Dr. Mohamed (Moh) Salem
Areas of Expertise
- PI of a grant funded by USDA/AFRI (SNP Markers for Muscle, Growth and Fillet Quality Traits in Rainbow Trout) (2014-2018, $500K).
- Co-PI of a grant funded by USDA/AFRI (Generation of a 50K SNP chip for genomic analysis in rainbow trout) (2011-2014, $675K).
- Co-PI and key investigator of the Rainbow Trout Genome Project USDA/ARS (2010-2012, $410K/year).
- Co-PI of a grant funded by USDA/NRI-Animal Genome (Molecular biomarkers for muscle atrophy and fillet quality in rainbow trout)(2007-2012, $382K).
Dr. Salem's interests are focused on using the state-of-the-art "genomics" technologies and experiments to study and characterize various physiological processes in non-model species. He uses high throughput omics and bioinformatics approaches to study gene networks/pathways that regulate different physiological traits at genomics, transcriptomics, post-transcriptomics and proteomics levels. His projects include but are not limited to utilization of genomic approaches to examine and enhance fish production traits with particular interest in muscle growth and quality.
- Salem M, Al-Tobasei R, Ali A, Lourenco D, Gao G, Palti Y, Kenney PB, Leeds TD: Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout.
- Salem M, Al-Tobasei R, Ali A, Lourenco D, Gao G, Palti Y, Kenney PB, Leeds TD: Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout. Frontiers in Genetics 2018, 9.
- Ali A, Al-Tobasei R, Kenney B, Leeds T, Salem M: Integrated analysis of lncRNA and mRNA expression in rainbow trout families showing variation in muscle growth and fllet quality traits. Sci Rep 2018, 8:12111
- Paneru B, Ali A, Al-Tobasei R, Kenney B, Salem M: Crosstalk among lncRNAs, microRNAs and mRNAs in the muscle ‘degradome’ of rainbow trout. Sci Rep 2018, 8:8416
- Al-Tobasei R, Ali A, Leeds TD, Liu S, Palti Y, Kenney B, Salem M: Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seqsamples in rainbow trout. BMC Genomics 2017, 18:582
- Paneru B, Al-Tobasei R, Leeds TD, Kenney B, Salem M: RNA-Seq reveals MicroRNA expression signature and genetic polymorphism associated with growth and muscle quality traits in rainbow trout. Sci Rep 2017, 7:9078
- Aquaculture Genomics G, Breeding W, Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H et al: Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017, 18(1):191
- Paneru B, Al-Tobasei R, Palti Y, Wiens GD, Salem M: Differential expression of long non-coding RNAs in three genetic lines of rainbow trout in response to infection with Flavobacterium psychrophilum. Sci Rep 2016, 6:36032.
- Al-Tobasei R, Paneru B, Salem M: Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout. PLoS One 2016, 11(2):e0148940.
- Salem M, Paneru B, Al-Tobasei R, Abdouni F, Thorgaard GH, Rexroad CE, Yao J: Transcriptome Assembly, Gene Annotation and Tissue Gene Expression Atlas of the Rainbow Trout. PloS One 2015, 10(3):e0121778.
- Khadka M, Salem M, Leblond JD: Sterol Composition and Biosynthetic Genes of Vitrella brassicaformis, A Recently Discovered Chromerid: Comparison to Chromera velia and Phylogenetic Relationship to Apicomplexan Parasites. Journal of Eukaryotic Microbiology 2015.
- Palti Y, Gao G, Miller MR, Vallejo RL, Wheeler PA, Quillet E, Yao J, Thorgaard GH, Salem M, Rexroad CE: A resource of single nucleotide polymorphisms for rainbow trout generated by restriction site associated DNA sequencing of doubled haploids. Molecular ecology resources 2014, 14(3):588-596.
- Marancik D, Gao G, Paneru B, Ma H, Hernandez AG, Salem M, Yao J, Palti Y, Wiens GD: Whole-body transcriptome of selectively bred, resistant-, control-, and susceptible-line rainbow trout following experimental challenge with Flavobacterium psychrophilum. Frontiers in genetics 2014, 5.
- Khadka M, Dahmen JL, Salem M, Leblond JD: Comparative study of galactolipid composition and biosynthetic genes for galactolipid synthases in Vitrella brassicaformis and Chromera velia, two recently identified chromerids with red algal-derived plastids. Algological studies 2014, 144:73 - 93.
- Ali A, Rexroad CE, Thorgaard GH, Yao J, Salem M: Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. Frontiers in genetics 2014, 5.
- Salem M, Manor ML, Aussanasuwannakul A, Kenney PB, Weber GM, Yao J: Effect of sexual maturation on muscle gene expression of rainbow trout: RNA-Seq approach. Physiological reports 2013, 1(5):e00120.
- Salem M, Vallejo RL, Leeds TD, Palti Y, Liu S, Sabbagh A, Rexroad CE, Yao J: RNA-Seq identifies SNP markers for growth traits in rainbow trout. PLoS One 2012, 7(5):e36264-e36264.
- Salem M: Next-generation sequencing and functional genomic analysis in Rainbow Trout. Functional Genomics in Aquaculture,(Eds) M Saroglia and Z(John) Liu, Wiley-Blackwell 2012:321-337.
- Manor ML, Weber GM, Salem M, Yao J, Aussanasuwannakul A, Kenney PB: Effect of sexual maturation and triploidy on chemical composition and fatty acid content of energy stores in female rainbow trout, Oncorhynchus mykiss. Aquaculture 2012, 364:312-321.
- Aussanasuwannakul A, Weber GM, Salem M, Yao J, Slider S, Manor ML, Brett Kenney P: Effect of sexual maturation on thermal stability, viscoelastic properties, and texture of female rainbow trout, Oncorhynchus mykiss, fillets. Journal of food science 2012, 77(1):S77-S83.
- Aussanasuwannakul A, Slider SD, Salem M, Yao J, Brett Kenney P: Comparison of Variable Blade to Allo-Kramer Shear Method in Assessing Rainbow Trout (Oncorhynchus mykiss) Fillet Firmness. Journal of food science 2012, 77(9):S335-S341.
- Wang J, Salem M, Qi N, Kenney PB, Rexroad CE, Yao J: Molecular characterization of the MuRF genes in rainbow trout: Potential role in muscle degradation. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 2011, 158(3):208-215.
- Aussanasuwannakul A, Kenney PB, Weber GM, Yao J, Slider SD, Manor ML, Salem M: Effect of sexual maturation on growth, fillet composition, and texture of female rainbow trout (Oncorhynchus mykiss) on a high nutritional plane. Aquaculture 2011, 317(1):79-88.
- Tripurani SK, Xiao C, Salem M, Yao J: Cloning and analysis of fetal ovary microRNAs in cattle. Animal reproduction science 2010, 120(1):16-22.
- Salem M, Xiao C, Womack J, Rexroad III CE, Yao J: A microRNA repertoire for functional genome research in rainbow trout (Oncorhynchus mykiss). Marine biotechnology 2010, 12(4):410-429.
- Salem M, Rexroad CE, Wang J, Thorgaard GH, Yao J: Characterization of the rainbow trout transcriptome using Sanger and 454-pyrosequencing approaches. BMC genomics 2010, 11(1):564.
- Salem M, Kenney PB, Rexroad CE, Yao J: Proteomic signature of muscle atrophy in rainbow trout. Journal of proteomics 2010, 73(4):778-789.
- Aussanasuwannakul A, Kenney PB, Brannan RG, Slider SD, Salem M, Yao J: Relating Instrumental Texture, Determined by Variable Blade and Allo-Kramer Shear Attachments, to Sensory Analysis of Rainbow Trout, Oncorhynchus mykiss, Fillets. Journal of food science 2010, 75(7):S365-S374.
- Tripurani SK, Xiao C, Salem M, Yao J: Cloning and Expression Profiling of Fetal Ovary-Expressed MicroRNAs in Cattle. Biology of Reproduction 2009, 81(1 Supplement):345.
- Sánchez CC, Smith TP, Wiedmann RT, Vallejo RL, Salem M, Yao J, Rexroad CE: Single nucleotide polymorphism discovery in rainbow trout by deep sequencing of a reduced representation library. Bmc Genomics 2009, 10(1):559.
- Goravanahally MP, Salem M, Yao J, Inskeep EK, Flores JA: Differential gene expression in the bovine corpus luteum during transition from early phase to midphase and its potential role in acquisition of luteolytic sensitivity to prostaglandin F2 alpha. Biology of reproduction 2009, 80(5):980-988.
- Salem M, Kenney P, Rexroad C, Yao J: Development of a 37 k high-density oligonucleotide microarray: a new tool for functional genome research in rainbow trout. Journal of Fish Biology 2008, 72(9):2187-2206.
- Ramachandra RK, Salem M, Gahr S, Rexroad CE, Yao J: Cloning and characterization of microRNAs from rainbow trout (Oncorhynchus mykiss): their expression during early embryonic development. BMC developmental biology 2008, 8(1):41.
- Bettegowda A, Patel OV, Lee K-B, Park K-E, Salem M, Yao J, Ireland JJ, Smith GW: Identification of novel bovine cumulus cell molecular markers predictive of oocyte competence: functional and diagnostic implications. Biology of reproduction 2008, 79(2):301-309.
- Salem M, Silverstein J, Rexroad CE, Yao J: Effect of starvation on global gene expression and proteolysis in rainbow trout (Oncorhynchus mykiss). BMC genomics 2007, 8(1):328.
- Salem M, Kenney PB, Rexroad CE, Yao J: Microarray gene expression analysis in atrophying rainbow trout muscle: a unique nonmammalian muscle degradation model. Physiological Genomics 2007, 28(1):33-45.
- Salem M, Rexroad C, Yao J: Identification of a novel gill-specific calpain from rainbow trout (Oncorhynchus mykiss). Fish physiology and biochemistry 2006, 32(1):1-6.
- Salem M, Levesque H, Moon TW, Rexroad CE, Yao J: Anabolic effects of feeding β 2-adrenergic agonists on rainbow trout muscle proteases and proteins. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 2006, 144(2):145-154.
- Salem M, Kenney PB, Rexroad CE, Yao J: Molecular characterization of muscle atrophy and proteolysis associated with spawning in rainbow trout. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 2006, 1(2):227-237.
- Salem M, Yao J, Rexroad CE, Kenney PB, Semmens K, Killefer J, Nath J: Characterization of calpastatin gene in fish: its potential role in muscle growth and fillet quality. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 2005, 141(4):488-497.
- Salem M, Nath J, Rexroad CE, Killefer J, Yao J: Identification and molecular characterization of the rainbow trout calpains (Capn1 and Capn2): their expression in muscle wasting during starvation. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 2005, 140(1):63-71.
- Salem M, Nath J, Killefer J: Cloning of the calpain regulatory subunit cDNA from fish reveals a divergent domain-V. Animal biotechnology 2004, 15(2):145-157.
- Salem M, Kenney P, Killefer J, Nath J: Isolation and characterization of calpains from rainbow trout muscle and their role in texture development. Journal of Muscle Foods 2004, 15(4):245-255.
Omics approaches to study/enhance muscle growth in fish
I am interested in studying the complex interactions between various components of the muscle as a biological system, and how these interactions work under various biological and environmental conditions to give rise to variations in phenotypes. I am particularly interested in exploring the causative connections between genotypic and phenotypic variation in muscle under degenerative/regenerative conditions. I use...Read More »
Omics approaches to study/enhance muscle growth in fish
I am interested in studying the complex interactions between various components of the muscle as a biological system, and how these interactions work under various biological and environmental conditions to give rise to variations in phenotypes. I am particularly interested in exploring the causative connections between genotypic and phenotypic variation in muscle under degenerative/regenerative conditions. I use various genome-wide omics approaches including; transcriptomics, post-transcriptomics, genomics and proteomics, to obtain, integrate and analyze complex data from various experimental sources. I use bioinformatics tools to simultaneously analyze complex biological networks and integrate rigorous data from high-throughput functional omics experiments. The ultimate goal of my research is to maximize the synthesis of high-quality muscle fibers. Control of protein turnover is one of my research objectives to make progress toward this goal.
In my recent research, I used state-of-the-art "omics" technologies to study "system biology" in the context of muscle growth and quality. The particular focus of this work was transcriptional/post-transcriptional networks that regulate muscle degradation. As a component of the comparative "omics" approach, I used rainbow trout as a model of lower vertebrates and ectothermic animals to compare to the well-studied muscle of mammalian species. My studies include functional genomics and biochemistry of protein turnover, especially the proteolytic enzyme systems; cathepsins, caspases, proteasome and calpains.
Omics approaches to enhance the aquaculture production
Biotechnology can be used to make or change agriculture products. Recently, biotechnologyapplications have expanded exponentially, in particular due to the modern tool of "Omics" technologies. One major constraint to increasing the production efficiency of the aquaculture industry is the lack of genetically improved strains of fish for aquaculture. In terrestrial farm animals there is no terrestrial farm production based on genetically unimproved and undomesticated populations, whereas, the majority of aquaculture production is based on genetically unimproved stocks. The benefits of selective breeding and domestication in aquaculture were only appreciated recently. There is only limited genetic information on traits that could enhance production efficiency and yield a better quality fish. Identification and characterization of the genetics and fish physiology affecting aquaculture production traits will facilitate the development of genetically improved strains and science-based recommendations to farmers and hatchery managers to increase aquaculture production efficiency. Aquaculture biotechnology can help in developing germplasm, and farm management guidelines for improved growth, stress tolerance, fillet quality, disease resistance and feed conversion efficiency as well as control of reproduction cycle and age at sexual maturation. I believe that bringing together people with diverse backgrounds through interdisciplinary collaboration is essential to make progress toward achieving and sustaining a competitive aquaculture industry. For more than ten years, I have been involved in successful interdisciplinary collaborations with scientists from national, international and private entities including the USDA.
- Genetics BIOL 3250
- Genomics BIOL 7250/6250