New Genes for Phylogenetic Studies of Lichenized Fungi: Glyceraldehyde-3-Phosphate Dehydrogenase and Beta-Tubulin Genes

2002 ◽  
Vol 34 (3) ◽  
pp. 237-246 ◽  
Author(s):  
Leena Myllys ◽  
Soili Stenroos ◽  
Arne Thell
Keyword(s):  
Ssu Rdna ◽  
Lichenized Fungi ◽  
Beta Tubulin ◽  
Data Set ◽  
Tubulin Genes ◽  
New Genes ◽  
Phylogenetic Studies ◽  
Pcr Product ◽  
Codon Positions ◽  
Relationship Of

AbstractPrimers for amplification and sequencing of partial glyceraldehyde-3-phosphate dehydrogenase (gpd) gene were designed for lichenized fungi. The 5’ gpd primer is most probably fungal specific, since a BLAST search in GenBank found identical sequences only from ascomycetous taxa, whereas the 3’ gpd primer was more universal. Utility of the gpd primers and previously designed beta-tubulin primers was tested in nine lichen taxa. Both the gpd and beta-tubulin primer pairs amplified in most of the taxa examined: the gpd primers generated a c. 1100 nucleotide fragment, whereas the PCR product obtained from the beta-tubulin primers was c. 900 nucleotides long. The gpd amplification products of Cladonia arbuscula and C. rangiferina were sequenced and both were found to contain three introns, the length of which varied between 49 to 83 nucleotides. To examine the applicability of gpd sequences in resolving relationships within Ascomycota, trees were calculated from 22 fungal gpd sequences obtained from GenBank together with the two Cladonia sequences using parsimony jackknifing. The gpd tree was compared with the SSU rDNA tree of the respective species (or genera). A similar analysis of the beta-tubulin gene was not performed, because only a few beta-tublin sequences from the same taxa were available in GenBank. The gpd tree was well resolved but in conflict with the SSU rDNA tree. In contrast to the SSU rDNA tree, the gpd tree did not support the monophyly of the Ascomycota. Analysis of the combined data set produced a tree very similar to that of the SSU rDNA data. However, the relationship of Lecanorales to the other orders remained unresolved. Even though gpd and beta-tubulin are highly conserved proteins, the third codon positions and introns are variable and both genes have the potential for inferring phylogenetic relationships at the lower taxonomic levels in the lichenized fungi. The two genes may be useful even below species level, depending on the species investigated.

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

scholarly journals The Complete DNA Sequence of the Mitochondrial Genome of a “Living Fossil,” the Coelacanth (Latimeria chalumnae)

Genetics ◽  
1997 ◽  
Vol 146 (3) ◽  
pp. 995-1010 ◽  
Author(s):  
Rafael Zardoya ◽  
Axel Meyer
Keyword(s):  
Mitochondrial Genome ◽  
Tandem Repeats ◽  
Phylogenetic Analyses ◽  
Large Data ◽  
Molecular Data ◽  
Phylogenetic Position ◽  
Data Set ◽  
Living Fossil ◽  
Latimeria Chalumnae ◽  
Relationship Of

The complete nucleotide sequence of the 16,407-bp mitochondrial genome of the coelacanth (Latimeria chalumnae) was determined. The coelacanth mitochondrial genome order is identical to the consensus vertebrate gene order which is also found in all ray-finned fishes, the lungfish, and most tetrapods. Base composition and codon usage also conform to typical vertebrate patterns. The entire mitochondrial genome was PCR-amplified with 24 sets of primers that are expected to amplify homologous regions in other related vertebrate species. Analyses of the control region of the coelacanth mitochondrial genome revealed the existence of four 22-bp tandem repeats close to its 3′ end. The phylogenetic analyses of a large data set combining genes coding for rRNAs, tRNA, and proteins (16,140 characters) confirmed the phylogenetic position of the coelacanth as a lobe-finned fish; it is more closely related to tetrapods than to ray-finned fishes. However, different phylogenetic methods applied to this largest available molecular data set were unable to resolve unambiguously the relationship of the coelacanth to the two other groups of extant lobe-finned fishes, the lungfishes and the tetrapods. Maximum parsimony favored a lungfish/coelacanth or a lungfish/tetrapod sistergroup relationship depending on which transversion:transition weighting is assumed. Neighbor-joining and maximum likelihood supported a lungfish/tetrapod sistergroup relationship.

Tandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii

1983 ◽  
Vol 3 (6) ◽  
pp. 1070-1076
Author(s):  
S M Landfear ◽  
D McMahon-Pratt ◽  
D F Wirth
Keyword(s):  
Tandem Repeat ◽  
Blot Hybridization ◽  
Protozoan Parasite ◽  
Southern Blot Hybridization ◽  
Beta Tubulin ◽  
Developmentally Regulated ◽  
Alpha Tubulin ◽  
Tubulin Genes ◽  
Southern Blot Hybridization Analysis ◽  
Leishmania Enriettii

The arrangement of developmentally regulated alpha- and beta-tubulin genes has been studied in the parasitic protozoan Leishmania enriettii by using Southern blot hybridization analysis. The alpha-tubulin genes occur in a tandem repeat whose monomeric unit may be represented by a 2-kilobase PstI fragment. Similarly, the beta-tubulin genes probably occur in a separate tandem repeat consisting of approximately 4-kilobase units unlinked to the alpha-tubulin repeats.

Molecular Systematics of Tribe Physarieae (Brassicaceae) Based on Nuclear ITS, LUMINIDEPENDENS, and Chloroplast ndhF

2021 ◽  
Author(s):  
Sara Fuentes-Soriano ◽  
Elizabeth A. Kellogg
Keyword(s):  
Sequence Data ◽  
Plastid Dna ◽  
Sister Relationship ◽  
Data Set ◽  
Woody Perennial ◽  
History Of ◽  
Nuclear Its ◽  
Phylogenetic Framework ◽  
Phylogenetic Hypotheses ◽  
Relationship Of

Physarieae is a small tribe of herbaceous annual and woody perennial mustards that are mostly endemic to North America, with its members including a large amount of variation in floral, fruit, and chromosomal variation. Building on a previous study of Physarieae based on morphology and ndhF plastid DNA, we reconstructed the evolutionary history of the tribe using new sequence data from two nuclear markers, and compared the new topologies against previously published cpDNA-based phylogenetic hypotheses. The novel analyses included ca. 420 new sequences of ITS and LUMINIDEPENDENS (LD) markers for 39 and 47 species, respectively, with sampling accounting for all seven genera of Physarieae, including nomenclatural type species, and 11 outgroup taxa. Maximum parsimony, maximum likelihood, and Bayesian analyses showed that these additional markers were largely consistent with the previous ndhF data that supported the monophyly of Physarieae and resolved two major clades within the tribe, i.e., DDNLS (Dithyrea, Dimorphocarpa, Nerisyrenia, Lyrocarpa, and Synthlipsis)and PP (Paysonia and Physaria). New analyses also increased internal resolution for some closely related species and lineages within both clades. The monophyly of Dithyrea and the sister relationship of Paysonia to Physaria was consistent in all trees, with the sister relationship of Nerisyrenia to Lyrocarpa supported by ndhF and ITS, and the positions of Dimorphocarpa and Synthlipsis shifted within the DDNLS Clade depending on the employed data set. Finally, using the strong, new phylogenetic framework of combined cpDNA + nDNA data, we discussed standing hypotheses of trichome evolution in the tribe suggested by ndhF.

scholarly journals TARGETED ADVERTISING IN THE BREAKFAST CEREAL INDUSTRY

2017 ◽  
Vol 49 (3) ◽  
pp. 382-399 ◽  
Author(s):  
JOSHUA BERNING ◽  
ADAM N. RABINOWITZ
Keyword(s):  
Product Differentiation ◽  
Food Product ◽  
Television Advertising ◽  
Breakfast Cereal ◽  
Data Set ◽  
Policy Makers ◽  
Relationship Of ◽  
Cereal Industry ◽  
The Relationship ◽  
Insight Into

AbstractWe examine the relationship of product characteristics of ready-to-eat breakfast cereal and targeted television advertising to specific consumer segments. We compile a unique data set that includes brand-packaging characteristics, including on-box games, nutrition information, and cobranding. We find that the relationship of television advertising and a cereal's brand-packaging characteristics varies by target audience. Our results provide insight into understanding how manufacturers strategically utilize branding, packaging, and television advertising. This can help industry and policy makers develop food product advertising policy. This analysis extends to other product markets where extensive product differentiation and promotion are present as well.

scholarly journals Tandem arrangement of tubulin genes in the protozoan parasite Leishmania enriettii.

1983 ◽  
Vol 3 (6) ◽  
pp. 1070-1076 ◽  
Author(s):  
S M Landfear ◽  
D McMahon-Pratt ◽  
D F Wirth
Keyword(s):  
Tandem Repeat ◽  
Blot Hybridization ◽  
Protozoan Parasite ◽  
Southern Blot Hybridization ◽  
Beta Tubulin ◽  
Developmentally Regulated ◽  
Alpha Tubulin ◽  
Tubulin Genes ◽  
Southern Blot Hybridization Analysis ◽  
Leishmania Enriettii

The arrangement of developmentally regulated alpha- and beta-tubulin genes has been studied in the parasitic protozoan Leishmania enriettii by using Southern blot hybridization analysis. The alpha-tubulin genes occur in a tandem repeat whose monomeric unit may be represented by a 2-kilobase PstI fragment. Similarly, the beta-tubulin genes probably occur in a separate tandem repeat consisting of approximately 4-kilobase units unlinked to the alpha-tubulin repeats.

scholarly journals Hubungan Kekerabatan Sapi Aceh dengan Menggunakan Daerah Displacement-loop

2008 ◽  
Vol 8 (2) ◽  
pp. 9-14 ◽  
Author(s):  
Mohd. Agus Nashri Abdullah
Keyword(s):  
Whole Blood ◽  
Bos Indicus ◽  
Loop Analysis ◽  
Blood Samples ◽  
Bos Javanicus ◽  
Pcr Product ◽  
Two Samples ◽  
D Loop ◽  
Whole Blood Samples ◽  
Relationship Of

Relationship of aceh cattle using displacement-loop regionABSTRACT. The aims of this study were to describe relationship of D-loop of mtDNA Aceh cattle which is useful database for conducting conservation programme. The whole blood samples were collected (8 samples for D-loop analysis) from four locations which were Aceh Besar, Pidie, North Aceh regencies and Banda Aceh city. Out group whole blood samples were collected from two samples from Bali cattles (Bali Island), Madura cattle (Madura Island), Pesisir cattle (West Sumatera) respectively and one sample from PO cattle (West Java). Amplification of D-loop sequences of mtDNA with BIDLF and BIDLR primary have PCR product 980 bp. The Data were analyzed using Squint 1.02 and MEGA 4.0 programme. Result of analysis indicate that Aceh cattle have nearer relationship with zebu and there is items inset of genetik Bali cattle (Bos javanicus) at the end sequences start ke-354 situs up to 483, so that the origin Aceh cattle was from Bos indicus which have hybridization with Bos javanicus.

Czech civil sector face-to-face with freelance activism

2016 ◽  
Vol 36 (11/12) ◽  
pp. 774-791
Author(s):  
Pavol Frič ◽  
Martin Vávra
Keyword(s):  
Large Scale ◽  
Civil Society Organizations ◽  
Political Consumerism ◽  
Data Set ◽  
Content Type ◽  
Individual Level ◽  
Face To Face ◽  
Online Activism ◽  
Civil Sector ◽  
Relationship Of

Purpose The purpose of this paper is to answer following question: what is the relationship between member activism performed through civil society organizations (CSOs) and individualized freelance activism (in form of online activism, everyday making, political consumerism or checkbook activism) independent of organizational framework? Is it a relationship of mutual competition or support? Design/methodology/approach Analysis is carried out on data from 2009 questionnaire-based survey on volunteering, representative for adult Czech population. The data set allowed the authors to relate member activism with freelance activism and in case of member activism distinguish the type of organization and the level of its professionalization. Findings Dominant pattern the authors identified in data is mutual support of both types of volunteering documented by significant overlap of these forms of public engagement. The most striking is the overlap for active members of new advocacy NGOs and the weakest for traditional clubs. Regression analysis shows that on an individual level “mixed activism” (compared with “pure freelance activism”) is linked with higher education and higher confidence in civic organizations. Originality/value The civil practice of individualized freelance activism was described and analysed by various authors as an activity of specific types of activist, but there has not yet been any research giving reflection on such a large scale of freelance activism types as in the analysis. The authors set them together in contrast to the member (collective, organized) form of civic activism and also took into account the influence of professionalization and type of CSOs.

Identification of two human beta-tubulin isotypes

1983 ◽  
Vol 3 (5) ◽  
pp. 854-862
Author(s):  
J L Hall ◽  
L Dudley ◽  
P R Dobner ◽  
S A Lewis ◽  
N J Cowan
Keyword(s):  
Cdna Clone ◽  
Hela Cells ◽  
Untranslated Region ◽  
Genomic Sequence ◽  
Beta Tubulin ◽  
Tubulin Isotypes ◽  
Tubulin Genes ◽  
Processed Pseudogene ◽  
Carboxy Terminal ◽  
High Degree

The sequence of a human beta-tubulin cDNA clone (D beta-1) is described; our data revealed 95.6% homology compared with the sequence of a human beta-tubulin processed pseudogene derived by reverse transcription of a processed mRNA (Wilde et al., Nature [London] 297:83-84, 1982). However, the amino acid sequence encoded by this cDNA showed less homology with pig and chicken beta-tubulin sequences than the latter did to each other, with major divergence within the 15 carboxy-terminal amino acids. On the other hand, an independently isolated, functionally expressed genomic human beta-tubulin sequence (5 beta) possessed a very high degree of homology with chicken and pig beta-tubulins in this region. Thus, human cells appear to contain two distinct beta-tubulin isotypes. Both the intact beta-tubulin cDNA clone and a subclone containing only the 3' untranslated region detected two mRNA species in HeLa cells; these mRNAs were 1.8 and 2.6 kilobases long and were present in about equal amounts. Two independently subcloned probes constructed from the 3' untranslated region of the 5 beta genomic sequence also detected a 2.6-kilobase beta-tubulin mRNA. However, the 3'-untranslated-region probes from the cDNA clone and the genomic sequence did not cross-hybridize. Thus, at least two human beta-tubulin genes, each specifying a distinct isotype, are expressed in HeLa cells, and the 2.6-kilobase mRNA band is a composite of at least two comigrating beta-tubulin mRNAs.

Phenotypic consequences of tubulin overproduction in Saccharomyces cerevisiae: differences between alpha-tubulin and beta-tubulin

1990 ◽  
Vol 10 (10) ◽  
pp. 5295-5304
Author(s):  
B Weinstein ◽  
F Solomon
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Division ◽  
Microtubule Assembly ◽  
Beta Tubulin ◽  
Alpha Tubulin ◽  
Tubulin Genes ◽  
Data Support ◽  
Cell Biol

Overexpression of alpha- and beta-tubulin genes in Saccharomyces cerevisiae, separately or together, leads to accumulation of large excesses of each of the polypeptides and arrest of cell division. However, other consequences of overexpression of these genes differ in several ways. As shown previously (D. Burke, P. Gasdaska, and L. Hartwell, Mol. Cell. Biol. 9:1049-1059, 1989), overexpression of beta-tubulin leads, at early times, to loss of microtubule structures and loss of viability. Eventually, the excess beta-tubulin forms abnormal structures. We show here that, in contrast, overexpression of alpha-tubulin led to none of these phenotypes and in fact could suppress each of the phenotypes associated with beta-tubulin accumulation. Truncated forms of beta-tubulin that were not competent to carry out microtubule functions also failed to elicit the beta-tubulin-specific phenotypes when overexpressed. The data support the hypothesis that beta-tubulin in excess over alpha-tubulin is uniquely toxic, perhaps because it interferes with normal microtubule assembly.

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