Practical application of massively parallel reporter assay in biotechnology and medicine

The development and viability of an organism relies on tissue-specific gene programs. The genome regulatory elements play a key role in the regulation of such programs, whereas its disfunction can lead to the establishment of various pathologies, including cancer, congenital disorders, and autoimmune diseases. The development of high-throughput approaches in genomics has led to the emergence of massively parallel reporter assays (MPRA), which enable genome-wide screening and functional verification of regulatory elements. Although MPRA was originally used for investigation of fundamental aspects of epigenetics, it also has a great potential for clinical and practical biotechnology. Currently, MPRA is used for validation of clinically significant mutations, identification of tissue-specific regulatory elements, identification of the favorable loci for transgene integration, as well as represents an essential tool for creating highly efficient expression systems, with a wide range of applications from protein production and design of novel therapeutic antibody super-producers to gene therapy. In this review, the basic principles and areas of practical application of high-throughput reporter assays will be discussed

Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

Background During Drosophila spermatogenesis, testis-specific meiotic arrest complex (tMAC) and testis-specific TBP-associated factors (tTAF) contribute to activation of hundreds of genes required for meiosis and spermiogenesis. Intriguingly, tMAC is paralogous to the broadly expressed complex Myb-MuvB (MMB)/dREAM and Mip40 protein is shared by both complexes. tMAC acts as a gene activator in spermatocytes, while MMB/dREAM was shown to repress gene activity in many cell types. Results Our study addresses the intricate interplay between tMAC, tTAF, and MMB/dREAM during spermatogenesis. We used cell type-specific DamID to build the DNA-binding profiles of Cookie monster (tMAC), Cannonball (tTAF), and Mip40 (MMB/dREAM and tMAC) proteins in male germline cells. Incorporating the whole transcriptome analysis, we characterized the regulatory effects of these proteins and identified their gene targets. This analysis revealed that tTAFs complex is involved in activation of achi, vis, and topi meiosis arrest genes, implying that tTAFs may indirectly contribute to the regulation of Achi, Vis, and Topi targets. To understand the relationship between tMAC and MMB/dREAM, we performed Mip40 DamID in tTAF- and tMAC-deficient mutants demonstrating meiosis arrest phenotype. DamID profiles of Mip40 were highly dynamic across the stages of spermatogenesis and demonstrated a strong dependence on tMAC in spermatocytes. Integrative analysis of our data indicated that MMB/dREAM represses genes that are not expressed in spermatogenesis, whereas tMAC recruits Mip40 for subsequent gene activation in spermatocytes. Conclusions Discovered interdependencies allow to formulate a renewed model for tMAC and tTAFs action in Drosophila spermatogenesis demonstrating how tissue-specific genes are regulated

Genetic diversity in the Orenburg goat breed revealed by single-nucleotide polymorphism (SNP) analysis: Initial steps in saving a threatened population

Background/Objectives: For genomic selection to enhance the efficiency of broiler production, finding SNPs and candidate genes that define the manifestation of main selected traits is essential. We conducted a genome-wide association study (GWAS) for growth and meat productivity traits of roosters from a chicken F2 resource population (n = 152). Methods: The population was obtained by crossing two breeds with contrasting phenotypes for performance indicators, i.e., Russian White (slow-growing) and Cornish White (fast-growing). The birds were genotyped using the Illumina Chicken 60K SNP iSelect BeadChip. After LD filtering of the data, 54,188 SNPs were employed for the GWAS analysis that allowed us to reveal significant specific associations for phenotypic traits of interest and economic importance. Results: At the threshold value of p < 9.2 × 10−7, 83 SNPs associated with body weight at the age of 28, 42, and 63 days were identified, as well as 171 SNPs associated with meat qualities (average daily gain, slaughter yield, and dressed carcass weight and its components). Moreover, 34 SNPs were associated with a group of three or more traits, including 15 SNPs significant for a group of growth traits and 5 SNPs for a group of meat productivity indicators. Relevant to these detected SNPs, nine prioritized candidate genes associated with the studied traits were revealed, including WNT2, DEPTOR, PPA2, UNC80, DDX51, PAPPA, SSC4D, PTPRU, and TLK2. Conclusions: The found SNPs and candidate genes can serve as genetic markers for growth and meat performance characteristics in chicken breeding in order to achieve genetic improvement in broiler production

Bioinert coatings of Ti-Ta-N for medical implants obtained by electric explosion spraying and subsequent electron-ion-plasma modification

The purpose of the research was to form a Ti-Ta-N- system bioinert coating on Ti6Al4V alloy surface as well as to study its structure and properties. The main contribution of the research is in the following. Electro-explosion spraying of tantalum coating on VT6 titanium alloy surface was pioneered in the research. After that the processing of the coating by low-energy high-current electron beam and subsequent nitriding was carried out in a single technological cycle. It has been established that a nanocrystalline coating based on tantalum, nitrogen and titanium was formed as a result of the technological operations. The phase composition of the coatings has been detected. The variations in crystal lattice parameters being formed in coating of phases and coherent scallering regions of these phases depending on power density of electron beam have been determined. Structural characteristics of the coatings at nano- and microlevel have been detected. Tests of coatings for nanohardness, the Young modulus, wear resistance and friction factor have been carried out. By all technical characteristics Ti-Ta-N-system coating exceeds titanium of VT6 grade. The cause of the increase in mechanical characteristics of the Ti-Ta-N-system coating is their nanostructural state and strengthening phases. Tests for proliferation activity of fibroplasts and antimicrobial activity have shown better results in comparison with VT6 titanium alloy as well. It is due to escape of vanadium ions from VT6 alloy into nutrient cell medium and their destructive effect on cell cultures. Variations in proliferation and antimicrobial activity develop due to amplification of cell proliferation. A complex of the obtained characteristics makes it possible to recommend Ti-Ta-N-system coating for its application as a bioinert coating on different implants in furure

Chemical Synapses without Synaptic Vesicles: Purinergic Neurotransmission through a CALHM1 Channel-mitochondrial Signaling Complex

Conventional chemical synapses in the nervous system involve a presynaptic accumulation of neurotransmitter-containing vesicles, which fuse with the plasma membrane to release neurotransmitters that activate postsynaptic receptors. In taste buds, type II receptor cells do not have conventional synaptic features but nonetheless show regulated release of their afferent neurotransmitter, ATP, through a large-pore, voltage-gated channel, CALHM1. Immunohistochemistry revealed that CALHM1 was localized to points of contact between the receptor cells and sensory nerve fibers. Ultrastructural and super-resolution light microscopy showed that the CALHM1 channels were consistently associated with distinctive, large (1- to 2-μm) mitochondria spaced 20 to 40 nm from the presynaptic membrane. Pharmacological disruption of the mitochondrial respiratory chain limited the ability of taste cells to release ATP, suggesting that the immediate source of released ATP was the mitochondrion rather than a cytoplasmic pool of ATP. These large mitochondria may serve as both a reservoir of releasable ATP and the site of synthesis. The juxtaposition of the large mitochondria to areas of membrane displaying CALHM1 also defines a restricted compartment that limits the influx of Ca2+ upon opening of the nonselective CALHM1 channels. These findings reveal a distinctive organelle signature and functional organization for regulated, focal release of purinergic signals in the absence of synaptic vesicles

Afferent neurotransmission mediated by hemichannels in mammalian taste cells

In mammalian taste buds, ionotropic P2X receptors operate in gustatory nerve endings to mediate afferent inputs. Thus, ATP secretion represents a key aspect of taste transduction. Here, we characterized individual vallate taste cells electrophysiologically and assayed their secretion of ATP with a biosensor. Among electrophysiologically distinguishable taste cells, a population was found that released ATP in a manner that was Ca(2+) independent but voltage-dependent. Data from physiological and pharmacological experiments suggested that ATP was released from taste cells via specific channels, likely to be connexin or pannexin hemichannels. A small fraction of ATP-secreting taste cells responded to bitter compounds, indicating that they express taste receptors, their G-protein-coupled and downstream transduction elements. Single cell RT–PCR revealed that ATP-secreting taste cells expressed gustducin, TRPM5, PLCβ2, multiple connexins and pannexin 1. Altogether, our data indicate that tastant-responsive taste cells release the neurotransmitter ATP via a non-exocytotic mechanism dependent upon the generation of an action potential

The GLUEX beamline and detector

The GLUEX experiment at Jefferson Lab has been designed to study photoproduction reactions with a 9-GeV linearly polarized photon beam. The energy and arrival time of beam photons are tagged using a scintillator hodoscope and a scintillating fiber array. The photon flux is determined using a pair spectrometer, while the linear polarization of the photon beam is determined using a polarimeter based on triplet photoproduction. Charged-particle tracks from interactions in the central target are analyzed in a solenoidal field using a central straw-tube drift chamber and six packages of planar chambers with cathode strips and drift wires. Electromagnetic showers are reconstructed in a cylindrical scintillating fiber calorimeter inside the magnet and a lead-glass array downstream. Charged particle identification is achieved by measuring energy loss in the wire chambers and using the flight time of particles between the target and detectors outside the magnet. The signals from all detectors are recorded with flash ADCs and/or pipeline TDCs into memories allowing trigger decisions with a latency of 3.3 mu s. The detector operates routinely at trigger rates of 40 kHz and data rates of 600 megabytes per second. We describe the photon beam, the GLUEX detector components, electronics, data-acquisition and monitoring systems, and the performance of the experiment during the first three years of operation

The GlueX beamline and detector

The GlueX experiment at Jefferson Lab has been designed to study photoproduction reactions with a 9-GeV linearly polarized photon beam. The energy and arrival time of beam photons are tagged using a scintillator hodoscope and a scintillating fiber array. The photon flux is determined using a pair spectrometer, while the linear polarization of the photon beam is determined using a polarimeter based on triplet photoproduction. Charged-particle tracks from interactions in the central target are analyzed in a solenoidal field using a central straw-tube drift chamber and six packages of planar chambers with cathode strips and drift wires. Electromagnetic showers are reconstructed in a cylindrical scintillating fiber calorimeter inside the magnet and a lead-glass array downstream. Charged particle identification is achieved by measuring energy loss in the wire chambers and using the flight time of particles between the target and detectors outside the magnet. The signals from all detectors are recorded with flash ADCs and/or pipeline TDCs into memories allowing trigger decisions with a latency of 3.3 . The detector operates routinely at trigger rates of 40 kHz and data rates of 600 megabytes per second. We describe the photon beam, the GlueX detector components, electronics, data-acquisition and monitoring systems, and the performance of the experiment during the first three years of operation