Tools for generating and analyzing glycan microarray data

• Akul Y. Mehta,
• Jamie Heimburg-Molinaro and
• Richard D. Cummings

Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187

• experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and

• structural informatics tools. Keywords: data analysis; glycan binding; glycan microarray; glycomics; informatics; Introduction Glycans represent a major type of biomolecule in all living things, along with DNA, RNA, lipids and proteins [1]. In mammals, glycans commonly occur as post-translational

• microarray experiment. Such a centralized database would greatly help the glycoscience community and help develop newer software for glycan microarray data analysis. B) Data visualization/manual data analysis 1. GLAD: Status: Available. Address: https://glycotoolkit.com/GLAD/. Description: Traditionally

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• ). Origin 7.0 software, supplied by the manufacturer, was used for data analysis. During the titration of ct-DNA, d: poly(rA)–poly(rU), poly(dAdT)–poly(dAdT), and poly(dGdC)–poly(dGdC) with the compound 4, one aliquot of 2 μL and 27 aliquots of 10 μL of 4 (c = 1.0 × 10−4 M) were injected from rotating

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• automated software pipeline which integrates the complementary outputs of Byonic and Proteome Discoverer to allow high-throughput automated quantitative glycoproteomic data analysis. The output of GlypNirO is clearly structured, allowing manual interrogation, and is also appropriate for input into diverse

• robustness and throughput. Our workflow uses a collection of scripts built on an in-house sequence string handling library and the scientific Python data handling package pandas [24], and integrates outputs of two commonly used software packages in glycoproteomic MS data analysis, Proteome Discoverer (Thermo

• quantitative glycoproteomic data analysis. GlypNirO takes Byonic and Proteome Discover output files, and user-defined sample information and processing parameters, performs a series of automated data integration and computational steps, and provides informative and intuitive output files with site or peptide

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• optimization study. The key advantage of this computational approach is that all runs can be analyzed simultaneously with high accuracy in glycan identification and quantitation and there is no theoretical limit to the scale of this method. Keywords: capillary electrophoresis; clustering; data analysis

• different parameter settings for each electropherogram (or groups of similar electropherograms) requiring substantial human intervention to check correctness of the automated picked peaks and tuning parameters. This level of human manual data analysis is impractical when dealing with thousands of samples

• approach. The main reason quantitation was complicated by automated data analysis methods, whether using 32 Karat software [17] or HappyTools quantitation functions, was because of Gaussian peak approximation [16]. Using 32 Karat with a single set of default parameters there were difficulties with

Automated high-content imaging for cellular uptake, from the Schmuck cation to the latest cyclic oligochalcogenides

• Rémi Martinent,
• Javier López-Andarias,
• Dimitri Moreau,
• Yangyang Cheng,
• Naomi Sakai and
• Stefan Matile

Beilstein J. Org. Chem. 2020, 16, 2007–2016, doi:10.3762/bjoc.16.167

• automated HT format with image-based information. To summarize briefly what has been outlined previously in more detail [56], HCS requires automated high-speed microscopy, including robotic liquid handlers and plate washers, automated data analysis tools, and large data storage systems for the terabits of

Photophysics and photochemistry of NIR absorbers derived from cyanines: key to new technologies based on chemistry 4.0

• Bernd Strehmel,
• Christian Schmitz,
• Ceren Kütahya,
• Yulian Pang,
• Anke Drewitz and
• Heinz Mustroph

Beilstein J. Org. Chem. 2020, 16, 415–444, doi:10.3762/bjoc.16.40

• application [66]. Data collection [67] in combination with self-leaning software related to artificial intelligence (A.I.) drives their use in applications with more efficiency in large workflows. Such tools can recognize failures in industrial processes just by collection of data in a big database where data

• analysis of global production may solve issues related to the materials. Review Synthesis of cyanines absorbing in the NIR Cyanines comprising the patterns I–V (Scheme 1) have received much importance as NIR absorbers applied in different technologies [1][8][9][11][12][13][14][15][16][17][18][19][20][32

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• energies, Δ0[Τ1 − S0] for 11 and 12. All numerical values in kcal/mol, in aqueous solution. Supporting Information The Supporting Information features 1) general procedures for the synthesis of all compounds and data analysis; 2) 1H NMR and 13C NMR of amidoxime, ethanone oxime and aldoxime carbamates; 3

Ultrafast processes triggered by one- and two-photon excitation of a photochromic and luminescent hydrazone

• Alessandro Iagatti,
• Baihao Shao,
• Alberto Credi,
• Barbara Ventura,
• Ivan Aprahamian and
• Mariangela Di Donato

Beilstein J. Org. Chem. 2019, 15, 2438–2446, doi:10.3762/bjoc.15.236

• fitting method using Felix data analysis from Horiba Scientific Ltd. Transient absorption spectroscopy The apparatus used for the transient absorption spectroscopy (TAS) measurements is based on a Ti:sapphire regenerative amplifier (BMI Alpha 1000) system pumped by a Ti:sapphire oscillator (Spectra

Friedel–Crafts approach to the one-pot synthesis of methoxy-substituted thioxanthylium salts

• Kenta Tanaka,
• Yuta Tanaka,
• Mami Kishimoto,
• Yujiro Hoshino and
• Kiyoshi Honda

Beilstein J. Org. Chem. 2019, 15, 2105–2112, doi:10.3762/bjoc.15.208

• = 464 nm) showed a large red shift compared to thioxanthylium salt 4b (λmax = 383 nm), which has no methoxy groups (Figure 4 and Figure 5). Finally, we measured the cyclic voltammograms (CV) of thioxanthylium salts 3b and 4b (Figure 6). The CV data analysis implies that the reduction potential of 3b (E

Analysis of sesquiterpene hydrocarbons in grape berry exocarp (Vitis vinifera L.) using in vivo-labeling and comprehensive two-dimensional gas chromatography–mass spectrometry (GC×GC–MS)

• Philipp P. Könen and
• Matthias Wüst

Beilstein J. Org. Chem. 2019, 15, 1945–1961, doi:10.3762/bjoc.15.190

• ) mode at −70 eV. The ion source temperature was 250 °C and the detector voltage was set to −2236.8 V. Ions in the mass range 35–250 amu were acquired at a rate of 100 spectra s−1. All samples were analyzed in triplicate. Data analysis Data processing was performed using the software ChromSpace (Markes

Unexpected polymorphism during a catalyzed mechanochemical Knoevenagel condensation

• Sebastian Haferkamp,
• Andrea Paul,
• Adam A. L. Michalchuk and
• Franziska Emmerling

Beilstein J. Org. Chem. 2019, 15, 1141–1148, doi:10.3762/bjoc.15.110

• monitoring multi-phase reactions during ball milling. Keywords: ball milling; C–C coupling; in situ; mechanochemistry; multivariate data analysis; Introduction Mechanochemistry offers a wide array of applications. It is used widely for synthesis of inorganic, metal-organic, and organic molecules and

• diffraction data. Results of multivariate data analysis of Raman spectra for 30 Hz milling experiments. Principal component analysis (PCA) of Raman data, showing (a) scores, and (b) loadings for (black) PC1 and (blue) PC2. (a) PC1 scores show a decrease in spectral component of 1a in the first minutes – cf

• be observed. Catalyzed mechanochemical Knoevenagel condensation of fluorobenzaldehydes and malonodinitrile. The milling process is symbolized by the three balls, proposed by Hanusa et al. [20]. Supporting Information Supporting Information File 508: XRPD data and multivariate data analysis.

Hoveyda–Grubbs catalysts with an N→Ru coordinate bond in a six-membered ring. Synthesis of stable, industrially scalable, highly efficient ruthenium metathesis catalysts and 2-vinylbenzylamine ligands as their precursors

• Kirill B. Polyanskii,
• Kseniia A. Alekseeva,
• Pavel V. Raspertov,
• Pavel A. Kumandin,
• Eugeniya V. Nikitina,
• Atash V. Gurbanov and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2019, 15, 769–779, doi:10.3762/bjoc.15.73

• preparation of the “chloroform adduct” (9) [51][52][53][54][55]. Even though these approaches provide good yields they have some drawbacks such as the use of expensive reagents, difficulties in the purification process, and data analysis. Here we propose an alternative reliable procedure for the synthesis of

Repurposing the anticancer drug cisplatin with the aim of developing novel Pseudomonas aeruginosa infection control agents

• Mingjun Yuan,
• Song Lin Chua,
• Yang Liu,
• Daniela I. Drautz-Moses,
• Joey Kuok Hoong Yam,
• Thet Tun Aung,
• Roger W. Beuerman,
• May Margarette Santillan Salido,
• Stephan C. Schuster,
• Choon-Hong Tan,
• Michael Givskov,
• Liang Yang and
• Thomas E. Nielsen

Beilstein J. Org. Chem. 2018, 14, 3059–3069, doi:10.3762/bjoc.14.284

• vigorous protocol was used for a second round of DNase treatment (Ambion). The 16S, 23S and 5S rRNA was removed using the Ribo-Zero Magnetic Kit (Bacteria) (Epicentre). RNA sequencing and data analysis Gene expression analysis was conducted via Illumina RNA sequencing (RNA-Seq technology). RNA-Seq was

Defining the hydrophobic interactions that drive competence stimulating peptide (CSP)-ComD binding in Streptococcus pneumoniae

• Bimal Koirala,
• Robert A. Hillman,
• Erin K. Tiwold,
• Michael A. Bertucci and
• Yftah Tal-Gan

Beilstein J. Org. Chem. 2018, 14, 1769–1777, doi:10.3762/bjoc.14.151

• reported as percent activation, which is the ratio between the Miller units of the analog and of the positive control. For calculation of Miller units, please see data analysis below. Analogs that exhibited high activity in the initial screening (see Figures S1 and S2, Supporting Information File 1) were

Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• data analysis. The CLYCAM_06 force field [46] was applied to the atoms of β-CD, whereas GAFF parameters and AM1BCC charges were applied to the guest molecule using ANTECHAMBER [47]. The explicit solvent model TIP3P was used for water forming a periodic, octahedral box of at least 10 Å between the box

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles

• Ido Azuri,
• Anna Hirsch,
• Anthony M. Reilly,
• Alexandre Tkatchenko,
• Shai Kendler,
• Oded Hod and
• Leeor Kronik

Beilstein J. Org. Chem. 2018, 14, 381–388, doi:10.3762/bjoc.14.26

• for the mixed-polymorph TNT crystal, taken from [16], as captured by a data analysis program. All other spectra are computed for: (O) the orthorhombic structure and (M) the monoclinic structure, calculated with and without TS-vdW interactions. Colored horizontal lines appearing below various

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• /RNA helical axis. The other techniques mentioned in the Introduction (VCD, FDCD, and CPL) will be treated more shortly because of their relatively less widespread use in the context of interest. The particular aspects of data analysis and interpretation will be discussed for each method, while general

Position-dependent impact of hexafluoroleucine and trifluoroisoleucine on protease digestion

• Susanne Huhmann,
• Anne-Katrin Stegemann,
• Kristin Folmert,
• Damian Klemczak,
• Johann Moschner,
• Michelle Kube and
• Beate Koksch

Beilstein J. Org. Chem. 2017, 13, 2869–2882, doi:10.3762/bjoc.13.279

• /min, continuing with a linear gradient of 5–70% ACN over 25 min, flow rate: 20.0 mL/min. UV-detection occurred at 220 nm. Data analysis was performed with an EZChrom Elite-Software (Version 3.3.2 SP2, Agilent Technologies, Santa Clara, CA, USA). The fractions containing pure peptide were combined

Binding abilities of a chiral calix[4]resorcinarene: a polarimetric investigation on a complex case of study

• Marco Russo and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2698–2709, doi:10.3762/bjoc.13.268

• region only) and their 1:1 complex (purple). Possible depiction of the 1:1 and 1:2 complexes of 12. Binding constants for CAP anions with guests 6–12. Supporting Information Supporting Information File 396: Mathematical details on the derivation of the equations used for polarimetric data analysis, and

The effect of milling frequency on a mechanochemical organic reaction monitored by in situ Raman spectroscopy

• Patrick A. Julien,
• Ivani Malvestiti and
• Tomislav Friščić

Beilstein J. Org. Chem. 2017, 13, 2160–2168, doi:10.3762/bjoc.13.216

• reaction component xn (Figure 3). It is important to note that the herein presented approach to data analysis assumes that the Raman spectra of individual reactants or products are not significantly affected by the degree of crystallinity or changes in the composition of the reaction mixture. While Raman

Synthesis and enzymatic ketonization of the 5-(halo)-2-hydroxymuconates and 5-(halo)-2-hydroxy-2,4-pentadienoates

• Tyler M. M. Stack,
• William H. Johnson Jr. and
• Christian P. Whitman

Beilstein J. Org. Chem. 2017, 13, 1022–1031, doi:10.3762/bjoc.13.101

• equation. The initial rates were determined in triplicate, averaged, plotted versus initial substrate concentration, and fit to determine kcat and Km. Nonlinear regression data analysis was performed using Mathematica (Wolfram Research, Inc., Mathematica, Version 8.0, Champaign, IL 2010). The 4-OT

Use of costic acid, a natural extract from Dittrichia viscosa, for the control of Varroa destructor, a parasite of the European honey bee

• Kalliopi Sofou,
• Demosthenis Isaakidis,
• Apostolos Spyros,
• Anita Büttner,
• Athanassios Giannis and
• Haralambos E. Katerinopoulos

Beilstein J. Org. Chem. 2017, 13, 952–959, doi:10.3762/bjoc.13.96

• experiments which were performed in five replicates. In both cases the solvent was allowed to evaporate before covering the vials. The mortality of mites was recorded under a stereoscope binocular set after 5, 8, and 12 hours. Data analysis. All graphs and statistical analysis (one way ANOVA followed by the

Synthesis of multi-lactose-appended β-cyclodextrin and its cholesterol-lowering effects in Niemann–Pick type C disease-like HepG2 cells

• Keiichi Motoyama,
• Rena Nishiyama,
• Yuki Maeda,
• Taishi Higashi,
• Yoichi Ishitsuka,
• Yuki Kondo,
• Tetsumi Irie,
• Takumi Era and
• Hidetoshi Arima

Beilstein J. Org. Chem. 2017, 13, 10–18, doi:10.3762/bjoc.13.2

• of Filipin III area to cell area by the fluorescence microscope and BZ-II analyzer. Data analysis Quantitative data was expressed as the mean ± standard error of the mean (S.E.M.), while the statistical comparisons were made using the Scheffe's test. A p-value < 0.05 was considered statistically

The in situ generation and reactive quench of diazonium compounds in the synthesis of azo compounds in microreactors

• Faith M. Akwi and
• Paul Watts

Beilstein J. Org. Chem. 2016, 12, 1987–2004, doi:10.3762/bjoc.12.186

• the azo compound. However, highly alkaline conditions are usually avoided as they lead to diazonium salt decomposition. In the regression summary of the statistical data analysis (Table 2) of the observed data, it is seen from the p-values (0.067 and 0.084) associated with the estimated coefficients

• . The wavelength used for quantification of the 2-naphthol was 349 nm. Data analysis The total volume of samples collected (tvscollected) was calculated by multiplying the total flow rate of the reactant solutions (tfrABC) by the total sample collection time (tcollection). The reaction time was

• calculated by dividing the total reaction space volume i.e. the total volume of the two LTF-MS plates, the PTFE tubing used to join the two mixers and also that leading to the final outlet: the point of sample collection by the total flow rate of reactant solutions (tfrABC). For purposes of data analysis

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• acids. Thus, nucleoside phosphonate analogues 1a–q (Scheme 2) were isolated as their sodium salts with yields ranging from 21 to 77% over three steps. Structures of all final compounds were unambiguously confirmed on the basis of NMR (1H, 13C and 31P) and MS (MS and HRMS) data analysis (see Supporting