Tomás J Aragón

Messenger RNA targeting to endoplasmic reticulum stress signalling sites

Deficiencies in the protein-folding capacity of the endoplasmic reticulum (ER) in all eukaryotic cells lead to ER stress and trigger the unfolded protein response (UPR). ER stress is sensed by Ire1, a transmembrane kinase/endoribonuclease, which initiates the non-conventional splicing of the messenger RNA encoding a key transcription activator, Hac1 in yeast or XBP1 in metazoans. In the absence of ER stress, ribosomes are stalled on unspliced HAC1 mRNA. The translational control is imposed by a base-pairing interaction between the HAC1 intron and the HAC1 5′ untranslated region. After excision of the intron, transfer RNA ligase joins the severed exons, lifting the translational block and allowing synthesis of Hac1 from the spliced HAC1 mRNA to ensue. Hac1 in turn drives the UPR gene expression program comprising 7–8% of the yeast genome to counteract ER stress. Here we show that, on activation, Ire1 molecules cluster in the ER membrane into discrete foci of higher-order oligomers, to which unspliced HAC1 mRNA is recruited by means of a conserved bipartite targeting element contained in the 3′ untranslated region. Disruption of either Ire1 clustering or HAC1 mRNA recruitment impairs UPR signalling. The HAC1 3′ untranslated region element is sufficient to target other mRNAs to Ire1 foci, as long as their translation is repressed. Translational repression afforded by the intron fulfils this requirement for HAC1 mRNA. Recruitment of mRNA to signalling centres provides a new paradigm for the control of eukaryotic gene expression.

BiP Binding to the ER-Stress Sensor Ire1 Tunes the Homeostatic Behavior of the Unfolded Protein Response

Computational modeling and experimentation in the unfolded protein response reveals a role for the ER-resident chaperone protein BiP in fine-tuning the systems response dynamics.

The unfolded protein response in fission yeast modulates stability of select mRNAs to maintain protein homeostasis

The unfolded protein response (UPR) monitors the protein folding capacity of the endoplasmic reticulum (ER). In all organisms analyzed to date, the UPR drives transcriptional programs that allow cells to cope with ER stress. The non-conventional splicing of Hac1 (yeasts) and XBP1 (metazoans) mRNA, encoding orthologous UPR transcription activators, is conserved and dependent on Ire1, an ER membrane-resident kinase/endoribonuclease. We found that the fission yeast Schizosaccharomyces pombe lacks both a Hac1/XBP1 ortholog and a UPR-dependent-transcriptional-program. Instead, Ire1 initiates the selective decay of a subset of ER-localized-mRNAs that is required to survive ER stress. We identified Bip1 mRNA, encoding a major ER-chaperone, as the sole mRNA cleaved upon Ire1 activation that escapes decay. Instead, truncation of its 3′ UTR, including loss of its polyA tail, stabilized Bip1 mRNA, resulting in increased Bip1 translation. Thus, S. pombe uses a universally conserved stress-sensing machinery in novel ways to maintain homeostasis in the ER. DOI: http://dx.doi.org/10.7554/eLife.00048.001

Case-Control Study of Shigellosis in San Francisco: The Role of Sexual Transmission and HIV Infection

BACKGROUND Shigella species infect approximately 450,000 persons annually in the United States. Person-to-person transmission of Shigella species, which have a low infectious dose, occurs frequently, particularly in areas with poor sanitation and hygiene. Sexual transmission of Shigella species among men who have sex with men (MSM) has been inferred from outbreaks of shigellosis among that population, and limited studies have suggested the importance of human immunodeficiency virus (HIV) infection as a risk factor for shigellosis. No population-based study of sporadic shigellosis has evaluated the role of sexual practices (especially among MSM) and HIV infection along with other established risk factors for shigellosis. METHODS We conducted a population-based case-control study of shigellosis in adults in San Francisco, California, during the period 1998-1999. Cases of Shigella infection were identified through laboratory-based active surveillance conducted by the California Emerging Infections Program. Seventy-six case patients were matched by sex with 146 control subjects. Exposure data were collected on established risk factors, sexual practices, and HIV infection status. Bivariable and multivariable analyses were conducted. Population-attributable fractions were calculated. RESULTS From the multivariable analysis, for men, shigellosis was associated with MSM (odds ratio [OR], 8.24; 95% confidence interval [CI], 2.70-25.2), HIV infection (OR, 8.17; 95% CI, 2.71-24.6), direct oral-anal contact (OR, 7.50; 95% CI, 1.74-32.3), and foreign travel (OR, 20.0; 95% CI, 5.26-76.3), with population-attributable fractions of 0.72, 0.42, 0.31, and 0.18, respectively. For women, shigellosis was associated only with foreign travel (OR, 21.0; 95% CI, 2.52-899), with a population-attributable fraction of 0.37. CONCLUSIONS Among MSM, shigellosis is predominantly a sexually transmitted disease, with direct oral-anal contact conferring the highest risk and HIV infection likely contributing to increased host susceptibility.

HIV infection as a risk factor for shigellosis.

We investigated cases of shigellosis in San Francisco and Alameda Counties identified during 1996 by active laboratory surveillance to assess the role of HIV infection as a risk factor for shigellosis. Dramatically elevated rates of shigellosis in HIV-infected persons implicate HIV infection as an important risk factor for shigellosis in San Francisco.

Research findings from nonpharmaceutical intervention studies for pandemic influenza and current gaps in the research.

In June 2006, the Centers for Disease Control and Prevention released a request for applications to identify, improve, and evaluate the effectiveness of nonpharmaceutical interventions (NPIs)-strategies other than vaccines and antiviral medications-to mitigate the spread of pandemic influenza within communities and across international borders (RFA-CI06-010). These studies have provided major contributions to seasonal and pandemic influenza knowledge. Nonetheless, key concerns were identified related to the acceptability and protective efficacy of NPIs. Large-scale intervention studies conducted over multiple influenza epidemics, as well as smaller studies in controlled laboratory settings, are needed to address the gaps in the research on transmission and mitigation of influenza in the community setting. The current novel influenza A (H1N1) pandemic underscores the importance of influenza research.

Logistics of community smallpox control through contact tracing and ring vaccination: a stochastic network model

BackgroundPrevious smallpox ring vaccination models based on contact tracing over a network suggest that ring vaccination would be effective, but have not explicitly included response logistics and limited numbers of vaccinators.MethodsWe developed a continuous-time stochastic simulation of smallpox transmission, including network structure, post-exposure vaccination, vaccination of contacts of contacts, limited response capacity, heterogeneity in symptoms and infectiousness, vaccination prior to the discontinuation of routine vaccination, more rapid diagnosis due to public awareness, surveillance of asymptomatic contacts, and isolation of cases.ResultsWe found that even in cases of very rapidly spreading smallpox, ring vaccination (when coupled with surveillance) is sufficient in most cases to eliminate smallpox quickly, assuming that 95% of household contacts are traced, 80% of workplace or social contacts are traced, and no casual contacts are traced, and that in most cases the ability to trace 1–5 individuals per day per index case is sufficient. If smallpox is assumed to be transmitted very quickly to contacts, it may at times escape containment by ring vaccination, but could be controlled in these circumstances by mass vaccination.ConclusionsSmall introductions of smallpox are likely to be easily contained by ring vaccination, provided contact tracing is feasible. Uncertainties in the nature of bioterrorist smallpox (infectiousness, vaccine efficacy) support continued planning for ring vaccination as well as mass vaccination. If initiated, ring vaccination should be conducted without delays in vaccination, should include contacts of contacts (whenever there is sufficient capacity) and should be accompanied by increased public awareness and surveillance.

Calculating expected years of life lost for assessing local ethnic disparities in causes of premature death

BackgroundA core function of local health departments is to conduct health assessments. The analysis of death certificates provides information on diseases, conditions, and injuries that are likely to cause death – an important outcome indicator of population health. The expected years of life lost (Y LL) measure is a valid, stand-alone measure for identifying and ranking the underlying causes of premature death. The purpose of this study was to rank the leading causes of premature death among San Francisco residents, and to share detailed methods so that these analyses can be used in other local health jurisdications.MethodsUsing death registry data and population estimates for San Francisco deaths in 2003–2004, we calculated the number of deaths, Y LL, and age-standardized Y LL rates (ASY Rs). The results were stratified by sex, ethnicity, and underlying cause of death. The Y LL values were used to rank the leading causes of premature death for men and women, and by ethnicity.ResultsIn the years 2003–2004, 6312 men died (73,627 years of life lost), and 5726 women died (51,194 years of life lost). The ASY R for men was 65% higher compared to the ASY R for women (8971.1 vs. 5438.6 per 100,000 persons per year). The leading causes of premature deaths are those with the largest average Y LLs and are largely preventable. Among men, these were HIV/AIDS, suicide, drug overdose, homicide, and alcohol use disorder; and among women, these were lung cancer, breast cancer, hypertensive heart disease, colon cancer, and diabetes mellitus. A large health disparity exists between African Americans and other ethnic groups: African American age-adjusted overall and cause-specific Y LL rates were higher, especially for homicide among men. Except for homicide among Latino men, Latinos and Asians have comparable or lower Y LL rates among the leading causes of death compared to whites.ConclusionLocal death registry data can be used to measure, rank, and monitor the leading causes of premature death, and to measure and monitor ethnic health disparities.

Risks of serious complications and death from smallpox vaccination: a systematic review of the United States experience, 1963-1968.

BackgroundThe United States (US) has re-instituted smallpox vaccinations to prepare for an intentional release of the smallpox virus into the civilian population. In an outbreak, people of all ages will be vaccinated. To prepare for the impact of large-scale ring and mass vaccinations, we conducted a systematic review of the complication and mortality risks of smallpox vaccination. We summarized these risks for post-vaccinial encephalitis, vaccinia necrosum (progressive vaccinia), eczema vaccinatum, generalized vaccinia, and accidental infection (inadvertant autoinoculation).MethodsUsing a MEDLINE search strategy, we identified 348 articles, of which seven studies met our inclusion criteria (the number of primary vaccinations and re-vaccinations were reported, sufficient data were provided to calculate complication or case-fatality risks, and comparable case definitions were used). For each complication, we estimated of the complication, death, and case-fatality risks.ResultsThe life-threatening complications of post-vaccinial encephalitis and vaccinia necrosum were at least 3 and 1 per million primary vaccinations, respectively. Twenty-nine percent of vaccinees with post-vaccinial encephalitis died and 15% with vaccinia necrosum died. There were no deaths among vaccinees that developed eczema vaccinatum; however, 2.3% of non-vaccinated contacts with eczema vaccinatum died. Among re-vaccinees, the risk of post-vaccinial encephalitis was reduced 26-fold, the risk of generalized vaccinia was reduced 29-fold, and the risk of eczema vaccinatum was reduced 12-fold. However, the risk reductions of accidental infection and vaccinia necrosum were modest (3.8 and 1.5 fold respectively).

Endemic cryptosporidiosis and exposure to municipal tap water in persons with acquired immunodeficiency syndrome (AIDS): A case-control study

BackgroundIn persons with acquired immunodeficiency syndrome (AIDS), Cryptosporidium parvum causes a prolonged, severe diarrheal illness to which there is no effective treatment, and the risk of developing cryptosporidiosis from drinking tap water in non-outbreak settings remains uncertain. To test the hypothesis that drinking tap water was associated with developing cryptosporidiosis, we conducted a matched case-control study among persons with AIDS in San Francisco.MethodsAmong patients reported to the San Francisco AIDS Registry from May 1996 through September 1998, we compared patients who developed cryptosporidiosis to those who did not. Cases were individually matched to controls based on age, sex, race/ethnicity, CD4+ T lymphocyte count, date of CD4+ count, and date of case diagnosis. Population attributable fractions (PAFs) were calculated.ResultsThe study consisted of 49 cases and 99 matched controls. In the multivariable analysis with adjustments for confounders, tap water consumption inside and outside the home at the highest exposure categories was associated with the occurrence of cryptosporidiosis (inside the home: odds ratio (OR), 6.76; 95% CI 1.37–33.5, and outside the home: OR 3.16; 95% CI 1.23–8.13). The PAF was 85%; that is, the proportion of cases of cryptosporidiosis in San Francisco AIDS patients attributable to tap water consumption could have been as high as 85%.ConclusionsAlthough the results from this observational study cannot be considered definitive, until there is more data, we recommend persons with AIDS, especially those with compromised immune systems, consider avoiding tap water.