Developmental and Housekeeping Genes: Two Types of Genetic Organization in the Drosophila Genome.

We developed a procedure for locating genes on Drosophila melanogaster polytene chromosomes and described three types of chromosome structures (gray bands, black bands, and interbands), which differed markedly in morphological and genetic properties. This was reached through the use of our original methods of molecular and genetic analysis, electron microscopy, and bioinformatics data processing. Analysis of the genome-wide distribution of these properties led us to a bioinformatics model of the Drosophila genome organization, in which the genome was divided into two groups of genes. One was constituted by 65, in which the genome was divided into two groups, 62 genes that are expressed in most cell types during life cycle and perform basic cellular functions (the so-called "housekeeping genes"). The other one was made up of 3162 genes that are expressed only at particular stages of development ("developmental genes"). These two groups of genes are so different that we may state that the genome has two types of genetic organization. Different are the timings of their expression, chromatin packaging levels, the composition of activating and deactivating proteins, the sizes of these genes, the lengths of their introns, the organization of the promoter regions of the genes, the locations of origin recognition complexes (ORCs), and DNA replication timings.

Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing.

Studies on hereditary fixation of the tame-behavior phenotype during animal domestication remain relevant and important because they are of both basic research and applied significance. In model animals, gray rats Rattus norvegicus bred for either an enhancement or reduction in defensive response to humans, for the first time, we used high-throughput RNA sequencing to investigate differential expression of genes in tissue samples from the tegmental region of the midbrain in 2-month-old rats showing either tame or aggressive behavior. A total of 42 differentially expressed genes (DEGs; adjusted p-value < 0.01 and fold-change > 2) were identified, with 20 upregulated and 22 downregulated genes in the tissue samples from tame rats compared with aggressive rats. Among them, three genes encoding transcription factors (TFs) were detected: Ascl3 was upregulated, whereas Fos and Fosb were downregulated in tissue samples from the brains of tame rats brain. Other DEGs were annotated as associated with extracellular matrix components, transporter proteins, the neurotransmitter system, signaling molecules, and immune system proteins. We believe that these DEGs encode proteins that constitute a multifactorial system determining the behavior for which the rats have been artificially selected. We demonstrated that several structural subtypes of E-box motifs­known as binding sites for many developmental TFs of the bHLH class, including the ASCL subfamily of TFs­are enriched in the set of promoters of the DEGs downregulated in the tissue samples of tame rats'. Because ASCL3 may act as a repressor on target genes of other developmental TFs of the bHLH class, we hypothesize that the expression of TF gene Ascl3 in tame rats indicates longer neurogenesis (as compared to aggressive rats), which is a sign of neoteny and domestication. Thus, our domestication model shows a new function of TF ASCL3: it may play the most important role in behavioral changes in animals.

CisCross: A gene list enrichment analysis to predict upstream regulators in Arabidopsis thaliana.

Having DNA-binding profiles for a sufficient number of genome-encoded transcription factors (TFs) opens up the perspectives for systematic evaluation of the upstream regulators for the gene lists. Plant Cistrome database, a large collection of TF binding profiles detected using the DAP-seq method, made it possible for Arabidopsis. Here we re-processed raw DAP-seq data with MACS2, the most popular peak caller that leads among other ones according to quality metrics. In the benchmarking study, we confirmed that the improved collection of TF binding profiles supported a more precise gene list enrichment procedure, and resulted in a more relevant ranking of potential upstream regulators. Moreover, we consistently recovered the TF binding profiles that were missing in the previous collection of DAP-seq peak sets. We developed the CisCross web service (https://plamorph.sysbio.ru/ciscross/) that gives more flexibility in the analysis of potential upstream TF regulators for Arabidopsis thaliana genes.

Motif models proposing independent and interdependent impacts of nucleotides are related to high and low affinity transcription factor binding sites in Arabidopsis.

Position weight matrix (PWM) is the traditional motif model representing the transcription factor (TF) binding sites. It proposes that the positions contribute independently to TFs binding affinity, although this hypothesis does not fit the data perfectly. This explains why PWM hits are missing in a substantial fraction of ChIP-seq peaks. To study various modes of the direct binding of plant TFs, we compiled the benchmark collection of 111 ChIP-seq datasets for Arabidopsis thaliana, and applied the traditional PWM, and two alternative motif models BaMM and SiteGA, proposing the dependencies of the positions. The variation in the stringency of the recognition thresholds for the models proposed that the hits of PWM, BaMM, and SiteGA models are associated with the sites of high/medium, any, and low affinity, respectively. At the medium recognition threshold, about 60% of ChIP-seq peaks contain PWM hits consisting of conserved core consensuses, while BaMM and SiteGA provide hits for an additional 15% of peaks in which a weaker core consensus is compensated through intra-motif dependencies. The presence/absence of these dependencies in the motifs of alternative/traditional models was confirmed by the dependency logo DepLogo visualizing the position-wise partitioning of the alignments of predicted sites. We exemplify the detailed analysis of ChIP-seq profiles for plant TFs CCA1, MYC2, and SEP3. Gene ontology (GO) enrichment analysis revealed that among the three motif models, the SiteGA had the highest portions of genes with the significantly enriched GO terms among all predicted genes. We showed that both alternative motif models provide for traditional PWM greater extensions in predicted sites for TFs MYC2/SEP3 with condition/tissue specific functions, compared to those for TF CCA1 with housekeeping functions. Overall, the combined application of standard and alternative motif models is beneficial to detect various modes of the direct TF-DNA interactions in the maximal portion of ChIP-seq loci.

Predictive value of a day orthostatic loading test for the reversibility of the great saphenous vein reflux after phlebectomy of all varicous tributaries.

BACKGROUND: The aim of this study was to evaluate predictive value of a day orthostatic loading test (DOL-test) for the reversibility of the great saphenous vein (GSV) reflux after phlebectomy of all varicose tributaries (VTs). METHODS: Prospective cohort study. Patients with reflux in the GSV were included. Patients were treated by phlebectomy for all VTs of the GSV. GSV reflux was measured during a Duplex ultrasound examination with DOL-based on: 1) reflux location and donor vein; 2) reflux extent (RE) of the GSV was evaluated according to the number of zones of reflux (NZR) which included three thigh and three calf zones; 3) reflux duration (RD); 4) peak reflux velocity (PRV) in GSV reflux point of initiation; 5) the diameter of the GSV; 6) orthostatic gradient (OG) - difference between evening and morning values of the GSV diameter. We included 87 lower limbs (LLs) in 65 patients (51 women and 15 men) aged from 29 to 53 (mean age 36.7) years. RESULTS: In twelve months after the surgery the amount of limbs with eliminated reflux constituted 77.0%. In LLs with incompetence of SFJ the reversibility of the GSV was observed in 59.0% of cases in 12 months after treatment. В LLs without incompetence of SFJ the reversibility constituted 91.7%. In LLs with resolved GSV reflux (N.=67) the initial evening RE constituted 3.76 and reduced in the morning to 1.51, P=0.000001. In LLs with persistent GSV reflux (N.=20) the initial evening RE constituted 3,75 and reduced in the morning to 3.00, P=0.028418. In LLs with resolved GSV reflux the initial evening RD constituted 2.10 s and reduced in the morning to 0.93 s, P=0.000001. In LLs with persistent GSV reflux the initial evening RD constituted 2.13 s and reduced in the morning to 1.82 s, P=0.043115. In LLs with resolved GSV reflux the initial evening PRV constituted 173.46 mm/s and reduced in the morning to 101.57 mm/s, P=0.000001. In LLs with persistent GSV reflux the initial evening PRV constituted 172.50 mm/ and reduced in the morning to 158.50 mm/s, P=0.007686. In LLs with resolved reflux the initial OG was 0.93 mm with the initial evening GSV diameter of 7.20 mm. After the surgery OG reduced to 0.59 mm, P=0.000001. The evening vein diameter decreased to 5.07 mm, P=0.000001. In LLs with persistent reflux the OG and the GSV diameter decreased from 0.55 mm to 0.51 mm, P=0.017961 and evening GSV diameter from 7.75 mm initially to 7.55 mm after the treatment, P=0.067890 respectively. CONCLUSIONS: Characterizing GSV with minimum volume loading, DOL-test shows the degree of preservation of muscular-tonic properties of GSV and allows to predict the reversibility of the GSV reflux after phlebectomy. Being initially high, the GSV OG points that the potential of muscular-tonic function is saved. Its decrease after the surgery proves the decrease of the volume loading on GSV.

Secondary Varicose Small Pelvic Veins and Their Treatment with Micronized Purified Flavonoid Fraction.

The aim of this study was to examine secondary varicose small pelvic veins (VSPV) and their treatment with micronized purified flavonoid fraction (MPFF). We examined 70 patients with a history of acute iliac thrombosis of > 1 year. Patients with urination difficulties associated with other symptoms (n = 24) received MPFF 1,000 mg once daily for 1 month. Clinical manifestations were assessed by collecting complaints and analyzing results of physician examinations. VSPV was identified in 48 (68.6%) patients, the majority (58%) had grade 2 (7.0-9.0 mm) venous dilation. VSPV severity correlated with time since the thrombotic event. In most women, varicosities were found in the parametrial venous plexus (mean vein diameter 7.91 mm); retrograde flow during the Valsalva maneuver was found in 14 (78%). In men, all varicosities occurred in the paraprostatic plexus (mean vein diameter 7.20 mm); retrograde flow was found in 21 (70%). MPFF significantly reduced VSPV dilation in 18 (75%) patients (p = 0.0863) and returned ultrasonic indices to normal values in the remainder. Patients with bilateral varices decreased from 10 to 2. Only four patients had retrograde flow in the SPV plexus after treatment. MPFF decreased mean paraprostatic vein diameter in men and parametrial vein diameter in women to near-normal values. Clinical improvement was reported in 13 (54%) patients. Patients with pelvic pain decreased from 8 to 1 and patients with urination disorders from 24 to 9. VSPV is common in patients with a history of iliac vein thrombosis. MPFF decreases the diameter of affected veins, improves retrograde flow and pelvic hemodynamics, and significantly reduces the severity of the clinical manifestations.