What is Biotechnology ?

An interesting  quiz on Biotechnology from Roche.

Maintaining curiosity: a survey into science education in schools

 A recent report from Ofsted  provides an analysis of the  successful application of inquiry based learning to science  education.

" Physicians take an oath that commits them to ‘first do no harm’. The best science teachers, seen as part of this survey, set out to ‘first maintain curiosity’ in their pupils. The most successful schools visited during this survey had adopted this as a key principle in teaching science and this not only fostered enthusiasm for the subject in their pupils but helped them to fulfil their potential.

We need better science education to secure a strong foundation for a successful and technological society. The new National Curriculum for 2014 sets out why we teach science in schools:

‘A high-quality science education provides the foundations for understanding the world through the specific disciplines of biology, chemistry and physics. Science has changed our lives and is vital to the world’s future prosperity, and all pupils should be taught essential aspects of the knowledge, methods, processes and uses of science. Through building up a body of key foundational knowledge and concepts, pupils should be encouraged to recognise the power of rational explanation and develop a sense of excitement and curiosity about natural phenomena. They should be encouraged to understand how science can be used to explain what is occurring, predict how things will behave, and analyse causes.’

This report highlights the importance of teaching science for understanding. For pupils to achieve well in science, they must not only acquire the necessary knowledge, but also understand its value, enjoy the experience of working scientifically, and sustain their interest in learning it. Pupils in schools need to discover the concepts revealed through observing scientific phenomena and conducting experimental investigations for themselves. Then they are more likely to continue to study science and use that learning for work, for family, and to contribute as informed citizens."

Inquiry Exercise 20 - Patient sera challenge - Student Results November 2013

Excellent  results  !
All groups correctly identified patient 1 as negative and patients 2 and 3 as positive.  Some examples of Agarose Gel  electrophoresis of small RNAs in serum  are shown below:

Inquiry Exercise 20 - An Assay to Diagnose Cancer - Student results - Nov 2013

An excellent  interactive session in the lab today . Everyone worked together to get the analysis done ! Below is the agarose gel electrophoresis that we ran today. The small RNA can be seen in all samples ! Very cool !

Building it big in Texas: Community college program trains biotech workforce

A very useful review of the ways in which NSF-ATE  support,  BIO-Link  and Community Colleges  are  training a vigorous Biotech work force in Texas.

Inquiry Exercise 30 - Purification of plasmid DNA

Challenge - To  develop a purification method for plasmid DNA from first principles .

Students are provided with a bacterial culture that harbors plasmid DNA. After a review of the properties of plasmid and chromosomal DNA, students will develop a method to purify plasmid DNA.

Milestone

 Demonstration of the purity of the plasmid DNA preps.

Inquiry Exercise 21 - Identifying a factor that changes phenotype - The Griffith experiment Redux

Challenge:  To identify the factor that confers resistance to ampicillin.

Students are provided with almost identical bacterial strains that only differ in their sensitivity to ampicillin.  Students review classic experiments on the factors that confer phenotype. They then design experiments to isolate and  confirm the function of factors that militate resistance to ampicillin.

Milestone

Functional demonstration

Inquiry Exercise 18 - Fall 2013 - Student Results

Excellent work , all groups  were successfull in making DNA  ! Milestone validations are  below !

Inquiry Exercise 25 - The Diagnosis of AIDS

Challenge  -  To  develop  an assay for AIDS

Students  will review the  molecular basis of AIDS and will develop a diagnostic assay.  In these deliberations,  students  should  consider the basic  principles of  protein-protein interactions  as  outlined in the General Biology and Basic Techniques in Biotechnology course.

As in typical inquiry exercises , discuss with your group,  ask for materials  and perform experiments that may convince the instructor that you have indeed  established such an assay. 

The milestone  will be the  diagnosis of a provided set of serum samples ( N.B.   these samples  are mimics and are not real human samples ).   

Inquiry Exercise 20 - An Assay to Diagnose Cancer.

Challenge - Devise a serum  diagnostic assay  for Cancer

You have formed a small company  that seeks to  market a test that can  diagnose cancer before it is clinically apparent.  Angel investors have provided 5 million dollars.   In your analysis of the  current literature,  you have noted that  it has been observed that  tumor cells can shed cell content into  blood. Thus, it should be possible to identify such cell content in a serum sample  and predict the presence of cancer  before it is clinically observable.

  As in typical inquiry exercises , discuss with your group,  ask for materials  and perform experiments that may convince the instructor that you have indeed  established such an  assay.

The milestone of this inquiry exercise   will  be  the  correct diagnosis of a provided set of  patient sera ( N.B.  these are mimics and not real human sera ) .

Inquiry exercise 18 - Can you make DNA ?

Histopathologists at work !

This video  illustrates a real case study and the discussions  necessary to make conclusions  about immunohistochemical staining.

Is this site working on your mobile device ?

Given that desktop computers have almost disappeared and that it is only a  very small minority who still use laptops , the majority of  students now view  material through their own favorite  mobile device.  However, there is a huge variety of mobile platforms . So let us know if  this site works on your device and feel free to make suggestions to make access easier and faster.   

Amylase becomes a celebrity ?

Many think that  having a sense of humor   is key  to developing a critical  sense in science. This  feature from ONION ,  the well known  satirical web  site  offers a humorous  opportunity ! 

What is a Histotechnologist ?

Histotechnology is a sub discipline of Biotechnology.  It involves skills in preparing  tissue for microscopic analysis and   more recent techniques such as  IHC (Immunohistochemistry) and FISH  (Fluorescent in-Situ Hybridization) . This article provides links to careers in Histotechnolog. 

Basic Techniques in Biotechnology will be offered at Capital in Spring 2014

We are delighted to announce that  Basic Techniques in Biotechnology,   the gateway course to the  Associate  Degree program in Biotechnology  will be offered at Capital in Spring  2014.  This 4-credit course provides an introduction to the basic lab  skills needed by a Biotechnologist.  Such basic skills include accurate pippetting, preparation of solutions, growth of bacteria, basic microscopy, Bioinformatics, preparation of  DNA,  measuring  proteins and nucleic acids using NanoDrop Spectroscopy,  agarose gel electrophoresis,  PCR amplification  and subcloning of DNA fragments. 

For further information  email Dr Cleo Rolle 

An Excellent Talk on Selective Somatic Mutation Therapies in Cancer

This video produced by AACR,  presents a clear  summary of the current biotechnology   approaches to mutation directed cancer  therapies.

Organic Odorants are finding a Market

This article in the Times summarizes the current drive to produce natural odorants via synthetic biology.

Coverting Smart Phone to Digital Microcope

This article describes how to make a very economical  digital microscope  from a smart phone. Such devices will empower students to capture images of  Inquiry-based laboratory exercises.

Quest introduces BRCA1/2 test

Quest Diagnostics To Offer Cheaper Version Of Myriad's Breast Cancer Genetic Test

Biotechnology Training in the 21st Century

 An interesting article in Nature Biotechnology indicates trends that are important for training in  Biotechnology in the 21st century:
 "The introductory analysis highlights a common theme addressed by all interviewees and points to a clear shift in the industry's demand for talent away from the senior scientist positions that tend to be more highly specialized and narrowly focused, to a talent pool consisting of individuals who have interdisciplinary academic training with the ability to work broadly across multiple areas and in project teams where not everyone has to be an expert in everything. Specific skill sets desired among scientists, engineers, clinicians and management teams who work within the industry include strong communications skills that facilitate the translation of the science effectively to stakeholders, a commercial market-based mindset versus an academic mindset, the ability to apply skills to real world problems, comfort with big data management, the capacity to be creative and the willingness to push boundaries."

Nobel Prize for Medicine 2013

"Three scientists have won the Nobel Prize for medicine or physiology after discovering how cells precisely transport material."

New Biotech Test for Prostate Cancer; Unlike PSA Test, is Ultra-Specific for Prostate Cancer

This article describes a more selective assay for prostate cancer. Unlike the PSA test which can simply indicate inflammation. This test measure the presence of a unique RNA derived from a gene fusion event which is specific to prostate cancer cells. 

The Next-Generation Sequencing Revolution and Its Impact on Genomics

A superb ( and free !)  paper in Cell which reviews cutting edge  sequence analysis .

Google shifts to more complex questions , not just key words !

An interesting article in the Times on the revamping of Google search algorithm

Algae produced oils go mainstream

Unilever has decided to buy large quantities  of oil produced from algae designed by solazyme .

Introducing Biotechnology into High Schools

This article from the ATE@20 blog  illustrates how an initial ATE NSF grant to  train high school teachers in Biotechnology, has been  developed into a self sustaining program.

Tales from the Genome ? 23and Me and Udacity

23 and Me, the premier personal genomics company has set up a collaboration with Udacity to offer an  online genomics course   .  The course will integrate  student observations on their own genome  with  discussion on the likely function of  DNA sequence variants.

The Top Ten List of Sequencing Techniques

The journal Biotechniques has compiled  a list of the top ten sequencing techniques  complete with downloadable pdfs .

What are those pink inclusions ?

An inquiring  student  in API  wondered what these pink inclusions might be  ? The section  is from a tissue in an early stage of development and was stained with  H and E.  The student  took  the picture through the lens using a droid camera phone .

Free fellowships to develop web skills

A pioneering program in NYC offers  free fellowships to  adults who have not had any previous training  in web development technologies .

State's Quest To Be 'On The Bioscience Map' Progresses

Governor  Malloy is scheduled to sign  the  Bioscience Innovation Act which will provide funding to enable  new biotechnology  collaborations  between  universities and small companies in CT.    

Low GC content makes B. braunii good candidate for biofuel production.

  An article in  Phycologia suggests B. braunii is an attractive  algae for bio fuel production.

Inquiry Exercise - Introduction to Bioinformatics

Challenge
  
Diagnose and treat Cancer  by using Bioinformatics 

 It is the year 2014 and in this real world Bioinformatics exercise, you will play the role of a Molecular Pathologist. Your job is to analyze cancer at the genomic (DNA) level and to suggest molecular therapies.  The human genome ( 3 billion nucleotides of DNA sequence) was first sequenced in 2000 and cost about 3 billion dollars. At present, the cost of sequencing the human genome has decreased to $20,000. It is now economical to sequence the genome of human cancer cells to find out what has gone wrong and predict therapies that may work. In this introductory exercise, a preliminary analysis has been performed to identify sequences in a lung tumor that are different from the normal human sequence.  Your job is to determine whether these changes could cause cancer and where possible, suggest molecular therapies.


Click here to download   introductory exercise

Inquiry Exercise 12

Challenge :

Generate  an example of  cell specific gene expression.

Inquiry Exercise 8

Challenge:

Demonstrate  the catalytic conversion of Starch into Glucose    

Inquiry Exercise 5

Challenge:

Provide convincing  evidence that molecules move.

Prep of LB plates and LB media

LB media is the universal  growth media  in Molecular Biology. Although  LB  is often thought to  stand for  Luria Broth , in fact it was an abbreviation for lysogeny broth and LB should perhaps be more  correctly referred to as Luria Bertrani broth.  There are many variations,  but here  is our favorite  recipe:  

LB Agar plates
Dissolve  7.5 g of  Bacto Agar ( Difco ) and 12.5 g of   LB medium  ( MP Biochemicals)  in  water, Q to 500mL in a "Wheaton"  1 liter glass bottle.  Check that pH is 7, if not titrate with NaOH. Autoclave at 121 for 15 minutes and store at RT.  To pour plates, melt on hotplate and dispense.  If adding antibiotic , cool to 45 degrees centigrade, add the antibiotic and pour.

LB Media
Dissolve  12.5 g of   LB medium  ( MP Biochemicals)  in water, Q to 500mL in a "Wheaton"  1 liter glass bottle.  Check that pH is 7 , if not  titrate with NaOH.  Autoclave at 121 for 15 minutes and store at RT. 

The Biotech Revolution

The future of Biotechnology is here now !

Bridging the Gap Between Undergraduate Education and Research

An interesting  student  article on  Science Education.

"Undergraduate science education is changing.  Fading are the days of large introductory lectures, where faceless students are merely consumers of certain knowledge to be later regurgitated on an exam. That model of teaching might get the information across, but it fails to engage students.  Where the infamous ‘weed-out’ courses do succeed, however, is in depleting the science talent pool: only 40% of students intending to major in a STEM discipline actually graduate with that major. "

Kaiser - Looking at genomes before conception

The Kaiser Permanente Center in Portland has  been awarded an NIH grant to  sequence the genomes of couples before they have children.
“Most of the time, couples don’t find out that they carry these mutations until after the mother is already pregnant, or until after the child is born,” said Katrina Goddard, a genetic epidemiologist, principal investigator on the project and researcher with Kaiser’s Center for Health Research "

Paper Clips - Listen for 5 minutes and learn a biological concept !

The journal Cell produces a series of conversations with scientists  called paper clips. These audio segments are ideal to listen to when you are sitting on the bus, waiting for lectures to start  or  in the lab and waiting while  the gel is running. Here is the archive

Interns are the new best friend of the lean biotech startup !

Interesting article on the key role of interns in Biotech startups.

Loss of Function of the Melanocortin 2 Receptor Accessory Protein 2 Is Associated with Mammalian Obesity

Studies in mice indicated that loss of function of the Melanocortin 2 Receptor Accessory Protein 2 increased obesity. The investigators then looked at human subjects and found that mutations in this gene were associated with human  obesity. 

3D print your favorite protein !

It is often difficult to appreciate the nuances of protein structure by viewing a spinning image on a monitor. Being able to look at a solid model,  often reveals major insights.  In this blog article , a simple step by step  protocol is presented that enables students  to create a 3D model of their favorite protein. All you need is a 3D printer !

Inquiry Exercise 1

Student challenge:

What  is the  quantitative relationship between the volume and weight of water ?

Learning to do Science - Inquiry Exercises ?

Although there has been significant discussion in the education  community about  the need for   "doing science to learn science", most curricula  employ Inquiry laboratory exercises that are still simply "cook book "exercises in which the student cannot assume ownership.  Typically,  the hypothesis is already presented and the student  simply gets to choose a variable  in the experiment .  In the Capital  Biotechnology program,  we have been devising  novel Inquiry exercises that require  almost complete  independence  to achieve the objective. The exercises take the form of simple challenges. They are more difficult to run than  standard laboratory  exercises , since the students are likely to move in  unanticipated directions . Thus,  the instructor notes  are quite complex. In the following posts , we will describe our Inquiry Exercises , invite instructors to use them in their own courses,  and provide feedback .

Gene Signature Predicts Reponse to Aspirin

Many people take low doses of aspirin with the hope that  it may decrease the risk of heart attack  or stroke . It has been well known that only some people respond to this preventative therapy.  In this article in the NIH director's blog, Dr Francis Collins reviews new gene expression  data that may help to  identify the  people who will benefit from aspirin therapy.

Synthetic Biology Start Ups - The new Apples and Googles ?

Some interesting reflections on the new synthetic biology Start Ups. But....don't drop out ...take our Basic  Techniques in Biotechnology  course and learn to clone DNA !

Sentence Adverbs - To use or not to use ? Is that the(a) question?

Much of scientific writing  contains  stock phrases that  are universally recognized. A  bioinformatician ( with maybe too much time on his hands)  has analysed the use of the  "sentence adverb" in scientific papers.   Interestingly,  adding more to the  lexicon ?

An Organic Perfume ?

Steven Lergos is the first student to be enrolled in the new Basic Techniques in Biotechnology course at Capital. Steve is a typical non-traditional student in that he is coming to Capital to learn new job skills that will enable him to pursue a new career. Steve is an entrepreneur at heart and has become interested in the biomanufacturing of organic perfumes. Chemical synthesis of perfume is toxic to the environment and also does not efficiently produce the isomer with the desired aromatherapeutic effect. In his first bioengineering project,  he will be using the iGEM plasmid repository to generate and express a tagged form of jasmonic acid carboxyl methyltransferase. This is the enzyme that converts jasmonic acid to the highly desirable   methyl jasmonate or Jasmine. The tagged version of the enzyme  will enable it’s affinity purification and the production of a catalytic nano gel that will carry out the organic synthesis. 

Roche looking to buy Alexion for $23 billion ?

Rumors are flying that Roch intends to buy Alexion  and this would be one of the biggest Biotech deals this year.

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

-->

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.