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https://www.readbyqxmd.com/read/28730445/polycationic-probe-guided-nanopore-single-molecule-counter-for-selective-mirna-detection
#1
Kai Tian, Ruicheng Shi, Amy Gu, Michael Pennella, Li-Qun Gu
MicroRNAs (miRNAs) are a class of noncoding RNAs that are being explored as a new type of disease biomarkers. The nanopore single-molecule sensor offers a potential noninvasive tool to detect miRNAs for diagnostics and prognosis applications. However, one of the challenges that limits its clinical applications is the presence of a large variety of nontarget nucleic acids in the biofluid extracts. Upon interacting with the nanopore, nontarget nucleic acids produce "contaminative" nanopore signals that interfere with target miRNA discrimination, thus severely lowering the accuracy in target miRNA detection...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28728975/continuous-nitrogen-removal-by-a-single-stage-reactor-packed-with-ring-laced-string-medium
#2
Masahiro Tatara, Shu Ishikawa, Yoshiyuki Ueno
The efficiency of nitrogen removal by a partial-nitritation/anammox (PNA) reaction was investigated using a packed-bed reactor in which ring-laced strings were used as the supporting medium. A stable population of PNA microorganisms was established from typical activated sludge, after less than two months of acclimation in the packed-bed reactor, by applying a high nitrogen-loading rate (NLR: 0.53 kg/m(3)/d) and short hydraulic retention time (HRT: 1.8 h). The stability of reactor performance was confirmed in industrial wastewater (IW), demonstrating a nitrogen removal efficiency (NRE) of greater than 77% during 260 days of continuous operation, between 0...
July 17, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28709076/coupling-autotrophic-denitrification-with-partial-nitritation-anammox-pna-for-efficient-total-inorganic-nitrogen-removal
#3
Sunayna Dasgupta, Sha Wu, Ramesh Goel
The performance of and the microbial ecology in an integrated lab scale set up comprising of a PN/A bioreactor and an elemental sulfur-supported packed bed autotrophic denitrification (ESSAD) are reported. The PN/A reactor exhibited an average removal rate of 0.56±0.103kgNm(-3)d(-1), whereas the ESSAD reactor removed an average of 0.0018kg NO3(-)-Nm(-3)d(-1). The combined average removal rate was 0.6kgNm(-3)d(-1), yielding an overall total inorganic nitrogen efficiency of 97%. Based on 16S rRNA gene clone libraries from the ESSAD reactor, the extracted Operational Taxonomic Units (OTUs) formed a clade with Thiobacillus denitrificans sp...
June 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28704609/hydrophilic-and-cell-penetrable-pyrrolidinyl-peptide-nucleic-acid-pna-via-post-synthetic-modification-with-hydrophilic-side-chains
#4
Chaturong Suparpprom, Thanesuan Nuanyai, Haruthai Pansuwan, Tirayut Vilaivan, Supason Wanichwecharungruang, Boonsong Ditmangklo, Tanapat Palaga, Porntip Pan-In, Banphot Jiangchareon, Chotima Vilaivan
Peptide Nucleic Acid (PNA) is a nucleic acid mimic in which the deoxyribose-phosphate was replaced by a peptide-like backbone. The absence of negative charge in the PNA backbone leads to several unique behaviors including a stronger binding and salt-independency of the PNA-DNA duplex stability. However, PNA possesses poor aqueous solubility and cannot directly penetrate cell membranes. These are major obstacles that limited in vivo applications of PNA. In previous strategies, the PNA can be conjugated to macromolecular carrier, or modified with positively charged side chains such as guanidinium groups to improve the aqueous solubility and/or cell permeability...
July 13, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28699197/sperm-telomere-length-in-motile-sperm-selection-techniques-a-qfish-approach
#5
R Lafuente, E Bosch-Rue, J Ribas-Maynou, J Alvarez, C Brassesco, M J Amengual, J Benet, A Garcia-Peiró, M Brassesco
Several studies have associated telomere shortening with alterations in reproductive function. The objective of the present study was to determine telomere length (TL) in spermatozoa selected by either density-gradient centrifugation (DGC) or swim-up. The analysis of TL was performed using quantitative fluorescent in situ hybridisation (qFISH) using PNA probes in combination with a chromatin decompaction protocol in sperm cells. Results of TL were 24.64 ± 5.00 Kb and 24.95 ± 4.60 Kb before and after DGC, respectively, and 19...
July 11, 2017: Andrologia
https://www.readbyqxmd.com/read/28698463/peptide-nucleic-acids-as-mirna-target-protectors-for-the-treatment-of-cystic-fibrosis
#6
Federica Zarrilli, Felice Amato, Carmine Marco Morgillo, Brunella Pinto, Giuliano Santarpia, Nicola Borbone, Stefano D'Errico, Bruno Catalanotti, Gennaro Piccialli, Giuseppe Castaldo, Giorgia Oliviero
Cystic Fibrosis (CF) is one of the most common life shortening conditions in Caucasians. CF is caused by mutations in the CF Transmembrane Conductance Regulator (CFTR) gene which result in reduced or altered CFTR functionality. Several microRNAs (miRNAs) downregulate the expression of CFTR, thus causing or exacerbating the symptoms of CF. In this context, the design of anti-miRNA agents represents a valid functional tool, but its translation to the clinic might lead to unpredictable side effects because of the interference with the expression of other genes regulated by the same miRNAs...
July 8, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28696677/a-monolithic-peptide-nucleic-acid-hybrid-functioning-as-an-artificial-microperoxidase
#7
Koji Nakano, Junichi Tanabe, Ryoichi Ishimatsu, Toshihiko Imato
A new peptide nucleic acid (PNA) with an installed peroxidase function has been developed. Fmoc solid phase peptide synthesis prepared a PNA hybrid (VQKCAQCHTVE-(C2H4O)2CH2-[PNA(T)]6-G) that renders the microperoxidase backbone, followed by reconstitution with hemin. The resulting holocompound catalyzed the oxidation of 3,3',5,5'-tetramthylbenzidine by H2O2 to 50% that of natural microperoxidase-11, whereas the apo-form and hemin gave no responses. The peroxidase domain was found to be active toward direct electrochemistry and the PNA hybrid served for gene sensor; in the presence of the target DNA (5'-CATGTATAAAAAA-3'), an electrode-attached DNA probe (5'-TsTsTsTsTsTCTCATACATG-3') showed the ferric-to-ferrous quasi-reversible wave (-276 mV vs...
July 11, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28695635/taurine-does-not-improve-the-quality-of-short-term-stored-rabbit-spermatozoa-in-vitro
#8
D Paál, F Strejček, E Tvrdá, J Vašíček, A Baláži, P Chrenek, P Massányi
This study examines the impact of taurine on the viability, morphology and acrosome integrity of rabbit spermatozoa in vitro. Semen samples, obtained from four to five sexually mature and healthy New Zealand White rabbits, were pooled in heterospermic semen sample. This was divided and treated with taurine in a concentration of 0 (control), 1.5, 7, 12.5, 50 mM to a final concentration of 10(8)  spermatozoa/ml. The samples were then incubated at 37°C for 4 hr. A combination of fluorescent probes SYBR-14/propidium iodide/PNA-Alexa Fluor 647 was used to assess spermatozoa viability and acrosome integrity on a flow cytometer...
July 10, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28690651/mutations-of-the-epidermal-growth-factor-receptor-gene-in-triple-negative-breast-cancer
#9
Aeri Kim, Min Hye Jang, Soo Jung Lee, Young Kyung Bae
PURPOSE: Epidermal growth factor receptor (EGFR) is considered a potential therapeutic target for anti-EGFR therapy in triple-negative breast cancer (TNBC). However, the frequency of EGFR gene mutation in TNBC is low and varies with ethnicity. This study aimed to investigate the incidence of EGFR gene mutation in TNBC. METHODS: EGFR protein expression was evaluated by immunohistochemistry in tissue microarrays of 493 TNBC cases using four different primary antibodies, which included mutation-specific antibodies...
June 2017: Journal of Breast Cancer
https://www.readbyqxmd.com/read/28686972/peptide-nucleic-acids-pnas-currently-potential-bactericidal-agents
#10
REVIEW
Hanar Narenji, Pourya Gholizadeh, Mohammad Aghazadeh, Mohammad Ahangarzadeh Rezaee, Mohammad Asgharzadeh, Hossein Samadi Kafil
In recent years, the emergence of ESBL-producing and multi-drug resistant bacteria have been increased and designing novel components is necessary for confrontation these bacteria. Peptide nucleic acids (PNAs) are one of the synthetic components that bind to single strand DNA and RNA. Applications of these components are wide while, and one of the important applications of these components is inhibition of gene expression and knock downing the target gene follow as inhibition of bacterial growth. For PNA targeting gene, peptide-PNAs (PPNA) activity cannot be occurred without sequence homology, at the same time, it has been affected by sequence-based specific target and dose-dependent-based manner...
July 4, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28679838/fluorocitrate-mediated-depolarization-of-astrocytes-in-the-retrotrapezoid-nucleus-stimulates-breathing
#11
Cleyton R Sobrinho, Christopher M Gonçalves, Ana C Takakura, Daniel K Mulkey, Thiago S Moreira
Evidence indicates that CO2/H(+)-evoked ATP released from retrotrapezoid nucleus (RTN) astrocytes modulates the activity of CO2-sensitive neurons. RTN astrocytes also sense H+ by inhibition of Kir4.1 channels; however, the relevance of this pH-sensitive current remains unclear since ATP release appears to involve CO2-dependent gating of connexin 26 hemichannels. Considering that depolarization mediated by H(+) inhibition of Kir4.1 channels is expected to increase sodium bicarbonate cotransporter (NBC) conductance and favor Ca(2+) influx via the sodium calcium exchanger (NCX), we hypothesize that depolarization in the presence of CO2 is sufficient to facilitate ATP release and enhance respiratory output...
July 5, 2017: Journal of Neurophysiology
https://www.readbyqxmd.com/read/28678845/polymerase-free-measurement-of-microrna-122-with-single-base-specificity-using-single-molecule-arrays-detection-of-drug-induced-liver-injury
#12
David M Rissin, Barbara López-Longarela, Salvatore Pernagallo, Hugh Ilyine, A D Bastiaan Vliegenthart, James W Dear, Juan J Díaz-Mochón, David C Duffy
We have developed a single probe method for detecting microRNA from human serum using single molecule arrays, with sequence specificity down to a single base, and without the use of amplification by polymerases. An abasic peptide nucleic acid (PNA) probe-containing a reactive amine instead of a nucleotide at a specific position in the sequence-for detecting a microRNA was conjugated to superparamagnetic beads. These beads were incubated with a sample containing microRNA, a biotinylated reactive nucleobase-containing an aldehyde group-that was complementary to the missing base in the probe sequence, and a reducing agent...
2017: PloS One
https://www.readbyqxmd.com/read/28674833/cloning-purification-and-characterization-of-tripeptidyl-peptidase-from-streptomyces-herbaricolor-ty-21
#13
Keisuke Ekino, Shinichi Yonei, Hiroshi Oyama, Takuji Oka, Yoshiyuki Nomura, Takashi Shin
Tripeptidyl peptidase (TPP) is an exopeptidase that sequentially hydrolyzes tripeptides from the N-terminus of oligopeptides or polypeptides. We performed screening for isolating novel TPP-producing microorganisms from soil samples. TPP activity was observed in the culture supernatant of Streptomyces herbaricolor TY-21 by using Ala-Ala-Phe-p-nitroanilide (pNA) as the substrate. TPP from the culture supernatant was purified to approximately 790-fold. It was shown to cleave oxidized insulin B-chain, thereby with releasing tripeptide units, but not the N-terminal-protected peptide, Cbz-Ala-Ala-Phe-pNA...
July 3, 2017: Applied Biochemistry and Biotechnology
https://www.readbyqxmd.com/read/28657690/a-dna-based-encryption-method-based-on-dna-chip-and-pcr-amplification-techniques
#14
Yunpeng Zhang, Zhiwen Wang, Zhenzhen Wang, Xiaojing Yuan
Researchers have gained deeper understanding of DNA-based encryption and its effectiveness in enhancing information security in the security field in recent years. However, there are a lot of theoretical and technical issues about DNA-based encryption that need to be addressed before it can be effectively used in the field of information security. Currently most popular DNA-based encryption schemes are based on integrating traditional cryptography and existing DNA technology. They are not totally based on DNA computing and Bio-technology...
June 28, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28655215/development-of-a-new-method-based-on-unmodified-gold-nanoparticles-and-peptide-nucleic-acids-for-detecting-bovine-viral-diarrhea-virus-rna
#15
Maryam Askaravi, Seyedeh Elham Rezatofighi, Saadat Rastegarzadeh, Masoud Reza Seifi Abad Shapouri
A simple colorimetric assay is presented for detecting bovine viral diarrhea virus (BVDV)-RNA based on aggregation of gold nanoparticles (AuNPs) in the presence of charge-neutral peptide nucleic acids (PNA). Free charge-neutral PNA oligomers tended to be adsorbed onto AuNPs and act as a coagulant, whereas hybridizing complementary RNA with PNA disrupted PNA-induced AuNP aggregation, and the NPs remained stable. However, non-complementary RNA did not have this effect, and PNA induced aggregation of the AuNPs that resulted in a color change of the reaction from red to blue...
December 2017: AMB Express
https://www.readbyqxmd.com/read/28643380/microscopy-visualisation-confirms-multi-species-biofilms-are-ubiquitous-in-diabetic-foot-ulcers
#16
Khalid Johani, Matthew Malone, Slade Jensen, Iain Gosbell, Hugh Dickson, Honhua Hu, Karen Vickery
Increasing evidence within the literature has identified the presence of biofilms in chronic wounds and proposed that they contribute to delayed wound healing. This research aimed to investigate the presence of biofilm in diabetic foot ulcers (DFUs) using microscopy and molecular approaches and define if these are predominantly mono- or multi-species. Secondary objectives were to correlate wound observations against microscopy results in ascertaining if clinical cues are useful in detecting wound biofilm. DFU tissue specimens were obtained from 65 subjects...
June 23, 2017: International Wound Journal
https://www.readbyqxmd.com/read/28638803/peptide-nucleic-acid-knockdown-and-intra-host-cell-complementation-of-ehrlichia-type-iv-secretion-system-effector
#17
Pratibha Sharma, Omid Teymournejad, Yasuko Rikihisa
Survival of Ehrlichia chaffeensis depends on obligatory intracellular infection. One of the barriers to E. chaffeensis research progress has been the inability, using conventional techniques, to generate knock-out mutants for genes essential for intracellular infection. This study examined the use of Peptide Nucleic Acids (PNAs) technology to interrupt type IV secretion system (T4SS) effector protein expression in E. chaffeensis followed by intracellular complementation of the effector to determine its requirement for infection...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28629980/polymer-nanoassemblies-with-hydrophobic-pendant-groups-in-the-core-induce-false-positive-sirna-transfection-in-luciferase-reporter-assays
#18
Steven Rheiner, Derek Reichel, Piotr Rychahou, Tadahide Izumi, Hsin-Sheng Yang, Younsoo Bae
Poly(ethylene glycol)-conjugated polyethylenimine (PEG-PEI) is a widely studied cationic polymer used to develop non-viral vectors for siRNA therapy of genetic disorders including cancer. Cell lines stably expressing luciferase reporter protein typically evaluate the transfection efficacy of siRNA/PEG-PEI complexes, however recent findings revealed that PEG-PEI can reduce luciferase expression independent of siRNA. This study elucidates a cause of the false positive effect in luciferase assays by using polymer nanoassemblies (PNAs) made from PEG, PEI, poly-(l-lysine) (PLL), palmitate (PAL), and deoxycholate (DOC): PEG-PEI (2P), PEG-PEI-PAL (3P), PEG-PLL (2P'), PEG-PLL-PAL (3P'), and PEG-PEI-DOC (2PD)...
June 16, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28624242/facile-access-to-modified-and-functionalized-pnas-through-ugi-based-solid-phase-oligomerization
#19
Jacques Saarbach, Daniela Masi, Claudio Zambaldo, Nicolas Winssinger
Peptide nucleic acids (PNAs) derivatized with functional molecules are increasingly used in diverse biosupramolecular applications. PNAs have proven to be highly tolerant to modifications and different applications benefit from the use of modified PNAs, in particular modifications at the γ position. Herein we report simple protocols to access modified PNAs from iterative Ugi couplings which allow modular modifications at the α, β or γ position of the PNA backbone from simple starting materials. We demonstrate the utility of the method with the synthesis of several bioactive small molecules (a peptide ligand, a kinase inhibitor and a glycan)-PNA conjugates...
June 14, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28617037/quantitative-determination-of-a-sirna-ad00370-in-rat-plasma-using-peptide-nucleic-acid-probe-and-hplc-with-fluorescence-detection
#20
Qingguo Tian, Juan Rogness, Min Meng, Zheng Li
AIM: Toxicokinetic and pharmacokinetic studies of therapeutic oligonucleotides require validated bioanalytical methods for sensitive and specific quantification of oligonucleotide drug candidates in biological samples. RESULTS: A peptide nucleic acid (PNA) hybridization-based HPLC-fluorescence assay was developed and validated for quantification of Arrowhead Pharmaceuticals' proprietary siRNA in rat plasma samples via hybridization and anion-exchange-HPLC (AEX-HPLC) with fluorescence detection...
June 15, 2017: Bioanalysis
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