Search

Fragile X syndrome (FXS) is caused by the loss of fragile X messenger ribonucleoprotein (FMRP), a translational regulator that binds the transcripts of proteins involved in synaptic function and plasticity. Dysregulated protein synthesis is a central effect of FMRP loss, however, direct translational modulation has not been leveraged in the treatment of FXS. Thus, we examined the effect of the translational modulator integrated stress response inhibitor (ISRIB) in treating synaptic and behavioral symptoms of FXS. We show that FMRP loss dysregulates synaptic protein abundance, stabilizing dendritic spines through increased PSD-95 levels while preventing spine maturation through reduced glutamate receptor accumulation, thus leading to the formation of dense, immature dendritic spines, characteristic of FXS patients and Fmr1 knockout (KO) mice. ISRIB rescues these deficits and improves social recognition in Fmr1 KO mice. These findings highlight the therapeutic potential of targeting core translational mechanisms in FXS and neurodevelopmental disorders more broadly.

Duckweeds are widely distributed small, simply constructed aquatic higher plants (the Lemnaceae) found on quiet freshwater surfaces. Species inhabiting temperate climates may have to cope with long periods of severe cold during the winter season. Several duckweeds form compact resting structures from the assimilatory fronds of the growing season that can bridge inhospitable conditions in a quiescent state. Of these, turions separate from the mother fronds and overwinter on the water body bottom in a dormant state. They can surface, germinate, and sprout to resume active growth upon warming in the spring. The turions of the largest duckweed, Spirodela polyrhiza, have been intensively examined as to ultrastructure, the factors governing their formation and release from dormancy, and the signals driving their germination and sprouting and the accompanying starch degradation. Comparative transcriptomics of assimilatory fronds and dormant turions are revealing the molecular features of this developmental cycle. The results illustrate an elegant sequence of reactions that ensures aquatic survival of even severe winters by frost avoidance in a vegetative mode. Since little is known about other duckweed resting fronds, the S. polyrhiza turion developmental cycle cannot be considered to be representative of duckweed resting fronds in general but can serve as a reference for corresponding investigations. [ABSTRACT FROM AUTHOR]

In this study, nitrogen‐doped carbon nanodots (N‐CNDs) were synthesized from Citrus reticulata using microwave‐assisted process and material's genotoxic effects were investigated in Daphnia magna. Morphological size and shape variations of the synthesized N‐CNDs were evaluated by using zetasizer and transmission electron microscope. Acute/chronic toxicity experiments were performed using method by OECD (Organization for Economic Cooperation and Development) 202–212 guidelines. Daphnia magna was subjected to the N‐CNDs produced from Citrus reticulata at the different concentrations ranging between 0.04 and0.24 mg tangerine equivalent N‐CND/mL for 96 h at 20 °C. After 96 h, the LC50 (lethal concentration‐ at which 50% of cells) value of N‐CNDs was determined to be 0.1 mg equivalent N‐CND/mL using probit analysis. Based on toxicity levels determined by EU‐Directive 93/67/EEC, N‐CNDs are classified in the nontoxic category. The toxicological assessments of sublethal concentrations of N‐CNDs demonstrated that 0.013 mg tangerine equivalent N‐CND/mL dose group exhibited a similar profile to the control group, indicating its safety. Although the DNA damage frequency of the 0.03 and 0.06 mg equivalent N‐CND/mL dose groups was found to be higher than control group, these levels were observed almost 70% lower than the DNA damage frequency found in the mutagenic group/positive group. [ABSTRACT FROM AUTHOR]

Background: The family Batrachoididae are a group of ecologically important teleost fishes with unique life histories, behavior, and physiology that has made them popular model organisms. Batrachoididae remain understudied in the realm of genomics, with only four reference genome assemblies available for the family, with three being highly fragmented and not up to current assembly standards. Among these is the Gulf toadfish, Opsanus beta, a model organism for serotonin physiology which has recently been bred in captivity. Results: Here we present a new, de novo genome and transcriptome assemblies for the Gulf toadfish using PacBio long read technology. The genome size of the final assembly is 2.1 gigabases, which is among the largest teleost genomes. This new assembly improves significantly upon the currently available reference for Opsanus beta with a final scaffold count of 62, of which 23 are chromosome scale, an N50 of 98,402,768, and a BUSCO completeness score of 97.3%. Annotation with ab initio and transcriptome-based methods generated 41,076 gene models. The genome is highly repetitive, with ~ 70% of the genome composed of simple repeats and transposable elements. Satellite DNA analysis identified potential telomeric and centromeric regions. Conclusions: This improved assembly represents a valuable resource for future research using this important model organism and to teleost genomics more broadly. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Laboratory Animal Science & Practices / Laboratuvar Hayvanlari Bilimi ve Uygulamalari Dergisi is the property of Ataturk University Coordinatorship of Scientific Journals and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Abstract Background The family Batrachoididae are a group of ecologically important teleost fishes with unique life histories, behavior, and physiology that has made them popular model organisms. Batrachoididae remain understudied in the realm of genomics, with only four reference genome assemblies available for the family, with three being highly fragmented and not up to current assembly standards. Among these is the Gulf toadfish, Opsanus beta, a model organism for serotonin physiology which has recently been bred in captivity. Results Here we present a new, de novo genome and transcriptome assemblies for the Gulf toadfish using PacBio long read technology. The genome size of the final assembly is 2.1 gigabases, which is among the largest teleost genomes. This new assembly improves significantly upon the currently available reference for Opsanus beta with a final scaffold count of 62, of which 23 are chromosome scale, an N50 of 98,402,768, and a BUSCO completeness score of 97.3%. Annotation with ab initio and transcriptome-based methods generated 41,076 gene models. The genome is highly repetitive, with ~ 70% of the genome composed of simple repeats and transposable elements. Satellite DNA analysis identified potential telomeric and centromeric regions. Conclusions This improved assembly represents a valuable resource for future research using this important model organism and to teleost genomics more broadly.

ABSTRACTVirtually every major medical advance of the last century and at still has depended upon research with animals. Zebrafish's journey from the ocean to the laboratory leads to major scientific breakthroughs. Transparency structure of zebrafish helps in monitoring their internal structures and are permitting scientist to see effectes of nano particles in fish. Their organs share the same main features as humans and so can be used to study human developmental processes. Zebrafish congruence 70% of their genes with humans, and 84% of ailment-depended genes have zebrafish congruence. The zebrafish embryos can also genetically modified. Certain fishes like zebrafish are able to regenerate damaged retinal nerve cells. Müller galia cells in retina of zebrafish can transform in response to injury and act like stem cells to regrow the retina and replace all damaged neurons. Though humans have the same exact Müller galia cell, they don’t respond to damaged in the same way. Zebrafish are also very responsive to having their genomes edited. Zebrafish regenerate some tissue such as heart in during larval stage. In additionaly zebrafish are used as an animal model to study pharmocology – how drugs work and what they do to an organism’s body. Aim of this review, here, we review current knowledge of how these specialized structures and model organism by focusing on cellular behaviors and molecular mechanisms, highlighting findings from in vivo models and briefly discussing the recent advances in tissue cell culture and organoids. Review discusses the applications of human organoids models of disease on model organism and outlines the ailment treatments.

As an important model organism, Drosophila melanogaster has unique advantages in biological research because of its short life span, low culture cost, rich mutant resources and relatively simple gene operation. In recent years, with the vigorous development of food science, Drosophila melanogaster shows unique application value in screening new health food and pharmacological research. This paper reviews the methods and applications of establishing models of common human diseases and aging of Drosophila melanogaster, which lays a foundation for the study of the mechanism of diseases and aging, as well as the research and development of health food and drugs. [ABSTRACT FROM AUTHOR]

Cyanobacteria have great potential in CO2-based bio-manufacturing and synthetic biological studies. The filamentous cyanobacterium, Leptolyngbya sp. strain BL0902, is comparable to Arthrospira (Spirulina) platensis in commercialscale cultivation while proving to be more genetically tractable. Here, we report the analyses of the whole genome sequence, gene inactivation/overexpression in the chromosome and deletion of non-essential chromosomal regions in this strain. The genetic manipulations were performed via homologous double recombination using either an antibiotic resistance marker or the CRISPR/Cpf1 editing system for positive selection. A desD-overexpressing strain produced γ-linolenic acid in an open raceway photobioreactor with the productivity of 0.36 g·m-2·d-1. Deletion mutants of predicted patX and hetR, two genes with opposite effects on cell differentiation in heterocyst-forming species, were used to demonstrate an analysis of the relationship between regulatory genes in the non-heterocystous species. Furthermore, a 50.8-kb chromosomal region was successfully deleted in BL0902 with the Cpf1 system. These results supported that BL0902 can be developed into a stable photosynthetic cell factory for synthesizing high value-added products, or used as a model strain for investigating the functions of genes that are unique to filamentous cyanobacteria, and could be systematically modified into a genome-streamlined chassis for synthetic biological purposes. [ABSTRACT FROM AUTHOR]

The increasing global concern regarding plastic pollution has prompted the research into the consequences of microplastics (MPs) on aquatic ecosystems. Fairy shrimp Branchinella kugenumaensis are freshwater planktonic organisms that have existed for 250 million years. This study aimed to uncover the harmful effects of MPs, with a particular focus on their size variations (0.1, 1, and 5 µm), on the fairy shrimp. We focused on how MPs could significantly affect the survival and growth of fairy shrimp. Notably, larger MPs, especially those measuring 5 µm, caused higher mortality rates and hindered the growth compared to smaller ones. The impact of MPs continued even subsequent to depuration in clean water. The accumulation of MPs within the intestines of fairy shrimp resulted in intestinal blockages, disrupted excretory functions, and harmed intestinal epithelial cells. Examinations at the histological, cellular, and molecular levels showed that exposure to MPs triggered necroptosis in intestinal cells, accompanied by alterations in pathways related to transcription, translation, digestion, energy metabolism, and neurological functions. Furthermore, the effects of MPs on gene expression and pathways varied based on particle size, with larger MPs having a more significant effect and causing a strong response in xenobiotic biodegradation and metabolism pathways. We suggest that the increasing severity of MPs pollution could pose a significant threat to the survival of fairy shrimp. This study provided vital insights into the complex relationship between microplastics and aquatic organisms, and highlighted the urgent need to address the potential devastating impact of plastic pollution on freshwater ecosystems. Additionally, due to their rapid growth, strong reproductive capacity, sensitivity, and ease of cultivation, fairy shrimp hold the potential candidate to serve as a model organism for studying the effects of MPs and other pollutants on freshwater ecosystems. [ABSTRACT FROM AUTHOR]

DNA-binding proteins (DBPs) play critical roles in many biological processes, including gene expression, DNA replication, recombination and repair. Understanding the molecular mechanisms underlying these processes depends on the precise identification of DBPs. In recent times, several computational methods have been developed to identify DBPs. However, because of the generic nature of the models, these models are unable to identify species-specific DBPs with higher accuracy. Therefore, a species-specific computational model is needed to predict species-specific DBPs. In this paper, we introduce the computational DBPMod method, which makes use of a machine learning approach to identify species-specific DBPs. For prediction, both shallow learning algorithms and deep learning models were used, with shallow learning models achieving higher accuracy. Additionally, the evolutionary features outperformed sequence-derived features in terms of accuracy. Five model organisms, including Caenorhabditis elegans , Drosophila melanogaster , Escherichia coli , Homo sapiens and Mus musculus , were used to assess the performance of DBPMod. Five-fold cross-validation and independent test set analyses were used to evaluate the prediction accuracy in terms of area under receiver operating characteristic curve (auROC) and area under precision-recall curve (auPRC), which was found to be ~89–92% and ~89–95%, respectively. The comparative results demonstrate that the DBPMod outperforms 12 current state-of-the-art computational approaches in identifying the DBPs for all five model organisms. We further developed the web server of DBPMod to make it easier for researchers to detect DBPs and is publicly available at https://iasri-sg.icar.gov.in/dbpmod/. DBPMod is expected to be an invaluable tool for discovering DBPs, supplementing the current experimental and computational methods. [ABSTRACT FROM AUTHOR]

In humans, Entamoeba histolytica is the main pathogen causing various amoebiases, while E. moshkovskii falls between being a pathogen and non-pathogen. The two species have similar behavior patterns but differ significantly in pathogenicity, with previous studies and clinical data indicating that E. moshkovskii has a low level of pathogenicity. Meaningfully, the biological characteristics of E. moshkovskii make it a potential model organism and a protein display platform for studying the functions of important Entamoeba proteins. Here, an Amoeba-pcDNA3.1 vector capable of overexpressing E. histolytica-sourced Igl-C protein was constructed and successfully transfected into E. moshkovskii. High levels of expression of the Igl-C, EGFP, and NeoR genes were identified in Igl-C-transfected trophozoites using qRT-PCR, and they were subsequently confirmed using immunoblotting. Transfection of Igl-C protein improved the adherence and phagocytosis of E. moshkovskii, demonstrating that E. histolytica Igl mediated amoebic adhesion. Moreover, as a manifestation of protein virulence, the ability of post-transfected trophozoites to induce inflammation in host macrophages was also enhanced. In conclusion, this study utilizing the characteristics of E. moshkovskii confirmed its potential to serve as a model organism. E. moshkovskii could replace E. histolytica as the target of gene editing, allowing more efficient study of amoebic pathogenicity. [ABSTRACT FROM AUTHOR]

DNA adduction in the model yeast Saccharomyces cerevisiae was investigated after exposure to the fungicide penconazole and the reference genotoxic compound benzo(a)pyrene, for validating yeasts as a tool for molecular toxicity studies, particularly of environmental pollution. The effect of the toxicants on the yeast's growth kinetics was determined as an indicator of cytotoxicity. Fermentative cultures of S. cerevisiae were exposed to 2 ppm of Penconazole during different phases of growth; while 0.2 and 2 ppm of benzo(a)pyrene were applied to the culture medium before inoculation and on exponential cultures. Exponential respiratory cultures were also exposed to 0.2 ppm of B(a)P for comparison of both metabolisms. Penconazole induced DNA adducts formation in the exponential phase test; DNA adducts showed a peak of 54.93 adducts/109 nucleotides. Benzo(a)pyrene induced the formation of DNA adducts in all the tests carried out; the highest amount of 46.7 adducts/109 nucleotides was obtained in the fermentative cultures after the exponential phase exposure to 0.2 ppm; whereas in the respiratory cultures, 14.6 adducts/109 nucleotides were detected. No cytotoxicity was obtained in any experiment. Our study showed that yeast could be used to analyse DNA adducts as biomarkers of exposure to environmental toxicants. [ABSTRACT FROM AUTHOR]

Summary: The inwardly rectifying K+ channel Kir5.1 (Kcnj16) is essential in renal salt handling and blood pressure control. However, the underlying mechanisms are not fully understood. Here, we integrated transcriptomics and metabolomics to comprehensively profile the changes in genes and metabolites in the Dahl salt-sensitive (SS) rat lacking Kcnj16 to identify potential mechanisms. Consistent with the phenotype of knockout (KO) rats, the transcriptomic profile predicted reduced blood pressure, kidney damage, and increased ion transport. Canonical pathway analysis suggested activation of metabolic-related pathways while suppression of immune response-related pathways in KO rats. Untargeted metabolomic analysis revealed different metabolic profiles between wild-type (WT) and KO rats. Integration of transcriptomic and metabolomic profiles suggested altered tricarboxylic acid (TCA) cycle, amino acid metabolism, and reactive oxygen species (ROS) metabolism that are related to SS hypertension. In conclusion, besides increased ion transport, our data suggest suppressed immune response-related and altered metabolic-related pathways of SS rats lacking Kir5.1.

Summary: Given the resurgence of syphilis, research endeavors to improve current assays for serological diagnosis and management of this disease are a priority. A proteome-scale platform for high-throughput profiling of the humoral response to Treponema pallidum (T. pallidum) proteins during infection could identify antigens suitable to ameliorate the performance and capabilities of treponemal tests for syphilis. Additionally, because infection-induced immunity is partially protective, profiling the response to T. pallidum outer membrane proteins (OMPs) could help select vaccine candidates. Therefore, we developed a pan-proteome array (PPA) based on the Nichols and SS14 strain complete proteomes and used it to define the immunoglobulin M (IgM) and IgG humoral response to T. pallidum proteins in sera collected longitudinally from long-term infected rabbits and from rabbits that were infected, treated, and re-infected. We identified antigens that could facilitate early diagnosis and immunity to a core set of OMP that could explain protection upon reinfection.

Summary: The biological mechanisms underlying the development of myopia have not yet been completely elucidated. The retina is critical for visual signal processing, which primarily utilizes aerobic glycolysis to produce lactate as a metabolic end product. Lactate facilitates lysine lactylation (Kla), a posttranslational modification essential for transcriptional regulation. This study found increased glycolytic flux and lactate accumulation in the retinas of form-deprived myopic guinea pigs. Subsequently, a comprehensive analysis of Kla levels in retinal proteins revealed that Kla was upregulated at 124 sites in 92 proteins and downregulated at three sites in three proteins. Functional enrichment and protein interaction analyses showed significant enrichment in pathways related to energy metabolism, including glutathione metabolism, glycolysis, and the hypoxia-inducible factor-1 signaling pathway. Parallel-reaction monitoring confirmed data reliability. These findings suggest a connection between myopia and retinal energy metabolism imbalance, providing new insights into the pathogenesis of myopia.

With the continuous development of experimental biology, the limitations of commonly utilized model organisms are becoming increasingly apparent. Discrepancies between research conducted on laboratory animals and humans significantly impede the translational application of findings derived from animal experiments. This review introduces ascidian Ciona intestinalis as a novel model organism, an invertebrate that is evolutionarily closest to vertebrates and is a sister group to vertebrates. The review summarizes recent research progress on Ciona intestinalis in various fields to illustrate the significant advantages and promising application prospects of it as a model organism. The research progress outlined in the review mainly encompasses: (1) The whole-genome sequencing of Ciona intestinalis has been determined and numerous related databases have been established. Various embryonic gene editing technologies have been successfully applied, making it an animal model easy to manipulate genetically and study the functions and interactions of target genes visually. (2) In the field of neurobiology, Ciona intestinalis boasts a central nervous system structure similar to that of vertebrates and possesses numerous homologous neuropeptides and hormone molecules. These features grant it an edge in exploring the mechanisms and functional evolution of endocrine and neuroendocrine-related molecules. Additionally, the sensitivity and habituation of its larvae to light stimulation provide an avenue for exploring mechanisms related to behavioral plasticity. (3) In the field of immunology, Ciona intestinalis possesses a mature innate immune system and has evolved precursor genes to the adaptive immune system, with a relatively simple coding of immune-related genes. These features make it an exemplary model organism for immunological studies. (4) In the field of developmental biology, many studies have focused on the notochord development process in Ciona intestinalis and the regulatory mechanisms of gene expression within it, indicating common evolutionary developmental strategies among chordates. Additionally, insights into its heart development also significantly enhance our comprehension on the genetic network of human heart development. (5) In medical research, the ability of Ciona intestinalis to regenerate its neural complex and siphon, as well as the resilience of its heart to recover contractile function from substantial damage, renders it a valuable animal model for the study of regeneration and heart injury. It also has unique advantages as a research model for Alzheimer's disease and new drug development. Furthermore, its brief five-month lifespan facilitates the observation and recording of the entire aging process and the exploration of the effects of various factors on aging. In summary, this review aims to demonstrate that Ciona intestinalis stands out as a model organism with unique attributes and is expected to play a significant role in a wider range of scientific research areas.

Banana peel is one of the wastes that can be explored for various applications. Cavendish is among the most highly consumed bananas in the world, which implies a high amount of banana peel waste. Our study evaluated the potential of Cavendish banana peels as the source of antioxidant and anti-aging agents. Antioxidant was extracted using three different solvents, i.e., water, ethyl acetate, and methanol. Each extract was then assayed for antioxidant activity in vitro using a 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The antioxidant and anti-aging activity of the extracts were further evaluated at the cellular level using the yeast Schizosaccharomyces pombe as a model. Our data indicated that the methanol extract of banana peel showed the highest antioxidant activity with an IC50 value of 253.8 µg mL-1 compared to ethyl acetate and water, yet it was considered weak. Interestingly, the methanol extract (600 ppm) showed antioxidant and anti-aging activities at cellular levels in yeast S. pombe. Therefore, this research reveals the potential for developing banana peel methanol extract as a component of pharmaceutical or cosmetic products with antioxidant and anti-aging properties.

Introduction: Micro- and nanoplastics (MNPs) are emerging environmental pollutants that have raised serious concerns about their potential impact on ecosystem and organism health. Despite increasing efforts to investigate the impacts of micro- and nanoplastics (MNPs) on biota little is known about their potential impacts on terrestrial organisms, especially insects, at environmental concentrations. Objectives: To address this gap, we used an insect model, silkworm Bombyx mori to examine the potential long-term impacts of different sizes of polystyrene (PS) MNPs at environmentally realistic concentrations (0.25 to 1.0 μg/mL). Methods: After exposure to PS-MNPs over most of the larval lifetime (from second to last instar), the endpoints were examined by an integrated physiological (growth and survival) and multiomics approach (metabolomics, 16S rRNA, and transcriptomics). Results: Our results indicated that dietary exposures to PS-MNPs had no lethal effect on survivorship, but interestingly, increased host body weight. Multiomics analysis revealed that PS-MNPs exposure significantly altered multiple pathways, particularly lipid metabolism, leading to enriched energy reserves. Furthermore, the exposure changed the structure and composition of the gut microbiome and increased the abundance of gut bacteria Acinetobacter and Enterococcus. Notably, the predicted functional profiles and metabolite expressions were significantly correlated with bacterial abundance. Importantly, these observed effects were particle size-dependent and were ranked as PS-S (91.92 nm) > PS-M (5.69 µm) > PS-L (9.7 µm). Conclusion: Overall, PS-MNPs at environmentally realistic concentrations exerted stimulatory effects on energy metabolism that subsequently enhanced body weight in silkworms, suggesting that chronic PS-MNPs exposure might trigger weight gain in animals and humans by influencing host energy and microbiota homeostasis.

Sponges (Phylum Porifera) are aquatic sessile metazoans found worldwide in marine and freshwater environments. They are significant in the animal tree of life as one of the earliest-branching metazoan lineages and as filter feeders play crucial ecological roles, particularly in coral reefs, but are susceptible to the effects of climate change. In the face of the current biodiversity crisis, genomic data is crucial for species conservation efforts and predicting their evolutionary potential in response to environmental changes. However, there is a limited availability of culturable sponge species with annotated high-quality genomes to further comprehensive insights into animal evolution, function, and their response to the ongoing global change. Despite the publication of a few high-quality annotated sponge genomes, there remains a gap in resources for culturable sponge species. To address this gap, we provide high quality draft genomes of the two congeneric aquarium species Tethya wilhelma and Tethya minuta, small ball-shaped demosponges that are easily maintained long-term in ex situ culture. As such, they offer promising opportunities as laboratory models to contribute to advancing our understanding of sponge biology and provide valuable resources for studying animal evolution, function, and responses to environmental challenges.

Sponges (Phylum Porifera) are aquatic sessile metazoans found worldwide in marine and freshwater environments. They are significant in the animal tree of life as one of the earliest-branching metazoan lineages and as filter feeders play crucial ecological roles, particularly in coral reefs, but are susceptible to the effects of climate change. In the face of the current biodiversity crisis, genomic data is crucial for species conservation efforts and predicting their evolutionary potential in response to environmental changes. However, there is a limited availability of culturable sponge species with annotated high-quality genomes to further comprehensive insights into animal evolution, function, and their response to the ongoing global change. Despite the publication of a few high-quality annotated sponge genomes, there remains a gap in resources for culturable sponge species. To address this gap, we provide high quality draft genomes of the two congeneric aquarium species Tethya wilhelma and Tethya minuta, small ball-shaped demosponges that are easily maintained long-term in ex situ culture. As such, they offer promising opportunities as laboratory models to contribute to advancing our understanding of sponge biology and provide valuable resources for studying animal evolution, function, and responses to environmental challenges.

Summary: In humans, dietary patterns impact weight and metabolism differentially across individuals. To uncover genetic determinants for differential dietary effects, we subjected four genetically diverse mouse strains to humanized diets (American, Mediterranean, vegetarian, and vegan) with similar macronutrient composition, and performed body weight, metabolic parameter, and RNA-seq analysis. We observed pronounced diet- and strain-dependent effects on weight, and triglyceride and insulin levels. Differences in fat mass, adipose tissue, and skeletal muscle glucose uptake, and gene expression changes in most tissues were strain-dependent. In visceral adipose tissue, ∼400 genes responded to diet in a strain-dependent manner, many of them in metabolite transport and lipid metabolism pathways and several previously identified to modify diet effects in humans. Thus, genetic background profoundly impacts metabolism, though chosen dietary patterns modify the strong genetic effects. This study paves the way for future mechanistic investigations into strain-diet interactions in mice and translation to precision nutrition in humans.

Model organisms are instrumental substitutes for human studies to expedite basic, translational, and clinical research. Despite their indispensable role in mechanistic investigation and drug development, molecular congruence of animal models to humans has long been questioned and debated. Little effort has been made for an objective quantification and mechanistic exploration of a model organisms resemblance to humans in terms of molecular response under disease or drug treatment. We hereby propose a framework, namely Congruence Analysis for Model Organisms (CAMO), for transcriptomic response analysis by developing threshold-free differential expression analysis, quantitative concordance/discordance scores incorporating data variabilities, pathway-centric downstream investigation, knowledge retrieval by text mining, and topological gene module detection for hypothesis generation. Instead of a genome-wide vague and dichotomous answer of poorly or greatly mimicking humans, CAMO assists researchers to numerically quantify congruence, to dissect true cross-species differences from unwanted biological or cohort variabilities, and to visually identify molecular mechanisms and pathway subnetworks that are best or least mimicked by model organisms, which altogether provides foundations for hypothesis generation and subsequent translational decisions.

Objective To preliminarily analyze the effect of stomatitis mixture on embryo, liver and kidney development by using zebrafish as an animal model. Methods When zebrafish developed to 10 h after fertilization（10 hpf）,they were grouped by simple random method and added with gradient concentration of stomatitis mixture. After 72 h of drug action, the toxicity of stomatitis mixture on embryonic development and hepat orenal toxicity were observed under microscope and the image data were recorded. Results When the dilution concentration of stomatitis mixture was higher than 1. 625×10-5 g/mL,embryo developmental toxicity began to appear in 10hpf zebrafish, showing developmental delay and cardiac cavity stenosis. When the dilution concentration of stomatitis mixture was higher than 6. 500×10-5 g/mL,it had hepatorenal toxicity to 36 hpf zebrafish. The main manifestations were that the boundary between liver and surrounding tissues was not obvious, and the kidney and swim bladder area increased significantly, accompanied by edema and stasis. Conclusion The stomatitis mixture has certain embryo and liver and kidney toxicity. Pregnant women, lactating women, and patients with liver and kidney dysfunction, are not allowed to use this product in principle. It must be used with strict limits and careful use under the guidance of doctors. [ABSTRACT FROM AUTHOR]

WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast-paced C. elegans research, to provide better integration with other resources, and to be sustainable. Here, we discuss the current state of WormBase as well as progress and plans for moving core WormBase infrastructure to the Alliance of Genome Resources (the Alliance). As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features as needed, and curate key information from the literature and large-scale projects. [ABSTRACT FROM AUTHOR]

Mouse Genome Informatics (MGI) is a federation of expertly curated information resources designed to support experimental and computational investigations into genetic and genomic aspects of human biology and disease using the laboratory mouse as a model system. The Mouse Genome Database (MGD) and the Gene Expression Database (GXD) are core MGI databases that share data and system architecture. MGI serves as the central community resource of integrated information about mouse genome features, variation, expression, gene function, phenotype, and human disease models acquired from peer-reviewed publications, author submissions, and major bioinformatics resources. To facilitate integration and standardization of data, biocuration scientists annotate using terms from controlled metadata vocabularies and biological ontologies (e.g. Mammalian Phenotype Ontology, Mouse Developmental Anatomy, Disease Ontology, Gene Ontology, etc.), and by applying international community standards for gene, allele, and mouse strain nomenclature. MGI serves basic scientists, translational researchers, and data scientists by providing access to FAIR-compliant data in both human-readable and compute-ready formats. The MGI resource is accessible at https://informatics.jax.org. Here, we present an overview of the core data types represented in MGI and highlight recent enhancements to the resource with a focus on new data and functionality for MGD and GXD. [ABSTRACT FROM AUTHOR]

PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community. [ABSTRACT FROM AUTHOR]

Echinobase (www.echinobase.org) is a model organism knowledgebase serving as a resource for the community that studies echinoderms, a phylum of marine invertebrates that includes sea urchins and sea stars. Echinoderms have been important experimental models for over 100 years and continue to make important contributions to environmental, evolutionary, and developmental studies, including research on developmental gene regulatory networks. As a centralized resource, Echinobase hosts genomes and collects functional genomic data, reagents, literature, and other information for the community. This third-generation site is based on the Xenbase knowledgebase design and utilizes gene-centric pages to minimize the time and effort required to access genomic information. Summary gene pages display gene symbols and names, functional data, links to the JBrowse genome browser, and orthology to other organisms and reagents, and tabs from the Summary gene page contain more detailed information concerning mRNAs, proteins, diseases, and protein–protein interactions. The gene pages also display 1:1 orthologs between the fully supported species Strongylocentrotus purpuratus (purple sea urchin), Lytechinus variegatus (green sea urchin), Patiria miniata (bat star), and Acanthaster planci (crown-of-thorns sea star). JBrowse tracks are available for visualization of functional genomic data from both fully supported species and the partially supported species Anneissia japonica (feather star), Asterias rubens (sugar star), and L. pictus (painted sea urchin). Echinobase serves a vital role by providing researchers with annotated genomes including orthology, functional genomic data aligned to the genomes, and curated reagents and data. The Echinoderm Anatomical Ontology provides a framework for standardizing developmental data across the phylum, and knowledgebase content is formatted to be findable, accessible, interoperable, and reusable by the research community. [ABSTRACT FROM AUTHOR]

Simple Summary: The life expectancy of Drosophila melanogaster evolves in the laboratory in a downward direction over time. The comparison of two old laboratory-adapted strains, Canton-S and Harwich, suggested that they may be used as a multicellular eukaryote model for studying the effects of individual difference in aging processes on the physiological responses to various environmental factors, including low and high temperature, carbohydrate-heavy food, and caffeinated food in the presence of light-dark cyclicity and constant darkness. We found that the accelerated aging in Harwich was associated with a shorter lifespan, lower fecundity, faster rate of development, smaller body weight, lower concentrations of two main insect sugars, reduced locomotor activity, and larger amount of sleep. Such findings imply that, in the experimental studies of the aging accelerated effects of various adverse factors, the results obtained with only one of the laboratory-adapted strains cannot be generalized to other strains. The documented individual and strain-associated differences in the responses of their daily rhythms to aging and age-accelerated factors allow the recommendation to use at least two distinct strains characterized by a relatively fast and relatively slow aging processes, for the experimental elaboration of relationships between genes, environment, behavior, physiology, and health. Background: Drosophila melanogaster provides a powerful platform to study the physiology and genetics of aging, i.e., the mechanisms underpinnings healthy aging, age-associated disorders, and acceleration of the aging process under adverse environmental conditions. Here, we tested the responses of daily rhythms to age-accelerated factors in two wild-type laboratory-adapted strains, Canton-S and Harwich. Methods: On the example of the 24 h patterns of locomotor activity and sleep, we documented the responses of these two strains to such factors as aging, high temperature, carbohydrate diet, and diet with different doses of caffeine-benzoate sodium. Results: The strains demonstrated differential responses to these factors. Moreover, compared to Canton-S, Harwich showed a reduced locomotor activity, larger amount of sleep, faster rate of development, smaller body weight, lower concentrations of main sugars, lower fecundity, and shorter lifespan. Conclusions: It might be recommended to use at least two strains, one with a relatively fast and another with a relatively slow aging process, for the experimental elaboration of relationships between genes, environment, behavior, physiology, and health. [ABSTRACT FROM AUTHOR]

Copyright of Journal of Guangxi Normal University - Natural Science Edition is the property of Gai Kan Bian Wei Hui and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

With the continuous development of experimental biology, the limitations of commonly utilized model organisms are becoming increasingly apparent. Discrepancies between research conducted on laboratory animals and humans significantly impede the translational application of findings derived from animal experiments. This review introduces ascidian Ciona intestinalis as a novel model organism, an invertebrate that is evolutionarily closest to vertebrates and is a sister group to vertebrates. The review summarizes recent research progress on Ciona intestinalis in various fields to illustrate the significant advantages and promising application prospects of it as a model organism. The research progress outlined in the review mainly encompasses: (1) The whole-genome sequencing of Ciona intestinalis has been determined and numerous related databases have been established. Various embryonic gene editing technologies have been successfully applied, making it an animal model easy to manipulate genetically and study the functions and interactions of target genes visually. (2) In the field of neurobiology, Ciona intestinalis boasts a central nervous system structure similar to that of vertebrates and possesses numerous homologous neuropeptides and hormone molecules. These features grant it an edge in exploring the mechanisms and functional evolution of endocrine and neuroendocrine-related molecules. Additionally, the sensitivity and habituation of its larvae to light stimulation provide an avenue for exploring mechanisms related to behavioral plasticity. (3) In the field of immunology, Ciona intestinalis possesses a mature innate immune system and has evolved precursor genes to the adaptive immune system, with a relatively simple coding of immune-related genes. These features make it an exemplary model organism for immunological studies. (4) In the field of developmental biology, many studies have focused on the notochord development process in Ciona intestinalis and the regulatory mechanisms of gene expression within it, indicating common evolutionary developmental strategies among chordates. Additionally, insights into its heart development also significantly enhance our comprehension on the genetic network of human heart development. (5) In medical research, the ability of Ciona intestinalis to regenerate its neural complex and siphon, as well as the resilience of its heart to recover contractile function from substantial damage, renders it a valuable animal model for the study of regeneration and heart injury. It also has unique advantages as a research model for Alzheimer's disease and new drug development. Furthermore, its brief five-month lifespan facilitates the observation and recording of the entire aging process and the exploration of the effects of various factors on aging. In summary, this review aims to demonstrate that Ciona intestinalis stands out as a model organism with unique attributes and is expected to play a significant role in a wider range of scientific research areas. [ABSTRACT FROM AUTHOR]

Zebrafish (Danio rerio) are a popular model organism for scientific research, due to its small size, rapid development, and transparent embryos. One of the areas of study involving zebrafish is their teeth, which are continuously replaced throughout their lives. They have two types of teeth: incisors and pharyngeal teeth, compared to humans, who have only one type. Zebrafish teeth are replaced continuously throughout life, a process known as polyphyodonty, in contrast to humans, who are diphyodont and replace their teeth only once. Zebrafish teeth have been the subject of numerous experiments, including studies of tooth development, regeneration and evolution. In conclusion, zebrafish teeth are a fascinating subject of study in scientific research. In this review, we will describe zebrafish teeth, the experiments performed on them, and provide a comparative analysis with human teeth. [ABSTRACT FROM AUTHOR]

The Jardine River turtle (Emydura subglobosa) was selected as a potential model species for studies on freshwater turtles and general reptile physiology. Attempts to establish a freshwater turtle laboratory line were made when an adult pair of E. subglobosa was received in 2016 by the Laboratory of Inland Fisheries and Aquaculture (Poznań University of Life Sciences). The first generation of offspring was obtained in 2017, and the second generation in 2023. In each generation, unrelated specimens were added to the animal cohort to avoid inbreeding. Husbandry regimes were established, and a basal diet for nutritional experiments was developed and manufactured by two methods, producing extruded feed and a gelatinesolidified variant. The establishment of the Freshwater Turtle Laboratory Line (FTLL) provides an opportunity to improve the development of husbandry techniques, increase knowledge of reptile physiology, and use laboratory-raised animals as model species for research and education. [ABSTRACT FROM AUTHOR]

[Display omitted] • Environmental concentrations of PS-MNPs increased body weight without affecting survivorship. • Exposures induced significant alterations in host metabolome, microbiome, and transcriptome. • Gut metabolites were correlated with the microbiome. • The observed biomarkers' responses were particle size-dependent i.e., PS-S > PS-M > PS-L. • Metabolic disorder and microbiome dysbiosis are the main mechanisms of the observed phenotype. Micro- and nanoplastics (MNPs) are emerging environmental pollutants that have raised serious concerns about their potential impact on ecosystem and organism health. Despite increasing efforts to investigate the impacts of micro- and nanoplastics (MNPs) on biota little is known about their potential impacts on terrestrial organisms, especially insects, at environmental concentrations. To address this gap, we used an insect model, silkworm Bombyx mori to examine the potential long-term impacts of different sizes of polystyrene (PS) MNPs at environmentally realistic concentrations (0.25 to 1.0 μg/mL). After exposure to PS-MNPs over most of the larval lifetime (from second to last instar), the endpoints were examined by an integrated physiological (growth and survival) and multiomics approach (metabolomics, 16S rRNA, and transcriptomics). Our results indicated that dietary exposures to PS-MNPs had no lethal effect on survivorship, but interestingly, increased host body weight. Multiomics analysis revealed that PS-MNPs exposure significantly altered multiple pathways, particularly lipid metabolism, leading to enriched energy reserves. Furthermore, the exposure changed the structure and composition of the gut microbiome and increased the abundance of gut bacteria Acinetobacter and Enterococcus. Notably, the predicted functional profiles and metabolite expressions were significantly correlated with bacterial abundance. Importantly, these observed effects were particle size-dependent and were ranked as PS-S (91.92 nm) > PS-M (5.69 µm) > PS-L (9.7 µm). Overall, PS-MNPs at environmentally realistic concentrations exerted stimulatory effects on energy metabolism that subsequently enhanced body weight in silkworms, suggesting that chronic PS-MNPs exposure might trigger weight gain in animals and humans by influencing host energy and microbiota homeostasis. [ABSTRACT FROM AUTHOR]

Hydra, a member of the Phylum Cnidaria, has emerged as a versatile and valuable model organism for various scientific studies. Its remarkable regenerative capacity and perpetual reproductive capabilities make it an excellent candidate for research in multiple fields. In the realm of environmental studies, Hydra has been extensively utilized to assess the impact of pollutants and toxins on aquatic ecosystems. Its sensitivity to environmental changes and rapid asexual reproduction facilitates toxicity testing, making it an ideal indicator for monitoring environmental health and detecting subtle changes in ecological conditions. This review incorporates the last three decades of studies done on the Hydra model: with reference to toxicological studies. [ABSTRACT FROM AUTHOR]

Sponges (Phylum Porifera) are aquatic sessile metazoans found worldwide in marine and freshwater environments. They are significant in the animal tree of life as one of the earliest-branching metazoan lineages and as filter feeders play crucial ecological roles, particularly in coral reefs, but are susceptible to the effects of climate change. In the face of the current biodiversity crisis, genomic data is crucial for species conservation efforts and predicting their evolutionary potential in response to environmental changes. However, there is a limited availability of culturable sponge species with annotated high-quality genomes to further comprehensive insights into animal evolution, function, and their response to the ongoing global change. Despite the publication of a few high-quality annotated sponge genomes, there remains a gap in resources for culturable sponge species. To address this gap, we provide high quality draft genomes of the two congeneric aquarium species Tethya wilhelma and Tethya minuta, small ball-shaped demosponges that are easily maintained long-term in ex situ culture. As such, they offer promising opportunities as laboratory models to contribute to advancing our understanding of sponge biology and provide valuable resources for studying animal evolution, function, and responses to environmental challenges.

Summary: The regenerative functions associated with cytokines and growth factors have immense therapeutic potential; however, their poor pharmacokinetics, resulting from structural features, hinder their effectiveness. In this study, we aimed to enhance the pharmacokinetics of growth factors by designing receptor-binding macrocyclic peptides through in vitro mRNA display and grafting them into loops of immunoglobulin’s crystallizable region (Fc). As a model, we developed peptide-grafted Fc proteins with hepatocyte growth factor (HGF) functionality that exhibited a prolonged circulation half-life and could be administered subcutaneously. The Fc-based HGF mimetic alleviated liver fibrosis in a mouse model fed a choline-deficient high-fat diet, which induces hepatic features of non-alcoholic steatohepatitis, including fibrosis, showcasing its potential as a therapeutic intervention. This study provides a basis for developing growth factor and cytokine mimetics with improved pharmacokinetics, expanding their therapeutic applications.

Summary: Homologous recombination is initiated by the nucleolytic degradation (resection) of DNA double-strand breaks (DSBs). DSB resection is a two-step process. In the short-range step, the MRX (Mre11-Rad50-Xrs2) complex, together with Sae2, incises the 5′-terminated strand at the DSB end and resects back toward the DNA end. Then, the long-range resection nucleases Exo1 and Dna2 further elongate the resected DNA tracts. We found that mutations lowering proteasome functionality bypass the need for Sae2 in DSB resection. In particular, the dysfunction of the proteasome subunit Rpn11 leads to hyper-resection and increases the levels of both Exo1 and Dna2 to such an extent that it allows the bypass of the requirement for either Exo1 or Dna2, but not for both. These observations, along with the finding that Exo1 and Dna2 are ubiquitylated, indicate a role of the proteasome in restraining DSB resection by negatively controlling the abundance of the long-range resection nucleases.

Summary: Axolotls are uniquely able to completely regenerate the spinal cord after amputation. The underlying governing mechanisms of this regenerative response have not yet been fully elucidated. We previously found that spinal cord regeneration is mainly driven by cell-cycle acceleration of ependymal cells, recruited by a hypothetical signal propagating from the injury. However, the nature of the signal and its propagation remain unknown. In this theoretical study, we investigated whether the regeneration-inducing signal can follow a reaction-diffusion process. We developed a computational model, validated it with experimental data, and showed that the signal dynamics can be understood in terms of reaction-diffusion mechanism. By developing a theory of the regenerating outgrowth in the limit of fast reaction-diffusion, we demonstrate that control of regenerative response solely relies on cell-to-signal sensitivity and the signal reaction-diffusion characteristic length. This study lays foundations for further identification of the signal controlling regeneration of the spinal cord.

Summary: We utilized scRNA-seq to delineate the diversity of cell types in the zebrafish heart. Transcriptome profiling of over 50,000 cells at 48 and 72 hpf defined at least 18 discrete cell lineages of the developing heart. Utilizing well-established gene signatures, we identified a population of cells likely to be the primary pacemaker and characterized the transcriptome profile defining this critical cell type. Two previously uncharacterized genes, atp1b3b and colec10, were found to be enriched in the sinoatrial cardiomyocytes. CRISPR/Cas9-mediated knockout of these two genes significantly reduced heart rate, implicating their role in cardiac development and conduction. Additionally, we describe other cardiac cell lineages, including the endothelial and neural cells, providing their expression profiles as a resource. Our results established a detailed atlas of the developing heart, providing valuable insights into cellular and molecular mechanisms, and pinpointed potential new players in heart rhythm regulation.

Summary: The murine embryonic diaphragm is a primary model for studying myogenesis and neuro-muscular synaptogenesis, both representing processes regulated by spatially organized genetic programs of myonuclei located in distinct myodomains. However, a spatial gene expression pattern of embryonic mouse diaphragm has not been reported. Here, we provide spatially resolved gene expression data for horizontally sectioned embryonic mouse diaphragms at embryonic days E14.5 and E18.5. These data reveal gene signatures for specific muscle regions with distinct maturity and fiber type composition, as well as for a central neuromuscular junction (NMJ) and a peripheral myotendinous junction (MTJ) compartment. Comparing spatial expression patterns of wild-type mice with those of transgenic mice lacking either the skeletal muscle calcium channel CaV1.1 or β-catenin, reveals curtailed muscle development and dysregulated expression of genes potentially involved in NMJ formation. Altogether, these datasets provide a powerful resource for further studies of muscle development and NMJ formation in the mouse.

Summary: Ribonucleoside monophosphates (rNMPs) are abundantly found within genomic DNA of cells. The embedded rNMPs alter DNA properties and impact genome stability. Mutations in ribonuclease (RNase) H2, a key enzyme for rNMP removal, are associated with the Aicardi-Goutières syndrome (AGS), a severe neurological disorder. Here, we engineered orthologs of the human RNASEH2A-G37S and RNASEH2C-R69W AGS mutations in yeast Saccharomyces cerevisiae: rnh201-G42S and rnh203-K46W. Using the ribose-seq technique and the Ribose-Map bioinformatics toolkit, we unveiled rNMP abundance, composition, hotspots, and sequence context in these AGS-ortholog mutants. We found a high rNMP presence in the nuclear genome of rnh201-G42S-mutant cells, and an elevated rCMP content in both mutants, reflecting preferential cleavage of RNase H2 at rGMP. We discovered unique rNMP patterns in each mutant, showing differential activity of the AGS mutants on the leading or lagging replication strands. This study guides future research on rNMP characteristics in human genomes with AGS mutations.

Summary: Cardiac damage is widely present in patients with metabolic diseases, but the exact pathophysiological mechanisms involved remain unclear. The porcine heart is an ideal material for cardiovascular research due to its similarities to the human heart. This study evaluated pathological features and performed single-nucleus RNA sequencing (snRNA-seq) on myocardial samples from both wild-type and metabolic disease-susceptible transgenic pigs (previously established). We found that transgenic pigs exhibited lipid metabolism disturbances and myocardial injury after a high-fat high-sucrose diet intervention. snRNA-seq reveals the cellular landscape of healthy and metabolically disturbed pig hearts and identifies the major cardiac cell populations affected by metabolic diseases. Within metabolic disorder hearts, metabolically active cardiomyocytes exhibited impaired function and reduced abundance. Moreover, massive numbers of reparative LYVE1+ macrophages were lost. Additionally, proinflammatory endothelial cells were activated with high expression of multiple proinflammatory cytokines. Our findings provide insights into the cellular mechanisms of metabolic disease-induced myocardial injury.

Summary: The routine need for myonuclear turnover in skeletal muscle, together with more sporadic demands for hypertrophy and repair, are performed by resident muscle stem cells called satellite cells. Muscular dystrophies are characterized by muscle wasting, stimulating chronic repair/regeneration by satellite cells. Here, we derived and validated transcriptomic signatures for satellite cells, myoblasts/myocytes, and myonuclei using publicly available murine single cell RNA-Sequencing data. Our signatures distinguished disease from control in transcriptomic data from several muscular dystrophies including facioscapulohumeral muscular dystrophy (FSHD), Duchenne muscular dystrophy, and myotonic dystrophy type I. For FSHD, the expression of our gene signatures correlated with direct counts of satellite cells on muscle sections, as well as with increasing clinical and pathological severity. Thus, our gene signatures enable the investigation of myogenesis in bulk transcriptomic data from muscle biopsies. They also facilitate study of muscle regeneration in transcriptomic data from human muscle across health and disease.

Summary: The mechanisms governing autophagy of proteins and organelles have been well studied, but how other cytoplasmic components such as RNA and polysaccharides are degraded remains largely unknown. In this study, we examine autophagy of glycogen, a storage form of glucose. We find that cells accumulate glycogen in the cytoplasm during nitrogen starvation and that this carbohydrate is rarely observed within autophagosomes and autophagic bodies. However, sequestration of glycogen by autophagy is observed following prolonged nitrogen starvation. We identify a yet-uncharacterized open reading frame, Yil024c (herein Atg45), as encoding a cytosolic receptor protein that mediates autophagy of glycogen (glycophagy). Furthermore, we show that, during sporulation, Atg45 is highly expressed and is associated with an increase in glycophagy. Our results suggest that cells regulate glycophagic activity by controlling the expression level of Atg45.

Neurodevelopmental disorders (NDDs) are complex disorders with variable clinical features caused by a wide range of genetic variants which disrupt genes with pleiotropic effects. Model organisms allow for recapitulation of phenotypes related to the disorder and characterization of molecular mechanisms at varying throughput and resolution. Human induced pluripotent stem cells allow for evaluating patient-specific and cell-type-specific effects. The massively parallel reporter assay (MPRA) uses high-throughput sequencing to screen thousands of genomic fragments containing patient-specific noncoding mutations to quantify their regulatory effects. Single-cell RNA sequencing and its combination with CRISPR-based screens – such as CRISPR droplet sequencing (CROP-seq) and Perturb-seq – provide promising platforms to understand gene function during brain development. Neurodevelopmental disorders (NDDs) are associated with a wide range of clinical features, affecting multiple pathways involved in brain development and function. Recent advances in high-throughput sequencing have unveiled numerous genetic variants associated with NDDs, which further contribute to disease complexity and make it challenging to infer disease causation and underlying mechanisms. Herein, we review current strategies for dissecting the complexity of NDDs using model organisms, induced pluripotent stem cells, single-cell sequencing technologies, and massively parallel reporter assays. We further highlight single-cell CRISPR-based screening techniques that allow genomic investigation of cellular transcriptomes with high efficiency, accuracy, and throughput. Overall, we provide an integrated review of experimental approaches that can be applicable for investigating a broad range of complex disorders. [ABSTRACT FROM AUTHOR]

Symsagittifera roscoffensis forms a photosymbiotic relationship with the alga Tetraselmis convolutae within the intertidal zone. Juveniles lack algal symbionts at birth and acquire them from the environment. Requiring light for photosynthesis, they position themselves within the water column while also balancing the risk of being washed away. To understand their behavioural adaptations, we conducted experiments on their movement in response to algal cues (chemotaxis), light gradients (phototaxis), and mechanical vibrations. Aposymbiotic juveniles showed three times more positive displacement towards algae. Adults exhibited positive phototaxis but retreated from high light intensity. When introduced to a column with a light source, the worms remained just below the surface. In the mechanical vibration experiment, worms only descended when vibrations exceeded a threshold. These findings suggest that S. roscoffensis has chemotactic abilities crucial for acquiring algae and acquires light for photosynthesis while minimizing dispersal risk and photoinhibition, facilitating its life cycle in the intertidal zone. [ABSTRACT FROM AUTHOR]

Copyright of Caldasia is the property of Universidad Nacional de Colombia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)