Introduction to Biotechnology

An excellent  lecture by Eric Lander (MIT) on the conceptual basis  of recombinant DNA techology.

Implications of Biotechnology and Genomics for Nursing Practice

 As discussed in the video below, the Biotechnology revolution has  very  important implications for Nursing  Education and  Practice.

Next generation DNA sequencing strategies

Dr. Mardis, one of the pioneers in using next generation sequencing strategies to  understand human disease, talks about recent developments.

The Million Mutation Project: A new approach to genetics in Caenorhabditis elegans

This is an interesting resource paper. The investigators have generated  a library  of  mutagenized    C. Elegans strains. What's new is that  each member of the library  has been sequence verified to identify  mutant alleles that cover all known C. Elegans genes.  The paper is  from the Waterston lab and is open access.

CT's Alexion is one of the Three Best-run Biotechnology Companies in the USA !

Alexion was recently written up as  one of the three best-run Biotechnology companies  in the USA .

"Alexion's focus on ultra-rare diseases has led to ultra-rare results. The biotech achieved a 15.1% ROIC over the past year. Its five-year average of 21.6% is even better. 
Earnings growth has been stellar. Alexion's net income over a trailing 12-month window increased 49% during the last year. Over the past five years, Alexion saw earnings skyrocket by more than 460%.
The company's CEO, Dr. Leonard Bell, helped develop Soliris, which treats the rare diseases paroxysmal nocturnal hemoglobinuria and atypical hemolytic uremic syndrome. Bell co-founded Alexion in 1992 and led the company through its IPO four years later. He also was instrumental in Alexion gaining regulatory approval for Soliris and successfully launching the drug. Along the way, Alexion has received several honors, including being named the world's second-most innovative company by Forbes in 2012. "

The Origin of GENENTECH

A very interesting reflection on  GENENTECH, one of the  original Biotechnology companies.

Jobs in Academic Research Labs

Biotechnology graduates  typically look for jobs with large Biotechnology companies and are generally unaware of the excellent   career  development possibilities   presented by small academic research labs.  In small academic research labs,  there is often a more significant  focus on discovering  new technologies that are yet to be found in mainstream Biotechnology. Thus,  employment in an academic research lab often significantly  enhances the career trajectory of Biotechnologists.  In this post , we report the recent round of Stem Cell funding in CT, which will likely  have the effect of increasing the number of entry level positions  in academic  Biotechnology labs.


"Nine scientists at the University of Connecticut Health Center received grant awards Monday totaling $4.5 million from the Connecticut Stem Cell Research Program, making UConn the largest recipient of the $9.8 million total grants awarded this year."

CT Innovations funds new Biotech Companies

CT Innovations awarded  start-up funds totaling  $560k to  four new Biotech companies in the Hartford area.  

AMGEN is in Rhode Island

AMGEN, one of the original Biotechnology companies  has a manufacturing plant in R.I. It makes Enbrel and it runs 24/7 !

The discovery that launched Biotechnology

Herb Boyer and Stanley Cohen discuss their discovery of recombinant DNA cloning, the foundation stone of Biotechnology and Genomics.

Undergrads find improved antifreeze in beetles !!

A team of Yale undergraduates in the iGEM competition  has discovered the structure of  the most powerful known antifreeze to date!

Biotechnology and Cosmetics - Making Oils from Algae

An interesting article describing the road from  making  green fuels to  making  "niche"   oils for cosmetics. Want to know more about Biotech and algae check out the video !

Students at Salt Lake Community College form their own Biotech Company !

STUDENTfacturED a novel student-run company  is now up and running !

  "As many of you know, Salt Lake Community College has established a student-run company called STUDENTfacturED that provides students with an opportunity to "work" in a real, biotech manufacturing environment.  STUDENTfacturED is focused on making supplies to support biotechnology instruction.  The company is a NSF-funded project and involves not just students from our college's Biotechnology and Biomanufacturing programs, but also students, and faculty, from the School Business who provide the necessary business support to make STUDENTfacturED a complete business enterprise.
     We are about to launch our first product.  This product is a sample of a plasmid unknown.  Many of you teach the following skills in your courses:

• DNA concentration determination: sample preparation
• restriction mapping: restriction enzyme digestion set-up; restriction fragment prediction and analysis
• buffer preparation:  lab math calculations; measurement of dry and liquid materials; pH measurement
• agarose gel electrophoresis:  running buffer preparation; gel preparation; sample preparation; gel loading
• data analysis
• lab report writing

The plasmid unknown allows you to easily assess your students mastery of the concepts and techniques related to these skills.  An instructor's guide on how to execute these assessments is also available."

The iGEM DNA library is at Capital

The ability to create  new functions by combining  DNA elements is the heart of Biotechnology. Recently Capital joined the  iGEM competition and received the  2013 version of  the iGEM  DNA library.  This  iGEM  library  is a collection of  DNA plasmids   containing elements  that  are biosynthetic enzymes  , DNA  modification  enzymes ,  biosensor elements , fluorescent elements and gene regulatory elements. The key to the iGEM  system is the ability  to easily recombine these  elements to make new plasmids . Such plasmids may  provide new solutions to contemporary  societal and  environmental problems.   For example , one might be able to make a plasmid that permits  a bacterium  to covert carbon dioxide  into gasoline.

  Thus,  this library provides a unique  platform   that  may enable  the generation  of novel   synthetic biology projects  by faculty and students.

Beneath is an animation video produced by one of the iGEM teams, that explains the  concept.

iCell - An Educational app to view the Cell

iCell is a very cool educational app that allows neophytes and experts to view the cell.

What do biotechnology graduates get paid ?

What do biotechnology graduates get paid in California? CA Community Colleges publish salary info for different  degrees.

A Micro Benedict’s assay for the Determination of Glucose

The determination of glucose by Benedict's solution is a staple activity in Biotechnology  labs.  The classic format is to set up a large-scale reaction (5-10 ml) in glass tubes and boil until the desired reaction occurs. In the education lab this is a slow procedure and potentially fraught with problems.  Benedicts solution contains alkali and large volume boiling alkali solutions in an open tube are always a potential hazard.  Here, we suggest a micro procedure that can be done in a standard heating  block. 

Reactions are assembled in Eppendorf centrifuge tubes.  The unknown sample is Q’d to 250ul. Benedicts (250uL) is added and the tubes are closed (lid locks can be used if needed) and are heated at 70 degrees centigrade in a thermal block. Color development is monitored (usually takes 5-10 minutes) by negative and positive controls and the presence of glucose in the unknown determined.

In an inquiry driven exercise  this   rapid method is useful since it permits many determinations  of glucose in even a short lab session.

Here is an example from a recent  Inquiry exercise. 

 

Dr Robert Langer - How to be a Biotech Entrepreneur

In this article Dr  Robert Langer describes his experiences in  translating lab discoveries into Biotechnology start-up companies.  

New complex to be built by Alexion in New Haven may generate 200-300 Biotech Jobs

"Dr. Leonard Bell, founder and chief executive officer of Alexion, who heads a company with a presence in 30 countries, said he expects New Haven will become a major bio-pharmaceutical hub and drive economic growth here and elsewhere in Connecticut"

"The state has agreed to provide $51 million in assistance if Alexion generates 200 to 300 more full-time jobs by 2017, in addition to the 350 it will bring to the city in its move from Cheshire."


"U.S. Sen. Richard Blumenthal, D-Conn., said the groundbreaking is also “a celebration of individual daring and risk taking and adventure ... It’s because of people like Lenny Bell that the American economy and America itself are the greatest in the world. Risk-takers and the scientists who invest of themselves in new enterprises are what ultimately will distinguish our nation on the world scene."

Naturally occurring human sequences such as BRCA1 and BRCA2 are no longer patentable

The Supreme Court has decided that naturally occurring human  sequences are no longer patentable.  This case  was on the use of the gene patents for  BRCA1 and BRCA2 genes in the diagnosis of inherited breast or ovarian cancer.  However, the court indicated that  derived  cDNA sequences may be patentable.   This decision has profound general  implications for the Biotech industry and is discussed in this article

Genomics Impact on U.S. Economy Approaches $1 Trillion !

A recent article in the journal  Science indicates  that the research investment in Genomics has boosted the US economy by 1 trillion !

Large Scale Restriction Enzyme Digestion of DNA

The  preparative digestion of DNA with restriction enzymes is a core technique in all Biotechnology labs. Here we describe a best practices approach.  One of the key factors in obtaining complete digestion of plasmid DNA is the  quality of the DNA.  Its important that  RF1 (or supercoiled ) plasmid is the predominant form. Presence of  substantial amounts of RFIII is usually indicative  of significant  DNA nicking.  Usually  the most important factor is that the DNA  is free from  the reagents used to purify it. For example,  even very small  traces of Phenol and  SDS can exert a significant inhibition of restriction enzyme activity.  Elsewhere is this blog,  we will describe a robust routine  method  of  plasmid DNA purification.

In the example below, 20ug of  PBR322 plasmid  were incubated  in a reaction (20uL)  containing  1X NEB buffer 2  and 10 units of HindIII. Before adding the enzyme,  a sample (1ul)  was withdrawn.  After incubation for 30 minutes at 37 degrees, another sample (1uL)  was withdrawn from the reaction.   The "before " and "after " samples were run  on 1% agarose gel electrophorsis.
As can be seen from  the picture,  complete digestion was obtained.  Subsequent work up of the DNA digest depends on its future utility  and will be discussed in that context in other posts.

 

The Bradford Reagent for Protein Determination

The Bradford Reagent  is the current  standard for protein determination, but it is quite expensive .   Most educational  exercises still use  the Biuret method since it is much more economical. However, the Bradford method is the one that  most  Biotechnology graduates  will  use in the workplace and so  it is important  to use this reagent in Biotechnology technique courses.

 Here, we describe  how to make  Bradford reagent  in economical fashion  from  readily available laboratory reagents.

Add Commassie brilliant blue ( 50mg) to  Methanol (50ml) , then  slowly add  100ml of phosporic acid , Q to 1 litre with dH20 .

TAE - A Classic Electrophoresis Buffer

TAE is available  commercially but can readily  be made in the Biotechnology  lab. Here is the recipe for a 50X stock.

To make 1 litre :
 Add  Tris base (242g) to  57 mL of Acetic Acid  and 100ml of 0.5M EDTA.  Q to 1 litre with dH2O .

Tips on PUBMED

In the two year college environment,  it can be difficult to access the full text  version of research papers.  Typically, after a PUBMED search ,  students can be discouraged when  they are faced  with a  journal paywall. However, unless the paper is very recent ( within the last 6 months)  the vast majority of papers  are available  through  PMC ( the free access version of PUBMED) . So  just "google"  NCBI   PMC  and that will take you to the front door !
For very recent papers , one can request a  pdf from the author.  In many journals , this is expedited by a simple online request.

Connecticut Legislature Approves Transformational $1.5 Billion Investment in UConn

The next generation initiative  has passed  final approval  and will commit 1.5 billion dollars to an Institute of Systems  Genomics. Combined with the previous Bioscience initiative ( Jackson Labs ) , this will result in  a significant increase in  Biotechnology jobs in Connecticut.

An Economical Alternative to Ethidium Bromide for Visualization of DNA ?

Ethidium bromide is the classic reagent for the detection of nucleic acids on agarose gel electrophoresis. However, it is a recognized mutagen and care and attention are merited in its use. In the research lab, it is quite easy to regulate its use, since the personnel are aware of the  issues. However, in the education lab  the potential for accidental exposure is high.   Other less toxic reagents such as the SYBR series have  come into use, but they are significantly more expensive than Et BR.  So, in this post, we have examined whether the SYBR reagents can be directly added to the sample. If this works, it would avoid the need to include the visualization reagent in the agarose gel and thus be a significant saving, especially in an education environment. As shown in the picture,  increasing amounts of SYBR green  were added to 100ng of DNA marker ladders,  1ul of a 1/1000 dilution of SYBR green is sufficient to visualize 100ng of DNA (lane 3).

Thus SYBR  green  is a safe,  effective and economical reagent to visualize DNA.

Capital Loading Dye - Native Gel Electrophoresis

Sustainability is key to the running of Biotechnology courses. Paradoxically,  it's the small items that consume the most. One staple in the lab, is Native Gel loading dye which is used in  native gel electrophoresis  of DNA, ssRNA and Proteins.  Here is a reliable recipe  to make enough gel loading dye for a semester .

Fill up a  15ml  tube with  glycerol to  5ml , add  BPB (2ml of 1% ) , XC (2ml of 1% ) and EDTA ( 20uL  of 500mM) . Q with dH20  to 10 ml and aliquot  ( 100ul ). This provides a 10X loading dye.

The attached picture shows  plasmid DNA and ladder markers run  on a  1% agarose gel electrophoresis  in 1XTAE buffer using Capital Loading Dye. Image captured with iPhone .

50% of STEM jobs do not require a degree from a four year College !

A recent Brooking report  indicates that  50% of STEM  jobs do not require  a degree from a four year College and  these jobs pay $53,000 on average. 

Genomics and Us

An interesting article that makes the case  that Biotechnology should be more intensively applied to public health problems.

Sequencing the Genomes of a Million Veterans

The US Department of Veterans Affairs (VA) intends to sequence and analyze the complete genomes of more than 1,000,000 veterans.  It is hoped that these studies may shed light on the  inherited factors that may  modulate  the risks  of veteran associated disease.

A simple Semi-Quantitative Determination of Nucleic Acid

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Establishing a Biotechnology training program in a high school or two-year college environment is challenging.  Many of the basic techniques are quire sophisticated and use  “big ticket “ equipment items. In these posts we will explore ways to present Biotechnology using elements typically found in high school or two-year college labs.   One key problem with high school or two year environments is that   there are not working labs near by that can provide reagents that work, so troubleshooting is a significant endeavor.  Many Biotechnology methods take time to run, so it is an advantage to have a quick determination method. In this first example we are going to demonstrate a simple method to determine the presence of nucleic acids using SYBR  green, a UV light source and an iPhone or iPad.

Here is the protocol:

All volumes are in uL

Tube	tRNA (10mg/ml )	SYBR green 1/100	H2O (Q to)
1	-	1	100
2	1	1	100

tRNA is a convenient economical source of nucleic acid and has enough duplex structure. The reaction is assembled and placed on a UV transilluminator. A cardboard box with a hole serves as a portable darkroom and the image is recorded by an iPhone or iPad.

 

What is Biotechnology ?

A video  of a typical Biotechnology class 

Basic Techniques in Biotechnology will be offered at Capital in Fall 2013

 We are delighted to announce that "Basic Techniques in Biotechnology" will be offered at Capital in Fall 2013.  This 4-credit course provides training in the basic skills needed by a Biotechnologist.  Such basic skills include accurate pipetting, preparation of solutions, growth of bacteria, basic microscopy,  Bioinformatics, preparation of  DNA, agarose gel electrophoresis, and PCR amplification of DNA.