Biology subjects

Thompson, J. D.

Publications and source records attributed to Thompson, J. D..

9 recordsLinked to original sources

bioRxiv2026

Estrogen Receptor Expression Changes After Puberty in the Porcine Anterior Cruciate Ligament

Anterior cruciate ligament (ACL) injuries disproportionately affect female adolescent athletes, with hormonal influences implicated in this sex disparity. However, the relationship between pubertal hormonal changes and ACL gene and protein expression remains poorly understood. This study characterized hormone receptor expression and transcriptional profiles in the anteromedial (AM) and posterolateral (PL) bundles of female porcine ACLs before and after puberty. ACL bundles were collected from pre-pubescent (8 weeks) and post-pubescent (>8 months) female Yorkshire cross-breed pigs (n=6/group) and analyzed using gene expression profiling, western blotting, and immunofluorescence. Pre-pubescent ACLs exhibited greater expression of primary matrix genes (COL1A1, COL1A2, ELN, TNMD), suggesting active matrix synthesis, while post-pubescent ACLs showed elevated secondary matrix genes (COL3A1, LUM, COMP), indicating a homeostatic state. Notably, estrogen receptor alpha (ER) gene and protein expression were significantly greater in post-pubescent ACLs, particularly in AM bundles, whereas G-protein coupled estrogen receptor (GPR30) expression was elevated pre-puberty. Both receptors were distributed homogeneously throughout the tissue. Progesterone receptor protein expression was not detected in any samples. Histologically, post-pubescent ACLs demonstrated decreased cellularity and thicker fascicles compared to pre-pubescent tissues. These findings indicate that ACL sensitivity to estrogen varies across development, with increased ER expression post-puberty potentially rendering the ligament more responsive to circulating estrogen. This work provides foundational evidence for age-dependent hormonal responsiveness in the ACL and motivates further investigation into how sex hormones influence ACL injury risk in adolescent females.

bioengineering↗

bioRxiv2025

Buffering of genetic defects in animal development by regeneration programs

Regeneration programs enable animals to restore damaged or lost tissues, and the range of stimuli for these programs is incompletely understood. Here, we used zebrafish, a vertebrate species with exceptional regenerative capacity, to identify chemically induced mutations that alter regeneration-associated gene activation. Transgenic zebrafish with a permissive promoter and EGFP cassette inserted in the vicinity of the pro-regenerative factor gene fgf20a were mutagenized, and larvae homozygous for ENU-induced mutations were assessed for disruptions in fgf20a-directed reporter gene expression following fin fold amputation. One line was identified with heritable, elevated fgf20a:EGFP presence in the absence of experimental injury, localized to regions of fin fold tissue undergoing degeneration. Whole-genome sequencing (WGS) identified a mutation within exon 72 of the fraser syndrome 1 (fras1) gene, mutated in patients with inherited skin disease. fras1 mutant larvae spontaneously displayed elevated expression of other known injury/regeneration-responsive reporter lines in fin fold, and zebrafish crispants for homologs of other genes mutated in human developmental diseases also displayed regeneration-associated gene expression in regions of dysmorphology. Tempering Fgf signaling by transgenic expression of a dominant-negative Fgf receptor in fras1 mutants exacerbated the disease phenotype. Our findings provide evidence that regeneration programs are harnessed in response to developmental defects caused by genetic mutations, potentially buffering deleterious phenotypes.

developmental biology↗

bioRxiv2023

Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources

Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM) are frequently used for the elaboration of spatially exhaustive biodiversity diagnostics. Despite the paradigm of "garbage in - garbage out" that emphasises the importance of testing the suitability of data for SDM and priority conservation areas, the assessment of database sources remains relatively rare. In addition, the lack of practical recommendations for the use of open-access databases by SEA stakeholders remains a problem. The aim of this study is to explore the quality of data sources that can be used in SEA to assess priority conservation areas in SEA. The study used data for nine taxonomic groups (commonly used in inventories for environmental impact assessment) and three databases available to SEA stakeholders. Three local administrative entities in very different socio-ecological contexts were used to examine three main issues : (i) the suitability of local versus regional or country databases for assessing conservation priorities, (ii) differences among taxonomic groups or territories in terms of the suitability of databases, (iii) the importance of the quality of databases for the application of SDM to assess priority conservation areas. Our study provides several clear messages for potential users of open- access databases. First, the need for prudence in the interpretation of biodiversity maps. Second, the collection of individual databases at the country scale is necessary to complete local data and ensure the suitability of SDM in a local context. Third, a data driven approach can lead to the use of notably different species communities to identify priority conservation areas when compared to the community in the original database. Finally, we propose a workflow to guide SEA stakeholders through the process of data rationalization and use in conservation planning.

ecology↗

bioRxiv2023

Neo-natal castration leads to subtle differences in porcine anterior cruciate ligament morphology and function in adolescence

Female adolescent athletes are at a higher risk of tearing their anterior cruciate ligament (ACL) than male counterparts. While most work related to hormones has focused on the effects of estrogen to understand the increased risk of ACL injury, there are other understudied factors, including testosterone. The purpose of this study was to determine how surgical castration in the male porcine model influences ACL size and function across skeletal growth. Thirty-six male Yorkshire crossbreed pigs were raised to 3 (juvenile), 4.5 (early adolescent), and 6 months (adolescent) of age. Animals were either castrated (barrows) within 1-2 weeks after birth or were left intact (boars). Post-euthanasia, joint and ACL size were assessed via MRI, and biomechanics were assessed via a robotic testing system. Joint size increased throughout age, yet barrows had smaller joints than boars (p<0.001 for all measures). ACL cross-sectional area (CSA), length, volume, and stiffness increased with age (p<0.0001), as did ACL anteromedial (AM) bundle percent contribution to resisting loads (p=0.012). Boar ACL, AM bundle, and PL bundle volumes were 19% (p=0.002), 25% (p=0.003), and 15% (p=0.04) larger than barrows across ages. However, CSA, stiffness, and bundle contribution were similar between boars and barrows (p>0.05). The barrows had smaller temporal increases in AM bundle percent function than boars, but these data were highly variable. Thus, early and sustained loss in testosterone leads to subtle differences in ACL morphology, but may not influence measures associated with increased injury risk, such as CSA or bundle forces in response to applied loads.

bioengineering↗

bioRxiv2022

Degenerative changes are associated with severity of anterior cruciate ligament injury within the skeletally immature joint

Anterior cruciate ligament (ACL) injuries are a major problem in the pediatric and adolescent populations. Some of these injuries extend only partially through the tissue cross-section; yet, there is limited data to inform clinical treatment of such partial tears. In particular, it is unknown how injury severity impacts long-term degenerative changes in the joint. Here, we leverage a skeletally immature preclinical porcine model to evaluate joint biomechanics and degeneration after partial (isolated anteromedial (AM) or posterolateral (PL) bundle) or complete ACL injury. Six months after injury, joint laxity increases were minimal after PL bundle injury, minor after AM bundle injury, and major after ACL injury. Joint degeneration (evaluated in the cartilage and meniscus) was minimal after PL bundle injury, moderate after AM bundle injury, and substantial after ACL injury. With subjects grouped by clinical Lachman grade (indicating the extent of joint destabilization), degeneration was associated with increasing grade, irrespective of injury type. These findings point to the importance of considering joint laxity as a factor when treating young patients, particularly those with partial ACL injuries.

bioengineering↗

bioRxiv2022

CeGAL: revisiting a widespread fungal-specific TF family using an in silico error-aware approach to identify missing zinc cluster domains

Transcription factors (TF) regulate gene activity in eukaryotic cells by binding specific regions of genomic DNA. In fungi, the most abundant TF class contains a fungal-specific GAL4-like Zn2C6 DNA binding domain (DBD), while the second class contains another fungal-specific domain, known as fungal_trans or Middle Homology Domain (MHD), whose function remains largely uncharacterized. Remarkably, almost a third of MHD-containing TF in public sequence databases apparently lack DNA binding activity, since they are not predicted to contain a DBD. Here, we reassess the domain organization of these MHD-only proteins using an in silico error-aware approach. Our large-scale analysis of ~17000 MHD-only TF sequences showed that the vast majority (>90%) result from gene annotation errors, thus contradicting previous findings that the MHD-only TF are widespread in fungi. We show that they are in fact exceptional cases, and that the Zn2C6-MHD domain pair represents the canonical domain signature defining a new TF family composed of two fungal-specific domains. We call this family CeGAL, after the most characterized members: Cep3, whose 3D structure has been determined and GAL4, an archetypal eukaryotic TF. This definition should improve the classification of the Zn2C6 TF and provide critical insights into fungal gene regulatory networks. IMPORTANCEIn fungi, extensive efforts focus on genome-wide characterization of potential Transcription Factors (TFs) and their targets genes to provide a better understanding of fungal processes and a rational for transcriptional manipulation. The second most abundant families of fungal-specific TFs, characterized by a Middle Homology Domain, are major regulators of primary and secondary metabolisms, multidrug resistance and virulence. Remarkably, one third of these TFs do not have a DNA Binding Domain (DBD-orphan) and thus are excluded from genome-wide studies. This particularity has been the subject of debate for many years. By computationally inspecting the close genomic environment of about 20,000 DBD-orphan TFs from a wide range of fungal species, we reveal that more than 90% contained sequences encoding a zinc-finger DBD. This analysis implies that the arrays of DBD containing TFs and their control DNA-sequences in target genes need to be reconsidered and expands the combinatorial regulation degree of the crucial fungal processes controlled by this TF family.

bioinformatics↗

bioRxiv2020

From genotype to phenotype: maintenance of a chemical polymorphism in the context of high geneflow.

A major question in evolution is how to maintain many adaptive phenotypes within a species. In Mediterranean wild thyme, a staggering number of discrete chemical phenotypes (chemotypes) coexist in close geographic proximity. Plant chemotypes are defined by the dominant monoterpene produced in their essential oil. We study the genetics of six distinct chemotypes nested within two well established ecotypes. Ecotypes, and chemotypes within ecotypes, are spatially segregated, and their distribution tracks local differences in the abiotic environment. The ecotypes have undergone a rapid shift in distribution associated with current climate change. Here, combining genomic, phenotypic, and environmental data, we show how the genetics of ecotype determination can allow for such rapid evolutionary response despite high gene flow among ecotypes. Variation in three terpene-synthase loci explains almost all variation in ecotype identity, with one single locus accounting for as much as 78% of it. Phenotypic selection on ecotypes combined with low segregating genotypic redundancy and tight genetic determination leaves a clear footprint at the genomic level: alleles associated with ecotype identity track environmental variation despite extensive gene flow. Different chemotypes, nested within each ecotype, also track environmental variation. However, in contrast to ecotypes, chemotype identity is determined by more loci and show a wider range of genotypic redundancy, which dilutes the impact of phenotypic selection on alleles associated with different chemotypes. Identifying the genetics behind this polymorphism in thyme is a crucial step towards understanding the maintenance of this widespread chemical polymorphism found in many aromatic Lamiaceae.

evolutionary biology↗

bioRxiv2020

Enteroendocrine cells sense bacterial tryptophan catabolites to activate enteric and vagal neuronal pathways

The intestinal epithelium senses nutritional and microbial stimuli using epithelial sensory enteroendocrine cells (EECs). EECs can communicate nutritional information to the nervous system, but similar mechanisms for microbial information are unknown. Using in vivo real-time measurements of EEC and nervous system activity in zebrafish, we discovered that the bacteria Edwardsiella tarda specifically activates EECs through the receptor transient receptor potential ankyrin A1 (Trpa1) and increases intestinal motility in an EEC-dependent manner. Microbial, pharmacological, or optogenetic activation of Trpa1+EECs directly stimulates vagal sensory ganglia and activates cholinergic enteric neurons through 5-HT. We identified a subset of indole derivatives of tryptophan catabolism produced by E. tarda and other gut microbes that potently activates zebrafish EEC Trpa1 signaling and also directly stimulates human and mouse Trpa1 and intestinal 5-HT secretion. These results establish a molecular pathway by which EECs regulate enteric and vagal neuronal pathways in response to specific microbial signals.

physiology↗

bioRxiv2020

Characterization of accessory genes in coronavirus genomes

The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods. We propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes. We applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV. Our findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.

bioinformatics↗