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Want to Lose Weight?  Think About When You Eat.

It’s not just the what; it’s also the when. That’s what nutritional scientists are learning as they continue to study the ways in which our diets are complicated by other variables.

One trend that’s emerging, according to a recent write-up in the New York Times, is a body of evidence that connects the outcomes of our diets to our eating schedule and how our eating matches up with our circadian rhythms. Circadian rhythms are the internal clock common to most living things; they’ve been observed in animals, plants, fungi, and bacteria. They take signals from the natural world – the amount of available light, for example – and use that to rough out a daily cycle that regulates biological functions.

One important cue for circadian rhythms, it turns out, is food intake. Glucose levels, enzymes, digestion, internal signals related to hunger and more are tied to the internal cycles of the body. When we eat and when we sleep are both tied up in these signals. Align yourself with these cycles, and you’ll get better results with digestion and sleep. Swim against the stream, sleeping and eating whenever you like, and you may confuse your body – reducing the effectiveness of the sleep that you get, and changing the way that the digestive system processes food.

Circadian rhythm, as the Times article explains, isn’t just a function of a single master clock in the brain. Many of our biological systems have their own timers, working roughly in sync but independently of one another. Insulin, for example, is released more readily during the day, when most people are doing their eating, and slows down after sundown. Other functions related to digestion and eating (including the schedules of the bacteria that live in our guts) are similarly regulated.

If you push back against your natural sleep cycle, your body will likely react in kind. Staying up later than normal several nights in a row confuses your internal mechanisms. Insulin regulation gets sloppier, according to some of the research cited by the Times, and more of the food that you eat will be packed on as fat.

For people whose schedules work against their circadian rhythms, like security guards or gas station clerks assigned to the night shift, these changes can have serious implications. Disruption of insulin sensitivity is a risk factor for metabolic disease and diabetes. Weight gain is a risk factor for diabetes well; it can also lead to obesity and a number of related conditions.

Our bodies are primed for digestion in the morning; that’s when they’re the most sensitive to the appropriate level of insulin to break down glucose in the blood. We’re also primed to release the digestive enzymes that you need to break down food in the morning. The schedule of the body, in fact, dictates that most of our digestive-related resources are on hand for a relatively short window; most of what we need to break down food is available for the eight hours after we wake up.

In light of this, some scientists have recommended that we align our eating and sleeping schedules with our circadian rhythms. Restrict your diet to the eight-hour window of optimal digestion, the thinking goes, and you’ll have a better time of breaking the food down. Less will be converted into fat for the body to store, moving the needle on your bathroom scale to the left; you’ll see a smoother, more coordinated performance when it comes to the delicate interplay between glucose and insulin in the blood.

The link between circadian rhythm and the things that live in our gut has implications for food safety, too. If our body is primed for certain digestive responses at certain times of day, it stands to reason that it might be similarly primed for immune responses – an area that warrants further study. If someone is having trouble breaking down a certain food in their gut and experiences bloating, nausea, or flatulence because of it, it might be because their body wasn’t prepared to break that food down or prepared to do it at that particular time of day.

That’s a medical concern, which makes it a food safety one as well. The same can be said of circadian rhythms and insulin response; although diabetes isn’t what we normally think of when we think of food safety, it’s a medical condition that’s intimately tied up with when and what we eat. The development of diabetes, furthermore, is shaped by what we eat and when. Having diabetes is unsafe; thus, it too is a food safety issue by definition.

Circadian rhythm doesn’t just affect your food, of course: circadian rhythms are intimately tied to our sleep. Eating too late in the day sends mixed messages to the part of the body that determines when we feel tired. This gets back to something that I mentioned earlier: he body doesn’t run on a single clock, but rather has several that each regulate different functions roughly in sync. Generally, the digestive system responds to bright sunlight by priming for some eating. When the sun goes down, the brain releases a hormone called melatonin that primes the body for sleep.

If you’re consistently eating at night, the body is liable to get somewhat confused: the gut will slip out of sync with the brain. The orderly release of melatonin and digestive enzymes both will get somewhat muddled in response.

The details of this phenomenon are still being teased out, but several studies have already been done. Last year, scientists at the University of Texas put mice on carefully controlled feeding schedules to study the relationship between digestion and circadian rhythm. Their findings were written up by the website Science Daily

What they found was remarkable: the time of day that the mice ate was more important to weight loss than the total number of calories ingested. Several groups of the rodents were put on a reduced calorie plan by the scientists. The times at which they were fed, however, were scrambled throughout the day.

Despite their restricted diets, only the mice whose eating times matched natural circadian rhythms lost weight (mice are nocturnal, so their bodies are primed for eating after dark). Feeding the animals reduced-calorie meals during restricted periods left them sleep deprived and wide-awake during the day when they would normally be sleeping.

So: if you’re looking to lose weight, remember to watch the when of your eating alongside the what.

By: Sean McNulty, Contributing Writer (Non-Lawyer)

September 20, 2018
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Do Antibiotics in Meat Pose Risk to Our Guts?

An op-ed in the New York Times over Labor Day weekend this year raised important questions: do antibiotics in meat pose a risk to our guts? And are we doing enough to curb their overuse?

Before we delve into the risks that antibiotics in meat might pose, let’s answer why farmers might want to feed their livestock antibiotics in the first place. There is a lot of skepticism and distrust when the word “antibiotics” is thrown around.

One reason: using antibiotics early and often is one way to guard their animals against sickness. Meaning, to many farmers, using antibiotics is how they care for their animals, and help them survive happy, healthy lives. By proactively putting antibiotics in feed, it can kill off different types of bacteria before they have the chance to make an animal sick. It can also help to contain ongoing outbreaks to a handful of animals on the farm. A farm needs healthy animals, after all.

There are a couple of “upsides” to antibiotic use in animals, according to the Times. Chief upside amongst these advantages is that antibiotics allow animals to get fatter and bigger faster. A NYT article published in 2014 delved into this phenomenon. The exact causes are murky, but in humans, chicks, piglets, and calves, administration of antibiotics boosts growth dramatically. One early experiment on chicks found that those fed antibiotics grew to twice the weight of their compatriots in a control group. Tests on Navy recruits and developmentally disabled children in Florida found similarly dramatic gains.

The Upsides are not Necessarily Positive

If animals who never get sick and who grow to be twice as fat in half the time sounds too good to be true, that’s because it is. There are significant downsides to indiscriminate use of antibiotics. Chief amongst these is antibiotic resistance. When a course of antibiotics is administered, there’s a chance that some of the pathogens it would otherwise wipe out have random mutations that make them resistant or immune to the antibiotic in question. Once the course of antibiotics is over, those microbes will survive. They’ll then multiply and pass the resistance or immunity on to the next generations. If the same antibiotics were taken a second time, they wouldn’t be effective at killing off the new, drug-resistant strain. For anyone who has read Maryn McKenna’s book, Big Chicken, you have seen the argument that industrial chicken farms have misused antibiotics for decades, thus breeding generations of resistant bacteria alongside their mega large poultry.

We only have a handful of different kinds of antibiotics that are effective at what they do and safe to take as medicine. As use of antibiotics has become accessible and widespread, some strains bacteria have started to develop specific resistances to them. If a bacteria adapts to a single kind of antibiotic, it’s called drug resistant. If two or more antibiotics are no longer effective against it, it’s multiple drug resistant. If we only have one antibiotic treatment that works on the bacteria, it’s called extensively drug resistant. Pan drug resistant bacteria are immune to everything we can throw at them.

Extensive use of antibiotics in agriculture poses a few different kinds of risks, given the creeping nature of drug resistance. The first is that some of the pathogens found on the farm might become hardened to antibiotics. This poses a problem for the farmers; if an infection with some level of resistance spreads between their animals, sickening or killing them, then they’ll face lost productivity, mounting vet bills, or dead livestock that they’ll need to write off as a loss.

Health and safety standards are intended to protect the consumer against pathogens that might be present on the farm. There’s still a real possibility that you might find drug resistant bacteria in a product that you consume – by negligence or malfeasance, chance or design. Those bacteria can make you very sick, and the possibility of a bacteria like listeria hardening against the limited treatments casts a longer and darker shadow in light of this year’s deadly outbreak of extensively drug resistant typhoid in Pakistan.

There are other concerns with overuse of antibiotics. Circle back around to that op-ed in the NYT and you’ll find that some people are sounding the bell on the possibility that antibiotics used on the farm, along with drug-resistant bacteria, can make it into the digestive tract of the consumer through vectors like undercooked meat (an important side note: the science is still very much out on the half-life of antibiotics from farm to table). We’ve covered the bacteria. But what would the downside be of the odd trace antibiotic in the meat that you consume?

That brings us back to the gut – the place where we digest our food, and the biggest metro area in our body for the teeming hordes of microbiota that live inside of us. Most of our cells, you see, are not our own; our gut, along with the rest of our body, plays host to dense and complicated ecosystems of a multitude of beneficial bacteria. These tiny passengers help with a number of tasks; when it comes to food, they’re an essential part of the crew, helping to break nutrients down and move things along. Without a healthy gut biome, digestion and bowel movements become painful and difficult. So complicated and unique are these little worlds inside us that scientists have speculated that all kinds of conditions – including Alzheimer’s and Parkinson’s – may be linked to their disruption (this has not yet been borne out by strong evidence – it’s more of an inkling in the literature at this point).

Stray antibiotics from meat, then, have the possibility to disrupt and damage our particular little stomach Edens. That would make it harder for the gut to digest food, for one. Without a healthy microbiota, our guts are more susceptible to invaders – from standard bacteria to those weathered by the overuse of antibiotics. And, perhaps, it has a relationship to all kinds of conditions affecting your mood, your happiness, and your brain.

By:  Sean McNulty, Contributing Writer (Non-Lawyer)

July 31, 2018
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Get Some Culture: A Guide to Culture Independent Diagnostic Tests vs Benefits of Culture

Doctors and Epidemiologists share some common goals, but sometimes their perspectives diverge.  Doctors and Epidemiologist alike want to identify what is making patients sick so that they can receive the appropriate treatment.  Each would also like this answer as soon as possible.  The Doctor has a responsibility to his or her own patient, while the Epidemiologist has a responsibility to the community.  This is where their paths often fork.  Or rather, where the Doctor’s participation tapers off and the Epidemiologist participation picks up.

Doctor’s Choice for Diagnostics

Doctors have many choices when it comes to diagnosing the specific bug ailing their patient.  They can request from a variety of fast kits which are Culture Independent Diagnostic Tests or CIDTs or opt for a longer, but more thorough culture confirmation tests.  CIDTs are faster, but the culture confirmation tests have much more information.

CIDTs vs Culture

Let’s take a look at the differences between CIDTs and culture confirmation tests.

CIDTs can provide results in as little as a few hours and can even be performed in-house.  These tests often require less expensive equipment and less training for the test to be performed, thus reducing the overall cost of the tests.  CIDTs often detect antibodies or proteins that the bacteria produce very specific to a particular organism.  While the detection process may only take a few hours, bacteria count in the sample might be too low for the minimum detection limit.  These tests often take that into account offering a pre-enrichment step where the culture is allowed to grow for a short period of time – just enough to boost bacterial count to detectable levels.  This increases the result turn-around-time, but not significantly.  For a doctor who is trying to rule out different causes that might produce the same symptoms but would require different treatment depending on the result, CIDTs are a fast solution.

Cultures provide much more information in addition to organism identification.  Cultures allow the investigator to determine if the organism is alive or dead.  This makes a huge difference when it comes to identifying if the organism is what is making the patient sick.  Additionally, genomic information and DNA fingerprints can be obtained from growing the culture and purifying isolated DNA from the sample.  This allows for very specific data collection.  There are many strains or versions of the same organism.  Obtaining the DNA whole genome sequence of the pathogen responsible for making the patient sick allows investigators to compare the minor differences to others who are also sick with the same pathogen.  If the DNA fingerprints match, the two patients were likely sickened from the same source.  Taking cultures to make isolates and performing DNA fingerprinting analysis on potential food sources that come in in patient interviews will allow investigators to definitively determine what food is the source and appropriate agencies can issue recalls as necessary.

Epidemiologist Choice for Monitoring

While CIDTs allow fast surveillance at the local medical care level, unless this information is passed on to the local or state health departments it stays under the radar.  Epidemiologists often request that a sample be submitted for culture confirmation and analysis even though the pathogen has been identified and appropriate medical intervention has begun.

Once diagnosed, the process should not stop there.  Epidemiologist want to help prevent others in the community from falling ill from the same source if possible.  DNA fingerprinting allows for monitoring disease trends and outbreak investigations.  When healthcare providers stop at their end of diagnostics, it leaves a lot of information off the table when it comes to where epidemiology picks up.

CIDT Trends Affecting Epidemiology

This shift toward CIDTs and away from sending samples for culture and bacterial isolates has significantly affected the effectiveness of outbreak investigators.  The decline in culturing has become measurable.

FoodNet, also known as “The Foodborne Diseases Active Surveillance Network,” has been around since 1996.  This organization tracks foodborne illness trends for commonly transmitted infections.  According to the organization, FoodNet “estimates the number of foodborne illnesses, monitors trends in incidence of specific foodborne illnesses over time, attributes illnesses to specific foods and settings, and disseminates this information.”  According to FoodNet, Campylobacter diarrheal illness that was diagnosed by ONLY CIDTs in FoodNet sites showed an increase from 13% in the years of 2012 to 2014 to 24% in 2015 alone.

Potential Short-Term Solutions

The Center for Disease Control and Prevention (CDC) is soliciting the help of clinical laboratories to prevent this loss of information.  Together the two groups can come together to achieve a desired result that does not compromise patient care, but also does not compromise outbreak monitoring activities.

  • The CDC is encouraging clinical laboratories to continue culturing and isolating bacteria from patients who test CIDT positive for specific bacterial pathogens. This includes: Salmonella, Shiga toxin-producing coli, and Shigella.  Select laboratories are also requested to culture Campylobacter positive specimens.
  • The CDC is working to make the culture process a cheaper and easier for the clinical laboratories to encourage clinical laboratories to continue this practice.
  • The CDC is working with various organizations including the Association of Public Health Laboratories, regulatory agencies, public health officials, diagnostic laboratories, clinicians, and even CIDT kit manufacturers to be sure that cultures can be and are obtained so that public health laboratories have isolates to work with in the event CIDT produces a positive result.
  • One of the ways the CDC is working with CIDT manufacturers is encouraging them to design tests that keep the bacteria alive so that the sample can be cultured from it if the test produces a positive result.
  • As CIDTs are here to stay, the CDC is also working with surveillance systems (such as FoodNet and PulseNet) to update practices to include CIDT diagnosed results in their monitoring networks.

Potential Long-Term Solutions

The fast turn-around-time benefit of CIDTs is too great for the method to go away anytime soon.  At least until a better method becomes available.  Long-term, the CDC must come up with a compromise to avoid loss of the important genetic information.

The CDC is working to develop that next level diagnostic test.  One that is both fast but does not require bacterial isolates to obtain additional information.  Potential upstream information such as likelihood for antibiotic resistance and more specific information about the pathogen are some of the value-added aspects.

By:  Heather Van Tassell, Contributing Writer (Non-Lawyer)

July 29, 2018
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Keeping Us Safe – What’s Being Done in Food Safety Research

I frequently see various memes on social media proclaiming the virtues of being a baby boomer, a generational term that includes me. These memes colorfully describe what it was like “all those years ago”, when we left the house in the morning to play with our friends and weren’t seen again until dinner time, when crime wasn’t as heinous or prevalent, when lead-based paint was the norm, and when foodborne illnesses (known then as “food poisoning”) were practically unheard-of, and certainly not as publicized.

Since I’ve been writing for this website, I am endlessly fascinated by the research I conduct related to food safety practices as well as foodborne illnesses and other issues. The advances in food safety are astounding, and continue to improve in scope and purpose. What I, and perhaps many of my baby boomer contemporaries who ever experienced a bout of food poisoning attributed to “bad chicken, a bad stew, a bad piece of pie,” can now frequently be traced to a common source, and with ever-increasing specificity.

The following is a round-up of the most up-to-date scientific advances in ensuring our food safety.  Due to a stroke of genetic genius, I have spared readers my scientific clumsiness and confined myself to observing and writingabout those who truly know what to do with a Petri dish, microscope, and long, polysyllabic words. I bring you a brief summation of nucleic acid extraction dipstick methodology, gentamycin protection assay, amoebae, and other.What?

And You Thought a Dipstick Was Just For Checking Your Oil

At the University of Queensland, Australia, pathogens have been detected using untreated cellulose-based paper in a process known as nucleic acid extraction dipstick methodology. In this process, DNA and RNA from living organisms can be amplified without specialized equipment. According to Professor Jimmy Botella, a food science researcher, “we have successfully used the dipsticks in remote plantations in Papua New Guinea to diagnose sick trees and have applied it to livestock, human samples, pathogens in food, and in detecting [risks] such as E.colicontaminated water.” That’s exciting news in terms of identifying potential sources of this nasty bacterium.

Campylobacter as a Trojan Horse

In another study at Kingston University of London, England, researchers discovered that Campylobactercan use another organism’s cells as a kind of Trojan horse, infiltrating tiny organisms called amoebae and generally hiding themselves from harsh environmental conditions. Diabolical cowards.

But why is this important in terms of food safety? The researchers employed what, on the surface, appears to be a sneaky procedure in which they observed how campylobacterinvades healthy host cells. It’s called gentamycin protection assay. I visualize sort of a high-tech, but extremely tiny, episode of a TV detective show. On a serious note, the research could assist in preventing the spread of this type of infection. Those amoebic hosts often exist in the same environments such as in drinking water for chickens on poultry farms. This can, and often does, increase the risk of infection.

Social Media Can Help Identify Foodborne Illness Sources

New York’s Columbia University recently partnered with the New York City Health Department in detecting foodborne illnesses and outbreaks in New York City restaurants based on keywords in Yelp reviews. In addition to calls to 311 (a non-emergency phone number that is used to find information as well as register complaints), and reports from health care providers, the NYC Health Department has used a system developed by Columbia University’s Department of Computer Science to track foodborne illnesses based upon reviews left on the popular Yelp website. Launched in 2012, this computer system tracks foodborne illnesses based upon the identification of particular keywords that appear specifically in Yelp restaurant reviews. This implementation has helped NYC health department staff identify 1,500 complaints of foodborne illness in New York City each year, for a total of over 8,500 cases since July 2012. Both Columbia University and The New York City Health Department plan to expand this to include other social media sources such as Twitter, which was added to the system in November 2016. Without this system, some individuals may not report their symptoms, and many incidents of foodborne illness might otherwise go unnoticed and/or unreported. Professors of Computer Science at Columbia University Luis Gravano and Daniel Hsu stated that “Effective information extraction regarding foodborne illness from social media is of high importance  – online restaurants review sites are popular and many people are more likely to discuss food poisoning incidents in such sites [rather] than on official government channels.”

You Are What You Eat: The Implications of Blockchain Technology

With increased emphasis being placed on identifying the source(s) of foodborne pathogens and subsequent efforts to eradicate or diminish their threat, perhaps no recent technological emergence is as great as the blockchain revolution. It is revolutionary because the word itself implies great change, and blockchain technology offers transparency for consumers and brings huge advantages for individuals within the supply chain. For food producers, attempts to tamper with a food item can be immediately identified and prevented before the food reaches its destination via the blockchain. For grocery retailers, if a potentially contaminated food product appears on their shelves, the stores can identify and remove on the offending “batch” items. Frequent batch recalls can be extremely costly to retailers. And for consumers, blockchain offers the reassurance that the food that they consume is exactly what the label says it is.Additionally, the blockchain can take “the power of information” out of huge corporate food producers and place it squarely into the hands of the individual consumer. By using a simple QR code and a smartphone, consumers can scan a package at the point of sale and receive an instant and complete history of the food item’s journey from farm to table without having to differentiate true from false claims of authenticity. As for potential foodborne pathogen outbreaks, imagine having the ability to detect the source of contamination within seconds rather than days or weeks.

With the social, economic, and political impacts of foodborne illnesses in the US, it becomes almost effortless to realize how sustained research is essential to individuals. As consumers, awareness and proactivity regarding our food sources is equally essential, and being armed with information is critical. Here at MakeFoodSafe, we will keep you informed of relevant research in food safety for your and your family’s protection.

By: Kerry Bazany, Contributing Writers (Non-Lawyer)

April 8, 2018
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The World’s Smallest Data Recorder

In a groundbreaking study, researchers have converted a natural bacterial immune system into the world’s smallest microscopic data recorder. By using the bacterial CRISPR/Cas immune system to generate miniature living tape recorders, scientists have successfully opened a new path to carry out environmental or microbiological sensing, diagnose diseases, develop future treatments, and record changes in body organs or systems— such as the gut. This new science has potentially paved the way for the future development of many new technologies.

What can these data recorders actually help to achieve?

These biologically engineered bacteria can record their interactions with the immediate environment. They can also encode the information about the events that occur in their surroundings. These cells are able to monitor the other invisible changes without disrupting those surroundings. It will be able to record changes that happen in body organs or body systems.

These bacteria can record whatever they do and how they interact with their environments, making it possible for the development of the future diagnosis and treatments to an otherwise difficult medical situation. This microscopic tape recorder can keep track of all the changes that take place in the bacterial environment. The best part, as mentioned above, is it can achieve such a major role without changing anything in the environment.

Harris Wang, Assistant Professor in the Department of Pathology and Cell Biology and Systems Biology at Columbia University Medical Centre said, “Such bacteria, when swallowed by a patient, might be able to record the changes they have experienced through the whole digestive tract, yielding an unprecedented view of previously inaccessible phenomenon”. He also led the new research and is the senior author of the group’s published paper in Science which is entitled ‘Multiplex recording of cellular events over time on CRISPR Biological Tape’.

What is a CRISPR?

CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. It is a bacterial defense system and form the basis of the CRISPR-Ca9 genome editing technology. These systems can be used to target specific genetic codes and edit DNA at precise locations. This technology can be used to target certain genes in living organisms, and thus, correct certain mutations.

The bacterial CRISPR/Cas system is an example of a naturally occurring biological memory system. The cells CRISPR/Cas system cuts out short fragments of the foreign nucleic acid whenever a bacterium is infected by a genetic element. It, then integrates the sequence into the CRISPR spacers that are called as arrays. If, at any point in the future the same invader tries to infect the bacterium the second time, the immunity proteins can recognize and eliminate the invader. An important thing to note is the integration of foreign DNA occurs in a unidirectional fashion. This means that the CRISPR locus forms a chronological record of invading virus that passes down through bacterial generations.

The CRISPR/Cas is a natural biological memory device which is actually quite good from an engineering perspective. This is because the system has been naturally designed throughout the evolution to be really great at storing information.

The system that the researchers aimed to develop is actually something like a tape recorder. A tape recorder converts the temporary signals into recordable data written on the tape as it passes on through the recorder at a decided speed. The biological system is built pretty much around the same basis and is therefore called temporal recording in arrays by CRISPR expansion (TRACE).

CRISPR has been previously put to record and store books, poems and an experimental movie in DNA but this will be the first time it would be used to record cellular activity and trace and record its events. The authors have reported that using the CRISPR-Cas adaptation system to record biological signals and not simply sequence information of exogenous DNA has not been achieved till date. Within this framework, a biological input signal is first transformed into a change in the profuseness of a trigger DNA pool within the living cells. The spacer acquisition machinery is then employed to record the amount of trigger DNA into the CRISPR arrays in a unidirectional manner.

THE EXPERIMENT:

To achieve this bacterial recording system, the researchers used the laboratory strain of Escherichia coli to engineer two different plasmids. The first plasmid creates duplicates of itself in response to an external signal. The second plasmid accurately marks the time and expresses the required CRISPR/Cas system components. If, in case, there is no external signal the recording plasmid can insert the copies of the spacer sequence into the CRISPR locus.

When an external signal gets detected, the replicating plasmid becomes activated and inserts the signal sequences into the locus. The locus can then read using some computational tools. Initial tests within the TRACE system shows that the recorded information remains stable within the cell population for over 8 days.

Having a prototype system, the team demonstrates how it can easily be multiplied and helps them achieve a simultaneous recording of around three different signals – which in this case includes availability of metabolites like copper, trehalose and fructose – in the cell population environment over a period of three days. This work has easily enabled new application in biological recording. TRACE can be utilized to record metabolite fluctuations, gene expression changes, lineage associated information etc. It can help in getting information on difficult to study habitats such as the mammalian gut or open setting such as marine environment etc.

The team with Dr. Wang as the senior researcher is now planning to use the TRACE platform to investigate markers that indicate changes in normal or diseased states of gastrointestinal tract or any other bodily systems.

By: Pooja Sharma, Contributing Writer (Non-Lawyer)

April 8, 2018
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