Ethyl acetate fraction of oregano seed protects non-alcoholic fatty liver in high-fat diet-induced obese mice through modulation of Srebp-1c.

Oregano (Origanum vulgare) seed is used as spices and is known to have anti-inflammatory, antibacterial, and antioxidant effects. The anti-fatty liver effects of oregano seed ethyl acetate (OSEA) were evaluated in high-fat diet (HFD)-induced obese mice. OSEA was orally administered with HFD for 10 weeks. The body weight, aspartate aminotransferase, alanine aminotransferase, cholesterol, triglyceride, and low-density lipoprotein levels in the HFD with 100 mg/kg of OSEA significantly decreased by approximately 1.21-, 1.44-, 2.12-, 1.12-, 1.05, and 1.59 times, respectively, while high-density lipoprotein levels increased by approximately 1.05 times compared to those in the HFD group (p < .05). In addition, the distribution of liver fat in the HFD with 100 mg/kg OSEA (OSEA 100) group decreased significantly (p < .05). Therefore, OSEA supplementation can ameliorate fatty liver disease and reduce the accumulation of triglycerides in adipose tissue. The expression of genes involved in liver fat accumulation, such as sterol regulatory element-binding protein-1c (Srebp-1c), fatty acid synthase (Fas), stearoyl-CoA desaturase-1 (Scd1), and acetyl-CoA carboxylase 1 (Acc1), significantly decreased in OSEA 100 by approximately 2.6-, 1.74-, 1.89-, and 1.56-times, respectively (p < .05). Therefore, OSEA may modify obesity and liver fat accumulation by regulating the expression of genes involved in lipid metabolism.

The Impact of the Rapid Blood Culture Identification Panel on Antibiotic Treatment and Clinical Outcomes in Bloodstream Infections, Particularly Those Associated with Multidrug-Resistant Micro-Organisms.

We evaluated the impact of the FilmArray blood culture identification (BCID) panel on the time taken to administer effective antibiotics and the clinical outcomes of bloodstream infections. We retrospectively screened patients with bloodstream infections who underwent BCID testing and compared them to a historical control group that received conventional culture testing. A total of 144 and 214 patients who underwent BCID and conventional cultures, respectively, were compared. The 30-day mortality (BCID: 9.7% vs. conventional method: 10.7%, p = 0.755), time to effective antibiotic administration (3 h for both BCID and conventional method, p = 0.789), and time to appropriate antibiotic administration did not differ significantly between the groups. BCID was not significantly associated with 30-day mortality after adjusting for the Pitt bacteremia score and the Charlson comorbidity index (adjusted OR = 0.833, CI; 0.398-1.743). Compared with conventional methods, BCID reduced the time to administration of effective antibiotics in cases of carbapenem-resistant Enterobacterales (CRE) (39 h vs. 93 h, p = 0.012) and vancomycin-resistant enterococci (VRE) (50 h vs. 92 h, p < 0.001) bacteremia. BCID did not affect the clinical outcomes of overall bloodstream infections; however, it contributed to the early administration of effective antibiotics in cases of CRE and VRE bacteremia.

Large-Scale Clinical Evaluation of Rapid Blood Culture Identification Panels for Bloodstream Infections at a Tertiary Hospital.

The prompt implementation of optimal antibacterial therapy through the rapid identification of the causative organisms is essential for improving outcomes for critically ill patients with bloodstream infections. We evaluated the clinical performance of the FilmArray blood culture identification (BCID) panel for rapidly identifying causative pathogens in the bloodstream using large-scale clinical samples. We analyzed the results of identification using a BCID panel performed on 2005 positive blood culture bottles from September 2019 to June 2022. Pathogen detection efficiency and interval from Gram staining to identification using the BCID panel were compared to those of conventional identification systems-VITEK MS MALDI-TOF Mass Spectrometer and Vitek2-and antibiotic susceptibility testing-Vitek2. We detected 2167 isolates from 2005 positive blood culture bottles. In these isolates, the BCID panel showed 93% full agreement-both organisms and antimicrobial resistance genes were matched, and no off-target organisms were detected. Species-level discordance was found in 0.6% of tests. Sixty-five isolates (3.0%) were only detected by BCID, whereas 22 isolates (1.0%) from the on-target panel were not detected by BCID. This large-scale study demonstrated that the BCID panel was a reliable and rapid identification method for directly identifying bloodstream pathogens in a positive blood culture.

Genome-wide CRISPRi screen identifies enhanced autolithotrophic phenotypes in acetogenic bacterium Eubacterium limosum.

Acetogenic bacteria are a unique biocatalyst that highly promises to develop the sustainable bioconversion of carbon oxides (e.g., CO and CO2) into multicarbon biochemicals. Genotype-phenotype relationships are important for engineering their metabolic capability to enhance their biocatalytic performance; however, systemic investigation on the fitness contribution of individual gene has been limited. Here, we report genome-scale CRISPR interference screening using 41,939 guide RNAs designed from the E. limosum genome, one of the model acetogenic species, where all genes were targeted for transcriptional suppression. We investigated the fitness contributions of 96% of the total genes identified, revealing the gene fitness and essentiality for heterotrophic and autotrophic metabolisms. Our data show that the Wood-Ljungdahl pathway, membrane regeneration, membrane protein biosynthesis, and butyrate synthesis are essential for autotrophic acetogenesis in E. limosum. Furthermore, we discovered genes that are repression targets that unbiasedly increased autotrophic growth rates fourfold and acetoin production 1.5-fold compared to the wild-type strain under CO2-H2 conditions. These results provide insight for understanding acetogenic metabolism and genome engineering in acetogenic bacteria.

Evaluation of the Efficacy of COVID-19 Booster Vaccinations in Healthcare Personnel.

This study aimed to investigate the efficacy of different COVID-19 booster vaccines by measuring the serum antibody titer. SARS-CoV-2 anti-nucleocapsid protein antibody (N-Ab), anti-spike protein antibody (S-Ab), and neutralizing antibody (Neut.Ab) were measured before and 4-6 weeks after booster vaccinations in healthcare personnel with a previous vaccination within 3-6 months. Personnel who previously received two doses of ChAdOx1 vaccine or two doses of BNT162b2 vaccine received the BNT162b2 vaccine (AAP and PPP groups, respectively). Personnel who previously received two doses of mRNA-1273 received the same vaccine as a booster dose (MMM group). Of the 917 participants, the AAP, MMM, and PPP groups comprised 837 (91.3%), 27 (2.9%), and 53 (5.8%) participants, respectively. The pre-booster S-Ab and Neut.Ab titer were significantly lower in the AAP group. After the booster vaccination, all participants were positive for S-Ab and Neut.Ab; furthermore, the S-Ab and Neut.Ab titer significantly increased in all three groups, although the post-booster S-Ab was lower in the AAP group than in the other groups. The post-booster Neut.Ab titer showed no significant difference among the groups. Our study's results suggest that booster vaccination, after two prior vaccinations, shows a significant effect regardless of the type of vaccine administered.

Recent progress in the engineering of C1-utilizing microbes.

The global climate crisis has led to the transition toward the sustainable production of chemicals and fuels with a low carbon footprint. Microbial utilization of one-carbon (C1) substrates, such as carbon dioxide, carbon monoxide, methane, formate, and methanol, may be a promising replacement for the current fossil fuel-based industry. However, natural C1-utilizing microbes are currently unsuitable for industrial applications because of their slow growth and low carbon conversion efficiency, which results in low productivity and yield. Here, we review the recent achievements in engineering C1-utilizing microbes with improved carbon assimilation efficiency and describe the development of synthetic microorganisms by introducing natural C1 assimilation pathways in non-C1-utilizing microbes. Finally, we outline the future directions for realizing the industrial potential of C1-utilizing microbes.

Antibacterial activities of polyphenols against foodborne pathogens and their application as antibacterial agents.

Polyphenols are secondary metabolites produced in higher plants. They are known to possess various functional properties in the human body. Polyphenols also exhibit antibacterial activities against foodborne pathogens. Their antibacterial mechanism is based on inhibiting bacterial biofilm formation or inactivating enzymes. Food-derived polyphenols with such antibacterial activity are natural preservatives and can be used as an alternative to synthetic preservatives that can cause side effects, such as allergies, asthma, skin irritation, and cancer. Studies have reported that polyphenols have positive effects, such as decreasing harmful bacteria and increasing beneficial bacteria in the human gut microbiota. Polyphenols can also be used as natural antibacterial agents in food packaging system in the form of emitting sachets, absorbent pads, and edible coatings. We summarized the antibacterial activities, mechanisms and applications of polyphenols as antibacterial agents against foodborne bacteria.

Engineering Acetogenic Bacteria for Efficient One-Carbon Utilization.

C1 gases, including carbon dioxide (CO2) and carbon monoxide (CO), are major contributors to climate crisis. Numerous studies have been conducted to fix and recycle C1 gases in order to solve this problem. Among them, the use of microorganisms as biocatalysts to convert C1 gases to value-added chemicals is a promising solution. Acetogenic bacteria (acetogens) have received attention as high-potential biocatalysts owing to their conserved Wood-Ljungdahl (WL) pathway, which fixes not only CO2 but also CO. Although some metabolites have been produced via C1 gas fermentation on an industrial scale, the conversion of C1 gases to produce various biochemicals by engineering acetogens has been limited. The energy limitation of acetogens is one of the challenges to overcome, as their metabolism operates at a thermodynamic limit, and the low solubility of gaseous substrates results in a limited supply of cellular energy. This review provides strategies for developing efficient platform strains for C1 gas conversion, focusing on engineering the WL pathway. Supplying liquid C1 substrates, which can be obtained from CO2, or electricity is introduced as a strategy to overcome the energy limitation. Future prospective approaches on engineering acetogens based on systems and synthetic biology approaches are also discussed.

Systems Biology on Acetogenic Bacteria for Utilizing C1 Feedstocks.

With a presence of the Wood-Ljungdahl pathway, acetogenic bacteria are capable of converting C1 feedstocks into biomass and various metabolites, receiving industrial interest in microbial production of biochemicals derived from C1 substrates. To understand C1 feedstock fermentation using acetogenic bacteria, most of the studies have focused on revealing their carbon assimilation and energy conservation systems. Despite the determination of the essential mechanisms, a fundamental understanding of acetogenic bacteria and the associated complex regulatory systems remains unclear and is needed for rational strain design. For this purpose, systems biology is a suitable approach for investigating genome, transcription, translation, regulation systems, and metabolic flux, providing a glimpse of the relationship between the genotype and phenotype of the organisms. This chapter will cover recent systems biology applications on acetogenic bacteria and discuss the cellular responses during C1 feedstock fermentation along with the regulatory systems that orchestrate cellular processes.

Poly-3-hydroxybutyrate production in acetate minimal medium using engineered Methylorubrum extorquens AM1.

Acetate is regarded as a sustainable microbial feedstock that is synthesized from biowastes such as synthesis gas (syngas), carbon dioxide, lignocellulose, or organic waste. In this study, Methylorubrum extorquens AM1 was engineered to improve the production of bioplastic poly-3-hydroxybutyrate (PHB) using acetate as the sole carbon source. To utilize acetate as a carbon source and methanol as an energy source, acs encoding acetyl-CoA synthetase and fdh from Burkholderia stabilis were overexpressed, while ftfL involved in the assimilation of methanol into formyl-tetrahydrofolate was deleted. The yields of biomass and PHB from acetate significantly improved, and the growth rate and PHB content of the bacteria increased. In addition, sustainability of the PHB production was demonstrated using acetate derived from carbon dioxide and syngas. This study shows that biopolymers could be synthesized efficiently using acetate as the sole carbon source through metabolic engineering and the supply of energy cofactors.

Development of highly characterized genetic bioparts for efficient gene expression in CO2-fixing Eubacterium limosum.

Acetogenic bacteria demonstrate industrial potential for utilizing carbon dioxide (CO2) for biochemical production using the Wood-Ljungdahl pathway. However, the metabolic engineering of acetogenic bacteria has been hampered by the limited number of available genetic bioparts for gene expression. Here, we integrated RNA sequencing, ribosome profiling, differential RNA sequencing, and RNA 3'-end sequencing results of Eubacterium limosum to establish genetic bioparts, such as promoters, 5' untranslated regions, and transcript terminators, to regulate transcriptional and translational expression of genes composing of biosynthetic pathways. In addition, a transformation method for the strain was developed to efficiently deliver the obtained genetic bioparts into cells, resulting in a transformation efficiency of 2.5 × 105 CFU/µg DNA. Using this method, the genetic bioparts were efficiently introduced, and their strengths were measured, which were then applied to optimize the heterologous expression of acetolactate synthase and acetolactate decarboxylase for non-native biochemical acetoin production. The strategy developed in this study is the first report on integrating multi-omics data for biopart development of CO2 or syngas utilizing acetogenic bacteria, which lays a foundation for the efficient production of biochemicals from CO2 or syngas as a carbon feedstock under autotrophic growth conditions.

Risk of Absence of Measles Antibody in Healthcare Personnel and Efficacy of Booster Vaccination.

We aimed to identify the presence of the measles IgG antibody (mIgG-Ab) in healthcare personnel and finding out who needs the measles vaccination. The history of measles vaccination was obtained from the national vaccine registry. A baseline mIgG-Ab test was performed, and the measles vaccine was administered to participants who tested negative or equivocal for mIgG-Abs. During the study, 2885 (87.3%) of the 3303 employees were tested for measles serostatus. The baseline seropositivity rate for mIgG-Abs was 91.9%. Among the 234 seronegative cases, 82.9% were born after 1985. The seroprevalence rate was lower in those who received the measles-mumps-rubella (MMR) vaccine >10 years before the testing time, especially if they were born after 1985 and if there was only one previous record of vaccination. Among the 234 seronegative cases, MMR vaccination was administered in 174 cases, of which serostatus was evaluated in 146 cases. After the first dose, positive seroconversion was achieved in 126 participants (86.3%). After a second dose, 15 achieved (75.0%) positive seroconversion. In healthcare personnel born after the period when measles incidence significantly decreased, it may be necessary to reassess their immune status for measles if more than 10 years have elapsed since the last vaccination.

Acetogenic bacteria utilize light-driven electrons as an energy source for autotrophic growth.

Acetogenic bacteria use cellular redox energy to convert CO2 to acetate using the Wood-Ljungdahl (WL) pathway. Such redox energy can be derived from electrons generated from H2 as well as from inorganic materials, such as photoresponsive semiconductors. We have developed a nanoparticle-microbe hybrid system in which chemically synthesized cadmium sulfide nanoparticles (CdS-NPs) are displayed on the cell surface of the industrial acetogen Clostridium autoethanogenum The hybrid system converts CO2 into acetate without the need for additional energy sources, such as H2, and uses only light-induced electrons from CdS-NPs. To elucidate the underlying mechanism by which C. autoethanogenum uses electrons generated from external energy sources to reduce CO2, we performed transcriptional analysis. Our results indicate that genes encoding the metal ion or flavin-binding proteins were highly up-regulated under CdS-driven autotrophic conditions along with the activation of genes associated with the WL pathway and energy conservation system. Furthermore, the addition of these cofactors increased the CO2 fixation rate under light-exposure conditions. Our results demonstrate the potential to improve the efficiency of artificial photosynthesis systems based on acetogenic bacteria integrated with photoresponsive nanoparticles.

Transcriptome and translatome of CO2 fixing acetogens under heterotrophic and autotrophic conditions.

Acetogens are anaerobic bacteria that utilise gaseous feedstocks such as carbon monoxide (CO) and carbon dioxide (CO2) to synthesise biomass and various metabolites via the energetically efficient Wood-Ljungdahl pathway. Because of this pathway, acetogens have been considered as a novel platform to produce biochemicals from gaseous feedstocks, potentially replacing the conventional thermochemical processes. Despite their advantages, a lack of systematic understanding of the transcriptional and translational regulation in acetogens during autotrophic growth limits the rational strain design to produce the desired products. To overcome this problem, we presented RNA sequencing and ribosome profiling data of four acetogens cultivated under heterotrophic and autotrophic conditions, providing data on genome-scale transcriptional and translational responses of acetogens during CO2 fixation. These data facilitate the discovery of regulatory elements embedded in their genomes, which could be utilised to engineer strains to achieve better growth and productivity. We anticipate that these data will expand our understanding of the processes of CO2 fixation and will help in the designing of strains for the desired biochemical production.

Synthetic Biology on Acetogenic Bacteria for Highly Efficient Conversion of C1 Gases to Biochemicals.

Synthesis gas, which is mainly produced from fossil fuels or biomass gasification, consists of C1 gases such as carbon monoxide, carbon dioxide, and methane as well as hydrogen. Acetogenic bacteria (acetogens) have emerged as an alternative solution to recycle C1 gases by converting them into value-added biochemicals using the Wood-Ljungdahl pathway. Despite the advantage of utilizing acetogens as biocatalysts, it is difficult to develop industrial-scale bioprocesses because of their slow growth rates and low productivities. To solve these problems, conventional approaches to metabolic engineering have been applied; however, there are several limitations owing to the lack of required genetic bioparts for regulating their metabolic pathways. Recently, synthetic biology based on genetic parts, modules, and circuit design has been actively exploited to overcome the limitations in acetogen engineering. This review covers synthetic biology applications to design and build industrial platform acetogens.

Adaptive Laboratory Evolution of Eubacterium limosum ATCC 8486 on Carbon Monoxide.

Acetogens are naturally capable of metabolizing carbon monoxide (CO), a component of synthesis gas (syngas), for autotrophic growth in order to produce biomass and metabolites such as acetyl-CoA via the Wood-Ljungdahl pathway. However, the autotrophic growth of acetogens is often inhibited by the presence of high CO concentrations because of CO toxicity, thus limiting their biosynthetic potential for industrial applications. Herein, we implemented adaptive laboratory evolution (ALE) for growth improvement of Eubacterium limosum ATCC 8486 under high CO conditions. The strain evolved under syngas conditions with 44% CO over 150 generations, resulting in a significant increased optical density (600 nm) and growth rate by 2.14 and 1.44 folds, respectively. In addition, the evolved populations were capable of proliferating under CO concentrations as high as 80%. These results suggest that cell growth is enhanced as beneficial mutations are selected and accumulated, and the metabolism is altered to facilitate the enhanced phenotype. To identify the causal mutations related to growth improvement under high CO concentrations, we performed whole genome resequencing of each population at 50-generation intervals. Interestingly, we found key mutations in CO dehydrogenase/acetyl-CoA synthase (CODH/ACS) complex coding genes, acsA and cooC. To characterize the mutational effects on growth under CO, we isolated single clones and confirmed that the growth rate and CO tolerance level of the single clone were comparable to those of the evolved populations and wild type strain under CO conditions. Furthermore, the evolved strain produced 1.34 folds target metabolite acetoin when compared to the parental strain while introducing the biosynthetic pathway coding genes to the strains. Consequently, this study demonstrates that the mutations in the CODH/ACS complex affect autotrophic growth enhancement in the presence of CO as well as the CO tolerance of E. limosum ATCC 8486.

Risk factors associated with an increase in the size of ground-glass lung nodules on chest computed tomography.

BACKGROUND: The detection rate of ground-glass nodules (GGNs) in the lung has increased with the increased use of low-dose computed tomography (CT) of the chest for cancer screening; however, limited data is available on the natural history, follow-up, and treatment of GGNs. The aim of this study was to identify factors associated with an increase in the size of GGNs. METHODS: A total of 338 patients (mean ages, 59.8 years; males, 35.5%) with 689 nodules who underwent chest CT at our institute between June 2004 and February 2014 were included in this study. The cut-off date of follow-up was August 2018. We analyzed the size, solidity, number, and margins of the nodules compared with their appearance on previous chest CT images. The Cox proportional hazard model was used to identify risk factors associated with nodule growth. RESULTS: The median follow-up period was 21.8 months. Of the 338 patients, 38.5% had a history of malignancy, including lung cancer (8.9%). Among the 689 nodules, the median size of the lesions was 6.0 mm (IQR, 5-8 mm), and the proportion of nodules with size ≥10 mm and multiplicity was 17.1% and 66.3%, respectively. Compared to the nodules without an increase in size, the 79 nodules with an increase in size during the follow-up period were initially larger (growth group, 7.0 mm vs. non-growth group, 6.0 mm; P = 0.027), more likely to have a size ≥10 mm (26.6% vs. 15.9%; P = 0.018), and had less frequent multiplicity (54.4% vs. 67.9%, P = 0.028). In the multivariate analysis, nodule size ≥10 mm (hazard ratio [HR], 2.044; P = 0.005), a patient history of lung cancer (HR: 2.190, P = 0.006), and solitary nodule (HR: 2.499, P < 0.001) were independent risk factors for nodule growth. CONCLUSION: Careful follow-up of GGNs is warranted in patients with a history of malignancy, a large , or a solitary nodule.

Identification of distinctive clinical significance in hospitalized patients with endoscopic duodenal mucosal lesions.

BACKGROUND/AIMS: Duodenitis is not infrequent finding in patient undergoing endoscopy. However, hospitalized patients have a higher incidence of secondary duodenal mucosal lesions that might be related with inflammatory bowel disease (IBD), cytomegalovirus (CMV) infection, tuberculosis, immunologic disorders, or other rare infections. We aimed to identify clinicopathologic features of duodenal mucosal lesions in hospitalized patients. METHODS: All hospitalized patients having duodenal mucosal lesions were identified by endoscopic registration data and pathologic data query from 2011 to 2014. The diagnostic index was designed to be sensitive; however, a detailed review of medical record and endoscopic findings was undertaken to improve specificity. Secondary duodenal lesion was defined as having specific reason to explain the duodenal lesion. RESULTS: Among 6,334 hospitalized patients have undergone upper endoscopy, endoscopic duodenal mucosal lesions was detected in 475 patients. Secondary duodenal lesions was 21 patients (4.4%) and the most frequent secondary cause was IBD (n = 7). The mean age of secondary group was significantly lower than that in primary group (42.3 ± 18.9 years vs. 58.5 ± 16.8 years, p = 0.00), and nonsteroidal anti-inflammatory drugs were less frequently used in secondary group, but there was no differences of gender or presence of Helicobacter pylori. The involvement of distal part of duodenum including postbulbitis or panduodenitis was more frequently detected in secondary group than in primary group. By multivariate regression analysis, younger age of 29 years and the disease extent were significant predictors for the secondary mucosal lesions. CONCLUSIONS: Secondary duodenal mucosal lesions with different pathophysiology, such as IBD or CMV infection, are rare. Disease extent and age seems the most distinctive feature of secondary duodenal mucosal lesions.