scholarly journals mySpot: a versatile microfocussing station for scanning methods at BESSY II

2016 ◽  
Vol 2 ◽  
Author(s):  
Ivo Zizak
Keyword(s):  
Focal Spot ◽  
Structural Information ◽  
Chemical Information ◽  
Video Microscope ◽  
Capillary Optics ◽  
Sample Position ◽  
Molecular Information ◽  
Combination Of Methods ◽  
The Stability ◽  
Insight Into

mySpot is a versatile microfocussing station for scanning methods with resolution down to 1.5 µm, providing a combination of methods which can be performed simultaneously at the same sample position. It is especially designed (but not limited to) for the study of hierarchically structured biological samples. Structural information from different length scales (XRD - crystalline, SAXS - nanometer, Video-microscope - micrometer, sample translation - milimeter) can be combined with chemical information (XRF-mapping, EXAFS, XANES) and molecular information (Raman) providing unique insight into the mutual dependencies of different parameters.The beamline provides focal spot of about 500x50µm, which can be refocused at the sample using capillary optics. Capillary optics is used for two main reasons: 1) the focal spot does not depend on the energy which makes EXAFS and XANES measurements very simple, and 2) the optics is positioned very close to the sample which improves the stability of the focus at the sample. This allows the focal spot of 1.5 µm in 2D scans, as well as very parallel beam for scattering experiments down to 10µm, or volume element of 20µm diameter for 3D XRF mapping.

A Systematic Review on Popularity, Application and Characteristics of Protein Secondary Structure Prediction Tools

2019 ◽  
Vol 16 (2) ◽  
pp. 159-172 ◽  
Author(s):  
Elaheh Kashani-Amin ◽  
Ozra Tabatabaei-Malazy ◽  
Amirhossein Sakhteman ◽  
Bagher Larijani ◽  
Azadeh Ebrahim-Habibi
Keyword(s):  
Systematic Review ◽  
Secondary Structure ◽  
Structure Prediction ◽  
Web Of Science ◽  
Secondary Structure Prediction ◽  
Structural Information ◽  
Protein Secondary Structure ◽  
Structural Features ◽  
Prediction Tools ◽  
Insight Into

Background: Prediction of proteins’ secondary structure is one of the major steps in the generation of homology models. These models provide structural information which is used to design suitable ligands for potential medicinal targets. However, selecting a proper tool between multiple Secondary Structure Prediction (SSP) options is challenging. The current study is an insight into currently favored methods and tools, within various contexts. Objective: A systematic review was performed for a comprehensive access to recent (2013-2016) studies which used or recommended protein SSP tools. Methods: Three databases, Web of Science, PubMed and Scopus were systematically searched and 99 out of the 209 studies were finally found eligible to extract data. Results: Four categories of applications for 59 retrieved SSP tools were: (I) prediction of structural features of a given sequence, (II) evaluation of a method, (III) providing input for a new SSP method and (IV) integrating an SSP tool as a component for a program. PSIPRED was found to be the most popular tool in all four categories. JPred and tools utilizing PHD (Profile network from HeiDelberg) method occupied second and third places of popularity in categories I and II. JPred was only found in the two first categories, while PHD was present in three fields. Conclusion: This study provides a comprehensive insight into the recent usage of SSP tools which could be helpful for selecting a proper tool.

scholarly journals Transcriptomic and chemical analyses to identify candidate genes involved in color variation of sainfoin flowers

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Yu Qiao ◽  
Qiming Cheng ◽  
Yutong Zhang ◽  
Wei Yan ◽  
Fengyan Yi ◽  
...  
Keyword(s):  
Regulatory Networks ◽  
Flower Color ◽  
Color Variation ◽  
Anthocyanin Synthesis ◽  
Flower Formation ◽  
Factors Affecting ◽  
Phenylpropanoid Biosynthesis ◽  
Molecular Information ◽  
Illumina Hiseq4000 ◽  
Insight Into

Abstract Background Sainfoin (Onobrychis viciifolia Scop) is not only a high-quality legume forage, but also a nectar-producing plant. Therefore, the flower color of sainfoin is an important agronomic trait, but the factors affecting its flower phenotype are still unclear. To gain insights into the regulatory networks associated with metabolic pathways of coloration compounds (flavonoids or anthocyanins) and identify the key genes, we conducted a comprehensive analysis of the phenotype, metabolome and transcriptome of WF and AF of sainfoin. Results Delphinidin, petunidin and malvidin derivatives were the main anthocyanin compounds in the AF of sainfoin. These substances were not detected in the WF of sainfoin. The transcriptomes of WF and AF in sainfoin at the S1 and S3 stages were obtained using the Illumina HiSeq4000 platform. Overall, 10,166 (4273 upregulated and 5893 downregulated) and 15,334 (8174 upregulated and 7160 downregulated) DEGs were identified in flowers at S1 and S3 stages, respectively (WF-VS-AF). KEGG pathway annotations showed that 6396 unigenes were annotated to 120 pathways and contained 866 DEGs at S1 stages, and 6396 unigenes were annotated to 131 pathways and included 1546 DEGs at the S3 stage. Nine DEGs belonging to the “flavonoid biosynthesis”and “phenylpropanoid biosynthesis” pathways involved in flower color formation were identified and verified by RT-qPCR analyses. Among these DEGs, 4CL3, FLS, ANS, CHS, DFR and CHI2 exhibited downregulated expression, and F3H exhibited upregulated expression in the WF compared to the AF, resulting in a decrease in anthocyanin synthesis and the formation of WF in sainfoin. Conclusions This study is the first to use transcriptome technology to study the mechanism of white flower formation in sainfoin. Our transcriptome data will be a great enrichment of the genetic information for sainfoin. In addition, the data presented herein will provide valuable molecular information for genetic breeding and provide insight into the future study of flower color polymorphisms in sainfoin.

scholarly journals Bioinspired organometallic chemistry

2002 ◽  
Vol 74 (1) ◽  
pp. 115-122 ◽  
Author(s):  
Lanny S. Liebeskind ◽  
Jiri Srogl ◽  
Cecile Savarin ◽  
Concepcion Polanco
Keyword(s):  
Organometallic Chemistry ◽  
Refractory Metal ◽  
Redox Active ◽  
The Stability ◽  
New Procedures ◽  
Sulfur Containing ◽  
Insight Into

Given the stability of the bond between a mercaptide ligand and various redox-active metals, it is of interest that Nature has evolved significant metalloenzymatic processes that involve key interactions of sulfur-containing functionalities with metals such as Ni, Co, Cu, and Fe. From a chemical perspective, it is striking that these metals can function as robust biocatalysts in vivo, even though they are often "poisoned" as catalysts in vitro through formation of refractory metal thiolates. Insight into the nature of this chemical discrepancy is under study in order to open new procedures in synthetic organic and organometallic chemistry.

scholarly journals On the Trigonometric Descriptions of Colors

2016 ◽  
Vol 8 (3) ◽  
pp. 5
Author(s):  
Jirí Stavek
Keyword(s):  
Experimental Data ◽  
Transverse Energy ◽  
Gravitational Constant ◽  
Isaac Newton ◽  
Type Ia ◽  
New Interpretation ◽  
The Stability ◽  
Mass Evaporation ◽  
Supernovae Type Ia ◽  
Insight Into

<p class="1Body">An attempt is presented for the description of the spectral colors using the standard trigonometric tools in order to extract more information about photons. We have arranged the spectral colors on an arc of the circle with the radius R = 1 and the central angle θ = π/3 when we have defined cos (θ) = λ<sub>380</sub>/λ<sub>760</sub> = 0.5. Several trigonometric operations were applied in order to find the gravity centers for the scotopic, photopic, and mesopic visions. The concept of the center of gravity of colors introduced Isaac Newton. We have postulated properties of the long-lived photons with the new interpretation of the Hubble (Zwicky-Nernst) constant H<sub>0</sub> = 2.748… * 10<sup>-18</sup> kg kg<sup>-1 </sup>s<sup>-1</sup>, the specific mass evaporation rate (SMER) of gravitons from the source mass. The stability of international prototypes of kilogram has been regularly checked. We predict that those standard kilograms due to the evaporation of gravitons lost 8.67 μg kg<sup>-1</sup> century<sup>-1</sup>. The energy of long-lived photons was trigonometrically decomposed into three parts that could be experimentally tested: longitudinal energy, transverse energy and energy of evaporated gravitons. We tested the properties of the long-lived photons with the experimental data published for the best available standard candles: supernovae Type Ia. There was found a surprising match of those experimental data with the model of the long-lived photons. Finally, we have proposed a possible decomposition of the big G (Newtonian gravitational constant) and the small kappa κ (Einsteinian gravitational constant) in order to get a new insight into the mysterious gravitational force and/or the curvature concept.</p>

scholarly journals Influence of additives on suspension structure

2021 ◽  
Vol 10 (1) ◽  
pp. 37-40
Author(s):  
Vesna Savić ◽  
Milica Martinović ◽  
Ivana Nešić ◽  
Jelena Živković ◽  
Ivana Gajić
Keyword(s):  
Zinc Oxide ◽  
The Other ◽  
Stability Tests ◽  
Polysorbate 20 ◽  
The Stability ◽  
Carbomer Gel ◽  
Suspension Structure ◽  
Insight Into ◽  
Study Offer ◽  
Measured Hardness

The aim of this study was to compare the stability and texture of three zinc oxide suspensions with different additives. Suspension 1 was made as official magistral formulation Suspensio album 7.5% from Formulae magistrales 2008. Suspension 2 was prepared when 1% carbomer gel was added to suspension 1 and suspension 3 was prepared when polysorbate 20 was added to suspension 2. After stability tests, texture analysis was performed on all suspensions. Following parameters were measured: hardness cycle 1, hardness cycle 2, cohesiveness, adhesiveness, resilience and springiness. The study showed that suspension 3 had the lowest value of hardness, and therefore the best spreadability. Also, suspension 3 was the least sticky of all three, since it was characterized with the lowest adhesiveness. Further, suspension 3 was the most cohesive and is predicted to withstand the stress during packing and use longer than others. On the other hand, the highest values of resilience and springiness were detected for suspension 1, while the lowest was related to suspension 2. Therefore, the best textural characteristics were assigned to suspension 3. This result is in accordance with the results of performed stability tests. The results of our study offer insight into potential improvements of the current magistral formulation Suspensio album 7.5%.

scholarly journals Een geconstrueerd denken

1970 ◽  
Vol 61 ◽  
pp. 269-292
Author(s):  
Rajesh Heynickx
Keyword(s):  
Main Argument ◽  
Cultural Project ◽  
The Stability ◽  
Insight Into ◽  
The Way

In this article it is demonstrated that an analysis of how building metaphorswere used in the Flemish Catholic discourse of the interwar years can offermore insight into the way a community of believers tries to establish a culturalcohesiveness. The main argument is that in a period of deep transformations,building metaphors could become "instruments" for Catholics whowanted to defend and promote a traditional dimension of their religion.Building metaphors allowed Catholics to stress the stability of their own ideology(the fundaments) and to formulate their own cultural project (buildingplan). By analysing such strategic use of building metaphors in artistic andphilosophical discourses, it can become possible to shed more light on the roleneo-thomism, a main philosophical current in interwar Flanders, played inartistic debates and more specific in discussions on the modernisation of religiousart.

scholarly journals High-resolution structure of an α-spectrin SH3-domain mutant with a redesigned hydrophobic core

2010 ◽  
Vol 66 (9) ◽  
pp. 1023-1027 ◽  
Author(s):  
Ana Cámara-Artigas ◽  
Monserrat Andújar-Sánchez ◽  
Emilia Ortiz-Salmerón ◽  
Celia Cuadri ◽  
Eva S. Cobos ◽  
...  
Keyword(s):  
Structural Information ◽  
Sh3 Domain ◽  
Hydrophobic Core ◽  
Orthorhombic Space Group ◽  
Cell Parameters ◽  
High Resolution Structure ◽  
Model Protein ◽  
Distal Loop ◽  
Modular Domain ◽  
The Stability

The α-spectrin SH3 domain (Spc-SH3) is a small modular domain which has been broadly used as a model protein in folding studies and these studies have sometimes been supported by structural information obtained from the coordinates of Spc-SH3 mutants. The structure of B5/D48G, a multiple mutant designed to improve the hydrophobic core and as a consequence the protein stability, has been solved at 1 Å resolution. The crystals belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 24.79,b= 37.23,c= 62.95 Å. This mutant also bears a D48G substitution in the distal loop and this mutation has also been reported to increase the stability of the protein by itself. The structure of the B5/D48G mutant shows a highly packed hydrophobic core and a more ordered distal loop compared with previous Spc-SH3 structures.

scholarly journals Electrochemistry at the Synapse

2019 ◽  
Vol 12 (1) ◽  
pp. 297-321 ◽  
Author(s):  
Mimi Shin ◽  
Ying Wang ◽  
Jason R. Borgus ◽  
B. Jill Venton
Keyword(s):  
Mass Spectrometry ◽  
Electrochemical Measurements ◽  
Chemical Information ◽  
Fast Scan Cyclic Voltammetry ◽  
Spatially Resolved ◽  
Future Challenges ◽  
Insight Into ◽  
Partial Release ◽  
Electrochemical Cytometry ◽  
Made In

Electrochemical measurements of neurotransmitters provide insight into the dynamics of neurotransmission. In this review, we describe the development of electrochemical measurements of neurotransmitters and how they started with extrasynaptic measurements but now are pushing toward synaptic measurements. Traditionally, biosensors or fast-scan cyclic voltammetry have monitored extrasynaptic levels of neurotransmitters, such as dopamine, serotonin, adenosine, glutamate, and acetylcholine. Amperometry and electrochemical cytometry techniques have revealed mechanisms of exocytosis, suggesting partial release. Advances in nanoelectrodes now allow spatially resolved, electrochemical measurements in a synapse, which is only 20–100 nm wide. Synaptic measurements of dopamine and acetylcholine have been made. In this article, electrochemical measurements are also compared to optical imaging and mass spectrometry measurements, and while these other techniques provide enhanced spatial or chemical information, electrochemistry is best at monitoring real-time neurotransmission. Future challenges include combining electrochemistry with these other techniques in order to facilitate multisite and multianalyte monitoring.

scholarly journals Camelid VHH Antibodies that Neutralize Botulinum Neurotoxin Serotype E Intoxication or Protease Function

Toxins ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 611 ◽  
Author(s):  
Jacqueline M. Tremblay ◽  
Edwin Vazquez-Cintron ◽  
Kwok-Ho Lam ◽  
Jean Mukherjee ◽  
Daniela Bedenice ◽  
...  
Keyword(s):  
Botulinum Neurotoxin ◽  
Structural Information ◽  
Rapid Onset ◽  
Binding Properties ◽  
Large Panels ◽  
Tier 1 ◽  
Plastic Surface ◽  
Single Domain Antibodies ◽  
Vhh Antibodies ◽  
Insight Into

Botulinum neurotoxin (BoNT) serotype E is one of three serotypes that cause the preponderance of human botulism cases and is a Tier 1 Select Agent. BoNT/E is unusual among BoNT serotypes for its rapid onset and short duration of intoxication. Here we report two large panels of unique, unrelated camelid single-domain antibodies (VHHs) that were selected for their ability to bind to BoNT/E holotoxin and/or to the BoNT/E light chain protease domain (LC/E). The 19 VHHs which bind to BoNT/E were characterized for their subunit specificity and 8 VHHs displayed the ability to neutralize BoNT/E intoxication of neurons. Heterodimer antitoxins consisting of two BoNT/E-neutralizing VHHs, including one heterodimer designed using structural information for simultaneous binding, were shown to protect mice against co-administered toxin challenges of up to 500 MIPLD50. The 22 unique VHHs which bind to LC/E were characterized for their binding properties and 9 displayed the ability to inhibit LC/E protease activity. Surprisingly, VHHs selected on plastic-coated LC/E were virtually unable to recognize soluble or captured LC/E while VHHs selected on captured LC/E were poorly able to recognize LC/E coated to a plastic surface. This panel of anti-LC/E VHHs offer insight into BoNT/E function, and some may have value as components of therapeutic antidotes that reverse paralysis following BoNT/E exposures.

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