Ocean-bottom seismographs based on broadband MET sensors: architecture and deployment case study in the Arctic

The Arctic seas are now of particular interest due to their prospects in terms of hydrocarbon extraction, development of marine transport routes, etc. Thus, various geohazards, including those related to seismicity, require detailed studies, especially by instrumental methods. This paper is devoted to the ocean-bottom seismographs (OBS) based on broadband molecular–electronic transfer (MET) sensors and a deployment case study in the Laptev Sea. The purpose of the study is to introduce the architecture of several modifications of OBS and to demonstrate their applicability in solving different tasks in the framework of seismic hazard assessment for the Arctic seas. To do this, we used the first results of several pilot deployments of the OBS developed by Shirshov Institute of Oceanology of the Russian Academy of Sciences (IO RAS) and IP Ilyinskiy A.D. in the Laptev Sea that took place in 2018–2020. We highlighted various seismological applications of OBS based on broadband MET sensors CME-4311 (60 s) and CME-4111 (120 s), including the analysis of ambient seismic noise, registering the signals of large remote earthquakes and weak local microearthquakes, and the instrumental approach of the site response assessment. The main characteristics of the broadband MET sensors and OBS architectures turned out to be suitable for obtaining high-quality OBS records under the Arctic conditions to solve seismological problems. In addition, the obtained case study results showed the prospects in a broader context, such as the possible influence of the seismotectonic factor on the bottom-up thawing of subsea permafrost and massive methane release, probably from decaying hydrates and deep geological sources. The described OBS will be actively used in further Arctic expeditions

A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm–Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results)

Specific features of l-histidine production by Escherichia coli concerned with feedback control of AICAR formation and inorganic phosphate/metal transport

Abstract Background In the l-histidine (His) biosynthetic pathway of Escherichia coli, the first key enzyme, ATP-phosphoribosyltransferase (ATP-PRT, HisG), is subject to different types of inhibition. Eliminating the feedback inhibition of HisG by the His end product is an important step that enables the oversynthesis of His in breeding strains. However, the previously reported feedback inhibition-resistant mutant enzyme from E. coli, HisGE271K, is inhibited by purine nucleotides, particularly ADP and AMP, via competitive inhibition with its ATP substrate. 5-Aminoimidazole-4-carboxamide ribonucleotide (AICAR), which is formed not only during His biosynthesis but also during de novo purine biosynthesis, acts as a natural analog of AMP and substitutes for it in some enzymatic reactions. We hypothesized that AICAR could control its own formation, particularly through the His biosynthetic pathway, by negatively influencing HisG enzymatic activity, which would make preventing ATP-PRT transferase inhibition by AICAR crucial for His overproduction. Results For the first time, both the native E. coli HisG and the previously described feedback-resistant mutant HisGE271K enzymes were shown to be sensitive to inhibition by AICAR, a structural analog of AMP. To circumvent the negative effect that AICAR has on His synthesis, we constructed the new His-producing strain EA83 and demonstrated its improved histidine production. This increased production was particularly associated with the improved conversion of AICAR to ATP due to purH and purA gene overexpression; additionally, the PitA-dependent phosphate/metal (Me2+-Pi) transport system was modified by a pitA gene deletion. This His-producing strain unexpectedly exhibited decreased alkaline phosphatase activity at low Pi concentrations. AICAR was consequently hypothesized inhibit the two-component PhoBR system, which controls Pho regulon gene expression. Conclusions Inhibition of a key enzyme in the His biosynthetic pathway, HisG, by AICAR, which is formed in this pathway, generates a serious bottleneck during His production. The constructed His-producing strain demonstrated the enhanced expression of genes that encode enzymes involved in the metabolism of AICAR to ATP, which is a substrate of HisG, and thus led to improved His accumulation

Evaluation of Discrimination Performance in Case for Multiple Non-Discriminated Samples: Classification of Honeys by Fluorescent Fingerprinting

In this study we develop a variant of fluorescent sensor array technique based on addition of fluorophores to samples. A correct choice of fluorophores is critical for the successful application of the technique, which calls for the necessity of comparing different discrimination protocols. We used 36 honey samples from different sources to which various fluorophores were added (tris-(2,2′-bipyridyl) dichlororuthenium(II) (Ru(bpy)32+), zinc(II) 8-hydroxyquinoline-5-sulfonate (8-Ox-Zn), and thiazole orange in the presence of two types of deoxyribonucleic acid). The fluorescence spectra were obtained within 400–600 nm and treated by principal component analysis (PCA). No fluorophore allowed for the discrimination of all samples. To evaluate the discrimination performance of fluorophores, we introduced crossing number (CrN) calculated as the number of mutual intersections of confidence ellipses in the PCA scores plots, and relative position (RP) characterized by the pairwise mutual location of group centers and their most distant points. CrN and RP parameters correlated with each other, with total sensitivity (TS) calculated by Mahalanobis distances, and with the overall rating based on all metrics, with coefficients of correlation over 0.7. Most of the considered parameters gave the first place in the discrimination performance to Ru(bpy)32+ fluorophore

Generation of an induced pluripotent stem cell line HPCASRi002-A from a patient with neonatal severe primary hyperparathyroidism caused by a compound heterozygous mutation in the CASR gene

Neonatal severe primary hyperparathyroidism (NSHPT) is a rare autosomal recessive disorder of calcium homeostasis that manifests shortly after birth with hypercalcemia and bone disease. NSHPT, in most cases, is attributed to mutations in the calcium-sensing receptor (CASR) gene. We reprogrammed dermal fibroblasts derived from a patient with NSHPT carrying a compound heterozygous mutation in the CASR gene into induced pluripotent stem cells (iPSCs). The established iPSCs expressed pluripotency markers, maintained normal karyotype and differentiated into all three germ layers. This line is a valuable resource for modeling of hyperparathyroidism related to CASR mutations

Electron energy relaxation under terahertz excitation in (Cd1− x Zn x )3As2 Dirac semimetals

We demonstrate that measurements of the photo-electromagnetic effect using terahertz laser radiation provide an argument for the existence of highly conductive surface electron states with a spin texture in Dirac semimetals (Cd1-xZnx)(3)As-2. We performed a study on a range of (Cd1-xZnx)(3)As-2 mixed crystals undergoing a transition from the Dirac semimetal phase with an inverse electron energy spectrum to trivial a semiconductor with a direct spectrum in the crystal bulk by varying the composition x. We show that for the Dirac semimetal phase, the photo-electromagnetic effect amplitude is defined by the number of incident radiation quanta, whereas for the trivial semiconductor phase, it depends on the laser pulse power, irrespective of wavelength. We assume that such behavior is attributed to a strong damping of the interelectron interaction in the Dirac semimetal phase compared to the trivial semiconductor, which may be due to the formation of surface electron states with a spin texture in Dirac semimetals

Production of Fluorescent Dissolved Organic Matter by Microalgae Strains from the Ob and Yenisei Gulfs (Siberia)

Dissolved organic matter (DOM) is an important component of aquatic environments; it plays a key role in the biogeochemical cycles of many chemical elements. Using excitation–emission matrix fluorescence spectroscopy, we examined the fluorescent fraction of DOM (FDOM) produced at the stationary phase of growth of five strains of microalgae sampled and isolated from the Ob and Yenisei gulfs. Based on the morphological and molecular descriptions, the strains were identified as diatoms (Asterionella formosa, Fragilaria cf. crotonensis, and Stephanodiscus hantzschii), green microalgae (Desmodesmus armatus), and yellow-green microalgae (Tribonema cf. minus). Three fluorescent components were validated in parallel factor analysis (PARAFAC): one of them was characterized by protein-like fluorescence (similar to peak T), two others, by humic-like fluorescence (peaks A and C). The portion of fluorescence intensity of humic compounds (peak A) to the total fluorescence intensity was the lowest (27 ± 5%) and showed little variation between species. Protein-like fluorescence was most intense (45 ± 16%), but along with humic-like fluorescence with emission maximum at 470 nm (28 ± 14%), varied considerably for different algae strains. The direct optical investigation of FDOM produced during the cultivation of the studied algae strains confirms the possibility of autochthonous production of humic-like FDOM in the Arctic shelf regions

Upconversion Nanoparticles Intercalated in Large Polymer Micelles for Tumor Imaging and Chemo/Photothermal Therapy

Frontiers in theranostics are driving the demand for multifunctional nanoagents. Upconversion nanoparticle (UCNP)-based systems activated by near-infrared (NIR) light deeply penetrating biotissue are a powerful tool for the simultaneous diagnosis and therapy of cancer. The intercalation into large polymer micelles of poly(maleic anhydride-alt-1-octadecene) provided the creation of biocompatible UCNPs. The intrinsic properties of UCNPs (core@shell structure NaYF4:Yb3+/Tm3+@NaYF4) embedded in micelles delivered NIR-to-NIR visualization, photothermal therapy, and high drug capacity. Further surface modification of micelles with a thermosensitive polymer (poly-N-vinylcaprolactam) exhibiting a conformation transition provided gradual drug (doxorubicin) release. In addition, the decoration of UCNP micelles with Ag nanoparticles (Ag NPs) synthesized in situ by silver ion reduction enhanced the cytotoxicity of micelles at cell growth temperature. Cell viability assessment on Sk-Br-3, MDA-MB-231, and WI-26 cell lines confirmed this effect. The efficiency of the prepared UCNP complex was evaluated in vivo by Sk-Br-3 xenograft regression in mice for 25 days after peritumoral injection and photoactivation of the lesions with NIR light. The designed polymer micelles hold promise as a photoactivated theranostic agent with quattro-functionalities (NIR absorption, photothermal effect, Ag NP cytotoxicity, and Dox loading) that provides imaging along with chemo- and photothermal therapy enhanced with Ag NPs

Novel mouse monoclonal antibodies specifically recognize <i>Aspergillus fumigatus</i> galactomannan

<div><p>A panel of specific monoclonal antibodies (mAbs) against synthetic pentasaccharide β-D-Gal<i>f</i>-(1→5)-[β-D-Gal<i>f</i>-(1→5)]₃-α-D-Man<i>p</i>, structurally related to <i>Aspergillus fumigatus</i> galactomannan, was generated using mice immunized with synthetic pentasaccharide-BSA conjugate and by hybridoma technology. Two selected mAbs, 7B8 and 8G4, could bind with the initial pentasaccharide with affinity constants of approximately 5.3 nM and 6.4 nM, respectively, based on surface plasmon resonance-based biosensor assay. The glycoarray, built from a series of synthetic oligosaccharide derivatives representing different galactomannan fragments, demonstrated that mAb 8G4 could effectively recognize the parental pentasaccharide while mAb 7B8 recognizes its constituting trisaccharide parts. Immunofluorescence studies showed that both 7B8 and 8G4 could stain <i>A</i>. <i>fumigatus</i> cells in culture efficiently, but not the mutant strain lacking galactomannan. In addition, confocal microscopy demonstrated that <i>Candida albicans</i>, <i>Bifidobacterium longum</i>, <i>Lactobacillus plantarum</i>, and numerous gram-positive and gram-negative bacteria were not labeled by mAbs 7B8 and 8G4. The generated mAbs can be considered promising for the development of a new specific enzyme-linked assay for detection of <i>A</i>. <i>fumigatus</i>, which is highly demanded for medical and environmental controls.</p></div