scholarly journals Interbase FRET in RNA: from A to Z

2019 ◽  
Vol 47 (19) ◽  
pp. 9990-9997 ◽  
Author(s):  
Anders F Füchtbauer ◽  
Moa S Wranne ◽  
Mattias Bood ◽  
Erik Weis ◽  
Pauline Pfeiffer ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Structural Changes ◽  
Average Structure ◽  
Structure And Dynamics ◽  
Rna Conformation ◽  
First Time ◽  
Existing Structure ◽  
Fret Pair

Abstract Interbase FRET can reveal highly detailed information about distance, orientation and dynamics in nucleic acids, complementing the existing structure and dynamics techniques. We here report the first RNA base analogue FRET pair, consisting of the donor tCO and the non-emissive acceptor tCnitro. The acceptor ribonucleoside is here synthesised and incorporated into RNA for the first time. This FRET pair accurately reports the average structure of A-form RNA, and its utility for probing RNA structural changes is demonstrated by monitoring the transition from A- to Z-form RNA. Finally, the measured FRET data were compared with theoretical FRET patterns obtained from two previously reported Z-RNA PDB structures, to shed new light on this elusive RNA conformation.

scholarly journals Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

2018 ◽  
Vol 14 ◽  
pp. 114-129 ◽  
Author(s):  
Mattias Bood ◽  
Sangamesh Sarangamath ◽  
Moa S Wranne ◽  
Morten Grøtli ◽  
L Marcus Wilhelmsson
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Orientation Factor ◽  
Design Synthesis ◽  
Structure And Dynamics ◽  
Donor And Acceptor ◽  
Structure Investigations ◽  
Fret Pair

Förster resonance energy transfer (FRET) between a donor nucleobase analogue and an acceptor nucleobase analogue, base–base FRET, works as a spectroscopic ruler and protractor. With their firm stacking and ability to replace the natural nucleic acid bases inside the base-stack, base analogue donor and acceptor molecules complement external fluorophores like the Cy-, Alexa- and ATTO-dyes and enable detailed investigations of structure and dynamics of nucleic acid containing systems. The first base–base FRET pair, tCO–tCnitro, has recently been complemented with among others the adenine analogue FRET pair, qAN1–qAnitro, increasing the flexibility of the methodology. Here we present the design, synthesis, photophysical characterization and use of such base analogues. They enable a higher control of the FRET orientation factor, κ 2, have a different distance window of opportunity than external fluorophores, and, thus, have the potential to facilitate better structure resolution. Netropsin DNA binding and the B-to-Z-DNA transition are examples of structure investigations that recently have been performed using base–base FRET and that are described here. Base–base FRET has been around for less than a decade, only in 2017 expanded beyond one FRET pair, and represents a highly promising structure and dynamics methodology for the field of nucleic acids. Here we bring up its advantages as well as disadvantages and touch upon potential future applications.

scholarly journals Valorization of sugarcane bagasse by chemical pretreatment and enzyme mediated deconstruction

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Vihang S. Thite ◽  
Anuradha S. Nerurkar
Keyword(s):  
Cell Wall ◽  
Sugarcane Bagasse ◽  
Structural Changes ◽  
Enzymatic Saccharification ◽  
Dry Weight ◽  
Gravimetric Analysis ◽  
Chemical Pretreatment ◽  
Cell Wall Degrading Enzymes ◽  
First Time ◽  
Soluble Components

Abstract After chemical pretreatment, improved amenability of agrowaste biomass for enzymatic saccharification needs an understanding of the effect exerted by pretreatments on biomass for enzymatic deconstruction. In present studies, NaOH, NH4OH and H2SO4 pretreatments effectively changed visible morphology imparting distinct fibrous appearance to sugarcane bagasse (SCB). Filtrate analysis after NaOH, NH4OH and H2SO4 pretreatments yielded release of soluble reducing sugars (SRS) in range of ~0.17–0.44%, ~0.38–0.75% and ~2.9–8.4% respectively. Gravimetric analysis of pretreated SCB (PSCB) biomass also revealed dry weight loss in range of ~25.8–44.8%, ~11.1–16.0% and ~28.3–38.0% by the three pretreatments in the same order. Release of soluble components other than SRS, majorly reported to be soluble lignins, were observed highest for NaOH followed by H2SO4 and NH4OH pretreatments. Decrease or absence of peaks attributed to lignin and loosened fibrous appearance of biomass during FTIR and SEM studies respectively further corroborated with our observations of lignin removal. Application of commercial cellulase increased raw SCB saccharification from 1.93% to 38.84%, 25.56% and 9.61% after NaOH, H2SO4 and NH4OH pretreatments. Structural changes brought by cell wall degrading enzymes were first time shown visually confirming the cell wall disintegration under brightfield, darkfield and fluorescence microscopy. The microscopic evidence and saccharification results proved that the chemical treatment valorized the SCB by making it amenable for enzymatic saccharification.

scholarly journals Characterization of Each St and Y Genome Chromosome of Roegneria grandis Based on Newly Developed FISH Markers

2021 ◽  
pp. 213-222
Author(s):  
Dandan Wu ◽  
Xiaoxia Zhu ◽  
Lu Tan ◽  
Haiqin Zhang ◽  
Lina Sha ◽  
...  
Keyword(s):  
Structural Changes ◽  
Distribution Patterns ◽  
Proximal Region ◽  
Genome Chromosome ◽  
High Affinity ◽  
Complete Set ◽  
Genome Analyses ◽  
First Time ◽  
Homoeologous Chromosomes

The genera of the tribe Triticeae (family Poaceae), constituting many economically important plants with abundant genetic resources, carry genomes such as St, H, P, and Y. The genome symbol of <i>Roegneria</i> C. Koch (Triticeae) is StY. The St and Y genomes are crucial in Triticeae, and tetraploid StY species participate extensively in polyploid speciation. Characterization of St and Y nonhomologous chromosomes in StY-genome species could help understand variation in the chromosome structure and differentiation of StY-containing species. However, the high genetic affinity between St and Y genome and the deficiency of a complete set of StY nonhomologous probes limit the identification of St and Y genomes and variation of chromosome structures among <i>Roegneria</i> species. We aimed to identify St- and Y-enhanced repeat clusters and to study whether homoeologous chromosomes between St and Y genomes could be accurately identified due to high affinity. We employed comparative genome analyses to identify St- and Y-enhanced repeat clusters and generated a FISH-based karyotype of <i>R. grandis</i> (Keng), one of the taxonomically controversial StY species, for the first time. We explored 4 novel repeat clusters (StY_34, StY_107, StY_90, and StY_93), which could specifically identify individual St and Y nonhomologous chromosomes. The clusters StY_107 and StY_90 could identify St and Y addition/substitution chromosomes against common wheat genetic backgrounds. The chromosomes V_St, VII_St, I_Y, V_Y, and VII_Y displayed similar probe distribution patterns in the proximal region, indicating that the high affinity between St and Y genome might result from chromosome rearrangements or transposable element insertion among V_St/Y, VII_St/Y, and I_Y chromosomes during allopolyploidization. Our results can be used to employ FISH further to uncover the precise karyotype based on colinearity of Triticeae species by using the wheat karyotype as reference, to analyze diverse populations of the same species to understand the intraspecific structural changes, and to generate the karyotype of different StY-containing species to understand the interspecific chromosome variation.

scholarly journals Dynamic nanoscale morphology of the ER surveyed by STED microscopy

2018 ◽  
Vol 218 (1) ◽  
pp. 83-96 ◽  
Author(s):  
Lena K. Schroeder ◽  
Andrew E.S. Barentine ◽  
Holly Merta ◽  
Sarah Schweighofer ◽  
Yongdeng Zhang ◽  
...  
Keyword(s):  
Living Cells ◽  
Stimulated Emission ◽  
Membrane Structures ◽  
Spatiotemporal Resolution ◽  
Sted Microscopy ◽  
Superresolution Microscopy ◽  
Structure And Dynamics ◽  
First Time ◽  
Nanoscale Dynamics ◽  
Conventional Light Microscopy

The endoplasmic reticulum (ER) is composed of interconnected membrane sheets and tubules. Superresolution microscopy recently revealed densely packed, rapidly moving ER tubules mistaken for sheets by conventional light microscopy, highlighting the importance of revisiting classical views of ER structure with high spatiotemporal resolution in living cells. In this study, we use live-cell stimulated emission depletion (STED) microscopy to survey the architecture of the ER at 50-nm resolution. We determine the nanoscale dimensions of ER tubules and sheets for the first time in living cells. We demonstrate that ER sheets contain highly dynamic, subdiffraction-sized holes, which we call nanoholes, that coexist with uniform sheet regions. Reticulon family members localize to curved edges of holes within sheets and are required for their formation. The luminal tether Climp63 and microtubule cytoskeleton modulate their nanoscale dynamics and organization. Thus, by providing the first quantitative analysis of ER membrane structure and dynamics at the nanoscale, our work reveals that the ER in living cells is not limited to uniform sheets and tubules; instead, we suggest the ER contains a continuum of membrane structures that includes dynamic nanoholes in sheets as well as clustered tubules.

S-Edge-rich MoxSy arrays vertically grown on carbon aerogels as superior bifunctional HER/OER electrocatalysts

Nanoscale ◽  
2019 ◽  
Vol 11 (42) ◽  
pp. 20284-20294 ◽  
Author(s):  
Yu Cheng ◽  
Pengfei Yuan ◽  
Xiaohui Xu ◽  
Sijie Guo ◽  
Kanglei Pang ◽  
...  
Keyword(s):  
Raman Spectroscopy ◽  
Active Sites ◽  
Structural Changes ◽  
Carbon Aerogels ◽  
Clear Identification ◽  
First Time

Operando Raman spectroscopy is used for the first time for clear identification of the intrinsic active sites, intermediates and structural changes in Mo4S16@GCA.

27Al-MAS-NMR-Untersuchungen des thermischen Abbaus von NH4Al(SO4)2·12H2O / 27Al-MAS-NMR Studies on the Thermolysis of NH4Al(SO4)2· 12H2O

1991 ◽  
Vol 46 (11) ◽  
pp. 1515-1518 ◽  
Author(s):  
Gerhard Wegner ◽  
Gert Blumenthal ◽  
Dirk Müller ◽  
Dirk-Henning Menz ◽  
Antje Schmalstieg
Keyword(s):  
Nmr Spectroscopy ◽  
Structural Changes ◽  
Chemical Shifts ◽  
Mas Nmr ◽  
Nmr Studies ◽  
High Stage ◽  
27Al Mas Nmr ◽  
High Resolution Nmr ◽  
First Time

Products of the thermolysis of NH4Al-alum were prepared under dried air and characterized by X-ray powder diffraction, thermogravimetry, and for the first time by solid-state 27Al-MAS-NMR spectroscopy. It was found, that high resolution NMR spectroscopy is applicable to follow up the thermal decomposition and to indicate even minor structural changes. 27Al-MAS-NMR spectra show peaks with characteristic chemical shifts for octahedral Al-units up to a high stage of thermolysis. During the decomposition of Al2(SO4)3 to γ-Al2O3 we again observed three-peak spectra with the specific signal at ≈ 35 ppm for penta-coordinated Al ions as recently proved for the thermolysis of AlCl3 · 6 H2O.

Between Hammer and Anvil

2019 ◽  
pp. 256-303
Author(s):  
A. Wess Mitchell
Keyword(s):  
Ethnic Minority ◽  
Structural Changes ◽  
New Technologies ◽  
Great Power ◽  
Treaty Rights ◽  
Crimean War ◽  
Habsburg Monarchy ◽  
Buffer Zones ◽  
Revolution Of 1848 ◽  
First Time

This chapter traces the breakdown of the Metternichian system, from the time of the revolution of 1848 and Crimean War to the debilitating defeats by Italy in 1859 and Prussia in 1866. In the middle decades of the nineteenth century, the Habsburg Monarchy suffered defeats in a series of short, sharp wars that would bring an end to the Metternich system and pave the way for Austria’s demise as a Great Power. These changes occurred not primarily because of economic decay or the empire’s internal complexity but instead because Austria lost the tools that it had used in the past to manage the sequencing and duration of its wars. This was the result of both structural changes beyond its leaders’ control and avoidable errors and a deviation from the principles that had formerly shaped its past statecraft. Specifically, Austria’s leaders abandoned the flexible statecraft that had allowed them to control conflict sequencing and avoid isolation; rivals adopted new technologies that denied the monarchy’s armies the ability to use attrition and terrain to prolong conflict and outlast stronger militaries; and nationalism trumped treaty rights as a source of territorial legitimacy, allowing hostile polities to form in the areas that had previously served as the monarchy’s buffer zones. Deprived of its traditional strategic toolbox, Austria was forced by its strongest rival to accept cohabitation with its strongest ethnic minority and for the first time had to absorb the full costs of managing a 360-degree defensive position.

Gender and Industrial Creativity in Poland

2015 ◽  
pp. 230-243 ◽  
Author(s):  
Rafał Wisła
Keyword(s):  
Structural Changes ◽  
Technology Innovation ◽  
Economic Transformation ◽  
Innovation Activity ◽  
Creative Industry ◽  
Men And Women ◽  
Science Technology ◽  
Patent Statistics ◽  
First Time ◽  
Gender Aspect

The chapter deals with the problem of seeking possibilities to utilise patent databases in the research on dynamics and development directions in science, technology, innovation activity as well as on structural changes in economy, taking into account gender aspect. The key research objectives include: drawing a statistical picture of creative industry activity in Poland in the years 1995 - 2013, taking into account gender aspect; assessing the convergence as regards the patents obtained by men and women; identifying technological areas where women are present. The chapter, for the first time, presents a statistical picture of industrial creativity of men and women in Poland in the period of economic transformation, based on patent statistics.

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