scholarly journals Untargeted In Silico Compound Classification—A Novel Metabolomics Method to Assess the Chemodiversity in Bryophytes

2021 ◽  
Vol 22 (6) ◽  
pp. 3251
Author(s):  
Kristian Peters ◽  
Gerd Balcke ◽  
Niklas Kleinenkuhnen ◽  
Hendrik Treutler ◽  
Steffen Neumann
Keyword(s):  
In Silico ◽  
Structural Integrity ◽  
Environmental Changes ◽  
Light Availability ◽  
Biotic Interactions ◽  
Plant Ecology ◽  
Chemical Diversity ◽  
Classification Framework ◽  
Significant Difference ◽  
Compound Classification

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies.

Geographic variation of parasitic and predatory traces on mollusks in the northern Adriatic Sea, Italy: implications for the stratigraphic paleobiology of biotic interactions

Paleobiology ◽  
2015 ◽  
Vol 41 (1) ◽  
pp. 134-153 ◽  
Author(s):  
John Warren Huntley ◽  
Daniele Scarponi
Keyword(s):  
Environmental Changes ◽  
Temporal Trends ◽  
Biotic Interactions ◽  
Diversity Indices ◽  
Northern Adriatic Sea ◽  
Po River ◽  
Northern Adriatic ◽  
Ideal System ◽  
Significant Difference ◽  
Po Delta

AbstractParasitic trematode worms leave characteristic pits in their bivalve mollusk hosts and represent an ideal system for analyzing parasite-host interactions through space and time with statistically meaningful sample sizes. Previous work in Late Pleistocene–Holocene sequences from the Po plain revealed significant long-term fluctuations in trematode prevalence values: higher prevalence in retrogradational environments (TST) and negligible prevalence in progradational environments (HST). Here we expand upon this work by investigating traces of parasitism, kleptoparasitism, and predation on mollusk death assemblages from two domains along the northern Adriatic coastline. The domain north of the Po delta (TST-like) and the southern domain (including the Po delta; HST-like) comprise environments comparable to those recovered in late Holocene (<6 Kyr) subsurface progradational deposits. We collected 17,299 specimens representing 111 species from 11 locations on the northern Adriatic coast of Italy. Our results reveal high predation pressure, a high diversity of host taxa, and widespread presence of trematode infestation in starved, oligotrophic, environmentally more stable (i.e., TST-like) settings north of the Po delta. Immediately south of the Po delta, in settings with strong and variable sedimentary input, almost no infestation is recorded. The reappearance of infestation is evident in the southern portion of the study area (i.e., Cattolica-Montemarciano), relatively far from the highly stressed environments south of the Po River. There is no significant difference in trematode prevalence values between fossil and modern samples. The distribution of spionid traces (an indicator of stressed environments) was nearly the opposite of that displayed by trematodes. Drilling frequency is highest in TST-like environments and is not correlated with diversity indices. These results suggest that temporal trends of trematode prevalence (and possibly also other biotic interactions) in sedimentary successions are controlled by environmental changes driven by glacio-eustatic dynamics, and reaffirm the importance of interpreting temporal trends in the context of spatial variation.

Computational and In-Vitro Validation of Natural Molecules as Potential Acetylcholinesterase Inhibitors and Neuroprotective Agents

2019 ◽  
Vol 16 (2) ◽  
pp. 116-127 ◽  
Author(s):  
Ashwani Kumar ◽  
Vineet Mehta ◽  
Utkarsh Raj ◽  
Pritish Kumar Varadwaj ◽  
Malairaman Udayabanu ◽  
...  
Keyword(s):  
In Silico ◽  
Hippocampal Neurons ◽  
Symptomatic Relief ◽  
In Vitro Assays ◽  
Disease Modifying Drugs ◽  
In Silico Docking ◽  
Ache Inhibitors ◽  
Significant Difference ◽  
Disease Modifying

Background: Cholinesterase inhibitors are the first line of therapy for the management of Alzheimer’s disease (AD), however, it is now established that they provide only temporary and symptomatic relief, besides, having several inherited side-effects. Therefore, an alternative drug discovery method is used to identify new and safer ‘disease-modifying drugs’. Methods: Herein, we screened 646 small molecules of natural origin having reported pharmacological and functional values through in-silico docking studies to predict safer neuromodulatory molecules with potential to modulate acetylcholine metabolism. Further, the potential of the predicted molecules to inhibit acetylcholinesterase (AChE) activity and their ability to protect neurons from degeneration was determined through in-vitro assays. Results: Based on in-silico AChE interaction studies, we predicted quercetin, caffeine, ascorbic acid and gallic acid to be potential AChE inhibitors. We confirmed the AChE inhibitory potential of these molecules through in-vitro AChE inhibition assay and compared results with donepezil and begacestat. Herbal molecules significantly inhibited enzyme activity and inhibition for quercetin and caffeine did not show any significant difference from donepezil. Further, the tested molecules did not show any neurotoxicity against primary (E18) hippocampal neurons. We observed that quercetin and caffeine significantly improved neuronal survival and efficiently protected hippocampal neurons from HgCl2 induced neurodegeneration, which other molecules, including donepezil and begacestat, failed to do. Conclusion: Quercetin and caffeine have the potential as “disease-modifying drugs” and may find application in the management of neurological disorders such as AD.

Diatoms in Saline Lakes Paleoclimate and Paleoecology Interpretations

2007 ◽  
Vol 13 ◽  
pp. 149-168 ◽  
Author(s):  
Erik J. Ekdahl
Keyword(s):  
Climate Change ◽  
Global Warming ◽  
Global Climate Change ◽  
Water Conservation ◽  
Environmental Changes ◽  
Global Climate ◽  
Light Availability ◽  
Ionic Concentration ◽  
Mitigation Strategies ◽  
Environmental Response

Average global temperatures are predicted to rise over the next century and changes in precipitation, humidity, and drought frequency will likely accompany this global warming. Understanding associated changes in continental precipitation and temperature patterns in response to global change is an important component of long-range environmental planning. For example, agricultural management plans that account for decreased precipitation over time will be less susceptible to the effects of drought through implementation of water conservation techniques.A detailed understanding of environmental response to past climate change is key to understanding environmental changes associated with global climate change. To this end, diatoms are sensitive to a variety of limnologic parameters, including nutrient concentration, light availability, and the ionic concentration and composition of the waters that they live in (e.g. salinity). Diatoms from numerous environments have been used to reconstruct paleosalinity levels, which in turn have been used as a proxy records for regional and local paleoprecipitation. Long-term records of salinity or paleoprecipitation are valuable in reconstructing Quaternary paleoclimate, and are important in terms of developing mitigation strategies for future global climate change. High-resolution paleoclimate records are also important in groundtruthing global climate simulations, especially in regions where the consequences of global warming may be severe.

scholarly journals Spatial point-pattern analysis as a powerful tool in identifying pattern-process relationships in plant ecology: an updated review

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Mariem Ben-Said
Keyword(s):  
Spatial Patterns ◽  
Pattern Analysis ◽  
Biotic Interactions ◽  
Plant Ecology ◽  
Point Pattern Analysis ◽  
Point Pattern ◽  
Summary Statistics ◽  
Spatial Point Pattern ◽  
Spatial Point ◽  
Spatial Point Pattern Analysis

Abstract Background Ecological processes such as seedling establishment, biotic interactions, and mortality can leave footprints on species spatial structure that can be detectable through spatial point-pattern analysis (SPPA). Being widely used in plant ecology, SPPA is increasingly carried out to describe biotic interactions and interpret pattern-process relationships. However, some aspects are still subjected to a non-negligible debate such as required sample size (in terms of the number of points and plot area), the link between the low number of points and frequently observed random (or independent) patterns, and relating patterns to processes. In this paper, an overview of SPPA is given based on rich and updated literature providing guidance for ecologists (especially beginners) on summary statistics, uni-/bi-/multivariate analysis, unmarked/marked analysis, types of marks, etc. Some ambiguities in SPPA are also discussed. Results SPPA has a long history in plant ecology and is based on a large set of summary statistics aiming to describe species spatial patterns. Several mechanisms known to be responsible for species spatial patterns are actually investigated in different biomes and for different species. Natural processes, plant environmental conditions, and human intervention are interrelated and are key drivers of plant spatial distribution. In spite of being not recommended, small sample sizes are more common in SPPA. In some areas, periodic forest inventories and permanent plots are scarce although they are key tools for spatial data availability and plant dynamic monitoring. Conclusion The spatial position of plants is an interesting source of information that helps to make hypotheses about processes responsible for plant spatial structures. Despite the continuous progress of SPPA, some ambiguities require further clarifications.

scholarly journals Changes in Adherence to the 24-Hour Movement Guidelines and Overweight and Obesity among Children in Northeastern Japan: A Longitudinal Study before and during the COVID-19 Pandemic

Obesities ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 167-177
Author(s):  
Hyunshik Kim ◽  
Jiameng Ma ◽  
Junghoon Kim ◽  
Daolin Xu ◽  
Sunkyoung Lee
Keyword(s):  
Environmental Changes ◽  
Preventive Measures ◽  
Overweight And Obesity ◽  
Health Programs ◽  
Average Body Mass Index ◽  
Northeastern Japan ◽  
Significant Difference ◽  
Community Health Programs ◽  
Average Body Mass ◽  
Average Body

There are few studies comparing adherence to Canadian 24-hour Movement Guidelines (24-h MG) before and during the COVID-19 pandemic and exploring the pandemic’s effect on childhood obesity. This survey-based 2-year study investigated changes in obesity and adherence to the 24-h MG in children before and during the COVID-19 pandemic. Data were collected at two points in time: pre-COVID-19 (May 2019; T1; n = 247) and during-COVID-19 (May 2021; T2; n = 171). Participants were healthy elementary school children aged between 6–12 years in northeastern Japan. The questionnaire comprised items on physical activity, screen time, sleep duration, adherence to the 24-h MG, and anthropometric and demographic characteristics. Among all participants, a statistically significant difference (p < 0.001) between the average body mass index at T1 (M = 16.06 kg/m2, SD = 2.08 kg/m2) and T2 (M = 18.01 kg/m2, SD = 3.21 kg/m2) was observed, where 17.8% were overweight and obese at T1 and 24% at T2, and 10.9% adhered to all 24 h MG at T1 and 4.1% at T2. To prevent obesity in children during the COVID-19 pandemic, environmental changes should be evaluated and appropriate preventive measures taken, including pro-community health programs that encourage parent-children outdoor activities.

scholarly journals The Biomechanics of Erections: Modeling the Penis as a One-Comparment Pressurized Vessel vs. Modeling it as a Two-Compartments Pressurized Vessel

2009 ◽  
Vol 3 (2) ◽  
Author(s):  
A. Mohamed ◽  
A. Erdman ◽  
G. Timm
Keyword(s):  
Structural Integrity ◽  
Tunica Albuginea ◽  
Three Dimensional ◽  
The Body ◽  
Physical Models ◽  
Von Mises Stress ◽  
Two Dimensional ◽  
Biomechanical Models ◽  
Significant Difference ◽  
The One

Previous biomechanical models of the penis that have attempted to simulate penile erections have either been limited to two-dimensional geometry, simplified three-dimensional geometry or made inaccurate assumptions altogether. Most models designed the shaft of the penis as a one-compartment pressurized vessel fixed at one end, when in reality it is a two-compartments pressurized vessel, in which the compartments diverge as they enter the body and are fixed at two separate points. This study began by designing simplified two-dimensional and three-dimensional models of the erect penis using Finite Element Analysis (FEA) methods with varying anatomical considerations for analyzing structural stresses, axial buckling and lateral deformation. The study then validated the results by building physical models replicating the computer models. Finally a more complex and anatomically accurate model of the penis was designed and analyzed. There was a significant difference in the peak von-Mises stress distribution between the one-compartment pressurized vessel and the more anatomically correct two-compartments pressurized vessel. Furthermore, the two-compartments diverging pressurized vessel was found to have more structural integrity when subject to external lateral forces than the one-compartment pressurized vessel. This study suggests that Mother Nature has favored an anatomy of two corporal cavernosal bodies separated by a perforated septum as opposed to one corporal body, due to better structural integrity of the tunica albuginea when subject to external forces.

scholarly journals Acmella oleracea (L) R. K. Jansen Reproductive Toxicity in Zebrafish: An In Vivo and In Silico Assessment

2019 ◽  
Vol 2019 ◽  
pp. 1-19 ◽  
Author(s):  
Gisele Custodio de Souza ◽  
Arlindo César Matias Pereira ◽  
Muller Duarte Viana ◽  
Adriana Maciel Ferreira ◽  
Ianna Dias Ribeiro da Silva ◽  
...  
Keyword(s):  
Embryonic Development ◽  
In Silico ◽  
Reproductive Toxicity ◽  
Control Group ◽  
The North ◽  
Significant Difference ◽  
Hydroethanolic Extract ◽  
Primary Compound ◽  
F1 Generation

The plant species Acmella oleracea L. is used in the north of Brazil for the treatment of a range of illnesses, such as tuberculosis, flu, cough, and rheumatism and as an anti-inflammatory agent; besides, hydroethanolic formulations with this species are popularly used as a female aphrodisiac agent. However, currently, there are no studies performed evaluating its effect on embryonic development. Hence, this research aimed to evaluate the effects of the hydroethanolic extract of A. oleracea (EHFAo) on the reproductive performance (parental) and embryonic development (F1 generation) of zebrafish, at concentrations of 50, 100, and 200 μg/L. Histopathology of parental gonads after 21 days of exposure to EHFAo reveals few alterations in the ovaries and testes, not impairing the reproduction; an increase of eggs deposition was observed in animals treated with EHFAo at the highest concentrations. Nevertheless, concerning the embryonic development of F1, teratogenic effects were observed including tail deformation, cardiac and yolk edema, scoliosis, and growth retardation; these alterations were more prominent in the groups born from progenitors exposed to the highest concentrations (100 and 200 μg/L.); but only the occurrence of yolk and cardiac edema had a statistically significant difference when compared to the control group. The chromatographic analysis shows that spilanthol (affinin) was the primary compound found in the EHFAo. Hence, in silico assessment was performed to evaluate the pharmacokinetic and toxicological properties of this molecule and 37 metabolites derived from it. Overall, our data show that the treatment caused no detrimental changes in progenitors regarding their gonads or fertility but caused some potentially teratogenic activity in embryos, which may be due to the action of spilanthol’s metabolites M3, M6, M7, M8, M16, M28, and M31.

scholarly journals High light alongside elevated PCO2 alleviates thermal depression of photosynthesis in a hard coral (Pocillopora acuta)

2020 ◽  
Vol 223 (20) ◽  
pp. jeb223198
Author(s):  
Robert A. B. Mason ◽  
Christopher B. Wall ◽  
Ross Cunning ◽  
Sophie Dove ◽  
Ruth D. Gates
Keyword(s):  
Elevated Temperature ◽  
Ocean Acidification ◽  
Environmental Changes ◽  
Dark Respiration ◽  
Interactive Effect ◽  
Light Availability ◽  
Photosynthetic Apparatus ◽  
High Light ◽  
Photochemical Quenching ◽  
Strong Light

ABSTRACTThe absorbtion of human-emitted CO2 by the oceans (elevated PCO2) is projected to alter the physiological performance of coral reef organisms by perturbing seawater chemistry (i.e. ocean acidification). Simultaneously, greenhouse gas emissions are driving ocean warming and changes in irradiance (through turbidity and cloud cover), which have the potential to influence the effects of ocean acidification on coral reefs. Here, we explored whether physiological impacts of elevated PCO2 on a coral–algal symbiosis (Pocillopora acuta–Symbiodiniaceae) are mediated by light and/or temperature levels. In a 39 day experiment, elevated PCO2 (962 versus 431 µatm PCO2) had an interactive effect with midday light availability (400 versus 800 µmol photons m−2 s−1) and temperature (25 versus 29°C) on areal gross and net photosynthesis, for which a decline at 29°C was ameliorated under simultaneous high-PCO2 and high-light conditions. Light-enhanced dark respiration increased under elevated PCO2 and/or elevated temperature. Symbiont to host cell ratio and chlorophyll a per symbiont increased at elevated temperature, whilst symbiont areal density decreased. The ability of moderately strong light in the presence of elevated PCO2 to alleviate the temperature-induced decrease in photosynthesis suggests that higher substrate availability facilitates a greater ability for photochemical quenching, partially offsetting the impacts of high temperature on the photosynthetic apparatus. Future environmental changes that result in moderate increases in light levels could therefore assist the P. acuta holobiont to cope with the ‘one–two punch’ of rising temperatures in the presence of an acidifying ocean.

scholarly journals Destabilizing the structural integrity of COVID-19 by caulerpin and its derivatives along with some antiviral drugs: An in silico approaches for a combination therapy

2020 ◽  
Vol 31 (6) ◽  
pp. 2391-2412 ◽  
Author(s):  
Shimaa A. Ahmed ◽  
Doaa A. Abdelrheem ◽  
H. R. Abd El-Mageed ◽  
Hussein S. Mohamed ◽  
Aziz A. Rahman ◽  
...  
Keyword(s):  
Combination Therapy ◽  
In Silico ◽  
Structural Integrity ◽  
Antiviral Drugs

Study of the Feasibility of Conventional MR Images and Magnetic Resonance (MR)/Ultra-Short Echo Time (UTE) Technique in the Evaluation of Lumbar Disc Degeneration in the Axial Plane

2021 ◽  
Vol 11 (3) ◽  
pp. 817-821
Author(s):  
Peng Tang ◽  
Jingtao Xu ◽  
Wei Liu ◽  
Yu Li ◽  
Wei Fan ◽  
...  
Keyword(s):  
Low Back Pain ◽  
Back Pain ◽  
Intervertebral Disc ◽  
Disc Degeneration ◽  
Intervertebral Disc Degeneration ◽  
Structural Integrity ◽  
Low Back ◽  
Pain Group ◽  
Cartilage Endplate ◽  
Significant Difference

The advantage and value of magnetic resonance (MR)-ultra-short echo time (UTE) technique in the displaying the structures of degenerative intervertebral discs were observed through evaluating the lumbar disc degeneration in the axial plane by conventional MR image and MR-UTE technique. A total of 160 examinees screened by inclusion and exclusion criteria were enrolled, and a total of 800 intervertebral disks were involved, and the degree of intervertebral disc degeneration was classified by conventional MR image classification method. After the first echo image of MR-UTE technique was integrated with the contour, the image entered UTE cartilage endplate, fibrous ring and osseous endplate. The integrity of the intervertebral disc from the above and below the intervertebral disc and the correlation of the structural endplate with the integrities of cartilage endplate, fibrous ring and osseous endplate under double echo sequence were analyzed, and the correlation analysis of the two categorical variables was conducted using rank correlation analysis. Under the MR-UTE sequence, there was no statistical significant difference in structural integrity constituent ratio (intact structure only on one side, incomplete structure on both side) between the non-low back pain group and the low back pain group (P > 0.05), the proportion of complete structure disappearance was lowest, and the proportion of partial structure disappearance was highest; there was a significant difference in the structural integrity of fibrous ring between the non-low back pain group and the low back pain group (P < 0.05), there was a statistical significant difference in structural integrity of fibrous rings between the two groups (P < 0.05); there was a statistical significant difference in pain degree between the partial structure disappearance group and the complete structure disappearance group (P < 0.05). There was no significant difference in pain degree between the groups (intact structure only on one side and incomplete structure on both side); conventional MR images showed no significant difference in the intervertebral disc degeneration degree between the non-low back pain group and low back pain group (P > 0.05), and the intervertebral disc degeneration degree had no significant correlation with the lower back pain. MR-UTE sequence and T2WI sequence showed that there was a correlation between different intervertebral disc degeneration degrees and the structural integrity distributions of cartilage endplate, osseous endplate and fibrous rings in two groups of patients with or without low back pain (P < 0.05). Whether low back pain exists or not has little effect on the intervertebral disc degeneration degree on T2WI. MR-UTE double echo sequence scan reveals that the intervertebral disc degeneration degree is positively related to the integrity and integrity distribution of cartilage endplate, fibrous ring and bone endplate.

Sign in / Sign up

Export Citation Format

Share Document