Is HIV short-sighted? Insights from a multistrain nested model

An important component of pathogen evolution at the population level is evolution within hosts. Unless evolution within hosts is very slow compared to the duration of infection, the composition of pathogen genotypes within a host is likely to change during the course of an infection, thus altering the composition of genotypes available for transmission as infection progresses. We develop a nested modeling approach that allows us to follow the evolution of pathogens at the epidemiological level by explicitly considering within-host evolutionary dynamics of multiple competing strains and the timing of transmission. We use the framework to investigate the impact of short-sighted within-host evolution on the evolution of virulence of human immunodeficiency virus (HIV), and find that the topology of the within-host adaptive landscape determines how virulence evolves at the epidemiological level. If viral reproduction rates increase significantly during the course of infection, the viral population will evolve a high level of virulence even though this will reduce the transmission potential of the virus. However, if reproduction rates increase more modestly, as data suggest, our model predicts that HIV virulence will be only marginally higher than the level that maximizes the transmission potential of the virus

MAXIMAL THEORETICAL STRENGTH: METHODOLOGY AND APPLICATIONS

Introduction: We describe a new experimental method useful in the evaluation of strength, strength training and rehabilitation, and training control. Methods: The Maximal Theoretical Strength (Forza Massima Teorica - FMAXT) method has been developed from the equation F=P(1+a/g), which relates lifted weight (P) to muscular strength (F) used in lifting and to its acceleration (a). The test is carried out with a bench press and a multipower machine (for testing upper and lower limb strength), both equipped with a photocell-system chronometer and linked to a PC that elaborates the data. The test consists of five consecutive lifts from a motionless start, each carried out with increasing weight (P): We obtain, from the acceleration (a) expressed in the lifts (derived from the time measured by the photocells) the corresponding strength (F). F obtained in the previous lift is used as the weight in the next lift. Results: 1) Reporting the five pairs (P-F) on a Cartesian plane, the points draw up on a interpolating straight line (r=0.996) that, when intersecting the bisecting line of the plane itself, determines a condition (F=P) experimentally impossible to reach, because a=0. Such value (FMAXT value) can be calculated only theoretically; it can be considered as an ‘absolute’ strength value and is quantifiable as the average max isometric strength expressed in the totality of the movement. On the strength/velocity Hill’s curve, the FMAXT value is pointed out in the intersection of the curve with the axis of Strength, in correspondence to v=0. (This study phase was carried out with 255 subjects for the upper limbs and 144 for the lower limbs) 2) When the single test is carried out with a double lift, the first starting from a motionless position (evaluation of the unique Contractile Component-expressed strength), followed, without pause, by a second one beginning at the superior deadpoint reached in the first lift and divided into two phases, the falling phase (concentric phase with elastic energy accumulation in muscular Serial Elastic Component) and the second lifting phase (in which is expressed the strength derived from CC plus the CES-accumulated one), the FMAXT findings of the two lifts (motionless and with counter-movement) coincide. (this second study phase was carried out with 120 subjects). Conclusions: From the analysis of FMAXT test results some very significant data for personalized training programming can be obtained. These data are the maxFMAXT itself, the Maximal Concentric Power Peak, the Maximal Eccentric/Concentric Power Peak, the Maximal Elastic Energy Percentage Reutilization Peak. Each peak can be characterized by an absolute value and by a relative percentage FMAXT-related value. In training control, comparing the results of subsequent FMAXT tests, it is possible to evaluate whether the programmed training has or has not produced the supposed adaptive phenomena regarding the contractile and/or elastic component of muscular strength

Dysfunctional play and dopamine physiology in the Fischer 344 rat

Juvenile Fischer 344 rats are known to be less playful than other inbred strains, although the neurobiological substrate(s) responsible for this phenotype is uncertain. In the present study, Fischer 344 rats were compared to the commonly used outbred Sprague-Dawley strain on several behavioral and physiological parameters in order to ascertain whether the lack of play may be related to compromised activity of brain dopamine (DA) systems. As expected, Fischer 344 rats were far less playful than Sprague-Dawley rats, with Fischer 344 rats less likely to initiate playful contacts with a playful partner and less likely to respond playfully to these contacts. We also found that Fischer 344 rats showed less of a startle response and greater pre-pulse inhibition (PPI), especially at higher prepulse intensities. The increase in PPI seen in the Fischer 344 rat could be due to reduced DA modulation of sensorimotor gating and neurochemical measures were consistent with Fischer 344 rats releasing less DA than Sprague-Dawley rats. Fast scan cyclic voltammetry (FSCV) revealed Fischer 344 rats had less evoked DA release in dorsal and ventral striatal brain slices and high-performance liquid chromatography revealed Fischer 344 rats to have less DA turnover in the striatum and prefrontal cortex. We also found DA-dependent forms of cortical plasticity were deficient in the striatum and prefrontal cortex of the Fischer 344 rat. Taken together, these data indicate that deficits in play and enhanced PPI of Fischer 344 rats may be due to reduced DA modulation of corticostriatal and mesolimbic/mesocortical circuits critical to the execution of these behaviors

Information content of household-stratified epidemics

Household structure is a key driver of many infectious diseases, as well as a natural target for interventions such as vaccination programs. Many theoretical and conceptual advances on household-stratified epidemic models are relatively recent, but have successfully managed to increase the applicability of such models to practical problems. To be of maximum realism and hence benefit, they require parameterisation from epidemiological data, and while household-stratified final size data has been the traditional source, increasingly time-series infection data from households are becoming available. This paper is concerned with the design of studies aimed at collecting time-series epidemic data in order to maximize the amount of information available to calibrate household models. A design decision involves a trade-off between the number of households to enrol and the sampling frequency. Two commonly used epidemiological study designs are considered: cross-sectional, where different households are sampled at every time point, and cohort, where the same households are followed over the course of the study period. The search for an optimal design uses Bayesian computationally intensive methods to explore the joint parameter-design space combined with the Shannon entropy of the posteriors to estimate the amount of information in each design. For the cross-sectional design, the amount of information increases with the sampling intensity, i.e., the designs with the highest number of time points have the most information. On the other hand, the cohort design often exhibits a trade-off between the number of households sampled and the intensity of follow-up. Our results broadly support the choices made in existing epidemiological data collection studies. Prospective problem-specific use of our computational methods can bring significant benefits in guiding future study designs

Modeled Microgravity-Induced Protein Kinase C Isoform Expression in Human Lymphocytes

In long-term space travel, the crew is exposed to microgravity and radiation that invoke potential hazards to the immune system. T cell activation is a critical step in the immune response. Receptor-mediated signaling is inhibited both in microgravity and modeled microgravity (MMG) as reflected in diminished DNA synthess in peripheral blood lymphocytes and their locomotion through gelled type 1 collagen. Direct activation of Protein Kinase C (PKC) bypassing cell surface events using the phorbol ester PMA rescues MMG-inhibited lymphocyte activation and locomotion, whereas calcium ionophore ionomycin had no rescue effect. Thus calcium-independent PKC isoforms may be affected in MMG-induced locomotion inhibition and rescue. Both calcium-dependent isoforms and calcium-independent PKC isoforms were investigated to assess their expression in lymphocytes in 19 and MMG-culture. Human lymphocytes were cultured and harvested at 24, 48, 72 and 96 hours and serial samples assessed for locomotion using type I collagen and expression of PKC isoforms. Expression of PKC-alpha, -delta and -epsilon was assessed by RT-PCR, flow cytometry and immunoblotting. Results indicated that PKC isoforms delta and epsilon were down-regulated by more than 50% at the transcriptional and translational levels in MMG-cultured lymphocytes compared with 19 controls. Events upstream of PKC such as phosphorylation of Phospholipase C(gamma) (PLC-gamma) in MMG, revealed accumulation of inactive enzyme. Depressed Ca++ -independent PKC isoforms may be a consequence of an upstream lesion in the signal transduction pathway. The differential response among calcium-dependent and calcium-independent isoforms may actually result from MMG intrusion events earlier than, but after ligand-receptor interaction. Keywords: Signal transduction, locomotion, immunit

Microgravity and Immunity: Changes in Lymphocyte Gene Expression

Earlier studies had shown that modeled and true microgravity (MG) cause multiple direct effects on human lymphocytes. MG inhibits lymphocyte locomotion, suppresses polyclonal and antigen-specific activation, affects signal transduction mechanisms, as well as activation-induced apoptosis. In this study we assessed changes in gene expression associated with lymphocyte exposure to microgravity in an attempt to identify microgravity-sensitive genes (MGSG) in general and specifically those genes that might be responsible for the functional and structural changes observed earlier. Two sets of experiments targeting different goals were conducted. In the first set, T-lymphocytes from normal donors were activated with antiCD3 and IL2 and then cultured in 1g (static) and modeled MG (MMG) conditions (Rotating Wall Vessel bioreactor) for 24 hours. This setting allowed searching for MGSG by comparison of gene expression patterns in zero and 1 g gravity. In the second set - activated T-cells after culturing for 24 hours in 1g and MMG were exposed three hours before harvesting to a secondary activation stimulus (PHA) thus triggering the apoptotic pathway. Total RNA was extracted using the RNeasy isolation kit (Qiagen, Valencia, CA). Affymetrix Gene Chips (U133A), allowing testing for 18,400 human genes, were used for microarray analysis. In the first set of experiments MMG exposure resulted in altered expression of 89 genes, 10 of them were up-regulated and 79 down-regulated. In the second set, changes in expression were revealed in 85 genes, 20 were up-regulated and 65 were down-regulated. The analysis revealed that significant numbers of MGS genes are associated with signal transduction and apoptotic pathways. Interestingly, the majority of genes that responded by up- or down-regulation in the alternative sets of experiments were not the same, possibly reflecting different functional states of the examined T-lymphocyte populations. The responder genes (MGSG) might play an essential role in adaptation to MG and/or be responsible for pathologic changes encountered in Space and thus represent potential targets for molecular-based countermeasure

Enzymatic synthesis of lignin derivable pyridine based polyesters for the substitution of petroleum derived plastics

Following concerns over increasing global plastic pollution, interest in the production and characterization of bio-based and biodegradable alternatives is rising. In the present work, the synthesis of a series of fully bio-based alternatives based on 2,4-, 2,5-, and 2,6-pyridinedicarboxylic acid-derived polymers produced via enzymatic catalysis are reported. A similar series of aromatic-aliphatic polyesters based on diethyl-2,5-furandicarboxylate and of the petroleum-based diethyl terephthalate and diethyl isophthalate were also synthesized. Here we show that the enzymatic synthesis starting from 2,4-diethyl pyridinedicarboxylate leads to the best polymers in terms of molecular weights (M n = 14.3 and M w of 32.1 kDa when combined with 1,8-octanediol) when polymerized in diphenyl ether. Polymerization in solventless conditions were also successful leading to the synthesis of bio-based oligoesters that can be further functionalized. DSC analysis show a clear similarity in the thermal behavior between 2,4-diethyl pyridinedicarboxylate and diethyl isophthalate (amorphous polymers) and between 2,5-diethyl pyridinedicarboxylate and diethyl terephthalate (crystalline polymers)

Unsupervised identification of significant lineages of SARS-CoV-2 through scalable machine learning methods

Since its emergence in late 2019, SARS-CoV-2 has diversified into a large number of lineages and caused multiple waves of infection globally. Novel lineages have the potential to spread rapidly and internationally if they have higher intrinsic transmissibility and/or can evade host immune responses, as has been seen with the Alpha, Delta, and Omicron variants of concern. They can also cause increased mortality and morbidity if they have increased virulence, as was seen for Alpha and Delta. Phylogenetic methods provide the "gold standard" for representing the global diversity of SARS-CoV-2 and to identify newly emerging lineages. However, these methods are computationally expensive, struggle when datasets get too large, and require manual curation to designate new lineages. These challenges provide a motivation to develop complementary methods that can incorporate all of the genetic data available without down-sampling to extract meaningful information rapidly and with minimal curation. In this paper, we demonstrate the utility of using algorithmic approaches based on word-statistics to represent whole sequences, bringing speed, scalability, and interpretability to the construction of genetic topologies. While not serving as a substitute for current phylogenetic analyses, the proposed methods can be used as a complementary, and fully automatable, approach to identify and confirm new emerging variants

Textbook for nature entrepreneurship : product of the WURKS project Nature Entrepreneurship and Tourism within Green Education (NatureToGo)

In recent years, government funding for nature conservation and development has declined. As a result, links between nature conservation and entrepreneurship are increasingly being made in both practice and education. This comes with many questions and challenges. In Green Secondary Vocational Education and Higher Professional Education, educators want to incorporate social, economic and ecological factors in their courses in nature entrepreneurship. There is also a demand for tools for developing new business models for nature conservation and development. This textbook is meant to meet those demands, together with the other educational materials including a documentary and a number of PowerPoint presentation

Understanding potentials and restrictions of solvent-free enzymatic polycondensation of itaconic acid: an experimental and computational analysis

6siItaconic acid is a chemically versatile unsaturated diacid that can be produced by fermentation and potentially it can replace petrol based monomers such as maleic and fumaric acids in the production of curable polyesters or new biocompatible functionalized materials. Unfortunately, due to the presence of the unsaturated C=C bond, polycondensation of itaconic acid is hampered by cross reactivity and isomerization. Therefore, enzymatic polycondensations would respond to the need of mild and selective synthetic routes for the production of novel bio-based polymers. The present work analyses the feasibility of enzymatic polycondensation of diethyl itaconate and, for the first time, provides comprehensive solutions embracing both the formulation of the biocatalyst, the reaction conditions and the choice of the co-monomers. Computational docking was used to disclose the structural factors responsible for the low reactivity of dimethyl itaconate and to identify possible solutions. Surprisingly, experimental and computational analysis revealed that 1,4-butanediol is an unsuitable co-monomer for the polycondensation of dimethyl itaconate whereas the cyclic and rigid 1,4-cyclohexanedimethanol promotes the elongation of the oligomers.partially_openembargoed_20160430Corici, Livia; Pellis, Alessandro; Ferrario, Valerio; Ebert, Cynthia; Cantone, Sara; Gardossi, LuciaCorici, Livia; Pellis, Alessandro; Ferrario, Valerio; Ebert, Cynthia; Cantone, Sara; Gardossi, Luci