Deciphering temporal gene expression dynamics in multiple coral species exposed to heat stress: Implications for predicting resilience.

Coral reefs are facing unprecedented threats due to global climate change, particularly elevated sea surface temperatures causing coral bleaching. Understanding coral responses at the molecular level is crucial for predicting their resilience and developing effective conservation strategies. In this study, we conducted a comprehensive gene expression analysis of four coral species to investigate their long-term molecular response to heat stress.

Comparative transcriptome analysis reveals deep molecular landscapes in stony coral clade.

Coral reefs, among the most invaluable ecosystems in the world, face escalating threats from climate change and anthropogenic activities. To decipher the genetic underpinnings of coral adaptation and resilience, we undertook comprehensive transcriptome profiling of two emblematic coral species, and , leveraging PacBio Iso-Seq technology. These species were strategically selected for their ecological significance and their taxonomic proximity within the Anthozoa class.

Coaxial electrostatic spray-based preparation of localization missile liposomes on a microfluidic chip for targeted treatment of triple-negative breast cancer.

Due to triple-negative breast cancer (TNBC) lacking specific targets for efficient therapies, nanoparticles have been widely developed to enhance efficacy and reduce the toxicity of chemotherapeutics. We prepared unique liposomes containing PTX and DOX by microfluidics-based coaxial electrostatic spray method, which have a uniform particle size, high drug loading capacity, and good stability. Meanwhile, the cRGD peptide was fused with the lipid membrane to form PTX/DOX@cRGD-Lipo, which played a GPS role in locating tumor neovascularization and further targeting TNBC cells where both overexpress αβ.

Polyp-Canal Reconstruction Reveals Evolution Toward Complexity in Corals.

Modern scleractinian corals are classified into robust, complex, and basal clades through comparative molecular studies. However, only few morphological or biological criteria can systematically determine the evolutionary trajectories of these major scleractinian coral clades. Here, we obtained the structural information of 21 scleractinian coral species representing robust and complex clades: High-resolution micro-computed tomography was used to reconstruct the polyp-canal systems in their colonies and to visualize the dynamic polyp growth processes.

Utilizing an artificial intelligence system to build the digital structural proteome of reef-building corals.

Background: Reef-building corals play an important role in the marine ecosystem, and analyzing their proteomes from a structural perspective will exert positive effects on exploring their biology. Here we integrated mass spectrometry with newly published ColabFold to obtain digital structural proteomes of dominant reef-building corals.

Results: Of the 8,382 homologous proteins in Acropora muricata, Montipora foliosa, and Pocillopora verrucosa identified, 8,166 received predicted structures after about 4,060 GPU hours of computation.

Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circadian Genes.

Coral transcriptomic data largely rely on short-read sequencing, which severely limits the understanding of coral molecular mechanisms and leaves many important biological questions unresolved. Here, we sequence the full-length transcriptomes of four common and frequently dominant reef-building corals using the PacBio Sequel II platform. We obtain information on reported gene functions, structures, and expression profiles.

Symbiodiniaceae microRNAs and their targeting sites in coral holobionts: A transcriptomics-based exploration.

Corals should make excellent models for cross-kingdom research because of their natural animal-photobiont holobiont composition, yet a lack of studies and experimental data restricts their use. Here we integrate new full-length transcriptomes and small RNAs of four common reef-building corals with the published Cladocopium genomes to gain deeper insight into gene regulation in coral-Symbiodiniaceae holobionts. Eleven novel Symbiodiniaceae miRNAs get identified, and enrichment results of their target genes show that they might play a role in downregulating rejection from host coral cells, protecting symbiont from autophagy and apoptosis in parallel.

Full-Length Transcriptome Sequencing Reveals Tissue-Specific Gene Expression Profile of Mangrove Clam .

Mollusca is the second largest animal phylum and represents one of the most evolutionarily successful animal groups. , a species of Corbiculidae, plays an important role in mangrove ecology. It is highly adaptable and can withstand environmental pollution and microbial infections.

Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs.

Background: Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference.

Binding Pattern Reconstructions of FGF-FGFR Budding-Inducing Signaling in Reef-Building Corals.

Reef-building corals play an important role in marine ecosystems. However, owing to climate change, ocean acidification, and predation by invasive crown-of-thorns starfish, these corals are declining. As marine animals comprise polyps, reproduction by asexual budding is pivotal in scleractinian coral growth.

High-Strength Hydrogel Adhesive Formed via Multiple Interactions for Persistent Adhesion under Saline.

Hydrogel adhesives have been widely used in wet environments. Nonetheless, strong and stable persistent adhesion remains a challenge. Here, we report a facile yet powerful strategy to construct high-strength hydrogel adhesives for durable adhesion in a saline environment.

Full-Length Transcriptome Sequencing of the Scleractinian Coral Reveals the Gene Expression Profile of Coral-Zooxanthellae Holobiont.

Coral-zooxanthellae holobionts are one of the most productive ecosystems in the ocean. With global warming and ocean acidification, coral ecosystems are facing unprecedented challenges. To save the coral ecosystems, we need to understand the symbiosis of coral-zooxanthellae.

FEM: mining biological meaning from cell level in single-cell RNA sequencing data.

Background: One goal of expression data analysis is to discover the biological significance or function of genes that are differentially expressed. Gene Set Enrichment (GSE) analysis is one of the main tools for function mining that has been widely used. However, every gene expressed in a cell is valuable information for GSE for single-cell RNA sequencing (scRNA-SEQ) data and not should be discarded.

Exploring Nanotechnological Detection Background of Heat Shock Proteins (HSPs) in Coral .

Coral reefs are cornerstone of global marine ecosystems, providing shelter for over one third of marine organisms. Currently, along with global warming and increased human activities, large-scale decline of coral reefs has become a severe ecosystem problem, and now quantitative detection of heat shock protein (HSP) gene by nanotechnology has become a research hotspot in this field. However, is one of the most important dominant reef-building corals in Indo- Pacific region, encounter an urgent obstacle on the HSP detection research by nanoscience and nanotechnology for lack of sequence background.

BENviewer: a gene interaction network visualization server based on graph embedding model.

BENviewer is a brand-new online gene interaction network visualization server based on graph embedding models. With mature graph embedding algorithms applied on several interaction network databases, it provides human-friendly 2D visualization based on more than 2000 biological pathways, and these results present not only genes involved but also tightness of interactions in an intuitive way. As a unique visualization server introducing graph embedding application for the first time, it is expected to help researchers gain deeper insights into biological networks beyond generating results explainable by existing knowledge.

Microfluidic-based fabrication and characterization of drug-loaded PLGA magnetic microspheres with tunable shell thickness.

To overcome the shortcoming of conventional transarterial chemoembolization (cTACE) like high systemic release, a novel droplet-based flow-focusing microfluidic device was fabricated and the biocompatible poly(lactic-co-glycolic acid) (PLGA) magnetic drug-eluting beads transarterial chemoembolization (TACE) microspheres with tunable size and shell thickness were prepared via this device. Paclitaxel, as a model active, was loaded through O/O/W emulsion method with high efficiency. The size and the shell thickness vary when adjusting the flow velocity and/or solution concentration, which caters for different clinical requirements to have different drug loading and release behavior.

Single symbiotic cell transcriptome sequencing of coral.

Zooxanthellae and coral can form an intracellular symbiotic system. Yet, little is known about the molecular mechanism underlying this symbiosis. In this study, we characterized the symbiosis based on analyses of gene expression at the single-cell level.

Whole-genome resequencing reveals the pleistocene temporal dynamics of and populations.

Global climatic fluctuations governed the ancestral demographic histories of species and contributed to place the current population status into a more extensive ecological and evolutionary context. Genetic variations will leave unambiguous signatures in the patterns of intraspecific genetic variation in extant species since the genome of each individual is an imperfect mosaic of the ancestral genomes. Here, we report the genome sequences of 20 individuals by whole-genome resequencing strategy.

A high-strength double network polydopamine nanocomposite hydrogel for adhesion under seawater.

Mussel-inspired catechol-based strategy has been widely used in the development of underwater adhesives. Nonetheless, the properties of the adhesives were still severely limited under harsh environments. A facile approach was proposed herein to prepare a double network hydrogel adhesive with low swelling rate and high strength in seawater, where the first network was polyacrylamide (PAM) and the second network was alginate (Alg).

On the origin of vertebrate body plan: Insights from the endoderm using the hourglass model.

The vertebrate body plan is thought to be derived during the early Cambrian from a worm-like chordate ancestor. While all three germ layers were clearly involved in this innovation, the role of the endoderm remains elusive. According to the hourglass model, the optimal window for investigating the evolution of vertebrate endoderm-derived structures during cephalochordate development is from the Spemann's organizer stage to the opening of the mouth (Stages 1-7, described herein).

The 3D Reconstruction of Pocillopora Colony Sheds Light on the Growth Pattern of This Reef-Building Coral.

Coral reefs are formed by living polyps, and understanding the dynamic processes behind the reefs is crucial for marine ecosystem restoration. However, these processes are still unclear because the growth and budding patterns of living polyps are poorly known. Here, we investigate the growth pattern of a widely distributed reef-building coral Pocillopora damicornis from Xisha Islands using high-resolution computed tomography.

Characterization and Analysis of the Mitochondrial Genome of Common Bean () by Comparative Genomic Approaches.

The common bean () is a major source of protein and essential nutrients for humans. To explore the genetic diversity and phylogenetic relationships of , its complete mitochondrial genome (mitogenome) was sequenced and assembled. The mitogenome is 395,516 bp in length, including 31 unique protein-coding genes (PCGs), 15 transfer RNA (tRNA) genes, and 3 ribosomal RNA (rRNA) genes.