Ontogenic variations in the content and distribution of progesterone receptor isoforms in the reproductive tract and brain of chicks

Progesterone participates in the regulation of several functions in chicks such as ovulation, gonadal differentiation, and sexual and nesting behaviors. Many progesterone actions are mediated by specific intracellular receptors (PR) which are ligand-induced transactivators. Two PR isoforms that are functionally distinct in their ability to activate genes and regulate distinct physiological processes have been described in chicks: a full length form PR-B and the N-terminally truncated one PR-A which lacks the amino-terminal 128 amino acids of PR-B. PR isoforms have been detected in several tissues of both the adult and the embryo chick such as brain, ovary and oviduct. PR isoforms expression ratio varies among progesterone target tissues and under different hormonal and environmental conditions such as those presented during avian sexual maturity and the seasons of the year. These data let us to conclude that progesterone actions in brain, ovary, and oviduct highly depend on PR isoforms expression pattern and regulation.     

Nitric oxide production by haemocytes from Mytilus galloprovincialis shows seasonal variations

Nitric oxide (NO) has been identified as an important physiological modulator, with evidence of its role as a signalling molecule throughout the whole phylogenetic scale. In marine molluscs, it intervenes in processes related to the immune function of haemocytes. The presented results indicate that basal NO production by haemocytes of Mytilus galloprovincialis shows seasonal variations, with summer values statistically higher than those of winter. The presence of IL-2 increased NO production in winter. In summer, incubating the haemocytes with TNF-alpha for 6h slightly increased NO production. LPS, TGF-beta1 or PDGF did not induce significant effects on NO production by the haemocytes. Immunoblotting experiments detected two proteins that bind to vertebrate iNOS and eNOS antibodies, with different seasonal expression: the protein that binds to anti-iNOS antibody was expressed throughout the year, whereas the anti-eNOS antibody bound with a protein that was only detected in winter. IL-2 is suggested to start a signalling system dependent on the seasonal presence of winter protein. Such a system would activate the enzyme, thus favouring the higher NO production detected in winter.     

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

MOTIVATION: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. RESULTS: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. AVAILABILITY: http://sbg.cib.csic.es/Software/ADP_EM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

A general strategy to determine the congruence between a hierarchical and a non-hierarchical classification

Background  

Classification procedures are widely used in phylogenetic inference, the analysis of expression profiles, the study of biological networks, etc. Many algorithms have been proposed to establish the similarity between two different classifications of the same elements. However, methods to determine significant coincidences between hierarchical and non-hierarchical partitions are still poorly developed, in spite of the fact that the search for such coincidences is implicit in many analyses of massive data.     

Implication of PKC in the seasonal variation of the immune response of the hemocytes of Mytilus galloprovincialis Lmk. and its role in interleukin-2-induced nitric oxide synthesis

The hemocytes are the cells responsible for the immune response in marine mollusks. The role of NO in processes related to the activation of the hemocytes has turned out evident over the late years. In the case of the mussel Mytilus galloprovincialis Lmk., hemocyte NO basal production varies throughout the year, showing a maximum in summer and a minimum in winter. IL-2 reverts the low winter NO basal production through a process mediated by cAMP-dependent protein kinase and by an apparent side effect of protein kinase C. The seasonal variation of NO production in the presence of the PKC inhibitor bisindolylmaleimide (BSM) allows suggesting a model in which PKC would modulate the activity of the enzymes responsible for nitric oxide production.     

Nonlinear optical imaging to evaluate the impact of obesity on mammary gland and tumor stroma

Obesity is an established risk factor for breast cancer incidence and mortality. However, the mechanism that links obesity to tumorigenesis is not well understood. Here we combined nonlinear optical imaging technologies with an early-onset diet-induced obesity breast cancer animal model to evaluate the impact of obesity on the composition of mammary gland and tumor stroma. Using coherent anti-Stokes Raman scattering and second harmonic generation on the same platform, we simultaneously imaged mammary adipocytes, blood capillaries, collagen fibrils, and tumor cells without any labeling. We observed that obesity increases the size of lipid droplets of adipocytes in mammary gland and collagen content in mammary tumor stroma, respectively. Such impacts of obesity on mammary gland and tumor stroma could not be analyzed using standard two-dimensional histologic evaluation. Given the importance of mammary stroma to the growth and migration of tumor cells, our observation provides the first imaging evidence that supports the relationship between obesity and breast cancer risk.     

Trans-oligomerization of duplicated aminoacyl-tRNA synthetases maintains genetic code fidelity under stress

Aminoacyl-tRNA synthetases (aaRSs) play a key role in deciphering the genetic message by producing charged tRNAs and are equipped with proofreading mechanisms to ensure correct pairing of tRNAs with their cognate amino acid. Duplicated aaRSs are very frequent in Nature, with 25,913 cases observed in 26,837 genomes. The oligomeric nature of many aaRSs raises the question of how the functioning and oligomerization of duplicated enzymes is organized. We characterized this issue in a model prokaryotic organism that expresses two different threonyl-tRNA synthetases, responsible for Thr-tRNA^Thr synthesis: one accurate and constitutively expressed (T1) and another (T2) with impaired proofreading activity that also generates mischarged Ser-tRNA^Thr. Low zinc promotes dissociation of dimeric T1 into monomers deprived of aminoacylation activity and simultaneous induction of T2, which is active for aminoacylation under low zinc. T2 either forms homodimers or heterodimerizes with T1 subunits that provide essential proofreading activity in trans. These findings evidence that in organisms with duplicated genes, cells can orchestrate the assemblage of aaRSs oligomers that meet the necessities of the cell in each situation. We propose that controlled oligomerization of duplicated aaRSs is an adaptive mechanism that can potentially be expanded to the plethora of organisms with duplicated oligomeric aaRSs.     

First phylogenetic analysis of the family Neriidae (Diptera), with a study on the issue of scaling continuous characters

Neriidae are a small family of acalyptratae flies, mostly distributed in the tropics. Very little is known about their biology, and the evolutionary relationships among species have never been evaluated. We perform the first comprehensive phylogenetic analysis of the family, including 48 species from all biogeographic regions inhabited, as well as five species of Micropezidae and one Cypselosomatidae as outgroups. We build a morphological data matrix of 194 characters, including 72 continuous characters. We first explore ways to deal with the issue of scaling continuous characters, including rescaling ranges to unity and using implied weighting. We find that both strategies result in very different phylogenetic hypotheses, and that implied weighting reduces the problem of scaling, but only partially. Furthermore, using implied weighting after rescaling characters improves the congruence between partitions and results in higher values of group support. With respect to the Neriidae, we confirm the monophyly of the family and of most its genera, although we do not obtain any of the currently accepted suprageneric groups. We propose to restrict the Eoneria and Nerius groups exclusively to the Neotropical fauna, and synonymize Glyphidops subgenus Oncopsia Enderlein with Glyphidops subgenus Glyphidops Enderlein, eliminating the subgeneric divisions. This revised phylogeny presents a striking biogeographic consistency, and shows that previous main divisions of the family were based on events of convergence.     

Retraction: ‘Are European birds leaving traditional wintering grounds in the Mediterranean?’, by José Luis Tellería, Álvaro Ramírez and José Ignacio Aguirre

The above article, published online on 20 January 2015 in Wiley Online Library ( wileyonlinelibrary.com ), has been retracted by agreement between the authors, the journal Editors in Chief, Thomas Alerstam and Jan‐Åke Nilsson, the Nordic Society Oikos and John Wiley and Sons Ltd. The aim of this study was to answer the question, ‘Are European birds leaving traditional wintering grounds in the Mediterranean?’ Due to an analytical error the study only analysed EURING circumstance 20 ring records (see the EURING exchange code) which excludes birds hunted by shot and other ways, but not all hunted individuals. As a result, the effect of illegal hunting on ring recoveries was not controlled for in the analyses. This means that the data is affected by ring records from birds other than ‘alive and probably healthy and released by ringer’ (condition 8 in the EURING exchange code). The authors' intention always was to include both condition 8 and circumstance 20, but unfortunately this was not the case. When the data was reanalysed including both condition 8 and circumstance 20 recoveries, there is no longer any support for the main conclusion of the paper and the authors can only conclude that winter ring recoveries in Spain of some common passerines (robin, chiffchaff and blackcap) do not decrease. The authors apologise for this mistake and hope that the retraction will serve to prevent the spread of the unsound conclusions derived from this paper.