Annotated Bibliography

Baker, Monya. "Functional Genomics: The Changes That Count." Nature 482.7384 (2012): 257. MAS Ultra - School Edition. Web. 9 Feb. 2017.

"As more mutations are found across the genome, geneticists are focusing on learning which ones are likely to cause human disease, and how."

A change in the genome or variants can cause disease in the species. With bioinformatics, it has become more and more possible to analyze (using algorithms) the potential variants and which can cause a disease. For example, "VAAST (variant annotation, analysis and search tool; vaast.html), received a lot of attention last year when researchers used it on just two newly sequenced genomes to pinpoint the mutation that causes Ogden syndrome". The area of bioinformatics are growing rapidly due its ability with time to pinpoint what mutations in the genome can cause what diseases. By pinpointing the mutation, it can be easier to help the affected.

This article gave me a broad overview in the importance of bioinformatics and how it can affect the world. This is important in my project since this made it more clear to me how diseases can be linked to bioinformatics. I can use this new understanding to research ASD and understand more readily how I can analyze it.

Linnartz, B., Kopatz, J., Tenner, A. J., & Neumann, H. (2012). Sialic Acid on the Neuronal Glycocalyx Prevents Complement C1 Binding and Complement Receptor-3-Mediated Removal by Microglia. The Journal of Neuroscience : The Official Journal of the Society for Neuroscience, 32(3), 946–952.

"Moreover, during normal brain development or before degeneration of adult retinal neurons synapses and axons are marked by the complement components C1q and C3 before they akre removed (Stevens et al., 2007). "

Koyama, Ryuta, and Yuji Ikegaya. Microglia in the Pathogenesis of Autism Spectrum Disorders. : Elsevier, 25 June 2016. Web. 2 Mar. 2017.

Proper synaptic pruning is necessary for a properly developed neural circuits.

Microglia are cells that reside in the brain and pick up weak or less active synapses in order to refine the function of more active synapses. The process of microglia picking up weak or inactive synapses is synaptic pruning.

Less and more synaptic pruning can cause excitatory and inhibitory imbalance which is likely a link to neurodevelopment problems. It is thought to be a cause to the phenotypes of ASD including social impairments and repetitive behaviors.

"Furthermore, the risk genes for ASD include a number of synapse-related genes, such as mem- bers of the neuroligin and neurexin families, synaptic adhesion molecules whose expression is significantly upregulated during the perinatal period, suggesting that defects in synapse formation are likely involved in the pathogenesis of ASD"

"The comple- ment protein C1q, the initiating protein in this pathway, and the downstream complement protein C3 opsonize or tag unwanted cells or debris for removal by phagocytic macrophages via spe- cific complement receptors. These complement proteins are highly localized to immature synapses and are required for synaptic prun- ing in the retinogeniculate system (Stevens et al., 2007). Further, it was suggested that ‘weaker’ or less active RGC synapses are tagged by the C3 protein and then detected and pruned by microglia that express complement receptor 3 (CR3/cd11b) (Schafer et al., 2012). C1q expression was increased in the peripheral serum of children with ASD (Corbett et al., 2007), leading us to hypothe- size that elevated levels of complement proteins in the ASD brain promote synaptic pruning by microglia"

"C3 Gene - Genetics Home Reference." U.S. National Library of Medicine. National Institutes of Health, n.d. Web. 10 Apr. 2017.

C3 gene that provides instructions for complement component 3 that turns on the complement protein cascade.

Who, Shirley. "How to Write a Bioinformatics Research Paper." I Was Lost, but I Live Here Now. WordPress, 30 Sept. 2008. Web. 26 Feb. 2017.

In summary of the above article, a bioinformatics paper is written beginning with one liner about the thesis and how it relates to the field it researches. I, then, go into an abstract with the following structure:

        • Sentence 1: Describe the important unsolved problem.
        • Sentence 2: Emphasize the challenge/unsolved ness.
        • Sentence 3: Describe the critical sub-problem of interest.
        • Sentence 4: Describe the opportunity presented.
        • Sentences 5-6: Briefly summarize the methods.
        • Sentences 7-8: Briefly summarize the results, including a few exact numbers or findings.
        • Sentence 9: Describe the specific contribution this research makes to the field.

Following the abstract is a well designed introduction. This begins explaining past work that helped you in developing your project(background) and describing the potential for new or continued work off of other research projects. Then, very briefly review methods taken to research the topic.

The materials and methods are then shared just like in a regular science research paper, butin this case, the materials include data sets, pre processing on that data and specific algorithms used to manipulate the data. The methods are just describing the way you evaluate and analyzed the data. DO NOT include results.

The results are then shared in the result section. Write long caption on each screenshot of data and processing to explain what is shown. DO NOT describe results only explain what is shown. This section includes figures and tables. They must be clear, useful, and aesthetically pleasing data with legend. This is the main showing of the project, so this should be bulky.

At last, the discussion section is displayed. This should review the main point of your project. Describe the positive effects the research could have in the future as well as the negative aspects of the project. Explain controversial choices made in methods and analysis. End with a reflection of the work and how it could be continued in the future.

This Article will obviously help my project as I will be writing a bioinformatics research paper. This guide will be used when doing so.

"Autism Spectrum Disorder." National Institutes of Health. U.S. Department of Health and Human Services, Oct. 2016. Web. 26 Feb. 2017.

Autism Spectrum Disorder (ASD) includes a large range of disabilities and varies from each person greatly. It includes characteristics like difficulty communicating and interacting with others, repetitive behaviors, limited interests or symptoms that hurt individual's ability to function socially.

While previously Asperger’s syndrome or Autistic Disorder were categorized separately, they are both now under the umbrella of Autism Spectrum Disorder.

Symptoms are usually categorized into two categories: “restricted / repetitive behaviors” and “social communication / interaction behaviors.” Restrictive / repetitive behaviors can include "repeating certain behaviors or having unusual behaviors, having overly focused interests, such as with moving objects or parts of objects, having a lasting, intense interest in certain topics, such as numbers, details, or facts." Social communication / interaction behaviors include many more symptoms. Some include: being upset by changed routine or by new overstimulating environment, very little eye contact or not listening to others often, not sharing enjoyment of things with others, responding unusually to others expressing emotions like anger, distress, or affection, not responding when someone makes an attempt to gain their attention, difficulty maintaining back and forth conversations, speaking for long period of time concerning subject interest without noticing uninterested listeners, echolalia (repeating words or phrases heard), using words out of place or with special meaning to them, using body language that doesn't correspond with words, speaking with odd tones (monotone or sing-song like), or having trouble understanding others' point of view or predicting actions.

People affected by ASD often are sensitive to light or sound and can have troubles with sleep, digestion and irritability.

Strengths include: "having above-average intelligence – the CDC reports 46% of ASD children have above average intelligence, being able to learn things in detail and remember information for long periods of time, being strong visual and auditory learners, excelling in math, science, music, or art."

This research should help advance my project since my project is researching Autism in depth and then analyzing the genome of a human with ASD to then compare to other organisms. This will be in an attempt to understand the disorder in more depth and provide comparisons between other organisms and humans in the effects ASD creates.

"Research." Centers for Disease Control and Prevention. Centers for Disease Control and Prevention, 05 Dec. 2016. Web. 26 Feb. 2017.

Diagnosis of ASD is often in childhood and can be easily recognizable by doctors, but in adulthood, the symptoms can overlap with schizophrenia and ADHD causing it to be difficult to diagnosis. Children typically go through regular health check ups as babies and are screened for ASD. The first screening includes parental concerns with behavior and if the child is related to someone with ASD or with born premature. If the doctor recommends the child be further screened, they are screened in a second stage. This stage includes reviewing cognitive level, thinking skills, language ability, age appropriate skills to complete regular independent activities(eating, dressing, toileting). This may also include blood tests and hearing tests since ASD is commonly paired with other disabilities. Older children are usually evaluated by his or hers school's special education staff who look for difficulties making friends, understanding sarcasm or other subtle communication skills. Looking for ASD in adults is even more challenging. It includes a psychiatrist evaluation and evaluations from peers and family members.

Autism Spectrum Disorder's causes are not known, but there are many correlations that can be reviewed such that boys are more likely to have ASD, people related to someone with ASD are more likely to have it, children born to older parents, or children who also have other genetic problems such as Down syndrome or Fragile X syndrome.

This along with the research above will give me the starting knowledge of Autism in order to further my understanding and analyze its similarity in the humane genome to other species genomes.

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