Biology subjects

Nowick, K.

Publications and source records attributed to Nowick, K..

7 recordsLinked to original sources

bioRxiv2025

A chromosome-level genome assembly and resequencing data reveal low DNA methylation and reduced diversity in the solitary bee pollinator Osmia cornuta

Bees provide essential pollination services that contribute to ecosystem stability, as well as the sustainability of economic crop yields. Due to concerns over global and local declines, improving our understanding of these ecologically and commercially important species is crucial for determining their capacity to respond and adapt to environmental challenges. The European orchard bee (Osmia cornuta) is a solitary bee of increasing agricultural importance due to its role in the pollination of fruit crops, yet lacks genomic resources. Using cost-effective Nanopore-only long-read sequencing, we report the first genome assembly for O. cornuta, spanning 647.56Mb across 727 contigs (N50=3.94Mb) at a high level of completeness (99.88% BUSCO complete). In line with the expected number of chromosomes in this species, 16 major scaffolds were assembled to chromosome-level. Also, we provisionally investigated the epigenomic architecture of O. cornuta, finding low numbers of CG dinucleotides that were either 5-methylated or 5-hydroxymethylated, providing additional evidence for the limited role methylation plays in gene regulation in Hymenopterans. To generate improved gene annotations, we combined transcriptomic- and orthology-based approaches, leading to the prediction of 12,144 genes and 25,964 proteins, showing exceptionally high BUSCO completeness (99.64%). Lastly, through whole-genome resequencing of a representative dataset, we provisionally find patterns of reduced nucleotide diversity and lower recombination rates within O. cornuta compared to other bee species. Collectively, our study provides a novel insight into the genome architecture of a key pollinator, providing an important resource to facilitate further genomic studies. Significance statementSolitary bees are crucial pollinators for crops and wild plants, but scientists have lacked the genetic blueprints needed to understand how these species might adapt to environmental threats like climate change and habitat loss. Using modern and cost-effective technologies, we generated the complete genome of the European orchard bee, an economically important fruit pollinator. This comprehensive genetic resource provides the foundation for future research on solitary bee biology and conservation, necessary to understand their adaptive potential in the face of environmental challenges. In line with this, we analysed this species genetic variation across populations in Germany using a small, representative dataset and found surprisingly low genetic diversity and limited evidence of gene recombination during reproduction, which are factors that could restrict its capacity to evolve in response to environmental challenges.

genomics↗

bioRxiv2025

RNA promotes synapsin coacervation and modulates local translation

Condensates at synapses organize synaptic vesicle (SV) clusters and are essential for efficient neurotransmitter release. While it is established that RNA granules traffic along the axons, the function of RNA at the presynapse remains unclear. Here, we uncover a direct structural role of coding RNAs in organizing presynaptic condensates by focusing on SV clusters, condensates between synapsin-1 and lipid vesicles, a defining feature of nerve terminals. Using in vitro reconstitution systems, we show that RNA drives synapsin-1 coacervation, with bias toward structured RNAs being more effective at promoting phase transitions. The importance of RNA was confirmed in living synapses, where acute disruption of native RNA induces a dispersion of SVs and synapsin. Conversely, ectopically expressed SV-like condensates have the ability to recruit the translational machinery. The microscopy-based in vitro translation assay demonstrates increased translation efficiency within synapsin-1/RNA condensates. Together, our work indicates a novel structural role of RNAs in modulating SV condensates.

cell biology↗

bioRxiv2025

Integrative Gene Co-expression Network Analysis Reveals Protein-Coding and lncRNA Genes Associated with Alzheimer's Disease Pathology

Alzheimers disease (AD) is a complex neurodegenerative disorder marked by widespread molecular changes, many of which remain poorly understood. While AD pathology progresses through specific brain regions, it is unclear whether these regions are affected similarly. Long non-coding RNAs (lncRNAs), emerging as key cellular regulators, remain largely uncharacterized in AD. Understanding how lncRNAs interact with protein-coding genes across brain regions could shed light on AD mechanisms and progression. To investigate this, we performed consensus weighted gene co-expression network analysis on 396 postmortem brain RNA-seq samples using a meta-analytic approach. Our analysis revealed substantial network rewiring in AD, particularly in the temporal cortex compared to the frontal cortex. The temporal cortex exhibited adaptive changes in gene interactions, while the frontal cortex showed a breakdown of healthy correlations--possibly reflecting regional differences in disease progression. We identified 46 protein-coding genes and 27 lncRNAs as key components in the AD network of the temporal cortex. Using known functions of protein-coding genes as reference points, we inferred potential functions for over 100 lncRNAs across both regions. These findings highlight novel lncRNA candidates potentially involved in AD and provide insights into their roles in both healthy and diseased brain states.

neuroscience↗

bioRxiv2024

Covariation between metabolic and radioactive dose rates in Chornobyl rodents

High metabolic rate may provide fitness benefits for individuals. But high metabolic rates incur energetic costs and the need to ingest more food, increasing the risks of ingesting harmful substances from the environment. How organisms respond to elevated levels of ionizing radiation is an important question in the light of increasing pollution from nuclear accidents and waste, as well as ever-increasing reliance on radiation in medical diagnostics and therapies. We investigated how limits to metabolic rate, and aerobic metabolic scope (ceiling of energetic activity above maintenance levels), of wild rodents inhabiting a gradient of radioactive contamination from the Chernobyl accident covary with the biological burden of radionuclides in their bodies. Our results demonstrate that high biological dose rate correlates with high self-maintenance and low aerobic capacity in adults. In contrast, in subadults high dose rate correlates with high aerobic capacity. Consequently, high dose rate correlates with low aerobic scope in adults, but with high aerobic scope in subadults. Despite the uncertainty of the causal mechanisms, whether the dose rate affects the metabolic rate, the reverse or the reciprocal feedback prevail, it can be hypothesized that metabolic down-regulation could contribute to protection against radioactive exposure. Yet, metabolic down-regulation might be constrained by developmental obligations. Understanding the physiological mechanisms affecting responses to radiation exposure is key for risk assessment of environmental contamination, radiotherapies, and space exploration, and may help to rectify discordant opinions concerning the effects of radiation on the ecology of organisms living in Chornobyl.

ecology↗

bioRxiv2024

Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness. Here, we leverage novel methods for estimating locus-specific IBD from low coverage whole genome resequencing data to demonstrate the feasibility and value of resolving fine-scaled gradients of relatedness in free-living animals. Using primarily 4-6x coverage data from a rhesus macaque (Macaca mulatta) population with available long-term pedigree data, we show that we can call the number and length of IBD segments across the genome with high accuracy even at 0.5x coverage. The resulting estimates demonstrate substantial variation in genetic relatedness within kin classes, leading to overlapping distributions between kin classes. They identify cryptic genetic relatives that are not represented in the pedigree and reveal elevated recombination rates in females relative to males, which allows us to discriminate maternal and paternal kin using genotype data alone. Our findings represent a breakthrough in the ability to understand the predictors and consequences of genetic relatedness in natural populations, contributing to our understanding of a fundamental component of population structure in the wild.

ecology↗

bioRxiv2023

Regulatory networks of KRAB zinc finger genes and transposable elements changed during human brain evolution and disease

Evidence indicates that transposable elements (TEs) can contribute to the evolution of new traits, with some TEs acting as deleterious elements while others are repurposed for beneficial roles in evolution. In mammals, some KRAB-ZNF proteins can serve as a key defense mechanism to repress TEs, offering genomic protection. Notably, the family of KRAB-ZNF genes evolves rapidly and exhibits diverse expression patterns in primate brains, where some TEs, including autonomous LINE-1 and non-autonomous Alu and SVA elements remain mobile. This prompts questions about their interactions in primate brains and potential roles in human brain evolution and disease. For a systematic comparative analysis of TE interactions with other genes, we developed the tool TEKRABber, and focused on strong and experimentally validated cases. Our bipartite network analysis revealed significantly more interactions between KRAB-ZNF genes and TEs in humans than in other primates, especially with recently evolved, i.e. Simiiformes specific, TEs. Notably, ZNF528, under positive selection in humans, shows numerous human-specific TE interactions. Most negative interactions in our network, indicative of repression by KRAB-ZNF proteins, entail Alu TEs, while links to other TEs are generally positive. In Alzheimers patients, a subnetwork involving 21 interactions with an Alu module appears diminished or lost. Our findings suggest that KRAB-ZNF and TE interactions vary across TE families, have increased throughout human evolution, and may influence susceptibility to Alzheimers disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/569574v8_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@28e11forg.highwire.dtl.DTLVardef@1d3e356org.highwire.dtl.DTLVardef@1f23994org.highwire.dtl.DTLVardef@1a256cf_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2023

mtDNA "Nomenclutter" and its Consequences on the Interpretation of Genetic Data

Population-based studies of human mitochondrial genetic diversity often require the classification of mitochondrial DNA (mtDNA) haplotypes into more than 5400 described haplogroups, and further grouping those into hierarchically higher haplogroups. Such secondary haplogroup groupings (e.g., "macro-haplogroups") vary across studies, as they depend on the sample quality, technical factors of haplogroup calling, the aims of the study, and the researchers understanding of the mtDNA haplogroup nomenclature. Retention of historical nomenclature coupled with a growing number of newly described mtDNA lineages results in increasingly complex and inconsistent nomenclature that does not reflect phylogeny well. This "clutter" leaves room for grouping errors and inconsistencies across scientific publications, especially when the haplogroup names are used as a proxy for secondary groupings, and represents a source for scientific misinterpretation. Here we explore the effects of phylogenetically insensitive secondary mtDNA haplogroup groupings, and the lack of standardized secondary haplogroup groupings on downstream analyses and interpretation of genetic data. We demonstrate that frequency-based analyses produce inconsistent results when different secondary mtDNA groupings are applied, and thus allow for vastly different interpretations of the same genetic data. The lack of guidelines and recommendations on how to choose appropriate secondary haplogroup groupings presents an issue for the interpretation of results, as well as their comparison and reproducibility across studies. To reduce biases originating from arbitrarily defined secondary nomenclature-based groupings, we suggest that future updates of mtDNA phylogenies aimed for the use in mtDNA haplogroup nomenclature should also provide well-defined and standardized sets of phylogenetically meaningful algorithm-based secondary haplogroup groupings such as "macro-haplogroups", "meso-haplogroups", and "micro-haplogroups". Ideally, each of the secondary haplogroup grouping levels should be informative about different human population history events. Those phylogenetically informative levels of haplogroup groupings can be easily defined using TreeCluster, and then implemented into haplogroup callers such as HaploGrep3. This would foster reproducibility across studies, provide a grouping standard for population-based studies, and reduce errors associated with haplogroup nomenclatures in future studies.

genetics↗