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PubMed2026

Simplifying multiplex genome engineering in Saccharomyces cerevisiae with intron-mediated Random Assembly and INtegration (RAIN).

Engineering of multistep enzymatic pathways often involves extensive optimization of heterologous gene expression levels and requires cloning of promoter and open reading frames (ORFs) to generate expression cassettes. We present work on a nascent method for multiplex genome engineering in Saccharomyces cerevisiae that negates the requirement for cloning of expression cassettes. Our system, Random Assembly and INtegration (RAIN), uses intron-mediated homologous recombination (HR) for random in vivo assembly of exogenous promoter and ORF libraries, which are combined and cotransformed in a one-pot method. The libraries include consensus homology arms which target long terminal repeat regions of the Ty1 retrotransposon, providing over a hundred possible integration loci. In this way, our developmental system aims to negate the need for in vitro combinatorial cloning of promoters and ORFs to generate expression cassettes, simplifying in vitro DNA preparation before multiplex genome engineering. This paper presents findings from a series of experiments to demonstrate a proof of concept for the RAIN system. These include: the first reported use of intron-mediated assembly of promoters and ORFs for expression of a functional gene product; up to three markerless genomic integrations; and up to five integrations with antibiotic selection. We also present a number of innovations to improve integration efficiency during multiplex engineering in S. cerevisiae including: SGS1 gene knockout; disruption of heteroduplex rejection; modified Cas9 expression architecture; and overexpression of HR genes RAD52, MRE11, and RAD59. To demonstrate how our system can be used for single transformation phenotype engineering of multiple strains, we also transformed a library of methylotrophy associated genes to generate four new strains that were able to grow on a solid minimal medium with methanol as the sole additional carbon source. Our findings contribute to the ongoing efforts to improve multiplex genome engineering tools in S. cerevisiae, and provide the foundations for further development of a novel toolbox for generating useful genetic diversity for metabolic pathway engineering.

Saccharomyces cerevisiae↗
PubMed2000

Conotoxins - new vistas for peptide therapeutics.

There are approximately 500 species of predatory cone snails within the genus Conus. They comprise what is arguably the largest single genus of marine animals alive today. It has been estimated that the venom of each Conus species has between 50 and 200 components. These highly constrained sulfur rich components or conotoxins represent a unique arsenal of neuropharmacologically active peptides that have been evolutionarily tailored to afford unprecedented and exquisite selectivity for a wide variety of ion-channel subtypes. Remarkable divergence occurs when cone snails speciate. Consequently, the complement of venom peptides in any one Conus species is distinct from that of any other species. Hence many thousands of peptides that modulate ion channel function are present within Conus venoms. Evolutionary pressures have afforded a "pre-optimized," structurally sophisticated library that has been "fine tuned" over 50 million years. The statistics associated with sampling such libraries bear testimony to the validity and feasibility of this strategy. Although approximately 100 conotoxin sequences have been published in the scientific literature, representing a mere 0.2 % of the estimated library size, this sample has already afforded a peptide of proven clinical utility and several pre-clinical leads for CNS disorders. Conus libraries represent a rich pharmacopoeia and the potential to "therapeutically mine" such a resource appears limitless. The paucity of synthetic methodologies necessary to achieve the regioisomeric folding patterns present in these native peptides precludes access to synthetic conotoxin libraries, further validating the overall "mining" strategy. In this article, we will present a pragmatic overview of the molecular diversity as well as the neurobiological mechanisms that define each major class of conotoxin.

Amino Acid Motifs↗
PubMedDate not supplied

[Application of principles of evidence-based medicine in cancer of the urinary bladder].

Meta-analysis has been made to answer the question whether a proven advantage exists of chemotherapy of locally advanced and metastatic cancer of the urinary bladder (UB) with gemcitabine+cisplatin over the scheme M-VAC. The data for 1990-2002 obtained from the data base Medline, library of Cocrane Association, proceedings of the symposia and conferences, publications in domestic periodicals Urologiya, Voprosy Onkologii covered 3477 items on UB cancer. Nine publications were selected which seem to use significant information in terms of evidence-based medicine. The patients were divided into two groups. Group 1 consisted of patients with local and metastatic UB cancer treated with the combination gemcitabine+cisplatin (n = 390). Group 2 patients (n = 499) received chemotherapy with M-VAC. By principles of evidence-based medicine, group 1 patients had more frequent unfavourable outcomes (absence of complete and partial regressions)--50 and 42%, respectively. A decrease in the absolute risk is significant (p < 0.05, chi-square = 5.8). It is 8% in the confidence interval (CI) 4,12. A decrease in the relative risk was 19% (CI 13.7-24.3), odds ratio 1.39 in CI 1.3-1.48. Thus, at present there are no reliable data on advantages of local and metastatic UB cancer treatment with the scheme gemcitabine-cysplatin over standard treatment M-VAC.

Antineoplastic Combined Chemotherapy Protocols↗
PubMed2006

Research trends of nursing informatics in Korea.

In order to examine the research trends of Korean nursing informatics over the past 10 years starting from 1995 when the Journal of Korean Society of Medical Informatics started being published, to 2004, nursing informatics related studies were searched for on information search websites such as the National Digital Library, Korean Nurses Association, Korean Society of Medical Informatics, KoreaMed, and MedRIC. As a result of it, specified research trends were identified about Korean nursing informatics.

Humans↗
PubMedDate not supplied

[For a history of nursing care and nurses in Italy: the indications for research on sources and bibliography].

This is the final article of a series, where main problems and social conditions of italian nurses at the beginning of the century were analyzed, and a thorough (but not exhaustive) list of the main bibliographic sources is presented. Historical research on the recent origins of the nursing profession (beginning of the century) can be very awkward and time consuming because many of the original sources are not very well known, not readily available and scattered in several major and minor libraries and private associations. Knowing what is available and what has already been used for historical research can give a further impulse to the research and enrich the data base and information on readily available sources.

Historiography↗
PubMed2004

Cloning, recombinant expression and biochemical characterisation of novel esterases from Bacillus sp. associated with the marine sponge Aplysina aerophoba.

Two novel esterases (EstB1 and EstB2) were isolated from a genomic library of Bacillus sp. associated with the marine sponge Aplysina aerophoba. EstB1 shows low identity (26-44%) with the published hydrolases of the genus Bacillus, whereas EstB2 shows high identity (73-74%) with the carboxylesterases from B. cereus and B. anthracis. Both esterases were efficiently expressed in Escherichia coli under the control of T7 promoter using the vector pET-22b(+). Recombinant EstB1 was purified in a single step to electrophoretic homogeneity by IMAC. A method for the refolding of inclusion bodies formed by the recombinant EstB2 was established to obtain active enzyme. Substrate specificity of the two enzymes towards p-nitrophenyl and methyl esters and the respective kinetic parameters K(m) and V(max) were determined. The temperature optima of EstB1 and EstB2 were determined to be in the range of 30-50 degrees C and 20-35 degrees C, respectively. The pH optima were found to be in the range of 6.5-7.5 and 6.5-8.0, respectively. Both enzymes showed the highest stability in up to 50% (v/v) DMSO followed by methanol, ethanol and 2-propanol. The influence of high NaCl and KCl concentrations was tested. The inhibition effect of 10-50 mM Zn(2+) and 50 mM Mg(2+) and Ca(2+) ions was observed for both esterases. One to five millimolar PMSF deactivated the enzymes, whereas beta-mercaptoethanol, DTT and EDTA had no effect on the enzymes activity.

Animals↗
PubMed2001

Mimotopes for tumor-specific T lymphocytes in human cancer determined with combinatorial peptide libraries.

Mimotopes of a tumor-associated T cell epitope were determined using randomized and combinatorial peptide libraries and a CD8(+) T cell clone specific for the cutaneous T cell lymphoma cell line MyLa. Antigen recognition by this clone was found to be HLA-B8 restricted. More than 80 % of HLA-matched patients with cutaneous T cell lymphoma had mimotope-specific CD8(+) T cells in their peripheral blood. Mimotope-specific T cells isolated and expanded from a patient lysed MyLa cells in in vitro assays thus demonstrating their cytolytic capacity and tumor specificity. Mimotope vaccination of a patient without detectable mimotope-specific T cells induced frequencies of these cells of up to 1.82 % of the peripheral blood CD8(+) T cells.

Amino Acid Sequence↗
PubMed1993

A survey of health sciences libraries in hospitals: implications for the 1990s.

In response to an expressed need for comprehensive data on health sciences libraries in hospitals, the American Hospital Association (AHA) conducted a survey of all U.S. registered hospitals in 1990. The response rate was 57%. Results showed that 2,167 hospitals (31.6% of all U.S. registered hospitals) had on-site libraries that met four definitional criteria. Survey results also indicated that hospitals use diverse resources and approaches to provide information services to a wide array of health care providers and consumers. These baseline data, combined with an assessment of key environmental factors affecting hospitals, can provide guidance to hospital libraries as they face the challenges of the 1990s. The AHA has added the health sciences library to services tracked in its annual survey of hospitals; additional research opportunities in this area remain.

American Hospital Association↗
PubMed2002

Normalized cDNA libraries from a porcine model of orthopedic implant-associated infection.

Staphylococcal infections that result from an alteration in a patient's immune response at the surgical site are a major problem in procedures that incorporate biomaterials in trauma surgery and joint replacement. Diagnosis of infection based on pathogen detection is difficult and exacerbated by increasing numbers of partially or totally resistant strains of nosocomial pathogens, particularly Staphylococcus aureus. Expression profiling of a host's cellular immune response could facilitate the identification of the pathways involved in pathogen recognition and eradication and could lead to more rational design of drugs and therapies. To this end, we constructed and characterized ten individually tagged and directionally cloned cDNA libraries from peripheral blood cells (PBC), spleen (Sp), thymus (Th), lymph node (LN), and bone marrow (BM) from immunologically naive and challenged pigs as part of an implant-associated orthopedic model of deep infection. Three of these libraries were normalized at C(0)(t) values 5, 10, 20, and 30. The libraries comprise more than 20 million primary transformants with an average insert length >1.4 kb. Cluster analysis of 7620 ESTs revealed 1029 clusters containing an average of 3.6 sequences and 3846 singletons. Gene discovery is estimated to be approximately 64%. Searches of public databases resulted in 49.3% annotated porcine sequences, of which 22.2% had significant homologies to ESTs from a variety of species, and 28.5% were without a significant match in any public database. We also identified 9.1% ESTs as involved in host cell and organism defense and 11.5% related to cell signaling and communication. These sequences, together with the 28.5% appearing as novel, are of specific interest to the infectious disease process.

Amino Acid Sequence↗
PubMed2006

Dissecting virulence pathways of Mycobacterium tuberculosis through protein-protein association.

The sudden increase in information derived from the completed Mycobacterium tuberculosis (Mtb) genome sequences has revealed the need for approaches capable of converting raw genome sequence data into functional information. To date, an experimental system for studying protein-protein association in mycobacteria is not available. We have developed a simple system, termed mycobacterial protein fragment complementation (M-PFC), that is based upon the functional reconstitution of two small murine dihydrofolate reductase domains independently fused to two interacting proteins. Using M-PFC, we have successfully demonstrated dimerization of yeast GCN4, interaction between Mtb KdpD and KdpE, and association between Esat-6 and Cfp-10. We established the association between the sensor kinase, DevS, and response regulator, DevR, thereby demonstrating the potential of M-PFC to study protein associations in the mycobacterial membrane. To validate our system, we screened an Mtb library for proteins that associate with the secreted antigen Cfp-10 and consistently identified Esat-6 in our screens. Additional proteins that specifically associate with Cfp-10 include Rv0686 and Rv2151c (FtsQ), a component and substrate, respectively, of the evolutionary conserved signal recognition pathway; and Rv3596c (ClpC1), an AAA-ATPase chaperone involved in protein translocation and quality control. Our results provide empirical evidence that directly links the Mtb specialized secretion pathway with the evolutionary conserved signal recognition and SecA/SecYEG pathways, suggesting they share secretory components. We anticipate that M-PFC will be a major contributor to the systematic assembly of mycobacterial protein interaction maps that will lead to the development of better strategies for the control of tuberculosis.

Bacterial Proteins↗
PubMed2004

Encoded self-assembling chemical libraries.

The isolation of molecules capable of high-affinity and specific binding to biological targets is a central problem in chemistry, biology and pharmaceutical sciences. Here we describe the use of encoded self-assembling chemical (ESAC) libraries for the facile identification of molecules that bind macromolecular targets. ESAC technology uses libraries of organic molecules linked to individual oligonucleotides that mediate the self-assembly of the library and provide a code associated with each organic molecule. After panning ESAC libraries on the biomolecular target of interest, the 'binding code' of the selected compounds can be 'decoded' by a number of experimental techniques (e.g., hybridization on oligonucleotide microarrays). The potential of this technology was demonstrated by the affinity maturation (>40-fold) of binding molecules to human serum albumin and bovine carbonic anhydrase, leading to binders with dissociation constants in the nanomolar range.

Albumins↗
PubMed1985

Hospital library surveys for management and planning: past and future directions.

Since the survey of health sciences libraries by the American Medical Association in 1969, a number of other hospital library surveys have been conducted. Twelve hospital/health sciences library surveys published since the passage of the Medical Library Assistance Act are reviewed. The use of data from these surveys for management and planning is discussed and directions for future library survey development are suggested.

Libraries, Hospital↗
PubMed2004

Isolation of genes associated with developmentally competent bovine oocytes and quantitation of their levels during development.

We have performed suppressive subtraction hybridization (SSH) of populations of developmentally competent and incompetent bovine oocytes from large (> or =5-mm) and small (< or =2-mm) follicles to isolate messenger RNA associated with the attainment of developmental competency. RNA was amplified in a linear fashion and then subjected to the SSH procedure to produce a library enriched for genes associated with competency. One thousand clones of this library were subjected to a differential screening approach to identify 31 potentially upregulated isolates. Sequencing revealed these to represent 21 genes. To rigorously identify the degree of upregulation and reproducibility thereof, we examined the expression of these genes in three separate pools of developmentally competent and incompetent oocytes by quantitative real-time PCR. Results indicated that upregulation varied from zero to threefold, showing that accurate quantification is essential for the interpretation of such differential screening experiments. Furthermore, it appears that the molecular causes for poor developmental capacity may be highly complex and be reliant on many small changes. We further characterized a selection of these novel and known maternally expressed genes for their absolute expression levels during maturation in the presence or absence of an inhibitor of transcription and during preattachment development. Last, the effect of nuclear transfer on the levels of these genes was assayed. Nuclear transfer was found to differentially affect transcript levels of genes expressed after embryonic genome activation but did not prevent the degradation of maternal transcripts or result in activation of maternal genes that are silent at blastocyst stages.

Animals↗
PubMed2003

Development and characterization of a pooled Haemophilus influenzae genomic library for the evaluation of gene expression changes associated with mucosal biofilm formation in otitis media.

UNLABELLED: Haemophilus influenzae is one of the most important respiratory pathogens of man. It has been etiologically associated with otitis media, otorrhea, and chronic obstructive pulmonary disease. Identification of new genomic elements will provide novel targets to fight chronic infections caused by this organism. OBJECTIVE: The new paradigm that chronic infections are caused by bacterial biofilms prompted us to study the relationship between bacterial pathogenicity, biofilm formation and bacterial communal cooperation. To do this, it is essential to determine the virulence gene sets that are involved in the above processes and whether they are present in every bacterial cell or distributed in a "communal gene-pool", the distributed genome hypothesis (DGH). We designed, constructed and characterized a highly redundant genomic DNA library comprised of the genomes of ten low passage clinical isolates of H. influenzae carrying large numbers of genes that are not present in the laboratory strains of H. influenzae. METHODS: Genomic DNA fragments of the ten clinical strains were hydro-dynamically sheared to produce a mean fragment size of 1.5-2.5 kb. The ten sheared DNAs were than pooled and used in the construction of a genomic library with 76800 clones. RESULTS: Our restriction endonuclease and sequence analyses of 800 clones demonstrate that 75% of the clones carry an insert larger than 0.5 kb. The library has an approximately 1.5 kb average insert size, and therefore, better than 4.5x redundancy for each of the genomes of the ten clinical isolates. Our sequencing effort ( approximately 1 million nucleotides to date) reveals that a high percentage of genes (75 clones, 11% of the 686 sequenced clones) present in this library are not represented in the genome of the reference strain H. influenzae Rd. CONCLUSIONS: The library, based on the above results, has a better than 4.5x coverage for each of the ten constituent genomes. On the basis of our preliminary sequencing data ( approximately 1 million nucleotides) the library lacks of highly repeated sequences, therefore, the expected genome coverage (4.5x) is not degraded. Using the prevalence of non-Rd like sequences (11%) detected during characterization of the genomic library, we estimated that the library contains DNA sequences equivalent to approximately 2 million bp, which are not represented in the reference genome of the H. influenzae Rd strain and that is greater in size than the genome of this reference strain, providing ample targets for innovative drug design.

Base Sequence↗