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PubMed1993

Construction of primary and subtracted cDNA libraries from early embryos.

By modifying current cDNA cloning and electroporation methods, large and representative murine cDNA libraries were synthesized from 10 to 100 ng mRNA isolated from unfertilized egg and preimplantation mouse embryos. High cloning efficiency is essential for complete representation of genes expressed in egg and preimplantation embryos and for the isolation of stage-specific genes using subtractive hybridization. Because the mouse embryo contains no more than 50 pg of poly(A)+ mRNA at any stage of preimplantation development, approximately 5000-10,000 embryos are required to obtain enough mRNA to synthesize libraries using current methods. To obtain a representative library that also includes rare transcripts, the size of the library should be at least 10(6) clones. The average percent conversion of mRNA to single-stranded cDNA was 20-40%, so that a cloning efficiency of nearly 2 x 10(8) cfu/microgram cDNA is required for such a cDNA library. No previous methods have provided directional cloning of cDNA into plasmids with these high efficiencies. The advent of electroporation methods for the introduction of nucleic acids into bacteria has made possible the use of standard plasmid vectors for high-efficiency cDNA cloning. Plasmid vectors are currently available that can accommodate the directional cloning of cDNA such that T7 and T3 RNA polymerase promoter sequences can be used to generate sense and anti-sense transcripts for subtractive hybridization and riboprobe synthesis. The cDNA libraries we derived using this methodology are a reusable and abundant source of genetic information about the control of preimplantation development. Specialized subtractive cDNA libraries enriched for genes expressed exclusively at a predetermined time in development give access to genes expressed in a stage-specific manner. The ability to construct new cDNA libraries from limited amounts of starting material ensures the provision of new and important resources for the identification and study of novel genes or gene families, and it is an important new tool for understanding the molecular control of mammalian development.

Animals↗
PubMed1990

Prophage lambda libraries for isolating cDNA clones by functional screening.

Isolation of cDNA clones from lambda gt11 phage libraries by functional screening is limited by the low amount of lacZ-cDNA-encoded fusion protein synthesized in an isolated phage plaque. The amount of specific cDNA-encoded protein can be significantly enhanced by expression in bacterial colonies rather than phage plaques. Escherichia coli was lysogenized with a lambda gt11 cDNA expression library from Dictyostelium discoideum. Bacteria were selected for the presence of the lambda gt11 prophage by elimination of nonlysogenic parental cells with a lambda cI phage. The usefulness of the lysogen library was demonstrated by immuno-screening and functional screening with two different radiolabeled ligands. cDNA clones encoding a well-characterized D. discoideum protein, the regulatory subunit of the cAMP-dependent protein kinase, were isolated by screening the lysogen library with antibodies. Clones encoding this protein could also be identified by functional screening with [3H]cAMP, demonstrating that the limit of detection of positive clones by ligand screening is at least an order of magnitude lower for the lysogen library than for the corresponding phage library. We have subsequently used the lysogen library to isolate cDNA clones encoding calmodulin-binding protein(s) from D. discoideum by functional screening with [125I]calmodulin. For these clones, screening of the corresponding phage library had previously been found unsuccessful.

Bacteriophage lambda↗
PubMed1992

Microdissection of human chromosomal regions 8q23.3-q24.11 and 2q33-qter: construction of DNA libraries and isolation of their clones.

Human chromosomal regions 8q23.3-q24.11 and 2q33-qter were microdissected, DNAs from the regions were amplified with the primer-linker method of polymerase chain reaction (PCR), and their DNA libraries were constructed by cloning into pUC19. The primer-linker PCR involved Sau3AI digestion of microdissected chromosomal DNAs, ligation of the digests to a 10mer DNA linker and 24mer primer, filling the recessed 3' ends, and PCR amplification using the 24mer DNA as a primer. A total of 3.5 x 10(4) pUC19 recombinants (8q library) from the 8q region and 5.0 x 10(4) pUC clones (2q library) from the 2q region were obtained. From the 8q library, 60 pUC clones were selected, while 88 pUC-clones were selected from the 2q library. These clones were Southern blot analyzed on hybrid cell panels with or without human chromosome 8 or 2. Twelve (20%) of the 60 8q-derived clones were unique DNA sequences, and 9 were subjected to deletion analysis in the genomic DNA of two patients, one with trichorhino-phalangeal syndrome (TRPS) type I and the other with TRPS type II, both with del(8) (q23.3q24.13). Five of the 9 pUC clones tested showed a one-copy density in both patients, an indication that the clones map to the region deleted in both patients. Screening a genomic DNA library constructed in the phage revealed a clone with a 9.4-kb insert and a one-copy density in both patients. From the 2q library, 15 (17%) of the 88 pUC clones obtained were unique sequences. When a phage library was screened, 8 clones were obtained: 4 were identical and 2 were overlapping sequences.(ABSTRACT TRUNCATED AT 250 WORDS)

Abnormalities, Multiple↗
PubMed2005

Construction, evaluation and refinement of a large human antibody phage library based on the IgD and IgM variable gene repertoire.

The ability to isolate antibodies against any antigen of interest has become increasingly important as antibodies have proved their utility both in antigen detection, quantification and as specific in vivo targeting agents. To this end, we have constructed a large antibody phage library in the single chain Fv (scFv) phagemid format based on the naive human variable (V) gene repertoire dictated by IgD and IgM. Optimizing each step of the library construction has resulted in a highly diverse and functional library, as assessed by sequencing analysis, large-scale automated expression analysis and antigen screening. Furthermore, the versatile format of the library, which comprises 14 separate sub-libraries, adds considerably flexibility with respect to which part of the antibody repertoire that is to be probed. This versatility has been further exploited to generate a refined antibody library, which exhibits one of the highest prokaryotic expression levels reported to date for a naive repertoire. The construction of the refined library was based on the functional purification of expressed V genes in the context of the protein L interaction with correctly folded V genes of the kappa light chain family. Antigen screening of this library indicated that the functional purification improved the ability to retrieve antigen specific antibodies, but at the cost of potential loss of diversity in the isolated repertoire.

Amino Acid Sequence↗
PubMed2004

Phage-displayed antibody libraries of synthetic heavy chain complementarity determining regions.

A structure-based approach was used to design libraries of synthetic heavy chain complementarity determining regions (CDRs). The CDR libraries were displayed as either monovalent or bivalent single-chain variable fragments (scFvs) with a single heavy chain variable domain scaffold and a fixed light chain variable domain. Using the structure of a parent antibody as a guide, we restricted library diversity to CDR positions with significant exposure to solvent. We introduced diversity with tailored degenerate codons that ideally only encoded for amino acids commonly observed in natural antibody CDRs. With these design principles, we reasoned that we would produce libraries of diverse solvent-exposed surfaces displayed on stable scaffolds with minimal structural perturbations. The libraries were sorted against a panel of proteins and yielded multiple unique binding clones against all six antigens tested. The bivalent library yielded numerous unique sequences, while the monovalent library yielded fewer unique clones. Selected scFvs were converted to the Fab format, and the purified Fab proteins retained high affinity for antigen. The results support the view that synthetic heavy chain diversity alone may be sufficient for the generation of high-affinity antibodies from phage-displayed libraries; thus, it may be possible to dispense with the light chain altogether, as is the case in natural camelid immunoglobulins.

Amino Acid Sequence↗
PubMed2004

Identification of unique transcripts from a mouse full-length, subtracted inner ear cDNA library.

A small-scale full-length library construction approach was developed to facilitate production of a mouse full-length cDNA encyclopedia representing approximately 250 enriched, normalized, and/or subtracted cDNA libraries. One library produced using this approach was a subtracted adult mouse inner ear cDNA library (sIEa). The average size of the inserts was approximately 2.5 kb, with the majority ranging from 0.5 to 7.0 kb. From this library 22,574 sequence reads were obtained from 15,958 independent clones. Sequencing and chromosomal localization established 5240 clusters, with 1302 clusters being unique and 359 representing new ESTs. Our sIEa library contributed 56.1% of the 7773 nonredundant Unigene clusters associated with the four mouse inner ear libraries in the NCBI dbEST. Based on homologous chromosomal regions between human and mouse, we identified 1018 UniGene clusters associated with the deafness locus critical regions. Of these, 59 clusters were found only in our sIEa library and represented approximately 50% of the identified critical regions.

Amino Acid Sequence↗
PubMed2002

Phage versus phagemid libraries for generation of human monoclonal antibodies.

Non-immune (naïve) phage antibody libraries have become an important source of antibodies for reagent, diagnostic, and therapeutic use. To date, reported naïve libraries have been constructed in phagemid vectors as fusions to pIII, yielding primarily single copy (monovalent) display of antibody fragments. For this work, we subcloned the single chain Fv (scFv) gene repertoire from a naïve phagemid antibody library into a true phage vector to create a multivalently displayed scFv phage library. Compared to monovalently displayed scFv, multivalent phage display resulted in improved efficiency of display as well as antibody selection. A greater number of antibodies were obtained and at earlier rounds of selection. Such increased efficiency allows the screening for binding antibodies after a single round of selection, greatly facilitating automation. Expression levels of antigen-binding scFv were also higher than from the phagemid library. In contrast, the affinities of scFv from the phage library were lower than from the phagemid library. This could be overcome by utilizing the scFv in a multivalent format, by affinity maturation, or by converting the library to monovalent display after the first round of selection.

Amino Acid Sequence↗
PubMed2002

Air quality and well-being perception in subjects attending university libraries in Modena (Italy).

We studied four libraries in the University of Modena and Reggio Emilia (Northern Italy) to determine the presence of polluting agents such as total dusts, formaldehyde and other volatile organic compounds (VOCs) including benzene, toluene and xylenes and to assess the sense of well-being perceived by library users. This investigation was suggested by an increase in reported symptoms related to Sick Building Syndrome (SBS) observed in recent decades among people spending most of their time in various indoor environments, including libraries. The microclimatic conditions and the concentrations of pollutants indicated an acceptable situation on the whole, even though a wide range of total dust values (40-350 microg/m3) and total VOCs (203-749 microg/m3) was observed. However, the perception of the different environmental parameters by the 130 library users that were interviewed identified the existence of some discomfort mainly caused by the feeling of poor ventilation. Moreover, 78.5% of the subjects stated they had at least one of the 16 investigated symptoms potentially related to a SBS. The place of occurrence of the self-reported symptoms was also investigated, the symptoms arising during library attendance more frequently than elsewhere were only four, and in particular feeling hot, sore eyes, dry throat and breathing difficulties. Overall, our study has shown the existence of an association between microclimatic perceptions as reported by library users and subjective symptoms related to SBS, considering the four libraries separately, the highest prevalence of self-reported symptoms was found in the library where environmental discomfort as perceived by users was greatest. Nevertheless, an association between subjective self-reported symptoms and both microclimatic conditions as resulted by instrumental measurements and/or pollutants concentrations was not apparent.

Adult↗
PubMed2002

Polyclonal anti-colorectal cancer Fab phage display library selected in one round using density gradient centrifugation to separate antigen-bound and free phage.

A combinatorial Fab phage display library generated from antibody variable (V) region genes of BALB/c mice immunized with the human colorectal cancer cell lines SW480, SW948, and SW837, was used to isolate an anti-colorectal cancer library. In an attempt to preserve as many anti-colorectal cancer specificities as possible, the original Fab phage display library was selected for binding to a suspension of the human colorectal cancer cells using density gradient centrifugation, instead of washes, to separate cell-bound and free phage. The method consists of placing the cell-phage mixture on a layer of fetal bovine serum (FBS) which had been overlaid on a "cushion" of percoll density medium in a soft, polyallomer tube. After centrifugation, free phage remain on top of the serum layer, whereas the colorectal cancer cells with bound phage are recovered from the serum-percoll interface with a syringe. Analysis of the selected phage display library by enzyme linked immunosorbent assay (ELISA) and diagnostic restriction enzyme digests of individual members (fingerprinting), revealed about 90% anti-colorectal cancer diverse clones after only one round of selection. After conversion to a library of full-length antibodies, such an anti-cancer polyclonal library could be useful for therapeutic and/or diagnostic applications. The density gradient centrifugation method presented here holds great promise for the generation of polyclonal antibody libraries (PCALs) to complex antigens. It is also applicable for selection of peptide or other phage display libraries on any insoluble ligand.

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↗
PubMed2001

Comparative evaluation of 5'-end-sequence quality of clones in CAP trapper and other full-length-cDNA libraries.

To enhance the usefulness of the laboratory mouse and to facilitate the rapid assay of gene functions we have been collecting the entire set of mouse full-length cDNA by one-pass sequencing. To collect full-length cDNA clones efficiently, it is critical to construct high-quality cDNA libraries. In recent years, we have been developing a way to construct full-length cDNA libraries by using biotinylation of the cap structure (the 'CAP-trapper' method) coupled with treatment to increase reverse transcriptase efficiency at high temperature by the addition of trehalose. In this paper we report our evaluation of the quality of CAP trapper and a number of other full-length cDNA libraries, including the results of 5' end analysis of clones in CAP trapper and the other libraries. We used a procedure that compared the 5'-ends of cDNA clones with those of genes in the public databases. Our analysis showed that 63% of cDNA clones in CAP trapper libraries had sequences that were either the same length as those of equivalent genes in the public database or 5'-extended, and that 90% of these clones maintained their coding sequences. These results indicate that the CAP trapper library is a promising tool for collecting full-length cDNA in large-scale projects. Comparison of the quality of CAP trapper with that of other full-length-cDNA libraries confirmed the value of these libraries.

Algorithms↗
PubMed2001

Construction and characterization of a cDNA library from 4-week-old human embryo.

Development and differentiation studies of early human embryos have been severely impeded by general difficulties in obtaining suitable samples. In order to isolate and identify new genes expressed during early human development, we constructed and characterized a PCR-based cDNA library using a 4-week-old chorion-free human embryo. The constructed cDNA library contained 6.3 x 10(6) directional recombinants, and its insert size ranged from 0.4 to 1.8 kb. The cDNA library proportionally represents the mRNA population, containing beta-actin, tPA and LINE1 repetitive sequences at the expected frequencies as in other conventionally constructed and PCR-based cDNA libraries. PCR analyses of the library for specific genes have also revealed the presence of cDNAs for developmentally important genes such as CD59, MCP, Quox-1 and ZNF268. Among the 70 randomly selected cDNA clones, 53% encoded previously known genes, 26% matched with anonymous sequences, and 17% showed no sequence similarity and were designated as human early embryo-specific ESTs. These results demonstrate the sequence complexity and relatively low redundancy of our cDNA library. Furthermore, approximately 40% of those randomly analyzed clones contained full-length encoding regions. To our knowledge, this is the first description of the PCR-based cDNA library from a 4-week-old chorion-free human embryo, and the presence of novel sequences within this library makes it a valuable and unique resource for studying gene expression and regulatory mechanisms that underlie the early process of human embryogenesis.

Cloning, Molecular↗
PubMedDate not supplied

Combinatorial library design for diversity, cost efficiency, and drug-like character.

Most computational techniques for the design of combinatorial libraries have concentrated solely on maximizing the diversity of the selected subset or its similarity to a known target. However, such libraries can produce high-throughput screening hits with properties that make them unsuitable to take forward into medicinal chemistry. This article describes software that allows the design of library subsets to simultaneously optimize a library's diversity or similarity to a target, properties (such as drug likeness) of the library members, properties (such as cost) of the reagents required to make them, and efficiency of synthesis in arrays or mixtures. Example are given showing that libraries can be designed to contain drug-like molecules with only a small trade-off in terms of the maximum possible diversity, and that the cost of the library, in terms of the reagents required to make it, can be contained. Other examples show that libraries can be designed to minimize the deconvolution problem or to maximize the number of molecules predicted to be active while also being designed for efficiency of synthesis.

Algorithms↗
PubMed2002

Designing focused libraries using MoSELECT.

When designing a combinatorial library it is usually desirable to optimise multiple properties of the library simultaneously and often the properties are in competition with one another. For example, a library that is designed to be focused around a given target molecule should ideally have minimum cost and also contain molecules that are bioavailable. In this paper, we describe the program MoSELECT for multiobjective library design that is based on a multiobjective genetic algorithm (MOGA). MoSELECT searches the product-space of a virtual combinatorial library to generate a family of equivalent solutions where each solution represents a combinatorial subset of the virtual library optimised over multiple objectives. The family of solutions allows the relationships between the objectives to be explored and thus enables the library designer to make an informed choice on an appropriate compromise solution. Experiments are reported where MoSELECT has been applied to the design of various focused libraries.

Algorithms↗
PubMed2005

Active-site specificity of digestive aspartic peptidases from the four species of Plasmodium that infect humans using chromogenic combinatorial peptide libraries.

Two targeted chromogenic octapeptide combinatorial libraries, comprised of 38 pools each containing 361 different peptides, were used to analyze the enzyme/substrate interactions of five plasmepsins. The first library (P1 library) was based on a good synthetic aspartic peptidase substrate [Westling, J., Cipullo, P., Hung, S. H., Saft, H., Dame, J. B., and Dunn, B. M. (1999) Protein Sci. 8, 2001-2009; Scarborough, P. E., and Dunn, B. M. (1994) Protein Eng. 7, 495-502] and had the sequence Lys-Pro-(Xaa)-Glu-P1*Nph-(Xaa)-Leu. The second library (P1' library) incorporated results with the plasmepsins from the first library and had the sequence Lys-Pro-Ile-(Xaa)-Nph*P1'-Gln-(Xaa). In both cases, P1 and P1' were fixed residues for a given peptide pool, where Nph was a para-nitrophenylalanine chromogenic reporter and Xaa was a mixture of 19 different amino acids. Kinetic assays monitoring the rates of cleavage of these libraries revealed the optimal P1 and P1' residues for the five plasmepsins as hydrophobic substitutions. Extended specificity preferences were obtained utilizing liquid chromatography-mass spectrometry (LC-MS) to analyze the cleavage products produced by enzyme-catalyzed digestion of the best pools of each peptide library. LC-MS analysis of the P1-Phe and P1'-Phe pools revealed the favored amino acids at the P3, P2, P2', and P3' positions. These analyses have provided new insights on the binding preferences of malarial digestive enzymes that were used to design specific methyleneamino peptidomimetic inhibitors of the plasmepsins. Some of these compounds were potent inhibitors of the five plasmepsins, and their possible binding modes were analyzed by computational methods.

Animals↗
PubMed1999

A bacterial artificial chromosome library for soybean PI 437654 and identification of clones associated with cyst nematode resistance.

We have constructed a soybean bacterial artificial chromosome (BAC) library using the plant introduction (PI) 437654. The library contains 73 728 clones stored in 192 384-well microtiter plates. A random sampling of 230 BACs indicated an average insert size of 136 kb with a range of 20 to 325 kb, and less than 4% of the clones do not contain inserts. Ninety percent of BAC clones in the library have an average insert size greater than 100 kb. Based on a genome size of 1115 Mb, library coverage is 9 haploid genome equivalents. Screening the BAC library colony filters with cpDNA sequences showed that contamination of the genomic library with chloroplast clones was low (1.85%). Library screening with three genomic RFLP probes linked to soybean cyst nematode (SCN) resistance genes resulted in an average of 18 hits per probe (range 7 to 30). Two separate pools of forward and reverse suppression subtractive cDNAs obtained from SCN-infected and uninfected roots of PI437654 were hybridized to the BAC library filters. The 488 BACs identified from positive signals were fingerprinted and analyzed using FPC software (version 4.0) resulting in 85 different contigs. Contigs were grouped and analyzed in three categories: (1) contigs of BAC clones which hybridized to forward subtracted cDNAs, (2) contigs of BAC clones which hybridized to reverse subtracted cDNAs, and (3) contigs of BAC clones which hybridized to both forward and reverse subtracted cDNAs. This protocol provides an estimate of the number of genomic regions involved in early resistance response to a pathogenic attack.

Animals↗
PubMed2001

Construction and characterization of BAC libraries for three fish species; rainbow trout, carp and tilapia.

Bacterial artificial chromosome (BAC) libraries are important tools for genomic research. We have constructed seven genomic BAC libraries from three fish species, rainbow trout (Oncorhynchus mykiss), carp (Cyprinus carpio) and tilapia (Oreochromis niloticus). The two rainbow trout BAC libraries have average insert sizes of 58 and 110 kb. The average size of inserts in the carp BAC library is 160 kb. The average insert sizes of the four tilapia BAC libraries are 65, 105, 145 and 194 kb, respectively. These libraries represent good coverage of each genome (2-64 x coverage). The libraries can be screened by conventional colony hybridization and provide a starting point for the construction of high-density filtres or polymerase chain reaction (PCR) screening approaches. These BAC libraries will facilitate the positional cloning of quantitative trait loci (QTLs) for a variety of economically important traits in these species.

Animals↗
PubMed1998

Large scale isolation of osteoclast-specific genes by an improved method involving the preparation of a subtracted cDNA library.

BACKGROUND: Osteoclasts play crucial roles in bone resorption, which triggers bone remodeling. Molecular mechanisms underlying these osteoclast-specific biological functions remain elusive because only a limited number of osteoclast-specific genes have been identified. To circumvent this, we isolated a large number of osteoclast-specific genes by preparing a subtracted cDNA library of high quality. RESULTS: We first constructed a plasmid expression vector (pAP3neo) that allowed an efficient subtraction. Then, we improved the standard protocols for preparation of the cDNA library and the subsequent subtraction procedure. Using our protocol, we prepared a rabbit osteoclast cDNA library of high complexity. Subsequently, we prepared an osteoclast-specific cDNA library of high complexity by subtracting it with biotin-labelled mRNA, derived from rabbit spleen through the biotin-avidin method. The resulting library included a high proportion of full-length cDNA inserts. Using DNA dot blot analysis, we found that the osteoclast-specific cDNA clones were highly enriched in this subtracted cDNA library, i.e. nearly 70% of the analysed clones were primarily detected in osteoclasts but not in spleen. Multiple-tissue Northern analysis also showed that many of these clones were expressed almost exclusively in osteoclasts. DNA sequencing of randomly selected clones showed that 424 cDNA species out of 1136 analysed were novel. DNA sequencing also showed that our subtracted cDNA library was almost equalized, suggesting that the library may contain almost all of the osteoclast-specific genes. CONCLUSION: From these data, we conclude that our subtraction protocols, and the subsequent procedure for the analysis of the isolated clones developed here, are useful for the comprehensive isolation and identification of transcriptionally up- or down-regulated genes in general.

Animals↗