Biology subjects

Sage, J. M.

Publications and source records attributed to Sage, J. M..

4 recordsLinked to original sources

bioRxiv2017

Impaired Cu-Zn superoxide dismutase (SOD1) and calcineurin (Cn) interaction in ALS: A presumed consequence for TDP-43 and zinc aggregation in Tg SOD1G93A rodent spinal cord tissue.

Impaired interactions between Calcineurin (Cn) and (Cu/Zn) superoxide dismutase (SOD1) are suspected to be responsible for the formation of hyperphosphorylated protein aggregation in amyotrophic lateral sclerosis (ALS). Serine (Ser)-enriched TDP-43 protein aggregation appears in the spinal cord of ALS animal models, and may be linked to the reduced phosphatase activity of Cn. The mutant overexpressed SOD1G93A protein does not properly bind zinc (Zn) in animal models; hence, mutant SOD1G93A - Cn interaction weakens. Consequently, unstable Cn fails to dephosphorylate TDP-43 that yields hyperphosphorylated TDP-43 aggregates. Our previous studies had suggested that Cn and SOD1 interaction was necessary to keep Cn enzyme functional. We have observed low Cn level, increased Zn concentrations, and increased TDP-43 protein levels in cervical, thoracic, lumbar, and sacral regions of the spinal cord tissue homogenates. This study further supports our previous published work indicating that Cn stability depends on functional Cn-SOD1 interaction because Zn metal is crucial for maintaining the Cn stability. Less active Cn did not efficiently dephosphorylate TDP-43; hence TDP-43 aggregations appeared in the spinal cord tissue.

neuroscience↗

bioRxiv2017

Automated Structural Variant Verification In Human Genomes Using Single-Molecule Electronic DNA Mapping

The importance of structural variation in human disease and the difficulty of detecting structural variants larger than 50 base pairs has led to the development of several long-read sequencing technologies and optical mapping platforms. Frequently, multiple technologies and ad hoc methods are required to obtain a consensus regarding the location, size and nature of a structural variant, with no approach able to reliably bridge the gap of variant sizes between the domain of short-read approaches and the largest rearrangements observed with optical mapping.\n\nTo address this unmet need, we have developed a new software package, SV-Verify, which utilizes data collected with the Nabsys High Definition Mapping (HD-Mapping) system, to perform hypothesis-based verification of putative deletions. We demonstrate that whole genome maps, constructed from electronic detection of tagged DNA, hundreds of kilobases in length, can be used effectively to facilitate calling of structural variants ranging in size from 300 base pairs to hundreds of kilobase pairs. SV-Verify implements hypothesis-based verification of putative structural variants using a set of support vector machines and is capable of concurrently testing several thousand independent hypotheses. We describe support vector machine training, utilizing a well-characterized human genome, and application of the resulting classifiers to another human genome, demonstrating high sensitivity and specificity for deletions [≥]300 base pairs.

genomics↗

bioRxiv2017

High-Definition Electronic Genome Maps From Single Molecule Data

With the advent of routine short-read genome sequencing has come a growing recognition of the importance of long-range, structural information in applications ranging from sequence assembly to the detection of structural variation. Here we describe the Nabsys solid-state detector capable of detecting tags on single molecules of DNA 100s of kilobases in length as they translocate through the detector at a velocity greater than 1 megabase pair per second. Sequence-specific tags are detected with a high signal-to-noise ratio. The physical distance between tags is determined after accounting for viscous drag-induced intramolecular velocity fluctuations. The accurate measurement of the physical distance between tags on each molecule and the ability of the detector to resolve distances between tags of less than 300 base-pairs enables the construction of high-density genome maps.

genomics↗

bioRxiv2017

Platelet phosphorylated TDP-43: An exploratory study for a peripheral surrogate biomarker development for Alzheimer’s disease

Aim: Alzheimers disease (AD) and other forms of dementia create a non-curable disease population in Worlds societies. To develop a blood-based biomarker is important so that the remedial or disease-altering therapeutic intervention for AD patients would be available at the early stage. Materials & Methods: TDP-43 levels were analyzed in post-mortem brain tissue and platelets of AD and control subjects. Results: We observed an increased TDP-43 (<60%) in post-mortem AD brain regions and similar trends were also observed in patients platelets. Conclusion: Platelet TDP-43 could be used as a surrogate biomarker that is measurable, reproducible, and sensitive for screening the patients with some early clinical signs of AD and can be used to monitor disease prognosis.\n\nLay abstractIn this study, we explore to identify an Alzheimers disease-selective phospho-specific antibody that recognizes the diseased form of TDP-43 protein in patients blood-derived platelets. Our results suggest that selective anti-phosphorylated TDP-43 antibody discriminates Alzheimers disease from non-demented controls and patients with amyotrophic lateral sclerosis. Therefore, platelet screening with a selective antibody could potentially be a useful tool for diagnostic purposes for Alzheimers disease.

neuroscience↗