Comparative kinetics of cytosine nucleosides. Influence of a 6-methyl substituent on degradation rates and pathways in aqueous buffers

A major challenge for developmental biologists in coming years will be to place the vast number of newly identified genes into precisely ordered genetic and molecular pathways. This will require efficient methods to determine which genes interact directly and indirectly. One of the most comprehensive pathways currently under study is the genetic hierarchy that controls Drosophila segmentation. Yet, many of the potential interactions within this pathway remain untested or unverified. Here, we look at one of the best-characterized components of this pathway, the homeodomain-containing transcription factor Fushi tarazu (Ftz), and analyze the response kinetics of known and putative target genes. This is achieved by providing a brief pulse of Ftz expression and measuring the time required for genes to respond. The time required for Ftz to bind and regulate its own enhancer, a well-documented interaction, is used as a standard for other direct interactions. Surprisingly, we find that both positively and negatively regulated target genes respond to Ftz with the same kinetics as autoregulation. The rate-limiting step between successive interactions (<10 minutes) is the time required for regulatory proteins to either enter or be cleared from the nucleus, indicating that protein synthesis and degradation rates are closely matched for all of the proteins studied. The matching of these two processes is likely important for the rapid and synchronous progression from one class of segmentation genes to the next. In total, 11 putative Ftz target genes are analyzed, and the data provide a substantially revised view of Ftz roles and activities within the segmentation hierarchy.

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Stress–response relationships related to ageing and death of orthodox seeds: a study comparing viability and RNA integrity in soya bean (Glycine max) cv. Williams 82

Seed Science Research ◽

10.1017/s0960258520000197 ◽

2020 ◽

Vol 30 (2) ◽

pp. 161-172

Author(s):

Christina Walters ◽

Margaret B. Fleming ◽

Lisa M. Hill ◽

Emma J. Dorr ◽

Christopher M. Richards

Keyword(s):

Degradation Kinetics ◽

Rna Degradation ◽

Soya Bean ◽

Rna Integrity ◽

Viability Loss ◽

Rna Integrity Number ◽

Oxidative Stresses ◽

Degradation Rates ◽

Highly Correlated ◽

Kinetics Of

AbstractCharacterizing non-lethal damage within dry seeds may allow us to detect early signs of ageing and accurately predict longevity. We compared RNA degradation and viability loss in seeds exposed to stressful conditions to quantify relationships between degradation rates and stress intensity or duration. We subjected recently harvested (‘fresh’) ‘Williams 82’ soya bean seeds to moisture, temperature and oxidative stresses, and measured time to 50% viability (P50) and rate of RNA degradation, the former using standard germination assays and the latter using RNA Integrity Number (RIN). RIN values from fresh seeds were also compared with those from accessions of the same cultivar harvested in the 1980s and 1990s and stored in the refrigerator (5°C), freezer (−18°C) or in vapour above liquid nitrogen (−176°C). Rates of viability loss (P50−1) and RNA degradation (RIN⋅d−1) were highly correlated in soya bean seeds that were exposed to a broad range of temperatures [holding relative humidity (RH) constant at about 30%]. However, the correlation weakened when fresh seeds were maintained at high RH (holding temperature constant at 35°C) or exposed to oxidizing agents. Both P50−1 and RIN⋅d−1 parameters exhibited breaks in Arrhenius behaviour near 50°C, suggesting that constrained molecular mobility regulates degradation kinetics of dry systems. We conclude that the kinetics of ageing reactions at RH near 30% can be simulated by temperatures up to 50°C and that RNA degradation can indicate ageing prior to and independent of seed death.

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Determination of Aerobic Degradation Rates and Kinetics of Gaseous Hydrocarbons in Soil

Handbook of Hydrocarbon and Lipid Microbiology ◽

10.1007/978-3-540-77587-4_285 ◽

2010 ◽

pp. 3623-3630

Author(s):

P. Höhener

Keyword(s):

Aerobic Degradation ◽

Degradation Rates ◽

Gaseous Hydrocarbons ◽

Kinetics Of

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Membrane-bound Steel factor induces more persistent tyrosine kinase activation and longer life span of c-kit gene-encoded protein than its soluble form

Blood ◽

10.1182/blood.v85.3.641.bloodjournal853641 ◽

1995 ◽

Vol 85 (3) ◽

pp. 641-649 ◽

Cited By ~ 195

Author(s):

K Miyazawa ◽

DA Williams ◽

A Gotoh ◽

J Nishimaki ◽

HE Broxmeyer ◽

...

Keyword(s):

Cell Surface ◽

Tyrosine Kinase ◽

Life Span ◽

Protein Degradation ◽

Cell Line ◽

Soluble Form ◽

Steel Factor ◽

Degradation Rates ◽

Membrane Bound ◽

Kinetics Of

Alternative splicing of exon 6 results in the production of two isoforms of Steel factor (SLF): the membrane-bound and soluble forms. To investigate differences in the kinetics of c-kit tyrosine kinase activated by these two isoforms, we used a stromal cell line (SI/SI4) established from SI/SI homozygous murine embryo fetal liver and its stable transfectants containing either hSCF248 cDNA (including exon 6; secreted form) or hSCF220 cDNA (lacking exon 6; membrane-bound form) as the source of each isoform. Interaction of factor dependent myeloid cell line MO7e with stromal cells producing either isoform resulted in activated c-kit tyrosine kinase and induction of the same series of tyrosine phosphorylated cellular proteins in MO7e cells. However, SI4- h220 (membrane-bound form) induced more persistent activation of c-kit kinase than SI4-h248 (soluble form) did. Flow cytometric analysis and pulse-chase studies using [35S]methionine showed that SI4-h248 induced rapid downmodulation of cell-surface c-kit expression and its protein degradation in MO7e cells, whereas SI4-h220 induced more prolonged life span of c-kit protein. Addition of soluble recombinant human SLF to SI4- h220 cultures enhanced reduction of cell-surface c-kit expression and its protein degradation. Because the kinetics of c-kit inactivation strikingly fits with the protein degradation rates of c-kit under the conditions described above, rapid proteolysis of c-kit protein induced by soluble SLF stimulation may function as a “turn-off switch” for activated c-kit kinase.

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Fertimetro, a Principle and Device to Measure Soil Nutrient Availability for Plants by Microbial Degradation Rates on Differently-Spiked Buried Threads

Soil Systems ◽

10.3390/soilsystems3010003 ◽

2018 ◽

Vol 3 (1) ◽

pp. 3 ◽

Cited By ~ 1

Author(s):

Giuseppe Concheri ◽

Stefano Tiozzo ◽

Piergiorgio Stevanato ◽

Francesco Morari ◽

Antonio Berti ◽

...

Keyword(s):

Crop Yields ◽

Soil Nutrient ◽

Self Assessment ◽

Soil Nutrient Availability ◽

Degradation Rates ◽

Subsequent Crop ◽

User Friendly ◽

Fertilizer Rates ◽

Kinetics Of

A novel patented method (PCT/IB2012/001157: Squartini, Concheri, Tiozzo, University of Padova) and the corresponding application devices, suitable to measure soil fertility, are presented. The availability or deficiency of specific nutrients for crops is assessed by monitoring the kinetics of progressive weakening of cotton or silk threads due to in situ microbial activity. The method is based on a nutrient-primed incremented substrate degradation principle. Threads are buried as is or pre-impregnated with N or P solutions, and the acceleration of the degradation rate for the N-supplemented or P-supplemented thread, in comparison to the untreated thread, is proportional to the lack of the corresponding nutrient in that soil. Tests were validated on corn crops in plots receiving increasing fertilizer rates in a historical rotation that has been established since 1962. The measurement carried out in May significantly correlated with the subsequent crop yields recorded in October. The analysis allows an early, inexpensive, fast, and reproducible self-assessment at field level to improve fertilization rates. The device is envisaged as a user-friendly tool for agronomy, horticulture, and any environmental applications where organic matter cycling, soil quality, and specific nutrients excess or deficiency are critical considerations.

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Poly(Lactic Acid)-Based Nanobiocomposites with Modulated Degradation Rates

Materials ◽

10.3390/ma11101943 ◽

2018 ◽

Vol 11 (10) ◽

pp. 1943 ◽

Cited By ~ 9

Author(s):

Iozzino Valentina ◽

Askanian Haroutioun ◽

Leroux Fabrice ◽

Verney Vincent ◽

Pantani Roberto

Keyword(s):

Lactic Acid ◽

Succinic Acid ◽

Extrusion Process ◽

Poly Lactic Acid ◽

Melt Compounding ◽

Degradation Rates ◽

Rate Of Hydrolysis ◽

Plastic Industry ◽

Double Hydroxides ◽

Kinetics Of

In the field of biodegradable polymers such as poly(Lactic Acid) (PLA), it is quite well known that their kinetics of hydrolysis strongly depend on the pH of the hydrolyzing medium. The idea explored during this study focused on PLA, is the addition of additives that are able to control the pH of water when it diffuses inside the polymer. For instance, acids (i.e. succinic acid, also used as food additive) are bio- and eco- friendly additives that are able to play this role. In order to control the release of these molecules and their dispersion inside the polymer, their intercalation in biocompatible nanofillers like layered double hydroxides (LDH) is here considered. The additives have been dispersed in the polymer by melt compounding, commonly used in the plastic industry. Several composites of PLA (4032D) and LDH intercalated with organic acids (succinic, fumaric, and ascorbic acid) have been obtained by an extrusion process. From all extruded materials, PLA films obtained by compression molding were then subjected to hydrolysis tests. The results showed that the mentioned molecules, dispersed in the polymer, are able to control the rate of hydrolysis, and experimental results show an increase of degradation time for samples containing LDH-organic acid (in particular with LDH-succinic acid), making such hybrid additives an appropriate and efficient solution for PLA.

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Photocatalytic Performance of Electrospun Silk Fibroin/ZnO Mats to Remove Pesticide Residues from Water under Natural Sunlight

Catalysts ◽

10.3390/catal10010110 ◽

2020 ◽

Vol 10 (1) ◽

pp. 110 ◽

Cited By ~ 4

Author(s):

Isabel Garrido ◽

Salvador Aznar-Cervantes ◽

Marina Aliste ◽

María J. Yáñez-Gascón ◽

Nuria Vela ◽

...

Keyword(s):

Silk Fibroin ◽

Pesticide Residues ◽

Degradation Kinetics ◽

Catalyst Loading ◽

Similar Amount ◽

Experimental Conditions ◽

Electrospinning Technique ◽

Degradation Rates ◽

Kinetics Of ◽

Environmentally Friendly Approach

We have evaluated the efficiency of silk fibroin (SF) coated with ZnO nanoparticles in the photocatalytic disappearance of one acaricide (etoxazole) and three fungicides (difenoconazole, myclobutanil and penconazole) in water exposed to sunlight irradiation. Electrospun SF/ZnO mats were successfully synthesized by electrospinning technique and characterized by XRD, FE-SEM, XPS, XDS, FTIR, and BET. The influence of catalyst loading on the degradation kinetics of the different pesticides was examined in order to gain knowledge of maximum degradation efficiency. A significant increment in degradation rates was observed with the addition of ZnO. SF mats with 25 mg of ZnO were finally selected since no significant differences (p < 0.05) were detected when the loading was enlarged from 25 to 50 mg for the majority of the compounds. In the experimental conditions, the half-lives ranged from 33 min to 93 min for etoxazole and myclobutanil, respectively. The comparison of SF materials coated with similar amount of TiO2 and ZnO showed that the later was slightly more efficient to remove pesticide residues. Hence, the use of electrospun SF/ZnO nanostructures would provide an environmentally friendly approach with photocatalytic activity to be applied in the reclamation of water polluted by pesticides.

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Mutation of Candida tropicalis by Irradiation with a He-Ne Laser To Increase Its Ability To Degrade Phenol

Applied and Environmental Microbiology ◽

10.1128/aem.00677-06 ◽

2006 ◽

Vol 73 (1) ◽

pp. 226-231 ◽

Cited By ~ 16

Author(s):

Yan Jiang ◽

Jianping Wen ◽

Xiaoqiang Jia ◽

Qinggele Caiyin ◽

Zongding Hu

Keyword(s):

Mutant Strain ◽

Candida Tropicalis ◽

Phenol Hydroxylase ◽

Phenol Biodegradation ◽

Batch Cultures ◽

Yeast Extract Peptone Dextrose ◽

Degradation Rates ◽

Wide Range ◽

Mutant Strains ◽

Kinetics Of

ABSTRACT Candida tropicalis isolated from acclimated activated sludge was used in this study. Cell suspensions with 5 × 107 cells ml−1 were irradiated by using a He-Ne laser. After mutagenesis, the irradiated cell suspension was diluted and plated on yeast extract-peptone-dextrose (YEPD) medium. Plates with approximately 20 individual colonies were selected, and all individual colonies were harvested for phenol biodegradation. The phenol biodegradation stabilities for 70 phenol biodegradation-positive mutants, mutant strains CTM 1 to 70, ranked according to their original phenol biodegradation potentials, were tested continuously during transfers. Finally, mutant strain CTM 2, which degraded 2,600 mg liter−1 phenol within 70.5 h, was obtained on the basis of its capacity and hereditary stability for phenol biodegradation. The phenol hydroxylase gene sequences were cloned in wild and mutant strains. The results showed that four amino acids were mutated by irradiation with a laser. In order to compare the activity of phenol hydroxylase in wild and mutant strains, their genes were expressed in Escherichia coli BL21(DE3) and enzyme activities were spectrophotometrically determined. It was clear that the activity of phenol hydroxylase was promoted after irradiation with a He-Ne laser. In addition, the cell growth and intrinsic phenol biodegradation kinetics of mutant strain CTM 2 in batch cultures were also described by Haldane's kinetic equation with a wide range of initial phenol concentrations from 0 to 2,600 mg liter−1. The specific growth and degradation rates further demonstrated that the CTM 2 mutant strain possessed a higher capacity to resist phenol toxicity than wild C. tropicalis did.

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Pyrolytic kinetics of coconut shell waste using Ramped PyrOx

10.31224/osf.io/p6h49 ◽

2018 ◽

Author(s):

Imtiaz Ali ◽

Haitham Bahaitham ◽

Raed Naebulharam

Keyword(s):

Activation Energy ◽

Biomass Conversion ◽

Degradation Mechanism ◽

Coconut Shell ◽

Heating Rates ◽

Experimental Conditions ◽

Degradation Rates ◽

Shell Waste ◽

Mass Conversion ◽

Kinetics Of

Biomass pyrolysis is an efficient and economical conversion process. The kinetics of biomass conversion is still not fully understood mainly because this complex material is composed of numerous compounds with very different reactivities. In this work an inverse model is used to determine the nonparametric probability density function p(Ea) of activation energy (Ea) for coconut shell waste (CSW) pyrolysis via the Ramped PyrOx (RPO) method from the time-series and temperature-series mass conversion data. In this method, the degradation rates are described by inverting distributed activation energy model (DAEM). This method does not require p(Ea) to follow any particular parametric form furthermore the modelling results are independent of experimental conditions such as heating rates. The pyrolytic kinetics is modelled considering first-order degradation mechanism.

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Structure - Activity Relations for the Photodegradation Reactions of Monosubstituted Anilines in TiO2 Suspensions

Journal of Advanced Oxidation Technologies ◽

10.1515/jaots-2002-0111 ◽

2002 ◽

Vol 5 (1) ◽

Cited By ~ 1

Author(s):

Nevim San ◽

Zekiye Çımar

Keyword(s):

Rate Constants ◽

Molecular Orbital Calculations ◽

Hartree Fock ◽

Degradation Reactions ◽

Structure Activity ◽

Degradation Rates ◽

Structure Activity Relations ◽

Self Consistent Field ◽

Semi Empirical ◽

Kinetics Of

AbstractThe kinetics of the photocatalytic degradation reactions of nine different monosubstituted anilines have been investigated experimentally and theoretically. With the intention of finding certain indices in order to determine the degradation rates of aromatic pollutants, geometry optimizations of the anilines have been performed with the semi-empirical PM3 method. The molecular orbital calculations have been carried out by a self-consistent field SCF method using the restricted Hartree-Fock RHF formalism. The correlations between the apparent first-order rate constants and the molecular properties of the compounds have been examined. Three different quantitative structure-activity relationships, QSARs were developed expressing the logarithms of the rate constants in terms of the Brown constants σ

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