@article{clark_huayta_morton_meyer_san-miguel_2024, title={Morphological hallmarks of dopaminergic neurodegeneration are associated with altered neuron function in Caenorhabditis elegans}, volume={100}, ISSN={["1872-9711"]}, DOI={10.1016/j.neuro.2023.12.005}, abstractNote={Caenorhabditis elegans (C. elegans) is an excellent model system to study neurodegenerative diseases, such as Parkinson's disease, as it enables analysis of both neuron morphology and function in live animals. Multiple structural changes in neurons, such as cephalic dendrite morphological abnormalities, have been considered hallmarks of neurodegeneration in this model, but their relevance to changes in neuron function are not entirely clear. We sought to test whether hallmark morphological changes associated with chemically induced dopaminergic neuron degeneration, such as dendrite blebbing, breakage, and loss, are indicative of neuronal malfunction and result in changes in behavior. We adapted an established dopaminergic neuronal function assay by measuring paralysis in the presence of exogenous dopamine, which revealed clear differences between cat-2 dopamine deficient mutants, wildtype worms, and dat-1 dopamine abundant mutants. Next, we integrated an automated image processing algorithm and a microfluidic device to segregate worm populations by their cephalic dendrite morphologies. We show that nematodes with dopaminergic dendrite degeneration markers, such as blebbing or breakage, paralyze at higher rates in a dopamine solution, providing evidence that dopaminergic neurodegeneration morphologies are correlated with functional neuronal outputs.}, journal={NEUROTOXICOLOGY}, author={Clark, Andrew S. and Huayta, Javier and Morton, Katherine S. and Meyer, Joel N. and San-Miguel, Adriana}, year={2024}, month={Jan}, pages={100–106} }
 @article{clark_kalmanson_morton_hartman_meyer_san-miguel_2023, title={An unbiased, automated platform for scoring dopaminergic neurodegeneration in C. elegans}, volume={18}, ISSN={["1932-6203"]}, url={https://doi.org/10.1371/journal.pone.0281797}, DOI={10.1371/journal.pone.0281797}, abstractNote={Caenorhabditis elegans(C.elegans) has served as a simple model organism to study dopaminergic neurodegeneration, as it enables quantitative analysis of cellular and sub-cellular morphologies in live animals. These isogenic nematodes have a rapid life cycle and transparent body, making high-throughput imaging and evaluation of fluorescently tagged neurons possible. However, the current state-of-the-art method for quantifying dopaminergic degeneration requires researchers to manually examine images and score dendrites into groups of varying levels of neurodegeneration severity, which is time consuming, subject to bias, and limited in data sensitivity. We aim to overcome the pitfalls of manual neuron scoring by developing an automated, unbiased image processing algorithm to quantify dopaminergic neurodegeneration inC.elegans. The algorithm can be used on images acquired with different microscopy setups and only requires two inputs: a maximum projection image of the four cephalic neurons in theC.eleganshead and the pixel size of the user’s camera. We validate the platform by detecting and quantifying neurodegeneration in nematodes exposed to rotenone, cold shock, and 6-hydroxydopamine using 63x epifluorescence, 63x confocal, and 40x epifluorescence microscopy, respectively. Analysis of tubby mutant worms with altered fat storage showed that, contrary to our hypothesis, increased adiposity did not sensitize to stressor-induced neurodegeneration. We further verify the accuracy of the algorithm by comparing code-generated, categorical degeneration results with manually scored dendrites of the same experiments. The platform, which detects 20 different metrics of neurodegeneration, can provide comparative insight into how each exposure affects dopaminergic neurodegeneration patterns.}, number={7}, journal={PLOS ONE}, author={Clark, Andrew S. and Kalmanson, Zachary and Morton, Katherine and Hartman, Jessica and Meyer, Joel and San-Miguel, Adriana}, editor={Lajoie, PatrickEditor}, year={2023}, month={Jul} }
 @misc{an unbiased, automated platform for scoring dopaminergic neurodegeneration in c. elegans_2023, DOI={10.5061/dryad.cvdncjt82}, journal={Dryad}, year={2023}, month={May} }
 @article{clark_kalmanson_morton_hartman_meyer_san-miguel_2023, title={An unbiased, automated platform for scoring dopaminergic neurodegeneration inC. elegans}, url={https://doi.org/10.1101/2023.02.02.526781}, DOI={10.1101/2023.02.02.526781}, abstractNote={Abstract}, author={Clark, Andrew S. and Kalmanson, Zachary and Morton, Katherine and Hartman, Jessica and Meyer, Joel and San-Miguel, Adriana}, year={2023}, month={Feb} }
 @misc{data for: endogenous daf-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction_2023, DOI={10.5061/dryad.vx0k6djwt}, journal={Dryad}, year={2023}, month={Feb} }
 @article{huayta_crapster_san-miguel_2023, title={Endogenous DAF-16 spatiotemporal activity quantitatively predicts lifespan extension induced by dietary restriction}, volume={6}, ISSN={["2399-3642"]}, url={https://doi.org/10.1038/s42003-023-04562-2}, DOI={10.1038/s42003-023-04562-2}, abstractNote={Abstract}, number={1}, journal={COMMUNICATIONS BIOLOGY}, author={Huayta, Javier and Crapster, Joseph P. and San-Miguel, Adriana}, year={2023}, month={Feb} }
 @article{karakis_jabeen_britt_cordiner_mischler_li_miguel_rao_2023, title={Laminin switches terminal differentiation fate of human trophoblast stem cells under chemically defined culture conditions}, volume={299}, ISSN={["1083-351X"]}, DOI={10.1016/j.jbc.2023.104650}, abstractNote={Human trophoblast stem cells (hTSCs) have emerged as a powerful tool to model early placental development in vitro. Analogous to the epithelial cytotrophoblast in the placenta, hTSCs can differentiate into cells of the extravillous trophoblast (EVT) lineage or the multinucleate syncytiotrophoblast (STB). Here we present a chemically defined culture system for STB and EVT differentiation of hTSCs. Notably, in contrast to current approaches, we neither utilize forskolin for STB formation nor transforming growth factor-beta (TGFβ) inhibitors or a passage step for EVT differentiation. Strikingly, the presence of a single additional extracellular cue–laminin-111–switched the terminal differentiation of hTSCs from STB to the EVT lineage under these conditions. In the absence of laminin-111, STB formation occurred, with cell fusion comparable to that obtained with differentiation mediated by forskolin; however, in the presence of laminin-111, hTSCs differentiated to the EVT lineage. Protein expression of nuclear hypoxia-inducible factors (HIF1α and HIF2α) was upregulated during EVT differentiation mediated by laminin-111 exposure. A heterogeneous mixture of Notch1+ EVTs in colonies and HLA-G+ single-cell EVTs were obtained without a passage step, reminiscent of heterogeneity in vivo. Further analysis showed that inhibition of TGFβ signaling affected both STB and EVT differentiation mediated by laminin-111 exposure. TGFβ inhibition during EVT differentiation resulted in decreased HLA-G expression and increased Notch1 expression. On the other hand, TGFβ inhibition prevented STB formation. The chemically defined culture system for hTSC differentiation established herein facilitates quantitative analysis of heterogeneity that arises during hTSC differentiation and will enable mechanistic studies in vitro. Human trophoblast stem cells (hTSCs) have emerged as a powerful tool to model early placental development in vitro. Analogous to the epithelial cytotrophoblast in the placenta, hTSCs can differentiate into cells of the extravillous trophoblast (EVT) lineage or the multinucleate syncytiotrophoblast (STB). Here we present a chemically defined culture system for STB and EVT differentiation of hTSCs. Notably, in contrast to current approaches, we neither utilize forskolin for STB formation nor transforming growth factor-beta (TGFβ) inhibitors or a passage step for EVT differentiation. Strikingly, the presence of a single additional extracellular cue–laminin-111–switched the terminal differentiation of hTSCs from STB to the EVT lineage under these conditions. In the absence of laminin-111, STB formation occurred, with cell fusion comparable to that obtained with differentiation mediated by forskolin; however, in the presence of laminin-111, hTSCs differentiated to the EVT lineage. Protein expression of nuclear hypoxia-inducible factors (HIF1α and HIF2α) was upregulated during EVT differentiation mediated by laminin-111 exposure. A heterogeneous mixture of Notch1+ EVTs in colonies and HLA-G+ single-cell EVTs were obtained without a passage step, reminiscent of heterogeneity in vivo. Further analysis showed that inhibition of TGFβ signaling affected both STB and EVT differentiation mediated by laminin-111 exposure. TGFβ inhibition during EVT differentiation resulted in decreased HLA-G expression and increased Notch1 expression. On the other hand, TGFβ inhibition prevented STB formation. The chemically defined culture system for hTSC differentiation established herein facilitates quantitative analysis of heterogeneity that arises during hTSC differentiation and will enable mechanistic studies in vitro. The placenta is a complex fetal organ with a vast network of villi that ensures efficient exchange of nutrients and waste across the maternal-fetal interface. Epithelial cytotrophoblasts (CTBs) of the early human placenta give rise to all trophoblast cell types in the placenta (1Aplin J.D. Developmental cell biology of human villous trophoblast: current research problems.Int. J. Dev. Biol. 2010; 54: 323-329Crossref PubMed Scopus (95) Google Scholar, 2Knöfler M. Vasicek R. Schreiber M. Key regulatory transcription factors involved in placental trophoblast development - a review.Placenta. 2001; 22: S83-S92Crossref PubMed Scopus (45) Google Scholar, 3Knöfler M. Haider S. Saleh L. Pollheimer J. Gamage T.K.J.B. 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The STB is subsequently bathed in maternal blood at ∼10 weeks of gestation, when blood flow to the placenta is established (5Caniggia I. Winter J. Lye S.J. Post M. Oxygen and placental development during the first trimester: implications for the pathophysiology of pre-eclampsia.Placenta. 2000; 21: S25-S30Crossref PubMed Scopus (313) Google Scholar, 6Tuuli M.G. Longtine M.S. Nelson D.M. Review: oxygen and trophoblast biology - a source of controversy.Placenta. 2011; 32: S109-S118Crossref PubMed Scopus (120) Google Scholar, 7Zhou Y. Genbacev O. Damsky C.H. Fisher S.J. Oxygen regulates human cytotrophoblast differentiation and invasion: implications for endovascular invasion in normal pregnancy and in pre-eclampsia.J. Reprod. Immunol. 1998; 39: 197-213Crossref PubMed Scopus (94) Google Scholar). CTBs of placental villi anchored to the maternal decidua push through the syncytial layer and differentiate to extravillous trophoblasts (EVTs), first forming proliferative column trophoblasts adjacent to the villus tip (1Aplin J.D. Developmental cell biology of human villous trophoblast: current research problems.Int. J. Dev. Biol. 2010; 54: 323-329Crossref PubMed Scopus (95) Google Scholar, 3Knöfler M. Haider S. Saleh L. Pollheimer J. Gamage T.K.J.B. James J. Human placenta and trophoblast development: key molecular mechanisms and model systems.Cell. Mol. Life Sci. 2019; 76: 3479-3496Crossref PubMed Scopus (311) Google Scholar). At the distal end, column trophoblasts undergo an epithelial-to-mesenchymal transition (EMT) to become mature mesenchymal EVTs that invade the maternal decidua and parts of the myometrium (8Vićovac L. Aplin J.D. Epithelial-mesenchymal transition during trophoblast differentiation.Acta Anat. 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Preeclampsia is associated with failure of human cytotrophoblasts to mimic a vascular adhesion phenotype: one cause of defective endovascular invasion in this syndrome?.J. Clin. Invest. 1997; 99: 2152-2164Crossref PubMed Scopus (815) Google Scholar, 23Zhou Y. Gormley M.J. Hunkapiller N.M. Kapidzic M. Stolyarov Y. Feng V. et al.Reversal of gene dysregulation in cultured cytotrophoblasts reveals possible causes of preeclampsia.J. Clin. Invest. 2013; 123: 2862-2872Crossref PubMed Scopus (97) Google Scholar). Yet, despite the importance of EVT differentiation in placental health and pathology, molecular mechanisms underlying EVT differentiation and maturation to mesenchymal invasive EVTs remain poorly understood. Mechanistic studies on early human placental development have been impeded primarily due to lack of suitable model systems. There are substantial restrictions on research with fetal tissue and human embryos and significant differences between placental development in common experimental animals and humans (24Boer G.J. Ethical guidelines for the use of human embryonic or fetal tissue for experimental and clinical neurotransplantation and research.J. Neurol. 1994; 242: 1-13Crossref PubMed Scopus (106) Google Scholar, 25Pera M.F. Human embryo research and the 14-day rule.Development. 2017; 144: 1923-1925Crossref PubMed Scopus (52) Google Scholar, 26Soncin F. Khater M. To C. Pizzo D. Farah O. Wakeland A. et al.Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development.Development. 2018; 145dev156273Google Scholar, 27Lee K.Y. Demayo F.J. Animal models of implantation.Reproduction. 2004; 128: 679-695Crossref PubMed Scopus (213) Google Scholar, 28Malassine A. Frendo J.-L. Evain-Brion D. 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Models for study of human embryo implantation: choice of cell lines?.Biol. Reprod. 2010; 82: 235-245Crossref PubMed Scopus (237) Google Scholar). In this context, human trophoblast stem cells (hTSCs) derived from early gestation primary placental samples and blastocysts have emerged as powerful in vitro models of early human placental development (32Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. et al.Derivation of human trophoblast stem cells.Cell Stem Cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (432) Google Scholar). hTSCs, which model the CTB in vivo, can be maintained in cell culture and differentiate into STB or EVTs. In recent work, others and we have also shown that hTSCs can be derived from human pluripotent stem cells, including induced pluripotent stem cells (33Yu L. Wei Y. Duan J. Schmitz D.A. Sakurai M. 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Springer, Berlin Heidelberg2012Crossref Scopus (64) Google Scholar, 57Haider S. Meinhardt G. Saleh L. Kunihs V. Gamperl M. Kaindl U. et al.Self-renewing trophoblast organoids recapitulate the developmental program of the early human placenta.Stem Cell Rep. 2018; 11: 537-551Abstract Full Text Full Text PDF PubMed Scopus (207) Google Scholar, 62Plessl K. Haider S. Fiala C. Pollheimer J. Knöfler M. Expression pattern and function of notch2 in different subtypes of first trimester cytotrophoblast.Placenta. 2015; 36: 365-371Crossref PubMed Scopus (17) Google Scholar, 65Mccormick J. Whitley G.S.J. Le Bouteiller P. Cartwright J.E. Soluble HLA-G regulates motility and invasion of the trophoblast-derived cell line SGHPL-4.Hum. Reprod. 2009; 24: 1339-1345Crossref PubMed Scopus (35) Google Scholar). Subsequently, when these distal EVTs undergo EMT, they gain expression of ITGA1, express higher levels of HLA-G, and lose expression of markers that characterize the column trophoblasts (3Knöfler M. Haider S. Saleh L. Pollheimer J. Gamage T.K.J.B. James J. Human placenta and trophoblast development: key molecular mechanisms and model systems.Cell. Mol. Life Sci. 2019; 76: 3479-3496Crossref PubMed Scopus (311) Google Scholar, 66Fukushima K. Miyamoto S. Tsukimori K. Kobayashi H. Seki H. Takeda S. et al.Tumor necrosis factor and vascular endothelial growth factor induce endothelial integrin repertories, regulating endovascular differentiation and apoptosis in a human extravillous trophoblast cell Line1.Biol. Reprod. 2005; 73: 172-179Crossref PubMed Scopus (52) Google Scholar, 67Natenzon A. McFadden P. DaSilva-Arnold S.C. Zamudio S. Illsley N.P. Diminished trophoblast differentiation in early onset preeclampsia.Placenta. 2022; 120: 25-31Crossref PubMed Scopus (4) Google Scholar). Current protocols for EVT differentiation that include a passage step (32Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. et al.Derivation of human trophoblast stem cells.Cell Stem Cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (432) Google Scholar, 47Karvas R.M. Khan S.A. Verma S. Yin Y. Kulkarni D. Dong C. et al.Stem-cell-derived trophoblast organoids model human placental development and susceptibility to emerging pathogens.Cell Stem Cell. 2022; 29: 810-825.e8Abstract Full Text Full Text PDF PubMed Scopus (32) Google Scholar) do not capture EVT heterogeneity and the sequential nature of CTB differentiation as mature mesenchymal EVTs are formed. Here we present chemically defined culture conditions for differentiation of placenta- and hiPSC-derived hTSCs to EVTs and STB. Notably, our conditions do not involve a passage step and exclude forskolin and TGFβ inhibition during STB and EVT differentiation, respectively. Under these culture conditions, we identified laminin-111-mediated upregulation of hypoxia-inducible factor-alpha (HIFα) as the critical input that switches differentiation hTSCs from STB to the EVT lineage. We also investigated the effect of inhibiting TGFβ signaling on EVT and STB differentiation. Placenta-derived CT29 and CT30 hTSCs and hiPSC-derived SC102A-1 hTSCs were cultured in trophoblast stem cell medium (TSCM) as described previously (32Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. et al.Derivation of human trophoblast stem cells.Cell Stem Cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (432) Google Scholar, 38Mischler A. Karakis V. Mahinthakumar J. Carberry C.K. Miguel A.S. Rager J.E. et al.Two distinct trophectoderm lineage stem cells from human pluripotent stem cells.J. Biol. Chem. 2021; 296: 100386Abstract Full Text Full Text PDF PubMed Scopus (29) Google Scholar). Differentiation was induced by passaging hTSCs into a defined trophoblast differentiation medium (DTDM) supplemented with epidermal growth factor (EGF) and the ROCK inhibitor, Y-27632, at passage for 2 days, and culturing them for an additional 4 days in DTDM (Fig. 1A). Upon passage, we initially observed an increase in cell number, but b}, number={5}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, author={Karakis, Victoria and Jabeen, Mahe and Britt, John W. and Cordiner, Abigail and Mischler, Adam and Li, Feng and Miguel, Adriana San and Rao, Balaji M.}, year={2023}, month={May} }
 @article{prodromou_moore_chu_deal_san miguel_brown_daniele_pozdin_menegatti_2023, title={Molecular Engineering of Cyclic Azobenzene-Peptide Hybrid Ligands for the Purification of Human Blood Factor VIII via Photo-Affinity Chromatography}, volume={1}, ISSN={["1616-3028"]}, url={http://dx.doi.org/10.1002/adfm.202213881}, DOI={10.1002/adfm.202213881}, abstractNote={Abstract}, journal={ADVANCED FUNCTIONAL MATERIALS}, publisher={Wiley}, author={Prodromou, Raphael and Moore, Brandyn David and Chu, Wenning and Deal, Halston and San Miguel, Adriana and Brown, Ashley Carson and Daniele, Michael Angelo-Anthony and Pozdin, Vladimir Aleksandrovich and Menegatti, Stefano}, year={2023}, month={Jan} }
 @article{clark_huayta_morton_meyer_san-miguel_2023, title={Morphological hallmarks of dopaminergic neurodegeneration are associated with altered neuron function inCaenorhabditis elegans}, url={https://doi.org/10.1101/2023.08.22.554364}, DOI={10.1101/2023.08.22.554364}, abstractNote={Abstract}, author={Clark, Andrew S. and Huayta, Javier and Morton, Katherine S. and Meyer, Joel N. and San-Miguel, Adriana}, year={2023}, month={Aug} }
 @article{durmusoglu_haller_al’abri_day_sands_clark_san-miguel_vazquez-uribe_sommer_crook_2023, title={Programming Probiotics: Diet-responsive gene expression and colonization control in engineeredS. boulardii}, url={https://doi.org/10.1101/2023.11.17.567539}, DOI={10.1101/2023.11.17.567539}, abstractNote={Abstract}, author={Durmusoglu, Deniz and Haller, Daniel J. and Al’Abri, Ibrahim S. and Day, Katie and Sands, Carmen and Clark, Andrew and San-Miguel, Adriana and Vazquez-Uribe, Ruben and Sommer, Morten O. A. and Crook, Nathan C.}, year={2023}, month={Nov} }
 @article{midkiff_huayta_lichty_crapster_san-miguel_2022, title={Identifying C. elegans lifespan mutants by screening for early-onset protein aggregation}, volume={25}, ISSN={["2589-0042"]}, url={http://dx.doi.org/10.1016/j.isci.2022.105460}, DOI={10.1016/j.isci.2022.105460}, abstractNote={Genetic screens are widely used to identify genes that control specific biological functions. In Caenorhabditis elegans, forward genetic screens rely on the isolation of reproductively active mutants that can self-propagate clonal populations. Screens that target post-reproductive phenotypes, such as lifespan, are thus challenging. We combine microfluidic technologies and image processing to perform high-throughput automated screening for short-lived mutants using protein aggregation as a marker for aging. We take advantage of microfluidics for maintaining a reproductively active adult mutagenized population and for performing serial high-throughput analysis and sorting of animals with increased protein aggregation, using fluorescently-labeled PAB-1 as a readout. We demonstrate that lifespan mutants can be identified by screening for accelerated protein aggregation through quantitative analysis of fluorescently labeled aggregates while avoiding conditional sterilization or manual separation of parental and progeny populations. We also show that aged wildtypes and premature aggregation mutants differ in aggregate morphology, suggesting aggregate growth is time-dependent.}, number={11}, journal={ISCIENCE}, publisher={Elsevier BV}, author={Midkiff, Daniel F. and Huayta, Javier and Lichty, James D. and Crapster, Joseph P. and San-Miguel, Adriana}, year={2022}, month={Nov} }
 @article{clark_san-miguel_2021, title={A bioinspired, passive microfluidic lobe filtration system}, volume={21}, ISSN={["1473-0189"]}, url={http://dx.doi.org/10.1039/d1lc00449b}, DOI={10.1039/d1lc00449b}, abstractNote={Lobe filtration is a bioinspired, non-clogging microparticle filtration mechanism capable of high throughput processing. Simulations of complex velocity profiles provide a robust explanation for this microparticle filtration mechanism.}, number={19}, journal={LAB ON A CHIP}, publisher={Royal Society of Chemistry (RSC)}, author={Clark, Andrew S. and San-Miguel, Adriana}, year={2021}, month={Aug} }
 @article{arulalan_huayta_stallrich_san-miguel_2021, title={Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction}, url={https://doi.org/10.1101/2021.03.17.435857}, DOI={10.1101/2021.03.17.435857}, abstractNote={Abstract}, author={Arulalan, Karthik Suresh and Huayta, Javier and Stallrich, Jonathan W. and San-Miguel, Adriana}, year={2021}, month={Mar} }
 @article{arulalan_huayta_stallrich_san-miguel_2021, title={Antagonistic effects of chemical mixtures on the oxidative stress response are silenced by heat stress and reversed under dietary restriction}, volume={1}, url={https://doi.org/10.1093/exposome/osab005}, DOI={10.1093/exposome/osab005}, abstractNote={Abstract}, number={1}, journal={Exposome}, publisher={Oxford University Press (OUP)}, author={Arulalan, Karthik Suresh and Huayta, Javier and Stallrich, Jonathan W and San-Miguel, Adriana}, year={2021}, month={Apr} }
 @article{huayta_san-miguel_2021, title={Endogenous DAF-16 Spatiotemporal Activity Quantitatively Predicts Lifespan Extension Induced by Dietary Restriction}, url={https://doi.org/10.1101/2021.12.20.473576}, DOI={10.1101/2021.12.20.473576}, abstractNote={Summary}, author={Huayta, Javier and San-Miguel, Adriana}, year={2021}, month={Dec} }
 @article{prodromou_day_saberi-bosari_schneible_mabe_san miguel_daniele_pozdin_menegatti_2021, title={Engineering Next Generation Cyclized Peptide Ligands for Light-Controlled Capture and Release of Therapeutic Proteins}, volume={31}, ISSN={["1616-3028"]}, url={http://dx.doi.org/10.1002/adfm.202101410}, DOI={10.1002/adfm.202101410}, abstractNote={Abstract}, number={27}, journal={ADVANCED FUNCTIONAL MATERIALS}, publisher={Wiley}, author={Prodromou, Raphael and Day, Kevin N. and Saberi-Bosari, Sahand and Schneible, John D. and Mabe, Matthew D. and San Miguel, Adriana and Daniele, Michael A. and Pozdin, Vladimir and Menegatti, Stefano}, year={2021}, month={Jul} }
 @article{midkiff_san-miguel_2021, title={Identifying C. elegans Lifespan Mutants by Screening for Early-Onset Protein Aggregation}, url={https://doi.org/10.1101/2021.12.14.472506}, DOI={10.1101/2021.12.14.472506}, abstractNote={Summary}, author={Midkiff, Daniel F. and San-Miguel, Adriana}, year={2021}, month={Dec} }
 @article{smith_san-miguel_hsiao_2021, title={Local velocity of thermoresponsive colloidal gels in rate-driven flow}, volume={33}, ISSN={["1089-7666"]}, url={http://dx.doi.org/10.1063/5.0042109}, DOI={10.1063/5.0042109}, abstractNote={The interplay between flow and attractive interactions in colloidal gels results in complex particle trajectories and velocity profiles that are not evident from bulk rheological measurements. We use high-speed confocal microscopy to investigate the local velocity of a low volume fraction (ϕ = 0.20) thermogelling nanoemulsion system as it flows through a cylindrical capillary at temperatures below and above the gel point. The nanoemulsions are composed of poly(dimethyl siloxane) droplets in a continuous phase of sodium dodecyl sulfate, de-ionized water, and a gelator molecule, poly(ethylene glycol diacrylate). The trajectories of fluorescent polystyrene tracer beads in the oil-rich domains are tracked using two-dimensional image processing. While the velocity profiles agree with those computed from rheometry measurements for nanoemulsion suspensions below the gel point temperature, increasing attractive interactions above the gel point results in statistically significant deviations. Specifically, the velocity measurements indicate a higher yield stress and a larger degree of shear thinning than expected from bulk rheology measurements, resulting in a more plug-shaped velocity profile as temperature and associated interdroplet attraction increase. These deviations from theoretical predictions are likely due to structural heterogeneity. Confocal microscopy images show that small, fluidized clusters are found in high shear rate regions near the capillary walls, while large dense clusters form in low shear rate regions closer to the center of the capillary.}, number={3}, journal={PHYSICS OF FLUIDS}, publisher={AIP Publishing}, author={Smith, Kristine M. and San-Miguel, Adriana and Hsiao, Lilian C.}, year={2021}, month={Mar} }
 @inbook{clark_huayta_arulalan_san-miguel_2021, title={Microfluidic devices for imaging and manipulation of C. elegans}, url={http://dx.doi.org/10.1016/b978-0-12-823990-2.00013-1}, DOI={10.1016/b978-0-12-823990-2.00013-1}, abstractNote={The nematode Caenorhabditis elegans is a model organism widely used to study development, neuroscience, disease modeling, and aging. Due to their small size, transparent body, and fast growth, these animals have seen an increased use in answering questions related to fundamental biological processes. Nevertheless, the manipulation of C. elegans for culturing, imaging, and other routine techniques is labor-intensive, time-consuming, and not suitable for high-throughput approaches. Microfluidic devices and platforms are powerful and robust tools capable of improving C. elegans research by facilitating handling, strengthening experimental control, and increasing screening throughput. Microfluidic features such as immobilization channels, culture chambers, pillar structures, and versatile geometries are combined with hardware and software components to enable complex platforms with the ability to perform multiple experimental techniques. In this review, we will discuss microfluidic approaches that have emerged to improve the control and throughput of the imaging and manipulation of C. elegans. The first few sections discuss platforms developed to perform techniques such as immobilization, imaging, and culturing while the latter sections will delve into microfluidic technologies aimed at improve screening and stimuli delivery as well as studying development and behavior.}, booktitle={Micro and Nano Systems for Biophysical Studies of Cells and Small Organisms}, publisher={Elsevier}, author={Clark, Andrew S. and Huayta, Javier and Arulalan, Karthik Suresh and San-Miguel, Adriana}, year={2021}, pages={295–321} }
 @article{san-miguel_2021, title={Optogenetics gets the worm}, volume={6}, ISSN={["2470-9476"]}, url={http://dx.doi.org/10.1126/scirobotics.abj3937}, DOI={10.1126/scirobotics.abj3937}, abstractNote={
            Analysis of
            Caenorhabditis elegans
            natural movement and optogenetic control of its muscle cells enable controlled locomotion.
          }, number={55}, journal={SCIENCE ROBOTICS}, publisher={American Association for the Advancement of Science (AAAS)}, author={San-Miguel, Adriana}, year={2021}, month={Jun} }
 @article{mischler_karakis_mahinthakumar_carberry_san miguel_rager_fry_rao_2021, title={Two distinct trophectoderm lineage stem cells from human pluripotent stem cells}, volume={296}, ISSN={["1083-351X"]}, url={http://dx.doi.org/10.1016/j.jbc.2021.100386}, DOI={10.1016/j.jbc.2021.100386}, abstractNote={The trophectoderm layer of the blastocyst-stage embryo is the precursor for all trophoblast cells in the placenta. Human trophoblast stem (TS) cells have emerged as an attractive tool for studies on early trophoblast development. However, the use of TS cell models is constrained by the limited genetic diversity of existing TS cell lines and restrictions on using human fetal tissue or embryos needed to generate additional lines. Here we report the derivation of two distinct stem cell types of the trophectoderm lineage from human pluripotent stem cells. Analogous to villous cytotrophoblasts in vivo, the first is a CDX2- stem cell comparable with placenta-derived TS cells—they both exhibit identical expression of key markers, are maintained in culture and differentiate under similar conditions, and share high transcriptome similarity. The second is a CDX2+ stem cell with distinct cell culture requirements, and differences in gene expression and differentiation, relative to CDX2- stem cells. Derivation of TS cells from pluripotent stem cells will significantly enable construction of in vitro models for normal and pathological placental development. The trophectoderm layer of the blastocyst-stage embryo is the precursor for all trophoblast cells in the placenta. Human trophoblast stem (TS) cells have emerged as an attractive tool for studies on early trophoblast development. However, the use of TS cell models is constrained by the limited genetic diversity of existing TS cell lines and restrictions on using human fetal tissue or embryos needed to generate additional lines. Here we report the derivation of two distinct stem cell types of the trophectoderm lineage from human pluripotent stem cells. Analogous to villous cytotrophoblasts in vivo, the first is a CDX2- stem cell comparable with placenta-derived TS cells—they both exhibit identical expression of key markers, are maintained in culture and differentiate under similar conditions, and share high transcriptome similarity. The second is a CDX2+ stem cell with distinct cell culture requirements, and differences in gene expression and differentiation, relative to CDX2- stem cells. Derivation of TS cells from pluripotent stem cells will significantly enable construction of in vitro models for normal and pathological placental development. Specification of the trophectoderm and the inner cell mass is the first differentiation event during human embryonic development. The trophectoderm mediates blastocyst implantation in the uterus and is the precursor to all trophoblast cells in the placenta. Upon embryo implantation, the trophectoderm forms the cytotrophoblast (CTB), a putative stem cell that can differentiate to form the two major cell types in the placenta, the extravillous trophoblast (EVT) and the syncytiotrophoblast (STB) (1Bischof P. Irminger-Finger I. The human cytotrophoblastic cell, a mononuclear chameleon.Int. J. Biochem. Cel. Biol. 2005; 37: 1-16Crossref PubMed Scopus (125) Google Scholar, 2Benirschke Kurt. Baergen R.N. Burton G. Graham J. Pathology of the Human Placenta [electronic Resource]. Springer, Heidelberg2012Crossref Scopus (48) Google Scholar). The EVTs are involved in remodeling of uterine arteries, which is critical to ensure adequate perfusion of the placenta with maternal blood, whereas the multinucleated STB mediates the nutrient and gas exchange at the maternal–fetal interface (3Yabe S. Alexenko A.P. Amita M. Yang Y. Schust D.J. Sadovsky Y. Ezashi T. Roberts R.M. Comparison of syncytiotrophoblast generated from human embryonic stem cells and from term placentas.Proc. Natl. Acad. Sci. U. S. A. 2016; 113: E2598-E2607Crossref PubMed Scopus (68) Google Scholar, 4Moser G. Orendi K. Gauster M. Siwetz M. Helige C. Huppertz B. The art of identification of extravillous trophoblast.Placenta. 2011; 32: 197-199Crossref PubMed Scopus (29) Google Scholar). Abnormalities in trophoblast development are associated with pregnancy-related pathologies such as miscarriage, preeclampsia, and placenta accreta. Yet, despite its relevance to maternal and fetal health, constraints on research with human embryos and early fetal tissue impede mechanistic insight into early trophoblast development. Trophoblast stem (TS) cells derived from first-trimester human placental samples and blastocyst-stage embryos have emerged as an attractive in vitro model system for early human trophoblast (5Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. Kabayama Y. Suyama M. Sasaki H. Arima T. Derivation of human trophoblast stem cells.Cell stem cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). However, restricted accessibility of embryos and placental samples from early gestation and low genetic diversity of existing cell lines limit the use of this model. In contrast, human pluripotent stem cells (hPSCs) are a more accessible source for generating in vitro models of human trophoblast. Of more importance, unlike early gestation primary samples where the projected pregnancy outcome is uncertain, human induced pluripotent stem cells (hiPSCs) can potentially provide models of validated normal and pathological trophoblast development (6Sheridan M.A. Yang Y. Jain A. Lyons A.S. Yang P. Brahmasani S.R. Dai A. Tian Y. Ellersieck M.R. Tuteja G. Schust D.J. Schulz L.C. Ezashi T. Roberts R.M. Early onset preeclampsia in a model for human placental trophoblast.Proc. Natl. Acad. Sci. U. S. A. 2019; 116: 4336-4345Crossref PubMed Scopus (20) Google Scholar). However, whether bona fide trophoblast can be obtained from hPSCs has been a subject of intense debate (7Roberts R.M. Loh K.M. Amita M. Bernardo A.S. Adachi K. Alexenko A.P. Schust D.J. Schulz L.C. Telugu B.P.V.L. Ezashi T. Pedersen R.A. Differentiation of trophoblast cells from human embryonic stem cells: To be or not to be?.Reproduction (Cambridge, England). 2014; 147: D1-D12Crossref PubMed Scopus (45) Google Scholar). A rigorous head-to-head comparison between trophoblast derived from hPSCs and their in vivo counterparts has proven difficult owing to multiple reasons. Previous studies have used varying experimental protocols (8Roberts R.M. Ezashi T. Sheridan M.A. Yang Y. Specification of trophoblast from embryonic stem cells exposed to BMP4†.Biol. Reprod. 2018; 99: 212-224Crossref PubMed Scopus (22) Google Scholar); both primary placental samples and cultures of terminally differentiated trophoblast obtained from hPSCs exhibit heterogeneity and contain many cell types, and until recently self-renewing TS-like cells had not been derived from hPSCs (9Dong C. Beltcheva M. Gontarz P. Zhang B. Popli P. Fischer L.A. Khan S.A. Park K.-M. Yoon E.-J. Xing X. Kommagani R. Wang T. Solnica-Krezel L. Theunissen T.W. Derivation of trophoblast stem cells from naïve human pluripotent stem cells.eLife. 2020; 9: e52504Crossref PubMed Scopus (57) Google Scholar, 10Cinkornpumin J.K. Kwon S.Y. Guo Y. Hossain I. Sirois J. Russett C.S. Tseng H.W. Okae H. Arima T. Duchaine T.F. Liu W. Pastor W.A. Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and Methylome.Stem Cell Rep. 2020; 15: 198-213Abstract Full Text Full Text PDF PubMed Scopus (33) Google Scholar, 11Li Z. Kurosawa O. Iwata H. Development of trophoblast cystic structures from human induced pluripotent stem cells in limited-area cell culture.Biochem. Biophysical Res. Commun. 2018; 505: 671-676Crossref PubMed Scopus (5) Google Scholar, 12Gao X. Nowak-Imialek M. Chen X. Chen D. Herrmann D. Ruan D. Chen A.C.H. Eckersley-Maslin M.A. Ahmad S. Lee Y.L. Kobayashi T. Ryan D. Zhong J. Zhu J. Wu J. et al.Establishment of porcine and human expanded potential stem cells.Nat. Cell Biol. 2019; 21: 687-699Crossref PubMed Scopus (120) Google Scholar). In this study, we report the derivation and maintenance of two distinct trophectoderm lineage stem cell types from hPSCs, specifically human embryonic stem cells (hESCs) and hiPSCs, in chemically defined culture conditions. The first is a CDX2- stem cell that is comparable with TS cells derived from early-gestation placental samples and similar to the villous CTB. The second is a CDX2+ cell type with distinct cell culture requirements, and differences in gene expression and differentiation, relative to CDX2- stem cells. Critically, the isolation of self-renewing stem cell populations allowed a direct comparison of placenta-derived TS cells with TS cells from hPSCs; genome-wide transcriptomic analysis and functional differentiation assays demonstrate very high similarity between placenta- and hPSC-derived CDX2- TS cells. The routine derivation of TS cells from hPSCs will provide powerful tools for mechanistic studies on normal and pathological early trophoblast development. Media formulations in previous studies on trophoblast differentiation of hESCs included components such as knockout serum replacement (KSR) or bovine serum albumin (BSA) that act as carriers for lipids. Albumin-associated lipids have been implicated in activation of G-protein–coupled receptor–mediated signaling (13Yu F.-X. Zhao B. Panupinthu N. Jewell J.L. Lian I. Wang L.H. Zhao J. Yuan H. Tumaneng K. Li H. Fu X.-D. Mills G.B. Guan K.-L. Regulation of the Hippo-YAP pathway by G-protein-coupled receptor signaling.Cell. 2012; 150: 780-791Abstract Full Text Full Text PDF PubMed Scopus (974) Google Scholar, 14Mendelson K. Evans T. Hla T. Sphingosine 1-phosphate signalling.Development (Cambridge, England). 2014; 141: 5-9Crossref PubMed Scopus (165) Google Scholar). For instance, the phospholipid sphingosine-1 phosphate (S1P) present in KSR can activate YAP signaling. YAP plays a critical role in specification of the trophectoderm in mouse (15Yagi R. Kohn M.J. Karavanova I. Kaneko K.J. Vullhorst D. DePamphilis M.L. Buonanno A. Transcription factor TEAD4 specifies the trophectoderm lineage at the beginning of mammalian development.Development (Cambridge, England). 2007; 134: 3827-3836Crossref PubMed Scopus (353) Google Scholar, 16Knott J.G. Paul S. Transcriptional regulators of the trophoblast lineage in mammals with hemochorial placentation.Reproduction (Cambridge, England). 2014; 148: R121-R136Crossref PubMed Scopus (40) Google Scholar, 17Nishioka N. Yamamoto S. Kiyonari H. Sato H. Sawada A. Ota M. Nakao K. Sasaki H. Tead4 is required for specification of trophectoderm in pre-implantation mouse embryos.Mech. Dev. 2008; 125: 270-283Crossref PubMed Scopus (331) Google Scholar), as well as human trophoblast development (18Saha B. Ganguly A. Home P. Bhattacharya B. Ray S. Ghosh A. Rumi M.A.K. Marsh C. French V. Gunewardena S. Paul S. TEAD4 ensures postimplantation development by promoting trophoblast self-renewal: An implication in early human pregnancy loss.Proc. Natl. Acad. Sci. 2020; 117: 202002449Crossref Scopus (20) Google Scholar, 19Meinhardt G. Haider S. Kunihs V. Saleh L. Pollheimer J. Fiala C. Hetey S. Feher Z. Szilagyi A. Than N.G. Knöfler M. Pivotal role of the transcriptional co-activator YAP in trophoblast stemness of the developing human placenta.Proc. Natl. Acad. Sci. U. S. A. 2020; 117: 13562-13570Crossref PubMed Scopus (25) Google Scholar). We investigated the use of S1P in the context of trophoblast differentiation of hESCs under chemically defined culture conditions, by modifying our previous protocol that utilized KSR (20Sarkar P. Randall S.M. Collier T.S. Nero A. Russell T.A. Muddiman D.C. Rao B.M. Activin/nodal signaling Switches the terminal fate of human embryonic stem cell-derived trophoblasts.J. Biol. Chem. 2015; 290: 8834-8848Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar, 21Sarkar P. Mischler A. Randall S.M. Collier T.S. Dorman K.F. Boggess K.A. Muddiman D.C. Rao B.M. Identification of epigenetic factor proteins expressed in human embryonic stem cell-derived trophoblasts and in human placental trophoblasts.J. Proteome Res. 2016; 15: 2433-2444Crossref PubMed Scopus (6) Google Scholar). H1 and H9 hESCs cultured in E8 medium were differentiated for 6 days in E7 medium (E8 without transforming growth factor-beta1 [TGFβ1]) supplemented with S1P, by treatment with BMP4 and the activin/nodal inhibitor SB431542 (Fig. 1A). Under these conditions, we observed upregulation of the trophectoderm marker CDX2 and the CTB marker ELF5 (Fig. S1, A and B). Upregulation of TBX4 was observed after 6 days. However, overall there were no significant changes in markers associated with neural or mesodermal differentiation after 6 days suggesting that differentiation to these lineages did not occur (Fig. S1, A and B). Immunofluorescence analysis at day 6 confirmed expression of the pan-trophoblast marker KRT7, and CTB markers P63 and GATA3; expression of CDX2 was not observed (Figs. 1B and S1C). The putative CTB cells obtained at day 6 were investigated for their ability to differentiate to EVTs and STB, using protocols similar to those previously employed (20Sarkar P. Randall S.M. Collier T.S. Nero A. Russell T.A. Muddiman D.C. Rao B.M. Activin/nodal signaling Switches the terminal fate of human embryonic stem cell-derived trophoblasts.J. Biol. Chem. 2015; 290: 8834-8848Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar). We observed formation of mesenchymal cells from epithelial cells over a 6-day period when passaged into E8 medium supplemented with epidermal growth factor (EGF) and SB431542. Immunofluorescence analysis showed expression of KRT7 and the EVT markers VE-Cadherin and HLA-G (Figs. 1C, S1D). Alternatively, passaging CTB-like cells in E6 medium (E8 without TGFβ1 and fibroblast growth factor-2 [FGF2]) supplemented with activin and EGF resulted in the formation of KRT7+ multinucleate cells expressing the STB markers hCG and syncytin over an 8-day period (Figs. 1D, S1E). Removal of S1P from the medium during hESC differentiation to CTB-like cells abolished the formation of EVTs that express HLA-G and VE-Cadherin (Figs. 1E, S2A) under identical differentiation conditions (Fig. 1A). Differentiation to STB also did not occur in the absence of S1P, as evidenced by lack of expression of syncytin and KRT7 (Figs. 1F, S2B). Also, downregulation of the trophectoderm marker CDX2 and upregulation of transcripts of neural and mesoderm markers was observed in cells after 6 days of differentiation, upon removal of S1P (Fig. S2C). Taken together these results show that CTB-like cells, similar to those in previous studies utilizing more complex culture conditions (20Sarkar P. Randall S.M. Collier T.S. Nero A. Russell T.A. Muddiman D.C. Rao B.M. Activin/nodal signaling Switches the terminal fate of human embryonic stem cell-derived trophoblasts.J. Biol. Chem. 2015; 290: 8834-8848Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar), can be obtained by differentiation of hESCs in a chemically defined medium containing S1P. Furthermore, addition of exogenous S1P is necessary for hESC differentiation to trophoblast in our chemically defined culture medium. Rho GTPase signaling, downstream of G-protein–coupled receptors activated by S1P, has been implicated in nuclear localization of YAP (22Ohgushi M. Minaguchi M. Sasai Y. Rho-signaling-directed YAP/TAZ activity Underlies the long-term Survival and Expansion of human embryonic stem cells.Cell stem cell. 2015; 17: 448-461Abstract Full Text Full Text PDF PubMed Scopus (100) Google Scholar, 23Mo J.-S. Yu F.-X. Gong R. Brown J.H. Guan K.-L. Regulation of the Hippo-YAP pathway by protease-activated receptors (PARs).Genes Dev. 2012; 26: 2138-2143Crossref PubMed Scopus (195) Google Scholar). Both Rho/RhoA associated kinase (ROCK) and nuclear YAP play a critical role in trophectoderm specification in the mouse (24Nishioka N. Inoue K. Adachi K. Kiyonari H. Ota M. Ralston A. Yabuta N. Hirahara S. Stephenson R.O. Ogonuki N. Makita R. Kurihara H. Morin-Kensicki E.M. Nojima H. Rossant J. et al.The Hippo signaling pathway components Lats and Yap pattern Tead4 activity to distinguish mouse trophectoderm from inner cell mass.Dev. Cel. 2009; 16: 398-410Abstract Full Text Full Text PDF PubMed Scopus (657) Google Scholar, 25Kono K. Tamashiro D.A.A. Alarcon V.B. Inhibition of RHO-ROCK signaling enhances ICM and suppresses TE characteristics through activation of Hippo signaling in the mouse blastocyst.Dev. Biol. 2014; 394: 142-155Crossref PubMed Scopus (79) Google Scholar). Therefore, we investigated the role of Rho/ROCK signaling and YAP in trophoblast differentiation of hESCs. The Rho/ROCK inhibitor Y-27632 was included during differentiation of hESCs to CTB-like cells and subsequent differentiation to EVT and STB to investigate the role of Rho/ROCK signaling. Under these conditions, HLA-G expression was observed in cells obtained from H9 hESCs; however, VE-Cadherin expression was weak and observed in only a few cells (Fig. S3A). On the other hand, expression of EVT markers was not observed in cells derived from H1 hESCs. In addition, presence of ROCK inhibition abolished STB formation, as shown by the lack of expression of syncytin and KRT7 (Fig. S3B). To investigate the role of YAP signaling in CTB formation from hESCs, we used an hESC cell line (H9) that expresses an inducible shRNA against YAP (H9-YAP-ishRNA) or a scrambled shRNA control (26Hsiao C. Lampe M. Nillasithanukroh S. Han W. Lian X. Palecek S.P. Human pluripotent stem cell culture density modulates YAP signaling.Biotechnol. J. 2016; 11: 662-675Crossref PubMed Scopus (26) Google Scholar). YAP knockdown abolished differentiation to EVT and STB, as evidenced by lack of expression of the relevant markers. It is notable that high cell death was observed (Fig. S3, A and B). Gene expression analysis revealed a significant reduction in ELF5 upon YAP knockdown, relative to the scrambled shRNA control (Fig. S3C). Significant downregulation of the mesodermal genes TBX4 and LMO2 was observed, whereas T was upregulated, in H9-YAP-ishRNA, relative to the scrambled control. Taken together, these results show that Rho/ROCK signaling and YAP are necessary for differentiation of hESCs to functional CTB that can give rise to both EVTs and STB, in our chemically defined culture medium. S1P acts through both receptor-mediated and receptor-independent pathways (14Mendelson K. Evans T. Hla T. Sphingosine 1-phosphate signalling.Development (Cambridge, England). 2014; 141: 5-9Crossref PubMed Scopus (165) Google Scholar, 27Maceyka M. Harikumar K.B. Milstien S. Spiegel S. Sphingosine-1-phosphate signaling and its role in disease.Trends Cell Biol. 2012; 22: 50-60Abstract Full Text Full Text PDF PubMed Scopus (695) Google Scholar). To investigate the specific mechanism of S1P action during hESC differentiation to trophoblast, we replaced S1P with D-erythro-dihydrospingosine-1-phosphate (dhS1P) in our protocol. dhS1P acts as an agonist for the S1P receptors (S1PRs) but does not mediate an intracellular effect (28Van Brocklyn J.R. Lee M.-J. Menzeleev R. Olivera A. Edsall L. Cuvillier O. Thomas D.M. Coopman P.J.P. Thangada S. Liu C.H. Hla T. Spiegel S. Dual actions of sphingosine-1-phosphate: Extracellular through the G i -coupled receptor Edg-1 and intracellular to regulate proliferation and Survival.J. Cell Biol. 1998; 142: 229-240Crossref PubMed Scopus (444) Google Scholar). Replacing S1P with dhS1P yielded similar results—CTB-like cells showed expression of CDX2, GATA3, P63, and TEAD4 (Figs. 2A and S4A). Upon further differentiation as previously described (Fig. 1A), STB expressing KRT7 and hCG, and EVT expressing HLA-G and VE-Cadherin were obtained (Fig. 2, B and C; Fig. S4, B and C). These results suggest that S1PR signaling mediates the effect of exogenous S1P during hESC differentiation to trophoblast in our chemically defined medium. S1P acts extracellularly through S1PR1-5 (14Mendelson K. Evans T. Hla T. Sphingosine 1-phosphate signalling.Development (Cambridge, England). 2014; 141: 5-9Crossref PubMed Scopus (165) Google Scholar, 27Maceyka M. Harikumar K.B. Milstien S. Spiegel S. Sphingosine-1-phosphate signaling and its role in disease.Trends Cell Biol. 2012; 22: 50-60Abstract Full Text Full Text PDF PubMed Scopus (695) Google Scholar); however, TBs have been shown to only express S1PR1-3 (29Johnstone E.D. Chan G. Sibley C.P. Davidge S.T. Lowen B. Guilbert L.J. Sphingosine-1-phosphate inhibition of placental trophoblast differentiation through a G(i)-coupled receptor response.J. lipid Res. 2005; 46: 1833-1839Abstract Full Text Full Text PDF PubMed Scopus (34) Google Scholar). We further used selective chemical agonists for S1PR1-3—CYM5442 hydrochloride, CYM5520, and CYM5541, respectively—to replace S1P in differentiation protocols previously discussed. Expression of CDX2, GATA3, P63, and TEAD4 was observed in CTB-like cells for all three agonists (Figs. 2A and S4A). Similarly, use of each agonist resulted in expression of the EVT markers HLA-G and VE-Cadherin and formation of multinucleate STB expressing KRT7 and hCG (Fig. 2, B and C; Fig. S4, B and C). However, we observed some variability between the agonists (Fig. S5). For instance, use of the S1PR2 agonist resulted in strong cytoplasmic expression of P63 and high heterogeneity in staining at day 6 relative to the other agonists. Formation of large multinucleated STB was more pronounced when the S1PR2 or S1PR3 agonists were used, as compared with the S1PR1 agonist. On the other hand, the S1PR1 and S1PR3 agonists enhanced the formation of mesenchymal EVTs, relative to the S1PR2 agonist. Taken together, our results further confirmed that S1PR signaling mediates effects of exogenous S1P during trophoblast differentiation of hESCs in our culture system. Since our qualitative observations showed that use of the S1PR3 agonist resulted in expression of CTB markers, and both multinucleate STB and mesenchymal EVTs could be obtained when the S1PR3 agonist was used, we chose the S1PR3 agonist for subsequent studies. We investigated whether CTB-like cells obtained by treatment of hESCs with BMP4 and SB431542 in E7 medium supplemented with the S1PR3 agonist CYM5541 for 6 days could be passaged and maintained under conditions used for culture of blastocyst- and placenta-derived primary TS cells (5Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. Kabayama Y. Suyama M. Sasaki H. Arima T. Derivation of human trophoblast stem cells.Cell stem cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). Upon plating in trophoblast stem cell medium (TSCM) developed by Okae et al. (5Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. Kabayama Y. Suyama M. Sasaki H. Arima T. Derivation of human trophoblast stem cells.Cell stem cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar), hESC-derived CTB-like cells underwent differentiation and epithelial colonies could not be retained after a single passage. CDX2 expression is upregulated significantly in as little as 2 days after initiation of hESC differentiation but decreases by day 6 (Fig. S1, A and B). In addition, previous studies have reported differentiation of hESCs to CDX2+/p63+ cells upon treatment with BMP for 4 days (30Horii M. Li Y. Wakeland A.K. Pizzo D.P. Nelson K.K. Sabatini K. Laurent L.C. Liu Y. Parast M.M. Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease.Proc. Natl. Acad. Sci. United States America. 2016; 113: E3882-E3891Crossref PubMed Scopus (66) Google Scholar). Therefore, we explored the use of a shorter differentiation step for obtaining CTB-like cells (Fig. 3A). After 3 days of differentiation, H9 and H1 hESCs expressed nuclear CDX2, P63, and TEAD4 uniformly (Fig. 3B). However, by day 6 most differentiated H1 and H9 hESCs lose expression of CDX2 (Fig. 3C). Quantitative image analysis showed that nearly all cells are CDX2+ at day 3, in contrast to CTB-like cells at day 6. Of note, use of a 6-day protocol resulted in a significantly reduced fraction of CDX2+ cells in the case of H1 hESCs in comparison with the 3-day protocol; on the other hand, a significant fraction of H9 cells retained CDX2+ at day 6 (Fig. 3D). Transcriptome analysis using RNA sequencing identified 291 genes with significantly higher expression levels and 330 genes with significantly lower expression levels in day 3 differentiated hESCs versus undifferentiated hESCs (Tables S1 and S2).Expression of other trophectoderm-associated markers such as HAND1, GATA3, and TFAP2A, in addition to CDX2, was upregulated in differentiated hESCs at day 3, whereas expression of pluripotency-associated NANOG was downregulated. Gene set enrichment analysis of differentially expressed genes identified 567 and 202 gene ontology (GO) categories (of 9996 queried categories) associated with higher and lower gene expression in day 3 differentiated cells versus undifferentiated hESCs, respectively (Tables S3 and S4). Consistent with differentiation to epithelial trophoblast, genes associated with the GO terms for epithelium development, epithelial cell proliferation, and epithelial cell differentiation were upregulated in day 3 differentiated hESCs. CDX2+ cells at day 3 were passaged into a chemically defined medium containing four major components (denoted TM4), the S1PR3 agonist CYM5541, the GSK3β inhibitor CHIR99021, the TGFβ inhibitor A83-01, and FGF10. CHIR99021 and A83-01 are components of TSCM used for culture of primary TS cells; FGF10 was included because FGFR2b signaling is active in blastocyst- and placenta-derived TS cells and the early placenta (5Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. Kabayama Y. Suyama M. Sasaki H. Arima T. Derivation of human trophoblast stem cells.Cell stem cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). Cells in TM4 could be maintained as epithelial colonies for 30+ passages over the course of 5 months. In TM4 medium, cells derived from H9 and H1 hESCs retained expression of the trophoblast markers CDX2, TFAP2C, YAP, TEAD4, and GATA3 (Figs. 3E and S6) (15Yagi R. Kohn M.J. Karavanova I. Kaneko K.J. Vullhorst D. DePamphilis M.L. Buonanno A. Transcription factor TEAD4 specifies the trophectoderm lineage at the beginning of mammalian development.Development (Cambridge, England). 2007; 134: 3827-3836Crossref PubMed Scopus (353) Google Scholar, 17Nishioka N. Yamamoto S. Kiyonari H. Sato H. Sawada A. Ota M. Nakao K. Sasaki H. Tead4 is required for specification of trophectoderm in pre-implantation mouse embryos.Mech. Dev. 2008; 125: 270-283Crossref PubMed Scopus (331) Google Scholar, 31Choi I. Carey T.S. Wilson C.A. Knott J.G. Transcription factor AP-2γ is a core regulator of tight junction biogenesis and cavity formation during mouse early embryogenesis.Development (Cambridge, England). 2012; 139: 4623-4632Crossref PubMed Scopus (40) Google Scholar, 32Home P. Saha B. Ray S. Dutta D. Gunewardena S. Yoo B. Pal A. Vivian J.L. Larson M. Petroff M. Gallagher P.G. Schulz V.P. White K.L. Golos T.G. Behr B. et al.Altered subcellular localization of transcription factor TEAD4 regulates first mammalian cell lineage commitment.Proc. Natl. Acad. Sci. U. S. A. 2012; 109: 7362-7367Crossref PubMed Scopus (113) Google Scholar, 33Ralston A. Cox B.J. Nishioka N. Sasaki H. Chea E. Rugg-Gunn P. Guo G. Robson P. Draper J.S. Rossant J. Gata3 regulates trophoblast development downstream of Tead4 and in parallel to Cdx2.Development (Cambridge, England). 2010; 137: 395-403Crossref PubMed Scopus (299) Google Scholar, 34Niwa H. Toyooka Y. Shimosato D. Strumpf D. Takahashi K. Yagi R. Rossant J. Interaction between Oct3/4 and Cdx2 determines trophectoderm differentiation.Cell. 2005; 123: 917-929Abstract Full Text Full Text PDF PubMed Scopus (854) Google Scholar). In addition, cells expressed the pan-trophoblast marker KRT7 and low levels of P63. Of note, CDX2 expression has been strongly associated with the trophectoderm and is lost once placental villi are formed (30Horii M. Li Y. Wakeland A.K. Pizzo D.P. Nelson K.K. Sabatini K. Laurent L.C. Liu Y. Parast M.M. Human pluripotent stem cells as a model of trophoblast differentiation in both normal development and disease.Proc. Natl. Acad. Sci. United States America. 2016; 113: E3882-E3891Crossref PubMed Scopus (66) Google Scholar, 35Hemberger M. Udayashankar R. Tesar P. Moore H. Burton G.J. ELF5-enforced transcriptional networks define an epigenetically regulated trophoblast stem cell compartment in the human placenta.Hum. Mol. Genet. 2010; 19: 2456-2467Crossref PubMed Scopus (126) Google Scholar, 36Blakeley P. Fogarty N.M.E. del Valle I. Wamaitha S.E. Hu T.X. Elder K. Snell P. Christie L. Robson P. Niakan K.K. Defining the three cell lineages of the human blastocyst by single-cell RNA-seq.Development. 2015; 142: 3151-3165Crossref PubMed Scopus (262) Google Scholar, 37Knöfler M. Haider S. Saleh L. Pollheimer J. Gamage T.K.J.B. James J. Human placenta and trophoblast development: Key molecular mechanisms and model systems.Cell Mol. Life Sci. 2019; 76: 3479-3496Crossref PubMed Scopus (144) Google Scholar). To indicate that these cells are derived from hPSCs, and to distinguish these cells from TS cells that do not express CDX2, these cells are denoted as hPSC-TSCDX2 cells. We further evaluated the differentiation potential of hPSC-TSCDX2 cells using same protocols as those used by Okae et al. for differentiation of primary TS cells to EVTs and STB (5Okae H. Toh H. Sato T. Hiura H. Takahashi S. Shirane K. Kabayama Y. Suyama M. Sasaki H. Arima T. Derivation of human trophoblast stem cells.Cell stem cell. 2018; 22: 50-63.e6Abstract Full Text Full Text PDF PubMed Scopus (233) Google Scholar). Cells were able to form multinucleate STB that expressed hCG and KRT7 (Fig. 3F). However, upon EVT treatment, cells did not form mesenchymal elongated cells but acquired a flattened morphology. Upon passage, cells showed no HLA-G and minimal VE-Cadherin expression (Fig. 3G). Furthermore, cells maintained an epithelial flattened morp}, journal={JOURNAL OF BIOLOGICAL CHEMISTRY}, publisher={Elsevier BV}, author={Mischler, Adam and Karakis, Victoria and Mahinthakumar, Jessica and Carberry, Celeste K. and San Miguel, Adriana and Rager, Julia E. and Fry, Rebecca C. and Rao, Balaji M.}, year={2021} }
 @article{a reference map of the human binary protein interactome_2020, volume={580}, url={http://dx.doi.org/10.1038/s41586-020-2188-x}, DOI={10.1038/s41586-020-2188-x}, abstractNote={Global insights into cellular organization and genome function require comprehensive understanding of the interactome networks that mediate genotype–phenotype relationships1,2. Here we present a human ‘all-by-all’ reference interactome map of human binary protein interactions, or ‘HuRI’. With approximately 53,000 protein–protein interactions, HuRI has approximately four times as many such interactions as there are high-quality curated interactions from small-scale studies. The integration of HuRI with genome3, transcriptome4 and proteome5 data enables cellular function to be studied within most physiological or pathological cellular contexts. We demonstrate the utility of HuRI in identifying the specific subcellular roles of protein–protein interactions. Inferred tissue-specific networks reveal general principles for the formation of cellular context-specific functions and elucidate potential molecular mechanisms that might underlie tissue-specific phenotypes of Mendelian diseases. HuRI is a systematic proteome-wide reference that links genomic variation to phenotypic outcomes. A human binary protein interactome map that includes around 53,000 protein–protein interactions involving more than 8,000 proteins provides a reference for the study of human cellular function in health and disease.}, number={7803}, journal={Nature}, publisher={Springer Science and Business Media LLC}, year={2020}, month={Apr}, pages={402–408} }
 @article{crawford_san-miguel_2020, title={An inexpensive programmable optogenetic platform for controlled neuronal activation regimens in C. elegans}, volume={4}, ISSN={["2473-2877"]}, url={http://dx.doi.org/10.1063/1.5120002}, DOI={10.1063/1.5120002}, abstractNote={In Caenorhabditis elegans, optogenetic stimulation has been widely used to assess neuronal function, control animal movement, or assay circuit responses to controlled stimuli. Most studies are performed on single animals and require high-end components such as lasers and shutters. We present an accessible platform that enables controlled optogenetic stimulation of C. elegans in two modes: single animal stimulation with locomotion tracking and entire population stimulation for neuronal exercise regimens. The system consists of accessible electronic components: a high-power light-emitting diode, Arduino board, and relay are integrated with MATLAB to enable programmable optogenetic stimulation regimens. This system provides flexibility in optogenetic stimulation in freely moving animals while providing quantitative information of optogenetic-driven locomotion responses. We show the applicability of this platform in single animals by stimulation of cholinergic motor neurons in C. elegans and quantitative assessment of contractile responses. In addition, we tested synaptic plasticity by coupling the entire-population stimulation mode with measurements of synaptic strength using an aldicarb assay, where clear changes in synaptic strength were observed after regimens of neuronal exercise. This platform is composed of inexpensive components, while providing the illumination strength of high-end systems, which require expensive lasers, shutters, or automated stages. This platform requires no moving parts but provides flexibility in stimulation regimens.}, number={1}, journal={APL BIOENGINEERING}, publisher={AIP Publishing}, author={Crawford, Zachary and San-Miguel, Adriana}, year={2020}, month={Mar} }
 @article{saberi-bosari_flores_san-miguel_2020, title={Deep learning-enabled analysis reveals distinct neuronal phenotypes induced by aging and cold-shock}, volume={18}, ISSN={["1741-7007"]}, url={http://dx.doi.org/10.1186/s12915-020-00861-w}, DOI={10.1186/s12915-020-00861-w}, abstractNote={Abstract}, number={1}, journal={BMC BIOLOGY}, publisher={Springer Science and Business Media LLC}, author={Saberi-Bosari, Sahand and Flores, Kevin B. and San-Miguel, Adriana}, year={2020}, month={Sep} }
 @article{saberi-bosari_flores_san-miguel_2020, title={Deep learning-enabled phenotyping reveals distinct patterns of neurodegeneration induced by aging and cold-shock}, url={https://doi.org/10.1101/2020.03.08.982074}, DOI={10.1101/2020.03.08.982074}, abstractNote={Abstract}, author={Saberi-Bosari, Sahand and Flores, Kevin B. and San-Miguel, Adriana}, year={2020}, month={Mar} }
 @article{lee_luo_bae_san-miguel_2020, title={Genetic and Chemical Effects on Somatic and Germline Aging}, volume={2020}, ISSN={["1942-0994"]}, url={http://dx.doi.org/10.1155/2020/4684890}, DOI={10.1155/2020/4684890}, abstractNote={Department of Internal Medicine (Division of Hematology/Oncology), Brody School of Medicine at East Carolina University, Greenville, NC 27834, USA Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China Severance Biomedical Science Institute, Yonsei Biomedical Research Institute, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-gu, Seoul 03722, Republic of Korea Department of Chemical and Biomolecular Engineering, NC State University, Raleigh, NC 27695, USA}, journal={OXIDATIVE MEDICINE AND CELLULAR LONGEVITY}, publisher={Hindawi Limited}, author={Lee, Myon-Hee and Luo, Huai-Rong and Bae, Soo Han and San-Miguel, Adriana}, year={2020}, month={Jan} }
 @article{san miguel_ramirez_flores_2020, title={Lifelong Analysis of Key Aging Genes as Determinants of Lifespan in <it>C</it>. <it>elegans</it>}, volume={34}, ISSN={["1530-6860"]}, DOI={10.1096/fasebj.2020.34.s1.00160}, abstractNote={Aging is an integrative phenotype subject to a complex interplay of genetic, environmental, and life history factors, and a key risk factor for a multitude of human diseases. Research in model organisms has enabled the identification of key evolutionary conserved genetic pathways that play a role in aging. In particular, research on the model organism Caenorhabditis elegans has been crucial in our current understanding of the genetic and environmental regulation of lifespan. Although a multitude of pathways are known to affect longevity, how these pathways jointly respond to upstream stimuli, and how they integrate this information to drive lifespan is far from understood. A major limitation to answer this question is the technical difficulty associated with studying the spatiotemporal activity of multiple pathways throughout lifespan, and under a variety of environmental conditions. In this work, we present a system that enables in vivo tracking the endogenous spatiotemporal activity of key aging genes throughout C. elegans lifespan. This system hinges on an integrative experimental platform based on microfluidics, computer vision, and tagging of endogenous genes via CRISPR/Cas9 genetic engineering approaches. In contrast to traditional transgene expression, CRISPR/Cas9 enables insertion of a tag at precise genomic locations. This results in fluorescent protein levels representative of the endogenously expressed genes, and where all isoforms can be analyzed. Studying endogenous protein levels, however, poses a significant challenge, as these reporters are extremely dim in comparison to traditional multi‐copy insertion transgenes. To address this limitation, we have developed computer vision approaches to quantitatively determine the spatial location and levels of said proteins, which can be used as a metric for gene activity. Furthermore, the use of microfluidic devices enables culture, stimulation, and longitudinal high‐resolution imaging of animal populations under precise environmental conditions. Taking advantage of our computer vision algorithms, we can quantify protein levels, cellular compartmentalization, and tissue localization. Using this approach, we have studied the key transcription factor, DAF‐16/FOXO, the main regulator of Insulin/Insulin‐like Signaling in C. elegans. Under a variety of exposures to dietary restriction, a well‐known regulator of lifespan that acts through DAF‐16, we have observed patterns of activity that have not been identified with traditional transgenes. Integrating lifespan measurements under varied environmental conditions with quantitative analysis from DAF‐16 lifelong spatiotemporal activity, we are exploring the predictive power of this key transcription factor at the tissue‐level, using statistical and mathematical models. We are working on expanding our analysis to additional lifespan regulators to better understand how these interact in driving lifespan.}, journal={FASEB JOURNAL}, author={San Miguel, Adriana and Ramirez, Javier and Flores, Kevin}, year={2020}, month={Apr} }
 @article{saberi-bosari_omary_lavoie_prodromou_day_menegatti_san-miguel_2019, title={Affordable Microfluidic Bead-Sorting Platform for Automated Selection of Porous Particles Functionalized with Bioactive Compounds}, volume={9}, ISSN={["2045-2322"]}, url={http://dx.doi.org/10.1038/s41598-019-42869-5}, DOI={10.1038/s41598-019-42869-5}, abstractNote={Abstract}, number={1}, journal={SCIENTIFIC REPORTS}, publisher={Springer Science and Business Media LLC}, author={Saberi-Bosari, Sahand and Omary, Mohammad and Lavoie, Ashton and Prodromou, Raphael and Day, Kevin and Menegatti, Stefano and San-Miguel, Adriana}, year={2019}, month={May} }
 @article{mischler_karakis_san miguel_rao_2019, title={DERIVATION OF HUMAN TROPHOBLAST STEM CELLS FROM HUMAN PLURIPOTENT STEM CELLS}, volume={83}, ISSN={["1532-3102"]}, DOI={10.1016/j.placenta.2019.06.193}, abstractNote={Conventional soil maps contain valuable knowledge on soil–environment relationships. Such knowledge can be extracted for use when updating conventional soil maps with improved environmental data. Existing methods take all polygons of the same map unit on a map as a whole to extract the soil–environment relationship. Such approach ignores the difference in the environmental conditions represented by individual soil polygons of the same map unit. This paper proposes a method of mining soil–environment relationships from individual soil polygons to update conventional soil maps. The proposed method consists of three major steps. Firstly, the soil–environment relationships represented by each individual polygon on a conventional soil map are extracted in the form of frequency distribution curves for the involved environmental covariates. Secondly, for each environmental covariate, these frequency distribution curves from individual polygons of the same soil map unit are synthesized to form the overall soil–environment relationship for that soil map unit across the mapped area. And lastly, the extracted soil–environment relationships are applied to updating the conventional soil map with new, improved environmental data by adopting a soil land inference model (SoLIM) framework. This study applied the proposed method to updating a conventional soil map of the Raffelson watershed in La Crosse County, Wisconsin, United States. The result from the proposed method was compared with that from the previous method of taking all polygons within the same soil map unit on a map as a whole. Evaluation results with independent soil samples showed that the proposed method exhibited better performance and produced higher accuracy.}, journal={PLACENTA}, author={Mischler, Adam and Karakis, Victoria and San Miguel, Adriana and Rao, Balaji}, year={2019}, month={Aug}, pages={E59–E59} }
 @article{day_prodromou_bosari_lavoie_omary_market_san miguel_menegatti_2019, title={Discovery and Evaluation of Peptide Ligands for Selective Adsorption and Release of Cas9 Nuclease on Solid Substrates}, volume={30}, ISSN={["1520-4812"]}, url={http://dx.doi.org/10.1021/acs.bioconjchem.9b00703}, DOI={10.1021/acs.bioconjchem.9b00703}, abstractNote={The rapid expansion of CRISPR in biotechnology, medicine, and bioprocessing poses an urgent need for advanced manufacturing of Cas nucleases. The lack of Cas-targeting ligands, however, prevents the development of platform processes for purifying this class of molecules. This work represents the first effort at developing short synthetic Cas9-binding peptides and demonstrates their applicability as affinity ligands for the purification of a Cas nuclease. Candidate Cas9-targeting peptides were initially identified by screening a solid-phase peptide library against a model mixture of Streptococcus pyogenes Cas9 spiked in Escherichia coli cell lysate. An ensemble of homologous sequences were identified, conjugated on Toyopearl resin, and evaluated by Cas9 binding studies to identify sequences providing selective Cas9 capture and efficient release. In silico docking studies were also performed to evaluate the binding energy and site of the various peptides on Cas9. Notably, sequences GYYRYSEY and YYHRHGLQ were shown to target the RecII domain of Cas9, which is not involved in nuclease activity, and was targeted as ideal binding site. The peptide ligands were validated by purifying Cas9 from the E. coli lysate in dynamic conditions and through measurements of binding capacity and strength (Qmax and KD). The resulting values of Qmax = 4 - 5 mg Cas9 per mL of resin and KD ~ 0.1 - 0.3 μM, and product recovery (86 - 89%) and purity (91% - 93%) indicate that both peptides, and YYHRHGLQ in particular, can serve as capture ligands in a platform purification process of Cas9.}, number={12}, journal={BIOCONJUGATE CHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Day, Kevin and Prodromou, Raphael and Bosari, Sahand Saberi and Lavoie, Ashton and Omary, Mohammad and Market, Connor and San Miguel, Adriana and Menegatti, Stefano}, year={2019}, month={Dec}, pages={3057–3068} }
 @misc{midkiff_san-miguel_2019, title={Microfluidic Technologies for High Throughput Screening Through Sorting and On-Chip Culture of C. elegans}, volume={24}, ISSN={["1420-3049"]}, url={https://www.mdpi.com/1420-3049/24/23/4292}, DOI={10.3390/molecules24234292}, abstractNote={The nematode Caenorhabditis elegans is a powerful model organism that has been widely used to study molecular biology, cell development, neurobiology, and aging. Despite their use for the past several decades, the conventional techniques for growth, imaging, and behavioral analysis of C. elegans can be cumbersome, and acquiring large data sets in a high-throughput manner can be challenging. Developments in microfluidic “lab-on-a-chip” technologies have improved studies of C. elegans by increasing experimental control and throughput. Microfluidic features such as on-chip control layers, immobilization channels, and chamber arrays have been incorporated to develop increasingly complex platforms that make experimental techniques more powerful. Genetic and chemical screens are performed on C. elegans to determine gene function and phenotypic outcomes of perturbations, to test the effect that chemicals have on health and behavior, and to find drug candidates. In this review, we will discuss microfluidic technologies that have been used to increase the throughput of genetic and chemical screens in C. elegans. We will discuss screens for neurobiology, aging, development, behavior, and many other biological processes. We will also discuss robotic technologies that assist in microfluidic screens, as well as alternate platforms that perform functions similar to microfluidics.}, number={23}, journal={MOLECULES}, author={Midkiff, Daniel and San-Miguel, Adriana}, year={2019}, month={Dec} }
 @article{saberi-bosari_huayta_san-miguel_2018, title={A microfluidic platform for lifelong high-resolution and high throughput imaging of subtle aging phenotypes in C-elegans}, volume={18}, ISSN={["1473-0189"]}, url={http://dx.doi.org/10.1039/c8lc00655e}, DOI={10.1039/c8lc00655e}, abstractNote={Aging produces a number of changes in the neuronal structure and function throughout a variety of organisms.}, number={20}, journal={LAB ON A CHIP}, publisher={Royal Society of Chemistry (RSC)}, author={Saberi-Bosari, Sahand and Huayta, Javier and San-Miguel, Adriana}, year={2018}, month={Oct} }
 @article{san-miguel_kurshan_crane_zhao_mcgrath_shen_lu_2016, title={Deep phenotyping unveils hidden traits and genetic relations in subtle mutants}, volume={7}, ISSN={["2041-1723"]}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000388319200001&KeyUID=WOS:000388319200001}, DOI={10.1038/ncomms12990}, abstractNote={Abstract}, journal={NATURE COMMUNICATIONS}, author={San-Miguel, Adriana and Kurshan, Peri T. and Crane, Matthew M. and Zhao, Yuehui and McGrath, Patrick T. and Shen, Kang and Lu, Hang}, year={2016}, month={Nov} }
 @inbook{porto_rouse_san-miguel_lu_2016, place={Cham}, title={Microfluidic Platforms for Quantitative Biology Studies in Model Organisms}, DOI={10.1007/978-3-319-30019-1_1}, booktitle={Microfluidic Methods for Molecular Biology}, author={Porto, Daniel A. and Rouse, Tel M. and San-Miguel, Adriana and Lu, Hang}, editor={Lu, Chang and Verbridge, Scott S.Editors}, year={2016}, pages={1–18} }
 @article{he_kniss_san-miguel_rouse_kemp_lu_2015, title={An automated programmable platform enabling multiplex dynamic stimuli delivery and cellular response monitoring for high-throughput suspension single-cell signaling studies}, volume={15}, ISSN={1473-0197 1473-0189}, url={http://dx.doi.org/10.1039/C4LC01070A}, DOI={10.1039/C4LC01070A}, abstractNote={Microfluidic platform for generating dynamic profile of cell stimuli for non-adherent cells.}, number={6}, journal={Lab on a Chip}, publisher={Royal Society of Chemistry (RSC)}, author={He, Luye and Kniss, Ariel and San-Miguel, Adriana and Rouse, Tel and Kemp, Melissa L. and Lu, Hang}, year={2015}, pages={1497–1507} }
 @article{sahni_yi_taipale_fuxman bass_coulombe-huntington_yang_peng_weile_karras_wang_et al._2015, title={Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders}, volume={161}, ISSN={0092-8674}, url={http://dx.doi.org/10.1016/J.CELL.2015.04.013}, DOI={10.1016/J.CELL.2015.04.013}, abstractNote={How disease-associated mutations impair protein activities in the context of biological networks remains mostly undetermined. Although a few renowned alleles are well characterized, functional information is missing for over 100,000 disease-associated variants. Here we functionally profile several thousand missense mutations across a spectrum of Mendelian disorders using various interaction assays. The majority of disease-associated alleles exhibit wild-type chaperone binding profiles, suggesting they preserve protein folding or stability. While common variants from healthy individuals rarely affect interactions, two-thirds of disease-associated alleles perturb protein-protein interactions, with half corresponding to "edgetic" alleles affecting only a subset of interactions while leaving most other interactions unperturbed. With transcription factors, many alleles that leave protein-protein interactions intact affect DNA binding. Different mutations in the same gene leading to different interaction profiles often result in distinct disease phenotypes. Thus disease-associated alleles that perturb distinct protein activities rather than grossly affecting folding and stability are relatively widespread.}, number={3}, journal={Cell}, publisher={Elsevier BV}, author={Sahni, Nidhi and Yi, Song and Taipale, Mikko and Fuxman Bass, Juan I. and Coulombe-Huntington, Jasmin and Yang, Fan and Peng, Jian and Weile, Jochen and Karras, Georgios I. and Wang, Yang and et al.}, year={2015}, month={Apr}, pages={647–660} }
 @article{maeder_san-miguel_wu_lu_shen_2014, title={In Vivo Neuron-Wide Analysis of Synaptic Vesicle Precursor Trafficking}, volume={15}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000334571200003&KeyUID=WOS:000334571200003}, DOI={10.1111/tra.12142}, abstractNote={Abstract}, number={3}, journal={Traffic}, author={Maeder, Celine I. and San-Miguel, Adriana and Wu, Emily Ye and Lu, Hang and Shen, Kang}, year={2014}, pages={273–291} }
 @article{scrimgeour_san-miguel_curtis_behrens_2013, title={A generalized approach for measuring microcapsule permeability with Fluorescence Recovery After Photobleaching}, volume={48}, ISSN={0022-2461 1573-4803}, url={http://dx.doi.org/10.1007/S10853-012-6997-7}, DOI={10.1007/S10853-012-6997-7}, number={5}, journal={Journal of Materials Science}, publisher={Springer Science and Business Media LLC}, author={Scrimgeour, Jan and San-Miguel, Adriana and Curtis, Jennifer E. and Behrens, Sven H.}, year={2013}, month={Mar}, pages={2215–2223} }
 @article{san-miguel_lu_2013, title={Microfluidics as a tool for C. elegans research.}, url={http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=MEDLINE&KeyUT=MEDLINE:24065448&KeyUID=MEDLINE:24065448}, DOI={10.1895/wormbook.1.162.1}, abstractNote={Microfluidics has emerged as a set of powerful tools that have greatly advanced some areas of biological research, including research using C. elegans. The use of microfluidics has enabled many experiments that are otherwise impossible with conventional methods. Today there are many examples that demonstrate the main advantages of using microfluidics for C. elegans research, achieving precise environmental conditions and facilitating worm handling. Examples range from behavioral analysis under precise chemical or odor stimulation, locomotion studies in well-defined structural surroundings, and even long-term culture on chip. Moreover, microfluidics has enabled coupling worm handling and imaging thus facilitating genetic screens, optogenetic studies, and laser ablation experiments. In this article, we review some of the applications of microfluidics for C. elegans research and provide guides for the design, fabrication, and use of microfluidic devices for C. elegans research studies.}, journal={WormBook : the online review of C. elegans biology}, author={San-Miguel, Adriana and Lu, Hang}, year={2013}, pages={1–19} }
 @article{san-miguel_behrens_2012, title={Influence of Nanoscale Particle Roughness on the Stability of Pickering Emulsions}, volume={28}, ISSN={0743-7463 1520-5827}, url={http://dx.doi.org/10.1021/la302224v}, DOI={10.1021/la302224v}, abstractNote={The wetting behavior of solid surfaces can be altered dramatically by introducing surface roughness on the nanometer scale. Some of nature's most fascinating wetting phenomena are associated with surface roughness; they have inspired both fundamental research and the adoption of surface roughness as a design parameter for man-made functional coatings. So far the attention has focused primarily on macroscopic surfaces, but one should expect the wetting properties of colloidal particles to be strongly affected by roughness, too. Particle wettability, in turn, is a key parameter for the adsorption of particles at liquid interfaces and for the industrially important use of particles as emulsion stabilizers; yet, the consequence of particle roughness for emulsion stability remains poorly understood. In order to investigate the matter systematically, we have developed a surface treatment, applicable to micrometer-sized particles and macroscopic surfaces alike, that produces surface coatings with finely tunable nanoscale roughness and identical surface chemistry. Coatings with different degrees of roughness were characterized with regard to their morphology, charging, and wetting properties, and the results were correlated with the stability of emulsions prepared with coated particles of different roughness. We find that the maximum capillary pressure, a metric of the emulsions' resistance to droplet coalescence, varies significantly and in a nonmonotonic fashion with particle roughness. Surface topography and contact angle hysteresis suggest that particle roughness benefits the stability of our emulsions as long as wetting occurs homogeneously (Wenzel regime), whereas the transition toward heterogeneous wetting (Cassie-Baxter regime) is associated with a loss of stability.}, number={33}, journal={Langmuir}, publisher={American Chemical Society (ACS)}, author={San-Miguel, Adriana and Behrens, Sven H.}, year={2012}, month={Aug}, pages={12038–12043} }
 @article{rubin_san miguel_bommarius_behrens_2011, title={Correction to “Correlating Aggregation Kinetics and Stationary Diffusion in Protein–Sodium Salt Systems Observed with Dynamic Light Scattering”}, volume={115}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp206633a}, DOI={10.1021/jp206633a}, abstractNote={ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionORIGINAL ARTICLEThis notice is a correctionCorrection to “Correlating Aggregation Kinetics and Stationary Diffusion in Protein–Sodium Salt Systems Observed with Dynamic Light Scattering”Jonathan Rubin, Adriana San Miguel, Andreas S. Bommarius*, and Sven H. BehrensCite this: J. Phys. Chem. B 2011, 115, 36, 10778Publication Date (Web):August 18, 2011Publication History Published online18 August 2011Published inissue 15 September 2011https://doi.org/10.1021/jp206633aCopyright © 2011 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views336Altmetric-Citations2LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (1 MB) Get e-Alerts Get e-Alerts}, number={36}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Rubin, Jonathan and San Miguel, Adriana and Bommarius, Andreas S. and Behrens, Sven H.}, year={2011}, month={Sep}, pages={10778–10778} }
 @article{san miguel_behrens_2011, title={Permeability control in stimulus-responsive colloidosomes}, volume={7}, ISSN={1744-683X 1744-6848}, url={http://dx.doi.org/10.1039/c0sm01107j}, DOI={10.1039/c0sm01107j}, abstractNote={Self-assembly of colloidal particles in the liquid interface of double emulsion droplets can be used to fabricate “colloidosome” microcapsules, which have great potential as vehicles for the controlled delivery of drugs or other cargoes. Here we present a novel class of aqueous core colloidosomes that combine the benefit of low capsule permeability (good cargo retention) with the option of a stimulus-triggered fast release in a target environment. Complete or partial dissolution of the capsule walls in response to a mild pH change is achieved in each case through the use of responsive particles made from polymers with pH-switchable solubility. We demonstrate three methods of controlling the capsule permeability prior to release while maintaining the intended response to the release trigger.}, number={5}, journal={Soft Matter}, publisher={Royal Society of Chemistry (RSC)}, author={San Miguel, Adriana and Behrens, Sven H.}, year={2011}, pages={1948–1956} }
 @article{rubin_san miguel_bommarius_behrens_2010, title={Correlating Aggregation Kinetics and Stationary Diffusion in Protein−Sodium Salt Systems Observed with Dynamic Light Scattering}, volume={114}, ISSN={1520-6106 1520-5207}, url={http://dx.doi.org/10.1021/jp912126w}, DOI={10.1021/jp912126w}, abstractNote={This paper compares two manifestations of electrolyte-mediated interaction between globular proteins. Salt-induced protein aggregation is studied with dynamic light scattering (DLS) in solutions of lysozyme and bovine serum albumin (BSA) containing different types of sodium salts. The same types of ions are used in a second measurement series assessing the effect of more dilute electrolytes on protein diffusivity in non-aggregating protein dispersions. Both aggregation and stable diffusion exhibit strong ion specificity along the lines of the Hofmeister series: chaotropic counterions act as the strongest coagulants and, in stable protein solutions, lead to the lowest "protein interaction parameter", evaluated as the slope of protein diffusivity versus protein concentration. Within this common qualitative trend, lysozyme and BSA solutions show marked differences, including the sign of the interaction parameter for most of the tested solution compositions. Despite the different nature of lysozyme and BSA, a strong correlation is found in both cases between the ion-specific interaction parameter and the proteins' aggregation tendency as indicated by the salt concentration required for fast aggregation. The interaction parameter, available via quick and easy DLS measurements on stable protein solutions, may thus serve as a predictor of ion-specific aggregation trends.}, number={12}, journal={The Journal of Physical Chemistry B}, publisher={American Chemical Society (ACS)}, author={Rubin, Jonathan and San Miguel, Adriana and Bommarius, Andreas S. and Behrens, Sven H.}, year={2010}, month={Apr}, pages={4383–4387} }
 @article{san miguel_scrimgeour_curtis_behrens_2010, title={Smart colloidosomes with a dissolution trigger}, volume={6}, ISSN={1744-683X 1744-6848}, url={http://dx.doi.org/10.1039/c002930k}, DOI={10.1039/c002930k}, abstractNote={This paper reports the assembly and pH-triggered dissolution of a novel type of colloidosome microcapsules formed by self-assembly of responsive particles made from enteric coating polymers onto double emulsion templates; measurements of the capsules' permeability are complemented by evidence for fast and complete capsule dissolution in response to a mild pH stimulus.}, number={14}, journal={Soft Matter}, publisher={Royal Society of Chemistry (RSC)}, author={San Miguel, Adriana and Scrimgeour, Jan and Curtis, Jennifer E. and Behrens, Sven H.}, year={2010}, pages={3163} }