Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists

<p>Abstract</p> <p>Background</p> <p>The increasing protein family and domain based annotations constitute important information to understand protein functions and gain insight into relations among their codifying genes. To allow analyzing of gene proteomic annotations, we implemented novel modules within <it>GFINDer</it>, a Web system we previously developed that dynamically aggregates functional and phenotypic annotations of user-uploaded gene lists and allows performing their statistical analysis and mining.</p> <p>Results</p> <p>Exploiting protein information in Pfam and InterPro databanks, we developed and added in <it>GFINDer </it>original modules specifically devoted to the exploration and analysis of functional signatures of gene protein products. They allow annotating numerous user-classified nucleotide sequence identifiers with controlled information on related protein families, domains and functional sites, classifying them according to such protein annotation categories, and statistically analyzing the obtained classifications. In particular, when uploaded nucleotide sequence identifiers are subdivided in classes, the <it>Statistics Protein Families&Domains </it>module allows estimating relevance of Pfam or InterPro controlled annotations for the uploaded genes by highlighting protein signatures significantly more represented within user-defined classes of genes. In addition, the <it>Logistic Regression </it>module allows identifying protein functional signatures that better explain the considered gene classification.</p> <p>Conclusion</p> <p>Novel <it>GFINDer </it>modules provide genomic protein family and domain analyses supporting better functional interpretation of gene classes, for instance defined through statistical and clustering analyses of gene expression results from microarray experiments. They can hence help understanding fundamental biological processes and complex cellular mechanisms influenced by protein domain composition, and contribute to unveil new biomedical knowledge about the codifying genes.</p

Los dobles participios en español: Estudio de corpus

Some verbs in Spanish present in their non-finite verb form of past participles the possibility of possessing both a regular and an irregular form: 'Freído'/'frito'(fried), 'imprimido'/'impreso' (printed), etc. It is well known that the past participle may function both as a verb and as an adjective, and this universality makes it particularly interesting to observe how these doublets of participles are applied and in which contexts they appear in contemporary Spanish, aspect this investigation wish to elaborate. In order to delimit the investigation and to be able to provide sufficiently detailed descriptions, we will focus the study on the four participles pairs, that is, 'bendecido'/'bendito' (from the verb 'bendecir' [to bless]), 'freído'/'frito' (from the verb 'freír' [to fry]), 'imprimido'/'impreso' (from the verbo 'imprimir' [to print]) and 'corrompido'/'corrupto' (from the verb 'corromper' [to corrupt]). We have through in-depth analysis of examples found in various corpus of the Spanish language (i.e. El corpus de CREA and El corpus del Español de Davies) discovered that they show distributional differences when it comes to this double functionality of the participles. It appears that the regular forms 'bendecido', 'freído' and 'imprimido' are exclusively verbal forms, while the irregular participles 'bendito' and 'corrupto' always receive adjectival interpretations. The regular form 'corrompido' and the irregular participles 'frito' and 'impreso', on the other hand, may alternate between the two possible functions. Furthermore, this thesis relates the discoveries with two fundamental morphological theories, that is, lexicalism and constructionism. None of these two linguistic theories as they are formulated today provide appropriate explanations, and therefore we suggest that it is necessary to address each verb separately in order to understand the alternation between the two participial forms, considering the syntactic, semantic and even geographic factors of each verb

Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists-0

<p><b>Copyright information:</b></p><p>Taken from "Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists"</p><p>http://www.biomedcentral.com/1471-2105/8/S1/S14</p><p>BMC Bioinformatics 2007;8(Suppl 1):S14-S14.</p><p>Published online 8 Mar 2007</p><p>PMCID:PMC1885843.</p><p></p>ro entry (D: protein domain); Tree: tree label in the defined protein domain parent/child hierarchy, if any; Level: level in the related tree of the defined protein domain parent/child hierarchy, if any (higher levels correspond to more specific protein domains); Num. (%): absolute and percentage number of considered genes that codify proteins containing the specific protein domain (Category Name)

Basic properties of somatosensory-evoked responses in the dorsal hippocampus of the rat

Peer Reviewe

Tailoring light delivery for optogenetics by modal demultiplexing in tapered optical fibers

Optogenetic control of neural activity in deep brain regions ideally requires precise and flexible light delivery with non-invasive devices. To this end, Tapered Optical Fibers (TFs) represent a versatile tool that can deliver light over either large brain volumes or spatially confined sub-regions, while being sensibly smaller than flat-cleaved optical fibers. In this work, we report on the possibility of further extending light emission length along the taper in the range 0.4 mm-3.0 mm by increasing the numerical aperture of the TFs to NA = 0.66. We investigated the dependence between the input angle of light (θin) and the output position along the taper, finding that for θin > 10° this relationship is linear. This mode-division demultiplexing property of the taper was confirmed with a ray tracing model and characterized for 473 nm and 561 nm light in quasi-transparent solution and in brain slices, with the two wavelengths used to illuminate simultaneously two different regions of the brain using only one waveguide. The results presented in this manuscript can guide neuroscientists to design their optogenetic experiments on the base of this mode-division demultiplexing approach, providing a tool that potentially allow for dynamic targeting of regions with diverse extension, from the mouse VTA up to the macaque visual cortex

SU-8 based microprobes with integrated planar electrodes for enhanced neural depth recording

Here, we describe new fabrication methods aimed to integrate planar tetrode-like electrodes into a polymer SU-8 based microprobe for neuronal recording applications. New concepts on the fabrication sequences are introduced in order to eliminate the typical electrode-tissue gap associated to the passivation layer. Optimization of the photolithography technique and high step coverage of the sputtering process have been critical steps in this new fabrication process. Impedance characterization confirmed the viability of the electrodes for reliable neuronal recordings with values comparable to commercial probes. Furthermore, a homogeneous sensing behavior was obtained in all the electrodes of each probe. Finally, . in vivo action potential and local field potential recordings were successfully obtained from the rat dorsal hippocampus. Peak-to-peak amplitude of action potentials ranged from noise level to up to 400-500. μV. Moreover, action potentials of different amplitudes and shapes were recorded from all the four recording sites, suggesting improved capability of the tetrode to distinguish from different neuronal sources. © 2012 Elsevier B.V.This was supported by the Basque Government under the Etortek-Microsystems program, the ERANET-Neuron project EPINet (EUI2009-04093) and SAF2009-14724-C02-02 from the Spanish Ministry of Science and Innovation and the European Regional Development Fund.Peer Reviewe

Determinants of different deep and superficial CA1 pyramidal cell dynamics during sharp-wave ripples

Sharp-wave ripples represent a prominent synchronous activity pattern in the mammalian hippocampus during sleep and immobility. GABAergic interneuronal types are silenced or fire during these events, but the mechanism of pyramidal cell (PC) participation remains elusive. We found opposite membrane polarization of deep (closer to stratum oriens) and superficial (closer to stratum radiatum) rat CA1 PCs during sharp-wave ripples. Using sharp and multi-site recordings in combination with neurochemical profiling, we observed a predominant inhibitory drive of deep calbindin (CB)-immunonegative PCs that contrasts with a prominent depolarization of superficial CB-immunopositive PCs. Biased contribution of perisomatic GABAergic inputs, together with suppression of CA2 PCs, may explain the selection of CA1 PCs during sharp-wave ripples. A deep-superficial gradient interacted with behavioral and spatial effects to determine cell participation during sleep and awake sharp-wave ripples in freely moving rats. Thus, the firing dynamics of hippocampal PCs are exquisitely controlled at subcellular and microcircuit levels in a cell type–selective manner.This work was supported by a grant from the Spanish Ministerio de Economía y Competitividad (BFU2012-37156-C03-01). E.C. receives funding from the CSIC JAE Program, co-funded by the European Social Fund. M.V. was supported by the Spanish Ministry of Education, Culture and Sports (FPU12/03776) and by a short-term grant to visit the MRC Anatomical Neuropharmacological Unit in Oxford (FPU-EST13/01046). A.S.-A. is funded by the Universidad Complutense de Madrid. T.J.V. was supported by the UK Medical Research Council. R.G.A. was supported by an ERC Advanced grant (INTERIMPACT) to G. Tamás. D.G.-D. is funded by the Spanish Ministerio de Economía y Competitividad (BES-2013-064171)