Biology subjects

Voloshin, V.

Publications and source records attributed to Voloshin, V..

9 recordsLinked to original sources

bioRxiv2025

Machine Learning Reveals Immediate Disruption in Mosquito Flight when exposed to Olyset Nets

Insecticide-treated nets (ITNs) remain a critical intervention in controlling malaria transmission, yet the behavioural adaptations of mosquitoes in response to these interventions are not fully understood. This study examined the flight behaviour of insecticide-resistant (IR) and insecticide-susceptible (IS) Anopheles gambiae strains around an Olyset net (OL), a permethrin-impregnated ITN, versus an untreated net (UT). Using machine learning (ML) models, we classified mosquito flight trajectories with high accuracy (0.838) and ROC AUC (0.925). Contrary to assumptions that behavioural changes at OL would intensify over time, our findings show an immediate onset of convoluted, erratic flight paths for both IR and IS mosquitoes around the treated net. SHAP analysis identified three key predictive features of OL exposure: frequency of zero-crossings in flight angle change, first quartile of flight angle change, and zero-crossings in horizontal velocity. These suggest disruptive flight patterns, indicating insecticidal irritancy. While IS mosquitoes displayed rapid, disordered trajectories and mostly died within 30 minutes, IR mosquitoes persisted throughout the 2-hour experiments but exhibited similarly disturbed behaviour, suggesting resistance does not fully mitigate disruption. Our findings challenge literature suggesting permethrins repellency in solution form, instead supporting an irritant or contactdriven effect when incorporated into net fibres. This study highlights the value of ML-based trajectory analysis for understanding mosquito behaviour, refining ITN configurations and evaluating novel active ingredients aimed at disrupting mosquito flight behaviour. Future work should extend these methods to other ITNs to further illuminate the complex interplay between mosquito behaviour and insecticidal intervention.

animal behavior and cognition↗

bioRxiv2024

Discrimination of inherent characteristics of susceptible and resistant strains of Anopheles gambiae by explainable Artificial Intelligence Analysis of Flight Trajectories

Understanding mosquito behaviours is vital for development of insecticide-treated bednets (ITNs), which have been successfully deployed in sub-Saharan Africa to reduce disease transmission, particularly malaria. However, rising insecticide resistance (IR) among mosquito populations, owing to genetic and behavioural changes, poses a significant challenge. We present a machine learning pipeline that successfully distinguishes between IR and insecticide-susceptible (IS) mosquito behaviours by analysing trajectory data. Data driven methods are introduced to accommodate common tracking system shortcomings that occur due to mosquito positions being occluded by the bednet or other objects. Trajectories, obtained from room-scale tracking of two IR and two IS strains around a human-baited, untreated bednet, were analysed using features such as velocity, acceleration, and geometric descriptors. Using these features, an XGBoost model achieved a balanced accuracy of 0.743 and a ROC AUC of 0.813 in classifying IR from IS mosquitoes. SHAP analysis helped decipher that IR mosquitoes tend to fly slower with more directed flight paths and lower variability than IS--traits that are likely a fitness advantage by enhancing their ability to respond more quickly to bloodmeal cues. This approach provides valuable insights based on flight behaviour that can reveal the action of interventions and insecticides on mosquito physiology.

animal behavior and cognition↗

bioRxiv2024

Towards an unbiased characterization of genetic polymorphism

Our view of genetic polymorphism is shaped by methods that provide a limited and reference-biased picture. Long-read sequencing technologies, which are starting to provide nearly complete genome sequences for population samples, should solve the problem--except that characterizing and making sense of non-SNP variation is difficult even with perfect sequence data. Here we analyze 27 genomes of Arabidopsis thaliana in an attempt to address these issues, and illustrate what can be learned by analyzing whole-genome polymorphism data in an unbiased manner. Estimated genome sizes range from 135 to 155 Mb, with differences almost entirely due to centromeric and rDNA repeats that are difficult to assemble. The completely assembled chromosome arms comprise roughly 120 Mb in all accessions, but are full of structural variants, largely due to transposable elements. Even with only 27 accessions, a pan-genome coordinate system that includes the resulting variation ends up being [~] 70% larger than the size of any one genome. Our analysis reveals an incompletely annotated mobile-ome: we not only detect several novel TE families, but also find that existing TE annotation is a poor predictor of elements that have recently been active. In contrast to this, the genic portion, or "gene-ome", is highly conserved. By annotating each genome using accession-specific transcriptome data, we find that 13% of all (non-TE) genes are segregating in our 27 accessions, but most of these are transcriptionally silenced. Finally, we show that with short-read data we previously massively underestimated genetic variation of all kinds, including SNPs--mostly in regions where short reads could not be mapped reliably, but also where reads were mapped incorrectly. We demonstrate that SNP-calling errors can be biased by the choice of reference genome, and that RNA-seq and BS-seq results can be strongly affected by mapping reads only to a reference genome rather than to the genome of the assayed individual. In conclusion, while whole-genome polymorphism data pose tremendous analytical challenges, they also have the potential to revolutionize our understanding of genome evolution.

genomics↗

bioRxiv2023

Open access-enabled evaluation of epigenetic age acceleration in colorectal cancer and development of a classifier with diagnostic potential.

Aberrant DNA methylation (DNAm) is known to be associated with the aetiology of cancer, including colorectal cancer (CRC). In the past, the availability of open access data has been the main driver of innovative method development and research training. However, this is increasingly being eroded by the move to controlled access, particularly of medical data, including cancer DNAm data. To rejuvenate this valuable tradition, we leveraged DNAm data from 1,845 samples (535 CRC tumours, 522 normal colon tissues adjacent to tumours, 72 colorectal adenomas, and 716 normal colon tissues from healthy individuals) from 14 open access studies deposited in NCBI GEO and ArrayExpress. We calculated each samples epigenetic age (EA) using eleven epigenetic clock models and derived the corresponding epigenetic age acceleration (EAA). For EA, we observed that most first- and second-generation epigenetic clocks reflect the chronological age in normal tissues adjacent to tumours and healthy individuals (e.g. Horvath (r = 0.77 and 0.79), Zhang EN (r = 0.70 and 0.73)) unlike the epigenetic mitotic clocks (EpiTOC, HypoClock, MiAge) (r < 0.3). For EAA, we used PhenoAge, Wu, and the above mitotic clocks and found them to have distinct distributions in different tissue types, particularly between normal colon tissues adjacent to tumours and cancerous tumours, as well as between normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals. Finally, we harnessed these associations to develop a classifier using elastic net regression (with lasso and ridge regularisations) that predicts CRC diagnosis based on a patients sex and EAAs calculated from histologically normal controls (i.e. normal colon tissues adjacent to tumours and normal colon tissue from healthy individuals). The classifier demonstrated good diagnostic potential with ROC-AUC=0.886, which suggests that an EAA-based classifier trained on relevant data could become a tool to support diagnostic/prognostic decisions in CRC for clinical professionals. Our study also reemphasises the importance of open access clinical data for method development and training of young scientists. Obtaining the required approvals for controlled access data would not have been possible in the timeframe of this study.

genomics↗

bioRxiv2023

Insecticidal roof barriers mounted on untreated bednets can be as effective against Anopheles gambiae s.l. as insecticidal bednets

Barrier bednets (BBnets), regular bednets with a vertical insecticidal panel to target mosquitoes above the bednet roof, where activity is highest, have the potential to improve existing Insecticidal Treated Bednets (ITNs), by reducing quantity of insecticide required per net, reducing the toxic risks to those using the net, thus increasing the range of insecticides to choose from. We evaluated performance of different BBnet variants based on the PermaNet 3 (i.e., P3 BBnets with pyrethroid and piperonyl butoxide (PBO) on the roof or barrier; pyrethroid alone on the side walls) in room-scale bioassays, simultaneously video-recorded to track mosquitoes. Experimental results showed the longitudinal P3 barrier (P3L) to be highly effective: P3+P3L were consistently though not significantly more effective than the reference P3 bednet while performance of Ut+P3L was comparable to the reference P3. Comparing contact duration at the treated sections of each variant, the Ut+P3L accumulated 1273 contacts with 1374 seconds duration, all on the barrier, greatly exceeding the 792 seconds duration, from 8049 contacts, accumulated across the entire surface of the PermaNet 3 reference bednet. The BBnets potential to augment existing bednets and enhance their performance is considered.

animal behavior and cognition↗

bioRxiv2022

Behaviour of pyrethroid-resistant Anopheles gambiae at the interface of two dual active-ingredient bed nets, assessed by room-scale infrared video tracking

BackgroundThe success of Insecticide Treated Bednets (ITNs) for malaria vector control in Africa relies on the behaviour of the major malaria vectors, Anopheles species. Research into mosquito behavioural traits influencing the performance of ITNs has focused largely on time or location of biting. Here we investigated less tractable behaviours including timings of net contact, willingness to refeed and longevity post exposure to two next-generation nets, PermaNet(R) 3.0 (P3) and Interceptor(R) G2 (IG2) in comparison with a standard pyrethroid only net (Olyset (OL)) and an untreated net. MethodsSusceptible and resistant Anopheles gambiae mosquitoes were exposed to the nets with a human volunteer host in a room scale assay. Mosquito movements were tracked for two hours using an infrared video system, collecting flight trajectory, spatial position and net contact data. Post-assay, mosquitoes were monitored for a range of sublethal insecticide effects. ResultsOL, P3 and IG2 all killed over 90% of susceptible mosquitoes 24 hours after exposure, but this effect was not seen with resistant mosquitoes where mortality ranged from 16% to 72%. Total mosquito activity was higher around untreated nets than ITNs. There was no difference in total activity, the number, or duration, of net contact, between any mosquito strain, with similar behaviours recorded in susceptible and resistant strains at all ITNs. Net contact was focussed predominantly on the roof for all bednets. We observed a steep decay in activity for both susceptible strains when P3 and OL were present and with IG2 for one of the two susceptible strains. All treated nets reduced the willingness of resistant strains to re-feed when offered blood one-hour post-exposure, with a more pronounced effect seen with P3 and OL than IG2. ConclusionResults indicate that the effects of ITNs on mosquito behaviour are consistent, with no major differences in responses between strains of different pyrethroid susceptibility.

animal behavior and cognition↗

bioRxiv2022

Evaluation of epigenetic age acceleration scores and their associations with CVD related phenotypes in a population cohort

We evaluated associations between nine epigenetic age acceleration (EAA) scores and 18 cardio-metabolic phenotypes using an Eastern European ageing population cohort richly annotated for a diverse set of phenotypes (subsample, n = 306; aged 45-69 years). This was implemented by splitting the data into groups with positive and negative EAAs. We observed strong association between all epigenetic age acceleration scores and sex, suggesting that any analysis of EAAs should be adjusted by sex. We found that some sex-adjusted EAA scores were significantly associated with several phenotypes such as blood levels of gamma-glutamyl transferase and low-density lipoprotein, smoking status, annual alcohol consumption, multiple carotid plaques, and incident coronary heart disease status (not necessarily the same phenotypes for different EAAs). We demonstrated that even after adjusting EAAs for sex, EAA-phenotype associations remain sex-specific, which should be taken into account in any downstream analysis involving EAAs. The obtained results suggest that in some EAA-phenotype associations, negative EAA scores (i.e. epigenetic age below chronological age) indicated more harmful phenotype values, which is counter-intuitive. Among all considered epigenetic clocks, GrimAge was significantly associated with more phenotypes than any other EA scores in this Russian sample.

bioinformatics↗

bioRxiv2019

Diffuse retro-reflective imaging for improved mosquito tracking around human baited bednets

Robust imaging techniques for tracking insects have been essential tools in numerous laboratory and field studies on pests, beneficial insects and model systems. Recent innovations in optical imaging systems and associated signal processing have enabled detailed characterisation of nocturnal mosquito behaviour around bednets and improvements in bednet design, a global essential for protecting populations against malaria. Nonetheless, there remain challenges around ease of use for large scale in situ recordings and extracting data reliably in the critical areas of the bednet where the optical signal is attenuated. Here we introduce a retro-reflective screen at the back of the measurement volume, which can simultaneously provide diffuse illumination, and remove optical alignment issues whilst requiring only one-sided access to the measurement space. The illumination becomes significantly more uniform, although, noise removal algorithms are needed to reduce the effects of shot noise particularly across low intensity bednet regions. By systematically introducing mosquitoes in front and behind the bednet in lab experiments we are able to demonstrate robust tracking in these challenging areas. Overall, the retro-reflective imaging setup delivers mosquito segmentation rates in excess of 90% compared to less than 70% with back-lit systems.

animal behavior and cognition↗

bioRxiv2019

The Personal Genome Project-UK: an open access resource of human multi-omics data

Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.

bioinformatics↗