Biopharmaceutical Sciences

If you need access to the United States pharmacopoeia (USP) then you can get it by logging in through the IT Tallaght Library website. You can find the USP on the page at the link below. Just search for pharmacopoeia at the link below and click it. You will then be required to login using your IT Tallaght student details.

http://bit.ly/usptallaght

 

RefME is a platform I have talked about before as a useful piece of kit for managing your referencing. RefME has been purchased by another reference manager which has both free and premium (pay to use) versions called Cite this for me. RefME will shut down in due course so it might be worth considering moving to another manager. Cite this for me is a very simple to use reference manager but there are quite a few programs out there which offer both free and premium versions. A list of my top reference managers can be found below:

Zotero has chrome plugins to assist reference capture.

Test out your knowledge of Cells and Genetics at the links below:

Genetics

Cells

Áine, one of my colleagues who helps out in our practicals found a quiz on bacterial growth kinetics. It’s only short but I found a few more at the same location. Well worth having a go of to test your knowledge:

Growth Kinetics Quiz

Cell Biology

Lab Safety

Lab Balances

One of your colleagues found a very good book on Pharma Science on the web and it’s available free. The title of the book is: Pharmaceutics: The Science of Dosage Form Design 2nd Edition By Micheal E. Aulton and can be found at the link below.

http://bit.ly/pharmascienceebook

As an update to a previous post on this please note there is a newer and more often updated free desktop publishing software known as Libreoffice. Not everyone has or can afford Microsoft Office but there are plenty of free packages out there that do much the same as Microsoft office and are similarly easy to use. You can get a free office suite of programs from many companies and organisations but one of my favourites is Libre Office. Select the version open office for your system here:

https://www.libreoffice.org/download/libreoffice-fresh/

Medicines manufactured by the pharma sector cost significant amounts of money to go from discovery to market. This can mean that many medicines when they launch are beyond the ability of most people to afford them. In most cases the largest purchaser of pharmaceuticals are countries. Countries buy the drugs for their own national formularies. In an ideal world everyone would get the drugs they need to treat their illnesses. This unfortunately is not the case. Countries have limited budgets with which to buy essential medicines. Pharmacoeconomics is the study of the value of one drug or drug therapy over another. In Ireland the NCPE (National Centre for Pharmacoeconomic Evaluation) takes on the task of deciding which drugs should be made available freely from the state. Their mission is:

…to facilitate healthcare decisions on the reimbursement of technologies, by applying clinical and scientific evidence in a systematic framework, in order to maximise population wellness. The NCPE assess evidence for comparative effectiveness and cost-effectiveness of technologies for use by patients in Ireland. This is done through assessment of evidence submitted by manufacturers and independent systematic review. The NCPE also undertake research to inform national guidelines for health technology assessment.

NCPE

Below are two videos showing what goes into the process of fermentation, where the cells produce the product (part 1), to product separation and recovery (part 2). These illustrate many of the aspects we are discussing in class.

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If anyone would like to use an app instead of their browser when doing my in class revision quizzes feel free to download the app for Android or iPhone/iPad below.

Android:

https://play.google.com/store/apps/details?id=com.socrative.student

iOS

https://itunes.apple.com/us/app/socrative-student/id477618130

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The latest version of the Eudralex Volume 4, Good manufacturing practice (GMP) Guidelines can be found at this link:

http://ec.europa.eu/health/documents/eudralex/vol-4/index_en.htm

It’s well worth having a look at to see how GMP documents, such as the site master file, can be laid out.

Below are links (some requiring ITT Dublin library login details for full article access) to interesting articles about the use and potential use of CRISPR/cas9 editing in pharmaceutical bioprocessing. Well worth a read if you’re interested.

 

The impact of CRISPR-Cas9 on target identification and validation (requires ITT Dublin login)

CRISPR-Based Technologies and the Future of Food Science

Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool

Exploiting CRISPR–Cas immune systems for genome editing in bacteria

Small molecules targeting microRNA for cancer therapy: Promises and obstacles (requires ITT Dublin login)

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Clinical trial details that the US FDA is monitoring can be found at http://clinicaltrials.gov but if you want to see what’s happening in Europe check out http://clinicaltrialsregister.eu The European only launched recently (January 2016).

EU Clinical Trials Register

 

CRISPR/cas9 is a defense mechanism used by certain bacteria to protect themselves against viral (bacteriophage) attach (see figure below). The most commonly used CRISPR/Cas9 bacteria system comes from the bacteria Streptococcus pyogenes. Essentially as the bacteria is exposed to viruses it keeps portions of the viral genetic code (in the form of  short RNA sequences) around so it can recognise the virus again. The CRISPR system keeps a record of the viral genetic code and the cas9 enzyme does the cutting. If the CRISPR/cas9 system encounters a virus it recognises in the bacterium the cas9 enzymes chop up the viral DNA preventing the virus from replication.

Crispr Bacterial Defence

What’s so interesting about this? Well scientists have been able to extract this system from bacteria and use it to quickly and efficiently create transgenic organisms. The system allows for much more precise modification of a genome then traditional methods. Traditional methods of producing transgenic animals has involved injecting genetic material into embryos and hoping for homologous recombination. This technique not only had plenty of failures but also many non specific effects through in correct targeting of the sequence that the scientist wants altered. A successful transgenic animal could take up to a year to produce. With CRISPR/cas9 specificity this can be shortened to as little as 12 weeks. Below are some articles/papers explaining the system.

CRISPR = Clustered regularly-interspaced short palindromic repeats

The Health Sciences department in the University of Utah has a lovely website explaining many aspects of biology and molecular biology through videos and interactive animations. The home page is here : http://learn.genetics.utah.edu/ with lots of links to explore but I’ve put together some of the most relevant pages below.

 

 

The animations below will show you how both PCR and RT-PCR work.

The PCR instructional animation can be found at this link. You can either watch and interact with it on the page or download it for Mac or PC at the links on the page.

https://www.dnalc.org/resources/animations/pcr.html

 

The interactive RT-PCR instructional animation can be found at the link below.

http://www.bio.davidson.edu/courses/Immunology/Flash/RT_PCR.html

Scitable is a website run by Nature Publishing Group which provides biology students with resources on genetics and cell biology. It has great images, explanations (definitions), articles and much much more on everything to do with biology. Well worth checking out if you’re studying for exams or researching for assignments.

http://www.nature.com/scitable

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You can have a look around the ITT Dublin pilot plant using the embedded virtual tour below. For a full screen tour click the following link:
http://bit.ly/pilotplant

We will go through these videos in class but here is a playlist of what I think are very useful videos explaining different key aspects of biology that we’re studying. They are all from the organisation dnalc.org.

If you’re looking for past papers for any subject you are studying you can get them from the ITT Dublin Library website at this link:

http://millennium.it-tallaght.ie/search/r

 

 

The ITT Dublin Library has an agreement with openstax college who have made available a number of free books covering many subjects.

The full list of books can be found here:

https://www.openstaxcollege.org/books

I have reviewed the Biology, Microbiology and Concepts in Biology books and think they are all well written and applicable to the course. If you need to read extra material to help you understand your notes I can wholeheartedly recommend them. If you’ve any queries just give me a shout.

Biology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/biology

Concepts in Biology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/concepts-of-biology

Microbiology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/microbiology

Chemistry:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/chemistry

This is a short video on the basic operation of a spectrophotometer.

The links below describe in detail how to use either Harvard or Vancouver referencing styles for writing an essay/thesis. Harvard is probably the easier to use especially if you don’t have a reference manager program. This is due to the fact that it is very forgiving if you need to add additional detail to the article. Instead of having to re-number ever reference if you used Vancouver style, you can just add the surname and year to the new reference and just put the references in alphabetical order at the end of the article.

The most important thing to remember with referencing is to be consistent with what ever style you use. Use of web links is never appropriate for referencing!

IT- Tallaght

Harvard Style

Guide to Writing Styles and Citing Sources

 

UCD

Harvard Style Guide

Vancouver Style Guide

The image below allows you to navigate the biology lab where you will be doing your experiments. It is advisable to familiarise yourself with the location of items which will be used in the lab to facilitate laboratory induction and to allow us more time to focus on performing the experiments and getting the most out of the lab experience as possible. Make sure you note the different types of waste bins and what goes into each. You can also see the location of labcoats and the hand wash station which must be used upon entering the lab and before leaving it.

We have a small number of labcoats for students but if you are in a position to bring your own labcaot and/or safety glasses that will also help as our supplies are limited.

To navigate the image below hold down the left mouse button while your cursor is on the screen and move your mouse slowly left or right (or swipe with your finger if you are on a mobile device). To change positions in the laboratory click the turquoise arrows. You can also use the navigation buttons on screen to look around the lab too. If you want to see a full screen view click the link below:

ITT Dublin Lab Tour Full Screen

 

There’s a very good explanation for what the function of the CDER (Center for drug evaluation and research) at the FDA’s own FAQ page found here:

http://www.fda.gov/AboutFDA/CentersOffices/OfficeofMedicalProductsandTobacco/CDER/FAQsaboutCDER/#1

Wikipedia also has a good definition:

CDER reviews New Drug Applications to ensure that the drugs are safe and effective. Its primary objective is to ensure that all prescription and over-the-counter (OTC) medications are safe and effective when used as directed.

The plasma membrane is made up of the phospholipid bilayer, glycoproteins, carbohydrates and transport proteins amongst other molecules.

1280px-Cell_membrane_detailed_diagram_en.svg

The human genome is 3.3 billion base pairs in length. Compare that to the bacteria Pseudomonas aeruginosa which has 6.4 million base pairs. A base pair is A or T or G or C. In DNA, which has a double helix, (two strands attached together) these are:

A – Adenine binds to Thymine -T

T – Thymine binds to Adenine – A

G – Guanine binds to Cytosine – C

C – Cytosine binds to Guanine – G

DNA encodes for everything thing you are in the form of genes of which the human genome encodes for between 20,000 to 25,000 protein encoding genes. Your genes are capable of producing proteins which perform functions in your body including deciding your eye colour, hair colour, insulin production, immune system etc…Your 46 chromosomes are found in every cell in your body but not all the genes are switched on or activated in every cell. The cells in your eye do not need to activate proteins that would normally be found active in your liver and your liver would not activate the genes that control eye colour but the information for both is in every cell. When genes are activated in cells mRNA is produced from the DNA (a process called transcription) and this mRNA travels to the ribosomes to be turned into proteins (a process known as translation). mRNA has 4 base pairs but is only single stranded (unlike DNA) and has Uracil (U) instead of Thymine (T).

Human Amylase enzyme (which is found in your saliva and helps break down starch) has a gene size of 1544 base pairs and produces a protein 511 amino acids long. It takes 3 base pairs to encode/make an amino acid. You can see the final structure of the protein here:

http://www.rcsb.org/pdb/explore/jmol.do?structureId=4GQQ&opt=3&jmolMode=JAVA

Research papers are a great resource for learning. One of the largest databases of peer reviewed published research papers is housed by the US National Library of Medicine National Institutes of Health. You can find specific papers on techniques or new discoveries or review papers which offer a broad look at a particular topic. This should be your first stop for research on topics we’re discussing in lectures or for your assignments.

http://www.ncbi.nlm.nih.gov/pubmed/

This book by the US department of health and human sciences “Inside the Cell” is freely available on Google Books and offers a really nice explanation of the entire eukaryotic cell and all it’s components. Well worth a read.

You can have a look at it on Google Books here or download the pdf version from here

As well as the books in the library Google Books can offer a great resource for learning about biology.

This is a really nice and easy paper to read that explains why we need statistics and data records not only in the scientific world but also in the pharmaceutical and medical device industry.

Twenty tips for interpreting scientific claims

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Image Courtesy: http://mkweb.bcgsc.ca/