Proteome-Level Responses of Escherichia coli to Long-Chain Fatty Acids and Use of Fatty Acid Inducible Promoter in Protein Production

In Escherichia coli, a long-chain acyl-CoA is a regulatory signal that modulates gene expression through its binding to a transcription factor FadR. In this study, comparative proteomic analysis of E. coli in the presence of glucose and oleic acid was performed to understand cell physiology in response to oleic acid. Among total of 52 proteins showing altered expression levels with oleic acid presence, 9 proteins including AldA, Cdd, FadA, FadB, FadL, MalE, RbsB, Udp, and YccU were newly synthesized. Among the genes that were induced by oleic acid, the promoter of the aldA gene was used for the production of a green fluorescent protein (GFP). Analysis of fluorescence intensities and confocal microscopic images revealed that soluble GFP was highly expressed under the control of the aldA promoter. These results suggest that proteomics is playing an important role not only in biological research but also in various biotechnological applications

Prediction of Neighbor-Dependent Microbial Interactions From Limited Population Data

Modulation of interspecies interactions by the presence of neighbor species is a key ecological factor that governs dynamics and function of microbial communities, yet the development of theoretical frameworks explicit for understanding context-dependent interactions are still nascent. In a recent study, we proposed a novel rule-based inference method termed the Minimal Interspecies Interaction Adjustment (MIIA) that predicts the reorganization of interaction networks in response to the addition of new species such that the modulation in interaction coefficients caused by additional members is minimal. While the theoretical basis of MIIA was established through the previous work by assuming the full availability of species abundance data in axenic, binary, and complex communities, its extension to actual microbial ecology can be highly constrained in cases that species have not been cultured axenically (e.g., due to their inability to grow in the absence of specific partnerships) because binary interaction coefficients – basic parameters required for implementing the MIIA – are inestimable without axenic and binary population data. Thus, here we present an alternative formulation based on the following two central ideas. First, in the case where only data from axenic cultures are unavailable, we remove axenic populations from governing equations through appropriate scaling. This allows us to predict neighbor-dependent interactions in a relative sense (i.e., fractional change of interactions between with versus without neighbors). Second, in the case where both axenic and binary populations are missing, we parameterize binary interaction coefficients to determine their values through a sensitivity analysis. Through the case study of two microbial communities with distinct characteristics and complexity (i.e., a three-member community where all members can grow independently, and a four-member community that contains member species whose growth is dependent on other species), we demonstrated that despite data limitation, the proposed new formulation was able to successfully predict interspecies interactions that are consistent with experimentally derived results. Therefore, this technical advancement enhances our ability to predict context-dependent interspecies interactions in a broad range of microbial systems without being limited to specific growth conditions as a pre-requisite

Transcriptome and proteome analyses of adaptive responses to methyl methanesulfonate in Escherichia coli K-12 and ada mutant strains

<p>Abstract</p> <p>Background</p> <p>The Ada-dependent adaptive response system in <it>Escherichia coli </it>is important for increasing resistance to alkylation damage. However, the global transcriptional and translational changes during this response have not been reported. Here we present time-dependent global gene and protein expression profiles following treatment with methyl methanesulfonate (MMS) in <it>E. coli </it>W3110 and its <it>ada </it>mutant strains.</p> <p>Results</p> <p>Transcriptome profiling showed that 1138 and 2177 genes were differentially expressed in response to MMS treatment in the wild-type and mutant strains, respectively. A total of 81 protein spots representing 76 nonredundant proteins differentially expressed were identified using 2-DE and LC-MS/MS. In the wild-type strain, many genes were differentially expressed upon long-exposure to MMS, due to both adaptive responses and stationary phase responses. In the <it>ada </it>mutant strain, the genes involved in DNA replication, recombination, modification and repair were up-regulated 0.5 h after MMS treatment, indicating its connection to the SOS and other DNA repair systems. Interestingly, expression of the genes involved in flagellar biosynthesis, chemotaxis, and two-component regulatory systems related to drug or antibiotic resistance, was found to be controlled by Ada.</p> <p>Conclusion</p> <p>These results show in detail the regulatory components and pathways controlling adaptive response and how the related genes including the Ada regulon are expressed with this response.</p

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

TNF-α antagonist attenuates systemic lipopolysaccharide-induced brain white matter injury in neonatal rats

Background Systemic inflammation is an important risk factor for neurodevelopmental impairments in preterm infants. Premyelinating oligodendrocytes are main building blocks of white matter in preterm infants and vulnerable to oxidative stress and excitotoxic stress. Tumour necrosis factor-α (TNF-α) plays important roles in systemic inflammation and local inflammation leading to apoptosis of premyelinating oligodendrocytes and white matter injury (WMI) in brain tissue. This study was conducted to investigate whether etanercept, a TNF-α antagonist, could attenuate systemic lipopolysaccharide (LPS)-induced WMI in the immature brain. Results We found that intraperitoneal LPS administration caused systemic and local inflammation in brain tissue. Subsequent etanercept treatment significantly attenuated LPS-induced inflammation in brain tissue as well as in systemic circulation. Intraperitoneal LPS also induced microgliosis and astrocytosis in the cingulum and etanercept treatment reduced LPS-induced microgliosis and astrocytosis. Additionally, systemic LPS-induced apoptosis of oligodendrocyte precursor cells was observed, which was lessened by etanercept treatment. The concentration of etanercept in the CSF was higher when it was administrated with LPS than when administrated with a vehicle. Conclusions It appears that etanercept reduce WMI in the neonatal rat brain via attenuation of systemic and local inflammation. This study provides preclinical data suggesting etanercept-mediated modulation of inflammation as a promising approach to reduce WMI caused by sepsis or necrotizing enterocolitis in preterm infants.This research was supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2012R1A1A2044109 and 2017R1D1A1B03036383). The funding body played no role in the design and interpretation of the experiments

Minimal Interspecies Interaction Adjustment (MIIA): Inference of Neighbor-Dependent Interactions in Microbial Communities

An intriguing aspect in microbial communities is that pairwise interactions can be influenced by neighboring species. This creates context dependencies for microbial interactions that are based on the functional composition of the community. Context dependent interactions are ecologically important and clearly present in nature, yet firmly established theoretical methods are lacking from many modern computational investigations. Here, we propose a novel network inference method that enables predictions for interspecies interactions affected by shifts in community composition and species populations. Our approach first identifies interspecies interactions in binary communities, which is subsequently used as a basis to infer modulation in more complex multi-species communities based on the assumption that microbes minimize adjustments of pairwise interactions in response to neighbor species. We termed this rule-based inference minimal interspecies interaction adjustment (MIIA). Our critical assessment of MIIA has produced reliable predictions of shifting interspecies interactions that are dependent on the functional role of neighbor organisms. We also show how MIIA has been applied to a microbial community composed of competing soil bacteria to elucidate a new finding that – in many cases – adding fewer competitors could impose more significant impact on binary interactions. The ability to predict membership-dependent community behavior is expected to help deepen our understanding of how microbiomes are organized in nature and how they may be designed and/or controlled in the future

Electrical spin injection and accumulation in CoFe/MgO/Ge contacts at room temperature

We first report the all-electrical spin injection and detection in CoFe/MgO/moderately doped n-Ge contact at room temperature (RT), employing threeterminal Hanle measurements. A sizable spin signal of ~170 k{\Omega} {\mu}m^2 has been observed at RT, and the analysis using a single-step tunneling model gives a spin lifetime of ~120 ps and a spin diffusion length of ~683 nm in Ge. The observed spin signal shows asymmetric bias and temperature dependences which are strongly related to the asymmetry of the tunneling process.Comment: 28 pages, 5 figure

Clinical relevance of ground glass opacity in 105 patients with miliary tuberculosis

SummaryBackgroundAfter the application of chest computed tomography (CT), ground glass opacity (GGO) was introduced as one of major accompanying findings of miliary tuberculosis (MT) in addition to miliary nodules. However, little is known about whether GGO is associated with the clinical manifestations and outcomes of MT. Therefore, the present study examined the clinical relevance of GGO in patients with MT.MethodsChest radiographs and CT scans of MT patients were retrospectively reviewed. Clinical manifestations and outcomes were compared in terms of the extent of GGO revealed by chest CT.ResultsConfirmed 105 MT patients were included. GGO was observed in 70 (67%) patients. MT patients with an extent of GGO >50% (n = 21) had symptoms of shorter duration, more frequent dyspnea, and more pronounced changes in the levels of acute phase reactants. Miliary nodules were less discernible on CT in those with an extent of GGO >50%. MT patients with an extent of GGO >50% were significantly associated with a longer hospital stay (p = 0.02) and with acute respiratory failure (p < 0.001) than those with an extent of GGO ≤50%. However, mortality among MT patients was not associated with the extent of GGO.ConclusionMT patients with an extent of GGO >50% had more rapidly progressive manifestations and a greater potential for delayed diagnosis and poorer prognosis. Nevertheless, mortality was not higher in confirmed MT patients with an extent of GGO >50% than in those with an extent of GGO ≤50%

Comparison between a novel core knife and the conventional IT knife 2 for endoscopic submucosal dissection of gastric mucosal lesions

Background/Aims Few studies have compared the performances of endoscopic knives. This study aimed to compare the therapeutic outcomes of a novel core knife and the conventional IT knife 2 for endoscopic submucosal dissection (ESD) of gastric mucosal lesions. Methods This prospective, non-inferiority trial included patients diagnosed with gastric adenoma or early-stage adenocarcinoma at Keimyung University Dongsan Hospital between June and November 2020. The patients were randomly assigned to either the core knife or the IT knife 2 group. The operators and assistants scored the knives’ grip convenience and cutting abilities. Results A total of 39 patients were enrolled (core knife group, 20 patients; IT knife 2 group, 19 patients). There were no significant between-group differences in operator-assessed grip convenience (9.600 vs. 9.526, p=0.753), cutting ability (9.600 vs. 9.105, p=0.158), or assistant-assessed grip convenience (9.500 vs. 9.368, p=0.574). Conclusions The core knife achieved therapeutic outcomes that were comparable to those of the IT knife 2 for ESD of gastric mucosal lesions