CAN COMPLEX CELLULAR PROCESSES BE GOVERNED BY SIMPLE LINEAR RULES?

2009 ◽  
Vol 07 (01) ◽  
pp. 243-268 ◽  
Author(s):  
KUMAR SELVARAJOO ◽  
MASARU TOMITA ◽  
MASA TSUCHIYA
Keyword(s):  
Biological Networks ◽  
Biological Network ◽  
Living Systems ◽  
Regulatory Motifs ◽  
Cellular Processes ◽  
Self Organized ◽  
Wide Range ◽  
Activation Response ◽  
Physical Reasons

Complex living systems have shown remarkably well-orchestrated, self-organized, robust, and stable behavior under a wide range of perturbations. However, despite the recent generation of high-throughput experimental datasets, basic cellular processes such as division, differentiation, and apoptosis still remain elusive. One of the key reasons is the lack of understanding of the governing principles of complex living systems. Here, we have reviewed the success of perturbation–response approaches, where without the requirement of detailed in vivo physiological parameters, the analysis of temporal concentration or activation response unravels biological network features such as causal relationships of reactant species, regulatory motifs, etc. Our review shows that simple linear rules govern the response behavior of biological networks in an ensemble of cells. It is daunting to know why such simplicity could hold in a complex heterogeneous environment. Provided physical reasons can be explained for these phenomena, major advancement in the understanding of basic cellular processes could be achieved.

scholarly journals Cooperative subunit dynamics modulate p97 function

2018 ◽  
Vol 116 (1) ◽  
pp. 158-167 ◽  
Author(s):  
Rui Huang ◽  
Zev A. Ripstein ◽  
John L. Rubinstein ◽  
Lewis E. Kay
Keyword(s):  
Bound State ◽  
Nmr Studies ◽  
Biologically Relevant ◽  
Aaa Atpase ◽  
Cellular Processes ◽  
Allosteric Communication ◽  
Functional Dynamics ◽  
Nmr Study ◽  
Wide Range

p97 is an essential hexameric AAA+ ATPase involved in a wide range of cellular processes. Mutations in the enzyme are implicated in the etiology of an autosomal dominant neurological disease in which patients are heterozygous with respect to p97 alleles, containing one copy each of WT and disease-causing mutant genes, so that, in vivo, p97 molecules can be heterogeneous in subunit composition. Studies of p97 have, however, focused on homohexameric constructs, where protomers are either entirely WT or contain a disease-causing mutation, showing that for WT p97, the N-terminal domain (NTD) of each subunit can exist in either a down (ADP) or up (ATP) conformation. NMR studies establish that, in the ADP-bound state, the up/down NTD equilibrium shifts progressively toward the up conformation as a function of disease mutant severity. To understand NTD functional dynamics in biologically relevant p97 heterohexamers comprising both WT and disease-causing mutant subunits, we performed a methyl-transverse relaxation optimized spectroscopy (TROSY) NMR study on a series of constructs in which only one of the protomer types is NMR-labeled. Our results show positive cooperativity of NTD up/down equilibria between neighboring protomers, allowing us to define interprotomer pathways that mediate the allosteric communication between subunits. Notably, the perturbed up/down NTD equilibrium in mutant subunits is partially restored by neighboring WT protomers, as is the two-pronged binding of the UBXD1 adaptor that is affected in disease. This work highlights the plasticity of p97 and how subtle perturbations to its free-energy landscape lead to significant changes in NTD conformation and adaptor binding.

NMR studies of enzymatic rates in vitro and in vivo by magnetization transfer

1984 ◽  
Vol 17 (1) ◽  
pp. 83-124 ◽  
Author(s):  
J. R. Alger ◽  
R. G. Shulman
Keyword(s):  
Creatine Kinase ◽  
Chemical Reactions ◽  
Magnetization Transfer ◽  
Living Systems ◽  
Nmr Studies ◽  
Wide Range ◽  
Potential Applications

Magnetization transfer techniques are specialized NMR experiments which can measure the rate of chemical reactions while concentrations of products and reactants are maintained constant. These techniques are being used to measure the rates of enzyme catalysed reactions in a variety of living systems and in vitro. The magnetization transfer measurements in vivo of the ATP synthetase and the creatine kinase reactions have been particularly useful in describing rates of major energy transducing reactions involving ATP and phosphocreatine. As a result, a wide range of biomedicai scientists are becoming aware of the potentials of these techniques. The purpose of this review is thus threefold: first, to present a concise, conceptual review of the underlying principles for these non-specialists; secondly, to review the important biochemical applications of the method which have appeared, and thirdly, to discuss potential applications and limitations of the method.

scholarly journals Mitochondrial division, fusion and degradation

2019 ◽  
Vol 167 (3) ◽  
pp. 233-241 ◽  
Author(s):  
Daisuke Murata ◽  
Kenta Arai ◽  
Miho Iijima ◽  
Hiromi Sesaki
Keyword(s):  
Super Resolution ◽  
Healthy Population ◽  
Lipid Biochemistry ◽  
Mitochondrial Division ◽  
Cellular Processes ◽  
Size Number ◽  
Wide Range ◽  
Autophagic Degradation ◽  
And Function

Abstract The mitochondrion is an essential organelle for a wide range of cellular processes, including energy production, metabolism, signal transduction and cell death. To execute these functions, mitochondria regulate their size, number, morphology and distribution in cells via mitochondrial division and fusion. In addition, mitochondrial division and fusion control the autophagic degradation of dysfunctional mitochondria to maintain a healthy population. Defects in these dynamic membrane processes are linked to many human diseases that include metabolic syndrome, myopathy and neurodegenerative disorders. In the last several years, our fundamental understanding of mitochondrial fusion, division and degradation has been significantly advanced by high resolution structural analyses, protein-lipid biochemistry, super resolution microscopy and in vivo analyses using animal models. Here, we summarize and discuss this exciting recent progress in the mechanism and function of mitochondrial division and fusion.

scholarly journals Identification of Z nucleotides as an ancient signal for two-component system activation in bacteria

2020 ◽  
Vol 117 (52) ◽  
pp. 33530-33539
Author(s):  
Oscar J. Vázquez-Ciros ◽  
Adrián F. Alvarez ◽  
Dimitris Georgellis
Keyword(s):  
De Novo ◽  
Response Regulator ◽  
Phosphoryl Group ◽  
Response Regulators ◽  
Carbamoyl Phosphate ◽  
Cellular Processes ◽  
Wide Range ◽  
Two Component ◽  
Two Component Systems

Two-component systems (TCSs) in bacteria are molecular circuits that allow the perception of and response to diverse stimuli. These signaling circuits rely on phosphoryl-group transfers between transmitter and receiver domains of sensor kinase and response regulator proteins, and regulate several cellular processes in response to internal or external cues. Phosphorylation, and thereby activation, of response regulators has been demonstrated to occur by their cognate histidine kinases but also by low molecular weight phosphodonors such as acetyl phosphate and carbamoyl phosphate. Here, we present data indicating that the intermediates of the de novo syntheses of purines and histidine, 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5′-monophosphate (ZMP) and/or 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5′-triphosphate (ZTP), activate the response regulator UvrY, by promoting its autophosphorylation at the conserved aspartate at position 54. Moreover, these Z nucleotides are shown to also activate the nonrelated response regulators ArcA, CpxR, RcsB, and PhoQ. We propose that ZMP and/or ZTP act as alarmones for a wide range of response regulators in vivo, providing a novel mechanism by which they could impact gene expression in response to metabolic cues.

scholarly journals A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks

2020 ◽  
Author(s):  
Elva-María Novoa-del-Toro ◽  
Efrén Mezura-Montes ◽  
Matthieu Vignes ◽  
Frédérique Magdinier ◽  
Laurent Tichit ◽  
...  
Keyword(s):  
Genetic Algorithm ◽  
Biological Networks ◽  
Biological Network ◽  
Expression Data ◽  
Rna Seq ◽  
Multi Objective ◽  
Multiplex Networks ◽  
Cellular Processes ◽  
Functional Relationships ◽  
Multi Objective Genetic Algorithm

AbstractThe identification of subnetworks of interest - or active modules - by integrating biological networks with molecular profiles is a key resource to inform on the processes perturbed in different cellular conditions. We here propose MOGAMUN, a Multi-Objective Genetic Algorithm to identify active modules in multiplex biological networks. MOGAMUN optimizes both the density of interactions and the scores of the nodes (e.g., their differential expression).We compare MOGAMUN with state-of-the-art methods, representative of different algorithms dedicated to the identification of active modules in single networks. MOGAMUN identifies dense and high-scoring modules that are also easier to interpret. In addition, to our knowledge, MOGAMUN is the first method able to use multiplex networks. Multiplex networks are composed of different layers of physical and functional relationships between genes and proteins. Each layer is associated to its own meaning, topology, and biases; the multiplex framework allows exploiting this diversity of biological networks.We applied MOGAMUN to identify cellular processes perturbed in Facio-Scapulo-Humeral muscular Dystrophy, by integrating RNA-seq expression data with a multiplex biological network. We identified different active modules of interest, thereby providing new angles for investigating the pathomechanisms of this disease.AvailabilityMOGAMUN is available at https://github.com/elvanov/[email protected], [email protected]

scholarly journals Whole-Plant Measure of Temperature-Induced Changes in the Cytosolic pH of Potato Plants Using Genetically Encoded Fluorescent Sensor Pt-GFP

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1131
Author(s):  
Anna Pecherina ◽  
Marina Grinberg ◽  
Maria Ageyeva ◽  
Tatiana Zdobnova ◽  
Maria Ladeynova ◽  
...  
Keyword(s):  
Fluorescent Sensor ◽  
Signal Transmission ◽  
Ph Sensor ◽  
Threshold Temperature ◽  
Cytosolic Ph ◽  
Cellular Processes ◽  
Wide Range ◽  
Open Ground ◽  
Work Model

Cytosolic pH (pHcyt) regulates a wide range of cellular processes in plants. Changes in pHcyt occurring under the effect of different stressors can participate in signal transmission. The dynamics of pHcyt under the action of external factors, including significant factors for open ground crops such as temperature, remains poorly understood, which is largely due to the difficulty of intracellular pH registration using standard methods. In this work, model plants of potato (one of the essential crops) expressing a fluorescent ratiometric pH sensor Pt-GFP were created. The calibration obtained in vivo allowed for the determination of the pHcyt values of the cells of the leaves, which is 7.03 ± 0.03 pH. Cooling of the whole leaf caused depolarization and rapid acidification of the cytosol, the amplitude of which depended on the cooling strength, amounting to about 0.2 pH units when cooled by 15 °C. When the temperature rises to 35–40 °C, the cytosol was alkalized by 0.2 pH units. Heating above the threshold temperature caused the acidification of cytosol and generation of variation potential. The observed rapid changes in pHcyt can be associated with changes in the activity of H+-ATPases, which was confirmed by inhibitory analysis.

scholarly journals Mapping physiological ADP-ribosylation using Activated Ion Electron Transfer Dissociation (AI-ETD)

2020 ◽  
Author(s):  
Sara C. Buch-Larsen ◽  
Ivo A. Hendriks ◽  
Jean M. Lodge ◽  
Martin Rykær ◽  
Benjamin Furtwängler ◽  
...  
Keyword(s):  
Electron Transfer ◽  
Electron Transfer Dissociation ◽  
Post Translational Modification ◽  
Physiological Regulation ◽  
Physiological Conditions ◽  
Adp Ribosylation ◽  
Cellular Processes ◽  
Wide Range ◽  
Enrichment Strategy

SUMMARYADP-ribosylation (ADPr) is a post-translational modification that plays pivotal roles in a wide range of cellular processes. Mass spectrometry (MS)-based analysis of ADPr under physiological conditions, without relying on genetic or chemical perturbation, has been hindered by technical limitations. Here, we describe the applicability of Activated Ion Electron Transfer Dissociation (AI-ETD) for MS-based proteomics analysis of physiological ADPr using our unbiased Af1521 enrichment strategy. To benchmark AI-ETD, we profiled 9,000 ADPr peptides mapping to >5,000 unique ADPr sites from a limited number of cells exposed to oxidative stress, corresponding to 120% and 28% more ADPr peptides compared to contemporary strategies using ETD and EThcD, respectively. Under physiological conditions AI-ETD identified 450 ADPr sites on low-abundant proteins, including in vivo cysteine auto-modifications on PARP8 and tyrosine auto-modifications on PARP14, hinting at specialist enzymatic functions for these enzymes. Collectively, our data provides new insights into the physiological regulation of ADP-ribosylation.

Molecular and Nanometer-Scale Self-Organized System Generated by Protein Motor Functions

2007 ◽  
Vol 539-543 ◽  
pp. 3290-3296 ◽  
Author(s):  
Kazuhiro Oiwa ◽  
R. Kometani ◽  
Dong Yang Li ◽  
Y. Shitaka ◽  
R. Nakamori ◽  
...  
Keyword(s):  
Complex Adaptive Systems ◽  
Adaptive Systems ◽  
Nanometer Scale ◽  
Major Protein ◽  
Cellular Processes ◽  
Self Organized ◽  
Wide Range ◽  
Protein Motors ◽  
Complex Adaptive ◽  
Protein Motor

Creatures have evolved extremely intelligent and complex adaptive systems for conducting their movements. They are protein motors with typical sizes of a few tens of nanometers. Protein motors include three major protein families, myosin, kinesin and dynein, which participate in a wide range of cellular processes, using energy from the hydrolysis of adenosinetriphosphate ATP. To harness these protein motors to power nanometer-scale devices, we have investigated effective and non-destructive methods for immobilizing protein motors on surfaces and to arrange the output of these motors, e.g. force and movement, to be in a defined direction. We found NEB-22 to be useful for retaining the abilities of protein motors to support the movement of protein filaments. We fabricated various patterns of tracks of NEB-22 on coverslips and protein motors were introduced and immobilized on glass surface. The trajectories of protein polymers were confined to these tracks. Simple patterns readily biased and guide polymer movement confining it to be unidirectional. In addition, having used dynein c purified from Chlamydomonas flagellar axoneme, we showed that microtubules driven by surface-bound dynein were self-organized into dynamic streams through collisions between the microtubules and their subsequent joining.

Evaluation of 99mTc-Label led Vitamin K4 as an Agent for Testicular Imaging

1991 ◽  
Vol 30 (01) ◽  
pp. 35-39 ◽  
Author(s):  
H. S. Durak ◽  
M. Kitapgi ◽  
B. E. Caner ◽  
R. Senekowitsch ◽  
M. T. Ercan
Keyword(s):  
Soft Tissue ◽  
Room Temperature ◽  
Normal Subjects ◽  
Left Testis ◽  
Wide Range ◽  
Activity Ratios ◽  
The Right ◽  
Radioactivity Levels

Vitamin K4 was labelled with 99mTc with an efficiency higher than 97%. The compound was stable up to 24 h at room temperature, and its biodistribution in NMRI mice indicated its in vivo stability. Blood radioactivity levels were high over a wide range. 10% of the injected activity remained in blood after 24 h. Excretion was mostly via kidneys. Only the liver and kidneys concentrated appreciable amounts of radioactivity. Testis/soft tissue ratios were 1.4 and 1.57 at 6 and 24 h, respectively. Testis/blood ratios were lower than 1. In vitro studies with mouse blood indicated that 33.9 ±9.6% of the radioactivity was associated with RBCs; it was washed out almost completely with saline. Protein binding was 28.7 ±6.3% as determined by TCA precipitation. Blood clearance of 99mTc-l<4 in normal subjects showed a slow decrease of radioactivity, reaching a plateau after 16 h at 20% of the injected activity. In scintigraphic images in men the testes could be well visualized. The right/left testis ratio was 1.08 ±0.13. Testis/soft tissue and testis/blood activity ratios were highest at 3 h. These ratios were higher than those obtained with pertechnetate at 20 min post injection.99mTc-l<4 appears to be a promising radiopharmaceutical for the scintigraphic visualization of testes.

Ethnomedicinal uses, Phytochemistry and Pharmacological Aspects of the Genus Berberis Linn: A Comprehensive Review

2020 ◽  
Vol 23 ◽  
Author(s):  
Roohi Mohi-ud-din ◽  
Reyaz Hassan Mir ◽  
Prince Ahad Mir ◽  
Saeema Farooq ◽  
Syed Naiem Raza ◽  
...  
Keyword(s):  
Chemical Constituents ◽  
Pharmacological Activities ◽  
Traditional Use ◽  
Comprehensive Review ◽  
Wide Range ◽  
Anti Cancer ◽  
Comprehensive Survey ◽  
Ethnomedicinal Uses

Background: Genus Berberis (family Berberidaceae), which contains about 650 species and 17 genera worldwide, has been used in folklore and various traditional medicine systems. Berberis Linn. is the most established group among genera with around 450-500 species across the world. This comprehensive review will not only help researchers for further evaluation but also provide substantial information for future exploitation of species to develop novel herbal formulations. Objective: The present review is focussed to summarize and collect the updated review of information of Genus Berberis species reported to date regarding their ethnomedicinal information, chemical constituents, traditional/folklore use, and reported pharmacological activities on more than 40 species of Berberis. Conclusion: A comprehensive survey of the literature reveals that various species of the genus possess various phytoconstituents mainly alkaloids, flavonoid based compounds isolated from different parts of a plant with a wide range of pharmacological activities. So far, many pharmacological activities like anti-cancer, anti-hyperlipidemic, hepatoprotective, immunomodulatory, anti-inflammatory both in vitro & in vivo and clinical study of different extracts/isolated compounds of different species of Berberis have been reported, proving their importance as a medicinal plant and claiming their traditional use.

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