Biology subjects

Wilson, M. P.

Publications and source records attributed to Wilson, M. P..

7 recordsLinked to original sources

bioRxiv2026

Two-State Effective Connectivity Predicts the effect of Anterior Cingulate Cortex Excitatory / Inhibitory Balance on Posterior Cingulate Cortex

Aims Excitatory/inhibitory imbalance - the equilibrium between glutamatergic excitation and {gamma}-Aminobutyric acid (GABA)ergic inhibition - is implicated in psychosis and may precede psychosis onset. Methods To investigate whether excitatory/inhibitory balance relates to subclinical psychotic experiences, anxiety and depression, we developed a network-level measure integrating Magnetic Resonance Spectroscopy Glutamate/GABA ratios with effective connectivity during resting-state fMRI. In 20 healthy young adults (aged between 18-32; 50% female), we first measured excitatory/inhibitory balance, operationalised as Glutamate/GABA and Glutamate+Glutamine(Glx)/GABA ratio, in the dorsal anterior cingulate cortex. Second, we applied Two-state Dynamic Causal Modelling to assess effective connectivity of the default-mode network, using these ratios as empirical priors to determine how they translate into network connectivity. Third, we ran Bayesian Model Selection at the model and family levels to identify the optimal models. Results The two-state model with Glx/GABA ratio as direct input into the posterior cingulate cortex best explained the data. This best-fitting model incorporated the neurometabolite ratio with Glutamate and GABA and used two-state connectivity. Conclusions Excitatory/inhibitory balance underlies resting-state effective connectivity, with the Glx/GABA ratio shaping connectivity networks. This pathway highlights excitatory/inhibitory balance as a predictor of two-state brain networks, potentially aiding identification of high-risk individuals and informing new interventions.

neuroscience↗

bioRxiv2026

Dolichol biosynthesis in yeast traces the expanded reaction pathway of higher eukaryotes

The recent reassignment of Saccharomyces cerevisiae Dfg10 as a polyprenal reductase left two unresolved steps in yeast dolichol biosynthesis: the conversion of polyprenol to polyprenal and dolichal to dolichol. In humans, both of these steps are carried out by DHRSX, an enzyme with a unique dual specificity. We found that yeast Env9 catalyzes an NADPH-dependent reduction of dolichal to dolichol. However, in contrast to DHRSX, Env9 does not catalyze the conversion of polyprenol to polyprenal. Instead, our data indicates that this reaction is catalyzed by another yeast short chain oxidoreductase, Tda5. Thus, we provide evidence that the dual role of DHRSX in human dolichol synthesis is fulfilled by two dedicated yeast enzymes, Env9 and Tda5. Accordingly, deletion of ENV9 and TDA5 led to the accumulation of polyisoprenoid intermediates, transfer of immature lipid-linked oligosaccharides onto nascent proteins, and defective N-glycosylation. This is similar to what had been observed in DHRSX-deficient mammalian cells and yeast cells with DFG10 deleted. Furthermore, we discovered that loss of Dfg10 results in a deficiency of cell wall -mannan, revealing a critical sensitivity of yeast mannan biosynthesis to the quality of nascent N-linked glycans.

biochemistry↗

bioRxiv2024

The N-glycosylation defect in Lec5 and Lec9 CHO cells is caused by absence of the DHRSX gene

Glycosylation-deficient Chinese hamster ovary (CHO) cell lines have been instrumental in the discovery of N-glycosylation machinery. Yet, the molecular causes of the glycosylation defects in the Lec5 and Lec9 mutants have been elusive, even though for both cell lines a defect in dolichol formation from polyprenol was previously established. We recently found that dolichol synthesis from polyprenol occurs in three steps consisting of the conversion of polyprenol to polyprenal by DHRSX, the reduction of polyprenal to dolichal by SRD5A3 and the reduction of dolichal to dolichol, again by DHRSX. This led us to investigate defective dolichol synthesis in Lec5 and Lec9 cells. Both cell lines showed increased levels of polyprenol and its derivatives, concomitant with decreased levels of dolichol and derivatives, but no change in polyprenal levels, suggesting DHRSX deficiency. Accordingly, N-glycan synthesis and changes in polyisoprenoid levels were corrected by complementation with human DHRSX but not with SRD5A3. Furthermore, the typical polyprenol dehydrogenase and dolichal reductase activities of DHRSX were absent in membrane preparations derived from Lec5 and Lec9 cells, while the reduction of polyprenal to dolichal, catalyzed by SRD5A3, was unaffected. Long-read whole genome sequencing of Lec5 and Lec9 cells did not reveal mutations in the ORF of SRD5A3, but the genomic region containing DHRSX was absent. Lastly, we established the sequence of Chinese hamster DHRSX and validated that this protein has similar kinetic properties to the human enzyme. Our work therefore identifies the basis of the dolichol synthesis defect in CHO Lec5 and Lec9 cells.

biochemistry↗

bioRxiv2023

N-glycosylation as a eukaryotic protective mechanism against protein aggregation

The tendency for proteins to form aggregates is an inherent part of every proteome and arises from the self-assembly of short protein segments called aggregation-prone regions (APRs). While post-translational modifications (PTMs) have been implicated in modulating protein aggregation, their direct role in APRs remains poorly understood. In this study, we used a combination of proteome-wide computational analyses and biochemical techniques to investigate the potential involvement of PTMs in aggregation regulation. Our findings reveal that while most PTM types are disfavored near APRs, N-glycosylation is enriched and evolutionarily selected, especially in proteins prone to misfolding. Experimentally, we show that N-glycosylation inhibits the aggregation of peptides in vitro through steric hindrance. Moreover, mining existing proteomics data, we find that the loss of N-glycans at the flanks of APRs leads to specific protein aggregation in Neuro2a cells. Our results point towards a novel intrinsic role for N-glycosylation, directly preventing protein aggregation in eukaryotes.

molecular biology↗

bioRxiv2020

Developing and Deploying a Scalable Computing Platform to Support MOOC Education in Clinical Data Science

One of the challenges of teaching applied data science courses is managing individual students local computing environment. This is especially challenging when teaching massively open online courses (MOOCs) where students come from across the globe and have a variety of access to and types of computing systems. There are additional challenges with using sensitive health information for clinical data science education. Here we describe the development and performance of a computing platform developed to support a series of MOOCs in clinical data science. This platform was designed to restrict and log all access to health datasets while also being scalable, accessible, secure, privacy preserving, and easy to access. Over the 19 months the platform has been live it has supported the computation of more than 2300 students from 101 countries.

scientific communication and education↗

bioRxiv2020

Assessing the Utility and Accuracy of ICD10-CM Nontraumatic Subarachnoid Hemorrhage Codes for Intracranial Aneurysm Research

BackgroundThe 10th revision of International Classification of Disease, Clinical Modification (ICD10-CM) increased the number of codes to identify nontraumatic subarachnoid hemorrhage from one to twenty-two. ICD10-CM codes are able to specify the location of aneurysms causing subarachnoid hemorrhage (aSAH), however it is not clear how frequently or accurately these codes are being used in practice. ObjectiveTo systematically evaluate the usage and accuracy of location-specific ICD10-CM codes for aSAH. MethodsWe extracted all uses of ICD10-CM codes for nontraumatic subarachnoid hemorrhage (I60.x) during the first three years following the implementation of ICD10-CM from the billing module of the EHR for UCHealth. For those codes that specified aSAH location (I60.0-I60.6), EHR documentation was reviewed to determine whether there was an active aSAH, any patient history of aSAH, or unruptured intracranial aneurysm/s and the locations of those outcomes. ResultsBetween October 1, 2015 - September 30, 2018, there were 3,119 instances of nontraumatic subarachnoid hemorrhage ICD10-CM codes (I60.00-I60.9), of which 297 (9.5%) code instances identified aSAH location (I60.0-I60.6). These codes accurately identified current aSAH (64%), any patient history of aSAH (84%), and any patient history of intracranial aneurysm (87%). The accuracy of identified outcome location was 53% in current aSAH, 72% for any history of aSAH, and 76% for any history of an intracranial artery. ConclusionsResearchers should use ICD10-CM codes with caution when attempting to detect active aSAH and/or aneurysm location.

bioinformatics↗

bioRxiv2018

Mkk4 and Mkk7 are important for retinal development and axonal injury-induced retinal ganglion cell death

The mitogen activated protein kinase (MAPK) pathway has been shown to be involved in both neurodevelopment and neurodegeneration. c-Jun N-terminal kinase (JNK), a MAPK shown to be important in retinal development and after optic nerve crush injury, is regulated by two upstream kinases: MKK4 and MKK7. The specific requirements of MKK4 and MKK7 in retinal development and retinal ganglion cell (RGC) death after axonal injury, however, are currently undefined. Optic nerve injury is an important insult in many neurologic conditions including traumatic, ischemic, inflammatory, and glaucomatous optic neuropathies. Mice deficient in Mkk4, Mkk7, and both Mkk4 and Mkk7 were generated. Immunohistochemistry was used to study the distribution and structure of retinal cell types and to assess RGC survival after optic nerve injury (mechanical controlled optic nerve crush; CONC). Adult Mkk4 and Mkk7 deficient retinas had all retinal cell types. With the exception of small areas of lamination defects with photoreceptors in Mkk4 deficient mice, the retinas of both mutants were grossly normal. Deficiency of Mkk4 or Mkk7 reduced JNK signaling after axonal injury in RGCs. Mkk4 and Mkk7 deficient retinas had a significantly greater percentage of surviving RGCs 35 days after CONC as compared to wildtype controls (Mkk4: 51.5%, Mkk7: 29.1% WT: 15.2%; p<0.001). Combined deficiency of Mkk4 and Mkk7 caused failure of optic nerve formation, irregular retinal axonal trajectories, disruption of retinal lamination, clumping of RGC cell bodies, and dendritic fasciculation of dopaminergic amacrine cells. These results suggest that MKK4 and MKK7 may serve redundant and unique roles in molecular signaling important for retinal development and injury response following axonal insult.

neuroscience↗