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Nature Communications Jan 2024Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably...
Frogs are an ecologically diverse and phylogenetically ancient group of anuran amphibians that include important vertebrate cell and developmental model systems, notably the genus Xenopus. Here we report a high-quality reference genome sequence for the western clawed frog, Xenopus tropicalis, along with draft chromosome-scale sequences of three distantly related emerging model frog species, Eleutherodactylus coqui, Engystomops pustulosus, and Hymenochirus boettgeri. Frog chromosomes have remained remarkably stable since the Mesozoic Era, with limited Robertsonian (i.e., arm-preserving) translocations and end-to-end fusions found among the smaller chromosomes. Conservation of synteny includes conservation of centromere locations, marked by centromeric tandem repeats associated with Cenp-a binding surrounded by pericentromeric LINE/L1 elements. This work explores the structure of chromosomes across frogs, using a dense meiotic linkage map for X. tropicalis and chromatin conformation capture (Hi-C) data for all species. Abundant satellite repeats occupy the unusually long (~20 megabase) terminal regions of each chromosome that coincide with high rates of recombination. Both embryonic and differentiated cells show reproducible associations of centromeric chromatin and of telomeres, reflecting a Rabl-like configuration. Our comparative analyses reveal 13 conserved ancestral anuran chromosomes from which contemporary frog genomes were constructed.
Topics: Animals; Chromatin; Evolution, Molecular; Genome; Anura; Xenopus; Centromere
PubMed: 38233380
DOI: 10.1038/s41467-023-43012-9 -
Heliyon Apr 2024Given their pervasiveness in the environment, particularly in aquatic ecosystems, plastics are posing a growing concern worldwide. Many vertebrates and invertebrates in... (Review)
Review
Given their pervasiveness in the environment, particularly in aquatic ecosystems, plastics are posing a growing concern worldwide. Many vertebrates and invertebrates in marine, freshwater, and terrestrial ecosystems exhibit microplastic (MP) uptake and accumulation. Some studies have indicated the fatal impacts of MPs on animals and their possible transfer through food chains. Thus, it is crucial to study MP pollution and its impacts on environment-sensitive and globally threatened animal groups, such as amphibians, which also play an important role in the energy transfer between ecosystems. Unfortunately, research in this field is lacking and sources of organized information are also scarce. Hence, we systematically reviewed published literature on MPs in amphibians to fill the existing knowledge gap. Our review revealed that most of the previous studies have focused on MP bioaccumulation in amphibians, whereas, only a few research highlighted its impacts. We found that more than 80% of the studied species exhibited MP accumulation. MPs were reported to persist in different organs for a long time and get transferred to other trophic levels. They can also exhibit cytotoxic and mutagenic effects and may have fatal impacts. Moreover, they can increase the disease susceptibility of amphibians. Our study concludes the MPs as a potential threat to amphibians and urges increasing the scope and frequency of research on MP pollution and its impacts on this vulnerable animal group. We also provide a generalized method for studying MPs in amphibians with future perspectives and research directions. Our study is significant for extending the knowledge of MPs and their impacts on amphibians and guiding prospective research.
PubMed: 38560268
DOI: 10.1016/j.heliyon.2024.e28220 -
Anais Da Academia Brasileira de Ciencias 2024Fishermen-hunter-gatherers of sambaquis (Brazilian shell mounds) had an intimate affinity with marine-coastal environments, where they exploited a great variety of fish...
Fishermen-hunter-gatherers of sambaquis (Brazilian shell mounds) had an intimate affinity with marine-coastal environments, where they exploited a great variety of fish and mollusks that comprise the best documented fauna from sambaquis. However, other groups of animals as mammals, birds, reptiles, and amphibians are also present in these sites, but are relatively less studied. This paper is the first one focused exclusively on the Tetrapoda biodiversity of sambaquis and aimed to identify tetrapods of ten sites from southern Brazil. We present a faunal inventory and data regarding animal capture and environmental exploitation. We identified the specimens anatomically and taxonomically, analyzed them concerning fragmentation, and quantified the data for the number of identified specimens (NISP) and minimum number of individuals (MNI). Despite the high degree of fragmentation of remains, we identified 46 taxa. As expected, most were from marine animals: cetaceans (total NISP = 2,568 and MNI = 27), otariids (total NISP = 248 and MNI = 32), and seabirds (total NISP = 65 and MNI = 23), indicating great relevance of marine tetrapod fauna as a resource for sambaqui builders (79.39% of NISP). We thus document the close bond between fishermen-hunter-gatherers of sambaquis and the marine tetrapods in southern Brazil.
Topics: Animals; Brazil; Biodiversity; Birds; Reptiles; Cetacea
PubMed: 38747839
DOI: 10.1590/0001-3765202420230901 -
Communications Biology Jul 2023Metazoan genomes are duplicated by the coordinated activation of clusters of replication origins at different times during S phase, but the underlying mechanisms of this...
Metazoan genomes are duplicated by the coordinated activation of clusters of replication origins at different times during S phase, but the underlying mechanisms of this temporal program remain unclear during early development. Rif1, a key replication timing factor, inhibits origin firing by recruiting protein phosphatase 1 (PP1) to chromatin counteracting S phase kinases. We have previously described that Rif1 depletion accelerates early Xenopus laevis embryonic cell cycles. Here, we find that in the absence of Rif1, patterns of replication foci change along with the acceleration of replication cluster activation. However, initiations increase only moderately inside active clusters. Our numerical simulations suggest that the absence of Rif1 compresses the temporal program towards more homogeneity and increases the availability of limiting initiation factors. We experimentally demonstrate that Rif1 depletion increases the chromatin-binding of the S phase kinase Cdc7/Drf1, the firing factors Treslin, MTBP, Cdc45, RecQL4, and the phosphorylation of both Treslin and MTBP. We show that Rif1 globally, but not locally, restrains the replication program in early embryos, possibly by inhibiting or excluding replication factors from chromatin.
Topics: Animals; Cell Cycle; Cell Cycle Proteins; Chromatin; Replication Origin; Xenopus laevis
PubMed: 37516798
DOI: 10.1038/s42003-023-05172-8 -
International Journal of Molecular... Sep 2023Cancer is one of the major diseases that seriously threaten human life. Traditional anticancer therapies have achieved remarkable efficacy but have also some unavoidable... (Review)
Review
Cancer is one of the major diseases that seriously threaten human life. Traditional anticancer therapies have achieved remarkable efficacy but have also some unavoidable side effects. Therefore, more and more research focuses on highly effective and less-toxic anticancer substances of natural origin. Amphibian skin is rich in active substances such as biogenic amines, alkaloids, alcohols, esters, peptides, and proteins, which play a role in various aspects such as anti-inflammatory, immunomodulatory, and anticancer functions, and are one of the critical sources of anticancer substances. Currently, a range of natural anticancer substances are known from various amphibians. This paper aims to review the physicochemical properties, anticancer mechanisms, and potential applications of these peptides and proteins to advance the identification and therapeutic use of natural anticancer agents.
Topics: Humans; Animals; Peptides; Amphibians; Drug-Related Side Effects and Adverse Reactions; Esters; Immunomodulation
PubMed: 37762285
DOI: 10.3390/ijms241813985 -
Journal of Thermal Biology Oct 2023Increases in ultraviolet radiation (UVR) correlate spatially and temporally with global amphibian population declines and interact with other stressors such as disease...
Increases in ultraviolet radiation (UVR) correlate spatially and temporally with global amphibian population declines and interact with other stressors such as disease and temperature. Declines have largely occurred in high-altitude areas associated with greater UVR and cooler temperatures. UVR is a powerful mutagenic harming organisms largely by damaging DNA. When acutely exposed to UVR at cool temperatures, amphibian larvae have increased levels of DNA damage. Amphibians may compensate for the depressive effects of temperature on DNA damage through acclimatisation, but it is unknown whether they have this capacity. We reared striped marsh frog larvae (Limnodynastes peronii) in warm (25 °C) and cool (15 °C) temperatures under a low or moderate daily dose of UVR (10 and 40 μW cm UV-B for 1 h at midday, respectively) for 18-20 days and then measured DNA damage resulting from an acute high UVR dose (80 μW cm UV-B for 1.5 h) at a range of temperatures (10, 15, 20, 25, and 30 °C). Larvae acclimated to 15 °C and exposed to UVR at 15 °C completely compensated UVR-induced DNA damage compared with 25 °C acclimated larvae exposed to UVR at 25 °C. Additionally, warm-acclimated larvae had higher DNA damage than cold-acclimated larvae across test temperatures, which indicated a cost of living in warmer temperatures. Larvae reared under elevated UVR levels showed no evidence of UVR acclimation resulting in lower DNA damage following high UVR exposure. Our finding that thermal acclimation in L. peronii larvae compensated UVR-induced DNA damage at low temperatures suggested that aquatic ectotherms living in cool temperatures may be more resilient to high UVR than previously realised. We suggested individuals or species with less capacity for thermal acclimation of DNA repair mechanisms may be more at risk if exposed to changing thermal and UVR exposure regimes.
PubMed: 37717403
DOI: 10.1016/j.jtherbio.2023.103711 -
Scientific Reports Nov 2023The major evolutionary transition from fish to amphibian included Late Devonian tetrapods that were neither fish nor amphibian. They had thick necks and small limbs with...
The major evolutionary transition from fish to amphibian included Late Devonian tetrapods that were neither fish nor amphibian. They had thick necks and small limbs with many digits on elongate flexuous bodies more suitable for water than land. Habitats of Devonian tetrapods are of interest in assessing selective pressures on their later evolution for land within three proposed habitats: 1, tidal flats, 2, desert ponds, and 3, woodland streams. Here we assess paleoenvironments of the Late Devonian tetrapod Sinostega from paleosols in Shixiagou Canyon near Zhongning, Ningxia, China. Fossil tetrapods, fish, molluscs, and plants of the Zhongning Formation are associated with different kinds of paleosols, representing early successional vegetation, seasonal wetlands, desert shrublands, and riparian woodlands, and paleoclimates ranging from semiarid moderately seasonal to monsoonal subhumid. The tetrapod Sinostega was found in a paleochannel of a meandering stream below a deep-calcic paleosol supporting well drained progymnosperm woodland in a monsoonal subhumid paleoclimate. This habitat is similar to that of the tetrapods Densignathus, Hynerpeton, and an indeterminate watcheeriid from Pennsylvania, USA. Chinese and Pennsylvanian Late Devonian tetrapods lived in productive woodland streams, choked with woody debris as a refuge from large predators. Habitats of other Devonian tetrapods have yet to be assessed from studies of associated paleosols as evidence for their ancient climate and vegetation.
Topics: Animals; Biological Evolution; Fossils; Fishes; Amphibians; Ecosystem
PubMed: 37990036
DOI: 10.1038/s41598-023-47728-y -
Conservation Physiology 2023Infectious diseases are a major driver of the global amphibian decline. In addition, many factors, including genetics, stress, pollution, and climate change can...
Infectious diseases are a major driver of the global amphibian decline. In addition, many factors, including genetics, stress, pollution, and climate change can influence the response to pathogens. Therefore, it is important to be able to evaluate amphibian immunity in the laboratory and in the field. The phytohemagglutinin (PHA) assay is an inexpensive and relatively non-invasive tool that has been used extensively to assess immunocompetence, especially in birds, and more recently in amphibians. However, there is substantial variation in experimental methodology among amphibian PHA studies in terms of species and life stages, PHA doses and injection sites, and use of experimental controls. Here, we compile and compare all known PHA studies in amphibians to identify knowledge gaps and develop best practices for future work. We found that research has only been conducted on a limited number of species, which may not reflect the diversity of amphibians. There is also a lack of validation studies in most species, so that doses and timing of PHA injection and subsequent swelling measurements may not effectively evaluate immunocompetence. Based on these and other findings, we put forward a set of recommendations to make future PHA studies more consistent and improve the ability to utilize this assay in wild populations, where immune surveillance is greatly needed.
PubMed: 38090122
DOI: 10.1093/conphys/coad090 -
Global Change Biology Sep 2023Shifts between native and alien climatic niches pose a major challenge for predicting biological invasions. This is particularly true for insular species because...
Shifts between native and alien climatic niches pose a major challenge for predicting biological invasions. This is particularly true for insular species because geophysical barriers could constrain the realization of their fundamental niches, which may lead to underestimates of their invasion potential. To investigate this idea, we estimated the frequency of shifts between native and alien climatic niches and the magnitude of climatic mismatches using 80,148 alien occurrences of 46 endemic insular amphibian, reptile, and bird species. Then, we assessed the influence of nine potential predictors on climatic mismatches across taxa, based on species' characteristics, native range physical characteristics, and alien range properties. We found that climatic mismatch is common during invasions of endemic insular birds and reptiles: 78.3% and 55.1% of their respective alien records occurred outside of the environmental space of species' native climatic niche. In comparison, climatic mismatch was evident for only 16.2% of the amphibian invasions analyzed. Several predictors significantly explained climatic mismatch, and these varied among taxonomic groups. For amphibians, only native range size was associated with climatic mismatch. For reptiles, the magnitude of climatic mismatch was higher for species with narrow native altitudinal ranges, occurring in topographically complex or less remote islands, as well as for species with larger distances between their native and alien ranges. For birds, climatic mismatch was significantly larger for invasions on continents with higher phylogenetic diversity of the recipient community, and when the invader was more evolutionarily distinct. Our findings highlight that apparently common niche shifts of insular species may jeopardize our ability to forecast their potential invasions using correlative methods based on climatic variables. Also, we show which factors provide additional insights on the actual invasion potential of insular endemic amphibians, reptiles, and birds.
Topics: Animals; Introduced Species; Ecosystem; Phylogeny; Amphibians; Reptiles; Birds
PubMed: 37395619
DOI: 10.1111/gcb.16849 -
The Journal of Biological Chemistry Dec 2023The collagen IV (Col-IV) scaffold, the major constituent of the glomerular basement membrane (GBM), is a critical component of the kidney glomerular filtration barrier.... (Comparative Study)
Comparative Study
The collagen IV (Col-IV) scaffold, the major constituent of the glomerular basement membrane (GBM), is a critical component of the kidney glomerular filtration barrier. In Alport syndrome, affecting millions of people worldwide, over two thousand genetic variants occur in the COL4A3, COL4A4, and COL4A5 genes that encode the Col-IV scaffold. Variants cause loss of scaffold, a suprastructure that tethers macromolecules, from the GBM or assembly of a defective scaffold, causing hematuria in nearly all cases, proteinuria, and often progressive kidney failure. How these variants cause proteinuria remains an enigma. In a companion paper, we found that the evolutionary emergence of the COL4A3, COL4A4, COL4A5, and COL4A6 genes coincided with kidney emergence in hagfish and shark and that the COL4A3 and COL4A4 were lost in amphibians. These findings opened an experimental window to gain insights into functionality of the Col-IV scaffold. Here, using tissue staining, biochemical analysis and TEM, we characterized the scaffold chain arrangements and the morphology of the GBM of hagfish, shark, frog, and salamander. We found that α4 and α5 chains in shark GBM and α1 and α5 chains in amphibian GBM are spatially separated. Scaffolds are distinct from one another and from the mammalian Col-IV scaffold, and the GBM morphologies are distinct. Our findings revealed that the evolutionary emergence of the Col-IV scaffold enabled the genesis of a compact GBM that functions as an ultrafilter. Findings shed light on the conundrum, defined decades ago, whether the GBM or slit diaphragm is the primary filter.
Topics: Animals; Anura; Collagen Type IV; Glomerular Basement Membrane; Hagfishes; Mammals; Sharks; Species Specificity; Urodela
PubMed: 37977222
DOI: 10.1016/j.jbc.2023.105459