The spatial organization and microbial community structure of an epilithic biofilm.

Microbial biofilms are common on lithic surfaces, including stone buildings. However, the ecology of these communities is poorly understood. Few studies have focused on the spatial characteristics of lithobiontic biofilms, despite the fact that spatial structure has been demonstrated to influence ecosystem function (and hence biodegradation) and community diversity. Furthermore, relatively few studies have utilized molecular techniques to characterize these communities, even though molecular methods have revealed unexpected microbial diversity in other habitats. This study investigated (1) the spatial structure and (2) the taxonomic composition of an epilithic biofilm using molecular techniques, namely amplicon pyrosequencing and terminal restriction fragment length polymorphism. Dispersion indices and Mantel correlograms were used to test for the presence of spatial structure in the biofilm. Diversity metrics and rank-abundance distributions (RADs) were also generated. The study revealed spatial structure on a centimetre scale in eukaryotic microbes (fungi and algae), but not the bacteria. Fungal and bacterial communities were highly diverse; algal communities much less so. The RADs were characterized by a distinctive 'hollow' (concave up) profile and long tails of rare taxa. These findings have implications for understanding the ecology of epilithic biofilms and the spatial heterogeneity of stone biodeterioration.This work was supported by the Engineering and Physical Sciences Research Council (grant no. EP/G011338/1).This is the author accepted manuscript. The final version is available from OUP at http://femsec.oxfordjournals.org/content/91/3/fiu027

Genome-wide profiling of human cap-independent translation-enhancing elements.

We report an in vitro selection strategy to identify RNA sequences that mediate cap-independent initiation of translation. This method entails mRNA display of trillions of genomic fragments, selection for initiation of translation and high-throughput deep sequencing. We identified >12,000 translation-enhancing elements (TEEs) in the human genome, generated a high-resolution map of human TEE-bearing regions (TBRs), and validated the function of a subset of sequences in vitro and in cultured cells

Profiling microbial communities in manganese remediation systems treating coal mine drainage

Author Posting. © American Society for Microbiology, 2015. This article is posted here by permission of American Society for Microbiology for personal use, not for redistribution. The definitive version was published in Applied and Environmental Microbiology 81 (2015): 2189-2198, doi:10.1128/AEM.03643-14.Water discharging from abandoned coal mines can contain extremely high manganese levels. Removing this metal is an ongoing challenge. Passive Mn(II) removal beds (MRBs) contain microorganisms that oxidize soluble Mn(II) to insoluble Mn(III/IV) minerals, but system performance is unpredictable. Using amplicon pyrosequencing, we profiled the bacterial, fungal, algal and archaeal communities in four variably-performing MRBs in Pennsylvania to determine whether they differed among MRBs and from surrounding soil, and to establish the relative abundance of known Mn(II)-oxidizers. Archaea were not detected; PCRs with archaeal primers returned only non-target bacterial sequences. Fungal taxonomic profiles differed starkly between sites that remove the majority of influent Mn and those that do not, with the former dominated by Ascomycota (mostly Dothideomycetes) and the latter by Basidiomycota (almost entirely Agaricomycetes). Taxonomic profiles for the other groups did not differ significantly between MRBs, but OTU-based analyses showed significant clustering by MRB with all four groups (p<0.05). Soil samples clustered separately from MRBs in all groups except fungi, whose soil samples clustered loosely with their respective MRB. Known Mn(II) oxidizers accounted for a minor proportion of bacterial sequences (up to 0.20%) but a greater proportion of fungal sequences (up to 14.78%). MRB communities are more diverse than previously thought, and more organisms may be capable of Mn(II) oxidation than are currently known.This project was funded by Smithsonian Scholarly Studies and Next-Generation Sequencing grants to C.M.S., by a Smithsonian Postdoctoral Fellowship to D.L.C., and by the National Science Foundation, grant numbers EAR-1249489 (awarded to C.M.H.) and CBET-1336496 (awarded to C.M.H. and C.M.S.)

Les comportements patrimoniaux des ménages en France : évolutions et déterminants entre 2004 et 2010.

À la lumière des informations issues des enquêtes Patrimoine 2004 et 2010 de l’INSEE et des évaluations des comptes nationaux financiers établis par la Banque de France, l’article propose une première analyse des ajustements patrimoniaux des ménages français depuis 2007.épargne, ménages, portefeuilles, immobilier, risques.

Non-monotonic field-dependence of the ZFC magnetization peak in some systems of magnetic nanoparticles

We have performed magnetic measurements on a diluted system of gamma-Fe2O3 nanoparticles (~7nm), and on a ferritin sample. In both cases, the ZFC-peak presents a non-monotonic field dependence, as has already been reported in some experiments,and discussed as a possible evidence of resonant tunneling. Within simple assumptions, we derive expressions for the magnetization obtained in the usual ZFC, FC, TRM procedures. We point out that the ZFC-peak position is extremely sensitive to the width of the particle size distribution, and give some numerical estimates of this effect. We propose to combine the FC magnetization with a modified TRM measurement, a procedure which allows a more direct access to the barrier distribution in a field. The typical barrier values which are obtained with this method show a monotonic decrease for increasing fields, as expected from the simple effect of anisotropy barrier lowering, in contrast with the ZFC results. From our measurements on gamma-Fe2O3 particles, we show that the width of the effective barrier distribution is slightly increasing with the field, an effect which is sufficient for causing the observed initial increase of the ZFC-peak temperatures.Comment: LaTeX file 19 pages, 9 postscript figures. To appear in Phys. Rev. B (tentative schedule: Dec.97

Small Angle Scattering by Fractal Aggregates: A Numerical Investigation of the Crossover Between the Fractal Regime and the Porod Regime

Fractal aggregates are built on a computer using off-lattice cluster-cluster aggregation models. The aggregates are made of spherical particles of different sizes distributed according to a Gaussian-like distribution characterised by a mean $a_0$ and a standard deviation $\sigma$. The wave vector dependent scattered intensity $I(q)$ is computed in order to study the influence of the particle polydispersity on the crossover between the fractal regime and the Porod regime. It is shown that, given $a_0$, the location $q_c$ of the crossover decreases as $\sigma$ increases. The dependence of $q_c$ on $\sigma$ can be understood from the evolution of the shape of the center-to-center interparticle-distance distribution function.Comment: RevTex, 4 pages + 6 postscript figures, compressed using "uufiles", published in Phys. Rev. B 50, 1305 (1994

Giant alkali-metal-induced lattice relaxation as the driving force of the insulating phase of alkali-metal/Si(111):B

Ab initio density-functional theory calculations, photoemission spectroscopy (PES), scanning tunneling microscopy, and spectroscopy (STM, STS) have been used to solve the 2√3 x 2√3R30 surface reconstruction observed previously by LEED on 0.5 ML K/Si:B. A large K-induced vertical lattice relaxation occurring only for 3/4 of Si adatoms is shown to quantitatively explain both the chemical shift of 1.14 eV and the ratio 1/3 measured on the two distinct B 1s core levels. A gap is observed between valence and conduction surface bands by ARPES and STS which is shown to have mainly a Si-B character. Finally, the calculated STM images agree with our experimental results. This work solves the controversy about the origin of the insulating ground state of alkali-metal/Si(111):B semiconducting interfaces which were believed previously to be related to many-body effectsThis work has received the financial support of the French ANR SURMOTT program (ANR-09-BLAN- 0210-01) and the Spanish MICIIN under Project No. FIS2010-1604

Distinct RNA profiles in subpopulations of extracellular vesicles: apoptotic bodies, microvesicles and exosomes

Introduction: In recent years, there has been an exponential increase in the number of studies aiming to understand the biology of exosomes, as well as other extracellular vesicles. However, classification of membrane vesicles and the appropriate protocols for their isolation are still under intense discussion and investigation. When isolating vesicles, it is crucial to use systems that are able to separate them, to avoid cross-contamination. Method: EVs released from three different kinds of cell lines: HMC-1, TF-1 and BV-2 were isolated using two centrifugation-based protocols. In protocol 1, apoptotic bodies were collected at 2,000&#x00D7;g, followed by filtering the supernatant through 0.8 &#x00B5;m pores and pelleting of microvesicles at 12,200&#x00D7;g. In protocol 2, apoptotic bodies and microvesicles were collected together at 16,500&#x00D7;g, followed by filtering of the supernatant through 0.2 &#x00B5;m pores and pelleting of exosomes at 120,000&#x00D7;g. Extracellular vesicles were analyzed by transmission electron microscopy, flow cytometry and the RNA profiles were investigated using a Bioanalyzer&#x00AE;. Results: RNA profiles showed that ribosomal RNA was primary detectable in apoptotic bodies and smaller RNAs without prominent ribosomal RNA peaks in exosomes. In contrast, microvesicles contained little or no RNA except for microvesicles collected from TF-1 cell cultures. The different vesicle pellets showed highly different distribution of size, shape and electron density with typical apoptotic body, microvesicle and exosome characteristics when analyzed by transmission electron microscopy. Flow cytometry revealed the presence of CD63 and CD81 in all vesicles investigated, as well as CD9 except in the TF-1-derived vesicles, as these cells do not express CD9. Conclusions: Our results demonstrate that centrifugation-based protocols are simple and fast systems to distinguish subpopulations of extracellular vesicles. Different vesicles show different RNA profiles and morphological characteristics, but they are indistinguishable using CD63-coated beads for flow cytometry analysis

Lorenz function of Bi2_{2}Te3_{3}/Sb2_{2}Te3_{3} superlattices

Combining first principles density functional theory and semi-classical Boltzmann transport, the anisotropic Lorenz function was studied for thermoelectric Bi$_{2}$Te$_{3}$/Sb$_{2}$Te$_{3}$ superlattices and their bulk constituents. It was found that already for the bulk materials Bi$_{2}$Te$_{3}$ and Sb$_{2}$Te$_{3}$, the Lorenz function is not a pellucid function on charge carrier concentration and temperature. For electron-doped Bi$_{2}$Te$_{3}$/Sb$_{2}$Te$_{3}$ superlattices large oscillatory deviations for the Lorenz function from the metallic limit were found even at high charge carrier concentrations. The latter can be referred to quantum well effects, which occur at distinct superlattice periods

The Risk and Protective Factors for Adolescents with an Addicted Parent

This research project was a qualitative study that explored the risk and protective factors for adolescents who are growing up with a parent who is addicted to drugs and/or alcohol using a sample of eight participants. Specifically, this research looked at the possible protective factors that may help an adolescent from becoming addicted to drugs and/or alcohol themselves. Also, this research looked at the possible risk factors that may have helped an adolescent fall into addiction like his or her parents. In addition, the study explored possible behavioral patterns exhibited in adolescents who are growing up in a home with addiction and become addicted themselves. The themes that emerged from the data for risk factors for adolescents who grow up in a home with an addicted parent and who become addicted to drugs and/or alcohol themselves were a) parental chemical health modeling, b) traumatic experiences in adolescence and/or adulthood and c) genetic predisposition. In comparison, the themes that emerged for protective factors for adolescents who grow up in a home with an addicted parent and do not become addicted to drugs and/or alcohol were a) engagement with others and in activities, b) resilience and c) a faith in God. The predominant theme that emerged for the behavioral patterns of adolescents who grow up in an addicted home and become addicted to drugs and/or alcohol themselves was oppositional defiance. Overall, the data from this study had some similar findings as other research, but also provided new findings. It is imperative that clinicians continue to stay knowledgeable regarding the risk and protective factors for adolescents who are growing up in a home with parental addiction. Research showed that these factors are always changing and different for every adolescent. It is important for social workers to be aware of the diversity of these factors that could help or hinder an adolescent from following in their parent’s footsteps of addiction