author, reviewer, presenter. comma usage placement of punctuation in parenthesis and quotations...

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Author, reviewer, presenter.

George GarritySeptember 4, 2007

http://www.presentationzen.com/presentationzen/2007/04/powerpoint_some.html

http://www.youtube.com/watch?v=lj3iNxZ8Dww

This lecture will focus on the review articles

Preparing and submitting your manuscriptPeer review and editing of your manuscripts

From an author’s perspectiveFrom a reviewer’s perspectiveChecking for plagiarism

Preparing a mini-seminar based on your paper

Credits Portions of this lecture are based on the texts ofMichael Alley on scientific writing, editing, andpresentations.

Topics

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The manuscript: where to begin

BiotechnologyAcceptable topics Analytical methods

In silico biologyBioinformaticsFood, plant, chemical, and

pharmaceutical biotechnologyProtein and enzyme technologyCommercial enzymesBiochemical engineeringBiocatalysis


BiotechnologyMicrobiology

Acceptable topics

Microbial ecology and industrial microbiologyTechniquesHost-microbe interactionsMicrobial classification & identificationCell regulationMicrobial diversityGrowth and developmentAntimicrobialsGenomics


BiotechnologyMicrobiologyPharmacology

Acceptable topics

Out of scope Pure or theoretical research, clinical medicine,epidemiology

Cardiovascular and renalCancerImmunomodulationAntiinfectivesNew technologies (e.g., assays, screening)

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Gathering your information

The secondary literature (peer reviewed)Review articlesNews articles (Science, Nature, Microbe,

Microbiology Today, SIM News)Trade publications

ChemEngineering News, BioTechniques,Genome Technology, Forbes BiotechNewsletter, Science News, etc

NewspapersWall Street Journal, New York Times

Web sites Bio-IT World, The Scientist

Seminars

Where to start

The primary literature (peer reviewed)Patent literature

The next stop

Gathering your information (continued)

Background readingAt least 10-15 references from primary and

secondary literature (no more than threepapers from the secondary literature)

References should be current (published after2002)

Topic too broad?Topic too narrow?

How much?

Page length2250 words is equivalent to 11 manuscript

pages(12 pt Times Roman, double spaced)

Practical limits

Alley’s four principal constraints in scientific writing

Who will read the paper?Technical competenceBackground knowledgeInform or persuade?The importance of efficient writing

What to emphasize and when

Audience

How the content is arrangedRationaleFormat ≠style

StructureLanguage

PreciseClear, fluid, familiar, forthright, concise

Illustrations and tables

Format

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An example of a properly used figure

Viswanathan, K., 2006 MMG445 Basic Biotechnology eJournal Vol 1

The affects Weather has on growth

0

10

20

30

40

50

60

70

80

90

Florida Alaska

Cold

Warm

Hot

An example of a improperly used figure

Unpublished

An example of a properly used table

Wei, M., 2006 MMG445 Basic Biotechnology eJournal Vol 2

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Alley’s four principal constraints in scientific writing

Rules of grammar and punctuationDifficult to master because of complexities in

EnglishComma usagePlacement of punctuation in parenthesis

and quotationsHyphens, en-dashes, em-dashes

See Appendices in Alley, Craft of Scientific Writingand Alley, Craft of Scientific Editing

Mechanics

Need to remain honest vs. need to satisfy legal andorganization constraints

Politics

Things to think about while writing your manuscript

Tells the reader what the paper is aboutIdentifies the field of studyDistinguishes it from other paper in the fieldAvoid the TMI syndrome

Title

If the purpose of the paper is to inform, then itshould reveal the conclusions. It should not bea mystery

Repetition vs. redundancyShould only include the significant points

Abstract

An example of an informative title and abstract

Berger, A., 2006 MMG445 Basic Biotechnology eJournal Vol 2

Off-target Effects in RNAi Quieted by SpecificModifications in the siRNA Sequence

The analysis of gene function and treatment ofgenetic diseases are just two of the significantapplications RNAi can offer. However, extensiveoff-target effects in RNAi research applicationscause false positives and unintended silencing ofother genes. Initially, these nonspecific effectswere hoped to be resolved by creating sequence- specific siRNAs. Though more precise siRNAwere created, off-target effects still had a largeimpact on experiments. Modifications to thesiRNA sequence and structure to reduce off-targeteffects might be the key to continuing theuse of RNAi in the laboratory and widening theuse in clinical studies.

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Tells the reader what the paper is aboutIdentifies the field of studyDistinguishes it from other paper in the fieldAvoid the TMI syndrome

Title

If the purpose of the paper is to inform, then itshould reveal the conclusions. It should not bea mystery

Repetition vs. redundancyShould only include the significant points

Abstract

Should precisely describe the workInform readers why the work is importantProvide the background necessary to understand

the workDescribe how the work will be presented

Introduction

An example of a well written Introduction



The middle In a review article, it provides the reader with anorderly discussion about the status of the field,as interpreted by the author.

Material should be presented in a logical fashion(temporal, spatial, comparative, etc.)

Using sections and subsectionsImportance of consistency and parallelisms

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An example of well formed section headings

Off-target effects of RNAiInitial means of reducing off-target effectssiRNA seed region may be cause of many off-target effectsModification of siRNA to reduce off-target effectsMismatch of siRNA nucelotides by purine:purine base paringAddition of 2’-O-methyl ribose to nuceotides in the seed

regionConclusion

Berger, A., 2006 MMG445 Basic Biotechnology eJournal Vol 2


The middle In a review article, it provides the reader with anorderly discussion about the status of the field,as interpreted by the author.

Material should be presented in a logical fashion(temporal, spatial, comparative, etc.)

Using sections and subsectionsImportance of consistency and parallelisms

The end Need to provide closureProvide an analysis of your most important

findingsTreat the parts as a wholeProvide the reader with your idea about the

future of the fieldProvide information about marketability of the

technologyLength about 200-250 words

An example of a concise and well written Conclusions


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The back matter The bibliographyUnique aspects about the Current Opinions format

Author indicates those references of specialinterest and importance

AcknowledgementsTablesFiguresFigure legends


Writing in circles


By the year 2000, it appeared that LSPP was nowat the point where reactions needed to beoptimized. Already researchers were producing r-proteins that could be used for a plethora of usesranging from therapeutic, such as chemokines, toresearch oriented. The three main steps in theprocess begging to be looked at in greater detailwere transfection, purification and producingsoluble proteins, which relates to purification

The Miss SouthCarolina syndrome

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Things to think about before you begin writing: Deadlines

Week 2 - Topic selection and initial literature searchLecture/submission schedule

Week 3 - Submission of outlineWeek 6 - First submissions/presentations dueWeek 7 - First round of reviews dueWeek 14 - All assignments completed

The editorial workflow

Day 1

Day 7

Day 14

Day 15-28

Content/Form Form/Style

Form/Style

Reviewing and editing manuscripts

Rationale Reading and editing the work of others isinformativeLearning by example

Those who write betterThose who don’t

Your assignment Critically evaluate the scientific quality of eachassigned manuscript and provide feedback tothe author and editors

Edit the manuscriptFormatting errorsMechanical errorsStylistic errorsUse reviewing tools in MS Word to mark-up the

manuscriptRead in multiple passes

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Editing and reviewing manuscripts

Points to address

Is the paper in scope?Is the scientific content strong enough?What is the significance?Is the work original?Does the manuscript follow the Current Opinions

format?Should the paper be accepted, revised or rejected?Is there any evidence of plagiarism?Comments to the editors

Confidential remarks (eg. suspected plagiarism,poor quality of paper, outright rejection)

Comments to the authorSuggested changes

An example of the feedback authors receive from reviewers

A “memorable” paper

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If you can find it with Google, so can we.

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Three passagestaken out of contextand “woven” into theauthor’s paragraphwithout crediting thesource in thebibliography.

This lecture will focus on the review articles

Preparing and submitting your manuscriptPeer review and editing of your

manuscriptsFrom an author’s perspectiveFrom a reviewer’s perspectiveChecking for plagiarism

Preparing a mini-seminar based on yourpaper

Credits Portions of this lecture are based on the texts ofMichael Alley on scientific presentation.

Topics

Is this slide really necessary?

36 ptGaramond

italic

21 pt Arial

upright

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Once the manuscript is done, the presentation should be easy.

Scope Identical to the paperPresentation allows author to discuss their findings

Constraints Twenty minute presentation with five minutequestion and answer session.

Format Lecture fits into category one or two categoriesInformPersuadeInspire

Lecture flowIntroduction to orient the audienceMain body to present your findingsConcluding remarks to summarize your

findings and postulate about future researchdirections.

A few general suggestions for your consideration

Preparation time

Allow at least 8-16 hrs of preparation time for asimple presentation

Every graphic must have a purpose and must bediscussed

Complex graphics add to the prep time and requiretime to explain during the presentation

So do animations

Death byPowerPoint

Keep you slides simple, clean, and unclutteredMaintain visual balanceMaintain major elements in the same position

Use no more than three fontsPosition background elements that appear inevery slide consistently

Avoid flying text, sounds, and bulleted lists

It’s all about the science…

What to include

What not toinclude

Tables and figures from the primary literatureArrows, labels, or other “devices” to focus attention

on key points in figures and tablesCredit the source of material

FluffTextured or busy backgroundsClipartAnything that distracts from your message

Your goal is to communicate the science effectively

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When disaster strikes

Be prepared Do a projection test before submissionUpload PowerPoint file onto the OJS by 5:00 PM

on the day before presentationBring presentation on a USB “memory stick” or a

CDAnticipate a disaster and plan accordingly

Making smooth transitions between ideas

“…because as we know, there are known knowns; there are things we know we know.We also know there are known unknowns; that is to say we know there are somethings we do not know. But there are also unknown unknowns -- the ones we don'tknow we don't know.”

Rumsfeld’s axiom and knowledge bleed

But, there is something missing….

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The knowledge gradient

Unkno

wnun

know

ns

Known

know

ns

Basic and appliedresearch advances

knowledge

Knowledge bleedresults is a loss of

knowledge that hasalready been gained

Semantic resolutionprovides a mechanismto combat knowledge

bleed

Unkno

wnkn

owns

Known

unkn

owns

Let’s go to the video…

Magnetosomes are formed by invagination of the membrane

From: Komeili et al. 2006, Science 311:242

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Three dimensional reconstruction of an AMB-1 cell

Some tips and hints about getting it right

Create a Master slidePlace “constant” artwork such as logosTurn on Guides and RulersIdentify positions where text and graphics will

appearTurn off snapping to grid

Layout

Building a master slide in PowerPoint

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Some tips and hints about getting it right

Create a Master slidePlace “constant” artwork such as logosTurn on Guides and RulersIdentify positions where text and graphics will

appearTurn off snapping to grid

Layout

Raster graphics degrade. Always enlargeimage size before capturing.

Tools include Screen Capture key (PC) andGrab (Mac) for most circumstances. Alsoinsert figure (tif, png. jpg, pic, eps, ps

Crop the figure to fit on the slideFor PDF files use Acrobat (Professional)

Graphics

Extracting images from PDF files*

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PDF image to PowerPoint

Input image at 150% magnificationFrom Ward, A. and N. Bora. 2006Curr. Opin. Microbiol 9:279

PDF image to PowerPoint


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Extraction from the web page

Raster image (captured from HTML version of paper)


Some lessons from prior years

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From Rollins, S. 2005 MMG445 Basic Biotechnology eJournal


57 year old femaleleft breast


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Mood Disorders: AnOverview. Affects 1.4% to 6.4% of U.S. Population Deficiency of Monoamines in the brain

– Target of Antidepressants Bipolar Disorder (manic-depression)

– Depressive state with manic episodes Unipolar Disorder (depression)

– Depressive state Others

– Anxiety– Hypertension

From Chancy, O. 2005 MMG445 Basic Biotechnology eJournal

www.lbl.gov/Publications/Currents/Archive/Mar-05-2004.html

Bioremediation-ImportanceImportance

• Cascade effects of pollution– Environmental effects– Food chain– Human health

• Minamata Disease• http://www.vs-

c.de/vsengine/media/vsc/en/ch/16/uc/images/minamata1.jpg• http://healthandenergy.com/images/mercury_minamata.jpg

• Lead poisoning• http://www.osh.dol.govt.nz/kidz/gore/images/leadman.gif

From Simon, A. 2005 MMG445 Basic Biotechnology eJournal

What is hybridization?

The successful production ofat least some fertile offspringin a mating between twoparents not belonging to thesame gene pool.

From Bigelow, P. 2005 MMG445 Basic Biotechnology eJournal

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Bigger Problem:In a green house setting, researchers were able tohybridize jointed goatgrass with herbicide-resistant breadwheat

•The hybrids were herbicide-resistant, larger, andpossessed the hardiness of the weed species.

Weed characteristics of jointed goatgrass:•Able to germinate easily from 10 to 35 deg. C•Some germination occurs at down to 2 and up to 40 deg C•Able to survive burial up to 16 cm deep•Seeds remain viable in soil for up to 5 years.

Case One:

Problem:Natural hybrids of bread wheat and jointed goatgrasshave been found in both the US and Canada.

From Bigelow, P. 2005 MMG445 Basic Biotechnology eJournal

Hodeck,P, Trefil, P., Stiborová, M. (2002)

Flavonoid StructuresFlavanoid Structures

From Cherian, C. 2005 MMG445 Basic Biotechnology eJournal

Round 1

Round 2

Round 3

The DNA vaccine against PSA protectsThe DNA vaccine against PSA protectsmice from prostate cancermice from prostate cancer

Marshall et. al. Cancer Immunol Immunother. 2005 54(11):1082-94. From Viswanathan, K . 2005 MMG445 Basic Biotechnology eJournal

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Survivin as a lung cancer target forSurvivin as a lung cancer target forDNA vaccinesDNA vaccines

Survivin is a 16.5 Survivin is a 16.5 KDaKDaprotein that is involved inprotein that is involved incell cycle progression,cell cycle progression,and is an inhibitor ofand is an inhibitor ofapoptosis.apoptosis.

Belongs to the IAP familyBelongs to the IAP family Highly expressed inHighly expressed in

almost all cancer cells butalmost all cancer cells butalmost undetectable inalmost undetectable innormal tissue.normal tissue.

Zaffaroni N. et. al. J Cell Mol Med. 2005 9: 360-72.From Viswanathan, K . 2005 MMG445 Basic Biotechnology eJournal

Zinc Finger Proteins in NatureZinc Finger Proteins in Nature

More fingers = More specificityMore fingers = More specificity

From Barbas et al.

BackgroundBatch Fed Fermentation

http://www.cebtechservices.com/lys5.jpg

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Methods of GDNF DeliveryInd-Lentiviral Transfer Vectors

A derivative of SIN Tetracycline transactivator (tTA1) Gene expression inhibition can be induced by

addition of doxycycline – tetracycline derivative

MMG 4 4 5 Fall 2 0 0 6

Figure 2: Structures of ind-lenti-tTA transfer vector.

Evaluation of the presentation

Scientific contentUnderstanding of the topicOrganization of the presentationClarity of expressionPreparation and use of visual aidsResponse to questions

Written evaluation with 24hPost evaluation on the OJSScoring of six points aboveComments and suggestions

Scientific discussionPresentation style

Reviewer

Advantages and disadvantages of presentations

DisadvantagesOne shot for speaker and

audienceNo chance for audience to

lookup background info

Audience restricted tospeaker’s pace

Success based on speaker’sability to deliver

Difficulty of assemblingspeaker and audience ata single point in time

AdvantagesQ & A time after

presentation

On the spot revision

Modify delivery style foremphasis

Ability to use various typesof graphics

Assurance that the audiencehas witnessed theinformation

Questions?

author, reviewer, presenter. comma usage placement of punctuation in parenthesis and quotations...

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