HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.

The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues.

A High-Quality Phased Genome Assembly of Stinging Nettle ( ssp. ).

Stinging nettles () have a long history of association with human civilization, having been used as a source of textile fibers, food and medicine. Here, we present a chromosome-level, phased genome assembly for a diploid female clone of from Romania. Using a combination of PacBio HiFi, Oxford Nanopore, and Illumina sequencing, as well as Hi-C long-range interaction data (using a novel Hi-C protocol presented here), we assembled two haplotypes of 574.

Revealing the Complexity of Host-Parasite Relationships Between Syringophilid Mites and Sunbirds in Their Global Range.

This article emphasises the importance of parasitological research in understanding ecological dynamics and biodiversity conservation through a global analysis of quill mites (Syringophilidae) parasitising Sunbirds (Nectariniidae). Data from 764 Sunbird individuals across seventy-six species revealed twelve quill mite species, including three newly described species: Sikora and Unsoeld sp. n.

Chromosome-level genome assembly of Megachile sculpturalis Smith (Hymenoptera, Apoidea, Megachilidae).

Megachile sculpturalis Smith, 1853 native to East Asia, is an important solitary bee species that has invaded both Europe and the United States. This study provides the first chromosome-level genome assembly of M. sculpturalis using a combination of Nanopore long reads, Illumina short reads, and Hi-C data.

A left-to-right bias in number-space mapping across ages and cultures.

Number and space are inherently related. Previous research has provided evidence that numbers are aligned to a so-called "mental number line", which is malleable and affected by cultural factors mostly linked to literacy-related habits. However, preverbal humans and non-human animals also map numerosities into space, in a consistent left-to-right direction.

Bio-concentration of hazardous metals in migrant shorebirds in a key conservation reserve and adjoining areas on the west coast of India.

Heavy metal pollution is a growing environmental concern as it causes the degradation of wetlands by affecting the organisms at different trophic levels. Shorebirds typically feed on benthic invertebrates including polychaete worms, crustaceans and molluscs. Thus, the assessment of bioconcentration of heavy metals in shorebirds provides an insight into the extent of bioaccumulation of these hazardous metals in the upper trophic levels.

Functional optimality underpins the repeated evolution of the extreme "saber-tooth" morphology.

"Saber teeth"-elongate, blade-like canines-are a classic example of convergence, having evolved repeatedly throughout mammalian history. Within canine teeth, there is a trade-off between the aspects of shape that improve food fracture and those that increase tooth strength. Optimal morphologies strike a balance between these antagonistic functional criteria.

Complex tissue regeneration in reveals a phylogenetic signal for enhanced regenerative ability in deomyine rodents.

Identifying why complex tissue regeneration is present or absent in specific vertebrate lineages has remained elusive. One also wonders whether the isolated examples where regeneration is observed represent cases of convergent evolution or are instead the product of phylogenetic inertia from a common ancestral program. Testing alternative hypotheses to identify genetic regulation, cell states, and tissue physiology that explain how regenerative healing emerges in some species requires sampling multiple species among which there is variation in regenerative ability across a phylogenetic framework.

Development and validation of a high-throughput qPCR platform for the detection of soil-transmitted helminth infections.

Background: Historically, soil-transmitted helminth (STH) control and prevention strategies have relied on mass drug administration efforts targeting preschool and school-aged children. While these efforts have succeeded in reducing morbidity associated with STH infection, recent modeling efforts have suggested that expanding intervention to treatment of the entire community could achieve transmission interruption in some settings. Testing the feasibility of such an approach requires large-scale clinical trials, such as the DeWorm3 cluster randomized trial.

Anatomical variations in Eurasian wolf (Canis lupus lupus) (Carnivora: Canidae) of the salivary glands: A histological and histochemical investigation.

The study involved a gross anatomical description of the parotid gland, mandibular gland, monostomatic sublingual gland, polystomatic sublingual gland, and zygomatic gland in 12 adult Eurasian wolves (Canis lupus lupus) (wild free-ranging individuals and their zoo counterparts), including their morphometry and microscopic evaluation using hematoxylin & eosin, mucicarmine, azan trichrome, PAS, AB pH 1.0, AB pH 2.5; AB pH 2.

The formation, maintenance, and loss of island biodiversity.

Due to the unique geographical features of large numbers, isolated by water and diverse formation histories, islands have become natural laboratories for ecological and evolutionary research. Islands have a high proportion of endemic species and disharmony in representing the species compared with that in the continent, which provides a good opportunity to explore the formation of island biodiversity. In this review, we focuse on island ecosystems and describes the progress of research in island biogeography in recent years from three aspects: formation, maintenance, and loss of island biodiversity.

Heteronemin suppresses EGF‑induced proliferation through the PI3K/PD‑L1 signaling pathways in cholangiocarcinoma.

Epidermal growth factor (EGF) binds with its surface receptor to stimulate gene expression and cancer cell proliferation. EGF stimulates cancer cell growth via phosphoinositide 3‑kinase (PI3K) and programmed cell death ligand 1 (PD‑L1) pathways. As an integrin αvβ3 antagonist, heteronemin exhibits potent cytotoxic effects against cancer cells.

Contact zone of slow worms Linnaeus, 1758 and (Nordmann, 1840) in Poland.

Background: Legless lizards, the slow worms of the genus are forming secondary contact zones within their Europe-wide distribution.

Methods: We examined 35 populations of and to identify the level of morphological and genetic divergence in Poland. We applied a conventional study approach using metric, meristic, and categorial (coloration) features for a phenotype analysis, and two standard molecular markers, a mitochondrial (NADH-ubiquinone oxidoreductase chain 2; ) and a nuclear (V(D)J recombination-activating protein 1; ) one.

Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems.

Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools.

Phylogenomic insights into the taxonomy, ecology, and mating systems of the lorchel family Discinaceae (Pezizales, Ascomycota).

Lorchels, also known as false morels (Gyromitra sensu lato), are iconic due to their brain-shaped mushrooms and production of gyromitrin, a deadly mycotoxin. Molecular phylogenetic studies have hitherto failed to resolve deep-branching relationships in the lorchel family, Discinaceae, hampering our ability to settle longstanding taxonomic debates and to reconstruct the evolution of toxin production. We generated 75 draft genomes from cultures and ascomata (some collected as early as 1960), conducted phylogenomic analyses using 1542 single-copy orthologs to infer the early evolutionary history of lorchels, and identified genomic signatures of trophic mode and mating-type loci to better understand lorchel ecology and reproductive biology.

Tropical forest clearance impacts biodiversity and function, whereas logging changes structure.

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: (i) structure and environment, (ii) species traits, (iii) biodiversity, and (iv) ecosystem functions. Responses were highly heterogeneous and often complex and nonlinear.

Superstable lipid vacuoles endow cartilage with its shape and biomechanics.

Conventionally, the size, shape, and biomechanics of cartilages are determined by their voluminous extracellular matrix. By contrast, we found that multiple murine cartilages consist of lipid-filled cells called lipochondrocytes. Despite resembling adipocytes, lipochondrocytes were molecularly distinct and produced lipids exclusively through de novo lipogenesis.

Dietary breadth in kangaroos facilitated resilience to Quaternary climatic variations.

Identifying what drove the late Pleistocene megafaunal extinctions on the continents remains one of the most contested topics in historical science. This is especially so in Australia, which lost 90% of its large species by 40,000 years ago, more than half of them kangaroos. Determining causation has been obstructed by a poor understanding of their ecology.

Dispersal promotes stability and persistence of exploited yeast mutualisms.

Multi-species mutualistic interactions are ubiquitous and essential in nature, yet they face several threats, many of which have been exacerbated in the Anthropocene era. Understanding the factors that drive the stability and persistence of mutualism has become increasingly important in light of global change. Although dispersal is widely recognized as a crucial spatially explicit process in maintaining biodiversity and community structure, knowledge about how the dispersal of mutualists contributes to the persistence of mutualistic systems remains limited.

Plio-Pleistocene Environmental Changes Drove the Settlement of Aotearoa New Zealand by Australian Open-Habitat Bird Lineages.

In a changing environment, vacant niches can be filled either by adaptation of local taxa or range-expanding invading species. The relative tempo of these patterns is of key interest in the modern age of climate change. Aotearoa New Zealand has been a hotspot of biogeographic research for decades due to its long-term isolation and dramatic geological history.

Genomics Reveal Population Structure and Intergeneric Hybridization in an Endangered South American Bird: Implications for Management and Conservation.

Genomics is an invaluable tool for conservation, particularly for endangered species impacted by wildlife trafficking. This study uses genomic data to provide new insights to aid conservation and management of endangered species, using as a case study the Yellow cardinal (), a bird endemic to southern South America severely affected by illegal trade and the transformation of its natural habitat. We explore population structure within the Yellow cardinal, delimiting management units and describing connectivity among them.

Autonomous Reef Monitoring Structures (ARMS) as a tool to uncover neglected marine biodiversity: two new Solenogastres (Mollusca, Aplacophora) from the Gulf of Mexico.

Solenogastres is a group of mollusks with evolutionary and ecological importance. Nevertheless, their diversity is underestimated and knowledge about the distribution of the approximately 300 formally described species is limited. Factors that contribute to this include their small size and frequent misidentification by non-specialists.