Biology subjects

Nuzhdin, S. V.

Publications and source records attributed to Nuzhdin, S. V..

7 recordsLinked to original sources

bioRxiv2025

The reference genome for the northeastern Pacific bull kelp, Nereocystis luetkeana

Bull kelp, Nereocystis luetkeana, is a northeastern Pacific kelp with broad distribution from Alaska to central California. Its population declines have caused severe concerns in northern California, the Salish Sea in Washington, and recently in some populations in Oregon. Despite bull kelps accumulated ecological and physiological studies, an assembled and annotated genomic reference was still unavailable. Here, we report the complete and annotated genome of Nereocystis luetkeana, produced by the California Conservation Genomics Project (CCGP), which aims to reveal genomic diversity patterns across California by sequencing the complete genomes of approximately 150 carefully selected species. The genome was assembled into 1,562 scaffolds with 449.82 Mb, 80x of coverage and 22,952 gene models. BUSCO assembly showed a completeness score of 72% for the stramenopiles gene set. The mitochondria and chloroplast genome sequences have 37 Mb and 131 Mb, respectively. The orthology analysis between 10 Phaeophycean genomes showed 1,065 expanded and 286 unique orthogroups for this species. Pairwise comparisons showed 542 orthogroups present only in N. luetkeana and M. pyrifera, another large-body kelp. The enrichment analysis of these orthogroups showed important functions related to central metabolism and signaling due to ATPases enrichment in these two species. This genome assembly will provide an essential resource for the ecology, evolution, conservation, and breeding of bull kelp.

genomics↗

bioRxiv2025

Exploring the evolution of sex determination related genes through a cross-species genomics analysis

The molecular basis of sex determination (SD), while being extensively studied in model organisms, remains poorly understood in many animal groups. Bivalves, a diverse class of molluscs with a variety of reproductive modes, represent an ideal yet challenging clade for investigating SD and the evolution of sexual systems. However, the absence of a comprehensive framework has limited progress in this field, particularly regarding the study of sex-determination related genes (SRGs). In this study, we performed a genome-wide sequence evolutionary analysis of the Dmrt, Sox, and Fox gene families in more than 40 bivalve species. For the first time, we provide an extensive and phylogenetic-aware dataset of these SRGs, and we find support to the hypothesis that Dmrt-1L and Sox-H may act as primary sex-determining genes, by showing their high levels of sequence diversity within the bivalve genomic context. To validate our findings, we studied the same gene families in two well-characterized systems, mammals and Drosophila. In the former, we found that the male sex-determining gene Sry exhibits a pattern of amino acid sequence diversity similar to that of Dmrt-1L and Sox-H in bivalves, consistent with its role of master SD regulator. In contrast, no such pattern was observed among genes of the fruit fly SD cascade, which is controlled by a chromosomic mechanism. Overall, our findings highlight similarities in the sequence evolution of some mammal and bivalve SRGs, possibly driven by a comparable architecture of SD cascades. This work underscores once again the importance of employing a comparative approach when investigating understudied and non-model systems.

evolutionary biology↗

bioRxiv2023

Sex-biased expression is associated with chromatin state in D. melanogaster and D. simulans

We propose a new model for the association of chromatin state and sex-bias in expression. We hypothesize enrichment of open chromatin in the sex where we see expression bias (OS) and closed chromatin in the opposite sex (CO). In this study of D. melanogaster and D. simulans head tissue, sex-bias in expression is associated with H3K4me3 (open mark) in males for male-biased genes and in females for female-biased genes in both species. Sex-bias in expression is also largely conserved in direction and magnitude between the two species on the X and autosomes. In male-biased orthologs, the sex-bias ratio is more divergent between species if both species have H3K27me2me3 marks in females compared to when either or neither species has H3K27me2me3 in females. H3K27me2me3 marks in females are associated with male-bias in expression on the autosomes in both species, but on the X only in D. melanogaster. In female-biased orthologs the relationship between the species for the sex-bias ratio is similar regardless of the H3K27me2me3 marks in males. Female-biased orthologs are more similar in the ratio of sex-bias than male-biased orthologs and there is an excess of male-bias in expression in orthologs that gain/lose sex-bias. There is an excess of male-bias in sex-limited expression in both species suggesting excess male-bias is due to rapid evolution between the species. The X chromosome has an enrichment in male-limited H3K4me3 in both species and an enrichment of sex-bias in expression compared to the autosomes.

evolutionary biology↗

bioRxiv2021

Power Calculator for Detecting Allelic Imbalance Using Hierarchical Bayesian Model

Allelic imbalance (AI) is the differential expression of the two alleles in a diploid. AI can vary between tissues, treatments, and environments. Statistical methods for testing in this area exist, with impacts of explosive type I error in the presence of bias well understood. However, for study design, the more important and understudied problem is the type II error and power. As the biological questions for this type of study explode, and the costs of the technology plummet, what is more important: reads or replicates? How small of an interaction can be detected while keeping the type I error at bay? Here we present a simulation study that demonstrates that the proper model can control type I error below 5% for most scenarios. We find that a minimum of 2400, 480, and 240 allele specific reads divided equally among 12, 5, and 3 replicates is needed to detect a 10%, 20%, and 30%, respectively, deviation from allelic balance in a condition with power >80%. A minimum of 960 and 240 allele specific reads is needed to detect a 20% or 30% difference in AI between conditions with comparable power but these reads need to be divided amongst 8 replicates. Higher numbers of replicates increase power more than adding coverage without affecting type I error. We provide a Python package that enables simulation of AI scenarios and enables individuals to estimate type I error and power in detecting AI and differences in AI between conditions tailored to their own specific study needs.

bioinformatics↗

bioRxiv2021

Avalanches During Epithelial Tissue Growth; Uniform Growth and a Drosophila Eye Disc Model

In the physicists perspective, epithelial tissues constitute an exotic type of active matter with non-linear properties reminiscent of amorphous materials. In the context of a circular proliferating epithelium, modeled by the quasistatic vertex model, we identify novel discrete tissue scale rearrangements, i.e. cellular flow avalanches, which are a form of collective cell movement. During the avalanches, the cellular trajectories are radial in the periphery and form a vortex in the core. After the onset of these avalanches, the epithelial area grows discontinuously. The avalanches are found to be stochastic, and their strength is determined by the density of cells in the tissue. Overall, avalanches regularize the spatial tension distribution along tissue. Furthermore, the avalanche distribution is found to obey a power law, with an exponent consistent with sheer induced avalanches in amorphous materials. To decipher the role of avalanches in organ development, we simulate epithelial growth of the Drosophila eye disc during the third instar using a computational model, which includes both signaling and mechanistic signalling. During the third instar, the morphogenetic furrow (MF), a [~]10 cell wide wave of apical area constriction propagates through the epithelium, making it a system with interesting mechanical properties. These simulations are used to understand the details of the growth process, the effect of the MF on the growth dynamics on the tissue scale, and to make predictions. The avalanches are found to depend on the strength of the apical constriction of cells in the MF, with stronger apical constriction leading to less frequent and more pronounced avalanches. The results herein highlight the dependence of simulated tissue growth dynamics on relaxation timescales, and serve as a guide for in vitro experiments.

biophysics↗

bioRxiv2019

Tracking somatic drift reveals small effective population size of stem cells and high somatic mutation rate in asexual planaria

Planarian flatworms have emerged as highly promising models of body regeneration due to the many stem cells scattered through their bodies. Currently, there is no consensus as to the number of stem cells active in each cycle of regeneration or the equality of their relative contributions. We approached this problem with a population genetic model of somatic genetic drift. We modeled the fissiparous life cycle of asexual planarians as an asexual population of cells that goes through repeated events of splitting into two subpopulations followed by population growth to restore the original size. We sampled a pedigree of obligate asexual clones of Girardia cf. tigrina at multiple time points encompassing 14 generations. Effective population size of stem cells was inferred from the magnitude of temporal fluctuations in the frequency of somatic variants and under most of the examined scenarios was estimated to be in the range of a few hundreds. Average genomic nucleotide diversity was 0.00398. Assuming neutral evolution and mutation-drift equilibrium, the somatic mutation rate was estimated in the 10-5 - 10-7 range. Alternatively, we estimated Ne and somatic from temporal changes in nucleotide diversity{pi} without the assumption of equilibrium. This second method suggested even smaller Ne and larger . A key unknown parameter in our model on which estimates of Ne and depend is g, the ratio of cellular to organismal generations determined by tissue turnover rate. Small effective number of propagating stem cells might contribute to reducing reproductive conflicts in clonal organisms.

genetics↗

bioRxiv2018

Methane Reduction Potential of Two Pacific Coast Macroalgae During in-vitro Ruminant Fermentation.

With increasing interest in feed based methane mitigation strategies, fueled by local legal directives aimed at methane production from the agricultural sector in California, identifying local sources of biological feed additives will be critical in keeping the implementation of these strategies affordable. In a recent study, the red alga Asparagopsis taxiformis stood out as the most effective species of seaweed to reduce methane production from enteric fermentation. Due to the potential differences in effectiveness based on the location from where A. taxiformis is collected and the financial burden of collection and transport, we tested the potential of A. taxiformis, as well as the brown seaweed Zonaria farlowii collected in the nearshore waters off Santa Catalina Island, CA, USA, for their ability to mitigate methane production during in-vitro rumen fermentation. At a dose rate of 5% dry matter (DM), A. taxiformis reduced methane production by 74% (p [≤] 0.01) and Z. farlowii reduced methane production by 11% (p [≤] 0.04) after 48 hours and 24 hours of in-vitro rumen fermentation respectively. The methane reducing effect of A. taxiformis and Z. farlowii described here make these local macroalgae promising candidates for biotic methane mitigation strategies in the largest milk producing state in the US. To determine their real potential as methane mitigating feed supplements in the dairy industry, their effect in-vivo requires investigation.

systems biology↗