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Find video protocols related to scientific articles indexed in Pubmed.
Forensic interpretation of molecular variation on networks of disease transmission and genetic inheritance.
Electrophoresis
PUBLISHED: 10-07-2014
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This paper describes the inference-on-networks (ION) framework for forensic interpretat ION of molecular typing data in cases involving allegations of infectious microbial transmission, association of disease outbreaks with alleged sources, and identifying familial relationships using mitochondrial or Y chromosomal DNA. The framework is applicable to molecular typing data obtained using any technique, including those based on electrophoretic separations. A key insight is that the networks associated with disease transmission or DNA inheritance can be used to define specific testable relationships and avoid the ambiguity and subjectivity associated with the criteria used for inferring genetic relatedness now in use. We discuss specific applications of the framework to the 2003 severe acute respiratory syndrome (SARS) outbreak in Singapore and the 2001 foot-and-mouth disease virus (FMDV) outbreak in Great Britain.
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Characterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt.
BMC Genomics
PUBLISHED: 08-29-2014
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Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as "accessory genome". Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed.
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Microbial profiling of combat wound infection through detection microarray and next-generation sequencing.
J. Clin. Microbiol.
PUBLISHED: 05-14-2014
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Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden.
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Metagenomic Analysis of the Airborne Environment in Urban Spaces.
Microb. Ecol.
PUBLISHED: 05-08-2014
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The organisms in aerosol microenvironments, especially densely populated urban areas, are relevant to maintenance of public health and detection of potential epidemic or biothreat agents. To examine aerosolized microorganisms in this environment, we performed sequencing on the material from an urban aerosol surveillance program. Whole metagenome sequencing was applied to DNA extracted from air filters obtained during periods from each of the four seasons. The composition of bacteria, plants, fungi, invertebrates, and viruses demonstrated distinct temporal shifts. Bacillus thuringiensis serovar kurstaki was detected in samples known to be exposed to aerosolized spores, illustrating the potential utility of this approach for identification of intentionally introduced microbial agents. Together, these data demonstrate the temporally dependent metagenomic complexity of urban aerosols and the potential of genomic analytical techniques for biosurveillance and monitoring of threats to public health.
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Different paths to pathogenesis.
Trends Microbiol.
PUBLISHED: 02-24-2014
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In a recent issue of Cell Host & Microbe, Elsen and colleagues identify a novel hemolysin in a highly virulent Pseudomonas aeruginosa strain that lacks a type III secretion system. Their analysis provides another example of how individual strains of P. aeruginosa utilize different virulence mechanisms to cause severe infections.
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Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array.
Sci Rep
PUBLISHED: 02-12-2014
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Ancient human remains of paleopathological interest typically contain highly degraded DNA in which pathogenic taxa are often minority components, making sequence-based metagenomic characterization costly. Microarrays may hold a potential solution to these challenges, offering a rapid, affordable, and highly informative snapshot of microbial diversity in complex samples without the lengthy analysis and/or high cost associated with high-throughput sequencing. Their versatility is well established for modern clinical specimens, but they have yet to be applied to ancient remains. Here we report bacterial profiles of archaeological and historical human remains using the Lawrence Livermore Microbial Detection Array (LLMDA). The array successfully identified previously-verified bacterial human pathogens, including Vibrio cholerae (cholera) in a 19th century intestinal specimen and Yersinia pestis ("Black Death" plague) in a medieval tooth, which represented only minute fractions (0.03% and 0.08% alignable high-throughput shotgun sequencing reads) of their respective DNA content. This demonstrates that the LLMDA can identify primary and/or co-infecting bacterial pathogens in ancient samples, thereby serving as a rapid and inexpensive paleopathological screening tool to study health across both space and time.
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A mixed-methods observational study of human milk sharing communities on Facebook.
Breastfeed Med
PUBLISHED: 02-03-2014
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The Food and Drug Administration discourages the casual sharing of human milk because of the risk of pathogen transmission. No information is currently available on the prevalence of this practice. The purpose of this mixed-methods observational study is to describe the size and activity of online milk sharing communities.
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Zebrafish as a natural host model for Vibrio cholerae colonization and transmission.
Appl. Environ. Microbiol.
PUBLISHED: 12-27-2013
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The human diarrheal disease cholera is caused by the aquatic bacterium Vibrio cholerae. V. cholerae in the environment is associated with several varieties of aquatic life, including insect egg masses, shellfish and vertebrate fish. Here we describe a novel animal model for V. cholerae, the zebrafish. Pandemic V. cholerae strains specifically colonize the zebrafish intestinal tract after exposure in water with no manipulation of the animal required. Colonization occurs in close contact with the intestinal epithelium and mimics colonization observed in mammals. Zebrafish that are colonized by V. cholerae transmit the bacteria to naïve fish, which then become colonized. Striking differences in colonization between classical and El Tor biotype V. cholerae were apparent. The zebrafish natural habitat in Asia heavily overlaps cholera endemic areas, suggesting that zebrafish and V. cholerae evolved in close contact with each other. Thus, the zebrafish provides a natural host model for the study of V. cholerae colonization, transmission and environmental survival.
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Ultra-Deep Sequencing of Intra-host Rabies Virus Populations during Cross-species Transmission.
PLoS Negl Trop Dis
PUBLISHED: 11-01-2013
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One of the hurdles to understanding the role of viral quasispecies in RNA virus cross-species transmission (CST) events is the need to analyze a densely sampled outbreak using deep sequencing in order to measure the amount of mutation occurring on a small time scale. In 2009, the California Department of Public Health reported a dramatic increase (350) in the number of gray foxes infected with a rabies virus variant for which striped skunks serve as a reservoir host in Humboldt County. To better understand the evolution of rabies, deep-sequencing was applied to 40 unpassaged rabies virus samples from the Humboldt outbreak. For each sample, approximately 11 kb of the 12 kb genome was amplified and sequenced using the Illumina platform. Average coverage was 17,448 and this allowed characterization of the rabies virus population present in each sample at unprecedented depths. Phylogenetic analysis of the consensus sequence data demonstrated that samples clustered according to date (1995 vs. 2009) and geographic location (northern vs. southern). A single amino acid change in the G protein distinguished a subset of northern foxes from a haplotype present in both foxes and skunks, suggesting this mutation may have played a role in the observed increased transmission among foxes in this region. Deep-sequencing data indicated that many genetic changes associated with the CST event occurred prior to 2009 since several nonsynonymous mutations that were present in the consensus sequences of skunk and fox rabies samples obtained from 20032010 were present at the sub-consensus level (as rare variants in the viral population) in skunk and fox samples from 1995. These results suggest that analysis of rare variants within a viral population may yield clues to ancestral genomes and identify rare variants that have the potential to be selected for if environment conditions change.
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Gongylonema pulchrum infection in a resident of Williamsburg, Virginia, verified by genetic analysis.
Am. J. Trop. Med. Hyg.
PUBLISHED: 08-19-2013
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We describe the thirteenth reported case of human infection with Gongylonema spp. in the United States and the first to be confirmed as Gongylonema pulchrum. The parasite described was isolated from the oral cavity of a resident of Williamsburg, Virginia. The identity of the parasite was verified through morphological and genetic approaches, and provided the first genetic confirmation of a Gongylonema sp. in humans.
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Shanghai fever: a distinct Pseudomonas aeruginosa enteric disease.
Gut
PUBLISHED: 08-13-2013
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Shanghai fever, a community-acquired enteric illness associated with sepsis caused by Pseudomonas aeruginosa, was first described in 1918. The understanding of Shanghai fever is incomplete.
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Scalable metagenomic taxonomy classification using a reference genome database.
Bioinformatics
PUBLISHED: 07-04-2013
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Deep metagenomic sequencing of biological samples has the potential to recover otherwise difficult-to-detect microorganisms and accurately characterize biological samples with limited prior knowledge of sample contents. Existing metagenomic taxonomic classification algorithms, however, do not scale well to analyze large metagenomic datasets, and balancing classification accuracy with computational efficiency presents a fundamental challenge.
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Bacterial and clinical characteristics of health care- and community-acquired bloodstream infections due to Pseudomonas aeruginosa.
Antimicrob. Agents Chemother.
PUBLISHED: 06-03-2013
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Health care-associated infections, including Pseudomonas aeruginosa bloodstream infection, have been linked to delays in appropriate antibiotic therapy and an increased mortality rate. The objective of this study was to evaluate intrinsic virulence, bacterial resistance, and clinical outcomes of health care-associated bloodstream infections (HCABSIs) in comparison with those of community-acquired bloodstream infections (CABSIs) caused by P. aeruginosa. We conducted a retrospective multicenter study of consecutive P. aeruginosa bacteremia patients at two university-affiliated hospitals. Demographic, clinical, and treatment data were collected. Microbiologic analyses included in vitro susceptibility profiles and type III secretory (TTS) phenotypes. Sixty CABSI and 90 HCABSI episodes were analyzed. Patients with HCABSIs had more organ dysfunction at the time of bacteremia (P = 0.05) and were more likely to have been exposed to antimicrobial therapy (P < 0.001) than those with CABSIs. Ninety-two percent of the carbapenem-resistant P. aeruginosa infections were characterized as HCABSIs. The 30-day mortality rate for CABSIs was 26% versus 36% for HCABSIs (P = 0.38). The sequential organ failure assessment score at the time of bacteremia (hazard ratio [HR], 1.2; 95% confidence interval [CI], 1.1 to 1.3) and the TTS phenotype (HR 2.1; 95% CI, 1.1 to 3.9) were found to be independent predictors of the 30-day mortality rate. No mortality rate difference was observed between CABSIs and HCABSIs caused by P. aeruginosa. Severity of illness and expression of TTS proteins were the strongest predictors of the 30-day mortality rate due to P. aeruginosa bacteremia. Future P. aeruginosa bacteremia trials designed to neutralize TTS proteins are warranted.
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The nutritive and immunoprotective quality of human milk beyond 1 year postpartum: are lactation-duration-based donor exclusions justified?
J Hum Lact
PUBLISHED: 05-14-2013
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Donor human milk is critical for the fragile preterm infant who does not have access to his or her mothers milk, improving survival rates and quality of survival and decreasing hospital stay. Despite the opening of donor milk banks around the world, shortages continue as demand for donor milk exceeds supply. One potential means of increasing supply is by reducing exclusion criteria that prohibit mothers from donating milk based on duration of lactation. Minimal research has been done on the composition of human milk during the second year of lactation, with most research focusing on the nutritive compounds and not the immunoprotective compounds. Several immunoprotective compounds, including lysozyme, lactoferrin, secretory immunoglobulin A, and oligosaccharides, are abundant in human milk compared to bovine-based infant formula and are partially or fully retained during Holder pasteurization, making them an important differentiating feature of donor milk. A PubMed search was conducted to review studies in human milk composition during the second year of lactation. Limitations of existing research include sample collection protocols, small study sizes, and use of populations that may have been at risk for nutritional deficiencies. Stable concentrations of several components were reported including protein, lactose, iron, copper, lactoferrin, and secretory immunoglobulin A. Lysozyme concentration increased during extended lactation, while zinc and calcium concentrations declined into the second year. Conflicting findings were reported on fat content, and no information was available regarding oligosaccharide content. More research is needed to create evidence-based guidelines regarding the nutritive and immunoprotective value of donor milk throughout the course of lactation.
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Characterization of aerosol emissions from wastewater aeration basins.
J Air Waste Manag Assoc
PUBLISHED: 03-02-2013
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The emission of particulate matter (PM10 and PM2.5) and ammonia (NH3) by aeration processes at wastewater treatment plants (WWTPs) with and without odor control units was examined. Local concentrations of PM2.5, PM10, and NH3 at the aeration basins were within urban ranges. Emission fluxes of NH3 and PM2.5 for a medium-sized WWTP were determined to be 136 g day(-1) and 43 g day(-1), respectively, which are not substantial emission fluxes for urban environments. Odor control treatment using a granulated activated carbon bed reduced aerosol and NH3 emissions substantially. Detection of sterols, in particular the fecal sterol campesterol, in the PM clearly demonstrates aerosolization of wastewater components in the aeration process. The presence of campesterol in PM2.5 at a remote fenceline location in a WWTP facility illustrates that wastewater components are aerosolized in the fine PM fraction and transported beyond the facilities.
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Ultra-deep mutant spectrum profiling: improving sequencing accuracy using overlapping read pairs.
BMC Genomics
PUBLISHED: 02-06-2013
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High throughput sequencing is beginning to make a transformative impact in the area of viral evolution. Deep sequencing has the potential to reveal the mutant spectrum within a viral sample at high resolution, thus enabling the close examination of viral mutational dynamics both within- and between-hosts. The challenge however, is to accurately model the errors in the sequencing data and differentiate real viral mutations, particularly those that exist at low frequencies, from sequencing errors.
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A novel report of hatching plasticity in the phylum Echinodermata.
Am. Nat.
PUBLISHED: 01-26-2013
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Hatching plasticity occurs in response to a wide range of stimuli across many animal taxa, including annelids, arthropods, mollusks, and chordates. Despite the prominence of echinoderms in developmental biology and more than 100 years of detailed examination of their development under a variety of conditions, environmentally cued hatching plasticity has never been reported in the phylum Echinodermata. Here we report plasticity in the timing and stage of hatching of embryos of the sand dollar Echinarachnius parma in response to reductions in salinity. Embryos of E. parma increased their time to hatching more than twofold in response to ecologically relevant salinity reductions, while maintaining an otherwise normal developmental schedule. Embryos that experienced the greatest delay in hatching time emerged from the fertilization envelope as four-arm pluteus larvae rather than hatching as blastulae or early gastrulae. Salinity manipulations across multiple male-female pairs indicated high variability in hatching time both within and among clutches, suggesting significant intraspecific variation in developmental responses to salinity.
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The role of viral population diversity in adaptation of bovine coronavirus to new host environments.
PLoS ONE
PUBLISHED: 01-07-2013
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The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were "selected" from a pre-existing pool rather than through de novo mutation and subsequent population fixation.
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Improved power conversion efficiency in bulk heterojunction organic solar cells with radial electron contacts.
ACS Nano
PUBLISHED: 09-19-2011
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We incorporate radial electrical contacts penetrating a blended organic semiconductor active layer to shorten the electron collection pathway in poly(3-hexylthiophene):[6,6]-phenyl-C(61)-butyric acid methyl ester bulk heterojunction solar cells and simultaneously confine the blend material within nanometer-scale volumes. This architecture improves the active material performance by more than 50% compared to its performance in a bulk heterojunction with planar contacts, consistent with accelerated electron extraction. The radial contact solar cell achieves similar overall photovoltaic power conversion efficiency to control bulk heterojunction devices with planar contacts, despite containing less than half the volume of light-absorbing semiconductor material.
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The Streptococcus iniae transcriptional regulator CpsY is required for protection from neutrophil-mediated killing and proper growth in vitro.
Infect. Immun.
PUBLISHED: 09-12-2011
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The ability of a pathogen to metabolically adapt to the local environment for optimal expression of virulence determinants is a continued area of research. Orthologs of the Streptococcus iniae LysR family regulator CpsY have been shown to regulate methionine biosynthesis and uptake pathways but appear to influence expression of several virulence genes as well. An S. iniae mutant with an in-frame deletion of cpsY (?cpsY mutant) is highly attenuated in a zebrafish infection model. The ?cpsY mutant displays a methionine-independent growth defect in serum, which differs from the methionine-dependent defect observed for orthologous mutants of Streptococcus mutans and Streptococcus agalactiae. On the contrary, the ?cpsY mutant can grow in excess of the wild type (WT) when supplemented with proteose peptone, suggesting an inability to properly regulate growth. CpsY is critical for protection of S. iniae from clearance by neutrophils in whole blood but is dispensable for intracellular survival in macrophages. Susceptibility of the ?cpsY mutant to killing in whole blood is not due to a growth defect, because inhibition of neutrophil phagocytosis rescues the mutant to WT levels. Thus, CpsY appears to have a pleiotropic regulatory role for S. iniae, integrating metabolism and virulence. Furthermore, S. iniae provides a unique model to investigate the paradigm of CpsY-dependent regulation during systemic streptococcal infection.
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Utilization of dairy byproduct proteins, surfactants, and enzymes in frozen dough.
Crit Rev Food Sci Nutr
PUBLISHED: 03-25-2011
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Use of natural additives is gaining popularity among the masses as they are becoming more conscious about their diet and health. Frozen dough products are one of the recent examples of value-added cereal products which face stability problems during extended storage periods of times. Dairy whey proteins, surfactants, and certain enzymes are considered important natural additives which could be used to control the water redistribution problem in the dough structure during the storage condition. They interact with the starch and gluten network in a dough system and thus behave as dough improvers and strengtheners. These natural additives not only help to bind extra moisture but also to improve texture and sensory attributes in frozen dough bakery products.
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The peril of the plankton.
Integr. Comp. Biol.
PUBLISHED: 05-12-2010
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The pelagic environment is characterized by unevenly distributed resources and risks. Such unpredictability presents adaptive challenges to diverse planktonic organisms including the larvae of benthic marine invertebrates. Estimates of mortality during planktonic development are highly variable, ranging from 0% to 100% per day. Predation is considered a significant source of this mortality, but what explains the variability in estimates of the mortality of marine invertebrate larvae? While differential exposure of larval prey to predators may explain these widely variable estimates, adaptations that reduce vulnerability of marine larvae to predators may also be important. Although there are excellent reviews of predation upon larvae and of larval mortality and defenses, nearly 15 years have elapsed since these topics were formally reviewed. Here, we highlight recent advances in understanding the behavioral, chemical, and morphological defenses that larvae possess and assess their effectiveness in reducing the risk of predation. While recent work confirms that larval mortality is generally high, it also demonstrates that larvae can reduce their risk of predation in several ways, including: (1) temporarily escaping the benthos during vulnerable early stages, (2) producing chemical compounds that reduce palatability, (3) possessing morphological defenses such as spines and shells, and (4) exhibiting induced defensive responses whereby larvae can alter their behavior, morphology, and life histories in the presence of predators. Taken together, these studies indicate that marine invertebrate larvae possess a sophisticated suite of defensive phenotypes that have allowed them to persist in the life cycle of benthic invertebrates for eons.
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Synthetic musk emissions from wastewater aeration basins.
Water Res.
PUBLISHED: 05-12-2010
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Wastewater aeration basins at publicly owned treatment works (POTWs) can be emission sources for gaseous or aerosolized sewage material. In the present study, particle and gas phase emissions of synthetic musks from covered and uncovered aeration basins were measured. Galaxolide (HHCB), tonalide (AHTN), and celestolide (ADBI) were the most abundant, ranging from 6704 to 344,306 ng m(-3), 45-3816 ng m(-3), and 2-148 ng m(-3) in the gas phase with particle phase concentrations 3 orders of magnitude lower. The musk species were not significantly removed from the exhaust air by an odor control system, yielding substantial daily emission fluxes (? 200 g d(-1) for HHCB) into the atmosphere. However, simple dispersion modeling showed that the treatment plants are unlikely to be a major contributor to ambient air concentrations of these species. Emission of synthetic musk species during wastewater treatment is a substantial fate process; more than 14% of the influent HHCB is emitted to the atmosphere in a POTW as opposed to the <1% predicted by an octanol-water partition coefficient and fugacity-based US EPA fate model. The substantial atmospheric emission of these compounds is most likely due to active stripping that occurs in the aeration basins by bubbling air through the sludge.
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Understanding the effects of low salinity on fertilization success and early development in the sand dollar Echinarachnius parma.
Biol. Bull.
PUBLISHED: 04-24-2010
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Free-spawning marine invertebrates that live near shore or in estuaries may experience reduced fertilization success during low-salinity events. Although several studies have documented reproductive failure at reduced salinity in estuarine animals, few have looked at whether developmental failure is due to a failure of fertilization or to a failure of fertilized eggs to cleave. In this study, we examined the effects of salinities ranging from 18 to 32 psu on fertilization success and early development in the sand dollar Echinarachnius parma. In addition to decoupling the effects of low salinity on fertilization from its effects on early cleavage, we also assessed whether eggs or sperm were the weak link in accounting for reproductive failure. We found that both fertilization and cleavage failed at salinities below about 22 psu but that development could be partially rescued by returning zygotes to full-strength seawater. We also found that sperm remained active and capable of fertilizing eggs even after being exposed to low salinities for 30 min.. Taken together, these results suggest that reproductive failure at low salinities in E. parma is due more to an inability of the fertilized eggs to cleave than to an inability of sperm to fertilize eggs.
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Trolling for the ideal model host: zebrafish take the bait.
Future Microbiol
PUBLISHED: 04-01-2010
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As little as 10 years ago, murine models of infectious disease were the host of choice for analyzing interactions between the pathogen and host during infection. However, not all pathogens can infect mice, nor do they always replicate the clinical syndromes observed in human infections. Furthermore, in the current economic environment, using mammalian models for large-scale screens may be less economically feasible. The emergence of the zebrafish (Danio rerio) as an infectious disease host model, as well as a model for vertebrate immune system development, has provided new information and insights into pathogenesis that, in many instances, would not have been possible using a murine model host. In this article we highlight some of the key findings and the latest techniques along with the many advantages of using the zebrafish host model to gain new insights into pathogenic mechanisms in a live vertebrate host.
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How do changes in parental investment influence development in echinoid echinoderms?
Evol. Dev.
PUBLISHED: 11-03-2009
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Understanding the relationship between egg size, development time, and juvenile size is critical to explaining patterns of life-history evolution in marine invertebrates. Currently there is conflicting information about the effects of changes in egg size on the life histories of echinoid echinoderms. We sought to resolve this conflict by manipulating egg size and food level during the development of two planktotrophic echinoid echinoderms: the green sea urchin, Strongylocentrotus droebachiensis and the sand dollar, Echinarachnius parma. Based on comparative datasets, we predicted that decreasing food availability and egg size would increase development time and reduce juvenile size. To test our prediction, blastomere separations were performed in both species at the two-cell stage to reduce egg volume by 50%, producing whole- and half-size larvae that were reared to metamorphosis under high or low food levels. Upon settlement, age at metamorphosis, juvenile size, spine number, and spine length were measured. As predicted, reducing egg size and food availability significantly increased age at metamorphosis and reduced juvenile quality. Along with previous egg size manipulations in other echinoids, this study suggests that the relationship between egg size, development time, and juvenile size is strongly dependent upon the initial size of the egg.
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Scanning photocurrent microscopy analysis of Si nanowire field-effect transistors fabricated by surface etching of the channel.
Nano Lett.
PUBLISHED: 03-31-2009
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High-performance field-effect transistors were fabricated by etching the channel regions of surface-doped Si nanowires. On/off ratios of 10(6) and field effect mobilities up to 525 cm(2)/(V x s) represent significant improvements over transistors fabricated from uniformly doped n-Si nanowires. Analysis by scanning photocurrent microscopy (SPCM) confirmed that the devices function similarly to traditional metal-oxide semiconductor field-effect transistors; in accumulation, the device current is controlled by channel conductance modulation, while n(+)-n junctions determine subthreshold characteristics as the channel is depleted. The principles of operation and the drain current saturation mechanisms were investigated by correlating current versus voltage data with integrated photocurrent profiles from SPCM.
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A synergistic assembly of nanoscale lamellar photoconductor hybrids.
Nat Mater
PUBLISHED: 03-03-2009
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Highly ordered nanostructured organic/inorganic hybrids offer chemical tunability, novel functionalities and enhanced performance over their individual components. Hybrids of complementary p-type organic and n-type inorganic components have attracted interest in optoelectronics, where high-efficiency devices with minimal cost are desired. We demonstrate here self-assembly of a lamellar hybrid containing periodic and alternating 1-nm-thick sheets of polycrystalline ZnO separated by 2-3 nm layers of conjugated molecules, directly onto an electrode. Initially the electrodeposited inorganic is Zn(OH)(2), but pi-pi interactions among conjugated molecules stabilize synergistically the periodic nanostructure as it converts to ZnO at 150 degrees C. As photoconductors, normalized detectivities (D(*)) greater than 2x10(10) Jones, photocurrent gains of 120 at 1.2 V microm(-1) and dynamic ranges greater than 60 dB are observed on selective excitation of the organic. These are among the highest values measured for organic, hybrid and amorphous silicon, making them technologically competitive as low-power, wavelength-tunable, flexible and environmentally benign photoconductors.
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Source apportionment of lead-containing aerosol particles in Shanghai using single particle mass spectrometry.
Chemosphere
PUBLISHED: 02-20-2009
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Lead (Pb) in individual aerosol particles was measured using single particle aerosol mass spectrometer (ATOFMS) in the summer of 2007 in Shanghai, China. Pb was found in 3% of particles with diameters in the range 0.1-2.0 microm. Single particle data were analyzed focusing on the particles with high Pb content which were mostly submicron. Using the ART-2a neural network algorithm, these fine Pb-rich particles were classified into eight main classes by their mass spectral patterns. Based on the size distribution, temporal variation of number density, chemical composition and the correlation between different chemical species for each class, three major emission sources were identified. About 45% of the Pb-rich particles contained organic or elemental carbon and were attributed to the emission from coal combustion; particles with good correlation between Cl and Pb content were mostly attributed to waste incineration. One unique class of particles was identified by strong phosphate and Pb signals, which were assigned to emissions from phosphate industry. Other Pb-rich particles included aged sea salt and particles from metallurgical processes.
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Quantitative extraction of organic tracer compounds from ambient particulate matter collected on polymer substrates.
Talanta
PUBLISHED: 01-13-2009
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Organic compounds in ambient particulate matter (PM) samples are used as tracers for PM source apportionment. These PM samples are collected using high volume samplers; one such sampler is an impactor in which polyurethane foam (PUF) and polypropylene foam (PPF) are used as the substrates. The polymer substrates have the advantage of limiting particle bounce artifacts during sampling; however these substrates may contain background organic additives. A protocol of two extractions with isopropanol followed by three extractions with dichloromethane (DCM) was developed for both substrate precleaning and analyte extraction. Some residual organic contaminants were present after precleaning; expressed as concentrations in a 24-h ambient PM sample, the residual amounts were 1 microg m(-3) for plasticizers and antioxidants, and 10 ng m(-3) for n-alkanes with carbon number lower than 26. The quantification limit for all other organic tracer compounds was approximately 0.1 ng m(-3) in a 24-h ambient PM sample. Recovery experiments were done using NIST Standard Reference Material (SRM) Urban Dust (1649a); the average recoveries for polycyclic aromatic hydrocarbons (PAHs) from PPF and PUF substrates were 117+/-8% and 107+/-11%, respectively. Replicate extractions were also done using the ambient samples collected in Nogales, Arizona. The relative differences between repeat analyses were less than 10% for 47 organic tracer compounds quantified. After the first extraction of ambient samples, less than 7% of organic tracer compounds remained in the extracted substrates. This method can be used to quantify a suite of semi- and non-polar organic tracer compounds suitable for source apportionment studies in 24-h ambient PM samples.
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Conserved amino acid markers from past influenza pandemic strains.
BMC Microbiol.
PUBLISHED: 01-09-2009
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Finding the amino acid mutations that affect the severity of influenza infections remains an open and challenging problem. Of special interest is better understanding how current circulating influenza strains could evolve into a new pandemic strain. Influenza proteomes from distinct viral phenotype classes were searched for class specific amino acid mutations conserved in past pandemics, using reverse engineered linear classifiers.
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Chemical optimization of protein extraction from sweet potato (Ipomoea batatas) peel.
J. Food Sci.
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Proteins isolated from sweet potatoes (Ipomoea batatas) have been shown to possess antidiabetic, antioxidant, and antiproliferative properties. The objective of this study was to chemically optimize a process for extracting proteins from sweet potato peel. The extraction procedure involved mixing peel with saline solvent to dissolve proteins and then precipitating with CaCl(2). Quadratic and segmented models were used to determine the optimum NaCl concentration and peel to solvent ratio to maximize protein solubility while minimizing solvent usage. A segmented model was also used to optimize the concentration of CaCl(2) used for precipitation. The highest yield was obtained by mixing blanched peelings with 59.7 mL of 0.025 mM NaCl per g peel and then precipitating with 6.8 mM CaCl(2). The results of this study show that potentially valuable proteins can be extracted from peel generated during processing of sweet potatoes and industrial costs can be minimized by using these optimum conditions.
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Draft genome sequence of the Pseudomonas aeruginosa bloodstream isolate PABL056.
J. Bacteriol.
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Pseudomonas aeruginosa is an important cause of disease in hospitalized and immunocompromised patients. The genome of P. aeruginosa is among the largest of bacteria pathogenic to humans. We present the draft genome sequence of P. aeruginosa strain PABL056, a human bloodstream isolate with the largest genome yet reported in P. aeruginosa.
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Rapid protein global fold determination using ultrasparse sampling, high-dynamic range artifact suppression, and time-shared NOESY.
J. Am. Chem. Soc.
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In structural studies of large proteins by NMR, global fold determination plays an increasingly important role in providing a first look at a targets topology and reducing assignment ambiguity in NOESY spectra of fully protonated samples. In this work, we demonstrate the use of ultrasparse sampling, a new data processing algorithm, and a 4-D time-shared NOESY experiment (1) to collect all NOEs in (2)H/(13)C/(15)N-labeled protein samples with selectively protonated amide and ILV methyl groups at high resolution in only four days, and (2) to calculate global folds from this data using fully automated resonance assignment. The new algorithm, SCRUB, incorporates the CLEAN method for iterative artifact removal but applies an additional level of iteration, permitting real signals to be distinguished from noise and allowing nearly all artifacts generated by real signals to be eliminated. In simulations with 1.2% of the data required by Nyquist sampling, SCRUB achieves a dynamic range over 10000:1 (250× better artifact suppression than CLEAN) and completely quantitative reproduction of signal intensities, volumes, and line shapes. Applied to 4-D time-shared NOESY data, SCRUB processing dramatically reduces aliasing noise from strong diagonal signals, enabling the identification of weak NOE crosspeaks with intensities 100× less than those of diagonal signals. Nearly all of the expected peaks for interproton distances under 5 Å were observed. The practical benefit of this method is demonstrated with structure calculations for 23 kDa and 29 kDa test proteins using the automated assignment protocol of CYANA, in which unassigned 4-D time-shared NOESY peak lists produce accurate and well-converged global fold ensembles, whereas 3-D peak lists either fail to converge or produce significantly less accurate folds. The approach presented here succeeds with an order of magnitude less sampling than required by alternative methods for processing sparse 4-D data.
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Effect of added calcium, phosphorus, and infant formula on calcium and phosphorus dialyzability in preterm donor human milk.
J. Pediatr. Gastroenterol. Nutr.
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We studied the effect of preparing donor human milk (DHM) with commonly used nutritional additives on the dialyzability of calcium and phosphate. We hypothesized that the additives to DHM would decrease the dialyzability of calcium and phosphate when prepared according to hospital protocols.
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CpsY influences Streptococcus iniae cell wall adaptations important for neutrophil intracellular survival.
Infect. Immun.
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The ability of a pathogen to evade neutrophil phagocytic killing mechanisms is critically important for dissemination and establishment of a systemic infection. Understanding how pathogens overcome these innate defenses is essential for the development of optimal therapeutic strategies for invasive infections. CpsY is a conserved transcriptional regulator previously identified as an important virulence determinant for systemic infection of Streptococcus iniae. While orthologs of CpsY have been associated with the regulation of methionine metabolism and uptake pathways, CpsY additionally functions in protection from neutrophil-mediated killing. S. iniae does not alter neutrophil phagosomal maturation but instead is able to adapt to the extreme bactericidal environment of a mature neutrophil phagosome, a property dependent upon CpsY. This CpsY-dependent adaptation appears to involve stabilization of the cell wall through peptidoglycan O-acetylation and repression of cellular autolysins. Furthermore, S. iniae continues to be a powerful model for investigation of bacterial adaptations during systemic streptococcal infection.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.