mcb 3020l - syllabus fall 2015 microbio-1

8/19/2019 MCB 3020L - Syllabus Fall 2015 Microbio-1

http://slidepdf.com/reader/full/mcb-3020l-syllabus-fall-2015-microbio-1 1/21

Syllabus for MCB MicrobiologyLabsMCB3020L and 3023L

Contact Information - Course CoordinatorMonika W. Oli, PhD

e-Mail: [email protected]

Oce: RM 1049, MC !uildin"

Oce #ours: $!%

&e'site: (tt):**microcell.u.edu*director+*facult+*monia-oli*

lease contact +our /raduate $% and under"raduate $%s for an+section s)ecic uestions2 Contact me 3r. Oli5 an+ time if +ou (a6e

unresol6a'le )ro'lem 7it( an+ of +our $%s.

!orgina Olyss!, radua"! #!aching $ssis"an" %PhD&

e-Mail: "t(om)[email protected]

Oce: RM 180, MC !uildin"

Oce #ours: $!%

Cours! "i'! and loca"ion

a's 7ill 'e (eld in t(e Micro'iolo"+ and Cell cience !uildin", Museumri6e, Room 100 and 108; <teac(in" la's=. On t(e rst da+ (l!as! 'ak!

sur! you ar! in "h! righ" s!c"ion in "h! corr!c" roo'. lease c(ec onII for +our correct section 'efore +ou come to t(e rst la'. Mae sure +ouno7 7(o +our $% is.

Labs s"ar" during "h! )rs" *!!k of class!s. a's usuall+ last for all )eriods2

$a'le of Contents

Con"ac" +nfor'a"ion Cours! Coordina"or..............................-

Course time and location..........................................................................1W!lco'!.............................................................................3

Cours! O/!r/i!*...................................................................&(at +ou 7ill no7 at t(e end of t(e course............................................4a'orator+ ills........................................................................................>a'orator+ $(inin" ills.........................................................................>

#!1"books and !uir!d r!ading..................................................4Micro %)).................................................................................................. ;

1

http://microcell.ufl.edu/directory/faculty/monika-oli/

http://microcell.ufl.edu/directory/faculty/monika-oli/



!oos and references................................................................................;

!""ing s"ar"!d.....................................................................561(!c"a"ions of "h! s"ud!n"s.......................................................7

S"ud!n" !/alua"ion...............................................................7$""!ndanc! and Par"ici(a"ion %89&............................................................?

Lab 6"iu!""! %89&........................................................................................?:ui;;!s %-09&................................................................................................ 9Mid"!r' 61a' %289&....................................................................................9<inal 61a' %-09&..........................................................................................9Pro=!c"s, "alks %-09&....................................................................................96l!c"ronic lab no"!book %-09&....................................................................9S"ud!n" +ni"ia"!d !s!arch Pro=!c" %209&...............................................1061"ra cr!di" %no 'or! "han 89&................................................................10

/radin" and nal "rades.........................................................................10Mak!u( Policy...........................................................................-0S!a"ing and Lock!r assign'!n".................................................--Biosaf!"y in "h! Microbiology Labora"ory...................................--

>nd!rlying '!dical condi"ions...................................................--<u"ur! "!aching assis"an"s for 'icro labs and L!""!r ofr!co''!nda"ion.......................................................................--O"h!r >< (olici!s......................................................................--

%cademic #onest+...................................................................................11oft7are se........................................................................................... 18Cam)us #el)in" Resources..................................................................... 18er6ices for tudents 7it( isa'ilities.....................................................1

!n!ric *!!kly sch!dul!.....................................................-

Da"abas!s you *ill us!........................................................-4Airtual )ond di) B for 7et mount identication.......................................1;

C!I $aDonom+ <no )ass7ord=................................................................ 1;/ideon B to determine +our unno7n and for )u'lic (ealt( )roEect........1;% lims B to retrie6e +our 1;s % seuence.......................................1;!%$ B for seuence ali"nment.............................................................1;Food afet+ First B for "ro7t( cur6e simulation.......................................1;

O("ional sof"*ar! and da"abas!................................................-4Gndnote&e' Reference mana"ement )ro"ram.......................................1;#ealt(Ma)...............................................................................................1;

Microbiology ?id!os............................................................-4Microbiology in"ro.....................................................................-5

a' afet+ Rules......................................................................................1Hail+ Routines......................................................................................... 1H%se)tic $ec(niues..................................................................................1H

Basic M!"hods..........................................................................-5trea for isolation.................................................................................. 1H!asic %natom+ of a Microsco)e...............................................................1H&et Mount...............................................................................................1Hi)ettin"..................................................................................................1H

Co'(u"!r #u"orials...................................................................-5/ra)(in" 7it( GDcel................................................................................1H

8



/ro7t( cur6e and "ro7t( rate calculation..............................................1H?isuali;ing Microb!s.................................................................-5

/ram tain.............................................................................................. 1He"ati6e tain......................................................................................... 1HCa)sule tain..........................................................................................1HFla"ella tain...........................................................................................1H

#radi"ional Diagnos"ic M!"hods..................................................-7IM.......................................................................................................... 1?(enol Red !rot(.....................................................................................1?!lood %"ar...............................................................................................1?Mannitol alt %"ar................................................................................... 1?MacCone+ a"ar......................................................................................1?%se %"ar............................................................................................. 1?Citrate %"ar............................................................................................. 1?Catalase $est...........................................................................................1?%naero'e ar............................................................................................1?

Mol!cular Diagnos"ic "!s"..........................................................-7CR 1....................................................................................................... 1?

CR 8....................................................................................................... 1?CR ....................................................................................................... 1?

Bioinfor'a"ics..........................................................................-@euence retrie6al and !last...................................................................19!last tutorial and )(+lo"enetic tree........................................................19

Diagnos"ic "!s"s........................................................................-@GI%....................................................................................................... 19

Parasi"!s..................................................................................-@Fecal oat................................................................................................19

?ir"ual <i!ld #ri(s......................................................................-@ia"nostic la' F Aet c(ool...................................................................19

Docu'!n"ari!s A s"ud!n" (ro=!c"s..............................................-@+me documentar+..................................................................................19C(olera out'rea in #aiti <)u'lic (ealt(=.................................................19

Cool S"u.................................................................................-@Micro'es did +ou no7JJ......................................................................19&(+ micro'iolo"+K..................................................................................19Meet t(e MC facult+..............................................................................80

&elcome2&elcome to t(e Micro'iolo"+ a'orator+. In t(is course, 7e 7ill learntec(niues used in micro'iolo"+ and (o7 t(e+ aLect all as)ects of our li6es.

Man+ of +ou 7ill 'e familiar 7it( some of t(e to)ics co6ered in t(e la'eDercises, 'ut (ands-on eD)erience is in6alua'le to reall+ understand man+ of t(e tec(niues tau"(t. our $%s and I 7ill 7or closel+ 7it( +ou to ensure t(at+ou (a6e a "ood "ras) of t(e to)ics and met(ods co6ered.

&e (a6e incor)orated a num'er of )roEects and student initiated acti6ities into t(e s+lla'us as 7ell as student )resentations to )ro6ide +ou 7it( a 6ariet+of learnin" eD)eriences. Our ultimate "oal is for +ou to com)lete t(esemester 7it( t(e feelin" t(at micro'es are im)ortant in e6er+ as)ect of our



li6es B and 7it( t(e notion t(at +ou (a6e learned somet(in" +ou can use fort(e rest of +our life and not Eust to "et an %2

I 7ould lie to em)(asiNe t(at 7e are (ere to (el) +ou. our $%s and I (o)e tosee +ou all durin" o)en la' or our oce (ours <or '+ a))ointment=, es)eciall+if +ou (a6e uestions or need assistance.

Course O6er6ie7 $(is is an under"raduate la'orator+ course to learn and eD)lore a 6ariet+ ofmicro'iolo"ical tec(niues, sills and conce)ts. $o)ics t(at 7ill 'e co6eredinclude 6isualiNation and enumeration of micro'es, traditional, molecular andimmunolo"ical dia"nostic tec(niues, 'asic tec(niues used in )arasitolo"+,6irolo"+ and m+colo"+. tudents 7ill "enerate, anal+Ne and inter)ret data,desi"n and conduct a small researc( )roEect and "ain eD)erience in tec(nical7ritin" and )resentation sills. ou 7ill "ain a7areness a'out t(e u'iuit+and di6ersit+ of micro'es and t(e "ood and 'ad roles t(e+ )la+ in +our e6er+da+ life.

Wha" you *ill kno* a" "h! !nd of "h! cours!

% student successfull+ com)letin" 'asic micro'iolo"+ la' course 7illdemonstrate a'ilit+ to use, eD)lain and )racticeJ..

4



Labora"ory Saf!"y1. Microbiological (roc!dur!, includin", )ro)er la' etiuette <(and7as(in", disinfectin" la' 'enc(es and eui)ment=, follo7 met(ods for ase)tictransfer, re)ortin" all s)ills, understandin" O#%s !lood 'orne at(o"en

tandard, )ro)er dis)osal of diLerent t+)es of 7aste, follo7in" "ood la')ractice, includin" returnin" materials to )ro)er locations, )ro)er care and(andlin" of eui)ment

8. Pro"!c"i/! (roc!dur!s, Includin" t+in" lon" (air 'ac, 7earin" )ersonal)rotecti6e eui)ment <la' coats, "lo6es 7(en needed, closed toed s(oes=P oeatin" or drinin" in t(e la'orator+

. 6'!rg!ncy (roc!dur!s, includin", locatin" and )ro)erl+ usin"emer"enc+ eui)ment, re)ortin" all inEuries immediatel+ to t(e instructor

Labora"ory Skills

1. >s! a brigh" )!ld ligh" 'icrosco(! to 6ie7 and inter)ret slides,)ro)erl+ )re)are slides and 6arious stains to 6isualiNe micro'es

8. >s! 'icro(i(!""!s and understand t(e correct 6olume and )i)ette ti)s touse for eac( eD)eriment, com)re(end accurac+ and )recision to (a6e a "ood)i)ettin" tec(niue. Pro(!rly us! as!("ic "!chniu!s, to o'tain and maintain a )ure culture

4. +d!n"ify unkno*n organis's '+ usin" a))ro)riate micro'iolo"icalmedia and test s+stems, and molecular met(ods

>. 6s"i'a"! "h! nu'b!r of 'icrob!s usin" dilution tec(niues,s)ectro)(otometer and a (emoc+tometerP )redict (o7 6arious "ro7t(conditions aLect t(e num'er of life cells

;. erform and inter)ret a disk diusion assay and understand (o7 to testfor t(e eLecti6eness of a 6ariet+ antimicro'ial a"ents

H. erform and inter)ret an 6L+S$ assay and no7 tec(niues (o7 todetermine anti'od+ )re6alence in a )atients immune res)onse to )at(o"ensP

?. !e a'le to descri'e t(e )ro'lem of global *a"!r con"a'ina"ion, andunderstand t(e )re6alence of "lo'al occurrence of )arasites, )erform andinter)ret a f!cal oa" and conduct 7ater )urication met(ods to )re6ent7ater 'orn infections

9. se standard micro'iolo"+ labora"ory !ui('!n" correctl+ <includin",incu'ators, centrifu"es, 6orteD, s)ectro)(otometer, CR mac(ine, ima"in"

>



s+stem= and follo7 eD)erimental )rotocols

Labora"ory #hinking Skills

1. >nd!rs"and and a((ly "h! sci!n"i)c '!"hod, includin" formulation ofa clear, ans7era'le uestion and (+)ot(esisP researc( of )eer re6ie7edscientic literature, conduct and eDecute a))ro)riate eD)eriments 7it(correct controls, e6aluate, anal+Ne and inter)ret results8. $naly"ical skills, includin" collection and or"aniNin" data in as)reads(eet, anal+Ne and )resentin" data in an a))ro)riate from <"ra)(s,ta'les, "ures, or descri)ti6e )ara"ra)(s=, assessin" t(e 6alidit+ of t(e data<means, standard de6iation, si"nicance= and dra7in" a))ro)riateconclusions 'ased on t(e results. Co''unica"ion skills, includin" )re)aration of )resentations of currentto)ics in micro'iolo"+, de6elo)in" educational materials and )resentin" la'results or ndin"s to +our )eers4. Big (ic"ur!E skills, includin" understandin" (o7 micro'es )la+ a'enecial and detrimental role in our lo6es and t(e en6ironment. tudentss(ould 'e a'le to read and inter)ret current ne7s and )o)ular literaturerelatin" to micro'iolo"+ and e6aluate t(e scientic merit of t(e information)resented. %ll students s(ould com)re(end t(at science is not Q'lac and7(ite and t(at ne7 scientic ndin"s ma+ alter t(e inter)retation of olderdo"mas. Finall+ students s(ould "et a "lim)se of (o7 micro'es (a6e al7a+ss(a)ed (istor+ and aLect our e6er+ da+ life in a m+riad of 7a+s.

#!1"books and !uir!d r!ading

O %!M%% is reuired. %ll information 7ill 'e )osted in C%A% <)lease'are 7it( us durin" t(e transition )eriod2=

Micro $((

&e Eust 'uilt a ne7 %)) to )ro6ide +ou 7it( eas+access to all t(e la' modules. C(ec it out and let usno7 (o7 7e can im)ro6e it. i(one*iad 6ersion is)endin".

(tt):**studentsa)).mo'i*micro'iolo"+la's

Clic on t(e SR code and +ou 7ill automaticall+'e lined to our a)) in t(e maret a))ro)riate to t(eir)(one, or to t(e #$M> 6ersion if t(e+ dont (a6e an%ndroid or i(one.

Books and r!f!r!nc!s

ou ma+ nd t(ese references interestin" or t(e+ can 'e a "ood refres(er if+ou need more (el).

;

http://studentsapp.mobi/microbiologylabs

http://studentsapp.mobi/microbiologylabs



Pho"ogra(hic $"las for Microbiology Labs, 4t( ed <or an+ ot(er= '+e'oLe T ierce, I!U 9H?-0?9>?8-?H89

Lab Ma"hF $ Gandbook of M!asur!'!n"s, Calcula"ions, and O"h!r:uan"i"a"i/! Skills for >s! a" "h! B!nch '+ an+ )encer %dams(tt):**777.amaNon.com*a'-Mat(-Measurements-Calculations-

Suantitati6e*d)*0?H9;9;4;*refVsrW1W8KieV$F?TidV1>;H;1?HTsrV?-8Te+7ordsVatXt(eX'enc(

$" "h! B!nchF $ Labora"ory Ha/iga"or '+ Yat(+ !arer(tt):**777.amaNon.com*%t-!enc(-a'orator+-a6i"ator-)dated*d)*0?H9;9H0?

!" !ady for Microbiology '+ Y. /arrettIf +ou feel lie +ou (a6e deciencies in 'asic cell 'iolo"+,

mat( and ot(er areas 7e touc( on, +ou ma+ 7ant to loointo 'rus(in" u) 'asic sills 7it( t(is 'oo.

Modules, readin" material and ot(er instructional material 7ill 'e )osted inC%A%. our $% 7ill determine 7(ic( of t(e readin" materials 7ill 'eincluded in t(e uiNNes and assi"nments.

/ettin" startedCourse Corres)ondence as 7ell as la' eDercises, assi"nments and eDams 7ill'e a6aila'le 6ia eearnin" Can6as &e'site (tt):**lss.at.u.edu*. If +ou needan+ (el) 7it( t(e eearnin" s+stem )lease 6isit t(e eearnin" #el) )a"e at(tt)s:**lss.at.u.edu*(el).s(tml. ou ma+ also contact t(e F (el) des at>8-98-#G, O)tion 8.

H

https://lss.at.ufl.edu/help.shtml

https://lss.at.ufl.edu/help.shtml



our section s)ecic site is maintained and administered '+ +our $%s. ou areres)onsi'le for t(e material )osted in +our section. I do not c(ec email int(e indi6idual sections2

Furt(ermore:

1. ie t(e MC Face'oo )a"e for interestin" ne7s and current u)datesP t(e

)ostin"s can 'e )art of t(e class material2h""(FII***.fac!book.co'I><Microbiology

8. lease Remem'er to c(ec t(e $nnounc!'!n"s and Mail eac( da+ inCan6as. QI did not no7 a'out t(e assi"nment, deadlineJ is O$ anacce)ted eDcuse. For t(is course t(ere are t7o Can6as sites for t(e course.

our instructor 7ill (a6e (is*(er o7n Can6as 7e')a"e 7(ere section s)ecicinformation 7ill 'e )osted, and QMicro'iolo"+ is For %ll Of s 7ill )ost"eneral course information )ertinent to all students tain" Micro la'.

. lease bring your la("o( co'(u"!r or "abl!" "o !ach lab. &e often7ill do com)uter 'ased eDercises. !rin" a camera, cell )(one or ta'let to tae)ictures of +our la' results.

4. $(rou"(out t(e emester t(ere 7ill 'e O(!n Lab sessions to )ro6ide +ou7it( eDtra (ands on time and an o))ortunit+ to as uestions and "et moreeD)erience 7it( t(e tec(niues discussed in class. Information re"ardin"o)en la' 7ill 'e emailed as sc(edules are naliNed.

>. %ll assi"nments, )roEects and re)orts are eD)ected to 'e su'mittedelectronicall+ t(rou"( Can6as. Gac( assi"nment is )rocessed t(rou"(#urni"in.co' and as suc( is c(eced for )la"iarism.

;. $""!ndanc! is 'anda"ory. If +ou can (el) not missin" class )leasedont. Gac( da+ ne7 tec(niues are tau"(t and it is eas+ to fall 'e(ind2%rri6in" late and not comin" to class 7it(out an eDcused a'sence 7ill aLect+our attendance "rade <10Z=

H. /ot a SuestionK lease email me B I am are (ere to (el)2

61(!c"a"ions of "h! s"ud!n"s

Read t(e Syllabus to no7 +our deadlines and eDam sc(edules. our $%(o7e6er 7ill announce s)ecic da+s for +our o7n section so P$J$##6H#+OH

%s student, +ou are eD)ected to full+ !ngag! yours!lf in all as)ects of t(eclass

ou are eD)ected to COM6 P6P$6D to class and (a6e read t(e assi"nedreadin" material and es)eciall+ 7atc(ed t(e introductor+ 6ideos.

ou are eD)ected to <OLLOW O> L$B 6#+:>6##6 at all times <see neDtc(a)ter=. ou (a6e to res)ect t(e )otential )at(o"ens 7e are 7orin" 7it(.

Most im)ortantl+: 6HKOJ #G6 L$B

tudent e6aluation

?

http://www.facebook.com/UFMicrobiology

http://www.facebook.com/UFMicrobiology



tudent "rades are com)osed t(rou"( amultitude of acti6ities, includin" uiNNes, eDams,)resentations, )roEects, attendance and)artici)ation. FOO&I/ I$RC$IO I %M$ as 7ell as CRG%$IAI$ &I !GRG&%RG.

Attendance and Participation (5%)

$""!ndanc! to all la'orator+ sessions is'anda"ory and +our instructor 7ill recordattendance. (ould a conict arise, notif+ +ourla' instructor in ad6ance if )ossi'le and ndarran"ements to mae u) t(e missed materialand uiNNes. neDcused a'sences 7ill result in aNero for t(at da+s attendance. ou must e-mail+our instructor 7it(in 84( 'efore*after t(emissed la' to ualif+ for maeu) o))ortunit+

and )ro6ide 6alid 7ritten eDcuse.o c(eatin" and )la"iarism is allo7ed. ou 7illrecei6e an automatic 0 7it(out 7arnin" if cau"(t for a )articular assi"nment, )roEect oreDam.

Lab Etiquette (5%)a' etiuette is a class 'ased "rade. %ll t(e students to"et(er areres)onsi'le to lea6e t(e la' clean and to use t(e eui)ment 7it( care BGAGR &GGY . Poin"s *ill b! "ak!n o fro' 6?6JOH6 in "h!class if a class is obs!r/!d "o no" follo* "h! lab !"iu!""! rul!sA r!gardl!ss if on! s"ud!n" '!ss!s u( or "h! *hol! class.

$(is includes, 'ut is not restricted to:[ Gm)t+in" +our 'enc(to) tras( container <7it(out t(ro7in" a7a+ t(e

'a"=[ Cleanin" 'enc( 'efore and after la'[ Main" sure all items are in +our la' 'in 7(en +ou arri6e and 7(en

+ou lea6eo o 'roen, dama"ed or stained )i)etteso )i)ettes )er )air of studentso

o striers in t(e 'inJ.[ Main" sure t(at all items on +our 'enc( are )resent and in order[ Maintain t(e microsco)e: &i)in" oil of t(e 100\ oil lens, )ut co6er

on t(e sco)e, secure (e ca'le[ Rell ti) 'oDes and e))endorf tu'es, microsco)e slides and co6er

sli)s[ uttin" t(e tras( in t(e a))ro)riate and correct container <re"ular

tras(, 'io(aNard tras(, "lass tras(=

+"!'s rad!d 9 ?alu!

artici)ation,%ttendance

>

a' etiuette >

SuiNNes 80

Midterm GDam 8>

FinalGDam*)roEect

8>

roEects, tals 10

G 10

#o"al 100

GDtra credit >

9



[ c(ec 7it( +our $% for details

Quizzes (10%)

SuiNNes 7ill eit(er 'e "i6en in t(e la' or assi"ned to 'e com)leted in Can6as. $(is 7ill 'e u) to +our indi6idual $%s. SuiNNes 7ill contain material from t(eu)comin" la' and from an+ )re6ious module. SuiNNes can 'e assi"ned to t(e

6ideos to 'e 7atc(ed 'efore class. #h! lo*!s" ui; grad! *ill b!dro((!d.

Midterm Exam (25%)

GDams are desi"ned to test +our no7led"e of )ractical sills learned in classand also determine com)re(ension of t(e learned material.

ractical com)onent: a lar"e )art of t(e midterm is com)rised of a )racticaleDam 7(ere +ou (a6e to )erform t(e sills and tec(niues learned o6er t(erst 7ees of class. Final eDam could 'e a tae (ome or )ractical eDam.etails for eac( eDamination 7ill 'e eD)lained and discussed '+ +our $%.C(eatin" 7ill automaticall+ result in 0 )oints 7it(out 7arnin" and ma+ lead toa re)ort to t(e ean of tudents Oce <O=.

% "y(ical 'id"!r' 7ill test +ou on: microsco)+ <)arts and (o7 to use it=,7et mount, identication of or"anisms, strea for isolation, /ram stain <andot(er stains=, )i)ettin", "ra)(in" <meanX$GA=, "ro7t( cur6e*calculations,enumeration, la' mat(, identication of micro'es usin" /IGO andmolecular tec(niues <'ioinformatics - !%$=. Mae sure +ou GR$%t(e tec(niues, t(e instruments <Xmicrosco)e=, t(e )ur)ose and t(eim)ortance of eac( module.

Proects! ta"#s (10%)

our $% 7ill assi"n 6arious )roEects. lease follo7 t(e instructions of +our $%eDactl+. roEects can include )u'lic (ealt( )roEects 7it( role )la+,

)resentations, dia"nostic )roEect, etc.

E"ectronic "ab noteboo# (10%)

ou 7ill ee) an electronic la' note'oo <G=, 7(ic( contains all +our results,ans7ers to uestions, )roEects, o'ser6ations, etc. $(is 7ill (el) +ou tounderstand t(e material 'etter. ou can add an+ information into t(e G.#his s!'!s"!r you *ill HO# b! allo*!d "o us! your 6LH for "h! !1a'bu" you can 'ak! your o*n ch!a" sh!!"E "o h!l( you *i"h(roc!dur!s !"c. e)endin" on +our $% +ou ma+ 'e ased to com)l+ 7it( a)articular format. In "eneral +our G s(ould include t(e follo7in".

[ etailed eD)lanation of t(e conce)ts 'ein" learned t(at da+

[ Ye+ terms*Aoca'ular+

[ % )ro)er )rotocol

[ ata in t(e form of )ictures, "ra)(s, ta'les, etc

[ Results

[ Conclusion

[ %ns7er to end of c(a)ter uestions and ot(er material as directed'+ +our $%

Mak! sur! you also kno* "h! d!)ni"ions and "!r'inology.

10



$tudent nitiated &esearc' Proect (20%)

Gac( student (as t(e o))ortunit+ to 7or on an inde)endent researc( )roEectas )art of t(e class. ou can 7or in "rou)s and t(e )roEect (as to 'ea))ro6ed '+ +our $%. our a))roac( (as to follo7 t(e )rinci)les of scienticmet(od. ou (a6e to su'mit a small researc( )ro)osal and include current

)a)ers from t(e literature as 7ell as a 'ud"et for +our researc(. It is )ossi'leto conduct a 'ioinformatics stud+ usin" eDistin" data'ases. $(e nal )roEect7ill 'e )resented as a )oster durin" t(e last 7ee of class.

roEect su'missions

1. u'missions after t(e deadline 7ill 'e treated as late su'missions, and10Z of t(e total assi"nment )oints 7ill 'e deducted for eac( da+ after t(edeadline for > da+sP su'mission 7ill not 'e acce)ted after t(at.

8. If +ou eD)erience an+ )ro'lem 7it( e-earnin" s+stem or 7(ileu)loadin" assi"nments, contact t(e (el)des immediatel+ <>8= 98-4>H<select o)tion 8= or e-mail: learnin"-su))[email protected]. Retain+our e-mail or (el)des ticet num'er as documentation of +our )ro'lem.

Extra credit (no more t'an 5%)&it( t(e discression of +our $% +ou ma+ "et some eDtracredit 7(ic( can include

[ artici)ation in online discussion[ !rin"in"*s(arin" en6ironmental sam)les for 7et mount

eDamination[ !rin"in"*s(arin" fecal sam)les 7it( )otential )arasite e""s

for t(e fecal oat <)arasitolo"+= la'[ !rin"in"*s(arin" fermented food )roducts for t(e food la'[ (arin" interestin" ne7s and articles a'out micro'iolo"+

7it( +our class

GDtra Credit O))ortunities 7ill 'e a6aila'le t(rou"(out t(esemester at t(e discretion of +our $%. uc( GDtra CreditO))ortunities ma+ include: %ttendin" O)en a', resentationof current to)ic in class and )ostin" it to &ii, &ii )ostin"s,contri'ution to discussion 'oard

rading and )nal grad!s

#h! grading scal! 'ay b! ad=us"!d bas!d on class(!rfor'anc!. $f"!r +S+S allo*s you "o /i!* your )nal grad!. Jou ha/!2 *!!ks "o chall!ng! your grad! and r!u!s" a chang! of grad! bycon"ac"ing Dr. Oli %'oliu.!du&

Mak!u( Policy&e 7ill 7or 7it( +ou if +ou )ro6ide us 7it( a F acce)ted eDcuse for+our a'sence durin" la's or t(e eDam. (tt)s:**catalo".u.edu*u"rad*current*re"ulations*info *attendance.as)D.&e do acce)t inter6ie7s as eDcused a'sence - as lon" as +ou )ro6ide a7ritten in6itation to t(e inter6ie7 !GFORG +our a'sence. ou 7ill 7or

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11

mailto:[email protected]

https://catalog.ufl.edu/ugrad/current/regulations/info%20/attendance.aspx


https://catalog.ufl.edu/ugrad/current/regulations/info%20/attendance.aspx



7it( +our $% to mae u) missed 7or. Remem'er: o)en la' is O$intended for maeu) as t(ere 7ill 'e no actual instructor.

S!a"ing and Lock!r assign'!n"

lease tae t(e same seat in eac( class )eriod. &e 7ill mae notice of +ourlocation in t(e room and a seatin" c(art 7ill 'e (anded out t(e st da+ ofclass.

ou 7ill 'e assi"ned a )ersonal or s(ared locer for t(e )eriod of t(e class orsemester to lea6e +our la' coats and 'ac)ac durin" la' and 'et7een la')eriods. lease 'rin" a loc for securit+.

Biosaf!"y in "h! Microbiology Labora"ory

&e are re"ulated and ins)ected annuall+ '+ t(e F Gn6ironmental #ealt( andafet+ e)artment. &e follo7 t(eir "uidelines - and +ou follo7 ourinstructions - to )re6ent an+ accidents and )ro'lems 7it( contaminations. Formore information a'out t(e re"ulations "o to:

(tt):**777.e(s.u.edu*a'*G#intro.(tm

$o com)l+ 7it( t(e ni6ersit+ of Florida 'iosafet+ reuirements clos!d "o!dsho!s ar! 'anda"ory in t(e la'orator+. ou can lea6e a )air in +our locerso +ou dont for"et. Dis(osabl! lab coa"s *ill b! (ro/id!d "o you on t(erst da+ of class. It is mandator+ to 7ear t(em at all times. &rite +our nameson +our coats and ee) t(em in +our locers. o not tae t(em (ome. o nottae an+one else^s coat. a' coats 7ill 'e autocla6ed and dis)osed accordin"to F re"ulations on t(e last da+ of t(e semester.

>nd!rlying '!dical condi"ions

+f you ha/! any und!rlying '!dical condi"ions, *hich can a!c" youri''un! sys"!' or 'ak! you 'or! susc!("ibl! "o inf!c"ious dis!as!,

you 'us" infor' your #$ and consul" *i"h your (hysician b!for!*orking in "h! 'icrobiology labora"ory.

For students and $%s 7it( )reeDistin" conditions, includin" )re"nanc+, tain"immunosu))ressi6e dru"s, or 7(o (a6e ot(er medical conditions <e.".,dia'etes, immune s+stem disorder= t(at mi"(t necessitate s)ecial)recautions and it is recommended t(at t(e+ "et medical clearance from t(einrmar+.

(tt):**s(cc.u.edu*

If +ou notice an+ unusual s+m)toms or of an+ s)ills or accidents occur,contact +our $% immediatel+.

Please come and see Dr. Oli if you have any concerns ( [email protected] )

<u"ur! "!aching assis"an"s for 'icro labs and L!""!r ofr!co''!nda"ion

ou ma+ reuest a letter of recommendation onl+ if +ou attend t(e section Iam teac(in". I 7ill also 7rite recommendation letters for most students 7(osi"n u) to 'e $% t(e micro'iolo"+ la'oratories. $o si"n u) to $% after +ou (a6etaen t(e class, ll out t(e information in t(e online a))

18

http://www.ehs.ufl.edu/Lab/EHSintro.htm

http://shcc.ufl.edu/


http://www.ehs.ufl.edu/Lab/EHSintro.htm

http://shcc.ufl.edu/




(tt):**microcell.u.edu*$%Wa))* . $(e s)ots for $%s are limited and 7ill 'elled on a rst come rst ser6ed 'asis.

O"h!r >< (olici!s

$cad!'ic Gon!s"y

In 199> t(e F student 'od+ enacted an (onor code and 6oluntaril+committed itself to t(e (i"(est standards of (onest+ and inte"rit+. &(enstudents enroll at t(e uni6ersit+, t(e+ commit t(emsel6es to t(e standarddrafted and enacted '+ students.

$(e #onor led"e: &e, t(e mem'ers of t(e ni6ersit+ of Florida communit+,)led"e to (old oursel6es and our )eers to t(e (i"(est standards of (onest+and inte"rit+.

On all 7or su'mitted for credit '+ students at t(e uni6ersit+, t(e follo7in")led"e is eit(er reuired or im)lied: _On m+ (onor, I (a6e neit(er "i6en norrecei6ed unaut(oriNed aid in doin" t(is assi"nment._

tudents s(ould re)ort an+ condition t(at facilitates dis(onest+ to t(e

instructor, de)artment c(air, colle"e dean, tudent #onor Council, or tudentConduct and Conict Resolution in t(e ean of tudents Oce. It is assumedall 7or 7ill 'e com)leted inde)endentl+ unless t(e assi"nment is dened asa "rou) )roEect, in 7ritin" '+ t(e instructor. $(is )olic+ 7ill 'e 6i"orousl+u)(eld at all times in t(is course.

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<ource: 8011-8018 nder"raduate Catalo"=

Sof"*ar! >s!

%ll facult+, staL and students of t(e uni6ersit+ are reuired and eD)ected to

o'e+ t(e la7s and le"al a"reements "o6ernin" soft7are use. Failure to do socan lead to monetar+ dama"es and*or criminal )enalties for t(e indi6idual6iolator. !ecause suc( 6iolations are also a"ainst uni6ersit+ )olicies andrules, disci)linar+ action 7ill 'e taen as a))ro)riate.

W! r!uir! for !ach s"ud!n"s "o ha/! MS Oc! %Mac or PC& ins"all!don "h!irIa co'(u"!rs. Si'ilar gra(hing (rogra's ar! a/ailabl! foriPads and "abl!"s

Microsoft oft7are for F students

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$(e Oce of Information $ec(nolo"+ (as "reat ne7s for ni6ersit+ of Floridastudents2 If +ou 7ant to u)"rade +our o)eratin" s+stem or need Microsoft

Oce uite, t(is media 7ill 'e a6aila'le in t(e )rin" 8011 semester. $(ediLerent media a6aila'le are: &indo7s H o)eratin" s+stem )"rade,Microsoft Oce rofessional lus 8010 <8-'it*;4-'it= for C or MicrosoftOce for Mac 8011. Sof"*ar! is fr!! for >< s"ud!n"s.

$o c(ec for a6aila'ilit+ of t(e media and tec(nical reuirements, contact t(eF Com)utin" #el) es at <>8=98-#G<4>H=. Once t(e media isa6aila'le, +ou can "et it at t(e F Com)utin" #el) es or at t(e F!oostore .

1

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Ot(er soft7are trainin" o))ortunities are a6aila'le. For eDam)les t(rou"(+nda.com (tt):**777.l+nda.com*mem'er.as)D

Ca'(us G!l(ing !sourc!s

tudents eD)eriencin" crises or )ersonal )ro'lems t(at interfere 7it( t(eir"eneral 7ell-'ein" are encoura"ed to utiliNe t(e uni6ersit+s counselin"resources. $(e Counselin" T &ellness Center )ro6ides condential counselin"ser6ices at no cost for currentl+ enrolled students. Resources are a6aila'le oncam)us for students (a6in" )ersonal )ro'lems or lacin" clear career oracademic "oals, 7(ic( interfere 7it( t(eir academic )erformance.

ni6ersit+ Counselin" T &ellness Center, 190 Radio Road, >8-98-1>H>,777.counselin".u.edu*c7c*

Career Resource Center, First Floor &R, 98-1;01, 777.crc.u.edu*

S!r/ic!s for S"ud!n"s *i"h Disabili"i!s

lease come and tal to +our $% at t(e 'e"innin" of t(e semester a'out an+

accommodations reuired. &e 7ill mae sure t(at t(e students needs aremet to t(e 'est of our a'ilities in t(e la'orator+ settin".

$(e isa'ilit+ Resource Center coordinates t(e needed accommodations ofstudents 7it( disa'ilities. $(is includes re"isterin" disa'ilities, recommendin"academic accommodations 7it(in t(e classroom, accessin" s)ecial ada)ti6ecom)uter eui)ment, )ro6idin" inter)retation ser6ices and mediatin" facult+-student disa'ilit+ related issues.

0001 Reid #all, >8-98-?>;>, 777.dso.u.edu*drctudents 7it( isa'ilities

777.dso.u.edu*drc*

tudents reuestin" classroom accommodation must rst re"ister 7it( t(eean of tudents Oce in ea'od+ (all. $(e ean of tudent Oce 7ill

)ro6ide documentation to t(e student 7(o must t(en )ro6ide t(isdocumentation to t(e Instructor 7(en reuestin" accommodation at t(e'e"innin" of t(e semester.

14

http://www.lynda.com/member.aspx

http://www.counseling.ufl.edu/cwc/

http://www.crc.ufl.edu/

http://www.dso.ufl.edu/drcStudents

http://www.dso.ufl.edu/drc/

http://www.lynda.com/member.aspx

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/eneric &eel+ sc(edule

Modul!

?id!o 61!rcis!s

1

a' safet+, dail+routines. se of amicrosco)e, 7et

mount

Intro - s+lla'us, can6as, la' safet+, art of microsco)+, life in a dro) of 7ater,taDonom+*)(+lo"en+, euar+ote -

)roar+ote

8

/ram stain,)i)ettin",

ne"ati6e stain, oilimmersion

Microor"anisms in t(e en6ironment and on+ou, "ram stain, sim)le stain, ne"ati6e

stain, ase)tic tec(niue, )i)ettin"

/ra)(in" eDercisetutorial, "ro7t(

cur6e, $GA,"ro7t( rate

trea for isolation, scientic met(od,enumeration of 'acterial )o)ulations

CF*ml, "ro7t( cur6e, isolation of coloniesfrom a miDed culture,

4

ia"nostic la'6irtual eldtri),/ideon tutorial,

6arious testtutorials

ia"nostic micro'iolo"+ - selecti6e anddiLerential media, 'ioc(emical tests,

"ro7t( c(aracteristics.

> 1;s CR 6ideo/ideon data'ase, % isolation, 1;s R%

CR X "el electro)(oresis,

;!ioinformatics

tutorial!ioinformatics, )(+lo"en+

H%nti'io"ram,

MR%Re6ie7 - )roEect )ro)osals, steriliNation <ta

trainin"=

? Mid"!r' (rac"ical and /isual !1a'

9 Glisa anti'iotic dis diLusion susce)ti'ilit+ test

T t(e )ost anti'iotic aera, disinfectants andot(er antimicro'ials, GI%, MR% screen

1>



10 Fecal oat Fecal oat and 7ater la'

11 Micro'e art, m+colo"+

18 Fermented X rotten foods )re'iotics,

)ro'iotics , food sam)le,

1 <inish s"ud!n" (ro=!c"s

14 Pr!s!n"a"ions

1;



ata'ases +ou 7ill use?ir"ual (ond di( A for *!" 'oun" id!n"i)ca"ion(tt):**777.microsco)+-u.or".u*indeD.(tmlK(tt):**777.microsco)+-u.or".u*)onddi)*

HCB+ #a1ono'y <no )ass7ord=(tt):**777.nc'i.nlm.ni(."o6*taDonom+

id!on A "o d!"!r'in! your unkno*n and for (ublic h!al"h(ro=!c"

(tt):**7e'./IGOonline.com*lo"inD.)()KuserVufmicro <no )ass7ord=

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(tt):**777.ui'.u.edu*uf)roD+.(tml

DH$ li's A "o r!"ri!/! your -4s DH$ s!u!nc!

(tt):**dnalims.dnatools.com*c"i-'in*dna*)ass7ord.c"ilo"in: moniaoli

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(tt):**'last.nc'i.nlm.ni(."o6*!last.c"i

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Micro'iolo"+ Aideosour A *i"" "et +ou #no* *'en +ou 'a,e to *atc' eac' ,ideo-or *'ic' modu"e. ou ma+ 'a,e quizzes about t'e content o-t'e ,ideos

Ch!ck ou" "h! >< M+COB+OLOJ /id!o chann!l in ?i'!o(tt)s:**6imeo.com*c(annels*?>940>

1H

http://web.gideononline.com/loginx.php?user=ufmicro

http://www.uflib.ufl.edu/ufproxy.html

http://dnalims.dnatools.com/cgi-bin/dna/password.cgi

http://www.foodsafetyfirst.org/fsf_mgsp.html

https://vimeo.com/channels/859405

http://web.gideononline.com/loginx.php?user=ufmicro

http://www.uflib.ufl.edu/ufproxy.html

http://dnalims.dnatools.com/cgi-bin/dna/password.cgi

http://www.foodsafetyfirst.org/fsf_mgsp.html

https://vimeo.com/channels/859405



lease note all of t(e 6ideos are )roduced at t(e e)artment ofMicro'iolo"+ and Cell cience and man+ of t(em 7ere actuall+ madeas )art of t(e inde)endent student )roEect2222 Thanks to all ouramazing students!

$(ans to some of our amaNin" students 7e (a6e t7o ne7 tutorials,one for usin" Gndnote reference mana"ement(tt)s:**6imeo.com*114844?>4

and a "reat o6er6ie7 of 'ioinformatics2(tt)s:**6imeo.com*11;1;9H8

Microbiology in"ro

Lab Saf!"y ul!s

(tt)s:**6imeo.com*4;094>

Daily ou"in!s

(tt)s:**6imeo.com*4;0940?>

$s!("ic #!chniu!s

(tt)s:**6imeo.com*411>1;8

Basic M!"hods

S"r!ak for isola"ion

(tt)s:**6imeo.com*4?1;8H9HBasic $na"o'y of a Microsco(!(tt)s:**6imeo.com*44?80198

W!" Moun"

(tt)s:**6imeo.com*4?1;0HH9

Pi(!""ing

(tt)s:**6imeo.com*44?80191

Co'(u"!r #u"orials

ra(hing *i"h 61c!l

(tt)s:**6imeo.com*49>1?>H0

ro*"h cur/! and gro*"h ra"! calcula"ion

(tt)s:**6imeo.com*>81>084>

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?isuali;ing Microb!s

ra' S"ain

(tt)s:**6imeo.com*44?8019

H!ga"i/! S"ain

(tt)s:**6imeo.com*H;H0001

Ca(sul! S"ain

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<lag!lla S"ain

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#radi"ional Diagnos"ic M!"hods

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Ph!nol !d Bro"h

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Blood $gar

(tt)s:**6imeo.com*H;>;>91

Manni"ol Sal" $gar

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MacConk!y agar

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DH$s! $gar

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Ci"ra"! $gar

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Ca"alas! #!s"

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$na!rob! Kar

(tt)s:**6imeo.com*H;>>>1

19























Mol!cular Diagnos"ic "!s"

PC -

(tt)s:**6imeo.com*498H8;4

PC 2

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PC 3

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Bioinfor'a"ics

S!u!nc! r!"ri!/al and Blas"

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Blas" "u"orial and (hylog!n!"ic "r!!(tt)s:**6imeo.com*>194H?4

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80

















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Why 'icrobiology

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M!!" "h! MCS facul"y

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mcb 3020l - syllabus fall 2015 microbio-1

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