Comparative Structural Analysis Research Articles

The genetic structure of populations of Isthmiophora melis (Schrank, 1788) (Digenea: Echinostomatidae). Does the host’s diet matter?

BackgroundHere we provide a comparative analysis of the genetic structure of populations (based on nad1 mtDNA) of Isthmiophora melis isolated from the American mink (Neogale vison), an introduced invasive species, commonly occurring in the territory of Poland, and from the striped field mouse (Apodemus agrarius).MethodsA total of 133 specimens of I. melis were obtained from naturally infected N. vison collected from six localities in Poland (108 samples) and 25 individuals of I. melis from A. agrarius. All sequences of the nad1 gene obtained during the present study were assembled and aligned. The standard statistics for haplotype composition, i.e., the number of haplotypes, haplotype diversity, nucleotide diversity, and average number of nucleotide differences, were calculated. Haplotype analysis and visualization of haplotype frequency among populations were performed using a median-joining network.ResultsBased on the samples collected from different localities in Poland, our study revealed that the overall genetic diversity of I. melis isolated from the American mink and of the striped field mouse do not differ significantly. The median-joining network showed that the three main haplotypes are in the centre of a star-like structure, with the remaining haplotypes as the satellites, reflecting the recent expansion of the populations.ConclusionsThe overall genetic diversity of I. melis isolated from the American mink and striped field mouse reveals a high level of homogeneity. Moreover, regional differences in the food composition of the definitive hosts play an important role in shaping the genetic structure of the trematode populations.Graphical

Comparative analysis of structure and electronic properties of doped g-GaN/Al0.5Ga0.5N heterostructure

Comparative analysis of structure and electronic properties of doped g-GaN/Al0.5Ga0.5N heterostructure

Comparative Analysis of Surface-Attached Cooling Structure for Efficient Thermal Management of SPMM-TW

Efficient thermal management is the essential precondition for electrical machines to achieve high power density and reliable operation. This paper presents a surface-attached cooling structure (SACS) for the thermal management of slotless permanent magnet motor (SPMM) with toroidal winding. The SACS consists of several channels attached to the surface of the toroidal winding, and the shorter heat path guarantees that the heat generated in the winding can be effectively extracted. Three-dimensional electromagnetic finite-element analysis and the computational fluid dynamics are used to evaluate the losses of the SPMM and obtain the accurate convective heat transfer coefficient (CHTC). For predicting the winding temperature accurately, the layered winding model is proposed to simulate the actual winding conditions. In addition, the influence of different channel materials on temperature rise is experimentally evaluated on the same prototype. The experimental results show that the layered winding model can well simulate and predict the actual temperature distribution of the winding, and the SACS can effectively reduce the temperature rise of the winding compared with the housing water jacket cooling, where the SPMM with the SACS can withstand a continuous current density of 17.2 A/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and a peak current density of 28 A/mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .

Comparative Analysis of the Morphological Diversity Structure of Altai Osmans of the Genus Oreoleuciscus (Cyprinidae) in the Riverine Populations of Three Mongolian Water Systems

Analysis of the structure of the morphological diversity of the Altai osmans of the genus Oreoleuciscus in the Urt River (water system of the Tes River) indicates that this is a polymorphic population, consisting of three forms, clearly differentiated by a set of characters. The ratio of differences between these forms and forms previously identified in the Zavkhan (water system of the Great Lakes Hollow) and Tuin (water system of the Lake Valley) rivers suggests that the characters considered in the study are adaptively plastic, and the revealed structure of the morphological diversity of the genus is mostly determined by local patterns of environmental conditions.

Comparative structural and semantic analysis of English and Russian proverbs about greediness, prodigality, frugality and moderation in the context of their linguistic and cultural identity

Comparative structural and semantic analysis of English and Russian proverbs about greediness, prodigality, frugality and moderation in the context of their linguistic and cultural identity

Structural and semantic features and national specificity of English and Russian proverbs with the meaning "foresight", "caution".

The subject of this study is the structural and semantic features of English and Russian proverbs with the meanings of "foresight", "caution". Proverbs with the meanings "foresight", "caution" have not been sufficiently studied in terms of revealing their meaning and describing their structural and semantic characteristics. The scientific novelty lies in the fact that for the first time the general and unique meanings of English and Russian proverbs of this thematic group were considered in a comparative aspect, as well as an analysis of syntactic structures and a semantic analysis of the lexical components of proverbs and an analysis of figurative and expressive means reflecting their national and cultural identity were made. The results of the study can be used in the process of teaching English, as well as the basis for a deeper comparative study of the proverbs of the two languages of this thematic group. The study used descriptive and comparative methods, functional-stylistic analysis, structural and syntactic analysis. In the course of the analysis, we revealed the following pattern: in most of the presented thematic groups there are proverbs close in meaning that are not equivalents. They use the same syntactic structures (imperative sentences, complex sentences with subordinate conditions, time clause, subordinate concessions and subordinate attributive clauses, syntactic compression: ellipsis, incompleteness of sentences, non-conjunction, as well as complex sentences with an adversative meaning) and similar expressive techniques (antithesis, comparison, oxymoron, tautology, allegory, metaphor, including personifying metaphor), while differing in lexical content (emotional and expressive, evaluative vocabulary, vocabulary associated with the realities of everyday life, zoonyms, somatisms, archaisms). These differences are due to the peculiarities of climate, life, traditions, as well as the environment of their occurrence, which, on the one hand, indicates the universality of human experience, and on the other hand, indicates the national specificity of the thinking of the two peoples.

Comparative Analysis of Structure for Calamity by using Midas Gen, ETABS and STAAD pro

Abstract: During the past few years the earthquakes have dealt a lot of damage to life and property in India. To overcome this, the need for advancement in construction is necessary. With Scarcity of area and overgrowing population the need of constructing High Rise building has been increasing. Traditional high rise structures are tend to be weak against additional load pressure or earthquakes. To counter such situations and to reduce the effect of such calamity with the help of structural analysis and use of methods like Base Isolation, X bracing and Shear Wall, the intensity of such problem can be reduced to a wide extent. This paper represents the comparison of various methods on normal high rise building with the use of Midas Gen ,ETABS and STAAD pro..We took the case for Seismic zone 2 with medium soil category. Structural engineering software has progressed significantly in recent years. MIDAS GEN, ETABS and STAAD pro conducts structural design and analysis packages that support multiple types of concrete, steel, aluminum and timber international design codes.

Comparative Experiment and Analysis of a Base-Isolated Structure with Small Aspect Ratio on Multi-Layered Soft Soil Foundation and Rigid Foundation

Through conducting a comparative experimental study of small-aspect-ratio isolated structure models on multi-layered soft soil foundations and rigid foundations, this paper investigates the influence of soil–structure interaction (SSI) effects on the seismic response of small-aspect-ratio isolated structures on multi-layered soft soil foundations. An energy balance equation for isolated structure systems considering SSI effects is proposed, and the impact of SSI effects on the energy dissipation response of small-aspect-ratio isolated structures on multi-layered soft soil foundations is analyzed in depth. The analysis results reveal that SSI effects on multi-layered soft soil foundations reduce the first-order natural frequency of the isolated structure system and significantly increase the damping ratio of the system. Furthermore, the rotational effect of the isolated structure foundation is significant on multi-layered soft soil foundations, and the isolation layer has a certain amplification effect on the rotational effect of the foundation. The study shows that SSI effects on multi-layered soft soil foundations may either increase or decrease the seismic response of isolated structures. Moreover, due to the influence of SSI effects, the ratios of kinetic energy, damping energy dissipation, and hysteresis deformation energy dissipation of the isolated structure on multi-layered soft soil foundations are significantly different from those on rigid foundations. The research concludes that the influence of SSI effects is more significant during large earthquakes, where the ratios of kinetic energy and damping energy dissipation of the isolated structure increase, the hysteresis deformation energy dissipation ratio of the isolation layer decreases, and the magnitude of the decrease is related to the characteristics of the input seismic motion. This research has significant implications for improving the seismic design theory of small-aspect-ratio isolated structures on multi-layered soft soil foundations.

Structural Insights into Molecular Recognition and Receptor Activation in Chemokine-Chemokine Receptor Complexes.

The chemokine system is a key player in the functioning of the immune system and a sought-after target for drug candidates. The number of experimental structures of chemokines in complex with chemokine receptors has increased rapidly over the past few years, providing essential information for rational development of chemokine receptor ligands. Here, we perform a comparative analysis of all chemokine-chemokine receptor structures, with the aim of characterizing the molecular recognition processes and highlighting the relationships between chemokine structures and functional processes. The structures show conserved interaction patterns between the chemokine core and the receptor N-terminus, while interactions near ECL2 display subfamily-specific features. Detailed analyses of the interactions of the chemokine N-terminal domain in the 7TM cavities reveal activation mechanisms for CCR5, CCR2, and CXCR2 and a mechanism for biased agonism in CCR1.

Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus.

Entry inhibitors are an important resource in the response against emerging pathogens like the novel SARS-CoV-2, which enters human cells via interaction between the surface spike glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the spike to ACE2, docking experiments, and molecular dynamics simulations, we identified a stable fragment of ACE2 that binds to the spike, is soluble, and is not predicted to bind to its physiological ligand angiotensin II. From this fragment we computationally designed and experimentally validated a smaller, stable peptide that disrupts ACE2-spike interaction at nanomolar concentrations, suggesting its potential use as a decoy that could interfere with viral binding by competition.

In silico comparative structural and functional analysis of arsenite methyltransferase from bacteria, fungi, fishes, birds, and mammals

BackgroundArsenic, a ubiquitous toxic metalloid, is a threat to the survival of all living organisms. Bioaccumulation of arsenic interferes with the normal physiological pathway. To overcome arsenic toxicity, organisms have developed arsenite methyltransferase enzyme, which methylates inorganic arsenite to organic arsenic MMA (III) in the presence of S-adenosylmethionine (SAM). Bacteria-derived arsM might be horizontally transported to different domains of life as arsM or as3mt (animal ortholog). A systematic study on the functional diversity of arsenite methyltransferase from various sources will be used in arsenic bioremediation. ResultsSeveral arsenite methyltransferase protein sequences of bacteria, fungi, fishes, birds, and mammals were retrieved from the UniProt database. In silico physicochemical studies confirmed the acidic, hydrophilic, and thermostable nature of these enzymes. Interkingdom relationships were revealed by performing phylogenetic analysis. Homology modeling was performed by SWISS-MODEL, and that was validated through SAVES-v.6.0. QMEAN values ranged from − 0.93 to − 1.30, ERRAT score (83–96), PROCHECK (88–92%), and other parameters suggested models are statistically significant. MOTIF and PrankWeb discovered several functional motifs and active pockets within the proteins respectively. The STRING database showed protein–protein interaction networks. ConclusionAll of our in silico studies confirmed the fact that arsenite methyltransferase is a cytosolic stable enzyme with conserved sequences over a wide range of organisms. Thus, because of its stable and ubiquitous nature, arsenite methyltransferase could be employed in arsenic bioremediation.

Chloroplast Pan-Genomes and Comparative Transcriptomics Reveal Genetic Variation and Temperature Adaptation in the Cucumber.

Although whole genome sequencing, genetic variation mapping, and pan-genome studies have been done on a large group of cucumber nuclear genomes, organelle genome information is largely unclear. As an important component of the organelle genome, the chloroplast genome is highly conserved, which makes it a useful tool for studying plant phylogeny, crop domestication, and species adaptation. Here, we have constructed the first cucumber chloroplast pan-genome based on 121 cucumber germplasms, and investigated the genetic variations of the cucumber chloroplast genome through comparative genomic, phylogenetic, haplotype, and population genetic structure analysis. Meanwhile, we explored the changes in expression of cucumber chloroplast genes under high- and low-temperature stimulation via transcriptome analysis. As a result, a total of 50 complete chloroplast genomes were successfully assembled from 121 cucumber resequencing data, ranging in size from 156,616-157,641 bp. The 50 cucumber chloroplast genomes have typical quadripartite structures, consisting of a large single copy (LSC, 86,339-86,883 bp), a small single copy (SSC, 18,069-18,363 bp), and two inverted repeats (IRs, 25,166-25,797 bp). Comparative genomic, haplotype, and population genetic structure results showed that there is more genetic variation in Indian ecotype cucumbers compared to other cucumber cultivars, which means that many genetic resources remain to be explored in Indian ecotype cucumbers. Phylogenetic analysis showed that the 50 cucumber germplasms could be classified into 3 types: East Asian, Eurasian + Indian, and Xishuangbanna + Indian. The transcriptomic analysis showed that matK were significantly up-regulated under high- and low-temperature stresses, further demonstrating that cucumber chloroplasts respond to temperature adversity by regulating lipid metabolism and ribosome metabolism. Further, accD has higher editing efficiency under high-temperature stress, which may contribute to the heat tolerance. These studies provide useful insight into genetic variation in the chloroplast genome, and established the foundation for exploring the mechanisms of temperature-stimulated chloroplast adaptation.

Effect of the complex of natural terpenes and vitamin E Renotineх® on free radical processes in patients with urolithiasis

BACKGROUND: One of the leading links in the pathogenesis of urolithiasis is oxidative stress, which occurs as a result of the intensification of free radical oxidation with insufficient activity of the antioxidant defense system of the body.&#x0D; AIM: The aim of the study was to study the effect of a complex of natural terpenes and vitamin E Renotineх on the state of oxidative stress in patients with urolithiasis in the postoperative period after percutaneous nephrolithotripsy.&#x0D; MATERIALS AND METHODS: The study included 42 patients. Of the 35 people who underwent percutaneous nephrolithotripsy, 2 groups were formed. Patients of the main group (n = 20), in contrast to the control group (n = 15), received Renotinex (Polaris LLC, Russia) before and after surgery, 2 capsules (1 capsule 300 mg) twice a day. To determine the main indicators of the activity of free-radical processes in the body, all patients underwent a blood test on the 3rd day after surgery. The total activity of the pro- and antioxidant systems in blood plasma was determined by the method of induced chemiluminescence. The activity of lipid peroxidation was assessed by determining the concentration of active products of thiobarbituric acid secondary products of lipid peroxidation in blood erythrocytes. The activity of antioxidant enzymes was studied by spectrophotometric method. To determine the ability of blood plasma to crystallize in some of the same patients with urolithiasis while taking Renotinex, the method of wedge dehydration was used. For a comparative analysis of the crystal structure of dried blood plasma samples (facies), 7 healthy volunteers were included in the study, which made up the third group (comparison group).&#x0D; RESULTS: The results of the study reliably demonstrate that the composition of the complex of natural terpenes and vitamin E Renotinex has a positive effect on free-radical processes in patients with urolithiasis, biochemical parameters of blood plasma (indicators of induced chemiluminescence, catalase activity, malondialdehyde level), as well as on crystallization processes blood plasma, which is confirmed by the method of wedge dehydration of blood plasma. Any change in the body caused by excessive activity of free-radical oxidation processes is reflected in the composition of the blood, and specifically in the indicators of the mechanical characteristics of blood plasma (viscosity, structure, surface tension), which determine the shape of the resulting structures of the drying drop of biological fluid.&#x0D; CONCLUSIONS: The complex of natural terpenes and vitamin E Renotinex has a positive effect on free-radical processes, biochemical parameters of blood plasma, as well as on the systemic structural organization of blood plasma in patients operated on for urolithiasis. The inclusion of the combined product Renotinex in the treatment regimen for patients with urolithiasis is pathogenetically justified.

Emplacement of a lamprophyric sheet swarm under ductile transpression in continental crust. Insights from a Variscan magmatic complex in the West Armorican belt, Western France

We present structural data from a Variscan magmatic complex of dominantly lamprophyric (kersantite) and associated felsic (microgranodiorite) sheets - the West Armorican swarm (WAS) - injected into Paleozoic metasedimentary series at the western extremity of a transpressional system in the Armorican belt, Western France. The comparative structural analysis of nearly 100 individual intrusive sheets and their host-rocks demonstrates that the WAS complex is a syntectonic magmatic structure which intruded during the onset of regional shortening via successive pulses alternating with three strain episodes (D1-D2-D3). The moderate/high dipping attitude of a great majority of intrusions, along with their prominent orientation parallel to the regional cleavage (S1), i.e. orthogonal to the direction of shortening, challenge theoretical predictions about magma-filled fractures in contractional settings. These apparently atypical features are reconciled in a kinematic model which emphasizes the influence of both host-rock planar anisotropies (S1 cleavage and D3 shear patterns) and structural inheritance on magma pathways, and instead hypothesizes the negligible role of the ambient stress field. Comparisons are attempted with syncollisional lamprophyre systems present in the European Variscides, and more especially in the SE Bohemian massif.

Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited

In the DarTG toxin-antitoxin system, the DarT toxin ADP-ribosylates single-stranded DNA (ssDNA), which stalls DNA replication and plays a crucial role in controlling bacterial growth and bacteriophage infection. This toxic activity is reversed by the N-terminal macrodomain of the cognate antitoxin DarG. DarG also binds DarT, but the role of these interactions in DarT neutralization is unknown. Here, we report that the C-terminal domain of DarG (DarG toxin-binding domain [DarGTBD]) interacts with DarT to form a 1:1 stoichiometric heterodimeric complex. We determined the 2.2Å resolution crystal structure of the Mycobacterium tuberculosis DarT-DarGTBD complex. The comparative structural analysis reveals that DarGTBD interacts with DarT at the DarT/ssDNA interaction interface, thus sterically occluding substrate ssDNA binding and consequently inactivating toxin by direct protein-protein interactions. Our data support a unique two-layered DarT toxin neutralization mechanism of DarG, which is important in keeping the toxin molecules in check under normal growth conditions.

A computational investigation of pyrrole borane as a potential hydrogen storage system

A detailed theoretical analysis of the unsaturated adduct pyrrole borane and its dehydrogenated counterpart has been performed to explore its capabilities towards hydrogen storage. Thermochemical parameters at CCSD(T) and CBS-QB3 level, B-N bond dissociation energies at CCSD(T) level and the potential energy surface associated with dehydrogenation at CBS-QB3 level have been investigated. A comparative structural analysis revealed that pyrrole borane has a longer dative B-N bond distance, and consequently a lower bond dissociation energy, compared to pyrrolidine borane. The predicted enthalpies of dehydrogenation at various temperatures indicates the hydrogen elimination reaction of pyrrole borane is more exothermic and not much closer to thermoneutrality than related saturated systems. Transition state structures for the BH3-catalysed dehydrogenation reaction pathways revealed that dehydrogenation of pyrrole borane should still be favoured over dissociation and calculated rate constants at different temperatures indicates hydrogen release from pyrrole borane with BH3 catalyst can be favoured even at 298 K.

Vanol-Supported Lanthanide Complexes for Strong Circularly Polarized Luminescence at 1550 nm.

Strong circularly polarized luminescence (CPL) at 1550 nm is reported from lanthanide complexes supported by Vanol; these are the first examples of coordination of Vanol to lanthanides. A change in the ligand design from a 1,1'-bi-2-naphthol (in Binol) to a 2,2'-bi-1-naphthol (in Vanol) results in significantly improved dissymmetry factors for (Vanol)3ErNa3 (|glum| = 0.64) at 1550 nm. This is the highest reported dissymmetry factor to date in the telecom C-band region, and among the highest for any lanthanide complexes. Comparative solid-state structural analysis of (Vanol)3ErNa3 and (Binol)3ErNa3 suggests that a less distorted geometry around the metal center is in part responsible for the high chiroptical metrics of (Vanol)3ErNa3. This phenomenon was further evidenced in the analogous ytterbium complexes (Vanol)3YbNa3 that also exhibit significantly improved dissymmetry factors (|glum| = 0.21). This confirms and generalizes the same observation that was made in other visibly emitting, six-coordinate lanthanide complexes. Due to their strong CPL at 1550 nm, the reported complexes are potential candidates for applications in quantum communication technologies. More importantly, our structure-CPL activity relationship study provides guidance towards the generation of even better near infrared-CPL emitters.

Scalable precision wide-field imaging in radio interferometry – II. AIRI validated on ASKAP data

ABSTRACT Accompanying Part I, this sequel delineates a validation of the recently proposed AI for Regularization in radio-interferometric Imaging (AIRI) algorithm on observations from the Australian Square Kilometre Array Pathfinder (ASKAP). The monochromatic AIRI-ASKAP images showcased in this work are formed using the same parallelized and automated imaging framework described in Part I: ‘uSARA validated on ASKAP data’. Using a Plug-and-Play approach, AIRI differs from uSARA by substituting a trained denoising deep neural network (DNN) for the proximal operator in the regularization step of the forward–backward algorithm during deconvolution. We build a trained shelf of DNN denoisers that target the estimated image dynamic ranges of our selected data. Furthermore, we quantify variations of AIRI reconstructions when selecting the nearest DNN on the shelf versus using a universal DNN with the highest dynamic range, opening the door to a more complete framework that not only delivers image estimation but also quantifies epistemic model uncertainty. We continue our comparative analysis of source structure, diffuse flux measurements, and spectral index maps of selected target sources as imaged by AIRI and the algorithms in Part I – uSARA and WSClean. Overall, we see an improvement over uSARA and WSClean in the reconstruction of diffuse components in AIRI images. The scientific potential delivered by AIRI is evident in further imaging precision, more accurate spectral index maps, and a significant acceleration in deconvolution time, whereby AIRI is four times faster than its subiterative sparsity-based counterpart uSARA.

Description of the Wild Strain Rhizobium rosettiformans DSM26376, Reclassified under Peteryoungia rosettiformans comb.nov., for Producing Glucuronan.

Glucuronan is a polysaccharide composed of β-(1,4)-linked d-glucuronic acids having intrinsic properties and biological activities recoverable in many fields of application. Currently, the description of Sinorhyzobium meliloti M5N1CS mutant bacterial strain as the sole source of glucuronan makes it relevant to the exploration of new microorganisms producing glucuronan. In this study, the Peteryoungia rosettifformans strain (Rhizobia), was identified as a wild producer of an exopolysaccharide (RhrBR46) related to glucuronan. Structural and biochemical features, using colorimetric assays, Fourier infrared spectroscopy, nuclear magnetic resonance, high pressure size exclusion chromatography coupled to multi-angle light laser scattering, and enzymatic assays allowed the characterization of a polyglucuronic acid, having a molecular mass (Mw¯) of 1.85 × 105 Da, and being partially O-acetylated at C-2 and/or C-3 positions. The concentration of Mg2+ ions in the cultivation medium has been shown to impact the structure of RhrBR46, by reducing drastically its Mw¯ (73%) and increasing its DA (10%). Comparative structural analyses between RhrBR46 and the glucuronan from Sinorhyzobium meliloti M5N1CS strain revealed differences in terms of molecular weight, degree of acetylation (DA), and the distribution of acetylation pattern. These structural divergences of RhrBR46 might contribute to singular properties or biological activities of RhrBR46, offering new perspectives of application.

Structural insights into a regulatory mechanism of FIR RRM1-FUSE interaction.

FUBP-interacting repressor (FIR) is a suppressor of transcription of the proto-oncogene MYC. FIR binds to the far upstream element (FUSE) of the MYC promoter. Competition of FIR with FUSE-binding protein 1 (FUBP1) is a key mechanism of MYC transcriptional regulation. To gain insights into the structural mechanisms regulating FIR DNA interaction, we determined the crystal structure of two FIR RRM domains (RRM1-2) with single-stranded FUSE DNA sequences. These structures revealed an ability of the RRM domain to recognize diverse FUSE regions through distinct intermolecular interactions and binding modes. Comparative structural analyses against available RRM-ssDNA/RNA complexes showed that the nucleotide configurations in FIR were similar to those in other RRMs that harbour a tyrosine at the conserved aromatic position in the RNP2 motif (Y-type RRM), but not those with a phenylalanine (F-type RRM). Site-directed mutagenesis experiments demonstrated that a single substitution, Y115F, altered the binding affinities of oligonucleotides to FIR RRM, suggesting an important role of this conserved aromatic residue in ssDNA/RNA interactions. Our study provides the structural basis for further mechanistic studies on this important protein-DNA interaction.