Bioinformatics


Welcome to the first installation of Hourglass, a blog carnival devoted to the biology of aging. This first issue corresponds with the second blogiversary of Ouroboros, but mostly I consider it a celebration of the excellent (and growing) community of bloggers who are writing about biogerontology, lifespan extension technologies, and aging in general.

Without further ado, then, let’s get started:

Reason at Fight Aging! reports on AnAge, a curated database of longevity, aging, and life history in a wide range of animals. The database contains information about average and maximum longevity within species, and also cool features like lists of the “world-record” holders for the longest-lived organisms on the planet. AnAge will be a great tool for anyone interested in studying evolution of negligible senescence or exploiting lifespan diversity across related species to learn about mechanisms of aging. For those who are interested in databases of this kind, AnAge is a component of a larger project, the Human Ageing Genomic Resources.

The most widely studied technique for extending the lifespan of diverse animals is calorie restriction (CR), whose benefits in humans are still under careful study. One of the disadvantages of studying humans, of course, is that you can’t keep them in completely controlled environments, free from temptation to cheat on their defined diets — but this may be more than adequately compensated by the main advantage of human subjects, namely, that they can tell you how they’re feeling about the study while it’s underway. Over at Weekly Adventures of a Girl on a Diet, Elizabeth Ewen describes her experiences as a subject in the CALERIE study, a large-scale test of the effects of CR on humans (we’ve discussed CALERIE here before). In her post, Elizabeth describes the CALERIE study in detail, and also critically assesses some of its specific features — something that no mouse, however talented, could ever do.

While methods like CR may delay aging, or at least aspects thereof, they can’t stop it dead in its tracks — and they certainly can’t reverse large-scale age-related decline in tissue function. For those applications, we will have to look to more dramatic interventions, such as tissue engineering. In this exciting new field, biomedical engineers are seeking, essentially, to grow new organs for people whose originals have worn out due to injury, disease, or aging itself. One of the major challenges of tissue engineering is morphology: Even assuming that the appropriate sorts of stem cells are available, and that one can induce them to differentiate appropriately, how would one guarantee that they grow into the appropriate spatial architecture for efficient function? According to Attila Csordás at Partial Immortalization, one solution would be to use the “decellularized matrix hack“: to chemically or enzymatically remove the cells from cadaver organs, and then regrow new cells over the extracellular matrix left behind. (Since ECM is much more highly conserved than cell-surface markers, I suspect that such an approach could also be used to overcome immune rejection issues.) Attila’s post includes a video of the application of this concept to the heart.

Moving from the heart to the brain, we’re going to finish up with two huge posts about aging, mental fitness, and age-related changes in neurological function.

Ward Plunet at BrainHealthHacks writes about recent evidence that smarter people live longer. This is true whether your metric of intelligence is education (which could be problematic, as education levels are often correlated with lifelong affluence and access to medical care) or whether you’re looking at individual genetic variations correlated with both longevity and intelligence. It’s a giant post that quotes several articles from the primary literature as well as studies by international organizations. Nature, nurture, Ward has it all.

Assuming for the moment that long life and intelligence are associated — in which direction does the causal arrow point? We’re still unsure about that at the level of the whole organism, but in the case of brain health we know a bit more. At SharpBrains, Alvaro Fernandez interviews U. of Illinois’ Prof. Art Kramer, who describes ways that everyone can extend their mental healthspans and even delay the onset of age-related neurological dysfunction such as Alzheimer’s disease. That’s just the beginning of the lengthy interview, which goes on to talk about people’s desire for magical solutions to age-related declines in mental function, the results of prior studies, and the synergy between physical and cognitive exercise — among many other subjects.

Thanks for reading. I’m going to try to make Hourglass a monthly carnival on the second Tuesday of every month, so the next one will be held on August 12th. If you’re interested in hosting, please email me.

Advertisements

By now, some well-meaning friend has surely invited you to join an online community, for reasons either professional (e.g., LinkedIn) or personal (e.g., Friendster). I generally accept the invitations, if only because it seems a little rude not to.

Thus far, even the more professionally oriented networking systems have been of little use to me as a scientist. That might have just changed: The growing online empire of the Nature journals has started its own community, the Nature Network.

It works a lot like other networking communities: You can enter a personal profile, add links to your own publications, affiliate with subgroups of the network (like this one from the SENS Research folks), invite your colleagues to join up, and — presumably, someday — reap the benefits of massively parallel schmoozing, when a colleague of a friend of a graduate student of a former labmate realizes that the two of you should have started collaborating yesterday.

I’m still figuring out the bells and whistles, but I thought I’d notify those of you who happen to be scientists, so that you too can hop on board the MySpace of molecular biology…

(Via Partial Immortalization, where Attila Csordás has a detailed article on the features of Nature Network as compared to more established online social networking communities.)

The most recent issue of Nucleic Acids Research has a paper about something that I have no doubt will become a hugely valuable asset to those of us who are interested in age-related changes in gene expression: The Gene Aging Nexus. Pan et al.:

The recent development of microarray technology provided unprecedented opportunities to understand the genetic basis of aging. So far, many microarray studies have addressed aging-related expression patterns in multiple organisms and under different conditions. The number of relevant studies continues to increase rapidly. However, efficient exploitation of these vast data is frustrated by the lack of an integrated data mining platform or other unifying bioinformatic resource to enable convenient cross-laboratory searches of array signals. To facilitate the integrative analysis of microarray data on aging, we developed a web database and analysis platform ‘Gene Aging Nexus’ (GAN) that is freely accessible to the research community to query/analyze/visualize cross-platform and cross-species microarray data on aging. By providing the possibility of integrative microarray analysis, GAN should be useful in building the systems-biology understanding of aging. GAN is accessible at http://gan.usc.edu.

There’s such a flood of array data hitting the scientific presses every day, but everyone who wants to mine this data is basically stuck first solving a tedious, somewhat difficult common problem: Most experiments are different enough that it takes almost as much work to combine the data in a meaningful way as it would to repeat the experiments on a standard platform.

As anyone who’s tried to compare experiments performed on different arrays in different cell types (or species) in different labs can attest, this publicly available resource will be a huge boon to meta-analysis of gene expression data related to aging.

I just hope they’ll include some cellular senescence data, too, in subsequent versions of the database. Hint, hint.

Our short article on the Human Ageing Genomic Resources databases has been listed in the most recent issue of Bio::Blogs, a blog carnival devoted to “all bioinformatics and computational biology subjects.”

Bio::Blogs #2 is being hosted at Neil Saunders’ personal website, on his bioinformatics blog What You’re Doing is Quite Desperate. There are seven featured articles on a variety of subjects, four conference reviews, and a couple of other cool features.

I won’t ruin the surprise — if you aren’t coming here from there already, check it out. If you’ve stumbled across Ouroboros for the first time via Bio::Blogs, welcome.

(To Bio::Blogs readers: Welcome!)

I just discovered, and am in the process of checking out, Human Ageing Genomic Resources (HAGR) over at senescence.info, a site run by aging researcher João Pedro de Magalhães.

HAGR consists of two main parts: GenAge, a curated database of genes known or suspected to play a role in aging, and AnAge, a resource for comparative study of aging in different organisms (I am guessing that the “An-” comes from “Animal”). AnAge is big, with more than 3900 entries — most at the species level, but also at other limbs of the phylogenetic tree. GenAge is smaller, with only 243 entries, though these are hand-curated descriptions of every gene known to play a role in human aging, so it’s still a lot of information.

There is a bit more to the site, including a software package (the Ageing Research Computational Tools) and references to some tantalizing works in progress. One of these pertains to the evolution of aging in mammals and another (the Delta Projects) looks like it could evolve into a meta-analysis of expression profiles of aging. I find the last point particularly exciting: as someone who has done a bit of work trying to analyze multiple microarray data sets, I’m a firm believer that the more centralized resources there are within a field (to standardize data formats, at the very least), the better.

I’ll continue to explore the site, but I wanted to blog it in case it might come in handy for anyone else. If you want to do more reading, the resources are described in an 2005 article in Nucleic Acids Research.

« Previous Page