pathway evolution
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Marine Drugs ◽  
2022 ◽  
Vol 20 (1) ◽  
pp. 52
Author(s):  
Sam Afoullouss ◽  
Anthony R. Sanchez ◽  
Laurence K. Jennings ◽  
Younghoon Kee ◽  
A. Louise Allcock ◽  
...  

Sponges are at the forefront of marine natural product research. In the deep sea, extreme conditions have driven secondary metabolite pathway evolution such that we might expect deep-sea sponges to yield a broad range of unique natural products. Here, we investigate the chemodiversity of a deep-sea tetractinellid sponge, Characella pachastrelloides, collected from ~800 m depth in Irish waters. First, we analyzed the MS/MS data obtained from fractions of this sponge on the GNPS public online platform to guide our exploration of its chemodiversity. Novel glycolipopeptides named characellides were previously isolated from the sponge and herein cyanocobalamin, a manufactured form of vitamin B12, not previously found in nature, was isolated in a large amount. We also identified several poecillastrins from the molecular network, a class of polyketide known to exhibit cytotoxicity. Light sensitivity prevented the isolation and characterization of these polyketides, but their presence was confirmed by characteristic NMR and MS signals. Finally, we isolated the new betaine 6-methylhercynine, which contains a unique methylation at C-2 of the imidazole ring. This compound showed potent cytotoxicity towards against HeLa (cervical cancer) cells.


2021 ◽  
Author(s):  
Omid Safronov ◽  
Guleycan Lutfullahoglubal ◽  
Nina Sipari ◽  
Maya Wilkens ◽  
Pezhman Safdari ◽  
...  

Inonotus obliquus, Chaga mushroom, is a fungal species from Hymenochaetaceae family (Basidiomycota) which has been widely used for traditional medicine in Europe and Asia. Here, chaga genome was sequenced using Pacbio sequencing into a 50.7Mbp assembly consisting of 301 primary contigs with an N50 value of 375 kbp. Genome evolution analyses revealed a lineage-specific whole genome duplication event and an expansion of Cytochrome P450 superfamily. Fungal biosynthetic clusters were enriched for tandemly duplicated genes, suggesting that biosynthetic pathway evolution has proceeded through small-scale duplications. Metabolomic fingerprinting confirmed a highly complex terpene biosynthesis chemistry when compared against related fungal species lacking the genome duplication event.


The Breast ◽  
2021 ◽  
Vol 59 ◽  
pp. S45-S46
Author(s):  
Lefeuvre Claudia ◽  
Frenel Jean-Sebastien ◽  
Moley-Massol Isabelle ◽  
Guéroult-Accolas Laure ◽  
Debiais Dominique ◽  
...  

2021 ◽  
Vol 207 ◽  
pp. 106097
Author(s):  
Shichao Ji ◽  
Hongping He ◽  
Jianxi Zhu ◽  
Xing Ding ◽  
William E. Seyfried

2021 ◽  
Vol 11 (9) ◽  
pp. 4045
Author(s):  
Amilcar Duque-Prata ◽  
Carlos Serpa ◽  
Pedro J. S. B. Caridade

The photodegradation mechanism of 1-phenyl-4-allyl-tetrazol-5-one has been studied using (time-dependent) density functional theory with the M06-HF, B3LYP, and PBE0 functionals and the VDZ basis set. All calculations have been carried out using the polarizable continuum model to simulate the solvent effects of methanol. The reaction pathway evolution on the triplet state has been characterised to validate a previously postulated experimental-based mechanism. The transition states and minimums have been initially located by local scanning in partial constrained optimisation, followed by a fully relaxed search procedure. The UV spectra has shown to be better described with PBE0 functional when compared with the experimental results, having the M06-HF a shift of 40 nm. From the energetic point of view, the postulated mechanism has been validated in this work showing a concerted photoextrusion of the N2 molecule. The intramolecular proton transfer occurs at a later stage of the mechanism after cyclization of the allyl group on a triplet biradical intermediate. The photoproduct observed experimentally, a pyrimidinone, has been characterised. The infrared spectroscopic reaction profile has also been proposed.


Author(s):  
Maria Clara Tonini ◽  
Alessandra Fiorencis ◽  
Rosario Iannacchero ◽  
Mauro Zampolini ◽  
Antonietta Cappuccio ◽  
...  

Abstract Background Although migraine is widespread and disabling, stigmatisation and poor awareness of the condition still represent barriers to effective care; furthermore, research on migraine individual and social impact must be enhanced to unveil neglected issues, such as caregiving burden. The project investigated the migraine illness experience through Narrative Medicine (NM) to understand daily life, needs and personal resources of migraneurs, their caregivers and clinicians, and to provide insights for clinical practice. Methods The project involved 13 Italian headache centres and targeted migraneurs, their caregivers and migraine specialists at these centres. Written narratives, composed by a sociodemographic survey and illness plot or parallel chart, were collected through the project’s webpage. Illness plots and parallel charts employed open words to encourage participants’ expression. Narratives were analysed through Nvivo software, interpretive coding and NM classifications. Results One hundred and seven narratives were collected from patients and 26 from caregivers, as well as 45 parallel charts from clinicians. The analysis revealed migraine perception in social, domestic and work life within the care pathway evolution and a bond between chaos narratives and day loss due to migraine; furthermore, narratives suggested the extent of the caregiving burden and a risk of underestimation of migraine burden in patients’ and caregivers’ life. Conclusion The project represents the first investigation on migraine illness experience through NM simultaneously considering migraneurs’, caregivers’ and clinicians’ perspectives. Comparing narratives and parallel charts allowed to obtain suggestions for clinical practice, while NM emerged as able to foster the pursuing of migraine knowledge and awareness.


2020 ◽  
Vol 36 (14) ◽  
pp. 4116-4125 ◽  
Author(s):  
Idit Bloch ◽  
Dana Sherill-Rofe ◽  
Doron Stupp ◽  
Irene Unterman ◽  
Hodaya Beer ◽  
...  

Abstract Summary The exponential growth in available genomic data is expected to reach full sequencing of a million genomes in the coming decade. Improving and developing methods to analyze these genomes and to reveal their utility is of major interest in a wide variety of fields, such as comparative and functional genomics, evolution and bioinformatics. Phylogenetic profiling is an established method for predicting functional interactions between proteins based on similarities in their evolutionary patterns across species. Proteins that function together (i.e. generate complexes, interact in the same pathways or improve adaptation to environmental niches) tend to show coordinated evolution across the tree of life. The normalized phylogenetic profiling (NPP) method takes into account minute changes in proteins across species to identify protein co-evolution. Despite the success of this method, it is still not clear what set of parameters is required for optimal use of co-evolution in predicting functional interactions. Moreover, it is not clear if pathway evolution or function should direct parameter choice. Here, we create a reliable and usable NPP construction pipeline. We explore the effect of parameter selection on functional interaction prediction using NPP from 1028 genomes, both separately and in various value combinations. We identify several parameter sets that optimize performance for pathways with certain biological annotation. This work reveals the importance of choosing the right parameters for optimized function prediction based on a biological context. Availability and implementation Source code and documentation are available on GitHub: https://github.com/iditam/CompareNPPs. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.


2019 ◽  
Vol 59 (3) ◽  
pp. 585-598 ◽  
Author(s):  
L C Wheeler ◽  
S D Smith

Abstract The alteration of metabolic pathways is a common mechanism underlying the evolution of new phenotypes. Flower color is a striking example of the importance of metabolic evolution in a complex phenotype, wherein shifts in the activity of the underlying pathway lead to a wide range of pigments. Although experimental work has identified common classes of mutations responsible for transitions among colors, we lack a unifying model that relates pathway function and activity to the evolution of distinct pigment phenotypes. One challenge in creating such a model is the branching structure of pigment pathways, which may lead to evolutionary trade-offs due to competition for shared substrates. In order to predict the effects of shifts in enzyme function and activity on pigment production, we created a simple kinetic model of a major plant pigmentation pathway: the anthocyanin pathway. This model describes the production of the three classes of blue, purple, and red anthocyanin pigments, and accordingly, includes multiple branches and substrate competition. We first studied the general behavior of this model using a naïve set of parameters. We then stochastically evolved the pathway toward a defined optimum and analyzed the patterns of fixed mutations. This approach allowed us to quantify the probability density of trajectories through pathway state space and identify the types and number of changes. Finally, we examined whether our simulated results qualitatively align with experimental observations, i.e., the predominance of mutations which change color by altering the function of branching genes in the pathway. These analyses provide a theoretical framework that can be used to predict the consequences of new mutations in terms of both pigment phenotypes and pleiotropic effects.


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