KINETICS OF BIOLOGICAL PROCESSES AS A BASIS OF AUTOMATIC REGULATION

Abstract Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

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Kinetics of nitrogen removal processes in constructed wetlands

E3S Web of Conferences ◽

10.1051/e3sconf/20182600001 ◽

2018 ◽

Vol 26 ◽

pp. 00001 ◽

Cited By ~ 4

Author(s):

Magdalena Gajewska ◽

Katarzyna Skrzypiec

Keyword(s):

Constructed Wetlands ◽

Nitrogen Removal ◽

Kinetic Models ◽

Treatment Wetlands ◽

Rate Coefficients ◽

Biological Processes ◽

Monod Kinetics ◽

Removal Processes ◽

Kinetics Of ◽

Removal Model

The aim of this paper is to present a state-of-the-art review of the kinetics of nitrogen removal in constructed wetlands. Biological processes of nitrogen removal from wastewater can be described using equations and kinetic models. Hence, these kinetic models which have been developed and evaluated allow for predicting the removal of nitrogen in treatment wetlands. One of the most important, first order removal model, which is still applied, was analysed and its rate coefficients and factors were compared. This study also demonstrates the validity of Monod and multiple Monod kinetics, commonly seen today. Finally, a computational example of the reaction kinetics of nitrogen removal was also included in the study.

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Direct Monitoring of Bicarbonate Transport by Emission Spectroscopy

10.26434/chemrxiv.12624425.v2 ◽

2020 ◽

Author(s):

Luis Martínez-Crespo ◽

Sarah Hewitt ◽

Nicola Alessandro De Simone ◽

Vladimir Sindelar ◽

Anthony P. Davis ◽

...

Keyword(s):

Emission Spectroscopy ◽

High Sensitivity ◽

Bicarbonate Transport ◽

Biological Processes ◽

Indirect Methods ◽

The Past ◽

Low Concentrations ◽

Bicarbonate Transporters ◽

Fluorescence Spectrometer ◽

Kinetics Of

The transmembrane transport of bicarbonate is a key step in many important biological processes, while problems with bicarbonate transport are at the origin of various diseases. Over the past 10 years, many anionophores that have been developed for the transport of chloride, have also been tested as bicarbonate transporters. However, methodology to directly monitor the kinetics of transport of bicarbonate is lacking, hence indirect methods have been used, which mainly rely on the monitoring of chloride concentrations.Here we present an assay that allows the kinetics of bicarbonate transport into liposomes to be monitored directly, using emission spectroscopy. The assay utilises an encapsulated europium(III) complex, which exhibits a large increase in emission upon binding of bicarbonate. The advantages of this assay over existing methodology are that concentrations of bicarbonate are monitored directly and with a high sensitivity. This allows studies at very low concentrations of anionophores, and for the mechanisms of bicarbonate transport to be unravelled. We have distinguished classical antiport with bicarbonate from mechanisms involving CO2 diffusion and the dissipation of a pH gradient. Furthermore, the use of a standard fluorescence spectrometer and liposomes with a diameter ~200 nm makes this assay readily and reliably applicable in many laboratories, where it can facilitate the development of bicarbonate transporters for applications in physiological studies or therapies.

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Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure

10.1101/2021.12.17.473246 ◽

2021 ◽

Author(s):

Sophie Hertel ◽

Richard Spinney ◽

Stephanie Xu ◽

Thomas E Ouldridge ◽

Richard Morris ◽

...

Keyword(s):

Secondary Structure ◽

Dna Sequences ◽

Physical Factors ◽

Biological Processes ◽

Physical Mechanisms ◽

Mechanistic Insight ◽

Sequence Dependent ◽

Dna Hybridisation ◽

Kinetics Of ◽

Insight Into

The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridise at different rates are not well understood. Secondary structure is one predictable factor that influences hybridisation rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. Consequently, to achieve a good correlation with experimental data, current prediction algorithms require many parameters that provide little mechanistic insight into DNA hybridisation. In this context, we measured hybridisation rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify their hybridisation rates. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters, thus providing new insight into the physical factors underpinning DNA hybridisation rates.

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Thermodynamics and Kinetics of Biological Processes

10.1515/9783110845914 ◽

1982 ◽

Cited By ~ 1

Keyword(s):

Biological Processes ◽

Thermodynamics And Kinetics ◽

Kinetics Of

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Direct Monitoring of Bicarbonate Transport by Emission Spectroscopy

10.26434/chemrxiv.12624425.v3 ◽

2021 ◽

Author(s):

Luis Martínez-Crespo ◽

Sarah Hewitt ◽

Nicola Alessandro De Simone ◽

Vladimir Sindelar ◽

Anthony P. Davis ◽

...

Keyword(s):

Emission Spectroscopy ◽

High Sensitivity ◽

Bicarbonate Transport ◽

Biological Processes ◽

Indirect Methods ◽

The Past ◽

Low Concentrations ◽

Bicarbonate Transporters ◽

Fluorescence Spectrometer ◽

Kinetics Of

The transmembrane transport of bicarbonate is a key step in many important biological processes, while problems with bicarbonate transport are at the origin of various diseases. Over the past 10 years, many anionophores that have been developed for the transport of chloride, have also been tested as bicarbonate transporters. However, methodology to directly monitor the kinetics of transport of bicarbonate is lacking, hence indirect methods have been used, which mainly rely on the monitoring of chloride concentrations.Here we present an assay that allows the kinetics of bicarbonate transport into liposomes to be monitored directly, using emission spectroscopy. The assay utilises an encapsulated europium(III) complex, which exhibits a large increase in emission upon binding of bicarbonate. The advantages of this assay over existing methodology are that concentrations of bicarbonate are monitored directly and with a high sensitivity. This allows studies at very low concentrations of anionophores, and for the mechanisms of bicarbonate transport to be unravelled. We have distinguished classical antiport with bicarbonate from mechanisms involving CO2 diffusion and the dissipation of a pH gradient. Furthermore, the use of a standard fluorescence spectrometer and liposomes with a diameter ~200 nm makes this assay readily and reliably applicable in many laboratories, where it can facilitate the development of bicarbonate transporters for applications in physiological studies or therapies.

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Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with repressed chromatin compartment and reveals transcription dynamics

10.1101/859504 ◽

2019 ◽

Author(s):

Alexey A. Gavrilov ◽

Anastasiya A. Zharikova ◽

Aleksandra A. Galitsyna ◽

Artem V. Luzhin ◽

Natalia M. Rubanova ◽

...

Keyword(s):

Messenger Rna ◽

K562 Cells ◽

Biological Processes ◽

Rna Molecules ◽

Proximity Ligation ◽

Genome Wide ◽

Non Coding Rnas ◽

Genomic Regions ◽

Kinetics Of ◽

Inactive Chromatin

AbstractNon-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA–DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. We found two microRNAs—MIR3648 and MIR3687 transcribed from the rRNA locus—that are associated with inactive chromatin genome wide. These miRNAs favor bulk heterochromatin over Polycomb-repressed chromatin and interact preferentially with late-replicating genomic regions. Analysis of the RNA–DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

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Kinetics of Biological Oxidation

Water Quality Research Journal ◽

10.2166/wqrj.1966.003 ◽

1966 ◽

Vol 1 (1) ◽

pp. 53-80

Author(s):

B.E. Jank ◽

W.R. Drynan

Keyword(s):

Activated Sludge ◽

Future Development ◽

Process Design ◽

Industrial Wastes ◽

Biological Oxidation ◽

Biological Processes ◽

Activated Sludge Process ◽

Toxic Materials ◽

Basic Understanding ◽

Kinetics Of

Abstract The future development of the activated sludge process depends to a large extent upon a basic understanding of the kinetics of the biological processes involved and an evaluation of the effects of various factors on these kinetics. A realistic evaluation of the effects of such variables as influent quality and quantity, presence of toxic materials, shock loads, sludge age, pH, etc., on the activated sludge process can be made only if the kinetics of biological oxidation are well defined and reproducible under normal conditions. In addition, a knowledge of the kinetics for a given waste and sludge, particularly in the case of industrial wastes, should provide a more meaningful approach to process design.

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DNA hybridisation kinetics using single-molecule fluorescence imaging

Essays in Biochemistry ◽

10.1042/ebc20200040 ◽

2021 ◽

Author(s):

Rebecca Andrews

Keyword(s):

Nucleic Acid ◽

Single Molecule ◽

Biological Processes ◽

Single Molecule Fluorescence ◽

Extrinsic Factors ◽

Factors Affecting ◽

Dna Hybridisation ◽

Single Molecule Studies ◽

Kinetics Of ◽

Insight Into

Abstract Deoxyribonucleic acid (DNA) hybridisation plays a key role in many biological processes and nucleic acid biotechnologies, yet surprisingly there are many aspects about the process which are still unknown. Prior to the invention of single-molecule microscopy, DNA hybridisation experiments were conducted at the ensemble level, and thus it was impossible to directly observe individual hybridisation events and understand fully the kinetics of DNA hybridisation. In this mini-review, recent single-molecule fluorescence-based studies of DNA hybridisation are discussed, particularly for short nucleic acids, to gain more insight into the kinetics of DNA hybridisation. As well as looking at single-molecule studies of intrinsic and extrinsic factors affecting DNA hybridisation kinetics, the influence of the methods used to detect hybridisation of single DNAs is considered. Understanding the kinetics of DNA hybridisation not only gives insight into an important biological process but also allows for further advancements in the growing field of nucleic acid biotechnology.

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Mechanistic reconstruction of glycoprotein secretion through monitoring of intracellular N-glycan processing

Science Advances ◽

10.1126/sciadv.aax8930 ◽

2019 ◽

Vol 5 (11) ◽

pp. eaax8930 ◽

Cited By ~ 8

Author(s):

Ilaria Arigoni-Affolter ◽

Ernesto Scibona ◽

Chia-Wei Lin ◽

David Brühlmann ◽

Jonathan Souquet ◽

...

Keyword(s):

Secretory Pathway ◽

Current Knowledge ◽

Biological Processes ◽

Turnover Rates ◽

In Vivo Kinetics ◽

Glycoprotein Processing ◽

Glycoprotein Secretion ◽

Kinetics Of ◽

Model Based Analysis

N-linked glycosylation plays a fundamental role in determining the thermodynamic stability of proteins and is involved in multiple key biological processes. The mechanistic understanding of the intracellular machinery responsible for the stepwise biosynthesis of N-glycans is still incomplete due to limited understanding of in vivo kinetics of N-glycan processing along the secretory pathway. We present a glycoproteomics approach to monitor the processing of site-specific N-glycans in CHO cells. On the basis of a model-based analysis of structure-specific turnover rates, we provide a kinetic description of intracellular N-glycan processing along the entire secretory pathway. This approach refines and further extends the current knowledge on N-glycans biosynthesis and provides a basis to quantify alterations in the glycoprotein processing machinery.

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