scholarly journals Role of mRNA Stability during Genome-wide Adaptation of Lactococcus lactis to Carbon Starvation

2005 ◽  
Vol 280 (43) ◽  
pp. 36380-36385 ◽  
Author(s):  
Emma Redon ◽  
Pascal Loubière ◽  
Muriel Cocaign-Bousquet
Keyword(s):  
Lactococcus Lactis ◽  
Mrna Stability ◽  
Formal Method ◽  
Growth Conditions ◽  
Carbon Starvation ◽  
Reading Frame ◽  
Mrna Pool ◽  
Open Reading Frame Length ◽  
Wide Range ◽  
The Stability

The stability of mRNA was investigated for the first time at the genomic scale during carbon starvation adaptation of Lactococcus lactis IL1403. In exponential phase, mRNA half-lives were correlated positively to open reading frame length. A polypurine sequence, AGGAG, was identified as a putative 5′-stabilizer and inverted repeated sequences as a 3′-destabilizer. These original findings suggested that multiple pathways of mRNA degradation should coexist: internal cleavage, endonuclease cleavage initiated at the 5′-end, and exonuclease attack at the 3′-end. During carbon starvation adaptation, mRNA stability globally increased, but specific mechanisms allowing a wide range of stabilization factors between genes and differential kinetic evolution were involved. A formal method allowing the quantification of the relative influences of transcription and degradation on the mRNA pool control was developed and applied in L. lactis. Gene expression was mostly controlled by altered transcription prior to carbon source exhaustion, while the influence of mRNA stability increased during the starvation phase. This study highlighted that stability modulation in response to adverse growth conditions can govern gene regulation to the same extent as transcription in bacteria.

scholarly journals Regulation of Nramp1 mRNA stability by oxidants and protein kinase C in RAW264.7 macrophages expressing Nramp1Gly169

2000 ◽  
Vol 351 (3) ◽  
pp. 687-696 ◽  
Author(s):  
William P. LAFUSE ◽  
Gail R. ALVAREZ ◽  
Bruce S. ZWILLING
Keyword(s):  
Protein Kinase C ◽  
Protein Kinase ◽  
Mrna Stability ◽  
Pleiotropic Effects ◽  
Natural Resistance ◽  
Raw264.7 Macrophages ◽  
Kinase C ◽  
Wide Range ◽  
Macrophage Protein ◽  
The Stability

The murine Nramp1 (natural-resistance-associated macrophage protein) locus confers innate resistance against intracellular macrophage pathogens. The gene encodes a transporter molecule, which is rapidly recruited to the phagosome. Nramp1 functions as an iron transporter by transporting iron into the phagosome. Within the phagosome iron mediates anti-microbial killing by hydroxyl radical formation through the iron-catalysed Fenton/Haber–Weiss reaction. In addition to its effects on the growth of intracellular pathogens, Nramp1 exerts a wide range of pleiotropic effects in activated macrophages. One of these pleiotropic effects is the increased stability of a variety of mRNA species, including Nramp1 mRNA. In the present study, the stability of Nramp1 mRNA in Mycobacterium avium infected RAW264.7 macrophages expressing either the Nramp1Gly169 resistant allele or the Nramp1Asp169 susceptible allele was examined. Nramp1 mRNA stability was greater in Nramp1Gly169 macrophages than in Nramp1Asp169 macrophages. The increase in Nramp1 mRNA stability in resistant macrophages was inhibited by antioxidants and protein kinase C (PKC) inhibitors, suggesting that Nramp1 mRNA stability is regulated by an oxidant-generated signalling pathway that requires PKC activity. This was corroborated by treating Nramp1Asp169 macrophages with menadione, which generates reactive oxygen species within cells. Menadione increased Nramp1 mRNA stability to the level observed in resistant macrophages; this increase was also inhibited by a PKC inhibitor. Further, PKC activity was found to be greater in M. avium-infected Nramp1Gly169 macrophages than in infected Nramp1Asp169 macrophages and inhibited by treatment with an antioxidant.

Performance of Electronic Structure Methods for the Description of Hückel-Möbius Interconversions in Extended π-Systems

2019 ◽  
Author(s):  
Tatiana Woller ◽  
Ambar Banerjee ◽  
Nitai Sylvetsky ◽  
Xavier Deraet ◽  
Frank De Proft ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Basis Set ◽  
Dft Methods ◽  
Molecular Switching ◽  
Wide Range ◽  
Electronic Structure Methods ◽  
Explicitly Correlated ◽  
Relative Errors ◽  
The Stability ◽  
Basis Set Expansion

<p>Expanded porphyrins provide a versatile route to molecular switching devices due to their ability to shift between several π-conjugation topologies encoding distinct properties. Taking into account its size and huge conformational flexibility, DFT remains the workhorse for modeling such extended macrocycles. Nevertheless, the stability of Hückel and Möbius conformers depends on a complex interplay of different factors, such as hydrogen bonding, p···p stacking, steric effects, ring strain and electron delocalization. As a consequence, the selection of an exchange-correlation functional for describing the energy profile of topological switches is very difficult. For these reasons, we have examined the performance of a variety of wavefunction methods and density functionals for describing the thermochemistry and kinetics of topology interconversions across a wide range of macrocycles. Especially for hexa- and heptaphyrins, the Möbius structures have a pronouncedly stronger degree of static correlation than the Hückel and figure-eight structures, and as a result the relative energies of singly-twisted structures are a challenging test for electronic structure methods. Comparison of limited orbital space full CI calculations with CCSD(T) calculations within the same active spaces shows that post-CCSD(T) correlation contributions to relative energies are very minor. At the same time, relative energies are weakly sensitive to further basis set expansion, as proven by the minor energy differences between MP2/cc-pVDZ and explicitly correlated MP2-F12/cc-pVDZ-F12 calculations. Hence, our CCSD(T) reference values are reasonably well-converged in both 1-particle and n-particle spaces. While conventional MP2 and MP3 yield very poor results, SCS-MP2 and particularly SOS-MP2 and SCS-MP3 agree to better than 1 kcal mol<sup>-1</sup> with the CCSD(T) relative energies. Regarding DFT methods, only M06-2X provides relative errors close to chemical accuracy with a RMSD of 1.2 kcal mol<sup>-1</sup>. While the original DSD-PBEP86 double hybrid performs fairly poorly for these extended p-systems, the errors drop down to 2 kcal mol<sup>-1</sup> for the revised revDSD-PBEP86-NL, again showing that same-spin MP2-like correlation has a detrimental impact on performance like the SOS-MP2 results. </p>

Insights into Potent Therapeutical Antileukemic Agent L-glutaminase Enzyme Under Solid-state Fermentation: A Review

2020 ◽  
Vol 21 (3) ◽  
pp. 211-220 ◽  
Author(s):  
Chandrasai Potla Durthi ◽  
Madhuri Pola ◽  
Satish Babu Rajulapati ◽  
Anand Kishore Kola
Keyword(s):  
Solid State ◽  
Solid State Fermentation ◽  
Food Industry ◽  
Energy Requirement ◽  
Production Studies ◽  
Wide Range ◽  
Hybridoma Technology ◽  
Bacteria And Fungi ◽  
The Stability ◽  
Glutaminase Activity

Aim & objective: To review the applications and production studies of reported antileukemic drug L-glutaminase under Solid-state Fermentation (SSF). Overview: An amidohydrolase that gained economic importance because of its wide range of applications in the pharmaceutical industry, as well as the food industry, is L-glutaminase. The medical applications utilized it as an anti-tumor agent as well as an antiretroviral agent. L-glutaminase is employed in the food industry as an acrylamide degradation agent, as a flavor enhancer and for the synthesis of theanine. Another application includes its use in hybridoma technology as a biosensing agent. Because of its diverse applications, scientists are now focusing on enhancing the production and optimization of L-glutaminase from various sources by both Solid-state Fermentation (SSF) and submerged fermentation studies. Of both types of fermentation processes, SSF has gained importance because of its minimal cost and energy requirement. L-glutaminase can be produced by SSF from both bacteria and fungi. Single-factor studies, as well as multi-level optimization studies, were employed to enhance L-glutaminase production. It was concluded that L-glutaminase activity achieved by SSF was 1690 U/g using wheat bran and Bengal gram husk by applying feed-forward artificial neural network and genetic algorithm. The highest L-glutaminase activity achieved under SSF was 3300 U/gds from Bacillus sp., by mixture design. Purification and kinetics studies were also reported to find the molecular weight as well as the stability of L-glutaminase. Conclusion: The current review is focused on the production of L-glutaminase by SSF from both bacteria and fungi. It was concluded from reported literature that optimization studies enhanced L-glutaminase production. Researchers have also confirmed antileukemic and anti-tumor properties of the purified L-glutaminase on various cell lines.

Glycans in scaffold design in tissue reconstruction

2021 ◽  
pp. 088391152199784
Author(s):  
Nipun Jain ◽  
Shashi Singh
Keyword(s):  
Cell Attachment ◽  
Low Cost ◽  
Growth Conditions ◽  
Downstream Signaling ◽  
Cell Carrier ◽  
Wide Range ◽  
Proliferation And Differentiation ◽  
Different Types ◽  
Tissue Reconstruction ◽  
A Cell

Development of an artificial tissue by tissue engineering is witnessed to be one of the long lasting clarified solutions for the damaged tissue function restoration. To accomplish this, a scaffold is designed as a cell carrier in which the extracellular matrix (ECM) performs a prominent task of controlling the inoculated cell’s destiny. ECM composition, topography and mechanical properties lead to different types of interactions between cells and ECM components that trigger an assortment of cellular reactions via diverse sensing mechanisms and downstream signaling pathways. The polysaccharides in the form of proteoglycans and glycoproteins yield better outcomes when included in the designed matrices. Glycosaminoglycan (GAG) chains present on proteoglycans show a wide range of operations such as sequestering of critical effector morphogens which encourage proficient nutrient contribution toward the growing stem cells for their development and endurance. In this review we discuss how the glycosylation aspects are of considerable importance in everyday housekeeping functions of a cell especially when placed in a controlled environment under ideal growth conditions. Hydrogels made from these GAG chains have been used extensively as a resorbable material that mimics the natural ECM functions for an efficient control over cell attachment, permeability, viability, proliferation, and differentiation processes. Also the incorporation of non-mammalian polysaccharides can elicit specific receptor responses which authorize the creation of numerous vigorous frameworks while prolonging the low cost and immunogenicity of the substance.

scholarly journals Polymer-Drug Conjugates as Nanotheranostic Agents

2021 ◽  
Vol 2 (1) ◽  
pp. 63-81
Author(s):  
Sajana Manandhar ◽  
Erica Sjöholm ◽  
Johan Bobacka ◽  
Jessica M. Rosenholm ◽  
Kuldeep K. Bansal
Keyword(s):  
Drug Delivery ◽  
Drug Release ◽  
Treatment Options ◽  
The Body ◽  
Drug Conjugates ◽  
Imaging Characteristics ◽  
Wide Range ◽  
Systemic Side Effects ◽  
Theranostic Agents ◽  
The Stability

Since the last decade, the polymer-drug conjugate (PDC) approach has emerged as one of the most promising drug-delivery technologies owing to several benefits like circumventing premature drug release, offering controlled and targeted drug delivery, improving the stability, safety, and kinetics of conjugated drugs, and so forth. In recent years, PDC technology has advanced with the objective to further enhance the treatment outcomes by integrating nanotechnology and multifunctional characteristics into these systems. One such development is the ability of PDCs to act as theranostic agents, permitting simultaneous diagnosis and treatment options. Theranostic nanocarriers offer the opportunity to track the distribution of PDCs within the body and help to localize the diseased site. This characteristic is of particular interest, especially among those therapeutic approaches where external stimuli are supposed to be applied for abrupt drug release at the target site for localized delivery to avoid systemic side effects (e.g., Visudyne®). Thus, with the help of this review article, we are presenting the most recent updates in the domain of PDCs as nanotheranostic agents. Different methodologies utilized to design PDCs along with imaging characteristics and their applicability in a wide range of diseases, have been summarized in this article.

scholarly journals No-z Model for Magnetic Fields of Different Astrophysical Objects and Stability of the Solutions

Data ◽  
2021 ◽  
Vol 6 (1) ◽  
pp. 4
Author(s):  
Evgeny Mikhailov ◽  
Daniela Boneva ◽  
Maria Pashentseva
Keyword(s):  
Magnetic Field ◽  
Magnetic Fields ◽  
Large Scale ◽  
Point Of View ◽  
Accretion Discs ◽  
Wide Range ◽  
Astrophysical Objects ◽  
Alpha Effect ◽  
The Stability ◽  
The Magnetic Field

A wide range of astrophysical objects, such as the Sun, galaxies, stars, planets, accretion discs etc., have large-scale magnetic fields. Their generation is often based on the dynamo mechanism, which is connected with joint action of the alpha-effect and differential rotation. They compete with the turbulent diffusion. If the dynamo is intensive enough, the magnetic field grows, else it decays. The magnetic field evolution is described by Steenbeck—Krause—Raedler equations, which are quite difficult to be solved. So, for different objects, specific two-dimensional models are used. As for thin discs (this shape corresponds to galaxies and accretion discs), usually, no-z approximation is used. Some of the partial derivatives are changed by the algebraic expressions, and the solenoidality condition is taken into account as well. The field generation is restricted by the equipartition value and saturates if the field becomes comparable with it. From the point of view of mathematical physics, they can be characterized as stable points of the equations. The field can come to these values monotonously or have oscillations. It depends on the type of the stability of these points, whether it is a node or focus. Here, we study the stability of such points and give examples for astrophysical applications.

scholarly journals Tetracycline Induces Stabilization of mRNA in Bacillus subtilis

2002 ◽  
Vol 184 (4) ◽  
pp. 889-894 ◽  
Author(s):  
Yi Wei ◽  
David H. Bechhofer
Keyword(s):  
Bacillus Subtilis ◽  
Mrna Stability ◽  
The Other ◽  
Leader Region ◽  
Subinhibitory Concentration ◽  
Coding Sequence ◽  
Mrna Stabilization ◽  
Threefold Increase ◽  
The Stability

ABSTRACT The tet(L) gene of Bacillus subtilis confers low-level tetracycline (Tc) resistance. Previous work examining the >20-fold-inducible expression of tet(L) by Tc demonstrated a 12-fold translational induction. Here we show that the other component of tet(L) induction is at the level of mRNA stabilization. Addition of a subinhibitory concentration of Tc results in a two- to threefold increase in tet(L) mRNA stability. Using a plasmid-borne derivative of tet(L) with a large in-frame deletion of the coding sequence, the mechanism of Tc-induced stability was explored by measuring the decay of tet(L) mRNAs carrying specific mutations in the leader region. The results of these experiments, as well as experiments with a B. subtilis strain that is resistant to Tc due to a mutation in the ribosomal S10 protein, suggest different mechanisms for the effects of Tc on translation and on mRNA stability. The key role of the 5" end in determining mRNA stability was confirmed in these experiments. Surprisingly, the stability of several other B. subtilis mRNAs was also induced by Tc, which indicates that addition of Tc may result in a general stabilization of mRNA.

scholarly journals Sequence and regulation of a gene encoding a human 89-kilodalton heat shock protein.

1989 ◽  
Vol 9 (6) ◽  
pp. 2615-2626 ◽  
Author(s):  
E Hickey ◽  
S E Brandon ◽  
G Smale ◽  
D Lloyd ◽  
L A Weber
Keyword(s):  
Heat Shock ◽  
Heat Shock Protein ◽  
Normal Growth ◽  
Gene Families ◽  
Growth Conditions ◽  
Complete Sequence ◽  
Start Codon ◽  
Hybridization Probe ◽  
Reading Frame ◽  
Alpha Gene

Vertebrate cells synthesize two forms of the 82- to 90-kilodalton heat shock protein that are encoded by distinct gene families. In HeLa cells, both proteins (hsp89 alpha and hsp89 beta) are abundant under normal growth conditions and are synthesized at increased rates in response to heat stress. Only the larger form, hsp89 alpha, is induced by the adenovirus E1A gene product (M. C. Simon, K. Kitchener, H. T. Kao, E. Hickey, L. Weber, R. Voellmy, N. Heintz, and J. R. Nevins, Mol. Cell. Biol. 7:2884-2890, 1987). We have isolated a human hsp89 alpha gene that shows complete sequence identity with heat- and E1A-inducible cDNA used as a hybridization probe. The 5'-flanking region contained overlapping and inverted consensus heat shock control elements that can confer heat-inducible expression on a beta-globin reporter gene. The gene contained 10 intervening sequences. The first intron was located adjacent to the translation start codon, an arrangement also found in the Drosophila hsp82 gene. The spliced mRNA sequence contained a single open reading frame encoding an 84,564-dalton polypeptide showing high homology with the hsp82 to hsp90 proteins of other organisms. The deduced hsp89 alpha protein sequence differed from the human hsp89 beta sequence reported elsewhere (N. F. Rebbe, J. Ware, R. M. Bertina, P. Modrich, and D. W. Stafford (Gene 53:235-245, 1987) in at least 99 out of the 732 amino acids. Transcription of the hsp89 alpha gene was induced by serum during normal cell growth, but expression did not appear to be restricted to a particular stage of the cell cycle. hsp89 alpha mRNA was considerably more stable than the mRNA encoding hsp70, which can account for the higher constitutive rate of hsp89 synthesis in unstressed cells.

scholarly journals Stability and Instability in the Lysogenic State of Phage Lambda

2010 ◽  
Vol 192 (22) ◽  
pp. 6064-6076 ◽  
Author(s):  
John W. Little ◽  
Christine B. Michalowski
Keyword(s):  
Intrinsic Rate ◽  
Growth Conditions ◽  
Emergent Properties ◽  
Regulatory Circuits ◽  
Stability And Instability ◽  
Natural Range ◽  
Analysis Of Stability ◽  
Stable Association ◽  
The Stability ◽  
Gene Regulatory Circuits

ABSTRACT Complex gene regulatory circuits exhibit emergent properties that are difficult to predict from the behavior of the components. One such property is the stability of regulatory states. Here we analyze the stability of the lysogenic state of phage λ. In this state, the virus maintains a stable association with the host, and the lytic functions of the virus are repressed by the viral CI repressor. This state readily switches to the lytic pathway when the host SOS system is induced. A low level of SOS-dependent switching occurs without an overt stimulus. We found that the intrinsic rate of switching to the lytic pathway, measured in a host lacking the SOS response, was almost undetectably low, probably less than 10−8/generation. We surmise that this low rate has not been selected directly during evolution but results from optimizing the rate of switching in a wild-type host over the natural range of SOS-inducing conditions. We also analyzed a mutant, λprm240, in which the promoter controlling CI expression was weakened, rendering lysogens unstable. Strikingly, the intrinsic stability of λprm240 lysogens depended markedly on the growth conditions; lysogens grown in minimal medium were nearly stable but switched at high rates when grown in rich medium. These effects on stability likely reflect corresponding effects on the strength of the prm240 promoter, measured in an uncoupled assay system. Several derivatives of λprm240 with altered stabilities were characterized. This mutant and its derivatives afford a model system for further analysis of stability.

scholarly journals Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
T. M. Porter ◽  
M. Hajibabaei
Keyword(s):  
Markov Model ◽  
Hidden Markov Model ◽  
Dna Barcoding ◽  
Profile Analysis ◽  
Hidden Markov ◽  
Open Reading Frame ◽  
Protein Coding ◽  
Reading Frame ◽  
Frame Length ◽  
Open Reading Frame Length

Abstract Background Pseudogenes are non-functional copies of protein coding genes that typically follow a different molecular evolutionary path as compared to functional genes. The inclusion of pseudogene sequences in DNA barcoding and metabarcoding analysis can lead to misleading results. None of the most widely used bioinformatic pipelines used to process marker gene (metabarcode) high throughput sequencing data specifically accounts for the presence of pseudogenes in protein-coding marker genes. The purpose of this study is to develop a method to screen for nuclear mitochondrial DNA segments (nuMTs) in large COI datasets. We do this by: (1) describing gene and nuMT characteristics from an artificial COI barcode dataset, (2) show the impact of two different pseudogene removal methods on perturbed community datasets with simulated nuMTs, and (3) incorporate a pseudogene filtering step in a bioinformatic pipeline that can be used to process Illumina paired-end COI metabarcode sequences. Open reading frame length and sequence bit scores from hidden Markov model (HMM) profile analysis were used to detect pseudogenes. Results Our simulations showed that it was more difficult to identify nuMTs from shorter amplicon sequences such as those typically used in metabarcoding compared with full length DNA barcodes that are used in the construction of barcode libraries. It was also more difficult to identify nuMTs in datasets where there is a high percentage of nuMTs. Existing bioinformatic pipelines used to process metabarcode sequences already remove some nuMTs, especially in the rare sequence removal step, but the addition of a pseudogene filtering step can remove up to 5% of sequences even when other filtering steps are in place. Conclusions Open reading frame length filtering alone or combined with hidden Markov model profile analysis can be used to effectively screen out apparent pseudogenes from large datasets. There is more to learn from COI nuMTs such as their frequency in DNA barcoding and metabarcoding studies, their taxonomic distribution, and evolution. Thus, we encourage the submission of verified COI nuMTs to public databases to facilitate future studies.

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