All things anthropogeny
Established in 2008 by co-founders Ajit Varki, Margaret Schoeninger and Fred Gage, the Center for Academic Research and Training in Anthropogeny (CARTA) promotes transdisciplinary research in the study of human origins.
Anthropogeny is not a synonym for human evolution, but rather encompasses investigation of all factors involved in human origins, including climate, cultural, geographic, social and ecological. The word was popularized by the noted German zoologist Ernst Haeckel.
Not surprisingly, it’s a rich and diverse topic of conversation. Consider CARTA’s regular symposia, which have produced more than 150 scholarly presentations on subjects ranging from language and the biology of altruism to the evolution of nutrition and whether the human mind is unique. Future symposia will discuss child-rearing in human evolution and the role of male aggression and violence.
Recently, the number of online hits of CARTA videos topped 10 million in just four years – a big number in a blink of geologic time.
Each of us possesses our own unique genetic code, a fact that presents a monumental conundrum: How does that one singular sequence of DNA dictate the creation and function of our multitudinous and varied cells. Your skin cells, muscle cells and fat cells all share the same genetic information, but perform wildly different roles. What defines and determines those functions?
The answer, in a word, is the epigenome, a Greek-derived word that literally means “above the genome.” The epigenome consists of all of the chemical compounds that modify or mark the genome in a way that tells DNA what to do, where to do it and when.
The study of the epigenome is a relatively young endeavor, and much is not known. One of the tools of the epigenome is DNA methylation, a process in which a methyl group is added to cytosine DNA nucleotides, marking genes for repression, silencing repetitive elements and making genomic imprinting possible.
In normal mammalian development, DNA methylation dramatically changes as new cell lineages emerge. “This complex remodeling is evidently essential for development, as loss of the machinery that established DNA methylation results in embryonic lethality,” said Gary C. Hon, PhD, a postdoctoral fellow at the Ludwig San Diego, based at UC San Diego.
In a new paper published online Sunday in Nature Genetics, first author Hon, senior author Bing Ren, PhD, a Ludwig scientist and professor of cellular and molecular medicine at UC San Diego and colleagues probe deeper into the mysteries of epigenetics, reporting on how DNA methylation changes in different kinds of tissue.
“We created very high resolution maps of DNA methylation for 17 diverse tissues in an individual mouse,” said Hon. “Interestingly, we found that if you look at DNA methylation with a wide angle lens, you’ll find that it is generally constant between different tissues. But if you zoom in, there are a large number of short regions that show very tissue-specific DNA methylation, and the vast majority of these regions happened at the many regulatory elements encoded in the genome that control the genes specifically to a tissue.”
The epigenome reveals the current state of a cell and, in embryonic cells, portions of it can reflect the cell’s potential future developmental paths – what it will be when it grows up. Ren, Hon and colleagues discovered, to their surprise, that in adult tissues, some of these regions of tissue-specific DNA methylation involved regulatory elements that were no longer active, but had been during development.
“In this way, the epigenome of each adult tissue is imprinted with the regulatory memory of its past,” said Hon.
The findings are fundamental science. They “do not have immediate clinical relevance. They simply help understanding of development,” said Hon. But they may also auger greater import in the future, bolstering the recognized importance of DNA methylation and providing “an epigenetic signature that can be used to find regulatory elements active in development, but which are no longer active in adult tissues.”
Such a signature might be helpful to understanding the origins of diseases that occur early in developing life, a necessary step before science can take action to prevent them.
What happened to Douglas Prasher?
The Nobel Prize strictly limits shared awards to three people.
In 2008, the Prize in chemistry was famously shared by Roger Tsien of the UC San Diego School of Medicine, Martin Chalfie at Columbia University, and the Marine Biological Laboratory’s Osama Shimomura for their work on the discovery and development of green fluorescent proteins (GFP).
The fourth man out was Douglas Prasher, who had isolated and sequenced the gene for GFP, then generously provided the data to scientists like Tsien, Chalfie and Shimomura. When the 2008 prize was announced, though, Prasher was working as a courtesy shuttle driver for a Toyota dealership in Huntsville, Alabama.
Prasher’s story – a tale of professional and personal misfortune – has been widely reported, but it appears to have a happy – or at least happier – ending. Prasher has returned to science and, specifically, to Tsien’s UC San Diego lab, where he is working as a staff research associate on new ways to screen cell mutations for optical properties. You can read his updated story here in The Scientist.
Digging on the Altman CTRI
Local leaders and luminaries gathered Thursday, Jan. 10, to officially break ground on the Altman Clinical and Translational Research Institute (CTRI), a new structure that will bring together laboratory and clinical researchers in a collaborative search for faster, better ways to treat and cure disease.
Though the morning was notably cold and windy, a series of speakers brightly celebrated “the great day,” among them: UC San Diego Chancellor Pradeep Khosla, vice chancellor for Health Science and dean of the School of Medicine David Brenner, MD, CTRI director Gary Firestein, MD, UC San Diego Health System chief executive officer Paul S. Viviano, Department of Pediatrics chair Gabriel Haddad, MD, and San Diego Mayor Bob Filner.
All extolled the passion and investment of Steve and Lisa Altman, long-time San Diego philanthropists who have pledged $10 million toward construction of the $269 million, 7-story building that will rise near the UC San Diego Thornton Hospital, Moores Cancer Center, Sulpizio Cardiovascular Center and Jacobs Medical Center, which is currently under construction.
“We know translational medicine is the future. This building will be a centerpiece of that vision,” said Khosla, observing that engineers, doctors, computer scientists, geneticists, microbiologists and others will all work together under one roof. “They won’t be able to avoid each other.”
Brenner said places capable of combining the resources, people and vision to create something like the Altman CTRI are rare. “This will be a place where people can access the leading-edge care that only an academic medical center can offer,” he said.
The Altman CTRI is slated to open in early 2016.
Leech neurons stained with voltage-sensitive dye.
Top UCSD Health Sciences stories of 2012
The results are in from our first-ever faculty survey of the top UC San Diego Health Sciences stories for 2012.
Faculty were asked to pick their top three stories from 15 choices culled from the dozens of news reports and releases produced last year by the UC San Diego Health Sciences Marketing & Communications office.
The top spot went to Mark Tuszynski’s paper, published in the September 14 issue of Cell, in which he and colleagues were able to regenerate axonal growth at the site of severe spinal injury in rats using neural stem cells. The work has obvious implications for efforts to develop therapies to restore central nervous system and motor function.
In second place was a PNAS paper out of Roger Tsien’s lab which reported creating a new generation of fast-acting fluorescent dyes that optically highlight electrical activity in neuronal membranes. The achievement will help scientists better decipher how brain cells function and interact.
In third place was research by a multi-institution team, headed by Sharon Reed in the UC San Diego Departments of Pathology and Medicine and James McKerrow at the UC San Francisco Sandler Center for Drug Discovery, that identified an existing drug was also effective against Entamoeba histolytica. This parasite causes amebic dysentery and liver abscesses and results in the death of more than 70,000 people worldwide each year. The findings were published in the June issue of Nature Medicine.
You can read more about all of the 2012 selections below.
Fast-acting dyes highlight membrane activities of neurons (R. Tsien, E. Miller, et al.)
Researchers induce functional Alzheimer’s neurons in vitro from pluripotent stem cells (L. Goldstein, et al.)
New weight loss surgery folds stomach into smaller size (S. Horgan, et al.)
New surgical technique may reverse paralysis, restore use of hand (J. Brown, et al.)
New technology pinpoints source of irregular heart rhythms, improves treatment (S. Narayan, et al.)
Novel enzyme target identified for anti-malarial drug development (L. Bode, et al.)
New method indentifies whether leukemia will be aggressive or slow-moving (T. Kipps, et al.)
Patterns in adolescent brains could predict heavy alcohol use (S. Tapert, et al.)
Potency of statins linked to muscle pain and weakness (B. Golomb, et al.)
Neural stem cells regenerate axons in severe spinal cord injury (M. Tuszynski, et al.)
New way of fighting high cholesterol upends assumptions (C. Glass, et al.)
Blocking tumor-induced inflammation impacts cancer development (M. Karin, et al.)
Study finds potential new drug therapy for Crohn’s disease (W. Sanborn, et al.)
How the Nose Knows
Whether we’re awake or asleep, and whether an odor is familiar or new, appears to determine our response to smells. Since we know that smells are highly evocative as well as serving to warn us of danger like smoke or spoiled foods, how the brain perceives odors is of interest to scientists.
Researchers at the University of California, San Diego School of Medicine wondered how sensory representations, in this case the sense of smell, are shaped by the state of an animal and its history. They studied this question in the mouse olfactory bulb, the part of the brain involved in the perception of odors.
Their major conclusion is that the way in which sensory information such as odor is represented isn’t fixed or static, but highly dynamic and flexible. It is modulated by brain state such as wakefulness, experience, even by simple sensory exposure to smells. According to the researchers, his could be the basis of why novel or unfamiliar odors are such noticeable stimuli for humans, compared to familiar odors.
Using a powerful means for monitoring the activity of brain neurons in mammals – called two-photon calcium imaging – the UC San Diego team, headed by Takaki Komiyama, PhD, assistant professor in the UCSD Department of Neurosciences, recorded the activity of specific neuronal cell types in mice, following the activity of the same set of neurons over days, weeks and months.
With this technique, the researchers explored how wakefulness and odor experience modulate the activity of two neuron types in the olfactory bulb, namely mitral cells – the principal neurons of the bulb – and granule cells, very small brain cells that account for nearly half of the neurons in the central nervous system. Granule cells are the major class of interneurons that inhibit mitral cells.
The team imaged the activity of mitral and granule cell populations in awake mice, and subsequently anesthetized the mice to find out how odor representations differ between the awake and anesthetized state. They found that anesthesia increases odor responses of mitral cells. In contrast, granule cell activity is dramatically reduced with anesthesia. These results suggest that, in awake animals, mitral cell odor representations are made sparse by the action of local inhibitory circuits, and that studies in anaesthetized animals may have underestimated the actions of granule cells.
Next, the researchers looked at how mitral cell odor representations in awake mice are shaped by experience. By monitoring the response of same sets of mitral cells to a panel of odors, they found that repeated odor experience causes a gradual lessening of mitral cell responses which accumulates across days. This change is odor-specific – the same mitral cells still respond strongly to other smells. The plasticity, or ability of the neuronal connection to change in strength, recovers gradually over months.
“Intriguingly, this plasticity is not expressed when the mouse is tested under anesthesia, indicating that wakefulness plays a key role in the dynamic nature of mitral cell odor representations,” Komiyama said.
“All available evidence from comparative genetics and neuroanatomy suggests that mouse and human olfactory systems function similarly,” he added. “We have many reasons to believe that what we found in this study in mice directly translates to the perception of odors in humans.”
Card 10 in Hermann Rorschach’s original inkblot series. You can see the entire series and how Nazi leaders Adolph Eichmann, Hermann Goering and Albert Speer interpreted the images here, courtesy of Cabinet magazine
Judgments after Nuremberg
As a young professor of psychiatry in the 1970s, Joel E. Dimsdale studied concentration camp survivors – and their families – in the years after World War II. What were the psychological consequences of their suffering and trauma? What mechanisms did they use to cope?
One day a man came to visit Dimsdale at his Boston office. He had heard the professor speak and believed Dimsdale should study another group as well: the Nazi perpetrators who had conceived and implemented the camps that resulted in the murder of millions.
The man said he had met some of Nazi leaders.
The man had killed some of them.
“He was one of the executioners at the Nuremberg trials,” recalled Dimsdale, now a professor emeritus in the UC San Diego School of Medicine.
The trials, of course, were a series of highly publicized, history-making military tribunals held by Allied victors to judge and punish the surviving remnants of Nazi German leadership after the war. Scores of political, military and public officials were tried, most notably 22 defendants in the Bavarian city of Nuremberg over several months in 1945 and 1946.
These were some of Nazi Germany’s most notorious leaders: Field Marshall Hermann Goering, deputy Fuhrer Rudolf Hess, army head Wilhelm Keitel, SS leader Ernst Kaltenbrunner, and interior minister Wilhelm Frick, who had co-authored the Nazi’s anti-Semitic Race Laws introduced in 1935 in, ironically, Nuremberg.
Though Dimsdale continued and expanded his psychiatric research, ultimately conducting hundreds of studies about stress, sleep and how patients cope with severe illness over a long and distinguished career, he took the advice of the Nuremberg executioner and eventually wrote a book about the trials and efforts to better understand the psychology of the accused.
“One of the great questions of psychology is the anatomy of malice,” said Dimsdale, “and nowhere is that subject more compelling than in trying to explain the behavior of the accused war criminals at Nuremberg. Were they inherently depraved monsters or ordinary men corrupted by power and circumstances? Were they somewhere on a continuum of human behavior or distinctly different? How did they get that way?”
Meat your maker
When you sit down on Thursday and give thanks, start perhaps with the fact you’re not eating the (Petri) dish above. At least not yet.
What you’re looking at is not “synthetic” meat, but in vitro or cultured. Apparently, there’s a difference. Synthetic meat typically refers to imitation edible animal tissue made from a vegetable source, often soy or gluten. In vitro meat (which has other monikers, including the less-than-appetizing “shmeat”) is grown from scratch using muscle cells.
“This is real meat because it is made of the same cells that meat is composed of,” said Gabor Forgacs, one of the men behind Modern Meadow, a company with plans to use three-dimensional bioprinting to eventually produce in vitro edible meat products. (The company will start first with simple leather products because it’s easier to create and grow skin cells than muscle.)
While there’s no obvious demand for in vitro meat at the moment, its proponents say there is a need. Natural meat – the kind that originates from actual animals – is increasingly expensive, ecologically speaking. Using conventional methods, it takes 6.7 pounds of cattle feed, 52.8 gallons of water, 74.5 square feet of land and 1,036 BTUs of fossil fuel energy (enough energy to power a microwave oven for 18 minutes) to produce a quarter-pound of hamburger, according to the Journal of Animal Science.
In vitro meat production requires only a fraction of those resources.
However, don’t go looking for a lab-grown steak anytime soon. Technological advances have made bioprinting – a process in which biological elements like cells in a liquid form can be laid down upon each other in complex, three-dimensional formulations – more feasible, but nobody’s making anything yet that resembles a turkey breast or pork chop. Indeed, Modern Meadows short-term goal is to print edible slivers of meat two centimeters by one centimeter, less than half a millimeter thick.
The big cell
Proponents of the “3D Virtual Cell” hope the imagined project will do for biology what the Large Hadron Collider did for particle physics – without the cost and time involved in digging a giant hole in the ground.
The idea is to create a virtual, rather than physical, framework and resource to gather together every studied and known aspect of molecular and cellular biology in a way that can be understood and used by practicing scientists.
It’s a major undertaking, and with support from the National Science Foundation (NSF), researchers at the University of California, San Diego are taking some first steps with a year-long series of workshops. The first – “Toward the 3D Virtual Cell” – is scheduled for December 13-14 at the California Institute for Telecommunications and Information Technology (Calit2) on the UC San Diego campus.
“Many of the top names in cell biology and cyberinfrastructure will join us to explore critical areas and challenges facing anyone who attempts to build a resource of this magnitude,” said Phil Bourne, principal investigator on the NSF grant and a professor of pharmacology at UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences at UC San Diego.
“Cell biology occurs at many scales, and a resource for modeling and visualization must operate on an increasingly large, diverse, complex and widely-distributed body of digital biological data.”
To explore this field, conference attendees will be asked to address the grand challenges facing whole-cell modeling, and what computational, sociological or other obstacles must be overcome in order to the resource.
“You can think of it as a giant app store of freely-available, open-source software, data, educational materials and expertise that would become the go-to resource for researchers in the life sciences, no matter what biological scale they are working at,” said Bourne.
The workshop is open to university researchers as well as scientists from other La Jolla institutions that focus on life sciences research, among them the Salk Institute for Biological Studies, Sanford Burnham Medical Research Institute, The Scripps Research Institute, La Jolla Institute for Allergy & Immunology and the Sanford Consortium for Regenerative Medicine.
Click here for registration information or contact Stephanie Hagstrom at 858-534-1219 or email@example.com.