Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography

© The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Geisterfer, Z. M., Oakey, J., & Gatlin, J. C. . Microfluidic encapsulation of Xenopus laevis cell-free extracts using hydrogel photolithography. STAR Protocols, 1(3), (2020): 100221, doi:10.1016/j.xpro.2020.100221.Cell-free extract derived from the eggs of the African clawed frog Xenopus laevis is a well-established model system that has been used historically in bulk aliquots. Here, we describe a microfluidic approach for isolating discrete, biologically relevant volumes of cell-free extract, with more expansive and precise control of extract shape compared with extract-oil emulsions. This approach is useful for investigating the mechanics of intracellular processes affected by cell geometry or cytoplasmic volume, including organelle scaling and positioning mechanisms. For complete details on the use and execution of this protocol, please refer to Geisterfer et al. (2020).This work was made possible by an Institutional Development Award (IDeA) from the National Institute of General Medical Sciences of the National Institutes of Health under grant no. 2P20GM103432. It was also supported by additional funding provided by the NIGMS under grant no. R01GM113028, the NSF Faculty CAREER Program under award no. BBBE 1254608, Whitman Center fellowships at the Marine Biological Laboratory, and the Biomedical Scholars program of the Pew Charitable Trusts. We thank Drs. Aaron Groen and Tim Mitchison for their intellectual contributions and involvement in some of the pioneering experiments that set the foundation for this approach

Microtubule motors in eukaryotic spindle assembly and maintenance

The main function of the mitotic spindle is to accurately segregate replicated chromosomes during cell division. This dynamic, microtubule-based structure is assembled by a dividing cell and facilitates the orchestrated movement of chromosomes that is the hallmark of mitosis. Steady-state spindle size and morphology are relatively constant for cells of a specified type but vary considerably from one cell type to the next. Despite these differences, all eukaryotic spindles share basic architectural similarities, perhaps the most important of which is bipolar symmetry. At its core, assembling a bipolar spindle is a mechanical process that requires dynamic microtubules be moved and arranged to realize some ultimate functional form. These movements are the result of forces generated either by microtubule polymer dynamics or molecular motors. In this review we focus specifically on the motor-dependent mechanisms that shape the spindle and defer a more comprehensive treatment of spindle assembly and other motor functions during mitosis to others [1]

Spindle assembly in the absence of a RanGTP gradient requires localized CPC activity

Author Posting. © The Author(s), 2009. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Current Biology 19 (2009): 1210-1215, doi:10.1016/j.cub.2009.05.061.During animal cell division, a gradient of GTP-bound Ran is generated around mitotic chromatin. It is generally accepted that this RanGTP gradient is essential for organizing the spindle since it locally activates critical spindle assembly factors. Here, we show in Xenopus egg extract, where the gradient is best characterized, that spindles can assemble in the absence of a RanGTP gradient. Gradient-free spindle assembly occurred around sperm nuclei but not around chromatin-coated beads and required the chromosomal passenger complex (CPC). Artificial enrichment of CPC activity within hybrid bead arrays containing both immobilized chromatin and the CPC supported local microtubule assembly even in the absence of a RanGTP gradient. We conclude that RanGTP and the CPC constitute the two major molecular signals that spatially promote microtubule polymerization around chromatin. Furthermore, we hypothesize that the two signals mainly originate from discreet physical sites on the chromosomes to localize microtubule assembly around chromatin: a RanGTP signal from any chromatin, and a CPC-dependent signal predominantly generated from centromeric chromatin.This work was supported by the American Cancer Society (grant PF0711401 to T.J. Maresca), the National Cancer Institute (grant CA078048-09 to T.J. Mitchison) and the National Institutes of Health (grant F32GM080049 to J.C. Gatlin and grant GM24364 to E.D. Salmon)

Growth cone responses to growth and chemotropic factors

Abstract During nervous system development axons reach their target areas under the influence of numerous guidance cues that affect rate and direction of growth. This report addresses the unsettled question of whether and to what extent growth velocity and turning responses (attraction, repulsion) are interdependent. We exposed individual growth cones of fetal rat dorsal root ganglion neurons in culture asymmetrically to gradients of seven different factors and recorded their growth rates and turning angles. Growth cones exhibited divergent patterns of turning and growth responses. For example, hepatocyte growth factor (HGF), insulin-like growth factor-1 (IGF-1) and thrombin all promoted growth, but HGF was a powerful attractant, thrombin a potent repellent and IGF-1 did not elicit turning. Galanin and neuropeptide Y also affected growth and ⁄ or turning differentially. Finally, nerve growth factor in the culture medium not only inhibited the turning responses to HGF, but also converted growth promotion of HGF and IGF-1 into inhibition. Overall, our studies indicate that: (i) turning and advance are regulated independently, except that strong attractive or repulsive responses generally are accompanied by growth promotion; (ii) asymmetric growth factor application per se does not elicit attraction; (iii) regulation of the two parameters may occur through a single receptor; and (iv) the effects of combined growth factors may not be additive and can be inhibitory

Directly probing the mechanical properties of the spindle and its matrix

The spindle matrix does not make a significant mechanical contribution to metaphase spindle length.Several recent models for spindle length regulation propose an elastic pole to pole spindle matrix that is sufficiently strong to bear or antagonize forces generated by microtubules and microtubule motors. We tested this hypothesis using microneedles to skewer metaphase spindles in Xenopus laevis egg extracts. Microneedle tips inserted into a spindle just outside the metaphase plate resulted in spindle movement along the interpolar axis at a velocity slightly slower than microtubule poleward flux, bringing the nearest pole toward the needle. Spindle velocity decreased near the pole, which often split apart slowly, eventually letting the spindle move completely off the needle. When two needles were inserted on either side of the metaphase plate and rapidly moved apart, there was minimal spindle deformation until they reached the poles. In contrast, needle separation in the equatorial direction rapidly increased spindle width as constant length spindle fibers pulled the poles together. These observations indicate that an isotropic spindle matrix does not make a significant mechanical contribution to metaphase spindle length determination

Directly probing the mechanical properties of the spindle and its matrix

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. The definitive version was published in Journal of Cell Biology 188 (2010): 481-489, doi:10.1083/jcb.200907110.Several recent models for spindle length regulation propose an elastic pole to pole spindle matrix that is sufficiently strong to bear or antagonize forces generated by microtubules and microtubule motors. We tested this hypothesis using microneedles to skewer metaphase spindles in Xenopus laevis egg extracts. Microneedle tips inserted into a spindle just outside the metaphase plate resulted in spindle movement along the interpolar axis at a velocity slightly slower than microtubule poleward flux, bringing the nearest pole toward the needle. Spindle velocity decreased near the pole, which often split apart slowly, eventually letting the spindle move completely off the needle. When two needles were inserted on either side of the metaphase plate and rapidly moved apart, there was minimal spindle deformation until they reached the poles. In contrast, needle separation in the equatorial direction rapidly increased spindle width as constant length spindle fibers pulled the poles together. These observations indicate that an isotropic spindle matrix does not make a significant mechanical contribution to metaphase spindle length determination.This work was supported by National Institute of General Medicine grants to J.C. Gatlin (F32GM080049) and E.D. Salmon (GM24364). T.J. Mitchison was funded by a grant from the National Cancer Institute (CA078048-09)

Functional overlap of microtubule assembly factors in chromatin-promoted spindle assembly

Author Posting. © American Society for Cell Biology, 2009. This article is posted here by permission of American Society for Cell Biology for personal use, not for redistribution. The definitive version was published in Molecular Biology of the Cell 20 (2009): 2766-2773, doi:10.1091/mbc.E09-01-0043.Distinct pathways from centrosomes and chromatin are thought to contribute in parallel to microtubule nucleation and stabilization during animal cell mitotic spindle assembly, but their full mechanisms are not known. We investigated the function of three proposed nucleation/stabilization factors, TPX2, {gamma}-tubulin and XMAP215, in chromatin-promoted assembly of anastral spindles in Xenopus laevis egg extract. In addition to conventional depletion-add back experiments, we tested whether factors could substitute for each other, indicative of functional redundancy. All three factors were required for microtubule polymerization and bipolar spindle assembly around chromatin beads. Depletion of TPX2 was partially rescued by the addition of excess XMAP215 or EB1, or inhibiting MCAK (a Kinesin-13). Depletion of either {gamma}-tubulin or XMAP215 was partially rescued by adding back XMAP215, but not by adding any of the other factors. These data reveal functional redundancy between specific assembly factors in the chromatin pathway, suggesting individual proteins or pathways commonly viewed to be essential may not have entirely unique functions.This work was supported by the American Cancer Society (grant PF0711401 to T. J. Maresca), the National Cancer Institute (grant CA078048-09 to T. J. Mitchison) and the National Institutes of Health (grant F32GM080049 to J. C. Gatlin and grant GM24364 to E. D. Salmon)

Challenges and Opportunities in Finfish Nutrition

Much of the criticism leveled at aquaculture (e.g., dependency on animal-derived feedstuffs, nutrient-laden effluent discharges, and increased organic contamination in edible products) can be traced to the feeds in use. Accordingly, finfish nutritionists are being challenged to formulate feeds that not only meet the nutritional requirements of livestock but also minimize production costs, limit environmental impacts, and enhance product quality. These challenges not only add considerable complexity to finfish nutrition but also afford opportunities to avoid some of the mistakes made by other industries in the past. From a review of the current status of finfish nutrition with respect to major nutrient classes, we comment on future opportunities and promising avenues of research. Alternative protein sources, specifically those derived from marine bycatch, plants, and microbes, are discussed, as well as methods to facilitate their implementation in finfish feeds. Dietary lipid, its role in fish bioenergetics and physiology, and quality of aquaculture products is reviewed with special emphasis on alternative lipid sources and finishing diets. Carbohydrates and fiber are discussed in terms of nutrient-sparing, least-cost diet formulation and digestive physiology. Micronutrients are reviewed in terms of current knowledge of requirements and, along with other dietary immunostimulants, are given further consideration in a review of nutriceuticals and application in finfish feeds. The status of nutritional research in new aquaculture species is also outlined. By integrating classical approaches with emerging technologies, dietary formulations, and species, finfish nutritionists may identify means to increase production efficiency and sustainability and provide for the continued success of aquaculture