Patching the Leaks: Revitalizing and Reimagining the STEM Pipeline

We identify problematic areas throughout the Science, Technology, Engineering and Mathematics (STEM) pipeline that perpetuate racial disparities in academia. Distinct ways to curtail these disparities include early exposure and access to resources, supportive mentoring networks and comprehensive training programs specifically for racially minoritized students and trainees at each career stage. These actions will revitalize the STEM pipeline.

Mentoring during Uncertain Times

Scientific success is mainly supported by mentoring, which often occurs through face-to-face interactions. Changes to the research environment incurred by the Coronavirus 2019 (COVID-19) pandemic have necessitated mentorship adaptations. Here, we describe how mentors can broaden their mentorship to support trainee growth and provide reassurance about trainee development amid uncertain circumstances.

Re-examination of population structure in Arctic ringed seals using DArTseq genotyping

Although Arctic ringed seals Phoca hispida hispida are currently abundant and broadly distributed, their numbers are projected to decline substantially by the year 2100 due to climate warming. While understanding population structure could provide insight into the impact of environmental changes on this subspecies, detecting demographically important levels of exchange can be difficult in taxa with high abundance. We used a next-generation sequencing approach (DArTseq) to genotype ~5700 single nucleotide polymorphisms in 79 seals from 4 Pacific Arctic regions. Comparison of the 2 most geographically separated strata (eastern Bering vs. northeastern Chukchi-Beaufort Seas) revealed a statistically significant level of genetic differentiation (FST = 0.001, p = 0.005) that, while small, was 1 to 2 orders of magnitude greater than expected based on divergence estimated for similarly sized populations connected by low (1% yr-1) dispersal. A relatively high proportion (72 to 88%) of individuals within these strata could be genetically assigned to their stratum of origin. These results indicate that demographically important structure may be present among Arctic ringed seals breeding in different areas, increasing the risk that declines in the number of seals breeding in areas most negatively affected by environmental warming could occur.

Localized delivery of ibuprofen via a bilayer delivery system (BiLDS) for supraspinatus tendon healing in a rat model

The high prevalence of tendon retear following rotator cuff repair motivates the development of new therapeutics to promote improved tendon healing. Controlled delivery of non-steroidal anti-inflammatory drugs to the repair site via an implanted scaffold is a promising option for modulating inflammation in the healing environment. Furthermore, biodegradable nanofibrous delivery systems offer an optimized architecture and surface area for cellular attachment, proliferation, and infiltration while releasing soluble factors to promote tendon regeneration. To this end, we developed a bilayer delivery system (BiLDS) for localized and controlled release of ibuprofen (IBP) to temporally mitigate inflammation and enhance tendon remodeling following surgical repair by promoting organized tissue formation. In vitro evaluation confirmed the delayed and sustained release of IBP from Labrafil-modified poly(lactic-co-glycolic) acid microspheres within sintered poly(ε-caprolactone) electrospun scaffolds. Biocompatibility of the BiLDS was demonstrated with primary Achilles tendon cells in vitro. Implantation of the IBP-releasing BiLDS at the repair site in a rat rotator cuff injury and repair model led to decreased expression of proinflammatory cytokine, tumor necrotic factor-α, and increased anti-inflammatory cytokine, transforming growth factor-β1. The BiLDS remained intact for mechanical reinforcement and recovered the tendon structural properties by 8 weeks. These results suggest the therapeutic potential of a novel biocompatible nanofibrous BiLDS for localized and tailored delivery of IBP to mitigate tendon inflammation and improve repair outcomes. Future studies are required to define the mechanical implications of an optimized BiLDS in a rat model beyond 8 weeks or in a larger animal model.

Mentoring minority trainees: Minorities in academia face specific challenges that mentors should address to instill confidence

A toolkit for mentoring minority students and trainees in science.

Three-Dimensional Porous Trabecular Scaffold Exhibits Osteoconductive Behaviors In Vitro

In the USA, approximately 500,000 bone grafting procedures are performed annually to treat injured or diseased bone. Autografts and allografts are the most common treatment options but can lead to adverse outcomes such as donor site morbidity and mechanical failure within 10 years. Due to this, tissue engineered replacements have emerged as a promising alternative to the biological options. In this study, we characterize an electrospun porous composite scaffold as a potential bone substitute. Various mineralization techniques including electrodeposition were explored to determine the optimal method to integrate mineral content throughout the scaffold. In vitro studies were performed to determine the biocompatibility and osteogenic potential of the nanofibrous scaffolds. The presence of hydroxyapatite (HAp) and brushite throughout the scaffold was confirmed using energy dispersive X-ray fluorescence, scanning electron microscopy, and ash weight analysis. The active flow of ions via electrodeposition mineralization led to a threefold increase in mineral content throughout the scaffold in comparison to static and flow mineralization. Additionally, a ten-layer scaffold was successfully mineralized and confirmed with an alizarin red assay. In vitro studies confirmed the mineralized scaffold was biocompatible with human bone marrow derived stromal cells. Additionally, bone marrow derived stromal cells seeded on the mineralized scaffold with embedded HAp expressed 30% more osteocalcin, a primary bone protein, than these cells seeded on non-mineralized scaffolds and only 9% less osteocalcin than mature pre-osteoblasts on tissue culture polystyrene. This work aims to confirm the potential of a biomimetic mineralized scaffold for full-thickness trabecular bone replacement.

Mechanical and biological evaluation of a hydroxyapatite-reinforced scaffold for bone regeneration

With over 500,000 bone grafting procedures performed annually in the United States, the advancement of bone regeneration technology is at the forefront of medical research. Many tissue-engineered approaches have been explored to develop a viable synthetic bone graft substitute, but a major challenge is achieving a load-bearing graft that appropriately mimics the mechanical properties of native bone. In this study, sintered hydroxyapatite (HAp) was used to structurally reinforce a scaffold and yield mechanical properties comparable to native bone. HAp was packed into a cylindrical framework and processed under varying conditions to maximize its mechanical properties. The resulting HAp columns were further tested in a 6-week degradation study to determine their physical and mechanical response. The cellular response of sintered HAp was determined using a murine preosteoblast cell line, MC3T3-E1. Cell viability and morphology were studied over a one-week period and MC3T3-E1 differentiation was determined by measuring the alkaline phosphatase levels. Finite element analysis was used to determine the columns' geometric configuration and arrangement within our previously developed composite bone scaffold. It was determined that incorporating four cylindrical HAp columns, fabricated under 44 MPa of pressure and sintered at 1200°C for 5 hr, led to load-bearing properties that match the yield strength of native whole bone. These preliminary results indicate that the incorporation of a mechanically enhanced HAp structural support system is a promising step toward developing one of the first load-bearing bone scaffolds that can also support cell proliferation and osteogenic differentiation. © 2018 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 107A: 732-741, 2019.

Investigating processing techniques for bovine gelatin electrospun scaffolds for bone tissue regeneration

Tissue engineering has emerged as a promising solution to tissue regeneration in the case of significant bone loss due to disease or injury. The ability to promote cellular attachment, migration, and differentiation into tissue is dependent on the scaffold's surface properties and composition. Bovine gelatin is a natural polymer commonly used as a scaffolding material for tissue engineering applications. Nonetheless, due to the hydrophilic behavior of gelatin, cross-linking and additives are necessary to maintain the scaffold's structure and overall strength in vivo. In this article, we discuss various processing techniques to determine the optimal electrospinning, cross-linking, sintering, and mineralization parameters necessary to yield a porous, mechanically enhanced scaffold. The scaffolds were evaluated quantitatively using compressive mechanical testing, and qualitatively using scanning electron microscopy (SEM). Mechanical data concluded the use of biocompatible microbial transglutaminase (mTG) as a cross-linking agent, led to increased compressive strength. SEM images confirmed the presence of individual gelatin and polymeric nanofibers woven into one scaffold. Sintering before leaching the scaffold yielded structured pores throughout the three-dimensional scaffold when compared to the scaffolds that were leached prior to sintering. The results presented in this article will provide novel information about processing techniques that can be utilized to develop a hybrid synthetic and biological based biomimetic mineralized scaffold for trabecular bone tissue regeneration. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 105B: 1131-1140, 2017.

In vitro evaluation of three-dimensional single-walled carbon nanotube composites for bone tissue engineering

The purpose of this study was to develop three-dimensional single-walled carbon nanotube composites (SWCNT/PLAGA) using 10-mg single-walled carbon nanotubes (SWCNT) for bone regeneration and to determine the mechanical strength of the composites, and to evaluate the interaction of MC3T3-E1 cells via cell adhesion, growth, survival, proliferation, and gene expression. PLAGA (polylactic-co-glycolic acid) and SWCNT/PLAGA microspheres and composites were fabricated, characterized, and mechanical testing was performed. MC3T3-E1 cells were seeded and cell adhesion/morphology, growth/survival, proliferation, and gene expression analysis were performed to evaluate biocompatibility. Imaging studies demonstrated microspheres with uniform shape and smooth surfaces, and uniform incorporation of SWCNT into PLAGA matrix. The microspheres bonded in a random packing manner while maintaining spacing, thus resembling trabeculae of cancellous bone. Addition of SWCNT led to greater compressive modulus and ultimate compressive strength. Imaging studies revealed that MC3T3-E1 cells adhered, grew/survived, and exhibited normal, nonstressed morphology on the composites. SWCNT/PLAGA composites exhibited higher cell proliferation rate and gene expression compared with PLAGA. These results demonstrate the potential of SWCNT/PLAGA composites for musculoskeletal regeneration, for bone tissue engineering, and are promising for orthopedic applications as they possess the combined effect of increased mechanical strength, cell proliferation, and gene expression.

Fabrication and characterization of three-dimensional electrospun scaffolds for bone tissue engineering

When traumatic injury, tumor removal, or disease results in significant bone loss, reconstructive surgery is required. Bone grafts are used in orthopedic reconstructive procedures to provide mechanical support and promote bone regeneration. In this study, we applied a heat sintering technique to fabricate 3D electrospun scaffolds that were used to evaluate effects of mineralization and fiber orientation on scaffold strength. We electrospun PLLA/gelatin scaffolds with a layer of PDLA and heat sintered them into three-dimensional cylindrical scaffolds. Scaffolds were mineralized by incubation in 10× simulated body fluid for 6, 24, and 48 h to evaluate the effect of mineralization on scaffolds compressive mechanical properties. The effects of heat sintering hydroxyapatite (HA) microparticles directly to the scaffolds on mineral deposition, distribution and mechanical properties of the scaffolds were also evaluated. We found that orientation of the fibers had little effect on the compressive mechanical properties of the scaffolds. However, increasing the mineralization times resulted in an increase in compressive mechanical properties. Also, the direct addition of HA microparticles had no effect on the scaffold mechanical properties, but had a significant effect on the mineral deposition on PLLA/gelatin scaffolds.

The Swine Flu Triage (SwiFT) study: development and ongoing refinement of a triage tool to provide regular information to guide immediate policy and practice for the use of critical care services during the H1N1 swine influenza pandemic

OBJECTIVES

To use, existing critical care and early pandemic, data to inform care during the pandemic influenza A 2009 (H1N1) pandemic (with a possible use for triage - if the demand for critical care seriously exceeded supply). To monitor the impact of the H1N1 pandemic on critical care services, in real time, with regular feedback to critical care clinicians and other relevant jurisdictions to inform ongoing policy and practice.

DESIGN

Modelling of data and cohort study.

SETTING

Modelling - 148 adult, general critical care units in England, Wales and Northern Ireland in the Intensive Care National Audit & Research Centre Case Mix Programme. Cohort study - 192 acute hospitals in England, Wales, Northern Ireland, Scotland and the Republic of Ireland.

PARTICIPANTS

Modelling - 105,397 admissions to adult, general critical care units. Cohort study - 1728 H1N1 pandemic-related admissions referred and assessed as requiring critical care.

MAIN OUTCOME MEASURES

Modelling - requirement for organ support and acute hospital mortality. Cohort study - survival to the end of critical care.

RESULTS

Modelling - cancelled or postponed, elective or scheduled surgery resulted in savings in calendar days of critical, Level 3 and advanced respiratory care of 17, 11 and 10%, respectively. These savings varied across units. Using routine, physiological variables, the best triage models, for all and for acute respiratory admissions, achieved only satisfactory concordance of 0.79 and 0.75, respectively. Application of the best model on all admissions indicated that approximately 12.5% of calendar days of critical care could be saved. Cohort study - research governance approvals were achieved for 192 acute hospitals, for 91 within 1 day of central research and development approval across the five countries. A total of 1725 cases (562 confirmed) were reported. Confirmed cases were young (mean age of 40 years), had low severity of acute illness on presentation [61% CURB-65 (confusion, urea, respiratory rate, blood pressure, age over 65 years) 0-1], but had long stays in critical care (median 8.5 days) and were likely to be ventilated (77% for median 9 days). Risk factors for acute hospital death were similar to those for general critical care admissions.

CONCLUSIONS

SwiFT was rapidly established. Models based on routine physiology suggested limited value for triage. More data and further modelling are warranted. The magnitude of the pandemic did not approach the worst-case scenario modelling, and UK-confirmed H1N1 cases appeared similar to those reported internationally.

FUNDING

The National Institute for Health Research Health Technology Assessment programme.

Risk factors for hospitalisation and poor outcome with pandemic A/H1N1 influenza: United Kingdom first wave (May-September 2009)

BACKGROUND

During the first wave of pandemic H1N1 influenza in 2009, most cases outside North America occurred in the UK. The clinical characteristics of UK patients hospitalised with pandemic H1N1 infection and risk factors for severe outcome are described.

METHODS

A case note-based investigation was performed of patients admitted with confirmed pandemic H1N1 infection.

RESULTS

From 27 April to 30 September 2009, 631 cases from 55 hospitals were investigated. 13% were admitted to a high dependency or intensive care unit and 5% died; 36% were aged <16 years and 5% were aged > or = 65 years. Non-white and pregnant patients were over-represented. 45% of patients had at least one underlying condition, mainly asthma, and 13% received antiviral drugs before admission. Of 349 with documented chest x-rays on admission, 29% had evidence of pneumonia, but bacterial co-infection was uncommon. Multivariate analyses showed that physician-recorded obesity on admission and pulmonary conditions other than asthma or chronic obstructive pulmonary disease (COPD) were associated with a severe outcome, as were radiologically-confirmed pneumonia and a raised C-reactive protein (CRP) level (> or = 100 mg/l). 59% of all in-hospital deaths occurred in previously healthy people.

CONCLUSIONS

Pandemic H1N1 infection causes disease requiring hospitalisation of previously fit individuals as well as those with underlying conditions. An abnormal chest x-ray or a raised CRP level, especially in patients who are recorded as obese or who have pulmonary conditions other than asthma or COPD, indicate a potentially serious outcome. These findings support the use of pandemic vaccine in pregnant women, children <5 years of age and those with chronic lung disease.

Modelling the impact of an influenza A/H1N1 pandemic on critical care demand from early pathogenicity data: the case for sentinel reporting

Projected critical care demand for pandemic influenza H1N1 in England was estimated in this study. The effect of varying hospital admission rates under statistical uncertainty was examined. Early in a pandemic, uncertainty in epidemiological parameters leads to a wide range of credible scenarios, with projected demand ranging from insignificant to overwhelming. However, even small changes to input assumptions make the major incident scenario increasingly likely. Before any cases are admitted to hospital, 95% confidence limit on admission rates led to a range in predicted peak critical care bed occupancy of between 0% and 37% of total critical care bed capacity, half of these cases requiring ventilatory support. For hospital admission rates above 0.25%, critical care bed availability would be exceeded. Further, only 10% of critical care beds in England are in specialist paediatric units, but best estimates suggest that 30% of patients requiring critical care will be children. Paediatric intensive care facilities are likely to be quickly exhausted and suggest that older children should be managed in adult critical care units to allow resource optimisation. Crucially this study highlights the need for sentinel reporting and real-time modelling to guide rational decision making.

Modelling the impact of an influenza pandemic on critical care services in England

The UK Influenza Pandemic Contingency Plan does not consider the impact of a pandemic on critical care services. We modelled the demand for critical care beds in England with software developed by the Centers for Disease Control (Flusurge 1.0), using a range of attack rates and pandemic durations. Using inputs that have been employed in UK Department of Health scenarios (25% attack rate and 8-week pandemic duration) resulted in a demand for ventilatory support that exceeded 200% of present capacity. Demand remained unsustainably high even when more favourable scenarios were considered. Current critical care bed capacity in England would be unable to cope with the increased demand provided by an influenza pandemic. Appropriate contingency planning is essential.

The impact of low-risk intensive care unit admissions on mortality probabilities by SAPS II, APACHE II and APACHE III

A large proportion of intensive care unit patients are low-risk admissions. Mortality probabilities generated by predictive systems may not accurately reflect the mortality experienced by subpopulations of critically ill patients. We prospectively assessed the impact of low-risk admissions (mortality risk < 10%) on the mortality estimates generated by three prognostic models. We studied 1497 consecutive admissions to a general intensive care unit. The performance of the three models for subgroups and the whole population was analysed. The proportions of patients designated as low risk varied with the model and differences in model performance were most pronounced for these patients. The APACHE II mortality ratios (1.32 vs. 1.19) did not differ for low- and higher risk patients, but mortality ratios generated by APACHE III (2.38 vs. 1.23) and SAPS II (2.19 vs. 1.16) were nearly two-fold greater. Calibration for higher risk patients was similar for all three models but the APACHE III system calibrated worse than the other models for low-risk patients. This may have contributed to the poorer overall calibration of the APACHE III system (Hosmer-Lemeshow C-test: APACHE III chi(2) = 329; APACHE II chi(2) = 42; SAPS II chi(2) = 62). Imperfect characterisation of the large proportion of low-risk intensive care unit admissions may contribute to the deterioration of the models' predictive accuracies for the intensive care population as a whole.

The FAD-PAS domain as a sensor for behavioral responses in Escherichia coli

Aer, the aerotaxis receptor in Escherichia coli, is a member of a novel class of flavoproteins that act as redox sensors. The internal energy of the cell is coupled to the redox state of the electron transport system, and this status is sensed by Aer(FAD). This is a more versatile sensory response system than if E. coli sensed oxygen per se. Energy-depleting conditions that decrease electron transport also alter the redox state of the electron transport system. Aer responds by sending a signal to the flagellar motor to change direction. The output of other sensory systems that utilize redox sensors is more commonly transcriptional regulation than a behavioral response. Analysis in silico showed Aer to be part of a superfamily of PAS domain proteins that sense the intracellular environment. In Aer, FAD binds to the PAS domain. By using site-specific mutagenesis, residues critical for FAD binding and sensory transduction were identified in the PAS domain. The PAS domain appears to interact with a linker region in the C-terminus. The linker region is a member of a HAMP domain family, which has signal transduction roles in other systems.

Sports-related injuries in children

OBJECTIVE

To describe the demographics and types of sports-related injuries (SRIs) in children.

METHODS

The authors performed a retrospective chart review of children 5-18 years of age diagnosed as having an SRI in a pediatric emergency department (ED) during a two-year period. Patients were identified by ICD-9 codes. Data collected were age, sex, sport, ED interventions, consultations, mechanism, location, and injury type. Pairwise comparisons were reported as odds ratios with 95% confidence intervals.

RESULTS

Six hundred seventy-seven SRIs fit the inclusion criteria; 480 of the patients were male (71%). The mean ages of the males and females were 13.0 years (SD +/- 3.0 yr) and 12.4 years (SD +/- 2.9 yr), respectively. The six most common sports implicated were basketball (19.5%), football (17.1%), baseball/softball (14.9%), soccer (14.2%), in-line skating (Rollerblading)/skating (5.7%), and hockey (4.6%). Sprains/strains (32.0%), fractures (29.4%), contusions/abrasions (19. 3%), and lacerations (9.7%) accounted for 90% of injury types. Pairwise comparison of the four injury types in the six sports listed showed significant associations for contusions/abrasions in baseball, sprains/strains in basketball, fractures in Rollerblading/skating, and lacerations in hockey. Age variance, including all sports, of the younger group (5-11 yr) in fractures and the older group (12-18 yr) in sprains was significant. The most common injury location was wrist/hand (28%), followed by head/face (22%) and ankle/foot (18%). Each had significant sport-specific predilections. Contact with person or object was the mechanism for >50% of the SRIs. Sport-specific mechanisms followed lines drawn from the sport-specific injury types and locations.

CONCLUSIONS

The pediatric age group incurs a variety of injuries in numerous sports with diverse sex, age, mechanism, location, injury type, and sport-specific differences.

First policy then science: why a management unit based solely on genetic criteria cannot work

In contrast to the goals of the symposium from which this series of papers originated, we argue that attempts to apply unambiguously defined and general management unit criteria based solely on genetic parameters can easily lead to incorrect management decisions. We maintain that conservation genetics is best served by altering the perspective of data analysis so that decision making is optimally facilitated. To do so requires accounting for policy objectives early in the design and execution of the science. This contrasts with typical hypothesis testing approaches to analysing genetic data for determining population structure, which often aspire to objectivity by considering management objectives only after the analysis is complete. The null hypothesis is generally taken as panmixia with a strong predilection towards avoiding false acceptance of the alternative hypothesis (the existence of population structure). We show by example how defining management units using genetic data and standard scientific analyses that do not consider either the specific management objectives or the anthropogenic risks facing the populations being studied can easily result in a management failure by losing local populations. We then use the same example to show how an 'applied' approach driven by specific objectives and knowledge of abundance and mortality results in appropriate analyses and better decisions. Because management objectives stem from public policy, which differs among countries and among species groups, criteria for defining management units must be specific, not general. Therefore, we conclude that the most productive way to define management units is on a case-by-case basis. We also suggest that creating analytical tools designed specifically to address decision making in a management context, rather than re-tooling academic tools designed for other purposes, will increase and improve the use of genetics in conservation.

Aerotaxis and other energy-sensing behavior in bacteria

Energy taxis is widespread in motile bacteria and in some species is the only known behavioral response. The bacteria monitor their cellular energy levels and respond to a decrease in energy by swimming to a microenvironment that reenergizes the cells. This is in contrast to classical Escherichia coli chemotaxis in which sensing of stimuli is independent of cellular metabolism. Energy taxis encompasses aerotaxis (taxis to oxygen), phototaxis, redox taxis, taxis to alternative electron acceptors, and chemotaxis to a carbon source. All of these responses share a common signal transduction pathway. An environmental stimulus, such as oxygen concentration or light intensity, modulates the flow of reducing equivalents through the electron transport system. A transducer senses the change in electron transport, or possibly a related parameter such as proton motive force, and initiates a signal that alters the direction of swimming. The Aer and Tsr proteins in E. coli are newly recognized transducers for energy taxis. Aer is homologous to E. coli chemoreceptors but unique in having a PAS domain and a flavin-adenine dinucleotide cofactor that is postulated to interact with a component of the electron transport system. PAS domains are energy-sensing modules that are found in proteins from archaea to humans. Tsr, the serine chemoreceptor, is an independent transducer for energy taxis, but its sensory mechanism is unknown. Energy taxis has a significant ecological role in vertical stratification of microorganisms in microbial mats and water columns. It plays a central role in the behavior of magnetotactic bacteria and also appears to be important in plant-microbe interactions.

Loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of Azospirillum lipoferum

Laccase, a p-diphenol oxidase typical of plants and fungi, has been found recently in a proteobacterium, Azospirillum lipoferum. Laccase activity was detected in both a natural isolate and an in vitro-obtained phase variant that originated from the laccase-negative wild type. In this study, the electron transport systems of the laccase-positive variant and its parental laccase-negative forms were compared. During exponential (but not stationary) growth under fully aerobic (but not under microaerobic) conditions, the laccase-positive variant lost a respiratory branch that is terminated in a cytochrome c oxidase of the aa(3) type; this was most likely due to a defect in the biosynthesis of a heme component essential for the oxidase. The laccase-positive variant was significantly less sensitive to the inhibitory action of quinone analogs and fully resistant to inhibitors of the bc(1) complex, apparently due to the rearrangements of its respiratory system. We propose that the loss of the cytochrome c oxidase-containing branch in the variant is an adaptive strategy to the presence of intracellular oxidized quinones, the products of laccase activity.

PAS domains: internal sensors of oxygen, redox potential, and light

PAS domains are newly recognized signaling domains that are widely distributed in proteins from members of the Archaea and Bacteria and from fungi, plants, insects, and vertebrates. They function as input modules in proteins that sense oxygen, redox potential, light, and some other stimuli. Specificity in sensing arises, in part, from different cofactors that may be associated with the PAS fold. Transduction of redox signals may be a common mechanistic theme in many different PAS domains. PAS proteins are always located intracellularly but may monitor the external as well as the internal environment. One way in which prokaryotic PAS proteins sense the environment is by detecting changes in the electron transport system. This serves as an early warning system for any reduction in cellular energy levels. Human PAS proteins include hypoxia-inducible factors and voltage-sensitive ion channels; other PAS proteins are integral components of circadian clocks. Although PAS domains were only recently identified, the signaling functions with which they are associated have long been recognized as fundamental properties of living cells.

In search of higher energy: metabolism-dependent behaviour in bacteria

Bacteria use different strategies to navigate to niches where environmental factors are favourable for growth. Chemotaxis is a behavioural response mediated by specific receptors that sense the concentration of chemicals in the environment. Recently, a new type of sensor has been described in Escherichia coli that responds to changes in cellular energy (redox) levels. This sensor, Aer, guides the bacteria to environments that support maximal energy levels in the cells. A variety of stimuli, such as oxygen, alternative electron acceptors, light, redox carriers that interact with the electron transport system and metabolized carbon sources, effect changes in the cellular energy (redox) levels. These changes are detected by Aer and by the serine chemotaxis receptor Tsr and are transduced into signals that elicit appropriate behavioural responses. Diverse environmental signals from Aer and chemotaxis receptors converge and integrate at the level of the CheA histidine kinase. Energy sensing is widespread in bacteria, and it is now evident that a variety of signal transduction strategies are used for the metabolism-dependent behaviours. The occurrence of putative energy-sensing domains in proteins from cells ranging from Archaea to humans indicates the importance of this function for all living systems.

Rewiring a receptor: negative output from positive input

A point mutation or covalent modification in bacterial chemotaxis receptors causes bacteria to be repelled by attractants, and attracted to repellents. The variety of conditions causing inverse responses suggest that the signal transduction mechanism in receptors can be readily rewired to elicit inverse responses. A model is presented in which the orientation of a critical residue with respect to an active site determines whether the receptor produces normal or inverted signals. The model is consistent with observed responses and can be generalized to include receptors in other signal transduction systems.

The Aer protein and the serine chemoreceptor Tsr independently sense intracellular energy levels and transduce oxygen, redox, and energy signals for Escherichia coli behavior

We identified a protein, Aer, as a signal transducer that senses intracellular energy levels rather than the external environment and that transduces signals for aerotaxis (taxis to oxygen) and other energy-dependent behavioral responses in Escherichia coli. Domains in Aer are similar to the signaling domain in chemotaxis receptors and the putative oxygen-sensing domain of some transcriptional activators. A putative FAD-binding site in the N-terminal domain of Aer shares a consensus sequence with the NifL, Bat, and Wc-1 signal-transducing proteins that regulate gene expression in response to redox changes, oxygen, and blue light, respectively. A double mutant deficient in aer and tsr, which codes for the serine chemoreceptor, was negative for aerotaxis, redox taxis, and glycerol taxis, each of which requires the proton motive force and/or electron transport system for signaling. We propose that Aer and Tsr sense the proton motive force or cellular redox state and thereby integrate diverse signals that guide E. coli to environments where maximal energy is available for growth.

Oxygen-dependent growth of the obligate anaerobe Desulfovibrio vulgaris Hildenborough

Desulfovibrio vulgaris Hildenborough, a sulfate-reducing bacterium classified as an obligate anaerobe, swam to a preferred oxygen concentration of 0.02 to 0.04% (0.24 to 0.48 microM), a level which also supported growth. Oxygen concentrations of 0.08% and higher arrested growth. We propose that in zones of transition from an oxic to an anoxic environment, D. vulgaris protects anoxic microenvironments from intrusion of oxygen.

Magneto-aerotaxis in marine coccoid bacteria

Magnetotactic cocci swim persistently along local magnetic field lines in a preferred direction that corresponds to downward migration along geomagnetic field lines. Recently, high cell concentrations of magnetotactic cocci have been found in the water columns of chemically stratified, marine and brackish habitats, and not always in the sediments, as would be expected for persistent, downward-migrating bacteria. Here we report that cells of a pure culture of a marine magnetotactic coccus, designated strain MC-1, formed microaerophilic bands in capillary tubes and used aerotaxis to migrate to a preferred oxygen concentration in an oxygen gradient. Cells were able to swim in either direction along the local magnetic field and used magnetotaxis in conjunction with aerotaxis, i.e., magnetically assisted aerotaxis, or magneto-aerotaxis, to more efficiently migrate to and maintain position at their preferred oxygen concentration. Cells of strain MC-1 had a novel, aerotactic sensory mechanism that appeared to function as a two-way switch, rather than the temporal sensory mechanism used by other bacteria, including Magnetospirillum megnetotacticum, in aerotaxis. The cells also exhibited a response to short-wavelength light (< or = 500 nm), which caused them to swim persistently parallel to the magnetic field during illumination.

How do bacteria avoid high oxygen concentrations?

Bacteria, such as Escherichia coli and Azospirillum brasilense, avoid microenvironments with elevated oxygen concentrations, not by sensing reactive oxygen derivatives, but by sensing a metabolic down-shift that results from elevated oxygen levels. A novel protein, Aer, and the chemotaxis serine receptor, Tsr, have recently been identified as transducers for aerotaxis which monitor internal energy levels in the bacteria.

Glycerol elicits energy taxis of Escherichia coli and Salmonella typhimurium

Escherichia coli and Salmonella typhimurium show positive chemotaxis to glycerol, a chemical previously reported to be a repellent for E. coli. The threshold of the attractant response in both species was 10(-6) M glycerol. Glycerol chemotaxis was energy dependent and coincident with an increase in membrane potential. Metabolism of glycerol was required for chemotaxis, and when lactate was present to maintain energy production in the absence of glycerol, the increases in membrane potential and chemotactic response upon addition of glycerol were abolished. Methylation of a chemotaxis receptor was not required for positive glycerol chemotaxis in E. coli or S. typhimurium but is involved in the negative chemotaxis of E. coli to high concentrations of glycerol. We propose that positive chemotaxis to glycerol in E. coli and S. typhimurium is an example of energy taxis mediated via a signal transduction pathway that responds to changes in the cellular energy level.

Prediction of outcome from intensive care: a prospective cohort study comparing Acute Physiology and Chronic Health Evaluation II and III prognostic systems in a United Kingdom intensive care unit

OBJECTIVE

To evaluate the ability of two prognostic systems to predict hospital mortality in adult intensive care patients.

DESIGN

Prospective cohort study.

SETTING

A mixed medical and surgical intensive care unit (ICU) in the United Kingdom.

PATIENTS

A total of 1,144 patients consecutively admitted to the study.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

Acute Physiology and Chronic Health Evaluation (APACHE) II and III prognostic systems were applied to assess probabilities of hospital mortality, which were compared with the actual outcome. The overall goodness-of-fit of both models was assessed. Hospital death rates were higher than those predicted by each system. Risk estimates showed a strong positive correlation between both systems (nonsurvivors r2 = 0.756, p < .0001; survivors r2 = 0.787, p < .0001). Calibration of APACHE II (chi 2 = 98.6, Lemeshow-Hosmer) was superior to that of APACHE III (chi 2 = 129.8, Lemeshow-Hosmer). The total correct classification rate of APACHE III was greater for all decision criteria applied; the best overall total correct classification rate was 80.6% for APACHE III and 77.9% for APACHE II (both for a decision criterion of 40%). The areas under the receiver operating characteristic curves were 0.806 and 0.847 for APACHE II and III, respectively, confirming the better discrimination of APACHE III. When patients were classified by diagnostic categories, risk predictions did not fit uniformly across the spectrum of disease groups. For both models, mortality ratios were highest for trauma patients and lowest for the group with respiratory disease. APACHE II predictions for patients with gastrointestinal disease were significantly better. Risk estimates for surgical admissions were superior with APACHE II (MR = 1.27) compared with APACHE III (MR = 1.56), but were similar for medical patients (1.22 vs. 1.28 for APACHE II and III, respectively). Bias induced by factors reflecting the clinical practice in an individual ICU (e.g., admission criteria, treatment before admission) may have considerable impact on risk estimates. The identification of such factors appears to be a prerequisite for the meaningful interpretation of observed and predicted death rates on the individual ICU level.

CONCLUSIONS

Both predictive models demonstrated a similar degree of overall goodness-of-fit. APACHE II showed better calibration, but discrimination was better with APACHE III. Hospital mortality was higher than predicted by both models, but was underestimated to a greater degree by APACHE III. Risk estimates by both models showed considerable variation across the disease spectrum of ICU patients. Risk predictions for surgical patients and patients with gastrointestinal disease were better with APACHE II. Factors reflecting the clinical practice of an individual ICU are not accounted for by APACHE II and III. Overall, the performance of APACHE III was not superior to that of its predecessor for a cohort of United Kingdom ICU patients; for certain diagnostic categories, APACHE III performed worse than APACHE II despite an improved system of disease classification.