Open Access. Powered by Scholars. Published by Universities.®

Molecular Biology Commons

Open Access. Powered by Scholars. Published by Universities.®

Iowa State University

Discipline
Keyword
Publication Year
Publication
Publication Type

Articles 1 - 30 of 563

Full-Text Articles in Molecular Biology

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo Mar 2019

Development Of An Innovative And Sustainable One-Step Method For Rapid Plant Dna Isolation For Targeted Pcr Using Magnetic Ionic Liquids, Arianna Marengo, Cecilia Cagliero, Barbara Sgorbini, Jared L. Anderson, Miranda N. Emaus, Carlo Bicchi, Cinzia M. Bertea, Patrizia Rubiolo

Chemistry Publications

Background

Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids.

Results

In the present study, a MIL-based magnet-assisted dispersive liquid–liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal ...


Arginine In The Farm And Sarm: A Role In Chain-Length Determination For Arginine In The Aspartate-Rich Motifs Of Isoprenyl Diphosphate Synthases From Mycobacterium Tuberculosis, Raimund Nagel, Jill A. Thomas, Faith A. Adekunle, Francis M. Mann, Reuben J. Peters Oct 2018

Arginine In The Farm And Sarm: A Role In Chain-Length Determination For Arginine In The Aspartate-Rich Motifs Of Isoprenyl Diphosphate Synthases From Mycobacterium Tuberculosis, Raimund Nagel, Jill A. Thomas, Faith A. Adekunle, Francis M. Mann, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Isoprenyl chains are found in many important metabolites. These are derived from precursors of the appropriate length produced by isoprenyl diphosphate synthases (IDSs). The human pathogen Mycobacterium tuberculosis makes various isoprenoids/terpenoids, with important roles in their biosynthesis played by two closely related IDSs, encoded by grcC1 (Rv0562) and grcC2 (Rv0989c), with Rv0989c generating the 10-carbon precursor (E)-geranyl diphosphate (GPP), and Rv0562 the 20-carbon precursor (E,E,E)-geranylgeranyl diphosphate (GGPP). Intriguingly, while Rv0562 contains the prototypical trans-IDS first and second aspartate-rich (DDxxD) motifs (FARM and SARM, respectively), Rv0989c uniquely contains arginine in place of the second Asp in ...


Continuous Interdomain Orientation Distributions Reveal Components Of Binding Thermodynamics, Yang Qi, Jeffrey W. Martin, Adam W. Barb, Francois Thelot, Anthony Yan, Bruce R. Donald, Terrence G. Oas Sep 2018

Continuous Interdomain Orientation Distributions Reveal Components Of Binding Thermodynamics, Yang Qi, Jeffrey W. Martin, Adam W. Barb, Francois Thelot, Anthony Yan, Bruce R. Donald, Terrence G. Oas

Biochemistry, Biophysics and Molecular Biology Publications

The flexibility of biological macromolecules is an important structural determinant of function. Unfortunately, the correlations between different motional modes are poorly captured by discrete ensemble representations. Here, we present new ways to both represent and visualize correlated interdomain motions. Interdomain motions are determined directly from residual dipolar couplings, represented as a continuous conformational distribution, and visualized using the disk-on-sphere representation. Using the disk-on-sphere representation, features of interdomain motions, including correlations, are intuitively visualized. The representation works especially well for multidomain systems with broad conformational distributions.This analysis also can be extended to multiple probability density modes, using a Bingham mixture ...


Protein Dynamic Communities From Elastic Network Models Align Closely To The Communities Defined By Molecular Dynamics, Sambit Kumar Mishra, Robert L. Jernigan Jun 2018

Protein Dynamic Communities From Elastic Network Models Align Closely To The Communities Defined By Molecular Dynamics, Sambit Kumar Mishra, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Dynamic communities in proteins comprise the cohesive structural units that individually exhibit rigid body motions. These can correspond to structural domains, but are usually smaller parts that move with respect to one another in a protein’s internal motions, key to its functional dynamics. Previous studies emphasized their importance to understand the nature of ligand-induced allosteric regulation. These studies reported that mutations to key community residues can hinder transmission of allosteric signals among the communities. Usually molecular dynamic (MD) simulations (~ 100 ns or longer) have been used to identify the communities—a demanding task for larger proteins. In the present ...


Restricted Processing Of Cd16a/Fc Γ Receptor Iiia N-Glycans From Primary Human Nk Cells Impacts Structure And Function, Kashyap R. Patel, Jacob T. Roberts, Ganesh P. Subedi, Adam W. Barb Mar 2018

Restricted Processing Of Cd16a/Fc Γ Receptor Iiia N-Glycans From Primary Human Nk Cells Impacts Structure And Function, Kashyap R. Patel, Jacob T. Roberts, Ganesh P. Subedi, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

CD16a/Fc γ receptor IIIa is the most abundant antibody Fc receptor expressed on human natural killer (NK) cells and activates a protective cytotoxic response following engagement with antibody clustered on the surface of a pathogen or diseased tissue. Therapeutic monoclonal antibodies (mAbs) with greater Fc-mediated affinity for CD16a show superior therapeutic outcome; however, one significant factor that promotes antibody–CD16a interactions, the asparagine-linked carbohydrates (N-glycans), remains undefined. Here, we purified CD16a from the primary NK cells of three donors and identified a large proportion of hybrid (22%) and oligomannose N-glycans (23%). These proportions indicated restricted N-glycan ...


Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau Feb 2018

Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau

Genetics, Development and Cell Biology Publications

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate’s acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of ...


Seqstruct : A New Amino Acid Similarity Matrix Based On Sequence Correlations And Structural Contacts Yields Sequence-Structure Congruence, Kejue Jia, Robert L. Jernigan Feb 2018

Seqstruct : A New Amino Acid Similarity Matrix Based On Sequence Correlations And Structural Contacts Yields Sequence-Structure Congruence, Kejue Jia, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Protein sequence matching does not properly account for some well-known features of protein structures: surface residues being more variable than core residues, the high packing densities in globular proteins, and does not yield good matches of sequences of many proteins known to be close structural relatives. There are now abundant protein sequences and structures to enable major improvements to sequence matching. Here, we utilize structural frameworks to mount the observed correlated sequences to identify the most important correlated parts. The rationale is that protein structures provide the important physical framework for improving sequence matching. Combining the sequence and structure data ...


The Oligomerization State Of Bacterial Enzyme I (Ei) Determines Ei's Allosteric Stimulation Or Competitive Inhibition By Α-Ketoglutarate, Trang T. Nguyen, Rodolfo Ghirlando, Vincenzo Venditti Feb 2018

The Oligomerization State Of Bacterial Enzyme I (Ei) Determines Ei's Allosteric Stimulation Or Competitive Inhibition By Α-Ketoglutarate, Trang T. Nguyen, Rodolfo Ghirlando, Vincenzo Venditti

Chemistry Publications

The bacterial phosphotransferase system (PTS) is a signal transduction pathway that couples phosphoryl transfer to active sugar transport across the cell membrane. The PTS is initiated by phosphorylation of enzyme I (EI) by phosphoenolpyruvate (PEP). The EI phosphorylation state determines the phosphorylation states of all other PTS components and is thought to play a central role in the regulation of several metabolic pathways and to control the biology of bacterial cells at multiple levels, for example, affecting virulence and biofilm formation. Given the pivotal role of EI in bacterial metabolism, an improved understanding of the mechanisms controlling its activity could ...


Mouse Igg2c Fc Loop Residues Promote Greater Receptor-Binding Affinity Than Mouse Igg2b Or Human Igg1, Daniel J. Falconer, Adam W. Barb Feb 2018

Mouse Igg2c Fc Loop Residues Promote Greater Receptor-Binding Affinity Than Mouse Igg2b Or Human Igg1, Daniel J. Falconer, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

The structures of non-human antibodies are largely unstudied despite the potential for the identification of alternative structural motifs and physical properties that will benefit a basic understanding of protein and immune system evolution as well as highlight unexplored motifs to improve therapeutic monoclonal antibody. Here we probe the structure and receptor-binding properties of the mouse IgG2c crystallizable fragment (Fc) to compare to mouse IgG2b and human IgG1 Fcs. Models of mIgG2c Fc determined by x-ray crystallography with a complex-type biantennary (to 2.05 Å) or a truncated (1)GlcNAc asparagine-linked (N)-glycan attached (to 2.04 Å) show differences in ...


Comparisons Of Protein Dynamics From Experimental Structure Ensembles, Molecular Dynamics Ensembles, And Coarse-Grained Elastic Network Models, Kannan Sankar, Sambit K. Mishra, Robert L. Jernigan Jan 2018

Comparisons Of Protein Dynamics From Experimental Structure Ensembles, Molecular Dynamics Ensembles, And Coarse-Grained Elastic Network Models, Kannan Sankar, Sambit K. Mishra, Robert L. Jernigan

Biochemistry, Biophysics and Molecular Biology Publications

Predicting protein motions is important for bridging the gap between protein structure and function. With growing numbers of structures of the same, or closely related proteins becoming available, it is now possible to understand more about the intrinsic dynamics of a protein with principal component analysis (PCA) of the motions apparent within ensembles of experimental structures. In this paper, we compare the motions extracted from experimental ensembles of 50 different proteins with the modes of motion predicted by several types of coarse-grained elastic network models (ENMs) which additionally take into account more details of either the protein geometry or the ...


Automated Nmr Resonance Assignments And Structure Determination Using A Minimal Set Of 4d Spectra, Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes Jan 2018

Automated Nmr Resonance Assignments And Structure Determination Using A Minimal Set Of 4d Spectra, Thomas Evangelidis, Santrupti Nerli, Jiří Nováček, Andrew E. Brereton, P. Andrew Karplus, Rochelle R. Dotas, Vincenzo Venditti, Nikolaos G. Sgourakis, Konstantinos Tripsianes

Chemistry Publications

Automated methods for NMR structure determination of proteins are continuously becoming more robust. However, current methods addressing larger, more complex targets rely on analyzing 6–10 complementary spectra, suggesting the need for alternative approaches. Here, we describe 4D-CHAINS/autoNOE-Rosetta, a complete pipeline for NOE-driven structure determination of medium- to larger-sized proteins. The 4D-CHAINS algorithm analyzes two 4D spectra recorded using a single, fully protonated protein sample in an iterative ansatz where common NOEs between different spin systems supplement conventional through-bond connectivities to establish assignments of sidechain and backbone resonances at high levels of completeness and with a minimum error rate ...


Functions Of Maize Genes Encoding Pyruvate Phosphate Dikinase In Developing Endosperm, Ryan R. Lappe, John W. Baier, Susan K. Boehlein, Ryan Huffman, Qiaohui Lin, Fabrice Wattebled, A. Mark Settles, L. Curtis Hannah, Ljudmilla Borisjuk, Hardy Rolletschek, Jon D. Stewart, M. Paul Scott, Tracie A. Hennen-Bierwagen, Alan M. Myers Jan 2018

Functions Of Maize Genes Encoding Pyruvate Phosphate Dikinase In Developing Endosperm, Ryan R. Lappe, John W. Baier, Susan K. Boehlein, Ryan Huffman, Qiaohui Lin, Fabrice Wattebled, A. Mark Settles, L. Curtis Hannah, Ljudmilla Borisjuk, Hardy Rolletschek, Jon D. Stewart, M. Paul Scott, Tracie A. Hennen-Bierwagen, Alan M. Myers

Agronomy Publications

Maize opaque2 (o2) mutations are beneficial for endosperm nutritional quality but cause negative pleiotropic effects for reasons that are not fully understood. Direct targets of the bZIP transcriptional regulator encoded by o2 include pdk1 and pdk2 that specify pyruvate phosphate dikinase (PPDK). This enzyme reversibly converts AMP, pyrophosphate, and phosphoenolpyruvate to ATP, orthophosphate, and pyruvate and provides diverse functions in plants. This study addressed PPDK function in maize starchy endosperm where it is highly abundant during grain fill. pdk1 and pdk2 were inactivated individually by transposon insertions, and both genes were simultaneously targeted by endosperm-specific RNAi. pdk2 accounts for the ...


Investigating The Interplay Of Physiological And Molecular Mechanisms Underpinning Programmable Aspects Of Heat Stress In Pigs, Jacob Seibert Jan 2018

Investigating The Interplay Of Physiological And Molecular Mechanisms Underpinning Programmable Aspects Of Heat Stress In Pigs, Jacob Seibert

Graduate Theses and Dissertations

Heat stress (HS) undermines production efficiency in all animal agriculture, culminating in major economic losses annually. The effects of HS in pigs is realized through depressed growth, altered body composition, and impaired reproductive performance. Pigs, unlike other mammals, do not possess functional sweat glands, making them rely on other mechanisms to thermoregulate during a heat challenge. Continual investigation of hyperthermia in pigs is crucial for developing new strategies and/or technologies that mitigate the effects of HS imposed on the pork industry. The studies conducted in this dissertation investigate the complex interplay of whole-animal physiology as well as cellular and ...


Characterization Of A Mucopolysaccharidosis Type I And Galnac Transferase Deficiency Double Knockout Mouse, Karan Gera Jan 2018

Characterization Of A Mucopolysaccharidosis Type I And Galnac Transferase Deficiency Double Knockout Mouse, Karan Gera

Graduate Theses and Dissertations

The mucopolysaccharidoses (MPSs) are a group of lysosomal storage diseases (LSDs) which are characterized by the aberrant primary storage of glycosaminoglycans (GAGs) in lysosomes of multiple organ and tissue systems. The most commonly diagnosed is MPS Type I (MPS I), caused by mutations in the gene which codes for α-L-iduronidase (IDUA). Biochemically, MPS I is characterized by the aberrant primary lysosomal storage of incompletely degraded dermatan and heparan sulfates, along with a secondary accumulation of gangliosides and other compounds in lysosomes. Its clinical manifestation in severe form leads to early death, characterized by progressive central nervous system disease (with behavioral ...


Using Genomic And Gene Expression Methods To Understand The Phenotypic Response Of Soybean To Sudden Death Syndrome Caused By Fusarium Virguliforme, Alexander Stephen Luckew Jan 2018

Using Genomic And Gene Expression Methods To Understand The Phenotypic Response Of Soybean To Sudden Death Syndrome Caused By Fusarium Virguliforme, Alexander Stephen Luckew

Graduate Theses and Dissertations

Soybean sudden death syndrome (SDS) is one of the most important soybean diseases in the Midwestern United States, leading to average losses of $396 million per year from 1996 to 2015. The causal agent of SDS, soilborne fungus Fusarium virguliforme (Fv), causes root rot symptoms and releases phytotoxins taken up by the plant to produce chlorosis and necrosis in the leaves. The main management practice used to reduce the impact of SDS is planting resistant soybean cultivars. Resistance to SDS is known to be quantitative with 88 known quantitative trait loci (QTL) based on Soybase.org. Many of these QTL ...


Molecular Mechanisms Governing Plant Parasitic Nematode Signaling And Host Parasitism, Stacey Nicola Barnes Jan 2018

Molecular Mechanisms Governing Plant Parasitic Nematode Signaling And Host Parasitism, Stacey Nicola Barnes

Graduate Theses and Dissertations

Pathogen infection of crops causes large-scale annual yield losses for farmers worldwide and hinders global efforts to provide adequate amounts of nutrition for the ever-growing human population. Plant-parasitic nematodes (PPN) are among some of the most devastating pathogens due to their ability to parasitize an expansive variety of agriculturally important crops. In order to identify ways to attenuate PPN infection and limit yield losses it is vital that we increase our understanding of host-PPN interactions. Here we investigate the molecular mechanisms that are occurring both within PPN and at the interface between PPN and their host plants.

Research into PPN-derived ...


Impact Of Acute Heat Treatment On Autophagy And Insulin Signaling In C2c12 Myotubes, Corey Michael Summers Jan 2018

Impact Of Acute Heat Treatment On Autophagy And Insulin Signaling In C2c12 Myotubes, Corey Michael Summers

Graduate Theses and Dissertations

A major risk factor for the development of type 2 diabetes is reduced skeletal muscle insulin sensitivity. It is known that exercise and caloric restriction can improve skeletal muscle insulin resistance, but the mechanism by which this occurs is not completely elucidated. The AMP-activated protein kinase (AMPK), is thought to be a major contributor to the metabolic benefits observed after exercise training and caloric restriction. Activation of AMPK in skeletal muscle can have a wide range of effects, one of which is the initiation of macroautophagy (herein referred to as autophagy). Autophagy is the bulk degradation system of the cell ...


Comparison And Evaluation Of Two Rapid Diagnostic Assays For The Identification Of Mycoplasma Species, Aric James Mcdaniel Jan 2018

Comparison And Evaluation Of Two Rapid Diagnostic Assays For The Identification Of Mycoplasma Species, Aric James Mcdaniel

Graduate Theses and Dissertations

Members of the class Mollicutes are unique among bacteria in that they are unable to synthesize a cell wall. These organisms are also difficult to culture and very slow-growing with some species requiring up to 40 days to culture. Many of these bacteria are also significant pathogens in humans and animals, so rapid identification of isolates is a necessary diagnostic step. Many different tests are used for identification of pathogenic Mollicutes (primarily Mycoplasma and Ureaplasma species), however most tests are not cost or time efficient. Two relatively recent diagnostic tools are matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry and ...


Molecular Architectures Of Benzoic Acid-Specific Type Iii Polyketide Synthases, Charles Stewart Jr., Kate Woods, Greg Macias, Andrew C. Allan, Roger P. Hellens, Joseph P. Noel Dec 2017

Molecular Architectures Of Benzoic Acid-Specific Type Iii Polyketide Synthases, Charles Stewart Jr., Kate Woods, Greg Macias, Andrew C. Allan, Roger P. Hellens, Joseph P. Noel

Office of Biotechnology Publications

Biphenyl synthase and benzophenone synthase constitute an evolutionarily distinct clade of type III polyketide synthases (PKSs) that use benzoic acid-derived substrates to produce defense metabolites in plants. The use of benzoyl-CoA as an endogenous substrate is unusual for type III PKSs. Moreover, sequence analyses indicate that the residues responsible for the functional diversification of type III PKSs are mutated in benzoic acid-specific type III PKSs. In order to gain a better understanding of structure–function relationships within the type III PKS family, the crystal structures of biphenyl synthase from Malus × domestica and benzophenone synthase from Hypericum androsaemum were compared with ...


Biosynthesis Of Diterpenoids In Tripterygium Adventitious Root Cultures, Fainmarinat S. Inabuy, Justin T. Fischedick, Iris Lange, Michael Hartmann, Narayanan Srividya, Amber N. Parrish, Meimei Xu, Reuben J. Peters, B. Markus Lange Sep 2017

Biosynthesis Of Diterpenoids In Tripterygium Adventitious Root Cultures, Fainmarinat S. Inabuy, Justin T. Fischedick, Iris Lange, Michael Hartmann, Narayanan Srividya, Amber N. Parrish, Meimei Xu, Reuben J. Peters, B. Markus Lange

Biochemistry, Biophysics and Molecular Biology Publications

Adventitious root cultures were developed from Tripterygium regelii Sprague & Takeda and growth conditions optimized for the abundant production of diterpenoids, which can be collected directly from the medium. An analysis of publicly available transcriptome data sets collected with T. regelii roots and root cultures indicated the presence of a large gene family (with 20 members) for terpene synthases (TPSs). Nine candidate diterpene synthase genes were selected for follow-up functional evaluation, of which two belonged to the TPS-c, three to the TPS-e/f and four to the TPS-b subfamily. These genes were characterized by heterologous expression in a modular metabolic engineering ...


Mechanistic Insight Into Nanoparticle Surface Adsorption By Solution Nmr Spectroscopy In An Aqueous Gel, Timothy K. Egner, Pranjali Naik, Nicholas C. Nelson, Igor I. Slowing, Vincenzo Venditti Aug 2017

Mechanistic Insight Into Nanoparticle Surface Adsorption By Solution Nmr Spectroscopy In An Aqueous Gel, Timothy K. Egner, Pranjali Naik, Nicholas C. Nelson, Igor I. Slowing, Vincenzo Venditti

Chemistry Publications

Engineering nanoparticle (NP) functions at the molecular level requires a detailed understanding of the dynamic processes occurring at the NP surface. Herein we show that a combination of dark‐state exchange saturation transfer (DEST) and relaxation dispersion (RD) NMR experiments on gel‐stabilized NP samples enables the accurate determination of the kinetics and thermodynamics of adsorption. We used the former approach to describe the interaction of cholic acid (CA) and phenol (PhOH) with ceria NPs with a diameter of approximately 200 nm. Whereas CA formed weak interactions with the NPs, PhOH was tightly bound to the NP surface. Interestingly, we ...


Spatial Mapping And Profiling Of Metabolite Distributions During Germination, Adam D. Feenstra, Liza E. Alexander, Zhihong Song, Andrew R. Korte, Marna D. Yandeau-Nelson, Basil J. Nikolau, Young-Jin Lee Aug 2017

Spatial Mapping And Profiling Of Metabolite Distributions During Germination, Adam D. Feenstra, Liza E. Alexander, Zhihong Song, Andrew R. Korte, Marna D. Yandeau-Nelson, Basil J. Nikolau, Young-Jin Lee

Chemistry Publications

Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this paper, we utilize a combination of GC-MS, LC-fluorescence, and mass spectrometry imaging (MSI) approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize seeds, B73 and Mo17. GC and LC analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by GC-MS analysis of polar metabolites also ...


Carbohydrate–Polypeptide Contacts In The Antibody Receptor Cd16a Identified Through Solution Nmr Spectroscopy, Ganesh P. Subedi, Daniel J. Falconer, Adam W. Barb Jun 2017

Carbohydrate–Polypeptide Contacts In The Antibody Receptor Cd16a Identified Through Solution Nmr Spectroscopy, Ganesh P. Subedi, Daniel J. Falconer, Adam W. Barb

Biochemistry, Biophysics and Molecular Biology Publications

Asparagine-linked carbohydrates (N-glycans) are a common modification of eukaryotic proteins that confer multiple properties including the essential stabilization of therapeutic monoclonal antibodies. Here we present a rapid and efficient strategy to identify N-glycans that contact polypeptide residues and apply the method to profile the five N-glycans attached to the human antibody receptor CD16A (Fc γ receptor IIIA). Human embryonic kidney 293S cells expressed CD16A with [13CU]-labeled N-glycans using standard protein expression techniques and medium supplemented with 3 g/L [13CU]-glucose. Anomeric resonances on the protein-linked N-acetylglucosamine residue at the reducing end of the glycan are particularly well suited ...


Comparative Omega-3 Fatty Acid Enrichment Of Egg Yolks From First-Cycle Laying Hens Fed Flaxseed Oil Or Ground Flaxseed, I. J. Ehr, M. E. Persia, E. A. Bobeck Jun 2017

Comparative Omega-3 Fatty Acid Enrichment Of Egg Yolks From First-Cycle Laying Hens Fed Flaxseed Oil Or Ground Flaxseed, I. J. Ehr, M. E. Persia, E. A. Bobeck

Animal Science Publications

When laying hen diets are enriched with omega-3 polyunsaturated fatty acids to generate value-added eggs for human consumption markets, concentrations of alphalinolenic, eicosapentaenoic, and docosahexaenoic acids (ALA, EPA, and DHA) in the yolk can reach 250mg/50g whole egg. Flaxseed, a rich source of ALA, is commonly used for omega-3 enrichment; however, the impact of dietary flaxseed source (extracted oil vs. milled seed) on fatty acid transfer to egg yolk in laying hens is unknown. Therefore, transfer of ALA, EPA, and DHA into egg yolk from extracted flaxseed oil or milled flaxseed was evaluated in Hy-Line W-36 laying hens over ...


Investigating The Phylogenetic Range Of Gibberellin Biosynthesis In Bacteria, Raimund Nagel, Reuben J. Peters Apr 2017

Investigating The Phylogenetic Range Of Gibberellin Biosynthesis In Bacteria, Raimund Nagel, Reuben J. Peters

Biochemistry, Biophysics and Molecular Biology Publications

Certain plant-associated microbes can produce gibberellin (GA) phytohormones, as first described for the rice fungal pathogen Gibberella fujikuroi and, more recently, for bacteria, including several rhizobia and the rice bacterial pathogen Xanthomonas oryzae pv. oryzicola. The relevant enzymes are encoded by a biosynthetic operon that exhibits both a greater phylogenetic range and scattered distribution among plant-associated bacteria. Here, the phylogenetic distribution of this operon was investigated. To demonstrate conserved functionality, the enzymes encoded by the disparate operon from X. translucens pv. translucens, along with those from the most divergent example, found in Erwinia tracheiphila, were biochemically characterized. In both of ...


Validation Of A Hairy Roots System To Study Soybean-Soybean Aphid Interactions, Stephanie C. Morriss, Matthew E. Studham, Gregory L. Tylka, Gustavo C. Macintosh Mar 2017

Validation Of A Hairy Roots System To Study Soybean-Soybean Aphid Interactions, Stephanie C. Morriss, Matthew E. Studham, Gregory L. Tylka, Gustavo C. Macintosh

Plant Pathology and Microbiology Publications

The soybean aphid (Aphis glycines) is one of the main insect pests of soybean (Glycine max) worldwide. Genomics approaches have provided important data on transcriptome changes, both in the insect and in the plant, in response to the plant-aphid interaction. However, the difficulties to transform soybean and to rear soybean aphid on artificial media have hindered our ability to systematically test the function of genes identified by those analyses as mediators of plant resistance to the insect. An efficient approach to produce transgenic soybean material is the production of transformed hairy roots using Agrobacterium rhizogenes; however, soybean aphids colonize leaves ...


A Structural Biology Approach To The Problem Of Antibiotic Resistance In Bacteria, Jared Armand Delmar Jan 2017

A Structural Biology Approach To The Problem Of Antibiotic Resistance In Bacteria, Jared Armand Delmar

Graduate Theses and Dissertations

X-ray crystallography remains the most robust method to determine protein structure at the atomic level. We demonstrate how these structural studies can directly contribute to unsolved problems in biology, with a focus on the growing problem of antibiotic resistance in bacterial infections. Multi-drug efflux transporters are common and powerful resistance mechanisms that are capable of extruding a number of structurally unrelated antimicrobials, including antibiotics and toxic heavy metal ions, from the bacterial cell. We begin by presenting the crystal structures of the individual pump components of the Escherichia coli Cus system, a paradigm for efflux machinery, and speculate on how ...


Investigations Into Nutritional Quality, Commercial Productivity, And Genetic Purity Of Maize Grain For Organic Production Systems, Ryan Huffman Jan 2017

Investigations Into Nutritional Quality, Commercial Productivity, And Genetic Purity Of Maize Grain For Organic Production Systems, Ryan Huffman

Graduate Theses and Dissertations

Consumer demand for organic maize grain has steadily increased in the past decade which has resulted in an increased interest for this market class by plant breeders and geneticist. Each chapter in this dissertation investigates areas of concern to the organic community and possible solutions for improvement. Chapter 2 seeks to understand which combinations of genetic mechanisms are capable of a further increase in the methionine concentration of maize grain over individual mechanisms. Based on the genetic mechanisms evaluated, it was concluded that crosses combining dzr1 and recurrent selection in hybrid combination can elevate methionine concentration and overall grain nutritional ...


Insights Into Retinal Cell Fate Determination In Vertebrates Using Transcriptomic Profiling And Genome Editing, Rebecca Chowdhury Jan 2017

Insights Into Retinal Cell Fate Determination In Vertebrates Using Transcriptomic Profiling And Genome Editing, Rebecca Chowdhury

Graduate Theses and Dissertations

Deciphering the mechanisms of development of retinal neurons is not only of immense interest to developmental biologists, but is also vital for regenerative therapeutic applications. To attain this goal, it is critical to understand how specific intrinsic factors control cell fate decisions and neuronal maturation processes. In the retina, Atoh7 is a highly conserved transcription factor that is essential for retinal ganglion cell development in the developing mouse and zebrafish. Atoh7 labels a subset of cells in the developing retina that are progressing from a progenitor to a differentiated state. To capture cells during the window when the cell fate ...


Functions And Mechanism Of Wrky Transcription Factors In Brassinosteroid-Regulated Plant Growth And Stress Response, Jiani Chen Jan 2017

Functions And Mechanism Of Wrky Transcription Factors In Brassinosteroid-Regulated Plant Growth And Stress Response, Jiani Chen

Graduate Theses and Dissertations

Brassinosteroids (BRs), a family of plant steroid hormones, play important role in plant growth and development. BR signal is perceived by receptors BRI1 and BAK1, which transduce the hormonal signal to downstream transcription factors BES1/BZR1 to regulate the expression of thousands of BR target genes. BRs also play a vital role in both abiotic and biotic stress responses. However, the molecular mechanisms by which BRs regulate stress responses have just begun to be revealed. Here, we characterized three group III transcription factors, WRKY46, WRKY 54 and WRKY70, which are involved in BR-regulated plant growth and drought stress by cooperating ...