Host-microbiota interactions play a critical role in the hosts\' biology, and thus, it is crucial to elucidate the mechanisms that shape gut microbial communities. We leveraged threespine stickleback fish (Gasterosteus aculeatus) as a model system to investigate the contribution of host and environmental factors to gut microbiota variation. These fish offer a unique opportunity for experiments in naturalistic conditions; we reared benthic and limnetic ecotypes from three different lakes in experimental ponds, allowing us to assess the relative effects of shared environment (pond), geographic origin (lake-of-origin), trophic ecology and genetics (ecotype) and biological sex on gut microbiota α- and β-diversity. Host ecotype had the strongest influence on α-diversity, with benthic fish exhibiting higher diversity than limnetic fish, followed by the rearing environment. β-diversity was primarily shaped by rearing environment, followed by host ecotype, indicating that environmental factors play a crucial role in determining gut microbiota composition. Furthermore, numerous bacterial orders were differentially abundant across ponds, underlining the substantial contribution of environmental factors to gut microbiota variation. Our study illustrates the complex interplay between environmental and host ecological or genetic factors in shaping the stickleback gut microbiota and highlights the value of experiments conducted under naturalistic conditions for understanding gut microbiota dynamics.

Glucose has important roles in the development of zebrafish, the vertebrate animal model; however, in most oviparous animals, the amount of maternally provided glucose in the yolk is scarce. For these reasons, developing animals need some ways to supplement glucose. Recently, it was found that developing zebrafish, a teleost fish, undergo gluconeogenesis in the yolk syncytial layer (YSL), an extraembryonic tissue that surrounds the yolk. However, teleost YSL is evolutionarily unique, and it is not clear how other vertebrates supplement glucose. In this study, we used cloudy catshark (or Torazame catshark), an elasmobranch species which possesses a YSL-like tissue during development, and sought for possible gluconeogenic activities in this tissue. In their yolk sac, glucose increased, and our isotope tracking analysis detected gluconeogenic activities with glycerol most preferred substrate. In addition, many of gluconeogenic genes were expressed at the YSL-like tissue, suggesting that cloudy catshark engages in gluconeogenesis in this tissue. The gluconeogenesis in teleost YSL and a similar tissue in elasmobranch species implies conserved mechanisms of yolk metabolism between these two lineages. Future studies on other vertebrate taxa will be helpful to understand the evolutionary changes in the modes of yolk metabolism that vertebrates have experienced.

Microplastics and nanoplastics (MNPs) have received increasing attention due to their high detection rates in human matrices and adverse health implications. However, the toxicity of MNPs on embryo/fetal development following maternal exposure remains largely unexplored. Zebrafish, sharing genetic similarities with human, boast a shorter life cycle, rapid embryonic development, and the availability of many transgenic strains, is a suitable model for environmental toxicology studies. This review comprehensively explores the existing research on the impacts of MNPs on zebrafish embryo development. MNPs exposure induces a wide array of toxic effects, encompassing neurodevelopmental toxicity, immunotoxicity, gastrointestinal effects, microbiota dysbiosis, cardiac dysfunctions, vascular toxicity, and metabolic imbalances. Moreover, MNPs disrupt the balance between reactive oxygen species (ROS) production and antioxidant capacity, culminating in oxidative damage and apoptosis. This study also offers insight into the current omics- and multi-omics based approaches in MNPs research, which greatly expedite the discovery of biochemical or metabolic pathways, and molecular mechanisms underlying MNPs exposure. Additionally, this review proposes a preliminary adverse outcome pathway framework to predict developmental toxicity caused by MNPs. It provides a comprehensive overview of pathways, facilitating a clearer understanding of the exposure and toxicity of MNPs, from molecular effects to adverse outcomes. The compiled data in this review provide a better understanding for MNPs effects on early life development, with the goal of increasing awareness about the risks posed to pregnant women by MNPs exposure and its potential impact on the health of their future generations.

DNA barcoding employs standard molecular techniques (e.g., DNA extraction, PCR, and Sanger sequencing) to taxonomically identify biological samples. While DNA barcoding is a useful experimental workflow for in-class active learning exercises, extracting DNA from diverse sample types in a time and cost-effective manner can be challenging in a classroom setting. Here, we provide two time and cost-effective methods that have been used by novice students to successfully extract DNA from a variety of animal, fungal, algal, and plant tissues for DNA barcoding.

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as \"defaunation.\" This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data.

Horizontal transfer of transposable elements (HTT) has been reported across many species and the impact of such events on genome structure and function has been well described. However, few studies have focused on reptilian genomes, especially HTT events in Testudines (turtles). Here, as a consequence of investigating the repetitive content of Malaclemys terrapin terrapin (Diamondback turtle) we found a high similarity DNA transposon, annotated in RepBase as hAT-6_XT, shared between other turtle species, ray-finned fishes, and a frog. hAT-6_XT was notably absent in reptilian taxa closely related to turtles, such as crocodiles and birds. Successful invasion of DNA transposons into new genomes requires the conservation of specific residues in the encoded transposase, and through structural analysis, these residues were identified indicating some retention of functional transposition activity. We document six recent independent HTT events of a DNA transposon in turtles, which are known to have a low genomic evolutionary rate and ancient repeats.

Nocturnal activity of tropical otters is rarely reported. To date no studies have documented den use by sympatric giant (Pteronura brasiliensis) and neotropical otters (Lontra longicaudis). We used camera-traps to monitor den use by sympatric otters along an equatorial Amazonian river. Camera-traps provided evidence that giant otters were more nocturnal around dens than sympatric neotropical otters. Nocturnal activity was recorded in 11% of giant otter photos (n = 14 of 125 photos), but was recorded only once for neotropical otters. Den use by giant and neotropical otters overlapped spatially and temporally but not concurrently. We hypothesize that previously reported nocturnal activity in neotropical otters is facilitated by the absence or low density of giant otters. Our results also underscore the need to use complementary techniques together with den counts for monitoring otters as sympatric species can use the same dens.

Androgen(s) is one of the sex steroids that are involved in many physiological phenomena of vertebrate species. Although androgens were originally identified as male sex hormones, it is well known now that they are also essential in females. As in the case of other steroid hormones, androgen is produced from cholesterol through serial enzymatic reactions. Although testis is a major tissue to produce androgens in all species, androgens are also produced in ovary and adrenal (interrenal tissue). Testosterone is the most common and famous androgen. It represents a major androgen both in males and females of almost vertebrate species. In addition, testosterone is a precursor for producing significant androgens such as11-ketotestosterone, 5α-dihydrotestosterone, 11-ketodihydrotestosterones and 15α-hydroxytestosterone in a species- or sex-dependent manner for their homeostasis. In this article, we will review the significance and characteristics of these androgens, following a description of the history of testosterone discovery and its synthetic pathways.

In eukaryotes, cytosine methylation is a primary heritable epigenetic modification of the genome that regulates many cellular processes. In invertebrate, methylated cytosine generally located on specific genomic elements (e.g., gene bodies and silenced repetitive elements) to show a \"mosaic\" pattern. While in jawed vertebrate (teleost and tetrapod), highly methylated cytosine located genome-wide but only absence at regulatory regions (e.g., promoter and enhancer). Many studies imply that the evolution of DNA methylation reprogramming may have helped the transition from invertebrates to jawed vertebrates, but the detail remains largely elusive. In this study, we used the whole-genome bisulfite-sequencing technology to investigate the genome-wide methylation in three tissues (heart, muscle, and sperm) from the sea lamprey, an extant agnathan (jawless) vertebrate. Strikingly, we found that the methylation level of the sea lamprey is very similar to that in sea urchin (a deuterostome) and sea squirt (a chordate) invertebrates. In sum, the global pattern in sea lamprey is intermediate methylation level (around 30%), that is higher than methylation level in the genomes of pre-bilaterians and protostomes (1%-10%), but lower than methylation level appeared in jawed vertebrates (around 70%, teleost and tetrapod). We anticipate that, in addition to genetic dynamics such as genome duplications, epigenetic dynamics such as global methylation reprograming was also orchestrated toward the emergence and evolution of vertebrates.

With an increase in the progression of research and development in the medical field, the experimental use of animals for the efficacy and safety testing of pharmaceuticals is on rise. Every year, millions of animals are used for experimental testing during which these suffer from pain and are then eventually sacrificed. Besides bioethical issues, animal experimentation is associated with many disadvantages like high cost, the requirement of skilled manpower, approval, and is time-consuming. Therefore, attempts have been made by researchers to design and develop a number of alternative methods that could bypass animal experiments. These methods not only give accurate results but can also save lives of millions of animals annually. Research techniques, including computer and robotics together with molecular biology techniques, are applied to discover new methods to replace animal testing. Several alternative methods are discussed in this review. Some of these methods can predict the behavior of drugs accurately and are as reliable as in-vivo animal models. Furthermore, these alternative methods offer a variety of advantages over experimental animals. However, there is still a great need to discover and develop new, accurate, and reliable methods to replace experimental animals.