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Kinetics and mechanistic analysis of an extremely rapid carbon dioxide fixation reaction [Chemistry] (2011)

Huang, D., Makhlynets, O. V., Tan, L. L., Lee, S. C., Rybak-Akimova, E. V., Holm, R. H.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2011-01-26

Description: Carbon dioxide may react with free or metal-bound hydroxide to afford products containing bicarbonate or carbonate, often captured as ligands bridging two or three metal sites. We report the kinetics and probable mechanism of an extremely rapid fixation reaction mediated by a planar nickel complex [NiII(NNN)(OH)]1- containing a tridentate 2,6-pyridinedicarboxamidate pincer ligand and a terminal hydroxide ligand. The minimal generalized reaction is M-OH + CO2 → M-OCO2H; with variant M, previous rate constants are ≲103 M-1 s-1 in aqueous solution. For the present bimolecular reaction, the (extrapolated) rate constant is 9.5 × 105 M-1 s-1 in N,N′-dimethylformamide at 298 K, a value within the range of kcat/KM≈105–108 M-1 s-1 for carbonic anhydrase, the most efficient catalyst of CO2 fixation reactions. The enthalpy profile of the fixation reaction was calculated by density functional theory. The initial event is the formation of a weak precursor complex between the Ni-OH group and CO2, followed by insertion of a CO2 oxygen atom into the Ni-OH bond to generate a four center Ni(η2-OCO2H) transition state similar to that at the zinc site in carbonic anhydrase. Thereafter, the Ni-OH bond detaches to afford the Ni(η1-OCO2H) fragment, after which the molecule passes through a second, lower energy transition state as the bicarbonate ligand rearranges to a conformation very similar to that in the crystalline product. Theoretical values of metric parameters and activation enthalpy are in good agreement with experimental values [ΔH‡ = 3.2(5) kcal/mol].

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

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ASCL1 is a lung cancer lineage oncogene [Cell Biology] (2014)

Augustyn, A., Borromeo, M., Wang, T., Fujimoto, J., Shao, C., Dospoy, P. D., Lee, V., Tan, C., Sullivan, J. P., Larsen, J. E., Girard, L., Behrens, C., Wistuba, I. I., Xie, Y., Cobb, M. H., Gazdar, A. F., Johnson, J. E., Minna, J. D.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2014-10-15

Description: Aggressive neuroendocrine lung cancers, including small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), represent an understudied tumor subset that accounts for approximately 40,000 new lung cancer cases per year in the United States. No targeted therapy exists for these tumors. We determined that achaete-scute homolog 1 (ASCL1),...

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

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Lineage-negative progenitors mobilize to regenerate lung epithelium after major injury (2014)

A. E. Vaughan ; A. N. Brumwell ; Y. Xi ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 517(7536): 621-5. doi: 10.1038/nature14112.

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Publication Date: 2014-12-24

Description: Broadly, tissue regeneration is achieved in two ways: by proliferation of common differentiated cells and/or by deployment of specialized stem/progenitor cells. Which of these pathways applies is both organ- and injury-specific. Current models in the lung posit that epithelial repair can be attributed to cells expressing mature lineage markers. By contrast, here we define the regenerative role of previously uncharacterized, rare lineage-negative epithelial stem/progenitor (LNEP) cells present within normal distal lung. Quiescent LNEPs activate a DeltaNp63 (a p63 splice variant) and cytokeratin 5 remodelling program after influenza or bleomycin injury in mice. Activated cells proliferate and migrate widely to occupy heavily injured areas depleted of mature lineages, at which point they differentiate towards mature epithelium. Lineage tracing revealed scant contribution of pre-existing mature epithelial cells in such repair, whereas orthotopic transplantation of LNEPs, isolated by a definitive surface profile identified through single-cell sequencing, directly demonstrated the proliferative capacity and multipotency of this population. LNEPs require Notch signalling to activate the DeltaNp63 and cytokeratin 5 program, and subsequent Notch blockade promotes an alveolar cell fate. Persistent Notch signalling after injury led to parenchymal 'micro-honeycombing' (alveolar cysts), indicative of failed regeneration. Lungs from patients with fibrosis show analogous honeycomb cysts with evidence of hyperactive Notch signalling. Our findings indicate that distinct stem/progenitor cell pools repopulate injured tissue depending on the extent of the injury, and the outcomes of regeneration or fibrosis may depend in part on the dynamics of LNEP Notch signalling.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312207/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉 〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4312207/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Vaughan, Andrew E -- Brumwell, Alexis N -- Xi, Ying -- Gotts, Jeffrey E -- Brownfield, Doug G -- Treutlein, Barbara -- Tan, Kevin -- Tan, Victor -- Liu, Feng Chun -- Looney, Mark R -- Matthay, Michael A -- Rock, Jason R -- Chapman, Harold A -- F32 HL117600-01/HL/NHLBI NIH HHS/ -- R01 HL44712/HL/NHLBI NIH HHS/ -- U01 HL099995/HL/NHLBI NIH HHS/ -- U01 HL099999/HL/NHLBI NIH HHS/ -- U01 HL111054/HL/NHLBI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Jan 29;517(7536):621-5. doi: 10.1038/nature14112. Epub 2014 Dec 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, Cardiovascular Research Institute, University of California, San Francisco (UCSF), San Francisco, California 94143, USA. ; Department of Biochemistry, Stanford University School of Medicine and Howard Hughes Medical Institute, Stanford, California 94305, USA. ; Max Planck Institute for Evolutionary Anthropology, Department of Evolutionary Genetics, Deutscher Platz 6, 04103 Leipzig, Germany. ; Department of Anatomy, School of Medicine, University of California, San Francisco (UCSF), San Francisco, California 94143, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25533958" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Bleomycin ; Cell Lineage ; Cell Proliferation ; Cell Separation ; Cysts/metabolism/pathology ; Epithelial Cells/*cytology/metabolism/*pathology ; Female ; Humans ; Keratin-5/metabolism ; Lung/*cytology/*pathology/physiology ; Lung Injury/chemically induced/*pathology/virology ; Male ; Mice ; Orthomyxoviridae Infections/pathology/virology ; Phosphoproteins/genetics/metabolism ; *Re-Epithelialization ; Receptors, Notch/metabolism ; Signal Transduction ; Stem Cell Transplantation ; Stem Cells/*cytology/metabolism ; Trans-Activators/genetics/metabolism

Print ISSN: 0028-0836

Electronic ISSN: 1476-4687

Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics

Published by Nature Publishing Group (NPG)

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Mutations in bacterial genes induce unanticipated changes in the relationship between bacterial pathogens in experimental otitis media (2018)

Lakhani, V., Tan, L., Mukherjee, S., Stewart, W. C. L., Swords, W. E., Das, J.

Royal Society

In: Royal Society Open Science

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Publication Date: 2018-11-15

Description: Otitis media (OM) is a common polymicrobial infection of the middle ear in children under the age of 15 years. A widely used experimental strategy to analyse roles of specific phenotypes of bacterial pathogens of OM is to study changes in co-infection kinetics of bacterial populations in animal models when a wild-type bacterial strain is replaced by a specific isogenic mutant strain in the co-inoculating mixtures. As relationships between the OM bacterial pathogens within the host are regulated by many interlinked processes, connecting the changes in the co-infection kinetics to a bacterial phenotype can be challenging. We investigated middle ear co-infections in adult chinchillas ( Chinchilla lanigera ) by two major OM pathogens: non-typeable Haemophilus influenzae (NTHi) and Moraxella catarrhalis (Mcat), as well as isogenic mutant strains in each bacterial species. We analysed the infection kinetic data using Lotka–Volterra population dynamics, maximum entropy inference and Akaike information criteria-(AIC)-based model selection. We found that changes in relationships between the bacterial pathogens that were not anticipated in the design of the co-infection experiments involving mutant strains are common and were strong regulators of the co-infecting bacterial populations. The framework developed here allows for a systematic analysis of host–host variations of bacterial populations and small sizes of animal cohorts in co-infection experiments to quantify the role of specific mutant strains in changing the infection kinetics. Our combined approach can be used to analyse the functional footprint of mutant strains in regulating co-infection kinetics in models of experimental OM and other polymicrobial diseases.

Keywords: microbiology, biophysics, computational biology

Electronic ISSN: 2054-5703

Topics: Natural Sciences in General

Published by Royal Society

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Electronic Resource

The creep behavior of ideally atactic and commercial polymethylmethacrylate (1974)

Plazek, D. J. ; Tan, V. ; O'Rourke, V. M.

Springer

Rheologica acta 13 (1974), S. 367-376

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ISSN: 1435-1528

Source: Springer Online Journal Archives 1860-2000

Topics: Chemistry and Pharmacology , Physics

Notes: Summary The shear creep behavior of polymethylmethacrylate, PMMA, samples has been studied in the neighborhood of and above their glass temperatures. One of the materials studied was “ideally” atactic with equal numbers of random isotactic and syndiotactic placements, while the other was a commercial or “conventional” PMMA which was about 76% syndiotactic. The glass temperatures,T g , were found to be 106 and 117 °C respectively. Evacuation above the glass temperature for several weeks was necessary before reproducible creep compliance,J (t), curves could be obtained. It is believed that absorbed water plasticized the polar materials and its removal led to the shifting of theJ (t) curves to longer times. For both materials apparently successful temperature reduction was found to be possible within the temperature range of our investigations, i.e. up to 200 °C. Retardation spectra were calculated from the reduced curves and are compared. The temperature dependences, as described by the time scale shift factors,a T , were similar when allowance is made for the different glass temperature. Botha T curves could not be fitted to theWilliams, Landel, andFerry, WLF, free volume expression. These are the first examples of such a deviation for amorphous high polymers. It is proposed that the primary softening dispersion has two distinctly different groups of viscoelastic mechanisms contributing to it. On this basis the primary dispersion was decomposed into the two contributions. Both of the resulting temperature dependences were satisfactorily fitted to the WLF equation. Differences in the retardation spectra are noted. The glassy compliance of the commercial PMMA appears to be about twice that of the atactic PMMA.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF01521729

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Electronic Resource

Novel two-dimensional laser scanning technique

MacFarlane, D.L. ; Kim, W.Y. ; Nilvi, J.S. ; [et al.]

Amsterdam : Elsevier

Optics and Lasers in Engineering 17 (1992), S. 1-8

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ISSN: 0143-8166

Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002

Topics: Electrical Engineering, Measurement and Control Technology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics , Technology

Type of Medium: Electronic Resource

URL: http://linkinghub.elsevier.com/retrieve/pii/0143-8166(92)90022-Y

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Introduction of new traits into cotton through genetic engineering: insect resistance as example (1997)

Pannetier, C. ; Giband, M. ; Couzi, P. ; [et al.]

Springer

Euphytica 96 (1997), S. 163-166

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ISSN: 1573-5060

Keywords: Agrobacterium tumefaciens ; Bacillus thuringiensis ; cotton ; gene transfer ; Gossypium hirsutum ; insect resistance ; protease inhibitors ; regeneration

Source: Springer Online Journal Archives 1860-2000

Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition

Notes: Abstract The main goal of gene transfer into cotton is the development of insect-resistant varieties. The stakes are important since cotton protection against insects uses almost 24% of the world's chemical insecticides market, which is not without consequences on the environment. The first approach was to introduce and express in the cotton genome, genes from the bacterium Bacillus thuringiensis (B.t.) which produces entomopathogenic toxins. The development of an efficient Agrobacterium tumefaciens mediated transformation system was the first step. The expression of B.t. genes was studied and synthetic genes more adapted to a plant genome have been constructed. Studies on their expression in cotton is underway. The second focus was to develop strategies that would minimize the risks of inducing insect resistance. The main approach is to associate several genes coding for entomopathogenic proteins with different modes of action. Genes encoding protease inhibitors were chosen. One possibility is to associate a B.t. gene and a gene encoding a protease inhibitor. Several protease inhibitors were tested in artificial diets on major pests of cotton. The corresponding genes have been introduced into the cotton genome. These various orientations of the research program will be presented.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1002906308304

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Electronic Resource

Melt rheology of blends of semicrystalline polymers. I. Degradation and viscosity of poly(ethylene terephthalate)-polyamide-6,6 mixtures (1982)

Utracki, L. A. ; Catani, A. M. ; Bata, G. L. ; [et al.]

New York, NY [u.a.] : Wiley-Blackwell

Journal of Applied Polymer Science 27 (1982), S. 1913-1931

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ISSN: 0021-8995

Keywords: Chemistry ; Polymer and Materials Science

Source: Wiley InterScience Backfile Collection 1832-2000

Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics

Notes: Melt rheology of poly(ethylene terephthalate)-polyamide-6,6, and their blends was studied between 240°C and 300°C, in capillary and rotational rheometers. The flow curves were determined in the range of rate shear from about 10-2to 105 (s-1). The results indicate a considerable degree of compatibility, presence of associations between the two types of macromolecules, and cocrystallization. A new mechanism of flow for the blends has been proposed. The study also considers the kinetics of thermal degradation.

Additional Material: 18 Ill.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1002/app.1982.070270606

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