The three-dimensional genome drives the evolution of asymmetric gene duplicates via enhancer capture-divergence.

Previous evolutionary models of duplicate gene evolution have overlooked the pivotal role of genome architecture. Here, we show that proximity-based regulatory recruitment by distally duplicated genes is an efficient mechanism for modulating tissue-specific production of preexisting proteins. By leveraging genomic asymmetries, we performed a coexpression analysis on tissue data to show the generality of enhancer capture-divergence (ECD) as a significant evolutionary driver of asymmetric, distally duplicated genes.

Antarctic Streptomyces: Promising biocontrol agents for combating f. sp. cubense.

Fusarium wilt of Banana (FWB) caused by f. sp. (Foc) poses a significant threat to the banana industry, with current inadequate control measures.

: Unlocking the Value of This Duckweed for the Food and Feed Industry.

Duckweed ( L.) is a small floating aquatic plant that has an important economic impact in several industrial areas. With its high biomass production, reasonable protein content, and resilience to several climates, it has been attracting increasing interest for potential use in animal and human food systems.

Chromosome analysis of 303 pregnancy losses in Mexico.

Background: Chromosomal abnormalities are present in 50 to 60% of miscarriages and in 6 to 19% of stillbirths. Although microarrays are preferred for studying chromosomal abnormalities, many hospitals cannot offer this methodology.

Objective: To present the results of the cytogenetic analysis of 303 products of conception (POC), which included 184 miscarriages, 49 stillbirths and 17 cases of undefined age.

The Rapid Evolution of De Novo Proteins in Structure and Complex.

Recent studies in the rice genome-wide have established that de novo genes, evolving from noncoding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over time remain unclear. Here, we addressed these issues within a surprisingly short evolutionary timescale (<1 million years for 97% of Oryza de novo genes) with comparative approaches to gene duplicates.

Elucidating the semantics-topology trade-off for knowledge inference-based pharmacological discovery.

Leveraging AI for synthesizing the deluge of biomedical knowledge has great potential for pharmacological discovery with applications including developing new therapeutics for untreated diseases and repurposing drugs as emergent pandemic treatments. Creating knowledge graph representations of interacting drugs, diseases, genes, and proteins enables discovery via embedding-based ML approaches and link prediction. Previously, it has been shown that these predictive methods are susceptible to biases from network structure, namely that they are driven not by discovering nuanced biological understanding of mechanisms, but based on high-degree hub nodes.

Validation of a modified QuEChERS method for the quantification of residues of currently used pesticides in Cuban agricultural soils, using gas chromatography tandem mass spectrometry.

We present an analytical method to detect and quantify residues of currently used pesticides (CUPs), which include 31 active ingredients (ai) and seven transformation products (TPs) in tropical and agricultural soils of Cuba. Ten isotopically labeled analogous compounds served as internal standards (IL-IS). The novelty of this research is the inclusion of different tropical soils type scarcely studied for CUPs and TPs, based on the QuEChERS (quick, easy, cheap, effective, rugged and safe) method, followed by chromatography tandem mass spectrometry.

Examining the Effectiveness of a Digital Media Campaign at Reducing the Duration of Untreated Psychosis in New York State: Results From a Stepped-wedge Randomized Controlled Trial.

Background And Hypothesis: Longer duration of untreated psychosis (DUP) predicts worse outcomes in First Episode Psychosis (FEP). Searching online represents one of the first proactive step toward treatment initiation for many, yet few studies have informed how best to support FEP youth as they engage in early online help-seeking steps to care.

Study Design: Using a stepped-wedge randomized design, this project evaluated the effectiveness of a digital marketing campaign at reducing DUP and raising rates of referrals to FEP services by proactively targeting and engaging prospective patients and their adult allies online.

Inherited bone marrow failure syndromes: phenotype as a tool for early diagnostic suspicion at a major reference center in Mexico.

The inherited bone marrow failure syndromes (IBMFSs) are a group of rare disorders characterized by bone marrow failure (BMF), physical abnormalities, and an increased risk of neoplasia. The National Institute of Pediatrics (INP) is a major medical institution in Mexico, where patients with BMF receive a complete approach that includes paraclinical tests. Readily recognizable features, such as the hematological and distinctive physical phenotypes, identified by clinical dysmorphologists, remain crucial for the diagnosis and management of these patients, particularly in circumstances where next-generation sequencing (NGS) is not easily available.

Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection.

New genes (or young genes) are genetic novelties pivotal in mammalian evolution. However, their phenotypic impacts and evolutionary patterns over time remain elusive in humans due to the technical and ethical complexities of functional studies. Integrating gene age dating with Mendelian disease phenotyping, our research shows a gradual rise in disease gene proportion as gene age increases.

Associating biological context with protein-protein interactions through text mining at PubMed scale.

Inferring knowledge from known relationships between drugs, proteins, genes, and diseases has great potential for clinical impact, such as predicting which existing drugs could be repurposed to treat rare diseases. Incorporating key biological context such as cell type or tissue of action into representations of extracted biomedical knowledge is essential for principled pharmacological discovery. Existing global, literature-derived knowledge graphs of interactions between drugs, proteins, genes, and diseases lack this essential information.

Human gene age dating reveals an early and rapid evolutionary construction of the adaptive immune system.

T cells are a type of white blood cell that play a critical role in the immune response against foreign pathogens through a process called T Cell Adaptive Immunity (TCAI). However, the evolution of the genes and nucleotide sequences involved in TCAI is not well understood. To investigate this, we performed comparative studies of gene annotations and genome assemblies of 28 vertebrate species and identified sets of human genes that are involved in TCAI, carcinogenesis, and ageing.

Chemical Characterization of spp. Extracts with Antifungal Activity against Cocoa Pathogens.

Ecuador is one of the major cocoa producers worldwide, but its productivity has lately been affected by diseases. Endophytic biocontrol agents have been used to minimize pathogenic effects; however, compounds produced by endophytes are minimally understood. This work presents the chemical characterization of the species extracts that proved inhibition against cocoa pathogens.

Lung Transplantation Waitlist Mortality Among Sarcoidosis Patients by Lung Allocation Score Grouping.

Background: The Lung Allocation Score (LAS) system was designed to equalize and minimize waitlist mortality among candidiates for lung transplantation. The LAS stratifies sarcoidosis patients by mean pulmonary arterial pressure (mPAP) into group A (mPAP ≤30 mm Hg) and group D (mPAP >30 mm Hg). In this study, we aimed to analyze the effect of diagnostic grouping and patient characteristics on waitlist mortality among sarcoidosis patients.

A patient-driven clinicogenomic partnership for metastatic prostate cancer.

Molecular profiling studies have enabled discoveries for metastatic prostate cancer (MPC) but have predominantly occurred in academic medical institutions and involved non-representative patient populations. We established the Metastatic Prostate Cancer Project (MPCproject, mpcproject.org), a patient-partnered initiative to involve patients with MPC living anywhere in the US and Canada in molecular research.

No replication of previously reported association with genetic variants in the T cell receptor alpha (TRA) locus for myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS).

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disease with a variety of symptoms such as post-exertional malaise, fatigue, and pain, but where aetiology and pathogenesis are unknown. An increasing number of studies have implicated the involvement of the immune system in ME/CFS. Furthermore, a hereditary component is suggested by the reported increased risk for disease in relatives, and genetic association studies are being performed to identify potential risk variants.

Contexts and contradictions: a roadmap for computational drug repurposing with knowledge inference.

The cost of drug development continues to rise and may be prohibitive in cases of unmet clinical need, particularly for rare diseases. Artificial intelligence-based methods are promising in their potential to discover new treatment options. The task of drug repurposing hypothesis generation is well-posed as a link prediction problem in a knowledge graph (KG) of interacting of drugs, proteins, genes and disease phenotypes.

Digital Strategies to Accelerate Help-Seeking in Youth With Psychiatric Concerns in New York State.

Background: Mental illness in transition age youth is common and treatment initiation is often delayed. Youth overwhelmingly report utilizing the Internet to gather information while psychiatric symptoms emerge, however, most are not yet ready to receive a referral to care, forestalling the established benefit of early intervention.

Methods: A digital outreach campaign and interactive online care navigation platform was developed and deployed in New York State on October 22, 2020.

Heavy metals in soils of Mayabeque, Cuba: multifaceted and hardly discernable contributions from pedogenic and anthropogenic sources.

Cuba is a country with considerable potential for economic growth, and special efforts are made to increase the agricultural output. As food production depends on the quality of soils, heavy metal concentrations were measured in 39 soils in the province of Mayabeque, Cuba, and interpreted in light of anthropogenic activities and pedogenic conditions (soil type and properties). With median concentrations of 1.

Genetic association study in myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) identifies several potential risk loci.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a disease of unknown etiology and pathogenesis, which manifests in a variety of symptoms like post-exertional malaise, brain fog, fatigue and pain. Hereditability is suggested by an increased disease risk in relatives, however, genome-wide association studies in ME/CFS have been limited by small sample sizes and broad diagnostic criteria, therefore no established risk loci exist to date. In this study, we have analyzed three ME/CFS cohorts: a Norwegian discovery cohort (N = 427), a Danish replication cohort (N = 460) and a replication dataset from the UK biobank (N = 2105).

Rapid Cis-Trans Coevolution Driven by a Novel Gene Retroposed from a Eukaryotic Conserved CCR4-NOT Component in .

Young, or newly evolved, genes arise ubiquitously across the tree of life, and they can rapidly acquire novel functions that influence a diverse array of biological processes. Previous work identified a young regulatory duplicate gene in , that unexpectedly diverged rapidly from its parent, , an extremely conserved component in the CCR4-NOT machinery in post-transcriptional and post-translational regulation of eukaryotic cells, and took on roles in the male reproductive system. This neofunctionalization was accompanied by differential binding of the Zeus protein to loci throughout the   genome.

Species-specific partial gene duplication in Arabidopsis thaliana evolved novel phenotypic effects on morphological traits under strong positive selection.

Gene duplication is increasingly recognized as an important mechanism for the origination of new genes, as revealed by comparative genomic analysis. However, how new duplicate genes contribute to phenotypic evolution remains largely unknown, especially in plants. Here, we identified the new gene EXOV, derived from a partial gene duplication of its parental gene EXOVL in Arabidopsis thaliana.