J Comput Theor Nanosci 2013, 10:1–5.CrossRef 28. Neamen DA: Semiconductor Physics and Devices. 3rd edition. New York: McGraw-Hill; 2003. 29. Kargar A, Lee C: Graphene nanoribbon schottky diodes using asymmetric contacts. In Proceedings of the IEEE-NANO2009: 9th Conference on Nanotechnology, 2009: July 26–30 2009; Genoa. Piscataway: IEEE; 2009:243–245. 30. Jimenez D: A current–voltage model for Schottky-barrier graphene based transistors. Nanotechnology 2008, 19:345204.CrossRef 31. Ahmadi MT, Rahmani M, Ghadiry MH, Ismail R: Monolayer graphene nanoribbon homojunction characteristics. Sci Adv Mater 2012, 4:753–756.CrossRef 32. Sadeghi H, Ahmadi MT, Mousavi M, Ismail R: Channel conductance of ABA stacking GDC-0994 chemical structure trilayer graphene field

effect transistor. Mod Phys Lett B 2012, 26:1250047.CrossRef 33. Avetisyan AA, Partoens B, Peeters FM: Electric-field control of the band gap and Fermi energy in graphene multilayers by top and back gates. Phys Rev B 2009, 80:195401.CrossRef 34. McCann E, Koshino M: Spin-orbit coupling and

broken spin degeneracy in multilayer graphene. Phys Rev B 2010, 81:241409.CrossRef 35. Guinea F, Castro Neto AH, Peres NMR: Electronic states and Landau levels in graphene stacks. Phys Rev B 2006, 73:245426.CrossRef 36. Latil S, Meunier V, Henrard L: Massless fermions Selleck Adriamycin in multilayer graphitic systems with misoriented layers: ab initio calculations and experimental fingerprints. Phys Rev B 2007, 76:201402.CrossRef 37. Castro EV, Novoselov KS, Morozov SV, Peres NMR, Santos JMB L, Nilsson J, Guinea F, Geim AK, Castro AH: Electronic

properties of a biased graphene bilayer. J Phys PU-H71 cell line Condens Matter 2010, 22:175503.CrossRef 38. Kato T: Perturbation Theory for Linear Operators. Berlin: Springer; 1995:132. 39. Rahmani M, Ahamdi MT, Ghadiry MH, Anwar S, Ismail R: The effect of applied voltage on the carrier effective mass in ABA trilayer graphene nanoribbon. Comput Theor Nanosci 2012, 9:1–4.CrossRef acetylcholine 40. Guinea F, Castro Neto AH, Peres NMR: Interaction effects in single layer and multi-layer graphene. Eur Phys J Spec Top 2007, 148:117–125.CrossRef 41. Krompiewski S: Ab initio studies of Ni-Cu-Ni trilayers: layer-projected densities of states and spin-resolved photoemission spectra. J Phys Condens Matter 1998, 10:9663.CrossRef 42. Arora VK: Failure of Ohm’s law: its implications on the design of nanoelectronic devices and circuits. In Proceedings of the 2006 25th IEEE International Conference on Microelectronics: May 14–17 2006; Belgrade. Piscataway: IEEE; 2006:15–22. 43. Rahmani M, Ahmadi MT, Ismail R, Ghadiry MH: Quantum confinement effect on trilayer graphene nanoribbon carrier concentration. J Exp Nanosci in press 44. Kumar SB, Guoa J: Chiral tunneling in trilayer graphene. Appl Phys Lett 2012, 100:163102.CrossRef 45. Datta S: Electronic Transport in Mesoscopic Systems. Cambridge: Cambridge University Press; 2012. 46. Polyanin AD: Cubic equation. [http://​eqworld.​ipmnet.​ru/​en/​solutions/​ae/​ae0103.​pdf] 47.

Shannon’s index is affected by the selleck chemical species number and their equitability, check details or evenness. A greater number of species and an even distribution of abundances result in an elevated Shannon’s diversity index. The maximum Shannon’s diversity

index for a sample indicates that all species are nearly equally abundant. The Gini-Simpson’s diversity index is measured as the probability that two individuals randomly selected from a sample belong to the same species, with a range from 0 to 1. Value of 0 indicates lack of diversity, i.e., one dominant species or taxon in the community, and 1 suggests that the community contains an infinite number of taxa with all taxa present equally. Before alpha-diversity indices were calculated, multiple rarefactions were performed with our own Perl scripts. All fungal reads from each marker were resampled starting at the depth of 1,000 reads, stepping up to 385,000 reads with increments of 1,000, and ten replicates were done at each sampling depth. For illustrating fungal find more diversities, taxonomic

relationships of all detected fungal genera were converted to the Newick format and uploaded to the web-based tool Interactive Tree Of Life v2.2 (Letunic and Bork 2011), and the taxonomic trees for each barcode and for all barcodes combined were generated. Estimation of the taxon abundance based on copy numbers of PCR-amplified DNA reads for a mixture of homologous genes in a multi-template PCR can be biased due to the differences in the primer binding energy to the target (Kanagawa 2003). Consequently, the taxon diversity and proportion of any given operational taxonomic

unit (OTU) in the fungal community are expected to differ when using different sets of DNA barcodes. In this study, the percentage of reads for a taxon was calculated by dividing the total reads of fungi generated by individual barcodes (Table S3). Because of the bias in mafosfamide the taxonomic assignations of mtATP6, that was restricted to the class Agaricomycetes except for six reads, we excluded mtATP6 from estimating species abundance with multiple barcodes. The percentage of reads for each of the genera generated from five barcodes (ITS1/2, ITS3/4, nrLSU-LR, nrLSU-U and mtLSU) was then transformed to a rank score based on the abundance of each genus in the community using the formula 20 − 19 (rank − 1)/(N − 1). The ranks (1, 2, 3…to N) represent the order of abundance (percentage of reads) for all taxa; thus, a taxon with rank 1 is most abundant and receives the highest rank score (20). When several taxa have the same abundance, the highest rank of these taxa was used as representative. The highest rank score was set to 20 for a given taxon having the highest number of reads (rank = 1), and the lowest rank score was set to 1 for a given taxon having lowest number of reads (rank = N).

The MH cockroach hemolymph, which contains phagocytic hemocytes, was fixed and stained with DAPI. Figure 5A shows a representative field containing the blue-staining nuclei from multiple hemocytes. As expected, the non-nuclear regions of most hemocytes could not be visualized with this fluorescent DNA stain. Interestingly, each field also contained one or two hemocytes in which the nucleus and the surrounding cytosol could be easily visualized (Figure 5A, white arrows). We speculated that these particular hematocytes might contain cytosolic B. pseudomallei and we stained the hemolymph with a Salubrinal manufacturer polyclonal antibody that reacts with B. pseudomallei. Figure 5B and 5 C show a representative micrograph

of a hematocyte engorged with cytosolic B. pseudomallei, suggesting that the bacteria are multiplying to high numbers inside these cells. Free bacteria can also be visualized in the hemolymph outside the hemocyte, but it is unclear if these PARP inhibitor cells are alive or dead (Figure 5B and 5 C). Some infected hemocytes appear to have multiple nuclei and may be multinucleated giant cells (MNGCs) (Figure 5). MNGC have been observed in cases of human melioidosis [28] and are often formed when B.pseudomallei infects murine selleck compound macrophage-like cell lines in vitro [9]. The formation of B. pseudomallei-induced MNGCs in vivo in MH cockroaches is an exciting finding and indicates that

MNGCs can form in non-adherent cells freely flowing within the hemolymph. Figure 5 B. pseudomallei multiplies inside MH cockroach hemocytes. Panel A is a representative micrograph of hemolymph obtained from a MH cockroach infected with B. pseudomallei K96243 and stained with DAPI. The white arrows show hemocytes that harbor intracellular B. pseudomallei. The white scale bar is 100 μm. Panels B and C show a higher magnification of a B. pseudomallei-infected hemocyte using bright field microscopy (B) and stained with DAPI and a Burkholderia-specific rabbit polyclonal antibody (C). The secondary antibody used, Alexa Fluor 588 goat anti-rabbit IgG, stained B. pseudomallei green. The magnified inset in C shows individual bacilli within the hemocyte cytosol Bay 11-7085 and the white arrows show extracellular

bacteria in the hemolymph. The white scale bars in B and C are 20 μm. The results are representative images from eight MH cockroaches infected with ~ 103 cfu of B. pseudomallei K96243. Based on these results, we hypothesize that B. pseudomallei is able to survive the innate immune system of the MH cockroach by establishing an intracellular niche within the hemocyte. Infected hemocytes harboring numerous cytosolic bacteria may fuse with uninfected hemocytes to form MNGCs, which may serve as a reservoir for continued bacterial replication and protection from the antimicrobial peptides present in the surrounding hemolymph. The amplification of bacteria within phagocytic hemocytes, and their subsequent release, may eventually overwhelm the MH cockroach and lead to death.

The intercellular transmissibility of the mobile genetic elements with carried gene cassettes could constitute important driving forces in genome evolution and speciation of Vibrios, but also mediate the emergence, resurgence and spread of multiple drug resistant pathogens [17–19]. China has become the world’s largest producer of aquatic products since 2002 (People’s Republic of China, Fishery Products Annual Report). The East China Sea has been one of the major fishing grounds, especially

within the Yangtze River plume and its click here surrounding sea along China’s coast [20]. Along with improved aquaculture production, however, incidences of food-borne illnesses caused by consumption of aquatic products contaminated with Vibrios have www.selleckchem.com/products/jnk-in-8.html also rapidly increased, particularly in the littoral provinces [21]. Previous research suggested that acquisition of virulence and resistance traits through horizontal gene transfer might occur at high frequency through microbial contacts in the environment [22]. Nevertheless, to date, numerous studies have been conducted to identify ICEs-harboring Vibrios Milciclib manufacturer from clinical samples in different parts of the world [23], but very few information is available on environmental isolates. Thus, in this study, we focused on analyzing

the Vibrio strains bearing the SXT/R391-related ICEs that Liothyronine Sodium were isolated from aquatic products and environment in the Yangtze River Estuary in Shanghai, China.

Molecular structures of the ICEs and phenotypes of their hosts have been characterized. The information will facilitate the better understanding of possible mechanism underlying ICE evolution and dissemination of food-borne diseases mediated by the mobile genetic elements. Results and discussion Bacterial isolation, screening and identification of ICEs-positive strains The Yangze River, being the third largest river (about 6,300 km in length) in the world, originates from the Qingzhang plateau, runs through eleven Chinese provinces and regions, and finally enters into the East China Sea in Shanghai, China. Environmental surface water samples were collected from the Yangtze River Estuary in Shanghai during the years between 2010 and 2011, while aquatic products including shrimps and fish were sampled from fish markets distributed in Shanghai in 2011. Pure cultures of Vibrio isolates were transferred into sterile 96-well microtiter plates, and used for PCR-based screening of the conserved essential integrase gene (int) of SXT/R391-related ICEs (see the Methods). A total of one hundred and fifty three isolates were detected positive for the int gene from about forty one plates.

immitis infection. The upregulation of the ISGs CXCL9 and UBD in DBA/2 mice, which are predominantly modulated by Type II IFN [14, 27, 28], suggested that the interferon gamma (IFNG)

gene should also be upregulated in this mouse strain. However, IFNG was not a top 100 modulated gene (Figure 2) and upon closer examination of the microarray data was found to be expressed below background levels (data not shown). Since our initial time course may have missed the peak of induction of IFNG, a targeted analysis of cytokine expression was performed at an additional time point (day 15) using a complementary technology, namely the Mouse Common Cytokines Gene Array from SABiosciences (Frederick, MD, USA). This cytokine array confirmed that IFNG was expressed to a greater extent in DBA/2 compared to C57BL/6 mice with a log2 fold change of 1.50 (actual fold change of 2.82, Additional file 1: Figure S2). The cytokine with the greatest Wnt inhibitor differentially expression between mice strains at day 15 detected

by the Mouse Common Cytokines Gene Array was interleukin 17A (IL17A), which had a log2 fold change of 1.83 (actual fold change of 3.56). Therefore, IFNG and IL17A were also selected as targets for RT-qPCR analysis at days 14 and 16 in order to determine if this more sensitive technique could confirm expression of these cytokines at these time points. Real-time Smad3 signaling quantitative PCR analysis of interferon and hypoxia associated genes To validate microarray gene expression results and further confirm the role of responses to IFN-γ and HIF-1α in the resistance of DBA/2 mice to C. immitis infection, RT-qPCR analysis was performed at days 10 (Additional file 1: Figure S3A), 14 (Figure 7), and 16

(Additional file 1: Figure S3B) BI 2536 concentration post-infection for the following thirteen targets: CXCL9, HIF1A, IFNG, IL6, IL17A, IRGM1, ISG20, LYVE1, PSMB9, STAT1, THBS1, TNFA and UBD. The differential gene expression between mice strains detected by microarray was confirmed at day 14 by RT-qPCR for all targets at the 2-fold level (log2 fold change of 1) except for ISG20. In addition, although microarray analysis Cobimetinib in vitro did not indicate that IFNG and IL17A were differentially expressed between mice strains, RT-qPCR analysis confirmed that both were expressed to a greater extent in DBA/2 compared to C57BL/6 mice at day 14 post-infection with C. immitis. Even with a limited number of biological replicates at day 14, the majority of targets (CXCL9, HIF1A, IFNG, IL17A, IL6, IRGM1, PSMB9, STAT1, TNFA and UBD) were significantly differentially expressed (p <0.05, t-test) between mouse strains (Figure 7). Figure 7 Confirmation of gene expression differences by RT-qPCR between DBA/2 and C57BL/6 mice at day 14 following C. immitis infection. The fold change for each gene, calculated by dividing the expression level in DBA/2 mice by the expression level in C57BL/6 mice is presented for RT-qPCR data (grey bars).

brucei, TbPRMT1 [27]. Of particular interest to us are proteins whose functions might be affected by arginine methylation. Here, we report that TbPRMT1 directly interacts in both Far Western and co-immunoprecipitation assays with a novel protein. We termed this protein TbLpn, based on the presence of two URMC-099 mw conserved (N-LIP and C-LIP) domains

found in a family of proteins called lipins. We further demonstrate that, like TbPRMT1, TbLpn is cytoplasmic in PF T. brucei, consistent with a function in TbLpn methylation. Together, these data point to TbLpn as a candidate protein whose post-transcriptional NSC 683864 price gene regulatory functions are affected by arginine methylation. We demonstrated that, as predicted from the amino GSK458 nmr acid sequence, recombinant TbLpn, as other members of the lipin family, exhibits phosphatidic acid phosphatase enzymatic activity. Mutation of the conserved aspartic acid residues (Asp-445 and Asp- 447) to alanines results in a significant reduction in the enzymatic activity of TbLpn. These two aspartic acid residues are part

of the conserved DxDxT motif found in lipin proteins and other members of the haloacid dehalogenase (HAD)-like superfamily [53, 54]. Based on the crystal structure of L-2-haloacid dehalogenase from Pseudomonas, it is likely that Asp-445 in TbLpn acts as a nucleophile in the phosphoryl transfer reaction. Compared to the recombinant yeast PAH1 (3000 nmol/min/mg) and human Lipin-1 (1,600 nmol/min/mg), His ~ TbLpn displays a lower but still significant specific activity [43]. One possible explanation for this lower specific activity

is the fact that the recombinant protein may not contain the same post-translational modifications as those found in the native protein. It is of interest that several lipin Selleck Pazopanib homologues are highly modified at the post translational level. In rat and in mouse adipocytes, Lipin 1 contains at least 19 and as many as 23 sites that are phosphorylated in response to insulin [49, 55, 56]. Although it does not affect its intrinsic phosphatidic acid phosphatase activity, phosphorylation of Lipin-1 decreases the association with intracellular membranes, thus the active lipin fraction [49]. In addition, the lipin homologue SMP2 is phosphorylated by the cyclin-dependent kinase Cdc28/Cdk1 in budding yeast [57]. The authors have shown that phosphorylation of SMP2 by Cdc28/Cdk1 enhances its association with promoters of lipid biosynthetic genes, which leads to their transcriptional down-regulation. Careful analysis of TbLpn amino acid sequence revealed the presence of 5 conserved amino acid residues shown to be phosphorylated in either mouse (Mm) Lipin-1 or yeast (Sc) Smp2. These residues are Ser-102 (Ser-110 in Sc), Thr-239 (Thr-282 in Mm), Thr-255 (Thr-298 in Mm), Ser-282 (Ser-328 in Mm), and Ser-343 (Ser-392 in Mm). In addition, a previous analysis of the cytosolic phosphoproteome of BF T.

Our results imply that there are no E. coli strains that have generally high or low levels of persisters; instead, there are different types of persister cells within populations, and each type may be more or less persistent to different antibiotics. Importantly, the variation in persister fractions exists even for antibiotics with nearly identical modes of LDN-193189 action (ciprofloxacin and nalidixic acid). Mechanistically, this suggests that persistence through cell dormancy is not a single, general phenomenon. Instead, check details there

may be distinct physiological states of dormancy, each of which is differently susceptible to a particular antibiotic. The idea that there are different types of persister cells that arise from a variety of mechanisms has also been proposed in a recently published study [34]. We note that one complicating factor in this interpretation is that these different persister populations may have different Eltanexor order propensities to form colonies, and that this might explain some of the differences in the shapes of the kill curves that we observed. However, given the range of persister fractions that we observed (over four orders of magnitude), we do not think that this mechanism can fully explain the patterns that we find. It is also possible that

although the isolates that we studied have similar MIC values, they differ in their pharmacodynamics [35]. However, the persister fraction should largely be independent of

the pharmacodynamic behavior; thus this is unlikely to account for the differences that we observe between isolates [34]. Evidence of two different types of persister cells has been shown previously by Balaban et al. [6], and genotypic changes at different loci were associated with each phenotype. Similarly, genetic differences between different E. coli isolates, such as the presence or absence of TA various modules, may affect the production of persister cells (Figure 6). Gefen et al. [36] suggested that large differences in the measurement of persister fractions might arise because antibiotic Ponatinib in vitro exposure begins at different stages of exponential growth (before or after 1.5 hours of growth). However, by growing the cells for four hours, we hope to have minimized such effects, and propose that the large differences we find in persister fractions are not due to differences in growth stage, but to fundamental differences in the mechanisms of persister production. We note that the set of environment isolates that we have used are not known to be pathogenic, suggesting that many of them have had less exposure to antibiotics and the concomitant selection for resistant or persister phenotypes that arises from such exposure.

According to our Northern blot findings and previously published microarray data [35], gudB, encoding glutamate dehydrogenase, and rocD, encoding ornithine aminotransferase, seemed https://www.selleckchem.com/products/byl719.html to be co-transcribed. Interestingly, this operon contains three putative cre-sites (see Additional file 3: CcpA-dependent

down-regulation by glucose), suggesting a complex transcriptional regulation by CcpA, which could be confirmed by our Northern blot analyses, showing that rocD/gudB-transcription is largely affected by CcpA in response to glucose. Similarly, aldA, arg, and rocA transcription patterns determined by Northern analyses showed the same tendency as our microarray data (Fig. 2). Table 4 shows genes coding for transporters or lipoproteins which were regulated by glucose in a CcpA-dependent manner or which were partially controlled by CcpA. Seven of these genes contained putative cre-sites in their promoter regions, or as in the case of SA0186, SA0302, and

gntP, belonged to an operon which contained a putative cre-site and were probably under the direct control of CcpA. The up-regulation of the glucose uptake protein homologue (SA2053) may contribute to the rapid glucose consumption observed in the wild-type (Fig. 1). Many putative non-sugar-transporters were found to be regulated by CcpA: MM-102 research buy Amongst them, the selleck opu-operon, which is preceded by a putative cre-site and consists of opuCA-opuCB-opuCC-opuCD, coding for a glycine-betaine/carnitine/choline ABC transporter, acting in osmoprotection [36], was up-regulated by glucose. Interestingly, the same operon is also up-regulated in femAB mutants, due to a secondary effect compensating for an impaired cell envelope [37]. S. aureus possesses two systems involved in osmoprotection [36], the second system encoded

by the opuD gene did not appear to be regulated by CcpA. Table 4 CcpA-dependent genes coding for transport/binding proteins and lipoproteins regulated by glucose ID   Producta wt mut N315 Newman common   +/- Dolutegravir molecular weight b +/- b Down-regulated by glucose SA0100 NWMN_0049   similar to Na+ Pi-cotransporter 0.2 1.7 *SA0186 NWNM_0136   sucrose-specific PTS tranporter IIBC component protein 0.4 1.2 *SA0302 NWNM_0255   probable pyrimidine nucleoside transport protein 0.4 1.8 SA1848 NWNM_1950 nrgA probable ammonium transporter 0.4 0.8 SA2226 NWNM_2337   similar to D-serine/D-alanine/glycine transporter 0.2 0.9 SA2227 NWNM_2337   amino acid ABC transporter homologue 0.1 0.9 Up-regulated by glucose SA0166 NWNM_0116   similar to nitrate transporter 2.8 1.1 SA0167 NWNM_0117   similar to membrane lipoprotein SrpL 2.8 1.6 SA0168 NWNM_0118   similar to probable permease of ABC transporter 2.3 1.1 SA0214 NWMN_0158 uhpT hexose phosphate transport protein 2.1 1.1 SA0335 NWMN_0340   twin-arginine translocation protein TatA 2.2 1.4 SA0374 NWNM_0379 pbuX xanthine permease 7.2 1.1 *SA0655 NWNM_0669 fruA fructose specific permease 2.4 1.

Primers used for sequencing are displayed in Additional file 2 Table S2. PCR products were purified by using ExoSAP-IT (USB, Cleveland, USA) and DNA sequencing reactions were performed in both directions using BigDyeTerminator v3.1 (Applied Biosystems, Selleckchem CA4P Nieuwerkerk a/d IJssel, the Netherlands)

on a 48-capillary 3730 DNA Analyzer sequencer (Applied Biosystems, Nieuwerkerk a/d IJssel, the Netherlands). Accession numbers: HQ222846 to HQ222861 and HQ606074. PCR and real-time qPCR Oligonucleotides were synthesized by Biolegio (Biolegio, Nijmegen, the Netherlands). Conventional PCR was used to produce amplicons from signature sequences. Amplification was carried out using the HotStar Taq Master Mix Kit (Qiagen, Westburg, the Netherlands) and 400 nM primers in a total reaction volume of 50 μl. Primer sets were designed using Visual OMP software (Additional file 2 Table S2). Thermocycling conditions Temsirolimus mouse were as follows: 95°C for 15 min, 40 cycles at 95°C for 30 sec, 55°C for 30 sec and 72°C for 30 sec, followed by a final step at 72°C for 7 min.

Thermocycling reactions were carried out in a Px2 thermal cycler (Thermo Electron Corporation, Breda, the Netherlands). All qPCR reactions were carried out in a final volume of 20 μl containing iQ Multiplex Powermix (Bio-Rad, Veenendaal, the Netherlands), 200 nM of each primer and 100-300 nM hydrolysis probes and 3 μl of DNA template. Probes concentrations had been optimized to yield minimal spectral overlap between fluorescence level of the reporter dyes for each target in a multiplex assay and were 100, 200, 300 and 300 nM for FAM, JOE, CFR590 and Cy5 labeled probes respectively. The multiplex real-time qPCR selleck inhibitor assays had been designed for an optimal annealing temperature of 60°C and the thermal cycling conditions were as follows: First enzyme activation at 95°C for 5 min, followed by amplification and detection by 45 cycles at 95°C for 5 sec and 60°C for 35 sec. Each real-time

qPCR experiment included a negative (no template) control. Measurements were carried out on a Lightcycler 480 3-mercaptopyruvate sulfurtransferase (Roche, Almere, the Netherlands). An iQ5 (Bio-Rad) instrument was used for routine screening purposes. Analyses were performed on the instruments software: LightCycler 480 Software release 1.5.0. SP3 and iQ5 Optical Systems Software version 2.0. Cq values were calculated using the second derivative method on the LightCycler and the Base Line Subtracted Curve Fit method on the iQ5. Color compensations were carried out on both instruments as follows. PCR amplifications were performed using single primer-probe sets for each reporter dye and under identical reaction conditions as during multiplex amplification. The PCR reactions thus produced contained single dyes in relevant concentrations and these were used for color compensation runs according to the manufacturers’ guidelines.

Acknowledgments The authors are grateful to Mrs. Manuela Breiter, Mrs. Birgitt Hartmann, Mrs. Ilona Marquardt, and Mr. Joachim Döll, all from Ilmenau University of Technology, for their help with the sample preparation. This work was partially supported by a grant (NanoBatt TNA VII-1/2012) from the state of Thuringia (TMWAT by LEG Thüringen) and co-financed by the European Union within the frame of the European Funds for Regional Development (EFRD). Electronic supplementary material Additional

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