Week 05: Methods Presentations; Manuscript Formatting

Submitted by sbrewer on Sun, 10/02/2016 - 20:35

Meeting Location

BCRC (M311S)


This week, we will give you a chance to very briefly present your Methods paper. This is an opportunity to get feedback on the differences observed and factors identified. We will also spend a few minutes looking at manuscript submission guidelines for scientific journals and establishing a set of formatting guidelines for manuscript submission for this class.

Required Activities

I'm assumed you have already completed your own figure, have submitted your methods to me, and have been matched up with a partner (as was required before the last class meeting). Before class, please:

  1. Follow your partner's Methods.
  2. Post their figure at the course website.
  3. Once your figure has been duplicated, you should
    • Post your original figure.
    • Identify differences between your original figure and the duplicate created by your partner (to be summarized in the RESULTS of your final paper).
    • Identify the factors that caused the differences observed (to be summarized in the DISCUSSION).
    • Complete a rough draft of your complete Methods paper. (Please continue to use the same Google Doc that already contains your Methods).
  4. Find the manuscript submission guidelines for a scientific journal (here's a list of life science journals at the UMass library). Write a brief blog post that includes the title of the journal, a link to the guidelines, and a very brief summary of the requirements.

Jounal week 5

Submitted by astaubin on Fri, 02/24/2017 - 14:29

My grub-like organism has changed significantly over the last couple of days. The organism has changed from a light brown color to a very dark brown body color and has a dark color casing around its entire body. The shell seems to only be covering up half of its body almost like a cocoon. The organism still seems to be moving but not as much and spending lots of time staying completely still. Also, the organism seems to have stopped eating completely. I am unsure as to what exactly is going on but I think that it might be transforming. As I was reading online because I was curious, the organism or what I think is a “meal worm” is turning into a larvae which will then turn into a beetle. So I think it is going through the appropirate phases of its life cycle.

Animal Feed Science and Technology Journal

Submitted by rfredericks on Fri, 02/24/2017 - 13:41

For this journal, there is a long PDF including all of the requirements for submitting papers. They are stated very clealy. The submissions must include, numbered lines, double spacing and wide margins. Additionally it must have an introduction stating the objectives and providing background information. It must have a methods that would allow for the work to be replicated. If they methods have already been pushblished you must include a reference. If you have made any relevent modifications to the methods section you must state them. You must write a separate results and conclusion section.

The titale page must include the title, contributing authors and affiliation and and current residence/address as well as an email. You must include an abstract that is concise and no longer than 400 words. Immediately after the abstact you may list a maximum of 6 keywords. Any math equations included in your paper must be editable text, not images. You must use the international system of units to display data. A list of references must be included in any submissions

Regenerating pancreas

Submitted by johanthomas on Fri, 02/24/2017 - 13:22

Dr. Valter Longo published in Cell journal a potential new therapy to treat diabetes. He cycled a special diet in mice to regenerate beta cells in the pancreas which release insulin in the presence of sugar in the blood. The diet involved starving the mice and then feeding them again in cycles. The equivalent diet in humans would be low protein, low carbohydrate, and high unsaturated fats (very low calorie) for 5 days, and then eating whatever they want for 25 days. Experiments in mice showed improvement in both type 1 and type 2 diabetes. Type 1 diabetes is caused by the immune system destroying beta cells in the pancreas. Type 2 diabetes is caused by an accumulated resistance to insulin by overexposure (unhealthy lifestyle). Dr. Longo stated: "Scientifically, the findings are perhaps even more important because we've shown that you can use diet to reprogram cells without having to make any genetic alterations." When trying the diet with humans results included weight loss, lower blood pressure, lower levels of the cancer causing hormone IGF-1, and improved blood sugar levels.

Dr. Longo does not advise anyone to try this diet without the approval of a medical expert because it is more complex than people realize.


Manuscript Guidelines

Submitted by jiadam on Fri, 02/24/2017 - 13:02

Title: Journal of Cell Science

Link: http://jcs.biologists.org/content/manuscript-prep#2.

The requirements to submit material in this journal are outlined very clearly. The manuscripts are submitted using Bench>Press manuscript processing system. The article cannot be more than 8000 words, but that does not include abstract, reference list, title. Limit of 8 tables and figures which is why multi panel figures are very useful. File format is Microsoft Word, LaTeX, or rtf formatting. There should be a title page, summary statement, abstract, introduction, results, discussion, materials and methods, acknowledgements, competing interest, author contributions, funding, data availability, references, and figure legend in that particular order. Not every article will have those elements but each of those sections has strict guidelines to follow.

Perfect Paragraph Latrotoxin

Submitted by matjbaker on Fri, 02/24/2017 - 12:56

Latrotoxin has an especially high affinity for receptors located on neurons and endocrine cells. The protein is able to insert itself into the cell membrane of these cells.  Once embedded, latrotoxin works by essentially forming pores in the presynaptic membrane of neuronal cells. These pores are partially permeable to neurotransmitters, cations and water. Also, the venom may intereact with membrane bound transmitter release proteins and stimulate the depletion of neurotransmitters that way. But most importantly, the pores that the venom forms are permeable to positively charged calcium ions.

Manuscript Submission Guidelines

Submitted by johanthomas on Fri, 02/24/2017 - 12:55

The American Journal of Tropical Medicine and Hygiene has its submission guidelines posted at the website: http://www.ajtmh.org/site/misc/ifora.xhtml

To submit a manuscript the following components are necessary:

A cover letter, the title of the manuscript, a description of the significance of the manuscript, a confirmation that the manuscript is original work, disclosure of all conflicts of interest, names and signiatures of all authors, and the completion of a copyright form.

There are also specific formatting styles the journal requires to keep the material consistent and understandable.

Manuscript Submission Guidelines for Geriatric Orthopaedic Surgery & Rehabilitation (GOS)

Submitted by koganezova on Fri, 02/24/2017 - 12:54

The guidelines to submit a manuscript for Geriatric Orthopaedic Surgery & Rehabilitation journal could be found here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3789503/

The Geriatric Orthopaedic Surgery and Rehabilitation is a bimonthly peer-reviewed journal that provides information about musculoskeletal conditions that affect the aging population.


1) Make an account at  http://mc.manuscriptcentral.com/gos

2)Upload title page and main document seperately. Title page should include the title, authors name, degree, affiliation, contact info, authors disclosure or conflict of interest info, and grants/other acknowledgments. Main document should include title, abstract, keywords, text, references, tables/captions, and figures/captions.

Manuscript Submission Guidelines

Submitted by dkotorobay on Fri, 02/24/2017 - 12:44

The Journal of Molecular Biology has an eighteen page packet for manuscript submission guidelines, which can be found here https://www.elsevier.com/wps/find/journaldescription.cws_home/622890?gen...

As breifly as I can summarize eighteen pages any manuscript that is submitted must be reviewed by at least two other editors. There are also guidelines for composite images, they are not allowed to have more than four parts, graphs should be able to be edited. Footnotes should be used sparingly as the guidelines say, enough detail should be provided in the methods and materials section that the work could be reproduced. The discussion section should explore the significance of the results of the work, and a combined results and discussion section is usually appropriate and extensive citing and discussion of published literature shoudl be avoided.

The manuscript guidelines are extensive and thorough, answering any question imaginable relating to formatting and what is acceptable when attempting to submit a manuscript. 


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