Simultaneous Replication Research Articles

Prediction of Active Site and Distal Residues in E. coli DNA Polymerase III alpha Polymerase Activity.

The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA Pol III, which is a complex of 10 different subunits that coordinates simultaneous replication on the leading and lagging strands. The 1160-residue Pol III alpha subunit is responsible for the polymerase activity and copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to the activity of the polymerase subunit. Homology modeling and the computational methods of THEMATICS and POOL were used to predict functionally important amino acid residues through their computed chemical properties. Site-directed mutagenesis and biochemical assays were used to validate these predictions. Primer extension, steady-state single-nucleotide incorporation kinetics, and thermal denaturation assays were performed to understand the contribution of these residues to the function of the polymerase. This work shows that the top 15 residues predicted by POOL, a set that includes the three previously known catalytic aspartate residues, seven remote residues, plus five previously unexplored first-layer residues, are important for function. Six previously unidentified residues, R362, D405, K553, Y686, E688, and H760, are each essential to Pol III activity; three additional residues, Y340, R390, and K758, play important roles in activity.

Microrespirometric model calibration applied to wastewater processes

Microrespirometry is a recently developed method that combines classical respirometry and microreactor systems, for the characterization of microbial cultures. This method, which allows multiple simultaneous replicates from a single low-volume biomass sample, can improve and simplify the model calibration exercise by providing more and better experimental data. To follow up on the interest in microrespirometry, two model wastewater treatment processes were set up and used for model calibration: an aerobic degradation of 4-chlorophenol by acclimated sludge, and a synthetic wastewater treatment by activated sludge, which were well described by a Haldane model and a modified ASM3 model, respectively. For each process, the model parameters were estimated by model fitting, minimizing the objective function for each replicate independently, and minimizing the objective function for all replicates simultaneously (multiresponse approach). Parameter confidence intervals were determined for all parameter estimates, and the impacts of measurement errors, number of replicates, and parameter correlation were assessed. It was observed that the multiresponse approach presents several advantages, including single-step parameter estimation, independent of the number of replicates, and determination of confidence intervals that include the main sources of uncertainty. It was concluded that microrespirometry is a high-throughput and convenient method for model calibration.

Effect of dietary supplements in American bullfrogs reared in low and high stocking densities

The aim of this study was to evaluate the effect of the probiotic Bacillus subtillis and beta-glucan from the fungus Agaricus blazei on survival, growth and immunological capacity in bullfrogs (Lithobates catesbeianus) cultured in low and high stocking densities. Animals weighing 24.3±2.38g were randomly distributed into four treatments with four simultaneous replicates: D100: 100 frogs/m2 (control); D236: 236 frogs/m2; D236+Prob.: 236 frogs/m2 supplemented with probiotic; and D236+BG: 236 frogs/m2 supplemented with beta-glucan. The parameters evaluated were weight gain, survival, plasma corticosterone (CORT), phagocytic capacity (PC) and phagocytic index (PI), at 24h and 15 and 30days. There is significant interaction between treatments and time for CORT levels. At 30days, these values were very close for the D100 (control) and D236+BG groups. Meanwhile, no statistical differences were observed between treatments for PC and PI. These results indicate that beta-glucan reduced the effects of stress caused by high density in bullfrogs, but the probiotic did not reduce these effects. Both compounds are not efficient at increasing survival rates, weight gain and neither immune response of animals. Thus, the use of commercial food additives may not have the favorable impact desired by the farmer. Their use in aquaculture should be further studied in experiments involving a longer trial period and taking into account the cost of their use.

Surface Energy Mimicking: Simultaneous Replication of Hydrophilic and Superhydrophobic Micropatterns through Area‐Selective Monomers Self‐Assembly (Adv. Mater. Interfaces 17/2016)

Surface Energy Mimicking : Simultaneous Replication of Hydrophilic and Superhydrophobic Micropatterns through Area-Selective Monomers Self-Assembly (Adv. Mater. Interfaces 17/2016)

Simultaneous Replication of Hydrophilic and Superhydrophobic Micropatterns through Area‐Selective Monomers Self‐Assembly

The control and permanent modification of the surface properties of polymers is a critical enabler for many applications. Here, we demonstrate a strategy, which we call surface energy mimicking, fo ...

Chronic viral mixt-hepatitis: current clinical and epidemiological aspects

Objective: Improvement of the diagnosis and prognosis of liver disease of viral etiology based on the analysis of clinical and epidemiological characteristics of the course and outcome of viral mixt-hepatitis. Materials and methods There are presented results of the retrospective study of 106 patients with chronic viral mixt-hepatitis (study group), which were under the medical observation for a period from two to five years between 2010 and 2014. The comparison group was consisted of 1,913 patients with chronic hepatitis C. Results and discussion The morbidity of chronic viral mixt-hepatitis in the majority of cases is registered among socially active groups of young and middle age persons, more common among males. Frequent risk factors are the artificial factor (55%), the intravenous drug usage (25%), tattooing (19%). Typical concomitant illnesses are diseases of the gastrointestinal tract and the endocrine system. Chronic viral mixt-hepatitis is mainly caused by a combination of HCV and HBV, and HCV + HBV + HDV also. HCV replication is noted in 64% of cases, the replication of HBV - in 58%, HDV replication - in 20%. Transformation into cirrhosis in patients with mixt-hepatitis C+B+D was recorded in 25% of cases, in mixt-hepatitis C+B cases - in 7.1%. In the group of C+B+D hepatitis patients, viral replication of HBV and HDV without HCV replication transformation into cirrhosis was seen in 36%. In the case of HDV replication alone, the rate of cirrhosis was 25%, while in cases with isolated HBV replication - 14%. In patients with mixt-infection C+B, the development of cirrhosis was registered within subgroup with simultaneous replication of HBV and HCV viruses in 9% cases. An isolated HCV replication, in general was less often, and led to the transformation into cirrhosis in 6% cases. Conclusions. Simultaneous replication of more than one type of hepatitis virus promotes transformation into cirrhosis, in greater extent, simultaneous replication of HBV + HDV, and monoreplication of HDV virus also. In order to prevent further progression of the pathological process it is recommended the well-timed causal treatment order with account for the predominant virus replication.

Dietary cation-anion difference and day length have an effect on milk calcium content and bone accretion of dairy cows

Milk and dairy products are an important source of Ca for humans. Recent studies have shown fluctuations in cow milk Ca content during the year in France, with high values in winter and with corn silage diets, and a decrease during May and June and with grass diets. The aim of this study was to identify the reasons for this seasonal decrease in milk Ca content by testing the effect of 2 levels of dietary cation-anion differences (DCAD; 0mEq/kg of dry matter for DCAD 0 and 400mEq/kg for DCAD 400) and 2 day lengths (8h of light/d for short days: SD; and 16h/d for long days: LD) on the Ca balances of dairy cows. The DCAD treatments were designed to mimic diets based either on corn silage or on herbage. The cows were only illuminated by solarium lights providing UVA and UVB. The trial was conducted according to 2 simultaneous replicates of a 4×4 Latin square design using 8 dairy cows averaging 103±44 d in milk with 4 periods of 14d. Data were analyzed by ANOVA with a model including treatment, cow, and period effects. No significant interaction was found between day length and DCAD treatments. With DCAD 400 compared with DCAD 0, blood pH increased and plasma ionized Ca content decreased, whereas the plasma total Ca content did not differ between treatments. Milk Ca content, however, increased with DCAD 400 compared with DCAD 0, in relation to a decrease in the amount of Ca excreted in urine. The DCAD had no significant effect on protein and casein contents and DCAD 400 tended to decrease milk yield. This illustrates that the udder did not decrease Ca uptake from the blood at high DCAD even though DCAD 400 decreased the mammary availability of Ca by decreasing the proportion of blood ionized Ca. Milk Ca and casein contents were significantly lower with LD compared with SD, whereas day length had no effect on milk yield after 14d of treatment. Bone accretion of cows increased when the Ca content of milk increased (i.e., with DCAD 400 compared with DCAD 0 and with SD compared with LD). This work suggests that long and sunny days could explain part of the seasonal decrease in milk Ca content in summer and refutes the hypothesis that low milk Ca contents at grazing could be due to the high DCAD of herbage.

The progene hypothesis: the nucleoprotein world and how life began.

In this article, I review the results of studies on the origin of life distinct from the popular RNA world hypothesis. The alternate scenario postulates the origin of the first bimolecular genetic system (a polynucleotide gene and a polypeptide processive polymerase) with simultaneous replication and translation and includes the following key features:The bimolecular genetic system emerges not from mononucleotides and monoamino acids, but from progenes, namely, trinucleotides aminoacylated on 3′–end by a non-random amino acid (NpNpNp ~ pX ~ Aa, where N—deoxyribo- or ribonucleoside, p—phosphate, X—a bifunctional agent, for example ribose, Aa—amino acid, ~ macroerge bond). Progenes are used as substrates for simultaneous synthesis of a polynucleotide and a polypeptide. Growth of the system is controlled by the growing polypeptide, and the bimolecular genetic system emerges as an extremely rare event. The first living being (virus-like organism protoviroid, Protoviroidum primum) arises and reproduces in prebiotic liposome-like structures using progenes. A population of protoviroids possessing the genetic system evolves in accordance with the Darwinian principle. Early evolution from protoviroid world to protocell world is shortly described.The progene forming mechanism (NpNp + Np ~ pX ~ Aa) makes it possible to explain the emergence of the prebiotic physicochemical group genetic code, as well as the selection of organic compounds for the future genetic system from the racemic environment.The protoviroid is reproduced on a progene basis via replicative transcription-translation (RTT, the first molecular genetic process) that is similar to its modern counterparts. Nothing is required for the emergence and reproduction of the protoviroid except for progenes and conditions for their formation.The general scheme of early evolution is as follows: prebiotic world → protoviroid (nucleoprotein) world → protocell (DNA-RNA-protein) world → LUCA (Last Universal Common Ancestor) → modern cell world. This scheme exclude the existence of an independent RNA world as predecessor of the cellular world.ReviewersDr. Thomas Dandekar, Dr. Bojan Zagrovic and Dr. Anthony Poole

BULLFROG HEMOGRAM UNDER MANAGEMENT STRESS

Stress is one of the major obstacles in frog culture and can be caused by factors such as inappropriate farming systems; inadequate management among other situations. The objective of the present study was to assess the hemogram, erythrogram and leukogram of bullfrogs (L. catesbeianus) when exposed to stress caused by different types of management: density and handling (manipulation), developed in the laboratory and repeated in the field for the appropriate comparisons in a experimental period of 30 days. The density experiment was conducted with four treatments: 70 animals m-2 (D70); 100 animals m-2 (D100), Control; 150 animals m-2 (D150) and 200 animals m-2 (D200), with 10, 14, 21 and 28 animals/box in the laboratory, respectively. Each treatment was performed with three simultaneous replicates. The handling experiment was conducted with three treatments: Treatment Without Handling (WH); Treatment with Partial Handling (PH) every 15 days and Treatment with Total Handling (TH) every 15 days. Each treatment was performed with four simultaneous replications. The methodology of the blood analysis followed international recommendations. In the present study we could observe that the animals of the field experiment did not reflect the same stress response observed in the laboratory in both experiment, which demonstrated the plasticity of these animals.

Per-Ingvar Brånemark: 3 May 1929--20 December 2014.

The father of modern implants – Professor Per-Ingvar Brånemark, surgeon, scholar, scientist, visionary, humanitarian, who changed the lives of countless patients and contemporary oral health care – has died at the age of 85 in Gothenburg, Sweden after a brilliant career The vision of P-I Brånemark led to the development of what he termed osseointegration (the structural and functional attachment of a titanium implant into living bone) and with it the predictable surgical placement of endogenous dental and facial implants as the means by which oral and facial rehabilitation became the acceptable and now routine way to replace lost and missing teeth and tissues. The development fundamentally changed the way dental and oral clinicians considered rehabilitation of lost teeth and tissues to optimize patient care. It was an inspirational experience for clinicians committed to providing prosthodontic rehabilitation but who had previously been limited to removable prostheses and fixed bridgework involving teeth. Their good fortune was to learn about this approach and be part of its introduction. The basis of the procedure was an understanding of bone biology through studies which progressed to a specific design for root form implants, precision formed from commercially pure titanium which was a key element in the success, as it led to biological integration with the ability to sustain load and function. The international awareness of this new development in 1981 occurred with the first report in an international journal, which captured the innovation and predictable management of complete edentulism with osseointegrated implants and dramatically improved the quality of life of those unable to function with complete dentures. Later single tooth implants and short span implant bridgework continued to transform clinical management of restorative dentistry and prosthodontics. The Toronto Conference in 1982 brought the information to North America and was the catalyst for the rapid spread of the support industry and additional implant systems, some of which challenged the biology and science which underlined the original controlled development. Internationally, Australia became involved very early with simultaneous replication studies conducted at the University of Sydney and the University of Western Australia, together with subsequent involvement in university-sponsored training and education programmes. Australia was fortunate to enjoy a close collaboration with Professor Brånemark, and as a result has remained at the forefront of research, development, innovation and clinical application. Contemporary demands for immediacy in case management have been a driver for change in clinical practice. P-I emphasized a systematic approach involving clinical trials and the careful training of clinicians to ensure the delivery of optimum care. Competitive dental practice and industry initiatives need to reflect on this approach to ensure that professional standards initially set are maintained. The passing of our esteemed leader, colleague and friend, allows us to reflect on his life, his achievements, his passion and commitment to helping rehabilitate those in greatest need, and to marvel at the continual inspiration of the man and his contributions – a legacy of benefit to more and more grateful patients and clinicians who have had the privilege to be part of the osseointegration story and to acknowledge its transformation of clinical practice.

Different true-protein sources do not modify the metabolism of crossbred Bos taurus × Bos indicus growing heifers

The present study was conducted to investigate the effect of alternative true-protein sources to soybean meal, with different ruminal degradability, using a sugarcane-based diet, on nutrient digestion, ruminal fermentation, efficiency of microbial protein synthesis and passage rate in prepubertal dairy heifers. Eight crossbred rumen- and duodenum-cannulated Holstein × Gyr dairy heifers (202.0±11.5 kg BW) were evaluated in a 4 × 4 Latin square experimental design with four treatments and four periods in two simultaneous replicates. Dietary treatments were: soybean meal; cottonseed meal; peanut meal; and sunflower meal. When associated with diets containing sugarcane, the different protein sources did not affect intake or digestibility of dry mater, crude protein, organic matter and neutral detergent fiber. The average ruminal pH, NH3-N and concentration of total volatile fatty acids were not different among the diets supplied. The concentration of butyric acid was different among the protein sources, wherein the animals fed the diet with sunflower meal presented lower values than those fed the other sources. Diets did not affect nitrogen balance, microbial nitrogen, microbial synthesisefficiency, estimated dry matter flow, or passage rate. Alternative protein sources can be used to reduce the costs without changing the animal metabolism.

Temporal Workload-Aware Replicated Partitioning for Social Networks

Most frequent and expensive queries in social networks involve multi-user operations such as requesting the latest tweets or news-feeds of friends. The performance of such queries are heavily dependent on the data partitioning and replication methodologies adopted by the underlying systems. Existing solutions for data distribution in these systems involve hashor graph-based approaches that ignore the multi-way relations among data. In this work, we propose a novel data partitioning and selective replication method that utilizes the temporal information in prior workloads to predict future query patterns. Our method utilizes the social network structure and the temporality of the interactions among its users to construct a hypergraph that correctly models multi-user operations. It then performs simultaneous partitioning and replication of this hypergraph to reduce the query span while respecting load balance and I/O load constraints under replication. To test our model, we enhance the Cassandra NoSQL system to support selective replication and we implement a social network application (a Twitter clone) utilizing our enhanced Cassandra. We conduct experiments on a cloud computing environment (Amazon EC2) to test the developed systems. Comparison of the proposed method with hash- and enhanced graph-based schemes indicate that it significantly improves latency and throughput.

Competition and cooperation in dynamic replication networks.

The simultaneous replication of six coiled-coil peptide mutants by reversible thiol-thioester exchange reactions is described. Experimental analysis of the time dependent evolution of networks formed by the peptides under different conditions reveals a complex web of molecular interactions and consequent mutant replication, governed by competition for resources and by autocatalytic and/or cross-catalytic template-assisted reactions. A kinetic model, first of its kind, is then introduced, allowing simulation of varied network behaviour as a consequence of changing competition and cooperation scenarios. We suggest that by clarifying the kinetic description of these relatively complex dynamic networks, both at early stages of the reaction far from equilibrium and at later stages approaching equilibrium, one lays the foundation for studying dynamic networks out-of-equilibrium in the near future.

The organization of medical care for patients with chronic viral hepatitis in the Republic Sakha (Yakutia)

Aim. To identify the risk factors for primary liver cancer in patients with chronic viral hepatitis in the Republic of Sakha (Yakutia) and develop an organizational model of treatment and prevention of viral hepatitis and primary liver cancer. Methods. Clinical, epidemiological and molecular biological methods were used. Results. There is a high prevalence of chronic viral hepatitis B, C and D in the Republic of Sakha (Yakutia), as well as their distant adverse outcomes. Disclosed the problem of the combined effects of risk factors for primary liver cancer in people indigenous nationality of the Republic of Sakha (Yakutia), mostly male, living in rural areas, which is the simultaneous replication of hepatitis viruses B, C and D in patients with genetically predisposed changes in the activity of alcohol dehydrogenase and aldehyde dehydrogenase. The modernization of the training algorithms of patients for liver transplantation and management of patients with cirrhosis and liver cancer in the outcome of chronic viral hepatitis, liver transplantation is justified from a related donor with a high level of specific antibodies of patients with primary liver cancer, as well as phasing held medical diagnostic and organizational and methodological measures. Created was an annual Republican «liver-school» for physicians, gastroenterologists, internists, pediatricians, epidemiologists, introduced the publication of conference materials for use on the entire territory of the Republic of Sakha (Yakutia). Conclusion. Multi-component structural-functional model of service prevention and control of viral hepatitis has allowed to develop a program to address the medical and social protection of different groups of the population to create a unified register «Chronic viral hepatitis in the Republic of Sakha (Yakutia)», as well as long-term programs for complex vaccine prophylactics and modernization of services for prevention and control of viral hepatitis.

Is hypoxia a stressor to American bullfrog tadpoles?

The aim of this study was to evaluate alterations to the physiological profile of cortisol in pro-metamorphose phase tadpoles of Lithobates catesbeianus exposed to hypoxia stressor in a capture experiment and in a crowding experiment. The capture study was performed by the treatments: stress due to individual capture with a hand net, stress due to batch capture with a hand net and stress due to capture by emptying. Three simultaneous replicates was done witch 12 animals were sampled (6 normoxia - immediately blood collection) and 6 hypoxia - blood collection after 15 min of air exposition) in two collection times with 5 days by intervals. The crowding study was performed by the treatments 1 tadpole L-1, 5 tadpoles L-1 and 10 tadpoles L-1. Three simultaneous replicates was done witch 8 animals (4 normoxia and 4 hypoxia) were sampled in the zero moment (ZM) - blood collection before the experiment, 6 animals/treatment (3 normoxia and 3 hypoxia) to 4 and 8 days and 18 animals/treatment (9 normoxia and 9 hypoxia) to 12 days. The average values to plasmatic cortisol varying from 1.7 to 5.1ng mL-1 (capture study) and 1.0 to 4.2ng mL-1 (crowding study). It concludes that the biomarker tested (cortisol) showed no alterations front of the stressor used. Alternatively, a larger response pattern to these stimuli may have been expressed in another level of an unmeasured hormone (corticosterone). And the bullfrog has great ability to adapt to different management compared to other aquatic organisms, which demonstrates the plasticity of these animals.

Network and data location aware approach for simultaneous job scheduling and data replication in large-scale data grid environments

Data Grid integrates graphically distributed resources for solving data intensive scientific applications. Effective scheduling in Grid can reduce the amount of data transferred among nodes by submitting a job to a node, where most of the requested data files are available. Scheduling is a traditional problem in parallel and distributed system. However, due to special issues and goals of Grid, traditional approach is not effective in this environment any more. Therefore, it is necessary to propose methods specialized for this kind of parallel and distributed system. Another solution is to use a data replication strategy to create multiple copies of files and store them in convenient locations to shorten file access times. To utilize the above two concepts, in this paper we develop a job scheduling policy, called hierarchical job scheduling strategy (HJSS), and a dynamic data replication strategy, called advanced dynamic hierarchical replication strategy (ADHRS), to improve the data access efficiencies in a hierarchical Data Grid. HJSS uses hierarchical scheduling to reduce the search time for an appropriate computing node. It considers network characteristics, number of jobs waiting in queue, file locations, and disk read speed of storage drive at data sources. Moreover, due to the limited storage capacity, a good replica replacement algorithm is needed. We present a novel replacement strategy which deletes files in two steps when free space is not enough for the new replica: first, it deletes those files with minimum time for transferring. Second, if space is still insufficient then it considers the last time the replica was requested, number of access, size of replica and file transfer time. The simulation results show that our proposed algorithm has better performance in comparison with other algorithms in terms of job execution time, number of intercommunications, number of replications, hit ratio, computing resource usage and storage usage.

Randomization tests for single-case experiments: State of the art, state of the science, and state of the application

A single-case experimental design is a research design that can be used to evaluate the effect of an intervention for a single entity. There are two important schedules to include randomization into the design of single-case experiments: phase designs and alternation designs. We present these two schedules and provide a detailed example for each schedule. For both examples, we illustrate the use of a free software package that assists researchers in designing and analyzing single-case experiments using randomization tests. Furthermore, we discuss several additions (simultaneous and sequential replication designs; meta-analysis of single-case experimental studies) and alternatives (statistical and visual analysis methods).

Analysis of single-case data: Randomisation tests for measures of effect size

Single-case experiments can be used to evaluate the effect of an intervention or treatment for a single entity. The internal validity and statistical conclusion validity of single-case experiments can be improved by incorporating randomisation in their design. In this article, we explain how to design randomised single-case phase and alternation studies as well as randomised simultaneous and sequential replication studies, and how to conduct randomisation tests for these designs. Advantages and limitations of randomisation tests are discussed. In order to not only determine the (non)randomness of an intervention effect, but also the magnitude of this effect, we propose to use an effect size index as a test statistic for the randomisation test. We illustrate this combination for the design and analysis of an ABAB phase study, using a free software package.

Hopfield neural network for simultaneous job scheduling and data replication in grids

This paper presents a novel heuristic approach, named JDS-HNN, to simultaneously schedule jobs and replicate data files to different entities of a grid system so that the overall makespan of executing all jobs as well as the overall delivery time of all data files to their dependent jobs is concurrently minimized. JDS-HNN is inspired by a natural distribution of a variety of stones among different jars and utilizes a Hopfield Neural Network in one of its optimization stages to achieve its goals. The performance of JDS-HNN has been measured by using several benchmarks varying from medium- to very-large-sized systems. JDS-HNN’s results are compared against the performance of other algorithms to show its superiority under different working conditions. These results also provide invaluable insights into scheduling and replicating dependent jobs and data files as well as their performance related issues for various grid environments.

Successful computational prediction of active site and distal residues essential for function in DNA polymerase III alpha subunit

The process of DNA replication is carried out with high efficiency and accuracy by DNA polymerases. The replicative polymerase in E. coli is DNA pol III, which is a 10‐subunit complex that coordinates simultaneous replication on the leading and lagging strands. The 1160‐residue pol III alpha subunit copies DNA accurately, making one error per 105 nucleotide incorporations. The goal of this research is to determine the residues that contribute to this high fidelity and activity of the polymerase subunit. Homology modelingand the computational methods of Theoretical Microscopic Anomalous Titration Curve Shapes (THEMATICS) and Partial Order Optimum Likelihood (POOL)have been used to predict functionally important amino acid residues. Site‐directed mutagenesis and primer extension assays have been used to validate these predictions. This and previous work show that the top 11 residues predicted by POOL, including the three catalytic aspartates plus distal residues, are important for function. Fluorescence binding assays, thermal denaturation assays and steady‐state kinetic assays are being performed to better understand the contribution of these residues to the function of the polymerase. Work supported by NSF‐MCB‐0843603, NSF‐MCB‐0845033, NSF‐MCB‐1158176 and Research Corporation for Science Advancement.