Animal Science Review

Circadian rhythms and jet lag.  There, cyclic crowing behavior explained.

Quite a lot of people are discussing this study from Japan examining the effect of light on the crowing behavior of roosters. The authors observed several birds in experimental conditions where light intensity and duration were controlled, taking observations with audio recorders and cameras. The scenarios presented were a daylight cycle of 12 hours of light and dim light respectively, and constant dim light. Observations were recorded for a period of 14 days, producing this graph.

So many reporters on the study have run with this, making declarations about what great timekeepers roosters are, and how cool it is that they don’t need the sun to know when dawn is.

Well, approximately when dawn is.

“Under dimLL conditions, a free-running rhythm of crowing was observed with a period of 23.7 ± 0.1 h (n = 4), but this free-running rhythmicity gradually damped out”

Interesting, so the sun is unnecessary until it’s been gone for a while, then we start to get some variation. This dampening effect is even more obvious when you place testosterone implants in the roosters.

Don’t get me wrong, the fact that Roosters have this accurate of a circadian clock is impressive! It’s very interesting biologically, but it’s not some infallible atomic clock. While many news sites are toting that Roosters are independent of the sun, the opposite is true. Circadian rhythms are directly calibrated primarily by light cycling, with temperature being another important environmental cue. To confirm the roosters knew what time it was, the authors examined the effect of light or recorded crowing sounds at different times of day. They found that there were fewer crowing behaviors at random dawn times than at the “correct time” of day.

This doesn’t mean the roosters know it’s 5pm, but their circadian rhythm is telling them that it isn’t dawn. However, the sun still “came up” so we witness some halfhearted crowing. Anyone who has ever traveled out of their timezone knows exactly how this feels: these roosters have jet lag. While the sun may be coming up, their circadian clocks are telling them that it feels like a different time of day, so they crow in response to the light, but with reluctance and confusion, much in the same way you sleepily get up on vacation when the Louvre opens, even though it feels like 5PM to you.

“But Austin,” you tell me, “aren’t you anthropomorphizing?” While I admit roosters may not empathize with trans-Atlantic vacations, we know that chickens are dependent on daylight to calibrate their biological rhythms because we do it all the time. We increase egg production by simulating summer lighting year round, and alter feed intake in broilers by changing their daylight cycle. We also use this trick to bring mares into heat.

The loss of rhythm observed in 24 hour dim light is likely to become more and more sporadic, and even more so if the roosters were housed singly (as there is some group consensus due to competitive crowing). I would propose that if you could keep the roosters on a light cycle that progressively moved forward an hour a day until dawn was at 2pm, the roosters would crow with the same strict rhythm independent of the actual sun. If the authors of the study choose to pursue this hypothesis, an easy test would be to simply progress their artificial sun’s rise and fall over time.

Alternatively, we could fly several roosters with us to Paris, and see if they wake us up before the Louvre opens.

Shimmura, T., & Yoshimura, T. (2013). Circadian clock determines the timing of rooster crowing Current Biology, 23 (6) DOI: 10.1016/j.cub.2013.02.015

Hey all, taking a quick break from blogging as I’m busy with a personal research project I’ll report here on ASR soon, but I wanted to add a quick post for anyone subscribing to RSS or wondering if I’m still alive.

This article on ScienceDaily details a study going on at the University of Georgia, in which they’re recording flock vocalizations to find distinct patterns that can be associated with temperature levels, ammonia concentrations, and other detrimental environmental factors. This has possible implications not only for the welfare of the birds but for the efficiency of the operation.One example of a financial incentive that the article provided is that current ammonia detectors are expensive and short-lived, and if a computer instead could “listen” to the flock and identify specific vocalization changes related to ammonia levels those detectors could be made obsolete.

It’s a cool article, and an awesome example of how agriculture continues to keep up with technology. Check it out and I’ll be back to regular posting as soon as my other personal project is on it’s way!

An article recently published in Environmental Science and Technology details a study conducted at Johns Hopkins where when examining samples of commercially available feather meal (used as a protein supplement feed or fertilizer) they found trace amounts of fluoroquinolones, a class of antibiotics that have been banned for use in animal feed for 6 years. This is an interesting find, and definitely warrants further research before any broad sweeping conclusions can be made. You know…unless you publish a press release condemning the entire industry for breaking the law and trying to kill us all (question, if all the chicken consumers are dead, how does that lead to higher profits?).

The article itself is very well done. The authors collected samples of feather meal from several states and Canada and tested them for various pharmaceuticals. They also autoclaved the samples to see how the heating processes involved in creation of the product affected degradation/digestion of any of the compounds, and exposed E. Coli cultures to the meal to see if the presence of one or more of the compounds was enough to select for antibiotic resistant populations (they were).

The researchers examined each of the compounds of interest and proposed mechanisms for their presence. Some of them are used at various levels legally within the industry, and the presence of many others (such as caffeine) can be explained by their introduction through various feedstuffs (such as coffee pulp and green tea powder) (Love et al., 2012).

Obviously of most interest to the researchers were the levels of fluoroquinolones, and they hesitantly proposed possible mechanisms for their introduction into feather meal.

“Fluoroquinolones (enrofloxacin, norofloxacin, or ofloxacin) were detected in 6 of 10 U.S. samples, which was not expected because fluoroquinolone use in U.S. poultry production has been banned since 2005. These findings may suggest that the ban is not being adequately enforced or that other pathways, for example, through use of commodity feed products from livestock industries not covered by the ban, may inadvertently contaminate poultry feed with fluoroquinolones…To better interpret our findings, corroborating evidence in the form of antimicrobial usage practices and dosing amounts would be needed.” (Love et al., 2012)

Clearly we’re not ruling out the possibility of these antibiotics being fed, but there is no cause and effect relationship here. They also make note that feather’s contain antibiotics in higher concentrations than meat or other tissues, even after legally defined withdrawal times to remove them from edible tissue. The conclusions here are justly cautious, and place no blame or accusations upon the industry.

The other interesting find was that the feather meal tested would select for antibiotic resistant strains of E. Coli when exposed to cultures. However, this was only testable with autoclaved samples of the meal. And did we mention that the only samples tested here were sourced from China (who according to the article use many more antibiotics than we do in poultry production)?

“These initial results suggest, but cannot prove, that the inhibiting substance may be an antibiotic/bacteriostatic. Autoclaving may have attenuated the quantity and bioavailability of antimicrobial drugs originally present.” (Love et al., 2012)

Again, a cautious observation and hardly conclusive. Comparisons were made from standard cultures exposed to low levels of relevant antibiotics to see if the same strains were removed, but this data cannot be correctly compared as the feather meal was not controlled enough to isolate those compounds. The authors finish their discussion with an appreciation for the novel information they found and an invitation for others to verify, replicate, and build upon their results.

“We have previously described risks related to administration of medicated feed to food animals, which may promote selection for antimicrobial resistance. The presence of antimicrobials in feather meal, as determined in this study, is a previously unrecognized source of these drugs in animal feed. Because this is the first study of PPCPs in feather meal, we invite independent verification of our results by others. More work is needed to determine whether the detected levels of PPCPs in feather meal have an impact on the quality of food animal products and the safety of consumers.” (Love et al., 2012)

And there we have it, an exciting new study that presents a lot of questions to be used for follow-up research. So we’ll publish it and make sure to put out a press release so that not only those keeping up with the journals can read and understand what we’re currently researching.

Well…it seems like the authors like to be scientific when submitting journal articles, but prefer big headlines and sensationalizing when trying to popularize their research. In their official press release, these researchers quickly turn from cautious scientists to industry whistleblowers.

“The discovery of certain antibiotics in feather meal strongly suggests the continued use of these drugs, despite the ban put in place in 2005 by the FDA…The public health community has long been frustrated with the unwillingness of FDA to effectively address what antibiotics are fed to food animals.” – David Love, PhD

Comments from Keeve Nachman, PhD, show a level of conviction that I had no idea he possessed in the original article.

“In recent years, we’ve seen the rate of fluoroquinolone resistance slow, but not drop…With such a ban, you would expect a decline in resistance to these drugs. The continued use of fluoroquinolones and unintended antibiotic contamination of poultry feed may help explain why high rates of fluoroquinolone-resistant Campylobacter continue to be found on commercial poultry meat products over half a decade after the ban.” (I guess we know for sure they’re still being used in the US, I must have missed that citation in your introduction)

“A high enough concentration was found in one of the samples to select for bacteria that are resistant to drugs important to treat infections in humans” (Note: the concentration comment is true, however, your study stated that there was not controlled enough testing to prove that any specific compound present caused the bacterial selection)

“We strongly believe that the FDA should monitor what drugs are going into animal feed…Based on what we’ve learned, I’m concerned that the new FDA guidance documents, which call for voluntary action from industry, will be ineffectual. By looking into feather meal, and uncovering a drug banned nearly 6 years ago, we have very little confidence that the food animal production industry can be left to regulate itself.”

Wow, this press release from the actual authors of the article must be legit, after all, they wrote it, and they wouldn’t write/act completely differently so as to both dangle a carrot to the media and still get their research published in a peer-reviewed journal right?

Well, the press release did its job, and Nachman can be found interviewing left and right about how he was “floored” by the result, and how that the more he learns, “the more [he is] drawn to Organic”. There’s a severe lack of integrity here, and the misrepresentation of your data and analysis to cater to anti-big-Ag sentiments is irresponsible and unethical.

So, future scientific corespondents for the Daily Mail aside, what are some other proposed mechanisms for the presence of these banned antibiotics? After all, I’m suggesting that they aren’t being fed routinely as the authors apparently really believe. Let me rephrase that, I’m not ignoring multiple unproven mechanisms for the purpose of shock science.

I spoke with James Hermes PhD, a professor and Poultry Science Extension Specialist here at Oregon State University, about the article. He had obviously heard of it and shared with me some discussions he had had with his colleagues. Their proposed mechanism for the introduction of the pharmaceuticals was through groundwater.

“Feather meal is boiled at the rendering plant, it’s processed with a lot of water, so anything in the groundwater can end up in the meal…Just recently near [Corvallis] they did some testing and found nearly everything we use at home. For years they told us to flush our excess medications…It’s always been there, we’ve just only recently been able to look at such small concentrations 1 parts per billion, trillion, or even possibly quadrillion.” – James Hermes, PhD

So in addition to whatever chickens could be exposed to via drinking the water and concentrating pollutants in their feathers, additional water and pollutants are introduced during the rendering of the product. He encouraged me to find some research showing that ground water contains any and all of the things discovered in the feather meal, and I found it.

So is this a possible mechanism for the introduction of these contaminants? I suggest the authors of the study follow their own advice in the article and explore this mechanism. Perhaps see if the levels of the pharmaceuticals change in the feathers both prior to and after rendering/boiling, explore if they are present in organically produced feather meal, and find out if there are still large concentrations of fluoroquinolones in the groundwater of the areas processing feather meal. And hey, if they want to keep on trucking with scare tactics, I think finding this stuff in the water supply will be much more frightening to the public given that we can’t buy organic water (don’t start).

Finally, in evaluating consumer exposure to the present antibiotics in feather meal, we should keep in mind the steps necessary in the shortest route to the consumer. First, there have to be high concentrations of antibiotics in feather meal; second, that feather meal must be fed to an animal used for food, third; those antibiotics must be retained and remain active until slaughter of that animal at a high enough concentration; fourth, they have to survive gastric juices and be absorbed into the small intestine of the person eating the meat/milk. Nevermind that along the way, the authors of the relevant study note that at any point the vector for the antibiotics is heated most of them will degrade.

Obviously, if the feather meal is used as fertilizer instead of a by product feed, then there are a few more steps that need to take place to get those pollutants onto the plate.

Now if you’ll excuse me, I need to finish this compelling article on how those fat cats selling nautral almond extract are trying to murder me .

 

D.C. Love, R.U. Halden, M.F. Davis, & K.E. Nachman (2012). Feather Meal: A Previously Unrecognized Route for Reentry into the Food Supply of Multiple Pharmaceuticals and Personal Care Products (PPCPs) Environmental Science and Technology, 46, 3795-3802

Kolpin, D., Furlong, E., Meyer, M., Thurman, E., Zaugg, S., Barber, L., & Buxton, H. (2002). Pharmaceuticals, Hormones, and Other Organic Wastewater Contaminants in U.S. Streams, 1999−2000: A National Reconnaissance Environmental Science & Technology, 36 (6), 1202-1211 DOI: 10.1021/es011055j

 

 

Update: following this post I had a chance to talk with one of the Authors of the article, read about our discussion here.

A friend of mine thought this would interest me when I last visited him, and I had him send me the links discussing badger culling in the UK to control the spread of bovine tuberculosis (Mycobacterium bovis).  In addition to having an economic impact,  bovine TB also carries a zoonotic concern. I thought I would learn more about the issue, and see what the literature says about the success of the program.

Badger culling has been a part of TB control in the United Kingdom since 1973. Despite this and other programs in place, incidence of TB has only increased during that time. In the thousands of biological and environmental risk factors that have been associated with TB infection risk, Badgers have been identified as an important reservoir and potential vectors for the disease.

The politics surrounding the issue are interesting, and provides a great case example of how public perception can be skewed for certain species. The regular players are all there: the economically invested (in this case, cattle farmers and associated industries), the scientific community, outspoken animal interest groups, a generalized public perception, and the federal government trying to cater to the majority of voters (or campaign contributors, depending on the official and your own opinion). Lets break down these players.

The Economically Invested

On this issue, everyone seems to be on board that bovine TB is a problem in the UK. The ones who really care though are cattle producers, meat and dairy processing companies, and the retail ends associated with those products. When oppositional parties want to discredit this group, we see them described as “big corporations” only concerned about the bottom line. These claims are many times true, as even the small farmer has to maintain a decent profit margin to provide for him or herself. This group tends to be less publicly oppositional, preferring to exercise their strength through advertizing, lobbying, and funding research that can help support their position. Within this issue, I wasn’t able to find any ads produced by organizations in the UK, however, I did find some farmer concerns over the issue. One was the difficulty in getting approved for a badger cull in your area, and the other was the fear of response from activist groups if they did choose to participate in the program. The position of the farm interest groups is that the spread of bovine TB is an animal welfare and economic concern, and that badger culling will be critical in suppression of the disease. Local wildlife can often aid transmission of disease; however, we have also seen blame placed incorrectly on wildlife in other situations.

Animal Interest Groups

There are many groups in the UK that advocate for Animal interests, and they’re pretty much unanimous in the opinion that culling badgers is not an effective or ethical way to combat bovine TB prevalence. However, they do have different techniques in approaching opposition. While many of them strictly condemn the practice and advertize to sway public opinion, one group (with the support of many others), Gloucestershire Wildlife Trust, has been independently vaccinating wild badgers for bovine TB. At this time they haven’t investigated the effectiveness of the vaccine itself, but rather the economical viability of the process. Their results so far have shown that it would cost more than twice as much to vaccinate an entire hectare instead of culling. Typically these same groups in other controversial situations are very politically active.

The General Public

Generally the least informed and (arguably) the most powerful, the majority of public opinion represents the majority of voters and consumers. Regarding badger culling however, most of the general public has been shown in polls to oppose the practice. Agricultural controversies are often represented by government and industry actions that don’t necessarily mirror consumer or public preference, but instead are economically viable. Whether it’s often advocated for or not, above all else the majority of the public wants inexpensive food, and that benefit often outweighs other consumer preferences (though not always). An interesting examination of the public perception of badgers is discussed within this controversy, and this argument can also apply to other similar situations we have seen over the years. BBC explored the role of badgers in popular children’s stories, and related them to other species that receive special protection even if they are not endangered. An example from the states would be our attachment to wild horses as an icon of America, and some of the debates we’ve seen surrounding not only control of wild horses, but within discussions on using horses for food. Kevin Pierce from the article sums this feeling up well:

“It’s an image issue. A lot of farmers like badgers but we also want to control the disease. If your vector spreading TB was a rat, I’m sure that there’d be no problem for farmers in securing a license to take action.”

The Government

Tasked with the burden of trying to please everyone, the federal government often responds to the loudest collective voice along with their own advisers, analysts, and ethics. In this case, we do know that the government has moved forward with culling as they have in the past. Evaluating the motivation behind these decisions is an endless discussion, whether it’s a working system or corrupt is beyond the scope of this post. Feel free to express your opinions on the process in the comments below. The best I hope for is that while looking out for my interests, my officials attempt to remain objective, and speaking of objectivity…

The Scientific Community

I’ve left us for last. The example of objectivity and a lens of evidence to weigh a cost-benefit analysis of the issue not directed by personal interests, concepts of morality, or hidden goals. Or so we would hope. As a realistic scientist who has read a lot of peer-reviewed research, I know that we are never truly objective. All funding comes from somewhere, we interpret our own results, and while we try as hard as we can to be objective, there is no perfect experimental design immune to bias. However, as creator of this site, I obviously hold research in high esteem, so lets look at some of the literature regarding the effectiveness of badger culling in curbing the spread of bovine TB.

According to the sources I found, it appears that badger culling does have a positive effect on the rates of bovine tuberculosis, but strictly within the areas the culling occurs. There’s a beneficial cumulative effect after several years of a culling program (in the reduction of detrimental effects in surrounding areas), but it isn’t necessarily lasting, cost-effective, or repeatable in different situations. The consensus amongst several studies is that localized culling actually increases TB rates in the surrounding areas, due to the displacement of normally local badger populations, and additional factors that we don’t fully understand. Given these effects, there seems to be a general consensus in the literature I viewed that at best badger culling is not a cost effective way to reduce TB transmission, and at worst contributes to the spread of disease.

Culling programs always have fierce opposition from many sources, whether it be culling sea lions to protect Columbia river salmon, culling grey wolves to protect livestock, or culling tame geese that are causing damage to city parks. There are serious concerns from conservationists and animal activists about the effectiveness of such programs that can be well founded, and the controversy surrounding badger culling in the United Kingdom is a clear example  of why these decisions would be more effective if they are backed by empirical research and economic analysis before being presented as a moral dilemma.

Donnelly CA, Woodroffe R, Cox DR, Bourne J, Gettinby G, Le Fevre AM, McInerney JP, & Morrison WI (2003). Impact of localized badger culling on tuberculosis incidence in British cattle. Nature, 426 (6968), 834-7 PMID: 14634671
Donnelly CA, Wei G, Johnston WT, Cox DR, Woodroffe R, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Gettinby G, Gilks P, Jenkins HE, Le Fevre AM, McInerney JP, & Morrison WI (2007). Impacts of widespread badger culling on cattle tuberculosis: concluding analyses from a large-scale field trial. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, 11 (4), 300-8 PMID: 17566777
Donnelly CA, Woodroffe R, Cox DR, Bourne FJ, Cheeseman CL, Clifton-Hadley RS, Wei G, Gettinby G, Gilks P, Jenkins H, Johnston WT, Le Fevre AM, McInerney JP, & Morrison WI (2006). Positive and negative effects of widespread badger culling on tuberculosis in cattle. Nature, 439 (7078), 843-6 PMID: 16357869

N-terminal portion of pro C-type natriuretic peptide. Try to say that one three times fast. ScienceDaily has a cool article detailing a couple new studies showing that this peptide (Nt-pCNP) could be a solid indicator of sepsis as opposed to a generalized inflammatory response. It could potentially be added to current serum chemistry analysis, or packaged as an ELISA snap for quick, in-house diagnostics for pertinent cases.

Overuse of antibiotics has been a long term problem that is being well addressed in human medicine, however they are used much more broadly and liberally in animals due to their non-prescription access (especially in large animal work), and their use as a diagnostic tool for patients who can’t speak and often can’t afford thorough diagnostics. A veterinarian who’s client is unwilling to pay for a culture will often send broad spectrum antibiotics home anyway as a less expensive option in the hopes that they will take care of the problem.

I was unable to find a chemistry profile of Nt-pCNP, but the journal article itself talks a bit about C-type natriuretic peptide. CNP is produced by vascular endothelial cells and immune system macrophages. It “inhibits microbial growth and modifies pathogenicity of microorganisms” (DeClue, 2011). The problem with looking for just CNP as an indicator of sepsis is that it has a very short half life, and tends to degrade even faster in removed serum. Therefore, the researchers decided to use Nt-pCNP as their target molecule.  Nt-pCNP is created in a 1:1 ratio with CNP as a byproduct, and is much more durable and long-lived in both the bloodstream and collected serum.

The results of the study support the hypothesis  that CNP is a good indicator of sepsis, however like anything else, it’s not ideal. CNP was shown to be a poor indicator of sepsis when the infection was peritoneal. This includes gastrointestinal perforations or other possible infections found within the peritoneum (the authors mention that using peritoneal fluid as opposed to serum from a distal point may yield better sensitivity). Taking these false negatives into account, the test had a 65.5% sensitivity, for all other origins of sepsis in the study, sensitivity was 92%. Unfortunately, there appears to be a large potential for ambiguous negatives when peritoneal infection is suspected, but it’s always important to remember to educate clients that medicine is rarely black and white. It’s nice that House is able to identify exactly what’s wrong with each of his patients every week, but most of the time, we’re just going to give them supportive care based on the most likely result. Some of the limitations of the study that the authors mentioned were the small sample size and uncontrolled natures of the ailments that may have influenced the blood chemistry (samples taken from bacterial vs. viral infections, condition as of admission, underlying secondary infection or ailment, etc.).

In the case of this test and many other lab tests, positives are very definitive and help us out, while negatives are ambiguous. This is true whether it’s a heartworm test, fine needle aspirate, fecal flotation, radiology, or any number of other diagnostic tests. Every one is a tool, and hopefully looking at Nt-pCNP levels will give us another way to confirm sepsis while our cultures are growing at the lab, or perhaps offering another faster or less expensive option that the situation necessitates.

DeClue AE, Osterbur K, Bigio A, & Sharp CR (2011). Evaluation of serum NT-pCNP as a diagnostic and prognostic biomarker for sepsis in dogs. Journal of veterinary internal medicine / American College of Veterinary Internal Medicine, 25 (3), 453-9 PMID: 21457321