UFGI publications round-up week 12/19/2016

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: December 2016

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 ([INCREMENT]RIN = 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.



Cortisol and DHEA in Development and Psychopathology.

Author information: Kamin HS1, Kertes DA2.

1Department of Psychology, University of Florida, Gainesville, FL 32611, USA.
2Department of Psychology, University of Florida, Gainesville, FL 32611, USA; University of Florida Genetics Institute, University of Florida, Gainesville, FL 32611, USA. Electronic address: dkertes@ufl.edu.

Journal: Hormones and Behavior

Date of e-pub: December 2016

Abstract: Dehydroepiandrosterone (DHEA) and cortisol are the most abundant hormones of the human fetal and adult adrenals released as end products of a tightly coordinated endocrine response to stress. Together, they mediate short- and long-term stress responses and enable physiological and behavioral adjustments necessary for maintaining homeostasis. Detrimental effects of chronic or repeated elevations in cortisol on behavioral and emotional health are well documented. Evidence for actions of DHEA that offset or oppose those of cortisol has stimulated interest in examining their levels as a ratio, as an alternate index of adrenocortical activity and the net effects of cortisol. Such research necessitates a thorough understanding of the co-actions of these hormones on physiological functioning and in association with developmental outcomes. This review addresses the state of the science in understanding the role of DHEA, cortisol, and their ratio in typical development and developmental psychopathology. A rationale for studying DHEA and cortisol in concert is supported by physiological data on the coordinated synthesis and release of these hormones in the adrenal and by their opposing physiological actions. We then present evidence that researching cortisol and DHEA necessitates a developmental perspective. Age-related changes in DHEA and cortisol are described from the perinatal period through adolescence, along with observed associations of these hormones with developmental psychopathology. Along the way, we identify several major knowledge gaps in the role of DHEA in modulating cortisol in typical development and developmental psychopathology with implications for future research.



Metnase Mediates Loading of Exonuclease 1 onto Single-strand Overhang DNA for End Resection at Stalled Replication Forks.

Author information: Kim HS1, Williamson EA2, Nickoloff JA3, Hromas RA2, Lee SH4.

1Indiana University School of Medicine, United States.
2University of Florida at Gainesville, United States.
3Colorado State University, United States.
4Indiana University School of Medicine, United States; slee@iu.edu.

Journal: The Journal of Biological Chemistry

Date of e-pub: December 2016

Abstract: Stalling at DNA replication forks generates stretches of single-stranded (ss) DNA on both strands that are exposed to nucleolytic degradation, potentially compromising genome stability. One enzyme crucial for DNA replication fork repair and restart of stalled forks in human is Metnase (also known as SETMAR), a chimeric fusion protein consisting of a SET histone methylase and transposase nuclease domain. We previously showed that Metnase possesses a unique fork cleavage activity necessary for its function in replication restart and that its SET domain is essential for recovery from hydroxyurea-induced DNA damage. However, its exact role in replication restart is unclear. In this study we show that Metnase associates with exonuclease 1 (Exo1), a 5′ exonuclease crucial for 5 end resection to mediate DNA processing at stalled forks. Metnase’ DNA cleavage activity was not required for Exo1 5′ exonuclease activity on the lagging strand daughter DNA, but its DNA binding activity mediated loading of Exo1 onto ssDNA overhangs. Metnase-induced enhancement of Exo1-mediated DNA strand resection required the presence of these overhangs but did not require Metnase DNA cleavage activity. These results suggest that Metnase enhances Exo1-mediated exonuclease activity on the lagging-strand DNA by facilitating Exo1 loading onto a single-strand gap at the stalled replication fork.



Heritability of tic disorders: a twin-family study.

Author information: Zilhão NR1, Olthof MC2, Smit DJ1, Cath DC3, Ligthart L1, Mathews CA4, Delucchi K5, Boomsma DI1, Dolan CV1.

1Department of Biological Psychology,Vrije Universiteit,Amsterdam,The Netherlands.
2Department of Psychology,University of Amsterdam,The Netherlands.
3Department of Clinical Psychology,Utrecht University,The Netherlands.
4Department of Psychiatry,University of Florida,Gainesville, FL,USA.
5Department of Psychiatry,University of California,San Francisco, CA,USA.

Journal: Psychological Medicine

Date of e-pub: December 2016

Abstract: Genetic-epidemiological studies that estimate the contributions of genetic factors to variation in tic symptoms are scarce. We estimated the extent to which genetic and environmental influences contribute to tics, employing various phenotypic definitions ranging between mild and severe symptomatology, in a large population-based adult twin-family sample.

In an extended twin-family design, we analysed lifetime tic data reported by adult mono- and dizygotic twins (n = 8323) and their family members (n = 7164; parents and siblings) from 7311 families in the Netherlands Twin Register. We measured tics by the abbreviated version of the Schedule for Tourette and Other Behavioral Syndromes. Heritability was estimated by genetic structural equation modeling for four tic disorder definitions: three dichotomous and one trichotomous phenotype, characterized by increasingly strictly defined criteria.

Prevalence rates of the different tic disorders in our sample varied between 0.3 and 4.5% depending on tic disorder definition. Tic frequencies decreased with increasing age. Heritability estimates varied between 0.25 and 0.37, depending on phenotypic definitions. None of the phenotypes showed evidence of assortative mating, effects of shared environment or non-additive genetic effects.

Heritabilities of mild and severe tic phenotypes were estimated to be moderate. Overlapping confidence intervals of the heritability estimates suggest overlapping genetic liabilities between the various tic phenotypes. The most lenient phenotype (defined only by tic characteristics, excluding criteria B, C and D of DSM-IV) rendered sufficiently reliable heritability estimates. These findings have implications in phenotypic definitions for future genetic studies.



Structural and Biochemical Characterization of Cinnamoyl-CoA Reductases.

Author information: Sattler SA1, Walker AM1, Vermerris W2, Sattler SE3, Kang C4.

1Washington State University CITY: Pullman STATE: WA United States Of America [US].
2University of Florida CITY: Gainesville STATE: Florida POSTAL_CODE: 32610 United States Of America [US].
3USDA CITY: Lincoln STATE: Nebraska POSTAL_CODE: 68583-0737 United States Of America [US].
4Washington State University 264 Fulmer, Washington State University CITY: Pullman STATE: WA POSTAL_CODE: WA99164 United States Of America [US] chkang@wsu.edu.

Journal: Plant Physiology

Date of e-pub: December 2016

Abstract: Cinnamoyl-CoA reductase (CCR) catalyzes the reduction of hydroxycinnamoyl-CoA esters using NADPH to produce hydroxycinnamyl aldehyde precursors in lignin synthesis. The catalytic mechanism and substrate specificity of cinnamoyl-CoA reducases from Sorghum bicolor, a strategic plant for the bioenergy production, were deduced from crystal structures, site-directed mutagenesis, and kinetic and thermodynamic analyses. Although SbCCR1 displayed higher affinity for caffeoyl-CoA or p-coumaroyl-CoA than for feruloyl-CoA, the enzyme showed significantly higher activity for the latter substrate. Through molecular docking and comparisons between the crystal structures of the Vitis vinifera dihydroflavonol reductase and SbCCR1, residues Thr154 and Tyr310 were pinpointed as being involved in binding CoA-conjugated phenylpropanoids. Thr154 of SbCCR1 and other CCRs likely confers strong substrate specificity for feruloyl-CoA over other cinnamoyl-CoA thioesters and the T154Y mutation in SbCCR1 led to broader substrate specificity and faster turnover. Through data mining using our structural and biochemical information, four additional putative SbCCR genes were discovered from sorghum genomic data. One of these, SbCCR3 displayed greater activity toward p-coumaroyl-CoA than did SbCCR1, which could be indicative of playing a role in the synthesis of defense-related lignin. Taken together, these findings provide knowledge of critical residues on their substrate preference among CCRs, and provide the first three-dimensional structure information for a CCR from a monocot species.



Deazaguanine derivatives, examples of crosstalk between RNA and DNA modification pathways.

Author information: Hutinet G1, Swarjo MA2, de Crécy-Lagard V1.

1a Department of Microbiology and Cell Science , University of Florida , P.O. Box 110700 , Gainesville , FL 32611 , USA.
2b Department of Chemistry and Biochemistry , San Diego State University , 5500 Campanile Dr., San Diego , CA 92182 , USA.

Journal: RNA Biology

Date of e-pub: December 2016

Abstract: 7-deazapurine modifications were thought to be highly specific of tRNAs, but have now been discovered in DNA of phages and of phylogenetically diverse bacteria, illustrating the plasticity of these modification pathways. The intermediate 7-cyano-7-deazaguanine (preQ0) is a shared precursor in the pathways leading to the insetion of 7-deazapurine derivatives in both tRNA and DNA. It is also used as an intermediate in the synthesis of secondary metabolites such as toyocamacin. The presence of 7-deazapurine in DNA is proposed to be a protection mechanism against endonucleases. This makes preQ0 a metabolite of underappreaciated but central importance.

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