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Omega: A Software Tool For The Management, Analysis, And Dissemination Of Intracellular Trafficking Data That Incorporates Motion Type Classification And Quality Control, Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, Jeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, Caterina Strambio-De-Castilla 2018 University of Massachusetts Medical School

Omega: A Software Tool For The Management, Analysis, And Dissemination Of Intracellular Trafficking Data That Incorporates Motion Type Classification And Quality Control, Alessandro Rigano, Vanni Galli, Jasmine M. Clark, Lara E. Pereira, Loris Grossi, Jeremy Luban, Raffaello Giulietti, Tiziano Leidi, Eric Hunter, Mario Valle, Ivo F. Sbalzarini, Caterina Strambio-De-Castilla

University of Massachusetts Medical School Faculty Publications

MOTIVATION: Particle tracking coupled with time-lapse microscopy is critical for understanding the dynamics of intracellular processes of clinical importance. Spurred on by advances in the spatiotemporal resolution of microscopy and automated computational methods, this field is increasingly amenable to multi-dimensional high-throughput data collection schemes (Snijder et al, 2012). Typically, complex particle tracking datasets generated by individual laboratories are produced with incompatible methodologies that preclude comparison to each other. There is therefore an unmet need for data management systems that facilitate data standardization, meta-analysis, and structured data dissemination. The integration of analysis, visualization, and quality control capabilities into such systems would ...


Imp3 Stabilization Of Wnt5b Mrna Facilitates Taz Activation In Breast Cancer, Sanjoy Samanta, Santosh Guru, Ameer L. Elaimy, John J. Amante, Jianhong Ou, Jun Yu, Lihua Julie Zhu, Arthur M. Mercurio 2018 University of Massachusetts Medical School

Imp3 Stabilization Of Wnt5b Mrna Facilitates Taz Activation In Breast Cancer, Sanjoy Samanta, Santosh Guru, Ameer L. Elaimy, John J. Amante, Jianhong Ou, Jun Yu, Lihua Julie Zhu, Arthur M. Mercurio

University of Massachusetts Medical School Faculty Publications

Insulin-like growth factor-2 mRNA-binding protein 3 (IMP3) is an oncofetal protein associated with many aggressive cancers and implicated in the function of breast cancer stem cells (CSCs). The mechanisms involved, however, are poorly understood. We observed that IMP3 facilitates the activation of TAZ, a transcriptional co-activator of Hippo signaling that is necessary for the function of breast CSCs. The mechanism by which IMP3 activates TAZ involves both mRNA stability and transcriptional regulation. IMP3 stabilizes the mRNA of an alternative WNT ligand (WNT5B) indirectly by repressing miR145-5p, which targets WNT5B, resulting in TAZ activation by alternative WNT signaling. IMP3 also facilitates ...


Improving Techniques To Study Equine Cervical Mucociliary Clearance, Melissa A. Hawkes 2018 University of Maine

Improving Techniques To Study Equine Cervical Mucociliary Clearance, Melissa A. Hawkes

Electronic Theses and Dissertations

Bacterial uterine infections inflict major losses on the equine breeding industry. These infections usually arise from bacteria introduced at breeding. Micro-currents propelled by ciliated cells between the folds of the uterus and cervix have been proposed as a means by which contaminants are expelled. Previous data have shown possible ciliary micro-currents propelling carbon particles, occasionally rotating, through cervical folds. However, adherence to the epithelium may have interfered with movement of carbon in these studies. Therefore, we tested potentially non-adherent substances to reveal ciliary micro-currents on the equine cervix under high magnification video-endoscopy. We hypothesized that polyethylene green microspheres 1 - 5 ...


Melatonin-Micronutrients Osteopenia Treatment Study (Mots): A Translational Study Assessing The Effects Of Melatonin, Strontium Citrate, Vitamin D3 And Vitamin K2 On Bone Density, Bone Turnover Markers And Health-Related Quality Of Life In Postmenopausal Osteopenic Women Following A One-Year Double-Blind Randomized Placebo-Controlled Trial And On Osteoblast-Osteoclast Co-Cultures, Sifat Maria 2018 Duquesne University

Melatonin-Micronutrients Osteopenia Treatment Study (Mots): A Translational Study Assessing The Effects Of Melatonin, Strontium Citrate, Vitamin D3 And Vitamin K2 On Bone Density, Bone Turnover Markers And Health-Related Quality Of Life In Postmenopausal Osteopenic Women Following A One-Year Double-Blind Randomized Placebo-Controlled Trial And On Osteoblast-Osteoclast Co-Cultures, Sifat Maria

Electronic Theses and Dissertations

Objective: The purpose of this study was to assess if a novel combination of melatonin and three other natural bone-aiding micronutrients: strontium citrate, vitamins D3 and K2 (MSDK) could improve bone health by modulating the activity of osteoblasts and osteoclasts in favor of balanced bone remodeling and by improving the overall health-related quality of life in postmenopausal osteopenic women.

Methods: The Melatonin-micronutrients Osteopenia Treatment Study (MOTS) is a translational research study that used both clinical and in vitro approaches to assess the efficacy of MSDK on bone health in women and to identify potential mechanisms for its effects ...


Nmecas9 Is An Intrinsically High-Fidelity Genome Editing Platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer 2018 University of Massachusetts Medical School

Nmecas9 Is An Intrinsically High-Fidelity Genome Editing Platform, Nadia Amrani, Xin D. Gao, Pengpeng Liu, Alireza Edraki, Aamir Mir, Raed Ibraheim, Ankit Gupta, Kanae E. Sasaki, Tong Wu, Thomas G. Fazzio, Lihua Julie Zhu, Scot A. Wolfe, Erik J. Sontheimer

University of Massachusetts Medical School Faculty Publications

Background: The development of CRISPR genome editing has transformed biomedical research. Most applications reported thus far rely upon the Cas9 protein from Streptococcus pyogenes SF370 (SpyCas9). With many RNA guides, wild-type SpyCas9 can induce significant levels of unintended mutations at near-cognate sites, necessitating substantial efforts toward the development of strategies to minimize off-target activity. Although the genome-editing potential of thousands of other Cas9 orthologs remains largely untapped, it is not known how many will require similarly extensive engineering to achieve single-site accuracy within large (e.g. mammalian) genomes. In addition to its off-targeting propensity, SpyCas9 is encoded by a relatively ...


A Leap To Hybrid Governance For European Union Healthcare On Organ Donations, Tasnim Ahmed 2018 Liverpool John Moores University

A Leap To Hybrid Governance For European Union Healthcare On Organ Donations, Tasnim Ahmed

Journal of Law and Health

This article evaluates two proposals that the Organs Directive along with the commission’s Action Plan 2009-2015 can be viewed as a form of hybrid governance. The Organs Directive is the first legally-binding supranational risk regulation devised in the field of organ donation and transplantation. The Directive is modelled on the earlier Directive dealing with blood, tissue, and cells. The Action Plan, which is soft law, will complement the Directive. The Directive and Action Plan requires additional administration procedures from the Member States with the EU Commission regularly monitoring the implementation of the work programme to ensure it is manageable ...


Rip Kinase 1-Dependent Endothelial Necroptosis Underlies Systemic Inflammatory Response Syndrome, Matija Zelic, Justine E. Roderick, Joanne A. O'Donnell, Jesse Lehman, Sung Eun Lim, Harish P. Janardhan, Chinmay M. Trivedi, Manolis Pasparakis, Michelle A. Kelliher 2018 University of Massachusetts Medical School

Rip Kinase 1-Dependent Endothelial Necroptosis Underlies Systemic Inflammatory Response Syndrome, Matija Zelic, Justine E. Roderick, Joanne A. O'Donnell, Jesse Lehman, Sung Eun Lim, Harish P. Janardhan, Chinmay M. Trivedi, Manolis Pasparakis, Michelle A. Kelliher

Open Access Articles

Receptor interacting protein kinase 1 (RIPK1) has important kinase-dependent and kinase-independent scaffolding functions that activate or prevent apoptosis or necroptosis in a cell context-dependent manner. The kinase activity of RIPK1 mediates hypothermia and lethality in a mouse model of TNF-induced shock, reflecting the hyperinflammatory state of systemic inflammatory response syndrome (SIRS), where the proinflammatory "cytokine storm" has long been viewed as detrimental. Here, we demonstrate that cytokine and chemokine levels did not predict survival and, importantly, that kinase-inactive Ripk1D138N/D138N hematopoietic cells afforded little protection from TNF- or TNF/zVAD-induced shock in reconstituted mice. Unexpectedly, RIPK1 kinase-inactive mice transplanted with ...


The Systemic Quantification Of Immune Cell Populations In Various Murine Models: How Age, Tumor Burden, And Immunotherapy Affect The Immune Response, Kavita Sinha 2018 University of Connecticut

The Systemic Quantification Of Immune Cell Populations In Various Murine Models: How Age, Tumor Burden, And Immunotherapy Affect The Immune Response, Kavita Sinha

Honors Scholar Theses

Immunotherapy as a form of cancer treatment has become increasingly popular in the past few decades. Researchers have worked to figure out how to best use the body’s natural defense mechanism, the immune system, to fight off and destroy cancer cells. In particular, the goal has been to manipulate checkpoint blockades such as CTLA-4 and PD-1 in order to take the breaks off of the immune system, allowing for a prolonged immune response to the cancer. This work has led to the development of human versions of anti-CTLA4 antibodies (ipilimumab, tremelimumab) and anti-PD1 antibodies (pembrolizumab and Nivolumab) that are ...


A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, William Stafford Noble 2018 University of Washington

A Unified Encyclopedia Of Human Functional Dna Elements Through Fully Automated Annotation Of 164 Human Cell Types, Maxwell Wing Libbrecht, Oscar Rodriguez, Zhiping Weng, Michael Hoffman, Jeffrey A. Bilmes, William Stafford Noble

University of Massachusetts Medical School Faculty Publications

Semi-automated genome annotation methods such as Segway enable understanding of chromatin activity. Here we present chromatin state annotations of 164 human cell types using 1,615 genomics data sets. To produce these annotations, we developed a fully-automated annotation strategy in which we train separate unsupervised annotation models on each cell type and use a machine learning classifier to automate the state interpretation step. Using these annotations, we developed a measure of the functional importance of each genomic position called the "functionality score," which allows us to aggregate information across cell types into a multi-cell type view. This score provides a ...


Application Of Area Scaling Analysis To Identify Natural Killer Cell And Monocyte Involvement In The Grantoxilux Antibody Dependent Cell-Mediated Cytotoxicity Assay, Justin Pollara, Chiara Orlandi, Charles Beck, R Whitney Edwards, Yi Hu, Shuying Liu, Shixia Wang, Richard A. Koup, Thomas N. Denny, Shan Lu, Georgia D. Tomaras, Anthony DeVico, George K. Lewis, Guido Ferrari 2018 Duke University

Application Of Area Scaling Analysis To Identify Natural Killer Cell And Monocyte Involvement In The Grantoxilux Antibody Dependent Cell-Mediated Cytotoxicity Assay, Justin Pollara, Chiara Orlandi, Charles Beck, R Whitney Edwards, Yi Hu, Shuying Liu, Shixia Wang, Richard A. Koup, Thomas N. Denny, Shan Lu, Georgia D. Tomaras, Anthony Devico, George K. Lewis, Guido Ferrari

Open Access Articles

Several different assay methodologies have been described for the evaluation of HIV or SIV-specific antibody-dependent cell-mediated cytotoxicity (ADCC). Commonly used assays measure ADCC by evaluating effector cell functions, or by detecting elimination of target cells. Signaling through Fc receptors, cellular activation, cytotoxic granule exocytosis, or accumulation of cytolytic and immune signaling factors have been used to evaluate ADCC at the level of the effector cells. Alternatively, assays that measure killing or loss of target cells provide a direct assessment of the specific killing activity of antibodies capable of ADCC. Thus, each of these two distinct types of assays provides information ...


Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio 2018 University of Massachusetts Medical School

Profiling Of Pluripotency Factors In Individual Stem Cells And Early Embryos, Sarah J. Hainer, Ana Boskovic, Oliver J. Rando, Thomas G. Fazzio

University of Massachusetts Medical School Faculty Publications

Major cell fate decisions are governed by sequence-specific transcription factors (TFs) that act in small cell populations within developing embryos. To understand how TFs regulate cell fate it is important to identify their genomic binding sites in these populations. However, current methods cannot profile TFs genome-wide at or near the single cell level. Here we adapt the CUT&RUN method to profile chromatin proteins in low cell numbers, mapping TF-DNA interactions in single cells and individual pre-implantation embryos for the first time. Using this method, we demonstrate that the pluripotency TF NANOG is significantly more dependent on the SWI/SNF ...


Biochemical Analysis Of Dimethyl Suberimidate-Crosslinked Yeast Nucleosomes, Yuichi Ichikawa, Paul D. Kaufman 2018 University of Massachusetts Medical School

Biochemical Analysis Of Dimethyl Suberimidate-Crosslinked Yeast Nucleosomes, Yuichi Ichikawa, Paul D. Kaufman

Open Access Articles

Nucleosomes are the fundamental unit of eukaryotic chromosome packaging, comprised of 147 bp of DNA wrapped around two molecules of each of the core histone proteins H2A, H2B, H3, and H4. Nucleosomes are symmetrical, with one axis of symmetry centered on the homodimeric interaction between the C-termini of the H3 molecules. To explore the functional consequences of nucleosome symmetry, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, allowing us to compare cells with single or double H3 alterations. Our biochemical validation of the heterodimeric X-Y interaction included intra-nucleosomal H3 crosslinking using dimethyl suberimidate (DMS). Here, we ...


Fundamental Limits On Dynamic Inference From Single-Cell Snapshots, Caleb Weinreb, Samuel Wolock, Betsabeh K. Tusi, Merav Socolovsky, Allon M. Klein 2018 Harvard Medical School

Fundamental Limits On Dynamic Inference From Single-Cell Snapshots, Caleb Weinreb, Samuel Wolock, Betsabeh K. Tusi, Merav Socolovsky, Allon M. Klein

Open Access Articles

Single-cell expression profiling reveals the molecular states of individual cells with unprecedented detail. Because these methods destroy cells in the process of analysis, they cannot measure how gene expression changes over time. However, some information on dynamics is present in the data: the continuum of molecular states in the population can reflect the trajectory of a typical cell. Many methods for extracting single-cell dynamics from population data have been proposed. However, all such attempts face a common limitation: for any measured distribution of cell states, there are multiple dynamics that could give rise to it, and by extension, multiple possibilities ...


Enucleated Cells Reveal Differential Roles Of The Nucleus In Cell Migration, Polarity, And Mechanotransduction, Gunes Uzer 2018 Boise State University

Enucleated Cells Reveal Differential Roles Of The Nucleus In Cell Migration, Polarity, And Mechanotransduction, Gunes Uzer

Mechanical and Biomedical Engineering Faculty Publications and Presentations

The nucleus has long been postulated to play a critical physical role during cell polarization and migration, but that role has not been defined or rigorously tested. Here, we enucleated cells to test the physical necessity of the nucleus during cell polarization and directed migration. Using enucleated mammalian cells (cytoplasts), we found that polarity establishment and cell migration in one dimension (1D) and two dimensions (2D) occur without the nucleus. Cytoplasts directionally migrate toward soluble (chemotaxis) and surface-bound (haptotaxis) extracellular cues and migrate collectively in scratch-wound assays. Consistent with previous studies, migration in 3D environments was dependent on the nucleus ...


Cerebral Organoids Derived From Sandhoff Disease-Induced Pluripotent Stem Cells Exhibit Impaired Neurodifferentiation, Maria L. Allende, Emily K. Cook, Bridget C. Larman, Adrienne Nugent, Jacqueline M. Brady, Diane Golebiowski, Miguel Sena-Esteves, Cynthia J. Tifft, Richard L. Proia 2018 National Institutes of Health

Cerebral Organoids Derived From Sandhoff Disease-Induced Pluripotent Stem Cells Exhibit Impaired Neurodifferentiation, Maria L. Allende, Emily K. Cook, Bridget C. Larman, Adrienne Nugent, Jacqueline M. Brady, Diane Golebiowski, Miguel Sena-Esteves, Cynthia J. Tifft, Richard L. Proia

Open Access Articles

Sandhoff disease, one of the GM2 gangliosidoses, is a lysosomal storage disorder characterized by the absence of beta-hexosaminidase A and B activity and the concomitant lysosomal accumulation of its substrate, GM2 ganglioside. It features catastrophic neurodegeneration and death in early childhood. How the lysosomal accumulation of ganglioside might affect the early development of the nervous system is not understood. Recently, cerebral organoids derived from induced pluripotent stem (iPS) cells have illuminated early developmental events altered by disease processes. To develop an early neurodevelopmental model of Sandhoff disease, we first generated iPS cells from the fibroblasts of an infantile Sandhoff disease ...


Molecular Mechanisms Of Cell Death: Recommendations Of The Nomenclature Committee On Cell Death 2018, Lorenzo Galluzzi, Eric H. Baehrecke, Francis Ka-Ming Chan, Guido Kroemer 2018 Weill Cornell Medical College

Molecular Mechanisms Of Cell Death: Recommendations Of The Nomenclature Committee On Cell Death 2018, Lorenzo Galluzzi, Eric H. Baehrecke, Francis Ka-Ming Chan, Guido Kroemer

Open Access Articles

Over the past decade, the Nomenclature Committee on Cell Death (NCCD) has formulated guidelines for the definition and interpretation of cell death from morphological, biochemical, and functional perspectives. Since the field continues to expand and novel mechanisms that orchestrate multiple cell death pathways are unveiled, we propose an updated classification of cell death subroutines focusing on mechanistic and essential (as opposed to correlative and dispensable) aspects of the process. As we provide molecularly oriented definitions of terms including intrinsic apoptosis, extrinsic apoptosis, mitochondrial permeability transition (MPT)-driven necrosis, necroptosis, ferroptosis, pyroptosis, parthanatos, entotic cell death, NETotic cell death, lysosome-dependent cell ...


Emergence Of The Erythroid Lineage From Multipotent Hematopoiesis, Betsabeh K. Tusi, Samuel L. Wolock, Caleb Weinreb, Yung Hwang, Daniel Hidalgo, Rapolas Zilionis, Ari Waisman, Jun R. Huh, Allon M. Klein, Merav Socolovsky 2018 University of Massachusetts Medical School

Emergence Of The Erythroid Lineage From Multipotent Hematopoiesis, Betsabeh K. Tusi, Samuel L. Wolock, Caleb Weinreb, Yung Hwang, Daniel Hidalgo, Rapolas Zilionis, Ari Waisman, Jun R. Huh, Allon M. Klein, Merav Socolovsky

University of Massachusetts Medical School Faculty Publications

Red cell formation begins with the hematopoietic stem cell, but the manner by which it gives rise to erythroid progenitors, and their subsequent developmental path, remain unclear. Here we combined single-cell transcriptomics of murine hematopoietic tissues with fate potential assays to infer a continuous yet hierarchical structure for the hematopoietic network. We define the erythroid differentiation trajectory as it emerges from multipotency and diverges from 6 other blood lineages. With the aid of a new flow-cytometric sorting strategy, we validated predicted cell fate potentials at the single cell level, revealing a coupling between erythroid and basophil/mast cell fates. We ...


Biology Of Platelet Purinergic Receptors And Implications For Platelet Heterogeneity, Milka Koupenova-Zamor, Katya Ravid 2018 University of Massachusetts Medical School

Biology Of Platelet Purinergic Receptors And Implications For Platelet Heterogeneity, Milka Koupenova-Zamor, Katya Ravid

Open Access Articles

Platelets are small anucleated cells present only in mammals. Platelets mediate intravascular hemostatic balance, prevent interstitial bleeding, and have a major role in thrombosis. Activation of platelet purinergic receptors is instrumental in initiation of hemostasis and formation of the hemostatic plug, although this activation process becomes problematic in pathological settings of thrombosis. This review briefly outlines the roles and function of currently known platelet purinergic receptors (P1 and P2) in the setting of hemostasis and thrombosis. Additionally, we discuss recent novel studies on purinergic receptor distribution according to heterogeneous platelet size, and the possible implication of this distribution on hemostatic ...


Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging, Chuangqi Wang, Hee June Choi, Sung-Jin Kim, Aesha Desai, Namgyu Lee, Dohoon Kim, Yongho Bae, Kwonmoo Lee 2018 Worcester Polytechnic Institute

Deconvolution Of Subcellular Protrusion Heterogeneity And The Underlying Actin Regulator Dynamics From Live Cell Imaging, Chuangqi Wang, Hee June Choi, Sung-Jin Kim, Aesha Desai, Namgyu Lee, Dohoon Kim, Yongho Bae, Kwonmoo Lee

University of Massachusetts Medical School Faculty Publications

Cell protrusion is morphodynamically heterogeneous at the subcellular level. However, the mechanistic understanding of protrusion activities is usually based on the ensemble average of actin regulator dynamics at the cellular or population levels. Here, we establish a machine learning-based computational framework called HACKS (deconvolution of Heterogeneous Activity Coordination in cytosKeleton at a Subcellular level) to deconvolve the subcellular heterogeneity of lamellipodial protrusion in migrating cells. HACKS quantitatively identifies distinct subcellular protrusion phenotypes from highly heterogeneous protrusion activities and reveals their underlying actin regulator dynamics at the leading edge. Furthermore, it can identify specific subcellular protrusion phenotypes susceptible to pharmacological perturbation ...


A Standard Nomenclature For Referencing And Authentication Of Pluripotent Stem Cells, Andreas Kurtz, Stefanie Seltmann, Kelly P. Smith 2018 Charité - Universitätsmedizin Berlin

A Standard Nomenclature For Referencing And Authentication Of Pluripotent Stem Cells, Andreas Kurtz, Stefanie Seltmann, Kelly P. Smith

Open Access Articles

Unambiguous cell line authentication is essential to avoid loss of association between data and cells. The risk for loss of references increases with the rapidity that new human pluripotent stem cell (hPSC) lines are generated, exchanged, and implemented. Ideally, a single name should be used as a generally applied reference for each cell line to access and unify cell-related information across publications, cell banks, cell registries, and databases and to ensure scientific reproducibility. We discuss the needs and requirements for such a unique identifier and implement a standard nomenclature for hPSCs, which can be automatically generated and registered by the ...


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