41,627 research outputs found
Expression of Plasmodium falciparum genes involved in erythrocyte invasion varies among isolates cultured directly from patients.
No full textPlasmodium falciparum merozoites invade erythrocytes using a range of alternative ligands that includes erythrocyte binding antigenic proteins (EBAs) and reticulocyte binding protein homologues (Rh). Variation in the expression of some of these genes among culture-adapted parasite lines correlates with the use of different erythrocyte receptors. Here, expression profiles of four Rh genes and eba175 are analysed in a sample of 42 isolates cultured from malaria patients in Kenya. The profiles cluster into distinct groups, largely because of very strong negative correlations between the levels of expression of particular gene pairs (Rh1 versus Rh2b, eba175 versus Rh2b, and eba175 versus Rh4), previously associated with alternative invasion pathways in culture-adapted parasite lines. High levels of eba175 are seen in isolates in expression profile group I, and may be associated with sialic acid-dependent invasion. Groups II and III are, respectively, characterized by high levels of Rh2b and Rh4, and are more likely to be associated with sialic acid-independent invasion
Transcript-specific expression profiles derived from sequence-based analysis of standard microarrays
Full text linkBackground: Alternative mRNA processing mechanisms lead to multiple transcripts (i.e. splice isoforms) of a given gene
which may have distinct biological functions. Microarrays like Affymetrix GeneChips measure mRNA expression of genes
using sets of nucleotide probes. Until recently probe sets were not designed for transcript specificity. Nevertheless, the reanalysis of established microarray data using newly defined transcript-specific probe sets may provide information about expression levels of specific transcripts.
Methodology/Principal Findings: In the present study alignment of probe sequences of the Affymetrix microarray HGU133A with Ensembl transcript sequences was performed to define transcript-specific probe sets. Out of a total of 247,965 perfect match probes, 95,008 were designated ‘‘transcript-specific’’, i.e. showing complete sequence alignment, no crosshybridization, and transcript-, not only gene-specificity. These probes were grouped into 7,941 transcript-specific probe sets and 15,619 gene-specific probe sets, respectively. The former were used to differentiate 445 alternative transcripts of 215
genes. For selected transcripts, predicted by this analysis to be differentially expressed in the human kidney, confirmatory real-time RT-PCR experiments were performed. First, the expression of two specific transcripts of the genes PPM1A (PP2CA_HUMAN and P35813) and PLG (PLMN_HUMAN and Q5TEH5) in human kidneys was determined by the transcriptspecific array analysis and confirmed by real-time RT-PCR. Secondly, disease-specific differential expression of single transcripts of PLG and ABCA1 (ABCA1_HUMAN and Q5VYS0_HUMAN) was computed from the available array data sets and confirmed by transcript-specific real-time RT-PCR.
Conclusions: Transcript-specific analysis of microarray experiments can be employed to study gene-regulation on the
transcript level using conventional microarray data. In this study, predictions based on sufficient probe set size and foldchange are confirmed by independent mean
Using container flows to predict economic activity: An application to transpacific trade
No full textThere is a significant historical link between maritime trade and economic activity. With the rapid growth of containerised trade over the past 60 years, a significant share of global trade is transported by container nowadays. This suggests there is a connection between container flows and economic activity. There is also a time delay between containers with goods being imported and the announcement of quarterly Gross Domestic Product numbers. With US container imports and exports being publicly available information, this leads to the research question of this thesis: Can loaded and/or empty container flows be used to predict economic activity?” If so, this could prove to be valuable information for economists, policy makers and, as this thesis highlights, professional traders working at investment banks or hedge funds.This thesis focusses on analysing transpacific containerised trade as a potential so-called forward indicator of US GDP. To measure these transpacific flows, an aggregate of US West coast port data is produced and de-seasonalised. The container flows are separated into Loaded In, Empty Out and Loaded Out flows. It is important to understand the dynamics of container trade and the variables influencing it on this route. Variables are identified that could possibly affect the supply-side of container shipping and therefore the transpacific container flows (the demand-side is seen as an expression of economic activity).After analysing the Cross Correlation Functions (CCF) of the identified, data based influencing variables, five different GDP growth prediction models are constructed. This is done by performing OLS single and multivariate regressions of the individual container flows (together with the influencing variables) on historical GDP growth data from 2000 to 2017. The resulting models are tested against an existing, commonly used forward indicator: the Purchasing Managers Index (PMI). The results show that three models, all using a form of loaded containers, outperform the PMI when predicting the direction of US GDP growth 3-months ahead over the 17-year time period of the dataset used. The probability of large prediction errors with these models are also smaller than the PMI benchmark model.Marine Technology | Shipping Managemen
Evaluation of the expression of matrix metalloproteinase 9 and neutrophil gelatinase associated lipocalin in serum, urine and tumoral tissues of female dogs suffering from mammary gland tumors
Full text linkIn human medicine, it has been shown recently that the level of expression of matrix metalloproteinase-9 (MMP-9) and neutrophil gelatinase-associated lipocalin (NGAL) in serum, urine, and breast tissue were significantly increased in patients with breast cancer and correlated to several prognostic factors. In the first part, the author presents the MMP-9 and NGAL as a synthesis of current knowledge on their ability to serve as biomarkers of breast cancer in women. In the second, the author presents the production of canine MMP9 and NGAL recombinant proteins, the production of polyclonal antibodies, and their use in various techniques (ELISA, western blot, immunohistochemistry) to assess the level of expression of these proteins in the blood, urine and breast tissue of dogs suffering from mammary gland tumors and demonstrate a positive correlation between these proteins and the presence of a tumor disease of the mammary gland
Vascular endothelial growth factor restores delayed tumor progression in tumors depleted of macrophages
Full text linkGenetic depletion of macrophages in Polyoma Middle T oncoprotein (PyMT)-induced mammary tumors in mice delayed the angiogenic switch and the progression to malignancy. To determine whether vascular endothelial growth factor A (VEGF-A) produced by tumor-associated macrophages regulated the onset of the angiogenic switch, a genetic approach was used to restore expression of VEGF-A into tumors at the benign stages. This stimulated formation of a high-density vessel network and in macrophage-depleted mice, was followed by accelerated tumor progression. The expression of VEGF-A led to a massive infiltration into the tumor of leukocytes that were mostly macrophages. This study suggests that macrophage-produced VEGF regulates malignant progression through stimulating tumor angiogenesis, leukocytic infiltration and tumor cell invasion
High-level expression of Proteinase K from Tritirachium album Limber in Pichia pastoris using multi-copy expression strains
No full textProteinase K is widely used in scientific research and industries. This report was aimed to achieve high-level expression of proteinase K using Pichia pastoris GS115 as the host strain. The coding sequence of a variant of proteinase K that has higher activity than the wild type protein was chosen and optimized based on the codon usage preference of P. pastoris. The novel open reading frame was synthesized and a series of multi-copy expression vectors were constructed based on the pHBM905BOM plasmid, allowing for the tandem integration of multiple copies of the target gene into the genome of P. pastoris with a single recombination. These strains were used to study the correlation between the gene copy number and the expression level of proteinase K. The results of quantitative polymerase chain reaction (qPCR) indicated that the tandem expression cassettes were integrated into the host genome stably. Meanwhile, the results of qPCR and enzyme activity assays indicated that the mRNA and protein expression levels of the target gene increased as the gene copy number increased. Moreover, the effect of gene dosage on the expression level of the recombinant protein was more obvious using high-density fermentation. The maximum expression level and enzyme activity of proteinase K, which were obtained from the recombinant yeast strain bearing 5 copies of the target gene after an 84-h induction, were approximately 8.069 mg/mL and 108,295 1.1/mL, respectively. The recombinant proteinase was purified and characterized. The optimum pH and temperature for the activity of this protease were approximately pH 11 and 55 degrees C, respectively. (C) 2016 Elsevier Inc. All rights reserved.National 973 Program of China [2013CB910801]; Nature Science Fund for Creative Research Groups of Hubei Province of China [2012FFA034]; Foundation for High and New Technology Industrial Innovative Research Groups of the Wuhan Science and Technology Bureau [2014070504020239]SCI(E)[email protected]
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Commonsense Knowledge and Conceptual Structure in Container Metaphors
Full text linkCognitive grammar provides an analytic framework in which the semantic value of linguistic expressions is characterized relative to domains of presupposed knowledge. Cognitive metaphor theory holds that metaphorical language involves a mapping of conceptual structure from a source domain to a target domain. Containers are one such pervasive structure. This investigation proposes a detailed representation for the domain CONTAINER and applies it in the analysis of metaphorical expressions mapping CONTAINER onto target domains ARGUMENT and linguistic expression. Each source domain word is analyzed with respect to which aspects of the CONTAINER domain structure it refers, and whether it refers to a 2D or 3D bounded region. The pattern of aspects mapped suggest that spatial containment, content, and material container object comprise major aspects of the 3D CONTAINER domain. The target domains are demonstrated to be structured according this container organization. The results demonstrate that cognitive semantic analysis can reveal specific structures of commonsense knowledge which are prerequisite for language use
Disruption of the developmental programme of Trypanosoma brucei by genetic ablation of TbZFP1, a differentiation-enriched CCCH protein
Full text linkThe regulation of differentiation is particularly important in microbial eukaryotes that inhabit multiple environments. The parasite Trypanosoma brucei is an extreme example of this, requiring exquisite gene regulation during transmission from mammals to the tsetse fly vector. Unusually, trypanosomes rely almost exclusively on post-transcriptional mechanisms for regulated gene expression. Hence, RNA binding proteins are potentially of great significance in controlling stage-regulated processes. We have previously identified TbZFP1 as a trypanosome molecule transiently enriched during differentiation to tsetse midgut procyclic forms. This small protein (101 amino acids) contains the unusual CCCH zinc finger, an RNA binding motif. Here, we show that genetic ablation of TbZFP1 compromises repositioning of the mitochondrial genome, a specific event in the strictly regulated differentiation programme. Despite this, other events that occur both before and after this remain intact. Significantly, this phenotype correlates with the TbZFP1 expression profile during differentiation. This is the first genetic disruption of a developmental regulator in T. brucei. It demonstrates that programmed events in parasite development can be uncoupled at the molecular level. It also further supports the importance of CCCH proteins in key aspects of trypanosome cell function
The development of an assessment tool to gather evidence and evaluate the progress of performance skills of students in the Edgerton High School Band
Full text linkProject chair, Dr. Glenn C. Hayes.Because of the block schedule and the lack of certain basic music skills among the incoming band students at Edgerton High School, it is necessary to create a system to help students establish their basic performance skills. The purpose of this project is to design a set of assessment tools that will help students define and perform basic musical skills. A series of quarterly study sheets allows the student to study scales, rhythms, tone, and expression in a progressive manner through all grade levels. The student is required to master each form and the skill level demonstrated serves as a portion of his or her final grade. It is also necessary to have a way to assess the students’ skills. This project uses literature and methods from a variety of sources to develop a set of tools that will accomplish both of these objectives.
This project focuses on the four areas of skills basic to musical performance on a musical instrument including scales and arpeggios, rhythm, tone, and expression. The study of scales, arpeggios, and rhythm has been systematically designed to increase the technical skill of students on their instruments. Students will have studied the major, minor, and chromatic scales and arpeggios in a systematic method over a four-year course of study. Each term for four years (16 terms), the student will have studied one major scale, the relative minor scale, arpeggios, and the chromatic scale. In addition, the student will have studied a specific rhythm pattern each term. The chromatic scale study has been coordinated to the rhythm study for each term to help reinforce the rhythm pattern. The rhythm patterns began with the easiest whole rhythms (whole, half, and quarter notes) and get progressively more difficult with each term.
In addressing tone quality, the teacher will have assigned a phrase of music from the literature studied by the band. The student will have performed the phrase with the best tone quality he/she can produce. A rubric has been developed to assess the student’s level of tone production quality and to help the student begin to identify the qualities of an excellent tone.
Musical expression has been addressed in two manners. The first has been through a demonstration of expression during the same performance of the tone quality assignment. Students have been assessed on a rubric similar to the one designed for tone quality. In addition, the student has been presented with a blank phrase of music. The student then adds expression markings that they feel are appropriate and performs the excerpt. Again, a rubric has been designed to assess the work of the student
Differential expression analysis for sequence count data
Full text link*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.

*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. 

*Availability:* A free open-source R software package, _DESeq_, is available from the Bioconductor project and from "http://www-huber.embl.de/users/anders/DESeq":http://www-huber.embl.de/users/anders/DESeq
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