In-depth prospection of Avène Thermal Spring Water reveals an uncommon and stable microbial community.

BACKGROUND: Avène Thermal Spring Water (TSW) exhibits therapeutic properties in the treatment of skin pathologies. Arising from a dolomitic aquifer system, its physico-chemical properties are well-established and its bacteriological quality regularly monitored. The microbiota of this aquifer have been characterized. OBJECTIVES: We aimed to describe the structure of the bacterial community inhabiting the deep aquifer and to examine its dynamics over time. METHODS: The Avène TSW was collected at the catchment point and filtered through 0.1 µm pore size filters. The sampling was carried out every 3 months to generate a 4-year time series. The DNA extracted from filters was analysed using high-throughput 16S rRNA gene amplicon sequencing, and the microorganisms and their contribution were characterized by the taxonomic assignment of sequence variants generated from each sample. RESULTS: Bacteria were distributed into 39 phyla. Nitrospirae and Proteobacteria were the most prevalent, accounting for 38% and 23% of the total community on average, respectively. A stable pattern was observed throughout the study. A few bacterial species were always detected, forming a core community of likely chemolithoautotrophic organisms which might use energy sources and nutrients produced from water-bedrock interactions. Most of the species were distantly related to organisms described to date. CONCLUSIONS: Avène TSW provided by the deep aquifer system harbours a unique microbial community, shaped by the physico-chemical characteristics of the deep environment. Its remarkable stability over time has revealed a high level of confinement of the water resource.

Evidence for magnetic Weyl fermions in a correlated metal.

Weyl fermions have been observed as three-dimensional, gapless topological excitations in weakly correlated, inversion-symmetry-breaking semimetals. However, their realization in spontaneously time-reversal-symmetry-breaking phases of strongly correlated materials has so far remained hypothetical. Here, we report experimental evidence for magnetic Weyl fermions in Mn3Sn, a non-collinear antiferromagnet that exhibits a large anomalous Hall effect, even at room temperature. Detailed comparison between angle-resolved photoemission spectroscopy (ARPES) measurements and density functional theory (DFT) calculations reveals significant bandwidth renormalization and damping effects due to the strong correlation among Mn 3d electrons. Magnetotransport measurements provide strong evidence for the chiral anomaly of Weyl fermions-namely, the emergence of positive magnetoconductance only in the presence of parallel electric and magnetic fields. Since weak magnetic fields (approximately 10 mT) are adequate to control the distribution of Weyl points and the large fictitious fields (equivalent to approximately a few hundred T) produced by them in momentum space, our discovery lays the foundation for a new field of science and technology involving the magnetic Weyl excitations of strongly correlated electron systems such as Mn3Sn.

5 f -shell correlation effects in dioxides of light actinides studied by O 1s x-ray absorption and emission spectroscopies and first-principles calculations.

Soft x-ray emission and absorption spectroscopic data are reported for the O 1s region of a single crystal of UO2, a polycrystalline NpO2 sample, and a single crystal of PuO2. The experimental data are interpreted using first-principles correlated-electron calculations within the framework of the density functional theory with added Coulomb U interaction (DFT+U). A detailed analysis regarding the origin of different structures in the x-ray emission and x-ray absorption spectra is given and the effect of varying the intra-atomic Coulomb interaction-U for the 5 f electrons is investigated. Our data indicate that O 1s x-ray absorption and emission spectroscopies can, in combination with DFT+U calculations, successfully be used to study 5 f -shell Coulomb correlation effects in dioxides of light actinides. The values for the Coulomb U parameter in these dioxides are derived to be in the range of 4-5 eV.

Emergent antiferromagnetism out of the "hidden-order" state in URu2Si2: high magnetic field nuclear magnetic resonance to 40 T.

Very high field (29)Si-NMR measurements using a fully (29)Si-enriched URu(2)Si(2) single crystal were carried out in order to microscopically investigate the "hidden order" (HO) state and adjacent magnetic phases in the high field limit. At the lowest measured temperature of 0.4 K, a clear anomaly reflecting a Fermi surface instability near 22 T inside the HO state is detected by the (29)Si shift, (29)K(c). Moreover, a strong enhancement of (29)K(c) develops near a critical field H(c) ≃ 35.6 T, and the ^{29}Si-NMR signal disappears suddenly at H(c), indicating the total suppression of the HO state. Nevertheless, a weak and shifted (29)Si-NMR signal reappears for fields higher than H(c) at 4.2 K, providing evidence for a magnetic structure within the magnetic phase caused by the Ising-type anisotropy of the uranium ordered moments.

De novo basilar tip aneurysm. Case report and literature review.

The de novo aneurysms are the formation of new aneurysms in a location previously observed to be normal by a cerebral angiography or direct microsurgical exploration. In this report, we present a review of the theme and describe a case of a ruptured de novo basilar tip aneurysm in a patient previously treated with carotid occlusion for a giant intracavernous aneurysm and microsurgical clipping of contralateral posterior communicating artery aneurysm.

Fermi surface of CeIn3 above the Néel critical field.

We report measurements of the de Haas-van Alphen effect in CeIn(3) in magnetic fields extending to approximately 90 T, well above the Néel critical field of mu(0)H(c) approximately 61 T. The unreconstructed Fermi surface a sheet is observed in the high magnetic field polarized paramagnetic limit, but with its effective mass and Fermi surface volume strongly reduced in size compared to that observed in the low magnetic field paramagnetic regime under pressure. The spheroidal topology of this sheet provides an ideal realization of the transformation from a "large Fermi surface" accommodating f electrons to a "small Fermi surface" when the f-electron moments become polarized.

Mercury methylation by dissimilatory iron-reducing bacteria.

The Hg-methylating ability of dissimilatory iron-reducing bacteria in the genera Geobacter, Desulfuromonas, and Shewanella was examined. All of the Geobacter and Desulfuromonas strains tested methylated mercury while reducing Fe(III), nitrate, or fumarate. In contrast, none of the Shewanella strains produced methylmercury at higher levels than abiotic controls under similar culture conditions. Geobacter and Desulfuromonas are closely related to known Hg-methylating sulfate-reducing bacteria within the Deltaproteobacteria.

Growth hormone provocation tests and their prediction in the growth of children treated for acute lymphoblastic leukemia.

AIM: The aim of this study was to evaluate the positive predictive value of two growth hormone stimulation tests (insulin-induced hypoglycemia and clonidine) for stature below percentile 10 in patients treated for acute lymphoblastic leukemia in childhood. METHODS: The study population was a cohort of 30 patients (aged 14.1+/-2.9 years; 20 male) treated for acute lymphoblastic leukemia during childhood and then examined after insulin-induced hypoglycemia (30 patients) and clonidine (16 patients) tests. The follow-up time was 7.7+/-2.8 years since treatment and 2.3+/-1.3 years after administration of the tests. RESULTS: In the last evaluation, 12 patients (40%) were below and 18 (60%) were above percentile 10. The insulin-induced hypoglycemia test response was: 9 patients (30%) had growth hormone peak <5 ng/mL and 19 (63.3%) <7 ng/mL. The clonidine test response was: 7 patients had growth hormone peak <5 ng/mL and 8 (50%) <7 ng/mL. For stature below of the percentile 10, the positive predictive values of insulin-induced hypoglycemia test (33%) and clonidine (28%) were low when growth hormone peak <5 ng/mL was considered; however, when growth hormone peak <7 ng/mL was considered, the positive predictive values were 83% and 50% for the insulin-induced hypoglycemia and clonidine tests, respectively. CONCLUSIONS: In patients treated for acute lymphoblastic leukemia in childhood, the positive predictive values for statural deficit of both tests were low, except for the insulin-induced hypoglycemia test when a growth hormone peak <7 ng/mL was considered.

Catastrophic Fermi surface reconstruction in the shape-memory alloy AuZn.

AuZn undergoes a shape-memory transition at 67 K. The de Haas-van Alphen effect persists to 100 K enabling the observation of a change in the quantum oscillation spectrum indicative of a catastrophic Fermi surface reconstruction at the transition. The coexistence of both Fermi surfaces at low temperatures suggests an intrinsic phase separation in the bulk of the material. In addition, Dingle analysis reveals a sharp change in the scattering mechanism at a threshold cyclotron radius, attributable to the underlying microstructure driving the shape-memory effect.

Phylogenetic screening of ribosomal RNA gene-containing clones in Bacterial Artificial Chromosome (BAC) libraries from different depths in Monterey Bay.

Marine picoplankton are central mediators of many oceanic biogeochemical processes, but much of their biology and ecology remains ill defined. One approach to better defining these environmentally significant microbes involves the acquisition of genomic data that can provide information about genome content, metabolic capabilities, and population variability in picoplankton assemblages. Previously, we constructed and phylogenetically screened a Bacterial Artificial Chromosome (BAC) library from surface water picoplankton of Monterey Bay. To further describe niche partitioning, metabolic variability, and population structure in coastal picoplankton populations, we constructed and compared several picoplankton BAC libraries recovered from different depths in Monterey Bay. To facilitate library screening, a rapid technique was developed (ITS-LH-PCR) to identify and quantify ribosomal RNA (rRNA) gene-containing BAC clones in BAC libraries. The approach exploited natural length variations in the internal transcribed spacer (ITS) located between SSU and LSU rRNA genes, as well as the presence and location of tRNA-alanine coding genes within the ITS. The correspondence between ITS-LH-PCR fragment sizes and 16S rRNA gene phylogenies facilitated rapid identification of rRNA genes in BAC clones without requiring direct DNA sequencing. Using this approach, 35 phylogenetic groups (previously identified by cultivation or PCR-based rRNA gene surveys) were detected and quantified among the BAC clones. Since the probability of recovering chimeric rRNA gene sequences in large insert BAC clones was low, we used these sequences to identify potentially chimeric sequences from previous PCR amplified clones deposited in public databases. Full-length SSU rRNA gene sequences from picoplankton BAC libraries, cultivated bacterioplankton, and nonchimeric RNA genes were then used to refine phylogenetic analyses of planktonic marine gamma Proteobacteria, Roseobacter, and Rhodospirillales species.

Phylogenetic analysis of ribosomal RNA operons from uncultivated coastal marine bacterioplankton.

Analyses of small subunit ribosomal RNA genes (SSU rDNAs) have significantly influenced our understanding of the composition of aquatic microbial assemblages. Unfortunately, SSU rDNA sequences often do not have sufficient resolving power to differentiate closely related species. To address this general problem for uncultivated bacterioplankton taxa, we analysed and compared sequences of polymerase chain reaction (PCR)-generated and bacterial artificial chromosome (BAC)-derived clones that contained most of the SSU rDNAs, the internal transcribed spacer (ITS) and the large subunit ribosomal RNA gene (LSU rDNA). The phylogenetic representation in the rRNA operon PCR library was similar to that reported previously in coastal bacterioplankton SSU rDNA libraries. We observed good concordance between the phylogenetic relationships among coastal bacterioplankton inferred from SSU or LSU rDNA sequences. ITS sequences confirmed the close intragroup relationships among members of the SAR11, SAR116 and SAR86 clades that were predicted by SSU and LSU rDNA sequence analyses. We also found strong support for homologous recombination between the ITS regions of operons from the SAR11 clade.

Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5'-nuclease assays.

Few techniques are currently available for quantifying specific prokaryotic taxa in environmental samples. Quantification of specific genotypes has relied mainly on oligonucleotide hybridization to extracted rRNA or intact rRNA in whole cells. However, low abundance and cellular rRNA content limit the application of these techniques in aquatic environments. In this study, we applied a newly developed quantitative PCR assay (5'-nuclease assay, also known as TaqMan) to quantify specific small-subunit (SSU) rRNA genes (rDNAs) from uncultivated planktonic prokaryotes in Monterey Bay. Primer and probe combinations for quantification of SSU rDNAs at the domain and group levels were developed and tested for specificity and quantitative reliability. We examined the spatial and temporal variations of SSU rDNAs from Synechococcus plus Prochlorococcus and marine Archaea and compared the results of the quantitative PCR assays to those obtained by alternative methods. The 5'-nuclease assays reliably quantified rDNAs over at least 4 orders of magnitude and accurately measured the proportions of genes in artificial mixtures. The spatial and temporal distributions of planktonic microbial groups measured by the 5'-nuclease assays were similar to the distributions estimated by quantitative oligonucleotide probe hybridization, whole-cell hybridization assays, and flow cytometry.

Bacterial rhodopsin: evidence for a new type of phototrophy in the sea.

Extremely halophilic archaea contain retinal-binding integral membrane proteins called bacteriorhodopsins that function as light-driven proton pumps. So far, bacteriorhodopsins capable of generating a chemiosmotic membrane potential in response to light have been demonstrated only in halophilic archaea. We describe here a type of rhodopsin derived from bacteria that was discovered through genomic analyses of naturally occuring marine bacterioplankton. The bacterial rhodopsin was encoded in the genome of an uncultivated gamma-proteobacterium and shared highest amino acid sequence similarity with archaeal rhodopsins. The protein was functionally expressed in Escherichia coli and bound retinal to form an active, light-driven proton pump. The new rhodopsin exhibited a photochemical reaction cycle with intermediates and kinetics characteristic of archaeal proton-pumping rhodopsins. Our results demonstrate that archaeal-like rhodopsins are broadly distributed among different taxa, including members of the domain Bacteria. Our data also indicate that a previously unsuspected mode of bacterially mediated light-driven energy generation may commonly occur in oceanic surface waters worldwide.

Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage.

Cultivation-independent surveys of ribosomal RNA genes have revealed the existence of novel microbial lineages, many with no known cultivated representatives. Ribosomal RNA-based analyses, however, often do not provide significant information beyond phylogenetic affiliation. Analysis of large genome fragments recovered directly from microbial communities represents one promising approach for characterizing uncultivated microbial species better. To assess further the utility of this approach, we constructed large-insert bacterial artificial chromosome (BAC) libraries from the genomic DNA of planktonic marine microbial assemblages. The BAC libraries we prepared had average insert sizes of 80 kb, with maximal insert sizes > 150 kb. A rapid screening method assessing the phylogenetic diversity and representation in the library was developed and applied. In general, representation in the libraries agreed well with previous culture-independent surveys based on polymerase chain reaction (PCR)amplified rRNA fragments. A significant fraction of the genome fragments in the BAC libraries originated from as yet uncultivated microbial species, thought to be abundant and widely distributed in the marine environment. One entire BAC insert, derived from an uncultivated, surface-dwelling euryarchaeote, was sequenced completely. The planktonic euryarchaeal genome fragment contained some typical archaeal genes, as well as unique open reading frames (ORFs) suggesting novel function. In total, our results verify the utility of BAC libraries for providing access to the genomes of as yet uncultivated microbial species. Further analysis of these BAC libraries has the potential to provide significant insight into the genomic potential and ecological roles of many indigenous microbial species, cultivated or not.

Phylogenetic diversity of ultraplankton plastid small-subunit rRNA genes recovered in environmental nucleic acid samples from the Pacific and Atlantic coasts of the United States.

The scope of marine phytoplankton diversity is uncertain in many respects because, like bacteria, these organisms sometimes lack defining morphological characteristics and can be a challenge to grow in culture. Here, we report the recovery of phylogenetically diverse plastid small-subunit (SSU) rRNA gene (rDNA) clones from natural plankton populations collected in the Pacific Ocean off the mouth of Yaquina Bay, Oreg. (OCS clones), and from the eastern continental shelf of the United States off Cape Hatteras, N.C. (OM clones). SSU rRNA gene clone libraries were prepared by amplifying rDNAs from nucleic acids isolated from plankton samples and cloning them into plasmid vectors. The PCR primers used for amplification reactions were designed to be specific for bacterial SSU rRNA genes; however, plastid genes have a common phylogenetic origin with bacteria and were common in both SSU rRNA gene clone libraries. A combination of restriction fragment length polymorphism analyses, nucleic acid sequencing, and taxon-specific oligonucleotide probe hybridizations revealed that 54 of the 116 OCS gene clones were of plastid origin. Collectively, clones from the OCS and OM libraries formed at least eight unique lineages within the plastid radiation, including gene lineages related to the classes Bacillariophyceae, Cryptophyceae, Prymnesiophyceae, Chrysophyceae, and Prasinophyceae; for a number of unique clones, no close phylogenetic neighbors could be identified with confidence. Only a group of two OCS rRNA gene clones showed close identity to the plastid SSU rRNA gene sequence of a cultured organism [Emiliania huxleyi (Lohmann) Hay and Mohler; 99.8% similar]. The remaining clones could not be identified to the genus or species level. Although cryptic species are not as prevalent among phytoplankton as they are among their bacterial counterparts, this genetic survey nonetheless uncovered significant new information about phytoplankton diversity.

Bacterial diversity among small-subunit rRNA gene clones and cellular isolates from the same seawater sample.

Numerous investigations applying the cloning and sequencing of rRNA genes (rDNAs) to the study of marine bacterioplankton diversity have shown that the sequences of genes cloned directly from environmental DNA do not correspond to the genes of cultured marine taxa. These results have been interpreted as support for the hypothesis that the most abundant heterotrophic marine bacterioplankton species are not readily culturable by commonly used methods. However, an alternative explanation is that marine bacterioplankton can be easily cultured but are not well represented in sequence databases. To further examine this question, we compared the small-subunit (SSU) rDNAs of 127 cellular clones isolated from a water sample collected off the Oregon coast to 58 bacterial SSU rDNAs cloned from environmental DNAs from the same water sample. The results revealed little overlap between partial SSU rDNA sequences from the cellular clones and the environmental clone library. An exception was the SSU rDNA sequence recovered from a cellular clone belonging to the Pseudomonas subgroup of the gamma subclass of the class Proteobacteria, which was related to a single gene cloned directly from the same water sample (OCS181) (similarity, 94.6%). In addition, partial SSU rDNA sequences from three of the cultured strains matched a novel rDNA clone related to the gamma subclass of the Proteobacteria found previously in an environmental clone library from marine aggregates (AGG53) (similarity, 94.3 to 99.6%). Our results support the hypothesis that many of the most abundant bacterioplankton species are not readily culturable by standard methods but also show that heterotrophic bacterioplankton that are culturable on media with high organic contents include many strains for which SSU rDNA sequences are not available in sequence databases.

Studies on the mechanism of early onset macular degeneration in cynomolgus monkeys. II. Suppression of metallothionein synthesis in the retina in oxidative stress.

Initial investigations done in this laboratory detected increased albumin and decreased glyceraldehyde 3-phosphate dehydrogenase concentrations in the retina of an animal model manifesting early onset macular degeneration. Both glyceraldehyde 3-phosphate dehydrogenase and albumin are markers of oxidative stress in cells. In this study, we used the same animal model to study further biochemical and physiological processes which may be involved in the pathogenesis of early onset macular degeneration in monkeys. We detected 60% lower catalase and glutathione peroxidase activities in the affected retinas suggesting lower antioxidant activities and oxidative stress. One of the consequences of oxidative stress is the production of metallothionein, a low molecular weight protein also induced by high concentrations of heavy metals such as zinc. Metallothionein was detected by RT-PCR in these monkey retinas. However initial quantitative PCR studies on this protein showed that the synthesis of metallothionein in affected retinas appears to be less than in normal controls. The affected retinas also showed a fourfold lower zinc concentration compared with the normal controls. No significant difference, however, could be detected in the zinc concentrations in plasma samples. Since induction of metallothionein synthesis is mediated by transcription factors which require heavy metals such as zinc for binding to specific sites in the DNA, the lowered zinc concentration may, thus, correlate with the lowered metallothionein expression. And since metallothionein is suggested to function as a free radical scavenger, the lowered metallothionein synthesis may consequently contribute to increased peroxidation reactions in the affected retinas. It appears therefore, that oxidative stress and the decreased metallothionein synthesis may be involved in the pathogenesis of early onset macular degeneration in this animal model.

Studies on the mechanism of early onset macular degeneration in cynomolgus (Macaca fascicularis) monkeys. I. Abnormal concentrations of two proteins in the retina.

Cynomolgus (Macaca fascicularis) monkeys from three families, which showed symptoms of early onset macular degeneration was studied. Two proteins, albumin and glyceraldehyde 3-phosphate dehydrogenase, were found to have markedly altered concentrations in whole retina of the monkeys with early onset macular degeneration, compared with normal controls. SDS-polyacrylamide gel patterns detected a 40-70% increase in the concentration of albumin and about 65% decrease in the concentration of glyceraldehyde 3-phosphate dehydrogenase in these affected retinas. There was however no significant difference in the relative concentrations of albumin in the plasma samples of affected and normal monkeys belonging to the three families studied and to an unrelated family. These initial findings suggest that degradative as well as antioxidant enzymes might be involved in the mechanisms leading to macular degeneration. In addition, the results also correlate with a possible role of these two proteins in H2O2 toxicity and appear to indicate that oxidative stress is significant in the etiology of early onset macular degeneration.

Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR.

The PCR is used widely for the study of rRNA genes amplified from mixed microbial populations. These studies resemble quantitative applications of PCR in that the templates are mixtures of homologs and the relative abundance of amplicons is thought to provide some measure of the gene ratios in the starting mixture. Although such studies have established the presence of novel rRNA genes in many natural ecosystems, inferences about gene abundance have been limited by uncertainties about the relative efficiency of gene amplification in the PCR. To address this question, three rRNA gene standards were prepared by PCR, mixed in known proportions, and amplified a second time by using primer pairs in which one primer was labeled with a fluorescent nucleotide derivative. The PCR products were digested with restriction endonucleases, and the frequencies of genes in the products were determined by electrophoresis on an Applied Biosystems 373A automated DNA sequencer in Genescan mode. Mixtures of two templates amplified with the 519F-1406R primer pair yielded products in the predicted proportions. A second primer pair (27F-338R) resulted in strong bias towards 1:1 mixtures of genes in final products, regardless of the initial proportions of the templates. This bias was strongly dependent on the number of cycles of replication. The results fit a kinetic model in which the reannealing of genes progressively inhibits the formation of template-primer hybrids.

[Visual function of cynomolgus monkeys with macula degeneration and peripheral retinal degeneration].

Using the simplified method for judging visual function of the cynomolgus monkey that was established by the present authors (Suzuki et al., 1988), forty-four cynomolgus monkeys with normal ophthalmoscopic findings, eleven monkeys with macula degeneration and thirteen monkeys with peripheral retinal degeneration were examined for their visual function. It was demonstrated that the monkeys with macula degeneration were inferior in their visual function to the monkeys with normal fundus. In addition, the degree of visual function varied with the degree of macula degeneration. The monkeys with peripheral retinal degeneration showed about the same degree in their visual function as the monkeys with normal fundus.