FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution

The datasets on gene expression are the valuable source of information about the functional state of an organism. Recently, we have acquired the large dataset on expression of segmentation genes in the Drosophila blastoderm. To provide efficient access to the data, we have developed the FlyEx database (http://urchin.spbcas.ru/flyex). FlyEx contains 4716 images of 14 segmentation gene expression patterns obtained from 1579 embryos and 9 500 000 quantitative data records. Reference data are available for all segmentation genes in cycles 11–13 and all temporal classes of cycle 14A. FlyEx supports operations on images of gene expression patterns. The database can be used to examine the quality of data, analyze the dynamics of formation of segmentation gene expression domains, as well as to estimate the variability of gene expression patterns. Currently, a user is able to monitor and analyze the dynamics of formation of segmentation gene expression domains over the whole period of segment determination, that amounts to 1.5 h of development. FlyEx supports the data downloads and construction of personal reference datasets, that makes it possible to more effectively use and analyze data

Comparative population structure of <i>Plasmodium malariae</i> and <i>Plasmodium falciparum</i> under different transmission settings in Malawi

&lt;b&gt;Background:&lt;/b&gt; Described here is the first population genetic study of Plasmodium malariae, the causative agent of quartan malaria. Although not as deadly as Plasmodium falciparum, P. malariae is more common than previously thought, and is frequently in sympatry and co-infection with P. falciparum, making its study increasingly important. This study compares the population parameters of the two species in two districts of Malawi with different malaria transmission patterns - one seasonal, one perennial - to explore the effects of transmission on population structures. &lt;BR/&gt; &lt;b&gt;Methods:&lt;/b&gt; Six species-specific microsatellite markers were used to analyse 257 P. malariae samples and 257 P. falciparum samples matched for age, gender and village of residence. Allele sizes were scored to within 2 bp for each locus and haplotypes were constructed from dominant alleles in multiple infections. Analysis of multiplicity of infection (MOI), population differentiation, clustering of haplotypes and linkage disequilibrium was performed for both species. Regression analyses were used to determine association of MOI measurements with clinical malaria parameters. &lt;BR/&gt; &lt;b&gt;Results:&lt;/b&gt; Multiple-genotype infections within each species were common in both districts, accounting for 86.0% of P. falciparum and 73.2% of P. malariae infections and did not differ significantly with transmission setting. Mean MOI of P. falciparum was increased under perennial transmission compared with seasonal (3.14 vs 2.59, p = 0.008) and was greater in children compared with adults. In contrast, P. malariae mean MOI was similar between transmission settings (2.12 vs 2.11) and there was no difference between children and adults. Population differentiation showed no significant differences between villages or districts for either species. There was no evidence of geographical clustering of haplotypes. Linkage disequilibrium amongst loci was found only for P. falciparum samples from the seasonal transmission setting. &lt;BR/&gt; &lt;b&gt;Conclusions:&lt;/b&gt; The extent of similarity between P. falciparum and P. malariae population structure described by the high level of multiple infection, the lack of significant population differentiation or haplotype clustering and lack of linkage disequilibrium is surprising given the differences in the biological features of these species that suggest a reduced potential for out-crossing and transmission in P. malariae. The absence of a rise in P. malariae MOI with increased transmission or a reduction in MOI with age could be explained by differences in the duration of infection or degree of immunity compared to P. falciparum

Lateral Gene Expression in Drosophila Early Embryos Is Supported by Grainyhead-Mediated Activation and Tiers of Dorsally-Localized Repression

The general consensus in the field is that limiting amounts of the transcription factor Dorsal establish dorsal boundaries of genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, while repressors establish ventral boundaries. Yet recent studies have provided evidence that repressors act to specify the dorsal boundary of intermediate neuroblasts defective (ind), a gene expressed in a stripe along the DV axis in lateral regions of the embryo. Here we show that a short 12 base pair sequence (“the A-box”) present twice within the ind CRM is both necessary and sufficient to support transcriptional repression in dorsal regions of embryos. To identify binding factors, we conducted affinity chromatography using the A-box element and found a number of DNA-binding proteins and chromatin-associated factors using mass spectroscopy. Only Grainyhead (Grh), a CP2 transcription factor with a unique DNA-binding domain, was found to bind the A-box sequence. Our results suggest that Grh acts as an activator to support expression of ind, which was surprising as we identified this factor using an element that mediates dorsally-localized repression. Grh and Dorsal both contribute to ind transcriptional activation. However, another recent study found that the repressor Capicua (Cic) also binds to the A-box sequence. While Cic was not identified through our A-box affinity chromatography, utilization of the same site, the A-box, by both factors Grh (activator) and Cic (repressor) may also support a “switch-like” response that helps to sharpen the ind dorsal boundary. Furthermore, our results also demonstrate that TGF-β signaling acts to refine ind CRM expression in an A-box independent manner in dorsal-most regions, suggesting that tiers of repression act in dorsal regions of the embryo

Pharmacokinetic Interactions of Phenosanic Acid with Valproic Acid and Carbamazepine in Dogs

Phenosanic acid prevents convulsions, reduces the frequency of epileptic seizures, and improves cognitive, intellectual and mnestic functions in patients with epilepsy. Therefore, phenosanic acid-based medicinal products are promising candidates for inclusion in combination antiepileptic therapy. In order to combine medicinal products rationally and ensure that the therapy is safe, it is useful to study the pharmacokinetic interaction of medicinal products planned for clinical co-administration.The aim of the study was to examine single-dose pharmacokinetic interactions between Dibufelon® 200 mg capsules (PIQ-PHARMA LLC, Russia) and two medicinal products planned for clinical co-application with it, namely, valproic acid and carbamazepine, in sexually mature dogs.Materials and methods: the study included medicinal products of phenosanic acid (Dibufelon® 200 mg capsules by PIQ-PHARMA LLC, Russia), valproic acid (300 mg prolonged-release film-coated tablets), and carbamazepine (200 mg tablets). The medicinal products were administered to beagle dogs (2 groups of 9 males each) as a single oral dose separately and in the following combinations: phenosanic acid with valproic acid and phenosanic acid with carbamazepine. Dose selection involved adjusting maximum human therapeutic doses using interspecies conversion factors. Phenosanic acid was administered at a dose of 24 mg/kg; valproic acid and carbamazepine were administered at a dose of 60 mg/kg. Blood sampling took place at baseline and in 0.5, 0.75, 1, 2, 4, 6, 8, 10, and 24 h after dosing. Plasma concentrations of active substances were determined by HPLC-UV. Pharmacokinetic interactions were evaluated by changes in the main pharmacokinetic parameters (Сmax, Тmax, AUC0-24, MRT, Т1/2).Results: the study demonstrated rapid gastrointestinal absorption and prolonged systemic circulation of phenosanic acid administered separately (Tmax 2–4 h, T1/2 13–28 h) and combined with valproic acid (Tmax 2 h, T1/2 22 h). When administered with carbamazepine, phenosanic acid was eliminated from the systemic blood flow faster (T1/2 7.4 h).Conclusions: co-administration of phenosanic acid and valproic acid medicinal products had no significant effect on their respective pharmacokinetics. Whereas, the combination of phenosanic acid and carbamazepine demonstrated a significant decrease in the Tmax values of phenosanic acid and the MRT values of carbamazepine. The pharmacokinetic changes suggestive of a possible interaction between phenosanic acid and carbamazepine need further clinical investigation

Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

Preclinical Evaluation of Esomeprazole Safety and Toxicokinetics

Esomeprazole, the S-isomer of omeprazole, is a second-generation proton pump inhibitor widely used for acid-related diseases of the oesophagus, stomach, and duodenum (peptic ulcer, gastro-oesophageal reflux disease, etc.). Studies on esomeprazole safety and toxicokinetics (TK) are essential for increasing the number of modified-release esomeprazole products manufactured in Russia.The aim of the study was to compare the safety and toxicokinetics of a new esomeprazole product, 40 mg modifiedrelease capsules (Valenta Pharm JSC, Russia), and Nexium® 40 mg film-coated tablets (AstraZeneca AB, Sweden).Materials and methods. This toxicity study involved oral administration of esomeprazole 40 mg modified-release capsules (Valenta Pharm JSC, Russia) and Nexium® 40 mg film-coated tablets (AstraZeneca AB, Sweden) to 5 groups of rabbits (8 males and 8 females per group) for 28 days at a dose of 1 or 3 capsules, or tablets, corresponding to approximately 4.8 or 14.3 maximum human therapeutic doses (MHTDs), respectively. Comparisons included general toxicity, local tolerance, safety pharmacology, effects on immune system organs, reproductive toxicity, and basic TK parameters (Cmax, Tmax, AUC0-24, MRT, and T1/2).Results. No toxic effects, including local irritation and immunotoxicity, were observed for the test product. The safety pharmacology testing demonstrated the safety of repeated oral administration of the test product for the cardiovascular, excretory, respiratory systems and the liver. The test product did not affect the reproductive system of male and female rabbits. The No Observed Adverse Effect Level (NOAEL) was determined to be 14.3 MHTDs. According to the TK parameters evaluated after single and repeated oral administration, the test product and Nexium® demonstrated comparable TK profiles.Conclusions. The study demonstrated a favourable safety profile for the test product. All the test product parameters studied were comparable with those of Nexium®. Positive clinical experience with Nexium® supports the data obtained for the new esomeprazole product. Thea safety of these medicinal products may be considered similar

Considerations for the Bioanalytical Part of Equivalence Studies of Biosimilar Nadroparin Calcium

According to current regulatory views, a comparative study of the pharmacodynamics (PD) of low molecular weight heparin (LMWH) products and confirmation of their equivalence require comparing three PD markers: the anti-Xa activity, the anti-IIa activity, and the tissue factor pathway inhibitor (TFPI) concentration. The aim of this study was to analyse the features specific to the bioanalytical part of an equivalence study of a nadroparin calcium biosimilar after single subcutaneous administration. Material and methods: the anti-Xa and anti-IIa activity values and TFPI content were determined in human plasma samples obtained after single subcutaneous administration of the test and the reference product in the same dose, using commercially available reagent kits and pre-validated assays. The authors calculated the main PD parameters (surrogate pharmacokinetic markers), namely the maximum activity or concentration (Amax or Cmax), time to maximum activity or concentration (Tmax), area under the activity–time (or concentration–time) curve (AUC ), and half-life period (T1/2), by means of model-independent statistical moment analysis and carried out further statistical testing of the parameters. Results: the anti-Xa activity and TFPI concentration results provided for  the  possibility  of  calculating  and  comparing  the PD parameters (Amax or Cmax, AUC0-24, AUC0-∞, Tmax, T1/2) and estimating the confidence intervals that are necessary to confirm the bioequivalence of the studied products. The anti-IIa activity data had a characteristic pattern of slight fluctuations around one level, which prevented the calculation and comparison of PD parameters. Conclusion: the study identified specific features to consider when planning comparative PD studies of nadroparin calcium products. Firstly, it is feasible to divide samples into two test aliquots (one for anti-Xa and anti-IIa activity determination, the other for TFPI analysis) at the moment of collection in order to perform the analytical step correctly. Secondly, there is no need in full validation for the bioanalytical assays of the anti-Xa and anti-II activity and TFPI content in human plasma validated in the concentration ranges of 0.024–0.182 IU/mL, 0.0069–0.052 IU/mL and 1.56–100 ng/mL, respectively; a confirmation that the active ingredient does not interfere with the analytical procedure is adequate for the purpose. Finally, the data obtained may not allow for calculating PD parameters and comparing confidence intervals for all three markers. The listed considerations may be relevant for other LMWH products as well

Regional Genetic Structure in the Aquatic Macrophyte Ruppia cirrhosa Suggests Dispersal by Waterbirds

The evolutionary history of the genus Ruppia has been shaped by hybridization, polyploidisation and vicariance that have resulted in a problematic taxonomy. Recent studies provided insight into species circumscription, organelle takeover by hybridization, and revealed the importance of verifying species identification to avoid distorting effects of mixing different species, when estimating population connectivity. In the present study, we use microsatellite markers to determine population diversity and connectivity patterns in Ruppia cirrhosa including two spatial scales: (1) from the Atlantic Iberian coastline in Portugal to the Siculo-Tunisian Strait in Sicily and (2) within the Iberian Peninsula comprising the Atlantic-Mediterranean transition. The higher diversity in the Mediterranean Sea suggests that populations have had longer persistence there, suggesting a possible origin and/or refugial area for the species. The high genotypic diversities highlight the importance of sexual reproduction for survival and maintenance of populations. Results revealed a regional population structure matching a continent-island model, with strong genetic isolation and low gene flow between populations. This population structure could be maintained by waterbirds, acting as occasional dispersal vectors. This information elucidates ecological strategies of brackish plant species in coastal lagoons, suggesting mechanisms used by this species to colonize new isolated habitats and dominate brackish aquatic macrophyte systems, yet maintaining strong genetic structure suggestive of very low dispersal.Fundacao para a Cincia e Tecnologia (FCT, Portugal) [PTDC/MAR/119363/2010, BIODIVERSA/0004/2015, UID/Multi/04326/2013]Pew FoundationSENECA FoundationMurcia Government, Spain [11881/PI/09]FCT Investigator Programme-Career Development [IF/00998/2014]Spanish Ministry of Education [AP2008-01209]European Community [00399/2012]info:eu-repo/semantics/publishedVersio