Life Sciences Commons^™

Compass Plant Leaves And Apparent Randomness, Jeff Ploegstra

Faculty Work Comprehensive List

"Just because something appears random (and maybe actually is in a very real sense), does not mean that it has no purpose or cannot be shaped into a form."

Posting about ­­­­­­­­God's providence in nature from In All Things - an online journal for critical reflection on faith, culture, art, and every ordinary-yet-graced square inch of God’s creation.

https://inallthings.org/compass-plant-leaves-and-apparent-randomness/

Fatty Acid Biomarkers Of Dairy Fat Consumption And Incidence Of Type 2 Diabetes: A Pooled Analysis Of Prospective Cohort Studies, Fumiaki Imamura, Amanda Fretts, Matti Marklund, Andres V. Ardisson Korat, Wei-Sin Yang, Maria Lankinen, Waqas Qureshi, Catherine Helmer, Tzu-An Chen, Kerry Wong, Julie K. Bassett, Rachel Murphy, Nathan L. Tintle, Chaoyu Ian Yu, Ingeborg A. Brouwer, Kuo-Liong Chien, Alexis C. Frazier-Wood, Liana C. Del Gobbo, Luc Djousse, Johanna M. Geleijnse, Graham G. Giles, Janette De Goede, Vilmunder Gudnason, William S. Harris, Allison Hodge, Frank Hu, Interact Consortium, Albert Koulman, Markku Laakso, Lars Lind, Hung-Ju Lin, Barbara Mcknight, Kalina Rajaobelina, Ulf Riserus, Jennifer G. Robinson, Cecilia Samieri, David S. Siscovick, Sabita S. Soedamah-Muthu, Nona Sotoodehnia, Qi Sun, Michael Y. Tsai, Matti Uusitupa, Lynne E. Wageknecht, Nick J. Wareham, Jason Hy Wu, Renata Micha, Nita G. Forouhi, Rozenn N. Lemaitre, Dariush Mozaffarian, Fatty Acids And Outcomes Research Consortium

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Background

We aimed to investigate prospective associations of circulating or adipose tissue odd-chain fatty acids 15:0 and 17:0 and trans-palmitoleic acid, t16:1n-7, as potential biomarkers of dairy fat intake, with incident type 2 diabetes (T2D).

Methods and findings

Sixteen prospective cohorts from 12 countries (7 from the United States, 7 from Europe, 1 from Australia, 1 from Taiwan) performed new harmonised individual-level analysis for the prospective associations according to a standardised plan. In total, 63,682 participants with a broad range of baseline ages and BMIs and 15,180 incident cases of T2D over the average of 9 years of follow-up were …

Application Of Novel And Existing Methods To Identify Genes With Evidence Of Epigenetic Association: Results From Gaw20, Angga M. Fuady, Samantha Lent, Chloé Sarnowski, Nathan L. Tintle

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Background: The rise in popularity and accessibility of DNA methylation data to evaluate epigenetic associations with disease has led to numerous methodological questions. As part of GAW20, our working group of 8 research groups focused on gene searching methods.

Results: Although the methods were varied, we identified 3 main themes within our group. First, many groups tackled the question of how best to use pedigree information in downstream analyses, finding that (a) the use of kinship matrices is common practice, (b) ascertainment corrections may be necessary, and (c) pedigree information may be useful for identifying parent-of-origin effects. Second, many groups …

Epigenome Wide Association Study Of Snp–Cpg Interactions On Changes In Triglyceride Levels After Pharmaceutical Intervention: A Gaw20 Analysis, Jenna Veenstra, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Abbey Bos, Jordan Huisman, Lucas Vander Berg, Jason Vander Woude, Nathan L. Tintle

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In the search for an understanding of how genetic variation contributes to the heritability of common human disease, the potential role of epigenetic factors, such as methylation, is being explored with increasing frequency. Although standard analyses test for associations between methylation levels at individual cytosine-phosphateguanine (CpG) sites and phenotypes of interest, some investigators have begun testing for methylation and how methylation may modulate the effects of genetic polymorphisms on phenotypes. In our analysis, we used both a genome-wide and candidate gene approach to investigate potential single-nucleotide polymorphism (SNP)–CpG interactions on changes in triglyceride levels. Although we were able to identify …

Evaluating The Performance Of Gene-Based Tests Of Genetic Association When Testing For Association Between Methylation And Change In Triglyceride Levels At Gaw20, Jason Vander Woude, Jordan Huisman, Lucas Vander Berg, Jenna Veenstra, Abbey Bos, Anya Kalsbeek, Karissa Koster, Nathan Ryder, Nathan L. Tintle

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Although methylation data continues to rise in popularity, much is still unknown about how to best analyze methylation data in genome-wide analysis contexts. Given continuing interest in gene-based tests for next-generation sequencing data, we evaluated the performance of novel gene-based test statistics on simulated data from GAW20. Our analysis suggests that most of the gene-based tests are detecting real signals and maintaining the Type I error rate. The minimum pvalue and threshold-based tests performed well compared to single-marker tests in many cases, especially when the number of variants was relatively large with few true causal variants in the set.

Climate Change And Reasons To Care (Leader's Guide), Kevin Timmer

Study Guides for Faith & Science Integration

An introduction to the climate change discussion based on the video series Global Weirding by Katharine Hayhoe.

Why Forage Quality Matters, John Olthoff

Faculty Work Comprehensive List

No abstract provided.

Transcriptome Assembly And Annotation Of Johnsongrass (Sorghum Halepense) Rhizomes Identify Candidate Rhizome-Specific Genes, Nathan Ryder, Kevin M. Dorn, Mark Huitsing, Micah Adams, Jeff Ploegstra, Lee Dehaan, Steve Larson, Nathan L. Tintle

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Rhizomes facilitate the wintering and vegetative propagation of many perennial grasses. Sorghum halepense (johnsongrass) is an aggressive perennial grass that relies on a robust rhizome system to persist through winters and reproduce asexually from its rootstock nodes. This study aimed to sequence and assemble expressed transcripts within the johnsongrass rhizome. A de novo transcriptome assembly was generated from a single johnsongrass rhizome meristem tissue sample. A total of 141,176 probable protein-coding sequences from the assembly were identified and assigned gene ontology terms using Blast2GO. Estimated expression analysis and BLAST results were used to reduce the assembly to 64,447 high-confidence sequences. …

Agrarian Politics And The American Tradition, Jeff Taylor

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Agrarianism is a political philosophy and way of life known and prac­ticed among peoples of diverse nationalities and religions. While having ancient, medieval, and early-modern roots, agrarian politics blossomed most dramatically in America, during both its colonial and republican periods. Notable spokesmen for American agrarianism include Thomas Jefferson, William Jennings Bryan, and Robert La Follette. It has been in steady decline for the past century as cosmopolitan and centralizing forc­es have displaced tradition and smallness of scale. Still, there have been natural voices lamenting losses in the face of"progress": Distributists and Southern Agrarians, the Counterculture and the Green Party, Wendell …

Science For All Christians, Jeff Ploegstra

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"What questions should we endeavor to answer as we work out the relationship between our faith commitments and our scientific insight?"

Posting about a Reformed worldview on the complexities of creation from In All Things - an online journal for critical reflection on faith, culture, art, and every ordinary-yet-graced square inch of God’s creation.

https://inallthings.org/science-for-all-christians/

Comparing Strip Trials Of Chicken Litter, Compost, Hog Manure, And Wet Cattle Manure On Soil Fertility, Tanner Douma, Emily Hummel, Wendi Jo Vande Voort

Student Work

Utilizing agriculture animal and biodegradable waste can reduce the input costs of fertilizers while enhancing the soil. This comparative study focuses on the nutrient values soil receives from agricultural waste. The central objective was, “Due to the historical over-application of manure leading to environmental concerns, a comparative study of soil fertility and economic viability of manures and compost are analyzed in a one-year study”. On an 18.7 acre corn plot, 11 strips were applied with four different manure types, which were randomized, during the 2017 growing season. Chicken litter, compost, hog manure, wet cattle manure, and control strips were replicated …

A Genome-Wide Association Study Of Red-Blood Cell Fatty Acids And Ratios Incorporating Dietary Covariates: Framingham Heart Study Offspring Cohort, Anya Kalsbeek, Jenna Veenstra, Jason Westra, Craig Disselkoen, Kristin Koch, Katelyn A. Mckenzie, Jacob O'Bott, Jason Vander Woude, Karen Fischer, Greg C. Shearer, William S. Harris, Nathan L. Tintle

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Recent analyses have suggested a strong heritable component to circulating fatty acid (FA) levels; however, only a limited number of genes have been identified which associate with FA levels. In order to expand upon a previous genome wide association study done on participants in the Framingham Heart Study Offspring Cohort and FA levels, we used data from 2,400 of these individuals for whom red blood cell FA profiles, dietary information and genotypes are available, and then conducted a genome-wide evaluation of potential genetic variants associated with 22 FAs and 15 FA ratios, after adjusting for relevant dietary covariates. Our analysis …

What Can We Learn From Atheists? (Leader's Guide And Participant's Guide), Lydia Marcus

Study Guides for Faith & Science Integration

A study of Larry Tauton's The Faith of Christopher Hitchens: The Restless Soul of the World's Most Notorious Atheist

On Why Design Might Be Detectable, Tony N. Jelsma

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No abstract provided.

A Christian Look At The Biology Of Gender Dysphoria, Tony N. Jelsma

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"We should treat people suffering from gender dysphoria with the dignity, respect, and support that are due anyone created in the image of God, recognizing that their condition may not be resolved in this life."

Posting about the church's response to sexual identity issues from In All Things - an online journal for critical reflection on faith, culture, art, and every ordinary-yet-graced square inch of God’s creation.

https://inallthings.org/a-christian-look-at-the-biology-of-gender-dysphoria/

Analyzing Metabolomics Data For Association With Genotypes Using Two-Component Gaussian Mixture Distributions, Jason Westra, Nicholas Hartman, Bethany Lake, Gregory Shearer, Nathan L. Tintle

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Standard approaches to evaluate the impact of single nucleotide polymorphisms (SNP) on quantitative phenotypes use linear models. However, these normal-based approaches may not optimally model phenotypes which are better represented by Gaussian mixture distributions (e.g., some metabolomics data). We develop a likelihood ratio test on the mixing proportions of two-component Gaussian mixture distributions and consider more restrictive models to increase power in light of a priori biological knowledge. Data were simulated to validate the improved power of the likelihood ratio test and the restricted likelihood ratio test over a linear model and a log transformed linear model. Then, using real …

Internships In Kinesiology: Reconsidering Best Practices, Mark Urtel, Sara F. Michaliszyn, Craig L. Stiemsma

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The purpose of this paper is to summarize the 2018 American Kinesiology Association (AKA) pre-workshop on best practices in internships. This pre-workshop contained 2 keynote speakers, 5 ignite sessions, and 6 round-table discussions looking at the status of internships in departments of kinesiology, nationally. It is clear kinesiology does not have a common practice for implementing internships. Given the many variables in respect to offering an internship, such as: curricular mandates, faculty workload policy, community partner availability, program outcomes, student learning objectives, and assessment tools this is not surprising. Perhaps we should rethink the notion that there is a set …