Daniel Ian McSkimming

Daniel Ian McSkimming
University of South Florida | USF · Morsani College of Medicine

PhD

About

41
Publications
6,008
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776
Citations
Citations since 2017
31 Research Items
748 Citations
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2017201820192020202120222023050100150200250
2017201820192020202120222023050100150200250

Publications

Publications (41)
Article
Very low birth weight (VLBW) infants (<1500 g) are at risk for poor neurodevelopmental outcomes depending on gestational age (GA), birth weight (BW), and morbidity in early life. The contribution of the gut microbiome is not well understood. Stool samples were collected weekly in the neonatal intensive care unit (NICU) from 24 VLBW infants for 6 we...
Preprint
Full-text available
Background and Objectives Very Low Birth Weight (VLBW) infants, born weighing less than 1500 grams, are at risk for both gut dysbiosis and later neuropsychological developmental deficits. With gut dysbiosis there is a disequilibrium of the gut microbial community. The Gammaproteobacteriadominated gut dysbiosis in VLBW infants likely results from a...
Preprint
Full-text available
Background and Objectives Very Low Birth Weight (VLBW) infants, born weighing less than 1500 grams, are at risk for both gut dysbiosis and later neuropsychological developmental deficits. With gut dysbiosis there is a disequilibrium of the gut microbial community. The Gammaproteobacteriadominated gut dysbiosis in VLBW infants likely results from a...
Article
Background: This study investigated the association between menopausal hormone therapy (HT) use and the subgingival microbiome, for which published information is limited. Methods: This cross-sectional study included 1,270 postmenopausal women, aged 53-81 years, who completed clinical examinations. Detailed information on HT use (type, delivery...
Article
Full-text available
Abstract Limited research exists on carbohydrate intake and oral microbiome diversity and composition assessed with next-generation sequencing. We aimed to better understand the association between habitual carbohydrate intake and the oral microbiome, as the oral microbiome has been associated with caries, periodontal disease, and systemic diseases...
Article
Full-text available
Kinetoplastids, including Trypanosoma brucei, control gene expression primarily at the posttranscriptional level. Nuclear mRNA export is an important, but understudied, step in this process. The general heterodimeric export factors, Mex67/Mtr2, function in the export of mRNAs and tRNAs in T. brucei, but RNA binding proteins (RBPs) that regulate exp...
Preprint
Kinetoplastids, including Trypanosoma brucei, control gene expression primarily at the posttranscriptional level. Nuclear mRNA export is an important, but understudied, step in this process. The general heterodimeric export factors, Mex67/Mtr2, function in the export of mRNAs and tRNAs in T. brucei, but RNA binding proteins (RBPs) that regulate exp...
Article
Factor H (FH) is a critical regulator of the alternative complement pathway and its deficiency or mutation underlie kidney diseases such as dense deposit disease. Since vascular dysfunction is an important facet of kidney disease, maintaining optimal function of the lining endothelial cells is important for vascular health. To investigate the molec...
Article
Full-text available
Patients with chronic kidney disease (CKD) and end stage renal disease suffer from increased cardiovascular events and cardiac mortality. Prior studies have demonstrated a portion of this enhanced risk can be attributed to the accumulation of microbiota-derived toxic metabolites, with most studies focusing on the sulfonated form of p-cresol (PCS)....
Article
Systemic lupus erythematosus (lupus) is a global health problem where 20-80% patients display cognitive problems and central nervous system (CNS) dysfunction. Early diagnosis and treatment of lupus remains a clinical challenge. Exercise improves experimental lupus nephritis. However, the effects of exercise in CNS lupus remains unknown. This study...
Article
Full-text available
Corrections have been made to “Gut Microbiota and Immune System Interactions” [1], a review article published in Microorganisms, to remove text found in previously published work. While phrasing was adjusted throughout, the most extensive changes can be found in Sections 2.1 and 3.1. Within days of publication, the authors became aware of some unin...
Article
Background: The aim of this study was to quantify the association between subgingival microbiota and periodontal disease progression in older women, for which limited published data exist. Methods: A total of 1016 postmenopausal women, aged 53 to 81 years, completed baseline (1997 to 2001) and 5-year (2002 to 2006) dental exams that included pro...
Article
Full-text available
Dynamic interactions between gut microbiota and a host’s innate and adaptive immune systems play key roles in maintaining intestinal homeostasis and inhibiting inflammation. The gut microbiota metabolizes proteins and complex carbohydrates, synthesize vitamins, and produce an enormous number of metabolic products that can mediate cross-talk between...
Article
Full-text available
Background: The extent to which the composition and diversity of the oral microbiome varies with age is not clearly understood. Methods: The 16S rRNA gene of subgingival plaque in 1219 women, aged 53-81 years, was sequenced and its taxonomy annotated against the Human Oral Microbiome Database (v.14.5). Composition of the subgingival microbiome w...
Article
Full-text available
Understanding of the oral microbiome in relation to periodontal disease in older adults is limited. The composition and diversity of the subgingival microflora and their oligotypes in health and levels of periodontal disease were investigated in this study on older postmenopausal women. The 16S rRNA gene was sequenced using the Illumina MiSeq platf...
Article
Introduction A possible role of the oral microbiome, specifically oral nitrate reducing flora, in blood pressure (BP) homeostasis, if proven etiologic in nature, could lead to novel mechanism-based therapy to improve hypertension prevention and control. Aim This cross-sectional study characterized and compared the oral microbiome between four stud...
Article
Impact statement: The heterogeneity of the renal disease, therapeutic interventions, and the original cause of the renal failure, all directly affect the microbiota. We delineate in this report the direct effect of decreased renal function on the bacterial composition following stringent criteria to eliminate the possibilities of other confounding...
Article
Full-text available
Purpose The Buffalo Osteoporosis and Periodontal Disease (OsteoPerio) study is a prospective cohort study focused on the relationship between the microbiome and oral and systemic health outcomes in postmenopausal women. The cohort was established to examine how the oral microbiome is affected by (and how it affects) periodontal disease presence, se...
Article
Full-text available
Aging invokes physiological changes, such as immunosenescence and inflammation, that could increase host susceptibility to oral microbiome shifts that enable periodontitis progression in later life. At present, there is a dearth of studies specifically evaluating the oral microbiome and periodontitis in older adults. We used high-throughput untarge...
Article
Full-text available
Many bioinformatics resources with unique perspectives on the protein landscape are currently available. However, generating new knowledge from these resources requires interoperable workfows that support cross-resource queries. In this study, we employ federated queries linking information from the Protein Kinase Ontology, iPTMnet, Protein Ontolog...
Article
Full-text available
Reprogrammed cellular metabolism is a common characteristic observed in various cancers. However, whether metabolic changes directly regulate cancer development and progression remains poorly understood. Here we show that BCAT1, a cytosolic aminotransferase for branched-chain amino acids (BCAAs), is aberrantly activated and functionally required fo...
Article
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Background Signaling proteins such as protein kinases adopt a diverse array of conformations to respond to regulatory signals in signaling pathways. Perhaps the most fundamental conformational change of a kinase is the transition between active and inactive states, and defining the conformational features associated with kinase activation is critic...
Article
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FLT3 is frequently mutated and overexpressed in acute myelogenous leukemia (AML) and other hematologic malignancies. Although signaling events downstream of FLT3 receptor tyrosine kinase has been studied in depth, molecular mechanisms of how FLT3 expression is regulated at the post-transcriptional level in particular remain elusive. In this study,...
Article
Multiple sequence alignments (MSAs) are a fundamental analysis tool used throughout biology to investigate relationships between protein sequence, structure, function, evolutionary history, and patterns of disease-associated variants. However, their widespread application in systems biology research is currently hindered by the lack of user-friendl...
Conference Paper
Full-text available
SPARQLing presents a graphical SPARQL query builder, which allows users of domain ontologies and RDF datasets formulate queries through visual inspection of classes and properties in the ontology or RDF schema. Our approach takes into account the users' preferences in viewing the elements of the interface. 1 Introduction Domain-specific ontologies...
Conference Paper
Full-text available
The growing volume of biomedical data available on the Web has contributed to numerous scientific advancements. At the same time, the complex, versatile and disparate nature of the data can overburden the knowledge discovery and data-driven hypothesis generation by scientists. Ontologies have been proposed to address the data integration challenge,...
Article
Full-text available
Protein kinases represent a large and diverse family of evolutionarily related proteins that are abnormally regulated in human cancers. Although genome sequencing studies have revealed thousands of variants in protein kinases, translating "big" genomic data into biological knowledge remains a challenge. Here we describe an ontological framework for...
Article
Full-text available
Protein phosphorylation lies at the heart of cell signalling, and somatic mutation(s) in kinases drives and sustains a multitude of human diseases, including cancer. The human protein kinase superfamily (the kinome) encodes approximately 50 'pseudokinases', which were initially predicted to be incapable of dynamic cell signalling when compared with...
Data
Supp. Table S4. Catalytic Spine Variants generated using v69 of COSMIC
Data
Supp. Table S1. Canonical RD Pocket Variants generated using v69 of COSMIC
Data
Supp. Table S2. KE Salt Bridge variants generated using v69 of COSMIC
Data
Supp. Table S3. Regulatory Spine Variants generated using v69 of COSMIC

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