Sioux Center, IA, United States
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De Haan R.L.,Dordt College | Schuiteman M.A.,Sioux Center | Vos R.J.,Dordt College
PLoS ONE | Year: 2017

Many communities in the Midwestern United States obtain their drinking water from shallow alluvial wells that are vulnerable to contamination by NO3 -N from the surrounding agricultural landscape. The objective of this research was to assess cropping systems with the potential to produce a reasonable return for farmers while simultaneously reducing the risk of NO3 -N movement into these shallow aquifers. From 2009 to 2013 we conducted a field experiment in northwest Iowa in which we evaluated five cropping systems for residual (late fall) soil NO3 -N content and profitability. Soil samples were taken annually from the top 30 cm of the soil profile in June and August, and from the top 180 cm in November (late fall). The November samples were divided into 30 cm increments for analysis. Average residual NO3 -N content in the top 180 cm of the soil profile following the 2010 to 2013 cropping years was 134 kg ha-1 for continuous maize (Zea mays L.) with a cereal rye (Secale cereale L.) cover crop, 18 kg ha-1 for perennial grass, 60 kg ha-1 for a three year oat (Avena sativa L.)-alfalfa (Medicago sativa L.)-maize rotation, 85 kg ha-1 for a two year oat/red clover (Trifolium pratense L.)-maize rotation, and 90 kg ha-1 for a three year soybean (Glycine max (L.) Merr.)-winter wheat (Triticum aestivum L.)-maize rotation. However, residual NO3 -N in the 90 to 180 cm increment of the soil profile was not significantly higher in the oat-alfalfa-maize cropping system than the perennial grass system. For 2010 to 2013, average profit ($ ha-1 yr-1 ) was 531 for continuous corn, 347 for soybean-winter wheat-maize, 264 for oat-alfalfamaize, 140 for oat/red clover-maize, and -384 (loss) for perennial grass. Considering both residual soil NO3 -N and profitability data, the oat-alfalfa-maize rotation performed the best in this setting. However, given current economic pressures widespread adoption is likely to require changes in public policy. © 2017 De Haan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Martinuzzi K.,Mount Sinai School of Medicine | Barritt J.,Mount Sinai School of Medicine | Wei H.,Sioux Center | Chaubal S.,Sioux Center | Copperman A.B.,Mount Sinai School of Medicine
FASEB Journal | Year: 2010

A major challenge of assisted reproduction technologies (ARTs) is to mimic the natural environment required to sustain oocyte and embryo survival. Herein, we show that the ceramide-metabolizing enzyme, acid ceramidase (AC), is expressed in human cumulus cells and follicular fluid, essential components of this environment, and that the levels of this enzyme are positively correlated with the quality of human embryos formed in vitro. These observations led us to develop a new approach for oocyte and embryo culture that markedly improved the outcome of in vitro fertilization (IVF). The addition of recombinant AC (rAC) to human and mouse oocyte culture medium maintained their healthy morphology in vitro. Following fertilization, the number of mouse embryos formed in the presence of rAC also was improved (from ∼40 to 88%), leading to ∼5-fold more healthy births. To confirm these observations, immature bovine oocytes were matured in vitro and subjected to IVF in the presence of rAC. Significantly more high-grade blastocysts were formed, and the number of morphologically intact, hatched embryos was increased from ∼24 to 70%. Overall, these data identify AC as an important component of the in vivo oocyte and embryo environment, and provide a novel technology for enhancing the outcome of assisted fertilization. © FASEB.


Zhou W.,ViaGen Inc. | Gosch G.,Sioux Center | Guerra T.,ViaGen Inc. | Broek D.,Sioux Center | And 4 more authors.
Theriogenology | Year: 2014

Somatic cell nuclear transfer (SCNT), or cloning, is one of the assisted reproductive technologies currently used in agriculture. Commercial applications of SCNT are presently limited to the production of animals of high genetic merit or the production of the most elite show cattle owing to its relatively low efficiency. In current practice, 20% to 40% of SCNT pregnancies do not result in viable offspring. In an effort to better understand some of the anomalies associated with SCNT pregnancies, we investigated amino acid compositions of first trimester amniotic fluid. In this retrospective study, amniotic fluids were collected from SCNT and control IVF pregnancies at Day 75 of gestation and grouped according to the pregnancy results: control IVF (IVF), viable SCNT pregnancies that resulted in live healthy calves (SCNT-HL), nonviable SCNT pregnancies that were aborted before Day 150 (SCNT-ED), and nonviable SCNT pregnancies that were aborted after Day 150 or produced deceased calves (SCNT-LD). High-performance liquid chromatography (HPLC) was used to analyze the concentrations of 22 amino acids (AAs) in the amniotic fluid samples. There were no differences in average AA concentrations between IVF and SCNT-HL groups, whereas SCNT-LD and SCNT-ED had higher levels of total AA concentrations. Concentrations of asparagine, citruline, arginine, and valine were significantly higher in the SCNT-LD group. Both SCNT-LD and SCNT-ED groups had relatively large intragroup variances in AA concentrations. Urea concentration was also measured in the SCNT amniotic fluid samples. No correlations between urea concentrations and arginine concentrations or pregnancy outcomes were found. The findings in this study not only deepen the understanding onSCNT pregnancy anomalies, but also provide a potentially useful screening tool for assessing viable and nonviable SCNT pregnancies. © 2014 Elsevier Inc.


Kasinathan P.,Sioux Center | Wei H.,Sioux Center | Xiang T.,Sioux Center | Molina J.A.,Sioux Center | And 5 more authors.
Scientific Reports | Year: 2015

Genomic selection (GS) approaches, in combination with reproductive technologies, are revolutionizing the design and implementation of breeding programs in livestock species, particularly in cattle. GS leverages genomic readouts to provide estimates of breeding value early in the life of animals. However, the capacity of these approaches for improving genetic gain in breeding programs is limited by generation interval, the average age of an animal when replacement progeny are born. Here, we present a cost-effective approach that combines GS with reproductive technologies to reduce generation interval by rapidly producing high genetic merit calves. © 2015, Nature Publishing Group. All rights reserved.


Ehsani A.,University of Aarhus | Sorensen P.,University of Aarhus | Pomp D.,University of North Carolina at Chapel Hill | Allan M.,Sioux Center | Janss L.,University of Aarhus
BMC Genomics | Year: 2012

Background: To understand the genetic architecture of complex traits and bridge the genotype-phenotype gap, it is useful to study intermediate -omics data, e.g. the transcriptome. The present study introduces a method for simultaneous quantification of the contributions from single nucleotide polymorphisms (SNPs) and transcript abundances in explaining phenotypic variance, using Bayesian whole-omics models. Bayesian mixed models and variable selection models were used and, based on parameter samples from the model posterior distributions, explained variances were further partitioned at the level of chromosomes and genome segments.Results: We analyzed three growth-related traits: Body Weight (BW), Feed Intake (FI), and Feed Efficiency (FE), in an F2 population of 440 mice. The genomic variation was covered by 1806 tag SNPs, and transcript abundances were available from 23,698 probes measured in the liver. Explained variances were computed for models using pedigree, SNPs, transcripts, and combinations of these. Comparison of these models showed that for BW, a large part of the variation explained by SNPs could be covered by the liver transcript abundances; this was less true for FI and FE. For BW, the main quantitative trait loci (QTLs) are found on chromosomes 1, 2, 9, 10, and 11, and the QTLs on 1, 9, and 10 appear to be expression Quantitative Trait Locus (eQTLs) affecting gene expression in the liver. Chromosome 9 is the case of an apparent eQTL, showing that genomic variance disappears, and that a tri-modal distribution of genomic values collapses, when gene expressions are added to the model.Conclusions: With increased availability of various -omics data, integrative approaches are promising tools for understanding the genetic architecture of complex traits. Partitioning of explained variances at the chromosome and genome-segment level clearly separated regulatory and structural genomic variation as the areas where SNP effects disappeared/remained after adding transcripts to the model. The models that include transcripts explained more phenotypic variance and were better at predicting phenotypes than a model using SNPs alone. The predictions from these Bayesian models are generally unbiased, validating the estimates of explained variances. © 2012 Ehsani et al.; licensee BioMed Central Ltd.


PubMed | Sioux Center and University of Iowa
Type: Journal Article | Journal: Molecular & cellular oncology | Year: 2016

Large-animal cancer models are needed to advance the development of innovative and clinically applicable tumor diagnostic, therapeutic, and monitoring technologies. We developed a genetically modified porcine model of cancer based on a TP53 mutation, and established its utility for tracking tumorigenesis in vivo through non-invasive clinical imaging approaches.


PubMed | University of Vermont, University of Cagliari, Sioux Center, Tufts University and 2 more.
Type: Journal Article | Journal: Tissue engineering. Part C, Methods | Year: 2016

A novel potential approach for lung transplantation could be to utilize xenogeneic decellularized pig lung scaffolds that are recellularized with human lung cells. However, pig tissues express several immunogenic proteins, notably galactosylated cell surface glycoproteins resulting from alpha 1,3 galactosyltransferase (-gal) activity, that could conceivably prevent effective use. Use of lungs from -gal knock out (-gal KO) pigs presents a potential alternative and thus comparative de- and recellularization of wild-type and -gal KO pig lungs was assessed.Decellularized lungs were compared by histologic, immunohistochemical, and mass spectrometric techniques. Recellularization was assessed following compartmental inoculation of human lung bronchial epithelial cells, human lung fibroblasts, human bone marrow-derived mesenchymal stromal cells (all via airway inoculation), and human pulmonary vascular endothelial cells (CBF) (vascular inoculation).No obvious differences in histologic structure was observed but an approximate 25% difference in retention of residual proteins was determined between decellularized wild-type and -gal KO pig lungs, including retention of -galactosylated epitopes in acellular wild-type pig lungs. However, robust initial recellularization and subsequent growth and proliferation was observed for all cell types with no obvious differences between cells seeded into wild-type versus -gal KO lungs.These proof of concept studies demonstrate that decellularized wild-type and -gal KO pig lungs can be comparably decellularized and comparably support initial growth of human lung cells, despite some differences in retained proteins. -Gal KO pig lungs are a suitable platform for further studies of xenogeneic lung regeneration.


PubMed | University of Washington and Sioux Center
Type: | Journal: Scientific reports | Year: 2015

Genomic selection (GS) approaches, in combination with reproductive technologies, are revolutionizing the design and implementation of breeding programs in livestock species, particularly in cattle. GS leverages genomic readouts to provide estimates of breeding value early in the life of animals. However, the capacity of these approaches for improving genetic gain in breeding programs is limited by generation interval, the average age of an animal when replacement progeny are born. Here, we present a cost-effective approach that combines GS with reproductive technologies to reduce generation interval by rapidly producing high genetic merit calves.


News Article | November 17, 2015
Site: www.scientificcomputing.com

Austin, TX — Silicon Mechanics, a provider of servers, storage and high-performance computing solutions, announced the opening of its 5th Annual Research Cluster Grant (RCG) program at Supercomputing 2015. Two institutions will be selected, and both will be awarded a complete high-performance computing (HPC) cluster. The competition is open to all United States and Canadian qualified post-secondary institutions, university-affiliated research institutions, non-profit research institutions, and researchers at federal labs with university affiliations. "We designed the Research Cluster Grant program to provide computational and storage technology resources to researchers who may not have been able to keep pace with technology acquisitions through traditional grant-funding programs like those at the National Science Foundation or the National Institute of Health,” said Art Mann, Silicon Mechanics' Sr. Director, Life Sciences Practice. "With the ever-growing demand for more powerful IT infrastructure to support research, the RCG represents a tremendous opportunity to work with our technology partners and support these research efforts. I’m excited and truly honored to see the RCG program achieve its fifth year.” Silicon Mechanics created the RCG in 2012 as a way of giving back to the educational community, as obtaining needed research funding for technology advancements continues to be challenging and can limit future impact at some educational institutions. In particular, the program is helping to jumpstart research efforts where access to high-performance computing is limited, outdated or was not previously available. The RCG program also provides institutions with an opportunity to showcase how collaboration across departments and researchers by providing cluster technology can positively impact research efforts through the use of cluster technology. Previous RCG awardees include The City College of New York (CCNY) and Dordt College in 2015, Wayne State University in 2014, Tufts University in 2013 and Saint Louis University in 2012. Silicon Mechanics' partners currently committed to supporting this year’s grant include: Intel, NVIDIA, Mellanox, Supermicro, Bright Computing, HGST, Avago, Kingston, Micron and Seagate. At CCNY, the HPC cluster is being used for cutting-edge research in biochemistry, chemistry, biology, physics, earth and atmospheric sciences, computer science, engineering, medicine, mathematics, social science, humanities and writing pedagogy. "For many of our research programs, this computer cluster was the missing piece that lowered the barriers that kept our work from moving forward smoothly," said David Jeruzalmi, professor of chemistry and biochemistry in CCNY's Division of Science, who wrote the grant proposal last year. "This award has touched the research of many colleagues by bringing together researchers from across CCNY, many of whom never knew that their work could be positively impacted by colleagues down the hall or in the next building over." At Dordt College and at its research partner, Hope College, the HPC cluster supports eight STEM-based research groups and nine distinct faculty members focused on a wide variety of research activities. Those activities include bacterial statistical genetics, processing and analysis of RNA sequencing, phylogenetic trees, computational chemistry, engineering integrity, analyzing genomic sequencing data, population genetic data and more. "Dordt has traditionally been a liberal arts school," said Dr. Nathan Tintle, Dordt College's Director for Research and Scholarship. "In recent years, however, we have ramped up our research department in partnership with Hope College and, in doing so, created a demand for an HPC system. Unfortunately, we didn’t have the budget to purchase a cluster that would suit our computational needs. Fortunately, Silicon Mechanics offered the annual RCG, a program that we are proud to be involved with. We feel fortunate to have been awarded this grant." Submissions for the 2016 RCG will be accepted December 15, 2015, through March 1, 2016. The grant recipients will be announced April 2016. Submissions will be reviewed for merit and for the potential impact the research may have on the institution's mission. Silicon Mechanics strongly encourages collaboration, within and across departments of a single institution, or across multiple institutions. Details on RCG rules, application requirements, and cluster technical specifications are available at www.researchclustergrant.com. About The City College of New York Since 1847, The City College of New York has provided low-cost, high-quality education for New Yorkers in a wide variety of disciplines. More than 16,000 students pursue undergraduate and graduate degrees in: the College of Liberal Arts and Sciences; the Bernard and Anne Spitzer School of Architecture; the School of Education; the Grove School of Engineering; the Sophie Davis School of Biomedical Education, and the Colin Powell School for Civic and Global Leadership. Dordt College is a private institution of higher education, committed to the Reformed Christian perspective. With 1,400 students, the college’s STEM programs are leading enrollment growth. Located in Sioux Center, Iowa, Dordt College provides a holistic residential learning experience for students, in which they can develop Christian insight in all areas of life.


News Article | February 16, 2017
Site: www.businesswire.com

VISALIA, Calif.--(BUSINESS WIRE)--Edeniq, Inc., a biorefining and cellulosic technology company, today announced that Siouxland Energy Cooperative (“SEC”) has successfully installed Edeniq’s Cellunators and has started production of cellulosic ethanol using Edeniq’s Pathway Technology at its 60 million gallon per year ethanol plant located in Sioux Center, Iowa. With Edeniq providing technical support, SEC is preparing to file a registration with the United States Environmental Protection Agency for D3 RINs. The Cellunator high-shear milling equipment is a leading yield-enhancement technology that offers the most significant and consistent increase in ethanol yield and corn oil recovery, as well as enables the highest production of cellulosic ethanol when integrated with Edeniq’s Pathway Technology. Edeniq’s Pathway Technology is the lowest-cost solution for producing and measuring cellulosic ethanol from corn kernel fiber utilizing existing fermenters at corn ethanol plants and has produced up to 2.5% cellulosic ethanol, up to a 7% increase in overall ethanol yield, and additional corn oil recovery. “Edeniq met our every expectation,” said Jeff Altena, SEC’s Operations Director. “The installation of the Cellunators was on schedule and budget, and we are pleased with the increased yield of ethanol both from starch and cellulosic fiber. We would like to thank the USDA for grants toward the Cellunator installation.” “We really appreciated the cooperation from Jeff Larson, SEC’s plant manager, and his team to achieve a rapid and successful installation and start-up,” said Cam Cast, Chief Operating Officer for Edeniq. “We were pleased to complete the start-up in the fourth quarter of last year so that SEC can enjoy the high value of D3 RINs for 2017.” Edeniq has developed leading processes for producing low-cost cellulosic sugars and cellulosic ethanol. Edeniq’s capital light and operationally efficient solutions can be easily integrated into existing biorefineries that produce ethanol, other biofuels, biochemicals, and/or bio-based products. Edeniq currently sells or licenses its technologies to biorefineries in the United States. Edeniq was founded in 2008 and is headquartered in Visalia, California with a field office in Omaha, Nebraska. More information can be found at www.edeniq.com.

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