Lab 1 --Z3332863 11:47, 25 July 2012 (EST)
Lab 2 --Z3332863 10:20, 1 August 2012 (EST)
Lab 3 --Z3332863 10:05, 8 August 2012 (EST)
Lab 4 --Z3332863 10:18, 15 August 2012 (EST)
Lab 5 --Z3332863 10:01, 22 August 2012 (EST)
lab 6 --Z3332863 10:04, 29 August 2012 (EST)
Lab 7--Z3332863 09:59, 12 September 2012 (EST)
Lab 8 --Z3332863 10:10, 19 September 2012 (EST)
Lab 9--Z3332863 10:04, 26 September 2012 (EST)
Lab 10 --Z3332863 10:07, 3 October 2012 (EST)
Lab 11 --Z3332863 10:04, 10 October 2012 (EST)
lab 12--Z3332863 10:08, 17 October 2012 (EST)
Full lab attendance logged. --Mark Hill 07:38, 18 October 2012 (EST)
Individual Assessments and Practical work
Origin of Nobel Prize & Discoverer
In 2010, Robert G. Edwards won the Nobel Prize for developing In vitro Fertilisation. IVF originated in 1950s when Edwards began fertilizing human eggs in cell culture dishes as a way of treating infertility. In 1978, Edward's IVF technology gave the world's first IVF baby. Over the next few years, Edwards and his team fine-tuned the technique of IVF.
Research paper on fertilisation:
What does this paper tell us about fertilisation?
This article looks at the rise of aneuploidies in IVF embryos from women around 40yrs of age. To do this Handyside et al, used 'microarray comparative genomic hybridisation' technology to study the chromosome copy number in the zygote, the 1st and 2nd polar bodies in older women receiving IVF treatment. Handyside et al found that:
- Most of the aneuploidies of IVF embryos arose from the 2nd meiotic division of the oocyte. This is surprising because most aneuploidies in naturally fertilized embryos arise from Meiosis I of the oocyte.
- Aneuploidies in IVF zygotes were not due to non-disjunction of chromosomes in the oocyte. Instead, these Aneuploidies were due to predivision of the chromatids in the oocyte.
- In IVF zygotes made from aged oocytes, often there were multiple aneuploidies in 1 zygote.
By looking at the origin of aneuploidies in IVF zygotes, these scientists are trying to find a way to reduce these aneuploidies.
Mark Hill - Q1 identified nobel laureate and linked to source. Q2 This paper perhaps relates more to aneuploidies more than around fertilisation, though an abnormal oocyte can have developmental issues I don't see the direct "fertilisation" link. 9/10
Lab 2 Prac work
Prac class work (not the assessment - see section after this for assessment
Genes that display significant strain by stage variation fall into four main categories
Genes that display significant strain by stage variation fall into four main categories. The genes that show significant variation due to strain by stage interaction were clustered hierarchically. Four distinct patterns appear in the clustered data, identified by the letters A–D. CB4856 (H) are on the left, from the egg to the young adult, while N2 (N) are on the right, from the egg to the young adult. Missing values were imputed using KNN-impute and expression values represent the average from four replicates.
Capra et al were studying the variation in gene expression during the different stages of Development of different isolates of C. elegans. This image is a microarray result, showing genes that are expressed in different amounts in different strains of C. elegans during development. This Micrarray shows allow these differentially expressed genes to be classified into 4 groups. It’s likely the genes in the same cluster are regulated in the same way.
Copyright 2008 Capra et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
lab 2 Assessment
Q1. Paper & Image Related to Fertilization
Detection and Localisation of HPV in Sperms
a. Fluorescence in situ hybridization (fluorescence microscope) for HPV DNA on sperm from a patient with HPV16 in semen. Infected and noninfected sperm are shown. Red: HPV DNA (Texas red); blue: nuclear staining (DAPI). b. Immunofluorescence (confocal fluorescence microscope) for HPV16 capsid protein L1 on sperm from a control (left) and a patient with HPV16 in semen (right). Upper panel, L1 antibody; central panel, L1 antibody and Pisum Sativum (acrosome); lower panel, L1 antibody and Pisum Sativum after induction of the acrosome reaction. Red: HPV16 L1; green: Pisum Sativum; blue: nuclear staining (DAPI). c. PCR for HPV E7 gene from sperm DNA. Lane M: DNA marker (100 bp); 1: negative control (no template); 2: positive control (sperm transfected with recombinant plasmid pIRES2-AcGFP1-E6E7); 3: sperm from a patient with HPV16 in semen; 4: sperm from a control subject.
Outline of the Research:
The results of Foresta et al show that Human Papilloma Virus (HPV) can infect sperm through interactions between the virus’ capsid proteins and Syndecan-1 of the sperm. They also found these infected sperm can fertilize the egg and pass the virus into the oocyte
2011 Carlo et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
'Q2. Protein Involved in Implantation'
Franco et al discovered that WNT4 plays a crucial role inregulating uterine development, Progesterone signalling and decidualization during Embryo Implantation. They used a WNT4 deficient mouse model to show that without WNT4, there were:
- Defects in Endometrial stromal cell survival
- reduction in uterine glands
- reduced responsiveness of endometrial cells to progesterone.
Franco et al used a mouse with fully functional Wnt4 as a control and these abnormalities were not seen in the Wnt4 expressing mouse. These researchers studied the Implantation sites of WNT4 deficient versus the control mice. They discovered, while all of the control mice showed implantation sites, only 25% of the WNT4 deficient mice had evidence of implantation. This means without WNT4, implantation cannot take place in most mice. The area of the implantation site in WNT4 deficient mice was smaller than control.
In WNT4 deficient mice, there was also a reduction in Decidualization. Franco et al induced an artificial decidualization in these mice and found the WNT4 deficient mice had a smaller decidual horn (uterine horn) than the control mice with functional WNT4. They found Wnt4 drives decidualization by enhancing the survival and differentiation of the stromal cells in the endometrium.
They noticed that in the WNT4 deficient mouse, another protein Foxa2 was reduced, in comparison to WNT4 expressing mouse. Foxa2 is expressed in uterine glands and is important in their development. Furthermore, leukemia inhibitory factor (Lif), a protein secreted by uterine glands, was also reduced in WNT4 deficient mice but not the control.
Mark Hill - Q1 image uploaded successfully and summary contains all required information. Q2 - good detailed answer 10/10
Lab 3 Assessment
Q1. Identify the difference between "gestational age" and "post-fertilisation age" and explain why clinically "gestational age" is used in describing human development.
- Gestational age is the age of the Conceptus or Pregnancy. Gestational age is timed from the first day of the woman's last Menstrual Cycle. However, Post-fertilisation age is the time lapsed since fertilisation of the oocyte.
- Gestational age is used clinically because it is hard to pinpoint the exact day of Fertilisation. Ostetricians can ask the woman when was the first day of her last menstruation to work out the gestation age.
Q2. Identify using histological descriptions at least 3 different types of tissues formed from somites.
- Skeletal Muscle - Formed from the Myotome of the somites. Skeletal muscle is made up of contractile units called Sarcomeres. Components of sarcomeres can be seen using electron microscopes. The sarcomere has a Lightly coloured H band in the middle. This H band consists of actin filaments and myosin tails. The myosin heads interact with actin in the A band (just beside the H band). This gives the Dark band seen under the miscroscope. On the sides of each sarcomere is the Z disc where actin filaments of adjacent sarcomeres are attached.
- Dermis - formed from the Dermatome of the somites. dermis is the deep layer of skin, under the epidermis. Dermis is divided into 2 layers - Papillary layer and Reticular layer. Papillary layer has very fine collagen fibres and lots of cells and blood vessels. It is made up of loose connective tissue. Reticular layer is a dense connective tissue layer, made up of bundles of interlacing collagen fibres.
- Bone - Vertebral body and Intervertebral disc are formed from the Sclerotome of the Somites. Histologically, bone form 2 types of organisations - Compact bone and Trabecular bone. Vertebrae are made up of mainly trabecular bone. Trabecular bone is deposited in the form of lamellae but the lamellae do not form Haversian systems. Trabecular bone is made up of tiny bony bars with intervening spaces. A fully developed vertebral column is made up of 7 cervical, 12 thoracic, 5 lumbar, 5 (fused together) sacral and 1 coccygeal vertebrae. The Invertebral discs are made up of a gelatinous nucleus pulposus, enclosed in a fibrous annulus fibrosis. The annulus is made up of concentric rings of collagen fibres. These fibres fuse with the longitudinal ligaments. reference: <pubmed>16595436</pubmed>
Reference: Blue Histology 
Mark Hill - Good answers, you might have mentioned the approx. 2 week difference between the two timings. 10/10
Lab 4 Assessment
1. Identify the 2 invasive prenatal diagnostic techniques related to the placenta and 2 abnormalities that can be identified with these techniques.
Chorionic Villus Sampling (CVS)
Catheter is passed into the uterus to collect cells from the placental Chorionic Villi. Ultrasound is used to guide the catheter to the chorionic villi. CVS identifies the karyotype of fetus. CVS identifies chromosomal diseases like:
- Down’s Syndrome
- Cystic Fibrosis
- sickle cell anaemia
Fetal blood is taken from the Umbilical vein, at the placental end of the vein. Ultrasound imaging is used to guide the needle to the umbilical vein. Blood cells are analyzed in the lab. Cordocentesis looks for the following abnormalities:
- Infections like toxoplasmosis, Cytomeglovirus and rubella
- fetal Anaemia
- Down's Syndrome
2. Identify a paper that uses cord stem cells therapeutically and write a brief (2-3 paragraph) description of the paper's findings.
This paper investigates the therapeutic value of Umbilical Matrix Stem Cells (UMSC) which is found in Wharton’s Jelly of the umbilical cord. UMSC may be used to treat Parkinson’s disease. Rats with Parkinson’s disease (PD model rats) were given human UMSC as a transplant. One of their preliminary experiments showed there is no rejection of the transplanted cells. Severity of Parkinson’s disease in rats is measured by rotational behaviour of the rats – the more rotations, the worse the disease. Rats with UMSC implant showed a significant reduction in the number of rotations compared to those without UMSC transplant.
Weiss et al also found an increase in the number of Dopaminergic (DA) neurons in PD model rats that were given the UMSC transplant. Weiss et al found UMSC secrete large amounts of GDNF that can stimulate DA neuron growth and fibroblast growth factor 20 which can increase the survival of DA neurons. These factors secreted by UMSC may be responsible for the increased number of DA neurons seen in the rat’s brains after UMSC transplant. Low DA neurons, especially in the ventral tegmental area, are responsible for Parkinson’s disease. Thus by increasing the number of DA neurons UMSC may treat Parkinson’s disease in people.
Mark Hill - Good answers. 10/10
Lab 7 Assessment
1. (a) Provide a one sentence definition of a muscle satellite cell (b) In one paragraph, briefly discuss two examples of when satellite cells are activated ?
- A muscle satellite cell is stem cell located in skeletal muscle that promotes regeneration, growth and repair of skeletal muscle fibers. 
- Satellite cells can be activated after extreme exercise. A study was done by Darr et al where mice were vigorously exercised and the level of activated satellite cells were measured before and after their exercise.  This study showed exercise can increase the level of satellite cell proliferation which is needed to repair necrotic muscle fibers as a result of extreme exercise.  Exercising skeletal muscles may release mitogenic factors that increase satellite cell activation and proliferation.  Insulin-like Growth Factor I (IGF-1) can induce skeletal muscle hypertrophy.  This hypertrophy may be caused by activation satellite cells.  Activated satellite cells increases protein synthesis in muscle fibers to cause muscle hypertrophy.  Thus another example of satellite cell action is in IGF-1 induced muscle hypertrophy.  Satellite cells are aslo activated in Duchene's Muscular Dystrophy (DMD).  In DMD, fibres are lost due to a deficiency in Dystrophin which causes tearing in the cell membrane and activated satellite cells proliferate to replace these lost cells.  as the age of the DMD patients increase, the replicative potential of the satellite cells reduce, more so than the control (children without DMD). 
2. In one brief paragraph, describe what happens to skeletal muscle fibre type and size when the innervating motor nerve sustains long term damage such as in spinal cord injury?
In mice, cutting the spinal cord results in severe atrophy of the muscle fibers.  This is where muscle fibers reduce their size and cross-sectional fiber area.  Muscle fibers also seem to switch to a 'fast' phenotype, instead of slow fibers. Sustained motor neuron injury also increases the amount of Myosin Heavy chain 2b in skeletal muscle fibers. 
Mark Hill - Good answers, I would prefer a scientific source be used in your answers, not an online dictionary. 9/10
Lab 8 Assessment: Peer Review of Group Projects
Really funny image of the large eared dog is a great way to capture reader attention. It’s nice to see the importance of hearing in so many aspects of our lives. Finishing the introduction with an outline of the project is very appropriate because it sets up a framework of what you are going to talk about Overall, the introduction was very well written. The language is beautiful. However, there is a typo in ‘energy produced has be converted’.
Information presented in the history table was succinct and brief. It would be good to include proper references (in text citations) for each entry. There seems to be a gap between 1898 and 1978. Have there been any discoveries in those 80 years? It just seems like a big leap to go from the first portable electric hearing aid to a cochlear implant without any advances in hearing aid technology in between those years.
Anatomy of the ear was very clear. The text related to the picture nicely. The image enables readers to see all parts of the ear in relation to each other. It would nice to put an enlarged image of the inner ear and organ of Corti. Some people might not know what a ‘utricle’ or ‘saccule’ looks like and on that image it may be too hard to see.
With the development section, it would be good to include some images related to the development of outer, middle and inner ear. For example, include an image of week 5 embryo and label where the pharyngeal arches are so people with no background in embryology can understand what parts of the embryo you are referring to. Some of terminology, such as ‘auricular enlargement’, ‘tragus’ and ‘helix’, is hard to understand. Relevant images would help.
It would be good to put in text citations after important sentences in the paragraphs of outer, inner and middle ear development. This is because a couple of paragraphs (e.g. the middle ear paragraph) had several citations at the end of the paragraph and we don’t know which sentence or fact corresponds to which citation.
In the ‘Otic placode’ section, it’s great to see the images well referenced and have the correct copyright. ‘Early expression of Pax2 and Pax8 compared’ and ‘The expression of Sox2 and Sox3 during development of the ear’ images were useful because they reflected the processes outlined in the text. Maybe simplify the signalling information on the FGFs because I found it hard to understand. Maybe give a summary of the roles of the major factors – a table, showing ‘factor...process it controls’, would be nice.
‘Recent model related to sensory fate’ image made a complex process simple – this is great to see. ‘Establishing polarity and formation of inner ear structures’ section was very well written. Maybe put this under the same section as the inner ear. I feel the 2 sections are related.
Abnormal hearing section was very detailed and extensive. It covered so many hearing abnormalities. It would be good to include available treatments for some of the diseases and give a summary table – ‘causes...disease...description of disease...prevalence...treatments’. --Z3332863 14:35, 25 September 2012 (EST)
Great eye image at the start to capture attention. It's nice to see that it has the correct referencing and copyright.
The introduction is very clear and simple to read. Overall the written content is easy to understand and provides sufficient detail to cover the developmental stages of the eye and associated structures like the optic nerve and lacrimal glands.
The images throughout the project were very useful because they complement the text nicely. The student drawn diagrams made the optic vesicle formation easier to understand. However, I think the labels are a bit small - you can really only read them if you click on them and see the larger version. If you can put some labels on the orientation (such as the ventral side, posterior side, etc), that would be great too. Can you also put a reference as to where you got the information to draw these images from?
The images you got from the 'Atlas of development of man volume 2', can you put the copyright up? Not many textbooks allow using their images but if it is allowed for this book, you should definitely include the copyright there.
Sections that seemed incomplete are history and current research. with the current research information you uploaded, can you add a bit more text just to summarize what the study found out? There's a picture there with some description but it would be good if you can put into dot points what the significant findings are.
It would also be good if you can write something on the visual cortex of the brain. I think it links in with the section on Optic nerve. Maybe mention some of the genes related to the various stages of eye development. It doesn't have to be a lot of detail - just suggest what stage of development the genes are responsible for.
It would be good if you used more research papers instead of using the textbooks. If you are using the textbooks, it's good to track down the references the textbook used. This means you can put the relevant research papers as reference instead.
--Z3332863 16:09, 23 September 2012 (EST)
The introduction seemed to go into a lot of detail. for example, the information on Type II receptors should be placed in the same section as neural pathways, not the introduction. Can you also include in your introduction, an overview of what you are going to talk about in your project? That would give your project more structure.
With the neural pathway section, can you draw or find a diagram for that section? I find it hard to understand without one. The taste map section goes into a lot of detail which I think is unnecessary because this is a development project.
Current research section is very interesting. I don't think you need to add any more content on that section - that section to me looks complete, besides a few formatting and referencing issues with the images.
Overall, I felt there wasn't enough written on the development of taste, either the receptors (taste buds) or the neural pathways. Your project seem to focus on the anatomy and physiology or function of the taste system. This is alright to keep but the focus should be on development. You do have a Time-line of taste development that summarizes the development of the Gustatory system which is great to see. I think use that as a starting point and expand on each stage in text form, below the table. In week 12 development in this time-line, you mention 'epithelial types I and II', what are they? Are they similar to skin cells?
Overall, the balance between images and text is great. The colourful images work wonders in breaking up the text. Having said that, Many of your images did not have the correct PMID referencing. These images include:
- images of taste being revoked by visualizing ATP release
- CVP of WT and DKO mouse with H & E and SEM
- histology - can you give a more relevant title for this image? We know it's histology; we can see that. What is this image about?
- Abnormal of Tongue - it should say abnormality of tongue
The history section is excellent because it spans over such a long time - 350BC to 2010. The layout of a coloured table for history is beautiful, clear and concise.
--Z3332863 16:35, 23 September 2012 (EST)
The introduction was very interesting to read - 1000 genes related to olfactory system is amazing. The introduction isn't too long which is great. However, it would be good to include in text citations. Where did you get your information from?
The history section will look better if it was put into a table.
The 'Timeline of Development process' is excellent because it clearly presents so much information with respect to the time the differentiations took place. I can't wait to see the images though because some of the concepts were hard to understand without visual aids. For example, 'specialized areas in rostrolateral regions of head of olfactory placodes' - where is that on the embryo?
The normal function section was short. This is nice to see because this project is about development, not about the function. It would be good to include a diagram of the signaling pathway in this section, just to make it interesting.
The structure section needs a bit more information. Maybe put the olfactory bulb image in this section as it relates more to structure. You can also put some images of the cribiform plate in here too.
Abnormality section on Kallmann's syndrome was very well written. It had lots of detail, presented clearly in point form. Can you describe some of the other diseases in just as much detail as well? It just seems like Kallmann's syndrome is the main disease and there's not a lot of focus in other abnormalities.
In current research, 'the 'role of Odorant receptors' need to have some text and content in that section, not just the reference.
--Z3332863 16:58, 23 September 2012 (EST)
Abnormal vision development
Introduction gives an overview of your project. This gives structure to your project. The introduction is a little too brief. It would be nice to add some detail about the significance of eye abnormalities:
- how important is vision to humans
- how does vision abnormalities affect people
- how many people are suffering from major eye abnormalities, etc.
Great images. They highlight the severity of abnormalities associated with vision. It would be nice if you can make the images a little bigger or add more images. it just seem there's too much text and not enough images to break it up.
The normal development section is succinct and give sufficient background information so readers can understand the abnormalities section. It would be good if you can put this normal function part into point form or table. for example, 'stage...development'
The gene mutations section is very complicated. Maybe talk about the FOX genes and Pax6 genes in abnormal lens development and not as a separate section. This is so readers can associate the mutation with the disease immediately, without having to scroll to the bottom to find the consequences of such mutation. The layout makes the disease and gene section hard to understand. Maybe set it out as:
- Genetic mutation
- diseases from this mutation
- clinical symptoms of diseases
- treatments for the diseases
Most of the images are well referenced, except Albino Fundus image. for this image, you need the PMID reference style.
References 45-48 should be placed as one reference.
--Z3332863 17:26, 23 September 2012 (EST)
Mark Hill - Good peer assessment feedback provided in your comments. 10/10
Lab 9 Assessment
Identify and write a brief description of the findings of a recent research paper on development of one of the endocrine organs covered in today's practical.
This article looks at the senstivity of the melatonin secretion by the pineal gland in response to blood insulin levels. Previous studies have shown that insulin increases the amount of Norepinephrine (NE) stimulated melatonin relase. In this study, it was found that insulin potentiates the melatonin secretion at the beginning and the end of night time. many protiens of the insulin signalling pathway were observed in the pineal gland. This molecules include:
When these researchers blocked PI3K with a kinase inhibitor LY 294002, melatonin production by the pineal gland was reduced. So this pper showed tat melatonin release is stimulated by insulin during certain periods in the day and there is crosstalk between the pathways of insulin signalling and melatonin production.
Identify the embryonic layers and tissues that contribute to the developing teeth.
Embryonic Layers and tissues contributing to developing teeth:
- ectoderm of the first pharyngeal arch
- neural crest cells
- ectomesenchymal cells
These 3 embryonic tissues/layers give rise to:
- produce enamel
- comes from differentiation of pre-ameloblasts that rose from inner enamel epithelium
- Neural Crest - derived mesenchymal cells or odontoblasts:
- secrete predentin which calcifies into denti
- Periodontal Ligament:
- is the connective tissue that that surrounds the tooth root
- acts as a shock absorber and sensory apparatus
Mark Hill - there is also a mesoderm mesenchymal contribution. 10/10
Lab 11 Assessment
Q. Identify a recent research article (using the pubmed tags to cite) on iPS cells and summarise in a few paragraphs the main findings of the paper.
This research article has found that iPS cells can be subject to immune rejection by the recipient from which the iPS cells were derived. This is surprising because iPS cells are reprogrammed from cells that came from the same recipient. So technically, the iPS cells should have the same genetic content as the recipient and not be sujected to immune rejection. This immune rejection is not seen in embryonic stem cells (ESC). The scientists generated ESCs from inbred mice and when these ESC were implanted into the mice, these embryonic stem cells were not rejected. The aim of this paper was to find out why there is an immune rejection associated with iPS cells but not with ESCs.
To carry out this investigation, Zhao et al reprogrammed C57BL/6 (B6) mouse embryonic fibroblasts into iPS cells using 2 different methods. The retroviral method involves integration of the viral genome into the host cell's DNA and gives ViPSCs. This retroviral method involved using retroviruses carrying genetic information that encoded the Yamanaka factors (Oct4, SOX2, Klf4, c-Myc). Zhao et al also performed a new non-integrative, episomal method to give episomally derived iPS cells (EiPSCs). This episomal appraoch uses an episome vector which encoded the 4 Yamanaka factors. When Zhao et al placed these iPSCs into the recipient mice from which these cells were derived, they observed immune rejection with the teratomas formed by the ViPSCs. The teratomas formed by EiPSCs stimulated an immune response involving T cell infiltration and damage to tissues. when they put the EiPSC into mice with CD4+ and CD8+ T-cells knocked out, they didn't notice any regression of the EiPSC teratomas. Conversely, the teratomas formed by ESCs were not immune rejected at all.
These scientists then conducted a 'global gene expression analysis' on the EiPSC and ESC teratomas. From this analysis they found that EiPSCs overexpressed many genes that were not over expressed in the ESCs. These difference in gene expression could be a result of epigenetic reprogramming, although this wasn't tested in their study. It may also be possible that the genes of the iPSC have undergone mutations which lead to abnormal gene expression. They concluded that this gene over-expression may contribute to the induction of a T cell response against the EiPSC teratoma and so the immungenicty of iPS cells must be analysed for each patient before using these cells as a treatment.
Mark Hill - Good summary to the iPS paper. 10/10
Group Project notes and Articles
Article on Pain Development: