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At least 883 records · Page 49Linked to original sources
PubMed2005

Cell-type-specific transcriptomics in chimeric models using transcriptome-based masks.

Regulatory networks involving different cell types control inflammation, morphogenesis and tissue homeostasis. Cell-type-specific transcriptional profiling offers a powerful tool for analyzing such cross-talk but is often hampered by mingling of cells within a tissue. Here, we present a novel method that performs cell-type-specific expression measurements without prior cell separation. This involves inter-species transplantation or chimeric co-culture models among which the human mouse system is frequently used. Here, we exploit the sufficiently divergent transcriptomes of human and mouse in conjunction with high-density oligonucleotide arrays. This required a masking procedure based on transcriptome databases and exhaustive fuzzy mapping of oligonucleotide probes onto these data. The approach was tested in a human-mouse experiment, demonstrating that we can efficiently measure species-specific transcriptional profiles in chimeric RNA samples without physically separating cells. Our results stress the importance of transcriptome databases with accurate 3' mRNA termination for computational prediction of accurate probe masks. We find that most human and mouse 3'-untranslated region contain unique stretches to allow for an effective control of cross-hybridization between the two species. This approach can be applied to xenograft models studying tumor-host interactions, morphogenesis or immune responses.

Animals↗
PubMed2006

Classification of G-protein coupled receptors at four levels.

G-protein coupled receptors (GPCRs) are transmembrane proteins which via G-proteins initiate some of the important signaling pathways in a cell and are involved in various physiological processes. Thus, computational prediction and classification of GPCRs can supply significant information for the development of novel drugs in pharmaceutical industry. In this paper, a nearest neighbor method has been introduced to discriminate GPCRs from non-GPCRs and subsequently classify GPCRs at four levels on the basis of amino acid composition and dipeptide composition of proteins. Its performance is evaluated on a non-redundant dataset consisted of 1406 GPCRs for six families and 1406 globular proteins using the jackknife test. The present method based on amino acid composition achieved an overall accuracy of 96.4% and Matthew's correlation coefficient (MCC) of 0.930 for correctly picking out the GPCRs from globular proteins. The overall accuracy and MCC were further enhanced to 99.8% and 0.996 by dipeptide composition-based method. On the other hand, the present method has successfully classified 1406 GPCRs into six families with an overall accuracy of 89.6 and 98.8% using amino acid composition and dipeptide composition, respectively. For the subfamily prediction of 1181 GPCRs of rhodopsin-like family, the present method achieved an overall accuracy of 76.7 and 94.5% based on the amino acid composition and dipeptide composition, respectively. Finally, GPCRs belonging to the amine subfamily and olfactory subfamily of rhodopsin-like family were further analyzed at the type level. The overall accuracy of dipeptide composition-based method for the classification of amine type and olfactory type of GPCRs reached 94.5 and 86.9%, respectively, while the overall accuracy of amino acid composition-based method was very low for both subfamilies. In comparison with existing methods in the literature, the present method also displayed great competitiveness. These results demonstrate the effectiveness of our method on identifying and classifying GPCRs correctly. GPCRsIdentifier, a corresponding stand-alone executable program for GPCR identification and classification was also developed, which can be acquired freely on request from the authors for academic purposes.

Algorithms↗
PubMedDate not supplied

Characterization and work optimization of skeletal muscle as a VAD power source.

Powering a ventricular assist device (VAD) with skeletal muscle in a linear configuration will require the understanding of basic muscle mechanics and efficient use of available power. Accordingly, a mathematical model incorporating aspects of the Hill equation has been developed. This model relates whole muscle length, force, velocity, and time during cyclic contraction to investigate coupling with a hydraulically actuated VAD. Parameters of the model have been determined from in vivo isometric and isotonic measurements of electrically stimulated pig latissimus dorsi with the humerus insertion reattached to a hydraulic loading system. The in vivo results show an exponential passive force-length relationship and active isometric forces increasing from 2 to 8 kgf over a 5 cm change in length. The maximum shortening velocity extrapolated from isotonic data in 85 cm/sec. With the experimentally determined parameters, the model system of differential equations was optimized computationally. Predicted maximum cycle work and corresponding muscle force are nonlinear functions of contraction duration; an increase in duration yields little improvement in work output for longer contraction times. The model helps clarify VAD system design parameters for optimal muscle coupling; for example, the model predicts that operating at maximum instantaneous power does not optimize stroke work.

Animals↗
PubMed1979

Satisfaction with medical care: its measurement and relation to utilization.

Both the conceptualization and the measurement of satisfaction have been of major concern in medical care research. Some scholars used satisfaction as a determinant of utilization, others as a consequence of utilization. Measures of satisfaction are largely content oriented. Reliabilities are reported, but validity is usually assumed (face validity) or assessed through correlations with a criterion variable like "wish to change providers." Using multidimensional scaling techniques, this study identifies several components in the construct "satisfaction" and relates them to the utilization of services. A general satisfaction measure provides us with an assessment of physicians and the medical care delivered, a specific satisfaction measure assesses past experience with the regular source of the care. Both of these can be divided into a positive and negative subcluster. Regressions were computed predicting satisfaction from utilization, and utilization from satisfaction, each time controlling in a preceding step for sociodemographic factors. The relationships varied strongly by provider; as a rule, a larger proportion of the variance could be explained analyzing for one provider at a time than for all providers combined. Analyzing one provider at a time showed that satisfaction substantially increased the proportion of explained variance in utilization in hierarchical regression, but utilization did not increase the explained variance in satisfaction.

Black or African American↗
PubMed2006

Triplet ultrasound growth parameters.

OBJECTIVE: To create ultrasound growth curves for normal growth of fetal triplets using statistical methodology that properly accounts for similarities of growth of fetuses within a mother as well as repeated measurements over time for each fetus. METHODS: In this longitudinal study, all triplet pregnancies managed at a single tertiary center from 1992-2004 were reviewed. Fetuses with major anomalies, prior selective reduction, or fetal demise were excluded. Data from early and late gestation in which there were fewer than 30 fetal measurements available for analysis were excluded. We used multilevel models to account for variation in growth within a single fetus over time, variations in growth between multiple fetuses within a single mother, and variations in fetal growth between mothers. Medians (50th), 10th, and 90th percentiles were estimated by the creation of multiple quadratic growth models from bootstrap samples adapting a previously published method to compute prediction intervals. Estimated fetal weight was derived from Hadlock's formula. RESULTS: One hundred fifty triplet pregnancies were identified. Twenty-seven pregnancies were excluded for the following reasons: missing records (23), fetal demise (3), and fetal anomaly (1). The study group consisted of 123 pregnancies. The gestational age range was restricted to 14-34 weeks. Figures and tables were developed showing medians, 10th and 90th percentiles for estimated fetal weight, femur length, biparietal diameter, abdominal circumference, and head circumference. CONCLUSION: Growth curves for triplet pregnancies were derived. These may be useful for identification of abnormal growth in triplet fetuses. LEVEL OF EVIDENCE: III.

Anthropometry↗
PubMed2006

Kidney injury: an experimental investigation of blunt renal trauma.

BACKGROUND: The abdomen ranks third with regard to injured body regions, and urogenital trauma accounts for up to 10% of all abdominal injuries. Predictive numerical models are evolving as important tools for the development of preventative measures and preliminary clinical diagnostics. Such models require accurate biomechanical input data that at present is not sufficiently available. METHOD: The purpose of the present study was to determine the biomechanical response of whole, perfused porcine kidneys to blunt impact. Specifically of interest were the force-displacement characteristics of the organs, as well as the injury thresholds. Thirty nine young, adult pig kidneys (kidney mass 0.17 +/- 0.02 kg) were infused with physiologic saline solution, and impacted on their dorsal surface by a freely swinging right cylindrical pendulum. Two impact masses (2.1 and 4.7 kg) were used at varying impact velocities and corresponding impact energies. Resulting injuries were graded according to the AAST injury scale, and injury was related to impact mass, impact velocity, and impact energy. RESULTS AND CONCLUSIONS: It was determined that injury was best predicted by impact energy, and that for a given impact energy the resulting injury severity was relatively independent of either impact mass or impact velocity. For a moderate to severe injury, an impact energy threshold of 4 J, or a corresponding strain energy density of 25 kJ/m, was established. This information is essential to the development and implementation of accurate, predictive computational trauma models.

Animals↗
PubMed1994

Cruciform structure of a DNA motif of parvovirus minute virus of mice (prototype strain) involved in the attenuation of gene expression.

It has previously been reported that the region between nucleotides 259 and 383 immediately downstream from the P4 early promoter of parvovirus minute virus of mice, prototype strain (MVMp) is responsible for transcriptional attenuation. Attenuation results from the premature pausing of RNA polymerase II within this sequence (designated to as att) and seems to depend on potential RNA secondary structure. To assess the attenuation capacity of att under near physiological conditions, the early transcription unit of MVMp was replaced by the chloramphenicol acetyltransferase reporter gene under control of the early P4 promoter, in the presence or absence of att. The resulting recombinant vectors were encapsidated in parvovirus particles and replicated in cells after co-infection with the wild-type virus. The att fragment reduced the rate of expression of the reporter gene by approximately threefold, confirming previously reported data from transfection experiments performed in the same cellular system. This attenuation factor is unexpectedly high, considering that the 'readthrough' fold of the nascent viral transcript is thermodynamically more stable than the 'attenuation' configuration. In an attempt to elucidate this point, we sought for the presence of secondary structures in the template DNA molecule. In vitro nuclease probing of viral dsDNA revealed that the att fragment had a cruciform configuration with both complementary strands folding into the computer-predicted stem-loop 'attenuation' structure. These observations lead us to propose that the secondary structure of the DNA template may prompt the formation of the 'attenuation' stem-loop in nascent mRNAs by bringing corresponding self-complementary sequences into close proximity.

Base Sequence↗
PubMed1997

Secondary structure-dependent evolution of Cymbidium ringspot virus defective interfering RNA.

Mutational analysis of defective interfering (DI) RNAs of Cymbidium ringspot virus (CymRSV) was used to study the mechanism of DI RNA evolution. It was shown that a highly base-paired structure in the 3' region of the longer DI RNA directed the formation of smaller DI RNA molecules. Mutations which increased the stability of the computer-predicted, highly structured 3' region of the longest DI RNA of CymRSV significantly enhanced the generation and accumulation of the smaller derivatives. Sequence analysis of smaller progeny molecules revealed that the highly base-paired region was deleted from the precursor DI RNA. Moreover, sites of recombination were found in other regions of the DI RNA progenies due to transposition of the highly base-paired structure. It is likely that the deletion event was structure- and not sequence-specific, and operated when a foreign sequence containing a 37-nt-long base-paired stem was inserted at the appropriate position of DI RNA.

Base Sequence↗
PubMed2002

Early gene m18, a novel player in the immune response to murine cytomegalovirus.

The identification of all antigenic peptides encoded by a pathogen, its T cell 'immunome', is a research aim for rational vaccine design. Screening of proteome-spanning peptide libraries or computational prediction is used to identify antigenic peptides recognized by CD8 T cells. Based on their high coding capacity, cytomegaloviruses (CMVs) could specify numerous antigenic peptides. Yet, current evidence indicates that the memory CD8 T cell response in a given haplotype is actually focused on a few viral proteins. CMVs actively interfere with antigen processing and presentation by the expression of immune evasion proteins. In the case of murine CMV (mCMV), these proteins are effectual in the early (E) phase of the virus replication cycle and should thus preclude the presentation of peptides derived from E proteins. Notably, the m18 gene is here added to a growing list of mCMV E genes that encode antigenic peptides in spite of the E phase immune evasion strategies of the virus.

Animals↗
PubMed1989

Surface-exposed epitopes on the major outer-membrane protein of Chlamydia trachomatis defined with peptide antisera.

The surface exposure of computer-predicted, linear B-cell epitopes on the major outer-membrane protein (MOMP) of Chlamydia trachomatis serovar B was assessed using antibodies raised against synthetic peptides in conjunction with immunogold transmission electron microscopy. Several of the chosen peptides elicited antibodies which reacted with both denatured and native MOMP. The majority of the exposed epitopes were found within the variable segments of MOMP. For each of the epitopes identified, the extent of their surface accessibility varied both among individual organisms and different developmental forms. Evidence for two distinct subspecies-specific epitopes within VS4 is presented.

Amino Acid Sequence↗
PubMed1989

Cloning and sequence analysis of the 10 kDa antigen gene of Mycobacterium tuberculosis.

The gene encoding a major protein antigen of Mycobacterium tuberculosis has been cloned and sequenced using oligonucleotide probes derived from the N-terminal sequence of the analogous protein from Mycobacterium bovis BCG. The gene analysis revealed a sequence encoding a protein of 99 amino acid residues, with a molecular mass of 10.7 kDa. Computer prediction suggests that the protein contains three T-cell-determined epitopes (of which one has been demonstrated experimentally) and three B-cell-determined epitopes. The protein sequence was homologous to two prokaryote heat-shock proteins and the gene possessed heat-shock-like promoter sequences upstream of the initiation codon. A hairpin loop identified in the upstream sequence may also be important in regulation of the gene.

Antigens, Bacterial↗
PubMed1997

The general secretion pathway of Erwinia carotovora subsp. carotovora: analysis of the membrane topology of OutC and OutF.

The out gene cluster of Erwinia carotovora subsp. carotovora (Ecc) encodes the proteins of the type II or general secretory pathway (GSP) apparatus which is required for secretion of pectinase and cellulase. In this study, fusions between Ecc out genes and the topology probe blaM were constructed. The ability of Out protein domains to export BlaM across the cytoplasmic membrane in both Escherichia coli and the cognate host was utilized to confirm the computer-predicted cytoplasmic membrane topology of OutC and OutF, When outC was fused to blaM, the resulting phenotype suggested that the majority of OutC is targeted to the periplasm, typical of a type II bitopic conformation in the cytoplasmic membrane. In contrast, for the outF gene product, three transmembrane regions were identified which connect a large N-terminal cytoplasmic domain, a smaller periplasmic domain, and a large cytoplasmic loop. Fusions between blaM and outD and outE were used to further substantiate the locations of these gene products in the outer membrane and the cytoplasm respectively. The data derived suggest that a number of the Out apparatus components possess domains in the cytoplasm and/or the periplasm with potential for protein-protein interactions which facilitate the secretion of periplasmic enzyme intermediates across the outer membrane to the external milieu.

Bacterial Outer Membrane Proteins↗
PubMed2004

Identification of the nuclear localization signals within the Epstein-Barr virus EBNA-6 protein.

Epstein-Barr virus nuclear antigen (EBNA)-6 is essential for EBV-induced immortalization of primary human B-lymphocytes in vitro. Previous studies have shown that EBNA-6 acts as a transcriptional regulator of viral and cellular genes; however at present, few functional domains of the 140 kDa EBNA-6 protein have been completely characterized. There are five computer-predicted nuclear localization signals (NLS), four monopartite and one bipartite, present in the EBNA-6 amino acid sequence. To identify which of these NLS are functional, fusion proteins between green fluorescent protein and deletion constructs of EBNA-6 were expressed in HeLa cells. Each of the constructs containing at least one of the NLS was targeted to the nucleus of cells whereas a construct lacking all of the NLS was cytoplasmic. Site-directed mutation of these NLS demonstrated that only three of the NLS were functional, one at the N-terminal end (aa 72-80), one in the middle (aa 412-418) and one at the C-terminal end (aa 939-945) of the EBNA-6 protein.

Amino Acid Sequence↗
PubMed2004

Biochemical characterization of the respiratory syncytial virus P-P and P-N protein complexes and localization of the P protein oligomerization domain.

The RNA-dependent RNA polymerase complex of respiratory syncytial virus (RSV) is composed of the large polymerase (L), the phosphoprotein (P), the nucleocapsid protein (N) and the co-factors M2-1 and M2-2. The P protein plays a central role within the replicase-transcriptase machinery, forming homo-oligomers and complexes with N and L. In order to study P-P and N-P complexes, and the role of P phosphorylation in these interactions, the human RSV P and N proteins were expressed in E. coli as His-tagged or GST-fusion proteins. The non-phosphorylated status of recombinant P protein was established by mass spectrometry. GST-P and GST-N fusion proteins were able to interact with RSV proteins extracted from infected cells in a GST pull-down assay. When co-expressed in bacteria, GST-P and His-P were co-purified by glutathione-Sepharose affinity, showing that the RSV P protein can form oligomers within bacteria. This result was confirmed by chemical cross-linking experiments and gel filtration studies. The P oligomerization domain was investigated by a GST pull-down assay using a series of P deletion constructs. This domain was mapped to a small region situated in the central part of P (aa 120-150), which localized in a computer-predicted coiled-coil domain. When co-expressed in bacteria, RSV N and P proteins formed a soluble complex that prevented non-specific binding of N to bacterial RNA. Therefore, RSV P protein phosphorylation is not required for the formation of P-P and N-P complexes, and P controls the RNA binding activity of N.

Amino Acid Sequence↗
PubMed2006

Epstein-Barr virus nuclear antigen 3A contains six nuclear-localization signals.

The Epstein-Barr nuclear antigen 3A (EBNA3A) is one of only six viral proteins essential for Epstein-Barr virus-induced transformation of primary human B cells in vitro. Viral proteins such as EBNA3A are able to interact with cellular proteins, manipulating various biochemical and signalling pathways to initiate and maintain the transformed state of infected cells. EBNA3A has been reported to have one nuclear-localization signal and is targeted to the nucleus during transformation, where it associates with components of the nuclear matrix. By using enhanced green fluorescent protein-tagged deletion mutants of EBNA3A in combination with site-directed mutagenesis, an additional five functional nuclear-localization signals have been identified in the EBNA3A protein. Two of these (aa 63-66 and 375-381) were computer-predicted, whilst the remaining three (aa 394-398, 573-578 and 598-603) were defined functionally in this study.

Epstein-Barr Virus Nuclear Antigens↗
PubMed2025

Structure-based discovery of inhibitors of Mac1 domain of nonstructural protein-3 of SARS-CoV-2 by machine learning-augmented screening of chemical space.

Significant efforts have been recently dedicated to the discovery of small molecule inhibitors against the Macrodomain 1 (Mac1) of nonstructural protein 3 (NSP3) as potential antivirals for SARS-CoV-2. Thus, Mac1 has also been selected as the target for the Critical Assessment of Hit-finding Experiments (CACHE) challenge #3. As contestants in that challenge, we developed a computational strategy that ranked on the top among all 23 participants in the competition and resulted in the discovery of a novel chemical series of non-charged Mac1 inhibitors. Those have been identified through the combination of machine learning-accelerated virtual screening of Enamine REAL Diversity Subset of approximately 25 million compounds and consequent hit expansion into the entire Enamine REAL Space library. In particular, the initially identified hit compound CACHE3-HI_1706_56 (KD = 20 μM) was explored by probing 17 close analogues from a library of 44 billion molecules from the Enamine REAL. All those analogues effectively displaced the Mac1-binding ADP-ribose peptide, and 12 were confirmed to engage with Mac1 by the Surface Plasmon Resonance experiments, revealing a new chemical series of compounds for hit-to-lead optimization. The structure of the CACHE3-HI_1706_56-Mac1 complex was further determined at high resolution with crystallography, confirming initial computational predictions. Our results illustrate the effectiveness of ML-accelerated docking to rapidly identify novel chemical series and provide a strong foundation for the development of SARS-CoV-2 NSP3 Mac1 inhibitors.

CACHE challenge↗
PubMed2005

The developmental miRNA profiles of zebrafish as determined by small RNA cloning.

MicroRNAs (miRNAs) represent a family of small, regulatory, noncoding RNAs that are found in plants and animals. Here, we describe the miRNA profile of the zebrafish Danio rerio resolved in a developmental and cell-type-specific manner. The profiles were obtained from larger-scale sequencing of small RNA libraries prepared from developmentally staged zebrafish, and two adult fibroblast cell lines derived from the caudal fin (ZFL) and the liver epithelium (SJD). We identified a total of 154 distinct miRNAs expressed from 343 miRNA genes. Other experimental/computational sources support an additional 10 miRNAs encoded by 19 genes. The miRNAs can be classified into 87 distinct families. Cross-species comparison indicates that 81 families are conserved in mammals, 17 of which also have at least one member conserved in an invertebrate. Our analysis reveals that the zygotes are essentially devoid of miRNAs and that their expression begins during the blastula period with a zebrafish-specific family of miRNAs encoded by closely spaced multicopy genes. Computational predictions of zebrafish miRNA targets are provided that take into account the depth of evolutionary conservation. Besides miRNAs, we identified a prominent class of repeat-associated small interfering RNAs (rasiRNAs).

Animals↗
PubMed2004

Parallel genotyping of over 10,000 SNPs using a one-primer assay on a high-density oligonucleotide array.

The analysis of single nucleotide polymorphisms (SNPs) is increasingly utilized to investigate the genetic causes of complex human diseases. Here we present a high-throughput genotyping platform that uses a one-primer assay to genotype over 10,000 SNPs per individual on a single oligonucleotide array. This approach uses restriction digestion to fractionate the genome, followed by amplification of a specific fractionated subset of the genome. The resulting reduction in genome complexity enables allele-specific hybridization to the array. The selection of SNPs was primarily determined by computer-predicted lengths of restriction fragments containing the SNPs, and was further driven by strict empirical measurements of accuracy, reproducibility, and average call rate, which we estimate to be >99.5%, >99.9%, and>95%, respectively [corrected]. With average heterozygosity of 0.38 and genome scan resolution of 0.31 cM, the SNP array is a viable alternative to panels of microsatellites (STRs). As a demonstration of the utility of the genotyping platform in whole-genome scans, we have replicated and refined a linkage region on chromosome 2p for chronic mucocutaneous candidiasis and thyroid disease, previously identified using a panel of microsatellite (STR) markers.

Alleles↗