From Genes to Pathways: A Curated Gene Approach to Accurate Pathway Reconstruction in Teleost Fish Transcriptomics.

Interpreting the vast amounts of data generated by high-throughput sequencing technologies can often present a significant challenge, particularly for non-model organisms. While automated approaches like GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analyses are widely used, they often lack specificity for non-model organisms. To bridge this gap, we present a manually curated gene list tailored for teleost fish transcriptomics.

Extreme Drought Increases the Temporal Variability of Grassland Productivity by Suppressing Dominant Grasses.

Extreme droughts are intensifying, yet their impact on temporal variability of grassland functioning and its drivers remains poorly understood. We imposed a 6-year extreme drought in two semiarid grasslands to explore how drought influences the temporal variability of ANPP and identify potential stabilising mechanisms. Drought decreased ANPP while increasing its temporal variability across grasslands.

Harmonizing nature's timescales in ecosystem models.

Modeling complex, nonlinear ecosystem processes across different timescales presents a significant challenge. We identify two key issues: selecting a representative timestep that captures interconnected processes across various timescales, and simulating these processes in an appropriate sequence. By synthesizing existing ecosystem frameworks, we find shared compromises between biological realism and computational performance.

Trophic convergence of marine vertebrate communities worldwide.

Biogeographic regions arise due to constraints on species ranges, fostering lineage divergence as a result. Yet, convergent evolution means that evolutionary distinct lineages can share similar characteristics when subjected to similar environmental conditions. The ecological convergence of distinct regions has been demonstrated in terrestrial communities, but it remains uncertain if marine systems exhibit similar patterns, given the greater ease of dispersal in the ocean.

Absolute Number of Thalamic Parafascicular and Striatal Cholinergic Neurons, and the Three-Dimensional Spatial Array of Striatal Cholinergic Neurons, in the Sprague-Dawley Rat.

The absolute number of neurons and their spatial distribution yields important information about brain function and species comparisons. We studied thalamic parafascicular neurons and striatal cholinergic interneurons (CINs) because the parafascicular neurons are the main excitatory input to the striatal CINs. This circuit is of increasing interest due to research showing its involvement in specific types of learning and behavioral flexibility.

Loss of intracellular ATP affects axoplasmic viscosity and pathological protein aggregation in mammalian neurons.

Neurodegenerative diseases display synaptic deficits, mitochondrial defects, and protein aggregation. We show that intracellular adenosine triphosphate (ATP) regulates axoplasmic viscosity and protein aggregation in mammalian neurons. Decreased intracellular ATP upon mitochondrial inhibition leads to axoterminal cytosol, synaptic vesicles, and active zone component condensation, modulating the functional organization of mouse glutamatergic synapses.

PLK4: Master Regulator of Centriole Duplication and Its Therapeutic Potential.

Centrosomes catalyze the assembly of a microtubule-based bipolar spindle, essential for the precise chromosome segregation during cell division. At the center of this process lies Polo-Like Kinase 4 (PLK4), the master regulator that controls the duplication of the centriolar core to ensure the correct balance of two centrosomes per dividing cell. Disruptions in centrosome number or function can lead to genetic disorders such as primary microcephaly or drive tumorigenesis via centrosome amplification.

The complete mitogenome of an unidentified species.

Appendicularians are planktonic tunicates abundant all over the world. Currently, only two complete annotated mitochondrial genome assemblies are available for appendicularians, both for cryptic species of This underrepresentation of available appendicularian mitochondrial genomes limits environmental DNA sequencing (eDNA) studies that rely on mitochondrial markers as a taxonomic barcode. We report the complete mitochondrial genome assembly and annotation of an unknown appendicularian species isolated from the Amami Oshima island, Kagoshima prefecture, Japan, that has significant sequence difference with other currently available assemblies and will serve as a useful resource for ecological studies and further mitochondrial studies of appendicularians.

A fossil-informed pattern of body size increase and local extinction in dirt ants (Hymenoptera: Formicidae).

dirt ants are morphologically distinct and widely distributed members of Neotropical communities. These ants possess features that aid in leaf litter camouflage and are larger than other closely related lineages with similar cryptic adaptations. Here, we report the first fossil of this genus group, sp.

Assessing neighborhoods, wealth differentials, and perceived inequality in preindustrial societies.

Humans often live in neighborhoods, nested socio-spatial clusters within settlements of varying size and population density. In today's cities, neighborhoods are often characterized as relatively homogenous and may exhibit segregation along various socioeconomic dimensions. However, even within neighborhoods of similar social or economic status, there is often residential disparity, which in turn impacts perceived inequality.

Toward multiscalar measures of inequality in archaeology.

The Gini coefficient is a statistical measure commonly used to characterize distributions of socioeconomic quantities. Archaeologists and social scientists have recently adopted this method to analyze ancient inequality by targeting specific proxy variables (e.g.

Red blood cell lipid distribution in the pathophysiology and laboratory evaluation of chorea-acanthocytosis and McLeod syndrome patients.

The core neuroacanthocytosis syndromes, , chorea-acanthocytosis/VPS13A disease (ChAc) and McLeod syndrome/XK disease (MLS), are respectively due to mutations in and genes and share similar manifestations including the formation of acanthocytes. We previously showed by lipidomics of red blood cells (RBCs) from ChAc patients slight lipid changes compared to healthy controls. We here evaluated the consequences for RBC morphology, deformability, cytoskeleton and membrane lipid transversal and lateral distribution in five patients with ChAc and two patients with MLS.

Constraints on the optimization of gene product diversity.

RNA and proteins can have diverse isoforms due to post-transcriptional and post-translational modifications. A fundamental question is whether these isoforms are mostly beneficial or the result of noisy molecular processes. To assess the plausibility of these explanations, we developed mathematical models depicting different regulatory architectures and investigated isoform evolution under multiple population genetic regimes.

Infection of two cestode larvae, Nybelinia enterika sp. nov. and Phoreiobothrium sp. in oval squid Sepioteuthis lessoniana species complex.

Recently, oval squid of Sepioteuthis lessoniana species complex has gained importance in aquaculture due to its successful breeding in semi-intensive and intensive aquaculture systems. However, there is a lack of information regarding pathogens and diseases that can affect this species, prompting the need for further research. Two cestode species, Nybelinia enterika sp.

Global structural survey of the flagellotropic myophage φTE infecting agricultural pathogen Pectobacterium atrosepticum.

Bacteriophages offer a promising alternative to drug-based treatments due to their effectiveness and host specificity. This is particularly important in agriculture as a biocontrol agent of plant diseases. Phage engineering is facilitated by structural knowledge.

The multi-level effect of chlorpyrifos during clownfish metamorphosis.

Chemical pollution in coastal waters, particularly from agricultural runoff organophosphates, poses a significant threat to marine ecosystems, including coral reefs. Pollutants such as chlorpyrifos (CPF) are widely used in agriculture and have adverse effects on marine life and humans. In this paper, we investigate the impact of CPF on the metamorphosis of a coral reef fish model, the clownfish Amphiprion ocellaris, focusing on the disruption of thyroid hormone (TH) signalling pathways.

A geological timescale for bacterial evolution and oxygen adaptation.

Microbial life has dominated Earth's history but left a sparse fossil record, greatly hindering our understanding of evolution in deep time. However, bacterial metabolism has left signatures in the geochemical record, most conspicuously the Great Oxidation Event (GOE). We combine machine learning and phylogenetic reconciliation to infer ancestral bacterial transitions to aerobic lifestyles, linking them to the GOE to calibrate the bacterial time tree.

Use of videos to measure dynamic body acceleration as a proxy for metabolic costs in coral reef damselfish (Chromis viridis).

Quantifying the energy costs of various activities is critical to understand key aspects of animal behavior and ecology. Currently, calorimetry is the most widely used method to measure those costs in laboratory studies, whereas field studies use the doubly labeled water method, heart rate and dynamic body acceleration (DBA). However, these methods are limited or even biased because of restricted space for movement, low temporal resolution and/or the need for logger attachment or implantation.

Genomic insights and the conservation potential of captive breeding: The case of Chinese alligator.

Despite 40 years of conservation of the critically endangered Chinese alligator (), the genomic underpinnings of its status remained uncharted. Genome sequencing data of 244 individuals uncovered relatively low overall genomic diversity/heterozygosity and long runs of homozygosity, with captive populations exhibiting higher heterozygosity and smaller inbreeding coefficients compared to wild individuals. The decreased level of inbreeding in the captive population demonstrates the contribution of the large captive breeding population.

Tob negatively regulates NF-κB activation in breast cancer through its association with the TNF receptor complex.

NF-κB mediates transcriptional regulation crucial to many biological functions, and elevated NF-κB activity leads to autoimmune and inflammatory diseases, as well as cancer. Since highly aggressive breast cancers have few therapeutic molecular targets, clarification of key molecular mechanisms of NF-κB signaling would facilitate the development of more effective therapy. In this report, we show that Tob, a member of the Tob/BTG family of antiproliferative proteins, acts as a negative regulator of the NF-κB signal in breast cancer.

A family of crown-of-thorns starfish spine-secreted proteins modify adult conspecific behavior.

With growing interest in utilizing semiochemicals to control pest species, recent investigations have begun to consider semiochemicals to control outbreaks of crown-of-thorns starfish (CoTS; cf. ), a corallivore contributing to coral reef degradation. In this study, differential gene expression analysis of adult CoTS spines led to the identification of (1) numerous G-protein coupled receptor genes enriched at the reproductive stage, possibly reflecting enhanced sensitivity to semiochemicals and (2) genes encoding secreted proteins at the non-reproductive stage.

Non-covalent Molecular Wires of Double Thiahelicene on Cu(111): A nc-AFM Study at Room Temperature.

The fine control of molecules or atoms in self-assemblies on surfaces is a great challenge for future nanodevices, specially for unidimensional structure formations. In this context, our study explores the adsorption behavior of a benzo-fused double [7]thiahelicene (DT7H) on Cu(111). Using non-contact atomic force microscopy (nc-AFM) at room temperature, we prove their capability in the construction of linear-like shape adlayers.

Dscamb regulates cone mosaic formation in zebrafish via filopodium-mediated homotypic recognition.

Cone photoreceptors assemble to form a regular mosaic pattern in vertebrate retinas. In zebrafish, four distinct spectral cone types (red, green, blue, and ultraviolet), form a lattice-like pattern. However, the mechanism of cone mosaic formation has been unknown.

Structural insights into lab-coevolved RNA-RBP pairs and applications of synthetic riboswitches in cell-free system.

CS1-LS4 and CS2-LS12 are ultra-high affinity and orthogonal RNA-protein pairs that were identified by PD-SELEX (Phage Display coupled with Systematic Evolution of Ligands by EXponential enrichment). To investigate the molecular basis of the lab-coevolved RNA-RBP pairs, we determined the structures of the CS1-LS4 and CS2-LS12 complexes and the LS12 homodimer in an RNA-free state by X-ray crystallography. The structural analyses revealed that the lab-coevolved RNA-RBPs have acquired unique molecular recognition mechanisms, whereas the overall structures of the RNP complexes were similar to the typical kink-turn RNA-L7Ae complex.