In Vitro Tracking of Human Umbilical Vein Endothelial Cells Using Ultra-Sensitive Quantum Dot-Embedded Silica Nanoparticles.

The nanoscale spatiotemporal resolution of single-particle tracking (SPT) renders it a powerful method for exploring single-molecule dynamics in living cells or tissues, despite the disadvantages of using traditional organic fluorescence probes, such as the weak fluorescent signal against the strong cellular autofluorescence background coupled with a fast-photobleaching rate. Quantum dots (QDs), which enable tracking targets in multiple colors, have been proposed as an alternative to traditional organic fluorescence dyes; however, they are not ideally suitable for applying SPT due to their hydrophobicity, cytotoxicity, and blinking problems. This study reports an improved SPT method using silica-coated QD-embedded silica nanoparticles (QD2), which represent brighter fluorescence and are less toxic than single QDs. After treatment of QD2 in 10 µg/mL, the label was retained for 96 h with 83.76% of labeling efficiency, without impaired cell function such as angiogenesis. The improved stability of QD2 facilitates the visualization of in situ endothelial vessel formation without real-time staining. Cells retain QD2 fluorescence signal for 15 days at 4 °C without significant photobleaching, indicating that QD2 has overcome the limitations of SPT enabling long-term intracellular tracking. These results proved that QD2 could be used for SPT as a substitute for traditional organic fluorophores or single quantum dots, with its photostability, biocompatibility, and superior brightness.

High-quantum yield alloy-typed core/shell CdSeZnS/ZnS quantum dots for bio-applications.

BACKGROUND: Quantum dots (QDs) have been used as fluorophores in various imaging fields owing to their strong fluorescent intensity, high quantum yield (QY), and narrow emission bandwidth. However, the application of QDs to bio-imaging is limited because the QY of QDs decreases substantially during the surface modification step for bio-application. RESULTS: In this study, we fabricated alloy-typed core/shell CdSeZnS/ZnS quantum dots (alloy QDs) that showed higher quantum yield and stability during the surface modification for hydrophilization compared with conventional CdSe/CdS/ZnS multilayer quantum dots (MQDs). The structure of the alloy QDs was confirmed using time-of-flight medium-energy ion scattering spectroscopy. The alloy QDs exhibited strong fluorescence and a high QY of 98.0%. After hydrophilic surface modification, the alloy QDs exhibited a QY of 84.7%, which is 1.5 times higher than that of MQDs. The QY was 77.8% after the alloy QDs were conjugated with folic acid (FA). Alloy QDs and MQDs, after conjugation with FA, were successfully used for targeting human KB cells. The alloy QDs exhibited a stronger fluorescence signal than MQD; these signals were retained in the popliteal lymph node area for 24 h. CONCLUSION: The alloy QDs maintained a higher QY in hydrophilization for biological applications than MQDs. And also, alloy QDs showed the potential as nanoprobes for highly sensitive bioimaging analysis.

Highly sensitive near-infrared SERS nanoprobes for in vivo imaging using gold-assembled silica nanoparticles with controllable nanogaps.

BACKGROUND: To take advantages, such as multiplex capacity, non-photobleaching property, and high sensitivity, of surface-enhanced Raman scattering (SERS)-based in vivo imaging, development of highly enhanced SERS nanoprobes in near-infrared (NIR) region is needed. A well-controlled morphology and biocompatibility are essential features of NIR SERS nanoprobes. Gold (Au)-assembled nanostructures with controllable nanogaps with highly enhanced SERS signals within multiple hotspots could be a breakthrough. RESULTS: Au-assembled silica (SiO2) nanoparticles (NPs) (SiO2@Au@Au NPs) as NIR SERS nanoprobes are synthesized using the seed-mediated growth method. SiO2@Au@Au NPs using six different sizes of Au NPs (SiO2@Au@Au50-SiO2@Au@Au500) were prepared by controlling the concentration of Au precursor in the growth step. The nanogaps between Au NPs on the SiO2 surface could be controlled from 4.16 to 0.98 nm by adjusting the concentration of Au precursor (hence increasing Au NP sizes), which resulted in the formation of effective SERS hotspots. SiO2@Au@Au500 NPs with a 0.98-nm gap showed a high SERS enhancement factor of approximately 3.8 × 106 under 785-nm photoexcitation. SiO2@Au@Au500 nanoprobes showed detectable in vivo SERS signals at a concentration of 16 µg/mL in animal tissue specimen at a depth of 7 mm. SiO2@Au@Au500 NPs with 14 different Raman label compounds exhibited distinct SERS signals upon subcutaneous injection into nude mice. CONCLUSIONS: SiO2@Au@Au NPs showed high potential for in vivo applications as multiplex nanoprobes with high SERS sensitivity in the NIR region.

Synthesis of Gold-Platinum Core-Shell Nanoparticles Assembled on a Silica Template and Their Peroxidase Nanozyme Properties.

Bimetallic nanoparticles are important materials for synthesizing multifunctional nanozymes. A technique for preparing gold-platinum nanoparticles (NPs) on a silica core template (SiO2@Au@Pt) using seed-mediated growth is reported in this study. The SiO2@Au@Pt exhibits peroxidase-like nanozyme activity has several advantages over gold assembled silica core templates (SiO2@Au@Au), such as stability and catalytic performance. The maximum reaction velocity (Vmax) and the Michaelis-Menten constants (Km) were and 2.1 × 10-10 M-1∙s-1 and 417 µM, respectively. Factors affecting the peroxidase activity, including the quantity of NPs, solution pH, reaction time, and concentration of tetramethyl benzidine, are also investigated in this study. The optimization of SiO2@Au@Pt NPs for H2O2 detection obtained in 0.5 mM TMB; using 5 µg SiO2@Au@Pt, at pH 4.0 for 15 min incubation. H2O2 can be detected in the dynamic liner range of 1.0 to 100 mM with the detection limit of 1.0 mM. This study presents a novel method for controlling the properties of bimetallic NPs assembled on a silica template and increases the understanding of the activity and potential applications of highly efficient multifunctional NP-based nanozymes.

Highly Bright Silica-Coated InP/ZnS Quantum Dot-Embedded Silica Nanoparticles as Biocompatible Nanoprobes.

Quantum dots (QDs) have outstanding optical properties such as strong fluorescence, excellent photostability, broad absorption spectra, and narrow emission bands, which make them useful for bioimaging. However, cadmium (Cd)-based QDs, which have been widely studied, have potential toxicity problems. Cd-free QDs have also been studied, but their weak photoluminescence (PL) intensity makes their practical use in bioimaging challenging. In this study, Cd-free QD nanoprobes for bioimaging were fabricated by densely embedding multiple indium phosphide/zinc sulfide (InP/ZnS) QDs onto silica templates and coating them with a silica shell. The fabricated silica-coated InP/ZnS QD-embedded silica nanoparticles (SiO2@InP QDs@SiO2 NPs) exhibited hydrophilic properties because of the surface silica shell. The quantum yield (QY), maximum emission peak wavelength, and full-width half-maximum (FWHM) of the final fabricated SiO2@InP QDs@SiO2 NPs were 6.61%, 527.01 nm, and 44.62 nm, respectively. Moreover, the brightness of the particles could be easily controlled by adjusting the amount of InP/ZnS QDs in the SiO2@InP QDs@SiO2 NPs. When SiO2@InP QDs@SiO2 NPs were administered to tumor syngeneic mice, the fluorescence signal was prominently detected in the tumor because of the preferential distribution of the SiO2@InP QDs@SiO2 NPs, demonstrating their applicability in bioimaging with NPs. Thus, SiO2@InP QDs@SiO2 NPs have the potential to successfully replace Cd-based QDs as highly bright and biocompatible fluorescent nanoprobes.

Silver-Assembled Silica Nanoparticles in Lateral Flow Immunoassay for Visual Inspection of Prostate-Specific Antigen.

Prostate-specific antigen (PSA) is the best-known biomarker for early diagnosis of prostate cancer. For prostate cancer in particular, the threshold level of PSA <4.0 ng/mL in clinical samples is an important indicator. Quick and easy visual detection of the PSA level greatly helps in early detection and treatment of prostate cancer and reducing mortality. In this study, we developed optimized silica-coated silver-assembled silica nanoparticles (SiO2@Ag@SiO2 NPs) that were applied to a visual lateral flow immunoassay (LFIA) platform for PSA detection. During synthesis, the ratio of silica NPs to silver nitrate changed, and as the synthesized NPs exhibited distinct UV spectra and colors, most optimized SiO2@Ag@SiO2 NPs showed the potential for early prostate cancer diagnosis. The PSA detection limit of our LFIA platform was 1.1 ng/mL. By applying each SiO2@Ag@SiO2 NP to the visual LFIA platform, optimized SiO2@Ag@SiO2 NPs were selected in the test strip, and clinical samples from prostate cancer patients were successfully detected as the boundaries of non-specific binding were clearly seen and the level of PSA was <4 ng/mL, thus providing an avenue for quick prostate cancer diagnosis and early treatment.

Synthesis of Finely Controllable Sizes of Au Nanoparticles on a Silica Template and Their Nanozyme Properties.

The precise synthesis of fine-sized nanoparticles is critical for realizing the advantages of nanoparticles for various applications. We developed a technique for preparing finely controllable sizes of gold nanoparticles (Au NPs) on a silica template, using the seed-mediated growth and interval dropping methods. These Au NPs, embedded on silica nanospheres (SiO2@Au NPs), possess peroxidase-like activity as nanozymes and have several advantages over other nanoparticle-based nanozymes. We confirmed their peroxidase activity; in addition, factors affecting the activity were investigated by varying the reaction conditions, such as concentrations of tetramethyl benzidine and H2O2, pH, particle amount, reaction time, and termination time. We found that SiO2@Au NPs are highly stable under long-term storage and reusable for five cycles. Our study, therefore, provides a novel method for controlling the properties of nanoparticles and for developing nanoparticle-based nanozymes.

Synthesis and Application of Silica-Coated Quantum Dots in Biomedicine.

Quantum dots (QDs) are semiconductor nanoparticles with outstanding optoelectronic properties. More specifically, QDs are highly bright and exhibit wide absorption spectra, narrow light bands, and excellent photovoltaic stability, which make them useful in bioscience and medicine, particularly for sensing, optical imaging, cell separation, and diagnosis. In general, QDs are stabilized using a hydrophobic ligand during synthesis, and thus their hydrophobic surfaces must undergo hydrophilic modification if the QDs are to be used in bioapplications. Silica-coating is one of the most effective methods for overcoming the disadvantages of QDs, owing to silica's physicochemical stability, nontoxicity, and excellent bioavailability. This review highlights recent progress in the design, preparation, and application of silica-coated QDs and presents an overview of the major challenges and prospects of their application.

VnD: a structure-centric database of disease-related SNPs and drugs.

Numerous genetic variations have been found to be related to human diseases. Significant portion of those affect the drug response as well by changing the protein structure and function. Therefore, it is crucial to understand the trilateral relationship among genomic variations, diseases and drugs. We present the variations and drugs (VnD), a consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. VnD was built in three steps. First, we integrated various resources systematically to deduce catalogs of disease-related genes, single nucleotide polymorphisms (SNPs), protein mutations and relevant drugs. VnD contains 137,195 disease-related gene records (13,940 distinct genes) and 16,586 genetic variation records (1790 distinct variations). Next, we carried out structure modeling and docking simulation for wild-type and mutant proteins to examine the structural and functional consequences of non-synonymous SNPs in the drug-related genes. Conformational changes in 590 wild-type and 4437 mutant proteins from drug-related genes were included in our database. Finally, we investigated the structural and biochemical properties relevant to drug binding such as the distribution of SNPs in proximal protein pockets, thermo-chemical stability, interactions with drugs and physico-chemical properties. The VnD database, available at http://vnd.kobic.re.kr:8080/VnD/ or vandd.org, would be a useful platform for researchers studying the underlying mechanism for association among genetic variations, diseases and drugs.

Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome.

The genome of soybean (Glycine max), a commercially important crop, has recently been sequenced and is one of six crop species to have been sequenced. Here we report the genome sequence of G. soja, the undomesticated ancestor of G. max (in particular, G. soja var. IT182932). The 48.8-Gb Illumina Genome Analyzer (Illumina-GA) short DNA reads were aligned to the G. max reference genome and a consensus was determined for G. soja. This consensus sequence spanned 915.4 Mb, representing a coverage of 97.65% of the G. max published genome sequence and an average mapping depth of 43-fold. The nucleotide sequence of the G. soja genome, which contains 2.5 Mb of substituted bases and 406 kb of small insertions/deletions relative to G. max, is ∼0.31% different from that of G. max. In addition to the mapped 915.4-Mb consensus sequence, 32.4 Mb of large deletions and 8.3 Mb of novel sequence contigs in the G. soja genome were also detected. Nucleotide variants of G. soja versus G. max confirmed by Roche Genome Sequencer FLX sequencing showed a 99.99% concordance in single-nucleotide polymorphism and a 98.82% agreement in insertion/deletion calls on Illumina-GA reads. Data presented in this study suggest that the G. soja/G. max complex may be at least 0.27 million y old, appearing before the relatively recent event of domestication (6,000∼9,000 y ago). This suggests that soybean domestication is complicated and that more in-depth study of population genetics is needed. In any case, genome comparison of domesticated and undomesticated forms of soybean can facilitate its improvement.

Perovskite single-crystal thin films: preparation, surface engineering, and application.

Perovskite single-crystal thin films (SCTFs) have emerged as a significant research hotspot in the field of optoelectronic devices owing to their low defect state density, long carrier diffusion length, and high environmental stability. However, the large-area and high-throughput preparation of perovskite SCTFs is limited by significant challenges in terms of reducing surface defects and manufacturing high-performance devices. This review focuses on the advances in the development of perovskite SCTFs with a large area, controlled thickness, and high quality. First, we provide an in-depth analysis of the mechanism and key factors that affect the nucleation and crystallization process and then classify the methods of preparing perovskite SCTFs. Second, the research progress on surface engineering for perovskite SCTFs is introduced. Third, we summarize the applications of perovskite SCTFs in photovoltaics, photodetectors, light-emitting devices, artificial synapse and field-effect transistor. Finally, the development opportunities and challenges in commercializing perovskite SCTFs are discussed.

Wide-Band-Gap (2.0 eV) Perovskite Solar Cells with a VOC of 1.325 V Fabricated by a Green-Solvent Strategy.

Perovskite-based tandem solar cells are promising candidates for next-generation photovoltaic devices. However, the defects caused by ion migration cause a large deficit of open-circuit voltage (VOC) in conventional wide-band-gap perovskite films. Here, we present a new strategy that employs nontoxic acetic acid and isopropanol as solvents to deposit a perovskite film with a 2.0 eV band gap in an ambient atmosphere. The in situ formed acetate anions strongly stabilize the intrinsic defects in perovskite films. These features effectively improve the phase stability of 2.0 eV Cs0.2FA0.8PbI0.9Br2.1 perovskite, allowing the VOC to reach 1.325 V and the corresponding power conversion efficiency to reach 10.62%, which is close to the state-of-art performance of perovskite solar cells employing perovskite around a 2.0 eV band gap.

The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group.

We present the first Korean individual genome sequence (SJK) and analysis results. The diploid genome of a Korean male was sequenced to 28.95-fold redundancy using the Illumina paired-end sequencing method. SJK covered 99.9% of the NCBI human reference genome. We identified 420,083 novel single nucleotide polymorphisms (SNPs) that are not in the dbSNP database. Despite a close similarity, significant differences were observed between the Chinese genome (YH), the only other Asian genome available, and SJK: (1) 39.87% (1,371,239 out of 3,439,107) SNPs were SJK-specific (49.51% against Venter's, 46.94% against Watson's, and 44.17% against the Yoruba genomes); (2) 99.5% (22,495 out of 22,605) of short indels (< 4 bp) discovered on the same loci had the same size and type as YH; and (3) 11.3% (331 out of 2920) deletion structural variants were SJK-specific. Even after attempting to map unmapped reads of SJK to unanchored NCBI scaffolds, HGSV, and available personal genomes, there were still 5.77% SJK reads that could not be mapped. All these findings indicate that the overall genetic differences among individuals from closely related ethnic groups may be significant. Hence, constructing reference genomes for minor socio-ethnic groups will be useful for massive individual genome sequencing.

Aptamer-conjugated nano-liposome for immunogenic chemotherapy with reversal of immunosuppression.

Cancer cells have various immune evasion mechanisms that resist the immune cells by reprogramming the tumor microenvironment (TME), such as programmed death-ligand 1 (PD-L1) and indoleamine 2,3-dioxygenase-1 (IDO1) overexpression. One of the approaches to restore antitumor immune response by T-cells is through induction of immunogenic cell death (ICD). Thus, drug carrier containing IDO1 siRNA and ICD inducer would be effective anticancer regimen to modulate the immunosuppressive TME by reversing the IDO1-mediated immunosuppression in a synergistic combination with ICD induction. However, numerous nanocarrier platforms for co-delivery of multiple drugs mostly depend on the enhanced permeation and retention (EPR), which is insufficient to achieve selectivity in tumor sites harboring various types of cells. We designed a targeted drug delivery system using nano-sized liposomes functionalized with anti-CD44 and anti-PD-L1 DNA aptamers, which target breast cancer cells and inhibit PD-1/PD-L1 interaction between cancer cells and T-cells. To reverse immunosuppressive TME and reactivate immune response, cancer-targeting nano-liposomes were prepared to contain immunogenic cell death inducer (Doxorubicin, DOX) and IDO1 siRNA, namely Aptm[DOX/IDO1]. The Aptm[DOX/IDO1] specifically delivered the loaded DOX and IDO1 siRNA into target breast cancer cells through aptamer-mediated endocytosis. Cancer-targeted DOX/IDO1 siRNA delivery enhanced ICD and suppressed IDO1 expression with significantly high toxicity in cancer cells. We demonstrated that Aptm[DOX/IDO1] could achieve synergistic antitumor effects by facilitating ICD response and simultaneous reversal of the immunosuppressive TME with IDO1 knockdown in the subcutaneous breast cancer model mice, thus reducing tumor size. These antitumor effects were exerted with intratumoral infiltration of CD8+ cytotoxic T lymphocyte as well as attenuation of regulatory T-cell recruitment in the tumor sites. We further proved that our Aptm[DOX/IDO1] strategy significantly reduced tumor metastasis in tumor-xenograft mice through a synergistic combination of cancer cell-targeted ICD induction and reversal of the IDO1-mediated immunosuppressive TME. Our nanocarrier platform based on cationic liposomes containing DOX and IDO1 siRNA, which are conjugated with two DNA aptamers targeting the cancer cell surface, accomplished synergistic chemoimmunotherapy through tumor-specific immune modulation into immune-favorable TME in vivo.

Nonenzymatic Hydrogen Peroxide Detection Using Surface-Enhanced Raman Scattering of Gold-Silver Core-Shell-Assembled Silica Nanostructures.

Hydrogen peroxide (H2O2) plays important roles in cellular signaling and in industry. Thus, the accurate detection of H2O2 is critical for its application. Unfortunately, the direct detection of H2O2 by surface-enhanced Raman spectroscopy (SERS) is not possible because of its low Raman cross section. Therefore, the detection of H2O2 via the presence of an intermediary such as 3,3,5,5-tetramethylbenzidine (TMB) has recently been developed. In this study, the peroxidase-mimicking activity of gold-silver core-shell-assembled silica nanostructures (SiO2@Au@Ag alloy NPs) in the presence of TMB was investigated using SERS for detecting H2O2. In the presence of H2O2, the SiO2@Au@Ag alloy catalyzed the conversion of TMB to oxidized TMB, which was absorbed onto the surface of the SiO2@Au@Ag alloy. The SERS characteristics of the alloy in the TMB-H2O2 mixture were investigated. The evaluation of the SERS band to determine the H2O2 level utilized the SERS intensity of oxidized TMB bands. Moreover, the optimal conditions for H2O2 detection using SiO2@Au@Ag alloy included incubating 20 µg/mL SiO2@Au@Ag alloy NPs with 0.8 mM TMB for 15 min and measuring the Raman signal at 400 µg/mL SiO2@Au@Ag alloy NPs.

Gevab: a prototype genome variation analysis browsing server.

BACKGROUND: The first Korean individual diploid genome sequence data (KOREF) was publicized in December 2008. RESULTS: A Korean genome variation analysis and browsing server (Gevab) was constructed as a database and web server for the exploration and downloading of Korean personal genome(s). Information in the Gevab includes SNPs, short indels, and structural variation (SV) and comparison analysis between the NCBI human reference and the Korean genome(s). The user can find information on assembled consensus sequences, sequenced short reads, genetic variations, and relationships between genotype and phenotypes. CONCLUSION: This server is openly and publicly available online at http://koreagenome.org/en/ or directly http://gevab.org.

ssSNPTarget: genome-wide splice-site Single Nucleotide Polymorphism database.

Deep sequencing has shown that over 90% of human genes undergo alternative splicing. The splicing process requires exon-intron boundary recognition. SNPs located in the boundaries (splice sites) influence exon configuration. Also, splice site SNPs (ssSNPs) alter translation efficiency of the mRNA and lead to important changes in disease susceptibility. We developed the ssSNPTarget database to provide ssSNPs on human and mouse genes. It includes: 1) ssSNP distribution information in human and mouse genes; 2) effects of SNPs in splice sites: junction strength change, protein domain change, and alternative splicing events (exon skipping, 5'- or 3'-exon extension); 3) splice site conservation in eukaryotes; and 4) associated disease information derived from OMIM, GAD, and HGMD. ssSNPTarget contains 1,576 human ssSNPs associated with 1,193 genes and 538 mouse ssSNPs associated with 281 genes. Users can query ssSNPTarget with several types of search terms (gene symbol, SNP rs number, transcript ID, or genomic position), and the information can be accessed at http://variome.kobic.re.kr/ssSNPTarget/ or http://ssSNPTarget.org.

MitoVariome: a variome database of human mitochondrial DNA.

BACKGROUND: Mitochondrial sequence variation provides critical information for studying human evolution and variation. Mitochondrial DNA provides information on the origin of humans, and plays a substantial role in forensics, degenerative diseases, cancers, and aging process. Typically, human mitochondrial DNA has various features such as HVSI, HVSII, single-nucleotide polymorphism (SNP), restriction enzyme sites, and short tandem repeat (STR). RESULTS: We present a variome database (MitoVariome) of human mitochondrial DNA sequences. Queries against MitoVariome can be made using accession numbers or haplogroup/continent. Query results are presented not only in text but also in HTML tables to report extensive mitochondrial sequence variation information. The variation information includes repeat pattern, restriction enzyme site polymorphism, short tandem repeat, disease information as well as single nucleotide polymorphism. It also provides a graphical interface as Gbrowse displaying all variations at a glance. The web interface also provides the tool for assigning haplogroup based on the haplogroup-diagnostic system with complete human mitochondrial SNP position list and for retrieving sequences that users query against by using accession numbers. CONCLUSION: MitoVariome is a freely accessible web application and database that enables human mitochondrial genome researchers to study genetic variation in mitochondrial genome with textual and graphical views accompanied by assignment function of haplogrouping if users submit their own data. Hence, the MitoVariome containing many kinds of variation features in the human mitochondrial genome will be useful for understanding mitochondrial variations of each individual, haplogroup, or geographical location to elucidate the history of human evolution.

PDbase: a database of Parkinson's disease-related genes and genetic variation using substantia nigra ESTs.

BACKGROUND: Parkinson's disease (PD) is one of the most common neurodegenerative disorders, clinically characterized by impaired motor function. Since the etiology of PD is diverse and complex, many researchers have created PD-related research resources. However, resources for brain and PD studies are still lacking. Therefore, we have constructed a database of PD-related gene and genetic variations using the substantia nigra (SN) in PD and normal tissues. In addition, we integrated PD-related information from several resources. RESULTS: We collected the 6,130 SN expressed sequenced tags (ESTs) from brain SN normal tissues and PD patients SN tissues using full-cDNA library and normalized cDNA library construction methods from our previous study. The SN ESTs were clustered in 2,951 unigene clusters and assigned in 2,678 genes. We then found up-regulated 57 genes and down-regulated 48 genes by comparing normal and PD SN ESTs frequencies with over 0.9 cut-off probability of differential expression based on the Audic and Claverie method. In addition, we integrated disease-related information from public resources. To examine the characteristics of these PD-related genes, we analyzed alternative splicing events, single nucleotide polymorphism (SNP) markers located in the gene regions, repeat elements, gene regulation elements, and pathways and protein-protein interaction networks. CONCLUSION: We constructed the PDbase database to capture the PD-related gene, genetic variation, and functional elements. This database contains 2,698 PD-related genes through ESTs discovered from human normal and PD patients SN tissues, and through integrating several public resources. PDbase provides the mitochondrion proteins, microRNA gene regulation elements, single nucleotide polymorphisms (SNPs) markers within PD-related gene structures, repeat elements, and pathways and networks with protein-protein interaction information. The PDbase information can aid in understanding the causation of PD. It is available at http://bioportal.kobic.re.kr/PDbase/. Supplementary data is available at http://bioportal.kobic.re.kr/PDbase/suppl.jsp.

Automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries.

UNLABELLED: Bioinformatics involves the collection, organization and analysis of large amounts of biological data, using networks of computers and databases. Developing countries in the Asia-Pacific region are just moving into this new field of information-based biotechnology. However, the computational infrastructure and network bandwidths available in these countries are still at a basic level compared to that in developed countries. In this study, we assessed the utility of a BitTorrent-based Peer-to-Peer (btP2P) file distribution model for automatic synchronization and distribution of large amounts of biological data among developing countries. The initial country-level nodes in the Asia-Pacific region comprised Thailand, Korea and Singapore. The results showed a significant improvement in download performance using btP2P--three times faster overall download performance than conventional File Transfer Protocol (FTP). This study demonstrated the reliability of btP2P in the dissemination of continuously growing multi-gigabyte biological databases across the three Asia-Pacific countries. The download performance for btP2P can be further improved by including more nodes from other countries into the network. This suggests that the btP2P technology is appropriate for automatic synchronization and distribution of biological databases and software over low-bandwidth networks among developing countries in the Asia-Pacific region. AVAILABILITY: http://everest.bic.nus.edu.sg/p2p/