A Minimal Stochastic Model of Transcriptional and Splicing Regulation.

In the past decades an extensive mathematical literature was developed to model and analyze gene networks under both deterministic and stochastic formalisms. However, such literature is predominantly focused to deal with the modeling of transcriptional and translational regulation, but results related to post-transcriptional regulation and its connection with transcriptional regulation are poorly investigated. However, it is becoming of paramount importance the need for modeling post-transcriptional regulation via splicing especially for minor organisms or viruses.The aim of this study is to propose a first general basic modeling scheme for modeling gene expression via alternative splicing and investigating the basic deterministic and stochastic features of the pre-mRNA, mRNAs and proteins under different biological conditions.This first study showed the dynamical properties of alternative splicing, the faster kinetics of the pre-mRNA compared to the mRNA and the importance to stochastically model gene networks when considering the post-transcriptional regulation.

A Human Papillomavirus Early Promoter Minimal Model: Viral Population and Stochasticity.

HPV infection starts with the activation of the early promoter (EP) regulatory core and the replication of the viral particles to around 10-100 per cell at the beginning of the infection. For this reason, understanding the deterministic and stochastic role of the population number of viruses inside the cell is of pivotal importance to understand the regulation of the EP and the viral latency.The aim of this study is to extend a recently published minimal model of the EP transcriptional regulation in order to consider the effect of the viral population on gene regulation, to perform the bifurcation analysis and to understand the role of the stochasticity at the beginning of the infection.The bifurcation analysis showed how modeling the viral population number is pivotal to exhibit a bistable behavior, potentially linked to the viral latency. Moreover, the viral population number was identified as an important source of stochasticity, which is of paramount importance to drive the bistable switching mechanism in the first stages of infection.

Sensitivity Analysis of a Model of Human Papillomavirus Late Promoter Regulation.

A mathematical model of Human Papillomavirus late promoter regulation was recently developed, able to predict the main features of HPV gene expression during cellular differentiation under productive infection. A sensitivity analysis is performed to characterize the influence of transcriptional, post-transcriptional and translational regulations on the viral species related to E1, E2, E4 and Li genes. Sensitivity analysis indicates strong influence of parameters related to transcriptional and translational regulation. It also shows a strong influence on the parameters related to post-transcriptional regulation, showing the importance of modeling splicing regulation to well describe the biology of the late promoter.

Human Papillomavirus Early Promoter Regulatory Core as a Bistable Switch.

High risk human papillomavirus (HPV) can induce cervical and oropharyngeal cancerous lesions. Different HPV strains, as well as still unknown mechanisms can be associated to a range of biochemical parameters that can importantly affect the HPV gene expression dynamics. For this reason, it is of pivotal importance to investigate how parameters variation can induce interesting behaviors such as viral latency in place of the normal gene replication activity. The aim of this study is to perform bifurcation analysis on a minimal model of the early promoter regulatory core controlled by E2 transcriptional regulation. The bifurcation analysis showed how E2 regulation can induce a bistability on the early promoter gene expression that could explain the interplay between viral latency and gene replication regimen.

Stochastic Modeling of the Co-Regulation between Early and E8 Promoters in Human Papillomavirus.

High risk HPV can induce cervical and oropharyngeal cancerous Iesions. The initial phase of the infection is characterized by a fine regulation of the viral DNA replication, in order to maintain 10-100 DNA copies per cell. Such regulation is primarily controlled by El and E2 proteins produced by the early promoter. The recently discovered E8 promoter is capable to co-regulate the early one in order to maintain a low and constant viral DNA copy number.The aim of this study is to develop a novel stochastic mathematical model of the co-regulation between the E8 and the early promoter, with the main purpose to rigorously show the E8 promoter capability to finely regulate the HPV transcripts which control the DNA replication in the first stages of the infection.The model, condensing the biological knowledge present in literature, describes the interaction between the two promoters and shows how the E8 co-regulation is capable to reject the stochastic noise of E2 gene expression to a higher extent than the early promoter negative auto-feedback. This proves the capability of the E8 promoter to finely control the HPV genomes copy number.

Modeling HPV Late Promoter Regulation.

High risk HPV can induce cervical and oropharyngeal Iesions. HPV productive infection is strictly linked by differentiation-dependent control of the late promoter. This latter produces HPV transcripts at different epithelial layers through a complex post-transcriptional control. The aim of this study is to develop a novel mathematical model of the late promoter condensing the biological knowledge present in literature. The model describes the interaction among primary transcript, spliced transcripts and their proteins and includes the major splicing mechanisms. When used as an in silico tool it shows the crucial role of splicing regulation to explain the HPV gene expression. Novel testing hypothesis are then formulated to uncover this still elusive but pivotal promoter.

In Silico Modeling of the Antiplatelet Pharmacodynamics of Low-dose Aspirin in Health and Disease.

The influence of platelet turnover on cyclooxygenase (COX-1) inhibition by low-dose aspirin remains largely uncharacterized due to limited feasibility of studying aspirin pharmacodynamics in bone marrow precursors. We developed an in silico compartmental model describing the aspirin effects on COX-1 activity in a population of megakaryocytes (MK) and in peripheral platelets. Model parameters were inferred from the literature and calibrated using measurements of serum thromboxane B2 (sTXB2 ), as proxy of COX-1 activity in peripheral platelets, in 17 healthy subjects and 24 patients with essential thrombocythemia (ET). The model reproduced well the average time-course of sTXB2 inhibition in healthy (accuracy = 10.4%), the reduced inhibition of sTXB2 observed in ET, and the effect of different dosing regimens. In conclusion, the in silico model accurately describes COX-1 inactivation by low-dose aspirin in MK and platelets in different clinical settings, and might help personalize aspirin regimens in conditions of altered megakaryopoiesis.

Effects of redox conditions on the control of arsenic mobility in shallow alluvial aquifers on the Venetian Plain (Italy).

The Venetian Plain is known for the occurrence of areas with high concentrations of arsenic in groundwater (greater than 400 µg/L). The study area represents the typical residential, industrial and agricultural features of most Western countries and is devoid of hydrothermal, volcanic or anthropogenic sources of arsenic. The aim of the study is to model the arsenic mobilization and the water-rock interaction by a complete hydrogeochemical investigation (analyses of filtered and unfiltered groundwater sediment mineralogy and geochemistry). The groundwater arsenic contamination and redox conditions are highly variable. Groundwaters with oxidizing and strongly reducing potentials have much lower arsenic concentrations than do mildly reducing waters. The grain size of the aquifer sediments includes gravels, sands and silty-clays. A continuous range of organic material concentrations is observed (from zero to 40%). The amount of sedimentary organic matter is highly correlated with the arsenic content of the sediments (up to 300 mg/kg), whereas no relationships are detectable between arsenic and other chemical parameters. The occurrence of arsenic minerals was observed as a peculiar feature under the scanning electron microscope. Arsenic and sulfur are the sole constituents of small tufts or thin crystals concentrated in small masses. These arsenic minerals were clearly observed in the peat sediments, in agreement with the geochemical modeling that requires very reducing conditions for their precipitation from the groundwater. The modeling suggests that, under oxidizing conditions, arsenic is adsorbed; moreover, a continuous decrease in the redox potential causes increasing desorption of arsenic. If the reducing conditions become more intense, the formation of As-S minerals would explain the lower concentration of arsenic measured in the strongly reducing groundwater. Even if As-sulfides are rare under low-temperature conditions, the anomalous abundance of reductants (organic matter) can locally stabilize As-S minerals, which can scavenge large quantities of groundwater arsenic.

Modeling HPV early promoter regulation.

In high risk forms, human papillomaviruses (HPV) can either induce or promote cancerous lesions, especially cervical cancer which is considered the second most common cancer in the women worldwide. HPV life cycle is tightly linked to the infected cell differentiation program and its evolution is strictly joined to the switch between the early and the late viral polycistronic promoters.The aim of this study is to develop a novel mathematical model which collects and structures the available biologic knowledge on the early promoter regulation for HPV in episomal form. The model includes the main regulation by E2 viral protein as well as a novel discovered co-regulation function mediated by the viral E1 protein. Only by including both E2 and E1 regulatory effect the model is able to correctly predict the temporal behaviour of the early promoter switching off. A possible use of the model as in silico tool to evaluate new antiviral therapies is discussed.

Solid state and solution fine tuning of the linear and nonlinear optical properties of (2-pyrene-1-yl-vinyl)pyridine by protonation-deprotonation reactions.

The unexpected and acido-triggered reversible luminescence and nonlinear optical properties of (2-pyrene-1-yl-vinyl)pyridine, a simple and highly transparent chromophore, are studied both in solution and in the solid state. Remarkably, for the first time the acidomodulation of the NLO response of a poled thin film is reported.

The nested assembly of individual-resource networks.

1. Much of the current understanding of ecological systems is based on theory that does not explicitly take into account individual variation within natural populations. However, individuals may show substantial variation in resource use. This variation in turn may be translated into topological properties of networks that depict interactions among individuals and the food resources they consume (individual-resource networks). 2. Different models derived from optimal diet theory (ODT) predict highly distinct patterns of trophic interactions at the individual level that should translate into distinct network topologies. As a consequence, individual-resource networks can be useful tools in revealing the incidence of different patterns of resource use by individuals and suggesting their mechanistic basis. 3. In the present study, using data from several dietary studies, we assembled individual-resource networks of 10 vertebrate species, previously reported to show interindividual diet variation, and used a network-based approach to investigate their structure. 4. We found significant nestedness, but no modularity, in all empirical networks, indicating that (i) these populations are composed of both opportunistic and selective individuals and (ii) the diets of the latter are ordered as predictable subsets of the diets of the more opportunistic individuals. 5. Nested patterns are a common feature of species networks, and our results extend its generality to trophic interactions at the individual level. This pattern is consistent with a recently proposed ODT model, in which individuals show similar rank preferences but differ in their acceptance rate for alternative resources. Our findings therefore suggest a common mechanism underlying interindividual variation in resource use in disparate taxa.

Individual-level diet variation in four species of Brazilian frogs.

1. Many natural populations exploiting a wide range of resources are actually composed of relatively specialized individuals. 2. This interindividual variation is thought to be a consequence of the invasion of 'empty' niches in depauperate communities, generally in temperate regions. If individual niches are constrained by functional trade-offs, the expansion of the population niche is only achieved by an increase in interindividual variation, consistent with the 'niche variation hypothesis'. 3. According to this hypothesis, we should not expect interindividual variation in species belonging to highly diverse, packed communities. 4. In the present study, we measured the degree of interindividual diet variation in four species of frogs of the highly diverse Brazilian Cerrado, using both gut contents and delta(13)C stable isotopes. 5. We found evidence of significant diet variation in the four species, indicating that this phenomenon is not restricted to depauperate communities in temperate regions. 6. The lack of correlations between the frogs' morphology and diet indicate that trade-offs do not depend on the morphological characters measured here and are probably not biomechanical. The nature of the trade-offs remains unknown, but are likely to be cognitive or physiological. 7. Finally, we found a positive correlation between the population niche width and the degree of diet variation, but a null model showed that this correlation can be generated by individuals sampling randomly from a common set of resources. Therefore, albeit consistent with, our results cannot be taken as evidence in favour of the niche variation hypothesis.

Further notes on the natural history of the South American pepper frog, Leptodactylus labyrinthicus (Spix, 1824) (Anura, Leptodactylidae).

Leptodactylus labyrinthicus tadpoles reach a large size in the nest through consumption of trophic eggs. We previously suggested that the trophic eggs are laid just after amplexus has finished, but our new data do not support this hypothesis. We also present further details on the natural history of the species with regard to breeding activity, spawning site, retreats and the ability of tadpoles in preying upon fully-growth heterospecific tadpoles. We also show that the tadpoles are mainly nocturnal and take diurnal refuges. We collected the data in Brazil in three localities within the Cerrado Biome. We examined burrows used by L. labyrinthicus males, verified if females still contained mature eggs just after released from amplexus, and tested the ability of tadpoles in preying fully-growth heterospecific tadpoles. Field observations and experiments were conducted on tadpole activity time, hiding behaviour and level of susceptibility to predation by the bird leaf-scrapers in four sheltering situations. Reproduction could start before the first rains; this may be advantageous by allowing the tadpoles to exploit eggs of other frogs. We found one floating nest built in a temporary pool. The nest of the species is normally circumscribed in an excavated basin beside the water body. Adult males were found during the day with their head-out of the entrance of underwater burrows, which were perforations through dense root mats beside calling/spawning sites. Probably, these burrows in permanently water-filled soil are actively excavated by males. Females released all their eggs during the amplexus, so trophic eggs are not produced by the currently-accepted mechanism. Fully-grown heterospecific tadpoles were not preyed upon by L. labyrinthicus tadpoles, which can prey only slow-moving newly hatched ones. Field tadpoles took shelter under mud/dead leaves during daylight and became exposed on the bottom at night. Free-ranging leaf-scrapers removed dead leaves from a pool with their beaks and preyed upon tadpoles. In the experiments, the tadpoles sheltered under gravel/leaves during daylight, but they were exposed at night. Leaf-scrapers ate all exposed tadpoles, but no tadpole of the gravel/leaves trays was consumed. Hence the nocturnal habits and use of diurnal refuges may protect the tadpoles from visual predators, such as the leaf-scrapers.

Further notes on the natural history of the South American pepper frog, Leptodactylus labyrinthicus (Spix, 1824) (Anura, Leptodactylidae) / Notas complementares sobre a história natural da rã-pimenta sul-americana, Leptodactylus labyrinthicus (Anura, Leptodactylidae)

Leptodactylus labyrinthicus tadpoles reach a large size in the nest through consumption of trophic eggs. We previously suggested that the trophic eggs are laid just after amplexus has finished, but our new data do not support this hypothesis. We also present further details on the natural history of the species with regard to breeding activity, spawning site, retreats and the ability of tadpoles in preying upon fully-growth heterospecific tadpoles. We also show that the tadpoles are mainly nocturnal and take diurnal refuges. We collected the data in Brazil in three localities within the Cerrado Biome. We examined burrows used by L. labyrinthicus males, verified if females still contained mature eggs just after released from amplexus, and tested the ability of tadpoles in preying fully-growth heterospecific tadpoles. Field observations and experiments were conducted on tadpole activity time, hiding behaviour and level of susceptibility to predation by the bird leaf-scrapers in four sheltering situations. Reproduction could start before the first rains; this may be advantageous by allowing the tadpoles to exploit eggs of other frogs. We found one floating nest built in a temporary pool. The nest of the species is normally circumscribed in an excavated basin beside the water body. Adult males were found during the day with their head-out of the entrance of underwater burrows, which were perforations through dense root mats beside calling/spawning sites. Probably, these burrows in permanently water-filled soil are actively excavated by males. Females released all their eggs during the amplexus, so trophic eggs are not produced by the currently-accepted mechanism. Fully-grown heterospecific tadpoles were not preyed upon by L. labyrinthicus tadpoles, which can prey only slow-moving newly hatched ones. Field tadpoles took shelter under mud/dead leaves during daylight and became exposed on the bottom at night. Free-ranging leaf-scrapers removed...

Girinos de L. labyrinthicus crescem parcialmente no ninho consumindo ovos tróficos. Sugerimos anteriormente que os ovos tróficos seriam postos logo após o amplexo, porém nossos novos dados não corroboram esta hipótese. Apresentamos também mais detalhes da história natural da espécie relacionados à estação reprodutiva, local de desova, abrigos e capacidade dos girinos em predar girinos heteroespecíficos plenamente desenvolvidos. Demonstramos ainda que os girinos são noturnos e se utilizam de refúgios diurnos. Coletamos os dados no Brasil em três locais no Bioma Cerrado. Determinamos o formato e dimensões de buracos utilizados por machos, verificamos se fêmeas liberadas do amplexo ainda portavam óvulos maduros e testamos a capacidade dos girinos em predar girinos heteroespecíficos plenamente desenvolvidos. Realizamos observações naturalísticas e experimentais com girinos para descrever o horário de atividade, comportamento de refúgio e grau de suscetibilidade à predação pela ave sabiá-poca em diferentes tipos de substratos. Desovas podiam ocorrer antes das primeiras chuvas, possibilitando aos girinos explorar ovos de outros anuros no meio da estação chuvosa. Encontramos um ninho construído na superfície da água de uma poça temporária. Os ninhos da espécie geralmente são circunscritos em bacias escavadas às margens do corpo d'água. Machos adultos foram encontrados durante o dia em buracos subaquáticos, os quais eram perfurações adjacentes aos sítios de vocalização/desova. Provavelmente, esses buracos em solos encharcados são ativamente escavados pelos machos. As fêmeas liberam todos os óvulos durante o amplexo, portanto, os ovos tróficos não são produzidos pelo mecanismo aceito presentemente. Os girinos oferecidos nos testes não foram consumidos pelos girinos de L. labyrinthicus, os quais conseguem predar apenas recém-eclodidos. No campo, os girinos se refugiavam entre o lodo ou folhas mortas durante o dia, porém ficavam expostos sobre...

The sperm of Hylodinae species (Anura, Leptodactylidae): ultrastructural characteristics and their relevance to interspecific taxonomic relationships.

Hylodinae leptodactylids (sensu Lynch 1971) form a group of diurnal frogs, which is hypothesized on the basis of morphological traits to be the closest relatives of the dendrobatid frogs. Our study describes ultrastructural characteristics of sperm from three hylodine species (Hylodes phyllodes, Crossodactylus sp. n. and Megaelosia massarti) to reassess the intergeneric relationships within the Hylodinae, as well as the supposed relationship between the Hylodinae and Dendrobatidae. The ultrastructure of the sperm is very similar among the three species and is indicative of its conserved nature within the Hylodinae. The structure of the acrosomal complex was very similar to that of other leptodactylid species, to most of the remaining species included in the Bufonoidea lineage, and also to that observed in the dendrobatid species examined so far. Since such a structure has been considered a plesiomorphic trait, it contributes little to our understanding of the relationships between the Hylodinae and Dendrobatidae. The flagellar apparatus of Crossodactylus sp. n. is very similar to that of most leptodactylids. The sperm of Megaelosia massarti and Hylodes phyllodes display a distinctive condition in their axial and juxtaxonemal fibers. This distinctive flagellar condition expands the already known variability in sperm structure within the Leptodactylidae.

Detoxified glutaraldehyde cross-linked pericardium: tissue preservation and mineralization mitigation in a subcutaneous rat model.

BACKGROUND AND AIM OF THE STUDY: Glutaraldehyde is considered a promoter of calcification by the action of toxic aldehyde group residuals from cross-linking. Post-fixation treatment with homocysteic acid (HA), besides bonding aldehyde groups and neutralizing toxicity, should enhance biocompatibility due to the strongly electronegative sulfonic group. The aim of this investigation was to evaluate HA efficacy on tissue preservation and dystrophic calcification mitigation in glutaraldehyde cross-linked bovine pericardium (BP) using a subcutaneous rat model. METHODS: Four samples of BP, two with glutaraldehyde-HA and two with glutaraldehyde treatment, were implanted in each of 24 male Sprague-Dawley rats. Three rats were killed at 14 days, eight at 28 days, eight at 56 days and five at 84 days. Unimplanted glutaraldehyde-HA- and glutaraldehyde-treated samples served as controls. All samples were studied by gross examination, mammography, light transmission and scanning electron microscopy, and atomic absorption spectroscopy. The nature of mineralization was investigated by coupling techniques of scanning electron microscopy, electron microprobe analysis and X-ray powder diffraction. RESULTS: No histological and ultrastructural differences were found between glutaraldehyde-HA- and glutaraldehyde-treated BP, whether implanted or unimplanted. In both groups, calcification progressed with time, but significantly less after glutaraldehyde-HA treatment than after glutaraldehyde alone and at all time intervals (14.63 +/- 21.34 versus 43.17 +/- 15.99 at 28 days, p = 0.003; 56.42 +/- 40.20 versus 90.59 +/- 32.90 at 56 days, p = 0.008; 91.68 +/- 67.68 versus 156.23 +/- 17.85 at 84 days, p = 0.01). Differences were evident by mammography and histology (von Kossa stain). Electron microprobe analysis in both groups showed the composition of calcified nuclei to be calcium phosphate, stoichiometrically close to apatite (Ca5(PO4)3(OH)). The occurrence of crystallized apatite was supported by X-ray powder diffraction findings, the amount of crystallized apatite being higher in glutaraldehyde-treated samples. CONCLUSIONS: Post-fixation treatment with HA preserves BP structural properties and significantly mitigates mineralization of long-term subcutaneous implants.

[Carotid thromboendarterectomy. Comparison of two anesthesiologic techniques]. / Tromboendoarteriectomia carotidea. Confronto tra due tecniche anestesiologiche.

The authors have examined two homogeneous groups of patients suffering from "carotid stenosis", operated by TEAC with two different techniques of anaesthesia: general and local-regional (block). Neurological and cardiovascular complications have been recorded in pre and post-operative period. The results analysed statistically with the Pearson test, were homogeneous. However the authors, on the basis of their experience, prefer local-regional (block) anaesthesia for good haemodynamic stability and a better neurologic control. Moreover the block anaesthesia was better in patients.

[Block of the cervical plexus in surgery of the carotid artery. Our experience with 142 cases]. / Il blocco del plesso cervicale nella chirugia della carotide. Nostra esperienza su 142 casi.

The main anesthesiological problem in TEAC operations is the possibility of evaluating the degree of tolerance after carotid artery clamping. When facing this situation, some anesthesiologists prefer to administer general anesthesia, others prefer loco-regional anesthesia. On the basis of their background and experience, the Authors, from 1.1.1987 to 12.31.1988, have performed 142 nerve blocks of the superficial and the cervical plexus. The proposed technique is simple. No side effects are observed. Moreover it is gratifying for the surgeon and safe from risks for patients. Loco-regional anesthesia permits a close neurologic monitoring that is easily understandable and inexpensive. When performing this kind of surgery, this technique seems to be valid and effective.