Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 13 de 13
Filtrar
Mais filtros










Base de dados
Intervalo de ano de publicação
1.
BMC Bioinformatics ; 21(1): 528, 2020 Nov 17.
Artigo em Inglês | MEDLINE | ID: mdl-33203354

RESUMO

BACKGROUND: Next-generation sequencing technologies revolutionized genomics by producing high-throughput reads at low cost, and this progress has prompted the recent development of de novo assemblers. Multiple assembly methods based on de Bruijn graph have been shown to be efficient for Illumina reads. However, the sequencing errors generated by the sequencer complicate analysis of de novo assembly and influence the quality of downstream genomic researches. RESULTS: In this paper, we develop a de Bruijn assembler, called Clover (clustering-oriented de novo assembler), that utilizes a novel k-mer clustering approach from the overlap-layout-consensus concept to deal with the sequencing errors generated by the Illumina platform. We further evaluate Clover's performance against several de Bruijn graph assemblers (ABySS, SOAPdenovo, SPAdes and Velvet), overlap-layout-consensus assemblers (Bambus2, CABOG and MSR-CA) and string graph assembler (SGA) on three datasets (Staphylococcus aureus, Rhodobacter sphaeroides and human chromosome 14). The results show that Clover achieves a superior assembly quality in terms of corrected N50 and E-size while remaining a significantly competitive in run time except SOAPdenovo. In addition, Clover was involved in the sequencing projects of bacterial genomes Acinetobacter baumannii TYTH-1 and Morganella morganii KT. CONCLUSIONS: The marvel clustering-based approach of Clover that integrates the flexibility of the overlap-layout-consensus approach and the efficiency of the de Bruijn graph method has high potential on de novo assembly. Now, Clover is freely available as open source software from https://oz.nthu.edu.tw/~d9562563/src.html .


Assuntos
Algoritmos , Sequenciamento de Nucleotídeos em Larga Escala , Sequência de Bases , Cromossomos Humanos Par 14/genética , Análise por Conglomerados , Genoma Bacteriano , Genômica/métodos , Humanos , Software , Fatores de Tempo
2.
J Am Chem Soc ; 142(18): 8211-8222, 2020 05 06.
Artigo em Inglês | MEDLINE | ID: mdl-32281385

RESUMO

The synthesis of two-dimensional (2D) zeolites has garnered attention due to their superior properties for applications that span catalysis to selective separations. Prior studies of 2D zeolite catalysts demonstrated enhanced mass transport for improved catalyst lifetime and selectivity. Moreover, the significantly higher external surface area of 2D materials allows for reactions of bulky molecules too large to access interior pores. There are relatively few protocols for preparing 2D materials, owing to the difficultly of capping growth in one direction to only a few unit cells. To accomplish this, it is often necessary to employ complex, commercially unavailable organic structure-directing agents (OSDAs) prepared via multistep synthesis. However, a small subset of zeolite structures exist as naturally layered materials where postsynthesis steps can be used to exfoliate samples and produce ultrathin 2D nanosheets. In this study, we selected a common layered zeolite, the MWW framework, to explore methods of preparing 2D nanosheets via one-pot synthesis in the absence of complex organic templates. Using a combination of high-resolution microscopy and spectroscopy, we show that 2D MMW-type layers with an average thickness of 3.5 nm (ca. 1.5 unit cells) can be generated using the surfactant cetyltrimethylammonium (CTA), which operates as a dual OSDA and exfoliating agent to affect Al siting and to eliminate the need for postsynthesis exfoliation, respectively. We tested these 2D catalysts using a model reaction that assesses external (surface) Brønsted acid sites and observed a marked increase in the conversion relative to three-dimensional MWW (MCM-22) and 2D layers prepared from postsynthesis exfoliation (ITQ-2). Collectively, our findings identify a facile and effective route to directly synthesize 2D MWW-type materials, which may prove to be more broadly applicable to other layered zeolites.

3.
Angew Chem Int Ed Engl ; 58(19): 6255-6259, 2019 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-30912601

RESUMO

The adsorption and reaction properties of heterogeneous zeolite catalysts (e.g. for catalytic cracking of petroleum, partial oxidation of natural gas) depend strongly on the types and distributions of Al heteroatoms in the aluminosilicate frameworks. The origins of these properties have been challenging to discern, owing in part to the structural complexity of aluminosilicate zeolites. Herein, combined solid-state NMR and synchrotron X-ray powder diffraction analyses show the Al atoms locate preferentially in certain framework sites in the zeolite catalyst Al-SSZ-70. Through-covalent-bond 2D 27 Al{29 Si} J-correlation NMR spectra allow distinct framework Al sites to be identified and their relative occupancies quantified. The analyses show that 94 % of the Al atoms are located at the surfaces of the large-pore interlayer channels of Al-SSZ-70, while only 6 % are in the sub-nm intralayer channels. The selective siting of Al atoms accounts for the reaction properties of catalysts derived from SSZ-70.

4.
J Am Chem Soc ; 139(46): 16803-16812, 2017 11 22.
Artigo em Inglês | MEDLINE | ID: mdl-29068208

RESUMO

The structure of the calcined form of the high-silica zeolite SSZ-70 has been elucidated by combining synchrotron X-ray powder diffraction (XRPD), high-resolution transmission electron microscopy (HRTEM), and two-dimensional (2D) dynamic nuclear polarization (DNP)-enhanced NMR techniques. The framework structure of SSZ-70 is a polytype of MWW and can be viewed as a disordered ABC-type stacking of MWW-layers. HRTEM and XRPD simulations show that the stacking sequence is almost random, with each layer being shifted by ±1/3 along the ⟨110⟩ direction with respect to the previous one. However, a small preponderance of ABAB stacking could be discerned. DNP-enhanced 2D 29Si{29Si} J-mediated NMR analyses of calcined Si-SSZ-70 at natural 29Si isotopic abundance (4.7%) establish the through-covalent-bond 29Si-O-29Si connectivities of distinct Si sites in the framework. The DNP-NMR results corroborate the presence of MWW layers and, more importantly, identify two distinct types of Q3 silanol species at the surfaces of the interlayer regions. In the first, an isolated silanol group protrudes into the interlayer space pointing toward the pocket in the adjacent layer. In the second, the surrounding topology is the same, but the isolated -SiOH group is missing, leaving a nest of three Si-O-H groups in place of the three Si-O-Si linkages. The analyses clarify the structure of this complicated material, including features that do not exhibit long-range order. With these insights, the novel catalytic behavior of SSZ-70 can be better understood and opportunities for enhancement recognized.

5.
Angew Chem Int Ed Engl ; 56(43): 13366-13371, 2017 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-28771911

RESUMO

We report the most siliceous FAU-type zeolite, HOU-3, prepared via a one-step organic-free synthesis route. Computational studies indicate that it is thermodynamically feasible to synthesize FAU with SAR=2-7, though kinetic factors seemingly impose a more restricted upper limit for HOU-3 (SAR≈3). Our findings suggest that a slow rate of crystallization and/or low concentration of Na+ ions in HOU-3 growth mixtures facilitate Si incorporation into the framework. Interestingly, Q4 (nAl) Si speciation measured by solid-state NMR can only be modeled with a few combinations of Al positioning at tetrahedral sites in the crystal unit cell, indicating the distribution of Si(-O-Si)4-n (-O-Al)n species is spatially biased as opposed to being random. Achieving higher SAR is desirable for improved zeolite (hydro)thermal stability and enhanced catalytic performance, which we demonstrate in benchmark tests that show HOU-3 is superior to commercial zeolite Y.

6.
Phys Chem Chem Phys ; 17(38): 25449-54, 2015 Oct 14.
Artigo em Inglês | MEDLINE | ID: mdl-26365719

RESUMO

Here we present a systematic study of direct (27)Al Dynamic Nuclear Polarization (DNP) as induced by three different mono-radical probes with side groups of varying charge states. By employing 4-amino TEMPO that adsorbs to negatively charged surface sites of Al-SBA-15, we achieve a (27)Al signal enhancement factor of ∼13 compared to a signal enhancement factor of ∼3-4 from mono-radicals that do not adsorb as strongly to the surfaces of Al-SBA-15, here 4-carboxy- and 4-hydroxy-TEMPO. By performing Electron Spin Echo Envelope Modulation (ESEEM) experiments and continuous wave (cw) Electron Paramagnetic Resonance (EPR) lineshape analysis using various nitroxide probes imbibed in Al-SBA-15, we find that direct (27)Al DNP enhancements achieved with different spin probes can be attributed to proximity and local concentration of the spin probes to aluminum on the surface of mesoporous alumina-silica.

7.
Phys Chem Chem Phys ; 17(33): 21664-82, 2015 Sep 07.
Artigo em Inglês | MEDLINE | ID: mdl-26227574

RESUMO

Boron heteroatom distributions are shown to be significantly different in two closely related layered borosilicates synthesized with subtly different alkylammonium surfactant species. The complicated order and disorder near framework boron sites in both borosilicates were characterized at the molecular level by using a combination of multi-dimensional solid-state nuclear magnetic resonance (NMR) spectroscopy techniques and first-principles calculations. Specifically, two-dimensional (2D) solid-state J-mediated (through-bond) (11)B{(29)Si} NMR analyses provide direct and local information on framework boron sites that are covalently bonded to silicon sites through bridging oxygen atoms. The resolution and identification of correlated signals from distinct (11)B-O-(29)Si site pairs reveal distinct distributions of boron heteroatoms in layered borosilicate frameworks synthesized with the different C16H33N(+)Me3 and C16H33N(+)Me2Et structure-directing surfactant species. The analyses establish that boron atoms are distributed non-selectively among different types of silicon sites in the layered C16H33N(+)Me3-directed borosilicate framework, whereas boron atoms are preferentially incorporated into incompletely condensed Q(3)-type sites in the C16H33N(+)Me2Et-directed borosilicate material. Interestingly, framework boron species appear to induce framework condensation of their next-nearest-neighbor silicon sites in the C16H33N(+)Me3-directed borosilicate. By comparison, the incorporation of boron atoms is found to preserve the topology of the C16H33N(+)Me2Et-directed borosilicate frameworks. The differences in boron site distributions and local boron-induced structural transformations for the two surfactant-directed borosilicates appear to be due to different extents of cross-linking of the siliceous frameworks. The molecular-level insights are supported by density functional theory (DFT) calculations, which show the distinct influences of boron atoms on the C16H33N(+)Me3- and C16H33N(+)Me2Et-directed borosilicate frameworks, consistent with the experimental observations.

8.
J Am Chem Soc ; 136(4): 1462-71, 2014 Jan 29.
Artigo em Inglês | MEDLINE | ID: mdl-24401027

RESUMO

The work here describes the kinetic analyses of aluminum replacement for boron in a suite of borosilicate molecular sieves. While the method has been described before as a means of converting synthesized borosilicates (with weak inherent acidity) to aluminosilicates (with much stronger acid strength) when there are large pores in the structure, here we carry out the transformation under less than optimal replacement concentrations, in order to better follow the kinetics. We examined several zeolite structures with boundary conditions of boron MEL where there are only 10-ring (or intermediate) pore structures and no Al is taken up, to multidimensional large pore zeolites, like boron beta, where Al substitution can occur everywhere. We also studied materials with both intermediate and large pores, SSZ-56, 57, 70, and 82. In the case of 57 up to 90% of the structure is made up of boron MEL. We observe that the pH drop is proportional to the Al reinsertion and is the same for all zeolites we studied. In one case, we compared a zeolite (SSZ-24) with boron and then no boron sites and found that Al does not go into defect sites. It was again confirmed (shown in earlier work) that Al will go into nest sites created by boron hydrolysis out of the substrate before Al treatment. Along those lines we also made two new observations: (1) the profile for Al uptake, as followed by pH drop, is the same kinetically, whether the boron is there or not; and (2) NMR showed that the boron is leaving the structure faster than Al can go back in (SSZ-33 study), even when we treat a material with boron in the lattice.

9.
J Bacteriol ; 194(24): 6974, 2012 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-23209228

RESUMO

Acinetobacter baumannii has emerged recently as a major cause of health care-associated infections due to the extent of its antimicrobial resistance and its propensity to cause large nosocomial outbreaks. Here we report the genome sequence of Acinetobacter baumannii TYTH-1 isolated in Taiwan during 2008.


Assuntos
Acinetobacter baumannii/genética , Genoma Bacteriano , Infecções por Acinetobacter/microbiologia , Acinetobacter baumannii/efeitos dos fármacos , Acinetobacter baumannii/isolamento & purificação , Antibacterianos/farmacologia , Bacteriemia/microbiologia , Proteínas de Bactérias/genética , DNA Bacteriano/genética , Farmacorresistência Bacteriana Múltipla , Humanos , Dados de Sequência Molecular , RNA Bacteriano/genética , Análise de Sequência de DNA , Taiwan , beta-Lactamases/genética
10.
ACS Nano ; 6(5): 4434-44, 2012 May 22.
Artigo em Inglês | MEDLINE | ID: mdl-22502599

RESUMO

The design and synthesis of hollow/yolk-shell mesoporous structures with catalytically active ordered mesoporous shells can infuse new vitality into the applications of these attractive structures. In this study, we report that hollow/yolk-shell structures with catalytically active ordered mesoporous aluminosilica shells can be easily prepared by using silica spheres as the silica precursors. By simply treating with a hot alkaline solution in the presence of sodium aluminate (NaAlO(2)) and cetyltrimethylammonium bromide (CTAB), solid silica spheres can be directly converted into high-quality hollow mesoporous aluminosilica spheres with perpendicular pore channels. On the basis of the proposed formation mechanism of etching followed by co-assembly, the synthesis strategy developed in this work can be extended as a general strategy to prepare ordered mesoporous yolk-shell structures with diverse compositions and morphologies simply by replacing solid silica spheres with silica-coated nanocomposites. The reduction of 4-nitrophenol with yolk-shell structured Au@ordered mesoporous aluminosilica as the catalyst has clearly demonstrated that the highly permeable perpendicular pore channels of mesoporous aluminosilica can effectively prevent the catalytically active yolk from aggregating. Furthermore, with accessible acidity, the yolk-shell structured ordered mesoporous aluminosilica spheres containing Pd yolk exhibit high catalytic activity and recyclability in a one-pot two-step synthesis involving an acid catalysis and subsequent catalytic hydrogenation for desired benzimidazole derivative, which makes the proposed hollow ordered aluminosilica spheres a versatile and practicable scaffold for advanced catalytic nanoreactor systems.

11.
BMC Genomics ; 13 Suppl 7: S4, 2012.
Artigo em Inglês | MEDLINE | ID: mdl-23282187

RESUMO

BACKGROUND: The opportunistic enterobacterium, Morganella morganii, which can cause bacteraemia, is the ninth most prevalent cause of clinical infections in patients at Changhua Christian Hospital, Taiwan. The KT strain of M. morganii was isolated during postoperative care of a cancer patient with a gallbladder stone who developed sepsis caused by bacteraemia. M. morganii is sometimes encountered in nosocomial settings and has been causally linked to catheter-associated bacteriuria, complex infections of the urinary and/or hepatobiliary tracts, wound infection, and septicaemia. M. morganii infection is associated with a high mortality rate, although most patients respond well to appropriate antibiotic therapy. To obtain insights into the genome biology of M. morganii and the mechanisms underlying its pathogenicity, we used Illumina technology to sequence the genome of the KT strain and compared its sequence with the genome sequences of related bacteria. RESULTS: The 3,826,919-bp sequence contained in 58 contigs has a GC content of 51.15% and includes 3,565 protein-coding sequences, 72 tRNA genes, and 10 rRNA genes. The pathogenicity-related genes encode determinants of drug resistance, fimbrial adhesins, an IgA protease, haemolysins, ureases, and insecticidal and apoptotic toxins as well as proteins found in flagellae, the iron acquisition system, a type-3 secretion system (T3SS), and several two-component systems. Comparison with 14 genome sequences from other members of Enterobacteriaceae revealed different degrees of similarity to several systems found in M. morganii. The most striking similarities were found in the IS4 family of transposases, insecticidal toxins, T3SS components, and proteins required for ethanolamine use (eut operon) and cobalamin (vitamin B12) biosynthesis. The eut operon and the gene cluster for cobalamin biosynthesis are not present in the other Proteeae genomes analysed. Moreover, organisation of the 19 genes of the eut operon differs from that found in the other non-Proteeae enterobacterial genomes. CONCLUSIONS: This is the first genome sequence of M. morganii, which is a clinically relevant pathogen. Comparative genome analysis revealed several pathogenicity-related genes and novel genes not found in the genomes of other members of Proteeae. Thus, the genome sequence of M. morganii provides important information concerning virulence and determinants of fitness in this pathogen.


Assuntos
Genoma Bacteriano , Morganella morganii/genética , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Mapeamento de Sequências Contíguas , Farmacorresistência Bacteriana , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Morganella morganii/isolamento & purificação , Morganella morganii/patogenicidade , Proteus mirabilis/genética , Análise de Sequência de DNA
12.
J Chem Phys ; 131(17): 174709, 2009 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-19895037

RESUMO

Random pairing simulation and low temperature scanning tunneling microscopy (STM) are used to investigate the detailed O(2) dissociative adsorption processes at 200 K for various coverages. The distribution of oxygen adatoms shows a strong repulsion between the adsorbates with a radius of approximately 0.8 nm. The comparison between STM results and simulation reveals two prominent pairing distances of 2 and 4 nm and their branching ratio is about 2:1. These findings shed new light on the origin of the large intrapair distances found and on the process behind the empirical "eight-site rule."

13.
J Chem Phys ; 127(3): 034708, 2007 Jul 21.
Artigo em Inglês | MEDLINE | ID: mdl-17655456

RESUMO

The Cl abstraction by gas-phase H atoms from a Cl-terminated Si(100) surface was investigated by scanning tunneling microscopy (STM), high-resolution core level photoemission spectroscopy, and computer simulation. The core level measurements indicate that some additional reactions occur besides the removal of Cl. The STM images show that the Cl-extracted sites disperse randomly in the initial phase of the reaction, but form small clusters as more Cl is removed, indicating a correlation between Cl-extracted sites. These results suggest that the hot-atom process may occur during the atom-adatom collision.

SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA
...