Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction)

BACKGROUND: PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology. RESULTS: Here we present our results using a Universal DNA Microarray approach as an analytical tool for bacterial discrimination. The proposed procedure is based on the properties of the DNA ligation reaction and requires the design of two probes specific for each target sequence. One oligo carries a fluorescent label and the other a unique sequence (cZipCode or complementary ZipCode) which identifies a ligation product. Ligated fragments, obtained in presence of a proper template (a PCR amplified fragment of the 16s rRNA gene) contain either the fluorescent label or the unique sequence and therefore are addressed to the location on the microarray where the ZipCode sequence has been spotted. Such an array is therefore "Universal" being unrelated to a specific molecular analysis. Here we present the design of probes specific for some groups of bacteria and their application to bacterial diagnostics. CONCLUSIONS: The combined use of selective probes, ligation reaction and the Universal Array approach yielded an analytical procedure with a good power of discrimination among bacteria

Early life stress interacts with the diet deficiency of Omega-3 fatty acids during the life course increasing the metabolic vulnerability in adult rats

Early stress can cause metabolic disorders in adulthood. Omega-3 polyunsaturated fatty acids (n-3 PUFAs) deficiency has also been linked to the development of metabolic disorders. The aim of this study was to assess whether an early stressful event such as maternal separation interacts with the nutritional availability of n-3 PUFAs during the life course on metabolic aspects. Litters were randomized into: maternal separated (MS) and non-handled (NH). The MS group was removed from their dam for 3 hours per day and put in an incubator at 32uC on days 1u to 10u postnatal (PND). On PND 35, males were subdivided into diets that were adequate or deficient in n-3 PUFAs, and this intervention was applied during the subsequent 15 weeks. Animal’s body weight and food consumption were measured weekly, and at the end of the treatment tissues were collected. MS was associated with increased food intake (p = 0.047) and weight gain (p = 0.012), but no differences were found in the NPY hypothalamic content between the groups. MS rats had also increased deposition of abdominal fat (p,0.001) and plasma triglycerides (p = 0.018) when compared to the NH group. Interactions between early life stress and n-3 PUFAs deficiency were found in plasma insulin (p = 0.033), HOMA index (p = 0.049), leptin (p = 0.010) and liver PEPCK expression (p = 0.050), in which the metabolic vulnerability in the MS group was aggravated by the n-3 PUFAs deficient diet exposure. This was associated with specific alterations in the peripheral fatty acid profile. Variations in the neonatal environment interact with nutritional aspects during the life course, such as n-3 PUFAs diet content, and persistently alter the metabolic vulnerability in adulthood

Galaxy stellar mass functions of different morphological types in clusters, and their evolution between z=0.8 and z=0

We present the galaxy stellar mass function (MF) and its evolution in clusters from z~0.8 to the current epoch, based on the WIde-field Nearby Galaxy-cluster Survey (WINGS) (0.04<z<0.07), and the ESO Distant Cluster Survey (EDisCS) (0.4<z <0.8). We investigate the total MF and find it evolves noticeably with redshift. The shape at M*>10^11 M' does not evolve, but below M*~10^10.8 M' the MF at high redshift is flat, while in the Local Universe it flattens out at lower masses. The population of M* = 10^10.2 - 10^10.8 M' galaxies must have grown significantly between z=0.8 and z=0. We analyze the MF of different morphological types (ellipticals, S0s and late-types), and find that also each of them evolves with redshift. All types have proportionally more massive galaxies at high- than at low-z, and the strongest evolution occurs among S0 galaxies. Examining the morphology-mass relation (the way the proportion of galaxies of different morphological types changes with galaxy mass), we find it strongly depends on redshift. At both redshifts, ~40% of the stellar mass is in elliptical galaxies. Another ~43% of the mass is in S0 galaxies in local clusters, while it is in spirals in distant clusters. To explain the observed trends, we discuss the importance of those mechanisms that could shape the MF. We conclude that mass growth due to star formation plays a crucial role in driving the evolution. It has to be accompanied by infall of galaxies onto clusters, and the mass distribution of infalling galaxies might be different from that of cluster galaxies. However, comparing with high-z field samples, we do not find conclusive evidence for such an environmental mass segregation. Our results suggest that star formation and infall change directly the MF of late-type galaxies in clusters and, indirectly, that of early-type galaxies through subsequent morphological transformations.Comment: MNRAS in press, 24 pages, 19 figures and 8 table

Calcareous phytoplankton response to the half century of interannual climatic variability in Santa Barbara Basin (California)

A high-resolution study of calcareous phytoplankton in a box core from the Santa Barbara Basin (SBB) reveals floral assemblage fluctuations which can be related to climatic and paleoceanographic changes during the last half century (1940-1996). In particular, Gephyrocapsa oceanica production increased during El Niño periods, in response to high temperatures, silica depletion, and increased iron availability. Conversely, Helicosphaera carteri flux increases in conjunction with lower surface temperatures associated with La Niña episodes. Increasing abundances of Florisphaera profunda and Umbilicosphaera sibogae after 1970 reflect a warming trend and increased stratification within the basin associated with the warm phase of the Pacific Decadal Oscillation (PDO). Conversely, increased abundances of Coccolithus pelagicus and Calcidiscus leptoporus before 1970 mark the cold phase of PDO. These coccolithophore production rate data are consistent with instrumental records of surface and thermocline temperatures monitored since 1950. This is the first study to document the response of calcareous phytoplankton to surface water warming occurring in SBB since 197

Galaxy sizes as a function of environment at intermediate redshift from the ESO Distant Cluster Survey

In order to assess whether the environment has a significant effect on galaxy sizes, we compare the mass–size relations of cluster and field galaxies in the 0.41), with early-type/passive galaxies in higher density environments growing earlier. Such dependence disappears at lower redshifts. Therefore, if the reported difference at higher-z is real, the growth of field galaxies has caught up with that of cluster galaxies by z∼1. Any putative mechanism responsible for galaxy growth has to account for the existence of environmental differences at high redshift and their absence (or weakening) at lower redshifts

Endophytic and rhizospheric bacteria associated with Paspalum atratum and its potential for plant growth promotion with different phosphate sources

The genus Paspalum belongs to the family Poaceae and has several species that are native to Brazil. The Paspalum Germplasm Bank (GB) of the Brazilian Agricultural Research Corporation comprises approximately 450 accessions from 50 species. Among these accessions, Paspalum atratum (BGP 308) has economic potential for forage purposes. However, the endophytic and rhizospheric microbial communities within this accession and their ability to promote plant growth remain unknown. The present study aimed to isolate the endophytic and rhizospheric bacteria associated with P. atratum and to assess their potential for plant growth improvement, so-called plant growth-promoting bacteria (PGPB). For the in vitro tests, the ability of nitrogen-fixing bacteria (NFB), phosphate solubilization (PS) and indoleacetic acid (IAA) production were evaluated. A total of 116 endophytic and rhizosphere bacteria were obtained from the isolation. In the in vitro tests, 43 (37.00%) of these isolates showed positive NFB, PS, and IAA results. These isolates were identified by 16S rDNA sequencing. The phosphate solubilization index (PSI) ranged from 2 to 3.61, all 43 strains performed biological nitrogen fixation and the IAA production ranged from 12.85 to 431.41 μg ml−1. Eight of these 43 isolates were evaluated in vivo in a greenhouse using P. atratum caryopsis. The pots were filled with soil prepared with three different phosphate sources and one control without phosphate. After growth, the plants were submitted to morphological, bromatological and chemical determination. Data were analyzed using analysis of variance (ANOVA) and principal component analysis (PCA). In the in vivo test, treatments 105 (Pseudomonas sp.) and 458 (Pseudomonas sp.) were the most significant for the crystalline phosphate source, 109 (Bacillus sp.) for the sedimentary phosphate source and, as for the soluble phosphate source most treatments that received bacterial isolates had higher phosphorus content in the dry matter than the uninoculated soluble phosphate control. The 105FCR (crystalline phosphate + Pseudomonas sp.), 109FSE (sedimentary phosphate + Bacillus sp.), and 110 FSE (sedimentary phosphate + Enterobacter sp.) treatments showed the best results for plant growth promotion. This work made it possible to determine the bacterial community associated with P. atratum (BGP308) and to obtain new potential plant growth-promoting strains

Search for dark matter produced in association with bottom or top quarks in √s = 13 TeV pp collisions with the ATLAS detector

A search for weakly interacting massive particle dark matter produced in association with bottom or top quarks is presented. Final states containing third-generation quarks and miss- ing transverse momentum are considered. The analysis uses 36.1 fb−1 of proton–proton collision data recorded by the ATLAS experiment at √s = 13 TeV in 2015 and 2016. No significant excess of events above the estimated backgrounds is observed. The results are in- terpreted in the framework of simplified models of spin-0 dark-matter mediators. For colour- neutral spin-0 mediators produced in association with top quarks and decaying into a pair of dark-matter particles, mediator masses below 50 GeV are excluded assuming a dark-matter candidate mass of 1 GeV and unitary couplings. For scalar and pseudoscalar mediators produced in association with bottom quarks, the search sets limits on the production cross- section of 300 times the predicted rate for mediators with masses between 10 and 50 GeV and assuming a dark-matter mass of 1 GeV and unitary coupling. Constraints on colour- charged scalar simplified models are also presented. Assuming a dark-matter particle mass of 35 GeV, mediator particles with mass below 1.1 TeV are excluded for couplings yielding a dark-matter relic density consistent with measurements