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Articles 1 - 30 of 34
Full-Text Articles in Physical Sciences and Mathematics
Informing Wetland Management With Waterfowl Movement And Sanctuary Use Responses To Human-Induced Disturbance, Fiona Mcduie, Austen A. Lorenz, Robert C. Klinger, Cory T. Overton, Cliff L. Feldheim, Joshua T. Ackerman, Michael L. Casazza
Informing Wetland Management With Waterfowl Movement And Sanctuary Use Responses To Human-Induced Disturbance, Fiona Mcduie, Austen A. Lorenz, Robert C. Klinger, Cory T. Overton, Cliff L. Feldheim, Joshua T. Ackerman, Michael L. Casazza
Faculty Research, Scholarly, and Creative Activity
Long-term environmental management to prevent waterfowl population declines is informed by ecology, movement behavior and habitat use patterns. Extrinsic factors, such as human-induced disturbance, can cause behavioral changes which may influence movement and resource needs, driving variation that affects management efficacy. To better understand the relationship between human-based disturbance and animal movement and habitat use, and their potential effects on management, we GPS tracked 15 dabbling ducks in California over ~4-weeks before, during and after the start of a recreational hunting season in October/November 2018. We recorded locations at 2-min intervals across three separate 24-h tracking phases: Phase 1) two …
Characterization Of Cdom In The Elkhorn Slough Estuary Using Eem Spectroscopy And Its Potential For Macrophyte Monitoring, María Vila Duplá
Characterization Of Cdom In The Elkhorn Slough Estuary Using Eem Spectroscopy And Its Potential For Macrophyte Monitoring, María Vila Duplá
Faculty Research, Scholarly, and Creative Activity
The Elkhorn Slough estuary is an upwelling-influenced system located in Monterey Bay, California. It is of great ecological importance, as it provides essential habitat to over 750 species, and is one of the largest estuaries in California. The sources and distribution of chromophoric dissolved organic matter (cDOM) in Elkhorn Slough are strongly influenced by geochemical processes linked to the transition between sea and continent, and to anthropogenic activity from adjacent lands. In 2016, water samples were collected from across the Elkhorn Slough estuary to assess the sources and spatial dynamics of cDOM and its components throughout the system. Using EEM …
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Statistical Potentials For Rna-Protein Interactions Optimized By Cma-Es, Takayuki Kimura, Nobuaki Yasuo, Masakazu Sekijima, Brooke Lustig
Faculty Research, Scholarly, and Creative Activity
Characterizing RNA-protein interactions remains an important endeavor, complicated by the difficulty in obtaining the relevant structures. Evaluating model structures via statistical potentials is in principle straight-forward and effective. However, given the relatively small size of the existing learning set of RNA-protein complexes optimization of such potentials continues to be problematic. Notably, interaction-based statistical potentials have problems in addressing large RNA-protein complexes. In this study, we adopted a novel strategy with covariance matrix adaptation (CMA-ES) to calculate statistical potentials, successfully identifying native docking poses.
Draft Genome Sequences Of Three Monokaryotic Isolates Of The White-Rot Basidiomycete Fungus Dichomitus Squalens, Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, Steven Ahrendt, Vivian Ng, Kerrie Barry, Chris Daum, Igor Grigoriev, Kristiina Hildén, Miia Mäkelä, Ronald De Vries
Draft Genome Sequences Of Three Monokaryotic Isolates Of The White-Rot Basidiomycete Fungus Dichomitus Squalens, Sara Casado López, Mao Peng, Paul Daly, Bill Andreopoulos, Jasmyn Pangilinan, Anna Lipzen, Robert Riley, Steven Ahrendt, Vivian Ng, Kerrie Barry, Chris Daum, Igor Grigoriev, Kristiina Hildén, Miia Mäkelä, Ronald De Vries
Faculty Publications, Computer Science
Here, we report the draft genome sequences of three isolates of the wood-decaying white-rot basidiomycete fungus Dichomitus squalens. The genomes of these monokaryons were sequenced to provide more information on the intraspecies genomic diversity of this fungus and were compared to the previously sequenced genome of D. squalens LYAD-421 SS1.
Air Quality And Health Burden Of 2017 Northern California Wildfires, Susan O’Neill, Minghui Diao
Air Quality And Health Burden Of 2017 Northern California Wildfires, Susan O’Neill, Minghui Diao
Faculty Publications, Meteorology and Climate Science
No abstract provided.
A Lab-On-Chip Phosphate Analyzer For Long-Term In Situ Monitoring At Fixed Observatories: Optimization And Performance Evaluation In Estuarine And Oligotrophic Coastal Waters, Maxime Grand, Geraldine Clinton-Bailey, Alexander Beaton, Allison Schaap, Thomas Johengen, Mario Tamburri, Douglas Connelly, Matthew Mowlem, Eric Achterberg
A Lab-On-Chip Phosphate Analyzer For Long-Term In Situ Monitoring At Fixed Observatories: Optimization And Performance Evaluation In Estuarine And Oligotrophic Coastal Waters, Maxime Grand, Geraldine Clinton-Bailey, Alexander Beaton, Allison Schaap, Thomas Johengen, Mario Tamburri, Douglas Connelly, Matthew Mowlem, Eric Achterberg
Faculty Publications
The development of phosphate sensors suitable for long-term in situdeployments in natural waters, is essential to improve our understanding of the distribution, fluxes, and biogeochemical role of this key nutrient in a changing ocean. Here, we describe the optimization of the molybdenum blue method for in situ work using a lab-on-chip (LOC) analyzer and evaluate its performance in the laboratory and at two contrasting field sites. The in situ performance of the LOC sensor is evaluated using hourly time-series data from a 56-day trial in Southampton Water (UK), as well as a month-long deployment in the subtropical oligotrophic waters of …
Long-Term, High Frequency In Situ Measurements Of Intertidal Mussel Bed Temperatures Using Biomimetic Sensors, Brian Helmuth, Francis Choi, Allison Matzelle, Jessica Torossian, Scott Morello, K.A.S. Mislan, Lauren Yamane, Denise Strickland, P. Szathmary, Sarah Gilman, Alyson Tockstein, Thomas Hilbish, Michael Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa Foley, Angela Johnson, Megan Poole, Mae Noble, Erin Richmond, Matt Robart, Jonathan Robinson, Jerod Sapp, Jackie Sones, Bernardo Broitman, Mark Denny, Katharine Mach, Luke P. Miller, Michael O'Donnell, Philip Ross, Gretchen Hofmann, Mackenzie Zippay, Carol Blanchette, J. Macfarlan, Eugenio Carpizo-Ituarte, Benjamin Ruttenberg, Carlos Peña Mejía, Christopher Mcquaid, Justin Lathlean, Cristián Monaco, Katy Nicastro, Gerardo Zardi
Long-Term, High Frequency In Situ Measurements Of Intertidal Mussel Bed Temperatures Using Biomimetic Sensors, Brian Helmuth, Francis Choi, Allison Matzelle, Jessica Torossian, Scott Morello, K.A.S. Mislan, Lauren Yamane, Denise Strickland, P. Szathmary, Sarah Gilman, Alyson Tockstein, Thomas Hilbish, Michael Burrows, Anne Marie Power, Elizabeth Gosling, Nova Mieszkowska, Christopher Harley, Michael Nishizaki, Emily Carrington, Bruce Menge, Laura Petes, Melissa Foley, Angela Johnson, Megan Poole, Mae Noble, Erin Richmond, Matt Robart, Jonathan Robinson, Jerod Sapp, Jackie Sones, Bernardo Broitman, Mark Denny, Katharine Mach, Luke P. Miller, Michael O'Donnell, Philip Ross, Gretchen Hofmann, Mackenzie Zippay, Carol Blanchette, J. Macfarlan, Eugenio Carpizo-Ituarte, Benjamin Ruttenberg, Carlos Peña Mejía, Christopher Mcquaid, Justin Lathlean, Cristián Monaco, Katy Nicastro, Gerardo Zardi
Faculty Publications, Biological Sciences
At a proximal level, the physiological impacts of global climate change on ectothermic organisms are manifest as changes in body temperatures. Especially for plants and animals exposed to direct solar radiation, body temperatures can be substantially different from air temperatures. We deployed biomimetic sensors that approximate the thermal characteristics of intertidal mussels at 71 sites worldwide, from 1998-present. Loggers recorded temperatures at 10–30 min intervals nearly continuously at multiple intertidal elevations. Comparisons against direct measurements of mussel tissue temperature indicated errors of ~2.0–2.5 °C, during daily fluctuations that often exceeded 15°–20 °C. Geographic patterns in thermal stress based on biomimetic …
Evolutionary Game Dynamics In Populations With Heterogenous Structures, Wes Maciejewski, Feng Fu, Christoph Hauert
Evolutionary Game Dynamics In Populations With Heterogenous Structures, Wes Maciejewski, Feng Fu, Christoph Hauert
Faculty Research, Scholarly, and Creative Activity
Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours. In this article we show that such a conclusion largely depends on the individual-level interactions that take place. In particular, averaging payoffs garnered through game interactions rather than accumulating the payoffs can altogether remove the cooperative advantage of heterogeneous graphs while such a difference does not affect the outcome on homogeneous structures. In addition, …
Will Extreme Climatic Events Facilitate Biological Invasions?, Jeffrey M. Diez, Carla M. D'Antonio, Jeffrey S. Dukes, Edwin D. Grosholz, Julian D. Olden, Cascade J.B. Sorte, Dana M. Blumenthal, Bethany A. Bradley, Regan I. Early, Inés Ibáñez, Sierra J. Jones, Joshua J. Lawler, Luke P. Miller
Will Extreme Climatic Events Facilitate Biological Invasions?, Jeffrey M. Diez, Carla M. D'Antonio, Jeffrey S. Dukes, Edwin D. Grosholz, Julian D. Olden, Cascade J.B. Sorte, Dana M. Blumenthal, Bethany A. Bradley, Regan I. Early, Inés Ibáñez, Sierra J. Jones, Joshua J. Lawler, Luke P. Miller
Faculty Publications, Biological Sciences
Extreme climatic events (ECEs) – such as unusual heat waves, hurricanes, floods, and droughts – can dramatically affect ecological and evolutionary processes, and these events are projected to become more frequent and more intense with ongoing climate change. However, the implications of ECEs for biological invasions remain poorly understood. Using concepts and empirical evidence from invasion ecology, we identify mechanisms by which ECEs may influence the invasion process, from initial introduction through establishment and spread. We summarize how ECEs can enhance invasions by promoting the transport of propagules into new regions, by decreasing the resistance of native communities to establishment, …
Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede
Silica As A Matrix For Encapsulating Proteins:Surface Effects On Protein Structure Assessed By Circular Dichroism Spectroscopy, Daryl K. Eggers, P. J. Calabretta, M. C. Chancellor, C. Torres, G. R. Abel Jr., C. Neihaus, N. J. Birtwhistle, N. M. Khouderchah, G. H. Zemede
Faculty Publications, Chemistry
The encapsulation of biomolecules in solid materials that retain the native properties of the molecule is a desired feature for the development of biosensors and biocatalysts. In the current study, protein entrapment in silica-based materials is explored using the sol-gel technique. This work surveys the effects of silica confinement on the structure of several model polypeptides, including apomyoglobin, copper-zinc superoxide dismutase, polyglutamine, polylysine, and type I antifreeze protein. Changes in the secondary structure of each protein following encapsulation are monitored by circular dichroism spectroscopy. In many cases, silica confinement reduces the fraction of properly-folded protein relative to solution, but addition …
Global Change, Global Trade, And The Next Wave Of Plant Invasions, Bethany A. Bradley, Dana M. Blumenthal, Regan Early, Edwin D. Grosholz, Joshua J. Lawler, Luke P. Miller, Cascade J.B. Sorte, Carla M. D'Antonio, Jeffrey M. Diez, Jeffrey S. Dukes, Ines Ibanez, Julian D. Olden
Global Change, Global Trade, And The Next Wave Of Plant Invasions, Bethany A. Bradley, Dana M. Blumenthal, Regan Early, Edwin D. Grosholz, Joshua J. Lawler, Luke P. Miller, Cascade J.B. Sorte, Carla M. D'Antonio, Jeffrey M. Diez, Jeffrey S. Dukes, Ines Ibanez, Julian D. Olden
Faculty Publications, Biological Sciences
Many non-native plants in the US have become problematic invaders of native and managed ecosystems, but a new generation of invasive species may be at our doorstep. Here, we review trends in the horticultural trade and invasion patterns of previously introduced species and show that novel species introductions from emerging horticultural trade partners are likely to rapidly increase invasion risk. At the same time, climate change and water restrictions are increasing demand for new types of species adapted to warm and dry environments. This confluence of forces could expose the US to a range of new invasive species, including many …
Rumbling In The Benthos: Acoustic Ecology Of The California Mantis Shrimp Hemisquilla Californiensis, E. Staaterman, C. Clark, A. Gallagher, M. Devries, T. Claverie, S. Patek
Rumbling In The Benthos: Acoustic Ecology Of The California Mantis Shrimp Hemisquilla Californiensis, E. Staaterman, C. Clark, A. Gallagher, M. Devries, T. Claverie, S. Patek
Faculty Publications, Biological Sciences
Although much research has focused on acoustic mapping and exploration of the benthic environment, little is known about the acoustic ecology of benthic organisms, particularly benthic crustaceans. Through the use of a coupled audio–video system, a hydrophone array, and an autonomous recording unit, we tested several hypotheses about the field acoustics of a benthic marine crustacean, Hemisquilla californiensis. Living in muddy burrows in southern California, these large mantis shrimp produce low frequency ‘rumbles’ through muscle vibrations. First, we tested whether acoustic signals are similar in the field and in the laboratory, and discovered that field-produced rumbles are more acoustically and …
Efficient Unfolding Pattern Recognition In Single Molecule Force Spectroscopy Data, Bill Andreopoulos, Dirk Labudde
Efficient Unfolding Pattern Recognition In Single Molecule Force Spectroscopy Data, Bill Andreopoulos, Dirk Labudde
Faculty Publications, Computer Science
BackgroundSingle-molecule force spectroscopy (SMFS) is a technique that measures the force necessary to unfold a protein. SMFS experiments generate Force-Distance (F-D) curves. A statistical analysis of a set of F-D curves reveals different unfolding pathways. Information on protein structure, conformation, functional states, and inter- and intra-molecular interactions can be derived.ResultsIn the present work, we propose a pattern recognition algorithm and apply our algorithm to datasets from SMFS experiments on the membrane protein bacterioRhodopsin (bR). We discuss the unfolding pathways found in bR, which are characterised by main peaks and side peaks. A main peak is the result of the pairwise …
Synthesis Of Knowledge Of Extreme Fire Behavior: Volume I For Fire Managers, Paul Werth, Brian Potter, Craig Clements, Mark Finney, Scott Goodrick, Martin Alexander, Miguel Cruz, Jason Forthofer, Sara Mcallister
Synthesis Of Knowledge Of Extreme Fire Behavior: Volume I For Fire Managers, Paul Werth, Brian Potter, Craig Clements, Mark Finney, Scott Goodrick, Martin Alexander, Miguel Cruz, Jason Forthofer, Sara Mcallister
Faculty Publications, Meteorology and Climate Science
The National Wildfire Coordinating Group definition of extreme fire behavior (EFB) indicates a level of fire behavior characteristics that ordinarily precludes methods of direct control action. One or more of the following is usually involved: high rate of spread, prolific crowning/ spotting, presence of fire whirls, and strong convection column. Predictability is difficult because such fires often exercise some degree of influence on their environment and behave erratically, sometimes dangerously. Alternate terms include “blow up” and “fire storm.” Fire managers examining fires over the last 100 years have come to understand many of the factors necessary for EFB development. This …
A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers
A Bulk Water-Dependent Desolvation Energy Model For Analyzing The Effects Of Secondary Solutes On Biological Equilibria, Daryl K. Eggers
Faculty Publications, Chemistry
A new phenomenological model for interpreting the effects of solutes on biological equilibria is presented. The model attributes changes in equilibria to differences in the desolvation energy of the reacting species that, in turn, reflect changes in the free energy of the bulk water upon addition of secondary solutes. The desolvation approach differs notably from that of other solute models by treating the free energy of bulk water as a variable and by not ascribing the observed shifts in reaction equilibria to accumulation or depletion of solutes next to the surfaces of the reacting species. On the contrary, the partitioning …
Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight
Changes In Apparent Molar Water Volume And Dkp Solubility Yield Insights On The Hofmeister Effect, Daryl K. Eggers, A. Y. Payumo, R. M. Huijon, D. D. Mansfield, L. M. Belk, A. K. Bui, A. E. Knight
Faculty Publications, Chemistry
This study examines the properties of a 4 × 2 matrix of aqueous cations and anions at concentrations up to 8.0 M. The apparent molar water volume, as calculated by subtracting the mass and volume of the ions from the corresponding solution density, was found to exceed the molar volume of ice in many concentrated electrolyte solutions, underscoring the nonideal behavior of these systems. The solvent properties of water were also analyzed by measuring the solubility of diketopiperazine (DKP) in 2.000 M salt solutions prepared from the same ion combinations. Solution rankings for DKP solubility were found to parallel the …
Triangle Network Motifs Predict Complexes By Complementing High-Error Interactomes With Structural Information, Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
Triangle Network Motifs Predict Complexes By Complementing High-Error Interactomes With Structural Information, Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder
Faculty Publications, Computer Science
BackgroundA lot of high-throughput studies produce protein-protein interaction networks (PPINs) with many errors and missing information. Even for genome-wide approaches, there is often a low overlap between PPINs produced by different studies. Second-level neighbors separated by two protein-protein interactions (PPIs) were previously used for predicting protein function and finding complexes in high-error PPINs. We retrieve second level neighbors in PPINs, and complement these with structural domain-domain interactions (SDDIs) representing binding evidence on proteins, forming PPI-SDDI-PPI triangles.ResultsWe find low overlap between PPINs, SDDIs and known complexes, all well below 10%. We evaluate the overlap of PPI-SDDI-PPI triangles with known complexes from …
Word Sense Disambiguation In Biomedical Ontologies With Term Co-Occurrence Analysis And Document Clustering, Bill Andreopoulos, Dimitra Alexopoulou, Michael Schroeder
Word Sense Disambiguation In Biomedical Ontologies With Term Co-Occurrence Analysis And Document Clustering, Bill Andreopoulos, Dimitra Alexopoulou, Michael Schroeder
Faculty Publications, Computer Science
With more and more genomes being sequenced, a lot of effort is devoted to their annotation with terms from controlled vocabularies such as the GeneOntology. Manual annotation based on relevant literature is tedious, but automation of this process is difficult. One particularly challenging problem is word sense disambiguation. Terms such as |development| can refer to developmental biology or to the more general sense. Here, we present two approaches to address this problem by using term co-occurrences and document clustering. To evaluate our method we defined a corpus of 331 documents on development and developmental biology. Term co-occurrence analysis achieves an …
Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
Unraveling Protein Networks With Power Graph Analysis, Loïc Royer, Matthias Reimann, Bill Andreopoulos, Michael Schroeder
Faculty Publications, Computer Science
Networks play a crucial role in computational biology, yet their analysis and representation is still an open problem. Power Graph Analysis is a lossless transformation of biological networks into a compact, less redundant representation, exploiting the abundance of cliques and bicliques as elementary topological motifs. We demonstrate with five examples the advantages of Power Graph Analysis. Investigating protein-protein interaction networks, we show how the catalytic subunits of the casein kinase II complex are distinguishable from the regulatory subunits, how interaction profiles and sequence phylogeny of SH3 domains correlate, and how false positive interactions among high-throughput interactions are spotted. Additionally, we …
Favourable Influence Of Hydrophobic Surfaces On Protein Structure In Porous Organically-Modified Silica Glasses, Daryl K. Eggers, B. Menaa, M. Herrero, V. Rives, M. Lavrenko
Favourable Influence Of Hydrophobic Surfaces On Protein Structure In Porous Organically-Modified Silica Glasses, Daryl K. Eggers, B. Menaa, M. Herrero, V. Rives, M. Lavrenko
Faculty Publications, Chemistry
Organically-modified siloxanes were used as host materials to examine the influence of surface chemistry on protein conformation in a crowded environment. The sol–gel materials were prepared from tetramethoxysilane and a series of monosubstituted alkoxysilanes, RSi(OR′)3, featuring alkyl groups of increasing chain length in the R-position. Using circular dichroism spectroscopy in the far-UV region, apomyoglobin was found to transit from an unfolded state to a native-like helical state as the content of the hydrophobic precursor increased from 0 to 15%. At a fixed molar content of 5% RSi(OR′)3, the helical structure of apomyoglobin increased with the chain length of the R-group, …
Protein Adsorption Onto Organically-Modified Silica Glass Leads To A Different Structure Than Sol-Gel Encapsulation, Daryl K. Eggers, B, Menaa, C. Torres, M. Herrero, V. Rives, A. R.W Gilbert
Protein Adsorption Onto Organically-Modified Silica Glass Leads To A Different Structure Than Sol-Gel Encapsulation, Daryl K. Eggers, B, Menaa, C. Torres, M. Herrero, V. Rives, A. R.W Gilbert
Faculty Publications, Chemistry
The secondary structures of two proteins were examined by circular dichroism spectroscopy after adsorption onto a series of organically modified silica glasses. The glasses were prepared by the sol-gel technique and were varied in hydrophobicity by incorporation of 5% methyl, propyl, trifluoropropyl, or n-hexyl silane. Both cytochrome c and apomyoglobin were found to lose secondary structure after adsorption onto the modified glasses. In the case of apomyoglobin, the α-helical content of the adsorbed protein ranged from 21% to 28%, well below the 62% helix found in solution. In contrast, these same glasses led to a striking increase in apomyoglobin structure …
Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha
Hydrophobic, Organically-Modified Silica Gels Enhance The Structure Of Encapsulated Apomyoglobin, Daryl K. Eggers, V. A. Rocha
Faculty Publications, Chemistry
Insertion of hydrophobic groups in a silica matrix, by addition of propyl- or trifluoropropyltrimethoxysilane, leads to a surprising increase in the helical content of apomyoglobin following encapsulation by the sol–gel technique
Finding Molecular Complexes Through Multiple Layer Clustering Of Protein Interaction Networks, Bill Andreopoulos, Aijun An, Xiangji Huang, Xiaogang Wang
Finding Molecular Complexes Through Multiple Layer Clustering Of Protein Interaction Networks, Bill Andreopoulos, Aijun An, Xiangji Huang, Xiaogang Wang
Faculty Publications, Computer Science
Clustering protein-protein interaction networks (PINs) helps to identify complexes that guide the cell machinery. Clustering algorithms often create a flat clustering, without considering the layered structure of PINs. We propose the MULIC clustering algorithm that produces layered clusters. We applied MULIC to five PINs. Clusters correlate with known MIPS protein complexes. For example, a cluster of 79 proteins overlaps with a known complex of 88 proteins. Proteins in top cluster layers tend to be more representative of complexes than proteins in bottom layers. Lab work on finding unknown complexes or determining drug effects can be guided by top layer proteins.
Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang
Bi-Level Clustering Of Mixed Categorical And Numerical Biomedical Data, Bill Andreopoulos, Aijun An, Xiaogang Wang
Faculty Publications, Computer Science
Biomedical data sets often have mixed categorical and numerical types, where the former represent semantic information on the objects and the latter represent experimental results. We present the BILCOM algorithm for |Bi-Level Clustering of Mixed categorical and numerical data types|. BILCOM performs a pseudo-Bayesian process, where the prior is categorical clustering. BILCOM partitions biomedical data sets of mixed types, such as hepatitis, thyroid disease and yeast gene expression data with Gene Ontology annotations, more accurately than if using one type alone.
Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol
Farnesylated Lamins, Progeroid Syndromes And Farnesyl Transferase Inhibitors, Michael Sinensky, A. E. Rusinol
Faculty Publications, Biological Sciences
Three mammalian nuclear lamin proteins, lamin B1, lamin B2 and the lamin A precursor, prelamin A, undergo canonical farnesylation and processing at CAAX motifs. In the case of prelamin A, there is an additional farnesylation-dependent endoproteolysis, which is defective in two congenital diseases: Hutchinson-Gilford progeria (HGPS) and restrictive dermopathy (RD). These two diseases arise respectively from defects in the prelamin A substrate and the enzyme (ZmpSte24) that processes it. Recent work has shed light on the roles of the lamin proteins and the enzymes involved in their farnesylation-dependent maturation. Other experimental work, including mouse model studies, have examined the possibility …
Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou
Dna Damage Responses In Progeroid Syndromes Arise From Defective Maturation Of Prelamin A, Michael Sinensky, Y. Liu, A. Rusinol, Y. Wang, Y. Zou
Faculty Publications, Biological Sciences
The genetic diseases Hutchinson-Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) arise from accumulation of farnesylated prelamin A because of defects in the lamin A maturation pathway. Both of these diseases exhibit symptoms that can be viewed as accelerated aging. The mechanism by which accumulation of farnesylated prelamin A leads to these accelerated aging phenotypes is not understood. Here we present evidence that in HGPS and RD fibroblasts, DNA damage checkpoints are persistently activated because of the compromise in genomic integrity. Inactivation of checkpoint kinases Ataxia-telangiectasia-mutated (ATM) and ATR (ATM- and Rad3-related) in these patient cells can partially overcome their …
Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio
Reduced Macrophage Apoptosis Is Associated With Accelerated Atherosclerosis In Low-Denstiy Lipoprotein Receptor-Null Mice, Michael Sinensky, J. Liu, D. P. Thweke, Y. R. Su, M. F. Linton, S. Fazio
Faculty Publications, Biological Sciences
Objective— The majority of apoptotic cells in atherosclerotic lesions are macrophages. However, the pathogenic role of macrophage apoptosis in the development of atherosclerosis remains unclear. Elevated expression of Bax, one of the pivotal proapoptotic proteins of the Bcl-2 family, has been found in human atherosclerotic plaques. Activation of Bax also occurs in free cholesterol-loaded and oxysterol-treated mouse macrophages. In this study, we examined the effect of Bax deficiency in bone marrow-derived leukocytes on the development of atherosclerosis in low-density lipoprotein receptor-null (LDLR−/−) mice. Methods and Results— Fourteen 8-week-old male LDLR−/− mice were lethally irradiated and reconstituted with either wild-type (WT) …
Familial Als-Associated Mutations Decrease The Thermal Stability Of Distinctly Metallated Species Of Human Copper/Zinc Superoxide Dismutase, Daryl K. Eggers, J. A. Rodriguez, J. S. Valentine, J. A. Roe, A. Tiwari, R. H. Brown, L. J. Hayward
Familial Als-Associated Mutations Decrease The Thermal Stability Of Distinctly Metallated Species Of Human Copper/Zinc Superoxide Dismutase, Daryl K. Eggers, J. A. Rodriguez, J. S. Valentine, J. A. Roe, A. Tiwari, R. H. Brown, L. J. Hayward
Faculty Publications, Chemistry
We report the thermal stability of wild type (WT) and 14 different variants of human copper/zinc superoxide dismutase (SOD1) associated with familial amyotrophic lateral sclerosis (FALS). Multiple endothermic unfolding transitions were observed by differential scanning calorimetry for partially metallated SOD1 enzymes isolated from a baculovirus system. We correlated the metal ion contents of SOD1 variants with the occurrence of distinct melting transitions. Altered thermal stability upon reduction of copper with dithionite identified transitions resulting from the unfolding of copper-containing SOD1 species. We demonstrated that copper or zinc binding to a subset of “WT-like” FALS mutants (A4V, L38V, G41S, G72S, D76Y, …
Complexes Between Nascent Polypeptides And Their Molecular Chaperones In The Cytosol Of Mammalian Cells, Daryl K. Eggers, W. J. Welch, W. J. Hansen
Complexes Between Nascent Polypeptides And Their Molecular Chaperones In The Cytosol Of Mammalian Cells, Daryl K. Eggers, W. J. Welch, W. J. Hansen
Faculty Publications, Chemistry
Folding of newly synthesized proteins in vivo is believed to be facilitated by the cooperative interaction of a defined group of proteins known as molecular chaperones. We investigated the direct interaction of chaperones with nascent polypeptides in the cytosol of mammalian cells by multiple methods. A new approach using a polyclonal antibody to puromycin allowed us to tag and capture a population of truncated nascent polypeptides with no bias as to the identity of the bound chaperones. In addition, antibodies that recognize the cytosolic chaperones hsp70, CCT (TRiC), hsp40, p48 (Hip), and hsp90 were compared on the basis of their …
The Processing Pathway Of Prelamin A, Michael Sinensky, K. Fantle, M. Trujillo, T. Mclain, A. Kupfer, M. Dalton
The Processing Pathway Of Prelamin A, Michael Sinensky, K. Fantle, M. Trujillo, T. Mclain, A. Kupfer, M. Dalton
Faculty Publications, Biological Sciences
The conversion of mammalian prelamin A to mature lamin A proceeds through the removal of 18 amino acids from the carboxyl terminus. The initial step in this processing is the isoprenylation of a CAAX box cysteine. This proteolytic event is distinctive for prelamin A among the known prenylated mammalian proteins. Since the carboxyl terminus of prelamin A is removed during maturation, it is not obvious that this protein would undergo the two reactions subsequent to prenylation observed in other CAAX box proteins-the endoproteolytic removal of the carboxyl-terminal 3 amino acids and the subsequent methylation of the now carboxyl-terminal cysteine. To …