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https://www.readbyqxmd.com/read/28324600/light-sheet-fluorescence-microscopy-chemical-clearing-and-labeling-protocols-for-ultramicroscopy
#1
Nina Jährling, Klaus Becker, Saiedeh Saghafi, Hans-Ulrich Dodt
Light-sheet microscopy is an effective technique in neuroscience, developmental biology, and cancer research for visualizing and analyzing cellular networks and whole organs in three dimensions. Because this technique requires specimens to be translucent they commonly have to be cleared before microscopy inspection. Here, we provide 3DISCO based protocols for preparing cleared samples of immuno-stained neural networks, lectin-labeled vascular networks, and Methoxy-X04 labeled beta-amyloid plaques in mice. 3DISCO utilizes the lipophilic solvents tetrahydrofuran (THF) and dibenzylether (DBE) for dehydration and successive clearing...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324506/induction-of-site-specific-oxidative-damage-at-telomeres-by-killerred-fused-shelretin-proteins
#2
Rong Tan, Li Lan
Chronic oxidative stress is the major endogenous metabolic stress and contributes directly to telomere shortening and senescence. Understanding the dysfunction of telomeres under oxidative stress will greatly facilitate healthy aging and advance the treatment of aging-related diseases. Here, we describe the KR-TEL (KillerRed induced DNA damage at telomeres) system that induces site-specific oxidative damage at telomeres. We have developed the KR-TEL system by fusing killerred with the shelterin component TRF1 (KR-TRF1) or other shelterin proteins...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324485/maintenance-of-human-embryonic-stem-cells-by-sphingosine-1-phosphate-and-platelet-derived-growth-factor
#3
Raymond C B Wong, Martin F Pera, Alice Pébay
Human embryonic stem cells (hESCs) have historically been cultivated on feeder layers of primary mouse embryonic fibroblasts (MEF) in a medium supplemented with fetal calf serum (FCS). However, serum contains a wide variety of biologically active compounds that might adversely affect hESC growth and differentiation. Thus, cultivation of stem cells in FCS complicates experimental approaches to define the intracellular mechanisms required for hESC maintenance. This chapter describes the serum-free maintenance of hESCs in culture by addition of sphingosine-1-phosphate (S1P) and platelet-derived growth factor (PDGF)...
March 22, 2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28324279/soil-organic-matter-as-sole-indicator-of-soil-degradation
#4
S E Obalum, G U Chibuike, S Peth, Y Ouyang
Soil organic matter (SOM) is known to play vital roles in the maintenance and improvement of many soil properties and processes. These roles, which largely influence soil functions, are a pool of specific contributions of different components of SOM. The soil functions, in turn, normally define the level of soil degradation, viewed as quantifiable temporal changes in a soil that impairs its quality. This paper aims at providing a generalized assessment of the current state of knowledge on the usefulness of SOM in monitoring soil degradation, based on its influence on the physical, chemical and biological properties and processes of soils...
April 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/28320100/drosophila-melanogaster-a-potential-model-organism-for-identification-of-pharmacological-properties-of-plants-plant-derived-components
#5
REVIEW
Komal Panchal, Anand K Tiwari
Plants/plant-derived components have been used from ancient times to treat/cure several human diseases. Plants and their parts possess several chemical components that play the vital role in the improvement of human health and their life expectancy. Allopathic medicines have been playing a key role in the treatment of several diseases. Though allopathic medicines provide fast relief, long time consumption cause serious health concerns such as hyperallergic reactions, liver damage, etc. So, the study of medicinal plants which rarely cause any side effect is very important to mankind...
March 18, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28319869/biofilm-inhibition-formation-of-clinical-strains-of-pseudomonas-aeruginosa-mutans-photocatalytic-activity-of-azo-dye-and-gc-ms-analysis-of-leaves-of-lagerstroemia-speciosa
#6
V Sai Saraswathi, Neethu Kamarudheen, K V Bhaskara Rao, K Santhakumar
The investigation was conducted to analyse the bioactive compounds from the leaf extracts of L. speciosa by GC-MS. The extracts were screened for antibacterial and antibiofilm activities against potential clinical strains. The bioactive compounds from the leaves of L. speciosa were extracted by soxhlet continuous extraction method and their chemical composition was analysed by Gas Chromatography-Mass Spectroscopy (GC-MS). The antibacterial activity was evaluated against clinical strain like Staphylococcus aureus, Escherichia coli, P...
March 9, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28319856/systems-biology-solutions-for-biochemical-production-challenges
#7
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28319854/extremely-thermophilic-energy-metabolisms-biotechnological-prospects
#8
REVIEW
Christopher T Straub, Benjamin M Zeldes, Gerrit J Schut, Michael Ww Adams, Robert M Kelly
New strategies for metabolic engineering of extremely thermophilic microorganisms to produce bio-based fuels and chemicals could leverage pathways and physiological features resident in extreme thermophiles for improved outcomes. Furthermore, very recent advances in genetic tools for these microorganisms make it possible for them to serve as metabolic engineering hosts. Beyond providing a higher temperature alternative to mesophilic platforms, exploitation of strategic metabolic characteristics of high temperature microorganisms grants new opportunities for biotechnological products...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28319812/exploring-sequence-space-harnessing-chemical-and-biological-diversity-towards-new-peptide-leads
#9
REVIEW
Richard Obexer, Louise J Walport, Hiroaki Suga
From their early roots in natural products, peptides now represent an expanding class of novel drugs. Their modular structures make them ideal candidates for pooled library screening approaches. Key technologies for library generation and screening, such as SICLOPPS, phage display and mRNA display, give unparalleled access to tight binding peptides. Through combination with genetic code reprogramming and chemical modifications, access to more natural product-like libraries, spanning non-canonical peptide space, is readily achievable...
March 17, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28319747/integration-of-in-silico-methods-and-computational-systems-biology-to-explore-endocrine-disrupting-chemical-binding-with-nuclear-hormone-receptors
#10
P Ruiz, A Sack, M Wampole, S Bobst, M Vracko
Thousands of potential endocrine-disrupting chemicals present difficult regulatory challenges. Endocrine-disrupting chemicals can interfere with several nuclear hormone receptors associated with a variety of adverse health effects. The U.S. Environmental Protection Agency (U.S. EPA) has released its reviews of Tier 1 screening assay results for a set of pesticides in the Endocrine Disruptor Screening Program (EDSP), and recently, the Collaborative Estrogen Receptor Activity Prediction Project (CERAPP) data...
March 9, 2017: Chemosphere
https://www.readbyqxmd.com/read/28318906/analysis-of-molecular-mechanisms-of-atp-synthesis-from-the-standpoint-of-the-principle-of-electrical-neutrality
#11
REVIEW
Sunil Nath
Theories of biological energy coupling in oxidative phosphorylation (OX PHOS) and photophosphorylation (PHOTO PHOS) are reviewed and applied to ATP synthesis by an experimental system containing purified ATP synthase reconstituted into liposomes. The theories are critically evaluated from the standpoint of the principle of electrical neutrality. It is shown that the obligatory requirement to maintain overall electroneutrality of bulk aqueous phases imposes strong constraints on possible theories of energy coupling and molecular mechanisms of ATP synthesis...
March 8, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28318601/strategies-and-knowledge-gaps-for-improving-nanomaterial-biocompatibility
#12
REVIEW
Xiangang Hu, Anqi Sun, Weilu Kang, Qixing Zhou
With rapid development of nanotechnology and nanomaterials, nanosafety has attracted wide attention in all fields related to nanotechnology. As well known, a grand challenge in nanomaterial applications is their biocompatibility. It is urgent to explore effective strategies to control the unintentional effects. Although many novel methods for the synthesis of biocompatible and biodegradable nanomaterials are reported, the control strategy of nanotoxicity remains in its infancy. It is urgent to review the archived strategies for improving nanomaterial biocompatibility to clarify what we have done and where we should be...
March 15, 2017: Environment International
https://www.readbyqxmd.com/read/28318534/a-multidrug-and-toxic-compound-extrusion-transporter-mediates-berberine-accumulation-into-vacuoles-in-coptis-japonica
#13
Kojiro Takanashi, Yasuyuki Yamada, Takayuki Sasaki, Yoko Yamamoto, Fumihiko Sato, Kazufumi Yazaki
Plants produce a large variety of alkaloids, which have diverse chemical structures and biological activities. Many of these alkaloids accumulate in vacuoles. Although some membrane proteins on tonoplasts have been identified as alkaloid uptake transporters, few have been characterized to date, and relatively little is known about the mechanisms underlying alkaloid transport and accumulation in plant cells. Berberine is a model alkaloid. Although all genes involved in berberine biosynthesis, as well as the master regulator, have been identified, the gene responsible for the final accumulation of berberine at tonoplasts has not been determined...
March 16, 2017: Phytochemistry
https://www.readbyqxmd.com/read/28318300/bacteria-from-wheat-and-cucurbit-plant-roots-metabolize-pahs-and-aromatic-root-exudates-implications-for-rhizodegradation
#14
Cairn S Ely, Barth F Smets
The chemical interaction between plants and bacteria in the root zone can lead to soil decontamination. Bacteria which degrade PAHs have been isolated from the rhizospheres of plant species with varied biological traits, however, it is not known what phytochemicals promote contaminant degradation. One monocot and two dicotyledon plants were grown in PAH-contaminated soil from a manufactured gas plant (MGP) site. A phytotoxicity assay confirmed greater soil decontamination in rhizospheres when compared to bulk soil controls...
March 20, 2017: International Journal of Phytoremediation
https://www.readbyqxmd.com/read/28318088/twenty-five-years-of-dna-encoded-chemical-libraries
#15
EDITORIAL
Dario Neri
Reference library: The availability of DNA-encoded chemical libraries containing billions of compounds facilitates the discovery of binding molecules for pharmaceutical applications and for investigating biological processes. This Special Issue highlights the use of this library technology and some of the latest developments in the field.
March 20, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28317950/in-vivo-identification-of-potential-uranium-protein-targets-in-zebrafish-ovaries-after-chronic-waterborne-exposure
#16
Y Eb-Levadoux, S Frelon, O Simon, C Arnaudguilhem, R Lobinski, S Mounicou
Ecotoxicological studies have indicated the reprotoxicity of uranium (U) in zebrafish, but its molecular mechanisms remain unclear. Due to the non-covalent nature of U-protein complexes, canonical proteomics approaches are often not relevant as they usually use denaturating reagents or solvents. In this study, non-denaturating (ND) methods were used to obtain insight into the nature of U potential targets in ovaries of reproduced and non-reproduced zebrafish after 20 days of exposure to an environmentally relevant U concentration (20 μg L(-1))...
March 20, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28317922/optical-imaging-of-localized-chemical-events-using-programmable-diamond-quantum-nanosensors
#17
Torsten Rendler, Jitka Neburkova, Ondrej Zemek, Jan Kotek, Andrea Zappe, Zhiqin Chu, Petr Cigler, Jörg Wrachtrup
Development of multifunctional nanoscale sensors working under physiological conditions enables monitoring of intracellular processes that are important for various biological and medical applications. By attaching paramagnetic gadolinium complexes to nanodiamonds (NDs) with nitrogen-vacancy (NV) centres through surface engineering, we developed a hybrid nanoscale sensor that can be adjusted to directly monitor physiological species through a proposed sensing scheme based on NV spin relaxometry. We adopt a single-step method to measure spin relaxation rates enabling time-dependent measurements on changes in pH or redox potential at a submicrometre-length scale in a microfluidic channel that mimics cellular environments...
March 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28317887/nmr-spectroscopy-of-single-sub-nl-ova-with-inductive-ultra-compact-single-chip-probes
#18
Marco Grisi, Franck Vincent, Beatrice Volpe, Roberto Guidetti, Nicola Harris, Armin Beck, Giovanni Boero
Nuclear magnetic resonance (NMR) spectroscopy enables non-invasive chemical studies of intact living matter. However, the use of NMR at the volume scale typical of microorganisms is hindered by sensitivity limitations, and experiments on single intact organisms have so far been limited to entities having volumes larger than 5 nL. Here we show NMR spectroscopy experiments conducted on single intact ova of 0.1 and 0.5 nL (i.e. 10 to 50 times smaller than previously achieved), thereby reaching the relevant volume scale where life development begins for a broad variety of organisms, humans included...
March 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28317807/tetrahydro-2-furanyl-2-4-1h-3h-pyrimidinedione-derivatives-as-novel-antibacterial-compounds-against-mycobacterium
#19
Yuji Koseki, Hironori Kanetaka, Joji Tsunosaki, Héléne Munier-Lehmann, Shunsuke Aoki
OBJECTIVE/BACKGROUND: Mycobacterium tuberculosis thymidine monophosphate kinase (mtTMPK) is a potential enzymatic target for the treatment of tuberculosis (TB). MATERIALS AND METHODS: In this study, we performed pharmacophore-based in silico screening, targeting mtTMPK with a compound library of 461,383 chemicals. We evaluated the candidate compounds for inhibitory effects on the growth of the model mycobacteria, Mycobacterium smegmatis. RESULTS: The compound KTP3 completely inhibited the growth of M...
January 2017: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28317232/soil-parent-material-a-major-driver-of-plant-nutrient-limitations-in-terrestrial-ecosystems
#20
Laurent Augusto, David L Achat, Mathieu Jonard, David Vidal, Bruno Ringeval
Because the capability of terrestrial ecosystems to fix carbon is constrained by nutrient availability, understanding how nutrients limit plant growth is a key contemporary question. However, what drives nutrient limitations at global scale remains to be clarified. Using global data on plant growth, plant nutritive status, and soil fertility, we investigated to which extent soil parent materials explain nutrient limitations. We found that N limitation was not linked to soil parent materials, but was best explained by climate: ecosystems under harsh (i...
March 19, 2017: Global Change Biology
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