Kabuki Syndrome Disease Gene Identified

Kabuki syndrome, which has an estimated incidence of 1 in 32,000 births, was originally described by Japanese scientists in 1981. Patients with the disorder often have distinct facial features that resemble the make-up worn by actors of Kabuki, a Japanese theatrical form.

According to an article published in the advanced online edition of Nature Genetics (15 August 2010), using a new, rapid and less expensive DNA sequencing strategy, the genetic alterations that account for most cases of Kabuki syndrome, a rare disorder that causes multiple birth defects and mental retardation, have been discovered. Instead of sequencing the entire human genome, the new approach sequences just the exome, the 1-2 percent of the human genome that contains protein-coding genes.

The study sequenced the exomes of 10 unrelated individuals with Kabuki syndrome. Beginning with the premise that Kabuki syndrome is caused by alterations in just a single gene, the study compared the exomes of the 10 patients to the human genome sequence to look for differences shared by the affected individuals. Initially, none were identified. The study then tested the hypothesis that Kabuki syndrome is more genetically heterogeneous than originally assumed, and that multiple genes could potentially cause the disorder. Looking for novel variants in genes that were shared among subsets of the 10 patients’ exomes, novel, matching variants were found that were shared in three genes in nine of the patient’s exomes, shared in six genes in at least eight exomes, and shared in 16 genes among seven exomes.

With no obvious way to rank these gene candidates, the authors categorized each Kabuki case based on a subjective assessment of how well the patient matched the characteristics of Kabuki syndrome. The authors also looked in particular for variants in genes that led to a loss of function. The combined analysis pointed to gene called MLL2.

It was found novel variants which lead to a loss of function in the MLL2 gene in the four highest ranked cases, and in three of the remaining six cases. The variants were nonsense and frameshift mutations. The nonsense mutation substituted a single nucleotide (a molecule that links to form DNA) in the gene code, while the frameshift mutation resulted in a four nucleotide deletion in the gene. In these cases, each nonsense and frameshift mutation resulted in the production of a shortened, nonfunctional protein. The MLL2 gene normally encodes a protein important in the regulation of chromatin, a protein that helps package the DNA in a compact form and allows the chromosome to fit in the cell nucleus. Changes in chromatin structure are associated with DNA replication and turning genes on or off.

The findings were then validated using Sanger sequencing in 43 additional Kabuki syndrome cases. Novel MLL2 variants were found in 26 of the 43 cases. In the end, a total of 33 distinct MLL2 mutations were found in 35 of 53, or 66%, of patients with Kabuki syndrome. The authors also discovered that in each of the 12 cases for which DNA from both parents was available, the MLL2 variants reflected new mutations within the affected individual’s genome and were not present in either parent’s genomes.

Discovery Opens Door To Therapeutic Development For FSH Muscular Dystrophy

Facioscapulohumeral Muscular Dystrophy (FSHD) affects about 1 in 20,000 people, and is named for progressive weakness and wasting of muscles in the face, shoulders and upper arms. Although not life-threatening, the disease is disabling. The facial weakness in FSHD, for example, often leads to problems with chewing and speaking.

According to an article published in Science (19 August 2010) we are closer to understanding what triggers muscle damage in in FSHD. The new research was funded in part by the National Institutes of Health. Until now, there were few clues to the mechanism of FSHD and essentially no leads for potential therapies, beyond symptomatic treatments and this study presents a model of the disease that ties together many complex findings, and should allow researchers to test new theories and potential new treatments.

In the early 1990s, researchers found that FSHD is associated with a shortened DNA sequence located on chromosome 4. Experts predicted that discovery of one or more FSHD genes was imminent, but while a handful of candidate genes gradually emerged, none of them were found to have a key role in the disease. The mysteries surrounding FSHD deepened in 2002 when researchers, led by Silvere van der Maarel, Ph.D., at Leiden University in the Netherlands, found that the shortened DNA sequence on chromosome 4 is not enough to cause FSHD. They discovered that the disease occurs only among people who have the shortened DNA sequence plus other sequence variations on chromosome 4. That work was funded in part by NIH, the FSH Society and the Muscular Dystrophy Association.

The new study proposes a model that explains how the previous findings fit together. At one end of chromosome 4 is a chunk of repetitive DNA, called a tandem repeat array. Normally this region contains 10-100 repeating units of DNA, but in most people with FSHD, the array is smaller, with fewer than 10 repeats. Within each repeating unit is a gene called DUX4. The authors found that in people with FSHD, the DUX4 gene generates a piece of RNA that is toxic to muscle cells. RNA is a sister molecule to DNA with many critical functions. The authors also discovered that variations on chromosome 4 are important because they affect the durability of DUX4 RNA. People with FSHD have chromosome variations that add a trailing segment to the RNA called a poly(A) tail. With the poly(A) tail attached, the RNA is more stable and more likely to cause damage.

The authors came to these conclusions by creating artificial DNA constructs containing the short repeat array, in combination with different variations on chromosome 4. They inserted these constructs into muscle cells, and analyzed how the chromosome 4 variations affected the level of DUX4 RNA. They also studied FSHD families with unique chromosome rearrangements and showed that all families with FSHD shared chromosome 4 sequences encoding the poly(A) tail. In another set of experiments, they found they could detect DUX4 RNA in muscle cells from individuals with FSHD but not in cells from unaffected individuals. Meanwhile, previous studies have shown that DUX4 can trigger muscle cell death.

According to the authors, the study provides evidence that DUX4 RNA is likely a key part of the disease process in FSH muscular dystrophy, and justifies further investigation of its role and how to silence its effects.

Change in Prevalence of Hearing Loss in US Adolescents

Hearing loss is common and, in young persons, can compromise social development, communication skills, and educational achievement. As a result, a study published in the Journal of the American Medical Association (2010;304:772-778) was performed to examine the current prevalence of hearing loss in US adolescents and determine whether it has changed over time.

The study involved a cross-sectional analyses of US representative demographic and audiometric data derived from The Third National Health and Nutrition Examination Survey (NHANES III), 1988-1994, and NHANES 2005-2006 Survey. The  NHANES III trial examined 2,928 participants and NHANES 2005-2006 examined 1,771 participants, all aged 12 to 19 years.

For the study, the prevalence of hearing loss was determined in study participants after accounting for the complex survey design. Audiometrically determined hearing loss was categorized as either unilateral or bilateral for low frequency (0.5, 1, and 2 kHz) or high frequency (3, 4, 6, and 8 kHz), and as slight loss (>15 to <25 dB) or mild or greater loss (25 dB) according to hearing sensitivity in the worse ear. The prevalence of hearing loss from NHANES 2005-2006 was compared with the prevalence from NHANES III (1988-1994). The study also examined the cross-sectional relations between several potential risk factors and hearing loss.

Results showed that the prevalence of any hearing loss increased significantly from 14.9% in 1988-1994 to 19.5% in 2005-2006 (P = .02). In 2005-2006, hearing loss was more commonly unilateral (prevalence, 14.0% vs. 11.1%; P = .005). Individuals from families below the federal poverty threshold had significantly higher odds of hearing loss than those above the threshold.

TARGET HEALTH excels in Regulatory Affairs and Public Policy issues. Each week we highlight new information in these challenging areas.

Developing Products for Rare Diseases and Conditions

The FDA has charged the Office of Orphan Products Development (OOPD) to dedicate its mission to promoting the development of products that demonstrate promise for the diagnosis and/or treatment of rare diseases or conditions. In fulfilling that task, OOPD interacts with the medical and research communities, professional organizations, academia, governmental agencies, and the pharmaceutical industry, as well as rare disease groups.

The OOPD administers the major provisions of the Orphan Drug Act (ODA) which provide incentives for sponsors to develop products for rare diseases. The ODA has been very successful – more than 200 drugs and biological products for rare diseases have been brought to market since 1983. In contrast, the decade prior to 1983 saw fewer than ten such products come to market. 

In addition, the OOPD administers the Orphan Products Grants Program which provides funding for clinical research in rare diseases. The Office Of Orphan Products Development will also administer a new grant program, the Pediatric Device Consortia (PDC) Grant Program. The PDC Grant Program solicits grant applications from institutions/organizations that propose to develop nonprofit consortia to facilitate pediatric medical device development. FDA will provide grants to consortia whose business model and approach to device development will either result in, or substantially contribute to, market approval of medical devices designed specifically for use in children. Although administered by the OOPD, this grant program is intended to encompass devices used in all pediatric diseases, not just rare diseases.

For more information about our expertise in Medical Affairs, contact Dr. Mark Horn. For Regulatory Affairs, please contact Dr. Jules T. Mitchel or Dr. Glen Park.

Target Health (www.targethealth.com) is a full service eCRO with full-time staff dedicated to all aspects of drug and device development. Areas of expertise include Regulatory Affairs, comprising, but not limited to, IND (eCTD), IDE, NDA (eCTD), BLA (eCTD), PMA (eCopy) and 510(k) submissions, execution of Clinical Trials, Project Management, Biostatistics and Data Management, EDC utilizing Target e*CRF®, and Medical Writing.

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Science Weekly: Questioning gravity

Filed Under Uncategorized | Comments Off

The big questions about our universe; a sex scientist; zombie ants; plus, is the moon really getting smaller?

By Daniel J. DeNoon
WebMD Health News

Reviewed by Laura J. Martin, MD

Outbreak Traced to Supplier for Major Groceries, Restaurants

WebMD, Aug. 18, 2010 — Eggs are behind a nationwide salmonella outbreak that caused hundreds of illnesses each week in June and July.

The nationwide egg recall involves more than a dozen major brands that got eggs from Wright County Egg in Galt, Iowa.

CDC and state investigators in California, Colorado, and Minnesota found clusters of salmonella food poisoning among people who ate eggs at the same restaurants. Those restaurants got eggs that came from Wright County Egg.

Investigations continue in Arizona, Connecticut, Massachusetts, Maryland, North Carolina, Nevada, Oregon, Pennsylvania, Tennessee, and Texas. According to a CDC spokeswoman, the outbreak is “pretty much nationwide.”

Meanwhile, the FDA is conducting a thorough investigation of the Iowa firm to which the contaminated eggs were traced. The company says it already has sent all its remaining eggs to a breaker, where they will be pasteurized to kill any salmonella.

Shell eggs included in the recall were shipped since May to food wholesalers, distribution centers, and food service companies in eight states, from which they were distributed nationwide.

The brand names included in the recall are Lucerne, Albertson, Mountain Dairy, Ralph’s, Boomsma’s, Sunshine, Hillandale, Trafficanda, Farm Fresh, Shoreland, Lund, Dutch Farms, and Kemps. Recalled eggs are in six, dozen, and 18-egg cartons.

Stamped on the end of the recalled egg cartons are Julian dates ranging from 136 to 225 and plant numbers 1026, 1413, and 1946. The plant number begins with the letter P and then the number. The Julian date follows the plant number, for example: P-1946 223.  Recalled eggs may be returned to the store for a full refund.

The salmonella strain causing the outbreak is Salmonella Enteritidis, the most common salmonella strain. Usually the CDC gets about 50 reports a week of Salmonella Enteritidis food poisoning; beginning in May there was a fourfold increase in salmonella reports. Each week in late June and early July the CDC received some 200 salmonella samples isolated from patients, all with the same DNA fingerprint.

Symptoms of infection begin 12 to 72 hours after consuming contaminated foods or beverages and include fever, abdominal cramps, and diarrhea. Symptoms usually last four to seven days.

Most people recover without antibiotic treatment, but severe cases can be fatal. People prone to severe illness — particularly severe diarrhea — include the elderly, infants, and those with impaired immune systems, including people on immune suppressive therapy such as cancer chemotherapy.

Salmonella: Protect Yourself Against This Culprit

How to Avoid Food Poisoning From Eggs

If you like your eggs prepared over easy, you may want to change your egg-eating habits. Here’s the CDC’s advice on how to avoid food poisoning from eggs:

  • Don’t eat recalled eggs or products containing recalled eggs. Recalled eggs might still be in grocery stores, restaurants, and homes. Consumers who have recalled eggs should discard them or return them to their retailer for a refund.
  • People who think they might have become ill from eating recalled eggs should consult their health care providers.
  • Keep eggs refrigerated at least to 45 degrees F at all times.
  • Discard cracked or dirty eggs.
  • Wash hands, cooking utensils, and food preparation surfaces with soap and water after contact with raw eggs.
  • Eggs should be cooked until both the white and the yolk are firm and eaten promptly after cooking.
  • Do not keep eggs warm or at room temperature for more than two hours.
  • Refrigerate unused or leftover egg-containing foods promptly.
  • Avoid eating raw eggs.
  • Avoid restaurant dishes made with raw or undercooked, unpasteurized eggs. Restaurants should use pasteurized eggs in any recipe (such as Hollandaise sauce or Caesar salad dressing) that calls for raw eggs.
  • Consumption of raw or undercooked eggs should be avoided, especially by young children, elderly people, and people with weakened immune systems or debilitating illness.

Salmonella is a genus of rod-shaped, Gram-negative, non-spore forming, predominantly motile enterobacteria with diameters around 0.7 to 1.5 µm, lengths from 2 to 5 µm, and flagella which project in all directions (i.e. peritrichous). They are chemoorganotrophs, obtaining their energy from oxidation and reduction reactions using organic sources, and are facultative anaerobes. Most species produce hydrogen sulfide, which can readily be detected by growing them on media containing ferrous sulfate, such as TSI. Most isolates exist in two phases: a motile phase I and a nonmotile phase II. Cultures that are nonmotile upon primary culture may be switched to the motile phase using a Cragie tube. Salmonella is closely related to the Escherichia genus and are found worldwide in cold- and warm-blooded animals (including humans), and in the environment. They cause illnesses such as typhoid fever, paratyphoid fever, and the foodborne illness salmonellosis. Salmonella is properly ˌsælməˈnɛlə voicing the initial letter “L,” since it is named for pathologist Daniel Elmer Salmon.

Read more: http://www.righthealth.com/Health/Salmonella%20Pictures-s?lid=goog-ads-sb-8536643334#ixzz0wzWGGqK5

Medscape, by Steve Stiles, August 19, 2010 (Dallas, Texas) — Not that many would need further encouragement to eat chocolate regularly, but a prospective observational study of older women in Sweden suggests that partaking of it up to a few times a week can cut the risk of heart failure by about a third [1]. Although many studies of various kinds have linked intake of chocolate, especially flavanol-rich dark chocolate, to improved blood pressure and other cardiovascular benefits, the new population-based study may be the first of its kind to suggest the confection can improve the risk of heart failure in particular.

The adjusted risk of heart failure over nine years declined 26% for women who reported a monthly chocolate intake of one to three servings and by 32% for those who said they ate one or two servings per week; both findings were significant. The analysis, based on >30 000 members of the Swedish Mammography Cohort, was controlled for intake of other foods, body-mass index, exercise levels, family medical history, and other potential influences on heart-failure risk.

But women who reported eating chocolate more often than twice a week didn’t show a reduced heart-failure risk. “Chocolate still comes with a fair amount of calories from sugar and fat, which can be problematic,” observed senior author Dr Murray A Mittleman (Beth Israel Deaconess Medical Center, Boston MA). “We controlled for total calorie intake, so that means for women who were eating larger amounts of chocolate, it was displacing other foods that might be beneficial, such as fruits and vegetables,” he told heartwire .

qFor women who were eating larger amounts of chocolate, it was displacing other foods that might be beneficial, such as fruits and vegetables.

“We think the data are suggesting that if you’re going to have a treat, chocolate is a reasonable choice because it appears to have these beneficial effects, [as long as] you are careful not to overindulge.” His group’s report, with first author Elizabeth Mostofsky (Beth Israel Deaconess Medical Center), is published online August 17, 2010 in Circulation: Heart Failure.

Of course, any benefits depend on the type of chocolate. The flavanols in chocolate believed to confer cardiovascular benefits are concentrated in the cocoa solids (pure chocolate minus the cocoa butter)–so the greater the cocoa content, the better are chocolate’s health effects. Overwhelmingly, according to Mittleman, the chocolate consumed in Sweden is milk chocolate, but in accordance with European standards, its cocoa content is likely to be about 30%. It can therefore be richer in flavanols than some dark chocolate in the US, which is allowed to contain as little as 15% cocoa solids.

The analysis included 31 823 women the Swedish cohort who were 48 to 83 years old at baseline without a history of diabetes, MI, or heart failure who completed questionnaires on intake of specific foods, activity levels, body dimensions, and other issues. Over nine years of follow-up, the rate of hospitalization or death from heart failure was 15.1 cases per 10 000 person-years.

In a finding that mirrors other research, the adjusted heart-failure event hazard ratio (HR) associated with chocolate intake at various levels showed a J-shaped trend that was significant at p=0.0005, with risk falling off significantly in association with either one or two servings per week or one to three servings per month, compared with no regular intake. Risk was neither up or down significantly at higher consumption levels.

Hazard Ratio (95% CI) for Heart Failure Death or Hospitalization by Chocolate Consumption Over Nine Years, Compared to No Regular Chocolate Intake, in the Swedish Mammography Cohort

Frequency of chocolate intake HR (95% CI)*
1 to 3 servings/mo 0.74 (0.58–0.95)
1 to 2 servings/wk 0.68 (0.50–0.93)
3–6 servings/wk 1.09 (0.74–1.62)
>1 servings/d 1.23 (0.73–2.08)

*p for quadratic trend 0.0005

“The [caveat] with this kind of study, of course, is that it’s observational,” Mittleman acknowledged. “It was a prospective cohort study, whereas a number of the short-term studies [showing chocolate effects] on blood pressure were randomized. Having said that, we were able to adjust for a lot of things, like exercise and diet,” he said.

“There are data that show the effect of chocolate on blood pressure and other vascular markers are similar in men and women, so there’s no strong reason to believe the effects [seen in this study] would be any different in men,” according to Mittleman. “[However,] it would be important to get the data in men to be certain.”

The study was supported by the Swedish Research Council, the Swedish Foundation for International Cooperation in Research and Higher Education, and the US National Institutes of Health. The authors had no disclosures.

WsbMD, Laurie Barclay, MD, August 19, 2010 — Tai chi may be a helpful intervention for patients with fibromyalgia, according to the results of a single-blind, randomized trial reported in the August 19 issue of the New England Journal of Medicine.

“Previous research has suggested that tai chi offers a therapeutic benefit in patients with fibromyalgia,” write Chenchen Wang, MD, MPH, from Tufts Medical Center, Tufts University School of Medicine in Boston, Massachusetts, and colleagues. “…[Tai chi] combines meditation with slow, gentle, graceful movements, as well as deep breathing and relaxation, to move vital energy (or qi) throughout the body. It is considered a complex, multicomponent intervention that integrates physical, psychosocial, emotional, spiritual, and behavioral elements.”

Fibromyalgia was defined by American College of Rheumatology 1990 criteria. Participants (n = 66) were randomly assigned 1:1 to receive classic Yang-style tai chi or a control intervention consisting of wellness education and stretching. In both groups, participants received 60-minute sessions twice weekly for 12 weeks.

Fibromyalgia Impact Questionnaire (FIQ) score (ranging from 0 – 100) at the end of 12 weeks was the main study outcome, with higher scores indicating more severe symptoms. Secondary outcomes were summary scores on the physical and mental components of the Medical Outcomes Study 36-Item Short-Form Health Survey. To assess durability of the response, these tests were performed again at 24 weeks.

Improvements in the FIQ total score and quality of life in the tai chi group were clinically important. For this group, mean baseline and 12-week FIQ scores were 62.9 ± 15.5 and 35.1 ± 18.8, respectively, vs 68.0 ± 11 and 58.6 ± 17.6, respectively, in the control group. The mean between-group difference from baseline in the tai chi group vs the control group was −18.4 points (P < .001).

The tai chi group also fared better than the wellness intervention group in physical component scores of the Short-Form Health Survey (28.5 ± 8.4 and 37.0 ± 10.5 for the tai chi group vs 28.0 ± 7.8 and 29.4 ± 7.4 for the control group; between-group difference, 7.1 points; P = .001) and mental component scores (42.6 ± 12.2 and 50.3 ± 10.2 vs 37.8 ± 10.5 and 39.4 ± 11.9, respectively; between-group difference, 6.1 points; P = .03).

These improvements were still present at 24 weeks (FIQ score between-group difference, −18.3 points; P < .001), with no reported adverse events.

Limitations of this study include lack of double blinding, lack of generalizability because treatment was delivered by a single tai chi master at a single center, and follow-up limited to 24 weeks.

“In conclusion, our preliminary findings indicate that tai chi may be a useful treatment in the multidisciplinary management of fibromyalgia,” the study authors write. “Longer-term studies involving larger clinical samples are warranted to assess the generalizability of our findings and to deepen our understanding of this promising therapeutic approach.”

The National Center for Complementary and Alternative Medicine, the American College of Rheumatology Research and Education Foundation Health Professional Investigator Award, and the Boston Claude D. Pepper Older Americans Independence Center Research Career Development Award supported this study. The contents of the journal article are solely the responsibility of the study authors and do not necessarily represent the official views of the National Center for Complementary and Alternative Medicine or the National Institutes of Health. Disclosure forms provided by the study authors are available with the full text of the original article here .

N Engl J Med. 2010;363:743-754.

Colonies of Bacillus licheniformis, which detect their neighbors by “smelling” ammonia      Image: Reindert Nijland

When sensing the presence of other species, bacteria meet the textbook definition for olfaction

 

 


Bacteria have a sense of smell, which they may use to sniff out competitors and food sources, according to new research published this week in Biotechnology Journal.

A study led by Reindert Nijland, now at the University Medical Center in Utretcht, The Netherlands, found that Bacillus bacteria can sense each other’s presence through the air by sensing ammonia production.

“This is basic science that’s really, really interesting because if bacteria can really smell, that’s something unexpected,” Nijland told The Scientist.

Although researchers had known that bacteria could sense the presence of ammonia, “this is the first time it was shown that a gas is sensed for the purpose of regulating social behavior,” said Jörg Stülke, a microbiologist at the University of Göttingen in Germany, who did not participate in the study.

Nijland, then a post-doctoral fellow in the lab of Grant Burgess at the Dove Marine Laboratory at Newcastle University in the UK, was originally trying to figure out how different growth media affected the biofilm-forming abilities of Bacillus subtilis and B. licheniformis. Trying to save valuable lab space, Nijland set up several different experiments in the two Bacillus species on the same 96-well microtiter plate. On the left side of the plate, Nijland grew his bacteria in a nutrient-rich broth, while growing the same bacteria on the right side in media that encouraged them to form the sticky, slimy matrix of sugars and other compounds known as a biofilm. He assumed that the bacteria would not affect each other since they were physically separated.

As Nijland continued his experiments, he noticed something strange. The Bacillus species grown in biofilm-friendly media nearest the wells with the bacteria grown in nutrient-rich media formed larger biofilms that had a darker red pigment. As the bacteria in the biofilm-promoting media got farther away from the bacteria in the nutrient-rich media, the characteristic red pigmentation of Bacillus biofilms began to fade, indicating lower biofilm formation.

Since the bacteria were not physically connected to each other, Nijland could only conclude one thing: The Bacillus must be sensing the presence of the nearby bacteria through the air. Those bacteria growing in nutrient-rich media seemed to be producing some sort of signal that could be sensed by bacteria growing in a biofilm-promoting media. The bacteria must be responding to an airborne volatile compound, which meant the bacteria had fulfilled the textbook definition for olfaction. Only animals and other “higher” eukaryotes were thought to have a sense of smell, but Nijland’s work showed that bacteria also have an olfactory sense. The problem was: what compound were the bacteria sensing?

Nijland began testing all types of volatile chemicals, “basically anything that we had that was smelly,” he said. Nijland identified his volatile compound after placing purified ammonia in one row of wells on the microtiter plate and then growing B. licheniformis in biofilm-friendly media in the row of wells next to the purified ammonia. The B. licheniformis in the adjacent wells formed red pigmented biofilms, whereas the B. licheniformis growing in separate plates without ammonia did not form biofilms.

“Ammonia is the simplest available nitrogen source,” Nijland said. “All organisms need nitrogen to produce their proteins.” The ammonia is thought to signal both the presence of nutrients and the presence of other bacteria, since the biofilms Bacillus species produce in response to ammonia contain antibiotics that can kill competing bacteria. And the ability to “smell” ammonia “gives bacteria a way to sense nutrients where nutrients are and then migrate towards them,” he said.

Knowing more about how biofilms form might also lead to better ways to kill off these notoriously hardy and persistent infections, Nijland added.

Nijland, R. & Burgess, J. G. “Bacterial olfaction,” Biotechnology Journal, doi:10.1002/biot.201000174, 2010.

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