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https://www.readbyqxmd.com/read/28229259/acidicapsa-ferrireducens-sp-nov-acidicapsa-acidiphila-sp-nov-and-granulicella-acidiphila-sp-nov-novel-acidobacteria-isolated-from-metal-rich-acidic-waters
#1
Carmen Falagán, Bärbel Foesel, Barrie Johnson
Four novel strains of Acidobacteria were isolated from water samples taken from pit lakes at two abandoned metal mines in the Iberian Pyrite Belt mining district, south-west Spain. Three of the isolates belong to the genus Acidicapsa (MCF9(T), MCF10(T), and MCF14) and one of them to the genus Granulicella (MCF40(T)). All isolates are moderately acidophilic (pH growth optimum 3.8-4.1) and mesophilic (temperature growth optima 30-32 °C). Isolates MCF10(T) and MCF40(T) grew at pH lower (<3.0) than previously reported for all other acidobacteria...
February 22, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28213328/an-integrated-dual-functional-recognition-amplification-bio-label-for-the-one-step-impedimetric-detection-of-micro-rna-21
#2
Sawsen Azzouzi, Wing Cheung Mak, Kamalodin Kor, Anthony P F Turner, Mounir Ben Ali, Valerio Beni
Alteration in expression of miRNAs has been correlated with different cancer types, tumour stage and response to treatments. In this context, a structurally responsive oligonucleotide-based electrochemical impedimetric biosensor has been developed for the simple and sensitive detection of miRNA-21. A highly specific biotinylated DNA/LNA molecular beacon (MB) probe was conjugated with gold nanoparticles (AuNPs) to create an integrated, dual function bio-label (biotin-MB-AuNPs) for both biorecognition and signal generation...
February 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28207249/convection-driven-pull-down-assays-in-nanoliter-droplets-using-scaffolded-aptamers
#3
Xiangmeng Qu, Hongbo Zhang, Hong Chen, Ali Aldalbahi, Li Li, Yang Tian, David A Weitz, Hao Pei
One of the great challenges in cellular studies is to develop a rapid and biocompatible analytical tool for single-cell analysis. We report a rapid, DNA nanostructure-supported aptamer pull-down (DNaPull) assay under convective flux in a glass capillary for analyzing contents of droplets with nano or picoliter volumes. We have demonstrated that the scaffolded aptamer can greatly improve the efficiency of target molecules' pull-down. The convective flux enables complete reaction in less than 5 min, which is an 18-fold improvement compared to purely diffusive flux (traditional model of stationary case)...
February 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193507/identification-of-organ-tissue-types-and-skin-from-forensic-samples-by-microrna-expression-analysis
#4
Eva Sauer, Antje Extra, Philipp Cachée, Cornelius Courts
The identification of organ tissues in traces recovered from scenes and objects with regard to violent crimes involving serious injuries can be of considerable relevance in forensic investigations. Molecular genetic approaches are provably superior to histological and immunological assays in characterizing organ tissues, and micro-RNAs (miRNAs), due to their cell type specific expression patterns and stability against degradation, emerged as a promising molecular species for forensic analyses, with a range of tried and tested indicative markers...
February 5, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28193505/statistical-modelling-of-ion-pgm-hid-str-10-plex-mps-data
#5
Søren B Vilsen, Torben Tvedebrink, Helle Smidt Mogensen, Niels Morling
We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences...
February 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28179111/role-of-the-oxidized-form-of-xrcc1-in-protection-against-extreme-oxidative-stress
#6
REVIEW
Julie K Horton, Hannah J Seddon, Ming-Lang Zhao, Natalie R Gassman, Agnes K Janoshazi, Donna F Stefanick, Samuel H Wilson
The multi-domain protein XRCC1 is without catalytic activity, but can interact with a number of known repair proteins. The interaction between the N-terminal domain (NTD) of XRCC1 and DNA polymerase β (pol β) is critical for recruitment of pol β to sites of DNA damage and repair. Crystallographic and NMR approaches have identified oxidized and reduced forms of the XRCC1 NTD, and the corresponding forms of XRCC1 have been identified in cultured mouse fibroblast cells. Both forms of NTD interact with pol β, but the interaction is much stronger with the oxidized form...
February 4, 2017: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/28176928/n-3-hydroxymethyl-%C3%AE-carboline-1-yl-ethyl-2-yl-l-phe-development-toward-a-nanoscaled-antitumor-drug-capable-of-treating-complicated-thrombosis-and-inflammation
#7
Jianhui Wu, Ming Zhao, Yuji Wang, Yaonan Wang, Haimei Zhu, Shurui Zhao, Lin Gui, Xiaoyi Zhang, Shiqi Peng
It is well documented that the surfaces of cancer cells, activated platelets and inflammatory cells are rich in P-selectin. N-(3-hydroxymethyl-β-carboline-1-yl-ethyl-2-yl)-l-Phe (HMCEF) is a P-selectin inhibitor capable of simultaneously inhibiting thrombosis and inflammation. Based on the knowledge that P-selectin is a common target for antithrombotic, anti-inflammatory and antitumor drugs, the aim of this study article was to estimate the possibility of HMCEF as a nanoscaled antitumor drug. Images of transmission electron micro scopy, scanning electron microscopy and atomic force microscopy proved that HMCEF forms nanoparticles with a diameter of <120 nm that promote delivery in blood circulation...
2017: Drug Design, Development and Therapy
https://www.readbyqxmd.com/read/28169232/membrane-bound-versus-soluble-major-histocompatibility-complex-class-i-related-chain-a-and-major-histocompatibility-complex-class-i-related-chain-b-differential-expression-mechanisms-of-tumor-eradication-versus-evasion-and-current-drug-development-strategies
#8
REVIEW
P K Suresh
Major histocompatibility complex Class I-related chain A/chain B (MICA/MICB) is stress-inducible, highly polymorphic ligands whose expression at the transcript level has been detected in all tissues except the central nervous system. However, their restricted protein expression is due to their regulation at the posttranslational level. Its levels are elevated in virally infected and neoplastically transformed cells. Membrane expression of this NKG2DL marks the aberrant cells for elimination by those immune effector cells that express the cognate NKG2D receptor...
October 2016: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28168566/the-value-of-cultures-to-modern-microbiology
#9
Brian Austin
Since the late nineteenth century, pure cultures have been regarded as the cornerstone of bacteriology. However, not all bacteria will multiply sufficiently to produce visible colonies on solid media; some cells will produce micro-colonies that are invisible to the naked eye. Moreover, the proportion of culturable cells that produce visible growth will vary according to the species and the state of the cells-are they actively growing or comparatively inactive? The latter have a poorer rate of recovery in terms of cultivability...
February 6, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28168519/pcna-is-recruited-to-irradiated-chromatin-in-late-s-phase-and-is-most-pronounced-in-g2-phase-of-the-cell-cycle
#10
Eva Bártová, Jana Suchánková, Soňa Legartová, Barbora Malyšková, Matúš Hornáček, Magdalena Skalníková, Martin Mašata, Ivan Raška, Stanislav Kozubek
DNA repair is a complex process that prevents genomic instability. Many proteins play fundamental roles in regulating the optimal repair of DNA lesions. Proliferating cell nuclear antigen (PCNA) is a key factor that initiates recombination-associated DNA synthesis after injury. Here, in very early S-phase, we show that the fluorescence intensity of mCherry-tagged PCNA after local micro-irradiation was less than the fluorescence intensity of non-irradiated mCherry-PCNA-positive replication foci. However, PCNA protein accumulated at locally irradiated chromatin in very late S-phase of the cell cycle, and this effect was more pronounced in the following G2 phase...
January 20, 2017: Protoplasma
https://www.readbyqxmd.com/read/28159568/micro-rna-detection-based-on-fluorescence-resonance-energy-transfer-of-dna-carbon-quantum-dots-probes
#11
Faeze Khakbaz, Mohamad Mahani
Carbon quantum dots have been proposed as an effective platform for miRNA detection. Carbon dots were synthesized by citric acid. The synthesized dots were characterized by dynamic light scattering, UV-Vis spectrophotometry, spectrofluorimetry, transmission electron microscopy and FT-IR spectrophotometry. The fluorescence quantum yield of the synthesized dots was determined using quinine sulfate as the standard. The FAM-labeled single stranded DNA, as sensing element, was adsorbed on dots by π-π interaction...
January 31, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28157593/naphthalene-diimide-polyamine-hybrids-as-antiproliferative-agents-focus-on-the-architecture-of-the-polyamine-chains
#12
Andrea Milelli, Chiara Marchetti, Maria Laura Greco, Federica Moraca, Giosuè Costa, Eleonora Turrini, Elena Catanzaro, Nibal Betari, Cinzia Calcabrini, Claudia Sissi, Stefano Alcaro, Carmela Fimognari, Vincenzo Tumiatti, Anna Minarini
Naphthalene diimides (NDIs) have been widely used as scaffold to design DNA-directed agents able to target peculiar DNA secondary arrangements endowed with relevant biochemical roles. Recently, we have reported disubstituted linear- and macrocyclic-NDIs that bind telomeric and non-telomeric G-quadruplex with high degree of affinity and selectivity. Herein, the synthesis, biological evaluation and molecular modelling studies of a series of asymmetrically substituted NDIs are reported. Among these, compound 9 emerges as the most interesting of the series being able to bind telomeric G-quadruplex (ΔTm = 29 °C at 2...
January 22, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28155662/an-ensemble-micro-neural-network-approach-for-elucidating-interactions-between-zinc-finger-proteins-and-their-target-dna
#13
Shayoni Dutta, Spandan Madan, Harsh Parikh, Durai Sundar
BACKGROUND: The ability to engineer zinc finger proteins binding to a DNA sequence of choice is essential for targeted genome editing to be possible. Experimental techniques and molecular docking have been successful in predicting protein-DNA interactions, however, they are highly time and resource intensive. Here, we present a novel algorithm designed for high throughput prediction of optimal zinc finger protein for 9 bp DNA sequences of choice. In accordance with the principles of information theory, a subset identified by using K-means clustering was used as a representative for the space of all possible 9 bp DNA sequences...
December 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28151902/clinical-pathological-and-genetic-evaluations-of-chinese-patient-with-otodental-syndrome-and-multiple-complex-odontoma-case-report
#14
Anqi Liu, Meiling Wu, Xiaohe Guo, Hao Guo, Zhifei Zhou, Kewen Wei, Kun Xuan
Otodental syndrome is a rare autosomal-dominant disease characterized by globodontia, associated with sensorineural, high-frequency hearing loss. Here, we describe the clinical, pathological, and genetic evaluations of a 9-year-old girl with otodental syndrome and multiple complex odontoma.The patient presented with a draining sinus tract in her left cheek, globodontia, and hearing loss. The odontomas which caused the cutaneous sinus tracts were extracted because of the odontogenic infection. The extracted odontoma and primary tooth was studied by micro-CT and further observed histopathologically...
February 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28137364/nucleoplasmic-bridges-as-a-biomarker-of-dna-damage-exposed-to-radon
#15
C Meenakshi, K Sivasubramanian, B Venkatraman
Radon is a naturally occurring radionuclide in the environment, during decay it emits high linear energy transfer (LET) alpha particles. When radon exposure is accompanied by smoking it has been reported that lung cancer risk is higher. Blood samples were collected after prior consent, 25 smokers and 25 non smokers (only males) exposed in vitro to radon gas with doses ranging between 0.3-12.6mGy Ionizing radiation is a strong clastogenic agent and a potent inducer of MN. Cytokinesis-Blocked Micro Nucleus (CBMN) assay has proven to be a reliable, thoroughly validated and standardised technique in the field of radiation biology...
February 2017: Mutation Research
https://www.readbyqxmd.com/read/28128213/high-throughput-automated-microfluidic-sample-preparation-for-accurate-microbial-genomics
#16
Soohong Kim, Joachim De Jonghe, Anthony B Kulesa, David Feldman, Tommi Vatanen, Roby P Bhattacharyya, Brittany Berdy, James Gomez, Jill Nolan, Slava Epstein, Paul C Blainey
Low-cost shotgun DNA sequencing is transforming the microbial sciences. Sequencing instruments are so effective that sample preparation is now the key limiting factor. Here, we introduce a microfluidic sample preparation platform that integrates the key steps in cells to sequence library sample preparation for up to 96 samples and reduces DNA input requirements 100-fold while maintaining or improving data quality. The general-purpose microarchitecture we demonstrate supports workflows with arbitrary numbers of reaction and clean-up or capture steps...
January 27, 2017: Nature Communications
https://www.readbyqxmd.com/read/28122253/assessment-of-alterations-in-x-ray-irradiation-induced-dna-damage-of-glioma-cells-by-using-proton-nuclear-magnetic-resonance-spectroscopy
#17
Hongxia Li, Yanjie Xu, Wenqi Shi, Fuyan Li, Qingshi Zeng, Cui Yi
Glioma is one of the most common types of brain tumors. DNA damage is closely associated with glioma cell apoptosis induced by X-ray irradiation. Alterations of metabolites in glioma can be detected noninvasively by proton nuclear magnetic resonance (1H NMR) spectroscopy. To noninvasively explore the micro mechanism in X-ray irradiation-induced apoptosis, the relationship between metabolites and DNA damage in glioma cells was investigated. Three glioma cell lines (C6, U87 and U251) were randomly designated as control (0Gy) and treatment groups (1, 5, 10, 15Gy)...
January 22, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28110230/identification-of-the-autotrophic-denitrifying-community-in-nitrate-removal-reactors-by-dna-stable-isotope-probing
#18
Wei Xing, Jinlong Li, Yuan Cong, Wei Gao, Zhongjun Jia, Desheng Li
Autotrophic denitrification has attracted increasing attention for wastewater with insufficient organic carbon sources. Nevertheless, in situ identification of autotrophic denitrifying communities in reactors remains challenging. Here, a process combining micro-electrolysis and autotrophic denitrification with high nitrate removal efficiency was presented. Two batch reactors were fed organic-free nitrate influent, with H(13)CO3(-) and H(12)CO3(-) as inorganic carbon sources. DNA-based stable-isotope probing (DNA-SIP) was used to obtain molecular evidence for autotrophic denitrifying communities...
April 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28108868/morpho-molecular-characterization-of-soil-inhabitant-dermatophytes-from-ahvaz-southwest-of-iran-a-high-occurrence-of-microsporum-fulvum
#19
Ali Rezaei-Matehkolaei, Abbas Jahangiri, Ali Zarei Mahmoudabadi, Mohammad Javad Najafzadeh, Sadegh Nouripour-Sisakht, Koichi Makimura
Occurrence and diversity of dermatophyte mycoflora in 298 soil samples from Ahvaz, Southwest of Iran was investigated by using the hair-baiting technique. The samples were collected during spring (n = 210) and autumn (n = 88) of 2015, and the fungal isolates were identified based on the macro- and micro-morphology of colonies and with further ITS-rDNA RFLP and sequencing. Totally, 60 soil samples (20.1%) were positive for dermatophyte growth whose pH varied from 7.0 to 7.9. The highest (26.6%) and the lowest (14...
January 20, 2017: Mycopathologia
https://www.readbyqxmd.com/read/28108625/combined-parthenolide-and-balsalazide-have-enhanced-antitumor-efficacy-through-blockade-of-nf-%C3%AE%C2%BAb-activation
#20
Se-Lim Kim, Seong Hun Kim, Young Ran Park, Yu-Chuan Liu, Eun-Mi Kim, Hwan-Jeong Jeong, Yo Na Kim, Seung Young Seo, In Hee Kim, Seung Ok Lee, Soo Teik Lee, Sang-Wook Kim
: Balsalazide is a colon-specific prodrug of 5-aminosalicylate that is associated with a reduced risk of colon cancer in patients with ulcerative colitis. Parthenolide, a strong NF-κB inhibitor, has recently been demonstrated to be a promising therapeutic agent, promoting apoptosis of cancer cells. In the current study, the antitumor effect of balsalazide combined with parthenolide in human colorectal cancer cells and colitis-associated colon cancers (CAC) was investigated. The results demonstrate that the combination of balsalazide and parthenolide markedly suppress proliferation, nuclear translocation of NF-κB, IκB-α phosphorylation, NF-κB DNA binding, and expression of NF-κB targets...
November 14, 2016: Molecular Cancer Research: MCR
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