Author: Kari Kenefick

Novel Cell Surface Markers Identified that Differentiate White, Beige and Brown Adipocytes

Posted on by Kari Kenefick
2012 CDC-based data on U.S. obesity percentages by state.
2012 CDC-based data on U.S. obesity percentages by state.

Estimates of obesity in the U.S. range from 30% (Centers for Disease Control data) to 70% (persons selling online and television audience-focused weight-loss programs). We are a nation of fat or fat-obsessed persons, and rightfully so. CDC data shows that the cost of obesity, in 2008 dollars, was estimated at $147 billion. That amount of money would buy a lot of french fries or cheesecake or __ (name your poison).

We all help pay those high-dollar amounts in terms of rising healthcare costs, thus there is considerable interest in finding ways to not only avoid, but also to combat obesity.

In recent years researchers working to understand body fat biology have produced exciting information on differences in types of fat. For instance, we now understand that in addition to white adipose tissue, animals and humans also have brown and beige adipose tissue. White adipose tissue or WAT is commonly found in humans and mice subcutaneously and in visceral fat. Brown adipose tissue or BAT, and beige adipose, is less common, and in humans and mice, is found in deeper cervical, supraclavical and paraspinal areas.

Continue reading “Novel Cell Surface Markers Identified that Differentiate White, Beige and Brown Adipocytes”

Dark Chocolate Benefits Improved by Fiber

Posted on by Kari Kenefick
Add pomegranate to your chocolate, says researcher Finley, to aid it's digestion, health benefits.
Add pomegranate to your chocolate, says researcher Finley, to aid it’s digestion and health benefits.

For chocolate lovers (and chocolate makers) it has been a great decade or so. Scientific research continues to prove what our brains have been saying for years; chocolate really IS good for us.

Research over the past decade or so has studied dark chocolate and its polyphenolic compounds, such as catechin and epicatechin, for their effects on inflammation, and cardiac and endothelial cell function. Today, from the American Chemical Society meeting in Dallas, TX, we learn new details about how dark chocolate brings its health benefits.

Before beneficial compounds in dark chocolate can reach the heart and other tissues in the body, digestive processes must occur to release the beneficial compounds from the chocolate.

Researcher John Finley and cohorts from Louisiana State University created a model digestive system by which to study what happens when cocoa combines with typical gut bacteria.

Their research showed that bacterial species in the colon ferment the fiber found in cocoa, which in turn aids in digestion of the larger polyphenols in cocoa, into smaller, more easily absorbed molecules. These smaller molecules, the catechins and epicatechins then enter the bloodstream and exert their anti-inflammatory effects.

Finley emphasized the role of dietary fiber, such as the fiber in the cocoa powders tested in this research, in the digestion process. He noted that prebiotics, carbohydrates in foods like raw garlic or cooked whole wheat flour, while not digested by humans, aid digestion and absorption of healthful food components, in this case polyphenols in dark chocolate.  Continue reading “Dark Chocolate Benefits Improved by Fiber”

From Where, the Dog’s Ancient Ancestor

Posted on by Kari Kenefick

We’ve learned this year, 2013, that Europe may be the original home to domestic dogs, a title previously claimed by East Asia and the Middle East. A recent study published in Science magazine may put to rest the debate.

In their report, Thalmann and Wayne (1) used an evidential gold standard, DNA from mitochondria of fossilized ancient dog and wolf remains, to reach the conclusion that dogs originated from a now extinct line of European gray wolves.

In 2002, researchers from Sweden and China collaborated to compared first the mitochondrial DNA and later the complete mitochondrial genomes and Y chromosomes from a hundreds of wolves, coyotes and modern dogs from around the world (2). Their results showed the greatest genetic diversity from canids from East Asia. Such genetic diversity can be a marker of a species’ origin.

In 2010 Wayne, et al. (3) analyzed 48,000 markers from across the genome of gray wolves and dogs, again from around the world. The dogs were found to have more genetic material in common with Middle Eastern wolves than with those from East Asia. Wayne and colleagues found this a yes to dogs’ origins lying in the Middle East.

A criticism of the analysis done with modern dog DNA is that this DNA has been mixed with that from wolves. In addition, dog-dog breeding over the 15,000 to 30,000 years since this domestication, could confound results. Prior to the current study, critics called for analysis of ancient DNA remains only.

Wayne had collected DNA from ancient remains and due to recent collaboration with geneticist Thalmann, now had the lab-power to analyze those remains.

In this work, Wayne and Thalmann looked at mitochondrial DNA from ancient remains, those of 18 wolves and dogs. The fossils  ranging in age from 1,000 to 36,000 years. Eight of the samples were classified as dog-like and 10 samples were wolf-like in nature. They compared the ancient mitochondrial DNA samples to those of modern animals, including 77 dogs from an assortment of breeds, as well as 49 wolves and 4 coyotes. They then built a sort of a canid family tree, demonstrating relatedness in the animals whose DNA was analyzed.

Thalmann and Wayne’s finding showed that 1) the DNA of modern dogs more closely resembled that of ancient gray wolves than modern wolves, and 2) the geographic location of the wolves who’s DNA was most closely resembled, was Europe.

It is important to note that Thalmann and Wayne did not compare ancient remains from animals from the Middle East, nor did they have access to ancient remains from East Asia. In addition, there is criticism of the use of mitochondrial DNA, which represents only the maternal dog lineage. Thus there is more work to be done to finalize the ancestral home of the modern dog.

This work does, however, push back the origins of domesticated dogs to between 18,000 and 32,000 years ago, significant because the domestication timeline was previously believed to coincide with the rise of farming by our human ancestors. Domestic canines are now believed to have been part of humans lives far before farming was a way of life, back in the hunter-gatherer days.

There are those who believe that domestication of wolves, selectively bred to become modern dogs occurred simultaneously at more than one geographic region. Wolves were once found in many locations around the world and their usefulness to and domestication by humans would seem odd if only embraced by people from a single part of the world.

    References

  1. Thalmann, O. et al. Science (2013) 342, 871–874
  2. Savolainen P, Zhang YP, et al. (2002)
  3. Wayne, R.K. et al. (2010) Nature 464(7290), 898-902. 

Remembering Frederick Sanger and Sanger Sequencing

Posted on by Kari Kenefick

It is with sadness that we recognize the passing of Dr. Frederick Sanger. Sanger is known to molecular biologists and biochemists worldwide for his DNA sequencing technique, which won for him the 1980 Nobel prize in Chemistry.

Also noteworthy, Sanger’s laboratory accomplished the first complete genome sequence, that of a viral DNA genome more than 5,000 base pairs in length.

The 1980 prize was Sanger’s second Nobel award, his first awarded in 1958 for determining the chemical structure of proteins. In this work, Sanger elucidated not only the amino acids that comprised insulin but also the order in which the amino acids occurred.

About Sanger Sequencing
Sanger DNA sequencing is also known as the chain-termination method of sequencing. The Sanger technique uses dideoxynucleotides or ddNTPs in addition to typical deoxynucleotides (dNTPs) in the reaction. ddNTPs result in termination of the DNA strand because ddNTPs lack the 3’-OH group required for phosphodiester bond formation between nucleotides. Without this bond, the chain of nucleotides being formed is terminated.

Sanger sequencing requires a single-stranded DNA, a DNA primer (either radiolabeled or with a fluorescent tag), DNA polymerase, dNTPs and ddNTPs. Four reactions are set up, one for each nucleotide, G, A, T and C. In each reaction all four dNTPs are included, but only one ddNTP (ddATP, ddCTP, ddGTP or ddTTP) is added. The sequencing reactions are performed and the products denatured and separated by size using polyacrylamide gel electrophoresis.

Diagram of Sanger dideoxy sequencing. (Courtesy of Wikipedia and Estevez, J.)
Diagram of Sanger dideoxy sequencing. (Courtesy of Wikipedia and Estevez, J.)

This reaction mix results in various lengths of fragments representing, for instance, the location of each A nucleotide in the sequence, because while there is more dATP than ddATP in the reaction, there is enough ddATP that each ATP ultimately instead is replaced with a ddATP, resulting in chain termination. Separation by gel electrophoresis reveals the size of these ddATP-containing fragments, and thus the locations of all A nucleotide in the sequence. Similar information is provided for GTP, CTP and TTP.

The Maxam and Gilbert DNA sequencing method had the advantage at the time of being used with double-stranded DNA. However, this method required DNA strand separation or fractionation of the restriction enzyme fragments, resulting in a somewhat more time-consuming technique, compared to the 1977 method published by Sanger et al.

Dr. Sanger was born in Gloucestershire, U.K. in 1918, the son of a physician. Though he initially planned to follow his father into medicine, biochemistry became his life-long passion and area of research endeavor. Sanger retired at age 65, to spend more time at hobbies of gardening and boating.

References

Sanger, F. , Nicklen, S. and Coulson, A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74, 5463-7.

Maxam, A.M. and Gilbert, W. (1977) A New Method for Sequencing DNA. Proc. Natl. Acad. Sci. USA

There is something special about seeing the original Sanger publication from 1977, available here as a scan.

Hepatitis C: A Promising Animal Model, and Reasons to Get Tested

Posted on by Kari Kenefick
Hepatitis C virus infection by source, in the U.S. From Wikipedia.
Hepatitis C virus infection by source, in the U.S. From Wikipedia.

During graduate studies in Medical Microbiology and Immunology at the University of WI-Madison, a favorite class was an infectious disease course that included an exercise in designing the perfect pathogen. This was a thought experiment, a writing exercise. No laboratory experimentation was involved.

You might initially think of a perfect pathogen as one that produces the most spores, allowing the pathogen to spread or seed itself in many locations. Copious slime and mucus production and projectile vomiting and diarrhea were frequently suggested during discussions of the perfect pathogen. And it’s true that these features really get the attention of the infected person and her/his caregiver. There are some pretty scary microbial buggers out there, for instance those that cause hemolytic anemia and/or raging fevers; these are the attention getters of the infectious disease world. Continue reading “Hepatitis C: A Promising Animal Model, and Reasons to Get Tested”

Improving Fitness Using Your Weight

Posted on by Kari Kenefick
Push ups, yes. But the gym not needed for this routine.
Push ups, yes. But the gym not needed for this routine.

Body weight, that is.

It’s true. One of the more recent fitness trends is that of using body weight for resistance, in conjunction with high-intensity circuit training. Brett Klika and Chris Jordan published an article on this method in the American College of Sports Medicine’s Health & Fitness Journal, in the May/June 2013 issue.

Here is the Article:
 “High-Intensity Circuit Training: Using Body Weight: Maximal Results with Minimal Investment”

When it comes to fitness I’m mostly old school. Years of one- and two-a-day swim practices in high school and college, and long runs for track and cross-country practice off-season from swimming were part of the ‘more miles/time is better’ philosophy. You had to put in the time and miles to get the conditioning and strengthening, as well as cardiovascular benefits. Continue reading “Improving Fitness Using Your Weight”

Priming an Effective T cell Response to Cancer

Posted on by Kari Kenefick

Cancer vaccines have been in progress for some time now. But a vaccine that is highly effective against cancer is not currently available.

However, an interesting report from Stanford University School of Medicine researchers, Dr. Irving Weissman, et al. shows some promise in a development of an altered means of stimulating the immune system, that could result in a stronger immune response and ultimately a better cancer vaccine. The paper by Weissman et al. was published electronically ahead of print in PNAS USA, May 20, 2013: “Anti-CD47 antibody-mediated phagocytosis of cancer by macrophages primes an effective antitumor T-cell response.”

Schematic of a macrophage engulfing, digesting and presenting parts of a pathogen or foreign cell to the cell surface.
Schematic of a macrophage engulfing, digesting and presenting parts of a pathogen or foreign cell to the cell surface.

Continue reading “Priming an Effective T cell Response to Cancer”

Walking the Dog, Prefrontal Cortex Engaged

Posted on by Kari Kenefick
A favorite walk: the dog park.

A friend and I were recently at a local dog park, walking his Sheltie and Australian shepherd, and my two standard poodles. Our dogs are not daily visitors to the dog park, and while his dogs are well-behaved and subtle in their approach to other dogs, my poodles’ enthusiasm is not always in their best interest.

In addition, one of my dogs seems to take issue with certain of the protection dog breeds,  like German Shepherds, as well as some of the sled dog breeds. Generally, if a dog has pointed ears, I am on the alert for bad behavior.

For that matter, the protection dogs don’t seem to much care for fluffy, bouncy poodles. Annoying, you know? A dog’s trying to keep order and make the world safe, and here comes that poodle, bouncing along without a care in the world. There’s a lot of danger out there and the poodles are simply not paying attention. They jog along meeting people and dogs like they are running for mayor; darn poodles.

Occasionally it has seemed that the attitude problem is not exclusive to my dog.

People often say, “Oh, standard poodles are such smart dogs”. But you’d think a smart dog would not choose a big, guard dog breed with which to make trouble. Continue reading “Walking the Dog, Prefrontal Cortex Engaged”

A Food for Happiness? Go Fish

Posted on by Kari Kenefick
Salmon, smoked
Salmon is a good source of omega-3 fatty acids.

We’ve heard that omega-3 fatty acids, such as those from various fish sources, have important anti-inflammatory, as well as cardiac health benefits.

In fact, WebMD has an Omega-3 Fatty Acid Fact Sheet with so much positive health information that you may add “Buy wild-caught salmon” to your list of things to do on the way home tonight.

In other words, eating fish is a no-brainer, right? Continue reading “A Food for Happiness? Go Fish”

Catnip and Its Effect on Cats, Dogs and Humans

Posted on by Kari Kenefick
Feline in catnip.
Common cat behavior around catnip.

Cat owners—and those that care about cats—know the power that catnip has on cats. If you own a cat and bring catnip into the house, no matter where you put it, the cat will find it.

Once the cat gets the catnip (aka catmint, nepeta) she/he will rub her/his head and shoulders on the plant,  lie down on it or even dash about the house. Cats frequently chew on and eat catnip.

A report sought to explain why and how catmint affects cats. I eagerly read the report, having always been conflicted about giving catnip to my cats. Could they be killing brain cells by smelling or consuming catnip? Is it habit forming? Is catnip a gateway drug for cats? Continue reading “Catnip and Its Effect on Cats, Dogs and Humans”