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In JoVE (2)
- Alimentador livre adaptação, Cultura e Passaging de células iPS humanas usando Completa KnockOut Alimentador-Free substituição Serum Médio
- Criopreservação e recuperação das células humanas iPS usando KnockOut Completa Feeder livre de substituição de soro Médio
Other Publications (60)
- Genes & Development
- Theoretical Population Biology
- Pediatric Transplantation
- Proceedings (Baylor University. Medical Center)
- Pediatric Transplantation
- Liver Transplantation : Official Publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society
- International Journal of Audiology
- The Journal of Allergy and Clinical Immunology
- The Laryngoscope
- Pediatric Research
- Pediatric Transplantation
- Genome Biology
- Pediatric Research
- PloS One
- Genes & Development
- Journal of Clinical Periodontology
- The American Journal of Tropical Medicine and Hygiene
- Current Pain and Headache Reports
- JAMA : the Journal of the American Medical Association
- Obesity (Silver Spring, Md.)
- Ear and Hearing
- Diseases of Aquatic Organisms
- PLoS Biology
- PLoS Genetics
- The Journal of Allergy and Clinical Immunology
- Journal of the Royal Society, Interface / the Royal Society
- Health Psychology : Official Journal of the Division of Health Psychology, American Psychological Association
- Human Genetics
- BMC Biology
- Physiological and Biochemical Zoology : PBZ
- The Journal of Eukaryotic Microbiology
- Journal of Clinical Microbiology
- Journal of the Royal Society, Interface / the Royal Society
- Archives of Pediatrics & Adolescent Medicine
- Environmental Microbiology
- International Journal for Parasitology
- PloS One
- FEMS Microbiology Ecology
- Emerging Infectious Diseases
- PloS One
- PloS One
- The Annals of Otology, Rhinology, and Laryngology
- International Journal of Environmental Research and Public Health
- Nucleus (Austin, Tex.)
- PloS One
- Molecular Ecology
- Proceedings of the National Academy of Sciences of the United States of America
- Molecular Ecology Resources
- BMC Genomics
- Frontiers in Microbiology
- Science (New York, N.Y.)
- PloS One
- The New Zealand Medical Journal
- Noise & Health
- PM & R : the Journal of Injury, Function, and Rehabilitation
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Articles by David Welch in JoVE
Alimentador livre adaptação, Cultura e Passaging de células iPS humanas usando Completa KnockOut Alimentador-Free substituição Serum Médio
Kate Wagner, David Welch
GIBCO, Life Technologies
O protocolo a seguir fornece instruções para a adaptação humana tronco pluripotentes induzidas (iPS) células para alimentação livre de cultura usando completa KnockOut Feeder livre de substituição de soro médio (KSR-FF). Uma vez adaptado, instruções para a manutenção contínua também são fornecidos.
Criopreservação e recuperação das células humanas iPS usando KnockOut Completa Feeder livre de substituição de soro Médio
Kate Wagner, David Welch
GIBCO, Life Technologies
Este protocolo descreve o procedimento detalhado para a criopreservação de células iPS humanas no meio de criopreservação KnockOut SR e recuperação destas células em completa KnockOut Feeder SR Free (KSR-FF) médio ou alimentação baseada em médias KnockOut SR.
Other articles by David Welch on PubMed
Transplantation. Jun, 2003 | Pubmed ID: 12829908
A new class of monoclonal antibodies (non-T-cell depleting) has gained favor for induction therapy after transplantation. This study evaluated the non-T-cell depleting antibody to the CD25 cell, daclizumab, as a single-dose induction agent immediately after pediatric liver transplantation to spare the use of the calcineurin inhibitor, tacrolimus, for 7 days in respect to both efficacy and renal function.
Mosaic Analyses Using Marked Activation and Deletion Clones Dissect Arabidopsis SCARECROW Action in Asymmetric Cell Division
Genes & Development. Aug, 2004 | Pubmed ID: 15314023
In the Arabidopsis root meristem, ground tissue stem cell daughters perform an asymmetric division to form endodermis and cortex. The putative transcription factors SCARECROW (SCR) and SHORTROOT (SHR) regulate this radial patterning event, and the mixed cell fate in scr mutants suggests an atypical role of the SCR gene in asymmetric cell division. Here we use a newly developed site-specific gene activation/deletion system in which induced clones are positively marked with green fluorescent protein (GFP). Using this system, we show that SCR acts cell-autonomously to control asymmetric cell division within the ground tissue. We provide evidence that SCR gene expression is under autoregulatory control, that SCR limits SHR movement, and that transient SCR action is sufficient to separate endodermis and cortex fates by asymmetric cell division.
Integrating Genealogy and Epidemiology: the Ancestral Infection and Selection Graph As a Model for Reconstructing Host Virus Histories
Theoretical Population Biology. Jul, 2005 | Pubmed ID: 15927223
We model the genealogies of coupled haploid host-virus populations. Hosts reproduce and replace other hosts as in the Moran model. The virus can be transmitted between individuals of the same and succeeding generations. The epidemic model allows a selective advantage for susceptible over infected hosts. The coupled host-virus ancestry of a sample of hosts is embedded in a branching and coalescing structure that we call the Ancestral Infection and Selection Graph, a direct analogue to the Ancestral Selection Graph of Krone and Neuhauser [1997. Theoret. Population Biol. 51, 210-237]. We prove this and discuss various special cases. We show that the inter-host viral genealogy is a scaled coalescent. Using simulations, we compare the viral genealogy under this model to earlier published models and investigate the estimatability of the selection and infectious contact rates. We use simulations to compare the persistence of the disease with the time to the ultimate ancestor.
Low Incidence of Hepatic Artery Thrombosis After Pediatric Liver Transplantation Without the Use of Intraoperative Microscope or Parenteral Anticoagulation
Pediatric Transplantation. Aug, 2005 | Pubmed ID: 16048601
The risk of hepatic artery thrombosis (HAT) after pediatric liver transplantation (PLT) has been reported to range from 0 to 25%. We report our experience focusing on the interrelationships between risk factors, surgical technique and the incidence of HAT after liver transplantation in the pediatric age group. From February 18, 1997 to December 31, 2003, 150 consecutive liver transplants were performed in 132 pediatric patients. There were similar numbers of whole grafts when compared with partial grafts, 80 (53.3%) vs. 70 (46.7%), p = 0.30. Four grafts (2.7%) developed HAT. Of the grafts with HAT, three were successfully revascularized within the first 24 h. Only one graft (0.66%) was lost to HAT. A single surgeon utilizing 3.5-6.0 magnification loupes performed all but one hepatic arterial anastomoses. All patients were followed postoperatively by a daily ultrasound protocol and with anticoagulation of aspirin and alprostadil only. Living and deceased donor left lateral segment grafts had an increased rate of HAT when compared with whole liver grafts. HAT with subsequent graft loss may be minimized in PLT with the use of surgical loupes only, anticoagulation utilizing aspirin, alprostadil, and daily ultrasounds.
Proceedings (Baylor University. Medical Center). Jan, 2006 | Pubmed ID: 16424925
Liver Transplant in a Four-month-old Child with Biliary Atresia, Unilateral Pulmonary Agenesis, and Diaphragmatic Hernia: First Case Report
Pediatric Transplantation. Jun, 2006 | Pubmed ID: 16712613
Bilateral pulmonary agenesis (PA) is a rare embryological defect incompatible with life. Unilateral PA has a wide range of clinical presentations: its prognosis depends on the presence and severity of other associated anomalies. Fetal biliary atresia has been associated with a number of congenital anomalies, but the etiology is still not understood. An unusual case of a child with right PA, right diaphragmatic hernia, and delayed diagnosed biliary atresia leading to liver failure is presented herein. At the age of 4 months the patient was referred to the Transplant Department at Children Healthcare of Atlanta at Egleston with cholestasis and failure to thrive. With a rapidly progressive liver insufficiency, this child was evaluated for liver transplantation. In the absence of any respiratory symptom, the patient received a deceased donor size-matched left lateral segment liver transplant, which covered the diaphragmatic defect, with no further repair required. Twenty-seven months post-transplant, the patient has good graft function, a normal Z-score and is thriving. In spite of the increased physiological and surgical challenges (absence of right lung tissue, hemi-diaphragm, and ectopic position of the liver in the right chest), liver transplantation was performed with positive outcome in this high-risk child. Whether PA, may have developmentally contributed to expression of biliary atresia will need further investigation.
Successful ABO-incompatible Pediatric Liver Transplantation Utilizing Standard Immunosuppression with Selective Postoperative Plasmapheresis
Liver Transplantation : Official Publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society. Jun, 2006 | Pubmed ID: 16721774
Transplanting blood group A, B, or O (ABO)-incompatible (ABO-I) liver grafts has resulted in lower patient and graft survival with an increased incidence of vascular and biliary complications and rejection. We report that, without modification of our standard immunosuppression protocol, crossing blood groups is an acceptable option for children requiring liver transplantation. In our study, ABO-I liver grafts -- regardless of recipient age -- have comparable long-term survival (mean follow-up of 3.25 yr) with ABO-compatible grafts without any difference in rejection, vascular or biliary complications. From January 1, 1999 to October 1, 2005, we studied 138 liver transplants in 121 children: 16 (13.2%) received an ABO incompatible liver allograft. One-year actuarial patient survival for ABO-matched grafts vs. ABO-I grafts was 93.0% and 100%, respectively, whereas graft survival was 83.4% and 92.3%. Additionally, 6 of 16 (37.5%) ABO-I transplanted children had 8 rejection episodes, whereas 47 patients (44.8%) had 121 rejection episodes in the ABO-compatible group. There were no vascular complications and 2 biliary strictures in the ABO-I group. Plasmapheresis was not used for pretransplantation desensitization and was only required in 1 posttransplantation recipient. No child was splenectomized. Six of the 16 children were older than 13 yr of age, suggesting the possibility of successfully expanding this technique to an older population. In conclusion, our outcomes may support the concept of using ABO-I grafts in a more elective setting associated with split and living donor liver transplants.
International Journal of Audiology. Jun, 2006 | Pubmed ID: 16777782
Previous research has found that childhood otitis media leads to elevated adulthood acoustic reflex thresholds because of worsened audiometric thresholds in the stimulation ear, and abnormality of the tympanic membrane in the ear from which acoustic reflexes were measured. To confirm and expand this finding, our research utilized longitudinal data from 631 general-population-sampled children assessed between ages 5 and 15. Otitis media was assessed to age 9, audiometric thresholds were measured at age 11, and otoscopy and acoustic reflex thresholds testing were performed at age 15. Our findings support the earlier research, in that acoustic reflex threshold was higher in those with the worst experience of childhood otitis media. However, this was directly mediated not by audiometric threshold in the ear to which the stimulus was delivered, but by the amount of tympanic membrane abnormality in both the stimulus and probe ears. This appeared to have an effect independent of audiometric threshold. Furthermore, only those who suffered the worst, persistent, binaural childhood otitis media showed raised acoustic reflex thresholds.
The Journal of Allergy and Clinical Immunology. Mar, 2007 | Pubmed ID: 17141852
Several studies have found obesity to be associated with an increased prevalence of asthma. For reasons that remain unclear, this association has often been reported to be stronger in women than in men. One possible explanation might be that these studies have used body mass index to identify adiposity, which might be a less reliable measure of body fat in men than in women.
The Laryngoscope. Mar, 2007 | Pubmed ID: 17334307
To test the hypothesis that childhood middle-ear disease may have disadvantageous long-term psychosocial consequences in adulthood.
Variation in the Normal Hearing Threshold Predicts Childhood IQ, Linguistic, and Behavioral Outcomes
Pediatric Research. Jun, 2007 | Pubmed ID: 17426656
Childhood hearing level varies considerably within the range considered normal. Four classes of outcome were investigated for associations with hearing thresholds in this range: ability to identify speech in noise, neurocognitive ability, linguistic ability, and behavior. The research was conducted in a general population cohort of 711 children with mean hearing threshold of 15 dB HL or better. Some outcomes: speech in noise, intelligence, and certain linguistic abilities, were predicted in both boys and girls; effects were stronger in girls. In girls only, poorer hearing predicted worse behavior. These effects remained after statistical control for childhood socioeconomic status and otitis media. Variability in normal hearing, due to causes other than otitis media, is associated with the listening, language, and neurocognitive abilities of children, and the behavior of girls. We suggest that these effects may be present for three reasons, cochlear insults, neurodevelopmental factors, and psychological factors. We discuss how these may interact to produce the effects observed.
Pediatric Transplantation. Jun, 2007 | Pubmed ID: 17493216
NH is a rare disorder of iron storage in newborns resulting in rapid liver failure. Outcomes are dismal with 20-30% survival. We report our experience in eight children with NH. Assessment of liver function included admission PT and serum levels of FV and FVII. Medical treatment (antioxidant cocktail) was started in all patients, with chelation therapy in six. Of these six, three survived with medical treatment alone. The other three underwent liver transplant. One died 158 days after transplant to sepsis: two are well more than five yr after transplant. The two neonates who did not receive chelation therapy, died to multi-organ failure and sepsis. In summary, five children (62.5%) survived long-term. In the three transplanted, one- and five-yr-survival was 66%. Older children with compromised synthetic liver function (FVII levels < or = 15%) required liver replacement for survival. Early referral to a tertiary care center is essential to increase survival of these children with a rare and otherwise fatal disease. Single center experience of children with NH is here presented. Potentials for survival improvement with of medical and surgical treatment are examined.
Genome Biology. 2007 | Pubmed ID: 17659080
Massively parallel pyrosequencing systems have increased the efficiency of DNA sequencing, although the published per-base accuracy of a Roche GS20 is only 96%. In genome projects, highly redundant consensus assemblies can compensate for sequencing errors. In contrast, studies of microbial diversity that catalogue differences between PCR amplicons of ribosomal RNA genes (rDNA) or other conserved gene families cannot take advantage of consensus assemblies to detect and minimize incorrect base calls.
Pediatric Research. Oct, 2007 | Pubmed ID: 17667854
It is known that shorter stature is associated with sensorineural hearing loss; and that cochlear development is associated with activity of IGF 1, as are many important aspects of neurodevelopment. We hypothesized that this relation might be extrapolated to a normally hearing group, and that the strongest relation between hearing level and growth rate would be in late puberty, when serum IGF-1 levels are highest. We examined the statistical relation between childhood hearing threshold and rate of growth in height at different times during the life course up to age 32. We found mixed support for the hypothesis. The strongest relations were observed in late puberty, at the ages which previous research shows are associated with the highest serum concentrations of IGF-1 in males and females, but also in infancy and early childhood. The association between hearing and height is present in a normally hearing, general population sample, and is associated with growth in late adolescence. Our findings support the idea that childhood hearing threshold may be predictive of IGF-1 mediated developmental characteristics.
PloS One. 2007 | Pubmed ID: 17668053
Rotifers are among the most common non-arthropod animals and are the most experimentally tractable members of the basal assemblage of metazoan phyla known as Gnathifera. The monogonont rotifer Brachionus plicatilis is a developing model system for ecotoxicology, aquatic ecology, cryptic speciation, and the evolution of sex, and is an important food source for finfish aquaculture. However, basic knowledge of the genome and transcriptome of any rotifer species has been lacking.
Does Childhood Television Viewing Lead to Attention Problems in Adolescence? Results from a Prospective Longitudinal Study
Pediatrics. Sep, 2007 | Pubmed ID: 17766526
There is controversy over whether childhood television viewing causes attention problems. The findings from cross-sectional and longitudinal studies have been mixed. To our knowledge, no longitudinal studies have assessed the impact of children's television viewing on attention problems in adolescence. The objective of this study was to assess this association. DESIGN, PARTICIPANTS, AND SETTING: Study members were a general population birth cohort of 1037 participants (502 female) born in Dunedin, New Zealand, between April 1972 and March 1973. Parental estimates of children's television-viewing time were obtained at ages 5, 7, 9, and 11 years. Self-, parent-, and teacher-reported attention problems in adolescence were obtained at ages 13 and 15 years.
Arabidopsis JACKDAW and MAGPIE Zinc Finger Proteins Delimit Asymmetric Cell Division and Stabilize Tissue Boundaries by Restricting SHORT-ROOT Action
Genes & Development. Sep, 2007 | Pubmed ID: 17785527
In the Arabidopsis root, the SHORT-ROOT transcription factor moves outward to the ground tissue from its site of transcription in the stele and is required for the specification of the endodermis and the stem cell organizing quiescent center cells. In addition, SHORT-ROOT and the downstream transcription factor SCARECROW control an oriented cell division in ground tissue stem cell daughters. Here, we show that the JACKDAW and MAGPIE genes, which encode members of a plant-specific family of zinc finger proteins, act in a SHR-dependent feed-forward loop to regulate the range of action of SHORT-ROOT and SCARECROW. JACKDAW expression is initiated independent of SHORT-ROOT and regulates the SCARECROW expression domain outside the stele, while MAGPIE expression depends on SHORT-ROOT and SCARECROW. We provide evidence that JACKDAW and MAGPIE regulate tissue boundaries and asymmetric cell division and can control SHORT-ROOT and SCARECROW activity in a transcriptional and protein interaction network.
Cigarette Smoking and Periodontal Disease Among 32-year-olds: a Prospective Study of a Representative Birth Cohort
Journal of Clinical Periodontology. Oct, 2007 | Pubmed ID: 17850601
Smoking is recognized as the primary behavioural risk factor for periodontal attachment loss (AL), but confirmatory data from prospective cohort studies are scarce.
Transmission Dynamics of Cryptosporidium Infection in a Natural Population of Non-human Primates at Polonnaruwa, Sri Lanka
The American Journal of Tropical Medicine and Hygiene. Nov, 2007 | Pubmed ID: 17984333
Infections from Cryptosporidium parvum are of interest not only to public health, but also to wildlife conservation, particularly when humans and livestock encroach on nature and thereby increase the risk of cross-species transmissions. To clarify this risk, we used polymerase chain reaction to examine the hypervariable region of the C. parvum 18S rRNA gene in feces from three monkey species. Samples were isolated from regions where disease transmission between monkeys, livestock, and humans was likely (soiled habitat) or unlikely (clean habitat). Monkey individuals, their social groups, and different species shared multiple genotypes/isolates of C. parvum. Ecological and molecular analyses suggested that Cryptosporidium infection among Toque macaques in soiled habitats was mainly the bovine genotype C. parvum. Monkeys inhabiting clean habitat, particularly gray and purple-faced langurs, lacked Cryptosporidium species/types associated with bovines. Livestock apparently was a main source of infection for wild primates.
Current Pain and Headache Reports. Dec, 2007 | Pubmed ID: 18173981
The association between tension-type headache and cognitive ability was assessed among 971 members of a longitudinal birth cohort study. Primary headache status was determined at age 32 years according to 2004 International Headache Society criteria, frequent childhood headaches were identified from parent report from ages 7 to 13 years, and data relating to cognitive and academic performance from ages 3 to 32 years were analyzed. Adult study members with tension-type headache did not score worse on any of the cognitive measures relative to headache-free controls or headache-free tinnitus sufferers. Instead, a consistent relation was found between childhood headache (regardless of headache diagnosis in adulthood) and lower scores on most cognitive measures from age 3 years through adolescence (verbal and performance IQ, receptive language, and reading scores). The data indicate that cognitive performance deficits in childhood headache sufferers can probably be attributed to factors stemming from utero or early childhood.
JAMA : the Journal of the American Medical Association. Feb, 2008 | Pubmed ID: 18252882
Tobacco smoking is a recognized behavioral risk factor for periodontal disease (through its systemic effects), and cannabis smoking may contribute in a similar way.
Obesity (Silver Spring, Md.). Jun, 2008 | Pubmed ID: 18369346
To assess whether the long-term effects of childhood television viewing on BMI and cardiorespiratory fitness are mediated by adult viewing.
Ear and Hearing. Oct, 2008 | Pubmed ID: 18596645
Tinnitus has high prevalence and a wide range of etiologies and of impacts on sufferers. Our objective was to develop understanding of the role of personality in the perception of tinnitus in the general population. As a theoretical basis for this, we combined elements of a general model of signal detection with the ideas of ignition (development) and promotion (neural transmission) of tinnitus, and considered plausible roles for personality factors within this conceptual framework.
Molecular Characterization of Giardia Intestinalis Haplotypes in Marine Animals: Variation and Zoonotic Potential
Diseases of Aquatic Organisms. Aug, 2008 | Pubmed ID: 18828561
Giardia intestinalis is a microbial eukaryotic parasite that causes diarrheal disease in humans and other vertebrates worldwide. The negative effect on quality of life and economics caused by G. intestinalis may be increased by its potential status as a zoonosis, or a disease that can be transmitted from animals to humans. The zoonotic potential of G. intestinalis has been implied for over 2 decades, with human-infecting genotypes (belonging to the 2 major subgroups, Assemblages A and B) occurring in wildlife and domesticated animals. There are recent reports of G. intestinalis in shellfish, seals, sea lions and whales, suggesting that marine animals are also potential reservoirs of human disease. However, the prevalence, genetic diversity and effect of G. intestinalis in marine environments and the role that marine animals play in transmission of this parasite to humans are relatively unexplored. Here, we provide the first thorough molecular characterization of G. intestinalis in marine vertebrates. Using a multi-locus sequencing approach, we identify human-infecting G. intestinalis haplotypes of both Assemblages A and B in the fecal material of dolphins, porpoises, seals, herring gulls Larus argentatus, common eiders Somateria mollissima and a thresher shark Alopias vulpinus. Our results indicate that G. intestinalis is prevalent in marine ecosystems, and a wide range of marine hosts capable of harboring zoonotic forms of this parasite exist. The presence of G. intestinalis in marine ecosystems raises concerns about how this disease might be transmitted among different host species.
PLoS Biology. Oct, 2008 | Pubmed ID: 18959485
The mortality of salmon smolts during their migration out of freshwater and into the ocean has been difficult to measure. In the Columbia River, which has an extensive network of hydroelectric dams, the decline in abundance of adult salmon returning from the ocean since the late 1970s has been ascribed in large measure to the presence of the dams, although the completion of the hydropower system occurred at the same time as large-scale shifts in ocean climate, as measured by climate indices such as the Pacific Decadal Oscillation. We measured the survival of salmon smolts during their migration to sea using elements of the large-scale acoustic telemetry system, the Pacific Ocean Shelf Tracking (POST) array. Survival measurements using acoustic tags were comparable to those obtained independently using the Passive Integrated Transponder (PIT) tag system, which is operational at Columbia and Snake River dams. Because the technology underlying the POST array works in both freshwater and the ocean, it is therefore possible to extend the measurement of survival to large rivers lacking dams, such as the Fraser, and to also extend the measurement of survival to the lower Columbia River and estuary, where there are no dams. Of particular note, survival during the downstream migration of at least some endangered Columbia and Snake River Chinook and steelhead stocks appears to be as high or higher than that of the same species migrating out of the Fraser River in Canada, which lacks dams. Equally surprising, smolt survival during migration through the hydrosystem, when scaled by either the time or distance migrated, is higher than in the lower Columbia River and estuary where dams are absent. Our results raise important questions regarding the factors that are preventing the recovery of salmon stocks in the Columbia and the future health of stocks in the Fraser River.
Pediatrics. Nov, 2008 | Pubmed ID: 18977973
Associations between short sleep duration and increased BMI have been found in children and adults. However, it is not known whether short sleep time during childhood has long-term consequences. We assessed the association between sleep time in childhood and adult BMI in a birth cohort.
PLoS Genetics. Nov, 2008 | Pubmed ID: 19023400
Massively parallel pyrosequencing of hypervariable regions from small subunit ribosomal RNA (SSU rRNA) genes can sample a microbial community two or three orders of magnitude more deeply per dollar and per hour than capillary sequencing of full-length SSU rRNA. As with full-length rRNA surveys, each sequence read is a tag surrogate for a single microbe. However, rather than assigning taxonomy by creating gene trees de novo that include all experimental sequences and certain reference taxa, we compare the hypervariable region tags to an extensive database of rRNA sequences and assign taxonomy based on the best match in a Global Alignment for Sequence Taxonomy (GAST) process. The resulting taxonomic census provides information on both composition and diversity of the microbial community. To determine the effectiveness of using only hypervariable region tags for assessing microbial community membership, we compared the taxonomy assigned to the V3 and V6 hypervariable regions with the taxonomy assigned to full-length SSU rRNA sequences isolated from both the human gut and a deep-sea hydrothermal vent. The hypervariable region tags and full-length rRNA sequences provided equivalent taxonomy and measures of relative abundance of microbial communities, even for tags up to 15% divergent from their nearest reference match. The greater sampling depth per dollar afforded by massively parallel pyrosequencing reveals many more members of the "rare biosphere" than does capillary sequencing of the full-length gene. In addition, tag sequencing eliminates cloning bias and the sequences are short enough to be completely sequenced in a single read, maximizing the number of organisms sampled in a run while minimizing chimera formation. This technique allows the cost-effective exploration of changes in microbial community structure, including the rare biosphere, over space and time and can be applied immediately to initiatives, such as the Human Microbiome Project.
The Journal of Allergy and Clinical Immunology. Jan, 2008 | Pubmed ID: 18061657
Cigarette smoke has immunosuppressant effects, but its effect on allergic sensitization is unclear.
Approximate Bayesian Computation Scheme for Parameter Inference and Model Selection in Dynamical Systems
Journal of the Royal Society, Interface / the Royal Society. Feb, 2009 | Pubmed ID: 19205079
Approximate Bayesian computation (ABC) methods can be used to evaluate posterior distributions without having to calculate likelihoods. In this paper, we discuss and apply an ABC method based on sequential Monte Carlo (SMC) to estimate parameters of dynamical models. We show that ABC SMC provides information about the inferability of parameters and model sensitivity to changes in parameters, and tends to perform better than other ABC approaches. The algorithm is applied to several well-known biological systems, for which parameters and their credible intervals are inferred. Moreover, we develop ABC SMC as a tool for model selection; given a range of different mathematical descriptions, ABC SMC is able to choose the best model using the standard Bayesian model selection apparatus.
Health Psychology : Official Journal of the Division of Health Psychology, American Psychological Association. May, 2009 | Pubmed ID: 19450034
To investigate associations between personality traits in early adulthood (and changes in them) and change in smoking status.
Accelerated Decline in Lung Function in Cigarette Smokers is Associated with TP53/MDM2 Polymorphisms
Human Genetics. Oct, 2009 | Pubmed ID: 19521721
In vitro studies have shown that p53 mediates a protective response against DNA damage by causing either cell-cycle arrest and DNA repair, or apoptosis. These responses have not yet been demonstrated in humans. A common source of DNA damage in humans is cigarette smoke, which should activate p53 repair mechanisms. As the level of p53 is regulated by MDM2, which targets p53 for degradation, the G-allele of a polymorphism in intron 1 of MDM2 (rs2279744:G/T), that results in higher MDM2 levels, should be associated with a reduced p53 response and hence more DNA damage and corresponding tissue destruction. Similarly, the alleles of rs1042522 in TP53 that encode arginine (G-allele) or proline (C-allele) at codon 72, which cause increased pro-apoptotic (G-allele) or cell-cycle arrest activities (C-allele), respectively, may moderate p53's ability to prevent DNA damage. To test these hypotheses, we examined lung function in relation to cumulative history of smoking in a population-based cohort. The G-alleles in MDM2 and TP53 were found to be associated with accelerated smoking-related decline in lung function. These data support the hypothesis that p53 protects from DNA damage in humans and provides a potential explanation for the variation in lung function impairment amongst smokers.
BMC Biology. 2009 | Pubmed ID: 19740420
Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recognition pheromone. The mate recognition pheromone has been biochemically characterized, but little was known about the gene(s). We describe the isolation and characterization of the mate recognition pheromone gene through protein purification, N-terminal amino acid sequence determination, identification of the mate recognition pheromone gene from a cDNA library, sequencing, and RNAi knockdown to confirm the functional role of the mate recognition pheromone gene in rotifer mating.
Mechanisms Influencing the Timing and Success of Reproductive Migration in a Capital Breeding Semelparous Fish Species, the Sockeye Salmon
Physiological and Biochemical Zoology : PBZ. Nov-Dec, 2009 | Pubmed ID: 19780650
Two populations of homing sockeye salmon (Oncorhynchus nerka; Adams and Chilko) were intercepted in the marine approaches around the northern and southern ends of Vancouver Island (British Columbia, Canada) en route to a natal river. More than 500 salmon were nonlethally biopsied for blood plasma, gill filament tips, and gross somatic energy (GSE) and were released with either acoustic or radio transmitters. At the time of capture, GSE, body length, and circulating testosterone ([T]) differed between populations, differences that reflected known life-history variations. Within-population analyses showed that in Adams sockeye salmon, plasma glucose ([glu]), lactate ([lactate]), and ion concentrations were higher in the northern approach than in the southern approach, suggesting that the former was more stressful. GSE, [T], and gill Na(+),K(+)-ATPase activities also differed between the two locales, and each varied significantly with Julian date, suggesting seasonality. Despite these relative geographic differences, the timing of river entry and the ability to reach spawning areas were strongly correlated with energetic, reproductive, and osmoregulatory state. Salmon that delayed river entry and reached spawning areas had relatively high GSE and low [T] and gill ATPase. In contrast, salmon that entered the river directly but that ultimately failed to reach spawning areas had lower GSE and higher [T] and gill ATPase, and they also swam at significantly faster rates (failed fish approximately 20.0 km d(-1) vs. successful fish approximately 15.5 km d(-1)). Physiologically, salmon that did not enter the river at all but that presumably died in the marine environment exhibited high stress (plasma [glu] and [lactate]) and ionoregulatory measures (plasma [Na(+)], [Cl(-)], osmolality).
The Journal of Eukaryotic Microbiology. Nov-Dec, 2009 | Pubmed ID: 19883439
Meiotic sex evolved early in the history of eukaryotes. Giardia duodenalis (syn. Giardia lamblia, Giardia intestinalis), a parasitic protist belonging to an early diverging lineage of eukaryotes, shows no cytological or physiological evidence of meiotic or sexual processes. Recent molecular analyses challenge the idea that G. duodenalis is a strictly clonal organism by providing evidence of recombination between homologous chromosomes within one subgroup (Assemblage A) of this species as well as genetic transfer from one subgroup to another (Assemblage A-B). Because recombination is not well documented and because it is not known whether the observed inter-assemblage transfer represents true reciprocal genetic exchange or a non-sexual process, we analyzed genic sequences from all major subgroups (Assemblages A-G) of this species. For all assemblages, we detected molecular signatures consistent with meiotic sex or genetic exchange, including low levels of heterozygosity, as indicated by allelic sequence divergence within isolates, and intra- and inter-assemblage recombination. The identification of recombination between assemblages suggests a shared gene pool and calls into question whether it is appropriate to divide the genetically distinct assemblages of G. duodenalis into a species complex.
Role of Rapid Immunochromatographic Antigen Testing in Diagnosis of Influenza A Virus 2009 H1N1 Infection
Journal of Clinical Microbiology. Jan, 2010 | Pubmed ID: 20007399
Rapid antigen testing using immunochromatographic devices has become a diagnostic mainstay for detection of influenza virus and respiratory syncytial virus, the two major viruses infecting the respiratory tract. Recent studies have indicated that poor performance in the detection of the novel influenza A virus 2009 H1N1 should preclude their use. A survey of influenza diagnostic methods available on ClinMicroNet and Division C, the two ASM list servers, revealed that, despite this reported poor performance, a majority of the laboratories surveyed intend to continue to offer this testing during the current influenza season. Our two experts have been asked to consider the following question: what is the role of rapid immunochromatographic antigen testing in the laboratory diagnosis of influenza A virus infection during the current 2009 H1N1 pandemic?
Journal of the Royal Society, Interface / the Royal Society. Jul, 2010 | Pubmed ID: 20147314
With more emphasis being put on global infectious disease monitoring, viral genetic data are being collected at an astounding rate, both within and without the context of a long-term disease surveillance plan. Concurrent with this increase have come improvements to the sophisticated and generalized statistical techniques used for extracting population-level information from genetic sequence data. However, little research has been done on how the collection of these viral sequence data can or does affect the efficacy of the phylogenetic algorithms used to analyse and interpret them. In this study, we use epidemic simulations to consider how the collection of viral sequence data clarifies or distorts the picture, provided by the phylogenetic algorithms, of the underlying population dynamics of the simulated viral infection over many epidemic cycles. We find that sampling protocols purposefully designed to capture sequences at specific points in the epidemic cycle, such as is done for seasonal influenza surveillance, lead to a significantly better view of the underlying population dynamics than do less-focused collection protocols. Our results suggest that the temporal distribution of samples can have a significant effect on what can be inferred from genetic data, and thus highlight the importance of considering this distribution when designing or evaluating protocols and analysing the data collected thereunder.
Archives of Pediatrics & Adolescent Medicine. Mar, 2010 | Pubmed ID: 20194259
To examine associations between screen time (television, video or DVD, gaming, and computer use) and attachment to parents and peers in 2 cohorts of adolescents 16 years apart.
Environmental Microbiology. Jul, 2010 | Pubmed ID: 20236171
Deep sequencing of PCR amplicon libraries facilitates the detection of low-abundance populations in environmental DNA surveys of complex microbial communities. At the same time, deep sequencing can lead to overestimates of microbial diversity through the generation of low-frequency, error-prone reads. Even with sequencing error rates below 0.005 per nucleotide position, the common method of generating operational taxonomic units (OTUs) by multiple sequence alignment and complete-linkage clustering significantly increases the number of predicted OTUs and inflates richness estimates. We show that a 2% single-linkage preclustering methodology followed by an average-linkage clustering based on pairwise alignments more accurately predicts expected OTUs in both single and pooled template preparations of known taxonomic composition. This new clustering method can reduce the OTU richness in environmental samples by as much as 30-60% but does not reduce the fraction of OTUs in long-tailed rank abundance curves that defines the rare biosphere.
The Identification of a New Giardia Duodenalis Assemblage in Marine Vertebrates and a Preliminary Analysis of G. Duodenalis Population Biology in Marine Systems
International Journal for Parasitology. Aug, 2010 | Pubmed ID: 20361967
Giardia duodenalis is an intestinal parasite of many vertebrates. The presence of G. duodenalis in the marine environment due to anthropogenic and wildlife activity is well documented, including the contributions from untreated sewage and storm water, agricultural run-off and droppings from terrestrial animals. Recently, studies have detected this protistan parasite in the faeces of marine vertebrates such as whales, dolphins, seals and shore birds. To explore the population biology of G. duodenalis in marine life, we determined the prevalence of G. duodenalis in two species of seal (Halichoerus grypus, Phoca vitulina vitulina and Phoca vitulina richardsi) from the east and west coasts of the USA, sequenced two loci from G. duodenalis-positive samples to assess molecular diversity and examined G. duodenalis distribution amongst these seals and other marine vertebrates along the east coast. We found a significant difference in the presence of G. duodenalis between east and west coast seal species. Only the zoonotic lineages of G. duodenalis, Assemblages A and B and a novel lineage, which we designated as Assemblage H, were identified in marine vertebrates. Assemblages A and B are broadly distributed geographically and show a lack of host specificity. Only grey seal (Halichoerus grypus) samples and one gull sample (Larus argentatus) from a northern location of Cape Cod, Massachusetts, USA, showed the presence of Assemblage H haplotypes; only one other study of harbour seals from the Puget Sound region of Washington, USA previously recorded the presence of an Assemblage H haplotype. Assemblage H sequences form a monophyletic clade that appears as divergent from the other seven Assemblages of G. duodenalis as these assemblages are from each other. The discovery of a previously uncharacterised lineage of G. duodenalis suggests that this parasite has more genetic diversity and perhaps a larger host range than previously believed.
PloS One. 2010 | Pubmed ID: 20526367
To investigate reasons for the decline of an endangered population of coho salmon (O. kisutch), 190 smolts were acoustically tagged during three consecutive years and their movements and survival were estimated using the Pacific Ocean Shelf Tracking project (POST) array. Median travel times of the Thompson River coho salmon smolts to the lower Fraser River sub-array were 16, 12 and 10 days during 2004, 2005 and 2006, respectively. Few smolts were recorded on marine arrays. Freshwater survival rates of the tagged smolts during their downstream migration were 0.0-5.6% (0.0-9.0% s.e.) in 2004, 7.0% (6.2% s.e.) in 2005, and 50.9% (18.6% s.e.) in 2006. Overall smolt-to-adult return rates exhibited a similar pattern, which suggests that low freshwater survival rates of out-migrating smolts may be a primary reason for the poor conservation status of this endangered coho salmon population.
Isolated Communities of Epsilonproteobacteria in Hydrothermal Vent Fluids of the Mariana Arc Seamounts
FEMS Microbiology Ecology. Sep, 2010 | Pubmed ID: 20533947
Low-temperature hydrothermal vent fluids represent access points to diverse microbial communities living in oceanic crust. This study examined the distribution, relative abundance, and diversity of Epsilonproteobacteria in 14 low-temperature vent fluids from five volcanically active seamounts of the Mariana Arc using a 454 tag sequencing approach. Most vent fluids were enriched in cell concentrations compared with background seawater, and quantitative PCR results indicated that all fluids were dominated by bacteria. Operational taxonomic unit-based statistical tools applied to 454 data show that all vents from the northern end of the Mariana Arc grouped together, to the exclusion of southern arc seamounts, which were as distinct from one another as they were from northern seamounts. Statistical analysis also showed a significant relationship between seamount and individual vent groupings, suggesting that community membership may be linked to geographical isolation and not geochemical parameters. However, while there may be large-scale geographic differences, distance is not the distinguishing factor in the microbial community composition. At the local scale, most vents host a distinct population of Epsilonproteobacteria, regardless of seamount location. This suggests that there may be barriers to exchange and dispersal for these vent endemic microorganisms at hydrothermal seamounts of the Mariana Arc.
Emerging Infectious Diseases. Sep, 2010 | Pubmed ID: 20735916
Chronic granulomatous disease (CGD) is characterized by frequent infections, most of which are curable. Granulibacter bethesdensis is an emerging pathogen in patients with CGD that causes fever and necrotizing lymphadenitis. However, unlike typical CGD organisms, this organism can cause relapse after clinical quiescence. To better define whether infections were newly acquired or recrudesced, we use comparative bacterial genomic hybridization to characterize 11 isolates obtained from 5 patients with CGD from North and Central America. Genomic typing showed that 3 patients had recurrent infection months to years after apparent clinical cure. Two patients were infected with the same strain as previously isolated, and 1 was infected with a genetically distinct strain. This organism is multidrug resistant, and therapy required surgery and combination antimicrobial drugs, including long-term ceftriaxone. G. bethesdensis causes necrotizing lymphadenitis in CGD, which may recur or relapse.
PloS One. 2010 | Pubmed ID: 20805978
As the timing of spring productivity blooms in near-shore areas advances due to warming trends in global climate, the selection pressures on out-migrating salmon smolts are shifting. Species and stocks that leave natal streams earlier may be favoured over later-migrating fish. The low post-release survival of hatchery fish during recent years may be in part due to static release times that do not take the timing of plankton blooms into account. This study examined the effects of release time on the migratory behaviour and survival of wild and hatchery-reared coho salmon (Oncorhynchus kisutch) using acoustic and coded-wire telemetry. Plankton monitoring and near-shore seining were also conducted to determine which habitat and food sources were favoured. Acoustic tags (n = 140) and coded-wire tags (n = 266,692) were implanted into coho salmon smolts at the Seymour and Quinsam Rivers, in British Columbia, Canada. Differences between wild and hatchery fish, and early and late releases were examined during the entire lifecycle. Physiological sampling was also carried out on 30 fish from each release group. The smolt-to-adult survival of coho salmon released during periods of high marine productivity was 1.5- to 3-fold greater than those released both before and after, and the fish's degree of smoltification affected their downstream migration time and duration of stay in the estuary. Therefore, hatchery managers should consider having smolts fully developed and ready for release during the peak of the near-shore plankton blooms. Monitoring chlorophyll a levels and water temperature early in the spring could provide a forecast of the timing of these blooms, giving hatcheries time to adjust their release schedule.
PloS One. 2010 | Pubmed ID: 20886121
Migrations allow animals to find food resources, rearing habitats, or mates, but often impose considerable predation risk. Several behavioural strategies may reduce this risk, including faster travel speed and taking routes with shorter total distance. Descriptions of the natural range of variation in migration strategies among individuals and populations is necessary before the ecological consequences of such variation can be established.
The Annals of Otology, Rhinology, and Laryngology. Oct, 2010 | Pubmed ID: 21049852
Tinnitus is associated with hearing loss in adulthood, often resulting from noise or age, but it is not known whether children's hearing and/or middle ear health predispose them to tinnitus in adulthood.
Exploring the Relationship Between Noise Sensitivity, Annoyance and Health-related Quality of Life in a Sample of Adults Exposed to Environmental Noise
International Journal of Environmental Research and Public Health. Oct, 2010 | Pubmed ID: 21139850
The relationship between environmental noise and health is poorly understood but of fundamental importance to public health. This study estimated the relationship between noise sensitivity, noise annoyance and health-related quality of life in a sample of adults residing close to the Auckland International Airport, New Zealand. A small sample (n = 105) completed surveys measuring noise sensitivity, noise annoyance, and quality of life. Noise sensitivity was associated with health-related quality of life; annoyance and sleep disturbance mediated the effects of noise sensitivity on health.
Nucleus (Austin, Tex.). Jan-Feb, 2010 | Pubmed ID: 21327105
Lamin B receptor (LBR) is an integral membrane protein of the interphase nuclear envelope (NE). The N-terminal end resides in the nucleoplasm, binding to lamin B and heterochromatin, with the interactions disrupted during mitosis. The C-terminal end resides within the inner nuclear membrane, retreating with the ER away from condensing chromosomes during mitotic NE breakdown. Some of these properties are interpretable in terms of our current structural knowledge of LBR, but many of the structural features remain unknown. LBR apparently has an evolutionary history which brought together at least two ancient conserved structural domains (i.e., Tudor and sterol reductase). This convergence may have occurred with the emergence of the chordates and echinoderms. It is not clear what survival values have maintained LBR structure during evolution. But it seems likely that roles in post-mitotic nuclear reformation, interphase NE growth and compartmentalization of nuclear architecture might have provided some evolutionary advantage to preservation of the LBR gene.
Epidemics. Mar, 2011 | Pubmed ID: 21420658
Contact networks are playing an increasingly important role in the study of epidemiology. Most of the existing work in this area has focused on considering the effect of underlying network structure on epidemic dynamics by using tools from probability theory and computer simulation. This work has provided much insight on the role that heterogeneity in host contact patterns plays on infectious disease dynamics. Despite the important understanding afforded by the probability and simulation paradigm, this approach does not directly address important questions about the structure of contact networks such as what is the best network model for a particular mode of disease transmission, how parameter values of a given model should be estimated, or how precisely the data allow us to estimate these parameter values. We argue that these questions are best answered within a statistical framework and discuss the role of statistical inference in estimating contact networks from epidemiological data.
The Effect of Hatchery Release Strategy on Marine Migratory Behaviour and Apparent Survival of Seymour River Steelhead Smolts (Oncorhynchus Mykiss)
PloS One. 2011 | Pubmed ID: 21468320
Early marine migratory behaviour and apparent survival of hatchery-reared Seymour River steelhead (Oncorhynchus mykiss) smolts was examined over a four year period (2006-2009) to assess the impact of various management strategies on improving early marine survival. Acoustically tagged smolts were released to measure their survival using estuary and coastal marine receivers forming components of the Pacific Ocean Shelf Tracking (POST) array. Early marine survival was statistically indistinguishable between releases of summer run and winter run steelhead races, night and day releases, and groups released 10 days apart. In 2009, the survival of summer run steelhead released into the river was again trialed against groups released directly into the ocean at a distance from the river mouth. Apparent survival was improved significantly for the ocean released groups. The health and physiological status of the various release groups were monitored in years 2007-2009, and results indicate that the fish were in good health, with no clinical signs of disease at the time of release. The possibility of a disease event contributing to early marine mortality was further examined in 2009 by vaccinating half of the released fish against common fish diseases (vibriosis, furunculosis). The results suggest that marine survival may be enhanced using this approach, although not to the extent observed when the smolts were transported away from the river mouth before release. In summary, direct experimental testing of different release strategies using the POST array to measure ocean survival accelerated the scientific process by allowing rapid collection of data which enabled the rejection of several existing theories and allowed tentative identification of several new alternative approaches that might improve early marine survival of Seymour River steelhead.
Limited Ecological Population Connectivity Suggests Low Demands on Self-recruitment in a Tropical Inshore Marine Fish (Eleutheronema Tetradactylum: Polynemidae)
Molecular Ecology. Jun, 2011 | Pubmed ID: 21518062
The diversity of geographic scales at which marine organisms display genetic variation mirrors the biophysical and ecological complexity of dispersal by pelagic larvae. Yet little is known about the effect of larval ecology on genetic population patterns, partly because detailed data of larval ecology do not yet exist for most taxa. One species for which this data is available is Eleutheronema tetradactylum, a tropical Indo-West Pacific shorefish. Here, we use a partial sequence mitochondrial cytochrome oxidase subunit 1 (COI) marker and five microsatellite loci to survey the genetic structure of E. tetradactylum across northern Australia. Structure was found throughout the range and isolation by distance was strong, explaining approximately 87 and 64% of the genetic variation in microsatellites and mtDNA, respectively. Populations separated by as little as 15 km also showed significant genetic structure, implying that local populations are mainly insular and self-seeding on an ecological time frame. Because the larvae of E. tetradactylum have lower swimming performance and poor orientation compared with other tropical fishes, even modest larval abilities may permit self-recruitment rather than passive dispersal.
Proceedings of the National Academy of Sciences of the United States of America. May, 2011 | Pubmed ID: 21558442
Many salmon populations in both the Pacific and Atlantic Oceans have experienced sharply decreasing returns and high ocean mortality in the past two decades, with some populations facing extirpation if current marine survival trends continue. Our inability to monitor the movements of marine fish or to directly measure their survival precludes experimental tests of theories concerning the factors regulating fish populations, and thus limits scientific advance in many aspects of fisheries management and conservation. Here we report a large-scale synthesis of survival and movement rates of free-ranging juvenile salmon across four species, 13 river watersheds, and 44 release groups of salmon smolts (>3,500 fish tagged in total) in rivers and coastal ocean waters, including an assessment of where mortality predominantly occurs during the juvenile migration. Of particular importance, our data indicate that, over the size range of smolts tagged, (i) smolt survival was not strongly related to size at release, (ii) tag burden did not appear to strongly reduce the survival of smaller animals, and (iii) for at least some populations, substantial mortality occurred much later in the migration and more distant from the river of origin than generally expected. Our findings thus have implications for determining where effort should be invested to improve the accuracy of salmon forecasting, to understand the mechanisms driving salmon declines, and to predict the impact of climate change on salmon stocks.
A Mitochondrial Species Identification Assay for Australian Blacktip Sharks (Carcharhinus Tilstoni, C. Limbatus and C. Amblyrhynchoides) Using Real-time PCR and High-resolution Melt Analysis
Molecular Ecology Resources. Sep, 2011 | Pubmed ID: 21565127
Tropical Australian shark fisheries target two morphologically indistinguishable blacktip sharks, the Australian blacktip (Carcharhinus tilstoni) and the common blacktip (C. limbatus). Their relative contributions to northern and eastern Australian coastal fisheries are unclear because of species identification difficulties. The two species differ in their number of precaudal vertebrae, which is difficult and time consuming to obtain in the field. But, the two species can be distinguished genetically with diagnostic mutations in their mitochondrial DNA ND4 gene. A third closely related sister species, the graceful shark C. amblyrhynchoides, can also be distinguished by species-specific mutations in this gene. DNA sequencing is an effective diagnostic tool, but is relatively expensive and time consuming. In contrast, real-time high-resolution melt (HRM) PCR assays are rapid and relatively inexpensive. These assays amplify regions of DNA with species-specific genetic mutations that result in PCR products with unique melt profiles. A real-time HRM PCR species-diagnostic assay (RT-HRM-PCR) has been developed based on the mtDNA ND4 gene for rapid typing of C. tilstoni, C. limbatus and C. amblyrhynchoides. The assay was developed using ND4 sequences from 66 C. tilstoni, 33. C. limbatus and five C. amblyrhynchoides collected from Indonesia and Australian states and territories; Western Australia, the Northern Territory, Queensland and New South Wales. The assay was shown to be 100% accurate on 160 unknown blacktip shark tissue samples by full mtDNA ND4 sequencing.
Transcriptomic Assessment of Resistance to Effects of an Aryl Hydrocarbon Receptor (AHR) Agonist in Embryos of Atlantic Killifish (Fundulus Heteroclitus) from a Marine Superfund Site
BMC Genomics. 2011 | Pubmed ID: 21609454
Populations of Atlantic killifish (Fundulus heteroclitus) have evolved resistance to the embryotoxic effects of polychlorinated biphenyls (PCBs) and other halogenated and nonhalogenated aromatic hydrocarbons that act through an aryl hydrocarbon receptor (AHR)-dependent signaling pathway. The resistance is accompanied by reduced sensitivity to induction of cytochrome P450 1A (CYP1A), a widely used biomarker of aromatic hydrocarbon exposure and effect, but whether the reduced sensitivity is specific to CYP1A or reflects a genome-wide reduction in responsiveness to all AHR-mediated changes in gene expression is unknown. We compared gene expression profiles and the response to 3,3',4,4',5-pentachlorobiphenyl (PCB-126) exposure in embryos (5 and 10 dpf) and larvae (15 dpf) from F. heteroclitus populations inhabiting the New Bedford Harbor, Massachusetts (NBH) Superfund site (PCB-resistant) and a reference site, Scorton Creek, Massachusetts (SC; PCB-sensitive).
Viruses. Jun, 2011 | Pubmed ID: 21731813
Networks are often used to model the contact processes that allow pathogens to spread between hosts but it remains unclear which models best describe these networks. One question is whether clustering in networks, roughly defined as the propensity for triangles to form, affects the dynamics of disease spread. We perform a simulation study to see if there is a signal in epidemic transmission trees of clustering. We simulate susceptible-exposed-infectious-removed (SEIR) epidemics (with no re-infection) over networks with fixed degree sequences but different levels of clustering and compare trees from networks with the same degree sequence and different clustering levels. We find that the variation of such trees simulated on networks with different levels of clustering is barely greater than those simulated on networks with the same level of clustering, suggesting that clustering can not be detected in transmission data when re-infection does not occur.
Long Term Seasonal Dynamics of Synechococcus Population Structure in the Gulf of Aqaba, Northern Red Sea
Frontiers in Microbiology. 2011 | Pubmed ID: 21734910
Spatial patterns of marine Synechococcus diversity across ocean domains have been reported on extensively. However, much less is known of seasonal and multiannual patterns of change in Synechococcus community composition. Here we report on the genotypic diversity of Synechococcus populations in the Gulf of Aqaba, Northern Red Sea, over seven annual cycles of deep mixing and stabile stratification, using ntcA as a phylogenetic marker. Synechococcus clone libraries were dominated by clade II and XII genotypes and a total of eight different clades were identified. Inclusion of ntcA sequences from the Global Ocean Sampling database in our analyses identified members of clade XII from beyond the Gulf of Aqaba, extending its known distribution. Most of the Synechococcus diversity was attributed to members of clade II during the spring bloom, while clade III contributed significantly to diversity during summer stratification. Clade XII diversity was most prevalent in fall and winter. Clade abundances were estimated from pyrosequencing of the V6 hypervariable region of 16S rRNA. Members of clade II dominated Synechococcus communities throughout the year, whereas the less frequent genotypes showed a pattern of seasonal succession. Based on the prevailing nutritional conditions we observed that clade I members thrive at higher nutrient concentrations during winter mixing. Clades V, VI and X became apparent during the transition periods between mixing and stratification. Clade III became prominent during sumeer stratification. We propose that members of clades V, VI, and X, and clade III are Synechococcus ecotypes that are adapted to intermediate and low nutrient levels respectively. This is the first time that molecular analyses have correlated population dynamics of Synechococcus genotypes with temporal fluctuations in nutrient regimes. Since these Synechococcus genotypes are routinely observed in the Gulf of Aqaba we suggest that seasonal fluctuations in nutrient levels create temporal niches that sustain their coexistence.
Science (New York, N.Y.). Jul, 2011 | Pubmed ID: 21778400
The mechanism that drives the regular beating of individual cilia and flagella, as well as dense ciliary fields, remains unclear. We describe a minimal model system, composed of microtubules and molecular motors, which self-assemble into active bundles exhibiting beating patterns reminiscent of those found in eukaryotic cilia and flagella. These observations suggest that hundreds of molecular motors, acting within an elastic microtubule bundle, spontaneously synchronize their activity to generate large-scale oscillations. Furthermore, we also demonstrate that densely packed, actively bending bundles spontaneously synchronize their beating patterns to produce collective behavior similar to metachronal waves observed in ciliary fields. The simple in vitro system described here could provide insights into beating of isolated eukaryotic cilia and flagella, as well as their synchronization in dense ciliary fields.
PloS One. 2011 | Pubmed ID: 21931760
Marine microbial communities have been essential contributors to global biomass, nutrient cycling, and biodiversity since the early history of Earth, but so far their community distribution patterns remain unknown in most marine ecosystems.
The New Zealand Medical Journal. Jul, 2011 | Pubmed ID: 21946968
A total smoking ban in prisons comes into effect from July 2011. The ban, introduced by the Corrections Minister, Judith Collins, aims to provide a healthier environment for prison staff and inmates through the elimination of secondhand smoke. Overseas experience has shown that simply banning smoking will not necessarily result in prisoners giving up, nor will it result in the maintenance of abstinence by those who do stop smoking during incarceration. In order to reap maximum health gains from the total smoking ban in prison policy, comprehensive cessation support for all inmates needs to be provided to ensure that they quit during incarceration and continue to abstain from smoking upon release.
Noise & Health. Sep-Oct, 2011 | Pubmed ID: 21959113
We report a cross-sectional study comparing the health-related quality of life (HRQOL) of individuals residing in the proximity of a wind farm to those residing in a demographically matched area sufficiently displaced from wind turbines. The study employed a nonequivalent comparison group posttest-only design. Self-administered questionnaires, which included the brief version of the World Health Organization quality of life scale, were delivered to residents in two adjacent areas in semirural New Zealand. Participants were also asked to identify annoying noises, indicate their degree of noise sensitivity, and rate amenity. Statistically significant differences were noted in some HRQOL domain scores, with residents living within 2 km of a turbine installation reporting lower overall quality of life, physical quality of life, and environmental quality of life. Those exposed to turbine noise also reported significantly lower sleep quality, and rated their environment as less restful. Our data suggest that wind farm noise can negatively impact facets of HRQOL.