Database : MEDLINE
Search on : trees [Words]
References found : 171985 [refine]
Displaying: 1 .. 10   in format [Detailed]

page 1 of 17199 go to page                         

  1 / 171985 MEDLINE  
              next record last record
select
to print
Photocopy
Full text

[PMID]: 29506565
[Au] Autor:Sauvage T; Plouviez S; Schmidt WE; Fredericq S
[Ad] Address:Department of Biology, University of Louisiana at Lafayette, 410 E. Saint Mary Boulevard, Lafayette, LA, 70503, USA. tomsauv@gmail.com.
[Ti] Title:TREE2FASTA: a flexible Perl script for batch extraction of FASTA sequences from exploratory phylogenetic trees.
[So] Source:BMC Res Notes;11(1):164, 2018 Mar 05.
[Is] ISSN:1756-0500
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:OBJECTIVE: The body of DNA sequence data lacking taxonomically informative sequence headers is rapidly growing in user and public databases (e.g. sequences lacking identification and contaminants). In the context of systematics studies, sorting such sequence data for taxonomic curation and/or molecular diversity characterization (e.g. crypticism) often requires the building of exploratory phylogenetic trees with reference taxa. The subsequent step of segregating DNA sequences of interest based on observed topological relationships can represent a challenging task, especially for large datasets. RESULTS: We have written TREE2FASTA, a Perl script that enables and expedites the sorting of FASTA-formatted sequence data from exploratory phylogenetic trees. TREE2FASTA takes advantage of the interactive, rapid point-and-click color selection and/or annotations of tree leaves in the popular Java tree-viewer FigTree to segregate groups of FASTA sequences of interest to separate files. TREE2FASTA allows for both simple and nested segregation designs to facilitate the simultaneous preparation of multiple data sets that may overlap in sequence content.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:In-Process
[do] DOI:10.1186/s13104-018-3268-y

  2 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29506465
[Au] Autor:Badal VD; Kundrotas PJ; Vakser IA
[Ad] Address:Center for Computational Biology and Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas, 66047, USA.
[Ti] Title:Natural language processing in text mining for structural modeling of protein complexes.
[So] Source:BMC Bioinformatics;19(1):84, 2018 Mar 05.
[Is] ISSN:1471-2105
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:BACKGROUND: Structural modeling of protein-protein interactions produces a large number of putative configurations of the protein complexes. Identification of the near-native models among them is a serious challenge. Publicly available results of biomedical research may provide constraints on the binding mode, which can be essential for the docking. Our text-mining (TM) tool, which extracts binding site residues from the PubMed abstracts, was successfully applied to protein docking (Badal et al., PLoS Comput Biol, 2015; 11: e1004630). Still, many extracted residues were not relevant to the docking. RESULTS: We present an extension of the TM tool, which utilizes natural language processing (NLP) for analyzing the context of the residue occurrence. The procedure was tested using generic and specialized dictionaries. The results showed that the keyword dictionaries designed for identification of protein interactions are not adequate for the TM prediction of the binding mode. However, our dictionary designed to distinguish keywords relevant to the protein binding sites led to considerable improvement in the TM performance. We investigated the utility of several methods of context analysis, based on dissection of the sentence parse trees. The machine learning-based NLP filtered the pool of the mined residues significantly more efficiently than the rule-based NLP. Constraints generated by NLP were tested in docking of unbound proteins from the DOCKGROUND X-ray benchmark set 4. The output of the global low-resolution docking scan was post-processed, separately, by constraints from the basic TM, constraints re-ranked by NLP, and the reference constraints. The quality of a match was assessed by the interface root-mean-square deviation. The results showed significant improvement of the docking output when using the constraints generated by the advanced TM with NLP. CONCLUSIONS: The basic TM procedure for extracting protein-protein binding site residues from the PubMed abstracts was significantly advanced by the deep parsing (NLP techniques for contextual analysis) in purging of the initial pool of the extracted residues. Benchmarking showed a substantial increase of the docking success rate based on the constraints generated by the advanced TM with NLP.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[St] Status:In-Data-Review
[do] DOI:10.1186/s12859-018-2079-4

  3 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29471079
[Au] Autor:Bell CD; Gonzalez LA
[Ad] Address:Department of Biological Sciences, University of New Orleans, 2000 Lakeshore Drive, New Orleans, LA 70148, USA. Electronic address: cdbell1@uno.edu.
[Ti] Title:Exploring the utility of "next-generation" sequence data on inferring the phylogeny of the South American Valeriana (Valerianaceae).
[So] Source:Mol Phylogenet Evol;123:44-49, 2018 Feb 19.
[Is] ISSN:1095-9513
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:This study aimed to investigate the phylogenetic utility of genotyping-by-sequencing (GBS) data in the southern South American subclade of Valerianaceae (Dipsacales). The variety of forms that has arisen in this clade, presumably over the past 5-10 million years, has all the signatures of an adaptive and rapid radiation. While the phylogeny of Valerianaceae has received a great deal of attention in the last decade, species relationships have been hard to resolve using traditional phylogenetic markers. Here, we collected high-throughput genomic sequence data from reduced-representation libraries obtained through GBS protocols. Putative orthologs were identified using within- and among-sample clustering using the computer software pyRAD. We recovered over 3000 loci for 14 species of southern South AmericanValeriana,with 140 loci present across all samples.We analyzed a set of phylogenetic trees generated from each locus using maximum likelihood methods, as well as multispecies coalescent (∗BEAST) methods. For comparative purposes, we also used a supermatrix approach to infer the phylogeny for these taxa. Across different methods and data sets, we recovered consistent relationships for the southern South American valerians that we sampled with varying degrees of support.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  4 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29408693
[Au] Autor:Beghalem H; Aliliche K; Landoulsi A
[Ad] Address:Laboratory of Biochemistry and Molecular Biology, Carthage University, UR13ES34 Research Unit, Faculty of Sciences of Bizerte, Zarzouna, 7021, Bizerte, Tunisia. Electronic address: beghalemhamida@gmail.com.
[Ti] Title:Identification and sequence analysis of putative Sulla species nod factor receptor.
[So] Source:Microb Pathog;117:88-92, 2018 Feb 02.
[Is] ISSN:1096-1208
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:In legumes, LysM domains of receptors-like kinases (RLKs) mediate rhizobial NFs perception; which are required for infection and establishment of symbiosis without triggering the host immune response. In this study, we identify the LysM extracellular domain sequences of putative Sulla species Nod factor receptors (S. pallida, S. capitata and S. coronaria). The Blast search displayed high identity percentages with genes encoding LjNFR5-like of several legumes. Phylogenetic trees were built using the partial nod factor receptor and predicted amino acid sequences, which grouped Sulla in a separate clade. The multiple alignments of the LysM2 domains revealed that amino acids found to be important in other legume species are not conserved in Sulla species. Further examination of the predicted proteins sequences (LysM2 domain) showed that the three species were different in the two crucial sites for Nod factor perception.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1802
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher

  5 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 28467418
[Au] Autor:Khare S; Nick JA; Zhang Y; Galeano K; Butler B; Khoshbouei H; Rayaprolu S; Hathorn T; Ranum LPW; Smithson L; Golde TE; Paucar M; Morse R; Raff M; Simon J; Nordenskjöld M; Wirdefeldt K; Rincon-Limas DE; Lewis J; Kaczmarek LK; Fernandez-Funez P; Nick HS; Waters MF
[Ad] Address:Department of Neurology, University of Florida, Gainesville, FL, United States of America.
[Ti] Title:A KCNC3 mutation causes a neurodevelopmental, non-progressive SCA13 subtype associated with dominant negative effects and aberrant EGFR trafficking.
[So] Source:PLoS One;12(5):e0173565, 2017.
[Is] ISSN:1932-6203
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:The autosomal dominant spinocerebellar ataxias (SCAs) are a diverse group of neurological disorders anchored by the phenotypes of motor incoordination and cerebellar atrophy. Disease heterogeneity is appreciated through varying comorbidities: dysarthria, dysphagia, oculomotor and/or retinal abnormalities, motor neuron pathology, epilepsy, cognitive impairment, autonomic dysfunction, and psychiatric manifestations. Our study focuses on SCA13, which is caused by several allelic variants in the voltage-gated potassium channel KCNC3 (Kv3.3). We detail the clinical phenotype of four SCA13 kindreds that confirm causation of the KCNC3R423H allele. The heralding features demonstrate congenital onset with non-progressive, neurodevelopmental cerebellar hypoplasia and lifetime improvement in motor and cognitive function that implicate compensatory neural mechanisms. Targeted expression of human KCNC3R423H in Drosophila triggers aberrant wing veins, maldeveloped eyes, and fused ommatidia consistent with the neurodevelopmental presentation of patients. Furthermore, human KCNC3R423H expression in mammalian cells results in altered glycosylation and aberrant retention of the channel in anterograde and/or endosomal vesicles. Confirmation of the absence of plasma membrane targeting was based on the loss of current conductance in cells expressing the mutant channel. Mechanistically, genetic studies in Drosophila, along with cellular and biophysical studies in mammalian systems, demonstrate the dominant negative effect exerted by the mutant on the wild-type (WT) protein, which explains dominant inheritance. We demonstrate that ocular co-expression of KCNC3R423H with Drosophila epidermal growth factor receptor (dEgfr) results in striking rescue of the eye phenotype, whereas KCNC3R423H expression in mammalian cells results in aberrant intracellular retention of human epidermal growth factor receptor (EGFR). Together, these results indicate that the neurodevelopmental consequences of KCNC3R423H may be mediated through indirect effects on EGFR signaling in the developing cerebellum. Our results therefore confirm the KCNC3R423H allele as causative for SCA13, through a dominant negative effect on KCNC3WT and links with EGFR that account for dominant inheritance, congenital onset, and disease pathology.
[Mh] MeSH terms primary: Receptor, Epidermal Growth Factor/metabolism
Shaw Potassium Channels/genetics
Spinocerebellar Degenerations/genetics
[Mh] MeSH terms secundary: Animals
CHO Cells
Cricetinae
Cricetulus
Drosophila melanogaster
Female
Humans
Male
Pedigree
Protein Transport
[Pt] Publication type:JOURNAL ARTICLE
[Nm] Name of substance:0 (KCNC3 protein, human); 0 (Shaw Potassium Channels); EC 2.7.10.1 (Receptor, Epidermal Growth Factor)
[Em] Entry month:1709
[Cu] Class update date: 180311
[Lr] Last revision date:180311
[Js] Journal subset:IM
[Da] Date of entry for processing:170504
[St] Status:MEDLINE
[do] DOI:10.1371/journal.pone.0173565

  6 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29524097
[Au] Autor:Grünewald S; Long Y; Wu Y
[Ad] Address:CAS-MPG Partner Institute for Computational Biology, Chinese Academy of Sciences Key Laboratory of Computational Biology, 320 Yue Yang Road, Shanghai, 200032, China.
[Ti] Title:Reconstructing Unrooted Phylogenetic Trees from Symbolic Ternary Metrics.
[So] Source:Bull Math Biol;, 2018 Mar 09.
[Is] ISSN:1522-9602
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:Böcker and Dress (Adv Math 138:105-125, 1998) presented a 1-to-1 correspondence between symbolically dated rooted trees and symbolic ultrametrics. We consider the corresponding problem for unrooted trees. More precisely, given a tree T with leaf set X and a proper vertex coloring of its interior vertices, we can map every triple of three different leaves to the color of its median vertex. We characterize all ternary maps that can be obtained in this way in terms of 4- and 5-point conditions, and we show that the corresponding tree and its coloring can be reconstructed from a ternary map that satisfies those conditions. Further, we give an additional condition that characterizes whether the tree is binary, and we describe an algorithm that reconstructs general trees in a bottom-up fashion.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:Publisher
[do] DOI:10.1007/s11538-018-0413-7

  7 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29523202
[Au] Autor:Lagrée AC; Rouxel C; Kevin M; Dugat T; Girault G; Durand B; Pfeffer M; Silaghi C; Nieder M; Boulouis HJ; Haddad N
[Ad] Address:UMR BIPAR, Ecole Nationale Vétérinaire d'Alfort, Anses, INRA, Université Paris-Est, Maisons-Alfort, France.
[Ti] Title:Co-circulation of different A. phagocytophilum variants within cattle herds and possible reservoir role for cattle.
[So] Source:Parasit Vectors;11(1):163, 2018 Mar 09.
[Is] ISSN:1756-3305
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:BACKGROUND: Anaplasma phagocytophilum is a zoonotic tick-borne intracellular alpha-proteobacterium causing tick-borne fever, which leads to significant economic losses in domestic ruminants in Europe. Its epidemiological cycles are complex and reservoir host species of bovine strains have not yet been identified. Given that little genetic information is available on strains circulating within a defined bovine environment, our objective was to assess the genetic diversity of A. phagocytophilum obtained from the same farms over time. METHODS: Blood samplings were performed several times in two European herds. In the French herd, 169 EDTA-blood samples were obtained from 115 cows (32 were sampled two to four times). In the German herd, 20 cows were sampled six times (120 EDTA-blood samples). The presence of A. phagocytophilum DNA was assessed using a qPCR targeting msp2. The positive DNA samples underwent MLST at nine genetic markers (typA, ctrA, msp4, pleD, recG, polA, groEL, gyrA, and ankA). For each locus, sequences were aligned with available bacterial sequences derived from cattle, horse, dog, and roe deer hosts, and concatenated neighbor joining trees were constructed using three to six loci. RESULTS: Around 20% (57/289) of samples were positive. Forty positive samples from 23 French and six German cows (11 of them being positive at two time points) were sequenced. Six loci (typA, ctrA, msp4, pleD, recG, and polA) allowed to build concatenated phylogenetic trees, which led to two distinct groups of bovine variants in the French herd (hereafter called A and B), whereas only group A was detected in the German herd. In 42% of French samples, double chromatogram peaks were encountered in up to four loci. Eleven cows were found infected three weeks to 17 months after first sampling and harboured a new variant belonging to one or the other group. CONCLUSIONS: Our results demonstrate the occurrence of two major bovine strain groups and the simultaneous infection of single cows by more than one A. phagocytophilum strain. This challenges the role of cattle as reservoirs for A. phagocytophilum. This role may be facilitated via long-term bacterial persistence in individual cows and active circulation at the herd scale.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180310
[Lr] Last revision date:180310
[St] Status:In-Data-Review
[do] DOI:10.1186/s13071-018-2661-7

  8 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29522989
[Au] Autor:Furze ME; Trumbore S; Hartmann H
[Ad] Address:Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA 02138, USA. Electronic address: mfurze@fas.harvard.edu.
[Ti] Title:Detours on the phloem sugar highway: stem carbon storage and remobilization.
[So] Source:Curr Opin Plant Biol;43:89-95, 2018 Mar 06.
[Is] ISSN:1879-0356
[Cp] Country of publication:England
[La] Language:eng
[Ab] Abstract:For trees to survive, they must allocate resources between sources and sinks to maintain proper function. The vertical transport pathway in tree stems is essential for carbohydrates and other solutes to move between the canopy and the root system. To date, research and models emphasize the role of tree stems as 'express' sugar highways. However, recent investigations using isotopic markers suggest that there is considerable storage and exchange of phloem-transported sugars with older carbon (C) reserves within the stem. Thus, we suggest that stems play an important role not only in long-distance transport, but also in the regulation of the tree's overall C balance. A quantitative partitioning of stem C inputs among storage and sinks, including tissue growth, respiration, and export to roots, is still lacking. Combining methods to better quantify the dynamics and controls of C storage and remobilization in the stem will help to resolve central questions of allocation and C balance in trees.
[Pt] Publication type:JOURNAL ARTICLE; REVIEW
[Em] Entry month:1803
[Cu] Class update date: 180309
[Lr] Last revision date:180309
[St] Status:Publisher

  9 / 171985 MEDLINE  
              first record previous record next record last record
select
to print
Photocopy
Full text

[PMID]: 29522840
[Au] Autor:Hunt ER; Kendall C; Stanbury E; Sendova-Franks AB; Franks NR
[Ad] Address:School of Biological Sciences, University of Bristol, BS8 1TQ, UK. Electronic address: edmund.hunt@bristol.ac.uk.
[Ti] Title:Two route landmarks are more useful to navigating ant colonies when they are dissimilar.
[So] Source:Behav Processes;, 2018 Mar 06.
[Is] ISSN:1872-8308
[Cp] Country of publication:Netherlands
[La] Language:eng
[Ab] Abstract:Visual landmarks are important navigational aids to many animals, and when more than one is available their juxtaposition can convey valuable new information to a navigator about progress toward a goal, depending on the landmarks' comparative distinctiveness. We investigated the effect of presenting rock ant colonies (Temnothorax albipennis) with identical horizontal landmarks either side of their route, versus one horizontal landmark paired with a sloping landmark, as they navigated to a new nest site. Our findings suggest that ants can obtain more navigational information from a combination of dissimilar landmarks: the average tortuosity of the route taken between old and new nests was significantly lower when a horizontal landmark was paired with a monotonically downward sloping landmark (the paths were more direct). The impact on available navigational information from the similarity or dissimilarity of nearby landmarks is likely made through more distinctive visual panoramas, and could be an influential factor in individual and collective animal decision-making about which routes are followed. Furthermore, the effect of landmark complementarity may be relevant to a wide range of species, such as navigating honey bees relying on multiple landmarks, for example a straight line of trees and the sloping brow of a hill.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180309
[Lr] Last revision date:180309
[St] Status:Publisher

  10 / 171985 MEDLINE  
              first record previous record
select
to print
Photocopy
Matushima, Eliana R
Full text

[PMID]: 29522766
[Au] Autor:Cesar MO; Matushima ER; Zwarg T; de Oliveira AS; Sanches TC; Joppert AM; Keid LB; Oliveira TMFS; Ferreira HL; Llano HAB; Konradt G; Bianchi MV; Gregori F; Gondim LFP; Soares RM
[Ad] Address:Department of Pathology, University of São Paulo, São Paulo, SP, Brazil.
[Ti] Title:Multilocus characterization of Sarcocystis falcatula-related organisms isolated in Brazil supports genetic admixture of high diverse SAG alleles among the isolates.
[So] Source:Exp Parasitol;, 2018 Mar 06.
[Is] ISSN:1090-2449
[Cp] Country of publication:United States
[La] Language:eng
[Ab] Abstract:In a previous study in Brazil, six isolates of Sarcocystis spp. recovered from budgerigars fed sporocysts excreted by opossums of the genus Didelphis were characterized by means of sequencing fragments of gene coding cytochrome B (CYTB), internal transcribed spacer 1 (ITS1), and surface antigen genes (SAG2, SAG3 and SAG4). The isolates shared identical ITS1 and CYTB sequences, but differed at SAG2, SAG3 and SAG4: three allele variants of SAG2, 3 allele variants of SAG3 and 2 allele variants of SAG4 were encountered in three multilocus genotypes (MLGs) (MLG1, MLG2, and MLG3). At ITS1 and CYTB, all the isolates from budgerigars were identical to the Sarcocystis falcatula-like isolate 59-2016-RS-BR that was detected in a barefaced ibis (Phimosus infuscatus) causing necrotizing meningoencephalitis in Brazil. At ITS1 locus, all the above isolates were clearly distinct from Sarcocystis neurona, Sarcocystis falcatula, Sarcocystis lindsayi, and Sarcocystis speeri, the four known species of Sarcocystis that use opossums of the genus Didelphis as definitive hosts. Here, we replicated the experiment above to identify additional MLGs or other species of Sarcocystis. Fifteen budgerigars were experimentally infected with sporocysts of Sarcocystis spp. from 12 opossums of the genus Didelphis. All the birds died 9-19 days after infection and tissue samples containing merozoites and schizonts of Sarcocystis spp. were recovered. Fractions of sequences coding for 18S ribosomal RNA gene (18S), CYTB, ITS1, SAG2, SAG3 and SAG4 were PCR amplified and sequenced from the infected lungs. In addition, fractions of 18S, SAG2, SAG3 and SAG4 were sequenced from the isolate 59-2016-RS-BR and fractions of 18S were sequenced from the six isolates from budgerigars described above. From the results, all the isolates shared identical 18S, ITS1 and CYTB sequences. Among the 15 new isolates from budgerigars, three allele variants of SAG2, 3 allele variants of SAG3 and 2 allele variants of SAG4 were encountered in five MLGs, of which four were novel (MLG1, MLG4, MLG5, MLG6 and MLG7). Isolate 59-2016-RS-BR was assigned to an eighth MLG (MLG8). Molecular data pointed that Sarcocystis assigned to MLGs 1 to 8 are variants of the same species, but the SAG-based trees of the isolates conflicted, which supports genetic admixture among them. The sarcocystinae studied have high diversity of SAG alleles per locus and the correlation of such an abundant variety of SAG alleles to host specificity and pathogenicity needs to be assessed. Remains to be elucidated if the parasites studied here and S. falcatula are variants of the same species that have diverged to the point of possessing differences at ITS1 level, but that are still capable of exchanging genes.
[Pt] Publication type:JOURNAL ARTICLE
[Em] Entry month:1803
[Cu] Class update date: 180309
[Lr] Last revision date:180309
[St] Status:Publisher


page 1 of 17199 go to page                         
   


Refine the search
  Database : MEDLINE Advanced form   

    Search in field  
1  
2
3
 
           



Search engine: iAH v2.6 powered by WWWISIS

BIREME/PAHO/WHO - Latin American and Caribbean Center on Health Sciences Information