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PubMed2006

Novel facultative anaerobic acidotolerant Telmatospirillum siberiense gen. nov. sp. nov. isolated from mesotrophic fen.

Three facultative anaerobic acidotolerant Gram-negative motile spirilla strains designated 26-4b1, 26-2 and K-1 were isolated from mesotrophic Siberian fen as a component of methanogenic consortia. The isolates were found to grow chemoorganotrophically on several organic acids and glucose under anoxic and low oxygen pressure in the dark, tolerant up to 5kPa of oxygen. At low oxygen supply, faint autotrophic growth on the H(2):CO(2) mixture was also observed. All three isolates were able to fix N(2). Major cellular fatty acids were 18:1 omega7c, 17:0 cyclopropane and 16:0. Phylogenetic analyses of the 16S rRNA gene sequences revealed that they formed a deep branch within the family Rhodospirillaceae of the Alphaproteobacteria with the highest similarity of 90.9-92.5% with members of genera Phaeospirillum and Magnetospirillum. Phylogenetic study of nifH (nitrogenase) and cbbL (RuBisCO) amino acid sequence identities confirmed that the new isolates represent a novel group. Based on the phylogenetic analyses and distinct phenotypic characteristics, we are of the opinion that strains 26-4b1, 26-2 and K-1 represent a new species of a novel genus for which the name Telmatospirillum siberiense gen. nov. sp. nov. is proposed.

Acids↗
PubMed1999

Deep hypothermia and rewarming alters glutamate levels and glycogen content in cultured astrocytes.

BACKGROUND: Deep hypothermia has been associated with an increased incidence of postoperative neurologic dysfunction after cardiac surgery in children. Recent studies suggest an excitotoxic mechanism involving overstimulation of glutamate receptors. Extracellular glutamate uptake occurs primarily by astrocytes. Astrocytes also store glycogen, which may be used to sustain the energy-consuming glutamate uptake. Extracellular glutamate and glycogen content were studied during temperature changes mimicking cardiopulmonary bypass in vivo. METHODS: Primary cultures of cerebral cortical astrocytes were used in a specially designed incubator allowing continuous changes of temperature and ambient gas concentrations. The sequence of events was as follows: normothermia, rapid cooling (2.8 degrees C/min) followed by 60 min of deep hypothermia (15 degrees C), followed by rewarming (3.0 degrees C/min) and subsequent 5 h of mild hyperthermia (38.5 degrees C). Two different conditions of oxygenation were studied: (1) normoxia (25% O2, 70% N2, 5% CO2); or (2) hyperoxia (95% O2, 5% CO2). The extracellular glutamate concentrations and intracellular glycogen levels were measured at nine time points. RESULTS: One hundred sixty-two cultures were studied in four independent experiments. The extracellular concentration of glutamate in the normoxic group increased significantly from 35+/-10 nM/mg protein at baseline up to 100+/-15 nM/mg protein at the end of 5 h of mild hyperthermia (P < 0.05). In contrast, extracellular glutamate levels did not vary from control in the hyperoxic group. Glycogen levels decreased significantly from 260+/-85 nM/mg protein at baseline to < 25+/-5 nM/mg protein at the end of 5 h in the normoxic group (P < 0.05) but returned to control levels after rewarming in the hyperoxic group. No morphologic changes were observed in either group. CONCLUSION: The extracellular concentration of glutamate increases, whereas the intracellular glycogen content decreases when astrocytes are exposed to a sequence of deep hypothermia and rewarming. This effect of hypothermia is prevented when astrocytes are exposed to hyperoxic conditions.

Algorithms↗
PubMed1999

In situ detection of novel bacterial endosymbionts of Acanthamoeba spp. phylogenetically related to members of the order Rickettsiales.

Acanthamoebae are ubiquitous soil and water bactivores which may serve as amplification vehicles for a variety of pathogenic facultative bacteria and as hosts to other, presently uncultured bacterial endosymbionts. The spectrum of uncultured endosymbionts includes gram-negative rods and gram-variable cocci, the latter recently shown to be members of the Chlamydiales. We report here the isolation from corneal scrapings of two Acanthamoeba strains that harbor gram-negative rod endosymbionts that could not be cultured by standard techniques. These bacteria were phylogenetically characterized following amplification and sequencing of the near-full-length 16S rRNA gene. We used two fluorescently labelled oligonucleotide probes targeting signature regions within the retrieved sequences to detect these organisms in situ. Phylogenetic analyses demonstrated that they displayed 99.6% sequence similarity and formed an independent and well-separated lineage within the Rickettsiales branch of the alpha subdivision of the Proteobacteria. Nearest relatives included members of the genus Rickettsia, with sequence similarities of approximately 85 to 86%, suggesting that these symbionts are representatives of a new genus and, perhaps, family. Distance matrix, parsimony, and maximum-likelihood tree-generating methods all consistently supported deep branching of the 16S rDNA sequences within the Rickettsiales. The oligonucleotide probes displayed at least three mismatches to all other available 16S rDNA sequences, and they both readily permitted the unambiguous detection of rod-shaped bacteria within intact acanthamoebae by confocal laser-scanning microscopy. Considering the long-standing relationship of most Rickettsiales with arthropods, the finding of a related lineage of endosymbionts in protozoan hosts was unexpected and may have implications for the preadaptation and/or recruitment of rickettsia-like bacteria to metazoan hosts.

Acanthamoeba↗
PubMed2002

Pallidal stimulation for parkinsonism: improved brain activation during sequence learning.

We used (15)O-labeled water and positron emission tomography to assess the effect of deep brain stimulation of the internal globus pallidus on motor sequence learning in Parkinson's disease. Seven right-handed patients were scanned on and off stimulation while they were performing a motor sequence learning task and a kinematically matched motor execution reference task. The scans were performed after a 12-hour medication washout. Stimulation parameters were adjusted for maximal motor improvement; experimental task parameters were held constant across stimulation conditions. Internal globus pallidus stimulation improved motor ratings by 37% (p < 0.01). During the sequence learning task, stimulation improved performance as measured by several correct anticipatory movements (p < 0.01) and by verbal report (p < 0.001). Concurrent positron emission tomography imaging during learning demonstrated significant (p < 0.01) increases in brain activation with stimulation in the left dorsolateral prefrontal cortex, bilaterally in premotor cortex, and in posterior parietal and occipital association areas. Stimulation did not affect the activity of these regions during the performance of the motor execution reference task. These findings suggest that internal globus pallidus deep brain stimulation can enhance the activity of prefrontal cortico-striato-pallidothalamic loops and related transcortical pathways. Improved sequence learning with stimulation may be directly related to these functional changes.

Adult↗
PubMed1999

Genetic diversity of archaea in deep-sea hydrothermal vent environments.

Molecular phylogenetic analysis of naturally occurring archaeal communities in deep-sea hydrothermal vent environments was carried out by PCR-mediated small subunit rRNA gene (SSU rDNA) sequencing. As determined through partial sequencing of rDNA clones amplified with archaea-specific primers, the archaeal populations in deep-sea hydrothermal vent environments showed a great genetic diversity, and most members of these populations appeared to be uncultivated and unidentified organisms. In the phylogenetic analysis, a number of rDNA sequences obtained from deep-sea hydrothermal vents were placed in deep lineages of the crenarchaeotic phylum prior to the divergence of cultivated thermophilic members of the crenarchaeota or between thermophilic members of the euryarchaeota and members of the methanogen-halophile clade. Whole cell in situ hybridization analysis suggested that some microorganisms of novel phylotypes predicted by molecular phylogenetic analysis were likely present in deep-sea hydrothermal vent environments. These findings expand our view of the genetic diversity of archaea in deep-sea hydrothermal vent environments and of the phylogenetic organization of archaea.

Adaptation, Physiological↗
PubMed1995

The sequence, organization, and evolution of the Locusta migratoria mitochondrial genome.

The sequencing of the cloned Locusta migratoria mitochondrial genome has been completed. The sequence is 15,722 bp in length and contains 75.3% A+T, the lowest value in any of the five insect mitochondrial sequences so far determined. The protein coding genes have a similar A+T content (74.1%) but are distinguished by a high cytosine content at the third codon position. The gene content and organization are the same as in Drosophila yakuba except for a rearrangement of the two tRNA genes tRNAlys and tRNAasp. The A+T-rich region has a lower A+T nucleotide content than in other insects, and this is largely due to the presence of two G+C-rich 155-bp repetitive sequences at the 5'end of this section and the beginning of the adjacent small rRNA gene. The sizes of the large and small rRNA genes are 1,314 and 827 bp, respectively, and both sequences can be folded to form secondary structures similar to those previously predicted for Drosophila. The tRNA genes have also been modeled and these show a strong resemblance to the dipteran tRNAs, all anticodons apparently being conserved between the two species. A comparison of the protein coding nucleotide sequences of the locust DNA with the homologous sequences of five other arthropods (Drosophila yakuba, Anopheles quadrimaculatus, Anopheles gambiae, Apis mellifera, and Artemia franciscana) was performed. The amino acid composition of the encoded proteins in Locusta is similar to that of Drosophila, with a Dayhoff distance twice that of the distance between the fruit fly and the mosquitoes. A phylogenetic analysis revealed the locust genes to be more similar to those of the Dipterans than to those of the honeybee at both the nucleotide and amino acid levels. A comparative analysis of tRNA orders, using crustacean mtDNAs as outgroups, supported this. This high level of divergence in the Apis genome has been noted elsewhere and is possibly an effect of directional mutation pressure having resulted in an accelerated pattern of sequence evolution. If the general assumption that the Holometabola are monophyletic holds, then these results emphasize the difficulties of reconstructing phylogenies that include lineages with variable substitution rates and base composition biases. The need to exercise caution in using information about tRNA gene orders in phylogenetic analysis is also illustrated. However, if the honeybee sequence is excluded, the correspondence between the other five arthropod sequences supports the findings of previous studies which have endorsed the use of mtDNA sequences for studies of phylogeny at deep levels of taxonomy when mutation rates are equivalent.

Amino Acids↗
PubMed1999

Diffusion- and perfusion-weighted magnetic resonance imaging in deep cerebral venous thrombosis.

BACKGROUND: Diffusion-weighted (DWI) and perfusion-weighted (PI) MRI are highly sensitive techniques for early diagnosis of arterial infarction, but little data on venous cerebral ischemia are available. We describe a case in which DWI, PI, and fast T2-weighted sequences were performed in the acute phase of deep cerebral venous thrombosis (CVT). CASE DESCRIPTION: An 11-year-old girl with Crohn's disease developed deep CVT in which extensive edema was shown in the deep gray matter on T2-weighted sequence images. Isotropic echo-planar DWI demonstrated a local augmentation of the apparent diffusion coefficient (1.1 to 1.6x10(-3) mm2/s), consistent with vasogenic edema. In dynamic contrast-enhanced PI, the regional cerebral blood volume was increased and the passage time of the contrast bolus was markedly prolonged. Clinically, the patient recovered totally after intravenous full-dose heparinization. T2 abnormalities, apparent diffusion coefficient values (0.8 to 0.92x10(-3) mm2/s), and brain perfusion alterations resolved without damage to brain tissue. CONCLUSIONS: Unlike arterial infarction, DWI demonstrated vasogenic edema in a patient with deep CVT, which proved to be reversible in follow-up magnetic resonance imaging. PI showed areas with extensive venous congestion, but perfusion deficits were missing. Therefore, we believe that DWI and PI may play a role in detecting venous congestion in CVT and in prospective differentiation of vasogenic edema and venous infarction.

Brain Edema↗
PubMed1997

Biochemical and phylogenetic characterization of two novel deep-sea Thermococcus isolates with potentially biotechnological applications.

The partial 16S rDNA gene sequences of two thermophilic archaeal strains, TY and TYS, previously isolated from the Guaymas Basin hydrothermal vent site were determined. Lipid analyses and a comparative analysis performed with 16S rDNA sequences of similar thermophilic species showed that the strains isolated from deep-sea vents were not identical to the other species belonging to the genus Thermococcus. On the basis of the results of the phylogenetic analyses, lipid analyses, and previously reported physiological data, we believe that strains TY and TYS are significantly different from the previously described Thermococcus species. According to specific physiological and molecular features, we propose the use of these isolates as potential tools for the development of biotechnological applications in the field of starch processing and DNA technology.

Archaea↗
PubMed1998

Molecular phylogeny and evolution of the deep-sea fish genus Sternoptyx.

A portion of mitochondrially encoded 12S and 16S ribosomal RNA genes were sequenced from all four valid species of the midwater deep-sea fish genus Sternoptyx (Teleostei: Sternoptychidae) and four sternoptychid outgroup taxa. Secondary structure-based alignment resulted in a character matrix consisting of 865 bp of unambiguously aligned, combined sequences of the two genes, which were subjected to phylogenetic analyses using the maximum parsimony and maximum likelihood methods. The resultant tree topologies from the two methods were congruent and supported by various tree statistics. Although the single most parsimonious tree was not statistically different from the two second parsimonious trees, independent morphological evidence from the anal fin pterygiophore configuration and associated structures strongly supported the former as the preferred hypothesis. Mapping of the contemporary geographic distribution patterns of the four species onto the tree suggested that there was a common ancestor of Sternoptyx with a circumglobal distribution, which had been subdivided into southern and northern ancestral populations along 30 degrees S, possibly through some large-scale oceanographic event. There has been no discernible speciation event in the southern population, though the northern population has subsequently speciated into three contemporary species with largely allopatric/microallopatric distributions.

Animals↗
PubMed2001

Phylogenetic diversity of ribulose-1,5-bisphosphate carboxylase/oxygenase large-subunit genes from deep-sea microorganisms.

The phylogenetic diversity of the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO, E.C. 4.1.1.39) large-subunit genes of deep-sea microorganisms was analyzed. Bulk genomic DNA was isolated from seven samples, including samples from the Mid-Atlantic Ridge and various deep-sea habitats around Japan. The kinds of samples were hydrothermal vent water and chimney fragment; reducing sediments from a bathyal seep, a hadal seep, and a presumed seep; and symbiont-bearing tissues of the vent mussel, Bathymodiolus sp., and the seep vestimentiferan tubeworm, Lamellibrachia sp. The RuBisCO genes that encode both form I and form II large subunits (cbbL and cbbM) were amplified by PCR from the seven deep-sea sample DNA populations, cloned, and sequenced. From each sample, 50 cbbL clones and 50 cbbM clones, if amplified, were recovered and sequenced to group them into operational taxonomic units (OTUs). A total of 29 OTUs were recorded from the 300 total cbbL clones, and a total of 24 OTUs were recorded from the 250 total cbbM clones. All the current OTUs have the characteristic RuBisCO amino acid motif sequences that exist in other RuBisCOs. The recorded OTUs were related to different RuBisCO groups of proteobacteria, cyanobacteria, and eukarya. The diversity of the RuBisCO genes may be correlated with certain characteristics of the microbial habitats. The RuBisCO sequences from the symbiont-bearing tissues showed a phylogenetic relationship with those from the ambient bacteria. Also, the RuBisCO sequences of known species of thiobacilli and those from widely distributed marine habitats were closely related to each other. This suggests that the Thiobacillus-related RuBisCO may be distributed globally and contribute to the primary production in the deep sea.

Amino Acid Sequence↗
PubMed2004

Molecular diversity of new Thermococcales isolates from a single area of hydrothermal deep-sea vents as revealed by randomly amplified polymorphic DNA fingerprinting and 16S rRNA gene sequence analysis.

Members of the Thermococcales are anaerobic Archaea belonging to the kingdom Euryarchaea that are studied in many laboratories as model organisms for hyperthermophiles. We describe here a molecular analysis of 86 new Thermococcales isolates collected from six different chimneys of a single hydrothermal field located in the 13 degrees N 104 degrees W segment of the East Pacific ridge at a depth of 2,330 m. These isolates were sorted by randomly amplified polymorphic DNA (RAPD) fingerprinting into nine groups, and nine unique RAPD profiles were obtained. One RAPD group corresponds to new isolates of Thermococcus hydrothermalis, whereas all other groups and isolates with unique profiles are different from the 22 reference strains included in this study. Analysis of 16S rRNA gene sequences of representatives of each RAPD group and unique profiles showed that one group corresponds to Pyrococcus strains, whereas all the other isolates are Thermococcus strains. We estimated that our collection may contain at least 11 new species. These putative species, isolated from a single area of hydrothermal deep-sea vents, are dispersed in the 16S rRNA tree among the reference strains previously isolated from diverse hot environments (terrestrial, shallow water, hydrothermal vents) located around the world, suggesting that there is a high degree of dispersal of Thermococcales: About one-half of our isolates contain extrachromosomal elements that could be used to search for novel replication proteins and to develop genetic tools for hyperthermophiles.

Base Sequence↗
PubMed2004

Kangiella koreensis gen. nov., sp. nov. and Kangiella aquimarina sp. nov., isolated from a tidal flat of the Yellow Sea in Korea.

Two Gram-negative, non-motile, non-spore-forming, rod-shaped organisms, strains SW-125T and SW-154T, were isolated from tidal flat sediment of the Yellow Sea in Korea, and subjected to a polyphasic taxonomic study. Strains SW-125T and SW-154T grew optimally at 30-37 degrees C and in the presence of 2-3 % (w/v) NaCl. They contained ubiquinone-8 (Q-8) as the predominant respiratory lipoquinone and iso-C(15 : 0) as the major fatty acid. The DNA G + C contents of strains SW-125T and SW-154T were 44 mol%. Phylogenetic trees based on 16S rRNA gene sequences revealed that the two strains form deep evolutionary lineages of descent within the gamma-Proteobacteria. Strains SW-125T and SW-154T exhibited 16S rRNA gene sequence similarity levels of less than 90 % to members of the gamma-Proteobacteria used in this analysis. Strains SW-125T and SW-154T showed a 16S rRNA gene sequence similarity level of 98.5 % and a mean DNA-DNA relatedness level of 9.4 %. Therefore, on the basis of phenotypic, phylogenetic and genomic data, a new genus, Kangiella gen. nov., is proposed to accommodate the novel strains, comprising two novel species, Kangiella koreensis sp. nov. (type strain, SW-125T = KCTC 12182T = DSM 16069T) and Kangiella aquimarina sp. nov. (type strain, SW-154T = KCTC 12183T = DSM 16071T).

Bacterial Typing Techniques↗
PubMed1997

Phylogeny of cyanobacterial nifH genes: evolutionary implications and potential applications to natural assemblages.

DNA sequences of a fragment of nifH from diverse cyanobacteria were amplified, cloned and sequenced to determine the evolutionary relationship of nitrogenase within the cyanobacteria as a group, and to provide a basis for the identification of uncultivated strains of cyanobacteria in the environment. Analysis of 30 nitrogenase DNA and deduced amino acid sequences from cyanobacteria representing five major taxonomic subdivisions showed great variation in phylogenetic distances between the sequences. Sequences from heterocystous cyanobacteria formed a coherent cluster, in which branching forms did not form a clade distinct from the non-branching forms. Nitrogenase sequences from the unicellular cyanobacteria Gloeothece and Synechococcus sp. RF-1 formed a cluster, as did sequences from the genera Xenococcus and Myxosarcina. The nifH sequences of filamentous nonheterocystous cyanobacteria were not closely related to each other, forming deep branches with respect to the heterocystous cyanobacterial nifH sequences. The phylogeny of nifH based on amino acid sequences was consistent with taxonomic relationships among the strains; for example, a sequence obtained form a natural assemblage believed to be dominated by 'Lyngbya' clustered with nifH from Lyngbya lagerheimii. Results also indicate that the phylogeny of nifH among the cyanobacteria is largely consistent with the phylogeny of 16S rRNA, and furthermore that the nifH sequence can be used to identify uncultivated strains of nitrogen-fixing cyanobacteria.

Amino Acid Sequence↗
PubMed2003

Detection of an Ala601Thr mutation of plasminogen gene in 3 out of 36 Korean patients with deep vein thrombosis.

Plasminogen is a key proenzyme in the fibrinolytic and thrombolytic systems. Congenital deficiency of plasminogen and molecular abnormality of plasminogen (dysplasminogenemia) have been reported in association with the thrombotic tendency in human. In dysplasminogenemia, the level of immunoreactive plasminogen is normal, although the functional activity is reduced. Human plasminogen gene spans about 52.5 kb of DNA and consists of 19 exons. Three types of mutations (Ala601Thr, Val355Phe, and Asp676Asn) have been described in dysplasminogenemia. In this study, we measured the plasminogen activity in patients with deep vein thrombosis and analyzed the DNA sequence to detect three point mutations (Ala601Thr, Val355Phe and Asp676Asn) in patients with hypo/dysplasminogenemia. Dysplasminogenemia was identified in 3 (8.3%) of unrelated 36 patients with deep vein thrombosis and the Ala601Thr mutation was detected in all three patients with dysplasminogenemia. In conclusion, dysplasminogenemia is not rare in deep vein thrombosis, which suggests a risk factor for the thrombosis in Korean population.

Adult↗
PubMed2001

16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection.

Recently, anaerobic ammonium-oxidizing bacteria (AAOB) were identified by comparative 16S rDNA sequence analysis as a novel, deep-branching lineage within the Planctomycetales. This lineage consists currently of only two, not yet culturable bacteria which have been provisionally described as Candidatus 'Brocadia anammoxidans' and Candidatus 'Kuenenia stuttgartiensis'. In this study, a large fragment of the rDNA operon, including the 16S rDNA, the intergenic spacer region (ISR) and approximately 2 000 bases of the 23S rDNA, was polymerase chain reaction (PCR) amplified, cloned and sequenced from both AAOB. The retrieved 16S rDNA sequences of both species contain an insertion at helix 9 with a previously overlooked pronounced secondary structure (new subhelices 9a and 9b). This insertion, which is absent in all other known prokaryotes, is detectable by fluorescence in situ hybridization (FISH) and thus present in the mature 16S rRNA. In contrast with the genera Pirellula, Planctomyces and Gemmata that possess unlinked 16S and 23S rRNA genes, both AAOB have the respective genes linked together by an ISR of approximately 450 bp in length. Phylogenetic analysis of the obtained 23S rRNA-genes confirmed the deep branching of the AAOB within the Planctomycetales and allowed the design of additional specific FISH probes. Remarkably, the ISR of the AAOB also could be successfully detected by FISH via simultaneous application of four monolabelled oligonucleotide probes. Quantitative FISH experiments with cells of Candidatus 'Brocadia anammoxidans' that were inhibited by exposure to oxygen for different time periods demonstrated that the concentration of transcribed ISR reflected the activity of the cells more accurately than the 16S or 23S rRNA concentration. Thus the developed ISR probes might become useful tools for in situ monitoring of the activity of AAOB in their natural environment.

Bacteria, Anaerobic↗
PubMed1998

Assessment of depth of myometrial invasion by endometrial carcinoma: comparison of T2-weighted SE and contrast-enhanced dynamic GRE MR imaging.

A prospective study was undertaken to assess the value of both T2-weighted spin-echo (SE) and contrast-enhanced dynamic gradient-echo (GRE) sequences using MR imaging in differentiating the deep myometrial invasion from lower stages produced by endometrial carcinoma. For the correlation of MR findings with the histopathologic findings, patients who had no myometrial invasion (stage 1 a) and patients in whom tumors were confined to the superficial myometrium (stage 1 b) at pathologic examination were combined as lower stages. Twenty patients with endometrial carcinoma were studied using both techniques. The absence of any detectable tumor (stage 1 a) or the presence of a tumor confined to inner half of myometrium (stage 1 b) and extention of tumor to the outer half of myometrium (stage 1 c) were used as the diagnostic criteria. In pathologic examination of excised specimens, deep myometrial invasion was detected in 9 of 20 patients. The sensitivity, specificity, accuracy, positive predictive values (PPV) and negative predictive values (NPV) of T2-weighted SE in differentiating deep myometrial invasion from combined lower stages were 88, 91, 90, 88, and 91 %, respectively, whereas corresponding values for contrast-enhanced dynamic GRE sequences were 78, 100, 90, 100, and 85 %. Statistical difference between two sequences did not reach a significant level. We conclude that in cases of absence of visible junctional zone with SE sequence, contrast-enhanced dynamic GRE MR imaging may be helpful.

Adult↗
PubMed2004

Pulmonary consequences of a deep breath revisited.

About two decades ago, a model was proposed for surfactant release by lung distension. This model implies rapid fusion of lamellar bodies (LBs) with the plasma membrane followed by quick release of surfactant into the alveolus, as reflected by immediate facilitation of lung inflation after a single deep breath. Recent experimental evidence indicates that this two-pool model (intracellular versus alveolar surfactant pool) has to be refined by introducing a third pool, which resides in fused but non-released LBs. Here we discuss the implication of this additional pool for strain-induced surfactant secretion and propose a revised model for the sequence of events following a single deep breath.

Animals↗
PubMed2002

Phylogenetic composition of bacterioplankton assemblages from the Arctic Ocean.

We analyzed the phylogenetic composition of bacterioplankton assemblages in 11 Arctic Ocean samples collected over three seasons (winter-spring 1995, summer 1996, and summer-fall 1997) by sequencing cloned fragments of 16S rRNA genes. The sequencing effort was directed by denaturing gradient gel electrophoresis (DGGE) screening of samples and the clone libraries. Sequences of 88 clones fell into seven major lineages of the domain Bacteria: alpha(36%)-, gamma(32%)-, delta(14%)-, and epsilon(1%)-Proteobacteria; Cytophaga-Flexibacter-Bacteroides spp. (9%); Verrucomicrobium spp. (6%); and green nonsulfur bacteria (2%). A total of 34% of the cloned sequences (excluding clones in the SAR11 and Roseobacter groups) had sequence similarities that were <94% compared to previously reported sequences, indicating the presence of novel sequences. DGGE fingerprints of the selected samples showed that most of the bands were common to all samples in all three seasons. However, additional bands representing sequences related to Cytophaga and Polaribacter species were found in samples collected during the summer and fall. Of the clones in a library generated from one sample collected in spring of 1995, 50% were the same and were most closely affiliated (99% similarity) with Alteromonas macleodii, while 50% of the clones in another sample were most closely affiliated (90 to 96% similarity) with Oceanospirillum sp. The majority of the cloned sequences were most closely related to uncultured, environmental sequences. Prominent among these were members of the SAR11 group. Differences between mixed-layer and halocline samples were apparent in DGGE fingerprints and clone libraries. Sequences related to alpha-Proteobacteria (dominated by SAR11) were abundant (52%) in samples from the mixed layer, while sequences related to gamma-proteobacteria were more abundant (44%) in halocline samples. Two bands corresponding to sequences related to SAR307 (common in deep water) and the high-G+C gram-positive bacteria were characteristic of the halocline samples.

Arctic Regions↗