Mechanical Tensions Regulate Gene Expression in the Xenopus laevis Axial Tissues

During gastrulation and neurulation, the chordamesoderm and overlying neuroectoderm of vertebrate embryos converge under the control of a specific genetic programme to the dorsal midline, simultaneously extending along it. However, whether mechanical tensions resulting from these morphogenetic movements play a role in long-range feedback signaling that in turn regulates gene expression in the chordamesoderm and neuroectoderm is unclear. In the present work, by using a model of artificially stretched explants of Xenopus midgastrula embryos and full-transcriptome sequencing, we identified genes with altered expression in response to external mechanical stretching. Importantly, mechanically activated genes appeared to be expressed during normal development in the trunk, i.e., in the stretched region only. By contrast, genes inhibited by mechanical stretching were normally expressed in the anterior neuroectoderm, where mechanical stress is low. These results indicate that mechanical tensions may play the role of a long-range signaling factor that regulates patterning of the embryo, serving as a link coupling morphogenesis and cell differentiation.

Photochemically induced formation of adhesive hydrogels from sodium alginate, acrylamide, and iron sandwich complexes

Visible light irradiation of an aqueous solution of sodium alginate and organometallic complex [(C5H5)Fe(toluene)]BF4 transforms it into a rigid hydrogel due to crosslinking of the carboxylate groups by the iron ions. Irradiation of the same iron complex together with K2S2O8 initiates the polymerization of acrylamide, which provides an efficient method for light-controlled one-step preparation of alginate-polyacrylamide double network hydrogels, which are capable of gluing wet glass with 100-200 kPa shear strength.

A partial genome assembly of the miniature parasitoid wasp, Megaphragma amalphitanum

Body size reduction, also known as miniaturization, is an important evolutionary process that affects a number of physiological and phenotypic traits and helps animals conquer new ecological niches. However, this process is poorly understood at the molecular level. Here, we report genomic and transcriptomic features of arguably the smallest known insect-the parasitoid wasp, Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae). In contrast to expectations, we find that the genome and transcriptome sizes of this parasitoid wasp are comparable to other members of the Chalcidoidea superfamily. Moreover, compared to other chalcid wasps the gene content of M. amalphitanum is remarkably conserved. Intriguingly, we observed significant changes in M. amalphitanum transposable element dynamics over time, in which an initial burst was followed by suppression of activity, possibly due to a recent reinforcement of the genome defense machinery. Overall, while the M. amalphitanum genomic data reveal certain features that may be linked to the unusual biological properties of this organism, miniaturization is not associated with a large decrease in genome complexity.

The binding of monomeric amyloid β peptide to serum albumin is affected by major plasma unsaturated fatty acids

Human serum albumin (HSA) serves as a natural depot of amyloid β peptide (Aβ). Improvement of Aβ binding to HSA should impede Alzheimer's disease (AD). We developed a method for quantitation of the interaction between monomeric Aβ40/42 and HSA using surface plasmon resonance spectroscopy. The dissociation constant of HSA complex with recombinant Aβ40/42 is 0.2-0.3 μM. Flemish variant of Aβ40 has 2.5-10-fold higher affinity to HSA. The parameters of the HSA-Aβ interaction are selectively sensitive to HSA binding of major plasma unsaturated fatty acids and Cu²⁺. Linoleic and arachidonic acids promote the HSA-Aβ42 interaction. The developed methodology for quantitation of HSA-Aβ interaction may serve as a tool for search of compounds favoring HSA-Aβ interaction, thereby preventing AD progression.

Metagenomic analysis of microbial community of a parasitoid wasp Megaphragma amalphitanum

The vast majority of multicellular organisms coexist with bacterial symbionts that may play various roles during their life cycle. Parasitoid wasp Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae) belongs to the smallest known insects whose size is comparable with some bacteria. Using 16S rRNA gene sequencing and Whole Genome Sequencing (WGS), we described microbiota diversity for this arthropod and its potential impact on their lifecycle. Metagenomic sequences were deposited to SRA database which is available at NCBI with accession number SRX2363723 and SRX2363724. We found that small body size and limited lifespan do not lead to a significant reduction of bacterial symbionts diversity. At the same time, we show here a specific feature of microbiota composition in M. amalphitanum – the absence of the Rickettsiaceae family representatives that are known to cause sex-ratio distortion in arthropods and well represented in other populations of parasitoid wasps.

State of the Art of Chromosome 18-Centric HPP in 2016: Transcriptome and Proteome Profiling of Liver Tissue and HepG2 Cells

A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R² ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .

Identification of novel microRNA genes in freshwater and marine ecotypes of the three-spined stickleback (Gasterosteus aculeatus)

The three-spined stickleback (Gasterosteus aculeatus L.) is an important model organism for studying the molecular mechanisms of speciation and adaptation to salinity. Despite increased interest to microRNA discovery and recent publication on microRNA prediction in the three-spined stickleback using bioinformatics approaches, there is still a lack of experimental support for these data. In this paper, high-throughput sequencing technology was applied to identify microRNA genes in gills of the three-spined stickleback. In total, 595 miRNA genes were discovered; half of them were predicted in previous computational studies and were confirmed here as microRNAs expressed in gill tissue. Moreover, 298 novel microRNA genes were identified. The presence of miRNA genes in selected 'divergence islands' was analysed and 10 miRNA genes were identified as not randomly located in 'divergence islands'. Regulatory regions of miRNA genes were found enriched with selective SNPs that may play a role in freshwater adaptation.

Mitochondrial genome of Megaphragma amalphitanum (Hymenoptera: Trichogrammatidae)

The mitochondrial genome of the parasitic wasp Megaphragma amalphitanum is published in this paper. The mitochondrial DNA (mtDNA) is 15 041 base pairs (bp) in length and contained 13 protein-coding genes, 2 rRNA genes and 22 tRNA genes. The overall base composition of the genome in descending order was 45.67% A, 8.71% C, 39.63% T and 5.99% G, with a significant AT bias of 85.30%.

Nonhydrolyzable ATP analog 5'-adenylyl-imidodiphosphate (AMP-PNP) does not inhibit ATP-dependent scanning of leader sequence of mRNA

The objective of the present work was to determine whether it is possible to use a nonhydrolyzable analog of ATP (AMP-PNP) as an inhibitor of ATP-dependent scanning of the leader sequence of eukaryotic mRNA in translation initiation-. The formation of ribosomal 48S initiation complexes at the start codon of the capped mRNA leader sequence of rabbit β-globin mRNA was studied. The study was carried out in a system composed of individual components of translation initiation. The dependences of the efficiency of formation of 48S initiation complexes on ATP concentration and incubation time were obtained in the absence and presence of AMP-PNP. It was found that AMP-PNP did not affect the efficiency of formation of 48S initiation complexes in all cases under study. We conclude that the uncleavable analog of ATP, AMP-PNP, is not an inhibitor of translation initiation in eukaryotes.

Chromosome 18 transcriptoproteome of liver tissue and HepG2 cells and targeted proteome mapping in depleted plasma: update 2013

We report the results obtained in 2012-2013 by the Russian Consortium for the Chromosome-centric Human Proteome Project (C-HPP). The main scope of this work was the transcriptome profiling of genes on human chromosome 18 (Chr 18), as well as their encoded proteome, from three types of biomaterials: liver tissue, the hepatocellular carcinoma-derived cell line HepG2, and blood plasma. The transcriptome profiling for liver tissue was independently performed using two RNaseq platforms (SOLiD and Illumina) and also by droplet digital PCR (ddPCR) and quantitative RT-PCR. The proteome profiling of Chr 18 was accomplished by quantitatively measuring protein copy numbers in the three types of biomaterial (the lowest protein concentration measured was 10(-13) M) using selected reaction monitoring (SRM). In total, protein copy numbers were estimated for 228 master proteins, including quantitative data on 164 proteins in plasma, 171 in the HepG2 cell line, and 186 in liver tissue. Most proteins were present in plasma at 10(8) copies/μL, while the median abundance was 10(4) and 10(5) protein copies per cell in HepG2 cells and liver tissue, respectively. In summary, for liver tissue and HepG2 cells a "transcriptoproteome" was produced that reflects the relationship between transcript and protein copy numbers of the genes on Chr 18. The quantitative data acquired by RNaseq, PCR, and SRM were uploaded into the "Update_2013" data set of our knowledgebase (www.kb18.ru) and investigated for linear correlations.

[Phosphorescent microanalysis as a new technical platform for molecular diagnostics]

The authors developed a method of phosphorescent multiplex microanalysis (PHOSPHAN) as a new technological platform for a wide scope of molecular diagnostic tasks, and consider the prospects of its application in the article. PHOSPHAN combines the potential of solid-phase microplate analysis with the principle of microarray laser scanning of microzonules with biospecifically bound analyte on the surface of the bottom of microplate holes with consequent real-time registration of the phosphorescent signal. The sensitivity of the instrumental detection system is approximately 1000 molecules of Pt coproporphyrin mark in the illuminated area of scanning of 30 microns in diameter. PHOSPHAN makes it possible to detect separate microbial cells in samples and increases the sensitivity of analyte detection in microaliquots eluted from blood spots dried on paper blanks. All the key elements of this technology are protected with Russian patents.

[Treatment of patients with pneumonia, chronic obstructive bronchitis and mucoviscidosis with cefpirome]

Twenty two patients with inflammatory respiratory tract infection were treated with cefpirome. Among the patients 14 were with severe pneumonia, 4 with exacerbated obstructive chronic purulent bronchitis and 4 with mucoviscidosis. All the patients were subjected to clinical, laboratory and x-ray examinations, electrocardiography, estimation of the external respiration and sputum bacteriological tests. The cefpirome susceptibility was determined by the agar diffusion assay with standard disks from Roussel Uclaf. Cefpirome was administered by slow intravenous infusion in a daily dose of 2 to 4 g every 12 hours depending on the disease severity. After 2 or 3 days of the patient afebrile temperature and normal differential blood count the therapy was discontinued. The favourable time course of the disease was recorded in 12 out of the 14 patients with pneumonia. Recovery and clinical improvement were stated in 64.3 and 21.4 per cent of the cases respectively. In 2 patients the treatment failed. In all the patients with exacerbated severe chronic purulent bronchitis the cefpirome therapy resulted in the disease remission. The clinical effect of the mucoviscidosis treatment was observed in 3 out of the 4 patients. The drug tolerance in the doses used was good.

[The dependence of the cytokinetic effects of alkylating antitumor preparations on the phase of the hepatocyte cell cycle in regenerating liver]

Effects of alkylating antitumor drugs on resting (G0 phase of cell cycle) and proliferating (G1, S, G2 and M phases) hepatocytes were studied in regenerating mouse liver. Cell cycle kinetics (fraction of labeled mitoses, labeling and mitotic indices) were determined by 3H-thymidine autoradiography. Dipin and fotrin as a DNA-damaging agents attack mainly resting (G0) and proliferating (G1) cells. Effect of the damage results in the inhibition of DNA synthesis and G2 phase arrest in the following mitotic cycle. An alkylating drug phopurin as well as ara-C both suppress the mitotic progression in proliferating hepatocytes and do not influence the resting cells.

Interpretation of Snow-Climate Feedback as Produced by 17 General Circulation Models

Snow feedback is expected to amplify global warming caused by increasing concentrations of atmospheric greenhouse gases. The conventional explanation is that a warmer Earth will have less snow cover, resulting in a darker planet that absorbs more solar radiation. An intercomparison of 17 general circulation models, for which perturbations of sea surface temperature were used as a surrogate climate change, suggests that this explanation is overly simplistic. The results instead indicate that additional amplification or moderation may be caused both by cloud interactions and longwave radiation. One measure of this net effect of snow feedback was found to differ markedly among the 17 climate models, ranging from weak negative feedback in some models to strong positive feedback in others.

[Bioavailability of dalargin and its metabolism during intranasal administration to rats]

Bioavailability and metabolism of a peptide drug Dalargin with a chemical structure Tyr-D-Ala-Gly-Phe-Leu-Arg have been examined. Dalargin is applied for the treatment of gastric and duodenal ulcers. Bioavailability was estimated following intramuscular (i/m) and intranasal (i/n) routes of administration of 3H-dalargin in anesthetized dogs. The highest dalargin concentration was achieved about 10 min after i/m and i/n administration. Absolute dalargin bioavailability was 15% and 8%, while its elimination half-life was 23.2 min and 21.3 min, respectively. Tyrosine, N-terminated tetra- and pentapeptides were the main metabolites detected in the blood. The intranasal route of dalargin administration is concluded to be possible in the clinical practice.