Deciphering the Role of Filamin B Calponin-Homology Domain in Causing the Larsen Syndrome,Boomerang Dysplasia,and Atelosteogenesis Type I Spectrum Disorders via a Computational Approach

Filamins (FLN) are a family of actin-binding proteins involved in regulating the cytoskeleton and signaling phenomenon by developing a network with F-actin and FLN-binding partners. The FLN family comprises three conserved isoforms in mammals: FLNA, FLNB, and FLNC. FLNB is a multidomain monomer protein with domains containing an actin-binding N-terminal domain (ABD 1–242), encompassing two calponin-homology domains (assigned CH1 and CH2). Primary variants in FLNB mostly occur in the domain (CH2) and surrounding the hinge-1 region. The four autosomal dominant disorders that are associated with FLNB variants are Larsen syndrome, atelosteogenesis type I (AOI), atelosteogenesis type III (AOIII), and boomerang dysplasia (BD). Despite the intense clustering of FLNB variants contributing to the LS-AO-BD disorders, the genotype-phenotype correlation is still enigmatic. In silico prediction tools and molecular dynamics simulation (MDS) approaches have offered the potential for variant classification and pathogenicity predictions. We retrieved 285 FLNB missense variants from the UniProt, ClinVar, and HGMD databases in the current study. Of these, five and 39 variants were located in the CH1 and CH2 domains, respectively. These variants were subjected to various pathogenicity and stability prediction tools, evolutionary and conservation analyses, and biophysical and physicochemical properties analyses. Molecular dynamics simulation (MDS) was performed on the three candidate variants in the CH2 domain (W148R, F161C, and L171R) that were predicted to be the most pathogenic. The MDS analysis results showed that these three variants are highly compact compared to the native protein, suggesting that they could affect the protein on the structural and functional levels. The computational approach demonstrates the differences between the FLNB mutants and the wild type in a structural and functional context. Our findings expand our knowledge on the genotype-phenotype correlation in FLNB-related LS-AO-BD disorders on the molecular level, which may pave the way for optimizing drug therapy by integrating precision medicine.     

Understanding the factors controlling the photo-oxidation of natural DNA by enantiomerically pure intercalating ruthenium polypyridyl complexes through TA/TRIR studies with polydeoxynucleotides and mixed sequence oligodeoxynucleotides

Ruthenium polypyridyl complexes which can sensitise the photo-oxidation of nucleic acids and other biological molecules show potential for photo-therapeutic applications. In this article a combination of transient visible absorption (TrA) and time-resolved infra-red (TRIR) spectroscopy are used to compare the photo-oxidation of guanine by the enantiomers of [Ru(TAP)₂(dppz)]²⁺ in both polymeric {poly(dG-dC), poly(dA-dT) and natural DNA} and small mixed-sequence duplex-forming oligodeoxynucleotides. The products of electron transfer are readily monitored by the appearance of a characteristic TRIR band centred at ca. 1700 cm⁻¹ for the guanine radical cation and a band centered at ca. 515 nm in the TrA for the reduced ruthenium complex. It is found that efficient electron transfer requires that the complex be intercalated at a G-C base-pair containing site. Significantly, changes in the nucleobase vibrations of the TRIR spectra induced by the bound excited state before electron transfer takes place are used to identify preferred intercalation sites in mixed-sequence oligodeoxynucleotides and natural DNA. Interestingly, with natural DNA, while it is found that quenching is inefficient in the picosecond range, a slower electron transfer process occurs, which is not found with the mixed-sequence duplex-forming oligodeoxynucleotides studied.

Efficient electron transfer requires the complex to be intercalated at a G-C base-pair. Identification of preferred intercalation sites is achieved by TRIR monitoring of the nucleobase vibrations before electron transfer.     

NMR spectral analysis of strongly second-order 6-, 8-, 9- and 10- spin-systems (1H─19F, 19F─19F,and 13C─19F) in perfluorotoluyl- and tetrafluoro-pyridyl-aromatics using the lineshape method ANATOLIA

A simple to use nuclear magnetic resonance analysis method has been tested on complex ¹H, ¹⁹F, and ¹³C multiplets. This open-source line-shape analysis method analysis of total lineshape (ANATOLIA)¹ provides some significant advantages over traditional assign-iterate methods of NMR spectral analysis by avoiding false minima and progressing optimisation to the global minimum. The target molecules are 1-perfluorotol-4-yl-2-perfluorotol-4-yl-oxymethyl-1H-benzimidazole (molecule-I) and 1-tetrafluoropyrid-4-yl-2-tetrafluoropyrid-4-yl-thio-1H-benzimidazole (molecule-II) which were produced as part of a family of fluorinated drug scaffolds prepared for anticancer and antiparasitic screening. Spectra display significant second-order effects with ¹H Δδ = 3.68 and 4.67 Hz for the aromatic hydrogen “triplets”, with ¹⁹F ⁴J_AA', ⁴J_BB', ⁴J_XX', and ⁴J_YY' coupling constants range from +4.8 to −14.0 Hz and for ¹³C-isotopomers ¹⁹F Δδ of up to 111.56 Hz. A spin-system of six coupling nuclei (H_aH_bH_cH_d F_YF_Y') was analysed in 12 s, a spin-system of nine coupling fluorine nuclei (AA'BB'CCC-YY') was analysed within 2 min, and 10 coupling nuclei (XX'YY'ZZZ-BB'-H_d) was optimised in 6 min using a laptop computer. ANATOLIA was also robust enough to be able to yield accurate spectral values from inaccurate input values. In both compounds, a fluorine–fluorine coupling constant was identified between the two fluoro-aromatic rings (F_BB' and F_YY') of +4.05 and +4.67 Hz and attributed to a through-space interaction. Ab initio structure optimisations and coupling constant calculations provided useful input data for spectral analysis. A modern ¹⁹F nuclear magnetic resonance spectrum of perfluorotoluene (octafluorotoluene) and analysis from 1975 was used as a test data set to assess ANATOLIA.     

Iodine-transfer polymerization and CuAAC “click” chemistry: A versatile approach toward poly(vinylidene fluoride)-based amphiphilic triblock terpolymers

This study presents the synthesis and properties of linear PVDF-based amphiphilic triblock terpolymers with PS and PEO, [PVDF-b-PS-b-PEO], by adopting a procedure that involves: (a) iodine-transfer polymerization (ITP) of VDF with 1-iodoperfluorohexane (C₆F₁₃I) serving as chain-transfer agent (CTA) to afford C₆F₁₃-PVDF-I, (b) ITP of styrene with the C₆F₁₃-PVDF-I macromolecular-CTA to obtain C₆F₁₃-PVDF-b-PS-I diblock copolymer, (c) end-group exchange from iodo- to azido-group by nucleophilic substitution reaction with NaN_3, and (d) copper-catalyzed azide-alkyne cycloaddition (CuAAC) with alkyne-terminated PEO to achieve C₆F₁₃-PVDF-b-PS-b-PEO triblock terpolymers. The ¹H and ¹⁹F NMR spectroscopy confirmed the presence of all blocks, while gel permeation chromatography traces showed the living nature of ITP technique. The self-assembly of these terpolymers was investigated in films (atomic force microscopy and DSC), as well as in aqueous and organic solvents (DLS). The analysis of crystalline phases based on the FTIR spectroscopy indicated the conversion of PVDF α-phase into α + β-phases and β + γ-phases upon the incorporation of PS and PEO blocks, respectively. The synthesized amphiphilic copolymers were evaluated (fluorescence spectroscopy) as carriers of small hydrophobic molecules in water. © 2019 Wiley Periodicals, Inc. J. Polym. Sci. 2020 , 58, 163–171     

Design of a field flow system for the on-line spectrophotometric determination of phosphate, nitrite and nitrate in natural water and wastewater

This study describes the design and optimisation of a field flow system for the in-situ collection and on-line determination of phosphate, nitrate and nitrite by flow injection analysis-spectrophotometry. The method is based on the initial determination of phosphate as its phosphoantimonylmolybdenum blue complex which is then oxidized on-line by nitrite and the decrease in absorbance is monitored at 880 nm. Nitrate is determined as the difference between total and initial nitrite content in a separate flow after reduction to nitrite in a cadmium reductive column. The calibration curves were linear in the range 0–2.00 mg L⁻¹ P-phosphate, 0–10.00 mg L⁻¹ nitrite and 0–7.00 mg L⁻¹ nitrate with correlation coefficients of 0.9979, 0.9993 and 0.9995, respectively. The detection limits, calculated as 3S/N, were 0.15 mg L⁻¹ for P-phosphate, 0.17 mg L⁻¹ for nitrite and 0.09 mg L⁻¹ for nitrate. The reproducibility was below 3.0% (n = 7). Method validation in the analysis of natural water and wastewater samples revealed that it can efficiently be applied to the determination of the target analytes, with recoveries in the range of 92–108%. Correspondence: Athanasios G. Vlessidis, Laboratory of Analytical Chemistry, Department of Chemistry, University of Ioannina, Ioannina 45110, Greece     

Binding of nontarget microorganisms from food washes to anti-<Emphasis Type="Italic">Salmonella</Emphasis> and anti-<Emphasis Type="Italic">E. coli</Emphasis> O157 immunomagnetic beads: most probable composition of background Eubacteria

We present herein the composition of bacterial communities occurring in ground chicken and the changes which arise in these populations based upon nonselective partitioning by commercially-available Dynal anti-Salmonella and anti-E. coli O157 immunomagnetic beads (IMB). Our enumeration and colony selection protocol was based upon a 6 × 6 drop plate method (n = 18 for each 25-g sub-sampling) using a dilution which resulted in ca. 4–8 colonies per drop. An average of 82 ± 13 colonies were selected from three 25-g ground chicken subsamplings per batch, each of which was repeated seasonally for one year. DNA was extracted from each colony and the composition of Eubacteria in each of these harvests was determined by sequence-based identification of 16S rDNA amplicons. The Gram-positive bacteria Brochothrix thermosphacta and Carnobacterium maltaromticum were the most commonly found organisms in both the total chicken wash (PBS) and in the IMB-bound (PBS-washed) fractions. The remaining background organisms which also adhered to varying degrees to commercial IMBs were: Pseudomonas oleovorans, Acinetobacter lwoffi, Serratia spp., and one Rahnella spp. A large number of the organisms were also cladistically evaluated based on rDNA basepair disparities: all Brochothrices were monophyletic; twelve different Pseudomonads were found along with eight Carnobacteria, seven Acinetobacteres, four Serratiae, and two Rahnellae. Carnobacterium alone showed an IMB-based concentration enhancement (ca. two to sixfold). Any reference to a brand or firm name does not constitute endorsement of the US Department of Agriculture over others of a similar nature not mentioned     

HPTLC-based chromatographic studies in selected Justicia species for quality assessment

JPC – Journal of Planar Chromatography – Modern TLC - The genus Justicia (Acanthaceae) is a source of important pharmaceutical compounds. Justicia species are integral parts of several...     

Synchronized Esterification and Transesterification of Jatropha Curcas Using Ferric Sulfate Modified Snail Shells As a Bi-Functional Catalyst: A Box-Behken Optimization Approach

Russian Journal of Applied Chemistry - The study is focused on modelling and optimizing the process parameters on the production of biodiesel from Jatropha Curcas oil using achantinoidea shell...     

A close look at silver oxide colloid for surface-enhanced Raman scattering

A silver oxide hydrosol has been prepared by reacting silver nitrate with sodium hydroxide in an aqueous solution. The colloidal particle composition and particle size have been characterized by X-ray diffractometry and transmittance electron microscopy. We have demonstrated that the sol is surface-enhanced Raman scattering active. One major advantage of this sol is the absence of the spectral interference arising from reaction products of the sol formation process. The mechanism of surface-enhanced Raman scattering activity is essentially contributed by the silver particles generated from the photochemical process during the laser excitation.     

In Vivo Endoscopic Tissue Identification by Rapid Evaporative Ionization Mass Spectrometry (REIMS)

Gastrointestinal cancers are a leading cause of mortality, accounting for 23 % of cancer‐related deaths worldwide. In order to improve outcomes from these cancers, novel tissue characterization methods are needed to facilitate accurate diagnosis. Rapid evaporative ionization mass spectrometry (REIMS) is a technique developed for the in vivo classification of human tissue through mass spectrometric analysis of aerosols released during electrosurgical dissection. This ionization technique was further developed by utilizing surface induced dissociation and was integrated with an endoscopic polypectomy snare to allow in vivo analysis of the gastrointestinal tract. We tested the classification performance of this novel endoscopic REIMS method in vivo. It was shown to be capable of differentiating between healthy layers of the intestinal wall, cancer, and adenomatous polyps based on the REIMS fingerprint of each tissue type in vivo.