Synaptic Vesicle Dynamics: A Simple Model of Phasic Release

We present a simple model of phasic neurotransmitter release whichreproduces the salient features of chemical neurotransmission. The synapticvesicle cycle has been modelled as a set of biochemical reactionsrepresented by a system of coupled differential equations. These equationshave been solved analytically to obtain the time dependent behaviour of thesystem on perturbation from the steady state. The scheme of the synapticvesicle network has been emphasized and its role in determining some of themajor experimentally observed properties of synaptic transmission has beendiscussed, which includes the biphasic decay of the rate neurotransmitterrelease even under sustained stimulation. Another interesting outcome ofthis theoretical exercise is the saturation of total release with thecalcium dependent rate constant. The theoretically calculated values oftotal release fit very well into a sigmoidal saturating function with afourth order cooperativity exponent similar to the empiricalDodge–Rahamimoff equation. It appears that the synaptic vesiclenetwork itself is responsible for some of the major properties associatedwith chemical neurotransmission.     

Effects of Immigration on the Dynamics of Simple Population Models

Many simple population models exhibit the period doubling route to chaos as a single parameter, commonly the growth rate, is increased. Here we examine the effect of an immigration process on such models and explain why in the case of one-dimensional ("single-humped") maps, immigration often tends to suppress chaos and stabilise equilibrium behaviour or cyclical oscillations of long period. The conditions for which an increase of immigration "simplifies" population dynamics are examined.     

A Systematic Framework for Molecular Dynamics Simulations of Protein Post-Translational Modifications

By directly affecting structure, dynamics and interaction networks of their targets, post-translational modifications (PTMs) of proteins play a key role in different cellular processes ranging from enzymatic activation to regulation of signal transduction to cell-cycle control. Despite the great importance of understanding how PTMs affect proteins at the atomistic level, a systematic framework for treating post-translationally modified amino acids by molecular dynamics (MD) simulations, a premier high-resolution computational biology tool, has never been developed. Here, we report and validate force field parameters (GROMOS 45a3 and 54a7) required to run and analyze MD simulations of more than 250 different types of enzymatic and non-enzymatic PTMs. The newly developed GROMOS 54a7 parameters in particular exhibit near chemical accuracy in matching experimentally measured hydration free energies (RMSE = 4.2 kJ/mol over the validation set). Using this tool, we quantitatively show that the majority of PTMs greatly alter the hydrophobicity and other physico-chemical properties of target amino acids, with the extent of change in many cases being comparable to the complete range spanned by native amino acids.     

A Systematic Review of Pharmacological Treatment Options Used to Reduce Ischemia Reperfusion Injury in Rat Liver Transplantation

Background

Although animal studies models are frequently used for the purpose of attenuating ischemia reperfusion injury (IRI) in liver transplantation (LT), many of pharmacological agents have not become part of clinical routine.

Methods

A search was performed using the PubMed database to identify agents, from which 58 articles containing 2700 rat LT procedures were selected. The identified pharmacological agents were categorized as follows: I - adenosine agonists, nitric oxide agonists, endothelin antagonists, and prostaglandins, II – Kupffer cell inactivator, III - complement inhibiter, IV - antioxidant, V - neutrophil inactivator, VI -anti-apoptosis agent, VII - heat shock protein and nuclear factor kappa B inducer, VIII - metabolic agent, IX - traditional Chinese medicine, and X - others. Meta-analysis using 7-day-survival rate was also performed with Mantel-Haenszel''s Random effects model.

Results

The categorization revealed that the rate of donor-treated experiments in each group was highest for agents from Group II (70%) and VII (71%), whereas it was higher for agents from Group V (83%) in the recipient-treated experiments. Furthermore, 90% of the experiments with agents in Group II provided 7-day-survival benefits. The Risk Ratio (RR) of the meta-analysis was 2.43 [95% CI: 1.88-3.14] with moderate heterogeneity. However, the RR of each of the studies was too model-dependent to be used in the search for the most promising pharmacological agent.

Conclusion

With regard to hepatic IRI pathology, the categorization of agents of interest would be a first step in designing suitable multifactorial and pleiotropic approaches to develop pharmacological strategies.     

Retraction Note to: Simple Sequence Repeat and S-locus Genotyping to Explore Genetic Variability in Polyploid Prunus spinosa and P. insititia

Biochemical Genetics -     

Excited State Dynamics Can Be Used to Probe Donor-Acceptor Distances for H-Tunneling Reactions Catalyzed by Flavoproteins

In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H₄, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H₄-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.     

Excited State Dynamics Can Be Used to Probe Donor-Acceptor Distances for H-Tunneling Reactions Catalyzed by Flavoproteins

In enzyme systems where fast motions are thought to contribute to H-transfer efficiency, the distance between hydrogen donor and acceptor is a very important factor. Sub-ångstrom changes in donor-acceptor distance can have a large effect on the rate of reaction, so a sensitive probe of these changes is a vital tool in our understanding of enzyme function. In this study we use ultrafast transient absorption spectroscopy to investigate the photoinduced electron transfer rates, which are also very sensitive to small changes in distance, between coenzyme analog, NAD(P)H₄, and the isoalloxazine center in the model flavoenzymes morphinone reductase (wild-type and selected variants) and pentaerythritol tetranitrate reductase (wild-type). It is shown that upon addition of coenzyme to the protein the rate of photoinduced electron transfer is increased. By comparing the magnitude of this increase with existing values for NAD(P)H₄-FMN distances, based on charge-transfer complex absorbance and experimental kinetic isotope effect reaction data, we show that this method can be used as a sensitive probe of donor-acceptor distance in a range of enzyme systems.     

Simple Topological Features Reflect Dynamics and Modularity in Protein Interaction Networks

The availability of large-scale protein-protein interaction networks for numerous organisms provides an opportunity to comprehensively analyze whether simple properties of proteins are predictive of the roles they play in the functional organization of the cell. We begin by re-examining an influential but controversial characterization of the dynamic modularity of the S. cerevisiae interactome that incorporated gene expression data into network analysis. We analyse the protein-protein interaction networks of five organisms, S. cerevisiae, H. sapiens, D. melanogaster, A. thaliana, and E. coli, and confirm significant and consistent functional and structural differences between hub proteins that are co-expressed with their interacting partners and those that are not, and support the view that the former tend to be intramodular whereas the latter tend to be intermodular. However, we also demonstrate that in each of these organisms, simple topological measures are significantly correlated with the average co-expression of a hub with its partners, independent of any classification, and therefore also reflect protein intra- and inter- modularity. Further, cross-interactomic analysis demonstrates that these simple topological characteristics of hub proteins tend to be conserved across organisms. Overall, we give evidence that purely topological features of static interaction networks reflect aspects of the dynamics and modularity of interactomes as well as previous measures incorporating expression data, and are a powerful means for understanding the dynamic roles of hubs in interactomes.     

Systematic Review of the Measurement Properties of Tools Used to Measure Behaviour Problems in Young Children with Autism

Background

Behaviour problems are common in young children with autism spectrum disorder (ASD). There are many different tools used to measure behavior problems but little is known about their validity for the population.

Objectives

To evaluate the measurement properties of behaviour problems tools used in evaluation of intervention or observational research studies with children with ASD up to the age of six years.

Methods

Behaviour measurement tools were identified as part of a larger, two stage, systematic review. First, sixteen major electronic databases, as well as grey literature and research registers were searched, and tools used listed and categorized. Second, using methodological filters, we searched for articles examining the measurement properties of the tools in use with young children with ASD in ERIC, MEDLINE, EMBASE, CINAHL, and PsycINFO. The quality of these papers was then evaluated using the COSMIN checklist.

Results

We identified twelve tools which had been used to measure behaviour problems in young children with ASD, and fifteen studies which investigated the measurement properties of six of these tools. There was no evidence available for the remaining six tools. Two questionnaires were found to be the most robust in their measurement properties, the Child Behavior Checklist and the Home Situations Questionnaire—Pervasive Developmental Disorders version.

Conclusions

We found patchy evidence on reliability and validity, for only a few of the tools used to measure behaviour problems in young children with ASD. More systematic research is required on measurement properties of tools for use in this population, in particular to establish responsiveness to change which is essential in measurement of outcomes of intervention.

PROSPERO Registration Number

CRD42012002223     

Dynamics of Biological Macromolecules: Not a Simple Slaving by Hydration Water

We studied the dynamics of hydrated tRNA using neutron and dielectric spectroscopy techniques. A comparison of our results with earlier data reveals that the dynamics of hydrated tRNA is slower and varies more strongly with temperature than the dynamics of hydrated proteins. At the same time, tRNA appears to have faster dynamics than DNA. We demonstrate that a similar difference appears in the dynamics of hydration water for these biomolecules. The results and analysis contradict the traditional view of slaved dynamics, which assumes that the dynamics of biological macromolecules just follows the dynamics of hydration water. Our results demonstrate that the dynamics of biological macromolecules and their hydration water depends strongly on the chemical and three-dimensional structures of the biomolecules. We conclude that the whole concept of slaving dynamics should be reconsidered, and that the mutual influence of biomolecules and their hydration water must be taken into account.     

A Simple Open Flow System Used to Measure Acetylene Reduction Activity of Sesbania rostrata Stem and Root Nodules

A simple method for mixing gases for the assay of acetylenereduction using an open flow system is described. Gas mixturesare obtained using simple regulator valves (described) to obtainequal gas pressures and then providing a resistance to gas flowproportional to the flow of gas required. The system describedallows any number of gases to be mixed over a wide range ofratios, at a wide range of flow rates. Using this system, theactivity of Sesbania rostrata stem and root nodules was examinedin undisturbed plants. Nodules in either location had high ratesof acetylene reduction (270 µmol C₂H₄ g     

The Evolutionary Optimality of Oscillatory and Chaotic Dynamics in Simple Population Models

The problem is considered of whether natural selection favors genotypes characterized by oscillatory or chaotic population dynamics. This is done with reference to two simple one-dimensional models, which display a variety of dynamical patterns according to the different values of their parameters: the semelparous and iteroparous Ricker models. To lind the optimal genotype (or genotypes) within a given feasibility set, the concept of Continuously Stable Strategy (CSS) and a haploid model of competition between genotypes are used. The parameters subject to evolution are the intrinsic finite rate of increase and respectively the juvenile mortality in the semelparous model and the adult survival in the iteroparous one. In the semelparous case a single feasible CSS exists, while in the other case more than one CSS might exist. The dynamical nature of the optimal genotype (stable equilibrium, stable sustained oscillations or chaos) is basically determined by the shape of the set of feasibility for the parameters defining each genotype. However, if the feasibility set is drawn at random, the probability that the corresponding optimal genotype (or genotypes) be oscillatory or chaotic is quite low. This result, however, might not hold with more complex models.     

Photosystem II Function and Dynamics in Three Widely Used Arabidopsis thaliana Accessions

Columbia-0 (Col-0), Wassilewskija-4 (Ws-4), and Landsberg erecta-0 (Ler-0) are used as background lines for many public Arabidopsis mutant collections, and for investigation in laboratory conditions of plant processes, including photosynthesis and response to high-intensity light (HL). The photosystem II (PSII) complex is sensitive to HL and requires repair to sustain its function. PSII repair is a multistep process controlled by numerous factors, including protein phosphorylation and thylakoid membrane stacking. Here we have characterized the function and dynamics of PSII complex under growth-light and HL conditions. Ws-4 displayed 30% more thylakoid lipids per chlorophyll and 40% less chlorophyll per carotenoid than Col-0 and Ler-0. There were no large differences in thylakoid stacking, photoprotection and relative levels of photosynthetic complexes among the three accessions. An increased efficiency of PSII closure was found in Ws-4 following illumination with saturation flashes or continuous light. Phosphorylation of the PSII D1/D2 proteins was reduced by 50% in Ws-4 as compared to Col-0 and Ler-0. An increase in abundance of the responsible STN8 kinase in response to HL treatment was found in all three accessions, but Ws-4 displayed 50% lower levels than Col-0 and Ler-0. Despite this, the HL treatment caused in Ws-4 the lagest extent of PSII inactivation, disassembly, D1 protein degradation, and the largest decrease in the size of stacked thylakoids. The dilution of chlorophyll-protein complexes with additional lipids and carotenoids in Ws-4 may represent a mechanism to facilitate lateral protein traffic in the membrane, thus compensating for the lack of a full complement of STN8 kinase. Nevertheless, additional PSII damage occurs in Ws-4, which exceeds the D1 protein synthesis capacity, thus leading to enhanced photoinhibition. Our findings are valuable for selection of appropriate background line for PSII characterization in Arabidopsis mutants, and also provide the first insights into natural variation of PSII protein phosphorylation.     

一种简便的适用于酵母双杂交系统的酵母质粒提取方法

目的:建立一种适用于酵母双杂交系统的简便快捷的酵母质粒提取方法。方法:以酿酒酵母为供试材料,用玻璃珠振荡法破除酵母细胞壁,提取酵母总DNA,最后通过电转化大肠杆菌DH10B获得目的质粒。结果:粗提得到的质粒可直接转化DH10B,作为模板用于PCR分析及酵母双杂交后续的序列分析等,大大降低了工作量。结论:该方法简便快捷,经济实用,降低了成本,提高了效率,可以作为一种实验室酵母质粒提取方法。     

A Study on Mutational Dynamics of Simple Sequence Repeats in Relation to Mismatch Repair System in Prokaryotic Genomes

Mutational bias toward expansion or contraction of simple sequence repeats (SSRs) is referred to as directionality of SSR evolution. In this communication, we report the mutational bias exhibited by mononucleotide SSRs occurring in the non-coding regions of several prokaryotic genomes. Our investigations revealed that the strains or species lacking mismatch repair (MMR) system generally show higher number of polymorphic SSRs than those species/strains having MMR system. An exception to this observation was seen in the mycobacterial genomes that are MMR deficient where only a few SSR tracts were seen with mutations. This low incidence of SSR mutations even in the MMR-deficient background could be attributed to the high fidelity of the DNA polymerases as a consequence of high generation time of the mycobacteria. MMR system-deficient species generally did not show any bias toward mononucleotide SSR expansions or contractions indicating a neutral evolution of SSRs in these species. The MMR-proficient species in which the observed mutations correspond to secondary mutations showed bias toward contraction of polymononucleotide tracts, perhaps, indicating low efficiency of MMR system to repair SSR-induced slippage errors on template strands. This bias toward deletion in the mononucleotide SSR tracts might be a probable reason behind scarcity for long poly A|T and G|C tracts in prokaryotic systems which are mostly MMR proficient. In conclusion, our study clearly demonstrates mutational dynamics of SSRs in relation to the presence/absence of MMR system in the prokaryotic system.     

Evaluating Outcomes Used in Cardiothoracic Surgery Interventional Research: A Systematic Review of Reviews to Develop a Core Outcome Set

Background

When planning clinical trials, it is a key element to choose appropriate outcomes that ensure the comparability of effects of interventions in ways that minimise bias. We hypothesise that outcome measures in cardiothoracic surgical trials are inconsistent and without standard. Therefore, comparing the relative effectiveness of interventions across studies is problematic. We surmise that cardiothoracic research has focused habitually on the identification of risk factors and on the reduction of adverse outcomes with less consideration of factors that contribute to well being and positive health outcomes (salutogenesis).

Methods and Findings

We conducted a systematic review of reviews to determine both the type and number of outcomes reported in current cardiothoracic surgery interventional research, in order to identify a list of potential outcomes for a minimum core outcome set (COS). Special focus was placed on outcomes that emphasise salutogenesis. We interpreted salutogenic outcomes as those relating to optimum and/or positive health and well being. We searched Issue 7 (July 2014) of the Cochrane Database of Systematic Reviews. Systematic reviews of randomised trials on non-minimal-invasive off- or on-pump cardiothoracic surgery (elective and emergency, excluding transplants) investigating pre-, intra- or postsurgical interventions related to the outcome of the procedure were eligible for inclusion. We excluded protocols and withdrawn systematic reviews. Two review authors extracted outcome data independently. Unique lists of salutogenically and non-salutogenically focused outcomes were established. 15 systematic reviews involving 371 randomized trials and 58,253 patients were included in this review. Applied definitions of single and composite endpoints varied significantly, and patient-centred, salutogenically focused outcomes were seldom reported. One third of included reviews did not assess patient-centred outcomes at all; all other reviews were unable to perform meta-analyses due to an absence of data or heterogeneity in outcome measures. This compares to 36 non-salutogenically focused outcome domains representing 121 individual non-salutogenically focused outcomes, whereof 50% were assessed only once. Measures of mortality, cerebrovascular complications and hospitalisation were reported most frequently. Two reviews chose a composite endpoint as primary outcome. Pooled analysis of composite endpoints was not possible, as the required data was not reported per patient in all components.

Conclusion

In cardiothoracic surgical trials, choice and definition of non-salutogenically focused single and composite outcomes are inconsistent. There is an absence of patient centred, salutogenically focused outcome parameters in cardiac trials. We recommend the development of a core outcome set of salutogenically focused and non-salutogenically focused outcomes for cardiothoracic surgical research.     

Can a Threshold Value Be Used to Classify Chondrichthyan Reproductive Modes: Systematic Review and Validation Using an Oviparous Species

The maternal-embryonic nutritional relationship in chondrichthyans has been poorly explored. Consequently, accurately discerning between their different reproductive modes is difficult; especially lecithotrophy and incipient histotrophy. This present study is the first to assess changes in mass throughout embryonic development of an oviparous chondrichthyan other than Scyliorhinus canicula. Heterodontus portusjacksoni egg cases were collected and used to quantify the gain or loss of wet mass, dry mass, water content, inorganic and organic matter from freshly deposited eggs (without macroscopically visible embryos) to near full-term embryos. A loss in organic mass of ∼40% found from this study is approximately double the values previously obtained for S. canicula. This raises concerns for the validity of the current threshold value used to discern between lecithotrophic and matrotrophic species. Accordingly, 26 studies published in the primary literature between 1932 and 2012 addressing the maternal-embryonic nutritional relationship in sharks were reviewed. Values for changes in mass reported for over 20 different shark species were synthesised and recalculated, revealing multiple typographical, transcribing, calculation and rounding errors across many papers. These results suggest that the current threshold value of −20% established by previous studies is invalid and should be avoided to ascertain the reproductive mode of aplacental viviparous species.