Vulnerability to stress - Tet by Tet

Transition states like 5-hydroxymethylcytosine aren't really a new letter of the genetic alphabet – they’ve been there all along. We just didn’t see them Read more

Circadian rhythms go both ways: in and from retina

Removal of Bmal1 accelerates the deterioration of vision that comes with Read more

Genomics plus human intelligence

The power of gene sequencing to solve puzzles when combined with human Read more

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The unsweetened option

Pediatric hepatologist Miriam Vos is starting a new study testing the effects of a low-sugar diet in children with NAFLD (non-alcoholic fatty liver disease). The study is supported by the Nutrition Science Initiative and conducted in a partnership with UCSD/Rady Children’s Hospital, San Diego. See below for more on NUSI.

While there are no medications approved for NAFLD – a healthy diet and exercise are the standard of care – plenty of drugs are under development, as a recent article from Mitch Leslie in Science illustrates. As a reality check and benchmark, the NUSI study will address whether the low-tech intervention of altering diet can be effective.

Lab Land has delved into NAFLD and its increasing prevalence in previous posts. Plenty of correlational data shows that sugar intake is linked to NAFLD (a recent paper from the Framingham Heart Study), but Vos points out that there are no studies showing that reducing sugar is sufficient to drive improvement in the disease.

Diet is a challenge to examine in humans rigorously. In observational studies, investigators are always bumping up against the limits of memory and accurate reporting. In an interventional study with adults, it’s possible to provide them a completely defined menu for a short time in a closed environment, but that’s less practical for longer periods or with children.

The press release announcing the NUSI study says: half of the families will eat and drink what they normally do while the rest will be put on sugar-free meals and snacks, all of which will be provided for the participants and their families for eight weeks.

Miriam Vos, MD

I was curious about how this would work, especially for boys aged 11 to 16 (the participants in her study), so I asked Vos more about it for Lab Land.

“We try to provide them a diet that is otherwise similar to what the family is used to,” she says. “For example, if they’re accustomed to home-cooked meals, our team of nutritionists will work with them to find different recipes.” Read more

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Adaptive mutation mechanism may drive some forms of antibiotic resistance

Evolutionary theory says mutations are blind and occur randomly. But in the controversial phenomenon of adaptive mutation, cells can peek under the blindfold, increasing their mutation rate in response to stress.

Scientists at Winship Cancer Institute, Emory University have observed that an apparent “back channel” for genetic information called retromutagenesis can encourage adaptive mutation to take place in bacteria.

The results were published Tuesday, August 25 in PLOS Genetics.

“This mechanism may explain how bacteria develop resistance to some types of antibiotics under selective pressure, as well as how mutations in cancer cells enable their growth or resistance to chemotherapy drugs,” says senior author Paul Doetsch, PhD.

Doetsch is professor of biochemistry, radiation oncology and hematology and medical oncology at Emory University School of Medicine and associate director of basic research at Winship Cancer Institute. The first author of the paper is Genetics and Molecular Biology graduate student Jordan Morreall, PhD, who defended his thesis in April.

Retromutagenesis resolves the puzzle: if cells aren’t growing because they’re under stress, which means their DNA isn’t being copied, how do the new mutants appear?

The answer: a mutation appears in the RNA first. Read more

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Anti-aging tricks from dietary supplement seen in mice

Our recent news item on a Cell Reports paper from ShiQin Xiong and Wayne Alexander describes a connection between two important biological molecules: the exercise-induced transcription coactivator PGC1-alpha and the enzyme telomerase, sometimes described as a “fountain of youth” because telomeres protect the ends of chromosomes.

While the Emory researchers did not directly assess the effects of exercise in their experiments, their findings provide molecular clues to how exercise might slow the effects of aging or chronic disease in some cell types.

Xiong and Alexander found that the dietary supplement alpha lipoic acid (ALA) can stimulate telomerase, with positive effects in a mouse model of atherosclerosis. ALA is a sulfur-containing fatty acid used to treat diabetic neuropathy in Germany, and has previously been shown to combat atherosclerosis in animal models. The Emory authors’ main focus was on vascular smooth muscle cells and note that more study of ALA’s effects on other cell types is needed.

Below are four key references that may help you put the Cell Reports paper in context: Read more

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All the boulders at the same time

Emory is preparing to launch a center devoted to antibiotic resistance. On Wednesday, Arjun Srinivasan, one of the CDC’s point people for antibiotic use and hospital acquired infections, kicked off the preparations with a talk on the multifaceted nature of this problem.

Without attempting to cover everything related to antibiotic resistance (that would take a book — or several), I will note in an upcoming post how Emory and partners such as Children’s Healthcare of Atlanta already have begun assembling many of the necessary tools.

Tackling antibiotic resistance has to take into account the habits of physicians, the expectations of patient, improved surveillance and antibiotic overuse in agriculture, as well as research on new antibiotics and detecting dangerous bacteria. In short, it’s both a science and policy issue — captured well by the documentary Resistance.

At the end of his talk, Srinivasan made a remark that brought this home for me, saying “We just have to push all the boulders up the hill at the same time” in response to a question about balancing effort on science vs policy. Allusions to Sisyphus!

Yet he provided some hope too, highlighting a recent CDC study that models how a coordinated response to antibiotic resistance in health care facilities could substantially cut infections. Read more

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Providing the potent part of probiotics

A Emory News item on a helpful part of the microbiome focuses on how the same type of bacteria – lactobacilli – activates the same ancient signaling pathway in intestinal cells in both insects and mammals. It continues a line of research from Rheinallt Jones and Andrew Neish on how beneficial bacteria stimulate wound healing by activating ROS (reactive oxygen species).

Asma Nusrat, MD

A idea behind this research is: if we know what parts of the bacteria stimulate healing, perhaps doctors can deliver that material, or something very close, to patients directly to treat intestinal diseases such as Crohn’s or ulcerative colitis.

This idea has advanced experimentally, as demonstrated by two papers from Jones and Neish’s frequent collaborator, Asma Nusrat, who recently moved from Emory to the University of Michigan. This team had shown that a protein produced by human intestinal cells called annexin A1 activates ROS, acting through the same N-formyl peptide receptors that bacteria do.

Nusrat told me Friday her team began investigating annexins a decade ago at Emory, and it was fortuitous that Neish was working on beneficial bacteria right down the hall, since it is now apparent that annexin A1 and the bacteria are activating the same molecular signals. (Did you know there is an entire conference devoted to annexins? I didn’t until a few days ago.)

In a second Journal of Clinical Investigation paper published this February, Nusrat and her colleagues show that intestinal cells release vesicles containing annexin A1 following injury. The wound closure-promoting effects of these vesicles can be mimicked with nanoparticles containing annexin A1. The nanoparticles incorporate a form of collagen, which targets them to injured intestinal tissue. Read more

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Emory team part of undiagnosed conditions challenge

An Emory team of geneticists and genetics counselors is participating in the Clarity Undiagnosed competition, hosted by Boston Children’s Hospital and Harvard Medical School.

The team is led by genetics counselor Dawn Laney MS, CGC, CCRC. Team members include: Madhuri Hegde, PhD, William Wilcox, MD,PhD, Michael Gambello, MD, PhD, Rani Singh, PhD, RD, Suma Shankar, MD, PhD, Alekhya Narravula, MS,CGC, Kristin Cornell, MS, CRC, Cristina da Silva, MS, Sarah Richards, MS, CGC and Kimberly Lewis, MS, CGC.

In Clarity Undiagnosed, five families of patients with undiagnosed conditions provide DNA sequence information and clinical summaries to up to 30 competing teams. The teams then do their best to interpret the data and provide answers, and a $25,000 prize will go to the team that solves the mysteries in the most complete way.

At the discretion of the families, short videos of the patients may be available to investigators through producers of a forthcoming documentary film, Undiagnosed, but the teams are barred from direct interaction with the families. A glimpse of some of the families is possible by viewing the trailer. Teams have until September 21 to submit their reports and the results of the competition will be announced in November.

Boston Children’s and Harvard held a similar competition in 2012, which attracted teams from all over the world.

The competition grows out of the NIH-sponsored Undiagnosed Diseases Network; Emory pharmacologists Stephen Traynelis and Hongjie Yuan have been working with the related Undiagnosed Diseases Program based at NIH (very complex 2014 paper, blog post on personalized molecular medicine).

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Reversing liver fibrosis via adiponectin

Non-alcoholic fatty liver disease (NAFLD) is one of the most common liver conditions in the United States, affecting 30 percent of the population, and increasing — and likely to catch up in prevalence with obesity and diabetes. In NAFLD, fat content of the liver is elevated to 6 percent or more in people who drink in moderation or not at all. Patients will first present with elevated liver enzyme values in blood tests, but then an imaging test or tissue biopsy may be ordered to evaluate the extent of the damage. NAFLD is mostly asymptomatic and is variable in severity; a majority of those afflicted do not need drug treatments. However, NAFLD is thought to be a preliminary condition that can eventually progress to severe manifestations, such as cirrhosis, hepatocellular carcinoma, and end stage liver failure.

Progression of liver disease, from NIDDK.  This article is a guest post from Kristina Bargeron Clark, a graduate student at Emory and communications chair for Women in Bio-Atlanta. Her website is www.inkcetera.org.

Progression of liver disease, from NIDDK.
This is a guest post from Kristina Bargeron Clark, a MMG graduate student at Emory and communications chair for Women in Bio-Atlanta. Her website is www.inkcetera.org.

At Emory, Frank Anania, director of the Department of Medicine’s Division of Digestive Diseases, and his colleagues are developing a tool to treat liver disease. A recent publication in the FASEB Journal describes their investigation into the potential for the hormone adiponectin to modulate liver fibrosis.

Adiponectin is produced by adipose tissue, but is known to decrease in overweight people with metabolic disease. Research by others indicates that it may prevent heart and kidney fibrosis. The Emory team’s studies were conducted to determine if adiponectin could also reduce liver fibrosis.

Read more

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Bone-strengthening particles stimulate autophagy

Neale Weitzmann and George Beck have been publishing a series of papers describing how silica nanoparticles can increase bone mineral density in animals. Their findings could someday form the basis for a treatment for osteoporosis.

In 2012, we posted an article and video on this topic. We wanted to call attention to a few of the team’s recent papers, one of which probes the mechanism for a remarkable phenomenon: how can very fine silica particles stimulate bone formation?

The particles’ properties seem to depend on their size: 50 nanometers wide – smaller than a HIV or influenza vision. In a 2014 ACS Nano paper, Beck, Weitzmann and postdoc Shin-Woo Ha show that the particles interact with particular proteins involved in the process of autophagy, a process of “self digestion” induced by stress.

“These studies suggest that it is not the material per se that stimulates autophagy but rather size or shape,” they write. Read more

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A few links for BEINGS2015

Several well-known authors, scientists and bioethicists are in downtown Atlanta’s Tabernacle for the #BEINGS2015 conference. Paul Wolpe and the Center for Ethics have been central to organizing the event, and several Emory biomedical and genetics researchers will be involved in shaping the consensus documents that will emerge.

I won’t attempt to summarize the ongoing discussion at this point; with biotechnology, it is difficult to draw a circle around certain topics and say “we’re going to focus on this, but not this” and today was a good example. The border between existing agricultural biotechnology and new organisms seems hard to define.

Three interesting relevant links:

The National Academy of Sciences is launching an effort to guide decision making on human gene editing technologies such as Cas9/CRISPR

Collection of scientists’ comments on human gene editing and Cas9/CRISPR in Nature Biotechnology

Nature Chem Bio paper on engineered yeast that “paves way for home brew heroin”. Interesting role of FBI in overseeing this emerging area, and note that full production of opiates in yeast may look close, but is still not yet possible.

 

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Six beautiful images — choose your favorites

WoodruffMatthew1

Matthew Woodruff — Bali Pulendran lab

ImageJ=1.48g unit=micron

Kenneth Myers — James Zheng lab

Joshua_Strauss_OPE_Image

Joshua Strauss — Elizabeth Wright lab

AndersonJoAnna

JoAnna Anderson — Francisco Alvarez lab

AlexTamas

Alexey Tamas — Charles Searles lab

Emory’s Office of Postdoctoral Education is holding a Best Image contest. The deadline to vote is this Thursday, April 30. You can look at these beautiful images (and guess exactly what they are, based on what lab they come from), but to VOTE, you need to go to the OPE site.

This is part of the run up to their Postdoctoral Research Symposium at the end of May.

(Hat tip to Ashley Freeman in Dept of Medicine!)

Read more

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