scholarly journals Evolution of YidC/Oxa1/Alb3 insertases: three independent gene duplications followed by functional specialization in bacteria, mitochondria and chloroplasts

2011 ◽  
Vol 392 (1-2) ◽  
Author(s):  
Soledad Funes ◽  
Frank Kauff ◽  
Eli O. van der Sluis ◽  
Martin Ott ◽  
Johannes M. Herrmann
Keyword(s):  
Phylogenetic Analyses ◽  
Core Region ◽  
Functional Specialization ◽  
Gene Duplications ◽  
Hydrophobic Core ◽  
Core Domain ◽  
The Core ◽  
Independent Gene ◽  
The Family ◽  
Substrate Spectrum

Abstract Members of the YidC/Oxa1/Alb3 protein family facilitate the insertion, folding and assembly of proteins of the inner membranes of bacteria and mitochondria and the thylakoid membrane of plastids. All homologs share a conserved hydrophobic core region comprising five transmembrane domains. On the basis of phylogenetic analyses, six subgroups of the family can be distinguished which presumably arose from three independent gene duplications followed by functional specialization. During evolution of bacteria, mitochondria and chloroplasts, subgroup-specific regions were added to the core domain to facilitate the association with ribosomes or other components contributing to the substrate spectrum of YidC/Oxa1/Alb3 proteins.

scholarly journals Deletions and recombinations in the core region of hepatitis B virus genotype E strains from asymptomatic blood donors in Guinea, west Africa

2009 ◽  
Vol 90 (10) ◽  
pp. 2442-2451 ◽  
Author(s):  
Penelope Garmiri ◽  
André Loua ◽  
Nyankoye Haba ◽  
Daniel Candotti ◽  
Jean-Pierre Allain
Keyword(s):  
Hepatitis B Virus ◽  
Hepatitis B ◽  
West Africa ◽  
Phylogenetic Analyses ◽  
Core Gene ◽  
Core Region ◽  
Virus Genotype ◽  
The Core ◽  
B Virus ◽  
Genotype E

The prevalence of hepatitis B virus (HBV) surface antigen (HBsAg) chronic carriage in west Africa is the highest in the world, but its molecular epidemiology remains relatively poorly investigated. Plasma samples from random asymptomatic carriers of HBsAg in Conakry, Guinea, were studied and the complete genome sequences of 81 strains were obtained. Three additional samples from Kumasi, Ghana, were also included in the analysis. Phylogenetic analyses confirmed the dominance of genotype E (95.1 %), including 8.6 % of strains (viral load, 5×103–2.6×108 IU ml−1) comprising dominant variants with large deletions in the core region and minority wild-type variants. The presence of two different patterns of deletions in two and four donors suggested targeted genome fragility between nt 1979 and 2314. The remaining sequences included one subgenotype A3 (1 %) and six A/E recombinant forms (4–7 %). A/E strains with identical points of recombination in three donors suggested strongly that these recombinant HBV strains are circulating and transmitted in the population. Recombination points were concentrated in the core gene. The detection of similar A/E recombinant strains in Ghana suggested a geographical extension of recombinant HBV to the region. The quasispecies of one additional Ghanaian strain sequenced in the pre-surface/surface region resolved into dominant clones of either the A or E genotype, but also three different patterns of A/E recombinant variants. The observation that both deletions of genotype E strains and A/E recombination points are mostly located in the core gene at specific positions indicates a region of the genome where genetic rearrangements preferentially take place.

scholarly journals Plastome sequences help to improve the systematic position of trinerved Lindera species in the family Lauraceae

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7662 ◽  
Author(s):  
Xiangyu Tian ◽  
Junwei Ye ◽  
Yu Song
Keyword(s):  
Species Identification ◽  
Phylogenetic Analyses ◽  
Systematic Position ◽  
Variable Regions ◽  
The Core ◽  
The Family ◽  
Close Relationship ◽  
Lindera Obtusiloba ◽  
Hypervariable Loci

Lindera is a genus (c. 100 spp.) of trees belonging to the “core Laureae” group in the family Lauraceae. It is often confused with Litsea, and the systematics of the genus is unclear. Here, total 10 complete plastomes from nine trinerved Lindera species and another species Lindera obtusiloba (sect. Palminerviae Meissn.) were sequenced. Nine highly variable regions, trnH-GUG/psbA, psbM/trnD-GUC, petA/psbL, ndhF, trnL-UAG/ndhD, and ycf1, were identified among the 10 Lindera species. In addition, a total of 1,836 mutation events including six micro-inversions, 156 indels, and 1,674 substitutions, were also summarized. Comparing our sequences with other available plastomes in the “core Laureae,” we put forward that six hypervariable loci, trnH-GUG/psbA, ndhF, ndhF/rpl32, trl32/trnL-UAG, ndhD, and ycf1, could potentially be used as plastid barcode candidates for species identification. Further phylogenetic analyses were conducted using 49 complete Lauraceae plastomes. The results supported a close relationship among trinerved Lindera species and suggested an improved trinerved group comprising species of trinerved Lindera species and Iteadaphne caudate.

Intramitochondrial Viruses of Reptilian Cell Origin

1972 ◽  
Vol 30 ◽  
pp. 318-319
Author(s):  
Philip D. Lunger ◽  
H. Fred Clark
Keyword(s):  
Particle Production ◽  
Outer Zone ◽  
Density Variation ◽  
Core Region ◽  
Mitochondrial Membranes ◽  
Virus Particles ◽  
The Core ◽  
Vipera Russelli ◽  
Maturation Stages ◽  
Type Particle

In the course of fine structure studies of spontaneous “C-type” particle production in a viper (Vipera russelli) spleen cell line, designated VSW, virus particles were frequently observed within mitochondria. The latter were usually enlarged or swollen, compared to virus-free mitochondria, and displayed a considerable degree of cristae disorganization.Intramitochondrial viruses measure 90 to 100 mμ in diameter, and consist of a nucleoid or core region of varying density and measuring approximately 45 mμ in diameter. Nucleoid density variation is presumed to reflect varying degrees of condensation, and hence maturation stages. The core region is surrounded by a less-dense outer zone presumably representing viral capsid.Particles are usually situated in peripheral regions of the mitochondrion. In most instances they appear to be lodged between loosely apposed inner and outer mitochondrial membranes.

Exposure of protein VP7 on the surface of bluetongue virus

1990 ◽  
Vol 48 (3) ◽  
pp. 600-601
Author(s):  
A.D. Hyatt
Keyword(s):  
Bluetongue Virus ◽  
Structural Proteins ◽  
Major Constituent ◽  
Outer Coat ◽  
Virus Particles ◽  
Antibody Recognition ◽  
The Core ◽  
The Family ◽  
Electron Microscopical ◽  
Physical Accessibility

Bluetongue virus (BTV) is the type species os the genus orbivirus in the family Reoviridae. The virus has a fibrillar outer coat containing two major structural proteins VP2 and VP5 which surround an icosahedral core. The core contains two major proteins VP3 and VP7 and three minor proteins VP1, VP4 and VP6. Recent evidence has indicated that the core comprises a neucleoprotein center which is surrounded by two protein layers; VP7, a major constituent of capsomeres comprises the outer and VP3 the inner layer of the core . Antibodies to VP7 are currently used in enzyme-linked immunosorbant assays and immuno-electron microscopical (JEM) tests for the detection of BTV. The tests involve the antibody recognition of VP7 on virus particles. In an attempt to understand how complete viruses can interact with antibodies to VP7 various antibody types and methodologies were utilized to determine the physical accessibility of the core to the external environment.

‘To wise for a woman’

2018 ◽  
Author(s):  
Nicola Clark
Keyword(s):  
Marital Problems ◽  
The Core ◽  
The Family ◽  
Made In ◽  
The Way

While there were clear strategic aims in the way that marriages were made in the Howard dynasty during this period, the family was only unusual in that it operated at the very top of the aristocratic hierarchy and was therefore able to use marital alliances to successfully recover and bolster both status and finances. Where they were different, however, was in the experience of some of these women within marriage. By and large, the marriages made by and for members of the family, including women, seem to have been as successful as others of their class. However, three women close to the core of the dynasty experienced severe marital problems, even ‘failed’ marriages, almost simultaneously during the 1520s and 1530s. The records generated by these episodes tell us about the way in which the family operated as a whole, and the agency of women in this context, and this chapter therefore reconstructs these disputes for this purpose.

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.

scholarly journals Multiple Types of Novel Enteric Bopiviruses (Picornaviridae) with the Possibility of Interspecies Transmission Identified from Cloven-Hoofed Domestic Livestock (Ovine, Caprine and Bovine) in Hungary

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 66
Author(s):  
Zoltán László ◽  
Péter Pankovics ◽  
Gábor Reuter ◽  
Attila Cságola ◽  
Ádám Bálint ◽  
...  
Keyword(s):  
Novel Species ◽  
Phylogenetic Analyses ◽  
Interspecies Transmission ◽  
Background Information ◽  
Type Ii ◽  
Rt Pcr ◽  
Faecal Samples ◽  
The Family ◽  
Domestic Livestock

Most picornaviruses of the family Picornaviridae are relatively well known, but there are certain “neglected” genera like Bopivirus, containing a single uncharacterised sequence (bopivirus A1, KM589358) with very limited background information. In this study, three novel picornaviruses provisionally called ovipi-, gopi- and bopivirus/Hun (MW298057-MW298059) from enteric samples of asymptomatic ovine, caprine and bovine respectively, were determined using RT-PCR and dye-terminator sequencing techniques. These monophyletic viruses share the same type II-like IRES, NPGP-type 2A, similar genome layout (4-3-4) and cre-localisations. Culture attempts of the study viruses, using six different cell lines, yielded no evidence of viral growth in vitro. Genomic and phylogenetic analyses show that bopivirus/Hun of bovine belongs to the species Bopivirus A, while the closely related ovine-origin ovipi- and caprine-origin gopivirus could belong to a novel species “Bopivirus B” in the genus Bopivirus. Epidemiological investigation of N = 269 faecal samples of livestock (ovine, caprine, bovine, swine and rabbit) from different farms in Hungary showed that bopiviruses were most prevalent among <12-month-old ovine, caprine and bovine, but undetectable in swine and rabbit. VP1 capsid-based phylogenetic analyses revealed the presence of multiple lineages/genotypes, including closely related ovine/caprine strains, suggesting the possibility of ovine–caprine interspecies transmission of certain bopiviruses.

scholarly journals Effect of Molecular Architecture on Associating Behavior of Star-Like Amphiphilic Polymers Consisting of Plural Poly(ethylene oxide) and One Alkyl Chain

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 460
Author(s):  
Daisuke Kugimoto ◽  
Aoi Taniguchi ◽  
Masaki Kinoshita ◽  
Isamu Akiba
Keyword(s):  
Ethylene Oxide ◽  
Average Molecular Weight ◽  
Amphiphilic Polymers ◽  
Hydrophobic Core ◽  
Molecular Architecture ◽  
Polymer Micelles ◽  
The Core ◽  
X Ray Scattering ◽  
Poly Ethylene Oxide ◽  
Poly Ethylene

Associating behavior of star-like amphiphilic polymers consisting of two or three poly(ethylene oxide) (PEO) chains and one stearyl chain (C18) was investigated. Although the aggregation number (Nagg) of linear analogue of amphiphilic polymers monotonically decreased with increasing number-average molecular weight of PEO (Mn,PEO), the Nagg of micelles of star-like amphiphilic polymers with Mn,PEO = 550 g/mol was smaller than that with Mn,PEO = 750 g/mol, whereas that with Mn,PEO ≥ 750 g/mol showed general Mn,PEO dependence. Small-angle X-ray scattering analyses revealed that the occupied area of one PEO chain on the interface between hydrophobic core and corona layer in the micelles of star-like polymers was much narrower than that in the linear amphiphilic polymers. This result indica ted the PEO chains of star-like polymers partially took unfavorable conformation near the core–corona interface in polymer micelles. The effect of local conformation of PEO chains near the interface on the associating behavior became significant as Mn,PEO decreased. Therefore, in polymer micelles of star-like amphiphilic polymers containing PEO with Mn,PEO = 550 g/mol, the enlargement of occupied area of PEO on the core–corona interface should be caused to avoid the formation of unfavorable conformations of partial PEO chains, resulting in a decrease in Naggs.

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