Thoughts of public sector animal geneticist - all views are my own

Month: February 2016

Got pests?


Cattle grazing in Northern California

Over the past two weeks I have been speaking to livestock producers at locations from Bakersfield in Southern California to Montague on the Oregon border. I was a speaker at a number of “Winter Animal Health” meetings which are organized annually by the University of California Cooperative Extension.

As a geneticist, I was speaking about genetics and how to make better bull selection decisions. Not surprisingly (to all but a geneticist) genetics was only one of several topics covered, and many of the subjects were unrelated to my area of expertise.

Being located on the Davis campus, I relish the opportunity that extension meetings afford me to get out among actual producers and listen to their experiences, concerns and problems. And what really struck me about this series of meetings is that everything is trying to eat our lunch!

What I mean by that is that pests from all kingdoms – microbial, plant and animal – are competing for the resources used by the plants and animals that we eat, or are beating us to the punch by actually eating those same things for themselves!

The traditional definition of a pest is an epidemic disease associated with high mortality; specifically the plague or “pestilence”. It is also defined as something resembling a pest in destructiveness; especially a plant or animal detrimental to humans or human concerns (as in agriculture or livestock production).

The pests that were covered by this series of meetings included the traditional viruses and bacteria that result in animal diseases, weeds that compete with pasture and crops for scarce water and nutrients, a wide-ranging list of insects like ticks and mosquitos that carry disease, ground squirrels that eat vegetation and construct leg-breaking holes and destructive mounds in the middle of fields, wild deer that graze crops, pastures and even watermelons, and wild horses that compete for precious resources on the drought-stricken range.

Listening to the plethora of animal and plant pests discussed at these meetings, it is impressive that the producers are able to preserve any of their product to market for human consumers.

Control measures to address pests were as varied as the pests, and indeed the producers, themselves. Depending upon the production system requirements of their target market, producers are using a variety of chemical, physical, and  temporal pest management approaches.

One thing is constant – all production system face pests. Some pests are common to all – like threat of animal disease and weeds – whereas others are crop and/or species specific.

Google image search for “ideal farm”

Often images of agriculture show a utopian red barn in a green field, and rarely is there even a single pest present in the image. The animals are all healthy, the fields are all weed-free, and there is not a single ground squirrel, tick or other scourge in sight.

Skillful management can help approach that ideal through the judicious use of preventative measures like vaccines to forestall disease, and ploughing or tilling to manage undesired weeds. But in the open outdoor environment of agriculture it is hard to avoid airborne weed seeds, disease-causing microbes and insects, and grazing competition from wild herbivores. And then there are the predators that prey on the livestock themselves.

Failure to correctly or effectively manage pests can result in complete crop failure (i.e. no food), or catastrophic health outcomes for livestock. It has been estimated that without pesticides 70% of the world food crop would be lost and even with pesticide use, 42% is destroyed by insects and fungal damage. Dispensing with pesticides would require at least 90% more cropland to maintain present yields.

The producers present at these meetings spanned the range from backyard hobby farmers, to part-time ranchers with  day jobs in the city, to fulltime commercial family farmers and ranchers. They represented a range of farming systems, including some that prohibited the use of certain pest management methods such as certain herbicides, antibiotics, or selected insecticides.

What was  refreshing to me was that the different control methods and integrated pest management approaches were presented objectively, and the producers listened with respectful interest, rather than judgment, as to how their neighbors were managing their pest problems.

There were no black and white choices or magic silver bullets provided by the various speakers. Different approaches were presented along with their nuanced pros and cons; benefits and tradeoffs were discussed fairly and without prejudice in comparison among the different choices that are available.

In my 20 year experience working with farmers and ranchers, this set of meetings was not atypical. Extension has long presented objective information on solutions to agricultural problems through informal educational meetings.

I just wish more urban people could hear these discussions and see the level of technical competence, professionalism and thought that producers put into their production and pest management decisions, and appreciate the fact that at the end of the day some food remains for their dinner and dessert plates. Including this impressive spread of homemade pies on offer at the conclusion of the Montague cattle health meeting, aka “Pie Night” for obvious reasons. One of the lesser known and most enjoyable perks of an extension meeting in Northern California ! With thanks to Siskiyou County Cattlemen and Cattlewomen!

Home made pies at the Montague Cattle Health Meeting

Home made pies at the 2016 Montague Cattle Health Meeting


Time to Accelerate Real Change

The following abstract entitled “Twenty years of TARC: Time to Accelerate Real Change” appears in the February 2016 issue of Transgenic Research  Volume 25, Issue 1, pp 101-122

(Note: Since the 10th Biennial Transgenic Animal Research Conference (TARC X) conference was held in August 2015, the AquAdvantage salmon was technically approved by the FDA in November 2015, although currently it can still not be sold in the United States as explained here.)

bookThe first transgenic animal research conference (TARC I) was held in 1997 and the proceedings were summarized in a book optimistically titled, “Transgenic Animals in Agriculture”. The book contains some interesting quotes, including one attributed to Dr. Robert Wall, USDA-ARS in Beltsville, Maryland, who quipped, “the field of transgenic large animals is one of the few fields where there are more review papers than data papers.”

It is perhaps a useful exercise at this TARC X conference to go back to some of those original papers and see what progress we have made over the past 18 years. At the time it was posited that there were three major limitations to wide-scale application of transgenic technology to improve farm animals: 1) lack of knowledge concerning the genetic basis of factors limiting production traits, 2) identification of tissue and developmentally-specific regulatory sequences for use in developing gene constructs, expression vectors and in gene targeting, and 3) establishment of novel methods to increase the efficiency of transgenic animal production. Considerable progress has been made in all three of these areas in the past 2 decades.

Despite the hopeful projection offered by Dr. George Seidel of the Animal Reproduction and Biotechnology Laboratory at Colorado State University, “At this point in evolution, human society places great emphasis on applications of science and technology. Since use of transgenic technology in farm animals, almost by definition, is an application, this will be viewed favorably by both public and private funding sources”, limited progress has been made in the commercialization of transgenic animals.

Pharmaceutical proteins ATryn® and Ruconest®, produced in transgenic goats and rabbits, respectively, have been approved in both the European Union and the United States. Several varieties of fluorescent transgenic aquarium fish are being marketed throughout the United States as GloFish®, and open field trials of genetically engineered male insects produced by Oxitec have been carried out in several countries to reduce the population numbers for disease-spreading pests. However, no transgenic animal has yet been approved for food purposes anywhere in the world, despite an ongoing long-term attempt by AquaBounty to obtain a U.S. regulatory decision for their fast-growing Atlantic salmon.

GloFish Fluorescent Fish Group Photo with NEW Striped Green Barb

Fluorescent Genetically Engineered Aquarium Fish (Glofish)

The lack of progress on agricultural applications can be attributed to a scarcity of both public and private funding sources, and the absence of a clear path to market. Starting in the mid-2000s, the annual USDA request for grant applications included the following ominous text, “Applications whose primary aim is to improve the efficiency in the production of clones or transgenic animals through manipulation of the nucleus will no longer be accepted by the Animal Genome program”. This directive continued for almost a decade. There has likewise been little private sector interest in taking transgenic food animals, such as the phytase-expressing Enviropig™, through an expensive and unpredictable regulatory process. In the absence of any approved food animal applications, there has been little support or market pull for transgenic animals from the livestock breeding sector.

As a scientific community, we have continued to make progress in transgenic animal research methods, funded mostly by granting sources interested in the biomedical application of transgenic animals, and also the USDA Biotechnology Risk Assessment Grant (BRAG) program. This program has funded research to test some nontraditional hypotheses to provide rigorous scientific data for risk assessments.

Dr. Matthew Wheeler, University of Illinois, answered the question of whether transgenes can be transferred directly from transgenic pigs to control swine by physical association or contact, by mating, or from a transgenic dam to her non-transgenic offspring during lactation. Spoiler alert # 1: The data showed no transfer.

In another project, Dr. Elizabeth Maga, University of California, Davis (UCD) answered the question of whether transgenic goats expressing lysozyme in their milk behave differently to control goats. Spoiler alert # 2: The data showed no difference.

In the first chapter of “Transgenic Animals in Agriculture”, Dr. Jim Murray, UCD wrote, “Our role as scientists, consumers, and regulators is, in part, to decide at what level or stages and to what degree the development of agriculturally important transgenic animals must be monitored and regulated to ensure consumer safety and animal well-being, and address societal concerns. A further corollary to this responsibility is to ensure that the consuming public understands the processes to the extent that they can accept government approval of such animals in the food chain.”

I would argue that less progress has been made in this area. In the chapter penned by Dr. Joy Mench, UCD, which focused on the ethics and animal welfare of transgenic farm animals, she warned, “In the past scientists have tended to isolate themselves from these debates. This posture needs to change. Scientists need to become full and fully informed participants in the debate about the ethical effects of the technologies that their work is instrumental in developing. Otherwise, consumer confidence in science and scientists may well be lost.”

Is it finally time for the transgenic animal scientific community to take these suggestions to heart and address both the regulatory impasse and the consumer concerns head on? The current recombinant DNA (rDNA) process-based trigger for regulatory evaluation of transgenic animals is disincentivizing the development of beneficial transgenic animal applications. As a community, we need to push for sensible regulatory reform.

Regulatory effort should be proportional to the risks posed by the product. Required regulatory studies should be hypothesis-driven based upon the novel attributes of new varieties in relation to known risks associated with existing varieties, and not on the breeding method used to develop the new variety.

The closing speaker at the 1997 conference, Dr. George Seidel suggested, “One mistake that animal scientists are rightly accused of making is to emphasize production traits when low production is not a problem. More attention needs to be paid to non-production traits such as animal welfare, animal health, consumer acceptance, and so on.” I contend that we now have applications that address these non-production traits and it is time for scientists to more effectively communicate the compelling narratives associated with the potential benefits of these technologies.

It would be ironic if,  as was portended by Joy Mench at TARC I in 1997, “genetic engineering turned out to be the fastest and best solution for some of the welfare problems that we have created using traditional breeding methods like leg problems in broilers.”

Scientific and technological advances in disparate animal breeding research communities over the past two decades are now undergoing a form of scientific convergent evolution. The thousands of SNP markers discovered through livestock sequencing projects, the information obtained from numerous genome wide association studies, the discovery of causative SNP (QTNs), the development of genomic selection statistical methodology to include molecular data in genetic merit estimates, genome editing techniques, and transgenic technologies are all useful individually. But collectively, they offer a powerful approach to accelerate real genetic change in our food animal species to the advantage of food security and agricultural sustainability globally.

Omega-3 fatty acids and milk

I have had a long standing interest in omega-3 fatty acids. Increasing the intake of omega-3 fatty acids has been linked to beneficial health outcomes. Mammals cannot make omega-3 fatty acids, they must obtain them from their diet.

Milking mice

In fact, one of the first research projects I undertook when I started at UC Davis in 2002 was to produce genetically engineered mice (by adding an omega-3 desaturase gene) that could produce their own omega-3 fatty acids in their milk! Yes I have spent time milking mice – they have a lot of teats (10-12) compared to a cow (so this milking mice image is technically incorrect!).

When in 2004 I  wrote a follow on grant to take my preliminary research in mice onto larger animals (i.e. cows), the grant was not funded with the reviewer’s comment being  “Given the “pure and wholesome” public perception of milk products, it may be particularly difficult to gain widespread public acceptance for transgenic milk products – despite their health benefits.”

So began my decade plus of focusing my research on breeding methods other than genetic engineering. However, I still think that if cows could produce their own omega-3 fatty acids that would be a good thing for public health, and perhaps if the public sector had been able to obtain research funding to bring some of these consumer benefit traits to market then public acceptance of transgenic products might be different today.

But back to omega-3s in milk. Because cows cannot produce their own omega-3 fatty acids they must obtain them from their diet. And because cows are ruminants, almost all of the feed they consume is first “digested” by the microbes in their rumen. And bacteria love to derive energy by converting polyunsaturated fatty acids into saturated fatty acids (biohydrogenation).

Hence, ruminant products are relatively high in saturated fatty acids relative to single stomach animals who tend to more faithfully reflect the fatty acid composition of their diet. And one group that eat a lot of omega-3 fatty acids in their diet is oily fish, such as salmon, herring, mackerel, anchovies, menhaden, and sardines.

Like cows, fish do not synthesize omega-3 fatty acids; they obtain them from the plankton in their diets. Fish are a particularly valuable source of the long-chain omega-3 fatty acids (20:5 EPA and 22:6 DHA). Evidence supports a dietary recommendation of ≈ 0.5 g/d of EPA and DHA for cardiovascular disease risk reduction. As a result, the American Heart Association recommends eating fish (particularly fatty fish) at least two times (two servings) per week.

So is milk an important dietary source of omega-3 fatty acids? Not really. Not to criticize milk – it is valuable source of protein, Vitamin D, Riboflavin,  Vitamin B12, Phosphorus and Calcium, and my kids drink a glass of pasteurized milk with every meal.

I am not a trained dietician, but as a Mom I do feed humans nutrients and therefore compare the nutritional content of foods. According to the USDA standard reference database, an eight fluid ounce cup (244 g) of 3.25% fat milk has 0.183 grams of omega-3s, most of it 18:3 (ALA). A half fillet serving (178 g) of salmon has 4.023 grams of omega-3s,  most of it EPA and DHA. In other words I get more than 20 times the omega-3 fatty acids from a serving of salmon that I get from a glass of milk, and they are the long-chain varieties. And if the milk is non-fat or skim the amount goes down to 0.0049 grams of omega-3s, because – well they removed the fat!

Dairy cows on California drought-stricken pasture

Dairy cows on California drought-stricken pasture in Sonoma County in 2014

The omega-3 composition of milk can be influenced by the cow’s diet – if cows eat a diet high in omega-3 fatty acids, then a small fraction of them “bypass” biohydrogenation by the rumen microbes, and so make it to the true stomach. So feeding cows lush omega-3 rich green grass, rather than the drought-stricken pastures that have been on offer here in California for the past 4 years, is associated with a slight increase in omega-3 fatty acids. The high content of polyunsaturated fatty acids (especially ALA) in grasses at early stage of maturity is the main reason for the positive effects of pasture on the fatty acid composition of milk.

I should mention my husband (of 26 years as of today – Happy Anniversary!)  is also a researcher at UC Davis, and he works in aquaculture. So we have had a surf and turf rivalry going on for more than a quarter century in our house. I think we only survived together so long because we recognize that different foods – four legs, two legs, no legs – all have their pros and cons! And little of each in moderation seems to be a recipe that my whole family can live with.

Valentine’s Day 2016

Alison Van EenennaamShould I start a blog? I have been thinking about this question for a while. I certainly have plenty of other things to keep me occupied – students, grants, research, presentations to prepare, reports to write, oh and my own kids and husband (Happy Valentine’s day BTW) and family duties.

What really spurred me to actually bite the bullet and start a site was a couple of recent interactions with work colleagues. One was an email asking me if I had ever interacted with a particular journalist. The question was whether this journalist had a history of misrepresenting the science around animal breeding methods. The default assumption seemed to be that it was most likely that the scientifically-accurate information that was being freely given by this public sector scientist to the journalist would be spun to misrepresent what the scientist said or distort the facts.

And then there was a discussion with some faculty members in my department about correcting some misinformation regarding the consumption of animal products. There was a collective sigh that yes the information was incorrect, but was it worth our while to challenge it? Such things take time and energy, and often such challenges fall of deaf ears. And everyone has plenty of other pressing work to do with their own students, teaching, research etc. to more than occupy the day.

So who then is left to stand up for science, especially around agriculture, and speak out to challenge incorrect information which is often used as the basis of public policy? If not public sector scientists and researchers working in the field, then who? Unfortunately I think we all know the answer to that question.

I know as a researcher working in the field of animal biotechnology (my current research projects are listed on my faculty website – and are publicly funded), I deal with controversial topics. My interest is to use this blog to try to interject scientific nuance into these controversial and often politicized scientific topics.

Science is rarely black and white, and agriculture never is. I know you should never say never, but in this case I think never is warranted. I also remember thinking to myself  I would never write a blog. That is the beauty of science – you are allowed to change your mind based on new information.

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