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alginates ( fmc biopolymer ) and agarose were covalently coupled with the integrin binding peptide ( gly)4-arg - gly - asp - ala - ser - ser - lys - tyr ( peptides international)17,20 .
pegdm polymers were photo - crosslinked in the presence of acryloyl - peg - grgds21 . for cell encapsulation studies , mixtures of varying wt % polymer
were mixed with stem cells ( 20 million clonally derived mmsc ( d1 ) per ml , or 15 million hmsc / ml ) and crosslinked to form hydrogels .
the elastic modulus e of hydrogel matrices was measured using an instron 3342 mechanical apparatus at a compression rate of 1mm / min .
cell - encapsulating hydrogels were transferred to fbs - supplemented dulbecco s modified eagle media ( dmem , invitrogen ) containing a combination of osteogenic and adipogenic chemical supplements .
after 1 week in culture , lineage specification was assessed by in - situ staining for alkaline phosphatase activity ( fast blue ) and neutral lipids ( oil red o ) in the same samples , by ocn staining in cryosectioned matrices , or by biochemical analysis of cell lysates obtained by recovering cells from alginate matrices with 50 mm ethylenediaminetetraacetic acid ( edta ) in pbs .
western analysis of cell phenotype was performed to assess population - level expression levels of fn and coli , as well as adipogenic ( ppar- , adn ) and osteogenic ( cbfa-1 , osteopontin ) biomarkers . in certain experiments , cell , encapsulating , calcium - crosslinked alginate matrices were combined with cell - free alginate matrices in the same media so that the concentration of calcium ions available to cells could be controlled independent from the rigidity of cell - encapsulating matrices ( fig .
the relative diffusion coefficient for a model protein , bovine serum albumin ( bsa ; 67 kda ) was measured via release of rhodamine - labeled bsa from alginate matrices of varying rigidity ( fig .
after encapsulating cells , hydrogels were incubated in fbs - supplemented media for 2 hr .
hydrogels were dissolved into 250g / ml alginate lyase , and cell lysates were prepared with ripa buffer ( sigma ) .
equal amounts of protein were probed onto neutravidin - coated stripwells ( thermo scientific ) , and biotin - rgd - bound integrins were probed by elisa using polyclonal antibodies against either 5 or v integrin subunits , hrp - tagged secondary antibodies ( jackson immunolabs ) , and quantablue fluorogenic hrp substrate ( thermo scientific ) .
quantablue fluorescence was read in a biotek plate reader and the relative number of bonds between integrins and rgd was calculated according to equation 1 : 
 equation 1nb,x = rfisamplerfiblankrficontrolrfiblank where rfi refers to the relative fluorescence intensity of samples , controls or blank ( lysate from cells that were not encapsulated into alginate - rgd - biotin ) .
the control was a 3d , 22 kpa matrix modified with 15 m rgd - biotin ( fig .
fret analysis of integrin - adhesion ligand bonds was performed by monitoring energy transfer between a membrane - intercalating fluorescein dye and rhodamine labeled peptides as previously described by kong et al41 .
clonally derived mmsc ( d1 ) were labeled with 5-hexadecanoylaminofluorescein ( invitrogen ) for 24 hr , and encapsulated into alginate matrices presenting g4rgdassk(tetramethylrhodamine)y - oh .
hydrogels were formed by mixing cells with various alginate polymers and crosslinking either with caso4 ( calcium - alginate ) or poly(acrylamide - co - hydrazide ; alginate dialdehyde ) . after encapsulating cells
, hydrogels were incubated in fbs - supplemented media for 2 hr . the emission spectrum from hydrogels was collected using a fluorimeter ( jobin horiba ) with 488 nm excitation , and normalized to cell density by dissolving hydrogels into pbs containing 50mmol / l edta ( calcium alginate ) or 250g / ml alginate lyase ( alginate dialdehyde ) .
the degree of energy transfer ( dfret ) was calculated according to equation 2 : 
 equation 2dfret=1ii0 where i refers to emission intensity at 520 nm , i0 to the 520 nm emission intensity in a donor control sample with the same peptide density , elastic modulus and drug treatment but with rgd peptides rather than rgd - tamra peptides .
dfret was used to calculate the number of integrin - rgd bonds based on a linear calibration curve generated by performing parallel fret - binding and i - rgd binding studies in solution41 .
excitation was provided by an argon laser ( 488 nm ) , and fluorescein ( green , 500530 nm ) and rhodamine ( red , 565615 ) emission were collected simultaneously .
alginates ( fmc biopolymer ) and agarose were covalently coupled with the integrin binding peptide ( gly)4-arg - gly - asp - ala - ser - ser - lys - tyr ( peptides international)17,20 .
pegdm polymers were photo - crosslinked in the presence of acryloyl - peg - grgds21 . for cell encapsulation studies , mixtures of varying wt % polymer
were mixed with stem cells ( 20 million clonally derived mmsc ( d1 ) per ml , or 15 million hmsc / ml ) and crosslinked to form hydrogels .
the elastic modulus e of hydrogel matrices was measured using an instron 3342 mechanical apparatus at a compression rate of 1mm / min .
cell - encapsulating hydrogels were transferred to fbs - supplemented dulbecco s modified eagle media ( dmem , invitrogen ) containing a combination of osteogenic and adipogenic chemical supplements .
after 1 week in culture , lineage specification was assessed by in - situ staining for alkaline phosphatase activity ( fast blue ) and neutral lipids ( oil red o ) in the same samples , by ocn staining in cryosectioned matrices , or by biochemical analysis of cell lysates obtained by recovering cells from alginate matrices with 50 mm ethylenediaminetetraacetic acid ( edta ) in pbs .
western analysis of cell phenotype was performed to assess population - level expression levels of fn and coli , as well as adipogenic ( ppar- , adn ) and osteogenic ( cbfa-1 , osteopontin ) biomarkers . in certain experiments , cell , encapsulating , calcium - crosslinked alginate matrices were combined with cell - free alginate matrices in the same media so that the concentration of calcium ions available to cells could be controlled independent from the rigidity of cell - encapsulating matrices ( fig .
the relative diffusion coefficient for a model protein , bovine serum albumin ( bsa ; 67 kda ) was measured via release of rhodamine - labeled bsa from alginate matrices of varying rigidity ( fig .
g4rgeassk(biotin)y - oh presenting alginates were used as negative controls . after encapsulating cells , hydrogels were incubated in fbs - supplemented media for 2 hr .
hydrogels were dissolved into 250g / ml alginate lyase , and cell lysates were prepared with ripa buffer ( sigma ) .
equal amounts of protein were probed onto neutravidin - coated stripwells ( thermo scientific ) , and biotin - rgd - bound integrins were probed by elisa using polyclonal antibodies against either 5 or v integrin subunits , hrp - tagged secondary antibodies ( jackson immunolabs ) , and quantablue fluorogenic hrp substrate ( thermo scientific ) .
quantablue fluorescence was read in a biotek plate reader and the relative number of bonds between integrins and rgd was calculated according to equation 1 : 
 equation 1nb,x = rfisamplerfiblankrficontrolrfiblank where rfi refers to the relative fluorescence intensity of samples , controls or blank ( lysate from cells that were not encapsulated into alginate - rgd - biotin ) .
the control was a 3d , 22 kpa matrix modified with 15 m rgd - biotin ( fig .
fret analysis of integrin - adhesion ligand bonds was performed by monitoring energy transfer between a membrane - intercalating fluorescein dye and rhodamine labeled peptides as previously described by kong et al41 .
clonally derived mmsc ( d1 ) were labeled with 5-hexadecanoylaminofluorescein ( invitrogen ) for 24 hr , and encapsulated into alginate matrices presenting g4rgdassk(tetramethylrhodamine)y - oh .
hydrogels were formed by mixing cells with various alginate polymers and crosslinking either with caso4 ( calcium - alginate ) or poly(acrylamide - co - hydrazide ; alginate dialdehyde ) . after encapsulating cells
, hydrogels were incubated in fbs - supplemented media for 2 hr . the emission spectrum from hydrogels was collected using a fluorimeter ( jobin horiba ) with 488 nm excitation , and normalized to cell density by dissolving hydrogels into pbs containing 50mmol / l edta ( calcium alginate ) or 250g / ml alginate lyase ( alginate dialdehyde ) .
the degree of energy transfer ( dfret ) was calculated according to equation 2 : 
 equation 2dfret=1ii0 where i refers to emission intensity at 520 nm , i0 to the 520 nm emission intensity in a donor control sample with the same peptide density , elastic modulus and drug treatment but with rgd peptides rather than rgd - tamra peptides .
dfret was used to calculate the number of integrin - rgd bonds based on a linear calibration curve generated by performing parallel fret - binding and i - rgd binding studies in solution41 .
fret between cells and rgd was visualized using a laser scanning confocal microscope ( zeiss lsm 510 ) .
excitation was provided by an argon laser ( 488 nm ) , and fluorescein ( green , 500530 nm ) and rhodamine ( red , 565615 ) emission were collected simultaneously .
stem cells sense and respond to the mechanical properties of the extracellular matrix . 
 however , both the extent to which extracellular matrix mechanics affect stem cell fate in 3d micro - environments and the underlying biophysical mechanisms are unclear . 
 we demonstrate that the commitment of mesenchymal stem cell ( msc ) populations changes in response to the rigidity of 3d micro - environments , with osteogenesis occurring predominantly at 1130 kpa . 
 in contrast to previous 2d work , however , cell fate was not correlated with morphology . 
 instead , matrix stiffness regulated integrin binding as well as reorganization of adhesion ligands on the nanoscale , both of which were traction - dependent and correlated with osteogenic commitment of msc populations . 
 these findings suggest that cells interpret changes in the physical properties of adhesion substrates as changes in adhesion ligand presentation , and that cells themselves can be harnessed as tools to mechanically process materials into structures that feedback to manipulate their fate .