Topic: Applied Exercise 5 My Favorite Gene Exercise

Student’s Name (Last, First): DOUBLEYCLICKYANDYTYPEYLASTYNAMEYFIRSTYNAME

 

Deadline: Thursday, August19^th, midnight.
No extensions: Grades are due on August 20^th.

 

Please give your document a proper title! No proper title, no acceptance of submission. You may use something like this: Merrill, Susan-AppEx5.docx.

 

Submit via Canvas> Assignments—no email submissions, no excuses here either. Please use Microsoft Word (preferably save as .docx. Word’s Marked-Up text will be used to enter my reviews and corrections. Do not use WordPerfect, Pages, or Google docs.

 

Instructions

Be brief, one or two sentences at the most (“…brevity is the soul of wit”).>Failure to keep this space limit will result on return of your assignment for editing. Be careful with the gene nomenclature (e.g. italics for gene symbols, non-italics for gene products, etc.). Always cite your bibliographic sources and remember not to use Wikipedia.

 

I am a stickler for good bibliographies because it is part of your training as a major in the sciences. There is no excuse not to write bibliographies correctly if you follow the guidelines (see page 4) to create bibliographiesor check the Chicago Manual of Style.

 

You may research your gene in different databases, depending on the source organism. For example, OMIM for human genes, GRAMENE and PHYTOZOME for plant genes, MBGD for microbial genomes, KEGG for all biological systems, etc. About Homo sapiensgene names, “…the HUGO Gene Nomenclature Committee (HGNC) is the only worldwide authority that assigns standardized nomenclature to human genes.”

 

A final note: If you use a prior entry from previous students this will be detected because of (1) the University repository through Turnitin and (2) because we carefully read everything students submit. For example, in this version of the assignment there is no need for a narrative, just short answers consisting of two sentences maximum. Topic: Applied Exercise 5 My Favorite Gene Exercise

 

Questionnaire

 

• What is a gene? Find the most up-to-date definition that you can find. Hint: We spend some time in the course going over the history of the concept of gene, especially post-ENCODE. Topic: Applied Exercise 5 My Favorite Gene Exercise

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• What is your favorite gene? (E.g. )

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• What does it encode? (E.g.the LEP gene encodes a hormone called leptin.)

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• What is the function of the gene product? (E.g.Leptin is involved in the regulation of body weight in mammals and usually, the body’s fat cells release leptin in proportion to their size. As fat accumulates in cells, more leptin is produced, an indication that fat stores are increasing.) Notice the conciseness of this two–sentence-long answer.

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• What does your gene’s symbol mean? (E.g., the name LEP comes from the first three letters of the hormone’s name; it is written in capital letters according to HUGO’s Criteria for symbol assignment). If the meaning is obscure, try to find a rationale for why it is named that way.

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• Is there any health-related issue associated with your gene? If not, is there any special process associated with the product? (E.g., defense, cell-to-cell recognition, protection from a particular disease, association with an inherited disease.)

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• Consult Table 2.2 in Xiong’s Bioinformatics chapter selection (the reading for Minicourse 4iRAT) and familiarize yourself with the PubMed tags therein or in the NCBI Field Tags website.

DOUBLECCLICKCANDCSTARTCTYPINGCYOURCANSWERCHERE

 

• Using the suggested databases on the previous page, find at least one nucleotide and amino acid sequence for your gene.Write the corresponding entry (e.g. “Gene ID: 3952” is the NCBI Entrez for LEP).

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• Be adventurous and narrate more what you find about your entry:

 

1. Is there any publication listed that caught your attention?

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1. What chromosome is it located at (for example, in humans one may add small arm, p(petit), or long arm, q(queue) and what is its locus? (E.g.,LEP locates to the q arm of Chromosome 7from nucleotides 128,241,284 to 128,257,628).

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1. What can be found in the Clinical Synopsis of OMIM, for example?

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1. Be creative. This is your course, you learn as much as you want. Add anything that you consider has added to your knowledge of or interest in genes.

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• You may add a graph, a scheme or a mind map that would help other people understand your gene, its functions and its intricacies.

 

 

Bibliography:

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ApEx5 Rubric

 

These are the applicable criteria for your grade:

 

5. Student states why s/he chose her/his particular gene for ApEx5.

 

1. Student indicates the abbreviation for the gene, as per established standards (plant, human, bacterial, etc.) and the gene’s name, adding why this gene is called that way.

 

• Student names the discoverer(es) of the gene and/or the circumstances of the discovery (for example, if the gene is related to a disease or pathological state).

 

1. Student describes the function(s) of the gene if known, for example, if the gene codes for a structural protein, metabolic enzyme, or a non-(protein)-coding RNA.

 

1. Student mentions specific health issues associated with the gene product (e.g., mutation, chromosomal aberration, metabolic disorder, and the like).

 

1. Student presents a nucleotide or an amino acid sequence related to the chosen gene if available at the time of the assignment (i.e., you won’t be penalized if you choose a gene that interests you but that has not been sequenced). Topic: Applied Exercise 5 My Favorite Gene Exercise

 

 

Computation of grade

 

%	Criteria
90-100	Complete components i, ii, iii, iv, v, and vi
85-89	Missing one of the components above
80-84	Missing two of the components above
75-79	Missing three of the components above
70-74	Missing four of the components above
60-69	Missing five of the components above

 

 

 

Citation Style Guide✒

 

Citing a bibliography comprises two aspects: How to cite within the text and how to write down the references cited.

 

Citing works within the text you are writing

 

When citing as you write, there is a difference if the referenced work was produced by one or more authors. For example:

 

One author: (Nobel, 2003)

Two authors: (Schroeder and Hagiwara, 1990)

Three or more authors: (Bowsher et al., 2008)

 

Please notice several things: When citing in the text, do not write authors’ initials; only their last name should be written and respecting as much as possible the original spelling, e.g. (Lütcke, 1987), is preferred over (Lutcke, 1987). Regarding the locution et al., it comes from the Latin et alli(“and friends”), so there should not be a period the word et and no plural s after al. And finally the requirement for adding (or not) a comma between the author names and the year varies from journal to journal.

 

If you are describing work done by several people, both the name of the author(s) and the year should be in parenthesis: “Measurements of tendril tension were made daily (Matista and Silk, 1997).” If quoting or mentioning the name of the authors, it is correct to only write the year in parenthesis: “Nobel (2003) described an equation for K⁺ fluxes in guard cells.” Standard abbreviations are preferred when citing journals. You may omit the issue number, but the volume and the first and final page of the article should be indicated; the volume number should be either in bold type or underlined (see examples above).

 

You should not cite references that you did not consult, even if they are cited in articles that you actually read or at the end of the lab exercises in this manual. It is unethical to cite works that you did not read.

 

Examples of references from different bibliographic sources

 

Book

 

Voet D, Voet JG. Pratt CW (2016) Fundamentals of Biochemistry: Life at the Molecular Level, 5^th edition. Garland and Francis, Boston. Pp. 361-381.

 

Hunter LE (2009) The Processes of Life: An Introduction to Molecular Biology. The MIT Press, Cambridge, London. Pp. 119-138.

 

Biswal UC, Biswal B, Raval MK (2003) Chloroplast Biogenesis: From Proplastid to Gerontoplast. Kluwer Academic Publishers, Dordrecht, 353 pp.
[NB: This is not a citation from a portion of a publication, but the reference is to the book as a whole; hence, the abbreviation pp. goes after the number of pages.]

 

Review chapter in a book

 

Schroeder JI, Hagiwara S (1990) Voltage-dependent activation of Ca²⁺-regulated anion channels and K⁺ uptake channels in Vicia fabaguard cells. Pp. 144-150, in: Leonard, R.T. and P.K. Hepler (eds.), Calcium in Plant Growth and Development, Current Topics in Plant Physiology, Vol. 4. American Society of Plant Physiologists. Rockville, Maryland.

 

Robertson, D., I. Anderson, and M. Bachmann. 1978. Pigment-deficient mutants: Genetic, biochemical and developmental studies. Pp. 461-494, in: Walden, D. (ed.), Maize Breeding and Genetics. John Wiley & Sons, New York.

 

Journal article

 

Abduallah Y, Turki T, Byron K, Du Z, Cervantes-Cervantes M, Wang JT (2017) MapReduce Algorithms for Inferring Gene Regulatory Networks from Time-Series Microarray Data Using an Information-Theoretic Approach. Biomed Res Int 2017:6261802

 

Liu CI, Liu GY, Song Y, Yin F, Hensler ME, Jeng WY, Nizet V, Wang AH, Oldfield E (2008) A cholesterol biosynthesis inhibitor blocks Staphylococcus aureus virulence. Science 319:1391-1394.

 

Szabo CM, Matsumura Y, Fukura S, Martin MB, Sanders JM, Sengupta S, Cieslak JA, Loftus TC, Lea CR, Lee HJ, Koohang A, Coates RM, Sagami H, Oldfield E (2002) Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates and diphosphates: A potential route to new bone antiresorption and antiparasitic agents. J Med Chem 45:2185-2196.

 

Wentz CT, Magavi SSP (2009) Caffeine alters proliferation of neuronal precursors in the adult hippocampus. Neuropharmacology 56:994-1000.

 

Online-only journal articles

 

When searching the internet for bona fide, authentic scientific journal articles, you may find three different types of journals:

 

1. A) Exclusively online journals, e., those which were established in electronic format. For example, the several journals published under the umbrella of PLOS, the Public Library of Science (www.plos.org/publications/journals/).

 

1. B) Journals that are transitioning from printed form to electronic. So, it has been reported that the many journals and magazines published by the American Chemical Society will not be printed, but available only through the web (com/blogs/wiredcampus/chemistry-journals-go-digital-only/7264).

 

1. C) Printed journals (usually available in the library or in professor’s personal stacks) which also have online articles (e., their entire issues are available in both formats). Examples are: the prestigious journals Science, Nature, Cell and the Proceedings of the National Academy of Sciences of the U.S.A. (better known as PNAS).

 

In recent years, online-only journals have established a different way to cite. Since there are no paper pages, it suffices to have a number (i.e., an initial page) to indicate where the article starts. In addition, some journals offer downloadable citation files so writers are able to cite articles in a more standardized manner.

 

Zoppoli P, Morganella S, Ceccarelli M (2010) TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. BMC Bioinformatics 11:154.

 

Liang X-J, Xia Z, Zhang L-W, Wu F-X (2012) Inference of gene regulatory subnetworks from time course gene expression data. BMC Bioinformatics 13(Suppl 9):S3.

 

Another way to cite online articles, includes the Digital Object Identifier (DOI), which assigns a unique alphanumeric code to electronic papers. The DOI offers an excellent alternative to everchanging URLs. For example check the citation for an article from the Public Library of Science: Neglected Tropical Diseases:

 

Teixeira DE, Benchimol M, Crepaldi PH, de Souza W (2012) Interactive multimedia to teach the life cycle of Trypanosoma cruzi, the causative agent of Chagas disease. PLoSNegl Trop Dis 6(8): e1749. doi:10.1371/journal.pntd.0001749

 

Of course, DOIs can be used to cite papers that are published in print and online:

 

Brownlie, D. (2007). Toward effective poster presentations: An annotated bibliography. Eur J Marketing 41:1245-1283. doi:10.1108/03090560710821161

 

 

 

 

Internet article (not Internet journal article)

 

Given the wide variety of web pages, one may follow a very simple style (e.g. that of the American Psychological Association, which is: Contributors’ names (last edited date). Title of resource. Retrieved (date of retrieval) from web address for resource).

 

Angeli, E., Wagner, J., Lawrick, E., Moore, K., Anderson, M., Soderland, L., &Brizee, A. (2010, May 5). General format. Retrieved from owl.english.purdue.edu/owl/resource/560/01/

 

Julian Schroeder, Torrey Mesa Research Institute Chair in Plant Science, University of California-San Diego. Research. Retrieved January 27, 2018 from the World Wide Web:   biology.ucsd.edu/research/faculty/jischroeder

 

Wolf A, Beegle D (1995) Recommended soil tests for macronutrients: Phosphorus, potassium, calcium and magnesium. In: Recommended soil testing Procedures for the Northeastern United States, 2^nd Edition, Chapter 5, Delaware Cooperative Extension, Publications from the Soil Testing Laboratory. Northeastern Regional Publication N° 493.

Retrieved August 24, 2009 from the World Wide Web:

ag.udel.edu/extension/agnr/pdf/soiltesting/CHAP5-95.pdf.

 

A final brief note about using Internet citations: Many of the web pages you will find today will not be indefinitely available. Web page turnover is very fast! You should not cite more than 2-out-of-10 web pages per bibliography and that you save the corresponding HTML files for future reference (or print them as PDFs). The way to do this varies according to your computer; in the Mac environment you can print to PDF from any application.

 

You may check websites such as The Write Source of the Modern Language Association for examples of how to cite Internet references: www.thewritesource.com/mla/ or the Purdue Online Writing Lab (owl.english.purdue.edu/owl/resource/560/01/) cited above.

 

Another popular source for good citation style is the Chicago-Style Citation Quick Guide (www.chicagomanualofstyle.org/tools_citationguide.html). Follow the author-date system guidelines.

 

And please remember: No Wikipedia. No Ask! No dubious or other non-curated sources. You may try Google Scholar (scholar.google.com/schhp?hl=en&tab=ws, if you must use a popular engine) and the (truly) intelligently designed WolframAlpha (www.wolframalpha.com).

>Shakespeare W (1603) Hamlet, Act 2, Scene 2. Public Domain (The Complete Works of William Shakespeare at MIT).

✒    Adapted from: Cervantes-Cervantes M (2018) 120:202 Foundations of Biology: Cell and Molecular Biology Laboratory—Student Manual (Secure access via Blackboard). Department of Biological Sciences; Rutgers, The State University of New Jersey, Campus at Newark.