scholarly journals Evolutionary implications of infra- and interspecific molecular variability of pathogenesis-related proteins

2003 ◽  
Vol 63 (3) ◽  
pp. 437-448 ◽  
Author(s):  
L. B. Freitas ◽  
S. L. Bonatto ◽  
F. M. Salzano
Keyword(s):  
Phylogenetic Trees ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Rare Occurrence ◽  
Pr Protein ◽  
Interspecific Differences ◽  
The Family ◽  
Pathogenesis Related ◽  
Family Level ◽  
Related Proteins

We have examined phylogenetic relationships in seven pathogenesis-related (PR) protein families. Within-family comparisons involved 79 species, 166 amino acid sequences, and 1,791 sites. For 37 species, 124 different PR isoforms were identified (an average of 3.3 per species). Thirty-one of the 37 species investigated tended to cluster together (84%). Of the 17 clusters distinguished in the seven phylogenetic trees, 10 (59%) were in agreement with their taxonomic status, ascertained at the family level. The strong similarities among the intraspecific forms, as compared to interspecific differences, argue for some kind of gene conversion, but the rare occurrence of widely different isoforms also suggests diversifying selection. PRs 1, 6, and 4 seem to be less differentiated than PRs 3, 2, 10, and 5.

scholarly journals Taxonomic status of Bhanja and Kismayo viruses (family Bunyaviridae)

2012 ◽  
Vol 17 (4) ◽  
pp. 4-8
Author(s):  
A. S Klimentov ◽  
A. P Gmyl ◽  
A. M Butenko ◽  
L. V Gmyl ◽  
O. V Isaeva ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Nucleotide Sequence ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
The Family ◽  
L Segment

The nucleotide sequence of M= (1398 nucleotides and L= (6186 nucleotides) segments of the genome of Bhanja virus and L-segment (1297 nucleotides) of Kismayo virus has been partially determined. Phylogenetic analysis of deduced amino acid sequences showed that these viruses are novel members of the Flebovirus (Phlebovirus) genus in the family Bunyaviridae

Geometric morphometrics uncovers a new species of ponyfish (Teleostei: Leiognathidae: Equulites), with comments on the taxonomic status of Equula berbis Valenciennes

Zootaxa ◽  
2010 ◽  
Vol 2427 (1) ◽  
pp. 15 ◽  
Author(s):  
PROSANTA CHAKRABARTY ◽  
J.JEANETTE CHU ◽  
LUTHFUN NAHAR ◽  
JOHN S. SPARKS
Keyword(s):  
New Species ◽  
Taxonomic Status ◽  
Sexually Dimorphic ◽  
Light Organ ◽  
Geometric Morphometric ◽  
The Family ◽  
External Feature ◽  
Family Level ◽  
Male Specific ◽  
A New Species

A new species of Equulites is revealed using geometric morphometric techniques and is herein described. Based on features recovered in recent comparative analyses, members of Equulites have been diagnosed on the basis of internal and external male-specific traits related to their light-organ system (LOS; Sparks et al., 2005; Sparks, 2006; Sparks and Chakrabarty, 2007; Chakrabarty and Sparks, 2008). These sexually-dimorphic traits are hypothesized to allow males to signal to conspecific females in photic sexual displays using bacterially-generated luminescence (Woodland et al., 2002; Sasaki et al., 2003; Wada et al., 2005). The holotype and sole name-bearing type of Equulites leuciscus (BMNH 1858.4.21.243, 104.9 mm SL) is an adult female, and therefore lacks the diagnostic external feature of the LOS, a large, translucent flank patch, used to identify species in this genus. Geometric morphometric shape analysis of individuals ascribed to Equulites leuciscus, a traditionally widespread, "catch-all" taxon, reveals two discrete shape groups. Based on the results presented below, members of one of these groups correspond to a morphological variant that represents the new species (Equulites absconditus Chakrabarty & Sparks) described herein, whereas the other group corresponds to traditional E. leuciscus. In addition, the taxonomic status of Equula berbis Valenciennes, to which many female and poorly preserved specimens of the new species have erroneously been attributed, is reviewed and E. berbis is concluded to be a nomen dubium of uncertain placement beyond the family level.

scholarly journals Large-scale Phylogenomic Analysis Provides New Insights Into the Phylogeny of the Order Gadiformes and Evolution of Freshwater Gadiform Species Burbot (Lota lota)

2021 ◽  
Author(s):  
Zhiqiang Han ◽  
Chenyan Shou ◽  
Manhong Liu ◽  
Tianxiang Gao
Keyword(s):  
Amino Acid ◽  
Phylogenetic Relationships ◽  
Phylogenetic Trees ◽  
Large Scale ◽  
Amino Acid Sequences ◽  
Phylogenomic Analysis ◽  
Data Set ◽  
Lota Lota ◽  
The Family ◽  
Tree Building

Our understanding of phylogenetic relationships among Gadiformes fish is obtained through the analysis of a small number of genes, but uncertainty remains around critical nodes. A series of phylogenetic controversial exists at the suborder, family, subfamily, and species levels. A total of 1105 orthologous exon sequences and translated amino acid sequences from 36 genomes and 12 transcriptomes covering 33 species were applied to investigate the phylogenetic relationships within Gadiformes and address these problems. Phylogenetic trees reconstructed with the amino acid data set using different tree-building methods (RAxML and MrBayes) showed consistent topology. The monophyly of Gadifromes was confirmed in our study. However, the three suborders Muraenolepidoidei, Macrouroidei, and Gadoidei were not well recovered by our phy-logenomic study, rejecting the validity of suborder Muraenolepidoidei. Four major lineages were revealed in this study. The family Bregmacerotidae forming clade I was the basal lineage of Gadiformes. The family Merluciidae formed clade II. Clade III contained families Melanonidae, Muraenolepididae, Macrouridae (with subfamilies Trachyrincinae, Macrourinae, and Bathygadinae), and Moridae. Clade IV contained at least three families of suborder Gadoidei, i.e., Gadidae, Phycidae, and Ranicipitidae. The subspecies of Lota lota from Amur River were confirmed, indicating that exon markers were a valid high-resolution method for delimiting subspecies or distinct lineages within species level. The PSMC analysis of different populations of L. lota suggests a continuous decline since 2 Myr.

scholarly journals Morphological and molecular evidence that Culex nigripalpus baculovirus is an unusual member of the family Baculoviridae

2001 ◽  
Vol 82 (2) ◽  
pp. 283-297 ◽  
Author(s):  
Bettina A. Moser ◽  
James J. Becnel ◽  
Susan E. White ◽  
Claudio Afonso ◽  
Gerald Kutish ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Gc Content ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Molecular Evidence ◽  
Culex Nigripalpus ◽  
Double Stranded Dna ◽  
The Family ◽  
Occlusion Bodies ◽  
Infected Cells

We present evidence that a newly discovered mosquito virus from Culex nigripalpus is an unusual member of the family Baculoviridae. Development of this virus was restricted to nuclei of midgut epithelial cells in the gastric caeca and posterior stomach. The globular occlusion bodies were not enveloped, measured around 400 nm in diameter, occurred exclusively in nuclei of infected cells and typically contained four, sometimes up to eight, virions. The developmental sequence involved two virion phenotypes: an occluded form (ODV) that initiated infection in the midgut epithelial cells, and a budded form that spread the infection in the midgut. Each ODV contained one rod-shaped enveloped nucleocapsid (40×200 nm). The double-stranded DNA genome was approximately 105–110 kbp with an estimated GC content of 52%. We have sequenced approximately one-third of the genome and detected 96 putative ORFs of 50 amino acids or more including several genes considered to be unique to baculoviruses. Phylogenetic analysis of the amino acid sequences of DNApol and p74 placed this virus in a separate clade from the genera Nucleopolyhedrovirus and Granulovirus. We provisionally assign this virus in the genus Nucleopolyhedrovirus, henceforth abbreviated as CuniNPV (for Culex nigripalpus nucleopolyhedrovirus), and suggest that, awaiting additional data to clarify its taxonomic status, it may be a member of a new genus within the family Baculoviridae.

The complete mitochondrial genome of Pseudanoplocephala crawfordi and a comparison with closely related cestode species

2015 ◽  
Vol 90 (5) ◽  
pp. 588-595 ◽  
Author(s):  
G.H. Zhao ◽  
H.B. Wang ◽  
Y.Q. Jia ◽  
W. Zhao ◽  
X.F. Hu ◽  
...  
Keyword(s):  
Complete Mitochondrial Genome ◽  
Taxonomic Status ◽  
Amino Acid Sequences ◽  
Health Concern ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Economic Significance ◽  
The Family ◽  
Mt Genome ◽  
Rna Genes

AbstractPseudanoplocephala crawfordi is an important zoonotic cestode of economic significance and public health concern. In spite of its significance as a pathogen, the systematics, genetics, epidemiology and biology of this parasite remain poorly understood. In the present study, we sequenced and characterized the complete mitochondrial (mt) genome of P. crawfordi, which is 14,192 bp long and encodes 36 genes, including 12 protein-coding genes, 22 transfer RNA genes and two ribosomal RNA genes. Phylogenetic analysis of the concatenated amino acid sequences using the Bayesian inference (BI) method showed that P. crawfordi was closely related to the family Hymenolepididae. Considering that the taxonomic status of P. crawfordi has been controversial when based only on morphological features, the mt genome obtained here will provide novel molecular markers to ascertain the phylogenetic position of this parasite accurately.

Cuticular structures in the copulatory apparatus of Planorbis planorbis (Linnaeus, 1758) (Gastropoda: Pulmonata: Planorbidae)

2009 ◽  
Vol 18 (1) ◽  
pp. 11-16
Author(s):  
E.V. Soldatenko ◽  
A.A. Petrov
Keyword(s):  
Light Microscopy ◽  
Confocal Laser Scanning Microscopy ◽  
Laser Scanning ◽  
Taxonomic Status ◽  
Laser Scanning Microscopy ◽  
Confocal Laser Scanning ◽  
Confocal Laser ◽  
Copulatory Apparatus ◽  
The Family ◽  
Cuticular Structures

The morphology of the copulatory apparatus and associated cuticular structures in Planorbis planorbis was studied by light microscopy, SEM, TEM and confocal laser scanning microscopy. The significance of these cuticular structures for the taxonomic status of the species and for the systematics of the family Planorbidae in general is discussed.

Modulation of Hepatic MRP3/ABCC3 by Xenobiotics and Pathophysiological Conditions: Role in Drug Pharmacokinetics

2019 ◽  
Vol 26 (7) ◽  
pp. 1185-1223 ◽  
Author(s):  
Carolina I. Ghanem ◽  
Jose E. Manautou
Keyword(s):  
Abc Transporters ◽  
Basolateral Membrane ◽  
Clinical Use ◽  
Nucleotide Analogs ◽  
Synthetic Drugs ◽  
The Family ◽  
Hepatic Transporter ◽  
Related Proteins ◽  
Drug Pharmacokinetics ◽  
Conjugated Metabolites

Liver transporters play an important role in the pharmacokinetics and disposition of pharmaceuticals, environmental contaminants, and endogenous compounds. Among them, the family of ATP-Binding Cassette (ABC) transporters is the most important due to its role in the transport of endo- and xenobiotics. The ABCC sub-family is the largest one, consisting of 13 members that include the cystic fibrosis conductance regulator (CFTR/ABCC7); the sulfonylurea receptors (SUR1/ABCC8 and SUR2/ABCC9) and the multidrug resistanceassociated proteins (MRPs). The MRP-related proteins can collectively confer resistance to natural, synthetic drugs and their conjugated metabolites, including platinum-containing compounds, folate anti-metabolites, nucleoside and nucleotide analogs, among others. MRPs can be also catalogued into "long" (MRP1/ABCC1, -2/C2, -3/C3, -6/C6, and -7/C10) and "short" (MRP4/C4, -5/C5, -8/C11, -9/C12, and -10/C13) categories. While MRP2/ABCC2 is expressed in the canalicular pole of hepatocytes, all others are located in the basolateral membrane. In this review, we summarize information from studies examining the changes in expression and regulation of the basolateral hepatic transporter MPR3/ABCC3 by xenobiotics and during various pathophysiological conditions. We also focus, primarily, on the consequences of such changes in the pharmacokinetic, pharmacodynamic and/or toxicity of different drugs of clinical use transported by MRP3.

scholarly journals Towards a Natural Classification of Hyphodontia Sensu Lato and the Trait Evolution of Basidiocarps within Hymenochaetales (Basidiomycota)

2021 ◽  
Vol 7 (6) ◽  
pp. 478
Author(s):  
Xue-Wei Wang ◽  
Tom W. May ◽  
Shi-Liang Liu ◽  
Li-Wei Zhou
Keyword(s):  
Phylogenetic Analyses ◽  
Taxonomic Status ◽  
Ancestral State ◽  
Trait Evolution ◽  
Natural Classification ◽  
Multiple Loci ◽  
The Family ◽  
Phylogenetic Perspective ◽  
Taxonomic Framework ◽  
First Time

Hyphodontia sensu lato, belonging to Hymenochaetales, accommodates corticioid wood-inhabiting basidiomycetous fungi with resupinate basidiocarps and diverse hymenophoral characters. Species diversity of Hyphodontia sensu lato has been extensively explored worldwide, but in previous studies the six accepted genera in Hyphodontia sensu lato, viz. Fasciodontia, Hastodontia, Hyphodontia, Kneiffiella, Lyomyces and Xylodon were not all strongly supported from a phylogenetic perspective. Moreover, the relationships among these six genera in Hyphodontia sensu lato and other lineages within Hymenochaetales are not clear. In this study, we performed comprehensive phylogenetic analyses on the basis of multiple loci. For the first time, the independence of each of the six genera receives strong phylogenetic support. The six genera are separated in four clades within Hymenochaetales: Fasciodontia, Lyomyces and Xylodon are accepted as members of a previously known family Schizoporaceae, Kneiffiella and Hyphodontia are, respectively, placed in two monotypic families, viz. a previous name Chaetoporellaceae and a newly introduced name Hyphodontiaceae, and Hastodontia is considered to be a genus with an uncertain taxonomic position at the family rank within Hymenochaetales. The three families emerged between 61.51 and 195.87 million years ago. Compared to other families in the Hymenochaetales, these ages are more or less similar to those of Coltriciaceae, Hymenochaetaceae and Oxyporaceae, but much older than those of the two families Neoantrodiellaceae and Nigrofomitaceae. In regard to species, two, one, three and 10 species are newly described from Hyphodontia, Kneiffiella, Lyomyces and Xylodon, respectively. The taxonomic status of additional 30 species names from these four genera is briefly discussed; an epitype is designated for X. australis. The resupinate habit and poroid hymenophoral configuration were evaluated as the ancestral state of basidiocarps within Hymenochaetales. The resupinate habit mainly remains, while the hymenophoral configuration mainly evolves to the grandinioid-odontioid state and also back to the poroid state at the family level. Generally, a taxonomic framework for Hymenochaetales with an emphasis on members belonging to Hyphodontia sensu lato is constructed, and trait evolution of basidiocarps within Hymenochaetales is revealed accordingly.

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