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1.  Outcomes by Sex Following Treatment Initiation With Atazanavir Plus Ritonavir or Efavirenz With Abacavir/Lamivudine or Tenofovir/Emtricitabine 
Smith, Kimberly Y. | Tierney, Camlin | Mollan, Katie | Venuto, Charles S. | Budhathoki, Chakra | Ma, Qing | Morse, Gene D. | Sax, Paul | Katzenstein, David | Godfrey, Catherine | Fischl, Margaret | Daar, Eric S. | Collier, Ann C. | Bolivar, Hector H. | Navarro, Sandra | Koletar, Susan L. | Gochnour, Diane | Seefried, Edward | Hoffman, Julie | Feinberg, Judith | Saemann, Michelle | Patterson, Kristine | Pittard, Donna | Currin, David | Upton, Kerry | Saag, Michael | Ray, Graham | Johnson, Steven | Santos, Bartolo | Funk, Connie A. | Morgan, Michael | Jackson, Brenda | Tebas, Pablo | Thomas, Aleshia | Kim, Ge-Youl | Klebert, Michael K. | Santana, Jorge L. | Marrero, Santiago | Norris, Jane | Valle, Sandra | Cox, Gary Matthew | Silberman, Martha | Shaik, Sadia | Lopez, Ruben | Vasquez, Margie | Daskalakis, Demetre | Megill, Christina | Shore, Jessica | Taiwo, Babafemi | Goldman, Mitchell | Boston, Molly | Lennox, Jeffrey | del Rio, Carlos | Lane, Timothy W. | Epperson, Kim | Luetkemeyer, Annie | Payne, Mary | Gripshover, Barbara | Antosh, Dawn | Reid, Jane | Adams, Mary | Storey, Sheryl S. | Dunaway, Shelia B. | Gallant, Joel | Wiggins, Ilene | Smith, Kimberly Y. | Swiatek, Joan A. | Timpone, Joseph | Kumar, Princy | Moe, Ardis | Palmer, Maria | Gothing, Jon | Delaney, Joanne | Whitely, Kim | Anderson, Ann Marie | Hammer, Scott M. | Yin, Michael T. | Jain, Mamta | Petersen, Tianna | Corales, Roberto | Hurley, Christine | Henry, Keith | Bordenave, Bette | Youmans, Amanda | Albrecht, Mary | Pollard, Richard B. | Olusanya, Abimbola | Skolnik, Paul R. | Adams, Betsy | Tashima, Karen T. | Patterson, Helen | Ukwu, Michelle | Rogers, Lauren | Balfour, Henry H. | Fox, Kathy A. | Swindells, Susan | Van Meter, Frances | Robbins, Gregory | Burgett-Yandow, Nicole | Davis, Charles E. | Boyce, Colleen | O'Brien, William A. | Casey, Gerianne | Morse, Gene D. | Hsaio, Chiu-Bin | Meier, Jeffrey L. | Stapleton, Jack T. | Mildvan, Donna | Revuelta, Manuel | Currin, David | El Sadr, Wafaa | Loquere, Avelino | El-Daher, Nyef | Johnson, Tina | Gross, Robert | Maffei, Kathyrn | Hughes, Valery | Sturge, Glenn | McMahon, Deborah | Rutecki, Barbara | Wulfsohn, Michael | Cheng, Andrew | Dix, Lynn | Liao, Qiming
This clinical trial identifies a significantly earlier time to virologic failure in women randomized to atazanavir/ritonavir compared to women randomized to efavirenz.
Background. We aimed to evaluate treatment responses to atazanavir plus ritonavir (ATV/r) or efavirenz (EFV) in initial antiretroviral regimens among women and men, and determine if treatment outcomes differ by sex.
Methods. We performed a randomized trial of open-label ATV/r or EFV combined with abacavir/lamivudine (ABC/3TC) or tenofovir/emtricitabine (TDF/FTC) in 1857 human immunodeficiency virus type 1–infected, treatment-naive persons enrolled between September 2005 and November 2007 at 59 sites in the United States and Puerto Rico. Associations of sex with 3 primary study endpoints of time to virologic failure, safety, and tolerability events were analyzed using Cox proportional hazards models. Model-based population pharmacokinetic analysis was performed using nonlinear mixed effects modeling (NONMEM version VII).
Results. Of 1857 participants, 322 were women. Women assigned to ATV/r had a higher risk of virologic failure with either nucleoside reverse transcriptase inhibitor backbone than women assigned to EFV, or men assigned to ATV/r. The effects of ATV/r and EFV upon safety and tolerability risk did not differ significantly by sex. With ABC/3TC, women had a significantly higher (32%) safety risk compared to men; with TDF/FTC, the safety risk was 20% larger for women compared to men, but not statistically significant. Women had slower ATV clearance and higher predose levels of ATV compared to men. Self-reported adherence did not differ significantly by sex.
Conclusions. This is the first randomized clinical trial to identify a significantly earlier time to virologic failure in women randomized to ATV/r compared to women randomized to EFV. This finding has important clinical implications given that boosted protease inhibitors are often favored over EFV in women of childbearing potential.
Clinical Trials Registration NCT00118898.
PMCID: PMC3905755  PMID: 24253247
sex; atazanavir; efavirenz; abacavir; tenofovir
2.  Do pollinator distributions underlie the evolution of pollination ecotypes in the Cape shrub Erica plukenetii? 
Annals of Botany  2013;113(2):301-316.
Background and Aims
According to the Grant–Stebbins model of pollinator-driven divergence, plants that disperse beyond the range of their specialized pollinator may adapt to a new pollination system. Although this model provides a compelling explanation for pollination ecotype formation, few studies have directly tested its validity in nature. Here we investigate the distribution and pollination biology of several subspecies of the shrub Erica plukenetii from the Cape Floristic Region in South Africa. We analyse these data in a phylogenetic context and combine these results with information on pollinator ranges to test whether the evolution of pollination ecotypes is consistent with the Grant–Stebbins model.
Methods and Key Results
Pollinator observations showed that the most common form of E. plukenetii with intermediate corolla length is pollinated by short-billed Orange-breasted sunbirds. Populations at the northern fringe of the distribution are characterized by long corollas, and are mainly pollinated by long-billed Malachite sunbirds. A population with short corollas in the centre of the range was mainly pollinated by insects, particularly short-tongued noctuid moths. Bird exclusion in this population did not have an effect on fruit set, while insect exclusion reduced fruit set. An analysis of floral scent across the range, using coupled gas chromatography–mass spectrometry, showed that the scent bouquets of flowers from moth-pollinated populations are characterized by a larger number of scent compounds and higher emission rates than those in bird-pollinated populations. This was also reflected in clear separation of moth- and bird-pollinated populations in a two-dimensional phenotype space based on non-metric multidimensional scaling analysis of scent data. Phylogenetic analyses of chloroplast and nuclear DNA sequences strongly supported monophyly of E. plukenetii, but not of all the subspecies. Reconstruction of ancestral character states suggests two shifts from traits associated with short-billed Orange-breasted sunbird pollination: one towards traits associated with moth pollination, and one towards traits associated with pollination by long-billed Malachite sunbirds. The latter shift coincided with the colonization of Namaqualand in which Orange-breasted sunbirds are absent.
Conclusions Erica plukenetii
is characterized by three pollination ecotypes, but only the evolutionary transition from short- to long-billed sunbird pollination can be clearly explained by the Grant–Stebbins model. Corolla length is a key character for both ecotype transitions, while floral scent emission was important for the transition from bird to moth pollination.
PMCID: PMC3890384  PMID: 24071499
Helicoverpa armigera; speciation; benzene propanoids; phylogeny; niche; floral scent; bird pollination; floral trait; ancestral character state; Erica plukenetii; pollination ecotype; Cape flora
3.  A pollinator shift explains floral divergence in an orchid species complex in South Africa 
Annals of Botany  2013;113(2):277-288.
Background and Aims
Floral diversification driven by shifts between pollinators has been one of the key explanations for the radiation of angiosperms. According to the Grant–Stebbins model of pollinator-driven speciation, these shifts result in morphologically distinct ‘ecotypes’ which may eventually become recognizable as species. The current circumscription of the food-deceptive southern African orchid Eulophia parviflora encompasses a highly variable monophyletic species complex. In this study, two forms were identified within this complex that differ in distribution, floral morphology, scent chemistry and phenology, and a test was made of whether these differences represent adaptations for different pollinators.
Methods and Results
Multivariate analysis of floral and vegetative traits revealed that there are at least two discrete morphological forms in the species complex. Field observations revealed that each form is pollinated by a different insect species, and thus represent distinct ecotypes. The early-flowering coastal form which has long spurs and floral scent dominated by sesquiterpene compounds is pollinated exclusively by the long-tongued bee Amegilla fallax (Apidae, Anthophorinae), while the late-flowering inland form with short spurs and floral scent dominated by benzenoid compounds is pollinated exclusively by the beetle Cyrtothyrea marginalis (Cetoniinae; Scarabaeidae). Choice experiments in a Y-maze olfactometer showed that beetles are preferentially attracted to the scent of the short-spurred form. A spur-shortening experiment showed that long spurs are required for effective pollination of the bee-pollinated form. Although it was initially thought likely that divergence occurred across a geographical pollinator gradient, plants of the long-spurred form were effectively pollinated when transplanted to an inland locality outside the natural coastal range of this form. Thus, the underlying geographical basis for the evolution of ecotypes in the E. parviflora complex remains uncertain, although early flowering in the long-spurred form to exploit the emergence of naïve bees may restrict this form to coastal areas where there is no frost that would damage flower buds. Later flowering of the short-spurred form coincides closely with the emergence of the pollinating beetles following winter frosts.
This study identifies a shift between bee and beetle pollination as the main driver of floral divergence in an orchid species complex. Floral scent and spur length appear to be key traits in mediating this evolutionary transition.
PMCID: PMC3890387  PMID: 24107684
Grant–Stebbins model; pollinator-driven speciation; pollination ecotypes; scent; Eulophia; Orchidaceae; phenology; beetle pollination; Cetoniinae; bee pollination; Y-maze olfactometer; Amegilla
4.  Pollinator-driven ecological speciation in plants: new evidence and future perspectives 
Annals of Botany  2014;113(2):199-212.
The hypothesis that pollinators have been important drivers of angiosperm diversity dates back to Darwin, and remains an important research topic today. Mounting evidence indicates that pollinators have the potential to drive diversification at several different stages of the evolutionary process. Microevolutionary studies have provided evidence for pollinator-mediated floral adaptation, while macroevolutionary evidence supports a general pattern of pollinator-driven diversification of angiosperms. However, the overarching issue of whether, and how, shifts in pollination system drive plant speciation represents a critical gap in knowledge. Bridging this gap is crucial to fully understand whether pollinator-driven microevolution accounts for the observed macroevolutionary patterns. Testable predictions about pollinator-driven speciation can be derived from the theory of ecological speciation, according to which adaptation (microevolution) and speciation (macroevolution) are directly linked. This theory is a particularly suitable framework for evaluating evidence for the processes underlying shifts in pollination systems and their potential consequences for the evolution of reproductive isolation and speciation.
This Viewpoint paper focuses on evidence for the four components of ecological speciation in the context of plant-pollinator interactions, namely (1) the role of pollinators as selective agents, (2) floral trait divergence, including the evolution of ‘pollination ecotypes‘, (3) the geographical context of selection on floral traits, and (4) the role of pollinators in the evolution of reproductive isolation. This Viewpoint also serves as the introduction to a Special Issue on Pollinator-Driven Speciation in Plants. The 13 papers in this Special Issue range from microevolutionary studies of ecotypes to macroevolutionary studies of historical ecological shifts, and span a wide range of geographical areas and plant families. These studies further illustrate innovative experimental approaches, and they employ modern tools in genetics and floral trait quantification. Future advances to the field require better quantification of selection through male fitness and pollinator isolation, for instance by exploiting next-generation sequencing technologies. By combining these new tools with strategically chosen study systems, and smart experimental design, we predict that examples of pollinator-driven speciation will be among the most widespread and compelling of all cases of ecological speciation.
PMCID: PMC3890394  PMID: 24418954
Geography; floral odour; flower colour; flower shape; specialization; reproductive isolation; next-generation sequencing; pollination ecotypes; pollination; nectar tube; adaptation; natural selection; geographical mosaic of selection; Grant–Stebbins model
5.  Pediatric Stroke Presenting as a Seizure 
Background. Childhood arterial ischemic stroke (AIS) is rare and may be difficult to diagnose. Management of acute stroke in any age group is time sensitive, so awareness of the manifestations and appropriate diagnostic procedures for pediatric AIS is vital to establishing care. We present a pediatric case of arterial ischemic stroke that presented to the emergency department (ED) after two seizures. Case Report. A five-year-old female with an existing seizure disorder presented to a pediatric ED after having two seizures. Postictal upon arrival, she underwent a computed tomography (CT) scan of her head. Family reported that she had complained of a severe headache and vomited; her seizures were described as different from those she had experienced in the past. Loss of grey white matter differentiation on the CT warranted magnetic resonance imaging (MRI), which demonstrated a right-sided stroke. After a complicated course in the hospital, the patient was discharged to a rehabilitation hospital. Why Should an Emergency Physician Be Aware of This? It is important that emergency physicians recognize that a seizure may be the initial symptom of a pediatric stroke regardless of an established seizure history. Pediatric seizures are relatively common; however consideration of the diagnosis of pediatric stroke may prevent unnecessary delays in treatment.
PMCID: PMC4283395  PMID: 25587467
6.  Solid phase synthesis of functionalised SAM-forming alkanethiol–oligoethyleneglycols 
We present an efficient solid phase synthesis methodology that provides easy access to a range of functionalised long-chain alkanethiol–oligoethyleneglycols that form well-defined self-assembled monolayers on gold and are compatible with pre- or post-assembly conjugation of (bio)molecules. We demonstrate the versatility of our synthetic route by synthesising LCAT–OEGs with a range of functional moieties, including peptides, electro-active redox groups, chemical handles for post-assembly conjugation of (bio)molecules, and demonstrate the application of our LCAT–OEG monolayers in immunosensing, where they show good biocompatibility with minimal biofouling.
PMCID: PMC4229624  PMID: 25400934
7.  The evolution of floral nectaries in Disa (Orchidaceae: Disinae): recapitulation or diversifying innovation? 
Annals of Botany  2013;112(7):1303-1319.
Background and Aims
The Orchidaceae have a history of recurring convergent evolution in floral function as nectar production has evolved repeatedly from an ancestral nectarless state. However, orchids exhibit considerable diversity in nectary type, position and morphology, indicating that this convergence arose from alternative adaptive solutions. Using the genus Disa, this study asks whether repeated evolution of floral nectaries involved recapitulation of the same nectary type or diversifying innovation. Epidermis morphology of closely related nectar-producing and nectarless species is also compared in order to identify histological changes that accompanied the gain or loss of nectar production.
The micromorphology of nectaries and positionally equivalent tissues in nectarless species was examined with light and scanning electron microscopy. This information was subjected to phylogenetic analyses to reconstruct nectary evolution and compare characteristics of nectar-producing and nectarless species.
Key Results
Two nectary types evolved in Disa. Nectar exudation by modified stomata in floral spurs evolved twice, whereas exudation by a secretory epidermis evolved six times in different perianth segments. The spur epidermis of nectarless species exhibited considerable micromorphological variation, including strongly textured surfaces and non-secreting stomata in some species. Epidermis morphology of nectar-producing species did not differ consistently from that of rewardless species at the magnifications used in this study, suggesting that transitions from rewardlessness to nectar production are not necessarily accompanied by visible morphological changes but only require sub-cellular modification.
Independent nectary evolution in Disa involved both repeated recapitulation of secretory epidermis, which is present in the sister genus Brownleea, and innovation of stomatal nectaries. These contrasting nectary types and positional diversity within types imply weak genetic, developmental or physiological constraints in ancestral, nectarless Disa. Such functional convergence generated by morphologically diverse solutions probably also underlies the extensive diversity of nectary types and positions in the Orchidaceae.
PMCID: PMC3806529  PMID: 23997231
Disa; Disinae; Orchidaceae; orchid; deceit pollination; modified stoma; nectar; nectary; reward; rewardless; evolution; functional convergence
8.  Ancestral deceit and labile evolution of nectar production in the African orchid genus Disa 
Biology Letters  2013;9(5):20130500.
An outstanding feature of the orchid family is that approximately 30–40% of the species have non-rewarding flowers and deploy various modes of deception to attract pollinators, whereas the remaining species engage in pollination mutualisms based on provision of floral rewards. Here, we explore the direction, frequency and reversibility of transitions between deceptive and rewarding pollination systems in the radiation of the large African genus Disa, and test whether these transitions had consequences for diversification. By optimizing nectar production data for 111 species on a well-resolved phylogeny, we confirmed that floral deception was the ancestral condition and that nectar production evolved at least nine times and was lost at least once. Transitions to nectar production first occurred ca 17 million years ago but did not significantly affect either speciation or extinction rates. Nectar evolved independently of a spur, which was lost and gained multiple times. These results show that nectar production can be a highly labile trait and highlight the need for further studies of the genetic architecture of nectar production and the selective factors underlying transitions between deception and mutualism.
PMCID: PMC3971689  PMID: 23904568
diversification rates; floral deception; mimicry; nectary; phylogenetic signal; pollination
9.  Crystal Structure of the Bacillus subtilis Phosphodiesterase PhoD Reveals an Iron and Calcium-containing Active Site♦ 
The Journal of Biological Chemistry  2014;289(45):30889-30899.
Background: PhoD family enzymes liberate phosphate from organic compounds.
Results: The structure of PhoD reveals an active site with one Fe3+ and two Ca2+ ions.
Conclusion: PhoD represents a new class of phosphatase related to purple acid phosphatases.
Significance: The requirement of PhoD for iron ions may limit bacterial phosphate acquisition in low iron environments.
The PhoD family of extra-cytoplasmic phosphodiesterases are among the most commonly occurring bacterial phosphatases. The exemplars for this family are the PhoD protein of Bacillus subtilis and the phospholipase D of Streptomyces chromofuscus. We present the crystal structure of B. subtilis PhoD. PhoD is most closely related to purple acid phosphatases (PAPs) with both types of enzyme containing a tyrosinate-ligated Fe3+ ion. However, the PhoD active site diverges from that found in PAPs and uses two Ca2+ ions instead of the single extra Fe2+, Mn2+, or Zn2+ ion present in PAPs. The PhoD crystals contain a phosphate molecule that coordinates all three active site metal ions and that is proposed to represent a product complex. A C-terminal helix lies over the active site and controls access to the catalytic center. The structure of PhoD defines a new phosphatase active site architecture based on Fe3+ and Ca2+ ions.
PMCID: PMC4223295  PMID: 25217636
Bacterial Metabolism; Catalysis; Metalloenzyme; Phosphatase; Structural Biology
10.  Patterns of odour emission, thermogenesis and pollinator activity in cones of an African cycad: what mechanisms apply? 
Annals of Botany  2013;112(5):891-902.
Background and Aims
Ontogenetic patterns of odour emissions and heating associated with plant reproductive structures may have profound effects on insect behaviour, and consequently on pollination. In some cycads, notably Macrozamia, temporal changes in emission of specific odour compounds and temperature have been interpreted as a ‘push–pull’ interaction in which pollinators are either attracted or repelled according to the concentration of the emitted volatiles. To establish which mechanisms occur in the large Encephalartos cycad clade, the temporal patterns of volatile emissions, heating and pollinator activity of cones of Encephalartos villosus in the Eastern Cape (EC) and KwaZulu Natal (KZN) of South Africa were investigated.
Methods and Key Results
Gas chromatography–mass spectrometry (GC-MS) analyses of Encephalartos villosus cone volatiles showed that emissions, dominated by eucalyptol and 2-isopropyl-3-methoxypyrazine in EC populations and (3E)-1,3-octadiene and (3E,5Z)-1,3,5-octatriene in the KZN populations, varied across developmental stages but did not vary significantly on a daily cycle. Heating in male cones was higher at dehiscence than during pre- and post-dehiscence, and reached a maximum at about 1830 h when temperatures were between 7·0 and 12·0 °C above ambient. Daily heating of female cones was less pronounced and reached a maximum at about 1345 h when it was on average between 0·9 and 3·0 °C above ambient. Insect abundance on male cones was higher at dehiscence than at the other stages and significantly higher in the afternoon than in the morning and evening.
There are pronounced developmental changes in volatile emissions and heating in E. villosus cones, as well as strong daily changes in thermogenesis. Daily patterns of volatile emissions and pollinator abundance in E. villosus are different from those observed in some Macrozamia cycads and not consistent with the push–pull pattern as periods of peak odour emission do not coincide with mass exodus of insects from male cones.
PMCID: PMC3747810  PMID: 23887092
Encephalartos villosus; Zamiaceae; cycads; monoterpenes; developmental stages; nitrogen-containing compounds; unsaturated hydrocarbons; gas chromatography–mass spectrometry; push–pull; odour emission; floral volatiles; thermogensis; pollination
11.  Population-Based Passive Tick Surveillance and Detection of Expanding Foci of Blacklegged Ticks Ixodes scapularis and the Lyme Disease Agent Borrelia burgdorferi in Ontario, Canada 
PLoS ONE  2014;9(8):e105358.
We identified ticks submitted by the public from 2008 through 2012 in Ontario, Canada, and tested blacklegged ticks Ixodes scapularis for Borrelia burgdorferi and Anaplasma phagocytophilum. Among the 18 species of ticks identified, I. scapularis, Dermacentor variabilis, Ixodes cookei and Amblyomma americanum represented 98.1% of the 14,369 ticks submitted. Rates of blacklegged tick submission per 100,000 population were highest in Ontario's Eastern region; D. variabilis in Central West and Eastern regions; I. cookei in Eastern and South West regions; and A. americanum had a scattered distribution. Rates of blacklegged tick submission per 100,000 population were highest from children (0–9 years old) and older adults (55–74 years old). In two health units in the Eastern region (i.e., Leeds, Grenville & Lanark District and Kingston-Frontenac and Lennox & Addington), the rate of submission for engorged and B. burgdorferi-positive blacklegged ticks was 47× higher than the rest of Ontario. Rate of spread for blacklegged ticks was relatively faster and across a larger geographic area along the northern shore of Lake Ontario/St. Lawrence River, compared with slower spread from isolated populations along the northern shore of Lake Erie. The infection prevalence of B. burgdorferi in blacklegged ticks increased in Ontario over the study period from 8.4% in 2008 to 19.1% in 2012. The prevalence of B. burgdorferi-positive blacklegged ticks increased yearly during the surveillance period and, while increases were not uniform across all regions, increases were greatest in the Central West region, followed by Eastern and South West regions. The overall infection prevalence of A. phagocytophilum in blacklegged ticks was 0.3%. This study provides essential information on ticks of medical importance in Ontario, and identifies demographic and geographic areas for focused public education on the prevention of tick bites and tick-borne diseases.
PMCID: PMC4149368  PMID: 25171252
12.  Coral Reef Disturbance and Recovery Dynamics Differ across Gradients of Localized Stressors in the Mariana Islands 
PLoS ONE  2014;9(8):e105731.
The individual contribution of natural disturbances, localized stressors, and environmental regimes upon longer-term reef dynamics remains poorly resolved for many locales despite its significance for management. This study examined coral reefs in the Commonwealth of the Northern Mariana Islands across a 12-year period that included elevated Crown-of-Thorns Starfish densities (COTS) and tropical storms that were drivers of spatially-inconsistent disturbance and recovery patterns. At the island scale, disturbance impacts were highest on Saipan with reduced fish sizes, grazing urchins, and water quality, despite having a more favorable geological foundation for coral growth compared with Rota. However, individual drivers of reef dynamics were better quantified through site-level investigations that built upon island generalizations. While COTS densities were the strongest predictors of coral decline as expected, interactive terms that included wave exposure and size of the overall fish assemblages improved models (R2 and AIC values). Both wave exposure and fish size diminished disturbance impacts and had negative associations with COTS. However, contrasting findings emerged when examining net ecological change across the 12-year period. Wave exposure had a ubiquitous, positive influence upon the net change in favorable benthic substrates (i.e. corals and other heavily calcifying substrates, R2 = 0.17 for all reeftypes grouped), yet including interactive terms for herbivore size and grazing urchin densities, as well as stratifying by major reeftypes, substantially improved models (R2 = 0.21 to 0.89, lower AIC scores). Net changes in coral assemblages (i.e., coral ordination scores) were more sensitive to herbivore size or the water quality proxy acting independently (R2 = 0.28 to 0.44). We conclude that COTS densities were the strongest drivers of coral decline, however, net ecological change was most influenced by localized stressors, especially herbivore sizes and grazing urchin densities. Interestingly, fish size, rather than biomass, was consistently a better predictor, supporting allometric, size-and-function relationships of fish assemblages. Management implications are discussed.
PMCID: PMC4148314  PMID: 25165893
13.  Reproducibility and Consistency of In Vitro Nucleosome Reconstitutions Demonstrated by Invitrosome Isolation and Sequencing 
PLoS ONE  2014;9(8):e103752.
Nucleosomes and their positions in the eukaryotic genome play an important role in regulating gene expression by influencing accessibility to DNA. Many factors influence a nucleosome's final position in the chromatin landscape including the underlying genomic sequence. One of the primary reasons for performing in vitro nucleosome reconstitution experiments is to identify how the underlying DNA sequence will influence a nucleosome's position in the absence of other compounding cellular factors. However, concerns have been raised about the reproducibility of data generated from these kinds of experiments. Here we present data for in vitro nucleosome reconstitution experiments performed on linear plasmid DNA that demonstrate that, when coverage is deep enough, these reconstitution experiments are exquisitely reproducible and highly consistent. Our data also suggests that a coverage depth of 35X be maintained for maximal confidence when assaying nucleosome positions, but lower coverage levels may be generally sufficient. These coverage depth recommendations are sufficient in the experimental system and conditions used in this study, but may vary depending on the exact parameters used in other systems.
PMCID: PMC4122377  PMID: 25093869
14.  Utility of telephone survey methods in population-based health studies of older adults: an example from the Alberta Older Adult Health Behavior (ALERT) study 
BMC Public Health  2014;14:486.
Random digit dialing is often used in public health research initiatives to accrue and establish a study sample; however few studies have fully described the utility of this approach. The primary objective of this paper was to describe the implementation and utility of using random digit dialing and Computer Assisted Telephone Interviewing (CATI) for sampling, recruitment and data collection in a large population-based study of older adults [Alberta Older Adult Health Behavior (ALERT) study].
Using random digit dialing, older adults (> = 55 years) completed health behavior and outcome and demographic measures via CATI. After completing the CATI, participants were invited to receive a step pedometer and waist circumference tape measure via mail to gather objectively derived ambulatory activity and waist circumference assessments.
Overall, 36,000 telephone numbers were called of which 7,013 were deemed eligible for the study. Of those, 4,913 (70.1%) refused to participate in the study and 804 (11.4%) participants were not included due to a variety of call dispositions (e.g., difficult to reach, full quota for region). A total of 1,296 participants completed telephone interviews (18.5% of those eligible and 3.6% of all individuals approached). Overall, 22.8% of households did not have an age 55+ resident and 13.6% of individuals refused to participate, Average age was 66.5 years, and 43% were male. A total of 1,081 participants (83.4%) also submitted self-measured ambulatory activity (i.e., via step pedometer) and anthropometric data (i.e., waist circumference). With the exception of income (18.7%), the rate of missing data for demographics, health behaviors, and health measures was minimal (<1%).
Older adults are willing to participate in telephone-based health surveys when randomly contacted. Researchers can use this information to evaluate the feasibility and the logistics of planned studies using a similar population and study design.
PMCID: PMC4045920  PMID: 24884997
Health behavior; Computer-assisted telephone interviews (CATI); Random digit dialing; Response rate; Older adults
15.  Systemic cytokine response to three bouts of eccentric exercise 
Results in Immunology  2014;4:23-29.
This research examined the changes in inflammatory cytokines interleukin 6 (IL-6), IL-1ß, IL-10, as well as muscle force, muscle soreness, thigh circumference, and range of motion in response to 3 bouts of eccentric knee extension. Ten males were recruited to participate. The participants performed eccentric exercise on 3 consecutive days on the knee extensors on the right leg separated by 24??h. Participants performed 6 sets of 10 repetitions of isokinetic eccentric knee extension at 120° per second. Blood was sampled before and after each exercise bout and 24?h after the final exercise bout. Muscle isometric force, delayed onset muscle soreness (DOMS), thigh circumference, and range of motion were evaluated before and after each exercise bout and 24?h after the final exercise bout. There were no statistically significant differences noted for the changes in isometric strength, thigh circumference, and range of motion, or IL-6 over the 4 days (all p > 0.05). On the second day and third day there was a significant increase noted in DOMS as compared with baseline (p < 0.05). These results suggest that 3 consecutive days of eccentric exercise results in DOMS but does not produce a sustained systemic inflammatory reaction or changes in muscle function.
PMCID: PMC4009404  PMID: 24809007
Eccentric exercise; Inflammation; Interleukin 6; Delayed onset muscle soreness
16.  A Temporal Dimension to the Influence of Pollen Rewards on Bee Behaviour and Fecundity in Aloe tenuior 
PLoS ONE  2014;9(4):e94908.
The net effect of pollen production on fecundity in plants can range from negative – when self-pollen interferes with fecundity due to incompatibility mechanisms, to positive – when pollen availability is associated with increased pollinator visitation and fecundity due to its utilization as a reward. We investigated the responses of bees to pollen and nectar rewards, and the effects of these rewards on pollen deposition and fecundity in the hermaphroditic succulent shrub Aloe tenuior. Self-pollinated plants failed to set fruit, but their ovules were regularly penetrated by self-pollen tubes, which uniformly failed to develop into seeds as expected from ovarian self-incompatibility (or strong early inbreeding depression). Bees consistently foraged for pollen during the morning and early afternoon, but switched to nectar in the late afternoon. As a consequence of this differential foraging, we were able to test the relative contribution to fecundity of pollen- versus nectar-collecting flower visitors. We exposed emasculated and intact flowers in either the morning or late afternoon to foraging bees and showed that emasculation reduced pollen deposition by insects in the morning, but had little effect in the afternoon. Despite the potential for self-pollination to result in ovule discounting due to late-acting self-sterility, fecundity was severely reduced in artificially emasculated plants. Although there were temporal fluctuations in reward preference, most bee visits were for pollen rewards. Therefore the benefit of providing pollen that is accessible to bee foragers outweighs any potential costs to fitness in terms of gender interference in this species.
PMCID: PMC3995886  PMID: 24755611
17.  Orally Active Fumagillin Analogues: Transformations of a Reactive Warhead in the Gastric Environment 
ACS Medicinal Chemistry Letters  2013;4(4):381-386.
Semisynthetic analogues of fumagillin, 1, inhibit methionine aminopeptidase-2 (MetAP2) and have entered the clinic for the treatment of cancer. An optimized fumagillin analogue, 3 (PPI-2458), was found to be orally active, despite containing a spiroepoxide function that formed a covalent linkage to the target protein. In aqueous acid, 3 underwent ring-opening addition of water and HCl, leading to four products, 4–7, which were characterized in detail. The chlorohydrin, but not the diol, products inhibited MetAP2 under weakly basic conditions, suggesting reversion to epoxide as a step in the mechanism. In agreement, chlorohydrin 6 was shown to revert rapidly to 3 in rat plasma. In an ex vivo assay, rats treated with purified acid degradants demonstrated inhibition of MetAP2 that correlated with the biochemical activity of the compounds. Taken together, the results indicate that degradation of the parent compound was compensated by the formation of active equivalents leading to a pharmacologically useful level of MetAP2 inhibition.
PMCID: PMC4027436  PMID: 24900682
Fumagillin; MetAP2; PPI-2458; angiogenesis inhibitor; irreversible inhibitor
18.  Utility of a Clinical Risk Factor Scoring Model in Predicting Infection with Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae on Hospital Admission 
To validate the utility of a previously published scoring model (Italian) to identify patients infected with community-onset extended-spectrum β-lactamase-producing Enterobacteriaceae (ESBL-EKP) and develop a new model (Duke) based on local epidemiology.
This case-control study included patients 18 years of age or more admitted to Duke University Hospital between January 1, 2008, and December 31, 2010, with culture-confirmed infection due to an ESBL-EKP (cases). Uninfected controls were matched to cases (3 : 1). The Italian model was applied to our patient population for validation. The Duke model was developed through logistic-regression-based prediction scores calculated on variables independently associated with ESBL-EKP isolation. Sensitivities and specificities at various point cutoffs were determined, and determination of the area under the receiver operating characteristic curve (ROC AUC) was performed.
A total of 123 cases and 375 controls were identified. Adjusted odds ratios and 95% confidence intervals for variables previously identified in the Italian model were as follows: hospitalization (3.20 [1.62–6.55]), transfer (4.31 [2.15–8.78]), urinary catheterization (5.92 [3.09–11.60]), β-lactam and/or fluoroquinolone therapy (3.76 [2.06–6.95]), age 70 years or more (1.55 [0.79–3.01]), and Charlson Co-morbidity Score of 4 or above (1.06 [0.55–2.01]). Sensitivity and specificity were, respectively, more than or equal to 95% and less than or equal to 47% for scores 3 or below and were less than or equal to 50% and more than or equal to 96% for scores 8 or above. The ROC AUC was 0.88. Variables identified in the Duke model were as follows: hospitalization (2.63 [1.32–5.41]), transfer (5.30 [2.67–10.71]), urinary catheterization (6.89 [3.62–13.38]), β-lactam and/or fluoroquinolone therapy (3.47 [1.91–6.41]), and immunosuppression (2.34 [1.14–4.80]). Sensitivity and specificity were, respectively, more than or equal to 94% and less than or equal to 65% for scores 3 or below and were less than or equal to 58% and more than or equal to 95% for scores 8 or above. The ROC AUC was 0.89.
While the previously reported model was an excellent predictor of community-onset ESBL-EKP infection, models utilizing factors based on local epidemiology may be associated with improved performance.
PMCID: PMC3641565  PMID: 23466912
19.  Building a secreting nanomachine: a structural overview of the T3SS☆ 
Graphical abstract
•Flagellar and non-flagellar T3SS are built assembling homologous protein machineries.•Unified nomenclature for non-flagellar T3SS.•New model of the T3SS needle is consistent with the flagellar filament, both in terms of helical parameters and orientation.•Structural and functional implication of the new architecture of the T3SS export apparatus and ATPase complex.
To fulfill complex biological tasks, such as locomotion and protein translocation, bacteria assemble macromolecular nanomachines. One such nanodevice, the type III secretion system (T3SS), has evolved to provide a means of transporting proteins from the bacterial cytoplasm across the periplasmic and extracellular spaces. T3SS can be broadly classified into two highly homologous families: the flagellar T3SS which drive cell motility, and the non-flagellar T3SS (NF-T3SS) that inject effector proteins into eukaryotic host cells, a trait frequently associated with virulence. Although the structures and symmetries of ancillary components of the T3SS have diversified to match requirements of different species adapted to different niches, recent genetic, molecular and structural studies demonstrate that these systems are built by arranging homologous modular protein assemblies.
PMCID: PMC4045390  PMID: 24704748
20.  The Centrosome-Specific Phosphorylation of Cnn by Polo/Plk1 Drives Cnn Scaffold Assembly and Centrosome Maturation 
Developmental Cell  2014;28(6):659-669.
Centrosomes are important cell organizers. They consist of a pair of centrioles surrounded by pericentriolar material (PCM) that expands dramatically during mitosis—a process termed centrosome maturation. How centrosomes mature remains mysterious. Here, we identify a domain in Drosophila Cnn that appears to be phosphorylated by Polo/Plk1 specifically at centrosomes during mitosis. The phosphorylation promotes the assembly of a Cnn scaffold around the centrioles that is in constant flux, with Cnn molecules recruited continuously around the centrioles as the scaffold spreads slowly outward. Mutations that block Cnn phosphorylation strongly inhibit scaffold assembly and centrosome maturation, whereas phosphomimicking mutations allow Cnn to multimerize in vitro and to spontaneously form cytoplasmic scaffolds in vivo that organize microtubules independently of centrosomes. We conclude that Polo/Plk1 initiates the phosphorylation-dependent assembly of a Cnn scaffold around centrioles that is essential for efficient centrosome maturation in flies.
Graphical Abstract
•Plk1/Polo phosphorylates Cnn in vitro•Phosphorylation appears to occur specifically at centrosomes during mitosis•Phosphorylation allows Cnn to assemble into a dynamic scaffold around centrioles•Cnn scaffold assembly is required for proper centrosome maturation
Centrosomes, important cellular organizers, form when centrioles recruit pericentriolar material (PCM) around themselves. Conduit et al. shed light on PCM spreading/centrosome maturation during mitosis, showing that Polo kinase initiates phosphorylation-dependent assembly of PCM protein Cnn as a scaffold around centrioles. This scaffold then spreads outward to support an expanded PCM.
PMCID: PMC3988887  PMID: 24656740
21.  Nonfunctional Variant 3 Factor H Binding Proteins as Meningococcal Vaccine Candidates 
Infection and Immunity  2014;82(3):1157-1163.
Neisseria meningitidis is a human-specific pathogen and leading cause of meningitis and septicemia. Factor H binding protein (fHbp), a virulence factor which protects N. meningitidis from innate immunity by binding the human complement regulator factor H (fH) with high affinity, is also a key antigen in vaccines being developed to prevent meningococcal disease. fHbp can be divided into three variant groups (V1, V2, and V3) that elicit limited immunological cross-reactivity. The interaction of fH with fHbp could impair the immunogenicity of this antigen by hindering access to the antigenic epitopes in fHbp, providing the rationale for the development of nonfunctional fHbps as vaccine candidates. Here, we characterized the two nonfunctional V3 fHbps, fHbpT286A and fHbpE313A, which each contains a single amino acid substitution that leads to a marked reduction in affinity for fH without affecting the folding of the proteins. The immunogenicity of the nonfunctional fHbps was assessed in transgenic mice expressing a single chimeric fH containing domains of human fH involved in binding to fHbp. No differences in anti-V3 fHbp antibody titers were elicited by the wild-type V3 fHbp, V3 fHbpT286A, and V3 fHbpE313A, demonstrating that the nonfunctional fHbps retain their immunogenicity. Furthermore, the nonfunctional V3 fHbps elicit serum bactericidal activity that is equivalent to or higher than that observed with the wild-type protein. Our findings provide the basis for the rational design of next-generation vaccines containing nonfunctional V3 fHbps.
PMCID: PMC3958001  PMID: 24379280
22.  Polymorphisms in the Human Inhibitory Signal-regulatory Protein α Do Not Affect Binding to Its Ligand CD47* 
The Journal of Biological Chemistry  2014;289(14):10024-10028.
Background: CD47 interacts with SIRPα to down-regulate myeloid cell activity.
Results: The extensive polymorphisms in human SIRPα do not affect ligand binding, and a peptide from CD47 does not bind SIRPα.
Conclusion: The polymorphisms are being selected for other purposes such as evasion from pathogens.
Significance: The polymorphisms are not likely to affect this interaction currently of therapeutic interest.
CD47 is a widely distributed membrane protein that interacts with signal-regulatory protein α (SIRPα), an inhibitory receptor on myeloid cells that gives a “don't-eat-me” signal. Manipulation of the interaction is of considerable interest in the immunotherapy of cancer and in xenotransplantation. The amino-terminal ligand binding domain of SIRPα is highly polymorphic in contrast to the single Ig-like domain of CD47. There is confusion as to whether the polymorphisms will affect ligand binding, but this is an important point for this interaction and other paired receptors being considered as targets for therapy. We show by x-ray crystallography that one human SIRPα allele differing in 13 amino acid residues has a very similar binding site and that several different alleles all bind CD47 with similar affinity as expected because the residues are mostly surface-exposed and distant from the binding site. A peptide from the binding site of CD47 has been reported to mimic the CD47 interaction with SIRPα, but we could find no binding. We discuss the possible pitfalls in determining the affinity of weak interactions and also speculate on how SIRPα polymorphisms may have been selected by pathogens and how this may also be true in other paired receptors such as the KIRs.
PMCID: PMC3974974  PMID: 24550402
Cancer Therapy; Cell Surface Receptor; Immunology; Leukocyte; Membrane Proteins; Peptide Interactions; Protein Structure; CD47; Inhibitory Receptor; SIRPα
23.  Whole-Body Imaging of High-Dose Ionizing Irradiation-Induced Tissue Injuries Using 99mTc-Duramycin 
High-dose ionizing irradiation can cause extensive injuries in susceptible tissues. A noninvasive imaging technique that detects a surrogate marker of apoptosis may help characterize the dynamics of radiation-induced tissue damage. The goal of this study was to prove the concept of imaging the temporal and spatial distribution of damage in susceptible tissues after high-dose radiation exposure, using 99mTc-duramycin as a phosphatidylethanolamine-binding radiopharmaceutical.
Rats were subjected to 15 Gy of total-body irradiation with x-rays. Planar whole-body 99mTc-duramycin scanning (n = 4 per time point) was conducted at 24, 48, and 72 h using a clinical γ-camera. On the basis of findings from planar imaging, preclinical SPECT data were acquired on control rats and on irradiated rats at 6 and 24 h after irradiation (n = 4 per time point). Imaging data were validated by γ-counting and histology, using harvested tissues in parallel groups of animals (n = 4).
Prominent focal uptake was detected in the thymus as early as 6 h after irradiation, followed by a gradual decline in 99mTc-duramycin binding accompanied by extensive thymic atrophy. Early (6–24 h) radioactivity uptake in the gastrointestinal region was detected. Significant signal was seen in major bones in a slightly delayed fashion, at 24 h, which persisted for at least 2 d. This finding was paralleled by an elevation in signal intensity in the kidneys, spleen, and liver. The imaging results were consistent with ex vivo γ-counting results and histology. Relatively high levels of apoptosis were detected from histology in the thymus, guts, and bones, with the thymus undergoing substantial atrophy.
As a proof of principle, this study demonstrated a noninvasive imaging technique that allows characterization of the temporal and spatial dynamics of injuries in susceptible tissues during the acute phase after high-dose ionizing irradiation. Such an imaging capability will potentially be useful for global, whole-body, assessment of tissue damage after radiation exposure. These data, in turn, will contribute to our general knowledge of tissue susceptibility to ionizing irradiation, as well as the onset and progression of tissue injuries.
PMCID: PMC3894925  PMID: 23804327
99mTc-Duramycin; phosphatidylethanolamine; apoptosis; radiation injuries
24.  Chronic dopamine depletion augments the functional expression of K-ATP channels in the rat subthalamic nucleus 
Neuroscience letters  2012;531(2):104-108.
Symptoms of Parkinson’s disease caused by dopamine depletion are associated with burst firing in the subthalamic nucleus (STN). Moreover, regularization or suppression of STN neuronal activity is thought to improve symptoms of Parkinson’s disease. We reported recently that N-methyl-D-aspartate (NMDA) receptor stimulation of rat STN neurons evokes ATP-sensitive K+ (K-ATP) current via a Ca2+- and nitric oxide-dependent mechanism. The present studies were done to determine whether or not K-ATP channel function in STN neurons is altered in a model of chronic dopamine depletion. Brain slices were prepared from rats with unilateral dopamine depletion caused by intracerebral 6-hydroxydopamine (6-OHDA) injections. Whole-cell patch-clamp recordings showed that NMDA evoked more outward current at −70 mV and greater positive slope conductance in STN neurons located ipsilateral to 6-OHDA treatment compared to neurons located contralateral. Moreover, extracellular, loose-patch recordings showed that NMDA increased spontaneous firing rate in STN neurons in slices from normal rats, whereas NMDA produced a tolbutamide-sensitive inhibition of firing rate in STN neurons located ipsilateral to 6-OHDA treatment. These results show that K-ATP channel function in STN neurons is up-regulated by chronic dopamine deficiency. We suggest that K-ATP channel activation in the STN might benefit symptoms of Parkinson’s disease.
PMCID: PMC3513517  PMID: 23127848
ATP-sensitive K+ channel; subthalamic nucleus; N-methyl-D-aspartate; sulfonylurea; tolbutamide; brain slice
25.  A Statistically Based Acute Ischemia Detection Algorithm Suitable for an Implantable Device 
Annals of biomedical engineering  2012;40(12):2627-2638.
This study investigates the performance of a new statistically driven acute ischemia detection algorithm that can process data from two bipolar cutaneous or subcutaneous leads. During a start-up phase, the algorithm processes electrocardiogram signals to determine a normal range of ST-segment deviation as a function of heart rate. The algorithm then generates upper and lower ST-deviation thresholds based on the dispersion of the baseline ST-deviation data. After the start-up phase, persistent ST-deviation that is beyond either the upper or lower thresholds results in detection of acute ischemia. To test the algorithm, we performed long-term (10 day) Holter monitoring in a control group of 14 subjects. We also performed Holter monitoring during balloon angioplasty, and for 2 days after surgery, in 30 subjects who underwent elective percutaneous coronary interventions (“PCI”). We determined the percentage of balloon inflations the algorithm detected without producing false positive detections within the control group 10-day daily life data. The algorithm detected 17/17 LAD occlusions, 7/8 LCX occlusions, and 8/9 RCA occlusions. Our results suggest that automatically generated, subject-specific, heart-rate dependent ST-deviation thresholds can detect PCI induced myocardial ischemia without resulting in false positive detections in a small control group.
PMCID: PMC3480542  PMID: 22739698
Implantable acute ischemia monitor; ST-segment deviation; Balloon occlusion

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