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At least 271 records · Page 15Linked to original sources
PubMed1997

Bacillus subtilis 168 RecR protein-DNA complexes visualized as looped structures.

The Bacillus subtilis 168 RecR protein bound to duplex DNA in the presence of ATP and divalent cations (Mg2+ and Zn2+) was visualized by electron microscopy as a nearly spherical particle. A RecR homomultimer is frequently located at the intersection of two duplex DNA strands in an interwound DNA molecule, generating DNA loops of variable length. Two individual DNA molecules bound to the same protein are seen at a very low frequency, if at all. The association of RecR with the intersection of two duplex DNA strands is more often seen in supercoiled than with relaxed or linear DNA. The RecR protein displays a slight but significant preference for negatively supercoiled over linear DNA. The minimum substrate size for RecR protein is about 150 bp in length. A possible mechanism for RecR function in DNA repair is discussed.

Bacillus subtilis↗
PubMed2004

Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila.

BACKGROUND: The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quantify how comparative genomics can improve computational detection of such modules. RESULTS: We run the Stubb software on the entire D. melanogaster genome, to obtain predictions of modules involved in segmentation of the embryo. Stubb uses a probabilistic model to score sequences for clustering of transcription factor binding sites, and can exploit multiple species data within the same probabilistic framework. The predictions are evaluated using publicly available gene expression data for thousands of genes, after careful manual annotation. We demonstrate that the use of a second genome (D. pseudoobscura) for cross-species comparison significantly improves the prediction accuracy of Stubb, and is a more sensitive approach than intersecting the results of separate runs over the two genomes. The entire list of predictions is made available online. CONCLUSION: Evolutionary conservation of modules serves as a filter to improve their detection in silico. The future availability of additional fruitfly genomes therefore carries the prospect of highly specific genome-wide predictions using Stubb.

Algorithms↗
PubMed2005

Evolutionary innovations in the fossil record: the intersection of ecology, development, and macroevolution.

The origins of evolutionary innovations have been intensively studied, but relatively little is known about their large-scale ecological patterns. For post-Paleozoic benthic marine invertebrates, which have the richest and most densely sampled fossil record, order-level taxa tend to appear first in onshore, disturbed habitats, even in groups that are now exclusively deep-water (so that present-day distributions are not reliable indicators of original environments). New results presented here show that the onshore-origination pattern is robust to shifts in taxonomic methods and to new paleontological discoveries, and the few available studies suggest that this pattern can also be seen in terms of excursions in morphospace or the acquisition of derived character states, without reference to taxonomic categories. The environmental pattern at high levels contrasts significantly with the origin of low-level novelties (such as defined genera and families) in crinoids, echinoids, and bryozoans, where first appearances tend to conform to their clade-specific bathymetric diversity gradients. This discordance seems to eliminate potential driving mechanisms that simply scale up within-population genetic or ecological processes. Little is known about the factors that promote the onshore-offshore expansion of orders across the continental shelf, or that drive some clades to abandon ancestral habitats for an exclusively deep-water distribution. The origin of evolutionary innovation must ultimately reside in developmental changes, but the onshore-origination bias could emerge from two different dynamics: the pattern could be primarily genetic and developmental, i.e., innovations truly arise onshore; or primarily ecological, i.e., innovations arise randomly but preferentially survive onshore. Whatever the ultimate driving mechanisms, these macroevolutionary patterns show that theories of large-scale evolutionary novelty must include an ecological dimension.

Animals↗
PubMed2005

An electrographic analysis of the synchronous discharge patterns of GEPR-9s generalized seizures.

Previous results from our Laboratory have shown a synchronous discharge pattern (less than 1 ms apart) in monopolar recordings from electrodes placed in the cortex, inferior colliculus, and medulla of seizing GEPR-9s. However, the wave morphology of the ictal EEG is quite different for electrodes placed in different anatomical structures. These results lead us to hypothesize that wave morphology was indicative of neural circuitry involved in the GEPR9 seizure and that volume conduction was accounting for synchronous epileptiform EEG pattern. We decided to approach the problem by using a set of two experiments. Experiment 1: Perform a complete precollicular transection in GEPR-9s before inducing seizure in order to observe changes in EEG morphology after forebrain circuitry removal. Experiment 2: A novel methodological approach using a three-dimensional bipolar array enabled the reconstruction of a vector indicative of to which direction is voltage increasing. Such time-varying vector is indicative of the source direction of the high-amplitude epileptiform EEG signal. By placing such an array of electrodes, used to record the 3 bipolar EEGs, in the forebrain, midbrain, and hindbrain, we were able to use a simple intersection method to infer source localization. Our results suggest that the slow wave component of the GEPR9 epileptiform ictal EEG pattern is associated with a midbrain-forebrain circuit while the spike component is associated with a midbrain-hindbrain substrate. These results are supported by experiment 1 in which only the spike component of EEG remained after the precollicular transection.

Action Potentials↗
PubMed2000

Molecular genetics of pattern formation in the inner ear: do compartment boundaries play a role?

The membranous labyrinth of the inner ear establishes a precise geometrical topology so that it may subserve the functions of hearing and balance. How this geometry arises from a simple ectodermal placode is under active investigation. The placode invaginates to form the otic cup, which deepens before pinching off to form the otic vesicle. By the vesicle stage many genes expressed in the developing ear have assumed broad, asymmetrical expression domains. We have been exploring the possibility that these domains may reflect developmental compartments that are instrumental in specifying the location and identity of different parts of the ear. The boundaries between compartments are proposed to be the site of inductive interactions required for this specification. Our work has shown that sensory organs and the endolymphatic duct each arise near the boundaries of broader gene expression domains, lending support to this idea. A further prediction of the model, that the compartment boundaries will also represent lineage-restriction compartments, is supported in part by fate mapping the otic cup. Our data suggest that two lineage-restriction boundaries intersect at the dorsal pole of the otocyst, a convergence that may be critical for the specification of endolymphatic duct outgrowth. We speculate that the patterning information necessary to establish these two orthogonal boundaries may emanate, in part, from the hindbrain. The compartment boundary model of ear development now needs to be tested through a variety of experimental perturbations, such as the removal of boundaries, the generation of ectopic boundaries, and/or changes in compartment identity.

Animals↗
PubMed2002

Genetic analysis of the role of G protein-coupled receptor signaling in electrotaxis.

Cells display chemotaxis and electrotaxis by migrating directionally in gradients of specific chemicals or electrical potential. Chemotaxis in Dictyostelium discoideum is mediated by G protein-coupled receptors. The unique Gbeta is essential for all chemotactic responses, although different chemoattractants use different receptors and Galpha subunits. Dictyostelium amoebae show striking electrotaxis in an applied direct current electric field. Perhaps electrotaxis and chemotaxis share similar signaling mechanisms? Null mutation of Gbeta and cAMP receptor 1 and Galpha2 did not abolish electrotaxis, although Gbeta-null mutations showed suppressed electrotaxis. By contrast, G protein signaling plays an essential role in chemotaxis. G protein-coupled receptor signaling was monitored with PHcrac-green fluorescent protein, which translocates to inositol phospholipids at the leading edge of cells during chemotaxis. There was no intracellular gradient of this protein during electrotaxis. However, F-actin was polymerized at the leading edge of cells during electrotaxis. We conclude that reception and transduction of the electrotaxis signal are largely independent of G protein-coupled receptor signaling and that the pathways driving chemotaxis and electrotaxis intersect downstream of heterotrimeric G proteins to invoke cytoskeletal elements.

Actins↗
PubMed1989

Probabilistic models of genome shuffling.

The comparison of entire genomes in evolutionary studies gives rise to alignments characterized by many intersections, or inversions in the order of two fragments in different genomes. To model this, we suggest a random migration process for fragments, and discuss its equilibrium distribution in the case of linear and circular genomes. Simulations are carried out to explore "cut-off" behavior as the process approaches equilibrium. We define a new process to take into account the indistinguishability of two fragments which are adjacent in both genomes being compared. Questions of applicability of these models are discussed.

Biological Evolution↗
PubMed2005

The vitamin D receptor, Runx2, and the Notch signaling pathway cooperate in the transcriptional regulation of osteopontin.

Osteopontin (OPN), a glycosylated phosphoprotein that binds calcium, is present in bone extracellular matrix and has been reported to modulate both mineralization and bone resorption. Targeted disruption in mice of the vitamin D receptor (VDR) or Runx2 results in marked inhibition of OPN expression in osteoblasts. In this study, we addressed possible cross-talk between VDR and Runx2 in regulating OPN transcription. 1,25-Dihydroxyvitamin D(3) (1,25(OH)(2)D(3)) or Runx2 stimulated OPN transcription (mouse OPN promoter -777/+79) 2-3-fold. However, coexpression of Runx2 and VDR in COS-7 cells and treatment with 1,25(OH)(2)D(3) resulted in an 8-fold induction of OPN transcription, indicating for the first time functional cooperation between Runx2 and VDR in the regulation of OPN transcription. In ROS 17/2.8 and MC3T3-E1 cells that contain endogenous Runx2, AML-1/ETO, which acts as a repressor of Runx2, significantly inhibited 1,25(OH)(2)D(3) induction of OPN transcription, OPN mRNA, and protein expression. Both a Runx2 site (-136/-130) and the vitamin D response element (-757/-743) in the OPN promoter are needed for cooperative activation. Chromatin immunoprecipitation analyses showed that 1,25(OH)(2)D(3) can enhance VDR and Runx2 recruitment on the OPN promoter, further indicating cooperation between these two factors in the regulation of OPN. In osteoblastic cells, Hes-1, a downstream factor of the Notch signaling pathway, was found to enhance basal and 1,25(OH)(2)D(3)-induced OPN transcription. This enhancement was inhibited by AML-1/ETO, an inhibitor of Runx2. Immunoprecipitation assays indicated that Hes-1 and Runx2 interact and that 1,25(OH)(2)D(3) can enhance this interaction. Taken together, these findings define novel mechanisms involving the intersection of three pathways, Runx2, 1,25(OH)(2)D(3), and Notch signaling, that play a major role in the regulation of OPN in osteoblastic cells and therefore in the process of bone remodeling.

Animals↗
PubMed2026

Network-based stratification of allele-specific expression reveals patient subgroups in Huntington's disease.

MOTIVATION: Huntington's disease (HD) exhibits substantial variability in age of onset and disease progression that is not fully explained by CAG repeat length alone. Part of this residual variation is heritable, implicating additional genetic mechanisms. cis-regulatory variation, genetic variants that alter transcription and splicing of nearby genes, represents one such mechanism that can be quantified through allele-specific expression (ASE) analysis. However, methods for integrating ASE profiles into patient stratification frameworks remain underdeveloped, particularly for rare diseases with small cohorts and sparse data. RESULTS: We adapt a network-based stratification algorithm, originally developed for somatic tumour mutations, to ASE data. By propagating gene-level ASE imbalance profiles through a protein-protein interaction network, we stratified 20 HD patients into three distinct biological patient subgroups. Differential gene expression analysis highlights neuroinflammatory pathways, including microglial activation, immune cell activation, and cytokine regulation, as key sources of inter-patient heterogeneity, while differential ASE analysis implicates proteasomal and ubiquitin-dependent protein catabolic processes, immune activation, and central nervous system development. Intersection of differentially imbalanced and expressed genes identified FAM181B as a candidate gene with potential eQTL-mediated regulation, supported by independent cis-eQTL evidence for rs3780 in the caudate and putamen, the primary HD-affected striatal regions. FAM181B encodes a nuclear protein expressed in neural tissues acting as an interactor of the Hippo pathway TEAD transcription factors, implicating transcriptional regulatory variation as a potential contributor to molecular heterogeneity between patient subgroups. Differences in cortical and striatal neuropathological scores between clusters, even when adjusted for CAG repeat length, provide clinical support for the biological relevance of the identified subgroups. AVAILABILITY: All analysis code, Docker containers, and conda environments are available at https://github.com/macsbio/HD-ASE-NBS.

Huntington Disease↗
PubMed2003

Intersection of the Kap123p-mediated nuclear import and ribosome export pathways.

Kap123p is a yeast beta-karyopherin that imports ribosomal proteins into the nucleus prior to their assembly into preribosomal particles. Surprisingly, Kap123p is not essential for growth, under normal conditions. To further explore the role of Kap123p in nucleocytoplasmic transport and ribosome biogenesis, we performed a synthetic fitness screen designed to identify genes that interact with KAP123. Through this analysis we have identified three other karyopherins, Pse1p/Kap121p, Sxm1p/Kap108p, and Nmd5p/Kap119p. We propose that, in the absence of Kap123p, these karyopherins are able to supplant Kap123p's role in import. In addition to the karyopherins, we identified Rai1p, a protein previously implicated in rRNA processing. Rai1p is also not essential, but deletion of the RAI1 gene is deleterious to cell growth and causes defects in rRNA processing, which leads to an imbalance of the 60S/40S ratio and the accumulation of halfmers, 40S subunits assembled on polysomes that are unable to form functional ribosomes. Rai1p localizes predominantly to the nucleus, where it physically interacts with Rat1p and pre-60S ribosomal subunits. Analysis of the rai1/kap123 double mutant strain suggests that the observed genetic interaction results from an inability to efficiently export pre-60S subunits from the nucleus, which arises from a combination of compromised Kap123p-mediated nuclear import of the essential 60S ribosomal subunit export factor, Nmd3p, and a DeltaRAI1-induced decrease in the overall biogenesis efficiency.

Active Transport, Cell Nucleus↗
PubMed2005

X for intersection: retrotransposition both on and off the X chromosome is more frequent.

As the heteromorphic sex chromosomes evolved from a pair of autosomes, the sex chromosomes became increasingly different in gene content and structure from each other and from the autosomes. Although recently there has been progress in documenting and understanding these differences, the molecular mechanisms that have fashioned some of these changes remain unclear. A new study addresses the differential distribution of retroposed genes in human and mouse genomes. Surprisingly, chromosome X is a major source and a preferred target for retrotransposition.

Animals↗
PubMed2004

Continuous cycling of grouped vs. solitary strategy frequencies in a predator-prey model.

We present a model of predator and prey grouping strategies using game theory. As predators respond strategically to prey behavior and vice versa, the model is based on a co-evolution approach. Focusing on the "many eyes-many mouths" trade-off, this model considers the benefits and costs of being in a group for hunting predators and foraging prey: predators in a group have more hunting success than solitary predators but they have to share the prey captured; prey in a group face a lower risk of predation but greater competition for resources than lone prey. The analysis of the model shows that the intersections of four curves define distinct areas in the parameter space, corresponding to different strategies used by predators and prey at equilibrium. The model predictions are in accordance with empirical evidence that an open habitat encourages group living, and that low risks of predation favor lone prey. Under some conditions, continuous cycling of the relative frequencies of the different strategies may occur. In this situation, the proportions of grouped vs. solitary predators and prey oscillate over time.

Animals↗
PubMed2005

Drug-induced torsades de pointes: the evolving role of pharmacogenetics.

Drug-induced torsades de pointes (TdP) is a rare, but potentially lethal, unwanted effect of drugs, including many commonly prescribed noncardiac drugs. Despite its low frequency, drug-induced TdP has generated a great deal of angst among physicians and pharmaceutical companies as well as tragedy, albeit rare, among patients. Although in retrospect many patients who died suddenly as a result of drug-induced TdP had identifiable risk factors, prediction in individual cases remains problematic. Over the past decade, tremendous progress has been made with respect to elucidating the fundamental pathogenic mechanisms that underlie drug-induced TdP. The vast majority of drugs associated with "QT liability" and the potential for drug-induced TdP, including all of the drugs removed from the market because of this side effect, are "HERG (human ether-á-go-go-related gene) blockers." These drugs inhibit the KCNH2-encoded HERG potassium channel, which is one of the critical repolarizing forces involved in the exquisite orchestration of the heart's action potential. Consequently, myocyte repolarization is potentially delayed as evidenced by prolongation of the QT interval, thus providing the substrate for drug-induced TdP. Rare mutations in KCNH2 provide the pathogenic substrate for type 2 congenital long QT syndrome (LQTS), thus placing this cardiac potassium channel squarely in the intersection between congenital LQTS (the "Rosetta stone" of the heritable channelopathies) and acquired LQTS (drug-induced TdP). In addition, common polymorphisms residing in the LQTS-causing channel genes may confer heightened arrhythmogenic susceptibility and contribute to the makings of a vulnerable host. This review focuses on the present strategy of identifying "at-risk compounds" and the potential future strategy involving pharmacogenetics to pinpoint "at-risk hosts" in an effort to curb this rare, unintended, but potentially life-threatening side effect.

Antihypertensive Agents↗
PubMed2001

Gender, body, biomedicine: how some feminist concerns dragged reproduction to the center of social theory.

This article tracks the growth of medical anthropology in the United States in the decades since the 1970s, as it has intersected the expansion of feminist activism and scholarship. I argue that feminist attention to embodied inequalities quickly focused on reproduction as a site of investigation and intervention. Medical anthropology has benefited from feminist concern with stratified reproduction, especially its interrogation of nonnormative and stigmatized fertility and childbearing. When reproduction becomes problematic, it provides a lens through which cultural norms, struggles, and transformations can be viewed. Examples drawn from prenatal diagnosis are particularly revelatory of the diverse interests and stakes we all hold in reproduction.

Achondroplasia↗
PubMed2005

Glucocorticoid receptor-dependent gene regulatory networks.

While the molecular mechanisms of glucocorticoid regulation of transcription have been studied in detail, the global networks regulated by the glucocorticoid receptor (GR) remain unknown. To address this question, we performed an orthogonal analysis to identify direct targets of the GR. First, we analyzed the expression profile of mouse livers in the presence or absence of exogenous glucocorticoid, resulting in over 1,300 differentially expressed genes. We then executed genome-wide location analysis on chromatin from the same livers, identifying more than 300 promoters that are bound by the GR. Intersecting the two lists yielded 53 genes whose expression is functionally dependent upon the ligand-bound GR. Further network and sequence analysis of the functional targets enabled us to suggest interactions between the GR and other transcription factors at specific target genes. Together, our results further our understanding of the GR and its targets, and provide the basis for more targeted glucocorticoid therapies.

Animals↗
PubMed2003

Prostaglandin F2(alpha) stimulates growth of skeletal muscle cells via an NFATC2-dependent pathway.

Skeletal muscle growth requires multiple steps to form large multinucleated muscle cells. Molecules that stimulate muscle growth may be therapeutic for muscle loss associated with aging, injury, or disease. However, few factors are known to increase muscle cell size. We demonstrate that prostaglandin F2alpha (PGF2alpha) as well as two analogues augment muscle cell size in vitro. This increased myotube size is not due to PGF2alpha-enhancing cell fusion that initially forms myotubes, but rather to PGF2alpha recruiting the fusion of cells with preexisting multinucleated cells. This growth is mediated through the PGF2alpha receptor (FP receptor). As the FP receptor can increase levels of intracellular calcium, the involvement of the calcium-regulated transcription factor nuclear factor of activated T cells (NFAT) in mediating PGF2alpha-enhanced cell growth was examined. We show that NFAT is activated by PGF2alpha, and the isoform NFATC2 is required for PGF2alpha-induced muscle cell growth and nuclear accretion, demonstrating the first intersection between prostaglandin receptor activation and NFAT signaling. Given this novel role for PGF2alpha in skeletal muscle cell growth, these studies raise caution that extended use of drugs that inhibit PG production, such as nonsteroidal antiinflammatory drugs, may be deleterious for muscle growth.

Active Transport, Cell Nucleus↗
PubMed2006

Hypothesis testing approaches to the exon prediction problem.

MOTIVATION: Many gene identification methods assign scores to gene elements prior to their assembly into predicted genes. The scoring system is often based on log-likelihood ratios. These methods usually perform well but it is difficult to interpret how significant a score is. RESULTS: We have developed several tests of significance for the scores: (1) a sum-of-scores test (SST), (2) an intersection-union test (IUT), based on a multiple hypothesis testing interpretation of an exon's score and (3) a meta-analytical approach (MA), which combines several P-values, corresponding to the exon's parts, to yield a global P-value. We performed simulation studies, which show that the MA has better sensitivity and specificity than other methods and is easier to interpret by non-expert users. This is an improvement over other methods and is especially relevant for users who would like to predict incomplete gene sequences.

Algorithms↗
PubMed1998

Genetic analysis of iron uptake in the yeast Saccharomyces cerevisiae.

OBJECTIVE: We used the methods of yeast genetics to identify genes involved in acquisition of iron by eukaryotic cells. METHODS: Mutants were identified with defects in cellular iron uptake. These were organized into an upstream group and a downstream group. The upstream group was involved in the delivery of copper to the multicopper oxidase FET3. Mutants of this group were characterized by defective iron uptake that could be corrected by exposure of the cells to large amounts of copper. The downstream group was more directly involved in iron uptake. Mutant phenotypes from these genes could not be corrected by copper exposure. RESULTS: Genes in the upstream group encoded the regulator of copper transport, MAC1, and two copper transporters, CTR1 and CCC2. Genes in the downstream group encoded the multicopper oxidase FET3 and its partner the iron permease FTR1. In addition, the downstream genes encoded the surface reductases FRE1 and FRE2 and the iron regulatory protein AFT1. CONCLUSIONS: The iron and copper uptake processes in yeast intersect because the FET3 gene encodes a multicopper oxidase that is required for iron transport. In human beings, an analogous function may be served by ceruloplasmin, a multicopper oxidase with a role in iron homeostasis.

Ceruloplasmin↗