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Berlin Brandenburg

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  • 1
    Language: English
    In: Science (New York, N.Y.), 08 October 2010, Vol.330(6001), pp.201-4
    Description: The Deepwater Horizon blowout is the largest offshore oil spill in history. We present results from a subsurface hydrocarbon survey using an autonomous underwater vehicle and a ship-cabled sampler. Our findings indicate the presence of a continuous plume of oil, more than 35 kilometers in length, at approximately 1100 meters depth that persisted for months without substantial biodegradation. Samples collected from within the plume reveal monoaromatic petroleum hydrocarbon concentrations in excess of 50 micrograms per liter. These data indicate that monoaromatic input to this plume was at least 5500 kilograms per day, which is more than double the total source rate of all natural seeps of the monoaromatic petroleum hydrocarbons in the northern Gulf of Mexico. Dissolved oxygen concentrations suggest that microbial respiration rates within the plume were not appreciably more than 1 micromolar oxygen per day.
    Keywords: Biodegradation, Environmental ; Environmental Pollution ; Hydrocarbons ; Petroleum ; Seawater ; Water Pollutants ; Bacteria -- Metabolism
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States, Jan 22, 2013, Vol.110(4), p.1339(6)
    Description: Dynamic spatial patterns of signaling factors or macromolecular assemblies in the form of oscillations or traveling waves have emerged as important themes in cell physiology. Feedback mechanisms underlying these processes and their modulation by signaling events and reciprocal cross-talks remain poorly understood. Here we show that antigen stimulation of mast cells triggers cyclic changes in the concentration of actin regulatory proteins and actin in the cell cortex that can be manifested in either spatial pattern. Recruitment of FBP17 and active Cdc42 at the plasma membrane, leading to actin polymerization, are involved in both events, whereas calcium oscillations, which correlate with global fluctuations of plasma membrane PI(4,5)[P.sub.2], are tightly linked to standing oscillations and counteract wave propagation. These findings demonstrate the occurrence of a calcium-independent oscillator that controls the collective dynamics of factors linking the actin cytoskeleton to the plasma membrane. Coupling between this oscillator and the one underlying global plasma membrane PI(4,5)P2 and calcium oscillations spatially regulates actin dynamics, revealing an unexpected pattern-rendering mechanism underlying plastic changes occurring in the cortical region of the cell. curvature | pattern formation | plasticity | GTPase | frequency doi/10.1073/pnas.1221538110
    Keywords: Calcium (Nutrient) -- Physiological Aspects ; Calcium (Nutrient) -- Health Aspects ; Actin -- Physiological Aspects ; Actin -- Health Aspects ; Wave Motion -- Research ; Oscillations -- Research
    ISSN: 0027-8424
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  • 3
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 31 July 2018, Vol.115(31), pp.7849-7851
    Keywords: Potassium Channels, Voltage-Gated ; Shab Potassium Channels
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 4
    Language: English
    In: Science (New York, N.Y.), 10 August 2018, Vol.361(6402), pp.604-607
    Description: Neurotransmitter-containing synaptic vesicles (SVs) form tight clusters at synapses. These clusters act as a reservoir from which SVs are drawn for exocytosis during sustained activity. Several components associated with SVs that are likely to help form such clusters have been reported, including synapsin. Here we found that synapsin can form a distinct liquid phase in an aqueous environment. Other scaffolding proteins could coassemble into this condensate but were not necessary for its formation. Importantly, the synapsin phase could capture small lipid vesicles. The synapsin phase rapidly disassembled upon phosphorylation by calcium/calmodulin-dependent protein kinase II, mimicking the dispersion of synapsin 1 that occurs at presynaptic sites upon stimulation. Thus, principles of liquid-liquid phase separation may apply to the clustering of SVs at synapses.
    Keywords: Lipids -- Chemistry ; Synapsins -- Chemistry ; Synaptic Vesicles -- Chemistry ; Water -- Chemistry
    ISSN: 00368075
    E-ISSN: 1095-9203
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  • 5
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 07 April 2015, Vol.112(14), pp.4423-8
    Description: Prolonged T-cell receptor (TCR) signaling is required for the proliferation of T lymphocytes. Ligation of the TCR activates signaling, but also causes internalization of the TCR from the cell surface. How TCR signaling is sustained for many hours despite lower surface expression is unknown. Using genetic inhibition of endocytosis, we show here that TCR internalization promotes continued TCR signaling and T-lymphocyte proliferation. T-cell-specific deletion of dynamin 2, an essential component of endocytosis, resulted in reduced TCR signaling strength, impaired homeostatic proliferation, and the inability to undergo clonal expansion in vivo. Blocking endocytosis resulted in a failure to maintain mammalian target of rapamycin (mTOR) activity and to stably induce the transcription factor myelocytomatosis oncogene (c-Myc), which led to metabolic stress and a defect in cell growth. Our results support the concept that the TCR can continue to signal after it is internalized from the cell surface, thereby enabling sustained signaling and cell proliferation.
    Keywords: T-Cell Receptor ; Endocytosis ; Metabolism ; Proliferation ; Endocytosis ; Signal Transduction ; Dynamin II -- Physiology ; Receptors, Antigen, T-Cell -- Metabolism ; T-Lymphocytes -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 6
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 21 April 2015, Vol.112(16), pp.E2004-13
    Description: The close apposition between the endoplasmic reticulum (ER) and the plasma membrane (PM) plays important roles in Ca(2+) homeostasis, signaling, and lipid metabolism. The extended synaptotagmins (E-Syts; tricalbins in yeast) are ER-anchored proteins that mediate the tethering of the ER to the PM and are thought to mediate lipid transfer between the two membranes. E-Syt cytoplasmic domains comprise a synaptotagmin-like mitochondrial-lipid-binding protein (SMP) domain followed by five C2 domains in E-Syt1 and three C2 domains in E-Syt2/3. Here, we used cryo-electron tomography to study the 3D architecture of E-Syt-mediated ER-PM contacts at molecular resolution. In vitrified frozen-hydrated mammalian cells overexpressing individual E-Syts, in which E-Syt-dependent contacts were by far the predominant contacts, ER-PM distance (19-22 nm) correlated with the amino acid length of the cytosolic region of E-Syts (i.e., the number of C2 domains). Elevation of cytosolic Ca(2+) shortened the ER-PM distance at E-Syt1-dependent contacts sites. E-Syt-mediated contacts displayed a characteristic electron-dense layer between the ER and the PM. These features were strikingly different from those observed in cells exposed to conditions that induce contacts mediated by the stromal interaction molecule 1 (STIM1) and the Ca(2+) channel Orai1 as well as store operated Ca(2+) entry. In these cells the gap between the ER and the PM was spanned by filamentous structures perpendicular to the membranes. Our results define specific ultrastructural features of E-Syt-dependent ER-PM contacts and reveal their structural plasticity, which may impact on the cross-talk between the ER and the PM and the functions of E-Syts in lipid transport between the two bilayers.
    Keywords: E-Syt ; Tulip ; Cryo-Electron Microscopy ; Lipid Transfer ; Phosphoinositides ; Imaging, Three-Dimensional ; Cell Membrane -- Metabolism ; Endoplasmic Reticulum -- Metabolism ; Synaptotagmins -- Metabolism
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 7
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 18 August 2015, Vol.112(33), pp.10485-90
    Description: Natural transformation is one mechanism of horizontal gene transfer (HGT) in Vibrio cholerae, the causative agent of cholera. Recently, it was found that V. cholerae isolates from the Haiti outbreak were poorly transformed by this mechanism. Here, we show that an integrating conjugative element (ICE)-encoded DNase, which we name IdeA, is necessary and sufficient for inhibiting natural transformation of Haiti outbreak strains. We demonstrate that IdeA inhibits this mechanism of HGT in cis via DNA endonuclease activity that is localized to the periplasm. Furthermore, we show that natural transformation between cholera strains in a relevant environmental context is inhibited by IdeA. The ICE encoding IdeA is globally distributed. Therefore, we analyzed the prevalence and role for this ICE in limiting natural transformation of isolates from Bangladesh collected between 2001 and 2011. We found that IdeA(+) ICEs were nearly ubiquitous in isolates from 2001 to 2005; however, their prevalence decreased to ∼40% from 2006 to 2011. Thus, IdeA(+) ICEs may have limited the role of natural transformation in V. cholerae. However, the rise in prevalence of strains lacking IdeA may now increase the role of this conserved mechanism of HGT in the evolution of this pathogen.
    Keywords: Dnase ; Evolution ; Horizontal Gene Transfer ; Integrating Conjugative Element ; Gene Transfer, Horizontal ; Interspersed Repetitive Sequences ; Transformation, Bacterial ; Bacterial Proteins -- Genetics ; Vibrio Cholerae -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 8
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 17 June 2014, Vol.111(24), pp.8937-42
    Description: Editing bacterial genomes is an essential tool in research and synthetic biology applications. Here, we describe multiplex genome editing by natural transformation (MuGENT), a method for accelerated evolution based on the cotransformation of unlinked genetic markers in naturally competent microorganisms. We found that natural cotransformation allows scarless genome editing at unprecedented frequencies of ∼50%. Using DNA substrates with randomized nucleotides, we found no evidence for bias during natural cotransformation, indicating that this method can be used for directed evolution studies. Furthermore, we found that natural cotransformation is an effective method for multiplex genome editing. Because MuGENT does not require selection at edited loci in cis, output mutant pools are highly complex, and strains may have any number and combination of the multiplexed genome edits. We demonstrate the utility of this technique in metabolic and phenotypic engineering by optimizing natural transformation in Vibrio cholerae. This was accomplished by combinatorially editing the genome via gene deletions and promoter replacements and by tuning translation initiation of five genes involved in the process of natural competence and transformation. MuGENT allowed for the generation of a complex mutant pool in 1 wk and resulted in the selection of a genetically edited strain with a 30-fold improvement in natural transformation. We also demonstrate the efficacy of this technique in Streptococcus pneumoniae and highlight the potential for MuGENT to be used in multiplex genetic interaction analysis. Thus, MuGENT is a broadly applicable platform for accelerated evolution and genetic interaction studies in diverse naturally competent species.
    Keywords: Genetic Techniques ; Genome, Bacterial ; Transformation, Bacterial ; Streptococcus Pneumoniae -- Genetics ; Vibrio Cholerae -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 9
    Language: English
    In: Science, 24 February 2006, Vol.311(5764), pp.1113-1116
    Description: Bacteria use diverse small molecules for extra- and intracellular signaling. They scan small-molecule mixtures to access information about both their extracellular environment and their intracellular physiological status, and based on this information, they continuously interpret their circumstances and react rapidly to changes. Bacteria must integrate extra- and intracellular signaling information to mount appropriate responses to changes in their environment. We review recent research into two fundamental bacterial small-molecule signaling pathways: extracellular quorum-sensing signaling and intracellular cyclic dinucleotide signaling. We suggest how these two pathways may converge to control complex processes including multicellularity, biofilm formation, and virulence. We also outline new questions that have arisen from recent studies in these fields.
    Keywords: Biological sciences -- Biology -- Microbiology ; Physical sciences -- Physics -- Microphysics ; Biological sciences -- Biology -- Genetics ; Biological sciences -- Biology -- Microbiology ; Biological sciences -- Biochemistry -- Enzymology ; Applied sciences -- Materials science -- Materials ; Physical sciences -- Chemistry -- Chemical compounds ; Physical sciences -- Chemistry -- Chemical reactions ; Health sciences -- Health and wellness -- Public health ; Biological sciences -- Biology -- Genetics
    ISSN: 00368075
    E-ISSN: 10959203
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  • 10
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 22 January 2013, Vol.110(4), pp.1339-44
    Description: Dynamic spatial patterns of signaling factors or macromolecular assemblies in the form of oscillations or traveling waves have emerged as important themes in cell physiology. Feedback mechanisms underlying these processes and their modulation by signaling events and reciprocal cross-talks remain poorly understood. Here we show that antigen stimulation of mast cells triggers cyclic changes in the concentration of actin regulatory proteins and actin in the cell cortex that can be manifested in either spatial pattern. Recruitment of FBP17 and active Cdc42 at the plasma membrane, leading to actin polymerization, are involved in both events, whereas calcium oscillations, which correlate with global fluctuations of plasma membrane PI(4,5)P(2), are tightly linked to standing oscillations and counteract wave propagation. These findings demonstrate the occurrence of a calcium-independent oscillator that controls the collective dynamics of factors linking the actin cytoskeleton to the plasma membrane. Coupling between this oscillator and the one underlying global plasma membrane PI(4,5)P2 and calcium oscillations spatially regulates actin dynamics, revealing an unexpected pattern-rendering mechanism underlying plastic changes occurring in the cortical region of the cell.
    Keywords: Actins -- Metabolism ; Calcium Signaling -- Physiology
    ISSN: 00278424
    E-ISSN: 1091-6490
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