Three-dimensional stromatolites from Maastrichtian–Danian Yacoraite Formation, Argentina: modelling and assessing hydrodynamic controls on growth patterns

2021 ◽  
pp. 1-17
Author(s):  
Patricio Guillermo Villafañe ◽  
Carlos Cónsole-Gonella ◽  
Paolo Citton ◽  
Ignacio Díaz-Martínez ◽  
Silvina de Valais
Keyword(s):  
Environmental Factors ◽  
Methodological Approach ◽  
Three Dimensional ◽  
Growth Patterns ◽  
External Morphology ◽  
Water Dynamics ◽  
Microbial Composition ◽  
Depositional Processes ◽  
Run Off ◽  
Internal Arrangement

Abstract Stromatolites are biogenic sedimentary structures formed by the interplay of biological (microbial composition) and environmental factors (local hydrodynamic conditions, clastic input and/or water chemistry). Well-preserved, three-dimensional (3D) fossil stromatolites are key to assessing the environmental factors controlling their growth and resulting morphology in space and time. Here, we report the detailed analysis of well-exposed, highly informative stromatolite build-ups from a single stratigraphic horizon within the Maastrichtian–Danian Yacoraite Formation (Argentina). This study focuses on the analysis of depositional processes driving intertidal to shallow subtidal stromatolites. Overall depositional architecture, external morphology and internal arrangement (mega, macro, meso and microstructures) of stromatolite build-ups were analysed and combined with 3D photogrammetric models, allowing us to decipher the links between stromatolite structure and tidal dynamics. Results suggest that external morphology and architecture of elongated and parallel clusters grew under the influence of run-off channels. The internal morphology exhibits columnar structures where the space between columns is interpreted as recharge or discharge channels. This work supports the theory that stromatolites can be used as a high-resolution tool in the assessment of water dynamics, and provides a new methodological approach and data for the dynamic reconstruction of intertidal stromatolite systems through the geological record.

scholarly journals Detecting the Mechanism behind the Transition from Fixed Two-Dimensional Patterned Sika Deer (Cervus nippon) Dermal Papilla Cells to Three-Dimensional Pattern

2021 ◽  
Vol 22 (9) ◽  
pp. 4715
Author(s):  
Guanning Wei ◽  
Hongmei Sun ◽  
Haijun Wei ◽  
Tao Qin ◽  
Yifeng Yang ◽  
...  
Keyword(s):  
Culture Condition ◽  
Sika Deer ◽  
Three Dimensional ◽  
Cervus Nippon ◽  
Dermal Papilla ◽  
Growth Patterns ◽  
The Self ◽  
Dermal Papilla Cells ◽  
Aggregative Behavior ◽  
Cell Pattern

The hair follicle dermal papilla is critical for hair generation and de novo regeneration. When cultured in vitro, dermal papilla cells from different species demonstrate two distinguishable growth patterns under the conventional culture condition: a self-aggregative three dimensional spheroidal (3D) cell pattern and a two dimensional (2D) monolayer cell pattern, correlating with different hair inducing properties. Whether the loss of self-aggregative behavior relates to species-specific differences or the improper culture condition remains unclear. Can the fixed 2D patterned dermal papilla cells recover the self-aggregative behavior and 3D pattern also remains undetected. Here, we successfully constructed the two growth patterns using sika deer (Cervus nippon) dermal papilla cells and proved it was the culture condition that determined the dermal papilla growth pattern. The two growth patterns could transit mutually as the culture condition was exchanged. The fixed 2D patterned sika deer dermal papilla cells could recover the self-aggregative behavior and transit back to 3D pattern, accompanied by the restoration of hair inducing capability when the culture condition was changed. In addition, the global gene expressions during the transition from 2D pattern to 3D pattern were compared to detect the potential regulating genes and pathways involved in the recovery of 3D pattern and hair inducing capability.

scholarly journals Australia IBD Microbiome (AIM) Study: protocol for a multicentre longitudinal prospective cohort study

BMJ Open ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. e042493
Author(s):  
Astrid-Jane Williams ◽  
Ramesh Paramsothy ◽  
Nan Wu ◽  
Simon Ghaly ◽  
Steven Leach ◽  
...  
Keyword(s):  
Cohort Study ◽  
Environmental Factors ◽  
Prospective Cohort Study ◽  
Clinical Data ◽  
Prospective Cohort ◽  
Response To Therapy ◽  
Psychological State ◽  
Local Health ◽  
Microbial Composition ◽  
Patient Reported

IntroductionCrohn’s disease and ulcerative colitis are common chronic idiopathic inflammatory bowel diseases (IBD), which cause considerable morbidity. Although the precise mechanisms of disease remain unclear, evidence implicates a strong multidirectional interplay between diet, environmental factors, genetic determinants/immune perturbations and the gut microbiota. IBD can be brought into remission using a number of medications, which act by suppressing the immune response. However, none of the available medications address any of the underlying potential mechanisms. As we understand more about how the microbiota drives inflammation, much interest has focused on identifying microbial signals/triggers in the search for effective therapeutic targets. We describe the establishment of the Australian IBD Microbiota (AIM) Study, Australia’s first longitudinal IBD bioresource, which will identify and correlate longitudinal microbial and metagenomics signals to disease activity as evaluated by validated clinical instruments, patient-reported surveys, as well as biomarkers. The AIM Study will also gather extensive demographic, clinical, lifestyle and dietary data known to influence microbial composition in order to generate a more complete understanding of the interplay between patients with IBD and their microbiota.MethodsThe AIM Study is an Australian multicentre longitudinal prospective cohort study, which will enrol 1000 participants; 500 patients with IBD and 500 healthy controls over a 5-year period. Assessment occurs at 3 monthly intervals over a 24-month period. At each assessment oral and faecal samples are self-collected along with patient-reported outcome measures, with clinical data also collected at baseline, 12 and 24 months. Intestinal tissue will be sampled whenever a colonoscopy is performed. Dietary intake, general health and psychological state will be assessed using validated self-report questionnaires. Samples will undergo metagenomic, transcriptomic, proteomic, metabolomic and culturomic analyses. Omics data will be integrated with clinical data to identify predictive biomarkers of response to therapy, disease behaviour and environmental factors in patients with IBD.Ethics and disseminationEthical approval for this study has been obtained from the South Eastern Sydney Local Health District Research Ethics Committee (HREC 2019/ETH11443). Findings will be reported at national and international gastroenterology meetings and published in peer-reviewed journals.Trial registration numberACTRN12619000911190.

scholarly journals Validation of a three-dimensional model about sleep: Habits, personal factors and environmental factors

Sleep Science ◽  
2014 ◽  
Vol 7 (4) ◽  
pp. 197-202 ◽  
Author(s):  
Teresa Rebelo-Pinto ◽  
Joana Carneiro Pinto ◽  
Helena Rebelo-Pinto ◽  
Teresa Paiva
Keyword(s):  
Environmental Factors ◽  
Three Dimensional ◽  
Personal Factors ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Sleep Habits

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Epithelial Cell Chirality Revealed by Three-Dimensional Spontaneous Rotation

2018 ◽  
Vol 115 (48) ◽  
pp. 12188-12193 ◽  
Author(s):  
Amanda S. Chin ◽  
Kathryn E. Worley ◽  
Poulomi Ray ◽  
Gurleen Kaur ◽  
Jie Fan ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Cell Polarity ◽  
Three Dimensional ◽  
Intrinsic Property ◽  
Cell Aggregates ◽  
Mechanistic Studies ◽  
Directional Bias ◽  
Self Organized ◽  
Dependent Cell

Our understanding of the left–right (LR) asymmetry of embryonic development, in particular the contribution of intrinsic handedness of the cell or cell chirality, is limited due to the confounding systematic and environmental factors during morphogenesis and a ack of physiologically relevant in vitro 3D platforms. Here we report an efficient two-layered biomaterial platform for determining the chirality of individual cells, cell aggregates, and self-organized hollow epithelial spheroids. This bioengineered niche provides a uniform defined axis allowing for cells to rotate spontaneously with a directional bias toward either clockwise or counterclockwise directions. Mechanistic studies reveal an actin-dependent, cell-intrinsic property of 3D chirality that can be mediated by actin cross-linking via α-actinin-1. Our findings suggest that the gradient of extracellular matrix is an important biophysicochemical cue influencing cell polarity and chirality. Engineered biomaterial systems can serve as an effective platform for studying developmental asymmetry and screening for environmental factors causing birth defects.

scholarly journals Geomorphometric analysis of cave ceiling channels mapped with 3D terrestrial laser scanning

2016 ◽  
Author(s):  
Michal Gallay ◽  
Zdenko Hochmuth ◽  
Ján Kaňuk ◽  
Jaroslav Hofierka
Keyword(s):  
Laser Scanning ◽  
Methodological Approach ◽  
Three Dimensional ◽  
Terrestrial Laser Scanning ◽  
Scalar Fields ◽  
Complex Environments ◽  
Digital Elevation ◽  
Unique Manner ◽  
Elevation Model ◽  
Different Levels

Abstract. The change of hydrological conditions during the evolution of caves in carbonate rocks often results in a complex subterranean geomorphology which comprises specific landforms such as ceiling channels, anastomosing half tubes, or speleothems organised vertically in different levels. Studying such complex environments traditionally requires tedious mapping, however, this is being replaced with terrestrial laser scanning technology. Laser scanning overcomes the problem of reaching high ceilings providing new options to map underground landscapes with unprecedented level of detail and accuracy. The acquired point cloud can be handled conveniently with dedicated software, but applying traditional geomorphometry to analyse the cave surface is limited. This is because geomorphometry has been focused on parameterisation and analysis of surficial terrain. The theoretical and methodological concept has been based on two-dimensional scalar fields which is sufficient for most cases of the surficial terrain. The terrain surface is modelled with a bivariate function of altitude (elevation) and represented by a raster digital elevation model. However, the cave is a three-dimensional entity therefore a different approach is required for geomorphometric analysis. In this paper, we demonstrate the benefits of high resolution cave mapping and 3-D modelling to better understand the palaeohydrography of the Domica cave in Slovakia. This methodological approach adopted traditional geomorphometric methods in a unique manner and also new methods used in 3D computer graphics which can be applied to study other 3-D geomorphological forms

Pattern re-establishment — transplantation and regeneration of the leg in the cricket Teleogryllus commodus (Walker)

Development ◽  
1981 ◽  
Vol 61 (1) ◽  
pp. 87-101
Author(s):  
Robert J. Biggin
Keyword(s):  
Pattern Formation ◽  
Three Dimensional ◽  
External Morphology ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Teleogryllus Commodus ◽  
Cuticular Structures

Regeneration and grafting experiments were carried out on the prothoracic leg of the cricket Teleogryllus commodus (Walker) to examine the precision with which surface cuticular structures and internal epidermal derivatives are reformed. By comparing regenerated and grafted limbs with normal limbs it was found that the three-dimensional structure of epidermal derivatives is not restored. This is despite the fact that regenerated and grafted limbs appear similar in their external morphology to normal limbs. The implication of these results are discussed in the context of theories of pattern formation.

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