Erratum to: CO2/HCO3 − perturbations of simulated large scale gradients in a scale-down device cause fast transcriptional responses in Corynebacterium glutamicum

In large-scale bioreactors, gradients in cultivation parameters such as oxygen, substrate and pH result in fluctuating environments. pH fluctuations were identified as a critical parameter for bioprocess performance. Traditionally, scale-down systems at the laboratory scale are used to analyze the effects of fluctuating pH values on strain and thus process performance. Here, we demonstrate the application of dynamic microfluidic single-cell cultivation (dMSCC) as a novel scale-down system for the characterization of Corynebacterium glutamicum growth using oscillating pH conditions as a model parameter. A detailed comparison between two-compartment reactor (two-CR) scale-down experiments and dMSCC was performed for one specific pH oscillation between reference pH 7 (~8 min) and disturbed pH 6 (~2 min). Similar reductions in growth rates were observed in both systems (dMSCC 21% and two-CR 27%). Afterward, systematic experiments at different symmetric and asymmetric pH oscillations between pH ranges of 4 −6 and 8 −11 and different intervals from 1 minute to 20 minutes, were performed to demonstrate the unique application range and throughput of the dMSCC system. Finally, the strength of the dMSCC application was demonstrated by mimicking fluctuating environmental conditions within large-scale bioprocesses, which is difficult to conduct using two-CRs.

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Application of projection-based model reduction to finite-element plate models for two-dimensional traveling waves

Journal of Intelligent Material Systems and Structures ◽

10.1177/1045389x16679295 ◽

2016 ◽

Vol 28 (14) ◽

pp. 1886-1904 ◽

Cited By ~ 6

Author(s):

Vijaya VN Sriram Malladi ◽

Mohammad I Albakri ◽

Serkan Gugercin ◽

Pablo A Tarazaga

Keyword(s):

Finite Element ◽

Model Reduction ◽

Traveling Waves ◽

Large Scale ◽

Fe Model ◽

Plate Model ◽

Reduction Techniques ◽

State Frequency ◽

Scale Down ◽

The Stability

A finite element (FE) model simulates an unconstrained aluminum thin plate to which four macro-fiber composites are bonded. This plate model is experimentally validated for single and multiple inputs. While a single input excitation results in the frequency response functions and operational deflection shapes, two input excitations under prescribed conditions result in tailored traveling waves. The emphasis of this article is the application of projection-based model reduction techniques to scale-down the large-scale FE plate model. Four model reduction techniques are applied and their performances are studied. This article also discusses the stability issues associated with the rigid-body modes. Furthermore, the reduced-order models are utilized to simulate the steady-state frequency and time response of the plate. The results are in agreement with the experimental and the full-scale FE model results.

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Evaluation of staged air and overfire air in regulating air-staging conditions within a large-scale down-fired furnace

Applied Thermal Engineering ◽

10.1016/j.applthermaleng.2014.03.009 ◽

2014 ◽

Vol 67 (1-2) ◽

pp. 97-105 ◽

Cited By ~ 19

Author(s):

Min Kuang ◽

Zhengqi Li ◽

Zhongqian Ling ◽

Xianyang Zeng

Keyword(s):

Large Scale ◽

Scale Down ◽

Air Staging

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Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

10.1101/393637 ◽

2018 ◽

Author(s):

Ivan D. Mateus ◽

Frédéric G. Masclaux ◽

Consolée Aletti ◽

Edward C. Rojas ◽

Romain Savary ◽

...

Keyword(s):

Mycorrhizal Fungi ◽

Large Scale ◽

Molecular Mechanisms ◽

Arbuscular Mycorrhizal ◽

Mycorrhizal Symbiosis ◽

Rna Seq ◽

Plant Host ◽

Transcriptional Responses ◽

Plant Genes ◽

Fungal Genetic

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

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Sex differences in viral entry protein expression and host transcript responses to SARS-CoV-2

10.21203/rs.3.rs-100914/v2 ◽

2020 ◽

Author(s):

Mengying Sun ◽

Rama Shankar ◽

Meehyun Ko ◽

Christopher Daniel Chang ◽

Shan-Ju Yeh ◽

...

Keyword(s):

Gene Expression ◽

Sex Differences ◽

Viral Entry ◽

Large Scale ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Scale Analysis ◽

Transcriptional Responses ◽

Deconvolution Analysis ◽

Large Scale Analysis

Abstract Epidemiological studies suggest that men exhibit a higher mortality rate to COVID-19 than women, yet the underlying biology is largely unknown. Here, we seek to delineate sex differences in the gene expression of viral entry proteins ACE2 and TMPRSS2, and host transcriptional responses to SARS-CoV-2 through large-scale analysis of genomic and clinical data. We first compiled 220,000 human gene expression profiles from three databases and completed the meta-information through machine learning and manual annotation. Large scale analysis of these profiles indicated that male samples show higher expression levels of ACE2 and TMPRSS2 than female samples, especially in the older group (>60 years) and in the kidney. Subsequent analysis of 6,031 COVID-19 patients at Mount Sinai Health System revealed that men have significantly higher creatinine levels, an indicator of impaired kidney function. Further analysis of 782 COVID-19 patient gene expression profiles taken from upper airway and blood suggested men and women present distinct expression changes. Computational deconvolution analysis of these profiles revealed male COVID-19 patients have enriched kidney-specific mesangial cells in blood compared to healthy patients. Together, this study suggests biological differences in the kidney between sexes may contribute to sex disparity in COVID-19.

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AraR, an l-Arabinose-Responsive Transcriptional Regulator in Corynebacterium glutamicum ATCC 31831, Exerts Different Degrees of Repression Depending on the Location of Its Binding Sites within the Three Target Promoter Regions

Journal of Bacteriology ◽

10.1128/jb.00314-15 ◽

2015 ◽

Vol 197 (24) ◽

pp. 3788-3796 ◽

Cited By ~ 3

Author(s):

Takayuki Kuge ◽

Haruhiko Teramoto ◽

Masayuki Inui

Keyword(s):

Corynebacterium Glutamicum ◽

Binding Sites ◽

Large Scale ◽

Transcriptional Regulator ◽

Scale Production ◽

Primary Role ◽

Promoter Regions ◽

Independent Manner ◽

Content Type

ABSTRACTInCorynebacterium glutamicumATCC 31831, a LacI-type transcriptional regulator AraR, represses the expression ofl-arabinose catabolism (araBDA), uptake (araE), and the regulator (araR) genes clustered on the chromosome. AraR binds to three sites: one (BSB) between the divergent operons (araBDAandgalM-araR) and two (BSE1and BSE2) upstream ofaraE.l-Arabinose acts as an inducer of the AraR-mediated regulation. Here, we examined the roles of these AraR-binding sites in the expression of the AraR regulon. BSBmutation resulted in derepression of botharaBDAandgalM-araRoperons. The effects of BSE1and/or BSE2mutation onaraEexpression revealed that the two sites independently function as theciselements, but BSE1plays the primary role. However, AraR was shown to bind to these sites with almost the same affinityin vitro. Taken together, the expression ofaraBDAandaraEis strongly repressed by binding of AraR to a single site immediately downstream of the respective transcriptional start sites, whereas the binding site overlapping the −10 or −35 region of thegalM-araRandaraEpromoters is less effective in repression. Furthermore, downregulation ofaraBDAandaraEdependent onl-arabinose catabolism observed in the BSBmutant and the AraR-independentaraRpromoter identified withingalM-araRadd complexity to regulation of the AraR regulon derepressed byl-arabinose.IMPORTANCECorynebacterium glutamicumhas a long history as an industrial workhorse for large-scale production of amino acids. An important aspect of industrial microorganisms is the utilization of the broad range of sugars for cell growth and production process. MostC. glutamicumstrains are unable to use a pentose sugarl-arabinose as a carbon source. However, genes forl-arabinose utilization and its regulation have been recently identified inC. glutamicumATCC 31831. This study elucidates the roles of the multiple binding sites of the transcriptional repressor AraR in the derepression byl-arabinose and thereby highlights the complex regulatory feedback loops in combination withl-arabinose catabolism-dependent repression of the AraR regulon in an AraR-independent manner.

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A curated transcriptome dataset collection to investigate inborn errors of immunity

10.1101/526004 ◽

2019 ◽

Author(s):

Salim Bougarn ◽

Sabri Boughorbel ◽

Damien Chaussabel ◽

Nico Marr

Keyword(s):

Web Application ◽

Large Scale ◽

Mononuclear Cells ◽

Ex Vivo ◽

Clinical Manifestations ◽

Inherited Disorders ◽

Transcriptional Responses ◽

Control Subjects ◽

A Genome ◽

Wide Range

ABSTRACTPrimary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of nineteen (19) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at: http://pid.gxbsidra.org/dm3/geneBrowser/list.

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Intein-mediated intracellular production of active microbial transglutaminase in Corynebacterium glutamicum

10.21203/rs.3.rs-25081/v1 ◽

2020 ◽

Author(s):

Nan Zhang ◽

Shan Zhang ◽

Yongzhi He ◽

Xin Chen ◽

Yanfeng Zhang ◽

...

Keyword(s):

Corynebacterium Glutamicum ◽

Large Scale ◽

Microbial Transglutaminase ◽

Proteolytic Processing ◽

Site Directed Mutagenesis ◽

Recombinant Production ◽

Specific Manner ◽

Long Time ◽

Protease Treatment ◽

High Level

Abstract Background The microbial transglutaminase (mTGase) from Streptomyces mobaraense has been widely used in the food industry. Recombinant production of mTGase is tricky because the mTGase is synthesized as an inactive zymogen, which needs to be activated by proteolytic processing. Self-cleaving inteins have been applied to activate the zymogen in a simple and highly specific manner as compared with proteolytic processing. However, self-cleaving inteins suffer from the inherent problem of premature cleavage. Moreover, self-cleaving inteins normally require an additional step of long time incubation to induce the cleavage. These two inherent problems limit self-cleaving inteins for their potential application in the production of mTGase.Results In this study, the premature cleavage of intein Ssp DnaB was observed in Corynebacterium glutamicum when the Ssp DnaB was used to activate mTGase precursor protein. Rather than suppressing it, the premature cleavage was applied to produce active mTGase in C. glutamicum. The SDS-PAGE analysis and the mTGase activity assay indicated that the premature cleavage of intein Ssp DnaB was successfully applied to activate the mTGase intracellularly in C. glutamicum. The subsequent N-terminal amino acid sequencing and site-directed mutagenesis studies demonstrated that the premature cleavage activated the mTGase intracellularly in a highly specific manner. Finally, in a jar fermentor, the intracellular mTGase activity was up to 49 U/mL, which was the highest intracellular mTGase activity ever reported.Conclusions An efficient and simple approach with great potential for large-scale industrial production of active mTGase was presented in this study. This approach employed premature cleavage of intein Ssp DnaB to activate mTGase in C. glutamicum, resulting in high-level intracellular production of active mTGase. Moreover, this approach did not require any further processing steps such as protease treatment or long time incubation, greatly simplifying the production of active mTGase.

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Genome-wide profiling of transcribed enhancers during macrophage activation

10.1101/163519 ◽

2017 ◽

Author(s):

Elena Denisenko ◽

Reto Guler ◽

Musa Mhlanga ◽

Harukazu Suzuki ◽

Frank Brombacher ◽

...

Keyword(s):

Gene Expression ◽

Transcriptional Activation ◽

Large Scale ◽

Transcriptional Control ◽

Macrophage Activation ◽

Transcriptional Responses ◽

Protein Coding ◽

Genome Wide ◽

Ifn Γ ◽

Cap Analysis

AbstractMacrophages are sentinel cells essential for tissue homeostasis and host defence. Owing to their plasticity, macrophages acquire a range of functional phenotypes in response to microenvironmental stimuli, of which M(IFN-γ) and M(IL-4/IL-13) are well-known for their opposing pro- and anti-inflammatory roles. Enhancers have emerged as regulatory DNA elements crucial for transcriptional activation of gene expression. Using cap analysis of gene expression and epigenetic data, we identify on large-scale transcribed enhancers in mouse macrophages, their time kinetics and target protein-coding genes. We observe an increase in target gene expression, concomitant with increasing numbers of associated enhancers and find that genes associated to many enhancers show a shift towards stronger enrichment for macrophage-specific biological processes. We infer enhancers that drive transcriptional responses of genes upon M(IFN-γ) and M(IL-4/IL-13) macrophage activation and demonstrate stimuli-specificity of regulatory associations. Finally, we show that enhancer regions are enriched for binding sites of inflammation-related transcription factors, suggesting a link between stimuli response and enhancer transcriptional control. Our study provides new insights into genome-wide enhancer-mediated transcriptional control of macrophage genes, including those implicated in macrophage activation, and offers a detailed genome-wide catalogue to further elucidate enhancer regulation in macrophages.

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