Exchangeability of mammalian DNA ligases between base excision repair pathways

In mammalian cells, DNA ligase IIIalpha and DNA ligase I participate in the short- and long-patch base excision repair pathways, respectively. Using an in vitro repair assay employing DNA ligase-depleted cell extracts and DNA substrates containing a single lesion repaired either through short-patch (regular abasic site) or long-patch (reduced abasic site) base excision repair pathways, we addressed the question whether DNA ligases are specific to each pathway or if they are exchangeable. We find that immunodepletion of DNA ligase I did not affect the short-patch repair pathway but blocked long-patch repair, suggesting that DNA ligase IIIa is not able to substitute DNA ligase I during long-patch repair. In contrast, immunodepletion of DNA ligase IIIa did not significantly affect either pathway. Moreover, repair of normal abasic sites in wild-type and X-ray cross-complementing gene 1 (XRCC1)-DNA ligase IIIalpha-immunodepleted cell extracts involved similar proportions of short- and long-patch repair events. This suggests that DNA ligase I was able to efficiently substitute the XRCC1-DNA ligase IIIa complex during short-patch repair.

Repair of abasic sites in DNA

Repair of both normal and reduced AP sites is activated by AP endonuclease, which recognizes and cleaves a phosphodiester bond 5' to the AP site. For a short period of time an incised AP site is occupied by poly(ADP-ribose) polymerase and then DNA polymerase beta adds one nucleotide into the repair gap and simultaneously removes the 5'-sugar phosphate. Finally, the DNA ligase III/XRCC1 complex accomplishes repair by sealing disrupted DNA ends. However, long-patch BER pathway, which is involved in the removal of reduced abasic sites, requires further DNA synthesis resulting in strand displacement and the generation of a damage-containing flap that is later removed by the flap endonuclease. Strand-displacement DNA synthesis is accomplished by DNA polymerase delta/epsilon and DNA ligase I restores DNA integrity. DNA synthesis by DNA polymerase delta/epsilon is dependent on proliferating cell nuclear antigen, which also stimulates the DNA ligase I and flap endonuclease. These repair events are supported by multiple protein-protein interactions. (C) 2003 Elsevier B.V. All rights reserved.

Joint effects of population density and toxicant exposure on population dynamics of Capitella sp I

Very few studies have analyzed the dependence of population growth rate on population density, and even fewer have considered interaction effects of density and other stresses, such as exposure to toxic chemicals. Yet without such studies we cannot know whether chemicals harmful at low density have effects on carrying capacity or, conversely, whether chemicals reducing carrying capacity are also harmful at low density, impeding a population's capacity to recover from disturbance. This study examines the combined effects of population density and a toxicant (fluoranthene) on population growth rate (pgr) and carrying capacity using the deposit-feeding polychaete Capitella sp. I as a test organism. Populations were initiated with a stable age distribution, and population density and age/size distribution were followed during a period of 28 wk. Fluoranthene (FLU), population density, and their interaction influenced population growth rate. Population growth rate declined linearly with the logarithm of population biomass, but the slope of the relationship was steeper for the control populations than for populations exposed to 50 mug FLU/(g sediment dry mass). Populations exposed to 150 mug FLU/(g sediment dry mass) went extinct after 8 wk of exposure. Despite concerns that toxicant effects would be exacerbated at high density, we found the reverse to be the case, and effects of fluoranthene on population growth rate were much reduced in the region of carrying capacity. Fluoranthene did. reduce carrying capacity by 46%, and this could haven important implications for interacting species and/or sediment biogeochemical processes.

The joint effects of larval density and C-14-cypermethrin on the life history and population growth rate of the midge Chironomus riparius

1. Chemical effects on organisms are typically assessed using individual-level endpoints or sometimes population growth rate (PGR), but such measurements are generally made at low population densities. In contrast most natural populations are subject to density dependence and fluctuate around the environmental carrying capacity as a result of individual competition for resources. As ecotoxicology aims to make reliable population projections of chemical impacts in the field, an understanding of how high-density or resource-limited populations respond to environmental chemicals is essential. 2. Our objective was to determine the joint effects of population density and chemical stress on the life history and PGR of an important ecotoxicological indicator species, Chironomus riparius, under controlled laboratory conditions. Populations were fed the same ration but initiated at different densities and exposed to a solvent control and three concentrations of C-14-cypermethrin in a sediment-water test system for 67 days at 20 +/- 1 degreesC. 3. Density had a negative effect on all the measured life-history traits, and PGR declined with increasing density in the controls. Exposure to C-14-cypermethrin had a direct negative effect on juvenile survival, presumably within the first 24 h because the chemical rapidly dissipated from the water column. Reductions in the initial larval densities resulted in an increase in the available resources for the survivors. Subsequently, exposed populations emerged sooner and started producing offspring earlier than the controls. C-14-cypermethrin had no effect on estimated fecundity and adult body weight but interacted with density to reduce the time to first emergence and first reproduction. As a result, PGR increased with cypermethrin concentration when populations were initiated at high densities. 4. Synthesis and applications. The results showed that the effects of C-14-cypermethrin were buffered at high density, so that the joint effects of density and chemical stress on PGR were less than additive. Low levels of chemical stressors may increase carrying capacity by reducing juvenile competition for resources. More and perhaps fitter adults may be produced, similar to the effects of predators and culling; however, toxicant exposure may result in survivors that are less tolerant to changing conditions. If less than additive effects are typical in the field, standard regulatory tests carried out at low density may overestimate the effects of environmental chemicals. Further studies over a wide range of chemical stressors and organisms with contrasting life histories are needed to make general recommendations.

A novel repair model for imperfect maintenance

Commonly used repair rate models for repairable systems in the reliability literature are renewal processes, generalised renewal processes or non-homogeneous Poisson processes. In addition to these models, geometric processes (GP) are studied occasionally. The GP, however, can only model systems with monotonously changing (increasing, decreasing or constant) failure intensities. This paper deals with the reliability modelling of failure processes for repairable systems where the failure intensity shows a bathtub-type non-monotonic behaviour. A new stochastic process, i.e. an extended Poisson process, is introduced in this paper. Reliability indices are presented, and the parameters of the new process are estimated. Experimental results on a data set demonstrate the validity of the new process.

A novel repair model for imperfect maintenance

The basic repair rate models for repairable systems may be homogeneous Poisson processes, renewal processes or nonhomogeneous Poisson processes. In addition to these models, geometric processes are studied occasionally. Geometric processes, however, can only model systems with monotonously changing (increasing, decreasing or constant) failure intensity. This paper deals with the reliability modelling of the failure process of repairable systems when the failure intensity shows a bathtub type non-monotonic behaviour. A new stochastic process, an extended Poisson process, is introduced. Reliability indices and parameter estimation are presented. A comparison of this model with other repair models based on a dataset is made.

Joint importance of multistate systems

Importance measures in reliability engineering are used to identify weak areas of a system and signify the roles of components in either causing or contributing to proper functioning of the system. Traditional importance measures for multistate systems mainly concern reliability importance of an individual component and seldom consider the utility performance of the systems. This paper extends the joint importance concepts of two components from the binary system case to the multistate system case. A joint structural importance and a joint reliability importance are defined on the basis of the performance utility of the system. The joint structural importance measures the relationship of two components when the reliabilities of components are not available. The joint reliability importance is inferred when the reliabilities of the components are given. The properties of the importance measures are also investigated. A case study for an offshore electrical power generation system is given.

Peroxynitrite-modified collagen-II induces p38/ERK and NF-kappa B-dependent synthesis of prostaglandin E-2 and nitric oxide in chondrogenically differentiated mesenchyrnal progenitor cells

Objective: Peroxynitrite (ONOO-) is formed in the inflamed and degenerating human joint. Peroxynitrite-modified collagen-II (PMC-II) was recently discovered in the serum of patients with osteoarthritis (OA) and rheumatoid arthritis (RA). Therefore we investigated the cellular effects of PMC-II on human mesenchymal progenitor cells (MPCs) as a model of cartilage and cartilage repair cells in the inflamed and degenerating joint. Design: MPCs were isolated from the trabecular bone of patients undergoing reconstructive surgery and were differentiated into a chondrogenic lineage. Cells were exposed to PMC-II and levels of the proinflammatory mediators nitric oxide (NO) and prostaglandin E-2 (PGE(2)) measured. Levels of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), phosphorylated mitogen activated protein kinases (MAPKs) and nuclear factor kappa B (NF-kappa B) activation were measured by enzyme linked immunosorbent assay (ELISA) together with specific MAPK and NF-kappa B inhibitors. Results: PMC-II induced NO and PGE(2) synthesis through upregulation of iNOS and COX-2 proteins. PMC-II also lead to the phosphorylation of MAPKs, extracellularly regulated kinase 1/2 (ERK1/2) and p38 [but not c-Jun NH2-terminal kinase (JNK1/2)] and the activation of proinflammatory transcription factor NF-kappa B. Inhibitors of p38, ERK1/2 and NF-kappa B prevented PMC-II induced NO and PGE(2) synthesis, NOS and COX-2 protein expression and NF-kappa B activation. Conclusion: iNOS, COX-2, NF-KB and MAPK are known to be activated in the joints of patients with OA and RA. PMC-II induced iNOS and COX-2 synthesis through p38, ERK1/2 and NF-KB dependent pathways suggesting a previously unidentified pathway for the synthesis of the proinflammatory mediators, NO and PGE(2), further suggesting that inhibitors of these pathways may be therapeutic in the inflamed and degenerating human joint. (c) 2005 OsteoArthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

Accurate molecular structures of chlorothiazide and hydrochlorothiazide by joint refinement against powder neutron and X-ray diffraction data

The compounds chlorothiazide and hydrochlorothiazide (crystalline form II) have been studied in their fully hydrogenous forms by powder neutron diffraction on the GEM diffractometer. The results of joint Rietveld refinement of the structures against multi-bank neutron and single-bank X-ray powder data are reported and show that accurate and precise structural information can be obtained from polycrystalline molecular organic materials by this route.

The effect of cleft lip and palate, and the timing of lip repair on mother-infant interactions and infant development

Background: Children with cleft lip and palate are at risk for psychological problems. Difficulties in mother-child interactions may be relevant, and could be affected by the timing of lip repair. Method: We assessed cognitive development, behaviour problems, and attachment in 94 infants with cleft lip (with and without cleft palate) and 96 non-affected control infants at 18 months; mother-infant interactions were assessed at two, six and 12 months. Index infants received either 'early', neonatal, lip repair, or 'late' repair (3-4 months). Results: Index infants did not differ from controls on measures of behaviour problems or attachment, regardless of timing of lip repair; however, infants having late lip repair performed worse on the Bayley Scales of Mental Development; the cognitive development of early repair infants was not impaired. Difficulties in early mother-infant interactions mediated the effects of late lip repair on infant cognitive outcome. Conclusions: Early interaction difficulties between mothers and infants having late repair of cleft lip are associated with poor cognitive functioning at 18 months. Interventions to facilitate mother-infant interactions prior to surgical lip repair should be explored.

Does repairing a cleft lip neonatally have any effect on the longer-term attractiveness of the repair?

Objective: To determine whether attractiveness and success of surgical outcome differ according to the timing of cleft lip repair. Design: Three experiments were conducted: (1) surgeons rated postoperative medical photographs of infants having either neonatal or 3-month lip repair; (2) lay panelists rated the same photographs; (3) lay panelists rated dynamic video displays of the infants made at 12 months. Normal comparison infants were also rated. The order of stimuli was randomized, and panelists were blind to timing of lip repair and the purposes of the study. Setting: Four U.K. regional centers for cleft lip and palate. Participants: Infants with isolated clefts of the lip, with and without palate. Intervention: Early lip repair was conducted at median age 4 days (inter-quartile range [IQR] = 4), and late repair at 104 days (IQR = 57). Main Outcome Measures: Ratings of surgical outcome (Experiment 1 only) and attractiveness (all experiments) on 5-point Likert scales. Results: In Experiment 1 success of surgical outcome was comparable for early and late repair groups (difference = -0.08; 95% confidence interval [CI] = -0.43 to 0.28; p = .66). In all three experiments, attractiveness ratings were comparable for the two groups. Differences were, respectively, 0.10 (95% CI = -2.3 to 0.44, p = .54); -0.11 (95% CI = -0.42 to -0.19, p = .54); and 0.08 (95% CI = -0.11 to 0.28, p =.41). Normal infants were rated more attractive than index infants (difference = 0.38; 95% CI = 0.24 to 0.52; p < .001). Conclusion: Neonatal repair for cleft of the lip confers no advantage over repair at 3 months in terms of perceived infant attractiveness or success of surgical outcome.

A new algorithm for OFDM joint data detection and phase noise cancellation

This paper proposes a new iterative algorithm for OFDM joint data detection and phase noise (PHN) cancellation based on minimum mean square prediction error. We particularly highlight the problem of "overfitting" such that the iterative approach may converge to a trivial solution. Although it is essential for this joint approach, the overfitting problem was relatively less studied in existing algorithms. In this paper, specifically, we apply a hard decision procedure at every iterative step to overcome the overfitting. Moreover, compared with existing algorithms, a more accurate Pade approximation is used to represent the phase noise, and finally a more robust and compact fast process based on Givens rotation is proposed to reduce the complexity to a practical level. Numerical simulations are also given to verify the proposed algorithm.

Design of redundant drive joint with adjustable stiffness and damping mechanism to improve joint admittance

Improving admittance of robotic joints is the key issue for making rehabilitation robots safe. This paper describes a design of Redundant Drive Joint (RD-Joint) which allows greater flexibility in the design of robotic mechanisms. The design strategy of the RD-Joint employs a systematic approach which consists of 1) adopting a redundant joint mechanism with internal kinematical redundancy to reduce effective joint inertia, and 2) adopting an adjustable admittance mechanism with a novel Cross link Reduction Mechanism and mechanical springs and dampers as a passive second actuator. First, the basic concepts used to construct the redundant drive joint mechanism are explained, in particular the method that allows a reduction in effective inertia at the output joint. The basic structure of the RD-Joint is introduced based on the idea of reduced inertia along with a method to include effective stiffness and damping. Then, the basic design of the adjustable admittance mechanism is described. Finally, a prototype of RD-joint is described and its expected characteristics are discussed.