For many of the roughly 300 million people around the world with rare diseases, the road to diagnosis can be long, painful, expensive, and disheartening. Around eighty percent of very infrequently seen undiagnosed diseases are estimated to have a genetic basis, but even with modern DNA sequencing techniques, the causes are often unclear. In these cases, clinicians and their basic scientist collaborators are increasingly turning to laboratory models like fruit flies and zebrafish to help diagnose disease—and gain clues about how to treat it.

The teamwork between clinicians and model organism researchers goes both ways: clinicians can find candidate genes in patients to test in model organisms, or basic scientists can identify candidate disease genes through research on their organism of choice. In a review appearing in the September issue of GENETICS, Wangler et al. describe numerous tools clinicians and basic scientists have at hand to help them work together on puzzling rare diseases.

One such tool is GeneMatcher, a website that connects researchers who may be separately investigating the same genes. Using GeneMatcher, clinicians can find potential collaborators working on model organisms.

Another mechanism that connects clinicians with model organism researchers is the Canadian Rare Diseases Models and Mechanisms Network (RDMM). Via the RDMM, a clinician can submit a proposal to work with a model organism researcher—or vice versa. Uniquely, they can also use the tool to apply for quick-turnaround grants to fund their investigations of potential disease-causing variants.

Patients themselves can also contribute to this research. People with rare diseases that have resisted diagnosis by any other means can apply to the Undiagnosed Diseases Program (UDP) to spur investigations of their conditions. Not only have patients been diagnosed using the UDP’s combination of detailed clinical investigation and genetic analysis, but new disease genes have also been discovered. For example, mutations in the gene NT5E were found to cause a rare arterial calcification disorder—and as an unexpected bonus, this finding hinted that adenosine metabolism might be linked to more common vascular disorders as well.

The UDP has now been expanded into the Undiagnosed Diseases Network (UDN), a decentralized program involving researchers at several institutions. Using the UDN, a patient is first screened to see if their disease matches a known genetic condition after an extensive phenotypic work-up and sequencing of the whole genome or exome. If not, clinical findings and candidate genetic variants are sent to the Model Organisms Screening Center (MOSC). The MOSC starts by searching databases of known information about the candidate variants to determine which are worth testing in model organisms. The MOSC then looks for other individuals with similar clinical presentations and possible genetic causes.

Once the list of candidate genes is narrowed down, the MOSC researchers design experiments in flies or zebrafish to acquire more knowledge. The MOSC teams aim to match the variant in the human patient’s gene in the model organism. The goal is to learn more about the function of the gene, to determine whether the gene variant found in the patient is the likely cause of the disease, and to understand how the variant may cause problems.

Wangler et al. conclude by endorsing the continued support of these tools by government agencies such as the National Institutes of Health. Only with this financial backing, they say, will crucial improvements in the diagnosis and treatment of rare genetic diseases be possible. And since our understanding of rare diseases often drives discoveries about more common diseases, this research could even have more far-reaching impacts.

CITATION:

Wangler, M.; Yamamoto, S.; Chao, H.; Posey, J.; Westerfield, M.; Postlethwait, J.; Members of the Undiagnosed Diseases Network (UDN); Hieter, P.; Boycott, K.; Campeau, P.; Bellen, H. Model Organisms Facilitate Rare Disease Diagnosis and Therapeutic Research.
GENETICS, 207(1), 9-27.
DOI: 10.1534/genetics.117.203067
http://www.genetics.org/content/207/1/9

Thanks to more than a hundred years of working with Drosophila melanogaster, geneticists have many powerful tools for precisely manipulating its genes. It has also become a model system for studying speciation and molecular evolution together with the other members of the melanogaster species group: D. simulans, D. mauritiana, D. yakuba, and D. santomea. However, evolutionary genetic studies have been hampered by an inability to make transgenic lines within the less well-studied species. In the April issue of G3, Stern et al. present a panel of new transgenic strains of these species designed to make fine mapping and functional genetic studies possible. These resources provide new opportunities for unraveling the genetic mechanisms of speciation and evolution.

Transposable elements are selfish genetic elements that insert themselves into new genome locations. This natural machinery has been adapted by scientists to introduce carefully designed DNA constructs into genomes. Stern and colleagues used the piggyBac transposon system to insert a fluorescent reporter gene into hundreds of random locations in the genomes of five different Drosophila species. They mapped the location of each insertion and identified the unique insertions that could be maintained in homozygotes, resulting in 184 D. simulans lines, 122 D. mauritiana lines, 104 D. yakuba lines, and 64 D. santomea lines. Each line has an insertion in a unique genomic location coupled to a fluorescent reporter gene whose expression can be easily detected in the eyes with a microscope. The huge collection of unique locations will make fine mapping in these species much easier.

Coupled to many of the insertions is a landing site that can be used to add new insertions via plasmids carrying a suitable targeting sequence. The authors tested the integration efficiency at landing sites in unique genomic locations and identified those with high efficiency that could be maintained as homozygotes. They also tested the effects of insertion location on expression by transforming a fluorescent reporter gene linked to an enhancer of even-skipped, a developmental gene in D. melanogaster with well characterized expression patterns. In four of the five species tested, at least one strain showed the expected patterns of expression, suggesting that any gene of interest transformed into these sites will not be subject to ectopic expression from location effects. Additionally, they used CRISPR/Cas9 gene editing to knock out expression of the fluorescent eye reporter in a number of strains. Since strains still have the landing site in known locations, they can be used to examine expression of genes of interest in the eye without interference from the reporter.

Noni fruit is toxic to most other fruit flies, but <i>D. sechellia</i> loves it. Photo by Carmen via Flickr.

The fly species of D. melanogaster species group are notable not just for their close relationship with the famous D. melanogaster, but they also make excellent evolutionary models in their own right. D. melanogaster and D. simulans are cosmopolitan species that live wherever humans do, but the other members of the group are found only on islands off the coast of Africa. D. sechellia is a member of the group that feeds primarily on a fruit toxic to most other animals. Despite the adaptive differences that come with these divergent lifestyles, many of these species can still hybridize, making laboratory studies aimed at dissecting these differences possible. The transgenic lines presented in this paper will make studies on speciation and adaptation in these lineages more powerful and accessible than ever before.

Stern, D. L., Crocker, J., Ding, Y., Frankel, N., Kappes, G., Kim, E., Kuzmickas, R., Lemire, A., Mast, J.D. & Picard, S. (2017). Genetic and Transgenic Reagents for Drosophila simulans, D. mauritiana, D. yakuba, D. santomea, and D. virilis. G3: Genes, Genomes, Genetics, 7(4), 1339-1347.

http://www.g3journal.org/content/7/4/1339

Off the coast of North America drifts a jellyfish that has unknowingly revolutionized molecular biology. Aequorea victoria produces green fluorescent protein (GFP), a substance that adds a green tinge to the jelly’s bioluminescence, which can sometimes be seen around its margins. By inserting a slightly modified version of the GFP gene into the genomes of other organisms, researchers have visualized a stunning range of biological phenomena. But GFP isn’t without flaws. For some uses—for instance, tracking expression of some low-expression genes—the protein just isn’t bright enough.

Luckily, A. victoria isn’t the only organism to produce a fluorescent protein amenable to laboratory use. The tiny European lancelet Branchiostoma lanceolatum, an invertebrate found in the northeastern Atlantic Ocean, produces a multimeric yellow fluorescent protein called LanYFP. Recently, Shaner et al. modified the protein to make it a green fluorescing monomer, making it a possible stand-in for GFP that could be used with the same microscope filters already used for GFP. Their new protein, dubbed mNeonGreen, isn’t just a new GFP substitute—it’s actually three times brighter than GFP in vitro.

Although their results were a promising first step, Shaner et al. did not determine whether mNeonGreen’s better in vitro fluorescence actually makes a difference in vivo. In the January issue of G3, Hostettler et al. address that question by expressing the protein in Caenorhabditis elegans, a commonly used animal model with a transparent body that makes it particularly suitable for imaging studies.

Their results show the green color produced by mNeonGreen is significantly brighter than GFP in C. elegans, allowing visualization of low-expression genes that can’t be seen using GFP. The group also found that mNeonGreen works well for GFP’s typical applications, from tagging proteins to labelling subcellular compartments, and that the protein is as stable against photodegradation as GFP. These properties will make mNeonGreen a valuable asset to researchers—and in light of this, Hostletter et al. have kindly provided a plasmid set containing the gene for use by researchers everywhere.

CITATION:

Hostettler, L.; Grundy, L.; Käser-Pébernard, S.; Wicky, C.; Schafer, W.; Glauser, D. The Bright Fluorescent Protein mNeonGreen Facilitates Protein Expression Analysis In Vivo.
G3, 7(2), 607-615.
DOI: 10.1534/g3.116.038133
http://www.g3journal.org/content/7/2/607

The National Science Foundation’s Directorate for Biological Sciences (BIO) has put two funding programs on hiatus, pending an evaluation of the “long term resource needs and research priorities” within the directorate. The suspended programs are both within BIO’s Division of Biological Infrastructure (DBI).

Collections in Support of Biological Research (CSBR)

The Collections in Support of Biological Research program had been providing funding for three major activities:

• improvements to secure and organize collections that are significant to the NSF BIO-funded research community;
• secure collections-related data for sustained, accurate, and efficient accessibility to the biological research community; and
• transfer ownership of collections.

The collections supported by the program include established living stock/culture collections, non-living natural history collections, and ancillary collections such as preserved tissues and DNA libraries.

Those of particular interest to the GSA community include the San Diego Drosophila Species Stock Center, Chlamydomonas Resource Center, Arabidopsis Biological Resource Center, Bacillus Genetic Stock Center, and E. coli Genetic Stock Center.

The program also experienced a similar pause in funding in 2013 during a shift from an annual to biennial deadline cycle (which was later reversed). Although DBI acknowledges the importance of infrastructure provided by the CSBR program, they are concerned about the relationship of the program to other related NSF programs.

To that end, NSF is soliciting feedback from the community and is especially interested in responses to the following questions:

• Is the scope of collection support provided by CSBR adequate and appropriate to address the research and education community needs? If there are gaps, what are these and how should they be addressed?
• What is known about how the collections-related programs (CSBR, Advancing Digitization of Biodiversity Collections, and the Collections track of Postdoctoral Research Fellowships in Biology) leverage one another (anecdotal evidence is welcome!)?
• What are the impacts of the CSBR program that are innovative and/or transformative in understanding unanswered questions in biology or that significantly impact education or outreach?
• Are there other issues or metrics that should be considered during evaluation of the CSBR program; e.g., encouraging data publications that cite specimens, societal benefits (such as environmental impacts, education/workforce development, and economic benefits), etc.?

GSA is working with several living stocks collections—as well as our policy partners—to develop a formal response, but we encourage individuals to submit their own comments to NSF by writing to DBICSBR@nsf.gov.

The Drosophila Species Stock Center is asking its users to write a letter to NSF supporting the value of living collections, and describing how important the center is to their research and STEM training.

They encourage users to try to include any one (or all) of the following in their letter: 1) how they use the stocks in their research, 2) if/how they use stocks in STEM training, 3) how stocks have facilitated new and exciting research trajectories.

We also invite members of the community to share your perspectives with GSA through comments below or by email to society@genetics-gsa.org. Your input will help us develop a response that is appropriately inclusive.

Instrument Development for Biological Research (IDBR)

The Instrument Development for Biological Research program had been supporting the “development, production, and distribution of novel instrumentation” that address needs in areas of biological research supported by NSF BIO. This has included two types of proposals:

Type A – Innovation: Proposals for the development of novel instrumentation that provides new research capabilities or, where appropriate, that significantly improves current technologies by at least an order of magnitude in fundamental aspects such as accuracy, precision, resolution, throughput, flexibility, breadth of application, costs of construction or operation, or user-friendliness.

Type B – Bridging: Proposals for transforming ‘one of a kind’ prototypes or high-end instruments into devices that are broadly available and utilizable without loss of capacity. If appropriate, PIs should seek SBIR/STTR Program, or similar support mechanism for implementation of broad distribution following an IDBR award.

The program has not supported access to an instrument in a user facility nor to enhance research capabilities in a specific lab or institution.

Additional Information:

• Nala Rogers, “Biologists ask NSF to reconsider plan to pause collections funding program,” ScienceInsider, March 25, 2016.
• Anna Nowogrodzhi, “Biological specimen troves threatened by funding pause,” Nature News, March 21, 2016.
• National Science Collections Alliance, “NSCA and Others Urge NSF to Reconsider CSBR Hiatus,” March 24, 2016.
• Bethany Drehman, “NSF places two biological infrastructure programs on hiatus,” FASEB – The Washington Update, April 7, 2016.

An article in the most recent issue of Science highlights a growing concern about the continued support of the biological databases on which our community depends. Indeed, 2015 GSA President Jasper Rine was quoted as saying these resources are “critical for our daily life as geneticists and biomedical researchers.”

Many of the model organism databases (MODs) used by members of the GSA community—including FlyBase, WormBase, SGD, ZFIN, and MGI—have been supported by NIH’s National Human Genome Research Institute (NHGRI), along with others supporting human and other research—such as OMIM, the Gene Ontology Consortium, and UniProt. In data compiled by Science, NHGRI provided more than $17 million in funding to support the MODs that serve the C. elegans, Drosophila, mouse, yeast, and zebrafish communities, part of the $30 million it spends on all databases.

But as the data cataloged in these resources continues to extend beyond genomes, NHGRI is concerned that it is bearing all of the costs. As NHGRI Director Eric Green was quoted, “we’re not a good long-term home.” And with the continuing explosion in the amount of biological data and increasing pressures on funding, the challenges are only growing.

NIH is thinking about other funding models, including ways to recruit financial support from other sources, encourage infrastructure sharing among databases, or consider charging for the use of the databases. For example, when the National Science Foundation eliminated funding for The Arabidopsis Information Resource (TAIR), it was forced to move toward a subscription model.

GSA member Janan Eppig, who is PI for the Mouse Genome Database, and Monte Westerfield, who runs the Zebrafish Model Organism Database, are concerned about this precedent. They worry that access to the data will be restricted under subscription paywalls and make it even more difficult to link to data across databases.

This past summer, Rine participated in a meeting convened by NHGRI to discuss the future of these databases, and GSA has also worked to draw attention to this issue by other NIH institutes. The sustainability of MODs has also been a frequent topic of conversation between GSA and both NHGRI and the National Institute of General Medical Sciences (NIGMS). Indeed, NIGMS Director Jon Lorsch has stressed the importance of treating such resources as infrastructure, rather than research grants.

GSA has also emphasized the importance of the model organism databases in response to several NIH requests for information. For example, in a March 2015 comment, GSA indicated that these resources should not be forced to be self-sustaining as they are essential to the overall research enterprise and provide value significantly greater than the sum of the value to individual investigators. GSA also cautioned against a subscription model, saying that “even a small fee would be a disincentive for accessing validated and current data. It would also have a negative impact on the use of such resources by scientists working on other organisms—often motivated by hunches from other MODs—more casual users or those who lack significant funds, such as researchers at under-resourced institutions and those using such data repositories for educational purposes.”

In the long run, the National Library of Medicine (NLM) might become the home for such databases, as part of its mission to serve as the datascience hub at NIH. A search for the new NLM director is underway, with Green and Lorsch chairing the search committee.

Additional Information:

• Jocelyn Kaiser, “Funding for key data resources in jeopardy,” Science 351: 14.