A new common functional coding variant at the DDC gene change renal enzyme activity and modify renal dopamine function.

The intra-renal dopamine (DA) system is highly expressed in the proximal tubule and contributes to Na+ and blood pressure homeostasis, as well as to the development of nephropathy. In the kidney, the enzyme DOPA Decarboxylase (DDC) originating from the circulation. We used a twin/family study design, followed by polymorphism association analysis at DDC locus to elucidate heritable influences on renal DA production. Dense single nucleotide polymorphism (SNP) genotyping across the DDC locus on chromosome 7p12 was analyzed by re-sequencing guided by trait-associated genetic markers to discover the responsible genetic variation. We also characterized kinetics of the expressed DDC mutant enzyme. Systematic polymorphism screening across the 15-Exon DDC locus revealed a single coding variant in Exon-14 that was associated with DA excretion and multiple other renal traits indicating pleiotropy. When expressed and characterized in eukaryotic cells, the 462Gln variant displayed lower Vmax (maximal rate of product formation by an enzyme) (21.3 versus 44.9 nmol/min/mg) and lower Km (substrate concentration at which half-maximal product formation is achieved by an enzyme.)(36.2 versus 46.8 μM) than the wild-type (Arg462) allele. The highly heritable DA excretion trait is substantially influenced by a previously uncharacterized common coding variant (Arg462Gln) at the DDC gene that affects multiple renal tubular and glomerular traits, and predicts accelerated functional decline in chronic kidney disease

Structural and biophysical analysis of important biomedical enzymes and nano-architectures

Dopa decarboxylase (DDC) is an important enzyme in the catecholamine biosynthesis pathways. Catecholamines, e.g., dopamine, serotonin, etc. often are the major neuromodulators or neurotransmitters. Hence, DDC plays a key role in regulation of neurodegenerative diseases like Parkinson’s disease (PD). In order to achieve a medicine for PD, a successful inhibitor for DDC, that could reduce the activity of DDC in the blood while making it more effective in brain, is required. An effective design of an inhibitor requires a detailed structural study of human DDC. It was aimed to solve the DDC structure by X-ray crystallography. In order to have enough protein the DDC encoding gene has been cloned in the pET21d vector which was later termed as pET-DDC-His. However, it required numerous trials and errors until a suitable condition for soluble DDC expression was found. Addition of additives like PLP, ethanol, a complex of sorbitol and betaine in the growth medium of the bacteria did not help bring the protein in the soluble part as it formed inclusion bodies. Several soluble protein fusions with DDC, like Thioredoxin and Glutathione-S-transferase were also not quite helpful towards achieving soluble expression of DDC. Finally, a coexpression of DDC along with bacterial chaperone proteins, e.g., GroEL and GroES (after cotransforming both the DDC and Chaperone protein encoding plasmid in the same E.coli cell, used for expression) lead to solubilization of recombinant human DDC. This enzyme was then purified to homogeneity by successively passing the crude bacterial proteins through Ni-chelate-affinity chromatography and Size Exclusion Chromatography. The purified protein (>90 % purity) did not produce a good yield (4mg/ 8L culture), but this was enough to start the initial crystallization trial. Using a scale up to a 50 L culture, quite a good amount of protein was achieved. The homogeneity of DDC was further confirmed by using Multi-Angle Light Scattering and Blue Native PAGE. The dimeric enzyme preparation was then utilized for crystallization using the Hanging Drop Vapor Diffusion method. In a particular condition of the crystal screens trigonal bipyramidal crystals formed. However, these crystals did not show good diffraction when bombarded with X-ray beams. Later, this particular crystallization condition remained irreproducible. The peptide nanoparticle, designed and produced in our lab, could possibly be a very valuable tool in biomedical applications, e.g., in designing vaccines, delivering drugs, bioimaging, serodiagnosis, etc. The design of the peptide nanoparticles is based on the application of the symmetry elements of virus icosahedral capsid on a specially designed building block peptide. The designed peptide building block contains two oligomerization motifs, i.e., a trimeric coiled coil and a pentameric coiled coil joined by a linker region. Sixty such peptide units, upon self-assembly, would produce peptide nanoparticle mimicking a small icosahedral virus particle. The peptide chains in the building block provide flexibility in the design so that an additional peptide could be attached to it at the C-terminus in order to functionalize the peptide nanoparticle for various biomedical applications. First of all, the functional peptide at the C-terminus could be an epitope for the antibody of a life threatening disease like HIV. These peptide nanoparticles can then function as the potent vaccine candidate for that particular disease. In this thesis work, I have attached the two epitopes against the two broadly neutralizing classes of antibody for HIV infection, 2F5 and 4E10, to the peptide nanoparticle. Secondly, another sequence of peptide, which proved to have the capacity of seeding gold on its surface, was attached to the building block peptide unit. The nanoparticle, functionalized with such a peptide, can decorate a gold layer surrounding it. Gold coating on the peptide nanoparticle scaffold can provide a nanostructure, called ‘nanoshells’, which could be very important in the field of therapeutics because of its ability in easy detection and quick treatment of cancer cells. Lastly, I added three peptides; those are recognized in the culture filtrates of M.tuberculosis isolated from TB patients, separately, to the basic peptide construct to form three different nanoparticles. Also, I tried to make a single nanoparticle that displays all the three peptides on its surface. Such a nanoparticle could be a very useful tool in the serodiagnosis or the antibody-based rapid detection of the deadly disease- Tuberculosis. The nanoparticle formation in each of the above-mentioned cases was more or less successful. One of the constructs could successfully even produce gold shells on the peptide nanoparticle

Tyrosine Hydroxylase and DOPA Decarboxylase Gene Variants in Personality Traits

Personality influences several characteristics of normal and pathologic behaviors and it is associated with neurotransmitter systems that are under genetic control. The dopaminergic system has been proposed to play a role in the modulation of personality traits. In the present study, variants of the tyrosine hydroxylase (TH) and DOPA decarboxylase (DDC) genes (for TH: rs3842727, rs6356; for DDC: rs1451371, rs1470750, rs998850) were investigated in 111 suicide attempters and 289 healthy subjects to assess the involvement of the dopaminergic synthesis pathway in personality traits. No strong evidence was found for the associations between personality and TH or DDC in overall tests. An interaction effect of genotype and diagnosis was present, with TH and DDC SNPs having a greater effect on the respective personality dimensions in the group of suicide attempters. Because of the risk of false positives, these findings should be interpreted with highest caution. Direct replication attempts within independent groups of suicide attempters will help to resolve this question. Copyright (C) 2009 S. Karger AG, Base

Disassortativity of random critical branching trees

Random critical branching trees (CBTs) are generated by the multiplicative branching process, where the branching number is determined stochastically, independent of the degree of their ancestor. Here we show analytically that despite this stochastic independence, there exists the degree-degree correlation (DDC) in the CBT and it is disassortative. Moreover, the skeletons of fractal networks, the maximum spanning trees formed by the edge betweenness centrality, behave similarly to the CBT in the DDC. This analytic solution and observation support the argument that the fractal scaling in complex networks originates from the disassortativity in the DDC.Comment: 3 pages, 2 figure

HILT : a terminology mapping service with a DDC spine

The role of DDC in the ongoing HILT (High-level Thesaurus) project is discussed. A phased initiative, funded by JISC in the UK, HILT addresses an issue of likely interest to anyone serving users wishing to cross-search or cross-browse groups of networked information services, whether at regional, national or international level - the problem of subject-based retrieval from multiple sources using different subject schemes for resource description. Although all three phases of HILT to date are covered, the primary concern is with the subject interoperability solution piloted in phase II, and with the use of DDC as a spine in that approach

PENERAPAN SISTEM DDC (DWEY DECIMAL CLASSIFICATION) PADA PERPUSTAKAAN POLITEKNIK ATMI SURAKARTA

Penelitian ini bertujuan untuk meneliti prosedur penerapan sistem DDC,serta mengetahui kendala penerapan sistem DDC dan solusi atas kendala tersebut. Penelitian ini mengambil lokasi di perpustakaan Politeknik ATMI (Akademi Teknik Mesin Industri) Surakarta. Pada penulisan Tugas Akhir ini penulis menggunakan metode observasi, metode wawancara, dan metode studi pustaka dalam pengumpulan data penelitian. Tugas Akhir ini menitikberatkan pada penerapan sistem DDC buku di perpustakaan Politeknik ATMI Surakarta. Cara mengklasir buku menggunakan DDC yang paling kompleks dan sepesifik dengan langkah-langkah pada analisis subyek, kata pengantar, daftar isi.Hambatan-hambatan sistem penerapan klasifikasi yang ada di perpustakaan Politeknik ATMI Surakarta ada dua yaitu untuk judul buku yang berbahasa asing harus diterjemahkan terlebih dahulu, setelah itu baru bisa diklasir mengunakan DDC. Yang kedua petugas perpustakaan masih minimpengetahuanya tentang cara pengunaan DDC. Alternatif solusi yang dapat diberikan berdasarkan kendala-kendala yang ada adalah memberikan pelatihan pada petugas perpustakaan ATMI Surakarta. Pelatihan dapat dilakuhkan dengan mendatangkan tenaga ahli yang menguasai sistem DDC untuk melatih petugas perpustakaan Kata kunci: Perpustakaan, klasifikasi, DD

Ein semantisches Netz für die Suche mit der Dewey-Dezimalklassifikation - Optimiertes Retrieval durch die Verwendung versionierter DDC-Klassen

A semantic network for the search with the Dewy Decimal Classification - optimized retrieval by using versioned DDC classes: The Dewey Decimal Classification (DDC) is used to catalogue library holdings all over the world. In order to keep the classification up-to-date with scientific advancement, the DDC is revised regularly. As a result, particular topics might be relocated and the original DDC notation might not represent the topic of a resource any more. This can lead to incorrect search results. A possible solution for this problem is to assign a unique identifier to each version of a DDC class. By doing that, it is possible to explicitly label which version of a DDC class was used for the classification of a particular resource. Bibliographic resources, terms from the German Subject Headings, and the different versions of the DDC classes can then be used to build a semantic network. Using the semantic network with appropriate queries allows for better search results independent of modifications within the DDC