Stochastic models for the in silico simulation of synaptic processes

Background: Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual experiments to be performed in silico. Such experiments may result in easier, faster, and satisfying approximations of their in vitro/vivo counterparts. A promising approach is represented by the study of biological phenomena as a collection of interactive entities through process calculi equipped with stochastic semantics. These exploit formal grounds developed in the theory of concurrency in computer science, account for the not continuous, nor discrete, nature of many phenomena, enjoy nice compositional properties and allow for simulations that have been demonstrated to be coherent with data in literature. Results: Motivated by the need to address some aspects of the functioning of neural synapses, we have developed one such model for synaptic processes in the calyx of Held, which is a glutamatergic synapse in the auditory pathway of the mammalia. We have developed such a stochastic model starting from existing kinetic models based on ODEs of some sub-components of the synapse, integrating other data from literature and making some assumptions about non-fully understood processes. Experiments have confirmed the coherence of our model with known biological data, also validating the assumptions made. Our model overcomes some limitations of the kinetic ones and, to our knowledge, represents the first model of synaptic processes based on process calculi. The compositionality of the approach has permitted us to independently focus on tuning the models of the pre- and post- synaptic traits, and then to naturally connect them, by dealing with “interface” issues. Furthermore, we have improved the expressiveness of the model, e.g. by embedding easy control of element concentration time courses. Sensitivity analysis over several parameters of the model has provided results that may help clarify the dynamics of synaptic transmission, while experiments with the model of the complete synapse seem worth explaining short-term plasticity mechanisms. Conclusions: Specific presynaptic and postsynaptic mechanisms can be further analysed under various conditions, for instance by studying the presynaptic behaviour under repeated activations. The level of details of the description can be refined, for instance by further specifying the neurotransmitter generation and release steps. Taking advantage of the compositionality of the approach, an enhanced model could then be composed with other neural models, designed within the same framework, in order to obtain a more detailed and comprehensive model. In the long term, we are interested, in particular, in addressing models of synaptic plasticity, i.e. activity dependent mechanisms, which are the bases of memory and learning processes. More on the computer science side, we plan to follow some directions to improve the underlying computational model and the linguistic primitives it provides as suggested by the experiments carried out, e.g. by introducing a suitable notion of (spatial) locality

Elevated synaptic vesicle release probability in synaptophysin/gyrin family quadruple knockouts

Synaptophysins 1 and 2 and synaptogyrins 1 and 3 constitute a major family of synaptic vesicle membrane proteins. Unlike other widely expressed synaptic vesicle proteins such as vSNAREs and synaptotagmins, the primary function has not been resolved. Here, we report robust elevation in the probability of release of readily releasable vesicles with both high and low release probabilities at a variety of synapse types from knockout mice missing all four family members. Neither the number of readily releasable vesicles, nor the timing of recruitment to the readily releasable pool was affected. The results suggest that family members serve as negative regulators of neurotransmission, acting directly at the level of exocytosis to dampen connection strength selectively when presynaptic action potentials fire at low frequency. The widespread expression suggests that chemical synapses may play a frequency filtering role in biological computation that is more elemental than presently envisioned

Theoretical models of synaptic short term plasticity

Short term plasticity is a highly abundant form of rapid, activity-dependent modulation of synaptic efficacy. A shared set of mechanisms can cause both depression and enhancement of the postsynaptic response at different synapses, with important consequences for information processing. Mathematical models have been extensively used to study the mechanisms and roles of short term plasticity. This review provides an overview of existing models and their biological basis, and of their main properties. Special attention will be given to slow processes such as calcium channel inactivation and the effect of activation of presynaptic autoreceptors

Frequency-dependent mobilization of heterogeneous pools of synaptic vesicles shapes presynaptic plasticity

The segregation of the readily releasable pool of synaptic vesicles (RRP) in sub-pools that are differentially poised for exocytosis shapes short-term plasticity. However, the frequency-dependent mobilization of these sub-pools is poorly understood. Using slice recordings and modeling of synaptic activity at cerebellar granule cell to Purkinje cell synapses of mice, we describe two sub-pools in the RRP that can be differentially recruited upon ultrafast changes in the stimulation frequency. We show that at low frequency stimulations, a first sub-pool is gradually silenced, leading to full blockage of synaptic transmission. Conversely, a second pool of synaptic vesicles that cannot be released by a single stimulus is recruited within milliseconds by high-frequency stimulation and support an ultrafast recovery of neurotransmitter release after low-frequency depression. This frequency-dependent mobilization or silencing of sub-pools in the RRP in terminals of granule cells may play a role in the filtering of sensorimotor information in the cerebellum

Developmental Increase of Neocortical Presynaptic Efficacy via Maturation of Vesicle Replenishment

The efficacy of neocortical synapses to transmit during bursts of action potentials (APs) increases during development but the underlying mechanisms are largely unclear. We investigated synaptic efficacy at synapses between layer 5 pyramidal neurons (L5PNs) during development, using paired recordings, presynaptic two-photon Ca2+ imaging, and numerical simulations. Our data confirm a developmental increase in paired-pulse ratios (PPRs). Independent of age, Ca2+ imaging revealed no AP invasion failures and linear summation of presynaptic Ca2+ transients, making differences in Ca2+ signaling an unlikely reason for developmental changes in PPR. Cumulative excitatory postsynaptic current (EPSC) amplitudes indicate that neither the size of the readily-releasable pool (RRP) nor replenishment rates were different between age groups, while the time-courses of depression differed significantly. At young synapses, EPSCs depressed rapidly to near steady-state during the first four APs, and synaptic failures (Fsyn) increased from 0 to 30%. At mature synapses this drop was significantly slower and strongly biphasic, such that near steady-state depression was reached not before 18 APs with Fsyn remaining between 0 and 5%. While young synapses reliably transmitted during pairs of APs, albeit with strong depression, mature synapses maintained near 100% transfer efficacy with significantly less depression during high-frequency bursts of APs. Our analysis indicates that at mature synapses a replenishment pool (RepP) is responsible for their high efficacy during bursting activity, while this RepP is functionally immature at young synapses. Hence, our data provide evidence that the functional maturation of a RepP underlies increasing synaptic efficacy during the development of an excitatory cortical synapse

Sensory properties and consumer acceptance of novel hibiscus (hibiscus sabdariffa) beverages

As bebidas à base de extratos de hibisco são ricas em ácidos orgânicos, compostos fenólicos e polissacáridos, substâncias com potenciais benefícios para a saúde, sendo tradicionalmente consumidas na Africa Ocidental, na Ásia e na parte sul da América do Norte. A sua divulgação na Europa e dos Estados Unidos tem sido lenta e dirigida sobretudo a nichos de mercado, no entanto, o crescente interesse dos consumidores europeus e norte-americanos em bebidas com ingredientes únicos ou exóticos, com potenciais benefícios para a saúde, criaram recentemente novas oportunidades de mercado para bebidas de hibisco de alta qualidade. Entre 2010 e 2015, o projeto Europeu African Food Tradition rEvisited by Research (AFTER) investigou a produção, a comercialização e o consumo de bebidas de hibisco (Hibiscus sabdariffa var. sabdariffa ruber) no Senegal e na Europa, com o objetivo de otimizar a sua produção industrial, minimizando a degradação dos compostos fitoquímicos. Pouco se sabia sobre o perfil sensorial destes produtos, na sua forma tradicional ou melhorada e sobre como as mesmas eram avaliadas pelos consumidores, fatores essenciais para o sucesso destes produtos em particular fora dos seus mercados tradicionais. Esta dissertação teve como objetivo avaliar o impacto da otimização dos processos de produção industrial das bebidas de hibisco levadas a cabo pelo projeto AFTER (1) nas propriedades físico-químicas dos produtos resultantes com impacto na qualidade sensorial; (2) no seu perfil sensorial; (3) na perceção e aceitação por parte dos consumidores em mercados tradicionais (Senegal) e potenciais (França, Portugal e Reino Unido). O uso de cálices de hibisco secos à sombra e triturados das cultivares Vimto e Koor (50:50) e de condições moderadas de tempo e temperatura de extração e pasteurização, deu origem a novas bebidas com uma cor mais intensa e mais vermelha, maior concentração em antocianas monoméricas e polifenois e consequentemente maior capacidade antioxidante do que as bebidas convencionais, maior equilíbrio entre a concentração de açúcares e de ácidos e maior intensidade aromática. O estudo efetuado com consumidores no Senegal (N=150), mostrou que as novas bebidas foram positivamente avaliadas e melhor apreciadas que bebidas convencionais, sem que a perceção do caracter tradicional tenha sido alterada. Três segmentos de consumidores com distintos padrões de aceitação das bebidas foram identificados. A avaliação hedónica foi influenciada por preferências pessoais relativamente à cor, aroma e equilíbrio doçura-acidez, por características sociodemográficas e hábitos de consumo. Vinte e duas bebidas de hibisco foram avaliadas por painéis de provadores no Senegal e em Portugal. Léxicos em Português, Inglês e Francês contendo 21 descritores definidos, e referenciados foram desenvolvidos. As características distintivas das bebidas de hibisco eram a cor vermelha, o aroma floral (hibisco) e frutado (aronia/arando, ginja e framboesa) e o sabor predominantemente ácido (infusões de hibisco e bebidas preparadas a partir de concentrados) ou doce (bebidas preparadas a partir de xaropes). Eram ainda percetíveis aromas de chá preto, passa de uva, mel e feno, assim como sabor amargo e adstringência. O vocabulário usado por profissionais não-treinados (N=30) e por consumidores foi estudado usando entrevistas semiestruturadas (N=75) e questões Check-all-that-apply (N=490) no Senegal, em França, Portugal e Reino Unido. Léxicos gráficos contendo 27 atributos sensoriais e 15 termos gerais foram desenvolvidos. Diferenças com origem na cultura e familiaridade com o produto foram observadas. A comparação dos perfis sensoriais obtidos com provadores treinados e consumidores permitiu uma melhor compreensão da linguagem destes últimos. Estudos com consumidores em França, Portugal e Reino Unido (N=403) mostraram padrões similares de aceitação e perceção pelos consumidores. Diferenças importantes foram observadas relativamente ao Senegal. Na generalidade, os consumidores na Europa, gostaram menos das bebidas do que no Senegal, embora avaliações hedónicas médias positivas tenham sido observadas para todas as bebidas. No Senegal os consumidores avaliaram mais favoravelmente uma maior intensidade de cor e maior doçura e de forma mais depreciativa menor acidez. Na Europa e caracter floral e frutado das bebidas constituíram importantes fatores de aceitação das mesmas. Segmentos de consumidores foram identificados. A aceitação e perceção foram influenciadas pela familiaridade com o produto e com produtos com características de algum modo similares na Europa (caso dos sumos de frutos vermelhos); por características sociodemográficas; e por preferências individuais inatas ou culturalmente adquiridas. Foram observadas diferenças entre segmentos de consumidores na Europa relativamente ao perfil sensorial de uma bebida ideal, mas não no Senegal.Hibiscus beverages are rich in organic acids, phenolic compounds and polysaccharides, which have been demonstrated to be linked to important health benefits. They are traditionally consumed in West African countries, in Asia and in the Southern part of the North American continent. In Europe and United States of America, hibiscus beverages have slowly penetrated niche markets. Due to the rising number of health conscious consumers, along with the growing interest of North Americans and Europeans in beverages made from unique or exotic ingredients, new mainstream market opportunities for high quality hibiscus beverages have been recently created. Between 2010 and 2015, the African Food Tradition rEvisited by Research (AFTER) project, investigated the production, trading and consumption of hibiscus beverages made from dried hibiscus (Hibiscus sabdariffa var. sabdariffa ruber) calyx extracts in Senegal and Europe. Key improvements were proposed to increase production process efficiency and minimize degradation of phytochemical compounds. The aims of this thesis encompassed the evaluation of the impact of the reengineering processes held under AFTER project scope (1) in the main chemical-sensory properties of hibiscus beverages; (2) on their sensory profile; (3) on consumer acceptance in traditional markets (Senegal) and potential markets (France, Portugal and United Kingdom). The selection of a blend of shade dried ground hibiscus calyces (Vimto:Koor cultivars 50:50) and the use of mild water extraction and pasteurization conditions, led to the production of beverages with a more intense redder colour, higher monomeric anthocyanin, total phenolic content and higher antioxidant capacity than their conventional counterparts. Colour evaluation by trained panelists was mainly linked to colour density and to anthocyanin/polyphenol content, while flavour assessments were associated to titratable acidity and sugar-to-acid ratio. New beverages presented also a more intense aroma than conventional ones. Results of hedonic assessments held in Senegal (N=150), indicated that all improved beverages were liked by roughly three-quarters of consumers and were better accepted than a traditional one (baseline comparison). Three clusters of consumers with distinct overall liking patterns were identified. Acceptance was driven personal preferences regarding colour intensity, aromatic character, balance between sweetness and acidity but also by gender, age frequency of consumption and education level. Importantly, new beverages were still perceived by consumers as traditional products. Given the scarcity of information about hibiscus beverages sensory profile, sensory lexicons were developed in French, Portuguese and English. Twenty-two samples, including freshly prepared and ready-to-drink infusions, syrups, concentrates and an instant tea, were evaluated by trained panelists, resulting in 21 defined and referenced descriptors, subsequently assembled in a sensory wheel. A distinctive red colour, a floral (hibiscus) and fruity aroma (aronia/cranberry, sour cherry and raspberry) and a predominant acid (in case of infusions and beverages prepared from concentrates) or sweet taste (for beverages prepared from syrups) were the main sensory attributes. Also moderate or low intensities of black tea, honey, raisin and hay odours and of bitter taste and astringency were perceived in all products. The vocabulary used by untrained panelists was also investigated in Europe and Senegal through professional meetings (N=30), consumer focus groups (N=75) and check-all-that-apply questions (N=490), resulting in graphical lexicons with 27 sensory and 15 overall impression terms. Training, food culture and product familiarity influenced results. Trained panelists used precise terms to describe the aromatic profile of hibiscus beverages (e.g., reminiscent of dried hibiscus flowers, with berry, raisin, hay and sweet notes), whereas untrained ones were more prolific in general expressions (e.g., strong in hibiscus in Senegal; floral and fruity in Europe). Consumer studies in France, Portugal, United Kingdom (N=403), showed similar patterns of acceptance and perception for hibiscus beverages in European countries. Positive mean overall liking ratings were observed for all beverages. Major differences were observed relatively to Senegal where consumers favored higher intensities of red colour and sweetness. In Europe fruity and floral character constituted important drivers of liking. Consumer segments were identified. Perception and acceptance was influenced by consumers’ sociodemographic characteristics and by innate and culturally acquired preferences. Besides exposure to product category, also exposure and liking of familiar products, with somewhat similar characteristics to hibiscus beverages (like red fruit beverages), was shown to influence liking in Europe. Differences across consumer segments in the profile of an ideal beverage were observed in Europe but not in Senegal

Reliability of Synaptic Transmission at the Synapses of Held In Vivo under Acoustic Stimulation

BACKGROUND:The giant synapses of Held play an important role in high-fidelity auditory processing and provide a model system for synaptic transmission at central synapses. Whether transmission of action potentials can fail at these synapses has been investigated in recent studies. At the endbulbs of Held in the anteroventral cochlear nucleus (AVCN) a consistent picture emerged, whereas at the calyx of Held in the medial nucleus of the trapezoid body (MNTB) results on the reliability of transmission remain inconsistent. In vivo this discrepancy could be due to the difficulty in identifying failures of transmission. METHODS/FINDINGS:We introduce a novel method for detecting unreliable transmission in vivo. Based on the temporal relationship between a cells' waveform and other potentials in the recordings, a statistical test is developed that provides a balanced decision between the presence and the absence of failures. Its performance is quantified using simulated voltage recordings and found to exhibit a high level of accuracy. The method was applied to extracellular recordings from the synapses of Held in vivo. At the calyces of Held failures of transmission were found only rarely. By contrast, at the endbulbs of Held in the AVCN failures were found under spontaneous, excited, and suppressed conditions. In accordance with previous studies, failures occurred most abundantly in the suppressed condition, suggesting a role for inhibition. CONCLUSIONS/SIGNIFICANCE:Under the investigated activity conditions/anesthesia, transmission seems to remain largely unimpeded in the MNTB, whereas in the AVCN the occurrence of failures is related to inhibition and could be the basis/result of computational mechanisms for temporal processing. More generally, our approach provides a formal tool for studying the reliability of transmission with high statistical accuracy under typical in vivo recording conditions

Retention and growth of urinary stones: insights from imaging

Recent work in nephrolithiasis has benefited from 2 special kinds of imaging: endoscopic study of patient kidneys with high-quality instruments, and examination of stones with microscopic computed tomography (micro CT). The combination of these has provided new evidence that there is more than 1 mechanism by which stones are retained in the kidney until they achieve sizes to be clinically relevant. This review describes what is known about the formation of stones on Randall's plaque, the formation of stones on ductal plugs and the ways in which stones may grow in free solution within the calyceal or pelvic spaces. Studies of urolithiasis need to recognize that any group of "stone formers" likely includes patients who differ fundamentally regarding which mechanism of stone formation is the primary route for their stones. Separation of patients on the basis of which mechanism (or combination of mechanisms) underlies their disease will be important for advancing research in the area of urolithiasis

Systematic studies in Neotropical Myrtaceae with an emphasis on <i>Myrcia s.l.</i>: The evolution and biogeography of a large South American clade

Low morphological variation at all taxonomic levels give Neotropical Myrtaceae a reputation as a 'difficult' family to identify even to genus, resulting in a lack of taxonomic data on every front. The subtribal classification of the predominantly Neotropical and exclusively fleshy-fruited tribe Myrteae (49 genera and c. 2500 species) is unstable, as are generic boundaries within it. Neotropical Myrtaceae are particularly species rich in some of South America's most threatened habitats. The second largest Neotropical genus, Myrcia s.l., comprises >700 taxonomically 'difficult' species with species diversity reaching its peak in the Brazilian Atlantic rainforest and cerrado, habitats in urgent need of inventories of their plant species before conservation initiatives can be undertaken. Phylogenetic hypotheses are provided for evolutionary relationships within Myrteae and Myrcia s.l. based on nuclear ITS and ETS ribosomal DNA and plastid psbA-trnH and matK DNA sequences, using parsimony and Bayesian inference. Four morphological characters of Myrteae are optimized on the resulting trees and nineteen are used in a cladistic analysis of Myrcia s.l. Myrteae appear monophyletic, comprising seven clades plus two isolated taxa. Of the four previously accepted genera of subtribe Myrciinae sensu DC., two are polyphyletic and all emerge in a single clade treated here as Myrcia s.l. Morphological characters exhibit homoplasy at both ranks, although in combination are useful for clade diagnosis. Biogeographical analysis is inconclusive regarding tribal ancestral areas, but South American colonization before northern radiation via the Andes appears likely. The largest genera, Eugenia and Myrcia s.l., have western and southeastern South American origins, respectively. Nonmetric multidimensional scaling and ordination techniques are employed to divide the distribution of Myrcia s.l. into discrete areas of endemism and historical biogeographical scenarios are discussed. Finally, modern, natural, subtribal and infrageneric classifications are proposed and concluding inferences are drawn regarding drivers of large genera using Myrtaceae and Myrcia s.l. as case studies