Genomics-Based Identifcation of Microorganisms in Human Ocular Body Fluid

Abstract Advances in genomics have the potential to revolutionize clinical diagnostics. Here, we examine the microbiome of vitreous (intraocular body fluid) from patients who developed endophthalmitis following cataract surgery or intravitreal injection. Endophthalmitis is an inflammation of the intraocular cavity and can lead to a permanent loss of vision. As controls, we included vitreous from endophthalmitis-negative patients, balanced salt solution used during vitrectomy and DNA extraction blanks. We compared two DNA isolation procedures and found that an ultraclean production of reagents appeared to reduce background DNA in these low microbial biomass samples. We created a curated microbial genome database (>5700 genomes) and designed a metagenomics workflow with filtering steps to reduce DNA sequences originating from: (i) human hosts, (ii) ambiguousness/contaminants in public microbial reference genomes and (iii) the environment. Our metagenomic read classification revealed in nearly all cases the same microorganism that was determined in cultivation- and mass spectrometry-based analyses. For some patients, we identified the sequence type of the microorganism and antibiotic resistance genes through analyses of whole genome sequence (WGS) assemblies of isolates and metagenomic assemblies. Together, we conclude that genomics-based analyses of human ocular body fluid specimens can provide actionable information relevant to infectious disease management

Age before beauty? Relationships between fertilization success and age-dependent ornaments in barn swallows

When males become more ornamented and reproduce more successfully as they grow older, phenotypic correlations between ornament exaggeration and reproductive success can be confounded with age effects in cross-sectional studies, and thus say relatively little about sexual selection on these traits. This is exemplified here in a correlative study of male fertilization success in a large colony of American barn swallows (Hirundo rustica erythrogaster). Previous studies of this species have indicated that two sexually dimorphic traits, tail length and ventral plumage coloration, are positively correlated with male fertilization success, and a mechanism of sexual selection by female choice has been invoked. However, these studies did not control for potential age-related variation in trait expression. Here, we show that male fertilization success was positively correlated with male tail length but not with plumage coloration. We also show that 1-year-old males had shorter tails and lower fertilization success than older males. This age effect accounted for much of the covariance between tail length and fertilization success. Still, there was a positive relationship between tail length and fertilization success among older males. But as this group consisted of males from different age classes, an age effect may be hidden in this relationship as well. Our data also revealed a longitudinal increase in both tail length and fertilization success for individual males. We argue that age-dependent ornament expression and reproductive performance in males complicate inferences about female preferences and sexual selection

Assessing the Effects of Climate on Host-Parasite Interactions: A Comparative Study of European Birds and Their Parasites

[Background] Climate change potentially has important effects on distribution, abundance, transmission and virulence of parasites in wild populations of animals. [Methodology/Principal Finding] Here we analyzed paired information on 89 parasite populations for 24 species of bird hosts some years ago and again in 2010 with an average interval of 10 years. The parasite taxa included protozoa, feather parasites, diptera, ticks, mites and fleas. We investigated whether change in abundance and prevalence of parasites was related to change in body condition, reproduction and population size of hosts. We conducted analyses based on the entire dataset, but also on a restricted dataset with intervals between study years being 5–15 years. Parasite abundance increased over time when restricting the analyses to datasets with an interval of 5–15 years, with no significant effect of changes in temperature at the time of breeding among study sites. Changes in host body condition and clutch size were related to change in temperature between first and second study year. In addition, changes in clutch size, brood size and body condition of hosts were correlated with change in abundance of parasites. Finally, changes in population size of hosts were not significantly related to changes in abundance of parasites or their prevalence. [Conclusions/Significance] Climate change is associated with a general increase in parasite abundance. Variation in laying date depended on locality and was associated with latitude while body condition of hosts was associated with a change in temperature. Because clutch size, brood size and body condition were associated with change in parasitism, these results suggest that parasites, perhaps mediated through the indirect effects of temperature, may affect fecundity and condition of their hosts. The conclusions were particularly in accordance with predictions when the restricted dataset with intervals of 5–15 years was used, suggesting that short intervals may bias findings.The Academy of Finland is acknowledged for a grant to TE (project 8119367) and EK (project 250709). PLP was supported by a research grant (TE_291/2010) offered by the Romanian Ministry of Education and Science. T. Szép received funding from OTKA K69068 and JT from OTKA 75618. JMP was supported by a JAE grant from Consejo Superior de Investigaciones Científicas. SM-JM, FdL-AM, JF, JJS and FV were respectively supported by projects CGL2009-09439, CGL2012-36665, CGL2009- 11445, CGL2010-19233-C03-01 and CGL2008-00562 by the Spanish Ministry of Science and Innovation and FEDER and project EVITAR by the Spanish Ministry of Health. FV was also supported by the European Regional Development Fund. MACT was funded by a predoctoral FPU grant from the Spanish Ministry of Education (AP20043713). PM was supported by grant from the Polish Ministry of Science and Higher Education (project 2P04F07030), and the Foundation for Polish Science

Detection of molecular hydrogen at z=1.15 toward HE 0515-4414

A new molecular hydrogen cloud is found in the sub-damped Ly-alpha absorber [log N(HI)=19.88+/-0.05] at the redshift z=1.15 toward the bright quasar HE0515-4414 (zem = 1.71). More than 30 absorption features in the Lyman band system of H2 are identified in the UV spectrum of this quasar obtained with the Space Telescope Imaging Spectrograph (STIS) aboard the Hubble Space Telescope. The H2-bearing cloud shows a total H2 column density N(H2)=(8.7^{+8.7}_-{4.0}) 10^16 cm^-2, and a fractional molecular abundance f(H2)=(2.3^{+2.3}_{-1.1}) 10^-3 derived from the H2 lines arising from the J=0-5 rotational levels of the ground electronic vibrational state. The estimated rate of photodissociation at the cloud edge I_0<=1.8 10^{-8} s^-1 is much higher than the mean Galactic disk value, I_MW~=5.5 10^{-11} s^-1. This may indicate an enhanced star-formation activity in the z=1.15 system as compared with molecular clouds at z~=3 where I~=I_MW. We also find a tentative evidence that the formation rate coefficient of H2 upon grain surfaces at z=1.15 is a factor of 10 larger than a canonical Milky Way value, R_MW~=3 10^-17 cm^3 s^-1. The relative dust-to-gas ratio estimated from the [Cr/Zn] ratio is equal to k=0.89+/-0.19 (in units of the mean Galactic disk value), which is in good agreement with a high molecular fraction in this system. The estimated line-of-sight size of L~=0.25 pc may imply that the H2 is confined within small and dense filaments embedded in a more rarefied gas giving rise to the z=1.15 sub-damped Ly-alpha absorber.Comment: 10 pages, 7 figures, accepted for publication in A&

Certified causes of death in patients with mesothelioma in South East England

Background: Mesothelioma is a highly fatal cancer that is caused by exposure to asbestos fibres. In many populations, the occurrence of mesothelioma is monitored with the use of mortality data from death certification. We examine certified causes of death of patients who have been diagnosed with mesothelioma, and assess the validity of death certification data as a proxy for mesothelioma incidence.Methods: We extracted mesothelioma registrations in the South East of England area between 2000 and 2004 from the Thames Cancer Registry database. We retained for analysis 2200 patients who had died at the time of analysis, after having excluded seven dead cases where the causes of death were not known to the cancer registry. The 2200 deaths were classified hierarchically to identify (1) mesothelioma deaths, (2) deaths certified as lung cancer deaths or (3) deaths from unspecified cancer, and (4) deaths from other causes.Results: 87% of the patients had mesothelioma mentioned on the death certificate. 6% had no mention of mesothelioma but included lung cancer as a cause of death. Another 6% had no mention of mesothelioma or lung cancer, but included an unspecified cancer as a cause of death. Lastly, 2% had other causes of death specified on the death certificate.Conclusion: This analysis suggests that official mortality data may underestimate the true occurrence of mesothelioma by around 10%

Interaction between sodium chloride and texture in semi-hard Danish cheese as affected by brining time, dl -starter culture, chymosin type and cheese ripening

Reduced NaCl in semi-hard cheeses greatly affects textural and sensory properties. The interaction between cheese NaCl concentration and texture was affected by brining time (0–28 h), dl-starter cultures (C1, C2, and C3), chymosin type (bovine or camel), and ripening time (1–12 weeks). Cheese NaCl levels ranged from <0.15 to 1.90% (w/w). NaCl distribution changed during ripening; migration from cheese edge to core led to a more homogeneous NaCl distribution after 12 weeks. As ripening time increased, cheese firmness decreased. Cheeses with reduced NaCl were less firm and more compressible. Cheeses produced with C2 were significantly firmer than those produced with C1; cheeses produced with C3 had higher firmness and compressibility. In NaCl reduced cheese, use of camel chymosin as coagulant resulted in significantly higher firmness than that given using bovine chymosin. Overall, cheese NaCl content is reducible without significant textural impact using well-defined starter cultures and camel chymosin

N-terminal Pro B-type Natriuretic Peptide and the Evaluation of Cardiac Dysfunction and Severity of Disease in Cirrhotic Patients

Purpose: Cardiac dysfunction and hyperdynamic systemic circulation may be present in patients with cirrhosis. The purpose of this study was to identify relations between plasma levels of N-terminal-proBNP (NT-proBNP), reflecting early ventricular dysfunction, and the severity of liver disease and cardiac dysfunction in cirrhotic patients. Materials and Methods: Sixty-three cirrhotic patients and 15 controls (group 1) were enrolled in this study. Plasma levels of NT-proBNP were determined in echocardiographically examined patients, which were allocated to 1 of 3 groups according to Child-Pugh classification or into 2 groups, i.e., a compensated group without ascites (group 2) and decompensated group with ascites (group 3). Results: Plasma NT-proBNP levels were significantly higher in cirrhotic patients (groups 2 and 3) than in age-matched controls (155.9 and 198.3 vs. 40.3 pg/mL

The VVDS type-1 AGN sample: The faint end of the luminosity function

In a previous paper (Gavignaud et al. 2006), we presented the type-1 Active Galactic Nuclei (AGN) sample obtained from the first epoch data of the VIMOS-VLT Deep Survey (VVDS). The sample consists of 130 faint, broad-line AGN with redshift up to z=5 and 17.5< I <24.0, selected on the basis of their spectra. In this paper we present the measurement of the Optical Luminosity Function up to z=3.6 derived from this sample, we compare our results with previous results from brighter samples both at low and at high redshift. Our data, more than one magnitude fainter than previous optical surveys, allow us to constrain the faint part of the luminosity function up to high redshift. By combining our faint VVDS sample with the large sample of bright AGN extracted from the SDSS DR3 (Richards et al., 2006b) and testing a number of different evolutionary models, we find that the model which better represents the combined luminosity functions, over a wide range of redshift and luminosity, is a luminosity dependent density evolution (LDDE) model, similar to those derived from the major X-surveys. Such a parameterization allows the redshift of the AGN space density peak to change as a function of luminosity and explains the excess of faint AGN that we find at 1.0< z <1.5. On the basis of this model we find, for the first time from the analysis of optically selected samples, that the peak of the AGN space density shifts significantly towards lower redshift going to lower luminosity objects. This result, already found in a number of X-ray selected samples of AGN, is consistent with a scenario of "AGN cosmic downsizing", in which the density of more luminous AGN, possibly associated to more massive black holes, peaks earlier in the history of the Universe, than that of low luminosity ones.Comment: 13 pages, 10 figures, submitted to A&

Buses, cars, bicycles and walkers the influence of the type of human transport on the flight responses of waterbirds

One way to manage disturbance to waterbirds in natural areas where humans require access is to promote the occurrence of stimuli for which birds tolerate closer approaches, and so cause fewer responses. We conducted 730 experimental approaches to 39 species of waterbird, using five stimulus types (single walker, three walkers, bicycle, car and bus) selected to mimic different human management options available for a controlled access, Ramsar-listed wetland. Across species, where differences existed (56% of 25 cases), motor vehicles always evoked shorter flight-initiation distances (FID) than humans on foot. The influence of stimulus type on FID varied across four species for which enough data were available for complete cross-stimulus analysis. All four varied FID in relation to stimuli, differing in 4 to 7 of 10 possible comparisons. Where differences occurred, the effect size was generally modest, suggesting that managing stimulus type (e.g. by requiring people to use vehicles) may have species-specific, modest benefits, at least for the waterbirds we studied. However, different stimulus types have different capacities to reduce the frequency of disturbance (i.e. by carrying more people) and vary in their capacity to travel around important habita

Pleural cancer mortality in Spain: time-trends and updating of predictions up to 2020

Background A total of 2,514,346 metric tons (Mt) of asbestos were imported into Spain from 1906 until the ban on asbestos in 2002. Our objective was to study pleural cancer mortality trends as an indicator of mesothelioma mortality and update mortality predictions for the periods 2011–2015 and 2016–2020 in Spain.Methods Log-linear Poisson models were fitted to study the effect of age, period of death and birth cohort (APC) on mortality trends. Change points in cohort- and period-effect curvatures were assessed using segmented regression. Fractional power-link APC models were used to predict mortality until 2020. In addition, an alternative model based on national asbestos consumption figures was also used to perform long-term predictions.Results Pleural cancer deaths increased across the study period, rising from 491 in 1976–1980 to 1,249 in 2006–2010. Predictions for the five-year period 2016–2020 indicated a total of 1,319 pleural cancer deaths (264 deaths/year). Forecasts up to 2020 indicated that this increase would continue, though the age-adjusted rates showed a levelling-off in male mortality from 2001 to 2005, corresponding to the lower risk in post-1960 generations. Among women, rates were lower and the mortality trend was also different, indicating that occupational exposure was possibly the single factor having most influence on pleural cancer mortality.Conclusion The cancer mortality-related consequences of human exposure to asbestos are set to persist and remain in evidence until the last surviving members of the exposed cohorts have disappeared. It can thus be assumed that occupationally-related deaths due to pleural mesothelioma will continue to occur in Spain until at least 2040.The study was partially supported by a research grant from the Spanish Health Research Fund (FIS PI11/00871) and the HAR2009-07543 project of the Ministry of Science and Innovation. The Department of Labour of the Government of Catalonia provided the asbestos consumption data