Biology subjects

Dvorak, E.

Publications and source records attributed to Dvorak, E..

7 recordsLinked to original sources

bioRxiv2026

The Georgetown Reading in Aging Neuroimaging Dataset (GRAND): Reading and multimodal MRI data in older adults

Reading is a critical skill in modern society. Most research on reading is conducted in school age children or young adults. However, acquired brain disorders often affect reading ability, and these disorders tend to occur in older adults. It is therefore critical to examine the normative distribution of reading behavior and the brain basis of reading in older adults. Here, we provide trial-wise single word and pseudoword oral reading and lexical decision data, as well as structural, functional, and diffusion-weighted MRI data from 116 neurotypical adults aged 22 to 84 years (mean = 59). Accuracy, response times, and errors are provided for corpora that are parametrically modulated in frequency, imageability, and regularity for real words and consistency of spelling-sound mapping for pseudowords. This dataset includes both minimally processed behavior (trial-wise data) and MRI data, and participant- and item-wise summary metrics and processed MRI data. These data serve both as a normative sample for reading behavior in older adults, but also as a valuable resource for identifying novel brain-behavioral relationships.

neuroscience↗

bioRxiv2025

Phylogenomics of Plasmopara halstedii reveals genomic regions associated with the breakdown of sunflower downy mildew resistance genes

O_LIUnderstanding the genetic diversity and evolutionary history of plant pathogens is crucial for effective disease management strategies. Sunflower downy mildew, caused by the oomycete Plasmopara halstedii, is a worldwide threat to the sunflower oil crop. We aimed to explain through phylogenomic studies how downy mildew resistance breakdown occurred recurrently in the last decades in France, leading to new virulence profiles. C_LIO_LIWe assembled high-quality genomes of three founder pathotypes of Pl. halstedii. Performing comparative genomic analyses, population genetics, and phylogenomic analyses, we studied the genomic structure among the 16 reference French pathotypes of Pl. halstedii. C_LIO_LIWe revealed a conserved genomic organisation among pathotypes and a strong synteny with other Peronosporales species. The history of Pl. halstedii invasion in France over the last 60 years was documented by identifying founder strains and their admixture patterns. The emergence of pathotypes with broader virulence spectra and therefore capable of overcoming host resistance was associated with genomic reshuffling. We highlighted genomic mosaicism in admixed pathotypes and identified regions associated with the breakdown of host resistance genes harbouring putative effector genes. C_LIO_LIOur findings provide insights into evolutionary mechanisms underlying plant pathogen host adaptation, which has implications for a sustainable deployment of multiple resistance genes. C_LI

plant biology↗

bioRxiv2024

Recombination landscape and karyotypic variations revealed by linkage mapping in the grapevine downy mildew pathogen Plasmopara viticola

Plasmopara viticola, the causal agent of grapevine downy mildew, is a biotrophic oomycete engaged in atight coevolutionary relationship with its host. Rapid adaptation of the pathogen is favored by annual sexual reproduction which generates genotypic diversity. With the aim of studying the recombination landscape across the P. viticola genome, we generated two half-siblings F1 progenies (N=189 and 162). Offspring were genotyped by targeted sequencing of a set of 5,000 informative SNPs. This enabled the construction of unprecedented high-density linkage maps for this species. The reference genome could be assembled into 17 pseudo-chromosomes, anchoring 88% of its physical length. We observed a strong collinearity between parental genomes and extensive synteny with the downy mildew Peronospora effusa. In the consensus map, the median recombination rate was 13.8 cM/Mb. The local recombination rate was highly variable along chromosomes and recombination was suppressed in putative centromeric regions. Recombination rate was found negatively correlated with repeats coverage and positively correlated with gene coverage. However, genes encoding secreted proteins and putative effectors were under-represented in highly recombining regions. In both progenies, about 5% of the individuals presented karyotypic anomalies. Aneuploidies and triploidies almost exclusively originated from the male-transmitted chromosomes. Triploids resulted from fertilization by diploid gametes, but also from dispermy. Obligatory sexual reproduction each year may explain the lower level of karyotypic variation in P. viticola compared to other oomycetes. The linkage maps will be useful to guide future de novo chromosome-scale assemblies of P. viticola genomes and to perform forward genetics. SummarySexual reproduction contributes to the rapid adaptation of plant pathogens thanks to the recombination of genetic variants. By crossing strains of grapevine downy mildew, we built a set of linkage maps and describe the recombination landscape along the 17 chromosomes of the genome. The recombination rate varied greatly and was higher in gene-rich regions, but not in effector-rich regions. We observed an abnormal number of chromosomes in 5% of the offspring, which was mostly due to the male parent.

genetics↗

bioRxiv2024

Patterns and drivers of diatom diversity and abundance in the global ocean

Diatoms constitute one of the most diverse and ecologically important phytoplankton groups, yet their large-scale diversity patterns and drivers of abundance are unclear due to limited observations. Here, we utilize Tara Oceans molecular and morphological data, spanning pole to pole, to describe marine diatom diversity, abundance, and environmental adaptation and acclimation strategies. The dominance of diatoms among phytoplankton in terms of relative abundance and diversity was confirmed, and the most prevalent genera were Chaetoceros, Thalassiosira, Actinocyclus and Pseudo-nitzschia. We defined 25 distinct diatom communities with varying environmental preferences illustrative of different life strategies. The Arctic Ocean stands out as a diatom hotspot with 6 of the diatom communities being exclusive to it. Light harvesting and photoprotection were among the cellular functions in which natural diatom populations invested the bulk of their transcriptional efforts. This comprehensive study sheds light on marine diatom distributions, offering insights to assess impacts of global change and oceanic anthropogenic impacts.

ecology↗

bioRxiv2021

The organization of individually mapped structural and functional semantic networks in aging adults

Language function in the brain, once thought to be highly localized, is now appreciated as relying on a connected but distributed network. The semantic system is of particular interest in the language domain because of its hypothesized integration of information across multiple cortical regions. Previous work in healthy individuals has focused on group-level functional connectivity (FC) analyses of the semantic system, which may obscure interindividual differences driving variance in performance. These studies also overlook the contributions of white matter networks to semantic function. Here, we identified semantic network nodes with a semantic decision fMRI task in 53 typically-aging adults, characterized network organization using structural connectivity (SC), and quantified the segregation and integration of the network using FC. Hub regions were identified in left inferior frontal gyrus. The individualized semantic network was composed of three interacting modules: 1) default-mode module characterized by bilateral medial prefrontal and posterior cingulate regions and also including right-hemisphere homotopes of language regions; 2) left frontal module extending dorsally from inferior frontal gyrus to pre-motor area; and 3) left temporoparietal module extending from temporal pole to inferior parietal lobule. FC within Module3 and integration of the entire network related to a semantic verbal fluency task, but not a matched phonological task. These results support and extend the tri-network semantic model (Xu et al., 2017) and the controlled semantic cognition model (Chiou et al., 2018) of semantic function.

neuroscience↗

bioRxiv2021

Testing the perilesional neuroplastic recruitment hypothesis in aphasia

ObjectiveA prominent theory proposes that neuroplastic recruitment of perilesional tissue supports aphasia recovery, especially when language-capable cortex is spared by smaller lesions. This theory has rarely been tested directly, and findings have been inconclusive. Here, we test the perilesional plasticity hypothesis using two fMRI tasks in two groups of stroke survivors. MethodsTwo cohorts totaling 84 chronic left-hemisphere stroke survivors with prior aphasia diagnosis, and 80 control participants underwent fMRI using either a naming task or a reliable semantic decision task. Individualized perilesional tissue was defined by dilating anatomical lesions, and language regions were defined using meta-analyses. Mixed modeling examined differences in activity between groups. Relationships with lesion size and aphasia severity were examined. ResultsStroke survivors exhibited reduced activity in perilesional language tissue relative to controls in both tasks. Although a few cortical regions exhibited greater activity irrespective of distance from the lesion, or only when distant from the lesion, no regions exhibited increased activity only when near the lesion. Larger lesions were associated with reduced language activity irrespective of distance from the lesion. Using the reliable fMRI task, reduced language activity related to aphasia severity independent of lesion size. InterpretationWe find no evidence for neuroplastic recruitment of perilesional tissue in aphasia beyond its typical role in language. Rather, our findings are consistent with alternative hypotheses that left-hemisphere activation changes during recovery relate to normalization of language network dysfunction and possibly recruitment of alternate cortical processors. These findings clarify left-hemisphere neuroplastic mechanisms supporting language recovery after stroke. Summary for Social Media If AcceptedO_ST_ABSTwitter handleC_ST_ABS@crlgeorgetown What is the current knowledge on the topic?After left-hemisphere stroke, many individuals experience long-term language impairment (aphasia) while others recover their communication abilities. Although there are several hypotheses concerning the kind of brain neuroplasticity that allows some individuals to recover, these mechanisms are not understood in aphasia. What question did this study address?This study tested the perilesional plasticity hypothesis as it relates to aphasia recovery. This predominant theory posits that tissue around the stroke lesion boundary becomes recruited to support recovered language function in post-stroke aphasia. What does this study add to our knowledge?This study clarifies the mechanisms of neuroplasticity in stroke aphasia recovery. The results are not consistent with the conventional perilesional plasticity hypothesis, but rather favor an interpretation that recovery is supported by normalization of language network dysfunction and possibly recruitment of alternate brain regions How might this potentially impact on the practice of neurology?These conclusions will give practicing neurologists a better understanding of how the brain recovers from aphasia after stroke.

neuroscience↗

bioRxiv2020

Global distribution patterns of marine nitrogen-fixers by imaging and molecular methods

Biological nitrogen fixation plays a critical role in marine primary production, yet, our understanding of marine N2-fixers (diazotrophs) is hindered by limited observations. Here, we developed a quantitative image analysis pipeline in concert with mapping of molecular markers for mining >2,000,000 images and >1,300 metagenomes in surface, deep chlorophyll maximum and mesopelagic samples across 6 size fractions (<0.2-2000 m). Imaging and PCR-free molecular data were remarkably congruent. Sequences from diazotrophs were detected from the ultrasmall bacterioplankton (<0.2 m) to mesoplankton (180-2000 m), while images predicted symbiotic and colonial-forming diazotrophs (>20 {micro}m). Imaging and molecular data estimated that polyploidy can significantly impact gene abundances of symbiotic vs colonial-forming diazotrophs. In general our results support the canonical view that larger sized diazotrophs (>10 m) dominate the tropical belts, while sequences from unicellular cyanobacterial and non-cyanobacterial diazotrophs were globally distributed in surface and the mesopelagic. Co-occurring diazotrophic lineages of different lifestyles were frequently encountered, and several new high density regions of diazotrophs were identified in the global ocean. Overall, this work provides an update of marine diazotroph biogeographical diversity and contributes a new bio-imaging-informatic workflow.

microbiology↗