bioRxiv - Zoology最新文献

{"title":"Reproductive success of inbred strain MV31 of the ctenophore Mnemiopsis leidyi in a self-sustaining inland laboratory culture system","authors":"Pranav Garg, Cameron Frey, William E Browne, Steven S Plotkin","doi":"10.1101/2024.07.03.601798","DOIUrl":"https://doi.org/10.1101/2024.07.03.601798","url":null,"abstract":"Ctenophores are an attractive lineage for studying animal evolution due to their early divergence from other metazoans. Among Ctenophora, <em>Mnemiopsis leidyi</em> is a model system for developmental, cellular, molecular genetic, and evolutionary studies. Until recently, many of these studies were conducted on wild-caught animals, limiting access to researchers on the coast. Here we present significant advancements towards culturing <em>M. leidyi</em> in laboratories without coastal access, enabling its wider use as an experimental and genetic model system. We detail updated feeding regimes that take advantage of co-culturing <em>Brachionus</em> rotifers with <em>Apocyclops</em> copepods, and quantify the reproductive output of our <em>M. leidyi</em> lab strain on this diet. Our updated feeding regime maintains reproductive fitness comparable to wild-caught individuals. Importantly, we have eliminated the logistical complexities and costs of regularly feeding live larval fish to <em>M. leidyi</em>. Our updated protocols make it feasible to maintain continuous ctenophore cultures independent of access to both coastal populations of wild <em>M. leidyi</em> and larval fish culturing facilities.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571616","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The SmARTR pipeline: a modular workflow for the cinematic rendering of 3D scientific imaging data","authors":"Simone Macri, Nicolas Di-Poi","doi":"10.1101/2024.07.03.601651","DOIUrl":"https://doi.org/10.1101/2024.07.03.601651","url":null,"abstract":"Advancements in non-invasive surface and internal imaging techniques, along with computational methods, have revolutionized 3D visualization of organismal morphology. These breakthroughs not only enhance research and medical anatomical analysis, but also facilitate the preservation and digital archiving of scientific specimens. We introduce the SmARTR pipeline (Small Animal Realistic Three-dimensional Rendering), a comprehensive workflow integrating wet lab procedures, 3D data acquisition, and processing to produce photorealistic 3D scientific data through cinematic rendering. This versatile pipeline supports multi-scale visualizations, from tissue-level to whole-organism details across diverse living organisms and is adaptable to various imaging sources and platforms. Its modular design and customizable rendering scenarios, provided by detailed SmARTR networks in a free software environment, make it a powerful tool for 3D data analysis. Accessible to a broad audience, SmARTR serves as a valuable resource not only for multiple fields of research in life sciences but also for education, diagnosis, outreach, and artistic endeavors.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141571746","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Familiarity of an environment prevents song suppression in isolated zebra finches","authors":"Anja Tamara Zai, Diana Isabel Rodrigues, Anna E Stepien, Iris Adam, Corinna Lorenz, Nicolas Giret, Richard H.R. Hahnloser","doi":"10.1101/2024.07.02.601800","DOIUrl":"https://doi.org/10.1101/2024.07.02.601800","url":null,"abstract":"Despite the wide use of zebra finches as an animal model to study vocal learning and production, little is known about impacts on their welfare caused by routine experimental manipulations such as changing their social context. Here we conduct a post-hoc analysis of singing rate, an indicator of positive welfare, to gain insights into stress caused by social isolation, a common experimental manipulation. We find that isolation in an unfamiliar environment reduces singing rate for several days, indicating the presence of an acute stressor. However, we find no such decrease when social isolation is caused by either removal of a social companion or by transfer to a familiar environment. Furthermore, during repeated brief periods of isolation, singing rate remains high when isolation is induced by removal of social companions, but it fails to recover from a suppressed state when isolation is induced by recurrent transfer to an unknown environment. These findings suggest that stress from social isolation is negligible compared to stress caused by environmental changes and that frequent short visits of an unfamiliar environment are detrimental rather than beneficial. Together, these insights can serve to refine experimental studies and design paradigms maximizing the birds' wellbeing and vocal output.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141550455","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Morphological simulation tests the limits on phenotype discovery in 3D image analysis","authors":"Rachel A Roston, Sophie M Whikehart, Sara M Rolfe, A. Murat Maga","doi":"10.1101/2024.06.30.601430","DOIUrl":"https://doi.org/10.1101/2024.06.30.601430","url":null,"abstract":"In the past few decades, advances in 3D imaging have created new opportunities for reverse genetic screens. Rapidly growing datasets of 3D images of genetic knockouts require high-throughput, automated computational approaches for identifying and characterizing new phenotypes. However, exploratory, discovery-oriented image analysis pipelines used to discover these phenotypes can be difficult to validate because, by their nature, the expected outcome is not known a priori. Introducing known morphological variation through simulation can help distinguish between real phenotypic differences and random variation; elucidate the effects of sample size; and test the sensitivity and reproducibility of morphometric analyses. Here we present a novel approach for 3D morphological simulation that uses open-source, open-access tools available in 3D Slicer, SlicerMorph, and Advanced Normalization Tools in R (ANTsR). While we focus on diffusible-iodine contrast-enhanced micro-CT (diceCT) images, this approach can be used on any volumetric image. We then use our simulated datasets to test whether tensor-based morphometry (TBM) can recover our introduced differences; to test how effect size and sample size affect detectability; and to determine the reproducibility of our results. In our approach to morphological simulation, we first generate a simulated deformation based on a reference image and then propagate this deformation to subjects using inverse transforms obtained from the registration of subjects to the reference. This produces a new dataset with a shifted population mean while retaining individual variability because each sample deforms more or less based on how different or similar it is from the reference. TBM is a widely-used technique that statistically compares local volume differences associated with local deformations. Our results showed that TBM recovered our introduced morphological differences, but that detectability was dependent on the effect size, the sample size, and the region of interest (ROI) included in the analysis. Detectability of subtle phenotypes can be improved both by increasing the sample size and by limiting analyses to specific body regions. However, it is not always feasible to increase sample sizes in screens of essential genes. Therefore, methodical use of ROIs is a promising way to increase the power of TBM to detect subtle phenotypes. Generating known morphological variation through simulation has broad applicability in developmental, evolutionary, and biomedical morphometrics and is a useful way to distinguish between a failure to detect morphological difference and a true lack of morphological difference. Morphological simulation can also be applied to AI-based supervised learning to augment datasets and overcome dataset limitations.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141517718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lethal Disruption of the Symbiotic Gut Community in Eastern Subterranean Termite Caused by Boric Acid","authors":"Aaron R Ashbrook, Melbert Schwarz, Coby Schal, Aram Mikaelyan","doi":"10.1101/2024.06.26.600876","DOIUrl":"https://doi.org/10.1101/2024.06.26.600876","url":null,"abstract":"The Eastern subterranean termite, Reticulitermes flavipes (Kollar), is a significant pest, causing extensive damage to structures that amount to substantial economic losses. Traditional termite control methods have utilized boric acid, known for its broad-spectrum insecticidal properties, yet its impact on termite gut microbiomes and the implications of such effects remain understudied. Our study evaluates the dose-dependent mortality of R. flavipes upon being provided boric acid treated filter papers and investigates the resulting dysbiosis within the termite gut microbiome. Consistent with reports from other insects, mortality increased in a dose-dependent manner, with the highest boric acid concentration (203.7 ug/cm2 of filter paper) significantly reducing termite survival. 16S rRNA gene sequencing of the gut microbiome revealed notable shifts in composition, indicating boric acid-induced dysbiosis. Aside from an overall decrease in microbial diversity, the relative abundance of some symbionts essential for termite nutrition decreased in response to higher boric acid concentrations, while several putative pathogens increased. Our findings extend the understanding of boric acid's mode of action in termites, emphasizing its effect beyond direct toxicity to include significant microbiome modulation that can have dire effects on termite biology. Considering its potential to induce dysbiosis and potentially augment the effectiveness of entomopathogens, our study supports the continued use of boric acid and related compounds for termite-resistant treatments for wood.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507035","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Why didn’t the nudibranch cross the ocean? Understanding biogeographic and evolutionary relationships of Hermissenda (Nudibranchia: Myrrhinidae) Bergh, 1878","authors":"Katherine Olivia Montana, Terrence M. Gosliner, Sarah C. Crews, Lynn J. Bonomo, James T. Carlton, Rebecca F. Johnson","doi":"10.1101/2024.06.23.600287","DOIUrl":"https://doi.org/10.1101/2024.06.23.600287","url":null,"abstract":"In the aftermath of the 2011 east Japanese earthquake and tsunami, anthropogenic debris from the east coast of Japan floated across the Pacific Ocean to the west coast of North America. One such vessel from Iwate Prefecture arrived on the coast of Oregon, and the fouling community included specimens identified as the nudibranch Hermissenda crassicornis, which was previously thought to range from Japan to Baja California but has since been split into three species: H. crassicornis (Alaska to southern CA), H. opalescens (British Columbia to Baja California), and H. emurai (Japan, Korea, Russian Far East). Previous work suggested that all of the motile invertebrates found in the tsunami debris fouling community were either pelagic or Japanese in origin. Our study sought to determine whether the nudibranch specimens collected from the Iwate vessel were, according to the new classification system, only H. emurai or whether the Eastern Pacific Hermissenda were present as well. Results from DNA sequencing and morphological analysis suggest that specimens of H. crassicornis, as it is currently recognized, and H. opalescens were found on the vessel. This finding indicates either that these species settled after arrival to the west coast of North America or that H. crassicornis and H. opalescens is found in Japan, suggesting Hermissenda ranges need to be investigated further. Occurrence data shared on the iNaturalist platform were also used to assess current ranges. Our phylogenetic tree and haplotype network constructed from COI data from all Hermissenda species indicate that H. opalescens and H. emurai are most closely related with H. opalescens sister to the clade that contains H. opalescens and H. emurai. This study demonstrates the power of combining volunteer naturalist data with lab-collected data to understand evolutionary relationships, species ranges, and biogeography.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effect of Hexane and Methanol Extracts of Piper guineense (Schum and Thonn) Seeds against the Larger grain borer (Prostephanus truncatus) in Stored Cassava Chips","authors":"Emmanuel Odii, Nnaemeka Joe Okonkwo, Ibeabuchi Uko","doi":"10.1101/2024.06.17.599383","DOIUrl":"https://doi.org/10.1101/2024.06.17.599383","url":null,"abstract":"Methanolic and hexane extract of black pepper Piper guineense Schum &amp; Thonn was evaluated for its insecticidal against the larger grain borer Prostephanus truncatus in stored cassava chips. The extracts were applied at various concentrations (4000, 2000, 1000, 500, 250 μl/ml) with ordinary acetone as control. The experimental setup involved placing ten unsexed adults of each insect species into petri dishes treated with each of the extracts as applicable for residual treatment application. Also, cassava chips weighing twenty grams were treated with the different concentrations of the extracts and the control before being artificially infested with Prostephanus truncatus and left for a period of thirty-three days. All of the treatments significantly reduced emergence holes and grain damage compared with the control.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Morphology, biology and phylogeny of Xenos gadagkari sp.nov. (Strepsiptera: Xenidae): an endoparasite of Polistes wattii (Hymenoptera: Vespidae).","authors":"Deepak Nain, Anjali Rana, Rhitoban Raychoudhury, Ruchira Sen","doi":"10.1101/2024.06.18.599476","DOIUrl":"https://doi.org/10.1101/2024.06.18.599476","url":null,"abstract":"We report the morphology, biology and phylogeny of a new strepsipteran endoparasitic species: Xenos gadagkari, from the primitively eusocial wasp Polistes wattii from Punjab, India. We report a high abundance of the endoparasite in P. wattii population of our study area and provide the morphological description of adult males, male puparium and neotenic females. This species is sufficiently different from other Xenos sp reported from various social wasps and therefore, constitutes a new species, X. gadagkari Sen and Nain, sp. nov. Although there are a few reports of Strepsipteran parasites from India, this is the first confirmational report with a thorough description of a Xenos species from the Indian population of P. wattii and underscores the need for further investigation of the diversity and distribution of this group in India. Our findings contribute to the growing body of knowledge on Xenos and provide a foundation for future behavioural, microbial and molecular studies on this enigmatic group of insects.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507038","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"External morphometric and microscopic analysis of the reproductive system in in- vitro reared stingless bee queens, Heterotrigona itama, and their mating frequency","authors":"Kanyanat Wongsa, Orawan Duangphakdee, Pisit Poolprasert, ATSALEK RATTANAWANNEE","doi":"10.1101/2024.06.12.598741","DOIUrl":"https://doi.org/10.1101/2024.06.12.598741","url":null,"abstract":"Stingless bees, prevalent in tropical and subtropical regions, are a tribe of eusocial bees that are crucial pollinators for economic crops and native plants, producing honey and pollen. However, colony expansion is limited by a shortage of queens for new colonies. Therefore, mass artificial rearing of virgin queens could address this in commercially managed meliponiculture. Furthermore, the in vitro rearing of queen stingless bees can improve meliponiculture management and conservation efforts. Herein, we explored the efficacy of in vitro queen rearing for Heterotrigona itama assessing the queen’s body size, reproductive organ size (ovary and spermatheca), acceptance rate into new, small colonies, and mating frequency. H. itama larvae developed into queens when fed with 120 µL–150 µL of larval food, resulting in in vitro queens having body sizes similar to those of naturally produced queens. Microscopic analysis revealed well-developed ovaries and spermathecae in in vitro-reared queens, unlike the smaller ovaries and the absence of spermathecae in the naturally produced workers. Acceptance of in vitro-reared queens was independent of worker age, and mating frequency was low but not significantly different from naturally produced queens. These findings could enhance stingless beekeeping practices and conservation efforts for the native stingless bee species.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141507039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Muscone-specific olfactory protein reveals the putative scent-marking pheromone in the Sunda pangolin (Manis javanica)","authors":"Zhongbo Yu, Tao Meng, Luyao Yu, Yichen Zhou, Tengcheng Que, Meihong He, Haijing Wang, Yingjiao Li, Liling Liu, Wenjian Liu, Yinliang Wang, Bingzhong Ren","doi":"10.1101/2024.06.04.597258","DOIUrl":"https://doi.org/10.1101/2024.06.04.597258","url":null,"abstract":"The Sunda pangolin (Manis javanica) is a burrowing and nocturnal animal, and they have poor vision, thus, intraspecies communication relies on olfaction, such as mating, warning, and scent-marking. However, the intraspecies pheromone in pangolins remains unknown. In this study, all the odorant-binding proteins in Sunda pangolins were functionally expressed, and they were screened against a panel of 32 volatiles that were derived from the pangolin's urine, feces, and anal gland secretions. Reverse chemical ecology identified that M. javanica odorant-binding protein 3 (MjavOBP3) possesses the highest binding affinity to muscone. A subsequent behavior-tracking assay showed that only males can sense muscone; thus, we hypothesize that muscone is a male-specific scent-marking pheromone. Meanwhile, the structural study showed that Tyr117 contributes the most to muscone's binding, which was further validated by site-directed mutagenesis. The findings clarify the scent-marking mechanism in pangolins, and muscone could potentially be used to support the monitoring and conservation of this endangered animal.","PeriodicalId":501575,"journal":{"name":"bioRxiv - Zoology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141253185","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}