Molecular Diagnosis of Infectious Diseases

622 Pages·1998·37.372 MB·English

by  Peng Liang, Feilan Wang, Weimin Zhu, Robert P. O’Connell, Lidia Averboukh (auth.), Udo Reischl (eds.)

Molecular Diagnosis of Infectious Diseases
METHODS IN MOLECULAR MEDICINE"
John M. Walker, SERIESE DITOR
13. Molecular Diagnosis of Infectious Diseases, edited by Udo
Reischl, 1998
12. Diagnostic Virology Protocols, edited by John R. Stephenson
and Alan Warnes, 1998
11. Therapeutic Application of Ribozymes, edited by Kevin J.
Scanlon, 1998
10. Herpes Simplex Virus Protocols, edited by S. Moira Brown
and Alasdair MacLean, 1998
9. Lectin Methods and Protocols, edited by Jonathan M.
Rhodes and Jeremy D. Milton, 1998
8. Helicobacter pylori Protocols, edited by Christopher L.
Clayton and Harry L. T. Mobley, 1997
7. Gene Therapy Protocols, edited by Paul D. Robbins, 1997
6. Molecular Diagnosis of Cancer, edited by Finbarr Cotter,
1996
5. Molecular Diagnosis of Genetic Diseases, edited by Rob
Elles, 1996
4. Vaccine Protocols, edited by Andrew Robinson, Graham H.
Farrar, and Christopher N. Wiblin, 1996
3. Prion Diseases, edited by Harry F. Baker and Rosalind M.
Ridley, 1996
2. Human Cell Culture Protocols, edited by Gareth E. Jones,
1996
1. Antisense Therapeutics, edited by Sudhir Agrawal, 1996
Molecular Diagnosis
of Infectious
Diseases
Edited by
Udo Reischl
University of Regensburg, Germany
Foreword by
Hans Wolf
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Library of Congress Cataloging in Publication Data
Main entry under title:
Methods in molecularmediciner,.
Molecular diagnosis of infectious diseases / edited by Udo Reischh
p. cm. -- (Methods in molecular medicine r~ ; 13)
Includes index.
ISBN 0-89603-398-8 (combbound) 0-89603-485-2 (hardcover) (alk. paper)
1. Communicable Diseases--Molecular diagnosis. I. Reischl, Udo. I1. Series.
[DNLM: 1. Communicable Diseases--diagnosis. 2. Communicable Diseases--genetics.
3. Immunologic Tests. 4. Biological Assay. 5. Recombinant Proteins--diagnostic use. WC 100 M718
1998]
RC112,M652 1998
616.9'0475--dc21
DNLM/DLC 97-29087
for Library of Congress C1P
Foreword
In most societies the medical field is undergoing a dramatic reorienta-
tion. Fundamentally new technologies in diagnosis and therapy, as well as the
extension of life expectations, have increased health costs to an extent that
now nears the limits of acceptability.
One consequence has been a reevaluation of the need for and duration of
each individual hospitalization. For diagnostic laboratories, results must now
be obtained rapidly in order to include them in therapeutic decisions. Further-
more, therapeutic approaches to the control of infectious agents, limited by
the number of therapeutic compounds available and by the growing percent-
age of multiresistant agents, now require improvement in the precision of
diagnostic approaches. The necessity for maximal reduction of the risk of
infection by the development of appropriate pharmaceutical products demands
even higher levels of sensitivity in diagnostic tests.
Today's highly purified antigens---often from recombinantly generated
antigens or peptides, monoclonal or recombinant antibodies, and more sensi-
tive signal-production and signal-detection systems--have greatly advanced
immunologically based detection methodology. However, this approach has
biological limits that further enhancement of sensitivity cannot breach.
Fortunately nucleic acids have now been quite successfully added to the spec-
trum of diagnostic targets. Recombinant-produced antigens and the integration of
microelectronics and microfluidics offer new perspectives and possibilities.
The goals we hope to meet are precision and clinical relevance of test
results, as well as their rapid development in the interest of better and earlier
treatment and the prevention of further spread of infections. New test prin-
ciples and strategies can greatly support the achievement of these goals.
Our enthusiasm about what is now feasible must also take into account
the net financial effects on specific cases. Otherwise, progress may fail of
implementation owing to financial constraints.
Aware of this complexity, Dr. Udo Reischl and his colleagues have, in
Molecular Diagnosis of Infectious Diseases, provided a major new work that
should help us all secure both more sensitive and precise diagnoses.
Hans Wolf
Preface
Infectious diseases constitute one of the principal threats to public health.
During recent years, many improvements in antibiotic and antiviral therapy
have occurred; pathogens have nonetheless been able to develop mechanisms
that render them resistant toward many specific treatments. Furthermore, a
variety of recently discovered microorganisms, such as Helicobacter pylorL
hepatitis D and E virus, and HIV-2, have been newly identified as etiological
agents of human diseases.
In order to allow the rational and specific use of antibiotic and antiviral
pharmaceuticals, increasingly accurate detection and identification of the caus-
ative pathogen is of major importance, and imposes rising demands for better
specificity, sensitivity, and speed of the corresponding assay. The revolution-
ary progress associated with molecular biology-based technology, such as the
detection of DNA or the manufacture of recombinant antigens or antibodies,
has already produced major advances in medicine and will contribute to the
ongoing development of improved assay systems.
Basically, there are three different ways to detect specifically a given
pathogen: the detection of the pathogen itself(e.g., by microscopy, culture, or
biochemical characteristics); the direct detection of selected components of
the pathogen (e.g., nucleic acids, antigenic proteins); and, indirectly, by the
detection of specific antibodies generated by the infected organism.
Recently published books in the field of clinical microbiology are sub-
stantially focused on various aspects of PCR. As a consequence, most of
these fail to highlight the rapid methodological progress in serodiagnosis
that has been generated by recombinant proteins and antibodies. With per-
manently increasing demands of both cost per test and the clinical signifi-
cance of the results, the use of recombinant antigenic proteins and
recombinant antibodies for the serodiagnosis of infectious diseases has gained
even greater importance. Large quantities of recombinant proteins can now
be produced at comparatively low cost in suitable bacterial or cell culture
systems. Moreover, there is now available a wide variety of molecular bio-
logical techniques that have proved especially advantageous in the prepara-
tion of recombinant proteins.
v//
viii Preface
Apart from a brief description of the basic principles of immunological
assays, Molecular Diagnosis of Infectious Diseases describes both established
and novel strategies that have been successfully applied to the identification
of valuable diagnostic markers, to epitope mapping, to the production and
purification of recombinant antigens, and to their use as diagnostic reagents in
immunological assays. Basic problems in serological laboratory diagnosis are
also addressed. Some duplication of important topics has been purposely per-
mitted in order to offer the reader several approaches to the same problem.
Particular emphasis has been placed on the very promising area of biosensor
technology, and on recent developments in antibody engineering.
Instead of focusing on particular infectious agents, my hope is that the
present collection of detailed protocols will provide comprehensive and
up-to-date information, and so prove especially useful to those researchers
and students wishing to become more familiar with the principles of molecu-
lar diagnostics, guiding them in the development of test systems appropriately
tailored to their specific needs.
Since molecular biology-based tools are subject to ongoing improvement,
Molecular Diagnosis oflnfbctious Diseases does not attempt the impossible
task of covering every one of the many varied experimental approaches in the
field. Rather, it offers a kind of cross-section of the actual possibilities for
devising novel assays.
Undoubtedly further progress in the rapid and specific detection of patho-
genic organisms may be expected from modern molecular biology; the future
will reveal what kind of assay and what kind of diagnostic marker will ulti-
mately prove most useful in individual clinical situations.
I am especially indebted to Prof. Hans Wolf for giving me the opportu-
nity to gain substantial experience in the field of medical microbiology. With-
out his confidence and his continuous support, many things would not have
been possible. I wish to thank Prof. John Walker for his encouragement and
Humana Press for their excellent assistance during the assembly of this vol-
ume. I am also thankful to my wife Michaela for her patience and for placing
enough time at my disposal to launch this promising project. Finally, 1 am
grateful to all of the contributing authors for their constantly high level of
motivation and enthusiasm and, last but not least, for providing such good
manuscripts.
Udo Reischl
Contents
Foreword ........................................................................................................... v
Preface ........................................................................................................... vii
Contributors ................................................................................................... xiii
I RECOMBINANTP ROTEINS AND PEPTIDES ......................................................... I
IDENTIFICATION OF IMPORTANTA NTIGENS
1 Identification of Novel Diagnostic Markers by Differential Display,
Peng Liang, Feilan Wang, Weimin Zhu, Robert P. O'Connell,
and Lidia Averboukh ........................................................................ 3
2 Immunoprecipitation,
Karl Johansen and Lennart Svensson ............................................ 15
IDENTIFICATION OF CORRESPONDINGO PEN READING FRAMES
3 RT-PCR Methods and Applications,
Paul O. Siebert .................................................................................... 29
4 Quantitative RT-PCR,
Paul D. Siebert .................................................................................... 55
5 Cloning cDNA Ends Using RACE,
Yue Zhang and Michael A. Frohman ................................................ 81
IDENTIFICATION OF IMPORTANTA NTIGENIC EPITOPES
6 A Method for the Rapid Identification of Epitopes and Other
Functional Peptide Domains,
Robert C. Mierendorf, Beth Hammer, and Robert E. Novy .......... 107
7 Mapping of Linear B-Cell Epitopes on Viral Polypeptides by Multiple
Peptide Synthesis and Fine Tuning Sensitivity and Specificity of the
Identified Peptide Antigens for Application in Virus Diagnosis,
Ulla Wienhues, Wolfgang Kraas, Christoph Seidel, Hans Georg
Ihlenfeldt, and G~nther Jung ...................................................... 125
CLONING AND EXPRESSIONO F OPEN READING FRAMES IN PROKARYONTICS YSTEMS
8 Amplification of Genomic DNA by PCR,
Bruno Frey ......................................................................................... 143
/x
X Contents
9 PCR-Based Cloning and Subsequent Expression of Antigenic
Proteins in Escherichia coil,
Udo Reischl ....................................................................................... 157
10 Application of TEV Protease in Protein Production,
Deborah A. Polayes, T. Dawn Parks, Stephen A. Johnston,
and William G. Dougherty ........................................................... 169
CLONING AND EXPRESSIONO F OPEN READING FRAMESI N EUKARYONTICS YSTEMS
11 Stable Transfected Drosophila Schneider-2 Cells as a Novel Tool
to Produce Recombinant Antigens for Diagnostic, Therapeutic,
and Preventive Purposes,
Ludwig Deml and Ralf Wagner ....................................................... 185
12 Use of Recombinant Antigens as Diagnostic Reagents in Enzyme-
Linked Immunosorbent Assays,
Alan Warnes, Anthony R. Fooks, and John R. Stephenson ....... 201
13 Generation of Recombinant Baculovirus DNA in E. coil Using
a Baculovirus Shuttle Vector,
Valentina C. Ciccarone, Deborah A. Polayes,
and Verne A. Luckow ................................................................... 213
14 The SFV Gene Expression System,
Valentina C. Ciccarone, Joel A. Jessee, and Peter Liljestr5m ... 237
PURIFICATION OF RECOMBINANTP ROTEINS
15 Expression and Purification of Recombinant Proteins Using
the pET System,
Robert C. Mierendorf, Barbara B. Morris, Beth Hammer,
and Robert E. Novy ...................................................................... 257
16 Procedures for the Analysis and Purification of His-Tagged Proteins,
Richard E. Kneusel, Joanne Crowe, Melanie Wulbeck,
and Joachim Ribbe ...................................................................... 293
17 Detection and Immobilization of Proteins Containing
the 6xHis Tag,
Richard E. Kneusel, Melanie Wulbeck,
and Joachim Ribbe ...................................................................... 309
18 The Use of Recombinant Fusion Proteases in the Affinity Purification
of Recombinant Proteins,
Louis E. C. Leong ............................................................................. 323
19 Purification and Immunological Characterization of Recombinant
Antigens Expressed in the Form of Insoluble Aggregates
(Inclusion Bodies),
Udo Reischl ....................................................................................... 331
Contents xi
20 Purification of Recombinant Proteins Having High Isoelectric Points,
Raffaele A. Calogero and Anna Aulicino ....................................... 345
EVALUTION OF RECOMBINANT PROTEINS IN IMMUNOLOGICALT EST SYSTEMS
21 Immunoblotting,
Michael Kirschfink and Peter Terness ........................................... 361
22 Diagnostic Application of a Multiple-Channel Immunoblot Apparatus,
Shaun D. Black .................................................................................. 373
23 Immobilization of Immunoreactants on Solid Phases
for ELISAs,
Richard Decker and David Leahy ................................................... 397
24 Nonradioactive Labeling and Immunodetection of Recombinant Proteins,
Robert Oberfelder ............................................................................. 411
25 Flow Cytometry,
Volker Daniel ..................................................................................... 427
26 Basic Problems of Serological Laboratory Diagnosis,
Walter Fierz ........................................................................................ 443
27 Molecular Diagnostics Resources on the Internet,
Kevin J. O'Donnell ............................................................................ 473
II ANTIBODIES. ............................................................................................ 485
28 Monoclonal Antibody-Based Immunoassays,
Peter Appleby and Udo Reischl ...................................................... 487
BIOSENSOR TECHNOLOGY
29 Biosensor-Based Methods in Clinical Diagnosis,
Franz Aberl and Conrad K681inger ................................................ 503
30 The Quartz Crystal Microbalance (QCM)
as an Immunosensor,
Franz Aberl, Conrad K6Blinger, and Hans Weft ........................... 519
31 Biomolecular Interaction Analysis: Strategies for Antibody
and Antigen Characterization,
Uwe W. Roder and Francis Markey ................................................ 53 !
RECOMBINANT ANTIGENS
32 Recent Developments in Antibody Engineering,
Melvyn Little, Stefan D~bel, Sergey Kipriyanov,
and Frank Breitling ....................................................................... 555
33 Cloning and Expression of Single Chain Fragments (scFv)
from Mouse and Rat Hybridomas,
Frank Breitling and Stefan DEIbel ................................................... 581