually, can prove challenging, tedious, or error-prone. We present, cldla, a bioinformatics workflow implemented in nextflow which takes the vcf file and phenotype file as inputs and implements all the downstream processing required for cLDLA. Additionally, it also has a separate workflow to estimate SNP-based heritability and features for interactive visualization of the results. The workflow is freely available at: https://github.com/Popgen48/cldla.

bioinformatics↗

bioRxiv2022

A role for BCL2L13 and autophagy in germline purifying selection of mtDNA

Mammalian mitochondrial DNA (mtDNA) is inherited uniparentally through the female germline without undergoing recombination. This poses a major problem as deleterious mtDNA mutations must be eliminated to avoid a mutational meltdown over generations. At least two mechanisms that can decrease the mutation load during maternal transmission are operational: a stochastic bottleneck for mtDNA transmission from mother to child, and a directed purifying selection against transmission of deleterious mtDNA mutations. However, the molecular mechanisms controlling these processes remain unknown. In this study, we systematically tested whether decreased autophagy contributes to purifying selection by crossing the C5024T mouse model harbouring a single pathogenic heteroplasmic mutation in the tRNAAla gene of the mtDNA with different autophagy-deficient mouse models, including knockouts of Parkin, Bcl2l13, Ulk1, and Ulk2. Our study reveals a robust effect of knockout of Bcl2l13 on the selection process, and weaker evidence for the effect of Ulk1 and potentially Ulk2, while no statistically significant impact is seen for knockout of Parkin. This points at distinctive roles of these players in germline purifying selection. Overall, our approach provides a framework for investigating the roles of other important factors involved in the enigmatic process of purifying selection and guides further investigations for the role of BCL2L13 in the elimination of non-synonymous mutations in protein-coding genes.

genetics↗

bioRxiv2022

Fine-mapping and identification of candidate causal genes for tail length in the Merinolandschaf breed

BackgroundDocking the tails of young lambs in long-tailed sheep breeds is a common practice worldwide. This practice is associated with pain, suffering and damage to the affected animals. Breeding for a shorter tail in long-tailed sheep breeds could offer one of the alternatives. This study aimed to analyze the natural tail length variation in the most common German Merino variety, and to identify possible causal alleles for the short tail phenotype segregating within a typical long-tailed breed. ResultsHaplotype-based mapping in 362 genotyped (Illumina OvineSNP50) and phenotyped Merinolandschaf lambs resulted in a genome-wide significant mapping at position 37,111,462 bp on sheep chromosome 11 and on chromosome 2 at position 94,538,115 bp (Oar_v4.0). Targeted capture sequencing of these regions in 48 selected sheep and comparative analyses of WGS data of various long and short-tailed sheep breeds as well as wild sheep subspecies identified a SNP and a SINE element as the promising candidates. The PCR genotyping of these candidates revealed complete linkage of both the candidate variants. The SINE element is located in the promotor region of HOXB13, while the SNP was located in the first exon of HOXB13 and predicted to result in a nonsynonymous mutation. ConclusionsOur approach successfully identified HOXB13 as candidate genes and the likely causal variants for tail length segregating within a typical long-tailed Merino breed. This would enable more precise breeding towards shorter tails, improve animal welfare by amplification of ancestral alleles and contribute to a better understanding of differential embryonic development.

genomics↗

bioRxiv2020

RNA degradation sculpts the maternal transcriptome during Drosophila oogenesis

In sexually reproducing animals, the oocyte contributes a large supply of RNAs that are essential to launch development upon fertilization. The mechanisms that regulate the composition of the maternal RNA contribution during oogenesis are unclear. Here, we show that a subset of RNAs expressed during the early stages of oogenesis is subjected to regulated degradation during oocyte specification. Failure to remove these RNAs results in oocyte dysfunction and death. We identify the RNA-degrading Super Killer complex and No-Go Decay factor Pelota as key regulators of oogenesis via targeted clearance of RNAs expressed in germline stem cells. These regulators target RNAs enriched for cytidine sequences bound by the protein Half pint. Thus, RNA degradation helps orchestrate a germ cell-to-maternal transition by sculpting the maternal RNA contribution to the zygote.Competing Interest StatementThe authors have declared no competing interest.View Full Text

developmental biology↗

bioRxiv2020

A program to automate the discovery of drugs for West Nile and Dengue virus -- programmatic screening of over a billion compounds on PubChem, generation of drug leads and automated In Silico modelling

Our work is composed of a python program for programmatic data mining of PubChem to collect data to implement a machine learning based AutoQSAR algorithm to generate drug leads for the flaviviruses - Dengue and West Nile. The drug leads generated by the program are feed as programmatic inputs to AutoDock Vina package for automated In Silico modelling of interaction between the compounds generated as drug leads by the program and the chosen Dengue and West Nile drug target methyltransferase, whose inhibition leads to the control of viral replication. The machine learning based AutoQSAR algorithm involves feature selection, QSAR modelling, validation and prediction. The drug leads generated each time the program is run is reflective of the constantly growing PubChem database is an important dynamic feature of the program which facilitates fast and dynamic drug lead generation against the West Nile and Dengue virus in way which is reflective of the constantly growing PubChem database. The program prints out the top drug leads after screening PubChem library which is over a billion compounds. The leads generated by the program are fed as programmatic inputs to an In Silico modelling package. The interaction of top drug lead compounds generated by the program and drug targets of West Nile and Dengue virus, was modelled in an automated way through programmatic commands. Thus our program ushers in a new age of automatic ease in the virtual drug screening and drug identification through programmatic data mining of chemical data libraries and drug lead generation through machine learning based AutoQSAR algorithm and an automated In Silico modelling run through the program to study the interaction between the drug lead compounds and the drug target protein of West Nile and Dengue virus

bioinformatics↗

bioRxiv2019

MSL3 coordinates a transcriptional and translational meiotic program in female Drosophila

Gamete formation from germline stem cells (GSCs) is essential for sexual reproduction. However, the regulation of GSC differentiation and meiotic entry are incompletely understood. Set2, which deposits H3K36me3 modifications, is required for differentiation of GSCs during Drosophila oogenesis. We discovered that the H3K36me3 reader Male-specific lethal 3 (MSL3) and the histone acetyltransferase complex Ada2a-containing (ATAC) cooperate with Set2 to regulate entry into meiosis in female Drosophila. MSL3 expression is restricted to the mitotic and early meiotic stages of the female germline, where it promotes transcription of genes encoding synaptonemal complex components and a germline enriched ribosomal protein S19 paralog, RpS19b. RpS19b upregulation is required for translation of Rbfox1, a known meiotic cell cycle entry factor. Thus, MSL3 is a master regulator of meiosis, coordinating the expression of factors required for recombination and GSC differentiation. We find that MSL3 is expressed during mouse spermatogenesis, suggesting a conserved function during meiosis.

developmental biology↗