Lateral Flow Assay Biotesting by Utilizing Plasmonic Nanoparticles Made of Inexpensive Metals─Replacing Colloidal Gold.

Nanoparticles (NPs) can be conjugated with diverse biomolecules and employed in biosensing to detect target analytes in biological samples. This proven concept was primarily used during the COVID-19 pandemic with gold-NP-based lateral flow assays (LFAs). Considering the gold price and its worldwide depletion, here we show that novel plasmonic NPs based on inexpensive metals, titanium nitride (TiN) and copper covered with a gold shell (Cu@Au), perform comparable to or even better than gold nanoparticles. After conjugation, these novel nanoparticles provided high figures of merit for LFA testing, such as high signals and specificity and robust naked-eye signal recognition. Since the main cost of Au NPs in commercial testing kits is the colloidal synthesis, our development with the Cu@Au and the laser-ablation-fabricated TiN NPs is exciting, offering potentially inexpensive plasmonic nanomaterials for various bioapplications. Moreover, our machine learning study showed that biodetection with TiN is more accurate than that with Au.

Lateral Flow Assays Biotesting by Utilizing Plasmonic Nanoparticles Made of Inexpensive Metals - Replacing Colloidal Gold.

Nanoparticles (NPs) can be conjugated with diverse biomolecules and employed in biosensing to detect target analytes in biological samples. This proven concept was primarily used during the COVID-19 pandemic with gold NPs-based lateral flow assays (LFAs). Considering the gold price and its worldwide depletion, here we show that novel plasmonic nanoparticles (NPs) based on inexpensive metals, titanium nitride (TiN) and copper covered with a gold shell (Cu@Au), perform comparable or even better than gold nanoparticles. After conjugation, these novel nanoparticles provided high figures of merit for LFA testing, such as high signals and specificity and robust naked-eye signal recognition. To the best of our knowledge, our study represents the 1st application of laser-ablation-fabricated nanoparticles (TiN) in the LFA and dot-blot biotesting. Since the main cost of the Au NPs in commercial testing kits is in the colloidal synthesis, our development with TiN is very exciting, offering potentially very inexpensive plasmonic nanomaterials for various bio-testing applications. Moreover, our machine learning study showed that the bio-detection with TiN is more accurate than that with Au.

West-Siberian Chernozem: How Vegetation and Tillage Shape Its Bacteriobiome.

Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs' richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0-5 cm of the undisturbed soil. As for the ß-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production.

Pharmacokinetic and Pharmacogenetic Predictors of Major Bleeding Events in Patients with an Acute Coronary Syndrome and Atrial Fibrillation Receiving Combined Antithrombotic Therapy.

Objective: This study's objective was to evaluate the effects of pharmacokinetic and pharmacogenetic factors on major bleeding in patients with ACS and non-valvular AF receiving combined antithrombotic therapy consisting of rivaroxaban, clopidogrel, and aspirin as part of dual or triple therapy. Methods: A prospective observational study was conducted in two PCI centers in Moscow, the Russian Federation, from 2017 to 2018. One hundred patients with ACS and AF were enrolled. Prospective follow-ups continued for 12 months. Results: A total of 36 patients experienced bleeding events, with 10 experiencing major bleeding based on the BARC scale and 17 experiencing major bleeding based on the ISTH scale. The following predictors associated with an increased number of major bleeding events were identified: for the ISTH scale, a Css min. of rivaroxaban of >137 pg/mL (5.94 OR, (95% CI, 3.13-12.99; p < 0.004)) and carriage of the T allelic variant polymorphism ABCB1 rs4148738 (8.97 OR (95% CI, 1.48-14.49; p < 0.017)), as well as for the BARC scale (5.76 OR (95% CI, 2.36-9.87; p < 0.018)). Conclusions: Measuring residual steady-state rivaroxaban concentrations and determining the carriage of the T allelic variant polymorphism ABCB1 rs4148738 may be applicable to high-risk patients for subsequent antithrombotic therapy modification.

Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems.

The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.

Soil Mycobiome Diversity under Different Tillage Practices in the South of West Siberia.

Managing soil biodiversity by reduced or no tillage is an increasingly popular approach. Soil mycobiome in Siberian agroecosystems has been scarcely studied; little is known about its changes due to tillage. We studied mycobiome in Chernozem under natural steppe vegetation and cropped for wheat by conventional or no tillage in a long-term field trial in West Siberia, Russia, by using ITS2 rDNA gene marker (Illumina MiSeq sequencing). Half of the identified OTUs were Ascomycota with 82% of the total number of sequence reads and showing, like other phyla (Basidiomycota, Zygomycota, Mortierellomycota, Chytridiomycota, Glomeromycota), field-related differential abundance. Several dominant genera (Mortierella, Chaetomium, Clonostachys, Gibberella, Fusarium, and Hypocrea) had increased abundance in both cropped soils as compared with the undisturbed one and therefore can be safely assumed to be associated with wheat residues. Fungal OTUs' richness in cropped soils was less than in the undisturbed one; however, no tillage shifted soil mycobiome composition closer to the latter, albeit, it was still similar to the ploughed soil, despite different organic matter and wheat residue content. The study provided the first inventory of soil mycobiome under different tillage treatments in the south of West Siberia, where wheat production is an important section of the regional economy.

Potential of TiN/GaN Heterostructures for Hot Carrier Generation and Collection.

Herein, we find that TiN sputter-deposited on GaN displayed the desired optical properties for plasmonic applications. While this is a positive result indicating the possible use of p- or n-type GaN as a collector of plasmonically generated hot carriers, the interfacial properties differed considerably depending on doping conditions. On p-type GaN, a distinct Schottky barrier was formed with a barrier height of ~0.56 eV, which will enable effective separation of photogenerated electrons and holes, a typical approach used to extend their lifetimes. On the other hand, no transport barrier was found for TiN on n-type GaN. While the lack of spontaneous carrier separation in this system will likely reduce unprompted hot carrier collection efficiencies, it enables a bias-dependent response whereby charges of the desired type (e.g., electrons) could be directed into the semiconductor or sequestered in the plasmonic material. The specific application of interest would determine which of these conditions is most desirable.

Genome-wide DNA methylation profiling identifies epigenetic changes in CD4+ and CD14+ cells of multiple sclerosis patients.

Multiple sclerosis (MS) is a chronic autoimmune and degenerative disease of the central nervous system, which develops in genetically predisposed individuals upon exposure to environmental influences. Environmental triggers of MS, such as viral infections or smoking, were demonstrated to affect DNA methylation, and thus to involve this important epigenetic mechanism in the development of pathological process. To identify MS-associated DNA methylation hallmarks, we performed genome-wide DNA methylation profiling of two cell populations (CD4+ T-lymphocytes and CD14+ monocytes), collected from the same treatment-naive relapsing-remitting MS patients and healthy subjects, using Illumina 450 K methylation arrays. We revealed significant changes in DNA methylation for both cell populations in MS. In CD4+ cells of MS patients the majority of differentially methylated positions (DMPs) were shown to be hypomethylated, while in CD14+ cells - hypermethylated. Differential methylation of HLA-DRB1 gene in CD4+ and CD14+ cells was associated with carriage of DRB1*15 allele independently from the disease status. Besides, about 20% of identified DMPs were shared between two cell populations and had the same direction of methylation changes; they may be involved in basic epigenetic processes occuring in MS. These findings suggest that the epigenetic mechanism of DNA methylation in immune cells contributes to MS; further studies are now required to validate these results and understand their functional significance.

Surface- and Structural-Dependent Reactivity of Titanium Oxide Nanostructures with 2-Chloroethyl Ethyl Sulfide under Ambient Conditions.

Robust materials capable of heterogeneous reactivity are valuable for addressing toxic chemical clean up. Synthetic manipulations for generating titanium oxide nanomaterials have been utilized to alter both photochemical (1000 nm > λ > 400 nm) and chemical heterogeneous reactivity with 2-chloroethyl ethyl sulfide (2-CEES). Synthesizing TiO2 nanomaterials in the presence of long-chain alkylphosphonic acids enhanced the visible light-driven oxidation of the thioether sulfur of 2-CEES. Photooxidation reaction rates of 99 and 168 µmol/g/h (quantum yields of 5.07 × 10-4 and 8.58 × 10-4 molecules/photon, respectively) were observed for samples made with two different alkylphosphonic acids (C14H29PO3H2 and C9H19PO3H2, respectively). These observations are correlated with (i) generation of new surface defects/states (i.e., oxygen vacancies) as a result of TiO2 grafting by alkylphosphonic acid that may serve as reaction active sites, (ii) better light absorption by assemblies of nanorods and nanowires in comparison to individual nanorods, (iii) surface area differences, and (iv) the exclusion of OH groups due to the surface functionalization with alkylphosphonic acids via Ti-O-P bonds on the TiO2. Alternatively, nanowire-form H2Ti2O5·H2O was produced and found to be capable of highly efficient hydrolysis of the carbon-chlorine (C-Cl) bond of 2-CEES in the dark with a reaction rate of 279.2 µmol/g/h due to the high surface area and chemical nature of the titanate structure.

Complete Genome of Sinorhizobium meliloti AK76, a Symbiont of Wild Diploid Medicago lupulina from the Mugodgary Mountain Region.

Sinorhizobium meliloti is a symbiotic bacterial species forming nitrogen-fixing nodules on roots of annual and perennial Medicago spp. We report the full genome sequence of S. meliloti strain AK76, an effective symbiont of the wild diploid plant Medicago lupulina grown in the Mugodgary Mountain region, Kazakhstan.

Influence of Clinically Significant Genes on Antiplatelet Effect of Clopidogrel and Clinical Outcomes in Patients with Acute Coronary Syndrome and Atrial Fibrillation.

INTRODUCTION: The interindividual variability of the antiplatelet effect of clopidogrel is determined by multiple clinical and genetic factors. A lot of genotype-oriented studies have concentrated on the impact of CYP2C19 gene polymorphisms on platelet aggregation in patients receiving clopidogrel. However, the influence of this polymorphism may be only 12-20%, so other genetic markers should also be investigated. The aim of this work was to study the impact of carriage of CES1, PON1, ABCG2, CYP4F2, CYP3A4, IGTB3, P2Y12, PEAR1, and B4GALT2 polymorphisms on antiplatelet effect of clopidogrel and clinical outcomes in patients with acute coronary syndrome (ACS) and atrial fibrillation (AF). METHODS: 103 patients who underwent ACS with or without percutaneous coronary intervention and concomitant nonvalvular AF were included in an open multicenter prospective study to assess efficacy and safety of combined antithrombotic therapy. The study assessed the frequency of different primary clinical outcomes (incidence of major bleeding, hospital mortality, cardiovascular mortality, stroke and transient ischemic attacks (TIAs), renal mortality) and secondary outcomes (resistance to therapy - high residual platelet reactivity, excessive platelet suppression). Residual platelet reactivity was examined using the VerifyNow system (Accumetrics, Latham, NY, USA). RESULTS: None of the studied genetic markers had no statistically significant effect on the antiaggregant response to clopidogrel in patients with ACS and AF. However, CYP4F2 C(Val433Met) T, PEAR1 rs41273215 C>T were statistically significantly associated with an increased frequency of bleeding on antithrombotic therapy. B4GALT2 rs1061781 was statistically significantly associated with increased frequency of strokes and TIA. CONCLUSION: In our study, we determined that carriers of CYP4F2 gene polymorphisms C(Val433Met)T, PEAR1 rs41273215 C>T (CT+TT) were associated with lower safety of antithrombotic therapy in patients with ACS and AF. And, the B4GALT2 rs1061781 gene polymorphism was associated with a greater risk of insufficient efficacy of the therapy. The data obtained in our study may improve the understanding of the effect of less studied genetic markers on the efficacy and safety of antithrombotic therapy in patients with ACS and AF.

Complete Genome Sequence of Sinorhizobium meliloti S35m, a Salt-Tolerant Isolate from Alfalfa Rhizosphere in Soil Native to the Caucasus Region.

The genome of a symbiotically effective salt-tolerant strain, Sinorhizobium meliloti S35m, isolated from alfalfa rhizosphere in soil native to the Caucasus region, was sequenced. Genomic islands, prophages, and elements of a potential CRISPR/Cas I type (Cas3_0_I) system were identified in the genome.

Autographivirinae Bacteriophage Arno 160 Infects Pectobacterium carotovorum via Depolymerization of the Bacterial O-Polysaccharide.

Phytopathogenic bacteria belonging to the Pectobacterium and Dickeya genera (soft-rot Pectobacteriaceae) are in the focus of agriculture-related microbiology because of their diversity, their substantial negative impact on the production of potatoes and vegetables, and the prospects of bacteriophage applications for disease control. Because of numerous amendments in the taxonomy of P. carotovorum, there are still a few studied sequenced strains among this species. The present work reports on the isolation and characterization of the phage infectious to the type strain of P. carotovorum. The phage Arno 160 is a lytic Podovirus representing a potential new genus of the subfamily Autographivirinae. It recognizes O-polysaccahride of the host strain and depolymerizes it in the process of infection using a rhamnosidase hydrolytic mechanism. Despite the narrow host range of this phage, it is suitable for phage control application.

Evaluation of discriminative capacity of two formulas of CKD-EPI to predict complications after the first episode of heart failure with preserved ejection fraction.

Background: Determining the prognosis of heart failure with preserved ejection fraction (HFpEF) is problematic, as the ejection fraction cannot be used. Formulae that estimate glomerular filtration rate (eGFR) may be potential prognosticators for this condition, since renal dysfunction is a well-known predictor of poor outcomes of all forms of heart failure. Methods: A prospective observational study of 117 HFpEF patients (average age 71.6±9.1 years; 65.8% women) who had eGFR determined after their first episode of cardiac decompensation by two different chronic kidney disease epidemiology collaboration (CKD-EPI) equations. The ability to predict hospitalizations and mortality over 24 months by the two equations were compared. Results: The CKD-EPI formula based on serum creatinine only performed poorly. However, the CKD-EPI equation that used both serum creatinine and serum cystatin C was associated with unfavorable outcome: eGFR <45 mL/min/1.73 m2 predicted 24-month mortality (HR=4.21 [1.32;13.43], p=0.02) and the combined endpoint of mortality and hospitalization (HR 2.45 [1.42;4.22], p=0.001). . Conclusions: eGFR by the CKD-EPI equation based on serum creatinine and cystatin C levels, but not by the CKD-EPI creatinine only equation, predicts the outcome of HFpEF patients.

Draft Genome Sequence of Sinorhizobium meliloti Strain AK170.

Root nodule bacteria of Sinorhizobium meliloti species live in a symbiotic relationship with alfalfa plants. We report here the draft genome sequence of S. meliloti strain AK170, recovered from nodules of Medicago orthoceras (Kar. & Kir.) growing in an area impacted by salinization.

Draft Genome Sequence of Sinorhizobium meliloti AK555.

The inoculation of legume seeds with Sinorhizobium bacteria significantly improves pasture production. Here, we report the draft genome sequence of symbiotically efficient and salt-tolerant Sinorhizobium meliloti inoculant strain AK555, which substantially increases biomass yield of a number of Medicago sativa subsp. varia varieties, such as "Agniya," "Vega 87," and "Selena."

Draft Genome Sequence of Sinorhizobium meliloti Strain CXM1-105.

Sinorhizobium meliloti is a Gram-negative bacterium which fixes atmospheric nitrogen in symbiosis with Medicago spp. We report the draft genome sequence of S. meliloti strain CXM1-105, associated with nodules of Medicago sativa subsp. varia (Martyn) Arcang.

Draft Genome Sequence of Thermaerobacter sp. Strain PB12/4term, a Thermophilic Facultative Anaerobic Bacterium from Bottom Sediments of Lake Baikal, Russia.

Here, we report the draft genome sequence of Thermaerobacter sp. strain PB12/4term, a thermophilic facultative anaerobic bacterium from the bottom sediments of Lake Baikal, Russia, associated with the discharge zone of gas-bearing fluids.

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species.

Oxidation-stable plasmonic copper nanoparticles in photocatalytic TiO2 nanoarchitectures.

Ultraporous copper/titanium dioxide (Cu/TiO2) aerogels supporting <5 nm diameter copper nanoparticles are active for surface plasmon resonance (SPR)-driven photocatalysis. The extended nanoscale Cu‖TiO2 junctions in Cu/TiO2 composite aerogels-which arise as a result of photodepositing copper at the surface of the nanoparticulate-bonded TiO2 aerogel architecture-stabilize Cu against oxidation to an extent that preserves the plasmonic behavior of the nanoparticles, even after exposure to oxidizing conditions. The metallicity of the Cu nanoparticles within the TiO2 aerogel is verified by aberration-corrected scanning transmission electron microscopy, electron energy-loss spectroscopy, and infrared spectroscopy using CO binding as a probe to distinguish Cu(0) from Cu(i). In contrast, photoreduction of Cu(ii) at a commercial nanoscale anatase TiO2 powder with primary particle sizes significantly larger than those in the aerogel results in a copper oxide/TiO2 composite that exhibits none of the plasmonic character of Cu nanoparticles. We attribute the persistence of plasmonic Cu nanoparticles without the use of ligand stabilizers to the arrangement of Cu and TiO2 within the aerogel architecture where each Cu nanoparticle is in contact with multiple nanoparticles of the reducing oxide. The wavelength dependence of the photoaction spectra for Cu/TiO2 aerogel films reveals visible-light photocatalytic oxidation activity initiated by an SPR-driven process-as opposed to photo-oxidation initiated by excitation of narrow-bandgap copper oxides.