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Microscopy and Classification 2

Microscopy

"ow does a lens wor#$

%ptical propertiesrefraction

magnification

resol!tion

distortion

&imitations of a single lens

magnification

ill!mination

aberration 'i#ipedia lin#http://en.wiipedia.or!/wii/"ens#$2%optics$2&

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Microscopy and Classification 3

Some principles of a

compo!nd microscope

%c!lar lens

%b(ective lens

Condenser lens

"ow is magnification calc!lated$

&imitations to a compo!nd

microscope

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Microscopy and Classification '

Speed of light in vac!!m

Speed of light in medi!m

'hat were the #ey advances

 in light microscopy$

)* %il immersion lens

+* !sed lenses

* .dvanced optics

"ow do oil immersion andf!sed lenses improve resol!tion$

efractive index /

0orosilicate glass / )12+

.ir / )133

'ater / )1Immersion oil / )12+

!sed lenses combine different types of glass

-- compensate for aberrations

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Microscopy and Classification

.dvanced optics only improve contrast

Theoretical limit of resol!tion

  / 31+ !M

ar# field

manip!lates the

path of light

Phase contrast

  and IC 

manip!late

phase of light

ar# field

0right field

IC

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Microscopy and Classification

l!orescence Microscopy allows precise

staining of cells and cell!lar components

Standard fl!orescence

manip!lates the

path of light

Confocal  -- p!ts everything in foc!s

Standard l!orescence vs Confocal image of Tetrahymena

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Microscopy and Classification *

"ow does electron

microscopy yield

higher resol!tion$

esol!tion

- 5ye + 0.2 mm

  - &M + 0.2 ,M

  - 5M + 0.2 nM (0.0002 ,M)

'avelengths of 

6 of electrons 7 31332 nm

6 visible light 7 223 nm

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Microscopy and Classification %

'hat are types of

electron

microscopy$

Scanning vs Transmission 

STM is different

riscoll et al1 )8831

9at!re, 4:, :+;)

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Microscopy and Classification &

0iological classification

0iological taxa

-- M!ddled in the middle

-- 0l!rry at the bottom

0inomial naming

'riting conventions

 Staphylococcus aureusStaphylococc!s a!re!s

 S. aureus

Common names and strainsPne!moncocc!s

E. coli   %)2< "<

Domain: Bacteria

Kingdom: Eubacteria

Phylum: Firmicutes

Class: Bacilli

Order: Bacillales

Family: Staphylococcaceae

Genus: Staphylococcus

Species: aureus

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Microscopy and Classification 10

The Antiquity of Microbes

dam

!ad "em## Stric$land Gillilan

'hat are the domains of life$

 Eukarya – Archaea – Bacteria

'hat traits do .rchaea

and 0acteria share$  -- proaryotic cell str,ct,re

-- circ,lar chromosome

'hat traits do .rchaea

and 5!#aria share$ -- ,cleosomes

 -- M,ltiple olymerases

 -- iosome str,ct,re

Some .rchaea have !ni=!e properties  -- enetically distinctie

-- Cell memrane

  -- Cell wall str,ct,re

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Microscopy and Classification 11

'hat are the characteristics of

5!#aryotes vs Pro#aryotes$-- all >cell!lar organisms?

0asic similarities$

memrane

!enetic information

iochemistry

istinctive properties of e!#aryotes4 5 e,6 = tr,e 5aryo6 = n,cle,s4 si7e4 or!anelles

mitochondria8 chloroplasts8 etc

4 chromosomes

9s proaryotes 5pre-n,cle,s6

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Microscopy and Classification 12

rchaea E%tremophiles-- some notable ones…

 Pyrolobus fumarii   -- >ire lobe of the chimney? 

"yper-thermophile -- &0C ; 113C (10C)

hydrothermal ents

<train 121:

http://www.!enomenewsnetwor.or!/articles/0%#03/hottes

t.shtml

 Picrophilus spp. 

5xtreme acidophiles -- p >' (opt 0.*)

?olcanic steam ents

 alobacterium spp.

5xtreme halophiles -- 3 ; M salt

@ead seaA !reat salt laeA

<alted foods