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Molecular biology

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https://www.readbyqxmd.com/read/28528145/uv-induced-electron-transfer-between-triethylamine-and-5-bromo-2-deoxyuridine-a-puzzle-concerning-the-photochemical-debromination-of-labeled-dna
#1
Paweł Wityk, Magdalena Zdrowowicz, Justyna Wiczk, Janusz Rak
5-Bromo-2'-deoxyuridine (BrdU) photosensitizes DNA to strand break formation. However, this type of photodamage is completely quenched by the presence of triethylamine (TEA) which originates from RP-HPLC purification commonly employed by oligonucleotide providers. While the presence of TEA in oligonucleotide samples does not interfere with PCR or other molecular biology applications, the mechanism of photochemical reaction proceeding in the labeled DNA is dramatically changed due to the photoinduced electron transfer (PET) between the photoexcited BrdU and the ground state TEA...
May 11, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28528123/quantitative-biology-of-hydrogen-peroxide-signaling
#2
REVIEW
Fernando Antunes, Paula Matos Brito
Hydrogen peroxide (H2O2) controls signaling pathways in cells by oxidative modulation of the activity of redox sensitive proteins denominated redox switches. Here, quantitative biology concepts are applied to review how H2O2 fulfills a key role in information transmission. Equations described lay the foundation of H2O2 signaling, give new insights on H2O2 signaling mechanisms, and help to learn new information from common redox signaling experiments. A key characteristic of H2O2 signaling is that the ratio between reduction and oxidation of redox switches determines the range of H2O2 concentrations to which they respond...
May 8, 2017: Redox Biology
https://www.readbyqxmd.com/read/28527894/hfe-genotype-affects-exosome-phenotype-in-cancer
#3
Oliver D Mrowczynski, A B Madhankumar, Becky Slagle-Webb, Sang Y Lee, Brad E Zacharia, James R Connor
Neuroblastoma is the third most common childhood cancer, and timely diagnosis and sensitive therapeutic monitoring remain major challenges. Tumor progression and recurrence is common with little understanding of mechanisms. A major recent focus in cancer biology is the impact of exosomes on metastatic behavior and the tumor microenvironment. Exosomes have been demonstrated to contribute to the oncogenic effect on the surrounding tumor environment and also mediate resistance to therapy. The effect of genotype on exosomal phenotype has not yet been explored...
May 17, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28527627/a-kinetic-study-on-the-reactivity-of-azanone-hno-toward-its-selected-scavengers-insight-into-its-chemistry-and-detection
#4
Renata Smulik-Izydorczyk, Adrianna Mesjasz, Angelika Gerbich, Jan Adamus, Radosław Michalski, Adam Sikora
Recently, azanone (HNO), which is the protonated one-electron reduction product of (·)NO, has gained considerable attention due to its unique pharmacological effects. Although there has been much progress in understanding HNO biology and chemistry, it remains the most elusive reactive nitrogen species. Herein, we applied the competition kinetics method, based on two parallel HNO reactions with the different scavengers and molecular oxygen (kO2 = (1.8 ± 0.3) × 10(4) M(-1) s(-1)), to determine the rate constants for the reactions of HNO with its selected co-reactants...
May 17, 2017: Nitric Oxide: Biology and Chemistry
https://www.readbyqxmd.com/read/28527412/early-stage-detection-of-ve-cadherin-during-endothelial-differentiation-of-human-mesenchymal-stem-cells-using-spr-biosensor
#5
Farzaneh Fathi, Aysa Rezabakhsh, Reza Rahbarghazi, Mohammad-Reza Rashidi
Surface plasmon resonance (SPR) biosensors are most commonly applied for real-time dynamic analysis and measurement of interactions in bio-molecular studies and cell-surface analysis without the need for labeling processes. Up to present, SPR application in stem cell biology and biomedical sciences was underused. Herein, a very simple and sensitive method was developed to evaluate human mesenchymal stem cells trans-differentiation to endothelial lineage of over a period of 14 days based on VE-cadherin biomarker...
May 10, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28527288/-partial-purification-of-peptides-present-in-the-tityus-macrochirus-buthidae-scorpion-venom-and-preliminary-assessment-of-their-cytotoxicity
#6
Clara Andrea Rincón-Cortés, Edgar Antonio Reyes-Montaño, Nohora Angélica Vega-Castro
INTRODUCTION: Scorpion venom contains peptides with neurotoxic action primarily active on ion channels in the nervous system of insects and mammals. They are also characterized as cytolytic and anticancer, biological characteristics that have not yet been reported for the Tityus macrochirus venom. OBJECTIVE: To assess if the total T. macrochirus venom and the fraction of partially purified peptides decrease the viability of various tumor-derived cell lines. MATERIALS AND METHODS: The scorpion venom was collected by electrical stimulation and, subsequently, subjected to chromatography, electrophoresis, and ultrafiltration with Amicon Ultra 0...
June 1, 2017: Biomédica: Revista del Instituto Nacional de Salud
https://www.readbyqxmd.com/read/28527179/making-time-conservation-of-biological-clocks-from-fungi-to-animals
#7
Jay C Dunlap, Jennifer J Loros
The capacity for biological timekeeping arose at least three times through evolution, in prokaryotic cyanobacteria, in cells that evolved into higher plants, and within the group of organisms that eventually became the fungi and the animals. Neurospora is a tractable model system for understanding the molecular bases of circadian rhythms in the last of these groups, and is perhaps the most intensively studied circadian cell type. Rhythmic processes described in fungi include growth rate, stress responses, developmental capacity, and sporulation, as well as much of metabolism; fungi use clocks to anticipate daily environmental changes...
May 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28526922/advances-in-systemic-therapy-for-metastatic-breast-cancer-future-perspectives
#8
REVIEW
S P Corona, N Sobhani, A Ianza, G Roviello, G Mustacchi, M Bortul, F Zanconati, D Generali
Breast cancer (BC) is the most common cancer in women worldwide. One in eight women will develop the disease in her lifetime. Notwithstanding the incredible progress made in this field, BC still represents the second most common cause of cancer-related death in women. Targeted drugs have revolutionised breast cancer treatment and improved the prognosis as well as the life expectancy of millions of women. However, the phenomenon of primary and secondary pharmacological resistance is becoming increasingly evident, limiting the efficacy of these agents and calling for a better in-depth knowledge and understanding of the biology as well as the biochemical crosstalk underlying the disease...
July 2017: Medical Oncology
https://www.readbyqxmd.com/read/28526873/role-of-s-palmitoylation-by-zdhhc13-in-mitochondrial-function-and-metabolism-in-liver
#9
Li-Fen Shen, Yi-Ju Chen, Kai-Ming Liu, Amir N Saleem Haddad, I-Wen Song, Hsiao-Yuh Roan, Li-Ying Chen, Jeffrey J Y Yen, Yu-Ju Chen, Jer-Yuarn Wu, Yuan-Tsong Chen
Palmitoyltransferase (PAT) catalyses protein S-palmitoylation which adds 16-carbon palmitate to specific cysteines and contributes to various biological functions. We previously reported that in mice, deficiency of Zdhhc13, a member of the PAT family, causes severe phenotypes including amyloidosis, alopecia, and osteoporosis. Here, we show that Zdhhc13 deficiency results in abnormal liver function, lipid abnormalities, and hypermetabolism. To elucidate the molecular mechanisms underlying these disease phenotypes, we applied a site-specific quantitative approach integrating an alkylating resin-assisted capture and mass spectrometry-based label-free strategy for studying the liver S-palmitoylome...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28526728/genetic-subtraction-profiling-identifies-candidate-mirnas-involved-in-rice-female-gametophyte-abortion
#10
Liyu Yang, Ya Wu, Wenliang Wang, Bigang Mao, Bingran Zhao, Jianbo Wang
Female gametophyte is an important participant in sexual reproduction of plants. The molecular mechanism of its development has received much attention in recent years. As important regulators of gene expression, miRNAs have been certified to play a significant role in many biological processes of plants including sexual reproduction. In this study, to investigate the potential regulatory effects of miRNAs on rice female gametophytes abortion, we used the high-throughput sequencing method to compare the miRNA transcriptome in ovules of a high frequency female-sterile line (fsv1) and a rice wild-type line (Gui 99) during ovule development...
May 19, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28526692/understanding-the-interrelationship-between-the-synthesis-of-urea-and-gluconeogenesis-by-formulating-an-overall-balanced-equation
#11
Piero L Ipata, Rossana Pesi
It is well known that a strong metabolic interrelationship exists between ureagenesis and gluconeogenesis. In this paper, we present a detailed, overall equation, describing a possible metabolic link between ureagenesis and gluconeogenesis. We adopted a guided approach in which we strongly suggest that students, when faced with the problem of obtaining the overall equation of a metabolic pathway, carefully account for all atoms and charges of the single reactions, as well as the cellular localizations of the substrates, and the related transport systems...
June 1, 2017: Advances in Physiology Education
https://www.readbyqxmd.com/read/28526370/synthesis-and-biological-evaluation-of-kresoxim-methyl-analogues-as-novel-inhibitors-of-hypoxia-inducible-factor-hif-1-accumulation-in-cancer-cells
#12
Sanghyuck Lee, Oh Seok Kwon, Chang-Soo Lee, Misun Won, Hyun Seung Ban, Choon Sup Ra
We designed and synthesized strobilurin analogues as hypoxia-inducible factor (HIF) inhibitors based on the molecular structure of kresoxim-methyl. Biological evaluation in human colorectal cancer HCT116 cells showed that most of the synthesized kresoxim-methyl analogues possessed moderate to potent inhibitory activity against hypoxia-induced HIF-1 transcriptional activation. Three candidates, compounds 11b, 11c, and 11d were identified as potent inhibitors against HIF-1 activation with IC50 values of 0.60-0...
May 9, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28526134/molecular-biology-digest-of-cell-mitophagy
#13
I Matic, D Strobbe, F Di Guglielmo, M Campanella
The homeostasis of eukaryotic cells relies on efficient mitochondrial function. The control of mitochondrial quality is framed by the combination of distinct but interdependent mechanisms spanning biogenesis, regulation of dynamic network, and finely tuned degradation either through ubiquitin-proteasome system or autophagy (mitophagy). There is continuous evolution on the pathways orchestrating the mitochondrial response to stress signals and the organelle adaptation to quality control during acute and subtle dysfunctions...
2017: International Review of Cell and Molecular Biology
https://www.readbyqxmd.com/read/28525957/determining-dominant-driving-forces-affecting-controlled-protein-release-from-polymeric-nanoparticles
#14
Josh Smith, Kayla G Sprenger, Rick Liao, Andrea Joseph, Elizabeth Nance, Jim Pfaendtner
Enzymes play a critical role in many applications in biology and medicine as potential therapeutics. One specific area of interest is enzyme encapsulation in polymer nanostructures, which have applications in drug delivery and catalysis. A detailed understanding of the mechanisms governing protein/polymer interactions is crucial for optimizing the performance of these complex systems for different applications. Using a combined computational and experimental approach, this study aims to quantify the relative importance of molecular and mesoscale driving forces to protein release from polymeric nanoparticles...
May 19, 2017: Biointerphases
https://www.readbyqxmd.com/read/28525648/the-role-of-omics-in-the-application-of-adverse-outcome-pathways-for-chemical-risk-assessment
#15
Erica K Brockmeier, Geoff Hodges, Thomas H Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F Owen, Edward J Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, Francesco Falciani
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (e.g., transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/28525595/gut-transcriptome-analysis-shows-different-food-utilization-efficiency-by-the-grasshopper-oedaleous-asiaticus-orthoptera-acrididae
#16
Xunbing Huang, Mark Richard McNeill, Jingchuan Ma, Xinghu Qin, Xiongbing Tu, Guangchun Cao, Guangjun Wang, Xiangqun Nong, Zehua Zhang
Oedaleus asiaticus B. Bienko is a persistent pest occurring in north Asian grasslands. We found that O. asiaticus feeding on Stipa krylovii Roshev. had higher approximate digestibility (AD), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), compared with cohorts feeding on Leymus chinensis (Trin.) Tzvel, Artemisia frigida Willd., or Cleistogenes squarrosa (Trin.) Keng. Although this indicated high food utilization efficiency for S. krylovii, the physiological processes and molecular mechanisms underlying these biological observations are not well understood...
May 19, 2017: Journal of Economic Entomology
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#17
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28525356/synthesis-biological-activity-and-molecular-modeling-study-of-new-schiff-bases-incorporated-with-indole-moiety
#18
Ahmed H Halawa, Shimaa Mohamed Abd El-Gilil, Ahmed H Bedair, Mohamed Shaaban, Marcel Frese, Norbert Sewald, Essam M Eliwa, Ahmed M El-Agrody
A new series of heterocyclic Schiff bases 2-9 containing indole moiety were synthesized by facile and efficient condensation of indole-3/2/5-carboxaldehyde (1a/1b/1c) with different aromatic and heterocyclic primary amines using conventional and/or microwave irradiation methods. The structures of the obtained compounds were assigned by sophisticated spectroscopic and spectrometric techniques (1D-NMR, 2D-NMR and MS). The synthesized compounds were screened for their cytotoxicity and antibacterial activities...
May 18, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28525259/biodegradable-smart-polyphosphazenes-with-intrinsic-multi-functionality-as-intracellular-protein-delivery-vehicles
#19
Andre P Martinez, Bareera Qamar, Thomas R Fuerst, Silvia Muro, Alexander K Andrianov
A series of biodegradable drug delivery polymers with intrinsic multifunctionality have been designed and synthesized utilizing polyphosphazene macromolecular engineering approach. Novel water-soluble polymers, which contain carboxylic acid and pyrrolidone moieties attached to inorganic phosphorus-nitrogen backbone, were characterized by a suite of physico-chemical methods to confirm their structure, composition, and molecular sizes. All synthesized polyphosphazenes displayed composition dependent hydrolytic degradability in aqueous solutions at neutral pH...
May 19, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28524769/machine-learning-for-epigenetics-and-future-medical-applications
#20
Lawrence B Holder, M Muksitul Haque, Michael K Skinner
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigenetic transgenerational inheritance of disease and novel ML approaches to predict genome-wide locations of critical epimutations. A combination of Active Learning (ACL) and Imbalanced Class Learning (ICL) was used to address past problems with ML to develop a more efficient feature selection process and address the imbalance problem in all genomic data sets...
May 19, 2017: Epigenetics: Official Journal of the DNA Methylation Society
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