Category: Educational

“Meat 2.0”

Posted by – December 1, 2009

In synthetic biology conferences, engineering improvements of food is listed in the top three applications of the new technology. As an example, George Church’s lab developed a genetic engineering technology specifically aimed at evolving super-tomatoes containing high amounts of the anti-oxident lycopene, as proof-of-concept.  Frequent brainstorming “what could syn bio do?” sessions include ideas of growing thick beef steaks without the cow: in essence, this is presumed to be an improvement on quality, cleanliness, nutrition, and animal rights, than today’s factory-farming method of bringing steak to the table.

What if there is already a better “steak”?  Let’s call it Meat 2.0.  How about modifying Rhizopus oligosporus, the fungus used in making tempeh, to create new tastes or additional vitamins?  Note that the below article states, “cost of preparing 1.5 kg of tempeh was less than US$1.”

Nutritional and sensory evaluation of tempeh products made with soybean, ground-nut, and sunflower-seed combinations

M. P. Vaidehi, M. L. Annapurna, and N. R. Vishwanath
Department of Rural Home Science and Department of Agricultural Microbiology, University of Agricultural Sciences, Bangalore, India


Tempeh products made from soybeans and from combinations of soybeans with ground-nuts and sunflower seed at ratios of 52:48 and 46:54 respectively were tested for their appearance, texture, aroma, flavour, and over-all acceptability. In addition, tempeh was prepared with and without the addition of bakla (Vicia faba) to soybeans in various ratios to obtain a tempeh of acceptable quality and nutritional value (1). Bakla tempeh at a 1:1 ratio was found to be crisper and more palatable than plain soybean tempeh, but at 3:1 the tempeh had a mushroom odour.



Tempeh culture (Rhizopus oligosporus) was obtained from the New Age Food Study Center, Lafayette, California, USA. It was grown on a rice medium and inoculated while different blended tempehs were prepared. A 2.5 9 packet of culture was used for 250 9 of substrate on a dry weight basis.

Soybeans (Hardee), ground-nuts (TMV-30), and sunflower seed (Mordon) were obtained from the University of Agricultural Sciences, Bangalore. Three varieties of tempeh -100 per cent soy, soy-ground-nut (52:48), and soy” sunflower seed (46:54)-were prepared under identical conditions.

Preparation of Tempeh and Products


Stanford University: Programmable Microfluidics (2007) – Video

Posted by – March 2, 2009

October 3, 2007 lecture by Bill Thies for the Stanford University Computer Systems Colloquium (EE 380). Bill Thies provides an overview of microfluidic technologies from a computer science perspective, highlight areas in the which computer science researchers can contribute to this field; he will also describe recent work in developing new architectures, programming languages, and CAD tools for the microfluidic domain.

EE 380 | Computer Systems Colloquium:

Make some simple biology lab tools

Posted by – February 3, 2009

Sometimes biology lab tools are really simple, and ridiculously obvious (i.e., a petri dish?).   Yet most of the general public form the idea that biology, chemistry, or even nanotechnology, is impossible because we don’t have high-tech tools. Maybe it’s because the research papers always use big words, half of which are some form of Latin, or the tools are named after a dead guy with a crazy name (erlenmeyer flask anyone?).

Look at some of the tools used in most biology labs for proof.  Cheap office supplies are re-used as laboratory supplies.  Many biology tasks only need the most basic tool for pouring, scraping, mixing, holding, or electrocuting something.  These are easy jobs which only require simple tools.

A few more examples are provided in The Scientist article, Let’s Get Physical –
How to modify your tools to prevent pain at the bench
.   (Free registration might be required to view the article.)

Maybe some of the Makers out there will read this article and Make me something.  (Meredith wants to make something; I need simple lab tools.)

Play, the “Tetris-On-Steroids” game that solves protein folding

Posted by – January 29, 2009

“Protein folding” is what again?

It’s this: Foldit (curiously, at the web address: “”).  And it’s fun to play.  Addictive, really.  Check out the picture:

After I had been playing a while, my 8-year old niece came over to my laptop to see what the cute sound-effects were all about.  After a minute of watching, she said:  “Tell me the web site, I want to play too!”   Yeah, no kidding.


Web Seminar on Systems Biology: New Approaches, New Tools

Posted by – November 5, 2008

A 90-minute webinar (web seminar) on Systems Biology as a “new approach” in solving today’s health problems — includes summary of what systems biology is, how it is emerging as a current technology, and methods for addressing “systems medicine”.

Systems Biology: New Approaches, New Tools and Implications for Human Health Care

The original event was broadcast on:
Date: Thursday, October 30, 2008
Time: 1:00 PM EDT
Duration: 90-minutes

Presentation is performed by the Institute for Systems Biology.  Partially sponsored by Agilent Technologies.

My brief overview

Initial introduction includes overview of technical & market drivers, and convergence of science & technology to create the emerging field.

“P4” Medicine: predictive, preventive, participatory and personalized medicine.

What are the top revolutionary technologies today which will drive the next several years of research?

  • High throughput and inexpensive DNA sequencing
  • Using nanotechnology to measure proteins from small amounts of blood
  • Information technology

System Biology’s largest “unsolved problems”

  • Validated datasets are unavailable – the massive amount of data is not fully used and systems for analysis are not fully developed
    • Open-to-the-public databases for research information is very important

      • “it must be freely and publically available to all, including industry. […] Those publishing articles must take the extra step to continue improving the data after simply being published” – Akhilesh Pandey, M.D., Ph. D., Associate Professor, John Hopkins University
  • Proteomics is still in its infancy
  • Sharing data is difficult
  • Building blocks are still being built; building blocks means specific databases for specialized data
  • Drug industry develops many new drugs; “but what we really need is” to identify specific drug targets for specific diseases/conditions, for screening
  • Lack of qualified people working in the field
    • “Biologists have to take second major in an engineering science” — Leroy Hood, M.D., Ph. D., President, Institute for Systems Biology

A typical Proteomics and Metabolomics workflow

  • Reduce complexity – Fractionation (mRP/UV); immunodepletion; MRP, OGE; sample preparation for membrane proteins
  • Profiling differences – Profiling (ToF); glycan profiling; metabolite profiling; biomarker discovery
  • Identifying Compounds – Identification (IT, QToF); PTM; glycan ID; metabolite ID; biomarker discovery
  • Characterizing differences – Characterization (QToF); intact protein; de-novo sequencing; protein complexes; membrane proteins; metalloproteins
  • Targeted quantitation – Validation (QQQ); biomarker screening by MRM; metabolite screening (UV, GC/MS, QQQ, ToF, QToF, IT, CE-MS, ICP-MS)

Discussed web site links

In-Depth Review, Part 3 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – November 3, 2008

In my previous write-ups of Part 1 and Part 2, I traced the Perl code and examples in the first half of the book, Beginning Perl for Bioinformatics, by James Tisdall, highlighting different approaches to bioinformatics in Perl.  As I mentioned before, Perl provides many different (and often stylistic) methods to solving a software problem.  The different methods usually differ in execution speed, code size, code scalability, readability / maintainability, simplicity, and advanced Perl symantics.  Since this is a beginning text, the advanced Perl isn’t covered.. that means templates, which could be useful for parsing bioinformatics data, are one of the topics not included here.

Often, the fastest code is the smallest code, and contains subtle code tricks for optimization. This is a perfect setup, because, in Chapter 8, Tisdall starts parsing FASTA files.  With Perl’s parsing engine, the subtly of the tricks leaves a lot of room for optimizing software.

FASTA & Sequence Translation

Tisdall offers a software problem based on the FASTA data, so time to solve it:

Tisdall: When you try to print the “raw” sequence data, it can be a problem if the data is much longer than the width of the page. For most practical purposes, 80 characters is about the maximum length you should try to fit across a page. Let’s write a print_sequence subroutine that takes as its arguments some sequence and a line length and prints out the sequence, breaking it up into lines of that length.

Compare his solution to mine:

# Solution by Tisdall
# print_sequence
# A subroutine to format and print sequence data

sub print_sequence {

    my($sequence, $length) = @_;

    use strict;
    use warnings;

    # Print sequence in lines of $length
    for ( my $pos = 0 ; $pos < length($sequence) ; $pos += $length ) {
        print substr($sequence, $pos, $length), "\n";

The above is a straightforward, strings-based approach. I chose a regex approach, which took a couple minutes to work out, though should be faster during run-time:

sub dna_print {
  my $str = $_[0];
  do {
    $str =~ s/^([\w]{0,25})//;
    print "$1\n";
  } until (!length($str));

The above relies on the following method:


In-Depth Review, Part 2 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – September 8, 2008

My Part 1 of 5 review of the book, Beginning Perl for Bioinformatics, by James Tisdall, left off at Chapter 8, just before Tisdall explains associative arrays, gene expression, FASTA files, genomic databases, and restriction sites.

Tisdall: “For simplicity, let’s say you have the names for all the genes in the organism and a number for the expressed genes indicating the level of the expression in your experiment; the unexpressed genes have the number 0. Now let’s suppose you want to know if the genes were expressed, but not the expression levels, and you want to solve this programming problem using arrays. After all, you are somewhat familiar with arrays by this point. How do you proceed?”

Perl’s associative arrays are one of the most powerful aspects of the language.  This is a good problem to examine using hashes.  Solutions to this kind of problem in other languages (C or matlab) might create an N-dimensional array (or even NxM) as a matrix representation of the problem.  In C, it might be solved using a lookup table possibly using a linked list, and the code to drive that needs to be written from scratch or borrowed from an external library.  Perl has a built-in method to solve these kinds of problems.

The solution is to use a hash:

$gene_name = "triA";
$level = 10;
$expression_levels{$gene_name} = $level;  # save 'level' on per-gene basis

This leads Tisdall to review biological transcription and translation, including code for DNA->RNA and RNA->protein data conversion.  The code is given in long form and then optimized in further examples for speed using associative arrays.  Recall the central dogma of biology:


In-Depth Review, Part 1 of 5: “Beginning Perl for Bioinformatics” by James Tisdall

Posted by – September 6, 2008

As a specialized field, Bioinformatics is rather young.  It can be difficult to find universities which teach bioinformatics.  Bioinformatics can refer to many different types of tasks — from using programs and data without any computer science knowledge, to implementing database or web software, to writing data conversion programs which modify file formats between database storage methods, to writing algorithms for modeling and visualizing research problems.  Most of the work is described best as “computational biology”.

In the context of Perl (the famous computer language which runs underneath most web pages), Bioinformatics means computing text data retreived from biological databases.

The book, Beginning Perl for Bioinformatics, by James Tisdall, is for learning introductory software techniques in Perl, with a very brief biology review.  For biologists who have rarely programmed and need a starting language or need to learn Perl, this is a good place to start.  For technologists, note the copyright date on the book, to see how dated the information may be; since bioinformatics is still a young field, standards and technology are evolving rapidly.

Tisdall: “A large part of what you, the Perl bioinformatics programmer, will spend your time doing amounts to variations on the same theme as Examples 4-1 and 4-2. You’ll get some data, be it DNA, proteins, GenBank entries, or what have you; you’ll manipulate the data; and you’ll print out some results.”   (Chapter 4)

For software engineers or computer programmers, the biology field is also a completely new realm which is tough to get a handle on, and has it’s own language: Biology as a field (at least to me) has not yet differentiated itself between “soft, life science” and an engineering science.  For example, as a software engineer, the most basic software question is, “I need to write a look-up table for these elements, what are the all the possible strings for the field values?”  Yet this simple question can be very difficult to answer by consulting a biology textbook.  It is important to keep in mind that data manipulation for biology can involve massive amounts of information: also known as, very, very large strings; the strings represent DNA sequences which may range in practical usage from 10k to 100k.

Perl Bioinformatics Introductory Examples

The author states,

Tisdall: How do you start from scratch and come up with a program that counts the regulatory elements in some DNA? Read on.”

In chapter 4, there are the first simple Perl examples:  convert the DNA sequence to the corresponding RNA sequence.  In biology, the DNA uses A, T, G, C (representing the chemical names, of course); whereas RNA uses U instead of T.  Simple string manipulation provides the answer:  s/T/U/g;


Biology & Life Science Textbooks for Download via NIH

Posted by – July 6, 2008

Resources at NIH and National Center for Biotechnology Information (NCBI):

Entrez is the integrated, text-based search and retrieval system used at NCBI for the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others.

Of particular educational interest is the NCBI Bookshelf, a growing collection of biomedical books with fully readable content online and that can be searched directly.  For example, Harvey Lodish Molecular Cell Biology (4th edition) is downloadable or searchable; although this is an older version than currently published (2000), it is useful.

The first book to be made available at NCBI was Molecular Biology of the Cell, 3rd edn, by Bruce Alberts, Dennis Bray, Julian Lewis, Martin Raff, Keith Roberts, and James D. Watson, published by Garland Publishing, Inc. Molecular Biology of the Cell is one of the most widely used undergraduate textbooks in molecular and cell biology.

Can Microbiology Prove (the Intelligent Evolutionary Design of) God?

Posted by – October 2, 2007

DNA and biology is incredibly complex.  Is there any coherency to the design of organisms?  Is there an intelligent or systematic method involved in the creation of life and the reproduction of life?  There are exploratory studies on the study of the origin of life.

Antoine Danchin, Ph.D., Institut Pasteur

The Bacterial Core Genome is an Archive of the Origin of Life

speaking at the Institute for Systems Biology, 6th Annual International Symposium, 2007

Danchin is the first to repeatedly admit, “Don’t believe anything I am saying, I am a scientist, even I do not believe what I am saying [until it is repeatedly proven by data], I am not a priest, I am a scientist.”

By multidimensional data analysis, and years of looking at comparisons of genes and bases, he states that some similarities might be seen which hint at how evolution has happened through interesting and functionally required coincidence rather than a systematic or “intelligent” design.

Best not to argue with fundamentalists in the midwest at the current time, though.

How PCR Works to Modify DNA (& Build New Organisms)

Posted by – February 12, 2007

The fundamental construction step of building modified biological organisms is by using PCR.

The polymerase chain reaction (PCR) is used to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating millions or more copies of the DNA piece.  This is a chemical reaction involving a heat-stable DNA polymerase, such as Taq polymerase, which is an enzyme.  Small volumes of solutions are used, usually under 100 microliters (uL).  Using small amounts of solution saves on cost (the solutions are expensive) and can speed up the reaction.

An animation of PCR describes this process.

By using PCR, a customized piece of DNA can be replicated into an organism (typically a simple bacteria which reproduces rapidly).  When the bacteria reproduces, it makes a copy with the modified DNA.  After thousands of reproductions, a new colony of modified bacteria can be separated from the non-modified bacteria.  The genetically modified organism is saved, studied, and/or kept as a friendly pet.