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https://www.readbyqxmd.com/read/27924591/the-oral-microbiota-in-health-and-disease-an-overview-of-molecular-findings
#1
José F Siqueira, Isabela N Rôças
Culture-independent nucleic acid technologies have been extensively applied to the analysis of oral bacterial communities associated with healthy and diseased conditions. These methods have confirmed and substantially expanded the findings from culture studies to reveal the oral microbial inhabitants and candidate pathogens associated with the major oral diseases. Over 1000 bacterial distinct species-level taxa have been identified in the oral cavity and studies using next-generation DNA sequencing approaches indicate that the breadth of bacterial diversity may be even much larger...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924585/salivary-diagnostics-using-purified-nucleic-acids
#2
Paul D Slowey
Saliva is an easily accessible fluid that has led to increasing interest in the development of salivary diagnostics. This chapter describes some of the newer tools and procedures for collection, stabilization, and storage of oral fluid matrices that aid in the successful use of saliva as a test specimen. This chapter focuses particularly on nucleic acid components for downstream molecular diagnostic (MDx) testing, since this is probably the area where saliva is likely to have the greatest impact in improving healthcare for the general population...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924490/site-specific-fluorescent-labeling-of-argonaute-for-fret-based-bio-assays
#3
Sarah Willkomm, Adrian Zander, Dina Grohmann
Deciphering the molecular mechanisms of eukaryotic Argonaute proteins is crucial for the understanding of RNA interference (RNAi), a posttranscriptional gene silencing process. Fluorescence-based single-molecule studies like single-molecule Förster resonance energy transfer (FRET) between a donor and acceptor dye represent a versatile tool to gain a mechanistic understanding of the structural dynamics of a biomolecular complex. Until today it was not possible to site-specifically introduce fluorophores into eukaryotic Argonaute...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924479/assessing-the-off-target-effects-of-mirna-inhibitors-on-innate-immune-toll-like-receptors
#4
Geneviève Pépin, Jonathan Ferrand, Michael P Gantier
MicroRNAs (miRNAs) are involved in most cellular processes and are deregulated in several diseases. Antisense miRNA oligonucleotides (AMOs) therefore present novel therapeutic opportunities. Currently, in vivo delivery of AMOs often relies on high doses of nucleic acids, with nonspecific uptake by most tissues. Critically, AMOs accumulate in phagocytic cells where they can interfere with immune functions, such as the activation of Toll-Like Receptors (TLRs). In this chapter, we describe a method to assess the possible off-target effects of AMOs on TLR7, 8, and 9 sensing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924115/-genetic-coding-reconsidered-an-analysis-of-actual-usage
#5
Ulrich E Stegmann
This article reconsiders the theoretical role of the genetic code. By drawing on published and unpublished sources from the 1950s, I analyse how the code metaphor was actually employed by the scientists who first promoted its use. The analysis shows that the term 'code' picked out mechanism sketches, consisting of more or less detailed descriptions of ordinary molecular components, processes, and structural properties of the mechanism of protein synthesis. The sketches provided how-possibly explanations for the ordering of amino acids by nucleic acids (the 'coding problem')...
September 2016: British Journal for the Philosophy of Science
https://www.readbyqxmd.com/read/27924036/folding-and-misfolding-pathways-of-g-quadruplex-dna
#6
Adrien Marchand, Valérie Gabelica
G-quadruplexes adopt various folding topologies, but information on their folding pathways remains scarce. Here, we used electrospray mass spectrometry to detect and quantify the specifically bound potassium ions, and circular dichroism to characterize the stacking topology of each ensemble. For human telomeric (hTel) sequences containing the d((GGGTTA)3GGG) core, K(+) binding affinity and cooperativity strongly depends on the chosen construct. The shortest sequences bind only one K(+) at low KCl concentration, and this 2-quartet G-quadruplex is antiparallel...
October 19, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923932/nucleobase-modification-by-an-rna-enzyme
#7
Raghav R Poudyal, Phuong D M Nguyen, Melissa P Lokugamage, Mackenzie K Callaway, Jesse V Gavette, Ramanarayanan Krishnamurthy, Donald H Burke
Ribozymes can catalyze phosphoryl or nucleotidyl transfer onto ribose hydroxyls of RNA chains. We report a single ribozyme that performs both reactions, with a nucleobase serving as initial acceptor moiety. This unprecedented combined reaction was revealed while investigating potential contributions of ribose hydroxyls to catalysis by kinase ribozyme K28. For a 58nt, cis-acting form of K28, each nucleotide could be replaced with the corresponding 2'F analog without loss of activity, indicating that no particular 2'OH is specifically required...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923930/mg2-ions-do-they-bind-to-nucleobase-nitrogens
#8
Filip Leonarski, Luigi D'Ascenzo, Pascal Auffinger
Given the many roles proposed for Mg(2+) in nucleic acids, it is essential to accurately determine their binding modes. Here, we surveyed the PDB to classify Mg(2+) inner-sphere binding patterns to nucleobase imine N1/N3/N7 atoms. Among those, purine N7 atoms are considered to be the best nucleobase binding sites for divalent metals. Further, Mg(2+) coordination to N7 has been implied in several ribozyme catalytic mechanisms. We report that Mg(2+) assigned near imine nitrogens derive mostly from poor interpretations of electron density patterns and are most often misidentified Na(+), K(+), NH4(+) ions, water molecules or spurious density peaks...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923765/better-together-strategies-based-on-magnetic-particles-and-quantum-dots-for-improved-biosensing
#9
REVIEW
Laura Moro, Mehmet Turemis, Bruna Marini, Rudy Ippodrino, Maria Teresa Giardi
Novel technologies and strategies for sensitive detection of biological responses in healthcare, food and environmental monitoring continue to be a priority. The present review focuses on bioassay development based on the simultaneous use of quantum dots and magnetic beads. Due to the outstanding characteristics of both particles for biosensing applications and the large number of publications using a combined approach, we aim to provide a comprehensive overview of the literature on different bioassays, the most recent advances and innovative strategies on the topic, together with an analysis of the main drawbacks encountered and potential solutions offered, with a special emphasis on the requirements that the transfer of technologies from the laboratory to the market will demand for future commercialization ofbiodevices...
December 3, 2016: Biotechnology Advances
https://www.readbyqxmd.com/read/27923672/functional-characterization-of-two-novel-purine-transporters-from-the-basidiomycota-phanerochaete-chrysosporium
#10
Mariana Barraco-Vega, Héctor Romero, Mariana Richero, María Pía Cerdeiras, Gianna Cecchetto
Purine transporters as substrate entry points in organisms, are involved in a number of cellular processes such as nitrogen source uptake, energy metabolism and synthesis of nucleic acids. In this study, two nucleobase transporter genes (phZ, phU) from Phanerochaete chrysosporium were cloned, identified, and functionally characterized. Our results show that PhZ is a transporter of adenine and hypoxanthine, and a protein belonging to the AzgA-like family, whilst PhU belongs to the NAT/NCS2 family, transporting xanthine and uric acid...
December 3, 2016: Gene
https://www.readbyqxmd.com/read/27923656/the-novel-antioxidant-ta293-reveals-the-role-of-cytoplasmic-hydroxyl-radicals-in-oxidative-stress-induced-senescence-and-inflammation
#11
Takahiro Sakai, Jun Imai, Tomohiro Ito, Hidetsugu Takagaki, Michio Ui, Shinichi Hatta
The hydroxyl radical (OH) possesses the strongest oxidation potential among reactive oxygen species (ROS). Hydroxyl radicals react nonpreferentially with proteins, lipids, and nucleic acids. Additionally, mitochondrial localization of OH causes dysfunction in the mitochondria. The cytoplasmic targets of OH-induced oxidation are unknown. No cytoplasm-specific OH scavenger is available; thus, elucidating the cytoplasmic targets of OH-induced oxidation has proven difficult. Accordingly, we developed a cytoplasm-specific OH-targeted scavenger, TA293, and a mitochondrion-specific scavenger, mitoTA293...
December 3, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27923366/3c-digital-pcr-for-quantification-of-chromatin-interactions
#12
Meijun Du, Liang Wang
BACKGROUND: Chromosome conformation capture (3C) is a powerful and widely used technique for detecting the physical interactions between chromatin regions in vivo. The principle of 3C is to convert physical chromatin interactions into specific DNA ligation products, which are then detected by quantitative polymerase chain reaction (qPCR). However, 3C-qPCR assays are often complicated by the necessity of normalization controls to correct for amplification biases. In addition, qPCR is often limited to a certain cycle number, making it difficult to detect fragment ligations with low frequency...
December 6, 2016: BMC Molecular Biology
https://www.readbyqxmd.com/read/27922207/stimuli-responsive-dna-functionalized-metal-organic-frameworks-mofs
#13
Jason S Kahn, Lina Freage, Natalie Enkin, Miguel Angel Aleman Garcia, Itamar Willner
The synthesis of nucleic acid-functionalized metal-organic frameworks (MOFs) is described. The metal-organic frameworks are loaded with a dye being locked in the structures by means of stimuli-responsive nucleic acid caps. The pH and K(+) -ion-triggered release, and switchable release, are demonstrated.
December 6, 2016: Advanced Materials
https://www.readbyqxmd.com/read/27921323/the-application-of-strand-invasion-phenomenon-directed-by-peptide-nucleic-acid-pna-and-single-stranded-dna-binding-protein-ssb-for-the-recognition-of-specific-sequences-of-human-endogenous-retroviral-herv-w-family
#14
Grzegorz Machnik, Łukasz Bułdak, Jarosław Ruczyński, Tomasz Gąsior, Małgorzata Huzarska, Dariusz Belowski, Magdalena Alenowicz, Piotr Mucha, Piotr Rekowski, Bogusław Okopień
The HERV-W family of human endogenous retroviruses represents a group of numerous sequences that show close similarity in genetic composition. It has been documented that some members of HERV-W-derived expression products are supposed to play significant role in humans' pathology, such as multiple sclerosis or schizophrenia. Other members of the family are necessary to orchestrate physiological processes (eg, ERVWE1 coding syncytin-1 that is engaged in syncytiotrophoblast formation). Therefore, an assay that would allow the recognition of particular form of HERV-W members is highly desirable...
December 6, 2016: Journal of Molecular Recognition: JMR
https://www.readbyqxmd.com/read/27920668/getting-mirna-therapeutics-into-the-target-cells-for-neurodegenerative-diseases-a-mini-review
#15
REVIEW
Ming Ming Wen
miRNAs play important roles in modulating gene expression in varying cellular processes and disease pathogenesis, including neurodegenerative diseases. Several miRNAs are expressed in the brain, control brain development and are identified as important biomarkers in the pathogenesis of motor-and neuro-cognitive diseases such as Alzheimer's (AD), Huntington's and Parkinson's diseases (PD) and amyotrophic lateral sclerosis. These remarkable miRNAs could be used as diagnostic markers and therapeutic targeting potential for many stressful and untreatable progressive neurodegenerative diseases...
2016: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/27920649/hepatoid-carcinoma-of-the-pancreas-case-report-next-generation-tumor-profiling-and-literature-review
#16
James M Chang, Nitin N Katariya, Dora M Lam-Himlin, Danielle J Haakinson, Ramesh K Ramanathan, Thorvardur R Halfdanarson, Mitesh J Borad, Rahul Pannala, Douglas Faigel, Adyr A Moss, Amit K Mathur
Fewer than 25 cases of hepatoid carcinoma of the pancreas have been reported in the literature. We present a case in a 61-year-old male with a remote history of Hodgkin's lymphoma and gastric neuroendocrine cell hyperplasia. On surveillance endoscopic ultrasound, an 8 × 5 mm cystic lesion was seen in the tail of the pancreas. MRI showed a focal pancreatic duct cut-off with mild ductal dilation. Fine needle aspiration was performed, which was concerning for acinar cell carcinoma. The patient underwent distal pancreatectomy and recovered uneventfully...
September 2016: Case Reports in Gastroenterology
https://www.readbyqxmd.com/read/27920533/effect-of-inserted-spacer-in-hepatic-cell-penetrating-multifunctional-peptide-component-on-the-dna-intracellular-delivery-of-quaternary-complexes-based-on-modular-design
#17
Luchen Zhang, Zhenbo Li, Fangli Sun, Yuhong Xu, Zixiu Du
A safe and efficient quaternary gene delivery system (named Q-complexes) was constructed based on self-assembly of molecules through noncovalent bonds. This system was formulated through the cooperation and competing interactions of cationic liposomes, multifunctional peptides, and DNA, followed by coating hyaluronic acid on the surface of the ternary complexes. The multifunctional peptide was composed of two functional domains: penetrating hepatic tumor-targeted cell moiety (KRPTMRFRYTWNPMK) and a wrapping gene sequence (polyarginine 16)...
2016: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/27920430/biomimetic-antimicrobial-cloak-by-graphene-oxide-agar-hydrogel
#18
Massimiliano Papi, Valentina Palmieri, Francesca Bugli, Marco De Spirito, Maurizio Sanguinetti, Carlotta Ciancico, Maria Chiara Braidotti, Silvia Gentilini, Luca Angelani, Claudio Conti
Antibacterial surfaces have an enormous economic and social impact on the worldwide technological fight against diseases. However, bacteria develop resistance and coatings are often not uniform and not stable in time. The challenge is finding an antibacterial coating that is biocompatible, cost-effective, not toxic, and spreadable over large and irregular surfaces. Here we demonstrate an antibacterial cloak by laser printing of graphene oxide hydrogels mimicking the Cancer Pagurus carapace. We observe up to 90% reduction of bacteria cells...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920208/genetic-modification-of-er-hoxb8-osteoclast-precursors-using-crispr-cas9-as-a-novel-way-to-allow-studies-on-osteoclast-biology
#19
Irene Di Ceglie, Guus G H van den Akker, Giuliana Ascone, Bas Ten Harkel, Hans Häcker, Fons A J van de Loo, Marije I Koenders, Peter M van der Kraan, Teun J de Vries, Thomas Vogl, Johannes Roth, Peter L E M van Lent
Osteoclasts are cells specialized in bone resorption. Currently, studies on murine osteoclasts are primarily performed on bone marrow-derived cells with the use of many animals and limited cells available. ER-Hoxb8 cells are conditionally immortalized monocyte/macrophage murine progenitor cells, recently described to be able to differentiate toward functional osteoclasts. Here, we produced an ER-Hoxb8 clonal cell line from C57BL/6 bone marrow cells that strongly resembles phenotype and function of the conventional bone marrow-derived osteoclasts...
December 5, 2016: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/27919704/global-transcriptome-analysis-of-halolamina-sp-to-decipher-the-salt-tolerance-in-extremely-halophilic-archaea
#20
Aslıhan Kurt-Kızıldoğan, Büşra Abanoz, Sezer Okay
Extremely halophilic archaea survive in the hypersaline environments such as salt lakes or salt mines. Therefore, these microorganisms are good sources to investigate the molecular mechanisms underlying the tolerance to high salt concentrations. In this study, a global transcriptome analysis was conducted in an extremely halophilic archaeon, Halolamina sp. YKT1, isolated from a salt mine in Turkey. A comparative RNA-seq analysis was performed using YKT1 isolate grown either at 2.7M NaCl or 5.5M NaCl concentrations...
December 2, 2016: Gene
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