Biology subjects

Wood, B.

Publications and source records attributed to Wood, B..

6 recordsLinked to original sources

bioRxiv2026

Nanoscale insights into chromatin integrity molecular rearrangements upon DNA damage response

DNA Double Strand Breaks (DSBs) threaten genomic stability, leading to cell death, chromosomal rearrangements, and cancer-driving mutations. Therefore, the effective repair mechanisms are essential for maintaining genomic stability and ensuring cellular survival across diverse organisms. At the core of this process lies chromatin integrity, which facilitates the local DNA conformational changes, regulating accessibility to repair proteins and other biomolecules. To deepen our understanding of the DNA damage response pathway, the local molecular mechanisms regulating the interplay between DNA damage formation and alterations in chromatin conformation must be investigated at the nanoscale level. Here, we integrated atomic force microscope-infrared spectroscopy (AFM-IR) and confocal fluorescence microscopy to explore local chemical modifications in DNA structure and chromatin integrity in metaphase chromosomes and chromosomal aberrations isolated from cells treated with the chemotherapeutic agent, bleomycin. Our findings reveal changes in secondary protein structures, indicating the engagement of DNA repair proteins with high {beta}-sheet content. Nanospectroscopic mapping resolved the alterations in DNA condensation along the chromosomes. Moreover, we observed global DNA demethylation, particularly the conversion of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), correlating with increased DSBs. We conclude that these transitions in protein conformation and DNA methylation correlate with chromatin relaxation and enhanced accessibility for the repair protein.

biophysics↗

bioRxiv2023

Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model

The thymus is the site of T lymphocyte development and T cell education to recognize foreign, but not self, antigens. B cells also reside and develop in the thymus, although their functions are less clear. During thymic involution, a process of lymphoid atrophy and adipose replacement linked to sexual maturation, thymocytes decline. However, thymic B cells decrease far less than T cells, such that B cells comprise [~]1% of human neonatal thymocytes, but up to [~]10% in adults. All jawed vertebrates possess a thymus, and we and others have shown zebrafish (Danio rerio) also have thymic B cells. Here, we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte-specific, fluorophore-labeled transgenic lines, quantifying the changes in thymic T- and B-lymphocytes pre- vs. post-involution. Our results prove that, as in humans, zebrafish thymic B cells increase relative to T cells post-involution. We also performed RNA sequencing (RNA-seq) on D. rerio thymic and marrow lymphocytes of four novel double-transgenic lines, identifying distinct populations of immature T and B cells. Collectively, this is the first comprehensive analysis of zebrafish thymic involution, demonstrating its similarity to human involution, and establishing the highly genetically- manipulatable zebrafish model as a template for involution studies.

developmental biology↗

bioRxiv2023

Fusion crystallization reveals the behavior of both the 1TEL crystallization chaperone and the TNK1 UBA domain

Human thirty-eight-negative kinase-1 (TNK1) is implicated in cancer progression. The TNK1-UBA domain binds polyubiquitin and plays a regulatory role in TNK1 activity and stability. Sequence analysis suggests an unusual architecture for the TNK1 UBA domain, but an experimentally-validated molecular structure is undetermined. To gain insight into TNK1 regulation, we fused the UBA domain to the 1TEL crystallization chaperone and obtained crystals diffracting as far as 1.53 [A]. A 1TEL search model enabled solution of the X-ray phases. GG and GSGG linkers allowed the UBA to reproducibly find a productive binding mode against its host 1TEL polymer and to crystallize at protein concentrations as low as 0.1 mg/mL. Our studies support a mechanism of TELSAM fusion crystallization and show that TELSAM fusion crystals require fewer crystal contacts than traditional protein crystals. Modeling and experimental validation suggest the UBA domain may be selective for both the length and linkages of polyubiquitin chains.

biochemistry↗

bioRxiv2022

A new haplotype-resolved turkey genome to enable turkey genetics and genomics research

BackgroundThe domesticated turkey (Meleagris gallopavo) is a species of significant agricultural importance and is the second largest contributor, behind broiler chickens, to world poultry meat production. The previous genome is of draft quality and partly based on the chicken (Gallus gallus) genome. A high-quality reference genome of Meleagris gallopavo is essential for turkey genomics and genetics research and the breeding industry. ResultsBy adopting the trio-binning approach, we were able to assemble a high-quality chromosome-level F1 assembly and two parental haplotype assemblies, leveraging long-read technologies and genomewide chromatin interaction data (Hi-C). These assemblies cover 35 chromosomes in a single scaffold and show improved genome completeness and continuity. The three assemblies are of higher quality than the previous draft quality assembly and comparable to the current chicken assemblies (GRCg6a and GRCg7). Comparative analyses reveal a large inversion of around 19 Mbp on the Z chromosome not found in other Galliformes. Structural variation between the parent haplotypes were identified in genes involved in growth providing new target genes for breeding. ConclusionsCollectively, we present a new high quality chromosome level turkey genome, which will significantly contribute to turkey and avian genomics research and benefit the turkey breeding industry.

genomics↗

bioRxiv2020

Efficient long-range conduction in cable bacteria through nickel protein wires

Filamentous cable bacteria display unrivalled long-range electron transport, generating electrical currents over centimeter distances through a highly ordered network of fibers embedded in their cell envelope. The conductivity of these periplasmic wires is exceptionally high for a biological material, but their chemical structure and underlying electron transport mechanism remain unresolved. Here, we combine high-resolution microscopy, spectroscopy, and chemical imaging on individual cable bacterium filaments to demonstrate that the periplasmic wires consist of a conductive protein core surrounded by an insulating shell layer. The core proteins contain a sulfur-ligated nickel cofactor, and conductivity decreases when nickel is oxidized or selectively removed. The involvement of nickel as the active metal in biological conduction is remarkable, and suggests a hitherto unknown form of electron transport that enables efficient conduction in centimeter-long protein structures.

microbiology↗

bioRxiv2020

Cytonemes with complex geometries and composition extend into invaginations of target cells

Cytonemes are specialized filopodia that mediate paracrine signaling in Drosophila and other animals. Studies using fluorescence confocal microscopy (CM) established their general paths, cell targets, and essential roles in signaling. To investigate details unresolvable by CM, we used high pressure freezing and electron microscopy to visualize cytoneme structures, paths, contents, and contacts. We observed cytonemes previously seen by CM in the Drosophila wing imaginal disc system, including in disc, tracheal air sac primordium (ASP), and myoblast cytonemes, and identified cytonemes extending into invaginations of target cells and cytonemes connecting ASP cells and connecting myoblasts. Diameters of cytoneme shafts vary between wide (206 {+/-} 51.8 nm) and thin (55.9 {+/-}16.2 nm) segments at regular intervals. Actin, ribosomes, and membranous compartments are present throughout; rough endoplasmic reticulum and mitochondria are in wider proximal sections. These results reveal novel structural features of filopodia and provide a basis for understanding cytoneme cell biology and function. SummaryCytoneme signaling filopodia of Drosophila cells have regions defined by oscillating diameters, and contents that include ER, mitochondria and ribosomes, and form contacts along invaginations of target cell membranes.

cell biology↗