Molecular Biology and Biochemistry Publications (UMKC)
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Items in this collection are the scholarly output of the Division of Molecular Biology and Biochemistry faculty, staff, and students, either alone or as co-authors, and which may or may not have been published in an alternate format.
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Item Klamm’s Microbiology Laboratory Manual(University of Missouri -- Kansas City, 2019) Klamm, Loretta SandersonThis laboratory manual was developed for a microbiology laboratory course designed to give students in the health care professions basic knowledge and skills of the techniques used to study microbes. The course is taken by first-time college students in the 6-year medical program and by prepharmacy undergraduates. Because this is the only microbiology laboratory course these students take, the laboratory experiments are essential to illustrate microbiological principles and methods presented in lecture companion course. The laboratory exercises demonstrate basic concepts of microbiology with emphasis on infectious diseases and host defenses. Throughout the course, students gain competency in the following areas: Safe handling of microbes Knowledge of the techniques and media used to subculture microbes Use of the light microscope Staining techniques Quantitative methods Identification of microbes using biochemical tests and/or immunological techniques Interpretation of experimental results In the past, I supplemented a commercially published lab manual with detailed weekly instructions posted to the course website. My instructions summarized the theory presented, pointing out the important concepts. Based on past experience, I made changes to the lab procedure accommodating organisms that work well in the UMKC teaching lab. In addition, the instructions gave students clarification on the post lab questions, encouraging critical thinking and evaluation of their actual experimental results. Students were required to use both the manual and my handouts to fully understand the exercise. As much as I tried to make each week’s activities clear, there was often confusion about the procedure, observations and/or expectations on the post-lab questions. This work aims to put it all together in one place for the student. For this project, I have built upon much of my original supplementary material using several open educational resources, most notably, OpenStax Microbiology. I appreciate the funding and support from the UM-system and the UMKC Libraries. I am grateful to my students who make teaching fun and interesting and will be unwitting editors and evaluators of this work. Sincerely, Loretta Sanderson KlammItem FunnyBase: a systems level functional annotation of FundulusESTs for the analysis of gene expression(2004-12-20) Paschall, Justin E; Oleksiak, Marjorie F; VanWye, Jeffrey D; Roach, Jennifer L; Whitehead, J Andrew; Wyckoff, Gerald J; Kolell, Kevin J; Crawford, Douglas LAbstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to the understanding of patterns of gene expression that underlie biological processes. Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs) from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P < 0.001) enrichment in genes associated with amine metabolism. Conclusion The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.Item TILLING to detect induced mutations in soybean(2008-01-24) Cooper, Jennifer L; Till, Bradley J; Laport, Robert G; Darlow, Margaret C; Kleffner, Justin M; Jamai, Aziz; El-Mellouki, Tarik; Liu, Shiming; Ritchie, Rae; Nielsen, Niels; Bilyeu, Kristin D; Meksem, Khalid; Comai, Luca; Henikoff, StevenAbstract Background Soybean (Glycine max L. Merr.) is an important nitrogen-fixing crop that provides much of the world's protein and oil. However, the available tools for investigation of soybean gene function are limited. Nevertheless, chemical mutagenesis can be applied to soybean followed by screening for mutations in a target of interest using a strategy known as Targeting Induced Local Lesions IN Genomes (TILLING). We have applied TILLING to four mutagenized soybean populations, three of which were treated with ethyl methanesulfonate (EMS) and one with N-nitroso-N-methylurea (NMU). Results We screened seven targets in each population and discovered a total of 116 induced mutations. The NMU-treated population and one EMS mutagenized population had similar mutation density (~1/140 kb), while another EMS population had a mutation density of ~1/250 kb. The remaining population had a mutation density of ~1/550 kb. Because of soybean's polyploid history, PCR amplification of multiple targets could impede mutation discovery. Indeed, one set of primers tested in this study amplified more than a single target and produced low quality data. To address this problem, we removed an extraneous target by pretreating genomic DNA with a restriction enzyme. Digestion of the template eliminated amplification of the extraneous target and allowed the identification of four additional mutant alleles compared to untreated template. Conclusion The development of four independent populations with considerable mutation density, together with an additional method for screening closely related targets, indicates that soybean is a suitable organism for high-throughput mutation discovery even with its extensively duplicated genome.