scholarly journals Distribution of Therapeutic Efficacy of Ranunculales Plants Used by Ethnic Minorities on the Phylogenetic Tree of Chinese Species

2022 ◽  
Vol 2022 ◽  
pp. 1-10
Author(s):  
Da-Cheng Hao ◽  
Yulu Zhang ◽  
Chun-Nian He ◽  
Pei-Gen Xiao
Keyword(s):  
Phylogenetic Tree ◽  
Ethnic Minorities ◽  
Therapeutic Efficacy ◽  
Phylogenetic Trees ◽  
Therapeutic Effects ◽  
Distribution Law ◽  
R Language ◽  
Net Relatedness Index ◽  
Angiosperm Species ◽  
Taxonomic Groups

The medicinal properties of plants can be evolutionarily predicted by phylogeny-based methods, which, however, have not been used to explore the regularity of therapeutic effects of Chinese plants utilized by ethnic minorities. This study aims at exploring the distribution law of therapeutic efficacy of Ranunculales plants on the phylogenetic tree of Chinese species. We collected therapeutic efficacy data of 551 ethnomedicinal species belonging to five species-rich families of Ranunculales; these therapeutic data were divided into 15 categories according to the impacted tissues and organs. The phylogenetic tree of angiosperm species was used to analyze the phylogenetic signals of ethnomedicinal plants by calculating the net relatedness index (NRI) and nearest taxon index (NTI) in R language. The NRI results revealed a clustered structure for eight medicinal categories (poisoning/intoxication, circulatory, gastrointestinal, eyesight, oral, pediatric, skin, and urinary disorders) and overdispersion for the remaining seven (neurological, general, hepatobiliary, musculoskeletal, otolaryngologic, reproductive, and respiratory disorders), while the NTI metric identified the clustered structure for all. Statistically, NRI and NTI values were significant in 5 and 11 categories, respectively. It was found that Mahonia eurybracteata has therapeutic effects on all categories. iTOL was used to visualize the distribution of treatment efficacy on species phylogenetic trees. By figuring out the distribution of therapeutic effects of Ranunculales medicinal plants, the importance of phylogenetic methods in finding potential medicinal resources is highlighted; NRI, NTI, and similar indices can be calculated to help find taxonomic groups with medicinal efficacy based on the phylogenetic tree of flora in different geographic regions.

scholarly journals Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

2015 ◽  
Author(s):  
Jennifer Fouquier ◽  
Jai R Rideout ◽  
Evan Bolyen ◽  
John H Chase ◽  
Arron Shiffer ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Marker ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Sequence Data ◽  
Fungal Species ◽  
Bioinformatics Tool ◽  
Hybrid Gene ◽  
Fungal Database ◽  
Taxonomic Groups

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

scholarly journals Reconstructing the Phylogeny ofCapsosiphon fulvescens(Ulotrichales, Chlorophyta) from Korea Based onrbcL and 18S rDNA Sequences

2016 ◽  
Vol 2016 ◽  
pp. 1-6 ◽  
Author(s):  
Sang-Mi Sun ◽  
Seung Hwan Yang ◽  
Kirill S. Golokhvast ◽  
Bao Le ◽  
Gyuhwa Chung
Keyword(s):  
Phylogenetic Tree ◽  
18S Rdna ◽  
Phylogenetic Trees ◽  
Economic Value ◽  
Phylogenetic Position ◽  
Therapeutic Effects ◽  
Filamentous Green Algae ◽  
Rdna Sequences ◽  
18S Rdna Sequences ◽  
Taxonomic Studies

Capsosiphon fulvescensis a filamentous green algae in the class Ulvophyceae. It has been consumed as food with unique flavor and soft texture to treat stomach disorders and hangovers, and its economic value justifies studying its nutritional and potential therapeutic effects. In contrast to these applications, only a few taxonomic studies have been conducted onC. fulvescens. In particular, classification and phylogenetic relationships of theC. fulvescensbelow the order level are controversial. To determine its phylogenetic position in the class, we usedrbcL and 18S rDNA sequences as molecular markers to construct phylogenetic trees. The amplifiedrbcL and 18S rDNA sequences from 4C. fulvescensisolates (Jindo, Jangheung, Wando, and Koheung, Korea) were used for phylogenetic analysis by employing three different phylogenetic methods: neighbor joining (NJ), maximum parsimony (MP), and maximum likelihood (ML). TherbcL phylogenetic tree showed that all taxa in the order Ulvales were clustered as a monophyletic group and resolved the phylogenetic position ofC. fulvescensin the order Ulotrichales. The significance of our study is that the 18S rDNA phylogenetic tree shows the detailed taxonomic position ofC. fulvescens. In our result,C. fulvescensis inferred as a member of Ulotrichaceae, along withUrosporaandAcrosiphonia.

scholarly journals Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses

2015 ◽  
Author(s):  
Jennifer Fouquier ◽  
Jai R Rideout ◽  
Evan Bolyen ◽  
John H Chase ◽  
Arron Shiffer ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Genetic Marker ◽  
Phylogenetic Trees ◽  
Phylogenetic Diversity ◽  
Sequence Data ◽  
Fungal Species ◽  
Bioinformatics Tool ◽  
Hybrid Gene ◽  
Fungal Database ◽  
Taxonomic Groups

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.

scholarly journals Computing nearest neighbour interchange distances between ranked phylogenetic trees

2021 ◽  
Vol 82 (1-2) ◽  
Author(s):  
Lena Collienne ◽  
Alex Gavryushkin
Keyword(s):  
Cancer Research ◽  
Computational Complexity ◽  
Phylogenetic Tree ◽  
Shortest Path ◽  
Phylogenetic Trees ◽  
Shortest Paths ◽  
Nearest Neighbour ◽  
Tree Inference ◽  
Subtree Prune And Regraft ◽  
Comparison Algorithms

AbstractMany popular algorithms for searching the space of leaf-labelled (phylogenetic) trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are given by pairs of trees connected by one rearrangement operation (sometimes called a move). Most popular are the classical nearest neighbour interchange, subtree prune and regraft, and tree bisection and reconnection moves. The problem of computing distances, however, is $${\mathbf {N}}{\mathbf {P}}$$ N P -hard in each of these graphs, making tree inference and comparison algorithms challenging to design in practice. Although anked phylogenetic trees are one of the central objects of interest in applications such as cancer research, immunology, and epidemiology, the computational complexity of the shortest path problem for these trees remained unsolved for decades. In this paper, we settle this problem for the ranked nearest neighbour interchange operation by establishing that the complexity depends on the weight difference between the two types of tree rearrangements (rank moves and edge moves), and varies from quadratic, which is the lowest possible complexity for this problem, to $${\mathbf {N}}{\mathbf {P}}$$ N P -hard, which is the highest. In particular, our result provides the first example of a phylogenetic tree rearrangement operation for which shortest paths, and hence the distance, can be computed efficiently. Specifically, our algorithm scales to trees with tens of thousands of leaves (and likely hundreds of thousands if implemented efficiently).

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals Analysis of SARS-CoV-2 nucleocapsid protein sequence variations in ASEAN countries

2021 ◽  
Author(s):  
Mochammad Rajasa Mukti Negara ◽  
Ita Krissanti ◽  
Gita Widya Pradini
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Protein Sequences ◽  
Reference Sequence ◽  
N Protein ◽  
Asean Country ◽  
Sequence Variations ◽  
Complete Sequences ◽  
Asean Countries ◽  
Global Initiative

BACKGROUND Nucleocapsid (N) protein is one of four structural proteins of SARS-CoV-2  which is known to be more conserved than spike protein and is highly immunogenic. This study aimed to analyze the variation of the SARS-CoV-2 N protein sequences in ASEAN countries, including Indonesia. METHODS Complete sequences of SARS-CoV-2 N protein from each ASEAN country were obtained from Global Initiative on Sharing All Influenza Data (GISAID), while the reference sequence was obtained from GenBank. All sequences collected from December 2019 to March 2021 were grouped to the clade according to GISAID, and two representative isolates were chosen from each clade for the analysis. The sequences were aligned by MUSCLE, and phylogenetic trees were built using MEGA-X software based on the nucleotide and translated AA sequences. RESULTS 98 isolates of complete N protein genes from ASEAN countries were analyzed. The nucleotides of all isolates were 97.5% conserved. Of 31 nucleotide changes, 22 led to amino acid (AA) substitutions; thus, the AA sequences were 94.5% conserved. The phylogenetic tree of nucleotide and AA sequences shows similar branches. Nucleotide variations in clade O (C28311T); clade GR (28881–28883 GGG>AAC); and clade GRY (28881–28883 GGG>AAC and C28977T) lead to specific branches corresponding to the clade within both trees. CONCLUSIONS The N protein sequences of SARS-CoV-2 across ASEAN countries are highly conserved. Most isolates were closely related to the reference sequence originating from China, except the isolates representing clade O, GR, and GRY which formed specific branches in the phylogenetic tree.

P–802 The fate and regenerative efficiency of differently administered BMSCs in thin-endometrium rat models

2021 ◽  
Vol 36 (Supplement_1) ◽  
Author(s):  
Q Guo ◽  
Y Chang
Keyword(s):  
Therapeutic Efficacy ◽  
Bioluminescence Imaging ◽  
Basal Layer ◽  
Post Treatment ◽  
Clinical Settings ◽  
Positive Staining ◽  
Therapeutic Effects ◽  
Thin Endometrium ◽  
Therapeutic Efficiency ◽  
Sd Rats

Abstract Study question This study aims to compare the engraftment, retaining time and therapeutic efficiency of differently administered BMSCs and help to select an optimal therapeutic route in clinical settings. Summary answer Compared with intrauterine infusion, BMSCs could better promote angiogenesis by upregulating related cytokines, such as VEGF, when administered through the ipsilateral iliac artery. What is known already MSC-based therapy has become a promising method for endometrial disease(thin endomtrium or Ashernmen’s syndrowe). Therapeutic effects could always be observed even though different MSC administration routes or MSCs of different tissue sources were used in these studies. Only a few studies compared efficacy of different transplantation routes. However, the results seem to be controversial. Comparable therapeutic effects were reported in some studies, while others stated that systematic administration gave a better outcome than local administration. Study design, size, duration Experimental animal study. Forty-eight female Sprague-Dawley (SD) rats were used in this study. They were randomly assigned to 4 groups: normal, injured, intra-arterial and intra-uterine group. For all rats except for normal group, the thin endometrium models were established by infusing 95% ethanol into the uterine horns and BMSCs were transplanted either locally or intra-arterially after modeling. The therapeutic efficacy were evaluated in the following month. Participants/materials, setting, methods The thin endometrium models induced by ethanol in SD rats, GFP/Luciferin labeled BMSCs were injected either locally or intra-arterially. The retaining time and quantitative distribution were assessed by in vivo bioluminescence imaging and immune-histological analysis. The precise location and differentiation of differently administered BMSCs were determined by immunofluorescence methods. The endometrial fibrosis, angiogenesis were detected by immunohistochemistry and western blotting at a consecutive time after treatment to compare the therapeutic efficiency of two administration methods. Main results and the role of chance The engraftment and differentiation abiility were comparable in 2 groups. The luminescent signal both remained distinct and strong in the abdomen in the first 4 days post-treatment(7.98 × 105 and 6.02 × 105p/s for IU and IA group), indicating the precise and concentrated distribution of BMSCs administered both locally or intra-arterially. The luminescent signals disappeared under bioluminescence imaging over time. We further evaluated the precise distribution, differentiation ability and retaining time of the BMSCs delivered in two strategies by immunofluorescence analysis. All the GFP positive cell localized in stroma, but not in the epithelium or myometrium. Furthermore, there are significantly more positive staining in basal layer of the endometrium close to the glands and vessels than the outer layer of the endometrium in the intra-arterial group. At the 28th days post treatment, we could capture a few GFP staining in the basalis layel of endometrium in intra-arterial group and there were no GFP fluorescence signals detected in intra-uterine group(P < 0.05), suggesting a better survival of BMSCs administered intra-arterially. Differentiation ability of differently administered BMSCs were similar. A few BMSCs began to differentiate into stromal cell 12 days after therapy. Limitations, reasons for caution No pregnancy tests were carried out in these rats to further confirm the regeneration of thin endometrium and compare the therapeutic efficacy. Wider implications of the findings: Our study unveiled that the location of MSCs might determined their regenerarive ability and retaining time, and provided an optimal therapeutic route in clinical settings. Trial registration number Not applicable

INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS

2006 ◽  
Vol 04 (01) ◽  
pp. 59-74 ◽  
Author(s):  
YING-JUN HE ◽  
TRINH N. D. HUYNH ◽  
JESPER JANSSON ◽  
WING-KIN SUNG
Keyword(s):  
Approximation Algorithms ◽  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Evolutionary History ◽  
Phylogenetic Network ◽  
Evolutionary Relationships ◽  
Large Set ◽  
Tree Network ◽  
History Of ◽  
Overlapping Sets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set [Formula: see text] and none of the rooted triplets in another given set [Formula: see text]. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.

Visualizing Speciation in Artificial Cichlid Fish

2006 ◽  
Vol 12 (2) ◽  
pp. 243-257 ◽  
Author(s):  
Ross Clement
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Cichlid Fish ◽  
Natural Consequence ◽  
Open Problems ◽  
Visualization System ◽  
Low Level ◽  
Wide Range ◽  
Level Information ◽  
History Of

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

scholarly journals Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

2019 ◽  
Vol 37 (2) ◽  
pp. 599-603 ◽  
Author(s):  
Li-Gen Wang ◽  
Tommy Tsan-Yuk Lam ◽  
Shuangbin Xu ◽  
Zehan Dai ◽  
Lang Zhou ◽  
...  
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
R Package ◽  
External Data ◽  
Input And Output ◽  
Evolutionary Context ◽  
Tree Data ◽  
Downstream Analysis ◽  
Different Sources ◽  
Associated Data

Abstract Phylogenetic trees and data are often stored in incompatible and inconsistent formats. The outputs of software tools that contain trees with analysis findings are often not compatible with each other, making it hard to integrate the results of different analyses in a comparative study. The treeio package is designed to connect phylogenetic tree input and output. It supports extracting phylogenetic trees as well as the outputs of commonly used analytical software. It can link external data to phylogenies and merge tree data obtained from different sources, enabling analyses of phylogeny-associated data from different disciplines in an evolutionary context. Treeio also supports export of a phylogenetic tree with heterogeneous-associated data to a single tree file, including BEAST compatible NEXUS and jtree formats; these facilitate data sharing as well as file format conversion for downstream analysis. The treeio package is designed to work with the tidytree and ggtree packages. Tree data can be processed using the tidy interface with tidytree and visualized by ggtree. The treeio package is released within the Bioconductor and rOpenSci projects. It is available at https://www.bioconductor.org/packages/treeio/.

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