Vector Lambda Research Articles

Convolutional neural network based dictionary learning to create hash codes for content-based image retrieval

Abstract This study investigates the suitability of sparse vectors in the dictionary learning (DL) method for content-based image retrieval (CBIR) tasks. Since DL usually performs the learning process in an unsupervised manner, it cannot generate robust features for the retrieval task, especially if a complex background is involved. In order to overcome this drawback, a DL approach using the feature representation power of the convolutional neural network (CNN) is proposed. The initialization values of the dictionaries in the proposed CNN based DL method are taken randomly from the middle layers of the CNN architecture. The vector of each image obtained from the CNN architecture is used as DL input. The lambda vectors produced by the DL structure are converted into binaries. In this way, DL acts as a hash code generator. The performance of the proposed framework is tested on modified COREL dataset. The results prove that it is an open-to-improvement approach and is promising.

Localization of a P1A1 Epitope to the Amino Terminal 66 Residues of Platelet Glycoprotein IIIa

A platelet glycoprotein (GP) IIIa epitope library was constructed by insertion of randomly cleaved GPIIIa cDNA fragments in the prokaryotic expression vector lambda gt22 and screened with purified anti-PlA1 antibodies for clones expressing a PlA1 epitope. Five independent clones were isolated and characterized by nucleotide sequencing. The smallest anti-PlA1 reactive clone obtained encoded the amino terminal 66 residues of mature GPIIIa. Substitution of leucine33 (PlA1) with a proline33 (PlA2) by in vitro mutagenesis resulted in the loss of anti- PlA1 reactivity; however, this clone still reacted with anti-GPIIIa polyclonal antibodies. These data indicate that a PlA1 alloantigenic epitope is located within a small, unglycosylated fragment of GPIIIa containing the polymorphism responsible for the PIA phenotype. Furthermore, these results prove that small recombinant mimics of a PlA1 epitope may be synthesized and used for detection of these alloantibodies.

Noreen Elizabeth Murray CBE. 26 February 1935 — 12 May 2011

Noreen Murray was one of the architects of the recombinant DNA revolution that transformed the study of biology from the early 1970s. Her particular prowess for genetic manipulation of bacteria and their phage was critical in developing the bacteriophage lambda vectors that were a vital part of the early genetic engineering toolbox. Her skill as a microbial geneticist had earlier become apparent through her work on genetic recombination and complementation in the fungus Neurospora , especially as a postdoctoral researcher at Stanford where her work brought her to the attention of some of the giants of early molecular biology. Back in the UK, first at Cambridge and then, for the bulk of her career, at Edinburgh, she produced a remarkable body of work focused on uncovering the mechanisms and biology of restriction enzymes, and their adaptation as tools underpinning modern biological research and the rise of the biotechnology industry. Much of this work was done in collaboration with her husband Ken Murray FRS, whose biographical memoir accompanies this one. Together they were known not only for the quality of their research but also for their vast generosity both on a personal level and on a larger canvas through their philanthropy.

Protection of mice against Chlamydophila abortus infection with a bacteriophage-mediated DNA vaccine expressing the major outer membrane protein

A bacteriophage-delivered DNA vaccine against Chlamydophila abortus was constructed by cloning a eukaryotic cassette containing the ompA gene (which expresses the Major Outer Membrane Protein) into a bacteriophage lambda vector. Four groups, each of 20 BALB/c mice were inoculated separately with the phage vaccine, a conventional DNA vaccine based on the same ompA expression cassette, a live attenuated vaccine (strain 1B) or the empty phage vector. The phage and DNA vaccines and empty phage vector were administered intramuscularly on days 0, 14 and 28; the attenuated vaccine was given once on day 0. Half the animals in each group were challenged on day 42 by intraperitoneal injection of live C. abortus and sacrificed on day 49. Phage-vaccinated mice developed moderate antibody levels against C. abortus and yielded higher levels of IFN-γ and IL-2 compared with the attenuated live vaccine group. Clearance of chlamydiae from spleens was significantly better in the attenuated vaccine group compared with the phage vaccine group, while both groups were significantly superior to the DNA vaccine and control groups ( p < 0.01). Although levels of protection in the mouse model were lower in phage-vaccinated animals, than in 1B vaccinated animals, phage vaccines offer several other advantages, such as easier handling and safety, potentially cheaper production and no chance of reversion to virulence. Although these are preliminary results in a model system, it is possible that with further optimisation immunization with phage vaccines may provide a novel way to improve protection against C. abortus infection and trials in large animals are currently being initiated.

Integration of In Vivo Genotoxicity and Short-term Carcinogenicity Assays Using F344 gpt Delta Transgenic Rats: In Vivo Mutagenicity of 2,4-Diaminotoluene and 2,6-Diaminotoluene Structural Isomers

An important trend in current toxicology is the replacement, reduction, and refinement of the use of experimental animals (the 3R principle). We propose a model in which in vivo genotoxicity and short-term carcinogenicity assays are integrated with F344 gpt delta transgenic rats. Using this model, the genotoxicity of chemicals can be identified in target organs using a shuttle vector λ EG10 that carries reporter genes for mutations; short-term carcinogenicity is determined by the formation of glutathione S-transferase placenta form (GST-P) foci in the liver. To begin validating this system, we examined the genotoxicity and hepatotoxicity of structural isomers of 2,4-diaminotoluene (2,4-DAT) and 2,6-diaminotoluene (2,6-DAT). Although both compounds are genotoxic in the Ames/Salmonella assay, only 2,4-DAT induces tumors in rat livers. Male F344 gpt delta rats were fed diet containing 2,4-DAT at doses of 125, 250, or 500 ppm for 13 weeks or 2,6-DAT at a dose of 500 ppm for the same period. The mutation frequencies of base substitutions, mainly at G:C base pairs, were significantly increased in the livers of 2,4-DAT–treated rats at all three doses. In contrast, virtually no induction of genotoxicity was identified in the kidneys of 2,4-DAT–treated rats or in the livers of 2,6-DAT–treated rats. GST-P–positive foci were detected in the livers of rats treated with 2,4-DAT at a dose of 500 ppm but not in those treated with 2,6-DAT. Integrated genotoxicity and short-term carcinogenicity assays may be useful for early identifying genotoxic and nongenotoxic carcinogens in a reduced number of experimental animals.

Can painting human cells with exogenous maltoporin enable efficient therapeutic gene transfer by bacteriophage lambda vectors?

Many gene therapy strategies require transfer of highmolecular weight DNA into human cells. To enable clinical trials, these vectors need to be produced on a large scale and at low cost. The production of effective high-capacity vectors like HSV-amplicons and helperdependent adenoviral vectors is difficult to up-scale, so new inexpensive vectors are needed for the efficient delivery of high-molecular weight DNA to human cells. Bacteriophage lambda vectors can accommodate up to about 46 kb of therapeutic DNA and can be easily produced in an industrial setting. However, the lambda vectors transfer DNA into mammalian cells with only a low efficiency. It was shown that bacteriophage lambda virions ejected their DNA in the presence of the purified receptor for bacteriophage lambda, maltoporin (LamB protein), encoded by the malB gene of Shigella sonnei 3070. This property of S. sonnei maltoporin was exploited for the bacteriophage injection-driven DNA loading of liposomes and other polymer nanocontainers displaying maltoporin. Relying on the above evidence I hypothesize that the efficient gene transfer by industrially produced bacteriophage lambda vector virions, such as cosmid transducing particles, to human cells can be accomplished after incorporation (protein painting) of the purified S. sonnei maltoporin into the human plasma membrane.

Proteasome inhibitors enhance bacteriophage lambda (λ) mediated gene transfer in mammalian cells

Bacteriophage lambda vectors can transfer their genomes into mammalian cells, resulting in expression of phage-encoded genes. However, this process is inefficient. Experiments were therefore conducted to delineate the rate limiting step(s) involved, using a phage vector that contains a mammalian luciferase reporter gene cassette. The efficiency of phage-mediated gene transfer in mammalian cells was quantitated, in the presence or absence of pharmacologic inhibitors of cell uptake and degradation pathways. Inhibitors of lysosomal proteases and proteasome inhibitors strongly enhanced phage-mediated luciferase expression, suggesting that these pathways contribute to the destruction of intracellular phage particles. In contrast, inhibition of endosome acidification had no effect on phage-mediated gene transfer, presumably because phage lambda is tolerant to extended exposure to low pH. These findings provide insights into the pathways by which phage vectors enter and transduce mammalian cells, and suggest that it may be possible to pharmacologically enhance the efficiency of phage-mediated gene transfer in mammalian cells. Finally, the data also suggest that the proteasome complex may serve as an innate defense mechanism that restricts the infection of mammalian cells by diverse viral agents.

In vivo gene delivery and expression by bacteriophage lambda vectors

AimsBacteriophage vectors have potential as gene transfer and vaccine delivery vectors because of their low cost, safety and physical stability. However, little is known concerning phage-mediated gene transfer in mammalian hosts. We therefore performed experiments to examine phage-mediated gene transfer in vivo.Methods and ResultsMice were inoculated with recombinant lambda phage containing a mammalian expression cassette encoding firefly luciferase (luc). Efficient, dose-dependent in vivo luc expression was detected, which peaked within 24 h of delivery and declined to undetectable levels within a week. Display of an integrin-binding peptide increased cellular internalization of phage in vitro and enhanced phage-mediated gene transfer in vivo. Finally, in vivo depletion of phagocytic cells using clodronate liposomes had only a minor effect on the efficiency of phage-mediated gene transfer.ConclusionsUnmodified lambda phage particles are capable of transducing mammalian cells in vivo, and may be taken up – at least in part – by nonphagocytic mechanisms. Surface modifications that enhance phage uptake result in more efficient in vivo gene transfer.Significance and Impact of the StudyThese experiments shed light on the mechanisms involved in phage-mediated gene transfer in vivo, and suggest new approaches that may enhance the efficiency of this process.

Novel hydrolase diversity retrieved from a metagenome library of bovine rumen microflora

A metagenome expression library of bulk DNA extracted from the rumen content of a dairy cow was established in a phage lambda vector and activity-based screening employed to explore the functional diversity of the microbial flora. Twenty-two clones specifying distinct hydrolytic activities (12 esterases, nine endo-beta-1,4-glucanases and one cyclodextrinase) were identified in the library and characterized. Sequence analysis of the retrieved enzymes revealed that eight (36%) were entirely new and formed deep-branched phylogenetic lineages with no close relatives among known ester- and glycosyl-hydrolases. Bioinformatic analyses of the hydrolase gene sequences, and the sequences and contexts of neighbouring genes, suggested tentative phylogenetic assignments of the rumen organisms producing the retrieved enzymes. The phylogenetic novelty of the hydrolases suggests that some of them may have potential for new applications in biocatalysis.

Two-stage continuous operation of recombinant Escherichia coli using the bacteriophage λ Q − vector

A two-stage continuous culture of Escherichia coli in combination with a bacteriophage lambda system was performed in order to overcome the intrinsic plasmid instability that is frequently observed in recombinant fermentation. A phage lambda vector with a Q(-) mutation was used to enhance the expression of the lambda system. The optimal values of the important operational variables such as the substrate concentration, the dilution rate, and the mean residence time on the expression of the cloned gene were determined in both batch and continuous cultures. For all culturing modes, the full induction of the cloned gene was observed 4 h after the temperature shift. In the two stage continuous culture, the overproduction reached their maxima at D=0.25 h(-1) with 1.5 S(0) of the medium supply. The maximum productivity of the total beta-galactosidase was 16.3x10(6) U l(-1) h(-1), which was approximately seven times higher than that in the single-copy lysogenic stage. The recombinant cells were stable in the lysogenic state for more than 260 h, while they were stable for 40 h in the lytic state. The instability that developed rapidly in the second tank is believed to be due to the accumulation of lysis proteins as a result of vector leakage during the operation.

Stepwise occurrence of a complex unbalanced translocation in neuroblastoma leading to insertion of a telomere sequence and late chromosome 17q gain

In neuroblastoma, the most frequent genetic alterations are unbalanced translocations involving chromosome 17. To gain insights into these rearrangements, we have characterized a previously identified der(1)t(1;17) of the CLB-Bar cell line. The 17q breakpoint was mapped by FISH. Subsequently, a rearranged fragment was identified by Southern analysis, cloned in a lambda vector and sequenced. The chromosome rearrangement is more complex than expected due to the presence of an interstitial 4p telomeric sequence between chromosome 1p and 17q. Three different genes, which may play a role in neuroblastoma development, are disrupted by the translocation breakpoints. Indeed, the 3'UTR of the PIP5K2B gene on chromosome 17q is directly fused to the (TTAGGG)n repeat of the chromosome 4p telomere, and the (1;4) fusion disrupts the MACF1 (microtubule-actin crosslinking factor 1) and POLN genes, respectively. Interestingly, the (1;4) fusion was present at diagnosis and at relapse, whereas the (4;17) fusion was detected at relapse only, leading to a secondary 17q gain confirmed by array CGH therefore indicating that 17q gain may not be a primary event in neuroblastoma. Finally, screening of a panel of neuroblastoma cell lines identified interstitial telomeric sequences in three other cases, suggesting that this may be a recurrent mechanism leading to unbalanced translocations in neuroblastoma.

Identification of tumor-associated antigens by screening phage-displayed human cDNA libraries with sera from tumor patients.

Screening cDNA libraries from solid human tumors with sera of autologous patients (SEREX) has proven to be a powerful approach to identifying tumor antigens recognized by the humoral arm of the immune system. In many cases, application of this methodology has led to the discovery of novel tumor antigens as unknown gene products. We tried to improve the potency of the SEREX approach by combining it with phage-display technology. We designed a new lambda vector to express protein fragments as N-terminal fusions to the D capsid protein and generated high-complexity cDNA libraries from human breast carcinoma cell lines and solid tumors. Screening these phage-displayed libraries required limited amounts of sera from patients and efficiently identified several tumor antigens specifically reacting with sera from breast cancer patients.

Identification and cloning potentially protective antigens of Coxiella burnetii using sera from mice experimentally infected with Nine Mile phase I.

Coxiella burnetii is an obligate intracellular bacterium that causes acute Q fever and occasional chronic infections in humans. To determine the immunodominant antigens during infection with C. burnetii, sera from mice experimentally infected with Nine Mile phase I were tested by immunoblotting. The mouse sera recognized antigens with a variety of molecular weights, including proteins of 14, 22, 28, 34, and 60 kDa as immunodominant antigens. In order to clone potential protective antigens, a genomic DNA library of Nine Mile phase I was constructed in the expression vector Lambda ZAP Express and screened with sera from mice that recovered from C. burnetii infection. A total of 102 immunoreactive clones with various signal intensities were identified from about 8,000 plaques. These clones were purified and expressed in the excised plasmid pBK-CMV. The proteins expressed by these recombinant plasmids were analyzed by SDS-PAGE and immunoblotting. Fifty-four clones expressed immunoreactive proteins of molecular masses ranging from approximately 14 to 60 kDa. Sequence analysis and BLAST search of the recently completed genome sequence identified a variety of novel immunoreactive proteins. These proteins are logical vaccine candidates for testing protective activity against C. burnetii challenge. We established a sublethal challenge model in BALB/c mice with protection from the development of severe splenomegaly as an indicator of vaccinogenic activity. Further characterization of these proteins will provide essential information for developing novel, specific diagnostic reagents and potential subunit vaccine candidates against C. burnetii infection.

Pparity of charmed particles from associative photoproduction ofDandD*-mesons

We suggest to measure the triple polarization correlations in the exclusive associative charm particle photoproduction, vector gamma + vector p --> vector Lambda_c^{++} bar{D^0} with linearly polarized photons, as a method to determine the P-parity of the charmed D-meson. The dependence of these correlations on the parity P(N Lambda_c D) can be predicted in model independent way. The t-dependence of the differential cross section for vector meson photoproduction, gamma + p --> Lambda_c^{++} bar{D^{*0}}, in a model based on D-exchange, is also sensitive to P(N Lambda_c D).

Preparing lambda libraries for expression of proteins in prokaryotes or eukaryotes.

AbstractComplementary DNA (cDNA) libraries represent the information encoded in the messenger RNA (mRNA) of a particular tissue or organism. RNA molecules are exceptionally labile and difficult to amplify in their natural form. For this reason, a cDNA library is created by converting the information encoded by the RNA into a stable DNA duplex (cDNA) and then inserting it into a self-replicating lambda or plasmid vector. Individual cDNA representing the original genetic information can be isolated from the cDNA library and examined with relative ease. KeywordsPhagemid VectorEcoRI AdapterPackaging ExtractPhage StockPrimary LibraryThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

GENERATION AND CHARACTERIZATION OF CDNA CLONES FROM SARCOPTES SCABIEI VAR. HOMINIS FOR AN EXPRESSED SEQUENCE TAG LIBRARY: IDENTIFICATION OF HOMOLOGUES OF HOUSE DUST MITE ALLERGENS

Molecular studies on scabies, a disease of considerable human and veterinary significance, have been limited because of the difficulty of obtaining the causative organism Sarcoptes scabiei, the "itch mite." We have used skin from the bedding of crusted scabies patients as a source of mites for the construction of libraries of cDNAs from S. scabiei var. hominis in the bacteriophage lambda vector lambdaZAP express. Sequences of 145 clones established that the libraries predominantly contain sequences from S. scabiei, enabling a major sequencing program to begin. Among those sequenced to date, cDNAs encoding S. scabiei homologues of 3 house dust mite allergens-the M-177 apolipoprotein, glutathione S-transferase, and paramyosin--were identified. The availability of cDNA libraries from S. scabiei var. hominis and S. scabiei var. vulpes and the emerging public sequence databases from both opens up new possibilities in scabies research.

Biotin-tagged cDNA expression libraries displayed on lambda phage: a new tool for the selection of natural protein ligands

cDNA expression libraries displayed on lambda phage have been successfully employed to identify partners involved in antibody-antigen, protein- protein and DNA-protein interactions and represent a novel approach to functional genomics. However, as in all other cDNA expression libraries based on fusion to a carrier polypeptide, a major issue of this system is the absence of control over the translation frame of the cDNA. As a consequence, a large number of clones will contain lambda D/cDNA fusions, resulting in the foreign sequence being translated on alternative reading frames. Thus, many phage will not display natural proteins, but could be selected, as they mimic the binding properties of the real ligand, and will hence interfere with the selection outcome. Here we describe a novel lambda vector for display of exogenous peptides at the C-terminus of the capsid D protein. In this vector, translation of fusion peptides in the correct reading frame allows efficient in vivo biotinylation of the chimeric phage during amplification. Using this vector system we constructed three libraries from human hepatoma cells, mouse hepatocytic MMH cells and from human brain. Clones containing open reading frames (ORFs) were rapidly selected by streptavidin affinity chromatography, leading to biological repertoires highly enriched in natural polypeptides. We compared the selection outcome of two independent experiments performed using an anti-GAP-43 monoclonal antibody on the human brain cDNA library before and after ORF enrichment. A significant increase in the efficiency of identification of natural target peptides with very little background of false-positive clones was observed in the latter case.

Cloning of a complementary DNA encoding the unique dendritic cell antigen Ki-M9.

Human sinus-lining cells (SLC) of the lymph node sinuses most probably represent accessory cells for the primary humoral immune response and have been shown to express a unique antigen recognized by the monoclonal antibody Ki-M9. To characterize this SLC-specific antigen further, a spleen cDNA library established in the expression vector lambda gt-11 was searched immunochemically for clones expressing the Ki-M9 antigen. Two recombinant phage clones revealed a cDNA with an open reading frame of 1666 bp encoding a 68-kDa protein. When fused with an expression vector that codes for the bacterial maltose-binding protein (MBP), the purified MBP-Ki-M9 fusion protein could be clearly detected by Western blot analysis. Furthermore, in situ hybridization with Ki-M9 cDNA as a probe confirmed the SLC-specific expression of the cloned cDNA. Additionally, Ki-M9 mRNA transcripts were detected in follicular dendritic reticulum cells of the secondary germinal centers, in a few cells of the perifollicular zone of the spleen, in some sinusoidal cells of liver, and in thymic reticular cells. A sequence database research revealed a strong homology to a murine cDNA. By applying non-radioactive in situ hybridization on mouse tissue, strong expression in SLC of the lymph node and metallophilic cells of the spleen in mouse tissue could be seen indicating that the Ki-M9 cDNA is highly conserved in the two species. Further computer analysis of the deduced amino acid sequence of the Ki-M9 antigen showed a large number of potential glycosylation sites and a PEST motive, which are characteristic for rapidly degraded membrane bound proteins and represent prerequisites for the function of this cell system in initiating the humoral immune response.

Molecular characterisation of a major 29 kDa surface antigen of Sarcocystis neurona

A gene encoding a major 29 kDa surface antigen from Sarcocystis neurona, the primary causative agent of equine protozoal myeloencephalitis (EPM), was cloned, sequenced, and expressed as a recombinant protein. A cDNA library was prepared in the expression vector lambda ZAP from polyA+mRNA isolated from S. neurona merozoites cultivated in vitro. Random sequencing of 96 clones identified a clone of an abundant transcript having a translated amino acid sequence with 30% identity to the 31-kDa surface antigen of Sarcocystis muris cyst merozoites. Southern blot analysis indicated that the corresponding gene exists in low copy number within the S. neurona genome, but RNA blot analysis and other data indicated that the gene transcript is highly abundant. The sequence of the cDNA clone encoded an open reading frame specifying a polypeptide of 276 amino acids with a predicted size of 28.7 kDa. The deduced amino acid sequence displayed a hypothetical N-terminal signal peptide sequence followed by a polypeptide containing 12 cysteines. The coding region of the cDNA insert was subcloned into the expression vector pET14b, and a fusion protein expressed. The recombinant polypeptide was recognised by mAb 2A7 and mAb 1631, directed against a 29 kDa native protein found on the surface of cultured merozoites. Antibodies in serum and cerebrospinal fluid from a horse with EPM recognised a 29 kDa native protein of S. neurona merozoites and the 29 kDa recombinant protein. This S. neurona surface antigen is named SnSAG1.

Bacteriophage lambda and plasmid pUR288 transgenic fish models for detecting in vivo mutations.

We adapted transgenic rodent mutation assays based on fish carrying bacteriophage lambda and plasmid pUR288 vectors to address the needs for improved methods to assess health risks from exposure to environmental mutagens and also to establish new animal models to study in vivo mutagenesis. The approach entails separating the vectors from fish genomic DNA and then shuttling them into specialized strains of E. coli bacteria to analyze spontaneous and induced mutations in either lacI and cII or lacZ mutational targets. Fish exhibited low frequencies of spontaneous mutants comparable to the sensitivity of transgenic rodent models. Mutations detected after treating fish with chemical mutagens showed concentration-dependent, tissue-specific, and time-dependent relationships. Spontaneous and induced mutational spectra also were consistent with the specificity of known mutagens, further supporting the utility of transgenic fish for studies of in vivo mutagenesis.