scholarly journals 3D phytomer-based geometric modelling method for plants—the case of maize

AoB Plants ◽  
2021 ◽  
Vol 13 (5) ◽  
Author(s):  
Weiliang Wen ◽  
Yongjian Wang ◽  
Sheng Wu ◽  
Kai Liu ◽  
Shenghao Gu ◽  
...  

Abstract Geometric plant modelling is crucial in in silico plants. Existing geometric modelling methods have focused on the topological structure and basic organ profiles, simplifying the morphological features. However, the models cannot effectively differentiate cultivars, limiting FSPM application in crop breeding and management. This study proposes a 3D phytomer-based geometric modelling method with maize (Zea Mays) as the representative plant. Specifically, conversion methods between skeleton and mesh models of 3D phytomer are specified. This study describes the geometric modelling of maize shoots and populations by assembling 3D phytomers. Results show that the method can quickly and efficiently construct 3D models of maize plants and populations, with the ability to show morphological, structural and functional differences among four representative cultivars. The method takes into account both the geometric modelling efficiency and 3D detail features to achieve automatic operation of geometric modelling through the standardized description of 3D phytomers. Therefore, this study provides a theoretical and technical basis for the research and application of in silico plants.

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sameera Senanayake ◽  
Nicholas Graves ◽  
Helen Healy ◽  
Keshwar Baboolal ◽  
Adrian Barnett ◽  
...  

Abstract Background Economic-evaluations using decision analytic models such as Markov-models (MM), and discrete-event-simulations (DES) are high value adds in allocating resources. The choice of modelling method is critical because an inappropriate model yields results that could lead to flawed decision making. The aim of this study was to compare cost-effectiveness when MM and DES were used to model results of transplanting a lower-quality kidney versus remaining waitlisted for a kidney. Methods Cost-effectiveness was assessed using MM and DES. We used parametric survival models to estimate the time-dependent transition probabilities of MM and distribution of time-to-event in DES. MMs were simulated in 12 and 6 monthly cycles, out to five and 20-year time horizon. Results DES model output had a close fit to the actual data. Irrespective of the modelling method, the cycle length of MM or the time horizon, transplanting a low-quality kidney as compared to remaining waitlisted was the dominant strategy. However, there were discrepancies in costs, effectiveness and net monetary benefit (NMB) among different modelling methods. The incremental NMB of the MM in the 6-months cycle lengths was a closer fit to the incremental NMB of the DES. The gap in the fit of the two cycle lengths to DES output reduced as the time horizon increased. Conclusion Different modelling methods were unlikely to influence the decision to accept a lower quality kidney transplant or remain waitlisted on dialysis. Both models produced similar results when time-dependant transition probabilities are used, most notable with shorter cycle lengths and longer time-horizons.


Author(s):  
Guanyu Hu ◽  
Chaojun Huang ◽  
Fengjie Yin ◽  
Mark Cerkovnik ◽  
Guangqiang Yang

Abstract The Flexible joint is one of the most widely used hang-off systems for deep water catenary riser for its large rotation and load bearing capacity. The fatigue performance of riser hang-off region and fatigue load on the flexible joint highly depend on the rotational stiffness of the flexible joint. Thus, modelling the flexible joint stiffness to accurately simulate the behavior under cyclic bending cycles is critical in global riser fatigue analysis. The load-displacement relationship of a flexible joint typically follows a nonlinear curve, and it shows hysteresis behavior when subject to cyclic bending cycles. However, in current industry practice, the flexible joint stiffness is modelled either as a nonlinear curve or simplified as a fixed value. These simplified methods sometimes can lead to unconservative or over conservative results in riser design. Modelling the flexible joint stiffness in an accurate approach becomes more important especially when the riser fatigue is critical at the hang-off region. In addition, the design of flexible joint will also be impacted by the fatigue load extracted from global fatigue analysis, which is also largely affected by the flexible joint stiffness modelling method. Thus, modelling a flexible joint by accounting for the nonlinear hysteretic stiffness is recommended. This paper compares the different modelling methodologies of the flexible joint for catenary riser hang-off and presents the impact on fatigue performance considering hysteretic behavior. This study considers the effects of wave amplitude and hosting vessel offset. A case study is also presented on the application of all the modelling methods on fatigue performance of an SCR in the Gulf of Mexico. The fatigue behavior is compared for the different modelling methods considering long term wave motion and platform offsets. The impact on the results from different types of hosting platform is also discussed.


F1000Research ◽  
2021 ◽  
Vol 10 ◽  
pp. 2
Author(s):  
Yuliana Emiliani ◽  
Andrés Sánchez ◽  
Marlon Munera ◽  
Jorge Sánchez ◽  
Dilia Aparicio

Background: Phospholipases are enzymes with the capacity to hydrolyze membrane lipids and have been characterized in several allergenic sources, such as hymenoptera species. However, cross-reactivity among phospholipases allergens are little understood. The objective of this study was to determine potential antigenic regions involved in cross-reactivity among allergens of phospholipases using an in silico approach. Methods: In total, 18 amino acids sequences belonging to phospholipase family derived from species of the order hymenoptera were retrieved from the UniProt database to perform phylogenetic analysis to determine the closest molecular relationship. Multialignment was done to identify conserved regions and matched with antigenic regions predicted by ElliPro server. 3D models were obtained from modeling by homology and were used to locate cross-reactive antigenic regions. Results: Phylogenetic analysis showed that the 18 phospholipases split into four monophyletic clades (named here as A, B, C and D). Phospholipases from A clade shared an amino acid sequences’ identity of 79%. Antigenic patches predicted by Ellipro were located in highly conserved regions, suggesting that they could be involved in cross-reactivity in this group (Ves v 1, Ves a 1 and Ves m 1). Conclusions: At this point, we advanced to the characterization of potential antigenic sites involved in cross-reactivity among phospholipases. Inhibition assays are needed to confirm our finding.


2019 ◽  
Vol 12 (1) ◽  
pp. 18-29
Author(s):  
Javier Escobar-Perez ◽  
Katterine Ospina-Garcia ◽  
Zayda Lorena Corredor Rozo ◽  
Ricaurte Alejandro Marquez-Ortiz ◽  
Jaime E Castellanos ◽  
...  

Background: YlbF and YmcA are two essential proteins for the formation of biofilm, sporulation, and competence in Bacillus subtilis. In these two proteins, a new protein domain called com_ylbF was recently discovered, but its role and protein function has not yet been established. Objective: In this study, we identified and performed an “in silico” structural analysis of the YheA protein, another com_ylbF-containing protein, in the opportunistic pathogen Staphylococcus aureus. Methods: The search of the yheA gene was performed using BLAST-P and tBLASn algorithms. The three-dimensional (3D) models of YheA, as well as YlbF and YmcA proteins, were built using the I-TASSER and Quark programs. The identification of the native YheA in Staphylococcus aureus was carried out through chromatography using the FPLC system. Results: We found that YheA protein is more widely distributed in Gram-positive bacteria than YlbF and YmcA. Two new and important characteristics for YheA and other com_ylbF-containing proteins were found: a highly conserved 3D structure and the presence of a putative conserved motif located in the central region of the domain, which could be involved in its function. Additionally, we established that Staphylococcus aureus expresses YheA protein in both planktonic growth and biofilm. Finally, we suggest renaming YheA as glutamine-rich protein (Qrp) in S. aureus. Conclusion: The Grp (YheA), YlbF, and YmcA proteins adopt a highly conserved three-dimensional structure, harboring a protein-specific putative motif within the com_ylbF domain, which possibly favors the interaction with their substrates. Finally, Staphylococcus aureus expresses the Grp (YheA) protein in both planktonic and biofilm growth.


2021 ◽  
Vol 11 ◽  
Author(s):  
Laura Righetti ◽  
Enrico Rolli ◽  
Luca Dellafiora ◽  
Gianni Galaverna ◽  
Michele Suman ◽  
...  

While aflatoxin metabolism in animals has been clarified, very limited information is so far available on the possible biotransformation occurring in plants. Therefore, this work aimed at investigating whether AFB1 metabolites could occur in field-grown infected maize and the putative role of Zea mays L. metabolism in their production. For such scope, asymptomatic in vitro–grown plantlets and in silico evaluations of plant transforming enzymes were used to pinpoint how plants may handle these compounds. Our data demonstrated the role of maize plants in the production of Phase I hydroxylated aflatoxins, including, among others, AFM1, AFM2, and aflatoxicol, and suggest that plant cytochromes may be involved in this biotransformation of AFB1.


2021 ◽  
pp. 1-27
Author(s):  
Nikita Letov ◽  
Pavan Tejaswi Velivela ◽  
Siyuan Sun ◽  
Yaoyao Fiona Zhao

Abstract Ever since its introduction over five decades ago, geometric solid modelling has been crucial for engineering design purposes and is used in engineering software packages such as computer-aided design (CAD), computer-aided manufacturing (CAM), computer-aided engineering (CAE), etc. Solid models produced by CAD software have been used to transfer geometric information from designers to manufacturers. Since the emergence of additive manufacturing (AM), a CAD file can also be directly uploaded to a three-dimensional (3D) printer and used for production. AM techniques allow manufacturing of complex geometric objects such as bio-inspired structures and lattice structures. These structures are shapes inspired by nature and periodical geometric shapes consisting of struts interconnecting in nodes. Both structures have unique properties such as significantly reduced weight. However, geometric modelling of such structures has significant challenges due to the inability of current techniques to handle their geometric complexity. This calls for a novel modelling method that would allow engineers to design complex geometric objects. This survey paper reviews geometric modelling methods of complex structures to support bio-inspired design created for AM which includes discussing reasoning behind bio-inspired design, limitations of current modelling approaches applied to bio-inspired structures, challenges encountered with geometric modelling and opportunities that these challenges reveal. Based on the review, a need for a novel geometric modelling method for bio-inspired geometries produced by AM is identified. A framework for such bio-inspired geometric modelling method is proposed as a part of this work.


Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 708
Author(s):  
Su Datt Lam ◽  
Paul Ashford ◽  
Sandra Díaz-Sánchez ◽  
Margarita Villar ◽  
Christian Gortázar ◽  
...  

Coronavirus-like organisms have been previously identified in Arthropod ectoparasites (such as ticks and unfed cat flea). Yet, the question regarding the possible role of these arthropods as SARS-CoV-2 passive/biological transmission vectors is still poorly explored. In this study, we performed in silico structural and binding energy calculations to assess the risks associated with possible ectoparasite transmission. We found sufficient similarity between ectoparasite ACE and human ACE2 protein sequences to build good quality 3D-models of the SARS-CoV-2 Spike:ACE complex to assess the impacts of ectoparasite mutations on complex stability. For several species (e.g., water flea, deer tick, body louse), our analyses showed no significant destabilisation of the SARS-CoV-2 Spike:ACE complex, suggesting these species would bind the viral Spike protein. Our structural analyses also provide structural rationale for interactions between the viral Spike and the ectoparasite ACE proteins. Although we do not have experimental evidence of infection in these ectoparasites, the predicted stability of the complex suggests this is possible, raising concerns of a possible role in passive transmission of the virus to their human hosts.


Cancers ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 28 ◽  
Author(s):  
Florentin Baur ◽  
Sarah L. Nietzer ◽  
Meik Kunz ◽  
Fabian Saal ◽  
Julian Jeromin ◽  
...  

To improve and focus preclinical testing, we combine tumor models based on a decellularized tissue matrix with bioinformatics to stratify tumors according to stage-specific mutations that are linked to central cancer pathways. We generated tissue models with BRAF-mutant colorectal cancer (CRC) cells (HROC24 and HROC87) and compared treatment responses to two-dimensional (2D) cultures and xenografts. As the BRAF inhibitor vemurafenib is—in contrast to melanoma—not effective in CRC, we combined it with the EGFR inhibitor gefitinib. In general, our 3D models showed higher chemoresistance and in contrast to 2D a more active HGFR after gefitinib and combination-therapy. In xenograft models murine HGF could not activate the human HGFR, stressing the importance of the human microenvironment. In order to stratify patient groups for targeted treatment options in CRC, an in silico topology with different stages including mutations and changes in common signaling pathways was developed. We applied the established topology for in silico simulations to predict new therapeutic options for BRAF-mutated CRC patients in advanced stages. Our in silico tool connects genome information with a deeper understanding of tumor engines in clinically relevant signaling networks which goes beyond the consideration of single drivers to improve CRC patient stratification.


Author(s):  
Nils Piechaud ◽  
Anna Downie ◽  
Heather A. Stewart ◽  
Kerry L. Howell

ABSTRACTPredictive modelling of deep-sea species and assemblages with multibeam acoustic datasets as input variables is now a key tool in the provision of maps upon which spatial planning and management of the marine environment can be based. However, with a multitude of methods available, advice is needed on the best methods for the task at hand. In this study, we predictively modelled the distribution and extent of three vulnerable marine ecosystems (VMEs) at the assemblage level (‘Lophelia pertusa reef frameworks’; ‘Stylasterids and lobose sponges’; and ‘Xenophyophore fields’) on the eastern flank of Rockall Bank, using three modelling methods: MaxEnt; RandomForests classification with multiple assemblages (gRF); and RandomForests classification with the presence/absence of a single VME (saRF). Performance metrics indicated that MaxEnt performed the best, but all models were considered valid. All three methods broadly agreed with regard to broad patterns in distribution. However, predicted extent presented a variation of up to 35 % between the different methods, and clear differences in predicted distribution were observed. We conclude that the choice of method is likely to influence the results of predicted maps, potentially impacting political decisions about deep-sea VME conservation.


2018 ◽  
Vol 1 (1) ◽  
pp. e00008
Author(s):  
K.A. Shcherbakov ◽  
D.S. Shcherbinin ◽  
V.A. Kostin ◽  
V.A. Zolottsev ◽  
A.Yu. Misharin ◽  
...  

The ability of novel oxazolinyl derivatives of pregna-5,17(20)-diene to interact with the androgen receptor (AR) was investigated using molecular modelling methods. Six new derivatives differed in oxazolinyl radicals in 17 position were used. It was shown that all compounds were able to docked in the ligand-binding domain of AR only when the AR helix-12 was removed. It is suggested that these compounds have antagonistic properties. Results of docking and simulation of molecular dynamics with estimation of binding energy allow to predict that two compounds can be effective AR antagonists.


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