Environmental Sensors

I have been thinking of how to measure data in our upcoming field tests for the soil regeneration project. We need to be able to monitor several environmental parameters during these tests, such as temperature, humidity, light intensity, soil moisture, etc. We also want to be able to do this remotely, either with a wireless setup, a gpms shield, or RFID sensors, and be able to store the data onsite for future use. I stated thinking of how to do this best, so I did some research and it seems that using an Arduino / Raspberry Pi using Dragino or XBee style setup will probably work. Stay tuned for progress.

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.

OpenLabWare – demystifying the research process

OpenLabWare

George S. Zaidan ’08, while an undergraduate at MIT, ran into a conceptual problem while teaching a course for high school students (See The Tech article).  He asked his students to plan an experiment and in the process realized that most students did not understand the process of developing a scientific hypothesis and designing hypothesis driven experiments.  George conceived the idea of having an online presence for students interested in science to go and explore who was doing research and how they were doing it.  He called it  OpenLabWare. With the help of John Essigmann, his academic adviser, George started to assemble a working team.  He recruited other MIT undergraduates and worked tirelessly for three years, obtaining funding and academic support for his vision.

The process of research and scientific discovery still remains a mystery to most people.  But thanks to George’s ideas and hard work, more people can understand how scientists develop research programs and carry out their research.  OpenCourseWare provides a glimpse into the every day lives of the individuals who help develop the next generation of scientific and engineering discoveries.

What was your first experience with food or science?

Cooking at Lily's parents house in TivertonI remember the growing up and watching my grandfather cook.  He was a chef who loved French cuisine and made wonderful deserts.  I got my love of food and science from him.  He would sit there and tell me about what the heat would do to the sugar while I watched the sugar slowly caramelize.  I listened in rapture as he explained the changes in consistency the and flavor of caramel.  He also loved to make sauces and gelatin.  The gelatin kind of grossed me out, but the sauces always smelled so delicious and tasted even better.  I learned about blending the spices and about ratios and combination of ingredients.  I remember the care he always took in measuring ingredients, how he would clean and sterilize his work area.  How he seemed to cook from memory, but he always had his trusty notebook where he kept his notes on food and recipes.

These memories have wakened in me the desire to take the principles I practice in the lab, and transplant them into my kitchen. I love to experiment and think of new ways to prepare food.  Not just changing the flavor, but changing how it is cooked and prepared.  I am extremely lucky to have a partner who is as interested in cooking and creating good food as I am.  We share recipes, ideas, menus, and generally wreak havoc in the kitchen, but we create great meals.  She bakes and makes great deserts, while I love the salty and meaty foods.

I am lucky that I had a great introduction to food and the science of cooking at an early age.  I learned that food was much more than sustenance.  It excites and nourishes the soul just as it provides nourishment to our bodies.  Now more than ever, I miss my grandfather and I wish I could prepare a meal for him like the ones he prepared many times while I was growing up.

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