Enjoy dissection? Watch this one, of an Amur tiger

Siberian tigers

The Amur tiger almost became extinct in the 1940’s, with maybe just 40 individuals remaining in the wild. Their conservation and subsequent recovery, supported by WWF, has been slow work but now a population of about 550 exists in the far east of Russia, northern China and perhaps North Korea. They are the tigers with the largest home range of any tiger species – needing to cover huge distances in order to get subsistence from the inhospitable terrain which they inhabit.

A team in Scotland made a dissection of an Amur tiger and carefully recorded and annotated it on video.

Here is the full link to the BBC Earth web page: http://www.bbc.com/earth/story/20170302-discover-how-the-amazing-body-of-an-amur-tiger-works

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Gene therapy is successfully used to cure sickle celled anaemia. A first!

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GENE THERAPY SUCCESSFULLY USED TO TREAT A 13 YEAR OLD PATIENT WITH SICKLE CELLED ANAEMIA

2nd March 2017

Here is a link to a BBC summary about the way in which, for the very first time, gene therapy has been used to ‘correct’ the abnormal mutation which causes sickle celled anaemia. A 13 year old French boy with an advanced condition of sickle celled anaemia had bone marrow removed and then genetically modified using a lentivirus vector, before being reintroduced back into his body, where it has subsequently been producing largely faultless red cells. http://www.bbc.com/news/health-39142971

This hugely successful and significant gene therapy procedure  was described formally March 2nd 2017 in the New England Journal of Medicine (NEJM), from where it cannot be freely accessed. A version of the story with much more detail and science than the BBC version can be accessed on the Medscape web pages:  http://www.medscape.com/viewarticle/876505

In the field of gene therapy this procedure is hugely, hugely significant. For some decades now the dream has been that gene therapy will offer ‘wonder’ cures for several genetically inherited diseases but so far, successes have been limited. From the University of Utah’s Genetic Science Learning Center (Learn.Genetics), here is a summary of the more important successes:  http://learn.genetics.utah.edu/content/genetherapy/success/

(Let me plug, yet again, the University of Utah’s Genetic Science Learning Center. A fabulous resource!  http://learn.genetics.utah.edu/)

Check out Topic 3.1 Genes, on this Blog, to learn more about sickle celled anaemia:  https://johnosborneabcbiology.wordpress.com/genetics-topics-3-10/3-1-genes/

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Drunken Monkey Hypothesis: some serious evolutionary and molecular biology

humanalcohol

This has to be a good read! Not just because it might be amusing but also because there is some serious evolutionary and molecular biology here. Our craving for alcohol seems to have a long, long evolutionary history, with a neat mutating gene, ADH4 (No! Not anti-diuretic hormone but alcohol dehydrogenase enzyme), which speeds up the digestion of alcohol, beginning in the mouth. Several primates are known to feast on fermented fruits and there is good evidence that this pursuit of alcohol has or had a significant calorific value for those animals.

From BBC, 23 February 2017

http://www.bbc.com/earth/story/20170222-our-ancestors-were-drinking-alcohol-before-they-were-human


protein_adh5_pdb_1m6h

The evolutionary investigation done by Mathew Carrigan and his associates is so very interesting but of course way beyond what the IB might require. Nevertheless, if you are interested enough (Extended essay???) here is a link to the full text of Carrigan’s publication:  http://www.pnas.org/content/112/2/458.full. Early primate ancestors, about 50 million years ago, evidently possessed a gene to produce ADH in some form, and were able therefore to digest alcohol. Some 10 million years ago, primates began foraging on the ground and encountered fallen, fermenting fruit – an excellent source of sugar and thus calories. At about the same time the ADH4 gene underwent a significant, single mutation which enabled some primates to digest alcohol very much more efficiently and therefore be at a competitive and evolutionary advantage. In humans, this gene is one of a bunch of alcohol digesting genes on chromosome 4. The focus upon alcohol in different forms as a source of energy food, pre-dates the supposed time, maybe just 9,000 years ago, when humans apparently first began to enjoy alcohol as a drink and for its pleasurable effects of inebriation. Carrigan even argues that the pleasure ‘kick’ we modern humans get from alcohol can be explained by our ancient ancestors especially seeking out fermented fruits for their high energy value, and thus obtaining a cerebral ‘hit’ of satisfaction, even though they possibly did not obtain significant effects from inebriation.


I love this! it can go on and on and on ….!

What is the mutation? ADH is a zinc based enzyme. (See a molecular visualisation of it here:  http://www.proteopedia.org/wiki/index.php/3cos.) The mutation is one of the most frequent sorts of mutation – a ‘snip’ or SNP, SINGLE NUCLEOTIDE POLYMORPHISM, which occurs when just one nucleotide and its base is changed, resulting in a the synthesis of a modified protein. Research has shown that in humans there are two variants of the ADH1 SNP, with a resultant protein carrying either the amino acid histidine or arginine – effectively two different alleles. The first of these alleles, with the amino acid histidine, is much more effective at the breakdown of ethanol. People with this allele are consequently more tolerant to alcohol. A wonderful piece of research in China has shown how the less effective allele, containing arginine, was selected out of a population about 10,000 years ago. This time coincides with the early domestication of rice in Eastern Asia. Supposedly early humans commonly consumed alcohol derived from the fermented rice. Those with the arginine-coding allele were less tolerant to alcohol and were therefore less likely to have reproductive success, so the allele became uncommon.  (http://bmcevolbiol.biomedcentral.com/articles/10.1186/1471-2148-10-15)

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Cytochrome c and cladistics – and much more!

cytochrome_c

I love the way the new syllabus can bring together different themes, concepts and understandings, through a focus upon one, seemingly small component. An understanding of cytochrome c might bring together and help a comprehension of this lot:

  • protein structure structure (2.4 Proteins & HL 7.3 Translation)
  • function in cell respiration as an electron carrier (8.2 Cell respiration HL)
  • coding gene, CYCS, on chromosome 7 (3.1 Genes & 3.2 Chromosomes)
  • mutations of DNA (1.6 Cell division, 3.1 Genes, 3.4 Inheritance)
  • synthesis of a protein through transcription and translation (2.7 DNA replication, transcription and translation & HL 7.2 Transcription and gene expression & 7.3 Translation)
  • comparing gene sequences in different species to provide support for cladistics and evolutionary arguments (5.1 Evidence for evolution & 5.3 Classification and biodiversity)

What is the specific context? Topic 3.1 – Genes. The IB syllabus suggests that students make a comparison between the amino acid sequences of cytochrome c in different species, using Genbank or some other database. Why cytochrome c? Because this electron carrier in mitochondrial membranes has been studied in depth as molecular evidence for the 3 Domain proposal for the classification of living organisms. Read on …. it is fascinating!

Now comparing amino acid sequences in different species. This is from Biology Second Edition, C.J. Clegg, 2014, Hodder Education and seems to work fine for cytochrome c oxidase, if you follow the instructions and use your head!p-137-gene-bankp-138

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3.1 Genes

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Chris Paine’s BioKnowledgy presentation – very complete: http://www.slideshare.net/diverzippy/bioknowledgy-31-genes


READING – from Biology in Context for Cambridge International A Level, Glenn and usan Toole, 2013, Nelson Thornes

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READING – from Biology for the IB Diploma Second Edition, C.J. Clegg, 2014, Hodder Education

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THE HUMAN GENOME PROJECT

The HGP was an international attempt to map the entire base sequence of the human genome, including the 1% which constitutes coding genes, the 8% regulatory sequences and the remainder, not all of which has clear functions . The project launched in 1990, funded by the US government and comprising an the international consortium of geneticists from the United Kingdom, France, Australia, China and several other collaborators. The HGP was officially completed in 2003 but not after some controversy caused by a privately funded attempt to unravel the genome, using different sequencing technology, with the intention of commercially capitalising on their results. This research was run by Craig Venter and his company Celera Genomics, but once President Clinton declared that the human genome and its information could not be patented, Venter collaborated with the HGP.

This powerpoint is some years old now and has a special focus upon ethical issues but the presentation is good; it is understandable; and it suffices! human-genome-project-ppt

The Nature of Science focus is upon gene sequencing and how the technology has so dramatically developed, and continues to develop, meaning that sequencing a genome can now be completed in as little as two days. In 1975 Sanger provided the first truly viable sequencing technique, from which were developed the automated techniques which assisted the HGP and Craig Venter. These techniques have now been well overtaken by the so-called ‘next-gen’ techniques which enable extremely rapid sequencing. 

Genomes of a staggering number of species have now been sequenced and analysed. Some interesting comparisons and insights have emerged:genomes-different-species


DNA MUTATIONS AND SICKLE CELLED ANAEMIA

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COMPARISON OF NUMBER OF GENES IN HUMANS WITH OTHER SPECIES

(Note – this is not a comparison of the genome size but is a comparison of the total number of genes which code for proteins. Remember that this coding DNA constitutes just 1% of the genome.)

bioknowledgy-presentation-on-31-genes-5-638ib-biology-31-slides-genes-4-638


COMPARING BASE SEQUENCES IN DIFFERENT SPECIES USING A DATABASE – and much, much more!

cytochrome_c

I love the way the new syllabus can bring together different themes, concepts and understandings, through a focus upon one, seemingly small component. An understanding of cytochrome c might bring together and help a comprehension of this lot:

  • protein structure structure (2.4 Proteins & HL 7.3 Translation)
  • function in cell respiration as an electron carrier (8.2 Cell respiration HL)
  • coding gene, CYCS, on chromosome 7 (3.1 Genes & 3.2 Chromosomes)
  • mutations of DNA (1.6 Cell division, 3.1 Genes, 3.4 Inheritance)
  • synthesis of a protein through transcription and translation (2.7 DNA replication, transcription and translation & HL 7.2 Transcription and gene expression & 7.3 Translation)
  • comparing gene sequences in different species to provide support for cladistics and evolutionary arguments (5.1 Evidence for evolution & 5.3 Classification and biodiversity)

What is the specific context? Topic 3.1 – Genes. The IB syllabus suggests that students make a comparison between the amino acid sequences of cytochrome c in different species, using Genbank or some other database. Why cytochrome c? Because this electron carrier in mitochondrial membranes has been studied in depth as molecular evidence for the 3 Domain proposal for the classification of living organisms. Read on …. it is fascinating!

Now comparing amino acid sequences in different species. This is from Biology Second Edition, C.J. Clegg, 2014, Hodder Education and seems to work fine for cytochrome c oxidase, if you follow the instructions and use your head!p-137-gene-bankp-138

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Answering an ‘Extended Response’ question in Biology

specimen-extended-response-questions

The EXTENDED RESPONSE  questions (maybe you might refer to them as ‘essays’) are found after the data analysis and structured factual recall questions in Paper II.

SL students answer 1 from a choice of 2; HL students answer 2 from a choice of 3. (Very little choice!!!!).

The Extended Response question is broken down into three parts (a, b & c), giving a total of 15 marks. There is an additional mark available for “… the construction of the answer.” Usually one of the three parts carries significantly more marks than the other 2 – maybe 8 out of the 15.

The parts a, b & c are all loosely connected but in the new style of syllabus there is much greater width in the scope of those connections, so they may not at first seem too obvious. There may be components asking about the Nature of Science and Applications. Be careful in the choice of question!

Pay special attention to COMMAND TERMS! (Before you start this sort of exam ANSWER, you should completely understand what each command term requires in an answer.)

Again – Be very careful in choice of question to answer! It is worth roughly and quickly jotting down rough notes for each of the 3 components of each of the two (or three) Extended Response questions and then making an evaluation of which answer might garner most marks for you.

You should have 20-25 minutes to answer an Extended Response question. This includes planning time. Of course you do not hand in your planning but you should see it as OBLIGATORY before writing an answer.


WRITING AN ANSWER

  1. The Extended Response question is not answered as a conventional essay with which you are familiar in non-science subjects.
  2. Answer only inside the given, bordered space.
  3. Of course, it goes without saying that a written answer must be legible. The examiners are flexible people but if an answer cannot be read, it cannot be marked. Write in pen, except for any drawings.
  4. Pay attention to COMMAND TERMS – these tell you what sort of answer is required.
  5. Answers should be written in enumerated (numbered or bullet-pointed) form but should consist of complete sentences if appropriate.
  6. Never repeat the questions. Maybe abbreviate question parts as sub-headings only.
  7. DO specifically answer what is required. Examiners are very flexible – there may be several ways to obtain marks – but they will never give marks for anything which is not required by the question.
  8. Do not repeat yourself. A mark is a mark only once.
  9. Space answers out – leaving lines and putting sub-headings, etc.
  10. An Extended Response answer should probably total a maximum of two sides of normal writing, including any diagrams.
  11. You may use diagrams. If so, make them large and make them the focus of any part of an answer. Unless specifically required, a diagram will NOT add marks if it is simply repeating what has been written in the text. Diagrams, if drawn, must be drawn properly and with care; they should not simply be tiny, illiterate illustrations of your written answer.
  12. If you obligatorily spend time planning, then so must you obligatorily spend time checking your answer at the end.

EXAMPLE

In many, many ways the example below is not good!

  • It is too focussed upon one area of the syllabus and is not broad enough for an IB question.
  • The answer is too long! (This answer was written also as a learning tool, so almost everything and anything was included. Do remember that there are often several ways to obtain marks. There may well be some content which is obligatorily necessary in the answer, but there is just as likely a statement in the mark scheme which reads, ” …. award marks to any of ….”.)
  • No diagrams are included in the answer.
  • I had no lined, exam paper available!

Nevertheless the layout and content should be checked out as a reasonable model for an Extended Response answer.

COMMAND TERMS (in this question):

  • State: “Give a specific name, value or other brief answer without explanation or calculation.”
  • Describe: “Give a detailed account.”
  • Outline: “Give a brief account or summary.”

Here is (the question and) the answer in Word, as imaged by scribd (which does not do a very faithful job!):

Here are scans of the written answer:

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scan_20161211-2scan_20161211-3

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