scholarly journals Microbial Biofilms: Structural Plasticity and Emerging Properties

2022 ◽  
Vol 10 (1) ◽  
pp. 138
Author(s):  
Arnaud Bridier ◽  
Romain Briandet
Keyword(s):  
Spatial Organization ◽  
3D Structure ◽  
Three Dimensional ◽  
Original Data ◽  
Natural Environments ◽  
Natural Ecosystems ◽  
Chronic Infections ◽  
Ecological Processes ◽  
Microbial Biofilms ◽  
Technological Advances

Microbial biofilms are found everywhere and can be either beneficial or detrimental, as they are involved in crucial ecological processes and in severe chronic infections. The functional properties of biofilms are closely related to their three-dimensional (3D) structure, and the ability of microorganisms to collectively and dynamically shape the community spatial organization in response to stresses in such biological edifices. A large number of works have shown a relationship between the modulation of the spatial organization and ecological interactions in biofilms in response to environmental fluctuations, as well as their emerging properties essential for nutrient cycling and bioremediation processes in natural environments. On the contrary, numerous studies have emphasized the role of structural rearrangements and matrix production in the increased tolerance of bacteria in biofilms toward antimicrobials. In these last few years, the development of innovative approaches, relying on recent technological advances in imaging, computing capacity, and other analytical tools, has led to the production of original data that have improved our understanding of this close relationship. However, it has also highlighted the need to delve deeper into the study of cell behavior in such complex communities during 3D structure development and maturation— from a single-cell to a multicellular scale— to better control or harness positive and negative impacts of biofilms. For this Special Issue, the interplay between biofilm emerging properties and their 3D spatial organization considering different models, from single bacteria to complex environmental communities, and various environments, from natural ecosystems to industrial and medical settings are addressed.

scholarly journals COMPARISON OF COMMERCIAL STRUCTURE-FROM-MOTION PHOTOGRAMMETY SOFTWARE USED FOR UNDERWATER THREE-DIMENSIONAL MODELING OF CORAL REEF ENVIRONMENTS

2017 ◽  
Vol XLII-2/W3 ◽  
pp. 127-131 ◽  
Author(s):  
J. H. R. Burns ◽  
D. Delparte
Keyword(s):  
Coral Reef ◽  
Structural Characteristics ◽  
Spatial Scales ◽  
3D Structure ◽  
Light Availability ◽  
Three Dimensional ◽  
Structural Complexity ◽  
Physical Structure ◽  
Natural Environments ◽  
Ecological Processes

Structural complexity in ecosystems creates an assortment of microhabitat types and has been shown to support greater diversity and abundance of associated organisms. The 3D structure of an environment also directly affects important ecological parameters such as habitat provisioning and light availability and can therefore strongly influence ecosystem function. Coral reefs are architecturally complex 3D habitats, whose structure is intrinsically linked to the ecosystem biodiversity, productivity, and function. The field of coral ecology has, however, been primarily limited to using 2-dimensional (2D) planar survey techniques for studying the physical structure of reefs. This conventional approach fails to capture or quantify the intricate structural complexity of corals that influences habitat facilitation and biodiversity. A 3-dimensional (3D) approach can obtain accurate measurements of architectural complexity, topography, rugosity, volume, and other structural characteristics that affect biodiversity and abundance of reef organisms. Structurefrom- Motion (SfM) photogrammetry is an emerging computer vision technology that provides a simple and cost-effective method for 3D reconstruction of natural environments. SfM has been used in several studies to investigate the relationship between habitat complexity and ecological processes in coral reef ecosystems. This study compared two commercial SfM software packages, Agisoft Photoscan Pro and Pix4Dmapper Pro 3.1, in order to assess the cpaability and spatial accuracy of these programs for conducting 3D modeling of coral reef habitats at three spatial scales.

scholarly journals Spatial organization of the transcriptional regulatory network of Saccharomyces cerevisiae

2019 ◽  
Author(s):  
Dong-Qing Sun ◽  
Liu Tian ◽  
Bin-Guang Ma
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Regulatory Network ◽  
Spatial Organization ◽  
Target Genes ◽  
Transcriptional Regulatory Network ◽  
3D Structure ◽  
Three Dimensional ◽  
3D Genome ◽  
Transcriptional Regulatory ◽  
Four Levels

AbstractTranscriptional regulatory network (TRN) is a directed complex network composed of all regulatory interactions between transcription factors and corresponding target genes. Recently, the three-dimensional (3D) genomics studies have shown that the 3D structure of the genome makes a difference to the regulation of gene transcription, which provides us with a novel perspective. In this study, we constructed the TRN of the budding yeast Saccharomyces cerevisiae and placed it in the context of 3D genome model. We analyzed the spatial organization of the yeast TRN on four levels: global feature, central nodes, hierarchical structure and network motifs. Our results suggested that the TRN of S. cerevisiae presents an optimized structure in space to adapt to functional requirement.

scholarly journals Integration of Multiple Resolution Data in 3D Chromatin Reconstruction Using ChromStruct

Biology ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 338
Author(s):  
Claudia Caudai ◽  
Monica Zoppè ◽  
Anna Tonazzini ◽  
Ivan Merelli ◽  
Emanuele Salerno
Keyword(s):  
Spatial Organization ◽  
Local Level ◽  
3D Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Rna Seq ◽  
Chromosome Conformation ◽  
Experimental Protocols ◽  
Easy Integration

The three-dimensional structure of chromatin in the cellular nucleus carries important information that is connected to physiological and pathological correlates and dysfunctional cell behaviour. As direct observation is not feasible at present, on one side, several experimental techniques have been developed to provide information on the spatial organization of the DNA in the cell; on the other side, several computational methods have been developed to elaborate experimental data and infer 3D chromatin conformations. The most relevant experimental methods are Chromosome Conformation Capture and its derivatives, chromatin immunoprecipitation and sequencing techniques (CHIP-seq), RNA-seq, fluorescence in situ hybridization (FISH) and other genetic and biochemical techniques. All of them provide important and complementary information that relate to the three-dimensional organization of chromatin. However, these techniques employ very different experimental protocols and provide information that is not easily integrated, due to different contexts and different resolutions. Here, we present an open-source tool, which is an expansion of the previously reported code ChromStruct, for inferring the 3D structure of chromatin that, by exploiting a multilevel approach, allows an easy integration of information derived from different experimental protocols and referred to different resolution levels of the structure, from a few kilobases up to Megabases. Our results show that the introduction of chromatin modelling features related to CTCF CHIA-PET data, histone modification CHIP-seq, and RNA-seq data produce appreciable improvements in ChromStruct’s 3D reconstructions, compared to the use of HI-C data alone, at a local level and at a very high resolution.

scholarly journals Needs and Gaps in Optical Underwater Technologies and Methods for the Investigation of Marine Animal Forest 3D-Structural Complexity

2021 ◽  
Vol 8 ◽  
Author(s):  
Paolo Rossi ◽  
Massimo Ponti ◽  
Sara Righi ◽  
Cristina Castagnetti ◽  
Roberto Simonini ◽  
...  
Keyword(s):  
Benthic Communities ◽  
Three Dimensional ◽  
Structural Complexity ◽  
Marine Animal ◽  
Growth Data ◽  
Ecological Processes ◽  
Spatial And Temporal Scales ◽  
Technological Advances ◽  
Data Collection And Analysis ◽  
Data Acquisition And Processing

Marine animal forests are benthic communities dominated by sessile suspension feeders (such as sponges, corals, and bivalves) able to generate three-dimensional (3D) frameworks with high structural complexity. The biodiversity and functioning of marine animal forests are strictly related to their 3D complexity. The present paper aims at providing new perspectives in underwater optical surveys. Starting from the current gaps in data collection and analysis that critically limit the study and conservation of marine animal forests, we discuss the main technological and methodological needs for the investigation of their 3D structural complexity at different spatial and temporal scales. Despite recent technological advances, it seems that several issues in data acquisition and processing need to be solved, to properly map the different benthic habitats in which marine animal forests are present, their health status and to measure structural complexity. Proper precision and accuracy should be chosen and assured in relation to the biological and ecological processes investigated. Besides, standardized methods and protocols are strictly necessary to meet the FAIR (findability, accessibility, interoperability, and reusability) data principles for the stewardship of habitat mapping and biodiversity, biomass, and growth data.

3D flow measurements in regular breaking waves past a fixed submerged bar on an impermeable plane slope

2016 ◽  
Vol 802 ◽  
pp. 490-527 ◽  
Author(s):  
M. Clavero ◽  
S. Longo ◽  
L. Chiapponi ◽  
M. A. Losada
Keyword(s):  
Flow Field ◽  
3D Structure ◽  
Three Dimensional ◽  
Breaking Waves ◽  
Wave Crest ◽  
Natural Environments ◽  
Incoming Wave ◽  
Data Set ◽  
Flow Measurements ◽  
Wave Trough

The velocity fields induced by regular breaking waves past a fixed bar on a 1 : 10 rigid plane slope were measured and analysed using a volumetric particle-tracking velocimetry system. Under specific conditions, the interaction between waves and morphological features steepens the waves, which eventually break. The geometry of the boundaries of the present experiments is common in natural environments, where reefs, sand and gravel bars, and submerged coastal structures, interact with the incoming wave field, ‘affecting’ the transport budget of substances (sediment, nutrients and pollutants), with relevant consequences on the water quality. The aims of the present work are the analysis of the flow field in the breaker, and the quantification of the terms in the equations usually adopted for modelling the flow and the turbulence. Two sets of attacking monochromatic wave trains with different periods and heights were used to generate a data set of instantaneous velocity, which was further analysed to extract turbulence. The measurement volume extended from the wave crest to a portion of the domain below the wave trough. The balance of linear momentum for the average field and the balance of turbulence were scrutinized, and included all the terms in a three-dimensional (3D) approach. The analysed data and results are original and novel because they include all the contributions derived from the 3D structure of a real flow field, and constitute a huge data set for the calibration of numerical codes.

scholarly journals Assessing stationary distributions derived from chromatin contact maps

2019 ◽  
Author(s):  
Mark Segal ◽  
Kipper Fletez-Brant
Keyword(s):  
Spatial Organization ◽  
Accuracy Assessment ◽  
3D Structure ◽  
Three Dimensional ◽  
Accuracy Evaluation ◽  
Reconstruction Algorithms ◽  
Reconstruction Accuracy ◽  
Stationary Distributions ◽  
K Nearest Neighbors ◽  
3D Genome

Abstract Background Three dimensional (3D) genome spatial organization is critical for numerous cellular functions, including transcription. Genome architecture had been difficult to elucidate but the suite of chromatin conformation capture assays, notably Hi-C transformed understanding of chromatin organization, yielding numerous insights, many deriving from 3D reconstructions. In part, these benefits derive from the ability to superpose genomic features on the reconstruction. However, the advantages of 3D structure-based analyses are clearly conditional on the accuracy of the corresponding reconstruction, which is difficult to assess due to an absence of gold standards. Proponents of competing reconstruction algorithms have evaluated their accuracy by recourse to simulation of toy structures and limited FISH imaging that features a handful of low resolution probes. While newly advanced multiplexed FISH imaging offers possibilities for refined 3D reconstruction accuracy evaluation, availability of such data remains limited due to assay complexity and the resolution thereof is appreciably lower than the reconstructions being assessed. Accordingly, there is demand for new methods of reconstruction accuracy appraisal. Results Here we explore the potential of recently proposed stationary distributions, StatDns, derived from Hi-C contact matrices, to serve as a basis for reconstruction accuracy assessment. Current usage of such StatDns has focussed on the identification of highly interactive regions (HIRs): computationally defined regions of the genome purportedly involved in numerous long-range intra-chromosomal contacts. Consistent identification of HIRs would be informative with respect to inferred 3D architecture since the corresponding regions of the reconstruction would have an elevated number of k nearest neighbors ( k NNs). More generally, we anticipate a monotone decreasing relationship between StatDn values and k NN distances. After initially evaluating the reproducibility of StatDns across replicate Hi-C data sets, we use this implied StatDn - k NN relationship to gauge the utility of StatDns for reconstruction validation, making recourse to both real and simulated examples. Conclusions Our analyses demonstrate that, as constructed, StatDns do not provide a suitable measure for assessing the accuracy of 3D genome reconstructions. Whether this is attributable to specific choices surrounding normalization in defining StatDns or to the logic underlying their very formulation remains to be determined.

scholarly journals The 3D Genome: From Structure to Function

2021 ◽  
Vol 22 (21) ◽  
pp. 11585
Author(s):  
Tapan Kumar Mohanta ◽  
Awdhesh Kumar Mishra ◽  
Ahmed Al-Harrasi
Keyword(s):  
Spatial Organization ◽  
Rapid Development ◽  
3D Structure ◽  
Three Dimensional ◽  
Genome Chromosome ◽  
3D Genome ◽  
Topologically Associated Domains ◽  
Functional Part ◽  
A Cell ◽  
Microscopy Techniques

The genome is the most functional part of a cell, and genomic contents are organized in a compact three-dimensional (3D) structure. The genome contains millions of nucleotide bases organized in its proper frame. Rapid development in genome sequencing and advanced microscopy techniques have enabled us to understand the 3D spatial organization of the genome. Chromosome capture methods using a ligation approach and the visualization tool of a 3D genome browser have facilitated detailed exploration of the genome. Topologically associated domains (TADs), lamin-associated domains, CCCTC-binding factor domains, cohesin, and chromatin structures are the prominent identified components that encode the 3D structure of the genome. Although TADs are the major contributors to 3D genome organization, they are absent in Arabidopsis. However, a few research groups have reported the presence of TAD-like structures in the plant kingdom.

scholarly journals Chromatin Organization and Radio Resistance in the Bacterium Gemmata obscuriglobus

2008 ◽  
Vol 191 (5) ◽  
pp. 1439-1445 ◽  
Author(s):  
Arnon Lieber ◽  
Andrew Leis ◽  
Ariel Kushmaro ◽  
Abraham Minsky ◽  
Ohad Medalia
Keyword(s):  
Spatial Organization ◽  
Genetic Material ◽  
Three Dimensional ◽  
Chromatin Organization ◽  
End Joining ◽  
Technological Advances ◽  
Gemmata Obscuriglobus ◽  
Membrane Bound ◽  
High Doses ◽  
Nucleoid Structure

ABSTRACT The organization of chromatin has a major impact on cellular activities, such as gene expression. For bacteria, it was suggested that the spatial organization of the genetic material correlates with transcriptional levels, implying a specific architecture of the chromosome within the cytoplasm. Accordingly, recent technological advances have emphasized the organization of the genetic material within nucleoid structures. Gemmata obscuriglobus, a member of the phylum Planctomycetes, exhibits a distinctive nucleoid structure in which chromatin is encapsulated within a discrete membrane-bound compartment. Here, we show that this soil and freshwater bacterium tolerates high doses of UV and ionizing radiation. Cryoelectron tomography of frozen hydrated sections and electron microscopy of freeze-substituted cells have indicated a more highly ordered condensed-chromatin organization in actively dividing and stationary-phase G. obscuriglobus cells. These three-dimensional analyses revealed a complex network of double membranes that engulf the condensed DNA. Bioinformatics analysis has revealed the existence of a putative component involved in nonhomologous DNA end joining that presumably plays a role in maintaining chromatin integrity within the bacterium. Thus, our observations further support the notion that packed chromatin organization enhances radiation tolerance.

Methods for three-dimensional reconstruction of cellular components within a thick section

1986 ◽  
Vol 44 ◽  
pp. 18-21
Author(s):  
J. Frank ◽  
B. F. McEwen ◽  
M. Radermacher ◽  
C. L. Rieder
Keyword(s):  
Tilt Angle ◽  
Tomographic Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Thick Section ◽  
Three Dimensional Reconstruction ◽  
Axis Ratio ◽  
Dimensional Reconstruction ◽  
Cellular Components

The tomographic reconstruction from multiple projections of cellular components, within a thick section, offers a way of visualizing and quantifying their three-dimensional (3D) structure. However, asymmetric objects require as many views from the widest tilt range as possible; otherwise the reconstruction may be uninterpretable. Even if not for geometric obstructions, the increasing pathway of electrons, as the tilt angle is increased, poses the ultimate upper limitation to the projection range. With the maximum tilt angle being fixed, the only way to improve the faithfulness of the reconstruction is by changing the mode of the tilting from single-axis to conical; a point within the object projected with a tilt angle of 60° and a full 360° azimuthal range is then reconstructed as a slightly elliptic (axis ratio 1.2 : 1) sphere.

Cryomicroscopy of crotoxin complex crystals at 400 KV

1989 ◽  
Vol 47 ◽  
pp. 826-827
Author(s):  
Jaap Brink ◽  
Wah Chiu
Keyword(s):  
Signal To Noise Ratio ◽  
3D Structure ◽  
Three Dimensional ◽  
Carbon Films ◽  
Depth Of Field ◽  
Basic Subunit ◽  
Ewald Sphere ◽  
Diffraction Patterns ◽  
Complex Crystals ◽  
Acidic Subunit

The crotoxin complex is a potent neurotoxin composed of a basic subunit (Mr = 12,000) and an acidic subunit (M = 10,000). The basic subunit possesses phospholipase activity whereas the acidic subunit shows no enzymatic activity at all. The complex's toxocity is expressed both pre- and post-synaptically. The crotoxin complex forms thin crystals suitable for electron crystallography. The crystals diffract up to 0.16 nm in the microscope, whereas images show reflections out to 0.39 nm2. Ultimate goal in this study is to obtain a three-dimensional (3D-) structure map of the protein around 0.3 nm resolution. Use of 100 keV electrons in this is limited; the unit cell's height c of 25.6 nm causes problems associated with multiple scattering, radiation damage, limited depth of field and a more pronounced Ewald sphere curvature. In general, they lead to projections of the unit cell, which at the desired resolution, cannot be interpreted following the weak-phase approximation. Circumventing this problem is possible through the use of 400 keV electrons. Although the overall contrast is lowered due to a smaller scattering cross-section, the signal-to-noise ratio of especially higher order reflections will improve due to a smaller contribution of inelastic scattering. We report here our preliminary results demonstrating the feasability of the data collection procedure at 400 kV.Crystals of crotoxin complex were prepared on carbon-covered holey-carbon films, quench frozen in liquid ethane, inserted into a Gatan 626 holder, transferred into a JEOL 4000EX electron microscope equipped with a pair of anticontaminators operating at −184°C and examined under low-dose conditions. Selected area electron diffraction patterns (EDP's) and images of the crystals were recorded at 400 kV and −167°C with dose levels of 5 and 9.5 electrons/Å, respectively.

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