Biological Lignocellulose Solubilization: Comparative Evaluation Of Biocatalysts And Enhancement Via Cotreatment,
2016
Dartmouth College
Biological Lignocellulose Solubilization: Comparative Evaluation Of Biocatalysts And Enhancement Via Cotreatment, Julie M. D. Paye, Anna Guseva, Sarah K. Hammer, Erica Gjersing
Dartmouth Scholarship
Feedstock recalcitrance is the most important barrier impeding cost-effective production of cellulosic biofuels. Pioneer commercial cellulosic ethanol facilities employ thermochemical pretreatment and addition of fungal cellulase, reflecting the main research emphasis in the field. However, it has been suggested that it may be possible to process cellulosic biomass without thermochemical pretreatment using thermophilic, cellulolytic bacteria. To further explore this idea, we examine the ability of various biocatalysts to solubilize autoclaved but otherwise unpretreated cellulosic biomass under controlled but not industrial conditions.
Nitrogenase Femoco Investigated By Spatially Resolved Anomalous Dispersion Refinement,
2016
Albert-Ludwigs-Universitat Freiburg & California Institute of Technology
Nitrogenase Femoco Investigated By Spatially Resolved Anomalous Dispersion Refinement, Thomas Spatzal, Julia Schlesier, Eva-Maria Burger, Daniel Sippel, Limei Zhang, Susana L.A. Andrade, Douglas C. Rees, Oliver Einsle
Department of Biochemistry: Faculty Publications
The [Mo:7Fe:9S:C] iron-molybdenum cofactor (FeMoco) of nitrogenase is the largest known metal cluster and catalyses the 6-electron reduction of dinitrogen to ammonium in biological nitrogen fixation. Only recently its atomic structure was clarified, while its reactivity and electronic structure remain under debate. Here we show that for its resting S 1⁄4 3/2 state the common iron oxidation state assignments must be reconsidered. By a spatially resolved refinement of the anomalous scattering contributions of the 7 Fe atoms of FeMoco, we conclude that three irons (Fe1/3/7) are more reduced than the other four (Fe2/4/5/6). Our data are in agreement with the …
Activation Of Erk And Nf-Κb During Hare-Mediated Heparin Uptake Require Only One
Of The Four Endocytic Motifs,
2016
University of Oklahoma Health Sciences Center
Activation Of Erk And Nf-Κb During Hare-Mediated Heparin Uptake Require Only One Of The Four Endocytic Motifs, Madhu S. Pandey, Colton M. Miller, Edward N. Harris, Paul H. Weigel
Department of Biochemistry: Faculty Publications
Fifteen different ligands, including heparin (Hep), are cleared from lymph and blood by the Hyaluronan (HA) Receptor for Endocytosis (HARE; derived from Stabilin-2 by proteolysis), which contains four endocytic motifs (M1-M4). Endocytosis of HARE•Hep complexes is targeted to coated pits by M1, M2, and M3 (Pandey et al, Int. J. Cell Biol. 2015, article ID 524707), which activates ERK1/2 and NF-κB (Pandey et al J. Biol. Chem. 288, 14068–79, 2013). Here, we used a NF-κB promoter-driven luciferase gene assay and cell lines expressing different HARE cytoplasmic domain mutants to identify motifs needed for Hepmediated signaling. Deletion of M1, M2 or …
Systems Perturbation Analysis Of A
Large-Scale Signal Transduction
Model Reveals Potentially Influential
Candidates For Cancer Therapeutics,
2016
University of Nebraska-Lincoln
Systems Perturbation Analysis Of A Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates For Cancer Therapeutics, Bhanwar Lal Puniya, Laura Allen, Colleen Hochfelde, Mahbubul Majumder, Tomáš Helikar
Department of Biochemistry: Faculty Publications
Dysregulation in signal transduction pathways can lead to a variety of complex disorders, including cancer. Computational approaches such as network analysis are important tools to understand system dynamics as well as to identify critical components that could be further explored as therapeutic targets. Here, we performed perturbation analysis of a large-scale signal transduction model in extracellular environments that stimulate cell death, growth, motility, and quiescence. Each of the model's components was perturbed under both loss-of-function and gain-of-function mutations. Using 1,300 simulations under both types of perturbations across various extracellular conditions, we identified the most and least influential components based on …
Cadmium And Secondary Structure-Dependent Function Of A
Degron In The Pca1p Cadmium Exporter,
2016
University of Nebraska-Lincoln
Cadmium And Secondary Structure-Dependent Function Of A Degron In The Pca1p Cadmium Exporter, Nathan Smith, Wenzhong Wel, Miaoyun Zhao, Xiaojuan Quin, Javier Seravalli, Heejeong Kim, Jaekwon Lee
Department of Biochemistry: Faculty Publications
Protein turnover is a critical cellular process regulating biochemical pathways and destroying terminally misfolded or damaged proteins. Pca1p, a cadmium exporter in the yeast Saccharomyces cerevisiae, is rapidly degraded by the endoplasmic reticulum-associated degradation (ERAD) system via a cis-acting degron that exists at the 250–350 amino acid region of Pca1p and is transferable to other proteins to serve as a degradation signal. Cadmium stabilizes Pca1p in a manner dependent on the degron. This suggested that cadmium-mediated masking of the degron impedes its interaction with the molecular factors involved in the ERAD. The characteristics and mechanisms of action of the …
Chloroplast Membrane Remodeling During Freezing Stress Is Accompanied By Cytoplasmic Acidification Activating Sensitive To Freezing 2,
2016
University of Nebraska-Lincoln
Chloroplast Membrane Remodeling During Freezing Stress Is Accompanied By Cytoplasmic Acidification Activating Sensitive To Freezing 2, Allison C. Barnes, Christoph Benning, Rebecca Roston
Department of Biochemistry: Faculty Publications
Low temperature is a seasonal abiotic stress which restricts native plant ranges and crop distributions. Two types of low temperature stress can be distinguished: chilling and freezing. Much work has been done on the mechanisms by which chilling is sensed, but relatively little is known about how plants sense freezing. Recently, SENSITIVE TO FREEZING 2 (SFR2) was identified as a protein which responds in a non-transcriptional manner to freezing. Here, we investigate the cellular conditions which allow SFR2 activation. Using a combination of isolated organelle, whole tissue and whole plant assays, we provide evidence that SFR2 is activated by changes …
Oma1 Links Mitochondrial Protein Quality Control And Tor
Signaling To Modulate Physiological Plasticity And Cellular Stress Responses,
2016
University of Nebraska- Lincoln
Oma1 Links Mitochondrial Protein Quality Control And Tor Signaling To Modulate Physiological Plasticity And Cellular Stress Responses, Iryna Bohovych, Stavroula Kastora, Sara Christianson, Danelle Topil, Heejeong Kim, Teresa Fangman, You J. Zhou, Antoni Barrientos, Jaekwon Lee, Alistair J.P. Brown, Oleh Khalimonchuk
Department of Biochemistry: Faculty Publications
A network of conserved proteases known as the intramitochondrial quality control (IMQC) system is central to mitochondrial protein homeostasis and cellular health. IMQC proteases also appear to participate in establishment of signaling cues for mitochondrion- to-nucleus communication. However, little is known about this process. Here, we show that in Saccharomyces cerevisiae, inactivation of the membrane-bound IMQC protease Oma1 interferes with oxidative-stress responses through enhanced production of reactive oxygen species (ROS) during logarithmic growth and reduced stress signaling via the TORC1-Rim15- Msn2/Msn4 axis. Pharmacological or genetic prevention of ROS accumulation in Oma1-deficient cells restores this defective TOR signaling. Additionally, inactivation …
Regulation Of Dj-1 By Glutaredoxin 1 In Vivo – Implications For Parkinson’S Disease,
2016
Case Western Reserve University
Regulation Of Dj-1 By Glutaredoxin 1 In Vivo – Implications For Parkinson’S Disease, William M. Johnson, Marcin Golczak, Kyonghwan Choe, Pierce L. Curran, Olga Gorelenkova Miller, Chen Yao, Wenzhang Wang, Jiusheng Lin, Nicole M. Milkovic, Ajit Ray, Vijayalakshmi Ravindranath, Xiongwei Zhu, Mark A. Wilson, Amy L. Wilson-Delfosse, Shu G. Chen, John J. Mieyal
Department of Biochemistry: Faculty Publications
Parkinson’s disease (PD) is the second most common neurodegenerative disease worldwide, caused by the degeneration of the dopaminergic neurons in the substantia nigra. Mutations in PARK7 (DJ-1) result in early onset autosomal recessive PD, and oxidative modification of DJ-1 has been reported to regulate the protective activity of DJ-1 in vitro. Glutathionylation is a prevalent redox modification of proteins resulting from the disulfide adduction of the glutathione moiety to a reactive cysteine-SH; and glutathionylation of specific proteins has been implicated in regulation of cell viability. Glutaredoxin 1 (Grx1) is the principal deglutathionylating enzyme within cells, and it has …
Inhibiting Hexamer Disassembly Of Human Udp-Glucose Dehydrogenase By Photoactivated Amino Acid Crosslinking,
2016
University of Nebraska-Lincoln
Inhibiting Hexamer Disassembly Of Human Udp-Glucose Dehydrogenase By Photoactivated Amino Acid Crosslinking, George Grady, Ashley Thelen, Jaleen Albers, Tong Ju, Jiantao Guo, Joseph J. Barycki, Melanie A. Simpson
Department of Biochemistry: Faculty Publications
The enzyme UDP-glucose dehydrogenase (UGDH) catalyzes the reaction of UDP-glucose to UDP-glucuronate through two successive NAD+-dependent oxidation steps. Human UGDH apoprotein purifies as a mixture of dimeric and hexameric species. Addition of substrate and cofactor stabilizes the oligomeric state to primarily the hexameric form. To determine if the dynamic conformations of hUGDH are required for catalytic activity, we used site-specific unnatural amino acid incorporation to facilitate crosslinking of monomeric subunits into predominantly obligate oligomeric species. Optimal crosslinking was achieved by encoding p-benzoyl-L-phenylalanine at position 458, normally a glutamine located within the dimer-dimer interface, and exposing to long wavelength …
Tumor Suppressive Role Of Sestrin2 During
Colitis And Colon Carcinogenesis,
2016
University of Nebraska-Lincoln
Tumor Suppressive Role Of Sestrin2 During Colitis And Colon Carcinogenesis, Seung-Hyun Ro, Xiang Xue, Sadeesh K. Ramakrishnan, Chun-Seok Cho, Sim Namkoong, Insook Jang, Ian A. Semple, Allison Ho, Hwan-Woo Park, Yatrik M. Shah, Jun Hee Lee
Department of Biochemistry: Faculty Publications
The mTOR complex 1 (mTORC1) and endoplasmic reticulum (ER) stress pathways are critical regulators of intestinal inflammation and colon cancer growth. Sestrins are stress-inducible proteins, which suppress both mTORC1 and ER stress; however, the role of Sestrins in colon physiology and tumorigenesis has been elusive due to the lack of studies in human tissues or in appropriate animal models. In this study, we show that human SESN2 expression is elevated in the colon of ulcerative colitis patients but is lost upon p53 inactivation during colon carcinogenesis. In mouse colon, Sestrin2 was critical for limiting ER stress and promoting the recovery …
Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization,
2016
University of Nebraska - Lincoln
Antisense Oligonucleotides: Treatment Strategies And Cellular Internalization, Colton M. Miller, Edward N. Harris
Department of Biochemistry: Faculty Publications
The clinical application of antisense oligonucleotides (ASOs) is becoming more of a reality as several drugs have been approved for the treatment of human disorders and many others are in various phases in development and clinical trials. ASOs are short DNA/RNA oligos which are heavily modified to increase their stability in biological fluids and retain the properties of creating RNA-RNA and DNA-RNA duplexes that knock-down or correct genetic expression. This review outlines several strategies that ASOs utilize for the treatment of various congenital diseases and syndromes that develop with aging. In addition, we discuss some of the mechanisms for specific …
Polyglycine Acts As A Rejection Signal For
Protein Transport At The Chloroplast Envelope,
2016
University of California, Davis
Polyglycine Acts As A Rejection Signal For Protein Transport At The Chloroplast Envelope, Joshua K. Endow, Agostinho Gomes Rocha, Amy J. Baldwin, Rebecca L. Roston, Toshio Yamaguchi, Hironari Kamikubo, Kentaro Inoue
Department of Biochemistry: Faculty Publications
PolyGly is present in many proteins in various organisms. One example is found in a transmembrane β-barrel protein, translocon at the outer-envelope-membrane of chloroplasts 75 (Toc75). Toc75 requires its N-terminal extension (t75) for proper localization. t75 comprises signals for chloroplast import (n75) and envelope sorting (c75) in tandem. n75 and c75 are removed by stromal processing peptidase and plastidic type I signal peptidase 1, respectively. PolyGly is present within c75 and its deletion or substitution causes mistargeting of Toc75 to the stroma. Here we have examined the properties of polyGly-dependent protein targeting using two soluble passenger proteins, the mature portion …
Mutation In Atg5 Reduces Autophagy And
Leads To Ataxia With Developmental Delay,
2016
University of Michigan-Ann Arbor
Mutation In Atg5 Reduces Autophagy And Leads To Ataxia With Developmental Delay, Myungjin Kim, Erin Sandford, Damian Gatica, Yu Qiu, Xu Liu, Yumei Zheng, Brenda A. Schulman, Jishu Xu, Ian Semple, Seung-Hyun Ro, Boyoung Kim, R. Nehir Mavioglu, Aslihan Tolun, Andras Jipa, Szabolcs Takats, Manuela Karpati, Jun Z. Li, Zuhal Yapici, Gabor Juhasz, Jun Hee Lee, Daniel J. Klionsky, Margit Burmeister
Department of Biochemistry: Faculty Publications
Autophagy is required for the homeostasis of cellular material and is proposed to be involved in many aspects of health. Defects in the autophagy pathway have been observed in neurodegenerative disorders; however, no genetically-inherited pathogenic mutations in any of the core autophagy-related (ATG) genes have been reported in human patients to date. We identified a homozygous missense mutation, changing a conserved amino acid, in ATG5 in two siblings with congenital ataxia, mental retardation, and developmental delay. The subjects’ cells display a decrease in autophagy flux and defects in conjugation of ATG12 to ATG5. The homologous mutation in yeast …
Novel Acyltranserases And
Methods Of Using,
2016
Lincoln, NE
Novel Acyltranserases And Methods Of Using, Edgar B. Cahoon, Umidjon Iskandarov, Hae Jin Kim, Jillian Collins-Silva
Department of Biochemistry: Faculty Publications
Provided herein are novel acyltransferases and methods of using Such novel acyltransferases in making medium-chain fatty acids.
Can Chilling Tolerance Of C4 Photosynthesis In
Miscanthus Be Transferred To Sugarcane?,
2016
University of Illinois at Urbana-Champaign
Can Chilling Tolerance Of C4 Photosynthesis In Miscanthus Be Transferred To Sugarcane?, Katarzyna Glowacka, Aasifuddin Ahmed, Shailendra Sharma, Tom Abbott, Jack C. Comstock, Stephen P. Long, Erik J. Sacks
Department of Biochemistry: Faculty Publications
The goal of this study was to investigate whether chilling tolerance of C4 photosynthesis in Miscanthus can be transferred to sugarcane by hybridization. Net leaf CO2 uptake (Asat) and the maximum operating efficiency of photosystem II (ФPSII) were measured in warm conditions (25 °C/20 °C), and then during and following a chilling treatment of 10 °C/5 °C for 11 day in controlled environment chambers. Two of three hybrids (miscanes), ‘US 84-1058’ and ‘US 87-1019’, did not differ significantly from the chilling tolerant M. xgiganteus ‘Illinois’ (Mxg), for Asat, and Φ …
High-Throughput Mutation, Selection, And Phenotype Screening Of Mutant Methanogenic Archaea,
2016
University of Nebraska-Lincoln
High-Throughput Mutation, Selection, And Phenotype Screening Of Mutant Methanogenic Archaea, Mary E. Walter, Alicia Ortiz, Casey Sondgeroth, Nathan M. Sindt, Nikolas Duszenko, Jennie L. Catlett, You Zhou, Shah R. Valloppilly, Christopher Anderson, Samodha Fernando, Nicole R. Buan
Department of Biochemistry: Faculty Publications
Bacterial and archaeal genomes can contain 30% or more hypothetical genes with no predicted function. Phylogenetically deep-branching microbes, such as methane-producing archaea (methanogens), contain up to 50% genes with unknown function. In order to formulate hypotheses about the function of hypothetical gene functions in the strict anaerobe, Methanosarcina acetivorans, we have developed high-throughput anaerobic techniques to UV mutagenize, screen, and select for mutant strains in 96-well plates. Using these approaches we have isolated 10 mutant strains that exhibit a variety of physiological changes including increased or decreased growth rate relative to the parent strain when cells use methanol and/or …
Pluralistic And Stochastic Gene Regulation: Examples, Models And Consistent Theory,
2016
University of Nebraska-Lincoln
Pluralistic And Stochastic Gene Regulation: Examples, Models And Consistent Theory, Elisa N. Salas, Jiang Shu, Matyas F. Cserhati, Donald P. Weeks, Istvan Ladunga
Department of Biochemistry: Faculty Publications
We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of transcription factors, variable DNA motifs, and bursts in gene expression. Stochastic regulation is also indicated by frequently subdued effects of knockout mutants of regulators, their evolutionary losses/gains and massive rewiring of regulatory sites. We report wide-spread pluralistic regulation in ≈800 000 tightly co-expressed pairs of diverse human genes. Typically, half of ≈50 observed regulators bind to both …
Mutual Information Upper Bound Of Molecular Communication Based On Cell Metabolism,
2016
University of Nebraska - Lincoln
Mutual Information Upper Bound Of Molecular Communication Based On Cell Metabolism, Massimiliano Pierobon, Zahmeeth Sakkaff, Jennie L. Catlett, Nicole R. Buan
Department of Biochemistry: Faculty Publications
Synthetic biology is providing novel tools to engineer cells and access the basis of their molecular information processing, including their communication channels based on chemical reactions and molecule exchange. Molecular communication is a discipline in communication engineering that studies these types of communications and ways to exploit them for novel purposes, such as the development of ubiquitous and heterogeneous communication networks to interconnect biological cells with nano and biotechnology-enabled devices, i.e., the Internet of Bio-Nano Things. One major problem in synthetic biology stands in the development of reliable techniques to control the engineered cells from the external environment. In this …
Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant
Ovarian Cancer,
2016
Oregon State University
Mechanistic Nanotherapeutic Approach Based On Sirna-Mediated Dj-1 Protein Suppression For Platinum-Resistant Ovarian Cancer, Canan Schumann, Stephanie Chan, Oleh Khalimonchuk, Shannon Khal, Vitaliya Moskal, Vidhi Shah, Adam W. G. Alani, Olena Taratula, Oleh Taratula
Department of Biochemistry: Faculty Publications
We report an efficient therapeutic modality for platinum resistant ovarian cancer based on siRNAmediated suppression of a multifunctional DJ-1 protein that is responsible for the proliferation, growth, invasion, oxidative stress and overall survival of various cancers. The developed therapeutic strategy can work alone or in concert with a low dose of the first line chemotherapeutic agent cisplatin, to elicit a maximal therapeutic response. To achieve an efficient DJ-1 knockdown, we constructed the polypropylenimine dendrimer-based nanoplatform targeted to LHRH receptors overexpressed on ovarian cancer cells. The quantitative PCR and western immunoblotting analysis, revealed that the delivered DJ-1 siRNA downregulated the expression …
Engineering A Trifunctional Proline Utilization A
Chimaera By Fusing A Dna-Binding Domain To A
Bifunctional Puta,
2016
University of Nebraska-Lincoln
Engineering A Trifunctional Proline Utilization A Chimaera By Fusing A Dna-Binding Domain To A Bifunctional Puta, Benjamin W. Arentson, Erin L. Hayes, Weidong Zhu, John J. Tanner, Donald F. Becker
Department of Biochemistry: Faculty Publications
Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1-pyrroline-5- carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the …
