Insights into structural defect formation in individual InP/ZnSe/ZnS quantum dots under UV oxidation.

InP/ZnSe/ZnS quantum dots (QDs) stand as promising candidates for advancing QD-organic light-emitting diodes (QLED), but low emission efficiency due to their susceptibility to oxidation impedes applications. Structural defects play important roles in the emission efficiency degradation of QDs, but the formation mechanism of defects in oxidized QDs has been less investigated. Here, we investigated the impact of diverse structural defects formation on individual QDs and propagation during UV-facilitated oxidation using high-resolution (scanning) transmission electron microscopy. UV-facilitated oxidation of the QDs alters shell morphology by the formation of surface oxides, leaving ZnSe surfaces poorly passivated. Further oxidation leads to the formation of structural defects, such as dislocations, and induces strain at the oxide-QD interfaces, facilitating In diffusion from the QD core. These changes in the QD structures result in emission quenching. This study provides insight into the formation of structural defects through photo-oxidation, and their effects on emission properties of QDs.

Mycobacterium yongonense sp. nov., a slow-growing non-chromogenic species closely related to Mycobacterium intracellulare.

A slow-growing non-chromogenic mycobacterium was isolated from a patient with pulmonary disease. Phenotypically, strain 05-1390(T) was similar to Mycobacterium intracellulare ATCC 13950(T). The 16S rRNA gene sequence (1385 bp) of strain 05-1390(T) showed a high degree of similarity to those of the M. intracellulare complex, namely Mycobacterium marseillense 5351974(T) (100 %), M. intracellulare ATCC 13950(T) (99.8 %) and Mycobacterium chimaera DSM 44623(T) (99.9 %). Phylogenetic analysis based on internal transcribed spacer 1 (ITS1) and the hsp65 gene indicated that strain 05-1390(T) was closely related to M. intracellulare ATCC 13950(T), but that it was a distinct phylogenetic entity. Of particular interest, an analysis based on the rpoB gene (701 bp) showed that it is closely related to Mycobacterium parascrofulaceum ATCC BAA-614(T) (99.4 %), a scotochromogenic strain, rather than to the M. intracellulare-related strains. Unique MALDI-TOF MS profiles also supported the taxonomic status of this strain as a distinct species. These data support the conclusion that strain 05-1390(T) represents a novel mycobacterial species, for which the name Mycobacterium yongonense sp. nov. is proposed; the type strain is 05-1390(T) ( = DSM 45126(T) = KCTC 19555(T)).

Mycobacterium parakoreense sp. nov., a slowly growing non-chromogenic species related to Mycobacterium koreense, isolated from a human clinical specimen.

A previously undescribed, slowly growing, non-chromogenic Mycobacterium strain (299(T)) was isolated from the sputum sample of a patient with a symptomatic pulmonary infection. Phenotypically, strain 299(T) was generally similar to Mycobacterium koreense DSM 45576(T) and Mycobacterium triviale ATCC 23292(T). The 16S rRNA gene sequence of strain 299(T) was similar to that of M. koreense DSM 45576(T) (GenBank accession no. AY734996, 99.5% similarity); however, it differed substantially from that of M. triviale ATCC 23292(T) (X88924, 98.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 299(T) clustered together with M. koreense DSM 45576(T) and M. triviale ATCC 23292(T), supported by high bootstrapping values (99%). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 299(T) represents a novel mycobacterial species, for which the name Mycobacterium parakoreense sp. nov. is proposed. The type strain is 299(T) (=DSM 45575(T)=KCTC 19818(T)).

Method for 3D atomic structure determination of multi-element nanoparticles with graphene liquid-cell TEM.

Determining the 3D atomic structures of multi-element nanoparticles in their native liquid environment is crucial to understanding their physicochemical properties. Graphene liquid cell (GLC) TEM offers a platform to directly investigate nanoparticles in their solution phase. Moreover, exploiting high-resolution TEM images of single rotating nanoparticles in GLCs, 3D atomic structures of nanoparticles are reconstructed by a method called "Brownian one-particle reconstruction". We here introduce a 3D atomic structure determination method for multi-element nanoparticle systems. The method, which is based on low-pass filtration and initial 3D model generation customized for different types of multi-element systems, enables reconstruction of high-resolution 3D Coulomb density maps for ordered and disordered multi-element systems and classification of the heteroatom type. Using high-resolution image datasets obtained from TEM simulations of PbSe, CdSe, and FePt nanoparticles that are structurally relaxed with first-principles calculations in the graphene liquid cell, we show that the types and positions of the constituent atoms are precisely determined with root mean square displacement values less than 24 pm. Our study suggests that it is possible to investigate the 3D atomic structures of synthesized multi-element nanoparticles in liquid phase.

Mycobacterium koreense sp. nov., a slowly growing non-chromogenic species closely related to Mycobacterium triviale.

A novel slow-growing, non-chromogenic mycobacterium (strain 01-305(T)) was isolated from a patient with pulmonary dysfunction. Growth characteristics, acid-fastness and the results of 16S rRNA gene sequencing supported the placement of this strain within the genus Mycobacterium. Phenotypically, strain 01-305(T) was generally similar to Mycobacterium triviale ATCC 23292(T), but some unique biochemical characteristics were observed. The 16S rRNA gene sequence of strain 01-305(T) was similar to those of M. triviale ATCC 23290 (GenBank accession no. AY734996, 99.9 % similarity) and M. triviale ATCC 23291 (AY734995, 99.9 %); however, it differed substantially from that of M. triviale ATCC 23292(T) (X88924, 98.2 %). Phylogenetic analysis based on 16S rRNA gene sequences placed strain 01-305(T) in the slow-growing Mycobacterium group close to M. triviale ATCC 23290 and M. triviale ATCC 23291, but not M. triviale ATCC 23292(T). Unique mycolic acid profiles and phylogenetic analysis based on two different chronometer molecules, and the hsp65 and rpoB genes, strongly supported the taxonomic status of this strain as representing a distinct species. These data support the conclusion that strain 01-305(T) represents a novel mycobacterial species, for which the name Mycobacterium koreense sp. nov. is proposed. The type strain is 01-305(T) ( = DSM 45576(T) = KCTC 19819(T)).

PCR restriction fragment length polymorphism analysis (PRA)-algorithm targeting 644 bp Heat Shock Protein 65 (hsp65) gene for differentiation of Mycobacterium spp.

A method based on PCR-restriction fragment length polymorphism analysis (PRA) using a novel region of the hsp65 gene was developed for the rapid and exact identification of mycobacteria to the species level. A 644 bp region of hsp65 in 62 mycobacteria reference strains, and 4 related bacterial strains were amplified, and the amplified DNAs were subsequently digested with restriction enzymes, namely, AvaII, HphI, and HpaII. Most of the mycobacteria species were easily differentiated at the species level by the developed method. In particular, the method enabled the separation of M. avium, M. intracellulare and M. tuberculosis to the species level by AvaII digestion alone. An algorithm was constructed based on the results and a blind test was successfully performed on 251 clinical isolates, which had been characterized by conventional biochemical testing. Our results suggest that this novel PRA offers a simple, rapid, and accurate method for the identification of mycobacteria culture isolates at the species level.

Simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by polymerase chain reaction-single strand conformation polymorphism and sequence analysis of the RNA polymerase gene (rpoB).

Interspecies variations and mutations associated with rifampin resistance in rpoB of Mycobacterium allow for the simultaneous identification of rifampin-resistant Mycobacterium tuberculosis and nontuberculous mycobacteria by PCR-SSCP analysis and PCR- sequencing. One hundred and ten strains of rifampin-susceptible M. tuberculosis, 14 strains of rifampin-resistant M. tuberculosis, and four strains of the M. avium complex were easily identified by PCR-SSCP. Of another seven strains, which showed unique SSCP patterns, three were identified as rifampin-resistant M. tuberculosis and four as M. terrae complex by subsequent sequence analysis of their rpoB DNAs (306 bp). These results were concordant with those obtained by susceptibility testing, biochemical identification, and 16S rDNA sequencing.

Identification of Mycobacterium tuberculosis by PCR-linked reverse hybridization using specific rpoB oligonucleotide probes.

A reverse probe hybridization method using two different Mycobacterium tuberculosis-specific rpoB DNA probes in combination was evaluated for the identification of M. tuberculosis culture isolates. Among the 384 isolates tested, 354 strains were identified as M. tuberculosis, which included 37 rifampin-resistant strains, and 30 were nontuberculous mycobacteria (NTM). This result was in accord with partial rpoB sequence analysis and IS6110 polymerase chain reaction (PCR) results, but not with the results of biochemical testing, which produced two false negative results. Because of its high level of sensitivity and specificity, we suggest that M. tuberculosis-specific rpoB probes immobilized on micro-titer well plates or on other solid matrixes can be used efficiently for the rapid and convenient identification of M. tuberculosis.

Discovery of a novel hsp65 genotype within Mycobacterium massiliense associated with the rough colony morphology.

So far, genetic diversity among strains within Mycobacterium massiliense has rarely been studied. To investigate the genetic diversity among M. massiliense, we conducted phylogenetic analysis based on hsp65 (603-bp) and rpoB (711-bp) sequences from 65 M. massiliense Korean isolates. We found that hsp65 sequence analysis could clearly differentiate them into two distinct genotypes, Type I and Type II, which were isolated from 35 (53.8%) and 30 patients (46.2%), respectively. The rpoB sequence analysis revealed a total of four genotypes (R-I to R-IV) within M. massiliense strains, three of which (R-I, R-II and R-III) correlated with hsp65 Type I, and other (R-IV), which correlated with Type II. Interestingly, genotyping by the hsp65 method agreed well with colony morphology. Despite some exceptions, Type I and II correlated with smooth and rough colonies, respectively. Also, both types were completely different from one another in terms of MALDI-TOF mass spectrometry profiles of whole lipid. In addition, we developed PCR-restriction analysis (PRA) based on the Hinf I digestion of 644-bp hsp65 PCR amplicons, which enables the two genotypes within M. massiliense to be easily and reliably separated. In conclusion, two distinct hsp65 genotypes exist within M. massiliense strains, which differ from one another in terms of both morphology and lipid profile. Furthermore, our data indicates that Type II is a novel M. massiliense genotype being herein presented for the first time. The disparity in clinical traits between these two hsp65 genotypes needs to be exploited in the future study.

Accuracy and Safety of Bedside External Ventricular Drain Placement at Two Different Cranial Sites : Kocher's Point versus Forehead.

OBJECTIVE: External ventricular drain (EVD) is commonly performed with a freehand technique using surface anatomical landmarks at two different cranial sites, Kocher's point and the forehead. The aim of this study was to evaluate and compare the accuracy and safety of these percutaneous ventriculostomies. METHODS: A retrospectively review of medical records and head computed tomography scans were examined in 227 patients who underwent 250 freehand pass ventriculostomy catheter placements using two different methods at two institutions, between 2003 and 2009. Eighty-one patients underwent 101 ventriculostomies using Kocher's point (group 1), whereas 146 patients underwent 149 forehead ventriculostomies (group 2). RESULTS: In group 1, the catheter tip was optimally placed in either the ipsilateral frontal horn or the third ventricle, through the foramen of Monro (grade 1) in 82 (81.1%) procedures, in the contralateral lateral ventricle (grade 2) in 4 (3.9%), and into eloquent structures or non-target cerebrospinal space (grade 3) in 15 (14.8%). Intracerebral hemorrhage (ICH) >1 mL developed in 5 (5.0%) procedures. Significantly higher incidences of optimal catheter placements were observed in group 2. ICH>1 mL developed in 11 (7.4%) procedures in group 2, showing no significant difference between groups. In addition, the mean interval from the EVD to ventriculoperitoneal shunt was shorter in group 2 than in group 1, and the incidence of EVD-related infection was decreased in group 2. CONCLUSION: Accurate and safe ventriculostomies were achieved using both cranial sites, Kocher's point and the forehead. However, the forehead ventriculostomies provided more accurate ventricular punctures.

Mycobacterium paraseoulense sp. nov., a slowly growing, scotochromogenic species related genetically to Mycobacterium seoulense.

A previously unidentified, slowly growing, scotochromogenic Mycobacterium species, represented by strain 31118(T), was discovered during hsp65 sequence-based reidentification of Korean clinical isolates that had been previously identified as Mycobacterium scrofulaceum by conventional biochemical tests. Although the 16S rRNA gene sequence of strain 31118(T) was identical to that of the recently described Mycobacterium seoulense, phylogenetic analyses based on three independent alternative targets (rpoB, hsp65 and the 16S-23S internal transcribed spacer) showed that it was closely related to M. seoulense but was a distinct phylogenetic entity. Furthermore, the phenetic characteristics of this strain were more similar to those of M. scrofulaceum than to those of M. seoulense. Taken together, these results support the conclusion that this strain represents a novel mycobacterium species, for which the name Mycobacterium paraseoulense sp. nov. is proposed. The type strain is 31118(T) (=DSM 45000(T) =KCTC 19145(T)).

Mycobacterium paraterrae sp. nov. recovered from a clinical specimen: novel chromogenic slow growing mycobacteria related to Mycobacterium terrae complex.

A previously unidentified, slowly growing scotochromogenic Mycobacterium was isolated from a Korean patient with symptomatic pulmonary infection. Phenotypically, this strain was generally similar to Mycobacterium terrae complex strains, however it uniquely produced orange pigmentation. Unique mycolic acid profiles and phylogenetic analyses based on three alternative chronometer molecules, 16S rRNA gene, hsp65 and rpoB, confirmed the taxonomic status of this strain as a novel species. These results support that this strain represents a novel Mycobacterium species. The name Mycobacterium paraterrae sp. nov. is proposed. The type strain is 05-2522 (= DSM 45127 = KCTC 19556).

Mycobacterium senuense sp. nov., a slowly growing, non-chromogenic species closely related to the Mycobacterium terrae complex.

A previously undescribed, slowly growing, non-chromogenic mycobacterium, isolated from a Korean patient with a symptomatic pulmonary infection, is described as representing a novel species. Its 16S rRNA gene sequence was unique and phylogenetic analysis based on 16S rRNA gene sequences showed that this organism belonged to the Mycobacterium terrae subclade. Phenotypically, the strain was generally similar to M. terrae and Mycobacterium nonchromogenicum, but its growth rate was slower than those of other M. terrae complex strains. A unique mycolic acid profile and phylogenetic analysis based on two different alternative chronometer molecules, hsp65 and rpoB, confirm the taxonomic status of this strain as a representative of a novel species. The name Mycobacterium senuense sp. nov. is proposed, with the type strain 05-832(T) (=DSM 44999(T) =KCTC 19147(T)).

Direct application of AvaII PCR restriction fragment length polymorphism analysis (AvaII PRA) targeting 644 bp heat shock protein 65 (hsp65) gene to sputum samples.

To evaluate the usefulness of the AvaII PRA method targeting 644-bp hsp65 gene for the direct detection of pathogenic mycobacteria from clinical specimens, we applied this method to 40 sputum samples and compared the results to those obtained by IS 6110 PCR. Although this method showed a sensitivity slightly lower than IS 6110 PCR (97.5% vs. 100%), it detected infections of M. avium complex (MAC) in two patients, which was not possible by IS 6110 PCR. We conclude that AvaII PRA is a highly effective method for directly detecting pathogenic mycobacteria in primary clinical specimens.

Mycobacterium seoulense sp. nov., a slowly growing scotochromogenic species.

A previously undescribed, slowly growing, scotochromogenic mycobacterium was isolated from a patient with symptomatic pulmonary infection during hsp65 sequence-based identification of Korean clinical isolates. Phenetic characteristics of this strain were generally similar to those of Mycobacterium nebraskense and Mycobacterium scrofulaceum. However, some phenetic characteristics differentiated it from these two species. Its 16S rRNA gene sequences were unique and phylogenetic analysis based on 16S rRNA gene sequences placed the organism in the slowly growing Mycobacterium group close to M. nebraskense and M. scrofulaceum. Its unique mycolic acid profiles and the results of phylogenetic analysis based on two independent alternative chronometer molecules, hsp65 and rpoB, confirmed the taxonomic status of this strain as representing a novel species. These data support the conclusion that this strain represents a novel mycobacterial species, for which the name Mycobacterium seoulense sp. nov. is proposed. The type strain is strain 03-19(T) (=DSM 44998(T)=KCTC 19146(T)).

Differentiation of Mycobacterial species by hsp65 duplex PCR followed by duplex-PCR-based restriction analysis and direct sequencing.

Here we describe a novel duplex PCR method which can differentiate Mycobacterium tuberculosis and nontuberculosis mycobacteria (NTM) strains by amplifying hsp65 DNAs of different sizes (195 and 515 bp, respectively). The devised technique was applied to 54 reference and 170 clinical isolates and differentiated all strains into their respective groups with 100% sensitivity and specificity. Furthermore, a duplex PCR-restriction analysis (duplex PRA) and a direct sequencing protocol were developed to differentiate NTM strains at the species and subspecies levels based on previously reported hsp65 DNA sequences (H. Kim et al., Int. J. Syst. Evol. Microbiol. 55:1649-1656, 2005) and then applied to 105 NTM clinical isolates. All NTM isolates were clearly differentiated at the species and subspecies levels by subsequent procedures (PRA or direct sequencing) targeting 515-bp NTM duplex PCR amplicons. Our results suggest that novel duplex PCR-based methods are sensitive and specific for identifying mycobacterial culture isolates at the species level.

Analysis of magnetization in nanocomposite Nd4.5(Fe,Cr)77B18.5 by electron holography and simulation.

Magnetization distribution in nanocomposite Nd4.5(Fe,Cr)77B18.5 was studied by electron holography and computer simulation. In order to understand the detailed magnetization distribution, the magnetic flux distribution was calculated taking into account the magnetic charge or the stray field on the basis of magnetization models consisting of small magnetic dipoles and was compared with that in reconstructed phase images experimentally observed. Through the comparison, the characteristic feature in the distribution of the magnetization distribution in the nanocomposite magnetic materials was clarified, and the distribution was found to well correspond to their magnetic properties. It is pointed out that for understanding magnetization, the interpretation of reconstructed phase images should be done through computer simulation just as the analysis of high-resolution electron microscope images. Eventually, it was demonstrated that electron holography with computer simulation is quite useful to analyze detailed magnetization distribution in nanocrystalline magnetic materials at the nanometer scale.

Differentiation of Mycobacterium species by analysis of the heat-shock protein 65 gene (hsp65).

The nucleotide sequences (604 bp) of partial heat-shock protein genes (hsp65) from 161 Mycobacterium strains containing 56 reference Mycobacterium species and 105 clinical isolates were determined and compared. hsp65 sequence analysis showed a higher degree of divergence between Mycobacterium species than did 16S rRNA gene analysis. Generally, the topology of the phylogenetic tree based on the hsp65 DNA sequences was similar to that of the 16S rRNA gene, thus revealing natural relationships among Mycobacterium species. When a direct sequencing protocol targeting 422 bp sequences was applied to 70 non-tuberculous mycobacterium (NTM) clinical isolates, all NTMs were clearly identified. In addition, an XhoI PCR restriction fragment length polymorphism analysis method for the differentiation of Mycobacterium tuberculosis complex from NTM strains was developed during this study. The results obtained suggest that 604 bp hsp65 sequences are useful for the phylogenetic analysis and species identification of mycobacteria.

Electron holography on remanent magnetization distribution of melt-spun Nd-Fe-B magnets.

Microstructures and magnetic domain structures of melt-spun Nd-Fe-B permanent magnets were investigated in detail by analytical electron microscopy and electron holography. While the crystal orientation of matrix Nd2Fe14B grains was analyzed by nanobeam electron diffraction, precipitates of a few tens of nanometers at grain boundaries were identified to be alpha-Fe by energy-dispersive X-ray spectroscopy. The detailed magnetization distribution in Nd2Fe14B grains and at their boundaries was visualized by electron holography. Ex situ experimentation with an electromagnet revealed that the domain walls in the demagnetized state and remanent states were pinned at grain boundaries, and Fe precipitates at the grain boundary were situated at the center of the closure domain.

Transmission electron microscopy on thin film of high density magnetic composite prepared by FIB method.

A thin specimen of a high density magnetic composite (HDMC), which is a type of powder magnetic cores was prepared for transmission electron microscopy (TEM) using a focused ion beam (FIB) method. A homogeneous thin film containing an insulator boundary between the constituent Fe powders was obtained successfully. Using this thin film, detailed flow of magnetic flux was visualized by electron holography, and the magnetic flux density was estimated to be 1.73 +/- 0.09 T being consistent with that of a bulk HDMC (1.70 T). Moreover, through Lorentz microscopy, the characteristic magnetization process of HDMC was observed by applying the magnetic field up to approximately 8 kA/m.