Biology subjects

Ivanov, V.

Publications and source records attributed to Ivanov, V..

9 recordsLinked to original sources

bioRxiv2026

Closely related, yet phenotypically different - Genome assemblies of two sister species of widow spiders: Latrodectus hasselti and L. katipo, Theridiidae

Widow spiders of the genus Latrodectus are important animals for biomedical, pest and conservation research. Here, we present the assembled genomes of two closely related Latrodectus species: the Australian L. hasselti and the New Zealand endemic L. katipo. The genome of L. katipo consists of 13 scaffolds likely corresponding to chromosomes (90% of the total length) and 1267 short scaffolds (10%). It has a total length of 1.5 Gbp and BUSCO of 94.9%. The genome of L. hasselti consists of 379 scaffolds and has a total length of 1.7 Gbp and a BUSCO score of 95.4%. The repeat content is very similar in both genomes with a total proportion of 37.2% for L. katipo and 39.9% for L. hasselti. Genome annotation predicted 12706 and 15111 genes for L. katipo and L. hasselti respectively. An ortholog analysis shows large overlap between orthogroups suggesting either duplication events in L. hasselti or loss of genes in L. katipo.

genomics↗

bioRxiv2025

Continuous dynamics of cooperation and competition in social foraging

Real-life social interactions often unfold continuously and involve dynamic cooperation and competition, yet most studies rely on discrete games that do not capture the adaptive and graded nature of continuous sensorimotor decisions. To address this gap, we developed the Cooperation-Competition Foraging game -- an ecologically grounded paradigm in which pairs of participants (dyads) navigate a continuous shared space under face-to-face visibility, deciding in real-time to collect rewarded targets either individually or jointly. Dyads (n=58, 116 participants) spontaneously converged on distinct stable strategies along the cooperation-competition spectrum, forming three groups: cooperative, intermediate, and competitive. Despite the behavioral complexity, our computational model, which incorporated travel path minimization, sensorimotor communication, and recent choice history, predicted dyadic decisions with 87% accuracy, and linked prediction certainty with ensuing dynamics of spatiotemporal coordination. Further modeling revealed how sensorimotor factors, such as movement speed and skill, shape distinct strategies and payoffs. Crucially, we quantify the cost of cooperation, demonstrating that in many dyads prosocial tendencies outweigh the individual benefits of exploiting skill advantages. Our versatile framework provides a predictive, mechanistic account of how social and embodied drivers promote the emergence of dynamic cooperation and competition, and offers rigorous metrics for investigating the neural basis of naturalistic social interactions, and for linking personality traits to distinct strategies.

neuroscience↗

bioRxiv2022

A versatile semiautomated image analysis workflow for time-lapsed camera trap image classification.

O_LICamera trap arrays can generate thousands to millions of images that require exorbitant time and effort to classify and annotate by trained observers. Computer vision has evolved as an automated alternative to manual classification. The most popular computer vision solution is the supervised Machine Learning technique, which uses labeled images to train automated classification algorithms. C_LIO_LIWe propose a multi-step semi-automated workflow that consists of (1) identifying and separating bad-from good-quality images, (2) parsing good images into animals, humans, vehicles, and empty, and (3) cropping animals from images and classifying them into species for manual inspection. We trained, validated, and evaluated this approach using 548,627 images from 46 cameras in two regions of the Arctic (northeastern Norway, and Yamal Peninsula, Russia). C_LIO_LIWe obtained an accuracy of 0.959 for all three steps combined with the complete year test data set at Varanger and 0.922 at Yamal, reducing the number of images that required manual inspection to 7.9% of the original set from Varanger and 3.2% from Yamal. C_LIO_LIResearchers can modify this multi-step process to meet their specific needs for monitoring and surveying wildlife, providing greater flexibility than current options available for image classification. C_LI

ecology↗

bioRxiv2022

Adjuvant effects of multifunctional transcription factor and BCG ‎target YB-1: exogenous YB-1 enhances specific antibody ‎production in vivo and protects mice against lethal E. coli ‎challenge

There is growing interest in the beneficial effects of immune system boosting through the administration of adjuvants, not only in acute infections such as COVID but also in chronic degenerative disorders that are potentially associated with infection. The best-known immunopotentiators are Freunds complete adjuvant (FCA) and its relative Bacille Calmete-Guerin (BCG), both based on Mycobacterium species. The key pathogen-associated molecular patterns (PAMPs) in both FCA and BCG are muramyl dipeptides (MDPs and glucosaminyl-MDP, GMDP). We previously identified the evolutionarily conserved protein Y-box factor YB-1/YBX1 as a primary target for MDP/GMDP. Unlike other host receptors for PAMPs, YB-1 is a diffusible molecule, and we therefore explored whether in vivo administration of YB-1, rather than its PAMP ligands, might enhance the immune response to a bacterial antigen and/or influence survival in the face of bacterial infection. We report that mice receiving YB-1 plus GMDP in vivo mount a significantly increased B cell response versus GMDP alone against a test antigen (Yersinia pestis V antigen), and that YB-1 administration alone significantly promotes survival in the face of lethal bacterial (Escherichia coli) challenge in vivo. Independent confirmation is warranted because recombinant YB-1 and its ligands could hold great promise both as adjuvants and as therapeutics.

immunology↗

bioRxiv2022

Decision-making processes in perceptual learning depend on effectors

Visual perceptual learning is traditionally thought to arise in visual cortex. However, typical perceptual learning tasks also involve systematic mapping of visual information onto motor actions. Because the motor system contains both effector-specific and effector-unspecific representations, the question arises whether visual perceptual learning is effector-specific itself, or not. Here, we study this question in an orientation discrimination task. Subjects learn to indicate their choices either with joystick movements or with manual reaches. After training, we challenge them to perform the same task with eye movements. We dissect the decision-making process using the drift diffusion model. We find that learning effects on the rate of evidence accumulation depend on effectors, albeit not fully. This suggests that during perceptual learning, visual information is mapped onto effector-specific integrators. Overlap of the populations of neurons encoding motor plans for these effectors may explain partial generalization. Taken together, visual perceptual learning is not limited to visual cortex, but also affects sensorimotor mapping at the interface of visual processing and decision making.

neuroscience↗

bioRxiv2020

A rapid urban biodiversity blitz using aquatic environmental DNA

Background As global biodiversity declines, there’s an increasing need to create an educated and engaged society. Having people from all ages participate in measuring biodiversity where they live helps to create awareness. Recently, the use of environmental DNA (eDNA) for biodiversity surveys has gained momentum. Here, we test whether sampling eDNA and metabarcoding can be used for rapid urban biodiversity surveys for educational purposes.Materials & Methods We sampled 2×1 L of water from each of 15 locations in the city of Trondheim, Norway, including a variety of freshwater, marine and brackish habitats. DNA was extracted, amplified in triplicate for the COI gene and sequenced. The obtained data were analysed on the novel mBRAVE platform, an online open access software and computing resource.Results The water samples were collected in two days by two people and the lab analysis was completed in five days by one person. Overall, we detected the presence of 501 taxa identified as belonging to 435 species, representing 90 orders and 18 phyla. On average, only 5.4% of the taxa were shared among six replicates per site. Based on the observed diversity, three distinct clusters were detected and related to geographic distribution of sites. There were some taxa shared between the habitats, with a substantial presence of terrestrial biota.Discussion Our results match expected patterns of biodiversity in the landscape and show that with minimal sampling effort, hundreds of species can be detected. Thus, using eDNA analysis of water is promising for rapid biodiversity surveys, and it is likely that more detailed results could be obtained by optimising field and lab methods for particular groups of interest. We recommend that rapid eDNA surveys, with openly available services and softwares, can be used to raise awareness in the importance of biodiversity.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2020

New Viral Biogeochemical Roles Revealed Through Metagenomic Analysis of Lake Baikal

Lake Baikal is the largest body of liquid freshwater on Earth. Previous studies have described the microbial composition of this habitat but the viral communities from this ecosystem have not been characterized in detail. Here we describe the viral diversity of this habitat across depth and seasonal gradients. We discovered 19,475 bona fide viral sequences, which are derived from viruses predicted to infect abundant and ecologically important taxa that reside in Lake Baikal, such as Nitrospirota, Methylophilaceae and Crenarchaeota. Diversity analysis revealed significant changes in viral community composition between epipelagic and bathypelagic zones. Analysis of the gene content of individual viral populations allowed us to describe one of the first bacteriophages that infect Nitrospirota, and their extensive repertoire of auxiliary metabolic genes that might enhance carbon fixation through the reductive TCA cycle. We also described bacteriophages of methylotrophic bacteria with the potential to enhance methanol oxidation and the S-adenosyl-L-methionine cycle. These findings unraveled new ways by which viruses influence the carbon cycle in freshwater ecosystems, namely by using auxiliary metabolic genes that act upon metabolisms of dark carbon fixation and methylotrophy. Therefore, our results shed light on the processes through which viruses can impact biogeochemical cycles of major ecological relevance.

microbiology↗

bioRxiv2017

Distinct types of short open reading frames are translated in plant cells

Genomes contain millions of short (<100 codons) open reading frames (sORFs), which are usually dismissed during gene annotation. Nevertheless, peptides encoded by such sORFs can play important biological roles, and their impact on cellular processes has long been underestimated. Here, we analyzed approximately 70,000 transcribed sORFs in the model plant Physcomitrella patens (moss). Several distinct classes of sORFs that differ in terms of their position on transcripts and the level of evolutionary conservation are present in the moss genome. Over 5000 sORFs were conserved in at least one of ten plant species examined. Mass spectrometry analysis of proteomic and peptidomic datasets suggested that 584 sORFs located on distinct parts of mRNAs and long non-coding RNAs (lncRNAs) are translated, including 73 conservative sORFs. Translational analysis of the sORFs and main ORFs at a single locus suggested the existence of genes that code for multiple proteins and peptides with tissue-specific expression. Alternative splicing is likely involved in the excision of translatable sORFs from such transcripts. We identified a group of sORFs homologous to known protein domains and suggested they function as small interfering peptides. Functional analysis of candidate lncRNA-encoded peptides showed it to be involved in regulating growth and differentiation in moss. The high evolutionary rate and wide translation of sORFs suggest that they may provide a reservoir of potentially active peptides and their importance as a raw material for gene evolution. Our results thus open new avenues for discovering novel, biologically active peptides in the plant kingdom.

plant biology↗

bioRxiv2017

MinE recruits, stabilizes, releases, and inhibits MinD interactions with membrane to drive oscillation

The MinD and MinE proteins of Escherichia coli self-organize into a standing-wave oscillator on the membrane to help align division at mid-cell. When unleashed from cellular confines, we find that MinD and MinE form a wide spectrum of patterns on artificial bilayers - static amoebas, traveling waves, traveling mushrooms, and bursts with standing-wave dynamics. We recently focused our cell-free studies on bursts because their dynamics closely resemble those found in vivo. The data unveiled a patterning mechanism largely governed by MinE regulation of MinD interaction with membrane. We proposed that the MinD to MinE ratio on the membrane acts as a toggle switch between MinE-stimulated recruitment or release of MinD from the membrane. Here we provide data that further refines and extends our model that explains the remarkable spectrum of patterns supported by these two simple proteins.

microbiology↗