scholarly journals The Cryptococcus neoformans GeneDHA1 Encodes an Antigen That Elicits a Delayed-Type Hypersensitivity Reaction in Immune Mice

2000 ◽  
Vol 68 (11) ◽  
pp. 6196-6201 ◽  
Author(s):  
M. Alejandra Mandel ◽  
Greg G. Grace ◽  
Kris I. Orsborn ◽  
Fredda Schafer ◽  
Juneann W. Murphy ◽  
...  
Keyword(s):  
Amino Acid ◽  
Cryptococcus Neoformans ◽  
Culture Filtrate ◽  
Genomic Library ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Delayed Type Hypersensitivity ◽  
Pcr Analysis ◽  
Rt Pcr ◽  
Fruiting Body Formation

ABSTRACT When mice are vaccinated with a culture filtrate fromCryptococcus neoformans (CneF), they mount a protective cell-mediated immune response as detected by dermal delayed-type hypersensitivity (DTH) to CneF. We have identified a gene (DHA1) whose product accounts at least in part for the DTH reactivity. Using an acapsular mutant (Cap-67) of C. neoformans strain B3501, we prepared a culture filtrate (CneF-Cap67) similar to that used for preparing the commonly used skin test antigen made with C. neoformans 184A (CneF-184A). CneF-Cap67 elicited DTH in mice immunized with CneF-184A. Deglycosylation of CneF-Cap67 did not diminish its DTH activity. Furthermore, size separation by either chromatography or differential centrifugation identified the major DTH activity of CneF-Cap67 to be present in fractions that contained proteins of approximately 19 to 20 kDa. Using N-terminal and internal amino acid sequences derived from the 20-kDa band, oligonucleotide primers were designed, two of which produced a 776-bp amplimer by reverse transcription-PCR (RT-PCR) using RNA from Cap-67 to prepare cDNA for the template. The amplimer was used as a probe to isolate clones containing the full-lengthDHA1 gene from a phage genomic library prepared from strain B3501. The full-length cDNA was obtained by 5′ rapid amplification of cDNA ends and RT-PCR. Analysis of DHA1 revealed a similarity between the deduced open reading frame and that of a developmentally regulated gene from Lentinus edodes(shiitake mushroom) associated with fruiting-body formation. Also, the gene product contained several amino acid sequences identical to those determined biochemically from the purified 20-kDa peptide encoded byDHA1. Recombinant DHA1 protein expressed inEscherichia coli was shown to elicit DTH reactions similar to those elicited by CneF-Cap67 in mice immunized against C. neoformans. Thus, DHA1 is the first gene to be cloned from C. neoformans whose product has been shown to possess immunologic activity.

Cloning and Characterization of the Zebrafish mll Ortholog.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1249-1249
Author(s):  
Blaine W. Robinson ◽  
Giuseppe Germano ◽  
Yuanquan Song ◽  
Rita J. Balice-Gordon ◽  
Carolyn A. Felix
Keyword(s):  
Amino Acid ◽  
Blot Analysis ◽  
Temporal Pattern ◽  
Southern Blot Analysis ◽  
Early Embryogenesis ◽  
Amino Acid Sequences ◽  
Pcr Analysis ◽  
Adult Zebrafish ◽  
Wild Type ◽  
Rt Pcr

Abstract Introduction: Zebrafish enable studies of early embryogenesis and hematopoiesis like no other animal models. Many zebrafish orthologs of hematopoietic genes have been identified, and zebrafish models of leukemia are emerging but the zebrafish ortholog of MLL, a critical oncogene disrupted by leukemogenic translocations, has not yet been studied. We cloned the complete zmll cDNA and characterized its temporal expression as a framework for further studies of MLL where current knowledge is still incomplete. Methods: Bioinformatic tools were employed to interrogate the existence and relationship of a zmll ortholog and synteny with human MLL. Degenerate RT-PCR was used to determine whether MLL amino acid sequences in domains highly conserved across species could identify the orthologous zebrafish transcript. Cross-species Southern blot analysis was performed to determine if a predicted zmll gene from restriction map simulations of a projected genomic sequence could be detected with a human cDNA probe for the MLL breakpoint cluster region (bcr). The full-length zmll cDNA was obtained using a combination of 5′ RACE PCR, long-range and conventional PCR. The corresponding protein was analyzed in a phylogram tree. The temporal pattern of zmll RNA expression was examined using quantitative (Q) RT-PCR. Results: Bioinformatic analysis using the human MLL protein as the reference sequence identified two putative “similar to MLL proteins” and predicted two proximal transcript sequences on zebrafish chromosome 15. Gene prediction tools suggested a single genomic structure matching both protein sequences. A conserved block of synteny containing several linked genes surrounded the predicted zmll. Furthermore, zmll and human MLL were in the same map order in an uninterrupted segment with the gene for ubiquitination factor E4A. Degenerate RT-PCR analysis of wild-type adult zebrafish RNA based on cross-species amino acid sequences from highly conserved PHD and SET domains amplified the predicted transcript. Cross-species Southern blot analysis with the human probe detected the projected zmll genomic fragments corresponding to the MLL bcr in adult zebrafish genomic DNA. RT-PCR analysis of wild-type adult zebrafish RNA determined that the two predicted “similar to MLL proteins” were from a single gene. The full length 12657 bp, 35-exon zmll cDNA cloned from wild-type 24 hpf zebrafish embryo RNA predicted a 4218 amino acid protein with CXXC, PHD, Bromodomain, FYRN, FYRC, and SET domains and taspase cleavage sites with 45.8% sequence identity and 57.3% similarity to human MLL. Phylogram tree analysis suggested evolutionary divergence of mammals from teleosts but nonetheless conservation of critical functional domains. QRT-PCR demonstrated maternally supplied zmll mRNA during the earliest embryonic developmental timepoints, and expression of zygotic zmll mRNA during embryogenesis and in the zebrafish adult. Conclusions: These results indicate that there is a single zmll gene with highly conserved functional similarity to human MLL. The temporal pattern of expression, including maternal supply of transcript to the embryo, indicates that zmll is important from early embryogenesis through the entire lifespan of the fish. The high evolutionary conservation of critical domains creates the framework to use zebrafish for studying MLL in hematopoiesis and leukemia.

scholarly journals Sequence Analysis and Initial Characterization of Two Isozymes of Hydroxylaminobenzene Mutase from Pseudomonas pseudoalcaligenes JS45

2000 ◽  
Vol 66 (7) ◽  
pp. 2965-2971 ◽  
Author(s):  
John K. Davis ◽  
George C. Paoli ◽  
Zhongqi He ◽  
Lloyd J. Nadeau ◽  
Charles C. Somerville ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Genomic Library ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Pseudomonas Pseudoalcaligenes ◽  
E Coli ◽  
Specific Activities ◽  
Reading Frames

ABSTRACT Pseudomonas pseudoalcaligenes JS45 grows on nitrobenzene by a partially reductive pathway in which the intermediate hydroxylaminobenzene is enzymatically rearranged to 2-aminophenol by hydroxylaminobenzene mutase (HAB mutase). The properties of the enzyme, the reaction mechanism, and the evolutionary origin of the gene(s) encoding the enzyme are unknown. In this study, two open reading frames (habA and habB), each encoding an HAB mutase enzyme, were cloned from a P. pseudoalcaligenes JS45 genomic library and sequenced. The open reading frames encoding HabA and HabB are separated by 2.5 kb and are divergently transcribed. The deduced amino acid sequences of HabA and HabB are 44% identical. The HAB mutase specific activities in crude extracts of Escherichia coli clones synthesizing either HabA or HabB were similar to the specific activities of extracts of strain JS45 grown on nitrobenzene. HAB mutase activity in E. coli extracts containing HabB withstood heating at 85�C for 10 min, but extracts containing HabA were inactivated when they were heated at temperatures above 60�C. HAB mutase activity in extracts of P. pseudoalcaligenesJS45 grown on nitrobenzene exhibited intermediate temperature stability. Although both the habA gene and thehabB gene conferred HAB mutase activity when they were separately cloned and expressed in E. coli, reverse transcriptase PCR analysis indicated that only habA is transcribed in P. pseudoalcaligenes JS45. A mutant strain derived from strain JS45 in which the habA gene was disrupted was unable to grow on nitrobenzene, which provided physiological evidence that HabA is involved in the degradation of nitrobenzene. A strain in which habB was disrupted grew on nitrobenzene. Gene Rv3078 of Mycobacterium tuberculosisH37Rv encodes a protein whose deduced amino acid sequence is 52% identical to the HabB amino acid sequence. E. colicontaining M. tuberculosis gene Rv3078 cloned into pUC18 exhibited low levels of HAB mutase activity. Sequences that exhibit similarity to transposable element sequences are present between habA and habB, as well as downstream ofhabB, which suggests that horizontal gene transfer resulted in acquisition of one or both of the hab genes.

scholarly journals First Report of Lettuce chlorosis virus Infecting Bean in Spain

Plant Disease ◽  
2014 ◽  
Vol 98 (6) ◽  
pp. 857-857 ◽  
Author(s):  
M. L. Ruiz ◽  
A. Simón ◽  
M. C. García ◽  
D. Janssen
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequences ◽  
Green Bean ◽  
Pcr Analysis ◽  
Economic Damage ◽  
Rt Pcr ◽  
First Report ◽  
Bean Plants ◽  
Field Samples ◽  
Plant Pathol

In September 2011, symptoms typically associated with Bean yellow disorder virus (BYDV) such as intervenal mottling and yellowing on middle and lower leaves combined with brittleness were observed in green bean (Phaseolus vulgaris L.) produced in commercial greenhouses from Granada and Almeria provinces, Spain. The affected plants were all observed in greenhouses infested with Bemisia tabaci. However, collected samples tested negative for BYDV using a specific RT-PCR test (4). Electrophoretic double stranded (ds) RNA analysis from symptomatic plants revealed the presence of a slightly diffused high molecular weight dsRNA band of ~8.5 kb, similar to that produced by the crinivirus Lettuce cholorosis virus (LCV) (3). The dsRNA was purified and used for cDNA synthesis and PCR by uneven PCR (1) using primers derived from LCV genome sequences (GenBank FJ380118 and FJ380119). Amplified DNA fragments were cloned in pGEM-T Easy vector (Promega, Madison, WI) and sequenced. Two different sequences were obtained and the nucleotide and amino acid sequences were analysed using BLAST. Both showed the highest identity with different regions of the LCV genome. The sequence of the first product had 92% nucleotide and 98% amino acid sequence identity with the polyprotein (Orf1a) homologue from RNA1 of LCV (KC602376). The sequence from the second product (KC602375) revealed the highest nucleotide and amino acid identity with the heat shock protein 70 homologue from LCV (90% and 99%, respectively). Based on these sequences, two sets of specific primers were designed (LCVSP 3-forward 5′-AGTGACACAAGTTGGAGCCGAC-3′, LCVSP 4-low 5′-CAGTGTTTGTTGGATATCTGGGG-3′) and (LCVSP 1-forward 5′-TGTTGGAAGGTGGTGAGGTC-3′, LCVSP 2-low 5′-CAGAGACGAGTCATACGTACC-3′) and each produced amplicons of the expected size (463 and 434 nt, respectively) when used in RT-PCR from the collected field samples. Subsequent field surveys from 2012 to 2013 in commercial bean greenhouses confirmed the presence of LCV that apparently had replaced BYDV. Groups of 15 to 20 adults of B. tabaci introduced in clip cages were fed for 24 h on 12 green bean plants infected with LCV and later transferred to six seedlings of bean and six of lettuce (Lactuca sativa L.). After 2 and 4 weeks, total RNA from the lettuce and bean plants was extracted using Plant RNA Reagent (Invitrogen) and subjected to RT-PCR analysis with the LCV-SP 1-2 and LCVSP 3-4 primer sets. All six plants of bean and none of lettuce showed positive for LCV-SP and a repeat experiment revealed identical results. We also seeded and produced lettuce plants within a bean greenhouse that was naturally infected with the virus and infested with B tabaci whiteflies. Under these conditions, we observed that whiteflies migrated freely from the infected bean plants to lettuce. After 4 and 6 weeks, lettuce plants neither produced symptoms nor tested positive for LCV by RT-PCR. This result confirms the existence of a new putative strain of LCV, Lettuce chlorosis virus-SP, unable to infect lettuce plants. To date, natural infections of LCV have not been reported outside California, where the virus failed to infect P. vulgaris (2). This is also the first report of LCV in Spain that infects members of the family Leguminosae. Green bean in southeast Spain was produced in ~9,000 ha of greenhouses until the introduction of BYDV a decade ago, causing considerable economic damage. The recent finding of LCV-SP has urged the local phytosanitary inspections to include this virus in lab tests and to emphasize disease management strategies based on whitefly control. References: (1) X. Chen and R. Wu. Gene 185:195, 1997. (2) J. Duffus et al. Eur. J. Plant Pathol. 102:591, 1996. (3) N. M. Salem et al. Virology 390:45, 2009. (4) E. Segundo et al. Plant Pathol. 53:517, 2004.

scholarly journals Murine erythropoietin gene: cloning, expression, and human gene homology.

1986 ◽  
Vol 6 (3) ◽  
pp. 849-858 ◽  
Author(s):  
C B Shoemaker ◽  
L D Mitsock
Keyword(s):  
Amino Acid ◽  
Genomic Library ◽  
Cdna Probe ◽  
Amino Acid Sequences ◽  
Nucleotide Sequence Analysis ◽  
Coding Region ◽  
Transcription Control ◽  
Erythroid Progenitor ◽  
Human Genes ◽  
Cell Expression

The gene for murine erythropoietin (EPO) was isolated from a mouse genomic library with a human EPO cDNA probe. Nucleotide sequence analysis permitted the identification of the murine EPO coding sequence and the prediction of the encoded amino acid sequence based on sequence conservation between the mouse and human EPO genes. Both the coding DNA and the amino acid sequences were 80% conserved between the two species. Transformation of COS-1 cells with a mammalian cell expression vector containing the murine EPO coding region resulted in secretion of murine EPO with biological activity on both murine and human erythroid progenitor cells. The transcription start site for the murine EPO gene in kidneys was determined. This permitted tentative identification of the transcription control region. The region included 140 base pairs upstream of the cap site which was over 90% conserved between the murine and human genes. Surprisingly, the first intron and much of the 5'- and 3'-untranslated sequences were also substantially conserved between the genes of the two species.

Cloning of rabbit prolactin cDNA and prolactin gene expression in the rabbit mammary gland

1996 ◽  
Vol 16 (1) ◽  
pp. 27-37 ◽  
Author(s):  
L Gabou ◽  
M Boisnard ◽  
I Gourdou ◽  
H Jammes ◽  
J-P Dulor ◽  
...  
Keyword(s):  
Gene Expression ◽  
Mammary Gland ◽  
Amino Acid ◽  
Untranslated Regions ◽  
Pcr Analysis ◽  
Cdna Clones ◽  
Rt Pcr ◽  
Prolactin Gene ◽  
New Zealand White Rabbits ◽  
Rna Probe

ABSTRACT cDNA clones coding for rabbit prolactin were isolated from a pituitary library using a rat prolactin RNA probe. One cDNA contained 873 bases including the entire coding sequence of rabbit prolactin, its signal peptide and the 5′ and 3′ untranslated regions of 44 and 145 nucleotides respectively. The deduced amino acid sequence of the cloned prolactin cDNA presented a 93–78% identity with mink, porcine and human prolactins. The prolactin gene transcription was investigated by RT-PCR analysis in several organs of midlactating New Zealand White rabbits. The ectopic transcription of the prolactin gene was examined in more detail in the mammary gland. A strong PCR signal was detected in the mammary gland of virgin does and was also observed during pregnancy and at the beginning of lactation. This PCR signal was very weak in mid-lactating and absent in post-weaning mammary gland.

scholarly journals Evolutionary Algorithms for Improving De Novo Peptide Sequencing

2021 ◽  
Author(s):  
◽  
Samaneh Azari
Keyword(s):  
Amino Acid ◽  
De Novo ◽  
Peptide Identification ◽  
Peptide Sequencing ◽  
De Novo Sequencing ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Multi Objective ◽  
De Novo Peptide Sequencing ◽  
De Novo Peptide

<p>De novo peptide sequencing algorithms have been developed for peptide identification in proteomics from tandem mass spectra (MS/MS), which can be used to identify and discover novel peptides and proteins that do not have a database available. Despite improvements in MS instrumentation and de novo sequencing methods, a significant number of CID MS/MS spectra still remain unassigned with the current algorithms, often leading to low confidence of peptide assignments to the spectra. Moreover, current algorithms often fail to construct the completely matched sequences, and produce partial matches. Therefore, identification of full-length peptides remains challenging. Another major challenge is the existence of noise in MS/MS spectra which makes the data highly imbalanced. Also missing peaks, caused by incomplete MS fragmentation makes it more difficult to infer a full-length peptide sequence. In addition, the large search space of all possible amino acid sequences for each spectrum leads to a high false discovery rate. This thesis focuses on improving the performance of current methods by developing new algorithms corresponding to three steps of preprocessing, sequence optimisation and post-processing using machine learning for more comprehensive interrogation of MS/MS datasets. From the machine learning point of view, the three steps can be addressed by solving different tasks such as classification, optimisation, and symbolic regression. Since Evolutionary Algorithms (EAs), as effective global search techniques, have shown promising results in solving these problems, this thesis investigates the capability of EAs in improving the de novo peptide sequencing. In the preprocessing step, this thesis proposes an effective GP-based method for classification of signal and noise peaks in highly imbalanced MS/MS spectra with the purpose of having a positive influence on the reliability of the peptide identification. The results show that the proposed algorithm is the most stable classification method across various noise ratios, outperforming six other benchmark classification algorithms. The experimental results show a significant improvement in high confidence peptide assignments to MS/MS spectra when the data is preprocessed by the proposed GP method. Moreover, the first multi-objective GP approach for classification of peaks in MS/MS data, aiming at maximising the accuracy of the minority class (signal peaks) and the accuracy of the majority class (noise peaks) is also proposed in this thesis. The results show that the multi-objective GP method outperforms the single objective GP algorithm and a popular multi-objective approach in terms of retaining more signal peaks and removing more noise peaks. The multi-objective GP approach significantly improved the reliability of peptide identification. This thesis proposes a GA-based method to solve the complex optimisation task of de novo peptide sequencing, aiming at constructing full-length sequences. The proposed GA method benefits the GA capability of searching a large search space of potential amino acid sequences to find the most likely full-length sequence. The experimental results show that the proposed method outperforms the most commonly used de novo sequencing method at both amino acid level and peptide level. This thesis also proposes a novel method for re-scoring and re-ranking the peptide spectrum matches (PSMs) from the result of de novo peptide sequencing, aiming at minimising the false discovery rate as a post-processing approach. The proposed GP method evolves the computer programs to perform regression and classification simultaneously in order to generate an effective scoring function for finding the correct PSMs from many incorrect ones. The results show that the new GP-based PSM scoring function significantly improves the identification of full-length peptides when it is used to post-process the de novo sequencing results.</p>

Molecular cloning, characterization and tissue specificity of the expression in the TAC1 genes from Henan Huai goat (Capra hircus)

2019 ◽  
Author(s):  
Zhilong Tian ◽  
Yuqin Wang ◽  
Huibin Shi ◽  
Zhibo Wu ◽  
Xiaohui Zhang ◽  
...  
Keyword(s):  
Amino Acid ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Capra Hircus ◽  
Reading Frame ◽  
Relative Molecular Weight ◽  
Rapid Amplification ◽  
And Function

To further to understand the structure and function of the TAC1 gene, we cloned the full-length cDNAs of the TAC1 genes from goat by rapid amplification of cDNA ends-PCR and the qRT-PCR was used to analyze the TAC1 mRNA expression patterns of goat various tissues. The full-length cDNA of goat TAC1 was 1176 bp, with a 339 bp open reading frame encoding 112 amino acids. The amino acid sequence analysis revealed that goat TAC1 gene encoded a water-drain protein and its relative molecular weight and isoelectric point was 13,012.86 Da and 6.29 respectively. Alignment and phylogenetic analyses revealed that their amino acid sequences were highly similar to those of other vertebrates. TAC1 expression of the goat of the brain, cerebellum, medulla oblongata, heart, liver, spleen, lung, kidney, uterus, ovaries. These results serve as a foundation for further study on the Capra hircus TAC1 gene.

scholarly journals Characterization of Novel Carbazole Catabolism Genes from Gram-Positive Carbazole Degrader Nocardioides aromaticivorans IC177

2006 ◽  
Vol 72 (5) ◽  
pp. 3321-3329 ◽  
Author(s):  
Kengo Inoue ◽  
Hiroshi Habe ◽  
Hisakazu Yamane ◽  
Hideaki Nojiri
Keyword(s):  
Amino Acid ◽  
Gene Clusters ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Class Iii ◽  
Rt Pcr ◽  
Gram Positive ◽  
Mononuclear Iron ◽  
Reverse Transcription Pcr ◽  
Genes Encoding

ABSTRACT Nocardioides aromaticivorans IC177 is a gram-positive carbazole degrader. The genes encoding carbazole degradation (car genes) were cloned into a cosmid clone and sequenced partially to reveal 19 open reading frames. The car genes were clustered into the carAaCBaBbAcAd and carDFE gene clusters, encoding the enzymes responsible for the degradation of carbazole to anthranilate and 2-hydroxypenta-2,4-dienoate and of 2-hydroxypenta-2,4-dienoate to pyruvic acid and acetyl coenzyme A, respectively. The conserved amino acid motifs proposed to bind the Rieske-type [2Fe-2S] cluster and mononuclear iron, the Rieske-type [2Fe-2S] cluster, and flavin adenine dinucleotide were found in the deduced amino acid sequences of carAa, carAc, and carAd, respectively, which showed similarities with CarAa from Sphingomonas sp. strain KA1 (49% identity), CarAc from Pseudomonas resinovorans CA10 (31% identity), and AhdA4 from Sphingomonas sp. strain P2 (37% identity), respectively. Escherichia coli cells expressing CarAaAcAd exhibited major carbazole 1,9a-dioxygenase (CARDO) activity. These data showed that the IC177 CARDO is classified into class IIB, while gram-negative CARDOs are classified into class III or IIA, indicating that the respective CARDOs have diverse types of electron transfer components and high similarities of the terminal oxygenase. Reverse transcription-PCR (RT-PCR) experiments showed that the carAaCBaBbAcAd and carDFE gene clusters are operonic. The results of quantitative RT-PCR experiments indicated that transcription of both operons is induced by carbazole or its metabolite, whereas anthranilate is not an inducer. Biotransformation analysis showed that the IC177 CARDO exhibits significant activities for naphthalene, carbazole, and dibenzo-p-dioxin but less activity for dibenzofuran and biphenyl.

scholarly journals Identification of a Full-Length cDNA for an Endogenous Retrovirus of Miniature Swine

1998 ◽  
Vol 72 (5) ◽  
pp. 4503-4507 ◽  
Author(s):  
Donna E. Akiyoshi ◽  
Maria Denaro ◽  
Haihong Zhu ◽  
Julia L. Greenstein ◽  
Papia Banerjee ◽  
...  
Keyword(s):  
Amino Acid ◽  
Leukemia Virus ◽  
Endogenous Retrovirus ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Endogenous Retroviruses ◽  
Miniature Swine ◽  
Sequence Identity ◽  
Multiple Organs ◽  
Porcine Endogenous Retrovirus

ABSTRACT Endogenous retroviruses of swine are a concern in the use of pig-derived tissues for xenotransplantation into humans. The nucleotide sequence of porcine endogenous retrovirus taken from lymphocytes of miniature swine (PERV-MSL) has been characterized. PERV-MSL is a type C retrovirus of 8,132 bp with the greatest nucleic acid sequence identity to gibbon ape leukemia virus and murine leukemia virus. Constitutive production of PERV-MSL RNA has been detected in normal leukocytes and in multiple organs of swine. The copy numbers of full-length PERV sequences per genome (approximately 8 to 15) vary among swine strains. The open reading frames for gag, pol, andenv in PERV-MSL have over 99% amino acid sequence identity to those of Tsukuba-1 retrovirus and are highly homologous to those of endogenous retrovirus of cell line PK15 (PK15-ERV). Most of the differences in the predicted amino acid sequences of PK15-ERV and PERV-MSL are in the SU (cell attach- ment) region ofenv. The existence of these PERV clones will enable studies of infection by endogenous retroviruses in xenotransplantation.

scholarly journals First Report of Beet necrotic yellow vein virus on Red Table Beet in Brazil

Plant Disease ◽  
2015 ◽  
Vol 99 (3) ◽  
pp. 423-423 ◽  
Author(s):  
J. A. M. Rezende ◽  
V. M. Camelo ◽  
D. Flôres ◽  
A. P. O. A. Mello ◽  
E. W. Kitajima ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sugar Beet ◽  
Hairy Root ◽  
Contaminated Soil ◽  
The United States ◽  
Amino Acid Sequences ◽  
Yellow Vein ◽  
Polymyxa Betae ◽  
Rt Pcr ◽  
First Report

Beet necrotic yellow vein virus (BNYVV) is an economically important pathogen of sugar beet (Beta vulgaris var. saccharifera) in several European, and Asian countries and in the United States (3). The virus is transmitted by the soil-inhabiting plasmodiophorid Polymyxa betae and causes the rhizomania disease of sugar beet. In November 2012, plants of B. vulgaris subsp. vulgaris cv. Boro (red table beet) exhibiting mainly severe characteristic root symptom of rhizomania were found in a commercial field located in the municipality of São José do Rio Pardo, State of São Paulo, Brazil. No characteristic virus-inducing foliar symptom was observed on diseased plants. The incidence of diseased plants was around 70% in the two visited crops. As the hairy root symptom is indicative of infection by BNYVV, the present study aimed to detect and identify this virus associated with the diseased plants. Preliminary leaf dip analysis by transmission electron microscopy revealed the presence of very few benyvirus-like particles. Total RNA was extracted from roots of three symptomatic plants and one asymptomatic plant according to Toth et al. (3). One-step reverse-transcription–polymerase chain reaction (RT-PCR) was performed as described by Morris et al. (2) with primers that amplify part of the coat protein gene at RNA2. The initial assumption that the hairy root symptom was associated with BNYVV infection was confirmed by the amplification of a fragment of ~500 bp from all three symptomatic samples. No amplicon was obtained from the asymptomatic control plant. Amplicons were directly sequenced, and the consensus nucleotide and deduced amino acid sequences showed 100% identity. The nucleotide sequence for one amplicon (Accession No. KM433683) was compared with other sequences deposited in GenBank. The nucleotide (468 nt) and deduced amino acid (156 aa) sequences shared 93 to 100 and 97 to 99% identity, respectively with the corresponding nucleotide and amino acid sequences for other isolates of type A of BNYVV. The virus was transmitted to three of 10 red table beet plants inoculated with contaminated soil, and infection was confirmed by nested RT-PCR, as described by Morris et al. (1), and nucleotide sequencing. This is the first report on the occurrence of BNYVV in Brazil, which certainly will affect the yield of red table beet in the producing region. Therefore, mapping of the occurrence of BNYVV in red table beet-producing areas in Brazil for containment of the spread of the virus is urgent. In the meantime, precautions should be taken to control the movement of contaminated soil and beet roots, carrots, or any vegetable grown on infested land that might introduce the virus to still virus-free regions. References: (1) J. Morris et al. J. Virol. Methods 95:163, 2001. (2) D. D. Sutic et al. Handbook of Plant Virus Diseases. CRC Press, Boca Raton, Florida, 1999. (3) I. K. Toth et al. Methods for the Detection and Quantification of Erwinia carotovora subsp. atroseptica (Pectobacterium carotovorum subsb. atrosepticum) on Potatoes: A Laboratory Manual. Scottish Crop Research Institute, Dundee, Scotland, 2002.

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