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1.  CLIC5 Stabilizes Membrane-Actin Filament Linkages at the Base of Hair Cell Stereocilia in a Molecular Complex with Radixin, Taperin, and Myosin VI 
Cytoskeleton (Hoboken, N.J.)  2013;71(1):61-78.
Chloride intracellular channel 5 protein (CLIC5) was originally isolated from microvilli in complex with actin binding proteins including ezrin, a member of the Ezrin-Radixin-Moesin (ERM) family of membrane-cytoskeletal linkers. CLIC5 concentrates at the base of hair cell stereocilia and is required for normal hearing and balance in mice, but its functional significance is poorly understood. This study investigated the role of CLIC5 in postnatal development and maintenance of hair bundles. Confocal and scanning electron microscopy of CLIC5-deficient jitterbug (jbg) mice revealed progressive fusion of stereocilia as early as postnatal day 10. Radixin (RDX), protein tyrosine phosphatase receptor Q (PTPRQ), and taperin (TPRN), deafness-associated proteins that also concentrate at the base of stereocilia, were mislocalized in fused stereocilia of jbg mice. TPRQ and RDX were dispersed even prior to stereocilia fusion. Biochemical assays showed interaction of CLIC5 with ERM proteins, TPRN, and possibly myosin VI (MYO6). In addition, CLIC5 and RDX failed to localize normally in fused stereocilia of MYO6 mutant mice. Based on these findings, we propose a model in which these proteins work together as a complex to stabilize linkages between the plasma membrane and subjacent actin cytoskeleton at the base of stereocilia.
doi:10.1002/cm.21159
PMCID: PMC4484851  PMID: 24285636
chloride intracellular channel 5 (CLIC5); cytoskeleton; deafness; ezrin-radixin-moesin (ERM); hair cell; myosin VI (MYO6); PTPRQ; radixin; stereocilia; taperin
2.  Alpers disease mutations in human DNA polymerase gamma cause catalytic defects in mitochondrial DNA replication by distinct mechanisms 
Frontiers in Genetics  2015;6:135.
The human mitochondrial DNA polymerase gamma (Pol-γ) is nuclearly encoded and is responsible for the replication and repair of the mitochondrial genome. Mutations S305R and P1073L in the POLG gene have been reported to be associated with early childhood Alpers syndrome. One patient harboring both mutations as compound heterozygous died at 2 years of age after disease onset at 9 months. Quantitative kinetic analysis on purified enzyme showed that the S305R mutation reduces the DNA binding affinity by 10-fold, and reduces the specificity constant (kcat/Km) for correct nucleotide incorporation by fourfold. It also causes a ∼threefold reduction in the excision rate to remove mismatched nucleotides. Compared to the wild-type Pol-γ, the S305R mutant showed no product formation in a reconstituted rolling circle replisome assay. Interestingly, the P1073L mutant exhibited wild-type activity in single turnover kinetics to quantify changes in kcat/Km, kcat, kexo, or processivity, and showed a twofold decrease in the net polymerization rate in the reconstituted replisome assay, while in yeast, P1073L caused a 60–70% mtDNA reduction in haploid cells. The heterozygous diploid yeast cells carrying S305R and P1073L mutations in trans showed ∼75% reduction of mtDNA content, relative to homozygous diploid cells with two wild-type alleles. Taken together, we show clearly in both the rolling circle and the humanized yeast system that the P1073L mutation caused significant defects in mtDNA replication, and our results suggest a role for P1073 in the functioning of the Pol-γ with the mitochondrial DNA helicase, and provide a rationale for understanding the physiological consequences of the S305R/P1073L compound heterozygote in humans.
doi:10.3389/fgene.2015.00135
PMCID: PMC4391263  PMID: 25914719
human mitochondria; alpers; Pol-γ mutations; kinetics; yeast; replisome
3.  Anthropometric and Hormonal Risk Factors for Male Breast Cancer: Male Breast Cancer Pooling Project Results 
Background
The etiology of male breast cancer is poorly understood, partly because of its relative rarity. Although genetic factors are involved, less is known regarding the role of anthropometric and hormonally related risk factors.
Methods
In the Male Breast Cancer Pooling Project, a consortium of 11 case–control and 10 cohort investigations involving 2405 case patients (n = 1190 from case–control and n = 1215 from cohort studies) and 52013 control subjects, individual participant data were harmonized and pooled. Unconditional logistic regression generated study design–specific (case–control/cohort) odds ratios (ORs) and 95% confidence intervals (CIs), with exposure estimates combined using fixed effects meta-analysis. All statistical tests were two-sided.
Results
Risk was statistically significantly associated with weight (highest/lowest tertile: OR = 1.36; 95% CI = 1.18 to 1.57), height (OR = 1.18; 95% CI = 1.01 to 1.38), and body mass index (BMI; OR = 1.30; 95% CI = 1.12 to 1.51), with evidence that recent rather than distant BMI was the strongest predictor. Klinefelter syndrome (OR = 24.7; 95% CI = 8.94 to 68.4) and gynecomastia (OR = 9.78; 95% CI = 7.52 to 12.7) were also statistically significantly associated with risk, relations that were independent of BMI. Diabetes also emerged as an independent risk factor (OR = 1.19; 95% CI = 1.04 to 1.37). There were also suggestive relations with cryptorchidism (OR = 2.18; 95% CI = 0.96 to 4.94) and orchitis (OR = 1.43; 95% CI = 1.02 to 1.99). Although age at onset of puberty and histories of infertility were unrelated to risk, never having had children was statistically significantly related (OR = 1.29; 95% CI = 1.01 to 1.66). Among individuals diagnosed at older ages, a history of fractures was statistically significantly related (OR = 1.41; 95% CI = 1.07 to 1.86).
Conclusions
Consistent findings across case–control and cohort investigations, complemented by pooled analyses, indicated important roles for anthropometric and hormonal risk factors in the etiology of male breast cancer. Further investigation should focus on potential roles of endogenous hormones.
doi:10.1093/jnci/djt465
PMCID: PMC3975166  PMID: 24552677
4.  Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans 
Background
Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution.
Results
The sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution.
Conclusions
The structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.
doi:10.1186/s12900-015-0032-6
PMCID: PMC4350885  PMID: 25886944
DNA polymerase III β subunit; Deinococcus radiodurans; Radiation resistance
5.  Characterization of a Respiratory Syncytial Virus L Protein Inhibitor 
The respiratory syncytial virus (RSV) L protein is a viral RNA-dependent RNA polymerase that contains multiple enzyme activities required for RSV replication. The RSV L inhibitors described in literature are limited by their cytotoxicity or the lack of RSV B subtype coverage. Here, we characterize a new RSV L inhibitor with strong antiviral activity against both RSV A and B subtypes and no detectable cytotoxicity. This compound, AZ-27, was equally active against RSV live viruses and subgenomic replicons and demonstrated advantages over other classes of RSV inhibitors in time-of-addition and cell line dependency studies. Resistance studies identified a dominant mutation in the putative capping enzyme domain of L protein, which conferred strong resistance to the AZ-27 series but not other classes of RSV inhibitors, supporting RSV L protein as the direct target for AZ-27. This novel and broad-spectrum RSV L polymerase inhibitor may pave the way toward an efficacious RSV therapeutic and provide a new tool for interrogation of the L protein function.
doi:10.1128/AAC.02540-14
PMCID: PMC4068518  PMID: 24777090
6.  Subfractionation, characterization and in-depth proteomic analysis of glomerular membrane vesicles in human urine 
Kidney international  2013;85(5):1225-1237.
Urinary exosome-like vesicles (ELVs) are a heterogenous mixture (diameter 40–200nm) containing vesicles shed from all segments of the nephron including glomerular podocytes. Contamination with Tamm Horsfall protein (THP) oligomers has hampered their isolation and proteomic analysis. Here we improved ELV isolation protocols employing density centrifugation to remove THP and albumin, and isolated a glomerular membranous vesicle (GMV) enriched subfraction from 7 individuals identifying 1830 proteins and in 3 patients with glomerular disease identifying 5657 unique proteins. The GMV fraction was composed of podocin/podocalyxin positive irregularly shaped membranous vesicles and podocin/podocalyxin negative classical exosomes. Ingenuity pathway analysis identified integrin, actin cytoskeleton and RhoGDI signaling in the top three canonical represented signaling pathways and 19 other proteins associated with inherited glomerular diseases. The GMVs are of podocyte origin and the density gradient technique allowed isolation in a reproducible manner. We show many nephrotic syndrome proteins, proteases and complement proteins involved in glomerular disease are in GMVs and some were shed in the disease state (nephrin, TRPC6 and INF2 and PLA2R). We calculated sample sizes required to identify new glomerular disease biomarkers, expand the ELV proteome and provide a reference proteome in a database that may prove useful in the search for biomarkers of glomerular disease.
doi:10.1038/ki.2013.422
PMCID: PMC4008663  PMID: 24196483
Exosome; proteomics; podocyte; glomerular disease; Integrin; actin cytoskeleton; Rho GDI. Q-Exactive mass spectrometer
7.  Effect of Web-Based Messages on Girls’ Knowledge and Risk Perceptions Related to Cigarette Smoke and Breast Cancer: 6-Month Follow-Up of a Randomized Controlled Trial 
JMIR Research Protocols  2014;3(3):e53.
Background
Evidence indicating an association between cigarette smoke exposure and an increase in breast cancer risk highlights the need for health messages that aim to prevent smoking initiation and reduce secondhand smoke (SHS) exposure among adolescent girls.
Objective
This study aimed to evaluate the efficacy of targeted gender-sensitive, breast cancer-specific, Web-based messages about the increased risk of breast cancer associated with cigarette smoke exposure. Outcomes assessed 6 months postmessage delivery included nonsmoking adolescent girls’ knowledge of the link between cigarette smoke exposure and breast cancer, perceptions of breast cancer risk associated with cigarette smoke, smoking behavior and intentions, and stage of change related to avoidance of secondhand smoke.
Methods
A prospective randomized controlled trial was used to compare standard (control) messages with targeted gender- and Aboriginal status-sensitive, breast cancer-specific (intervention) messages. Messages were delivered online to 618 nonsmoking girls, aged 13 to 15 years, clustered in 74 Canadian secondary schools.
Results
Compared with the control group, girls in the intervention group were significantly more likely to report that breast cancer is an illness caused by cigarette smoke (adjusted relative risk [ARR] 1.33, 95% CI 1.05-1.68) and to agree that exposure to SHS increases their risk of breast cancer (ARR 1.10, 95% CI 1.02-1.20). No significant effects were observed for a change in smoking status, intention to try smoking, or stage of change related to avoidance of SHS.
Conclusions
Compared with standard messages, targeted gender-sensitive, breast cancer-specific messages had a stronger influence on girls’ knowledge and perceived risk of cigarette smoke exposure as a risk factor for breast cancer. Brief information-based interventions delivered over the Internet have the potential to provide effective health promotion that could be broadly disseminated and lead to long-term effects on girls’ knowledge and risk perceptions about cigarette exposure and breast cancer.
doi:10.2196/resprot.3282
PMCID: PMC4210946  PMID: 25271096
secondhand smoke; breast cancer; Web-based health promotion; adolescents
8.  Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi) 
A structural and biophysical study of the interactions between cod and human uracil-DNA N-glycosylase (UNG) and their inhibitor Ugi is presented. The stronger interaction between cod UNG and Ugi can be explained by a greater positive electrostatic surface potential.
Uracil-DNA N-glycosylase from Atlantic cod (cUNG) shows cold-adapted features such as high catalytic efficiency, a low temperature optimum for activity and reduced thermal stability compared with its mesophilic homologue human UNG (hUNG). In order to understand the role of the enzyme–substrate interaction related to the cold-adapted properties, the structure of cUNG in complex with a bacteriophage encoded natural UNG inhibitor (Ugi) has been determined. The interaction has also been analyzed by isothermal titration calorimetry (ITC). The crystal structure of cUNG–Ugi was determined to a resolution of 1.9 Å with eight complexes in the asymmetric unit related through noncrystallographic symmetry. A comparison of the cUNG–Ugi complex with previously determined structures of UNG–Ugi shows that they are very similar, and confirmed the nucleotide-mimicking properties of Ugi. Biophysically, the interaction between cUNG and Ugi is very strong and shows a binding constant (K b) which is one order of magnitude larger than that for hUNG–Ugi. The binding of both cUNG and hUNG to Ugi was shown to be favoured by both enthalpic and entropic forces; however, the binding of cUNG to Ugi is mainly dominated by enthalpy, while the entropic term is dominant for hUNG. The observed differences in the binding properties may be explained by an overall greater positive electrostatic surface potential in the protein–Ugi interface of cUNG and the slightly more hydrophobic surface of hUNG.
doi:10.1107/S1399004714011699
PMCID: PMC4118823  PMID: 25084329
cold adaptation; uracil-DNA N-glycosylase; Atlantic cod; protein–inhibitor complex; protein–protein interactions; isothermal titration calorimetry; binding affinity
9.  Straight-Chain Alkyl Isocyanides Open the Distal Histidine Gate in Crystal Structures of Myoglobin† 
Biochemistry  2010;49(24):4977-4986.
Crystal structures of methyl, ethyl, propyl and butyl isocyanide bound to sperm whale myoglobin (Mb) reveal two major conformations. In the in conformer, His(E7) is in a “closed” position, forcing the ligand alkyl chain to point inward. In the out conformer, His(E7) is in an “open” position, allowing the ligand side chain to point outward. A progressive increase in the population of the out conformer is observed with increasing ligand length in P21 crystals of native Mb at pH 7.0. This switch from in to out with increasing ligand size also occurs in solution as measured by the decrease in the relative intensity of the low (~2075 cm 1) versus high frequency (~2125 cm 1) isocyano bands. In contrast, all four isocyanides in P6 crystals of wild type recombinant Mb occupy the in conformation. However, mutating either His64 to Ala, creating a “hole” to solvent, or Phe46 to Val, freeing rotation of His64, causes bound butyl isocyanide to point completely outward in P6 crystals. Thus, the unfavorable hindrance caused with crowding a large alkyl side chain into the distal pocket appears to be roughly equal to that for pushing open the His(E7) gate and is easily affected by crystal packing. This structural conclusion supports the “side path” kinetic mechanism for O2 release, in which the dissociated ligand first moves toward the protein interior and then encounters steric resistance, which is roughly equal to that for escaping to solvent through the His(E7) channel.
doi:10.1021/bi1001739
PMCID: PMC4074459  PMID: 20481504
myoglobin; alkyl isocyanide; isonitrile; X-ray crystallography; FTIR; infrared; vibrational spectroscopy; iron coordination
10.  A Lack of Immune System Genes Causes Loss in High Frequency Hearing but Does Not Disrupt Cochlear Synapse Maturation in Mice 
PLoS ONE  2014;9(5):e94549.
Early cochlear development is marked by an exuberant outgrowth of neurites that innervate multiple targets. The establishment of mature cochlear neural circuits is, however, dependent on the pruning of inappropriate axons and synaptic connections. Such refinement also occurs in the central nervous system (CNS), and recently, genes ordinarily associated with immune and inflammatory processes have been shown to play roles in synaptic pruning in the brain. These molecules include the major histocompatibility complex class I (MHCI) genes, H2-Kb and H2-Db, and the complement cascade gene, C1qa. Since the mechanisms involved in synaptic refinement in the cochlea are not well understood, we investigated whether these immune system genes may be involved in this process and whether they are required for normal hearing function. Here we report that these genes are not necessary for normal synapse formation and refinement in the mouse cochlea. We further demonstrate that C1qa expression is not necessary for normal hearing in mice but the lack of expression of H2-Kb and H2-Db causes hearing impairment. These data underscore the importance of the highly polymorphic family of MHCI genes in hearing in mice and also suggest that factors and mechanisms regulating synaptic refinement in the cochlea may be distinct from those in the CNS.
doi:10.1371/journal.pone.0094549
PMCID: PMC4012943  PMID: 24804771
11.  CorA Is a Copper Repressible Surface-Associated Copper(I)-Binding Protein Produced in Methylomicrobium album BG8 
PLoS ONE  2014;9(2):e87750.
CorA is a copper repressible protein previously identified in the methanotrophic bacterium Methylomicrobium album BG8. In this work, we demonstrate that CorA is located on the cell surface and binds one copper ion per protein molecule, which, based on X-ray Absorption Near Edge Structure analysis, is in the reduced state (Cu(I)). The structure of endogenously expressed CorA was solved using X-ray crystallography. The 1.6 Å three-dimensional structure confirmed the binding of copper and revealed that the copper atom was coordinated in a mononuclear binding site defined by two histidines, one water molecule, and the tryptophan metabolite, kynurenine. This arrangement of the copper-binding site is similar to that of its homologous protein MopE* from Metylococcus capsulatus Bath, confirming the importance of kynurenine for copper binding in these proteins. Our findings show that CorA has an overall fold similar to MopE, including the unique copper(I)-binding site and most of the secondary structure elements. We suggest that CorA plays a role in the M. album BG8 copper acquisition.
doi:10.1371/journal.pone.0087750
PMCID: PMC3912023  PMID: 24498370
12.  A Combined Bioinformatics and Chemoinformatics Approach for Developing Asymmetric Bivalent AMPA Receptor Positive Allosteric Modulators as Neuroprotective Agents 
ChemMedChem  2012;8(2):226-230.
doi:10.1002/cmdc.201200554
PMCID: PMC3733225  PMID: 23281122
bioinformatics and chemoinformatics; chemical and biological space; drug design; physicochemical properties; neuroprotective agents
14.  Hispanic Assimilation and Fertility in New Destinations 
This paper evaluates comparative patterns of fertility in new Hispanic destinations and established gateways using pooled cross-sectional data from the 2005–2009 microdata files of the American Community Survey. Changing Hispanic fertility provides a useful indicator of cultural incorporation. Analyses show that high fertility among Hispanics has been driven in part by the Mexican-origin and other new immigrant populations (e.g., noncitizens, those with poor English language skills, etc.). However, high fertility rates among Hispanics – and Mexican-origin Hispanics in particular – cannot be explained entirely by socio-demographic characteristics that place them at higher risk of fertility. For 2005–2009, Hispanic fertility rates were 48 percent higher than fertility among whites; they were roughly 25 percent higher after accounting for differences in key social characteristics, such as age, nativity, county of origin, and education. Contrary to most previous findings of spatial assimilation among in-migrants, fertility rates among Hispanics in new destinations exceeded fertility in established gateways by 18 percent. In the multivariate analyses, Hispanics in new destinations were roughly 10 percent more likely to have had a child in the past year than those living in established gateways. Results are consistent with sub-cultural explanations of Hispanic fertility and raise new questions about the spatial patterning of assimilation and the formation of ethnic enclaves outside traditional settlement areas.
doi:10.1111/imre.12000
PMCID: PMC3544406  PMID: 23325987
15.  Initial Impact of Tailored Web-Based Messages About Cigarette Smoke and Breast Cancer Risk on Boys’ and Girls’ Risk Perceptions and Information Seeking: Randomized Controlled Trial 
JMIR Research Protocols  2013;2(2):e53.
Background
Recent evidence indicates a causal link between both active smoking and secondhand smoke (SHS) exposure and breast cancer (BC).
Objective
The objective of the present study was to evaluate the initial reactions of girls and boys to tailored Web-based messages that describe the relationship between SHS and BC, using a parallel, single-blinded cluster randomized controlled trial.
Methods
This trial was nested within a cycle of an ongoing longitudinal study of 1498 students from 74 secondary schools. Self-reported assessments were used to evaluate the impact of study messages on participants’ risk perception and interest in obtaining additional information after participants were randomized by schools to control or intervention groups. The intervention group received a tailored visual message (based on gender and Aboriginal status) about BC and tobacco smoke. The control group received a standard visual message about smoking and cancer.
Results
SHS exposure was identified as a BC risk factor by 380/1488 (25.54%) participants, during the preintervention analysis. Compared to the female participants in the control group (491/839, 58.5%), girls who received the intervention (339/649, 52.2%) were 14% more likely to agree that exposure to SHS increased their BC risk (relative risk [RR] 1.14, 95% CI 1.07-1.21). Nonsmoking girls who received the intervention were 14% more likely to agree that starting smoking would increase their BC risk (RR 1.14, 95% CI 1.07-1.21). Compared to the male participants in control group (348/839, 41.5%), boys who received the intervention (310/649, 47.8%) were 10% more likely to agree that girls’ exposure to SHS increased their BC risk (RR 1.10, 95% CI 1.02-1.18). Compared to controls, girls who received the intervention were 52% more likely to request additional information about SHS and BC (RR 1.52, 95% CI 1.12-2.06).
Conclusions
Brief gender-sensitive messages delivered via the Internet have the potential to increase awareness and to stimulate information seeking about the risk for BC associated with SHS.
doi:10.2196/resprot.2858
PMCID: PMC3868973  PMID: 24326101
breast cancer; secondhand smoke; cancer prevention; youth; gender
16.  TMHS is an Integral Component of the Mechanotransduction Machinery of Cochlear Hair Cells 
Cell  2012;151(6):1283-1295.
SUMMARY
Hair cells are mechanosensors for the perception of sound, acceleration and fluid motion. Mechanotransduction channels in hair cells are gated by tip links, which connect the stereocilia of a hair cell in the direction of their mechanical sensitivity. The molecular constituents of the mechanotransduction channels of hair cells are not known. Here we show that mechanotransduction is impaired in mice lacking the tetraspan TMHS. TMHS binds to the tip-link component PCDH15 and regulates tip-link assembly, a process that is disrupted by deafness-causing Tmhs mutations. TMHS also regulates transducer channel conductance and is required for fast channel adaptation. TMHS therefore resembles other ion channel regulatory subunits such as the TARPs of AMPA receptors that facilitate channel transport and regulate the properties of pore-forming channel subunits. We conclude that TMHS is an integral component of the hair cells mechanotransduction machinery that functionally couples PCDH15 to the transduction channel.
doi:10.1016/j.cell.2012.10.041
PMCID: PMC3522178  PMID: 23217710
17.  A Pre-Steady State Kinetic Analysis of the αY60W mutant of trans-3-Chloroacrylic Acid Dehalogenase: Implications for the Mechanism of the Wild-type Enzyme† 
Biochemistry  2012;51(46):9420-9435.
The bacterial degradation of the nematicide 1,3-dichloropropene, an isomeric mixture, requires the action of trans- and cis-3-chloracrylic acid dehalogenase (CaaD and cis-CaaD, respectively). Both enzymes are tautomerase superfamily members and share a core catalytic mechanism for the hydrolytic dehalogenation of the respective isomer of 3-haloacrylate. The observation that cis-CaaD requires two additional residues raises the question of how CaaD carries out a comparable reaction with fewer catalytic residues. As part of an effort to determine the basis for the apparently simpler CaaD-catalyzed reaction, the kinetic mechanism was determined by stopped-flow and chemical quench techniques using a fluorescent mutant form of the enzyme, αY60W-CaaD, and trans-3-bromoacrylate as the substrate. The data from these experiments as well as bromide inhibition studies are best accommodated by a six-step model that provides individual rate constants for substrate binding, chemistry, and a proposed conformational change occurring after chemistry followed by release of malonate semialdehyde and bromide. The conformational change and product release rates are comparable and together they limit the rate of turnover. The kinetic analysis and modeling studies validate the αY60W-CaaD mutant as an accurate reporter of active site events during the course of the enzyme-catalyzed reaction. The kinetic mechanism for the αY60W-CaaD-catalyzed reaction is comparable to that obtained for the cis-CaaD-catalyzed reaction. The kinetic model and the validated αY60W-CaaD mutant set the stage for an analysis of active site mutants to explore the contributions of individual catalytic residues and the basis for the simplicity of the reaction.
doi:10.1021/bi3010686
PMCID: PMC3518313  PMID: 23110338
18.  β-actin and fascin-2 cooperate to maintain stereocilia length 
Stereocilia are actin-based protrusions on auditory sensory hair cells that are deflected by sound waves to initiate the conversion of mechanical energy to neuronal signals. Stereocilia maintenance is essential because auditory hair cells are not renewed in mammals. This process requires both β-actin and γ-actin as knockout mice lacking either isoform develop distinct stereocilia pathology during aging. In addition, stereocilia integrity may hinge on immobilizing actin, which outside of a small region at stereocilia tips turns over with a very slow, months-long half-life. Here, we establish that β-actin and the actin crosslinking protein fascin-2 cooperate to maintain stereocilia length and auditory function. We observed that mice expressing mutant fascin-2 (p.R109H) or mice lacking β-actin share a common phenotype including progressive, high-frequency hearing loss together with shortening of a defined subset of stereocilia in the hair cell bundle. Fascin-2 binds β-actin and γ-actin filaments with similar affinity in vitro and fascin-2 does not depend on β-actin for localization in vivo. Nevertheless, double mutant mice lacking β-actin and expressing fascin-2 p.R109H have a more severe phenotype suggesting that each protein has a different function in a common stereocilia maintenance pathway. Since the fascin-2 p.R109H mutant binds but fails to efficiently crosslink actin filaments, we propose that fascin-2 crosslinks function to slow actin depolymerization at stereocilia tips to maintain stereocilia length.
doi:10.1523/JNEUROSCI.0238-13.2013
PMCID: PMC3718021  PMID: 23658152
19.  Association of a citrate synthase missense mutation with age-related hearing loss in A/J mice 
Neurobiology of Aging  2011;33(8):1720-1729.
We previously mapped a locus (ahl4) on distal Chromosome 10 that contributes to the age-related hearing loss of A/J strain mice. Here, we report on a refined genetic map position for ahl4 and its association with a mutation in the citrate synthase gene (Cs). We mapped ahl4 to the distal-most 7 Mb of Chromosome 10 by analysis of a new linkage backcross and then further narrowed the interval to 5.5 Mb by analysis of eight C57BL/6J congenic lines with different A/J-derived segments of Chr 10. A nucleotide variant in exon 3 of Cs is the only known DNA difference within the ahl4 candidate gene interval that is unique to the A/J strain and that causes a nonsynonymous codon change. Multiple lines of evidence implicate this missense mutation (H55N) as the underlying cause of ahl4-related hearing loss, likely through its effects on mitochondrial ATP and free radical production in cochlear hair cells. The A/J mouse thus provides a new model system for in vivo studies of mitochondrial function and hearing loss.
doi:10.1016/j.neurobiolaging.2011.05.009
PMCID: PMC3206989  PMID: 21803452
mouse; genetics; inbred strain; A/J; age-related hearing loss; ahl4; citrate synthase; oxidative stress; mitochondria
20.  Inhibition of the PLP-dependent enzyme serine palmitoyltransferase by cycloserine: evidence for a novel decarboxylative mechanism of inactivation 
Molecular bioSystems  2010;6(9):1682-1693.
Cycloserine (CS, 4-amino-3-isoxazolidone) is a cyclic amino acid mimic that is known to inhibit many essential pyridoxal 5′-phosphate (PLP)-dependent enzymes. Two CS enantiomers are known; d-cycloserine (DCS, also known as Seromycin), is a natural product that is used to treat resistant Mycobacterium tuberculosis infections as well as neurological disorders since it is a potent NMDA receptor agonist, and l-cycloserine (LCS), is a synthetic enantiomer whose usefulness as a drug has been hampered by its inherent toxicity arising through inhibition of sphingolipid metabolism. Previous studies on various PLP-dependent enzymes revealed a common mechanism of inhibition by both enantiomers of CS; the PLP cofactor is disabled by forming a stable 3-hydroxyisoxazole/pyridoxamine 5′-phosphate (PMP) adduct at the active site where the cycloserine ring remains intact. Here we describe a novel mechanism of CS inactivation of the PLP-dependent enzyme serine palmitoyltransferase (SPT) from Sphingomonas paucimobilis. SPT catalyses the condensation of l-serine and palmitoyl-CoA, the first step in the de novo sphingolipid biosynthetic pathway. We have used a range of kinetic, spectroscopic and structural techniques to postulate that both LCS and DCS inactivate SPT by transamination to form a free pyridoxamine 5′-phosphate (PMP) and β-aminooxyacetaldehyde that remain bound at the active site. We suggest this occurs by ring opening of the cycloserine ring followed by decarboxylation. Enzyme kinetics show that inhibition is reversed by incubation with excess PLP and that LCS is a more effective SPT inhibitor than DCS. UV-visible spectroscopic data, combined with site-directed mutagenesis, suggest that a mobile Arg378 residue is involved in cycloserine inactivation of SPT.
doi:10.1039/c003743e
PMCID: PMC3670083  PMID: 20445930
21.  How Conformational Dynamics of DNA Polymerase Select Correct Substrates: Experiments and Simulations 
Structure(London, England:1993)  2012;20(4):618-627.
Summary
Nearly every enzyme undergoes a significant change in structure after binding it’s substrate. New experimental and theoretical analyses of the role of changes in HIV reverse transcriptase structure in selecting a correct substrate are presented. Atomically detailed simulations using the Milestoning method predict a rate and free energy profile of the conformational change commensurate with experimental data. A large conformational change occurring on a ms timescale locks the correct nucleotide at the active site, but promotes release of a mismatched nucleotide. The positions along the reaction coordinate that decide the yield of the reaction are not determined by the chemical step. Rather, the initial steps of weak substrate binding and protein conformational transition significantly enrich the yield of a reaction with a correct substrate, while the same steps diminish the reaction probability of an incorrect substrate.
doi:10.1016/j.str.2012.02.018
PMCID: PMC3322391  PMID: 22483109
22.  Reaction of cis-3-Chloroacrylic Acid Dehalogenase with an Allene Substrate, 2,3-Butadienoate: Hydration Via an Enamine 
cis -3-Chloroacrylic acid dehalogenase (cis-CaaD) catalyzes the hydrolytic dehalogenation of cis-3-haloacrylates to yield malonate semialdehyde. The enzyme processes other substrates including an allene (2,3-butadienoate) to produce acetoacetate. In the course of a stereochemical analysis of the cis-CaaD-catalyzed reaction using this allene, the enzyme was unexpectedly inactivated in the presence of NaBH4 by the reduction of a covalent enzyme-substrate bond. Covalent modification was surprising because the accumulated evidence for cis-CaaD dehalogenation favored a mechanism involving direct substrate hydration mediated by Pro-1. However, the results of subsequent mechanistic, pre-steady state and full progress kinetic experiments are consistent with a mechanism in which an enamine forms between Pro-1 and the allene. Hydrolysis of the enamine or an imine tautomer produces acetoacetate. Reduction of the imine species is likely responsible for the observed enzyme inactivation. This is the first reported observation of a tautomerase superfamily member functioning by covalent catalysis. The result may suggest that some fraction of the cis-CaaD-catalyzed dehalogenation of cis-3-haloacrylates also proceeds by covalent catalysis.
doi:10.1021/ja206873f
PMCID: PMC3257395  PMID: 22129074
23.  Retrotransposon Insertion in the T-cell Acute Lymphocytic Leukemia 1 (Tal1) Gene Is Associated with Severe Renal Disease and Patchy Alopecia in Hairpatches (Hpt) Mice 
PLoS ONE  2013;8(1):e53426.
“Hairpatches” (Hpt) is a naturally occurring, autosomal semi-dominant mouse mutation. Hpt/Hpt homozygotes die in utero, while Hpt/+ heterozygotes exhibit progressive renal failure accompanied by patchy alopecia. This mutation is a model for the rare human disorder “glomerulonephritis with sparse hair and telangiectases" (OMIM 137940). Fine mapping localized the Hpt locus to a 6.7 Mb region of Chromosome 4 containing 62 known genes. Quantitative real time PCR revealed differential expression for only one gene in the interval, T-cell acute lymphocytic leukemia 1 (Tal1), which was highly upregulated in the kidney and skin of Hpt/+ mice. Southern blot analysis of Hpt mutant DNA indicated a new EcoRI site in the Tal1 gene. High throughput sequencing identified an endogenous retroviral class II intracisternal A particle insertion in Tal1 intron 4. Our data suggests that the IAP insertion in Tal1 underlies the histopathological changes in the kidney by three weeks of age, and that glomerulosclerosis is a consequence of an initial developmental defect, progressing in severity over time. The Hairpatches mouse model allows an investigation into the effects of Tal1, a transcription factor characterized by complex regulation patterns, and its effects on renal disease.
doi:10.1371/journal.pone.0053426
PMCID: PMC3534690  PMID: 23301070
24.  Genetic background effects on age-related hearing loss associated with Cdh23 variants in mice 
Hearing Research  2011;283(1-2):80-88.
Inbred strain variants of the Cdh23 gene have been shown to influence the onset and progression of age-related hearing loss (AHL) in mice. In linkage backcrosses, the recessive Cdh23 allele (ahl) of the C57BL/6J strain, when homozygous, confers increased susceptibility to AHL, while the dominant allele (Ahl+) of the CBA/CaJ strain confers resistance. To determine the isolated effects of these alleles on different strain backgrounds, we produced the reciprocal congenic strains B6.CBACa-Cdh23Ahl+and CBACa.B6-Cdh23ahl and tested 15-30 mice from each for hearing loss progression. ABR thresholds for 8 kHz, 16 kHz, and 32 kHz pure-tone stimuli were measured at 3, 6, 9, 12, 15 and 18 months of age and compared with age-matched mice of the C57BL/6J and CBA/CaJ parental strains. Mice of the C57BL/6N strain, which is the source of embryonic stem cells for the large International Knockout Mouse Consortium, were also tested for comparisons with C57BL/6J mice. Mice of the C57BL/6J and C57BL/6N strains exhibited identical hearing loss profiles: their 32 kHz ABR thresholds were significantly higher than those of CBA/CaJ and congenic strain mice by 6 months of age, and their 16 kHz thresholds were significantly higher by 12 months. Thresholds of the CBA/CaJ, the B6.CBACa-Cdh23Ahl+, and the CBACa.B6-Cdh23ahl strain mice differed little from one another and only slightly increased throughout the 18-month test period. Hearing loss, which corresponded well with cochlear hair cell loss, was most profound in the C57BL/6J and C57BL/6NJ strains. These results indicate that the CBA/CaJ-derived Cdh23Ahl+ allele dramatically lessens hearing loss and hair cell death in an otherwise C57BL/6J genetic background, but that the C57BL/6J-derived Cdh23ahl allele has little effect on hearing loss in an otherwise CBA/CaJ background. We conclude that although Cdh23ahl homozygosity is necessary, it is not by itself sufficient to account for the accelerated hearing loss of C57BL/6J mice.
doi:10.1016/j.heares.2011.11.007
PMCID: PMC3277672  PMID: 22138310
age-related hearing loss; Cdh23; ahl; C57BL/6J; C57BL/6N; CBA/CaJ; inbred mouse strains; congenic mouse strains; cochleograms; ABR thresholds; hair cells
25.  Occupational exposure to asbestos and lung cancer in men: evidence from a population-based case-control study in eight Canadian provinces 
BMC Cancer  2012;12:595.
Background
Asbestos is classified as a human carcinogen, and studies have consistently demonstrated that workplace exposure to it increases the risk of developing lung cancer. Few studies have evaluated risks in population-based settings where there is a greater variety in the types of occupations, and exposures.
Methods
This was a population based case–control study with 1,681 incident cases of lung cancer, and 2,053 controls recruited from 8 Canadian provinces between 1994 and 1997. Self-reported questionnaires were used to elicit a lifetime occupational history, including general tasks, and information for other risk factors. Occupational hygienists, who were blinded to case–control status, assigned asbestos exposures to each job on the basis of (i) concentration (low, medium, high), (ii) frequency (<5%, 5-30%, and >30% of the time in a normal work week), and (iii) reliability (possible, probable, definite). Logistic regression was used to estimate odds ratios (ORs) and their corresponding 95% confidence intervals (CI).
Results
Those occupationally exposed to (i) low, and (ii) medium or high concentrations of asbestos had ORs for lung cancer of 1.17 (95% CI=0.92 – 1.50) and 2.16 (95% CI=1.21-3.88), respectively, relative to those who were unexposed. Medium or high exposure to asbestos roughly doubled the risk for lung cancer across all three smoking pack-year categories. The joint relationship between smoking and asbestos was consistent with a multiplicative risk model.
Conclusions
Our findings provide further evidence that exposure to asbestos has contributed to an increased risk of lung cancer in Canadian workplaces, and suggests that nearly 3% of lung cancers among Canadian men are caused by occupational exposure to asbestos.
doi:10.1186/1471-2407-12-595
PMCID: PMC3534484  PMID: 23234401
Lung cancer; Asbestos; Cigarette smoking; Case–control; Occupational epidemiology

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