Impact of essential and optional ingredients on microbial and metabolic profiles of kimchi

This study aimed to examine the impacts of essential and optional ingredients on the microbial and metabolic profiles of kimchi during 100 days of fermentation, using a mix-omics approach. Kimchi manufactured without essential ingredients (e.g., red pepper, garlic, ginger, green onion, and radish) had lower lactic acid content. The absence of garlic was associated with a higher proportion of Latilactobacillus and Lactococcus, while the absence of red pepper was associated with a greater proportion of Leuconostoc than the control group. In addition, red pepper and garlic served as primary determinants of the levels of organic acids and biogenic amines. Sugar was positively correlated with the levels of melibiose, and anchovy sauce was positively correlated with the levels of amino acids such as methionine, leucine, and glycine. These findings contribute to a fundamental understanding of how ingredients influence kimchi fermentation, offering valuable insights for optimizing kimchi production to meet various preferences.

Functional mining of novel terpene synthases from metagenomes

BACKGROUND

Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the genomes of uncultivated organisms living in the soil, indicating a vast array of putative terpenoids waiting to be discovered.

RESULTS

We aimed to develop a high-throughput functional metagenomic screening system for identifying novel terpene synthases from bacterial metagenomes by relieving the toxicity of terpene biosynthesis precursors to the Escherichia coli host. The precursor toxicity was achieved using an inducible operon encoding the prenyl pyrophosphate synthetic pathway and supplementation of the mevalonate precursor. Host strain and screening procedures were finely optimized to minimize false positives arising from spontaneous mutations, which avoid the precursor toxicity. Our functional metagenomic screening of human fecal metagenomes yielded a novel β-farnesene synthase, which does not show amino acid sequence similarity to known β-farnesene synthases. Engineered S. cerevisiae expressing the screened β-farnesene synthase produced 120 mg/L β-farnesene from glucose (2.86 mg/g glucose) with a productivity of 0.721 g/L∙h.

CONCLUSIONS

A unique functional metagenomic screening procedure was established for screening terpene synthases from metagenomic libraries. This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats.

A Tunable and Expandable Transactivation System in Probiotic Yeast Saccharomyces boulardii

Precise transcriptional modulation is a key requirement for developing synthetic probiotics with predictably tunable functionalities. In this study, an expandable and tunable transactivation system was constructed and validated in probiotic yeast Saccharomyces boulardii. The use of nuclease-null Cas9 and scaffold RNA (scRNA) directed regulation enabled transactivation under the control of a synthetic promoter in S. boulardii. A synthetic promoter consisting of the scRNA target sequence and the core GAL7 promoter region restricted interference from the native galactose regulon. The system was readily expanded by introducing new target sequences to the promoter and scRNA. Complementarity between the promoter and scRNA, and binding specificity between scRNA and transcriptional activator, served as two layers of orthogonality of the transactivation. In addition, activator expression under the control of an inducible promoter enabled control of the transactivation via chemical inducer. The described system has the potential to enable engineering of probiotic yeast to more precisely perform therapeutic functions.

2'-Fucosyllactose production in engineered Escherichia coli with deletion of waaF and wcaJ and overexpression of FucT2

2'-Fucosyllactose (2'-FL), a major oligosaccharide of human breast milk, and is currently supplemented into infant formula. For the overproduction of 2'-FL via fucosylation of lactose, conventional approaches have focused on the episomal overexpression of de novo or salvage GDP-L-fucose biosynthetic pathway and α-1,2-fucosyltransferase (FucT2) through T7 RNA polymerase expression system in engineered E. coli. However, these approaches have drawbacks of metabolic burden, plasmid instability, and inclusion body formation. In this study, a deletion mutant of waaF coding for ADP-heptose:LPS heptosyltransferase II was employed for 2'-FL production. As the waaF deletion induces accumulation of colanic acid, additional deletion of wcaJ coding for UDP-glucose-1-phosphate transferase in the waaF deletion mutant resulted in enhanced accumulation of GDP-L-fucose. Besides, 2'-FL yields and titers were drastically improved when T7 promoter was replaced with Trc promoter for α-1,2 fucosyltransferase expressions in the waaF and wcaJ deleted strain. As a result, when FucT2 was expressed under Trc promoter in the E. coli JM109(DE3) ΔwaaFΔwcaJ, 14.7 g/L of 2'-FL was produced with a productivity of 0.31 g/L/h in a fed-batch fermentation. We envision that the deletion-based metabolic design and decreased promoter strength for fucosyltransferase expression can resolve the drawbacks of T7 RNA polymerase-based expression design for 2'-FL production in E. coli.

Impact of atrial fibrillation on the progression and outcomes of isolated mild functional tricuspid regurgitation

Background

Atrial fibrillation (AF) is increasingly recognized as a cause of tricuspid regurgitation (TR) in the structurally normal tricuspid valve. However, there are limited data regarding the impact of AF on TR progression and its long-term cardiovascular outcomes.

Purpose

We aimed to investigate the association of AF with the significant TR progression and its impact on clinical outcomes among patients with isolated mild functional TR.

Methods

We studied 834 patients with mild function TR identified on the echocardiography between 2007 and 2019, whose follow-up echocardiography beyond 1-year was available. Major exclusion criteria were the overt causes of primary and secondary TR (i.e., concomitant left-sided heart disease). Primary endpoint was the significant TR progression to more than a moderate degree on the follow-up echocardiography. Composite cardiac event was defined as cardiovascular death, TR surgery, and heart failure admission due to TR.

Results

Of 834 patients with isolated mild functional TR (mean age 65.6 years, 41% men), 292 (35.0%) patients had AF at the baseline. Patients with AF were older and had larger left atrium compared to those without. During the median of 4.55 years follow-up (interquartile interval 2.56–7.24 years), 36 patients developed a significant TR ≥ moderate degree. The cumulative rate of TR progression was significantly higher in patients with AF than those without (11.3% versus 0.6%, P<0.001) (Figure 1). Multivariable Cox analyses showed that AF was associated with a 3-fold higher risk of TR progression (adjusted hazard ratio 3.50, 95% confidence interval 1.42–8.65). Regarding the cardiovascular outcomes, patients who developed significant TR had a higher rate of composite cardiac events compared to those who did not (cardiac events: 38.9% versus 6.3% P<0.001) (Figure 2).

Conclusions

AF is a strong risk factor for TR progression among patients with isolated mild functional TR. In addition, the development of significant TR is associated with worse cardiovascular outcomes. These findings highlight the important pathophysiology of AF on TR development and its clinical consequences.

Funding Acknowledgement

Type of funding sources: None.

Demonstration of reduced neoclassical energy transport in Wendelstein 7-X

Research on magnetic confinement of high-temperature plasmas has the ultimate goal of harnessing nuclear fusion for the production of electricity. Although the tokamak1 is the leading toroidal magnetic-confinement concept, it is not without shortcomings and the fusion community has therefore also pursued alternative concepts such as the stellarator. Unlike axisymmetric tokamaks, stellarators possess a three-dimensional (3D) magnetic field geometry. The availability of this additional dimension opens up an extensive configuration space for computational optimization of both the field geometry itself and the current-carrying coils that produce it. Such an optimization was undertaken in designing Wendelstein 7-X (W7-X)2, a large helical-axis advanced stellarator (HELIAS), which began operation in 2015 at Greifswald, Germany. A major drawback of 3D magnetic field geometry, however, is that it introduces a strong temperature dependence into the stellarator's non-turbulent 'neoclassical' energy transport. Indeed, such energy losses will become prohibitive in high-temperature reactor plasmas unless a strong reduction of the geometrical factor associated with this transport can be achieved; such a reduction was therefore a principal goal of the design of W7-X. In spite of the modest heating power currently available, W7-X has already been able to achieve high-temperature plasma conditions during its 2017 and 2018 experimental campaigns, producing record values of the fusion triple product for such stellarator plasmas3,4. The triple product of plasma density, ion temperature and energy confinement time is used in fusion research as a figure of merit, as it must attain a certain threshold value before net-energy-producing operation of a reactor becomes possible1,5. Here we demonstrate that such record values provide evidence for reduced neoclassical energy transport in W7-X, as the plasma profiles that produced these results could not have been obtained in stellarators lacking a comparably high level of neoclassical optimization.

Neural network surrogates of Bayesian diagnostic models for fast inference of plasma parameters

We present a framework for training artificial neural networks (ANNs) as surrogate Bayesian models for the inference of plasma parameters from diagnostic data collected at nuclear fusion experiments, with the purpose of providing a fast approximation of conventional Bayesian inference. Because of the complexity of the models involved, conventional Bayesian inference can require tens of minutes for analyzing one single measurement, while hundreds of thousands can be collected during a single plasma discharge. The ANN surrogates can reduce the analysis time down to tens/hundreds of microseconds per single measurement. The core idea is to generate the training data by sampling them from the joint probability distribution of the parameters and observations of the original Bayesian model. The network can be trained to learn the reconstruction of plasma parameters from observations and the model joint probability distribution from plasma parameters and observations. Previous work has validated the application of such a framework to the former case at the Wendelstein 7-X and Joint European Torus experiments. Here, we first give a description of the general methodological principles allowing us to generate the training data, and then we show an example application of the reconstruction of the joint probability distribution of an effective ion charge Z_eff-bremsstrahlung model from data collected at the latest W7-X experimental campaign. One key feature of such an approach is that the network is trained exclusively on data generated with the Bayesian model, requiring no experimental data. This allows us to replicate the training scheme and generate fast, surrogate ANNs for any validated Bayesian diagnostic model.

Stratifying the prognostic capability of cardiovascular magnetic resonance in severe aortic stenosis: a machine learning approach

Background

Cardiovascular magnetic resonance (CMR) demonstrates promise in improving patient risk stratification in aortic stenosis (AS). We explored whether machine learning might provide further insights into the prognostic capability of CMR parameters.

Methods

Severe AS patients (n=440) undergoing AVR were prospectively enrolled across 10 international sites, and CMR performed prior to AVR. A machine learning prediction model using a random survival forest (RSF) was trained with 29 variables, including 13 CMR, 4 echocardiography, and 12 clinical parameters, using post-AVR mortality as an outcome. The impact of the important variables on the outcome (partial dependency) was examined.

Results

The most predictive CMR parameters in the RSF model were the extracellular volume fraction (ECV%), followed by right ventricular ejection fraction (RVEF), late gadolinium enhancement (LGE%), and indexed left ventricular end-diastolic volume (LVEDVi). Regarding the partial effects, the predicted mortality increased strongly once the ECV% exceeded 26.5% (Figure 1A). The LGE% was associated with an increased risk of mortality, which reached a plateau beyond the level of 2% (Figure 1C). There were U-shaped relationships between mortality and both RVEF and LVEDVi, with the lowest mortality seen at RVEF 70% and LVEDVi 68ml/m2 (Figure 1B, D). These trends of predicted outcomes by each variable were verified in the Kaplan-Meier curves and Cox analyses (Table). In both Cox and RSF models, the predictability was substantially increased when these four CMR parameters were added to conventional clinical risk factors. An AS-CMR risk score comprised of these four parameters presented a stepwise increase in mortality with increasing adverse CMR features (p<0.001).

Conclusions

Our machine learning analysis using RSF has identified ECV%, RVEF, LGE%, and LVEDVi as key prognostic markers in severe AS with a nonlinear influence of each parameter on mortality post-AVR.

Figure 1

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): This study was supported by grants from the Korean Health Technology R & D Project, Ministry of Health, Welfare & Family Affairs, Republic of Korea (HI16C0225 and HI15C0399) and the National Institute for Health Research (NIHR) infrastructure at Leeds.

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial

BACKGROUND

Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome.

RESULTS

All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts toward average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel "transplantation index" metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs.

CONCLUSIONS

Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome. Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients' microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product-a proxy for the donor-than an antibiotic perturbed state.

TRIAL REGISTRATION

ClinicalTrials.gov, NCT02299570 . Registered 19 November 2014 Video Abstract.

Fipronil upregulates inflammatory cytokines and MUC5AC expression in human nasal epithelial cells

BACKGROUND

Airway inflammation and excessive mucin production are pathophysiological characteristics of airway diseases. Fipronil, a pesticide, is being extensively used in agriculture and veterinary medicine worldwide. However, this compound impairs immune function in non-target organisms. The present study aimed to evaluate the effect of fipronil on pro-inflammatory cytokine and mucus production and signalling pathways in human primary nasal METHODOLOGY: The effect of fipronil on pro-inflammatory cytokine and MUC5AC expression and the signalling pathway of fipronil were investigated using real-time PCR, enzyme immunoassays, immunofluorescence, and immunoblot analysis with specific inhibitors and small interfering RNA.

RESULTS

Fipronil treatment increased pro-inflammatory cytokine interleukin (IL)-1beta, IL-6, IL-8, and MUC5AC expression in human primary nasal epithelial cells. It also induced phosphorylation of extracellular signal-regulated kinase 1/2 (ERK1/2) mitogenactivated protein kinase (MAPK), p38 MAPK, and nuclear factor kappa-light-chain-enhancer of activated B cells (NF-kB). MAPK and NF-kB inhibitor treatment significantly inhibited increases in IL-1beta, IL-6, IL-8, and MUC5AC expression. Ex vivo data confirmed that fipronil-induced MUC5AC expression occurs through ERK1/2, p38, and NF-kB signalling pathways in nasal inferior turbinate tissue.

CONCLUSIONS

Fipronil induced pro-inflammatory cytokine IL-1beta, IL-6, IL-8, and MUC5AC expression via ERK1/2 MAPK, p38 MAPK, and NF-kB in human primary nasal epithelial cells.

P785 Left ventricular geometry and myocardial contractility modulate impact of statins on prognosis in patients with acute heart failure

Funding Acknowledgements

N/A

Background/Introduction: The benefit of statins in patients with heart failure (HF) remains controversial and the mechanism of action is largely speculative. We investigated whether survival benefit with statins differs according to left ventricular (LV) geometry and myocardial contractility in acute HF patients.

Methods

We enrolled 1792 acute HF patients receiving statins and 2296 patients not receiving statins admitted from 2009 to 2016. The LV and right ventricular (RV) global longitudinal strain (GLS) was assessed as a measure of myocardial contractility. Patients were classified into 2 groups based on ischemic etiology of HF and further divided into 4 subgroups according to the median values of LV-GLS or RV-GLS. The primary outcome was 5-year all-cause mortality. The study protocol was approved by the ethics committee at each institute and complied with the Declaration of Helsinki. The need for written informed consent was waived.

Results

During the 5-year follow-up, 1740 (40.4%) patients died and they had more unfavorable baseline characteristics. Statin therapy was significantly associated with improved survival in overall patients and in both groups with and without ischemic etiology (all p <0.001). Patients with concentric remodeling/hypertrophy and eccentric hypertrophy demonstrated survival benefit with statin therapy (P = 0.033, 0.004, and 0.008, respectively), while those with normal geometry did not (p = 0.123). In the non-ischemic HF group, survival benefit with statin therapy was confined to patients with low LV-GLS (p = 0.045) or those with low RV-GLS p = 0.003). On the contrary, in ischemic HF group, survival benefit with statin therapy was observed in all patients regardless of the values of LV-GLS or RV-GLS. Significant interactions were present between statin use and diabetes mellitus and IHD (p for interaction = 0.027 and 0.003, respectively) regarding mortality.

Conclusions

LV geometry and myocardial contractility may modulate the effects of statins in patients with acute HF. These echocardiographic measures can provide prognostic information to guide tailored statin treatment in this population. Our findings may also help to develop more well-designed prospective studies, in terms of a more homogenous study population, to confirm survival benefit with statin therapy.

Abstract P785 Figure. Multivariate Cox survival curves

P5002The impact of diabetes mellitus on global longitudinal strain of patients with acute heart failure

Introduction

Diabetes mellitus (DM) aggravates the clinical features and the prognosis of heart failure (HF) patients. However, the impact of DM on the ventricular systolic function of HF patients is not well delineated.

Purpose

The present study aimed to investigate the impact of DM on HF, regarding the systolic function presented by the global longitudinal strain (GLS).

Methods

In 4312 patients with acute HF, left ventricle (LV) and right ventricle (RV) GLS were acquired by speckle-tracking echocardiography. HF patients with DM were compared to those without DM from the entire cohort (n=4312), as well as the propensity-score matched cohort (n=3034).

Results

Our cohort consisted of 1750 DM patients (40.6%). Both LV-GLS and LVEF were significantly lower within the patients with DM (10.1±4.8% vs. 11.3±5.1%, p<0.001 for LV-GLS; 39.1±15.5% vs. 41.7±15.6%, p<0.001 for LVEF) in the entire cohort. In the propensity-score matched cohort, LV-GLS was significantly reduced in the patients with DM compared to those without DM (10.2±4.9% vs. 10.9±5.0%, p<0.001), even with the matched LVEF (Table 1). Decreased LV-GLS in the DM patients was consistently identified in both subgroups of preserved EF and reduced EF (Table 1). Although RV-GLS was slightly lower in the patients with DM from the matched cohort, it was not significant in neither the preserved EF nor the reduced EF subgroup. When comparing the adverse outcome in the propensity-score matched cohort, the survival of patients with DM was significantly lower (Figure 1-A, 1-B), except for the preserved EF group (Figure 1-C).

Comparison between heart failure patients with and without diabetes in the matched cohort Matched cohort p-value HFrEF (matched) p-value HFpEF (matched) p-value No-DM (n=1517) DM (n=1517) No-DM (n=823) DM (n=801) No-DM (n=652) DM (n=669) Age, years 71±14 71±11 0.962 69±14 70±11 0.305 75±11 74±10 0.061 Ischemic heart disease, n (%) 545 (35) 575 (37) 0.275 375 (36) 402 (39) 0.238 150 (34) 147 (34) 0.945 GFR, mL/min/1.73m2 56±27 55±27 0.282 58±28 56±27 0.253 54±27 54±26 1.000 HbA1C, % 5.7±0.4 7.3±1.4 <0.001 5.7±0.4 7.3±1.4 <0.001 5.7±0.4 7.2±1.4 <0.001 LV ejection fraction, % 39±15 39±15 0.871 31±9 31±10 0.99 59±5 59±6 0.279 LV-GLS, % 10.9±5.0 10.2±4.9 <0.001 9.1±3.8 8.3±3.6 <0.001 15.5±4.5 14.9±4.5 0.036 RV-GLS, % 13.1±6.5 12.7±6.2 0.045 12.1±6.2 11.8±5.9 0.188 15.6±6.5 15.0±6.4 0.157

Figure 1. Outcome by DM status

Conclusions

DM is associated with the impaired LV systolic function presented by GLS in HF patients, even with the adjustment of LVEF. The result indicates that GLS is a more sensitive marker of systolic function than LVEF, in terms of the DM status among the HF patients.

An extra copy of the β-glucosidase gene improved the cellobiose fermentation capability of an engineered Saccharomyces cerevisiae strain

In a previously engineered Saccharomyces cerevisiae recombinant, the cellobiose fermentation rate was significantly lower than the glucose fermentation rate. Thus, we implemented a genome-wide perturbation library to find gene targets for improving the cellobiose fermentation capability of the yeast strain. Unexpectedly, we discovered a transformant that contained an additional β-glucosidase gene (gh1-1), possibly through homologous recombination between the plasmids. The additional β-glucosidase led to the fastest cellobiose fermentation activity among all the transformants evaluated, and the strain demonstrated significantly higher β-glucosidase activity than the control strain, especially during the initial exponential growth phase. The present work revealed the benefit of the extra gh1-1 copy for efficient cellobiose fermentation in the engineered S. cerevisiae strain.

1438MicroRNA editing is integral for interleukin-6 trans-signalling and leukocyte trafficking to ischemic tissues

Background/Aim

Adenosine to inosine RNA editing is an essential post-transcriptional RNA modification catalysed by adenosine deaminase acting on RNA-1 and -2 (ADAR1; ADAR2). Endothelial cells (ECs) attract and guide leukocytes to sites of ischemic tissue injury. Here we studied the role of RNA editing in ischemic disease.

Methods

Primary human and murine vascular endothelial cell cultures were used to assess the EC responses to interleukin-6 (IL-6) or ischemia. For the animal studies, the effect of ADAR2 in acute and chronic ischemic disease was evaluated in cremaster muscle microcirculation by intravital microscopy, in peritoneal cavity after sterile peritonitis and in gastrocnemius muscle after hind-limb ischemia by 8-colour flow cytometry and immunohistochemistry (IHC) studies of Adar2−/−/tg as well as of i(nducible)EC-ADAR2 knockout (KO) mice. For the mechanistic studies, deep RNA sequencing, qRT-PCR, western blot, confocal microscopy, target-specific microRNA (miRNA) editing studies, RNA-immunoprecipitation, miRNA/plasmid silencing/overexpression and luciferase reporter assays were used among others. For human studies, ischemic tissues derived from patients with acute or chronic ischemic heart disease were processed.

Results

ADAR2, but not ADAR1, expression is induced by >2-fold in hypoxic ECs and in ischemic vascular ECs in mice and humans. Unbiased gene ontology analysis of the EC transcriptome indicated that ADAR2 controls inflammatory responses and predominantly the expression of interleukin-6-signal transducer (IL6ST), the co-receptor of IL-6. Subsequently, ADAR2 controls IL-6 trans-signalling in ECs as documented by the STAT3 phosphorylation and expression of the downstream leukocyte adhesion molecules, E-selectin and VCAM-1. IL-6-inflamed cremaster muscles showed that rolling and adhesion of leukocyte subsets to vascular wall were severely impaired in Adar2−/−/tg mice. Leukocyte transmigration was also diminished by >2-fold in Adar2−/−/tg and in iEC-ADAR2 KO mice in response to IL-6 or ischemia. Similar results were obtained for leukocyte rolling, adhesion and infiltration after acute (4h) and chronic (3d; 21d) ischemia from iEC-ADAR2 KO mice and human ischemic muscle tissues. Next we studied how ADAR2 controls IL6ST expression. ADAR2-deficient vascular EC miRNAome revealed the upregulation of a conserved group of miRNAs targeting the IL6ST mRNA including miR-199a-5p and miR-335-3p. At a single-nucleotide level, ADAR2-induced RNA editing of the stem loops of the primary miR-199a1/2 and miR-335 directly disrupted Drosha recruitment to both and thus inhibited their maturation process. Accordingly, rescue experiments using miRNA-inhibitors restored IL6ST levels after ADAR2 deficiency.

Conclusion

Taking together, inhibition of the microRNA maturation process by ADAR2-mediated RNA editing is integral for IL-6 trans-signalling in vascular endothelium and subsequent leukocyte trafficking to ischemic tissues in mice and humans.

Vitamin A Production by Engineered Saccharomyces cerevisiae from Xylose via Two-Phase in Situ Extraction

Vitamin A is an essential human micronutrient and plays critical roles in vision, reproduction, immune system, and skin health. Current industrial methods for the production of vitamin A rely on chemical synthesis from petroleum-derived substrates, such as acetone and acetylene. Here, we developed a biotechnological method for production of vitamin A from an abundant and nonedible sugar. Specifically, we engineered Saccharomyces cerevisiae to produce vitamin A from xylose-the second most abundant sugar in plant cell wall hydrolysates-by introducing a β-carotene biosynthetic pathway, and a gene coding for β-carotene 15,15'-dioxygenase (BCMO) into a xylose-fermenting S. cerevisiae. The resulting yeast strain produced vitamin A from xylose at a titer 4-fold higher than from glucose. When a two-phase in situ extraction strategy with dodecane or olive oil as an extractive agent was employed, vitamin A production improved additional 2-fold. Furthermore, a xylose fed-batch fermentation with dodecane in situ extraction achieved a final titer of 3350 mg/L vitamin A, which consisted of retinal (2094 mg/L) and retinol (1256 mg/L). These results suggest that potential limiting factors of vitamin A production in yeast, such as insufficient supply of isoprenoid precursors, and limited intracellular storage capacity, can be effectively addressed by using xylose as a carbon source, and two-phase in situ extraction. The engineered S. cerevisiae and fermentation strategies described in this study might contribute to sustainable and economic production of vitamin A, and vitamin A-enriched bioproducts from renewable biomass.

Redirection of the Glycolytic Flux Enhances Isoprenoid Production in Saccharomyces cerevisiae

Sufficient supply of reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a prerequisite of the overproduction of isoprenoids and related bioproducts in Saccharomyces cerevisiae. Although S. cerevisiae highly depends on the oxidative pentose phosphate (PP) pathway to produce NADPH, its metabolic flux toward the oxidative PP pathway is limited due to the rigid glycolysis flux. To maximize NADPH supply for the isoprenoid production in yeast, upper glycolytic metabolic fluxes are reduced by introducing mutations into phosphofructokinase (PFK) along with overexpression of ZWF1 encoding glucose-6-phosphate (G6P) dehydrogenase. The PFK mutations (Pfk1 S724D and Pfk2 S718D) result in less glycerol production and more accumulation of G6P, which is a gateway metabolite toward the oxidative PP pathway. When combined with the PFK mutations, overexpression of ZWF1 caused substantial increases of [NADPH]/[NADP⁺ ] ratios whereas the effect of ZWF1 overexpression alone in the wild-type strain is not noticeable. Also, the introduction of ZWF1 overexpression and the PFK mutations into engineered yeast overexpressing acetyl-CoA C-acetyltransferase (ERG10), truncated HMG-CoA reductase isozyme 1 (tHMG1), and amorphadiene synthase (ADS) leads to a titer of 497 mg L^-1 of amorphadiene (3.7-fold over the parental strain). These results suggest that perturbation of upper glycolytic fluxes, in addition to ZWF1 overexpression, is necessary for efficient NADPH supply through the oxidative PP pathway and enhanced production of isoprenoids by engineered S. cerevisiae.

First Observation of a Stable Highly Dissipative Divertor Plasma Regime on the Wendelstein 7-X Stellarator

For the first time, the optimized stellarator Wendelstein 7-X has operated with an island divertor. An operation regime in hydrogen was found in which the total plasma radiation approached the absorbed heating power without noticeable loss of stored energy. The divertor thermography recorded simultaneously a strong reduction of the heat load on all divertor targets, indicating almost complete power detachment. This operation regime was stably sustained over several energy confinement times until the preprogrammed end of the discharge. The plasma radiation is mainly due to oxygen and is located at the plasma edge. This plasma scenario is reproducible and robust at various heating powers, plasma densities, and gas fueling locations. These experimental results show that the island divertor concept actually works and displays good power dissipation potential, producing a promising exhaust concept for the stellarator reactor line.

Biosynthetic Routes for Producing Various Fucosyl-Oligosaccharides

Fucosyl-oligosaccharides (FOSs) play physiologically important roles as prebiotics, neuronal growth factors, and inhibitors of enteropathogens. However, challenges in designed synthesis and mass production of FOSs hamper their industrial applications. Here, we report flexible biosynthetic routes to produce various FOSs, including unnatural ones, through in vitro enzymatic reactions of various sugar acceptors, such as glucose, cellobiose, and agarobiose, and GDP-l-fucose as the fucose donor by using α1,2-fucosyltransferase (FucT2). Also, the whole-cell conversion for fucosylation of various sugar acceptors by overexpressing the genes associated with GDP-l-fucose production and fucT2 gene in Escherichia coli was demonstrated by producing 17.74 g/L of 2'-fucosylgalactose (2'-FG). Prebiotic effects of 2'-FG were verified on the basis of selective fermentability of 2'-FG by probiotic bifidobacteria. These biosynthetic routes can be used to engineer industrial microorganisms for more economical, more flexible, and safer production of FOSs than chemical synthesis of FOSs.

Biosynthesis of a Functional Human Milk Oligosaccharide, 2'-Fucosyllactose, and l-Fucose Using Engineered Saccharomyces cerevisiae

2'-fucosyllactose (2-FL), one of the most abundant human milk oligosaccharides (HMOs), has received much attention due to its health-promoting activities, such as stimulating the growth of beneficial gut microorganisms, inhibiting pathogen infection, and enhancing the host immune system. Consequently, large quantities of 2-FL are on demand for food applications as well as in-depth investigation of its biological properties. Biosynthesis of 2-FL has been attempted primarily in Escherichia coli, which might not be the best option to produce food and cosmetic ingredients due to the presence of endotoxins on the cell surface. In this study, an alternative route to produce 2-FL via a de novo pathway using a food-grade microorganism,  Saccharomyces cerevisiae, has been devised. Specifically, heterologous genes, which are necessary to achieve the production of 2-FL from a mixture of glucose and lactose, were introduced into S. cerevisiae. When the lactose transporter (Lac12), de novo GDP-l-fucose pathway (consisting of GDP-d-mannose-4,6-dehydratase (Gmd) and GDP-4-keto-6-deoxymannose-3,5-epimerase-4-reductase (WcaG)), and α1,2-fucosyltransferase (FucT2) were introduced, the resulting engineered strain (D452L-gwf) produced 0.51 g/L of 2-FL from a batch fermentation. In addition, 0.41 g/L of l-fucose was produced when α-l-fucosidase was additionally expressed in the 2-FL producing strain (D452L-gwf). To our knowledge, this is the first report of 2-FL and l-fucose production in engineered S. cerevisiae via the de novo pathway. This study provides the possibility of producing HMOs by a food-grade microorganism S. cerevisiae and paves the way for more HMO production in the future.

Bayesian uncertainty calculation in neural network inference of ion and electron temperature profiles at W7-X

We make use of a Bayesian description of the neural network (NN) training for the calculation of the uncertainties in the NN prediction. Having uncertainties on the NN prediction allows having a quantitative measure for trusting the NN outcome and comparing it with other methods. Within the Bayesian framework, the uncertainties can be calculated under different approximations. The NN has been trained with the purpose of inferring ion and electron temperature profile from measurements of a X-ray imaging diagnostic at W7-X. The NN has been trained in such a way that it constitutes an approximation of a full Bayesian model of the diagnostic, implemented within the Minerva framework. The network has been evaluated using measured data and the uncertainties calculated under different approximations have been compared with each other, finding that neglecting the noise on the NN input can lead to an underestimation of the error bar magnitude in the range of 10%-30%.

Production of a human milk oligosaccharide 2'-fucosyllactose by metabolically engineered Saccharomyces cerevisiae

BACKGROUND

2'-Fucosyllactose (2-FL), one of the most abundant oligosaccharides in human milk, has potential applications in foods due to its health benefits such as the selective promotion of bifidobacterial growth and the inhibition of pathogenic microbial binding to the human gut. Owing to the limited amounts of 2-FL in human milk, alternative microbial production of 2-FL is considered promising. To date, microbial production of 2-FL has been studied mostly in Escherichia coli. In this study, 2-FL was produced alternatively by using a yeast Saccharomyces cerevisiae, which may have advantages over E. coli.

RESULTS

Fucose and lactose were used as the substrates for the salvage pathway which was constructed with fkp coding for a bifunctional enzyme exhibiting L-fucokinase and guanosine 5'-diphosphate-L-fucose phosphorylase activities, fucT2 coding for α-1,2-fucosyltransferase, and LAC12 coding for lactose permease. Production of 2-FL by the resulting engineered yeast was verified by mass spectrometry. 2-FL titers of 92 and 503 mg/L were achieved from 48-h batch fermentation and 120-h fed-batch fermentation fed with ethanol as a carbon source, respectively.

CONCLUSIONS

This is the first report on 2-FL production by using yeast S. cerevisiae. These results suggest that S. cerevisiae can be considered as a host engineered for producing 2-FL via the salvage pathway.

Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass

BACKGROUND

Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae. Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites.

RESULTS

Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively.

CONCLUSIONS

The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.

Transporter engineering for cellobiose fermentation under lower pH conditions by engineered Saccharomyces cerevisiae

The aim of this study was to engineer cellodextrin transporter 2 (CDT-2) from Neurospora crassa for improved cellobiose fermentation under lower pH conditions by Saccharomyces cerevisiae. Through directed evolution, a mutant CDT-2 capable of facilitating cellobiose fermentation under lower pH conditions was obtained. Specifically, a library of CDT-2 mutants with GFP fusion was screened by flow cytometry and then serial subcultured to isolate a CDT-2 mutant capable of transporting cellobiose under acidic conditions. The engineered S. cerevisiae expressing the isolated mutant CDT-2 (I96N/T487A) produced ethanol with a specific cellobiose consumption rate of 0.069g/gcell/h, which was 51% and 55% higher than those of the strains harboring wild-type CDT-1 and CDT-2 in a minimal medium with 2g/L of acetic acid.

Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective

Efficient xylose utilization is one of the most important pre-requisites for developing an economic microbial conversion process of terrestrial lignocellulosic biomass into biofuels and biochemicals. A robust ethanol producing yeast Saccharomyces cerevisiae has been engineered with heterologous xylose assimilation pathways. A two-step oxidoreductase pathway consisting of NAD(P)H-linked xylose reductase and NAD⁺-linked xylitol dehydrogenase, and one-step isomerase pathway using xylose isomerase have been employed to enable xylose assimilation in engineered S. cerevisiae. However, the resulting engineered yeast exhibited inefficient and slow xylose fermentation. In order to improve the yield and productivity of xylose fermentation, expression levels of xylose assimilation pathway enzymes and their kinetic properties have been optimized, and additional optimizations of endogenous or heterologous metabolisms have been achieved. These efforts have led to the development of engineered yeast strains ready for the commercialization of cellulosic bioethanol. Interestingly, xylose metabolism by engineered yeast was preferably respiratory rather than fermentative as in glucose metabolism, suggesting that xylose can serve as a desirable carbon source capable of bypassing metabolic barriers exerted by glucose repression. Accordingly, engineered yeasts showed superior production of valuable metabolites derived from cytosolic acetyl-CoA and pyruvate, such as 1-hexadecanol and lactic acid, when the xylose assimilation pathway and target synthetic pathways were optimized in an adequate manner. While xylose has been regarded as a sugar to be utilized because it is present in cellulosic hydrolysates, potential benefits of using xylose instead of glucose for yeast-based biotechnological processes need to be realized.

Recycling Carbon Dioxide during Xylose Fermentation by Engineered Saccharomyces cerevisiae

Global climate change caused by the emission of anthropogenic greenhouse gases (GHGs) is a grand challenge to humanity. To alleviate the trend, the consumption of fossil fuels needs to be largely reduced and alternative energy technologies capable of controlling GHG emissions are anticipated. In this study, we introduced a synthetic reductive pentose phosphate pathway (rPPP) into a xylose-fermenting Saccharomyces cerevisiae strain SR8 to achieve simultaneous lignocellulosic bioethanol production and carbon dioxide recycling. Specifically, ribulose-1,5-bisphosphate carboxylase/oxygenase from Rhodospirillum rubrum and phosphoribulokinase from Spinacia oleracea were introduced into the SR8 strain. The resulting strain with the synthetic rPPP was able to exhibit a higher yield of ethanol and lower yields of byproducts (xylitol and glycerol) than a control strain. In addition, the reduced release of carbon dioxide by the engineered strain was observed during xylose fermentation, suggesting that the carbon dioxide generated by pyruvate decarboxylase was partially reassimilated through the synthetic rPPP. These results demonstrated that recycling of carbon dioxide from the ethanol fermentation pathway in yeast can be achieved during lignocellulosic bioethanol production through a synthetic carbon conservative metabolic pathway. This strategy has a great potential to alleviate GHG emissions during the production of second-generation ethanol.

Effects of genetic variation and growing condition of prairie cordgrass on feedstock composition and ethanol yield

Prairie cordgrass (Spartina pectinata L.) has the potential to be a feedstock for bioethanol. It is native to North America, and has extensive genetic diversity. Eleven natural populations of prairie cordgrass harvested in 2011 and 2012 were studied. Compositions of the samples showed significant differences within the same year, and between the two years. Two highest, one medium and two lowest glucan concentration samples from each year were selected to evaluate ethanol yield after dilute acid pretreatment and simultaneous saccharification and co-fermentation using Saccharomycescerevisiae SR8 that can ferment both glucose and xylose. Up to 88% of theoretical ethanol yields were achieved. Our research demonstrates the potential of prairie cordgrass as a dedicated energy crop with ethanol yields of 205.0-275.6 g/kg biomass and 1748-4368 L/ha, depending on feedstock composition and biomass yield. These ethanol yields are comparable with those of switchgrass, corn stover and bagasse.

Spontaneous Zone III rupture of the flexor tendons of the ulnar three digits in elderly Korean farmers

Spontaneous flexor tendon rupture is a rare condition and the aetiology is not clear. We report 12 elderly Korean farmers with spontaneous flexor tendon ruptures. We found the rupture in the dominant hand in ten patients. A rupture in the little finger was found in all 12 patients (seven with both flexor tendons ruptured and five with only the profundus ruptured), in the ring finger in four patients (the profundus ruptured in all and both flexor tendons in two patients), and in the middle finger a partial rupture of the profundus in one patient. The tendons were ruptured close to the hook of the hamate. Repetitive friction between the flexor tendons and the hamate hook may cause the ruptures. The hamate hook was excised and the ruptured profundus tendons were reconstructed with tendon transfers with quite favourable functional recovery at follow-up of 1 to 2 years. The ruptured superficialis tendons were not reconstructed. Level of Evidence IV.

Yeast synthetic biology toolbox and applications for biofuel production

Yeasts are efficient biofuel producers with numerous advantages outcompeting bacterial counterparts. While most synthetic biology tools have been developed and customized for bacteria especially for Escherichia coli, yeast synthetic biological tools have been exploited for improving yeast to produce fuels and chemicals from renewable biomass. Here we review the current status of synthetic biological tools and their applications for biofuel production, focusing on the model strain Saccharomyces cerevisiae We describe assembly techniques that have been developed for constructing genes, pathways, and genomes in yeast. Moreover, we discuss synthetic parts for allowing precise control of gene expression at both transcriptional and translational levels. Applications of these synthetic biological approaches have led to identification of effective gene targets that are responsible for desirable traits, such as cellulosic sugar utilization, advanced biofuel production, and enhanced tolerance against toxic products for biofuel production from renewable biomass. Although an array of synthetic biology tools and devices are available, we observed some gaps existing in tool development to achieve industrial utilization. Looking forward, future tool development should focus on industrial cultivation conditions utilizing industrial strains.

Biosynthesis of 3-hydroxypropionic acid from glycerol in recombinant Escherichia coli expressing Lactobacillus brevis dhaB and dhaR gene clusters and E. coli K-12 aldH

3-Hydroxypropionic acid (3-HP) is a value-added chemical for polymer synthesis. For biosynthesis of 3-HP from glycerol, two dhaB and dhaR clusters encoding glycerol dehydratase and its reactivating factor, respectively, were cloned from Lactobacillus brevis KCTC33069 and expressed in Escherichia coli. Coexpression of dhaB and dhaR allowed the recombinant E. coli to convert glycerol to 3-hydroxypropionaldehyde, an intermediate of 3-HP biosynthesis. To produce 3-HP from glycerol, fed-batch fermentation with a two-step feeding strategy was designed to separate the cell growth from the 3-HP production stages. Finally, E. coli JHS00947 expressing L .brevis dhaB and dhaR, and E. coli aldH produced 14.3g/L 3-HP with 0.26 g/L-h productivity, which were 14.6 and 8.53 times higher than those of the batch culture. In conclusion, overexpression of L. brevis dhaB and dhaR clusters and E. coli aldH, and implementation of the two-step feeding strategy enabled recombinant E. coli to convert glycerol to 3-HP efficiently.

Gender difference in susceptibility to smoking in Korean lung cancer patients having smoking habits

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Background: There were some controversies whether women were more or less susceptible to the carcinogenic effect of cigarette smoke and the decline of forced expiratory volume in 1 second (FEV1) to pack-years compared to men. Methods: In this study, we included all lung cancer patients having smoking habits who was histologically diagnosed and performed pulmonary function testing at the time of diagnosis from September 2001 through December 2005. We estimated individual susceptibility to smoking using a formula (SI, susceptibility index) of (100% predicted FEV1)/pack-years. Results: Of 858 lung cancer patients, sex ratio (M/F) was 14.6 (803/55). Past smokers were in 236 (29.3%) for men, 11 (20.0%) for women. Most common hsitologic type was squamous cell carcinoma (477), adenocarcinoma (191), small cell carcinoma (147), adenosquamous cell carcinoma (14), large cell carcinoma (14), NSCLC cell type not specified (15). Pack-years were 41.3 ± 18.9 for men, 29.2 ± 20.4 for women (P = 0.000). FEV1 % was 78.7 ± 23.3 for men, 79.4 ± 22.9 for women (P = 0.832). As for SI, there were no differences between men (0.65 ± 1.1) and women (0.72 ± 1.6) (P = 0.688). Conclusions: Although lung cancer women having smoking habits showed lower pack-years, there were no gender differences in terms of FEV1 decline to cigarette smoking.

No significant financial relationships to disclose.

Hemiparkinsonism associated with a mesencephalic tumor

A 66-year-old woman presented with a 3-year history of progressive right-sided hemiparkinsonism manifested by a right-hand resting tremor and right-sided bradykinesia. Magnetic resonance imaging (MRI) of the brain revealed a non-enhanced polycystic mass in the left midbrain. (11)C-methylspiperone ((11)C-NMSP) and (18)F-fluorodopa ((18)F-DOPA) positron emission tomography (PET) revealed a striatal hypometabolism that was restricted to the left side. These findings are consistent with a dysfunction in the left nigrostriatal dopaminergic pathway that is presumably induced by the cystic mass in the left midbrain. This case is significant due to the paucity of reports regarding the occurrence of a relatively pure parkinsonism that is associated with a mesencephalic space-occupying lesion.