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https://www.readbyqxmd.com/read/28550309/the-ppsu-plasmids-for-generating-dna-molecular-weight-markers
#1
Ryan C Henrici, Turner J Pecen, James L Johnston, Song Tan
Visualizing nucleic acids by gel electrophoresis is one of the most common techniques in molecular biology, and reference molecular weight markers or ladders are commonly used for size estimation. We have created the pPSU1 & pPSU2 pair of molecular weight marker plasmids which produce both 100 bp and 1 kb DNA ladders when digested with two common restriction enzymes. The 100 bp ladder fragments have been optimized to migrate appropriately on both agarose and native polyacrylamide, unlike many currently available DNA ladders...
May 26, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28549437/p-p-ddt-induces-testicular-oxidative-stress-induced-apoptosis-in-adult-rats
#2
Neila Marouani, Dorsaf Hallegue, Mohsen Sakly, Moncef Benkhalifa, Khémais Ben Rhouma, Olfa Tebourbi
BACKGROUND: The 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (p,p'-DDT) is a known persistent organic pollutant and male reproductive toxicant. The present study is designed to test the hypothesis that oxidative stress mediates p,p'-DDT-induced apoptosis in testis. METHODS: Male Wistar rats received an intraperitoneal (ip) injection of the pesticide at doses of 50 and 100mg/kg for 10 consecutive days. The oxidative stress was evaluated by biomarkers such lipid peroxidation (LPO) and metallothioneins (MTs) levels...
May 26, 2017: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/28537375/flexible-and-wearable-fiber-micro-supercapacitors-based-on-carbon-nanotube-agarose-gel-composite-electrodes
#3
Sung Kon Kim, Hyung-Jun Koo, Jinyun Liu, Paul V Braun
Fiber electrodes provide interesting opportunities for energy storage by providing both mechanical flexibility and the opportunity to impart multifunctionality to fabrics. We show here carbon nanotube (CNTs)-embedded agarose gel composite fiber electrodes with a diameter of ~120 μm consisting of 60 wt% CNTs that can serve as the basis for flexible and wearable fiber micro-supercapacitors (mSCs). Via an extrusion process, CNT bundles are induced to align in an agarose filament matrix. Due to the shear alignment of the CNT bundles, the dehydrated filaments have an electrical conductivity as high as 8...
May 24, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28535444/passive-detection-of-pb-in-water-using-rock-phosphate-agarose-beads
#4
Harry M Edenborn, Bret H Howard, James I Sams, Dorothy J Vesper, Sherie L Edenborn
In this study, passive detectors for Pb were prepared by immobilizing powdered rock phosphate in agarose beads. Rock phosphate has been used to treat Pb-contaminated waters and soil by fixing the metal as an insoluble pyromorphite mineral. Under lab conditions, Pb was rapidly adsorbed from aqueous solution by the beads over time, consistent with the acidic dissolution of rock phosphate, the precipitation of pyromorphite within the pore space of the agarose gel matrix, and surface exchange reactions. Net accumulation of Pb occurred when beads were exposed to simulated periodic releases of Pb over time...
April 15, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28534993/analysis-of-the-cdr3-length-repertoire-and-the-diversity-of-t-cell-receptor-%C3%AE-and-%C3%AE-chains-in-swine-cd4-and-cd8-t-lymphocytes
#5
Chun-Yan Wang, Yong-Xiang Fang, Guo-Hua Chen, Huai-Jie Jia, Shuang Zeng, Xiao-Bing He, Yuan Feng, Shou-Jie Li, Qi-Wang Jin, Wen-Yu Cheng, Zhi-Zhong Jing
The T cell receptor (TCR) is a complex heterodimer that recognizes fragments of antigens as peptides and binds to major histocompatibility complex molecules. The TCR α and β chains possess three hypervariable regions termed complementarity determining regions (CDR1, 2 and 3). CDR3 is responsible for recognizing processed antigen peptides. Immunoscope spectratyping is a simple technique for analyzing CDR3 polymorphisms and sequence length diversity, in order to investigate T cell function and the pattern of TCR utilization...
May 18, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28531233/in-silico-development-and-characterization-of-tri-nucleotide-simple-sequence-repeat-markers-in-hazelnut-corylus-avellana-l
#6
Gehendra Bhattarai, Shawn A Mehlenbacher
Plant genomes are now sequenced rapidly and inexpensively. In silico approaches allow efficient development of simple sequence repeat markers, also known as microsatellite markers, from these sequences. A search of the genome sequence of 'Jefferson' hazelnut (Corylus avellana L.) identified 8,708 tri-nucleotide simple sequence repeats with at least five repeat units, and stepwise removal of the less promising sequences led to the development of 150 polymorphic markers. Fragments in the 'Jefferson' sequence containing tri-nucleotide repeats were used as references and aligned with genomic sequences from seven other cultivars...
2017: PloS One
https://www.readbyqxmd.com/read/28530597/dna-agarose-gel-electrophoresis-for-antioxidant-analysis-development-of-a-quantitative-approach-for-phenolic-extracts
#7
Sara Silva, Eduardo M Costa, Sandra Vicente, Mariana Veiga, Conceição Calhau, Rui M Morais, Manuela E Pintado
Most of the fast in vitro assays proposed to determine the antioxidant capacity of a compound/extract lack either biological context or employ complex protocols. Therefore, the present work proposes the improvement of an agarose gel DNA electrophoresis in order to allow for a quantitative estimation of the antioxidant capacity of pure phenolic compounds as well as of a phenolic rich extract, while also considering their possible pro-oxidant effects. The result obtained demonstrated that the proposed method allowed for the evaluation of the protection of DNA oxidation [in the presence of hydrogen peroxide (H2O2) and an H2O2/iron (III) chloride (FeCl3) systems] as well as for the observation of pro-oxidant activities, with the measurements registering interclass correlation coefficients above 0...
October 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/28527284/-new-multiplex-pcr-for-species-specific-diagnosis-of-human-candidiasis
#8
Liliana Torcoroma García, Liany Johanna Luna, Tania Katherine Velasco, Beatriz Elena Guerra
INTRODUCTION: Candidiases is a group of opportunistic infections caused by yeasts belonging to the genus Candida. Candida albicans is the most prevalent species in both superficial and deep infections, however, the clinical importance of non-albicans Candida has increased during the last decade, driving an urgent need for diagnostic tests that allow for species-level resolution and selection of the optimum therapeutic approach. OBJECTIVE: To design and to optimize a new multiplex PCR assay for the simultaneous identification of the five most relevant species of Candida involved in human candidiasis etiology...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28526345/facile-fabrication-of-3d-porous-hybrid-sphere-by-co-immobilization-of-multi-enzyme-directly-from-cell-lysates-as-an-efficient-and-recyclable-biocatalyst-for-asymmetric-reduction-with-coenzyme-regeneration-in-situ
#9
Mingan Yu, Duqiang Liu, Lili Sun, Jing Li, Qian Chen, Lijun Pan, Jingchuan Shang, Shurong Zhang, Wei Li
Ni(2+)-agarose bead-wrapped multi-enzyme/inorganic hybrid sphere composed of the immobilized enzymes as organic component and NaH2PO4 and NaCl as inorganic component was developed by co-immobilizing extracellular His-tagged 3-quinuclidinone reductases and glucose dehydrogenase without pre-purification. The resulting biocatalysts has 3D porous architectures as confirmed by SEM and FESEM, and it enabled the continuous biotransformation of 3-quinuclidone to (R)-3-quinuclidinol with cofactor regeneration in situ...
May 17, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28523047/alpha-thalassemia-deletions-found-in-suspected-cases-of-beta-thalassemia-major-in-pakistani-population
#10
Saba Shahid, Muhammad Nadeem, Danish Zahid, Jawad Hassan, Saqib Ansari, Tahir Shamsi
BACKGROUND & OBJECTIVE: Alpha (α) thalassemia is a hereditary disorder and is caused by deletions or mutations in globin genes. It is present in two clinically significant forms: hemoglobin Bart hydrops fetalis (Hb Bart) syndrome and hemoglobin H (HbH) disease. It is highly prevalent in South-East Asia or Mediterranean countries. The most common deletion reported in alpha thalassemia in Pakistani population was -α(3.7) with a frequency of 8.3%, and the rare forms were -α(4.2) (0.2%) and ααα(anti3...
March 2017: Pakistan Journal of Medical Sciences Quarterly
https://www.readbyqxmd.com/read/28522396/ultrafast-spectroscopy-on-dna-cleavage-by-endonuclease-in-molecular-crowding
#11
Priya Singh, Susobhan Choudhury, Shreyasi Dutta, Aniruddha Adhikari, Siddhartha Bhattacharya, Debasish Pal, Samir Kumar Pal
The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG...
May 15, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28516285/intracellular-morphological-changes-in-staphylococcus-aureus-induced-by-treatment-with-sodium-hypochlorite
#12
Shiori Ujimine, Shigenobu Tone, Mineki Saito, Sakuo Yamada
Sodium hypochlorite (NaOCl) is commonly used as a disinfectant; however, its bactericidal mechanism has not yet been clarified. In the present study, the bactericidal mechanism of NaOCl was examined using microscopy and gel electrophoresis techniques with Staphylococcus aureus strain 209P. S. aureus cells treated with 500 and 1000 ppm NaOCl for 5 and 15 min were observed by SEM and TEM. SEM images of the bacterial cells treated with NaOCl showed an irregular surface, with cells being partially invaginated...
May 17, 2017: Medical Molecular Morphology
https://www.readbyqxmd.com/read/28516051/evaluation-of-mr-thermometry-with-proton-resonance-frequency-method-at-7t
#13
Ping Wang
Quantitative and non-invasive temperature mapping using magnetic resonance imaging (MRI) provides a unique way to measure temperature evolution inside biological tissues. The method is widely used in thermal ablation procedures with magnetic fields at or below 3T. In this paper, the sensitivity of the MRI thermometry at 7T was studied using a proton resonance frequency (PRF)-based technique. We first used an agarose gel phantom with MR-compatible thermometry to calibrate the temperature coefficient, and then this temperature coefficient was employed to measure the internal temperature in both ex vivo (beef muscle) and in vivo (rat) experiments using focused ultrasound heating...
April 2017: Quantitative Imaging in Medicine and Surgery
https://www.readbyqxmd.com/read/28511875/visible-light-switched-cytosol-release-of-sirna-by-amphiphilic-fullerene-derivative-to-enhance-rnai-efficacy-in-vitro-and-in-vivo
#14
Jing Wang, Lifei Xie, Tao Wang, Fengxin Wu, Jie Meng, Jian Liu, Haiyan Xu
Cationic macromolecules are attractive for use as small interfering RNA (siRNA) carriers due to their performance in non-immunological reactions, customization during synthesis, and low costs compared to viral carriers. However, their low transfection efficiency substantially hinders their application in both clinical practices and academic research, which is mostly attributable to the low capacity of siRNA/cationic macromolecule complexes to escape lysosomes. To address this challenge, we designed an amphiphilic fullerene derivative (C60-Dex-NH2) for efficient and controllable siRNA delivery...
May 13, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28510360/analysis-of-human-papillomavirus-genome-replication-using-two-and-three-dimensional-agarose-gel-electrophoresis
#15
Liisi Henno, Eva-Maria Tombak, Jelizaveta Geimanen, Marit Orav, Ene Ustav, Mart Ustav
This unit includes the necessary information to conduct neutral/neutral and neutral/alkaline two-dimensional and neutral/neutral/alkaline three-dimensional agarose gel electrophoresis. The methodology has been optimized over the years to gain a better outcome from the hard-to-interpret signals of human papilloma virus replication intermediates obtained from two- and three-dimensional agarose gels. Examples of typical results and interpretation of replication intermediate patterns are included, and the outcomes of multiple-dimension assays are assessed using previously published experimental data...
May 16, 2017: Current Protocols in Microbiology
https://www.readbyqxmd.com/read/28505860/nonmonotonic-dna-length-dependent-mobility-in-pluronic-gels
#16
Seungyong You, Ling Wei, Sachin Shanbhag, David H Van Winkle
Two-dimensional electrophoresis was used to analyze the mobility of DNA fragments in micellar gels of pluronic F127 (EO_{100}PO_{70}EO_{100}) and pluronic P123 (EO_{20}PO_{70}EO_{20}). The 20-3500 base pair DNA fragments were separated by size first in agarose gels, and then in pluronic gels at room temperature. In agarose gels, the DNA mobility decreases monotonically with increasing DNA length. In pluronic gels, however, the mobility varies nonmonotonically according to fragment lengths that are strongly correlated with the diameter of the spherical micelles...
April 2017: Physical Review. E
https://www.readbyqxmd.com/read/28504278/high-frequency-linear-rheology-of-hydrogels-probed-by-ultrasound-driven-microbubble-dynamics
#17
Akaki Jamburidze, Marco De Corato, Axel Huerre, Angelo Pommella, Valeria Garbin
Ultrasound-driven microbubble dynamics are central to biomedical applications, from diagnostic imaging to drug delivery and therapy. In therapeutic applications, the bubbles are typically embedded in tissue, and their dynamics are strongly affected by the viscoelastic properties of the soft solid medium. While the behaviour of bubbles in Newtonian fluids is well characterised, a fundamental understanding of the effect on ultrasound-driven bubble dynamics of a soft viscoelastic medium is still being developed...
May 15, 2017: Soft Matter
https://www.readbyqxmd.com/read/28494726/chlorella-vulgaris-induces-apoptosis-of-human-non-small-cell-lung-carcinoma-nsclc-cells
#18
Zhi-Dong Zhang, Kai Liang, Kun Li, Guo-Quan Wang, Ke-Wei Zhang, Lei Cai, Shui-Ting Zhai, Kuo-Chen Chou
PURPOSE: Chlorella vulgaris(C. vulgaris), a unicellular green microalga, has been widely used as a food supplement and reported to have antioxidant and anticancer properties. The current study was designed to assess the cytotoxic, apoptotic, and DNA-damaging effects of C. vulgaris growth factor (CGF), hot water C. vulgaris extracts, in lung tumor A549 and NCI-H460 cell lines. METHODS: A549 cells, NCI-H460 cells, and normal human fibroblasts were treated with CGF at various concentrations (0-300 μg/ml) for 24 hr...
May 9, 2017: Medicinal Chemistry
https://www.readbyqxmd.com/read/28492219/kappa-free-light-chains-in-cerebrospinal-fluid-of-patients-with-identified-oligoclonal-immunoglobulin-g
#19
Marina Vasilj, Miro Klarić, Nada Vrkić, Ivanka Mikulić, Marijana Marković Boras, Nevenka Jelić-Knezović, Violeta Šoljić
BACKGROUND: Production of kappa free light chains (KFLC) represents a part of humoral immune response, along with the synthesis of intrathecal immunoglobulins. Increased concentrations of immunoglobulin G light chains, kappa and lambda chains, were identified through research of numerous diseases of central nervous system. The qualitative method of isoelectric focusing (IEF) followed by immunofixation currently represents the accepted standard in identifying oligoclonal bands (OCB), but establishing a sensitive immunonephelometric method for quantification of kappa free light chains (KFLC) in cerebrospinal fluid (CSF) has paved a way for new diagnostic possibilities...
May 2017: Psychiatria Danubina
https://www.readbyqxmd.com/read/28477115/zn-ii-phos-tag-sds-page-for-separation-and-detection-of-a-dna-damage-related-signaling-large-phosphoprotein
#20
Eiji Kinoshita, Emiko Kinoshita-Kikuta, Tohru Koike
In this chapter, we provide a standard protocol for phosphate-affinity sodium dodecyl sulfate-polyacrylamide gel electrophoresis (Zn(2+)-Phos-tag SDS-PAGE). This technique uses a dizinc(II) complex of the phosphate-binding molecule Phos-tag in conjunction with a neutral-pH gel system, Tris [tris(hydroxymethyl)aminomethane], and acetic acid (Tris-AcOH), to detect shifts in the mobility of phosphorylated ataxia telangiectasia-mutated (ATM) kinase. This protocol, which employs a 3% (w/v) polyacrylamide gel strengthened with 0...
2017: Methods in Molecular Biology
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