2,338 research outputs found
Two mini-preparation protocols to DNA extraction from plants with high polysaccharide and secondary metabolites
Were standardized two previously reported standard plant DNA extraction methods, but improved them on mini preparations to use the samples for population genetic analysis. The combination of CTAB lysis procedure-solvent extraction and DNA column purification (DNeasy plant mini kit modification) enables a faster and reliable DNA extraction from all samples tested: Piper, Quercus, Zea and cacti species (considered “hard” extraction species), and this protocol uses smaller tissue samples than other mini or midi-prep protocols. We obtained high quality and DNA yields in all samples tested. This alternative protocol (CTAB lysis-solvent extraction based) is an excellent option if there are many samples to process and it is also a non expensive protocol. This method also produces good DNA quality but fewer yields. Both two protocols produce reproducible PCR pattern-bands amplification with all the genetic markers tested (RAPD’s and microsatellites). The DNA obtained was used in other molecular biology standard analysis methods, like enzymptic restriction patterns, ligation, sequencing and cloning with good results too
Bacillus subtilis RarA Acts as a Positive RecA Accessory Protein
Ubiquitous RarA AAA+ ATPases play crucial roles in the cellular response to blocked replication forks in pro- and eukaryotes. Here, we provide evidence that RarA regulates the activity of the central player in homologous recombination (HR), RecA, in response to DNA damage. During unperturbed growth, absence of RarA reduced the viability of recA, recO and recF15 cells, and during repair of H2O2- or MMS-induced DNA damage, rarA was epistatic to recA, recO and recF. Conversely, the inactivation of rarA partially suppressed the HR defect of mutants lacking end-resection (addAB, recJ, recQ, recS) or branch migration (ruvAB, recG, radA) activity. RarA contributes to RecA thread formation, that are thought to be the active forms of RecA during homology search. The absence of RarA reduced RecA accumulation, and the formation of visible RecA threads in vivo upon DNA damage. When rarA was combined with mutations in genuine RecA accessory genes, RecA accumulation was further reduced in rarA recU and rarA recX double mutant cells, and was blocked in rarA recF15 cells. These results suggest that RarA contributes to the assembly of RecA nucleoprotein filaments onto single-stranded DNA (ssDNA), in concert with RecF, and possibly antagonizes RecA filament disassembly by RecX or RecU.Peer reviewe
Modular classes of skew algebroid relations
Skew algebroid is a natural generalization of the concept of Lie algebroid.
In this paper, for a skew algebroid E, its modular class mod(E) is defined in
the classical as well as in the supergeometric formulation. It is proved that
there is a homogeneous nowhere-vanishing 1-density on E* which is invariant
with respect to all Hamiltonian vector fields if and only if E is modular, i.e.
mod(E)=0. Further, relative modular class of a subalgebroid is introduced and
studied together with its application to holonomy, as well as modular class of
a skew algebroid relation. These notions provide, in particular, a unified
approach to the concepts of a modular class of a Lie algebroid morphism and
that of a Poisson map.Comment: 20 page
Crowd Learning with Candidate Labeling: an EM-based Solution
Crowdsourcing is widely used nowadays in machine learning for data labeling. Although in the traditional case annotators are
asked to provide a single label for each instance, novel approaches allow annotators, in case of doubt, to choose a subset of labels as a way to extract more information from them. In both the traditional and these novel approaches, the reliability of the labelers can be modeled based on the collections of labels that they provide. In this paper, we propose an Expectation-Maximization-based method for crowdsourced data with candidate sets. Iteratively the likelihood of the parameters that model
the reliability of the labelers is maximized, while the ground truth is estimated. The experimental results suggest that the proposed method performs better than the baseline aggregation schemes in terms of estimated accuracy.BES-2016-078095
SVP-2014-068574
IT609-13
TIN2016-78365-
Mitocondrial COI and 16S rDNA sequences support morphological identification and biogeography of deep-sea red crabs of the genus Chaceon (Crustacea, Decapoda, Geryonidae) in the Eastern Central and South Atlantic Ocean
The geographical spreading of new fishing activities and the increasingly deeper locations of these activities have shown the worldwide distribution of gerionid crabs and new descriptions of Chaceon taxa. However, incomplete penetrance, variable expressivity, and phenotypic overlap make the morphometric identification of these species difficult. In this study, partial sequences of the cytochrome c oxidase subunit 1 (COI) and 16S mitochondrial ribosomal RNA (16S rRNA) genes have been analyzed in Chaceon species from the Eastern Central and South Atlantic and compared with sequences of species from Western Atlantic. Our results corroborate the proposed morphological species and highlight the significant separation of the Eastern Atlantic species and those from Atlantic coasts of South America for both markers (97% Bayesian posterior probability, BPP / 83% Bootstrap replicates, BT). Interestingly, Chaceon sanctaehelenae shows a closer relationship with the species of the American coast than with those from the Eastern Atlantic. On the other hand, while COI marker clearly separates Chaceon atopus and Chaceon erytheiae species (99 BPP / 91% BT), these species share haplotypes for the 16S rRNA marker, pointing to a recent speciation process. Moreover, a close relationship was observed between Chaceon maritae and Chaceon affinis (94% BPP / 77% BT). The topologies of the trees obtained indicate that the ancestor of this genus was closer related to those species from South America than to those from the Eastern Atlantic.Versión del edito
Impact of Insecticides on Parasitoids of the Leafminer, Liriomyza trifolii, in Pepper in South Texas
Liriomyza leafminers (Diptera: Agromyzidae) are cosmopolitan, polyphagous pests of horticultural plants and many are resistant to insecticides. Producers in South Texas rely on insecticides as the primary management tool for leafminers, and several compounds are available. The objective of this study is to address the efficacy of these compounds for controlling Liriomyza while minimizing their effects against natural enemies. Research plots were established at Texas AgriLife research center at Weslaco, Texas in fall 2007 and spring 2008 seasons, and peppers were used as a model crop. Plots were sprayed with novaluron, abamectin, spinetoram, lambda-cyhalothrin and water as treatments according to leafminer infestation; insecticide efficacy was monitored by collecting leaves and infested foliage. Plant phenology was also monitored. Novaluron was the most effective insecticide and lambda-cyhalothrin showed resurgence in leafminer density in fall 2007 and no reduction in spring 2008. Other compounds varied in efficacy. Novaluron showed the least number of parasitoids per leafminer larva and the lowest parasitoid diversity index among treatments followed by spinetoram. Liriomyza trifolii (Burgess) was the sole leafminer species on peppers, and 19 parasitoid species were found associated with this leafminer. Application of these insecticides for management of leafminers with conservation of natural enemies is discussed
Non-L\'evy mobility patterns of Mexican Me'Phaa peasants searching for fuelwood
We measured mobility patterns that describe walking trajectories of
individual Me'Phaa peasants searching and collecting fuelwood in the forests of
"La Monta\~na de Guerrero" in Mexico. These one-day excursions typically follow
a mixed pattern of nearly-constant steps when individuals displace from their
homes towards potential collecting sites and a mixed pattern of steps of
different lengths when actually searching for fallen wood in the forest.
Displacements in the searching phase seem not to be compatible with L\'evy
flights described by power-laws with optimal scaling exponents. These findings
however can be interpreted in the light of deterministic searching on heavily
degraded landscapes where the interaction of the individuals with their scarce
environment produces alternative searching strategies than the expected L\'evy
flights. These results have important implications for future management and
restoration of degraded forests and the improvement of the ecological services
they may provide to their inhabitants.Comment: 15 pages, 4 figures. First version submitted to Human Ecology. The
final publication will be available at http://www.springerlink.co
Measuring every particle's size from three-dimensional imaging experiments
Often experimentalists study colloidal suspensions that are nominally
monodisperse. In reality these samples have a polydispersity of 4-10%. At the
level of an individual particle, the consequences of this polydispersity are
unknown as it is difficult to measure an individual particle size from
microscopy. We propose a general method to estimate individual particle radii
within a moderately concentrated colloidal suspension observed with confocal
microscopy. We confirm the validity of our method by numerical simulations of
four major systems: random close packing, colloidal gels, nominally
monodisperse dense samples, and nominally binary dense samples. We then apply
our method to experimental data, and demonstrate the utility of this method
with results from four case studies. In the first, we demonstrate that we can
recover the full particle size distribution {\it in situ}. In the second, we
show that accounting for particle size leads to more accurate structural
information in a random close packed sample. In the third, we show that crystal
nucleation occurs in locally monodisperse regions. In the fourth, we show that
particle mobility in a dense sample is correlated to the local volume fraction.Comment: 7 pages, 5 figure
Scaling properties of protein family phylogenies
One of the classical questions in evolutionary biology is how evolutionary
processes are coupled at the gene and species level. With this motivation, we
compare the topological properties (mainly the depth scaling, as a
characterization of balance) of a large set of protein phylogenies with a set
of species phylogenies. The comparative analysis shows that both sets of
phylogenies share remarkably similar scaling behavior, suggesting the
universality of branching rules and of the evolutionary processes that drive
biological diversification from gene to species level. In order to explain such
generality, we propose a simple model which allows us to estimate the
proportion of evolvability/robustness needed to approximate the scaling
behavior observed in the phylogenies, highlighting the relevance of the
robustness of a biological system (species or protein) in the scaling
properties of the phylogenetic trees. Thus, the rules that govern the
incapability of a biological system to diversify are equally relevant both at
the gene and at the species level.Comment: Replaced with final published versio
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