Great new chapter of WormBook in GENETICS!

There’s a great new chapter of WormBook in GENETICS by Meera V. Sundaram and Matthew Buechner: The Caenorhabditis elegans Excretory System: A Model for Tubulogenesis, Cell Fate Specification, and Plasticity.

The excretory system of the nematode Caenorhabditis elegans is a superb model of tubular organogenesis involving a minimum of cells. The system consists of just three unicellular tubes (canal, duct, and pore), a secretory gland, and two associated neurons. Just as in more complex organs, cells of the excretory system must first adopt specific identities and then coordinate diverse processes to form tubes of appropriate topology, shape, connectivity, and physiological function. The unicellular topology of excretory tubes, their varied and sometimes complex shapes, and the dynamic reprogramming of cell identity and remodeling of tube connectivity that occur during larval development are particularly fascinating features of this organ. The physiological roles of the excretory system in osmoregulation and other aspects of the animal’s life cycle are only beginning to be explored. The cellular mechanisms and molecular pathways used to build and shape excretory tubes appear similar to those used in both unicellular and multicellular tubes in more complex organs, such as the vertebrate vascular system and kidney, making this simple organ system a useful model for understanding disease processes.

Check out the first chapter of WormBook in GENETICS!

The first chapter of WormBook in GENETICS, CRISPR-Based Methods for Caenorhabditis elegans Genome Engineering, by Daniel J. Dickinson and Bob Goldstein, is now available!

The advent of genome editing techniques based on the clustered regularly interspersed short palindromic repeats (CRISPR)–Cas9 system has revolutionized research in the biological sciences. CRISPR is quickly becoming an indispensible experimental tool for researchers using genetic model organisms, including the nematode Caenorhabditis elegans. Here, we provide an overview of CRISPR-based strategies for genome editing in C. elegans. We focus on practical considerations for successful genome editing, including a discussion of which strategies are best suited to producing different kinds of targeted genome modifications.

REMINDER!! – Gene Ontology (GO) Survey – Closes Sunday, November 15th

Attention GO users!!  The Gene Ontology Consortium would love to hear your feedback about GO.  Please assist the GO project by completing a short survey. The results will help us learn more about how you use GO, how GO can serve your research needs better, and will aid in preparation for the upcoming GO grant renewal. Surveys completed by November 15th 2015 will be eligible for a prize drawing for a $400 Apple Store voucher.  Thanks in advance for your time!

WormBook in Genetics: access and choices

Dear All,

I would like to address some questions that have come up regarding the partnership with the GSA and access to WormBook in the journal GENETICS.

As I said in a quote to the GSA blog, “WormBook in GENETICS will continue a great community tradition and will strengthen our longstanding association with GENETICS, which began with the publication in 1974 of Sydney Brenner’s landmark paper.   That association has grown, which is apparent in the many papers that appear every year in GENETICS and G3, as well as in the GSA’s sponsorship of the C. elegans meetings.”

GSA provides a sustainable platform for publishing WormBook, as well as the editorial and production resources of GENETICS.  However, because the GSA will be fully funding publication of new WormBook content, WormBook chapters will adhere to the journal’s current access policies, unless authors or institutions choose to subsidize immediate open access, including a Creative Commons license.

In practice, the journal’s access policy will not make much difference for most members of the community, who will continue to have immediate access to GENETICS content through their libraries and GSA memberships–which includes very low cost membership categories.  Furthermore, anyone who cannot pay may request individual article PDFs from the GENETICS Editorial Office.

The access issue was the subject of much discussion before we finalized the relationship.  But it is important to understand that there are costs to publishing, even on the web, and full open-access of WormBook at Caltech was possible only while they had sufficient funds to support it.  However, available funding, including some from WormBase, has been reduced to the point that WormBook was no longer sustainable.  Thus, the choice was to freeze WormBook in its current form altogether or find another way forward.

Several options were considered, and this association with the GSA emerged as the best option to finance and produce WormBook going forward.  Whether this arrangement should continue can be evaluated in 4-5 years.  For now, we have a fantastic opportunity, and the Section Editors are already commissioning great chapters.

It is too complicated to respond to questions about the economics of open access versus subscription publishing here–and I’m not an expert, though I know from having served as an editor of Development during the rise of the web and now, as an editor of PNAS and member of the PNAS Publications Committee, that it is very expensive to publish papers.*  Different journals have different business models, but the current access model used by GENETICS (and PNAS) is one way to keep costs down for authors, readers, and libraries.

So, thank you for your interest in, and continued support for, WormBook.

Best regards,


* It may interest some of you to see this report about the true cost of publishing a paper, where they calculate the cost in eLife as $14,000, and Nature itself estimates the cost of publishing in its own journal of $10,000!  (See