Ribosomal RNA (rRNA) is the most highly abundant component of RNA, comprising the majority (>80% to 90%) of the molecules present in a total RNA sample. Depletion of this rRNA fraction is desirable prior to performing an RNA-seq reaction, so that sequencing capacity can be focused on more informative parts of the transcriptome. This unit describes an rRNA depletion method based on selective hybridization of oligonucleotides to rRNA, recognition with a hybrid-specific antibody, and removal of the antibody-hybrid complex on magnetic beads.

The problem of dynamically modeling a chemostat is addressed. Using the results of continuous culture experiments for the growth of a strain of Saccharomyces cerevisiae on a glucose-limited medium, a general approach to developing dynamic models is discussed. The approach to develop and verify the model involves three different types of experiments: steady-state, dynamic step response, and feedback identification.

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We have developed a new research assay that combines sequence-specific sample preparation and isothermal amplification for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae infections. The assay targets both the omp gene and the cryptic plasmid of C. trachomatis and the multicopy opa gene of N. gonorrhoeae, which are amplified and detected in a single reaction. We evaluated the ability of the assay to detect C. trachomatis and N. gonorrhoeae infections in first-catch urine, swab, and liquid-based cytology samples. Total agreement between the new assay and APTIMA Combo 2 varied between 95.3% and 100%, depending on the sample type and target detected. Total agreement between the new assay and BD ProbeTec varied between 96.7% and 100%, depending on the sample type and target detected. The assay has a simple work flow, and endpoint results can be achieved in 3 h, including sample preparation. The assay described here was evaluated for research use and was compared to commercially available assays.Chlamydia trachomatis and Neisseria gonorrhoeae are among the most common causes of sexually transmitted infections (3). Infection with these organisms is often asymptomatic, which hinders diagnosis or treatment. Persistent infection can have serious negative consequences, including pelvic inflammatory disease and infertility. Untreated and undiagnosed infections also contribute to the further spread of the disease. Screening programs are recommended to prevent these consequences (17). Of the various testing methods currently available, nucleic acid amplification tests are among the most sensitive and specific methods for detection of C. trachomatis and N. gonorrhoeae organisms in clinical specimens (7, 9). The high sensitivity of nucleic acid amplification tests allows them to be used with less-invasive clinical samples, such as first-catch urine, which facilitates establishment of screening programs.The assay described here combines sequence-specific sample preparation and isothermal amplification for the detection of C. trachomatis and N. gonorrhoeae infections. Sequence-specific sample preparation is based on antibody capture of DNA-RNA hybrids. Ribo-oligonucleotide probes hybridize to specific target sequences, and the resulting hybrids are captured by antibodies specific for DNA-RNA hybrids. This process enriches the desired nucleic acid sequences in the sample. Antibodies are coupled to magnetic beads. Target amplification is accomplished by thermophilic helicase-dependent amplification (tHDA) (16). Amplification of captured strands of the DNA target occurs directly on magnetic beads through the combined action of primers, thermostable DNA polymerase, and helicase. Target DNA is detected by use of dually labeled probes in either endpoint or real-time detection modes. C. trachomatis and N. gonorrhoeae targets are amplified and detected simultaneously in a single closed reaction vessel.We investigated the ability of the assay to detect C. trachomatis and N. gonorrhoeae infections in clinical specimens. R...