scholarly journals Automated Rational Strain Construction Based on High-Throughput Conjugation

2020 ◽  
Author(s):  
Niklas Tenhaef ◽  
Robert Stella ◽  
Julia Frunzke ◽  
Stephan Noack

Molecular cloning is the core of Synthetic Biology, as it comprises the assembly of DNA and its expression in target hosts. At present, however, cloning is most often a manual, time-consuming and repetitive process that highly benefits from automation. The automation of a complete rational cloning procedure, i.e., from DNA part creation to expression in the target host, involves the integration of different operations and machines. Examples of such workflows are sparse, especially when the design is rational (i.e., the DNA sequence design is fixed, and not based on randomized libraries) and the target host is less genetically tractable (e.g., not sensitive to heat-shock transformation). In this study, an automated workflow for the rational construction of plasmids and their subsequent conjugative transfer into the biotechnological platform organism Corynebacterium glutamicum is presented. The whole workflow is accompanied by a custom-made software tool. As an application example, a rationally designed library of transcription factor biosensors based on the regulator Lrp was constructed and characterized. A sensor with an improved dynamic range was obtained, and insights from the screening provided evidence for a dual regulator function of C. glutamicum Lrp.

1988 ◽  
Vol 129 ◽  
pp. 27-28
Author(s):  
S. C. Unwin ◽  
R. J. Davis

We present a new high dynamic range map of the quasar 3C 273, made from observations with a VLBI network of 12 telescopes. This new map at 18 cm wavelength has one of the highest dynamic ranges yet achieved with VLBI, and it shows the ‘jet’ extending to at least 180 milliarcsec, or 330 pc from the nucleus of the quasar. Strong limits can be placed on the brightness of any ‘counter-jet’ on kiloparsec-scales, as no emission is visible on the opposite side of the ‘core’. Combining with other VLBI, VLA and MERLIN maps shows that the jet is visible and continuous over a very large range of scales, from 1 pc to 40 kpc.


2021 ◽  
Vol 129 (Suppl_1) ◽  
Author(s):  
Bryana N Harris ◽  
Laura Woo ◽  
Jeffrey J Saucerman

Rationale: Heart failure is caused by the inability of adult mammalian hearts to overcome the loss of cardiomyocytes (CMs). This is due partly to the limited proliferative capacity of CMs, which exit the cell cycle and do not undergo cell division. Current knowledge in cardiac regeneration lacks an understanding of the molecular regulatory networks that determine whether CMs will progress through the cell cycle to proliferate. Our goal is to use computational modeling to understand the expression and activation levels of the core cell cycle network, specifically cyclins and cyclin-cyclin-dependent kinase (CDK) complexes. Methods: A model of core cell cycle dynamics was curated using previously published studies of CM proliferation regulators. This model incorporates those regulators known to stimulate G1/S and G2/M transitions through the core CDKs. The activity of each of the 22 network nodes (22 reactions) was predicted using a logic-based differential equation approach. The CDK model was then coupled with a minimal ODE model of cell cycle phase distributions and validated based on descriptions and experimental data from the literature. To prioritize key nodes for experimental validation, we performed a sensitivity analysis by stimulating individual knockdown for every node in the network, measuring the fractional activity of all nodes. Results: Our model confirmed that the knockdown of p21 and Rb protein and the overexpression of E2F transcription factor and cyclinD-cdk4 showed an increase in cells going through DNA synthesis and entering mitosis. A combined knockdown of p21 and p27 showed an increase of cells entering mitosis. Cyclin D-cdk4 and p21 overexpression showed a decrease and increase of Rb expression, respectively. Of the 14 model predictions, 12 agreed with experimental data in the literature. A comprehensive knockdown of the model nodes suggests that E2F (a key transcription factor driving DNA synthesis) is positively regulated by cyclin D while negatively regulated by GSK3B, SMAD3, and pRB. Conclusion: This model enables us to predict how cardiomyocytes respond to stimuli in the CDK network and identify potential therapeutic regulators that induce cardiomyocyte proliferation.


Author(s):  
Johan Dib ◽  
Ivan Lewon ◽  
Boris Martin

Using classical Finite Element (FE) tools to model heat exchangers emphasizes the need to elaborate specific methods to reduce the size of the numerical problem. Among these methods, homogenization techniques can be adapted and used for Brazed Aluminum Plate-Fins Heat Exchangers (BAHX) including layers of periodic structures. Actually the core is formed by stacking single layers consisting of periodic corrugated fins, side-bar and parting sheets which are all made of aluminum base metals, and brazed in a furnace. So in this paper a global methodology of BAHX modeling and design is presented. It integrates homogenization techniques to perform FE calculation and localization techniques to allow applying the appropriate design criteria. Finally, to validate this methodology, results are then compared on a basic heat exchanger modeled both by classical FE tools and a dedicated software tool encapsulating both homogenization and localization techniques.


1991 ◽  
Vol 11 (9) ◽  
pp. 4297-4305
Author(s):  
C Jones ◽  
K A Lee

The cellular factors E4F and ATF-2 (a member of the activating transcription factor [ATF] family) bind to common sites in the adenovirus E4 promoter and have both been suggested to mediate transcriptional activation by the viral E1A protein. To assess the role of E4F, we have introduced mutations into the E4F/ATF binding sites of the E4 promoter and monitored promoter activity in HeLa cells. We find that the core motif (TGACG) of the E4F/ATF binding site is important for E4 promoter activity. However, a point mutation adjacent to the core motif that reduces E4F binding (but has no effect on ATF binding) has no effect on E4 promoter activity. Together with previous results, these findings indicate that there are at least two cellular factors (a member of the ATF family and E4F) that can function with E1A to induce transcription of the E4 promoter. We also find that certain mutations strongly reduce E4 transcription in vivo but have no effect on ATF-2 binding in vitro. These results are therefore incompatible with the possibility that (with respect to members of the ATF family) ATF-2 alone can function with E1A to transactivate the E4 promoter in HeLa cells.


1986 ◽  
Vol 119 ◽  
pp. 211-214
Author(s):  
R.J. Davis

The ‘superluminal’ motion observed in the cores of radio sources such as 3C273 is now accepted as evidence of relativistic motion within a few parsecs of the centre, but it is less clear whether such speeds persist out to kiloparsec scales. The one-sidedness of such sources is often cited as evidence of relativistic Doppler beaming, but could equally be intrinsic. New MERLIN maps of 3C273 at 151 MHz and 408 MHz have been made with dynamic range of 4.103:1 and 104:1 respectively. These show that (i) there is an extended region or lobe to the south of the main jet; (ii) the radio emission of the jet is continuous from the core to beyond the limit of the optical jet; (iii) no counter-component can be found in the opposite direction to the jet. The ridge-line of the jet shows a ‘wiggle’, the wavelength of which decreases by a factor of 6 along its length. This is interpreted as a deceleration of the bulk flow along the jet.


1992 ◽  
Vol 02 (03) ◽  
pp. 451-482 ◽  
Author(s):  
WALTER J. FREEMAN

Those classical models are reviewed that are most widely used by neurobiologists to explain the dynamics of neurons and neuron populations, and by modelers to implement artificial neural networks. Each neuron has input fibers called dendrites that integrate and an axon that transmits the output. The differing fiber architectures reflect these dissimilar dynamic operations. The basic tools to describe them are the RC model of the membrane, the core conductor model of the fibers, the Hodgkin–Huxley model of the trigger zone, and the modifiable synapse. Populations additionally require description of macroscopic state variables, the types of nonlinearity (most importantly the sigmoid curve and the dynamic range compression at the input to the cortex), and the types and strengths of connections. The properties of these neural masses can be characterized with the tools of nonlinear dynamics. These include description of point, limit cycle, and chaotic attractors for the cerebal cortex, as well as the types and mechanisms for the state transitions between basins of attraction during learning and perception.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 3426-3426
Author(s):  
Fang Fang ◽  
Mangju Wang ◽  
Quan Qiu ◽  
Dingfang Bu ◽  
Wei Liu ◽  
...  

Abstract Quiescent state of lymphocyte is a critical mechanism for immunity homeostasis. Until recently it has been recognized that quiescent state is not a passive default mode which also needs many signal molecular and transcriptional factors involvement. However, the mechanism of T cell quiescence remains incompletely understood. In quiescent cell, KLF3 is a highly expressed transcriptional factor, but once T lymphocyte is activated, KLF3 expression is reduced to an undetectable level. The Src homology 2 domain tyrosine phosphatase (SHP-1) is mainly expressed in hematopoietic cells and has been known to plays a negative effect on T cell activation. SHP-1 mutant mice (SHP-1me/me) exhibits multiple hematopoietic cells proliferation disorder and systemic inflammation. Compare to SHP-1me/me mice, KLF3 knock-out mice shows a myeloproliferative disorder and systematic inflammatory responses likewise. Accumulating evidence indicates KLF3 is a crucial transcription factor in T cell quiescent. Based on similarity between SHP-1me/me mice and KLF3 knock-out mice, we explore whether KLF3 cooperate with SHP-1 to maintain cell quiescence. SHP-1 consists two promoter regions that one locates upstream of exon1, mainly expressed in epithelial cell and the other one locates in intron 1 which mainly serves for hematopoietic cell. According to literature, the core promoter element which plays a critical role in SHP-1 gene regulation locates upstream 120bp of transcriptional site. Two cacc boxes (5'---caccc----3') were found among the core promoter elements. We constructed a reporter gene vector named pGL3-SHP1-luci1 which consist two cacc boxes. We also constructed another three vectors based on pGL3-SHP1-luci1. (figure1 left). We process dual-luciferase assay at 72h post transfection (figure1 right). when the proximal cacc box is mutated, the promoter activity is 1.7 times as high as the promoter activity of normal promoter sequence (luci1 vector) (p<0.05). The transcription factor KLF3 functions as a repressor to interact with SHP-1 P2 promoter. We prepare two dioxin-labelled probes based on cacc box motif to verify the binding activities between KLF3 and SHP-1. The probe I is consist of the distal cacc box and the probe II possesses the proximal cacc box. Two specific bands (A,B)were observed when probe target I or target II was adding into DNA-protein mixture (Figure2, lane2, 5). This band specifically disappeared by the addition of excess unlabeled target as a competitor (Figure2, lane 3, 6) which indicates probe can be a target of nuclear proteins from Jurkat cell. To verify KLF3 is the transcription factor involving in the interaction with labelled-probe, we added anti-KLF3 antibody to the EMSA binding reaction. The results show band A disappeared in the presence of target I and it became weaker in the presence of target II, but band B were still present after addition of anti-KLF3 antibody to the mixture (Figure2, lane4, 8). The band A, but not band B, disappeared or become weaken in the presence of anti-KLF3 antibody, indicates KLF3 interacts with SHP-1 P2 promoter. To test the ability of KLF3 binding to SHP-1 promoter 2 (P2) in vivo, we performed chromatin immunoprecipitation (ChIP) analysis using antibodies for KLF3 and compared it with the IgG-negative control. We design one promoter primer targeting a region from -135bp to 53bp which contains a potential KLF3 binding site and one SHP-1 exon15 promoter as a control for antibody enriched DNA analysis. By promoter primer or exon15 primer, specific DNA bands were observed in input. However, only anti-KLF3 enriched DNA can amplify a specific band with promoter primer. By contrast, the IgG negative control enriched DNA fail to amplify positive bands with promoter primer. And for the exon15 primer, it hardly amplified positive bands neither from anti-KLF3-enriched DNA nor from IgG negative control-enriched DNA (figure3). These data demonstrates that KLF3 proteins directly regulate SHP-1 expression. Our study suggests KLF3, as the candidate of programing T cell quiescence, can regulate SHP-1 to maintain quiescent phenotype. Figure 1. Figure 1. Figure 2. Figure 2. Figure 3. Figure 3. Disclosures No relevant conflicts of interest to declare.


1998 ◽  
Vol 258 (2) ◽  
pp. 101-104 ◽  
Author(s):  
Jonas Ekblom ◽  
Håkan Garpenstrand ◽  
Mattias Damberg ◽  
Kevin Chen ◽  
Jean C Shih ◽  
...  

2004 ◽  
Vol 279 (50) ◽  
pp. 51719-51721 ◽  
Author(s):  
Mohamed Ouhammouch ◽  
Finn Werner ◽  
Robert O. J. Weinzierl ◽  
E. Peter Geiduschek

The core components of the archaeal transcription apparatus closely resemble those of eukaryotic RNA polymerase II, while the DNA-binding transcriptional regulators are predominantly of bacterial type. Here we report the construction of an entirely recombinant system for positively regulated archaeal transcription. By omitting individual subunits, or sets of subunits, from thein vitroassembly of the 12-subunit RNA polymerase from the hyperthermophileMethanocaldococcus jannaschii, we describe a functional dissection of this RNA polymerase II-like enzyme, and its interactions with the general transcription factor TFE, as well as with the transcriptional activator Ptr2.


2005 ◽  
Vol 25 (6) ◽  
pp. 2147-2157 ◽  
Author(s):  
Thi T. Nguyen ◽  
Kyucheol Cho ◽  
Sabrina A. Stratton ◽  
Michelle Craig Barton

ABSTRACT We performed chromatin immunoprecipitation (ChIP) analyses of developmentally staged solid tissues isolated from wild-type and p53-null mice to determine specific histone N-terminal modifications, histone-modifying proteins, and transcription factor interactions at the developmental repressor region (−850) and core promoter of the hepatic tumor marker alpha-fetoprotein (AFP) gene. Both repression of AFP during liver development and silencing in the brain, where AFP is never expressed, are associated with dimethylation of histone H3 lysine 9 (DiMetH3K9) and the presence of heterochromatin protein 1 (HP1). These heterochromatic markers remain localized to AFP during developmental repression but spread to the upstream albumin gene during silencing. Developmentally regulated decreases in levels of acetylated H3 (AcH3K9) and H4 (AcH4) and of di- and trimethylated H3K4 (DiMetH3K4 and TriMetH3K4) occur at both the core promoter and distal repressor regions of AFP. Hepatic expression of AFP correlates with FoxA interaction at the repressor region and the binding of RNA polymerase II and TATA-binding protein to the core promoter. p53 acts as a developmental repressor of AFP in the liver by binding to chromatin, excluding FoxA interaction and targeting mSin3A/HDAC1 to the distal repressor region. p53-null mice exhibit developmentally delayed AFP repression, concomitant with acetylation of H3K9, methylation of H3K4, and loss of DiMetH3K9, mSin3A/HDAC1, and HP1 interactions.


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