CED: a conformational epitope database

BACKGROUND: Antigen epitopes provide valuable information useful for disease prevention, diagnosis, and treatment. Recently, more and more databases focusing on different types of epitopes have become available. Conformational epitopes are an important form of epitope formed by residues that are sequentially discontinuous but close together in three-dimensional space. These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes. DESCRIPTION: We describe CED, a special database of well defined conformational epitopes. CED provides a collection of conformational epitopes and related information including the residue make up and location of the epitope, the immunological property of the epitope, the source antigen and corresponding antibody of the epitope. All entries in this database are manually curated from articles published in peer review journals. The database can be browsed or searched through a user-friendly web interface. Most epitopes in CED can also be viewed interactively in the context of their 3D structures. In addition, the entries are also hyperlinked to various databases such as Swiss-Prot, PDB, KEGG and PubMed, providing wide background information. CONCLUSION: A conformational epitope database called CED has been developed as an information resource for investigators involved in both theoretical and applied immunology research. It complements other existing specialised epitope databases. The database is freely available a

Elastin Variants in Two Angiographic PCV Subtypes

Objective To compare the association of elastin (ELN) gene variants between two different angiographic phenotypes of polypoidal choroidal vasculopathy (PCV). Methods We included 411 treatment-naïve PCV patients and 350 controls in the present study. PCV was classified into two phenotypes (152 Type 1 and 259 Type 2) according to the presence or absence of feeding vessels found in indocyanine-green angiography. Single nucleotide polymorphisms (SNPs) in the ELN region including rs868005, rs884843, rs2301995, rs13239907 and rs2856728 were genotyped using TaqMan Genotyping Assays. Results In the allelic association analyses, rs868005 showed the strongest association with Type 2 PCV (allelic odds ratio 1.56; p = 7.4x10-6), while no SNP was significantly associated with Type 1 PCV. Genotype association analyses revealed the significant association of rs868005 with Type 2 PCV in log additive model and predominant model (odds ratio 1.75; p = 1.5x10-6 and odds ratio 1.60; p = 0.0044, respectively), but not with Type 1 PCV. These findings were further corroborated by another control group in the literature. Conclusions There may be significantly different associations in genetic variants of elastin between two angiographic phenotypes of PCV

A Case of Bilateral Macular Holes Showing Onset and Spontaneous Closure over Very Short Intervals

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Early Responses to Intravitreal Ranibizumab in Typical Neovascular Age-Related Macular Degeneration and Polypoidal Choroidal Vasculopathy

Purpose. To evaluate the early response to intravitreal ranibizumab (IVR) in two different phenotypes of age-related macular degenerations (AMD): typical neovascular AMD (tAMD) and polypoidal choroidal vasculopathy (PCV). Methods. Sixty eyes from 60 patients (tAMD 28, PCV 32 eyes) were recruited. Three consecutive IVR treatments (0.5 mg) were performed every month. Change in the best-corrected visual acuity (BCVA) and central retinal thickness (CRT) was then compared between the tAMD and PCV groups. Results. The mean BCVA logMAR was significantly improved at month 1 and month 3 after the initial IVR in the tAMD group, but there was no change in the PCV group. Both phenotypes showed significant improvements in the CRT during the 3 months after the initial IVR. There were no significant differences in the improvements of the CRT in the tAMD versus the PCV group. In the stepwise analysis, a worse pretreatment BCVA and tAMD lesions were significantly beneficial for a greater improvement of BCVA at 3 months after the initial IVR. Conclusions. The phenotype of tAMD showed a significantly better early response to IVR than PCV in terms of BCVA improvement

A calmodulin inhibitor, W-7 influences the effect of cyclic adenosine 3', 5'-monophosphate signaling on ligninolytic enzyme gene expression in Phanerochaete chrysosporium

The capacity of white-rot fungi to degrade wood lignin may be highly applicable to the development of novel bioreactor systems, but the mechanisms underlying this function are not yet fully understood. Lignin peroxidase (LiP) and manganese peroxidase (MnP), which are thought to be very important for the ligninolytic property, demonstrated increased activity in Phanerochaete chrysosporium RP-78 (FGSC #9002, ATCC MYA-4764™) cultures following exposure to 5 mM cyclic adenosine 3', 5'-monophosphate (cAMP) and 500 μM 3'-isobutyl-1-methylxanthine (IBMX), a phosphodiesterase inhibitor. Real-time reverse transcription polymerase chain reaction (RT-PCR) analysis revealed that transcription of most LiP and MnP isozyme genes was statistically significantly upregulated in the presence of the cAMP and IBMX compared to the untreated condition. However, 100 μM calmodulin (CaM) inhibitor N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), which had insignificant effects on fungal growth and intracellular cAMP concentration, not only offset the increased activity and transcription induced by the drugs, but also decreased them to below basal levels. Like the isozyme genes, transcription of the CaM gene (cam) was also upregulated by cAMP and IBMX. These results suggest that cAMP signaling functions to increase the transcription of LiP and MnP through the induction of cam transcription

Nucleation of the Primary Al Phase on TiAl 3 during Solidification in Hot-Dip Zn-11%Al-3%Mg-0.2%Si-Coated Steel Sheet * 1

The solidification structure of a hot-dip Zn-11%Al-3%Mg-0.2%Si coated steel sheet with a slight Ti addition was investigated by EBSD. In every center of the primary Al phase of the alloy-coating layer, TiAl 3 was observed by a scanning electron microscope, which suggests that TiAl 3 acts as a heterogeneous nucleation site of the primary Al phase. The latter was revealed to have perfect lattice coherency with the nucleus TiAl 3 phase. The crystal orientation relationships between TiAl 3 and the primary Al are ð001Þ TiAl3 == ð001Þ Al and ½100 TiAl3 == ½100 Al , ð100Þ TiAl3 == ð001Þ Al and ½001 TiAl3 == ½100 Al , ð102Þ TiAl3 == ð110Þ Al and ½ 2 201 TiAl3 == ½ 1 110 Al , ð110Þ TiAl3 == ð110Þ Al and ½ 1 110 TiAl3 == ½ 1 110 Al , indicating that the primary Al phase grows in an epitaxial manner from the nucleus TiAl 3 phase. The planar disregistry between the two phases was calculated to be less than 5%, owing to this good lattice coherency. The TiAl 3 phase is considered to decrease the degree of undercooling necessary for the nucleation of the primary Al phase