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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
Wenjia Li, Huanhuan Shi, Bo Dong, Kaixuan Nie, Zhengchun Liu, Nongyue He
Targeting double-stranded DNA (dsDNA) with high affinity and specificity has become a hot topic in biochemistry and molecular biology research. Gene diagnosis and therapy, DNA manipulation, and gene expression regulation could be achieved based on certain recognition principles through specific interactions between dsDNA and natural nucleotides or synthesized ligands. Some ligands (e.g., peptide nucleic acids (PNAs), triple helix-forming oligonucleotides (TFOs), oligopolyamides, and zinc-finger peptides) show sufficient affinity and specificity for targeting dsDNA sequences...
October 28, 2016: Current Medicinal Chemistry
Brunella Pinto, Giulia Rusciano, Stefano D'Errico, Nicola Borbone, Antonio Sasso, Vincenzo Piccialli, Luciano Mayol, Giorgia Oliviero, Gennaro Piccialli
BACKGROUND: G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS: The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS)...
November 29, 2016: Biochimica et Biophysica Acta
Takaya Sato, Yusuke Sato, Seiichi Nishizawa
A series of triplex-forming PNA probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base...
November 29, 2016: Chemistry: a European Journal
Euna Oh, Byeonghwa Jeon
Peptide nucleic acid (PNA) is an oligonucleotide mimic that recognizes and binds to nucleic acids. The strong binding affinity of PNA to mRNA coupled with its high sequence specificity enable antisense PNA to selectively inhibit (i.e., knockdown) the protein synthesis of a target gene. This novel technology provides a powerful tool for Campylobacter studies because molecular techniques have been relatively less well-developed for this bacterium as compared to other pathogens, such as Escherichia coli and Salmonella...
2017: Methods in Molecular Biology
Gemin Fang, Oliver Seitz
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached via covalent bonds to an oligonucleotide probe. However, the additional conjugation step increases costs. Herein we introduce a method that avoids the requirement for the preparation of fluorescence labeled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid probes to form a bipartite tetracysteine motif which binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH...
November 24, 2016: Chembiochem: a European Journal of Chemical Biology
Mainak Dutta, Dibakar Haldar
OBJECTIVE: To optimize the outcome of transnasal endoscopic sphenopalatine artery ligation (TESPAL) by determining the key surgical steps and applying them accordingly. METHODS: This is a case-control study carried out in a tertiary care teaching institution on subjects who underwent TESPAL during the period of October 2010 to September 2015. Their surgical and clinical records were reviewed, and success (no re-bleed) and failure (return with re-bleed) were considered the main outcome measures of TESPAL...
November 18, 2016: Auris, Nasus, Larynx
Tamaki Endoh, Chiara Annoni, Dziyana Hnedzko, Eriks Rozners, Naoki Sugimoto
Peptide nucleic acid (PNA) modified with unnatural nucleobases enables the formation of a highly stable triplex with a double-stranded RNA at physiological pH. In this communication, we evaluated kinetics and thermodynamics of PNA/RNA triplex formation as a function of both pH and temperature. Protonation entropy was found to be the major factor responsible for the destabilization of the triplex and for the progressive decrease in the association rate at more basic pHs.
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
Frank Persson, Carolina Suarez, Malte Hermansson, Elzbieta Plaza, Razia Sultana, Britt-Marie Wilén
Partial nitritation-anammox (PNA) permits energy effective nitrogen removal. Today PNA is used for treatment of concentrated and warm side streams at wastewater treatment plants, but not the more diluted and colder main stream. To implement PNA in the main stream, better knowledge about microbial communities at the typical environmental conditions is necessary. In order to investigate the response of PNA microbial communities to decreasing substrate availability, we have operated a moving bed biofilm reactor (MBBR) at decreasing reactor concentrations (311-27 mg-N l(-1) of ammonium) and low temperature (13°C) for 302 days and investigated the biofilm community using high throughput amplicon sequencing; quantitative PCR; and fluorescence in situ hybridization...
November 14, 2016: Microbial Biotechnology
Jinbei Wei, Baoyan Liang, Ruihong Duan, Zong Cheng, Chenglong Li, Tianlei Zhou, Yuanping Yi, Yue Wang
The design and preparation of metal-free organic materials that exhibit room-temperature phosphorescence (RTP) is a very attractive topic owing to potential applications in organic optoelectronic devices. Herein, we present a facile approach to efficient and long-lived organic RTP involving the doping of N-phenylnaphthalen-2-amine (PNA) or its derivatives into a crystalline 4,4'-dibromobiphenyl (DBBP) matrix. The resulting materials showed strong and persistent RTP emission with a quantum efficiency of approximately 20 % and a lifetime of a few to more than 100 milliseconds...
November 15, 2016: Angewandte Chemie
Poulomi Ray, Ami J Hughes, Misha Sharif, Susan C Chapman
Cartilage morphogenesis during endochondral ossification follows a progression of conserved developmental events. Cells are specified towards a prechondrogenic fate and subsequently undergo condensation followed by overt differentiation. Currently available molecular markers of prechondrogenic and condensing mesenchyme rely on common regulators of the chondrogenic program that are not specific to the tissue type or location. Therefore tissue-specific condensations cannot be distinguished based on known molecular markers...
November 16, 2016: Journal of Anatomy
Helen Bergquist, Cristina S J Rocha, Rubén Álvarez-Asencio, Chi-Hung Nguyen, Mark W Rutland, C I Edvard Smith, Liam Good, Peter E Nielsen, Rula Zain
Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich's ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions...
2016: PloS One
Michaela Lackner, Cornelia Lass-Flörl
The increasing interest in molecular diagnostics is a result of tremendously improved knowledge on fungal infections in the past 20 years and the rapid development of new methods, in particular polymerase chain reaction. High expectations have been placed on molecular diagnostics, and the number of laboratories now using the relevant technology is rapidly increasing-resulting in an obvious need for standardization and definition of laboratory organization. In the past 10 years, multiple new molecular tools were marketed for the detection of DNA, antibodies, cell wall components, or other antigens...
2017: Methods in Molecular Biology
Norma Estrada, Edwin Velázquez, Carmen Rodríguez-Jaramillo, Felipe Ascencio
Hemocytes represent one of the most important defense mechanisms against foreign material in Crustacea and are also involved in a variety of other physiological responses. Fluorescent lectin-binding assays and cytochemical reactions were used to identify specificity and distribution of carbohydrate moieties and presence of several hydrolytic enzymes, in hemocytes of whiteleg shrimp Litopenaeus vannamei. Two general classes of circulating hemocytes (granular and agranular) exist in L. vannamei, which express carbohydrates residues for FITC-conjugated lectins WGA, LEA, and PNA; UEA and Con-A were not observed...
2016: International Journal of Cell Biology
Artem P Lisachov, Pavel M Borodin
Most true lizards (Lacertidae) share a conservative karyotype, consisting of 18 pairs of macrochromosomes and one microchromosome pair. Homeologues of the microchromosome are present in other squamates and even in chickens. No structural autosomal microchromosome polymorphisms have been described previously in lizards. We found homozygous and heterozygous carriers of a microchromosome variant in a Siberian population of the sand lizard, Lacerta agilis Linnaeus, 1758. The variant microchromosome was almost twice as long as the standard one...
2016: Comparative Cytogenetics
Markus Nörrlinger, Sven Hafner, Thomas Ziegler
Four glycoconjugate building blocks for the construction of combinatorial PNA like glycopeptide libraries were prepared in 75-79% yield by condensing tert-butyl N-[2-(N-9-fluorenylmethoxycarbonylamino)ethyl]glycinate (AEG) 5 with 3-oxo-3-(2,3,4,6-tetra-O-acetyl-β-D-glucopyranosylamino)- (6a), 3-oxo-3-(β-D-galactopyranosylamino)- (6b), 3-oxo-3-(2-acetamido-2-deoxy-3,4,6-tetra-O-acetyl-β-D-glucopyranosylamino)- (6c) and 3-oxo-3-(2-acetamido-2-deoxy-3,4,6-tetra-O-acetyl-β-D-galactopyranosylamino)propanoic acid (6d), respectively...
2016: Beilstein Journal of Organic Chemistry
Subhasis Roy Choudhury, Niyaz Ahmed Khan, Rahul Saxena, Partap Singh Yadav, Jigar N Patel, Rajiv Chadha
AIM: Although liver abscess (LA) is prevalent worldwide, especially in developing countries, there is a paucity of data regarding the protocol for management of LA in children. The aim of this study was to analyze the outcome of a protocol-based management of pediatric LA from a single institution. MATERIALS AND METHODS: This prospective observational study was conducted in a tertiary-care children's hospital and included all patients with LA managed over a 5-year period...
November 8, 2016: Pediatric Surgery International
Maria Mastrodonato, Donatella Mentino, Angela Lopedota, Annalisa Cutrignelli, Giovanni Scillitani
Intracellular glycans in the urothelium of urinary bladder of 10 adult male Landrace pigs were characterized in situ by immunohistochemical detection of Muc1 mucin by anti MUC1 from rabbit, conventional histochemical techniques (Periodic-Acid Schiff, Alcian Blue pH 2.5, High-Iron Diamine), and binding with 13 lectins (PNA, DBA, RCA-I, WGA, SBA, BSI-B4, ConA, AAA, UEA-I, LTA, LFA, MAA-II, SNA) combined with chemical and enzymatic pre-treatments (β-elimination, desulfation and neuraminidase) to gather reference data for this model animal...
November 1, 2016: Microscopy Research and Technique
Si-Ying Wu, Gil-Yong Park, So-Hee Kim, John Hulme, Seong Soo A An
The aim of this study was to investigate the bacteriostatic and bactericidal effects of diminazene aceturate (DA) against five strains of pathogenic bacteria and two strains of nonpathogenic bacteria. The results showed that 5 μg/mL of DA suppressed the growth of pathogenic Escherichia coli by as much as 77% compared with the controls. Enterohemorrhagic E. coli EDL933 (an E. coli O157:H7 strain) was the most sensitive to DA with a minimum inhibitory concentration of 20 μg/mL. Additional investigations showed that DA induced the highest level of intracellular reactive oxygen species in EDL933...
2016: Drug Design, Development and Therapy
Alex Manicardi, Alessandro Bertucci, Andrea Rozzi, Roberto Corradini
A synthetic strategy for the production of polyfunctional PNAs bearing substituent groups both on the nucleobase and on the backbone C5 carbon of the same monomer is described; this is based on the use of a tris-orthogonally protected monomer and subsequent solid-phase selective functionalization. This strategy can be used for synthesizing PNAs that are not readily accessible by use of preformed modified monomers. As an example, a PNA-based probe that undergoes a switch in its fluorescence emission upon hybridization with a target oligonucleotide, induced by tailor-made movement of two pyrene substituent groups, was synthesized...
October 21, 2016: Organic Letters
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