UFGI publication round-up week 01/30/2017

Association among gestation length and health, production, and reproduction in Holstein cows and implications for their offspring.

Author information: Vieira-Neto A1, Galvão KN2, Thatcher WW1, Santos JE3.

1Department of Animal Sciences, Gainesville 32611; D. H. Barron Reproductive and Perinatal Biology Research Program, Gainesville 32611.
2D. H. Barron Reproductive and Perinatal Biology Research Program, Gainesville 32611; Department of Large Animal Clinical Sciences, University of Florida, Gainesville 32611.
3Department of Animal Sciences, Gainesville 32611; D. H. Barron Reproductive and Perinatal Biology Research Program, Gainesville 32611. Electronic address: jepsantos@ufl.edu.
Journal: Journal of Dairy Science

Date of e-pub: February 2017

Abstract: Objectives were to evaluate associations among gestation length (GL) and performance in Holstein cows and their offspring. A total of 8,095 Holstein cows and 3,635 female offspring born alive on 2 farms using only artificial insemination (AI) were evaluated. Gestation length averaged 276 ± 6 d in the 8,095 dams, and it was categorized as short (SGL; at least 1 SD below the population mean; mean = 266 d, range 256 to 269 d), average (AGL; population mean ± 1 SD; mean = 276 d, range 270 to 282 d), or long (LGL; at least 1 SD above the population mean; mean = 285 d, range 283 to 296 d). Responses evaluated in dams included incidence of diseases within 90 d in milk (DIM), pregnancy at first AI and by 300 DIM, and time to pregnancy. Milk yield and removal from the herd by culling or death were recorded for the first 300 DIM. Responses evaluated in female offspring born alive included removal from the herd and reproductive performance. Within primiparous cows, those with SGL had greater incidence of stillbirth, retained placenta, and metritis than primiparous with AGL or LGL; however, within multiparous cows, those with SGL or LGL had greater incidence of dystocia, stillbirth, retained placenta, and metritis than cows with AGL. Morbidity and rate of morbidity were greater for SGL and LGL than AGL. Rate of removal of dams from the herd was 38% faster for SGL than AGL. Milk production was greatest in AGL cows, but responses depended on parity. For primiparous cows, milk production was less in SGL and LGL than in AGL (AGL = 35.4, SGL = 34.6, LGL = 33.0 ± 0.4 kg/d), whereas for multiparous cows, production was less in SGL but greater in LGL than in AGL (AGL = 41.6, SGL = 38.6, LGL = 42.4 ± 0.3 kg/d). A smaller proportion of cows with SGL received at least one AI, but pregnancy at first AI did not differ among groups. Rate of pregnancy was 11% slower for LGL multiparous than for AGL multiparous. By 300 DIM, pregnancy was greater in AGL than SGL. Pregnancy by 300 DIM in multiparous cows was also greater for AGL than LGL. Heifers from dams with GL that deviated from AGL had greater mortality postweaning (AGL = 3.2 vs. SGL = 6.5 vs. LGL = 5.4%). The rate of removal from the herd was greater for SGL (adjusted hazard ratio = 1.78; 95% CI: 1.26 to 2.52) and LGL (adjusted hazard ratio = 2.00; 95% CI: 1.45 to 2.76) than for AGL heifers. Pregnancy at first AI was lowest for LGL and by 500 d of age a larger proportion of AGL heifers were pregnant than LGL (AGL = 82.3 vs. SGL = 79.2 vs. LGL = 74.0%). Cows with GL within 1 SD of the population mean (270 to 282 d) had improved health, production, and reproduction. Heifers from cows with GL within 1 SD of the population mean had improved health and reproduction. Gestation length affects performance of both dams and their offspring.



Oral Tolerance Induction in Hemophilia B Dogs Fed with Transplastomic Lettuce.

Author information: Herzog RW1, Nichols TC2, Su J3, Zhang B3, Sherman A1, Merricks EP2, Raymer R2, Perrin GQ1, Häger M4, Wiinberg B4, Daniell H5.

1Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
2Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, Chapel Hill, NC 25716, USA.
3Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
4Global Research, Novo Nordisk A/S, Måløv 2760, Denmark.
5Department of Biochemistry, School of Dental Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: hdaniell@upenn.edu.
Journal: Molecular Therapy: the Journal of the American Society of Gene Therapy

Date of e-pub: February 2017

Abstract: Anti-drug antibodies in hemophilia patients substantially complicate treatment. Their elimination through immune tolerance induction (ITI) protocols poses enormous costs, and ITI is often ineffective for factor IX (FIX) inhibitors. Moreover, there is no prophylactic ITI protocol to prevent anti-drug antibody (ADA) formation. Using general immune suppression is problematic. To address this urgent unmet medical need, we delivered antigen bioencapsulated in plant cells to hemophilia B dogs. Commercial-scale production of CTB-FIX fusion expressed in lettuce chloroplasts was done in a hydroponic facility. CTB-FIX (∼1 mg/g) in lyophilized cells was stable with proper folding, disulfide bonds, and pentamer assembly after 30-month storage at ambient temperature. Robust suppression of immunoglobulin G (IgG)/inhibitor and IgE formation against intravenous FIX was observed in three of four hemophilia B dogs fed with lyophilized lettuce cells expressing CTB-FIX. No side effects were detected after feeding CTB-FIX-lyophilized plant cells for >300 days. Coagulation times were markedly shortened by intravenous FIX in orally tolerized treated dogs, in contrast to control dogs that formed high-titer antibodies to FIX. Commercial-scale production, stability, prolonged storage of lyophilized cells, and efficacy in tolerance induction in a large, non-rodent model of human disease offer a novel concept for oral tolerance and low-cost production and delivery of biopharmaceuticals.



rAAV8-733-Mediated Gene Transfer of CHIP/Stub-1 Prevents Hippocampal Neuronal Death in Experimental Brain Ischemia.

Author information: Cabral-Miranda F1, Nicoloso-Simões E1, Adão-Novaes J1, Chiodo V2, Hauswirth WW2, Linden R1, Chiarini LB1, Petrs-Silva H3.

1Departamento de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil.
2Retinal Gene Therapy Group, Department of Ophthalmology, University of Florida, Gainesville, FL 32611, USA.
3Departamento de Neurobiologia, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil. Electronic address: hilda@biof.ufrj.br.
Journal: Molecular Therapy: the Journal of the American Society of Gene Therapy

Date of e-pub: February 2017

Abstract: Brain ischemia is a major cause of adult disability and death, and it represents a worldwide health problem with significant economic burden for modern society. The identification of the molecular pathways activated after brain ischemia, together with efficient technologies of gene delivery to the CNS, may lead to novel treatments based on gene therapy. Recombinant adeno-associated virus (rAAV) is an effective platform for gene transfer to the CNS. Here, we used a serotype 8 rAAV bearing the Y733F mutation (rAAV8-733) to overexpress co-chaperone E3 ligase CHIP (also known as Stub-1) in rat hippocampal neurons, both in an oxygen and glucose deprivation model in vitro and in a four-vessel occlusion model of ischemia in vivo. We show that CHIP overexpression prevented neuronal degeneration in both cases and led to a decrease of both eIF2α (serine 51) and AKT (serine 473) phosphorylation, as well as reduced amounts of ubiquitinated proteins following hypoxia or ischemia. These data add to current knowledge of ischemia-related signaling in the brain and suggest that gene therapy based on the role of CHIP in proteostasis may provide a new venue for brain ischemia treatment.



Gilles de la Tourette syndrome.

Author information: Robertson MM1,2, Eapen V3,4, Singer HS5, Martino D6, Scharf JM7,8,9, Paschou P10,11, Roessner V12, Woods DW13, Hariz M14,15, Mathews CA16, Črnčec R3,4, Leckman JF17.

1Department of Neuropsychiatry, UCL Division of Psychiatry, 6th Floor, Maple House, 149 Tottenham Court Road, London W1T 7NF, UK.
2Department of Psychiatry, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa.
3Infant, Child and Adolescent Psychiatry, School of Psychiatry, University of New South Wales, Sydney, New South Wales, Australia.
4Academic Unit of Child Psychiatry, South Western Sydney Local Health District and Ingham Institute, Liverpool Hospital, Mental Health Centre, Locked Bag 7103, Liverpool, 1871, New South Wales, Australia.
5Department of Neurology and Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
6Department of Clinical Neurosciences, University of Calgary, Calgary, Canada.
7Departments of Neurology and Psychiatry, Center for Human Genetics Research, Massachusetts General Hospital, Boston, Massachusetts, USA.
8Division of Cognitive and Behavioral Neurology, Brigham &Women’s Hospital, Boston, Massachusetts, USA.
9Department of Neurology, Harvard Medical School, Boston, Massachusetts, USA.
10Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.
11Department of Molecular Biology and Genetics, Democritus University of Thrace, Alexandroupoli, Greece.
12Department of Child and Adolescent Psychiatry, Faculty of Medicine, TU Dresden, Dresden, Germany.
13Department of Psychology, Marquette University, Milwaukee, Wisconsin, USA.
14Unit of Functional Neurosurgery, UCL Institute of Neurology, London, UK.
15Department of Clinical Neuroscience, Umeå University, Umeå, Sweden.
16Department of Psychiatry and Genetics Institute, University of Florida, Gainesville, Florida, USA.
17Department of Psychiatry, Pediatrics, and Psychology, Child Study Center, Yale University, New Haven, Connecticut, USA.
Journal: Nature Reviews. Disease Primers

Date of e-pub: February 2017

Abstract: Gilles de la Tourette syndrome (GTS) is a childhood-onset neurodevelopmental disorder that is characterized by several motor and phonic tics. Tics usually develop before 10 years of age, exhibit a waxing and waning course and typically improve with increasing age. A prevalence of approximately 1% is estimated in children and adolescents. The condition can result in considerable social stigma and poor quality of life, especially when tics are severe (for example, with coprolalia (swearing tics) and self-injurious behaviours) or when GTS is accompanied by attention-deficit/hyperactivity disorder, obsessive-compulsive disorder or another neuropsychiatric disorder. The aetiology is complex and multifactorial. GTS is considered to be polygenic, involving multiple common risk variants combined with rare, inherited or de novo mutations. These as well as non-genetic factors (such as perinatal events and immunological factors) are likely to contribute to the heterogeneity of the clinical phenotype, the structural and functional brain anomalies and the neural circuitry involvement. Management usually includes psychoeducation and reassurance, behavioural methods, pharmacotherapy and, rarely, functional neurosurgery. Future research that integrates clinical and neurobiological data, including neuroimaging and genetics, is expected to reveal the pathogenesis of GTS at the neural circuit level, which may lead to targeted interventions.




Author information: Langlo CS1, Erker LR, Parker M, Patterson EJ, Higgins BP, Summerfelt P, Razeen MM, Collison FT, Fishman GA, Kay CN, Zhang J, Weleber RG, Yang P, Pennesi ME, Lam BL, Chulay JD, Dubra A, Hauswirth WW, Wilson DJ, Carroll J; ACHM-001 study group.

1*Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, Milwaukee, Wisconsin; †Casey Eye Institute, Oregon Health & Science University, Portland, Oregon; ‡Department of Ophthalmology, Medical College of Wisconsin, Milwaukee, Wisconsin; §Alexandria Faculty of Medicine, University of Alexandria, Alexandria, Egypt; ¶Pangere Center for Inherited Retinal Diseases, The Chicago Lighthouse, Chicago, Illinois; **Vitreo Retinal Associates, Gainesville, Florida; ††Bascom Palmer Eye Institute, University of Miami, Miami, Florida; ‡‡Applied Genetics Technologies Corporation (AGTC), Alachua, Florida; §§Department of Biophysics, Medical College of Wisconsin, Milwaukee, Wisconsin; and ¶¶Department of Ophthalmology, University of Florida, Gainesville, Florida.

Journal: Retina (Philadelphia, Pa.)

Date of e-pub: January 2017

Abstract: Congenital achromatopsia is an autosomal recessive disease causing substantial reduction or complete absence of cone function. Although believed to be a relatively stationary disorder, questions remain regarding the stability of cone structure over time. In this study, the authors sought to assess the repeatability of and examine longitudinal changes in measurements of central cone structure in patients with achromatopsia.

Forty-one subjects with CNGB3-associated achromatopsia were imaged over a period of between 6 and 26 months using optical coherence tomography and adaptive optics scanning light ophthalmoscopy. Outer nuclear layer (ONL) thickness, ellipsoid zone (EZ) disruption, and peak foveal cone density were assessed.

ONL thickness increased slightly compared with baseline (0.184 μm/month, P = 0.02). The EZ grade remained unchanged for 34/41 subjects. Peak foveal cone density did not significantly change over time (mean change 1% per 6 months, P = 0.126).

Foveal cone structure showed little or no change in this group of subjects with CNGB3-associated achromatopsia. Over the time scales investigated (6-26 months), achromatopsia seems to be a structurally stable condition, although longer-term follow-up is needed. These data will be useful in assessing foveal cone structure after therapeutic intervention.This is an open-access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal.



Prediction of in vivo and in vitro infection model results using a semimechanistic model of avibactam and aztreonam combination against multidrug resistant organisms.

Author information: Sy S1, Zhuang L1, Xia H2, Beaudoin ME3, Schuck VJ3, Derendorf H1.

1Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida, USA.
2Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, Florida, USA.
3AstraZeneca, Waltham, Massachusetts, USA.
Journal: CPT: Pharmacometrics & Systems Pharmacology

Date of e-pub: February 2017

Abstract: The combination of aztreonam-avibactam is active against multidrug-resistant Enterobacteriaceae that express metallo-β-lactamases. A complex synergistic interaction exists between aztreonam and avibactam bactericidal activities that have not been quantitatively explored. A two-state semimechanistic pharmacokinetic/pharmacodynamic (PK/PD) logistic growth model was developed to account for antimicrobial activities in the combination of bacteria-mediated degradation of aztreonam and the inhibition of aztreonam degradation by avibactam. The model predicted that changing regimens of 2 g aztreonam plus 0.375 and 0.6 g avibactam as a 1-hour infusion were qualitatively similar to that observed from in vivo murine thigh infection and hollow-fiber infection models previously reported in the literature with 24-hour log kill ≥1. The current approach to characterize the effect of avibactam in enhancing aztreonam activity from time-kill study was accomplished by shifting the half-maximal effective concentration (EC50 ) of aztreonam in increasing avibactam concentration using a nonlinear equation as a function of avibactam concentration, providing a framework for translational predictions.



Skewing in Arabidopsis roots involves disparate environmental signaling pathways.

Author information: Schultz ER1,2, Zupanska AK1, Sng NJ1, Paul AL1, Ferl RJ3,4.

1Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA.
2Present address: Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA.
3Department of Horticultural Sciences, Program in Plant Molecular and Cellular Biology, University of Florida, Gainesville, FL, 32611, USA. robferl@ufl.edu.
4Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32610, USA. robferl@ufl.edu.
Journal: BMC Plant Biology

Date of e-pub: February 2017

Abstract: Skewing root patterns provide key insights into root growth strategies and mechanisms that produce root architectures. Roots exhibit skewing and waving when grown on a tilted, impenetrable surface. The genetics guiding these morphologies have been examined, revealing that some Arabidopsis ecotypes skew and wave (e.g. WS), while others skew insignificantly but still wave (e.g. Col-0). The underlying molecular mechanisms of skewing and waving remain unclear. In this study, transcriptome data were derived from two Arabidopsis ecotypes, WS and Col-0, under three tilted growth conditions in order to identify candidate genes involved in skewing.

This work identifies a number of genes that are likely involved in skewing, using growth conditions that differentially affect skewing and waving. Comparing the gene expression profiles of WS and Col-0 in different tilted growth conditions identified 11 candidate genes as potentially involved in the control of skewing. These 11 genes are involved in several different cellular processes, including sugar transport, salt signaling, cell wall organization, and hormone signaling.

This study identified 11 genes whose change in expression level is associated with root skewing behavior. These genes are involved in signaling and perception, rather than the physical restructuring of root. Future work is needed to elucidate the potential role of these candidate genes during root skewing.



Integrated analysis of genetic variation and gene expression reveals novel variant for increased warfarin dose requirement in African Americans.

Author information: Hernandez W1, Gamazon ER2,3, Aquino-Michaels K1, Smithberger E1, O’Brien TJ4, Harralson AF5,6, Tuck M7, Barbour A5, Cavallari LH8, Perera MA1.

1University of Chicago, Department of Medicine, Section of Genetic Medicine, Chicago, IL.
2Vanderbilt University, Department of Medicine, Division of Genetic Medicine, Nashville, TN.
3University of Amsterdam, Academic Medical Center, Amsterdam, The Netherlands.
4George Washington University, Department of Pharmacology and Physiology, Washington, DC.
5George Washington University, Department of Medicine, Washington, DC.
6Bernard J. Dunn School of Pharmacy, Shenandoah University, Winchester, VA.
7Veterans Affairs Medical Center, Washington, DC.
8University of Florida, College of Pharmacy, Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, Gainesville, FL.
Journal: Journal of Thrombosis and Haemostasis: JTH

Date of e-pub: January 2017

Abstract: Warfarin is commonly used to control and prevent thromboembolic disorders. However, due to warfarin’s complex dose-requirement relationship, safe and effective use is challenging. Pharmacogenomics-guided warfarin dosing algorithms that include the well-established VKORC1 and CYP2C9 polymorphisms explain only a small proportion of inter-individual variability in African Americans (AAs).

We aimed to assess whether transcriptomic analyses could be used to identify regulatory variants associated with warfarin dose response in AAs.

We identified a total of 56 eQTLs for CYP2C9, VKORC1, and CALU derived from human livers and evaluated their association to warfarin dose response in two independent AA warfarin patient cohorts.

We found rs4889606, a strong cis-eQTL for VKORC1 (log10 Bayes Factor = 12.02), is significantly associated with increased warfarin dose requirement (p = 8.18×10-6 ) in the Discovery Cohort (N=305) and in the Replication Cohort (p = 0.01; N = 141) even after conditioning on VKORC1 -1639G>A (rs9923231) variant. Inclusion of rs4889606 genotypes, along with CYP2C9 alleles, rs9923231 genotypes, and clinical variables explained 31% of the interpatient variability in warfarin dose requirement. We demonstrate different linkage disequilibrium patterns in the region encompassing rs4889606 and rs9923231 between AAs and Europe Americans which may explain the increased dose requirement found in AAs.

Our approach of interrogating eQTLs identified in liver has revealed a novel predictor of warfarin dose response in AAs. Our work highlights the utility of leveraging information from regulatory variants mapped in the liver to uncover novel variants associated with drug response and the importance of population-specific research. This article is protected by copyright. All rights reserved.



A Global Perspective on the Population Structure and Reproductive System of Phyllosticta citricarpa.

Author information: Carstens E1, Linde C2, Slabbert R3, Miles A4, Donovan N5, Li HY6, Zhang K7, Dewdney MM8,9, Rollins JA10, Glienke C11, Schutte GC12, Fourie P13,14, McLeod A15.

1Stellenbosch University, 26697, Plant Pathology , Stellenbosch University , Private Bag X1 , Matieland , Matieland, South Africa , 7602 ; ec@cri.co.za.
2Australian National University, School of Botany and Zoology, Daley Rd , The Australian National University , Bldg 116 , Canberra, Australia , 0200 ; celeste.linde@anu.edu.au.
3Stellenbosch University, 26697, Central Analytical Facilities, Matieland, South Africa ; rslabbrt@sun.ac.za.
4University of Queensland, 1974, Centre for Plant Science, Brisbane, Queensland, Australia ; a.miles@uq.edu.au.
5Elizabeth Macarthur Agricultural Institute, 153388, Menangle, New South Wales, Australia ; nerida.donovan@dpi.nsw.gov.au.
6Institute of Biotechnology, Zhejiang University, Zhejiang University , Yuhangtang Road 866, Hangzhou city, Zhejiang Provinice , Hangzhou, Zhejiang, China , 310058 ; hyli@zju.edu.cn.
7University of Florida, CREC, Lake Alfred, Florida, United States ; zhangke625@ufl.edu.
8University of Florida, CREC , 700 Experiment Station Road , Lake Alfred, Florida, United States , 33850.
9University of Florida, Plant Pathology ; mmdewdney@ufl.edu.
10Univ of Florida, PO Box 110680 – Plant Path Dept , 1453 Fifield Hall , Gainesville, Florida, United States , 32611-0680 ; rollinsj@ufl.edu.
11Federal University of Paraná, Genetics , Francisco Heraclito dos Santos , Curitiba, Paraná, Brazil , 81531990 ; ch.glienke@gmail.com.
12Citrus Research International, Disease Management, Nelspruit, South Africa ; ts@cri.co.za.
13Citrus Research International, Disease Management , PO Box 2201 , Stellenbosch, South Africa , 7602.
14University of Stellenbosch, Plant Pathology , Private Bag X1 , Stellenbosch, South Africa , 7602 ; phfourie@sun.ac.za.
15Stellenbosch University, Plant Pathology , Private Bag X1 , Stellenbosch, Western Cape, South Africa , 7602 ; adelem@sun.ac.za.
Journal: Phytopathology

Date of e-pub: January 2017

Abstract: The citrus pathogen Phyllosticta citricarpa was first described 117 years ago in Australia, and subsequently from the summer rainfall citrus-growing regions in China, Africa, South America and recently the United States of America (USA). Limited information is available on the pathogen’s population structure, mode of reproduction and introduction pathways, which were investigated by genotyping 383 isolates representing 12 populations from South Africa, USA, Australia, China and Brazil. Populations were genotyped using seven published and eight newly developed polymorphic simple sequence repeat (SSR) markers. The Chinese and Australian populations had the highest genetic diversities, whereas populations from Brazil, USA and South Africa exhibited characteristics of founder populations. The USA population was clonal. Based on principal coordinate and minimum spanning network analyses the Chinese populations were distinct from the other populations. Population differentiation and clustering analyses revealed high connectivity and possibly linked introduction pathways between South Africa, Australia and Brazil. With the exception of the clonal USA populations that only contained one mating type, all the other populations contained both mating types in a ratio that did not deviate significantly from 1:1. Whilst most populations exhibited sexual reproduction, linkage disequilibrium analyses indicated that asexual reproduction is important in the pathogen’s life cycle.



The Arabidopsis Elongator complex is required for nonhost resistance against the bacterial pathogens Xanthomonas citri subsp. citri and Pseudomonas syringae pv. phaseolicola NPS3121.

Author information: An C1, Wang C1, Mou Z1.

1Department of Microbiology and Cell Science, University of Florida, PO Box 110700, Gainesville, FL, 32611, USA.

Journal: The New Phytologist

Date of e-pub: January 2017

Abstract: Although in recent years nonhost resistance has attracted considerable attention for its broad spectrum and durability, the genetic and mechanistic components of nonhost resistance have not been fully understood. We used molecular and histochemical approaches including quantitative PCR, chromatin immunoprecipitation, and 3,3′-diaminobenzidine and aniline blue staining. The evolutionarily conserved histone acetyltransferase complex Elongator was identified as a major component of nonhost resistance against Xanthomonas citri subsp. citri (Xcc) and Pseudomonas syringae pv. phaseolicola (Psp) NPS3121. Mutations in Elongator genes inhibit Xcc-, Psp NPS3121- and/or flg22-induced defense responses including defense gene expression, callose deposition, and reactive oxygen species (ROS) and salicylic acid (SA) accumulation. Mutations in Elongator also attenuate the ROS-SA amplification loop. We show that suppressed ROS and SA accumulation in Elongator mutants is correlated with reduced expression of the Arabidopsis respiratory burst oxidase homologue AtrbohD and the SA biosynthesis gene ISOCHORISMATE SYNTHASE1 (ICS1). Furthermore, we found that the Elongator subunit ELP2 is associated with the chromatin of AtrbohD and ICS1 and is required for maintaining basal histone H3 acetylation levels in these key defense genes. As both AtrbohD and ICS1 contribute to nonhost resistance against Xcc, our results reveal an epigenetic mechanism by which Elongator regulates nonhost resistance in Arabidopsis.



Evolution of floral diversity: genomics, genes and gamma.

Author information: Chanderbali AS1,2, Berger BA3, Howarth DG3, Soltis DE1,2,4, Soltis PS5,4.

1Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA.
2Department of Biology, University of Florida, Gainesville, FL 32611, USA.
3Department of Biological Sciences, St John’s University, Queens, NY 11439, USA.
4Genetics Institute, University of Florida, Gainesville, FL 32610, USA.
5Florida Museum of Natural History, University of Florida, Gainesville, FL 32611, USA psoltis@flmnh.ufl.edu.
Journal: Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

Date of e-pub: February 2017

Abstract: A salient feature of flowering plant diversification is the emergence of a novel suite of floral features coinciding with the origin of the most species-rich lineage, Pentapetalae. Advances in phylogenetics, developmental genetics and genomics, including new analyses presented here, are helping to reconstruct the specific evolutionary steps involved in the evolution of this clade. The enormous floral diversity among Pentapetalae appears to be built on a highly conserved ground plan of five-parted (pentamerous) flowers with whorled phyllotaxis. By contrast, lability in the number and arrangement of component parts of the flower characterize the early-diverging eudicot lineages subtending Pentapetalae. The diversification of Pentapetalae also coincides closely with ancient hexaploidy, referred to as the gamma whole-genome triplication, for which the phylogenetic timing, mechanistic details and molecular evolutionary consequences are as yet not fully resolved. Transcription factors regulating floral development often persist in duplicate or triplicate in gamma-derived genomes, and both individual genes and whole transcriptional programmes exhibit a shift from broadly overlapping to tightly defined expression domains in Pentapetalae flowers. Investigations of these changes associated with the origin of Pentapetalae can lead to a more comprehensive understanding of what is arguably one of the most important evolutionary diversification events within terrestrial plants.This article is part of the themed issue ‘Evo-devo in the genomics era, and the origins of morphological diversity’.



Factors That Influence the Quality of RNA From the Pancreas of Organ Donors.

Author information: Philips T1, Kusmartseva I, Gerling IC, Campbell-Thompson M, Wasserfall C, Pugliese A, Longmate JA, Schatz DA, Atkinson MA, Kaddis JS.

1From the *Departments of Pathology, Immunology, & Laboratory Medicine, University of Florida, Gainesville, FL; †Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN; ‡Diabetes Research Institute and Departments of Medicine, Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL; §Department of Information Sciences, ∥Division of Biostatistics, City of Hope, Duarte, CA; and ¶Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL.

Journal: Pancreas

Date of e-pub: February 2017

Abstract: Attaining high-quality RNA from the tissues or organs of deceased donors used for research can be challenging due to physiological and logistical considerations. In this investigation, METHODS: RNA Integrity Number (RIN) was determined in pancreatic samples from 236 organ donors and used to define high (≥6.5) and low (≤4.5) quality RNAs. Logistic regression was used to evaluate the potential effects of novel or established organ and donor factors on RIN.

Univariate analysis revealed donor cause of death (odds ratio [OR], 0.35; 95% confidence interval [CI], 0.15-0.77; P = 0.01), prolonged tissue storage before RNA extraction (OR, 0.65; 95% CI, 0.52-0.79; P < 0.01), pancreas region sampled (multiple comparisons, P < 0.01), and sample type (OR, 0.32; 95% CI, 0.15-0.67; P < 0.01) negatively influenced outcome. Conversely, duration of final hospitalization (OR, 3.95; 95% CI, 1.59-10.37; P < 0.01) and sample collection protocol (OR, 8.48; 95% CI, 3.96-19.30; P < 0.01) positively impacted outcome. Islet RNA obtained via laser capture microdissection improved RIN when compared with total pancreatic RNA from the same donor (ΔRIN = 1.3; 95% CI, 0.6-2.0; P < 0.01).

A multivariable model demonstrates that autopsy-free and biopsy-free human pancreata received, processed, and preserved at a single center, using optimized procedures, from organ donors dying of anoxia with normal lipase levels increase the odds of obtaining high-quality RNA.



Differentiation of Diabetes by Pathophysiology, Natural History, and Prognosis.

Author information: Skyler JS1, Bakris GL2, Bonifacio E3, Darsow T4, Eckel RH5, Groop L6, Groop PH7,8,9, Handelsman Y10, Insel RA11, Mathieu C12, McElvaine AT13, Palmer JP14, Pugliese A1, Schatz DA15, Sosenko JM16, Wilding JP17, Ratner RE4.

1Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL.
2The University of Chicago Medicine, Chicago, IL.
3Technische Universität Dresden, Dresden, Germany.
4American Diabetes Association, Arlington, VA.
5University of Colorado Anschutz Medical Campus, Aurora, CO.
6Lund University, Skåne University Hospital, Malmö, Sweden.
7Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.
8Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland.
9Baker IDI Heart and Diabetes Institute, Melbourne, Australia.
10Metabolic Institute of America, Tarzana, CA.
11JDRF, New York, NY.
12Katholieke Universiteit Leuven, Leuven, Belgium.
13American Diabetes Association, Arlington, VA amcelvaine@diabetes.org.
14University of Washington and VA Puget Sound Health Care System, Seattle, WA.
15University of Florida College of Medicine, Gainesville, FL.
16University of Miami Miller School of Medicine, Miami, FL.
17University Hospital Aintree, Liverpool, U.K.
Journal: Diabetes

Date of e-pub: February 2017

Abstract: The American Diabetes Association, JDRF, the European Association for the Study of Diabetes, and the American Association of Clinical Endocrinologists convened a research symposium, “The Differentiation of Diabetes by Pathophysiology, Natural History and Prognosis” on 10-12 October 2015. International experts in genetics, immunology, metabolism, endocrinology, and systems biology discussed genetic and environmental determinants of type 1 and type 2 diabetes risk and progression, as well as complications. The participants debated how to determine appropriate therapeutic approaches based on disease pathophysiology and stage and defined remaining research gaps hindering a personalized medical approach for diabetes to drive the field to address these gaps. The authors recommend a structure for data stratification to define the phenotypes and genotypes of subtypes of diabetes that will facilitate individualized treatment.



Laboratory and field evaluation of brown dog tick behavioral responses to potential semiochemicals.

Author information: Carnohan LP1, Kaufman PE2, Allan SA3, Gezan SA4, Weeks EN1.

1Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, United States.
2Entomology and Nematology Department, University of Florida, Gainesville, FL 32611, United States. Electronic address: pkaufman@ufl.edu.
3USDA-ARS, Center for Medical, Agricultural and Veterinary Entomology, 1600/1700 SW 23rd Dr., Gainesville, FL 32608, United States.
4School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, United States.
Journal: Ticks and Tick-borne Diseases

Date of e-pub: February 2017

Abstract: The brown dog tick, Rhipicephalus sanguineus sensu lato (Parasitiformis: Ixodidae), is an ectoparasite of dogs that can be found worldwide. This tick poses unique difficulties in management because it can complete its entire life cycle indoors and has demonstrated acaricide resistance. The ability to monitor for tick presence and abundance is necessary for developing effective control programs. As such, an evaluation of adult brown dog tick behavioral responses to 16 potential semiochemicals was undertaken using Y-tube and straight-tube olfactometers. Both sexes of ticks were activated by nine of the 16 semiochemicals tested, including 300μg of 1-octen-3-ol, benzaldehyde, benzyl alcohol, hexanoic acid, nonanoic acid, methyl salicylate, o-nitrophenol, 2,6-dichlorophenol and salicylaldehyde. Rhipicephalus sanguineus s.l. behaviors including movement speed, direction and duration, as well as turning, were quantified following exposure to the same nine chemicals in a straight-tube olfactometer, individually at 300μg and as mixtures. Three individual chemicals, 1-octen-3-ol, hexanoic acid, and methyl salicylate induced strong responses. These three chemicals were evaluated in a semi-field setting using a modified bed bug trap but were found to provide no significant increase in attraction compared with CO2 alone. The results of these studies provide a foundation for future research regarding semiochemicals of R. sanguineus s.l.



Identification of miRNA from Bouteloua gracilis, a drought tolerant grass, by deep sequencing and their in silico analysis.

Author information: Ordóñez-Baquera PL1, González-Rodríguez E2, Aguado-Santacruz GA3, Rascón-Cruz Q4, Conesa A5, Moreno-Brito V6, Echavarria R7, Dominguez-Viveros J8.

1Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico R. Almada Km. 1C.P. 31453, Chihuahua, México. Electronic address: plordonez@uach.mx.
2Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico R. Almada Km. 1C.P. 31453, Chihuahua, México. Electronic address: evegonzal@uach.mx.
3Programa de Posgrado, Instituto Tecnológico de Roque, Km. 8 Carretera Celaya-Juventino Rosas C.P. 38110, Celaya, Guanajuato, México; BIOqualitum S.A. de C.V., Oriente 7 # 158, Ciudad Industrial Sur, Celaya, Gto. CP 38010, México. Electronic address: gaguado@prodigy.net.mx.
4Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Campus Universitario No. 2 Circuito Universitario, C.P. 31125, Chihuahua, México. Electronic address: qrascon@uach.mx.
5Genomics of Gene Expression Laboratory, Prince Felipe Research Center, Av. Eduardo Primo Yúfera 3, 46012 Valencia, Spain; Microbiology and Cell Science Department, Institute for Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States. Electronic address: aconesa@cipf.es.
6Facultad de Medicina y Ciencias Biomédicas, Universidad Autónoma de Chihuahua, Campus Universitario No. 2 Circuito Universitario, C.P. 31125 Chihuahua, México. Electronic address: vmoreno@uach.mx.
7Conacyt-Centro de Investigaciones Biomédicas de Occidente, Guadalajara, México. Electronic address: rechavarria.z@conacyt.mx.
8Facultad de Zootecnia y Ecología, Universidad Autónoma de Chihuahua, Periférico R. Almada Km. 1C.P. 31453, Chihuahua, México. Electronic address: joeldominguez@hotmail.com.
Journal: Computational Biology and Chemistry

Date of e-pub: February 2017

Abstract: MicroRNAs (miRNAs) are small non-coding RNA molecules that regulate signal transduction, development, metabolism, and stress responses in plants through post-transcriptional degradation and/or translational repression of target mRNAs. Several studies have addressed the role of miRNAs in model plant species, but miRNA expression and function in economically important forage crops, such as Bouteloua gracilis (Poaceae), a high-quality and drought-resistant grass distributed in semiarid regions of the United States and northern Mexico remain unknown.

We applied high-throughput sequencing technology and bioinformatics analysis and identified 31 conserved miRNA families and 53 novel putative miRNAs with different abundance of reads in chlorophyllic cell cultures derived from B. gracilis. Some conserved miRNA families were highly abundant and possessed predicted targets involved in metabolism, plant growth and development, and stress responses. We also predicted additional identified novel miRNAs with specific targets, including B. gracilis ESTs, which were detected under drought stress conditions.

Here we report 31 conserved miRNA families and 53 putative novel miRNAs in B. gracilis. Our results suggested the presence of regulatory miRNAs involved in modulating physiological and stress responses in this grass species.



Novel encapsulation improves recovery of probiotic strains in fecal samples of human volunteers.

Author information: Mai V1, Waugh S2, Byrd D2, Simpson D2, Ukhanova M2.

1Department of Epidemiology, Emerging Pathogens Institute, PHHP/COM, University of Florida, Gainesville, FL, USA. vmai@ufl.edu.
2Department of Epidemiology, Emerging Pathogens Institute, PHHP/COM, University of Florida, Gainesville, FL, USA.
Journal: Applied Microbiology and Biotechnology

Date of e-pub: February 2017

Abstract: Probiotic supplements can contribute to maintaining health and ameliorating various disease symptoms. Probiotics can be delivered in many forms with crucial differences in their survival during gastrointestinal (GI) passage. Previously, a novel encapsulation, Probiotic Pearls™ Acidophilus, Integrative Therapeutics, LLC, USA (Pearls), was shown to increase survival in vitro after exposure to gastric conditions. Here, we compare fecal recovery in human volunteers consuming Pearls or a conventional hard-shelled gelatin capsule. We performed a randomized double-blinded, two-armed trial, with six healthy subjects in each 12-day study arm. In fecal samples collected at baseline, twice during the intervention period, and after washout, we compared colony counts between the two encapsulation methods. The identity of the colonies was confirmed by colony morphology, strain-specific PCR, and 16S rRNA gene sequencing. We further performed a comprehensive 16S rRNA gene sequencing-based analysis to identify differential effects on overall microbiota composition. We detected an average log increase in bifidobacteria of 0.152 cfu/g with gelatin and 0.651 cfu/g with Pearls capsules (p > 0.05). Total lactobacilli counts increased in both groups with no difference between the groups. However, the supplemented Lactobacillus acidophilus NCFM decreased to baseline levels within 7 days after end of supplementation with gelatin capsules while 3.11 log cfu/g higher counts compared to baseline (p = 0.05) remained for Pearls. Targeted qPCR largely confirmed the trends observed by viable plate counts. Protecting the probiotic strains by Pearls encapsulation results in higher recovery rates of the supplemented lactobacilli and bifidobacteria in fecal samples and increased persistence, suggesting an improved survival and viability that might increase efficacy towards achieving desired health benefits.



The C-terminal MIR-containing region in the Pmt1 O-mannosyltransferase restrains sporulation and is dispensable for virulence in Beauveria bassiana.

Author information: He Z1, Luo L1, Keyhani NO2, Yu X1, Ying S3, Zhang Y4.

1College of Plant Protection, Biotechnology Research Center, Southwest University, Chongqing, 400715, People’s Republic of China.
2Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, 32611, USA.
3Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, People’s Republic of China.
4College of Plant Protection, Biotechnology Research Center, Southwest University, Chongqing, 400715, People’s Republic of China. yjzhang@swu.edu.cn.
Journal: Applied Microbiology and Biotechnology

Date of e-pub: February 2017

Abstract: Protein O-mannosyltransferases (Pmts) belong to a highly conserved protein family responsible for the initiation of O-glycosylation of many proteins. Pmts contain one dolichyl-phosphate-mannose-protein mannosyltransferases (PMT) domain and three MIR motifs (mannosyltransferase, inositol triphosphate, and ryanodine receptor) that are essential for activity in yeast. We report that in the insect fungal pathogen, Beauveria bassiana, deletion of the C-terminal Pmt1 MIR-containing region (Pmt1∆ 311-902) does not alter O-mannosyltransferase activity, but does increase total cell wall protein O-mannosylation levels and results in phenotypic changes in fungal development and cell wall stability. B. bassiana mutants harboring the Pmt1 ∆ 311-902 mutation displayed a significant increase in conidiation with up-regulation of conidiation-associated genes and an increase in biomass accumulation as compared to the wild-type parent. However, decreased vegetative growth and blastospore production was noted, and Pmt1 ∆ 311-902 mutants were altered in cell wall composition and cell surface features. Insect bioassays revealed little effect on virulence for the Pmt1 ∆ 311-902 strain via cuticle infection or intrahemocoel injection assays, although differences in hyphal body differentiation in the host hemolymph and up-regulation of virulence-associated genes were noted. These data suggest novel roles for Pmt1 in negatively regulating conidiation and demonstrate that the C-terminal Pmt1 MIR-containing region is dispensable for enzymatic activity and organismal virulence.



The sensitivity of exome sequencing in identifying pathogenic mutations for LGMD in the United States.

Author information: Reddy HM1, Cho KA1, Lek M2,3, Estrella E4, Valkanas E2,3, Jones MD1, Mitsuhashi S5, Darras BT5, Amato AA6, Lidov HG7, Brownstein CA4,8, Margulies DM4,8, Yu TW4, Salih MA9, Kunkel LM4, MacArthur DG2,3, Kang PB1,5,10,11.

1Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL, USA.
2Analytic and Translational Genetics Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
3Program in Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA.
4Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA.
5Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA.
6Department of Neurology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA.
7Department of Pathology, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA.
8Research Connection and Manton Center for Orphan Disease Research, Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, MA, USA.
9Department of Pediatrics, Division of Neurology, College of Medicine and King Khalid University Hospital, King Saud University, Riyadh, Kingdom of Saudi Arabia.
10Department of Neurology and Department of Molecular Genetics and Microbiology, University of Florida College of Medicine, Gainesville, FL, USA.
11Genetics Institute, University of Florida, Gainesville, FL, USA.
Journal: Journal of Human Genetics

Date of e-pub: February 2017

Abstract: The current study characterizes a cohort of limb-girdle muscular dystrophy (LGMD) in the United States using whole-exome sequencing. Fifty-five families affected by LGMD were recruited using an institutionally approved protocol. Exome sequencing was performed on probands and selected parental samples. Pathogenic mutations and cosegregation patterns were confirmed by Sanger sequencing. Twenty-two families (40%) had novel and previously reported pathogenic mutations, primarily in LGMD genes, and also in genes for Duchenne muscular dystrophy, facioscapulohumeral muscular dystrophy, congenital myopathy, myofibrillar myopathy, inclusion body myopathy and Pompe disease. One family was diagnosed via clinical testing. Dominant mutations were identified in COL6A1, COL6A3, FLNC, LMNA, RYR1, SMCHD1 and VCP, recessive mutations in ANO5, CAPN3, GAA, LAMA2, SGCA and SGCG, and X-linked mutations in DMD. A previously reported variant in DMD was confirmed to be benign. Exome sequencing is a powerful diagnostic tool for LGMD. Despite careful phenotypic screening, pathogenic mutations were found in other muscle disease genes, largely accounting for the increased sensitivity of exome sequencing. Our experience suggests that broad sequencing panels are useful for these analyses because of the phenotypic overlap of many neuromuscular conditions. The confirmation of a benign DMD variant illustrates the potential of exome sequencing to help determine pathogenicity.



The ability of quaternary ammonium groups attached to a urethane bandage to inhibit bacterial attachment and biofilm formation in a mouse wound model.

Author information: Tran PL1, Huynh E1, Hamood AN2, de Souza A3, Schultz G4, Liesenfeld B5, Mehta D3, Webster D6, Reid TW1,2.

1Departments of Ophthalmology and Visual Sciences, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX, USA.
2Departments of Molecular Microbiology and Immunology, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
3Viridis BioPharma Pvt. Ltd, Mumbai, India.
4Department of Obstetrics and Gynecology, University of Florida, College of Medicine, Gainesville, FL, USA.
5Quick Med Technologies, Inc., Gainesville, FL, USA.
6Departments of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX, USA.
Journal: International Wound Journal

Date of e-pub: February 2017

Abstract: For proper wound healing, control of bacteria or bacterial infections is of major importance. While caring for a wound, dressing material plays a key role as bacteria can live in the bandage and keep re-infecting the wound. They do this by forming biofilms in the bandage, which slough off planktonic bacteria and overwhelm the host defense. It is thus necessary to develop a wound dressing that will inhibit bacterial growth. This study examines the effectiveness of a polyurethane foam wound dressing bound with polydiallyl-dimethylammonium chloride (pDADMAC) to inhibit the growth of bacteria in a wound on the back of a mouse. This technology does not allow pDADMAC to leach away from the dressing into the wound, thereby preventing cytotoxic effects. Staphylococcus aureus, Pseudomonas aeruginosa and Acinetobacter baumannii were chosen for the study to infect the wounds. S. aureus and P. aeruginosa are important pathogens in wound infections, while A. baumannii was selected because of its ability to acquire or upregulate antibiotic drug resistance determinants. In addition, two different isolates of methicillin-resistant S. aureus (MRSA) were tested. All the bacteria were measured in the wound dressing and in the wound tissue under the dressing. Using colony-forming unit (CFU) assays, over six logs of inhibition (100%) were found for all the bacterial strains using pDADMAC-treated wound dressing when compared with control-untreated dressing. The CFU assay results obtained with the tissues were significant as there were 4-5 logs of reduction (100%) of the test organism in the tissue of the pDADMAC-covered wound versus that of the control dressing-covered wound. As the pDADMAC cannot leave the dressing (like other antimicrobials), this would imply that the dressing acts as a reservoir for free bacteria from a biofilm and plays a significant role in the development of a wound infection.


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