comparative / phylogenetic analysis

Effects of land-use intensification on nectar resources, bird assemblages and bird-flower interaction networks in the Western Ghats, India

The paper examines how land-use intensification affects nectar resources, bird communities, and bird-flower interaction networks in the Western Ghats, finding that agroforests support more diverse bird-flower interactions than monocultures or forests.

Exploring Probiotic Potential: A Comparative Genomics and In Silico Assessment of Genes within the Genus Geobacillus

This study assesses the probiotic potential of Geobacillus by analyzing its genomic features, revealing safety traits and absence of virulence factors.

Plasmodium killing and antimicrobial lineal or cyclic-peptides computationally targeted the circumsporozoite CSP protein

The paper computationally identifies cyclic peptides targeting Plasmodium falciparum's circumsporozoite protein with high affinity and stability, suggesting potential for antimalarial development.

Comparative cistromic analysis reveals a shift in tamoxifen-associated endometrial tumor ERα binding toward sites less frequently shared by progesterone receptors

The paper compares ERα cistromes in endometrial tumors from tamoxifen users and non-users to ERα and PR cistromes in Ishikawa cells, finding shifts in ERα binding patterns associated with tamoxifen exposure.

Beyond bacterial paradigms: uncovering the functional significance and first biogenesis machinery of archaeal lipoproteins

The paper identifies and characterizes archaeal lipoprotein biogenesis components, showing their essential role in archaeal cell physiology and revealing distinct enzymatic activities.

Evolution of the olfactory system during the radiation of Heliconiini butterflies

This study examines olfactory system evolution in Heliconiini butterflies, finding that antennal lobe size variation results from glomerular and hub volume shifts, with developmental plasticity influenced by environmental conditions.

Computational Modeling of Motor-Driven Extension of Microtubule Bundles in Axons

This study uses a computational model to show that intermediate cross-linking density and microtubule stiffness maximize axonal outgrowth by balancing buckling resistance and mechanical load.

Transcription-based dissection of floral identity and trichome biosynthesis pathways in Cannabis sativa L.

This study identifies MADS-box transcription factors and biosynthetic gene expression patterns in Cannabis sativa, linking them to floral identity and trichome metabolism.

Cultivation and genomic characterisation of novel methanogens from a desert biocrust

This study cultivates and genomes seven new methanogenic cultures from desert biocrusts, revealing their genetic adaptations to oxic and arid environments.

Comparative genomics of sex determination related genes reveals shared evolutionary patterns between bivalves and mammals, but not Drosophila

This study compares the sequence evolution of sex-determination related genes in bivalves, mammals, and Drosophila, finding shared patterns in bivalves and mammals but not in Drosophila.

Evolutionary Rewiring of Anthocyanin Biosynthesis Pathway in Poaceae

The paper examines anthocyanin biosynthesis gene evolution in Poaceae, identifying independent lineage replacements and gene losses in Brachypodium.

Anatomy and habitat shape the oxygen sensing machinery of angiosperms

The paper analyzes the evolution of oxygen sensing machinery in angiosperms, finding that habitat and anatomy shape diversification of Cys-NDP components while retaining a conserved transcriptional core.

Seasonal influenza viruses show distinct adaptive dynamics during growth in chicken eggs

The paper examines adaptive mutations in seasonal influenza viruses grown in chicken eggs, finding most mutations cluster around the HA receptor-binding pocket and show varying background dependence across subtypes.

EVOLUTIONARY CO-OPTION OF AN ANCESTRAL CLOACAL REGULATORY LANDSCAPE DURING THE EMERGENCE OF DIGITS AND GENITALS

The paper shows that the regulatory landscape controlling Hoxd gene expression in limbs was co-opted from an ancestral cloacal program in tetrapods.

Structural basis for color tuning and passive ion conductance in red-shifted pump-fold channelrhodopsin ChR024

This study presents cryo-EM structures of ChR024, revealing its color-tuning mechanism and transition from a proton pump to a light-gated channel.

A plant-centric investigation of Class B Flavin-dependent Monooxygenase evolution and structural diversity

This study investigates the evolution and structural diversity of Class B Flavin-dependent Monooxygenases (FMOs) in plants, identifying eight families and refining conserved motifs.

Gene duplication, translocation and molecular evolution of Dmrt1 and related sex-determining genes in anurans

This study investigates the evolution of sex-determining genes in anurans, finding that gene duplication is rare and sex chromosome turnover is driven by mutations in developmental pathway genes rather than translocation.

Long-term balancing selection maintains cryptic color polymorphism in frogs

This study identifies a genomic region under balancing selection maintaining green/brown color polymorphism in frogs and shows its impact on evolutionary dynamics.

Extracellular Polymeric Substances Drive Curvibacter Host Adaptation and Co-Speciation with Hydra

This study shows Curvibacter bacteria co-evolve with Hydra through extracellular polymeric substances, enabling host-specific colonization and symbiosis stability.

Phage-encoded homing endonucleases attenuate bacterial immunity

This study shows phage-encoded homing endonucleases reduce bacterial immunity by inhibiting GAPS4, a DNase defense system, thereby enhancing phage fitness.

Improved genome assembly of whale shark, the world's biggest fish: revealing "chromocline" in intragenomic heterogeneity

The paper presents an improved chromosome-level genome assembly of the whale shark, revealing a chromocline effect in substitution rates across chromosomes.

A choanoflagellate cGLR-STING pathway reveals evolutionary links between bacterial and animal immunity

The paper identifies a cGLR-STING signaling pathway in choanoflagellates, showing evolutionary links between bacterial and animal immunity.

Evolutionary diversification of ancestral genes across vertebrates and insects

The paper analyzes sequence and expression divergence of 7,000 conserved genes across vertebrates and insects to identify patterns of molecular diversification and lineage-specific evolution.

BBX transcription factor evolution in the green plant lineage

This study investigates the evolutionary history of BBX transcription factors across green plants, identifying structural groups, domain dynamics, and lineage-specific innovations.

Diploid genomes of the booklouse reveal evolutionary consequences ofasexuality

This paper provides strong evidence for the Meselson Effect in the parthenogenetic booklouse using diploid genomes, showing intra-individual SNP divergence exceeding inter-population levels.

Gene family expansions underpin context-dependency of the oldest mycorrhizal symbiosis.

The paper shows gene family expansions, mainly from tandem duplications, underpin context-dependent regulation of mycorrhizal symbiosis and its impact on plant fitness.

Evolution of drug-binding residues in eukaryotic ribosomes

The paper traces the evolutionary divergence of ribosomal drug-binding residues across eukaryotic clades to assess similarities and differences with humans and bacteria.

Mining genes underlying perennial-to-annual transitions in Oryza with comparative genomics

The paper identifies 91 gene families associated with perenniality in Oryza species through comparative genomics and co-expression analysis.

Chemo-mechanotherapy of fibrosis: dynamic control of biological materials through tissue-architecture-dependent crosslink disruption

This study shows that mechanical stretching can disrupt pathological crosslinks in fibrotic tissues, reversing fibrosis in mice when combined with pharmacological treatment.

Tracking tRNA evolution in closely related mouse strains

The paper analyzes tRNA gene variation across 17 closely related mouse strains to understand evolutionary dynamics and identifies conserved and strain-specific tRNA features.