Intro to Bio-processing

Looking to play videos or audio recordings such as lectures? If you are having trouble playing them try using the free player VLC. It can be downloaded for many types of devices including mobile OS. Links are below:

iTunes

Google Play Store (Android)

PC

MAC

 

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.

January 2017 Exam Timetables are now available here:

http://www.it-tallaght.ie/examtimetables

The Openstax organisation offer free books that are peer-reviewed by scientists and other academic individuals. There are currently a number of books available by them related to biology but they have now launched a new microbiology book well worth having a read of. It may help you with your studies. You can download the Microbiology book at the link below:

https://d3bxy9euw4e147.cloudfront.net/oscms-prodcms/media/documents/Microbiology-OP.pdf

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

Below are two links to sets of videos giving very basic explanations of how various chromatographic methods work.

Chromatographic Methods:

Mr Simple Science:

The link below will take you to a very useful bit of software created using excel that allows you to explore the effects of various parameters on the elution profile of a product. You can play around with column length, elution method (gradient or isocratic), injection volume, temperature and much more and see their effect on resolution and retention time. The first link gives a good overview of the software’s capabilities and the second link is to the program itself which you can download for free and run on PC or Mac.

Among the offered possibilities, it allows you to:

  1. Illustrate the concept of chromatographic resolution including the impact of retention, selectivity and efficiency on resolution.
  2. Understand the van Deemter equation and kinetic performance in HPLC.
  3. Recognize the importance of analytes lipophilicity (log P) on retention and selectivity in reversed phase HPLC mode (RPLC).
  4. Handle the RPLC retention, taking into account the acido-basic properties (pKa) of compounds and mobile phase pH.
  5. Simulate the impact of mobile phase temperature on HPLC separations
  6. Understand the behavior of a mixture of diverse compounds in both isocratic and elution gradient modes.
  7. Show the influence of instrumentation (injected volume and tubing geometry) on kinetic performance and sensitivity in HPLC.
  8. Demonstrate the impact of analytes molecular weight on thermodynamic (retention and selectivity) and kinetic (efficiency) performance.

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/

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.

logo_new

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

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)

2016-03-18_15-36-09

 

 

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

2016-02-23_07-26-24

 

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.

Palm oil is a vegetable oil derived from the oil palm tree. It is widely used in food products and so due to the high yields on cultivating the trees this has lead to deforestation to make space for planting, water pollution and increased greenhouse gas emissions. Now scientists in Bath University have developed an oily yeast that matches palm oil’s key properties almost identically. For more information check out this link here.

There’s a Moodle mobile app available for iOS and Android devices. It might be useful accessing information away from your PC/Mac. The apps are available from the links below:

iOS

Android

 

RefME is a free reference manager. It can help you capture references on the web and put them together into file format you can export and use in your thesis submission or project submission. For some general info on how it works and what it’s compatible with see this earlier post on LectureHub here. The video below will show you how to capture references on ncbi.nlm.nih.gov/pubmedbiopharminternational.com and books.google.ie to start with but it can do so much more. Well worth considering using it to help you with your thesis/essay writing.

RefME is a free reference manager that works as an add-on to a desktop browser and also as a mobile app. It is available as an app for iOS and Android. With the apps you can scan barcodes of books or search for references and then add them to your account.

It also works with Google Chrome Browser. This app and browser plugin will help you capture (from pubmed or any other web page where you have a potential reference) and manage references to go into your thesis. Once you’ve captured your references and used them in your thesis you can then export all references in the proper format (Harvard is probably the best format) and copy and paste them into your thesis.

You can sign up with a google or facebook account plus it’s completely free. More info can be found at the link below and I’ll put together a short video on how to use it later this week.

http://the12appsofchristmas.zohosites.com/App7.html

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

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

Sample paragraph showing multiple references:

“TLR3 recognizes viral dsRNA and endogenous dsRNA derived from necrotic cells during inflammation (11, 12). In humans, defective TLR3 function has been associated with enhanced susceptibility to viral infection and in particular, herpes simplex encephalitis (13). Recently, a functional TLR3 polymorphism, Leu412Phe (TLR3 L412F, rs3775291) was described which results in attenuated NF-B- and IRF3-signaling in affected cells (14). TLR3 412F has also been shown to confer protection against geographic atrophy in macular degeneration by attenuating TLR3-induced retinal epithelial cell apoptosis (15).”

References should be used throughout the essays. The above piece is in Vancouver Style. Other referencing styles can be found here. Details of what Vancouver style is and how to use it for different types of references can be found here:

Vancouver Style

Plagiarism includes:
  1. Using another author’s words without proper citation
  2. Using another author’s ideas without proper citation
  3. Citing a source but reproducing the exact word without quotation marks
  4. Borrowing the structure of another author’s phrases/sentences without giving the source
  5. Borrowing all or part of another student’s paper
  6. Using paper-writing service or having a friend write the paper

Avoid using significant amounts of quotes to in your essay as this is not appropriate. Put things you’ve read and understand in to your own words.

The links below are to resources you can use which will help you with your literature surveys/essays or studies in general.

ITT Dublin Library Medscape
The Cochrane Library Google Scholar
National Library of Medicine Web of Science
Google Books FDA
Clinical Trials HPRA
Biocheminternational  PharmaTech

 

This is advice taken from Carlton University in Canada from their department of economics but it is very useful in general for writing academic essays.

Academic Essay Writing

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.