Target Discovery and Validation Reviews and Protocols

Target Discovery and Validation Reviews and Protocols
Author: Mouldy Sioud
Publisher: Springer Science & Business Media
Total Pages: 360
Release: 2008-02-04
Genre: Medical
ISBN: 1597451657

Target discovery is a field that has existed for several years but is so vibrant today because of the recent progress in our understanding of the molecular mechanisms of many human diseases and the technical advances in target identification and validation. More sophisticated gene profiling technologies, such as DNA microarrays and serial analysis of gene expression, permit rapid identification of lead targets. Moreover, analysis of gene networks in living organisms allows the identification of target genes that operate in defined physiological pathways. With the sequencing of several genomes completed and the rapidly growing gene expression databases, there is now greater impetus than ever before for in silico discovery of therapeutic targets. Also, recent advances in genetic technologies have increased our ability to generate mouse models for human diseases. The implications of these genetically modified animals in drug development are several, including identification of new drug targets, predicting efficacy, and uncovering possible side effects. Together, these recent technical advances should allow researchers to make the most informed choice early and advance the chosen targets toward clinical studies. Regarding cancers, any difference between a cancer and a normal cell could potentially be exploited as a therapeutic target. The hope is that drugs targeting specific constituents or pathways in cancer cells will provide more effective therapy, either alone or in combination with other currently used anticancer drugs. In addition to drug targets, identifying new target antigens remains as much of a challenge as improving tumor vaccines already in the clinic.

Target Discovery and Validation Reviews and Protocols

Target Discovery and Validation Reviews and Protocols
Author: Mouldy Sioud
Publisher: Humana Press
Total Pages: 354
Release: 2006-10-15
Genre: Medical
ISBN: 9781588296566

Target discovery is a field that has existed for several years but is so vibrant today because of the recent progress in our understanding of the molecular mechanisms of many human diseases and the technical advances in target identification and validation. More sophisticated gene profiling technologies, such as DNA microarrays and serial analysis of gene expression, permit rapid identification of lead targets. Moreover, analysis of gene networks in living organisms allows the identification of target genes that operate in defined physiological pathways. With the sequencing of several genomes completed and the rapidly growing gene expression databases, there is now greater impetus than ever before for in silico discovery of therapeutic targets. Also, recent advances in genetic technologies have increased our ability to generate mouse models for human diseases. The implications of these genetically modified animals in drug development are several, including identification of new drug targets, predicting efficacy, and uncovering possible side effects. Together, these recent technical advances should allow researchers to make the most informed choice early and advance the chosen targets toward clinical studies. Regarding cancers, any difference between a cancer and a normal cell could potentially be exploited as a therapeutic target. The hope is that drugs targeting specific constituents or pathways in cancer cells will provide more effective therapy, either alone or in combination with other currently used anticancer drugs. In addition to drug targets, identifying new target antigens remains as much of a challenge as improving tumor vaccines already in the clinic.

Agrobacterium Protocols

Agrobacterium Protocols
Author: Kan Wang
Publisher: Springer Science & Business Media
Total Pages: 474
Release: 2008-02-04
Genre: Science
ISBN: 1597451304

Agrobacterium tumefaciens is a soil bacterium that for more than a century has been known as a pathogen causing the plant crown gall disease. Unlike many other pathogens, Agrobacterium has the ability to deliver DNA to plant cells and permanently alter the plant genome. The discovery of this unique feature 30 years ago has provided plant scientists with a powerful tool to genetically transform plants for both basic research purposes and for agricultural development. Compared to physical transformation methods such as particle bomba- ment or electroporation, Agrobacterium-mediated DNA delivery has a number of advantages. One of the features is its propensity to generate a single or a low copy number of integrated transgenes with defined ends. Integration of a single transgene copy into the plant genome is less likely to trigger “gene silencing” often associated with multiple gene insertions. When the first edition of Agrobacterium Protocols was published in 1995, only a handful of plants could be routinely transformed using Agrobacterium. Agrobacterium-mediated transformation is now commonly used to introduce DNA into many plant species, including monocotyledon crop species that were previously considered non-hosts for Agrobacterium. Most remarkable are recent developments indicating that Agrobacterium can also be used to deliver DNA to non-plant species including bacteria, fungi, and even mammalian cells.

YAC Protocols

YAC Protocols
Author: Alasdair MacKenzie
Publisher: Springer Science & Business Media
Total Pages: 209
Release: 2007-10-26
Genre: Science
ISBN: 1597451584

It is now 10 years since the first edition of YAC Protocols was published in 1996. YAC Protocols was first produced to address the huge demand within the research community for a lab-based text that described in detail the wide range of uses for large insert yeast artificial chromosome (YAC) DNA clones. In doing this, the original editor, David Markie, and the many different contri- tors who provided descriptions of the protocols they used and developed, did a magnificent job. Indeed many of the techniques described within the first e- tion require little change and have stood up admirably to the test of time. Since the first edition, the use of YACs has proved invaluable for addressing a wide range of new biological problems ranging from those of basic biochemistry to assisting in the mapping and sequencing of the human genome. The requirement for a second edition of YAC Protocols was prompted by a number of major advances in biology since the publication of the first edition. These advances have included the sequencing of the human genome, and the genomes of a wide variety of other organisms, and the increased use of transgenic animals for understanding the molecular basis of human and animal disease.

Glycobiology Protocols

Glycobiology Protocols
Author: Inka Brockhausen
Publisher: Springer Science & Business Media
Total Pages: 388
Release: 2008-02-04
Genre: Science
ISBN: 1597451673

Glycobiology involves studies of complex carbohydrates and posttrans- tional modifications of proteins, and has become an important interdiscip- nary field encompassing chemistry, biochemistry, biology, physiology, and pathology. Although initial research was directed toward elucidation of the different carbohydrate structures and the enzymes synthesizing them, the field has now moved toward identifying the functions of carbohydrates. The pro- cols described in Glycobiology Protocols form a solid basis for investigations of glycan functions in health and disease. The cloning of many of the genes participating in glycosylation processes has helped to enhance our knowledge of how glycosylation is controlled, but has also added another dimension of complexity to the great heterogeneous variety of the structures of the oligos- charides of glycoproteins, proteoglycans, and glycolipids. A family of similar enzyme proteins exists for each glycosylation step. Glycosyltransferases are extremely specific for both the nucleotide sugar donor and the acceptor s- strate, but many other factors control sugar transfer, including the locali- tion and topology of enzymes, cofactors, possible chaperone proteins, and the availability of sugar acceptor substrates. The analysis of the intracellular organization of glycosylation and of the factors controlling the activities of the participating enzymes in the cell are important areas that need more research efforts. Another challenge for future research is to understand the glycodynamics of a cell, that is, how the cell responds to stimuli leading to biological and pathological changes in terms of alterations in glycosylation, and how this affects the biology of the cell.

Protein Folding Protocols

Protein Folding Protocols
Author: Yawen Bai
Publisher: Springer Science & Business Media
Total Pages: 332
Release: 2008-02-04
Genre: Science
ISBN: 1597451894

Covering experiment and theory, bioinformatics approaches, and state-of-the-art simulation protocols for better sampling of the conformational space, this volume describes a broad range of techniques to study, predict, and analyze the protein folding process. Protein Folding Protocols also provides sample approaches toward the prediction of protein structure starting from the amino acid sequence, in the absence of overall homologous sequences.

Nuclear Transfer Protocols

Nuclear Transfer Protocols
Author: Paul J. Verma
Publisher: Springer Science & Business Media
Total Pages: 684
Release: 2008-02-02
Genre: Science
ISBN: 1597451541

Nuclear Transfer Protocols: Cell Reprogramming and Transgenesis is a comprehensive review of nuclear transfer technology in vertebrates, aimed at reprogramming differentiated nuclei and effecting targeted gene transfer. The emphasis here is on providing readily reproducible techniques for the gene- tion of cloned embryos and animals in a number of key research and commercially important vertebrates. Additional chapters provide alternative cutting-edge methods for nuclear transfer, such as zona-free nuclear transfer and serial nuclear transfer. Of immense practical benefit are descriptions of procedures associated with cloning, such as in vitro maturation of oocytes, activation and culture of cloned embryos, maintenance of pregnancy, and neonatal care of clones. Nuclear Transfer Protocols: Cell Reprogramming and Transgenesis also provides an understanding of the factors involved in nuclear reprogramming, which is imperative for the success of cloning. A section dealing with such cloning-related issues as aging and normality of clones is also included making this an essential comprehensive handbook for research and commercial labo- tories involved in, or intending to work on, nuclear transfer. The volume will prove beneficial to molecular biologists, stem cell biologists, clinicians, biotechnologists, students, veterinarians, and animal care technicians involved with reprogramming, nuclear transfer, and transgenesis.

Protein Engineering Protocols

Protein Engineering Protocols
Author: Kristian Müller
Publisher: Springer Science & Business Media
Total Pages: 318
Release: 2007-10-26
Genre: Science
ISBN: 1597451878

Protein engineering is a fascinating mixture of molecular biology, protein structure analysis, computation, and biochemistry, with the goal of developing useful or valuable proteins. Protein Engineering Protocols will consider the two general, but not mutually exclusive, strategies for protein engineering. The first is known as rational design, in which the scientist uses detailed knowledge of the structure and function of the protein to make desired changes. The s- ond strategy is known as directed evolution. In this case, random mutagenesis is applied to a protein, and selection or screening is used to pick out variants that have the desired qualities. By several rounds of mutation and selection, this method mimics natural evolution. An additional technique known as DNA shuffling mixes and matches pieces of successful variants to produce better results. This process mimics recombination that occurs naturally during sexual reproduction. The first section of Protein Engineering Protocols describes rational p- tein design strategies, including computational methods, the use of non-natural amino acids to expand the biological alphabet, as well as impressive examples for the generation of proteins with novel characteristics. Although procedures for the introduction of mutations have become routine, predicting and und- standing the effects of these mutations can be very challenging and requires profound knowledge of the system as well as protein structures in general.