Catalogue Search | MBRL
Are you sure you want to remove the book from the shelf?
{{itemTitle}}
147
result(s) for
"Rush, Matthew"
Sort by:
Mitochondrial protein functions elucidated by multi-omic mass spectrometry profiling
Proteomics, lipidomics and metabolomics of single gene deletion yeast strains sheds light on mitochondrial protein biology.
Mitochondrial dysfunction is associated with many human diseases, including cancer and neurodegeneration, that are often linked to proteins and pathways that are not well-characterized. To begin defining the functions of such poorly characterized proteins, we used mass spectrometry to map the proteomes, lipidomes, and metabolomes of 174 yeast strains, each lacking a single gene related to mitochondrial biology. 144 of these genes have human homologs, 60 of which are associated with disease and 39 of which are uncharacterized. We present a multi-omic data analysis and visualization tool that we use to find covariance networks that can predict molecular functions, correlations between profiles of related gene deletions, gene-specific perturbations that reflect protein functions, and a global respiration deficiency response. Using this multi-omic approach, we link seven proteins including Hfd1p and its human homolog ALDH3A1 to mitochondrial coenzyme Q (CoQ) biosynthesis, an essential pathway disrupted in many human diseases. This Resource should provide molecular insights into mitochondrial protein functions.
Journal Article
Defining mitochondrial protein functions through deep multiomic profiling
Mitochondria are epicentres of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles
1
and have linked their dysfunction to more than 150 distinct disorders
2
,
3
. Still, hundreds of mitochondrial proteins lack clear functions
4
, and the underlying genetic basis for approximately 40% of mitochondrial disorders remains unresolved
5
. Here, to establish a more complete functional compendium of human mitochondrial proteins, we profiled more than 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multiomics analyses. This effort generated approximately 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that
PIGY
upstream open reading frame (PYURF) is an
S
-adenosylmethionine-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis and is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitochondrial ribosomes and OxPhos integrity and established
RAB5IF
as the second gene harbouring pathogenic variants that cause cerebrofaciothoracic dysplasia. Our data, which can be explored through the interactive online MITOMICS.app resource, suggest biological roles for many other orphan mitochondrial proteins that still lack robust functional characterization and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.
A multiomics resource characterizing human mitochondrial proteins enables identification of biological functions and supports genetic diagnosis of mitochondrial pathologies.
Journal Article
Morphology investigation on direct current pulsed gas tungsten arc welded additive layer manufactured Ti6Al4V alloy
The effects of pulsed gas tungsten arc welding parameters on the morphology of additive layer manufactured Ti6Al4V has been investigated in this study. The peak/base current ratio and pulse frequency are found to have no significant effect on the refinement of prior beta grain size. However, it is found that the wire feed rate has a considerable effect on the prior beta grain refinement at a given heat input. This is due to the extra wire input being able to supply many heterogeneous nucleation sites and also results in a negative temperature gradient in the front of the liquidus which blocks the columnar growth and changes the columnar growth to equiaixal growth.
Journal Article
A Calibration Routine for Efficient ETD in Large-Scale Proteomics
Electron transfer dissociation (ETD) has been broadly adopted and is now available on a variety of commercial mass spectrometers. Unlike collisional activation techniques, optimal performance of ETD requires considerable user knowledge and input. ETD reaction duration is one key parameter that can greatly influence spectral quality and overall experiment outcome. We describe a calibration routine that determines the correct number of reagent anions necessary to reach a defined ETD reaction rate. Implementation of this automated calibration routine on two hybrid Orbitrap platforms illustrate considerable advantages, namely, increased product ion yield with concomitant reduction in scan rates netting up to 75% more unique peptide identifications in a shotgun experiment.
Graphical Abstract
ᅟ
Journal Article
Sulfur Pentafluoride is a Preferred Reagent Cation for Negative Electron Transfer Dissociation
Negative mode proteome analysis offers access to unique portions of the proteome and several acidic post-translational modifications; however, traditional collision-based fragmentation methods fail to reliably provide sequence information for peptide anions. Negative electron transfer dissociation (NETD), on the other hand, can sequence precursor anions in a high-throughput manner. Similar to other ion–ion methods, NETD is most efficient with peptides of higher charge state because of the increased electrostatic interaction between reacting molecules. Here we demonstrate that NETD performance for lower charge state precursors can be improved by altering the reagent cation. Specifically, the recombination energy of the NETD reaction—largely dictated by the ionization energy (IE) of the reagent cation—can affect the extent of fragmentation. We compare the NETD reagent cations of C
16
H
10
●+
(IE = 7.9 eV) and SF
5
●+
(IE = 9.6 eV) on a set of standard peptides, concluding that SF
5
●+
yields greater sequence ion generation. Subsequent proteome-scale nLC-MS/MS experiments comparing C
16
H
10
●
+
and SF
5
●+
further supported this outcome: analyses using SF
5
●+
yielded 4637 peptide spectral matches (PSMs) and 2900 unique peptides, whereas C
16
H
10
●
+
produced 3563 PSMs and 2231 peptides. The substantive gain in identification power with SF
5
●+
was largely driven by improved identification of doubly deprotonated precursors, indicating that increased NETD recombination energy can increase product ion yield for low charge density precursors. This work demonstrates that SF
5
●+
is a viable, if not favorable, reagent cation for NETD, and provides improved fragmentation over the commonly used fluoranthene reagent.
Graphical Abstract
ᅟ
Journal Article
Assessment of Variable Rate Nitrogen Application on Rice Cultivars Using Remote Sensing
Application of the right time and amount of fertilizer N is challenging in rice fertilization because crop N supply is highly variable in the field. Research plots were established at four research plot fields and one commercial field in Arkansas. Independent variables included six nitrogen (N) application rates (0, 67, 101, 134.5, 168, and 202 kg N ha-1), multiple rice cultivars, and five locations. The response variable was 24 vegetative indices values using high spatio-temporal multispectral and thermal imagery obtained from an Unmanned Aerial Vehicle (UAV). The 134 and 168 kg N ha-1 rates were identified as the control group (recommended rate), indicating deficient and sufficient N application could be detected using sensing technologies when visual inspection fails to detect such differences. The results showed that in-season assessments of rice N-demand using remote sensing indices might provide a useful N-management tool for in-season N-management and recommendations for both grain yield and profit.
Dissertation
Defining mitochondrial protein functions through deep multi-omic profiling
Mitochondria are epicenters of eukaryotic metabolism and bioenergetics. Pioneering efforts in recent decades have established the core protein componentry of these organelles1 and have linked their dysfunction to over 150 distinct disorders2,3. Still, hundreds of mitochondrial proteins lack clear functions4, and 40% of mitochondrial disorders remain unresolved5. To establish a more complete functional compendium of human mitochondrial proteins, we profiled over 200 CRISPR-mediated HAP1 cell knockout lines using mass spectrometry-based multi-omics analyses. This effort generated 8.3 million distinct biomolecule measurements, providing a deep survey of the cellular responses to mitochondrial perturbations, and laying a foundation for mechanistic investigations into protein function. Guided by these data, we discovered that PYURF is a SAM-dependent methyltransferase chaperone that supports both complex I assembly and coenzyme Q biosynthesis, and that is disrupted in a previously unresolved multisystemic mitochondrial disorder. We further linked the putative zinc transporter SLC30A9 to mitoribosome and OxPhos integrity and established RAB5IF as the second gene harboring pathogenic variants causing cerebrofaciothoracic dysplasia. Our data—which can be explored through an interactive online MITOMICS.app resource—suggest biological roles for many other orphan mitochondrial proteins still lacking robust functional characterization, and define a rich cell signature of mitochondrial dysfunction that can support the genetic diagnosis of mitochondrial diseases.
Journal Article
The Role of Principal and Teacher Leadership within Professional Learning Communities: A Cultural Theory Perspective
The purpose of this study was through cultural theory, to explore principals’ and teachers’ roles in professional learning communities in selected school contexts. Professional learning communities (PLCs) are powerful models designed to promote system-wide school improvement. While PLCs are designed to promote system-wide school improvement, research indicated that these goals are accomplished in some instances (DuFour et al, 2005; Saphier, 2005; Schmoker, 2005), and not accomplished in others (Carroll, 2010; Chenowith, 2009; Fullan, 2007; Hattie, 2009; Sims & Penny, 2015; Supovitz & Christman, 2003; Talbert, 2011). One way to explain these discrepancies is through cultural theory, which posits that cultural members’ roles and the rules associated with those roles are important variables in contextual practices and interactions (Douglas, 1995; Giles-Sims & Lockhart, 2005; Harris, 2005). For example, teachers’ and principals’ roles may inhibit or promote the success of PLCs in a given school environment. (Fullan, 2006; Hord, 2004; Leithwood, & Riehl, 2003). This study used naturalistic inquiry methods (Erlandson, Harris, Skipper & Allen, 1993), which allows the researcher to understand the everyday life of the people involved in the educational environment. The naturalistic inquiry method was chosen to provide a holistic picture of what the impact is on the lives of the teachers, school culture, and the principal, within the school context. This study was bound to two middle schools and explored the PLC structure, through Douglas’s (1982, 1986) Cultural Theory.
Dissertation
Chemically Modified Monolayer Surfaces Influence Valvular Interstitial Cell Attachment and Differentiation for Heart Valve Tissue Engineering
As a cell mediated-process, valvular heart disease (VHD) results in significant morbidity and mortality world-wide. In the US alone, valvular heart disease VHD is estimated to affect 2.5% of the population with a disproportionate impact on an increasing elderly populous. It is well understood that the primary driver for valvular calcification is the differentiation of valvular interstitial cells (VICs) into an osteoblastic-like phenotype. However, the factors leading to the onset of osteoblastic-like VICs (obVICs) and resulting calcification are not fully understood and a more complete characterization of VIC differentiation and phenotypic change is required before treatment of valve disease or growth of tissue engineered heart valves (TEHVs) can be realized. By investigating the microenvironmental cues at the cell-material interface, surface chemistry, protein adhesion, and integrin expression we have identified cell-material signaling that may be responsible for heart valve tissue calcification as well as healthy in vitro growth environments. A three-dimensional hydrogel system was developed for the study of VICs in a more physically relevant cell culture system.
Dissertation