Fall is here; faculty job search begins

The first hints of fall are in the air. The cool evenings herald the end of the summer and the beginning of the fall. What a summer it has been. I married the love of my life and we traveled to London, Tanzania, and Zanzibar in a three-week honeymoon. Africa turned out to be all that it was purported to be, enchanting Lily and I. We know that this will not be the last time we visit.

Now that summer is coming to an end, a new season begins. Most of you will think of fall and of leaves changing. In some sense I will be thinking of that too. But the fall also means the beginning of the faculty search cycle. This year I will be joining that cycle. There are many things that need to be done. Proposals are being written and rewritten, talks need to be arranged and prepared, and trips around the country are being organized. I have prepared for it, as much as I can, but it is still a daunting and foreboding path. I am stepping out from a secure and relatively safe environment of working in someone else’s laboratory and crossing the line to being the leader in my own laboratory.

I am excited about the chance to talk to other scientists and researchers about my ideas and how I think that I can contribute to the institutions that I will be applying to. I know there will be some moments over the next few months that this will seem a daunting task, but I am lucky to have good mentors and a great support group. Stay tuned to progress reports and I’ll see you on the other side.

Thermoplasma acidophilum -a model organism to study iron stress in microbes?

Thermoplasma acidophilum. Linda Stannard, UCT/Photo Science Library.Microbes require iron (Fe) as an essential element for growth and development.  It has two environmentally stable oxidation states (II and III) readily participating in redox reactions covering a wide magnitude of biological electron transport and redox reactions including respiration, oxygen activation and binding, degradation of peroxides and superoxides, synthesis of DNA, proteins, and other organic molecules, and energy fixation pathways.  At the same time, unregulated iron uptake can lead to toxicity, reactive oxygen species (ROS) and to inhibition of growth.

Microbes have evolved an iron storage mechanism used to store iron under limiting or environmental stress.  The most studied system is that in Escherichia coli which produces three structurally and chemically related storage proteins; ferritins, bacterioferritins, and Dps (DNA-binding proteins during stationary phase).  Ferritin and bacterioferritin are a tetracosameric structures capable of storing 2,500 and 1,800 iron atoms respectively. Bacterioferritin differs from ferritins in that they have an iron protoporphyrin IX (heme) at the interphase of each subunit.  Dps is a dodecameric ferritin, which is induced under stationary phase of growth or by oxidative stress.  These supramolecular structures help sequester iron in the cytoplasm and prevent toxicity of free iron in the cytoplasm.

Microbes living in low pH environments are subject to high concentrations of metals, in particular iron.  How these microbes respond to metal stress is key to understanding how organisms control energy producing metabolic reactions in the cell.  Recently, the genome of T. acidophilum was completed affording us a glimpse of the possible biochemical pathways responsible for the survival of this organism in an acidic environment, but analysis of the T. acidophilum genome did not reveal any molecular pathways for the production of known iron storage proteins ferritin, bacterioferritin, or Dps.

How does T. acidophilum manage the high concentrations of soluble iron, or other metals, liberated by its acidic environment?  Does this organism have a novel iron storage mechanism?   What are the cellular responses to stress to T. acidophilum cause by high metal concentration in the cytoplasm or by ROS?  This is one of the questions that I am trying to answer using transcriptomics to look at differential gene expression of this Archeaon under varying iron and other  environmental stress conditions.

Joost Bonsen – Maximizing Progress

I ran into Joost on Thursday of last week at Bosworth’s Cafe in Lobby 7 at MIT.  As usual, ended talking about one of our favorite subjects, emerging technologies and the developing countries.  Joost is a good friend with whom I have shared many beers at the Muddy Charles pub.  He is one of those people that makes MIT such a great place to be.  Joost is interested in everything dealing with global startups, social enterprises, sustainability, innovation, and technology.  He runs the blog Maximizing Progress, in which he shares stories about people, ideas, technology, and just plain cool stuff that happens around MIT and the world.

I love spending time with Joost as we usually end up kicking back some tasty brews, discussing and sometimes pushing to the limit ideas dealing with the plight of humanity and how science, technology, and engineering can provide answers to some of the issues facing the developing world.  Just a little of what he does around MIT and Cambridge: HighTech Fever on Cambridge Community TV; teaches various seminars and classes at MIT; The Muddy Charles Pub; Techlink; MIT Enterprise Forum; HowToons.  If you see him around campus, definitely stop him and introduce yourself.

TED: Ideas Worth Spreading

TED Logo

I remember the first time I visited the a TED conference (it stands for Technology, Entertainment, and Design) website.  Jarrett, a good friend who I blogged about, introduced me to a video from Aubrey de Grey called Why we age and how we can avoid it.   de Grey  has very interesting ideas regarding the disease called aging and what modern science and engineering can accomplish to minimize and prevent the causes and effects of aging and dying.  I instantly became hooked on TED!a

Since then I have become a regular visitor to the TED site, logging on and listening to talks ranging from evolution and god, to design and emerging technologies.  This is one of the few places that I can go and get inspired by the stories and the vision of incredible thinkers and doers.  TED expanded my view of the relationship between ideas, design, innovation, and the development of technology to benefit every part of humanity.