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HDinHD (Huntington’s Disease in High Definition; HDinHD.org) is an open online portal for the HD research community that presents a synthesized view of HD-related scientific data. Here, we present a broad overview of HDinHD and highlight the newly launched HDinHD Explorer tool that enables researchers to discover and explore a wide range of diverse yet interconnected HD-related data. We demonstrate the utility of HDinHD Explorer through data mining of a single collection of newly released in vivo therapeutic intervention study reports alongside previously published reports.

The human multidrug resistance gene MDR3 encodes a P-glycoprotein that belongs to the ATP-binding cassette transporter family (ABCB4). MDR3 is a critical trans-locator for phospholipids across canalicular membranes of hepatocytes, evidenced by the fact that human MDR3 deficiencies result in progressive familial intrahepatic cholestasis type III. It has been reported previously that MDR3 expression is modulated by hormones, cellular stress, and xenobiotics. Here we show that the MDR3 gene is trans-activated by the farnesoid X receptor (FXR) via a direct binding of FXR/retinoid X receptor alpha heterodimers to a highly conserved inverted repeat element (a FXR response element) at the distal promoter (-1970 to -1958). In FXR trans-activation assays, both the endogenous FXR agonist chenodeoxycholate and the synthetic agonist GW4064 activated the MDR3 promoter. Deletion or mutation of this inverted repeat element abolished FXR-mediated MDR3 promoter activation. Consistent with these data, MDR3 mRNA was significantly induced by both chenodeoxycholate and GW4064 in primary human hepatocytes in time- and dose-dependent fashions. In conclusion, we demonstrate that MDR3 expression is directly up-regulated by FXR. These results, together with the previous report that the bile salt export pump is a direct FXR target, suggest that FXR coordinately controls secretion of bile salts and phospholipids. Results of this study further support the notion that FXR is a master regulator of lipid metabolism.

Genome Analyzer (GenoA) with a relational database back-end, was developed to extract information from mammalian genomic sequences. This data mining and visualization tool-set enables laboratory bench scientists to identify and assemble virtual cDNA from genomic exon sequences, and provides a starting point to identify potential alternative splice variants and polymorphisms in silico. The study described in this paper demonstrates the use of GenoA to study human brain hyperpolarization-activated cation channel genes HCN1 and HCN3.

Human kininogen belongs to the plasma kallikreinkinin system. High molecular weight kininogen is the precursor for two-chain kinin-free kininogen and bradykinin. It has been shown that the two-chain kinin-free kininogen has the properties of anti-adhesion, anti-platelet aggregation, and anti-thrombosis, whereas bradykinin is a potent vasodilator and mediator of inflammation. In this study we show that the human kininogen gene is strongly up-regulated by agonists of the farnesoid X receptor (FXR), a nuclear receptor for bile acids. In primary human hepatocytes, both the endogenous FXR agonist chenodeoxycholate and synthetic FXR agonist GW4064 increased kininogen mRNA with a maximum induction of 8-10-fold. A more robust induction of kininogen expression was observed in HepG2 cells, where kininogen mRNA was increased by chenodeoxycholate or GW4064 up to 130-140-fold as shown by real time PCR. Northern blot analysis confirmed the up-regulation of kininogen expression by FXR agonists. To determine whether kininogen is a direct target of FXR, we examined the sequence of the kininogen promoter and identified a highly conserved FXR response element (inverted repeat, IR-1) in the proximity of the kininogen promoter (-66/-54). FXR/RXRalpha heterodimers specifically bind to this IR-1. A construct of a minimal promoter with the luciferase reporter containing this IR-1 was transactivated by FXR. Deletion or mutation of this IR-1 abolished FXR-mediated promoter activation, indicating that this IR-1 element is responsible for the promoter transactivation by FXR. We conclude that kininogen is a novel and direct target of FXR, and bile acids may play a role in the vasodilation and anti-coagulation processes.

The C-type lectin human dendritic cell (DC)-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin (DC-SIGN) plays important roles in pattern recognition by dendritic cells in the immune system. In addition to binding human immunodeficiency virus (HIV), this type II membrane protein binds with high affinity to the adhesion molecules ICAM-3 and -2 to promote important dendritic cell interactions with naive T cells and endothelial cells, respectively. DC-SIGNR, a human DC-SIGN homologue expressed on sinusoidal endothelial cells in liver and lymph node, also binds and transmits HIV virus. We describe the cloning and characterization of a family of murine complementary DNAs (cDNAs) called SIGNR1, expressed in skin and spleen, that encode C-type lectins highly related to human DC-SIGN and DC-SIGNR. We also report the genomic structure of the SIGNR1 gene and compare it to that of human DC-SIGN and DC-SIGNR. The different transcripts (alpha, beta, gamma, delta) are generated by differences in 5' untranslated sequences, alternative splicing and/or the use of different polyadenylation sites. The predicted open reading frames encoded by the cDNAs are most closely related to human DC-SIGN and DC-SIGNR in the cytoplasmic domain, the transmembrane region and the carbohydrate recognition domain. Moreover, the alternatively spliced transcripts encode proteins that lack the transmembrane region or have modified carbohydrate recognition domains. Northern hybridization experiments with several different SIGNR1 cDNA probes reveal transcripts of 1.3 and 2.1 kb that are expressed in a tissue-restricted fashion in murine skin, spleen and lung. In situ hybridization and immunocytochemistry experiments demonstrate that, like human DC-SIGN, the murine messenger RNAs are expressed in subsets of dendritic cells in the spleen and skin.

Ligands for peroxisome proliferator activated receptors (PPARs) are used as hypolipidemic agents and for the treatment of type II diabetes, PPARa and PPARg, respectively. PPARs are members of the nuclear receptor family of ligand activated transcription factors which exert their effects primarily by regulating gene transcription. We have used gene microarrays to characterize PPAR ligands (profiling) and to investigate their mechanism of action. Compound profiles based on gene expression allow for novel ligand groupings when compared with groupings based on compound structure or on the results from single variable assays.

3,4-Epoxy-1-butene (I), prepared by the selective oxidation of butadiene, is an unusual difunctional monomer containing polymerizable vinyl and epoxy groups. As expected, free radical homopolymerization of I and its cyclic ketal derivatives was found to be very sluggish, as expected, for the allylic monomer structures. However, I was found to form alternating copolymers with maleic anhydride with both 1,2- and 1,5- enchainment observed. The structures of the alternating copolymers were observed to be solvent dependent with the in situ formation of cyclic ketals and their incorporation into the copolymers in polymerizations done in ketone solvents. Various cyclic ketal monomers derived from I readily formed alternating copoymers with maleic anhydride. Thermally activated self-crosslinking of these resins was observed.

A rigorous analysis of the Merck-sponsored EST data with respect to known gene sequences increases the utility of the data set and helps refine methods for building a gene index. A highly curated human transcript data base was used as a reference data set of known genes. A detailed analysis of EST sequences derived from known genes was performed to assess the accuracy of EST sequence annotation. The EST data was screened to remove low-quality and low-complexity sequences. A set of high-quality ESTs similar to the transcript data base was identified using BLAST; this subset of ESTs was compared with the set of known genes using the Smith-Waterman algorithm. Error rates of several types were assessed based on a flexible match criterion defining sequence identity. The rate of lane-tracking errors is very low, approximately 0.5%. Insert size data is accurate within approximately 20%. Reversed clone and internal priming error rates are approximately 5% and 2.5%, respectively, contributing to the incorrect identification of reads as 3' ends of genes. Follow-up investigation reveals that a significant number of clones, miscategorized as reversed, represent overlapping genes on the opposite strand of entries in the transcript data base. Relevance of these results to the creation of a high-quality index to the human genome capable of supporting diverse genomic investigations is discussed.

A new method is described for the synthesis of polyimides utilizing bis(o-iodo esters) and primary diamines in the presence of carbon monoxide (CO) and a palladium catalyst. A goal of isolating the intermediate poly(amide esters) from these reactions was not realized. Under all conditions examined in the model systems, neutralizing bases suitable for promoting the carbonylation reaction also induced cyclization to the fully imidized product; intermediate amide esters were not observed. Hydrogen iodide traps such as olefins were also examined, but did not give the desired amide esters. Polyimides formed by this method were fully imidized and had thermal stability commensurate with conventionally prepared polymers. However, the synthetic scope of this method was limited to fully imidized polymers that were soluble in dipolar aprotic solvents

High molecular weight poly(imide-amides) can be readily formed by the palladium-mediated carbonylation and condensation reactions of activated chlorophthalimide monomers and aromatic diamines. The presence of iodide ion greatly accelerates the rate of reaction and increases the ultimate molecular weight of the polymer. Polymerizations proceed best using a protocol of high CO pressure (90 psig) for 2-4 h, followed by lower CO pressure (20 psig) in DMAc or NMPfor 24-48 h at 100°C using 0.3-3.0% PdCl 2 L 2 (L=PPh 3 ) as the catalyst with 2-6 equiv of PPh 3 /Pd and 0.3-1.0 equiv of an iodide/ chloro group

NMR View is a computer program designed for the visualization and analysis of NMR data. It allows the user to interact with a practically unlimited number of 2D, 3D and 4D NMR data files. Any number of spectral windows can be displayed on the screen in any size and location. Automatic peak picking and facilitated peak analysis features are included to aid in the assignment of complex NMR spectra. NMR View provides structure analysis features and data transfer to and from structure generation programs, allowing for a tight coupling between spectral analysis and structure generation. Visual correlation between structures and spectra can be done with the Molecular Data Viewer, a molecular graphics program with bidirectional communication to NMR View. The user interface can be customized and a command language is provided to allow for the automation of various tasks.

High molecular weight poly(imide-amides) can be readily formed by the palladium-mediated carbonylation and condensation reactions of diiodo imide monomers and aromatic diamines. Reaction conditions for polymerization are 100-120°C, 90 psig CO, 3-6% PdCl 2 L 2 (L=PPh 3 ), and 2.4 equiv of DBU for 2-4h in DMAc or NMP. This route offers the flexibility of incorporating different ratios of amide and imide groups in the polymer backbone in a controlled manner. The imide moiety is preformed, which eliminates the possibility of postpolymerization curing

High molecular weight aromatic polyamides can be synthesized by the palladium-catalyzed carbonylation and condensation of diiodoaromatics and aromatic diamines. This process is tolerant of a variety of functionality and, in one optimized system, was found to work best sligth a slight excess of the diamine monomer. At elevated CO pressures, a dramatic difference in reactivity between the m-diiodobenzene monomer and the corresponding bromo analogue was observed. In the former case, high molecular weight aromatic polyamide was formed in 1 h, and in the latter, only oligomers were isolated after 24 h

Wholly aromatic polyamides, including poly(1,4-phenyleneisophthalamide) and poly(1,4-phenyleneterephthalamide) are N-methylated to render them soluble in N,N-dimethylformamide, a common size-exclusion chromatography eluent. The procedure N-methylates 50–55% of the total amide linkages in these two examples, permitting reproducible measurement of their absolute molecular weight distributions using differential viscometry detection. There is no observable degradation in molecular weight resulting from the N-methylation, provided the excess methylating reagent is destroyed shortly after completion of the derivatization by quenching with potassium acetate. The validity of the molecular weight data obtained by the method is confirmed by light-scattering measurements on derivatized polymer and by comparison to the molecular weight of underivatized polymer that can be approximated from the intrinsic viscosity in concentrated sulfuric acid. The method is applicable to a variety of wholly aromatic polyamide structures. Examples are given.

Motivation: Many bioinformatic approaches exist for finding novel genes within genomic sequence data. Traditionally, homology search-based methods are often the first approach employed in determining whether a novel gene exists that is similar to a known gene. Unfortunately, distantly related genes or motifs often are difficult to find using single query-based homology search algorithms against large sequence datasets such as the human genome. Therefore, the motivation behind this work was to develop an approach to enhance the sensitivity of traditional single query-based homology algorithms against genomic data without losing search selectivity. Results: We demonstrate that by searching against a genome fragmented into all possible reading frames, the sensitivity of homology-based searches is enhanced without degrading its selectivity. Using the ETS-domain, bromodomain and acetyl-CoA acetyltransferase gene as queries, we were able to demonstrate that direct protein–protein searches using BLAST2P or FASTA3 against a human genome segmented among all possible reading frames and translated was substantially more sensitive than traditional protein–DNA searches against a raw genomic sequence using an application such as TBLAST2N. Receiver operating characteristic analysis was employed to demonstrate that the algorithms remained selective, while comparisons of the algorithms showed that the protein–protein searches were more sensitive in identifying hits. Therefore, through the overprediction of reading frames by this method and the increased sensitivity of protein–protein based homology search algorithms, a genome can be deeply mined, potentially finding hits overlooked by protein–DNA searches against raw genomic data.

Summary: We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications. Availability: The database schema, DTD file, and source codes are available from the authors via email. Contact: guochun_xie@merck.com

MULTICLUSTAL is a Perl script designed to automate the process of alignment parameter choice for Clustal W with the goal of generating high quality multiple sequence alignments.

MOTIVATION: To make effective use of the vast amounts of expressed sequence tag (EST) sequence data generated by the Merck-sponsored EST project and other similar efforts, sequences must be organized into gene classes, and scientists must be able to 'mine' the gene class data in the context of related genomic data. RESULTS: This paper presents the Merck Gene Index browser, an easily extensible, World Wide Web-based system for mining the Merck Gene Index (MGI) and related genomic data. The MGI is a non-redundant set of clones and sequences, each representing a distinct gene, constructed from all high-quality 3' EST sequences generated by the Merck-sponsored EST project. The MGI browser integrates data from a variety of sources and storage formats, both local and remote, using an eclectic integration strategy, including a federation of relational databases, a local data warehouse and simple hypertext links. Data currently integrated include: LENS cDNA clone and EST data, dbEST protein and non-EST nucleic acid similarity data, WashU sequence chromatograms. Entrez sequence and Medline entries, and UniGene gene clusters. Flatfile sequence data are accessed using the Bioapps server, an internally developed client-server system that supports generic sequence analysis applications. Browser data are retrieved and formatted by means of the Bioinformatics Data Integration Toolkit (B-DIT), a new suite of Perl routines.

The analysis of matrix-assisted laser desorption ionization post-source decay (MALDI-PSD) mass spectra of peptides by using the cross-correlation method for database searching is illustrated. MALDI-PSD mass spectra are shown to contain sufficient fragmentation information to uniquely identify the correct amino acid sequence from large protein databases (approximately 160,000 entries). A search employing the MALDI-PSD mass spectrum of a phosphorylated peptide that correctly identifies the amino acid sequence and the site of phosphorylation is also illustrated.

Copolymers of allyl methacrylate and propargyl methacrylate have very high speed as electron-beam and x-ray resists. They produce polymers of a structural complexity not often encountered in addition polymerization. The structural variety available in allyl methacrylate polymers gives them unusual properties, which consequently enhance their microlithographic performance.

A new application program, the BIOINFORMATICS PROFILER, is described which simplifies the analysis of new genome sequence information appearing on a daily basis. Control tasks are defined through an intuitive graphical user interface and are executed at user defined nightly intervals. Electronic mail is sent to indicate that search results have been found. All task output is presented to users in the form of hypertext (HTML), allowing easy browsing. Currently supported tasks include BLAST and FastA sequence searching, keyword based searching of network news articles and WAIS databases, examination of GenBank sequence entries using regular expressions and boolean operations and protein sequence motif searching.