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Ramón Cervantes-Rivera et al.
Bio-protocol, 10(18), e3757-e3757 (2021-03-05)
Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are
Cell-internalization SELEX: method for identifying cell-internalizing RNA aptamers for delivering siRNAs to target cells
<BIG>Thiel WH, et al.</BIG>
Methods in Molecular Biology, 187-199 (2015)
Sun Min Kim et al.
Bioresource technology, 183, 70-77 (2015-02-28)
Prairie cordgrass (Spartina pectinata L.) has the potential to be a feedstock for bioethanol. It is native to North America, and has extensive genetic diversity. Eleven natural populations of prairie cordgrass harvested in 2011 and 2012 were studied. Compositions of
Jean M Bonasera et al.
Journal of microbiological methods, 103, 138-143 (2014-06-14)
We have developed a method for the identification of Gram-negative bacteria, particularly members of the Enterobacteriaceae, based on sequence variation in a portion of the gyrB gene. Thus, we identified, in most cases to species level, over 1000 isolates from
Alejandra Escudero-Lara et al.
Bio-protocol, 10(18), e3763-e3763 (2021-03-05)
Endometriosis is a common gynecological disease characterized by the presence of endometrial tissue outside the uterine cavity. It is frequently associated with pain, infertility and a reduced quality of life, and it lacks adequate treatment. Several rodent models of endometriosis
Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine
<BIG>Afonin KA, et al.</BIG>
Nature Protocols, 6, 2022-2022 (2011)
A A Bhat et al.
Oncogene, 34(35), 4570-4580 (2014-12-17)
In normal colon, claudin-7 is one of the highly expressed claudin proteins and its knockdown in mice results in altered epithelial cell homeostasis and neonatal death. Notably, dysregulation of the epithelial homeostasis potentiates oncogenic transformation and growth. However, the role
Soonsil Hyun et al.
Chembiochem : a European journal of chemical biology, 15(11), 1651-1659 (2014-07-06)
A library of Trp-containing amphiphilic peptides was synthesized and screened for the ability to bind to pre-miRNA targets. Two members of this family, peptides Ac-WKKLLKWLKKLLKLAG-NH2 (2 b) and Ac-WKKLLKWLKKLLDabLAG-NH2 (4 b) were found to have nanomolar binding affinities to pre-let7a-1. Peptides 2 b
Masao Ota et al.
Nature protocols, 2(11), 2857-2864 (2007-11-17)
Accurate analysis of DNA sequence variation in not only humans and animals but also other organisms has played a significant role in expanding our knowledge about genetic variety and diversity in a number of different biological areas. The search for
Srikanth Dasari et al.
Dalton transactions (Cambridge, England : 2003), 44(46), 19844-19855 (2015-10-29)
The europium(III) and terbium(III) complexes, namely [Eu(dpq)(DMF)2(NO3)3] (1), [Eu(dppz)2(NO3)3] (2), [Tb(dpq)(DMF)2Cl3] (3), and [Tb(dppz)(DMF)2Cl3] (4), where dipyrido[3,2-d:2',3'-f]quinoxaline (dpq in 1 and 3), dipyrido[3,2-a:2',3'-c]phenazine (dppz in 2 and 4) and N,N'-dimethylformamide (DMF) have been isolated, characterized from their physicochemical data, luminescence
Riku Nagai et al.
Methods and protocols, 4(3) (2021-07-22)
The rates of translation elongation or termination in eukaryotes are modulated through cooperative molecular interactions involving mRNA, the ribosome, aminoacyl- and nascent polypeptidyl-tRNAs, and translation factors. To investigate the molecular mechanisms underlying these processes, we developed an in vitro translation
Sarah Gadel et al.
Drug metabolism and disposition: the biological fate of chemicals, 43(7), 994-1001 (2015-04-22)
Methadone is a long-acting opioid with considerable unexplained interindividual variability in clearance. Cytochrome P450 2B6 (CYP2B6) mediates clinical methadone clearance and metabolic inactivation via N-demethylation to 2-ethyl-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP). Retrospective studies suggest that individuals with the CYP2B6*6 allelic variant have higher
Neal J Dawson et al.
Biochimica et biophysica acta, 1850(1), 97-106 (2014-10-16)
The North American wood frog, Rana sylvatica, is able to overcome subzero conditions through overwintering in a frozen state. Freezing imposes ischemic and oxidative stress on cells as a result of cessation of blood flow. Superoxide dismutases (SODs) catalyze the
Maria Cardona et al.
PloS one, 10(6), e0131411-e0131411 (2015-06-30)
Executioner caspase-3 and -7 are proteases promoting cell death but non-apoptotic roles are being discovered. The heart expresses caspases only during development, suggesting they contribute to the organ maturation process. Therefore, we aimed at identifying novel functions of caspases in
Luyan Zhang et al.
G3 (Bethesda, Md.), 5(3), 427-439 (2015-01-17)
In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that
Farzin Haque et al.
Nature protocols, 8(2), 373-392 (2013-01-26)
Over the past decade, nanopores have rapidly emerged as stochastic biosensors. This protocol describes the cloning, expression and purification of the channel of the bacteriophage phi29 DNA-packaging nanomotor and its subsequent incorporation into lipid membranes for single-pore sensing of double-stranded
Single nucleotide polymorphism detection by polymerase chain reaction-restriction fragment length polymorphism
<BIG>Ota M, et al.</BIG>
Nature Protocols, 2857-2857 (2007)
Patrick S Aranda et al.
Electrophoresis, 33(2), 366-369 (2012-01-10)
RNA-based applications requiring high-quality, non-degraded RNA are a foundational element of many research studies. As such, it is paramount that the integrity of experimental RNA is validated prior to cDNA synthesis or other downstream applications. In the absence of expensive
T Yokoyama et al.
Lupus, 23(7), 635-642 (2014-02-05)
We investigated possible associations between neurotoxic inflammatory mediators (IMs) and anti-U1RNP antibodies (Abs) in cerebrospinal fluid (CSF) of neuropsychiatric systemic lupus erythematosus (NPSLE). Serum and CSF anti-U1RNP Abs were detected using an RNA-immunoprecipitation assay and CSF anti-U1RNP Ab levels were
Yuly A Henao-Díaz et al.
Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc, 30(5), 671-677 (2018-07-22)
Routine collection and testing of oral fluid (OF) samples facilitates porcine reproductive and respiratory syndrome virus (PRRSV) surveillance in commercial swine herds in a cost-effective, welfare-friendly fashion. However, OFs often contain environmental contaminants that may affect liquid handling and test
Katrina M Morris et al.
BMC genomics, 16, 1017-1017 (2015-11-28)
The Tasmanian devil (Sarcophilus harrisii) is being threatened with extinction in the wild by a disease known as devil facial tumour disease (DFTD). In order to prevent the spread of this disease a thorough understanding of the Tasmanian devil immune
Salvatore Delogu et al.
Oncotarget, 6(4), 2222-2234 (2014-12-30)
Mounting evidence indicates that S-Phase Kinase-Associated Protein 2 (SKP2) is overexpressed in human hepatocellular carcinoma (HCC). However, the role of SKP2 in hepatocarcinogenesis remains poorly delineated. To elucidate the function(s) of SKP2 in HCC, we stably overexpressed the SKP2 gene
Xingxiu Pan et al.
Molecular brain, 8, 36-36 (2015-06-06)
p21-activated kinase 1 (PAK1) is a serine/threonine kinase known to be activated by the Rho family small GTPases and to play a key role in cytoskeletal reorganization, spine morphology and synaptic plasticity. PAK1 is also implicated in a number of
Poly(A)-specific ribonuclease deficiency impacts telomere biology and causes dyskeratosis congenita.
Hemanth Tummala et al.
The Journal of clinical investigation, 125(5), 2151-2160 (2015-04-22)
Dyskeratosis congenita (DC) and related syndromes are inherited, life-threatening bone marrow (BM) failure disorders, and approximately 40% of cases are currently uncharacterized at the genetic level. Here, using whole exome sequencing (WES), we have identified biallelic mutations in the gene
A M Maxam et al.
Proceedings of the National Academy of Sciences of the United States of America, 74(2), 560-564 (1977-02-01)
DNA can be sequenced by a chemical procedure that breaks a terminally labeled DNA molecule partially at each repetition of a base. The lengths of the labeled fragments then identify the positions of that base. We describe reactions that cleave
Nicolás Cara et al.
Bio-protocol, 10(13), e3671-e3671 (2021-03-05)
Methylation-Sensitive Amplification Polymorphism (MSAP) is a versatile marker for analyzing DNA methylation patterns in non-model species. The implementation of this technique does not require a reference genome and makes it possible to determine the methylation status of hundreds of anonymous
Y Bao et al.
The Journal of general virology, 74 ( Pt 8), 1611-1616 (1993-08-01)
A virus-specific small nucleic acid (strong-stop DNA) was identified in rice plants infected with rice tungro bacilliform virus, but not in the virus particles. This nucleic acid was shown to consist of about 595 deoxyribonucleotides with about 70 ribonucleotides covalently
Electrophoresis in agarose and acrylamide gels.
R C Ogden et al.
Methods in enzymology, 152, 61-87 (1987-01-01)
Jeremy J Heit et al.
Journal of neurointerventional surgery, 7(1), 56-61 (2014-01-05)
Cerebral vasospasm following subarachnoid hemorrhage (SAH) results in significant morbidity and mortality. Intra-arterial administration of calcium channel blockers or intracranial angioplasty may be performed when non-invasive medical management fails to prevent neurologic deterioration. Technical improvements in balloon catheters are expected
Xiancheng Chen et al.
Medicine, 94(19), e873-e873 (2015-05-20)
The diagnosis of Xp11.2 translocation renal cell carcinoma (tRCC), which relies on morphology and immunohistochemistry (IHC), is often either missed in the diagnosis or misdiagnosed. To improve the accuracy of diagnosis of Xp11.2 tRCC and ASPL-TFE3 renal cell carcinoma (RCC)
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