Digital Commons Network^™

Prediction Of Agricultural Implement Hydraulic Power Requirements Using Controller Area Network Bus Data, Gabriel P. Stoll, Rodney A. Rohrer, Santosh K. Pitla, Joe D. Luck

Department of Agricultural and Biological Systems Engineering: Faculty Publications

One of the important challenges in agricultural machinery research is the ability to effectively determine power requirements of a given field operation. The Controller Area Network (CAN) Bus, also known as ISOBUS, has proven to be an effective digital tool for tractor and implement data collection. This study attempted to determine implement hydraulic power requirements using a combination of existing public tractor CAN messages and minimal added sensors. The sensor signals were published on the CAN bus for ease of simultaneous sensor signal and CAN message data collection. Based upon the available CAN messages, this study attempted to measure hydraulic …

Effects Of Alternate Wetting And Drying Irrigation Regime And Nitrogen Fertilizer On Yield And Nitrogen Use Efficiency Of Irrigated Rice In The Sahel, Koffi Djaman, Valere C. Mel, Lamine Diop, Abdoulaye Sow, Raafat El-Namaky, Baboucarr Manneh, Kazuki Saito, Koichi Futakuchi, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

The objectives of this study were to investigate water saving strategies in the paddy field and to evaluate the performance of some of the newly released rice varieties. Field experiments were conducted at Fanaye in the Senegal River Valley during two rice growing seasons in 2015. Three irrigation regimes ((i) continuous flooding, (ii) trigging irrigation at soil matric potential (SMP) of 30 kPa, (iii) trigging irrigation at SMP of 60 kPa) were tested in an irrigated lowland rice field. Irrigation regimes (ii) and (iii) are alternate wetting and drying (AWD) cycles. Four inbred rice varieties (NERICA S-21, NERICA S-44, Sahel …

Crop Evapotranspiration, Irrigationwater Requirement And Water Productivity Of Maize From Meteorological Data Under Semiarid Climate, Koffi Djaman, Michael O'Neill, Curtis K. Owen, Daniel Smeal, Komlan Koudahe, Margaret West, Samuel Allen, Kevin Lombard, Suat Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Under the semiarid climate of the Southwest United States, accurate estimation of crop water use is important for water management and planning under conservation agriculture. The objectives of this study were to estimate maize water use and water productivity in the Four Corners region of New Mexico. Maize was grown under full irrigation during the 2011, 2012, 2013, 2014 and 2017 seasons at the Agricultural Science Center at Farmington (NM). Seasonal amounts of applied irrigation varied from 576.6 to 1051.6 mm and averaged 837.7 mm and the total water supply varied from 693.4 to 1140.5 mm. Maize actual evapotranspiration was …

Hydrologic Evaluation Of Residential Rain Gardens Using A Stormwater Runoff Simulator, A. R. Anderson, T. G. Franti, D. P. Shelton

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Engineered bioretention cells with underdrains have shown water quality and hydrologic benefits for abating urban stormwater problems. Less is known about the hydrologic performance of residential rain gardens that rely on in situ soil infiltration as the primary mechanism of volume control. Eleven residential rain gardens in Lincoln, Nebraska, were evaluated using a variable-rate stormwater runoff simulator. A volume-based water quality volume (WQV) design storm of 3.0 cm was applied to each rain garden as an SCS Type II runoff hydrograph until the system began overflowing to test the rain gardens for surface and subsurface storage capacity, drawdown rate, ponding …

Registration For Optical Multimodal Remote Sensing Images Based On Fast Detection,Window Selection, And Histogram Specification, Xiaoyang Zhao, Jian Zhang, Chenghai Yang, Huaibo Song, Yeyin Shi, Xingen Zhou, Dongyan Zhang, Guozhong Zhang

Department of Agricultural and Biological Systems Engineering: Faculty Publications

In recent years, digital frame cameras have been increasingly used for remote sensing applications. However, it is always a challenge to align or register images captured with different cameras or different imaging sensor units. In this research, a novel registration method was proposed. Coarse registration was first applied to approximately align the sensed and reference images. Window selection was then used to reduce the search space and a histogram specification was applied to optimize the grayscale similarity between the images. After comparisons with other commonly-used detectors, the fast corner detector, FAST (Features from Accelerated Segment Test), was selected to extract …

Impact Of Eastern Redcedar Proliferation On Water Resources In The Great Plains Usa—Current State Of Knowledge, Chris B. Zou, Dirac Twidwell, Christine H. Bielski, Dillon T. Fogarty, Aaron R. Mittelstet, Patrick J. Starks, Rodney E. Will, Yu Zhong, Bharat Sharma Acharya

Department of Agricultural and Biological Systems Engineering: Faculty Publications

In the Great Plains of the central United States, water resources for human and aquatic life rely primarily on surface runoff and local recharge from rangelands that are under rapid transformation to woodland by the encroachment of Eastern redcedar (redcedar; Juniperus virginiana) trees. In this synthesis, the current understanding and impact of redcedar encroachment on the water budget and water resources available for non-ecosystem use are reviewed. Existing studies concluded that the conversion from herbaceous-dominated rangeland to redcedar woodland increases precipitation loss to canopy interception and vegetation transpiration. The decrease of soil moisture, particularly for the subsurface soil layer, …

Investigation Of Organic Solvents’ Effects On Kenaf (Hibiscus Cannabinus L.) Biomass Conversion In Subcritical Water, Bahar Meryemoglu, Arif Hasanoglu, Mehtap Kurtulus, Sibel Irmak

Department of Agricultural and Biological Systems Engineering: Faculty Publications

Kenaf biomass was hydrolyzed under subcritical water conditions in the presence of various organic solvents. The solvents tested were tetrahydrofuran (THF), acetone, xylene (mixed isomers) and methanol. The organic compounds released into hydrolysates, total organic contents, water-soluble total phenols, and the molecular weight distributions of the polysaccharides in the hydrolysates, solid residues leftover after hydrolysis and gaseous products formed during the solubilization process were determined. The results showed that organic solvents significantly enhanced the dissolution of kenaf biomass (methanol < (omp)xylene ≤ acetone ~ tetrahydrofuran). The hydrolysis percentage was found to be between 75-82% depending on the type of the solvent. Hydrolysis yield and total organic carbons released into hydrolysates highly differed when the solubilization process was performed under carbon dioxide pressure and this effect considerably varied based on the type of solvent used in hydrolysis process. The main gas product formed during hydrolysis process was carbon dioxide with ~80% composition. Morphological measurements of the solid biomass residues left after hydrolysis showed substantial degradations with increasing number of pores on the biomass surfaces.

Convergent Body Size Evolution Of Crocodyliformes Upon Entering The Aquatic Realm, William Gearty, Jonathan Payne

School of Biological Sciences: Presentations

Twenty-four species of crocodile populate the globe today, but this richness represents a minute fraction of the diversity and disparity of Crocodyliformes since their origin early in the Triassic. Across this clade, three major diversification events into the aquatic realm have occurred. Aquatic and terrestrial habitats impose differing selective pressures on body size. However, previous research on this topic in Crocodyliformes remains qualitative in nature. In this study, our goal was to quantify the influence of habitat (terrestrial versus aquatic) on the evolution of body size in Crocodyliformes. We find a history of repeated body size increase and convergence following …

Total Mercury Determination In Muscle And Liver Tissue Samples From Brazilian Amazon Fish Using Slurry Sampling, João Vitor De Queiroz, José Cavalcante Souza Vieira, Izabela Da Cunha Bataglioli, Alis Correia Bittarello, Camila Pereira Braga, Grasieli De Oliveira, Cilene Do Carmo Federici Padilha, Pedro De Magalhães Padilha

Department of Biochemistry: Faculty Publications

This paper presents a slurry sampling method for total mercury determination by graphite furnace atomic absorption spectrometry (GFAAS) in tissue of fish from the Amazon. The tissue samples were lyophilized and macerated, and then the slurry samples were prepared by putting 20 mg of tissue, added to a solution containing Triton X-100, Suprapur HNO₃, and zirconium nitrate directly in sampling vials of a spectrometer. Mercury standard solutions were prepared under the same conditions as the slurry samples. The slurry samples and the mercury standard solutions were sonicated for 20 s. Twenty microliters of slurry samples were injected into …

Cancerdiscover: An Integrative Pipeline For Cancer Biomarker And Cancer Class Prediction From High-Throughput Sequencing Data, Akram Mohammed, Greyson Biegert, Jiri Adamec, Tomáš Helikar

Department of Biochemistry: Faculty Publications

Accurate identification of cancer biomarkers and classification of cancer type and subtype from High Throughput Sequencing (HTS) data is a challenging problem because it requires manual processing of raw HTS data from various sequencing platforms, quality control, and normalization, which are both tedious and timeconsuming. Machine learning techniques for cancer class prediction and biomarker discovery can hasten cancer detection and significantly improve prognosis. To date, great research efforts have been taken for cancer biomarker identification and cancer class prediction. However, currently available tools and pipelines lack flexibility in data preprocessing, running multiple feature selection methods and learning algorithms, therefore, developing …

Towards The Synthetic Design Of Camelina Oil Enriched In Tailored Acetyl-Triacylglycerols With Medium-Chain Fatty Acids, Sunil Bansal, Hae Jin Kim, Gunnam Na, Megan E. Hamilton, Edgar B. Cahoon, Chaofu Lu, Timothy P. Durrett

Department of Biochemistry: Faculty Publications

The ability to manipulate expression of key biosynthetic enzymes has allowed the development of genetically modified plants that synthesise unusual lipids that are useful for biofuel and industrial applications. By taking advantage of the unique activities of enzymes from different species, tailored lipids with a targeted structure can be conceived. In this study we demonstrate the successful implementation of such an approach by metabolically engineering the oilseed crop Camelina sativa to produce 3-acetyl-1,2-diacyl-sn-glycerols (acetyl-TAGs) with medium-chain fatty acids (MCFAs). Different transgenic camelina lines that had been genetically modified to produce MCFAs through the expression of MCFA-specific thioesterases and …

Single-Molecule Unbinding Forces Between The Polysaccharide Hyaluronan And Its Binding Proteins, Fouzia Bano, Markku I. Tammi, David W. Kang, Edward N. Harris, Ralf P. Richter

Department of Biochemistry: Faculty Publications

The extracellular polysaccharide hyaluronan (HA) is ubiquitous in all vertebrate tissues, where its various functions are encoded in the supramolecular complexes and matrices that it forms with HA-binding proteins (hyaladherins). In tissues, these supramolecular architectures are frequently subjected to mechanical stress, yet how this affects the intermolecular bonding is largely unknown. Here, we used a recently developed single-molecule force spectroscopy platform to analyze and compare the mechanical strength of bonds between HA and a panel of hyaladherins from the Link module superfamily, namely the complex of the proteoglycan aggrecan and cartilage link protein, the proteoglycan versican, the inflammation-associated protein TSG-6, …

Endosomal Escape Of Antisense Oligonucleotides Internalized By Stabilin Receptors Is Regulated By Rab5c And Eea1 During Endosomal Maturation, Colton M. Miller, W. Brad Wan, Punit P. Seth, Edward N. Harris

Department of Biochemistry: Faculty Publications

Second-generation (Gen 2) Antisense oligonucleotides (ASOs) show increased nuclease stability and affinity for their RNA targets, which has translated to improved potency and therapeutic index in the clinic. Gen 2 ASOs are typically modified using the phosphorothioate (PS) backbone modification, which enhances ASO interactions with plasma, cell surface, and intracellular proteins. This facilitates ASO distribution to peripheral tissues and also promotes cellular uptake after injection into animals. Previous work identified that Stabilin receptors specifically internalize PS-ASOs in the sinusoidal endothelial cells of the liver and the spleen. By modulating expression of specific proteins involved in the trafficking and maturation of …

Purification Of Hepatocytes And Sinusoidal Endothelial Cells From Mouse Liver Perfusion, Fatima Cabral, Colton M. Miller, Katrina M. Kudrna, Blake E. Hass, Jocelyn G. Daubendiek, Brianna M. Kellar, Edward N. Harris

Department of Biochemistry: Faculty Publications

This protocol demonstrates a method for obtaining high yield and viability for mouse hepatocytes and sinusoidal endothelial cells (SECs) suitable for culturing or for obtaining cell lysates. In this protocol, the portal vein is used as the site for catheterization, rather than the vena cava, as this limits contamination of other possible cell types in the final liver preparation. No special instrumentation is required throughout the procedure. A water bath is used as a source of heat to maintain the temperature of all the buffers and solutions. A standard peristaltic pump is used to drive the fluid, and a refrigerated …

A Tlr/Akt/Foxo3 Immune Tolerance–Like Pathway Disrupts The Repair Capacity Of Oligodendrocyte Progenitors, Taasin Srivastava, Parham Diba, Justin M. Dean, Fatima Banine, Daniel Shaver, Matthew Hagen, Xi Gong, Weiping Su, Ben Emery, Daniel L. Marks, Edward N. Harris, Bruce Baggentoss, Paul H. Weigel, Larry S. Sherman, Stephen A. Back

Department of Biochemistry: Faculty Publications

Cerebral white matter injury (WMI) persistently disrupts myelin regeneration by oligodendrocyte progenitor cells (OPCs). We identified a specific bioactive hyaluronan fragment (bHAf) that downregulates myelin gene expression and chronically blocks OPC maturation and myelination via a tolerance-like mechanism that dysregulates pro-myelination signaling via AKT. Desensitization of AKT occurs via TLR4 but not TLR2 or CD44. OPC differentiation was selectively blocked by bHAf in a maturation-dependent fashion at the late OPC (preOL) stage by a noncanonical TLR4/TRIF pathway that induced persistent activation of the FoxO3 transcription factor downstream of AKT. Activated FoxO3 selectively localized to oligodendrocyte lineage cells in white matter …

3-O Sulfation Of Heparin Leads To Hepatotropism And Longer Circulatory Half-Life, Colton M. Miller, Yongmei Xu, Katrina M. Kudrna, Blake E. Hass, Brianna M. Kellar, Andrew W. Egger, Jian Liu, Edward N. Harris

Department of Biochemistry: Faculty Publications

Introduction: Heparins are common blood anticoagulants that are critical for many surgical and biomedical procedures used in modern medicine. In contrast to natural heparin derived from porcine gut mucosa, synthetic heparins are homogenous by mass, polymer length, and chemistry.

Materials & methods: Stable cell lines expressing the human and mouse Stabilin receptors were used to evaluate endocytosis of natural and synthetic heparin. We chemoenzymatically produced synthetic heparin consisting of 12 sugars (dodecamers) containing 14 sulfate groups resulting in a non-3-O sulfated structure (n12mer). Half of the n12mer was modified with a 3-O sulfate on a single GlcNS sugar producing the …

Characterization Of A Recurrent Missense Mutation In The Forkhead Dna-Binding Domain Of Foxp1, Tyler B. Johnson, Keegan Mechels, Ruth Ellen Anderson, Jacob T. Cain, David A. Sturdevant, Stephen Braddock, Hailey Pinz, Mark A. Wilson, Megan Landsverk, Kyle J. Roux, Jill M. Weimer

Department of Biochemistry: Faculty Publications

Haploinsufficiency of Forkhead box protein P1 (FOXP1), a highly conserved transcription factor, leads to developmental delay, intellectual disability, autism spectrum disorder, speech delay, and dysmorphic features. Most of the reported FOXP1 mutations occur on the C-terminus of the protein and cluster around to the forkhead domain. All reported FOXP1 pathogenic variants result in abnormal cellular localization and loss of transcriptional repression activity of the protein product. Here we present three patients with the same FOXP1 mutation, c.1574G>A (p.R525Q), that results in the characteristic loss of transcription repression activity. This mutation, however, represents the first reported FOXP1 mutation that does …

Editorial: Structure And Function Of Chloroplasts, Rebecca L. Roston, Juliette Jouhet, Fei Yu, Hongbo Gao

Department of Biochemistry: Faculty Publications

The primary energy resource of life on earth is the sun, whose energy is captured in the form of usable carbons by a process called photosynthesis. Photosynthesis occurs within a cellular organelle adapted to that purpose, called the chloroplast. Chloroplasts are unique metabolic and sensory organelles restricted to plants, algae, and a few protists. In this special topic, we aimed to gather new research, hypotheses, and reviews that would help us to better understand the important role of chloroplasts in all photosynthetic organisms. We were fortunate enough to have submissions from many talented chloroplast researchers. This topic contains a total …

Identification Of Genes Encoding Enzymes Catalyzing The Early Steps Of Carrot Polyacetylene Biosynthesis, Lucas Busta, Won Cheol Yim, Evan William Labrant, Peng Wang, Lindsey Grimes, Kiah Malyszka, John C. Cushman, Patricia Santos, Dylan K. Kosma, Edgar B. Cahoon

Department of Biochemistry: Faculty Publications

Polyacetylenic lipids accumulate in various Apiaceae species after pathogen attack, suggesting that these compounds are naturally occurring pesticides and potentially valuable resources for crop improvement. These compounds also promote human health and slow tumor growth. Even though polyacetylenic lipids were discovered decades ago, the biosynthetic pathway underlying their production is largely unknown. To begin filling this gap and ultimately enable polyacetylene engineering, we studied polyacetylenes and their biosynthesis in the major Apiaceae crop carrot (Daucus carota subsp. sativus). Using gas chromatography and mass spectrometry, we identified three known polyacetylenes and assigned provisional structures to two novel polyacetylenes. We …

Role Of Selenof As A Gatekeeper Of Secreted Disulfide-Rich Glycoproteins, Sun Hee Yim, Robert A. Everley, Frank A. Schildberg, Sang-Goo Lee, Andrea Orsi, Zachary R. Barbati, Kutay Karatepe, Dmitry E. Fomenko, Petra A. Tsuji, Hongbo R. Luo, Steven P. Gygi, Roberto Sitia, Arlene H. Sharpe, Dolph L. Hatfield, Vadim N. Gladyshev

Department of Biochemistry: Faculty Publications

Selenof (15-kDa selenoprotein; Sep15) is an endoplasmic reticulum (ER)-resident thioredoxin-like oxidoreductase that occurs in a complex with UDPglucose: glycoprotein glucosyltransferase. We found that Selenof deficiency in mice leads to elevated levels of non-functional circulating plasma immunoglobulins and increased secretion of IgM during in vitro splenic B cell differentiation. However, Selenof knockout animals show neither enhanced bacterial killing capacity nor antigen-induced systemic IgM activity, suggesting that excess immunoglobulins are not functional. In addition, ER-to-Golgi transport of a target glycoprotein was delayed in Selenof knockout embryonic fibroblasts, and proteomic analyses revealed that Selenof deficiency is primarily associated with antigen presentation and ER-to-Golgi …

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle E. Howell, Karin V. Van Dijk, Christine S. Booth, Tomáš Helikar, Brian A. Couch, Rebecca Roston

Department of Biochemistry: Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7).

Structural Basis For The Substrate Inhibition Of Proline Utilization A By Proline, David A. Korasick, Travis A. Pemberton, Benjamin W. Arentson, Donald F. Becker, John J. Tanner

Department of Biochemistry: Faculty Publications

Proline utilization A (PutA) is a bifunctional flavoenzyme that catalyzes the two-step oxidation of L-proline to L-glutamate using spatially separated proline dehydrogenase (PRODH) and L-glutamate-y-semialdehyde dehydrogenase (GSALDH) active sites. Substrate inhibition of the coupled PRODH-GSALDH reaction by proline is a common kinetic feature of PutAs, yet the structural basis for this phenomenon remains unknown. To understand the mechanism of substrate inhibition, we determined the 2.15 Å resolution crystal structure of Bradyrhizobium japonicum PutA complexed with proline. Proline was discovered in five locations remote from the PRODH active site. Most notably, strong electron density indicated that proline bound tightly to the …

Lncrna Meg3 Protects Endothelial Function By Regulating The Dna Damage Response, Mohamed Sham Shihabudeen Haider Ali, Xiao Cheng, Matthew Moran, Stefan Haemmig, Michael J. Naldrett, Sophie Alvarez, Mark W. Feinberg, Xinghui Sun

Department of Biochemistry: Faculty Publications

The role of long non-coding RNAs (lncRNAs) in regulating endothelial function through the DNA damage response (DDR) remains poorly understood. In this study, we demonstrate that lncRNA maternally expressed gene 3 (Meg3) interacts with the RNA binding protein polypyrimidine tract binding protein 3 (PTBP3) to regulate gene expression and endothelial function through p53 signaling a major coordinator of apoptosis and cell proliferation triggered by the DDR. Meg3 expression is induced in endothelial cells (ECs) upon p53 activation. Meg3 silencing induces DNA damage, activates p53 signaling, increases the expression of p53 target genes, promotes EC apoptosis, and inhibits EC proliferation. Mechanistically, …

Long-Chain Omega-3 Polyunsaturated Fatty Acids Modulate Mammary Gland Composition And Inflammation, Saraswoti Khadge, Geoffrey M. Thiele, J. Graham Sharp, Timothy R. Mcguire, Lynell W. Klassen, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Studies in rodents have shown that dietary modifications as mammary glands (MG) develop, regulates susceptibility to mammary tumor initiation. However, the effects of dietary PUFA composition on MGs in adult life, remains poorly understood. This study investigated morphological alterations and inflammatory microenvironments in the MGs of adult mice fed isocaloric and isolipidic liquid diets with varying compositions of omega (ω)-6 and long-chain (Lc)-ω3FA that were pair-fed. Despite similar consumption levels of the diets, mice fed the ω-3 diet had significantly lower body-weight gains, and abdominal-fat and mammary fat pad (MFP) weights. Fatty acid analysis showed significantly higher levels of Lc-ω-3FAs …

Dietary Omega-3 And Omega-6 Polyunsaturated Fatty Acids Modulate Hepatic Pathology, Saraswoti Khadge, J. Graham Sharp, Geoffrey M. Thiele, Timothy R. Mcguire, Lynell W. Klassen, Michael J. Duryee, Holly C. Britton, Jordan Beck, Paul N. Black, Concetta Dirusso, James Talmadge

Department of Biochemistry: Faculty Publications

Recent evidence has suggested that dietary polyunsaturated fatty acids (PUFAs) modulate inflammation; however, few studies have focused on the pathobiology of PUFA using isocaloric and isolipidic diets and it is unclear if the associated pathologies are due to dietary PUFA composition, lipid metabolism or obesity, as most studies compare diets fed ad libitum. Our studies used isocaloric and isolipidic liquid diets (35% of calories from fat), with differing compositions of omega (ω)-6 or long chain (Lc) ω-3 PUFA that were pair-fed and assessed hepatic pathology, inflammation and lipid metabolism. Consistent with an isocaloric, pair-fed model we observed no significant difference …

Adenosine Has Two Faces: Regionally Dichotomous Adenosine Tone In A Model Of Epilepsy With Comorbid Sleep Disorders, Ted J. Warren, Timothy A. Simeone, D. David Smith, Ryan Grove, Jiri Adamec, Kaeli K. Samson, Harrison M. Roundtree, Deepak Madhavan, Kristina A. Simeone

Department of Biochemistry: Faculty Publications

Objective: Adenosine participates in maintaining the excitatory/inhibitory balance in neuronal circuits. Studies indicate that adenosine levels in the cortex and hippocampus increase and exert sleep pressure in sleep-deprived and control animals, whereas in epilepsy reduced adenosine tone promotes hyperexcitability. To date, the role of adenosine in pathological conditions that result in both seizures and sleep disorders is unknown. Here, we determined adenosine tone in sleep and seizure regulating brain regions of Kv1.1 knockout (KO) mice, a model of temporal epilepsy with comorbid sleep disorders.

Methods: 1) Reverse phase-high performance liquid chromatography (RP-HPLC) was performed on brain tissue to determine levels …

The Development And Application Of Bioinformatics Core Competencies To Improve Bioinformatics Training And Education, Nicola Mulder, Russell Schwartz, Michelle D. Brazas, Cath Brooksbank, Bruno Gaeta, Sarah L. Morgan, Mark A. Pauley, Anne Rosenwald, Gabriella Rustici, Michael Sierk, Tandy Warnow, Lonnie Welch

School of Biological Sciences: Faculty Publications

Bioinformatics is recognized as part of the essential knowledge base of numerous career paths in biomedical research and healthcare. However, there is little agreement in the field over what that knowledge entails or how best to provide it. These disagreements are compounded by the wide range of populations in need of bioinformatics training, with divergent prior backgrounds and intended application areas. The Curriculum Task Force of the International Society of Computational Biology (ISCB) Education Committee has sought to provide a framework for training needs and curricula in terms of a set of bioinformatics core competencies that cut across many user …

Gene Turnover And Diversification Of The Α- And Β- Globin Gene Families In Sauropsid Vertebrates, Federico G. Hoffmann, Michael W. Vandewege, Jay F. Storz, Juan C. Opazo

School of Biological Sciences: Faculty Publications

The genes that encode the α- and β-chain subunits of vertebrate hemoglobin have served as a model system for elucidating general principles of gene family evolution, but little is known about patterns of evolution in amniotes other than mammals and birds. Here,we report a comparative genomic analysis of the α- and β-globin gene clusters in sauropsids (archosaurs and nonavian reptiles). The objectives were to characterize changes in the size and membership composition of the α- and β-globin gene families within and among the major sauropsid lineages, to reconstruct the evolutionary history of the sauropsid α- and β-globin genes, to resolve …

Influenza D Virus M2 Protein Exhibits Ion Channel Activity In Xenopus Laevis Oocytes, Evan Kesinger, Jianing Liu, Aaron Jensen, Catherine P. Chia, Andrew Demers, Hideaki Moriyama

School of Biological Sciences: Faculty Publications

A new type of influenza virus, known as type D, has recently been identified in cattle and pigs. Influenza D virus infection in cattle is typically asymptomatic; however, its infection in swine can result in clinical disease. Swine can also be infected with all other types of influenza viruses, namely A, B, and C. Consequently, swine can serve as a "mixing vessel" for highly pathogenic influenza viruses, including those with zoonotic potential. Currently, the only antiviral drug available targets influenza M2 protein ion channel is not completely effective. Thus, it is necessary to develop an M2 ion channel blocker capable …

Ecoevo-Maps: An Ecology And Evolution Assessment For Introductory Through Advanced Undergraduates, Mindi M. Summers, Brian A. Couch, Jennifer K. Knight, Sara E. Brownell, Alison J. Crowe, Katharine Semsar, Christian D. Wright, Michelle K. Smith

School of Biological Sciences: Faculty Publications

A new assessment tool, Ecology and Evolution–Measuring Achievement and Progression in Science or EcoEvo-MAPS, measures student thinking in ecology and evolution during an undergraduate course of study. EcoEvo-MAPS targets foundational concepts in ecology and evolution and uses a novel approach that asks students to evaluate a series of predictions, conclusions, or interpretations as likely or unlikely to be true given a specific scenario. We collected evidence of validity and reliability for EcoEvo-MAPS through an iterative process of faculty review, student interviews, and analyses of assessment data from more than 3000 students at 34 associate’s-, bachelor’s-, master’s-, and doctoral-granting institutions. The …