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UFGI publication round-up week 4/3/17

Predicted coreceptor usage at end-stage HIV disease in tissues derived from subjects on antiretroviral therapy with an undetectable plasma viral load.

Author information: Lamers SL1, Fogel GB2, Liu ES2, Nolan DJ3, Salemi M4, Barbier AE5, Rose R5, Singer EJ6, McGrath MS7.

1Bioinfoexperts, LLC, Thibodaux, LA, USA. Electronic address: susanna@bioinfox.com.
2Natural Selection, Inc., San Diego, CA, USA.
3Bioinfoexperts, LLC, Thibodaux, LA, USA; The University of Florida Emerging Pathogens Institute and the Department of Pathology and Laboratory Medicine, Gainesville, FL, USA.
4The University of Florida Emerging Pathogens Institute and the Department of Pathology and Laboratory Medicine, Gainesville, FL, USA.
5Bioinfoexperts, LLC, Thibodaux, LA, USA.
6The National Neurological AIDS Bank, University of California, Los Angeles, CA, USA; David Geffen School of Medicine and Olive View-UCLA Medical Center, Department of Pathology and Laboratory Medicine, Los Angeles, USA.
7The AIDS and Cancer Specimen Resource, San Francisco, CA, USA; The University of California Department of Medicine, San Francisco, CA, USA.
Journal: Infection, Genetics and Evolution : Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases

Date of e-pub: April 2017

Abstract: HIV cure research is increasingly focused on anatomical tissues as sites for residual HIV replication during combined antiretroviral therapy (cART). Tissue-based HIV could contribute to low-level immune activation and viral rebound over the course of infection and could also influence the development of diseases, such as atherosclerosis, neurological disorders and cancers. cART-treated subjects have a decreased and irregular presence of HIV among tissues, which has resulted in a paucity of actual evidence concerning how or if HIV persists, replicates and evolves in various anatomical sites during therapy. In this study, we pooled 1806 HIV envelope V3 loop sequences from twenty-six tissue types (seventy-one total tissues) of six pre-cART subjects, four subjects with an unknown cART history who died with profound AIDS, and five subjects who died while on cART with an undetectable plasma viral load. A computational approach was used to assess sequences for their ability to utilize specific cellular coreceptors (R5, R5 and X4, or X4). We found that autopsied tissues obtained from virally suppressed cART+ subjects harbored both integrated and expressed viruses with similar coreceptor usage profiles to subjects with no or ineffective cART therapy (i.e., significant plasma viral load at death). The study suggests that tissue microenvironments provide a sanctuary for the continued evolution of HIV despite cART.

 

 

Deep reticulation and incomplete lineage sorting obscure the diploid phylogeny of rain-lilies and allies (Amaryllidaceae tribe Hippeastreae).

Author information: García N1, Folk RA2, Meerow AW3, Chamala S4, Gitzendanner MA5, Souza de Oliveira R6, Soltis DE7, Soltis PS8.

1Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Av. Santa Rosa 11315, La Pintana, Santiago, Chile; Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: nicogarciab@gmail.com.
2Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA. Electronic address: ryanfolk@ufl.edu.
3USDA-ARS-SHRS-National Germplasm Repository, 13601 Old Cutler Road, Miami, FL 33158, USA. Electronic address: Alan.Meerow@ars.usda.gov.
4Department of Biology, University of Florida, Gainesville, FL 32611, USA; Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL 32610, USA. Electronic address: srikarchamala@gmail.com.
5Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA. Electronic address: magitz@ufl.edu.
6GaTE Laboratory, Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, IBUSP, Rua do Matão 277, CEP: 05508-090 São Paulo, SP, Brazil. Electronic address: rsolive1@gmail.com.
7Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: dsoltis@ufl.edu.
8Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA; Department of Biology, University of Florida, Gainesville, FL 32611, USA; Genetics Institute, University of Florida, Gainesville, FL 32610, USA. Electronic address: psoltis@flmnh.ufl.edu.
Journal: Molecular Phylogenetics and Evolution

Date of e-pub: April 2017

Abstract: Hybridization is a frequent and important force in plant evolution. Next-generation sequencing (NGS) methods offer new possibilities for clade resolution and ambitious sampling of gene genealogies, yet difficulty remains in detecting deep reticulation events using currently available methods. We reconstructed the phylogeny of diploid representatives of Amaryllidaceae tribe Hippeastreae to test the hypothesis of ancient hybridizations preceding the radiation of its major subclade, Hippeastrinae. Through hybrid enrichment of DNA libraries and NGS, we obtained data for 18 nuclear loci through a curated assembly approach and nearly complete plastid genomes for 35 ingroup taxa plus 5 outgroups. Additionally, we obtained alignments for 39 loci through an automated assembly algorithm. These data were analyzed with diverse phylogenetic methods, including concatenation, coalescence-based species tree estimation, Bayesian concordance analysis, and network reconstructions, to provide insights into the evolutionary relationships of Hippeastreae. Causes for gene tree heterogeneity and cytonuclear discordance were examined through a Bayesian posterior predictive approach (JML) and coalescent simulations. Two major clades were found, Hippeastrinae and Traubiinae, as previously reported. Our results suggest the presence of two major nuclear lineages in Hippeastrinae characterized by different chromosome numbers: 1) Tocantinia and Hippeastrum with 2n = 22, and 2) Eithea, Habranthus, Rhodophiala, and Zephyranthes mostly with 2n = 12, 14, and 18. Strong cytonuclear discordance was confirmed in Hippeastrinae, and a network scenario with at least six hybridization events is proposed to reconcile nuclear and plastid signals, along a backbone that may also have been affected by incomplete lineage sorting at the base of each major subclade.

 

 

Sexual Reproduction in the Citrus Black Spot Pathogen, Phyllosticta citricarpa.

Author information: Tran NT1, Miles AK1, Dietzgen RG1, Dewdney MM1, Zhang K1, Rollins JA1, Drenth A1.

1First, second, and seventh authors: Centre for Plant Science, Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Ecosciences Precinct, 41 Boggo Road, Dutton Park, QLD 4102, Australia; third author: Centre for Plant Science, QAAFI, The University of Queensland, Queensland Bioscience Precinct, St. Lucia, QLD 4072, Australia; fourth and fifth authors: Citrus Research and Education Centre, University of Florida, Lake Alfred; and sixth author: Department of Plant Pathology, University of Florida, Gainesville.
Journal: Phytopathology

Date of e-pub: April 2017

Abstract: Citrus black spot (Phyllosticta citricarpa) causes fruit blemishes and premature fruit drop, resulting in significant economic losses in citrus growing areas with summer rainfall across the globe. The mating type locus of P. citricarpa has recently been characterized, revealing the heterothallic nature of this pathogen. However, insight into the occurrence of mating and the impact of completing the sexual cycle of P. citricarpa was lacking. To investigate the occurrence and impact of sexual reproduction, we developed a method to reliably, and for the first time, produce ascospores of P. citricarpa on culture media. To demonstrate meiosis during the mating process, we identified recombinant genotypes through multilocus genotyping of single ascospores. Because the process of fertilization was not well understood, we experimentally determined that fertilization of P. citricarpa occurs via spermatization. Our results demonstrate that P. citricarpa is heterothallic and requires isolates of different MAT idiomorphs to be in direct physical contact, or for spermatia to fulfill their role as male elements to fertilize the receptive organs, in order to initiate the mating process. The impact of mating on the epidemiology of citrus black spot in the field is discussed.

 

 

Obsessive-Compulsive Disorder: Advances in Diagnosis and Treatment.

Author information: Hirschtritt ME1, Bloch MH2, Mathews CA3.

1Department of Psychiatry, University of California, San Francisco.
2Department of Psychiatry and Yale Child Study Center, Yale University School of Medicine, New Haven, Connecticut.
3Department of Psychiatry and University of Florida Genetics Institute, Gainesville.
Journal: JAMA

Date of e-pub: April 2017

Abstract: Obsessive-compulsive disorder (OCD) is a neuropsychiatric disorder associated with significant impairment and a lifetime prevalence of 1% to 3%; however, it is often missed in primary care settings and frequently undertreated.

To review the most current data regarding screening, diagnosis, and treatment options for OCD.

We searched PubMed, EMBASE, and PsycINFO to identify randomized controlled trials (RCTs), meta-analyses, and systematic reviews that addressed screening and diagnostic and treatment approaches for OCD among adults (≥18 years), published between January 1, 2011, and September 30, 2016. We subsequently searched references of retrieved articles for additional reports. Meta-analyses and systematic reviews were prioritized; case series and reports were included only for interventions for which RCTs were not available.

Among 792 unique articles identified, 27 (11 RCTs, 11 systematic reviews or meta-analyses, and 5 reviews/guidelines) were selected for this review. The diagnosis of OCD was revised for the Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition, which addresses OCD separately from anxiety disorders and contains specifiers to delineate the presence of tics and degree of insight. Treatment advances include increasing evidence to support the efficacy of online-based dissemination of cognitive behavioral therapies, which have demonstrated clinically significant decreases in OCD symptoms when conducted by trained therapists. Current evidence continues to support the use of selective serotonin reuptake inhibitors as first-line pharmacologic interventions for OCD; however, more recent data support the adjunctive use of neuroleptics, deep-brain stimulation, and neurosurgical ablation for treatment-resistant OCD. Preliminary data suggest safety of other agents (eg, riluzole, ketamine, memantine, N-acetylcysteine, lamotrigine, celecoxib, ondansetron) either in combination with selective serotonin reuptake inhibitors or as monotherapy in the treatment of OCD, although their efficacy has not yet been established.

The dissemination of computer-based cognitive behavioral therapy and improved evidence supporting it represent a major advancement in treatment of OCD. Although cognitive behavioral therapy with or without selective serotonin reuptake inhibitors remains a preferred initial treatment strategy, increasing evidence that supports the safety and efficacy of neuroleptics and neuromodulatory approaches in treatment-resistant cases provides alternatives for patients whose condition does not respond to first-line interventions.

 

 

Mutant Huntingtin Disrupts the Nuclear Pore Complex.

Author information: Grima JC1, Daigle JG2, Arbez N3, Cunningham KC4, Zhang K2, Ochaba J5, Geater C5, Morozko E5, Stocksdale J5, Glatzer JC2, Pham JT6, Ahmed I7, Peng Q7, Wadhwa H8, Pletnikova O9, Troncoso JC10, Duan W11, Snyder SH3, Ranum LP12, Thompson LM5, Lloyd TE13, Ross CA3, Rothstein JD14.

1Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
2Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
3Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
4Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
5Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA 92697, USA.
6Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
7Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
8Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
9Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
10Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
11Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Psychiatry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
12Center for NeuroGenetics, Departments of Molecular Genetics and Microbiology and Neurology, College of Medicine, Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA.
13Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
14Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Brain Science Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Program in Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA. Electronic address: jrothstein@jhmi.edu.
Journal: Neuron

Date of e-pub: April 2017

Abstract: Huntington’s disease (HD) is caused by an expanded CAG repeat in the Huntingtin (HTT) gene. The mechanism(s) by which mutant HTT (mHTT) causes disease is unclear. Nucleocytoplasmic transport, the trafficking of macromolecules between the nucleus and cytoplasm, is tightly regulated by nuclear pore complexes (NPCs) made up of nucleoporins (NUPs). Previous studies offered clues that mHTT may disrupt nucleocytoplasmic transport and a mutation of an NUP can cause HD-like pathology. Therefore, we evaluated the NPC and nucleocytoplasmic transport in multiple models of HD, including mouse and fly models, neurons transfected with mHTT, HD iPSC-derived neurons, and human HD brain regions. These studies revealed severe mislocalization and aggregation of NUPs and defective nucleocytoplasmic transport. HD repeat-associated non-ATG (RAN) translation proteins also disrupted nucleocytoplasmic transport. Additionally, overexpression of NUPs and treatment with drugs that prevent aberrant NUP biology also mitigated this transport defect and neurotoxicity, providing future novel therapy targets.

 

 

QueF-Like, a Non-Homologous Archaeosine Synthase from the Crenarchaeota.

Author information: Bon Ramos A1, Bao L2, Turner B3, de Crécy-Lagard V4, Iwata-Reuyl D5.

1Department of Chemistry, Portland State University, Portland, OR 97207, USA. efectegerundi@gmail.com.
2Department of Chemistry, Portland State University, Portland, OR 97207, USA. bold@imau.edu.cn.
3Department of Chemistry, Portland State University, Portland, OR 97207, USA. beturner@pdx.edu.
4The Department of Microbiology and Cell Science Department, University of Florida, Gainesville, FL 32611, USA. vcrecy@ufl.edu.
5Department of Chemistry, Portland State University, Portland, OR 97207, USA. iwatard@pdx.edu.
Journal: Biomolecules

Date of e-pub: April 2017

Abstract: Archaeosine (G⁺) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G⁺ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis. In the Euryarchaeota, the last step of the archaeosine biosynthetic pathway involves the amidation of a nitrile group on an archaeosine precursor to give formamidine, a reaction catalyzed by the enzyme Archaeosine Synthase (ArcS). Most Crenarchaeota lack ArcS, but possess two proteins that inversely distribute with ArcS and each other, and are implicated in G⁺ biosynthesis. Here, we describe biochemical studies of one of these, the protein QueF-like (QueF-L) from Pyrobaculum calidifontis, that demonstrate the catalytic activity of QueF-L, establish where in the pathway QueF-L acts, and identify the source of ammonia in the reaction.

 

 

Alpha-1 Antitrypsin PI MZ Genotype Is Associated with COPD in Two Racial Groups.

Author information: Foreman MG1, Wilson C2, DeMeo DL3, Hersh CP4, Beaty TH5, Cho MH6, Ziniti J7, Curran-Everett D8, Criner G9, Hokanson JE10, Brantly M11, Rouhani FN12, Sandhaus RA13, Crapo JD14, Silverman EK15,16; COPDGene Investigators.

1Morehouse School of Medicine, Pulmonary and Critical Care , 720 Westview Dr. SW , Atlanta, Georgia, United States , 30310 ; mforeman@msm.edu.
2National Jewish Health, Denver, Colorado, United States ; WilsonC@NJHealth.org.
3Brigham and Womens, Boston, Massachusetts, United States ; redld@channing.harvard.edu.
4Brigham and Women’s Hospital, Channing Laboratory , 181 Longwood Ave , Boston, Massachusetts, United States , 02115 ; craig.hersh@channing.harvard.edu.
5Bloombert School of Public Health, Baltimore, Maryland, United States ; tbeaty1@jhu.edu.
6Harvard Medical School, Channing Division of Respiratory Medicine , 181 Longwood Avenue , Boston, Massachusetts, United States , 02115 ; remhc@channing.harvard.edu.
7Channing Laboratory, Boston, Massachusetts, United States ; rejpz@channing.harvard.edu.
8National Jewish Health, Denver, Colorado, United States ; everettd@njhealth.org.
9Temple University Hospital, Pulm & Crit Care Medicine, Philadelphia, Pennsylvania, United States ; gerard.criner@tuhs.temple.edu.
10University of Colorado Anschutz Medical Campus, Epidemiology , 13001 E 17th Place , Mail Stop B119 , Aurora, Colorado, United States , 80045 ; John.Hokanson@ucdenver.edu.
11University of Florida College of Medicine, 12233, Division of Pulmonary, Critical Care and Sleep Medicine, Gainesville, Florida, United States ; Mark.Brantly@medicine.ufl.edu.
12University of Florida College of Medicine, 12233, Gainesville, Florida, United States ; Farshid.Rouhani@medicine.ufl.edu.
13National Jewish Health, Denver, Colorado, United States ; sandhausr@njhealth.org.
14National Jewish Medical & Research Ctr. , Professor of Medicine & Pathology , 1400 Jackson Street , Denver, Colorado, United States , 80205 ; crapoj@njhealth.org.
15Brigham and Women’s Hospital, Channing Division of Network Medicine, Boston, Massachusetts, United States.
16Brigham and Women’s Hospital, Division of Pulmonary Critical Care Medicine, Boston, Massachusetts, United States ; reeks@channing.harvard.edu.
Journal: Annals of the American Thoracic Society

Date of e-pub: April 2017

Abstract: Alpha-1 antitrypsin deficiency, primarily caused by homozygosity for the Z allele of the SERPINA1 gene, is a well-established genetic cause of chronic obstructive pulmonary disease (COPD). Whether the heterozygous PI MZ genotype for alpha-1 antitrypsin confers increased risk for COPD has been debated.

We analyzed 8271 subjects in the COPDGene Study, hypothesizing that PI MZ would independently associate with COPD and COPD-related phenotypes.

The Genetic Epidemiology of COPD (COPDGene) Study is a multi-ethnic, crosssectional, observational cohort of Non-Hispanic White and African American current and former smokers with > 10 pack-years of smoking enrolled for detailed clinical and genetic studies of COPD and COPD-related traits. We performed multivariate logistic regression analysis for moderate-to-severe COPD and assessed PI genotype with other relevant covariates in models stratified by race. We analyzed quantitative characteristics from volumetric computed tomography with generalized linear models controlling for genotype, scanner type, and similar covariates.

White PI MZ COPDGene subjects had significantly lower lung function, FEV1 percent predicted 68 + 28 vs. 75 + 27 (p = 0.0005) and FEV1/FVC ratio 0.59 + 0.18 vs. 0.63 + 0.17 (p = 0.0008), and more radiographic emphysema (p = 0.001), than subjects without alpha-1 antitrypsin Z risk alleles. Similarly, African American PI MZ subjects had lower lung function, FEV1 percent predicted 65 + 33 vs. 84 + 25 (p = 0.009) and FEV1/FVC 0.61 + 0.21 vs. 0.71 + 0.15, (p = 0.03).

In the COPDGene Study, we demonstrate that PI MZ heterozygous individuals who smoke are at increased risk for COPD and obstructive lung function impairment compared to non-Z-allele carriers, regardless of race. Although severe alpha-1 antitrypsin deficiency is uncommon in African Americans, our study adds further support for initial targeted detection of all COPD subjects for alpha-1 antitrypsin deficiency, including African Americans. Clinical Trial registered with clinicaltrials.gov (NCT 00608784).

 

 

Functional characterization of LotP from Liberibacter asiaticus.

Author information: Loto F1,2, Coyle JF1, Padgett KA1,3, Pagliai FA1, Gardner CL1, Lorca GL1, Gonzalez CF1.

1Department of Microbiology and Cell Science, Genetics Institute, Institute of Food and Agricultural Sciences, University of Florida, 2033 Mowry road, PO Box 103610, Gainesville, FL 32610-3610, USA.
2PROIMI Planta Piloto de Procesos Industriales Microbiológicos, CONICET, Tucumán, Argentina.
3Department of Microbiology and Cell Science, Undergraduate Research Program, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, USA.
Journal: Microbial Biotechnology

Date of e-pub: April 2017

Abstract: Liberibacter asiaticus is an unculturable parasitic bacterium of the alphaproteobacteria group hosted by both citrus plants and a psyllid insect vector (Diaphorina citri). In the citrus tree, the bacteria thrive only inside the phloem, causing a systemically incurable and deadly plant disease named citrus greening or Huanglongbing. Currently, all commercial citrus cultivars in production are susceptible to L. asiaticus, representing a serious threat to the citrus industry worldwide. The technical inability to isolate and culture L. asiaticus has hindered progress in understanding the biology of this bacterium directly. Consequently, a deep understanding of the biological pathways involved in the regulation of host-pathogen interactions becomes critical to rationally design future and necessary strategies of control. In this work, we used surrogate strains to evaluate the biochemical characteristics and biological significance of CLIBASIA_03135. This gene, highly induced during early stages of plant infection, encodes a 23 kDa protein and was renamed in this work as LotP. This protein belongs to an uncharacterized family of proteins with an overall structure resembling the LON protease N-terminus. Co-immunoprecipitation assays allowed us to identify the Liberibacter chaperonin GroEL as the main LotP-interacting protein. The specific interaction between LotP and GroEL was reconstructed and confirmed using a two-hybrid system in Escherichia coli. Furthermore, it was demonstrated that LotP has a native molecular weight of 44 kDa, corresponding to a dimer in solution with ATPase activity in vitro. In Liberibacter crescens, LotP is strongly induced in response to conditions with high osmolarity but repressed at high temperatures. Electrophoretic mobility shift assay (EMSA) results suggest that LotP is a member of the LdtR regulon and could play an important role in tolerance to osmotic stress.

 

 

The Causes of Dispersal and the Cost of Carryover Effects for an Endangered Bird in a Dynamic Wetland Landscape.

Author information: Robertson EP1, Fletcher RJ Jr1, Austin JD1.

1Department of Wildlife Ecology and Conservation, University of Florida, PO Box 110430, 110 Newins-Ziegler Hall, Gainesville, FL, 32611-0430, USA.
Journal: The Journal of Animal Ecology

Date of e-pub: April 2017

Abstract: 1.The decision to disperse or remain philopatric between breeding seasons has important implications for both ecology and evolution, including the potential for carryover effects, where an individual’s previous history affects their current performance. Carryover effects are increasingly documented although underlying mechanisms remain unclear. 2.Here we test for potential carryover effects and their mechanisms by uniting hypotheses for the causes and consequences of habitat selection and dispersal across space and time. We linked hypotheses regarding different types of factors and information (environmental conditions, personal and public information) predicted to impact reproductive success and dispersal for an endangered, wetland-dependent bird, the snail kite (Rostrhamus sociabilis plumbeus). To do so, we coupled structural equation modeling with 20 years of mark-recapture and nesting data across the breeding range of this species to isolate potential direct and indirect effects of these factors. 3.We found that water depth at nest sites explained subsequent emigration rates via an indirect path through the use of personal, not public, information. Importantly, we found that these dispersers tended to initiate nests later the following breeding season. This pattern explained a phenological mismatch of nesting with hydrological conditions, whereby immigrants tended to nest later, late nesters tended to experience lower water depths, higher nest failure occurred at lower water depths, and higher nest failure explained subsequent breeding dispersal. 4.These results identified a novel potential mechanism for carryover effects: a phenological mismatch with environmental conditions (water depth) that occurred potentially due to time costs of dispersal. Our results also highlighted a substantial benefit of philopatry-NDASH-earlier initiation of reproduction-NDASH-which allows philopatric individuals to better coincide with environmental conditions that are beneficial for successful reproduction. 5.These results have implications for our mechanistic understanding and prediction of carryover effects, and emphasize that local conservation strategies, such as water management, can explain future demography at distant sites connected through dispersal. This article is protected by copyright. All rights reserved.

 

 

Dual-Phase Iontophoresis for the Delivery of Antisense Oligonucleotides.

Author information: Gibson DJ1, Tuli SS2, Schultz GS1.

1Institute for Wound Research, University of Florida , Gainesville, Florida.
2Department of Ophthalmology, University of Florida , Gainesville, Florida.
Journal: Nucleic Acid Therapeutics

Date of e-pub: April 2017

Abstract: In support of ongoing research in the study of corneal and skin wound healing, we sought to improve on previously published results by using iontophoresis to deliver RNA interference-based oligonucleotides. By using a electromechanics-based approach, we were able to devise a two-phase solution that separated the buffering solution from the antisense oligonucleotide (ASO) solution. The separation was obtained by making the drug solution a higher density than the buffer, leading it to sink directly onto the tissue surface. This change immediately decreased the distance that the ASO would have to travel before delivery. The changes enabled delivery into ex vivo skin and corneas in 10 or fewer minutes and into in vivo corneas in 5 min. In vivo studies demonstrated short-term bioavailability of at least 24 h, a lack of chemical or thermal injury, a lack of interference in the healing of a corneal injury, and an antisense effect till at least day 7, but not day 14. The only side-effect observed was postdelivery edema that was not present when the vehicle alone was iontophoresed. This suggests that electro-osmotic flow from the delivery chamber was not the mechanism, but that the delivered solute likely increased the tissue’s osmolarity. These results support the continued development and utilization of this ASO delivery approach in research-grade oligonucleotides to probe molecular biological pathways and in support of testing therapeutic ASOs in the skin and cornea.

 

 

Lung Tissue Concentrations of Pyrazinamide among Patients with Drug-Resistant Pulmonary Tuberculosis.

Author information: Kempker RR1, Heinrichs MT2, Nikolaishvili K3, Sabulua I3, Bablishvili N3, Gogishvili S3, Avaliani Z3, Tukvadze N3, Little B4, Bernheim A4, Read TD5, Guarner J6, Derendorf H2, Peloquin CA2, Blumberg HM5,7, Vashakidze S3.

1Division of Infectious Diseases Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA. rkempke@emory.edu.
2University of Florida, College of Pharmacy, Gainesville, FL, USA.
3National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia.
4Department of Radiology, Emory University School of Medicine.
5Division of Infectious Diseases Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.
6Department of Pathology and Laboratory Medicine, Emory University School of Medicine.
7Departments of Epidemiology and Global Health, Rollins School of Public Health, Emory University.
Journal: Antimicrobial Agents and Chemotherapy

Date of e-pub: April 2017

Abstract: Background: Improved knowledge regarding tissue penetration of anti-tuberculosis drugs may help optimize drug management.Methods: Patients with drug-resistant pulmonary tuberculosis undergoing adjunctive surgery were enrolled. Serial serum samples were collected and microdialysis was performed using ex vivo lung tissue to measure pyrazinamide drug concentrations.Results: Among ten patients, the median pyrazinamide dose was 24.7 mg/kg. Imaging revealed predominant lung lesions as cavitary (6), mass-like (3), or consolidative (1). On histopathology examination, all tissue samples had necrosis; eight had a pH ≤5.5. Two patients had positive tissue cultures for M. tuberculosis (pH of 5.5, 7.2). Nine of 10 patients had a serum pyrazinamide Cmax within the recommended range of 20-60 μg/ml. The median free pyrazinamide lung tissue concentration was 20.96 μg/ml. The median tissue to serum pyrazinamide concentration ratio was 0.77 (range 0.54-0.93). There was a significant inverse correlation between tissue pyrazinamide concentrations and the amount of necrosis (r=-0.66, p=0.04) and acid-fast bacilli (r=-0.75, p=0.01) identified by histopathology.Discussion: We found good penetration of pyrazinamide into lung tissue among pulmonary TB patients with a variety of radiological lesion types. Our pH tissue results revealed most lesions had a pH conducive to pyrazinamide activity. The tissue penetration of pyrazinamide highlights its importance in both drug-susceptible and drug-resistant anti-tuberculosis treatment regimens.

 

 

Structure Determination of Mycobacterium tuberculosis Serine Protease Hip1 (Rv2224c).

Author information: Naffin-Olivos JL1, Daab A1,2, White A1, Goldfarb NE3, Milne AC1, Liu D4, Baikovitz J5, Dunn BM6, Rengarajan J7, Petsko GA8, Ringe D1.

1Rosenstiel Basic Medical Sciences Research Center, Brandeis University , Waltham, Massachusetts 02454, United States.
2Department of Biochemistry, Brandeis University , Waltham, Massachusetts 02454, United States.
3Department of Pharmaceutical and Biomedical Sciences, California Health Sciences University , Clovis, California 93612, United States.
4Department of Chemistry and Biochemistry, Loyola University Chicago , Chicago, Illinois 60660, United States.
5Department of Biology, Brandeis University , Waltham, Massachusetts 02454, United States.
6Department of Biochemistry and Molecular Biology, University of Florida , Gainesville, Florida 32610, United States.
7Division of Infectious Diseases, Department of Medicine, Emory Vaccine Center, Emory University School of Medicine , Atlanta, Georgia 30329, United States.
8Appel Alzheimer’s Disease Research Institute, Weill Cornell Medical College , New York, New York 10021, United States.
Journal: Biochemistry

Date of e-pub: April 2017

Abstract: The Mycobacterium tuberculosis (Mtb) serine protease Hip1 (hydrolase important for pathogenesis; Rv2224c) promotes tuberculosis (TB) pathogenesis by impairing host immune responses through proteolysis of a protein substrate, Mtb GroEL2. The cell surface localization of Hip1 and its immunomodulatory functions make Hip1 a good drug target for new adjunctive immune therapies for TB. Here, we report the crystal structure of Hip1 to a resolution of 2.6 Å and the kinetic studies of the enzyme against model substrates and the protein GroEL2. The structure shows a two-domain protein, one of which contains the catalytic residues that are the signature of a serine protease. Surprisingly, a threonine is located within the active site close enough to hydrogen bond with the catalytic residues Asp463 and His490. Mutation of this residue, Thr466, to alanine established its importance for function. Our studies provide insights into the structure of a member of a novel family of proteases. Knowledge of the Hip1 structure will aid in designing inhibitors that could block Hip1 activity.

 

 

Molecular Recognition-Based DNA Nanoassemblies on the Surfaces of Nanosized Exosomes.

Author information: Wan S1, Zhang L1,2, Wang S1, Liu Y1,2, Wu C1,2, Cui C1, Sun H1, Shi M1,2, Jiang Y1,2, Li L1, Qiu L1,2, Tan W1,2.

1Center for Research at Bio/Nano Interface, Department of Chemistry and Department of Physiology and Functional Genomics, UF Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States.
2Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Life Sciences, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha 410082, China.
Journal: Journal of the American Chemical Society

Date of e-pub: April 2017

Abstract: Exosomes are membrane-enclosed extracellular vesicles derived from cells, carrying biomolecules that include proteins and nucleic acids for intercellular communication. Owning to their advantages of size, structure, stability, and biocompatibility, exosomes have been used widely as natural nanocarriers for intracellular delivery of theranostic agents. Meanwhile, surface modifications needed to endow exosomes with additional functionalities remain challenging by their small size and the complexity of their membrane surfaces. Current methods have used genetic engineering and chemical conjugation, but these strategies require complex manipulations and have only limited applications. Herein, we present an aptamer-based DNA nanoassemblies on exosome surfaces. This in situ assembly method is based on molecular recognition between DNA aptamers and their exosome surface markers, as well as DNA hybridization chain reaction initiated by an aptamer-chimeric trigger. It further demonstrated selective assembly on target cell-derived exosomes, but not exosomes derived from nontarget cells. The present work shows that DNA nanostructures can successfully be assembled on a nanosized organelle. This approach is useful for exosome modification and functionalization, which is expected to have broad biomedical and bioanalytical applications.

 

 

The Balance between CD8+ T Cell-Mediated Clearance of AAV-Encoded Antigen in the Liver and Tolerance Is Dependent on the Vector Dose.

Author information: Kumar SR1, Hoffman BE1, Terhorst C2, de Jong YP3, Herzog RW4.

1Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
2Division of Immunology, Harvard Medical Center, Boston, MA 02115, USA.
3Division of Gastroenterology and Hepatology, Weill Cornell Medicine, New York, NY 10021, USA.
4Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610, USA. Electronic address: rherzog@ufl.edu.
Journal: Molecular Therapy : The Journal of the American Society of Gene Therapy

Date of e-pub: April 2017

Abstract: The liver continuously receives antigens from circulation and the gastrointestinal tract. A complex immune regulatory system has evolved in order to both limit inflammation and promote tolerance in the liver. Although in situ immune tolerance mechanisms enable successful gene therapy and liver transplantation, at the same time they facilitate chronic infections by pathogens such as hepatitis viruses. It is, however, poorly understood why hepatocytes infected with hepatitis viruses or transduced with adeno-associated virus (AAV)-based vectors may be rejected by CD8+ T cells several months later. We found that hepatic transfer of limited doses of an AAV-ovalbumin vector rapidly induced antigen-specific CD8+ T cells that only became functionally competent after >2 months. At this time, CD8+ T cells had downregulated negative checkpoint markers, e.g., the programmed death 1 [PD-1] receptor, and upregulated expression of relevant cytokines. At further reduced vector dose, only intrahepatic rather than systemic CD8+ T cell responses occurred, showing identical delay in antigen clearance. In contrast, PD-1-deficient mice rapidly cleared ovalbumin. Interestingly, higher vector dose directed sustained transgene expression without CD8+ T cell responses. Regulatory T cells, IL-10 expression, and Fas-L contributed to high-dose tolerance. Thus, viral vector doses profoundly impact CD8+ T cell responses.

 

 

First Synthesis of an Oridonin-Conjugated Iridium(III) Complex for the Intracellular Tracking of NF-κB in Living Cells.

Author information: Wang W1, Yang C2, Lin S1, Vellaisamy K1, Li G2, Tan W3,4, Leung CH2, Ma DL1.

1Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong, P. R. China.
2State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, P. R. China.
3Department of Chemistry, and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, USA.
4Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, Department of Chemistry, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha, P. R. China.
Journal: Chemistry (Weinheim an der Bergstrasse, Germany)

Date of e-pub: April 2017

Abstract: NF-κB is a critical transcription factor that plays an important role in mediating inflammation, the immune response, and cell proliferation. The activation of NF-κB leads to an enhancement of proinflammatory mediator expression, which is implicated in the pathogenesis of a variety of diseases. Therefore, methods that allow the intracellular tracking of NF-κB are particularly attractive because they can provide information regarding the pathways or stimulation responses that are involved in the activation of NF-κB. In this work, we report a novel platform to track intracellular NF-κB by employing the conjugated iridium(III) complex 1, which was synthesized through the unique combination of a luminescent iridium(III) moiety with the natural product oridonin. Experiments conducted with p50 knockdown cells revealed that complex 1 could detect the p50 subunit of NF-κB in cellulo. Furthermore, complex 1 tracked NF-κB translocation induced by tumor necrosis factor-α (TNF-α) as a model stimulus, without affecting the translocation process itself. To the best of our knowledge, complex 1 is the first metal-based compound that has been reported to be capable of monitoring intracellular NF-κB in living cells.

 

 

Systemic Injection of RPE65-Programmed Bone Marrow-Derived Cells Prevents Progression of Chronic Retinal Degeneration.

Author information: Qi X1, Pay SL2, Yan Y3, Thomas J Jr4, Lewin AS4, Chang LJ4, Grant MB1, Boulton ME5.

1Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
2Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
3Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610, USA.
4Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA.
5Department of Ophthalmology, Eugene and Marilyn Glick Eye Institute, Indiana University School of Medicine, Indianapolis, IN 46202, USA. Electronic address: mboulton@iupui.edu.
Journal: Molecular Therapy : The Journal of the American Society of Gene Therapy

Date of e-pub: April 2017

Abstract: Bone marrow stem and progenitor cells can differentiate into a range of non-hematopoietic cell types, including retinal pigment epithelium (RPE)-like cells. In this study, we programmed bone marrow-derived cells (BMDCs) ex vivo by inserting a stable RPE65 transgene using a lentiviral vector. We tested the efficacy of systemically administered RPE65-programmed BMDCs to prevent visual loss in the superoxide dismutase 2 knockdown (Sod2 KD) mouse model of age-related macular degeneration. Here, we present evidence that these RPE65-programmed BMDCs are recruited to the subretinal space, where they repopulate the RPE layer, preserve the photoreceptor layer, retain the thickness of the neural retina, reduce lipofuscin granule formation, and suppress microgliosis. Importantly, electroretinography and optokinetic response tests confirmed that visual function was significantly improved. Mice treated with non-modified BMDCs or BMDCs pre-programmed with LacZ did not exhibit significant improvement in visual deficit. RPE65-BMDC administration was most effective in early disease, when visual function and retinal morphology returned to near normal, and less effective in late-stage disease. This experimental paradigm offers a minimally invasive cellular therapy that can be given systemically overcoming the need for invasive ocular surgery and offering the potential to arrest progression in early AMD and other RPE-based diseases.

 

NOTE: These abstracts were retrieved from the U.S. National Library of Medicine website managed in collaboration with the U.S. National Library of Medicine

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