2009 Video, as part of State of Tomorrow aging TV series

December 4, 2008 Lecture

Video tutorial for a high-throughput method for quantitative measurement of chronological life span. This method involves aging the cells in a defined medium under agitation and at constant temperature. At each age-point, a sub-population of cells is removed from the aging culture and inoculated into rich growth medium. A high-resolution growth curve is then obtained for this sub-population of aged cells using a Bioscreen C MBR machine. An algorithm is then applied to determine the relative proportion of viable cells in each sub-population based on the growth kinetics at each age-point.

We developed a web-based database server, called Gerontome, which contains aging-related gene information and user-friendly analysis pipelines. To construct the Gerontome database, we integrated aging-related genes and their annotation data. The aging-related genes were categorized by a set of structural terms from Gene Ontology (GO). The analysis pipelines for promoter analysis and protein-ligand docking were developed. The promoter analysis pipeline allows users to investigate age-dependent regulation of gene expression. The protein-ligand docking pipeline provides information of the position and orientation of a ligand in age-related protein surface.

The Digital Ageing Atlas is a portal of changes covering different biological levels. There are currently portals for both humans and mice. The idea is to integrate molecular, physiological and pathological age-related data and create an interactive portal that serves as the first centralised collection of ageing changes and pathologies. The portal provides a centralised source for the database as well as basic tools to query and view the data stored within; For a more detailed analysis you are able to download the entire database. For more information on how to use the portal please consult our help page

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 721,721 binding data, for 6,179 protein targets and 316,172 small molecules.

"As research budgets tighten at universities and federal financing agencies, a new crop of Web-savvy scientists is hoping the wisdom

Interesting to see how tree aging compares with yeast/animal aging

The Brain Systems, Connections, Associations, and Network Relationships (a phrase with more words than strictly necessary in order to bootstrap a good acronym) assumes that somewhere in all the chaos and noise of the more than 20 million papers on PubMed, there must be some order and rationality.

To that end, we have created a dictionary of hundreds of brain region names, cognitive and behavioral functions, and diseases (and their synonyms!) to find how often any two phrases co-occur in the scientific literature. We assume that the more often two terms occur together (at the exclusion of those words by themselves, without each other), the more likely they are to be associated.

"Much of the literature describing the search for agents that increase the life span of rodents was found to suffer from confounds. One-hundred-six studies, absent 20 contradictory melatonin studies, of compounds or combinations of compounds were reviewed. "