Baked (Moist) Halibut with Creamy Red Pepper/Miso Sauce & Capers
This delicious sauce keeps the halibut moist ©Joyce Hays, Target Health Inc.
3 red bell peppers roasted in oven
1 yellow pepper roasted in oven
1 can (15 ounces) chickpeas, drained through strainer then on paper towel
1.5 teaspoons golden miso which is the same as traditional white miso
1 container of tofutti (8 ounces of tofu cream cheese)
3 anchovy fillets, minced
2 garlic cloves, minced or sliced
Pinch chili flakes (optional)
Pinch kosher or sea salt
Pinch black pepper (or grind to your taste)
2 (6- to 8-ounce) halibut fillets
2 Tablespoons drained capers, patted dry
Juice of 1/2 to 1 lime, plus first use zest of 1/2 lime
Fresh chopped parsley, for serving
1. Preheat oven to 400.
2. Clean the peppers, cut in half, remove seeds and roast for about 30-40 minutes or until soft, but not burned. Remove and cool slightly
3. Clean your fish.
4. One spray of olive oil or canola, onto a baking dish. With a brush spread the oil around to cover the dish.
5. Combine all the ingredients except fish and the parsley, in a food processor. Pulse until smooth. .
6. Use a spatula to get all of the sauce out and pour all of the sauce over the fish
7. Lower temperature to 350 and bake for 20 minutes.
8. Remove and serve with parsley sprinkled over the fish
Just poured the sauce over the halibut ©Joyce Hays, Target Health Inc.
Going into the oven ©Joyce Hays, Target Health Inc.
Oven to table, and sprinkled fresh parsley on top ©Joyce Hays, Target Health Inc.
Friday night was a fabulous meal.
We started with two different white wines, Hall (Napa)Vineyards Sauvignon Blanc and Cloudy Bay (New Zealand) Sauvignon Blanc, just to compare the two. We both love Hall cabernet, so assumed we’d like the Hall whites.
Jules loved the Hall (I didn’t) so he had that and I drank the Cloudy Bay. Hall Vineyards is a highly respected winery and I expected to like their white, and the taste buds in the front of my mouth were okay with it, but then the lingering taste was so sharply acidic (grapefruity), I couldn’t go on and had to switch to the Cloudy Bay and then onto my favorite, so far, Te Koko, from the same New Zealand vineyard.
Hall Vineyards Sauvignon Blanc ©Joyce Hays, Target Health Inc.
Cloudy Bay Sauvignon Blanc ©Joyce Hays, Target Health Inc.
After a toast, which we always do, we started with a fresh tomato/avocado salad with a simple lemon/oil dressing; Then the baked halibut with tiny elbow pasta and the baked zucchini circles, which I’m still trying to perfect before presenting in the On Target Newsletter. Jules gave the halibut with red sauce 5 stars (from 1 to 5, with 5 being tops).
I would say that the sauce has secret ingredients, that took a fair amount of experimenting to arrive at. I’ve found that chick peas pureed, give a dish a certain body and anchovies used in exactly the right amount add a rich flavor that you would never say is fishy. Anchovies are a mysterious ingredient like a spice. In the right amount, the flavor is heightened and you would never guess it was there.
I’ve been using tofutti for so long I sort of take it for granted, but it’s a wonderful addition to many of my recipes; plus perfect for weekend brunch bagels & cream cheese substitute, with our neighborhood’s delicate thinly sliced nova salmon.
I’m starting to experiment more with miso and finding it an excellent ingredient. More with miso in recipes to come.
For dessert we are loving my recent discovery of Cara Cara orange segments. First of all, they are a beautiful color, so even before you taste them, they’re inviting. We like to spear them with a tiny fork. These oranges are so sweet, that if you were thinking about a fattening sweet dessert, like, say, chocolate layer cake, you would be satisfied after eating these Cara Cara. We shared one container of them, and Jules drinks the small amount of juice down to the last drop.
This was a wonderful dinner!
Luscious sweet Cara Cara Orange Segments from California, at their peak right now. ©Joyce Hays, Target Health Inc.
PS: If you’re wondering what to buy tickets for, when you come to Manhattan, try the new musical, Dr Zhivago, which we just saw with family from Seattle. The music for the most part is lovely and good voices; the history is correct; and how can a show miss with a plot based on one of the great novels of the 20th Century. (Nobel prize for Boris Pasternak)
If you’re in Manhattan, let us know.
From Our Table to Yours!
A long-lived patch of warm water off the West Coast, about 1 to 4 degrees Celsius (2 to 7 degrees Fahrenheit) above normal, is part of what’s wreaking much of this mayhem, according to two University of Washington papers to appear in Geophysical Research Letters, a journal of the American Geophysical Union.
“In the fall of 2013 and early 2014 we started to notice a big, almost circular mass of water that just didn’t cool off as much as it usually did, so by spring of 2014 it was warmer than we had ever seen it for that time of year,” said Nick Bond, a climate scientist at the UW-based Joint Institute for the Study of the Atmosphere and Ocean, a joint research center of the UW and the U.S. National Oceanic and Atmospheric Administration.
Bond coined the term “the blob” last June in his monthly newsletter as Washington’s state climatologist. He said the huge patch of water — 1,000 miles in each direction and 300 feet deep — had contributed to Washington’s mild 2014 winter and might signal a warmer summer.
Ten months later, the blob is still off our shores, now squished up against the coast and extending about 1,000 miles offshore from Mexico up through Alaska, with water about 2 degrees Celsius (3.6 degrees Fahrenheit) warmer than normal. Bond says all the models point to it continuing through the end of this year.
The new study explores the blob’s origins. It finds that it relates to a persistent high-pressure ridge that caused a calmer ocean during the past two winters, so less heat was lost to cold air above. The warmer temperatures we see now aren’t due to more heating, but less winter cooling.
Co-authors on the paper are Meghan Cronin at NOAA in Seattle and a UW affiliate professor of oceanography, Nate Mantua at NOAA in Santa Cruz and Howard Freeland at Canada’s Department of Fisheries and Oceans.
The authors look at how the blob is affecting West Coast marine life. They find fish sightings in unusual places, supporting recent reports that West Coast marine ecosystems are suffering and the food web is being disrupted by warm, less nutrient-rich Pacific Ocean water.
The blob’s influence also extends inland. As air passes over warmer water and reaches the coast it brings more heat and less snow, which the paper shows helped cause current drought conditions in California, Oregon and Washington.
The blob is just one element of a broader pattern in the Pacific Ocean whose influence reaches much further — possibly to include two bone-chilling winters in the Eastern U.S.
A study in the same journal by Dennis Hartmann, a UW professor of atmospheric sciences, looks at the Pacific Ocean’s relationship to the cold 2013-14 winter in the central and eastern United States.
Despite all the talk about the “polar vortex,” Hartmann argues we need to look south to understand why so much cold air went shooting down into Chicago and Boston.
His study shows a decadal-scale pattern in the tropical Pacific Ocean linked with changes in the North Pacific, called the North Pacific mode, that sent atmospheric waves snaking along the globe to bring warm and dry air to the West Coast and very cold, wet air to the central and eastern states.
“Lately this mode seems to have emerged as second to the El Niño Southern Oscillation in terms of driving the long-term variability, especially over North America,” Hartmann said.
In a blog post last month, Hartmann focused on the more recent winter of 2014-15 and argues that, once again, the root cause was surface temperatures in the tropical Pacific.
That pattern, which also causes the blob, seems to have become stronger since about 1980 and lately has elbowed out the Pacific Decadal Oscillation to become second only to El Niño in its influence on global weather patterns.
“It’s an interesting question if that’s just natural variability happening or if there’s something changing about how the Pacific Ocean decadal variability behaves,” Hartmann said. “I don’t think we know the answer. Maybe it will go away quickly and we won’t talk about it anymore, but if it persists for a third year, then we’ll know something really unusual is going on.”
Bond says that although the blob does not seem to be caused by climate change, it has many of the same effects for West Coast weather.
“This is a taste of what the ocean will be like in future decades,” Bond said. “It wasn’t caused by global warming, but it’s producing conditions that we think are going to be more common with global warming.”
- Nicholas A. Bond, Meghan F. Cronin, Howard Freeland, Nathan Mantua. Causes and Impacts of the 2014 Warm Anomaly in the NE Pacific. Geophysical Research Letters, 2015; DOI: 10.1002/2015GL063306
Source: University of Washington. “‘Warm blob’ in Pacific Ocean linked to weird weather across the US.” ScienceDaily. ScienceDaily, 9 April 2015. <www.sciencedaily.com/releases/2015/04/150409143041.htm>.
During 2014, the outbreak of the West African Makona strain of Ebola Zaire virus killed nearly 10,000 and caused worldwide concern. With increasing population growth in West Africa, the frequency of contact between humans and natural Ebola virus hosts such as bats will likely rise, potentially leading to more catastrophic outbreaks.
Many vaccine approaches have shown promise in being able to protect nonhuman primates against Ebola Zaire. In response to the Ebola Zaire outbreak, several of these vaccines have been fast tracked for human use.
One of those vaccines, developed by UTMB and Profectus, has been undergoing testing in the Galveston National Laboratory, the only fully operational Biosafety Level 4 laboratory on an academic campus in the U.S.
“These findings may pave the way for the identification and manufacture of safer, single dose, high efficiency vaccines to combat current and future Ebola outbreaks,” said Thomas Geisbert, UTMB professor of Mmicrobiology and Iimmunology. “We are excited at the possibility of helping develop a way to stop this deadly disease. We have a lot of more work to accomplish but it’s important to note that this is a big step.”
The research team developed a vaccine effective against Ebola Zaire with a single dose in a nonhuman primate model. This new vaccine employs a virus not harmful to humans called vesicular stomatitis virus that had a part of the Ebola virus inserted into it. This “Trojan horse” vaccine safely triggered an immune response against Ebola Zaire.
To address any possible safety concerns associated with this vaccine, the team developed two next generation candidate vaccines that contain further weakened forms of the vaccine. Both of these vaccines produced an approximately ten-fold lower level of virus in the blood compared to the first generation vaccine.
“It was not known whether any of these vaccines could provide protection against the new outbreak West African Makona strain of Ebola Zaire currently circulating in Guinea,” said John Eldridge, Chief Scientific Officer-Vaccines at Profectus Biosciences, Inc. “Our findings show that our candidate vaccines provided complete, single dose protection from a lethal amount of the Makona strain of Ebola virus.”
Both weakened vaccines have features of the Mayinga strain of Ebola virus, as do most other candidate Ebola Zaire vaccines currently under evaluation. The original 1976 Mayinga strain and the new West African Makona strain are quite similar. The researchers said it was important to test their candidate vaccines on the Makona strain to ensure that even small differences between the strains didn’t impact the effectiveness of the vaccine.
- Chad E. Mire, Demetrius Matassov, Joan B. Geisbert, Theresa E. Latham, Krystle N. Agans, Rong Xu, Ayuko Ota-Setlik, Michael A. Egan, Karla A. Fenton, David K. Clarke, John H. Eldridge, Thomas W. Geisbert. Single-dose attenuated Vesiculovax vaccines protect primates against Ebola Makona virus. Nature, 2015; DOI: 10.1038/nature14428
Source: University of Texas Medical Branch at Galveston. “Ebola vaccine effective in a single dose.” ScienceDaily. ScienceDaily, 8 April 2015. <www.sciencedaily.com/releases/2015/04/150408133050.htm>.
CDC and public health partners investigated several recent clusters of shigellosis in Massachusetts, California and Pennsylvania and found that nearly 90 percent of the cases tested were resistant to ciprofloxacin (Cipro), the first choice to treat shigellosis among adults in the United States. Shigellosis can spread very quickly in groups like children in childcare facilities, homeless people and gay and bisexual men, as occurred in these outbreaks.
“These outbreaks show a troubling trend in Shigellainfections in the United States,” said CDC Director Tom Frieden, M.D., M.P.H. “Drug-resistant infections are harder to treat and because Shigella spreads so easily between people, the potential for more — and larger — outbreaks is a real concern. We’re moving quickly to implement a national strategy to curb antibiotic resistance because we can’t take for granted that we’ll always have the drugs we need to fight common infections.”
In the United States, most Shigella is already resistant to the antibiotics ampicillin and trimethoprim/sulfamethoxazole. Globally, Shigella resistance to Cipro is increasing. Cipro is often prescribed to people who travel internationally, in case they develop diarrhea while out of the United States. More study is needed to determine what role, if any, the use of antibiotics during travel may have in increasing the risk of antibiotic-resistant diarrhea infections among returned travelers.
“The increase in drug-resistant Shigella makes it even more critical to prevent shigellosis from spreading,” said Anna Bowen, M.D., M.P.H., a medical officer in CDC’s Waterborne Diseases Prevention Branch and lead author of the study. “Washing your hands with soap and water is important for everyone. Also, international travelers can protect themselves by choosing hot foods and drinking only from sealed containers.”
CDC’s PulseNet lab network identified an increase in Shigella sonnei infections with an uncommon genetic fingerprint in December 2014. Further testing at CDC’s National Antimicrobial Resistance Monitoring System (NARMS) lab found that the bacteria were resistant to Cipro. PulseNet detected several large clusters: 45 cases in Massachusetts; 25 cases in California; and 18 cases in Pennsylvania. About half of the PulseNet cases with patient information were associated with international travel, mostly to the Dominican Republic and India. The San Francisco Department of Public Health reported another 95 cases (nine of them among those identified by PulseNet), with almost half occurring among the homeless or people living in single-room occupancy hotels.
Shigella causes an estimated 500,000 cases of diarrhea in the United States every year. It spreads easily and rapidly from person to person and through contaminated food and recreational water. It can cause watery or bloody diarrhea, abdominal pain, fever, and malaise. Although diarrhea caused by Shigella typically goes away without treatment, people with mild illnesses are often treated with antibiotics to stop the diarrhea faster. Until recently, Cipro resistance has occurred in just 2 percent ofShigella infections tested in the United States, but was found in 90 percent of samples tested in the recent clusters.
Because Cipro-resistant Shigella is spreading, CDC recommends doctors use lab tests to determine which antibiotics will effectively treat shigellosis. Doctors and patients should consider carefully whether an infection requires antibiotics at all.
To prevent the spread of shigellosis, CDC recommends that people wash their hands often with soap and water, especially after using the toilet and before preparing food or eating; keep children home from childcare and other group activities while they are sick with diarrhea; avoid preparing food for others while ill with diarrhea; and avoid swimming for a few weeks after recovering. Improving access to toilets and soap and water for washing hands may help prevent Shigella transmission among the homeless.
Travelers to developing countries can take additional precautions to avoid diarrhea and minimize infection with resistant bacteria. Choose safe foods and beverages, such as food that is steaming hot and drinks from sealed containers (download CDC’s app “Can I Eat This?” to help you make safer food and beverage choices when you travel). Wash hands frequently, particularly before eating and after using the toilet. Take bismuth subsalicylate to prevent travelers’ diarrhea and treat it with over-the-counter drugs like bismuth subsalicylate or loperamide. Try to reserve antibiotics for severe cases of travelers’ diarrhea.
Health care providers should test stool samples from patients with symptoms consistent with shigellosis, re-test stool if patients do not improve after taking antibiotics, and test bacteria for antibiotic resistance.
Source: Centers for Disease Control and Prevention. “Multidrug-resistant shigellosis spreading in the United States.” ScienceDaily. ScienceDaily, 7 April 2015. <www.sciencedaily.com/releases/2015/04/150407112100.htm>.
To find the answer, the team designed a study that measured the connections between different brain regions while participants learned to play a simple game.
The researchers discovered that the neural activity in the quickest learners was different from that of the slowest. Their analysis provides new insight into what happens in the brain during the learning process and sheds light on the role of interactions between different regions. The findings, which appear online today inNature Neuroscience, suggest that recruiting unnecessary parts of the brain for a given task — similar to overthinking the problem — plays a critical role in this important difference.
“It’s useful to think of your brain as housing a very large toolkit,” said Grafton, a professor in UCSB’s Department of Psychological & Brain Sciences. “When you start to learn a challenging new skill, such as playing a musical instrument, your brain uses many different tools in a desperate attempt to produce anything remotely close to music. With time and practice, fewer tools are needed and core motor areas are able to support most of the behavior. What our laboratory study shows is that beyond a certain amount of practice, some of these cognitive tools might actually be getting in the way of further learning.”
At UCSB’s Brain Imaging Center, study participants played a simple game while their brains were scanned with fMRI. The technique measures neural activity by tracking the flow of blood in the brain, highlighting which regions are involved in a given task.
Participants responded to a sequence of color-coded notes by pressing the corresponding button on a hand-held controller. Six predetermined sequences of 10 notes each were shown multiple times during the scanning sessions. Subjects were instructed to play the sequences as quickly and as accurately as possible, responding to the cues they saw on a screen.
The study continued with participants practicing at home while researchers monitored their activity remotely. Subjects returned to the Brain Imaging Center at two-, four- and six-week intervals for new scans that demonstrated how well practice had helped them master the skill. Completion time for all participants dropped over the course of the study but did so at different rates. Some picked up the sequences immediately, while others gradually improved over the six-week period.
The complexities of learning
Lead author Danielle Bassett, an expert in network science, developed novel analysis methods to determine what was happening in the participants’ brains that correlated with these differences. But rather than trying to find a single spot in the brain that was more or less active, the team investigated the learning process as the function of a complex, dynamic network involving various regions of the brain.
“We weren’t using the traditional fMRI approach where you pick a region of interest and see if it lights up,” said Bassett, the Skirkanich Assistant Professor of Innovation at the University of Pennsylvania. “We looked at the whole brain at once and saw which parts were communicating with each other the most.”
The investigators compared the activation patterns of 112 anatomical regions of the brain and measured the degree to which they mirrored one another. The more the patterns of two regions matched, the more they were considered to be in communication. By graphing those connections, the team found that hotspots of highly interconnected regions emerged.
“When network scientists look at these graphs, they see what is known as community structure,” Bassett said. “There are sets of nodes in a network that are really densely interconnected to each other. Everything else is either independent or very loosely connected with only a few lines.”
The team used a technique known as dynamic community detection, a method that employs algorithms to determine which nodes are incorporated into these clusters and how their interactions change over time. This allowed the researchers to measure how common it was for any two nodes to remain in the same cluster while subjects practiced the same sequence some 10 times. Through these comparisons, they found overarching trends about how regions responsible for different functions worked together.
The researchers discovered that the visual and the motor blocks had a lot of connectivity during the first few trials, but as the experiment progressed they became essentially autonomous. For example, the part of the brain that controls finger movement and the part that processes visual stimulus didn’t really interact at all by the end of the experiment.
According to Grafton, in some ways this trend was not surprising since the team was essentially seeing the learning process on the neurological level, with the participants’ brains reorganizing the flow of activity as they mastered this new skill.
“Previous brain imaging research has mostly looked at skill learning over — at most — a few days of practice, which is silly,” said Grafton, who is also a member of UCSB’s Institute for Collaborative Biotechnologies. “Who ever learned to play the violin in an afternoon? By studying the effects of dedicated practice over many weeks, we gain insight into never before observed changes in the brain. These reveal fundamental insights into skill learning that are akin to the kinds of learning we must achieve in the real world.”
Comparing executive function
With the neurological correlates of the learning process coming into focus, the scientists were able to delve into the differences among participants in order to explain why some learned the sequences faster than others. Counterintuitive as it may seem, the participants who showed decreased neural activity learned the fastest. The critical distinction was in areas not directly related to seeing the cues or playing the notes: the frontal cortex and the anterior cingulate cortex.
These cognitive control centers are thought to be most responsible for what is known as executive function. “This neurological trait is associated with making and following through with plans, spotting and avoiding errors and other higher-order types of thinking,” Grafton said. “In fact, good executive function is necessary for complex tasks but might actually be a hindrance to mastering simple ones.”
Grafton also noted that the frontal cortex and the anterior cingulate cortex are among the last brain regions to fully develop in humans, which may help explain why children are able to acquire new skills quickly as compared to adults.
“It’s the people who can turn off the communication to these parts of their brain the quickest who have the steepest drop-off in their completion times,” said Bassett. “It seems like those other parts are getting in the way for the slower learners. It’s almost like they’re trying too hard and overthinking it.”
Additional studies will delve into why some people are better than others at shutting down the connections in these parts of the brains.
University of California – Santa Barbara. “The brain game: How decreased neural activity may help you learn faster.” ScienceDaily. ScienceDaily, 6 April 2015. <www.sciencedaily.com/releases/2015/04/150406121348.htm>.
Regulatory Affairs at Target Health
Target Health now represents 36 companies at FDA from all over the world. Our regulatory team is led by Glen Park, PharmD with terrific support from Mary Shatzoff MS, who just returned to Target Health after a brief hiatus, and Adam Harris MS, Tony Pinto MA, Lydia Battaglia and Carlos Figueroa. Jules Mitchel, MBA, PhD also supports all aspects of regulatory affairs and consults with the team as needed. Programs include but not limited to: orphan diseases, oncology, gastroenterology, dermatology, endocrinology, neurology and wound healing. Target Health provides regulatory agency, strategic planning, FDA meetings, eCTD publishing and all regulatory submissions.
The Survivor Tree
A Callery pear tree became known as the Survivor Tree after enduring the September 11, 2001 terror attacks at the World Trade Center. In October 2001, the tree was discovered at Ground Zero severely damaged, with snapped roots and burned and broken branches. The tree was removed from the rubble and placed in the care of the New York City Department of Parks and Recreation. After its recovery and rehabilitation, the tree was recently returned to the Memorial. New, smooth limbs extended from the gnarled stumps, creating a visible demarcation between the tree’s past and present. Today, the tree stands as a living reminder of resilience, survival and rebirth.
ON TARGET is the newsletter of Target Health Inc., a NYC-based, full-service, contract research organization (eCRO), providing strategic planning, regulatory affairs, clinical research, data management, biostatistics, medical writing and software services to the pharmaceutical and device industries, including the paperless clinical trial.
For more information about Target Health contact Warren Pearlson (212-681-2100 ext. 104). For additional information about software tools for paperless clinical trials, please also feel free to contact Dr. Jules T. Mitchel or Ms. Joyce Hays. The Target Health software tools are designed to partner with both CROs and Sponsors. Please visit the Target Health Website.
Joyce Hays, Founder and Editor in Chief of On Target
Jules Mitchel, Editor
Diagram of the human body showing the relative abundances of various types of microbes in each region. “ “Skin Microbiome20169-300″ by Darryl Leja, NHGRI
The scientific study of microbiology, which led to important discoveries such as Louis Pasteur’s germ theory of disease, grew out of society’s desire to eradicate infectious diseases.
The human microbiome is composed of the microbes, as well as their genes and genomes, that live in and on the human 1) ___. These resident microbes maintain our immune systems, contribute to the digestion of our food, and act as first line of defense against pathogens. There are many diseases that may be the result of disturbed microbiomes; however, microbiome-based medical treatments and applications are not completely mainstream and will be a part of future preventative 2) ___. Advances in medicine, now view humans and microbes as a co-evolved system for the mutual benefit of both the host and resident 3) ___. Most of the microbes we come in contact with are not germs, but beneficial microbes that digest many things in our diet – like vegetables – that we could not digest without microbial enzymes. They provide energy for our metabolism, make essential vitamins, and act as a first line of defense against potential pathogens.
The human microbiome is primarily composed of bacteria, but also includes numerous and diverse viruses, fungi and protozoa. The human body is made up of about 10 times more microbial cells (~1014) than human cells (~1013). It is thought that there are millions more microbial genes than human genes in this human microbiome system. Scientists now believe that infants are sterile (free of microbes) in the womb and receive their first inoculum of microbes from the mother during natural childbirth (not C-section). This inoculum goes on to colonize the newborn and initiate a succession of events leading to the development of the child’s own 4) ___. The newborn relies on this maternal vaginal microbial inoculum and the additional inoculum of microbes from mother’s breast milk for microbial colonization of all exposed surfaces in and on the infant’s body (e.g., oral, nasal/airways, gut, urogenital, skin). This is a dynamic process in which microbial abundances increase from effectively zero at birth to over six orders of magnitude (more than a million times) within just the first few weeks of life, with wide swings in the microbial membership of these communities until the microbiota largely stabilize in composition and numbers after approximately three years of life.
The characteristics of human microbiota change over time in response to varying environmental conditions and life stages. Image courtesy: US National Library of Medicine. Image source: Ottman N, Smidt H, de Vos WM and Belzer C (2012)
The newborn’s gut microbiota trigger development and maturation of the newborn’s 5) ___ system. Although there is still a great deal of research needed to understand precisely what happens in this developmental process, it appears the maturing immune system relies on the presence of microbial communities, and especially the presence of these early microbes, to distinguish self from nonself. It is these particular microbes that shape our immune systems. Once the immune system has matured, it will consult its memory banks if another microbe is encountered in order to determine if this microbe is considered self or nonself and to mount defenses against the microbe if it is recognized as a pathogen. Most of these microbes are growing in our large 6) ___, but each region of our body has its own distinct community of microbes living in or on it. For example, we have a particular kind of microbial community that prefers to grow on skin or in the nose. Our mouths have a rich mixture of microbes, with specific microbes that prefer teeth versus those that prefer gums. Even though the tongue is in constant contact with the roof of the mouth, microbes growing on the roof of the mouth are, very different from those growing on the tongue. Current research is grappling with which factors regulate microbial colonization in areas of the body that are just millimeters apart.
Researchers believe that what is eaten, combined with our hormones, bodily fluids, skin oils, genetic makeup, where we live, and many other factors, contribute to the colonization and growth of these microbes. Bathing, shampooing, washing hands, brushing teeth remove some microbes, which eventually grow back; however, too much washing may deplete valuable microbes, which could weaken the immune system. Each of us has a personal, group of microbial species and strains making each person’s microbiome 7) ___. Routine practices, including the use of antibiotics, may alter the human microbiome by reducing nontargeted bacteria and creating antibiotic resistant strains. Scientists are concerned about human behaviors that may disturb this delicate system. Antibiotic use is just one example of a common medical practice that may be altering the human microbiome by reducing, removing, or changing fundamental elements.
Antibiotics have been in broad use for treating infectious diseases in humans for over 70 years. As with vaccines, antibiotics have proven to be a very important medical advance, effectively eliminating many infectious diseases that have plagued human history. Today, as a result of antibiotics and vaccines, children do not die of the infectious diseases that killed them even 50 years ago. However, routine use of 8) ___ may cause collateral damage to our microbial flora in two ways: through the unintended death of nontargeted bacteria and through the emergence of antibiotic-resistant bacteria. Antibiotics can have unintended consequences and kill off beneficial bacteria in our microbiomes that are not the original target of the antibiotic?so-called nontarget bacteria. There is thought to be a relationship between the disturbance of the human microbiome through antibiotic use and the unexpected rise in autoimmune 9) ___ and allergies, particularly in Western countries. Autoimmunity is the failure of our own immune systems to distinguish self from nonself. This failure can lead to an immune response being mounted against our own cells and tissues. Examples of autoimmune diseases include rheumatoid arthritis, lupus, diabetes and celiac disease. The current line of thinking is that loss of normal microbiome constituents through antibiotic use may remove the necessary trigger for normal immune system development. As a result, an underdeveloped immune system might possibly allow autoimmune diseases to develop. Currently, much research is being conducted to better understand the relationship between the human microbiome and autoimmune diseases, and to find better treatments and cures.
The disappearing microbiota hypothesis postulates that, as a consequence of routine customs in modern societies – such as clean water, sanitation, caesarean birth and antibacterial soaps – practiced over many generations, the normal inoculum on which the newborn is dependent for microbiome and immune system development has become depleted in the mother. This hypothesis further suggests that we might be losing key members of our normal microbiome, generation after generation, because of the increasingly impoverished microbiomes of mothers, resulting in a cumulative loss of the normal microbiota needed to support human health. Whether this hypothesis is supported awaits rigorous scientific testing, but it does help frame the question of why we are currently seeing epidemics in 10) ___autoimmune diseases that have been relatively rare throughout human history. Perhaps disturbances to our microbiome are key to understanding why these diseases are increasing; in turn, this understanding may lead to the treatment and, ultimately, prevention of such diseases. (Part 2 next week.)
ANSWERS: 1) body; 2) medicine; 3) microbes; 4) microbiome; 5) immune; 6) intestine; 7) unique; 8) antibiotics; 9) diseases; 10) autoimmune
Antonie van Leeuwenhoek (1632-1723)
Portrait of Antonie van Leeuwenhoek (1632-1723)
Editor’s note: We give thanks to all the scientists and great thinkers, who, throughout history, ignored the derision of many, and courageously continued focused exploration of great ideas. They have been the drivers of human progress.
The Secretary of the Royal Society, London, wrote the following letter to van Leeuwenhoek, on the 20th of October, 1676; Dear Mr. Anthony van Leeuwenhoek, Your letter of October 10th has been received here with amusement. Your account of myriad little animals seen swimming in rainwater, with the aid of your so-called microscope,caused the members of the society considerable merriment when read at our most recent meeting. Your novel descriptions of the sundry anatomies and occupations of these invisible creatures led one member to imagine that your rainwater might have contained an ample portion of distilled spirits–imbibed by the investigator. Another member raised a glass of clear water and exclaimed, Behold, the Africk of Leeuwenhoek. For myself, I withhold judgment as to the sobriety of your observations and the veracity of your instrument. However, a vote having been taken among the members (accompanied, I regret to inform you, by considerable giggling) it has been decided not to publish your communication in the Proceedings of this esteemed society. However, all here wish your little animals health, prodigality and good husbandry by their ingenious discoverer.
Antonie Philips van Leeuwenhoek was a Dutch tradesman and scientist. He is commonly known as the Father of Microbiology, and considered to be the world’s first microbiologist. He is best known for his work on the improvement of the microscope and for his contributions towards the establishment of microbiology. Raised in Delft, Netherlands, Leeuwenhoek worked as a draper in his youth, and founded his own shop in 1654. He made a name for himself in municipal politics, and eventually developed an interest in lens making. Using his handcrafted microscopes, he was the first to observe and describe single-celled organisms, which he originally referred to as animalcules, and which are now referred to as microorganisms. He was also the first to record microscopic observations of muscle fibers, bacteria, spermatozoa, and blood flow in capillaries (small blood vessels). Leeuwenhoek did not author any books; his discoveries came to light through correspondence with the Royal Society, which published his letters.
Antonie van Leeuwenhoek was born in Delft, Dutch Republic, on October 24, 1632 of Dutch ancestry. His father, Philips Antonysz van Leeuwenhoek, was a basket maker who died when Antony was five years old. His mother, Margaretha (Bel van den Berch), came from a well-to-do brewer’s family, and married Jacbon Jansz Molijn, a painter, after Philips’ death. Antony had four older sisters, Margriete, Geertruyt, Neeltge, and Catharina. Little is known of his early life; he attended school near Leyden for a short time before being sent to live in Benthuizen with his uncle, an attorney and town clerk. He became an apprentice at a linen-draper’s shop in Amsterdam at the age of 16. He married Barbara de Mey in July 1654, with whom he would have one surviving daughter, Maria (four other children died in infancy). That year he returned to Delft, where he would live and study for the rest of his life. He opened a draper’s shop, which he ran throughout the 1650s. His status in Delft grew throughout the following years, although he would remain an obscure figure outside of the city. He received a lucrative municipal title as chamberlain for the Delft sheriffs’ assembly chamber in 1660, a position which he would hold for almost 40 years. In 1669 he was named a surveyor by the Court of Holland; later he would become a municipal wine-gauger in charge of the city’s wine imports.
Leeuwenhoek was a contemporary of another famous Delft citizen, painter Johannes Vermeer, who was baptized just four days earlier. It has been suggested that he is the man portrayed in two of Vermeer’s paintings of the late 1660s, The Astronomer and The Geographer. However, others argue that there appears to be little physical similarity. Because they were both relatively important men in a city with only 24,000 inhabitants, it is likely that they were at least acquaintances. Also, it is known that Leeuwenhoek acted as the executor of the will when the painter died in 1675. While running his draper’s shop, Leeuwenhoek began to develop an interest in lens making, although few records exist of his early activity. Leeuwenhoek’s interest in microscopes and a familiarity with glass processing led to one of the most significant, and simultaneously well-hidden, technical insights in the history of science. By placing the middle of a small rod of soda lime glass in a hot flame, Leeuwenhoek could pull the hot section apart to create two long whiskers of glass. Then, by reinserting the end of one whisker into the flame, he could create a very small, high-quality glass sphere. These spheres became the lenses of his microscopes, with the smallest spheres providing the highest magnifications.
Microscopic section through one-year-old Ash tree (Fraxinus) wood, drawing made by Leeuwenhoek
After developing his method for creating powerful lenses and applying them to study of the microscopic world, Leeuwenhoek introduced his work to his friend, the prominent Dutch physician Reinier de Graaf. When the Royal Society in London published the groundbreaking work of an Italian lensmaker in their journal Philosophical Transactions of the Royal Society, de Graaf wrote to the journal’s editor Henry Oldenburg with a ringing endorsement of Leeuwenhoek’s microscopes which, he claimed, far surpass those which we have hitherto seen. In response the Society published in 1673 a letter from Leeuwenhoek, which included his microscopic observations on mold, bees, and lice.
Van Leeuwenhoek wrote his letters to the Royal Society by hand in Dutch, the only language he knew, before publication in the Philosophical Transactions
Leeuwenhoek’s work fully captured the attention of the Royal Society, and he began regularly corresponding with the Society regarding his observations. He had at first been reluctant to publicize his findings, regarding himself as a businessman with little scientific, artistic, or writing background, but de Graaf urged him to be more confident in his work. By his death in 1723, he had written 190 letters to the Society, detailing his findings in a wide variety of fields, centered around his work in microscopy. He only wrote letters, in his own colloquial flavor of Dutch; he never published a proper scientific paper. He had strongly preferred to work alone, distrusting the sincerity of those who offered their assistance. The letters were translated into Latin or English by the German Oldenburg, who learnt Dutch in order to be able to do so. Despite the initial success of Leeuwenhoek’s relationship with the Royal Society, this relationship was soon severely strained. In 1676, his credibility was questioned when he sent the Royal Society a copy of his first observations of microscopic single-celled organisms. Previously, the existence of single-celled organisms was entirely unknown. Thus, even with his established reputation with the Royal Society as a reliable observer, his observations of microscopic life were initially met with both skepticism and open ridicule. Eventually, in the face of Leeuwenhoek’s insistence, the Royal Society arranged for Alexander Petrie, minister to the English Reformed Church in Delft, Benedict Haan, at that time Lutheran minister at Delft, and Henrik Cordes, then Lutheran minister at the Hague, accompanied by Sir Robert Gordon and four others to determine whether it was in fact Leeuwenhoek’s ability to observe and reason clearly, or perhaps the Royal Society’s theories of life itself that might require reform. Finally in 1677 Leeuwenhoek’s observations were fully vindicated by the Society. Leeuwenhoek was elected to the Royal Society in February 1680 on the nomination of William Croone, a then-prominent physician. Leeuwenhoek was taken aback at the nomination, which he considered a high honor, although he did not attend the induction ceremony in London, nor did he ever attend a Royal Society meeting. By the end of the 17th century, Leeuwenhoek had a virtual monopoly on microscopic study and discovery. His contemporary Robert Hooke, an early microscope pioneer, bemoaned that the field had come to rest entirely on one man’s shoulders. He was visited over the years by many notable individuals, such as Russian Tsar Peter the Great.
To the disappointment of his guests, Leeuwenhoek refused to reveal the cutting-edge microscopes he relied on for his discoveries, instead showing visitors a collection of average-quality lenses. An experienced businessman, Leeuwenhoek realized that if his simple method for creating the critically important lens was revealed, the scientific community of his time would likely disregard or even forget his role in microscopy. He therefore allowed others to believe that he was laboriously spending most of his nights and free time grinding increasingly tiny lenses to use in microscopes, even though this belief conflicted both with his construction of hundreds of microscopes and his habit of building a new microscope whenever he chanced upon an interesting specimen that he wanted to preserve. He made about 200 microscopes with different magnification. He was visited by Leibniz, William III of Orange and his wife, the Amsterdam burgemeester (the mayor) Johan Huydecoper, the latter very interested in collecting and growing plants for the Hortus Botanicus Amsterdam and all gazed at the tiny creatures. Nicolaes Witsen sent him a map of Tartaria and a mineral found near the origin of the river Amur. In 1698 Leeuwenhoek was invited in the boat of Tsar Peter the Great. On the occasion Leeuwenhoek presented the Tsar an eel-viewer, so Peter could study the blood circulation, whenever he wanted.
Leeuwenhoek made more than 500 optical lenses. He also created at least 25 microscopes, of differing types, of which only nine survived. His microscopes were made of silver or copper frames, holding hand-made lenses. Those that have survived are capable of magnification up to 275 times. It is suspected that Leeuwenhoek possessed some microscopes that could magnify up to 500 times. Although he has been widely regarded as a dilettante or amateur, his scientific research was of remarkably high quality. The microscopes were relatively small devices, the biggest being about 5 cm long. They are used by placing the lens very close in front of the eye, while looking in direction of the sun. The other side of the microscope had a pin, where the sample was attached in order to stay close to the lens. There were also three screws that allowed the viewer to move the pin, and the sample, along three axes: one axis to change the focus, and the two other axes to navigate through the sample. Leeuwenhoek maintained throughout his life that there are aspects of microscope construction which I only keep for myself, in particular his most critical secret of how he created lenses. For many years no-one was able to reconstruct Leeuwenhoek’s design techniques. However, in 1957 C.L. Stong used thin glass thread fusing instead of polishing, and successfully created some working samples of a Leeuwenhoek design microscope. Such a method was also discovered independently by A. Mosolov and A. Belkin at the Russian Novosibirsk State Medical Institute.
Replica of microscope by Leeuwenhoek
Leeuwenhoek used samples and measurements to estimate numbers of microorganisms in units of water. He also made good use of the huge lead provided by his method. He studied a broad range of microscopic phenomena, and shared the resulting observations freely with groups such as the English Royal Society. Such work firmly established his place in history as one of the first and most important explorers of the microscopic world. He was one of the first people to discover cells, along with Robert Hooke. Leeuwenhoek’s main discoveries are the:
infusoria (protists in modern zoological classification), in 1674
bacteria, (e.g., large Selenomonads from the human mouth), in 1676
vacuole of the cell.
spermatozoa in 1677.
banded pattern of muscular fibers, in 1682.
In 1687 he reported his research on the coffee bean. He roasted the bean, cut it into slices and saw a spongeous interior. The bean was pressed, and an oil appeared. He boiled the coffee with rain water twice, set it aside. Like Robert Boyle and Nicolaas Hartsoeker, Leeuwenhoek was interested in the dried cochineal, trying to find out if the dye came from a berry or an insect.
Leeuwenhoek was also a Dutch Reformed Calvinist. He often referred with reverence to the wonders God designed in making creatures great and small. He believed that his amazing discoveries were merely further proof of the great wonder of God’s creation. Leeuwenhoek’s discovery that smaller organisms procreate similarly to larger organisms challenged the contemporary belief, generally held by the 17th-century scientific community, that such organisms generated spontaneously. The position of the Church on the exact nature of the spontaneous generation of smaller organisms was ambivalent.
Antonie van Leeuwenhoek is buried in the Oude kerk in Delft
By the end of his life, Leeuwenhoek had written approximately 560 letters to the Society and other scientific institutions concerning his observations and discoveries. Even when dying, Leeuwenhoek kept sending letters full of observations to London. The last few also contained a precise description of his own illness. He suffered from a rare disease, an uncontrolled movement of the midriff, which is now named Van Leeuwenhoek’s disease. He died at the age of 90, on August 26, 1723 and was buried four days later in the Oude Kerk (Delft).
In 1981 the British microscopist, Brian J. Ford found that Leeuwenhoek’s original specimens had survived in the collections of the Royal Society of London. They were found to be of high quality, and were all well preserved. Ford carried out observations with a range of microscopes, adding to our knowledge of Leeuwenhoek’s work.
Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children
High proportions of autistic children suffer from gastrointestinal (GI) disorders, implying a link between autism and abnormalities in gut microbial functions. Increasing evidence from recent high-throughput sequencing analyses indicates that disturbances in composition and diversity of gut microbiome are associated with various disease conditions. However, microbiome-level studies on autism are limited and mostly focused on pathogenic bacteria.
As a result, a study published online in PLOS 1 (3 July 2013), was performed to define systemic changes in gut microbiome associated with autism and autism-related GI problems. The study recruited 20 neurotypical and 20 autistic children accompanied by a survey of both autistic severity and GI symptoms. By pyrosequencing the V2/V3 regions in bacterial 16S rDNA from fecal DNA samples, a comparison was made of gut microbiomes of GI symptom-free neurotypical children with those of autistic children mostly presenting GI symptoms. Unexpectedly, the presence of autistic symptoms, rather than the severity of GI symptoms, was associated with less diverse gut microbiomes. Further, rigorous statistical tests with multiple testing corrections showed significantly lower abundances of the genera Prevotella, Coprococcus, and unclassified Veillonellaceae in autistic samples. These organisms are intriguingly versatile carbohydrate-degrading and/or fermenting bacteria, suggesting a potential influence of unusual diet patterns observed in autistic children. However, multivariate analyses showed that autism-related changes in both overall diversity and individual genus abundances were correlated with the presence of autistic symptoms but not with their diet patterns.
Taken together, autism and accompanying GI symptoms were characterized by distinct and less diverse gut microbial compositions with lower levels of Prevotella, Coprococcus, and unclassified Veillonellaceae.
Precocious GEM: Shape-Shifting Sensor Can Report Conditions from Deep in the Body
Novel geometrically encoded magnetic sensors (GEMs), developed by researchers from NIST and NIH, respond to local biochemical conditions such as a change in acidity near inflammation sites – by changing their shape and response to radio frequencies. Credit: Kelley/NIST PML
Scientists working at the National Institute of Standards and Technology (NIST) and the National Institutes of Health (NIH) have devised and demonstrated a new, shape-shifting probe, about one-hundredth as wide as a human hair, which is capable of sensitive, high-resolution remote biological sensing that is not possible with current technology. If eventually put into widespread use, the design could have a major impact on research in medicine, chemistry, biology and engineering. Ultimately, it might be used in clinical diagnostics.
To date, most efforts to image highly localized biochemical conditions such as abnormal pH and ion concentration – critical markers for many disorders – rely on various nanosensors that are probed using light at optical frequencies. But the sensitivity and resolution of the resulting optical signals decrease rapidly with increasing depth into the body. That has limited most applications to less obscured, more optically accessible regions. The new shape-shifting probe devices, described online in the journal Nature (16 March2015) are not subject to those limitations. They make it possible to detect and measure localized conditions on the molecular scale deep within tissues, and to observe how they change in real time. The design is based on completely different operating principles. Instead of optically based sensing, the shape-changing probes are designed to operate in the radio frequency (RF) spectrum, specifically to be detectable with standard nuclear magnetic resonance (NMR) or magnetic resonance imaging (MRI) equipment. In these RF ranges, signals are, for example, not appreciably weakened by intervening biological materials. As a result, they can get strong, distinctive signals from very small dimensions at substantial depths or in other locations impossible to probe with optically based sensors.
The novel devices, called geometrically encoded magnetic sensors (GEMs), are microengineered metal-gel sandwiches about 5 to 10 times smaller than a single red blood cell, one of the smallest human cells. Each consists of two separate magnetic disks that range from 0.5 to 2 micrometers (millionths of a meter) in diameter and are just tens of nanometers (billionths of a meter) thick. Between the disks is a spacer layer of a hydrogel. A hydrogel is a cross-linked network of polymers that can absorb various amounts of water depending on their chemical composition and structure as well as the environment around it. The hydrogels used in the NIST-NIH project were engineered to swell in neutral environments and to shrink in low-pH environments. Swelling or shrinking of the gel changes the distance (and hence, the magnetic field strength) between the two disks, and that, in turn, changes the frequency at which the protons in water molecules around and inside the gel resonate in response to radio-frequency radiation. Scanning the sample with a range of frequencies quickly identifies the current shape of the nanoprobes, effectively measuring the remote conditions through the changes in resonance frequencies caused by the shape-changing agents.
In the experiments reported in Nature, the authors tested the sensors in solutions of varying pH, in solutions with ion concentration gradients, and in a liquid growth medium containing living canine kidney cells as their metabolism went from normal to nonfunctional in the absence of oxygen. That phenomenon caused the growth medium to acidify, and the change over time was sensed by the GEMs and recorded through real-time shifting in resonant frequencies. Even for the un-optimized, first-generation probes used, the frequency shifts resulting from changes in pH were easily resolvable and orders of magnitude larger than any equivalent frequency shifting observed through traditional magnetic resonance spectroscopy approaches.
Tracking highly localized pH values in living organisms can be difficult. (A blood test cannot necessarily do it because the sample mixes blood from numerous locations.) Yet local pH changes can provide invaluable early signals of many pathologies. For example, the pH around a cancer cell is slightly lower than normal, and internal inflammation generally leads to local change in pH level. Detecting such changes might reveal, for example, the presence of an unseen tumor or show whether an infection has developed around a surgical implant.
The long-term goal is to improve techniques to the point at which GEMs can be employed for biomedical uses. However, that would require, among other things, further miniaturization. The 0.5 to 2 ?m diameter GEMs in the experiments are already small enough for many in vitro and other possible non-biological applications, as well as possibly for some in vivo cellular related applications. But preliminary estimates by the experimenters indicate that the sensors can be reduced substantially from their current size, and might conceivably be made smaller than 100 nanometers in diameter. That would open up many additional biomedical applications. One of the most significant features of GEMs is that they can be tuned in fabrication to respond to different biochemical states and to resonate in different parts of the RF spectrum by altering the gel composition and the magnet shapes and materials, respectively. So placing two different populations of GEMs at the same site makes it possible to track changes in two different variables at the same time – a capability the authors demonstrated by placing GEMs with two different dimensions in the same location and detecting the signals from both simultaneously. NIST Tech Beat: 27 March 2015