The most conserved genome segments for life detection on Earth and other planets.

On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets.

Miniprimer PCR, a new lens for viewing the microbial world.

Molecular methods based on the 16S rRNA gene sequence are used widely in microbial ecology to reveal the diversity of microbial populations in environmental samples. Here we show that a new PCR method using an engineered polymerase and 10-nucleotide "miniprimers" expands the scope of detectable sequences beyond those detected by standard methods using longer primers and Taq polymerase. After testing the method in silico to identify divergent ribosomal genes in previously cloned environmental sequences, we applied the method to soil and microbial mat samples, which revealed novel 16S rRNA gene sequences that would not have been detected with standard primers. Deeply divergent sequences were discovered with high frequency and included representatives that define two new division-level taxa, designated CR1 and CR2, suggesting that miniprimer PCR may reveal new dimensions of microbial diversity.

Daptomycin for the treatment of gram-positive bacteremia and infective endocarditis: a retrospective case series of 31 patients.

STUDY OBJECTIVE: To evaluate the outcomes in patients with bacteremia and/or infective endocarditis who were treated with daptomycin. DESIGN: Retrospective chart review. SETTING: A university-affiliated medical center in Chicago, Illinois, and a regional hospital in Fountain Valley, California. PATIENTS: Thirty-one inpatients treated with daptomycin for bacteremia and/or infective endocarditis. MEASUREMENTS AND MAIN RESULTS: Patients were given daptomycin 4-6 mg/kg intravenously every 24-48 hours based on the practitioner's discretion and depending on the patient's clinical condition and presence of comorbidities. Primary end points were resolution of signs and symptoms of infection and discharge from the hospital. Methicillin-resistant Staphylococcus aureus ([MRSA] 11 patients) and vancomycin-resistant entercocci ([VRE] 11 patients) were the most common pathogens, whereas 7 patients had methicillin-sensitive S. aureus infection and 1 patient had coagulasenegative Staphylococcus infection. One patient with endocarditis had a negative culture result. Overall, 24 (77%) of the 31 patients achieved clinical resolution and were discharged, including all patients infected with MRSA; 7 patients died, 6 of whom had VRE infection. Duration of treatment for infective endocarditis lasted longer (typically 22-43 days) than that for bacteremia only (< or = 14 days), and no patients discontinued daptomycin because of adverse events. CONCLUSION: In these patients, daptomycin was safe and well tolerated even for extended durations of treatment. Daptomycin may provide an effective option for treating drug-resistant gram-positive bloodstream infections and endocarditis.

Use of daptomycin to treat drug-resistant Gram-positive bone and joint infections.

OBJECTIVE: Drug-resistant, Gram-positive bacteria are a growing concern in treating bone and joint infections, including osteomyelitis. This report describes the experience in a series of cases of the use of a novel antibiotic, daptomycin, for the treatment of bone and joint infections. RESEARCH DESIGN AND METHODS: This retrospective analysis included patients from two medical centers diagnosed with Gram-positive bone and joint infections and treated with daptomycin. RESULTS: A total of 10 patients were included in this report, of which nine received previous antibiotic therapy, including vancomycin, linezolid, and quinupristin/dalfopristin. Methicillin-resistant Staphylococcus aureus was isolated from eight patients while the remaining patients were infected with enterococci or streptococci. All patients initially resolved the infection while undergoing daptomycin treatment and were discharged from the hospital. One patient was switched to ampicillin (after receiving daptomycin for 4 days) once the infection was identified due to vancomycin-susceptible enterococcus. However, one patient was readmitted after 18 days due to a clinical relapse, possibly caused by under-dosing of daptomycin. CONCLUSION: Eight out of nine patients who received daptomycin for at least 8 days were successfully treated with the agent for Gram-positive bone and joint infections. Daptomycin was found to be well tolerated, even up to 44 days of treatment.

A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro.

Mechanisms that allow replicative DNA polymerases to attain high processivity are often specific to a given polymerase and cannot be generalized to others. Here we report a protein engineering-based approach to significantly improve the processivity of DNA polymerases by covalently linking the polymerase domain to a sequence non-specific dsDNA binding protein. Using Sso7d from Sulfolobus solfataricus as the DNA binding protein, we demonstrate that the processivity of both family A and family B polymerases can be significantly enhanced. By introducing point mutations in Sso7d, we show that the dsDNA binding property of Sso7d is essential for the enhancement. We present evidence supporting two novel conclusions. First, the fusion of a heterologous dsDNA binding protein to a polymerase can increase processivity without compromising catalytic activity and enzyme stability. Second, polymerase processivity is limiting for the efficiency of PCR, such that the fusion enzymes exhibit profound advantages over unmodified enzymes in PCR applications. This technology has the potential to broadly improve the performance of nucleic acid modifying enzymes.