Biology subjects

Yampolsky, L. Y.

Publications and source records attributed to Yampolsky, L. Y..

15 recordsLinked to original sources

bioRxiv2026

Aging and reproductive "rejuvenation" at a single nuclei resolution

Aging is a multifaceted process that occurs on the background of and is significantly driven by transcriptional and cell type abundance changes. Aging-related transcriptional changes may include reduced transcription of maintenance, repair and DNA methylation genes, de-differentiation, or increased transcription of transposons. Unbiased detection of these changes and full understanding of their physiological effects requires single-cell resolution. We studied single-nuclei transcriptomes of a model microcrustacean Daphnia magna sampled from 3 age- and reproductive status groups: young, old reproductively senescent, and old, regaining reproductive function late in life. We detected 17 cell clusters, some identifiable as ovary or fat body-, midgut-, epithelium-, and neural tissue-related, some escaping unambiguous identification. At the same time, some well-characterized cell types were not detected, such as hemocytes or myocytes. We detect significant changes of cell type abundance with age and with reproductive "rejuvenation" in ovary- and gut-related clusters. We also detect several patterns of functional transcriptional differences between age classes with nearly all cell types, with changes between old reproductive and old non-reproductive Daphnia often reversing age-related changes, and often in good concordance with previous bulk RNAseq data.

developmental biology↗

bioRxiv2025

Circulating hemocytes continue to proliferate throughout lifespan in Daphnia

Daphnia is a classic model organism for the study of circulation and hemocyte biology. Despite the ease of observation and separation of hemocytes, it is not known whether the circulating hemocytes continue to be produced throughout Daphnia lifespan, and if yes, whether they are generated in any specific hemopoietic tissue or represent a reproducing population as known in some arthropods. We detected de novo DNA synthesis by means of EdU staining in a significant portion of circulating hemocytes in adult D. magna. This portion did not significantly vary among phases of molting/ovary cycle and showed only a slight decrease with age. We did not detect any matching newly synthesized DNA anywhere in any other tissues of adult daphnids, eliminating the hypothesis of the existence of a population of hemopoietic stem cells. Rather, it appears that circulating hemocytes are a reproducing population with mitoses continuing throughout life. Hemocytes showed average ploidy of 4, with a considerable variation around that value indicating that either some endomitoses were also present or a significant portion of hemocytes were sampled in G2. However, while there was no difference in total DNA content measured by Hoechst fluorescence between hemocytes that showed and did not show recent DNA synthesis, among EdU-positive hemocytes there was a positive correlation between Hoechst and EdU fluorescence, indicating that many cells were sampled during S-phase. It is not known whether the total number of hemocytes increases with age or the observed proliferation compensates for losses of hemocytes, as well as whether the EdU-positive hemocytes represent a separate mitotically active stem subpopulation of circulating hemocytes.

developmental biology↗

bioRxiv2025

Beta-Hydroxybutyrate but not NMN supplementation mimics caloric restriction reducing early mortality in Daphnia

NAD+ homeostasis is an important determinant of lifespan and may be a key mechanism of caloric restriction (CR) expansion of lifespan. Ketone bodies such as beta-hydroxybutyrate (BHB) that regulate NAD+ abundance and NAD+ precursors such nicotinamide mononucleotide (NMN), as are known to extend life in experimental animals and ameliorate age-related conditions in humans. We tested the hypothesis that chronic BHB and NMN exposure separately or in combination can extend lifespan in a model organism Daphnia, a freshwater zooplankton crustacean with the magnitude similar to that of the CR treatment. We also measured fecundity, lipofuscin accumulation, and lipid investments into offspring in Daphnia fed the full diet, full diet with BHB, NMN, and combined treatments, and fed the CR diet (25% of the full diet). We also conducted an RNAseq experiment comparing the two diets and the two exposure treatments. We show that BHB exposure, but not NMN exposure reduces early life mortality in Daphnia fed the full diet to levels similar to those observed under CR without compromising fecundity. We also observed that in a combined exposure cohort, NMN nearly eliminates the beneficial effect of BHB. None of the treatments affected lipofuscin accumulation, but the NMN and the combined treatment mimicked the effect of CR on neonate size in older females. We show that BHB-treated Daphnia change expression of a variety of genes, including genes with known longevity extending effects, but differential expression of few genes is consistent with the effects of CR and their functionality is not clear.

biochemistry↗

bioRxiv2025

Ketone body b-Hydroxybutyrate does not extend lifespan, but upregulates fecundity in food-limited Daphnia, with a transgenerational effect

Ketone bodies accumulate on ketogenic diets and are known to have numerous beneficial health and longevity effects. Here we investigate the effects of exposure to environmental b-hydroxybutyrate (BHB), a ketone body, on longevity and fecundity of a model organism Daphnia magna, a plankton crustacean, maintained at limited food availability. We report that exposure to continuous or intermittent lifetime exposure to 2.5 - 10 mM of BHB reduces Daphnia lifespan, while intermittent exposure administered for 20-day periods has little effect on post-exposure survival, regardless of the age at exposure onset. On the other hand, various BHB exposure regimes significantly increased fecundity, including fecundity up to 100 days past a 20-day exposure. We further demonstrate that even relatively brief early life maternal exposure to BHB can increase daughters fecundity, although this transgenerational effect is genotype-specific. We argue that this effect must have a signaling nature rather than simply manifestation of additional source of energy provided by BHB and discuss potential significance of genetic variation in transmission of such signals.

ecology↗

bioRxiv2024

Genome-wide DNA Methylation Patterns in Daphnia magna Reveal Targeting to 5' Exons

Studying DNA methylation in Daphnia magna, a model organism in ecological and evolutionary research, offers valuable insights into pharmaceutical toxicity and behavioral ethology. In this study, we characterized DNA methyltransferases and mapped DNA methylation across the D. magna genome using whole-genome bisulfite sequencing. Our analysis revealed a highly expressed, nonfunctional de novo methyltransferase (DNMT3.1) alongside lowly expressed functional de novo methyltransferase DNMT3.2 and maintenance methyltransferase DNMT1. D. magna displays overall low DNA methylation, targeting primarily CpG dinucleotides. Methylation is sparse at promoters but elevated in the first exons downstream of transcription start sites, with these exons showing hypermethylation relative to adjacent introns. In contrast to prior studies, we observed minimal age-related changes in DNA methylation patterns that were not sufficiently robust to build an accurate epigenetic clock. These findings expand our understanding of the epigenetic landscape in D. magna.

systems biology↗

bioRxiv2024

Single Cell Transcriptome Defines Cell Type Repertoire of Adult Daphnia magna.

Detailed knowledge of transcriptional responses to environmental and developmental cues is impossible without single cell (SC) resolution data. We performed two SC RNAseq experiments surveying transcriptional profiles of females and males of D. magna, a freshwater plankton crustacean which is both a classic and emerging new model for eco-physiology, toxicology, and evolutionary genomics. We were able to identify over 30 distinct cell types about half of which could be functionally annotated. First, we identified ovaries- and testis-related cell types by focusing on female- and male-specific clusters. Second, we compared markers between SC clusters and bulk RNAseq data on transcriptional profiles of early embryos, circulating hemocytes, midgut, heads (containing brain, eyes, muscles and hepatic caeca), antennae II, and carapace. Finally, we compared transcriptional profiles of Daphnia cell clusters with orthologous markers of 250+ cell types annotated in Drosophila cell atlas. This allowed us to recognize striated muscle cells, gut enterocytes, cuticular cells, as well as 5 different neuron types, including photoreceptors and 3 ovaries-related clusters, one of which tentatively identified as the germ line cells. One well-defined cluster showed a significant enrichment in markers of both hemocytes and fat body of Drosophila, but not with bulk RNAseq data from circulating hemocytes, allowing us to hypothesize the existence of non-circulating, fat body-associated population of hemocytes in Daphnia. On the other hand, the circulating hemocytes express numerous cuticular proteins suggesting their role, in addition to macrophagy, in wound repair. At the same time numerous cell types remain unidentified, including those that map to FCA groups ambiguously or are characterized by Daphnia-specific markers with no clear orthology in the fruitfly. Likewise, many known or presumed cell types or tissues in Daphnia have not been identified to SC clusters. A detailed in-situ hybridization study would be necessary to match not yet annotated SC clusters to functional cell groups. HighlightsO_LIFirst single-cell transcriptomic atlas for Daphnia magna, identifies > 30 distinct cell types. C_LIO_LINovel cell type representing circulating hemocytes may play a role in cuticle regeneration. C_LIO_LIEvidence for non-circulating hemocyte-like cells associated with the fat body in Daphnia. C_LIO_LICuticle/epithelial cells expressing photoreceptors, suggesting light-sensing capabilities. C_LIO_LISubfunctionalization of divergent paralogs across cell types for ecological versatility. C_LI

cell biology↗

bioRxiv2024

Post-senescence reproductive rebound in Daphnia does not accelerate mortality and is associated with reversal of age-related transcriptional changes in lipid and protein metabolism

A long-lived species of zooplankton microcrustaceans, Daphnia magna, sometimes exhibits late-life rebound of reproduction, briefly reversing reproductive senescence. Such events are often interpreted as terminal investment in anticipation of imminent mortality. We demonstrate that such post-senescence reproductive events (PSREs) neither cause not anticipate increased mortality. We analyze an RNAseq experiment comparing young, old reproductively senescent, and old PSRE Daphnia females. We first show that overall age-related transcriptional changes are dominated by the increase transcription of guanidine monophosphate synthases and guanylate cyclases, as well as two groups of presumed transposon-encoded proteins and by a drop in transcription of protein synthesis-related genes. We then focus on gene families and functional groups in which full or partial reversal of age-related transcriptional changes occur. This analysis reveals reversal, in the PSRE individuals, of age-related up-regulation of apolipoproteins D, lysosomal lipases, and peptidases and of age-related down-regulation of E3 ubiquitin kinases, V-type proton ATPases, and numerous proteins related to mitochondrial and muscle functions. While it is not certain which of these changes enable reproductive rejuvenation, and which are by-products of processes that lead to it, we present some evidence that post-senescence reproductive events are associated with the reversal of age-related protein and lipid aggregates removal, apoptosis, and with restoration of mitochondrial integrity. Significance statementAdvances in aging studies revealed the need to extend the old-age health and functionality data from the Drosophila-C.elegans-yeast triad of model organisms to include those that combine the advantages of non-vertebrate models with stronger similarities to mammalian aging. This paper presents a previously unreported phenomenon: reproductive "rejuvenation" in Daphnia - a classic and a re-emerging choice model for longevity studies. These postsenescence reproductive episodes result in fecundity similar to that of young individuals and are accompanied by transcriptional shifts, often reverting age-related changes to youthful levels. Transcripts that show such reversal point to restoration of aggregate removal and of mitochondrial function. We believe that this finding opens a novel window of research towards mechanistic understanding of healthy aging.

ecology↗

bioRxiv2024

Short lifespan is one's fate, long lifespan is one's achievement: lessons from Daphnia

Studies of longevity and senescence rely on baseline life expectancy of reference genotypes measured in standardized conditions such as food level and group size. Variation in baseline lifespan data across labs and protocols and among genotypes can make longevity intervention studies difficult to compare, particularly when GxE interactions exist. Furthermore, extending the lifespan of a short-lived genotype or of any genotype under suboptimal conditions may be of a lesser theoretical and translational value than extending the maximal possible lifespan. Daphnia is rapidly becoming a model organism of choice for longevity research complementing data obtained on traditional models. In this study we report baseline longevity of several genotypes (parthenogenetic clones) of a long-lived species D. magna under a variety of laboratory protocols, aiming to document the highest possible lifespan, factors reducing it, and physiological parameters that change with age and correlate with longevity. Combining data from 25 different experiments across two labs we report strong differences among clones of different geographic origin, moderate effects of group size and medium composition on longevity, and strong GxE with respect to food level. Specifically, short-lived clones that tend to originate from small intermittent habitats show little or no caloric restriction (CR) longevity extension, while long-lived ones expand their lifespan even further when maintained at 25% of the ad libitum food. We find no evidence of any trade-offs between longevity and fecundity across clones or correlations with age-specific feeding rate. We find that in the short-lived, CR non-responsive clones show little correlation between longevity and two measures of lipid peroxidation (LPO: lipid hydroperoxides and MDA abundance). In contrast, the long-lived, CR-responsive clones show a positive longevity correlation with lipid hydroperoxide abundance at any age, and a negative correlation with MDA concentration measured at about median lifespan. This indicates differences among genotypes in longevity-related accumulation of LPO targets, efficiency of detoxification of LPO products, and/or their effects on longevity. Our observations support the hypothesis that a long lifespan can be affected by food availability and levels of oxidative damage, while genetically determined short lifespan remains short regardless. We suggest a set of condition and genotypes to be used as a reference for longevity studies in Daphnia.

ecology↗

bioRxiv2023

Differential Expression of Gluconeogenesis-Related Transcripts in a Freshwater Zooplankton Model Organism Suggests a Role of the Cori Cycle in Hypoxia Tolerance

O_LIGluconeogenesis (GNG) is the process of regenerating glucose and NAD+ that allows continuing ATP synthesis by glycolysis during fasting or in hypoxia. Recent data from C. elegans and crustaceans challenged with hypoxia show differential and tissue-specific expression of GNG-specific genes. C_LIO_LIHere we report differential expression of several GNG-specific genes in the head and body of a model organism, Daphnia magna, a planktonic crustacean, in normoxic and acute hypoxic conditions. We predict that GNG-specific transcripts will be enriched in the body, where most of the fat tissue is located, rather than in the head, where the tissues critical for survival in hypoxia, the central nervous system and locomotory muscles, are located. We measured the relative expression of GNG-specific transcripts in each body part by qRT-PCR and normalized them by either the expression of a reference gene or the rate-limiting glycolysis enzyme pyruvate kinase (PK). C_LIO_LIOur data show that of the three GNG-specific transcripts tested, pyruvate carboxylase (PC) showed no differential expression in either the head or body. Phosphoenolpyruvate carboxykinase (PEPCK-C), on the other hand, is upregulated in hypoxia in both body parts. Fructose-1,6-bisphosphatase (FBP) is upregulated in the body relative to the head and upregulated in hypoxia relative to normoxia, with a stronger body effect in hypoxia when normalized by PK expression. C_LIO_LIThese results support our hypothesis that Daphnia can survive hypoxic conditions by implementing the Cori cycle, where body tissues supply glucose and NAD+ to the brain and muscles, enabling them to continuously generate ATP by glycolysis. C_LI

biochemistry↗

bioRxiv2022

Prior selection affects phenotypic and transcriptional response to hypoxia

Hypoxia has profound and diverse effects on aerobic organisms, disrupting oxidative phosphorylation and activating several protective pathways. Predictions have been made that exposure to mild intermittent hypoxia may be protective against more severe exposure and may extend lifespan. Both effects are likely to depend on prior selection on phenotypic and transcriptional plasticity in response to hypoxia, and may therefore show signs of local adaptation. Here we report the lifespan effects of chronic, mild, intermittent hypoxia (CMIH) and short-term survival in acute severe hypoxia (ASH) in four clones of Daphnia magna originating from either permanent or intermittent habitats, the latter regularly drying up with frequent hypoxic conditions. We show that CMIH extended the lifespan in the two clones originating from intermittent habitats but had the opposite effect in the two clones from permanent habitats, which also showed lower tolerance to ASH. Exposure to CMIH did not protect against ASH; to the contrary, Daphnia from the CMIH treatment had lower ASH tolerance than normoxic controls. Few transcripts changed their abundance in response to the CMIH treatment in any of the clones. After 12 hours of ASH treatment, the transcriptional response was more pronounced, with numerous protein-coding genes with functionality in mitochondrial and respiratory metabolism, oxygen transport, and gluconeogenesis showing up-regulation. While clones from intermittent habitats showed somewhat stronger differential expression in response to ASH than those from permanent habitats, there were no significant hypoxia-by-habitat of origin or CMIH-by-ASH interactions. GO enrichment analysis revealed a possible hypoxia tolerance role by accelerating the molting cycle and regulating neuron survival through up-regulation of cuticular proteins and neurotrophins, respectively.

ecology↗

bioRxiv2021

Inverse Lansing effect: maternal age and provisioning affecting daughters' longevity and male offspring production

Maternal age effects on life history of offspring has been demonstrated in a variety of organisms, more often than not offspring of older mothers having lower life expectancy (Lansing effect). However, there is no consensus on how general this phenomenon is and what are the genetic and epigenetic mechanisms behind it. We tested the predictions of Lansing effect in several Daphnia magna clones in and observed a significant genotype-by-maternal age interaction, indicating clone-specific magnitude and direction of the effect of maternal age on daughters longevity. We then repeated this experiment with more detailed life-history and offspring provisioning data focusing on 2 clones with contrasting life-histories. One of these clones demonstrating the inverse Lansing effect, with daughters of older mothers living longer than those of young mothers. Individuals from a single-generation maternal age reversal treatment showed intermediate lifespan. We also report genotype-specific, ambidirectional, and largely fecundity-independent effects of maternal age on daughters propensity to produce male offspring, with daughters of older mothers showing higher male production than daughters of younger mothers in the least male-producing clone and vise versa. We tested whether both effects can be explained by either lipid provisioning of embryos by mothers of different age, or by properties of mitochondria transmitted by mothers of different age to their offspring, using rhodamine-123 assay of mitochondrial membrane potential as a measure of mitochondria quality. We show that once lipid provisioning is accounted for, the effects of maternal age on lifespan and male production disappear and that the effect of lipid provisioning itself is clone-dependent, confirming that maternal provisioning sets daughters life history parameters. In the clone showing the inverse Lansing effect we demonstrated that, contrary to the predictions, neonates produced by older mothers were characterized by higher mitochondrial membrane potential in neural tissues than their counterparts born to younger mothers. We conclude that, in at least some genotypes, a reverse Lansing effect is possible, and hypothesize that it may be a result of lower lipid provisioning creating calorically restricted environment during embryonic development.

developmental biology↗

bioRxiv2021

Lack of Age-related Respiratory Changes in Daphnia

Aging is a multifaceted process of accumulation of damages and waste in cells and tissues; age-related changes in mitochondria and in respiratory metabolism have been in the focus of aging research for decades. Here we investigated age-related changes in respiration rates, lactate/pyruvate ratio, a commonly used proxy for NAD+/NADH balance, and mitochondrial membrane potential in 4 genotypes of an emerging model organism for aging research, a cyclic parthenogen Daphnia magna. We show that total body weight-adjusted respiration rate decreases with age, although this decrease is small in magnitude and not observed in anaesthetized animals, thus likely to be accounted for by decrease in locomotion and feeding activity. Lactate/pyruvate ratio and mitochondrial membrane potential ({Psi}mt) showed no age-related changes, with a possible exception of {Psi}mt measured in the optical lobe and in epipodites (excretory organs) in which {Psi}mt showed a maximum at middle age. We conclude that actuarial senescence in Daphnia is not caused by a decline in respiratory metabolism and discuss possible mechanisms of maintaining mitochondrial healthspan throughout the lifespan.

physiology↗

bioRxiv2021

"Smart Tanks": An Intelligent High-Throughput Intervention Testing Platform in Daphnia

We present a novel platform for testing the effect of interventions on life- and health-span of a short-lived semi transparent freshwater organism, sensitive to drugs with complex behavior and physiology - the planktonic crustacean Daphnia magna. Within this platform, dozens of complex behavioural features of both routine motion and response to stimuli are continuously accurately quantified for large homogeneous cohorts via an automated phenotyping pipeline. We build predictive machine learning models calibrated using chronological age and extrapolate onto phenotypic age. We further apply the model to estimate the phenotypic age under pharmacological perturbation. Our platform provides a scalable framework for drug screening and characterization in both life-long and instant assays as illustrated using long term dose response profile of metformin and short term assay of such well-studied substances as caffeine and alcohol.

bioengineering↗

bioRxiv2019

Quantitative proteomics reveals remodeling of protein repertoire across life phases of Daphnia pulex

The microcrustacean Daphnia is becoming an organism of choice for genomic and proteomic studies of the effects of environmental stressors. However, the changes in protein expression across the life cycle have not been fully characterized. We analyzed the proteomes of adult females, juveniles, asexually produced embryos, and the ephippia - resting stages containing two sexually produced diapausing freezing- and desiccation-resistant embryos. Overall, we were significantly more likely to detect proteins with known molecular functions than proteins with no detectable orthology. Similarly we could detect those with stronger gene model support, as judged by mutual best BLAST hits between two independent genome assemblies than those without such support. This suggests that we could apply our proteomics pipeline to verify hypothesized proteins, even given less-than-perfect reference gene models. In particular, we observed up-regulation of vitellogenins and down-regulation of actins and myosins in embryos of both types, as compared to juveniles and adults and overrepresentation of cell-cycle related proteins in the developing embryos, as compared to both diapausing embryos and adults. We found upregulation of small heat-shock proteins and redox peroxidases, as well as overrepresentation of stress-response proteins in the ephippium relative to the asexually produced non-diapausing embryos. The ephippium also showed up-regulation of three trehalose-synthesis proteins and down-regulation of a trehalose hydrolase, consistent with the role of trehalose in protection against freezing and desiccation.\n\nStatement of significance of the studyFreshwater plankton crustacean Daphnia is rapidly becoming a model organism of choice for ecological and developmental genomics. While there have been several advances towards establishing the protocols and reference datasets for proteomics, a detailed dataset covering several main steps of asexual and sexual phases of Daphnia life cycle is not yet available. Moreover, different versions of D. pulex genome differ in the number of protein-coding genes identified; it is unclear whether these differences are caused by differences between sequenced genotypes or between gene model methodology used. In this study we report LC-MS2/MS3 proteomes of whole body adult females, juvenile females, asexually produces embryos and diapausing eggs capable of surviving freezing and desiccation.

systems biology↗

bioRxiv2018

Rearing temperature and fatty acid supplementation jointly affect membrane fluidity and heat tolerance in Daphnia

The homeoviscous adaptation hypothesis states that the relative abundance of polyunsaturated fatty acids (PUFA) decreases in the membrane phospholipids of ectothermic organisms at higher temperatures to maintain vital membrane properties. We hypothesized that the well-documented reduced heat tolerance of cold-reared Daphnia is due to the accumulation of PUFA in their body tissues and that heat-reared Daphnia contain reduced amounts of PUFA even when receiving a high dietary supply of PUFA. In Daphnia reared at 15{degrees}C, supplementation of a PUFA-deficient food with the long-chain PUFA eicosapentaenoic acid (EPA) resulted in an increase in the relative abundance of EPA in body tissues and a decrease in heat tolerance. However, the same was observed in Daphnia reared at 25{degrees}C, indicating that the ability of heat-acclimated Daphnia to adjust EPA body concentrations is limited when exposed to high dietary EPA concentrations. Daphnia reared at 25{degrees}C showed the lowest change in membrane fluidity, measured as fluorescence polarization. For Daphnia reared at three different temperatures, thermal tolerance (time to immobility at a lethally high temperature) and increasing dietary EPA concentrations correlated with fluorescence polarization and the degree of fatty acid unsaturation. Overall, our results support the homeoviscous adaptation hypothesis by showing that cold-reared Daphnia, which accumulate PUFA within their tissues, are more susceptible to heat than hot-reared Daphnia, which contain less PUFA.

ecology↗