|Student Information (expand to read)|
Please leave this template on top of your student page as I will add your assessment items here.
Beginning your online work - Working Online in this course
|Lab 1 Assessment - Researching a Topic|
|In the lab I showed you how to find the PubMed reference database and search it using a topic word. Lab 1 assessment will be for you to use this to find a research reference on "fertilization" and write a brief summary of the main finding of the paper.
|Lab 2 Assessment - Uploading an Image|
OK you are now in a group
Initially the topic can be as specific or as broad as you want.
Chicken embryo E-cad and P-cad gastrulation
|Lab 4 Assessment - GIT Quiz|
Design 4 quiz questions based upon gastrointestinal tract. Add the quiz to your own page under Lab 4 assessment and provide a sub-sub-heading on the topic of the quiz.
An example is shown below (open this page in view code or edit mode). Note that it is not just how you ask the question, but also how you explain the correct answer.
|Lab 5 Assessment - Course Review|
|Complete the course review questionnaire and add the fact you have completed to your student page.|
|Lab 6 Assessment - Cleft Lip and Palate|
|Lab 7 Assessment - Muscular Dystrophy|
|Lab 8 Assessment - Quiz|
|A brief quiz was held in the practical class on urogenital development.|
|Lab 9 Assessment - Peer Assessment|
|Lab 10 Assessment - Stem Cells|
|As part of the assessment for this course, you will give a 15 minutes journal club presentation in Lab 10. For this you will in your current student group discuss a recent (published after 2011) original research article (not a review!) on stem cell biology or technology.
|Lab 11 Assessment - Heart Development|
|Read the following recent review article on heart repair and from the reference list identify a cited research article and write a brief summary of the paper's main findings. Then describe how the original research result was used in the review article.
ANAT2341 Lab 1 Lab 1
Lab 1 Assessment
This research article aimed to study the effects of elevated progesterone levels on the trigger day of in-vitro fertilization and intracytoplasmic sperm injection (ICSI) cycles. 4106 IVF cycles were analysed, with the primary measure being live birth rate. The effects of increased progesterone that were studied include oocyte retrieval rates, fertilization and implantation rates as well as clinical pregnancy rates (measured when a heartbeat is detected) and live birth rates. All these outcomes were analysed among both groups of frozen embryo transfer and fresh transfer cycles. The negative impacts on oocyte and embryo quality found in previous studies, as well as potential negative impacts on fertilization and pregnancy rates were also closely observed. Progesterone levels only slightly increased on the trigger days of these cycles, but these increases were not found to be significant enough to be considered as more than a phenomenon. The implantation, clinical pregnancy rates and live birth rates were similar among the groups of fresh and frozen embryo transfer cycles, thus revealing that raised progesterone levels on the trigger day of these cycles had no impact on embryo quality and implantation, pregnancy and live birth rates, and no negative effects were detected.
|Mark Hill 18 August 2016 - You have added the citation correctly and written a reasonable summary of the article findings. Your summary should have included an explanation/description for what the 2 key components of this study, Medroxyprogesterone acetate (MPA) and Human Menotrophins Gonadotrophin (hMG ).||Assessment 4/5|
Lab 2 Assessment
This image is from an article titled "The Relationship between Cell Number, Division Behavior and Developmental Potential of Cleavage Stage Human Embryos: A Time-Lapse Study", found through the Public Library of Science. The graph conveys the results of one part of the study, that is, the cell number distribution for all embryos in this study on day 3. All embryos studied were human.
|Mark Hill 29 August 2016 - Copyright and Student Image template correctly included with the file. The reference was not formatted correctly with the file or one your page here.
This is the code you need with the file <pubmed>27077739</pubmed> to display the reference correctly.
This is the code you need or a citation as shown correctly on your page here.<ref name="PMID27077739"><pubmed>27077739</pubmed></ref>
FYI - I have added the figure (resized) with a legend and the citation below.
Cell number distribution for human embryos on day 3
Lab 3 Assessment
|Mark Hill 31 August 2016 - Lab 3 Assessment Quiz - Mesoderm and Ectoderm development.
Question 5 - maternal diet (half mark)
Lab 4 Assessment : Quiz
|Mark Hill 17 October 2016 - GIT quiz questions on a range of topics. Question 1 needs a clearer question format, I understand but it does not clearly ask about "recanalization" and true/false are never testing questions. Question 2 should be to identify the major divisions of the GIT. Question 3 is not precise, the duct epithelium is endoderm and the underlying connective tissue is splanchnic mesoderm.||Assessment 4/5|
Lab 5 Assessment
|Mark Hill 17 October 2016 - Course questionnaire completed.||Assessment 5/5|
Lab 6 Assessment
The deletion or mutation of the epidermal growth factor receptor at the medial edge epithelium where the Transforming Growth Factor a is expressed is one of the identified genetic mutations that results in cleft palate.
A recent research article on this gene: Parental cigarette smoking, transforming growth factor-alpha gene variant and the risk of orofacial cleft in Iranian infants
TGFA is concentrated in the epithelial tissue located in the medial edges of palatal shelves. In normal development, this gene assists in the production of extracellular matrix and also enables the palate to fuse without disruption by promoting normal movement and positioning of mesenchymal cells. The receptor, epidermal growth factor, is expressed on the medial edge epithelium which degenerates in healthy embryonic development. Three mutations of TGFA associated with cleft palate are RsaI, and TaqI in intron 5 and BamHI in exon 6. When this gene and receptor are mutated, an abnormal or incomplete formation of the palate occurs.
|Mark Hill 17 October 2016 - TGFA is a factor related to this abnormality. The journal used is not a very high impact journal and you should look first at the major journals, the reference needed correct citation method. It would have been good to also include the signaling pathway involved.
Duchenne muscular dystrophy (DMD) is caused by the absence of dystrophin protein, characterised by muscle fiber damage during contraction. The only current treatment for DMD are corticosteroids which reduce the inflammation of the muscle. However, there are several side effects as well as low efficacy of this treatment. However, there have been significant reports regarding the recovery from muscle atrophy through the use of pro-inflammatory or anti-inflammatory factors, by either inhibiting them or intensifying them. Reactive oxygen species, nuclear factor-κB signaling factors and calcium channels are all targets of pharmaceuticals regulating the inflammatory response in skeletal muscle affected by DMD. Current research is being undertaken to combine anti-inflammatory pharmecutical treatment with oligonucleotide-based exon skipping therapy which restores dystrophin expression.
Animal Models include MDX.
|Mark Hill 17 October 2016 - Answers are correct, I would have liked to see included the citation of the sources used in developing your answers.||Assessment 4.5/5|
Peer Review Assessment
These are very good reviews of the project pages, with some good specific examples. They include a balanced critical assessment, perhaps a little too on the positive side, given the existing status of some of these pages. 8/10
GROUP 1 A great start to this group project has been made, with a substantial amount of textual information. No images have been included, limiting the visual engagement of the readers. The signalling pathways discussed extensively in the text would be easier to understand if images as well as diagrams and flowcharts were included. These flowcharts could summarise the processes in the Canonical and non-canonical pathways, as well as the Planar cell polarity pathway, the PCP pathway and the Wnt Calcium pathway. Since a range of pathways are described in this web page, it is essential that diagrams are included to simplify these, allowing the audience to consolidate their knowledge of these processes. Another addition could be short movies that would aid in the visualisation of these processes. Student drawn images should also be included to reflect the depth of knowledge of the individuals producing this web page. An interesting and potentially humorous image could also be included at the beginning of the web page to attract the reader’s attention and add interest to the page. One of the criteria to be fulfilled is that the wiki has an element of teaching at a peer level using the student's own innovative diagrams, tables or figures and/or using interesting examples or explanations. Hence, making these additions to the page would satisfy this criteria.
An extensive list of references have been included throughout the paper. However, no in text referencing has been carried out. For example, at the end of Caroline’s sections, references including PMIDs have been included, but the lack of in text referencing means that the specific papers used for each piece of information can not be easily identified by the reader for further reading. Other members of the group have also placed their references at the end of their respective sections, rather than using in-text referencing. Compiling all the references at the end, after in-text referencing has been completed, will improve the cohesiveness of the paper, rather than having a separate list of references for each section. This would also improve the organisation and aestheticism of the page. One member of the group has commented “I’m not sure how to reference things that aren’t from pubmed” on the page. The solution to this problem would be to either ask fellow group members and colleagues from the class, or to ask Dr Hill as to how he would like these references to be made, ie. which style of referencing he would prefer. Other good resources such as OMIM have been identified, which is commended, and looking in places other than PubMed will create an extensive reference list and a range of information from various sources. This would fulfill the criteria that the page should demonstrate that the group has researched adequately on the topic.
Subheadings have been included, organising the web page well. Names of the group members should be removed from subheadings when possible as these are visually distracting and unnecessary. Some subheadings also have not been formatted correctly, such as the “===What can go wrong?===” subheading, which needs to be fixed so that it is formatted in a similar manner to the other headings. More coherent formatting could also created in combining Tony’s “Abnormalities” and Arsalan’s “What can go wrong” sections. Many subheadings need completion with more information, including the “WnT-Calcium Ion Pathway - Tony”. In this section, the dot points “abnormalities”, “main components” and “functions” dot points should be made into subheadings and completed. The “Studies” section should also be elaborated on with more textual information, including specific researchers and dates. This section could be developed into a timeline of the history of the research associated with WnT signalling pathways, presenting this information in an accessible and interesting manner. A wide range of research has taken place, evident in the extensive list of references at the bottom of this section. This section can be enhanced by referencing other studies more specifically by naming the scientists involved, and when this research was carried out. This would be better than referring to research as “a study”. Ensure in-text referencing is carried out effectively in this section so the readers are able to easily find these research papers should they require more information.
The “Things to do/reference” list at the top of the web page should be resolved as soon as possible so that these notes can be removed from the top of the web page so that the page can begin with relevant information. The comments and dates at the top of the web page shows a progression of this project over time as well as group communication, which is commended. The glossary section should also be developed at the bottom of the page to contain definitions for words like glycolipoproteins, the TCF/LEF family, abbreviations like CaMKII, Osteoprogenitor markers such as Alp, Opn, Ocn and Bsp in Tony’s sections and other terminology that may require a brief description to provide the readers with a more comprehensive understanding. Overall, this web page is developing well, but there are still many areas for improvement.
GROUP 2 This web page is developing very well, with comprehensive information and textual information. Relevant images and diagrams have been included and accurately referenced, which is to be commended. Student produced images, diagrams and flowcharts should also be included to reflect depth of knowledge on this topic. More images would enhance the readers’ understanding of topics like the development of the Atrioventricular Canal, heart valve and outflow tract, all of which are subheadings. Short movies and animations should also be included to assist the readers in visualising these signalling pathways and embryological developments being discussed. An interesting and potentially humorous image could also be included at the beginning of the web page to attract the reader’s attention and add interest to the page, such as an image of an ordinary notch at the top of the page.
The subheadings included in this web page are appropriate and have been well organised, ensuring consistency and cohesiveness in this project. The introduction is well written, as it covers a range of topics including an overview of the role of the Notch signalling pathway as well as an introduction to the abnormalities associated with mutations in the functional components of the pathway. The timeline could also be improved by including developments in research over the last 20 years, as well as the direction current research is moving in and where future research could be headed. An elaboration on 1914 by further explaining why this is called the “Notch signalling pathway” with the aid of an image would also be useful. More information on John S. Dexter and his research process, his team and initial findings would also add depth and interest to the web page. Another table could be included in this web page to help the readers differentiate between the four Notch genes in Mammals, including further information on each gene, their respective locations on chromosomes, functions and an image of each if possible. The location of the locus of the Notch gene on the 3C7 band of the X chromosome is included, as well as the NOTCH3 located on chromosome 19p13, showing detailed knowledge and extensive research by the group. Images, potentially student drawn, of where these locations physically are would also reflect a deeper understanding.
The ‘Roles in Embryonic Development’ section and its respective subheadings have also been well organised and structured. There are several headings in this web page that require completion before the submission date, including the ‘non-canonical pathway’ and ‘transcriptional regulation of notch signalling’ headings. More animal models can also be included, with the subheadings in this section also requiring completion. An abnormalities section has also begun well and is detailed and well referenced. It still requires completion as some of the sub-headings are still empty. Images of symptoms of these abnormalities such as the rib and spine abnormalities associated with Spondylocostal Dysostosis, and the eye conditions and facial features associated with Alagille syndrome would add depth to this section. A glossary section has also been started, but can definitely be added to to improve the understanding of the readers. Terms to be added could include proteolytic reactions, ligands and descriptions of signalling molecules such as MyoD, Mash1 and GATA2.
Referencing has been carried out well, with in-text referencing throughout the web page. The introduction was well referenced, as well as the “Roles in Embryonic development”, “Animal Models” and “Abnormalities” sections. However, no in-text referencing has been carried out for the “Overview of Molecular Mechanisms” section and the timeline. This should be resolved as soon as possible so that external links are easily accessed by the readers should they want to seek further information. Complete and proper referencing would also satisfy one of the criteria of this assessment, that the content is correctly cited and referenced.
GROUP 3 This page is developing well, as extensive headings have been well organised, with substantial written and visual information. A fantastic student produced image has been included, showing the different steps in the signalling pathway in a flowchart. It is very clear and neat, and the group is highly commended for this. An interesting and potentially humorous image can be included at the beginning of the web page to attract the reader’s attention and add interest to the page. Another image showing the ‘FGF and FGFR expression patterns during endochondral and intramembranous bone development’ has been included and is very clear and relevant. Another flowchart in the “Limb Bud formation” section would also help the reader summarise the different processes and the FGFR subtypes involved in each step. Adding short animations or movies would also be very helpful in aiding the reader understand these processes, particularly in the ‘Patterning Of The Embryonic Axis’ subheading. Images in the abnormalities sections, such as what the hands, broad thumbs, feet and medially deviated broad great toes of those with Pfeiffer Syndrome look like would also add depth to the web page.
Extensive and well organised headings have been included in this project, although some headings are still incomplete. A history section has been included in this web page. The timeline in this section requires more information as only two years, 1973 and 1999, have been included. More information is needed on the research carried out over the last decade, as well as gaps in this research, where future studies are heading and what is currently being researched in relation to this signalling process. The naming of researchers and where this research took place would also show depth of knowledge and extensive research, as required in the criteria. A heading at the bottom of the web page has been included titled “New and Emerging Research Into FG” and needs more information added to it. A summary of the current findings and research should also be added to the timeline higher up on the page when this section is further worked on.
Other sections including the glossary and “Animal models” sections have been started. Further terms to define in the glossary should include full names of terms such as RAS and AER included in the web page. The “Animal models” section is a comprehensive addition to the web page but is empty and requires further research. Ensure images of the animal models being explored are included in this section to enhance the textual information and to improve the readers’ understanding of these animal models. A table of the FGFR Subtypes has been included which is commended, however, needs much more elaboration as it is still quite bare. Images of these different FGFR Subtypes would also add depth to this web page.
In text referencing has been carried out well so far in this project. The writers often need to use references again when researchers and their research is mentioned again. For example, Mathias et al. (2001) is mentioned in the Subheading “Patterning Of The Embryonic Axis”. This research was referenced in the paragraph before the researchers were specifically mentioned, and thus should be referenced again with the same reference number. In the Limb Bud formation heading, a link to the lecture notes for Limb Development has been included. This is a very good way to allow the readers to easily access more information relevant to the topic.
GROUP 4 This web page is developing well, but has many areas that need completion. Starting the web page with the flowchart of the hedgehog signalling pathway is not recommended, as the reader has not been introduced to the topic at all and does not know what any of the terms and abbreviations mean. This image would serve better further down in the web page where the reader has knowledge of this signalling process and what is involved to then apply and consolidate in the image. More images can also be included in this web page, such as an image of a hedgehog at the top of the page, which would be an interesting and humorous way to grab the reader’s attention, which is required to fulfil the criteria for this assessment. Images in the animal model section would also enhance the reader’s understanding.
Many subheadings have been included, but could be improved on their clarity. For example, the heading “Mechanism” is not very specific and thus could be improved to identify which mechanisms are being spoken about. A “History” subheading has also been included with no information. A timeline of the history of research associated with the hedgehog signalling pathway would be very comprehensive, including where future research is headed. This research should include why there are question marks (“?”) in yellow in the diagram at the top of the web page, as these could be areas where future research is heading. Ensure this table/timeline is well referenced, including names of researchers for depth of information. A glossary section should also be included to enable to reader to keep track of the different terms and abbreviations used in this web page. Terms in this list could include information on the abbreviations in the diagram included: Cos2, PKA, Slimb and a range of other terms.
A “Human disease” heading has also been included. No information has been added to this section as more research by the group members must be carried out. This heading could be more specific, such as titling it as “abnormalities” as “Human disease” can be in reference to a wide range of issues, whereas “abnormalities” or something similar is more topic specific. Images of the effects of these abnormalities would also be an interesting addition, including treatments for the diseases and their symptoms as well as future research areas. The “Animal Models” section contains substantial textual information. Images would enhance this section, such as images of the animals being studied and short videos of their embryological development. A greater focus on human embryology is needed throughout the entire web page as there is a substantial amount of information on the hedgehog signalling pathway in animals.
In text referencing has been carried out throughout the web page which is commended, and an extensive reference list is developing well. Be sure to reference information twice (using the same reference number) when they are being mentioned, so that the reader has a direct link to where this is being sourced from. For example, another reference for when “Chiang et al., 2001” is mentioned would be appropriate, as the preceding paragraph referenced this work without specifically mentioning Chiang. More in-text referencing in the “Blockage of Shh Signalling in Forebrain Neuroectoderm of Chick Embryos” section would also be appropriate, even if the same references are being re-used. This would make it easier for the readers of the web page to easily access further information at any point in the web page.
GROUP 6 This web page is slowly developing, and in comparison to the other web pages, is lacking in information, meaning there are many improvements that must be made before submission. Headings have been included which are relevant and cohesive. However, the information beneath these headings should be more substantial in text and images. Two comprehensive diagrams have been included, however they are not properly labelled or referenced. Including student drawn diagrams, tables or figures would be a great addition to the web page and would fulfil the criteria for including student's own innovative diagrams, tables or figures and/or interesting examples or explanations. The images included would serve better further down in the web page where the reader has knowledge of this signalling process and what is involved to then apply and consolidate in the image. When they are placed so high up in the web page before the reader has learnt about the process, it often makes the images seem irrelevant until this information is read. Seeing terms for the first time on an image is not the purpose of a diagram. Rather, they should consolidate and summarise the information that has just been read. Other inclusions could be a video or short movie showing processes discussed, such as the bone and cartilage formation, mesoderm induction and patterning and dorso-ventral patterning controlled by the TGF superfamily.
Several things could be included to make this web page more substantial. A table comparing and summarising the different members of the TGF family would add to the depth of this page. This table would compare the family members: TGF-beta 1, 2 and 3, Activins, Inhibins, Lefty, Nodal, Growth Differentiation Factors (GDFs), Bone Morphogenetic Proteins (BMPs), Glial-derived Neurotrophic Factors (GDNFs) and Mullierian Inhibiting Substance (MIS). This would provide evidence of significant research, which would satisfy the criteria of this project. Many of the headings and sections have not been completed. For example, a glossary section has been started but needs to be more substantial. This could include more terms such as explanations for the abbreviations used in the first diagram at the top of the page - LTBP1, LTBP2, LTBP3, LTBP4 and more.
A “History of TGF-Beta signalling pathway” has also been included with minimal information. This section would be made more accessible and easier to read by arranging it on a timeline. A “Current research” heading has also been added but again needs more information. This section is important as it highlights current gaps in knowledge. It should also be summarised to be included in the “History of TGF-Beta signalling pathway” timeline. The “Limitations” heading is not very clear. Changing this title to “Abnormalities” or something similar would be more relevant, and again more information is needed to enhance the reader’s understanding of the topic. Images could also be included here to describe the symptoms or characteristics of the diseases associated with Mutations in the TGF-beta RII gene.
Many improvements can be made to the referencing of the information in this project. No in-text referencing has been included. A few internet links have been placed under a “References” heading. This is not sufficient as the reader does not know exactly where each piece of information has come from, and hence are not able to search for the exact research paper for more information on a specific section. A wider range of references would also show comprehensiveness in the research of the group, and that they have widely researched this topic, again satisfying the criteria of this project.
|Lab 10 - Stem Cell Presentations 2016|
|Group Mark||Assessor General Comments|
Group 1: 15/20
Group 2: 19/20
Group 3: 20/20
Group 4: 19/20
Group 5: 16/20
Group 6: 16/20
|The students put great effort in their presentation and we heard a nice variety of studies in stem cell biology and regenerative medicine today. The interaction after the presentation was great.
As general feedback I would like to advise students to:
This paper discusses the impact of cyclin A2 on cardiac growth and enlargement. It has been discovered that proliferation of cardiomyocytes in adult hearts is limited after birth. Thus, the concept of stimulating mitotic divisions in cardiomyocytes can have many advantages for cardiomyocyte regeneration and can be used in the treatment of cardiovascular disease. Cyclin A2, normally silenced after birth, was shown to regulate the transition through the G1/S and G2/M stages of mitosis. Mouse models were used to test the impact of cyclin A2 on cardiomyocyte mitosis. These tests showed cardiac enlargement due to cardiomyocyte hyperplasia, which is linked to an increase in cardiomyocytes mitosis in adults and cardiac enlargement. Thus, it was concluded that cyclin A2 impacts cell division and plays an important role in cardiomyocyte cell cycle exit and cardiomyocyte hyperplasia. In the article, this research paper was referenced under the heading “The growth and homeostasis of established cardiac structure.” It was used to identify different research papers and methods of stimulating cardiomyocyte mitosis and its impacts in cardiogenisis.