Facilitated and Controlled Strontium Ranelate Delivery Using GCS-HA Nanocarriers Embedded into PEGDA Coupled with Decortication Driven Spinal Regeneration.

BACKGROUND AND PURPOSE: Strontium ranelate (SrR) is an oral pharmaceutical agent for osteoporosis. In recent years, numerous unwanted side effects of oral SrR have been revealed. Therefore, its clinical administration and applications are limited. Hereby, this study aims to develop, formulate, and characterize an effective SrR carrier system for spinal bone regeneration. METHODS: Herein, glycol chitosan with hyaluronic acid (HA)-based nanoformulation was used to encapsulate SrR nanoparticles (SrRNPs) through electrostatic interaction. Afterward, the poly(ethylene glycol) diacrylate (PEGDA)-based hydrogels were used to encapsulate pre-synthesized SrRNPs (SrRNPs-H). The scanning electron microscope (SEM), TEM, rheometer, Fourier-transform infrared spectroscopy (FTIR), and dynamic light scattering (DLS) were used to characterize prepared formulations. The rabbit osteoblast and a rat spinal decortication models were used to evaluate and assess the developed formulation biocompatibility and therapeutic efficacy. RESULTS: In vitro and in vivo studies for cytotoxicity and bone regeneration were conducted. The cell viability test showed that SrRNPs exerted no cytotoxic effects in osteoblast in vitro. Furthermore, in vivo analysis for new bone regeneration mechanism was carried out on rat decortication models. Radiographical and histological analysis suggested a higher level of bone regeneration in the SrRNPs-H-implanted groups than in the other experimental groups. CONCLUSION: Local administration of the newly developed formulated SrR could be a promising alternative therapy to enhance bone regeneration in bone-defect sites in future clinical applications.

Strontium ranelate-laden near-infrared photothermal-inspired methylcellulose hydrogel for arthritis treatment.

Rheumatoid arthritis (RA) is of foremost concern among long-term autoimmune disorders, as it leads to inflammation, exudates, chondral degeneration, and painful joints. Because RA severity often fluctuates over time, a local drug delivery method that titrates release of therapeutics to arthritis bioactivity should represent a promising paradigm of RA therapy. Given the local nature of RA chronic illnesses, polysaccharide-drug delivering systems have the promise to augment therapeutic outcomes by offering controlled release of bioactive materials, diminishing the required frequency of administration, and preserving therapeutic levels in affected pathological regions. Herein, an intra-articular photothermal-laden injectable methylcellulose (MC) polymeric hydrogel carrier incorporating strontium ranelate (SrR) and sodium chloride was investigated to resolve these issues. Physicochemical and cellular characteristics of the MC carrier system were thoroughly evaluated. The slow release of SrR, enhancement of the material mechanical strength, and the potential of the non-invasive near-infrared photothermal gel to improve blood circulation and suppress inflammation in a mini-surgical model of RA were examined. Biocompatibility and suppression of intracellular ROS-induced inflammation were observed. This multifunctional photothermal MC hydrogel carrier is anticipated to be an alternative approach for future orthopedic disease treatment.

On the influenza vaccination policy through mathematical modeling.

OBJECTIVES: Aimed at mitigating influenza transmission, this study assessed the timing of the vaccination program and took vaccine capacity, strain mismatch and priority group into consideration. METHODS: An age-structured dynamic transmission model was fitted to the laboratory data of the national influenza surveillance system to reconstruct a baseline scenario with which the vaccination scenarios of interest could be compared. Outcome measures were defined as the impacts on the seasonal epidemic: decompression of the epidemic peak, reduction of the epidemic burden and change of the epidemic peak time. RESULTS: It was found that vaccine capacity building, although indispensable, could not guarantee substantial impact on the seasonal influenza epidemic. Vaccine mismatch might greatly offset vaccine capacity building. Notably, advance vaccine distribution could compensate for some vaccine underperformance. In the case of a well-matched vaccine, advance vaccine distribution could even exploit its utility. CONCLUSIONS: This study indicated that timely vaccine distribution should be put high on the agenda of seasonal influenza control policies. It provided a tangible platform for the policymakers to evaluate health policy impacts and to enhance risk communication with the public through mathematical modeling.

Data-driven interdisciplinary mathematical modelling quantitatively unveils competition dynamics of co-circulating influenza strains.

BACKGROUND: Co-circulation of influenza strains is common to seasonal epidemics and pandemic emergence. Competition was considered involved in the vicissitudes of co-circulating influenza strains but never quantitatively studied at the human population level. The main purpose of the study was to explore the competition dynamics of co-circulating influenza strains in a quantitative way. METHODS: We constructed a heterogeneous dynamic transmission model and ran the model to fit the weekly A/H1N1 influenza virus isolation rate through an influenza season. The construction process started on the 2007-2008 single-clade influenza season and, with the contribution from the clade-based A/H1N1 epidemiological curves, advanced to the 2008-2009 two-clade influenza season. Pearson method was used to estimate the correlation coefficient between the simulated epidemic curve and the observed weekly A/H1N1 influenza virus isolation rate curve. RESULTS: The model found the potentially best-fit simulation with correlation coefficient up to 96% and all the successful simulations converging to the best-fit. The annual effective reproductive number of each co-circulating influenza strain was estimated. We found that, during the 2008-2009 influenza season, the annual effective reproductive number of the succeeding A/H1N1 clade 2B-2, carrying H275Y mutation in the neuraminidase, was estimated around 1.65. As to the preceding A/H1N1 clade 2C-2, the annual effective reproductive number would originally be equivalent to 1.65 but finally took on around 0.75 after the emergence of clade 2B-2. The model reported that clade 2B-2 outcompeted for the 2008-2009 influenza season mainly because clade 2C-2 suffered from a reduction of transmission fitness of around 71% on encountering the former. CONCLUSIONS: We conclude that interdisciplinary data-driven mathematical modelling could bring to light the transmission dynamics of the A/H1N1 H275Y strains during the 2007-2009 influenza seasons worldwide and may inspire us to tackle the continually emerging drug-resistant A/H1N1pdm09 strains. Furthermore, we provide a prospective approach through mathematical modelling to solving a seemingly unintelligible problem at the human population level and look forward to its application at molecular level through bridging the resolution capacities of related disciplines.

SMART: Statistical Metabolomics Analysis-An R Tool.

Metabolomics data provide unprecedented opportunities to decipher metabolic mechanisms by analyzing hundreds to thousands of metabolites. Data quality concerns and complex batch effects in metabolomics must be appropriately addressed through statistical analysis. This study developed an integrated analysis tool for metabolomics studies to streamline the complete analysis flow from initial data preprocessing to downstream association analysis. We developed Statistical Metabolomics Analysis-An R Tool (SMART), which can analyze input files with different formats, visually represent various types of data features, implement peak alignment and annotation, conduct quality control for samples and peaks, explore batch effects, and perform association analysis. A pharmacometabolomics study of antihypertensive medication was conducted and data were analyzed using SMART. Neuromedin N was identified as a metabolite significantly associated with angiotensin-converting-enzyme inhibitors in our metabolome-wide association analysis (p = 1.56 × 10(-4) in an analysis of covariance (ANCOVA) with an adjustment for unknown latent groups and p = 1.02 × 10(-4) in an ANCOVA with an adjustment for hidden substructures). This endogenous neuropeptide is highly related to neurotensin and neuromedin U, which are involved in blood pressure regulation and smooth muscle contraction. The SMART software, a user guide, and example data can be downloaded from http://www.stat.sinica.edu.tw/hsinchou/metabolomics/SMART.htm .

Mycobacterium tuberculosis nucleic acid amplification tests reduce nosocomial tuberculosis exposure in intensive care units: A nationwide cohort study.

BACKGROUND AND OBJECTIVE: This retrospective national surveillance study investigated the burden of and risk factors for nosocomial exposure of pulmonary tuberculosis (TB) in intensive care units. METHODS: Patients admitted to intensive care units were identified from the National Health Insurance Research Database. During 2004-2009, there were 1 387 707 intensive care unit admissions of 900 562 adult patients. Pulmonary tuberculosis association was considered if the patient was diagnosed with pulmonary tuberculosis during admission or within 3 months after discharge. Nosocomial transmissible period was calculated based on the length of anti-tuberculosis treatment and negative-pressure isolation during admission. RESULTS: Pulmonary tuberculosis was associated with 1.20% of all intensive care unit admissions and 6731 (38.9%) started anti-TB treatment during admission. For the other 10 583 admissions, the diagnosis was made after discharge and anti-TB treatment was not prescribed during admission. The probability paralleled the regional tuberculosis incidence. On average, 2794 pulmonary tuberculosis associated intensive care unit admissions contributed to 42 999-44 062 days of nosocomial exposure per year. The length of nosocomial transmissible period decreased with the gradual implementation of Mycobacterium tuberculosis nucleic acid amplification tests in intensive care practice. Multivariate linear regression analysis revealed that the length of nosocomial transmissible period was inversely associated with male gender, airway symptoms prior to admission and performing M. tuberculosis nucleic acid amplification tests and mycobacterial culture. CONCLUSIONS: Nosocomial tuberculosis exposure is not uncommon in intensive care units. Performing rapid molecular diagnostic tests in those suspected of tuberculosis is recommended to reduce the risk of nosocomial exposure.

Optimal duration of anti-TB treatment in patients with diabetes: nine or six months?

BACKGROUND: Diabetes mellitus (DM) increases the risk of TB recurrence. This study investigated whether 9-month anti-TB treatment is associated with a lower risk of TB recurrence within 2 years after complete treatment than 6-month treatment in patients with DM with an emphasis on the impact of directly observed therapy, short course (DOTs). METHODS: Patients with pulmonary but not extrapulmonary TB receiving treatment of 173 to 277 days between 2002 and 2010 were identified from the National Health Insurance Research Database of Taiwan. Patients with DM were then selected and classified into two groups based on anti-TB treatment duration (9 months vs 6 months). Factors predicting 2-year TB recurrence were explored using Cox regression analysis. RESULTS: Among 12,688 patients with DM and 43,195 patients without DM, the 2-year TB recurrence rate was 2.20% and 1.38%, respectively (P < .001). Of the patients with DM, recurrence rate decreased from 3.54% to 1.19% after implementation of DOTs (P < .001). A total of 4,506 (35.5%) were classified into 9-month anti-TB treatment group. Although a 9-month anti-TB treatment was associated with a lower recurrence rate (hazard ratio, 0.76 [95% CI, 0.59-0.97]), the benefit disappeared (hazard ratio, 0.69 [95% CI, 0.43-1.11]) under DOTs. Other predictors of recurrence included older age, male sex, malignancy, earlier TB diagnosis year, culture positivity after 2 months of anti-TB treatment, and anti-TB treatment being ≤ 80% consistent with standard regimen. CONCLUSIONS: The 2-year TB recurrence rate is higher in a diabetic population in Taiwan and can be reduced by treatment supervision. Extending the anti-TB treatment by 3 months may also decrease the recurrence rate when treatment is not supervised.

A fault-tolerant method for HLA typing with PacBio data.

BACKGROUND: Human leukocyte antigen (HLA) genes are critical genes involved in important biomedical aspects, including organ transplantation, autoimmune diseases and infectious diseases. The gene family contains the most polymorphic genes in humans and the difference between two alleles is only a single base pair substitution in many cases. The next generation sequencing (NGS) technologies could be used for high throughput HLA typing but in silico methods are still needed to correctly assign the alleles of a sample. Computer scientists have developed such methods for various NGS platforms, such as Illumina, Roche 454 and Ion Torrent, based on the characteristics of the reads they generate. However, the method for PacBio reads was less addressed, probably owing to its high error rates. The PacBio system has the longest read length among available NGS platforms, and therefore is the only platform capable of having exon 2 and exon 3 of HLA genes on the same read to unequivocally solve the ambiguity problem caused by the "phasing" issue. RESULTS: We proposed a new method BayesTyping1 to assign HLA alleles for PacBio circular consensus sequencing reads using Bayes' theorem. The method was applied to simulated data of the three loci HLA-A, HLA-B and HLA-DRB1. The experimental results showed its capability to tolerate the disturbance of sequencing errors and external noise reads. CONCLUSIONS: The BayesTyping1 method could overcome the problems of HLA typing using PacBio reads, which mostly arise from sequencing errors of PacBio reads and the divergence of HLA genes, to some extent.

Risk factors for pulmonary tuberculosis in patients with chronic obstructive airway disease in Taiwan: a nationwide cohort study.

BACKGROUND: An association between chronic obstructive pulmonary disease (COPD) and tuberculosis (TB) has been described, mainly due to smoking and corticosteroid use. Whether inhaled corticosteroid (ICS) therapy is associated with an increased risk of TB remains unclear. METHODS: We selected COPD cases by using six diagnostic scenarios and control subjects from a nationwide health insurance database, and applied time-dependent Cox regression analysis to identify the risk factors for TB. RESULTS: Among 1,000,000 beneficiaries, 23,594 COPD cases and 47,188 non-COPD control subjects were selected. Cox regression analysis revealed that age, male gender, diabetes mellitus, end-stage renal disease, and cirrhosis, as well as COPD (hazard ratio = 2.468 [2.205-2.762]) were independent risk factors for TB. Among the COPD cases, those who developed TB received more oral corticosteroids and oral ß-agonists. Time-dependent Cox regression analysis revealed that age, male gender, diabetes mellitus, low income, oral corticosteroid dose, and oral ß-agonist dose, but not ICS dose, were independent risk factors for TB. The identified risk factors and their hazard ratios were similar among the COPD cases selected using different scenarios. CONCLUSION: Keeping a high suspicion and regularly monitoring for the development of pulmonary TB in COPD patients are necessary, especially for those receiving higher doses of oral corticosteroids and other COPD medications. Although ICS therapy has been shown to predispose COPD patients to pneumonia in large randomized clinical trials, it does not increase the risk of TB in real world practice.

In-silico drug screening and potential target identification for hepatocellular carcinoma using Support Vector Machines based on drug screening result.

Hepatocellular carcinoma (HCC) is a severe liver malignancy with few drug treatment options. In finding an effective treatment for HCC, screening drugs that are already FDA-approved will fast track the clinical trial and drug approval process. Connectivity Map (CMap), a large repository of chemical-induced gene expression profiles, provides the opportunity to analyze drug properties on the basis of gene expression. Support Vector Machines (SVM) were utilized to classify the effectiveness of drugs against HCC using gene expression profiles in CMap. The results of this classification will help us (1) identify genes that are chemically sensitive, and (2) predict the effectiveness of remaining chemicals in CMap in the treatment of HCC and provide a prioritized list of possible HCC drugs for biological verification. Four HCC cell lines were treated with 146 distinct chemicals, and cell viability was examined. SVM successfully classified the effectiveness of the chemicals with an average Area Under ROC Curve (AUROC) of 0.9. Using reported HCC patient samples, we identified chemically sensitive genes that may be possible HCC therapeutic targets, including MT1E, MYC, and GADD45B. Using SVM, several known HCC inhibitors, such as geldanamycin, alvespimycin (HSP90 inhibitors), and doxorubicin (chemotherapy drug), were predicted. Seven out of the 23 predicted drugs were cardiac glycosides, suggesting a link between this drug category and HCC inhibition. The study demonstrates a strategy of in silico drug screening with SVM using a large repository of microarrays based on initial in vitro drug screening. Verifying these results biologically would help develop a more accurate chemical sensitivity model.

Pulmonary tuberculosis and delay in anti-tuberculous treatment are important risk factors for chronic obstructive pulmonary disease.

OBJECTIVE: Tuberculosis (TB) remains the leading cause of death among infectious diseases worldwide. It has been suggested as an important risk factor of chronic obstructive pulmonary disease (COPD), which is also a major cause of morbidity and mortality. This study investigated the impact of pulmonary TB and anti-TB treatment on the risk of developing COPD. DESIGN, SETTING, AND PARTICIPANTS: This cohort study used the National Health Insurance Database of Taiwan, particularly the Longitudinal Health Insurance Database 2005 to obtain 3,176 pulmonary TB cases and 15,880 control subjects matched in age, sex, and timing of entering the database. MAIN OUTCOME MEASURES: Hazard ratios of potential risk factors of COPD, especially pulmonary TB and anti-TB treatment. RESULTS: The mean age of pulmonary TB cases was 51.9±19.2. The interval between the initial study date and commencement of anti-TB treatment (delay in anti-TB treatment) was 75.8±65.4 days. Independent risk factors for developing COPD were age, male, low income, and history of pulmonary TB (hazard ratio 2.054 [1.768-2.387]), while diabetes mellitus was protective. The impact of TB persisted for six years after TB diagnosis and was significant in women and subjects aged >70 years. Among TB patients, delay in anti-TB treatment had a dose-response relationship with the risk of developing COPD. CONCLUSIONS: Some cases of COPD may be preventable by controlling the TB epidemic, early TB diagnosis, and prompt initiation of appropriate anti-TB treatment. Follow-up care and early intervention for COPD may be necessary for treated TB patients.

Gene expression-based chemical genomics identifies potential therapeutic drugs in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is an aggressive tumor with a poor prognosis. Currently, only sorafenib is approved by the FDA for advanced HCC treatment; therefore, there is an urgent need to discover candidate therapeutic drugs for HCC. We hypothesized that if a drug signature could reverse, at least in part, the gene expression signature of HCC, it might have the potential to inhibit HCC-related pathways and thereby treat HCC. To test this hypothesis, we first built an integrative platform, the "Encyclopedia of Hepatocellular Carcinoma genes Online 2", dubbed EHCO2, to systematically collect, organize and compare the publicly available data from HCC studies. The resulting collection includes a total of 4,020 genes. To systematically query the Connectivity Map (CMap), which includes 6,100 drug-mediated expression profiles, we further designed various gene signature selection and enrichment methods, including a randomization technique, majority vote, and clique analysis. Subsequently, 28 out of 50 prioritized drugs, including tanespimycin, trichostatin A, thioguanosine, and several anti-psychotic drugs with anti-tumor activities, were validated via MTT cell viability assays and clonogenic assays in HCC cell lines. To accelerate their future clinical use, possibly through drug-repurposing, we selected two well-established drugs to test in mice, chlorpromazine and trifluoperazine. Both drugs inhibited orthotopic liver tumor growth. In conclusion, we successfully discovered and validated existing drugs for potential HCC therapeutic use with the pipeline of Connectivity Map analysis and lab verification, thereby suggesting the usefulness of this procedure to accelerate drug repurposing for HCC treatment.

Influence of pressure control levels on the pulse pressure variations: an animal study using healthy piglets.

Pulse pressure variation (PPV) is a promising predictor for volume responsiveness. However, recent studies have criticized its validity during small tidal volume (TV) ventilation. The present study evaluated the influence of pressure control level (PCL) on PPV. Six anesthetized healthy piglets simulating hemorrhagic shock underwent five stages of intravascular volume status change. Each stage comprised four cycles of PCL manipulation. In each cycle, five different PCLs were applied in random order. Among 600 arterial pressure tracings obtained during PCL manipulations, 26 tracings were excluded because of signal artifact or ectopic beats. For the remaining 574 tracings, the percentage of normal beats among total recorded beats in each tracing was 99.80% ± 0.85%. When manipulating PCL causing an abrupt change within -16 ∼ +8 cmH(2)O, the PPV responded rapidly and stabilized within 60 s after manipulation. With higher increment in PCL (+12 ∼ +16 cmH(2)O), it required 90 s for PPV to stabilize. Under each cycle of PCL manipulation, the PPVs are linearly correlated to the PCL (r = 0.84 ± 0.21) and TV (r = 0.83 ± 0.22). The PPV as well as the slopes of the trend lines decreased from hypovolemic stages toward hypervolemic stages. Pulse pressure variation responds rapidly to change in ventilator setting and is linearly correlated with the PCL and TV. These characteristics may have important applications in critical care to improve the interpretation of PPV in accord to different ventilator settings.

The extent of linkage disequilibrium and computational challenges of single nucleotide polymorphisms in genome-wide association studies.

Single Nucleotide Polymorphisms (SNPs) are the most abundant form of genetic variations observed in the human genome. With the advent of high-throughput genotyping arrays and next-generation sequencing (NGS) platforms, tens of millions of SNPs have been uncovered in several human populations. However, the huge amount of SNPs bring new challenges in subsequent analysis. In reality, a number of SNPs may not be genotyped, and non-mutant bases may be falsely reported as SNPs in the microarray and NGS platforms. Furthermore, the identification of disease susceptibility genes are often confounded by numerous SNPs correlated by chance. In this paper, we review existing approaches for calling SNPs using microarrays and next-generation sequencing (NGS) platforms. Methods for measuring linkage disequilibrium (LD) and applications of the LD structure are discussed. Finally, we compare methods for inferring haplotypes from genotypes using microarray and NGS platforms and present the challenges of using SNPs in large-scale association studies.

Linear-time algorithms for the multiple gene duplication problems.

A fundamental problem arising in the evolutionary molecular biology is to discover the locations of gene duplications and multiple gene duplication episodes based on the phylogenetic information. The solutions to the MULTIPLE GENE DUPLICATION problems can provide useful clues to place the gene duplication events onto the locations of a species tree and to expose the multiple gene duplication episodes. In this paper, we study two variations of the MULTIPLE GENE DUPLICATION problems: the EPISODE-CLUSTERING (EC) problem and the MINIMUM EPISODES (ME) problem. For the EC problem, we improve the results of Burleigh et al. with an optimal linear-time algorithm. For the ME problem, on the basis of the algorithm presented by Bansal and Eulenstein, we propose an optimal linear-time algorithm.

CNVDetector: locating copy number variations using array CGH data.

UNLABELLED: CNVDetector is a program for locating copy number variations (CNVs) in a single genome. CNVDetector has several merits: (i) it can deal with the array comparative genomic hybridization data even if the noise is not normally distributed; (ii) it has a linear time kernel; (iii) its parameters can be easily selected; (iv) it evaluates the statistical significance for each CNV calling. AVAILABILITY: CNVDetector (for Windows platform) can be downloaded from http:www.csie.ntu.edu.tw/~kmchao/tools/CNVDetector/. The manual of CNVDetector is also available.

PhosphoPOINT: a comprehensive human kinase interactome and phospho-protein database.

MOTIVATION: To fully understand how a protein kinase regulates biological processes, it is imperative to first identify its substrate(s) and interacting protein(s). However, of the 518 known human serine/threonine/tyrosine kinases, 35% of these have known substrates, while 14% of the kinases have identified substrate recognition motifs. In contrast, 85% of the kinases have protein-protein interaction (PPI) datasets, raising the possibility that we might reveal potential kinase-substrate pairs from these PPIs. RESULTS: PhosphoPOINT, a comprehensive human kinase interactome and phospho-protein database, is a collection of 4195 phospho-proteins with a total of 15 738 phosphorylation sites. PhosphoPOINT annotates the interactions among kinases, with their down-stream substrates and with interacting (phospho)-proteins to modulate the kinase-substrate pairs. PhosphoPOINT implements various gene expression profiles and Gene Ontology cellular component information to evaluate each kinase and their interacting (phospho)-proteins/substrates. Integration of cSNPs that cause amino acids change with the proteins with the phosphoprotein dataset reveals that 64 phosphorylation sites result in a disease phenotypes when changed; the linked phenotypes include schizophrenia and hypertension. PhosphoPOINT also provides a search function for all phospho-peptides using about 300 known kinase/phosphatase substrate/binding motifs. Altogether, PhosphoPOINT provides robust annotation for kinases, their downstream substrates and their interaction (phospho)-proteins and this should accelerate the functional characterization of kinomemediated signaling. AVAILABILITY: PhosphoPOINT can be freely accessed in http://kinase. bioinformatics.tw/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A new framework for the selection of tag SNPs by multimarker haplotypes.

This paper proposes a new framework for the selection of tag SNPs based on haplotypes instead of on a single SNP. The tag SNPs found by this framework form a set of haplotypes completely predictive of the alleles of all untyped SNPs. We refer to this problem as MTMH, which is defined as follows: given a set of SNPs, find a minimum subset of SNPs (called tag SNPs) which defines a set of haplotypes completely predictive of the alleles of all untyped SNPs. The MTMH problem is solved by dividing into three subproblems, two of which are shown to be NP-hard. Several exact and approximation algorithms are proposed to solve these subproblems. We describe a framework which integrates these algorithms and develop a program called HapTagger for finding tag SNPs. HapTagger is compared with existing methods as well as the official tagging tool (called Haploview) of the International HapMap project using a variety of real data sets. Our theoretical analysis and experimental results indicate that HapTagger consistently identifies a smaller set of tag SNPs and runs much faster than existing methods. HapTagger avoids the need of incorporating a linkage disequilibrium statistic and thus significantly improves the computational efficiency. We also present an algorithm (specific to HapTagger) for reconstructing alleles of untyped SNPs. It is worth mentioning that these predictive haplotypes selected by HapTagger can be used as signatures of recent positive selection or co-evolution. HapTagger is available at http://www.csie.ntu.edu.tw/~kmchao/tools/HapTagger/.

Distant HNF1 site as a master control for the human class I alcohol dehydrogenase gene expression.

Gene duplication and divergence have contributed to the biochemical diversity of the alcohol dehydrogenase (ADH) family. Class I ADH is the major enzyme that catalyzes alcohol to acetaldehyde in the liver. To investigate the mechanism(s) controlling tissue-specific and temporal regulation of the three human class I ADH genes (ADH1A, ADH1B, and ADH1C), we compared genomic sequences for the human and mouse ADH loci and analyzed human ADH gene expression in BAC transgenic mice carrying different lengths of the upstream sequences of the class I ADH. A conserved noncoding sequence, located between the class I and class IV ADH (ADH7) genes, was found to be essential for directing class I ADH gene expression in fetal and adult livers. Within this region, a 275-bp fragment displaying liver-specific DNase I hypersensitivity was bound by HNF1. The HNF1-containing upstream sequence enhanced all three class I ADH promoters in an orientation-dependent manner, and the transcriptional activation depended on binding to the HNF1 site. Deletion of the conserved HNF1 site in the BAC led to the shutdown of human class I ADH gene expression in the transgenic livers, leaving ADH1C gene expression in the stomach unchanged. Moreover, interaction between the upstream element and the class I ADH gene promoters was demonstrated by chromosome conformation capture, suggesting a DNA looping mechanism is involved in gene activation. Taken together, our data indicate that HNF1 binding, at approximately 51 kb upstream, plays a master role in controlling human class I ADH gene expression and may govern alcohol metabolism in the liver.

A greedier approach for finding tag SNPs.

MOTIVATION: Recent studies have shown that a small subset of Single Nucleotide Polymorphisms (SNPs) (called tag SNPs) is sufficient to capture the haplotype patterns in a high linkage disequilibrium region. To find the minimum set of tag SNPs, exact algorithms for finding the optimal solution could take exponential time. On the other hand, approximation algorithms are more efficient but may fail to find the optimal solution. RESULTS: We propose a hybrid method that combines the ideas of the branch-and-bound method and the greedy algorithm. This method explores larger solution space to obtain a better solution than a traditional greedy algorithm. It also allows the user to adjust the efficiency of the program and quality of solutions. This algorithm has been implemented and tested on a variety of simulated and biological data. The experimental results indicate that our program can find better solutions than previous methods. This approach is quite general since it can be used to adapt other greedy algorithms to solve their corresponding problems. AVAILABILITY: The program is available upon request.