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https://www.readbyqxmd.com/read/28639193/mirna-mediated-rna-activation-in-mammalian-cells
#1
Ramani Ramchandran, Pradeep Chaluvally-Raghavan
MicroRNA (miRNA or miR) is a small noncoding RNA molecule ~22 nucleotides in size, which is found in plants, animals, and some viruses. miRNAs are thought to primarily down regulate gene expression by binding to 3' untranslated regions of target transcripts, thereby triggering mRNA cleavage or repression of translation. Recently, evidence has emerged that miRNAs can interact with the promoter and activate gene expression. This mechanism, called RNA activation (RNAa), is a process of transcriptional activation where the direct interaction of miRNA on the promoter triggers the recruitment of transcription factors and RNA-Polymerase-II on the promoter to activate gene transcription...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28639190/target-recognition-mechanism-and-specificity-of-rna-activation
#2
Huiqing Cao, Xing Meng, Xiaoxia Wang, Zicai Liang
Small activating RNA (saRNA)-mediated gene activation has opened a new avenue for upregulating the expression of target genes by promoting endogenous transcription, a phenomenon known as RNA activation (RNAa). RNAa is distinct from the established RNAi mechanistic framework, although AGO2 is required by both. The precise mechanism of RNAa is currently disputable and has become a bottleneck in the development of this new technology. saRNA may achieve activation of target genes by directly binding to DNA targets in promoter, or interacting with antisense transcripts transcribed from overlapping promoter sequences, or by silencing other genes...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28631029/syngas-biorefinery-and-syngas-utilization
#3
Sashini De Tissera, Michael Köpke, Sean D Simpson, Christopher Humphreys, Nigel P Minton, Peter Dürre
Autotrophic acetogenic bacteria are able to capture carbon (CO or CO2) through gas fermentation, allowing them to grow on a spectrum of waste gases from industry (e.g., steel manufacture and oil refining, coal, and natural gas) and to produce ethanol. They can also consume syn(thesis) gas (CO and H2) made from the gasification of renewable/sustainable resources, such as biomass and domestic/agricultural waste. Acetogenic gas fermentation can, therefore, produce ethanol in any geographic region without competing for food or land...
June 20, 2017: Advances in Biochemical Engineering/biotechnology
https://www.readbyqxmd.com/read/28629512/erythropoietin-receptor-structural-domains
#4
Qingxin Li, CongBao Kang
Erythropoietin (EPO) is a hormone that is important for regulating red blood cell production. It is functional through binding to its receptor-EpoR. EpoR is a single-span membrane protein. It contains an extracellular region, a transmembrane domain, and a C-terminus. The extracellular region is important for binding to EPO, and its conformation is critical for signal transduction. The transmembrane domain contains 21 residues forming a helix which plays an important role in transferring ligand-induced conformational changes of the extracellular domain across the cell membrane...
2017: Vitamins and Hormones
https://www.readbyqxmd.com/read/28620761/medicinal-chemistry-of-%C3%AF-1-receptor-ligands-pharmacophore-models-synthesis-structure-affinity-relationships-and-pharmacological-applications
#5
Frauke Weber, Bernhard Wünsch
In the first part of this chapter, we summarize the various pharmacophore models for σ1 receptor ligands. Common to all of them is a basic amine flanked by two hydrophobic regions, representing the pharmacophoric elements. The development of computer-based models like the 3D homology model is described as well as the first crystal structure of the σ1 receptor. The second part focuses on the synthesis and biological properties of different σ1 receptor ligands, identified as 1-9. Monocyclic piperazines 1 and bicyclic piperazines 2 and 3 were developed as cytotoxic compounds, thus the IC50 values of cell growth and survival inhibition studies are given for all derivatives...
June 16, 2017: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/28608349/identification-and-evolutionary-characterization-of-argonaute-binding-platforms
#6
Joshua T Trujillo, Rebecca A Mosher
ARGONAUTE (AGO) proteins are eukaryotic RNA silencing effectors that interact with their binding partners via short peptide motifs known as AGO hooks. AGO hooks tend to cluster in one region of the protein to create an AGO-binding platform. In addition to the presence of AGO hooks, AGO-binding platforms are intrinsically disordered, contain tandem repeat arrays, and have weak sequence conservation even between close relatives. These characteristics make it difficult to identify and perform evolutionary analysis of these regions...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28608346/computational-analysis-of-genome-wide-argonaute-dependent-dna-methylation-in-plants
#7
Kai Tang, Cheng-Guo Duan, Huiming Zhang, Jian-Kang Zhu
Whole-genome bisulfite sequencing (WGBS) has become a powerful tool to dissect genome-wide methylation profiles at single-base resolution. In this chapter we describe in detail the bioinformatics pipeline used for the analysis of ARGONAUTE-dependent DNA methylation in Arabidopsis thaliana. We provide tools and command lines used for mapping bisulfite sequencing reads, for estimating methylation levels at individual cytosine sites, for identifying differentially methylated regions (DMRs), and for calculating methylation levels of DMRs...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28589363/tracking-b-cell-repertoires-and-clonal-histories-in-normal-and-malignant-lymphocytes
#8
Nicola J Weston-Bell, Graeme Cowan, Surinder S Sahota
Methods for tracking B-cell repertoires and clonal history in normal and malignant B-cells based on immunoglobulin variable region (IGV) gene analysis have developed rapidly with the advent of massive parallel next-generation sequencing (mpNGS) protocols. mpNGS permits a depth of analysis of IGV genes not hitherto feasible, and presents challenges of bioinformatics analysis, which can be readily met by current pipelines. This strategy offers a potential resolution of B-cell usage at a depth that may capture fully the natural state, in a given biological setting...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28584982/rational-design-of-t-lymphocyte-epitope-based-vaccines-against-coccidioides-infection
#9
Brady J Hurtgen, Chiung-Yu Hung
Coccidioidomycosis is a potentially life-threatening mycosis endemic to the Southwestern USA and some arid regions of Central and South America. A vaccine against Coccidioides infection would benefit over 30-million people who reside in or visit the endemic regions. Vaccine candidates against systemic fungal infections come in many forms. Live attenuated vaccines are derived from disease-causing pathogens and generally stimulate excellent protective immunity. Since attenuated vaccines contain living microbes, there is a degree of unpredictability raising concerns regarding safety and stability...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28573617/nonradioactive-northern-blot-analysis-to-detect-ebola-virus-minigenomic-mrna
#10
Kristina Brauburger, Tessa Cressey, Elke Mühlberger
In this chapter, we describe the detection of Ebola virus minigenomic mRNA using a nonradioactive Northern hybridization. This protocol comprises all steps beginning with the synthesis of a digoxigenin-labeled riboprobe, harvest of transcribed mRNA from cells transfected with the Ebola virus minigenome system, separation of mRNA species by denaturing RNA gel electrophoresis, transfer of the mRNA to nylon membranes by vacuum blotting, and finally the detection of minigenome-specific mRNA through hybridization with a labeled riboprobe directed against the reporter gene...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28573609/ebolavirus-an-overview-of-molecular-and-clinical-pathogenesis
#11
Veronica Vine, Dana P Scott, Heinz Feldmann
Ebolaviruses cause severe, often fatal hemorrhagic fever in Central, East, and West Africa. Until recently, they have been viewed as rare but highly pathogenic infections with regional, but limited, global public health impact. This view has changed with the emergence of the first epidemic of Ebola hemorrhagic fever in West Africa. In this chapter we provide an introduction of the pathogenesis of ebolaviruses as well as a description of clinical disease features. We also describe the current animal models used in ebolavirus research, detailing each model's unique strengths and weaknesses...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28552236/brain-repair-from-intrinsic-cell-sources-turning-reactive-glia-into-neurons
#12
Olof Torper, Magdalena Götz
The replacement of lost neurons in the brain due to injury or disease holds great promise for the treatment of neurological disorders. However, logistical and ethical hurdles in obtaining and maintaining viable cells for transplantation have proven difficult to overcome. In vivo reprogramming offers an alternative, to bypass many of the restrictions associated with an exogenous cell source as it relies on a source of cells already present in the brain. Recent studies have demonstrated the possibility to target and reprogram glial cells into functional neurons with high efficiency in the murine brain, using virally delivered transcription factors...
2017: Progress in Brain Research
https://www.readbyqxmd.com/read/28540699/long-fragment-polymerase-chain-reaction
#13
Eng Wee Chua, Simran Maggo, Martin A Kennedy
Polymerase chain reaction (PCR) is an oft-used preparatory technique in amplifying specific DNA regions for downstream analysis. The size of an amplicon was initially limited by errors in nucleotide polymerization and template deterioration during thermal cycling. A variant of PCR, designated long-range PCR, was devised to counter these drawbacks and enable the amplification of large fragments exceeding a few kb. In this chapter we describe a protocol for long-range PCR, which we have adopted to obtain products of 6...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540698/introduction-on-using-the-fastpcr-software-and-the-related-java-web-tools-for-pcr-and-oligonucleotide-assembly-and-analysis
#14
Ruslan Kalendar, Timofey V Tselykh, Bekbolat Khassenov, Erlan M Ramanculov
This chapter introduces the FastPCR software as an integrated tool environment for PCR primer and probe design, which predicts properties of oligonucleotides based on experimental studies of the PCR efficiency. The software provides comprehensive facilities for designing primers for most PCR applications and their combinations. These include the standard PCR as well as the multiplex, long-distance, inverse, real-time, group-specific, unique, overlap extension PCR for multi-fragments assembling cloning and loop-mediated isothermal amplification (LAMP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540681/exploring-microrna-target-regulatory-interactions-by-computing-technologies
#15
Yue Hu, Wenjun Lan, Daniel Miller
MiRNA genes (miRNA precursor genes) share some common structural elements with protein genes. As with protein genes, the promoters of miRNA genes are necessary to regulate the expression of miRNA. The computation methods used to find the promoter regions of the protein genes have been applied to miRNA genes and some methods have been designed specifically to find the promoter regions of miRNA genes. The transcription factors (TFs), miRNA, and the targeted genes can form complex regulatory networks in the cells that can be divided into circuits...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540680/computational-prediction-of-microrna-target-genes-target-prediction-databases-and-web-resources
#16
Justin T Roberts, Glen M Borchert
MicroRNA (miRNA) mediated silencing and repression of mRNA molecules requires complementary base pairing between the "seed" region of the miRNA and the "seed match" region of target mRNAs. While this mechanism is fairly well understood, accurate prediction of valid miRNA targets remains challenging due to factors such as imperfect sequence specificity, target site availability, and the thermodynamic stability of the mRNA structure itself. As knowledge of what genes are being targeted by each miRNA is arguably the most important facet of miRNA biology, many approaches have been developed to address the need for reliable prediction and ranking of putative targets, with most using a combination of various strategies such as evolutionary conservation, statistical inference, and distinct features of the target sequences themselves...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28540674/microrna-expression-protein-participants-in-microrna-regulation
#17
Valeria M King, Glen M Borchert
MiRNAs are ~20 nt small RNAs that regulate networks of proteins using a seed region of nucleotides 2-8 to complement the 3' UTR of target mRNAs. The biogenesis and function of miRNAs as translational repressors is facilitated by protein counterparts that process primary and precursor miRNAs to maturity (Drosha/DCGR8 and Dicer/TRBP respectively) and incorporate miRNAs into the protein complex RISC to recognize and repress target mRNAs (RISC proteins: Ago/TRBP1/TRBP2/DICER). Similarly, siRNAs through comparable mechanisms are loaded into the protein complex RITS to heterochromatin formation of DNA and suppress transcription of particular genes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28537344/evaluation-of-the-topic-lists-used-in-two-world-congresses-2015-and-2016-in-physical-and-rehabilitation-medicine
#18
Boya Nugraha, Tatjana Paternostro-Sluga, Othmar Schuhfried, Gerold Stucki, Franco Franchignoni, Lydia Abdul Latif, Julia Patrick Engkasan, Zaliha Omar, Christoph Gutenbrunner
BACKGROUND: Evaluation of the initial list of proposed abstract topics for Congresses of Physical and Rehabilitation Medicine (PRM) was needed in order to ensure its feasibility for use in future congress announcements and invitations for abstract submission. METHODS: The initial proposals were based on 5 main areas of PRM research: biosciences in rehabilitation, biomedical rehabilitation sciences and engineering, clinical PRM sciences, integrative rehabilitation sciences, and human functioning sciences...
May 24, 2017: Journal of Rehabilitation Medicine
https://www.readbyqxmd.com/read/28523503/hierarchical-cluster-analysis-to-aid-diagnostic-image-data-visualization-of-ms-and-other-medical-imaging-modalities
#19
Arul N Selvan, Laura M Cole, Lynne Spackman, Sarah Naylor, Chris Wright
Perceiving abnormal regions in the images of different medical modalities plays a crucial role in diagnosis and subsequent treatment planning. In medical images to visually perceive abnormalities' extent and boundaries requires substantial experience. Consequently, manually drawn region of interest (ROI) to outline boundaries of abnormalities suffers from limitations of human perception leading to inter-observer variability. As an alternative to human drawn ROI, it is proposed the use of a computer-based segmentation algorithm to segment digital medical image data...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508370/a-proteomic-evaluation-of-sympathetic-activity-biomarkers-of-the-hypothalamus-pituitary-adrenal-axis-by-western-blotting-technique-following-experimental-traumatic-brain-injury
#20
Hale Zerrin Toklu, Yasemin Sakarya, Nihal Tümer
Endocrine disorders and autonomic dysfunction are common paradigms following traumatic brain injury (TBI). Alterations in the hypothalamus-pituitary-adrenal (HPA) axis following TBI may result in impaired vasopressor response, energy imbalance, fatigue, depression, or neurological disorders. Autonomic dysfunction is a common disorder following TBI. The sympathetic activity markers on HPA axis can be measured by Western blot protein analysis. Tyrosine hydroxylase, dopamine beta hydroxylase are the key enzymes for the synthesis of norepinephrine; and neuropeptide Y (NPY) is the peptide that is co-stored and co-released with norepinephrine...
2017: Methods in Molecular Biology
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