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Full-Text Articles in Life Sciences

Breeding Maize Maternal Haploid Inducers, Henrique Uliana Trentin, Ursula K. Frei, Thomas Lubberstedt May 2020

Breeding Maize Maternal Haploid Inducers, Henrique Uliana Trentin, Ursula K. Frei, Thomas Lubberstedt

Agronomy Publications

Maize doubled haploid (DH) lines are usually created in vivo, through crosses with maternal haploid inducers. These inducers have the inherent ability of generating seeds with haploid embryos when used to pollinate other genotypes. The resulting haploid plants are treated with a doubling agent and self-pollinated, producing completely homozygous seeds. This rapid method of inbred line production reduces the length of breeding cycles and, consequently, increases genetic gain. Such advantages explain the wide adoption of this technique by large, well-established maize breeding programs. However, a slower rate of adoption was observed in medium to small-scale breeding programs. The high price ...


Iron-Mediated Organic Matter Decomposition In Humid Soils Can Counteract Protection, Chunmei Chen, Steven J. Hall, Elizabeth Coward, Aaron Thompson May 2020

Iron-Mediated Organic Matter Decomposition In Humid Soils Can Counteract Protection, Chunmei Chen, Steven J. Hall, Elizabeth Coward, Aaron Thompson

Ecology, Evolution and Organismal Biology Publications

Soil organic matter (SOM) is correlated with reactive iron (Fe) in humid soils, but Fe also promotes SOM decomposition when oxygen (O2) becomes limited. Here we quantify Fe-mediated OM protection vs. decomposition by adding 13C dissolved organic matter (DOM) and 57FeII to soil slurries incubated under static or fluctuating O2. We find Fe uniformly protects OM only under static oxic conditions, and only when Fe and DOM are added together: de novo reactive FeIII phases suppress DOM and SOM mineralization by 35 and 47%, respectively. Conversely, adding 57FeII alone increases SOM mineralization by 8% following oxidation to 57FeIII. Under O2 ...


Ragweed And Sagebrush Pollen Can Distinguish Between Vegetation Types At Broad Spatial Scales, Hannah M. Carroll, Alan D. Wanamaker, Lynn G. Clark, Brian J. Wilsey May 2020

Ragweed And Sagebrush Pollen Can Distinguish Between Vegetation Types At Broad Spatial Scales, Hannah M. Carroll, Alan D. Wanamaker, Lynn G. Clark, Brian J. Wilsey

Ecology, Evolution and Organismal Biology Publications

Patterns of vegetation distribution at regional to subcontinental scales can inform understanding of climate. Delineating ecoregion boundaries over geologic time is complicated by the difficulty of distinguishing between prairie types at broad spatial scales using the pollen record. Pollen ratios are sometimes employed to distinguish between vegetation types, although their applicability is often limited to a geographic range. The Neotoma Paleoecology Database offers an unparalleled opportunity to synthesize a large number of pollen datasets. Ambrosia (ragweed) is a genus of mesic‐adapted species sensitive to summer moisture. Artemisia (sagebrush, wormwood, mugwort) is a genus of dry‐mesic‐adapted species resilient ...


Soybean Aphid Biotype 1 Genome: Insights Into The Invasive Biology And Adaptive Evolution Of A Major Agricultural Pest, Rosanna Giordano, Ravi Kiran Donthu, Jonathan H. Badger, Glen L. Hartman, Arian Avalos, Brad S. Coates, Doris Lagos-Kutz, Matthew E. O'Neal, Sijun Liu, Et Al. May 2020

Soybean Aphid Biotype 1 Genome: Insights Into The Invasive Biology And Adaptive Evolution Of A Major Agricultural Pest, Rosanna Giordano, Ravi Kiran Donthu, Jonathan H. Badger, Glen L. Hartman, Arian Avalos, Brad S. Coates, Doris Lagos-Kutz, Matthew E. O'Neal, Sijun Liu, Et Al.

Entomology Publications

The soybean aphid, Aphis glycines Matsumura (Hemiptera: Aphididae) is a serious pest of the soybean plant, Glycine max, a major world-wide agricultural crop. We assembled a de novo genome sequence of Ap. glycines Biotype 1, from a culture established shortly after this species invaded North America. 20.4% of the Ap. glycines proteome is duplicated. These in-paralogs are enriched with Gene Ontology (GO) categories mostly related to apoptosis, a possible adaptation to plant chemistry and other environmental stressors. Approximately one-third of these genes show parallel duplication in other aphids. But Ap. gossypii, its closest related species, has the lowest number ...


Whole Genome Sequencing For Mutation Discovery In A Single Case Of Lysosomal Storage Disease (Mps Type 1) In The Dog, Tamer A. Mansour, Kevin D. Woolard, Karen L. Vernau, Devin M. Ancona, Sara M. Thomasy, Lionel Sebbag, Bret A. Moore, Marguerite F. Knipe, Haitham A. Seada, Tina M. Cowan, Miriam Aguilar, C. Titus Brown, Danika L. Bannasch Apr 2020

Whole Genome Sequencing For Mutation Discovery In A Single Case Of Lysosomal Storage Disease (Mps Type 1) In The Dog, Tamer A. Mansour, Kevin D. Woolard, Karen L. Vernau, Devin M. Ancona, Sara M. Thomasy, Lionel Sebbag, Bret A. Moore, Marguerite F. Knipe, Haitham A. Seada, Tina M. Cowan, Miriam Aguilar, C. Titus Brown, Danika L. Bannasch

Veterinary Clinical Sciences Publications

Mucopolysaccharidosis (MPS) is a metabolic storage disorder caused by the deficiency of any lysosomal enzyme required for the breakdown of glycosaminoglycans. A 15-month-old Boston Terrier presented with clinical signs consistent with lysosomal storage disease including corneal opacities, multifocal central nervous system disease and progressively worsening clinical course. Diagnosis was confirmed at necropsy based on histopathologic evaluation of multiple organs demonstrating accumulation of mucopolysaccharides. Whole genome sequencing was used to uncover a frame-shift insertion affecting the alpha-L-iduronidase (IDUA) gene (c.19_20insCGGCCCCC), a mutation confirmed in another Boston Terrier presented 2 years later with a similar clinical picture. Both dogs were homozygous ...


Preemergence Herbicide Application Timings: Pros And Cons, Robert G. Hartzler, Meaghan J. B. Anderson, Prashant Jha Apr 2020

Preemergence Herbicide Application Timings: Pros And Cons, Robert G. Hartzler, Meaghan J. B. Anderson, Prashant Jha

Integrated Crop Management News

Preemergence herbicides are the foundation of herbicide-based weed management systems, and effective use of these products is essential to protect crop yields and reduce selection pressure for herbicide resistant weeds. In a perfect world, applying preemergence herbicides immediately after planting would provide the greatest likelihood of maximum performance, but equipment and labor availability limit many farms from using this approach. This article will provide a brief overview of the pros and cons of different application strategies


Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. Mccallum, Amidou N’Diaye, Ron M. Depauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. Mccartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer Apr 2020

Mapping Quantitative Trait Loci Associated With Leaf Rust Resistance In Five Spring Wheat Populations Using Single Nucleotide Polymorphism Markers, Firdissa E. Bokore, Ron E. Knox, Richard D. Cuthbert, Curtis J. Pozniak, Brent D. Mccallum, Amidou N’Diaye, Ron M. Depauw, Heather L. Campbell, Catherine Munro, Arti Singh, Colin W. Hiebert, Curt A. Mccartney, Andrew G. Sharpe, Asheesh K. Singh, Dean Spaner, D. B. Fowler, Yuefeng Ruan, Samia Berraies, Brad Meyer

Agronomy Publications

Growing resistant wheat (Triticum aestivum L) varieties is an important strategy for the control of leaf rust, caused by Puccinia triticina Eriks. This study sought to identify the chromosomal location and effects of leaf rust resistance loci in five Canadian spring wheat cultivars. The parents and doubled haploid lines of crosses Carberry/AC Cadillac, Carberry/Vesper, Vesper/Lillian, Vesper/Stettler and Stettler/Red Fife were assessed for leaf rust severity and infection response in field nurseries in Canada near Swift Current, SK from 2013 to 2015, Morden, MB from 2015 to 2017 and Brandon, MB in 2016, and in New ...


Are You Planting On A Level Playing Field?, Ryan W. Bergman Apr 2020

Are You Planting On A Level Playing Field?, Ryan W. Bergman

Integrated Crop Management News

Springtime on a farm is typically filled with the hustle and bustle of gearing up for planting season. This is the time of year when most farmers focus on de-winterizing the sprayer, changing oil in the tractors and checking the seed meters on the planter. If you use a field cultivator, it is also important to make sure it is properly adjusted to help provide a uniform seedbed for the upcoming planting season. Whether this is the first season or the thirtieth season for the field cultivator, there are a few items to check before making your way to the ...


Pesticide Applications – Are You Prepared?, Elizabeth Danielson, Kristine J. P. Schaefer Apr 2020

Pesticide Applications – Are You Prepared?, Elizabeth Danielson, Kristine J. P. Schaefer

Integrated Crop Management News

With the critical need for respirators and other personal protective equipment (PPE) for health care, there is a potential shortage of PPE, particularly N95 respirators, in the marketplace for agriculture and pesticide applications.


(-)-Α-Pinene Reduces Quorum Sensing And Campylobacter Jejuni Colonization In Broiler Chickens, Katarina Šimunović, Orhan Sahin, Jasna Kovač, Zhangqi Shen, Anja Klančnik, Qijing Zhang, Sonja Smole Možina Apr 2020

(-)-Α-Pinene Reduces Quorum Sensing And Campylobacter Jejuni Colonization In Broiler Chickens, Katarina Šimunović, Orhan Sahin, Jasna Kovač, Zhangqi Shen, Anja Klančnik, Qijing Zhang, Sonja Smole Možina

Veterinary Microbiology and Preventive Medicine Publications

Campylobacter jejuni is one of the most prevalent causes of bacterial gastroenteritis worldwide, and it is largely associated with consumption of contaminated poultry. Current Campylobacter control measures at the poultry production level remain insufficient, and hence there is the need for alternative control strategies. We evaluated the potential of the monoterpene (-)-α-pinene for control of C. jejuni in poultry. The antibacterial and resistance-modulatory activities of (-)-α-pinene were also determined against 57 C. jejuni strains. In addition, the anti-quorum-sensing activity of (-)-α-pinene against C. jejuni NCTC 11168 was determined for three subinhibitory concentrations (125, 62.5, 31.25 mg/L) over ...


Spring Forage Fertilization Considerations, Brian J. Lang, Rebecca K. Vittetoe Apr 2020

Spring Forage Fertilization Considerations, Brian J. Lang, Rebecca K. Vittetoe

Integrated Crop Management News

Fertilization is just as important for forages as it is for row crops to maximize productivity. This article addresses spring fertilization considerations for forage crops and pastures.


The Soybean Aphid Suction Trap Network: Sampling The Aerobiological “Soup”, Doris Lagos-Kutz, David J. Voegtlin, David Onstad, David Hogg, David Ragsdale, Kelley Tilmon, Erin Hodgson, Christina Difonzo, Russell Groves, Christian Krupke, Joseph Laforest, Nicholas J. Selter, Emily Duerr, Benjamin Bradford, Glen L. Hartman Apr 2020

The Soybean Aphid Suction Trap Network: Sampling The Aerobiological “Soup”, Doris Lagos-Kutz, David J. Voegtlin, David Onstad, David Hogg, David Ragsdale, Kelley Tilmon, Erin Hodgson, Christina Difonzo, Russell Groves, Christian Krupke, Joseph Laforest, Nicholas J. Selter, Emily Duerr, Benjamin Bradford, Glen L. Hartman

Entomology Publications

The initiation of the soybean aphid suction trap network (STN) in 2001 marked the beginning of a rich and fruitful collaborative effort that has produced a wealth of data about the soybean aphid, other insect species, and other organisms that make up the aerobiological “soup.” Collaboration among researchers, extension specialists, and agriculturalists has provided information about seasonal migration patterns of the soybean aphid and monitoring of other insect species. The physical collections of the “soup” have been stored and used for past research, and will serve as a foundation for future research.


A Syringe-Based Biosensor To Rapidly Detect Low Levels Of Escherichia Coli (Ecor13) In Drinking Water Using Engineered Bacteriophages, Troy C. Hinkley, Spencer Garing, Paras Jain, John Williford, Anne-Laure M. Le Ny, Kevin P. Nichols, Joseph E. Peters, Joey N. Talbert, Sam R. Nugen Mar 2020

A Syringe-Based Biosensor To Rapidly Detect Low Levels Of Escherichia Coli (Ecor13) In Drinking Water Using Engineered Bacteriophages, Troy C. Hinkley, Spencer Garing, Paras Jain, John Williford, Anne-Laure M. Le Ny, Kevin P. Nichols, Joseph E. Peters, Joey N. Talbert, Sam R. Nugen

Food Science and Human Nutrition Publications

A sanitized drinking water supply is an unconditional requirement for public health and the overall prosperity of humanity. Potential microbial and chemical contaminants of drinking water have been identified by a joint effort between the World Health Organization (WHO) and the United Nations Children’s Fund (UNICEF), who together establish guidelines that define, in part, that the presence of Escherichia coli (E. coli) in drinking water is an indication of inadequate sanitation and a significant health risk. As E. coli is a nearly ubiquitous resident of mammalian gastrointestinal tracts, no detectable counts in 100 mL of drinking water is the ...


Deadline Waived For Iowa Pesticide Applicators To Renew Certification, Kristine J. P. Schaefer Mar 2020

Deadline Waived For Iowa Pesticide Applicators To Renew Certification, Kristine J. P. Schaefer

Integrated Crop Management News

The Iowa Department of Agriculture and Land Stewardship (IDALS) has waived the deadline for pesticide applicators to meet recertification requirements, following a proclamation by Iowa Gov. Kim Reynolds March 22.


Observations Show That Wind Farms Substantially Modify The Atmospheric Boundary Layer Thermal Stratification Transition In The Early Evening, Daniel A. Rajewski, Eugene S. Takle, Andy Vanloocke, Samantha L. Purdy Mar 2020

Observations Show That Wind Farms Substantially Modify The Atmospheric Boundary Layer Thermal Stratification Transition In The Early Evening, Daniel A. Rajewski, Eugene S. Takle, Andy Vanloocke, Samantha L. Purdy

Agronomy Publications

Single wind turbines and large wind farms modify local scales of atmospheric boundary layer (ABL) turbulence through different mechanisms dependent on location within the wind farm. These changes in turbulence scales would most likely have notable influence on surface fluxes and microclimate during the afternoon and early evening stability transition. Profiles of Richardson number and shear and buoyancy from 1‐Hz tall tower measurements in and near a wind farm in an agricultural landscape were used to quantify departures in stability characteristics during the fallow seasons. A single turbine wake decoupled turbulent connection between the surface and above the wind ...


The Opportunities And Challenges With Hemp, Chad Hart Mar 2020

The Opportunities And Challenges With Hemp, Chad Hart

Integrated Crop Management News

Over the past several years as row crop prices declined, farmers and landowners across the nation have searched for alternative crops that might improve the financial bottom line. With the passage of the 2014 and 2018 farm bills, industrial hemp became one of those possible alternative crops. The 2014 farm bill established industrial hemp (hemp with a tetrahydrocannabinol [THC] concentration of 0.3% or less) as a potential crop, separating it from its illegal relative, marijuana. The 2018 farm bill removed hemp from the list of controlled substances and established hemp as an agricultural commodity, including the provision of crop ...


Terminating Cover Crops This Spring, Meaghan J. B. Anderson, Rebecca K. Vittetoe, Robert G. Hartzler Mar 2020

Terminating Cover Crops This Spring, Meaghan J. B. Anderson, Rebecca K. Vittetoe, Robert G. Hartzler

Integrated Crop Management News

As temperatures warm this spring, cover crop termination is on the to-do list for some Iowa fields. Killing cover crops with herbicides is the most common termination method. The effectiveness of herbicides at terminating a cover crop depends primarily on three things:

1. Cover crop species and growth stage

2. Herbicide and rate used

3. Environment


Recommendations To Achieve High Quality Dry Fertilizer Applications, Ryan W. Bergman Mar 2020

Recommendations To Achieve High Quality Dry Fertilizer Applications, Ryan W. Bergman

Integrated Crop Management News

Claims of poor fertilizer application and visual striping in fields have increased in recent years. This issue impacts all sectors of the supply chain including growers, custom applicators, cooperatives and agribusiness insurance companies. An increase in documented application problems is primarily driven by a broader use of aerial imagery that can easily detect problems and an increase in use of dry nitrogen fertilizers. Cases of poor-quality application are seen less frequently with phosphorus or potassium products than with nitrogen because corn is not as sensitive to varying rates of these nutrients. Prior to applying dry fertilizer, follow these guidelines to ...


Crop Sulfur Fertilization This Spring, John E. Sawyer Mar 2020

Crop Sulfur Fertilization This Spring, John E. Sawyer

Integrated Crop Management News

Significant sulfur (S) deficiency in Iowa crops was first documented about 15 years ago. First identified in alfalfa and then corn and soybean. Since then about 150 trials with corn (along with trials with alfalfa and soybean) have been conducted across the state, with approximately 50% of trials having a statistically significant yield increase. A main reason for the yield response to S in recent years, as compared to many years prior, has been reduction in atmospheric deposition as a result of the Clean Air Act. Other factors for increased S responses include fields with no manure applications, increased crop ...


Managing Winter Annual Weeds This Spring, Meaghan J. B. Anderson, Robert G. Hartzler Mar 2020

Managing Winter Annual Weeds This Spring, Meaghan J. B. Anderson, Robert G. Hartzler

Integrated Crop Management News

After another relatively wet fall, late harvest season, and mild winter, early weed management may be important this spring for those who have persistent issues with winter annuals such as field pennycress and horseweed/marestail in no-till. Winter annuals resume growth soon after the arrival of warm temperatures, so as soon as fields are fit, the weeds will be susceptible to spray.


Management Considerations For Slugs: Do Insecticides Work?, Ashley Dean, Erin W. Hodgson Mar 2020

Management Considerations For Slugs: Do Insecticides Work?, Ashley Dean, Erin W. Hodgson

Integrated Crop Management News

With recent weather patterns, specifically high rainfall leading to wet soil conditions, some farmers have experienced damaging populations of slugs in their no-till fields. No-till fields are particularly affected since increased residue provides a stable, cool, and wet environment for these animals that are prone to desiccation (drying out). Oftentimes, farmers wonder if insecticides or seed treatments are effective at managing these noninsect pests. We will discuss management options for slugs in this article.


Legally Operating A Drone In The Agriculture Industry, Ryan W. Bergman Mar 2020

Legally Operating A Drone In The Agriculture Industry, Ryan W. Bergman

Integrated Crop Management News

Drone activity in agriculture continues to increase, and the aerial imagery generated can provide unique insight throughout the crop production season. Over the past decade the Federal Aviation Administration (FAA) has continued to evolve the requirements for the operation of small unmanned aerial systems (sUAS, UAS, UAV or drones) to create a reasonable legal pathway for use in agriculture.


Management Considerations For Millipedes And Isopods: Do Insecticides Work?, Ashley Dean, Erin W. Hodgson Mar 2020

Management Considerations For Millipedes And Isopods: Do Insecticides Work?, Ashley Dean, Erin W. Hodgson

Integrated Crop Management News

Many states, including Iowa, received a record amount of precipitation in 2019. In fact, the past two growing seasons have been especially wet. Consequently, this has created a number of issues for farmers, including reports of millipedes damaging crops under no-till production in Iowa, which is likely due to a combination of wet conditions and high residue. People that experience millipedes under these conditions frequently ask if insecticides or seed treatments will provide control of these pests. Although millipedes are not insects, they commonly fall under the realm of entomology, alongside many other animals (spiders, centipedes, mites, etc.). We will ...


Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt Mar 2020

Impact Of Spontaneous Haploid Genome Doubling In Maize Breeding, Nicholas A. Boerman, Ursula K. Frei, Thomas Lubberstedt

Agronomy Publications

Doubled haploid (DH) technology has changed the maize-breeding landscape in recent years. Traditionally, DH production requires the use of chemical doubling agents to induce haploid genome doubling and, subsequently, male fertility. These chemicals can be harmful to humans and the plants themselves, and typically result in a doubling rate of 10%–30%. Spontaneous genome doubling and male fertility of maize haploids, without using chemical doubling agents, have been observed to a limited extent, for nearly 70 years. Rates of spontaneous haploid genome doubling (SHGD) have ranged from less than 5% to greater than 50%. Recently, there has been increased interest ...


High Speed Planting Technology, Ryan W. Bergman Mar 2020

High Speed Planting Technology, Ryan W. Bergman

Integrated Crop Management News

Iowa State University (ISU) recently completed a five-year study of high-speed planter equipment in corn and soybeans. The study utilized a 12-row planter equipped with the Precision Planting SpeedTube high speed planter system and a 24-row planter equipped with the John Deere ExactEmerge high speed planter system (Figure 1). Both planters utilized individual row hydraulic downforce and were tested using a side-by-side strip trial experimental design. Each planter was used on approximately 400 acres per year. Additionally, a third planter with a standard drop tube seed delivery system was included in select fields for seed spacing comparisons.


Genetic And Genomic Characterization Of Vulva Size Traits In Yorkshire And Landrace Gilts, Flor-Anita Corredor, Leticia P. Sanglard, Richard J. Leach, Jason W. Ross, Aileen F. Keating, Nick V. L. Serão Mar 2020

Genetic And Genomic Characterization Of Vulva Size Traits In Yorkshire And Landrace Gilts, Flor-Anita Corredor, Leticia P. Sanglard, Richard J. Leach, Jason W. Ross, Aileen F. Keating, Nick V. L. Serão

Animal Science Publications

Background: Reproductive performance is critical for efficient swine production. Recent results indicated that vulva size (VS) may be predictive of reproductive performance in sows. Study objectives were to estimate genetic parameters, identify genomic regions associated, and estimate genomic prediction accuracies (GPA) for VS traits.

Results: Heritability estimates of VS traits, vulva area (VA), height (VH), and width (VW) measurements, were moderately to highly heritable in Yorkshire, with 0.46 ± 0.10, 0.55 ± 0.10, 0.31 ± 0.09, respectively, whereas these estimates were low to moderate in Landrace, with 0.16 ± 0.09, 0.24 ± 0.11, and 0 ...


Spring Corn Nitrogen Fertilization Considerations, John E. Sawyer Mar 2020

Spring Corn Nitrogen Fertilization Considerations, John E. Sawyer

Integrated Crop Management News

Perhaps you did not get planned nitrogen (N) applications accomplished last fall. Or you are pondering what the spring 2020 weather conditions might be – another wet spring? Are you are considering use of different products; if so how should they be handled?


Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital Mar 2020

Crispr-Cas12a Has Widespread Off-Target And Dsdna-Nicking Effects, Karthik Murugan, Arun S. Seetharam, Andrew J. Severin, Dipali G. Sashital

Office of Biotechnology Publications

Cas12a (Cpf1) is an RNA-guided endonuclease in the bacterial type V-A CRISPR-Cas anti-phage immune system that can be repurposed for genome editing. Cas12a can bind and cut dsDNA targets with high specificity in vivo, making it an ideal candidate for expanding the arsenal of enzymes used in precise genome editing. However, this reported high specificity contradicts Cas12a’s natural role as an immune effector against rapidly evolving phages. Here, we employed high-throughput in vitro cleavage assays to determine and compare the native cleavage specificities and activities of three different natural Cas12a orthologs (FnCas12a, LbCas12a, and AsCas12a). Surprisingly, we observed pervasive ...


Rs Content And Egi Value Of Cooked Noodles (I): Effect Of Cooking Methods, Yu Tian, Ming Li, Aoxing Tang, Jay-Lin Jane, Sushil Dhital, Boli Guo Mar 2020

Rs Content And Egi Value Of Cooked Noodles (I): Effect Of Cooking Methods, Yu Tian, Ming Li, Aoxing Tang, Jay-Lin Jane, Sushil Dhital, Boli Guo

Food Science and Human Nutrition Publications

Noodles are widely consumed in China, which can be cooked in different ways. The effects of different cooking methods (boiling, steaming, microwave heating, stir-frying and frying) on the resistance starch (RS) content and digestive properties (digestion rate, digestibility and estimated glycemic index (eGI) value) of noodles were investigated. The RS content was greatly affected by the cooking time, and it was varied when the noodles were optimally cooked using different cooking methods. The RS contents of the microwaved and stir-fried noodles were relatively high (0.59%–0.99%), but it was lower (0.43%–0.44%) in the boiled and ...


Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele Mar 2020

Pyrpipe: A Python Package For Rna-Seq Workflows, Urminder Singh, Jing Li, Arun Seetharam, Eve Syrkin Wurtele

Genetics, Development and Cell Biology Publications

Implementing RNA-Seq analysis pipelines is challenging as data gets bigger and more complex. With the availability of terabytes of RNA-Seq data and continuous development of analysis tools, there is a pressing requirement for frameworks that allow for fast and efficient development, modification, sharing and reuse of workflows. Scripting is often used, but it has many challenges and drawbacks. We have developed a python package, python RNA-Seq Pipeliner (pyrpipe) that enables straightforward development of flexible, reproducible and easy-to-debug computational pipelines purely in python, in an object-oriented manner. pyrpipe provides high level APIs to popular RNA-Seq tools. Pipelines can be customized by ...