599 research outputs found
Mars Sample Return: The Value of Depth Profiles
Sample return from Mars offers the promise of data from Martian materials that have previously only been available from meteorites. Return of carefully selected samples may yield more information about the history of water and possible habitability through Martian history. Here we propose that samples collected from Mars should include depth profiles of material across the interface between weathered material on the surface of Mars into unweathered parent rock material. Such profiles have the potential to yield chemical kinetic data that can be used to estimate the duration of water and information about potential habitats on Mars
Variable Curvature Slab Molecular Dynamics as a Method to Determine Surface Stress
A thin plate or slab, prepared so that opposite faces have different surface
stresses, will bend as a result of the stress difference. We have developed a
classical molecular dynamics (MD) formulation where (similar in spirit to
constant-pressure MD) the curvature of the slab enters as an additional
dynamical degree of freedom. The equations of motion of the atoms have been
modified according to a variable metric, and an additional equation of motion
for the curvature is introduced. We demonstrate the method to Au surfaces, both
clean and covered with Pb adsorbates, using many-body glue potentials.
Applications to stepped surfaces, deconstruction and other surface phenomena
are under study.Comment: 16 pages, 8 figures, REVTeX, submitted to Physical Review
Eph receptors in breast cancer: roles in tumor promotion and tumor suppression
Eph receptor tyrosine kinase signaling regulates cancer initiation and metastatic progression through multiple mechanisms. Studies of tumor-cell-autonomous effects of Eph receptors demonstrate their dual roles in tumor suppression and tumor promotion. In addition, Eph molecules function in the tumor microenvironment, such as in vascular endothelial cells, influencing the ability of these molecules to promote carcinoma progression and metastasis. The complex nature of Eph receptor signaling and crosstalk with other receptor tyrosine kinases presents a unique challenge and an opportunity to develop therapeutic intervention strategies for targeting breast cancer
Eph/Ephrin Profiling in Human Breast Cancer Reveals Significant Associations between Expression Level and Clinical Outcome
Pre-clinical studies provide compelling evidence that Eph family receptor tyrosine kinases (RTKs) and ligands promote cancer growth, neovascularization, invasion, and metastasis. Tumor suppressive roles have also been reported for the receptors, however, creating a potential barrier for clinical application. Determining how these observations relate to clinical outcome is a crucial step for translating the biological and mechanistic data into new molecularly targeted therapies. We investigated eph and ephrin expression in human breast cancer relative to endpoints of overall and/or recurrence-free survival in large microarray datasets. We also investigated protein expression in commercial human breast tissue microarrays (TMA) and Stage I prognostic TMAs linked to recurrence outcome data. We found significant correlations between ephA2, ephA4, ephA7, ephB4, and ephB6 and overall and/or recurrence-free survival in large microarray datasets. Protein expression in TMAs supported these trends. While observed no correlation between ephrin ligand expression and clinical outcome in microarray datasets, ephrin-A1 and EphA2 protein co-expression was significantly associated with recurrence in Stage I prognostic breast cancer TMAs. Our data suggest that several Eph family members are clinically relevant and tractable targets for intervention in human breast cancer. Moreover, profiling Eph receptor expression patterns in the context of relevant ligands and in the context of stage may be valuable in terms of diagnostics and treatment
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Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Inflammatory bowel diseases, which include Crohn's disease and ulcerative colitis, affect several million individuals worldwide. Crohn's disease and ulcerative colitis are complex diseases that are heterogeneous at the clinical, immunological, molecular, genetic, and microbial levels. Individual contributing factors have been the focus of extensive research. As part of the Integrative Human Microbiome Project (HMP2 or iHMP), we followed 132 subjects for one year each to generate integrated longitudinal molecular profiles of host and microbial activity during disease (up to 24 time points each; in total 2,965 stool, biopsy, and blood specimens). Here we present the results, which provide a comprehensive view of functional dysbiosis in the gut microbiome during inflammatory bowel disease activity. We demonstrate a characteristic increase in facultative anaerobes at the expense of obligate anaerobes, as well as molecular disruptions in microbial transcription (for example, among clostridia), metabolite pools (acylcarnitines, bile acids, and short-chain fatty acids), and levels of antibodies in host serum. Periods of disease activity were also marked by increases in temporal variability, with characteristic taxonomic, functional, and biochemical shifts. Finally, integrative analysis identified microbial, biochemical, and host factors central to this dysregulation. The study's infrastructure resources, results, and data, which are available through the Inflammatory Bowel Disease Multi'omics Database ( http://ibdmdb.org ), provide the most comprehensive description to date of host and microbial activities in inflammatory bowel diseases
Amplification Dynamics of Platy-1 Retrotransposons in the Cebidae Platyrrhine Lineage
Platy-1 elements are Platyrrhine-specific, short interspersed elements (SINEs) originally discovered in the Callithrix jacchus (common marmoset) genome. To date, only the marmoset genome has been analyzed for Platy-1 repeat content. Here, we report full-length Platy-1 insertions in other New World monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared to the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilies were discovered in the marmoset genome. All of the lineage-specific insertions found in the squirrel and capuchin monkeys were fixed present. However, ∼15% of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared to their respective consensus sequences, suggesting minimal ongoing retrotransposition in Aotus genus and no current activity in the Saimiri, Cebus and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in the marmoset genome is an exception among NWM analyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes
Amplification dynamics of platy-1 retrotransposons in the cebidae platyrrhine lineage
© 2019 The Author(s). Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Platy-1 elements are Platyrrhine-specific, short interspersed elements originally discovered in the Callithrix jacchus (common marmoset) genome. To date,only themarmoset genomehas been analyzed for Platy-1 repeat content.Here,we report full-length Platy-1 insertions in other NewWorld monkey (NWM) genomes (Saimiri boliviensis, squirrel monkey; Cebus imitator, capuchin monkey; and Aotus nancymaae, owl monkey) and analyze the amplification dynamics of lineage-specific Platy-1 insertions. A relatively small number of full-length and lineage-specific Platy-1 elements were found in the squirrel, capuchin, and owl monkey genomes compared with the marmoset genome. In addition, only a few older Platy-1 subfamilies were recovered in this study, with no Platy-1 subfamilies younger than Platy-1-6. By contrast, 62 Platy-1 subfamilieswere discovered in themarmoset genome.All of the lineagespecific insertions found in the squirrel and capuchin monkeys were fixed present. However, 15%of the lineage-specific Platy-1 loci in Aotus were polymorphic for insertion presence/absence. In addition, two new Platy-1 subfamilies were identified in the owl monkey genome with low nucleotide divergences compared with their respective consensus sequences, suggesting minimal ongoing retrotransposition in the Aotus genus and no current activity in the Saimiri, Cebus, and Sapajus genera. These comparative analyses highlight the finding that the high number of Platy-1 elements discovered in themarmoset genome is an exception among NWManalyzed thus far, rather than the rule. Future studies are needed to expand upon our knowledge of Platy-1 amplification in other NWM genomes
Lithocholic Acid Is an Eph-ephrin Ligand Interfering with Eph-kinase Activation
Eph-ephrin system plays a central role in a large variety of human cancers. In
fact, alterated expression and/or de-regulated function of Eph-ephrin system
promotes tumorigenesis and development of a more aggressive and metastatic
tumour phenotype. In particular EphA2 upregulation is correlated with tumour
stage and progression and the expression of EphA2 in non-trasformed cells
induces malignant transformation and confers tumorigenic potential. Based on
these evidences our aim was to identify small molecules able to modulate
EphA2-ephrinA1 activity through an ELISA-based binding screening. We identified
lithocholic acid (LCA) as a competitive and reversible ligand inhibiting
EphA2-ephrinA1 interaction (Ki = 49 µM). Since each
ephrin binds many Eph receptors, also LCA does not discriminate between
different Eph-ephrin binding suggesting an interaction with a highly conserved
region of Eph receptor family. Structurally related bile acids neither inhibited
Eph-ephrin binding nor affected Eph phosphorylation. Conversely, LCA inhibited
EphA2 phosphorylation induced by ephrinA1-Fc in PC3 and HT29 human prostate and
colon adenocarcinoma cell lines (IC50 = 48 and
66 µM, respectively) without affecting cell viability or other receptor
tyrosine-kinase (EGFR, VEGFR, IGFR1β, IRKβ) activity. LCA did not
inhibit the enzymatic kinase activity of EphA2 at 100 µM (LANCE method)
confirming to target the Eph-ephrin protein-protein interaction. Finally, LCA
inhibited cell rounding and retraction induced by EphA2 activation in PC3 cells.
In conclusion, our findings identified a hit compound useful for the development
of molecules targeting ephrin system. Moreover, as ephrin signalling is a key
player in the intestinal cell renewal, our work could provide an interesting
starting point for further investigations about the role of LCA in the
intestinal homeostasis
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