The lion's share of bacteria in various environments cannot be cloned in the laboratory and thus cannot be sequenced using existing technologies. A major goal of single-cell genomics is to complement gene-centric metagenomic data with whole-genome assemblies of uncultivated organisms. Assembly of single-cell data is challenging because of highly non-uniform read coverage as well as elevated levels of sequencing errors and chimeric reads. We describe SPAdes, a new assembler for both single-cell and standard (multicell) assembly, and demonstrate that it improves on the recently released E+V-SC assembler (specialized for single-cell data) and on popular assemblers Velvet and SoapDeNovo (for multicell data). SPAdes generates single-cell assemblies, providing information about genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. SPAdes is available online ( http://bioinf.spbau.ru/spades ). It is distributed as open source software.

SPAdes, a new genome assembly algorithm and its applications to single-cell sequencing ( 7th Annual SFAF Meeting, 2012)

Prospective Cohort Study

Osteoclasts are specialized cells derived from the monocyte/macrophage haematopoietic lineage that develop and adhere to bone matrix, then secrete acid and lytic enzymes that degrade it in a specialized, extracellular compartment. Discovery of the RANK signalling pathway in the osteoclast has provided insight into the mechanisms of osteoclastogenesis and activation of bone resorption, and how hormonal signals impact bone structure and mass. Further study of this pathway is providing the molecular basis for developing therapeutics to treat osteoporosis and other diseases of bone loss.

Osteoclast differentiation and activation

The TNF and TNF receptor superfamilies: integrating mammalian biology.

Osteoporosis, a disease endemic in Western society, typically reflects an imbalance in skeletal turnover so that bone resorption exceeds bone formation. Bone resorption is the unique function of the osteoclast, and anti-osteoporosis therapy to date has targeted this cell. The osteoclast is a specialized macrophage polykaryon whose differentiation is principally regulated by macrophage colony-stimulating factor, RANK ligand, and osteoprotegerin. Reflecting integrin-mediated signals, the osteoclast develops a specialized cytoskeleton that permits it to establish an isolated microenvironment between itself and bone, wherein matrix degradation occurs by a process involving proton transport. Osteopetrotic mutants have provided a wealth of information about the genes that regulate the differentiation of osteoclasts and their capacity to resorb bone.

https://science.sciencemag.org/content/sci/289/5484/1504.full.pdf

Bone Resorption by Osteoclasts

Air travel by individuals with active tuberculosis: reporting patterns and epidemiologic characteristics, Canada 2006-2008.

In 2000, syphilis mass treatment using oral azithromycin was delivered to at-risk British Columbians during a sex trade-related outbreak. The initiative included education, counselling and referral. This cross-sectional, observational study examines knowledge, attitudes and self-reported behaviour after one year among mass treatment participants compared with eligible non-participants. Participants self-reported positive changes: reduction in sexual partners overall (P=0.001) and for sex workers (P<0.01), decrease in unprotected oral sex (P=0.03), knowledge of asymptomatic syphilis (P=0.02), positive attitudes to mass treatment (P=0.02) and to the street nurses (P=0.01). Increased awareness was associated with increased condom use for vaginal sex overall (P=0.02) and for sex workers (P=0.03) and increased condom use for oral sex (P=0.05). There was no difference in syphilis incidence. Syphilis outbreak interventions that include education, support and referral can result in long-term positive behaviour changes.

The impact of syphilis mass treatment one year later: self-reported behaviour change among participants.

When modern epidemiology first took shape, there was only one kind of epidemiology – epidemiology, period. Over time has come specialisation into chronic and infectious disease epidemiology. Does this segregation into chronic and infectious disease epidemiologies benefit public health?

Dividing epidemiology into chronic disease and infectious disease “camps” is, in itself, problematic, in that each is based on an incompatible classification system. One classification is based on cause (infectious and non-infectious diseases) while the second is based on effect (chronic and acute diseases).1 Many chronic diseases have …

Bringing chronic disease epidemiology and infectious disease epidemiology back together

Since the publication of our recent public health article about early congenital syphilis,[1][1] we have been able to obtain patient consent for publication of photographs and details pertaining to 2 pregnant women who delivered babies with congenital syphilis. Both cases provide important

/pdf/early-congenital-syphilis-3vl2wl86en.pdf

Early congenital syphilis

INTRODUCTION: Genital herpes (GH) is the most common cause of genital ulceration, but is not reportable in Canada. Research in the United States has found that less than 10% of seropositive persons reported a diagnosis of GH. The present article investigates the rates of diagnosed cases of GH in Canada from 2002 to 2007.METHODS: Primary case diagnosis data on GH for the period between 2002 and 2007 were obtained from the Canadian Disease and Therapeutic Index, a proprietary database maintained by Intercontinental Medical Statistics (IMS) Health Canada. Of the 45,000 to 49,000 office-based physicians in Canada, IMS Health collected diagnosis-specific prescription diaries from a sample of 652, stratified according to geographic region and representing all major specialties, during this period.RESULTS: Between 2002 and 2007, there were approximately 84,398 to 122,456 medically attended GH cases annually in Canada. Approximately 74% to 93% of these diagnosed cases made one physician visit per year. The annual rate of medically attended GH cases ranged from 261.2 per 100,000 population to 386.6 per 100,000 population.DISCUSSION: The present report is the first time that administrative data have been used to estimate the annual rate of medically attended GH cases in Canada. The data include both incident and prevalent cases and are likely an underestimate of the actual number of cases because they only represent diagnosed cases presenting for medical care. Further seroepidemiological and clinical research studies would be helpful to assess the burden of infection and to plan appropriate diagnostic, treatment and preventive counselling services.

/pdf/genital-herpes-in-canada-deciphering-the-hidden-epidemic-4bm2euoy5s.pdf

Tom Wong

Papers

Air travel by individuals with active tuberculosis: reporting patterns and epidemiologic characteristics, Canada 2006-2008.

The impact of syphilis mass treatment one year later: self-reported behaviour change among participants.

Bringing chronic disease epidemiology and infectious disease epidemiology back together

Early congenital syphilis

Genital Herpes in Canada: Deciphering the Hidden Epidemic