Other search tools

About this data

The publication data currently available has been vetted by Vanderbilt faculty, staff, administrators and trainees. The data itself is retrieved directly from NCBI's PubMed and is automatically updated on a weekly basis to ensure accuracy and completeness.

If you have any questions or comments, please contact us.

Results: 1 to 10 of 40

Publication Record


The human body at cellular resolution: the NIH Human Biomolecular Atlas Program.
HuBMAP Consortium
(2019) Nature 574: 187-192
MeSH Terms: Aging, Atlases as Topic, Biomedical Research, Female, Health, Humans, International Cooperation, Male, Models, Anatomic, Molecular Biology, National Institutes of Health (U.S.), Organ Specificity, Single-Cell Analysis, United States
Show Abstract · Added January 22, 2020
Transformative technologies are enabling the construction of three-dimensional maps of tissues with unprecedented spatial and molecular resolution. Over the next seven years, the NIH Common Fund Human Biomolecular Atlas Program (HuBMAP) intends to develop a widely accessible framework for comprehensively mapping the human body at single-cell resolution by supporting technology development, data acquisition, and detailed spatial mapping. HuBMAP will integrate its efforts with other funding agencies, programs, consortia, and the biomedical research community at large towards the shared vision of a comprehensive, accessible three-dimensional molecular and cellular atlas of the human body, in health and under various disease conditions.
0 Communities
1 Members
0 Resources
MeSH Terms
Reconstitution of the Cytoplasmic Regulation of the Wnt Signaling Pathway Using Xenopus Egg Extracts.
Hyde AS, Hang BI, Lee E
(2016) Methods Mol Biol 1481: 101-9
MeSH Terms: Animals, Cell Cycle, Chromatin Assembly and Disassembly, DNA Replication, Embryonic Development, Microtubules, Molecular Biology, Oocytes, Proteolysis, Wnt Proteins, Wnt Signaling Pathway, Xenopus laevis, beta Catenin
Show Abstract · Added February 13, 2017
The regulation of β-catenin turnover is the central mechanism governing activation of the Wnt signaling pathway. All components of the pathway are present in the early embryo of Xenopus laevis, and Xenopus egg extracts have been used to recapitulate complex biological reactions such as microtubule dynamics, DNA replication, chromatin assembly, and phases of the cell cycle. Herein, we describe a biochemical method for analyzing β-catenin degradation using radiolabeled and luciferase-fusion proteins in Xenopus egg extracts. We show that in such a biochemical system, cytoplasmic β-catenin degradation is regulated by soluble components of the Wnt pathway as well as small molecules.
0 Communities
1 Members
0 Resources
13 MeSH Terms
An unbiased metric of antiproliferative drug effect in vitro.
Harris LA, Frick PL, Garbett SP, Hardeman KN, Paudel BB, Lopez CF, Quaranta V, Tyson DR
(2016) Nat Methods 13: 497-500
MeSH Terms: Cell Line, Tumor, Cell Proliferation, Computer Simulation, Dose-Response Relationship, Drug, Drug Discovery, Humans, Microscopy, Fluorescence, Models, Theoretical, Molecular Biology, Sensitivity and Specificity, Small Molecule Libraries, Time Factors
Show Abstract · Added May 3, 2016
In vitro cell proliferation assays are widely used in pharmacology, molecular biology, and drug discovery. Using theoretical modeling and experimentation, we show that current metrics of antiproliferative small molecule effect suffer from time-dependent bias, leading to inaccurate assessments of parameters such as drug potency and efficacy. We propose the drug-induced proliferation (DIP) rate, the slope of the line on a plot of cell population doublings versus time, as an alternative, time-independent metric.
2 Communities
4 Members
0 Resources
12 MeSH Terms
Epidermis-Derived Semaphorin Promotes Dendrite Self-Avoidance by Regulating Dendrite-Substrate Adhesion in Drosophila Sensory Neurons.
Meltzer S, Yadav S, Lee J, Soba P, Younger SH, Jin P, Zhang W, Parrish J, Jan LY, Jan YN
(2016) Neuron 89: 741-55
MeSH Terms: Animals, Animals, Genetically Modified, Cell Communication, Dendrites, Drosophila, Drosophila Proteins, Epidermis, Focal Adhesion Kinase 1, Gene Expression Regulation, Developmental, Green Fluorescent Proteins, Immunoprecipitation, Larva, Mechanistic Target of Rapamycin Complex 2, Molecular Biology, Multiprotein Complexes, Mutation, Nerve Tissue Proteins, Receptors, Cell Surface, Semaphorins, Sensory Receptor Cells, TOR Serine-Threonine Kinases, Transfection
Show Abstract · Added February 9, 2016
Precise patterning of dendritic arbors is critical for the wiring and function of neural circuits. Dendrite-extracellular matrix (ECM) adhesion ensures that the dendrites of Drosophila dendritic arborization (da) sensory neurons are properly restricted in a 2D space, and thereby facilitates contact-mediated dendritic self-avoidance and tiling. However, the mechanisms regulating dendrite-ECM adhesion in vivo are poorly understood. Here, we show that mutations in the semaphorin ligand sema-2b lead to a dramatic increase in self-crossing of dendrites due to defects in dendrite-ECM adhesion, resulting in a failure to confine dendrites to a 2D plane. Furthermore, we find that Sema-2b is secreted from the epidermis and signals through the Plexin B receptor in neighboring neurons. Importantly, we find that Sema-2b/PlexB genetically and physically interacts with TORC2 complex, Tricornered (Trc) kinase, and integrins. These results reveal a novel role for semaphorins in dendrite patterning and illustrate how epidermal-derived cues regulate neural circuit assembly.
Copyright © 2016 Elsevier Inc. All rights reserved.
1 Communities
0 Members
0 Resources
22 MeSH Terms
Small Cell Lung Cancer: Can Recent Advances in Biology and Molecular Biology Be Translated into Improved Outcomes?
Bunn PA, Minna JD, Augustyn A, Gazdar AF, Ouadah Y, Krasnow MA, Berns A, Brambilla E, Rekhtman N, Massion PP, Niederst M, Peifer M, Yokota J, Govindan R, Poirier JT, Byers LA, Wynes MW, McFadden DG, MacPherson D, Hann CL, Farago AF, Dive C, Teicher BA, Peacock CD, Johnson JE, Cobb MH, Wendel HG, Spigel D, Sage J, Yang P, Pietanza MC, Krug LM, Heymach J, Ujhazy P, Zhou C, Goto K, Dowlati A, Christensen CL, Park K, Einhorn LH, Edelman MJ, Giaccone G, Gerber DE, Salgia R, Owonikoko T, Malik S, Karachaliou N, Gandara DR, Slotman BJ, Blackhall F, Goss G, Thomas R, Rudin CM, Hirsch FR
(2016) J Thorac Oncol 11: 453-74
MeSH Terms: Animals, Humans, Lung Neoplasms, Molecular Biology, Small Cell Lung Carcinoma
Added February 16, 2016
0 Communities
1 Members
0 Resources
5 MeSH Terms
Biology coming full circle: joining the whole and the parts.
Wikswo JP, Porter AP
(2015) Exp Biol Med (Maywood) 240: 3-7
MeSH Terms: Animals, Humans, Molecular Biology, Systems Biology
Show Abstract · Added February 2, 2015
The new cover of Experimental Biology and Medicine features the hermeneutic circle of biology, a concept we have adapted from the hermeneutic principle that one understands the whole only in terms of each part and the parts only in terms of the whole. Our hermeneutic circle summarizes the course of experimental biology through 2500 years of the achievements of reductionist research (understanding the parts), which culminates in our ability to rapidly sequence the genome. Rather than returning along the same path in a constructionist approach that simply builds upon this knowledge, but in reverse, an alternative is to close the circle with synthetic constructions that seek to integrate the full complexity of biological and physiological systems (understanding the whole), of which organs-on-chips are one example. This closing of the circle cannot be a comprehensively accurate representation of biology, but it can be a synthetic one that effectively defines particular biological subsystems. The illustration of the hermeneutic circle of biology is also intended to suggest both the multiple cycles that may be required to reach such a synthesis and the expansion of the circle in an outward spiral as knowledge increases. Our commentary explains the symbolism of the new cover in a philosophical and scientific discussion.
© The Author(s) 2015 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.
1 Communities
2 Members
0 Resources
4 MeSH Terms
Control of gene expression in Helicobacter pylori using the Tet repressor.
McClain MS, Duncan SS, Gaddy JA, Cover TL
(2013) J Microbiol Methods 95: 336-41
MeSH Terms: Bacterial Proteins, Blotting, Western, Gene Expression Regulation, Bacterial, Genetics, Microbial, Helicobacter pylori, Molecular Biology, Operator Regions, Genetic, Recombination, Genetic, Repressor Proteins, Tetracyclines, Transcriptional Activation
Show Abstract · Added January 13, 2014
The lack of a versatile system to control gene expression in Helicobacter pylori has hampered efforts to study H. pylori physiology and pathogenesis. To overcome these limitations, we evaluated the utility of an inducible system based on the well-characterized Tet repressor (TetR) and Tet operator (tetO). As validation of this system, we introduced three copies of tetO into the promoter region upstream of the cagUT operon (encoding two virulence factors required for function of the H. pylori Cag type IV secretion system) and expressed tetR by introducing a codon-optimized gene into the chromosomal ureA locus. Introduction of the tetO copies upstream of cagUT did not disrupt promoter activity, as determined by immunoblotting for CagT. The subsequent introduction of tetR, however, did repress CagT synthesis. Production of CagT was restored when strains were cultured in the presence of the inducer, anhydrotetracycline. To demonstrate one potential application of this new tool, we analyzed the function of the Cag type IV secretion system. When the modified H. pylori strains were co-cultured with AGS cells, activity of the Cag type IV secretion system was dependent on the presence of anhydrotetracycline as evidenced by inducer-dependent induction of IL-8 secretion, CagA translocation, and appearance of type IV secretion system pili at the bacteria-host interface. These studies demonstrate the effectiveness of the tetR-tetO system to control gene expression in H. pylori and provide an improved system for studying H. pylori physiology and pathogenesis.
© 2013.
1 Communities
3 Members
0 Resources
11 MeSH Terms
Synthetic and tissue-derived models for studying rigidity effects on invadopodia activity.
Weaver AM, Page JM, Guelcher SA, Parekh A
(2013) Methods Mol Biol 1046: 171-89
MeSH Terms: Actins, Cell Line, Tumor, Extracellular Matrix, Humans, Molecular Biology, Neoplasm Metastasis, Neoplasms, Peptide Hydrolases, Proteolysis, Substrate Specificity
Show Abstract · Added March 10, 2014
Invasion by cancer cells through the extracellular matrix (ECM) of tissues is a critical step in cancer progression and metastasis. Actin-rich subcellular protrusions known as invadopodia are thought to facilitate this process by localizing proteinases which degrade the ECM and allow for cancer cell penetration. We have shown in vitro that invadopodia activity is regulated by the rigidity of the ECM, which suggests that matrix remodeling in vivo may also be regulated by the mechanical properties of tissues. In order to study rigidity effects on invadopodia activity in a controlled manner, we have developed assays in which we have conjugated degradable fluorescent matrix molecules to tunable synthetic substrates. In addition, we have also utilized ex vivo tissue-derived substrates to corroborate our findings. In this chapter, we present detailed protocols describing the synthesis and preparation of our synthetic substrates, polyacrylamide gels and polyurethane elastomers, for use in these matrix degradation assays as well as the steps required to utilize our tissue-derived substrates.
2 Communities
3 Members
0 Resources
10 MeSH Terms
New trends in cytochrome p450 research at the half-century mark.
Guengerich FP
(2013) J Biol Chem 288: 17063-4
MeSH Terms: Animals, Biomedical Research, Cytochrome P-450 Enzyme System, Humans, Inactivation, Metabolic, Molecular Biology, Oxidation-Reduction, Steroids
Show Abstract · Added March 7, 2014
Cytochrome P450 enzymes have major roles in the metabolism of steroids, drugs, carcinogens, eicosanoids, and numerous other chemicals. The P450s are collectively considered the most diverse catalysts known in biochemistry, although they operate from a basic structural fold and catalytic mechanism. The four minireviews in this thematic series deal with the unusual aspects of catalytic reactions and electron transfer pathway organization, the structural diversity of P450s, and the expanding roles of P450s in disease and medicine.
0 Communities
1 Members
0 Resources
8 MeSH Terms
Molecular determinants of lung development.
Morrisey EE, Cardoso WV, Lane RH, Rabinovitch M, Abman SH, Ai X, Albertine KH, Bland RD, Chapman HA, Checkley W, Epstein JA, Kintner CR, Kumar M, Minoo P, Mariani TJ, McDonald DM, Mukouyama YS, Prince LS, Reese J, Rossant J, Shi W, Sun X, Werb Z, Whitsett JA, Gail D, Blaisdell CJ, Lin QS
(2013) Ann Am Thorac Soc 10: S12-6
MeSH Terms: Biomedical Research, Cell Differentiation, Humans, Lung, Molecular Biology, Morphogenesis
Show Abstract · Added May 26, 2015
Development of the pulmonary system is essential for terrestrial life. The molecular pathways that regulate this complex process are beginning to be defined, and such knowledge is critical to our understanding of congenital and acquired lung diseases. A recent workshop was convened by the National Heart, Lung, and Blood Institute to discuss the developmental principles that regulate the formation of the pulmonary system. Emerging evidence suggests that key developmental pathways not only regulate proper formation of the pulmonary system but are also reactivated upon postnatal injury and repair and in the pathogenesis of human lung diseases. Molecular understanding of early lung development has also led to new advances in areas such as generation of lung epithelium from pluripotent stem cells. The workshop was organized into four different topics, including early lung cell fate and morphogenesis, mechanisms of lung cell differentiation, tissue interactions in lung development, and environmental impact on early lung development. Critical points were raised, including the importance of epigenetic regulation of lung gene expression, the dearth of knowledge on important mesenchymal lineages within the lung, and the interaction between the developing pulmonary and cardiovascular system. This manuscript describes the summary of the discussion along with general recommendations to overcome the gaps in knowledge in lung developmental biology.
0 Communities
1 Members
0 Resources
6 MeSH Terms