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Laura Elizabeth Satterwhite, Jessica A M Yeates, Niles Lehman
Origins-of-life research requires searching for a plausible transition from simple chemicals to larger macromolecules that can both hold information and catalyze their own production. We have previously shown that some group I intron ribozymes possess the ability to help synthesize other ribozyme genotypes by recombination reactions in small networks in an autocatalytic fashion. By simplifying these recombination reactions, using fluorescent anisotropy, we quantified the thermodynamic binding strength between two nucleotides of two group I intron RNA fragments for all 16 possible genotype combinations...
2016: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Yuanyuan Li, Dan Zhao, Zhonglei Chen, Haitao Li
Recent research reveals that the YEATS domains preferentially recognize crotonylated lysines on histones. Here, we discuss the molecular mechanisms that enable this recognition and the biological significances of this interaction. The dynamics of histone crotonylation and its potential roles in the regulation of gene expression will also be discussed.
September 23, 2016: Transcription
Lisa C Barry, Dorothy B Wakefield, Robert L Trestman, Yeates Conwell
OBJECTIVE: The study objective was to determine if disability in activities of daily living specific to prison, prison activities of daily living (PADLs), is associated with depression and severity of suicidal ideation (SI) in older prisoners, a rapidly growing population at high risk of suicide. METHODS: Cross-sectional design using data from a study of prisoners age ≥50 years (N = 167). Depression was operationalized as a score of ≥15 on the 9-item Physician Health Questionnaire (PHQ-9)...
September 21, 2016: International Journal of Geriatric Psychiatry
Bao-Liang Zhong, Helen F K Chiu, Yeates Conwell
BACKGROUND: The number of older adults (OAs) is growing rapidly and the elderly suicide rate (ESR) is highest among all age-groups in China. Examining the epidemiology of elderly suicide (ES) may facilitate population-specific suicide prevention efforts, however, little is known about the patterns of ES in China. OBJECTIVE: To describe the rates and characteristics of ES in China during 2013-14. METHODS: Suicide mortality data by gender, quinquennial age-group, residence (urban/rural) and geographic location (east/central/west) were obtained from China's Integrated National Mortality Surveillance System for 2013-14...
September 13, 2016: Journal of Affective Disorders
Megan E Narad, Keith O Yeates, H Gerry Taylor, Terry Stancin, Shari L Wade
OBJECTIVE : Examine differences in maternal and paternal coping and distress following traumatic brain injury (TBI) and orthopedic injuries (OI).  METHOD : Concurrent cohort/prospective design with five assessments between 1 and an average of 7 years after injury of children aged 3-6 years hospitalized for TBI (n = 87) or OI (n = 119). Mixed models analyses were used to examine hypotheses. RESULTS : Overall, fathers reported greater depression and general distress than mothers 18 months after injury, but not at long-term follow-up...
September 15, 2016: Journal of Pediatric Psychology
Alisa O'Riley, Michael R Nadorff, Yeates Conwell, Barry Edelstein
Little information about suicidal ideation and behavior in long-term care (LTC) facilities is available. Nonetheless, the implementation of the Minimum Data Set 3.0 requires that LTC facilities screen their residents for suicide risk and have protocols in place to effectively manage residents' responses. In this article, the authors briefly discuss the risk factors of suicide in the elderly and the problems that suicidal ideation and behavior pose in the LTC environment. The authors explain issues that arise when trying to manage suicide risk in the elderly LTC population with general, traditional approaches...
June 2013: Annals of Long-term Care: the Official Journal of the American Medical Directors Association
Jordan T Feigerle, P Anthony Weil
The evolutionarily conserved TFIID complex is composed of TATA-box Binding Protein (TBP) and 13 TBP-associated factors (Tafs). The mechanisms by which many Taf subunits contribute to the essential function of TFIID are only poorly understood. To address this gap in knowledge, we present the results of a molecular genetic dissection of the TFIID subunit Taf2. Through systematic site-directed mutagenesis, we have discovered 12 taf2 temperature sensitive alleles (Ts). Two of these alleles display growth defects that can be strongly suppressed by overexpression of the yeast-specific TFIID subunit TAF14 but not by overexpression of any other TFIID subunit...
September 1, 2016: Journal of Biological Chemistry
Chiranjit Chowdhury, Sunny Chun, Michael R Sawaya, Todd O Yeates, Thomas A Bobik
Bacterial microcompartments (MCPs) are complex organelles that consist of metabolic enzymes encapsulated within a protein shell. In this study, we investigate the function of the PduJ MCP shell protein. PduJ is 80% identical in amino acid sequence to PduA and both are major shell proteins of the 1,2-propanediol (1,2-PD) utilization (Pdu) MCP of Salmonella. Prior studies showed that PduA mediates the transport of 1,2-PD (the substrate) into the Pdu MCP. Surprisingly, however, results presented here establish that PduJ has no role 1,2-PD transport...
September 2016: Molecular Microbiology
Qiang Zhang, Lei Zeng, Chengcheng Zhao, Ying Ju, Tsuyoshi Konuma, Ming-Ming Zhou
Histone lysine acylations play an important role in the regulation of gene transcription in chromatin. Unlike histone acetyl-lysine, molecular recognition of a recently identified crotonyl-lysine mark is much less understood. Here, we report that the YEATS domain of AF9 preferentially binds crotonyl-lysine over acetyl-lysine in histone H3. Nuclear magnetic resonance structural analysis reveals that crotonyl-lysine of histone H3 lysine 18 is engulfed deep in an aromatic cage of the YEATS domain where the carbonyl oxygen of crotonyl-lysine forms a hydrogen bond with the backbone amide of protein residue Tyr78...
September 6, 2016: Structure
Trevor H Yeats, Chris R Somerville
SHAVEN3 (SHV3) and its homolog SHAVEN3-like 1 (SVL1) encode glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) that are involved in cellulose biosynthesis and hypocotyl elongation in Arabidopsis thaliana. In a recent report, we showed that the cellulose and hypocotyl elongation defects of the shv3svl1 double mutant are greatly enhanced by exogenous sucrose in the growth medium. Further investigation of this phenomenon showed that shv3svl1 exhibits a hyperpolarized plasma membrane (PM) proton gradient that is coupled with enhanced accumulation of sucrose via the PM sucrose/proton symporter SUC1...
September 2016: Plant Signaling & Behavior
Amery Treble-Barna, Huaiyu Zang, Nanhua Zhang, Lisa J Martin, Keith Owen Yeates, H Gerry Taylor, Shari L Wade, Brad G Kurowski
OBJECTIVES: To examine whether apolipoprotein e4 (APOE) status moderates the association of family environment with child functioning following early traumatic brain injury (TBI). METHODS: Sixty-five children with moderate to severe TBI and 70 children with orthopedic injury (OI) completed assessments 6, 12, 18 months, and 3.5 and 6.8 years post injury. DNA was extracted from saliva samples and genotyped for APOE e4 status. Linear mixed models examined moderating effects of APOE e4 status on associations between two family environment factors (parenting style, home environment) and three child outcomes (executive functioning, behavioral adjustment, adaptive functioning)...
September 2016: Journal of the International Neuropsychological Society: JINS
Todd O Yeates, Yuxi Liu, Joshua Laniado
In nature, protein molecules have evolved as building blocks for the assembly of diverse and complex structures, many of which exhibit a high degree of symmetry. This observation has motivated a number of recent engineering efforts in which the advantages of symmetry have been exploited to design novel self-assembling protein structures of great size. Materials ranging from cages to extended two and three-dimensional arrays have been demonstrated. Especially for extended arrays, a vast number of geometrically different design types are possible...
August 2016: Current Opinion in Structural Biology
Nicole M Wheatley, Kevin D Eden, Joanna Ngo, Justin S Rosinski, Michael R Sawaya, Duilio Cascio, Michael Collazo, Hamidreza Hoveida, Wayne L Hubbell, Todd O Yeates
Autotrophic bacteria rely on various mechanisms to increase intracellular concentrations of inorganic forms of carbon (i.e., bicarbonate and CO2) in order to improve the efficiency with which they can be converted to organic forms. Transmembrane bicarbonate transporters and carboxysomes play key roles in accumulating bicarbonate and CO2, but other regulatory elements of carbon concentration mechanisms in bacteria are less understood. In this study, after analyzing the genomic regions around α-type carboxysome operons, we characterize a protein that is conserved across these operons but has not been previously studied...
October 9, 2016: Journal of Molecular Biology
Jacob B Bale, Shane Gonen, Yuxi Liu, William Sheffler, Daniel Ellis, Chantz Thomas, Duilio Cascio, Todd O Yeates, Tamir Gonen, Neil P King, David Baker
Nature provides many examples of self- and co-assembling protein-based molecular machines, including icosahedral protein cages that serve as scaffolds, enzymes, and compartments for essential biochemical reactions and icosahedral virus capsids, which encapsidate and protect viral genomes and mediate entry into host cells. Inspired by these natural materials, we report the computational design and experimental characterization of co-assembling, two-component, 120-subunit icosahedral protein nanostructures with molecular weights (1...
July 22, 2016: Science
Megan E Narad, Amery Treble-Barna, James Peugh, Keith O Yeates, H Gerry Taylor, Terry Stancin, Shari L Wade
OBJECTIVE: To identify latent trajectories of executive functioning (EF) recovery overtime after childhood traumatic brain injury (TBI) and examine the predictive value of known risk factors within and across recovery trajectories using latent class growth modeling (LCGM). METHOD: A total of 206 children between the ages of 3 and 7 years with a moderate to severe TBI or orthopedic injury (OI) were included. LCGM was applied to identify longitudinal trajectories of postinjury EF as assessed by the Behavior Rating Inventory of Executive Functioning General Executive Composite (GEC)...
July 21, 2016: Journal of Head Trauma Rehabilitation
David K Yeates, Karen Meusemann, Michelle Trautwein, Brian Wiegmann, Andreas Zwick
Our understanding on the phylogenetic relationships of insects has been revolutionised in the last decade by the proliferation of next generation sequencing technologies (NGS). NGS has allowed insect systematists to assemble very large molecular datasets that include both model and non-model organisms. Such datasets often include a large proportion of the total number of protein coding sequences available for phylogenetic comparison. We review some early entomological phylogenomic studies that employ a range of different data sampling protocols and analyses strategies, illustrating a fundamental renaissance in our understanding of insect evolution all driven by the genomic revolution...
February 2016: Current Opinion in Insect Science
Adam V S Parry, Alexander J Straub, Eva M Villar-Alvarez, Takdanai Phuengphol, Jonathan E R Nicoll, Xavier Lim W K, Lianne M Jordan, Katie L Moore, Pablo Taboada, Stephen G Yeates, Steve Edmondson
Using an electrostatic-based super inkjet printer we report the high-resolution deposition of polyelectrolyte macroinitiators and subsequent polymer brush growth using SI-ARGET-ATRP. We go on to demonstrate for the first time a submicron patterning phenomenon through the addition of either a like charged polyelectrolyte homopolymer or through careful control of ionic strength. As a result patterning of polymer brushes down to ca. 300 nm is reported. We present a possible mechanistic model and consider how this may be applied to other polyelectrolyte-based systems as a general method for submicron patterning...
July 27, 2016: Journal of the American Chemical Society
Richard H Ffrench-Constant, Robin Somers-Yeates, Jonathan Bennie, Theodoros Economou, David Hodgson, Adrian Spalding, Peter K McGregor
The ecological impact of night-time lighting is of concern because of its well-demonstrated effects on animal behaviour. However, the potential of light pollution to change plant phenology and its corresponding knock-on effects on associated herbivores are less clear. Here, we test if artificial lighting can advance the timing of budburst in trees. We took a UK-wide 13 year dataset of spatially referenced budburst data from four deciduous tree species and matched it with both satellite imagery of night-time lighting and average spring temperature...
June 29, 2016: Proceedings. Biological Sciences
Kyle H Yeates, Ava D Segal, Rick R Neptune, Glenn K Klute
Stepping on coronally-uneven and unpredictable terrain is a common gait disturbance that can lead to injurious falls. This study identified the biomechanical response to a step on coronally-uneven and unpredictable terrain through observation of participants traversing a walkway with a middle step that could be blinded to participants, and positioned either 15° inverted, 15° everted, or flush. The isolated disturbance was intended to simulate stepping on a rock, object, or other transient coronal disturbance and allow for observation of the subsequent balance recovery...
June 15, 2016: Journal of Biomechanics
Erin D Bigler, Brandon A Zielinski, Naomi Goodrich-Hunsaker, Garrett M Black, B S Trevor Huff, Zachary Christiansen, Dawn-Marie Wood, Tracy J Abildskov, Maureen Dennis, H Gerry Taylor, Kenneth Rubin, Kathryn Vannatta, Cynthia A Gerhardt, Terry Stancin, Keith Owen Yeates
In a sample of children with traumatic brain injury, this magnetic resonance imaging (MRI)-based investigation examined whether presence of a focal lesion uniquely influenced cortical thickness in any brain region. Specifically, the study explored the relation of cortical thickness to injury severity as measured by Glasgow Coma Scale score and length of stay, along with presence of encephalomalacia, focal white matter lesions or presence of hemosiderin deposition as a marker of shear injury. For comparison, a group of children without head injury but with orthopedic injury of similar age and sex were also examined...
October 2016: Journal of Child Neurology
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