377 research outputs found
Intriguing symmetry in statistical structures of Siberian larch transcriptome
No full textThe paper presents a novel approach to infer a structuredness in a set of symbol sequences such as transcriptome nucleotide sequences. A distribution pattern of triplet frequencies in the Siberian larch (\textit{Larix sibirica}~Ledeb.) transcriptome sequences was investigated in the presented study. It was found that the larch transcriptome demonstrates a number of unexpected symmetries in the statistical and combinatorial properties
Chloroplast Genome Yields Unusual Seven-Cluster Structure C
No full textWe studied the structuredness in a chloroplast genome of Siberian larch. The clusters in 63-dimensional space were identified with elastic map technique, where the objects to be clusterized are the different fragments of the genome. A seven-cluster structure in the distribution of those fragments reported previously has been found. Unlike the previous results, we have found the drastically other composition of the clusters comprising the fragments extracted from coding and non-coding regions of the genome
Symmetry in a Four-Cluster Triangle Structure of the Siberian Stone Pine (Pinus sibirica Du Tour) Transcriptome
No full textThe RNA isolated from three different tissues of Siberian stone pine—cambium, needles and buds—were sequenced and assembled for each tissue separately. [...
Symmetry in the Transcriptome and Genome Sequences of Siberian Larch (Larix sibirica Ledeb.)
No full textWe studied the structuredness and order in draft assemblies of the Siberian larch [...
Proline-rich tyrosine kinase 2 mediates gonadotropin-releasing hormone signaling to a specific extracellularly regulated kinase-sensitive transcriptional locus in the luteinizing hormone beta-subunit gene
No full textG protein-coupled receptor regulation of gene transcription primarily occurs through the phosphorylation of transcription factors by MAPKs. This requires transduction of an activating signal via scaffold proteins that can ultimately determine the outcome by binding signaling kinases and adapter proteins with effects on the target transcription factor and locus of activation. By investigating these mechanisms, we have elucidated how pituitary gonadotrope cells decode an input GnRH signal into coherent transcriptional output from the LH beta-subunit gene promoter. We show that GnRH activates c-Src and multiple members of the MAPK family, c-Jun NH2-terminal kinase 1/2, p38MAPK, and ERK1/2. Using dominant-negative point mutations and chemical inhibitors, we identified that calcium-dependent proline-rich tyrosine kinase 2 specifically acts as a scaffold for a focal adhesion/cytoskeleton-dependent complex comprised of c-Src, Grb2, and mSos that translocates an ERK-activating signal to the nucleus. The locus of action of ERK was specifically mapped to early growth response-1 (Egr-1) DNA binding sites within the LH beta-subunit gene proximal promoter, which was also activated by p38MAPK, but not c-Jun NH2-terminal kinase 1/2. Egr-1 was confirmed as the transcription factor target of ERK and p38MAPK by blockade of protein expression, transcriptional activity, and DNA binding. We have identified a novel GnRH-activated proline-rich tyrosine kinase 2-dependent ERK-mediated signal transduction pathway that specifically regulates Egr-1 activation of the LH beta-subunit proximal gene promoter, and thus provide insight into the molecular mechanisms required for differential regulation of gonadotropin gene expression
Comparative analysis of alignment-free genome clustering and whole genome alignment-based phylogenomic relationship of coronaviruses
No full textThe SARS-CoV-2 is the third coronavirus in addition to SARS-CoV and MERS-CoV that causes severe respiratory syndrome in humans. All of them likely crossed the interspecific barrier between animals and humans and are of zoonotic origin, respectively. The origin and evolution of viruses and their phylogenetic relationships are of great importance for study of their pathogenicity and development of antiviral drugs and vaccines. The main objective of the presented study was to compare two methods for identifying relationships between coronavirus genomes: phylogenetic one based on the whole genome alignment followed by molecular phylogenetic tree inference and alignment-free clustering of triplet frequencies, respectively, using 69 coronavirus genomes selected from two public databases. Both approaches resulted in well-resolved robust classifications. In general, the clusters identified by the first approach were in good agreement with the classes identified by the second using K -means and the elastic map method, but not always, which still needs to be explained. Both approaches demonstrated also a significant divergence of genomes on a taxonomic level, but there was less correspondence between genomes regarding the types of diseases they caused, which may be due to the individual characteristics of the host. This research showed that alignment-free methods are efficient in combination with alignment-based methods. They have a significant advantage in computational complexity and provide valuable additional alternative information on the genomes relationships.Open-Access-Publikationsfonds 202
Strategic Time-Based Metering that Assures Separation for Integrated Operations in a Terminal Airspace
No full textThis paper reports an algorithm for strategic time-based metering of air traffic arriving and departing from a large ( tens of nautical miles) area (called here, the commitment region) around an airport or metroplex. The algorithm assures separation continuously in time and avoids a dictation of intent to an aircraft crew. This is accomplished by allowing an aircraft (specifically, its Flight Management System) to specify, and commit to, an intended route and ground speed profile along that route within the commitment region, and by supplying the time at which to enter the region to the aircraft crew. The airspace that comprises the commitment region need not be confined to the terminal airspace and can include some of the enroute space: the size and shape of the commitment region are parameters in the algorithm. An exact formula for including speed profile uncertainty in the algorithm is provided. The algorithm is applied to a number of data sets recorded during actual air traffic operations in the Southern California TRACON in July of 2014 and the Atlanta TRACON in November and December of 2013. The results of the numerical simulations indicate that the algorithm succeeds at keeping the aircraft separated, but introduces, in its current implementation, more separation than that observed in actual operations. This excess separation can be reduced by modeling more accurately the Visual Flight Rules separation practices, a direction for future research
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