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Garden croton (Codiaeum variegatum L.) plants showing typical begomovirus symptoms of vein twisting, enation and curling were collected from different gardens at Varanasi, Uttar Pradesh state of India ranged from 20 to 30%. All the 10 ten (CR1-CR10) infected samples of garden croton resulted in expected amplicon of 1.2 Kb in PCR specific to begomoviruses. No amplification was obtained for betasatellite and alphasatellite specific primers. The complete genome sequence of DNA-A and DNA-B for two isolates (CR1 and CR2) was obtained through rolling cycle amplification (RCA) and comparisons were made with other begomoviruses using Sequence Demarcation Tool (SDT) which revealed that, DNA-A of two isolates, CR1 (Acc.No.: MW816855) and CR2 (Acc.No.: MW816856) showed maximum nucleotide (nt) identity of 85.7-85.9% with Tomato leaf curl Karnataka virus, which is below the threshold percentage of begomovirus species demarcation, hence considered as novel begomovirus and proposed the name Garden croton enation leaf curl virus (CroELCuV) [IN: Varanasi: Croton: 18]. Further, DNA-B these isolates shared maximum nt identity of 91.0-92.2% (DNA-B) with Tomato leaf curl New Delhi virus. Recombination and GC plot analysis showed that the recombination occured at in low GC content regions of DNA-A and DNA-B of the CroELCuV and are derived from the previously reported several begomoviruses. This is the first record of novel bipartite begomovirus associated with vein twisting, enation and leaf curling of disease of garden garden croton in India and world. Supplementary Information: The online version contains supplementary material available at 10.1007/s13337-022-00772-0.

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PURPOSE: In Japan, the introduction of pneumococcal conjugate vaccine (PCV) in children has decreased vaccine-type (VT) pneumococcal infections caused by penicillin (PEN)-non-susceptible Streptococcus pneumoniae. PEN-non-susceptible strains have gradually emerged among non-vaccine types (NVT). In this study, we aim to investigate the pbp gene mutations and the characteristics of PEN-binding proteins (PBPs) that mediate PEN resistance in NVT strains. MATERIALS AND METHODS: Pneumococcal 41 strains of NVT isolated from patients with invasive pneumococcal infection were randomly selected. Nucleotide sequences for pbp genes encoding PBP1A, PBP2X, and PBP2B were analyzed, and amino acid (AA) substitutions that contribute to ß-lactam resistance were identified. In addition, the three-dimensional (3D) structure of abnormal PBPs in the resistant strain was compared with that of a reference R6 strain via homology modeling. RESULTS: In PEN-non-susceptible NVT strains, Thr to Ala or Ser substitutions in the conserved AA motif (STMK) were important in PBP1A and PBP2X. In PBP2B, substitutions from Thr to Ala, adjacent to the SSN motif, and from Glu to Gly were essential. The 3D structure modeling indicated that AA substitutions are characterized by accumulation around the enzymatic active pocket in PBPs. Many AA substitutions detected throughout the PBP domains were not associated with resistance, except for AA substitutions in or adjacent to AA motifs. Clonal complexes and sequence types showed that almost all NVT cases originated in other countries and spread to Japan via repeat mutations. CONCLUSIONS: NVT with diverse AA substitutions increased gradually with pressure from both antimicrobial agents and vaccines.

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INTRODUCTION: Hepatitis C virus (HCV) shows great structural variability. Based on genome sequencing and phylogenetical analysis, 7 types and 67 subtypes can be differentiated with varying geographical distribution. It is very important to determine the HCV type/subtype prior to starting direct antiviral therapy (DAA), which has been available since 2014, because the type, dose and optimal length of medication depends on these. AIM: In Hungary, the treatment of chronic HCV patients started in 1992 with the relevant special diagnostic tests being carried out in our Molecular Diagnostic Laboratory. Determination of the nucleotide sequence of the Hungarian HCV1b NS5A/PKR-BR region and the type and subtype distribution of Hungarian patients have already been carried out. The current summary discusses the results of 6092 chronic HCV patients (175 serotypes, 5917 genotypes) based on age, gender, regions and genotype distribution changes over the period between 1996 and 2017. METHOD: Serotyping (1996-1999). Genotyping: hybridization (2000-2016), real-time PCR (2016-; Cobas 4800 HCV GT). RESULTS: Genotype distribution: GT1a: 5.6%; GT1b: 84.6%; GT1a + 1b: 5.1%; GT2: 0.1%; GT3: 1.8%; GT4: 0.1%; mixed: 1.6%; GT1 (non-differentiated subtype): 1,1%. Women/men ratio: 52%/48%. The most common age category is 50-60 years (37% of all cases). There was no genotype asymmetry among the four Hungarian regions and Budapest. Over time, the prevalence of genotype 3 increased from 1.6% to 2.8% and the number of patients under the age of 40 doubled. CONCLUSION: There have been no substantial changes in the HCV type/subtype distribution in Hungary over the past 20 years, 1b remaining the most common. The introduction of real-time PCR method for genotyping has resulted in a major quality improvement including only a few mixed subtype results leading to more efficient drug selection. Orv Hetil. 2018; 159(Suppl 2): 2-8.

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This study analyzed the nucleotide sequences of the hypervariable region III (HVRIII) of mitochondrial DNA in Thai individuals. Buccal swab samples were randomly obtained from 100 healthy, unrelated, adult (18-60 years old), volunteer donors living in Thailand. Eighteen different haplotypes were found, of which 11 haplotypes were unique. The most frequent haplotypes observed were 522D-523D. Nucleotide transition from Thymine (T) to Cytosine (C) at position 489 (43%) was the most frequent substitution. Nucleotide transversions were also observed at position 433 (Adenine (A) to C, 1%) and position 499 (Guanine (G) to C, 1%). Fifty-three samples presented nucleotide insertion and deletion of C and A (CA) at position 514-523. Insertion of 1AC (3%) and 2AC (2%) were observed. Deletion of 1CA (53%) and 2CA (2%) at position 514-523 were revealed. The deletion of T at position 459 was observed. The haplotype diversity, random match probability, and discrimination power were calculated to be 0.7770, 0.2308, and 0.7692, respectively.

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Interactions of living organisms with their environment mainly involve modulation of gene expression by stimulation or silencing. One of the epigenetic mechanisms that regulate translation and the levels of transcripts is RNA interference, in which microRNAs (miRNAs) address RNA-induced silencing complexes (RISCs) to degrade specific mRNAs or to silence their translation. In this mechanism, double stranded RNA structure is crucial for miRNA biogenesis and the action of RISCs. RNA molecules can be modified structurally by reactive oxygen and nitrogen species (ROS and RNS) that are produced in cells of all aerobic organisms and may be induced by environmental factors. Here we describe experiments in which changes of ROS and transcript levels are induced by X-irradiation and measured using flow cytometer and the fluorescent dye 2',7'-dichlorofluorescein diacetate and microarray methods in cultured human K562, Me45 and HCT116 cells. Analysis of the nucleotide sequences of mRNAs which are up- or down-regulated after irradiation shows significant differences in the distributions of miRNA-targeted motives between these two groups. Immediately after irradiation most miRNAs behave as "up-regulators", showing more targets in up-than in down-regulated transcripts, and this changes about 12h later when we also observe changes in ROS and miRNA levels. Our results suggest that the changes in the transcriptome could result from changes in RNA interference and that these effects could be related to the changed ROS levels in irradiated cells. We propose that such modulation of gene expression at the mRNA level may be implicated more generally in cellular responses to stresses where ROS levels change.

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Genetic diversities, population genetic structures and demographic histories of the thread-sail filefish Stephanolepis cirrhifer were investigated by nucleotide sequencing of 336 base pairs of the mitochondrial DNA (mtDNA) control region in 111 individuals collected from six populations in Korean coastal waters. A total of 70 haplotypes were defined by 58 variable nucleotide sites. The neighbor-joining tree of the 70 haplotypes was shallow and did not provide evidence of geographical associations. Expansion of S. cirrhifer populations began approximate 51,000 to 102,000 years before present, correlating with the period of sea level rise since the late Pleistocene glacial maximum. High levels of haplotype diversities (0.974±0.029 to 1.000±0.076) and nucleotide diversities (0.014 to 0.019), and low levels of genetic differentiation among populations inferred from pairwise population F ST values (-0.007 to 0.107), support an expansion of the S. cirrhifer population. Hierarchical analysis of molecular variance (AMOVA) revealed weak but significant genetic structures among three groups (F CT = 0.028, p<0.05), and no genetic variation within groups (0.53%; F SC = 0.005, p = 0.23). These results may help establish appropriate fishery management strategies for stocks of S. cirrhifer and related species.

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Objective By sequenceing the Cj1136,Cj1138 and Cj1139 gene of Campylobacter jejuni(C. Jejuni) strains associated with Guillain-Barre Syndrome(GBS),features of Cj1136,Cj1138 and Cj1139 gene were studied.Results were compared with the C.jejuni strain NCTC11168, to find the mutations in sequence of C.jejuni which inducing GBS and their polygenetic relationship was analyzed.Methotis Three GBS-associated C.jejuni strains were isolated from stools of GBS patients from Hebei province who had been diagnosed as clinical AMAN pattern and electrophysiological tests were performed.After distilling and sequencing Cj1136,Cj1138 and Cj1139 genes,results were spliced and assembled into a complete sequence by the terminals overlapped with each other.Sequences of Cj1136,Cj1138 and Cj1139 genes were compared with NCTC11168,to find the mutations and gene feature.Results The Cj1136,Cj1138 and Cj1139 gene of the three GBS-associated C.jejuni strains were composed by 1173 base pairs,1170 base pairs,912 base pairs respectively. The alignment with the related sequence of NCTC11168 showed that there were two same mutations in the Cj1138 gene of the three C.jejuni stains.Data from phylogenetic analysis demonstrated that the three C.jejuni strains were genetically closed to NCTC11168,with the biggest phylogenetic distance between the three of them as 2.1%.Conclusion When compared with NCTC11168 the Cj1138 gene of the three GBS-associated C.jejuni strains had the same mutations which might be related to the development of GBS.Relation between the variation and GBS-pathogenesis remained to be confirmed.The mutations found in the three C.jejuni strains established the foundation for exploring the biological characteristics of GBS-associated C.jejuni strains and demonstrated that the GBS-associated C.jejuni strains of Hebei province having its regional features.

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Objective To investigate the characteristic of sequences of WLAX gene in Campylobacter jejuni(C.jejuni)strains.Methods WLAX gene and the neighbouring sequences were amplified by polymerase chain reaction(PCR).The PCR products were cloned into the vectors of plasmid.The positive recombinants were sequenced and the results were processed by software DNAstar.Results The variation frequency of WLAX sequences in GBS-related C.jejuni was higher than that in non-GBSrelated C.jejuni.The nucleotide sequences of WLAX gene in all the strains in the present study differed from that in genome sequencing strain NCTC11168.The phylogenic tree reflected the regional feature of C.jejuni.Conclusions The probability of sequence variation of WLAX in GBS-related C.jejuni is significantly higher than non-GBS-associated C.jejuni strains,the relation between the variation and GBS-pathogenesis remains to be further confirmed.

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The leguminous weed Macroptilium lathyroides is considered a potential host of the Bean golden yellow mosaic virus (BGYMV; BGMV = Mesoamerican isolates). To determine if M. lathyroides could be a host for BGYMV, an infectivity cycle was established between this weed and Phaseolus vulgaris. Virus transmission was carried out using the whitefly, Bemisia argentifolli, as a vector. Inoculated plants of both species were examined for symptoms such as mosaic, stunting, and leaf distortion. P. vulgaris and M. lathyroides showed golden yellow mosaic symptoms during all infectivity cycle stages. Symptomatic plants of both species were tested for BGYMV using polymerase chain reaction (PCR) and nucleotide sequence analysis. Two degenerate primers sets were used for PCR to detect viral DNA: PAL1v1978/PAR1c715 and PCRc2/PBL12039. PCR analysis using primers PCRc2/PBL12039 amplified viral DNA for component B from both plant species. Nucleotide sequence analysis revealed a 93% identity between the virus isolated from M. lathyroides and the Puerto Rican isolate of BGYMV. These results confirmed that M. lathyroides could serve as an alternative host of BGYMV and that an infectivity cycle of BGYMV could possibly occur between P. vulgaris and M. lathyroides in Puerto Rico.

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An attractive target for anti-herpes chemotherapy is the herpes simplex virus 1 (HSV-1) protease encoded by the UL26 gene. HSV-1 protease is essential for DNA packaging and virus maturation. To perform high throughput for potent inhibitors, the efficient production of larger amounts of highly purified enzyme and protease activity assay method must be established. In this report, expression in E. coli and purification of the protease gene of HSV-1 strain F was investigated. The protease gene was cloned pET28, and the nucleotide sequence of protease catalytic domain of HSV-1 compared strain F with other strains (KOS and CL101). In these results the F strain was different in base sequence. However, the amino acid sequence was identifical. The HSV-1 protease was purified with His-tagged affinity column. The analysis of HSV-1 protease activity Was performed by high performance liquid chromatography.

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Limited nucleotide sequences of human T-cell lymphotropic virus type I (HTLV-1) provirus isolated from the first case of a Korean patient with HTLV-I associated myelopathy and tropical spastic paraparesis (HAM/TSP) were analysed and compared with other isolates from different regions of the world. The sequences of the env, LTR regions (536bp, 690bp respectively) showed 98.7%, 99.3% homologies with the prototype HTLV-I, ATK-1, isolated from a Japanese Adult T-cell leukemia (ATL) patient. A comparison between other isolates from different geographical origins revealed that the Korean HTLV-I isolate is more closely related to Japanese isolates than to those from other geographical origins

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We determined the nucleotide sequences of enzymatically amplified second exons of DRB1and DRB3 genes derived from three Chinese DRw12 homozygous cells and found two distinctDRw12 haplotypes.The combinations between DRB1 and DRB3 genes of the two haplotypeswere different from that in Caucasoid DRw12 HTCa.Thise result might explain the consquenceof generating“new”Dw specificities by cellular assay.