The Mitochondrial Genomes of Siboglinum plumosum and Oligobrachia dogieli (Annelida: Siboglinidae) and Their Phylogenetic Analysis.

Frenulates are a group of sedentary Annelida within the family Siboglinidae that inhabit the ocean floor and present a unique challenge for comprehensive molecular and phylogenetic investigations. In this study, we focused on the frenulates, specifically assembling the mitochondrial genomes of Siboglinum plumosum and Oligobrachia dogieli. The phylogenetic reconstruction placed S. plumosum as a sister taxon to S. ekmani, and O. dogieli as a sister taxon to S. fiordicum, supporting the non-monophyletic nature of the genus Siboglinum. Overall, this study supports the phylogeny of the family Siboglinidae while highlighting the need for additional molecular data within frenulates.

Spin Crossover and Thermochromism in Iron(II) Complexes with 2,6-Bis(1H-imidazol-2-yl)-4-methoxypyridine.

New iron(II) complexes with 2,6-bis(1H-imidazol-2-yl)-4-methoxypyridine (L) of the composition [FeL2]An∙mH2O (A = SO42-, n = 1, m = 2 (I); A = ReO4-, n = 2, m = 1 (II); A = Br-, n = 2, m = 2 (III)) have been synthesized and investigated. To determine the coordination ability of the ligand, a single crystal of a copper(II) complex of the composition [CuLCl2] (IV) was obtained and studied by X-ray technique. Compounds I-III were studied using methods of X-ray phase analysis, electron (diffuse reflection spectra), infrared and Mössbauer spectroscopy, static magnetic susceptibility. The study of the µeff(T) dependence showed that the 1A1 ↔ 5T2 spin crossover manifests itself in the compounds. The spin crossover is accompanied by thermochromism: there is a distinct color change orange ↔ red-violet.

Tear nanoDSF Denaturation Profile Is Predictive of Glaucoma.

Primary open-angle glaucoma (POAG) is a frequent blindness-causing neurodegenerative disorder characterized by optic nerve and retinal ganglion cell damage most commonly due to a chronic increase in intraocular pressure. The preservation of visual function in patients critically depends on the timeliness of detection and treatment of the disease, which is challenging due to its asymptomatic course at early stages and lack of objective diagnostic approaches. Recent studies revealed that the pathophysiology of glaucoma includes complex metabolomic and proteomic alterations in the eye liquids, including tear fluid (TF). Although TF can be collected by a non-invasive procedure and may serve as a source of the appropriate biomarkers, its multi-omics analysis is technically sophisticated and unsuitable for clinical practice. In this study, we tested a novel concept of glaucoma diagnostics based on the rapid high-performance analysis of the TF proteome by differential scanning fluorimetry (nanoDSF). An examination of the thermal denaturation of TF proteins in a cohort of 311 ophthalmic patients revealed typical profiles, with two peaks exhibiting characteristic shifts in POAG. Clustering of the profiles according to peaks maxima allowed us to identify glaucoma in 70% of cases, while the employment of artificial intelligence (machine learning) algorithms reduced the amount of false-positive diagnoses to 13.5%. The POAG-associated alterations in the core TF proteins included an increase in the concentration of serum albumin, accompanied by a decrease in lysozyme C, lipocalin-1, and lactotransferrin contents. Unexpectedly, these changes were not the only factor affecting the observed denaturation profile shifts, which considerably depended on the presence of low-molecular-weight ligands of tear proteins, such as fatty acids and iron. Overall, we recognized the TF denaturation profile as a novel biomarker of glaucoma, which integrates proteomic, lipidomic, and metallomic alterations in tears, and monitoring of which could be adapted for rapid non-invasive screening of the disease in a clinical setting.

High-Temperature Spin Crossover in Iron(II) Complexes with 2,6-Bis(1H-imidazol-2-yl)pyridine.

Novel iron(II) coordination compounds containing a ligand 2,6-bis(1H-imidazol-2-yl)pyridine (L), having such a composition as [FeL2]SO4·0.5H2O, [FeL2]Br2·H2O, [FeL2](ReO4)2, [FeL2]B10H10∙H2O, [FeL2]B12H12∙1.5H2O had been synthesized and studied using UV-Vis (diffuse reflectance), infrared, extended X-ray absorption fine structure (EXAFS), and Mössbauer spectroscopy methods, as well as X-ray diffraction and static magnetic susceptibility methods. The analysis of the µeff(T) dependence in the temperature range of 80-600 K have shown that all the obtained complexes exhibit a high-temperature spin crossover 1A1 ↔ 5T2.

Interplay of Environmental, Individual and Genetic Factors in Rheumatoid Arthritis Provocation.

In this review, we explore systemization of knowledge about the triggering effects of non-genetic factors in pathogenic mechanisms that contribute to the development of rheumatoid arthritis (RA). Possible mechanisms involving environmental and individual factors in RA pathogenesis were analyzed, namely, infections, mental stress, sleep deprivation ecology, age, perinatal and gender factors, eating habits, obesity and smoking. The non-genetic factors modulate basic processes in the body with the impact of these factors being non-specific, but these common challenges may be decisive for advancement of the disease in the predisposed body at risk for RA. The provocation of this particular disease is associated with the presence of congenital loci minoris resistentia. The more frequent non-genetic factors form tangles of interdependent relationships and, thereby, several interdependent external factors hit one vulnerable basic process at once, either provoking or reinforcing each other. Understanding the specific mechanisms by which environmental and individual factors impact an individual under RA risk in the preclinical stages can contribute to early disease diagnosis and, if the factor is modifiable, might be useful for the prevention or delay of its development.

Morphological and Structural Transformations of Fe-Pd Powder Alloys Formed by Galvanic Replacement, Annealing and Acid Treatment.

In this article, we report the preparation and structural features of Fe-Pd powder alloys formed by galvanic replacement, annealing and selective dissolution of iron via acid treatment. The alloys were studied by the X-ray diffraction phase analysis, Mössbauer spectroscopy, scanning electron microscopy, and energy-dispersive spectroscopy. The Fe@Pd core-shell particles were obtained by a galvanic replacement reaction occurring upon treatment of a body-centered cubic (bcc) iron powder by a solution containing PdCl42- ions. It was found that the shells are a face-centered cubic (fcc) Pd(Fe) solid solution. HCl acid treatment of the Fe@Pd core-shell particles resulted in the formation of hollow Pd-based particles, as the bcc phase was selectively dissolved from the cores. Annealing of the Fe@Pd core-shell particles at 800 °C led to the formation of fcc Fe-Pd solid solution. Acid treatment of the Fe-Pd alloys formed by annealing of the core-shell particles allowed selectively dissolving iron from the bcc Fe-based phase (Fe(Pd) solid solution), while the fcc Fe-rich Fe-Pd solid solution remained stable (resistant to acid corrosion). It was demonstrated that the phase composition and the Fe/Pd ratio in the alloys (phases) can be tailored by applying annealing and/or acid treatment to the as-synthesized Fe@Pd core-shell particles.

Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome.

The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations.

Identifying Performance Descriptors in CO2 Hydrogenation over Iron-Based Catalysts Promoted with Alkali Metals.

Alkali metal promoters have been widely employed for preparation of heterogeneous catalysts used in many industrially important reactions. However, the fundamentals of their effects are usually difficult to access. Herein, we unravel mechanistic and kinetic aspects of the role of alkali metals in CO2 hydrogenation over Fe-based catalysts through state-of-the-art characterization techniques, spatially resolved steady-state and transient kinetic analyses. The promoters affect electronic properties of iron in iron carbides. These carbide characteristics determine catalyst ability to activate H2 , CO and CO2 . The Allen scale electronegativity of alkali metal promoter was successfully correlated with the rates of CO2 hydrogenation to higher hydrocarbons and CH4 as well as with the rate constants of individual steps of CO or CO2 activation. The derived knowledge can be valuable for designing and preparing catalysts applied in other reactions where such promoters are also used.

Elimination of Composition Segregation in 33Al-45Cu-22Fe (at.%) Powder by Two-Stage High-Energy Mechanical Alloying.

In the present work, complex powder alloys containing spinel as a minor phase were produced by mechanical alloying in a high-energy planetary ball mill from a 33Al-45Cu-22Fe (at.%) powder blend. These alloys show characteristics suitable for the synthesis of promising catalysts. The alloying was conducted in two stages: at the first stage, a Cu+Fe powder mixture was ball-milled for 90 min; at the second stage, Al was added, and the milling process was continued for another 24 min. The main products of mechanical alloying formed at each stage were studied using X-ray diffraction phase analysis, Mössbauer spectroscopy, transmission electron microscopy, and energy-dispersive spectroscopy. At the end of the first stage, crystalline iron was not found. The main product of the first stage was a metastable Cu(Fe) solid solution with a face-centered cubic structure. At the second stage, the Cu(Fe) solid solution transformed to Cu(Al), several Fe-containing amorphous phases, and a spinel phase. The products of the two-stage process were different from those of the single-stage mechanical alloying of the ternary elemental powder mixture; the formation of undesirable intermediate phases was avoided, which ensured excellent composition uniformity. A sequence of solid-state reactions occurring during mechanical alloying was proposed. Mesopores and a spinel phase were the features of the two-stage milled material (both are desirable for the target catalyst).

New iodine-apatites: synthesis and crystal structure.

The paper describes methods for the preparation of compounds with an apatite structure containing only iodine atoms in the "halogen" position. The crystal structure of the compounds was refined by the Rietveld method. The resulting apatites have a structure with a space group P63/m and have the following unit cell parameters: Ba4 f 1.78(2)Ba6 h 2.75(2)(PO4)3I0.04(2) (a = 10.18609(34) Å, c = 7.71113(30) Å, V = 692.889(54) Å3, R = 5.448 %), Pb4 f 1.82(2)Pb6 h 2.75(2)(PO4)3I0.13(2) (a = 9.87882(18) Å, c = 7.43222(16) Å, V = 628.144(26) Å3, R = 8.533 %), Pb4 f 1.90(2)Pb6 h 2.68(2)(PO4)3I0.16(2) (a = 9.87058(48) Å, c = 7.41255(46) Å, V = 625.437(72) Å3, R = 5.433 %). The study of the crystal structure showed a relatively low efficiency of the binding of iodine in the apatite matrix.

Combination of Multiple Microsatellite Analysis and Genome-Wide SNP Genotyping Helps to Solve Wildlife Crime: A Case Study of Poaching of a Caucasian tur (Capra caucasica) in Russian Mountain National Park.

Poaching is one of the major types of wildlife crime in Russia. Remnants of goats (presumably the wild endemic species, the Caucasian tur) were found in an area of the Caucasian mountains. The case study involves a suspected poacher whose vehicle was found to have two duffel bags containing pieces of a carcass, which he claimed was that of a goat from his flock. The aim of the forensic genetic analysis for this case was to (i) establish individual identity and (ii) perform species identification. DNA typing based on fourteen microsatellites revealed that STR-genotypes generated from pieces of evidence found at crime scene fully matched those obtained from the evidence seized from the suspect. The results of genome-wide SNP-genotyping, using Illumina Goat SNP50 BeadChip, provided evidence that the poached animal was a wild Caucasian tur (Capra caucasica). Thus, based on comprehensive molecular genetic analysis, evidence of poaching was obtained and sent to local authorities. To our knowledge, this case study is the first to attempt to use DNA chips in wildlife forensics of ungulates.

Targeted Lipidomic Analysis of Aqueous Humor Reveals Signaling Lipid-Mediated Pathways in Primary Open-Angle Glaucoma.

Primary open-angle glaucoma (POAG) is characterized by degeneration of retinal ganglion cells associated with an increase in intraocular pressure (IOP) due to hindered aqueous humor (AH) drainage through the trabecular meshwork and uveoscleral pathway. Polyunsaturated fatty acids and oxylipins are signaling lipids regulating neuroinflammation, neuronal survival and AH outflow. Among them, prostaglandins have been previously implicated in glaucoma and employed for its treatment. This study addressed the role of signaling lipids in glaucoma by determining their changes in AH accompanying IOP growth and progression of the disease. Eye liquids were collected from patients with POAG of different stages and cataract patients without glaucoma. Lipids were identified and quantified by UPLC-MS/MS. The compounds discriminating glaucoma groups were recognized using ANCOVA and PLS-DA statistic approaches and their biosynthetic pathways were predicted by bioinformatics. Among 22 signaling lipids identified in AH, stage/IOP-dependent alterations in glaucoma were provided by a small set of mediators, including 12,13-DiHOME, 9- and 13-HODE/KODE, arachidonic acid and lyso-PAF. These observations correlated with the expression of cytochromes P450 (CYPs) and phospholipases A2 in the ocular tissues. Interestingly, tear fluid exhibited similar lipidomic alterations in POAG. Overall, POAG may involve arachidonic acid/PAF-dependent pathways and oxidative stress as evidenced from an increase in its markers, KODEs and 12,13-DiHOME. The latter is a product of CYPs, one of which, CYP1B1, is known as POAG and primary congenital glaucoma-associated gene. These data provide novel targets for glaucoma treatment. Oxylipin content of tear fluid may have diagnostic value in POAG.

Simulation of collision-induced absorption spectra based on classical trajectories and ab initio potential and induced dipole surfaces. II. CO2-Ar rototranslational band including true dimer contribution.

This paper presents further development of the new semi-classical trajectory-based formalism described in Paper I [Chistikov et al., J. Chem. Phys. 151, 194106 (2019)]. We report the results of simulation and analysis of the low-frequency collision-induced absorption (CIA) in CO2-Ar, including its true dimer component. Our consideration relies on the use of ab initio intermolecular potential energy and induced dipole surfaces for CO2-Ar calculated in an assumption of a rigid CO2 structure using the CCSD(T) method. The theory, the details of which are reported in Paper I [Chistikov et al., J. Chem. Phys. 151, 194106 (2019)], permits taking into account the effect of unbound and quasi-bound classical trajectories on the CIA in the range of a rototranslational band. This theory is largely extended by trajectory-based simulation of the true bound dimer absorption in the present paper. The spectra are obtained from a statistical average over a vast ensemble of classical trajectories restricted by properly chosen domains in the phase space. Rigorous classical theory is developed for two low-order spectral moments interpreted as the Boltzmann-weighted average of the respective dipole functions. These spectral moments were then used to check the accuracy of our trajectory-based spectra, for which both spectral moments can be evaluated independently in terms of specific integrals over the trajectory-based calculated spectral profiles. Good agreement between the spectral moments calculated as integrals over the frequency domain or the phase space largely supports the reliability of our simulated CIA spectra, which conform with the available microwave and far-infrared observations.

Seroprevalence and B1 gene genotyping of Toxoplasma gondii in farmed European mink in the Republic of Tatarstan, Russia.

Toxoplasma gondii is a protozoan parasite that infects almost all species of mammals and birds, including fur-bearing animals. However, the prevalence of T. gondii among Russian fur-bearing animals is unknown. In this study, the seroprevalence of T. gondii in European mink in Russia was investigated. In total, 100, 119 and 61 serum samples were collected from a fur farm, located in the Republic of Tatarstan, Russia, in autumn 2016, 2017 and 2018, respectively. The seroprevalence of T. gondii in 2016, 2017 and 2018 was 32% (23.2%-42.2%, 95% confidence interval [CI]), 31.1% (23.1%-40.3%, 95% CI) and 41.0% (28.8%-54.3%, 95% CI), respectively. In total, 50 brain samples from 100 animals whose blood was sampled in 2016 were analyzed by PCR to detect T. gondii DNA. T. gondii DNA was detected in 14% (7/50) of the mink brain samples. To examine single nucleotide polymorphisms (SNPs) in the partial B1 gene, we sequenced an 836-bp fragment, which contains a few SNPs, from the detected T. gondii DNA. The sequences of the fragments were identical to those of two of the major lineages, Type II and Type III, but differed from that of the Type I lineage.

Simulation of collision-induced absorption spectra based on classical trajectories and ab initio potential and induced dipole surfaces. I. Case study of N2-N2 rototranslational band.

This paper presents theoretical formalism and some results of the collision-induced absorption (CIA) spectral simulation based on the classical trajectory analysis. Our consideration relies on the use of ab initio potential energy and dipole moment surfaces for two interacting rigid monomers. Rigorous intermolecular Hamiltonian is represented and used in the body-fixed reference frame. The complete set of dynamical equations with Boltzmann-weighted initial conditions is solved to render a large number of classical trajectories. The spectral shape is calculated as an ensemble-averaged Fourier spectrum issued from the time-dependent induced dipole along individual scattering trajectories. Considering a pair of N2 molecules as an example, we have calculated the rototranslational CIA band profiles at T = 78, 89, 109, 129, 149, 179, 228, 300, and 343 K. The classical trajectory-based spectral shape was corrected to satisfy the quantum principle of detailed balance. Good accuracy of our semiclassical approach was demonstrated by comparison with available experimental data as well as with results of the previously published purely quantum simulation by Karman et al. [J. Chem. Phys. 142, 084306 (2015)] in which the same ab initio calculated N2-N2 potential energy and induced dipole moment surfaces were used.

Comprehensive classical analysis of partition function and some observables for weakly interacting polyatomic dimers.

This paper presents the systematic classical consideration of a statistical averaging procedure that permits the calculation of partition function, equilibrium constant, and some observables for polyatomic dimers composed of weakly interacting rigid monomers. It was shown that the number of independent internal coordinates in a body-fixed frame is a crucial parameter that largely determines the temperature dependence of the partition function irrespective of the kinematic coupling within various degrees of freedom. The kinetic energy was derived for the molecular pair of arbitrary complexity in the body-fixed frame. Rigorous expression was obtained for the partition function over a pre-selected domain in the phase space. A similar expression was applicable to perform statistical averaging of some observables. Taking a linear molecule-atom as an example, it was shown how the suggested general approach permits the calculation of the equilibrium constant for true bound dimer formation or zeroth spectral moment of a collision-induced absorption band.

A technique of hand digit reconstruction using scarred and deformed donor segments.

BACKGROUND: Hand digit reconstruction with transposition of hand segments in cases of hand injury is not used frequently by surgeons, at least in part because of potential ischemic complications after cicatricial changes in tissues. The aim of this study was to investigate the opportunities for expanding the set of indications for hand digit reconstruction using scarred and deformed donor segments. METHODS: We developed a technique of ischemic preconditioning and preforming the segment before transfer to improve macro-circulation and micro-circulation in scarred donor segments with a view to preventing ischemic complications in reconstructed digits. It was validated using clinical, radiological, morphological, and biophysical (IR imaging, laser Doppler flowmetry, rheovasography) methods. RESULTS: A total of 184 patients were included. Primary digit reconstruction was performed in 19 patients while secondary reconstruction-in 165 patients. Single-stage transfer was performed in 122 hands, delayed transfer-in 67 hands. The total number of reconstructed thumbs and fingers was 203. Digit viability, stability, mobility and range of motion were very good with the use of new technique. CONCLUSIONS: When transferring hand segments with severe and highly severe deformations, tissue scarring and vascular damage, it is beneficial to pre-train the donor segment against hypoxia by both exsanguination and surgical methods.

Musculoskeletal and nervous systems of the attachment organ in three species of Diplectanum (Monogenea: Dactylogyroidea).

The taxonomy of Diplectanum Diesing, 1858, a genus of monopisthocotylean monogeneans, remains unsettled and needs to be revised based on new morphological criteria. Recent studies in monopisthocotyleans have shown that the muscle arrangement in the posterior attachment organ (haptor) differs between congeneric species and can be used as an additional criterion in genus-level taxonomy. To explore the possibility of using the haptoral musculature and nervous system in the taxonomy of Diplectanum, we conducted a detailed confocal-microscopy study of three species of Diplectanum (D. aculeatum Parona et Perugia, 1889, D. sciaenae van Beneden et Hesse, 1863 and D. similis Bychowsky, 1957) with phalloidin staining for muscle and indirect immunostaining for 5HT and FMRFamide. A further goal was to clarify the functional mechanics of the haptor and the role of its essential components (squamodiscs and anchors) in attachment to the host. The system of connecting bars and gaffing anchors was found to have a complex musculature consisting of 23 muscles in D. aculeatum and D. sciaenae, and 21 muscles in D. similis. The squamodiscs were shown to be operated by several groups of muscles attached primarily to the area termed the squamodisc fulcrum. Most of the haptoral musculature is identical in D. aculeatum and D. sciaenae and these species differ only in the presence of a muscle sheath around the tissue strand between the squamodiscs in D. sciaenae and in the different patterns of superficial squamodisc muscles. Diplectanum similis shows more significant differences from the other two species: besides lacking two of the haptoral muscles, it also differs in the shapes and arrangement of several other muscles. The nervous system of all three species conforms to the general pattern typical for the Dactylogyroidea and shows little variation between species.

Rapid spread of influenza A(H1N1)pdm09 viruses with a new set of specific mutations in the internal genes in the beginning of 2015/2016 epidemic season in Moscow and Saint Petersburg (Russian Federation).

A dramatic increase of influenza activity in Russia since week 3 of 2016 significantly differs from previous seasons in terms of the incidence of influenza and acute respiratory infection (ARI) and in number of lethal cases. We performed antigenic analysis of 108 and whole-genome sequencing of 77 influenza A(H1N1)pdm09 viruses from Moscow and Saint Petersburg. Most of the viruses were antigenically related to the vaccine strain. Whole-genome analysis revealed a composition of specific mutations in the internal genes (D2E and M83I in NEP, E125D in NS1, M105T in NP, Q208K in M1, and N204S in PA-X) that probably emerged before the beginning of 2015/2016 epidemic season.

Neoadjuvant Chemotherapy Using Reduced-Dose Docetaxel Followed by Radical Prostatectomy for Patients With Intermediate and High-Risk Prostate Cancer: A Single-Center Study.

BACKGROUND: To assess safety, pathologic response rate, and long-term oncologic outcomes of radical prostatectomy (RP) after neoadjuvant chemotherapy using reduced-dose docetaxel without androgen-deprivation therapy in prostate cancer (PCa) patients of intermediate- and high-risk groups. METHODS: Forty-four patients with PCa (PSA > 10 ng/ml, Gleason score 7 or more, or clinical stage cT2c or more) were included with a median follow-up of 11.4 years after RP. One group (NCT/RP) received neoadjuvant treatment 3-weekly with docetaxel (36 mg/m(2) for up to six cycles, 21 patients), the other (control) group (RP, 23 patients) received RP only. RESULTS: Toxicities were mild with grade 3 events not exceeding 10%. A statistically significant reduction of PSA > 50% post-chemotherapy was observed in 52.4% cases. Cancer-specific survival (CSS) was 90% in the NCT/RP group and 60.9% in the RP group (P = 0.042). The biochemical recurrence-free survival was 68.5% in the NCT/RP and 37.7% in the RP groups; overall survival was 75.5% and 54.6%, respectively (both P > 0.05). CONCLUSIONS: The use of neoadjuvant chemotherapy before RP in a selected regimen and dose represents a safe strategy and results in benefits in CSS. Given the limitations of the study, this concept should be evaluated in large, prospective, controlled studies. Prostate 76: 1345-1352, 2016. © 2016 Wiley Periodicals, Inc.