A resource for cell line authentication, annotation and quality control.

Cell line misidentification, contamination and poor annotation affect scientific reproducibility. Here we outline simple measures to detect or avoid cross-contamination, present a framework for cell line annotation linked to short tandem repeat and single nucleotide polymorphism profiles, and provide a catalogue of synonymous cell lines. This resource will enable our community to eradicate the use of misidentified lines and generate credible cell-based data.

Using major outer membrane protein typing as an epidemiological tool to investigate outbreaks caused by milk-borne Campylobacter jejuni isolates in California.

We describe using major outer membrane protein (MOMP) typing as a screen to compare the Campylobacter jejuni porA gene sequences of clinical outbreak strains from human stool with the porA sequences of dairy farm strains isolated during two milk-borne campylobacteriosis outbreak investigations in California. The genetic relatedness of clinical and environmental strains with identical or closely related porA sequences was confirmed by multilocus sequence typing and pulsed-field gel electrophoresis analysis. The first outbreak involved 1,644 C. jejuni infections at 11 state correctional facilities and was associated with consumption of pasteurized milk supplied by an on-site dairy (dairy A) at a prison in the central valley. The second outbreak involved eight confirmed and three suspect C. jejuni cases linked to consumption of commercial raw milk and raw chocolate colostrum at another central valley dairy (dairy B). Both dairies bottled fluid milk on the farm and distributed the finished product to off-site locations. Altogether, C. jejuni was isolated from 7 of 15 (46.7%) bovine fecal, 12 of 20 (60%) flush alley water, and 1 of 20 (5%) lagoon samples collected on dairy A. At dairy B, C. jejuni was cultured from 9 of 26 (34.6%) bovine fecal samples. Environmental strains indistinguishable from the clinical outbreak strains were found in five flush alley water samples (dairy A) and four bovine fecal samples (dairy B). The findings demonstrate that MOMP typing is a useful tool to triage environmental isolates prior to conducting more labor-intensive molecular typing methods.

Recurrent wound botulism among injection drug users in California.

BACKGROUND: Botulism is an acute neurologic illness characterized by cranial nerve palsies and descending flaccid paralysis. Botulism is a rare disease and recurrent botulism even more rare. We review cases of recurrent wound botulism (WB) among injection drug users (IDUs) in California from 1993 through 2006 and describe 2 case patients. METHODS: From botulism surveillance data for 1993-2006, we identified patients with >1 episode of clinical WB, defined as acute descending paralysis with a visible wound or recent history of injection drug use. For each patient, ≥1 of their WB episodes was laboratory confirmed. We extracted demographic, clinical, and laboratory information from case and laboratory reports and compared clinical characteristic frequency of initial and second WB episodes. RESULTS: During 1993-2006, 17 IDUs had recurrent WB, 14 with 1 recurrence and 3 with 2 recurrences. Of 25 laboratory-confirmed episodes, 22 were confirmed through serum testing and 3 through wound testing. Patients were 32-61 years old, and 94% were male. All patients reported heroin injections; 88% specified black tar heroin use and 76% reported subcutaneous injection. The most common presentations were having a visible wound, speech difficulty, double vision, respiratory difficulty, and trouble swallowing. There were no significant differences in clinical presentation between initial and second episodes. CONCLUSIONS: As the California epidemic of WB among IDUs continues, WB episodes are recurring. Both clinicians and IDUs should be aware of the potential for WB to recur among IDUs to enable timely diagnosis and early botulinum antitoxin administration and supportive care.

Increased Coccidioidomycosis Among Inmates at a California Prison: Initial Investigation in 2005 to 2006.

Since 2005, coccidioidomycosis has increased among inmates at a California prison. Our initial investigation found an incidence of 3,323 cases/100,000 persons. Black race, age ≥41 years, and residence on Yard C were significantly associated with coccidioidomycosis ( p < .05). Inmates at this prison have continued to be at risk for coccidioidomycosis.

The evidence base for public health informing policy at the Centers for Disease Control and Prevention.

BACKGROUND: As part of a major re-examination of its organization, in 2004, the Centers for Disease Control and Prevention (CDC) assessed the evidence base for the effectiveness of population-based public health intervention programs. METHODS: For the leading causes of disease, injury, and disability, evidence was systematically reviewed for modifiable risk factors and their attributable fractions, and for public health interventions and their preventable fractions. RESULTS: For 31 conditions, 194 modifiable risk factors were identified, and attributable fractions were found for 65 (33.5%). For 137 (70.6%) of the risk factors, 702 population-based interventions were found. Preventable fractions were found for 31 (4.4%) of the interventions. CONCLUSIONS: Despite considerable information about both modifiable risk factors and interventions designed to reduce the risks of the major causes of disease, injury, and disability, the evidence base that describes the effectiveness of these interventions is limited. The CDC is committed to support research that will set priorities for program development and identify effective public health interventions.

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.

A large-scale effort, termed the Secreted Protein Discovery Initiative (SPDI), was undertaken to identify novel secreted and transmembrane proteins. In the first of several approaches, a biological signal sequence trap in yeast cells was utilized to identify cDNA clones encoding putative secreted proteins. A second strategy utilized various algorithms that recognize features such as the hydrophobic properties of signal sequences to identify putative proteins encoded by expressed sequence tags (ESTs) from human cDNA libraries. A third approach surveyed ESTs for protein sequence similarity to a set of known receptors and their ligands with the BLAST algorithm. Finally, both signal-sequence prediction algorithms and BLAST were used to identify single exons of potential genes from within human genomic sequence. The isolation of full-length cDNA clones for each of these candidate genes resulted in the identification of >1000 novel proteins. A total of 256 of these cDNAs are still novel, including variants and novel genes, per the most recent GenBank release version. The success of this large-scale effort was assessed by a bioinformatics analysis of the proteins through predictions of protein domains, subcellular localizations, and possible functional roles. The SPDI collection should facilitate efforts to better understand intercellular communication, may lead to new understandings of human diseases, and provides potential opportunities for the development of therapeutics.