Manipulation and Expression of Recombinant DNA

Cover image courtesy of Ravisha Weerasinghe.
Fluorescence images of plant epidermal and root hair cells expressing Green Fluorescent Protein (GFP)
fused with microtubule associated protein, MAP4 (left-hand panel) and actin binding protein, Talin
(right-hand panel). These constructs provide an excellent system to monitor cytoskeletal dynamics in
living cells. New evidence confirms that root knot nematodes and rhizobia produce an essentially identical
response in cytoskeletal dynamics. See article by Weerasinghe, Bird, and Allen. PNAS, Feb. 22, 2005.
Elsevier Academic Press
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Molecular Biology of The Cell

All living creatures are made of cells - small membrane-bounded compartments filled with a concentrated aqueous solution of chemicals. The simplest forms of life are solitary cells that propagate by dividing in two. Higher organisms, such as ourselves, are like cellular cities in which groups of cells perform specialized functions and are linked by intricate systems of communication. Cells occupy a halfway point in the scale of biological complexity. We study them to learn, on the one hand, how they are made from molecules and, on the other, how they cooperate to make an organism as complex as a human being. All organisms, and all of the cells that constitute them, are believed to have descended from a common ancestor cell through evolution by natural selection. This involves two essential processes: (1) the occurrence of random variation in the genetic information passed from an individual to its descendants and (2) selection in favor of genetic information that helps its possessors to survive and propagate. Evolution is the central principle of biology, helping us to make sense of the bewildering variety in the living world.

This chapter, like the book as a whole, is concerned with the progression from molecules to multicellular organisms. It discusses the evolution of the cell, first as a living unit constructed from smaller parts and then as a building block for larger structures. Through evolution, we introduce the cell components and activities that are to be treated in detail, in broadly similar sequence, in the chapters that follow. Beginning with the origins of the first cell on earth, we consider how the properties of certain types of large molecules allow hereditary information to be transmitted and expressed and permit evolution to occur. Enclosed in a

membrane, these molecules provide the essentials of a self-replicating cell. Following this, we describe the major transition that occurred in the course of evolution, from small bacteriumlike cells to much larger and more complex cells such as are found in present-day plants and animals. Lastly, we suggest ways in which single free-living cells might have given rise to large multicellular organisms, becoming specialized and cooperating in the formation of such intricate organs as the brain.

Clearly, there are dangers in introducing the cell through its evolution: the large gaps in our knowledge can be filled only by speculations that are liable to be wrong in many details. We cannot go back in time to witness the unique molecular events that took place billions of years ago. But those ancient events have left many traces for us to analyze. Ancestral plants, animals, and even bacteria are preserved as fossils. Even more important, every modern organism provides evidence of the character of living organisms in the past. Present-day biological molecules, in particular, are a rich source of information about the course of

evolution, revealing fundamental similarities between the most disparate of living organisms and allowing us to map out the differences between them on an objective universal scale. These molecular similarities and differences present us with a problem like that which confronts the literary scholar who seeks to establish the original text of an ancient author by comparing a mass of variant manuscripts that have been corrupted through repeated copying and editing. The task is hard, and the evidence is incomplete, but it is possible at least to make intelligent guesses about the major stages in the evolution of living cells.

BLAST

The fact that the human genome is often referred to as the Book of Life is an apt
description because nucleic acids and proteins are often represented (and manipulated)
as text files. Chapter 3 described common algorithms for aligning sequences of
letters, and score is the metric used to determine the best alignment. This chapter
shows what scores really are. Some of the introduced terms come from information
theory, so the chapter begins with a brief introduction to this branch of mathematics.
It then explores the typical ways to measure sequence similarity. You’ll see that
this approach fits well with the sequence-alignment algorithms described in
Chapter 3. The last part of the chapter focuses on the statistical significance of
sequence similarity in a database search. The theories discussed in this chapter apply
only to local alignment. There is currently no theory for global alignment

BIOTECHNOLOGY FOR WASTE AND WASTEWATER TREATMENT

Copyright 0 1996 by Nicholas P. Cheremisinoff
No part of this book may be reproduced or utilized in
any form or by any means, electronic or mechanical,
including photocopying, recording or by any information
storage and retrieval system, without permission
in writing from the Publisher.
Library of Congress Catalog Card Number:
Printed in the United States
ISBN: 0-8155-1409-3
Published in the United States of America by
Noyes Publications
Fairview Avenue, Westwood, New Jersey 07675
10 9 8 7 6 5 4 3 2 1

Biotechnology and Communication

Copyright Ó 2004 by Lawrence Erlbaum Associates, Inc.
All rights reserved. No part of this book may be reproduced in
any form, by photostat, microform, retrieval system, or any other
means, without the prior written permission of the publisher.
Lawrence Erlbaum Associates, Inc., Publishers
10 Industrial Avenue
Mahwah, New Jersey 07430
Cover photograph by Graham Murdock
Cover design by Kathryn Houghtaling Lacey
Library of Congress Cataloging-in-Publication Data
Biotechnology and communication : the meta-technologies of information / edited by
Sandra Braman.
p. cm. — (LEA’s communication series)
Includes bibliographical references and index.
ISBN 0-8058-4304-3 (alk. paper)
1. Biotechnology—Social aspects. 2. Communication. 3. Information technology.
4. Information theory. 5. Bioinformatics. I. Braman, Sandra. II. Series.
TP248.23.B56 2004
303.48¢3—dc21 2003059933
CIP
Books published by Lawrence Erlbaum Associates are printed on acid-free paper,
and their bindings are chosen for strength and durability.
Printed in the United States of America

Biotech Industry

This book is printed on acid-free paper. ∞
Copyright © 2004 by John Wiley & Sons, Inc. All rights reserved.
Published by John Wiley & Sons, Inc., Hoboken, New Jersey
Published simultaneously in Canada
All figures created by Bryan Bergeron.
No part of this publication may be reproduced, stored in a retrieval system, or
transmitted in any form or by any means, electronic, mechanical, photocopying,
recording, scanning, or otherwise, except as permitted under Section 107 or 108 of
the 1976 United States Copyright Act, without either the prior written permission
of the Publisher, or authorization through payment of the appropriate per-copy fee
to the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA
01923, 978-750-8400, fax 978-646-8600, or on the web at www.copyright.com.
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Limit of Liability/Disclaimer of Warranty: While the publisher and author have
used their best efforts in preparing this book, they make no representations or
warranties with respect to the accuracy or completeness of the contents of this
book and specifically disclaim any implied warranties of merchantability or fitness
for a particular purpose. No warranty may be created or extended by sales
representatives or written sales materials. The advice and strategies contained
herein may not be suitable for your situation. You should consult with a
professional where appropriate. Neither the publisher nor author shall be liable
for any loss of profit or any other commercial damages, including but not limited
to special, incidental, consequential, or other damages.
For general information on our other products and services, or technical support,
please contact our Customer Care Department within the United States at 800-
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Library of Congress Cataloging-in-Publication Data:
Bergeron, Bryan P.
Biotech industry : a global, economic, and financing overview / Bryan
Bergeron
p. cm.
Includes bibliographical references and index.
ISBN 0–471–46561–5 (CLOTH)
1. Biotechnology industries. I. Title.
HD9999.B442B47 2004
338.4'76606—dc22 2003017976
Printed in the United States of America
10 9 8 7 6 5 4 3 2 1

MICROBIAL PHYSIOLOGY Fourth Edition Albert G. Moat John W. Foster Michael P. Spector

Cover images (clockwise from upper-left corner): 1) Coralline shape of the bacterial nucleoid. Reprinted
with permission from Bohrmann, B. et al. 1991. J. Bacteriol. 173:3149–3158 (see Chapter 7), 2) Cell
envelope-free nucleoid from E. coli (left frame RNAase treated, right frame washed). Reprinted with
permission from Kavenoff, R. and B.C. Bowen, 1976. Chromosome 59:89–101 (see Chapter 7), 3) Pili
(fimbriae) and flagella of Proteus mirabilis. Reprinted with permission from Hoeniger, J.F.M. 1965.
J. Gen. Microbiol. 40:29. 4) Cell envelope-free nucleoid from E. coli. Reprinted with permission from
Kavenoff, R. and B.C. Bowen, 1976. Chromosome 59:89–101 (see Chapter 7).
This book is printed on acid-free paper.
Copyright  2002 by Wiley-Liss, Inc., New York. All rights reserved.
Published simultaneously in Canada.
No part of this publication may be reproduced, stored in a retrieval system or transmitted in any form
or by any means, electronic, mechanical, photocopying, recording, scanning or otherwise, except as
permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the
prior written permission of the Publisher, or authorization through payment of the appropriate per-copy
fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923,
(978) 750-8400, fax (978) 750-4744. Requests to the Publisher for permission should be addressed to the
Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012,
(212) 850-6011, fax (212) 850-6008, E-mail: PERMREQ@WILEY.COM.
For ordering and customer service information please call 1-800-CALL-WILEY.
Library of Congress Cataloging-in-Publication Data:
Moat, Albert G.
Microbial physiology / Albert G. Moat, John W. Foster, Michael P. Spector.–4th ed.
p.cm.
Includes bibliographical references and index.
ISBN 0-471-39483-1 (paper: alk. paper)
1. Microorganisms—Physiology. I. Foster, John Watkins. II. Spector, Michael P.
III. Title.
QR84.M64 2002
571.29–dc21 2002071331
Printed in the United States of America.
10 9 8 7 6 5 4 3 2 1

Basic Cell Culture Protocols

Basic Cell Culture Protocols 
THIRD EDITION
Edited by
Cheryl D. Helgason
Cindy L. Miller

Culture of Primary Adherent Cells

and a Continuously Growing Nonadherent Cell Line

Cheryl D. Helgason

Summary

Cell culture is an invaluable tool for investigators in numerous fields. It facilitates

analysis of biological properties and processes that are not readily accessible at the level

of the intact organism. Successful maintenance of cells in culture, whether primary or

immortalized, requires knowledge and practice of a few essential techniques. The purpose

of this chapter is to explain the basic principles of cell culture using the maintenance

of a nonadherent cell line, the P815 mouse mastocytoma cell line, and the isolation

and culture of adherent primary mouse embryonic fibroblasts (MEFs) as examples.

Procedures for thawing, culture, determination of cell numbers and viability, and

cryopreservation are described.

Bioinformatics The Machine Learning Approach A Bradford

All rights reserved. No part of this book may be reproduced in any form
by any electronic or mechanical means (including photocopying, recording,
or information storage and retrieval) without permission in writing from the
publisher.
This book was set in Lucida by the authors and was printed and bound in the
United States of America.
Library of Congress Cataloging-in-Publication Data
Baldi, Pierre.
Bioinformatics : the machine learning approach / Pierre Baldi,
Søren Brunak.—2nd ed.
p. cm.—(Adaptive computation and machine learning)
"A Bradford Book"
Includes bibliographical references (p. ).
ISBN 0-262-02506-X (hc. : alk. paper)
1. Bioinformatics. 2. Molecular biology—Computer simulation. 3. Molecular
biology—Mathematical models. 4. Neural networks (Computer science). 5.
Machine learning. 6. Markov processes. I. Brunak, Søren. II. Title. III. Series.
QH506.B35 2001
572.8 01 13—dc21
2001030210

Bioinformatics_Genomes_to_Drugs_by_Lengauer

Bioinformatics_Genomes_to_Drugs_by_Lengauer

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition Andreas D. Baxevanis, B.F. Francis Ouellette

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition
Andreas D. Baxevanis, B.F. Francis Ouellette
Copyright 2001 John Wiley & Sons, Inc.
ISBNs: 0-471-38390-2 (Hardback); 0-471-38391-0 (Paper); 0-471-22392-1 (Electronic)

A Practical Guide to Cellular and Molecular Immunology

In the first week of this course we will begin to acquire some of the basic skills
needed to examine several components of the inflammatory cascade, a series of
responses that are integrally intertwined with the immune system. First we will begin
to acquire some basic skills in tissue culture, and the purification of selected cells
associated with the immunoinflammatory system (i.e., peripheral blood [PBL]
monocytes and neutrophils [PMN or polymorphonuclear cells]). Then we will learn
how to identify them using morphologic criteria, and how to assess a couple of
functions associated with monocytes/macrophages - phagocytosis (a subfunction of
antibody-dependent cellular cytotoxicity) and activation-dependent monokine
production.

Screening for NewMetabolites from Marine Microorganisms

This article gives an overview of current analysis techniques for the screening

and the activity analysis of metabolites from marine (micro)organisms. The sequencing

of marine genomes and the techniques of functional genomics (including transcriptome,

proteome, and metabolome analyses) open up new possibilities for the screening of new

metabolites of biotechnological interest. Although the sequencing of microbial marine

genomes has been somewhat limited to date, selected genome sequences of marine bacteria

and algae have already been published. This report summarizes the application

of the techniques of functional genomics, such as transcriptome analysis in combination

with high-resolution two-dimensional polyacrylamide gelelectrophoresis and mass

spectrometry, for the screening for bioactive compounds of marine microorganisms.

Furthermore, the target analysis of antimicrobial compounds by proteome or transcriptome

analysis of bacterial model systems is described. Recent high-throughput screening

techniques are explained. Finally, new approaches for the screening of metabolites from

marine microorganisms are discussed.

Download Marine Biotechnology volume 1

Download Marine Biotechnology volume 2

Bacterial and Bacteriophage Genetics Fifth Edition

Cover illustration: Micrographs courtesy of Dr. Yuri Lyubchenko and Dr. Luda Shlyakhtenko, Department
of Pharmaceutical Sciences, College of Pharmacy, 986025 Nebraska Medical Center, Omaha, Nebraska.
Library of Congress Control Number: 2005923811
ISBN-10: 0-387-23919-7
ISBN-13: 978-0387-23919-4
Printed on acid-free paper.
© 2006, 2000, 1994, 1988, 1984 Springer Science+Business Media, Inc.
All rights reserved. This work may not be translated or copied in whole or in part without the written permission
of the publisher (Springer Science+Business Media, Inc., 233 Spring Street, New York, NY 10013,
USA), except for brief excerpts in connection with reviews or scholarly analysis. Use in connection with
any form of information storage and retrieval, electronic adaptation, computer software, or by similar or
dissimilar methodology now known or hereafter developed is forbidden.
The use in this publication of trade names, trademarks, service marks, and similar terms, even if they are
not identified as such, is not to be taken as an expression of opinion as to whether or not they are subject
to proprietary rights.
Printed in the United States of America. (SPI/MVY)

ANIMAL BIOTECHNOLOGY: SCIENCE-BASED CONCERNS

Animal biotechnology: science-based concerns / Committee on Defining Sciencebased
Concerns Associated with Products of Animal Biotechnology, Committee on
Agricultural Biotechnology, Health, and the Environment, Board on Agriculture and
Natural Resources, Board on Life Sciences, Division on Earth and Life Studies.
p. cm.
Includes bibliographical references and index.
ISBN 0-309-08439-3 (pbk.)
1. Animal biotechnology. I. National Research Council (U.S.).
Committee on Defining Science-based Concerns Associated with Products of
Animal Biotechnology.
SF140.B54 A58 2002
660'.65—dc21
2002151075
Additional copies of this report are available from the National Academies Press,
500 Fifth Street, N.W., Lockbox 285, Washington, DC 20055; (800) 624-6242 or
(202) 334-3313 (in the Washington metropolitan area); Internet, http://www.nap.edu.
Copyright 2002 by the National Academy of Sciences. All rights reserved.
Printed in the United States of America