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At least 307 records · Page 17Linked to original sources
PubMed1992

An 80-kilodalton antigen from Histoplasma capsulatum that has homology to heat shock protein 70 induces cell-mediated immune responses and protection in mice.

An extract of the cell wall and cell membrane from Histoplasma capsulatum yeast cells was assayed by Western blot (immunoblot) for reactivity with two monoclonal antibodies to heat shock protein 70. Four bands with molecular masses of 80, 66, 54, and 32 kDa bound both antibodies. The 80-kDa protein was isolated, analyzed for homology to heat shock protein 70, and tested for antigenicity and immunogenicity in C57BL/6 mice. The 80-kDa protein reacted with monoclonal antibody to heat shock protein 70. Sera from mice immunized with the antigen recognized H. capsulatum heat shock protein 70. Moreover, the amino-terminal sequence of the 80-kDa protein revealed substantial homology with heat shock protein 70 from several species. The 80-kDa protein induced delayed-type hypersensitivity responses in mice immunized with either viable yeast cells or antigen. Splenocytes from mice immunized with yeast cells or with antigen responded in vitro to the 80-kDa antigen. Immunization of mice with the antigen enhanced host resistance against a sublethal inoculum of H. capsulatum yeast cells, but it did not reduce the mortality of mice given a lethal challenge of yeast cells. Thus, this antigen manifests homology with members of the heat shock protein 70 family. Furthermore, the 80-kDa protein elicits cellular immune responses to H. capsulatum, and it mediates protective immunity.

Amino Acid Sequence↗
PubMed2025

An updated compendium and reevaluation of the evidence for nuclear transcription factor occupancy over the mitochondrial genome.

In most eukaryotes, mitochondrial organelles contain their own genome, usually circular, which is the remnant of the genome of the ancestral bacterial endosymbiont that gave rise to modern mitochondria. Mitochondrial genomes are dramatically reduced in their gene content due to the process of endosymbiotic gene transfer to the nucleus; as a result most mitochondrial proteins are encoded in the nucleus and imported into mitochondria. This includes the components of the dedicated mitochondrial transcription and replication systems and regulatory factors, which are entirely distinct from the information processing systems in the nucleus. However, since the 1990s several nuclear transcription factors have been reported to act in mitochondria, and previously we identified 8 human and 3 mouse transcription factors (TFs) with strong localized enrichment over the mitochondrial genome using ChIP-seq (Chromatin Immunoprecipitation) datasets from the second phase of the ENCODE (Encyclopedia of DNA Elements) Project Consortium. Here, we analyze the greatly expanded in the intervening decade ENCODE compendium of TF ChIP-seq datasets (a total of 6,153 ChIP experiments for 942 proteins, of which 763 are sequence-specific TFs) combined with interpretative deep learning models of TF occupancy to create a comprehensive compendium of nuclear TFs that show evidence of association with the mitochondrial genome. We find some evidence for chrM occupancy for 50 nuclear TFs and two other proteins, with bZIP TFs emerging as most likely to be playing a role in mitochondria. However, we also observe that in cases where the same TF has been assayed with multiple antibodies and ChIP protocols, evidence for its chrM occupancy is not always reproducible. In the light of these findings, we discuss the evidential criteria for establishing chrM occupancy and reevaluate the overall compendium of putative mitochondrial-acting nuclear TFs.

Genome, Mitochondrial↗
PubMed1999

Molecular cloning, characterization, and expression of the M antigen of Histoplasma capsulatum.

The major diagnostic antigens of Histoplasma capsulatum are the H and M antigens, pluripotent glycoproteins that elicit both humoral and T-cell-mediated immune responses. These antigens may play a role in the pathogenesis of histoplasmosis. M antigen is considered immunodominant because antibodies against it are the first precipitins to arise in acute histoplasmosis and are commonly present during all phases of infection. The biological activity of monomolecular M antigen and its ability to elicit a protective immune response to H. capsulatum are largely unknown. A molecular approach was used to identify the biological nature of M antigen, including its purification from histoplasmin, partial digestion with proteinases, and reverse-phase high-performance liquid chromatography to separate the released peptides. The amino acid sequences of the purified peptides were obtained by Edman degradation, and using degenerate oligonucleotide primers for PCR, a 321-bp fragment of the gene encoding the M antigen was amplified from genomic H. capsulatum DNA. This fragment was used to screen an H. capsulatum genomic DNA library, leading to the isolation, cloning, and sequencing of the full-length gene. The M gene consists of 2, 187-bp DNA encoding a protein of 80,719 Da, which has significant homology to catalases from Aspergillus fumigatus, Aspergillus niger, and Eimericella nidulans. A cDNA was generated by reverse transcription-PCR and cloned into the expression vector pQE40. The identity of the cloned, expressed protein was confirmed by Western blotting. The recombinant fusion protein was immunoreactive with monoclonal antibodies raised against M antigen, with polyclonal mouse anti-M antiserum, and with a serum sample from a patient with histoplasmosis. The gene encoding the major immunodominant M antigen of H. capsulatum is a presumptive catalase, and the recombinant protein retains serodiagnostic activity.

Amino Acid Sequence↗
PubMed1996

Cellular immune responses to recombinant heat shock protein 70 from Histoplasma capsulatum.

Heat shock protein (hsp) 70 from several microbes is antigenic in mammals. In this study we sequenced and expressed the gene encoding this protein from Histoplasma capsulatum to study its immunological activity. The deduced amino acid sequence of the gene demonstrated 71 and 76% identity to hsp7O from humans and Saccharomyces cerevisiae, respectively. A cDNA was synthesized by reverse transcription-PCR and was expressed in Escherichia coli. Recombinant protein reacted with a mouse monoclonal antibody raised against human hsp7O. Splenocytes from C57BL/6 mice immunized with recombinant hsp7O emulsified in adjuvant, but not yeast cells, reacted in vitro to the antigen. Recombinant hsp7O elicited a cutaneous delayed-type hypersensitivity response in mice immunized with protein or with viable yeast cells. Mice were injected with recombinant hsp7O and challenged intranasally with a sublethal inoculum of yeast cells. Vaccination did not confer protection in this model. Thus, recombinant hsp7O can induce a cell-mediated immune response but does not induce a protective response.

Amino Acid Sequence↗
PubMed2001

A potential source of organic pollutants into the northeastern Atlantic: the outflow of the Mediterranean deep-lying waters through the Gibraltar Strait.

Small and large-size particles were collected in the water column (50-3000 m) of a Northeastern Atlantic area where deep Mediterranean waters, outflowing through the Strait of Gibraltar, are incorporated at mid-depth. Particles collected by water filtration (0.7 micron pore size) and by vertical hauls of a neuston net (50 microns mesh size) were analyzed for organic pollutants, namely aliphatic and aromatic hydrocarbons, and organochlorine compounds. Small-size particles represented the largest bulk of particulate organic carbon as well as of hydrophobic organic pollutants. Surface concentrations of n-alkanes [C14-C35), aromatic hydrocarbons (12 parent compounds), PCBs (7 congeners), and DDTs (DDT + DDE) were, respectively, in the range of 50-63 ng/L, 23-68 pg/L, 8-13 pg/L, and 0.05-1.7 pg/L. These concentrations showed a general decrease with depth, particularly significant in the upper 200 m, consistently with the POC contents. Compositional changes with depth were also evident in small-size particles and included the depletion of low molecular weight n-alkanes and low chlorinated PCB congeners as well as a decrease of the fossil to pyrolytic PAHs ratio. Unusual increases of concentrations were observed at mid-depths (900-1100 m), indicating additional particle inputs, either by in-situ formation or by advective transport from the Mediterranean. The latter was recognized because small-size particles within these water veins exhibited distribution patterns out of the vertical sequence and similar to those of deep Mediterranean waters. An input of 8 and 0.5 tons per year of the above PAH and PCB compounds, respectively, has tentatively been calculated as the contribution of these Mediterranean waters to the Northeastern Atlantic.

Atlantic Ocean↗
PubMed2024

Nanopore sequencing to detect A-to-I editing sites.

Adenosine-to-inosine (A-to-I) RNA editing, mediated by the ADAR family of enzymes, is pervasive in metazoans and functions as an important mechanism to diversify the proteome and control gene expression. Over the years, there have been multiple efforts to comprehensively map the editing landscape in different organisms and in different disease states. As inosine (I) is recognized largely as guanosine (G) by cellular machineries including the reverse transcriptase, editing sites can be detected as A-to-G changes during sequencing of complementary DNA (cDNA). However, such an approach is indirect and can be confounded by genomic single nucleotide polymorphisms (SNPs) and DNA mutations. Moreover, past studies rely primarily on the Illumina platform, which generates short sequencing reads that can be challenging to map. Recently, nanopore direct RNA sequencing has emerged as a powerful technology to address the issues. Here, we describe the use of the technology together with deep learning models that we have developed, named Dinopore (Detection of inosine with nanopore sequencing), to interrogate the A-to-I editome of any organism.

Inosine↗
PubMed1999

The correlation between morphological and phylogenetic classification of myxobacteria.

In order to determine whether morphological criteria are suitable to affiliate myxobacterial strains to species, a phylogenetic analysis of 16S rDNAs was performed on 54 myxobacterial strains that represented morphologically 21 species of the genera Angiococcus, Archangium, Chondromyces, Cystobacter, Melittangium, Myxococcus, Polyangium and Stigmatella, five invalid species and three unclassified isolates. The analysis included 12 previously published sequences. The branching pattern confirmed the deep trifurcation of the order Myxococcales. One lineage is defined by the genera Cystobacter, Angiococcus, Archangium, Melittangium, Myxococcus and Stigmatella. The study confirms the genus status of 'Corallococcus', previously 'Chondrococcus', within the family Myxococcaceae. The second lineage contains the genus Chondromyces and the species Polyangium ('Sorangium') cellulosum, while the third lineage is comprised of Nannocystis and a strain identified as Polyangium vitellinum. With the exception of a small number of strains that did not cluster phylogenetically with members of the genus to which they were assigned by morphological criteria ('Polyangium thaxteri' Pl t3, Polyangium cellulosum ATCC 25531T, Melittangium lichenicola ATCC 25947T and Angiococcus disciformis An d1), the phenotypic classification should provide a sound basis for the description of neotype species in those cases where original strain material is not available or is listed as reference material.

Bacterial Typing Techniques↗
PubMed2025

Robustness of Ancestral Sequence Reconstruction to Among-site and Among-lineage Evolutionary Heterogeneity.

Ancestral sequence reconstruction is typically performed using homogeneous evolutionary models, which assume that the same substitution propensities affect all sites and lineages. These assumptions are routinely violated: heterogeneous structural and functional constraints favor different amino acids at different sites, and these constraints often change among lineages as epistatic substitutions accrue at other sites. To evaluate how violations of the homogeneity assumption affect ancestral sequence reconstruction under realistic conditions, we developed site-specific substitution models and parameterized them using data from deep mutational scanning experiments on three protein families; we then used these models to perform ancestral sequence reconstruction on the empirical alignments and on alignments simulated under heterogeneous conditions derived from the experiments. Extensive among-site and -lineage heterogeneity is present in these datasets, but the sequences reconstructed from empirical alignments are almost identical when heterogeneous or homogeneous models are used for ancestral sequence reconstruction. Using models fit to deep mutational scanning data from distantly related proteins in which mutational effects are very different also has a minimal impact on ancestral sequence reconstruction. The rare differences occur primarily where phylogenetic signal is weak-at fast-evolving sites and nodes connected by long branches. When ancestral sequence reconstruction is performed on simulated data, errors in the reconstructed sequences become more likely as branch lengths increase, but incorporating heterogeneity into the model does not improve accuracy. These data establish that ancestral sequence reconstruction is robust to unincorporated realistic forms of evolutionary heterogeneity, because the primary determinant of ancestral sequence reconstruction is phylogenetic signal, not the substitution model. The best way to improve accuracy is therefore not to develop more elaborate models but to apply ancestral sequence reconstruction to densely sampled alignments that maximize phylogenetic signal at the nodes of interest.

Phylogeny↗
PubMed2006

Peripheral region for core cross-beta plays important role in amyloidogenicity.

The role of the peripheral sequence neighboring the core cross-beta region was investigated using a peptide library constructed with all possible combinations of Lys, Glu, Ser, and Leu at three residue positions (X1-X3) forming the N-terminal region linked to the amyloid core sequence of the barnase-derived segment (A4-K22). By means of CD spectra and thioflavin T binding assay for 64 peptides, not only the composition but also the sequence in the peripheral region were found to be responsible for amyloid formation. The preferences of amino acid residues in the peripheral region of the amyloid-forming peptides were in the order of Leu approximately SerGlu>>Lys. A balance of positive and negative charges was found to be essential for amyloid formation, suggesting that the electrostatic interaction at the surface of the amyloid fibrils is relevant to their stability. On the basis of the maximum fluorescence wavelength of fibril-bound thioflavin T, the highly amyloidogenic peptides were classified into two classes, which exhibited the sequence preferences of (Leu, Ser/Glu, and Leu) and (Glu, Leu, and Ser) for the peripheral sequence (X1, X2, and X3). The former class can be rationally assigned to the structural model with deep grooves along the fibril axis. Thus, the peripheral sequence regulates the manner of molecular packing in the fibrils as well as the amyloidogenicity. In addition, the chains of the peripheral sequence are most likely to form thioflavin T binding sites.

Amino Acids↗
PubMed2000

Phylogenetic analysis of psychrophilic bacteria isolated from the Japan Trench, including a description of the deep-sea species Psychrobacter pacificensis sp. nov.

Phylogenetic positions of psychrophilic bacteria isolated from the Japan Trench were determined by sequencing analysis of PCR-amplified bacterial small subunit (16S) rRNA genes. Between surface and deep-sea psychrophiles, distinct positions clearly differed within the gamma-Proteobacteria. In phylogenetic analysis using neighbour-joining, maximum-parsimony and maximum-likelihood, strains from surface seawater were inferred to be located in the Halomonas aquamarina-meridiana clade within the family Halomonadaceae. Strains from deep seawater (5000-6000 m), however, formed a novel monophyletic clade within the Moraxella-Psychrobacter branch in the family Moraxellaceae, showing separation from terrestrial and Antarctic relatives. These deep-sea strains were also discriminated from other known Psychrobacter species in phenotype, e.g. limited growth in the absence of NaCl (optimum at about 3% NaCl), positive urease activity, acid production from xylose and arabinose, and the presence of multiple fimbriae. DNA relatedness values among six deep-sea strains were > 85% in DNA-DNA hybridization experiments and > 98% in aligned 16S rDNA sequences. From this evidence, a new species, Psychrobacter pacificensis, is proposed for these deep-sea psychrophiles; the type strain of Psychrobacter pacificensis is strain NIBH P2K6T (= IFO 16270T). Occurrence of psychrobacters in cold Japan Trench deep seawater and at the Antarctic sea surface suggests that deep-sea bacterial habitation and evolution have been mediated by global deep-ocean circulation linked to the sinking of cooled seawater in polar regions.

Cold Temperature↗
PubMed1996

Ribulose-1,5-bisphosphate carboxylase/oxygenase gene expression and diversity of Lake Erie planktonic microorganisms.

Carbon dioxide fixation is carried out primarily through the Calvin-Benson-Bassham reductive pentose phosphate cycle, in which ribulose-1, 5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme. The primary structure of the large subunit of form I RubisCO is well conserved; however, four distinct types, A, B, C, and D, may be distinguished, with types A and B and types C and D more closely related to one another. To better understand the environmental regulation of RubisCO in Lake Erie phytoplanktonic microorganisms, we have isolated total RNA and DNA from four Lake Erie sampling sites. Probes prepared from RubisCO large-subunit genes (rbcL) of the freshwater cyanobacterium Synechococcus sp. strain PCC6301 (representative of type IB) and the diatom Cylindrotheca sp. strain N1 (representative of type ID) were hybridized to the isolated RNA and DNA. To quantitate rbcL gene expression for each sample, the amount of gene expression per gene dose (i.e., the amount of mRNA divided by the amount of target DNA) was determined. With a limited number of sampling sites, it appeared that type ID (diatom) rbcL gene expression per gene dose decreased as the sampling sites shifted toward open water. By contrast, a similar trend was not observed for cyanobacterial (type IB) rbcL gene expression per gene dose. Complementary DNA specific for rbcL was synthesized from Lake Erie RNA samples and used as a template for PCR amplification of portions of various rbcL genes. Thus far, a total of 21 clones of rbcL genes derived from mRNA have been obtained and completely sequenced from the Ballast Island site. For surface water samples, deduced amino acid sequences of five of six clones appeared to be representative of green algae. In contrast, six of nine sequenced rbcL clones from 10-m-deep samples were of chromophytic and rhodophytic lineages. At 5 m deep, the active CO2-fixing planktonic organisms represented a diverse group, including organisms related to Chlorella ellipsoidea, Cylindrotheca sp. strain N1, and Olisthodiscus luteus. Although many more samplings at diverse sites must be accomplished, the discovery of distinctly different sequences of rbcL mRNA at different water depths suggests that there is a stratification of active CO2-fixing organisms in western Lake Erie.

Amino Acid Sequence↗
PubMed1999

Membrane skeleton in cultured chick cardiac myocytes revealed by high resolution immunocytochemistry.

Distribution of cytoskeletal proteins with emphasis on the membrane-cytoskeleton interface was examined in cultured cardiac myocytes. Using specific antibodies recognizing alpha-sarcomeric actin, desmin, beta-tubulin, spectrin/alpha-fodrin and ankyrin, respectively, the cellular localization of these cytoskeletal proteins was detected by laser scanning confocal microscopy. In addition, the fine filamentous structure of these proteins was identified by combining silver-enhanced immunogold labelling with electron microscopy. The latter technique employed the sequence of quick-freezing, deep-etching and rotary shadowing of the specimens. Conventional transmission electron microscopy of the spherical cardiac myocytes revealed a filamentous submembranous layer, approximately 100 nm thick. Specific immunolabelling of alpha-sarcomeric actin and spectrin/alpha-fodrin as well as ankyrin was seen beneath the plasmalemma. A three-dimensional meshwork of spectrin/alpha-fodrin was shown. Numerous desmin filaments that exhibited a tortuous course throughout the cells were also observed running in parallel with the surface in the submembranous area, whereas beta-tubulin was infrequently detected in these areas. In conclusion, the present study shows that spherical cardiac myocytes contain a distinct and complex three-dimensional membrane skeleton. Major constituents of this distinct submembranous layer were spectrin/alpha-fodrin fibres as well as actin and desmin filaments.

Animals↗
PubMed2001

Molecular identification of Wolbachia from the filarial nematode Mansonella ozzardi.

Mansonella ozzardi, a filarial parasite of humans in Latin America, has been shown to harbour intracellular bacteria not yet identified. Here we show that these bacteria, like those of other filarial nematodes, belong to the genus Wolbachia (alpha 2 Proteobacteria; Rickettsiales). Their unambiguous placement in the Wolbachia group was shown by 16S rDNA sequence analysis. However, the exact position of the Wolbachia from M. ozzardi relative to the other wolbachiae is not clear. Indeed, 16S rDNA sequence analysis places this bacterium at a deep branch in Wolbachia evolution. It is interesting that analysis of the 5S rDNA gene spacer of the nematode host also suggests that the genus Mansonella, together with the genus Loa, could represent a deep-branching lineage in filarial evolution.

Animals↗
PubMedDate not supplied

Comparison of train-of-four and posttetanic response as guides for endotracheal intubation in children.

STUDY OBJECTIVE: To evaluate and compare the predictive values of the absence of train-of-four (TOF) or posttetanic response as guides for endotracheal intubation in children. DESIGN: Prospective controlled study in children. SETTING: Induction of anesthesia and endotracheal intubation at a university-affiliated hospital. PATIENTS: Thirty pediatric patients age 1 to 10 years, ASA physical status I, who were undergoing elective surgery were divided into two equal groups. INTERVENTIONS: Anesthesia was induced with halothane and maintained at 1% inspired concentration. Fifteen children were stimulated with the TOF (2 Hz for 2 seconds) technique and 15 with the twitch-tetanus-twitch sequence. All the patients received atracurium 0.4 mg/kg. Upon abolishment of the TOF or tetanus-twitch sequence, endotracheal intubation was performed and the conditions for intubation were evaluated. MEASUREMENTS AND MAIN RESULTS: In the group of patients stimulated by the TOF technique, the neuromuscular response was ablated in 1.7 +/- 0.1 minutes, a significantly shorter time than in those stimulated by the tetanus-twitch sequence (4.0 +/- 0.4 minutes; p less than 0.0001). Conditions for intubation did not differ between the two groups. CONCLUSIONS: Good intubating conditions can generally be counted on when the TOF has disappeared; additional waiting for the disappearance of posttetanic response is unnecessary. The observation that the disappearance of the tetanus-twitch sequence is a good indicator of deep neuromuscular blockade during recovery from atracurium in children cannot be extrapolated to the induction period.

Anesthesia, Inhalation↗
PubMed1998

Diffuse neurofibroma of the ankle.

PURPOSE: To correlate the imaging and histological findings in diffuse neurofibroma. PATIENTS AND METHODS: Retrospective review of clinical, imaging and histological findings in two patients with diffuse neurofibroma. RESULTS: CT demonstrates diffuse infiltration of the deep and subcutaneous fat, isodense to muscle. Magnetic resonance imaging shows extensive infiltration of the subcutaneous and deep fat that envelops tendons and vessels but does not involve bone. Superficial masses enhance homogeneously after intravenous gadolinium. The reticular nature of the deep infiltration is seen on all sequences but is most conspicuous on post-gadolinium T1-weighted images which show tumour enhancement and non-enhancing hypointense soft tissue strands. Magnetic resonance angiography and Doppler ultrasound may show enlarged vessels, high blood flow and vascular pools. CONCLUSION: Diffuse neurofibroma has a characteristic appearance on magnetic resonance that is best shown on post-gadolinium T1-weighted images.

Adolescent↗
PubMed1985

Canine inherited ataxia: ultrastructural observations.

Canine Inherited Ataxia is inherited as an autosomal recessive trait in Gordon Setters. This animal model shares features with certain human cerebellar degenerations and offers the opportunity to examine brain tissue at various stages during the evolution of disease. The present investigation focuses on the morphometric and ultrastructural changes of cerebellar neurons. Purkinje and granule cells are the principal intrinsic neurons at risk. The size of Purkinje cells decreases, axonal degeneration is an important feature of the pathology, and synaptic abnormalities occur in the cerebellar glomeruli and deep nuclei of the cerebellum. The sequence and nature of synaptic changes in the molecular layer suggest that the degenerative process begins in Purkinje cells and that granule cells may be secondarily affected.

Afferent Pathways↗
PubMed1992

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont.

The polymerase chain reaction (PCR) was used to amplify small-subunit ribosomal DNA from the anaerobic ciliated protozoon Metopus palaeformis, and from its uncultured endosymbiotic bacteria. This was accomplished directly from total DNA extracted from protozoa without prior isolation or enrichment for symbiont cells. The double-stranded amplification products were precipitated and directly sequenced using the linear PCR reaction. Fluorescent oligonucleotide probes were designed and used in whole-cell hybridizations to provide direct visual evidence that the sequences originated from the host ciliate and from the endosymbiont. Phylogenetic analysis of the Metopus palaeformis sequence consistently placed it as a deep-branching lineage near the root of the ciliate tree. However, the present data were insufficient to resolve the detailed relationship between Blepharisma and Metopus and thus to determine if the heterotrichs are mono- or paraphyletic. Phylogenetic analysis of the symbiont partial sequence clearly demonstrated that it is an archaeobacterium and that it is closely related to, but distinct from, Methanobacterium formicicum.

Animals↗
PubMed1998

Bacteria in post-glacial freshwater sediments.

Prokaryote communities in post-glacial profundal freshwater sediments of Windermere, representing 10-12,000 years of deposition, were examined for culturability, viability and community structure. The potential for active geochemical cycles was inferred from the presence of specific groups of bacteria. Direct count procedures revealed 10(12) cells (g dry wt sediment)-1 in the surface sediments, which declined to approximately 10(9) cells (g dry wt sediment)-1 at 6 m depth of core (Representing approximately 10,000 years of deposition). The majority of the cells in the upper sediments were metabolically active when challenged with viability probes and responded to the direct viable count method. Below 250 cm, viability shown by 5-cyano-2,3-diotyl tetrazolium chloride (CTC) dye was not significantly different from the direct count; however, counts obtained with 5-carboxyfluorescein diacetate (CFDA) and the direct viable count both declined significantly from the direct count below 250 cm and 1 m, respectively. Culture was achieved from samples throughout the core, although the numbers of culturable bacteria decreased significantly with depth, from 10(7) c.f.u. (g dry wt sediment)-1 to 10(1)-10(2) c.f.u. (g dry wt sediment)-1 below 3 m depth. Among culturable isolates, Gram-positives and Gram-negatives were found at all levels of the core, and spore-forming heterotrophs dominated. Although sulphate-reducing bacteria were not detected below 20 cm, isolates demonstrating denitrifying activity were detected at all depths. PCR performed on samples taken below 3 m (deposited more than 7000 years ago) using eubacterial and archaeal primers revealed sequences similar to those found in deep sediments of the Pacific Ocean and the presence of methanogenic archaea. These observations indicate that bacteria and archaea are capable of long-term persistence and activity in deep, aged freshwater sediments.

Archaea↗