bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fine-tuning the space, time, and host distribution of mycobacteria in wildlife
Authors: Gortazar Christian , Torres Maria J , Acevedo Pelayo , Aznar Javier , Negro Juan J , de la Fuente Jose , Vicente Joaquín 
Published: February 2011

Abstract

Background
We describe the diversity of two kinds of mycobacteria isolates, environmental mycobacteria and Mycobacterium bovis collected from wild boar, fallow deer, red deer and cattle in Doñana National Park (DNP, Spain), analyzing their association with temporal, spatial and environmental factors.

Results
High diversity of environmental mycobacteria species and M. bovis typing patterns (TPs) were found. When assessing the factors underlying the presence of the most common types of both environmental mycobacteria and M. bovis TPs in DNP, we evidenced (i) host species differences in the occurrence, (ii) spatial structuration and (iii) differences in the degree of spatial association of specific types between host species. Co-infection of a single host by two M. bovis TPs occurred in all three wild ungulate species. In wild boar and red deer, isolation of one group of mycobacteria occurred more frequently in individuals not infected by the other group. While only three TPs were detected in wildlife between 1998 and 2003, up to 8 different ones were found during 2006-2007. The opposite was observed in cattle. Belonging to an M. bovis-infected social group was a significant risk factor for mycobacterial infection in red deer and wild boar, but not for fallow deer. M. bovis TPs were usually found closer to water marshland than MOTT.

Conclusions
The diversity of mycobacteria described herein is indicative of multiple introduction events and a complex multi-host and multi-pathogen epidemiology in DNP. Significant changes in the mycobacterial isolate community may have taken place, even in a short time period (1998 to 2007). Aspects of host social organization should be taken into account in wildlife epidemiology. Wildlife in DNP is frequently exposed to different species of non-tuberculous, environmental mycobacteria, which could interact with the immune response to pathogenic mycobacteria, although the effects are unknown. This research highlights the suitability of molecular typing for surveys at small spatial and temporal scales.
The Renilla luciferase gene as a reference gene for normalization of gene expression in transiently transfected cells
Authors: Jiwaji Meesbah , Daly Rónán , Pansare Kshama , McLean Pauline , Yang Jingli , Kolch Walter , Pitt Andrew R 
Published: February 2011

Abstract

Background
The importance of appropriate normalization controls in quantitative real-time polymerase chain reaction (qPCR) experiments has become more apparent as the number of biological studies using this methodology has increased. In developing a system to study gene expression from transiently transfected plasmids, it became clear that normalization using chromosomally encoded genes is not ideal, at it does not take into account the transfection efficiency and the significantly lower expression levels of the plasmids. We have developed and validated a normalization method for qPCR using a co-transfected plasmid.

Results
The best chromosomal gene for normalization in the presence of the transcriptional activators used in this study, cadmium, dexamethasone, forskolin and phorbol-12-myristate 13-acetate was first identified. qPCR data was analyzed using geNorm, Normfinder and BestKeeper. Each software application was found to rank the normalization controls differently with no clear correlation. Including a co-transfected plasmid encoding the Renilla luciferase gene (Rluc) in this analysis showed that its calculated stability was not as good as the optimised chromosomal genes, most likely as a result of the lower expression levels and transfection variability. Finally, we validated these analyses by testing two chromosomal genes (B2M and ActB) and a co-transfected gene (Rluc) under biological conditions. When analyzing co-transfected plasmids, Rluc normalization gave the smallest errors compared to the chromosomal reference genes.

Conclusions
Our data demonstrates that transfected Rluc is the most appropriate normalization reference gene for transient transfection qPCR analysis; it significantly reduces the standard deviation within biological experiments as it takes into account the transfection efficiencies and has easily controllable expression levels. This improves reproducibility, data validity and most importantly, enables accurate interpretation of qPCR data.
Evaluation of suitable reference genes for gene expression studies in bronchoalveolar lavage cells from horses with inflammatory airway disease
Authors: Beekman Laura , Tohver Triin , Dardari Rkia , Léguillette Renaud 
Published: February 2011

Abstract

Background
The stability of reference genes has a tremendous effect on the results of relative quantification of genes expression by quantitative polymerase chain reaction. Equine Inflammatory Airway Disease (IAD) is a common condition often treated with corticosteroids. The diagnosis of IAD is based on clinical signs and bronchoalveolar lavage (BAL) fluid cytology. The aim of this study was to identify reference genes with the most stable mRNA expression in the BAL cells of horses with IAD irrespective of corticosteroids treatment.

Results
The expression stability of seven candidate reference genes (B2M, HPRT, GAPDH, ACTB, UBB, RPL32, SDHA) was determined by qRT-PCR in BAL samples taken pre- and post- treatment with dexamethasone and fluticasone propionate for two weeks in 7 horses with IAD. Primers' efficiencies were calculated using LinRegPCR. NormFinder, GeNorm and qBasePlus softwares were used to rank the genes according to their stability. GeNorm was also used to determine both the ideal number and the best combination of reference genes. GAPDH was found to be the most stably expressed gene with the three softwares. GeNorm ranked B2M as the least stable gene. Based on the pair-wise variation cut-off value determined with GeNorm, the number of genes required for optimal normalization was four and included GAPDH, SDHA, HPRT and RPL32.

Conclusion
The geometric mean of GAPDH, HPRT, SDHA and RPL32 is recommended for accurate normalization of quantitative PCR data in BAL cells of horses with IAD treated with corticosteroids. If only one reference gene can be used, then GAPDH is recommended.
Spatial distribution of Na+-K+-ATPase in dendritic spines dissected by nanoscale superresolution STED microscopy
Authors: Blom Hans , Rönnlund Daniel , Scott Lena , Spicarova Zuzana , Widengren Jerker , Bondar Alexander , Aperia Anita , Brismar Hjalmar 
Published: February 2011

AbstractBackgroundThe Na+,K+-ATPase plays an important role for ion homeostasis in virtually all mammalian cells, including neurons. Despite this, there is as yet little known about the isoform specific distribution in neurons.ResultsWith help of superresolving stimulated emission depletion microscopy the spatial distribution of Na+,K+-ATPase in dendritic spines of cultured striatum neurons have been dissected. The found compartmentalized distribution provides a strong evidence for the confinement of neuronal Na+,K+-ATPase (α3 isoform) in the postsynaptic region of the spine.ConclusionsA compartmentalized distribution may have implications for the generation of local sodium gradients within the spine and for the structural and functional interaction between the sodium pump and other synaptic proteins. Superresolution microscopy has thus opened up a new perspective to elucidate the nature of the physiological function, regulation and signaling role of Na+,K+-ATPase from its topological distribution in dendritic spines.
High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cerealeL.) genes involved in frost response
Authors: Li Yongle , Haseneyer Grit , Schön Chris-Carolin , Ankerst Donna , Korzun Viktor , Wilde Peer , Bauer Eva 
Published: February 2011

Abstract

Background
Rye (Secale cereale L.) is the most frost tolerant cereal species. As an outcrossing species, rye exhibits high levels of intraspecific diversity, which makes it well-suited for allele mining in genes involved in the frost responsive network. For investigating genetic diversity and the extent of linkage disequilibrium (LD) we analyzed eleven candidate genes and 37 microsatellite markers in 201 lines from five Eastern and Middle European rye populations.

Results
A total of 147 single nucleotide polymorphisms (SNPs) and nine insertion-deletion polymorphisms were found within 7,639 bp of DNA sequence from eleven candidate genes, resulting in an average SNP frequency of 1 SNP/52 bp. Nucleotide and haplotype diversity of candidate genes were high with average values π = 5.6 × 10-3 and Hd = 0.59, respectively. According to an analysis of molecular variance (AMOVA), most of the genetic variation was found between individuals within populations. Haplotype frequencies varied markedly between the candidate genes. ScCbf14, ScVrn1, and ScDhn1 were dominated by a single haplotype, while the other 8 genes (ScCbf2, ScCbf6, ScCbf9b, ScCbf11, ScCbf12, ScCbf15, ScIce2, and ScDhn3) had a more balanced haplotype frequency distribution. Intra-genic LD decayed rapidly, within approximately 520 bp on average. Genome-wide LD based on microsatellites was low.

Conclusions
The Middle European population did not differ substantially from the four Eastern European populations in terms of haplotype frequencies or in the level of nucleotide diversity. The low LD in rye compared to self-pollinating species promises a high resolution in genome-wide association mapping. SNPs discovered in the promoters or coding regions, which attribute to non-synonymous substitutions, are suitable candidates for association mapping.
Response to written feedback of clinical data within a longitudinal study: a qualitative study exploring the ethical implications
Authors: Lorimer Karen , Gray Cindy M , Hunt Kate , Wyke Sally , Anderson Annie , Benzeval Michaela 
Published: February 2011

AbstractBackgroundThere is a growing ethical imperative to feedback research results to participants but there remains a striking lack of empirical research on how people respond to individualised feedback. We sought to explore longitudinal study participants' response to receiving individual written feedback of weight-related and blood results, and to consider the balance of harms against benefits.MethodsA qualitative study with face-to-face and telephone interviews conducted with 50 men and women who had participated in the fifth and most recent wave of the cohort study 'West of Scotland Twenty-07' and received a feedback letter containing body mass index (BMI), body fat percentage, cholesterol and glycated haemoglobin A1c(HbA1c) results.ResultsExpectations of, and response to, the feedback of their individual results varied. Whilst half of the participants were on the whole 'pleased' with their results or held neutral views, half reported negative responses such as 'shock' or 'concern', particularly in relation to the weight-related results. Participants who were overweight and obese used the most negative language about their results, with some being quite distressed and reporting feelings of powerlessness, low self-image and anxiety over future health. Nevertheless, some people reported having implemented lifestyle changes in direct response to the feedback, resulting in significant weight-loss and/or dietary improvements. Others reported being motivated to change their behaviour. Age and gender differences were apparent in these narratives of behaviour change.ConclusionsThe potential harm caused to some participants may be balanced against the benefit to others. More evaluation of the impact of the format, content and means of individualised feedback of research findings in non-trial studies is required given the growing ethical imperative to offer participants a choice of receiving their results, and the likelihood that a high percentage will choose to receive them.
The impact of maternal HIV infection on cord blood lymphocyte subsets and cytokine profile in exposed non-infected newborns
Authors: Borges-Almeida Eliane , Milanez Helaine MBPM , Vilela Maria Marluce S , Cunha Fernanda GP , Abramczuk Beatriz M , Reis-Alves Suiellen C , Metze Konradin , Lorand-Metze Irene 
Published: February 2011

AbstractBackgroundChildren born to HIV+ mothers are exposed intra-utero to several drugs and cytokines that can modify the developing immune system, and influence the newborn's immune response to infections and vaccines. We analyzed the relation between the distribution of cord blood lymphocyte subsets and cytokine profile in term newborns of HIV+ mothers using HAART during pregnancy and compared them to normal newborns.MethodsIn a prospective, controlled study, 36 mother-child pairs from HIV+ mothers and 15 HIV-uninfected mothers were studied. Hematological features and cytokine profiles of mothers at 35 weeks of pregnancy were examined. Maternal and cord lymphocyte subsets as well as B-cell maturation in cord blood were analyzed by flow cytometry. The non-stimulated, as well as BCG- and PHA-stimulated production of IL2, IL4, IL7, IL10, IL12, IFN-γ and TNF-alpha in mononuclear cell cultures from mothers and infants were quantified using ELISA.ResultsAfter one year follow-up none of the exposed infants became seropositive for HIV. An increase in B lymphocytes, especially the CD19/CD5+ ones, was observed in cord blood of HIV-exposed newborns. Children of HIV+ hard drug using mothers had also an increase of immature B-cells. Cord blood mononuclear cells of HIV-exposed newborns produced less IL-4 and IL-7 and more IL-10 and IFN-γ in culture than those of uninfected mothers. Cytokine values in supernatants were similar in infants and their mothers except for IFN-γ and TNF-alpha that were higher in HIV+ mothers, especially in drug abusing ones. Cord blood CD19/CD5+ lymphocytes showed a positive correlation with cord IL-7 and IL-10. A higher maternal age and smoking was associated with a decrease of cord blood CD4+ cells.Conclusionsin uninfected infants born to HIV+ women, several immunological abnormalities were found, related to the residual maternal immune changes induced by the HIV infection and those associated with antiretroviral treatment. Maternal smoking was associated to changes in cord CD3/CD4 lymphocytes and maternal hard drug abuse was associated with more pronounced changes in the cord B cell line.
A first assessment of the genetic diversity of Mycobacterium tuberculosis complex in Cambodia
Authors: Zhang Jian , Heng Seiha , Le Moullec Stéphanie , Refregier Guislaine , Gicquel Brigitte , Sola Christophe , Guillard Bertrand 
Published: February 2011

Abstract

Background
Cambodia is among the 22 high-burden TB countries, and has one of the highest rates of TB in South-East Asia. This study aimed to describe the genetic diversity among clinical Mycobacterium tuberculosis complex (MTC) isolates collected in Cambodia and to relate these findings to genetic diversity data from neighboring countries.

Methods
We characterized by 24 VNTR loci genotyping and spoligotyping 105 Mycobacterium tuberculosis clinical isolates collected between 2007 and 2008 in the region of Phnom-Penh, Cambodia, enriched in multidrug-resistant (MDR) isolates (n = 33).

Results
Classical spoligotyping confirmed that the East-African Indian (EAI) lineage is highly prevalent in this area (60%-68% respectively in whole sample and among non-MDR isolates). Beijing lineage is also largely represented (30% in whole sample, 21% among non-MDR isolates, OR = 4.51, CI95% [1.77, 11.51]) whereas CAS lineage was absent. The 24 loci MIRU-VNTR typing scheme distinguished 90 patterns with only 13 multi-isolates clusters covering 28 isolates. The clustering of EAI strains could be achieved with only 8 VNTR combined with spoligotyping, which could serve as a performing, easy and cheap genotyping standard for this family. Extended spoligotyping suggested relatedness of some unclassified "T1 ancestors" or "Manu" isolates with modern strains and provided finer resolution.

Conclusions
The genetic diversity of MTC in Cambodia is driven by the EAI and the Beijing families. We validate the usefulness of the extended spoligotyping format in combination with 8 VNTR for EAI isolates in this region.
KCNE1D85N polymorphism — a sex-specific modifier in type 1 long QT syndrome?
Authors: Lahtinen Annukka M , Marjamaa Annukka , Swan Heikki , Kontula Kimmo 
Published: February 2011

Abstract

Background
Long QT syndrome (LQTS) is an inherited ion channel disorder manifesting with prolongation of the cardiac repolarization phase and severe ventricular arrhythmias. The common KCNE1 D85N potassium channel variant prolongs QT interval by inhibiting IKs (KCNQ1) and IKr (KCNH2) currents and is therefore a suitable candidate for a modifier gene in LQTS.

Methods
We studied the effect of D85N on age-, sex-, and heart rate-adjusted QT-interval duration by linear regression in LQTS patients carrying the Finnish founder mutations KCNQ1 G589D (n = 492), KCNQ1 IVS7-2A>G (n = 66), KCNH2 L552S (n = 73), and KCNH2 R176W (n = 88). We also investigated the association between D85N and clinical variables reflecting the severity of the disease.

Results
D85N was associated with a QT prolongation by 26 ms (SE 8.6, p = 0.003) in males with KCNQ1 G589D (n = 213), but not in females with G589D (n = 279). In linear regression, the interaction between D85N genotype and sex was significant (p = 0.028). Within the KCNQ1 G589D mutation group, KCNE1 D85N carriers were more often probands of the family (p = 0.042) and were more likely to use beta blocker medication (p = 0.010) than non-carriers. The number of D85N carriers in other founder mutation groups was too small to assess its effects.

Conclusions
We propose that KCNE1 D85N is a sex-specific QT-interval modifier in type 1 LQTS and may also associate with increased severity of disease. Our data warrant additional studies on the role of KCNE1 D85N in other genetically homogeneous groups of LQTS patients.
Cognitive function and quality of life in multiple sclerosis patients: a cross-sectional study
Authors: Baumstarck-Barrau Karine , Simeoni Marie-Claude , Reuter Françoise , Klemina Irina , Aghababian Valérie , Pelletier Jean , Auquier Pascal 
Published: February 2011

Abstract

Background
Nearly half of all patients diagnosed with multiple sclerosis (MS) will develop cognitive dysfunction. Studies highlighted from no/weak impact to a strong impact of cognitive impairment on quality of life (QoL). The aim of this study was to assess the impact of cognitive dysfunction on self-reported QoL in MS patients while considering key confounding factors.

Methods
Design: cross-sectional study. Inclusion criteria: MS patients of any disease subtype. Data collection: sociodemographic (age, gender, marital status, education level, and occupational activity) and clinical data (MS subtype, disease duration); MS disability (Expanded Disability Status Scale, EDSS); depression (Beck Depression Inventory); fatigue (Modified Fatigue Impact Scale); QoL (SF36 and MusiQoL); and neuropsychological performance (Brief Repeatable Battery of Neuropsychological Tests, BRB-N). Statistical analysis: multiple linear regressions (forward-stepwise selection).

Results
One hundred and twenty-four patients were enrolled. Performance on BRB-N subtests varied widely (6% to 70% abnormal). The BRB-N classified 37-78% of the patients as cognitively impaired, depending on the definition of cognitive impairment. No links were found between the MusiQoL index and cognitive subtests, whereas marital status, EDSS, and depression were found to be independent predictive factors.

Conclusions
The present study demonstrated the weak and scarce association between cognitive impairment and QoL, when the key confounding factors were considered. These results need to be confirmed with larger samples and more accurate tests of cognitive function.
Re-expression of ARHI (DIRAS3) induces autophagy in breast cancer cells and enhances the inhibitory effect of paclitaxel
Authors: Zou Chun-Fang , Jia Luoqi , Jin Hongyan , Yao Ming , Zhao Naiqing , Huan Jin , Lu Zhen , Bast Robert C , Feng Youji , Yu Yinhua 
Published: February 2011

Abstract

Background

ARHI is a Ras-related imprinted gene that inhibits cancer cell growth and motility. ARHI is downregulated in the majority of breast cancers, and loss of its expression is associated with its progression from ductal carcinoma in situ (DCIS) to invasive disease. In ovarian cancer, re-expression of ARHI induces autophagy and leads to autophagic death in cell culture; however, ARHI re-expression enables ovarian cancer cells to remain dormant when they are grown in mice as xenografts. The purpose of this study is to examine whether ARHI induces autophagy in breast cancer cells and to evaluate the effects of ARHI gene re-expression in combination with paclitaxel.

Methods
Re-expression of ARHI was achieved by transfection, by treatment with trichostatin A (TSA) or by a combination of TSA and 5-aza-2'-deoxycytidine (DAC) in breast cancer cell cultures and by liposomal delivery of ARHI in breast tumor xenografts.

Results
ARHI re-expression induces autophagy in breast cancer cells, and ARHI is essential for the induction of autophagy. When ARHI was re-expressed in breast cancer cells treated with paclitaxel, the growth inhibitory effect of paclitaxel was enhanced in both the cell culture and the xenografts. Although paclitaxel alone did not induce autophagy in breast cancer cells, it enhanced ARHI-induced autophagy. Conversely, ARHI re-expression promoted paclitaxel-induced apoptosis and G2/M cell cycle arrest.

Conclusions
ARHI re-expression induces autophagic cell death in breast cancer cells and enhances the inhibitory effects of paclitaxel by promoting autophagy, apoptosis, and G2/M cell cycle arrest.
FLT3 mutations in canine acute lymphocytic leukemia
Authors: Suter Steven E , Small George W , Seiser Eric L , Thomas Rachael , Breen Matthew , Richards Kristy L 
Published: February 2011

Abstract

Background
FMS-like tyrosine kinase 3 (FLT3) is a commonly mutated protein in a variety of human acute leukemias. Mutations leading to constitutively active FLT3, including internal tandem duplications of the juxtamembrane domain (ITD), result in continuous cellular proliferation, resistance to apoptotic cell death, and a poorer prognosis. A better understanding of the molecular consequences of FLT3 activation would allow improved therapeutic strategies in these patients. Canine lymphoproliferative diseases, including lymphoma and acute leukemias, share evolutionarily conserved chromosomal aberrations and exhibit conserved mutations within key oncogenes when compared to their human counterparts. A small percentage of canine acute lymphocytic leukemias (ALL) also exhibit FLT3 ITD mutations.

Methods
We molecularly characterized FLT3 mutations in two dogs and one cell line, by DNA sequencing, gene expression analysis via quantitative real-time PCR, and sensitivity to the FLT3 inhibitor lestaurtinib via in vitro proliferation assays. FLT 3 and downstream mediators of FLT3 activation were assessed by Western blotting.

Results
The canine B-cell leukemia cell line, GL-1, and neoplastic cells from 2/7 dogs diagnosed cytologically with ALL were found to have FLT3 ITD mutations and FLT3 mRNA up-regulation. Lestaurtinib, a small molecule FLT3 inhibitor, significantly inhibited the growth of GL-1 cells, while not affecting the growth of two other canine lymphoid cell lines without the FLT3 mutation. Finally, western blots were used to confirm the conserved downstream mediators of FLT3 activating mutations.

Conclusions
These results show that ALL and FLT3 biology is conserved between canine and human patients, supporting the notion that canine ALL, in conjunction with the GL-1 cell line, will be useful in the development of a relevant large animal model to aid in the study of human FLT3 mutant leukemias.