scholarly journals Corchorus yellow vein virus, a New World geminivirus from the Old World

2006 ◽  
Vol 87 (4) ◽  
pp. 997-1003 ◽  
Author(s):  
Cuong Ha ◽  
Steven Coombs ◽  
Peter Revill ◽  
Rob Harding ◽  
Man Vu ◽  
...  
Keyword(s):  
New World ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Yellow Vein ◽  
Bipartite Begomovirus ◽  
Degenerate Pcr ◽  
Old World ◽  
Reading Frame ◽  
Corchorus Capsularis ◽  
World Begomoviruses

A bipartite begomovirus infecting Jute mallow (Corchorus capsularis, Tilliaceae) in Vietnam was identified using novel degenerate PCR primers. Analysis of this virus, which was named Corchorus yellow vein virus (CoYVV), showed that it was more similar to New World begomoviruses than to viruses from the Old World. This was based on the absence of an AV2 open reading frame, the presence of an N-terminal PWRLMAGT motif in the coat protein and phylogenetic analysis of the DNA A and DNA B nucleotide and deduced amino acid sequences. Evidence is provided that CoYVV is probably indigenous to the region and may be the remnant of a previous population of New World begomoviruses in the Old World.

Identification of mariner-like elements in Sitodiplosis mosellana (Diptera: Cecidomyiidae)

2006 ◽  
Vol 138 (2) ◽  
pp. 138-146 ◽  
Author(s):  
O. Mittapalli ◽  
R.H. Shukle ◽  
I.L. Wise
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Blot Analysis ◽  
Copy Number ◽  
Southern Blot Analysis ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Degenerate Pcr ◽  
Sitodiplosis Mosellana ◽  
Wheat Midge

AbstractMariner-like element sequences were recovered from the genome of the orange wheat midge, Sitodiplosis mosellana (Géhin), with degenerate PCR primers designed to conserved regions of mariner transposases. The deduced amino acid sequences of the mariner-like transposases from S. mosellana showed 67% to 78% identity with the peptide sequences of other mariner transposases. A phylogenetic analysis revealed that the mariner-like elements from S. mosellana grouped in the mauritiana subfamily of mariner transposons. Results from Southern blot analysis suggest mariner-like elements are at a moderate copy number in the genome of S. mosellana.

scholarly journals Molecular characterization of begomoviruses and DNA satellites from Vietnam: additional evidence that the New World geminiviruses were present in the Old World prior to continental separation

2008 ◽  
Vol 89 (1) ◽  
pp. 312-326 ◽  
Author(s):  
Cuong Ha ◽  
Steven Coombs ◽  
Peter Revill ◽  
Rob Harding ◽  
Man Vu ◽  
...  
Keyword(s):  
New World ◽  
Bipartite Begomoviruses ◽  
Bipartite Begomovirus ◽  
Stem Loop ◽  
Old World ◽  
Recombinant Viruses ◽  
Virus Diversity ◽  
High Degree ◽  
First Time

Sixteen viruses, belonging to 16 species of begomovirus, that infect crops and weeds in Vietnam were identified. Sequence analysis of the complete genomes showed that nine of the viruses (six monopartite and three bipartite) belong to novel species and five of them were identified in Vietnam for the first time. Additionally, eight DNA-β and three nanovirus-like DNA-1 molecules were also found associated with some of the monopartite viruses. Five of the DNA-β molecules were novel. Importantly, a second bipartite begomovirus, Corchorus golden mosaic virus, shared several features with the previously characterized virus Corchorus yellow vein virus and with other bipartite begomoviruses from the New World, supporting the hypothesis that New World-like viruses were present in the Old World. This, together with a high degree of virus diversity that included putative recombinant viruses, satellite molecules and viruses with previously undescribed variability in the putative stem–loop sequences, suggested that South-East Asia, and Vietnam in particular, is one of the origins of begomovirus diversity.

Characterization and comparative analysis of three low molecular weight glutenin C-subunit genes isolated from Aegilops tauschii

2007 ◽  
Vol 87 (2) ◽  
pp. 273-280 ◽  
Author(s):  
Yu-He Pei ◽  
Ai-Li Wang ◽  
Xue-Li An ◽  
Xiao-Hui Li ◽  
Yan-Zhen Zhang ◽  
...  
Keyword(s):  
Molecular Weight ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Aegilops Tauschii ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Low Molecular Weight ◽  
Primitive Form ◽  
Reading Frame ◽  
Specific Pcr

Three low molecular weight glutenin subunit (LMW-GS) genes from T121, T128 and T132 accessions of Aegilops tauschii (DD, 2n = 2x = 14) were amplified using allelic-specific PCR primers. The amplified products with a size of about 900 bp were cloned and sequenced. Three complete coding sequences of LMW-GS with 918 bp, 921 bp and 918 bp were obtained and named as LMW-T121, LMW-T128, LMW-T132, respectively. Each gene contained a complete open reading frame and had no introns. The deduced amino acid sequences showed that all belonged to LMW-m type subunit with a predicted molecular weight of about 32 kDa, corresponding to the size of LMW C-subunits. All three subunits possessed eight cysteine residues and had greater homology with previously characterized LMW-m subunits from bread wheat and related species than LMW-s or LMW-i sequences. Some amino acid substitutions and insertion/deletion variations among the sequences were detected. The corresponding three C-subunits in seed endosperm encoded by LMW-T121, LMW-T128, LMW-T132, respectively, were identified and confirmed by SDS-PAGE, MALDI-TOF-MS and direct N-terminal amino acid sequencing. Phylogenetic analysis demonstrated that LMW-m and LMW-s type subunit genes possessed higher identity and they were obviously separated from LMW-i type subunit genes. The LMW-m type might be the primitive form while the LMW-s and LMW-i types are variant forms. Key words: Aegilops tauschii, LMW-GS, AS-PCR, phylogenetic analysis

scholarly journals Cloning of a rat brain succinic semialdehyde reductase involved in the synthesis of the neuromodulator γ-hydroxybutyrate

1998 ◽  
Vol 334 (1) ◽  
pp. 43-50 ◽  
Author(s):  
Christian ANDRIAMAMPANDRY ◽  
Jean-Claude SIFFERT ◽  
Michèle SCHMITT ◽  
Jean-Marie GARNIER ◽  
Adrien STAUB ◽  
...  
Keyword(s):  
Molecular Mass ◽  
Rat Brain ◽  
Cdna Library ◽  
Brain Tissue ◽  
Broad Band ◽  
Pcr Primers ◽  
Amino Acid Sequences ◽  
Succinic Semialdehyde ◽  
Tissue Slices ◽  
Reading Frame

The γ-hydroxybutyrate biosynthetic enzyme succinic semialdehyde reductase (SSR) was purified to homogeneity from rat brain. Peptides were generated by tryptic cleavage and sequenced. PCR primers were designed from the amino acid sequences of two of the peptides showing a similarity (75–85%) to a mitochondrial aldehyde dehydrogenase. A PCR-amplified DNA fragment was generated from recombinant plasmids prepared by a mass excision procedure from a rat hippocampal cDNA library and used as a probe to screen this cDNA library. One cDNA of 1341 bp had an open reading frame encoding a protein of 447 residues with a deduced molecular mass of 47967 Da. The enzyme was expressed in Escherichia coli. Immunoblotting analysis revealed the existence of a protein with the same electrophoretic mobility as the SSR purified from rat brain and with an estimated molecular mass of 45 kDa. Northern blot experiments showed that this enzyme was not expressed in the kidney or in the liver. In the brain tissue, a single but rather broad band was labelled under high stringency conditions, suggesting the presence of more than one messenger species coding for SSR. Hybridization in situ performed on brain tissue slices showed specific labelling of the hippocampus, the upper cortex layer, the thalamus, the substantia nigra, the cerebellum, the pons medulla and the olfactory tract. The recombinant enzyme showed catalytic properties similar to those of the SSR purified from rat brain, particularly in regard to its substrate affinities and Ki for inhibition by phthalaldehydic acid. Valproic acid did not inhibit the cloned SSR. This enzyme had 20–35% identity in highly conserved regions involved in NADPH binding with four other proteins belonging to the aldo–oxo reductase family.

scholarly journals Amerigo Vespucci's Contribution to the Modernization of Cartographic Representation

2020 ◽  
Author(s):  
Gyula Pápay
Keyword(s):  
New World ◽  
De Novo ◽  
Old World ◽  
University Library ◽  
The City

AbstractIn 2019, the Rostock University Library acquired the report by Amerigo Vespucci (1454–1512) on transatlantic discoveries, which was published in 1505 by the city secretary Hermann Barckhusen (c 1460–1528/29) in Rostock under the title “Epistola Albericij. De novo mundo” [1505] and, unlike other editions, was published with a map. The special feature of the map is that it is the oldest map with a globular projection. Vespucci reported in a letter dated July 18, 1500 to Lorenzo di Pierfrancesco de' Medici about his voyage 1499–1500, which is an important source for the fact that his longitude determinations contributed to the realization that the transatlantic discoveries were about a continent. The letter also contains evidence that Vespucci was the originator of the globular projection. This marked the beginning of a departure from ancient traditions regarding the projections for world maps. To enable the combined representation of the “old world” together with the “new world” in one map, Vespucci's projection was later modified into an oval map, which was used, for example, by Franzesco Rosselli, Sebastian Münster and Abraham Ortelius.

scholarly journals SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates

Genetics ◽  
2001 ◽  
Vol 157 (2) ◽  
pp. 777-784
Author(s):  
Jürgen Schmitz ◽  
Martina Ohme ◽  
Hans Zischler
Keyword(s):  
New World ◽  
World Monkey ◽  
Old World ◽  
Alu Elements ◽  
Alu Sequences ◽  
Short Interspersed Elements ◽  
Divergence Point ◽  
Tarsius Bancanus ◽  
Cladistic Analyses ◽  
The Common

Abstract Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

Efficiency of whole‐exome sequencing in old world and new world primates using human capture reagents

2021 ◽  
Author(s):  
Jeannie Chan ◽  
Wen Yao ◽  
Timothy D. Howard ◽  
Gregory A. Hawkins ◽  
Michael Olivier ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
New World ◽  
New World Primates ◽  
Old World ◽  
Whole Exome
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