Honey bee as an alternative model invertebrate organism

Insects perfectly fit the flagship principle of animal research – 3R: to reduce (the number of animals), to replace (animals with alternative models) and to refine (methods). Bees have the most important advantages of a model organism: they cause minimal ethical controversy, they have a small and fully known genome, and they permit the use of many experimental techniques. Bees have a fully functional DNMT toolkit. Therefore, they are used as models in biomedical/genetic research, e.g. in research on the development of cancer or in the diagnostics of mental and neuroleptic diseases in humans. The reversion of aging processes in bees offers hope for progress in gerontology research. The cellular mechanisms of learning and memory coding, as well as the indicators of biochemical immunity parameters, are similar or analogous to those in humans, so bees may become useful in monitoring changes in behavior and metabolism. Bees are very well suited for studies on the dose of the substance applied to determine the lethal dose or the effect of a formula on life expectancy. Honeybees have proven to be an effective tool for studying the effects of a long-term consumption of stimulants, as well as for observing behavioral changes and developing addictions at the individual and social levels, as well as for investigating the effects of continuously delivering the same dose of a substance. The genomic and physiological flexibility of bees in dividing tasks among workers in a colony makes it possible to create a Single- Cohort Colony (SCC) in which peers compared perform different tasks. Moreover behavioral methods (e.g. Proboscis Extension Reflex – PER, Sting Extension Reflex – SER, free flying target discrimination tasks or the cap pushing response) make it possible to analyse changes occurring in honeybee brains during learning and remembering. Algorithms of actions are created based on the behavior of a colony or individual, e.g. Artificial Bee Colony Algorithm (ABCA). Honeybees are also model organisms for profiling the so-called intelligence of a swarm or collective intelligence. Additionally, they serve as models for guidance systems and aviation technologies. Bees have inspired important projects in robotics, such as B-droid, Robobee and The Green Brain Project. It has also been confirmed that the apian sense of smell can be used to detect explosive devices, such as TNT, or drugs (including heroin, cocaine, amphetamines and cannabis). This inconspicuous little insect can revolutionize the world of science and contribute to the solution of many scientific problems as a versatile model.

Gender Identification and Classification of Drosophila melanogaster Flies Using Machine Learning Techniques

Drosophila melanogaster is an important genetic model organism used extensively in medical and biological studies. About 61% of known human genes have a recognizable match with the genetic code of Drosophila flies, and 50% of fly protein sequences have mammalian analogues. Recently, several investigations have been conducted in Drosophila to study the functions of specific genes exist in the central nervous system, heart, liver, and kidney. The outcomes of the research in Drosophila are also used as a unique tool to study human-related diseases. This article presents a novel automated system to classify the gender of Drosophila flies obtained through microscopic images (ventral view). The proposed system takes an image as input and converts it into grayscale illustration to extract the texture features from the image. Then, machine learning (ML) classifiers such as support vector machines (SVM), Naive Bayes (NB), and K -nearest neighbour (KNN) are used to classify the Drosophila as male or female. The proposed model is evaluated using the real microscopic image dataset, and the results show that the accuracy of the KNN is 90%, which is higher than the accuracy of the SVM classifier.

The dgc2 gene encoding di-guanylate cyclase suppresses both motility and biofilm formation in the filamentous cyanobacterium Leptolyngbya boryana.

Colony pattern formations of bacteria with motility manifest complicated morphological self-organization phenomena. Leptolyngbya boryana is the filamentous cyanobacterial species, which has been used as a genetic model organism for studying metabolism including photosynthesis and nitrogen-fixation. Although a widely used type strain (wild type) of this species has not been reported to show any motile activity, we isolated a spontaneous mutant strain which shows active motility (gliding activity) to give rise to complicated colony patters, including comet-like wandering clusters and disk-like rotating vortices on solid media. Whole-genome resequencing identified multiple mutations on the genome in the mutant strain. We confirmed that inactivation of a candidate gene, dgc2 (LBDG_02920), in the wild type background was sufficient to give rise to motility and the morphological colony patterns. This gene encodes a protein, containing the GGDEF motif, which is conserved at the catalytic domain of diguanylate cyclase (DGC). Although DGC has been reported to be involved in biofilm formation, the mutant strain lacking dgc2 significantly facilitated biofilm formation, suggesting a role of DGC for suppressing both gliding motility and biofilm formation. Thus, L. boryana provides an excellent genetic model to study dynamic colony pattern formation, and novel insight on a role of c-di-GMP for biofilm formation.

Metformin Alters the Chemotaxis and Flagellar Motility of Escherichia coli

Metformin is a biguanide molecule that is widely prescribed to treat type 2 diabetes and metabolic syndrome. Although it is known that metformin promotes the lifespan by altering intestinal microorganism metabolism, how metformin influences and alters the physiological behavior of microorganisms remains unclear. Here we studied the effect of metformin on the behavior alterations of the model organism Escherichia coli (E. coli), including changes in chemotaxis and flagellar motility that plays an important role in bacterial life. It was found that metformin was sensed as a repellent to E. coli by tsr chemoreceptors. Moreover, we investigated the chemotactic response of E. coli cultured with metformin to two typical attractants, glucose and α-methyl-DL-aspartate (MeAsp), finding that metformin prolonged the chemotactic recovery time to the attractants, followed by the recovery time increasing with the concentration of stimulus. Metformin also inhibited the flagellar motility of E. coli including the flagellar motor rotation and cell swimming. The inhibition was due to the reduction of torque generated by the flagellar motor. Our discovery that metformin alters the behavior of chemotaxis and flagellar motility of E. coli could provide potential implications for the effect of metformin on other microorganisms.

The Mycotoxin Fumonisin B1 Induces Metabolic and Molecular Perturbations Leading to Cell Death in Arabidopsis Cell Culture

Fumonisin B1 (FB1) is a fungal toxin produced by Fusarium spp. able to exert pleiotropic toxicity in plants. FB1 is known to be a strong inducer of the programmed cell death (PCD); however, the exact mechanism underling the plant-toxin interactions and the molecular events that lead to PCD are still unclear. Therefore, in this work we provided a comprehensive investigation of the response of the model organism Arabidopsis thaliana at the nuclear, transcriptional, and biochemical level after the treatment with FB1 at two different concentrations, namely 1 and 5µM during a time-course of 96 h. FB1 induced oxidative and nitrosative bursts and a rapid cell death in Arabidopsis cell cultures, which resembled a HR-like PCD event. Different genes involved in the regulation of PCD, antioxidant metabolism, photosynthesis, resistance, and sugar transport were upregulated, especially during the late treatment time and with higher FB1 concentration. Among the antioxidant enzymes and compounds studied, only glutathione appeared to be highly induced in both treatments, suggesting that it might be an important defense molecule induced during FB1 exposure. Collectively, these findings highlight the complexity of the defense network of A. thaliana and provide important information for the understanding of the physiological, molecular, and biochemical responses to counteract FB1-induced toxicity.

Maturation of Social-Vocal Communication in Prairie Vole (Microtus ochrogaster) Pups

Impairments in social communication are common among neurodevelopmental disorders. While traditional animal models have advanced our understanding of the physiological and pathological development of social behavior, they do not recapitulate some aspects where social communication is essential, such as biparental care and the ability to form long-lasting social bonds. Prairie voles (Microtus ochrogaster) have emerged as a valuable rodent model in social neuroscience because they naturally display these behaviors. Nonetheless, the role of vocalizations in prairie vole social communication remains unclear. Here, we studied the ontogeny [from postnatal days (P) 8–16] of prairie vole pup ultrasonic vocalizations (USVs), both when isolated and when the mother was present but physically unattainable. In contrast to other similarly sized rodents such as mice, prairie vole pups of all ages produced isolation USVs with a relatively low fundamental frequency between 22 and 50 kHz, often with strong harmonic structure. Males consistently emitted vocalizations with a lower frequency than females. With age, pups vocalized less, and the acoustic features of vocalizations (e.g., duration and bandwidth) became more stereotyped. Manipulating an isolated pup's social environment by introducing its mother significantly increased vocal production at older (P12–16) but not younger ages, when pups were likely unable to hear or see her. Our data provide the first indication of a maturation in social context-dependent vocal emission, which may facilitate more active acoustic communication. These results help lay a foundation for the use of prairie voles as a model organism to probe the role of early life experience in the development of social-vocal communication.

Phosphoglycolate phosphatase homologs act as glycerol-3-phosphate phosphatase to control stress and healthspan in C. elegans

Metabolic stress due to nutrient excess and lipid accumulation is at the root of many age-associated disorders and the identification of therapeutic targets that mimic the beneficial effects of calorie restriction has clinical importance. Here, using C. elegans as a model organism, we study the roles of a recently discovered enzyme at the heart of metabolism in mammalian cells, glycerol-3-phosphate phosphatase (G3PP) (gene name Pgp) that hydrolyzes glucose-derived glycerol-3-phosphate to glycerol. We identify three Pgp homologues in C. elegans (pgph) and demonstrate in vivo that their protein products have G3PP activity, essential for glycerol synthesis. We demonstrate that PGPH/G3PP regulates the adaptation to various stresses, in particular hyperosmolarity and glucotoxicity. Enhanced G3PP activity reduces fat accumulation, promotes healthy aging and acts as a calorie restriction mimetic at normal food intake without altering fertility. Thus, PGP/G3PP can be considered as a target for age-related metabolic disorders.

The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life

Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.

Consensus nomenclature for dyneins and associated assembly factors

Dyneins are highly complex, multicomponent, microtubule-based molecular motors. These enzymes are responsible for numerous motile behaviors in cytoplasm, mediate retrograde intraflagellar transport (IFT), and power ciliary and flagellar motility. Variants in multiple genes encoding dyneins, outer dynein arm (ODA) docking complex subunits, and cytoplasmic factors involved in axonemal dynein preassembly (DNAAFs) are associated with human ciliopathies and are of clinical interest. Therefore, clear communication within this field is particularly important. Standardizing gene nomenclature, and basing it on orthology where possible, facilitates discussion and genetic comparison across species. Here, we discuss how the human gene nomenclature for dyneins, ODA docking complex subunits, and DNAAFs has been updated to be more functionally informative and consistent with that of the unicellular green alga Chlamydomonas reinhardtii, a key model organism for studying dyneins and ciliary function. We also detail additional nomenclature updates for vertebrate-specific genes that encode dynein chains and other proteins involved in dynein complex assembly.