A clinical and genotype-phenotype analysis of MACF1 variants.

Microtubule-actin cross-linking factor 1 (MACF1) is a large protein of the spectraplakin family, which is essential for brain development. MACF1 interacts with microtubules through the growth arrest-specific 2 (Gas2)-related (GAR) domain. Heterozygous MACF1 missense variants affecting the zinc-binding residues in this domain result in a distinctive cortical and brain stem malformation.

Inter-evaluator bias and applicability of feline body condition score from visual assessment.

Body Condition Score (BCS) is an effective tool for assessing body weight and fat mass, as well as diagnosing obesity and abnormal weight loss. A method for visual assessment of BCS in cats would be useful to expand access for feline health and research. The goal of this study is to determine whether BCS can be accurately assessed solely from photographs of cats, and to measure inter-evaluator bias in visually assessed BCS.

Automated chromatin profiling with spa-ChIP seq uncovers the impacts of condition variations.

Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a well-established method for studying the genomic localization of DNA-associated proteins. Yet, while useful, most ChIP-seq protocols include multiple manual steps that can introduce inconsistency and make it burdensome to analyze large sample sets, limiting the inclusion of appropriate replicates and other controls. Although some of these challenges were addressed by incorporation of liquid handling platforms, most of those previous efforts have automated only a subset of the ChIP-seq steps.

Characterization of the complete plastid genome sequence of Á.J. Pérez & E. Rea (Magnoliaceae), a newly described species endemic to the Ecuadorian Andes.

Á.J.Pérez & E.

Chromosome level assembly and annotation of Cuscuta campestris Yunck. ("field dodder"), a model parasitic plant.

We present the first chromosome-level genome assembly and annotation for the genus Cuscuta, a twining and leafless parasitic plant of the morning glory family (Convolvulaceae). C. campestris, the study species, is a widely studied model parasite, due in part to its worldwide occurrence as a weed of agricultural and natural plant communities.

An X-linked sex determination mechanism in cannabis and hop.

Sex chromosomes in cannabis and hop were identified a century ago because of their obvious visible differences in size (heteromorphy). However, we know little about the genes they contain that control the development of the inflorescences. Here we assembled genomes, with phased sex chromosomes, for hop and cannabis.

Mesopolyploidy as a taxonomic clade marker for Brassica and relatives (tribe Brassiceae).

Background And Aims: Whole Genome Duplications (WGD) are rampant in flowering plant genomes. Within Brassicaceae, the genus Brassica (including crop mustards) and relatives (tribe Brassiceae) are hypothesized to share an ancient mesohexaploidy, or whole genome triplication (WGT), resulting from two WGD events (Br-⍺ WGT). However, the phylogenetic boundaries of the Br-α WGT remain unknown.

When families bridge the research-clinical divide: An exploration of values regarding cascade screening in genomic research.

Purpose: Genetic results are important for both patients and their biological relatives. However, cascade screening (CS) uptake is low, especially when testing occurs through research programs and not clinical care. Ethical guidance is needed for CS implementation when individuals receive clinical genetic results through research.

Methyl-CpG-binding domain as a protein interaction partner in promoter regulation and neurodevelopment through evolutionary expanded entanglement.

There is increasing evidence that the methyl-binding domain (MBD) is a protein-protein interaction motif that can function independently of methylated DNA binding. The MBD proteins found throughout plants and invertebrates duplicated into multiple vertebrate DNA and non-DNA-binding members (MBD1, MBD2, MBD3, MBD4, MBD5, MBD6, MECP2, BAZ2A, BAZ2B, SETDB1, and SETDB2). Although many invertebrate species possess MBD proteins that can bind and recognize DNA methylation, the DNA-binding function has been independently lost multiple times, with only minor alterations to the protein interaction residues.

Testing for the Genomic Footprint of Conflict Between Life Stages in an Angiosperm and Moss Species.

The maintenance of genetic variation by balancing selection is of considerable interest to evolutionary biologists. An important but understudied potential driver of balancing selection is antagonistic pleiotropy between diploid and haploid stages of the plant life cycle. Despite sharing a common genome, sporophytes (2n) and gametophytes (n) may undergo differential or even opposing selection.

Parental impacts on industry-relevant offspring performance traits using blue catfish, Ictalurus furcatus (Valenciennes, 1840), cryopreserved sperm.

Catfish accounts for ∼70 % of U.S. finfish aquaculture production with the channel catfish (Ictalurus punctatus) female by blue catfish (I.

Comparative Analyses of Four Reference Genomes Reveal Exceptional Diversity and Weak Linked Selection in the Yellow Monkeyflower (Mimulus guttatus) Complex.

Yellow monkeyflowers (Mimulus guttatus complex, Phrymaceae) are a powerful system for studying ecological adaptation, reproductive variation, and genome evolution. To initiate pan-genomics in this group, we present four chromosome-scale assemblies and annotations of accessions spanning a broad evolutionary spectrum: two from a single M. guttatus population, one from the closely related selfing species M.

Through the lens of bioenergy crops: advances, bottlenecks, and promises of plant engineering.

Advances in engineering of bioenergy crops were driven over the past years by adapting technological breakthroughs and accelerating conventional applications but also exposed intriguing challenges. New tools revealed rich interconnectivity in the exponentially growing and dynamic 'big' omics data' of metabolomes, transcriptomes, and genomes at previously inaccessible magnitude (global, cross-species, meta-) and resolution (single cell). Insights enabled fresh hypotheses and stimulated disciplines such as functional genomics with discovery of broad regulatory networks and their determinants, that is, DNA parts, including promoters, regulatory elements, and transcription factors.

Ionic liquid-assisted seed genomic DNA extraction for advanced sequencing applications.

Background: Modern plant breeding strategies rely on the intensive use of advanced genomic tools to expedite the development of improved crop varieties. Genomic DNA extraction from crop seeds eliminates the need to grow plants in contrast to fresh leaf tissue; however, it can still be a bottleneck due to the presence of stored compounds and the complexity of the matrix. The interaction of environmentally benign choline-based ionic liquids (ILs) with DNA offers an innovative approach to enhance the quality of extracted DNA from seeds.

Accelerating domestication of perennial plants with genomics.

Perennial crops are promising candidates for building climate resilient agricultural systems because they can sustain production in challenging environments and their deep roots mitigate soil erosion, nutrient leaching and preserve soil carbon. However, these plants are challenging to breed with classical approaches due to self-incompatibility, polyploidy, and large complex genomes. These factors have been a barrier to cultivar development, but with the advances in genomic technologies, this can change.

Synthetic feed-forward loop circuit boosts transgene expression in sugarcane.

A new GAL4-based feed-forward loop circuit enhances β-glucuronidase (GUS) reporter gene expression in leaves and stems of stably transformed sugarcane plants.

Genome assembly and annotation of Babesia rossi, a protozoan parasite for canine babesiosis.

Background: Apicomplexan parasite, Babesia rossi, is an Ixodid tick-transmitted pathogen that causes the most severe form of canine babesiosis disease. Compared to other Babesia pathogens of dogs, B. rossi exhibits unique pathophysiology, virulence, and a responsiveness to drugs that differs from the small Babesia parasites.

Single-cell transcriptome analysis reveals abnormal angiogenesis and placentation by loss of imprinted glutaminyl-peptide cyclotransferase.

Imprinted genes play a key role in regulating mammalian placental and embryonic development. Here, we generated glutaminyl-peptide cyclotransferase-knockout () mice utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) platform and identified as a novel anti-angiogenic factor in regulating mouse placentation. Compared with mice, placentae and embryos ( and ) showed significant overgrowth at embryonic Day 12.

Fine-mapping genomic loci refines bipolar disorder risk genes.

Bipolar disorder is a heritable mental illness with complex etiology. While the largest published genome-wide association study identified 64 bipolar disorder risk loci, the causal SNPs and genes within these loci remain unknown. We applied a suite of statistical and functional fine-mapping methods to these loci and prioritized 17 likely causal SNPs for bipolar disorder.

Cell-type specific reductions in interneuron gene expression within the cingulate gyrus of schizophrenia and bipolar disorder subjects.

Schizophrenia (SZ) and bipolar disorder (BP) patients share overlapping neurocognitive deficits of varied magnitude. Neuroimaging in patients and postmortem gene expression analyses suggest that compromised cingulate gyrus GABA-ergic interneurons may contribute to cognitive impairments in SZ and BP. To address this, we used radioactive in situ hybridization to investigate potential gene expression signatures for SZ and BP using interneuron cell-type specific markers including glutamic acid decarboxylase (GAD67), parvalbumin (PV), somatostatin (SST), and vasoactive intestinal peptide (VIP) within specific Brodmann's areas (BA) of the cingulate gyrus.

Comparative Transcriptomic Analysis of Soybean Recombinant Inbred Lines Differing at the Locus for Resistance to During Early Stages of Nematode Infection.

Root-knot nematodes ( spp.) are a continuing threat to soybean production, with being the predominant species. The deployment of Mi-resistant soybean cultivars is a primary management strategy, but the underlying molecular mechanisms contributing to resistance remain unknown.

Non-coding variation in dementias: mechanisms, insights, and challenges.

Dementia encompasses many neurodegenerative disorders. While some causal coding variants are known, most GWAS variants are in non-coding regions of the genome, making understanding functional impacts challenging. This review explores the role of non-coding variation in dementia, covering methods to identify enhancers and their target genes, prioritize GWAS variants, and validate the functional effects of variation, providing a comprehensive framework for investigating non-coding variation and its implications in dementia research.

Biallelic LGI1 and ADAM23 variants cause hippocampal epileptic encephalopathy via the LGI1-ADAM22/23 pathway.

Monoallelic pathogenic variants in LGI1 cause autosomal dominant epilepsy with auditory features with onset in childhood/adolescence. LGI1 is a secreted neuronal protein, functions as a ligand for ADAM22/23, and regulates excitatory synaptic transmission and neuronal excitability in the brain. While biallelic ADAM22 variants cause developmental and epileptic encephalopathy (DEE), the whole picture of LGI1-ADAM22/23 pathway-related diseases remains incompletely understood.

A haplotype-resolved reference genome for Eucalyptus grandis.

Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts.