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Phylogenetics

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https://www.readbyqxmd.com/read/28445658/a-time-and-a-place-for-everything-phylogenetic-history-and-geography-as-joint-predictors-of-oak-plastome-phylogeny
#1
Kasey Khanh Pham, Andrew L Hipp, Paul S Manos, Richard C Cronn
Due to high rates of introgressive hybridization, the plastid genome is poorly suited to fine-scale DNA barcoding and phylogenetic studies of the oak genus (Quercus, Fagaceae). At the tips of the oak plastome phylogeny, recent gene migration and reticulation generally cause topology to reflect geographic structure, while deeper branches reflect lineage divergence. In this study, we quantify the simple and partial effects of geographic proximity and nucleome-inferred phylogenetic history on oak plastome phylogeny at different evolutionary scales...
April 26, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28445514/the-complexity-underlying-invasiveness-precludes-the-identification-of-invasive-traits-a-comparative-study-of-invasive-and-non-invasive-heterocarpic-atriplex-congeners
#2
Jana Doudová, Jan Douda, Bohumil Mandák
Heterocarpy enables species to effectively spread under unfavourable conditions by producing two or more types of fruit differing in ecological characteristics. Although it is frequent in annuals occupying disturbed habitats that are vulnerable to invasion, there is still a lack of congeneric studies addressing the importance of heterocarpy for species invasion success. We compared two pairs of heterocarpic Atriplex species, each of them comprising one invasive and one non-invasive non-native congener. In two common garden experiments, we (i) simulated the influence of different levels of nutrients and population density on plants grown from different types of fruits and examined several traits that are generally positively associated with invasion success, and (ii) grew plants in a replacement series experiment to evaluate resource partitioning between them and to compare their competitive ability...
2017: PloS One
https://www.readbyqxmd.com/read/28445493/polyphyly-of-the-extinct-family-oviparosiphidae-and-its-implications-for-inferring-aphid-evolution-hemiptera-sternorrhyncha
#3
Dagmara Żyła, Agnieszka Homan, Piotr Wegierek
Aphidoidea, the so-called "true aphids" are one of the most challenging groups in terms of solving the phylogenetic relationships. Morphology-based analyses were strongly affected by widespread homoplasy, while the molecular-based attempts struggled with the lack of sufficient phylogenetic signal. Despite significant improvements, the higher classification still remains unresolved and rather controversial. However, the use of the fossil record, one of the most valuable sources of information, was mainly limited to calibration of a phylogenetic tree, without a direct inclusion into the analysis...
2017: PloS One
https://www.readbyqxmd.com/read/28445469/phylogenetic-ctdna-analysis-depicts-early-stage-lung-cancer-evolution
#4
Christopher Abbosh, Nicolai J Birkbak, Gareth A Wilson, Mariam Jamal-Hanjani, Tudor Constantin, Raheleh Salari, John Le Quesne, David A Moore, Selvaraju Veeriah, Rachel Rosenthal, Teresa Marafioti, Eser Kirkizlar, Thomas B K Watkins, Nicholas McGranahan, Sophia Ward, Luke Martinson, Joan Riley, Francesco Fraioli, Maise Al Bakir, Eva GrÖnroos, Francisco Zambrana, Raymondo Endozo, Wenya Linda Bi, Fiona M Fennessy, Nicole Sponer, Diana Johnson, Joanne Laycock, Seema Shafi, Justyna Czyzewska-Khan, Andrew Rowan, Tim Chambers, Nik Matthews, Samra Turajlic, Crispin Hiley, Siow Ming Lee, Martin D Forster, Tanya Ahmad, Mary Falzon, Elaine Borg, David Lawrence, Martin Hayward, Shyam Kolvekar, Nikolaos Panagiotopoulos, Sam M Janes, Ricky Thakrar, Asia Ahmed, Fiona Blackhall, Yvonne Summers, Dina Hafez, Ashwini Naik, Apratim Ganguly, Stephanie Kareht, Rajesh Shah, Leena Joseph, Anne Marie Quinn, Phil Crosbie, Babu Naidu, Gary Middleton, Gerald Langman, Simon Trotter, Marianne Nicolson, Hardy Remmen, Keith Kerr, Mahendran Chetty, Lesley Gomersall, Dean A Fennell, Apostolos Nakas, Sridhar Rathinam, Girija Anand, Sajid Khan, Peter Russell, Veni Ezhil, Babikir Ismail, Melanie Irvin-Sellers, Vineet Prakash, Jason F Lester, Malgorzata Kornaszewska, Richard Attanoos, Haydn Adams, Helen Davies, Dahmane Oukrif, Ayse U Akarca, John A Hartley, Helen L Lowe, Sara Lock, Natasha Iles, Harriet Bell, Yenting Ngai, Greg Elgar, Zoltan Szallasi, Roland F Schwarz, Javier Herrero, Aengus Stewart, Sergio A Quezada, Peter Van Loo, Caroline Dive, C Jimmy Lin, Matthew Rabinowitz, Hugo Jwl Aerts, Allan Hackshaw, Jacqui A Shaw, Bernhard G Zimmermann, Charles Swanton
The early detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a tumour-specific phylogenetic approach to ctDNA profiling in the first 100 TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28445464/burgess-shale-fossils-illustrate-the-origin-of-the-mandibulate-body-plan
#5
Cédric Aria, Jean-Bernard Caron
Retracing the evolutionary history of arthropods has been one of the greatest challenges in biology. During the past decade, phylogenetic analyses of morphological and molecular data have coalesced towards the conclusion that Mandibulata, the most diverse and abundant group of animals, is a distinct clade from Chelicerata, in that its members possess post-oral head appendages specialized for food processing, notably the mandible. The origin of the mandibulate body plan, however, which encompasses myriapods, crustaceans and hexapods, has remained poorly documented...
April 26, 2017: Nature
https://www.readbyqxmd.com/read/28445096/protection-from-oxidative-stress-in-immunocytes-of-the-colonial-ascidian-botryllus-schlosseri-transcript-characterization-and-expression-studies
#6
Nicola Franchi, Francesca Ballin, Loriano Ballarin
Botryllus schlosseri is a cosmopolitan colonial ascidian that undergoes cyclical generation changes, or take-overs, during which adult zooids are resorbed and replaced by their buds. At take-over, adult tissues undergo diffuse apoptosis and effete cells are massively ingested by circulating phagocytes, with a consequent increase in oxygen consumption and in production of reactive oxygen species (ROS). The latter are responsible for the death of phagocytes involved in the clearance of apoptotic cells and corpses by phagocytosis-induced apoptosis...
February 2017: Biological Bulletin
https://www.readbyqxmd.com/read/28444865/a-high-rate-of-hiv-1-acquisition-post-immigration-among-migrants-in-sweden-determined-by-a-cd4-t-cell-decline-trajectory-model
#7
J Brännström, A Sönnerborg, V Svedhem, U Neogi, G Marrone
OBJECTIVES: There is a lack of knowledge about the extent to which migrants become HIV-1 infected after arrival in European countries. The objective of this study was to assess the extent to which migrants to Sweden become HIV-1 infected post immigration using a CD4 T-cell decline trajectory model. METHODS: All migrants (n = 2268) who were ≥ 15 years old, were diagnosed with HIV-1 infection in the period 1983-2013, had a known year of arrival in Sweden, did not have primary HIV infection and were not infected via mother-to-child transmission were included in the study...
April 26, 2017: HIV Medicine
https://www.readbyqxmd.com/read/28444795/systematics-and-molecular-phylogeny-of-the-ciliate-genus-pseudokeronopsis-ciliophora-hypotrichia
#8
Ju Li, Zifeng Zhan, Kuidong Xu
A still challenging study on ciliate systematics is to clarify the taxonomic and phylogenetic confusions of the fascinating pigmented Pseudokeronopsis species because of their high inter-specific similarities. We evaluated the identities and internal relationships within Pseudokeronopsis based on morphological descriptions in combination with the 18S and ITS-5.8S rDNA genetic distances, ITS2 secondary structures and phylogenetic analyses. Results showed that (1) Pseudokeronopsis pararubra, a species ever synonymized as Pseudokeronopsis carnea, is a valid species; (2) most Chinese populations identified as Pseudokeronopsis rubra represent a new species namely Pseudokeronopsis songi sp...
April 26, 2017: Journal of Eukaryotic Microbiology
https://www.readbyqxmd.com/read/28444606/species-evolution-and-quality-evaluation-of-four-coptis-herbal-medicinal-materials-in-southwest-china
#9
Hanting Chen, Gang Fan, Yang He
Coptis herbs, which are important herbal medicinal materials, are the dried rhizomes of various plants. In China's herbal market, drying herbs can severely influence morphological markers such as shape, color, and odor, which make consumers difficult to precisely identify the herbs and effectively evaluate the quality. Here, we present the phylogenetic analysis of four Coptis herbal medicinal materials based on internal transcribed spacer sequences. C. chinensis, C. omeiensis, C. deltoidea and C. teeta constituted a monophyletic group...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444595/cloning-and-characterization-of-auxin-efflux-carrier-genes-ecpin1a-and-ecpin1b-from-finger-millet-eleusine-coracana-l
#10
Tapan Kumar Mohanta, Hanhong Bae
Auxin signaling events in plants play important role in developmental regulation as well as gravitropic responses and plays crucial role in the development of root, lateral root and root hairs. The gene that is known to be most important in the development of root, lateral root and root hairs is commonly known as auxin efflux carrier (PIN). Being commonly known as orphan plant, the genome sequence of Eleusine coracana is not known yet, and hence it was very difficult to conduct advanced research in root development in this plant...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444592/molecular-characterization-of-phytoplasma-of-16sri-b-group-association-with-acalypha%C3%A2-indica-in-india
#11
Ajay K Tiwari, M S Khan, Pradeep Kumar, Akhilesh Tiwari
The typical phytoplasma symptoms of little leaf, yellowing, chlorosis, witches' broom, and stunting growth were observed on Acalypha indica plants during the field survey conducted at Lucknow and surrounding districts in year 2015-2016. To confirm the association and possibility of phytoplasma etiology, PCR assays were performed using universal primer pairs (P1/P6) and nested primer pairs (R16F2n/R2) in a total of five diseased samples along with control. A ~1.2 Kb amplicon was observed in nested PCR assay in diseased sample; however, no band was observed in control sample...
May 2017: 3 Biotech
https://www.readbyqxmd.com/read/28444538/occurrence-and-genetic-diversity-analysis-of-apple-stem-pitting-virus-isolated-from-apples-in-china
#12
Guo-Jun Hu, Ya-Feng Dong, Zun-Ping Zhang, Xu-Dong Fan, Fang Ren, Zhengnan Li
Two primer pairs were used to detect apple stem pitting virus (ASPV) using a reverse transcription (RT)-PCR test. 82 out of the 141 randomly collected samples, from ten orchards in five provinces and regions of China, tested positive. In the positive samples forty-five (55%) were infected by ASPV and two other viruses. The full coat protein (CP) and the triple gene block (TGB) gene 1, 2 and 3 of partial ASPV isolates were subsequently cloned. The nucleotide and amino acid identities of 39 CP sequence variants from 31 Chinese apple samples were compared with that of previously reported ASPV isolates and were 67...
April 25, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28444444/bioinformatic-and-expression-analyses-on-carotenoid-dioxygenase-genes-in-fruit-development-and-abiotic-stress-responses-in-fragaria-vesca
#13
Yong Wang, Guanqun Ding, Tingting Gu, Jing Ding, Yi Li
Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved...
April 25, 2017: Molecular Genetics and Genomics: MGG
https://www.readbyqxmd.com/read/28444351/comparative-genomic-analysis-of-set-domain-family-reveals-the-origin-expansion-and-putative-function-of-the-arthropod-specific-smyda-genes-as-histone-modifiers-in-insects
#14
Feng Jiang, Qing Liu, Yanli Wang, Jie Zhang, Huimin Wang, Tianqi Song, Meiling Yang, Xianhui Wang, Le Kang
The SET domain is an evolutionarily conserved motif present in histone lysine methyltransferases, which are important in the regulation of chromatin and gene expression in animals. In this study, we searched for SET domain-containing genes (SET genes) in all of the 147 arthropod genomes sequenced at the time of carrying out this experiment to understand the evolutionary history by which SET domain have evolved in insects. Phylogenetic and ancestral state reconstruction analysis revealed an arthropod-specific SET gene family, named SmydA, which is ancestral to arthropod animals and specifically diversified during insect evolution...
April 22, 2017: GigaScience
https://www.readbyqxmd.com/read/28444190/biological-aging-and-the-human-gut-microbiota
#15
Vincent J Maffei, Sangkyu Kim, Eugene Blanchard, Meng Luo, S Michal Jazwinski, Christopher M Taylor, David A Welsh
The human gastrointestinal microbiota plays a key homeostatic role in normal functioning of physiologic processes commonly undermined by aging. We used a previously validated 34-item frailty index (FI34) to identify changes in gut microbiota community structure associated with biological age of community-dwelling adults. Stool 16S rRNA cDNA libraries from 85 subjects ranging in age (43-79) and FI34 score (0-0.365) were deep sequenced, denoised, and clustered using DADA2. Subject biological age but not chronological age correlated with a decrease in stool microbial diversity...
April 25, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28443999/first-reported-enterovirus-d68-infection-in-pediatric-patients-from-the-caribbean-region-evidence-of-spread-from-the-u-s-outbreak
#16
SueMin Nathaniel, Shalauddin Ahmed, Jennifer Wilson, Cristina Gutierrez, Dave D Chadee, Babatunde Olowokure, Pablo M de Salazar
The 2014 enterovirus D68 (EV-D68) outbreak in the United States raised concerns about the introduction of the virus in the Caribbean region. The objective of this study was to provide rapid evidence of the introduction of EV-D68 strains in the Caribbean region during the 2014 outbreak in the United States, using a relatively simple phylogenetic approach. From October 2014 to May 2015, four EV-D68 cases from two countries (Bermuda and Dominica) were detected at the regional referral laboratory at the Caribbean Public Health Agency (Port of Spain, Trinidad and Tobago) based on molecular testing of respiratory specimens...
April 20, 2017: Revista Panamericana de Salud Pública, Pan American Journal of Public Health
https://www.readbyqxmd.com/read/28443724/genetic-diversity-of-hiv-1-gene-vif-among-treatment-na%C3%A3-ve-brazilians
#17
Fabiola Villanova, Marta Barreiros, Luiz Mario Janini, Ricardo Sobhie Diaz, Elcio Leal
HIV-1 has the Vif protein, which binds to human antiviral proteins APOBEC3 to form complexes to be degraded by cellular proteolysis. To further explore HIV-1 diversity at the population level, we analyzed blood samples from 317 treatment-naïve patients in Brazil. Here, we explored the correlations of Vif polymorphisms with clinical parameters of the patients and found that mutation K22H is associated with low CD4+ cell counts and higher viral loads. Phylogenetic analysis of the vif gene indicated that subtype B was predominant in ∼77% (243/317) of the patients, followed by HIV-1 F ∼18% (56/317) and subtype C ∼4% (12/317); five samples were BF recombinants (∼1% of patients), and one was an AG recombinant...
April 26, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28443684/genetic-variants-of-hiv-type-1-in-msm-in-russia
#18
Elena Kazennova, Vita Laga, Konstantin Gromov, Natalya Lebedeva, Eugenia Zhukova, Alexander Pronin, Liliya Grezina, Nataliya Dement'eva, Andrey Shemshura, Marina Bobkova
The MSM population infected with HIV is poorly studied in Russia due to stigma and discrimination. In the first years of the HIV epidemic, the only HIV genetic variant that circulated among MSM was subtype B, usually acquired abroad. Meanwhile, the massive epidemic of HIV in Russia was caused by a highly homogenic subtype A variant, AFSU (A6), and spread mainly among drug users. In this study, 155 HIV pol sequences from MSM collected during the period of 2006-2016 were analyzed. Phylogenetic analysis found that 19...
April 26, 2017: AIDS Research and Human Retroviruses
https://www.readbyqxmd.com/read/28443126/genome-wide-identification-characterization-and-expression-analysis-of-pht1-phosphate-transporters-in-wheat
#19
Wan Teng, Yan-Yan Zhao, Xue-Qiang Zhao, Xue He, Wen-Ying Ma, Yan Deng, Xin-Ping Chen, Yi-Ping Tong
The PHT1 family of phosphate (Pi) transporters mediates phosphorus (P) uptake and re-mobilization in plants. A genome-wide sequence analysis of PHT1 genes in wheat (Triticum aestivum) was conducted, and their expression locations and responses to P availability were further investigated. We cloned 21 TaPHT1 genes from the homologous alleles at TaPHT1.1 to 1.10 through screening a BAC library and amplifying genomic sequences. The TaPHT1 transporters were clustered into five branches in the phylogenetic tree of PHT1 proteins, and the TaPHT1 genes from a given branch shared high similarities in sequences, expression locations, and responses to P availability...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28443114/tadir1-2-a-wheat-ortholog-of-lipid-transfer-protein-atdir1-contributes-to-negative-regulation-of-wheat-resistance-against-puccinia-striiformis-f-sp-tritici
#20
Soyed M Ahmed, Peng Liu, Qinghe Xue, Changan Ji, Tuo Qi, Jia Guo, Jun Guo, Zhensheng Kang
Very few LTPs have been shown to act through plasma membrane receptors or to be involved in the hypersensitive response (HR). DIR1, a new type of plant LTP interacts with lipids in vitro, moves to distant tissues during systemic acquired resistance (SAR) and therefore is thought to be involved in long-distance signaling during SAR. However, the exact functions of DIR1 orthologs in cereal species under biotic and abiotic stresses have not been thoroughly defined. In this study, a novel wheat ortholog of the DIR1 gene, TaDIR1-2, was isolated from Suwon11, a Chinese cultivar of wheat and functionally characterized...
2017: Frontiers in Plant Science
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