Pathway landscapes and epigenetic regulation in breast cancer and melanoma cell lines

Understanding how developmental systems evolve over time is a key question in stem cell and developmental biology research. However, due to hurdles of existing experimental techniques, our understanding of these systems as a whole remains partial and coarse. In recent years, we have been constructing in-silico models that synthesize experimental knowledge using software engineering tools. Our approach integrates known isolated mechanisms with simplified assumptions where the knowledge is limited. This has proven to be a powerful, yet underutilized, tool to analyze the developmental process. The models provide a means to study development in-silico by altering the model’s specifications, and thereby predict unforeseen phenomena to guide future experimental trials. To date, three organs from diverse evolutionary organisms have been modeled: the mouse pancreas, the C. elegans gonad, and partial rodent brain development. Analysis and execution of the models recapitulated the development of the organs, anticipated known experimental results and gave rise to novel testable predictions. Some of these results had already been validated experimentally. In this paper, I review our efforts in realistic in-silico modeling of stem cell research and developmental biology and discuss achievements and challenges. I envision that in the future, in-silico models as presented in this paper would become a common and useful technique for research in developmental biology and related research fields, particularly regenerative medicine, tissue engineering and cancer therapeutics.     

The CarD/CarG regulatory complex is required for the action of several members of the large set of Myxococcus xanthus extracytoplasmic function σ factors

Extracytoplasmic function (ECF) σ factors are critical players in signal transduction networks involved in bacterial response to environmental changes. The Myxococcus xanthus genome reveals ～45 putative ECF‐σ factors, but for the overwhelming majority, the specific signals or mechanisms for selective activation and regulation remain unknown. One well‐studied ECF‐σ, CarQ, binds to its anti‐σ, CarR, and is inactive in the dark but drives its own expression from promoter P_QRS on illumination. This requires the CarD/CarG complex, the integration host factor (IHF) and a specific CarD‐binding site upstream of P_QRS. Here, we show that DdvS, a previously uncharacterized ECF‐σ, activates its own expression in a CarD/CarG‐dependent manner but is inhibited when specifically bound to the N‐terminal zinc‐binding anti‐σ domain of its cognate anti‐σ, DdvA. Interestingly, we find that the autoregulatory action of 11 other ECF‐σ factors studied here depends totally or partially on CarD/CarG but not IHF. In silico analysis revealed possible CarD‐binding sites that may be involved in direct regulation by CarD/CarG of target promoter activity. CarD/CarG‐linked ECF‐σ regulation likely recurs in other myxobacteria with CarD/CarG orthologous pairs and could underlie, at least in part, the global regulatory effect of the complex on M. xanthus gene expression.     

Micelle‐enhanced spectrofluorimetric method for determination of sitagliptin and identification of potential alkaline degradation products using LC‐MS

A novel, quick, simple and highly sensitive spectrofluorimetric method was developed and validated for the determination of sitagliptin (SG) in its pharmaceutical formulations. The proposed method is based on investigation of the fluorescence spectral behavior of sitagliptin in an SDS micellar system. In an aqueous solution of phosphate buffer pH 4.0, the fluorescence intensity of SG in the presence of SDS was greatly enhanced, by 200%, i.e. twofold enhancement. The fluorescence intensity of SG was measured at 300 nm after excitation at 270 nm. The method showed good linearity in the range 0.03–10.0 µg/mL with a good correlation coefficient (r = 0.9998). The limits of detection and quantitation values were 5.31 and 16.1 ng/mL, respectively. The proposed method was successfully applied to the analysis of SG in its single and co‐formulated commercial tablets; the results were in good agreement with those obtained using a reference method. Application of the proposed method was extended to stability studies of SG after exposure to different forced degradation conditions according to the ICH guidelines, such as acidic, alkaline, thermal, photo‐ and oxidative stress. The chemical structure of certain potential degradation products (DPs) were investigated using LC‐MS. Copyright © 2013 John Wiley & Sons, Ltd.     

Steady‐state and synchronous spectrofluorimetric methods for simultaneous determination of aliskiren hemifumarate and amlodipine besylate in dosage forms

Aliskiren hemifumarate (ALS) and amlodipine besylate (AML) were simultaneously determined by two different spectrofluorimetric techniques. The first technique depends on direct measurement of the steady‐state fluorescence intensities of ALS and AML at 313 nm and 452 nm upon excitation at 290 and 375 nm, respectively, in a solvent composed of methanol and water (10: 90, v/v) . The second technique utilizes synchronous fluorimetric quantitative screening of the emission spectra of ALS and AML at 272 and 366 nm, respectively using Δλ of 97 nm. Effects of different solvents and surfactants on relative fluorescence intensity were studied. The method was validated according to ICH guidelines. Linearity, accuracy and precision were found to be satisfactory in both techniques over the concentration ranges of 1–15 and 0.4–4 µg/mL for ALS and AML, respectively. In the first technique, limit of detection and limit of quantification were estimated and found to be 0.256 and 0.776 µg/mL for ALS as well as 0.067 and 0.204 µg/mL for AML, respectively. Also, limit of detection and limit of quantification were calculated in the synchronous method and found to be 0.293 and 0.887 µg/mL for ALS as well as 0.034 and 0.103 µg/mL for AML, respectively. The methods were successfully applied for the determination of the two drugs in their co‐formulated tablets. The results were compared statistically with reference methods and no significant difference was found. The developed methods are rapid, sensitive, inexpensive and accurate for the quality control and routine analysis of the cited drugs in bulk and in pharmaceutical preparations without pre‐separation. Copyright © 2014 John Wiley & Sons, Ltd.     

Seed germination at different temperatures and seedling emergence at different depths of Rhamnus spp

Rhamnus alaternus and R. ludovici-salvatoris, two Mediterranean shrubs with different geographic distributions, have shown important differences in seedling recruitment capacity. The objectives of this work were to determine the ability of these species to germinate seeds under different temperature ranges, as well as the capacity of seedlings to emerge from different burial depths, in order to better understand their regeneration processes. Two different experiments were performed. In the first one, seed germination was studied in Petri dishes and in the dark at different temperature regimes: a) 5–15°C, b) 10–20°C and c) 15–25°C (12h/12h). In the second experiment, seedling emergence capacity from different burial depths (0.5, 2 and 5 cm) was tested. R. ludovici-salvatoris showed a significantly higher final germination rates, a lower dormancy period, and average time response at 10–20°C than at other temperature ranges, although differences were much greater when seeds were subjected to the 5–15°C temperature regime. By contrast, R. alaternus did not show significant differences between treatments (5–15°C and 10–20°C) in germination behavior. Seedling emergence of both species was lower and slower when seeds were buried at 5 cm. However, R. ludovici-salvatoris always showed a lower seedling emergence capacity than R. alaternus at any burial depth. The low ability of R. ludovici-salvatoris to germinate seeds and emerge between 5–15°C, even from shallow depths, is discussed in relation to its low regeneration capacity and declining geographic distribution.     

Hepatic HMOX1 Expression Positively Correlates with Bach-1 and miR-122 in Patients with HCV Mono and HIV/HCV Coinfection

Aim

To analyze the expression of HMOX1 and miR-122 in liver biopsy samples obtained from HCV mono-and HIV/HCV co-infected patients in relation to selected clinical parameters, histological examination and IL-28B polymorphism as well as to determine whether HMOX1 expression is dependent on Bach-1.

Materials and Methods

The study group consisted of 90 patients with CHC: 69 with HCV mono and 21 with HIV/HCV co-infection. RT-PCR was used in the analysis of HMOX1, Bach-1 and miR-122 expression in liver biopsy samples and in the assessment of IL-28B single-nucleotide polymorphism C/T (rs12979860) in the blood. Moreover in liver biopsy samples an analysis of HO-1 and Bach-1 protein level by Western Blot was performed.

Results

HCV mono-infected patients, with lower grading score (G<2) and higher HCV viral load (>600000 IU/mL) demonstrated higher expression of HMOX1. In patients with HIV/HCV co-infection, the expression of HMOX1 was lower in patients with lower lymphocyte CD4 count and higher HIV viral load. IL28B polymorphism did not affect the expression of either HMOX1 or miR-122. Higher HMOX1 expression correlated with higher expression of Bach-1 (Spearman’s ρ = 0.586, p = 0.000001) and miR-122 (Spearman’s ρ = 0.270, p = 0.014059).

Conclusions

HMOX1 and miR-122 play an important role in the pathogenesis of CHC in HCV mono-and HIV/HCV co-infected patients. Reduced expression of HMOX1 in patients with HIV/HCV co-infection may indicate a worse prognosis in this group. Our results do not support the importance of Bach-1 in repression of HMOX1 in patients with chronic hepatitis C.     

Piericidin A Aggravates Tau Pathology in P301S Transgenic Mice

ObjectiveThe P301S mutation in exon 10 of the tau gene causes a hereditary tauopathy. While mitochondrial complex I inhibition has been linked to sporadic tauopathies. Piericidin A is a prototypical member of the group of the piericidins, a class of biologically active natural complex I inhibitors, isolated from streptomyces spp. with global distribution in marine and agricultural habitats. The aim of this study was to determine whether there is a pathogenic interaction of the environmental toxin piericidin A and the P301S mutation.MethodsTransgenic mice expressing human tau with the P301S-mutation (P301S^+/+) and wild-type mice at 12 weeks of age were treated subcutaneously with vehicle (N = 10 P301S^+/+, N = 7 wild-type) or piericidin A (N = 9 P301S^+/+, N = 9 wild-type mice) at a dose of 0.5 mg/kg/d for a period of 28 days via osmotic minipumps. Tau pathology was measured by stereological counts of cells immunoreative with antibodies against phosphorylated tau (AD2, AT8, AT180, and AT100) and corresponding Western blot analysis.ResultsPiericidin A significantly increased the number of phospho-tau immunoreactive cells in the cerebral cortex in P301S^+/+ mice, but only to a variable and mild extent in wild-type mice. Furthermore, piericidin A led to increased levels of pathologically phosphorylated tau only in P301S^+/+ mice. While we observed no apparent cell loss in the frontal cortex, the synaptic density was reduced by piericidin A treatment in P301S^+/+ mice.DiscussionThis study shows that exposure to piericidin A aggravates the course of genetically determined tau pathology, providing experimental support for the concept of gene-environment interaction in the etiology of tauopathies.     

Household Transmission of Influenza A(H1N1)pdm09 in the Pandemic and Post-Pandemic Seasons

Background

The transmission of influenza viruses occurs person to person and is facilitated by contacts within enclosed environments such as households. The aim of this study was to evaluate secondary attack rates and factors associated with household transmission of laboratory-confirmed influenza A(H1N1)pdm09 in the pandemic and post-pandemic seasons.

Methods

During the 2009–2010 and 2010–2011 influenza seasons, 76 sentinel physicians in Navarra, Spain, took nasopharyngeal and pharyngeal swabs from patients diagnosed with influenza-like illness. A trained nurse telephoned households of those patients who were laboratory-confirmed for influenza A(H1N1)pdm09 to ask about the symptoms, risk factors and vaccination status of each household member.

Results

In the 405 households with a patient laboratory-confirmed for influenza A(H1N1)pdm09, 977 susceptible contacts were identified; 16% of them (95% CI 14–19%) presented influenza-like illness and were considered as secondary cases. The secondary attack rate was 14% in 2009–2010 and 19% in the 2010–2011 season (p = 0.049), an increase that mainly affected persons with major chronic conditions. In the multivariate logistic regression analysis, the risk of being a secondary case was higher in the 2010–2011 season than in the 2009–2010 season (adjusted odds ratio: 1.72; 95% CI 1.17–2.54), and in children under 5 years, with a decreasing risk in older contacts. Influenza vaccination was associated with lesser incidence of influenza-like illness near to statistical significance (adjusted odds ratio: 0.29; 95% CI 0.08–1.03).

Conclusion

The secondary attack rate in households was higher in the second season than in the first pandemic season. Children had a greater risk of infection. Preventive measures should be maintained in the second pandemic season, especially in high-risk persons.     

Railway Embankments as New Habitat for Pollinators in an Agricultural Landscape

Pollinating insect populations, essential for maintaining wild plant diversity and agricultural productivity, rely on (semi)natural habitats. An increasing human population is encroaching upon and deteriorating pollinator habitats. Thus the population persistence of pollinating insects and their associated ecosystem services may depend upon on man-made novel habitats; however, their importance for ecosystem services is barely understood. We tested if man-made infrastructure (railway embankments) in an agricultural landscape establishes novel habitats that support large populations of pollinators (bees, butterflies, hoverflies) when compared to typical habitats for these insects, i.e., semi-natural grasslands. We also identified key environmental factors affecting the species richness and abundance of pollinators on embankments. Species richness and abundance of bees and butterflies were higher for railway embankments than for grasslands. The occurrence of bare (non-vegetated) ground on embankments positively affected bee species richness and abundance, but negatively affected butterfly populations. Species richness and abundance of butterflies positively depended on species richness of native plants on embankments, whereas bee species richness was positively affected by species richness of non-native flowering plants. The density of shrubs on embankments negatively affected the number of bee species and their abundance. Bee and hoverfly species richness were positively related to wood cover in a landscape surrounding embankments. This is the first study showing that railway embankments constitute valuable habitat for the conservation of pollinators in farmland. Specific conservation strategies involving embankments should focus on preventing habitat deterioration due to encroachment of dense shrubs and maintaining grassland vegetation with patches of bare ground.     

The Increased Risk of Road Crashes in Attention Deficit Hyperactivity Disorder (ADHD) Adult Drivers: Driven by Distraction? Results from a Responsibility Case-Control Study

Background and Objective

Both distractions (external and internal) and attention-deficit/hyperactivity disorder (ADHD) are serious risk factors for traffic crashes and injuries. However, it is still unknown if ADHD (a chronic condition) modifies the effect of distractions (irregular hazards) on traffic crashes. The objective of this study was to assess the effects of distractions and ADHD on traffic crash responsibility.

Methods

A responsibility case-control study was conducted in the adult emergency department of Bordeaux University Hospital, France. Subjects were recruited among drivers injured in a motor vehicle crash between April 2010 and August 2011. Responsibility levels were estimated using a standardized method. Frequencies of exposures were compared between drivers responsible and drivers not responsible for the crash. Independent risk factors were identified using a multivariate logistic regression including test interactions between distractions and ADHD.

Results

A total of 777 subjects were included in the analysis. Factors associated with responsibility were distraction induced by an external event (adjusted OR (aOR)  = 1.47; 95% confidence interval (CI) [1.06–2.05]), distraction induced by an internal thought (aOR = 2.38; CI: [1.50–3.77]) and ADHD (aOR = 2.18 CI: [1.22–3.88]). The combined effect of ADHD and external distractions was strongly associated with responsibility for the crash (aOR = 5.79 CI: [2.06–16.32]). Interaction assessment showed that the attributable proportion due to the interaction among participants with both exposures was 68%.

Discussion

Adults with ADHD are a population at higher risk of being responsible for a road traffic crash when exposed to external distractions. This result reinforces the need to diagnose adult ADHD and to include road safety awareness messages delivered by the physician. Developing advanced driver assistance systems devoted to the management of attention lapses is also increasingly relevant for these drivers.