scholarly journals Prevalence of GII.4 Sydney Norovirus Strains and Associated Factors of Acute Gastroenteritis in Children: 2019/2020 Season in Guangzhou, China

2021 ◽  
Author(s):  
Lei Duan ◽  
Xiaohan Yang ◽  
Jia Xie ◽  
Wenli Zhan ◽  
Changbin Zhang ◽  
...  
Keyword(s):  
Acute Gastroenteritis ◽  
Continuous Monitoring ◽  
Gene Sequence ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Severe Diarrhoea ◽  
Chain Reaction ◽  
Women And Children ◽  
Polymerase Chain ◽  
Reading Frames

AbstractNorovirus, the leading cause of non-bacterial acute gastroenteritis (AGE) worldwide, is constantly mutating. Continuous monitoring of the evolution of epidemic genotypes and emergence of novel genotypes is, therefore, necessary. This study determined the prevalence and clinical characteristics of norovirus strains in AGE in Guangzhou, China in 2019/2020 season. This study included children aged 2–60 months diagnosed with AGE in Guangzhou Women and Children Hospital, from August 2019 to January 2020. Norovirus was detected by real-time polymerase chain reaction and clinical data were obtained. Genotyping and phylogenetic analyses were performed with partial gene sequence fragments located within the open reading frames 1 and 2. During the study period, 168 children (61.3% males) were confirmed as norovirus infectious AGE. The main symptoms were diarrhoea and vomiting and 38 patients (22.6%) had seizures. Norovirus was mainly prevalent in October and November, and GII.4 Sydney[P31] was the major genotype circulating in Guangzhou. The phylogenetic tree showed that the Guangzhou strains had high homology with the strains circulating in 2017–2019 worldwide. GII.4 Sydney was the main prevalent norovirus genotype in Guangzhou from August 2019 to January 2020, which had more severe diarrhoea than those of other genotypes. These findings provide a valuable reference for the prevention, control, and treatment of norovirus in the future.

scholarly journals The Previously Unidentified, Divergent Badnavirus Species Cacao red vein-banding virus is Associated with Cacao Swollen Shoot Disease in Nigeria

Plant Disease ◽  
2019 ◽  
Vol 103 (6) ◽  
pp. 1302-1308 ◽  
Author(s):  
Nomatter Chingandu ◽  
Lelia Dongo ◽  
Osman A. Gutierrez ◽  
Judith K. Brown
Keyword(s):  
Phylogenetic Analyses ◽  
Pcr Amplification ◽  
West African ◽  
Open Reading Frames ◽  
Nucleotide Identity ◽  
Genome Sequences ◽  
Foliar Symptoms ◽  
Field Samples ◽  
Polymerase Chain ◽  
Reading Frames

Cacao swollen shoot disease (CSSD) of Theobroma cacao was reported in Nigeria in 1944; however, no badnaviral genome sequences have been found associated with the symptomatic trees. In 2017, leaf samples (n = 18) were collected from cacao trees from Osun and Oyo, Nigeria showing foliar symptoms that included red vein-banding and shoot swelling, and variable secondary mosaic, mottling, and fern-like pattern symptoms. Abutting primers designed around previously determined 500-bp intergenic region sequences were used for polymerase chain reaction (PCR) amplification. Of the 18 samples, 9 yielded an approximately 7,000-bp, apparently genome-size product. The nine genomes were sequenced and found to encode four open reading frames, and to share 86 to 99% nucleotide identity. Pairwise analysis of the Nigerian genomes with 21 previously reported CSSD badnaviruses, at the complete genome and reverse-transcription ribonuclease H (1,230 bp) sequence levels, indicated 71 to 75 and 72 to 76% nucleotide identity, respectively. Phylogenetic analysis of the nine complete genomes indicated that the closest relatives of the divergent Nigerian isolates were previously described West African CSSD badnaviruses. Based on pairwise comparisons and phylogenetic analyses, the Nigerian CSSD isolates constitute a previously unrecognized Badnavirus sp., herein named Cacao red vein-banding virus (CRVBV). Primers designed based on the CRVBV genome sequences amplified a 1,068-bp fragment from 16 of 18 field samples tested by PCR, suggesting the possible existence of additional CRVBV variants.

scholarly journals Analysis of pFQ12, a 22.4-kbFrankiaplasmid

2001 ◽  
Vol 47 (7) ◽  
pp. 608-617 ◽  
Author(s):  
Theodore R John ◽  
Jeffrey M Rice ◽  
Jerry D Johnson
Keyword(s):  
Amino Acids ◽  
Woody Plants ◽  
Codon Bias ◽  
Open Reading Frames ◽  
Rt Pcr ◽  
Chain Reaction ◽  
Rich Region ◽  
Filter Hybridization ◽  
Polymerase Chain ◽  
Reading Frames

Frankia are gram-positive, filamentous bacteria capable of fixing atmospheric dinitrogen in symbiosis with a wide variety of woody plants and shrubs. Some isolates of Frankia harbor plasmids of 8.5 (pFQ11) and 22.4 kb (pFQ12) that have no known function but are transmitted through many generations in culture. We have sequenced the 22 437-bp pFQ12 plasmid that is present in isolates CpI1 and ArI3. This sequence, with 76% G+C, is almost totally unrelated to that of pFQ11 found in the same cells. However, four regions of identity, 40-90 bp each, are dispersed around the plasmids. The 22.4-kb plasmid has >50 open reading frames (ORFs) that encode putative proteins of more than 100 amino acids, with the largest being 2226 amino acids. Twenty of these ORFs are likely to encode proteins based on their codon bias as determined by two different algorithms. Transcripts from nine of these regions have been identified by reverse transcriptase-polymerase chain reaction (RT-PCR) or filter hybridization. The two Frankia plasmids each encode a protein similar to the korSA protein that regulates transmission of pSAM2 in Streptomyces. The origin of replication (ORI) region of pFQ12 was localized by intrastrand AT and GC equivalence switch. It includes a 40-bp, intergenic, A+T-rich region that has a strong identity in pFQ11.Key words: ORI analysis, RT-PCR, Glimmer, DNA sequence.

scholarly journals Expression of HERV-K proviruses in human leukocytes

Blood ◽  
1993 ◽  
Vol 81 (9) ◽  
pp. 2369-2374
Author(s):  
I Brodsky ◽  
B Foley ◽  
D Haines ◽  
J Johnston ◽  
K Cuddy ◽  
...  
Keyword(s):  
Human Blood ◽  
Blood Cells ◽  
Open Reading Frames ◽  
Chain Reaction ◽  
Blood Leukocytes ◽  
Normal Individuals ◽  
Class 1 ◽  
Polymerase Chain ◽  
Ribonuclease Protection ◽  
Reading Frames

HERV-K is a 50-copy, human endogenous, class 1 retroviral element that contains some polycistrons with gag, pol, and env open reading frames. Although expression of HERV-K proviruses has been shown in cultured human cell lines, expression of these elements has not been shown in human blood leukocytes. Using both reverse transcriptase-polymerase chain reaction and ribonuclease protection techniques, we show HERV-K pol gene expression in human blood leukocytes. Expression in blood leukocytes from 7 normal individuals was from a variety of different HERV-K proviruses, while restricted expression was observed in blood cells of 5 leukemia patients and 3 polycythemia vera patients. Evidence is presented suggesting that the restricted expression in leukemia blood cells is a result of gene regulation, not gene amplification.

scholarly journals Expression of HERV-K proviruses in human leukocytes

Blood ◽  
1993 ◽  
Vol 81 (9) ◽  
pp. 2369-2374 ◽  
Author(s):  
I Brodsky ◽  
B Foley ◽  
D Haines ◽  
J Johnston ◽  
K Cuddy ◽  
...  
Keyword(s):  
Human Blood ◽  
Blood Cells ◽  
Open Reading Frames ◽  
Chain Reaction ◽  
Blood Leukocytes ◽  
Normal Individuals ◽  
Class 1 ◽  
Polymerase Chain ◽  
Ribonuclease Protection ◽  
Reading Frames

Abstract HERV-K is a 50-copy, human endogenous, class 1 retroviral element that contains some polycistrons with gag, pol, and env open reading frames. Although expression of HERV-K proviruses has been shown in cultured human cell lines, expression of these elements has not been shown in human blood leukocytes. Using both reverse transcriptase-polymerase chain reaction and ribonuclease protection techniques, we show HERV-K pol gene expression in human blood leukocytes. Expression in blood leukocytes from 7 normal individuals was from a variety of different HERV-K proviruses, while restricted expression was observed in blood cells of 5 leukemia patients and 3 polycythemia vera patients. Evidence is presented suggesting that the restricted expression in leukemia blood cells is a result of gene regulation, not gene amplification.

scholarly journals Expanding the Diversity of the IS630-Tc1-mariner Superfamily: Discovery of a Unique DD37E Transposon and Reclassification of the DD37D and DD39D Transposons

Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1103-1115 ◽  
Author(s):  
Hongguang Shao ◽  
Zhijian Tu
Keyword(s):  
Phylogenetic Analyses ◽  
Mosquito Species ◽  
Open Reading Frames ◽  
Inverted Repeats ◽  
Sequence Comparisons ◽  
Wide Range ◽  
Multiple Copies ◽  
Catalytic Motif ◽  
Open The Doors ◽  
Reading Frames

Abstract A novel transposon named ITmD37E was discovered in a wide range of mosquito species. Sequence analysis of multiple copies in three Aedes species showed similar terminal inverted repeats and common putative TA target site duplications. The ITmD37E transposases contain a conserved DD37E catalytic motif, which is unique among reported transposons of the IS630-Tc1-mariner superfamily. Sequence comparisons and phylogenetic analyses suggest that ITmD37E forms a novel family distinct from the widely distributed Tc1 (DD34E), mariner (DD34D), and pogo (DDxD) families in the IS630-Tc1-mariner superfamily. The inclusion in the phylogenetic analysis of recently reported transposons and transposons uncovered in our database survey provided revisions to previous classifications and identified two additional families, ITmD37D and ITmD39D, which contain DD37D and DD39D motifs, respectively. The above expansion and reorganization may open the doors to the discovery of related transposons in a broad range of organisms and help illustrate the evolution and structure-function relationships among these distinct transposases in the IS630-Tc1-mariner superfamily. The presence of intact open reading frames and highly similar copies in some of the newly characterized transposons suggests recent transposition. Studies of these novel families may add to the limited repertoire of transgenesis and mutagenesis tools for a wide range of organisms, including the medically important mosquitoes.

scholarly journals Pectobacterium spp. Associated with Bacterial Stem Rot Syndrome of Potato in Canada

2012 ◽  
Vol 102 (10) ◽  
pp. 937-947 ◽  
Author(s):  
S. H. De Boer ◽  
X. Li ◽  
L. J. Ward
Keyword(s):  
Gene Sequence ◽  
Blackleg Disease ◽  
Chain Reaction ◽  
Biochemical Tests ◽  
Pectobacterium Atrosepticum ◽  
Physiological Characterization ◽  
Specific Polymerase Chain Reaction ◽  
Sequence Identification ◽  
Carotovorum Subsp ◽  
Polymerase Chain

Pectobacterium atrosepticum, P. carotovorum subsp. brasiliensis, P. carotovorum subsp. carotovorum, and P. wasabiae were detected in potato stems with blackleg symptoms using species- and subspecies-specific polymerase chain reaction (PCR). The tests included a new assay for P. wasabiae based on the phytase gene sequence. Identification of isolates from diseased stems by biochemical or physiological characterization, PCR, and multi-locus sequence typing (MLST) largely confirmed the PCR detection of Pectobacterium spp. in stem samples. P. atrosepticum was most commonly present but was the sole Pectobacterium sp. detected in only 52% of the diseased stems. P. wasabiae was most frequently present in combination with P. atrosepticum and was the sole Pectobacterium sp. detected in 13% of diseased stems. Pathogenicity of P. wasabiae on potato and its capacity to cause blackleg disease were demonstrated by stem inoculation and its isolation as the sole Pectobacterium sp. from field-grown diseased plants produced from inoculated seed tubers. Incidence of P. carotovorum subsp. brasiliensis was low in diseased stems, and the ability of Canadian strains to cause blackleg in plants grown from inoculated tubers was not confirmed. Canadian isolates of P. carotovorum subsp. brasiliensis differed from Brazilian isolates in diagnostic biochemical tests but conformed to the subspecies in PCR specificity and typing by MLST.

Gene sequences of the pcpB gene of pentachlorophenol-degrading Sphingomonas chlorophenolica found in nondegrading bacteria

1998 ◽  
Vol 44 (7) ◽  
pp. 667-675 ◽  
Author(s):  
Vandana M Saboo ◽  
Michael A Gealt
Keyword(s):  
Polymerase Chain Reaction ◽  
Gene Sequence ◽  
Acid Methyl Ester ◽  
Solid Support ◽  
Contaminated Site ◽  
Chain Reaction ◽  
Hybridization Data ◽  
Acid Methyl ◽  
Sphingomonas Chlorophenolica ◽  
Polymerase Chain

Bacteria isolated from a pentachlorophenol (PCP) contaminated site grew in the presence of 50 µg PCP/mL but were not able to degrade it in either liquid medium or the presence of 1% sterile potting soil as a solid support. Probes developed using the gene sequence of PCP-4-monooxygenase (pcpB) from Sphingomonas chlorophenolica sp.nov hybridized to two separate isolates. Identification based on fatty acid methyl ester profiles (Sherlock™), substrate utilization (BIOLOG™), and 16S rRNA showed that the two strains were different from each other and from Sphingomonas chlorophenolica. Sequences from these isolates, amplified by polymerase chain reaction, confirmed the homology with pcpB. The presence of pcpB sequences in these nondegraders indicated that growth and hybridization data alone were insufficient for predicting degradation capability. Key words: pentachlorophenol, Sphingomonas chlorophenolica, pcpB gene, pentachlorophenol-4-monooxygenase.

scholarly journals Evolutionary History of Cucumber Mosaic Virus Deduced by Phylogenetic Analyses

2002 ◽  
Vol 76 (7) ◽  
pp. 3382-3387 ◽  
Author(s):  
Marilyn J. Roossinck
Keyword(s):  
Cucumber Mosaic Virus ◽  
Mosaic Virus ◽  
Virus Isolate ◽  
Phylogenetic Analyses ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Nontranslated Region ◽  
History Of ◽  
Evolutionary Success ◽  
Reading Frames

ABSTRACT Cucumber mosaic virus (CMV) is an RNA plant virus with a tripartite genome and an extremely broad host range. Previous evolutionary analyses with the coat protein (CP) and 5′ nontranslated region (NTR) of RNA 3 suggested subdivision of the virus into three groups, subgroups IA, IB, and II. In this study 15 strains of CMV whose nucleotide sequences have been determined were used for a complete phylogenetic analysis of the virus. The trees estimated for open reading frames (ORFs) located on the different RNAs were not congruent and did not completely support the subgrouping indicated by the CP ORF, indicating that different RNAs had independent evolutionary histories. This is consistent with a reassortment mechanism playing an important role in the evolution of the virus. The evolutionary trees of the 1a and 3a ORFs were more compact and displayed more branching than did those of the 2a and CP ORFs. This may reflect more rigid host-interactive constraints exerted on the 1a and 3a ORFs. In addition, analysis of the 3′ NTR that is conserved among all RNAs indicated that evolutionary constraints on this region are specific to the RNA component rather than the virus isolate. This indicates that functions other than replication are encoded in the 3′ NTR. Reassortment may have led to the genetic diversity found among CMV strains and contributed to its enormous evolutionary success.

scholarly journals Association of Alcaligenes Faecalis Strain in Juvenile Earthworms, from Cocoons of Eudrilus Eugeniae

2019 ◽  
Vol 9 (2S2) ◽  
pp. 688-692
Keyword(s):  
16S Rrna ◽  
Gene Sequence ◽  
Agar Medium ◽  
Alcaligenes Faecalis ◽  
Rrna Gene ◽  
Eudrilus Eugeniae ◽  
Zone Of Inhibition ◽  
Chain Reaction ◽  
Nutrient Agar Medium ◽  
Polymerase Chain

Cocoons of earthworm Eudrilus eugeniae were collected from vermiculture bed and found that it had antibacterial activity. The size of zone of inhibition was directly proportional to the size of cocoons examined. Along with nutritious fluid and embryos, culturable bacterial community was found inside the cocoons. Bacterial colonies were isolated from the trails of newly hatched, juvenile worms in the nutrient agar medium and examined. Gram negative, rod shaped bacterium was found to be abundant in the trails of juvenile earthworms. Polymerase chain reaction was performed from this bacterium to amplify the gene of 16S rRNA and analyzed. Subsequent bi-directional DNA sequencing revealed that this abundant bacterium is highly related to 16S rRNA gene sequence of a strain, Alcaligenes faecalis. Based on available literature, we hypothesize that this bacterium could be symbiotically associated with cocoons of earthworms.

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