Culture-independent analysis of diversity in microbial communities: pros and cons of the partial sequence-based profiling

Among the culture-independent techniques developed so far, DGGE/TGGE analysis of amplified 16S rRNA fragments is currently used to a great extent for the characterization of microbial consortia, due to its fast response and highly descriptive power. This approach relies on the separations of partial 16S rRNA gene amplicons targeting two specific hypervariable regions, namely V3 and V6-V8. Separation is followed by sequencing and identification of different bands based on BLAST comparisons. Some case studies are presented here concerning the identification of bacterial species and genera - belonging to different phyla such as Actinobacteria (Bifidobacterium, Rhodococcus), Firmicutes (Bacillus, Enterococcus, and Lactobacillus), Alphaproteobacteria (Sinorhizobium), Betaproteobacteria (Burkholderia), and Gammaproteobacteria (Pseudomonas) \u2013 all relevant to environmental and industrial biotechnology

Metabarcoding analysis of gut microbiota of healthy individuals reveals impact of probiotic and maltodextrin consumption

In a previously published double-blind, placebo-controlled study, we showed that probiotics intake exerted a positive effect on sleep quality and a general improvement across time in different aspects of the profile of mood state, like sadness, anger, and fatigue in 33 healthy individuals. The present work investigates the impact of the probiotic product, constituted of Limosilactobacillus fermentum LF16, Lacticaseibacillus rhamnosus LR06, Lactiplantibacillus plantarum LP01 (all former members of Lactobacillus genus), and Bifidobacterium longum 04, on the gut microbiota composition of the same cohort through a metabarcoding analysis. Both the placebo and probiotic treatments had a significant impact on the microbiota composition. Statistical analysis showed that the microbiota of the individuals could be clustered into three groups, or bacteriotypes, at the baseline, and, inherently, bacterial compositions were linked to different responses to probiotic and placebo intakes. Interestingly, L. rhamnosus and L. fermentum were retrieved in the probiotic-treated cohort, while a bifidogenic effect of maltodextrin, used as placebo, was observed. The present study shed light on the importance of defining bacteriotypes to assess the impact of interventions on the gut microbiota and allowed to reveal microbial components which could be related to positive effects (i.e. sleep quality improvement) to be verified in further studies

Two-dimensional X-ray diffraction as a tool for the rapid, non-destructive detection of low calcite quantities in aragonitic corals

Paleoclimate reconstructions based on reef corals require precise detection of diagenetic alteration. Secondary calcite can significantly affect paleotemperature reconstructions at very low amounts of ~1%. X-ray powder diffraction is routinely used to detect diagenetic calcite in aragonitic corals. This procedure has its limitations as single powder samples might not represent the entire coral heterogeneity. A conventional and a 2-D X-ray diffractometer were calibrated with gravimetric powder standards of high and low magnesium calcite (0.3% to 25% calcite). Calcite contents <1% can be recognized with both diffractometer setups based on the peak area of the calcite [104] reflection. An advantage of 2-D-XRD over convenient 1-D-XRD methods is the nondestructive and rapid detection of calcite with relatively high spatial resolution directly on coral slabs. The calcite detection performance of the 2-D-XRD setup was tested on thin sections from fossil Porites sp. samples that, based on powder XRD measurements, showed <1% calcite. Quantification of calcite contents for these thin sections based on 2-D-XRD and digital image analysis showed very similar results. This enables spot measurements with diameters of ∼4 mm, as well as systematic line scans along potential tracks previous to geochemical proxy sampling. In this way, areas affected by diagenetic calcite can be avoided and alternative sampling tracks can be defined. Alternatively, individual sampling positions that show dubious proxy results can later be checked for the presence of calcite. The presented calibration and quantification method can be transferred to any 2-D X-ray diffractometer

Dark matter searches using superheated liquids

Direct detection of dark matter is one of the most important topics in modern physics. It is estimated that 22% of universe matter is composed by dark matter in front of 0.4% of ordinary matter like stars, galaxies planets and all kind of known astrophysical objects. Several kinds of experiments are nowadays involved in detection of one of the more accepted particle candidates to be dark matter: WIMPs (Weakly Interacting Massive Particles). These detectors, using several kinds of techniques: Cryogenic semiconductors, scintillation materials like I Na or noble gas chambers among others, are reporting very interesting but inconclusive results. In this paper a review of detectors that are using the superheated liquid technique in bubble chambers in order to detect WIMPs is reported. Basically, we will report about Coupp (Chicagoland observatory for underground particle physics), PICO that is composed by Coupp and Picasso researchers having the aim to build a ton experiment and also about a new detector named MOSCAB (Materia oscura a bolle) that recently published a first results of a test chamber that uses also superheated liquid technique but as a Geyser chamber.Bou Cabo, M.; Ardid Ramírez, M.; Felis-Enguix, I. (2016). Dark matter searches using superheated liquids. EPJ Web of Conferences. 121(06007):1-8. doi:10.1051/epjconf/201612106007S1812106007Rayleigh L., On the pressure developed in a liquid during the collapse of a spherical cavity (Philos. Mag34, 94, 1917)Plesset M.S., The growth of vapor bubbles in superheated liquid (J. Appl. Phys.25, 9493, 1954)Forster H.K., Growth of vapor bubbles in superheated liquid (J. Appl. Phys.05, 474, 1954)Seitz F. (Phys. Fluids1, 2, 1958)Behnke E. et al., Coupp Collaboration, First dark matter search results from a 4-kg CF3I bubble chamber operated in a deep underground site (Phys. Rev. D86, 2012)Behnke et al., Coupp Collaboration, Direct measurement of the bubble-nucleation energy threshold in a CF3I bubble chamber (Phys. Rev. D88, 2013)Archambault S., Picasso Collaboration, Dark Matter Spin-Dependent Limits for WIMPs Interactions on19F by PICASSO(Phys. Lett. B, 2009)Bertoni R. et al., A new technique for direct investigation of dark matter (Nuclear Instruments and Methods in Physics Research, A, 61–68, 2014)Bou-Cabo M. et al., LOW Radioactivity Techniques 2013 (LRT 2013): Proceedings of the IV International Workshop in Low Radioactivity Techniques, V:1549, 142 – 147Ardid M. et al., MOSCAB: Direct dark matter search using the Geyser technique, Proc. ICHEP 2014 Conf., Nucl. Phys. B: Proc. Supp. (in press

A compact array calibrator to study the feasibility of acoustic neutrino detection

[EN] Underwater acoustic detection of ultra-high-energy neutrinos was proposed already in 1950s: when a neutrino interacts with a nucleus in water, the resulting particle cascade produces a pressure pulse that has a bipolar temporal structure and propagates within a &#64258;at disk-like volume. A telescope that consists of thousands of acoustic sensors deployed in the deep sea can monitor hundreds of cubic kilometres of water looking for these signals and discriminating them from acoustic noise. To study the feasibility of the technique it is critical to have a calibrator able to mimic the neutrino signature that can be operated from a vessel. Due to the axial-symmetry of the signal, their very directive short bipolar shape and the constraints of operating at sea, the development of such a calibrator is very challenging. Once the possibility of using the acoustic parametric technique for this aim was validated with the &#64257;rst compact array calibrator prototype, in this paper we describe the new design for such a calibrator composed of an array of piezo ceramic tube transducers emitting in axial direction.We acknowledge the financial support of the Spanish Ministerio de Economía y Competitividad, Grants FPA2012-37528-C02-02, and Consolider MultiDark CSD2009-00064, of the Generalitat Valenciana, Grants ACOMP/2015/175 PrometeoII/2014/079 and of the European FEDER funds.Ardid Ramírez, M.; Camarena Femenia, F.; Felis-Enguix, I.; Herrero Debón, A.; Llorens Alvarez, CD.; Martínez Mora, JA.; Saldaña-Coscollar, M. (2016). A compact array calibrator to study the feasibility of acoustic neutrino detection. EPJ Web of Conferences. 116(03001):1-4. https://doi.org/10.1051/epjconf/201611603001S141160300

The genome of Bifidobacterium pseudocatenulatum IPLA 36007, a human intestinal strain with isoflavone-activation activity

Background: Bifidobacterium species, including Bifidobacterium pseudocatenulatum, are among the dominant microbial populations of the human gastrointestinal tract. They are also major components of many commercial probiotic products. Resident and transient bifidobacteria are thought to have several beneficial health effects. However, our knowledge of how these bacteria interact and communicate with host cells remains poor. This knowledge is essential for scientific support of their purported health benefits and their rational inclusion in functional foods. Results: This work describes the draft genome sequence of Bifidobacterium pseudocatenulatum IPLA 36007, a strain isolated as dominant from the feces of a healthy human. Besides several properties of probiosis, IPLA 36007 exhibited the capability of releasing aglycones from soy isoflavone glycosides. The genome contains 1,851 predicted genes, including 54 genes for tRNAs and fie copies of unique 16S, 23S and 5S rRNA genes. As key attributes of the IPLA 36007 genome we can mention the presence of a lysogenic phage, a cluster encoding type IV fimbriae, and a locus encoding a clustered, regularly interspaced, short, palindromic repeat (CRISPR)-Cas system. Four open reading frames (orfs) encoding \u3b2-glucosidases belonging to the glycosyl hydrolase family 3, which may act on isoflavone glycosides, were encountered. Additionally, one gene was found to code for a glycosyl hydrolase of family 1 that might also have \u3b2-glucosidase activity. Conclusion: The availability of the B. pseudocatenulatum IPLA 36007 genome should allow the enzyme system involved in the release of soy isoflavone aglycones from isoflavone glycosides, and the molecular mechanisms underlying the strain's probiotic properties, to be more easily understood

The Red Sea, Coastal Landscapes, and Hominin Dispersals

This chapter provides a critical assessment of environment, landscape and resources in the Red Sea region over the past five million years in relation to archaeological evidence of hominin settlement, and of current hypotheses about the role of the region as a pathway or obstacle to population dispersals between Africa and Asia and the possible significance of coastal colonization. The discussion assesses the impact of factors such as topography and the distribution of resources on land and on the seacoast, taking account of geographical variation and changes in geology, sea levels and palaeoclimate. The merits of northern and southern routes of movement at either end of the Red Sea are compared. All the evidence indicates that there has been no land connection at the southern end since the beginning of the Pliocene period, but that short sea crossings would have been possible at lowest sea-level stands with little or no technical aids. More important than the possibilities of crossing the southern channel is the nature of the resources available in the adjacent coastal zones. There were many climatic episodes wetter than today, and during these periods water draining from the Arabian escarpment provided productive conditions for large mammals and human populations in coastal regions and eastwards into the desert. During drier episodes the coastal region would have provided important refugia both in upland areas and on the emerged shelves exposed by lowered sea level, especially in the southern sector and on both sides of the Red Sea. Marine resources may have offered an added advantage in coastal areas, but evidence for their exploitation is very limited, and their role has been over-exaggerated in hypotheses of coastal colonization

Search for muon-neutrino emission from GeV and TeV gamma-ray flaring blazars using five years of data of the ANTARES telescope

The ANTARES telescope is well-suited for detecting astrophysical transient neutrino sources as it can observe a full hemisphere of the sky at all times with a high duty cycle. The background due to atmospheric particles can be drastically reduced, and the point-source sensitivity improved, by selecting a narrow time window around possible neutrino production periods. Blazars, being radio-loud active galactic nuclei with their jets pointing almost directly towards the observer, are particularly attractive potential neutrino point sources, since they are among the most likely sources of the very high-energy cosmic rays. Neutrinos and gamma rays may be produced in hadronic interactions with the surrounding medium. Moreover, blazars generally show high time variability in their light curves at different wavelengths and on various time scales. This paper presents a time-dependent analysis applied to a selection of flaring gamma-ray blazars observed by the FERMI/LAT experiment and by TeV Cherenkov telescopes using five years of ANTARES data taken from 2008 to 2012. The results are compatible with fluctuations of the background. Upper limits on the neutrino fluence have been produced and compared to the measured gamma-ray spectral energy distribution.Comment: 27 pages, 16 figure

Biodegradation of herbicide diuron by streptomycetes isolated from soil

The diuron degrading activity of 17 streptomycete strains, obtained from agricultural and non-agricultural soils, was determined in the laboratory. All strains were identified as Streptomyces sp. by phenotypic characteristics and PCR-based assays. The strains were cultivated in liquid medium with diuron (4mgL(-1)) at 25 degrees C for 15 days. Biodegradation activity was deter-mined by high-performance liquid chromatography. The results indicated that all strains were able to degrade diuron, but to different amounts. Twelve strains degraded the herbicide by up to 50% and four of them by up to 70%. Strain A7-9, belonging to S. albidoflavus cluster, was the most efficient organism in the degradation of diuron, achieving 95% degradation after five days of incubation and no herbicide remained after 10 days. Overall, the strains isolated from agricultural soils exhibited higher degradation percentages and rates than those isolated from non-agricultural soils. Given the high degradation activity observed here, the streptomycete strains show a good potential for bioremediation of soils contaminated with diuron. (c) 2006 Elsevier Ltd. All rights reserved.Castillo López, MÁ.; Felis Reig, N.; Aragón Revuelta, P.; Cuesta Amat, G.; Sabater Marco, C. (2006). Biodegradation of herbicide diuron by streptomycetes isolated from soil. International Biodeterioration and Biodegradation. 58(3-4):196-202. doi:10.1016/j.ibiod.2006.06.020S196202583-