June 10, 2013

The Latest on Immune Tolerance

Posted by Bench Marks under Immunology
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Immune ToleranceThe campus here at CSHL was abuzz last week with the 78th annual Cold Spring Harbor Symposium, where scientists from around the world assembled to discuss immunity and tolerance – also the topic of our new book Immune Tolerance.

“Immunological tolerance is a phenomenon that has fascinated immunologists for decades,” explained Diane Mathis in an interview at the meeting last week. “The immune system was set up to fight a whole diversity of different kinds of challenges. But sometimes [immune cells] are able to see a component of the body itself. There must be ways to deal with this issue . . . so they can’t attack the body’s own cells.”

In the book, which Diane coedited with Alexander Rudensky, the contributors discuss our current understanding of the mechanisms involved in establishing and maintaining immune tolerance, ensuring that the immune system responds to foreign molecules and not to self-molecules. The contributors also describe factors that underlie the breakdown of tolerance, leading to autoimmune diseases such as rheumatoid arthritis, lupus, and multiple sclerosis, and strategies to restore tolerance in clinical settings. The book will be a valuable reference for all immunologists and clinicians wishing to understand or develop treatments for autoimmune diseases.

For more information on the book, click here.

 

May 13, 2013

New Book on DNA Replication

Posted by Bench Marks under Molecular Biology
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DNA ReplicationDNA replication is a fundamental biological process that occurs in all living organisms. Ensuring that it occurs with high fidelity exactly once each time a cell divides is a complex task. Our latest book, DNA Replication, covers all aspects of the replication mechanism and its control. The book was edited by Stephen Bell, Marcel Méchali, and Melvin DePamphilis.

The contributors examine the molecular machinery involved in the assembly of replication origin complexes, the establishment of replication forks, unzipping of the double helix, priming of DNA synthesis, and elongation of daughter strands. Chromatin organization and dynamics, lagging-strand maturation, telomere replication, and mechanisms to handle errors and damage in DNA are also discussed.

“This is a truly exciting field in which to work—the rate of progress of the development of techniques and concepts is remarkable,” write the editors. “As will be apparent from the contents of the book, the full complement of state-of-the-art techniques have been exploited with remarkable effect to tease apart these intricate processes.”

For more information on the book, click here.

 

April 5, 2013

Looking at Protein-DNA Interactions from Multiple Perspectives

Posted by Bench Marks under Molecular Biology
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Introduction to Protein-DNA InteractionsThe manipulation of DNA by proteins is central to the life of a cell. It is critical for processes ranging from replication and recombination to transcription and the repair of DNA damage. Introduction to Protein-DNA Interactions, written by Gary Stormo, provides an up-to-date and interdisciplinary perspective on protein-DNA interactions, with an emphasis on DNA-binding proteins that control gene expression.

“The regulation of gene expression has fascinated me since my graduate school days,” writes Stormo. “The majority of my efforts have been focused on understanding how networks of transcription factors regulate gene expression and control cell fates and phenotypes. The primary goal of this volume is to provide an introduction to protein-DNA interactions from multiple perspectives.”

Three general types of approaches have been used to study protein-DNA interactions: structural, thermodynamic, and bioinformatic. Stromo describes what we know about protein-DNA interactions from each of these perspectives, and emphasizes how insights from experimental work can be translated into specific computational approaches to create a unified view of the field.

Because of the book’s cross-disciplinary approach, experts working in all fields are certain to learn something new. For more information on the book, click here.

 

March 8, 2013

New Book on a “Fascinating Organelle”

Posted by Bench Marks under Cell Biology
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The Endoplasmic ReticulumPresent in all eukaryotic cells, the endoplasmic reticulum (ER) is an extensive network of membranes that folds, modifies, and transports proteins, and manufactures lipids. This key organelle is the focus of a new book, The Endoplasmic Reticulum.

“The endoplasmic reticulum is one of the most intriguing and fascinating organelles,” write the editors, Susan Ferro-Novick, Tom Rapoport, and Randy Schekman. “This book attempts to capture in a single volume our current knowledge of this organelle and highlights many unresolved questions.”

Contributors examine how proteins translocate across the ER membrane, the folding and modification processes that occur inside the ER lumen, and how the proteins are packaged into vesicles and transported to the Golgi. They also review quality-control mechanisms that are employed by the ER to detect and eliminate misfolded or unassembled proteins. Lipid synthesis and transport are also discussed.

The Endoplasmic Reticulum is an indispensable reference for cell biologists interested in understanding the numerous functions of the ER. For more details on the book, click here.

 

February 11, 2013

Informatics for Next-Generation Sequencing

Posted by Bench Marks under Bioinformatics/Genomics
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Next -Generation DNA Sequencing InformaticsOur new book Next-Generation DNA Sequencing Informatics is the first of its kind to address the informatics needs of scientists who wish to take advantage of the explosion of research opportunities offered by new DNA sequencing technologies.

Edited by Stuart Brown, the book includes contributions from researchers at New York University’s Langone Medical Center, which invested heavily and early in next-generation sequencing (NGS) technology and informatics capacity. “In this book, building on our own extensive experience that spans collaborations on more than 30 National Institutes of Health-funded projects, and by critically evaluating and synthesizing the literature in the field, we provide an overview of many core types of next-generation sequencing projects, a discussion of methods embodied in popular software, and detailed descriptions of our own best practice workflows,” writes Brown.

 Topics include data visualization, sequence alignment, genome assembly and annotation, variant discovery, RNA-seq, ChIP-seq, and metagenomics, as well as the history of DNA sequencing and informatics. An accompanying website, seqinformatics.com, offers tutorials and resources for NGS. For additional details on the book, click here.

 

January 11, 2013

Innovative Lab Exercises for Teaching Biology

Posted by Bench Marks under New from CSHL Press
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Genome ScienceDo you teach a biology or biotechnology course involving genes or genomes? Are you looking to update or refresh the course? Our new book Genome Science contains 19 innovative laboratory exercises for high school and college teaching. The exercises can be used to enhance existing courses, start new courses, or support student research projects.

Developed by the world-renowned DNA Learning Center at Cold Spring Harbor Laboratory, the exercises illustrate key concepts of genome biology in humans, plants, and the worm C. elegans. “Genome Science aims to help beginners use modern tools to explore the unseen world of genes and genomes,” write David Micklos, Bruce Nash, and Uwe Hilgert, the book’s authors. “All labs stress the modern synthesis of molecular biology and computation, integrating in vitro experimentation with in silico bioinformatics.”

Molecular techniques such as polymerase chain reaction (PCR), DNA sequencing, and RNA interference (RNAi) are used to analyze DNA mutations, detect epigenetic modifications, silence genes, identify transposon insertions, detect genetically modified foods, and trace evolutionary histories. Computational tools are used to search, view, annotate, align, and compare DNA sequences. The labs are complemented by illustrated introductory text that provides an historical and conceptual framework. The book is complete with advice for instructors, laboratory planning guidelines, recipes for solutions, and answers to student questions.

For more information about the book, click here.

 

December 10, 2012

New Book on Wnt Signaling

Posted by Bench Marks under Cell Biology, Developmental Biology
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A wide range of biological phenomena – from embryonic development to diseases such as cancer – involve Wnt proteins and their signaling pathways. Our recent book Wnt Signaling contains 24 chapters covering all aspects of Wnt biology, from the molecular mechanisms involved in Wnt signal transduction to the effects of these pathways on normal development and physiology, as well as human disease.

 One chapter describes the history of Wnt research. It was written by Roel Nusse and Harold Varmus, who discovered the first Wnt gene 30 years ago. “Since the identification of the first Wnt gene, research in the Wnt field has taken flight,” write Roel Nusse, Xi He, and Renée van Amerongen, the book’s editors. “Wnt-related investigations continue to reveal fascinating principles of embryonic patterning, cell growth and differentiation, the wiring of the nervous system, the pathogenic mechanisms underlying cancer as well as degenerative disease, stem cell and regenerative biology, and potential therapeutic applications.”

 “It is our hope that this volume serves as a stepping-stone for the reader to guide and encourage further exploration and, perhaps, to open up novel avenues of investigation, particularly applications in the fields of bioengineering, regenerative medicine, and cancer treatment,” they continue. Wnt Signaling will be a fascinating read for cell and developmental biologists, as well as those who are interested in targeting the Wnt pathway for therapeutic purposes. For more information about the book, click here.

 

November 12, 2012

New Book on the Biology of Drug Addiction

Posted by Bench Marks under Neuroscience
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Drug and alcohol abuse elicits significant biological changes in the brain that drive compulsive behavior and lead to addiction. A new book from CSHL Press, Addiction, reviews the cell and molecular biology of drug addiction. It was edited by R. Christopher Pierce and Paul J. Kenny.

“Our goal was to highlight a cross-section of innovative contemporary addiction research,” write Pierce and Kenny. Contributors explore the biological basis of addiction to alcohol, nicotine, and other psychoactive drugs. They describe the molecular targets of these drugs, the resulting changes to neural networks, and the various genetic, developmental, and behavioral factors that influence the progression from abuse to addiction.

Addiction will be a useful resource for neuroscientists and all who are interested in reducing the public health burden of substance abuse.  For more details on the book, click here.

 

October 9, 2012

Lab Manual Provides “Gory Detail” for Successful Imaging

Posted by Bench Marks under Imaging/Microscopy, Neuroscience
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Imaging in Neuroscience, the manual from our imaging series that focuses on methods for studying neurons and their circuits, is given a positive review in the current issue of The Quarterly Review of Biology.

 “The most important feature of the manual is the protocol[s] provided,” write Lynne Oland and Patty Jansma. “These are clearly written with the intent of providing the gory detail needed to actually use the protocols successfully, and most chapters include troubleshooting hints, which are most helpful.”

 Oland and Jansma feel that the protocols on glial cells and brain pathology “will make the manual especially useful.” Some of these protocols are available online from Cold Spring Harbor Protocols: For example, check out how to visualize microglia in the mouse cortex, label astrocytes with sulforhodamine 101, and study neural networks in mouse models of Alzheimer’s disease. For more information on the manual, click here.

 

September 19, 2012

New Book on Translational Control

Posted by Bench Marks under Cell Biology
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Protein Synthesis and Translational Control“Situated at the nexus between nucleic acids and proteins, the importance of translational control, now appreciated for its role in establishing the cell’s proteome, is comparable to that of transcriptional control,” write John Hershey, Nahum Sonenberg, and Michael Mathews, editors of our recently released book Protein Synthesis and Translational Control. “It is especially important in defining the proteome, maintaining homeostasis, and controlling cell proliferation, growth, and development.”

The book covers our current understanding of all aspects of protein synthesis and its regulation. Contributors describe the fundamental steps in protein synthesis (initiation, elongation, and termination), the factors involved, and high-resolution structures of the translational machinery where this takes place.  They also review the targets of translational control (e.g., initiation factors and mRNAs) and how signaling pathways modulate this machinery.  The book will be useful to cell and molecular biologists, as well as cancer biologists and others who study human diseases associated with translation dysfunction. For more information, click here.

 

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