Prokaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of ...microbes. Restricted by current sequencing techniques, the massive sequencing of 16S rRNA gene amplicons encompassing the full length of genes is not yet feasible. Thus, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is still debated. In the present study, several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences.
The correlation of seven sub-regions was inferred from the geodesic distance, a parameter that is applied to quantitatively compare the topology of different phylogenetic trees constructed using the sequences from different sub-regions. The relationship between different sub-regions based on the geodesic distance indicated that V4-V6 were the most reliable regions for representing the full-length 16S rRNA sequences in the phylogenetic analysis of most bacterial phyla, while V2 and V8 were the least reliable regions.
Our results suggest that V4-V6 might be optimal sub-regions for the design of universal primers with superior phylogenetic resolution for bacterial phyla. A potential relationship between function and the evolution of 16S rRNA is also discussed.
Bacterial 16S ribosomal DNA (rDNA) amplicons have been widely used in the classification of uncultured bacteria inhabiting environmental niches. Primers targeting conservative regions of the rDNAs ...are used to generate amplicons of variant regions that are informative in taxonomic assignment. One problem is that the percentage coverage and application scope of the primers used in previous studies are largely unknown. In this study, conservative fragments of available rDNA sequences were first mined and then used to search for candidate primers within the fragments by measuring the coverage rate defined as the percentage of bacterial sequences containing the target. Thirty predicted primers with a high coverage rate (>90%) were identified, which were basically located in the same conservative regions as known primers in previous reports, whereas 30% of the known primers were associated with a coverage rate of <90%. The application scope of the primers was also examined by calculating the percentages of failed detections in bacterial phyla. Primers A519-539, E969-983, E1063-1081, U515 and E517, are highly recommended because of their high coverage in almost all phyla. As expected, the three predominant phyla, Firmicutes, Gemmatimonadetes and Proteobacteria, are best covered by the predicted primers. The primers recommended in this report shall facilitate a comprehensive and reliable survey of bacterial diversity in metagenomic studies.
Abstract
The two-dimensional topological insulators host a full gap in the bulk band, induced by spin–orbit coupling (SOC) effect, together with the topologically protected gapless edge states. ...However, it is usually challenging to suppress the bulk conductance and thus to realize the quantum spin Hall (QSH) effect. In this study, we find a mechanism to effectively suppress the bulk conductance. By using the quasiparticle interference technique with scanning tunneling spectroscopy, we demonstrate that the QSH candidate single-layer 1
T
’-WTe
2
has a semimetal bulk band structure with no full SOC-induced gap. Surprisingly, in this two-dimensional system, we find the electron–electron interactions open a Coulomb gap which is always pinned at the Fermi energy (
E
F
). The opening of the Coulomb gap can efficiently diminish the bulk state at the
E
F
and supports the observation of the quantized conduction of topological edge states.
Atomically thin 2D crystals have gained tremendous attention owing to their potential impact on future electronics technologies, as well as the exotic phenomena emerging in these materials. ...Monolayers of α‐phase Sb (α‐antimonene), which shares the same puckered structure as black phosphorous, are predicted to be stable with precious properties. However, the experimental realization still remains challenging. Here, high‐quality monolayerα‐antimonene is successfully grown, with the thickness finely controlled. The α‐antimonene exhibits great stability upon exposure to air. Combining scanning tunneling microscopy, density functional theory calculations, and transport measurements, it is found that the electron band crossing the Fermi level exhibits a linear dispersion with a fairly small effective mass, and thus a good electrical conductivity. All of these properties make the α‐antimonene promising for future electronic applications.
Monolayer α‐phase antimonene, a structural analog to black phosphorous, is fabricated on a WTe2 substrate. The α‐antimonene exhibits great stability upon exposure to air. Its electron band crossing the Fermi level exhibits a linear dispersion with a fairly small effective mass, and thus a good electrical conductivity. All of these properties make α‐antimonene promising in future electronic applications.
For successful wastewater reclamation, advanced oxidation processes have attracted attention for elimination of emerging contaminants. In this study, the synergistic treatment with UV irradiation and ...chlorine (UV/chlorine) was used to degrade carbamazepine (CBZ). Neither UV irradiation alone nor chlorination alone could efficiently degraded CBZ. UV/chlorine oxidation showed a significant synergistic effect on CBZ degradation through generation of radical species (OH and Cl), and this process could be well depicted by pseudo first order kinetic. The degradation rate constants (kobs,CBZ) of CBZ increased linearly with increasing UV irradiance and chlorine dosage. The degradation of CBZ by UV/chlorine in acidic solutions was more efficient than that in basic solutions mainly due to the effect of pH on the dissociation of HOCl and OCl− and then on the quantum yields and radical species quenching of UV/chlorine. When pH was increased from 5.5 to 9.5, the rate constants of degradation of CBZ by OH decreased from 0.65 to 0.14 min−1 and that by Cl decreased from 0.40 to 0.11 min−1. The rate constant for the reaction between Cl and CBZ was 5.6 ± 1.6 × 1010 M−1 s−1. Anions of HCO3− (1–50 mM) showed moderate inhibition of CBZ degradation by UV/chlorine, while Cl− did not. UV/chlorine could efficiently degrade CBZ in wastewater treatment plant effluent, although the degradation was inhibited by about 30% compared with that in ultrapure water with chlorine dosage of 0.14–0.56 mM. Nine main oxidation products of the CBZ degradation by UV/chlorine were identified using the HPLC-QToF MS/MS. Initial oxidation products arose from hydroxylation, carboxylation and hydrogen atom abstraction of CBZ by OH and Cl, and were then further oxidized to generate acylamino cleavage and decarboxylation products of acridine and acridione.
•UV/chlorine showed synergistic degradation of carbamazepine than UV and chlorination.•Carbamazepine degraded through both OH and Cl ways during UV/chlorine oxidation•Carbamazepine could be efficiently degraded by UV/chlorine in UPW and WWTP effluent.•The second order rate constant between carbamazepine and Cl were examined
Better understanding of the mechanisms of antifouling compounds is recognized to be of high value in establishing sensitive biomarkers, allowing the targeted optimization of antifouling compounds and ...guaranteeing environmental safety. Despite vigorous efforts to find new antifouling compounds, information about the mechanisms of antifouling is still scarce. This review summarizes the progress into understanding the molecular mechanisms underlying antifouling activity since 2012. Non-toxic mechanisms aimed at specific targets, including inhibitors of transmembrane transport, quorum sensing inhibitors, neurotransmission blockers, adhesive production/release inhibitors and enzyme/protein inhibitors, are put forward for natural antifouling products or shelf-stable chemicals. Several molecular targets show good potential for use as biomarkers in future mechanistic screening, such as acetylcholine esterase for neurotransmission, phenoloxidase/tyrosinase for the formation of adhesive plaques,
-acyl homoserine lactone for quorum sensing and intracellular Ca
levels as second messenger. The studies on overall responses to challenges by antifoulants can be categorized as general targets, including protein expression/metabolic activity regulators, oxidative stress inducers, neurotransmission blockers, surface modifiers, biofilm inhibitors, adhesive production/release inhibitors and toxic killing. Given the current situation and the knowledge gaps regarding the development of alternative antifoulants, a basic workflow is proposed that covers the indispensable steps, including preliminary mechanism- or bioassay-guided screening, evaluation of environmental risks, field antifouling performance, clarification of antifouling mechanisms and the establishment of sensitive biomarkers, which are combined to construct a positive feedback loop.
Proteins in cellular environments are highly susceptible. Local perturbations to any residue can be sensed by other spatially distal residues in the protein molecule, showing long-range correlations ...in the native dynamics of proteins. The long-range correlations of proteins contribute to many biological processes such as allostery, catalysis, and transportation. Revealing the structural origin of such long-range correlations is of great significance in understanding the design principle of biologically functional proteins. In this work, based on a large set of globular proteins determined by X-ray crystallography, by conducting normal mode analysis with the elastic network models, we demonstrate that such long-range correlations are encoded in the native topology of the proteins. To understand how native topology defines the structure and the dynamics of the proteins, we conduct scaling analysis on the size dependence of the slowest vibration mode, average path length, and modularity. Our results quantitatively describe how native proteins balance between order and disorder, showing both dense packing and fractal topology. It is suggested that the balance between stability and flexibility acts as an evolutionary constraint for proteins at different sizes. Overall, our result not only gives a new perspective bridging the protein structure and its dynamics but also reveals a universal principle in the evolution of proteins at all different sizes.
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