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At least 595 records · Page 33Linked to original sources
PubMed2005

AU-rich transient response transcripts in the human genome: expressed sequence tag clustering and gene discovery approach.

Transient response genes regulate critical biological responses that include cell proliferation, signal transduction events, and responses to exogenous agents such as inflammatory stimuli, microbes, and radiation. An important feature that ensures a timely response is the short half-life of the messenger RNA (mRNA), which is thought to be predominantly mediated by adenylate uridylate-rich sequence elements (AREs) in the 3' untranslated region (3' UTR). The repertoire and extent of transient response genes in the human genome are not known. We used a computational approach to delineate those genes that code for transient ARE mRNAs. We utilized a 3' UTR-specific ARE motif to retrieve and cluster 3'-end ESTs using a refined extraction protocol. With the availability of the entire human genome, we were able to utilize ARE EST clusters for further mining and computational prediction of ARE genes. The described approaches led to the finding of more than 1500 ARE genes in the human genome. In particular, "hidden" ARE mRNAs and alternative forms due to 3'UTR completeness, variant polyadenylation, and splicing were uncovered.

3' Untranslated Regions↗
PubMed2006

Computer-aided NMR assay for detecting natively folded structural domains.

Structural genomics projects require strategies for rapidly recognizing protein sequences appropriate for routine structure determination. For large proteins, this strategy includes the dissection of proteins into structural domains that form stable native structures. However, protein dissection essentially remains an empirical and often a tedious process. Here, we describe a simple strategy for rapidly identifying structural domains and assessing their structures. This approach combines the computational prediction of sequence regions corresponding to putative domains with an experimental assessment of their structures and stabilities by NMR and biochemical methods. We tested this approach with nine putative domains predicted from a set of 108 Thermus thermophilus HB8 sequences using PASS, a domain prediction program we previously reported. To facilitate the experimental assessment of the domain structures, we developed a generic 6-hour His-tag-based purification protocol, which enables the sample quality evaluation of a putative structural domain in a single day. As a result, we observed that half of the predicted structural domains were indeed natively folded, as judged by their HSQC spectra. Furthermore, two of the natively folded domains were novel, without related sequences classified in the Pfam and SMART databases, which is a significant result with regard to the ability of structural genomics projects to uniformly cover the protein fold space.

Computational Biology↗
PubMed2003

Near-infrared fluorescence contrast-enhanced imaging with area illumination and area detection: the forward imaging problem.

Fluorescence frequency-domain photon migration measurements were acquired from tissue phantoms, each containing a fluorescent target, by means of area illumination and area detection on the same surface and for the first time, to our knowledge, compared with predictions computed with a numerical solution to the coupled photon diffusion equations. We accomplished area illumination and area detection using a planar, intensity-modulated excitation light source and a gain-modulated intensified charge-coupled device camera, respectively. A 1-ml vessel containing 1-microm solution of Indocyanine Green in 1% Liposyn was immersed 1 cm deep in each 512-ml tissue phantom. For most tissue phantoms, the background surrounding the 1-ml target was composed of Liposyn solution containing Indocyanine Green or 3,3'-Diethylthiatricarbocyanine Iodide such that the target-to-background ratio of fluorescence yield was > or = 10:1. Measurements of fluorescence modulation amplitude and phase were predicted with a mean error ranging from 10.1% to 13.6% and 0.56 degrees to 1.72 degrees, respectively. These numbers are similar to those obtained by use of single-pixel frequency-domain photon migration techniques and validate the potential use of area illumination and area detection for biomedical imaging of tissues. Results also demonstrate that target-to-background ratios of fluorescence yield and fluorescence lifetime significantly affect target detectability.

Contrast Media↗
PubMed2003

FRAME and the Royal Commission on Environmental Pollution: common recommendations for assessing risks posed by chemicals under the EU REACH system.

This document discusses recommendations made by FRAME and the Royal Commission on Environmental Pollution (RCEP) with regard to the current European Commission proposals on the Registration, Evaluation and Authorisation of Chemicals (REACH) system for assessing the risks of chemicals to humans, wildlife and the environment. Of several common aims and recommendations, the two most important are: a) the greater use of non-animal testing methods, especially computational prediction methods (for example, [quantitative] structure-activity relationships, expert systems and biokinetic modelling) for prioritising chemicals for hazard assessment; and b) the greater use of intelligent exposure-based targeted risk assessment, with less emphasis being placed on tonnage-triggers. FRAME has produced a decision-tree testing scheme to illustrate the way in which these approaches could be used, together with in vitro test methods. This scheme has been slightly modified to take account of proposals subsequently made by the RCEP. In addition, FRAME points out that new and improved computational methods are needed through more coordinated research, and that these and existing methods need to be validated. The similarities between the independent publications of FRAME and the RCEP add weight to the recommendations that each have made concerning the implementation of the REACH system.

Animal Testing Alternatives↗
PubMed2006

FRAME and the Royal Commission on Environmental Pollution: common recommendations for assessing risks posed by chemicals under the EU REACH system.

This document discusses recommendations made by FRAME and the Royal Commission on Environmental Pollution (RCEP) with regard to the current European Commission proposals on the Registration, Evaluation and Authorisation of Chemicals (REACH) system for assessing the risks of chemicals to humans, wildlife and the environment. Of several common aims and recommendations, the two most important are: a) the greater use of non-animal testing methods, especially computational prediction methods (for example, [quantitative] structure-activity relationships, expert systems and biokinetic modelling) for prioritising chemicals for hazard assessment; and b) the greater use of intelligent exposure-based targeted risk assessment, with less emphasis being placed on tonnage-triggers. FRAME has produced a decision-tree testing scheme to illustrate the way in which these approaches could be used, together with in vitro test methods. This scheme has been slightly modified to take account of proposals subsequently made by the RCEP. In addition, FRAME points out that new and improved computational methods are needed through more coordinated research, and that these and existing methods need to be validated. The similarities between the independent publications of FRAME and the RCEP add weight to the recommendations that each have made concerning the implementation of the REACH system.

Journal Article↗
PubMed1994

Impact of using stated instead of measured height upon screening spirometry.

This study examined the impact of using stated height instead of measured height on predicted normal values and clinical interpretation of screening spirometry in an outpatient referral population. In a prospective fashion, we evaluated 210 patients, 20 to 89 yr of age, referred for spirometry to our pulmonary function laboratory by obtaining both stated height (HTs) and measured height (HTm). The mean difference between stated and measured height progressively increased with age, from 0.80 cm (20 to 29 yr; p = 0.01) to 5.70 cm (80 to 89 yr; p < 0.001). For men and women, use of HTs instead of HTm produced a mean difference for all ages in computing predicted FEV1 and FVC values of 3.9 and 4.3%, respectively. This effect was more prominent in the older age groups (80 to 89 yr, n = 30); mean differences were 11.0% (211 ml) and 11.7% (303 ml), respectively. Use of HTs instead of HTm altered the detection of restriction by reduced FVC in 17 patients and the detection of obstruction by reduced FEV1/FVC ratio in four patients. Use of HTs altered the clinical assessment of severity by FEV1 in 15 of 108 (13.9%) obstructed patients and altered the assessment of severity by FVC in 11 of 32 (34.4%) restricted patients, with older patients more frequently affected than younger patients. We conclude that the use of stated height instead of measured height in the performance of screening spirometry can have significant impact on the calculation of predicted normal values. These discrepancies can potentially influence the clinical interpretation of screening spirometry, affecting the detection of abnormality and the assessment of severity of disease, particularly among older patients.

Adult↗
PubMed1995

Dosimetry and treatment planning of complex electron arc therapy.

Electron arc therapy has been primarily utilized for treatment of the post-mastectomy chest wall. Its clinical usefulness and benefits have been proven. Casting procedures and blocking techniques have been discussed. We have successfully applied electron arc therapy to the treatment of the nasal cavity and associated nodal regions. When compared to the chest wall, the smaller radii and pronounced irregularity of the surface anatomy of the facial region presents multiple new dosimetric and treatment planning challenges. We will discuss these challenges, along with those encountered in the casting procedures and reproduction of patient characteristics required for the execution of this treatment. Many aspects of dosimetry were utilized in unique ways to produce the treatment plans, cast and bolus needed. Due to the insertion of bolus into the nostrils, a unique hollow bite block was constructed to allow patient respiration during treatment. Film dosimetry was used to verify computer predictions and to compare this electron arc treatment technique with alternative fixed electron beam techniques. The potential benefits and difficulties of this technique will be discussed.

Carcinoma, Squamous Cell↗
PubMed1993

Identification of B-cell epitopes on the S4 subunit of pertussis toxin.

The main purpose of the present study was to identify B-cell epitopes on the S4 subunit of pertussis toxin (PT) by the synthetic peptide approach. Two strategies were followed: (i) screening of two series of overlapping peptides (12- and 25-residue peptides) covering the entire S4 sequence by a panel of murine monoclonal anti-PT antibodies and various polyclonal anti-PT antisera in an enzyme-linked immunosorbent assay (ELISA), and (ii) analysis of the S4 amino acid sequence by a predictive algorithm followed by synthesis and immunization of mice with the predicted peptides coupled to diphtheria toxoid. The anti-peptide conjugate antisera were tested in an ELISA for cross-reactivity with native PT, B oligomer, and S4. Screening of the free peptides in an ELISA by the PT antisera indicated the presence of six B-cell epitope-containing domains covered by residues 18 to 32, 33 to 46, 39 to 52, 51 to 65, 71 to 84, and 91 to 106. None of the peptides, however, were recognized by the monoclonal anti-PT antibodies in an ELISA. Immunization with six computer-predicted peptides (B1 to B6) and three potential T-cell epitopes (T1 to T3) gave rise to very high antibody responses towards the homologous conjugates. With the exception of the anti-T1/diphtheria toxoid antisera, all anti-peptide conjugate antisera cross-reacted with PT in an ELISA at different levels. None of these anti-peptide conjugate antisera, however, showed any PT-neutralizing effect as measured by the Chinese hamster ovary cell assay and the leukocytosis-promoting activity test. The results of the present study suggest that discontinuous epitopes are predominant in the S4 subunit of native PT.

Amino Acid Sequence↗
PubMed2004

The KEGG resource for deciphering the genome.

A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledge-based approach for network prediction, which is to predict, given a complete set of genes in the genome, the protein interaction networks that are responsible for various cellular processes. KEGG at http://www.genome.ad.jp/kegg/ is the reference knowledge base that integrates current knowledge on molecular interaction networks such as pathways and complexes (PATHWAY database), information about genes and proteins generated by genome projects (GENES/SSDB/KO databases) and information about biochemical compounds and reactions (COMPOUND/GLYCAN/REACTION databases). These three types of database actually represent three graph objects, called the protein network, the gene universe and the chemical universe. New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database.

Animals↗
PubMed1988

Computer modeling of thoracic response to blast.

Primary blast injury affects the gas-containing structures of the body. Damage to the lungs with resultant respiratory insufficiency and arterial embolization of air from alveolar pulmonary venous fistulae is the predominant cause of morbidity and mortality following high-level blast exposure. In an effort to generate a widely applicable damage-risk criterion for thoracic injury from blast we are developing a complex computer finite element model (FEM) of the thorax. Taking an engineering approach, a horizontal cross-section of the thorax is divided into small discrete units (finite elements) of homogeneous structure. The necessary physical properties (density, bulk modulus, etc.) are then determined for each element. Specifying the material constants and geometry of the elements, the computer can load the surface of the structure with some force-time function (blast pressure-time history) and calculate the resultant physical events such as displacement, compression, stress, strain, etc. Computer predictions of pressure wave phenomena in the lung parenchyma are compared with trans-bronchially measured pressures in blast-exposed animals. The model should prove useful in assessing the risk of blast injury in diverse overpressure environments and may give insight into pathophysiologic mechanisms and strategies for protection.

Animals↗
PubMed2000

The 630-kb lung cancer homozygous deletion region on human chromosome 3p21.3: identification and evaluation of the resident candidate tumor suppressor genes. The International Lung Cancer Chromosome 3p21.3 Tumor Suppressor Gene Consortium.

We used overlapping and nested homozygous deletions, contig building, genomic sequencing, and physical and transcript mapping to further define a approximately 630-kb lung cancer homozygous deletion region harboring one or more tumor suppressor genes (TSGs) on chromosome 3p21.3. This location was identified through somatic genetic mapping in tumors, cancer cell lines, and premalignant lesions of the lung and breast, including the discovery of several homozygous deletions. The combination of molecular manual methods and computational predictions permitted us to detect, isolate, characterize, and annotate a set of 25 genes that likely constitute the complete set of protein-coding genes residing in this approximately 630-kb sequence. A subset of 19 of these genes was found within the deleted overlap region of approximately 370-kb. This region was further subdivided by a nesting 200-kb breast cancer homozygous deletion into two gene sets: 8 genes lying in the proximal approximately 120-kb segment and 11 genes lying in the distal approximately 250-kb segment. These 19 genes were analyzed extensively by computational methods and were tested by manual methods for loss of expression and mutations in lung cancers to identify candidate TSGs from within this group. Four genes showed loss-of-expression or reduced mRNA levels in non-small cell lung cancer (CACNA2D2/alpha2delta-2, SEMA3B [formerly SEMA(V), BLU, and HYAL1] or small cell lung cancer (SEMA3B, BLU, and HYAL1) cell lines. We found six of the genes to have two or more amino acid sequence-altering mutations including BLU, NPRL2/Gene21, FUS1, HYAL1, FUS2, and SEMA3B. However, none of the 19 genes tested for mutation showed a frequent (>10%) mutation rate in lung cancer samples. This led us to exclude several of the genes in the region as classical tumor suppressors for sporadic lung cancer. On the other hand, the putative lung cancer TSG in this location may either be inactivated by tumor-acquired promoter hypermethylation or belong to the novel class of haploinsufficient genes that predispose to cancer in a hemizygous (+/-) state but do not show a second mutation in the remaining wild-type allele in the tumor. We discuss the data in the context of novel and classic cancer gene models as applied to lung carcinogenesis. Further functional testing of the critical genes by gene transfer and gene disruption strategies should permit the identification of the putative lung cancer TSG(s), LUCA, Analysis of the approximately 630-kb sequence also provides an opportunity to probe and understand the genomic structure, evolution, and functional organization of this relatively gene-rich region.

Carcinoma, Non-Small-Cell Lung↗
PubMed2006

A method for induced-fit docking, scoring, and ranking of flexible ligands. Application to peptidic and pseudopeptidic beta-secretase (BACE 1) inhibitors.

Inhibition of beta-secretase (BACE 1) has recently been investigated as a promising therapeutic approach in the treatment of Alzheimer's disease, and a growing number of BACE 1 inhibitors and crystal structures of BACE 1/inhibitors complexes have been reported. We report herein a predictive computational method and its application to potential BACE 1 inhibitors. Using a training set of 50 known highly flexible inhibitors, we developed a docking method that accounts for the flexibility of both the protein and the inhibitors. Protein flexibility is accounted for using a specifically designed genetic algorithm. We next developed a scoring function consisting of force field evaluation of the inhibitor/protein interactions and two additional terms for hydrogen bonding and entropy change upon binding. Discarding three outliers from the training set, our protocol was found to perform well with an rmsd of 1.19 kcal/mol. Evaluation of the predictive power was next carried out by virtual screening of 80 synthetic compounds. The significant enrichment at the top of the ranking list in active compounds demonstrated the ability of the docking and scoring protocol to rank the compounds relative to their activities.

Algorithms↗
PubMed2006

Origin of syn/anti diastereoselectivity in aldehyde and ketone crotylation reactions: a combined theoretical and experimental study.

We report on experimentally determined and computationally predicted diastereoselectivities of (a) multicomponent crotylation (MCC) reactions of simple aliphatic aldehydes and ketones and (b) of acetal substitution (AS) reactions of aldehyde dimethyl acetals with E- and Z-configurated crotyl trimethylsilane to give homoallylic methyl ethers bearing two newly formed stereogenic centers. We found that corresponding MCC and AS reactions give nearly equal syn/anti ratios. While the crotylations of acetaldehyde and propionaldehyde mainly result in the syn product for E-configurated silane and in the anti product for Z-configurated silane, the syn product is found as main product for the crotylation of pivaldehyde regardless of substrate double bond geometry. Using butanone as substrate, the anti product is found as main product in both cases. By computational investigation employing the B3LYP/6-31+G(d) level of theory in dichloromethane solution (PCM/UAKS), we found that the attack of O-methyl-substituted carboxenium ions by crotyl silane explains the experimentally observed selectivities, indicating that these crotylations in fact proceed in an S(N)1-type reaction via this ionic intermediate. Comparison of relevant open transition-state structures leads to a rationalization of the observed selectivities. For all systems studied, three transition-state conformations are necessary and sufficient to determine the selectivity. This has been confirmed by studying the MCC reactions of isobutyraldehyde. Activation energies for the stereogenic step have been determined by calculation of the transition state and substrate structures in dichloromethane solution at the B3LYP/6-311+G(2d,p)//B3LYP/6-31+G(d) level of theory in dichloromethane solution. The possibility to predict simple diastereoselectivity in general Lewis acid-mediated crotylations of aldehydes and ketones is discussed.

Aldehydes↗
PubMed2003

A nonlinear finite element analysis of the periodontal ligament under orthodontic tooth loading.

The stressed state of the periodontal ligament (PDL) is understood to play a critical role in the tooth movement initiated by orthodontic treatment. Finite element simulations have been used to describe PDL stresses for orthodontic loading; however, these models have predominantly assumed linear mechanical properties for the PDL. The present study sought to determine the importance of using nonlinear mechanical properties and nonuniform geometric data in computer predictions of periodontal ligament stresses and tooth movements. A 2-dimensional plane-strain finite element model of a mandibular premolar was constructed based on anatomic data of transverse sections of tooth, PDL, and bone from a 24-year-old cadaveric man. A second model was constructed of the same tooth but with a PDL of uniform thickness. Each of these was prescribed linear or nonlinear elastic mechanical properties, as obtained in our own experiments. Predictions of the maximum and minimum principal stresses and von Mises stresses in the PDL were determined for extrusive and tipping forces. The results indicated that biofidelic finite element models predicted substantially different stresses in the PDL for extrusive loading than did the uniform thickness model, suggesting that incorporation of the hourglass shape of the PDL is warranted. In addition, incorporation of nonlinear mechanical properties for the PDL resulted in dramatic increases in the stresses at the apex and cervical margin as compared with the linear models.

Adult↗
PubMed1992

Development and validation of a computer program using Bayes's theorem to support diagnosis of rheumatic disorders.

A computer program has been developed to support the differential diagnosis of major rheumatic disease categories. Knowledge for the program was derived from the sensitivity and specificity of findings in a group of 1052 consecutive patients of a rheumatological outpatient clinic. Computer predictions based on two variations of Bayes's theorem were compared with 'gold standard' diagnoses in 570 test cases from the same clinic. The results demonstrate the feasibility of this approach, but also that refinements of both the method of calculation and the knowledge are required.

Adolescent↗
PubMed2005

HLA-A*0201, HLA-A*1101, and HLA-B*0702 transgenic mice recognize numerous poxvirus determinants from a wide variety of viral gene products.

In virus models explored in detail in mice, CTL typically focus on a few immunodominant determinants. In this study we use a multipronged approach to understand the diversity of CTL responses to vaccinia virus, a prototypic poxvirus with a genome approximately 20-fold larger than that of the model RNA viruses typically studied in mice. Based on predictive computational algorithms for peptide binding to HLA supertypes, we synthesized a panel of 2889 peptides to begin to create an immunomic map of human CTL responses to poxviruses. Using this panel in conjunction with CTLs from vaccinia virus-infected HLA transgenic mice, we identified 14 HLA-A*0201-, 4 HLA-A*1101-, and 3 HLA-B*0702-restricted CD8(+) T cell determinants distributed over 20 distinct proteins. These peptides were capable of binding one or multiple A2, A3, and B7 supertype molecules with affinities typical of viral determinants. Surprisingly, many of the viral proteins recognized are predicted to be late gene products, in addition to the early intermediate gene products expected. Nearly all of the determinants identified have identical counterparts encoded by modified vaccinia virus Ankara as well as variola virus, the agent of smallpox. These findings have implications for the design of new smallpox vaccines and the understanding of immune responses to large DNA viruses in general.

Animals↗
PubMed1996

Secondary structure model of the coat protein gene of turnip yellow mosaic virus RNA: long, C-rich, single-stranded regions.

The RNA of all tymoviruses, a group of ssRNA plant viruses, has a base composition that is different from that of most other viruses. The excess of cytosines (35-42%) and the low number of guanosines (15-17%) must impel an RNA structure with a relatively low amount of base pairing and a high incidence of unpaired cytosines. These unpaired cytosines probably function in RNA-protein interactions. To gain Insight into the way the RNA is positioned inside the virion, the secondary structure has been determined of a part of TYMV RNA, including the so-called tymobox, the coat protein gene, and the 3' untranslated region, by structure probing, sequence comparison, and computer predictions. Conservation of secondary structure elements in tymoviruses is not high and does not parallel the conservation of the primary structure. A combination of structure prediction and probing experiments, however, results in a model consisting of structured domains of 100-200 nucleotides interspersed by long unpaired cytosine-rich regions. The latter may interact with the coat protein inside the virion. The structure of some functionally interesting regions of the 3' part of TYMV RNA is also discussed.

Base Sequence↗
PubMed2003

An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome.

BACKGROUND: While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent annotation approaches have resulted in the same number of potential genes, but a careful comparison revealed only limited overlap. This indicates that only the combination of different computational prediction methods and experimental evaluation of such in silico data will provide more complete genome annotations. In order to get a more complete gene content of the Drosophila melanogaster genome, we based our new D. melanogaster whole-transcriptome microarray, the Heidelberg FlyArray, on the combination of the Berkeley Drosophila Genome Project (BDGP) annotation and a novel ab initio gene prediction of lower stringency using the Fgenesh software. RESULTS: Here we provide evidence for the transcription of approximately 2,600 additional genes predicted by Fgenesh. Validation of the developmental profiling data by RT-PCR and in situ hybridization indicates a lower limit of 2,000 novel annotations, thus substantially raising the number of genes that make a fly. CONCLUSIONS: The successful design and application of this novel Drosophila microarray on the basis of our integrated in silico/wet biology approach confirms our expectation that in silico approaches alone will always tend to be incomplete. The identification of at least 2,000 novel genes highlights the importance of gathering experimental evidence to discover all genes within a genome. Moreover, as such an approach is independent of homology criteria, it will allow the discovery of novel genes unrelated to known protein families or those that have not been strictly conserved between species.

Animals↗