bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of effects of connexin-mimetic peptides in rat mesenteric small arteries
Authors: Matchkov Vladimir V. , Rahman Awahan , Bakker Linda M. , Griffith Tudor M. , Nilsson Holger , Aalkjær Christian
Published: January 2006

Synthetic peptides homologous to the extracellular loops of the major vascular connexins represent a novel class of gap junction blockers that have been used to assess the role of direct cellular communication in arteries and veins. However, the specificity of action of such peptides on the coupling between smooth muscle cells (SMCs) has not yet been fully characterized. Isolated third-order rat mesenteric arteries were therefore studied with respect to isometric tension (myography), intracellular Ca2+concentraton ([Ca2+]i) (Ca2+-sensitive dyes), membrane potential, and input resistance (sharp intracellular glass electrodes). Confocal imaging was used for visualization of [Ca2+]ievents in individual SMCs in the arterial wall and membrane currents (patch clamp) measured in individual SMCs isolated from the same arteries. A triple peptide combination (37,43Gap 27 +40Gap 27 +43Gap 26) increased intercellular resistance (measured as input resistance) in intact arterial segments without affecting the membrane conductance of individual cells and also interrupted electrical coupling between pairs of rat aortic A7r5 myocytes. In intact arterial segments, the peptides desynchronized [Ca2+]itransients in individual SMCs and abolished vasomotion without suppressing Ca2+transients in individual cells. They also depolarized SMCs, increased [Ca2+]i, and attenuated acetylcholine-induced, endothelium-dependent smooth muscle hyperpolarization. Experiments with endothelium-denuded arteries suggested that the depolarization produced by the peptides under basal conditions was in part secondary to electrical uncoupling of the endothelium from SMCs with loss of a tonic hyperpolarizing effect of the endothelium. Taken together, the results indicate that connexin-mimetic peptides block electrical signaling in rat mesenteric small arteries without exerting major nonjunctional effects.
Rac1 and RhoA as regulators of endothelial phenotype and barrier function in hypoxia-induced neonatal pulmonary hypertension
Authors: Wojciak-Stothard Beata , Tsang Lillian Yen Fen , Paleolog Ewa , Hall Susan M. , Haworth Sheila G.
Published: January 2006

Hypoxia is a common cause of persistant pulmonary hypertension in the newborn (PPHN), a condition associated with endothelial dysfunction and abnormal pulmonary vascular remodeling. The GTPase RhoA has been implicated in the pathogenesis of PPHN, but its contribution to endothelial remodeling and function is not known. We studied pulmonary artery endothelial cells (PAECs) taken from piglets with chronic hypoxia-induced pulmonary hypertension and from healthy animals and analyzed the roles of Rho GTPases in the regulation of the endothelial phenotype and function under basal normoxic conditions, acute hypoxia, and reoxygenation. The activities of RhoA, Rac1, and Cdc42 were correlated with changes in the endothelial cytoskeleton, adherens junctions, permeability, ROS production, VEGF levels, and activities of transcription factors hypoxia-inducible factor (HIF)-1α and NF-κB. Adenoviral gene transfer was used to express dominant-negative GTPases, kinase-dead p21-activated kinase (PAK)-1, and constitutively activated Rac1 in cells. PAECs from pulmonary hypertensive piglets had a stable abnormal phenotype with a sustained reduction in Rac1 activity and an increase in RhoA activity, which correlated with an increase in actin stress fiber formation, increased permeability, and a decrease in VEGF and ROS production. Cells from pulmonary hypertensive animals were still able to respond to acute hypoxia. They also showed high activities of HIF-1α and NF-κB, likely to result from changes in the activities of Rho GTPases. Activation of Rac1 and its effector PAK-1 as well as inhibition of RhoA restored the abnormal phenotype and permeability of hypertensive PAECs to normal.
Intracellular Cl−fluxes play a novel role in Ca2+handling in airway smooth muscle
Authors: Hirota Simon , Trimble Nancy , Pertens Evi , Janssen Luke J.
Published: January 2006

Intracellular Ca2+is actively sequestered into the sarcoplasmic reticulum (SR), whereas the release of Ca2+from the SR can be triggered by activation of the inositol 1,4,5-trisphosphate and ryanodine receptors. Uptake and release of Ca2+across the SR membrane are electrogenic processes; accumulation of positive or negative charge across the SR membrane could electrostatically hinder the movement of Ca2+into or out of the SR, respectively. We hypothesized that the movement of intracellular Cl−(Cl[Formula: see text]) across the SR membrane neutralizes the accumulation of charge that accompanies uptake and release of Ca2+. Thus inhibition of SR Cl−fluxes will reduce Ca2+sequestration and agonist-induced release. The Cl−channel blocker 5-nitro-2-(3-phenylpropylamino)benzoic acid (NPPB; 10−4M), previously shown to inhibit SR Cl−channels, significantly reduced the magnitude of successive acetylcholine-induced contractions of airway smooth muscle (ASM), suggesting a “run down” of sequestered Ca2+within the SR. Niflumic acid (10−4M), a structurally different Cl−channel blocker, had no such effect. Furthermore, NPPB significantly reduced caffeine-induced contraction and increases in intracellular Ca2+concentration ([Ca2+]i). Depletion of Cl[Formula: see text], accomplished by bathing ASM strips in Cl−-free buffer, significantly reduced the magnitude of successive acetylcholine-induced contractions. In addition, Cl−depletion significantly reduced caffeine-induced increases in [Ca2+]i. Together these data suggest a novel role for Cl[Formula: see text] fluxes in Ca2+handling in smooth muscle. Because the release of sequestered Ca2+is the predominate source of Ca2+for contraction of ASM, targeting Cl[Formula: see text] fluxes may prove useful in the control of ASM hyperresponsiveness associated with asthma.
Role of hydrogen sulfide in cecal ligation and puncture-induced sepsis in the mouse
Authors: Zhang Huili , Zhi Liang , Moore Philip K. , Bhatia Madhav
Published: January 2006

Endogenous hydrogen sulfide (H2S) is naturally synthesized in various types of mammalian cells from l-cysteine in a reaction catalyzed by two enzymes, cystathionine-γ-lyase (CSE) and/or cystathionine-β-synthase. The latest studies have implied that H2S functions as a vasodilator and neurotransmitter. However, so far there is little information about the role played by H2S in systemic inflammation such as sepsis. Thus the aim of this study was to investigate the potential role of endogenous H2S in cecal ligation and puncture (CLP)-induced sepsis. Male Swiss mice were subjected to CLP-induced sepsis and treated with saline (ip), dl-propargylglycine (PAG, 50 mg/kg ip), a CSE inhibitor, or sodium hydrosulfide (NaHS; 10 mg/kg ip). PAG was administered either 1 h before or 1 h after the induction of sepsis, whereas NaHS was given at the same time of CLP. CLP-induced sepsis significantly increased the plasma H2S level and the liver H2S synthesis 8 h after CLP compared with sham operation. Induction of sepsis also resulted in a significant upregulation of CSE mRNA in liver. On the other hand, prophylactic as well as therapeutic administration of PAG significantly reduced sepsis-associated systemic inflammation, as evidenced by myeloperoxidase activity and histological changes in lung and liver, and attenuated the mortality of CLP-induced sepsis. Injection of NaHS significantly aggravated sepsis-associated systemic inflammation. Therefore, the effect of inhibition of H2S formation and administration of NaHS suggests that H2S plays a proinflammatory role in regulating the severity of sepsis and associated organ injury.
Characterization of Naturally Occurring and Lamivudine-Induced Surface Gene Mutants of Hepatitis B Virus in Patients with Chronic Hepatitis B in India
Authors: Kazim Syed Naqui , Sarin Shiv Kumar , Sharma Barjesh Chander , Khan Luqman Ahmad , Hasnain Seyed Ehtesham
Published: January 2006

Background: Besides vaccine escape or immune escape hepatitis B virus (HBV) mutants, naturally occurring and drug-induced mutations have been reported in the surface gene (S-gene) of HBV. Aim: To investigate the frequency and profile of naturally occurring S-gene mutants and the influence of long-term lamivudine therapy in patients with chronic hepatitis B (CHB). Materials and Methods: 57 patients with histologically proven CHB, on lamivudine 100 mg/day for more than 24 months, were included. Viral DNA was extracted at baseline and from on-therapy serum samples. The region encoding the complete major hydrophilic region (MHR) and flanking regions (nucleotides 425–840) of major S-gene that overlapped with the viral polymerase was PCR amplified and sequenced. End-of-therapy response (ETR) was assessed. Results: Two (3.5%) patients had naturally occurring HBV mutants, sP127S and sS143L seen in the ‘a’ determinant of the S-gene. Following lamivudine therapy, 14 of 57 (24.5%) patients developed 16 types of S-gene mutations (sP120S, sA128V, sS143L, sW182St., sT189I, sV190A, sS193L, sI195M, sW196L, sW196St., sS207R, sI208T, sS210E, sF219S, sF220L and sC221G). Thirteen (81.2%) of these mutations emerged downstream to the MHR. Nine of 16 types of S-gene mutations observed with lamivudine therapy were also associated with the corresponding changes in the polymerase gene. Baseline viral DNA was significantly higher (2,093 vs. 336 pg/ml; p < 0.05) among patients developing S-gene mutants and the ETR in them was significantly lower [3 of 16 (18.8%) vs. 17 of 41 (41.5%); p < 0.05]. Conclusions: Naturally occurring S-gene mutations are uncommon and are restricted to the ‘a’ determinant region. Mutations develop in about a quarter of the patients on lamivudine therapy, mostly downstream to the MHR. They may contribute to non-response to the antiviral therapy.
Guidelines for Prevention of Stroke in Patients With Ischemic Stroke or Transient Ischemic Attack
Authors: Sacco Ralph L. , Adams Robert , Albers Greg , Alberts Mark J. , Benavente Oscar , Furie Karen , Goldstein Larry B. , Gorelick Philip , Halperin Jonathan , Harbaugh Robert , Johnston S. Claiborne , Katzan Irene , Kelly-Hayes Margaret , Kenton Edgar J. , Marks Michael , Schwamm Lee H. , Tomsick Thomas
Published: January 2006

The aim of this new statement is to provide comprehensive and timely evidence-based recommendations on the prevention of ischemic stroke among survivors of ischemic stroke or transient ischemic attack. Evidence-based recommendations are included for the control of risk factors, interventional approaches for atherosclerotic disease, antithrombotic treatments for cardioembolism, and the use of antiplatelet agents for noncardioembolic stroke. Further recommendations are provided for the prevention of recurrent stroke in a variety of other specific circumstances, including arterial dissections; patent foramen ovale; hyperhomocysteinemia; hypercoagulable states; sickle cell disease; cerebral venous sinus thrombosis; stroke among women, particularly with regard to pregnancy and the use of postmenopausal hormones; the use of anticoagulation after cerebral hemorrhage; and special approaches for the implementation of guidelines and their use in high-risk populations. (Stroke. 2006;37:577-617.)
Temporal Trends in the Utilization of Diagnostic Testing and Treatments for Cardiovascular Disease in the United States, 1993–2001
Authors: Lucas F.L. , DeLorenzo Michael A. , Siewers Andrea E. , Wennberg David E.
Published: January 2006

Background—

Rates of invasive testing and treatment for coronary artery disease have increased over time. Less is known about trends in the utilization of noninvasive cardiac testing for coronary artery disease. The objective of this study was 2-fold: to explore temporal trends in the utilization of noninvasive and invasive cardiac services in relation to changes in the prevalence of cardiac disease, and to examine whether temporal increases have been targeted to potentially underserved populations.

Methods and Results—

We performed an annual cross-sectional population-based study of Medicare patients from 1993 to 2001. We identified stress testing, cardiac catheterization, and revascularization procedures, as well as hospitalizations for acute myocardial infarction, during each year and calculated population-based rates for each using the total fee-for-service Medicare population as the denominator and adjusting for age, gender, and race. We observed marked growth in the utilization rates of cardiac services over time, with relative rates nearly doubling for most services. Acute myocardial infarction hospitalization rates have remained stable over the study period. Although rates of all procedures except coronary artery bypass increased in all subgroups, differences in rates of cardiac testing and treatment between nonblack men and other subgroups persisted over time.

Conclusions—

Temporal increases in the use of noninvasive and invasive cardiac services are not explained by changes in disease prevalence and have not succeeded in narrowing preexisting treatment differences by gender and race. Such increases, although conferring benefit for some, may expose others to risk and cost without benefit.
Fingolimod (FTY720) in Severe Hepatic Impairment: Pharmacokinetics and Relationship to Markers of Liver Function
Authors: Kovarik John M. , Schmouder Robert L. , Hartmann Stefan , Riviere Gilles‐Jacques , Picard Franck , Voss Brigitta , Weiss Markus , Wagner Frank , Schmidt Hartmut H.‐J.
Published: January 2006

The authors assessed the impact of severe hepatic impairment on the disposition of fingolimod—a sphingosine‐1‐phosphate receptor immunomodulator primarily metabolized by CYP4F2—in 6 patients and 6 matched healthy controls who received a single 5‐mg oral dose. Compared with healthy controls, severe hepatic‐impaired subjects had a doubled area under the concentration time curve (AUC) and 50% prolonged elimination half‐life but a similar peak blood concentration. When these data were combined with those from a previous study in mild and moderate hepatic‐impaired subjects, there were significant positive correlations between fingolimod AUC versus bilirubin (r = 0.683) and prothrombin time (r = 0.777) and a significant negative correlation versus albumin (r = 0.578), confirming the importance of liver function for fingolimod clearance. For patients with severe hepatic impairment (Child‐Pugh class C), a standard first dose of fingolimod could be given followed by a maintenance dose that is reduced by half from the normal maintenance dose.
Limited Sampling Models for Oral Midazolam: Midazolam Plasma Concentrations, Not the Ratio of 1‐Hydroxymidazolam to Midazolam Plasma Concentrations, Accurately Predicts AUC as a Biomarker of CYP3A Activity
Authors: Lee Lois S. , Bertino Joseph S. , Nafziger Anne N.
Published: January 2006

Oral midazolam is used as a phenotyping probe for cytochrome P450 (CYP) 3A activity and requires multiple plasma samples to measure drug exposure. Limited sampling is a useful strategy for optimizing sampling and reducing costs and labor. We studied limited sampling models using multiple linear regressions to predict the area under the concentration versus time curve (AUC) of midazolam using either midazolam plasma concentrations or the ratio of 1‐hydroxymidazolam (1‐OH MDZ) to midazolam plasma concentrations. CYP3A baseline activity data for oral midazolam from previous studies were used (45 healthy adults for models using midazolam plasma concentrations and 41 healthy adults for models using the ratios of 1‐OH MDZ to midazolam plasma concentrations). Limited sampling models were derived, validated, and evaluated for precision and bias. Two equations using the time points at 0.5 and 6 hours and 0.5, 2, and 6 hours were acceptable and predictive of midazolam AUC using midazolam plasma concentrations. No 1‐OH MDZ to midazolam plasma concentration ratios accurately predicted midazolam AUC.
Effect of R667, a Novel Emphysema Agent, on the Pharmacokinetics of Midazolam in Healthy Men
Authors: Brennan Barbara J. , Brown Angus B. , Kolis Stanley J. , Rutman Olga , Gooden Calvin , Davies Brian E.
Published: January 2006

The purpose of this study was to investigate the potential for a CYP3A4‐mediated drug interaction between R667 and midazolam (MDZ) in healthy subjects. R667 is metabolized by CYP3A4 and therefore may interact with CYP3A4 substrates. In the present study, 18 healthy male subjects received a single 15‐mg oral dose of MDZ with and without R667 coadministration. Serial blood samples were collected predose and up to 24 hours after each MDZ dose for pharmacokinetic (PK) evaluation. The PK parameters for MDZ, R667, and metabolites were estimated using noncompartmental methods. MDZ exposure was very similar in the presence and absence of R667 (Cmax = 50.8 vs 46.2 ng/mL; AUC0‐last = 215 vs 216 ng•h/mL; AUC0‐last ratio = 0.26 vs 0.26, respectively). R667 exposure was not affected by midazolam coadministration as compared with historical data. Based on the results of this study, no significant pharmacokinetic interaction should be anticipated between R667 and CYP3A4 substrates.
Variability in Renal Clearance of Substrates for Renal Transporters in Chinese Subjects
Authors: Yin Ophelia Q. P. , Tomlinson Brian , Chow Moses S. S.
Published: January 2006

The authors evaluated the inter‐ and intraindividual variability in the renal clearance of substrates of organic anion transporters (OAT) or organic cation transporters (OCT) using repeated drug application procedures. Two OAT substrates (ampicillin and cephalexin) and 2 OCT substrates (famotidine and metformin) were selected. Each drug was administered orally twice to healthy subjects, with sample sizes ranging from 12 to 28 (using bioequivalent formulations of each drug). The inter‐ (δinter) and intrasubject (δintra) variances in renal clearance were estimated based on analysis of variance, and the genetic contribution (rGC) was calculated as (δinter ‐ intra)/δinter. The renal clearances of ampicillin, cephalexin, famotidine, and metformin averaged 5.21 (range, 2.87–11.20), 3.01 (range, 1.50–3.82), 4.96 (range, 2.84–8.17), and 9.44 (range, 5.66–15.43) mL/min/kg, with mean intraindividual coefficients of variation of 17.7%, 7.3%, 13.5%, and 9.0% and rGC values of 0.75, 0.89, 0.81, and 0.93, respectively. These high rGC values suggest a potential significant genetic contribution by the renal OATs and OCTs in Chinese subjects. Further studies in a larger population are needed to confirm the importance of these results as well as to identify specific genetic variants in these transporters responsible for such variability.
A high level interface to SCOP and ASTRAL implemented in Python
Authors: Casbon James A , Crooks Gavin E , Saqi Mansoor AS
Published: January 2006

Background

Benchmarking algorithms in structural bioinformatics often involves the construction of datasets of proteins with given sequence and structural properties. The SCOP database is a manually curated structural classification which groups together proteins on the basis of structural similarity. The ASTRAL compendium provides non redundant subsets of SCOP domains on the basis of sequence similarity such that no two domains in a given subset share more than a defined degree of sequence similarity. Taken together these two resources provide a 'ground truth' for assessing structural bioinformatics algorithms. We present a small and easy to use API written in python to enable construction of datasets from these resources.

Results

We have designed a set of python modules to provide an abstraction of the SCOP and ASTRAL databases. The modules are designed to work as part of the Biopython distribution. Python users can now manipulate and use the SCOP hierarchy from within python programs, and use ASTRAL to return sequences of domains in SCOP, as well as clustered representations of SCOP from ASTRAL.

Conclusion

The modules make the analysis and generation of datasets for use in structural genomics easier and more principled.
Automatic discovery of cross-family sequence features associated with protein function
Authors: Brameier Markus , Haan Josien , Krings Andrea , MacCallum Robert M
Published: January 2006

Background

Methods for predicting protein function directly from amino acid sequences are useful tools in the study of uncharacterised protein families and in comparative genomics. Until now, this problem has been approached using machine learning techniques that attempt to predict membership, or otherwise, to predefined functional categories or subcellular locations. A potential drawback of this approach is that the human-designated functional classes may not accurately reflect the underlying biology, and consequently important sequence-to-function relationships may be missed.

Results

We show that a self-supervised data mining approach is able to find relationships between sequence features and functional annotations. No preconceived ideas about functional categories are required, and the training data is simply a set of protein sequences and their UniProt/Swiss-Prot annotations. The main technical aspect of the approach is the co-evolution of amino acid-based regular expressions and keyword-based logical expressions with genetic programming. Our experiments on a strictly non-redundant set of eukaryotic proteins reveal that the strongest and most easily detected sequence-to-function relationships are concerned with targeting to various cellular compartments, which is an area already well studied both experimentally and computationally. Of more interest are a number of broad functional roles which can also be correlated with sequence features. These include inhibition, biosynthesis, transcription and defence against bacteria. Despite substantial overlaps between these functions and their corresponding cellular compartments, we find clear differences in the sequence motifs used to predict some of these functions. For example, the presence of polyglutamine repeats appears to be linked more strongly to the "transcription" function than to the general "nuclear" function/location.

Conclusion

We have developed a novel and useful approach for knowledge discovery in annotated sequence data. The technique is able to identify functionally important sequence features and does not require expert knowledge. By viewing protein function from a sequence perspective, the approach is also suitable for discovering unexpected links between biological processes, such as the recently discovered role of ubiquitination in transcription.
OpWise: Operons aid the identification of differentially expressed genes in bacterial microarray experiments
Authors: Price Morgan N , Arkin Adam P , Alm Eric J
Published: January 2006

Background

Differentially expressed genes are typically identified by analyzing the variation between replicate measurements. These procedures implicitly assume that there are no systematic errors in the data even though several sources of systematic error are known.

Results

OpWise estimates the amount of systematic error in bacterial microarray data by assuming that genes in the same operon have matching expression patterns. OpWise then performs a Bayesian analysis of a linear model to estimate significance. In simulations, OpWise corrects for systematic error and is robust to deviations from its assumptions. In several bacterial data sets, significant amounts of systematic error are present, and replicate-based approaches overstate the confidence of the changers dramatically, while OpWise does not. Finally, OpWise can identify additional changers by assigning genes higher confidence if they are consistent with other genes in the same operon.

Conclusion

Although microarray data can contain large amounts of systematic error, operons provide an external standard and allow for reasonable estimates of significance. OpWise is available athttp://microbesonline.org/OpWise.
Prediction of protein structural class with Rough Sets
Authors: Cao Youfang , Liu Shi , Zhang Lida , Qin Jie , Wang Jiang , Tang Kexuan
Published: January 2006

Background

A new method for the prediction of protein structural classes is constructed based on Rough Sets algorithm, which is a rule-based data mining method. Amino acid compositions and 8 physicochemical properties data are used as conditional attributes for the construction of decision system. After reducing the decision system, decision rules are generated, which can be used to classify new objects.

Results

In this study, self-consistency and jackknife tests on the datasets constructed by G.P. Zhou (Journal of Protein Chemistry, 1998, 17: 729–738) are used to verify the performance of this method, and are compared with some of prior works. The results showed that the rough sets approach is very promising and may play a complementary role to the existing powerful approaches, such as the component-coupled, neural network, SVM, and LogitBoost approaches.

Conclusion

The results with high success rates indicate that the rough sets approach as proposed in this paper might hold a high potential to become a useful tool in bioinformatics.
Metabolic pathways variability and sequence/networks comparisons
Authors: Tun Kyaw , Dhar Pawan K , Palumbo Maria Concetta , Giuliani Alessandro
Published: January 2006

Background

In this work a simple method for the computation of relative similarities between homologous metabolic network modules is presented. The method is similar to classical sequence alignment and allows for the generation of phenotypic trees amenable to be compared with correspondent sequence based trees. The procedure can be applied to both single metabolic modules and whole metabolic network data without the need of any specific assumption.

Results

We demonstrate both the ability of the proposed method to build reliable biological classification of a set of microrganisms and the strong correlation between the metabolic network wiringand involved enzymes sequence space.

Conclusion

The method represents a valuable tool for the investigation of genotype/phenotype correlationsallowing for a direct comparison of different species as for their metabolic machinery. In addition the detection of enzymes whose sequence space is maximally correlated with the metabolicnetwork space gives an indication of the most crucial (on an evolutionary viewpoint) steps of the metabolic process.
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration
Authors: Teber Erdahl T , Crawford Edward , Bolton Kent B , Van Dyk Derek , Schofield Peter R , Kapoor Vimal , Church W Bret
Published: January 2006

Background

There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences.

Results

Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant.

Conclusion

Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence annotations relating to a gene, its transcripts and translations. The mechanism of transcript definition and creation, and subsequent navigation and exploration of features, are very intuitive and demand only a short learning curve. Ultimately, Djinn Lite can form the basis for providing valuable clues to plan new experiments, providing storage of sequences and annotations for dedication to customised projects. The application is appropriate for Windows 98-ME-2000-XP-2003 operating systems.
OligoSpawn: a software tool for the design of overgo probes from large unigene datasets
Authors: Zheng Jie , Svensson Jan T , Madishetty Kavitha , Close Timothy J , Jiang Tao , Lonardi Stefano
Published: January 2006

Background

Expressed sequence tag (EST) datasets represent perhaps the largest collection of genetic information. ESTs can be exploited in a variety of biological experiments and analysis. Here we are interested in the design of overlapping oligonucleotide (overgo) probes from large unigene (EST-contigs) datasets.

Results

OLIGOSPAWN is a suite of software tools that offers two complementary services, namely (1) the selection of "unique" oligos each of which appears in one unigene but does not occur (exactly or approximately) in any other and (2) the selection of "popular" oligos each of which occurs (exactly or approximately) in as many unigenes as possible. In this paper, we describe the functionalities of OLIGOSPAWN and the computational methods it employs, and we report on experimental results for the overgo probes designed with it.

Conclusion

The algorithms we designed are highly efficient and capable of processing unigene datasets of sizes on the order of several tens of Mb in a few hours on a regular PC. The software has been used to design overgo probes employed to screen a barley BAC library (Hordeum vulgare). OLIGOSPAWN is freely available at http://oligospawn.ucr.edu/.
Examination of actin and microtubule dependent APC localisations in living mammalian cells
Authors: Langford Kelly J , Askham Jon M , Lee Tracy , Adams Matthew , Morrison Ewan E
Published: January 2006

Background

The trafficking of the adenomatous polyposis coli (APC) tumour suppressor protein in mammalian cells is a perennially controversial topic. Immunostaining evidence for an actin-associated APC localisation at intercellular junctions has been previously presented, though live imaging of mammalian junctional APC has not been documented.

Results

Using live imaging of transfected COS-7 cells we observed intercellular junction-associated pools of GFP-APC in addition to previously documented microtubule-associated GFP-APC and a variety of minor localisations. Although both microtubule and junction-associated populations could co-exist within individual cells, they differed in their subcellular location, dynamic behaviour and sensitivity to cytoskeletal poisons. GFP-APC deletion mutant analysis indicated that a protein truncated immediately after the APC armadillo repeat domain retained the ability to localise to adhesive membranes in transfected cells. Supporting this, we also observed junctional APC immunostaining in cultures of human colorectal cancer cell line that express truncated forms of APC.

Conclusion

Our data indicate that APC can be found in two spatially separate populations at the cell periphery and these populations can co-exist in the same cell. The first localisation is highly dynamic and associated with microtubules near free edges and in cell vertices, while the second is comparatively static and is closely associated with actin at sites of cell-cell contact. Our imaging confirms that human GFP-APC possesses many of the localisations and behaviours previously seen by live imaging of Xenopus GFP-APC. However, we report the novel finding that GFP-APC puncta can remain associated with the ends of shrinking microtubules. Deletion analysis indicated that the N-terminal region of the APC protein mediated its junctional localisation, consistent with our observation that truncated APC proteins in colon cancer cell lines are still capable of localising to the cell cortex. This may have implications for the development of colorectal cancer.
Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals
Authors: Danchin Etienne GJ , Gouret Philippe , Pontarotti Pierre
Published: January 2006

Background

Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes) but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability.

Results

We report 11 gene families conserved throughout eukaryotes from yeasts (such as Saccharomyces cerevisiae) to bilaterian animals (such as Drosophila melanogaster or Caenorhabditis elegans). This evolutionarily wide conservation suggests they were present in the last common ancestors of fungi and metazoan animals. None of these 11 gene families are found in human nor mouse genomes, and their absence generally extends to all vertebrates. A total of 8 out of these 11 gene families have orthologs in plants, suggesting they were present in the Last Eukaryotic Common Ancestor (LECA). We investigated known functional information for these 11 gene families. This allowed us to correlate some of the lost gene families to loss of capabilities.

Conclusion

Mammalian and vertebrate genomes lost evolutionary conserved ancestral genes that are probably otherwise not dispensable in eukaryotes. Hence, the human genome, which is generally viewed as being the result of increased complexity and gene-content, has also evolved through simplification and gene losses. This acknowledgement confirms, as already suggested, that the genome of our far ancestor was probably more complex than ever considered.
Haseman-Elston weighted by marker informativity
Authors: Franke Daniel , Kleensang André , Elston Robert C , Ziegler Andreas
Published: January 2006

In the Haseman-Elston approach the squared phenotypic difference is regressed on the proportion of alleles shared identical by descent (IBD) to map a quantitative trait to a genetic marker. In applications the IBD distribution is estimated and usually cannot be determined uniquely owing to incomplete marker information. At Genetic Analysis Workshop (GAW) 13, Jacobs et al. [BMC Genet 2003, 4(Suppl 1):S82] proposed to improve the power of the Haseman-Elston algorithm by weighting for information available from marker genotypes. The authors did not show, however, the validity of the employed asymptotic distribution. In this paper, we use the simulated data provided for GAW 14 and show that weighting Haseman-Elston by marker information results in increased type I error rates. Specifically, we demonstrate that the number of significant findings throughout the chromosome is significantly increased with weighting schemes. Furthermore, we show that the classical Haseman-Elston method keeps its nominal significance level when applied to the same data. We therefore recommend to use Haseman-Elston with marker informativity weights only in conjunction with empirical p-values. Whether this approach in fact yields an increase in power needs to be investigated further.
Whole-genome association analysis to identify markers associated with recombination rates using single-nucleotide polymorphisms and microsatellites
Authors: Huang Song , Wang Shuang , Liu Nianjun , Chen Liang , Oh Cheongeun , Zhao Hongyu
Published: January 2006

Recombination during meiosis is one of the most important biological processes, and the level of recombination rates for a given individual is under genetic control. In this study, we conducted genome-wide association studies to identify chromosomal regions associated with recombination rates. We analyzed genotype data collected on the pedigrees in the Collaborative Study on the Genetics on Alcoholism data provided by Genetic Analysis Workshop 14. A total of 315 microsatellites and 10,081 single-nucleotide polymorphisms from Affymetrix on 22 autosomal chromosomes were used in our association analysis. Genome-wide gender-specific recombination counts for family founders were inferred first and association analysis was performed using multiple linear regressions. We used the positive false discovery rate (pFDR) to account for multiple comparisons in the two genome-wide scans. Eight regions showed some evidence of association with recombination counts based on the single-nucleotide polymorphism analysis after adjusting for multiple comparisons. However, no region was found to be significant using microsatellites.
Application of the regression of offspring on mid-parent method to detect associations between single-nucleotide polymorphisms and the beta 2 electroencephalogram phenotype in the COGA data
Authors: Roy-Gagnon Marie-Hélène , Mathias Rasika A , Wilson Alexander F
Published: January 2006

The beta 2 electroencephalogram (EEG) phenotype is used as a quantitative measure related to alcoholism, and evidence of linkage and association has previously been reported in the Collaborative Study on the Genetics of Alcoholism data. In this study, associations between the beta 2 EEG phenotype and single nucleotide polymorphisms from whole-genome Illumina and Affymetrix panels were investigated with the regression of offspring on mid-parent method to identify significant genetic effects and to estimate their heritability. Separate regressions on father and mother were performed to identify parent-specific effects. Estimates of the heritability of the beta 2 EEG phenotype were 0.68 ± 0.12 and 0.52 ± 0.07 based on father-offspring and mother-offspring pairs, respectively. Significant associations at the 0.0005 level, some of which were parent-specific, were found on chromosomes 1, 2, 5, 6, 7, 8, 11, 12, 15, 16, 17, 18, and 19 with heritability attributable to each SNP ranging from 0.01 to 8%.
A comparison of discrete versus continuous environment in a variance components-based linkage analysis of the COGA data
Authors: Viel Kevin R , Warren Diane M , Buil Alfonso , Dyer Thomas D , Howard Tom E , Almasy Laura
Published: January 2006

Background

The information content of a continuous variable exceeds that of its categorical counterpart. The parameterization of a model may diminish the benefit of using a continuous variable. We explored the use of continuous versus discrete environment in variance components based analyses examining gene × environment interaction in the electrophysiological phenotypes from the Collaborative Study on the Genetics of Alcoholism.

Results

The parameterization using the continuous environment produced a greater number of significant gene × environment interactions and lower AICs (Akaike's information criterion). In these cases, the genetic variance increased with increasing cigarette pack-years, the continuous environment of interest. This did not, however, result in enhanced LOD scores when linkage analyses incorporated the gene × continuous environment interaction.

Conclusion

Alternative parameterizations may better represent the functional relationship between the continuous environment and the genetic variance.
Optimizing the evidence for linkage by permuting marker order
Authors: Jun Gyungah , Song Yeunjoo , Iyengar Sudha K , Elston Robert C
Published: January 2006

We developed a new marker-reordering algorithm to find the best order of fine-mapping markers for multipoint linkage analysis. The algorithm searches for the best order of fine-mapping markers such that the sum of the squared differences in identity-by-descent distribution between neighboring markers is minimized. To test this algorithm, we examined its effect on the evidence for linkage in the simulated and the Collaborative Studies on Genetics of Alcoholism (COGA) data. We found enhanced evidence for linkage with the reordered map at the true location in the simulated data (p-value decreased from 1.16 × 10-9 to 9.70 × 10-10). Analysis of the White population from the COGA data with the reordered map for alcohol dependence led to a significant change of the linkage signal (p = 0.0365 decreased to p = 0.0039) on chromosome 1 between marker D1S1592 and D1S1598. Our results suggest that reordering fine-mapping markers in candidate regions when the genetic map is uncertain can be a critical step when considering a dense map.
Will the real disease gene please stand up?
Authors: Shephard Neil , John Sally , Cardon Lon , McCarthy Mark I , Zeggini Eleftheria
Published: January 2006

A common dilemma arising in linkage studies of complex genetic diseases is the selection of positive signals, their follow-up with association studies and discrimination between true and false positive results. Several strategies for overcoming these issues have been devised. Using the Genetic Analysis Workshop 14 simulated dataset, we aimed to apply different analytical approaches and evaluate their performance in discerning real associations. We considered a) haplotype analyses, b) different methods adjusting for multiple testing, c) replication in a second dataset, and d) exhaustive genotyping of all markers in a sufficiently powered, large sample group. We found that haplotype-based analyses did not substantially improve over single-point analysis, although this may reflect the low levels of linkage disequilibrium simulated in the datasets provided. Multiple testing correction methods were in general found to be over-conservative. Replication of nominally positive results in a second dataset appears to be less stringent, resulting in the follow-up of false positives. Performing a comprehensive assay of all markers in a large, well-powered dataset appears to be the most effective strategy for complex disease gene identification.
Strategies for selecting subsets of single-nucleotide polymorphisms to genotype in association studies
Authors: Butler Joe M , Bishop D Timothy , Barrett Jennifer H
Published: January 2006

In genetic association studies, linkage disequilibrium (LD) within a region can be exploited to select a subset of single-nucleotide polymorphisms (SNPs) to genotype with minimal loss of information. A novel entropy-based method for selecting SNPs is proposed and compared to an existing method based on the coefficient of determination (R
2) using simulated data from Genetic Analysis Workshop 14. The effect of the size of the sample used to investigate LD (by estimating haplotype frequencies) and hence select the SNPs is also investigated for both measures. It is found that the novel method and the established method select SNP subsets that do not differ greatly. The entropy-based measure may thus have value because it is easier to compute than R
2. Increasing the sample size used to estimate haplotype frequencies improves the predictive power of the subset of SNPs selected. A smaller subset of SNPs chosen using a large initial sample to estimate LD can in some instances be more informative than a larger subset chosen based on poor estimates of LD (using a small initial sample). An initial sample size of 50 individuals is sufficient in most situations investigated, which involved selection from a set of 7 SNPs, although to select a larger number of SNPs, a larger initial sample size may be required.
Fine-scale mapping in case-control samples using locus scoring and haplotype-sharing methods
Authors: Humphreys Keith , Iles Mark M
Published: January 2006

Both haplotype-based and locus-based methods have been proposed as the most powerful methods to employ when fine mapping by association. Although haplotype-based methods utilize more information, they may lose power as a result of overparameterization, given the large number of haplotypes possible over even a few loci. Recently methods have been developed that cluster haplotypes with similar structure in the hope that this reflects shared genealogical ancestry. The aim is to reduce the number of parameters while retaining the genotype information relating to disease susceptibility. We have compared several haplotype-based methods with locus-based methods. We utilized 2 regions (D2 and D4) simulated to be in linkage disequilibrium and to be associated with disease susceptibility, combining 5 replicates at a time to produce 4 datasets that were analyzed. We found little difference in the performance of the haplotype-based methods and the locus-based methods in this dataset.
Haplotype-sharing analysis for alcohol dependence based on quantitative traits and the Mantel statistic
Authors: Kleensang Andre , Franke Daniel , König Inke R , Ziegler Andreas
Published: January 2006

Haplotype-based methods have become increasingly popular in the last decade because shared lengths in haplotypes can be used for disease localization. In this contribution, we propose a novel linkage-based haplotype-sharing approach for quantitative traits based on the class of Mantel statistics which is closely related to the weighted pair-wise correlation statistic. Because these statistics are known to be liberal, we propose a permutation test to evaluate significance. We applied the Mantel statistic to the autosomal data from the genome-wide scan of the Collaborative Study on the Genetics of Alcoholism with the Affymetrix Genotype 10 K array that was provided for the Genetic Analysis Workshop 14. Four regions on chromosome 4, 8, 16, and 20 showed p-values less than 0.005 with a minimum p-value of < 0.0001 on chromosome 16 (tsc0520638 at 72.8 cM). Three of these four regions located on chromosome 4, 16, and 20 have been reported previously in the Genetic Analysis Workshop 11.