The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis.

Mycorrhizal symbioses--the union of roots and soil fungi--are universal in terrestrial ecosystems and may have been fundamental to land colonization by plants. Boreal, temperate and montane forests all depend on ectomycorrhizae. Identification of the primary factors that regulate symbiotic development and metabolic activity will therefore open the door to understanding the role of ectomycorrhizae in plant development and physiology, allowing the full ecological significance of this symbiosis to be explored. Here we report the genome sequence of the ectomycorrhizal basidiomycete Laccaria bicolor (Fig. 1) and highlight gene sets involved in rhizosphere colonization and symbiosis. This 65-megabase genome assembly contains approximately 20,000 predicted protein-encoding genes and a very large number of transposons and repeated sequences. We detected unexpected genomic features, most notably a battery of effector-type small secreted proteins (SSPs) with unknown function, several of which are only expressed in symbiotic tissues. The most highly expressed SSP accumulates in the proliferating hyphae colonizing the host root. The ectomycorrhizae-specific SSPs probably have a decisive role in the establishment of the symbiosis. The unexpected observation that the genome of L. bicolor lacks carbohydrate-active enzymes involved in degradation of plant cell walls, but maintains the ability to degrade non-plant cell wall polysaccharides, reveals the dual saprotrophic and biotrophic lifestyle of the mycorrhizal fungus that enables it to grow within both soil and living plant roots. The predicted gene inventory of the L. bicolor genome, therefore, points to previously unknown mechanisms of symbiosis operating in biotrophic mycorrhizal fungi. The availability of this genome provides an unparalleled opportunity to develop a deeper understanding of the processes by which symbionts interact with plants within their ecosystem to perform vital functions in the carbon and nitrogen cycles that are fundamental to sustainable plant productivity.

Novel structural elements within the nonproteolytic clostridium botulinum type F toxin gene cluster.

We sequenced for the first time the complete neurotoxin gene cluster of a nonproteolytic Clostridium botulinum type F. The neurotoxin gene cluster contained a novel gene arrangement that, compared to other C. botulinum neurotoxin gene clusters, lacked the regulatory botR gene and contained an intergenic is element between its orfX2 and orfX3 genes.

Analysis of ten Brucella genomes reveals evidence for horizontal gene transfer despite a preferred intracellular lifestyle.

The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact beta-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the "domino theory" of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.

Regulatory mechanisms of hemoglobin oxygen affinity in acidosis and alkalosis.

The recent reports of the effect of 2,3-diphosphoglycerate (2,3-DPG) on hemoglobin affinity for oxygen suggested that this substance may play a role in man's adaptation to acidosis and alkalosis.A study of the effect of induced acidosis and alkalosis on the oxyhemoglobin dissociation curve of normal man was therefore carried out, and the mechanisms involved in the physiological regulation of hemoglobin oxygen affinity examined.In acute changes of plasma pH there was no alteration in red cell 2,3-DPG content. However, there were changes in hemoglobin oxygen affinity and these correlated with changes in mean corpuscular hemoglobin concentration (MCHC). With maintained acidosis and alkalosis, red cell 2,3-DPG content was altered and correlated with the changes in hemoglobin oxygen affinity. Both of these mechanisms shift the hemoglobin oxygen dissociation curve opposite to the direct pH (Bohr) effect, and providing the rate of pH change is neither too rapid nor too large, they counteract the direct pH effect and the in vivo hemoglobin oxygen affinity remains unchanged. It is also shown that approximately 35% of the change in hemoglobin oxygen affinity resulting from an alteration in red cell 2,3-DPG, is explained by effect of 2,3-DPG on the red cell pH.

Effect of increased blood oxygen affinity on work performance of rats.

Influence of altered blood oxygen affinity on maximal performance ability was evaluated in trained rats exercising to exhaustion in a graded treadmill test. Modification of blood oxygen affinity was achieved both by 2,3-diphosphoglycerate depletion, accomplished by exposure of animals to CO(2) and by exchange transfusion with blood exposed to bisulfite or stored in acid citrate dextrose, and by carbamylation of hemoglobin, produced by exchange transfusion of blood incubated with potassium cyanate. A decrease in oxygen tension at half-saturation of hemoglobin (P(50)) from 36 to 23 mm Hg produced a decrease in resting central venous oxygen pressure of about 12 mm Hg. During exercise it caused an average decrease in work performance of about 10%, which was equivalent to that performance decrement caused by a decrease in hemoglobin concentration of approximately 10%. When superimposed on anemia, this change in blood oxygen affinity again caused a similar decrease in performance over and above that due to anemia alone. A marked rightward shift of the in vivo oxygen dissociation curve during severe exercise may have compensated for the reduced in vitro P(50).

Complete Genome Sequence of Alkaliphilus metalliredigens Strain QYMF, an Alkaliphilic and Metal-Reducing Bacterium Isolated from Borax-Contaminated Leachate Ponds.

Alkaliphilus metalliredigens strain QYMF is an anaerobic, alkaliphilic, and metal-reducing bacterium associated with phylum Firmicutes QYMF was isolated from alkaline borax leachate ponds. The genome sequence will help elucidate the role of metal-reducing microorganisms under alkaline environments, a capability that is not commonly observed in metal respiring-microorganisms.

Complete Genome Sequence of Anaeromyxobacter sp. Fw109-5, an Anaerobic, Metal-Reducing Bacterium Isolated from a Contaminated Subsurface Environment.

We report the genome sequence of Anaeromyxobacter sp. Fw109-5, isolated from nitrate- and uranium-contaminated subsurface sediment of the Oak Ridge Integrated Field-Scale Subsurface Research Challenge (IFC) site, Oak Ridge Reservation, TN. The bacterium's genome sequence will elucidate its physiological potential in subsurface sediments undergoing in situ uranium bioremediation and natural attenuation.

Chromosomal localization and complete genomic sequence of the murine autoimmune regulator gene (Aire).

We have recently cloned the murine autoimmune regulator (Aire) gene, the homologue of human AIRE responsible for the autoimmune polyglandular syndrome type 1 (APS1) or autoimmune polyendocrinopathy candidiasis ectodermal dystrophy (APECED). Here, we report the genomic sequence (18,413 bp) for the entire Aire gene and its 5' flanking region, which contains putative regulatory sequences. Comparison of the genomic and cDNA sequences indicates that the Aire gene is composed of 14 exons and the coding sequence shares high similarities between mouse and human. The sizes of the homologous introns in the two species are conserved; however, the introns do not share significant sequence homologies except the sequences near the splice donor and acceptor sites. Sequence analyses of the 5' regulatory region and the complete coding region in three mouse strains (B6, NOD and SJL) did not reveal any sequence variation, suggesting sequence conservation between different inbred mouse strains. Using one of the six microsatellite markers identified by genomic sequencing and a B6 x Cast backcross mapping panel, we mapped the mouse Aire gene to chromosome 10, a syntenic region containing the Cdl18 and Pfkl genes on human chromosome 21q22.

A novel deletion of the entire alpha globin locus causing alpha-thalassemia-1 in a northern European family.

alpha-Thalassemia, though one of the most common genetic abnormalities in humans, is uncommon outside of tropical or subtropical regions of the world. The authors describe a family of northern European ancestry with a clinical presentation consistent with alpha-thalassemia-1, or deletion of both alpha globin genes on chromosome 16 in cis. Genomic mapping studies show that the deletion in this family spans 36.5-40 kbp and removes the entire alpha globin locus. This represents a novel deletion causing alpha-thalassemia-1, here termed "--RT." The 5' breakpoint is localized near the 5' breakpoints of previously described deletions in Thai and Filipino persons, consistent with this being an unstable region of chromosome 16.

Platelet counts in capillary blood.

Samples of venous and capillary blood were collected simultaneously from healthy adults to assess the accuracy of platelet counts in capillary blood as determined by an automated particle counter. The difference between the mean venous blood platelet count (248,300) and the mean capillary blood count (215,500) was highly significant (P less than .001). For 24% (7/29) of the subjects, the capillary blood platelet count underestimated the venous blood count by greater than or equal to 25%, with three subjects erroneously classified as thrombocytopenic. A heterogeneous group of thrombocytopenic patients showed a similar difference in mean platelet counts (venous blood: 72,500/microliter; capillary blood: 65,400/microliter; P = 0.01). In most clinical situations, capillary blood platelet counts were adequate for patient evaluation; however, when an accurate platelet count is necessary, venous blood should be used.

Whole-blood hemoglobin determinations: a comparison of methodologies.

The Coulter Model S provides an accurate measurement of total hemoglobin (Hb) content in peripheral blood even when elevated levels of carboxyhemoglobin (HbCO) are present. Commercial standards and diluents for spectrophotometric determinations of cyanmethemoglobin (HiCN) are variable in quality. All diluents studied produce turbidity in some samples, and this may explain why manual Hb determinations tend to be higher than hemoglobin measurement on the Coulter S. The most reliable diluent was the reagent described by Van Kampen and Zijlstra. Its reliability is enhanced by centrifugation of sample in diluent. The use of a narrow-band-pass spectrophotometer for routine HiCN determinations in a clinical laboratory is not recommended because of its sensitivity to turbidity and HbCO.

Positional cloning of the Chediak-Higashi syndrome gene: genetic mapping of the beige locus on mouse chromosome 13.

BACKGROUND: Chediak-Higashi syndrome (CHS) is a systemic disorder of human and mouse (beige, bg) that is characterized by aberrant intracellular protein kinesis and lysosomal trafficking. Affected individuals exhibit a severe primary immune deficiency that principally affects the function of granulocytes and cytolytic lymphocytes and partial oculocutaneous albinism, platelet dysfunction, and neurodegeneration. Chediak-Higashi syndrome is inherited as an autosomal recessive Mendelian trait in human and mouse and maps on proximal mouse Chromosome 13. METHODS: To clone positionally the defective gene in CHS, we have generated a large number of backcross mice who segregate for beige. Genomic DNA from these mice was genotyped for 26 genetic markers known to map on proximal mouse Chromosome 13. RESULTS: By segregation analysis, bg was localized to a 0.24 centiMorgan interval and was shown to cosegregate with 6 genetic markers (Nid, Estm9, D13Mit56, D13Mit162, D13Mit237, and D13Mit240). Two of these loci, Nid and Estm9, are genes and represent candidates for bg. Nidogen (Nid) encodes an extracellular matrix protein that is a component of basement membranes. Estm9 is a sequence that is transcribed ubiquitously in mouse embryos and encodes a protein of unknown function. Mutation analysis of Nid and Estm9 was undertaken in 6 bg alleles; no differences were observed between bg and coisogenic controls by analysis of Northern blots, Southern blots, or by quantitative reverse transcription and polymerase chain reaction. CONCLUSIONS: These studies indicate that a genomic rearrangement affecting Nid or Estm9 does not underlie bg. The bg locus has been localized on mouse Chromosome 13 with sufficient precision to enable rapid cloning of the bg non-recombinant interval and eventual identification of the gene for Chediak-Higashi syndrome among sequences within the interval.

The reliability of laboratory data from blood samples collected through pulmonary artery catheters.

Blood samples obtained through quadruple-lumen Swan-Ganz catheters in ten critically ill patients provided reliable results after withdrawal of a total of 2.2 mL (including 1.2 mL of dead space) for hematocrit tests and 3.2 mL (including 1.2 mL of dead space) for plasma sodium tests.

Screening for alpha-thalassemia. Correlation of hemoglobin H inclusion bodies with DNA-determined genotype.

We evaluated potential screening protocols for alpha-thalassemia in a group of 80 patients whose genotypes were determined by Southern blot analysis with alpha- and zeta-globin DNA probes. Erythrocyte inclusion bodies were measured by a modified brilliant cresyl blue test. Erythrocyte indices and iron status were also measured. The brilliant cresyl blue test reliably detects couples at risk for hemoglobin Bart's hydrops fetalis. Measurement of the number of inclusion bodies differentiates the alpha-thalassemia genotypes in the absence of a coincident beta-chain synthesis deficiency, such as hemoglobin E or beta-thalassemia. The test appears to identify patients, such as those with the Thai and Filipino deletion variants, whose alpha-thalassemia cannot be definitively characterized by DNA testing when only alpha- and zeta-globin probes are used in the analysis. We also found evidence of elevated serum ferritin levels in many patients with deletion of two or three alpha-globin genes. This study shows that most routine screening for alpha-thalassemia can be performed with three simple tests: (1) the brilliant cresyl blue inclusion study, (2) erythrocyte indices, and (3) iron studies. Analysis with DNA probes is needed in only some circumstances.

Accurate coagulation studies from heparinized radial artery catheters.

We studied the feasibility of obtaining accurate coagulation studies from indwelling, heparinized radial artery catheters in 28 patients after cardiac surgery. PTT assay was chosen because of its frequent clinical use. Thrombin time assay was chosen because it is a component of the coagulation screening panel and because it is useful in assessing heparin contamination of specimens. We conclude that PTT results are reliable when the dwell volume (0.6 ml for the catheter and extension tubing in our study) and an additional 4.5 ml have been discarded (5.1 ml total discard volume). We recommend the collection of samples for thrombin time assay from a separate venous site because results on samples from heparinized arterial catheters are unpredictable.

Obtaining reliable plasma sodium and glucose determinations from pulmonary artery catheters.

In critically ill patients, blood specimens are frequently withdrawn from intravascular catheters without consideration of possible infusate contamination, of test accuracy, or of undue blood loss. The reliability of sodium (Na+) and glucose determinations withdrawn from the venous infusion port of a pulmonary artery catheter was studied in 30 patients after cardiac surgery. Catheter patency was maintained by a saline and heparin infusate. Venipuncture samples for Na+ and glucose served as controls. A sample containing the dwell volume of the catheter and the stopcock (1 ml) was withdrawn and discarded, followed by fifteen 1 ml samples being taken for analysis. It was concluded that Na+ values are stable after discard of the catheter dwell volume and an additional milliliter of blood. Minimal clinical differences were found in the glucose values after discard of the catheter dwell volume and two additional milliliters of blood.

Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling.

The complete genomes of Thermus oshimai JL-2 and T. thermophilus JL-18 each consist of a circular chromosome, 2.07 Mb and 1.9 Mb, respectively, and two plasmids ranging from 0.27 Mb to 57.2 kb. Comparison of the T. thermophilus JL-18 chromosome with those from other strains of T. thermophilus revealed a high degree of synteny, whereas the megaplasmids from the same strains were highly plastic. The T. oshimai JL-2 chromosome and megaplasmids shared little or no synteny with other sequenced Thermus strains. Phylogenomic analyses using a concatenated set of conserved proteins confirmed the phylogenetic and taxonomic assignments based on 16S rRNA phylogenetics. Both chromosomes encode a complete glycolysis, tricarboxylic acid (TCA) cycle, and pentose phosphate pathway plus glucosidases, glycosidases, proteases, and peptidases, highlighting highly versatile heterotrophic capabilities. Megaplasmids of both strains contained a gene cluster encoding enzymes predicted to catalyze the sequential reduction of nitrate to nitrous oxide; however, the nitrous oxide reductase required for the terminal step in denitrification was absent, consistent with their incomplete denitrification phenotypes. A sox gene cluster was identified in both chromosomes, suggesting a mode of chemolithotrophy. In addition, nrf and psr gene clusters in T. oshmai JL-2 suggest respiratory nitrite ammonification and polysulfide reduction as possible modes of anaerobic respiration.

The Calyptogena magnifica chemoautotrophic symbiont genome.

Chemoautotrophic endosymbionts are the metabolic cornerstone of hydrothermal vent communities, providing invertebrate hosts with nearly all of their nutrition. The Calyptogena magnifica (Bivalvia: Vesicomyidae) symbiont, Candidatus Ruthia magnifica, is the first intracellular sulfur-oxidizing endosymbiont to have its genome sequenced, revealing a suite of metabolic capabilities. The genome encodes major chemoautotrophic pathways as well as pathways for biosynthesis of vitamins, cofactors, and all 20 amino acids required by the clam.

The genome of the obligately intracellular bacterium Ehrlichia canis reveals themes of complex membrane structure and immune evasion strategies.

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, alpha-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associated with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).

Hemoglobin G trait and S trait in the same patient.

We describe a subject who had a positive sickle solubility test and a routine alkaline electrophoretic pattern showing three major hemoglobulin bands migrating to the A, S, and A2 positions. In addition, the non-heme protein carbonic anhydrase appeared to be increased, suggesting the presence of a split A2. Two major hemoglobin bands separated on agar gel electrophoresis using a citrate buffer, pH 6.2. A non-S hemoglobin migrating to the position of Hb S was identified as GPhiladelphia. The electrophoretic pattern of GPhil/S trait most closely resembles S/beta+ thalassemia or sickle cell trait. Careful study is essential to avoid misdiagnosis and unfairly stigmatizing patients whose benign abnormality may be confused with more severe disease entities.