Category Archives: Book Reviews

Book Review: Cryptococcus – From Human Pathogen To Model Yeast

I wrote the following book review for the Mycological Society of America‘s Inoculum newsletter and I think the book is a great resource if you study Cryptococcus — so I am reproducing my review here.  You can also find a copy of the review here.

cryptococcus book cover for web

Cryptococcus: From Human Pathogen To Model Yeast. 2010.  Joseph Heitman, Thomas R. Kozel, Kyung J. Kwon-Chung, John R Perfect, and Arturo Casadevall (Eds.).  ASM Press, Washington, DC.

The yeast-forming basidiomycete genus, Cryptococcus, has emerged as a significant model for both fungal genetics and pathogenicity.  A long history of research compounded with numerous laboratory resources, as well as two sequenced genomes, have yielded a great deal of information on this enigmatic fungus.  The new book Cryptococcus: From Human Pathogen To Model Yeast, edited by Heitman, Kozel, Kwon-Chung, Perfect, and Casadevall, features contributions from 123 authors and summarizes a vast amount of data as well as synthesizes disparate concepts on the biology of Cryptococcus.  If you consider Casadevall & Perfect’s 1998 tome Cryptococcus neoformans as the groundwork for this book, then these 646 pages are evidence for the explosive advance of knowledge on Cryptococcus that has accrued over the last 12 years.

Cryptococcus species, arguably the most important fungal pathogen of mammals, are common in immuno-compromised hosts; HIV-associated cryptococcosis alone infects more than 1 million people per year.  For example, Cryptococcus has been laboratory confirmed in Sub-Saharan African countries to be responsible for anywhere from 10 to 70% of fatal meningitis cases over the last two decades.  A well-publicized outbreak of a particularly virulent strain of C. gattii was determined to be the causative agent of more than 200 cases of human meningitis in non-immuno compromised individuals within the Pacific Northwest over the last decade.  A concerted global consortium of medical mycology researchers ­ the majority of whom are authors of chapters in this book ­have provided the foundation for establishing Cryptococcus as the model system for understanding fungal pathogenesis in both a medical and veterinary setting.

Species of Cryptococcus entered my personal radar when they kept turning up in plant-associated environmental samples.  Wanting to get up to speed with natural history, population genetics, and methods for typing Cryptococcal diversity, this book was an obvious entry point for me.  Chapters here are dedicated to identification from environmental niches – such as the description of avian- or plant-associated vectors – as well as population biology to phylogeography, and species complexes to hybridization.

Copiously illustrated throughout, notable figures include those documenting Cryptococcus morphology, cell and molecular biological networks, secondary metabolite chemistry, and gene and genome structure.  Chapters devoted to phylogeography and species complexes have detailed phylogenetic trees and distribution maps.  Additionally, this wouldn’t be a clinical textbook if it didn’t include a series of color and monochrome plates of human and animal infections that remind you why you have – or haven’t – studied medical mycology.

Mycologists aren’t the only ones who will find this resource useful.  Geared toward a wide array of specialists, this book is equally applicable to the interests of clinicians and physicians, microbiologists and immunologists, disease ecologists and epidemiologists, and, to a lesser extent, public health and policy administrators.  The book succeeds in connecting and interpreting basic research science and applying this knowledge in a clinical context.

The book consists of a whopping 44 chapters separated into seven sections.  These sections are devoted to general biology; genetics and genomics; virulence; environmental interactions and population biology; immune host responses; pathogenesis; and diagnosis, treatment, and prevention.  Each of the sections consist of five to eight chapters and each informative chapter stands on its own – concise enough to allow for discrete chunks of reading without overwhelming the reader.  In fact, I would argue that the book’s greatest strength is cohesive breadth blended with factual depth.  My only criticism ­ and this is an extremely minor one ­ is that the book as a whole is slightly overwhelming in scope.  This by no means indicates a lack of vision from the authors or editors, but reflects their desire to take into consideration the complete state of knowledge relating to Cryptococcus and its biology.  As a result, the contributors have not only provided a truly fascinating and utterly comprehensive collection of everything Cryptococcus, but have set the bar high for the best treatise on fungal biology at the genus level.  I would consider this book essential for anyone working directly with Cryptococcus ­ or wanting to get up to speed ­ and for mycologists looking for a framework to fully grasp the biology of an important model fungus.

Book Review: Practical Computing For Biologists

I have a couple of book reviews in the pipeline, so I am starting a new category for review of books I find useful (or not so useful).  I wrote this review for this great book months ago, but, like many things in my life, I’m just now getting it online.

practical computing for biologists
Like many people, my research has been changing in recent years.  I have been spending an increasing amount of time in front of a computer and less time at the lab bench.  I can’t see myself ever forsaking the wet lab or field experiments, but I’m using computers more than ever before.  There’s now so much data to process – mostly text in the form of sequence data – and I’ve become increasingly reliant on a computer to search large data sets and convert data file formats.  Even if you aren’t a biologist in the area of genomics/genetics, new data collection instruments for physiology, ecology, and atmospheric sciences are recording data at incredible rates, and, additionally, sorting through citations is getting more and more time consuming.  It’s impossible to ignore the data revolution that is taking place no matter where your foundation within the biological sciences (or physics, chemistry, etc.) lies.

I wish the book Practical Computing For Biologists (and Companion Website), by Steven H. D. Haddock & Casey W. Dunn, would have come along sooner, but I am so glad it’s available now, because learning to deal with data more efficiently is where this book comes in.  When considering my research and use of time, this book has been the most important book I’ve read in the last year, perhaps the last decade.  If you’re a biologist (or anyone for that matter) who finds themselves clicking away at a database file (such as Excel) or cutting and pasting from online data repositories (such as GenBank, national weather databases, etc.) then this book is for you.  In reality, this book is for anyone who wants to use a computer to work more efficiently with data.

The book can be broken up into six sections dedicated to the following topics: (1) manipulating and searching text files, (2) working within your computer’s shell, (3) basic programming for biologists, (4) combining methods (this is a section on database management and tool selection), (5) dealing with graphics for data communication, and (6) advanced topics such as remote computer access and installing software.

This book devotes a large portion, and rightfully so, to addressing how to manipulate text files and other file formats used to store and communicate data.  Beginning with text editing using regular expressions, what I learned in the initial chapters immediately saved me time during large text processing and parsing of sequencing data.  A section at the end of the book focused on remote access and remote scripting helped me to start dealing with text and files on other computers.

The book focuses on Unix based platforms (Linux, OSX) due to ease of programming, but it does not ignore DOS (Windows) based platforms.  An appendix at the end of the book is useful in translating one platform to another.  When the book recommends the use of specific software, which is rare, the focus is on free open-source options.  The programming language Python is the language of choice for much of the book, but an Appendix at the end of the book helps to sort out differences in the many programming languages used in biology.  The open-source MySQL database platform is addressed for storing and communicating data.  One important goal of the programming and data organization aspect of the book is to standardize reproducibility and improve collaborative work through automation and transparency.

Surprisingly little attention is given to the actual communication of data in graduate coursework and training, so it’s refreshing to see a focus on image basics communicated here across a few chapters in the book.  These sections focus on basic image creation and manipulation using both commercial and open-source options.

Striking a perfect balance by guiding you through tutorials and nudging your own self-exploration, the book has just enough guided direction to not annoy or overwhelm.  This text is not a solution cookbook, but, more importantly, a guide to help get you started in data analysis and file format manipulation and to help you think for yourself to address your research problems.  While this book will help you deal with text, it doesn’t address software for word processing (Word, OpenOffice), Presentation (Powerpoint, Keynote), Spreadsheet (Excel), or statistics (R, SAS, SPSS, etc.), as this would create a huge giant book.  This book does not cover software for phylogenetics or population genetics and I don’t think it should.

Just to be clear, I’m not being paid here to promote this book.  I just honestly have found this book extremely helpful to my own research and I want to communicate that.  I haven’t read many books which have been able to change my life in a self-actualizing way, but this book helped (…and is still helping) me to do what I was doing before, but more efficiently.