High-energy-resolution off-resonant spectroscopy with self-seeded x-ray free-electron laser pulses.

This paper presents the implementation of high-energy-resolution off-resonant spectroscopy (HEROS) measurements using self-seeded x-ray free-electron laser (XFEL) pulses. This study systematically investigated XFEL conditions, including photon energy and accumulated shot numbers, to optimize the measurement efficiency for copper foil samples near the K-edge. The x-ray absorption spectra reconstructed using HEROS were compared with those derived from fluorescence-yield measurements. The HEROS-based spectra exhibited consistent line shapes independent of the sample thickness. The potential application of HEROS to high-temperature copper was also explored. HEROS offers distinct advantages including scan-free measurement of x-ray absorption spectra with reduced core-hole lifetime broadening and self-absorption effects. Using self-seeded XFEL pulses, HEROS facilitates single-shot-based pump-probe measurements to investigate the ultrafast dynamics in various materials and diverse conditions.

Role of soil microplastic pollution in climate change.

In recent decades, environmental pollution from microplastic (MPs: <5 mm) and climate change have received international attention. However, these two issues have been primarily investigated separately hitherto, although they exhibit a cause-and-effect relationship. Studies considering MPs and climate change as causal entities have focused only on MP pollution in marine environments as a contributor to climate change. Meanwhile, systematic causal studies have not been performed inadequately to understand the role of soil, which is a primary terrestrial sink of greenhouse gases (GHGs) in the context of MP pollution, in climate change. In this study, the causal effect of soil MP pollution on GHG emissions as direct and indirect contributors to climate change is systematically analyzed. The mechanisms underlying the contribution of soil MPs to climate change are discussed, and future research perspectives are suggested. Approximately 121 research manuscripts pertaining to MP pollution and its associated effects on GHGs, carbon sinks, and soil respiration, recorded between 2018 and 2023, are selected and cataloged from seven database categories in PubMed, Google Scholar, Nature's database, and Web of Science. Several studies demonstrated that soil MP pollution directly contributes to climate change by accelerating the emission of GHGs from the soil to the atmosphere and indirectly by promoting soil respiration and adversely affecting natural carbon sinks, such as trees. Other studies correlated the release of GHGs from the soil to mechanisms such as the alteration of soil aeration, methanogen activity, and carbon and nitrogen cycles, and improved the abundance of carbon and nitrogen soil microbial functional genes adhering to plant roots to create anoxic conditions for plant growth. In general, soil MP pollution increases the release of GHGs into the atmosphere, thereby contributing to climate change. However, further research is to be conducted by investigating the underlying mechanisms using more practical field-scale data.

Investigation of Nonequilibrium Electronic Dynamics of Warm Dense Copper with Femtosecond X-Ray Absorption Spectroscopy.

Ultrafast optical excitation of matter leads to highly excited states that are far from equilibrium. In this study, femtosecond x-ray absorption spectroscopy was used to visualize the ultrafast dynamics in photoexcited warm dense Cu. The rich dynamical features related to d vacancies are observed on femtosecond timescales. Despite the success in explaining x-ray absorption data in the picosecond regime, the new femtosecond data are poorly understood through the traditional two-temperature model based on the fast thermalization concept and the static electronic structure for high-temperature metals. An improved understanding can be achieved by including the recombination dynamics of nonthermal electrons and changes in the screening of the excited d block. The population balance between the 4sp and 3d bands is mainly determined by the recombination rate of nonthermal electrons, and the underpopulated 3d block is initially strongly downshifted and recovered in several hundreds of femtoseconds.

Evaluation of PCR-reverse blot hybridization assay, REBA Sepsis-ID test, for simultaneous identification of bacterial pathogens and mecA and van genes from blood culture bottles.

BACKGROUND: The aim of this study was to evaluate a newly developed PCR-based reverse blot hybridization assay (PCR-REBA), REBA Sepsis-ID (M&D, Wonju, Korea), to rapidly detect the presence of bacteremia and antimicrobial resistance gene in blood culture samples. METHODS: One thousand four hundred consecutive blood culture samples from patients with a delta neutrophil index greater than 2.7% were selected from March to July in 2013. Three hundred positive and 1,100 negative for bacterial growth in blood culture bottles samples were tested by conventional and real-time PCR-REBA, respectively. RESULTS: The overall agreement between the conventional identification test and the REBA Sepsis-ID test was 95.3% (286/300). Agreement for gram-positive bacteria, gram-negative bacteria, fungi, and polymicrobials was 94.5% (190/201), 97.3% (71/73), 100% (14/14), and 91.7% (11/12), respectively. The detection rate of the mecA gene from methicillin-resistant Staphylococcus isolates was 97.8% (90/92). The vanA gene was detected in one blood culture sample from which vancomycin-resistant Enterococcus was isolated. When the cycle threshold for real-time PCR was defined as 30.0, 2.4% (26/1,100) of negative blood culture samples tested positive by real-time PCR. CONCLUSIONS: The REBA Sepsis-ID test is capable of simultaneously and quickly detecting both causative agents and antimicrobial resistance genes, such as mecA and van, in blood culture positive samples.

Antibiotic resistance in Helicobacter pylori strains and its effect on H. pylori eradication rates in a single center in Korea.

BACKGROUND: Clarithromycin, amoxicillin, metronidazole, tetracycline, and levofloxacin have been commonly used for the eradication of Helicobacter pylori. We compared the change in antibiotic resistance of H. pylori strains during two separate periods and investigated the effect of antibiotic resistance on H. pylori eradication. METHODS: H. pylori strains were isolated from 71 patients between 2009 and 2010 and from 94 patients between 2011 and 2012. The distribution of minimal inhibitory concentration (MIC) of 5 antibiotics was assessed using the agar dilution method, and H. pylori eradication based on the antimicrobial susceptibility of the isolates was investigated retrospectively. RESULTS: Antibiotic resistance rate against clarithromycin, amoxicillin, tetracycline, metronidazole, and levofloxacin for the 2009-2010 isolates were 7.0% (5/71), 2.8% (2/71), 0% (0/71), 45.1% (32/71), and 26.8% (19/71), respectively, and for the 2011-2012 isolates were 16.0% (15/94), 2.1% (2/94), 0% (0/94), 56.3% (53/94), and 22.3% (21/94), respectively. Multi-drug resistance for 2 or more antibiotics increased slightly from 16.9% (12/71) in the 2009-2010 isolates to 23.4% (22/94) in the 2011-2012 isolates. In follow-up testing of 66 patients, first-line treatment successfully eradicated H. pylori in 50 patients (75.8%) and failed in 4 of 7 patients (57.1%) in a clarithromycin-resistant and amoxicillin-susceptible group. CONCLUSIONS: We observed an increase in resistance to clarithromycin and an overall increase in multi-drug resistance during the 2 study periods. The effectiveness of the eradication regimen was low with combinations of clarithromycin and amoxicillin, particularly in the clarithromycin-resistant group. Thus, eradication of H. pylori depends upon periodic monitoring of antimicrobial susceptibility.

PCR-reverse blot hybridization assay for screening and identification of pathogens in sepsis.

Rapid and accurate identification of the pathogens involved in bloodstream infections is crucial for the prompt initiation of appropriate therapy, as this can decrease morbidity and mortality rates. A PCR-reverse blot hybridization assay for sepsis, the reverse blot hybridization assay (REBA) Sepsis-ID test, was developed; it uses pan-probes to distinguish Gram-positive and -negative bacteria and fungi. In addition, the assay was designed to identify bacteria and fungi using six genus-specific and 13 species-specific probes; it uses additional probes for antibiotic resistance genes, i.e., the mecA gene of methicillin-resistant Staphylococcus aureus (MRSA) and the vanA and vanB genes of vancomycin-resistant enterococci (VRE). The REBA Sepsis-ID test successfully identified clinical isolates and blood culture samples as containing Gram-positive bacteria, Gram-negative bacteria, or fungi. The results matched those obtained with conventional microbiological methods. For the REBA Sepsis-ID test, of the 115 blood culture samples tested, 47 (40.8%) and 49 (42.6%) samples were identified to the species and genus levels, respectively, and the remaining 19 samples (16.5%), which included five Gram-positive rods, were identified as Gram-positive bacteria, Gram-negative bacteria, or fungi. The antibiotic resistances of the MRSA and VRE strains were identified using both conventional microbiological methods and the REBA Sepsis-ID test. In conclusion, the REBA Sepsis-ID test developed for this study is a fast and reliable test for the identification of Gram-positive bacteria, Gram-negative bacteria, fungi, and antibiotic resistance genes (including mecA for MRSA and the vanA and vanB genes for VRE) in bloodstream infections.

Inhibitory effects of anthocyanins on secretion of Helicobacter pylori CagA and VacA toxins.

Anthocyanins have been studied as potential antimicrobial agents against Helicobacter pylori. We investigated whether the biosynthesis and secretion of cytotoxin-associated protein A (CagA) and vacuolating cytotoxin A (VacA) could be suppressed by anthocyanin treatment in vitro. H. pylori reference strain 60190 (CagA(+)/VacA(+)) was used in this study to investigate the inhibitory effects of anthocyanins; cyanidin 3-O-glucoside (C3G), peonidin 3-O-glucoside (Peo3G), pelargonidin 3-O-glucoside (Pel3G), and malvidin 3-O-glucoside (M3G) on expression and secretion of H. pylori toxins. Anthocyanins were added to bacterial cultures and Western blotting was used to determine secretion of CagA and VacA. Among them, we found that C3G inhibited secretion of CagA and VacA resulting in intracellular accumulation of CagA and VacA. C3G had no effect on cagA and vacA expression but suppressed secA transcription. As SecA is involved in translocation of bacterial proteins, the down-regulation of secA expression by C3G offers a mechanistic explanation for the inhibition of toxin secretion. To our knowledge, this is the first report suggesting that C3G inhibits secretion of the H. pylori toxins CagA and VacA via suppression of secA transcription.

Mutational hotspots in the mitochondrial genome of lung cancer.

We determined the somatic mutations in the mitochondrial genomes of 70 lung cancer patients by pair-wise comparative analyses of the normal- and tumor-genome sequences acquired using Affymetrix Mitochondrial Resequencing Array 2.0. The overall mutation rates in lung cancers were Approximately 100 fold higher than those in normal cells, with significant statistical correlation with smoking (p=0.00088). Total of 532 somatic mutations were evenly distributed in 499 positions with very low overall frequency (1.07/bp), but the non-synonymous mutations causing amino acid substitution occurred more frequently (1.83/bp), particularly at two positions, 8701 and 10398 (10.5/bp) that code for ATPase6 and NADH dehydrogenase 3, respectively. Despite the randomness or even distribution of the mutations, these two mutations occurred together in 86% of the cases. The linkage between the two most frequent mutations suggests that they were selected together, possibly due to their cooperative role during cancer development. Indeed, the mutation at 10398 was shown by Canter, Pezzotti, and their colleagues in 2009, as a risk factor for breast cancer. In this study, we identified two potential biomarkers that might be functionally linked together during the development of cancer.

Prevalence and resistance patterns of extended-spectrum and AmpC ß-lactamase in Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, and Salmonella serovar Stanley in a Korean tertiary hospital.

A total of 100 clinical isolates of Escherichia coli (n = 35), Klebsiella pneumoniae (n = 63), Proteus mirabilis (n = 1), and Salmonella serovar Stanley (n = 1), showing resistance to cefoxitin, or returning positive in extended-spectrum ß-lactamase (ESBL) by Clinical and Laboratory Standards Institute (CLSI) ESBL confirmatory method, were studied. The isolates were examined by the boronic acid (BA) disk test, polymerase chain reaction, and pulsed-field gel electrophoresis (PFGE) to investigate genetic similarities. The concurrence rates for ESBLs by the CLSI and the BA disk test were 97% for E. coli and 96.7% for K. pneumoniae. A total of 41 isolates showing cefoxitin resistance yielded all positive by the BA disk test. All the 33 K. pneumoniae isolates, which showed positive by the BA disk test, were carrying AmpC genes. The TEM and CTX-M types were predominant in E. coli and the SHV and the CIT and/or DHA types were predominant in K. pneumoniae. PFGE analysis showed almost 75% of genetic similarities among K. pneumoniae isolates producing ESBLs and/or AmpC ß-lactamases (AmpCs) as each K. pneumoniae carried variable genes and showed variable antibiotic patterns. Clearly, the BA disk test was a useful method for the detection of ESBLs and AmpCs. In particular, cefoxitin resistance and BA-positive trait of K. pneumoniae do reflect the presence of AmpC genes in the organism.

Identification of the repeated number of C and D regions of tyrosine phosphorylation motifs in Helicobacter pylori cagA using multiplex PCR.

Various tyrosine phosphorylation motif regions of H. pylori cagA exist. The number of these regions was found to have some influence on cell signaling, which was found to be more pronounced when in D (ESS) region than in C (WSS) region. A molecular biological method with multiplex PCR was developed to distinguish C and D regions, and to identify the repetition number of tyrosine phosphorylation of the cagA gene. Multiplex PCR using novel primer sets was performed on 73 strains of H. pylori isolated from Korean patients with upper gastrointestinal diseases. The Western cagA was identified in only 3 strains (4.1%) whereas East Asia cagA was identified in 69 strains (94.5%). These results were reconfirmed through a sequencing analysis. The method developed in this study would be useful for monitoring the repeated number of C and D regions of tyrosine phosphorylation motifs in H. pylori cagA.

In vitro antibacterial activity of echinomycin and a novel analogue, YK2000, against vancomycin-resistant enterococci.

The in vitro inhibitory and bactericidal activity of echinomycin and its the novel synthetic analogues of echinomycin,YK2000 and YK2005, were evaluated using 93 clinical isolates of vancomycin-resistant enterococci (VRE). In agar dilution tests, the MIC(90) of echinomycin and YK2000 were 0.125 and 8 mg/l, respectively, using Mueller-Hinton II agar, while that of YK2005 was 32 mg/l. Bactericidal activity of echinomycin and YK2000 were two to four times higher than the MIC in time-kill assay experiments. These results suggest that echinomycin and its analogues might be useful as anti-VRE drugs.