Biology subjects

Johnson, E. B.

Publications and source records attributed to Johnson, E. B..

6 recordsLinked to original sources

bioRxiv2025

Calcite Precipitation by a Nitrogen-Fixing Cyanobacterium

Microbiologically induced calcium carbonate precipitation (MICP) is the process through which the metabolic activity of microorganisms causes the precipitation of calcium carbonate, which can result in solidification of sediment. In cyanobacteria, MICP is thought to occur primarily because cells sequester bicarbonate for the photosynthetic process, thereby lowering the pH of the surrounding media. However, these mechanisms are still poorly understood. Here we show direct evidence of MICP caused by the filamentous cyanobacterium Anabaena. Anabaena differentiates into photosynthetic vegetative cells and nitrogen-fixing heterocysts. Using quantitative microscopy, we show that MICP occurs due to two distinct mechanisms: Firstly, mechanical stress on vegetative cells can cause leakage and/or lysis, releasing sequestered bicarbonate into the environment, resulting in formation of new crystals. Secondly, contact between a heterocyst and a calcite crystal seed appears to cause rapid crystal growth. Our results suggest an evolutionary benefit of contact-mediated precipitation to anchor cyanobacteria growing in tidal regions. By providing greater insight into MICP caused by Anabaena, these results could be used to optimize bio-cement production, thereby enabling a green construction material that could assist with carbon sequestration and reducing the impact of climate change.

microbiology↗

bioRxiv2021

Timing of selective basal ganglia white matter loss in Huntington's disease

ObjectivesTo investigate the timeframe prior to symptom onset when cortico-basal ganglia white matter (WM) loss begins in premanifest Huntingtons disease (preHD), and which striatal and thalamic sub-region WM tracts are most vulnerable. MethodsWe performed fixel-based analysis, which allows resolution of crossing WM fibres at the voxel level, on diffusion tractography derived WM tracts of striatal and thalamic sub-regions in two independent cohorts; TrackON-HD, which included 72 preHD (approx. 11 years before disease onset) and 85 controls imaged at three time points over two years; and the HD young adult study (HD-YAS), which included 54 preHD (approx. 25 years before disease onset) and 53 controls, imaged at one time point. Group differences in fibre density and cross section (FDC) were investigated. ResultsWe found no significant group differences in cortico-basal ganglia sub-region FDC in preHD gene carriers 25 years before onset. In gene carriers 11 years before onset, there were reductions in striatal (limbic and caudal motor) and thalamic (premotor, motor and sensory) FDC at baseline, with no significant change over 2 years. Caudal motor-striatal, pre-motor-thalamic, and primary motor-thalamic FDC at baseline, showed significant correlations with the Unified Huntingtons disease rating scale (UHDRS) total motor score (TMS). Limbic cortico-striatal FDC and apathy were also significantly correlated. ConclusionsOur findings suggest that the initiation of disease modifying therapies 25 years before onset could protect these important brain networks from undergoing neurodegeneration and highlight selectively vulnerable sub-regions of the striatum and thalamus that may be important targets for future therapies.

neuroscience↗

bioRxiv2019

Progress toward the identification and stacking of crucial domestication traits in pennycress

The oilseed species Thlaspi arvense (pennycress) is being domesticated as a new crop that can provide both important ecosystem services and intensify farmland output. Through the use of high throughput sequencing and phenotyping, along with classical mutagenesis key traits needed for pennycress domestication have been identified. Domestication traits identified herein include reduced pod shatter, early maturity, reduced seed glucosinolate levels, and improved oil fatty acid content. By taking advantage of pennycress close genetic relationship with Arabidopsis thaliana, the causative mutations responsible for each of these traits have been identified. These mutations have been used to develop molecular markers to begin to stack the traits into individual lines.

plant biology↗

bioRxiv2019

Dynamics of cortical degeneration over a decade in Huntington's Disease

The neurodegenerative process is typically slowly progressive and complex. While simple models of neurodegeneration suggest that brain changes progress at a near constant rate, previous research shows regional variation within the temporal progression of atrophy, indicating that over the course of neurodegeneration, different regions may undergo changing rates of atrophy. Characterization of long-term dynamic brain changes in neurodegeneration requires both extensive longitudinal MRI datasets and an advanced modeling framework. Until recently, both of these elements were not available. Here, we implement a novel dynamic systems approach to infer patterns of regional progression spatially and temporally in a unique longitudinal dataset with up to seven annual individual brain scans per participant from 49 Huntingtons Disease (HD) gene-carriers. We map participant-and group-level trajectories of cortical atrophy in HD using a decade of data that encompasses motor symptom onset and, for the first time, show that neurodegenerative brain changes exhibit complex temporal dynamics of atrophy with substantial regional variation in progressive cortical atrophy. Some fronto-occipital cortical areas show an almost constant rate of atrophy, while medial-inferior temporal areas undergo only minor change. Interestingly, cortical sensory-motor areas were found to show a noticeable acceleration of atrophy following HD diagnosis. Furthermore, we establish links between individual atrophy and genetic markers of HD (CAG repeat length), as well as showing that cortical motor network changes predict subsequent decline in task-based motor performance, demonstrating face-validity of the model. Our findings highlight the complex pattern of dynamic cortical change occurring in HD that can help to resolve the biological underpinnings of HD progression.

neuroscience↗

bioRxiv2017

Measuring Selection Across HIV Gag: Combining Physico-Chemistry and Population Genetics

We present physico-chemical based model grounded in population genetics. Our model predicts the stationary probability of observing an amino acid residue at a given site. Its predictions are based on the physico-chemical properties of the inferred optimal residue at that site and the sensitivity of the proteins functionality to deviation from the physico-chemical optimum at that site. We contextualize our physico-chemical model by comparing our model fit and parameters it to the more general, but less biologically meaningful entropy based metric: site sensitivity or 1/E. We show mathematically that our physico-chemical model is a more restricted form of the entropy model and how 1/E is proportional to the log-likelihood of a parameter-wise saturated model. Next, we fit both our physico-chemical and entropy models to sequences for subtype Cs Gag poly-protein in the LANL HIV database. Comparing our models site sensitivity parameters G' to 1/E we find they are highly correlated. We also compare the ability of G', 1/E, and other indirect measures of HIV fitness to empirical in vitro and in vivo measures. We find G' does a slightly better job predicting empirical fitness measures of in vivo viral escape time and in vitro spreading rates. While our predictive gain is modest, our model can be modified to test more complex or alternative biological hypotheses. More generally, because of its explicit biological formulation, our model can be easily extended to test for stabilizing vs. diversifying selection. We conjecture that our model could also be extended include epistasis in a more realistic manner than Ising models, while requiring many fewer parameters than Potts models.

evolutionary biology↗

bioRxiv2017

Spring flowering habit in field pennycress (Thlaspi arvense) has arisen multiple independent times

- Pennycress (Thlaspi arvense L.) is currently being developed as a new cold-season oilseed crop. Like many Brassicaceae, pennycress can exhibit either a winter or spring annual phenotype. In Arabidopsis, mutations in negative regulators of flowering, including FLOWERING LOCUS C (FLC) and FRIGIDA can cause the transition to a spring annual habit. The genetics underlying the difference between spring and winter annual pennycress are currently unknown.\n\n- Using whole genome sequencing across wild spring annual pennycress accessions, co-segregation analyses, and comparative genomics approaches, we identify new alleles of TaFLC and explore their geographic distribution.\n\n- We report that loss of function mutations in TaFLC confer the spring annual phenotype in pennycress. We have also identified four natural alleles of TaFLC that confer a spring annual growth habit. The two spring annual FLC alleles present in European accessions were only identified in accessions collected in Montana, USA.\n\n- In pennycress, the spring annual habit has arisen several independent times. Accessions harboring the two European alleles were introduced to North America, likely after the species became a widespread on the continent. These findings provide new information on the natural history of the introduction and spread of the spring annual phenotype in pennycress.

plant biology↗