scholarly journals A structure–function based approach to floc hierarchy and evidence for the non-fractal nature of natural sediment flocs

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kate L. Spencer ◽  
Jonathan A. T. Wheatland ◽  
Andrew J. Bushby ◽  
Simon J. Carr ◽  
Ian G. Droppo ◽  
...  
Keyword(s):  
Fractal Theory ◽  
3D Structure ◽  
Three Dimensions ◽  
Predictive Capacity ◽  
Natural Sediment ◽  
Floc Size ◽  
Emergent Systems ◽  
Floc Size Distributions ◽  
And Function ◽  
Sediment Carbon

AbstractNatural sediment flocs are fragile, highly irregular, loosely bound aggregates comprising minerogenic and organic material. They contribute a major component of suspended sediment load and are critical for the fate and flux of sediment, carbon and pollutants in aquatic environments. Understanding their behaviour is essential to the sustainable management of waterways, fisheries and marine industries. For several decades, modelling approaches have utilised fractal mathematics and observations of two dimensional (2D) floc size distributions to infer levels of aggregation and predict their behaviour. Whilst this is a computationally simple solution, it is highly unlikely to reflect the complexity of natural sediment flocs and current models predicting fine sediment hydrodynamics are not efficient. Here, we show how new observations of fragile floc structures in three dimensions (3D) demonstrate unequivocally that natural flocs are non-fractal. We propose that floc hierarchy is based on observations of 3D structure and function rather than 2D size distribution. In contrast to fractal theory, our data indicate that flocs possess characteristics of emergent systems including non-linearity and scale-dependent feedbacks. These concepts and new data to quantify floc structures offer the opportunity to explore new emergence-based floc frameworks which better represent natural floc behaviour and could advance our predictive capacity.

Modelling the activated sludge flocculation process combining laser light diffraction particle sizing and population balance modelling (PBM)

2002 ◽  
Vol 45 (6) ◽  
pp. 41-49 ◽  
Author(s):  
I. Nopens ◽  
C.A. Biggs ◽  
B. De Clercq ◽  
R. Govoreanu ◽  
B.-M. Wilén ◽  
...  
Keyword(s):  
Experimental Data ◽  
Laser Light ◽  
Population Balance ◽  
Light Diffraction ◽  
Balance Model ◽  
Floc Size ◽  
Shear Rates ◽  
Breakage Rate ◽  
On Line ◽  
Floc Size Distributions

A technique based on laser light diffraction is shown to be successful in collecting on-line experimental data. Time series of floc size distributions (FSD) under different shear rates (G) and calcium additions were collected. The steady state mass mean diameter decreased with increasing shear rate G and increased when calcium additions exceeded 8 mg/l. A so-called population balance model (PBM) was used to describe the experimental data. This kind of model describes both aggregation and breakage through birth and death terms. A discretised PBM was used since analytical solutions of the integro-partial differential equations are non-existing. Despite the complexity of the model, only 2 parameters need to be estimated: the aggregation rate and the breakage rate. The model seems, however, to lack flexibility. Also, the description of the floc size distribution (FSD) in time is not accurate.

scholarly journals Consistent global structures of complex RNA states through multidimensional chemical mapping

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Clarence Yu Cheng ◽  
Fang-Chieh Chou ◽  
Wipapat Kladwang ◽  
Siqi Tian ◽  
Pablo Cordero ◽  
...  
Keyword(s):  
Secondary Structure ◽  
3D Structure ◽  
Three Dimensions ◽  
Biological Processes ◽  
Chemical Mapping ◽  
Entry Site ◽  
Tertiary Structures ◽  
Internal Ribosome Entry ◽  
Non Coding Rna ◽  
Paired End Sequencing

Accelerating discoveries of non-coding RNA (ncRNA) in myriad biological processes pose major challenges to structural and functional analysis. Despite progress in secondary structure modeling, high-throughput methods have generally failed to determine ncRNA tertiary structures, even at the 1-nm resolution that enables visualization of how helices and functional motifs are positioned in three dimensions. We report that integrating a new method called MOHCA-seq (Multiplexed •OH Cleavage Analysis with paired-end sequencing) with mutate-and-map secondary structure inference guides Rosetta 3D modeling to consistent 1-nm accuracy for intricately folded ncRNAs with lengths up to 188 nucleotides, including a blind RNA-puzzle challenge, the lariat-capping ribozyme. This multidimensional chemical mapping (MCM) pipeline resolves unexpected tertiary proximities for cyclic-di-GMP, glycine, and adenosylcobalamin riboswitch aptamers without their ligands and a loose structure for the recently discovered human HoxA9D internal ribosome entry site regulon. MCM offers a sequencing-based route to uncovering ncRNA 3D structure, applicable to functionally important but potentially heterogeneous states.

scholarly journals Cytolethal Distending Toxin Subunit B: A Review of Structure–Function Relationship

Toxins ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 595 ◽  
Author(s):  
Benoît J. Pons ◽  
Julien Vignard ◽  
Gladys Mirey
Keyword(s):  
Pathogenic Bacteria ◽  
Molecular Mechanisms ◽  
3D Structure ◽  
Cytolethal Distending Toxin ◽  
Experimental Systems ◽  
Bacterial Virulence Factor ◽  
Function Relationship ◽  
And Function ◽  
Key Residues ◽  
Cell Cycle Block

The Cytolethal Distending Toxin (CDT) is a bacterial virulence factor produced by several Gram-negative pathogenic bacteria. These bacteria, found in distinct niches, cause diverse infectious diseases and produce CDTs differing in sequence and structure. CDTs have been involved in the pathogenicity of the associated bacteria by promoting persistent infection. At the host-cell level, CDTs cause cell distension, cell cycle block and DNA damage, eventually leading to cell death. All these effects are attributable to the catalytic CdtB subunit, but its exact mode of action is only beginning to be unraveled. Sequence and 3D structure analyses revealed similarities with better characterized proteins, such as nucleases or phosphatases, and it has been hypothesized that CdtB exerts a biochemical activity close to those enzymes. Here, we review the relationships that have been established between CdtB structure and function, particularly by mutation experiments on predicted key residues in different experimental systems. We discuss the relevance of these approaches and underline the importance of further study in the molecular mechanisms of CDT toxicity, particularly in the context of different pathological conditions.

scholarly journals Effect of Weightlessness on the 3D Structure Formation and Physiologic Function of Human Cancer Cells

2019 ◽  
Vol 2019 ◽  
pp. 1-17 ◽  
Author(s):  
Zheng-Yang Chen ◽  
Song Guo ◽  
Bin-Bin Li ◽  
Nan Jiang ◽  
Ao Li ◽  
...  
Keyword(s):  
Cancer Cells ◽  
Human Cancer ◽  
Space Exploration ◽  
Rapid Development ◽  
3D Structure ◽  
Cell Aggregation ◽  
Migration Ability ◽  
Human Cancer Cells ◽  
Cell Cycle Inhibition ◽  
And Function

With the rapid development of modern medical technology and the deterioration of living environments, cancer, the most important disease that threatens human health, has attracted increasing concerns. Although remarkable achievements have been made in tumor research during the past several decades, a series of problems such as tumor metastasis and drug resistance still need to be solved. Recently, relevant physiological changes during space exploration have attracted much attention. Thus, space exploration might provide some inspiration for cancer research. Using on ground different methods in order to simulate microgravity, structure and function of cancer cells undergo many unique changes, such as cell aggregation to form 3D spheroids, cell-cycle inhibition, and changes in migration ability and apoptosis. Although numerous better experiments have been conducted on this subject, the results are not consistent. The reason might be that different methods for simulation have been used, including clinostats, random positioning machine (RPM) and rotating wall vessel (RWV) and so on. Therefore, we review the relevant research and try to explain novel mechanisms underlying tumor cell changes under weightlessness.

Polymorphism of follicle stimulating hormone receptor influences the 3D structure and its binding pattern to FSH in Bos taurus

2017 ◽  
Author(s):  
Hamny Hamny ◽  
Muhammad Jalaluddin ◽  
Siti Aisyah ◽  
Sri Wahyuni ◽  
Widodo . ◽  
...  
Keyword(s):  
Bos Taurus ◽  
Follicle Stimulating Hormone ◽  
3D Structure ◽  
Amino Acid Residues ◽  
Fshr Gene ◽  
Intracellular Process ◽  
Cattle Reproduction ◽  
And Function ◽  
Alignment Analysis ◽  
Stimulating Hormone

Follicle stimulating hormone (FSH) bond with the extracellular domain of the FSH receptor (FSHR) stimulates a cascade of the intracellular process that leads to folliculogenesis. This study aimed to elucidate the effects of FSHR polymorphism of its structure and function on Bos taurus through computational technology. The FSHR sequences were retrieved from Genebank. The polymorphism was identified using alignment analysis and the 3D structure of the FSHR was done by Swiss models. Results showed that FSHR of Bos taurus has three polymorphisms that located at amino acid residues 18th to 259th. The polymorphisms may alter its ability to bind with FSH. Molecular docking analysis indicated that all variant of FSHR potentially changes the pattern and affinity binding into FSH that may have an impact on reproduction status of Bos taurus. The study is a warrant for further investigation to explore biomarker of cattle reproduction status based on FSHR gene.

scholarly journals Deciphering the 3D Structure and Function of Phosphofructokinase from Fission Yeast

2014 ◽  
Vol 20 (S3) ◽  
pp. 1246-1247
Author(s):  
Shaun Benjamin ◽  
Michael Radermacher ◽  
Teresa Ruiz
Keyword(s):  
Fission Yeast ◽  
3D Structure ◽  
Structure And Function ◽  
And Function

scholarly journals Matching of PDB chain sequences to information in public databases as a prerequisite for 3D functional site visualization

2004 ◽  
Vol 1 (1) ◽  
pp. 80-89
Author(s):  
Guido Dieterich ◽  
Dirk W. Heinz ◽  
Joachim Reichelt
Keyword(s):  
Genetic Disorders ◽  
Protein Structures ◽  
3D Structure ◽  
Data Bank ◽  
Mendelian Inheritance ◽  
Biological Information ◽  
Structure Comparison ◽  
3D Structures ◽  
Functional Sites ◽  
And Function

Abstract The 3D structures of biomacromolecules stored in the Protein Data Bank [1] were correlated with different external, biological information from public databases. We have matched the feature table of SWISS-PROT [2] entries as well InterPro [3] domains and function sites with the corresponding 3D-structures. OMIM [4] (Online Mendelian Inheritance in Man) records, containing information of genetic disorders, were extracted and linked to the structures. The exhaustive all-against-all 3D structure comparison of protein structures stored in DALI [5] was condensed into single files for each PDB entry. Results are stored in XML format facilitating its incorporation into related software. The resulting annotation of the protein structures allows functional sites to be identified upon visualization.

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