Biochemical Species Research Articles

Подбор устойчивых видов Rosa L. для целей лесомелиорации, озеленения и использования в биотехнологии (на примере Волгоградской области)

Selection of sustainable and ornamental rosehip species is relevant for their widespread use in forest reclamation and landscaping of settlements in the arid region. The objects of research were rosehips with different areas of natural expansion: R. rugosa, including form alba War Rehder, R. cinnamomea, R. beggeriana, R. acicularis, R. spinosissima, R. canina growing at points of introduction on different soils. In 2018, June was the hottest month, while February was the coldest month in Volgograd region. The maximum deviation from the average monthly temperature was observed in March. July and January were the hottest and the coldest months, respectively, in Samara region. During the research period, the species of wild roses retained the life form of habitus, and their height varied from 1.0–2.0 m (medium-grown species) to 0.7–0.9 m (short species). Data on the resistance of rosehip species to the maximum and minimum temperatures can be the factual basis of systemarealogical forecasting for geographical points of introduction. The degree of demand of rosehips to soil fertility and light was revealed by poor-demanding species: R. beggeriana, R. cinnamomea, R. rugosa and R. spinosissima. The observing method of the Main Botanical garden, field and laboratory observations allowed to establish the duration of the phenological phases of the studied species. Rosehips, being ornamental throughout the growing season, are useful in forest reclamation and landscaping, depending on the growth and color of their flowers. Types of diseases and parasitic fungi were determined by mycological analysis and reference data. The most common disease of the studied species of rosehips is powdery mildew from the genus Sphaerotheca. Amino acid profile of rosehip fruits was determined by the capillary electrophoresis system “Kapel” at a wavelength of 250 nm and allowed to identify the most valuable by biochemical composition species. In the period of monitoring the winter hardiness of rosehips, the best result was shown by the species R. rugosa, R. cinnamomea and R. canina, belonging to the North American, European and Far Eastern collections. The method of a priori ranking of fruiting indicators based on the division of factors in the descending order of their contribution revealed the most promising species for use in bio technology. The total sum of ranks and the sum of squares of deviations were determined; the concordance coefficient and the degree of consistency of the researchers’ opinions are obtained in accordance with the degrees-of-freedom breakdown. It was found that the use of biotechnological methods in modern seed production is the most pressing; the obtained results will contribute to the improvement and acceleration of the seed production process in the arid conditions of Volgograd region. Recommendations are given for the cultivation of rosehips depending on the natural and climatic conditions of the different districts of the region. For citation: Solomentseva A.S., Lebed’ N.I., Kolmukidi S.V., Mezhevova A.S. Selection of Resistant Species of Rosa L. for the Purposes of Forest Reclamation, Landscaping and Use in Biotechnology (On the Example of Volgograd Region). Lesnoy Zhurnal [Russian Forestry Journal], 2020, no. 1, pp. 49–62. DOI: 10.37482/0536-1036-2020-1-49-62

Microarray Expression Profiling and Raman Spectroscopy Reveal Anti-Fatty Liver Action of Berberine in a Diet-Induced Larval Zebrafish Model.

Background: The prevalence of non-alcohol fatty liver disease (NAFLD) is increasing in children and adolescents who are mostly resulted from overfeeding. Previous studies demonstrate that berberine (BBR), a compound derived from plant, has beneficial effects on NAFLD in adults but poorly understood in the pediatric population. This study employed a larval zebrafish model to mimic the therapeutic effects of BBR in the pediatric population and the mechanisms underlying its hepatoprotection. Methods: High-cholesterol diet (HCD)-fed zebrafish exposed to BBR at doses of 0, 1, 5, and 25 μM. After the larvae were treated with BBR for 10 days, its effect on hepatic steatosis was evaluated. We introduced Raman imaging and three-dimensional (3D) molecular imaging to detect changes in the biochemical composition and reactive oxygen species (ROS) levels of zebrafish liver. Gene expression microarray was performed to identify differentially expressed genes (DEGs) followed by gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and functional category analysis. Results: BBR (5 and 25 μM) administration prevented HCD-induced liver lipid accumulation in larval zebrafish. The result was further confirmed by the pathological observation. Raman mapping indicated that the biochemical composition in the liver of BBR-treated group shifted to the control. The quantitative analysis of 3D imaging showed that the ROS level was significantly decreased in the liver of BBR-treated larvae. In the livers of the BBR group, we found 468 DEGs, including 172 genes with upregulated expression and 296 genes with downregulated expression. Besides, GO enrichment, KEGG pathway, and functional category analysis showed that various processes related to glucolipid metabolism, immune response, DNA damage and repair, and iron were significantly enriched with DEGs. The expression levels of the crucial genes from the functional analysis were also confirmed by quantitative PCR (qPCR). Conclusion: BBR can significantly improve hepatic steatosis in HCD-fed zebrafish larvae. Its mechanisms might be associated with the regulation of lipid metabolism, oxidative stress, and iron homeostasis. Raman imaging in larval zebrafish might become a useful tool for drug evaluation. Mainly, the gene expression profiles provide molecular information for BBR on the prevention and treatment of pediatric NAFLD.

Quantifying Nitric Oxide Flux Distributions.

Nitric oxide (NO) is a radical that is used as an attack molecule by immune cells. NO can interact and damage a range of biomolecules, and the biological outcome for bacteria assaulted with NO will be governed by how the radical distributes within their biochemical reaction networks. Measurement of those NO fluxes is complicated by the low abundance and transience of many of its reaction products. To overcome this challenge, we use computational modeling to translate measurements of several biochemical species (e.g., NO, O2, NO2-) into NO flux distributions. In this chapter, we provide a detailed protocol, which includes experimental measurements and computational modeling, to estimate the NO flux distribution in an Escherichia coli culture. Those fluxes will have uncertainty associated with them and we also discuss how further experiments and modeling can be employed for flux refinement.

Maximum Entropy Framework for Predictive Inference of Cell Population Heterogeneity and Responses in Signaling Networks.

Predictive models of signaling networks are essential for understanding cell population heterogeneity and designing rational interventions in disease. However, using computational models to predict heterogeneity of signaling dynamics is often challenging because of the extensive variability of biochemical parameters across cell populations. Here, we describe a maximum entropy-based framework for inference of heterogeneity in dynamics of signaling networks (MERIDIAN). MERIDIAN estimates the joint probability distribution over signaling network parameters that is consistent with experimentally measured cell-to-cell variability of biochemical species. We apply the developed approach to investigate the response heterogeneity in the EGFR/Akt signaling network. Our analysis demonstrates that a significant fraction of cells exhibits high phosphorylated Akt (pAkt) levels hours after EGF stimulation. Our findings also suggest that cells with high EGFR levels predominantly contribute to the subpopulation of cells with high pAkt activity. We also discuss how MERIDIAN can be extended to accommodate various experimental measurements.

New Advances in In Vivo Applications of Gated Mesoporous Silica as Drug Delivery Nanocarriers.

One appealing concept in the field of hybrid materials is related to the design of gated materials. These materials are prepared in such a way that the release of chemical or biochemical species from voids of porous supports to a solution is triggered upon the application of external stimuli. Such gated materials are mainly composed of two subunits: i) a porous inorganic scaffold in which a cargo is stored, and ii) certain molecular or supramolecular entities, grafted onto the external surface, that can control mass transport from the interior of the pores. On the basis of this concept, a large number of examples are developed in the past ten years. A comprehensive overview of gated materials used in drug delivery applications in in vivo models from 2016 to date is thus given here.

Microfluidic chip electrophoresis for biochemical analysis.

Microfluidic chip electrophoresis has been widely employed for separation of various biochemical species owing to its advantages of low sample consumption, low cost, fast analysis, high throughput, and integration capability. In this article, we reviewed the development of four different modes of microfluidics-based electrophoresis technologies including capillary electrophoresis, gel electrophoresis, dielectrophoresis, and field (electric) flow fractionation. Coupling detection schemes on microfluidic electrophoresis platform were also reviewed such as optical, electrochemical, and mass spectrometry method. We further discussed the innovative applications of microfluidic electrophoresis for biomacromolecules (nucleic acids and proteins), biochemical small molecules (amino acids, metabolites, ions, etc.), and bioparticles (cells and pathogens) analysis. The future direction of microfluidic chip electrophoresis was predicted.

Salvianolic acid B exerts a protective effect in acute liver injury by regulating the Nrf2/HO-1 signaling pathway.

Salvianolic acid B (Sal B) exerts strong antioxidant activity and eliminates the free radical effect. However, how it affects the antioxidant pathway is not very clear. The objective of this study was to investigate the underlying mechanism of Sal B in CCl4-induced acute liver injury, especially its effect on the Nrf2/HO-1 signaling pathway. For the in vivo experiment, an acute liver injury model was induced using CCl4 and treated with Sal B. For the in vitro experiment, an oxidative damage model was established followed by Sal B treatment. Serum biochemical indicators and reactive oxygen species activity were detected using corresponding kits. Oxidant/antioxidant status was determined based on the levels of malondialdehyde, glutathione, and superoxide dismutase. Nrf2 and HO-1 levels were analyzed by Western blotting and immunohistochemical staining. Sal B treatment improved liver histology, decreased the aminotransferase levels, and attenuated oxidative stress in the acute liver injury model. Nrf2 and HO-1 levels were increased both in vivo and in vitro. Sal B suppresses acute liver injury and Nrf2/HO-1 signaling plays a key role in this process.

Fabrication of refractive index sensors using polarization independent metamaterial and their application to chemical concentration measurement and DNA detection

AbstractBiochemical sensors are used for discrimination of biochemical species, concentration measurement, and so on. Because metamaterial responds to slight changes in the ambient refractive index, it is possible to realize ultrasensitive biochemical sensors. We designed and fabricated refractive index sensors using polarization independent metamaterial and examined their application as biochemical sensors. Refractive index sensitivity, concentration measurement, and DNA detection were carried out.

Homogenization results for a coupled system of reaction–diffusion equations

The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction–diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying several metabolic processes taking place in living cells, in which biochemical species can diffuse in the cytosol and react both in the cytosol and also on the organellar membranes. The coupling of the concentrations of the biochemical species is realized via various properly scaled nonlinear reaction terms. These nonlinearities, which model, at the microscopic scale, various volume or surface reaction processes, give rise in the macroscopic model to different effects, such as the appearance of additional source or sink terms or of a non-standard diffusion matrix.

Multivariate information processing characterizes fitness of a cascaded gene-transcription machinery.

We report that a genetic two-step activation cascade processes diverse flavors of information, e.g., synergy, redundancy, and unique information. Our computations measuring reduction in Shannon entropies and reduction in variances produce differently behaving absolute magnitudes of these informational flavors. We find that similarity can be brought in if these terms are evaluated in fractions with respect to corresponding total information. Each of the input signal and final gene-product is found to generate common or redundant information fractions (mostly) to predict each other, whereas they also complement one another to harness synergistic information fraction, predicting the intermediate biochemical species. For an optimally growing signal to maintain fixed steady-state abundance of activated downstream gene-products, the interaction information fractions for this cascade module shift from net-redundancy to information-independence.

A sensitive voltammetric sertraline nanosensor based on ZnFe2O4 nanoparticles modified screen printed electrode

Electro catalytic competency was exhibited by ZnFe2O4 nanoparticles modified screen printed electrode (SPE) for sertraline oxidation. This study showed that the sensor has exceptional electron mediating property for sertraline oxidation in 0.1 M phosphate buffer solution (PBS) at pH 7.0. ZnFe2O4 nanoparticles/SPE application in differential pulse voltammetry (DPV) is proved to entail apparent response for sertraline oxidation. In the concentration range 0.07–300.0 μM in a PBS, pH 7.0, the responses were linear and sertraline detection limit for this method was 0.02 μM (S/N = 3). This adjusted electrode was implemented to detect sertraline within real samples and proved to have sufficient results. Such results validate the fact that ZnFe2O4 nanoparticles are suitable for being applied in electrochemical sensors to analyze biochemical species.

Identification and typing of Yersinia enterocolitica and Yersinia pseudotuberculosis isolated from human clinical specimens in England between 2004 and 2018.

PurposeandMethodology. Epidemiological and microbiological data on Yersinia enterocolitica (n=699) and Yersinia pseudotuberculosis (n=35) isolated from human clinical specimens in England between April 2004 and March 2018 were reviewed. Traditional biochemical species identification and serological typing results were compared with species identifications and serotypes derived from whole-genome sequencing (WGS) data for a sub-set of these isolates (n=179).Results. Most Y. enterocolitica isolates were from faecal specimens (74.4%) from adults (80.7%) and 50.7 % of isolates were from male patients. Most Y. pseudotuberculosis isolates were from blood cultures (68.6%) from adults (91%) and 60.0 % of isolates were from male patients. All sequenced isolates of Y. enterocolitica (n=158) and Y. pseudotuberculosis (n=21), as well as isolates belonging to other Yersinia species (n=21), were correctly identified from genomic data using a kmer-based identification approach. Traditional phenotypic serotyping typed 82/158 and 12/21 isolates of Y. enterocolitica and Y. pseudotuberculosis, respectively, while 118/158 and 21/21 isolates of Y. enterocolitica and Y. pseudotuberculosis, respectively, were typed by the genome-derived serotyping method. In addition, WGS data provided a multi-locus sequence type profile and virulence gene profile for all isolates.Conclusion. The use of WGS for typing Y. enterocolitica and Y. pseudotuberculosis at Public Health England will facilitate the monitoring of animal-to-human transmission of these important foodborne pathogens in the UK and improve public health surveillance of the pathogenic lineages.

Tracing Size and Surface Chemistry-Dependent Endosomal Uptake of Gold Nanoparticles Using Surface-Enhanced Raman Scattering.

Surface-enhanced Raman scattering (SERS)-based single-cell analysis is an emerging approach to obtain molecular level information from molecular dynamics in a living cell. In this study, endosomal biochemical dynamics was investigated based on size and surface chemistry-dependent uptake of gold nanoparticles (AuNPs) on single cells over time using SERS. MDA-MB-231 breast cancer cells were exposed to 13 and 50 nm AuNPs and their polyadenine oligonucleotide-modified forms by controlling the order and combination of AuNPs. The average spectra obtained from 20 single cells were analyzed to study the nature of the biochemical species or processes taking place on the AuNP surfaces. The spectral changes, especially from proteins and lipids of endosomal vesicles, were observed depending on the size, surface chemistry, and combination as well as the duration of the AuNP treatment. The results demonstrate that SERS spectra are sensitive to trace biochemical changes not onlythe size, surface chemistry, and aggregation status of AuNPsbut alsotheendosomal maturation steps over time, which can be simple and fast way for understanding the AuNP behavior in single cell and useful for the assisting and controlling of AuNP-based gene or drug delivery applications.

Enhancement strategies of targetability, response and photostability for in vivo bioimaging

Analyses of the physiology and pathology of active biochemical species in their native contexts are critical for early diagnosis and therapy. Optical imaging has emerged as one of the promising modalities for noninvasive and real-time visualization of important biomolecules or biological events, and it has witnessed major advances in the field of imaging in vitro and in vivo . In this review, we present a survey of common approaches and tactics for enhanced targetability, response rate, and photostability in bioimaging applications. Recently developed and representative examples are illustrated on the cellular and tissue levels.

Kinetic Modeling of Coagulation and Fibrinolysis

Thromboelastic testing provides an assessment of a patient’s coagulation and fibrinolytic systems. In recent years, thromboelastic testing has become an important point of care technique. However, its direct connection with the underlying biochemistry of coagulation and clot formation is not obvious. Toward this issue, we describe a validated reduced order mathematical model of coagulation and fibrinolysis, consisting of 22 ordinary differential equations, which described clot formation from initiation of the coagulation cascade through the degradation of polymerized fibrin by plasmin. We trained the model via leave one out cross validation on ROTEM measurements, a common thromboelastic test, on four patients, and then predicted ROTEM trajectories on four unseen patients, in whole blood and whole blood with the addition of 2 nM tissue plasminogen activator. Following model validation, sensitivity analysis suggested which biochemical interactions and species controlled the system response. Lastly, we investigated if we could estimate protein concentrations from commonly reported thromboelastic metrics. These estimation studies suggested we could (on average) relearn the initial fibrinogen concentration to within 20% of its true value. Taken together, this work presents a model which connects the underlying biochemistry of coagulation and clot formation in patients to a common point of care thrombelastographic test.

Tissue Intrinsic Fluorescence Spectra-Based Digital Pathology of Liver Fibrosis by Marker-Controlled Segmentation.

Tissue intrinsic emission fluorescence provides useful diagnostic information for various diseases. Because of its unique feature of spectral profiles depending on tissue types, spectroscopic imaging is a promising tool for accurate evaluation of endogenous fluorophores. However, due to difficulties in discriminating those sources, quantitative analysis remains challenging. In this study, we quantitatively investigated spectral-spatial features of multi-photon excitation fluorescence in normal and diseased livers. For morphometrics of multi-photon excitation spectra, we examined a marker-controlled segmentation approach and its application to liver fibrosis assessment by employing a mouse model of carbon tetrachloride (CCl4)-induced liver fibrosis. We formulated a procedure of internal marker selection where markers were chosen to reflect typical biochemical species in the liver, followed by image segmentation and local morphological feature extraction. Image segmentation enabled us to apply mathematical morphology analysis, and the local feature was applied to the automated classification test based on a machine learning framework, both demonstrating highly accurate classifications. Through the analyses, we showed that spectral imaging of native fluorescence from liver tissues have the capability of differentiating not only between normal and diseased, but also between progressive disease states. The proposed approach provides the basics of spectroscopy-based digital histopathology of chronic liver diseases, and can be applied to a range of diseases associated with autofluorescence alterations.

Ratiometric analysis using Raman spectroscopy as a powerful predictor of structural properties of fatty acids.

Raman spectroscopy has been used extensively for the analysis of biological samples in vitro, ex vivo and in vivo. While important progress has been made towards using this analytical technique in clinical applications, there is a limit to how much chemically specific information can be extracted from a spectrum of a biological sample, which consists of multiple overlapping peaks from a large number of species in any particular sample. In an attempt to elucidate more specific information regarding individual biochemical species, as opposed to very broad assignments by species class, we propose a bottom-up approach beginning with a detailed analysis of pure biochemical components. Here, we demonstrate a simple ratiometric approach applied to fatty acids, a subsection of the lipid class, to allow the key structural features, in particular degree of saturation and chain length, to be predicted. This is proposed as a starting point for allowing more chemically and species-specific information to be elucidated from the highly multiplexed spectrum of multiple overlapping signals found in a real biological sample. The power of simple ratiometric analysis is also demonstrated by comparing the prediction of degree of unsaturation in food oil samples using ratiometric and multivariate analysis techniques which could be used for food oil authentication.

Optimization of a liquid refractive index sensor based on an integrated optic slot-waveguide directional coupler

An integrated optic silica slot-waveguide directional coupler is investigated here for its ability to measure the refractive index (n) of a liquid biochemical species. The geometrical dimensions of the directional coupler are optimized so that the output power of the directional coupler is linear when refractive index of the liquid species changes from 1.33 to 1.38. The best geometrical dimensions achieved here from a simulation with the beam propagation method (BPM) were a waveguide width of 6um, a gap of 2um, a slot-widht of 0.5um, and a channel length of 2,000um. The proposed directional coupler type of biochemical sensor changes its output power linearly from 2 to 24% when the refractive index of the liquid species varies from 1.33 to 1.38.

Interplay of synergy and redundancy in diamond motif.

The formalism of partial information decomposition provides a number of independent components which altogether constitute the total information provided by the source variable(s) about the target variable(s). These non-overlapping terms are recognized as unique information, synergistic information, and redundant information. The metric of net synergy conceived as the difference between synergistic and redundant information is capable of detecting effective synergy, effective redundancy, and information independence among stochastic variables. The net synergy can be quantified using appropriate combinations of different Shannon mutual information terms. The utilization of the net synergy in network motifs with the nodes representing different biochemical species, involved in information sharing, uncovers rich store for exciting results. In the current study, we use this formalism to obtain a comprehensive understanding of the relative information processing mechanism in a diamond motif and two of its sub-motifs, namely, bifurcation and integration motif embedded within the diamond motif. The emerging patterns of effective synergy and effective redundancy and their contribution toward ensuring high fidelity information transmission are duly compared in the sub-motifs. Investigation on the metric of net synergy in independent bifurcation and integration motifs are also executed. In all of these computations, the crucial roles played by various systemic time scales, activation coefficients, and signal integration mechanisms at the output of the network topologies are especially emphasized. Following this plan of action, we become confident that the origin of effective synergy and effective redundancy can be architecturally justified by decomposing a diamond motif into bifurcation and integration motif. According to our conjecture, the presence of a common source of fluctuations creates effective redundancy. Our calculations reveal that effective redundancy empowers signal fidelity. Moreover, to achieve this, input signaling species avoids strong interaction with downstream intermediates. This strategy is capable of making the diamond motif noise-tolerant. Apart from the topological features, our study also puts forward the active contribution of additive and multiplicative signal integration mechanisms to nurture effective redundancy and effective synergy.

A Magnetic Heterogeneous Biocatalyst Composed of Immobilized Laccase and 2,2,6,6‐Tetramethylpiperidine‐1‐oxyl (TEMPO) for Green One‐Pot Cascade Synthesis of 2‐Substituted Benzimidazole and Benzoxazole Derivatives under Mild Reaction Conditions

AbstractThe design of reusable high‐performance heterogeneous catalysts via the immobilization of chemical and biochemical species on magnetic nanoparticles increases the efficiency of catalytic systems by facilitating easy, fast, and clean separation processes. Laccase and 4‐amino‐2,2,6,6‐tetramethylpiperidine‐1‐oxyl were separately immobilized on amine functionalized iron (II, III) oxide nanoparticles with covalent bonding using glutaraldehyde as a coupling reagent. The prepared catalyst was used to synthesize 12 benzoxazole and benzimidazole derivatives. The one‐pot, two‐step enzymatic aerobic oxidation reaction included the condensation of in situ‐produced salicylaldehyde derivatives with aromatic amines, followed by an enzymatic dehydrogenation process. Optimal reaction conditions consisted of a citrate buffer (10 mM, pH 4.5) at 40 °C for an incubation time of 10 h and a heterogeneous catalyst containing immobilized laccase (80 mg, 100 U) and immobilized 2,2,6,6‐tetramethylpiperidine‐1‐oxyl (TEMPO) (40 mg, 2 mol%). The catalyst retained more than 85% of its initial activity after 10 runs. In addition to the potential for reuse without significant losses in performance, eco‐friendly attributes of this catalytic system include its high catalytic activity and the ease with which it can be recovered from the reaction mixture using an external magnet.magnified image