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N Vidal

Publications and source records attributed to N Vidal.

At least 19 recordsLinked to original sources
PubMed2006

Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy.

A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.

Genes, env↗
PubMed2006

Identification and molecular characterization of subsubtype A4 in central Africa.

Phylogenetic analysis on partial env sequences of HIV-1-positive samples obtained from sentinel population groups in HIV serosurveillance studies in 1997 and 2002 in the Democratic Republic of Congo (DRC) revealed a high genetic diversity in the number of cocirculating subtypes/CRFs as well as intrasubtype diversity. A cluster of three strains that formed a distinct and well-separated group within the subtype A radiation was observed. To determine a more precise structure of these viruses, the full-length genomes were sequenced. Phylogenetic tree and bootscan analysis showed that all three newly characterized viruses formed a new nonrecombinant lineage that was more closely related to subtype A. The SUDI (Subtype Distance) program showed that the distances of the newly derived HIV-1 sequences to subtype A references fell in the range of distances previously characterized for subsubtypes. According to current nomenclature rules, we have thus designated this new lineage as subsubtype A4. Analysis of viral sequences from other African countries suggests that the A4 strains seem restricted to DRC where they already circulated at the onset of the HIV/AIDS epidemic.

Africa, Central↗
PubMed2006

HIV type 1 pol gene diversity and antiretroviral drug resistance mutations in the Democratic Republic of Congo (DRC).

To study recombination and the natural polymorphism in pol of HIV-1 strains in the Democratic Republic of Congo (DRC) we sequenced the protease and RT genes for 70 HIV-1 strains previously characterized in the env V3-V5 region from a sentinel surveillance study in 2002. For 41 of the 70 (58.6%) strains, the same subtype/ CRF designations were observed in pol and env. Twenty-three (32.9%) of 70 pol sequences were complex recombinants involving two to five subtypes as well as fragments that could not be classified into any of the known subtypes. All subtypes were involved in recombination events. Unclassified (U) and env subtype H strains were very likely to be recombinant strains. Overall, many minor mutations were identified in the protease sequences. Although at the time of our study ARV use was not yet widespread in DRC, three strains were identified with one major mutation associated with drug resistance: L90M and M46L in protease and K103N in RT.

Democratic Republic of the Congo↗
PubMed2004

Familial Alzheimer disease associated with A713T mutation in APP.

Mutations in APP are associated with familial early-onset Alzheimer disease (FAD). Examination of the genomic sequence in one patient with FAD revealed a change located in the axon 17 of the APP gene at position 275329G>A (GenBank accession number: D87675; GI: 2429080); cDNA sequence 2137G>A (GenBank accession number: X06989; GI: 28720). This corresponds to the mutation A713T in APP. AD stage VI of neurofibrillary degeneration and stage C of Abeta-amyloid burden was found at the post-mortem neuropathological examination. Previous studies have suggested that the mutation A713T in APP is a silent mutation or polymorphism. However, we have not found this change in APP in a control population analyzed by the amplification-refractory mutation system (ARMS). It is concluded that A713T in APP is implicated in the pathogenesis of AD. Since the immunohistochemical study indicates that A713T mutation is not likely to relate with Abeta-amyloid processing, the causative role of this rare mutation remains to be warranted.

Alanine↗
PubMed2003

Developmental stages during the rooting of in-vitro-cultured Quercus robur shoots from material of juvenile and mature origin.

In-vitro-cultured shoots of clones initiated from shoots of the basal parts (BS) and the crown (C) of two mature Quercus robur L. trees were subjected to rooting experiments to relate rooting with shoot topophysical origin. The BS shoots exhibited morphologically juvenile characteristics and rooted more easily after indole-3-butyric acid (IBA) treatment than C shoots. When naphthylphthalamic acid (NPA) was applied to BS shoots, rooting capacity decreased and root emergence was delayed at least 2 days compared with shoots treated with IBA only. During the first days of the rooting process, endogenous indole-3-acetic acid (IAA) concentration was higher in C shoots than in BS shoots, regardless of whether the shoots were treated with NPA. Mitotic figures were observed in cells from the basal part of both BS and C shoots 24 h after IBA treatment. After 4 days of IBA treatment, the occurrence of histological events differed between BS shoots and C shoots. Cells of BS shoots became meristematic, giving rise to meristemoids and root primordia, whereas no differentiation of root meristemoids occurred in cells of C shoots. Thus, although adult oak material (C shoots) is capable of responding to the initial stimulus of auxin during the adventitious rooting process, the endogenous IAA concentration is not the factor limiting rooting in adult material.

Indoleacetic Acids↗
PubMed2003

Phosphorylated protein kinases associated with neuronal and glial tau deposits in argyrophilic grain disease.

Tau phosphorylation was examined in argyrophilic grain disease (AGD) by using the phosphospecific tau antibodies Thr181, Ser202, Ser214, Ser 396 and Ser422, and antibodies to non-phosphorylated and phosphorylated mitogen-activated protein kinase (MAPK), extracellular signal-regulated kinases (ERK), stress-activated kinase (SAPK), c-Jun N-terminal kinase (JNK), p38 kinase (p-38), alpha-calcium/calmodulin-dependent kinase II (alphaCaM kinase II), and glycogen synthase kinase-3 (GSK-3), all of which regulate phosphorylation at specific sites of tau. This is the first study in which the role of protein kinases in tau phosphorylation has been examined in AGD. Hyperphosphorylated tau accumulated in grains and pre-tangles in the hippocampus, dentate gyrus, entorhinal and trans-entorhinal cortices, and amygdala in all cases. Ballooned neurons in the amygdala, entorhinal, insular and cingulate cortex, and claustrum contained alphaB-crystallyn and phosphorylated neurofilament epitopes. Some astrocytes and scattered oligodendrocytes containing coiled bodies were recognized with anti-tau antibodies. A few tangles were observed in the entorhinal cortex and hippocampus corresponding to Alzheimer's disease (AD) stages I-III of Braak and Braak. None of the present cases was associated with progressive supranuclear palsy or with alpha-synuclein pathology. Two bands of phospho-tau of 64 and 68 kDa were observed in Western blots of sarkosyl-insoluble fractions enriched with abnormal filaments in AGD, a pattern that contrasts with the 4-band pattern obtained in AD. No modifications in the expression of non-phosphorylated MEK-1, ERK2 and GSK-3alpha/beta, as revealed by immunohistochemistry, were seen in AGD, but sarkosyl-insoluble fractions were particularly enriched in JNK-1 and alphaCaM kinase II. Increased expression of the phosphorylated (P) forms of MAPK/ERK, SAPK/JNK, p38 and GSK-3beta was found in grains and tau-containing cells in AGD. MAPK/ERK-P immunoreactivity was observed in pre-tangles and, diffusely, in the cytoplasm of ballooned neurons, but not in grains. Strong SAPK/JNK-P and P38-P, and moderate GSK-3b-P immunoreactivities selectively occured in grains, in neurons with pre-tangles and in the peripheral region of the cytoplasm of ballooned neurons. MAPK/ERK-P, SAPK/JNK-P, p38-P and GSK-3beta-P were expressed in tau-containing astrocytes and in oligodendrocytes with coiled bodies. Western blots revealed kinase expression in sarkosyl-insoluble fractions but none of the phospho-kinase antibodies recognized hyper-phosphorylated tau protein. These findings indicate complex, specific profiles of tau phosphorylation and concomitant activation of precise kinases that have the capacity to phosphorylate tau at specific sites in AGD. These kinases co-localize abnormal tau in selected structures and cells, including neurons with pre-tangles, ballooned neurons, astrocytes and oligodendrocytes. Most of these kinases are involved in cell death and cell survival in certain experimental paradigms. However, double-labeling studies with the method of in situ end-labeling of nuclear DNA fragmentation and cleaved (active) caspase-3 immunohistochemistry show no expression of apoptosis and death markers in cells bearing phosphorylated kinases.

Aged↗
PubMed2001

Evidence of two distinct subsubtypes within the HIV-1 subtype A radiation.

Members of HIV-1 group M are responsible for the vast majority of AIDS cases worldwide and have been classified on the basis of their phylogenetic relationships into nine roughly equidistant clades, termed subtypes. Although there are no known phenotypic correlates for these genotypes, the disproportionate spread of certain of these lineages has been taken to indicate that subtype-specific biological differences may exist. The subtype nomenclature thus remains an important molecular epidemiological tool with which to track the course of the group M pandemic. In this study, we have characterized HIV-1 strains described previously as unusual subtype A variants on the basis of partial sequence analysis. Six such strains from Cyprus (CY), South Korea (KR), and the Democratic Republic of Congo (CD) were PCR amplified from infected cell culture or patient PBMC DNA, cloned, and sequences in their entirety (94CY017, 97KR004, 97CDKTB48, and 97CDKP58) or as half genomes (97CDKS10 and 97CDKFE4). Distance and phylogenetic analyses showed that four of these viruses (94CY017, 97CDKTB48, 97CDKFE4, and 97CDKS10) were closely related to each other, but quite divergent from all other HIV-1 strains, except for subtype A viruses, which represented their closest relatives. In phylogenetic trees from gag, pol, env, and nef regions, the four newly characterized HIV-1 strains formed a distinct sister clade to subtype A, which was as closely related to subtype A as subsubtypes F1 and F2 are to each other. According to current nomenclature rules, this defines a subsubtype, which we have tentatively termed A2. The two other viruses, 97KR004 and 97CDKP58, as well as a full-length HIV-1 sequence from the sequence database (ZAM184), were found to represent complex A2/D, A2/G, and A2/C recombinants, respectively. These results indicate that HIV-1 subtype A is composed of two subsubtypes (A1 and A2), both of which appear to have a widespread geographic distribution. The A2 viruses described here represent the first reference reagents for this new group M lineage.

Cyprus↗
PubMed2000

Identification of a complex env subtype E HIV type 1 virus from the democratic republic of congo, recombinant with A, G, H, J, K, and unknown subtypes.

Up to now, all known env subtype E viruses (CRF01-AE) have had the same mosaic structure with subtype A, and no other env subtype E HIV-1 viruses with non-A subtypes in their genomes have been described. In this report we describe the full-length genome sequence of an env subtype E isolate with a recombinant genome different from the prototype CRF01-AE strains. The 97CD-KTB49 strain, obtained from a tuberculosis patient in Kinshasa, has a complex mosaic genome involving subtypes A, E, G, H, J, K, and several unknown fragments. The U sequences formed well-separated clusters together with previously described unknown fragments from CRF04-cpx (subtype I), and from Z321, the oldest intersubtype recombinant isolated in 1976 in the Democratic Republic of Congo. The complex recombinant virus from our study is not an isolated strain; partial sequencing of a second strain, 97CD-KFE45, confirmed the breakpoints observed in the 97CD-KTB49 strain in the regions sequenced. The complexity of these recombinant strains suggests a longstanding presence of subtype E in Central Africa.

Democratic Republic of the Congo↗
PubMed2000

Near-full-length genome sequencing of divergent African HIV type 1 subtype F viruses leads to the identification of a new HIV type 1 subtype designated K.

We recently reported a high divergence among African subtype F strains. Three well-separated groups (F1, F2, and F3) have been shown based on the phylogenetic analysis of the p24 gag and envelope sequences with genetic distances similar to those observed for known subtypes. In this study, we characterized the near-full-length genomes of two strains from epidemiological unlinked individual belonging to each of the subgroups: F1 (96FR-MP411), F2 (95CM-MP255 and 95CM-MP257), and F3 (96CM-MP535 and 97ZR-EQTB11). Phylogenetic analysis of the near-full-length sequences and for each of the genes separately showed the same three groups, supported by high bootstrap values. Diversity plotting, BLAST subtyping, and bootstrap plotting confirmed that the divergent F strains correspond to nonrecombinant viruses. The divergence between F1 and F2 is consistently lower than that seen in any other intersubtype comparison, with the exception of subtypes B and D. Based on all the different analyses, we propose to divide subtype F into two subclades, with F1 gathering the known subtype F strains from Brazil and Finland, and our African strain (96FR-MP411), and F2 containing the 95CM-MP255 and 95CM-MP257 strains from Cameroon. The F3 strains, 97ZR-EQTB11 from the Democratic Republic of Congo and 96CM-MP535 from Cameroon, meet the criteria of a new subtype designated as K. The equidistance of subtype K to the other subtypes of HIV-1 suggests that this subtype existed as long as the others, the lower distance between B and D, and between F1 and F2 suggest a more recent subdivision for these latter strains.

Africa↗
PubMed2000

Phylogenetic relationships of xenodontine snakes inferred from 12S and 16S ribosomal RNA sequences.

The phylogenetic relationships of xenodontine snakes are inferred from sequence analyses of portions of two mitochondrial genes (12S and 16S ribosomal RNA) in 85 species. Although support values for most of the basal nodes are low, the general pattern of cladogenesis observed is congruent with many independent molecular, morphological, and geographical data. The monophyly of xenodontines and the basal position of North American xenodontines in comparison with Neotropical xenodontines are favored, suggesting an Asian-North American origin of xenodontines. West Indian xenodontines (including endemic genera and members of the genus Alsophis) appear to form a monophyletic group belonging to the South American clade. Their mid-Cenozoic origin by dispersal using ocean currents is supported. Within South American mainland xenodontines, the tribes Hydropsini, Pseudoboini, and Xenodontini are monophyletic. Finally, our results suggest that some morphological and ecological traits concerning maxillary dentition, macrohabitat use, and foraging strategy have appeared multiple times during the evolution of xenodontine snakes.

Animals↗
PubMed2000

Unprecedented degree of human immunodeficiency virus type 1 (HIV-1) group M genetic diversity in the Democratic Republic of Congo suggests that the HIV-1 pandemic originated in Central Africa.

The purpose of this study was to document the genetic diversity of human immunodeficiency virus type 1 (HIV-1) in the Democratic Republic of Congo (DRC; formerly Zaire). A total of 247 HIV-1-positive samples, collected during an epidemiologic survey conducted in 1997 in three regions (Kinshasa [the capital], Bwamanda [in the north], and Mbuyi-Maya [in the south]), were genetically characterized in the env V3-V5 region. All known subtypes were found to cocirculate, and for 6% of the samples the subtype could not be identified. Subtype A is predominant, with prevalences decreasing from north to south (69% in the north, 53% in the capital city, and 46% in the south). Subtype C, D, G, and H prevalences range from 7 to 9%, whereas subtype F, J, K, and CRF01-AE strains represent 2 to 4% of the samples; only one subtype B strain was identified. The highest prevalence (25%) of subtype C was in the south, and CRF01-AE was seen mainly in the north. The high intersubtype variability among the V3-V5 sequences is the most probable reason for the low (45%) efficiency of subtype A-specific PCR and HMA (heteroduplex mobility assay). Eighteen (29%) of 62 samples had discordant subtype designations between env and gag. Sequence analysis of the entire envelope from 13 samples confirmed the high degree of diversity and complexity of HIV-1 strains in the DRC; 9 had a complex recombinant structure in gp160, involving fragments of known and unknown subtypes. Interestingly, the unknown fragments from the different strains did not cluster together. Overall, the high number of HIV-1 subtypes cocirculating, the high intrasubtype diversity, and the high numbers of possible recombinant viruses as well as different unclassified strains are all in agreement with an old and mature epidemic in the DRC, suggesting that this region is the epicenter of HIV-1 group M.

Africa, Central↗
PubMed1999

High diversity of HIV-1 subtype F strains in Central Africa.

In this paper, we studied the variability of HIV-1 subtype F strains in Africa. For 11 viruses, mainly of Central African origin, different parts of the genome were genetically characterized. For all strains the V3-V5 region of the envelope gene was sequenced, and for 7 strains, the entire envelope gene was studied. For 10 strains, the p24 region of the gag gene was also sequenced. For each region studied, three subgroups in the F subtype were identified, F1, F2, and F3. These three subgroups were supported by high bootstrap values and the intra- and inter-subgroup F distances were comparable to those obtained for the known subtypes A, B, C, D, E, G, and H. In subgroup F1, some African strains clustered with previously described strains from Brazil and Romania, suggesting an African origin of the HIV-1 epidemic in these countries. A more detailed analysis of the gag and the envelope sequences allowed the identification of four recombinant viruses. Our data show a high diversity among subtype F strains, suggesting the presence of new subtypes in the regions studied. If biological differences exist among subtypes, it is important that these subtypes be well defined. The data from our study show that there is a need to clearly identify the different subgroups within the F subtype.

Acquired Immunodeficiency Syndrome↗
PubMed1999

Ganciclovir resistance and UL97 gene mutations in cytomegalovirus blood isolates from patients with AIDS treated with ganciclovir.

BACKGROUND: Treatment of cytomegalovirus (CMV) diseases with protracted administration of ganciclovir can promote the development of resistant CMV that is associated with a poor response to therapy. It has been shown that the majority of ganciclovir-resistant CMV isolates carry mutations in the UL97 phosphotransferase gene. OBJECTIVES: To evaluate the frequency of CMV resistance to ganciclovir in patients with AIDS treated with ganciclovir and to identify the UL97 gene mutations associated with ganciclovir resistance. STUDY DESIGN: Analysis of CMV blood isolates obtained over 1 year from patients treated with ganciclovir. CMV susceptibility to ganciclovir was determined by an immediate early antigen plaque reduction assay; UL97 gene mutations were identified by restriction enzyme digest analysis and sequencing. RESULTS: Twenty-nine patients were followed-up; 17 CMV blood isolates were obtained from 10 ganciclovir-experienced patients. Thirteen (76%) of these isolates, obtained from seven (24%) patients after a median treatment duration of 5.5 months, were resistant to ganciclovir. Five of the seven patients who had a ganciclovir-resistant CMV in blood showed retinitis progression. UL97 gene mutations were identified in nine CMV isolates at codons 460 (M --> V), 594 (A --> V and A --> T), and 595(L --> S). Three patients developed a ganciclovir-resistant virus after a ganciclovir treatment shorter than 60 days (28-58 days). In another patient, we observed that ganciclovir resistance persisted 4 months after discontinuation of ganciclovir therapy. CONCLUSION: Our results indicate that ganciclovir resistance due to UL97 gene mutations is common in subjects with AIDS-related CMV diseases treated with ganciclovir. Detection of these mutations represents a tool for the management of patients with ganciclovir therapy.

AIDS-Related Opportunistic Infections↗
PubMed1998

Lazaroid-enhanced survival of grafted dopamine neurons does not increase target innervation.

The lazaroid U-74006F enhances survival of grafted ventral mesencephalic neurons. In this study the intraocular grafting model was used and survival and outgrowth from fetal ventral mesencephalic grafts treated with U-74006F was evaluated in nigrostriatal co-grafts. Fetal lateral ganglionic eminence was implanted into the anterior eye chamber and left to mature. Fetal ventral mesencephalon was then implanted and the eyes were treated with U-74006F. The lazaroid treatment enhanced survival of tyrosine hydroxylase (TH)-positive neurons, but did not enhance TH-positive nerve fiber growth into the striatal portions of the co-grafts. However, a marked increase in nerve fiber formation was found within the ventral mesencephalic grafts. In conclusion, increased cell survival enhanced nerve fiber formation within the ventral mesencephalic portion of the co-graft and not, as expected, in the striatal part.

Acetylcholinesterase↗