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Full-Text Articles in Life Sciences

Using Publicly Available Genbank Data To Teach Plant Phylogeny In High School Classrooms, Madhav P. Nepal, Ethan J. Andersen Feb 2019

Using Publicly Available Genbank Data To Teach Plant Phylogeny In High School Classrooms, Madhav P. Nepal, Ethan J. Andersen

iLEARN Teaching Resources

In this teaching module, students will learn about NCBI GenBank, search for DNA/protein sequences from multiple plant species of a gene that encodes Rubisco enzyme, construct and interpret a phylogenetic tree, and discuss traits that allowed plants to adapt their life on land.


Minque: An R Package For Analyzing Various Linear Mixed Models, Jixiang Wu Feb 2019

Minque: An R Package For Analyzing Various Linear Mixed Models, Jixiang Wu

SDSU Data Science Symposium

Linear mixed model (LMM) approaches offer much more flexibility comparing ANOVA (analysis of variance) based methods. There are three commonly used LMM approaches: maximum likelihood, restricted maximum likelihood, and minimum norm quadratic unbiased estimation. These three approaches, however, sometimes could also lead low testing power compared to ANOVA methods. Integration of resampling techniques like jackknife could help improve testing power based on both our simulation studies. In this presentation, I will introduce a R package, minque, which integrates LMM approaches and resampling techniques and demonstrate the use of this packages in various linear mixed model analyses.


Understanding Greenhouse Gases, Julie M. Mueller, Laura Edwards, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White Jan 2019

Understanding Greenhouse Gases, Julie M. Mueller, Laura Edwards, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White

iLEARN Teaching Resources

Students will conduct hands-on experiments to see how greenhouse gases interact with the Earth’s atmosphere and how greenhouse gases affect temperature. This lesson introduces National Geographic’s Geo-Inquiry Process, where students will identify a Geo-inquiry question, collect data, and create a project around the answer to their question. Students will then present their findings to their peers and evaluate their Geo-Inquiry process.


Using A Case Study Approach To Teach Invasive Species And Climate Change, Amanda Hoover, Bradley Blaha, Jacob Englin, Madhav P. Nepal, Larry B. Browning, Matt L. Miller, P. Troy White Jan 2019

Using A Case Study Approach To Teach Invasive Species And Climate Change, Amanda Hoover, Bradley Blaha, Jacob Englin, Madhav P. Nepal, Larry B. Browning, Matt L. Miller, P. Troy White

iLEARN Teaching Resources

In this teaching module, students will explore emerald ash borer (EAB), its impacts on the ash trees, and how warming temperatures could affect EAB populations. The emerald ash borer is a green buprestid or jewel beetle native to north-eastern Asia that causes devastating disease in ash trees.


Climate Change Within A Biome, Tyone Kruse, Lisa Forcier, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White Jan 2019

Climate Change Within A Biome, Tyone Kruse, Lisa Forcier, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White

iLEARN Teaching Resources

In this iLEARN lesson, students will investigate impacts of climate change on the native plants and animals, as well as the fisheries, agriculture, and forestry, within a biome of their choosing, and then develop and refine a solution for one of the impacts resulting from the climate change.


Jackrabbit Dairy And Food Review, Vikram V. Mistry Jan 2019

Jackrabbit Dairy And Food Review, Vikram V. Mistry

The Jackrabbit Dairy & Food Review

This is the Winter 2017- 2018 Jackrabbit Dairy and Food Review. It contains the following articles and information: Message from the Department Head, 2017 Graduates, David A. Thompson Endowment, New Faculty and Visitors, information on the Dairy Club and Food Science Club, Judging Activities, Student Accomplishments, Professional Activities of Faculty and Staff, Distinguished Alumni, Dairy Facilities, a list of Scholarships and Dairy and Food Science Students, information on Departmental Outreach and Research Highlights.


Level Of Satisfaction Among Food Pantry Clients, Staff/Volunteers, And Directors And Its Association With Client Choice In Food Pantry Layouts, Myranda Dunmire Jan 2019

Level Of Satisfaction Among Food Pantry Clients, Staff/Volunteers, And Directors And Its Association With Client Choice In Food Pantry Layouts, Myranda Dunmire

Electronic Theses and Dissertations

Objectives: Food insecurity is an issue in rural communities, particularly among food pantry clients. Food pantries may not provide clients with the opportunity to choose their own foods (client choice), and instead may just give a set amount and type of foods. Client choice is important in regards to client health status as well as perceptions of autonomy and quality of life. Although client choice can be promoted in food pantries, it may be difficult to grasp the process of food pantry transitioning and how well changes such as these may be perceived by clients or food pantry personnel. We ...


Animal Science Department News, Department Of Animal Science Jan 2019

Animal Science Department News, Department Of Animal Science

Animal Science Newsletter

No abstract provided.


Three Sister Crops: Understanding American Indian Agricultural Practices Of Corn, Beans And Squash, Sara Colombe, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White Dec 2018

Three Sister Crops: Understanding American Indian Agricultural Practices Of Corn, Beans And Squash, Sara Colombe, Madhav P. Nepal, Larry B. Browning, Matthew L. Miller, P. Troy White

iLEARN Teaching Resources

American Indians have practiced an inter-planting system to produce corn, beans, and squash, for generations. These crops are known as the “Three Sisters”. In this lesson developed for secondary agriscience curriculum, students will understand the past, current and future production practices of the three important crops. Students will also apply their knowledge to understand the crop selection process and relate to the changing environment.


Parliamentary Procedure Interactive Notebook, Amie Carter, P. Troy White, Laura Hasselquist, Madhav Nepal Oct 2018

Parliamentary Procedure Interactive Notebook, Amie Carter, P. Troy White, Laura Hasselquist, Madhav Nepal

Curriculum Resources

These resources were developed as an undergraduate student research experience. During the summer and fall of 2018, the Agricultural Education faculty in the Department of Teaching, Learning & Leadership recruited teachers and students to pilot and suggest revisions to these resources and to report their effectiveness in promoting engagement and learning of Parliamentary Procedure.

This item contains three downloadable files. Student and teacher notebooks are designed to be printed on 8.5"x14" pages in booklet format. The cutouts are on standards letter size paper.


Voices For Food: Methodologies For Implementing A Multi-State Community-Based Intervention In Rural, High Poverty Communities., Suzanne Stluka, Lindsay Moore, Heather A Eicher-Miller, Lisa Franzen-Castle, Becky Henne, Donna Mehrle, Daniel Remley, Lacey Mccormack Aug 2018

Voices For Food: Methodologies For Implementing A Multi-State Community-Based Intervention In Rural, High Poverty Communities., Suzanne Stluka, Lindsay Moore, Heather A Eicher-Miller, Lisa Franzen-Castle, Becky Henne, Donna Mehrle, Daniel Remley, Lacey Mccormack

Health and Nutritional Sciences Faculty Publications

BACKGROUND: Rural communities experience unique barriers to food access when compared to urban areas and food security is a public health issue in rural, high poverty communities. A multi-leveled socio-ecological intervention to develop food policy councils (FPCs), and improve food security in rural communities was created. Methods to carry out such an intervention were developed and are described.
METHODS: A longitudinal, matched treatment and comparison study was conducted in 24 rural, high poverty counties in South Dakota, Indiana, Missouri, Michigan, Nebraska and Ohio. Counties were assigned to a treatment (n = 12) or comparison (n = 12) group. Intervention activities focus on ...


Introduction To Integrated Crop-Livestock Systems, P. Troy White Jul 2018

Introduction To Integrated Crop-Livestock Systems, P. Troy White

Curriculum Resources

This presentation is an introductory lesson on integration of crop-livestock systems in the United States. The lesson includes national Agriculture, Food, and Natural Resources Standards, objectives, and a student project. This lesson is intended to be inquiry-based, and as such only foundational information is presented. Students are expected to take the introductory information and fins specific information needed to sold the problem posed at the beginning of the presentation. It is expected that at a minimum this lesson will take three 50-minute class periods and could take longer based on teacher preferences.


Daily Dietary Intake Patterns Improve After Visiting A Food Pantry Among Food-Insecure Rural Midwestern Adults., Breanne N Wright, Regan L Bailey, Bruce A Craig, Richard D Mattes, Lacey Mccormack, Suzanne Stluka, Lisa Franzen-Castle, Becky Henne, Donna Mehrle, Dan Remley, Heather A Eicher-Miller May 2018

Daily Dietary Intake Patterns Improve After Visiting A Food Pantry Among Food-Insecure Rural Midwestern Adults., Breanne N Wright, Regan L Bailey, Bruce A Craig, Richard D Mattes, Lacey Mccormack, Suzanne Stluka, Lisa Franzen-Castle, Becky Henne, Donna Mehrle, Dan Remley, Heather A Eicher-Miller

Health and Nutritional Sciences Faculty Publications

Emergency food pantries provide food at no cost to low-resource populations. The purpose of this study was to evaluate single-day dietary intake patterns before and after visiting a food pantry among food-secure and food-insecure pantry clients. This observational cohort study comprised a paired, before-and-after design with a pantry visit as the intervention. Participants (n = 455) completed a demographic and food security assessment, and two 24-h dietary recalls. Adult food security was measured using the U.S. Household Food Security Survey Module. Dietary intake patterns were assessed using Automated Self-Administered 24-h Recall data and classified by Healthy Eating Index (HEI-2010) scores ...


Quality Of Life Associated With Physical Activity But Not Sedentary Time In Youth, K. Kattelmann, E. Hofer, C. Merfeld, J. Meendering, M. Olfert, J. White, S. Colby, R. Meade, L. Franzen-Castle, T. Aquirre, D. Matthews, A. White May 2018

Quality Of Life Associated With Physical Activity But Not Sedentary Time In Youth, K. Kattelmann, E. Hofer, C. Merfeld, J. Meendering, M. Olfert, J. White, S. Colby, R. Meade, L. Franzen-Castle, T. Aquirre, D. Matthews, A. White

Health and Nutritional Sciences Faculty Publications

Purpose: It has been reported that youth who engaged in more screen time had lower quality of life scores compared to those that were more physically active. Furthermore, increased sedentary behavior increases health risks particularly the risk for obesity. A cross-sectional analysis was completed to examine the relationship between healthrelated quality-of-life (HRQOL) and accelerometer-measured sedentary time (ST) and physical activity (PA) in 9-10-yearold youth who were recruited for the family-based, childhood obesity intervention, iCook 4-H. It was hypothesized that objectively measured ST would be negatively correlated and PA would be positively correlated with HRQOL.
Methods: A subset of participants (n ...


Dairy Digest 2018: Home Is Where The Cows Are, South Dakota State University Dairy Club Apr 2018

Dairy Digest 2018: Home Is Where The Cows Are, South Dakota State University Dairy Club

Dairy Digest

This is the 2018 Dairy Digest published annually by the South Dakota State University Dairy Club. The Digest contains information and news about the activities and members of the SDSU Dairy Club for the academic year 2017 - 2018.


The Healthfulness Of Entrées And Students' Purchases In A University Campus Dining Environment, Krista Leischner, Lacey Arneson Mccormack, Brian C. Britt, Greg Heiberger, Kendra Kattelmann Mar 2018

The Healthfulness Of Entrées And Students' Purchases In A University Campus Dining Environment, Krista Leischner, Lacey Arneson Mccormack, Brian C. Britt, Greg Heiberger, Kendra Kattelmann

Health and Nutritional Sciences Faculty Publications

The purpose of this study is to determine the availability of "more healthful" (MH) versus "less healthful" (LH) entrée items in the campus dining and if students' purchases are reflective of what is offered. This is an observational study in which purchases of the available entrée items in the campus dining at South Dakota State University in one academic year were collected and categorized as either MH or LH according to the American Heart Association guidelines. Chi-square tests were used to determine the differences between the proportion of purchased MH and LH versus those available. Odds ratio estimates with 95 ...


The Journal Of Undergraduate Research: 2017 Mar 2018

The Journal Of Undergraduate Research: 2017

The Journal of Undergraduate Research

This is the complete issue of the South Dakota State University Journal of Undergraduate Research, Volume 15.


Quantifying Undisturbed (Native) Lands In Northwestern South Dakota: 2013, Pete Bauman, Benjamin Carlson, Tanner Butler, Brad Richardson Jan 2018

Quantifying Undisturbed (Native) Lands In Northwestern South Dakota: 2013, Pete Bauman, Benjamin Carlson, Tanner Butler, Brad Richardson

Quantifying Undisturbed (Native) Lands in Northwestern South Dakota: 2013

We employed simple GIS methods primarily utilizing the South Dakota Farm Service Agency’s Common Land Unit (CLU) data layers from 2013 and the 2012 United States Department of Agriculture (USDA) National Agriculture Imagery Program (NAIP) county mosaic aerial imagery to evaluate 7,347,812 acres of land in northwestern South Dakota. The analysis area includes: Harding, Perkins, and Butte counties along with portions of Lawrence and Meade counties outside of the Black Hills Core Highlands and Plateau Ecoregions.

We utilized the FSA CLU data layer queried to show current and former cropland to identify and remove any areas with ...


Immunization By Radiotherapy: Enhancing An Immune-Mediated Abscopal Effect, Amy Steffen Jan 2018

Immunization By Radiotherapy: Enhancing An Immune-Mediated Abscopal Effect, Amy Steffen

Biology and Microbiology Graduate Students Plan B Research Projects

Radiotherapy aims to destroy tumors by inducing DNA damage in their cells at the local irradiation site. Its immune-mediated systemic effects, called abscopal effect, has shown to enhance anti-tumor immunity when combined with immune therapies and thus, have gained attention by researchers and clinicians to investigate. Below is a summary of the fundamentals of cancer and the immune system’s response to it, as well as the changes in the phenotype and microenvironment of tumor cells after exposure to radiation. Impacts of the abscopal effect and the induction of effective antitumor immunity with various immune therapy strategies will be outlined ...


Increasing The Clinical Efficacy Of Radiotherapeutics For Solid Tumors By Inhibition Of Hypoxia Inducible Factor-1a, Austin Levi Walz Jan 2018

Increasing The Clinical Efficacy Of Radiotherapeutics For Solid Tumors By Inhibition Of Hypoxia Inducible Factor-1a, Austin Levi Walz

Biology and Microbiology Graduate Students Plan B Research Projects

Radiotherapy is commonly used in a variety of tumor types and is effective in control of long term progression and may be curative under certain circumstances. Radiotherapeutics have been shown to be the single most effective therapeutic for cancer and only account for 5% of the total cost. However, treatment of cells with radiation causes the tumor microenvironment to undergo changes and leads to cycles of hypoxia inside the tumor which allows for the cell to undergo angiogenesis, metastasize and may lead to repopulation of the tumor. Current systemic chemotherapeutics typically have an additive toxicity due to the unintended targeting ...


A Biological Review Of Mental Illness: An Overview Of Genetics And Pathophysiology Of Schizophrenia, Major Depression, And Addiction, Christopher R. Angerhofer Jan 2018

A Biological Review Of Mental Illness: An Overview Of Genetics And Pathophysiology Of Schizophrenia, Major Depression, And Addiction, Christopher R. Angerhofer

Biology and Microbiology Graduate Students Plan B Research Projects

Novel approaches in understanding mental illness present solutions to current issues in treatment and diagnosis. With advancements in genetics and neurology, the etiology and pathophysiology of mental illness is slowly unwrapping. In discovering biomarkers for depression, addiction, and schizophrenia, the precision for preventing, diagnosing, and treating these disorders increases. The aim of this paper is to review current research for addiction, major depression, and schizophrenia in genetics and physiology, while also clarifying the need for reclassifying mental illness as diseases with a pathophysiological basis, not syndromal, idiopathic disorders. Mental illness is dynamic in that it encompasses both environmental and biological ...


Transcranial Magnetic Stimulaton: In-Depth Review Of Methods, Efficacy And Future Applications, Matthew Carpenter Jan 2018

Transcranial Magnetic Stimulaton: In-Depth Review Of Methods, Efficacy And Future Applications, Matthew Carpenter

Biology and Microbiology Graduate Students Plan B Research Projects

Transcranial magnetic stimulation (TMS) has been regarded as a novel technique of neuromodulation with applications that span from the treatment of depression or depression related symptoms to the mapping of cerebral regions. This review takes an in depth look into the different forms of magnetic stimulation including repetitive TMS, theta-burst stimulation, and navigated TMS. The efficacy of these different forms of stimulation is addressed as well as comparisons made to current standards being used. Potential clinically relevant future applications of TMS are also discussed from the treatment of obsessive compulsive disorder to improving motor function after stroke. The purpose of ...


A Review Of Multiple Sclerosis Treatments: Interferon Beta, Glatiramer Acetate, Fingolimod, And Natalizumab, Ryan Golden Jan 2018

A Review Of Multiple Sclerosis Treatments: Interferon Beta, Glatiramer Acetate, Fingolimod, And Natalizumab, Ryan Golden

Biology and Microbiology Graduate Students Plan B Research Projects

Multiple Sclerosis (MS) is an autoimmune disease in which the body’s own immune system works to demyelinate the myelin sheaths in the central nervous system. The beginning of the review will concentrate on the history of MS while also describing how MS, the disease, differs from that of normal immune responses. The review then shifts to the four different stages of MS and how to differentiate between the stages, since the treatment options are often dependent on the stage of MS that the patient is in. The main focus of this review is to take an in depth look ...


Mild Traumatic Brain Injuries And Cte: A Review Highlighting The Connection Between The Two, Leandre Kennedy Jan 2018

Mild Traumatic Brain Injuries And Cte: A Review Highlighting The Connection Between The Two, Leandre Kennedy

Biology and Microbiology Graduate Students Plan B Research Projects

Chronic Traumatic Encephalopathy (CTE) is a traumatic brain injury based disease that is garnering a lot of attention in the United States. The purpose of this paper is to conduct an extensive review of the information available about the condition. Recently there has been a limited amount of published information and treatment opportunities are rare since the only way of diagnosing has come post mortem. Various literary reviews and experiments were analyzed for appropriate information regarding CTE’s pathology and treatments and only peer reviewed published works were allowed in this paper. This resulted in promising information about the disease ...


Jackrabbit Dairy And Food Review, Vikram V. Mistry Jan 2018

Jackrabbit Dairy And Food Review, Vikram V. Mistry

The Jackrabbit Dairy & Food Review

This is the Winter 2017- 2018 Jackrabbit Dairy and Food Review.
It contains the following articles and information: Message from the Department Head, 2017 Graduates, New Faculty and Visitors, information on the Dairy Club and Food Science Club, Judging Activities, Student Accomplishments, Professional Activities of Faculty and Staff, Distinguished Alumni, Dairy Facilities, a list of Scholarships and Dairy and Food Science Students, information on Departmental Outreach and Research Highlights.


Comparison Of Three Assembly Strategies For A Heterozygous Grapevine Genome Assembly, Sagar Patel, Erliang Zeng, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Anne Fennell Jan 2018

Comparison Of Three Assembly Strategies For A Heterozygous Grapevine Genome Assembly, Sagar Patel, Erliang Zeng, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Anne Fennell

Comparison of Three Assembly Strategies for a Heterozygous Grapevine Genome Assembly

Each folder includes the following files.

  1. Assembly.fa: Genome assembly in scaffolds.
  2. Blast2GO_results.b2g: The full annotation of coding sequences.
  3. Coding_sequences.fa: The predicted coding sequences from masked assembly.
  4. Gene_models.gff: Gene predictions from masked assembly.
  5. Masked_assembly.fa: The masked genome assembly.
  6. Protein.fa: The predicted protein sequences.

PLAT*_GC contains chromosomal assembly and annotation as "pseudo_chromosomal_assembly" folder.

SnpEff folder contains results from SnpEff as SnpEff_summary, genes affected are described as vini_snp.txt.genes and vini_snpeff is output from SnpEff.


Qualitative Analysis Of Grocery Store And Farmers Market Manager Perceptions Regarding Use Of Fruit And Vegetable Educational Materials, Lacey Mccormack, Shelly Brandenburger, Karlys Wells, Suzanne Stluka Jan 2018

Qualitative Analysis Of Grocery Store And Farmers Market Manager Perceptions Regarding Use Of Fruit And Vegetable Educational Materials, Lacey Mccormack, Shelly Brandenburger, Karlys Wells, Suzanne Stluka

Health and Nutritional Sciences Faculty Publications

The Pick it! Try it! Like it! (PTL) educational resource set, developed to display in grocery stores and farmers markets, teaches individuals how to shop for and prepare healthy fruit and vegetable dishes. Because program buy-in must be obtained from location managers before implementation occurs, the purpose of this study was to qualitatively examine the perceptions that grocery store and farmers market managers have regarding PTL implementation. Locations that requested PTL materials during 2013-14 were contacted and asked to answer 13 questions. Responses were analyzed using the content analysis method with themes generated and frequencies reported. Analyses examined manager perceptions ...


The Journal Of Undergraduate Research: 2018 Jan 2018

The Journal Of Undergraduate Research: 2018

The Journal of Undergraduate Research

This is the complete issue of the South Dakota State University Journal of Undergraduate Research , Volume 16.


Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch Jan 2018

Identification Of Qtl Modifying The Activity Of The Tcb1-S Locus And Characterization And Sequencing Of Two Plutonium-Beryllium Induced Reduced Gametophyte Transmission Mutants In Maize, Merritt Bryer Burch

Electronic Theses and Dissertations

This thesis is split into two independent projects both involving the male gametophyte generation of maize. The first project looks at how pollen interacts with the female gametophyte to reduce its transmission in cross-incompatible reactions controlled by the unilateral cross-incompatibility system, teosinte crossing barrier 1. The second project explores two plutonium-beryllium induced male gametophyte mutants and attempts to uncover their genetic basis.

Identification of QTL Modifying the Activity of the Tcb1-s Locus
Teosinte crossing barrier 1 (Tcb1) is a unilateral cross-incompatibility system present in maize that provides a pre-zygotic pistil barrier to plants carrying Tcb1-s (strong allele) from pollen not ...


Role Of Bovine Ileal Sub-Epithelial Myofibroblasts And Epithelial Cells In Innate Immunity, Tirth Uprety Jan 2018

Role Of Bovine Ileal Sub-Epithelial Myofibroblasts And Epithelial Cells In Innate Immunity, Tirth Uprety

Electronic Theses and Dissertations

Gastro-intestinal (GI) tract harbors largest number of microbiota as well as the largest number of immune cells for a given tissue. The host needs to mount an effective immune response against invading pathogens and tolerance against commensals. Thus, regulatory mechanism and barrier function of the GI tract are of utmost importance for appropriate host microbe interaction and gut homeostasis. Intestinal epithelial cells (IECs) act as the first line of defense against invading pathogens. IECs recognize pathogens and commensals and mount an effective innate immune response. Such recognition of pathogens is mediated through germ line encoded pattern recognition receptors (PRRs). Intestinal ...