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1.
J Phys Chem Lett ; 12(33): 8039-8045, 2021 Aug 26.
Artigo em Inglês | MEDLINE | ID: mdl-34402624

RESUMO

Calcite dissolution is initiated by the formation of a nanoscale etch pit followed by step edge propagation and hence strongly influenced by the interactions between surface diffusing ions and step edges. However, such atomic-scale dynamics are mostly inaccessible with current imaging tools. Here, we overcome this limitation by using our recent development of high-speed frequency modulation atomic force microscopy. By visualizing atomic-scale structural changes of the etch pits at the calcite surface in water, we found the existence of mobile and less-mobile surface adsorption layers (SALs) in the etch pits. We also found that some etch pits maintain their size for a long time without expansion, and their step edges are often associated with less-mobile SALs, suggesting their step stabilization effect.


Assuntos
Carbonato de Cálcio/química , Microscopia de Força Atômica/métodos , Nanoestruturas/química , Adsorção , Cristalografia , Estrutura Molecular , Solubilidade , Propriedades de Superfície , Água/química
2.
J Phys Chem Lett ; 12(31): 7605-7611, 2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34350760

RESUMO

Mineral-water interfaces play an important role in many natural as well as technological fields. Fundamental properties of these interfaces are governed by the presence of the interfacial water and its specific structure at the surface. Calcite is particularly interesting as a dominant rock-forming mineral in the earth's crust. Here, we combine atomic force microscopy, sum-frequency generation spectroscopy, and molecular dynamics simulations to determine the position and orientation of the water molecules in the hydration layers of the calcite surface with high resolution. While atomic force microscopy provides detailed information about the position of the water molecules at the interface, sum-frequency generation spectroscopy can deduce the orientation of the water molecules. Comparison of the calcite-water interface to the interfaces of magnesite-water, magnesite-ethanol, and calcite-ethanol reveals a comprehensive picture with opposite water orientations in the first and second layer of the interface, which is corroborated by the molecular dynamics simulations.

3.
ISME J ; 15(5): 1434-1444, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33349653

RESUMO

The ocean is a net source of N2O, a potent greenhouse gas and ozone-depleting agent. However, the removal of N2O via microbial N2O consumption is poorly constrained and rate measurements have been restricted to anoxic waters. Here we expand N2O consumption measurements from anoxic zones to the sharp oxygen gradient above them, and experimentally determine kinetic parameters in both oxic and anoxic seawater for the first time. We find that the substrate affinity, O2 tolerance, and community composition of N2O-consuming microbes in oxic waters differ from those in the underlying anoxic layers. Kinetic parameters determined here are used to model in situ N2O production and consumption rates. Estimated in situ rates differ from measured rates, confirming the necessity to consider kinetics when predicting N2O cycling. Microbes from the oxic layer consume N2O under anoxic conditions at a much faster rate than microbes from anoxic zones. These experimental results are in keeping with model results which indicate that N2O consumption likely takes place above the oxygen deficient zone (ODZ). Thus, the dynamic layer with steep O2 and N2O gradients right above the ODZ is a previously ignored potential gatekeeper of N2O and should be accounted for in the marine N2O budget.


Assuntos
Óxido Nitroso , Oxigênio , Cinética
4.
Beilstein J Nanotechnol ; 11: 891-898, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32566439

RESUMO

Calcite and magnesite are important mineral constituents of the earth's crust. In aqueous environments, these carbonates typically expose their most stable cleavage plane, the (10.4) surface. It is known that these surfaces interact with a large variety of organic molecules, which can result in surface restructuring. This process is decisive for the formation of biominerals. With the development of 3D atomic force microscopy (AFM) it is now possible to image solid-liquid interfaces with unprecedented molecular resolution. However, the majority of 3D AFM studies have been focused on the arrangement of water at carbonate surfaces. Here, we present an analysis of the assembly of ethanol - an organic molecule with a single hydroxy group - at the calcite and magnesite (10.4) surfaces by using high-resolution 3D AFM and molecular dynamics (MD) simulations. Within a single AFM data set we are able to resolve both the first laterally ordered solvation layer of ethanol on the calcite surface as well as the following solvation layers that show no lateral order. Our experimental results are in excellent agreement with MD simulations. The qualitative difference in the lateral order can be understood by the differing chemical environment: While the first layer adopts specific binding positions on the ionic carbonate surface, the second layer resides on top of the organic ethyl layer. A comparison of calcite and magnesite reveals a qualitatively similar ethanol arrangement on both carbonates, indicating the general nature of this finding.

5.
Nanoscale ; 12(24): 12856-12868, 2020 Jun 25.
Artigo em Inglês | MEDLINE | ID: mdl-32520063

RESUMO

In this study, we have investigated the influence of the tip on the three-dimensional scanning force microscopy (3D-SFM) images of calcite-water interfaces by experiments and simulations. We calculated 3D force images by simulations with the solvent tip approximation (STA), Ca, CO3 and OH tip models. For all the 3D images, the z profiles at the surface Ca and CO3 sites alternately show oscillatory peaks corresponding to the hydration layers. However, the peak heights and spacings become larger when the mechanical stability of the tip becomes higher. For analyzing the xy slices of the 3D force images, we developed the extended STA (E-STA) model which allowed us to reveal the strong correlation between the hydration structure just under the tip and the atomic-scale force contrasts. Based on these understandings on the image features showing the strong tip dependence, we developed a method for objectively estimating the similarity between 3D force images. With this method, we compared the simulated images with the three experimentally obtained ones. Among them, two images showed a relatively high similarity with the image obtained by the simulation with the Ca or the CO3 tip model. Based on these agreements, we characterized the hydration structure and mechanical stability of the experimentally used tips. The understanding and methodology presented here should help us to derive accurate information on the tip and the interfacial structure from experimentally obtained 3D-SFM images.

6.
Sci Rep ; 9(1): 20122, 2019 12 27.
Artigo em Inglês | MEDLINE | ID: mdl-31882935

RESUMO

Many prokaryotes encode protein-based encapsulin nanocompartments, including anaerobic ammonium oxidizing (anammox) bacteria. This study expands the list of known anammox encapsulin systems from freshwater species to include the marine genus Scalindua. Two novel systems, identified in "Candidatus Scalindua rubra" and "Candidatus Scalindua sp. SCAELEC01 167" possess different architectures than previously studied freshwater anammox encapsulins. Characterization of the S. rubra encapsulin confirms that it can self-assemble to form compartments when heterologously expressed in Escherichia coli. BLASTp and HMMER searches of additional genomes and metagenomes spanning a range of environments returned 26 additional novel encapsulins, including a freshwater anammox encapsulin identified in "Candidatus Brocadia caroliniensis". Phylogenetic analysis comparing these 28 new encapsulin sequences and cargo to that of their closest known relatives shows that encapsulins cluster by cargo protein type and therefore likely evolved together. Lastly, prokaryotic encapsulins may be more common and diverse than previously thought. Through searching a small sample size of all public metagenomes and genomes, many new encapsulin systems were unearthed by this study. This suggests that many additional encapsulins likely remain to be discovered.


Assuntos
Bactérias/classificação , Bactérias/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , Microbiologia Ambiental , Ordem dos Genes , Loci Gênicos , Geografia , Metagenoma , Metagenômica/métodos , Filogenia , Multimerização Proteica , Análise de Sequência de DNA
7.
Sci Adv ; 4(4): eaar7181, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29662955

RESUMO

Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)-a tool to directly resolve chemical structures-is one of the most promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution. This elemental-sensitive measurement takes an important step in the analysis of functionalized two-dimensional carbon materials.

8.
ACS Nano ; 11(8): 8122-8130, 2017 08 22.
Artigo em Inglês | MEDLINE | ID: mdl-28712296

RESUMO

According to Hückel theory, an anti-aromatic molecule possessing (4n)π-electrons becomes unstable. Although the stabilization has been demonstrated by radialene-type structures-fusing aromatic rings to anti-aromatic rings-in solution, such molecules have never been studied at a single molecular level. Here, we synthesize a cyclobutadiene derivative, dibenzo[b,h]biphenylene, by an on-surface intramolecular reaction. With a combination of high-resolution atomic force microscopy and density functional theory calculations, we found that a radialene structure significantly reduces the anti-aromaticity of the cyclobutadiene core, extracting π-electrons, while the small four-membered cyclic structure keeps a high density of the total charge.

9.
Nano Lett ; 17(7): 4083-4089, 2017 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-28650174

RESUMO

The microscopic understanding of the crystal growth and dissolution processes have been greatly advanced by the direct imaging of nanoscale step flows by atomic force microscopy (AFM), optical interferometry, and X-ray microscopy. However, one of the most fundamental events that govern their kinetics, namely, atomistic events at the step edges, have not been well understood. In this study, we have developed high-speed frequency modulation AFM (FM-AFM) and enabled true atomic-resolution imaging in liquid at ∼1 s/frame, which is ∼50 times faster than the conventional FM-AFM. With the developed AFM, we have directly imaged subnanometer-scale surface structures around the moving step edges of calcite during its dissolution in water. The obtained images reveal that the transition region with typical width of a few nanometers is formed along the step edges. Building upon insight in previous studies, our simulations suggest that the transition region is most likely to be a Ca(OH)2 monolayer formed as an intermediate state in the dissolution process. On the basis of this finding, we improve our understanding of the atomistic dissolution model of calcite in water. These results open up a wide range of future applications of the high-speed FM-AFM to the studies on various dynamic processes at solid-liquid interfaces with true atomic resolution.

10.
Sci Adv ; 3(5): e1603258, 2017 May.
Artigo em Inglês | MEDLINE | ID: mdl-28508080

RESUMO

The hydrogen atom-the smallest and most abundant atom-is of utmost importance in physics and chemistry. Although many analysis methods have been applied to its study, direct observation of hydrogen atoms in a single molecule remains largely unexplored. We use atomic force microscopy (AFM) to resolve the outermost hydrogen atoms of propellane molecules via very weak C═O⋅⋅⋅H-C hydrogen bonding just before the onset of Pauli repulsion. The direct measurement of the interaction with a hydrogen atom paves the way for the identification of three-dimensional molecules such as DNAs and polymers, building the capabilities of AFM toward quantitative probing of local chemical reactivity.

11.
Langmuir ; 33(1): 125-129, 2017 01 10.
Artigo em Inglês | MEDLINE | ID: mdl-27960056

RESUMO

Solid-liquid interfaces are decisive for a wide range of natural and technological processes, including fields as diverse as geochemistry and environmental science as well as catalysis and corrosion protection. Dynamic atomic force microscopy nowadays provides unparalleled structural insights into solid-liquid interfaces, including the solvation structure above the surface. In contrast, chemical identification of individual interfacial atoms still remains a considerable challenge. So far, an identification of chemically alike atoms in a surface alloy has only been demonstrated under well-controlled ultrahigh vacuum conditions. In liquids, the recent advent of three-dimensional force mapping has opened the potential to discriminate between anionic and cationic surface species. However, a full chemical identification will also include the far more challenging situation of alike interfacial atoms (i.e., with the same net charge). Here we demonstrate the chemical identification capabilities of dynamic atomic force microscopy at solid-liquid interfaces by identifying Ca and Mg cations at the dolomite-water interface. Analyzing site-specific vertical positions of hydration layers and comparing them with molecular dynamics simulations unambiguously unravels the minute but decisive difference in ion hydration and provides a clear means for telling calcium and magnesium ions apart. Our work, thus, demonstrates the chemical identification capabilities of dynamic AFM at the solid-liquid interface.

12.
Nanotechnology ; 27(41): 415709, 2016 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-27609045

RESUMO

Frequency modulation atomic force microscopy (FM-AFM) experiments were performed on the calcite (10[Formula: see text]4) surface in pure water, and a detailed analysis was made of the 2D images at a variety of frequency setpoints. We observed eight different contrast patterns that reproducibly appeared in different experiments and with different measurement parameters. We then performed systematic free energy calculations of the same system using atomistic molecular dynamics to obtain an effective force field for the tip-surface interaction. By using this force field in a virtual AFM simulation we found that each experimental contrast could be reproduced in our simulations by changing the setpoint, regardless of the experimental parameters. This approach offers a generic method for understanding the wide variety of contrast patterns seen on the calcite surface in water, and is generally applicable to AFM imaging in liquids.

13.
J Phycol ; 51(2): 332-42, 2015 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-26986528

RESUMO

The abundance of Aulacoseira granulata (Ehrenburg) Simonsen and Gloeocystis planctonica (West & G.S.West) Lemmermann was assessed during the summers of 2005 and 2010 in the eutrophic Fox River, Wisconsin, USA. In both years, a mid-summer bloom of G. planctonica was followed by the rapid growth of A. granulata. Laboratory experiments in which A. granulata was grown in cell-free filtrate of a G. planctonica culture revealed that the growth of A. granulata was stimulated in the G. planctonica-treated medium relative to controls. This effect was detected when dormant A. granulata cells were used as the source culture for the experiment but not when actively growing cells were used. Dormant A. granulata also grew more rapidly in river water collected after the 2010 G. planctonica bloom relative to river water collected before the bloom. These results suggest that the summer bloom of A. granulata in the river was stimulated by G. planctonica. This relationship can be described as stimulated rejuvenation, an interaction where the transition of an algal resting stage into active growth is triggered by exposure to another species.

14.
Emerg Infect Dis ; 16(12): 1896-904, 2010 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-21122219

RESUMO

We investigated carriage of avian influenza viruses by wild birds in Australia, 2005-2008, to assess the risks to poultry industries and human health. We collected 21,858 (7,357 cloacal, 14,501 fecal) samples and detected 300 viruses, representing a detection rate of ≈1.4%. Rates were highest in autumn (March-May) and differed substantially between bird types, areas, and years. We typed 107 avian influenza viruses and identified 19 H5, 8 H7, and 16 H9 (40% of typed viruses). All were of low pathogenicity. These viruses formed clearly different phylogenetic clades to lineages from Eurasia or North America, suggesting the potential existence of Australian lineages. H7 viruses were similar to highly pathogenic H7 strains that caused outbreaks in poultry in Australia. Several periods of increased detection rates (numbers or subtypes of viruses) were identified. This study demonstrates the need for ongoing surveillance to detect emerging pathogenic strains and facilitate prevention of outbreaks.


Assuntos
Aves/virologia , Monitoramento Ambiental , Vírus da Influenza A/isolamento & purificação , Influenza Aviária/epidemiologia , Influenza Aviária/virologia , Influenza Humana/epidemiologia , Migração Animal , Animais , Austrália/epidemiologia , Cloaca/virologia , Monitoramento Epidemiológico , Fezes/virologia , Humanos , Vírus da Influenza A/classificação , Vírus da Influenza A/patogenicidade , Influenza Aviária/genética , Filogenia , RNA Viral/análise , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Estações do Ano
15.
J Parasitol ; 95(5): 1177-82, 2009 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-19463035

RESUMO

Plagioporus kolipinskii n. sp. (Trematoda: Opecoelidae) is described from the intestine of the threespine stickleback, Gasterosteus aculeatus L., from Lobos Creek, a freshwater stream in Presidio, San Francisco County, California. Plagioporus kolipinskii is morphologically somewhat similar to 4 (P. serotinus , P. angusticollis , P. macrouterinus , and P. shawi []) of the 12 currently recognized North American species of the genus, but can be readily distinguished from all 4 in possessing a much larger acetabulum and a larger ovary relative to the testes. In addition, the new species can be distinguished from P. angusticollis by a smaller cirrus sac; from P. macrouterinus by the elongated shape of its body and reduced extent of its uterus (the uterus of P. macrouterinus extends posteriorly to the intersection of the testes); from P. shawi by a much-shorter cirrus sac (which reaches the ovary in P. shawi), an unlobed ovary (as opposed to a quadrilobed ovary in P. shawi), and fewer eggs that are also larger relative to body size.


Assuntos
Doenças dos Peixes/parasitologia , Enteropatias Parasitárias/veterinária , Smegmamorpha/parasitologia , Trematódeos/classificação , Infecções por Trematódeos/veterinária , Animais , California , Água Doce , Enteropatias Parasitárias/parasitologia , Intestinos/parasitologia , Trematódeos/anatomia & histologia , Trematódeos/isolamento & purificação , Infecções por Trematódeos/parasitologia
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