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D Serre

Publications and source records attributed to D Serre.

15 recordsLinked to original sources
PubMed2025

The UTRs of Leishmania donovani vary in length and are enriched in potential regulatory structures.

Leishmania spp. regulate gene expression largely post-transcriptionally, yet untranslated regions (UTRs) remain poorly delineated. We generated high-quality genome and transcriptome datasets for Leishmania donovani strain 1S2D (Ld1S) by combining PacBio HiFi de novo assembly with Oxford Nanopore direct RNA sequencing of promastigotes and axenic amastigotes. The genome assembly consists of 65 scaffolds totaling ~33.3 Mb. Structural comparisons to LdBPK282A1 revealed numerous rearrangements, including some reshuffling genes among polycistronic transcription units and validated by polycistronic reads from RNA sequencing. Promastigote and amastigote RNA sequencing produced 469,010 and 46,729 monocistronic reads containing a spliced-leader and a polyA tail sequences, defining 8,479 transcripts and supporting 7,415 of the 7,969 annotated protein coding genes, as well as 604 putative long non-coding RNAs. We annotated UTRs for 4,921 genes and observed that putative RNA G-quadruplexes were markedly enriched in UTRs. We also noted that 31.9% and 11.5% were expressed into multiple isoforms in promastigotes and amastigotes, respectively. Collectively, these data provide a comprehensive annotation of L. donovani genes and their UTRs and reveal widespread and stage-specific UTR length polymorphisms, and, overall, points to an important role of 3' UTR in post-transcriptional regulation in L. donovani.

Journal Article↗
PubMed2006

In vitro antiseptic properties of an ammonium compound combined with denture base acrylic resin.

BACKGROUND: Denture base acrylic resin is easily colonised by oral endogenous bacteria and Candida spp., and eventually by extra-oral species such as Staphylococcus spp., Pseudomonadaceae or members of Enterobacteriaceae. This microbial reservoir can be responsive for denture related stomatitis and aspiration pneumonia, a life-threatening infection especially in geriatric patients. However, the oral and denture hygiene of dependent elderly individuals is extremely poor. OBJECTIVE: This in vitro study aimed to determine the per cent of a quaternary ammonium compound heat-polymerised in acrylic resin necessary to obtain denture base displaying antiseptic properties. DESIGN: Acrylic resin discs containing 2-50% ammonium polymer (Poly 202063A; 0% control) were soaked in artificial saliva for 4 weeks. Resin discs were incubated for 24 hours with Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa [37 degrees C, brain-heart infusion (BHI) broth and phosphate-buffered saline (PBS) buffer] and Candida albicans (30 degrees C, Schaedler broth), in 15 ml (168 discs) and 600 microl (168 discs) of inoculum. Microbial growth was verified at t 0 hours and t 24 hours. Data were recorded as the mean of three colony forming unit (CFU) numerations. The borderline of antimicrobial effect was determined at 0.1% viable cells. RESULTS: In 600 microl of PBS inoculum, resin specimens had a bactericidal effect (E. coli and S. aureus: 2%; P. aeruginosa: 10%) and a fungicidal effect (C. albicans: 50%). Long-term stability and toxicity in vivo studies are now required. CONCLUSION: A 2% quaternary ammonium compound polymerised with a denture acrylic resin displayed antiseptic properties after a 4-week soaking period in artificial saliva. Such antiseptic denture base could help geriatric patients to improve their oral health.

Acrylic Resins↗
PubMed2005

Nuclear insertions help and hinder inference of the evolutionary history of gorilla mtDNA.

Numts are fragments of mitochondrial DNA (mtDNA) that have been translocated to the nucleus, where they can persist while their mitochondrial counterparts continue to rapidly evolve. Thus, numts represent 'molecular fossils' useful for comparison with mitochondrial variation, and are particularly suited for studies of the fast-evolving hypervariable segment of the mitochondrial control region (HV1). Here we used information from numts found in western gorillas (Gorilla gorilla) and eastern gorillas (Gorilla beringei) to estimate that these two species diverged about 1.3 million years ago (Ma), an estimate similar to recent calculations for the divergence of chimpanzee and bonobo. We also describe the sequence of a gorilla numt still possessing a segment lost from all contemporary gorilla mtDNAs. In contrast to that sequence, many numts of the HV1 are highly similar to authentic mitochondrial organellar sequences, making it difficult to determine whether purported mitochondrial sequences truly derive from that genome. We used all available organellar HV1 and corresponding numt sequences from gorillas in a phylogenetic analysis aimed at distinguishing these two types of sequences. Numts were found in several clades in the tree. This, in combination with the fact that only a limited amount of the extant variation in gorillas has been sampled, suggests that categorization of new sequences by the indirect means of phylogenetic comparison would be prone to uncertainty. We conclude that for taxa such as gorillas that contain numerous numts, direct approaches to the authentication of HV1 sequences, such as amplification strategies relying upon the circularity of the mtDNA molecule, remain necessary.

Animals↗
PubMed2004

Mutations induced by ancient DNA extracts?

We have investigated whether some factor in ancient DNA extracts induces site-specific mutations in modern DNA. We find no evidence for higher mutation rates when extracts from three different Pleistocene mammals are added to modern DNA than when water or extraction blanks are added. We also fail to find evidence that any such factor affects ancient DNA sequences determined from the same extracts. This as well as the patterns of nucleotide substitutions seen in DNA sequences determined from hundreds of other specimens leads us to doubt that a previously unknown mutagenic factor can be a general feature of extracts from old tissues.

Animals↗
PubMed2004

In vitro new dialysis protocol to assay the antiseptic properties of a quaternary ammonium compound polymerized with denture acrylic resin.

AIMS: To develop an in vitro protocol in order to assess the antiseptic properties of a quaternary ammonium compound polymerized with acrylic denture resin base, using experimental resin discs and dialysis membranes. METHODS AND RESULTS: Experimental acrylic resin discs were polymerized with Poly 202063A, an ammonium compound (2-50%). Antiseptic properties were assayed against two reference strains (Escherichia coli, Staphylococcus aureus) and a laboratory strain (Candida albicans), using three different conditions (test A, B and C). In test A, according to classical protocols the resin discs were first soaked in large volumes of microbial inoculum (45 ml). An original dialysis protocol was then designed to recreate the small biofilm volume on the prosthetic surface. In test B, discs and bacterial inoculum (600 microl) were introduced in a dialysis bag and dialysed against a sterile buffer. A bactericidal effect was observed against E. coli and Staph. aureus (<0.1% viable cells in initial bacterial suspension). A dose-dependent fungistatic effect was observed against C. albicans. Finally, in test C discs and sterile buffer (600 microl) were introduced in a dialysis bag and dialysed against microbial inoculum. Reduced activity was found outside the dialysis bag, demonstrating that free ammonium was able to diffuse through the dialysis membrane, displaying antiseptic properties. CONCLUSIONS: The present protocol demonstrated that a quaternary ammonium compound remains efficient after heat polymerization with an acrylic denture base resin, both in immediate and distant microbial environments. SIGNIFICANCE AND IMPACT OF THE STUDY: Such removable prosthetic devices with intrinsic antiseptic properties would contribute to improve the long-term management of denture stomatitis.

Acrylic Resins↗
PubMed2001

DNA sequences from multiple amplifications reveal artifacts induced by cytosine deamination in ancient DNA.

We show that DNA molecules amplified by PCR from DNA extracted from animal bones and teeth that vary in age between 25 000 and over 50 000 years carry C-->T and G-->A substitutions. These substitutions can reach high proportions among the molecules amplified and are due to the occurrence of modified deoxycytidine residues in the template DNA. If the template DNA is treated with uracil N-glycosylase, these substitutions are dramatically reduced. They are thus likely to result from deamination of deoxycytidine residues. In addition, 'jumping PCR', i.e. the occurrence of template switching during PCR, may contribute to these substitutions. When DNA sequences are amplified from ancient DNA extracts where few template molecules initiate the PCR, precautions such as DNA sequence determination of multiple clones derived from more than one independent amplification are necessary in order to reduce the risk of determination of incorrect DNA sequences. When such precautionary measures are taken, errors induced by damage to the DNA template are unlikely to be more frequent than approximately 0.1% even under the unlikely scenario where each amplification starts from a single template molecule.

Animals↗
PubMed2001

Ancient DNA.

DNA that has been recovered from archaeological and palaeontological remains makes it possible to go back in time and study the genetic relationships of extinct organisms to their contemporary relatives. This provides a new perspective on the evolution of organisms and DNA sequences. However, the field is fraught with technical pitfalls and needs stringent criteria to ensure the reliability of results, particularly when human remains are studied.

Animals↗
PubMed1993

Multiple juvenile xanthogranulomas without foam cells and giant cells.

A 4-month-old boy had numerous nodular lesions. Microscopic findings revealed a histiocytic proliferation without foam cells and giant cells. Immunohistochemical studies showed that the histiocytes belonged to the monocyte-macrophage system and not to the Langerhans cell system. This case is an unusual variant of juvenile xanthogranuloma that, when congenital, may be difficult to differentiate from Hashimoto-Pritzker disease.

Histiocytes↗
PubMed1990

[Immunohistochemical study of cells of invasive cancer of the vaginal part of the cervix uteri].

Immunohistochemical study of cervical carcinoma used EE21-06d monoclonal antibodies which identify five cytokeratin polypeptides inherent in the squamous epithelium. PAP-method and reaction of immunofluorescence were employed. Initial stages of squamous cell carcinoma invasion were characterized by bleaching or complete cell discoloring of most tumor cells. However, in deeply invading tumors, the share of intensively stained cells was markedly increased. The results point to expression of different cytokeratins or cell clones replacement with tumor progression. The peculiarities of cytokeratin distribution may serve to determine the degree of invasion and differentiation of tumor cells.

Adult↗