Life Sciences Commons^™

Genome Sequences And Annotation Of Two Urinary Isolates Of E.Coli, Travis Kyle Price, Arya Mehtash, Laurynas Kalesinskas, Kema Malki, Evann Elizabeth Hilt, Catherine Putonti, Alan J. Wolfe

Bioinformatics Faculty Publications

The genus Escherichia includes pathogens and commensals. Bladder infections (cystitis) result most often from colonization of the bladder by uropathogenic E. coli strains. In contrast, a poorly defined condition called asymptomatic bacteriuria results from colonization of the bladder with E. coli strains without symptoms. As part of an on-going attempt to identify and characterize the newly discovered female urinary microbiota, we report the genome sequences and annotation of two urinary isolates of E. coli: one (E78) was isolated from a female patient who self-reported cystitis; the other (E75) was isolated from a female patient who reported that she did …

Purification Of 26s Proteasomes And Their Subcomplexes From Plants, Richard S. Marshall, David C. Gemperline, Richard D. Vierstra

Biology Faculty Research

The 26S proteasome is a highly dynamic, multisubunit, ATP-dependent protease that plays a central role in cellular housekeeping and many aspects of plant growth and development by degrading aberrant polypeptides and key cellular regulators that are first modified by ubiquitin. Although the 26S proteasome was originally enriched from plants over 30 years ago, only recently have significant advances been made in our ability to isolate and study the plant particle. Here, we describe two robust methods for purifying the 26S proteasome and its subcomplexes from Arabidopsis thaliana; one that involves conventional chromatography techniques to isolate the complex from wild-type …

A Note On The Implications Of Brexit, E. Wesley F. Peterson, Marianna Khachaturyan

Cornhusker Economics

On June 23, 2016, the citizens of the United Kingdom (UK) voted by a narrow margin to withdraw from the European Union (EU) and on October 2, 2016, the recently chosen Prime Minister, Theresa May, announced that her government would invoke Article 50 of the Lisbon Treaty by the end of March 2017 triggering the process of exiting the EU. The purpose of this note is to review the history of the EU and the procedures a country has to follow to withdraw from it. The implications of the British exit, commonly referred to as “Brexit,” for US-European trade and …

Scorpions Of The Horn Of Africa (Arachnida: Scorpiones). Part Ix. Lanzatus, Orthochirus, And Somalicharmus (Buthidae), With Description Of Lanzatus Somalilandus Sp. N. And Orthochirus Afar Sp. N., František Kovařík, Graeme Lowe, František Šťáhlavský

Euscorpius

The rare Horn of Africa buthid genera Lanzatus Kovařík, 2001, Orthochirus Karsch, 1891, and Somalicharmus Kovařík, 1998 were newly collected. Lanzatus is reported for the first time from Somaliland, and Orthochirus for the first time from Ethiopia. We describe two new species, Lanzatus somalilandus sp. n. from Somaliland, and Orthochirus afar sp. n. from Ethiopia, both discovered during scorpiological expeditions in 2011–2016. Information is provided for all Horn of Africa species belonging to these three genera: their taxonomy, distribution, and ecology, fully complemented with color photos of live and preserved specimens, as well as their habitat. …

Noncanonical Sqstm1/P62-Nrf2 Pathway Activation Mediates Proteasome Inhibitor Resistance In Multiple Myeloma Cells Via Redox, Metabolic And Translational Reprogramming., Irene Riz, Teresa S Hawley, Jeffrey W Marsal, Robert G Hawley

Anatomy and Regenerative Biology Faculty Publications

Multiple Myeloma (MM) is a B-cell malignancy characterized by the accumulation of clonal plasma cells in the bone marrow, with drug resistance being a major cause of therapeutic failure. We established a carfilzomib-resistant derivative of the LP-1 MM cell line (LP-1/Cfz) and found that the transcription factor NF-E2 p45-related factor 2 (Nrf2; gene symbol NFE2L2) contributes to carfilzomib resistance. The mechanism of Nrf2 activation involved enhanced translation of Nrf2 as well as its positive regulator, the autophagy receptor sequestosome 1 (SQSTM1)/p62. The eukaryotic translation initiation factor gene EIF4E3 was among the Nrf2 target genes upregulated in LP-1/Cfz cells, suggesting existence …

How Did Zika Virus Emerge In The Pacific Islands And Latin America?, John Pettersson, Stephen J. Seligman, Didier Musso, Antoine Nougairède, Remi Charrel, Xavier De Lamballerie

NYMC Faculty Publications

The unexpected emergence of Zika virus (ZIKV) in the Pacific Islands and Latin America and its association with congenital Zika virus syndrome (CZVS) (which includes microcephaly) and Guillain-Barré syndrome (GBS) have stimulated wide-ranging research. High densities of susceptible Aedes spp., immunologically naive human populations, global population growth with increased urbanization, and escalation of global transportation of humans and commercial goods carrying vectors and ZIKV undoubtedly enhanced the emergence of ZIKV. However, flavivirus mutations accumulate with time, increasing the likelihood that genetic viral differences are determinants of change in viral phenotype. Based on comparative ZIKV complete genome phylogenetic analyses and temporal …

El Toro, Glo No. 275, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Ex-Mission Soledad (Soberanes), Glo No. 294, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

El Piojo, Glo No. 310, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

El Tucho, Glo No. 259, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Encinal Y Buena Esperanza, Glo No. 269, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

El Sur, Glo No. 288, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

El Potrero De San Carlos, Glo No. 286, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Mitochondrial Superoxide Signaling Contributes To Norepinephrine-Mediated T-Lymphocyte Cytokine Profiles., Adam J. Case, Colton T. Roessner, Jun Tian, Matthew C. Zimmerman

Journal Articles: Cellular & Integrative Physiology

Norepinephrine (NE) produces multifaceted regulatory patterns in T-lymphocytes. Recently, we have shown that NE utilizes redox signaling as evidenced by increased superoxide (O2●-) causally linked to the observed changes in these cells; however, the source of this reactive oxygen species (ROS) remains elusive. Herein, we hypothesized that the source of increased O2●- in NE-stimulated T-lymphocytes is due to disruption of mitochondrial bioenergetics. To address this hypothesis, we utilized purified mouse splenic CD4+ and CD8+ T-lymphocytes stimulated with NE and assessed O2●- levels, mitochondrial metabolism, cellular proliferation, and cytokine profiles. We demonstrate that the increase in O2●- levels in response to …

Speed And Rhythm Affect Temporal Structure Of Variability In Reaching Poststroke: A Pilot Study, Amit Sethi, Nicholas Stergiou, Tara Patterson, Carolynn Patten, Lorie G. Richards

Journal Articles

Temporal structure reveals the potential adaptive strategies employed during upper extremity movements. The authors compared the temporal structure of upper extremity joints under 3 different reaching conditions: preferred speed, fast speed, and reaching with rhythmic auditory cues in 10 individuals poststroke. They also investigated the temporal structure of these 3 reaching conditions in 8 healthy controls to aid in the interpretation of the observed patterns in the poststroke cohort. Approximate entropy (ApEn) was used to measure the temporal structure of the upper extremity joints. ApEn was similar between conditions in controls. After stroke, ApEn was significantly higher for shoulder, elbow, …

Optimisation Of Fucoxanthin Extraction From Irish Seaweeds By Response Surface Methodology, Emer Shannon, Nissreen Abu-Ghannam

Articles

Fucoxanthin is a xanthophyll pigment which occurs in marine brown algae (Phaeophyceae). The anti-diabetic, anti-obesity, anti-cancer, and antioxidant properties of fucoxanthin have been widely reported. Macroalgae, particularly brown seaweeds, grow prolifically around Irish coasts, representing a valuable resource of nutraceuticals such as fucoxanthin for functional food applications. The aim of this study was to maximise the solvent extraction yield from three anatomically discrete regions of the seaweed thallus: blade, stipe, and holdfast. Response surface methodology was applied to determine optimum parameters for extraction of fucoxanthin from the seaweed, Fucus vesiculosus, as a model species. A central composite design was …

Combined Effects Of Fertilizer, Irrigation, And Paclobutrazol On Yield And Fruit Quality Of Mango, Babul C. Sarker, Mohammad A. Rahim, Douglas D. Archbold

Horticulture Faculty Publications

Combinations of fertilizer rates, foliar N sprays, irrigation practices, and paclobutrazol were studied to determine how much they could alter and/or improve mango (Mangifera indica L.) growth, flowering, and yield. Two treatment combinations derived from several years of prior studies of individual practices were compared: one combination was comprised of the best (BT) individual practices from the prior studies and included three applications of fertilizer, a 4% KNO₃ spray application before flowering, paclobutrazol at 7.5 g/L, and weekly irrigation, and the other combination was comprised of the next best (NB) individual practices including two applications of the same …

Comparison Of Carnivore, Omnivore, And Herbivore Mammalian Genomes With A New Leopard Assembly, Soonok Kim, Yun Sung Cho, Hak Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, Je Hoon Jun, Hye Jin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee

Biology Faculty Articles

Background: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. Results: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild …

Guadalupe Y Llanitos De Los Correos, Glo No. 273, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Consciousness And The Unity Of Mind, Mark Rowlands

Animal Sentience

Several types of objection have been raised against the arguments I presented in my target article, “Are animals persons?” Among the objections are the following: (1) the claim that animals are persons is of little significance, (2) my use of the Lockean conception of the person is questionable, (3) whether a creature qualifies as a person is a matter of social construction rather than objective fact, (4) reflective consciousness is more important than I realize, (5) my reliance on implicit self-awareness in the account of personhood is ill-advised, (6) my account entails that too many creatures qualify as persons, and …

Los Gatos Or Santa Rita, Glo No. 253, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Los Carneros (Mcdougal)​, Glo No. 246, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Atomic Tiles: Manipulative Resources For Exploring Bonding And Molecular Structure, Alan L. Kiste, Rebecca G. Hooper, Gregory E. Scott, Seth Bush

Chemistry and Biochemistry

A simple manipulative resource, Atomic Tiles, is described for scaffolding the learning of Lewis structures without using algorithmic, rule-based methods of drawing. Students use Atomic Tiles to (1) create models of bonding that lead to drawing Lewis structures, (2) use the structures they create to infer patterns required for rational structures and common organic functional groups, (3) translate between Lewis structures and molecular models, and (4) use molecular models to identify isomers.

Las Salinas, Glo No. 257, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Llano De Buena Vista, Glo No. 226, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Los Carneros (Littlejohn), Glo No. 244, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Fedrr: Fast, Exhaustive Detection Of Redundant Hierarchical Relations For Quality Improvement Of Large Biomedical Ontologies, Guangming Xing, Guo-Qiang Zhang, Licong Cui

Institute for Biomedical Informatics Faculty Publications

Background: Redundant hierarchical relations refer to such patterns as two paths from one concept to another, one with length one (direct) and the other with length greater than one (indirect). Each redundant relation represents a possibly unintended defect that needs to be corrected in the ontology quality assurance process. Detecting and eliminating redundant relations would help improve the results of all methods relying on the relevant ontological systems as knowledge source, such as the computation of semantic distance between concepts and for ontology matching and alignment.

Results: This paper introduces a novel and scalable approach, called FEDRR – Fast, Exhaustive …

Genomics-Assisted Characterization Of A Breeding Collection Of Apios Americana, An Edible Tuberous Legume, Vikas Belamkar, Andrew Farmer, Nathan T. Weeks, Scott R. Kalberer, William J. Blackmon, Steven B. Cannon

Department of Agronomy and Horticulture: Faculty Publications

For species with potential as new crops, rapid improvement may be facilitated by new genomic methods. Apios (Apios americana Medik.), once a staple food source of Native American Indians, produces protein-rich tubers, tolerates a wide range of soils, and symbiotically fixes nitrogen. We report the first high-quality de novo transcriptome assembly, an expression atlas, and a set of 58,154 SNP and 39,609 gene expression markers (GEMs) for characterization of a breeding collection. Both SNPs and GEMs identify six genotypic clusters in the collection. Transcripts mapped to the Phaseolus vulgaris genome–another phaseoloid legume with the same chromosome number–provide provisional genetic …

Los Coches (Soberances), Glo No. 296, Monterey County, Diseños And Associated Historical Documents.

Monterey County

Diseños - Hand-drawn Spanish-Mexican map demonstrating the physical boundaries of land granted to Mexican citizens by the Spanish or Mexican.

Expediente – Hand-written Spanish-Mexican land grant document issued to Mexican citizens in Alta California for land in Alta-California.

Work Progress Administration Abstract (WPA Abstract) – A summary document prepared in 1938 under the Work Progress Administration program detailing the history of a rancho beginning with the Spanish-American land through the U.S. patenting process.

Hoffman Notes -- Summary of information concerning claims made for the Rancho lands from the Appendix listing Table of Land Claims in the Reports of Land Cases …

Antimicrobial Susceptibility Testing Of Neisseria Gonorrhoeae Isolates In Pakistan By Etest Compared To Calibrated Dichotomous Sensitivity And Clinical Laboratory Standards Institute Disc Diffusion Techniques., Pushpa Bhawan Mal, Kauser Jabeen, Joveria Farooqi, Magnus Unemo, Erum Khan

Department of Pathology and Laboratory Medicine

Background

Accurate detection of Neisseria gonorrhoeae antimicrobial resistance is essential for appropriate management and prevention of spread of infection in the community. In this study Calibrated Dichotomous Sensitivity (CDS) and Clinical Laboratory Standards Institute (CLSI) disc diffusion methods were compared with minimum inhibitory concentration (MIC) by Etest in Neisseria gonorrhoeae isolates from Karachi, Pakistan. CDS and CLSI disc diffusion techniques, and Etest for ceftriaxone, penicillin G, spectinomycin and ciprofloxacin against 100 isolates from years 2012–2014 were performed. Due to lack of CLSI breakpoints for azithromycin, it was interpreted using cut-offs from British Society of Antimicrobial Chemotherapy (BSAC). Due to lack …