Biology

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

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 some images and a video from two of the students in the class, Radu Morosan and Jolanta Wolff. These were taken with a camera phone straight down the microscope and have some excellent detail. If you weren’t able to see any images on the lab day then take a look at these. Click the images to enlarge them. If people take any nice images of the Gram stain in our next lab please send them on to me.

Hair 1 Onion cells 1 Hair 5 Escherchia coli stained in methylene blue

Onion cells 2 Labelled Cheeck cells methylene blue Labelled

The link below is to a really useful website explaining concisely all the terms used in speaking about HPLC/LC systems. Well worth book marking:

http://bit.ly/hplclcterms

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/

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.

 

 

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

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

 

From the BBC website

Reckitt Benckiser, the maker of a range of Nurofen products based on the active ingredient ibuprofen lysine, has been ordered by an Australian court to remove a number of its products, including Nurofen Back Pain, Nurofen Period Pain, Nurofen Migraine Pain and Nurofen Tension Headache, from shop shelves.

The action was taken by the Australian consumer watchdog, Australian Competition and Consumer Commission (ACCC), who argued in court that there was no difference between the different branded drugs used to treat different types of pain but which all contained the same levels of the active ingredient, ibuprofen lysin. The Federal Court of Australia has given the company 3 months to remove the products from Australian shelves.

The move has no effect in other jurisdictions around the world but may prompt further investigations. A spokesperson for Reckitt Benckiser said “Nurofen did not set out to mislead consumers”.

Update: The UK’s Advertising Standards Authority (ASA) is now investigating a number of complaints made against Nurofen about an ad on Nurofen Express. Similar complaints are being investgated in New Zealand too.

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

Here’s a nice “peer reviewed” article published in 1999 on “Antiseptics and Disinfectants: Activity, Action, and Resistance”. Well worth a read if you’re interested in understanding more about disinfection.

Antiseptics and Disinfectants: Activity, Action, and Resistance

The pdf version of the article is available at the above link to.

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

Polymixins are a type of antibiotic of which Colistin is one. Polymixins and in particular colistin are one of our last lines of defense against serious bacterial infection. While resistance has been seen against these antibiotics it has only occurred through mutations in the chromosome of the bacteria making resistance difficult to pass on to other bacteria. A new research article in The Lancet Infectious Diseases has reported that, for the first time, resistance to colistin has been detected on a plasmid. This is of significance as bacteria can transfer/share plasmids readily and thus spread resistance much more quickly then through mutations in the chromosome.

This raises the real possibility of the emergence of untreatable diseases. Are we at the beginning of a new era of bacterial superiority?

http://www.bbc.com/news/health-34857015

Once a patent expires for a drug (after 20 years) other manufacturers will step in to start selling the same drug but marketed as a generic. A recent investigation by skynews reported that the differences between some of these generic drugs (specifically pain killers) and their branded equivalents were few and far between.

…consumers in the UK are spending more on painkillers than ever before, a Sky News investigation reveals branded pills that claim to target pain can cost up to four times more than unbranded tablets…Jayne Lawrence, professor of biophysical pharmaceutics at Kings College London, said: “Some people believe that by taking a more expensive preparation, perhaps a branded formulation, they’ll get better pain relief.

“If it’s the same dose of drug, in the same formulation, the customer will experience no difference.”

Courtesy Skynews

Here’s a video explaining scientific notation:

And here’s a web page to help further understand what scientific notation is and how it works.

https://www.mathsisfun.com/numbers/scientific-notation.html

 

Botulinum toxin is a neurotoxic protein (destructive to nerve tissue) produced by the bacterium Clostridium botulinumIt also has medical applications, when use in tiny quantities, including in the treatment of dystonia (a muscle contraction disorder) and muscle spasms in cerebral palsy. Probably it’s most famous application is as a cosmeceutical which prevents the development of wrinkles by paralysing facial muscles. The brand name for this product is Botox and is produced by Allergan in Ireland.

SANYO DIGITAL CAMERA

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

 

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 Open Office. Select the version open office for your system here:

https://www.openoffice.org/download/index.html

Here’s two videos explaining serial dilutions and cfu/ml calculations which I can go though again on Wednesday.

 

 

The Centres for Disease Control has published a guide on Disinfection and Sterilization in Healthcare Facilities. It covers information on:

Cleaning:

http://www.cdc.gov/hicpac/Disinfection_Sterilization/5_0cleaning.html

—–

Disinfection:

http://www.cdc.gov/hicpac/Disinfection_Sterilization/6_0disinfection.html

—–

Sterilisation:

http://www.cdc.gov/hicpac/Disinfection_Sterilization/13_0Sterilization.html

—–

Factors Affecting The Efficacy Of Disinfection And Sterilization:

http://www.cdc.gov/hicpac/Disinfection_Sterilization/4_0efficacyDS.html

The link below is to an article exploring “Antibiotics and Bacterial Resistance in the 21st Century”. It’s long but it’s an interesting read. Not essential for any exams but a worthwhile read anyway.

Antibiotics and Bacterial Resistance in the 21st Century

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

Proteins are made up of 4 categories of structure:

Primary – Amino acid sequence

Secondary – Alpha helix and Beta pleated sheets

Tertiary – 3D Structure created by protein folding

Quaternary – Arrangement of multiple folded proteins

 

2014-11-05_21-38-35

 

If you want to look at some 3D structures you can click the following links:

Macrophage Migration Inhibitory Protein

Haemoglobin Protein

This is a website showing a nice animation of the differences between Gram positive and Gram negative bacteria:

http://www.cellsalive.com/cells/bactcell.htm

2014-10-17_17-27-01

The streak technique used in this video is the quadrant streak.

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

 

mRNA is synthesised from DNA via a process called transcription which in turn leave the nucleus and travels to the ribosomes on the rough endoplasmic reticulum before being converted into a protein by a process called translation. Proteins are made up of chains of amino acids.

 

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

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.