Mehmet Candas

Professional Preparation

Ph.D. - Molecular Biology and Genetics
Southern Methodist University Dallas, Texas - 1995

M.S. - Biochemistry
Middle East Technical University, Ankara, Turkey - 1988

B.S. - Biochemistry
Middle East Technical University, Ankara, Turkey - 1985

Research Areas

Research Background and Interests

After earning my bachelor’s and master's degrees with specialties in biochemistry and cancer biology, I completed my doctoral dissertation with studies focusing on glutathione metabolism and oxidative stress in the aging process. In 1995, I joined a biotechnology company and worked on recombinant protein expression and live-bacteria vaccine delivery technologies for immune stimulation, particularly for treatment of infectious diseases and cancer. In 1997, I became associated with The University of Texas at Dallas where I started as a research scientist and studied metabolic features of bacterial virulence expression. Later, in 1999-2006, I served as the Research Manager for Center for Applied Biology (Center for Biotechnology and Bioinformatics). During this time, I focused my studies on bacterial and insect systems as paradigms for microbe-host interactions and investigated structural and functional aspects of cell adhesion receptors in cell death signaling cascades. The studies provided new insight into the action of insecticidal Bt toxins as well as how changes in proteomic expression profiles in insect gut epithelium consolidate with physiological responses associated with resistance to biopesticides. At the Center, I also helped develop a spin-off company emphasizing agricultural and environmental biotechnology. As a scientific co-founder and internal scientific consultant to the company, I implemented an integrated technology platform involving genomic, proteomic and bioinformatic applications for constructing versatile gene libraries and generating protein expression systems for cell-based assays.
My current interests focus on overlapping themes that underline the metabolic basis of phenotypic adaptation and how cells integrate metabolic responses with signaling pathways. What motivates me to work in this field is the continuing challenge to understand biological systems and their emergent properties through better use of scientific data and interdisciplinary technology applications. Main approaches that I employ include bioinformatics, in silico methods (databases, conceptual clustering, homology modeling, virtual screening, ontology and semantic analysis), functional genomics and proteomics applications along with traditional biochemistry, molecular biology, microbiology and cell biology techniques. My goal is to bring new insights into the evolutionary significance of metabolic adaptation and construct phenotypic and process models that can be exploited in biotechnology and medicine.

Publications

Identification of Molecular Compounds Targeting Bacterial Propionate Metabolism with Topological Machine Learning 2024 - publications

Changes in Electrical Capacitance of Cell Membrane Reflect Drug Partitioning-Induced Alterations in Lipid Bilayer. Micromachines 2023, 14(2), 316; https://doi.org/10.3390/mi14020316 2023 - Publication

Univalent Binding of the Cry1Ab Toxin of Bacillus thuringiensis to a Conserved Structural Motif in the Cadherin Receptor BT-R1. Biochemistry, 46 (35), 10001 -10007 (2007). 2007 - Publication

A mechanism of cell death involving an adenylyl cyclase/PKA signaling pathway is induced by the Cry1Ab toxin of Bacillus thuringiensis. Proc. Natl. Acad. Sci., U S A. 103:9897-902 (2006). 2006 - Publication

Cytotoxicity of Bacillus thuringiensis Cry1Ab Toxln Depends on Specific Binding of Toxin to the Cadherin Receptor BT-R1 Expressed in Insect Cells. Cell Death Differ. 12, 1407-1416 (2005). 2005 - Publication

Selective antagonism to the cadherin BT-R1 interferes with calcium-induced adhesion of epithelial membrane vesicles. Biochemistry 43:1393-1400 (2004). 2004 - Publication

Insect resistance to Bacillus thuringiensis: Alterations in the Indianmeal moth larval gut proteome. Mol. Cell Proteomics 2:19-28 (2003). 2003 - Publication

Expression of a midgut-specific cadherin BT-R1 during the development of Manduca sexta larva. Comp. Biochem. Physiol. 135:125-137 (2003). 2003 - Publication

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Appointments

Professor
The University of Texas at Dallas [2006–Present]

Research Engineering Scientist
The University of Texas at Dallas [1999–2006]

Chief Science & Technology Officer
Biological Targets, Inc., Dallas, Texas [1999–2006]

Research Scientist
The University of Texas at Dallas [1997–1999]

Lead Scientist - Recombinant Vaccines
Cytoclonal Pharmaceutics, Inc., Dallas, TX [1995–1997]

Research and Teaching
Southern Methodist University [1989–1995]

Research
Middle East Technical University, Ankara, Turkey [1987–1989]

Research and Teaching Fellow - Medical Biology and Genetics
The University of Ankara Medical School, Ankara, Turkey [1986–1987]

Technical Associate - Clinical Biochemistry
Duzen Laboratories, Inc., Ankara, Turkey [1984–1986]

Projects

Targeting Phenotypic Adaptation for Antimicrobial Development

2004/05–2020/12 Virulence and resistance of bacterial pathogens during infection involve phenotypic adaptation in which pathogens modulate their metabolic activity in response to changing environment and nutrient availability in the host. This phenotypic adaptation is a survival strategy and allows pathogens to persist under severely-limited nutritional environments by utilizing molecules acquired from the host during infection.

During infection, under limited glucose availability in host, invading pathogens need to utilize metabolites arising from utilization of complex carbon sources like cholesterol, odd chain fatty acid, and certain amino acids as well as fermentation of various sugars. Effective inhibition of the production or the activity of certain enzymes abolishes key metabolic pathways in bacteria, resulting in significant reduction in bacterial growth and virulence expression, including biofilm production.

A novel antimicrobial target enzyme with classifiable substrate and catalytic function was identified, providing a promising approach for discovery of new anti-microbial, anti-infective, and anti-bacterial compounds as well as biofilm control agents.

University of Texas at Dallas
http://utdallas.technologypublisher.com/technology/28857

Characterization of enzyme active sites and potential ligand interactions through comparative modeling of protein three-dimensional structures.

2012/01–2020/11 University of Texas at Dallas
Undergraduate Research Program

Homology modeling and virtual screening of protein structure for potential ligand interactions.

2012/01–2020/10 University of Texas at Dallas
Undergraduate Research Program

Bioinformatics framework for conceptual mapping of relationships between folic acid and neural tube defects.

2011/08–2012/05 Information associated with genes and proteins are continuously increasing as high-throughput laboratory experimentation and massively-parallel computation methods facilitate faster data generation. However, accumulation of vast information and emergence of information silos pose a serious challenge to assimilation of information and effective analysis of functional correlations in biology and medicine. Thus extraction, integration and interpretation of information that is not coherently connected to each other, could help translating biomedical knowledge to practical applications.

Gene Ontology infrastructure has been described to facilitate semantic interoperability in mining, annotation, analysis, and integration of information about genes and proteins. These ontologies descibe attributes related to molecular function, cellular location and biological processes. We explored the utility of ontologies associated with neural tube folding and folic acid biology to find possible mechanistic relationship concerning folic acid deficiency and neural tube malformation. Results implicate the folate receptor 1 as a potential culprit in the formation of neural tube defects. Reduced folate transport may limit folate availability in developing embryo. We postulated that folate limitation may occur if the transport protein is down regulated as a result of excess folate supplementation, or the process may be limiting due to insufficient level and/or activity of the transport protein.

In addition, we show that conceptual mapping of gene-phenotype associations with GO is a useful approach to construct or validate a plausible hypothesis. The integrative and translational aspect of information re-use, as exploited in this study, could help reconcile disconnected information in the biomedical databases, and facilitate discovery of unrealized relationships. This could lead to applications critical to biomedical research and healthcare industry, including personalized medical treatments, pharmaceutical drug repositioning, bioinformatics and medical informatics

Structuring multidisciplinary biology courses - A case study: Cellular Microbiology.

2010/05–2010/05 University of Texas at Dallas

ASBMB Experimental Biology

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Additional Information

Teaching Activities

Biochemistry I (BIOL 3361) – Structures and chemical properties of amino acids; protein purification and characterization; protein structure; thermodynamics of protein folding; catalytic mechanisms, kinetics and regulation of enzymes; energetic of biochemical reactions; metabolism; roles of coenzymes and prosthetic groups; redox reactions; pathways for carbohydrate oxidation; glycogen metabolism; glucose synthesis; pentose phosphate pathway; electron transport and oxidative phosphorylation.

Biochemistry II (BIOL 3362) – Structure and functional properties of biological lipids (phospholipids, ceramides, glycolipids, waxes, isoprene-based compounds, and steroids); physical and chemical properties of membranes; membrane organization and dynamics; membrane proteins and transport processes across cell membrane; regulation of lipid metabolism; biosynthesis, breakdown and interconversion of fatty acids, cholesterol, isoprenoids and eicosanoids; hormone action, organ specialization; integration of metabolism, metabolic disorders, and biochemical basis of certain pathological processes; nitrogen metabolism and fixation; nucleotide metabolism; structure and properties of nucleic acids; sequencing and genetic engineering; replication, transcription, and translation; chromosome structure.

Host-Pathogen Interactions (BIOL 5370) / Cellular Microbiology (BIOL 4310) - The course covers infectious diseases in the context of pathogen evolution, host cell properties, and immune responses. Emphasis is given to the theme that microorganisms co-evolve with their hosts and ecological and evolutionary associations determine the dynamic nature of symbiosis (mutualism, commensalism, parasitism). It reflects on the different properties of example bacterial and viral pathogens and describes their virulence and pathogenicity by incorporating mechanistic aspects of horizontal gene transfer, the mode of action of bacterial toxins, manipulation of host cell functions, and impact of microbial metabolites on host physiology. The course also explores studies in the field of microbial genomics, human microbiome, probiotics, and applications of functional genomics and proteomics platforms to molecular microbiology and infectious diseases research, particularly for the development of antimicrobial drugs, vaccines, and molecular diagnostics.

Nutrition and Metabolism (BIOL 4325) / Nutritional Physiology (5325) - This course explores nutrient utilization and requirements, focusing on the links between diet, health, genetics, microbiome, and diseases. It covers nutritional physiology and metabolic homeostasis in human development, aging, exercise, and disease. Topics include energy metabolism, macronutrients, vitamins, minerals, and protective food compounds. The course examines how nutrient imbalances contribute to chronic diseases like heart disease, diabetes, and cancer. It also looks at diet in human evolution and societal contexts, addressing public health, sustainable food, and nutrition security. Additionally, it introduces microbiomics, nutrigenomics, nutrigenetics, and chrononutrition, highlighting gene-nutrient interactions and the impact of diet and sleep on metabolism.

Biotechnology Laboratory (BIOL 6684) – Applications of biotechnology methods in a laboratory setting; isolation and analysis of DNA, proteomics (theories and concepts related to research and clinical studies, 1D and 2D SDS PAGE, liquid chromatography, instrumentation basics of mass spectrometry, ionization techniques, peptide fragmentation, peptide fingerprinting, and protein identification and bioinformatics applications for protein sequence analysis and BLAST Searching), real time PCR, ELISA, FACS cell sorting, transfection of animal cells, immunocytochemistry and confocal microscopy.

Ecosystems (BIOL 3V00) - This course explores the fundamental characteristics of ecosystems, integrating biological and environmental sciences to understand Earth’s biodiversity and interconnectedness. It examines the structure and function of terrestrial, freshwater, and marine ecosystems, emphasizing interdependence of communities. Topics include biodiversity, sustainability, and human impact on ecosystems. Natural processes like matter and energy flow, carbon and nutrient cycling, and the effects of climate change and global change drivers (e.g., agriculture, food production, land use change, and altered disturbance regimes) are reviewed. The course also addresses conservation, resource management, and the importance of ecosystem goods and services for survival and economic development, particularly for food, feed, fiber, fuel, medicine, and industrial raw material production. Ecosystem science is presented as essential for understanding ecological networks and dynamics.

Biotechnology Product Design (BIOL 6V51) – This course guides students in designing theoretical applications to solve biotechnological problems. It enhances multidisciplinary knowledge and integrative skills through case-based learning. Students develop self-guided projects, proposing innovative products in fields like medicine, agriculture, energy, or the environment. Projects might include therapeutic drugs, bioanalytical tools, genetically modified plants, biofuels, or ecosystem bioremediation. Emphasis is on problem definition, scientific evaluation, and real-life application. Projects are assessed on procedural, integrative, and organizational aspects, with critical evaluations at three stages. The final report should demonstrate understanding of background information, scientific methodology, and application design. Ideal for students interested in engineering principles and multidimensional approaches.

Comparative Analysis of Genes and Proteins (BIOL 6V59) – Self-guided study focuses on proteins’ diverse properties, aiming to equip students with bioinformatics and AI tools to explore protein structures and functions. Projects integrate alignment, clustering, structure modeling, and virtual screening to evaluate molecular features. Studies include identifying sequence motifs, analyzing conserved domains, visualizing 3D structures, classifying unstructured regions, constructing phylogenetic profiles, speculating on mutation effects, and interpreting physicochemical descriptors in ligand binding, enzyme catalysis, protein interactions, and drug action.

Eukaryotic Molecular Cell Biology (BIOL 3302) – Structural organization of eukaryotic cells; regulation of cellular activities; membranes and transport across cell membrane; cell specialization; cell signaling molecules and cell surface receptors; signal transduction pathways that control gene activity; the organization and control of the eukaryotic cytoskeleton; mechanisms of protein targeting to cellular organelles; vesicle traffic, secretion and endocytosis; the molecular regulation of the eukaryotic cell cycle, and aspects of the molecular basis of cancer.
Independent Study - Research and Advanced Writing (BIOL 4390) – Planning and conducting thematic research; strategies for scientific literature analysis, examining original research articles, communicating facts and theories by coherent writing.

Modern Biology I (BIOL 2311) – Fundamental concepts in modern biology with an emphasis on molecular and cellular basis of biological phenomena. Topics include the basic biochemistry of biological molecules; cellular metabolism, organization of prokaryotic and eukaryotic cells, introductory classical and molecular genetics, essentials of mammalian physiology, organizational and operation principles of endocrine, immune, and nervous systems, and selected aspects of developmental biology, as well as study of major groups of biological organisms such as bacteria, viruses and fungi.

Modern Biology II (BIOL 2312) – Fundamental aspects of mammalian physiology with an emphasis on the human body systems, physiological evolution, organ development, regulation of organ functions and physiological mechanisms regulating the internal environment (homeostasis).

Natural Science & Mathematics Freshmen Seminar (NATS1101) - An overview of approaches to basic study and learning strategies, critical thinking, problem solving, group work and other skills as well as studentship and professional ethics; inter-disciplinary and cross-disciplinary connections within the programs of the School of Natural Science and Mathematics as well as their relationship to other scientific, technology and engineering fields and interdisciplinary applications. Emphasis is given to discussions on current and emerging themes of scientific research, education and technology applications in the 21st century.
Cell and Molecular Biology Laboratory (BIOL 4380)– DNA manipulation, cloning, bacterial transformation, plasmid mapping, PCR, DNA fingerprinting, mutagenesis and AMES test, centrifugation, cell fractionation, enzyme assays, mammalian cell culture techniques, transfection and ion-trapping

Body Systems (BIOL 1300) – Introductory to human physiology in relation to molecular, cellular and anatomical structures; examination of human body and organ systems with model-based lab exercises; physiological functions associated with homeostasis and integration of metabolism, basic information about diseases and disorders with special considerations to preventative and self-care approaches.

Introduction to Biotechnology (BIOL 5V00)– overview of techniques utilized in biomedical research and bioprocessing/biomanufacturing applications in the pharmaceutical, agricultural and environmental biotechnology industries; principles of common methods involving protein chemistry, molecular and cell biology; macromolecular separation, purification and analysis of biological molecules, chromatography, electrophoresis, molecular and cellular labeling, detection and assay methods, use of antibodies, DNA sequencing, recombinant DNA, protein engineering, nucleic acid primers, amplification and hybridization-based methods, PCR, RT-PCR, qPCR, gene libraries, genotyping, gene expression analysis, microarrays, bioinformatics, genomics, proteomics, DIGE, ICAT, mass spectroscopy, and systems biology-based approaches; molecular diagnostics, biomarkers and clinical trials

Biology of Aging – (under development): concepts and theories of aging; the evolution and genetics of aging; oxidative processes in aging; nutritional and physiological aspects of aging and longevity; mammalian metabolism in aging; dietary restriction, health and longevity; effect of age on gene expression; instability of the nuclear genome and alterations of the mitochondrial genome during aging; cell proliferation in mammalian aging; pathophysiology of aging and age-related diseases.

Medical Biochemistry – (under development): This upper-level undergraduate course revisits fundamental biochemical principles through the lens of case studies and clinical insights. It explores the biochemical basis of human health and disease, focusing on metabolic pathways, enzyme function, and molecular interactions. The course integrates theoretical knowledge with practical applications, emphasizing real-world clinical scenarios to illustrate key concepts. By analyzing case studies, students will gain a deeper understanding of biochemical processes and their implications in medical practice. The course aims to prepare students for advanced studies and careers in medical and health sciences, fostering critical thinking and problem-solving skills.

Activities

Affiliations

ASBMB - American Society for Biochemistry and Molecular Biology
Sigma Xi Scientific Research Honors SocietyNational Center for Case Study Teaching in ScienceThe Retina Foundation of the Southwest

Board for Knowledge, Southern Methodist University (Dallas, TX)
Medical Technology Program Board, UT Southwestern Medical School (Dallas, TX)
Association of Clinical Research Professionals (Alexandria, VA)
American Association for Advancement of Science (Washington, DC)
American Chemical Society (Washington, DC)
Society of Industrial Microbiology (Fairfax, VA)
New York Academy of Sciences (New York, NY)
American Society for Microbiology (Washington, DC) American Society for Tropical Medicine (Northbrook, IL)