Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content

BACKGROUND

Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding.

RESULTS

We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil.

CONCLUSIONS

This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.

Alternative splicing during mammalian organ development

Alternative splicing (AS) is pervasive in mammalian genomes, yet cross-species comparisons have been largely restricted to adult tissues and the functionality of most AS events remains unclear. We assessed AS patterns across pre- and postnatal development of seven organs in six mammals and a bird. Our analyses revealed that developmentally dynamic AS events, which are especially prevalent in the brain, are substantially more conserved than nondynamic ones. Cassette exons with increasing inclusion frequencies during development show the strongest signals of conserved and regulated AS. Newly emerged cassette exons are typically incorporated late in testis development, but those retained during evolution are predominantly brain specific. Our work suggests that an intricate interplay of programs controlling gene expression levels and AS is fundamental to organ development, especially for the brain and heart. In these regulatory networks, AS affords substantial functional diversification of genes through the generation of tissue- and time-specific isoforms from broadly expressed genes.

Development of a low-density panel for genomic selection of pigs in Russia

Genomic selection is routinely used worldwide in agricultural breeding. However, in Russia, it is still not used to its full potential partially due to high genotyping costs. The use of genotypes imputed from the low-density chips (LD-chip) provides a valuable opportunity for reducing the genotyping costs. Pork production in Russia is based on the conventional 3-tier pyramid involving 3 breeds; therefore, the best option would be the development of a single LD-chip that could be used for all of them. Here, we for the first time have analyzed genomic variability in 3 breeds of Russian pigs, namely, Landrace, Duroc, and Large White and generated the LD-chip that can be used in pig breeding with the negligible loss in genotyping quality. We have demonstrated that out of the 3 methods commonly used for LD-chip construction, the block method shows the best results. The imputation quality depends strongly on the presence of close ancestors in the reference population. We have demonstrated that for the animals with both parents genotyped using high-density panels high-quality genotypes (allelic discordance rate < 0.05) could be obtained using a 300 single nucleotide polymorphism (SNP) chip, while in the absence of genotyped ancestors at least 2,000 SNP markers are required. We have shown that imputation quality varies between chromosomes, and it is lower near the chromosome ends and drops with the increase in minor allele frequency. Imputation quality of the individual SNPs correlated well across breeds. Using the same LD-chip, we were able to obtain comparable imputation quality in all 3 breeds, so it may be suggested that a single chip could be used for all of them. Our findings also suggest that the presence of markers with extremely low imputation quality is likely to be explained by wrong mapping of the markers to the chromosomal positions.

[Cycloferon efficacy in treatment of upper respiratory tract infections: systematic review and meta-analysis]

Medical scientific sources about randomized clinical trials of Cycloferon were studied as a single plot of 531 articles. AIM was to get the generalized cycloferon efficacy's assessment in comparison with basic therapies curing the otorhinolaryngologic diseases. Groups heterogeneity and responding parameters' variability were estimated also. Comparison groups were symmetric enough to annihilate end-point variabilities, so the results' interpretations were clear enough and vector of clinical effects was detectable. Comparison groups were integrated to increase statistical power of metaanalysis. In result, cycloferon additional administration in treatment of otorhinolaryngologic diseases added 25% to absolute and relative usefulness of medical intervention. Also cycloferon increased 3,5 times the chances of recovery and absence of recurrent exacerbation.

Conservation, evolution, and regulation of splicing during prefrontal cortex development in humans, chimpanzees, and macaques

Changes in splicing are known to affect the function and regulation of genes. We analyzed splicing events that take place during the postnatal development of the prefrontal cortex in humans, chimpanzees, and rhesus macaques based on data obtained from 168 individuals. Our study revealed that among the 38,822 quantified alternative exons, 15% are differentially spliced among species, and more than 6% splice differently at different ages. Mutations in splicing acceptor and/or donor sites might explain more than 14% of all splicing differences among species and up to 64% of high-amplitude differences. A reconstructed trans-regulatory network containing 21 RNA-binding proteins explains a further 4% of splicing variations within species. While most age-dependent splicing patterns are conserved among the three species, developmental changes in intron retention are substantially more pronounced in humans.

[Clinical efficacy of the immunomodulatory agent cycloferon (tablets) in viral respiratory infections: Results of a systematic review and meta-analysis]

The authors carried out a systematic review and subsequent meta-analysis of randomized clinical trials evaluating the efficacy of the immunomodulator agent cycloferon as tablets in adults and children with viral respiratory diseases. A total estimate of its clinical efficacy was obtained in terms of compared heterogeneous groups and response variables. The data published in 16 articles were used to calculate the formal parameters of the clinical efficacy of cycloferon (increased absolute and relative benefits, odds ratio (OR); the number of patients needed to be additionally treated with cycloferon to achieve a favorable outcome or to prevent a poor outcome in one patient, etc.). High heterogeneity hampered the unequivocal interpretation of results; however, combining the compared homogeneous groups in the meta-analysis (with adjustments for fixed and random effects) increased the statistical power of the investigation. In children aged 6 to 18 years, the OR for the positive effect of the drug (no new cases after its preventive administration) was 5.3 (95% confidence interval (CI), 4.8-5.9), heterogeneity test, χ² = 249.5; p=0.000...; I² = 94.8% (95% CI, 92.7-96.3%). This suggested the heterogeneity of clinical trial data and extrapolated this estimate to medical practice. The use of cycloferon in adults to treat acute respiratory viral infection enhanced their chances of enduring the disease in a mild form and avoiding serious complications: the OR for positive outcomes was 9.7 (95% CI, 7.0-13.0), while the effect was more homogeneous than in children (heterogeneity test, χ² = 7.4; p=0.061...; I² = 59.4% (95% CI, 0-86.5). Thus, the use of cycloferon to treat and prevent acute viral respiratory infections showed a more than 5-fold increase in the probability of avoiding the disease or enduring the latter in a mild form.

[Meta-analytic assessment of parenteral cytoflavin effectiveness in different neurologic disorders]

AIM

To carry out an integral quantitative assessment of the clinical efficacy of parenteral use of cytoflavin in treatment of patients with CNS disorders based on the systemic selection of published controlled clinical trials and their meta-analysis.

MATERIAL AND METHODS

Twenty-one high evidence-based studies on the efficacy of parenteral use of cytoflavin in different CNS disorders (4314 patients) have been analyzed. Comparisons with basic treatment groups were undertaken to clarify the drug clinical effects adjusted for heterogeneity and variability of response parameters.

RESULTS AND CONCLUSION

An analysis of formalized efficacy indicators (increase in the absolute and relative value, odds ratio (OR) etc.) has demonstrated the advantages of cytoflavin. Group combination has increased the statistical power of the meta-analysis. Two models with fixed (Mantel-Haenszel amendment) and random effects were used. All the estimation protocols in different clinical groups of patients with neurologic diseases provided similar results and confirmed the stability of calculated values irrespective of heterogeneity of data arrays. OR of positive outcomes in neuropathologies treated with cytoflavin was 3,02 with χ2 heterogeneity 427,3 and p = 0,000…, I2= 85,7% (82%; 88%).

[ADJUVANT ENERGY PROTECTION WITH REAMBERIN IN PRACTICE OF INTENSIVE CARE AND RESUSCITATION: META-ANALYSIS DATA ABOUT EFFECTIVENESS (SYSTEMATIC REVIEW).]

THE AIM

a synthesis of evaluations ofReamberin's clinical efficacy as energy protectorfor the results of a meta-analysis of published data obtained during controlled clinical studies with the same design and a high level of evidence.

MATERIALS AND METHODS

To estimate succinic acid based remedy for infusions (reamberin), the meta-analysis was undertaken with data of reamberin use in intensive care, resuscitation departments, in critical post surgery period, in oncology (multiple chemotherapy of tumors), in emergent toxicology and pediatrics. 32 controlled randomized trials and all together 6221 patients were included.

RESULTS

Unified indicators of clinical efficiency were systemically and thoroughly processed with advanced statistic tools, resulting data were sufficient for association and assessment of their heterogeneity in different articles. The adjuvant effects of reamberin were proven, as good outcome frequency enlarged more than by 25%, absolute and relative treatment benefits increased more than by 50%, positive outcome chance grew twice and more.

CONCLUSIONS

According to sensitivity analysis and this meta-analysis results reamberin may be positioned as adjuvant energetic protector valid to improve effectiveness of pharmacologic correction during the treatment of emergencies joint with hypoxia, energy deficiencies and vegetative disregulations.

[Metaanalytic Approach to Evaluate Clinical Effectiveness of Infusion Succinnate-Containing Remaxol in Liver Pathologies of Diverse Genesis]

Metaanalysis was applied to the published data on the randomized clinical trials of Remaxol in the treatment of various diseases associated with the liver injury: chronic hepatitis B and C, severe ethanol intoxication, drug-induced pathologies due to tuberculosis chemotherapy, leptospirosis, psoriasis, tumor polychemotherapy. The database included information on 2250 patients. The total number of the patients of the control group (n = 1099) were treated according to the routine schemes (active placebo) and that of the main group (n = 1151) were additionally treated with Remaxol. Combination of the frequency characteristics of the positive outcomes (% of elimination of the main clinical symptoms and complications) in the patients of the reference groups allowed to estimate the general clinical efficacy of Remaxol, that was equal to 1.75 by the outcome frequency characteristics. The odds ratio of the positive outcomes equaled 5.3 [1.8; 17.0] and the number of the patients needed to treat (NPNT) equaled 8 [6; 14]. Therefore, the infusion Remaxol hepatoprotector based on succinic acid was shown to have statistically and clinically significant therapeutic efficacy in pharmacologic correction of the liver pathologies of diverse genesis.

Transcriptome analysis reveals novel regulatory mechanisms in a genome-reduced bacterium

The avian bacterial pathogen Mycoplasma gallisepticum is a good model for systems studies due to small genome and simplicity of regulatory pathways. In this study, we used RNA-Seq and MS-based proteomics to accurately map coding sequences, transcription start sites (TSSs) and transcript 3′-ends (T3Es). We used obtained data to investigate roles of TSSs and T3Es in stress-induced transcriptional responses. We identified 1061 TSSs at a false discovery rate of 10% and showed that almost all transcription in M. gallisepticum is initiated from classic TATAAT promoters surrounded by A/T-rich sequences. Our analysis revealed the pronounced operon structure complexity: on average, each coding operon has one internal TSS and T3Es in addition to the primary ones. Our transcriptomic approach based on the intervals between the two nearest transcript ends allowed us to identify two classes of T3Es: strong, unregulated, hairpin-containing T3Es and weak, heat shock-regulated, hairpinless T3Es. Comparing gene expression levels under different conditions revealed widespread and divergent transcription regulation in M. gallisepticum. Modeling suggested that the core promoter structure plays an important role in gene expression regulation. We have shown that the heat stress activation of cryptic promoters combined with the hairpinless T3Es suppression leads to widespread, seemingly non-functional transcription.

DNA repair in Mycoplasma gallisepticum

Background

DNA repair is essential for the maintenance of genome stability in all living beings. Genome size as well as the repertoire and abundance of DNA repair components may vary among prokaryotic species. The bacteria of the Mollicutes class feature a small genome size, absence of a cell wall, and a parasitic lifestyle. A small number of genes make Mollicutes a good model for a “minimal cell” concept.

Results

In this work we studied the DNA repair system of Mycoplasma gallisepticum on genomic, transcriptional, and proteomic levels. We detected 18 out of 22 members of the DNA repair system on a protein level. We found that abundance of the respective mRNAs is less than one per cell. We studied transcriptional response of DNA repair genes of M. gallisepticum at stress conditions including heat, osmotic, peroxide stresses, tetracycline and ciprofloxacin treatment, stationary phase and heat stress in stationary phase.

Conclusions

Based on comparative genomic study, we determined that the DNA repair system M. gallisepticum includes a sufficient set of proteins to provide a cell with functional nucleotide and base excision repair and mismatch repair. We identified SOS-response in M. gallisepticum on ciprofloxacin, which is a known SOS-inducer, tetracycline and heat stress in the absence of established regulators. Heat stress was found to be the strongest SOS-inducer. We found that upon transition to stationary phase of culture growth transcription of DNA repair genes decreases dramatically. Heat stress does not induce SOS-response in a stationary phase.

[The clinical efficacy of a succinate-containing infusion drug during pharmacotherapy for hepatic lesions of varying genesis: results of meta-analysis]

AIM

To pool the published results of trials of the new infusion hepatoprotector remaxol for the integral quantification of the magnitude of its clinical efficacy.

SUBJECTS AND METHODS

The authors made a systematized review of the published results of randomized clinical trials of the succinate-containing infusion hepatoprotector remaxol in diseases associated with hepatic lesions (chronic hepatitis B and C, severe ethanol intoxication in the presence of alcohol dependence, drug-induced liver lesion during treatment of tuberculosis, and metabolic syndrome). The pooled database included information on 935 patients. The combined control group (n = 447) received traditional pharmacotherapy drugs (active placebo), the treatment group (n = 628) additionally took remaxol.

RESULTS

Meta-analysis of the frequency characteristics of positive outcomes (the rate of disappearance of major clinical symptoms and complications) and the activity range for the enzymes characterizing hepatocyte cytolysis (alanine aminotransferase and aspartate aminotransferase) and cholestasis (alkaline phosphatase and gamma-glutamate transpeptidase) in the compared groups could provide an integral evaluation of the clinical efficacy of remaxol, which was 1.57 for enzymatic activity and 1.78 for the frequency characteristics of outcomes. The odds ratio of positive outcomes was 2.9 (range 1.9 to 3.9) and the number of patients who needed to be treated with remaxol during the follow-up to prevent a poor outcome in one patient was 6 (range 4 to 8).

CONCLUSION

The succinic acid-based infusion hepatoprotector remaxol provides a statistically and clinically significant therapeutic effect in the drug correction of hepatic lesions of varying genesis.

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

Background

Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.

Results

We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server http://bioinf.fbb.msu.ru/SDPfoxWeb/ and a stand-alone Java application available from the website.

Conclusions

SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.