PMCC PMCC

Search tips
Search criteria

Advanced
Results 1-25 (79)
 

Clipboard (0)
None

Select a Filter Below

Year of Publication
more »
1.  Structure and function of the DNA ligases encoded by the mammalian LIG3 gene 
Gene  2013;531(2):10.1016/j.gene.2013.08.061.
Among the mammalian genes encoding DNA ligases (LIG), the LIG3 gene is unique in that it encodes multiple DNA ligase polypeptides with different cellular functions. Notably, this nuclear gene encodes the only mitochondrial DNA ligase and so is essential for this organelle. In the nucleus, there is significant functional redundancy between DNA ligase IIIα and DNA ligase I in excision repair. In addition, DNA ligase IIIα is essential for DNA replication in the absence of the replicative DNA ligase, DNA ligase I. DNA ligase IIIα is a component of an alternative non-homologous end joining (NHEJ) pathway for DNA double-strand break (DSB) repair that is more active when the major DNA ligase IV-dependent pathway is defective. Unlike its other nuclear functions, the role of DNA ligase IIIα in alternative NHEJ is independent of its nuclear partner protein, X-ray repair cross-complementing protein 1 (XRCC1). DNA ligase IIIα is frequently overexpressed in cancer cells, acting as a biomarker for increased dependence upon alternative NHEJ for DSB repair and it is a promising novel therapeutic target.
doi:10.1016/j.gene.2013.08.061
PMCID: PMC3881560  PMID: 24013086
2.  DNA ligase I, the replicative DNA ligase 
Sub-cellular biochemistry  2012;62:10.1007/978-94-007-4572-8_17.
Multiple DNA ligation events are required to join the Okazaki fragments generated during lagging strand DNA synthesis. In eukaryotes, this is primarily carried out by members of the DNA ligase I family. The C-terminal catalytic region of these enzymes is composed of three domains: a DNA binding domain, an adenylation domain and an OB-fold domain. In the absence of DNA, these domains adopt an extended structure but transition into a compact ring structure when they engage a DNA nick, with each of the domains contacting the DNA. The non-catalytic N-terminal region of eukaryotic DNA ligase I is responsible for the specific participation of these enzymes in DNA replication. This proline-rich unstructured region contains the nuclear localization signal and a PCNA interaction motif that is critical for localization to replication foci and efficient joining of Okazaki fragments. DNA ligase I initially engages the PCNA trimer via this interaction motif which is located at the extreme N-terminus of this flexible region. It is likely that this facilitates an additional interaction between the DNA binding domain and the PCNA ring. The similar size and shape of the rings formed by the PCNA trimer and the DNA ligase I catalytic region when it engages a DNA nick suggest that these proteins interact to form a double-ring structure during the joining of Okazaki fragments. DNA ligase I also interacts with replication factor C, the factor that loads the PCNA trimeric ring onto DNA. This interaction, which is regulated by phosphorylation of the non-catalytic N-terminus of DNA ligase I, also appears to be critical for DNA replication.
doi:10.1007/978-94-007-4572-8_17
PMCID: PMC3881551  PMID: 22918593
Lagging strand DNA synthesis; Okazaki fragments; genome instability; cancer predisposition; phosphodiester bond formation
3.  Polyclonal Outbreak of KPC-3-Producing Enterobacter cloacae at a Single Hospital in Montréal, Québec, Canada 
Journal of Clinical Microbiology  2013;51(7):2406-2408.
From September 2010 to December 2011, 26 KPC-3-producing Enterobacter cloacae isolates were identified from 16 patients at a single hospital. Analyses revealed the blaKPC gene to be localized on multiple plasmids in a diverse nonclonal E. cloacae genetic background. These findings highlight the potential complexity of a KPC outbreak at a single hospital.
doi:10.1128/JCM.02480-12
PMCID: PMC3697733  PMID: 23637289
4.  DNA ligases as therapeutic targets 
During DNA replication, DNA joining events link Okazaki fragments on the lagging strand. In addition, they are required to repair DNA single- and double-strand breaks and to complete repair events initiated by the excision of mismatched and damaged bases. In human cells, there are three genes encoding DNA ligases. These enzymes are ATP-dependent and contain a conserved catalytic region. Biophysical studies have shown that the catalytic region contains three domains that, in the absence of DNA, are in an extended conformation. When the catalytic region engages a DNA nick, it adopts a compact, ring structure around the DNA nick with each of the three domains contacting the DNA.
Protein-protein interactions involving the regions flanking the conserved catalytic regions of human DNA ligases play a major role in directing these enzymes to participate in specific DNA transactions. Among the human LIG genes, the LIG3 gene is unique in that it encodes multiple DNA ligase polypeptides with different N- and C-termini. One of these polypeptides is targeted to mitochondria where it plays an essential role in the maintenance of the mitochondrial genome. In the nucleus, DNA ligases I, III and IV have distinct but overlapping functions in DNA replication and repair.
Small molecule inhibitors of human DNA ligases have been identified using structure-based approaches. As expected, these inhibitors are cytotoxic and also potentiate the cytotoxicity of DNA damaging agents. The results of preclinical studies with human cancer cell lines and mouse models of human cancer suggest that DNA ligase inhibitors may have utility as anti-cancer agents.
PMCID: PMC3819426  PMID: 24224145
Cancer; DNA replication; DNA repair; genome instability; mitochondria; DNA ligase
5.  Research priorities for child and adolescent physical activity and sedentary behaviours: an international perspective using a twin-panel Delphi procedure 
Background
The quantity and quality of studies in child and adolescent physical activity and sedentary behaviour have rapidly increased, but research directions are often pursued in a reactive and uncoordinated manner.
Aim
To arrive at an international consensus on research priorities in the area of child and adolescent physical activity and sedentary behaviour.
Methods
Two independent panels, each consisting of 12 experts, undertook three rounds of a Delphi methodology. The Delphi methodology required experts to anonymously answer questions put forward by the researchers with feedback provided between each round.
Results
The primary outcome of the study was a ranked set of 29 research priorities that aimed to be applicable for the next 10 years. The top three ranked priorities were: developing effective and sustainable interventions to increase children’s physical activity long-term; policy and/or environmental change and their influence on children’s physical activity and sedentary behaviour; and prospective, longitudinal studies of the independent effects of physical activity and sedentary behaviour on health.
Conclusions
These research priorities can help to guide decisions on future research directions.
doi:10.1186/1479-5868-10-112
PMCID: PMC3853883  PMID: 24228891
Physical activity; Sedentary behaviour; Research priorities; Children; Adolescents
6.  IL4RA Polymorphisms are Predictors of a Pharmacogenetic Response to a Novel IL4/IL13 Antagonist 
doi:10.1016/j.jaci.2010.08.001
PMCID: PMC3772526  PMID: 20920778
IL4RA; genetics; pharmacogenetics; interleukin 4; interleukin 13; interleukin 4 receptor; allergen; asthma therapy
7.  Targeting abnormal DNA double strand break repair in tyrosine kinase inhibitor-resistant chronic myeloid leukemias 
Oncogene  2012;32(14):1784-1793.
Resistance to imatinib (IM) and other BCR-ABL1 tyrosine kinase inhibitors (TKI)s is an increasing problem in leukemias caused by expression of BCR-ABL1. Since chronic myeloid leukemia (CML) cell lines expressing BCR-ABL1 utilize an alternative non-homologous end-joining pathway (ALT NHEJ) to repair DNA double strand breaks (DSB)s, we asked whether this repair pathway is a novel therapeutic target in TKI-resistant disease. Notably, the steady state levels of two ALT NHEJ proteins, poly-(ADP-ribose) polymerase 1 (PARP1) and DNA ligase IIIα were increased in the BCR-ABL1-positive CML cell line K562 and, to a greater extent, in its imatinib resistant (IMR) derivative. Incubation of these cell lines with a combination of DNA ligase and PARP inhibitors inhibited ALT NHEJ and selectively decreased survival with the effect being greater in the IMR derivative. Similar results were obtained with TKI-resistant derivatives of two hematopoietic cell lines that had been engineered to stably express BCR-ABL1. Together our results show that the sensitivity of cell lines expressing BCR-ABL1 to the combination of DNA ligase and PARP inhibitors correlates with the steady state levels of PARP1 and DNA ligase IIIα, and ALT NHEJ activity. Importantly, analysis of clinical samples from CML patients confirmed that the expression levels of PARP1 and DNA ligase IIIα correlated with sensitivity to the DNA repair inhibitor combination. Thus, the expression levels of PARP1 and DNA ligase IIIα serve as biomarkers to identify a subgroup of CML patients who may be candidates for therapies that target the ALT NHEJ pathway when treatment with TKIs has failed.
doi:10.1038/onc.2012.203
PMCID: PMC3752989  PMID: 22641215
Chronic myeloid leukemia; DNA ligase IIIα; PARP1; NHEJ; PARP inhibitors; DNA ligase I and III inhibitors
8.  Increased Risk of Lung Cancer Associated with a Functionally Impaired Polymorphic Variant of the Human DNA Glycosylase NEIL2 
DNA Repair  2012;11(6):570-578.
Human NEIL2, one of five oxidized base-specific DNA glycosylases, is unique in preferentially repairing oxidative damage in transcribed genes. Here we show that depletion of NEIL2 causes a 6- to 7-fold increase in spontaneous mutation frequency in the HPRT gene of the V79 Chinese hamster lung cell line. This prompted us to screen for NEIL2 variants in lung cancer patients’ genomic DNA. We identified several polymorphic variants, among which R103Q and R257L were frequently observed in lung cancer patients. We then characterized these variants biochemically, and observed a modest decrease in DNA glycosylase activity relative to the wild type (WT) only with the R257L mutant protein. However, in reconstituted repair assays containing WT NEIL2 or its R257L and R103Q variants together with other DNA base excision repair (BER) proteins (PNKP, Polβ, Lig IIIα and XRCC1) or using NEIL2-FLAG immunocomplexes, an ~ 5-fold decrease in repair was observed with the R257L variant compared to WT or R103Q NEIL2, apparently due to the R257L mutant’s lower affinity for other repair proteins, particularly Polβ. Notably, increased endogenous DNA damage was observed in NEIL2 variant (R257L)-expressing cells relative to WT cells. Taken together, our results suggest that the decreased DNA repair capacity of the R257L variant can induce mutations that lead to lung cancer development.
doi:10.1016/j.dnarep.2012.03.005
PMCID: PMC3361577  PMID: 22497777
9.  A High-Throughput Scintillation Proximity-Based Assay for Human DNA Ligase IV 
Abstract
Ionizing radiation (IR) and certain chemotherapeutic drugs are designed to generate cytotoxic DNA double-strand breaks (DSBs) in cancer cells. Inhibition of the major DSB repair pathway, nonhomologous end joining (NHEJ), will enhance the cytotoxicity of these agents. Screening for inhibitors of the DNA ligase IV (Lig4), which mediates the final ligation step in NHEJ, offers a novel target-based drug discovery opportunity. For this purpose, we have developed an enzymatic assay to identify chemicals that block the transfer of [α-33P]-AMP from the complex Lig4-[α-33P]-AMP onto the 5′ end of a double-stranded DNA substrate and adapted it to a scintillation proximity assay (SPA). A screen was performed against a collection of 5,280 compounds. Assay statistics show an average Z′ value of 0.73, indicative of a robust assay in this SPA format. Using a threshold of >20% inhibition, 10 compounds were initially scored as positive hits. A follow-up screen confirmed four compounds with IC50 values ranging from 1 to 30 μM. Rabeprazole and U73122 were found to specifically block the adenylate transfer step and DNA rejoining; in whole live cell assays, these compounds were found to inhibit the repair of DSBs generated by IR. The ability to screen and identify Lig4 inhibitors suggests that they may have utility as chemo- and radio-sensitizers in combination therapy and provides a rationale for using this screening strategy to identify additional inhibitors.
doi:10.1089/adt.2011.0404
PMCID: PMC3374410  PMID: 22192310
10.  Electron microscopy visualization of DNA-protein complexes formed by Ku and DNA ligase IV 
DNA Repair  2011;11(1):74-81.
The repair of DNA double-stranded breaks (DSBs) is essential for cell viability and genome stability. Aberrant repair of DSBs has been linked with cancer predisposition and aging. During the repair of DSBs by non-homologous end joining (NHEJ), DNA ends are brought together, processed and then joined. In eukaryotes, this repair pathway is initiated by the binding of the ring-shaped Ku heterodimer and completed by DNA ligase IV. The DNA ligase IV complex, DNA ligase IV/XRRC4 in humans and Dnl4/Lif1 in yeast, is recruited to DNA ends in vitro and in vivo by an interaction with Ku and, in yeast, Dnl4/Lif1 stabilizes the binding of yKu to in vivo DSBs. Here we have analyzed the interactions of these functionally conserved eukaryotic NHEJ factors with DNA by electron microscopy. As expected, the ring-shaped Ku complex bound stably and specifically to DNA ends at physiological salt concentrations. At a ratio of 1 Ku molecule per DNA end, the majority of DNA ends were occupied by a single Ku complex with no significant formation of linear DNA multimers or circular loops. Both Dnl4/Lif1 and DNA ligase IV/XRCC4 formed complexes with Ku-bound DNA ends, resulting in intra- and intermolecular DNA end bridging even with non-ligatable DNA ends. Together these studies, which provide the first visualization of the conserved complex formed by Ku and DNA ligase IV at juxtaposed DNA ends by electron microscopy, suggest that the DNA ligase IV complex mediates end-bridging by engaging two Ku-bound DNA ends.
doi:10.1016/j.dnarep.2011.10.023
PMCID: PMC3253911  PMID: 22088982
non-homologous end joining; DNA ligase; Ku; end-bridging
11.  Targeting abnormal DNA repair in therapy-resistant breast cancers 
Molecular Cancer Research  2011;10(1):96-107.
Although hereditary breast cancers have defects in the DNA damage response that result in genomic instability, DNA repair abnormalities in sporadic breast cancers have not been extensively characterized. Recently we showed that, relative to non-tumorigenic breast epithelial MCF10A cells, estrogen receptor- and progesterone receptor-positive (ER/PR+) MCF7 breast cancer cells have reduced steady state levels of DNA ligase IV, a component of the major DNA-PK dependent non-homologous end-joining (NHEJ) pathway, whereas the steady state level of DNA ligase IIIα, a component of the highly error-prone alternative NHEJ (ALT NHEJ) pathway, is increased. Here we show that tamoxifen- and aromatase-resistant derivatives of MCF7 cells and ER/PR- cells have even higher steady state levels of DNA ligase IIIα and increased levels of poly (ADP-ribose) polymerase (PARP1), another ALT NHEJ component. This results in increased dependence upon microhomology-mediated ALT NHEJ to repair DNA double strand breaks (DSB)s and the accumulation of chromosomal deletions. Notably, therapy-resistant derivatives of MCF7 cells and ER/PR- cells exhibited significantly increased sensitivity to a combination of PARP and DNA ligase III inhibitors that increased the number of DSBs. Biopsies from ER/PR- tumors had elevated levels of ALT NHEJ and reduced levels of DNA-PK-dependent NHEJ factors. Thus, our results show that ALT NHEJ is a novel therapeutic target in breast cancers that are resistant to frontline therapies and suggest that changes in NHEJ protein levels may serve as biomarkers to identify tumors that are candidates for this therapeutic approach.
doi:10.1158/1541-7786.MCR-11-0255
PMCID: PMC3319138  PMID: 22112941
breast cancer; therapy resistant breast cancers; DNA damage; DNA repair; Non homologous end-joining
12.  The Sirtuin 2 microtubule deacetylase is an abundant neuronal protein that accumulates in the aging CNS 
Human Molecular Genetics  2011;20(20):3986-3996.
Sirtuin 2 (SIRT2) is one of seven known mammalian protein deacetylases homologous to the yeast master lifespan regulator Sir2. In recent years, the sirtuin protein deacetylases have emerged as candidate therapeutic targets for many human diseases, including metabolic and age-dependent neurological disorders. In non-neuronal cells, SIRT2 has been shown to function as a tubulin deacetylase and a key regulator of cell division and differentiation. However, the distribution and function of the SIRT2 microtubule (MT) deacetylase in differentiated, postmitotic neurons remain largely unknown. Here, we show abundant and preferential expression of specific isoforms of SIRT2 in the mammalian central nervous system and find that a previously uncharacterized form, SIRT2.3, exhibits age-dependent accumulation in the mouse brain and spinal cord. Further, our studies reveal that focal areas of endogenous SIRT2 expression correlate with reduced α-tubulin acetylation in primary mouse cortical neurons and suggest that the brain-enriched species of SIRT2 may function as the predominant MT deacetylases in mature neurons. Recent reports have demonstrated an association between impaired tubulin acetyltransferase activity and neurodegenerative disease; viewed in this light, our results showing age-dependent accumulation of the SIRT2 neuronal MT deacetylase in wild-type mice suggest a functional link between tubulin acetylation patterns and the aging brain.
doi:10.1093/hmg/ddr326
PMCID: PMC3203628  PMID: 21791548
13.  Testing the activitystat hypothesis: a randomised controlled trial protocol 
BMC Public Health  2012;12:851.
Background
The activitystat hypothesis proposes that when physical activity or energy expenditure is increased or decreased in one domain, there will be a compensatory change in another domain to maintain an overall, stable level of physical activity or energy expenditure. To date, there has been no experimental study primarily designed to test the activitystat hypothesis in adults. The aim of this trial is to determine the effect of two different imposed exercise loads on total daily energy expenditure and physical activity levels.
Methods
This study will be a randomised, multi-arm, parallel controlled trial. Insufficiently active adults (as determined by the Active Australia survey) aged 18–60 years old will be recruited for this study (n=146). Participants must also satisfy the Sports Medicine Australia Pre-Exercise Screening System and must weigh less than 150 kg. Participants will be randomly assigned to one of three groups using a computer-generated allocation sequence. Participants in the Moderate exercise group will receive an additional 150 minutes of moderate to vigorous physical activity per week for six weeks, and those in the Extensive exercise group will receive an additional 300 minutes of moderate to vigorous physical activity per week for six weeks. Exercise targets will be accumulated through both group and individual exercise sessions monitored by heart rate telemetry. Control participants will not be given any instructions regarding lifestyle. The primary outcome measures are activity energy expenditure (doubly labeled water) and physical activity (accelerometry). Secondary measures will include resting metabolic rate via indirect calorimetry, use of time, maximal oxygen consumption and several anthropometric and physiological measures. Outcome measures will be conducted at baseline (zero weeks), mid- and end-intervention (three and six weeks) with three (12 weeks) and six month (24 week) follow-up. All assessors will be blinded to group allocation.
Discussion
This protocol has been specifically designed to test the activitystat hypothesis while taking into account the key conceptual and methodological considerations of testing a biologically regulated homeostatic feedback loop. Results of this study will be an important addition to the growing literature and debate concerning the possible existence of an activitystat.
Trial registration
Australian New Zealand Clinical Trials Registry ACTRN12610000248066
doi:10.1186/1471-2458-12-851
PMCID: PMC3503831  PMID: 23043381
Protocol; Randomised controlled trial; Physical activity; Activitystat
15.  Nucleosome Disruption by DNA Ligase III-XRCC1 Promotes Efficient Base Excision Repair ▿ ‡  
Molecular and Cellular Biology  2011;31(22):4623-4632.
Each day, approximately 20,000 oxidative lesions form in the DNA of every nucleated human cell. The base excision repair (BER) enzymes that repair these lesions must function in a chromatin milieu. We have determined that the DNA glycosylase hNTH1, apurinic endonuclease (APE), and DNA polymerase β (Pol β), which catalyze the first three steps in BER, are able to process their substrates in both 601- and 5S ribosomal DNA (rDNA)-based nucleosomes. hNTH1 formed a discrete ternary complex that was displaced by the addition of APE, suggesting an orderly handoff of substrates from one enzyme to the next. In contrast, DNA ligase IIIα-XRCC1, which completes BER, was appreciably active only at concentrations that led to nucleosome disruption. Ligase IIIα-XRCC1 was also able to bind and disrupt nucleosomes containing a single base gap and, because of this property, enhanced both its own activity and that of Pol β on nucleosome substrates. Collectively, these findings provide insights into rate-limiting steps that govern BER in chromatin and reveal a unique role for ligase IIIα-XRCC1 in enhancing the efficiency of the final two steps in the BER of lesions in nucleosomes.
doi:10.1128/MCB.05715-11
PMCID: PMC3209256  PMID: 21930793
16.  Patterns of hospital admission with epistaxis for 26,725 patients over an 18-year period in Wales, UK 
INTRODUCTION
Epistaxis is the one of the most common otorhinolaryngology emergencies. This study examined the age and sex distribution of all patients admitted with epistaxis to National Health Service (NHS) hospitals in Wales, UK, over a period of 18 years and 9 months.
METHODS
The Patient Episode Database for Wales was examined for all patient admissions with a diagnosis of epistaxis between April 1991 and December 2009. The age and sex of these patients was recorded and the proportion of the underlying population affected was calculated by comparing admission rates to the population data derived from the 1991 and 2001 national population censuses for Wales.
RESULTS
A total of 26,725 patients were admitted to NHS hospitals in Wales with epistaxis over the period studied. The proportion of the population admitted with epistaxis increased from the age of 40 onwards. For all ages except patients in the 10–14 years group, a higher proportion of the male population was admitted with epistaxis than the comparable female population. This discrepancy was most pronounced between the ages of 15 and 49 years, with the female-to-male ratio of hospital admissions with epistaxis being 0.55. These ages (15 and 49 years) approximate the average age of menarche and menopause respectively in the UK.
CONCLUSIONS
Women of menstrual age have fewer hospital admissions with epistaxis. This may be due to oestrogens providing protection to the nasal vasculature (as they do to other areas of the vascular tree).
doi:10.1308/003588412X13373405386691
PMCID: PMC3954281  PMID: 23131225
Epistaxis; Epidemiology; Incidence; Sex; Menopause
17.  Targeting abnormal DNA double strand break repair in cancer 
A major challenge in cancer treatment is the development of therapies that target cancer cells with little or no toxicity to normal tissues and cells. Alterations in DNA double strand break (DSB) repair in cancer cells include both elevated and reduced levels of key repair proteins and changes in the relative contributions of the various DSB repair pathways. These differences can result in increased sensitivity to DSB-inducing agents and increased genomic instability. The development of agents that selectively inhibit the DSB repair pathways that cancer cells are more dependent upon will facilitate the design of therapeutic strategies that exploit the differences in DSB repair between normal and cancer cells. Here, we discuss the pathways of DSB repair, alterations in DSB repair in cancer, inhibitors of DSB repair and future directions for cancer therapies that target DSB repair.
doi:10.1007/s00018-010-0493-5
PMCID: PMC3014093  PMID: 20697770
Homologous recombination; Non-homologous end-joining
18.  Replication protein A safeguards genome integrity by controlling NER incision events 
The Journal of Cell Biology  2011;192(3):401-415.
Continued association of RPA with sites of incomplete nucleotide excision repair averts further incision events until repair is completed.
Single-stranded DNA gaps that might arise by futile repair processes can lead to mutagenic events and challenge genome integrity. Nucleotide excision repair (NER) is an evolutionarily conserved repair mechanism, essential for removal of helix-distorting DNA lesions. In the currently prevailing model, NER operates through coordinated assembly of repair factors into pre- and post-incision complexes; however, its regulation in vivo is poorly understood. Notably, the transition from dual incision to repair synthesis should be rigidly synchronized as it might lead to accumulation of unprocessed repair intermediates. We monitored NER regulatory events in vivo using sequential UV irradiations. Under conditions that allow incision yet prevent completion of repair synthesis or ligation, preincision factors can reassociate with new damage sites. In contrast, replication protein A remains at the incomplete NER sites and regulates a feedback loop from completion of DNA repair synthesis to subsequent damage recognition, independently of ATR signaling. Our data reveal an important function for replication protein A in averting further generation of DNA strand breaks that could lead to mutagenic and recombinogenic events.
doi:10.1083/jcb.201006011
PMCID: PMC3101093  PMID: 21282463
19.  Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States† 
Biochemistry  2010;49(29):6165-6176.
Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases DNA nick-joining and intermolecular DNA ligation. Yet, the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small angle x-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) form a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) -OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick-sensing and the transition from nick-sensing by the ZnF to nick-joining by the catalytic core. The collective results support a “jackknife model” whereby the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.
doi:10.1021/bi100503w
PMCID: PMC2922849  PMID: 20518483
20.  Low-Level Laser Therapy Activates NF-kB via Generation of Reactive Oxygen Species in Mouse Embryonic Fibroblasts 
PLoS ONE  2011;6(7):e22453.
Background
Despite over forty years of investigation on low-level light therapy (LLLT), the fundamental mechanisms underlying photobiomodulation at a cellular level remain unclear.
Methodology/Principal Findings
In this study, we isolated murine embryonic fibroblasts (MEF) from transgenic NF-kB luciferase reporter mice and studied their response to 810 nm laser radiation. Significant activation of NF-kB was observed at fluences higher than 0.003 J/cm2 and was confirmed by Western blot analysis. NF-kB was activated earlier (1 hour) by LLLT compared to conventional lipopolysaccharide treatment. We also observed that LLLT induced intracellular reactive oxygen species (ROS) production similar to mitochondrial inhibitors, such as antimycin A, rotenone and paraquat. Furthermore, we observed similar NF-kB activation with these mitochondrial inhibitors. These results, together with inhibition of laser induced NF-kB activation by antioxidants, suggests that ROS play an important role in the laser induced NF-kB signaling pathways. However, LLLT, unlike mitochondrial inhibitors, induced increased cellular ATP levels, which indicates that LLLT also upregulates mitochondrial respiration.
Conclusion
We conclude that LLLT not only enhances mitochondrial respiration, but also activates the redox-sensitive NFkB signaling via generation of ROS. Expression of anti-apoptosis and pro-survival genes responsive to NFkB could explain many clinical effects of LLLT.
doi:10.1371/journal.pone.0022453
PMCID: PMC3141042  PMID: 21814580
21.  Family physicians who provide intrapartum care and those who do not 
Canadian Family Physician  2011;57(4):e139-e147.
Abstract
Objective
To examine FPs’ attitudes toward birth for those providing intrapartum care (IPC) and those providing only antepartum care (APC).
Design
National, cross-sectional Web- and paper-based survey.
Setting
Canada.
Participants
A total of 897 Canadian FPs: 503 providing both IPC and APC (FPIs), 252 providing only APC but who previously provided IPC (FPPs), and 142 providing only APC who never provided IPC (FPNs).
Main outcome measures
Respondents’ views (measured on a 5-point Likert scale) on routine electronic fetal monitoring, epidural analgesia, routine episiotomy, doulas, pelvic floor benefits of cesarean section, approaches to reducing cesarean section rates, maternal choice and the mother’s role in her own child’s birth, care providers’ fears of vaginal birth for themselves or their partners, and safety by mode or place of birth.
Results
Results showed that FPIs and FPPs were more likely than FPNs were to take additional training or advanced life support courses. The FPIs consistently demonstrated more positive attitudes toward vaginal birth than did the other 2 groups. The FPPs and FPNs showed significantly more agreement with use of routine electronic fetal monitoring and routine epidural analgesia (P < .001). The FPIs displayed significantly more acceptance of doulas (P < .001) and more disagreement with the pelvic floor benefits of cesarean section than other FPs did (P < .001). The FPIs were significantly less fearful of vaginal birth for themselves or their partners than were FPPs and FPNs (P < .001). All FP groups agreed on rejection of elective cesarean section, in the absence of indications, for themselves or their partners and on support for vaginal birth in the presence of uterine scar. While all FP groups supported licensed midwifery, three-quarters thought home birth was more dangerous than hospital birth and showed ambivalence toward birth plans. Only 7.8% of FPIs would choose obstetricians for their own or their partners’ maternity care.
Conclusion
The FPIs had a more positive, evidence-based view of birth. It is likely that FPs providing only APC are influencing women in their practices toward a relatively negative view of birth before referral to obstetricians, FPIs, or midwives for the actual birth. The relatively negative views of birth held by FPs providing only APC need to be addressed in family practice education and in continuing education.
PMCID: PMC3076498  PMID: 21490345
22.  Pharmacokinetics and tolerability of zibotentan (ZD4054) in subjects with hepatic or renal impairment: two open-label comparative studies 
Background
Zibotentan (ZD4054) is a specific endothelin A (ETA) receptor antagonist being investigated for the treatment of prostate cancer. As zibotentan is eliminated by renal and metabolic routes, clearance may be reduced in patients with hepatic or renal impairment, leading to greater drug exposure.
Methods
Open-label studies investigated the PK and tolerability of zibotentan in subjects with hepatic or renal impairment, compared with those with normal organ function. In the hepatic and renal studies, respectively, subjects were divided into categories using Child-Pugh classification or 24-hour urine creatinine clearance (mild, moderate, or severe impairment and normal function). Each subject received a single oral dose of zibotentan 10 mg and PK sampling was undertaken. Within the hepatic study, AUC and Cmax were expressed as the ratio of geometric means and 90% CI for each impairment group compared with the normal function group. The possibility that hepatic impairment had a clinically relevant effect on exposure was considered if the upper 90% CI for the ratio exceeded 2. In the renal study, AUC, Cmax and t1/2 were analyzed using linear regression fitting effects for creatinine clearance and age.
Results
In the hepatic and renal studies respectively, 32 subjects (eight per group) and 48 subjects received treatment (n = 18 normal, n = 12 mild, n = 9 moderate, n = 9 severe). Zibotentan Cmax was not significantly affected by hepatic or renal impairment. Compared with the normal function group, zibotentan AUC was 40% (1.40; 90% CI 0.91-2.17), 45% (1.45; 90% CI 0.94-2.24) and 190% (2.90; 90% CI 1.88-4.49) higher in subjects with mild, moderate and severe hepatic impairment, respectively, and 66% (1.66; 90% CI 1.38-1.99), 89% (1.89; 90% CI 1.50-2.39) and 117% (2.17; 90% CI 1.64-2.86) higher in subjects with mild, moderate and severe renal impairment, respectively. In both studies mean t1/2 increased and zibotentan clearance decreased with the degree of impairment. Headache was the most common AE in all groups.
Conclusions
Zibotentan absorption was unchanged, however, exposure was higher in subjects with hepatic or renal impairment due to slower clearance. This increased exposure did not result in differences in the range or severity of AEs observed.
Trial Registration
ClinicalTrials.gov: NCT00672581 and AstraZeneca study number D4320C00016 (renal trial; conducted in Germany).
doi:10.1186/1472-6904-11-3
PMCID: PMC3070638  PMID: 21414193
23.  Eukaryotic DNA Ligases: Structural and Functional Insights 
Annual review of biochemistry  2008;77:313-338.
DNA ligases are required for DNA replication, repair, and recombination. In eukaryotes, there are three families of ATP-dependent DNA ligases. Members of the DNA ligase I and IV families are found in all eukaryotes, whereas DNA ligase III family members are restricted to vertebrates. These enzymes share a common catalytic region comprising a DNA-binding domain, a nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The catalytic region encircles nicked DNA with each of the domains contacting the DNA duplex. The unique segments adjacent to the catalytic region of eukaryotic DNA ligases are involved in specific protein-protein interactions with a growing number of DNA replication and repair proteins. These interactions determine the specific cellular functions of the DNA ligase isozymes. In mammals, defects in DNA ligation have been linked with an increased incidence of cancer and neurodegeneration.
doi:10.1146/annurev.biochem.77.061306.123941
PMCID: PMC2933818  PMID: 18518823
cancer; genome stability; neurodegeneration; recombination; repair; replication
24.  Distinct kinetics of human DNA ligases I, IIIα, IIIβ, and IV reveal direct DNA sensing ability and differential physiological functions in DNA repair 
DNA repair  2009;8(8):961-968.
The three human LIG genes encode polypeptides that catalyze phosphodiester bond formation during DNA replication, recombination and repair. While numerous studies have identified protein partners of the human DNA ligases (hLigs), there has been little characterization of the catalytic properties of these enzymes. In this study, we developed and optimized a fluorescence-based DNA ligation assay to characterize the activities of purified hLigs. Although hLigI joins DNA nicks, it has no detectable activity on linear duplex DNA substrates with short, cohesive single-strand ends. By contrast, hLigIIIβ and the hLigIIIα/XRCC1 and hLigIV/XRCC4 complexes are active on both nicked and linear duplex DNA substrates. Surprisingly, hLigIV/XRCC4, which is a key component of the major non-homologous end joining (NHEJ) pathway, is significantly less active than hLigIII on a linear duplex DNA substrate. Notably, hLigIV/XRCC4 molecules only catalyze a single ligation event in the absence or presence of ATP. The failure to catalyze subsequent ligation events reflects a defect in the enzyme-adenylation step of the next ligation reaction and suggests that, unless there is an in vivo mechanism to reactivate DNA ligase IV/XRCC4 following phosphodiester bond formation, the cellular NHEJ capacity will be determined by the number of adenylated DNA ligaseIV/XRCC4 molecules.
doi:10.1016/j.dnarep.2009.06.002
PMCID: PMC2734511  PMID: 19589734
25.  The DNA binding domain of human DNA ligase I interacts with both nicked DNA and the DNA sliding clamps, PCNA and hRad9-hRad1-hHus1 
DNA repair  2009;8(8):912-919.
The participation of the DNA ligase (hLigI) encoded by the human LIG1 gene in DNA replication and repair is mediated by an interaction with proliferating cell nuclear antigen (PCNA), a homotrimeric DNA sliding clamp. Interestingly, the catalytic fragment of hLigI encircles a DNA nick forming a ring that is similar in size and shape to the PCNA ring. Here we show that the DNA binding domain (DBD) within the hLigI catalytic fragment interacts with both PCNA and the heterotrimeric cell-cycle checkpoint clamp, hRad9-hRad1-hHus1 (9-1-1). The DBD preferentially binds to trimeric PCNA and the hRad1 subunit of 9-1-1. Unlike the majority of PCNA interacting proteins, the DBD does not interact with the interdomain connector loop region of PCNA but instead appears to interact with regions adjacent to the intersubunit interfaces within the PCNA trimer. Notably, the DBD not only binds specifically to DNA nicks but also mediates the formation of DNA protein complexes with PCNA. Based on these results, we suggest that the interface between the DBD and PCNA acts as a pivot facilitating the transition of the hLigI catalytic region fragment from an extended conformation to a ring structure when it engages a DNA nick.
doi:10.1016/j.dnarep.2009.05.002
PMCID: PMC2759717  PMID: 19523882

Results 1-25 (79)