Predicting octanol/water partition coefficients and pKa for the SAMPL7 challenge using the SM12, SM8 and SMD solvation models.

Blind predictions of octanol/water partition coefficients and pKa at 298.15 K for 22 drug-like compounds were made for the SAMPL7 challenge. Octanol/water partition coefficients were predicted from solvation free energies computed using electronic structure calculations with the SM12, SM8 and SMD solvation models. Within these calculations we compared the use of gas- and solution-phase optimized geometries of the solute. Based on these calculations we found that in general the use of solution phase-optimized geometries increases the affinity of the solutes for water as compared to octanol, with the use of gas-phase optimized geometries resulting in the better agreement with experiment. The pKa is computed using the direct approach, scaled solvent-accessible surface model, and the inclusion of an explicit water molecule, where the latter two methods have previously been shown to offer improved predictions as compared to the direct approach. We find that the use of an explicit water molecule provides superior predictions, and that the predicted macroscopic pKa is sensitive to the employed microstates.

First report of the metacestode Caulobothrium sp. in the Peruvian scallop Argopecten purpuratus from Sechura Bay, Piura, Peru.

In recent parasitological surveys performed on the Peruvian scallop, Argopecten purpuratus, from bottom cultures of Sechura Bay, Piura, Peru, free and encysted metacestodes were frequently found in their gonads. The objective of this study was to identify this metacestode, determine their prevalence and intensity and briefly assess the histopathological impact in the affected tissues. A parasitological study of 890 scallops over a 3-year period was performed in order to determine the parasite prevalence and intensity. Microscopical observation of details of the scolex and histopathological study of the affected host tissues were performed as well as molecular characterization of the parasite based on 18S and 28S rDNA sequences. The prevalence of the metacestode was 82.2% in August of 2013, 90.4% in November of 2014, and 83.1% and 85.6% in April and September of 2015, respectively. The highest average intensity (218.4) was found in spring of 2014. The histopathological study showed that plerocercoids reduced the gonadal space where the ovules develop. The molecular characterization and phylogenetic analysis revealed that the metacestodes belong to the genus Caulobothrium having high sequence similarity to Caulobothrium opisthorchis. This study constitutes the first report of Caulobothrium metacestodes in the scallop A. purpuratus.

Cellular Uptake and Efflux of Palbociclib In Vitro in Single Cell and Spheroid Models.

Adequate drug distribution through tumors is essential for treatment to be effective. Palbociclib is a cyclin-dependent kinase 4/6 inhibitor approved for use in patients with hormone receptor positive, human epidermal growth factor receptor 2 negative metastatic breast cancer. It has unusual physicochemical properties, which may significantly influence its distribution in tumor tissue. We studied the penetration and distribution of palbociclib in vitro, including the use of multicellular three-dimensional models and mathematical modeling. MCF-7 and DLD-1 cell lines were grown as single cell suspensions (SCS) and spheroids; palbociclib uptake and efflux were studied using liquid chromatography-tandem mass spectrometry. Intracellular concentrations of palbociclib for MCF-7 SCS (C max 3.22 µM) and spheroids (C max 2.91 µM) were 32- and 29-fold higher and in DLD-1, 13- and 7-fold higher, respectively, than the media concentration (0.1 µM). Total palbociclib uptake was lower in DLD-1 cells than MCF-7 cells in both SCS and spheroids. Both uptake and efflux of palbociclib were slower in spheroids than SCS. These data were used to develop a mathematical model of palbociclib transport that quantifies key parameters determining drug penetration and distribution. The model reproduced qualitatively most features of the experimental data and distinguished between SCS and spheroids, providing additional support for hypotheses derived from the experimental data. Mathematical modeling has the potential for translating in vitro data into clinically relevant estimates of tumor drug concentrations. SIGNIFICANCE STATEMENT: This study explores palbociclib uptake and efflux in single cell suspension and spheroid models of cancer. Large intracellular concentrations of palbociclib are found after drug exposure. The data from this study may aid understanding of the intratumoural pharmacokinetics of palbociclib, which is useful in understanding how drug distributes within tumor tissue and optimizing drug efficacy. Biomathematical modelling has the potential to derive intratumoural drug concentrations from plasma pharmacokinetics in patients.

Assessing real-time Zika risk in the United States.

BACKGROUND: Confirmed local transmission of Zika Virus (ZIKV) in Texas and Florida have heightened the need for early and accurate indicators of self-sustaining transmission in high risk areas across the southern United States. Given ZIKV's low reporting rates and the geographic variability in suitable conditions, a cluster of reported cases may reflect diverse scenarios, ranging from independent introductions to a self-sustaining local epidemic. METHODS: We present a quantitative framework for real-time ZIKV risk assessment that captures uncertainty in case reporting, importations, and vector-human transmission dynamics. RESULTS: We assessed county-level risk throughout Texas, as of summer 2016, and found that importation risk was concentrated in large metropolitan regions, while sustained ZIKV transmission risk is concentrated in the southeastern counties including the Houston metropolitan region and the Texas-Mexico border (where the sole autochthonous cases have occurred in 2016). We found that counties most likely to detect cases are not necessarily the most likely to experience epidemics, and used our framework to identify triggers to signal the start of an epidemic based on a policymakers propensity for risk. CONCLUSIONS: This framework can inform the strategic timing and spatial allocation of public health resources to combat ZIKV throughout the US, and highlights the need to develop methods to obtain reliable estimates of key epidemiological parameters.

Divergent predation environment between two sister species of livebearing fishes (Cyprinodontiformes: Poeciliidae) predicts boldness, activity, and exploration behavior / Ambientes de depredación divergente para dos especies hermanas de peces vivíparos (Cyprinodontiformes: Poeciliidae) predicen el comportamiento de audacia, actividad y exploración

Abstract:Predators can influence a variety of prey traits, including behavior. Traits such as boldness, activity rate, and tendency to explore can all be shaped by predation risk. Our study examines the effects of predation on these behaviors by considering a natural system in which two sister species of livebearing fishes, Brachyrhaphis roseni and B. terrabensis, experience divergent predation environments. In February of 2013, we collected fish in the Río Chiriquí Nuevo drainage, Chiriquí, Panama, and conducted behavioral assays. Using open-field behavioral assays, we evaluated both juveniles and adults, and males and females, to determine if there were differences in behavior between ontogenetic stages or between sexes. We assessed boldness as 'time to emerge' from a shelter into a novel environment, and subsequently measured activity and exploration within that novel environment. We predicted that B. roseni (a species that co-occurs with predators) would be more bold, more active, and more prone to explore, than B. terrabensis (a species that does not co-occur with predators). In total, we tested 17 juveniles, 21 adult males, and 20 adult females of B. roseni, and 19 juveniles, 19 adult males, and 18 adult females of B. terrabensis. We collected all animals from streams in Chiriquí, Panama in February 2013, and tested them following a short acclimation period to laboratory conditions. As predicted, we found that predation environment was associated with several differences in behavior. Both adult and juvenile B. roseni were more active and more prone to explore than B. terrabensis. However, we found no differences in boldness in either adults or juveniles. We also found a significant interaction between 'sex' and 'species' as predictors of boldness and exploration, indicating that predation environment can affect behaviors of males and females differently in each species. Our work demonstrates the importance of considering sex and life history stage when evaluating the evolution of behavior. Rev. Biol. Trop. 65 (1): 267-277. Epub 2017 March 01.

ResumenLos depredadores pueden influenciar una variedad de rasgos de la presa, incluyendo el comportamiento. Los rasgos tales como la audacia, nivel de actividad, y la tendencia a explorar; pueden ser moldeados por el riesgo de depredación. Nuestro estudio examina los efectos de la depredación en el comportamiento al considerar un sistema natural en el que dos especies hermanas de peces vivíparos, Brachyrhaphis roseni y B. terrabensis, se presentan en ambientes de depredación divergente. En febrero 2013, recolectamos peces en el drenaje del Río Chiriquí Nuevo, Chiriquí, Panamá y llevamos a cabo ensayos de comportamiento. Al usar ensayos de comportamiento en campo abierto, se evaluó el comportamiento en juveniles y adultos, machos y hembras, para determinar si los patrones de divergencia diferían entre las etapas ontogenéticas o entre sexos. Se evaluó la audacia como "tiempo en salir" de un refugio a un ambiente nuevo, y posteriormente se midió la actividad y la exploración dentro de ese nuevo ambiente. Nosotros predijimos que B. roseni (una especie que se presenta con los depredadores) sería más audaz, activa y propensa a explorar que B. terrabensis (una especie que no se presenta con los depredadores). En total, probamos 17 jóvenes, 21 machos adultos, y 20 hembras adultas de B. roseni, y 19 jóvenes, 19 machos adultos, y 18 hembras adultas de B. terrabensis. Recogimos todos los animales en Chiriquí, Panamá en Febrero 2013, y los probamos después de un corto período de aclimatación a las condiciones de laboratorio. Como se predijo, se encontró que la depredación ambiental se asoció con varias diferencias en el comportamiento. Tanto adultos y jóvenes de B. roseni eran más activos y más propensos a explorar que B. terrabensis. Sin embargo, no se encontraron diferencias en la audacia en adultos o menores. También se encontró una interacción significativa entre "sexo" y "especie" como predictores de la audacia y la exploración, lo que indica que la depredación puede afectar el comportamiento de los machos y hembras de manera diferente en cada especie. Nuestro estudio demuestra la importancia de considerar el sexo y la etapa del ciclo de vida al evaluar la evolución del comportamiento.

Divergent predation environment between two sister species of livebearing fishes (Cyprinodontiformes: Poeciliidae) predicts boldness, activity, and exploration behavior.

Predators can influence a variety of prey traits, including behavior. Traits such as boldness, activity rate, and tendency to explore can all be shaped by predation risk. Our study examines the effects of predation on these behaviors by considering a natural system in which two sister species of livebearing fishes, Brachyrhaphis roseni and B. terrabensis, experience divergent predation environments. In February of 2013, we collected fish in the Río Chiriquí Nuevo drainage, Chiriquí, Panama, and conducted behavioral assays. Using open-field behavioral assays, we evaluated both juveniles and adults, and males and females, to determine if there were differences in behavior between ontogenetic stages or between sexes. We assessed boldness as 'time to emerge' from a shelter into a novel environment, and subsequently measured activity and exploration within that novel environment. We predicted that B. roseni (a species that co-occurs with predators) would be more bold, more active, and more prone to explore, than B. terrabensis (a species that does not co-occur with predators). In total, we tested 17 juveniles, 21 adult males, and 20 adult females of B. roseni, and 19 juveniles, 19 adult males, and 18 adult females of B. terrabensis. We collected all animals from streams in Chiriquí, Panama in February 2013, and tested them following a short acclimation period to laboratory conditions. As predicted, we found that predation environment was associated with several differences in behavior. Both adult and juvenile B. roseni were more active and more prone to explore than B. terrabensis. However, we found no differences in boldness in either adults or juveniles. We also found a significant interaction between 'sex' and 'species' as predictors of boldness and exploration, indicating that predation environment can affect behaviors of males and females differently in each species. Our work demonstrates the importance of considering sex and life history stage when evaluating the evolution of behavior.

Inhibition of Orexin Signaling Promotes Sleep Yet Preserves Salient Arousability in Monkeys.

STUDY OBJECTIVES: In addition to enhancing sleep onset and maintenance, a desirable insomnia therapeutic agent would preserve healthy sleep's ability to wake and respond to salient situations while maintaining sleep during irrelevant noise. Dual orexin receptor antagonists (DORAs) promote sleep by selectively inhibiting wake-promoting neuropeptide signaling, unlike global inhibition of central nervous system excitation by gamma-aminobutyric acid (GABA)-A receptor (GABAaR) modulators. We evaluated the effect of DORA versus GABAaR modulators on underlying sleep architecture, ability to waken to emotionally relevant stimuli versus neutral auditory cues, and performance on a sleepiness-sensitive cognitive task upon awakening. METHODS: DORA-22 and GABAaR modulators (eszopiclone, diazepam) were evaluated in adult male rhesus monkeys (n = 34) with continuous polysomnography recordings in crossover studies of sleep architecture, arousability to a classically conditioned salient versus neutral acoustical stimulus, and psychomotor vigilance task (PVT) performance if awakened. RESULTS: All compounds decreased wakefulness, but only DORA-22 sleep resembled unmedicated sleep in terms of underlying sleep architecture, preserved ability to awaken to salient-conditioned acoustic stimuli while maintaining sleep during neutral acoustic stimuli, and no congnitive impairment in PVT performance. Although GABAaR modulators induced lighter sleep, monkeys rarely woke to salient stimuli and PVT performance was impaired if monkeys were awakened. CONCLUSIONS: In nonhuman primates, DORAs' targeted mechanism for promoting sleep protects the ability to selectively arouse to salient stimuli and perform attentional tasks unimpaired, suggesting meaningful differentiation between a hypnotic agent that works through antagonizing orexin wake signaling versus the sedative hypnotic effects of the GABAaR modulator mechanism of action.

Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes.

The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analysis of Brachyrhaphis by using four molecular markers (3mtDNA, 1nucDNA) to infer relationships among species in this genus. We tested the validity of this genus as a monophyletic group using extensive outgroup sampling based on recent phylogenetic hypotheses of Poeciliidae. We also tested the validity of recently described species of Brachyrhaphis that are part of the B. episcopi complex in Panama. Finally, we examined the impact of historical events on diversification of Brachyrhaphis, and made predictions regarding the role of different ecological environments on evolutionary diversification where known historical events apparently fail to explain speciation. Based on our results, we reject the monophyly of Brachyrhaphis, and question the validity of two recently described species (B. hessfeldi and B. roswithae). Historical biogeography of Brachyrhaphis generally agrees with patterns found in other freshwater taxa in Lower Central America, which show that geological barriers frequently predict speciation. Specifically, we find evidence in support of an 'island' model of Lower Central American formation, which posits that the nascent isthmus was partitioned by several marine connections before linking North and South America. In some cases where historic events (e.g., vicariance) fail to explain allopatric species breaks in Brachyrhaphis, ecological processes (e.g., divergent predation environments) offer additional insight into our understanding of phylogenetic diversification in this group.

Benthic foraminifera show some resilience to ocean acidification in the northern Gulf of California, Mexico.

Extensive CO2 vents have been discovered in the Wagner Basin, northern Gulf of California, where they create large areas with lowered seawater pH. Such areas are suitable for investigations of long-term biological effects of ocean acidification and effects of CO2 leakage from subsea carbon capture storage. Here, we show responses of benthic foraminifera to seawater pH gradients at 74-207m water depth. Living (rose Bengal stained) benthic foraminifera included Nonionella basispinata, Epistominella bradyana and Bulimina marginata. Studies on foraminifera at CO2 vents in the Mediterranean and off Papua New Guinea have shown dramatic long-term effects of acidified seawater. We found living calcareous benthic foraminifera in low pH conditions in the northern Gulf of California, although there was an impoverished species assemblage and evidence of post-mortem test dissolution.

Glycerol and arabitol production by an intergeneric hybrid, PB2, obtained by protoplast fusion between Saccharomyces cerevisiae and Torulaspora delbrueckii.

An intergeneric osmotolerant hybrid yeast, PB2, was used together with the parental strains to study glycerol and arabitol production in batch culture. This fusion product was previously obtained by protoplast fusion between Torulaspora delbrueckii and Saccharomyces cerevisiae. Polyols and biomass production were determined in batch culture under aerobic conditions. Under the conditions tested, using PB2 hybrid and both parental strains, the best results were obtained with the hybrid. Arabitol reached a final concentration of 70 g/l and glycerol was increased to up to 50 g/l.

Non-conventional yeasts.

In the beginning there was yeast, and it raised bread, brewed beer, and made wine. After many not days but centuries and even millenia later, it was named Saccharomyces cerevisiae. After more years and centuries there was another yeast, and it was named Schizosaccharomyces pombe; now there were two stars in the yeast heaven. In only a few more years there were other yeasts, and then more, and more, and more. The era of the non-conventional yeasts had begun.

Further biochemical characterization of Mycobacterium leprae laminin-binding proteins.

It has been demonstrated that the alpha2 chain of laminin-2 present on the surface of Schwann cells is involved in the process of attachment of Mycobacterium leprae to these cells. Searching for M. leprae laminin-binding molecules, in a previous study we isolated and characterized the cationic proteins histone-like protein (Hlp) and ribosomal proteins S4 and S5 as potential adhesins involved in M. leprae-Schwann cell interaction. Hlp was shown to bind alpha2-laminins and to greatly enhance the attachment of mycobacteria to ST88-14 Schwann cells. In the present study, we investigated the laminin-binding capacity of the ribosomal proteins S4 and S5. The genes coding for these proteins were PCR amplified and their recombinant products were shown to bind alpha2-laminins in overlay assays. However, when tested in ELISA-based assays and in adhesion assays with ST88-14 cells, in contrast to Hlp, S4 and S5 failed to bind laminin and act as adhesins. The laminin-binding property and adhesin capacity of two basic host-derived proteins were also tested, and only histones, but not cytochrome c, were able to increase bacterial attachment to ST88-14 cells. Our data suggest that the alanine/lysine-rich sequences shared by Hlp and eukaryotic H1 histones might be involved in the binding of these cationic proteins to laminin.

Further biochemical characterization of Mycobacterium leprae laminin-binding proteins

It has been demonstrated that the alpha2 chain of laminin-2 present on the surface of Schwann cells is involved in the process of attachment of Mycobacterium leprae to these cells. Searching for M. leprae laminin-binding molecules, in a previous study we isolated and characterized the cationic proteins histone-like protein (Hlp) and ribosomal proteins S4 and S5 as potential adhesins involved in M. leprae-Schwann cell interaction. Hlp was shown to bind alpha2-laminins and to greatly enhance the attachment of mycobacteria to ST88-14 Schwann cells. In the present study, we investigated the laminin-binding capacity of the ribosomal proteins S4 and S5. The genes coding for these proteins were PCR amplified and their recombinant products were shown to bind alpha2-laminins in overlay assays. However, when tested in ELISA-based assays and in adhesion assays with ST88-14 cells, in contrast to Hlp, S4 and S5 failed to bind laminin and act as adhesins. The laminin-binding property and adhesin capacity of two basic host-derived proteins were also tested, and only histones, but not cytochrome c, were able to increase bacterial attachment to ST88-14 cells. Our data suggest that the alanine/lysine-rich sequences shared by Hlp and eukaryotic H1 histones might be involved in the binding of these cationic proteins to laminin

Dynamics of metabolism and its interactions with gene expression during sporulation in Saccharomyces cerevisiae.

The dynamics of metabolism has been shown to be involved in the triggering of events that are concurrent with sporulation of the budding yeast Saccharomyces cerevisiae. Indeed, quantitative correlations have been demonstrated between sporulation and the rate of carbon substrate or oxygen consumption, and the fluxes through gluconeogenic and glyoxylate cycle pathways. The results suggest that an imbalance between catabolic and anabolic fluxes influences the occurrence of the differentiation process. The hypothesis that the initiation of sporulation is triggered by the accumulation of an intracellular metabolite is confronted with the notion that intermediary metabolism and the expression of genes involved in sporulation interact to trigger the differentiation process. Several pieces of evidence indicate that derepression of the gluconeogenic pathway is crucial for the initiation of sporulation. One of the possible pathways through which glucose repression hampers sporulation might be the repression of gluconeogenesis as well as that of respiratory activity, in turn modulating the expression of IMEL++. The stages defined in the dynamics of sporulating cultures, namely readiness and commitment, are related to metabolic events associated with sporulation. An interpretation in terms of metabolic flux dynamics is given to the reversal of commitment occurring when the normal progression to sporulation is somehow blocked. The quantitative data are here integrated in a model attempting to simulate the dynamics of metabolic as well as cellular events during sporulation. The model is envisaged as a test of the hypothesis that an imbalance between anabolism and catabolism is involved in initiation of the sporulation process. It is proposed that such an imbalance may be a signal for differential gene expression associated with the differentiation pathway.

Expression of lymphocyte-endothelial receptor-ligand pairs, alpha4beta7/MAdCAM-1 and OX40/OX40 ligand in the colon and jejunum of patients with inflammatory bowel disease.

BACKGROUND: The interaction between leucocytes and vascular endothelial cells is essential for leucocyte migration into inflammatory sites. AIMS: To study the local expression of the pairs of complementary molecules, alpha4beta7/mucosal addressin cell adhesion molecule (MAdCAM-1) and OX40/OX40 ligand in the lamina propria of the colon and jejunum of patients with inflammatory bowel disease. METHODS: Ten patients with active ulcerative colitis (UC), nine with active Crohn's disease (CD), and seven irritable bowel syndrome (IBS) controls were submitted to endoscopic and peroral jejunal biopsies. Specimens were immunostained by indirect alkaline phosphatase using antibodies against CD3, intercellular adhesion molecule (ICAM) 1, alpha4beta7, MAdCAM-1, and OX40. An OX40-mouse-IgG fusion protein was used to detect OX40 ligand on frozen sections. Immunohistological analysis was carried out by optical microscopy using a computer assisted image analyser. RESULTS: Colonic lamina propria of patients with CD and UC showed increased density of CD3+, alpha4beta7+, and OX40+ cells compared with IBS controls. ICAM-1, MAdCAM-1, and OX40 ligand positive vessels were also increased compared with IBS controls. No significant difference was found in the density of any of these cells in the jejunal mucosa of patients compared with IBS controls. CONCLUSIONS: The expression of MAdCAM-1 and OX40 ligand on gut endothelial and OX40+ cells is increased in sites of mucosal inflammation in patients with inflammatory bowel disease. No evidence was found for increased lamina propria T cells or increased vascular adhesion molecule expression in the proximal intestine of patients with distal inflammatory bowel disease.

Modulation of sporulation and metabolic fluxes in Saccharomyces cerevisiae by 2 deoxy glucose.

Quantitative studies of metabolic fluxes during Saccharomyces cerevisiae sporulation on acetate in the presence of the glucose analog, 2-deoxy glucose (2dG) are reported. We have studied the inhibition of sporulation and associated catabolic or anabolic fluxes by 2dG. Sporulation frequencies decreased from 50% to 2% asci per cell at 2dG concentrations in the range of 0.03 to 0.30 g l-1, respectively. Under the same conditions, the acetate consumption flux was inhibited up to 60% and the glyoxylate cycle and gluconeogenic fluxes decreased from 0.7 and 0.3 mmol h-1 g-1 dw, respectively, to negligible values. We observed a linear correlation of the acetate consumption rate with the sporulation frequency by varying the 2dG concentration. The linear correlation was also verified between the frequency of sporulation and the fluxes through glyoxylate cycle and gluconeogenic pathways. In addition, the same association of inhibition of sporulation and metabolic fluxes was found in other S. cerevisiae strains displaying different potentials of sporulation. The results presented suggest that inhibition of sporulation in the presence of the glucose analog may be attributed, at least in part, to the inhibition of anabolic fluxes and might be associated with catabolite repression.