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Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model.

The transformation between a gel and a fluid phase in dipalmitoyl-phosphatidylcholine (DPPC) bilayers has been simulated using a coarse grained (CG) model by cooling bilayer patches composed of up to 8000 lipids. The critical step in the transformation process is the nucleation of a gel cluster consisting of 20-80 lipids, spanning both monolayers. After the formation of the critical cluster, a fast growth regime is entered. Growth slows when multiple gel domains start interacting, forming a percolating network. Long-lived fluid domains remain trapped and can be metastable on a microsecond time scale. From the temperature dependence of the rate of cluster growth, the line tension of the fluid-gel interface was estimated to be 3+/-2 pN. The reverse process is observed when heating the gel phase. No evidence is found for a hexatic phase as an intermediate stage of melting. The hysteresis observed in the freezing and melting transformation is found to depend both on the system size and on the time scale of the simulation. Extrapolating to macroscopic length and time scales, the transition temperature for heating and cooling converges to 295+/-5 K, in semi-quantitative agreement with the experimental value for DPPC (315 K). The phase transformation is associated with a drop in lateral mobility of the lipids by two orders of magnitude, and an increase in the rotational correlation time of the same order of magnitude. The lipid headgroups, however, remain fluid. These observations are in agreement with experimental findings, and show that the nature of the ordered phase obtained with the CG model is indeed a gel rather than a crystalline phase. Simulations performed at different levels of hydration furthermore show that the gel phase is stabilized at low hydration. A simulation of a small DPPC vesicle reveals that curvature has the opposite effect.

1,2-Dipalmitoylphosphatidylcholine↗

Familial clusters of nasopharyngeal carcinoma and salivary gland carcinomas in Greenland natives.

BACKGROUND: Nasopharyngeal carcinoma (NPC) and anaplastic salivary gland carcinoma (SGC), both associated with Epstein-Barr virus (EBV), are common among Inuit from Greenland, Canada, and Alaska. Because immigrant studies have shown that factors acting early in life are important for the development of NPC, the authors interviewed new patients in Greenland with either NPC or SGC about their lifestyles during childhood and additional cases in their families. METHODS: On admission, new patients from Greenland with either NPC or SGC were interviewed about childhood life-style, family size, and other cases of NPC or SGC within the family. Additional cases were confirmed by review of the medical records concerning these patients. RESULTS: During the 11 years from 1980 through 1990, 17 of 63 (27%) cases in Greenland were found in familial clusters among first-degree relatives. There were no differences in the life-styles of multiple-case families and single-case families. CONCLUSIONS: The high rate of familial clusters among natives of Greenland is of interest because EBV is believed to play a role in the origin of these two diseases similar to that of Marek disease in neurolymphomatosis of chickens. Therefore, the familial clustering of NPC and SGC may indicate that an enhanced oncogenic potential of an EBV strain may occur more frequently in Greenland than in other parts of the world.

Adolescent↗

Functions of mitochondrial ISCU and cytosolic ISCU in mammalian iron-sulfur cluster biogenesis and iron homeostasis.

Iron-sulfur (Fe-S) clusters are required for the functions of mitochondrial aconitase, mammalian iron regulatory protein 1, and many other proteins in multiple subcellular compartments. Recent studies in Saccharomyces cerevisiae indicated that Fe-S cluster biogenesis also has an important role in mitochondrial iron homeostasis. Here we report the functional analysis of the mitochondrial and cytosolic isoforms of the human Fe-S cluster scaffold protein, ISCU. Suppression of human ISCU by RNAi not only inactivated mitochondrial and cytosolic aconitases in a compartment-specific manner but also inappropriately activated the iron regulatory proteins and disrupted intracellular iron homeostasis. Furthermore, endogenous ISCU levels were suppressed by iron deprivation. These results provide evidence for a coordinated response to iron deficiency that includes activation of iron uptake, redistribution of intracellular iron, and decreased utilization of iron in Fe-S proteins.

Aconitate Hydratase↗

Prophylaxis of migraine, transformed migraine, and cluster headache with topiramate.

OBJECTIVE: To assess the efficacy and tolerability of topiramate for prophylaxis of migraine and cluster headache via a retrospective chart analysis. BACKGROUND: Topiramate has multiple mechanisms of action that could potentially contribute to migraine prophylaxis. We conducted a retrospective chart review to assess the efficacy of topiramate as add-on therapy in patients with transformed migraine or cluster headache, and as first-line therapy in patients with episodic migraine. METHODS: Patients diagnosed with transformed migraine, episodic migraine, or cluster headache, who received topiramate either as add-on therapy or monotherapy were selected via retrospective chart review. Patients had begun topiramate therapy at 25 mg/day for the first week and increased their dosage by 25 mg/week to a maximum of 200 mg/day. Topiramate was used as add-on therapy for patients with transformed migraine and cluster headache, and as a first-line monotherapy in patients with episodic migraine who had no previous prophylactic therapy. The outcome parameters examined included a mean 28-day migraine frequency, migraine severity, number of headache days/month, number of abortive medication tablets/month, patient global evaluation, and the MIDAS scale. RESULTS: One hundred seventy-eight patients (transformed migraine: n = 96; episodic migraine: n = 70; and cluster headache: n = 12) were included in the retrospective analysis. The mean dose of topiramate for all patients was 87.5 mg/day. For patients with transformed migraine, mean migraine frequency decreased from 6.3/28 days to 3.7 (P = 0.005). Mean severity decreased from 7.1 to 3.8 on a 10-point scale, with 10 representing the most severe pain (P = 0.003). The mean number of headache days/month decreased from 22.1 to 9.6 (P = 0.001), and the mean number of abortive medication tablets decreased from 28.7/month to 10.6 (P = 0.001). Patient global evaluation indicated substantial or moderate improvement in 53% of patients with transformed migraine who used topiramate as add-on therapy. Mean MIDAS scale values decreased from 90.2 to 24.9 (P< 0.0001). The 70 episodic migraine patients who were administered topiramate as first-line therapy exhibited a decrease in mean migraine frequency (5.8/28 days to 1.9, P = 0.001), while mean migraine severity decreased from 8.1 to 2.0 (P = 0.003). Sixty-one percent of patients reported marked improvement. Nine of the 12 cluster headache patients exhibited substantial or moderate improvement in symptoms, whereas three had no improvement. The most common adverse effects were paresthesias (12%), cognitive effects (11%), and dizziness (6%). Eight patients discontinued topiramate due to adverse effects; cognitive effects were the most common reason. No patient discontinued topiramate treatment due to lack of efficacy. Twelve percent of patients lost more than 5 lbs during treatment (a range of 5-120 lbs). CONCLUSION: For both patients with transformed migraine (add-on therapy) and patients with episodic migraine (first-line monotherapy), topiramate yielded significant reductions in migraine frequency, migraine severity, number of headache days/month, and use of abortive medications. Topiramate also appears to be well tolerated and useful in the adjunctive treatment of cluster headache. Prospective double-blind, placebo-controlled trials will be required to confirm our results.

Adult↗

Receptor cluster formation during activation by bacterial products.

The recognition of bacterial products, such as lipopolysaccharide (LPS) by the innate immune system lead to a strong pro-inflammatory response that can eventually lead to fatal sepsis syndrome in humans. Although CD14 and TLR4 have been identified as the key molecules involved in LPS-induced signal transduction, accumulating evidence indicates that multiple receptors are also involved. Our group has recently identified a cluster of receptors, involving heat-shock proteins 70 and 90, chemokine receptor 4 as well as growth differentiation factor 5, that are formed following LPS stimulation. In addition, we present data demonstrating that these molecules associate with TLR4 and accumulate in membrane microdomains following LPS ligation. Our results suggest that the entire bacterial recognition is based around the recruitment of multiple signalling molecules, in addition to CD14 and TLRs, within the lipid rafts. We propose that different combinational associations of receptors within activation clusters determine the different responses to a variety of bacterial stimuli.

Animals↗

Organization and synaptic relationships of the projection from the primary sensory to the primary motor cortex in the cat.

It is known from previous studies that fibers originating from cells in area 2 of the cat primary somatosensory cortex project topographically to area 4 of the motor cortex and that they terminate preferentially in the caudal region of the cruciate sulcus. We examined this pathway to determine more precisely the distribution pattern of fibers and the laminar arrangement of axon terminals in the motor cortex. The recently developed technique of PHA-L staining enabled us to label anterogradely the axons that form this projection. Iontophoretic injections of PHA-L were made into the rostral bank of the ansate sulcus (area 2). After 7 days the cats were perfused and the tissue was processed immunohistochemically to stain the PHA-L filled fibers. Light microscopic examination revealed that a small cluster of cells in the sensory cortex gave rise to multiple foci of labeled axons in area 4. The labeled fibers formed columnlike arrays, which were located for the most part in the posterior bank of the cruciate sulcus and were separated by irregular intervals of cortex devoid of labeled fibers. Clusters of labeled fibers were also found in the anterior region of the cruciate sulcus in some of the animals. The dimensions of the labeled areas and the small number of cells that gave rise to each group of fibers suggested that axonal branches of cells within the injection site formed the multiple foci. Variations in the immunohistochemical staining enabled us to study the laminar distribution of sensory cortex axon terminals with the electron microscope. Whereas some PHA-L labeled terminals were found in the deep cortical layers, the majority (82%) were spread throughout layers I-III. Differences in the laminar distribution of sensory cortex afferents that formed axodendritic or axospinous synapses were noted. Synapses formed with dendritic shafts were relatively sparse (28%) and were confined to the superficial layers. Some of the more numerous axospinous synapses, which accounted for 72% of identified synapses, were found in layers V and VI, although most were in layers I-III. The distribution pattern of terminals showed little variation between columns in different areas of the motor cortex, including that in the anterior cruciate region. The pattern of termination of the sensory to motor cortex projection is discussed in relation to the physiological characteristics of this pathway.

Animals↗

Terminal arbors of individual "feedback" axons projecting from area V2 to V1 in the macaque monkey: a study using immunohistochemistry of anterogradely transported Phaseolus vulgaris-leucoagglutinin.

In the present study, the anterograde tracer Phaseolus vulgaris-leucoagglutinin (PHA-L) was injected into area V2 in order to demonstrate the precise morphology of individual axons from area V2 to V1. On the basis of 28 complete axon reconstructions, several characteristic features have been identified. 1) Individual axons arborize in multiple layers: 1, 2, 5, and (inconstantly) 3. A single axon may have numerous terminal clusters in layers 1 and 2, but at most one in layer 3. 2) Axons typically ascend to layer 1, turn asymmetrically in one direction, and travel for long distances in this layer (1.10-4.30 mm; dimensions uncorrected for shrinkage). A few axons (three of 28 reconstructed) were found to have a single terminal cluster (0.3-0.5 mm wide) in layers 1 and 2. 3) Collaterals in layer 5 seem to extend over shorter distances (0.60 mm or less). 4) Delicate sprays of boutons (both beads and spines) are clustered along the main trunk. Spacing is variable but usually ranges from 0.35 mm to 0.65 mm. 5) In addition to clustered boutons, there can be linear collaterals, continuously studded with boutons, parallel to the main axon in layer 1. These results indicate that axons from V2 have complex radial and tangential distributions in V1. Terminations in different layers may be directed to different sets of neurons or to different portions of the dendritic tree (for example, distal portions of pyramidal neuron apical dendrites in layers 1 and 2, but more proximal portions in layer 3). Clustered terminations over wide tangential areas may imply a divergent innervation by a single axon of multiple compartmental structures, such as ocular dominance columns or cytochrome oxidase patches.

Animals↗

A novel mechanism of carbohydrate recognition by the C-type lectins DC-SIGN and DC-SIGNR. Subunit organization and binding to multivalent ligands.

DC-SIGN and DC-SIGNR are cell-surface receptors that mediate cell-cell interactions within the immune system by binding to intercellular adhesion molecule-3. The receptor polypeptides share 77% amino acid sequence identity and are type II transmembrane proteins. The extracellular domain of each comprises seven 23-residue tandem repeats and a C-terminal C-type carbohydrate-recognition domain (CRD). Cross-linking, equilibrium ultracentrifugation, and circular dichroism studies of soluble recombinant fragments of DC-SIGN and DC-SIGNR have been used to show that the extracellular domain of each receptor is a tetramer stabilized by an alpha-helical stalk. Both DC-SIGN and DC-SIGNR bind ligands bearing mannose and related sugars through the CRDs. The CRDs of DC-SIGN and DC-SIGNR bind Man(9)GlcNAc(2) oligosaccharide 130- and 17-fold more tightly than mannose, and affinity for a glycopeptide bearing two such oligosaccharides is increased by a further factor of 5- to 25-fold. These results indicate that the CRDs contain extended or secondary oligosaccharide binding sites that accommodate mammalian-type glycan structures. When the CRDs are clustered in the tetrameric extracellular domain, their arrangement provides a means of amplifying specificity for multiple glycans on host molecules targeted by DC-SIGN and DC-SIGNR. Binding to clustered oligosaccharides may also explain the interaction of these receptors with the gp120 envelope protein of human immunodeficiency virus-1, which contributes to virus infection.

Amino Acid Sequence↗

Genetic association study between senile dementia of Alzheimer's type and APOE/C1/C2 gene cluster.

Senile dementia of Alzheimer's type (SDAT) is characterized by progressive deficits of multiple cognitive functions in elderly more than 65 years of age. The APOE-epsilon 4 allele has been shown to be a risk factor for SDAT. To investigate the genetic interactions between SDAT and the APOE/APOC1/APOC2 gene cluster located at 19q13.2, we genotyped these genes in patients with SDAT and nondemented controls. Although allelic associations were found between the APOC1 locus and SDAT (p = 0.0022) as well as between the APOE locus and SDAT (p < 0.0001), no associations were detected between the APOC2 locus and SDAT. And the association between the APOE and APOC1 locus in SDAT was statistically more significant than that in controls (p < 0.001). Estimation of the haplotype frequencies indicated that the association between the APOE/APOC1 haplotype and SDAT was more significant than linkage disequilibrium between the APOE and APOC1 locus (p < 0.01). These results suggest that genetic interaction between the APOE and APOC1 gene could modify a risk factor of APOE-epsilon 4 for SDAT. The APOE/APOC1 locus was estimated to be responsible for 54.8% of SDAT in the Japanese population.

Aged↗

A cluster of Drosophila homeobox genes involved in mesoderm differentiation programs.

Although genes involved in common developmental programs are usually scattered throughout the metazoan genome, there are some important examples of functionally interconnected regulatory genes that display close physical linkage. In particular the homeotic genes, which determine the identities of body parts, are clustered in the Hox complexes and clustering is thought to be crucial for the proper execution of their developmental programs. Here we describe the organization and functional properties of a more recently identified cluster of six homeobox genes at 93DE on the third chromosome of Drosophila. These genes, which include tinman, bagpipe, ladybird early, ladybird late, C15, and slouch, all participate in mesodermal patterning and differentiation programs and show multiple regulatory interactions among each other. We propose that their clustering, through unknown mechanisms, is functionally significant and discuss the similarities and differences between the 93DE homeobox gene cluster and the Hox complexes.

Amino Acid Sequence↗

Documenting patterns of nursing interventions using cluster analysis.

Use of inferential statistics in research applications of the Nursing Intervention Classification has been rare, yet use of these statistical techniques is needed to answer questions related to intervention patterns. Using data from a descriptive study of 3,733 visits documented by 19 adult nurse practitioner students, hierarchical agglomerative cluster analysis was used to determine whether meaningful nursing intervention patterns could be depicted. Eight intervention clusters were derived, replicated, and validated. Clusters of intervention classes differed in the type of nursing and medical diagnosis, amount of time the nurse spent during the visit, cost of visit, and the age of the patient. Clustering supported the utility of standardized nursing diagnosis and intervention typologies to identify actual practice patterns of adult nurse practitioner students. Cluster analysis is a valuable data analysis strategy when analyzing multiple related variables.

Adolescent↗

Phenotypic and genotypic characterization of two penicillin-susceptible serotype 6B Streptococcus pneumoniae clones circulating in Italy.

Twenty-nine penicillin-susceptible serotype 6B strains isolated from patients with invasive diseases and from healthy carriers were examined by different genotyping methods. Ten groups were identified on the basis of the pulsed-field gel electrophoresis (PFGE) profiles, and two of these contained multiple isolates and were analyzed further. PFGE group 1 comprised 12 isolates, the majority of which had a multiresistant phenotype (resistance to erythromycin, clindamycin, tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole), corresponding to that of a clone previously described in the Mediterranean area and related to penicillin-resistant clone Spain(6B)-2. The pbp2b, pbp2x, dhf, and pspA genes of the isolates had identical restriction profiles; and the partial sequence of pspA was identical to that of clone Spain(6B)-2. In all isolates the resistance determinants erm(B) and tet(M) were inserted in a Tn1545-like element; 11 isolates carried cat as part of the integrated plasmid pC194. Multilocus sequence typing (MLST) performed with two isolates confirmed that their profiles corresponded to that of the Mediterranean clone. PFGE group 2 comprised nine strains, of which the majority showed no antibiotic resistance. Their pspA profiles were different, and the partial sequences obtained for two representative isolates indicated the presence of PspA proteins of different clades. The MLST profile of one strain was identical to that of a serotype 6B strain from the United Kingdom, while two other isolates were novel one-allele variants. This clone appears to be related (five of seven identical alleles) to two other internationally disseminated clones, Hungary(19A)-6 and Poland(23F)-16, both of which are penicillin resistant. The presence of antibiotic-susceptible isolates of this clone suggests that traits other than antibiotic resistance can make a clone successful.

Adult↗

A hierarchical clustering algorithm for MIMD architecture.

Hierarchical clustering is the most often used method for grouping similar patterns of gene expression data. A fundamental problem with existing implementations of this clustering method is the inability to handle large data sets within a reasonable time and memory resources. We propose a parallelized algorithm of hierarchical clustering to solve this problem. Our implementation on a multiple instruction multiple data (MIMD) architecture shows considerable reduction in computational time and inter-node communication overhead, especially for large data sets. We use the standard message passing library, message passing interface (MPI) for any MIMD systems.

Algorithms↗

An experimental analysis of treatment effects on consonant clusters and ambisyllabic consonants in two adults with developmental phonological problems.

The effect of treatment on errors in consonant clusters and in ambisyllabic consonants were investigated in two adults with histories of developmental phonological problems. Using a multiple baseline across behaviors, ambisyllabic consonant errors were treated in bisyllabic words and consonant cluster errors were treated in two different cluster classes. Results indicated that treatment, consisting of a sound-referenced rebus approach, affected change in production of trained words as well as generalization to untrained words for targeted behaviors.

Adult↗

Prostaglandin analog mechanisms are not effective in refractory chronic cluster headache.

Prostaglandin E analogs have been shown to be effective in the treatment of refractory trigeminal neuralgia in patients with multiple sclerosis. Prostaglandin E inhibits the functions of T lymphocytes which are involved in the pathophysiology of cluster headache. Therefore, a double-blind, placebo-controlled, crossover study on the efficacy of misoprostol in chronic refractory cluster headache was performed. Eight patients were treated with 600 micrograms misoprostol and with placebo for a 2-week period. No differences in attack frequency, intensity, global impression, and side effects could be detected, suggesting that prostaglandin E analogs are not effective in the treatment of chronic cluster headache.

Adult↗

highSpaClone enables copy number alteration inference and tumor subclone analysis for high-resolution spatial transcriptomics.

High-resolution spatially resolved transcriptomics (SRT) offers unprecedented opportunities to investigate tumor heterogeneity but poses substantial computational and analytical challenges. Here, we present highSpaClone, a computational framework for copy number alteration (CNA) inference and tumor subclone identification from high-resolution SRT data across multiple spatial scales. By integrating spatial constraints into CNA estimation and clonal clustering, highSpaClone enables neighboring spatial locations to share information, thereby improving the robustness of genomic signals and the accuracy of subclone delineation. Across multiple Xenium and Visium HD datasets, highSpaClone revealed unique transcriptional programs, clonal evolutionary trajectories, and distinct tumor-microenvironment interactions. Furthermore, in human colorectal cancer samples, highSpaClone detected CNA events in histologically normal epithelial regions, highlighting early genomic alterations associated with field cancerization. These findings establish highSpaClone as a scalable framework for studying clonal architecture and tumor evolution.

CP: cancer biology↗

Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation.

BACKGROUND: Activation of naïve B lymphocytes by extracellular ligands, e.g. antigen, lipopolysaccharide (LPS) and CD40 ligand, induces a combination of common and ligand-specific phenotypic changes through complex signal transduction pathways. For example, although all three of these ligands induce proliferation, only stimulation through the B cell antigen receptor (BCR) induces apoptosis in resting splenic B cells. In order to define the common and unique biological responses to ligand stimulation, we compared the gene expression changes induced in normal primary B cells by a panel of ligands using cDNA microarrays and a statistical approach, CLASSIFI (Cluster Assignment for Biological Inference), which identifies significant co-clustering of genes with similar Gene Ontology annotation. RESULTS: CLASSIFI analysis revealed an overrepresentation of genes involved in ion and vesicle transport, including multiple components of the proton pump, in the BCR-specific gene cluster, suggesting that activation of antigen processing and presentation pathways is a major biological response to antigen receptor stimulation. Proton pump components that were not included in the initial microarray data set were also upregulated in response to BCR stimulation in follow up experiments. MHC Class II expression was found to be maintained specifically in response to BCR stimulation. Furthermore, ligand-specific internalization of the BCR, a first step in B cell antigen processing and presentation, was demonstrated. CONCLUSION: These observations provide experimental validation of the computational approach implemented in CLASSIFI, demonstrating that CLASSIFI-based gene expression cluster analysis is an effective data mining tool to identify biological processes that correlate with the experimental conditional variables. Furthermore, this analysis has identified at least thirty-eight candidate components of the B cell antigen processing and presentation pathway and sets the stage for future studies focused on a better understanding of the components involved in and unique to B cell antigen processing and presentation.

Algorithms↗

Where and when do somatic mtDNA mutations occur?

It is generally assumed that somatic mtDNA mutations are originally created in the cells where these mutations are currently found. Accumulating data indicate, however, that cells with a particular mtDNA mutation tend to "cluster," that is, occur repeatedly within a given sample, but not in the others. Clusters likely are clonal, which implies that mtDNA mutations do not originate in the cells that currently carry them, but rather in those cells' progenitors, such as stem or satellite cells, or even earlier in the development. Importantly, a majority of mtDNA mutations appear to belong to such clusters, and thus mutational events in progenitor cells may be one of the major sources of mtDNA mutations in healthy aging tissue. More research including the analysis of multiple samples per individual is needed to confirm the existence of clustering and to distinguish between the possible clustering mechanisms.

Aging↗