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https://www.readbyqxmd.com/read/29318095/green-and-red-fluorescent-dyes-for-translational-applications-in-imaging-and-sensing-analytes-a-dual-color-flag
#1
REVIEW
Elisabete Oliveira, Emilia Bértolo, Cristina Núñez, Viviane Pilla, Hugo M Santos, Javier Fernández-Lodeiro, Adrian Fernández-Lodeiro, Jamila Djafari, José Luis Capelo, Carlos Lodeiro
Red and green are two of the most-preferred colors from the entire chromatic spectrum, and red and green dyes are widely used in biochemistry, immunohistochemistry, immune-staining, and nanochemistry applications. Selective dyes with green and red excitable chromophores can be used in biological environments, such as tissues and cells, and can be irradiated with visible light without cell damage. This critical review, covering a period of five years, provides an overview of the most-relevant results on the use of red and green fluorescent dyes in the fields of bio-, chemo- and nanoscience...
January 2018: ChemistryOpen
https://www.readbyqxmd.com/read/29310782/the-biochemistry-and-immunohistochemistry-of-versican
#2
Stephen P Evanko, Christina K Chan, Pamela Y Johnson, Charles W Frevert, Thomas N Wight
Versican is a chondroitin sulfate proteoglycan found in the extracellular matrix that is important for changes in cell phenotype associated with development and disease. Versican has been shown to be involved in cardiovascular disorders, as well as lung disease and fibrosis, inflammatory bowel disease, cancer, and several other diseases that have an inflammatory component. Versican was first identified as a fibroblast proteoglycan and forms large multimolecular complexes with hyaluronan and other components of the provisional matrix during wound healing and inflammation...
2018: Methods in Cell Biology
https://www.readbyqxmd.com/read/29300163/robust-model-based-analysis-of-single-particle-tracking-experiments-with-spot-on
#3
Anders S Hansen, Maxime Woringer, Jonathan B Grimm, Luke D Lavis, Robert Tjian, Xavier Darzacq
Single-particle tracking (SPT) has become an important method to bridge biochemistry and cell biology since it allows direct observation of protein binding and diffusion dynamics in live cells. However, accurately inferring information from SPT studies is challenging due to biases in both data analysis and experimental design. To address analysis bias, we introduce 'Spot-On', an intuitive web-interface. Spot-On implements a kinetic modeling framework that accounts for known biases, including molecules moving out-of-focus, and robustly infers diffusion constants and subpopulations from pooled single-molecule trajectories...
January 4, 2018: ELife
https://www.readbyqxmd.com/read/29278892/tauopathies-mechanisms-and-therapeutic-strategies
#4
Chen-Chen Tan, Xiao-Yan Zhang, Lan Tan, Jin-Tai Yu
Tauopathies are morphologically, biochemically, and clinically heterogeneous neurodegenerative diseases defined by the accumulation of abnormal tau proteins in the brain. There is no effective method to prevent and reverse the tauopathies, but this gloomy picture has been changed by recent research advances. Evidences from genetic studies, experimental animal models, and molecular and cell biology have shed light on the main mechanisms of the diseases. The development of radiology and biochemistry, especially the development of PET imaging, will provide important biomarkers for the clinical diagnosis and treatment...
2018: Journal of Alzheimer's Disease: JAD
https://www.readbyqxmd.com/read/29274248/stem-cell-education-for-medical-students-at-tongji-university-primary-cell-culture-and-directional-differentiation-of-rat-bone-marrow-mesenchymal-stem-cells
#5
Caixia Jin, Haibin Tian, Jiao Li, Song Jia, Siguang Li, Guo-Tong Xu, Lei Xu, Lixia Lu
Stem cells are cells that can self-renew and differentiate into a variety of cell types under certain conditions. Stem cells have great potential in regenerative medicine and cell therapy for the treatment of certain diseases. To deliver knowledge about this frontier in science and technology to medical undergraduate students, we designed an innovative practical experiment for freshmen in their second semester. The lab exercise focused on rat bone marrow mesenchymal stem cell (BMSC) isolation, cell culture and differentiation, and it aimed to help students master the aseptic techniques for cell culture, the basic methods and procedures for the primary culture and passage of BMSCs, the basic procedure for the directional differentiation of BMSCs into adipocytes and their subsequent identification by oil-red-O staining...
December 23, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29259528/%C3%A2-yeast-still-a-beast-diverse-applications-of-crispr-cas-editing-technology-in-s-cerevisiae%C3%A2
#6
REVIEW
Rachael M Giersch, Gregory C Finnigan
The recent discovery and use of CRISPR/Cas9 gene editing technology has provided new opportunities for scientific research in many fields of study including agriculture, genetic disorders, human disease, biotechnology, and basic biological research. The ability to precisely target DNA sequences and either remove, modify, or replace genetic sequences provides a new level of control in nearly all eukaryotic organisms, including budding yeast. Given the many discoveries made in Saccharomyces cerevisiae over the past decades spanning genetics, cell biology, and biochemistry, as well as the development of new technologies that have allowed high throughput screening, robotic automation, and a platform for synthetic genome engineering, the yeast community has also started to recognize the utility and complementary nature of CRISPR-based methodologies...
December 2017: Yale Journal of Biology and Medicine
https://www.readbyqxmd.com/read/29247800/de-novo-rna-seq-based-transcriptome-analysis-of-papiliotrema-laurentii-strain-ry1-under-nitrogen-starvation
#7
Soumyadev Sarkar, Somnath Chakravorty, Avishek Mukherjee, Debanjana Bhattacharya, Semantee Bhattacharya, Ratan Gachhui
Nitrogen is a key nutrient for all cell forms. Most organisms respond to nitrogen scarcity by slowing down their growth rate. On the contrary, our previous studies have shown that Papiliotrema laurentii strain RY1 has a robust growth under nitrogen starvation. To understand the global regulation that leads to such an extraordinary response, we undertook a de novo approach for transcriptome analysis of the yeast. Close to 33 million sequence reads of high quality for nitrogen limited and enriched condition were generated using Illumina NextSeq500...
December 13, 2017: Gene
https://www.readbyqxmd.com/read/29242887/chemical-methods-for-mapping-cysteine-oxidation
#8
REVIEW
Lisa J Alcock, Michael V Perkins, Justin M Chalker
Cysteine residues in proteins are subject to diverse redox chemistry. Oxidation of cysteine to S-nitrosocysteine, cysteine sulfenic and sulfinic acids, disulfides and persulfides are a few prominent examples of these oxidative post-translational modifications. In living organisms, these modifications often play key roles in cell signalling and protein function, but a full account of this biochemistry is far from complete. It is therefore an important goal in chemical biology to identify what proteins are subjected to these modifications and understand their physiological function...
December 15, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/29238927/metal-tolerant-thermophiles-metals-as-electron-donors-and-acceptors-toxicity-tolerance-and-industrial-applications
#9
Preeti Ranawat, Seema Rawat
Metal-tolerant thermophiles are inhabitants of a wide range of extreme habitats like solfatara fields, hot springs, mud holes, hydrothermal vents oozing out from metal-rich ores, hypersaline pools and soil crusts enriched with metals and other elements. The ability to withstand adverse environmental conditions, like high temperature, high metal concentration and sometimes high pH in their niche, makes them an interesting subject for understanding mechanisms behind their ability to deal with multiple duress simultaneously...
December 14, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29230441/detection-of-a%C3%AE-plaque-associated-astrogliosis-in-alzheimer-s-disease-brain-by-spectroscopic-imaging-and-immunohistochemistry
#10
Francesca Palombo, Francesco Tamagnini, J Charles G Jeynes, Sara Mattana, Imogen Swift, Jayakrupakar Nallala, Jane Hancock, Jonathan T Brown, Andrew D Randall, Nick Stone
Recent work using micro-Fourier transform infrared (μFTIR) imaging has revealed that a lipid-rich layer surrounds many plaques in post-mortem Alzheimer's brain. However, the origin of this lipid layer is not known, nor is its role in the pathogenesis of Alzheimer's disease (AD). Here, we studied the biochemistry of plaques in situ using a model of AD. We combined FTIR, Raman and immunofluorescence images, showing that astrocyte processes co-localise with the lipid ring surrounding many plaques. We used μFTIR imaging to rapidly measure chemical signatures of plaques over large fields of view, and selected plaques for higher resolution analysis with Raman microscopy...
December 12, 2017: Analyst
https://www.readbyqxmd.com/read/29208279/collagen-alginate-as-bioink-for-three-dimensional-3d-cell-printing-based-cartilage-tissue-engineering
#11
Xingchen Yang, Zhenhui Lu, Huayu Wu, Wei Li, Li Zheng, Jinmin Zhao
Articular cartilage repair is still a huge challenge for researchers and clinicians. 3D bioprinting could be an innovative technology for cartilage tissue engineering. In this study, we used collagen type I (COL) or agarose (AG) mixed with sodium alginate (SA) to serve as 3D bioprinting bioinks and incorporated chondrocytes to construct in vitro 3D printed cartilage tissue. Swelling ratio, mechanical properties, scanning electron microscopy (SEM), cell viability and cytoskeleton, biochemistry analysis and quantitative real-time polymerase chain reaction (qRT-PCR) were performed to investigate the function of different bioinks in 3D printing cartilage tissue engineering applications...
February 1, 2018: Materials Science & Engineering. C, Materials for Biological Applications
https://www.readbyqxmd.com/read/29201965/salivary-chemical-factors-in-relation-with-oral-cancer-in-smokers-and-non-smokers-a-literature-review
#12
REVIEW
Tahereh Nosratzehi
Squamous cell carcinoma of oral cavity is of malignant tumors, which causes cancerous complications. DNA damage, mainly because of products of oxidative stress like reactive oxygen species, is a frequent mutagenic that triggers carcinoma. Smoking increases the probability of cancer incidence. Saliva is the first biological medium to interact with external compounds, especially smoking substances. The present study overviews the salivary level of some remarkable compounds in relation with smoking and squamous cell carcinoma...
December 2017: Journal of Dentistry
https://www.readbyqxmd.com/read/29200271/the-next-frontier-quantitative-biochemistry-in-living-cells
#13
Alf Honigmann, André Nadler
Researchers striving to convert biology into an exact science foremost rely on structural biology and biochemical reconstitution approaches to obtain quantitative data. However, cell biological research is moving at an ever-accelerating speed into areas where these approaches loose much of their edge. Intrinsically unstructured proteins and biochemical interaction networks composed of interchangeable, multivalent and unspecific interactions pose unique challenges to quantitative biology, as do processes that occur in discrete cellular microenvironments...
December 4, 2017: Biochemistry
https://www.readbyqxmd.com/read/29170613/an-efficient-synthesis-of-indolo-2-3-b-quinoline-guanidine-derivatives-with-their-in-vitro-and-in-vivo-study
#14
Katarzyna Sidoryk, Marta Świtalska, Piotr Rózga, Joanna Wietrzyk, Iwona Bujak, Bartłomiej Żerek, Łukasz Kaczmarek, Marcin Cybulski
An optimization of the guanidylation process by verifying the efficacy of common guanylation reagents in order to obtain the guanidine derivatives of indolo[2,3-b]quinoline has been performed. As a result, a high-yield procedure using N,N'-di-Boc-N''-triflylguanidine was applied to synthesize the guanidine derivative of indolo[2,3-b]quinoline 1 in a gram scale for specific in vitro and in vivo biological research. Extensive studies on the antiproliferative activity against eight human tumor cell lines were completed...
2017: Medicinal Chemistry Research
https://www.readbyqxmd.com/read/29164638/the-piwi-interacting-rna-molecular-pathway-insights-from-cultured-silkworm-germline-cells
#15
Kazuhiro Sakakibara, Mikiko C Siomi
The PIWI-interacting RNA (piRNA) pathway, one of the major eukaryotic small RNA silencing pathways, is a genome surveillance system that silences selfish genes in animal gonads. piRNAs guide PIWI protein to target genes through Watson-Crick RNA-RNA base-parings. Loss of piRNA function causes genome instability, inducing failure in gametogenesis and infertility. Studies using fruit flies and mice as key experimental models have resulted in tremendous progress in understanding the mechanism underlying the piRNA pathway...
November 22, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/29155548/site-selective-rna-splicing-nanozyme-dnazyme-and-rtcb-conjugates-on-a-gold-nanoparticle
#16
Jessica R Petree, Kevin Yehl, Kornelia Galior, Roxanne Glazier, Brendan Deal, Khalid Salaita
Modifying RNA through either splicing or editing is a fundamental biological process for creating protein diversity from the same genetic code. Developing novel chemical biology tools for RNA editing has potential to transiently edit genes and to provide a better understanding of RNA biochemistry. Current techniques used to modify RNA include the use of ribozymes, adenosine deaminase and tRNA endonucleases. Herein, we report a nanozyme that is capable of splicing of virtually any RNA stem-loop. This nanozyme is comprised of a gold nanoparticle functionalized with three enzymes: two catalytic DNA strands with ribonuclease function and an RNA ligase...
November 20, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29154193/fundamentals-on-the-biochemistry-of-peroxynitrite-and-protein-tyrosine-nitration
#17
REVIEW
Silvina Bartesaghi, Rafael Radi
In this review we provide an analysis of the biochemistry of peroxynitrite and tyrosine nitration. Peroxynitrite is the product of the diffusion-controlled reaction between superoxide (O2(•)(-)) and nitric oxide ((•)NO). This process is in competition with the enzymatic dismutation of O2(•-) and the diffusion of (•)NO across cells and tissues and its reaction with molecular targets (e.g. guanylate cyclase). Understanding the kinetics and compartmentalization of the O2(•-) / (•)NO interplay is critical to rationalize the shift of (•)NO from a physiological mediator to a cytotoxic intermediate...
September 19, 2017: Redox Biology
https://www.readbyqxmd.com/read/29145976/not-only-p-glycoprotein-amplification-of-the-abcb1-containing-chromosome-region-7q21-confers-multidrug-resistance-upon-cancer-cells-by-coordinated-overexpression-of-an-assortment-of-resistance-related-proteins
#18
Ilaria Genovese, Andrea Ilari, Yehuda G Assaraf, Francesco Fazi, Gianni Colotti
The development of drug resistance continues to be a dominant hindrance toward curative cancer treatment. Overexpression of a wide-spectrum of ATP-dependent efflux pumps, and in particular of ABCB1 (P-glycoprotein or MDR1) is a well-known resistance mechanism for a plethora of cancer chemotherapeutics including for example taxenes, anthracyclines, Vinca alkaloids, and epipodopyllotoxins, demonstrated by a large array of published papers, both in tumor cell lines and in a variety of tumors, including various solid tumors and hematological malignancies...
May 2017: Drug Resistance Updates: Reviews and Commentaries in Antimicrobial and Anticancer Chemotherapy
https://www.readbyqxmd.com/read/29131508/an-interactive-computer-lab-of-the-galvanic-cell-for-students-in-biochemistry
#19
Emma Ahlstrand, Antoine Buetti-Dinh, Ran Friedman
We describe an interactive module that can be used to teach basic concepts in electrochemistry and thermodynamics to first year natural science students. The module is used together with an experimental laboratory and improves the students' understanding of thermodynamic quantities such as Δr G, Δr H, and Δr S that are calculated but not directly measured in the lab. We also discuss how new technologies can substitute some parts of experimental chemistry courses, and improve accessibility to course material...
November 13, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29131507/the-disruptive-effect-of-lysozyme-on-the-bacterial-cell-wall-explored-by-an-in-silico-structural-outlook
#20
Emiliano D Primo, Lisandro H Otero, Francisco Ruiz, Sebastián Klinke, Walter Giordano
The bacterial cell wall, a structural unit of peptidoglycan polymer comprised of glycan strands consisting of a repeating disaccharide motif [N-acetylglucosamine (NAG) and N-acetylmuramylpentapeptide (NAM pentapeptide)], encases bacteria and provides structural integrity and protection. Lysozymes are enzymes that break down the bacterial cell wall and disrupt the bacterial life cycle by cleaving the linkage between the NAG and NAM carbohydrates. Lab exercises focused on the effects of lysozyme on the bacterial cell wall are frequently incorporated in biochemistry classes designed for undergraduate students in diverse fields as biology, microbiology, chemistry, agronomy, medicine, and veterinary medicine...
November 13, 2017: Biochemistry and Molecular Biology Education
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