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#Genomics

10 posts10 participants0 posts today
Public
flypapers

📰 "Genome-wide analysis reveals genes mediating resistance to paraquat neurodegeneration in Drosophila"
biorxiv.org/content/10.1101/20
#Drosophila #Genomics

bioRxiv · Genome-wide analysis reveals genes mediating resistance to paraquat neurodegeneration in DrosophilaParkinson's disease (PD) is thought to develop through a complex interplay of genetic and environmental factors. Epidemiological studies have linked exposure to certain pesticides such as paraquat with elevated PD risk, although how a person's genetic makeup influences disease risk upon exposure remains unknown. Here, we used a genome-wide approach to uncover genes that play a role in resistance to paraquat-induced dopaminergic neurodegeneration in Drosophila. We developed a paraquat exposure model displaying delayed-onset dopaminergic (DA) neurodegeneration to recapitulate this aspect of human disease. We reveal that genetic background is a strong determinant of paraquat-induced DA neurodegeneration susceptibility across a series of nearly 200 fly strains called the Drosophila genetic reference panel (DGRP). Through unbiased genome-wide analysis and follow-up validation, we identify two candidate paraquat resistance genes, luna and CG32264. In gene-level studies, decreased expression of luna or CG32264 is associated with paraquat-induced DA neuron loss while overexpression of either gene prevents neurodegeneration in vivo. The mammalian ortholog of CG32264 is Phactr2, which has previously been linked to human idiopathic PD risk in several populations. Hence, our results reveal genes regulating paraquat-induced DA neuron loss that intersect with human PD risk variants, supporting the potential relevance of our findings to PD and underscoring a role for gene-environment interactions in pesticide-related DA neurodegeneration. ### Competing Interest Statement The authors have declared no competing interest.
Public
flypapers

📰 "The Evolutionary Flexibility of the Drosophila Circadian Clock: Network Constraints or Adaptive Freedom?"
biorxiv.org/content/10.1101/20
#Evolution
#Circadian
#Drosophila #Genomics

bioRxiv · The Evolutionary Flexibility of the Drosophila Circadian Clock: Network Constraints or Adaptive Freedom?The study of network evolution is critical to understanding how complex biological processes arise and adapt over time. Protein networks, composed of interacting components, can exhibit varying degrees of conservation and flexibility, enabling organ- isms to fine-tune their responses to environmental changes. Using the circadian clock system in Drosophila as a case study, we explore how such networks evolve. We leverage the recently published 101 Drosophilidae genome project to analyze the evolution and co-evolution of 11 core clock proteins across 65 species spanning about 60 million years of evolution. A sliding window analysis of coding regions reveals substantial heterogeneity in nucleotide divergence, with Clk and per exhibiting high divergence, whereas Pdp1 and sgg show virtually no evolutionary change. Additionally, we assessed interdependent amino acid evolution across different proteins, identifying 67 co-evolving site pairs, primarily between CLK-PER, CLK-CWO, and SGG-PER. Using codon-based models of evolution we found four genes ( cwo , jet , per , and sgg ) showing evidence of positive selection. Since several clock proteins are pleiotropic, we tested whether their multifunctionality influences their evolutionary constraints. Using alternative approaches to assess pleiotropy, we found no significant correlation between pleiotropy and the non-synonymous substitution rate (Ka) in 440 Drosophila proteins, including circadian clock ones. Overall, our findings suggest that the circadian clock network does not impose strong constraints on the evolution of its components. This flexibility may facilitate species-specific adaptation of the clock and allow the pleiotropic functions of clock proteins. ### Competing Interest Statement The authors have declared no competing interest.
Public
GHGA

GHGA Retreat – Day 1 at Kloster Schöntal kicked off with exciting discussions on a wide range of topics! From data portals to international connectivity (#FEGA, #ELIXIR, #EOSC), legal challenges, patient communication, and training plans, GHGA 2 is taking shape across all fronts. Perspectives from data producers and data hubs, along with workflow use cases, rounded off a fantastic first session. #GHGA #GHGAretreat #Genomics #OpenScience #Collaboration

Photograph of a room full of people at the GHGA retreat, viewed from the floor. People are sitting at tables and looking at a screen, following a presentation. No specific individuals are recognizable.
Public *
Radical Anthropology

More on #genomics, this is obviously crazy since the #world's #genetic #diversity is contained within #Africa. Yet African DNA is underrepresented! Oh dear, it should not be only African scientists noticing this.

'African scientists say the world is missing vital medical insights by ignoring the continent’s vast genetic diversity. Less than 2 percent of human genome sequencing worldwide comes from African populations.'

rfi.fr/en/africa/20250404-scie

Public
flypapers

📰 "HyDrop v2: Scalable atlas construction for training sequence-to-function models"
biorxiv.org/content/10.1101/20
#Drosophila #Genomics #Embryo

bioRxiv · HyDrop v2: Scalable atlas construction for training sequence-to-function modelsDeciphering cis-regulatory logic underlying cell type identity is a fundamental question in biology. Single-cell chromatin accessibility (scATAC-seq) data has enabled training of sequence-to-function deep learning models allowing decoding of enhancer logic and design of synthetic enhancers. Training such models requires large amounts of high-quality training data across species, organs, development, aging, and disease. To facilitate the cost-effective generation of large scATAC-seq atlases for model training, we developed a new version of the open-source microfluidic system HyDrop with increased sensitivity and scale: HyDrop v2. We generated HyDrop v2 atlases for the mouse cortex and Drosophila embryo development and compared them to atlases generated on commercial platforms. HyDrop v2 data integrates seamlessly with commercially available chromatin accessibility methods (10x Genomics). Differentially accessible regions and motif enrichment across cell types are equivalent between HyDrop-v2 and 10x atlases. Sequence-to-function models trained on either atlas are comparable as well in terms of enhancer predictions, sequence explainability, and transcription factor footprinting. By offering accessible data generation, enhancer models trained on HyDrop-v2 and mixed atlases can contribute to unraveling cell-type specific regulatory elements in health and disease. ### Competing Interest Statement The authors have declared no competing interest.
Public
Benjamin Carr, Ph.D. 👨🏻‍💻🧬

#Genetic data site #openSNP to close and delete data over #privacy concerns
openSNP, a platform for sharing genetic and phenotypic data, will shut down, and delete all user submissions over privacy concerns and risk of misuse by authoritarian governments.
Announced earlier this week by co-founder Bastian Greshake Tzovaras, who expressed concerns about how personal #genomics data is subject to abuse today and how fundamentally landscape has changed over the last 14 years.
bleepingcomputer.com/news/secu

BleepingComputer · Genetic data site openSNP to close and delete data over privacy concernsBy Bill Toulas
Public
ResearchBuzz: Firehose

Bleeping Computer: Genetic data site openSNP to close and delete data over privacy concerns. “The openSNP project, a platform for sharing genetic and phenotypic data, will shut down on April 30, 2025, and delete all user submissions over privacy concerns and the risk of misuse by authoritarian governments.”

https://rbfirehose.com/2025/04/03/bleeping-computer-genetic-data-site-opensnp-to-close-and-delete-data-over-privacy-concerns/

#genetics#Genomics#opensource
Public
ResearchBuzz: Firehose

Ars Technica: FTC: 23andMe buyer must honor firm’s privacy promises for genetic data. “Federal Trade Commission Chairman Andrew Ferguson said he’s keeping an eye on 23andMe’s bankruptcy proceeding and the company’s planned sale because of privacy concerns related to genetic testing data.”

https://rbfirehose.com/2025/04/02/ftc-23andme-buyer-must-honor-firms-privacy-promises-for-genetic-data-ars-technica/

#23andme#bankruptcy#biometrics
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