Numerical characterization of protein sequences based on the generalized Chou\u27s pseudo amino acid composition

The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical-chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a (21+λ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins

Roles of TGFβ and FGF signals during growth and differentiation of mouse lens epithelial cell in vitro.

Transforming growth factor β (TGFβ) and fibroblast growth factor (FGF) signaling pathways play important roles in the proliferation and differentiation of lens epithelial cells (LECs) during development. Low dosage bFGF promotes cell proliferation while high dosage induces differentiation. TGFβ signaling regulates LEC proliferation and differentiation as well, but also promotes epithelial-mesenchymal transitions that lead to cataracts. Thus far, it has been difficult to recapitulate the features of germinative LECs in vitro. Here, we have established a LEC culture protocol that uses SB431542 (SB) compound to inhibit TGFβ/Smad activation, and found that SB treatment promoted mouse LEC proliferation, maintained LECs' morphology and distinct markers including N-cadherin, c-Maf, Prox1, and αA-, αB-, and β-crystallins. In contrast, low-dosage bFGF was unable to sustain those markers and, combined with SB, altered LECs' morphology and β-crystallin expression. We further found that Matrigel substrate coatings greatly increased cell proliferation and uniquely affected β-crystallin expression. Cultured LECs retained the ability to differentiate into γ-crystallin-positive lentoids by high-dosage bFGF treatment. Thus, a suppression of TGFβ/Smad signaling in vitro is critical to maintaining characteristic features of mouse LECs, especially expression of the key transcription factors c-Maf and Prox1

Activation of extracellular signal-regulated protein kinase 5 is essential for cystitis- and nerve growth factor-induced calcitonin gene-related peptide expression in sensory neurons

Background Cystitis causes considerable neuronal plasticity in the primary afferent pathways. The molecular mechanism and signal transduction underlying cross talk between the inflamed urinary bladder and sensory sensitization has not been investigated. Results In a rat cystitis model induced by cyclophosphamide (CYP) for 48 h, the mRNA and protein levels of the excitatory neurotransmitter calcitonin gene-related peptide (CGRP) are increased in the L6 dorsal root ganglia (DRG) in response to bladder inflammation. Cystitis-induced CGRP expression in L6 DRG is triggered by endogenous nerve growth factor (NGF) because neutralization of NGF with a specific NGF antibody reverses CGRP up-regulation during cystitis. CGRP expression in the L6 DRG neurons is also enhanced by retrograde NGF signaling when NGF is applied to the nerve terminals of the ganglion-nerve two-compartmented preparation. Characterization of the signaling pathways in cystitis- or NGF-induced CGRP expression reveals that the activation (phosphorylation) of extracellular signal-regulated protein kinase (ERK)5 but not Akt is involved. In L6 DRG during cystitis, CGRP is co-localized with phospho-ERK5 but not phospho-Akt. NGF-evoked CGRP up-regulation is also blocked by inhibition of the MEK/ERK pathway with specific MEK inhibitors U0126 and PD98059, but not by inhibition of the PI3K/Akt pathway with inhibitor LY294002. Further examination shows that cystitis-induced cAMP-responsive element binding protein (CREB) activity is expressed in CGRP bladder afferent neurons and is co-localized with phospho-ERK5 but not phospho-Akt. Blockade of NGF action in vivo reduces the number of DRG neurons co-expressing CGRP and phospho-CREB, and reverses cystitis-induced increases in micturition frequency. Conclusions A specific pathway involving NGF-ERK5-CREB axis plays an essential role in cystitis-induced sensory activation

Coronal condensations caused by magnetic reconnection between solar coronal loops

Employing Solar Dynamics Observatory (SDO)/Atmospheric Imaging Assembly (AIA) multi-wavelength images, we report the coronal condensation during the magnetic reconnection (MR) between a system of open and closed coronal loops. Higher-lying magnetically open structures, observed in AIA 171 A images above the solar limb, move downward and interact with the lower-lying closed loops, resulting in the formation of dips in the former. An X-type structure forms at the interface. The interacting loops reconnect and disappear. Two sets of newly-reconnected loops then form and recede from the MR region. During the MR process, bright emission appears sequentially in the AIA 131 A and 304 A channels repeatedly in the dips of higher-lying open structures. This indicates the cooling and condensation process of hotter plasma from ~0.9 MK down to ~0.6 MK, and then to ~0.05 MK, also supported by the light curves of the AIA 171 A, 131 A, and 304 A channels. The part of higher-lying open structures supporting the condensations participate in the successive MR. The condensations without support by underlying loops then rain back to the solar surface along the newly-reconnected loops. Our results suggest that the MR between coronal loops leads to the condensation of hotter coronal plasma and its downflows. MR thus plays an active role in the mass cycle of coronal plasma because it can initiate the catastrophic cooling and condensation. This underlines that the magnetic and thermal evolution has to be treated together and cannot be separated, even in the case of catastrophic cooling.Comment: 10 pages, 6 figure

2-Chloro-4-(3,3-dichloro­all­yloxy)-1-nitro­benzene

In the crystal structure of the title compound, C9H6Cl3NO3, mol­ecules are connected by C—H⋯O hydrogen bonds, forming chains along the b axis. The dihedral angle between the benzene ring and the plane of the nitro group is 16.2 (1)° and that between the benzene ring and the plane of the dichloro­allyl group is 10.2 (1)°

Solid electrochemical mass spectrometry (SEMS) for investigation of supported metal catalysts under high vacuum

A new experimental set-up, coupling electrochemistry and mass spectroscopic techniques, for the investigation of a solid electrochemical cell under high vacuum conditions (HV) is presented. Two configurations are realized allowing the investigation of both the electrochemical and electrocatalytical behavior of a thin Pt layer on yttria stabilized zirconia (YSZ). We can readily select the atmosphere down to 10−6 Pa partial pressure and determine the response of the system in less than 1s. Under HV conditions, YSZ appears electrochemically active and we have identified, in the cathodic potential domain, the reduction/oxidation process of zirconia and in the anodic domain, the platinum oxidation/reduction and the oxygen evolution reactions. In a catalytic active gas mixture, despite the Faradaic enhancement of the CO oxidation observed over Pt/YSZ during an anodic polarization, an intriguing sustainable enhanced Pt/YSZ catalyst activity is achieved after current interruptio