Biology subjects

Uppal, A.

Publications and source records attributed to Uppal, A..

6 recordsLinked to original sources

bioRxiv2026

ProtoPure: Literature Mining and Analysis of Protein Purification Protocols at Proteome Scale

Protein purification is a fundamental step for analyzing individual proteins and protein complexes and identifying interactions with other proteins, DNA, or RNA. A variety of protein purification strategies exist to address desired scale, throughput, and downstream applications. However, selecting an effective experimental procedure remains a largely empirical process that a quick literature review can help guide. Researchers typically survey on the order of a dozen publications for proteins with similar biochemical properties, assessing conditions on a case-by-case basis, leaving no systematic framework for comparison and decision-making at the scale of entire protein families. As protein engineering and design evolve, identifying effective purification conditions remains critical for obtaining sufficient quantities of properly folded and functional proteins. To address this gap, we developed ProtoPure, an LLM-based workflow and database that automates the extraction, standardization and analysis of protein purification conditions from peer-reviewed literature at scale. Given a user-defined UniProt table-enabling flexible selection of proteins by family, organism, or proteome. ProtoPure retrieves associated publications, classifies them based on the presence of purification protocols, and extracts a standardized set of 12 purification parameters (e.g., buffer composition, elution conditions). By transforming dispersed experimental descriptions into a structured resource, ProtoPure makes it possible to compare purification strategies across thousands of proteins. The resulting dataset revealed quantitative convergence toward a limited set of recombinant expression practices, with BL21(DE3)-based systems dominating protein production and recurrent combinations of expression host, inducer, growth medium, and plasmid occurring substantially more frequently than expected by chance. In contrast, downstream purification parameters exhibited greater diversity, revealing a workflow architecture that combines standardized expression infrastructure with more flexible biochemical components.

biophysics↗

bioRxiv2025

Gene model for the ortholog of Ilp4 in Drosophila eugracilis

Gene Model for Insulin-like peptide 4 (Ilp4) in the D. eugracilis (DeugGB2) assembly (GCA_000236325.2). The characterization of this ortholog was carried out as part of a larger, ongoing dataset designed to explore the evolution of the insulin/insulin-like growth factor signaling (IIS) pathway across the genus Drosophila, utilizing the Genomics Education Partnership gene annotation protocol within Course-based Undergraduate Research Experiences.

genomics↗

bioRxiv2022

Ecological relevance of laboratory studies with brown trout embryos: hatchling size, carotenoids, and sex predict juvenile performance in the wild

Laboratory studies on embryos of salmonids, such as the brown trout (Salmo trutta), have been extensively used to study environmental stress and how responses vary within and between natural populations. These studies are based on the implicit assumption that early life-history traits are relevant for stress tolerance in the wild. Here we test this assumption by combining two datasets from studies on the same 60 full-sib families. These families had been experimentally produced from wild breeders to determine, in separate samples, (i) stress tolerances of singly kept embryos in the laboratory and (ii) growth of juveniles during 6 months in the wild. We found that growth in the wild was well predicted by larval size of their full sibs in the laboratory, especially if these siblings had been experimentally exposed to a pathogen. Exposure to the pathogen had not caused elevated mortality among the embryos but induced early hatching. The strength of this stress-induced change of life history was a significant predictor of juvenile growth in the wild: the stronger the response in the laboratory, the slower the growth in the wild. We conclude that embryo performance in controlled environments can be useful predictors of juvenile performance in the wild.

ecology↗

bioRxiv2019

Prediction of the Effect of Naturally Occurring Missense Mutations on Cellular N-Acetyl-Glucosaminidase Enzymatic Activity

In 2015, the Critical Assessment of Genome Interpretation (CAGI) proposed a challenge to devise a computational method for predicting the phenotypic consequences of genetic variants of a lysosomal hydrolase enzyme known as -N-acetylglucosaminidase (NAGLU). In 2014, the Human Gene Mutation Database released that 153 NAGLU mutations associated with MPS IIIB and 90 of them are missense mutations. The ExAC dataset catalogued 189 missense mutations NAGLU based on exome sequence data from about 60,000 individual and 24 of them are known to be disease associated. Biotechnology company, BioMarin, has quantified the relative functionality of NAGLU for the remaining subset of 165 missense mutations. For this particular challenge, we examined the subset missense mutations within the ExAC dataset and predicted the probability of a given mutation being deleterious and relating this measure to the capacity of enzymatic activity. In doing so, we hoped to learn the degree to which changes in amino acid physicochemical properties are tolerable for NAGLU function.\n\nAmino acid substitution (AAS) prediction methods are mainly based on the sequence and structure information. Simple comparisons between different AAS methods are not only difficult, but also irrational because each method was tested on various datasets and based on varied versions of databases. Currently, several AAS prediction methods have been introduced. PolyPhen-2, an updated version of PolyPhen, is a tool used to predict possible impacts of an amino acid substitution on the structure and function. Users are required to provide protein or SNP identifiers, protein sequences, substitution positions, etc. A score is provided, ranging from 0 to 1, corresponding to the probability of a mutation resulting in no functionality for the enzyme\n\nOnce the probability scores were generated, the dataset was then run through multiple machine learning algorithms to generate an applicable model for predicting the enzymatic activity of MPS IIIB-related mutations. This prediction was generated using the PolyPhen-2 probability score and other information about the mutation (amino acid type, location, allele frequency, etc.) as input feature variables. This generated a predicted aggregate score for each mutation, which was then reported back to CAGI. The results of the analysis are significant enough to hold confidence that the scores are decent predictors of enzymatic activity given a mutation in the NAGLU amino acid sequence.

bioinformatics↗

bioRxiv2017

Toxicity of 2 pg ethynylestradiol in brown trout embryos (Salmo trutta)

Endocrine disrupting chemicals are a threat to natural fish populations in the aquatic environment. Their toxicity is usually discussed relative to concentrations in the water the fish are exposed to. In the case of the synthetic compound 17-alpha-ethynylestradiol (EE2), a common and persistent estrogen, concentrations around 1 ng/L have repeatedly been found to induce toxic effects in fish. Here, we used brown trout (Salmo trutta) from a natural population to study EE2 take up and how it affects early life-history. We collected adults during the spawning season, produced 730 families in vitro (to control for potential maternal and paternal effects on embryo stress tolerance), and singly raised 7,300 embryos (in a 2 mL static system) that were either exposed to one dose of EE2 at 1 ng/L (i.e., 2 pg/embryo) or sham-treated. We found that EE2 concentration did not significantly change over a period of 3 months in control containers without embryos. Embryos took up most of the 2 pg EE2 within about 4 weeks at 4.6{degrees}C. EE2 treated embryos experienced higher mortality, delayed hatching of the survivors, and had reduced size at hatching. Our findings suggest that the toxicity of EE2 is often underestimated when discussed at the level of concentrations in water only.

ecology↗

bioRxiv2017

Sex Differentiation In Grayling (Salmonidae) Goes Through An All-Male Stage And Is Delayed In Genetic Males Who Instead Grow Faster

Fish can be threatened by distorted sex ratios that arise during sex differentiation. It is therefore important to understand sex determination and differentiation, especially in river-dwelling fish that are often exposed to environmental factors that may interfere with sex differentiation. However, sex differentiation is not sufficiently understood in keystone taxa such as the Thymallinae, one of the three salmonid subfamilies. Here we study a wild grayling (Thymallus thymallus) population that suffers from distorted sex ratios. We found sex determination in the wild and in captivity to be genetic and linked to the sdY locus. We therefore studied sex-specific gene expression in embryos and early larvae that were bred and raised under different experimental conditions, and we studied gonadal morphology in five monthly samples taken after hatching. Significant sex-specific changes in gene expression (affecting about 25,000 genes) started around hatching. Gonads were still undifferentiated three weeks after hatching, but about half of the fish showed immature testes around seven weeks after hatching. Over the next few months, this phenotype was mostly replaced by the \"testis-to-ovary\" or \"ovaries\" phenotypes. The gonads of the remaining fish, i.e. approximately half of the fish in each sampling period, remained undifferentiated until six months after fertilization. Genetic sexing of the last two samples revealed that fish with undifferentiated gonads were all males, who, by that time, were on average larger than the genetic females (verified in 8-months old juveniles raised in another experiment). Only 12% of the genetic males showed testicular tissue six months after fertilization. We conclude that sex differentiation starts around hatching, goes through an all-male stage for both sexes (which represents a rare case of \"undifferentiated\" gonochoristic species that usually go through an all-female stage), and is delayed in males who, instead of developing their gonads, grow faster than females during these juvenile stages.\n\nAuthor contributionMRR and CW initiated the project. DM, OS, AU, LMC, LW, and CW sampled the adult fish, did the experimental in vitro fertilizations, and prepared the embryos for experimental rearing in the laboratory. All further manipulations on the embryos and the larvae were done by DM, OS, AU, LMC, and LW. The RNA-seq data were analyzed by OS, JR, and MRR, the histological analyses were done by DM, supervised by SK, and the molecular genetic sexing was performed by DM, OS, AU, and KBM. DM, OS, and CW performed the remaining statistical analyses and wrote the first version of the manuscript that was then critically revised by all other authors.

developmental biology↗