We present the complete genome sequence and proteogenomic map for Acholeplasma laidlawii PG-8A (class Mollicutes, order Acholeplasmatales, family Acholeplasmataceae). The genome of A. laidlawii is ...represented by a single 1,496,992-bp circular chromosome with an average G+C content of 31 mol%. This is the longest genome among the Mollicutes with a known nucleotide sequence. It contains genes of polymerase type I, SOS response, and signal transduction systems, as well as RNA regulatory elements, riboswitches, and T boxes. This demonstrates a significant capability for the regulation of gene expression and mutagenic response to stress. Acholeplasma laidlawii and phytoplasmas are the only Mollicutes known to use the universal genetic code, in which UGA is a stop codon. Within the Mollicutes group, only the sterol-nonrequiring Acholeplasma has the capacity to synthesize saturated fatty acids de novo. Proteomic data were used in the primary annotation of the genome, validating expression of many predicted proteins. We also detected posttranslational modifications of A. laidlawii proteins: phosphorylation and acylation. Seventy-four candidate phosphorylated proteins were found: 16 candidates are proteins unique to A. laidlawii, and 11 of them are surface-anchored or integral membrane proteins, which implies the presence of active signaling pathways. Among 20 acylated proteins, 14 contained palmitic chains, and six contained stearic chains. No residue of linoleic or oleic acid was observed. Acylated proteins were components of mainly sugar and inorganic ion transport systems and were surface-anchored proteins with unknown functions.
The global problem of emerging resistance of microorganisms to antibiotics makes the search for new natural substances with antibacterial properties relevant. Such substances include peptidoglycan ...recognition proteins (PGLYRP), which are the components of the innate immunity of many organisms, including humans. These proteins have a unique mechanism of action that allows them to evade the resistance of bacteria to them, as well as to be active against both Gram-positive and Gram-negative bacteria. However, the use of antimicrobial recombinant proteins is not always advisable due to the complexity of local delivery of the proteins and their stability; in this regard it seems appropriate to activate the components of the innate immunity. The aim of this study was to increase the expression level of native peptidoglycan recognition protein genes in HeLa cells using genome-editing technology with synergistic activation mediators (CRISPR/Cas9-SAM) and evaluate antichlamydial effect of PGLYRP. We demonstrated activation of the chlamydial two-component gene system (
ctcB
-
ctcC
), which played a key role in the mechanism of action of the peptidoglycan recognition proteins. We generated the HeLa cell line transduced with lentiviruses encoding CRISPR/Cas9-SAM activation system with increased PGLYRP gene expression. It was shown that activation of the own peptidoglycan recognition proteins gene expression in the cell line caused inhibition of the chlamydial infection development. The proposed approach makes it possible to use the capabilities of innate immunity to combat infectious diseases caused by Gram-positive and Gram-negative bacteria.
The rise of antibiotic resistance has necessitated the development of alternative strategies for the treatment of infectious diseases. Antimicrobial peptides (AMPs), components of the innate immune ...response in various organisms, are promising next-generation drugs against bacterial infections. The ability of the medicinal leech Hirudo medicinalis to store blood for months with little change has attracted interest regarding the identification of novel AMPs in this organism. In this study, we employed computational algorithms to the medicinal leech genome assembly to identify amino acid sequences encoding potential AMPs. Then, we synthesized twelve candidate AMPs identified by the algorithms, determined their secondary structures, measured minimal inhibitory concentrations against three bacterial species (Escherichia coli, Bacillus subtilis, and Chlamydia thrachomatis), and assayed cytotoxic and haemolytic activities. Eight of twelve candidate AMPs possessed antimicrobial activity, and only two of them, 3967 (FRIMRILRVLKL) and 536–1 (RWRLVCFLCRRKKV), exhibited inhibition of growth of all tested bacterial species at a minimal inhibitory concentration of 10 μmol. Thus, we evidence the utility of the developed computational algorithms for the identification of AMPs with low toxicity and haemolytic activity in the medicinal leech genome assembly.
Display omitted
•Twelve candidate AMPs of medicinal leech H. medicinalis were identified by the computational algorithms and synthesized.•Peptides 3967 and 536–1 inhibit the growth of Gram-positive and Gram-negative bacteria at a MIC of 10 μM.•Peptides 3967 and 536–1 exhibit low haemolytic activity with no cytotoxic effects.•Structure determination of the peptides in a membrane-mimetic environment was carried out by NMR spectroscopy.
Data on the aggregate-size distribution (dry sifting method) in humus horizons of chernozems were processed by principal components analysis (PCA) with the centered logratio transformation of the ...initial data set. The analysis of the positions of treatments in the space of principal components coupled with the analysis of eigenvector magnitudes made it possible to identify several size fractions of aggregates, whose contents in the soils reflect soil degradation or progradation processes. These groups fitted well to the partial lognormal curves of aggregate sizes. In addition, the distribution of water-stable aggregates in coarse aggregate fractions (>10, 10–7, 7–5, and 5–3 mm) was analyzed. The integral analysis of the obtained data made it possible to propose the following conceptual model of the recovery of the structure of tilled chernozems. In the course of tillage, soil particles <0.25 mm in size are formed due to comminution. These particles are unstable and may stick together to shape large (>10 mm) water-unstable aggregates (clods). With the removal of tillage loads, large aggregates interact with fresh organic matter, and the water stability of aggregates increases. At the same time, the largest aggregates (mainly >10 mm) tend to transform into aggregates of smaller sizes.
Specific features in the content and accumulation of organic carbon and nitrogen in the aggregates of typical chernozems (Protocalcic Chernozems) of long-term experimental plots with different land ...management systems are assessed. The size fractions in the aggregates of >10, 10–3, 2–1, 1–0.25, and <0.25 mm are examined. The carbon and nitrogen contents are shown to depend on the land management system in a statistically significant manner. The dependence of carbon content on the size of aggregates is observed in five land use systems of the seven examined ones (permanent tilled fallow, unmanaged fallow after permanent tilled fallow, permanent corn and potato fields, shelterbelt, and annually mown steppe). As for nitrogen content, such pattern is observed in three land use variants. The specific features in carbon and nitrogen contents in the size fractions of soil aggregates depend on the type of land use. The carbon content under herbaceous vegetation (steppe) increases with a decrease in the size of aggregates reaching its maximum in the fraction of 1–0.25 mm. As for tree stands (shelterbelt), the maximum carbon content is observed in the fractions of >10 and <0.25 mm. All aggregates <2 mm of the chernozem under herbaceous vegetation in the process of restoration contain considerably higher amount of carbon as compared with the coarser fractions. The nitrogen content in the size fractions of the soil of steppe and shelterbelt plots follows the patterns similar to those of the carbon content.
The structure of the 001-oriented single crystalline tungsten probes sharpened in ultra-high vacuum using electron beam heating and ion sputtering has been studied using scanning and transmission ...electron microscopy. The electron microscopy data prove reproducible fabrication of the single-apex tips with nanoscale pyramids grained by the {011} planes at the apexes. These sharp, 001-oriented tungsten tips have been successfully utilized in high resolution scanning tunneling microscopy imaging of HOPG(0001), SiC(001) and graphene/SiC(001) surfaces. The electron microscopy characterization performed before and after the high resolution STM experiments provides direct correlation between the tip structure and picoscale spatial resolution achieved in the experiments.
The purpose of the work is a comparative study of the molecular composition of thermolabile (volatilizes at 300°C) and thermostable (volatilizes at 500°C) fractions of organic matter from humus ...horizons of typical chernozems by double-shot pyrolysis followed by gas chromatographic separation and mass detection of the products. The objects of the study are typical chernozems under different land use types differing in the prevalent trends of organic matter transformation. As is shown, polysaccharides, furfural, and methylfurfural are the major contributors to the pyrolysis products of the chernozem thermolabile matter. The largest share of the pyrolysis products of thermostable matter belongs to nitrogen-containing compounds. It is demonstrated for the first time that the principal component analysis of the data on molecular composition of thermolabile organic matter makes it possible to divide the studied chernozems under different land uses into the groups reflecting the quasi-equilibrium state of soil organic matter, its degradation, or accumulation.
—
The specific features in accumulation and distribution of organic carbon and nitrogen in the aggregates of typical, ordinary, and southern chernozems (Protocalcic Chernozems, Endocalcic Chernozems, ...and Pantocalcic Chernozems, respectively) during the transition from conventional farming to a no-till system are evaluated. For this purpose, the contents of organic carbon and nitrogen were determined in different aggregate size fractions (>10, 10–2, 2–1, 1–0.25, and <0.25 mm). All three chernozem subtypes differ in the content of organic carbon in a statistically significant manner. The carbon content in all no-till chernozems is higher as compared with the control (conventionally tilled chernozems). The no-till and conventional variants display no statistically significant differences in the nitrogen content. However, the nitrogen content statistically significantly depends on the aggregate size in no-till variants in contrast to conventional farming. In Protocalcic Chernozems, the higher nitrogen content is observed in all agronomically valuable aggregate size fractions (10–0.25 mm); in Endocalcic Chernozems, in the fractions of 2–0.25 mm; and in Pantocalcic Chernozems, in the fractions of <0.25 mm and 2–1 mm. In addition, characteristic of no-till Endocalcic Chernozem is the dependence of carbon content on the aggregate size. The use of no-till system significantly changes the transformation patterns of soil organic matter and biological activity in chernozems.
The extractable fractions of organic matter (OM) differing in their mobility
—
water-extractable organic matter, labile humic substances, and humic substances
—
have been isolated from ...different-sized aggregates of a typical chernozem (Haplic Chernozem (Loamic, Pachic)). The first two fractions characterize the active OM pool, and the latter fraction characterizes the slow OM pool. Overall, the extractable OM fractions make it possible to assess the content and qualitative composition of the active and slow OM pools and, in an indirect manner, of the passive OM pool. The content of dissolved organic carbon in the extracts is used to quantify the yield of fractions, and the spectral characteristics of light absorption in the ultraviolet and visible ranges attest to their qualitative composition. The main attention is focused on the OM recovery in the chernozems after an extreme regime (permanent tilled fallow) and on the differences in the OM of soil aggregates in dependence on their size. A large part of plant residues entering the soil during the recovery of the chernozem after the extreme conditions of tilled fallow is fixed in the passive OM pool. The qualitative composition of active pools is restored much faster than their quantity typical of the undisturbed cenoses. The optical descriptors
E
2
/
E
3
of labile humic substances and
E
4
/
E
6
of humic substances significantly depends on the size of aggregates.
Major internal components of WWER-type nuclear reactors are made from annealed 18Cr10NiTi steel, a close analog to AISI 321. Void swelling of the baffle ring in particular could be a major factor ...limiting operation of the reactor beyond the current 30 years license. A predictive swelling equation is needed to forecast the spatial variation of swelling so as to identify those areas requiring additional attention. Available data on the swelling of this steel arising from irradiation in the BOR-60 fast reactor was combined with data from a heavy ion accelerator at higher displacement rates to formulate a predictive equation of swelling for the WWER-relevant range of temperature, irradiation dose and dose rates. This equation was used to estimate the swelling distribution over a cross-section of the baffle ring of a WWER reactor during a service life up to 60 years, reaching a local maximum of ~30% swelling. It was shown that void swelling extends over a larger portion of the baffle ring than previously expected and exhibits a very complex and irregular distribution in response to complex distributions of temperature and dpa rate. Most importantly, as operation is extended beyond 30 years several areas of the ring may experience swelling in excess of 10% where void-induced embrittlement begins and one area may exceed 20% after 45 years, a swelling level where a complete loss of ductility is known to occur.
PDF
![Fabrication of [001]-orient...](http://api.summon.serialssolutions.com/2.0.0/image/issn/XR4PS5YY4K/2045-2322/small "Fabrication of [001]-oriented tungsten tips for high resolution scanning tunneling microscopy")
