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At least 55 records · Page 3

Deeply conserved synteny resolves early events in vertebrate evolution

Although it is widely believed that early vertebrate evolution was shaped by ancient whole-genome duplications, the number, timing and mechanism of these events remain elusive. Here, we infer the history of vertebrates through genomic comparisons with a new chromosome-scale sequence of the invertebrate chordate amphioxus. We show how the karyotypes of amphioxus and diverse vertebrates are derived from 17 ancestral chordate linkage groups (and 19 ancestral bilaterian groups) by fusion, rearrangement and duplication. We resolve two distinct ancient duplications based on patterns of chromosomal conserved synteny. All extant vertebrates share the first duplication, which occurred in the mid/late Cambrian by autotetraploidization (that is, direct genome doubling). In contrast, the second duplication is found only in jawed vertebrates and occurred in the mid–late Ordovician by allotetraploidization (that is, genome duplication following interspecific hybridization) from two now-extinct progenitors. This complex genomic history parallels the diversification of vertebrate lineages in the fossil record.

59 BASIC BIOLOGICAL SCIENCES↗

Carotenoid cleavage enzymes evolved convergently to generate the visual chromophore

The retinal light response in animals originates from the photoisomerization of an opsin-coupled 11-cis-retinaldehyde chromophore. This visual chromophore is enzymatically produced through the action of carotenoid cleavage dioxygenases. Vertebrates require two carotenoid cleavage dioxygenases, β-carotene oxygenase 1 and retinal pigment epithelium 65 (RPE65), to form 11-cis-retinaldehyde from carotenoid substrates, whereas invertebrates such as insects use a single enzyme known as Neither Inactivation Nor Afterpotential B (NinaB). RPE65 and NinaB couple trans–cis isomerization with hydrolysis and oxygenation, respectively, but the mechanistic relationship of their isomerase activities remains unknown. Here we report the structure of NinaB, revealing details of its active site architecture and mode of membrane binding. Structure-guided mutagenesis studies identify a residue cluster deep within the NinaB substrate-binding cleft that controls its isomerization activity. Our data demonstrate that isomerization activity is mediated by distinct active site regions in NinaB and RPE65—an evolutionary convergence that deepens our understanding of visual system diversity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Influence of aluminum incorporation and aqueous conditions on metal ion release of high-Ni transition metal oxide nanomaterials

Developing a materials perspective of how to control the degradation and negative impact of complex metal oxides requires an integrated understanding of how these nanomaterials transform in the environment and interact with biological systems. Doping with aluminum is known to stabilize oxide materials, but has not been assessed cohesively from synthesis to environmental fate and biological impact. In the present study, the influence of aluminum doping on metal ion release from transition metal oxides was investigated by comparing aqueous transformations of lithium nickel cobalt aluminum oxide (LiNi 0.82 Co 0.15 Al 0.03 O 2 ; NCA) and lithium nickel cobalt oxide (LiNi 0.80 Co 0.20 O 2 ; NC) nanoparticles and by calculating the energetics of metal release using a density functional theory (DFT) and thermodynamics method. Two model environmental organisms were used to assess biological impact, and metal ion release was compared for NCA and NC nanoparticles incubated in their respective growth media: moderately hard reconstituted water (MHRW) for the freshwater invertebrate Daphnia magna (D. magna) and minimal growth medium for the Gram-negative bacterium Shewanella oneidensis MR-1 (S. oneidensis). Further, the amount of metal ions released was reduced for NCA compared to NC in MHRW, which correlated to changes in the modeled energetics of release upon Al substitution in the lattice. In minimal medium, metal ion release was approximately an order of magnitude higher compared to MHRW and was similar to the stoichiometry of the bulk nanoparticles for both NCA and NC. Interpretation of the release profiles and modeling indicated that the increase in total metal ion release and the reduced influence of Al doping arises from lactate complexation of metal ions in solution. The relative biological impacts of NC and NCA exposure for both S. oneidensis and D. magna were consistent with the metal release trends observed for minimal medium and MHRW, respectively. Together, these results demonstrate how a combined experimental and computational approach provides valuable insight into the aqueous transformations and biological impacts of complex metal oxide nanoparticles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The myosin interacting-heads motif present in live tarantula muscle explains tetanic and posttetanic phosphorylation mechanisms

Striated muscle contraction involves sliding of actin thin filaments along myosin thick filaments, controlled by calcium through thin filament activation. In relaxed muscle, the two heads of myosin interact with each other on the filament surface to form the interacting-heads motif (IHM). A key question is how both heads are released from the surface to approach actin and produce force. Here we used time-resolved synchrotron X-ray diffraction to study tarantula muscle before and after tetani. The patterns showed that the IHM is present in live relaxed muscle. Tetanic contraction produced only a very small backbone elongation, implying that mechanosensing—proposed in vertebrate muscle—is not of primary importance in tarantula. Rather, thick filament activation results from increases in myosin phosphorylation that release a fraction of heads to produce force, with the remainder staying in the ordered IHM configuration. After the tetanus, the released heads slowly recover toward the resting, helically ordered state. During this time the released heads remain close to actin and can quickly rebind, enhancing the force produced by posttetanic twitches, structurally explaining posttetanic potentiation. Taken together, these results suggest that, in addition to stretch activation in insects, two other mechanisms for thick filament activation have evolved to disrupt the interactions that establish the relaxed helices of IHMs: one in invertebrates, by either regulatory light-chain phosphorylation (as in arthropods) or Ca 2+ -binding (in mollusks, lacking phosphorylation), and another in vertebrates, by mechanosensing.

59 BASIC BIOLOGICAL SCIENCES↗

Evolution of single gyroid photonic crystals in bird feathers

Vivid, saturated structural colors are conspicuous and important features of many animals. A rich diversity of three-dimensional periodic photonic nanostructures is found in the chitinaceous exoskeletons of invertebrates. Three-dimensional photonic nanostructures have been described in bird feathers, but they are typically quasi-ordered. Here, we report bicontinuous single gyroid β-keratin and air photonic crystal networks in the feather barbs of blue-winged leafbirds ( Chloropsis cochinchinensis sensu lato ), which have evolved from ancestral quasi-ordered channel-type nanostructures. Self-assembled avian photonic crystals may serve as inspiration for multifunctional applications, as they suggest efficient, alternative routes to single gyroid synthesis at optical length scales, which has been experimentally elusive.

59 BASIC BIOLOGICAL SCIENCES↗

Synapse-specific catecholaminergic modulation of neuronal glutamate release

Norepinephrine in vertebrates and its invertebrate analog, octopamine, regulate the activity of neural circuits. We find that, when hungry,Drosophilalarvae switch activity in type II octopaminergic motor neurons (MNs) to high-frequency bursts, which coincide with locomotion-driving bursts in type I glutamatergic MNs that converge on the same muscles. Optical quantal analysis across hundreds of synapses simultaneously reveals that octopamine potentiates glutamate release by tonic type Ib MNs, but not phasic type Is MNs, and occurs via the G q -coupled octopamine receptor (OAMB). OAMB is more abundant in type Ib terminals and acts through diacylglycerol and its target Unc13A, a key component of the glutamate release machinery. Potentiation varies significantly—by up to 1,000%—across synapses of a single Ib axon, with synaptic Unc13A levels determining both release probability and potentiation. We propose that a dual molecular mechanism—an upstream neuromodulator receptor and a downstream transmitter release controller—fine-tunes catecholaminergic modulation so that strong tonic synapses exhibit large potentiation, while weaker tonic and all phasic synapses maintain consistency, yielding a sophisticated regulation of locomotor behavior.

Science & Technology - Other Topics↗

Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system

The soft corals (Cnidaria, Octocorallia), a diverse group of colonial marine invertebrates, can reversibly tune their body stiffness in response to external stimuli. This capability is attributed to their dynamic skeletal systems, which consist of thousands of mineralized skeletal elements, called sclerites, embedded within a gel-like matrix that swells/deswells and unjams/jams the sclerites, thus modulating skeletal stiffness. While sclerite morphology is widely used for species identification, its role in the mechanical performance of a soft coral’s skeletal system is largely unknown. Here, we investigated structure-jamming relationships in sclerite-based skeletal architectures using the red gorgonian octocoral Leptogorgia chilensis as a model system. The sclerites of L. chilensis exhibit a shaft-like geometry with two axial branches and two sets of triradiate side branches, which are aligned with the crystallographic symmetry of the constituent magnesium-containing calcite. By combining multiscale three-dimensional (3D) structural characterization, parametric geometrical modeling, 3D printing, mechanical testing, and discrete element simulations, we demonstrate how sclerite geometry achieves a balanced jamming performance in terms of stiffness, weight, strength, and fracture resistance in comparison to alternative geometries parametrically modified from the native sclerites (e.g., changes in the length and number of side branches). Here, we also found that these performance metrics are achieved through the effective interlocking among side and axial branches, which is further enhanced by the fractal-like microscopic spikes on the branch tips. The findings in this natural jamming system offer insights for designing synthetic mechanotunable material architectures for a wide range of applications, from soft robotics to mechanical dampeners.

36 MATERIALS SCIENCE↗

Dynamic zinc fluxes regulate meiotic progression in Caenorhabditis elegans

Abstract Zinc influx and efflux events are essential for meiotic progression in oocytes of several mammalian and amphibian species, but it is less clear whether this evolutionary conservation of zinc signals is also important in late-stage germline development in invertebrates. Using quantitative, single cell elemental mapping methods, we find that Caenorhabditis elegans oocytes undergo significant stage-dependent fluctuations in total zinc content, rising by over sevenfold from Prophase I through the beginning of mitotic divisions in the embryo. Live imaging of the rapid cell cycle progression in C. elegans enables us to follow changes in labile zinc pools across meiosis and mitosis in single embryo. We find a dynamic increase in labile zinc prior to fertilization that then decreases from Anaphase II through pronuclear fusion and relocalizes to the eggshell. Disruption of these zinc fluxes blocks extrusion of the second polar body, leading to a range of mitotic defects. We conclude that spatial temporal zinc fluxes are necessary for meiotic progression in C. elegans and are a conserved feature of germ cell development in a broad cross section of metazoa.

59 BASIC BIOLOGICAL SCIENCES↗

Accumulation of trace elements in soil and fauna within a site historically contaminated with coal combustion residues

Legacy contaminants tied to energy production are a worldwide concern. Coal combustion residues (CCRs) contain high concentrations of potentially toxic trace elements such as arsenic (As), mercury (Hg), and selenium (Se), which can persist for decades after initial contamination. Coal combustion residue disposal methods, including aquatic settling basins and landfills, can facilitate environmental exposure through intentional and accidental releases. Wildlife exposed to CCRs can experience numerous deleterious effects, such as on development, reproduction, and survival. In the current study, we quantified and compared concentrations of As, Hg, Se, and strontium (Sr) within soils and target fauna (three vertebrate and three invertebrate taxa) from a CCR-contaminated site and a reference site within the U.S. Department of Energy’s Savannah River Site, South Carolina, United States. Our objectives were to (1) compare current concentrations of tested elements in soil and resident fauna to levels from our reference site, (2) assess natural attenuation of elements in soils by comparing current concentrations to historic levels, and (3) evaluate the biomagnification potential of the elements measured via body burden and trophic position correlations among fauna. Here, element concentrations were higher in contaminated soils than reference soils; however, concentrations in 2022 were unchanged from concentrations measured in 2003, suggesting no natural attenuation of tested elements. Additionally, target fauna had elevated As, Se, and Sr levels in comparison to reference samples. A positive correlation was observed in southern toads between Sr concentrations and trophic position, as assessed by nitrogen stable isotope ratios, suggesting potential for biomagnification of Sr within our study system. Collectively, our results demonstrate that legacy contaminants are still present and bioaccumulate in a diversity of taxa in a CCR-contaminated site that has not received effluents in more than 50 years, suggesting monitoring programs in CCR-contaminated sites should be maintained long term in the absence of remediation.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

Involvement of the Streptococcus mutans PgfE and GalE 4-epimerases in protein glycosylation, carbon metabolism, and cell division

Streptococcus mutans is a key pathogen associated with dental caries and is often implicated in infective endocarditis. This organism forms robust biofilms on tooth surfaces and can use collagen-binding proteins (CBPs) to efficiently colonize collagenous substrates, including dentin and heart valves. One of the best characterized CBPs of S. mutans is Cnm, which contributes to adhesion and invasion of oral epithelial and heart endothelial cells. These virulence properties were subsequently linked to post-translational modification (PTM) of the Cnm threonine-rich repeat region by the Pgf glycosylation machinery, which consists of 4 enzymes: PgfS, PgfM1, PgfE, and PgfM2. Inactivation of the S. mutans pgf genes leads to decreased collagen binding, reduced invasion of human coronary artery endothelial cells, and attenuated virulence in the Galleria mellonella invertebrate model. The present study aimed to better understand Cnm glycosylation and characterize the predicted 4-epimerase, PgfE. Using a truncated Cnm variant containing only 2 threonine-rich repeats, mass spectrometric analysis revealed extensive glycosylation with HexNAc2. Compositional analysis, complemented with lectin blotting, identified the HexNAc2 moieties as GlcNAc and GalNAc. Comparison of PgfE with the other S. mutans 4-epimerase GalE through structural modeling, nuclear magnetic resonance, and capillary electrophoresis demonstrated that GalE is a UDP-Glc-4-epimerase, while PgfE is a GlcNAc-4-epimerase. While PgfE exclusively participates in protein O-glycosylation, we found that GalE affects galactose metabolism and cell division. Furthermore, this study further emphasizes the importance of O-linked protein glycosylation and carbohydrate metabolism in S. mutans and identifies the PTM modifications of the key CBP, Cnm.

4-epimerases↗

Climate, food and humans predict communities of mammals in the United States

Abstract Aim The assembly of species into communities and ecoregions is the result of interacting factors that affect plant and animal distribution and abundance at biogeographic scales. Here, we empirically derive ecoregions for mammals to test whether human disturbance has become more important than climate and habitat resources in structuring communities. Location Conterminous United States. Time Period 2010–2021. Major Taxa Studied Twenty‐five species of mammals. Methods We analysed data from 25 mammal species recorded by camera traps at 6645 locations across the conterminous United States in a joint modelling framework to estimate relative abundance of each species. We then used a clustering analysis to describe 8 broad and 16 narrow mammal communities. Results Climate was the most important predictor of mammal abundance overall, while human population density and agriculture were less important, with mixed effects across species. Seed production by forests also predicted mammal abundance, especially hard‐mast tree species. The mammal community maps are similar to those of plants, with an east–west split driven by different dominant species of deer and squirrels. Communities vary along gradients of temperature in the east and precipitation in the west. Most fine‐scale mammal community boundaries aligned with established plant ecoregions and were distinguished by the presence of regional specialists or shifts in relative abundance of widespread species. Maps of potential ecosystem services provided by these communities suggest high herbivory in the Rocky Mountains and eastern forests, high invertebrate predation in the subtropical south and greater predation pressure on large vertebrates in the west. Main Conclusions Our results highlight the importance of climate to modern mammals and suggest that climate change will have strong impacts on these communities. Our new empirical approach to recognizing ecoregions has potential to be applied to expanded communities of mammals or other taxa.

Kays, Roland↗

Water Temperature, Prey Concentration and Salmonid Density Influence Daily Growth of Wild Juvenile Salmonids in Tributaries of the Upper Salmon River, Idaho ( USA )

ABSTRACT Theory, experiments and field studies indicate that the somatic growth rate of freshwater consumers is shaped by the individual, additive and multiplicative effects of multiple factors, including consumer size and condition, temperature, prey resources and biotic interactions. While our understanding of how these factors affect wild populations of freshwater consumers is improving, the topic remains poorly studied, especially with respect to mobile species. Here, we report on an 8‐year, seven‐stream ( n = 49 stream‐year combinations) observational study examining the individual and interactive effects of invertebrate prey concentration (F, mg/m 3 ), mean daily water temperature (T, °C) and juvenile Chinook salmon ( Oncorhynchus tshawytscha ) density (D, fish/100 m 2 ) on summer daily growth rates (%/d) of mobile, anadromous, juvenile Chinook salmon (age‐0+, n = 382) and sub‐yearling (age‐0+, n = 61) and yearling (age‐1+) steelhead trout ( O. mykiss , n = 70) rearing in cold (mean daily summer: 12.1°C, range: 4.2°C–16.7°C) mountain tributaries of the Salmon River basin in central Idaho (USA). AIC c model selection indicated that daily juvenile salmonid growth positively correlated with water temperature, prey biomass concentration, local juvenile Chinook density and the interaction between water temperature and food but with species and age‐specific differences. Water temperature was a covariate in all top‐ranked models, with daily growth (%/day) rate increasing (0.05%–0.23%/d) linearly with mean daily summer water temperature. In addition to a direct positive relationship with daily growth rate, there was evidence that prey concentration positively interacted with water temperature to accelerate daily growth (F × T). The positive relationship between juvenile salmonid daily growth rate and juvenile Chinook density is difficult to explain and could result from confounding factors. The individual success observed in these streams may contribute to population‐level benefits for the focal consumers, as prey‐rich, warm summers may result in larger individuals with higher energy reserves at the end of the summer/autumn growing season, contributing to improved overwinter survival. Our results, taken in combination with evidence from models, experiments and observational studies, have climate change implications. Current and predicted increases in water temperature will necessitate higher rates of prey consumption by aquatic ectothermic consumers to offset accelerated metabolic demands. Thus, to improve the resilience of mobile freshwater consumers in a warming climate, we suggest that natural resource managers not only consider physical and chemical habitat conditions but also biotic conditions, including the spatiotemporal quantity and quality of prey resources.

Kiffney, Peter. M. [Fish Ecology, Northwest Fisher↗

Vacant niches help predict invasion risk by birds

Abstract Aim If communities have a ceiling determining the number of species that can coexist, then the ability of alien species to establish at any given location should be related to the quantity of vacant niches available. We developed a new approach to estimate the extent to which niches are vacant and then explored the relationship between vacant niches and alien species. Location Global with focal tests in Europe and North America. Taxon Birds. Methods Drawing on a global classification of trophic structures for birds, we calculated a ‘vacant niche ratio’ metric to quantify the expected level of saturation (i.e. number of vacant niches) for each 1° × 1° grid cell globally, based on the difference between expected and observed numbers of bird species for all trophic guilds. Next, we used random forests to examine if the presence of plant‐invertivore (whose food source represents plants, seeds, fruits and invertebrates) and granivore alien bird species was associated with the vacant niche ratio across well‐sampled regions. Results In Europe, we found a significant relationship between alien species and vacant niches, with greater numbers of alien species being found in communities that offered greater numbers of vacant niches overall, and across habitat types. In North America, we found no significant relationship between plant‐invertivores and vacant niches, while for granivores, we found that areas with fewer vacant niches had greater numbers of alien species, especially in forests. However, vacant niches alone correctly predict 69% of the presence of alien bird species when combining both regions and trophic guilds. Main Conclusions Most regions of the world have unsaturated bird communities, with the level of saturation in communities varying within regions and trophic guilds. We found that although often‐neglected, vacant niches are likely to be, at least partially, related with the successful establishment of alien bird species.

González‐del‐Pliego, Pamela↗

Description of Freudenthalidium gen. nov. and Halluxium gen. nov. to Formally Recognize Clades Fr3 and H as Genera in the Family Symbiodiniaceae (Dinophyceae)

The Symbiodiniaceae are a family of marine dinoflagellates known mostly for their endosymbiotic interactions with invertebrates and protists, but facultatively and exclusively free‐living life histories in this family are also evident. A recent systematic revision of the Symbiodiniaceae replaced the clade‐based nomenclature of seven divergent lineages of “ Symbiodinium ” sensu lato with one based on formally described genera. The revised taxonomy was not extended to the whole group because type species to describe a new genus for each of the remaining clades and subclades were lacking. In an effort to characterize benthic habitats of symbiodiniaceans in sediments at Heron Island (Great Barrier Reef, Australia), we isolated >100 monoclonal Symbiodiniaceae cultures. Four of these belonged to Symbiodiniaceae ‘subclade’ Fr3, and three to Clade H, based on nucleotide sequence similarity (ITS2, LSU, cp23S, and mtCOB), representing the first cultures of these taxa. Based on these isolates, we propose two new genera: Freudenthalidium gen. nov. and Halluxium gen. nov., circumscribing Clades Fr3 and H, respectively. Three new species are described: Freudenthalidium heronense , F. endolithicum , and Halluxium pauxillum . Kofoidian tabulations of motile cells confirm previous observations that amphiesmal vesicle arrangements are generally conserved across the family. These descriptions are an important step toward completing the systematic revision of the Symbiodiniaceae. That this contribution was enabled by isolates from an endopsammic habitat highlights the potential of discovering new symbiodiniacean species in the environment, the study of which will lead to a deeper understanding of free‐living versus symbiotic life histories in this ecologically important family of dinoflagellates.

Nitschke, Matthew R.↗

Contrasting effects of bioenergy crops on biodiversity

Agriculture is driving biodiversity loss, and future bioenergy cropping systems have the potential to ameliorate or exacerbate these effects. Using a long-term experimental array of 10 bioenergy cropping systems, we quantified diversity of plants, invertebrates, vertebrates, and microbes in each crop. For many taxonomic groups, alternative annual cropping systems provided no biodiversity benefits when compared to corn (the business-as-usual bioenergy crop in the United States), and simple perennial grass–based systems provided only modest gains. In contrast, for most animal groups, richness in plant-diverse perennial systems was much higher than in annual crops or simple perennial systems. Microbial richness patterns were more eclectic, although some groups responded positively to plant diversity. Future agricultural landscapes incorporating plant-diverse perennial bioenergy cropping systems could be of high conservation value. However, increased use of annual crops will continue to have negative effects, and simple perennial grass systems may provide little improvement over annual crops.

09 BIOMASS FUELS↗

cotH Genes Are Necessary for Normal Spore Formation and Virulence in Mucor lusitanicus

Mucormycosis is an invasive fungal infection caused by certain members of the fungal order of Mucorales. The species most frequently identified as the etiological agents of mucormycosis belong to the genera Rhizopus , Lichtheimia , and Mucor . The frequency of systemic mucormycosis has been increasing, mainly because of increasing numbers of susceptible patients. Furthermore, Mucorales display intrinsic resistance to the majority of routinely used antifungal agents (e.g., echinocandins and short-tailed azoles), which limits the number of possible therapeutic options. All the above-mentioned issues urge the improvement of molecular identification methods and the discovery of new antifungal targets and strategies. Spore coat proteins (CotH) constitute a kinase family present in many pathogenic bacteria and fungi and participate in the spore formation in these organisms. Moreover, some of them can act as virulence factors being receptors of the human GRP78 protein during Rhizopus delemar-induced mucormycosis. We identified 17 cotH -like genes in the Mucor lusitanicus genome database. Successful disruption of five cotH genes in Mucor was performed using the CRISPR-Cas9 system. The CotH3 and CotH4 proteins play a role in adaptation to different temperatures as well as in developing the cell wall structure. We also show CotH4 protein is involved in spore wall formation by affecting the total chitin content and, thus, the composition of the spore wall. The role of CotH3 and CotH4 proteins in virulence was confirmed in two invertebrate models and a diabetic ketoacidosis (DKA) mouse model.

59 BASIC BIOLOGICAL SCIENCES↗

Intestinal microbiome profile of the brown rock sea cucumber ( Holothuria glaberrima ) using ITS and 16S rDNA amplicons from direct mechanical, enzymatic, and chemical metagenomic extraction

Using direct mechanical, enzymatic, and chemical extraction methods, the intestinal microbiome of the marine invertebrate Holothuria glaberrima was obtained. ITS and 16S rDNA regions were sequenced to enrich and investigate the prokaryotic and fungal diversity profiles from different anatomical regions within the sea cucumber’s intestinal biology.

16S↗

The Roseibium album (Labrenzia alba) Genome Possesses Multiple Symbiosis Factors Possibly Underpinning Host-Microbe Relationships in the Marine Benthos

Here, we announce the genomes of eight Roseibium album (synonym Labrenzia alba ) strains that were obtained from the octocoral Eunicella labiata . Genome annotation revealed multiple symbiosis factors common to all genomes, such as eukaryotic-like repeat protein- and multidrug resistance-encoding genes, which likely underpin symbiotic relationships with marine invertebrate hosts.

59 BASIC BIOLOGICAL SCIENCES↗