655 research outputs found
Capturing coevolutionary signals in repeat proteins
The analysis of correlations of amino acid occurrences in globular proteins
has led to the development of statistical tools that can identify native
contacts -- portions of the chains that come to close distance in folded
structural ensembles. Here we introduce a statistical coupling analysis for
repeat proteins -- natural systems for which the identification of domains
remains challenging. We show that the inherent translational symmetry of repeat
protein sequences introduces a strong bias in the pair correlations at
precisely the length scale of the repeat-unit. Equalizing for this bias reveals
true co-evolutionary signals from which local native-contacts can be
identified. Importantly, parameter values obtained for all other interactions
are not significantly affected by the equalization. We quantify the robustness
of the procedure and assign confidence levels to the interactions, identifying
the minimum number of sequences needed to extract evolutionary information in
several repeat protein families. The overall procedure can be used to
reconstruct the interactions at long distances, identifying the characteristics
of the strongest couplings in each family, and can be applied to any system
that appears translationally symmetric
The use of the ACC deaminase producing bacterium Pseudomonas putida UW4 as a biocontrol agent for pine wilt disease
Pine wilt disease, caused by the nematode Bursaphelenchus xylophilus, is responsible for the devastation of worldwide pine forestlands. Until today, the only effective solution to this serious threat resides on the destruction of infected trees, which is both economic and ecologically unacceptable. The use of ACC deaminase-producing plant growth promoting bacteria has been shown to be a useful strategy in order to reduce biotic and abiotic constraints that affect plant health and development. In this sense, we report the use of the ACC deaminase-producing bacterium Pseudomonas putida UW4 as a potential biological control agent for pine wilt disease. An inoculation assay was performed in 3-4 months Pinus pinaster (maritime pine) seedlings obtained from a nursery in Portugal. The bacteria P. putida UW4 wild-type and ACC deaminase mutant strains were inoculated in the roots of pine seedlings followed by stem inoculation of B. xylophilus. The inoculation of the P. putida UW4 wild-type strain lead to a significant reduction of B. xylophilus induced symptoms. Moreover, regardless the inoculation with B. xylophilus, seedlings inoculated with P. putida UW4 also demonstrated an increased root and shoot development. In addition, P. putida UW4 ACC deaminase knockout mutant was unable to promote pine seedling growth or to decrease B. xylophilus induced symptoms. The results obtained indicate that the inoculation of ACC deaminase-producing bacteria in pine seedlings growing in a nursery system might constitute a novel strategy to obtain B. xylophilus resistant pine trees. This is the first report on the use of ACC deaminase-producing bacteria as potential biological control agents for tree diseases
Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space
The notion of energy landscapes provides conceptual tools for understanding
the complexities of protein folding and function. Energy Landscape Theory
indicates that it is much easier to find sequences that satisfy the "Principle
of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G.
Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci.
U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be
fundamentally related to landscapes with multiple embedded funnels. Here we
present analytical tools to detect and compare structural repetitions in
protein molecules. By an exhaustive analysis of the distribution of structural
repeats using a robust metric we define those portions of a protein molecule
that best describe the overall structure as a tessellation of basic units. The
patterns produced by such tessellations provide intuitive representations of
the repeating regions and their association towards higher order arrangements.
We find that some protein architectures can be described as nearly periodic,
while in others clear separations between repetitions exist. Since the method
is independent of amino acid sequence information we can identify structural
units that can be encoded by a variety of distinct amino acid sequences
Villagorgin A and B : new type of indole alkaloids with acetylcholine antagonist activity from the gorgonian Villagorgia rubra
La declaración unilateral de independencia de Kosovo a la luz de la Opinión Consultiva de la Corte Internacional de Justicia, de 22 de julio de 2010 y de las declaraciones, opiniones individuales y disidentes a la misma
The Opinion of the International Court of Justice on the unilateral declaration of independence of Kosovo is an example of what the Court should not do. Saying only that international law does not prohibit declarations of independence and refusing to answer the matters related to this claim, the Court's opinion adopts a vacuum of legal terms and irresponsible
Tests of star formation metrics in the low metallicity galaxy NGC 5253 using ALMA observations of H30 line emission
We use Atacama Large Millimeter/submillimeter Array (ALMA) observations of
H30 (231.90 GHz) emission from the low metallicity dwarf galaxy NGC
5253 to measure the star formation rate (SFR) within the galaxy and to test the
reliability of SFRs derived from other commonly-used metrics. The H30
emission, which originates mainly from the central starburst, yields a
photoionizing photon production rate of (1.90.3)10 s
and an SFR of 0.0870.013 M yr based on conversions that
account for the low metallicity of the galaxy and for stellar rotation. Among
the other star formation metrics we examined, the SFR calculated from the total
infrared flux was statistically equivalent to the values from the H30
data. The SFR based on previously-published versions of the H flux that
were extinction corrected using Pa and Pa lines were lower than
but also statistically similar to the H30 value. The mid-infrared (22
m) flux density and the composite star formation tracer based on H
and mid-infrared emission give SFRs that were significantly higher because the
dust emission appears unusually hot compared to typical spiral galaxies.
Conversely, the 70 and 160 m flux densities yielded SFR lower than the
H30 value, although the SFRs from the 70 m and H30 data
were within 1-2 of each other. While further analysis on a broader
range of galaxies are needed, these results are instructive of the best and
worst methods to use when measuring SFR in low metallicity dwarf galaxies like
NGC 5253.Comment: 14 pages, 5 figures, accepted for publication in MNRA
Chemistry in isolation: High CCH/HCO+ line ratio in the AMIGA galaxy CIG 638
Multi-molecule observations towards an increasing variety of galaxies have
been showing that the relative molecular abundances are affected by the type of
activity. However, these studies are biased towards bright active galaxies,
which are typically in interaction. We study the molecular composition of one
of the most isolated galaxies in the local Universe where the physical and
chemical properties of their molecular clouds have been determined by intrinsic
mechanisms. We present 3 mm broad band observations of the galaxy CIG 638,
extracted from the AMIGA sample of isolated galaxies. The emission of the J=1-0
transitions of CCH, HCN, HCO+, and HNC are detected. Integrated intensity
ratios between these line are compared with similar observations from the
literature towards active galaxies including starburst galaxies (SB), active
galactic nuclei (AGN), luminous infrared galaxies (LIRG), and GMCs in M33. A
significantly high ratio of CCH with respect to HCN, HCO+, and HNC is found
towards CIG 638 when compared with all other galaxies where these species have
been detected. This points to either an overabundance of CCH or to a relative
lack of dense molecular gas as supported by the low HCN/CO ratio, or both. The
data suggest that the CIG 638 is naturally a less perturbed galaxy where a
lower fraction of dense molecular gas, as well as a more even distribution
could explain the measured ratios. In this scenario the dense gas tracers would
be naturally dimmer, while the UV enhanced CCH, would be overproduced in a less
shielded medium.Comment: Letter accepted for publication in A&
Comunicación corta. Exportación de los macroelementos mayoritarios por los frutos de diferentes cultivares de almendro
The amount of the major macroelements required to produce a given crop has been determined for a set of 11 almond (Prunus amygdalus Batsch) cultivars growing in the Middle Ebro Valley (NE Spain). A wide diversity of nutrient exports was found among the different cultivars. Although the production of kernels is the main objective when growing almonds, all the different fruit components: the mesocarp (hull), the endocarp (shell) and the seed (kernel), were taken into account. The different fruit components showed a great variation among cultivars, and the amount of fruit dry matter required for producing 1 kg of kernel ranged from 4.32 kg in ‘Guara’ to 10.56 kg in ‘Desmayo Largueta’. Similarly, the macroelement requirements to produce a given amount of kernels varied among the different cultivars. ‘Guara’ has proved to be the most effective cultivar in taking advantage of the mineral elements for producing a crop, showing that this efficiency is independent of the shell type. Se determinó la cantidad de macroelementos mayoritarios necesarios para producir una determinada cantidad de cosecha en un grupo de 11 cultivares de almendro (Prunus amygdalus Batsch) cultivados en el Valle Medio del Ebro (NE de España). Se encontró una gran diversidad de requerimientos entre los diferentes cultivares. Aunque la producción de pepitas es el objetivo principal en el cultivo del almendro, todos los componentes del fruto se han de tener en cuenta en este cálculo: el mesocarpo (la piel), el endocarpo (la cáscara) y la semilla (la pepita). Estos tres componentes del fruto mostraron una gran variabilidad entre los cultivares y la cantidad de materia seca necesaria para producir 1 kg de pepita osciló entre 4,32 kg en ‘Guara’ y 10,56 kg en ‘Desmayo Largueta’. Igualmente, los requisitos en macroelementos para producir una cantidad determinada de pepita varió entre los diferentes cultivares. ‘Guara’ mostró ser el cultivar más eficiente en la utilización de los elementos minerales para la producción de una cosecha, mostrando que esta eficiencia es independiente del tipo de cáscara
Investigation of the pathways related to intrinsic miltefosine tolerance in Leishmania (Viannia) braziliensis clinical isolates reveals differences in drug uptake
In Brazil, cutaneous leishmaniasis is caused predominantly by L. (V.) braziliensis. The few therapeutic drugs available exhibit several limitations, mainly related to drug toxicity and reduced efficacy in some regions. Miltefosine (MF), the only oral drug available for leishmaniasis treatment, is not widely available and has not yet been approved for human use in Brazil. Our group previously reported the existence of differential susceptibility among L. (V.) braziliensis clinical isolates. In this work, we further characterized three of these isolates of L. (V.) braziliensis chosen because they exhibited the lowest and the highest MF half maximal inhibitory concentrations and were therefore considered less tolerant or more tolerant, respectively. Uptake of MF, and also of phosphocholine, were found to be significantly different in more tolerant parasites compared to the less sensitive isolate, which raised the hypothesis of differences in the MF transport complex Miltefosine Transporter (MT)-Ros3. Although some polymorphisms in those genes were found, they did not correlate with the drug susceptibility phenotype. Drug efflux and compartmentalization were similar in the isolates tested, and amphotericin B susceptibility was retained in MF tolerant parasites, suggesting that increased fitness was also not the basis of observed differences. Transcriptomic analysis revealed that Ros3 mRNA levels were upregulated in the sensitive strain compared to the tolerant ones. Increased mRNA abundance in more tolerant isolates was validated by quantitative PCR. Our results suggest that differential gene expression of the MT transporter complex is the basis of the differential susceptibility in these unselected, naturally occurring parasites
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