Agard DA, Villa E, Pogliano J (2019) Viral
capsid trafficking along treadmilling tubulin
filaments in bacteria. Cell 177(7):1771–1780.
e12
7. Khanna K, Lopez-Garrido J, Zhao Z,
Watanabe R, Yuan Y, Sugie J, Pogliano K,
Villa E (2019) The molecular architecture of
engulfment during Bacillus subtilis sporulation. elife 8:e45257
8. Rast A, Schaffer M, Albert S, Wan W, Pfeffer S,
Beck F, Plitzko JM, Nickelsen J, Engel BD
(2019) Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma
membrane. Nat Plants 5(4):436–446
9. Weiss GL, Kieninger AK, Maldener I,
Forchhammer K, Pilhofer M (2019) Structure
and function of a bacterial gap junction analog.
Cell 178(2):374–384.e15
10. Lopez-Garrido J, Ojkic N, Khanna K, Wagner
FR, Villa E, Endres RG, Pogliano K (2018)
Chromosome translocation inflates bacillus
forespores and impacts cellular morphology.
Cell 172(4):758–770.e14
11. Noble JM, Lubieniecki J, Savitzky BH,
Plitzko J, Engelhardt H, Baumeister W, Kourkoutis LF (2018) Connectivity of centermost
chromatophores in rhodobacter sphaeroides
bacteria. Mol Microbiol 109(6):812–825
12. Mosalaganti S, Kosinski J, Albert S, Schaffer M,
Strenkert D, Salome ´ PA, Merchant SS, Plitzko
JM, Baumeister W, Engel BD, Beck M (2018)
In situ architecture of the algal nuclear pore
complex. Nat Commun 9(1):2361
13. Schaffer M, Mahamid J, Engel BD, Laugks T,
Baumeister W, Plitzko JM (2017) Optimized
cryo-focused ion beam sample preparation
aimed at in situ structural studies of membrane
proteins. J Struct Biol 197(2):73–82
14. Chaikeeratisak V, Nguyen K, Khanna K, Brilot
AF, Erb ML, Coker JKC, Vavilina A, Newton
GL, Buschauer R, Pogliano K, Villa E, Agard
DA, Pogliano J (2017) Assembly of a nucleuslike structure during viral replication in bacteria. Science 355(6321):194–197
15. Rosenzweig ESF, Xu B, Cuellar LK, MartinezSanchez A, Schaffer M, Strauss M, Cartwright
HN, Ronceray P, Plitzko JM, Fo ¨rster F, Wingreen NS, Engel BD, Mackinder LC, Jonikas
MC (2017) The eukaryotic co2-concentrating
organelle is liquid-like and exhibits dynamic
reorganization. Cell 171(1):148–162.e19
16. B€ auerlein FJ, Saha I, Mishra A, Kalemanov M,
Martı ´nez-Sa ´nchez A, Klein R, Dudanova I,
Hipp MS, Hartl FU, Baumeister W, Ferna ´ndez-Busnadiego R (2017) In situ architecture
and cellular interactions of polyq inclusions.
Cell 171(1):179–187.e10
17. Mahamid J, Pfeffer S, Schaffer M, Villa E,
Danev R, Kuhn Cuellar L, Fo ¨rster F, Hyman
AA, Plitzko JM, Baumeister W (2016) Visualizing the molecular sociology at the hela cell
nuclear
periphery.
Science
351
(6276):969–972
18. Zhang J, Ji G, Huang X, Xu W, Sun F (2016)
An improved cryo-fib method for fabrication of
frozen hydrated lamella. J Struct Biol 194
(2):218–223
19. Engel BD, Schaffer M, Kuhn Cuellar L, Villa E,
Plitzko JM, Baumeister W (2015) Native architecture of the Chlamydomonas chloroplast
revealed by in situ cryo-electron tomography.
elife 4:e04889
20. Harapin J, Bo ¨rmel M, Sapra KT, Brunner D,
Kaech A, Medalia O (2015) Structural analysis
of multicellular organisms with cryo-electron
tomography. Nat Methods 12:634–636
21. Villa E, Schaffer M, Plitzko JM, Baumeister W
(2013) Opening windows into the cell:
focused-ion-beam milling for cryo-electron
tomography. Curr Opin Struct Biol 23
(5):771–777. Protein-carbohydrate interactions/biophysical methods
22. Wang K, Strunk K, Zhao G, Gray JL, Zhang P
(2012) 3d structure determination of native
mammalian cells using cryo-fib and cryoelectron tomography. J Struct Biol 180
(2):318–326
23. Rigort A, B€ auerlein FJB, Villa E, Eibauer M,
Laugks T, Baumeister W, Plitzko JM (2012)
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc
Natl Acad Sci 109(12):4449–4454
24. Marko M, Hsieh C, Schalek R, Frank J, Mannella C (2007) Focused-ion-beam thinning of
frozen-hydrated biological specimens for cryoelectron microscopy. Nat Methods 4:215
25. Rajput NS, Luo X (2015) Chapter 3: FIB
micro-/nano-fabrication.
In:
Qin
Y
(ed) Micromanufacturing engineering and
technology, Micro and Nano Technologies,
2nd edn. William Andrew Publishing, Boston,
pp 61–80
26. Volkert CA, Minor AM (2007) Focused ion
beam microscopy and micromachining. MRS
Bull 32(5):389–399
27. Chyr I, Steckl AJ (2001) Gan focused ion beam
micromachining with gas-assisted etching. J
Vacuum Sci Technol B 19(6):2547–2550
28. Schaffer M, Pfeffer S, Mahamid J, Kleindiek S,
Laugks T, Albert S, Engel BD, Rummel A,
Smith AJ, Baumeister W, Plitzko JM (2019) A
cryo-fib lift-out technique enables molecularresolution cryo-et within native caenorhabditis
elegans tissue. Nat Methods 16(8):757–762
Practical Approaches for Cryo-FIB Milling
81
capsid trafficking along treadmilling tubulin
filaments in bacteria. Cell 177(7):1771–1780.
e12
7. Khanna K, Lopez-Garrido J, Zhao Z,
Watanabe R, Yuan Y, Sugie J, Pogliano K,
Villa E (2019) The molecular architecture of
engulfment during Bacillus subtilis sporulation. elife 8:e45257
8. Rast A, Schaffer M, Albert S, Wan W, Pfeffer S,
Beck F, Plitzko JM, Nickelsen J, Engel BD
(2019) Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma
membrane. Nat Plants 5(4):436–446
9. Weiss GL, Kieninger AK, Maldener I,
Forchhammer K, Pilhofer M (2019) Structure
and function of a bacterial gap junction analog.
Cell 178(2):374–384.e15
10. Lopez-Garrido J, Ojkic N, Khanna K, Wagner
FR, Villa E, Endres RG, Pogliano K (2018)
Chromosome translocation inflates bacillus
forespores and impacts cellular morphology.
Cell 172(4):758–770.e14
11. Noble JM, Lubieniecki J, Savitzky BH,
Plitzko J, Engelhardt H, Baumeister W, Kourkoutis LF (2018) Connectivity of centermost
chromatophores in rhodobacter sphaeroides
bacteria. Mol Microbiol 109(6):812–825
12. Mosalaganti S, Kosinski J, Albert S, Schaffer M,
Strenkert D, Salome ´ PA, Merchant SS, Plitzko
JM, Baumeister W, Engel BD, Beck M (2018)
In situ architecture of the algal nuclear pore
complex. Nat Commun 9(1):2361
13. Schaffer M, Mahamid J, Engel BD, Laugks T,
Baumeister W, Plitzko JM (2017) Optimized
cryo-focused ion beam sample preparation
aimed at in situ structural studies of membrane
proteins. J Struct Biol 197(2):73–82
14. Chaikeeratisak V, Nguyen K, Khanna K, Brilot
AF, Erb ML, Coker JKC, Vavilina A, Newton
GL, Buschauer R, Pogliano K, Villa E, Agard
DA, Pogliano J (2017) Assembly of a nucleuslike structure during viral replication in bacteria. Science 355(6321):194–197
15. Rosenzweig ESF, Xu B, Cuellar LK, MartinezSanchez A, Schaffer M, Strauss M, Cartwright
HN, Ronceray P, Plitzko JM, Fo ¨rster F, Wingreen NS, Engel BD, Mackinder LC, Jonikas
MC (2017) The eukaryotic co2-concentrating
organelle is liquid-like and exhibits dynamic
reorganization. Cell 171(1):148–162.e19
16. B€ auerlein FJ, Saha I, Mishra A, Kalemanov M,
Martı ´nez-Sa ´nchez A, Klein R, Dudanova I,
Hipp MS, Hartl FU, Baumeister W, Ferna ´ndez-Busnadiego R (2017) In situ architecture
and cellular interactions of polyq inclusions.
Cell 171(1):179–187.e10
17. Mahamid J, Pfeffer S, Schaffer M, Villa E,
Danev R, Kuhn Cuellar L, Fo ¨rster F, Hyman
AA, Plitzko JM, Baumeister W (2016) Visualizing the molecular sociology at the hela cell
nuclear
periphery.
Science
351
(6276):969–972
18. Zhang J, Ji G, Huang X, Xu W, Sun F (2016)
An improved cryo-fib method for fabrication of
frozen hydrated lamella. J Struct Biol 194
(2):218–223
19. Engel BD, Schaffer M, Kuhn Cuellar L, Villa E,
Plitzko JM, Baumeister W (2015) Native architecture of the Chlamydomonas chloroplast
revealed by in situ cryo-electron tomography.
elife 4:e04889
20. Harapin J, Bo ¨rmel M, Sapra KT, Brunner D,
Kaech A, Medalia O (2015) Structural analysis
of multicellular organisms with cryo-electron
tomography. Nat Methods 12:634–636
21. Villa E, Schaffer M, Plitzko JM, Baumeister W
(2013) Opening windows into the cell:
focused-ion-beam milling for cryo-electron
tomography. Curr Opin Struct Biol 23
(5):771–777. Protein-carbohydrate interactions/biophysical methods
22. Wang K, Strunk K, Zhao G, Gray JL, Zhang P
(2012) 3d structure determination of native
mammalian cells using cryo-fib and cryoelectron tomography. J Struct Biol 180
(2):318–326
23. Rigort A, B€ auerlein FJB, Villa E, Eibauer M,
Laugks T, Baumeister W, Plitzko JM (2012)
Focused ion beam micromachining of eukaryotic cells for cryoelectron tomography. Proc
Natl Acad Sci 109(12):4449–4454
24. Marko M, Hsieh C, Schalek R, Frank J, Mannella C (2007) Focused-ion-beam thinning of
frozen-hydrated biological specimens for cryoelectron microscopy. Nat Methods 4:215
25. Rajput NS, Luo X (2015) Chapter 3: FIB
micro-/nano-fabrication.
In:
Qin
Y
(ed) Micromanufacturing engineering and
technology, Micro and Nano Technologies,
2nd edn. William Andrew Publishing, Boston,
pp 61–80
26. Volkert CA, Minor AM (2007) Focused ion
beam microscopy and micromachining. MRS
Bull 32(5):389–399
27. Chyr I, Steckl AJ (2001) Gan focused ion beam
micromachining with gas-assisted etching. J
Vacuum Sci Technol B 19(6):2547–2550
28. Schaffer M, Pfeffer S, Mahamid J, Kleindiek S,
Laugks T, Albert S, Engel BD, Rummel A,
Smith AJ, Baumeister W, Plitzko JM (2019) A
cryo-fib lift-out technique enables molecularresolution cryo-et within native caenorhabditis
elegans tissue. Nat Methods 16(8):757–762
Practical Approaches for Cryo-FIB Milling
81