Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes

BACKGROUND: The minor histocompatibility antigens (mHags) are self-peptides derived from common cellular proteins and presented by MHC class I and II molecules. Disparities in mHags are a potential risk for the development of graft-versus-host disease (GvHD) in the recipients of bone marrow from HLA-identical donors. Two alleles have been identified in the mHag HA-1. The correlation between mismatches of the mHag HA-1 and GvHD has been suggested and methods to facilitate large-scale testing were afterwards developed. METHODS: We used sequence specific primer (SSP) PCR and direct sequencing to detect HA-1 gene polymorphisms in a sample of 131 unrelated Italian subjects. We then set up a novel melting temperature (Tm) assay that may help identification of HA-1 alleles without oligonucleotide probes. RESULTS: We report the frequencies of HA-1 alleles in the Italian population and the presence of an intronic 5 base-pair deletion associated with the immunogeneic allele HA-1(H). We also detected novel variable sites with respect to the consensus sequence of HA-1 locus. Even though recombination/gene conversion events are documented, there is considerable linkage disequilibrium in the data. The gametic associations between HA-1(R/H )alleles and the intronic 5-bp ins/del polymorphism prompted us to try the Tm analysis with SYBR(® )Green I. We show that the addition of dimethylsulfoxide (DMSO) during the assay yields distinct patterns when amplicons from HA-1(H )homozygotes, HA-1(R )homozygotes, and heterozygotes are analysed. CONCLUSION: The possibility to use SYBR(® )Green I to detect Tm differences between allelic variants is attractive but requires great caution. We succeeded in allele discrimination of the HA-1 locus using a relatively short (101 bp) amplicon, only in the presence of DMSO. We believe that, at least in certain assets, Tm assays may benefit by the addition of DMSO or other agents affecting DNA strand conformation and stability

The IgA nephropathy Biobank. An important starting point for the genetic dissection of a complex trait

BACKGROUND: IgA nephropathy (IgAN) or Berger's disease, is the most common glomerulonephritis in the world diagnosed in renal biopsied patients. The involvement of genetic factors in the pathogenesis of the IgAN is evidenced by ethnic and geographic variations in prevalence, familial clustering in isolated populations, familial aggregation and by the identification of a genetic linkage to locus IGAN1 mapped on 6q22–23. This study seems to imply a single major locus, but the hypothesis of multiple interacting loci or genetic heterogeneity cannot be ruled out. The organization of a multi-centre Biobank for the collection of biological samples and clinical data from IgAN patients and relatives is an important starting point for the identification of the disease susceptibility genes. DESCRIPTION: The IgAN Consortium organized a Biobank, recruiting IgAN patients and relatives following a common protocol. A website was constructed to allow scientific information to be shared between partners and to divulge obtained data (URL: ). The electronic database, the core of the website includes data concerning the subjects enrolled. A search page gives open access to the database and allows groups of patients to be selected according to their clinical characteristics. DNA samples of IgAN patients and relatives belonging to 72 multiplex extended pedigrees were collected. Moreover, 159 trios (sons/daughters affected and healthy parents), 1068 patients with biopsy-proven IgAN and 1040 healthy subjects were included in the IgAN Consortium Biobank. Some valuable and statistically productive genetic studies have been launched within the 5(th )Framework Programme 1998–2002 of the European project No. QLG1-2000-00464 and preliminary data have been published in "Technology Marketplace" website: . CONCLUSION: The first world IgAN Biobank with a readily accessible database has been constituted. The knowledge gained from the study of Mendelian diseases has shown that the genetic dissection of a complex trait is more powerful when combined linkage-based, association-based, and sequence-based approaches are performed. This Biobank continuously expanded contains a sample size of adequately matched IgAN patients and healthy subjects, extended multiplex pedigrees, parent-child trios, thus permitting the combined genetic approaches with collaborative studies

Cortical Plasticity Induced by Transcranial Magnetic Stimulation during Wakefulness Affects Electroencephalogram Activity during Sleep

BACKGROUND:Sleep electroencephalogram (EEG) brain oscillations in the low-frequency range show local signs of homeostatic regulation after learning. Such increases and decreases of slow wave activity are limited to the cortical regions involved in specific task performance during wakefulness. Here, we test the hypothesis that reorganization of motor cortex produced by long-term potentiation (LTP) affects EEG activity of this brain area during subsequent sleep. METHODOLOGY/PRINCIPAL FINDINGS:By pairing median nerve stimulation with transcranial magnetic stimulation over the contralateral motor cortex, one can potentiate the motor output, which is presumed to reflect plasticity of the neural circuitry. This paired associative stimulation increases M1 cortical excitability at interstimulus intervals of 25 ms. We compared the scalp distribution of sleep EEG power following paired associative stimulation at 25 ms to that following a control paradigm with 50 ms intervals. It is shown that the experimental manipulation by paired associative stimulation at 25 ms induces a 48% increase in amplitude of motor evoked potentials. This LTP-like potentiation, induced during waking, affects delta and theta EEG power in both REM and non-REM sleep, measured during the following night. Slow-wave activity increases in some frontal and prefrontal derivations and decreases at sites neighboring and contralateral to the stimulated motor cortex. The magnitude of increased amplitudes of motor evoked potentials by the paired associative stimulation at 25 ms predicts enhancements of slow-wave activity in prefrontal regions. CONCLUSIONS/SIGNIFICANCE:An LTP-like paradigm, presumably inducing increased synaptic strength, leads to changes in local sleep regulation, as indexed by EEG slow-wave activity. Enhancement and depression of slow-wave activity are interpreted in terms of a simultaneous activation of both excitatory and inhibitory circuits consequent to the paired associative stimulation at 25 ms

Genetic studies of IgA nephropathy: past, present, and future

Immunoglobulin A nephropathy (IgAN) is the most common form of primary glomerulonephritis worldwide and an important cause of kidney disease in young adults. Highly variable clinical presentation and outcome of IgAN suggest that this diagnosis may encompass multiple subsets of disease that are not distinguishable by currently available clinical tools. Marked differences in disease prevalence between individuals of European, Asian, and African ancestry suggest the existence of susceptibility genes that are present at variable frequencies in these populations. Familial forms of IgAN have also been reported throughout the world but are probably underrecognized because associated urinary abnormalities are often intermittent in affected family members. Of the many pathogenic mechanisms reported, defects in IgA1 glycosylation that lead to formation of immune complexes have been consistently demonstrated. Recent data indicates that these IgA1 glycosylation defects are inherited and constitute a heritable risk factor for IgAN. Because of the complex genetic architecture of IgAN, the efforts to map disease susceptibility genes have been difficult, and no causative mutations have yet been identified. Linkage-based approaches have been hindered by disease heterogeneity and lack of a reliable noninvasive diagnostic test for screening family members at risk of IgAN. Many candidate-gene association studies have been published, but most suffer from small sample size and methodological problems, and none of the results have been convincingly validated. New genomic approaches, including genome-wide association studies currently under way, offer promising tools for elucidating the genetic basis of IgAN

Electrical Brain Stimulation During a Retrieval-Based Learning Task Can Impair Long-Term Memory

Anodal transcranial direct current stimulation (tDCS) to the left dorsolateral prefrontal cortex (DLPFC) has been shown to improve performance on a multitude of cognitive tasks. These are, however, often simple tasks, testing only one cognitive domain at a time. Therefore, the efficacy of brain stimulation for complex tasks has yet to be understood. Using a task designed to increase learning efficiency, this study investigates whether anodal tDCS over the left DLPFC can modulate both learning ability and subsequent long-term memory retention. Using a within-subject design, participants (N = 25) took part in 6 training sessions over consecutive days in which active or sham stimulation was administered randomly (3 of each). A computer-based task was used, containing flags from countries unknown to the participants. Each training session consisted of the repetition of 8 pairs of flag/country names. Subsequently, in three testing sessions, free, cued, and timed cued recall, participants were assessed on all 48 flags they had learnt. No difference in learning speed between active and sham tDCS was found. Furthermore, in the timed cued recall phase, flags learnt in the sham tDCS sessions were recalled significantly better than flags learnt in the active tDCS sessions. This effect was stronger in the second testing session. It was also found that for the flags answered incorrectly; thus, meaning they were presented more frequently, subsequent long-term retention was improved. These results suggest that for a complex task, anodal tDCS is ineffective at improving learning speed and potentially detrimental to long-term retention when employed during encoding. This serves to highlight the complex nature of brain stimulation, providing a greater understanding of its limitations and drawbacks

Landslide initiation and runout susceptibility modeling in the context of hill cutting and rapid urbanization: a combined approach of weights of evidence and spatial multi-criteria

Rainfall induced landslides are a common threat to the communities living on dangerous hill-slopes in Chittagong Metropolitan Area, Bangladesh. Extreme population pressure, indiscriminate hill cutting, increased precipitation events due to global warming and associated unplanned urbanization in the hills are exaggerating landslide events. The aim of this article is to prepare a scientifically accurate landslide susceptibility map by combining landslide initiation and runout maps. Land cover, slope, soil permeability, surface geology, precipitation, aspect, and distance to hill cut, road cut, drainage and stream network factor maps were selected by conditional independence test. The locations of 56 landslides were collected by field surveying. A weight of evidence (WoE) method was applied to calculate the positive (presence of landslides) and negative (absence of landslides) factor weights. A combination of analytical hierarchical process (AHP) and fuzzy membership standardization (weighs from 0 to 1) was applied for performing a spatial multi-criteria evaluation. Expert opinion guided the decision rule for AHP. The Flow-R tool that allows modeling landslide runout from the initiation sources was applied. The flow direction was calculated using the modified Holmgren’s algorithm. The AHP landslide initiation and runout susceptibility maps were used to prepare a combined landslide susceptibility map. The relative operating characteristic curve was used for model validation purpose. The accuracy of WoE, AHP, and combined susceptibility map was calculated 96%, 97%, and 98%, respectively

A backward dynamical methodology for estimation of rainfall threshold associated to debris-flow

A novel, dynamical-based method for the determination of the intensity and duration of the rainfall pertaining to a debris-flow event is presented. The method has been used for the determination of a rainfall threshold for a study area