keyword
MENU ▼
Read by QxMD icon Read
search

Phylogenic tree

keyword
https://www.readbyqxmd.com/read/28966259/phylogenic-analysis-and-evaluation-of-ephedra-plants-and-aconites-for-medicinal-use
#1
Nobuko Kakiuchi
 Although Kampo medicine is now fully integrated into the modern Japanese healthcare system, most Kampo formulations depend on imported crude drugs from limited foreign areas. To prepare for possible shortages of crude drugs in the future, a wider scope for the supply of medicinal plants is necessary. We conducted field research and collaborated with international laboratories for phylogenic analysis and evaluation of medicinal plant resources. Our research on ephedra plants from a wide region of Eurasia has, for example, confirmed their phylogenic structure: based on DNA sequencing analysis of nuclear ribosomal internal transcribed spacer region 1 (ITS1) as well as the chloroplast intergenic spacer between trnL and trnF (trnL-F), the 8 major Chinese species and related plants grown on the continent could be divided into 3 groups...
2017: Yakugaku Zasshi: Journal of the Pharmaceutical Society of Japan
https://www.readbyqxmd.com/read/28961520/food-poisoning-outbreak-in-tokyo-japan-caused-by-staphylococcus-argenteus
#2
Yasunori Suzuki, Hiroaki Kubota, Hisaya K Ono, Makiko Kobayashi, Konomi Murauchi, Rei Kato, Akihiko Hirai, Kenji Sadamasu
Staphylococcus argenteus is a novel species subdivided from Staphylococcus aureus. Whether this species can cause food poisoning outbreaks is unknown. This study aimed to investigate the enterotoxigenic activities of two food poisoning isolates suspected to be S. argenteus (Tokyo13064 and Tokyo13069). The results for phylogenic trees, constructed via whole genome sequencing, demonstrated that both isolates were more similar to a type strain of S. argenteus (MSHR1132) than any S. aureus strain. Moreover, the representative characteristics of S...
December 4, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28840340/trait-shifts-associated-with-the-subshrub-life-history-strategy-in-a-tropical-savanna
#3
A B Giroldo, A Scariot, W A Hoffmann
Over the past 10 million years, tropical savanna environments have selected for small growth forms within woody plant lineages. The result has been the evolution of subshrubs (geoxyles), presumably as an adaptation to frequent fire. To evaluate the traits associated with the shift from tree to subshrub growth forms, we compared seed biomass, germination, survival, resprouting, biomass allocation, and photosynthesis between congeneric trees and subshrubs, and quantified phylogenetic conservatism. Despite large differences in adult morphology between trees and subshrub species, the differences are modest in seedlings, and most of the variation in traits was explained by genus, indicating considerable phylogenic conservatism...
August 24, 2017: Oecologia
https://www.readbyqxmd.com/read/28780378/homblocks-a-multiple-alignment-construction-pipeline-for-organelle-phylogenomics-based-on-locally-collinear-block-searching
#4
Guiqi Bi, Yunxiang Mao, Qikun Xing, Min Cao
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multi-gene alignments. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multi-gene alignment in a few hours...
August 2, 2017: Genomics
https://www.readbyqxmd.com/read/28642977/molecular-characteristics-and-prevalence-of-small-ruminant-lentiviruses-in-goats-in-japan
#5
Saki Kokawa, Mami Oba, Teppei Hirata, Shiro Tamaki, Miki Omura, Shinobu Tsuchiaka, Makoto Nagai, Tsutomu Omatsu, Tetsuya Mizutani
Small ruminant lentiviruses (SRLVs), which comprise caprine arthritis-encephalitis virus (CAEV) and maedi-visna virus (MVV), are prevalent in goats and sheep worldwide, including in Japan. However, little is known about the molecular characteristics of goat lentiviruses in Japan. In this study, a molecular and phylogenetic analysis of the long gag region was performed. The phylogenic tree demonstrated that all samples belonged to SRLV subtype B1. Two clusters were identified, with one cluster distinct from previously reported strains of subtype B1...
June 22, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28491250/prevalence-of-hepatitis-c-virus-genotype-3a-in-patients-with-hodgkin-and-non-hodgkin-lymphoma
#6
Hashem Radmehr, Manoochehr Makvandi, Alireza Samarbafzadeh, Ali Teimoori, Niloofar Neisi, Mojtaba Rasti, Sara Abasifar, Hasan Soltani, Samaneh Abbasi, Hadis Kiani, Hamide Mehravaran, Azarakhsh Azaran, Toran Shahani
BACKGROUND AND OBJECTIVES: Hepatitis C virus (HCV) is a major public health problem worldwide. Replication and persistence of HCV genome have been described in the liver tissue as well as B cells lymphocyte. Several investigations have reported that long-term persistence of HCV in B cells may result in Hodgkin and Non-Hodgkin lymphoma. This study was aimed to determine frequency of HCV RNA in histological tissues obtained from patients suffered from Hodgkin and Non-Hodgkin lymphoma. MATERIALS AND METHODS: 52 formalin-fixed paraffin-embedded tissue blocks including 23 (44...
December 2016: Iranian Journal of Microbiology
https://www.readbyqxmd.com/read/28466379/bayesian-and-phylogenic-approaches-for-studying-relationships-among-table-olive-cultivars
#7
Rayda Ben Ayed, Karim Ennouri, Fathi Ben Amar, Fabienne Moreau, Mohamed Ali Triki, Ahmed Rebai
To enhance table olive tree authentication, relationship, and productivity, we consider the analysis of 18 worldwide table olive cultivars (Olea europaea L.) based on morphological, biological, and physicochemical markers analyzed by bioinformatic and biostatistic tools. Accordingly, we assess the relationships between the studied varieties, on the one hand, and the potential productivity-quantitative parameter links on the other hand. The bioinformatic analysis based on the graphical representation of the matrix of Euclidean distances, the principal components analysis, unweighted pair group method with arithmetic mean, and principal coordinate analysis (PCoA) revealed three major clusters which were not correlated with the geographic origin...
August 2017: Biochemical Genetics
https://www.readbyqxmd.com/read/28440467/structural-and-evolutionary-divergence-of-aquaporins-in-parasites-review
#8
Zi-Xin Ni, Jian-Min Cui, Nian-Zhang Zhang, Bao-Quan Fu
Aquaporins are ubiquitous proteins that belong to the major intrinsic protein family. Previous studies have indicated that aquaporins are involved in multiple physiological processes in parasites, such as nutrient absorption and end product efflux, and thus, would be promising pharmacological agents in the fight against parasite infection. In the present paper, the authors analyzed the evolutionary relationship of parasitic aquaporins by re‑constructing of a phylogenic tree using neighbor‑joining and maximum likelihood methods...
June 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28352258/180-nucleotide-duplication-in-the-g-gene-of-human-metapneumovirus-a2b-subgroup-strains-circulating-in-yokohama-city-japan-since-2014
#9
Miwako Saikusa, Chiharu Kawakami, Naganori Nao, Makoto Takeda, Shuzo Usuku, Tadayoshi Sasao, Kimiko Nishimoto, Takahiro Toyozawa
Human metapneumovirus (HMPV), a member of the family Paramyxoviridae, was first isolated in 2001. Seroepidemiological studies have shown that HMPV has been a major etiological agent of acute respiratory infections in humans for more than 50 years. Molecular epidemiological, genetic, and antigenetic evolutionary studies of HMPV will strengthen our understanding of the epidemic behavior of the virus and provide valuable insight for the control of HMPV and the development of vaccines and antiviral drugs against HMPV infection...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28318778/stenotrophomonas-maltophilia-healthcare-associated-infections-identification-of-two-main-pathogenic-genetic-backgrounds
#10
C Corlouer, B Lamy, M Desroches, J Ramos-Vivas, E Mehiri-Zghal, O Lemenand, J-M Delarbre, J-W Decousser
BACKGROUND: Stenotrophomonas maltophilia is an opportunistic multi-drug-resistant bacterium responsible for healthcare-associated infections. Strategies for in-hospital infection control and management of carriers and environmental reservoirs remain controversial. AIM: To determine the population structure of S. maltophilia strains in hospitalized infected patients and to identify putative highly pathogenic subpopulations that require upgraded infection control measures...
June 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28285130/phylogenic-and-phosphorylation-regulation-difference-of-phosphoenolpyruvate-carboxykinase-of-c3-and-c4-plants
#11
Zhuo Shen, Xiu-Mei Dong, Zhi-Fang Gao, Qing Chao, Bai-Chen Wang
In C4 plants, phosphoenolpyruvate carboxykinase (PEPCK) plays a key role in the C4 cycle. PEPCK is also involved in gluconeogenesis and is conserved in both lower and higher organisms, including in animals and plants. A phylogenic tree constructed from PEPCK sequences from bacteria to higher plants indicates that the C4 Poaceae PEPCKs are conserved and have diverged from the PEPCKs of C3 plants. The maximum enzymatic activities of wild-type and phosphorylation mimic PEPCK proteins indicate that there is a significant difference between C3 and C4 plant PEPCKs...
February 27, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28266604/effects-of-biophysical-constraints-climate-and-phylogeny-on-forest-shrub-allometries-along-an-altitudinal-gradient-in-northeast-china
#12
Han Sun, Xiangping Wang, Yanwen Fan, Chao Liu, Peng Wu, Qiaoyan Li, Weilun Yin
Whether there is a general allometry law across plant species with different sizes and under different environment has long been controversial and shrubs are particularly useful to examine these questions. Here we sampled 939 individuals from 50 forest shrub species along a large altitudinal gradient. We tested several allometry models with four relationships simultaneously (between stem diameter, height, leaf, stem and aboveground biomass), including geometric, elastic and stress similarity, and metabolic scaling theory's predictions on small plants (MSTs) and trees (MSTt)...
March 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28264351/molecular-phylogenetic-analysis-of-the-orthoptera-arthropoda-insecta-based-on-hexamerin-sequences
#13
Xiaohong Zhang, Jinfeng Hao, Y U Xia, Yage Chang, Daochuan Zhang, Hong Yin
The higher taxa classification and phylogeny of the insect order Orthoptera have long been controversial. Hexamerin, as a member of the highly conserved arthropod hemocyanin superfamily, has been shown to be a good marker for the phylogenetic study of insects. However, few studies have used hexamerins on the phylogeny of Orthoptera. In this study, we determined twenty-seven different hexamerin subunit type sequences in seventeen speices of Orthoptera. In order to infer the phylogenetic relationships among the superfamilies within Orthoptera and test the monophyly of Orthoptera, phylogenic trees were reconstructed using Neighbor-Joining (NJ) and Bayesian inference (BI) methods with two dipluran and three hymenopteran hexamerin sequences as outgroups...
February 20, 2017: Zootaxa
https://www.readbyqxmd.com/read/28188871/cloning-characterization-and-subcellular-localization-of-nuclear-lim-interactor-interacting-factor-gene-from-leishmania-donovani
#14
R Ravinder, N Goyal
LIM domains are zinc-binding motifs that mediate protein-protein interactions and are found in a wide variety of cytoplasmic and nuclear proteins. The nuclear LIM domain family members have a number of different functions including transcription factors, gene regulation, cell fate determination, organization of the cytoskeleton and tumour formation exerting their function through various LIM domain interacting protein partners/cofactors. Nuclear LIM domain interacting proteins/factors have not been reported in any protozoan parasites including Leishmania...
May 5, 2017: Gene
https://www.readbyqxmd.com/read/28111450/the-complete-mitochondrial-genome-sequence-of-the-indigenous-i-pig-sus-scrofa-in-vietnam
#15
Hieu Duc Nguyen, Tuan Anh Bui, Phuong Thanh Nguyen, Oanh Thi Phuong Kim, Thuy Thi Bich Vo
OBJECTIVE: The I pig is a long nurtured longstanding breed in Vietnam, and contains excellent indigenous genetic resources. However, after 1970s, I pig breeds have become a small population because of decreasing farming areas and increasing pressure from foreign breeds with a high growth rate. Thus, there is now the risk of the disappearance of the I pigs breed. The aim of this study was to focus on classifying and identifying the I pig genetic origin and supplying molecular makers for conservation activities...
July 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28107076/characterization-of-an-avipoxvirus-from-a-bald-eagle-haliaeetus-leucocephalus-using-novel-consensus-pcr-protocols-for-the-rpo147-and-dna-dependent-dna-polymerase-genes
#16
Alexa A Stephen, Angelique M Leone, David E Toplon, Linda L Archer, James F X Wellehan
A juvenile female bald eagle ( Haliaeetus leucocephalus ) was presented with emaciation and proliferative periocular lesions. The eagle did not respond to supportive therapy and was euthanatized. Histopathologic examination of the skin lesions revealed plaques of marked epidermal hyperplasia parakeratosis, marked acanthosis and spongiosis, and eosinophilic intracytoplasmic inclusion bodies. Novel polymerase chain reaction (PCR) assays were done to amplify and sequence DNA polymerase and rpo147 genes. The 4b gene was also analyzed by a previously developed assay...
December 2016: Journal of Avian Medicine and Surgery
https://www.readbyqxmd.com/read/28053614/multilocus-sequence-typing-analysis-of-pseudomonas-aeruginosa-isolated-from-pet-chinese-stripe-necked-turtles-ocadia-sinensis
#17
Mitchell Wendt, Gang-Joon Heo
Our research sought to characterize the phylogeny of Pseudomonas aeruginosa isolated from pet Chinese stripe-necked turtles (Ocadia sinensis) to better understand its evolutionary relation to other isolates and increase understanding of a potential zoonotic pathogen transmitted through direct contact with pet turtles. Thirty-one Pseudomonas aeruginosa isolates were obtained from both immature and adult turtles sold in pet shops in Korea. To characterize the phylogenic position of Chinese stripe-necked turtle-borne P...
December 2016: Laboratory Animal Research
https://www.readbyqxmd.com/read/28018379/comparative-transcriptomics-of-strawberries-fragaria-spp-provides-insights-into-evolutionary-patterns
#18
Qin Qiao, Li Xue, Qia Wang, Hang Sun, Yang Zhong, Jinling Huang, Jiajun Lei, Ticao Zhang
Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557-82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27989861/identification-and-activity-of-a-paralog-of-cathepsin-s-from-yellow-catfish-pelteobagrus-fulvidraco-involved-in-immune-response
#19
Yun Wang, Xin Liu, Shuai Lv, Jinnan Ren, Fei Ke
Cathepsin S, a papain-like cysteine peptidase, is an important regulator and signaling molecule with diverse biological actions in addition to immune presentation. However, our understanding of its structure and properties remains limited. Herein, a full-length cathepsin Sa from yellow catfish was cloned and named PfCTSSa. It contained 1366 bp, including a 981 bp ORF flanked by a 123 bp 5'-untranslated region (UTR) and a 262 bp 3'-UTR. This ORF encoded a 36.5 kD cysteine protease with the deduced amino acid sequence having a 76% sequence identity with Ictalurus punctatus ctssa...
February 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27870689/zika-virus-and-diagnostics
#20
Claudia Raja Gabaglia
PURPOSE OF REVIEW: The purpose of this review is to present what is known about the Zika virus (ZIKV) at the time of writing this review. The viral structure and its phylogeny, as well as the limitations of current available techniques used for diagnosis, are discussed. RECENT FINDINGS: Crystallography and cryo-electron microscopy of the whole ZIKV, or a few of its proteins, are confirming its overall antigenic relatedness to other flaviviruses. Sequencing has revealed its dynamic genetic variation and has placed the Western cluster of Zika isolates within the Asian phylogenic tree...
February 2017: Current Opinion in Pediatrics
keyword
keyword
120687
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"