A multifarious exploration of synaptic tagging and capture hypothesis in synaptic plasticity: Development of an integrated mathematical model and computational experiments

The synaptic tagging and capture (STC) hypothesis not only explain the integration and association of synaptic activities, but also the formation of learning and memory. The synaptic pathways involved in the synaptic tagging and capture phenomenon are called STC pathways. The STC hypothesis provides a potential explanation of the neuronal and synaptic processes underlying the synaptic consolidation of memories. Several mechanisms and molecules have been proposed to explain the process of memory allocation and synaptic tags, respectively. However, a clear link between the STC hypothesis and memory allocation is still missing because the encoding of memories in neural circuits is mainly associated with strongly recurrently connected groups of neurons. To explore the mechanisms of potential synaptic tagging candidates and their involvement in the process of memory allocation, we develop a mathematical model for a single dendritic spine based on five essential criteria of a synaptic tag. By developing a mathematical model, we attempt to understand the roles of the potentially critical molecular networks underlying the STC and the essential attributes of a synaptic tag. We include essential memory molecules in the STC model that have been identified in earlier studies as crucial for STC pathways. CaMKII activation is critical for the setting of the initial tag; however, coordinated activities with other kinases and the biochemical pathways are necessary for the tag to be stable. PKA modulates NMDAR-mediated Ca²⁺ signalling. Similarly, PKA and ERK crosstalk is essential for Ca²⁺ - mediated protein synthesis during l-LTP. Our theoretical model explains the quantitative contribution of Tags and protein synthesis during l-LTP in synaptic strength.

A system of recurrent neural networks for modularising, parameterising and dynamic analysis of cell signalling networks

In this paper, we show how to extend our previously proposed novel continuous time Recurrent Neural Networks (RNN) approach that retains the advantage of continuous dynamics offered by Ordinary Differential Equations (ODE) while enabling parameter estimation through adaptation, to larger signalling networks using a modular approach. Specifically, the signalling network is decomposed into several sub-models based on important temporal events in the network. Each sub-model is represented by the proposed RNN and trained using data generated from the corresponding ODE model. Trained sub-models are assembled into a whole system RNN which is then subjected to systems dynamics and sensitivity analyses. The concept is illustrated by application to G1/S transition in cell cycle using Iwamoto et al. (2008) ODE model. We decomposed the G1/S network into 3 sub-models: (i) E2F transcription factor release; (ii) E2F and CycE positive feedback loop for elevating cyclin levels; and (iii) E2F and CycA negative feedback to degrade E2F. The trained sub-models accurately represented system dynamics and parameters were in good agreement with the ODE model. The whole system RNN however revealed couple of parameters contributing to compounding errors due to feedback and required refinement to sub-model 2. These related to the reversible reaction between CycE/CDK2 and p27, its inhibitor. The revised whole system RNN model very accurately matched dynamics of the ODE system. Local sensitivity analysis of the whole system model further revealed the most dominant influence of the above two parameters in perturbing G1/S transition, giving support to a recent hypothesis that the release of inhibitor p27 from Cyc/CDK complex triggers cell cycle stage transition. To make the model useful in a practical setting, we modified each RNN sub-model with a time relay switch to facilitate larger interval input data (≈20min) (original model used data for 30s or less) and retrained them that produced parameters and protein concentrations similar to the original RNN system. Results thus demonstrated the reliability of the proposed RNN method for modelling relatively large networks by modularisation for practical settings. Advantages of the method are its ability to represent accurate continuous system dynamics and ease of: parameter estimation through training with data from a practical setting, model analysis (40% faster than ODE), fine tuning parameters when more data are available, sub-model extension when new elements and/or interactions come to light and model expansion with addition of sub-models.

Modelling the dynamics of CaMKII-NMDAR complex related to memory formation in synapses: the possible roles of threonine 286 autophosphorylation of CaMKII in long term potentiation

A synaptic protein, Ca(2+)/Calmodulin dependent protein kinase II (CaMKII), has complex state transitions and facilitates the emergence of long term potentiation (LTP), which is highly correlated to memory formation. Two of the state transitions are critical for LTP: (1) threonine 286 autophosphorylation of CaMKII; and (2) binding to N-methyl-d-aspartate receptor (NMDAR) in the postsynaptic density (PSD) to form CaMKII-NMDAR complex. Both of these state transitions retain the activity of CaMKII when the induction signal disappears which is very important for the long-lasting characteristics of LTP. However, the possible relationships between the state transitions in the emergence of LTP are not well understood. We develop a mathematical model of the formation of CaMKII-NMDAR complex with the full state transitions of CaMKII, including the autophosphorylation, based on ordinary differential equations. In addition, we formulate a probabilistic framework for the binding between CaMKII and NMDAR. The model gives accurate predictions of the behaviours of CaMKII in comparisons to the experimental observations. Using the model, we show that: (1) the formation of CaMKII-NMDAR complex is dependent not only on the binding affinity between CaMKII and NMDAR, but also on the translocation of CaMKII into PSD; and (2) the autophosphorylation is not a requirement for the formation of CaMKII-NMDAR complex, but is important for the rapid formation of CaMKII-NMDAR complex during LTP.

The meiotic-mitotic initiation switch in budding yeast maintains its function robustly against sensitive parameter perturbations

Experiments show that the meiotic-mitotic initiation switch in budding yeast functions robustly during the early hours of meiosis initiation. In this study, we explain these experimental observations first by understanding how this switching occurs during the early hours of meiosis by studying the temporal variation of this switch at the gene expression level. Then, we investigate the effects on this meiotic-mitotic switching from the perturbations of the most sensitive parameters in budding yeast meiosis initiation network. We use a mathematical model of meiosis initiation in budding yeast for this task and find the most sensitive group of parameters that influence the expressions of meiosis and mitosis initiators at all stages of the meiotic-mitotic switch. The results indicate that the transition region of the switch, where a double negative feedback loop between meiosis (Ime2) and mitosis (Cdk1/Cln3) initiators plays a major role, shows lower robustness. Feedback loops are frequently observed serving as a major robust adaption mechanism in many biological networks. Consequences of this less robust region appear in the transition region of the resulting switches. Most importantly, despite the differences observed in the transition region, we find that the meiotic-mitotic switch robustly maintains its main function of transition from meiosis to mitosis when the nutrients are re-supplied, against the perturbations in the sensitive parameters.

Systems biology of synaptic plasticity: a review on N-methyl-D-aspartate receptor mediated biochemical pathways and related mathematical models

Synaptic plasticity, an emergent property of synaptic networks, has shown strong correlation to one of the essential functions of the brain, memory formation. Through understanding synaptic plasticity, we hope to discover the modulators and mechanisms that trigger memory formation. In this paper, we first review the well understood modulators and mechanisms underlying N-methyl-D-aspartate receptor dependent synaptic plasticity, a major form of synaptic plasticity in hippocampus, and then comment on the key mathematical modelling approaches available in the literature to understand synaptic plasticity as the integration of the established functionalities of synaptic components.

Remote and rapid pathological diagnosis in a resource challenged unit

Malawi is one of the world's poorest countries, but despite this, has a dedicated paediatric oncology service. The service has been hampered by the inability to make a timely cytological diagnosis in the majority of patients. A telemedicine programme was commenced to help overcome this problem, and the results for the first 197 consecutive patients are described. The results are compared with the local reports where available. Most samples were fine needle aspirates (104/197-53%), but others included bone marrow aspirates, peripheral blood films and other fluid collections. A diagnosis was arrived at in 52% of the samples; there were 46 discordant results, 38 were when one or other of the local or distant teams were unable to make a diagnosis, and only 8 where the diagnoses of the 2 teams differed. Diagnoses were made and reports were compiled by the 'distant' team within 24 h and sent to the centre in Malawi. This simple telepathology initiative has had a positive impact on clinical management, and could be used in other less resourced centres twinned with better resourced ones.

A nutrient dependant switch explains mutually exclusive existence of meiosis and mitosis initiation in budding yeast

Nutrients from living environment are vital for the survival and growth of any organism. Budding yeast diploid cells decide to grow by mitosis type cell division or decide to create unique, stress resistant spores by meiosis type cell division depending on the available nutrient conditions. To gain a molecular systems level understanding of the nutrient dependant switching between meiosis and mitosis initiation in diploid cells of budding yeast, we develop a theoretical model based on ordinary differential equations (ODEs) including the mitosis initiator and its relations to budding yeast meiosis initiation network. Our model accurately and qualitatively predicts the experimentally revealed temporal variations of related proteins under different nutrient conditions as well as the diverse mutant studies related to meiosis and mitosis initiation. Using this model, we show how the meiosis and mitosis initiators form an all-or-none type bistable switch in response to available nutrient level (mainly nitrogen). The transitions to and from meiosis or mitosis initiation states occur via saddle node bifurcation. This bidirectional switch helps the optimal usage of available nutrients and explains the mutually exclusive existence of meiosis and mitosis pathways.

Retrospective study of alemtuzumab vs ATG-based conditioning without irradiation for unrelated and matched sibling donor transplants in acquired severe aplastic anemia: a study from the British Society for Blood and Marrow Transplantation

This retrospective national study compared the use of alemtuzumab-based conditioning regimens for hematopoietic SCT (HSCT) in acquired severe aplastic anemia with antithymocyte globulin (ATG)-based regimens. One hundred patients received alemtuzumab and 55 ATG-based regimens. A matched sibling donor (MSD) was used in 87 (56%), matched unrelated donor (MUD) in 60 (39%) and other related or mismatched unrelated donor (UD) in 8 (5%) patients. Engraftment failure occurred in 9% of the alemtuzumab group and 11% of the ATG group. Five-year OS was 90% for the alemtuzumab and 79% for the ATG groups, P=0.11. For UD HSCT, OS of patients was better when using alemtuzumab (88%) compared with ATG (57%), P=0.026, although smaller numbers of patients received ATG. Similar outcomes for MSD HSCT using alemtuzumab or ATG were seen (91% vs 85%, respectively, P=0.562). A lower risk of chronic GVHD (cGVHD) was observed in the alemtuzumab group (11% vs 26%, P=0.031). On multivariate analysis, use of BM as stem cell source was associated with better OS and EFS, and less acute and cGVHD; young age was associated with better EFS and lower risk of graft failure. This large study confirms successful avoidance of irradiation in the conditioning regimens for MUD HSCT patients.

Robustness of circadian rhythms in the presence of molecular fluctuations: an investigation based on a mechanistic, statistical theory and a simulation algorithm

After a very brief introduction to a mechanistic and statistical theory of molecular fluctuations in chemical reactions developed by Joel Keizer, we explore the robustness of a circadian rhythm model by using the theory and the exact stochastic simulation (ESS). The comparative study shows that the theory reflects the effects of the dynamics of the model on the robustness more than ESS does. Even though the theory is a macroscopic one, the robustness of the model compares well with that computed from the ESS when the system size is larger than 50. The robustness increases nonlinearly with the system size and it reaches an asymptotic value at higher system sizes. As we can expect from the dynamics of the system, the robustness is minimum near the bifurcation point and as the most sensitive parameter increases away from the bifurcation point the robustness according to the theory as well as the ESS increases and then reaches to a steady value.

Increasing the nonlinear character of microbubble oscillations at low acoustic pressures

The nonlinear response of gas bubbles to acoustic excitation is an important phenomenon in both the biomedical and engineering sciences. In medical ultrasound imaging, for example, microbubbles are used as contrast agents on account of their ability to scatter ultrasound nonlinearly. Increasing the degree of nonlinearity, however, normally requires an increase in the amplitude of excitation, which may also result in violent behaviour such as inertial cavitation and bubble fragmentation. These effects may be highly undesirable, particularly in biomedical applications, and the aim of this work was to investigate alternative means of enhancing nonlinear behaviour. In this preliminary report, it is shown through theoretical simulation and experimental verification that depositing nanoparticles on the surface of a bubble increases the nonlinear character of its response significantly at low excitation amplitudes. This is due to the fact that close packing of the nanoparticles restricts bubble compression.

Health status of primary schoolchildren in Sri Lanka

OBJECTIVE

To assess health status of 9-10-year old school children in Sri Lanka.

DESIGN

A cross-sectional, descriptive study. Schools were selected to obtain a sample representative at national and provincial levels and 20 children were randomly selected from Grade 5 classes in each school.

MEASUREMENTS

Children were examined for Bitot's spots and goitre. Height, weight, and visual acuity were measured according to standard procedures. Haemoglobin level was measured using finger-prick blood and a HemoCue meter. Geohelminth infections were quantified by faecal examination using the modified Kato-Katz technique. Height for age Z-scores (HAZ) and body mass index (BMI) were calculated as indicators of nutritional status.

RESULTS

Two thousand five hundred and twenty eight children (1351 boys) from 144 schools (140 state schools and four private schools) were examined. Nationally, 15.5% of children were stunted (HAZ lower than -2.0 SD); 52.6% were thin (BMI < 5th centile of age- and sex-matched reference population); 3.1% were overweight (BMI > 85th centile); 12.1% were anaemic; 0.3% had Bitot's spots; 3% had a visible or palpable goitre; 4.6% were shortsighted; and 6.9% had one or more soil-transmitted nematode infection. Among children on whom anthropometry, haemoglobin and faecal examinations were all done, 64.6% (1332/2063) were thin, stunted, anaemic or infected with worms. A much higher proportion of children in the Northern and Eastern provinces had health problems when compared to the other provinces.

CONCLUSIONS

The majority of older primary schoolchildren in Sri Lanka are undernourished. Anaemia, vitamin A deficiency, iodine deficiency and soil-transmitted nematode infections affect a much smaller proportion of them.

Improved outcome for children with disseminated adenoviral infection following allogeneic stem cell transplantation

Adenovirus (AdV) infections are a frequent cause of morbidity and mortality following allogeneic stem cell transplantation (SCT), and disseminated infection is associated with high mortality, particularly in paediatric SCT. Here, we describe an approach to reduce mortality from adenoviraemia by combining prospective monitoring for the occurrence of adenoviraemia using a sensitive polymerase chain reaction method, early antiviral therapy and prompt withdrawal of immunosuppression. A total of 155 consecutive paediatric SCT procedures were prospectively monitored, of which 113 (73%) transplants involved donors other than matched siblings and 126 (83%) employed T-cell depletion. Adenoviraemia was detected in 26/155 (17%) transplants and developed exclusively in patients who had received T-cell-depleted grafts. Withdrawal of immunosuppression coupled with early antiviral therapy led to resolution of adenoviraemia in 19/26 (81%) patients with only five patients succumbing to disseminate AdV infection. Survival from adenoviraemia was associated with lymphocyte recovery to above 0.3x10(9)/l. Mortality was closely linked with the absence of lymphocyte recovery because of profound T-cell depletion of the graft with CD34+ magnetic-activated cell sorting. Mortality from disseminated AdV infection was 5/26 (19%) in this study, which is significantly lower than previously reported.

Improving prediction of aphid flights by temporal analysis of input data for an artificial neural network

Weather data in its raw form frequently contains irrelevant and noisy information Often the hardest task in model development regardless of the technique used is translating independent variables from their raw form into data relevant to a particular model A sequential or cascading temporal correlation analysis was used to identify weather sequences that were strongly correlated with aphid trap catches recorded at Lincoln Canterbury New Zealand over 19822000 Trap catches in the previous year and 13 weather sequences associated with eight climate variables were identified as significant predictors of aphid trap catch during the autumn flight period The variables were used to train artificial neural network (ANN) models to predict the size of autumn aphid migrations into cereal crops in Canterbury Such models would assist cereal growers to make better informed and more timely pest management decisions ANN predictive performance was compared with multiple regression predictions using jackknifed data The ANN gave superior prediction compared with multiple regression over 13 jackknifed years

Analysis of AMPA receptor subunit mRNA expression in control and ALS spinal cord

The distribution of glutamate receptor subunits in human spinal cord has yet to be fully elucidated. The aim of this study was to examine the distribution of mRNAs for the subunits of the AMPA type of glutamate receptor (GluR A, B, C and D) in control human spinal cord using in situ hybridization and to examine in parallel the expression of these mRNAs in patients with sporadic amyotrophic lateral sclerosis (ALS). We also quantitated mRNA levels for these subunits in spinal cord homogenates. The relative abundances of the receptor subunits were as follows: GluR A > GluR B > GluR D > GluR C with A, B and D expressed in foci corresponding to the medial, lateral and ventral clusters of motor neurones. Quantitation of homogenates revealed a significant decrease (38%) in GluR A mRNA in ALS spinal cord compared with controls, and a 67% decrease of GluR B mRNA compared with controls. Levels of GluR C and D were too low to analyse densitometrically.

Distribution of the N-methyl-D-aspartate glutamate receptor subunit NR2A in control and amyotrophic lateral sclerosis spinal cord

The distribution of the different glutamate receptor subunits in human spinal cord has yet to be fully elucidated. The aim of this study was to examine the distribution of the N-methyl-D-aspartate (NMDA) glutamate receptor modulatory subunit NR2A, in control human spinal cord and to examine in parallel the expression of the mRNA in amyotrophic lateral sclerosis (ALS). The aetiology of ALS is poorly understood, although abnormalities in glutamate and glycine transport have been reported as well as alterations in NMDA receptors including the NR1 subunit; suggesting a role for glutamate in the disease process. We have used the technique of in situ hybridisation to localise this receptor subunit to the laminae of human spinal cord and have found that it shows a widespread distribution similar to that previously reported for the universal NMDA receptor subunit NR1. Quantitation of mRNA expression in control and ALS cases showed a significant widespread loss of NR2A from both dorsal and ventral horns with losses of 55% and 78%, respectively, in ALS as compared to control. These results were substantiated by analysis of spinal cord homogenates, which showed a significant total decrease of 50% in ALS spinal cord as compared to control.

Pressure effects on dipalmitoylphosphatidylcholine bilayers measured by 2H nuclear magnetic resonance

The effects of pressure, up to 5 kbar, on multilamellar vesicles of 1,2-dipalmitoyl-sn-phosphatidylcholine perdeuterated in the acyl chains (DPPC-d62) were examined by using high-pressure NMR techniques. A deuterium probe was built, and the quadrupole splitting was measured against pressure at various temperatures. The experiments were performed on pure lipid bilayers in the liquid-crystalline state and on bilayers in the liquid-crystalline state containing the local anesthetic tetracaine. The results show that the order parameter of all segments of the acyl chains increases with pressure in the liquid-crystalline state. The more highly ordered regions of the chains are affected slightly more than the regions near the methyl ends. The addition of tetracaine increases the disorder of the chains, and pressure reverses the effect of anesthetic on the lipid as seen by the reversal of the changes in line shape and the measured order parameter.

Loa loa in a Sri Lankan expatriate from Nigeria

A worm was extracted from the subconjunctival space of the left eye in a 14-year old Sri Lankan girl, who returned to Sri Lanka in 1983 after spending six years in Nigeria. It was identified as a male Loa loa. A history of evanescent (Calabar) swellings was obtained. She also had significant eosinophilia. Microfilariae were not detected in the blood. This is the first case of Loa loa infection reported from Sri Lanka.