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At least 487 records · Page 27Linked to original sources
PubMed2002

Evidence for a susceptibility gene (SLEH1) on chromosome 11q14 for systemic lupus erythematosus (SLE) families with hemolytic anemia.

Hemolytic anemia is a forme fruste of systemic lupus erythematosus (SLE), being observed months or even years before the onset of other clinical manifestations in some patients. We hypothesized that hemolytic anemia in those SLE-affected patients would identify a group of SLE pedigrees that share a high degree of genetic homogeneity. From 160 multiplex SLE pedigrees, we sought evidence for linkage in 35 (16 African-American, 17 European-American, and 2 Hispanic) who had at least one SLE-affected patient with hemolytic anemia. Significant linkage was present at 11q14 in the 16 African-American pedigrees, yielding a maximum two-point logarithm of odds (LOD) score of 4.5 at D11S2002. The segregation pattern of SLE in these African-American pedigrees suggested a dominant mode of inheritance and, when maximized across penetrance and disease allele frequencies, produced a multipoint LOD of 4.7. Multipoint analysis yielded a multipoint heterogeneity LOD score of 3.6 (alpha = 0.63), again with maximum LOD at D11S2002. Finally, markers typed 7 centimorgans to either side of D11S2002 achieved LOD scores of 3 or better by using the maximized model, supporting linkage to 11q14. Clearly, pedigree ascertainment based on select clinical manifestations is an important tool, capable of revealing otherwise cryptic genetic linkages in complex genetic diseases. Thus, we show strong evidence for an SLE susceptibility gene, SLEH1, near D11S2002 in African-American pedigrees multiplex for SLE that have at least one SLE-affected patient with hemolytic anemia.

Anemia, Hemolytic↗
PubMed2004

Structure of the regulatory subunit of CK2 in the presence of a p21WAF1 peptide demonstrates flexibility of the acidic loop.

A truncated form of the regulatory subunit of the protein kinase CK2beta (residues 1-178) has been crystallized in the presence of a fragment of the cyclin-dependent kinase inhibitor p21WAF1 (residues 46-65) and the structure solved at 2.9 A resolution by molecular replacement. The core of the CK2beta dimer shows a high structural similarity with that identified in previous structural analyses of the dimer and the holoenzyme. However, the electron density corresponding to the substrate-binding acidic loop (residues 55-64) indicates two conformations that differ from that of the holoenzyme structure [Niefind et al. (2001), EMBO J. 20, 5320-5331]. Difference electron density near the dimerization region in each of the eight protomers in the asymmetric unit is attributed to between one and eight amino-acid residues of a complexed fragment of p21WAF1. This binding site corresponds to the solvent-accessible part of the conserved zinc-finger motif.

Amino Acid Motifs↗
PubMed2004

Biophysical characterization of the interaction of Limulus polyphemus endotoxin neutralizing protein with lipopolysaccharide.

Endotoxin-neutralizing protein (ENP) of the horseshoe crab is one of the most potent neutralizers of endotoxins [bacterial lipopolysaccharide (LPS)]. Here, we report on the interaction of LPS with recombinant ENP using a variety of physical and biological techniques. In biological assays (Limulus amebocyte lysate and tumour necrosis factor-alpha induction in human mononuclear cells), ENP causes a strong reduction of the immunostimulatory ability of LPS in a dose-dependent manner. Concomitantly, the accessible negative surface charges of LPS and lipid A (zeta potential) are neutralized and even converted into positive values. The gel to liquid crystalline phase transitions of LPS and lipid A shift to higher temperatures indicative of a rigidification of the acyl chains, however, the only slight enhancement of the transition enthalpy indicates that the hydrophobic moiety is not strongly disturbed. The aggregate structure of lipid A is converted from a cubic into a multilamellar phase upon ENP binding, whereas the secondary structure of ENP does not change due to the interaction with LPS. ENP contains a hydrophobic binding site to which the dye 1-anilino-8-sulfonic acid binds at a K(d) of 19 micro m, which is displaced by LPS. Because lipopolysaccharide-binding protein (LBP) is not able to bind to LPS when ENP and LPS are preincubated, tight binding of ENP to LPS can be deduced with a K(d) in the low nonomolar range. Importantly, ENP is able to incorporate by itself into target phospholipid liposomes, and is also able to mediate the intercalation of LPS into the liposomes thus acting as a transport protein in a manner similar to LBP. Thus, LPS-ENP complexes might enter target membranes of immunocompetent cells, but are not able to activate due to the ability of ENP to change LPS aggregates from an active into an inactive form.

Animals↗
PubMed2003

Identification by subtractive hybridization of a novel insertion element specific for two widespread Burkholderia cepacia genomovar III strains.

Species of the Burkholderia cepacia complex cause chronic and life-threatening infections in persons with cystic fibrosis. Epidemic strains infect multiple patients, reside primarily in genomovar III, and have an apparent enhanced capacity for human infection and/or interpatient transmission. By using subtractive hybridization, a novel insertion element, designated IS1363, was identified in epidemic strain PHDC, known to infect many cystic fibrosis patients in the mid-Atlantic region of the United States. IS1363 was also found in most isolates of the ET12 lineage, responsible for infecting large numbers of patients in Ontario, Canada, and the United Kingdom. Southern blot analysis demonstrated that whereas multiple copies of IS1363 were present in strain PHDC, only one copy was present in ET12 isolates. IS1363 was used to probe a collection of 943 B. cepacia complex isolates, representing all nine genomovars, recovered from 761 cystic fibrosis patients or the natural environment. IS1363 was not found in other genomovar III strains and, with the exception of B. ambifaria, was absent from other B. cepacia complex species. Genotyping analyses of all IS1363-positive isolates demonstrated that strain PHDC was more widely distributed in the United States than previously appreciated; 212 cystic fibrosis patients in 24 states were identified as being infected with PHDC.

Bacterial Typing Techniques↗
PubMed2003

Dynamic properties of nucleosomes during thermal and ATP-driven mobilization.

The fundamental subunit of chromatin, the nucleosome, is not a static entity but can move along DNA via either thermal or enzyme-driven movements. Here we have monitored the movements of nucleosomes following deposition at well-defined locations on mouse mammary tumor virus promoter DNA. We found that the sites to which nucleosomes are deposited during chromatin assembly differ from those favored during thermal equilibration. Taking advantage of this, we were able to track the movement of nucleosomes over 156 bp and found that this proceeds via intermediate positions spaced between 46 and 62 bp. The remodeling enzyme ISWI was found to direct the movement of nucleosomes to sites related to those observed during thermal mobilization. In contrast, nucleosome mobilization driven by the SWI/SNF and RSC complexes were found to drive nucleosomes towards sites up to 51 bp beyond DNA ends, with little respect for the sites favored during thermal repositioning. The dynamic properties of nucleosomes we describe are likely to influence their role in gene regulation.

Adenosine Triphosphatases↗
PubMed2005

Human dicer: purification, properties, and interaction with PAZ PIWI domain proteins.

Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21-nt small interfering RNAs (siRNAs) during RNA interference and excises microRNAs (miRNAs) from precursor hairpins. PAZ and PIWI domain (PPD) proteins, also involved in RNAi and miRNA function, are the best-characterized proteins known to interact with Dicer. PPD proteins are the core constituents of effector complexes, RISCs and miRNPs, mediating siRNA and miRNA function. In this chapter we describe overexpression and purification of recombinant human Dicer, its biochemical properties, and mapping of domains responsible for Dicer-PPD protein interactions.

Amino Acid Sequence↗
PubMed2005

Insertion of acrylonitrile into palladium methyl bonds in neutral and anionic Pd(II) complexes.

The reactions of a series of Pd(II) methyl compounds of general formula LPd(NCCH(3))CH(3), where L is a bulky phenoxydiazene or phenoxyaldimine ligand with the polar olefin acrylonitrile (AN), are reported. The compounds react with an excess of AN to give the products of 2,1 insertion into the Pd-Me bond, yielding dimers and/or trimers which feature bridging alpha-cyano groups. The reactions were studied by low temperature (1)H NMR spectroscopy, revealing an initial formation of compounds featuring N-bound AN, which isomerized to an (unobserved) pi-bound species that rapidly underwent 2,1 insertion into the Pd-Me bond. Intermediate oligomeric complexes retaining a Pd-Me function were observed at low [AN] in these reactions. Under pseudo first-order conditions, k(obs) values of 8.5 x 10(-5) to 2.68 x 10(-3) M(-1) (-22 degrees C to 10 degrees C, 100 equiv of AN) and activation parameters of DeltaH++ = 14.4(5) kcal mol(-1) and DeltaS++ = -19(5) eu were obtained in one case. Comparison of the overall rates of insertion between two LPd(NCCH(3))CH(3), differing in the overall charge on the supporting ligand L, showed that the complex bearing a negatively charged ligand reacts with AN twice as fast as one with no anionic charge. The rates of insertion in both of these complexes are significantly faster than reported rates for analogous reactions in cationic Pd(II) derivatives, indicating that increasing the negative charge on the complex enhances the rate of AN insertion. These results provide fundamental mechanistic insights into a crucial reaction for incorporation of polar comonomers into alpha olefins via a coordination polymerization mechanism.

Journal Article↗
PubMed2005

Development of a recA gene-based identification approach for the entire Burkholderia genus.

Burkholderia is an important bacterial genus containing species of ecological, biotechnological, and pathogenic interest. With their taxonomy undergoing constant revision and the phenotypic similarity of several species, correct identification of Burkholderia is difficult. A genetic scheme based on the recA gene has greatly enhanced the identification of Burkholderia cepacia complex species. However, the PCR developed for the latter approach was limited by its specificity for the complex. By alignment of existing and novel Burkholderia recA sequences, we designed new PCR primers and evaluated their specificity by testing a representative panel of Burkholderia strains. PCR followed by restriction fragment length polymorphism analysis of an 869-bp portion of the Burkholderia recA gene was not sufficiently discriminatory. Nucleotide sequencing followed by phylogenetic analysis of this recA fragment differentiated both putative and known Burkholderia species and all members of the B. cepacia complex. In addition, it enabled the design of a Burkholderia genus-specific recA PCR that produced a 385-bp amplicon, the sequence of which was also able to discriminate all species examined. Phylogenetic analysis of 188 novel recA genes enabled clarification of the taxonomic position of several important Burkholderia strains and revealed the presence of four novel B. cepacia complex recA lineages. Although the recA phylogeny could not be used as a means to differentiate B. cepacia complex strains recovered from clinical infection versus the natural environment, it did facilitate the identification of clonal strain types of B. cepacia, B. stabilis, and B. ambifaria capable of residing in both niches.

Bacterial Typing Techniques↗
PubMed2006

Effect of vitamin B12 treatment on haptocorrin.

BACKGROUND: Haptocorrin (HC) carries the major part of circulating cobalamin, but whether HC is altered on treatment with vitamin B12 remains unknown. METHODS: Our study included 3 populations: a population of vegan men (n = 174; vegan population), of whom 63 were treated daily with 5 mg of oral vitamin B12 for 3 months; a group of patients with a previous methylmalonic acid (MMA) concentration >0.4 micromol/L (n = 140; population with suspected deficiency), of which 69 were treated with weekly vitamin B12 injections (1 mg) for 4 weeks; and a subgroup of participants in a vitamin B intervention study (n = 88; nondeficient population), of whom 45 were treated daily with 0.4 mg of oral vitamin B12 for 3 months. Total HC and holoHC were measured by ELISA. Cobalamin was measured by an intrinsic factor (IF)-based assay. Samples were collected at baseline and 3 months after start of treatment. RESULTS: Compared with baseline results for the 3 study populations, total HC and holoHC increased 30 pmol/L for every 100 pmol/L increase in cobalamin. After treatment with vitamin B12, holoHC (P <0.0001) and total HC (P <0.0001) increased significantly in the vegan population. Only holoHC increased in the population with suspected deficiency (P <0.0001), whereas no alteration was observed in the nondeficient population. CONCLUSIONS: The HC concentration is decreased in severely cobalamin-deficient individuals and increases on treatment. The concentration of cobalamin also relates significantly to the HC concentration in nondeficient individuals.

Biomarkers↗
PubMed2005

Deletion of IKK2 in hepatocytes does not sensitize these cells to TNF-induced apoptosis but protects from ischemia/reperfusion injury.

The inhibitor of NF-kappaB (I-kappaB) kinase (IKK) complex consists of 3 subunits, IKK1, IKK2, and NF-kappaB essential modulator (NEMO), and is involved in the activation of NF-kappaB by various stimuli. IKK2 or NEMO constitutive knockout mice die during embryogenesis as a result of massive hepatic apoptosis. Therefore, we examined the role of IKK2 in TNF-induced apoptosis and ischemia/reperfusion (I/R) injury in the liver by using conditional knockout mice. Hepatocyte-specific ablation of IKK2 did not lead to impaired activation of NF-kappaB or increased apoptosis after TNF-alpha stimulation whereas conditional NEMO knockout resulted in complete block of NF-kappaB activation and massive hepatocyte apoptosis. In a model of partial hepatic I/R injury, mice lacking IKK2 in hepatocytes displayed significantly reduced liver necrosis and inflammation than wild-type mice. AS602868, a novel chemical inhibitor of IKK2, protected mice from liver injury due to I/R without sensitizing them toward TNF-induced apoptosis and could therefore emerge as a new pharmacological therapy for liver resection, hemorrhagic shock, or transplantation surgery.

Animals↗
PubMed2003

The F-box protein Skp2 participates in c-Myc proteosomal degradation and acts as a cofactor for c-Myc-regulated transcription.

The transcription regulatory oncoprotein c-Myc controls genes involved in cell growth, apoptosis, and oncogenesis. c-Myc is turned over very quickly through the ubiquitin/proteasome pathway. The proteins involved in this process are still unknown. We have found that Skp2 interacts with c-Myc and participates in its ubiquitylation and degradation. The interaction between Skp2 and c-Myc occurs during the G1 to S phase transition of the cell cycle in normal lymphocytes. Surprisingly, Skp2 enhances c-Myc-induced S phase transition and activates c-Myc target genes in a Myc-dependent manner. Further, Myc-induced transcription was shown to be Skp2 dependent, suggesting interdependence between c-Myc and Skp2 in activation of transcription. Moreover, Myc-dependent association of Skp2, ubiquitylated proteins, and subunits of the proteasome to a c-Myc target promoter was demonstrated in vivo. The results suggest that Skp2 is a transcriptional cofactor for c-Myc and indicates a close relationship between transcription activation and transcription factor ubiquitination.

Animals↗
PubMed2006

ERK modulates DNA bending and enhancesome structure by phosphorylating HMG1-boxes 1 and 2 of the RNA polymerase I transcription factor UBF.

Transcription of the ribosomal RNA genes of mammals by RNA polymerase I is rapidly activated by epidermal growth factor via the MAP-kinase (ERK) signaling cascade. This activation is mediated by direct phosphorylation of the HMG box DNA binding domains of the architectural transcription factor UBF. Mutation of the ERK sites of UBF inhibits its normal function and blocks growth factor activation of ribosomal transcription. UBF has little or no DNA sequence selectivity and binds throughout the ribosomal genes, defining a specialized chromatin. Indeed, the HMG boxes of UBF induce looping of the ribosomal DNA to create the enhancesome, a structure somewhat reminiscent of the nucleosome. Here, we show that both ERK phosphorylation and mutations that simulate this phosphorylation decrease the affinity of the individual HMG boxes of UBF for linear ribosomal DNA but have little or no effect on the capacity of these HMG boxes to bind to pre-bent DNA and do not affect the overall binding constant of UBF for the DNA. Electron spectroscopic imaging showed that ERK site UBF mutants do not induce the characteristic DNA looping of the enhancesome and associate with no more than half of the enhancesomal DNA. The data demonstrate that ERK phosphorylation of UBF prevents DNA bending by its first two HMG boxes, leading to a cooperative unfolding of the enhancesome.

Amino Acid Sequence↗
PubMed2003

Organization of the mouse Zfhx1b gene encoding the two-handed zinc finger repressor Smad-interacting protein-1.

SIP1, a member of the deltaEF1 family of two-handed zinc finger transcriptional repressors, has been identified as a Smad-binding protein. Recently, mutations in the human SIP1 gene (ZFHX1B) have been implicated in Hirschsprung disease. Here we document extensively the structure and transcriptional pattern of the mouse SIP1 gene (Zfhx1b) and compare it to homologues from other species. The overall structure of Zfhx1b is highly similar to that of the deltaEF1 gene (Zfhx1a), confirming their close evolutionary relationship. In contrast to Zfhx1a, the 5' untranslated region of the SIP1-encoding mouse gene is very complex and includes several alternative exons. The corresponding 5'-UTR splicing pattern seems to be conserved between species and suggests a role in its transcriptional and/or translational regulation. The gene also codes for an antisense transcript that is highly conserved between human and mouse.

Alternative Splicing↗
PubMed2002

Three-dimensional structure of the bacterial protein-translocation complex SecYEG.

Transport and membrane integration of polypeptides is carried out by specific protein complexes in the membranes of all living cells. The Sec transport path provides an essential and ubiquitous route for protein translocation. In the bacterial cytoplasmic membrane, the channel is formed by oligomers of a heterotrimeric membrane protein complex consisting of subunits SecY, SecE and SecG. In the endoplasmic reticulum membrane, the channel is formed from the related Sec61 complex. Here we report the structure of the Escherichia coli SecYEG assembly at an in-plane resolution of 8 A. The three-dimensional map, calculated from two-dimensional SecYEG crystals, reveals a sandwich of two membranes interacting through the extensive cytoplasmic domains. Each membrane is composed of dimers of SecYEG. The monomeric complex contains 15 transmembrane helices. In the centre of the dimer we observe a 16 x 25 A cavity closed on the periplasmic side by two highly tilted transmembrane helices. This may represent the closed state of the protein-conducting channel.

Cell Membrane↗
PubMed2006

Deregulation of cdk5 in Hippocampal sclerosis.

Hippocampal sclerosis (HS) is the most common cause of chronic medically refractory epilepsy in adults. Histologically, HS is characterized by segmental neuronal loss and gliosis. Although neuronal loss is important to the pathophysiology of HS, the molecular mechanisms underlying the neuronal loss remain uncertain. Recently, it has been appreciated that proteins important in neurodevelopment may also have a role in neurodegeneration. Cyclin-dependent kinase 5 (cdk5), known to be crucial in development of the normal cerebral cortex, has now been shown as pivotal in several cell death paradigms, including apoptosis and necrosis. Deregulation of cdk5 by p25 causes hyperphosphorylation of tau and may contribute to pathology in several neurodegenerative conditions. Furthermore, it has been shown that after transient forebrain ischemia, cdk5 causes specific death of CA1 neurons in the rat hippocampus by direct phosphorylation of the NR2A subunit of the NMDA receptor and subsequent excitotoxicity. Because apoptosis, necrosis, and excitotoxicity are all thought to contribute to neuronal loss in HS, we hypothesized that abnormalities of the cdk5 pathway would accompany this disorder. Surgically resected cases of HS with adjacent histologically normal lateral temporal cortex were examined for cdk5 and its activator p35/p25. We consistently found increased immunoreactivity for p35/p25 in surviving neurons within areas of neuronal loss compared with areas where neurons were preserved. Western blots showed the ratio of p25 to p35 to be greater in diseased hippocampi than in the adjacent histologically normal temporal lobe. Histone-based kinase assays demonstrated increased activity of the p25-cdk5 complex in HS compared with the temporal lobe despite neuronal loss in the hippocampal samples. Our results suggest that p25 is pathologically increased in HS and that deregulation of cdk5 by p25 might contribute to neuronal death in this condition.

Adult↗
PubMed2006

The effects of mild and severe traumatic brain injury on speed of information processing as measured by the computerized tests of information processing (CTIP).

In spite of the fact that reaction time (RT) measures are sensitive to the effects of traumatic brain injury (TBI), few RT procedures have been developed for use in standard clinical evaluations. The computerized test of information processing (CTIP) [Tombaugh, T. N., & Rees, L. (2000). Manual for the computerized tests of information processing (CTIP). Ottawa, Ont.: Carleton University] was designed to measure the degree to which TBI decreases the speed at which information is processed. The CTIP consists of three computerized programs that progressively increase the amount of information that is processed. Results of the current study demonstrated that RT increased as the difficulty of the CTIP tests increased (known as the complexity effect), and as severity of injury increased (from mild to severe TBI). The current study also demonstrated the importance of selecting a non-biased measure of variability. Overall, findings suggest that the CTIP is an easy to administer and sensitive measure of information processing speed.

Adolescent↗
PubMed2006

A conserved dimer and global conformational changes in the structure of apo-PknE Ser/Thr protein kinase from Mycobacterium tuberculosis.

The "eukaryotic-like" receptor Ser/Thr protein kinases (STPKs) are candidates for the sensors that mediate environmental adaptations of Mycobacterium tuberculosis (Mtb). To define the mechanisms of regulation and substrate recognition, we determined the crystal structure of the ligand-free, activated kinase domain (KD) of the Mtb STPK, PknE. Remarkably, the PknE KD formed a dimer similar to that first observed in the structure of the ATPgammaS complex of the Mtb paralog, PknB. This structural similarity, which occurs despite little sequence conservation between the PknB and PknE dimer interfaces, supports the idea that dimerization regulates the Mtb receptor STPKs. Insertion of the DFG motif into the ATP-binding site and other conformational differences compared the ATPgammaS:PknB complex suggest that apo-PknE is not pre-organized to bind nucleotides. This structure may represent an inactive conformation stabilized by dimerization or, alternatively, an active conformation that reveals shifts that mediate nucleotide exchange and order substrate binding.

Amino Acid Motifs↗
PubMed2004

The effect of labor and/or ovariectomy on rodent continence mechanism--the neuronal changes.

Many women develop stress urinary incontinence (SUI) after childbirth, but the exact neuronal changes are largely unknown. This study is designed to identify the neuronal changes associated with pregnancy, delivery and ovariectomy. A total of 10 virgin and 48 pregnant rats were used. Cystometry and stress/sneeze tests were performed in the virgin once and the pregnant rats at certain time points. Postpartum the rats were equally grouped as follows: group I: delivery, group II: delivery + ballooning, group III: delivery + ovariectomy, group IV: delivery + ballooning + ovariectomy. Tissues from bladder, bladder neck, and urethra were analyzed by immunostaining for PGP 9.5, CGRP, SP, NPY, VIP, TH, n-NOS. We found complex innervation changes in the different tissue samples. Since the bladder neck and the mid-urethra play an important role in the continence mechanism the neuronal changes in these areas contribute to the observed functional changes.

Animals↗