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PubMed1993

MULCOX2: a general computer program for the Cox regression analysis of multivariate failure time data.

Multivariate failure time data is commonly encountered in biomedicine, because each study subject may experience multiple events or because there exists clustering of subjects such that failure times within the same cluster are correlated. MULCOX2 implements a general statistical methodology for analyzing such data. This approach formulates the marginal distributions of multivariate failure times by Cox proportional hazards models without specifying the nature of dependence among related failure times. The baseline hazard functions for the marginal models may be identical or different. A variety of statistical inference can be made regarding the effects of (possibly time-dependent) covariates on the failure rates. Although designed primarily for the marginal approach, MULCOX2 is general enough to implement several alternative methods. The program runs on any computer with a FORTRAN compiler. The running time is minimal. Two illustrative examples are provided.

Age Factors↗
PubMed2026

Efficient rDNA-mediated multi-copy integration of gene clusters in Aureobasidium melanogenum.

Aureobasidium melanogenum is a promising non-conventional yeast chassis for synthetic biology. However, techniques recombining large genetic fragments, such as gene clusters, are still unavailable, hindering further metabolic reprogramming in this chassis. To achieve multi-copy integration of genes, we employed highly repetitive ribosomal DNA (rDNA) sequences in A. melanogenum as homologous recombination sites for large genetic fragments. First, integration efficiency of three different regions of A. melanogenum rDNA were investigated: RNA polymerase I promoter region (rDNA1, 1.0 kb), partial 26S rDNA region (rDNA2, 1.0 kb), and RNA polymerase I terminator region (rDNA3, 1.0 kb). Our findings revealed that the highest copy numbers and expression stability were observed for the short heterologous green fluorescent protein gene (gfp, 0.7 kb) and the long native polyketide synthase gene (pks, 7.0 kb) after rDNA1-mediated integration. Specifically, the copy numbers reached 7.0 and 8.0 for gfp and pks, respectively, and they remained stably expressed in the genome after 120-h subculturing. Furthermore, an 11.0 kb gene cluster (comprising the native pks, phosphopantetheinyl transferase (npg1), and scytalone dehydratase genes (scd) responsible for melanin biosynthesis) was integrated at the rDNA1 site, resulting in stable recombination with 15.0 copies and an approximately 12-fold increase in melanin production. Overall, the convenience and efficiency of the proposed rDNA-mediated multi-copy insertion strategy will facilitate superior metabolic engineering of A. melanogenum chassis cells.

Multigene Family↗
PubMed2005

RAPD for the typing of coagulase-negative staphylococci implicated in catheter-related bloodstream infection.

OBJECTIVES: A rapid random amplification of polymorphic DNA (RAPD) technique was developed to distinguish between strains of coagulase-negative staphylococci (CoNS) involved in central venous catheter (CVC)-related bloodstream infection. Its performance was compared with that of pulsed-field gel electrophoresis (PFGE). METHODS: Patients at the University Hospital Birmingham NHS Foundation Trust, U.K. who underwent stem cell transplantation and were diagnosed with CVC-related bloodstream infection due to CoNS whilst on the bone marrow transplant unit were studied. Isolates of CoNS were genotyped by PFGE and RAPD, the latter employing a single primer and a simple DNA extraction method. RESULTS: Both RAPD and PFGE were highly discriminatory (Simpson's diversity index, 0.96 and 0.99, respectively). Within the 49 isolates obtained from blood cultures of 33 patients, 20 distinct strains were identified by PFGE and 25 by RAPD. Of the 25 strains identified by RAPD, nine clusters of CoNS contained isolates from multiple patients, suggesting limited nosocomial spread. However, there was no significant association between time of inpatient stay and infection due to any particular strain. CONCLUSION: The RAPD technique presented allows CoNS strains to be genotyped with high discrimination within 4h, facilitating real-time epidemiological investigations. In this study, no single strain of CoNS was associated with a significant number of CVC-related bloodstream infections.

Adolescent↗
PubMed2006

AFLP fingerprinting for the analysis of genetic diversity within Necator americanus.

In the present study, we utilised the method of AFLP to screen for genetic variation within and among individuals of the blood-feeding human hookworm Necator americanus (Nematoda) from Africa, Asia and South America. A total of 45 adult worms (i.e. 20 from Ghana, 16 from Colombia and 9 from Nepal) were subjected to analysis using the restriction enzyme/primer combination HindIII+AG/BglII+AC. Cluster analysis divided N. americanus into multiple, genetically distinct groups, consistent with previous findings using ribosomal and mitochondrial DNA data sets. The results demonstrated the usefulness of AFLP fingerprinting for establishing genetic variation within N. americanus and reinforce its applicability to other parasitic helminths of human and/or veterinary health importance.

Animals↗
PubMed2005

Fusion oncogenes in tumor development.

Currently, all identified fusion oncogenes are found in rare tumor forms, and most of them only in specific tumor types. Some fusion oncogenes are frequent in healthy individuals suggesting that they rarely induce tumor growth. Multiple double-strand breaks that cluster in time and space increases the risk for formation of fusion oncogenes genes. The normal cell type specific spatial distribution of chromatin and genes in interphase nuclei may affect the risk for fusion of specific genes. Transcriptional orientation, splicing of reading frames, size and sequences of breakpoint introns are other risk factors. The biological activity of fusion oncoproteins is the most important factor for penetrance. The effects in specific target cells may explain the tumor type specificity of most fusion oncogenes.

Animals↗
PubMed2006

Labeling and intracellular tracking of functionally active plasmid DNA with semiconductor quantum dots.

Semiconductor nanocrystal quantum dots (QDs) allow long-term imaging in the cellular environment with high photostability. QD biolabeling techniques have previously been developed for tagging proteins and peptides as well as oligonucleotides. In this contribution, QD-decorated plasmid DNA was utilized for the first time for long-term intracellular and intranuclear tracking studies. Conjugation of plasmid DNA with phospholipid-coated QDs was accomplished using a peptide nucleic acid (PNA)-N-succinimidyl-3-(2-pyridylthio) propionate linker. Gel electrophoresis and confocal and atomic force microscopy (AFM) were used to confirm the structure of QD-DNA conjugates. AFM imaging also revealed that multiple QDs were attached in a cluster at the PNA-reactive site of the plasmid DNA. These QD-DNA conjugates were capable of expressing the reporter protein, enhanced green fluorescent protein, following transfection in Chinese hamster ovary (CHO-K1) cells with an efficiency of ca. 62%, which was comparable to the control (unconjugated) plasmid DNA.

Animals↗
PubMed2003

Mass spectrometry and site-directed mutagenesis identify several autophosphorylated residues required for the activity of PrkC, a Ser/Thr kinase from Bacillus subtilis.

We have shown recently that PrkC, which is involved in developmental processes in Bacillus subtilis, is a Ser/Thr kinase with features of the receptor kinase family of eukaryotic Hanks kinases. In this study, we expressed and purified from Escherichia coli the cytoplasmic domain of PrkC containing the kinase and a short juxtamembrane region. This fragment, which we designate PrkCc, undergoes autophosphorylation in E.coli. PrkCc is further autophosphorylated in vitro, apparently through a trans-kinase, intermolecular reaction. PrkC also displays kinase activity with myelin basic protein. Using high mass accuracy electrospray tandem mass spectrometry (LC-MS/MS) and nanoelectrospray tandem mass spectrometry, we identified seven phosphorylated threonine and one serine residue in PrkCc. All the corresponding residues were replaced by systematic site-directed mutagenesis and the purified mutant proteins were tested for in vitro kinase activity. Single and multiple replacement of four threonine residues, clustered between residues 162 and 167 in a putative activation loop, substantially reduced kinase activity and the effect was clearly additive. Replacement of the other three threonine residues, clustered between residues 290 and 320, had relatively little effect on activity. In contrast, substitution of Ser214, which is conserved in closely related receptor kinase-like bacterial proteins, independently affected activity and may represent a novel regulatory mechanism. When projected onto a 3D structure of PrkC modelled on the structure of known Hanks kinases, the first cluster of phospho-threonine residues falls precisely in the activation loop, controlling the access of substrate and ATP to the catalytic site of many eukaryotic receptor kinases, whereas the second cluster is located in the juxtamembrane region. These results indicate that regulation of PrkC kinase activity (and presumably autophosphorylation) includes a conserved activation loop mechanism. The juxtamembrane phospho-threonine residues may be essential, for example for the recruitment of other proteins necessary for a PrkC signalling cascade or for coupling to other signalling pathways. This is the first structure-function analysis of a bacterial receptor-like kinase of the Hanks family.

Adenosine Triphosphate↗
PubMed1996

Isolation and characterization of a TATA-less promoter for the human RAG-1 gene.

Human recombination activating gene-1 (RAG-1) genomic DNA clones containing the first exon coding for the 5' untranslated region and the second exon coding for the remaining 5' untranslated region, coding region, and 3' untranslated region were cloned. Primer extension analysis and RNase protection analysis demonstrated the multiple RAG-1 transcription start sites, clustered in a 31 nucleotide (nt) region. Sequence analysis showed that the RAG-1 promoter lacked a TATA box as well as an initiator sequence. Transient expression assays using a luciferase reporter gene with truncated promoter fragments and substitution mutants, showed that the 5' promoter region containing the CCAAT box between -110 and -86, is indispensable for its basal promoter activity in RAG-1 expressing Nalm 6 cell line. Comparative transient expression assays in various cell lines revealed that the 854 nt upstream promoter region was active, not only in RAG-1 expressing cell lines but also in RAG-1 non-expressing cell lines. These data indicate that the 854 nt upstream region of RAG-1 gene confer basal promoter activity, and that the tissue- and stage-specific expression of RAG-1 is controlled by elements present outside of the promoter region and/or differential chromatin structure(s) of the individual cells.

Base Sequence↗
PubMed2003

The major surface protease (MSP or GP63) of Leishmania sp. Biosynthesis, regulation of expression, and function.

Leishmania sp. are digenetic protozoa that cause an estimated 1.5-2 million new cases of leishmaniasis per year worldwide. Among the molecular factors that contribute to Leishmania sp. virulence and pathogenesis is the major surface protease, alternately called MSP, GP63, leishmanolysin, EC3.4.24.36, and PSP, which is the most abundant surface protein of leishmania promastigotes. Recent studies using gene knockout, antisense RNA and overexpression mutants have demonstrated a role for MSP in resistance of promastigotes to complement-mediated lysis and either a direct or indirect role in receptor-mediated uptake of leishmania. The MSP gene clusters in different Leishmania sp. include multiple distinct MSPs that tend to fall into three classes, which can be distinguished by their sequences and by their differential expression in parasite life stages. Regulated expression of MSP class gene products during the parasite life cycle occurs at several levels involving both mRNA and protein metabolism. In this review we summarize advances in MSP research over the past decade, including organization of the gene families, crystal structure of the protein, regulation of mRNA and protein expression, biosynthesis and possible functions. The MSPs exquisitely demonstrate the multiple levels of post-transcriptional gene regulation that occur in Leishmania sp. and other trypanosomatid protozoa.

Amino Acid Sequence↗
PubMed2001

Mouse melanocortin-4 receptor gene 5'-flanking region imparts cell specific expression in vitro.

Weight homeostasis is exquisitely sensitive to changes in the abundance of melanocortin-4 receptor (MC4-R). To begin to understand the factors that regulate MC4-R gene expression, we determined there are no introns in the gene, there are multiple starts of transcription, and a cluster of 3' ends. A series of MC4-R-luciferase gene reporter chimerics was developed and transfected into cell lines expressing (UMR106; GT1-7; HEK293) and not expressing (Neuro 2A) endogenous MC4-R mRNA. The longest construct, which includes approximately 3.3 kb 5'-flanking, 425 bp 5'-untranslated (UTR) and 1852 bp 3'-flanking, significantly increased luciferase reporter gene expression 24-, 13-, and 3-fold compared to pGL3-basic when expressed in HEK293, UMR106, and GT1-7 cells, respectively. Deletion analysis of mMC4-R 5'-flanking cDNA identified full mMC4-R promoter activity within 178 bp upstream of the major start of transcription. The mMC4-R gene structure and reporter chimerics provide a fundamental framework for the identification of specific factors regulating MC4-R gene expression.

3' Flanking Region↗
PubMed1997

Stereotaxic needle-core biopsy and fine-needle aspiration biopsy in the diagnosis of nonpalpable breast lesions: controversies and future prospects.

OBJECTIVE: To determine the advantages and limitations of a combined stereotaxic fine-needle aspiration biopsy and needle-core biopsy in the diagnosis of 353 nonpalpable breast lesions with special attention given to the collection of follow-up data. METHODS AND MATERIAL: 353 nonpalpable breast lesions underwent 'one pass' stereotaxic fine-needle aspiration (21 gauge needle) and needle-core biopsy (18 gauge needle) at our institution from January 1990 to October 1993. Stereotaxic biopsies were carried out by means of an 'add-on unit'. Surgical biopsy was usually recommended for highly suspicious radiologic patterns and/or needle biopsy reports classified as atypical or malignant. In all other cases mammographic follow-up was advised at 6 months and then annually for 3 years. The data were collected retrospectively during September 1995 (theoretical average follow-up of greater than 3 years). RESULTS: Following the combined needle biopsy technique procedure, surgery was recommended for 83 lesions. Fifty-four cancers were associated to these suspicious lesions. Because of changing radiological or clinical pattern during follow-up (mean follow-up: 22 months), 11 cancers were detected among the 270 lesions initially considered not to need surgery. Forty-three percent of the 65 malignant lesions were initially read as having less than highly suspicious mammographic features. There was no significant difference between the sensitivity and the specificity of one pass fine-needle aspiration biopsy (57% and 96% respectively) and needle-core biopsy (60% and 97% respectively), but noncontributive samples were not included in the false negative diagnoses and atypical samples were included in the true positive diagnoses. Of the 11 missed cancers, nine were manifested initially by clusters of calcifications. Our diagnostic approach was significantly less sensitive (P = 0.006) and less specific (P = 0.032) in cases of clusters of calcifications (31% false negative diagnoses) than in cases of soft-tissue masses (5.5% false negative diagnoses). In this study, an average delay in diagnoses of 22 months was responsible for a significantly increased percentage of axillary node positive invasive cancer (P < 0.001) and six of the 11 missed cancers were palpable at the time of the delayed diagnosis. For the nine cancers initially manifested by calcifications, the 22 months delay in diagnosis was responsible for a nonsignificant increase of microinvasive type at the expense of carcinoma in situ. CONCLUSION: Our enthusiasm with the sensitivity of this double stereotaxic needle sampling has been tempered by the results of this reanalysis in the light of a mean theoretical follow-up of three years. Our diagnostic approach was adequate in the presence of soft-tissue masses but not valid in the presence of clustered calcifications. When dealing with calcifications, multiple samplings must be done in order to improve the sensitivity of the diagnosis. Furthermore, this study does not favour the theory that the majority of mammographically detected cancers are indolent and highlights the poor sensitivity of the mammographic follow-up of nonpalpable lesions.

Biopsy, Needle↗
PubMed2003

A Th2 cytokine LCR. Adding a new piece to the regulatory puzzle.

DNase I hypersensitivity assays and phylogenetic analyses previously led to the identification of multiple enhancers in the Th2 cytokine cluster. As described in this issue of Immunity, Lee et al. have now used a transgenic mouse assay to identify a locus control region (LCR) that supports integration site-independent, copy number-dependent transcription of Il4 and Il13.

Animals↗
PubMed2003

Caldesmon binding to actin is regulated by calmodulin and phosphorylation via different mechanisms.

Smooth muscle caldesmon (CaD) binds F-actin and inhibits actomyosin ATPase activity. The inhibition is reversed by Ca2+/calmodulin (CaM). CaD is also phosphorylated upon stimulation at sites specific for mitogen-activated protein kinases (MAPKs). Because of these properties, CaD is thought to be involved in the regulation of smooth muscle contraction. The molecular mechanism of the reversal of inhibition is not well understood. We have expressed His6-tagged fragments containing the sequence of the C-terminal region of human (from M563 to V793) and chicken (from M563 to P771) CaD as well as a variant of the chicken isoform with a Q766C point mutation. By cleavages with proteases, followed by high-speed cosedimentation with F-actin and mass spectrometry, we found that within the C-terminal region of CaD there are multiple actin contact points forming two clusters. Intramolecular fluorescence resonance energy transfer between probes attached to cysteine residues (the endogenous C595 and the engineered C766) located in these two clusters revealed that the C-terminal region of CaD is elongated, but it becomes more compact when bound to actin. Binding of CaM restores the elongated conformation and facilitates dissociation of the C-terminal CaD fragment from F-actin. When the CaD fragment was phosphorylated with a MAPK, only one of the two actin-binding clusters dissociated from F-actin, whereas the other remained bound. Taken together, these results demonstrate that while both Ca2+/CaM and MAPK phosphorylation govern CaD's function via a conformational change, the regulatory mechanisms are different.

Actins↗
PubMed1998

Solution structures of the Ca2+-free and Ca2+-bound C2A domain of synaptotagmin I: does Ca2+ induce a conformational change?

C2 domains are widespread Ca2+-binding modules that are particularly abundant in proteins involved in membrane traffic and signal transduction. The C2A domain of synaptotagmin I is believed to play a key role in neurotransmitter release through its Ca2+-dependent interactions with syntaxin and phospholipids. Elucidating the structural consequences of Ca2+ binding to the C2A domain is critical for understanding its mechanism of action and for models of the functions of other C2 domains. We have determined the solution structure of the Ca2+-free and Ca2+-bound forms of the C2A domain of synaptotagmin I by NMR spectroscopy. Our data represent the first structure determination of a C2 domain in its Ca2+-free and Ca2+-bound forms. Three Ca2+ ions were included in the Ca2+-bound structure, yielding a Ca2+-binding motif that involves five aspartate side chains and one serine side chain. Ca2+ immobilizes the structure of the C2A domain but does not produce a significant conformational change from a well-defined conformation to another. Thus, the mechanism of action of the C2A domain of synaptotagmin I is different from that used by Ca2+-binding proteins of the EF-hand family. The main effect of Ca2+ binding on the C2A domain is to change its electrostatic potential rather than its structure. These results support a model whereby the C2A domain functions as an electrostatic switch in neurotransmitter release. The similarity between the structures of the synaptotagmin I C2A domain and the PLC-delta1 C2 domain suggests that the latter binds four Ca2+ ions and acts by a similar mechanism. This mechanism may also be valid for other C2 domains that share the unusual ability to bind multiple Ca2+ ions in a tight cluster at the tip of the domain.

Calcium↗
PubMed1999

Solution structure of Syrian hamster prion protein rPrP(90-231).

NMR has been used to refine the structure of Syrian hamster (SHa) prion protein rPrP(90-231), which is commensurate with the infectious protease-resistant core of the scrapie prion protein PrPSc. The structure of rPrP(90-231), refolded to resemble the normal cellular isoform PrPC spectroscopically and immunologically, has been studied using multidimensional NMR; initial results were published [James et al. (1997) Proc. Natl. Acad. Sci. U.S.A. 94, 10086-10091]. We now report refinement with better definition revealing important structural and dynamic features which can be related to biological observations pertinent to prion diseases. Structure refinement was based on 2778 unambiguously assigned nuclear Overhauser effect (NOE) connectivities, 297 ambiguous NOE restraints, and 63 scalar coupling constants (3JHNHa). The structure is represented by an ensemble of 25 best-scoring structures from 100 structures calculated using ARIA/X-PLOR and further refined with restrained molecular dynamics using the AMBER 4.1 force field with an explicit shell of water molecules. The rPrP(90-231) structure features a core domain (residues 125-228), with a backbone atomic root-mean-square deviation (RMSD) of 0.67 A, consisting of three alpha-helices (residues 144-154, 172-193, and 200-227) and two short antiparallel beta-strands (residues 129-131 and 161-163). The N-terminus (residues 90-119) is largely unstructured despite some sparse and weak medium-range NOEs implying the existence of bends or turns. The transition region between the core domain and flexible N-terminus, i.e., residues 113-128, consists of hydrophobic residues or glycines and does not adopt any regular secondary structure in aqueous solution. There are about 30 medium- and long-range NOEs within this hydrophobic cluster, so it clearly manifests structure. Multiple discrete conformations are evident, implying the possible existence of one or more metastable states, which may feature in conversion of PrPC to PrPSc. To obtain a more comprehensive picture of rPrP(90-231), dynamics have been studied using amide hydrogen-deuterium exchange and 15N NMR relaxation times (T1 and T2) and 15N{1H} NOE measurements. Comparison of the structure with previous reports suggests sequence-dependent features that may be reflected in a species barrier to prion disease transmission.

Amino Acid Sequence↗
PubMed2005

Correlating second harmonic optical responses of single Ag nanoparticles with morphology.

Femtosecond laser excited second harmonic (SH) activity from single Ag nanoparticles is reported. A correlation of SH single-particle measurements with high-resolution imaging of particle morphology by TEM was achieved by creating position markers on an optical and electron transparent substrate (Si3N4 thin film, approximately 100 nm). We compared the SH activity of single Ag nanoparticles (nanospheres versus nanorods) and cluster structures (composed of two or multiple particles, e.g., dimers and trimers). The direct correlation of single-particle structures and SH activity, spectral and power dependence, strongly suggests one-photon resonant driven nonlinear oscillator response mechanism.

Microscopy, Electron, Transmission↗
PubMed2006

Turkevich method for gold nanoparticle synthesis revisited.

The growth of gold nanoparticles by reduction by citrate and ascorbic acid has been examined in detail to explore the parameter space of reaction conditions. It is found that gold particles can be produced in a wide range of sizes, from 9 to 120 nm, with defined size distribution, following the earlier work of Turkevich and Frens. The reaction is initiated thermally or in comparison by UV irradiation, which results in similar final products. The kinetics of the extinction spectra show the multiple steps of primary and secondary clustering leading to polycrystallites.

Journal Article↗