Publications by authors named "Nick V Grishin"

The evolutionary classification of protein domains (ECOD) classifies protein domains using a combination of sequence and structural data (http://prodata.swmed.edu/ecod).

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The Pfam protein families database is a comprehensive collection of protein domains and families used for genome annotation and protein structure and function analysis (https://www.ebi.ac.

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The Karner blue butterfly, () , is an endangered North American climate change-vulnerable species that has undergone substantial historical habitat loss and population decline. To better understand the species' genetic status and support Karner blue conservation, we sampled 116 individuals from 22 localities across the species' geographical range in Wisconsin (WI), Michigan (MI), Indiana (IN), and New York (NY). Using genomic analysis, we found that these samples were divided into three major geographic groups, NY, WI, and MI-IN, with populations in WI and MI-IN each further divided into three subgroups.

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Classification of protein domains based on homology and structural similarity serves as a fundamental tool to gain biological insights into protein function. Recent advancements in protein structure prediction, exemplified by AlphaFold, have revolutionized the availability of protein structural data. We focus on classifying about 9000 Pfam families into ECOD (Evolutionary Classification of Domains) by using predicted AlphaFold models and the DPAM (Domain Parser for AlphaFold Models) tool.

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Targeting Meis1 and Hoxb13 transcriptional activity could be a viable therapeutic strategy for heart regeneration. In this study, we performd an in silico screening to identify FDA-approved drugs that can inhibit Meis1 and Hoxb13 transcriptional activity based on the resolved crystal structure of Meis1 and Hoxb13 bound to DNA. Paromomycin (Paro) and neomycin (Neo) induced proliferation of neonatal rat ventricular myocytes in vitro and displayed dose-dependent inhibition of Meis1 and Hoxb13 transcriptional activity by luciferase assay and disruption of DNA binding by electromobility shift assay.

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Article Synopsis
  • - This paper evaluates predictions for the "HMBS" challenge from the 2021 Critical Assessment of Genome Interpretation, focusing on how well participants predicted the effects of missense variants in the HMBS gene on yeast growth.
  • - Despite using various algorithms, most predictors showed similar performance with correlation coefficients around 0.3, though some top predictors had a slightly better median correlation of ≥ 0.34 with experimental results.
  • - Predictors were moderately effective in distinguishing between harmful and harmless variants, but overall accuracy remained low compared to experimental controls, highlighting a need for significant improvements in prediction methods, especially for variants in specific regions like the insertion loop.
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Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity.

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Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs).

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Cancer cells exhibit distinct metabolic activities and nutritional dependencies compared to normal cells. Thus, characterization of nutrient demands by individual tumor types may identify specific vulnerabilities that can be manipulated to target the destruction of cancer cells. We find that MYC-driven liver tumors rely on augmented tryptophan (Trp) uptake, yet Trp utilization to generate metabolites in the kynurenine (Kyn) pathway is reduced.

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  • The Ornate Moth has been an important subject in chemical ecology research for many years, much like the Monarch butterfly, particularly due to its chemical defenses which help them thrive in various environments.
  • Recent advancements in genomic techniques have shifted its role to being a model species for diverse studies, including wing pattern development, detoxification, and evolutionary biology.
  • The study presents genomic findings indicating gene duplications tied to detoxification, enabling the moth to consume toxic plants, alongside analysis of over 100 museum specimens that may reveal genetic influences on wing pattern diversity in Lepidoptera.
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Protein structure prediction has now been deployed widely across several different large protein sets. Large-scale domain annotation of these predictions can aid in the development of biological insights. Using our Evolutionary Classification of Protein Domains (ECOD) from experimental structures as a basis for classification, we describe the detection and cataloging of domains from 48 whole proteomes deposited in the AlphaFold Database.

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The most critical step in the clinical diagnosis workflow is the pathological evaluation of each tumor sample. Deep learning is a powerful approach that is widely used to enhance diagnostic accuracy and streamline the diagnosis process. In our previous study using omics data, we identified 2 distinct subtypes of pure seminoma.

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Adolescent idiopathic scoliosis (AIS) is a common and progressive spinal deformity in children that exhibits striking sexual dimorphism, with girls at more than fivefold greater risk of severe disease compared to boys. Despite its medical impact, the molecular mechanisms that drive AIS are largely unknown. We previously defined a female-specific AIS genetic risk locus in an enhancer near the gene.

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The genus Fabricius, 1807 includes numerous taxa and forms with uncertain status and taxonomic position. Among such taxa are Alphéraky, 1897 and Staudinger, 1897, interpreted in the literature either as conspecific forms, as subspecies of different but morphologically somewhat similar species or as distinct species-level taxa. Based on mitochondrial and nuclear DNA markers, we reconstructed a phylogeographic pattern of the taxa in question.

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Increased nucleolar size and activity correlate with aberrant ribosome biogenesis and enhanced translation in cancer cells. One of the first and rate-limiting steps in translation is the interaction of the 40S small ribosome subunit with mRNAs. Here, we report the identification of the zinc finger protein 692 (ZNF692), a MYC-induced nucleolar scaffold that coordinates the final steps in the biogenesis of the small ribosome subunit.

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Control of eukaryotic cellular function is heavily reliant on the phosphorylation of proteins at specific amino acid residues, such as serine, threonine, tyrosine, and histidine. Protein kinases that are responsible for this process comprise one of the largest families of evolutionarily related proteins. Dysregulation of protein kinase signaling pathways is a frequent cause of a large variety of human diseases including cancer, autoimmune, neurodegenerative, and cardiovascular disorders.

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Genomic sequencing and analysis of holotypes from the MIZA collection (Maracay, Venezuela) and their comparison with other species and their type specimens advances our understanding of their taxonomy. Jemadia demarmelsi Orellana, [2010] is confirmed as a species-level taxon and its female is genetically verified. The following are species-level taxa, not subspecies: Amenis pedro O.

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Genomic sequencing (or morphology when indicated) and analysis of Hesperiidae that includes a number of primary type specimens reveals inconsistencies between the phylogenetic trees and the current classification that are resolved here. The following taxonomic changes are proposed. Oeonus Godman, 1900, stat.

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The recent progress in the prediction of protein structures marked a historical milestone. AlphaFold predicted 200 million protein models with an accuracy comparable to experimental methods. Protein structures are widely used to understand evolution and to identify potential drug targets for the treatment of various diseases, including cancer.

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Article Synopsis
  • - Adolescent idiopathic scoliosis (AIS) predominantly affects girls and is linked to genetic factors, with a specific genetic locus identified that increases the risk of severe cases compared to boys.
  • - A large genetic study of over 10,000 AIS patients revealed a significant genetic variant associated with collagen production that may contribute to spinal deformity.
  • - The study indicates that both genetic variations and estrogen signaling interfere with normal spinal development, suggesting a new model for understanding the mechanisms behind AIS.
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The mitochondrial DNA COI barcode segment sequenced from American Anthocharis specimens across their distribution ranges partitions them into four well-separated species groups and reveals different levels of differentiation within these groups. The lanceolata group experienced the deepest divergence. About 2.

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Here, we untangle an oversight surrounding the application of the name Papilio marcus Fabricius, 1787 (Hesperiidae: Hesperiinae), currently in Troyus Warren & Turland, 2012, which has eluded taxonomists for nearly two centuries. First, we note that P. marcus is a junior primary homonym of Papilio marcus Schaller, 1785, a species currently in Morpho Fabricius, 1807 (Nymphalidae: Satyrinae).

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Recent advances in protein structure prediction have generated accurate structures of previously uncharacterized human proteins. Identifying domains in these predicted structures and classifying them into an evolutionary hierarchy can reveal biological insights. Here, we describe the detection and classification of domains from the human proteome.

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Comparative analyses of genomic data reveal further insights into the phylogeny and taxonomic classification of butterflies presented here. As a result, 2 new subgenera and 2 new species of Hesperiidae are described: Grishin, (type species Watson, 1937) and Grishin, (type species Bell, 1931) of Scudder, 1872, () Grishin, (type locality in Mexico: Sonora), and Grishin, (type locality in Bolivia: Yungas, La Paz). The is designated for Plötz, 1882.

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