Orthology inference at scale with FastOMA.

The surge in genome data, with ongoing efforts aiming to sequence 1.5 M eukaryotes in a decade, could revolutionize genomics, revealing the origins, evolution and genetic innovations of biological processes. Yet, traditional genomics methods scale poorly with such large datasets.

Repairing a deleterious domestication variant in a floral regulator gene of tomato by base editing.

Crop genomes accumulate deleterious mutations-a phenomenon known as the cost of domestication. Precision genome editing has been proposed to eliminate such potentially harmful mutations; however, experimental demonstration is lacking. Here we identified a deleterious mutation in the tomato transcription factor SUPPRESSOR OF SP2 (SSP2), which became prevalent in the domesticated germplasm and diminished DNA binding to genome-wide targets.

Equipping a Wyatt multiangle, multidetector instrument for real-time particle and polymer sizing by simultaneous multiple-angle dynamic and static light scattering.

Well-constructed instruments may continue to perform beyond their manufacturer-supported service lifetime, which is typically limited by computer operating system compatibility or the availability of spare parts. Often, such equipment is condemned to surplus and destroyed. End-of-life plans that retain some of the material and energy used to create scientific instruments are of interest, just as in other manufacturing sectors.

Quest for Orthologs in the Era of Biodiversity Genomics.

The era of biodiversity genomics is characterized by large-scale genome sequencing efforts that aim to represent each living taxon with an assembled genome. Generating knowledge from this wealth of data has not kept up with this pace. We here discuss major challenges to integrating these novel genomes into a comprehensive functional and evolutionary network spanning the tree of life.

When less is more: sketching with minimizers in genomics.

The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes.

Impact of occupational stress on healthcare workers' family members before and during COVID-19: A systematic review.

We aimed to explore the experiences, needs, and mental health impact of family members of healthcare workers (HCWs) before and during the COVID-19 pandemic. Eleven quantitative and nine qualitative studies were included in this review. Based on the narrative synthesis, we identified five outcomes: 'Mental health outcomes', 'Family relationships, 'Coping skills and resilience', 'Quality of life and social life', and 'Practical outcomes'.

Lung outcomes and related risk factors in patients after SARS-CoV-2 infection: a hospitalised single-centre cohort from Johannesburg, South Africa.

Background: Sequelae post-SARS-CoV-2 infection, including lung and functional impairment, pose a significant challenge post-recovery. We explored the burden and risk factors for post-COVID-19 sequelae in an African population with prevalent comorbidities including tuberculosis (TB) and HIV.

Methods: We conducted an observational cohort study on hospitalised adults with confirmed SARS-CoV-2 infection from 20 March to 06 October 2021 at Chris Hani Baragwanath Academic Hospital, South Africa.

DrosOMA: the Orthologous Matrix browser.

Background: Comparative genomic analyses to delineate gene evolutionary histories inform the understanding of organismal biology by characterising gene and gene family origins, trajectories, and dynamics, as well as enabling the tracing of speciation, duplication, and loss events, and facilitating the transfer of gene functional information across species. Genomic data are available for an increasing number of species from the genus Drosophila, however, a dedicated resource exploiting these data to provide the research community with browsable results from genus-wide orthology delineation has been lacking.

Methods: Using the OMA Orthologous Matrix orthology inference approach and browser deployment framework, we catalogued orthologues across a selected set of Drosophila species with high-quality annotated genomes.

Quality assessment of gene repertoire annotations with OMArk.

In the era of biodiversity genomics, it is crucial to ensure that annotations of protein-coding gene repertoires are accurate. State-of-the-art tools to assess genome annotations measure the completeness of a gene repertoire but are blind to other errors, such as gene overprediction or contamination. We introduce OMArk, a software package that relies on fast, alignment-free sequence comparisons between a query proteome and precomputed gene families across the tree of life.

Bringing science to the public in the light of evolution.

Evolution stands as a foundational pillar within modern biology, shaping our understanding of life. Studies related to evolution, for example constructing phylogenetic trees, are often carried out using DNA or protein sequences. These data, readily accessible from public databases, represent a treasure trove of resources that can be harnessed to create engaging activities with the public.

Expressed emotion in the South Asian diaspora living in the UK: A qualitative study.

Background: 'Expressed Emotion (EE)' captures ways in which emotions are expressed within a family environment. Research has found that EE in families has an impact on psychiatric illness, in particular psychosis, such that it increases risk of relapse. EE was conceptualised by research conducted in the UK.

OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem.

In this update paper, we present the latest developments in the OMA browser knowledgebase, which aims to provide high-quality orthology inferences and facilitate the study of gene families, genomes and their evolution. First, we discuss the addition of new species in the database, particularly an expanded representation of prokaryotic species. The OMA browser now offers Ancestral Genome pages and an Ancestral Gene Order viewer, allowing users to explore the evolutionary history and gene content of ancestral genomes.

Biomechanical effect of neurologic dance training (NDT) for breast cancer survivors with chemotherapy-induced neuropathy: study protocol for a randomized controlled trial and preliminary baseline data.

Background: Breast cancer (BC) is among the most common forms of cancer experienced by women. Up to 80% of BC survivors treated with chemotherapy experience chemotherapy-induced neuropathy (CIN), which degrades motor control, sensory function, and quality of life. CIN symptoms include numbness, tingling, and/or burning sensations in the extremities; deficits in neuromotor control; and increased fall risk.

Biomechanical effect of neurologic dance training (NDT) for breast cancer survivors with chemotherapy-induced neuropathy: study protocol for a randomized controlled trail and preliminary baseline data.

Background Breast cancer (BC) is among the most common forms of cancer experienced by women. Up to 80% of BC survivors treated with chemotherapy experience chemotherapy-induced neuropathy (CIN), which degrades motor control, sensory function, and quality of life. CIN symptoms include numbness, tingling, and/or burning sensations in the extremities; deficits in neuromotor control; and increased fall risk.

Protein length distribution is remarkably uniform across the tree of life.

Background: In every living species, the function of a protein depends on its organization of structural domains, and the length of a protein is a direct reflection of this. Because every species evolved under different evolutionary pressures, the protein length distribution, much like other genomic features, is expected to vary across species but has so far been scarcely studied.

Results: Here we evaluate this diversity by comparing protein length distribution across 2326 species (1688 bacteria, 153 archaea, and 485 eukaryotes).

An experimental assessment of detection dog ability to locate great crested newts (Triturus cristatus) at distance and through soil.

Detection dogs are increasingly used to locate cryptic wildlife species, but their use for amphibians is still rather underexplored. In the present paper we focus on the great crested newt (Triturus cristatus), a European species which is experiencing high conservation concerns across its range, and assess the ability of a trained detection dog to locate individuals during their terrestrial phase. More specifically, we used a series of experiments to document whether a range of distances between target newts and the detection dog (odour channelled through pipes 68 mm in diameter) affects the localisation, and to assess the ability and efficiency of target newt detection in simulated subterranean refugia through 200 mm of two common soil types (clay and sandy soil, both with and without air vents to mimic mammal burrows, a common refuge used by T.

Protein S-acylation controls the subcellular localization and biological activity of PHYTOCHROME KINASE SUBSTRATE.

PHYTOCHROME KINASE SUBSTRATE (PKS) proteins are involved in light-modulated changes in growth orientation. They act downstream of phytochromes to control hypocotyl gravitropism in the light and act early in phototropin signaling. Despite their importance for plant development, little is known about their molecular mode of action, except that they belong to a protein complex comprising phototropins at the plasma membrane (PM).

Deep Divergence and Genomic Diversification of Gut Symbionts of Neotropical Stingless Bees.

Social bees harbor conserved gut microbiotas that may have been acquired in a common ancestor of social bees and subsequently codiversified with their hosts. However, most of this knowledge is based on studies on the gut microbiotas of honey bees and bumblebees. Much less is known about the gut microbiotas of the third and most diverse group of social bees, the stingless bees.

A New Virtual Reality: Benefits and Barriers to Providing Pediatric Gender-Affirming Health Care Through Telehealth.

Purpose: Access to early, multidisciplinary, gender-affirming health care significantly improves the psychosocial well-being of transgender and gender diverse youth. The Doernbecher Gender Clinic (DGC) is an interdisciplinary pediatric gender clinic consisting of endocrinology, psychology, and social work. Following the initiation of modified operations in March 2020 due to the COVID-19 pandemic, the DGC converted all interdisciplinary new patient appointments to telehealth.

A systematic review and narrative synthesis of indirect psychological intervention in acute mental health inpatient settings.

Objectives: Psychologists frequently deliver indirect psychological interventions in mental health inpatient settings to support staff to reflect upon and improve their clinical practice. However, research into these interventions is sparse. Therefore, this study aimed to undertake a systematic review and narrative synthesis of the indirect psychological interventions used in mental health inpatient settings.

Third-Order Fiducial Predictions for Drell-Yan Production at the LHC.

The Drell-Yan process at hadron colliders is a fundamental benchmark for the study of strong interactions and the extraction of electroweak parameters. The outstanding precision of the LHC demands very accurate theoretical predictions with a full account of fiducial experimental cuts. In this Letter we present a state-of-the-art calculation of the fiducial cross section and of differential distributions for this process at third order in the strict fixed-order expansion in the strong coupling, as well as including the all-order resummation of logarithmic corrections.

The influence of receiving real-time visual feedback on breathing during treadmill running to exhaustion.

Breathing plays a vital role in everyday life, and specifically during exercise it provides working muscles with the oxygen necessary for optimal performance. Respiratory inductance plethysmography (RIP) monitors breathing through elastic belts around the chest and abdomen, with efficient breathing defined by synchronous chest and abdomen movement. This study examined if providing runners with visual feedback through RIP could increase breathing efficiency and thereby time to exhaustion.

Experiences and views of frontline healthcare workers' family members in the UK during the COVID-19 pandemic: a qualitative study.

Background: The COVID-19 pandemic has had a well-documented negative impact on the mental health and wellbeing of frontline healthcare workers (HCWs). Whilst no research has to date been carried out to explore the challenges experienced by the families of HCWs, some previous research has been conducted with military families, demonstrating that family members of deployed military personnel may also be affected seriously and negatively.

Objectives: This study aimed to explore the experiences, views, and mental health impact on frontline HCWs' families during the COVID-19 pandemic in the UK and what support the families of frontline HCWs may need.