Identification of a Mitofusin specificity region that confers unique activities to Mfn1 and Mfn2.
Abstract Mitochondrial structure can be maintained at steady state or modified in response to changes in cellular physiology. This is achieved by the coordinated regulation of dynamic properties including mitochondrial fusion, division and transport. Disease states, including neurodegeneration, are associated with defects in these processes. In vertebrates, two Mitofusin paralogs, Mfn1 and Mfn2, are required for efficient mitochondrial fusion. The Mitofusins share a high degree of homology and have very similar domain architecture, including an amino terminal GTPase domain and two extended helical bundles that are...
Source: Mol Biol Cell - June 12, 2019 Category: Molecular Biology Authors: Sloat SR, Whitley BN, Engelhart EA, Hoppins S Tags: Mol Biol Cell Source Type: research

The Drosophila Afadin and ZO-1 homologs Canoe and Polychaetoid act in parallel to maintain epithelial integrity when challenged by adherens junction remodeling.
Abstract During morphogenesis cells must change shape and move without disrupting tissue integrity. This requires cell-cell junctions to allow dynamic remodeling while resisting force generated by the actomyosin cytoskeleton. Multiple proteins play roles in junctional-cytoskeletal linkage, but the mechanisms by which they act remain unclear. Drosophila Canoe maintains adherens junction-cytoskeletal linkage during gastrulation. Canoe's mammalian homolog Afadin plays similar roles in cultured cells, working in parallel with ZO-1 proteins, particularly at multicellular junctions. We took these insights back into the ...
Source: Mol Biol Cell - June 12, 2019 Category: Molecular Biology Authors: Manning LA, Perez-Vale KZ, Schaefer KN, Sewell MT, Peifer M Tags: Mol Biol Cell Source Type: research

Augmentation of CFTR function in human bronchial epithelial cells via SLC6A14-dependent amino acid uptake: Implications for treatment of Cystic Fibrosis.
CONCLUSION: SLC6A14-mediated L-arginine transport augments residual F508del-CFTR channel function via a non-canonical, NO pathway. This effect is enhanced with increasing pharmacological rescue of F508del-CFTR to the membrane. The current study demonstrates how endogenous pathways can be utilized for the development of companion therapy in CF. PMID: 31189070 [PubMed - as supplied by publisher] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 12, 2019 Category: Molecular Biology Authors: Ahmadi S, Wu YS, Li M, Ip W, Lloyd-Kuzik A, Di Paola M, Du K, Xia S, Lew A, Bozoky Z, Forman-Kay J, Bear CE, Gonska T Tags: Am J Respir Cell Mol Biol Source Type: research

Rapid evolution of gained essential developmental functions of a young gene via interactions with other essential genes.
Abstract New genes are of recent origin and only present in a subset of species in a phylogeny. Accumulated evidence suggests that new genes, like old genes that are conserved across species, can also take on important functions and be essential for the survival and reproductive success of organisms. While there are detailed analyses of the mechanisms underlying new genes' gaining fertility functions, how new genes rapidly become essential for viability remains unclear. We focused on a young retro-duplicated gene (CG7804, which we named Cocoon) in Drosophila that originated between 4-10 million years ago. We found...
Source: Mol Biol Cell - June 11, 2019 Category: Molecular Biology Authors: Lee YCG, Ventura IM, Rice GR, Chen DY, Colmenares SU, Long M Tags: Mol Biol Evol Source Type: research

Frontiers of Pluripotency.
Abstract Humans develop from a unique group of pluripotent cells in early embryos that can produce all cells of the human body. While pluripotency is only transiently manifest in the embryo, scientists have identified conditions that sustain pluripotency indefinitely in the laboratory. Pluripotency is not a monolithic entity, however, but rather comprises a spectrum of different cellular states. Questions regarding the scientific value of examining the continuum of pluripotent stem (PS) cell states have gained increased significance in light of attempts to generate interspecies chimeras between humans and animals....
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: De Los Angeles A Tags: Methods Mol Biol Source Type: research

Highly Efficient Derivation of Pluripotent Stem Cells from Mouse Preimplantation and Postimplantation Embryos in Serum-Free Conditions.
We describe generation of mouse naïve PS cells using LIF and inhibitors of MEK and GSK3 kinases and of mouse primed PS cells using FGF2 and IWR1 compound which induces the stabilization of Axin proteins. PMID: 31175643 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: De Los Angeles A, Okamura D, Wu J Tags: Methods Mol Biol Source Type: research

Derivation of Hematopoietic Stem and Progenitor Cells from Human Pluripotent Stem Cells.
Abstract Hematopoietic stem cell (HSC) transplantation is a curative treatment for hematologic malignancies and innate immunodeficiency, but its applications are limited to matched donors, and the availability of umbilical cord blood of immune types. Therefore, derivation of HSCs from patient-specific human induced pluripotent stem cells (hiPSCs) is a holy grail in regenerative medicine. However, derivation of HSCs from iPSCs has proven elusive. Here, the authors developed a method to derive hematopoietic stem and progenitor cells (HSPCs) by combining two established methods. The first method mimics embryonic deve...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Sugimura R Tags: Methods Mol Biol Source Type: research

Cancer Stem Cells: Concepts, Challenges, and Opportunities for Cancer Therapy.
Abstract Cancer stem cells (CSCs) are a subpopulation of cancer cells with self-renewal capacity, that fuel tumor growth and contribute to the heterogeneous nature of tumors. First identified in hematological malignancies, CSC populations have to date been proposed in solid tumors in various organs. In vitro and in vivo assays, mouse genetic models, and more recently single-cell sequencing technologies and other '-omics' methodologies have not only facilitated the identification of novel CSC populations but also revealed and clarified novel properties of CSCs. Increasingly, both cell-autonomous and CSC niche ...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Lee MY, Giraddi RR, Tam WL Tags: Methods Mol Biol Source Type: research

Informed Consent Issues for Cell Donors.
Abstract Stem cell-based chimera research depends on the free and voluntary provision of human biomaterials necessary for the derivation of pluripotent stem cell lines. Informed consent requirements for the procurement of human embryos, gametes, and somatic cells must take into account unique features of biomedical research involving the use of immortal cell lines that carry their donors' genetic information. The extent and basis for donors' rights, including the right to withdraw from research, are explored here in detail. PMID: 31175646 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Hyun I Tags: Methods Mol Biol Source Type: research

Chick Models and Human-Chick Organizer Grafts.
Abstract The combination of affordability, large size, and ease of access at almost every stage of development renders the chick an excellent model organism for studying vertebrate development. Not only is it a great system in and of itself, but these qualities make it a great host for interspecies chimera experiments. In this chapter we highlight some notable examples of mammalian-chick chimeras, and show how one can for instance use the chick to push mammalian stem cell experiments further to learn about the behavior and capabilities of these cells in vivo. In particular, here we present the methodology necessar...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Martyn I, Kanno TY, Brivanlou AH Tags: Methods Mol Biol Source Type: research

The Engraftment of Lentiviral Vector-Transduced Human CD34+ Cells into Humanized Mice.
Abstract Humanized mouse models have been developed to study human hematopoiesis and therapeutic application of hematopoietic stem cell transplantation. To evaluate the safety and efficacy of lentiviral vectors for gene therapy, human CD34+ cells have been transduced with lentiviral vectors and transplanted into the humanized mice. Recipient mice are monitored over time and sacrificed for bone marrow analyses with regard to human cell engraftment, lineage distribution, and vector transduction. This chapter details the procedure for lentiviral transduction and transplantation of human hematopoietic stem/progenitor ...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Kim YS, Wielgosz M, Ryu B Tags: Methods Mol Biol Source Type: research

Pig Chimeric Model with Human Pluripotent Stem Cells.
Abstract Interspecies chimera formation provides a unique platform for studying donor cell developmental potential, modeling disease in vivo, as well as in vivo production of tissues and organs. The derivation of human pluripotent stem cells (hPSC) from either human embryos or somatic cell reprogramming facilitates our understanding of human development, as well as accelerates our exploration of regenerative medicine for human health. Due to similar organ size, close anatomy, and physiology between pig and human, human-Pig interspecies chimeric model in which pig serves as the host species may open new avenues for...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Zhong C, Wu J, Izpisua Belmonte JC Tags: Methods Mol Biol Source Type: research

Embryonic Chimeras with Human Pluripotent Stem Cells.
We describe how to generate interspecies primate-mouse chimeras at the blastocyst and postimplantation embryo stages. Systematic evaluation of the chimeric competency of human and primate PS cells will aid in efforts to overcome species barriers and achieve higher grade chimerism in postimplantation conceptuses that could enable organ-specific enrichment of human xenogeneic PS cell derivatives in large animals such as pigs and sheep. PMID: 31175650 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: De Los Angeles A, Sakurai M, Wu J Tags: Methods Mol Biol Source Type: research

Neural Stem Cell Transplantation into a Mouse Model of Stroke.
Abstract Stroke is the fifth leading cause of death among Americans each year. Current standard-of-care treatment for stroke deploys intravenous tissue-type plasminogen activator (tPA), mechanical thrombolysis, or delivery of fibrinolytics. Although these therapies have reduced stroke-induced damage, therapeutic options still remain limited. Transplantation of patient-specific neural stem (NS) cells represents a promising strategy for the treatment of stroke. Basic science research has shown that transplanted NS cells can differentiate in the brain of rodent models of stroke and promote behavioral recovery. Clinic...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: De Los Angeles A Tags: Methods Mol Biol Source Type: research

Ethical Standards for Chimera Research Oversight.
Abstract Ethical standards for stem cell-based chimera research should build on current ethical standards for all animal research, adding stem cell-specific guidance only when necessary to address potential negative effects on animal welfare resulting from heavy biological modification. PMID: 31175652 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Hyun I Tags: Methods Mol Biol Source Type: research

Isolation, Cryopreservation, and Transplantation of Spermatogonial Stem Cells.
Abstract Spermatogonial stem cell (SSC) culture and transplantation pave the way for clinical restoration of fertility in male prepubertal cancer survivors. In this chapter we detail the steps for isolating and freezing testicular tissue along with protocols for the subsequent recovery from cryopreservation and transplantation of cells into a recipient testis. Transplantation of cultured or thawed SSCs provides not only a functional assay for identification of stem cells, a critical tool for the study of the germline stem cell niche in model organisms, but also a framework for reconstitution of spermatogenesis in ...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Sinha N, Whelan EC, Brinster RL Tags: Methods Mol Biol Source Type: research

Human-Monkey Chimeras for Modeling Human Disease: Opportunities and Challenges.
Abstract The search for a better animal model to simulate human disease has been a "holy grail" of biomedical research for decades. Recent identification of different types of pluripotent stem cells (PS cells) and advances in chimera research might soon permit the generation of interspecies chimeras from closely related species, such as those between humans and other primates. Here, we suggest that the creation of human-primate chimeras-specifically, the transfer of human stem cells into (non-ape) primate hosts-could surpass the limitations of current monkey models of neurological and psychiatric disease...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: De Los Angeles A, Hyun I, Latham SR, Elsworth JD, Redmond DE Tags: Methods Mol Biol Source Type: research

Mouse Models of Yersiniosis.
Abstract Yersiniosis is common foodborne gastrointestinal disease caused by the enteric pathogens Yersinia enterocolitica and Yersinia pseudotuberculosis. The mouse model of oral infection serves as a useful tool to study enteropathogenic Yersinia infection in mammals. The following protocol describes two distinct oral infection methods: the commonly used oral gavage method in which the bacterial inoculum is instilled directly into the mouse stomach using a feeding needle, and an alternative method in which mice are fed bread soaked with Yersinia culture. PMID: 31177430 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Hooker-Romero D, Schwiesow L, Wei Y, Auerbuch V Tags: Methods Mol Biol Source Type: research

Intravital Confocal Microscopy of Dermal Innate Immune Responses to Flea-Transmitted Yersinia pestis.
Abstract The technique known as intravital microscopy (IVM), when used in conjunction with transgenic mice expressing fluorescent proteins in various cell populations, is a powerful tool with the potential to provide new insights into host-pathogen interactions in infectious disease pathogenesis in vivo. Yersinia pestis, the causative agent of plague, is typically deposited in a host's skin during feeding of an infected flea. IVM has been used to characterize the innate immune response to Y. pestis in the skin and identify differences between the responses to needle-inoculated and flea-transmitted bacteria that wo...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Shannon JG, Hinnebusch BJ Tags: Methods Mol Biol Source Type: research

Detection of Cells Translocated with Yersinia Yops in Infected Tissues Using β-Lactamase Fusions.
Detection of Cells Translocated with Yersinia Yops in Infected Tissues Using β-Lactamase Fusions. Methods Mol Biol. 2019;2010:117-139 Authors: Nguyen GT, McCabe AL, Fasciano AC, Mecsas J Abstract Development of the TEM-CCF2/4-AM FRET-based system has enabled investigators to track translocation of effector proteins into mammalian cells during infection. This allows for separation of translocated and non-translocated cell populations for further study. Yersinia strains expressing translational Yop-TEM fusions, containing the secretion and translocation signals of a Yop with the TEM-1 portion of &b...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Nguyen GT, McCabe AL, Fasciano AC, Mecsas J Tags: Methods Mol Biol Source Type: research

Drosophila as a Model for Understanding the Insect Host of Yersinia pestis.
Abstract With the limited availability of genomic sequence information and no established methods for genetic knockdowns or the creation of transgenic fleas and flea cell lines, we have adopted Drosophila melanogaster as a model for the study of the insect life cycle of Yersinia pestis. Infection of Drosophila larvae can be used to model early colonization of fleas, while the established embryonic cell lines can be used to model insect-pathogen interactions that underlie the unique capacity of Y. pestis to colonize the gut of its flea host. In this chapter, we present the methods we developed for infection of Dros...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Ludlow AB, Pauling CD, Marketon MM, Anderson DM Tags: Methods Mol Biol Source Type: research

Intracellular Assays to Monitor Survival and Growth of Yersinia pestis Within Macrophages.
Abstract Yersinia pestis is able to survive and replicate within macrophages, while also being able to live in the extracellular milieu of the host. Assays that facilitate better understanding of how Y. pestis survives intracellularly and subverts normal host antimicrobial defenses require the ability to monitor intracellular Y. pestis survival and replication. In this chapter three different assays for monitoring intracellular survival and replication will be described, along with the formulas and methods to quantify and present the acquired data. These assays are fundamental to answering a multitude of questions...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Pulsifer AR, VanCleave TT, Lawrenz MB Tags: Methods Mol Biol Source Type: research

Human Neutrophil Isolation and Degranulation Responses to Yersinia pestis Infection.
We describe a cell culture model for the infection of human neutrophils with Y. pestis. Neutrophils are isolated from human peripheral blood at high purity and subsequently infected with Y. pestis. We specifically focus on the application of this in vitro infection assay to the analysis of neutrophil degranulation responses. PMID: 31177440 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Eichelberger KR, Goldman WE Tags: Methods Mol Biol Source Type: research

Measurement of Yersinia Translocon Pore Formation in Erythrocytes.
Abstract Many Gram-negative pathogens produce a type III secretion system capable of intoxicating eukaryotic cells with immune-modulating effector proteins. Fundamental to this injection process is the prior secretion of two translocator proteins destined for injectisome translocon pore assembly within the host cell plasma membrane. It is through this pore that effectors are believed to travel to gain access to the host cell interior. Yersinia species especially pathogenic to humans and animals assemble this translocon pore utilizing two hydrophobic translocator proteins-YopB and YopD. Although a full molecular un...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Costa TRD, Francis MK, Farag SI, Edgren T, Francis MS Tags: Methods Mol Biol Source Type: research

Analysis of Inflammasome Activation in Response to Yersinia Infection by Fluorescence Microscopy Detection of Active Caspase-1 Puncta.
Abstract The type of cell death triggered by a particular environmental stimulus influences the outcome of infection or inflammatory disease processes. The ability to identify the cell death pathway that is activated in response to infection is essential for understanding the pathogenesis and host response to infection. Activation of the cysteine protease caspase-1 in various inflammasome complexes indicates that cells are undergoing pyroptosis, a regulated, proinflammatory cell death. Inflammasome assembly and caspase activation can be measured by various methods ranging from detection of inflammasome-dependent c...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Zwack EE, Brodsky IE Tags: Methods Mol Biol Source Type: research

Methods for Detection of Pyrin Inflammasome Assembly in Macrophages Infected with Yersinia spp.
Abstract The Yersinia effector proteins YopE and YopT are important bacterial virulence factors that are secreted into infected host cells and can inactivate Rho GTPases, like RhoA, Rac1, and Cdc42. In order to compensate for the consequences of this effect, the host cell can sense RhoA modifications and trigger a proinflammatory reaction to control the infection. This host response, known as pyrin inflammasome assembly, is normally prevented by another important effector, YopM, allowing Yersinia to counteract this conserved innate immune response. Once assembled, the pyrin inflammasome can activate caspase-1 via ...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Medici NP, Bliska JB Tags: Methods Mol Biol Source Type: research

T Cell: Primary Culture from Peripheral Blood.
Abstract Peripheral blood mononuclear cells (PBMCs) can be used to assess cell-mediated immunity in general or via antigen-specific stimulation to detect previous exposure to a variety of antigens/allergens and to monitor the response to immunotherapies. Peripheral blood is the most common source of mononuclear cells for in vitro cultures, although mononuclear cells can be obtained from other sources involved in the allergic reaction. PBMCs from individuals previously exposed to an antigen proliferate in vitro when stimulated with the specific antigen. Proliferation is measured by the incorporation of (3H)-thymidi...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Raulf M Tags: Methods Mol Biol Source Type: research

Measurement of Allergen-Specific Inhibitory Antibody Activity.
Abstract Specific allergen immunotherapy (AIT) is an effective treatment for IgE-mediated allergic diseases and involves T- and B-cell-mediated events. IgE receptors on the surface of antigen-presenting cells facilitate the presentation of allergens in the presence of specific IgE antibody resulting in T-cell activation. Interference with these IgE-dependent mechanisms by "blocking" IgG antibodies suppresses pro-inflammatory Th2 cell responses and manifests as a reduction in allergic responses in vivo.In vitro assays used to measure the inhibition of binding of allergen-IgE complexes have previously util...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Shamji MH, Francis JN Tags: Methods Mol Biol Source Type: research

Monocyte-Derived Dendritic Cells as Antigen-Presenting Cells in T-Cell Proliferation and Cytokine Production.
Abstract Dendritic cells (DC) are the most potent antigen-presenting cells that link innate with adaptive immunity. They circulate the body and sample the microenvironments for maintaining homeostasis and for mounting T-cell responses against invading pathogens, foreign antigens, and aberrant self-proteins. In humans, DC derived from blood monocytes (MDC) by cytokine treatment provide the most abundant and versatile source for studying DC and T-cell biology, and for use as adjuvants in cancer therapy. In asthma patients, T-cell functions are studied by using autologous MDC as accessory cells for allergen presentat...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Sung SJ Tags: Methods Mol Biol Source Type: research

The Use of Dual-Cell-Tracker Dye Staining for the Identification and Characterization of Peanut-Specific T-Cell Subsets.
Abstract Cell-tracker fluorescent dye labeling is widely used for investigating antigen-specific immune responses in vitro and in vivo. Here we describe a development of this technique-the use of dual-cell-tracker dye staining for the identification and characterization of the responses of different T-cell subsets to peanut proteins in vitro. PMID: 31177497 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Dunsterville C, Stephens AC, Lack G, Turcanu V Tags: Methods Mol Biol Source Type: research

The Use of pMHCII Tetramer Technology for the Identification and Characterization of CD4+ T Cells.
Abstract Understanding the mechanism underlying allergic disease is dependent upon definition of the heterogeneity and complexity of the cellular immune response toward allergens both in the context of disease and clinical intervention. Among all components of the immune system, CD4+ T cells play a key role in the orchestration of immune response toward allergen and have become a dynamic area of research. Because of their unique ability to identify antigen-specific CD4+ T cells irrespective of functional outputs, fluorescently labeled peptide-MHC class II (pMHCII) tetramers in combination with multiparameter flow ...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Wambre E Tags: Methods Mol Biol Source Type: research

Isolation and Characterization of Lymphocytes from Human Mucosal Biopsies.
Abstract The important role of the local mucosal environment in both the initiation and progression of allergic disease is well established. Analysis of tissue-resident lymphocyte subsets by flow cytometry requires isolation of viable cells from mucosal samples.Here we describe an advanced method to dissociate lymphocytes from human mucosal (e.g., nasal, bronchial) biopsies. Single-cell suspensions are obtained through a combination of gentle mechanical disruption and incubation of tissue with proteolytic enzymes. This method fully utilizes limited clinical samples and is amenable to a variety of downstream applic...
Source: Mol Biol Cell - June 10, 2019 Category: Molecular Biology Authors: Upton NEG, Hayday TS, James LK Tags: Methods Mol Biol Source Type: research

Isolation of Competitive Phage Display-Modified Bacteriophage T4 with Affinity Chromatography.
Abstract Phage recovery from various solutions, including physiological samples, as well as phage purification from crude lysates often requires a specific isolation method. Here, we demonstrate that T4-like phages can be efficiently isolated by affinity chromatography. This approach employs specific affinity tags (GST (glutathione S-transferase) or His-tag) that allow for the isolation of the phage. These affinity tags are exposed on the phage head using phage display. By combining competitive phage display and affinity chromatography, wild-type phages can be specifically recovered from mixtures with other phage/...
Source: Mol Biol Cell - June 9, 2019 Category: Molecular Biology Authors: Dąbrowska K Tags: Methods Mol Biol Source Type: research

Mol Biol Cell; +174 new citations
174 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: Mol Biol Cell These pubmed results were generated on 2019/06/07PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 8, 2019 Category: Molecular Biology Tags: Report Source Type: research

Mol Biol Cell; +136 new citations
136 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: Mol Biol Cell These pubmed results were generated on 2019/06/06PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 6, 2019 Category: Molecular Biology Tags: Report Source Type: research

Mol Biol Cell; +114 new citations
114 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: Mol Biol Cell These pubmed results were generated on 2019/06/05PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites. (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 5, 2019 Category: Molecular Biology Tags: Report Source Type: research

Building Portable and Reproducible Cancer Informatics Workflows: An RNA Sequencing Case Study.
Abstract The Seven Bridges Cancer Genomics Cloud (CGC) is part of the National Cancer Institute Cloud Resource project, which was created to explore the paradigm of co-locating massive datasets with the computational resources to analyze them. The CGC was designed to allow researchers to easily find the data they need and analyze it with robust applications in a scalable and reproducible fashion. To enable this, individual tools are packaged within Docker containers and described by the Common Workflow Language (CWL), an emerging standard for enabling reproducible data analysis. On the CGC, researchers can de...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Kaushik G, Davis-Dusenbery B Tags: Methods Mol Biol Source Type: research

Predictive Modeling of Anti-Cancer Drug Sensitivity from Genetic Characterizations.
Abstract Accurately predicting sensitivity of tumor cells to anti-cancer drugs based on genetic characterizations is a significant challenge for personalized cancer therapy. This chapter provides a computational procedure to design predictive models from individual genomic characterizations and combine them to arrive at an integrated predictive model. Integrated modeling employs the complementary information from heterogeneous genetic characterizations to improve the prediction error as well as lowering the error confidence interval. PMID: 30378080 [PubMed - indexed for MEDLINE] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Rahman R, Pal R Tags: Methods Mol Biol Source Type: research

Modeling Growth of Tumors and Their Spreading Behavior Using Mathematical Functions.
Abstract Computer simulations of the spread of malignant tumor cells in an entire organism provide important insights into the mechanisms of metastatic progression. Key elements for the usefulness of these models are the adequate selection of appropriate mathematical models describing the tumor growth and its parametrization as well as a proper choice of the fractal dimension of the blood vessels in the primary tumor. In addition, survival in the bloodstream and evasion into the connective spaces of the target organ of the future metastasis have to be modeled. Determination of these from experimental models is com...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Hoffmann B, Frenzel T, Schmitz R, Schumacher U, Wedemann G Tags: Methods Mol Biol Source Type: research

Overview of BCL-2 Family Proteins and Therapeutic Potentials.
Abstract BCL-2 family proteins interact in a network that regulates apoptosis. The BH3 amino acid sequence motif serves to bind together this conglomerate protein family, both literally and figuratively. BH3 motifs are present in antiapoptotic and proapoptotic BCL-2 homologs, and in a separate group of unrelated BH3-only proteins often appended to the BCL-2 family. BH3-containing helices mediate many of their physical interactions to determine cell death versus survival, leading to the development of BH3 mimetics as therapeutics. Here we provide an overview of BCL-2 family interactions, their relevance in health a...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Huska JD, Lamb HM, Hardwick JM Tags: Methods Mol Biol Source Type: research

Database and Bioinformatic Analysis of BCL-2 Family Proteins and BH3-Only Proteins.
Abstract BCL-2 proteins correspond to a structurally, functionally, and phylogenetically heterogeneous group of regulators that play crucial roles in the life and death of animal cells. Some of these regulators also represent therapeutic targets in human diseases including cancer. In the omics era, there is great need for easy data retrieval and fast analysis of the molecular players involved in cell death. In this chapter, we present generic and specific computational resources (such as the reference database BCL2DB) as well as bioinformatics tools that can be used to investigate BCL-2 homologs and BH3-only prote...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Aouacheria A, Navratil V, Combet C Tags: Methods Mol Biol Source Type: research

Application of Mito-Priming to Generate BCL-2 Addicted Cells.
Abstract The majority of apoptotic stimuli trigger cell death through the mitochondrial pathway of apoptosis. Invariably, mitochondrial apoptosis requires engagement of mitochondrial outer membrane permeabilization or MOMP to initiate cell death. We have developed a new method, called mito-priming, that allows for rapid and synchronous induction of mitochondrial apoptosis in an on-target manner. Mito-priming uses coexpression of pro- and antiapoptotic Bcl-2 proteins to render cells sensitive to the addition of Bcl-2 targeting BH3-mimetic drugs. This chapter describes how to design mito-priming constructs and apply...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Lopez J, Tait SWG Tags: Methods Mol Biol Source Type: research

BH3 Profiling: A Functional Assay to Measure Apoptotic Priming and Dependencies.
Abstract Apoptosis (programmed cell death) is activated by a wide variety of cellular stresses or insults and is vital for proper mammalian development as well as the maintenance of organismal homeostasis. The apoptosis pathway is also engaged by many common types of anticancer therapies and ionizing radiation, which contributes to the regressions of tumors or the toxic side effects of treatment. Due to the importance of maintaining healthy cell survival or the efficient clearance of cancer cells, the BH3 profiling assay was developed to functionally measure the state of the apoptosis pathway in any given cells. T...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Fraser C, Ryan J, Sarosiek K Tags: Methods Mol Biol Source Type: research

Flow Cytometry-Based Detection and Analysis of BCL-2 Family Proteins and Mitochondrial Outer Membrane Permeabilization (MOMP).
Abstract The BCL-2 family of proteins orchestrates a complex signaling network that governs the balance between cellular survival and death. A comprehensive understanding of the mechanistic interactions between these proteins continues to evolve in normal and malignant cells. The functional variation by individual BCL-2 proteins in different cell types has driven clinical therapeutic development in targeting individual BCL-2 members with the goal of fine-tuning cell death in diseased cells. Given the importance of understanding and validating the effect of activating or inhibiting BCL-2 protein interactions in ind...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Ludwig LM, Maxcy KL, LaBelle JL Tags: Methods Mol Biol Source Type: research

Liposomal Permeabilization Assay to Study the Functional Interactions of the BCL-2 Family.
Abstract Apoptosis, a form of programmed cell death that is important for development and homeostasis, is regulated by the BCL-2 family of proteins. Over twenty BCL-2 family members have been classified in three groups based on structural homology and function. The multidomain antiapoptotic proteins promote survival, whereas the multidomain and the BH3-only proapoptotic members induce cell death. Because the interaction among the BCL-2 family members occurs primarily at the mitochondrial outer membrane, biochemical assays using artificial liposomes have been developed to study the functional relationship between t...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Reyna DE, Gavathiotis E Tags: Methods Mol Biol Source Type: research

Assessment of Dynamic BCL-2 Protein Shuttling Between Outer Mitochondrial Membrane and Cytosol.
Abstract BCL-2 proteins control stress-dependent commitment to the programmed cell death apoptosis. In nonapoptotic cells the proapoptotic BCL-2 proteins BAX and BAK but also prosurvival family members, like BCL-xL or MCL-1, translocate to the outer mitochondrial membrane (OMM) and retrotranslocate from the mitochondria back into the cytosol. The resulting equilibrium produces a broad range of localization pattern observed for BAX and BAK in human cells and shows correlation between relative BAX and BAK localizations and cellular predisposition to apoptosis. The retrotranslocation of BCL-2 proteins from the OMM ca...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Lauterwasser J, Fimm-Todt F, Edlich F Tags: Methods Mol Biol Source Type: research

Quantification of BCL-2 Family Members by Flow Cytometry.
Abstract Flow cytometry is a powerful technique for the detection and quantification of cell surface and intracellular proteins. It enables the ability to measure the expression levels of specific proteins in a cell population of interest without the need to physically separate out the cells from within a heterogeneous population by using the appropriate cell-specific markers. It also requires fewer cells than other traditional techniques such as Western blotting. Here we describe a robust and reproducible method to measure the expression levels of the BCL-2 family members, BCL-2, BCL-XL, and MCL-1 by quantitative...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Smith ML, Tahir SK Tags: Methods Mol Biol Source Type: research

Methods to Probe Conformational Activation and Mitochondrial Activity of Proapoptotic BAK.
We describe methods to purify mitochondria for MOMP assays and to detect conformational changes in native BAK associated with MOMP by using limited proteolysis and cross-linking analyses. PMID: 30536007 [PubMed - indexed for MEDLINE] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Singh G, Moldoveanu T Tags: Methods Mol Biol Source Type: research

Probing BAK and BAX Activation and Pore Assembly with Cytochrome c Release, Limited Proteolysis, and Oxidant-Induced Linkage.
Abstract Mitochondrial permeabilization is a key event in the intrinsic pathway of apoptosis, and is mediated by either of the BCL-2 family members BAK or BAX. These two proteins generate pores in the mitochondrial outer membrane that release factors such as cytochrome c into the cytosol to trigger caspase activation and apoptotic cell death. To generate pores, BAK and BAX undergo major changes including BAX translocation to the outer membrane, and partial unfolding, dimerization, and oligomerization. Here we describe biochemical protocols that can be used on most cell types to gain a population overview of BAK an...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Iyer S, Uren RT, Kluck RM Tags: Methods Mol Biol Source Type: research

BCL-2 Protein Family Interaction Analysis by Nuclear Magnetic Resonance Spectroscopy.
Abstract Biomolecular nuclear magnetic resonance (NMR) is a powerful and versatile method for studying both protein-protein interactions (PPIs) and protein-small molecule binding. NMR has been used extensively in the investigation of BCL-2 family proteins revealing the structure of key family members, identifying binding partners and interaction sites, and screening small molecule modulators. In this chapter we discuss the application of NMR to identify interaction sites and structure determination of protein-protein and protein-small molecule complexes using two examples. PMID: 30536009 [PubMed - indexed for...
Source: Mol Biol Cell - June 3, 2019 Category: Molecular Biology Authors: Garner TP, Gavathiotis E Tags: Methods Mol Biol Source Type: research