bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prion protein self-peptides modulate prion interactions and conversion
Authors: Rigter Alan , Priem Jan , Timmers-Parohi Drophatie , Langeveld Jan PM , van Zijderveld Fred G , Bossers Alex 
Published: December 2009

Abstract

Background
Molecular mechanisms underlying prion agent replication, converting host-encoded cellular prion protein (PrPC) into the scrapie associated isoform (PrPSc), are poorly understood. Selective self-interaction between PrP molecules forms a basis underlying the observed differences of the PrPC into PrPSc conversion process (agent replication). The importance of previously peptide-scanning mapped ovine PrP self-interaction domains on this conversion was investigated by studying the ability of six of these ovine PrP based peptides to modulate two processes; PrP self-interaction and conversion.

Results
Three peptides (octarepeat, binding domain 2 -and C-terminal) were capable of inhibiting self-interaction of PrP in a solid-phase PrP peptide array. Three peptides (N-terminal, binding domain 2, and amyloidogenic motif) modulated prion conversion when added before or after initiation of the prion protein misfolding cyclic amplification (PMCA) reaction using brain homogenates. The C-terminal peptides (core region and C-terminal) only affected conversion (increased PrPres formation) when added before mixing PrPC and PrPSc, whereas the octarepeat peptide only affected conversion when added after this mixing.

Conclusion
This study identified the putative PrP core binding domain that facilitates the PrPC-PrPSc interaction (not conversion), corroborating evidence that the region of PrP containing this domain is important in the species-barrier and/or scrapie susceptibility. The octarepeats can be involved in PrPC-PrPSc stabilization, whereas the N-terminal glycosaminoglycan binding motif and the amyloidogenic motif indirectly affected conversion. Binding domain 2 and the C-terminal domain are directly implicated in PrPC self-interaction during the conversion process and may prove to be prime targets in new therapeutic strategy development, potentially retaining PrPC function. These results emphasize the importance of probable PrPC-PrPC and required PrPC-PrPSc interactions during PrP conversion. All interactions are probably part of the complex process in which polymorphisms and species barriers affect TSE transmission and susceptibility.
Derivation of an amino acid similarity matrix for peptide:MHC binding and its application as a Bayesian prior
Authors: Kim Yohan , Sidney John , Pinilla Clemencia , Sette Alessandro , Peters Bjoern 
Published: December 2009

Abstract

Background
Experts in peptide:MHC binding studies are often able to estimate the impact of a single residue substitution based on a heuristic understanding of amino acid similarity in an experimental context. Our aim is to quantify this measure of similarity to improve peptide:MHC binding prediction methods. This should help compensate for holes and bias in the sequence space coverage of existing peptide binding datasets.

Results
Here, a novel amino acid similarity matrix (PMBEC) is directly derived from the binding affinity data of combinatorial peptide mixtures. Like BLOSUM62, this matrix captures well-known physicochemical properties of amino acid residues. However, PMBEC differs markedly from existing matrices in cases where residue substitution involves a reversal of electrostatic charge. To demonstrate its usefulness, we have developed a new peptide:MHC class I binding prediction method, using the matrix as a Bayesian prior. We show that the new method can compensate for missing information on specific residues in the training data. We also carried out a large-scale benchmark, and its results indicate that prediction performance of the new method is comparable to that of the best neural network based approaches for peptide:MHC class I binding.

Conclusion
A novel amino acid similarity matrix has been derived for peptide:MHC binding interactions. One prominent feature of the matrix is that it disfavors substitution of residues with opposite charges. Given that the matrix was derived from experimentally determined peptide:MHC binding affinity measurements, this feature is likely shared by all peptide:protein interactions. In addition, we have demonstrated the usefulness of the matrix as a Bayesian prior in an improved scoring-matrix based peptide:MHC class I prediction method. A software implementation of the method is available at: http://www.mhc-pathway.net/smmpmbec.
Aberrant trafficking of NSCLC-associated EGFR mutants through the endocytic recycling pathway promotes interaction with Src@
Authors: Chung Byung Min , Raja Srikumar M , Clubb Robert J , Tu Chun , George Manju , Band Vimla , Band Hamid 
Published: December 2009

Abstract

Background
Epidermal growth factor receptor (EGFR) controls a wide range of cellular processes, and altered EGFR signaling contributes to human cancer. EGFR kinase domain mutants found in non-small cell lung cancer (NSCLC) are constitutively active, a trait critical for cell transformation through activation of downstream pathways. Endocytic trafficking of EGFR is a major regulatory mechanism as ligand-induced lysosomal degradation results in termination of signaling. While numerous studies have examined mutant EGFR signaling, the endocytic traffic of mutant EGFR within the NSCLC milieu remains less clear.

Results
This study shows that mutant EGFRs in NSCLC cell lines are constitutively endocytosed as shown by their colocalization with the early/recycling endosomal marker transferrin and the late endosomal/lysosomal marker LAMP1. Notably, mutant EGFRs, but not the wild-type EGFR, show a perinuclear accumulation and colocalization with recycling endosomal markers such as Rab11 and EHD1 upon treatment of cells with endocytic recycling inhibitor monensin, suggesting that mutant EGFRs preferentially traffic through the endocytic recycling compartments. Importantly, monensin treatment enhanced the mutant EGFR association and colocalization with Src, indicating that aberrant transit through the endocytic recycling compartment promotes mutant EGFR-Src association.

Conclusion
The findings presented in this study show that mutant EGFRs undergo aberrant traffic into the endocytic recycling compartment which allows mutant EGFRs to engage in a preferential interaction with Src, a critical partner for EGFR-mediated oncogenesis.
A modifier screen in the Drosophila eye reveals that aPKC interacts with Glued during central synapse formation
Authors: Ma Lisha , Johns Louise A , Allen Marcus J 
Published: December 2009

Abstract

Background
The Glued gene of Drosophila melanogaster encodes the homologue of the vertebrate p150Glued subunit of dynactin. The Glued
1 mutation compromises the dynein-dynactin retrograde motor complex and causes disruptions to the adult eye and the CNS, including sensory neurons and the formation of the giant fiber system neural circuit.

Results
We performed a 2-stage genetic screen to identify mutations that modified phenotypes caused by over-expression of a dominant-negative Glued protein. We screened over 34,000 flies and isolated 41 mutations that enhanced or suppressed an eye phenotype. Of these, 12 were assayed for interactions in the giant fiber system by which they altered a giant fiber morphological phenotype and/or altered synaptic function between the giant fiber and the tergotrochanteral muscle motorneuron. Six showed interactions including a new allele of atypical protein kinase C (aPKC). We show that this cell polarity regulator interacts with Glued during central synapse formation. We have mapped the five other interacting mutations to discrete chromosomal regions.

Conclusion
Our results show that an efficient way to screen for genes involved in central synapse formation is to use a two-step strategy in which a screen for altered eye morphology precedes the analysis of central synaptogenesis. This has highlighted a role for aPKC in the formation of an identified central synapse.
Metagenomic islands of hyperhalophiles: the case of Salinibacter ruber
Authors: Pašić Lejla , Rodriguez-Mueller Beltran , Martin-Cuadrado Ana-Belen , Mira Alex , Rohwer Forest , Rodriguez-Valera Francisco 
Published: December 2009

AbstractBackgroundSaturated brines are extreme environments of low diversity.Salinibacter ruberis the only bacterium that inhabits this environment in significant numbers. In order to establish the extent of genetic diversity in natural populations of this microbe, the genomic sequence of reference strain DSM 13855 was compared to metagenomic fragments recovered from climax saltern crystallizers and obtained with 454 sequencing technology. This kind of analysis reveals the presence of metagenomic islands, i.e. highly variable regions among the different lineages in the population.ResultsThree regions of the sequenced isolate were scarcely represented in the metagenome thus appearing to vary among co-occurringS. rubercells. These metagenomic islands showed evidence of extensive genomic corruption with atypically low GC content, low coding density, high numbers of pseudogenes and short hypothetical proteins. A detailed analysis of island gene content showed that the genes in metagenomic island 1 code for cell surface polysaccharides. The strain-specific genes of metagenomic island 2 were found to be involved in biosynthesis of cell wall polysaccharide components. Finally, metagenomic island 3 was rich in DNA related enzymes.ConclusionThe genomic organisation ofS. rubervariable genomic regions showed a number of convergences with genomic islands of marine microbes studied, being largely involved in variable cell surface traits. This variation at the level of cell envelopes in an environment devoid of grazing pressure probably reflects a global strategy of bacteria to escape phage predation.
Computational prediction of essential genes in an unculturable endosymbiotic bacterium, Wolbachia of Brugia malayi
Authors: Holman Alexander G , Davis Paul J , Foster Jeremy M , Carlow Clotilde KS , Kumar Sanjay 
Published: December 2009

AbstractBackgroundWolbachia(wBm) is an obligate endosymbiotic bacterium ofBrugia malayi, a parasitic filarial nematode of humans and one of the causative agents of lymphatic filariasis. There is a pressing need for new drugs against filarial parasites, such asB. malayi. AswBm is required forB. malayidevelopment and fertility, targetingwBm is a promising approach. However, the lifecycle of neitherB. malayinorwBm can be maintainedin vitro. To facilitate selection of potential drug targets we computationally ranked thewBm genome based on confidence that a particular gene is essential for the survival of the bacterium.ResultswBm protein sequences were aligned using BLAST to the Database of Essential Genes (DEG) version 5.2, a collection of 5,260 experimentally identified essential genes in 15 bacterial strains. A confidence score, the Multiple Hit Score (MHS), was developed to predict eachwBm gene's essentiality based on the top alignments to essential genes in each bacterial strain. This method was validated using a jackknife methodology to test the ability to recover known essential genes in a control genome. A second estimation of essentiality, the Gene Conservation Score (GCS), was calculated on the basis of phyletic conservation of genes acrossWolbachia'sparent orderRickettsiales. Clusters of orthologous genes were predicted within the 27 currently available complete genomes. Druggability ofwBm proteins was predicted by alignment to a database of protein targets of known compounds.ConclusionRankingwBm genes by either MHS or GCS predicts and prioritizes potentially essential genes. Comparison of the MHS to GCS produces quadrants representing four types of predictions: those with high confidence of essentiality by both methods (245 genes), those highly conserved acrossRickettsiales(299 genes), those similar to distant essential genes (8 genes), and those with low confidence of essentiality (253 genes). These data facilitate selection ofwBm genes for entry into drug design pipelines.
Comparison of the sensitivity of culture, PCR and quantitative real-time PCR for the detection of Pseudomonas aeruginosain sputum of cystic fibrosis patients
Authors: Deschaght Pieter , De Baere Thierry , Van Simaey Leen , Van daele Sabine , De Baets Frans , De Vos Daniel , Pirnay Jean-Paul , Vaneechoutte Mario 
Published: December 2009

Abstract

Background

Pseudomonas aeruginosa is the major pathogen involved in the decline of lung function in cystic fibrosis (CF) patients. Early aggressive antibiotic therapy has been shown to be effective in preventing chronic colonization. Therefore, early detection is important and sensitive detection methods are warranted. In this study, we used a dilution series of P. aeruginosa positive sputa, diluted in a pool of P. aeruginosa negative sputa, all from CF patients - to mimick as closely as possible the sputa sent to routine laboratories - to compare the sensitivity of three culture techniques versus that of two conventional PCR formats and four real-time PCR formats, each targeting the P. aeruginosa oprL gene. In addition, we compared five DNA-extraction protocols.

Results
In our hands, all three culture methods and the bioMérieux easyMAG Nuclisens protocol Generic 2.0.1, preceded by proteinase K pretreatment and followed by any of the 3 real-time PCR formats with probes were most sensitive and able to detect P. aeruginosa up to 50 cfu/ml, i.e. the theoretical minimum of one cell per PCR mixture, when taking into account the volumes used in this study of sample for DNA-extraction, of DNA-elution and of DNA-extract in the PCR mixture.

Conclusion
In this study, no difference in sensitivity could be found for the detection of P. aeruginosa from sputum between microbiological culture and optimized DNA-extraction and real-time PCR. The results also indicate the importance of the optimization of the DNA-extraction protocol and the PCR format.
Subcutaneous administration of TC007 reduces disease severity in an animal model of SMA
Authors: Mattis Virginia B , Fosso Marina Y , Chang Cheng-Wei , Lorson Christian L 
Published: December 2009

Abstract

Background
Spinal Muscular Atrophy (SMA) is the leading genetic cause of infantile death. It is caused by the loss of functional Survival Motor Neuron 1 (SMN1). There is a nearly identical copy gene, SMN2, but it is unable to rescue from disease due to an alternative splicing event that excises a necessary exon (exon 7) from the majority of SMN2-derived transcripts. While SMNΔ7 protein has severely reduced functionality, the exon 7 sequences may not be specifically required for all activities. Therefore, aminoglycoside antibiotics previously shown to suppress stop codon recognition and promote translation read-through have been examined to increase the length of the SMNΔ7 C-terminus.

Results
Here we demonstrate that subcutaneous-administration of a read-through inducing compound (TC007) to an intermediate SMA model (Smn-/-; SMN2+/+; SMNΔ7) had beneficial effects on muscle fiber size and gross motor function.

Conclusion
Delivery of the read-through inducing compound TC007 reduces the disease-associated phenotype in SMA mice, however, does not significantly extend survival.
Far from easy and accurate - detection of metabolic syndrome by general practitioners
Authors: Helminen Eeva-Eerika , Mäntyselkä Pekka , Nykänen Irma , Kumpusalo Esko 
Published: December 2009

Abstract

Background
Metabolic syndrome (MetS) is a major public health challenge. General practitioners (GPs) could play a key role in its recognition. However, it often remains undiagnosed in primary care. This study assesses how well GPs and patients recognise MetS among patients with coronary heart disease or at least one of its risk factors.

Methods
Twenty-six health centres around Finland were randomly selected for the purpose of identifying, over a two-week period in April 2005, patients meeting the inclusion criteria of coronary heart disease or one of its risk factors. GPs and identified patients (n = 1880) were asked to complete surveys that included a question about the patient's MetS status. A trained nurse conducted health checks (n = 1180) of the identified patients, utilising criteria of MetS modified from the National Cholesterol Program. Data from the GPs' survey were compared with those from the health check to establish the extent of congruence of identification of MetS.

Results
Almost half (49.4%) of the patients met the criteria of MetS as established by objective measures. However, in the GPs' survey responses, only 28.5% of the patients were identified as having MetS. Additionally, these groups of MetS patients were not congruent. The sensitivity of the GPs' diagnosis of MetS was 0.31 with a specificity of 0.73. Only 7.1% of the study patients stated that they were suffering from MetS.

Conclusion
Detection of MetS is inaccurate among GPs in Finland. Most patients were not aware of having MetS. The practical relevance of MetS in primary care should be reconsidered.
Polymorphism in the oxytocin promoter region in patients with lactase non-persistence is not related to symptoms
Authors: Truedsson Mikael , Carlson Joyce , Simrén Magnus , Ohlsson Bodil 
Published: December 2009

Abstract

Background
Oxytocin and the oxytocin receptor have been demonstrated in the gastrointestinal (GI) tract and have been shown to exert physiological effects on gut motility. The role for oxytocin in the pathophysiology of GI complaints is unknown. The aim of this study was to examine genetic variations or polymorphism of oxytocin (OXT) and its receptor (OXTR) genes in patients with GI complaints without visible organic abnormalities.

Methods
Genetic variants in the OXT promoter region, and in the OXTR gene in DNA samples from 131 rigorously evaluated patients with Irritable Bowel Syndrome (IBS), 408 homozygous subjects referred for lactase (LCT-13910 C>T, rs4988235) genotyping, and 299 asymptomatic blood donors were compared. One polymorphism related to the OXT gene (rs6133010 A>G) and 4 related to the OXTR gene (rs1465386 G>T, rs3806675 G>A, rs968389 A>G, rs1042778 G>T) were selected for genotyping using Applied Biosystems 7900 HT allele discrimination assays.

Results
There were no statistically significant differences in the genotype or allele frequencies in any of the SNPs when IBS patients were compared to healthy controls. Among subjects referred for lactase genotyping, the rs6133010 A>G OXT promoter A/G genotype tended to be more common in the 154 non-persistent (27.3%) subjects than in the 254 lactase persistant (18.1%) subjects and in the healthy controls (19.4%) (p = 0.08). When direct comparing, the A/G genotype was less common in the OXT promoter region in controls (p = 0.09) and in subjects with lactase persistence (p = 0.03) compared to subjects with lactase non-persistence. When healthy controls were viewed according to their own LCT-13910 genotypes, the C/C lactase non-persistent controls had a higher frequency for the OXT promoter A/G genotype than LCT-13910 T/T lactase persistent controls (41.2% vs 13.1%).
No significant differences in frequencies of the investigated OXTR SNPs were noted in this study.

Conclusion
The results suggest that polymorphism in the promoter region of the OXT gene is most common in subjects with lactase non-persistence. This polymorphism may not be related to GI symptoms, as it is related to lactase non-persistence also in healthy controls.
A comparison of urinary tract pathology and morbidity in adult populations from endemic and non-endemic zones for urinary schistosomiasis on Unguja Island, Zanzibar
Authors: Lyons Beatrice , Stothard Russel , Rollinson David , Khamis Simba , Simai Khamis A , Hunter Paul R 
Published: December 2009

Abstract

Background
Renal tract involvement is implicated in both early and late schistosomiasis leading to increased disease burden. Despite there being good estimates of disease burden due to renal tract disease secondary to schistosomiasis at the global level, it is often difficult to translate these estimates into local communities. The aim of this study was to assess the burden of urinary tract pathology and morbidity due to schistosomiasis in Zanzibar and identify reliable clinical predictors of schistosomiasis associated renal disease.

Methods
A cross-sectional comparison of Ungujan men and women living within either high or low endemic areas for urinary schistosomiasis was conducted. Using urine analysis with reagent strips, parasitological egg counts, portable ultrasonography and a qualitative case-history questionnaire. Data analysis used single and multiple predictor variable logistic regression.

Results
One hundred and sixty people were examined in the high endemic area (63% women and 37% men), and 101 people in the low endemic area (61% women and 39% men). In the high endemic area, egg-patent schistosomiasis and urinary tract pathology were much more common (p = 1 × 10-3, 8 × 10-6, respectively) in comparison with the low endemic area. Self-reported frothy urine, self-reported haematuria, dysuria and urgency to urinate were associated with urinary tract pathology (p = 1.8 × 10-2, p = 1.1 × 10-4, p = 1.3 × 10-6, p = 1.1 × 10-7, respectively) as assessed by ultrasonography. In a multi-variable logistic regression model, self-reporting of schistosomiasis in the past year, self-reporting of urgency to urinate and having an egg-positive urine sample were all independently associated with detectable urinary tract abnormality, consistent with schistosomiasis-specific disease. Having two or more of these features was moderately sensitive (70%) as a predictor for urinary tract abnormality with high specificity (92%).

Conclusion
Having two out of urgency to urinate, self reporting of previous infections and detection of eggs in the urine were good proxy predictors of urinary tract abnormality as detected by ultrasound.
Evaluation of alternative respiratory syndromes for specific syndromic surveillance of influenza and respiratory syncytial virus: a time series analysis
Authors: Schindeler Suzanne K , Muscatello David J , Ferson Mark J , Rogers Kris D , Grant Paul , Churches Tim 
Published: December 2009

Abstract

Background
Syndromic surveillance is increasingly being evaluated for its potential for early warning of increased disease activity in the population. However, interpretation is hampered by the difficulty of attributing a causative pathogen. We described the temporal relationship between laboratory counts of influenza and respiratory syncytial virus (RSV) detection and alternative groupings of Emergency Department (ED) respiratory diagnoses.

Methods
ED and laboratory data were obtained for the south-eastern area of Sydney, NSW for the period 1 June 2001 - 1 December 2006. Counts of ED visits and laboratory confirmed positive RSV and influenza cases were aggregated by week. Semi-parametric generalized additive models (GAM) were used to determine the association between the incidence of RSV and influenza and the incidence of respiratory syndrome ED presentations while controlling for temporal confounders.

Results
For every additional RSV laboratory count, ED diagnoses of bronchiolitis increased by 3.1% (95%CI: 2.7%-3.5%) in the same week. For every additional influenza laboratory count, ED diagnoses of influenza-like illness increased by 4.7% (95%CI: 4.2%-5.2%) one week earlier.

Conclusion
In this study, large increases in ED diagnoses of bronchiolitis and influenza-like illness were independent and proxy indicators for RSV and influenza activity, respectively.