The curse of dimensionality associated with the Hilbert space of spin systems provides a significant obstruction to the study of condensed matter systems. Tensor networks have proven an important ...tool in attempting to overcome this difficulty in both the numerical and analytic regimes. These notes form the basis for a seven lecture course, introducing the basics of a range of common tensor networks and algorithms. In particular, we cover: introductory tensor network notation, applications to quantum information, basic properties of matrix product states, a classification of quantum phases using tensor networks, algorithms for finding matrix product states, basic properties of projected entangled pair states, and multiscale entanglement renormalisation ansatz states. The lectures are intended to be generally accessible, although the relevance of many of the examples may be lost on students without a background in many-body physics/quantum information. For each lecture, several problems are given, with worked solutions in an ancillary file.
In recent years, tensor representation (TR)-based hyperspectral anomaly detection (HAD) approaches have attracted more and more attention. However, two urgent issues still need to be addressed: 1) ...existing tensor decomposition approaches for HAD cannot make full use of the spectral-spatial correlation of background components in hyperspectral images (HSIs) and 2) most approaches based on TR overlook the piecewise-smooth of background components that exist simultaneously in the spectral and spatial domains. To this end, with the aid of an advanced multiscale entanglement renormalization ansatz (MERA) tensor network, this article proposes an algorithm based on MERA decomposition and enhanced total variation regularization (MERAETV) for HAD. Specifically, MERA decomposes the background tensor by contracting a top-level factor with the remaining semiorthogonal and orthogonal factors. Due to the intricate interplay between semiorthogonal (low-rank) and orthogonal factors, low-rank MERA approximation exhibits a robust representational capacity that effectively captures the spectral-spatial correlation of the background component. Meanwhile, an enhanced total variation (ETV) regularization is devised to capture the inherent piecewise-smooth of the background component in both spectral and spatial domains. Furthermore, our algorithm incorporates group sparsity constraint and Gaussian noise term to enhance the discrimination between anomalies and background. Finally, a highly efficient update scheme based on the alternating direction method of multipliers (ADMM) is designed. A large number of experiments on one synthetic and seven real HSIs demonstrate the superiority of our proposed approach.
Mercury (Hg) is a highly toxic element due to its high affinity for protein sulfhydryl groups, which upon binding, can destabilize protein structure and decrease enzyme activity. Prokaryotes have ...evolved enzymatic mechanisms to detoxify inorganic Hg and organic Hg (e.g., MeHg) through the activities of mercuric reductase (MerA) and organomercury lyase (MerB), respectively. Here, the taxonomic distribution and evolution of MerAB was examined in 84,032 archaeal and bacterial genomes, metagenome assembled genomes, and single-cell genomes. Homologs of MerA and MerB were identified in 7.8 and 2.1% percent of genomes, respectively. MerA was identified in the genomes of 10 archaeal and 28 bacterial phyla previously unknown to code for this functionality. Likewise, MerB was identified in 2 archaeal and 11 bacterial phyla previously unknown to encode this functionality. Surprisingly, homologs of MerB were identified in a number of genomes (∼50% of all MerB-encoding genomes) that did not encode MerA, suggesting alternative mechanisms to detoxify Hg(II) once it is generated in the cytoplasm. Phylogenetic reconstruction of MerA place its origin in thermophilic Thermoprotei (Crenarchaeota), consistent with high levels of Hg(II) in geothermal environments, the natural habitat of this archaeal class. MerB appears to have been recruited to the
operon relatively recently and likely among a mesophilic ancestor of Euryarchaeota and Thaumarchaeota. This is consistent with the functional dependence of MerB on MerA and the widespread distribution of mesophilic microorganisms that methylate Hg(II) at lower temperature. Collectively, these results expand the taxonomic and ecological distribution of
-encoded functionalities, and suggest that selection for Hg(II) and MeHg detoxification is dependent not only on the availability and type of mercury compounds in the environment but also the physiological potential of the microbes who inhabit these environments. The expanded diversity and environmental distribution of MerAB identify new targets to prioritize for future research.
Over the past few decades, Indian agriculture is increasingly confronting a range of social, economic and ecological challenges putting the livelihood security of millions of resource poor farmers at ...risk. The ills plaguing the farm sector have received critical policy attention leading to the launch of several farmer-centric policies and programs aimed at infusing resilience into the ailing croplands, making agriculture a remunerative activity and for driving the rural poor out of poverty. One such initiative called 'Mera Gaon, Mera Gaurav' (My Village, My Pride) was launched in 2015 with the goal of revolutionizing the pace of technology transfer to the farmers' doorsteps in a time bound manner. In this article, we propose a new model consisting of five propositions for improving the modus operandi of 'Mera Gaon, Mera Gaurav'program such that it does not merely remain a tool of technology dissemination but instead serves as a viable platform for the co-production of agricultural knowledge which is more sustainable, inclusive and compatible to resolving the current and emerging agricultural issues.
The prevalence of methicillin-resitant Staphylococcus aureus (MRSA) in hospitals and the community poses an increasing health burden, which requires the discovery of alternative antimicrobials. ...Allicin (diallyl thiosulfinate) from garlic exhibits broad-spectrum antimicrobial activity against many multidrug resistant bacteria. The thiol-reactive mode of action of allicin involves its S-thioallylations of low molecular weight (LMW) thiols and protein thiols. To investigate the mode of action and stress response caused by allicin in S. aureus, we analyzed the transcriptome signature, the targets for S-thioallylation in the proteome and the changes in the bacillithiol (BSH) redox potential (EBSH) under allicin stress. Allicin caused a strong thiol-specific oxidative and sulfur stress response and protein damage as revealed by the induction of the PerR, HypR, QsrR, MhqR, CstR, CtsR, HrcA and CymR regulons in the RNA-seq transcriptome. Allicin also interfered with metal and cell wall homeostasis and caused induction of the Zur, CsoR and GraRS regulons. Brx-roGFP2 biosensor measurements revealed a strongly increased EBSH under allicin stress. In the proteome, 57 proteins were identified with S-thioallylations under allicin treatment, including translation factors (EF-Tu, EF-Ts), metabolic and redox enzymes (AldA, GuaB, Tpx, KatA, BrxA, MsrB) as well as redox-sensitive MarR/SarA-family regulators (MgrA, SarA, SarH1, SarS). Phenotype and biochemical analyses revealed that BSH and the HypR-controlled disulfide reductase MerA are involved in allicin detoxification in S. aureus. The reversal of protein S-thioallylation was catalyzed by the Brx/BSH/YpdA pathway. Finally, the BSSB reductase YpdA was shown to use S-allylmercaptobacillithiol (BSSA) as substrate to regenerate BSH in S. aureus. In conclusion, allicin results in an oxidative shift of EBSH and protein S-thioallylation, which can be reversed by YpdA and the Brx/BSH/YpdA electron pathways in S. aureus to regenerate thiol homeostasis.
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•Allicin causes a thiol-specific oxidative stress response in S. aureus.•The mode of action of allicin involves S-thioallylation of 57 proteins.•S-thioallylated proteins are redox-sensitive enzymes and MarR-family regulators.•BSH and the disulfide reductase MerA are involved in allicin detoxification.•BrxAB/BSH/YpdA pathway functions in reversal of protein S-thioallylation.
Martani NS, Notobroto HB, Wasito EB, Jabal AR. 2022. The role of merA Gene of Mercury-resistant Escherichia coli from Kahayan River, Central Kalimantan, Indonesia in emerging antibiotic resistance. ...Biodiversitas 23: 6629-6634. This study collected nine water samples from the upstream, middle, and downstream parts of the Kahayan river, which was heavily contaminated with mercury (Hg). The water was sampled following the collection method of surface water sample (SNI 6989.57-2008). Escherichia coli has been found in the four samples out of nine samples collected. The merA gene of bacteria was identified at 1695 base pairs (bp), bla at 199 bp, tet at 494 bp, cat at 623 bp, and gyrA at 577 bp. The merA gene from S1 from the PCR results was identified at 219 bp. However, the merA gene was not amplified with a primer measuring 1695 bp. Then, sequencing was performed, and the results indicated a 48.551% homology with E. coli Tn5075 nucleotide sequences. On examination of the cat gene, all samples are positive, or target-specific bands are observed (i.e., samples 1, 5, 6, and 7). Following sequencing, 623 bp were found to have nucleotide sequences that were 100% identical to E. coli. In all samples, the gyrA gene is either positive or has a band that corresponds to the target. Meanwhile, the results of nucleotide sequence homology of 99.826% were identical to E. coli at 586 bp. No bla gene or tet gene was identified. Sample 1 plate 1, 3, 4, 5, and sample 5 plate 3 exhibited intermediate results for ampicillin antibiotics, while the remaining results are sensitive to the tested antibiotics. Therefore, the mercury-resistant merA gene found in E. coli from the Kahayan river in Central Kalimantan has not been conclusively linked to antibiotic resistance.
The Amazon region abounds in precious mineral resources including gold, copper, iron, and coltan. Artisanal and small-scale gold mining (ASGM) poses a severe risk in this area due to considerable ...mercury release into the surrounding ecosystems. Nonetheless, the impact of mercury on both the overall microbiota and the microbial populations involved in mercury transformation is not well understood. In this study we evaluated microbial diversity in samples of soil, sediment and water potentially associated with mercury contamination in two localities (Taraira and Tarapacá) in the Colombian Amazon Forest. To this end, we characterized the bacterial community structure and mercury-related functions in samples from sites with a chronic history of mercury contamination which today have different levels of total mercury content. We also determined mercury bioavailability and mobility in the samples with the highest THg and MeHg levels (up to 43.34 and 0.049 mg kg−1, respectively, in Taraira). Our analysis of mercury speciation showed that the immobile form of mercury predominated in soils and sediments, probably rendering it unavailable to microorganisms. Despite its long-term presence, mercury did not appear to alter the microbial community structure or composition, which was primarily shaped by environmental and physicochemical factors. However, an increase in the relative abundance of merA genes was detected in polluted sediments from Taraira. Several Hg-responsive taxa in soil and sediments were detected in sites with high levels of THg, including members of the Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes and Chloroflexi phyla. The results suggest that mercury contamination at the two locations sampled may select mercury-adapted bacteria carrying the merA gene that could be used in bioremediation processes for the region.
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•In long-polluted sites bacterial communities are more affected by environmental variables than by Hg.•MerA was more abundant in Taraira sediments in line with higher mercury levels.•The Hg-immobile form was dominant, probably limiting microorganism access.•Proteobacteria, Acidobacteria, Actinobacteria, Firmicutes, and Chloroflexi dominated in high Hg sites.
Abstract Background and aims Mercury (Hg) contamination poses severe human and environmental health risks. We aimed to evaluate the colonization of Hg-contaminated sites by native plants and the ...prokaryotic composition of rhizosphere soil communities of the dominant plant species. Methods A field study was conducted at a Hg-contaminated site in Romania. Metal concentrations in soil and plant samples were analyzed using portable X-ray fluorescence spectrometry. The prokaryotic composition of rhizosphere soil communities was determined through 16S rRNA amplicon sequencing and community functionality was predicted through PICRUSt2. Results Site-specific trace metal distribution across the site drove plant species distribution in the highly contaminated soil, with Lotus tenuis and Diplotaxis muralis associated with higher Hg concentrations. In addition, for the bacterial communities in the rhizosphere soil of D. muralis , there was no observable decrease in alpha diversity with increasing soil Hg levels. Notably, Actinomycetota had an average of 24% relative abundance in the rhizosphere communities that also tested positive for the presence of merA , whereas in the absence of merA the phylum’s relative abundance was approximately 2%. merA positive rhizosphere communities also displayed an inferred increase in ABC transporters. Conclusions The results suggest a dependence of species-wise plant survival on local trace metal levels in soil, as well as an intricate interplay of the latter with rhizosphere bacterial diversity. Knowledge of these interdependencies could have implications for phytoremediation stakeholders, as it may allow for the selection of plant species and appropriate soil microbial inoculates with elevated Hg tolerance.
Mercury (Hg) pollution is a worldwide problem and increasing day by day due to natural and anthropogenic sources. In this study, mercury-resistant (Hg
R
) bacterial isolates were isolated from ...industrial wastewater of Ittehad Chemicals Ltd., Kala Shah Kaku, Lahore, Pakistan. Out of 65 bacterial isolates, five isolates were screened out based on showing resistance at 30–40 μg/ml against HgCl
2
. Selected Hg-resistant bacterial isolates were characterized as
Bacillus subtilis
AA-16 (OK562835),
Bacillus cereus
AA-18 (OK562834),
Bacillus
sp. AA-20 (OK562833),
Bacillus paramycoides
AA-30 (OK562836), and
Bacillus thuringiensis
AA-35 (OK562837).
B. cereus
AA-18 showed promising results in the resistance of HgCl
2
(40 μg/ml) due to the presence of
mer
A gene. Scanning electron microscopy (SEM) analysis of immobilized
B. cereus
AA-18 showed the accumulation Hg on the cell surface. The inoculation of immobilized
B. cereus
AA-18 remediated 86% Hg of industrial wastewater up to 72 h at large scale (
p
< 0.05).
In silico
analysis showed structural determination of MerA protein encoded by
mer
A gene of
B. cereus
AA-18 (OK562598) using ProtParam, Pfam, ConSurf Server, InterPro, STRING, Jpred4, PSIPRED, I-TASSER, COACH server, TrRosetta, ERRAT, VERIFY3D, Ramachandran plot, and AutoDock Vina (PyRx 8.0). These bioinformatics tools predicted the structural-based functional homology of MerA protein (mercuric reductase) associated with
mer
operon harboring bacteria involved in Hg-bioremediation system.
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