28 research outputs found
Memory in Microbes: Quantifying History-Dependent Behavior in a Bacterium
Memory is usually associated with higher organisms rather than bacteria. However, evidence is mounting that many regulatory networks within bacteria are capable of complex dynamics and multi-stable behaviors that have been linked to memory in other systems. Moreover, it is recognized that bacteria that have experienced different environmental histories may respond differently to current conditions. These “memory” effects may be more than incidental to the regulatory mechanisms controlling acclimation or to the status of the metabolic stores. Rather, they may be regulated by the cell and confer fitness to the organism in the evolutionary game it participates in. Here, we propose that history-dependent behavior is a potentially important manifestation of memory, worth classifying and quantifying. To this end, we develop an information-theory based conceptual framework for measuring both the persistence of memory in microbes and the amount of information about the past encoded in history-dependent dynamics. This method produces a phenomenological measure of cellular memory without regard to the specific cellular mechanisms encoding it. We then apply this framework to a strain of Bacillus subtilis engineered to report on commitment to sporulation and degradative enzyme (AprE) synthesis and estimate the capacity of these systems and growth dynamics to ‘remember’ 10 distinct cell histories prior to application of a common stressor. The analysis suggests that B. subtilis remembers, both in short and long term, aspects of its cell history, and that this memory is distributed differently among the observables. While this study does not examine the mechanistic bases for memory, it presents a framework for quantifying memory in cellular behaviors and is thus a starting point for studying new questions about cellular regulation and evolutionary strategy
Higher COVID-19 pneumonia risk associated with anti-IFN-α than with anti-IFN-ω auto-Abs in children
We found that 19 (10.4%) of 183 unvaccinated children hospitalized for COVID-19 pneumonia had autoantibodies (auto-Abs) neutralizing type I IFNs (IFN-alpha 2 in 10 patients: IFN-alpha 2 only in three, IFN-alpha 2 plus IFN-omega in five, and IFN-alpha 2, IFN-omega plus IFN-beta in two; IFN-omega only in nine patients). Seven children (3.8%) had Abs neutralizing at least 10 ng/ml of one IFN, whereas the other 12 (6.6%) had Abs neutralizing only 100 pg/ml. The auto-Abs neutralized both unglycosylated and glycosylated IFNs. We also detected auto-Abs neutralizing 100 pg/ml IFN-alpha 2 in 4 of 2,267 uninfected children (0.2%) and auto-Abs neutralizing IFN-omega in 45 children (2%). The odds ratios (ORs) for life-threatening COVID-19 pneumonia were, therefore, higher for auto-Abs neutralizing IFN-alpha 2 only (OR [95% CI] = 67.6 [5.7-9,196.6]) than for auto-Abs neutralizing IFN-. only (OR [95% CI] = 2.6 [1.2-5.3]). ORs were also higher for auto-Abs neutralizing high concentrations (OR [95% CI] = 12.9 [4.6-35.9]) than for those neutralizing low concentrations (OR [95% CI] = 5.5 [3.1-9.6]) of IFN-omega and/or IFN-alpha 2
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Light-based treatment of pediatric port-wine birthmarks.
Port-wine birthmarks (PWBs) are progressive vascular malformations with significant disfigurement and psychosocial morbidity; early light-based treatment has shown improved outcomes in the pediatric population. Somatic mosaic mutations underly the progressive nature of PWBs and explain the significant differences in response and heterogeneity of vessel architecture in the pediatric population when compared to the adult cohort. Here, we summarize a review of pediatric specific literature on the various light-based treatment modalities, including pulsed dye laser, near-infrared lasers, and intense pulsed light, providing the various indications, tips, advantages, and disadvantages for the pediatric dermatologist
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Light-based treatment of pediatric port-wine birthmarks.
Port-wine birthmarks (PWBs) are progressive vascular malformations with significant disfigurement and psychosocial morbidity; early light-based treatment has shown improved outcomes in the pediatric population. Somatic mosaic mutations underly the progressive nature of PWBs and explain the significant differences in response and heterogeneity of vessel architecture in the pediatric population when compared to the adult cohort. Here, we summarize a review of pediatric specific literature on the various light-based treatment modalities, including pulsed dye laser, near-infrared lasers, and intense pulsed light, providing the various indications, tips, advantages, and disadvantages for the pediatric dermatologist
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The complete genome of the uncultivated bacterium Desulforudis audaxviator from 2.8 km beneath earth's surface
A more complete picture of life on Earth, and even life in the Earth, has recently become possible through the application of environmental genomics. We have obtained the complete genome sequence of a new genus of the Finnicutes, the uncultivated sulfate reducing bacterium Desulforudis audaxviator, by filtering fracture water from a borehole at 2.8 km depth in a South African gold mine. The DNA was sequenced using a combination of Sanger sequencing and 454 pyrosequencing, and asserrlbled into just one genome, indicating the planktonic community is extremely low in diversity. We analyzed the genome of D. audaxviator using the MicrobesOnline annotation pipeline and toolkit (http://www.microbesonline.org), which offers powerful resources for comparative genome analysis, including operon predictions and treebased comparative genome browsing. MicrobesOnline allowed us to compare the D. audaxviator genome with other sequenced members of the Firmicutes in the same clade (primarily Pelotomaculum thennoproprionicum, Desulfotomaculum reducens, Carboxydothennus hydrogenoformans, and Moorella thennoacetica), as well as other known sulfate reducers and thermophilic organisms. D. audaxviator gives a view to the set of tools necessary for what appears to be a self-contained, independent lifestyle deep in the Earth's crust. The genome is not very streamlined, and indicates a motile, endospore forming sulfate reducer with pili that can fix its own nitrogen and carbon. D. audaxviator is an obligate anaerobe, and lacks obvious homologs of many of the traditional 02 tolerance genes, consistent with the low concentration of O2 in the fracture water and its long-term isolation from the surface. D. audaxviator provides a complete genome representative of the Gram-positive bacteria to further our understanding of dissimilatory sulfate reducing bacteria and archaea. Additionally, study of the deep subsurface has offered access to the simplest community yet studied by environmental genomics, perhaps consisting of just a single species that is capable of performing all of the tasks necessary for life
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The complete genome of the uncultivated ultra-deep subsurface bacterium Desulforudis audaxviator obtained by environmental genomics
A more complete picture of life on Earth, and even life in the Earth, has recently become possible through the application of environmental genomics. We have obtained the complete genome sequence of a new genus of the Firmicutes, the uncultivated sulfate reducing bacterium Desulforudis audaxviator, by filtering fracture water from a borehole at 2.8 km depth in a South African gold mine. The DNA was sequenced at the JGI using a combination of traditional Sanger sequencing and 454 pyrosequencing, and assembled into just one genome, indicating the planktonic community is extremely low in diversity. We analyzed the genome of D. audaxviator using the MicrobesOnline annotation pipeline and toolkit (http://www.microbesonline.org, and see MicrobesOnline abstract), which offers powerful resources for comparative genome analysis, including operon predictions and tree-based comparative genome browsing. MicrobesOnline allowed us to compare the D. audaxviator genome with other sequenced members of the Firmicutes in the same clade (primarily Pelotomaculum thermoproprionicum, Desulfotomaculum reducens, Carboxydothermus hydrogenoformans, and Thermoanaerobacter tengcongensis), as well as other known sulfate reducers (including Archaeoglobus fulgidus and Desulfovibrio vulgaris). D. audaxviator gives a view to the set of tools necessary for what appears to be a self-contained, independent lifestyle deep in the Earth's crust. The genome is not very streamlined, and indicates a motile, endospore forming sulfate reducer with pili that can fix its own nitrogen and carbon. D. audaxviator is an obligate anaerobe, and lacks obvious homologs of many of the traditional O2 tolerance genes, consistent with the low concentration of O2 in the fracture water and its long-term isolation from the surface. D. audaxviator provides a complete genome representative of the Gram-positive bacteria to further our understanding of dissimilatory sulfate reducing bacteria and archaea, and offers the full complement of genes necessary for an independent lifestyle based solely on interactions with the geochemistry of the deep subsurface