• T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees

      Carbone, Ignazio; White, James B; Miadlikowska, Jolanta; Arnold, A Elizabeth; Miller, Mark A; Magain, Nicolas; U'Ren, Jana M; Lutzoni, François; Univ Arizona, Dept Biosyst Engn; Univ Arizona, Sch Plant Sci; et al. (MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 2019-07-18)
      The Tree-Based Alignment Selector (T-BAS) toolkit combines phylogenetic-based placement of DNA sequences with alignment and specimen metadata visualization tools in an integrative pipeline for analyzing microbial biodiversity. The release of T-BAS version 2.1 makes available reference phylogenies, supports multilocus sequence placements and permits uploading and downloading trees, alignments, and specimen metadata.
    • Table cartogram

      Evans, William; Felsner, Stefan; Kaufmann, Michael; Kobourov, Stephen G.; Mondal, Debajyoti; Nishat, Rahnuma Islam; Verbeek, Kevin; Univ Arizona, Dept Comp Sci (ELSEVIER SCIENCE BV, 2018-03)
      A table cartogram of a two dimensional m x n table A of non-negative weights in a rectangle R, whose area equals the sum of the weights, is a partition of R into convex quadrilateral faces corresponding to the cells of A such that each face has the same adjacency as its corresponding cell and has area equal to the cell's weight. Such a partition acts as a natural way to visualize table data arising in various fields of research. In this paper, we give a O (mn)-time algorithm to find a table cartogram in a rectangle. We then generalize our algorithm to obtain table cartograms inside arbitrary convex quadrangles, circles, and finally, on the surface of cylinders and spheres. (c) 2017 Elsevier B.V. All rights reserved.
    • TAF1-gene editing alters the morphology and function of the cerebellum and cerebral cortex

      Janakiraman, Udaiyappan; Yu, Jie; Moutal, Aubin; Chinnasamy, Dhanalakshmi; Boinon, Lisa; Batchelor, Shelby N; Anandhan, Annaduri; Khanna, Rajesh; Nelson, Mark A; Univ Arizona, Coll Med, Dept Pathol; et al. (ACADEMIC PRESS INC ELSEVIER SCIENCE, 2019-12-01)
      TAF1/MRSX33 intellectual disability syndrome is an X-linked disorder caused by loss-of-function mutations in the TAF1 gene. How these mutations cause dysmorphology, hypotonia, intellectual and motor defects is unknown. Mouse models which have embryonically targeted TAF1 have failed, possibly due to TAF1 being essential for viability, preferentially expressed in early brain development, and intolerant of mutation. Novel animal models are valuable tools for understanding neuronal pathology. Here, we report the development and characterization of a novel animal model for TAF1 ID syndrome in which the TAF1 gene is deleted in embryonic rats using clustered regularly interspaced short palindromic repeats (CRISPR) associated protein 9 (Cas9) technology and somatic brain transgenesis mediated by lentiviral transduction. Rat pups, post-natal day 3, were subjected to intracerebroventricular (ICV) injection of either gRNA-control or gRNA-TAF1 vectors. Rats were subjected to a battery of behavioral tests followed by histopathological analyses of brains at post-natal day 14 and day 35. TAF1-edited rats exhibited behavioral deficits at both the neonatal and juvenile stages of development. Deletion of TAF1 lead to a hypoplasia and loss of the Purkinje cells. We also observed a decreased in GFAP positive astrocytes and an increase in Iba1 positive microglia within the granular layer of the cerebellum in TAF1-edited animals. Immunostaining revealed a reduction in the expression of the CaV3.1 T-type calcium channel. Abnormal motor symptoms in TAF1-edited rats were associated with irregular cerebellar output caused by changes in the intrinsic activity of the Purkinje cells due to loss of pre-synaptic CaV3.1. This animal model provides a powerful new tool for studies of neuronal dysfunction in conditions associated with TAF1 abnormalities and should prove useful for developing therapeutic strategies to treat TAF1 ID syndrome.
    • Taguchi Design for Heat Treatment of Rene 65 Components

      Katsari, Christina Maria; Wessman, Andrew; Yue, Stephen; Univ Arizona, Dept Mat Sci & Engn (Springer Science and Business Media LLC, 2020-04-17)
      Rene 65 is a nickel-based superalloy used in aerospace components such as turbine blades and disks. The microstructure in the as-received condition of the superalloy consists of ~ 40% volume fraction of gamma prime precipitates, which gives such a high strength that thermomechanical processing is problematic. The goal of this study was to improve the processability of Rene 65 by developing a heat treatment to lower the strength through changes in the size distribution and volume fraction of those precipitates. Gamma prime in this alloy is observed in three sizes, ranging from a few mu m to tens of nm. For the design of the heat treatments, Taguchi's L8 matrix design of experiments was used. The four factors that are examined are cooling rate, hold temperature, hold time and cooling method to room temperature. The levels of the factors were two (high and low) with replication. Microstructures were characterized by scanning electron microscopy and mechanical properties by Vickers microhardness testing. Regression analysis on the results revealed that the most significant factor for this design is hold temperature. The softest sample and the hardest sample have a significant difference microstructurally, with the latter having a trimodal distribution of precipitates which is believed to cause the strength.
    • Tai Chi in Chinese adults with metabolic syndrome: A pilot randomized controlled trial

      Leung, Leona Yuen-Ling; Chan, Aileen Wai-Kiu; Sit, Janet Wing-Hung; Liu, Ting; Taylor-Piliae, Ruth E; Univ Arizona, Coll Nursing (CHURCHILL LIVINGSTONE, 2019-10-01)
      Objective: To determine the feasibility, acceptability and effects of a 12-week Tai Chi exercise program on cardiometabolic risk factors and quality of life in community-dwelling Chinese adults with metabolic syndrome. Design: A single blind, pilot randomized controlled trial. Setting/location: A general outpatient clinic of a community-based hospital in Hong Kong. Subjects: Ethnic Chinese, 18 years and older, who had at least three of the five criteria of metabolic syndrome defined by the National Cholesterol Education- Adult Treatment Panel III. Intervention: The Tai Chi group attended a 1-h Tai Chi class, twice a week for 12 weeks, plus 30-minutes home practice three-times per week. The control group maintained their usual daily activities. Outcome measures: Primary outcomes were feasibility and acceptability of the Tai Chi intervention. Secondary outcome measures were cardiometabolic risk factors, quality of life, stress and Tai Chi exercise self-efficacy. Results: Study retention rate was 65% (n = 35). Overall satisfaction of completers with the Tai Chi intervention was 4.5 +/- 0.63 (possible range = 1-5). When compared to controls, the Tai Chi group had significantly lower systolic blood pressure (p = 0.037) at 12-weeks. Significant within group changes for the Tai Chi group included lower diastolic blood pressure (p = 0.015), higher fasting blood glucose (p = 0.009), higher waist circumference (females only, p = 0.007), and better perceived mental health (p = 0.046); while controls had significantly higher fasting blood glucose (p = 0.031), and higher waist circumference (females only, p = 0.003). Conclusion: The study intervention was feasible and acceptable for Chinese adults with metabolic syndrome. While not powered to find statistically significant differences, positive and negative changes were observed in some cardiometabolic risk factors and quality of life. Further investigation with a larger sample size and longer study period is needed to explore potential environmental factors that may have influenced the study results.
    • Tail Wags the Dog? Functional Gene Classes Driving Genome-Wide GC Content in Plasmodium spp

      Castillo, Andreina I; Nelson, Andrew D L; Lyons, Eric; Univ Arizona, Sch Plant Sci; Univ Arizona, Sch Plant Sci, BIO5 Inst (OXFORD UNIV PRESS, 2019-02)
      Plasmodium parasites are valuable models to understand how nucleotide composition affects mutation, diversification, and adaptation. No other observed eukaryotes have undergone such large changes in genomic Guanine-Cytosine (GC) content as seen in the genus Plasmodium (approximate to 30% within 35-40 Myr). Although mutational biases are known to influence GC content in the human-infective Plasmodium vivax and Plasmodium falciparum; no study has addressed how different gene functional classes contribute to genus-wide compositional changes, or if Plasmodium GC content variation is driven by natural selection. Here, we tested the hypothesis that certain gene processes and functions drive variation in global GC content between Plasmodium species. We performed a large-scale comparative genomic analysis using the genomes and predicted genes of 17 Plasmodium species encompassing a wide genomic GC content range. Genic GC content was sorted and divided into ten equally sized quantiles that were then assessed for functional enrichment classes. In agreement that selection on gene classes may drive genomic GC content, trans-membrane proteins were enriched within extreme GC content quantiles (Q1 and Q10). Specifically, variant surface antigens, which primarily interact with vertebrate immune systems, showed skewed GC content distributions compared with other trans-membrane proteins. Although a definitive causation linking GC content, expression, and positive selection within variant surface antigens from Plasmodium vivax, Plasmodium berghei, and Plasmodium falciparum could not be established, we found that regardless of genomic nucleotide composition, genic GC content and expression were positively correlated during trophozoite stages. Overall, these data suggest that, alongside mutational biases, functional protein classes drive Plasmodium GC content change.
    • Tailoring phonon band structures with broken symmetry by shaping spatiotemporal modulations of stiffness in a one-dimensional elastic waveguide

      Deymier, Pierre A.; Gole, Vitthal; Lucas, Pierre; Vasseur, Jérôme O.; Runge, Keith; Univ Arizona, Dept Mat Sci & Engn (AMER PHYSICAL SOC, 2017-08-17)
      Spatiotemporal modulations of the elastic properties of materials can be used to break time and parity symmetry of elastic waves. We show that the form of the elastic band structure depends not only on the spatial and temporal periodicity of a spatiotemporal modulation but also on its shape through its Fourier components. We demonstrate that hybridization gaps open from interactions between the Bloch modes of the periodic medium in absence of the temporal variation of the modulation and the combined sinusoidal components of the Fourier decomposition of the periodic modulation.
    • The Tajik Basin: A composite record of sedimentary basin evolution in response to tectonics in the Pamir

      Chapman, James B.; Carrapa, Barbara; DeCelles, Peter G.; Worthington, James; Mancin, Nicoletta; Cobianchi, Miriam; Stoica, Marius; Wang, Xin; Gadoev, Mustafo; Oimahmadov, Ilhomjon; et al. (WILEY, 2019)
      Investigation of a >6-km-thick succession of Cretaceous to Cenozoic sedimentary rocks in the Tajik Basin reveals that this depocentre consists of three stacked basin systems that are interpreted to reflect different mechanisms of subsidence associated with tectonics in the Pamir Mountains: a Lower to mid-Cretaceous succession, an Upper Cretaceous-Lower Eocene succession and an Eocene-Neogene succession. The Lower to mid-Cretaceous succession consists of fluvial deposits that were primarily derived from the Triassic Karakul-Mazar subduction-accretion complex in the northern Pamir. This succession is characterized by a convex-up (accelerating) subsidence curve, thickens towards the Pamir and is interpreted as a retroarc foreland basin system associated with northward subduction of Tethyan oceanic lithosphere. The Upper Cretaceous to early Eocene succession consists of fine-grained, marginal marine and sabkha deposits. The succession is characterized by a concave-up subsidence curve. Regionally extensive limestone beds in the succession are consistent with late stage thermal relaxation and relative sea-level rise following lithospheric extension, potentially in response to Tethyan slab rollback/foundering. The Upper Cretaceous-early Eocene succession is capped by a middle Eocene to early Oligocene (ca. 50-30 Ma) disconformity, which is interpreted to record the passage of a flexural forebulge. The disconformity is represented by a depositional hiatus, which is 10-30 Myr younger than estimates for the initiation of India-Asia collision and overlaps in age with the start of prograde metamorphism recorded in the Pamir gneiss domes. Overlying the disconformity, a >4-km-thick upper Eocene-Neogene succession displays a classic, coarsening upward unroofing sequence characterized by accelerating subsidence, which is interpreted as a retro-foreland basin associated with crustal thickening of the Pamir during India-Asia collision. Thus, the Tajik Basin provides an example of a long-lived composite basin in a retrowedge position that displays a sensitivity to plate margin processes. Subsidence, sediment accumulation and basin-forming mechanisms are influenced by subduction dynamics, including periods of slab-shallowing and retreat.
    • TAK1 activation of alpha-TAT1 and microtubule hyperacetylation control AKT signaling and cell growth

      Shah, Nirav; Kumar, Sanjay; Zaman, Naveed; Pan, Christopher C.; Bloodworth, Jeffrey C.; Lei, Wei; Streicher, John M.; Hempel, Nadine; Mythreye, Karthikeyan; Lee, Nam Y.; et al. (NATURE PUBLISHING GROUP, 2018-04-27)
      Acetylation of microtubules (MT) confers mechanical stability necessary for numerous functions including cell cycle and intracellular transport. Although alpha TAT1 is a major MT acetyltransferase, how this enzyme is regulated remains much less clear. Here we report TGF-beta-activated kinase 1 (TAK1) as a key activator of alpha TAT1. TAK1 directly interacts with and phosphorylates alpha TAT1 at Ser237 to critically enhance its catalytic activity, as mutating this site to alanine abrogates, whereas a phosphomimetic induces MT hyperacetylation across cell types. Using a custom phospho-alpha TAT1-Ser237 antibody, we screen various mouse tissues to discover that brain contains some of the highest TAK1-dependent alpha TAT1 activity, which, accordingly, is diminished rapidly upon intra-cerebral injection of a TAK1 inhibitor. Lastly, we show that TAK1 selectively inhibits AKT to suppress mitogenic and metabolism-related pathways through MT-based mechanisms in culture and in vivo. Collectively, our findings support a fundamental new role for TGF-beta signaling in MT-related functions and disease.
    • Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

      U'Ren, Jana; Schupp, James; Pearson, Talima; Hornstra, Heidie; Friedman, Christine; Smith, Kimothy; Daugherty, Rebecca; Rhoton, Shane; Leadem, Ben; Georgia, Shalamar; et al. (BioMed Central, 2007)
      BACKGROUND:The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations.RESULTS:B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria.CONCLUSION:The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous typing methods. Given the health threat to humans and livestock and the potential for B. pseudomallei to be released intentionally, MLVA could prove to be an important tool for fine-scale epidemiological or forensic tracking of this increasingly important environmental pathogen.
    • Tangled pasts, healthier futures: Nursing strategies to improve American Indian/Alaska Native health equity

      Pool, Natalie M; Stauber, Leah S; Univ Arizona, Coll Nursing; Univ Arizona, Coll Nursing, Dept Mexican Amer Studies, Inst LGBT Studies (WILEY, 2020-06-16)
      American Indian/Alaska Native (AI/AN) populations in the United States continue to experience overall health inequity, despite significant improvement in health status for nearly all other racial-ethnic groups over the past 30 years. Nurses comprise the bulk of healthcare providers in the U.S. and are in an optimal position to improve AI/AN health by transforming both nursing education and practice. This potential is dependent, however, on nurses' ability to recognize the distinct historical and political conditions through which AI/AN health inequities have been produced and sustained. Nurse providers, educators, and leaders must in turn recognize how the sustained conditions of marginalization and expropriation that underpin current AI/AN health inequities continue to shape contemporary AI/AN health outcomes. This manuscript builds upon the extant literature of AI/AN historical health policy and utilizes decolonial theorizations of nursing and a cultural safety framework to propose a series of immediately actionable steps for nursing intervention into AI/AN health inequity. Ultimately, we suggest that it is crucial for nurses to collaborate with AI/AN individuals and communities across educational and clinical settings to further refine these approaches in alignment with the disciplinary obligation of promoting social justice within healthcare.
    • TaPT: Temperature-Aware Dynamic Cache Optimization for Embedded Systems

      Adegbija, Tosiron; Gordon-Ross, Ann; Univ Arizona, Dept Elect & Comp Engn (MDPI, 2018-03)
      Embedded systems have stringent design constraints, which has necessitated much prior research focus on optimizing energy consumption and/or performance. Since embedded systems typically have fewer cooling options, rising temperature, and thus temperature optimization, is an emergent concern. Most embedded systems only dissipate heat by passive convection, due to the absence of dedicated thermal management hardware mechanisms. The embedded system's temperature not only affects the system's reliability, but can also affect the performance, power, and cost. Thus, embedded systems require efficient thermal management techniques. However, thermal management can conflict with other optimization objectives, such as execution time and energy consumption. In this paper, we focus on managing the temperature using a synergy of cache optimization and dynamic frequency scaling, while also optimizing the execution time and energy consumption. This paper provides new insights on the impact of cache parameters on efficient temperature-aware cache tuning heuristics. In addition, we present temperature-aware phase-based tuning, TaPT, which determines Pareto optimal clock frequency and cache configurations for fine-grained execution time, energy, and temperature tradeoffs. TaPT enables autonomous system optimization and also allows designers to specify temperature constraints and optimization priorities. Experiments show that TaPT can effectively reduce execution time, energy, and temperature, while imposing minimal hardware overhead.
    • Target Capture Sequencing Unravels Rubus Evolution

      Carter, Katherine A; Liston, Aaron; Bassil, Nahla V; Alice, Lawrence A; Bushakra, Jill M; Sutherland, Brittany L; Mockler, Todd C; Bryant, Douglas W; Hummer, Kim E; Univ Arizona, Dept Ecol & Evolutionary Biol (FRONTIERS MEDIA SA, 2019-12-20)
      Rubus (Rosaceae) comprises more than 500 species with additional commercially cultivated raspberries and blackberries. The most recent (> 100 years old) global taxonomic treatment of the genus defined 12 subgenera; two subgenera were subsequently described and some species were rearranged. Intra- and interspecific ploidy levels and hybridization make phylogenetic estimation of Rubus challenging. Our objectives were to estimate the phylogeny of 94 taxonomically and geographically diverse species and three cultivars using chloroplast DNA sequences and target capture of approximately 1,000 low copy nuclear genes; estimate divergence times between major Rubus clades; and examine the historical biogeography of species diversification. Target capture sequencing identified eight major groups within Rubus. Subgenus Orobatus and Subg. Anoplobatus were monophyletic, while other recognized subgenera were para- or polyphyletic. Multiple hybridization events likely occurred across the phylogeny at subgeneric levels, e.g., Subg. Rubus (blackberries) × Subg. Idaeobatus (raspberries) and Subg. Idaeobatus × Subg. Cylactis (Arctic berries) hybrids. The raspberry heritage within known cultivated blackberry hybrids was confirmed. The most recent common ancestor of the genus was most likely distributed in North America. Multiple distribution events occurred during the Miocene (about 20 Ma) from North America into Asia and Europe across the Bering land bridge and southward crossing the Panamanian Isthmus. Rubus species diversified greatly in Asia during the Miocene. Rubus taxonomy does not reflect phylogenetic relationships and subgeneric revision is warranted. The most recent common ancestor migrated from North America towards Asia, Europe, and Central and South America early in the Miocene then diversified. Ancestors of the genus Rubus may have migrated to Oceania by long distance bird dispersal. This phylogeny presents a roadmap for further Rubus systematics research. In conclusion, the target capture dataset provides high resolution between species though it also gave evidence of gene tree/species tree and cytonuclear discordance. Discordance may be due to hybridization or incomplete lineage sorting, rather than a lack of phylogenetic signal. This study illustrates the importance of using multiple phylogenetic methods when examining complex groups and the utility of software programs that estimate signal conflict within datasets.
    • Target patterns in a 2D array of oscillators with nonlocal coupling

      Jaramillo, Gabriela; Venkataramani, Shankar; Univ Arizona, Dept Math (Institute of Physics, London, 2018-07-26)
      We analyze the effect of adding a weak, localized, inhomogeneity to a two dimensional array of oscillators with nonlocal coupling. We propose and also justify a model for the phase dynamics in this system. Our model is a generalization of a viscous eikonal equation that is known to describe the phase modulation of traveling waves in reaction–diffusion systems. We show the existence of a branch of target pattern solutions that bifurcates from the spatially homogeneous state when , the strength of the inhomogeneity, is nonzero and we also show that these target patterns have an asymptotic wavenumber that is small beyond all orders in . The strategy of our proof is to pose a good ansatz for an approximate form of the solution and use the implicit function theorem to prove the existence of a solution in its vicinity. The analysis presents two challenges. First, the linearization about the homogeneous state is a convolution operator of diffusive type and hence not invertible on the usual Sobolev spaces. Second, a regular perturbation expansion in does not provide a good ansatz for applying the implicit function theorem since the nonlinearities play a major role in determining the relevant approximation, which also needs to be 'correct' to all orders in . We overcome these two points by proving Fredholm properties for the linearization in appropriate Kondratiev spaces and using a refined ansatz for the approximate solution which was obtained using matched asymptotics.
    • Target Selection for the SDSS-IV APOGEE-2 Survey

      Zasowski, G.; Cohen, R. E.; Chojnowski, S. Drew; Santana, F.; Oelkers, R. J.; Andrews, B.; Beaton, R. L.; Bender, C.; Bird, J. C.; Bovy, Jo; et al. (IOP PUBLISHING LTD, 2017-10-25)
      APOGEE-2 is a high-resolution, near-infrared spectroscopic survey observing similar to 3. x. 10(5) stars across the entire sky. It is the successor to APOGEE and is part of the Sloan Digital Sky Survey IV (SDSS-IV). APOGEE-2 is expanding on APOGEE's goals of addressing critical questions of stellar astrophysics, stellar populations, and Galactic chemodynamical evolution using (1) an enhanced set of target types and (2) a second spectrograph at Las Campanas Observatory in Chile. APOGEE-2 is targeting red giant branch and red clump stars, RR Lyrae, lowmass dwarf stars, young stellar objects, and numerous other Milky Way and Local Group sources across the entire sky from both hemispheres. In this paper, we describe the APOGEE-2 observational design, target selection catalogs and algorithms, and the targeting-related documentation included in the SDSS data releases.
    • Targeting a Potassium Channel/Syntaxin Interaction Ameliorates Cell Death in Ischemic Stroke

      Yeh, Chung-Yang; Bulas, Ashlyn M.; Moutal, Aubin; Saloman, Jami L.; Hartnett, Karen A.; Anderson, Charles T.; Tzounopoulos, Thanos; Sun, Dandan; Khanna, Rajesh; Aizenman, Elias; et al. (SOC NEUROSCIENCE, 2017-06-07)
      The voltage-gated K+ channel Kv2.1 has been intimately linked with neuronal apoptosis. After ischemic, oxidative, or inflammatory insults, Kv2.1 mediates a pronounced, delayed enhancement of K+ efflux, generating an optimal intracellular environment for caspase and nuclease activity, key components of programmed cell death. This apoptosis-enabling mechanism is initiated via Zn2+-dependent dual phosphorylation of Kv2.1, increasing the interaction between the channel's intracellular C-terminus domain and the SNARE(soluble N-ethylmaleimide-sensitive factor activating protein receptor) protein syntaxin 1A. Subsequently, an upregulation of de novo channel insertion into the plasma membrane leads to the critical enhancement of K+ efflux in damaged neurons. Here, we investigated whether a strategy designed to interfere with the cell death-facilitating properties of Kv2.1, specifically its interaction with syntaxin 1A, could lead to neuroprotection following ischemic injury in vivo. The minimal syntaxin 1A-binding sequence of Kv2.1 C terminus (C1aB) was first identified via a far-Western peptide screen and used to create a protherapeutic product by conjugating C1aB to a cell-penetrating domain. The resulting peptide (TAT-C1aB) suppressed enhanced whole-cell K+ currents produced by a mutated form of Kv2.1 mimicking apoptosis in a mammalian expression system, and protected cortical neurons from slow excitotoxic injury in vitro, without influencing NMDA-induced intracellular calcium responses. Importantly, intraperitoneal administration of TAT-C1aB in mice following transient middle cerebral artery occlusion significantly reduced ischemic stroke damage and improved neurological outcome. These results provide strong evidence that targeting the proapoptotic function of Kv2.1 is an effective and highly promising neuroprotective strategy.
    • Targeting adenosine monophosphate-activated protein kinase (AMPK) in preclinical models reveals a potential mechanism for the treatment of neuropathic pain

      Melemedjian, Ohannes; Asiedu, Marina; Tillu, Dipti; Sanoja, Raul; Yan, Jin; Lark, Arianna; Khoutorsky, Arkady; Johnson, Jessica; Peebles, Katherine; Lepow, Talya; et al. (BioMed Central, 2011)
      Neuropathic pain is a debilitating clinical condition with few efficacious treatments, warranting development of novel therapeutics. We hypothesized that dysregulated translation regulation pathways may underlie neuropathic pain. Peripheral nerve injury induced reorganization of translation machinery in the peripheral nervous system of rats and mice, including enhanced mTOR and ERK activity, increased phosphorylation of mTOR and ERK downstream targets, augmented eIF4F complex formation and enhanced nascent protein synthesis. The AMP activated protein kinase (AMPK) activators, metformin and A769662, inhibited translation regulation signaling pathways, eIF4F complex formation, nascent protein synthesis in injured nerves and sodium channel-dependent excitability of sensory neurons resulting in a resolution of neuropathic allodynia. Therefore, injury-induced dysregulation of translation control underlies pathology leading to neuropathic pain and reveals AMPK as a novel therapeutic target for the potential treatment of neuropathic pain.
    • Targeting NEK2 attenuates glioblastoma growth and radioresistance by destabilizing histone methyltransferase EZH2

      Wang, Jia; Cheng, Peng; Pavlyukov, Marat S.; Yu, Hai; Zhang, Zhuo; Kim, Sung-Hak; Minata, Mutsuko; Mohyeldin, Ahmed; Xie, Wanfu; Chen, Dongquan; et al. (AMER SOC CLINICAL INVESTIGATION INC, 2017-07-24)
      Accumulating evidence suggests that glioma stem cells (GSCs) are important therapeutic targets in glioblastoma (GBM). In this study, we identified NIMA-related kinase 2 (NEK2) as a functional binding protein of enhancer of zeste homolog 2 (EZH2) that plays a critical role in the posttranslational regulation of EZH2 protein in GSCs. NEK2 was among the most differentially expressed kinase-encoding genes in GSC-containing cultures (glioma spheres), and it was required for in vitro clonogenicity, in vivo tumor propagation, and radioresistance. Mechanistically, the formation of a protein complex comprising NEK2 and EZH2 in glioma spheres phosphorylated and then protected EZH2 from ubiquitination-dependent protein degradation in a NEK2 kinase activity-dependent manner. Clinically, NEK2 expression in patients with glioma was closely associated with EZH2 expression and correlated with a poor prognosis. NEK2 expression was also substantially elevated in recurrent tumors after therapeutic failure compared with primary untreated tumors in matched GBM patients. We designed a NEK2 kinase inhibitor, compound 3a (CMP3a), which efficiently attenuated GBM growth in a mouse model and exhibited a synergistic effect with radiotherapy. These data demonstrate a key role for NEK2 in maintaining GSCs in GBM by stabilizing the EZH2 protein and introduce the small-molecule inhibitor CMP3a as a potential therapeutic agent for GBM.
    • Targeting the Cohesive Cluster Phenotype in Chordoma via β1 Integrin Increases Ionizing Radiation Efficacy.

      Harryman, William L; Gard, Jaime M C; Pond, Kelvin W; Simpson, Skyler J; Heppner, Lucas H; Hernandez-Cortes, Daniel; Little, Andrew S; Eschbacher, Jennifer M; Cress, Anne E; Univ Arizona, Canc Ctr, 1515 N Campbell Ave, Tucson, AZ 85724 USA; et al. (ELSEVIER SCIENCE INC, 2017-11-01)
      Chordoma is a rare, radiation-resistant, skull-base and spinal tumor with high local recurrence containing mixed cell-adhesion phenotypes. We characterized DNA damage response (DDR) signaling (γH2AX, pKAP1, pATM) and survival response to ionizing radiation (IR) in human chordoma samples (42 resections, 23 patients) to test if blocking cell adhesion sensitizes U-CH1 tumor cells to IR. U-CH1 cells expressed brachyury, YAP, and laminin adhesion receptors (CD49c, CD49f, CD44), and approximately 15% to 20% of U-CH1 cells featured an α6 integrin-dependent (CD49f) cohesive cluster phenotype, which confers therapeutic resistance and aids metastasis. DDR to IR in U-CH1 cells was compared to normal prostate epithelial (PrEC) and tumor cells (DU145). Flow cytometry showed a dose- and time-dependent increase in γH2AX and pKAP1 expression in all cell lines. However, nearly 50% of U-CH1 cells exhibited nonresponsive phenotype to IR (measured by γH2AX and pKAP1) independent of cell cycle status. Immunofluorescence microscopy verified that only 15% of U-CH1 clustered cells were γH2AX or pKAP1 positive (versus 80% of nonclustered cells) 2 hours following 2-Gy IR. Conversely, both tumor cell lines were uniformly defective in pATM response. HYD1, a synthetic ECM ligand, inhibited DDR through an unresolved γH2AX response. β1 integrin-blocking antibody (AIIB2) decreased cell survival 50% itself and approximately doubled the IR-induced cell kill at all IR doses observed at 2 and 4 weeks posttreatment. These results suggest that a heterogeneity of DDR to IR exists within a chordoma population. Blocking integrin function alone and/or as an adjuvant to IR may eradicate chordomas containing the cohesive cluster phenotype.
    • Targeting the Non-catalytic RVxF Site of Protein Phosphatase-1 With Small Molecules for Ebola Virus Inhibition

      Lin, Xionghao; Ammosova, Tatiana; Choy, Meng S.; Pietzsch, Colette A.; Ivanov, Andrey; Ahmad, Asrar; Saygideğer, Yasemin; Kumari, Namita; Kovalskyy, Dmytro; Üren, Aykut; et al. (FRONTIERS MEDIA SA, 2019-09-13)
      Ebola virus (EBOV) is a non-segmented negative-sense RNA virus that causes a severe human disease. The ongoing EBOV outbreak in the Eastern part of Democratic Republic of the Congo has resulted to date in over 2500 confirmed cases including over 1500 deaths. Difficulties with vaccine administration indicate the necessity for development of new general drugs and therapeutic strategies against EBOV. Host Ser/Thr protein phosphatases, particularly PP1 and PP2A, facilitate EBOV transcription by dephosphorylating the EBOV VP30 protein and switching activity of the polymerase complex toward replication. Previously, we developed small molecule 1E7-03 that targeted host protein phosphatase-1 (PP1) and induces phosphorylation of EBOV VP30 protein thus shifting transcription-replication balance and inhibiting EBOV replication. Here, we developed a new EBOV inhibitor, 1E7-07, that potently inhibits EBOV replication and displays significantly improved metabolic stability when compared to previously described 1E7-03. Proteome analysis of VP30 shows that 1E7-07 increases its phosphorylation on Thr-119 and Ser-124 over 3-fold with p < 0.001, which likely contributes to EBOV inhibition. We analyzed 1E7-07 binding to PP1 using a mass spectrometry-based protein painting approach. Combined with computational docking, protein painting shows that 1E7-07 binds to several PP1 sites including the RVxF site, C-terminal groove and NIPP1-helix binding pocket. Further analysis using surface plasmon resonance and a split NanoBiT system demonstrates that 1E7-07 binds primarily to the RVxF site. Together, detailed analysis of 1E7-07 binding to PP1 and identification of the RVxF site as the main binding site opens up an opportunity for future development of PP1-targeting EBOV inhibitors.