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UFGI Publications Round-Up Week 11/07/2016

Identification of Two Heritable Cross-Disorder Endophenotypes for Tourette Syndrome.

Author information: Darrow SM1, Hirschtritt ME1, Davis LK1, Illmann C1, Osiecki L1, Grados M1, Sandor P1, Dion Y1, King R1, Pauls D1, Budman CL1, Cath DC1, Greenberg E1, Lyon GJ1, Yu D1, McGrath LM1, McMahon WM1, Lee PC1, Delucchi KL1, Scharf JM1, Mathews CA1; Tourette Syndrome Association International Consortium for Genetics1.

1From the Department of Psychiatry, University of California, San Francisco; the Department of Medicine, Vanderbilt University Medical Center, Nashville; the Psychiatric and Neurodevelopmental Genetics Unit, Department of Psychiatry, Massachusetts General Hospital, Boston; the Department of Psychiatry and Behavioral Sciences, Johns Hopkins University School of Medicine, Baltimore; the Department of Psychiatry and University Health Network, University of Toronto, Toronto; the Youthdale Treatment Centres, Toronto; the Department of Psychiatry, University of Montreal, Montreal; the Yale Child Study Center and the Department of Genetics, Yale University School of Medicine, New Haven, Conn.; the Feinstein Institute for Medical Research, North Shore/Long Island Jewish Health System, Manhasset, N.Y.; the Faculty of Social and Behavioral Sciences, Utrecht University, Utrecht, The Netherlands; the Stanley Institute for Cognitive Genomics, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.; the Department of Psychology, University of Denver, Denver; the Department of Psychiatry, University of Utah, Salt Lake City; the Department of Behavioral Health, Tripler Army Medical Center, Honolulu; the Departments of Neurology, Brigham and Women’s Hospital and Massachusetts General Hospital,, Boston; and the Department of Psychiatry, University of Florida, Gainesville.

Journal: American Journal of Psychiatry

Date of e-pub: November 2016

Abstract: Phenotypic heterogeneity in Tourette syndrome is partly due to complex genetic relationships among Tourette syndrome, obsessive-compulsive disorder (OCD), and attention deficit hyperactivity disorder (ADHD). Identifying symptom-based endophenotypes across diagnoses may aid gene-finding efforts.

Assessments for Tourette syndrome, OCD, and ADHD symptoms were conducted in a discovery sample of 3,494 individuals recruited for genetic studies. Symptom-level factor and latent class analyses were conducted in Tourette syndrome families and replicated in an independent sample of 882 individuals. Classes were characterized by comorbidity rates and proportion of parents included. Heritability and polygenic load associated with Tourette syndrome, OCD, and ADHD were estimated.

The authors identified two cross-disorder symptom-based phenotypes across analyses: symmetry (symmetry, evening up, checking obsessions; ordering, arranging, counting, writing-rewriting compulsions, repetitive writing tics) and disinhibition (uttering syllables/words, echolalia/palilalia, coprolalia/copropraxia, and obsessive urges to offend/mutilate/be destructive). Heritability estimates for both endophenotypes were high and statistically significant (disinhibition factor=0.35, SE=0.03; symmetry factor=0.39, SE=0.03; symmetry class=0.38, SE=0.10). Mothers of Tourette syndrome probands had high rates of symmetry (49%) but not disinhibition (5%). Polygenic risk scores derived from a Tourette syndrome genome-wide association study (GWAS) were significantly associated with symmetry, while risk scores derived from an OCD GWAS were not. OCD polygenic risk scores were significantly associated with disinhibition, while Tourette syndrome and ADHD risk scores were not.

The analyses identified two heritable endophenotypes related to Tourette syndrome that cross traditional diagnostic boundaries. The symmetry phenotype correlated with Tourette syndrome polygenic load and was present in otherwise Tourette-unaffected mothers, suggesting that this phenotype may reflect additional Tourette syndrome (rather than OCD) genetic liability that is not captured by traditional DSM-based diagnoses.

 

 

Effects of Long-Term Exercise on Age-Related Hearing Loss in Mice.

Author information: Han C1, Ding D2, Lopez MC3, Manohar S2, Zhang Y4, Kim MJ1, Park HJ1,5, White K1, Kim YH6, Linser P5, Tanokura M7, Leeuwenburgh C1, Baker HV3, Salvi RJ2, Someya S8.

1Department of Aging and Geriatric Research.
2Center for Hearing and Deafness, State University of New York at Buffalo, Buffalo, New York 14214, and.
3Department of Molecular Genetics and Microbiology.
4Gene Expression and Genotyping, Interdisciplinary Center for Biotechnology Research, and.
5Whitney Laboratory, University of Florida, St. Augustine, Florida 32080.
6Department of Physiology and Functional Genomics, University of Florida, Gainesville, Florida 32610.
7Department of Applied Biological Chemistry, University of Tokyo, Yayoi, Tokyo, 113, Japan.
8Department of Aging and Geriatric Research, someya@ufl.edu.

Journal: Journal of Neuroscience

Date of e-pub: November 2016

Abstract: Regular physical exercise reduces the risk for obesity, cardiovascular diseases, and disability and is associated with longer lifespan expectancy (Taylor et al., 2004; Pahor et al., 2014; Anton et al., 2015; Arem et al., 2015). In contrast, decreased physical function is associated with hearing loss among older adults (Li et al., 2013; Chen et al., 2015). Here, we investigated the effects of long-term voluntary wheel running (WR) on age-related hearing loss (AHL) in CBA/CaJ mice, a well established model of AHL (Zheng et al., 1999). WR activity peaked at 6 months of age (12,280 m/d) and gradually decreased over time. At 24 months of age, the average WR distance was 3987 m/d. Twenty-four-month-old runners had less cochlear hair cell and spiral ganglion neuron loss and better auditory brainstem response thresholds at the low and middle frequencies compared with age-matched, non-WR controls. Gene ontology (GO) enrichment analysis of inner ear tissues from 6-month-old controls and runners revealed that WR resulted in a marked enrichment for GO gene sets associated with immune response, inflammatory response, vascular function, and apoptosis. In agreement with these results, there was reduced stria vascularis (SV) atrophy and reduced loss of capillaries in the SV of old runners versus old controls. Given that SV holds numerous capillaries that are essential for transporting oxygen and nutrients into the cochlea, our findings suggest that long-term exercise delays the progression of AHL by reducing age-related loss of strial capillaries associated with inflammation.

Nearly two-thirds of adults aged 70 years or older develop significant age-related hearing loss (AHL), a condition that can lead to social isolation and major communication difficulties. AHL is also associated with decreased physical function among older adults. In the current study, we show that regular exercise slowed AHL and cochlear degeneration significantly in a well established murine model. Our data suggest that regular exercise delays the progression of AHL by reducing age-related loss of strial capillaries associated with inflammation.

 

 

Does abiotic stress cause functional B vitamin deficiency?

Author information: Hanson AD1, Beaudoin GA2, McCarty DR3, Gregory JF2.

1University of Florida CITY: Gainesville STATE: Florida POSTAL_CODE: 32611-0690 United States Of America [US] adha@ufl.edu.
2University of Florida CITY: Gainesville STATE: Florida United States Of America [US].
3University of Florida, IFAS CITY: Gainesville STATE: Florida POSTAL_CODE: 32611-0690 United States Of America [US].

Journal: Plant Physiology

Date of e-pub: November 2016

Abstract: N/A

 

 

Comparing Avocado, Swamp Bay, and Camphortree as Hosts of Raffaelea lauricola Using a Green Fluorescent Protein (GFP)-Labeled Strain of the Pathogen.

Author information: Campbell AS1, Ploetz RC1, Rollins JA1.

1First and second authors: Tropical Research & Education Center, University of Florida, Homestead 33031; and third author: Plant Pathology, University of Florida, Gainesville 32611.

Journal: Phytopathology

Date of e-pub: November 2016

Abstract: Raffaelea lauricola, a fungal symbiont of the ambrosia beetle Xyleborus glabratus, causes laurel wilt in members of the Lauraceae plant family. North American species in the family, such as avocado (Persea americana) and swamp bay (P. palustris), are particularly susceptible to laurel wilt, whereas the Asian camphortree (Cinnamomum camphora) is relatively tolerant. To determine whether susceptibility is related to pathogen colonization, a green fluorescent protein-labeled strain of R. lauricola was generated and used to inoculate avocado, swamp bay, and camphortree. Trees were harvested 3, 10, and 30 days after inoculation (DAI), and disease severity was rated on a 1-to-10 scale. By 30 DAI, avocado and swamp bay developed significantly more severe disease than camphortree (mean severities of 6.8 and 5.5 versus 1.6, P < 0.003). The extent of xylem colonization was recorded as the percentage of lumena that were colonized by the pathogen. More xylem was colonized in avocado than camphortree (0.9% versus 0.1%, P < 0.03) but colonization in swamp bay (0.4%) did not differ significantly from either host. Although there were significant correlations between xylem colonization and laurel wilt severity in avocado (r = 0.74), swamp bay (r = 0.82), and camphortree (r = 0.87), even severely affected trees of all species were scarcely colonized by the pathogen.

 

 

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation.

Author information: Zhang B1,2, Tieman DM1, Jiao C3,4, Xu Y3,4, Chen K2, Fe Z3,4, Giovannoni JJ3,4, Klee HJ5.

1Horticultural Sciences, Plant Innovation Center, Genetics Institute, University of Florida, Gainesville, FL 32611.
2Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Hangzhou 310058, People’s Republic of China.
3Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853.
4US Department of Agriculture-Agricultural Research Service Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853.
5Horticultural Sciences, Plant Innovation Center, Genetics Institute, University of Florida, Gainesville, FL 32611; hjklee@ufl.edu.

Journal: Proceedings of the National Academies of Sciences

Date of e-pub: November 2016

Abstract: Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.Commercial tomatoes are widely perceived by consumers as lacking flavor. A major part of that problem is a postharvest handling system that chills fruit. Low-temperature storage is widely used to slow ripening and reduce decay. However, chilling results in loss of flavor. Flavor-associated volatiles are sensitive to temperatures below 12 °C, and their loss greatly reduces flavor quality. Here, we provide a comprehensive view of the effects of chilling on flavor and volatiles associated with consumer liking. Reduced levels of specific volatiles are associated with significant reductions in transcripts encoding key volatile synthesis enzymes. Although expression of some genes critical to volatile synthesis recovers after a return to 20 °C, some genes do not. RNAs encoding transcription factors essential for ripening, including RIPENING INHIBITOR (RIN), NONRIPENING, and COLORLESS NONRIPENING are reduced in response to chilling and may be responsible for reduced transcript levels in many downstream genes during chilling. Those reductions are accompanied by major changes in the methylation status of promoters, including RIN Methylation changes are transient and may contribute to the fidelity of gene expression required to provide maximal beneficial environmental response with minimal tangential influence on broader fruit developmental biology.

 

 

Transcriptome assessment of the Pompe (Gaa-/-) mouse spinal cord indicates widespread neuropathology.

Author information: Turner SM1,2,3, Falk DJ3,4,5, Byrne BJ3,4,5, Fuller DD6,2,3.

1Department of Physical Therapy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
2McKnight Brain Institute, University of Florida, Gainesville, Florida.
3Center for Respiratory Research and Rehabilitation, University of Florida, Gainesville, Florida.
4Department of Pediatrics, Divisions of Cellular and Molecular Therapy and Pediatric Cardiology, College of Medicine, University of Florida, Gainesville, Florida; and.
5Powell Gene Therapy Center, University of Florida, Gainesville, Florida.
6Department of Physical Therapy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida; ddf@phhp.ufl.edu.

Journal: Physiological Genomics

Date of e-pub: November 2016

Abstract: Pompe disease, caused by deficiency of acid alpha-glucosidase (GAA), leads to widespread glycogen accumulation and profound neuromuscular impairments. There has been controversy, however, regarding the role of central nervous system pathology in Pompe motor dysfunction. We hypothesized that absence of GAA protein causes progressive activation of neuropathological signaling, including pathways associated with cell death. To test this hypothesis, genomic data (Affymetrix Mouse Gene Array 2.0ST) from the midcervical spinal cord in 6 and 16 mo old Pompe (Gaa-/-) mice were evaluated (Broad Institute Molecular Signature Database), along with spinal cord histology. The midcervical cord was selected because it contains phrenic motoneurons, and phrenic-diaphragm dysfunction is prominent in Pompe disease. Several clinically important themes for the neurologic etiology of Pompe disease emerged from this unbiased genomic assessment. First, pathways associated with cell death were strongly upregulated as Gaa-/- mice aged, and motoneuron apoptosis was histologically verified. Second, proinflammatory signaling was dramatically upregulated in the Gaa-/- spinal cord. Third, many signal transduction pathways in the Gaa-/- cervical cord were altered in a manner suggestive of impaired synaptic function. Notably, glutamatergic signaling pathways were downregulated, as were “synaptic plasticity pathways” including genes related to neuroplasticity. Fourth, many genes and pathways related to cellular metabolism are dysregulated. Collectively, the data unequivocally confirm that systemic absence of GAA induces a complex neuropathological cascade in the spinal cord. Most importantly, the results indicate that Pompe is a neurodegenerative condition, and this underscores the need for early therapeutic intervention capable of targeting the central nervous system.

 

 

Dietary Zinc Regulates Apoptosis through the Phosphorylated Eukaryotic Initiation Factor 2α/Activating Transcription Factor-4/C/EBP-Homologous Protein Pathway during Pharmacologically Induced Endoplasmic Reticulum Stress in Livers of Mice.

Author information: Kim MH1, Aydemir TB1, Cousins RJ2.

1Food Science and Human Nutrition, and Center for Nutritional Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL.
2Food Science and Human Nutrition, and Center for Nutritional Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville, FL cousins@ufl.edu.

Journal: Journal of Nutrition

Date of e-pub: November 2016

Abstract: Several in vitro studies have shown that zinc deficiency could induce endoplasmic reticulum (ER) stress, resulting in activation of the unfolded protein response.

We aimed to determine whether consumption of a zinc-deficient diet (ZnD) triggers ER stress and to understand the impact of dietary zinc intake on ER stress-induced apoptosis using a mouse model.

Young adult (8-16 wk of age) male mice of strain C57BL/6 were fed either a ZnD (<1 mg/kg diet), or a zinc-adequate diet (ZnA; 30 mg/kg diet). After 2 wk, liver, pancreas, and serum samples were collected and analyzed for indexes of ER stress. In another experiment, mice were fed either a ZnD, a ZnA, or a zinc-supplementation diet (ZnS; 180 mg/kg diet). After 2 wk, vehicle or tunicamycin (TM; 2 mg/kg body weight) was administered to mice to model ER stress. Liver and serum were analyzed for indexes of ER stress to evaluate the effects of zinc status.

Mice fed a ZnD did not activate the apoptotic and ER stress markers in the liver or pancreas. During the TM challenge, mice fed a ZnD showed greater C/EBP-homologous protein expression in the liver (3.8-fold, P < 0.01) than did ZnA-fed mice. TM-treated mice fed a ZnD also had greater terminal deoxynucleotidyl transferase deoxyuridine triphosphate nick-end labeling-positive cells in the liver (2.2-fold, P < 0.05), greater hepatic triglyceride accumulation (1.5-fold, P < 0.05), greater serum alanine aminotransferase activity (1.6-fold, P < 0.05), and greater protein-tyrosine phosphatase 1B activity (1.5-fold, P < 0.05), respectively, than did those fed a ZnA. No significant differences were observed in these parameters between mice fed ZnAs and ZnSs.

Consumption of a ZnD per se is not a critical factor for induction of ER stress in mice; however, once ER stress is triggered, adequate dietary zinc intake is required for suppressing apoptotic cell death and further insults in the liver of mice.

 

 

Genome-Wide and Gene-Based Meta-Analyses Identify Novel Loci Influencing Blood Pressure Response to Hydrochlorothiazide.

Author information: Salvi E1, Wang Z2, Rizzi F2, Gong Y2, McDonough CW2, Padmanabhan S2, Hiltunen TP2, Lanzani C2, Zaninello R2, Chittani M2, Bailey KR2, Sarin AP2, Barcella M2, Melander O2, Chapman AB2, Manunta P2, Kontula KK2, Glorioso N2, Cusi D2, Dominiczak AF2, Johnson JA2, Barlassina C2, Boerwinkle E2, Cooper-DeHoff RM2, Turner ST2.

1From the Department of Health Sciences, University of Milan, Italy (E.S., F.R., M.C., M.B., C.B.); Human Genetics and Institute of Molecular Medicine, University of Texas Health Science Center, Houston (Z.W., E.B.); Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy (Y.G., C.W.M., J.A.J., R.M.C.-D.) and Division of Cardiovascular Medicine, Department of Medicine (J.A.J., R.M.C.-D.), University of Florida, Gainesville; Institute of Cardiovascular and Medical Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, United Kingdom (S.P., A.F.D.); Department of Medicine, University of Helsinki and Helsinki University Hospital, Finland (T.P.H., K.K.K.); Nephrology and Dialysis and Hypertension Unit, San Raffaele Scientific Institute, Università Vita Salute San Raffaele, Milano, Italy (C.L., P.M.); Hypertension and Related Disease Centre, AOU-University of Sassari, Italy (R.Z., N.G.); Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (K.R.B.) and Division of Nephrology and Hypertension, Department of Internal Medicine (S.T.T.), Mayo Clinic, Rochester, Minnesota; Institute for Molecular Medicine Finland FIMM, University of Helsinki, Finland (A.-P.S); Department of Clinical Sciences, Lund University, Malmö, Sweden (O.M.); Section of Nephrology, Department of Medicine, University of Chicago, Illinois (A.B.C.); Institute of Biomedical Technologies, National Research Centre of Italy, Segrate, Milan, Italy (D.C.); and Sanipedia srl, Bresso, Italy (D.C.). erika.salvi@unimi.it.
2From the Department of Health Sciences, University of Milan, Italy (E.S., F.R., M.C., M.B., C.B.); Human Genetics and Institute of Molecular Medicine, University of Texas Health Science Center, Houston (Z.W., E.B.); Department of Pharmacotherapy and Translational Research, Center for Pharmacogenomics, College of Pharmacy (Y.G., C.W.M., J.A.J., R.M.C.-D.) and Division of Cardiovascular Medicine, Department of Medicine (J.A.J., R.M.C.-D.), University of Florida, Gainesville; Institute of Cardiovascular and Medical Sciences, College of Medical Veterinary and Life Sciences, University of Glasgow, United Kingdom (S.P., A.F.D.); Department of Medicine, University of Helsinki and Helsinki University Hospital, Finland (T.P.H., K.K.K.); Nephrology and Dialysis and Hypertension Unit, San Raffaele Scientific Institute, Università Vita Salute San Raffaele, Milano, Italy (C.L., P.M.); Hypertension and Related Disease Centre, AOU-University of Sassari, Italy (R.Z., N.G.); Division of Biomedical Statistics and Informatics, Department of Health Sciences Research (K.R.B.) and Division of Nephrology and Hypertension, Department of Internal Medicine (S.T.T.), Mayo Clinic, Rochester, Minnesota; Institute for Molecular Medicine Finland FIMM, University of Helsinki, Finland (A.-P.S); Department of Clinical Sciences, Lund University, Malmö, Sweden (O.M.); Section of Nephrology, Department of Medicine, University of Chicago, Illinois (A.B.C.); Institute of Biomedical Technologies, National Research Centre of Italy, Segrate, Milan, Italy (D.C.); and Sanipedia srl, Bresso, Italy (D.C.).

Journal: Hypertension

Date of e-pub: October 2016

Abstract: This study aimed to identify novel loci influencing the antihypertensive response to hydrochlorothiazide monotherapy. A genome-wide meta-analysis of blood pressure (BP) response to hydrochlorothiazide was performed in 1739 white hypertensives from 6 clinical trials within the International Consortium for Antihypertensive Pharmacogenomics Studies, making it the largest study to date of its kind. No signals reached genome-wide significance (P<5×108), and the suggestive regions (P<10-5) were cross-validated in 2 black cohorts treated with hydrochlorothiazide. In addition, a gene-based analysis was performed on candidate genes with previous evidence of involvement in diuretic response, in BP regulation, or in hypertension susceptibility. Using the genome-wide meta-analysis approach, with validation in blacks, we identified 2 suggestive regulatory regions linked to gap junction protein α1 gene (GJA1) and forkhead box A1 gene (FOXA1), relevant for cardiovascular and kidney function. With the gene-based approach, we identified hydroxy-delta-5-steroid dehydrogenase, 3 β- and steroid δ-isomerase 1 gene (HSD3B1) as significantly associated with BP response (P<2.28×10-4). HSD3B1 encodes the 3β-hydroxysteroid dehydrogenase enzyme and plays a crucial role in the biosynthesis of aldosterone and endogenous ouabain. By amassing all of the available pharmacogenomic studies of BP response to hydrochlorothiazide, and using 2 different analytic approaches, we identified 3 novel loci influencing BP response to hydrochlorothiazide. The gene-based analysis, never before applied to pharmacogenomics of antihypertensive drugs to our knowledge, provided a powerful strategy to identify a locus of interest, which was not identified in the genome-wide meta-analysis because of high allelic heterogeneity. These data pave the way for future investigations on new pathways and drug targets to enhance the current understanding of personalized antihypertensive treatment.

 

 

Uterine Microbiota and Immune Parameters Associated with Fever in Dairy Cows with Metritis.

Author information: Jeon SJ1, Cunha F1, Ma X1, Martinez N2, Vieira-Neto A2, Daetz R1, Bicalho RC3, Lima S3, Santos JE2, Jeong KC2,4, Galvão KN1,5.

1Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville, Florida, United States of America.
2Department of Animal Sciences, University of Florida, Gainesville, Florida, United States of America.
3Department of Population Medicine and Diagnostic Sciences, Cornell University, Ithaca, New York, United States of America.
4Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.
5D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville, Florida, United States of America.

Journal: PLoS One

Date of e-pub: November 2016

Abstract: This study aimed to evaluate bacterial and host factors causing a fever in cows with metritis. For that, we investigated uterine microbiota using a metagenomic sequencing of the 16S rRNA gene (Study 1), and immune response parameters (Study 2) in metritic cows with and without a fever.

Bacterial communities were similar between the MNoFever and MFever groups based on distance metrics of relative abundance of bacteria. Metritic cows showed a greater prevalence of Bacteroidetes, and Bacteroides and Porphyromonas were the largest contributors to that difference. A comparison of relative abundance at the species level pointed to Bacteroides pyogenes as a fever-related species which was significantly abundant in the MFever than the MNoFever and Healthy groups; however, absolute abundance of Bacteroides pyogenes determined by droplet digital PCR (ddPCR) was similar between MFever and MNoFever groups, but higher than the Healthy group. The same trend was observed in the total number of bacteria.

The activity of polymorphonuclear leukocyte (PMN) and the production of TNFα, PGE2 metabolite, and PGE2 were evaluated in serum, before disease onset, at 0 and 3 DPP. Cows in the MNoFever had decreased proportion of PMN undergoing phagocytosis and oxidative burst compared with the MFever. The low PMN activity in the MNoFever was coupled with the low production of TNFα, but similar PGE2 metabolite and circulating PGE2.

Our study is the first to show a similar microbiome between metritic cows with and without a fever, which indicates that the host response may be more important for fever development than the microbiome. Bacteroides pyogenes was identified as an important pathogen for the development of metritis but not fever. The decreased inflammatory response may explain the lack of a febrile response in the MNoFever group.

 

 

Isolation of Coronavirus NL63 from Blood from Children in Rural Haiti: Phylogenetic Similarities with Recent Isolates from Malaysia.

Author information: Beau De Rochars VM1,2, Lednicky J1,3, White S1,3, Loeb J1,3, Elbadry MA1,3, Telisma T1,4, Chavannes S1,4, Anilis MG1,4, Cella E1,5,6, Ciccozzi M6, Okech BA1,3, Salemi M1,5, Morris JG Jr7,8.

1Emerging Pathogens Institute, University of Florida, Gainesville, Florida.
2Department of Health Services Research, Management and Policy, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
3Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, Florida.
4Christianville Foundation, School Clinic, Gressier, Haiti.
5Department of Pathology, Immunology and Laboratory Sciences, College of Medicine, University of Florida, Gainesville, Florida.
6Department of Infectious Parasitic and Immunomediated Diseases, Reference Centre on Phylogeny, Molecular Epidemiology and Microbial Evolution (FEMEM)/Epidemiology Unit, Istituto Superiore di Sanita, Rome, Italy.
7Emerging Pathogens Institute, University of Florida, Gainesville, Florida. jgmorris@epi.ufl.edu.
8Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida.

Journal: American Journal of Tropical Medicine and Hygiene

Date of e-pub: October 2016

Abstract: Human coronavirus (HCoV) NL63 is recognized as a common cause of upper respiratory infections and influenza-like illness. In screening children with acute undifferentiated febrile illness in a school cohort in rural Haiti, we identified HCoV-NL63 in blood samples from four children. Cases clustered over an 11-day period; children did not have respiratory symptoms, but two had gastrointestinal complaints. On phylogenetic analysis, the Haitian HCoV-NL63 strains cluster together in a highly supported monophyletic clade linked most closely with recently reported strains from Malaysia; two respiratory HCoV-NL63 strains identified in north Florida in the same general period form a separate clade, albeit again with close linkages with the Malaysian strains. Our data highlight the variety of presentations that may be seen with HCoV-NL63, and underscore the apparent ease with which CoV strains move among countries, with our data consistent with recurrent introduction of strains into the Caribbean (Haiti and Florida) from Asia.

 

 

Paradoxical leanness in the imprinting centre deletion mouse model for Prader-Willi syndrome.

Author information: Golding DM1, Rees DJ2, Davies JR3, Relkovic D4, Furby HV5, Guschina IA6, Hopkins AL7, Davies JS8, Resnick JL9, Isles AR10, Wells T11.

1D Golding, School of Biosciences, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
2D Rees, Institute of Life Sciences, College of Medicine, Swansea University, Swansea, United Kingdom of Great Britain and Northern Ireland.
3J Davies, Neuroscience and Mantal Health Research Institute, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
4D Relkovic, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
5H Furby, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
6I Guschina, School of Biosciences, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
7A Hopkins, School of Biosciences, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
8J Davies, Institute of Life Sciences, College of Medicine, Swansea University, Swansea, United Kingdom of Great Britain and Northern Ireland.
9J Resnick, College of Medicine, University of Florida, Gainesville, United States.
10A Isles, Neuroscience and Mental Health Research Institute, Cardiff University, Cardiff, United Kingdom of Great Britain and Northern Ireland.
11T Wells, School of Biosciences, Cardiff University, Cardiff, CF10 3US, United Kingdom of Great Britain and Northern Ireland wellst@cardiff.ac.uk.

Journal: Journal of Endocrinology

Date of e-pub: October 2016

Abstract: Prader-Willi syndrome (PWS), a neurodevelopmental disorder caused by loss of paternal gene expression from 15q11-q13, is characterised by growth retardation, hyperphagia, and obesity. However, since single gene mutation mouse models for this condition display an incomplete spectrum of the PWS phenotype, we have characterised the metabolic impairment in a mouse model for “full” PWS, in which deletion of the imprinting centre (IC) abolishes paternal gene expression from the entire PWS-cluster. We show that PWS-ICdel mice displayed post-natal growth retardation, with reduced body weight, hyperghrelinaemia and marked abdominal leanness; proportionate retroperitoneal, epididymal/omental and inguinal white adipose tissue (WAT) weights being reduced by 82%, 84% and 67% respectively. PWS-ICdel mice also displayed a 48% reduction in proportionate interscapular brown adipose tissue (isBAT) weight with significant ‘beiging’ of abdominal WAT, and a 2°C increase in interscapular surface body temperature. Maintenance of PWS-ICdel mice under thermoneutral conditions (30°C) suppressed thermogenic activity in PWS-ICdel males, but failed to elevate abdominal WAT weight, possibly due to a normalisation of caloric intake. Interestingly, PWS-ICdel mice also showed exaggerated food hoarding behaviour with standard and high-fat diets, but, despite becoming hyperphagic when switched to a high-fat diet, PWS-ICdel mice failed to gain weight. This evidence indicates that, unlike humans with PWS, loss of paternal gene expression from the PWS-cluster in mice results in abdominal leanness. While reduced subcutaneous insulation may lead to exaggerated heat loss and thermogenesis, abdominal leanness is likely to arise from a reduced lipid storage capacity rather than increased energy utilisation in BAT.

 

 

The tale of the shrinking weapon: seasonal changes in nutrition affect weapon size and sexual dimorphism, but not contemporary evolution.

Author information: Miller CW1, McDonald GC2, Moore AJ3.

1Entomology and Nematology Department, University of Florida, Gainesville, FL, USA. cwmiller@ufl.edu.
2Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK.
3Department of Genetics, University of Georgia, Athens, GA, USA.

Journal: Journal of Evolutionary Biology

Date of e-pub: November 2016

Abstract: Sexually selected traits are often highly variable in size within populations due to their close link with the physical condition of individuals. Nutrition has a large impact on physical condition, and thus, any seasonal changes in nutritional quality are predicted to alter the average size of sexually selected traits as well as the degree of sexual dimorphism in populations. However, although traits affected by mate choice are well studied, we have a surprising lack of knowledge of how natural variation in nutrition affects the expression of sexually selected weapons and sexual dimorphism. Further, few studies explicitly test for differences in the heritability and mean-scaled evolvability of sexually selected traits across conditions. We studied Narnia femorata (Hemiptera: Coreidae), an insect where males use their hind legs as weapons and the femurs are enlarged, to understand the extent to which weapon expression, sexual dimorphism and evolvability change across the actual range of nutrition available in the wild. We found that insects raised on a poor diet (cactus without fruit) are nearly monomorphic, whereas those raised on a high-quality diet (cactus with ripe fruit) are distinctly sexually dimorphic via the expression of large hind leg weapons in males. Contrary to our expectations, we found little evidence of a potential for evolutionary change for any trait measured. Thus, although we show weapons are highly condition dependent, and changes in weapon expression and dimorphism could alter evolutionary dynamics, our populations are unlikely to experience further evolutionary changes under current conditions.

 

 

Longitudinal Patterns of Thalidomide Neuropathy in Children and Adolescents.

Author information: Liew WK1, Pacak CA2, Visyak N3, Darras BT3, Bousvaros A4, Kang PB5.

1Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA; Neurology Service, Department of Pediatrics, KK Women’s and Children’s Hospital, Singapore.
2Child Health Research Institute, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL.
3Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA.
4Division of Gastroenterology, Hepatology, and Nutrition, Boston Children’s Hospital and Harvard Medical School, Boston, MA.
5Department of Neurology, Boston Children’s Hospital and Harvard Medical School, Boston, MA; Division of Pediatric Neurology, Department of Pediatrics, University of Florida College of Medicine, Gainesville, FL. Electronic address: pbkang@ufl.edu.

Journal: Journal of Pediatrics

Date of e-pub: November 2016

Abstract: To characterize the longitudinal clinical and electrophysiological patterns of thalidomide neuropathy in children and adolescents.

Retrospective analysis of clinical records at a tertiary care children’s hospital, including serial electrophysiological studies.

Sixteen patients aged 6-24 years received thalidomide to treat Crohn’s disease from 2002 to 2012. Nine subjects had electrophysiological evidence of sensorimotor axonal polyneuropathy, 8 of whom had sensory and/or motor symptoms. The patients with polyneuropathy received thalidomide for 5 weeks to 52 months, with cumulative doses ranging from 1.4 to 207.7 g. All subjects with cumulative doses greater than 60 g developed polyneuropathy, and 4 of the 5 subjects who received thalidomide for more than 20 months developed polyneuropathy. The 7 subjects who had normal neurophysiological studies received therapy for 1 week to 25 months, with cumulative doses ranging from 0.7 to 47 g. In contrast to some previous reports, several patients had sensorimotor polyneuropathies, rather than pure sensory neuropathies. In patients with neuropathy who received therapy for more than 24 months and had 3 or more electromyography studies, the severity of the neuropathy plateaued.

Factors in addition to the total dose may contribute to the risk profile for thalidomide neuropathy, including pharmacogenetic susceptibilities. The severity of the neuropathy does not worsen relentlessly. Children, adolescents, and young adults receiving thalidomide should undergo regular neurophysiological studies to monitor for neuropathy.

 

 

Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane.

Author information: Jung JH1,2, Kannan B1, Dermawan H1, Moxley GW3, Altpeter F4,5,6.

1Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA.
2Institute of Life Science and Natural Resources, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul, 02841, South Korea.
3Novozymes North America Inc, Franklinton, NC, 27525, USA.
4Agronomy Department, IFAS, University of Florida, PO Box 110500, Gainesville, FL, 32611, USA. altpeter@ufl.edu.
5Plant Molecular and Cellular Biology Program, IFAS, University of Florida, PO Box 110300, Gainesville, FL, 32611, USA. altpeter@ufl.edu.
6University of Florida Genetics Institute, PO Box 103610, Gainesville, FL, 32610, USA. altpeter@ufl.edu.

Journal: Plant Molecular Biology

Date of e-pub: November 2016

Abstract: Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5 % along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52-76 % improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.

 

 

Biopsychosocial Influence on Shoulder Pain: Influence of Genetic and Psychological Combinations on Twelve-Month Postoperative Pain and Disability Outcomes.

Author information: George SZ1, Wu SS2, Wallace MR3, Moser MW2, Wright TW2, Farmer KW2, Greenfield WH 3rd2, Dai Y2, Li H3, Fillingim RB2.

1University of Florida, Gainesville. szgeorge@phhp.ufl.edu.
2University of Florida, Gainesville.
3University of Florida Genetics Institute, University of Florida, Gainesville.

Journal: Arthritis Care & Research

Date of e-pub: November 2016

Abstract: To identify novel combinations of genetic and psychological factors that predicted 12-month postoperative pain and disability outcomes following arthroscopic shoulder surgery.

A prospective presurgical cohort (n = 150) was recruited to complete validated psychological questionnaires and have their DNA collected from saliva. DNA was genotyped for a priori selected genes involved with pain modulation (ADRB2, OPRM1, AVPR1A, GCH1, and KCNS1) and inflammation (IL1B, TNF/LTA, and IL6). The outcome measures of interest were the Brief Pain Inventory and Disabilities of the Arm, Shoulder, and Hand questionnaire. Followup for the cohort was at 3, 6, and 12 months postoperatively. After controlling for age, sex, race, and preoperative status, genetic and psychological factors were entered as main effects and interaction terms in separate general linear models for predicting postoperative pain and disability outcomes.

Seven interactions involving pain-modulatory genes were identified. Three provided strong statistical evidence for different outcomes, including KCNS1 and kinesiophobia for preoperative pain intensity, ADRB2 and depressive symptoms for postoperative course, and GCH1 and anxiety symptoms for 12-month pain-intensity outcome. Ten interactions involving inflammatory genes were identified. Three provided strong statistical evidence for the 12-month postoperative course outcome, including 2 different IL6 single-nucleotide polymorphism and pain catastrophizing, and IL6 and depressive symptoms.

The current study identified novel genetic and psychological interactions that can be used in future studies to further understand the development of persistent postoperative pain and investigate the effectiveness of tailored treatment.

 

 

Modification of embryonic resistance to heat shock in cattle by melatonin and genetic variation in HSPA1L.

Author information: Ortega MS1, Rocha-Frigoni NA2, Mingoti GZ2, Roth Z3, Hansen PJ4.

1Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville 32611-0910.
2School of Veterinary Medicine, Laboratory of Reproductive Physiology, Universidade Estadual Paulista, Araçatuba, SP 16050-680, Brazil; Graduate Program in Veterinary Medicine, School of Agrarian and Veterinary Sciences, Department of Animal Reproduction, Universidade Estadual Paulista, Jaboticabal, SP 16050-680, Brazil.
3Department of Animal Sciences, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University, Rehovot 76100, Israel.
4Department of Animal Sciences, D.H. Barron Reproductive and Perinatal Biology Research Program and Genetics Institute, University of Florida, Gainesville 32611-0910. Electronic address: pjhansen@ufl.edu.

Journal: Journal of Dairy Science

Date of e-pub: November 2016

Abstract: The objectives were to test whether (1) melatonin blocks inhibition of embryonic development caused by heat shock at the zygote stage, and (2) the frequency of a thermoprotective allele for HSPA1L is increased in blastocysts formed from heat-shocked zygotes as compared with blastocysts from control zygotes. It was hypothesized that melatonin prevents effects of heat shock on development by reducing accumulation of reactive oxygen species (ROS) and that embryos inheriting the thermoprotective allele of HSPA1L would be more likely to survive heat shock. Effects of 1 µM melatonin on ROS were determined in experiments 1 and 2. Zygotes were cultured at 38.5 or 40°C for 3 h in the presence of CellROX reagent (ThermoFisher Scientific, Waltham, MA). Culture was in a low [5% (vol/vol)] oxygen (experiment 1) or low or high [21% (vol/vol)] oxygen environment (experiment 2). Heat shock and high oxygen increased ROS; melatonin decreased ROS. Development was assessed in experiments 3 and 4. In experiment 3, zygotes were cultured in low oxygen ± 1 µM melatonin and exposed to 38.5 or 40°C for 12 h (experiment 1) beginning 8 h after fertilization. Melatonin did not protect the embryo from heat shock. Experiment 4 was performed similarly except that temperature treatments (38.5 or 40°C, 24 h) were performed in a low or high oxygen environment (2×2 × 2 factorial design with temperature, melatonin, and oxygen concentration as main effects), and blastocysts were genotyped for a deletion (D) mutation (C→D) in the promoter region of HSPA1L associated with thermotolerance. Heat shock decreased percent of zygotes developing to the blastocyst stage independent of melatonin or oxygen concentration. Frequency of genotypes for HSPA1L was affected by oxygen concentration and temperature, with an increase in the D allele for blastocysts that developed in high oxygen and following heat shock. It was concluded that (1) lack of effect of melatonin or oxygen concentration on embryonic development means that the negative effects of heat shock on the zygote are not mediated by ROS, (2) previously reported effect of melatonin on fertility of heat-stressed cows might involve actions independent of the antioxidant properties of melatonin, and (3) the deletion mutation in the promoter of HSPA1L confers protection to the zygote from heat shock and high oxygen. Perhaps, embryonic survival during heat stress could be improved by selecting for thermotolerant genotypes.

 

 

Clinical response after chitosan microparticle administration and preliminary assessment of efficacy in preventing metritis in lactating dairy cows.

Author information: Daetz R1, Cunha F1, Bittar JH1, Risco CA1, Magalhaes F2, Maeda Y3, Santos JE4, Jeong KC5, Cooke RF6, Galvão KN7.

1Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville 32610.
2School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, SP 05508 270, Brazil.
3School of Veterinary Medicine, Kitasato University, Towada, Aomori, 034-8628, Japan.
4Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville 32610.
5Department of Animal Sciences, College of Agricultural and Life Sciences, University of Florida, Gainesville 32610; Emerging Pathogens Institute, University of Florida, Gainesville 32610.
6Eastern Oregon Agricultural Research Center, Oregon State University, Burns 97720.
7Department of Large Animal Clinical Sciences, College of Veterinary Medicine, University of Florida, Gainesville 32610; D. H. Barron Reproductive and Perinatal Biology Research Program, University of Florida, Gainesville 32610. Electronic address: galvaok@ufl.edu.

Journal: Journal of Dairy Science

Date of e-pub: November 2016

Abstract: The objectives were to evaluate the clinical response to intrauterine administration of chitosan microparticles (CM) and to assess efficacy for preventing metritis in dairy cows. Holstein cows (n=104; 40 primiparous and 64 multiparous) at increased risk for metritis (cows that had abortion, dystocia, twins, stillbirth, or retained placenta) were randomly assigned to 1 of 2 treatments at 1d in milk (DIM; 24h postpartum): CM group (n=52), daily intrauterine infusion of 8g of CM dissolved in 40mL of sterile water for 5d; control (CON) group (n=52), daily intrauterine infusion of 40mL of sterile water for 5d. Clinical response was assessed by evaluation of parameters associated with inflammation (rectal temperature and plasma haptoglobin concentration) and metabolism [plasma nonesterified fatty acid (NEFA) and β-hydroxybutyrate (BHB) concentrations] up to 14 DIM, and daily milk yield up to 30 DIM. Uterine discharge pH was evaluated at 4, 7, 10, and 14 DIM as an indicator of bacterial load and acid byproduct production. The cumulative incidence of metritis was evaluated up to 4, 7, 10, and 14 DIM. Continuous and dichotomous outcomes were evaluated with mixed linear and logistic regression analysis, respectively. Treatment with CM did not affect rectal temperature (39.17±0.04 vs. 39.14±0.04°C), haptoglobin (1.10±0.05 vs. 1.07±0.05mg/mL), NEFA (0.64±0.04 vs. 0.63±0.04mmol/L), BHB (0.61±0.03 vs. 0.57±0.03mmol/L), or milk yield (30.3±0.92 vs. 30.1±0.97kg/d) compared with CON. An interaction between treatment and time showed that NEFA concentrations were lower for CM than CON at 10 DIM (0.46±0.06 vs. 0.64±0.06mmol/L). Treatment with CM resulted in greater uterine discharge pH than CON (6.91±0.03 vs. 6.83±0.02). Cows that developed metritis had increased concentrations of haptoglobin and BHB, and decreased uterine discharge pH and milk yield. Treatment with CM resulted in decreased incidence of metritis up to 7 DIM compared with CON (46.2 vs. 65.4%); however, no differences were found at 4 (11.5 vs. 17.3%), 10 (61.5 vs. 73.1%), and 14 DIM (63.5 vs. 73.1%) for CM versus CON, respectively. In conclusion, CM did not alter clinical parameters of cows at risk for metritis, and may merit further investigation for prevention of metritis. However, the duration of treatment may have to be extended to effectively reduce the incidence of metritis during the high-risk period.

 

 

Circuitry Linking the Catabolite Repression and Csr Global Regulatory Systems of Escherichia coli.

Author information: Pannuri A1, Vakulskas CA1, Zere T1, McGibbon LC2, Edwards AN3, Georgellis D4, Babitzke P2, Romeo T5.

1Department of Microbiology and Cell Science, University of Florida, Institute of Food and Agricultural Sciences, Gainesville, Florida, USA.
2Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.
3Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA.
4Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
5Department of Microbiology and Cell Science, University of Florida, Institute of Food and Agricultural Sciences, Gainesville, Florida, USA tromeo@ufl.edu.

Journal: Journal of Bacteriology

Date of e-pub: October 2016

Abstract: Cyclic AMP (cAMP) and the cAMP receptor protein (cAMP-CRP) and CsrA are the principal regulators of the catabolite repression and carbon storage global regulatory systems, respectively. cAMP-CRP controls the transcription of genes for carbohydrate metabolism and other processes in response to carbon nutritional status, while CsrA binds to diverse mRNAs and regulates translation, RNA stability, and/or transcription elongation. CsrA also binds to the regulatory small RNAs (sRNAs) CsrB and CsrC, which antagonize its activity. The BarA-UvrY two-component signal transduction system (TCS) directly activates csrB and csrC (csrB/C) transcription, while CsrA does so indirectly. We show that cAMP-CRP inhibits csrB/C transcription without negatively regulating phosphorylated UvrY (P-UvrY) or CsrA levels. A crp deletion caused an elevation in CsrB/C levels in the stationary phase of growth and increased the expression of csrB-lacZ and csrC-lacZ transcriptional fusions, although modest stimulation of CsrB/C turnover by the crp deletion partially masked the former effects. DNase I footprinting and other studies demonstrated that cAMP-CRP bound specifically to three sites located upstream from the csrC promoter, two of which overlapped the P-UvrY binding site. These two proteins competed for binding at the overlapping sites. In vitro transcription-translation experiments confirmed direct repression of csrC-lacZ expression by cAMP-CRP. In contrast, cAMP-CRP effects on csrB transcription may be mediated indirectly, as it bound nonspecifically to csrB DNA. In the reciprocal direction, CsrA bound to crp mRNA with high affinity and specificity and yet exhibited only modest, conditional effects on expression. Our findings are incorporated into an emerging model for the response of Csr circuitry to carbon nutritional status.

Csr (Rsm) noncoding small RNAs (sRNAs) CsrB and CsrC of Escherichia coli use molecular mimicry to sequester the RNA binding protein CsrA (RsmA) away from lower-affinity mRNA targets, thus eliciting major shifts in the bacterial lifestyle. CsrB/C transcription and turnover are activated by carbon metabolism products (e.g., formate and acetate) and by a preferred carbon source (glucose), respectively. We show that cAMP-CRP, a mediator of classical catabolite repression, inhibits csrC transcription by binding to the upstream region of this gene and also inhibits csrB transcription, apparently indirectly. We propose that glucose availability activates pathways for both synthesis and turnover of CsrB/C, thus shaping the dynamics of global signaling in response to the nutritional environment by poising CsrB/C sRNA levels for rapid response.

 

 

A norovirus detection architecture based on isothermal amplification and expanded genetic systems.

Author information: Yaren O1, Bradley KM1, Moussatche P2, Hoshika S1, Yang Z1, Zhu S3, Karst SM3, Benner SA4.

1Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, # 7, Alachua, FL 32615, USA.
2Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA.
3Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville FL 32611, USA; The Emerging Pathogens Institute, University of Florida, Gainesville FL 32611, USA.
4Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, # 17, Alachua, FL 32615, USA. Electronic address: manuscripts@ffame.org.

Journal: Journal of Virological Methods

Date of e-pub: November 2016

Abstract: Noroviruses are the major cause of global viral gastroenteritis with short incubation times and small inoculums required for infection. This creates a need for a rapid molecular test for norovirus for early diagnosis, in the hope of preventing the spread of the disease. Non-chemists generally use off-the shelf reagents and natural DNA to create such tests, suffering from background noise that comes from adventitious DNA and RNA (collectively xNA) that is abundant in real biological samples, especially feces, a common location for norovirus. Here, we create an assay that combines artificially expanded genetic information systems (AEGIS, which adds nucleotides to the four in standard xNA, pairing orthogonally to A:T and G:C) with loop-mediated isothermal amplification (LAMP) to amplify norovirus RNA at constant temperatures, without the power or instrument requirements of PCR cycling. This assay was then validated using feces contaminated with murine norovirus (MNV). Treating stool samples with ammonia extracts the MNV RNA, which is then amplified in an AEGIS-RT-LAMP where AEGIS segments are incorporated both into an internal LAMP primer and into a molecular beacon stem, the second lowering background signaling noise. This is coupled with RNase H nicking during sample amplification, allowing detection of as few as 10 copies of noroviral RNA in a stool sample, generating a fluorescent signal visible to human eye, all in a closed reaction vessel.

 

 

Islet cell hyperexpression of HLA class I antigens: a defining feature in type 1 diabetes.

Author information: Richardson SJ1, Rodriguez-Calvo T2, Gerling IC3, Mathews CE4, Kaddis JS5, Russell MA6, Zeissler M6, Leete P6, Krogvold L7,8, Dahl-Jørgensen K7,8, von Herrath M2, Pugliese A9,10, Atkinson MA4, Morgan NG11.

1Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building (Level 4), Barrack Road, Exeter, EX2 5DW, UK. s.richardson@exeter.ac.uk.
2La Jolla Institute for Allergy and Immunology, San Diego, CA, USA.
3Department of Medicine, University of Tennessee, Memphis, TN, USA.
4Department of Pathology, University of Florida, Gainesville, FL, USA.
5Department of Information Sciences, City of Hope, Duarte, CA, USA.
6Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building (Level 4), Barrack Road, Exeter, EX2 5DW, UK.
7Paediatric Department, Oslo University Hospital, Oslo, Norway.
8Faculty of Medicine, University of Oslo, Oslo, Norway.
9Diabetes Research Institute, Department of Medicine, Division of Diabetes, Endocrinology and Metabolism, University of Miami Miller School of Medicine, Miami, FL, USA.
10Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA.
11Islet Biology Exeter (IBEx), Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, RILD Building (Level 4), Barrack Road, Exeter, EX2 5DW, UK. n.g.morgan@exeter.ac.uk.

Journal: Diabetologia

Date of e-pub: November 2016

Abstract: Human pancreatic beta cells may be complicit in their own demise in type 1 diabetes, but how this occurs remains unclear. One potentially contributing factor is hyperexpression of HLA class I antigens. This was first described approximately 30 years ago, but has never been fully characterised and was recently challenged as artefactual. Therefore, we investigated HLA class I expression at the protein and RNA levels in pancreases from three cohorts of patients with type 1 diabetes. The principal aims were to consider whether HLA class I hyperexpression is artefactual and, if not, to determine the factors driving it.

Pancreas samples from type 1 diabetes patients with residual insulin-containing islets (n = 26) from the Network for Pancreatic Organ donors with Diabetes (nPOD), Diabetes Virus Detection study (DiViD) and UK recent-onset type 1 diabetes collections were immunostained for HLA class I isoforms, signal transducer and activator of transcription 1 (STAT1), NLR family CARD domain containing 5 (NLRC5) and islet hormones. RNA was extracted from islets isolated by laser-capture microdissection from nPOD and DiViD samples and analysed using gene-expression arrays.

Hyperexpression of HLA class I was observed in the insulin-containing islets of type 1 diabetes patients from all three tissue collections, and was confirmed at both the RNA and protein levels. The expression of β2-microglobulin (a second component required for the generation of functional HLA class I complexes) was also elevated. Both ‘classical’ HLA class I isoforms (i.e. HLA-ABC) as well as a ‘non-classical’ HLA molecule, HLA-F, were hyperexpressed in insulin-containing islets. This hyperexpression did not correlate with detectable upregulation of the transcriptional regulator NLRC5. However, it was strongly associated with increased STAT1 expression in all three cohorts. Islet hyperexpression of HLA class I molecules occurred in the insulin-containing islets of patients with recent-onset type 1 diabetes and was also detectable in many patients with disease duration of up to 11 years, declining thereafter.

Islet cell HLA class I hyperexpression is not an artefact, but is a hallmark in the immunopathogenesis of type 1 diabetes. The response is closely associated with elevated expression of STAT1 and, together, these occur uniquely in patients with type 1 diabetes, thereby contributing to their selective susceptibility to autoimmune-mediated destruction.

 

 

A single amino acid (Asp159) from the dog prion protein suppresses the toxicity of the mouse prion protein in Drosophila.

Author information: Sanchez-Garcia J1, Jensen K1, Zhang Y1, Rincon-Limas DE2, Fernandez-Funez P3.

1McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, FL 32611, USA.
2McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, FL 32611, USA; Department of Neuroscience, Genetics Institute and Center for Translational Research on Neurodegenerative Disorders, University of Florida, Gainesville, FL 32611, USA.
3McKnight Brain Institute, Department of Neurology, University of Florida, Gainesville, FL 32611, USA; Department of Neuroscience, Genetics Institute and Center for Translational Research on Neurodegenerative Disorders, University of Florida, Gainesville, FL 32611, USA. Electronic address: pedro.ffunez@gmail.com.

Journal: Neurobiology of Disease

Date of e-pub: November 2016

Abstract: Misfolding of the prion protein (PrP) is the key step in the transmission of spongiform pathologies in humans and several animals. Although PrP is highly conserved in mammals, a few changes in the sequence of endogenous PrP are proposed to confer protection to dogs, which were highly exposed to prion during the mad-cow epidemics. D159 is a unique amino acid found in PrP from dogs and other canines that was shown to alter surface charge, but its functional relevance has never been tested in vivo. Here, we show in transgenic Drosophila that introducing the N159D substitution on mouse PrP decreases its turnover. Additionally, mouse PrP-N159D demonstrates no toxicity and accumulates no pathogenic conformations, suggesting that a single D159 substitution is sufficient to prevent PrP conformational change and pathogenesis. Understanding the mechanisms mediating the protective activity of D159 is likely to lessen the burden of prion diseases in humans and domestic animals.

 

 

Vaccinia virus dissemination requires p21-activated kinase 1.

Author information: Andrade LG1,2, Albarnaz JD1,2,3, Mügge FL1,2, David BA4, Abrahão JS2, da Fonseca FG5, Kroon EG2, Menezes GB4, McFadden G6, Bonjardim CA7,8.

1Signal Transduction Group, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
2Viruses Laboratory, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
3Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, UK.
4Immunobiophotonics Laboratory, Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
5Laboratory of Basic and Applied Virology, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil.
6Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, USA.
7Signal Transduction Group, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Campus Pampulha, Belo Horizonte, Minas Gerais, 31270-901, Brazil. claudio.bonjardim@pq.cnpq.br.
8Viruses Laboratory, Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 31270-901, Brazil. claudio.bonjardim@pq.cnpq.br.

Journal: Archives of Virology

Date of e-pub: November 2016

Abstract: The orthopoxvirus vaccinia virus (VACV) interacts with both actin and microtubule cytoskeletons in order to generate and spread progeny virions. Here, we present evidence demonstrating the involvement of PAK1 (p21-activated kinase 1) in the dissemination of VACV. Although PAK1 activation has previously been associated with optimal VACV entry via macropinocytosis, its absence does not affect the production of intracellular mature virions (IMVs) and extracellular enveloped virions (EEVs). Our data demonstrate that low-multiplicity infection of PAK1(-/-) MEFs leads to a reduction in plaque size followed by decreased production of both IMVs and EEVs, strongly suggesting that virus spread was impaired in the absence of PAK1. Confocal and scanning electron microscopy showed a substantial reduction in the amount of VACV-induced actin tails in PAK1(-/-) MEFs, but no significant alteration in the total amount of cell-associated enveloped virions (CEVs). Furthermore, the decreased VACV dissemination in PAK1(-/-) cells was correlated with the absence of phosphorylated ARPC1 (Thr21), a downstream target of PAK1 and a key regulatory subunit of the ARP2/3 complex, which is necessary for the formation of actin tails and viral spread. We conclude that PAK1, besides its role in virus entry, also plays a relevant role in VACV dissemination.

 

 

Patterns of abiotic niche shifts in allopolyploids relative to their progenitors.

Author information: Blaine Marchant D1,2, Soltis DE3,4,5, Soltis PS4,5.

1Department of Biology, University of Florida, Gainesville, FL, 32611, USA. dbmarchant@ufl.edu.
2Florida Museum of Natural History, Gainesville, FL, 32611, USA. dbmarchant@ufl.edu.
3Department of Biology, University of Florida, Gainesville, FL, 32611, USA.
4Florida Museum of Natural History, Gainesville, FL, 32611, USA.
5Genetics Institute, University of Florida, Gainesville, FL, 32611, USA.

Journal: New Phylotology

Date of e-pub: November 2016

Abstract: Polyploidy has extensive genetic, physiological, morphological, and ecological ramifications. While the patterns underlying the genetic and morphological consequences of polyploidy are being rapidly elucidated, the effects on ecological niche are still largely unknown. This study investigated 13 allopolyploid systems in North America (10 ferns and three angiosperms) using digitized natural history museum specimens. The abiotic niches of the allopolyploids were compared with those of their diploid progenitors using ecological niche modeling, niche analyses, and multivariate analyses. We identified four patterns of niche shifts through our analyses: niche expansion, niche contraction, niche intermediacy, and niche novelty. The classification of these shifts depended on the amount of niche overlap and breadth between the polyploid and progenitors. The most common niche shift was niche intermediacy in which the polyploid inhabited a geographic range between that of the progenitors and had a high degree of niche overlap. Each polyploid had at least partial geographic sympatry and abiotic niche overlap with one of its progenitors, suggesting that biotic and/or microclimate factors may play a larger role in polyploid establishment than previously hypothesized. This study provides a baseline for future comparisons of the diverse outcomes of genome merger and duplication on abiotic niche preference.

 

 

Mating Type and Simple Sequence Repeat Markers Indicate a Clonal Population of Phyllosticta citricarpa in Florida.

Author information: Wang NY1, Zhang K1, Huguet-Tapia JC1, Rollins JA1, Dewdney MM1.

1All authors: Department of Plant Pathology, University of Florida, Gainesville, and first, second, and fifth authors: Citrus Research and Education Center, University of Florida, Lake Alfred.

Journal: Phytopathology

Date of e-pub: November 2016

Abstract: Phyllosticta citricarpa, the citrus black spot pathogen, was first identified in Florida in March 2010. Subsequently, this pathogen has become established in Florida but can be easily confused with the endemic nonpathogenic citrus endophyte P. capitalensis. In this study, the mating-type (MAT) loci of P. citricarpa and P. capitalensis were identified via draft genome sequencing and were characterized at the structural and sequence levels. P. citricarpa was determined to have an idiomorphic, heterothallic MAT locus structure, whereas P. capitalensis was found to have a single MAT locus consistent with a homothallic mating system. A survey of P. citricarpa isolates from Florida revealed that only the MAT1-2 idiomorph existed in the Floridian population. In contrast, isolates collected from Australia exhibited a 1:1 ratio of MAT1-1 and MAT1-2 isolates. Development and analysis of simple sequence repeat markers revealed a single multilocus genotype (MLG) in the Floridian population (n = 70) and 11 MLG within the Australian population (n = 24). These results indicate that isolates of P. citricarpa from Florida are likely descendent from a single clonal lineage and are reproducing asexually. The disease management focus in Florida will need to be concentrated on the production and dispersal of pycnidiospores.

 

 

Brain quantitative proteomic responses reveal new insight of benzotriazole neurotoxicity in female Chinese rare minnow (Gobiocypris rarus).

Author information: Liang X1, Martyniuk CJ2, Zha J3, Wang Z4.

1Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Environment and Resources, Inner Mongolia University, Hohhot 010021, China.
2Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida, Gainesville, FL 32611, USA.
3Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Beijing Key Laboratory of Industrial Wastewater Treatment and Reuse, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China. Electronic address: jmzha@rcees.ac.cn.
4Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; State Key Laboratory of Environmental Aquatic Chemistry, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.

Journal: Aquatic Toxicology

Date of e-pub: November 2016

Abstract: Benzotriazole (BT) is a high-production volume chemical which has been ubiquitously detected in aquatic environments. Although adverse effects from acute and chronic exposure to BT have been reported, the neurotoxic effect of BT and the mechanisms of toxicity are not well documented. In this study, adult female Chinese rare minnow (Gobiocypris rarus) were exposed to 0.05, 0.5, and 5mg/L BT for 28days. The brain proteome showed that BT exposure mainly involved in metabolic process, signal transduction, stress response, cytoskeleton, and transport. Pathway analysis revealed that cellular processes affected by BT included cellular respiration, G-protein signal cascades, Ca2+-dependent signaling, cell cycle and apoptosis. Moreover, data on relative mRNA levels demonstrated that genes related to these toxic pathways were also significantly affected by BT. Furthermore, proteins affected by BT such as CKBB, GS, HPCA, VDAC1, and FLOT1A are associated with neurological disorders. Therefore, our finding suggested that BT induced molecular responses in the brain and could provide new insight into BT neurotoxicity in Chinese rare minnow.

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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