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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 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

This image below outlines the step by step process for HPLC Method Development.

Method Development

Courtesy: Researchgate

Agilent has a few nice guides on HPLC which I’ve attached below.

Agilent HPLC Basics

Agilent HPLC Separation Fundamentals

Agilent Rapid HPLC Method Development

Ray D’arcy had Prof. Michael Barry of the NCPE (National Centre for Pharmacoeconomics) on his radio show. Prof. Barry discussed the recent orkambi decision and the role the NCPE has in the national formulary. Really interesting conversation and well worth a listen. The podcast can be downloaded from the link below:

NCPE on Ray D’arcy

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

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.

The website below is a great resource for staying current on topics in relation to liquid chromatography and gas chromatography. Sections of the site include:

  • Publications on LC and GC systems
  • Information on techniques including:
  • LC
  • HPLC
  • UPLC
  • GC
  • Mass Spec
  • Sample Prep
  • LC/GC Television and Multimedia
  • eBooks (Free)

http://bit.ly/lcgcresource

Below is a link to some interesting review papers on HPLC/LC systems. Well worth a read to help you better understand the topic. Explore more on your own by visiting pubmed.gov. Remember to use the filters on the left hand side of the page to help you narrow your searches.

http://bit.ly/hplcpapers

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/

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

The EMA (European Medicines Agency) which is the EU regulator of the pharmaceutical, bio-pharmaceutical and medical device sector currently has its head offices for all of Europe in London. Following the vote on Brexit, and once the UK follows through on leaving the EU, the EMA will have to fine a new home for it’s HQ in a European country. Ireland may be well placed to become home to the new HQ due to the size of the sector in the country. We’ll have to watch and wait for now.

In 2013 it was agreed by European Pharmaceutical Associations that a new policy around disclosure of payments was to be implemented by member Associations. The IPHA (Irish Pharmaceutical and Healthcare Association) who are a member of the EFPIA set up a website to document all payments made from Pharmaceutical companies in Ireland to Irish healthcare professionals. The code is voluntary unlike the open payments system in the US which came in under the sunshine act. The first data disclosed related to 2015 and was published in a central industry report on the IPHA website on 30th June 2016. As the code is voluntary, Irish healthcare professionals can refuse to be listed and currently according to the IPHA about 55% of them are partaking in the voluntary code. You can find more details at the links below:

Transfer of Value

An explanation of the code

Search the database

 

 

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

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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)

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.

The links below are to some tips on how to plan and deliver a presentation on you project. I’ve also attached a “rough” template of a PowerPoint presentation you could use to help you with your planning. Feel free to come up with some nice designs of your own.

Presentation Tips

PowerPoint Presentation Sample Template

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

 

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.

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

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

If you are working on the time management exercise at the moment for learning 2 learn you can consider using an app for your smartphone to capture the time you are doing a specific thing. If you use one of the apps below I’ll accept a screen shot from the app showing the graph of % of time doing the different things outlined in the assignment instructions on Moodle as proof of completion of the assignment. Below are two apps (one for Apple devices and one for Android devices) which you might find useful for time management.

Any queries feel free to post below.

Courtesy of the Assistive Technology Blog in ITT Dublin here’s an app for Apple devices:

Assistive Technology in ITT Dublin

 

And here’s one for Android devices:

aTimeLogger – Time Tracker

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

 

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 VARK questionnaire can help you explore what type of learner you are. The VARK was developed by Neil Fleming back in 1987. It can identify which sensory modality a learner has a preference for. The four modalities are:

  1. Visual learning
  2. Auditory learning
  3. Read/write learning
  4. Kinesthetic (touch and feel) learning

Originally people could identify their primary preferred form of learning but nowadays we recognise that learners can be a combination of two forms. The VARK can help people with identifying not only their learning strengths but also in identifying their weaknesses thus enabling them to focus more on any areas they may struggle with.

Take the questionnaire yourself at the link below:

http://bit.ly/thevark

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

 

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.

Wondering what level you are studying at? Check out the chart below from Quality and Qualifications Ireland.

2015-06-12_08-54-34

Please note as previously mentioned, if any CLP images come up in the exams they will be based on the new images being brought in this June by the EU. You can familiarise yourself with them here:

New CLP regulations – June 2015

 

Take the CLP quiz from the ECHA!

I found a nice article explaining some of the key terms we’ve discussed in relation to sampling plans. Might be worth a read:

http://wps.prenhall.com/wps/media/objects/7117/7288732/65767_28_SuppG.pdf

 

Lot Tolerance Percent Defective (LTPD): The upper limit on the percentage of defects that a consumer is willing to accept.

Consumers Risk: The probability that a lot containing defects exceeding the LTPD will be accepted.

Producers Risk: The probability that a lot containing the AQL will be rejected.

Operating characteristics curve (OC): The ability of a sampling plan to discriminate between lots of high and low quality is described by it’s operating characteristics curve. The steeper the slope of the OC curve the more discriminating the sampling plan. It can be made steeper by increasing the number of samples to be tested or reducing the number of rejects acceptable.

This is a peer reviewed journal article on “Analytical techniques in pharmaceutical analysis” outlining the different techniques used in industry. The citation (Reference) is Siddiqui MR, AlOthman ZA, Rahman N. Analytical techniques in pharmaceutical analysis: A review. Arabian Journal of Chemistry. April 2013. The paper can be found here:

http://dx.doi.org/10.1016/j.arabjc.2013.04.016

The FDA publishes Guidance for Industry documents. One such document is for the Investigating Out-of-Specification (OOS) Test Results for Pharmaceutical Production which details guidance that applies to chemistry-based laboratory testing of drugs regulated by CDER. It is directed toward traditional drug testing and release methods.

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The HSA has a website called BeSmart.ie. The site, stands for Business electronic Safety Management And Risk assessment Tool, helps small business owners/managers to prepare risk assessments and a safety statement for their workplace. The system prepares risk assessment documents based on how you answer a series of questions. If you want to check it out without registering just click the “guest user login” on the home page here then enter the business type and choose a hazard.

The image below shows how Process Capability (standard deviation) relates to Process quality.

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Check out the video here for more information and it’s related video here

This video explains standard deviation and mean as well as cp/cpk

Pharmacopoeias are books which contain information on how to identify medicinal compounds. Some of the more common pharmacopoeias published include the European, United States and the WHO.

This is an example of a protocol for testing sterility from the WHO’s pharmacopoeia

TEST FOR STERILITY

Here is an example of the protocol for identifying the medicinal product Asprin (Acetylsalicylic acid).

Asprin-Acetylsalicylic acid Specification

Statistics is the study of the collection, organization, analysis, interpretation and presentation of data (wikipedia). To this end some averages (the middle) and standard deviations (the variation from the middle) are some of the basic calculations in statistics which we use every day. The average of three numbers can be calculated by adding them all together and dividing by the number of numbers there are. For example in the following sequence: 1, 2, 3 there are three numbers (we write this as “n=3”). The average can be calculated by adding them together: 1+2+3 = 6 and dividing this total by the number of numbers to calculate the average: 6/3=2. The average of 1, 2, 3 is 2. The “average” can also be called the “mean”. Both words describe the same thing. Symbol wise we can also call the “average” or “mean” x-bar and write it as an “x” with a line over as in: xbarSo the Average = Ave = Mean = xbar

The standard deviation is the difference between the x̄ and the other numbers in the sequence. we usually calculate standard deviation using calculators or excel but it can be easy to work out for some sequences. So back to the sequence 1, 2, 3 where the x̄ was 2 the standard deviation is 1 because x̄ + 1 is 3 (the upper number in our sequence) and x̄ – 1 is 1 the lower number in our sequence. Symbol wise we can also write the “standard deviation” as a p on it’s side: σ

So the Standard Deviation = StDev = σ

When we display data in figures to assess it’s quality we will often use histograms. These figures consist of an “x” and “y” axis. The x being the horizontal axis and the y being the vertical axis. Each axis is used to display data of some sort such as sample weight on the “x” axis and the number of samples of a particular weight on the “y” axis (also known as the frequency). If we re order the collected data on sample weights such that samples with the smallest weights are to the left of the “x” axis and the samples with the highest weights are to the right of the “x” axis we can in most cases produce a a bell shaped histogram such as the one below.

hist_normal

This is known as a “bell shaped curve” or “normal distribution” or a “Gaussian curve”.

To go with the new CLP regulations coming in to law from June 1st 2015 the European Chemicals Agency has created a quiz to test you on your knowledge. Check it out here: http://echa.europa.eu/clp-quiz

clp_banner_narrow_en

The European environment state and outlook report (SOER)  2015  delivers a comprehensive assessment of the European environment’s state, trends and prospects, in a global context. It highlights a number of factors of concerns in relation to the pharmaceutical industry in it’s 20 year plus outlook citing:

Emerging pollutants, such as from pharmaceuticals and personal care products, may be a future concern, as may be algal blooms and pathogenic microorganisms.

Chemicals from pharmaceuticals, personal care products, and other consumer products can have adverse effects on the environment and on human health. Endocrine disruption, which impacts the body’s hormonal system, is of particular concern. Unfortunately, the environmental pathways and potential human health impacts of these chemicals are poorly understood, especially when people are exposed to mixtures of chemicals, or when exposure occurs in vulnerable population groups such as pregnant women, small children and people suffering from certain diseases (EEA, 2011d; Larsson et al., 2007; EEA, 2012f; EEA/JRC, 2013). Reducing chemical pollution at source has become an important resource efficiency measure, as advanced wastewater treatment and treatment of drinking water is energy and chemicals intensive.

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According to the FDA 21 CFR 58.3 the definition of raw data is:

any laboratory worksheets, records, memoranda, notes, or exact copies thereof, that are the result of original observations and activities of a nonclinical laboratory study and are necessary for the reconstruction and evaluation of the report of that study. In the event that exact transcripts of raw data have been prepared (e.g., tapes which have been transcribed verbatim, dated, and verified accurate by signature), the exact copy or exact transcript may be substituted for the original source as raw data. Raw data may include photographs, microfilm or microfiche copies, computer printouts, magnetic media, including dictated observations, and recorded data from automated instruments.

The link below is to the FDA’s guide to electronic signatures and records – scope and application

 

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http://www.fda.gov/downloads/RegulatoryInformation/Guidances/ucm125125.pdf

From June 2015 the EU will harmonise CLP labelling under the ECHA (European Chemicals Agency). The regulations will apply to the classification and labelling of both substances and mixtures. Earlier EU legislation will be repealed. The head of the ECHA stated, “An enormous number of products must be re-labelled to comply with CLP, including consumer items such as paints or detergents, as well as industrial mixtures.”

Some of the new symbols can be seen here:

http://echa.europa.eu/chemicals-in-our-life/clp-pictograms

Many of the symbols previously used will be changed for example:

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A leaflet is available from this link and offers a brief guide to the new classifications:

http://echa.europa.eu/documents/10162/13556/echa_clp_leaflet_en.pdf

 

 

The United Nations Development Programme published a report on methods, tools and good practices for fighting corruption. The full report can be found by clicking Anticorruption-Methods-and-Tools-in-Health-final.

The report found 10 lessons were critical for fighting corruption:

Lesson one. There is no ‘one size fits all’ approach to mitigating corruption in the health sector. Practitioners need to give careful attention as to what potential strategy or strategies would work most effectively in view of the specific risks identified by use of diagnostics.
Lesson two. More than one anti-corruption intervention should be employed to deal with one risk. For example, wage increases may help to curb the likelihood of absenteeism, but they are likely to be more effective when there are systems in place to document absentee rates and when sanctions for absence are imposed.
Lesson three. Prioritization is key: governments and others involved in health projects and programming should prioritize areas of the health system that are most susceptible to corruption and implement appropriate interventions. Often even ‘low hanging fruit’ can produce significant anti-corruption impacts. For example, the act of posting medical supply and pharmaceutical product pricing can help deter price gouging. The identification of priority areas is particularly important when resources are scare.
Lesson four. It is important to work with other sectors. Corruption cannot be curbed in the health sector without the involvement of other critical sectors, such as infrastructure and finance.
Lesson five. Health policy goals should include anti-corruption considerations. Investments in health may be wasted unless anti-corruption strategies are built into all health projects. Preventative interventions can protect investments made.
Lesson six. Prevention is the best strategy: therefore, it is best not to wait for corruption to happen before beginning to deal with it. One of the biggest failings in the health sector is the implementation of anti-corruption interventions only after corruption is suspected or confirmed. Regular monitoring of the health sector for discrepancies in standards is vital.
Lesson seven. Numerous empirical diagnostic tools should be employed. Given the complexity of the health sector, more than one diagnostic tool may be of value to ensure accurate information. This also requires proper measuring and re-measuring. Regular ‘check-ups’ can measure how effectively anti-corruption strategies are working in a given point in the health care system.
Lesson eight. Partners with experience in implementing anti-corruption strategies and tactics should be identified and contacted for technical support. This study has identified a number of NGOs, international development institutions, research groups and experts involved in implementing anti- corruption strategies and tactics in the health sector.
Lesson nine. Broad participation in health policy and planning helps. Involving NGOs, citizens and designated experts in health budgeting, monitoring, and consulting, as a few examples, can help heighten transparency and lessen the likelihood of corruption.
Lesson ten. Good behaviour should be rewarded, and bad behaviour punished. This can be done by setting up appropriate incentive structures that help promote adherence to good behaviour, such as performance-based financing. It is also important to sanction those individuals who are engaged in corrupt activities where possible. This sends an important message that corruption is not tolerated.

Apart from outright corruption there are many important reasons for regulation of the pharmaceutical sector. The links below are to a few stories that indicate the need for regulation.

Pharmaceutical companies make huge profits and as a sector it is matched only by the banking sector for the largest profits. Many of the worlds best known pharma companies spend more on marketing then they do on R&D: http://www.bbc.com/news/business-28212223

The US Justice Department is so concerned about the marketing prowess of the pharma companies that it released a 2001 recording of a sales executive meeting for GSK which you can view here and the first 30 seconds speaks for itself.

When the US government brought in the affordable care act they also launched a website that patients/public could search to see what perks their doctor has received. It can be found here: https://openpaymentsdata.cms.gov/ A report into the site found some suprising statistics: http://projects.propublica.org/docdollars/ The types of work doctors do for pharma compneis include partaking in clinical trials, giving speeches and directly workign for a company.

Here is a list of what the fees to doctors are paid for: http://projects.propublica.org/docdollars/companies

Forbes magazine produced an article on the coffee supply chain with a very useful graphic indicating the many links that connect together to get you your daily coffee. You can see that at any point along this chain there is the possibility for corruption without regulation.

Vega-Typical-Supply-Chain-sRGB-1

Duties of employers and employees under the Safety, Health and Welfare at Work Act 2005. Taken from the HSA website.

Employer Duties
The core of the legislation is the risk assessment approach and the legal duty on employers to prepare a written health and safety document referred to as a Safety Statement. Employers (including self-employed persons) are also responsible for creating and maintaining a safe and healthy workplace.

Employer’s duties include:

  • Managing and conducting all work activities so as to ensure as reasonably as practicable the safety, health and welfare of people at work
  • Designing, providing and maintaining a safe place of work that has safe access and egress, and uses plant and equipment that is safe and without risk to health
  • Providing information, instruction, training and supervision regarding safety and health to employees
  • Providing and maintaining welfare facilities for employees at the workplace
  • Preventing risks to other people at the place of work including, for example, visitors, customers, suppliers and sales representatives
  • Have plans in place for emergencies

Employee Duties
Employees, including those employed on a part-time or temporary basis, also have duties including:

  • Comply with relevant laws and protect their own safety and health, as well as the safety and health of anyone who may be affected by their acts or omissions at work
  • Ensure that they are not under the influence of any intoxicant to the extent that they could be a danger to themselves or others while at work
  • Cooperate with their employer with regard to safety, health and welfare at work
  • Use in the correct manner any item provided for protection
  • Participate in safety and health training offered by their employer
  • Report any dangerous situations, practices or defects that might endanger a person’s safety, health or welfare
  • Not to engage in any improper conduct that could endanger their safety or health or that of anyone else

The links below will take you to some of the common reasons for receiving FDA warning letters:

FDA warning letters: the most common violations highlighted

Analysis of FDA Warning Letters Shows Patient Safety Violations, Inadequate Record Keeping Common in Clinical Trial Concerns

2012 FDA Warning Letters: What Can Be Learned?

An analysis of the warning letters issued by the FDA to pharmaceutical manufacturers regarding misleading health outcomes claims.

FDA warning letters, known as Form FDA 483 is defined as

…a correspondence that notifies regulated industry about violations that FDA has documented during its inspections or investigations. Typically, a Warning Letter notifies a responsible individual or firm that the Agency considers one or more products, practices, processes, or other activities to be in violation of the Federal Food, Drug, and Cosmetic Act (the Act), its implementing regulations and other federal statutes. Warning Letters should only be issued for violations of regulatory significance, i.e., those that may actually lead to an enforcement action if the documented violations are not promptly and adequately corrected. A Warning Letter is one of the Agency’s principal means of achieving prompt voluntary compliance with the Act

They demand a prompt response from the organisation/company that receives such a letter. You can search the letters which are all published on the FDA website by clicking here.

 

Here’s one of my own videos (also available on Moodle) explaining how to calculate the cfu/ml.

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

Peer reviewed material is material published in scientific journals (or other types of journals). These articles have been published in these journals only following review of the articles by other scientists who assess the quality and validity of the material.

News articles and websites are not peer reviewed and anyone can right anything there whether it is true or not. In scientific essays you should focus on referencing peer reviewed material first and foremost before utilising other material.

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.

Vaccines

A vaccine is a biological preparation that improves immunity to a particular disease.Whether that’s a disease caused by a bacteria or a virus.
 
Antibodies

An antibody (Ab), also known as an immunoglobulin (Ig), is a large Y-shape protein produced by plasma cells that is used by the immune system to identify and neutralize foreign objects such as bacteria and viruses. The antibody recognizes a unique part of the foreign target, called an antigen.
 
Cytokines

Cytokines (Greek cyto-, cell; and -kinos, movement) are a broad and loose category of small proteins (~5–20 kDa) that are important in cell signaling. They are released by cells and affect the behavior of other cells, and sometimes the releasing cell itself. Cytokines include chemokines, interferons, interleukins, lymphokines, tumour necrosis factor but generally not hormones or growth factors (despite some terminologic overlap). Cytokines are produced by a broad range of cells, including immune cells like macrophages, B lymphocytes, T lymphocytes and mast cells, as well as endothelial cells, fibroblasts, and various stromal cells; a given cytokine may be produced by more than one type of cell.
 
Hormones

A hormone (from Greek ὁρμή, “impetus”) is a class of signaling molecules produced by glands in multicellular organisms that are transported by the circulatory system to target distant organs to regulate physiology and behaviour. Hormones have diverse chemical structures that include eicosanoids, steroids, amino acid derivatives, peptides, and proteins. The glands that secrete hormones comprise the endocrine signaling system. The term hormone is sometimes extended to include chemicals produced by cells that affect the same cell (autocrine or intracrine signalling) or nearby cells (paracrine signalling).
 
Gene Therapy

Gene therapy is the use of DNA as a drug to treat disease by delivering therapeutic DNA into a patient’s cells. The most common form of gene therapy involves using DNA that encodes a functional, therapeutic gene to replace a mutated gene. Other forms involve directly correcting a mutation, or using DNA that encodes a therapeutic protein drug (rather than a natural human gene) to provide treatment. In gene therapy, DNA that encodes a therapeutic protein is packaged within a “vector”, which is used to get the DNA inside cells within the body. Once inside, the DNA becomes expressed by the cell machinery, resulting in the production of therapeutic protein, which in turn treats the patient’s disease.

 

Stem Cells

Stem cells are undifferentiated biological cells that can differentiate into specialized cells and can divide (through mitosis) to produce more stem cells. They are found in multicellular organisms. In mammals, there are two broad types of stem cells: embryonic stem cells, which are isolated from the inner cell mass of blastocysts, and adult stem cells, which are found in various tissues. In adult organisms, stem cells and progenitor cells act as a repair system for the body, replenishing adult tissues. In a developing embryo, stem cells can differentiate into all the specialized cells—ectoderm, endoderm and mesoderm (see induced pluripotent stem cells)—but also maintain the normal turnover of regenerative organs, such as blood, skin, or intestinal tissues.
 
Blood Products

A blood substitute (also called artificial blood or blood surrogates) is a substance used to mimic and fulfill some functions of biological blood. It aims to provide an alternative to blood transfusion, which is transferring blood or blood-based products from one person into another. Thus far, there are no well-accepted oxygen-carrying blood substitutes, which is the typical objective of a red blood cell transfusion; however, there are widely available non-blood volume expanders for cases where only volume restoration is required. These are helping doctors and surgeons avoid the risks of disease transmission and immune suppression, address the chronic blood donor shortage, and address the concerns of Jehovah’s Witnesses and others who have religious objections to receiving transfused blood.

Taken from Wikipedia

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 document at the link below is to a guide to writing reflective journals. It gives examples of what a reflective journal is and is not.

Reflective Learning

Courtesy DCU

The website Pharmacology Corner looks to me to be a great resource for drug discovery, targets and receptors information. Well worth checking out to help with your studies and essays.

2014-09-30_11-49-41

The image below shows the effect of agonists and antagonists on a biological reaction. In figure “A” the agonist alone causes a reaction but add the agonist and competitive antagonist this changes the reaction. You now need more agonist to get the same effect (this is competitive antagonist). In figure “B” you see again the effect an agonist has on a biological reaction but when we add the agonist together with a non-competitive irreversible antagonist we see the effect is to reduce the rate of the reaction.

 

competitive-antagonist

 

Courtesy: Pharmacology Corner

The image below is a detailed description of the HIV virus life-cycle and the targets in this life-cycle we can use drugs on. Click the image to see the full size pic.

 

2007 aids

The image below is from the article Steroid hormones: Interactions with membrane-bound receptorsIt shows three ways that a steroid hormone (drug) can interact with a cell. (a) The classical model. The steroid hormone dissociates from its plasma carrier protein and diffuses across the cell membrane. After gaining entry to the cell, the free hormone binds to an intracellular receptor and alters gene transcription. (b) Receptor-mediated endocytosis. The steroid hormone, bound to its plasma carrier protein, is brought into the cell via a cell-surface receptor. The complex is broken down inside the lysosome, and free steroid hormone diffuses into the cell, where it subsequently exerts its action at the genomic level or undergoes metabolism. (c) Signalling through cell-surface receptors. The free steroid hormone alters intracellular signalling by binding to cell-surface receptors. The steroid hormone could exert these effects directly or could alter signalling by blocking the actions of peptide hormones.

 

gr1

The EudraLex V29  September 2014 has just been release. It is a substantial document but if you wanted to have a look at it you can download it from the link below. Warning the file size is 910mbs so it’s very large and will take a while to download on a slow connection.

http://ec.europa.eu/health/documents/eudralex/cd/index_en.htm

For individual sections of the Eudralex you can have a look at this link:

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

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 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

The link below is a sample 1500 word essay from the University of York which contains also tutor comments on the layout and structure of the students essay. Well worth a read for your own studies.

Sample 1500 word Essay on referencing