Origin of Distinct Insulating Domains in the Layered Charge Density Wave Material 1T-TaS2.

Vertical charge order shapes the electronic properties in layered charge density wave (CDW) materials. Various stacking orders inevitably create nanoscale domains with distinct electronic structures inaccessible to bulk probes. Here, the stacking characteristics of bulk 1T-TaS2 are analyzed using scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. It is observed that Mott-insulating domains undergo a transition to band-insulating domains restoring vertical dimerization of the CDWs. Furthermore, STS measurements covering a wide terrace reveal two distinct band insulating domains differentiated by band edge broadening. These DFT calculations reveal that the Mott insulating layers preferably reside on the subsurface, forming broader band edges in the neighboring band insulating layers. Ultimately, buried Mott insulating layers believed to harbor the quantum spin liquid phase are identified. These results resolve persistent issues regarding vertical charge order in 1T-TaS2, providing a new perspective for investigating emergent quantum phenomena in layered CDW materials.

Bioengineered amyloid peptide for rapid screening of inhibitors against main protease of SARS-CoV-2.

The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has evoked a worldwide pandemic. As the emergence of variants has hampered the neutralization capacity of currently available vaccines, developing effective antiviral therapeutics against SARS-CoV-2 and its variants becomes a significant challenge. The main protease (Mpro) of SARS-CoV-2 has received increased attention as an attractive pharmaceutical target because of its pivotal role in viral replication and proliferation. Here, we generated a de novo Mpro-inhibitor screening platform to evaluate the efficacies of Mpro inhibitors based on Mpro cleavage site-embedded amyloid peptide (MCAP)-coated gold nanoparticles (MCAP-AuNPs). We fabricated MCAPs comprising an amyloid-forming sequence and Mpro-cleavage sequence, mimicking in vivo viral replication process mediated by Mpro. By measuring the proteolytic activity of Mpro and the inhibitory efficacies of various drugs, we confirmed that the MCAP-AuNP-based platform was suitable for rapid screening potential of Mpro inhibitors. These results demonstrated that our MCAP-AuNP-based platform has great potential for discovering Mpro inhibitors and may accelerate the development of therapeutics against COVID-19.

Melting of Unidirectional Charge Density Waves across Twin Domain Boundaries in GdTe3.

Solids undergoing a transition from order to disorder experience a proliferation of topological defects. The melting process generates transient quantum states. However, their dynamic nature with a femtosecond lifetime hinders exploration with atomic precision. Here, we suggest an alternative approach to the dynamic melting process by focusing on the interface created by competing degenerate quantum states. We use a scanning tunneling microscope (STM) to visualize the unidirectional charge density wave (CDW) and its spatial progression ("static melting") across a twin domain boundary (TDB) in the layered material GdTe3. Combining the STM with a spatial lock-in technique, we reveal that the order parameter amplitude attenuates with the formation of dislocations and thus two different unidirectional CDWs coexist near the TDB, reducing the CDW anisotropy. Notably, we discovered a correlation between this anisotropy and the CDW gap. Our study provides valuable insight into the behavior of topological defects and transient quantum states.

Can microbes be harnessed to reduce atmospheric loads of greenhouse gases?

Reducing atmospheric loads of greenhouse gases (GHGs), especially CO2 and CH4 , has been considered the key to alleviating global crises we are facing, such as climate change, sea level elevation and ocean acidification. To this end, development of strategies and technologies for carbon capture, sequestration and utilization (CCSU) is urgently needed. Although physicochemical methods have been the most actively studied in the early stages of developing CCSU technologies, there have recently been growing interests in developing microbe-based CCSU processes. In this article, we discuss advantages of microbe-based CCSU technologies over physicochemical approaches and even plant-based approaches. Next, various parts of the global carbon cycle where microorganisms can contribute, such as sequestering atmospheric GHGs, facilitating the carbon cycle, and slowing down the depletion of carbon reservoirs are described, emphasizing the impacts of microbes on the carbon cycle. Strategies to upgrade microbes and increase their performance in assimilating GHGs or converting GHGs to value-added chemicals are also provided. Moreover, several examples of exploiting microbes to address environmental crises are discussed. Finally, we discuss things to overcome in microbe-based CCSU technologies and provide future perspectives.

Biomimetically Engineered Amyloid-Shelled Gold Nanocomplexes for Discovering α-Synuclein Oligomer-Degrading Drugs.

The assembly of α-synuclein (αS) oligomers is recognized as the main pathological driver of synucleinopathies. While the elimination of toxic αS oligomers shows promise for the treatment of Parkinson's disease (PD), the discovery of αS oligomer degradation drugs has been hindered by the lack of proper drug screening tools. Here, we report a drug screening platform for monitoring the efficacy of αS-oligomer-degrading drugs using amyloid-shelled gold nanocomplexes (ASGNs). We fabricate ASGNs in the presence of dopamine, mimicking the in vivo generation process of pathological αS oligomers. To test our platform, the first of its kind for PD drugs, we use αS-degrading proteases and various small molecular substances that have shown efficacy in PD treatment. We demonstrate that the ASGN-based in vitro platform has strong potential to discover effective αS-oligomer-targeting drugs, and thus it may reduce the attrition problem in drug discovery for PD treatment.

Efficient Wear Simulation Methodology for Predicting Nonlinear Wear Behavior of Tools in Sheet Metal Forming.

In conventional wear simulation, the geometry must be updated for succeeding iterations to predict the accumulated wear. However, repeating this procedure up to the desired iteration is rather time consuming. Thus, a wear simulation process capable of reasonable quantitative wear prediction in reduced computational time is needed. This study aimed to develop an efficient wear simulation method to predict quantitative wear reasonably in reduced computational time without updating the geometry for succeeding iterations. The wear resistance of a stamping tool was quantitatively evaluated for different punch shapes (R3.0 and R5.5) and coating conditions (physical vapor deposition of CrN and AlTiCrN coatings) by using a progressive die set. To capture the nonlinear wear behavior with respect to strokes, a nonlinear equation from a modified form of Archard's wear model was proposed. By utilizing the scale factor representing the changes in wear properties with respect to wear depth as input, the simulation can predict the behavior of rapidly increasing wear depth with respect to strokes after failure initiation. Furthermore, the proposed simulation method is efficient in terms of computational time because it does not need to perform geometry updates.

Synthetic Formatotrophs for One-Carbon Biorefinery.

The use of CO2 as a carbon source in biorefinery is of great interest, but the low solubility of CO2 in water and the lack of efficient CO2 assimilation pathways are challenges to overcome. Formic acid (FA), which can be easily produced from CO2 and more conveniently stored and transported than CO2, is an attractive CO2-equivalent carbon source as it can be assimilated more efficiently than CO2 by microorganisms and also provides reducing power. Although there are native formatotrophs, they grow slowly and are difficult to metabolically engineer due to the lack of genetic manipulation tools. Thus, much effort is exerted to develop efficient FA assimilation pathways and synthetic microorganisms capable of growing solely on FA (and CO2). Several innovative strategies are suggested to develop synthetic formatotrophs through rational metabolic engineering involving new enzymes and reconstructed FA assimilation pathways, and/or adaptive laboratory evolution (ALE). In this paper, recent advances in development of synthetic formatotrophs are reviewed, focusing on biological FA and CO2 utilization pathways, enzymes involved and newly developed, and metabolic engineering and ALE strategies employed. Also, future challenges in cultivating formatotrophs to higher cell densities and producing chemicals from FA and CO2 are discussed.

Escherichia coli is engineered to grow on CO2 and formic acid.

We engineered Escherichia coli to grow on CO2 and formic acid alone by introducing the synthetic CO2 and formic acid assimilation pathway, expressing two formate dehydrogenase genes, fine-tuning metabolic fluxes and optimizing the levels of cytochrome bo3 and bd-I ubiquinol oxidase. Our engineered strain can grow to an optical density at 600 nm of 7.38 in 450 h, and shows promise as a platform strain growing on CO2 and formic acid alone.

Assimilation of formic acid and CO2 by engineered Escherichia coli equipped with reconstructed one-carbon assimilation pathways.

Gaseous one-carbon (C1) compounds or formic acid (FA) converted from CO2 can be an attractive raw material for bio-based chemicals. Here, we report the development of Escherichia coli strains assimilating FA and CO2 through the reconstructed tetrahydrofolate (THF) cycle and reverse glycine cleavage (gcv) pathway. The Methylobacterium extorquens formate-THF ligase, methenyl-THF cyclohydrolase, and methylene-THF dehydrogenase genes were expressed to allow FA assimilation. The gcv reaction was reversed by knocking out the repressor gene (gcvR) and overexpressing the gcvTHP genes. This engineered strain synthesized 96% and 86% of proteinogenic glycine and serine, respectively, from FA and CO2 in a glucose-containing medium. Native serine deaminase converted serine to pyruvate, showing 4.5% of pyruvate-forming flux comes from FA and CO2 The pyruvate-forming flux from FA and CO2 could be increased to 14.9% by knocking out gcvR, pflB, and serA, chromosomally expressing gcvTHP under trc, and overexpressing the reconstructed THF cycle, gcvTHP, and lpd genes in one vector. To reduce glucose usage required for energy and redox generation, the Candida boidinii formate dehydrogenase (Fdh) gene was expressed. The resulting strain showed specific glucose, FA, and CO2 consumption rates of 370.2, 145.6, and 14.9 mg⋅g dry cell weight (DCW)-1⋅h-1, respectively. The C1 assimilation pathway consumed 21.3 wt% of FA. Furthermore, cells sustained slight growth using only FA and CO2 after glucose depletion, suggesting that combined use of the C1 assimilation pathway and C. boidinii Fdh will be useful for eventually developing a strain capable of utilizing FA and CO2 without an additional carbon source such as glucose.

Membrane engineering via trans-unsaturated fatty acids production improves succinic acid production in Mannheimia succiniciproducens.

Engineering of microorganisms to produce desired bio-products with high titer, yield, and productivity is often limited by product toxicity. This is also true for succinic acid (SA), a four carbon dicarboxylic acid of industrial importance. Acid products often cause product toxicity to cells through several different factors, membrane damage being one of the primary factors. In this study, cis-trans isomerase from Pseudomonas aeruginosa was expressed in Mannheimia succiniciproducens to produce trans-unsaturated fatty acid (TUFA) and to reinforce the cell membrane of M. succiniciproducens. The engineered strain showed significant decrease in membrane fluidity as production of TUFA enabled tight packing of fatty acids, which made cells to possess more rigid cell membrane. As a result, the membrane-engineered M. succiniciproducens strain showed higher tolerance toward SA and increased production of SA compared with the control strain without membrane engineering. The membrane engineering approach employed in this study will be useful for increasing tolerance to, and consequently enhancing production of acid products.

Formic acid as a secondary substrate for succinic acid production by metabolically engineered Mannheimia succiniciproducens.

There has been much effort exerted to reduce one carbon (C1) gas emission to address climate change. As one promising way to more conveniently utilize C1 gas, several technologies have been developed to convert C1 gas into useful chemicals such as formic acid (FA). In this study, systems metabolic engineering was utilized to engineer Mannheimia succiniciproducens to efficiently utilize FA. 13 C isotope analysis of M. succiniciproducens showed that FA could be utilized through formate dehydrogenase (FDH) reaction and/or the reverse reaction of pyruvate formate lyase (PFL). However, the naturally favored forward reaction of PFL was found to lower the SA yield from FA. In addition, FA assimilation via FDH was found to be more efficient than the reverse reaction of PFL. Thus, the M. succiniciproducens LPK7 strain, which lacks in pfl, ldh, pta, and ack genes, was selected as a base strain. In silico metabolic analysis confirmed that utilization of FA would be beneficial for the enhanced production of SA and suggested FDH as an amplification target. To find a suitable FDH, four different FDHs from M. succiniciproducens, Methylobacterium extorquens, and Candida boidinii were amplified in LPK7 strain to enhance FA assimilation. High-inoculum density cultivation using 13 C labeled sodium formate was performed to evaluate FA assimilation efficiency. Fed-batch fermentations of the LPK7 (pMS3-fdh2 meq) strain was carried out using glucose, sucrose, or glycerol as a primary carbon source and FA as a secondary carbon source. As a result, this strain produced 76.11 g/L SA with the yield and productivity of 1.28 mol/mol and 4.08 g/L/h, respectively, using sucrose and FA as dual carbon sources. The strategy employed here will be similarly applicable in developing microorganisms to utilize FA and to produce valuable chemicals and materials from FA.

Cordycepin induces human lung cancer cell apoptosis by inhibiting nitric oxide mediated ERK/Slug signaling pathway.

Nitric oxide (NO) is an important signaling molecule and a component of the inflammatory cascade. Besides, it is also involved in tumorigenesis. Aberrant upregulation and activation of the ERK cascade by NO often leads to tumor cell development. However, the role of ERK inactivation induced by the negative regulation of NO during apoptosis is not completely understood. In this study, treatment of A549 and PC9 human lung adenocarcinoma cell lines with cordycepin led to a reduction in their viability. Analysis of the effect of cordycepin treatment on ERK/Slug signaling activity in the A549 cell line revealed that LPS-induced inflammatory microenvironments could stimulate the expression of TNF-α, CCL5, IL-1ß, IL-6, IL-8 and upregulate NO, phospho-ERK (p-ERK), and Slug expression. In addition, constitutive expression of NO was observed. Cordycepin inhibited LPS-induced stimulation of iNOS, NO, p-ERK, and Slug expression. L-NAME, an inhibitor of NOS, inhibited p-ERK and Slug expression. It was also found that cordycepin-mediated inhibition of ERK downregulated Slug, whereas overexpression of ERK led to an upregulation of Slug levels in the cordycepin-treated A549 cells. Inhibition of Slug by siRNA induced Bax and caspase-3, leading to cordycepin-induced apoptosis. Cordycepin-mediated inhibition of ERK led to a reduction in phospho-GSK3ß (p-GSK3ß) and Slug levels, whereas LiCl, an inhibitor of GSK3ß, upregulated p-GSK3ß and Slug. Overall, the results obtained indicate that cordycepin inhibits the ERK/Slug signaling pathway through the activation of GSK3ß which, in turn, upregulates Bax, leading to apoptosis of the lung cancer cells.

L-lactate production from seaweed hydrolysate of Laminaria japonica using metabolically engineered Escherichia coli.

Renewable and carbon neutral, marine algal biomass could be an attractive alternative substrate for the production of biofuel and various biorefinery products. Thus, the feasibility of brown seaweed (Laminaria japonica) hydrolysate as a carbon source was investigated here for L-lactate production. This work reports the homofermentative route for L-lactate production by introducing Streptococcus bovis/equinus L-lactate dehydrogenase in an engineered Escherichia coli strain where synthesis of the competing by-product was blocked. The engineered strain utilized both glucose and mannitol present in the hydrolysate under microaerobic condition and produced 37.7 g/L of high optical purity L-lactate at 80 % of the maximum theoretical value. The result shown in this study implies that algal biomass would be as competitive with lignocellulosic biomass in terms of lactic acid production and that brown seaweed can be used as a feedstock for the industrial production of other chemicals.

Microbiological characteristics of acute prostatitis after transrectal prostate biopsy.

PURPOSE: We aimed to identify microbiological characteristics in patients with acute prostatitis after transrectal prostate biopsy to provide guidance in the review of prevention and treatment protocols. MATERIALS AND METHODS: A retrospective analysis of medical records was performed in 1,814 cases who underwent prostate biopsy at Seoul St. Mary's Hospital and St. Vincent's Hospital over a 5 year period from 2006 to 2011. Cases in which acute prostatitis occurred within 7 days after the biopsy were investigated. Before starting treatment with antibiotics, sample collections were done for culture of urine and blood. Culture and drug susceptibility was identified by use of a method established by the Clinical and Laboratory Standards Institute. RESULTS: A total of 1,814 biopsy procedures were performed in 1,541 patients. For 1,246 patients, the procedure was the first biopsy, whereas for 295 patients it was a repeat biopsy. Twenty-one patients (1.36%) were identified as having acute bacterial prostatitis after the biopsy. Fifteen patients (1.2%) had acute prostatitis after the first biopsy, and 6 patients (2.03%) experienced acute prostatitis after a repeat biopsy. Even though the incidence of acute bacterial prostatitis was higher after repeat biopsy than that after the first biopsy, there was no statistically significant intergroup difference in terms of incidence (χ(2)=1.223, p=0.269). When the collected urine and blood samples were cultured, Escherichia coli was found in samples from 15 patients (71.4%), Klebsiella pneumoniae in 3 patients (14.3%), Enterobacter intermedius in 1 patient (4.8%), E. aerogenes in 1 patient (4.8%), and Pseudomonas aeruginosa in 1 patient (4.8%). A fluoroquinolone-resistant strain was confirmed in 5 cases (23.8%) in total. Three cases of E. coli and 1 case of Klebsiella had extended-spectrum ß-lactamase activity. CONCLUSIONS: Empirical treatment of acute prostatitis should be done with consideration of geographical prevalence and drug resistance. This study will provide meaningful information for the management of acute prostatitis after transrectal prostate biopsy.

Analysis of the distribution of bacteria within urinary catheter biofilms using four different molecular techniques.

BACKGROUND: Most nosocomial urinary tract infections are associated with the long-term use of urinary catheters. Such urinary catheter-associated infections are caused by bacteria that reside in biofilms. We determined the distribution of fastidious/nonculturable bacteria in biofilm of urinary catheters and evaluated the availability of concurrent applying various molecular techniques. METHODS: The biofilms were isolated from urinary catheters that had been installed in patients for 3 or 4 weeks and examined by the following 4 different 16S ribosomal RNA (rRNA) analysis techniques: capillary electrophoresis, terminal restriction fragment length polymorphism (T-RFLP), denaturing gradient gel electrophoresis (DGGE), and pyrosequencing. RESULTS: A total of 329 isolates was identified by capillary electrophoresis. The most common genera were Edwardsiella, Enterobacter, Escherichia, and Pseudomonas. A total of 32 bacterial strains was identified by T-RFLP. Escherichia, Pseudomonas, Enterobacter, Moraxella, Proteus, Serratia, and Yersinia were the most represented genera. Similarly, Escherichia, Pseudomonas, and Enterobacter were the most prevalent according to DGGE. Burkholderia, Corynebacterium, Achromobacter, Alcaligenes, Citrobacter, Stenotrophomonas, and Streptococcus were also detected. Escherichia and Pseudomonas were abundantly detected by pyrosequencing. Enterobacter, Bacteroides, Klebsiella, Corynebacterium were also seen. CONCLUSION: These 4 techniques detected different kinds of bacteria, suggesting that the simultaneous application of multiple techniques is necessary to accurately detect fastidious/nonculturable bacteria. Because bacterial growth within urinary catheter biofilms may be associated with urinary tract infections, further comprehensive studies are required.