A Multifunctional Reactor with Dry-Stored Reagents for Enzymatic Amplification of Nucleic Acids

To enable inexpensive molecular detection at the point-of-care and at home with minimal or no instrumentation, it is necessary to streamline unit operations and store reagents refrigeration-free. To address this need, a multifunctional enzymatic amplification reactor that combines solid-phase nucleic acid extraction, concentration, and purification; refrigeration-free storage of reagents with just-in-time release; and enzymatic amplification is designed, prototyped, and tested. A nucleic acid isolation membrane is placed at the reactor's inlet, and paraffin-encapsulated reagents are prestored within the reactor. When a sample mixed with chaotropic agents is filtered through the nucleic acid isolation membrane, the membrane binds nucleic acids from the sample. Importantly, the sample volume is decoupled from the reaction volume, enabling the use of relatively large sample volumes for high sensitivity. When the amplification reactor's temperature increases to its operating level, the paraffin encapsulating the reagents melts and moves out of the way. The reagents are hydrated, just-in-time, and the polymerase reaction proceeds. The amplification process can be monitored, in real-time. We demonstrate our reactors' ability to amplify both DNA and RNA targets using polymerase with both reverse-transcriptase and strand displacement activities to obtain sensitivities on-par with benchtop equipment and a shelf life exceeding 6 months.

Complete Genome Sequence of Thermus aquaticus Y51MC23

Thermus aquaticus Y51MC23 was isolated from a boiling spring in the Lower Geyser Basin of Yellowstone National Park. Remarkably, this T. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. Y51MC23 is a Gram-negative, rod-shaped organism that grows well between 50°C and 80°C with maximum growth rate at 65°C to 70°C. Growth studies suggest that Y51MC23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular proteases and peptidases as well as transporter systems for amino acids and peptides. The genome was assembled de novo using a 350 bp fragment library (paired end sequencing) and an 8 kb long span mate pair library. A closed and finished genome was obtained consisting of a single chromosome of 2.15 Mb and four plasmids of 11, 14, 70, and 79 kb. Unlike other Thermus species, functions usually found on megaplasmids were identified on the chromosome. The Y51MC23 genome contains two full and two partial prophage as well as numerous CRISPR loci. The high identity and synteny between Y51MC23 prophage 2 and that of Thermus sp. 2.9 is interesting, given the 8,800 km separation of the two hot springs from which they were isolated. The anaerobic lifestyle of Y51MC23 is complex, with multiple morphologies present in cultures. The use of fluorescence microscopy reveals new details about these unusual morphological features, including the presence of multiple types of large and small spheres, often forming a confluent layer of spheres. Many of the spheres appear to be formed not from cell envelope or outer membrane components as previously believed, but from a remodeled peptidoglycan cell wall. These complex morphological forms may serve multiple functions in the survival of the organism, including food and nucleic acid storage as well as colony attachment and organization.

Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park

Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.

Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes

CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B′) as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B′ genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B′, but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as “viritopes” to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

Genome signature analysis of thermal virus metagenomes reveals Archaea and thermophilic signatures

Background

Metagenomic analysis provides a rich source of biological information for otherwise intractable viral communities. However, study of viral metagenomes has been hampered by its nearly complete reliance on BLAST algorithms for identification of DNA sequences. We sought to develop algorithms for examination of viral metagenomes to identify the origin of sequences independent of BLAST algorithms. We chose viral metagenomes obtained from two hot springs, Bear Paw and Octopus, in Yellowstone National Park, as they represent simple microbial populations where comparatively large contigs were obtained. Thermal spring metagenomes have high proportions of sequences without significant Genbank homology, which has hampered identification of viruses and their linkage with hosts. To analyze each metagenome, we developed a method to classify DNA fragments using genome signature-based phylogenetic classification (GSPC), where metagenomic fragments are compared to a database of oligonucleotide signatures for all previously sequenced Bacteria, Archaea, and viruses.

Results

From both Bear Paw and Octopus hot springs, each assembled contig had more similarity to other metagenome contigs than to any sequenced microbial genome based on GSPC analysis, suggesting a genome signature common to each of these extreme environments. While viral metagenomes from Bear Paw and Octopus share some similarity, the genome signatures from each locale are largely unique. GSPC using a microbial database predicts most of the Octopus metagenome has archaeal signatures, while bacterial signatures predominate in Bear Paw; a finding consistent with those of Genbank BLAST. When using a viral database, the majority of the Octopus metagenome is predicted to belong to archaeal virus Families Globuloviridae and Fuselloviridae, while none of the Bear Paw metagenome is predicted to belong to archaeal viruses. As expected, when microbial and viral databases are combined, each of the Octopus and Bear Paw metagenomic contigs are predicted to belong to viruses rather than to any Bacteria or Archaea, consistent with the apparent viral origin of both metagenomes.

Conclusion

That BLAST searches identify no significant homologs for most metagenome contigs, while GSPC suggests their origin as archaeal viruses or bacteriophages, indicates GSPC provides a complementary approach in viral metagenomic analysis.

A comparison between continuous central venous pressure measurement from right atrium and abdominal vena cava or common iliac vein

OBJECTIVE

To determine the accuracy of mean continuous central venous pressure (CVP) measurements in the abdominal vena cava.

DESIGN

We simultaneously measured the CVP at the superior vena cava or right atrium and at the abdominal vena cava or common iliac vein. The study was conducted at the pediatric intensive care unit of a major university-affiliated medical center.

PATIENTS

Nine patients, aged 6 months to 14 years, were included in our study.

MEASUREMENTS AND RESULTS

Eleven continuous recordings of 12 to 68 min were taken, eight of them while the children were mechanically ventilated. Mean overall CVP ranged from 3 to 30 mmHg. A total of 519 simultaneous recordings were made, of which 515 (99.2%) were within the accepted limits of agreement of +/- 2 mmHg: 301 (58%) with delta CVP of +/- 0 mmHg, 189 (36,4%) with delta CVP of +/- 1 mmHg, and 25 (4.8%) with delta CVP of +/- 2 mmHg. The mean pressure difference was -0.22 +/- 1.52 mmHg. Accuracy was maintained within all ranges of CVP (3-10, 11-20, and 21-30 mmHg) and was not influenced by mechanical ventilation or abdominal fluid collection.

CONCLUSION

In children with no obstruction of blood flow from the abdominal vena cava to the right atrium, the pressure in the abdominal vena cava or common iliac vein accurately reflects the pressure in the right atrium.

SgfI, a new type-II restriction endonuclease that recognizes the octanucleotide sequence 5'-GCGAT/CGC-3'

A new restriction endonuclease (ENase), SgfI, has been isolated from the bacterium Streptomyces sp. SgfI recognizes the 8-bp palindrome 5'-GCGATCGC-3' and cleaves double-stranded DNA after the T in this sequence, producing a two-base 3' overhang compatible with PvuI termini. SgfI is a rare-cutting ENase and should be useful for megabase mapping experiments.

Bca77I: a new type-II restriction endonuclease from Bacillus caldolyticus cutting at the (A/T) increases CCGG(A/T) site

We describe a new restriction enzyme recognizing a degenerate hexanucleotide sequence and cleaving the 5'-W increases CCGGW site (W = A or T). This enzyme cuts with high efficiency all four permutations of this sequence; ACCGGA (TCCGGT on the opposite strand), ACCGGT and TCCGGA. Methylation of the external cytosine completely blocks restriction while methylation of the internal cytosine only decreases the rate of restriction activity.

Bst71I: an isoschizomer of the type-IIS restriction enzyme, BbvI, recognizing the GCAGC(8/12) site

A new type-IIS restriction enzyme, Bst71I, with the specificity 5'-GCAGC(N)8/3'-CGTCG(N)12 was isolated from Bacillus stearothermophilus (Promega No. 71). This enzyme is an isoschizomer of BbvI with somewhat improved characteristics for use by molecular biologists.

Dactinomycin potentiation of radiation pneumonitis: a forgotten interaction

No mention of dactinomycin potentiation of pulmonary radiation was found in a review of the literature of the past 12 years. Before that, this complication was well described and investigators had calculated that dactinomycin increased the toxic effect of lung radiation by a factor of 1.3 and reduced the radiation tolerance of the lung by at least 20%. An example of such a toxic effect is described in the treatment of a 7-year-old girl with lung metastases from Ewing's sarcoma. The chemotherapy protocol followed contained cyclophosphamide, vincristine, dactinomycin, adriamycin, cisplatinum, VP16, and radiotherapy. The treatment was associated with fatal pulmonary fibrosis following the reintroduction of dactinomycin after radiotherapy. Our experience suggests that there is clinical significance to this complication in sarcoma therapy when dactinomycin-containing protocols are used with radiation in the treatment of pulmonary metastases.

Multiple proteins are produced from the dec-1 eggshell gene in Drosophila by alternative RNA splicing and proteolytic cleavage events

The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. A distinctive feature of the gene is the production of multiple products by both alternative RNA splicing and proteolytic processing events. DNA and protein sequencing studies have revealed several dec-1 protein products. The predominant translation product, fc106, has a vitelline membrane-like N-terminal domain followed by a glutamine, methionine-rich central region, largely in the form of 26 amino acid repeats. During late stage 10 the N-terminal portion of fc106 is cleaved, yielding s80, a major eggshell protein. Conceptual translation of the DNA sequence as well as molecular analyses of several dec-1 mutants suggest that the less abundant alternatively spliced RNAs encode primary translation products with different carboxy terminal ends. These results are discussed with respect to previous genetic analyses of dec-1 mutants as well as with respect to potential protein-protein interactions which may underlie stabilization of this complex extracellular structure.

Purification and characterization of an isoschizomer of Asu II from Clostridium sporogenes

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Adenovirus type 3 infection with systemic manifestation in apparently normal children

Between July 1983 and February 1984, eight children with adenovirus Type 3 infection, proven by virus isolation from sputum, stool or nasopharyngeal swabs and a fourfold increase in complement fixation antibody titers against the virus, were treated in our department. All eight patients had fever lasting at least 7 days, hepatomegaly, diffuse pulmonary infiltrates and abnormal liver function tests. Seven of the patients exhibited dyspnea and pulmonary wheezing. Six of the patients developed changes in state of consciousness, and three had repeated convulsions. EEG patterns in three of the patients were compatible with encephalopathy. Other clinical manifestations included: follicular tonsillitis in two patients, diarrhea in two, pneumothorax in one, and shock with disseminated intravascular coagulation in one. The spectrum of adenovirus Type 3 infection reported here has been described previously only in the viral hemorrhagic fevers. This adenovirus Type 3 infection shares the potential for disseminated disease that has been described previously for Type 7, simulating Reye's syndrome.