scholarly journals Molecular characterization of Penicillium chrysogenum virus: reconsideration of the taxonomy of the genus Chrysovirus

2004 ◽  
Vol 85 (7) ◽  
pp. 2111-2121 ◽  
Author(s):  
Daohong Jiang ◽  
Said A. Ghabrial
Keyword(s):  
Molecular Characterization ◽  
Penicillium Chrysogenum ◽  
Sequence Similarity ◽  
Minor Component ◽  
Amino Acid Sequences ◽  
Nucleotide Sequencing ◽  
Dsrna Segment ◽  
Cdna Clones

Molecular cloning and complete nucleotide sequencing of Penicillium chrysogenum virus (PcV) dsRNAs indicated that PcV virions contained four dsRNA segments with sizes of 3562, 3200, 2976 and 2902 bp. Each dsRNA segment had unique sequences and contained a single large open reading frame (ORF). In vitro translation of transcripts derived from full-length cDNA clones of PcV dsRNAs yielded single products of sizes similar to those predicted from the deduced amino acid sequences of the individual ORFs. Sequence similarity searches revealed that dsRNA1 encodes a putative RNA-dependent RNA polymerase. In this study, it was determined that dsRNA2 encodes the major capsid protein and that p4, encoded by dsRNA4, is virion-associated as a minor component. All four dsRNAs of PcV, like the genomic segments of viruses with multipartite genomes, were found to have extended regions of highly conserved terminal sequences at both ends. In addition to the strictly conserved 5′-terminal 10 nt, a second region consisting of reiteration of the sequence CAA was found immediately upstream of the AUG initiator codon. These (CAA) n repeats are reminiscent of the translational enhancer elements of tobamoviruses. The 3′-terminal 14 nt were also strictly conserved. As PcV and related viruses with four dsRNA segments (genus Chrysovirus) have not been previously characterized at the molecular level, they were provisionally classified in the family Partitiviridae, comprising viruses with bipartite genomes. This study represents the first report on molecular characterization of a chrysovirus and the results suggest the creation of a new family of mycoviruses with multipartite dsRNA genomes to accommodate PcV and related viruses.

scholarly journals Molecular characterization of three newly recognized rat parvoviruses

2002 ◽  
Vol 83 (8) ◽  
pp. 2075-2083 ◽  
Author(s):  
Cho-Hua Wan ◽  
Maria Söderlund-Venermo ◽  
David J. Pintel ◽  
Lela K. Riley
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Molecular Characterization ◽  
Amino Acid Sequences ◽  
Minute Virus ◽  
Genomic Nucleotide Sequence ◽  
Kilham Rat Virus

Rodent parvoviruses have been documented to interfere with both in vivo and in vitro research. In this study, three rat parvoviruses distinct from previously characterized rodent parvoviruses were identified from naturally infected rats obtained from four discrete sources. These three newly recognized parvoviruses were designated rat minute virus (RMV)-1a, -1b and -1c. In this study, the genomic nucleotide sequence and the predicted amino acid sequences of proteins for each of the three RMV-1 variants and Kilham rat virus (KRV) were determined and compared with previously characterized rodent parvoviruses. The three RMV-1 variants were shown to be closely related to each other, to be distinct from but closely related to KRV and H-1 virus, and to be significantly different from the previously identified rat parvovirus isolate, RPV-1a.

scholarly journals Biological and Molecular Characterization of a U.S. Isolate of Hosta virus X

2012 ◽  
Vol 102 (12) ◽  
pp. 1176-1181 ◽  
Author(s):  
Carola M. De La Torre ◽  
Feng Qu ◽  
Margaret G. Redinbaugh ◽  
Dennis J. Lewandowski
Keyword(s):  
Molecular Characterization ◽  
Sequence Similarity ◽  
Direct Repeat ◽  
Complete Sequence ◽  
Full Length ◽  
Full Length Sequence ◽  
High Level ◽  
Systemic Infections

Hosta virus X (HVX) is rapidly becoming a serious pathogen of commercially important hosta plants worldwide. We report here biological and molecular characterization of a U.S. isolate of HVX, HVX-37. HVX-37 infectivity was tested in 21 hosta cultivars over three growth seasons, and three types of responses were defined based upon the ability of the virus to cause local and/or systemic infections. Four cultivars resistant to systemic HVX infection were identified. The full-length sequence of the HVX-37 genome was determined, the first complete sequence of a U.S. HVX isolate. Comparison with the previously sequenced HVX-Korea (Kr) genome revealed a high level of sequence similarity, as well as some differences. Notably, a 105-nucleotide long, near-perfect direct repeat in the Kr isolate is absent in HVX-37. The accuracy of the HVX-37 genome sequence was confirmed by infectivity of in vitro transcripts synthesized from a full-length HVX-37 cDNA on Nicotiana benthamiana and hosta plants.

scholarly journals SureSelect targeted enrichment, a new cost effective method for the whole genome sequencing of Candidatus Liberibacter asiaticus

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Weili Cai ◽  
Schyler Nunziata ◽  
John Rascoe ◽  
Michael J. Stulberg
Keyword(s):  
Whole Genome Sequencing ◽  
Molecular Characterization ◽  
Genome Sequencing ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Coverage ◽  
Metagenomic Sample ◽  
Liberibacter Asiaticus

AbstractHuanglongbing (HLB) is a worldwide deadly citrus disease caused by the phloem-limited bacteria ‘Candidatus Liberibacter asiaticus’ (CLas) vectored by Asian citrus psyllids. In order to effectively manage this disease, it is crucial to understand the relationship among the bacterial isolates from different geographical locations. Whole genome sequencing approaches will provide more precise molecular characterization of the diversity among populations. Due to the lack of in vitro culture, obtaining the whole genome sequence of CLas is still a challenge, especially for medium to low titer samples. Hundreds of millions of sequencing reads are needed to get good coverage of CLas from an HLB positive citrus sample. In order to overcome this limitation, we present here a new method, Agilent SureSelect XT HS target enrichment, which can specifically enrich CLas from a metagenomic sample while greatly reducing cost and increasing whole genome coverage of the pathogen. In this study, the CLas genome was successfully sequenced with 99.3% genome coverage and over 72X sequencing coverage from low titer tissue samples (equivalent to 28.52 Cq using Li 16 S qPCR). More importantly, this method also effectively captures regions of diversity in the CLas genome, which provides precise molecular characterization of different strains.

scholarly journals Synaptopodin: An Actin-associated Protein in Telencephalic Dendrites and Renal Podocytes

1997 ◽  
Vol 139 (1) ◽  
pp. 193-204 ◽  
Author(s):  
Peter Mundel ◽  
Hans W. Heid ◽  
Thomas M. Mundel ◽  
Meike Krüger ◽  
Jochen Reiser ◽  
...  
Keyword(s):  
Dendritic Spines ◽  
Cultured Cells ◽  
Rat Kidney ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Globular Domain ◽  
Postnatal Maturation ◽  
Human And Mouse

Synaptopodin is an actin-associated protein of differentiated podocytes that also occurs as part of the actin cytoskeleton of postsynaptic densities (PSD) and associated dendritic spines in a subpopulation of exclusively telencephalic synapses. Amino acid sequences determined in purified rat kidney and forebrain synaptopodin and derived from human and mouse brain cDNA clones show no significant homology to any known protein. In particular, synaptopodin does not contain functional domains found in receptor-clustering PSD proteins. The open reading frame of synaptopodin encodes a polypeptide with a calculated Mr of 73.7 kD (human)/74.0 kD (mouse) and an isoelectric point of 9.38 (human)/9.27 (mouse). Synaptopodin contains a high amount of proline (∼20%) equally distributed along the protein, thus virtually excluding the formation of any globular domain. Sequence comparison between human and mouse synaptopodin revealed 84% identity at the protein level. In both brain and kidney, in vivo and in vitro, synaptopodin gene expression is differentiation dependent. During postnatal maturation of rat brain, synaptopodin is first detected by Western blot analysis at day 15 and reaches maximum expression in the adult animal. The exclusive synaptopodin synthesis in the telencephalon has been confirmed by in situ hybridization, where synaptopodin mRNA is only found in perikarya of the olfactory bulb, cerebral cortex, striatum, and hippocampus, i.e., the expression is restricted to areas of high synaptic plasticity. From these results and experiments with cultured cells we conclude that synaptopodin represents a novel kind of proline-rich, actin-associated protein that may play a role in modulating actin-based shape and motility of dendritic spines and podocyte foot processes.

scholarly journals Molecular Characterization of cDNA Clones Encoding Flavanone 3-Hydroxylase from Dutch Iris(Iris ^|^times; hollandica)

CYTOLOGIA ◽  
2012 ◽  
Vol 77 (3) ◽  
pp. 359-367
Author(s):  
Noriko Yoshihara ◽  
Masako Fukuchii-mizutani ◽  
Hiroaki Okuhara ◽  
Yoshikazu Tanaka ◽  
Tsutomu Yabuya
Keyword(s):  
Molecular Characterization ◽  
Cdna Clones

Structure and expression of ferritin genes in a human promyelocytic cell line that differentiates in vitro

1986 ◽  
Vol 6 (2) ◽  
pp. 566-573
Author(s):  
C C Chou ◽  
R A Gatti ◽  
M L Fuller ◽  
P Concannon ◽  
A Wong ◽  
...  
Keyword(s):  
Cell Line ◽  
Terminal Differentiation ◽  
Amino Acid Sequences ◽  
Multigene Families ◽  
Cdna Clones ◽  
Macrophage Differentiation ◽  
Time Points ◽  
Human Ferritin ◽  
Complex Manner

HL-60 is a human promyelocytic cell line with the capability of differentiating in vitro to give neutrophils, macrophages, or eosinophils. We screened libraries of HL-60 cDNA clones representing different time points during these differentiation processes to isolate clones corresponding to mRNAs whose expression is regulated during terminal differentiation. Upon sequencing this group of regulated clones, one clone encoding the heavy subunit and two clones encoding the light subunit of human ferritin were identified by reference to published amino acid sequences. Southern blot analyses showed that these clones are encoded by distinct multigene families. These clones identify two mRNAs whose ratios vary in a complex manner during both neutrophil and macrophage differentiation.

scholarly journals Molecular characterization of Prunus necrotic ringspot virus isolated from rose in Brazil

2015 ◽  
Vol 45 (12) ◽  
pp. 2197-2200 ◽  
Author(s):  
Thor Vinícius Martins Fajardo ◽  
Monique Bezerra Nascimento ◽  
Marcelo Eiras ◽  
Osmar Nickel ◽  
Gilvan Pio-Ribeiro
Keyword(s):  
Amino Acid ◽  
Molecular Characterization ◽  
Molecular Analysis ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Causal Agent ◽  
Ringspot Virus ◽  
Prunus Necrotic Ringspot Virus ◽  
First Time

ABSTRACT: There is no molecular characterization of Brazilian isolates of Prunus necrotic ringspot virus (PNRSV), except for those infecting peach. In this research, the causal agent of rose mosaic was determined and the movement (MP) and coat (CP) protein genes of a PNRSV isolate from rose were molecularly characterized for the first time in Brazil. The nucleotide and deduced amino acid sequences of MP and CP complete genes were aligned and compared with other isolates. Molecular analysis of the MP and CP nucleotide sequences of a Brazilian PNRSV isolate from rose and others from this same host showed highest identities of 96.7% and 98.6%, respectively, and Rose-Br isolate was classified in PV32 group.

scholarly journals Molecular Characterization of HOXA2 and HOXA3 Binding Properties

2021 ◽  
Vol 9 (4) ◽  
pp. 55
Author(s):  
Joshua Mallen ◽  
Manisha Kalsan ◽  
Peyman Zarrineh ◽  
Laure Bridoux ◽  
Shandar Ahmad ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Characterization ◽  
Sequence Motif ◽  
Body Parts ◽  
Binding Affinities ◽  
Binding Properties ◽  
Functional Consequences

The highly conserved HOX homeodomain (HD) transcription factors (TFs) establish the identity of different body parts along the antero–posterior axis of bilaterian animals. Segment diversification and the morphogenesis of different structures is achieved by generating precise patterns of HOX expression along the antero–posterior axis and by the ability of different HOX TFs to instruct unique and specific transcriptional programs. However, HOX binding properties in vitro, characterised by the recognition of similar AT-rich binding sequences, do not account for the ability of different HOX to instruct segment-specific transcriptional programs. To address this problem, we previously compared HOXA2 and HOXA3 binding in vivo. Here, we explore if sequence motif enrichments observed in vivo are explained by binding affinities in vitro. Unexpectedly, we found that the highest enriched motif in HOXA2 peaks was not recognised by HOXA2 in vitro, highlighting the importance of investigating HOX binding in its physiological context. We also report the ability of HOXA2 and HOXA3 to heterodimerise, which may have functional consequences for the HOX patterning function in vivo.

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