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https://www.readbyqxmd.com/read/28212484/on-surface-site-selective-cyclization-of-corrole-radicals
#1
Stefano Tebi, Mateusz Paszkiewicz, Hazem Aldahhak, Francesco Allegretti, Sabrina Gonglach, Michael Haas, Mario Waser, Peter S Deimel, Pablo Casado Aguilar, Yi-Qi Zhang, Anthoula C Papageorgiou, David Andrew Duncan, Johannes V Barth, Wolf Gero Schmidt, Reinhold Koch, Uwe Gerstmann, Eva Rauls, Florian Klappenberger, Wolfgang Schöfberger, Stefan Müllegger
Radical cyclization is among the most powerful and versatile reactions for constructing mono- and polycyclic systems, but has, to date, remained unexplored in the context of on-surface synthesis. We report the controlled on-surface synthesis of stable corrole radicals on Ag(111) via site-specific dehydrogenation of a pyrrole N H bond in the 5,10,15-tris(pentafluoro-phenyl)-corrole triggered by annealing at 330 K under ultra-high vacuum conditions. We reveal a thermally-induced regioselective cyclization reaction mediated by a radical cascade and resolve the reaction mechanism of the pertaining cyclodefluorination reaction at the single-molecule level...
February 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/28211479/decoupling-absorption-and-emission-processes-in-super-resolution-localization-of-emitters-in-a-plasmonic-hotspot
#2
David L Mack, Emiliano Cortés, Vincenzo Giannini, Peter Török, Tyler Roschuk, Stefan A Maier
The absorption process of an emitter close to a plasmonic antenna is enhanced due to strong local electromagnetic (EM) fields. The emission, if resonant with the plasmonic system, re-radiates to the far-field by coupling with the antenna via plasmonic states, whose presence increases the local density of states. Far-field collection of the emission of single molecules close to plasmonic antennas, therefore, provides mixed information of both the local EM field strength and the local density of states. Moreover, super-resolution localizations from these emission-coupled events do not report the real position of the molecules...
February 17, 2017: Nature Communications
https://www.readbyqxmd.com/read/28208282/general-sensitive-detecting-strategy-of-ions-through-plasmonic-resonance-energy-transfer-from-gold-nanoparticles-to-rhodamine-spirolactam
#3
Ming Xuan Gao, Hong Yan Zou, Yuan Fang Li, Cheng Zhi Huang
Plasmonic resonance energy transfer (PRET), which occurs between the plasmonic nanoparticles and organic dyes, has significant potential in target sensing chemistry owing to its sensitivity at the single nanoparticle level. In this contribution, by using AuNPs, which has localized surface plasmonic resonance light scattering (LSPR-LS) around 550 nm, as the donor of PRET, a general sensitive detecting strategy of ions were developed. Targets can specifically react with a ring-close structured rhodamine spirolactam, which was prepared from rhodamines in the presence of different primary amine wherein the option of the primary amine is up to the targets, forming ring-open structured rhodamine spirolactam with the strong absorption around 550 nm...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28207833/structure-kinetic-characterization-and-subcellular-localization-of-the-two-ribulose-5-phosphate-epimerase-isoenzymes-from-trypanosoma-cruzi
#4
Soledad Natalia Gonzalez, Wanda Mariela Valsecchi, Dante Maugeri, José María Delfino, Juan José Cazzulo
The enzyme of the pentose phosphate pathway (PPP) ribulose-5-phosphate-epimerase (RPE) is encoded by two genes present in the genome of Trypanosoma cruzi CL Brener clone: TcRPE1 and TcRPE2. Despite high sequence similarity at the amino acid residue level, the recombinant isoenzymes show a strikingly different kinetics. Whereas TcRPE2 follows a typical michaelian behavior, TcRPE1 shows a complex kinetic pattern, displaying a biphasic curve, suggesting the coexistence of -at least- two kinetically different molecular forms...
2017: PloS One
https://www.readbyqxmd.com/read/28207240/interfaces-in-heterogeneous-catalysts-advancing-mechanistic-understanding-through-atomic-scale-measurements
#5
Wenpei Gao, Zachary D Hood, Miaofang Chi
Developing novel catalysts with high efficiency and selectivity is critical for enabling future clean energy conversion technologies. Interfaces in catalyst systems have long been considered the most critical factor in controlling catalytic reaction mechanisms. Interfaces include not only the catalyst surface but also interfaces within catalyst particles and those formed by constructing heterogeneous catalysts. The atomic and electronic structures of catalytic surfaces govern the kinetics of binding and release of reactant molecules from surface atoms...
February 16, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28206693/plasmid-and-clonal-interference-during-post-horizontal-gene-transfer-evolution
#6
S Bedhomme, D Perez Pantoja, I G Bravo
Plasmids are nucleic acid molecules that can drive their own replication in a living cell. They can be transmitted horizontally and can thrive in the host cell to high copy numbers. Plasmid replication and gene expression consume cellular resources and cells carrying plasmids incur fitness costs. But many plasmids carry genes that can be beneficial under certain conditions, allowing the cell to endure in the presence of antibiotics, toxins, competitors or parasites. Horizontal transfer of plasmid-encoded genes can thus instantaneously confer differential adaptation to local or transient selection conditions...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28198579/tweezing-of-magnetic-and-non-magnetic-objects-with-magnetic-fields
#7
REVIEW
Jaakko V I Timonen, Bartosz A Grzybowski
Although strong magnetic fields cannot be conveniently "focused" like light, modern microfabrication techniques enable preparation of microstructures with which the field gradients - and resulting magnetic forces - can be localized to very small dimensions. This ability provides the foundation for magnetic tweezers which in their classical variant can address magnetic targets. More recently, the so-called negative magnetophoretic tweezers have also been developed which enable trapping and manipulations of completely nonmagnetic particles provided that they are suspended in a high-magnetic-susceptibility liquid...
February 15, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28196667/stress-granules-assembly-affects-detection-of-mrna-in-living-cells-by-the-nanoflares-an-important-aspect-of-the-technology
#8
Magdalena Wolczyk, Paulina Podszywalow-Bartnicka, Lukasz Bugajski, Katarzyna Piwocka
The recently announced new methodologies to detect mRNA molecules in single cells offer opportunities for research, medicine and molecular diagnostics. The NanoFlare RNA Detection Probes are tools for characterizing RNA content (not localization) using fluorescence-based approaches in living cells. Combined with flow cytometry NanoFlares have expanded the available possibilities of quantitative analysis of mRNA level in a single cell. Herein we present, that the specific NanoFlare probes (SmartFlares), in some cases detect different amounts of mRNA compared to qPCR...
February 11, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28196307/molecule-counts-in-localization-microscopy-with-organic-fluorophores
#9
Mike Heilemann, Franziska Fricke, Christos Karathanasis, Gerhard Hummer
Single-molecule localization microscopy (SMLM) can be used to count fluorescently labeled molecules even when they are not individually resolved. We demonstrate SMLM molecule counting for nucleic acids labeled with the organic fluorophore Alexa Fluor 647 and imaged under photoswitching conditions. From the observed distributions of the number of fluorophore blinking events, we extracted the number of fluorophores per spot using a statistical model. We validate the molecule counting method for single Alexa Fluor 647 fluorophores, and for trimers of Alexa Fluor 647 constructed on a DNA origami structure...
February 14, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28195693/assembly-domain-based-optogenetic-system-for-the-efficient-control-of-cellular-signaling
#10
Akihiro Furuya, Fuun Kawano, Takahiro Nakajima, Yoshibumi Ueda, Moritoshi Sato
We previously developed the Magnet system, which consists of two distinct Vivid protein variants, one positively and one negatively charged, designated the positive Magnet (pMag) and negative Magnet (nMag), respectively. These two proteins bind to each other through electrostatic interactions, preventing unwanted homodimerization and providing selective light-induced heterodimerization. The Magnet system enables the manipulation of cellular functions such as protein-protein interactions and genome editing, although the system could be improved further...
February 14, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28194956/direct-imaging-of-single-plasmonic-metal-nanoparticles-in-capillary-with-laser-light-sheet-scattering-imaging
#11
Xuan Cao, Jingjing Feng, Qi Pan, Bin Xiong, Yan He, Edward S Yeung
Understanding the heterogeneous distribution of the physical and chemical properties of plasmonic metal nanoparticles is fundamentally important to their basic and applied research. Traditionally, they are obtained either indirectly via bulk spectroscopic measurements plus electron microscopic characterizations, or through single molecule/particle imaging of nanoparticles immobilized on planar substrates. In this study, by using light-sheet scattering microscopy with a supercontinuum white laser, highly sensitive imaging of individual MNPs flowing inside a capillary, driven by either pressure or electric field, was achieved for the first time...
February 13, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28193002/organic-cyanide-decorated-sers-active-nanopipettes-for-quantitative-detection-of-hemeproteins-and-fe-3-in-single-cells
#12
Sumaira Hanif, Hailing Liu, Ming Chen, Pir Muhammad, Yue Zhou, Jiao Cao, Saud Asif Ahmed, Jingjuan Xu, Xinghua Xia, Hongyuan Chen, Kang Wang
It is challenging to develop a robust nanoprobe for real-time operational and accurate detection of heavy metals in single cells. Fe-CN coordination chemistry has been well studied to determine the structural characteristics of hemeproteins by different techniques. However, the frequently used cyanide ligands are inorganic molecules that release cyanide anion under particular conditions and cause cyanide poisoning. In the present study, organic cyanide (4-mercaptobenzonitrile, MBN) was utilized for the first time in developing a facile nanoprobe based on surface-enhanced Raman scattering (SERS) for quantitative detection of hemeproteins (oxy-Hb) and trivalent iron (Fe(3+)) ions...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28192299/single-molecule-analysis-of-fluorescent-carbon-dots-towards-localization-based-super-resolution-microscopy
#13
Navneet C Verma, Syamantak Khan, Chayan K Nandi
The advancement of high-resolution bioimaging has always been dependent on the discovery of bright and easily available fluorescent probes. Fluorescent carbon nanodots, an interesting class of relatively new nanomaterials, have emerged as a versatile alternative due to their superior optical properties, non-toxicity, cell penetrability and easy routes to synthesis. Although a plethora of reports is available on bioimaging using carbon dots, single-molecule-based super-resolution imaging is rare in the literature...
October 11, 2016: Methods and Applications in Fluorescence
https://www.readbyqxmd.com/read/28188480/sexual-reproduction-and-sex-determination-in-green-algae
#14
Hiroyuki Sekimoto
The sexual reproductive processes of some representative freshwater green algae are reviewed. Chlamydomonas reinhardtii is a unicellular volvocine alga having two mating types: mating type plus (mt(+)) and mating type minus (mt(-)), which are controlled by a single, complex mating-type locus. Sexual adhesion between the gametes is mediated by sex-specific agglutinin molecules on their flagellar membranes. Cell fusion is initiated by an adhesive interaction between the mt(+) and mt(-) mating structures, followed by localized membrane fusion...
February 10, 2017: Journal of Plant Research
https://www.readbyqxmd.com/read/28185197/multiplex-immunohistochemistry-for-mapping-the-tumor-microenvironment
#15
Jessica Kalra, Jennifer Baker
Multiplex Immunohistochemistry (mIHC) allows for the simultaneous detection of multiple targets of interest in a single tissue section. Using this method it is therefore possible to evaluate several effectors of a signal transduction pathway at one time, co-localization of markers, or distribution of molecules relative to one another within tissues. This method plays an important role in characterizing molecular signaling and the outcome of signal ablation when assessing mechanisms of drug action. Additionally, this approach can be used to characterize: the tumor microenvironment including vascular architecture and hypoxia, cellular proliferation, cell death as well as drug distribution...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28170245/direct-pathway-to-molecular-photodissociation-on-metal-surfaces-using-visible-light
#16
Emiko Kazuma, Jaehoon Jung, Hiromu Ueba, Michael Trenary, Yousoo Kim
We demonstrate molecular photodissociation on single-crystalline metal substrates, driven by visible-light irradiation. The visible-light-induced photodissociation on metal substrates has long been thought to never occur, either because visible-light energy is much smaller than the optical energy gap between the frontier electronic states of the molecule or because the molecular excited states have short lifetimes due to the strong hybridization between the adsorbate molecular orbitals (MOs) and metal substrate...
February 17, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28165249/low-temperature-magnetic-force-microscopy-on-single-molecule-magnet-based-microarrays
#17
Michele Serri, Matteo Mannini, Lorenzo Poggini, Emilio Velez-Fort, Brunetto Cortigiani, Philippe Sainctavit, Donella Rovai, Andrea Caneschi, Roberta Sessoli
The magnetic properties of some single molecule magnets (SMM) on surfaces can be strongly modified by the molecular packing in nanometric films/aggregates or by interactions with the substrate, which affect the molecular orientation and geometry. Detailed investigations of the magnetism of thin SMM films and nanostructures are necessary for the development of spin-based molecular devices, however this task is challenged by the limited sensitivity of laboratory based magnetometric techniques and often requires access to synchrotron light sources to perform surface sensitive X-ray magnetic circular dichroism (XMCD) investigations...
February 6, 2017: Nano Letters
https://www.readbyqxmd.com/read/28158244/dna-graphene-interactions-during-translocation-through-nanogaps
#18
Hiral N Patel, Ian Carroll, Rodolfo Lopez, Sandeep Sankararaman, Charles Etienne, Subba Ramaiah Kodigala, Mark R Paul, Henk W Ch Postma
We study how double-stranded DNA translocates through graphene nanogaps. Nanogaps are fabricated with a novel capillary-force induced graphene nanogap formation technique. DNA translocation signatures for nanogaps are qualitatively different from those obtained with circular nanopores, owing to the distinct shape of the gaps discussed here. Translocation time and conductance values vary by ∼ 100%, which we suggest are caused by local gap width variations. We also observe exponentially relaxing current traces...
2017: PloS One
https://www.readbyqxmd.com/read/28155142/single-cell-cytochemistry-illustrated-by-the-demonstration-of-glucose-6-phosphate-dehydrogenase-deficiency-in-erythrocytes
#19
Anna L Peters, Cornelis J F van Noorden
Cytochemistry is the discipline that is applied to visualize specific molecules in individual cells and has become an essential tool in life sciences. Immunocytochemistry was developed in the sixties of last century and is the most frequently used cytochemical application. However, metabolic mapping is the oldest cytochemical approach to localize activity of specific enzymes, but in the last decades of the previous century and the first decade of the present century it almost became obsolete. The popularity of this approach revived in the past few years...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28153411/linking-chromatin-fibers-to-gene-folding-by-hierarchical-looping
#20
REVIEW
Gavin Bascom, Tamar Schlick
While much is known about DNA structure on the basepair level, this scale represents only a fraction of the structural levels involved in folding the genomic material. With recent advances in experimental and theoretical techniques, a variety of structures have been observed on the fiber, gene, and chromosome levels of genome organization. Here we view chromatin architecture from nucleosomes and fibers to genes and chromosomes, highlighting the rich structural diversity and fiber fluidity emerging from both experimental and theoretical techniques...
February 7, 2017: Biophysical Journal
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