Leahy BD, Jang W-D, Yang HY, Struyven R, Wei D, Sun Z, Lee KR, Royston C, Cam L, Kalma Y, et al. Automated Measurements of Key Morphological Features of Human Embryos for IVF. arXiv. 2020. Publisher's VersionAbstract
A major challenge in clinical In-Vitro Fertilization (IVF) is selecting the highest quality embryo to transfer to the patient in the hopes of achieving a pregnancy. Time-lapse microscopy provides clinicians with a wealth of information for selecting embryos. However, the resulting movies of embryos are currently analyzed manually, which is time consuming and subjective. Here, we automate feature extraction of timelapse microscopy of human embryos with a machine-learning pipeline of five convolutional neural networks (CNNs). Our pipeline consists of (1) semantic segmentation of the regions of the embryo, (2) regression predictions of fragment severity, (3) classification of the developmental stage, and object instance segmentation of (4) cells and (5) pronuclei. Our approach greatly speeds up the measurement of quantitative, biologically relevant features that may aid in embryo selection. Please see here for more information: 
Choi J, Zhou H, Landig R, Wu H-Y, Yu X, Stetina SEV, Kucsko G, Mango SE, Needleman DJ, Samuel ADT, et al. Probing and manipulating embryogenesis via nanoscale thermometry and temperature control. PNAS. 2020. Publisher's Version Download Paper
Sanchez T, Venturas M, Aghvami SA, Yang X, Fraden S, Sakkas D, Needleman D. Combined noninvasive metabolic and spindle imaging as potential tools for embryo and oocyte assessment. Human Reproduction. 2019 :1-13. Download Paper
Jauregui LA, Joe AY, Pistunova K, Wild DS, High AA, Zhou Y, Scuri G, De Greve K, Sushko A, Yu C-H, et al. Electrical control of interlayer exciton dynamics in atomically thin heterostructures. Science. 2019;336 (6467) :870-875. Publisher's VersionAbstract
A van der Waals heterostructure built from atomically thin semiconducting transition metal dichalcogenides (TMDs) enables the formation of excitons from electrons and holes in distinct layers, producing interlayer excitons with large binding energy and a long lifetime. By employing heterostructures of monolayer TMDs, we realize optical and electrical generation of long-lived neutral and charged interlayer excitons. We demonstrate that neutral interlayer excitons can propagate across the entire sample and that their propagation can be controlled by excitation power and gate electrodes. We also use devices with ohmic contacts to facilitate the drift motion of charged interlayer excitons. The electrical generation and control of excitons provide a route for achieving quantum manipulation of bosonic composite particles with complete electrical tunability.
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Fürthauer S, Lemma  B, Foster PJ, Ems-McClung SC, Yu7 C-H, Walczak CE, Dogic Z, Needleman DJ, Shelley MJ. Self-straining of actively crosslinked microtubule networks. Nature Physics. 2019.Abstract
Cytoskeletal networks are foundational examples of active matter and central to self-organized structures in the cell. In vivo, these networks are active and densely crosslinked. Relating their large-scale dynamics to the properties of their constituents remains an unsolved problem. Here, we study an in vitro active gel made from aligned microtubules and XCTK2 kinesin motors. Using photobleaching, we demonstrate that the gel’s aligned microtubules, driven by motors, continually slide past each other at a speed independent of the local microtubule polarity and motor concentration. This phenomenon is also observed, and remains unexplained, in spindles. We derive a general framework for coarse graining microtubule gels crosslinked by molecular motors from microscopic considerations. Using microtubule–microtubule coupling through a force–velocity relationship for kinesin, this theory naturally explains the experimental results: motors generate an active strain rate in regions of changing polarity, which allows microtubules of opposite polarities to slide past each other without stressing the material.
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Needleman D, Shelley M. The stormy fluid dynamics of the living cell. Physics Today. 2019;72 (9). Publisher's VersionAbstract
Cell biology has its beginnings in the first observations of cells through primitive microscopes and in the formulation of cell theory, which postulates that cells are the fundamental building blocks of life. Light microscopes showed that the insides of cells contained complex structures, such as nuclei, spindles, and chromosomes. The advent of electron microscopy in the mid 20th century brought the first truly detailed views of cell innards. Images revealed complexity at all observable scales, including cell-spanning networks of polymers, intricate organelles made of membranes, and a variety of micron- to nanometer-sized sacs and granules such as vesicles, lipid droplets, and ribosomes. (For a glossary of cellular components, see the Quick Study by Ned Wingreen, PHYSICS TODAY, September 2006, page 80.) Those structures are immersed in or part of the aqueous cytoplasm—the cell’s fluidic medium.
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MBoC Paper of the Year Award Winner: Yu C-H*, Redemann* S, Wu H-Y, Kiewisz R, Yoo TY, Conway W, Farhadifar R, Müller-Reichert T, Needleman D. Central-spindle microtubules are strongly coupled to chromosomes during both anaphase A and anaphase B. Molecular Biology of the Cell. 2019;30 :2503-2514. Publisher's VersionAbstract

Spindle microtubules, whose dynamics vary over time and at different locations, cooperatively drive chromosome segregation. Measurements of microtubule dynamics and spindle ultrastructure can provide insight into the behaviors of microtubules, helping elucidate the mechanism of chromosome segregation. Much work has focused on the dynamics and organization of kinetochore microtubules, that is, on the region between chromosomes and poles. In comparison, microtubules in the central-spindle region, between segregating chromosomes, have been less thoroughly characterized. Here, we report measurements of the movement of central-spindle microtubules during chromosome segregation in human mitotic spindles and Caenorhabditis elegans mitotic and female meiotic spindles. We found that these central-spindle microtubules slide apart at the same speed as chromosomes, even as chromosomes move toward spindle poles. In these systems, damaging central-spindle microtubules by laser ablation caused an immediate and complete cessation of chromosome motion, suggesting a strong coupling between central-spindle microtubules and chromosomes. Electron tomographic reconstruction revealed that the analyzed anaphase spindles all contain microtubules with both ends between segregating chromosomes. Our results provide new dynamical, functional, and ultrastructural characterizations of central-spindle microtubules during chromosome segregation in diverse spindles and suggest that central-spindle microtubules and chromosomes are strongly coupled in anaphase.

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Sanchez T, Zhang M, Needleman D, Seli E. Metabolic imaging via fluorescence lifetime imaging microscopy for egg and embryo assessment. Fertility and Sterility. 2019;111 (2) :212 - 218. Publisher's VersionAbstract
Current strategies for embryo assessment in the assisted reproductive technology laboratories rely primarily on morphologic parameters that have limited accuracy for determining embryo viability. Even with the addition of invasive diagnostic interventions such as preimplantation genetic testing for aneuploidy alone or in combination with mitochondrial DNA copy number assessment, at least one third of embryos fail to implant. Therefore, at a time when the clinical benefits of single ET are widely accepted, improving viability assessment of embryos is ever more important. Building on the previous work demonstrating the importance of metabolic state in oocytes and embryos, metabolic imaging via fluorescence lifetime imaging microscopy offers new and potentially useful diagnostic method by detecting natural fluorescence of FAD and NADH, the two electron transporters that play a central role in oxidative phosphorylation. Recent studies demonstrate that fluorescence lifetime imaging microscopy can detect oocyte and embryo metabolic function and dysfunction in a multitude of experimental models and provide encouraging evidence for use in scientific investigation and possibly for clinical application.
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Foster PJ, Fürthauer S, Shelley MJ, Needleman DJ. From cytoskeletal assemblies to living materials. Current Opinion in Cell Biology. 2019;56 :109–114. Download Paper
Sanchez T, Wang T, Pedro MV, Zhang M, Esencan E, Sakkas D, Needleman D, Seli E. Metabolic imaging with the use of fluorescence lifetime imaging microscopy (FLIM) accurately detects mitochondrial dysfunction in mouse oocytes. Fertility and sterility. 2018;110 (7) :1271. Download Paper
Yoo TY, Choi J-M, Conway W, Yu C-H, Pappu RV, Needleman DJ. Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments. eLife. 2018 :7:e36392. Publisher's Version Download Paper
Oriola D, Needleman DJ, Brugués J. The Physics of the Metaphase Spindle. Annual review of biophysics. 2018;47 :655–673. Download Paper
Kaye B, Stiehl O, Foster PJ, Shelley M, Needleman DJ, Fürthauer S. Measuring and modeling polymer concentration profiles near spindle boundaries argues that spindle microtubules regulate their own nucleation. New Journal of Physics. 2018. Download Paper
Penfield L, Wysolmerski B, Mauro M, Farhadifar R, Martinez MA, Biggs R, Wu H-Y, Broberg C, Needleman D, Bahmanyar S. Dynein pulling forces counteract lamin-mediated nuclear stability during nuclear envelope repair. Molecular biology of the cell. 2018;29 (7) :852–868. Download Paper
Racowsky C, Needleman DJ. Cumulus cell gene expression as a potential biomarker for oocyte quality. Fertility and Sterility. 2018 :109(3):438-439. Download Paper
Sherman DJ, Xie R, Taylor RJ, George AH, Okuda S, Foster PJ, Needleman DJ, Kahne D. Lipopolysaccharide is transported to the cell surface by a membrane-to-membrane protein bridge. Science. 2018;359 (6377) :798–801. Publisher's VersionAbstract
The outer membrane of Gram-negative bacteria is composed of lipopolysaccharide, a large glycolipid that prevents drugs from entering the cells. Disrupting lipopolysaccharide assembly hypersensitizes bacteria to antibiotics. Sherman et al. used biochemical tools to observe lipopolysaccharide transport. Seven proteins, which are conserved in all Gram-negative bacteria, appear to form a protein bridge that uses adenosine triphosphate to power transport of lipopolysaccharide from one membrane to another. The ability to monitor intermembrane transport of lipopolysaccharide will help in efforts to develop and characterize inhibitors.Science, this issue p. 798Gram-negative bacteria have an outer membrane that serves as a barrier to noxious agents in the environment. This protective function is dependent on lipopolysaccharide, a large glycolipid located in the outer leaflet of the outer membrane. Lipopolysaccharide is synthesized at the cytoplasmic membrane and must be transported to the cell surface. To understand this transport process, we reconstituted membrane-to-membrane movement of lipopolysaccharide by incorporating purified inner and outer membrane transport complexes into separate proteoliposomes. Transport involved stable association between the inner and outer membrane proteoliposomes. Our results support a model in which lipopolysaccharide molecules are pushed one after the other in a PEZ dispenser–like manner across a protein bridge that connects the inner and outer membranes.
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Tan R, Foster PJ, Needleman DJ, McKenney RJ. Cooperative accumulation of dynein-dynactin at microtubule minus-ends drives microtubule network reorganization. Developmental Cell. 2018;44 (2) :233–247. Download Paper
Foster PJ, Yan W, Fürthauer S, Shelley M, Needleman DJ. Connecting macroscopic dynamics with microscopic properties in active microtubule network contraction. New Journal of Physics. 2017. Download Paper
Sanchez T, Seidler EA, Gardner DK, Needleman D, Sakkas D. Will noninvasive methods surpass invasive for assessing gametes and embryos?. Fertility and Sterility. 2017;108 (5) :730–737. Download Paper
Nazockdast E, Rahimian A, Needleman D, Shelley M. Cytoplasmic flows as signatures for the mechanics of mitotic positioning. Molecular Biology of the Cell. 2017 :mbc–E16. Download Paper