| 1. |
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| 2. |
- Hwang, Sunbin, et al.
(författare)
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Two-in-One Device with Versatile Compatible Electrical Switching or Data Storage Functions Controlled by the Ferroelectricity of P(VDF-TrFE) via Photocrosslinking
- 2019
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Ingår i: ACS Applied Materials and Interfaces. - : AMER CHEMICAL SOC. - 1944-8244 .- 1944-8252. ; 11:28, s. 25358-25368
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Tidskriftsartikel (refereegranskat)abstract
- Organic electronics demand new platforms that can make integrated circuits and undergo mass production while maintaining diverse functions with high performance. The field-effect transistor has great potential to be a multifunctional device capable of sensing, data processing, data storage, and display. Currently, transistor-based devices cannot be considered intrinsic multifunctional devices because all installed functions are mutually coupled. Such incompatibilities are a crucial barrier to developing an all-in-one multifunctional device capable of driving each function individually. In this study, we focus on the decoupling of electric switching and data storage functions in an organic ferroelectric memory transistor. To overcome the incompatibility of each function, the high permittivity needed for electrical switching and the ferroelectricity needed for data storage become compatible by restricting the motion of poly(vinylidene fluoride-trifluoroethylene) via photocrosslinking with bis-perfluorobenzoazide. The two-in-one device consisting of a photocrosslinked ferroelectric layer exhibits reversible and individual dual-functional operation as a typical transistor with nonvolatile memory. Moreover, a p-MOS depletion load inverter composed of the two transistors with different threshold voltages is also demonstrated by simply changing only one of the threshold voltages by polarization switching. We believe that the two-in-one device will be considered a potential component of integrated organic logic circuits, including memory, in the future.
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| 3. |
- Imran, Qari Muhammad, et al.
(författare)
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Transcriptome wide identification and characterization of NO-responsive WRKY transcription factors in Arabidopsis thaliana L.
- 2018
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Ingår i: Environmental and Experimental Botany. - : Elsevier. - 0098-8472 .- 1873-7307. ; 148, s. 128-143
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Tidskriftsartikel (refereegranskat)abstract
- WRKY transcription factors are important plant-specific regulatory genes characterized by one or two conserved WRKY domain(s) usually followed by a zinc-finger motif. In this study using Arabidopsis thaliana, the RNA-Seq based transcriptomic analysis showed differential expression of 33 genes encoding WRKY TFs in response to the nitric oxide (NO) donor S-Nitrosocysteine (CySNO). Interestingly, 93.9% of these TFs were up-regulated with at least 2-fold change, suggesting their putative involvement in NO mediated gene regulation. GO- analysis of all the 33 transcriptomic elements showed their putative involvement in biological processes such as abiotic stress tolerance and defense against fungal pathogens (89.39 fold enrichment). Analysis of the NO-responsive AtWRKY TFs promoter region revealed the presence of the cis-acting elements such as ABRE, EIRE, ERE, and MBS involved in osmotic stress response, maximal elicitor-mediated activation, and drought-stress regulation. The analysis of NO-responsive AtWRKY TF motifs and their comparison with rice, soybean, and tomato orthologs suggested that members of the WRKY family belonging to the same group shared similar motifs and phylogenetic tree suggested that these TFs were highly conserved. Validation of transcriptomic data through quantitative real time-PCR showed a high correlation coefficient (0.85) indicating the high reliability and similarity of both types of analysis. Comparison of the NO-responsive and non-responsive WRKYs showed the presence of tyrosine (T) and cysteine (C) residues at a distance of 7 residues from the WRKYGQK motif which may serve as potential targets for modification by NO via tyrosine nitration and S-nitrosylation. We also validated the response of WRKYs through in vivo analysis using atwrky62 loss of function mutant and the results indicated a negative role of AtWRKY62 in plant growth. Furthermore, atwrky62 showed significantly less SNO contents compared to wild type plants indicating putative role of AtWRKY62 in NO metabolism.
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| 4. |
- Imran, Qari Muhammad, et al.
(författare)
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WRKYs, the Jack-of-various-Trades, Modulate Dehydration Stress in Populus davidiana-A Transcriptomic Approach
- 2019
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Ingår i: International Journal of Molecular Sciences. - : MDPI. - 1661-6596 .- 1422-0067. ; 20:2
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Tidskriftsartikel (refereegranskat)abstract
- Populus davidiana, native to Korea and central Asian countries, is a major contributor to the Korean forest cover. In the current study, using high-throughput RNA-seq mediated transcriptome analysis, we identified about 87 P. davidiana WRKY transcription factors (PopdaWRKY TFs) that showed differential expression to dehydration stress in both sensitive and tolerant cultivars. Our results suggested that, on average, most of the WRKY genes were upregulated in tolerant cultivars but downregulated in sensitive cultivars. Based on protein sequence alignment, P. davidiana WRKYs were classified into three major groups, I, II, III, and further subgroups. Phylogenetic analysis showed that WRKY TFs and their orthologs in Arabidopsis and rice were clustered together in the same subgroups, suggesting similar functions across species. Significant correlation was found among qRT-PCR and RNA-seq analysis. In vivo analysis using model plant Arabidopsis showed that atwrky62 (orthologous to Potri.016G137900) knockout mutants were significantly sensitive to dehydration possibly due to an inability to close their stomata under dehydration conditions. In addition, a concomitant decrease in expression of ABA biosynthetic genes was observed. The AtHK1 that regulates stomatal movement was also downregulated in atwrky62 compared to the wild type. Taken together, our findings suggest a regulatory role of PopdaWRKYs under dehydration stress.
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| 5. |
- Lee, Sang Wook, et al.
(författare)
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A sol-gel integrated dual-readout microarray platform for quantification and identification of prostate-specific antigen
- 2018
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Ingår i: Analytical Sciences. - : Springer Science and Business Media LLC. - 0910-6340 .- 1348-2246. ; 34:3, s. 317-321
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Tidskriftsartikel (refereegranskat)abstract
- Here, we report a sol-gel integrated affinity microarray for on-chip matrix-assisted laser desorption/ionization time-offlight mass spectrometry (MALDI-TOF-MS) that enables capture and identification of prostate-specific antigen (PSA) in samples. An anti-PSA antibody (H117) was mixed with a sol-gel, and the mixture was spotted onto a porous silicon (pSi) surface without additional surface modifications. The antibody easily penetrates the sol-gel macropore fluidic network structure, making possible high affinities. To assess the capture affinity of the platform, we performed a direct assay using fluorescein isothiocyanate-labeled PSA. Pure PSA was subjected to on-chip MALDI-TOF-MS analysis, yielding three clear mass peptide peaks (m/z = 1272, 1407, and 1872). The sol-gel microarray platform enables dual readout of PSA both fluorometric and MALDI-TOF MS analysis in biological samples. Here we report a useful method for a means for discovery of biomarkers in complex body fluids.
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| 6. |
- Mun, Bong-Gyu, et al.
(författare)
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Analysis of transcription factors among differentially expressed genes induced by drought stress in Populus davidiana
- 2017
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Ingår i: 3 Biotech. - : Springer. - 2190-5738 .- 2190-572X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Populus davidiana is native to the Korean Peninsula and is one of the most dominant and abundantly growing forest trees in eastern Asia. Compared to other Populus species such as P. trichocarpa, P. euphratica, and P. tremula, relatively little is known about P. davidiana. Here, we performed transcriptomic analysis of P. davidiana under drought stress induced by 10% polyethylene glycol. A total of 12,403 and 12,414 differentially expressed genes (DEGs) were successfully annotated with the P. trichocarpa reference genome after 6 and 12 h of treatment, respectively. Of these, a total of 404 genes (238 up-regulated and 166 down-regulated) after 6 h and 359 genes (187 up-regulated and 172 down-regulated) after 12 h of treatment were identified as transcription factors. Transcription factors known to be key genes for drought stress response, such as AP2-EREB, WRKY, C2H2, and NAC, were identified. This results suggesting that early induction of these genes affected initiation of transcriptional regulation in response to drought stress. Quantitative real-time PCR results of selected genes showed highly significant (R = 0.93) correlation with RNA-Seq data. Interestingly, the expression pattern of some transcription factors was P. davidiana specific. The sequence of P. davidiana ortholog of P. trichocarpa gene POPTR_0018s10230, which plays an important role in plant response to drought, was further analyzed as our RNA-Seq results showed highly significant changes in the expression of this gene following the stress treatment. Sequence of the gene was compared to P. trichocarpa gene sequence using cloning-based sequencing. Additionally, we generated a predicted 3D protein structure for the gene product. Results indicated that the amino acid sequence of P. davidiana-specific POPTR_0018s10230 is different at six different positions compared to P. trichocarpa, resulting in a significantly different structure of the protein. Identifying the transcription factors expressed in P. davidiana under drought stress will not only offer clues for understanding the underlying mechanisms involved in drought stress physiology but also serve as a basis for future molecular studies on this species.
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| 7. |
- Asaf, Sajjad, et al.
(författare)
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The complete chloroplast genome of wild rice (Oryza minuta) and its comparison to related species
- 2017
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Oryza minuta, a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O. minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata. Thus, the complete O. minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.
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| 8. |
- Bilal, Saqib, et al.
(författare)
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Endophytic microbial consortia of phytohormones-producing fungus Paecilomyces formosus LHL10 and bacteria Sphingomonas sp. LK11 to Glycine max L. regulates physio-hormonal changes to attenuate aluminum and zinc stresses
- 2018
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- The compatible microbial consortia containing fungal and bacterial symbionts acting synergistically are applied to improve plant growth and eco-physiological responses in extreme crop growth conditions. However, the interactive effects of phytohormones-producing endophytic fungal and bacterial symbionts plant growth and stress tolerance under heavy metal stress have been least known. In the current study, the phytohormones-producing endophytic Paecilomyces formosus LHL10 and Sphingomonas sp. LK11 revealed potent growth and tolerance during their initial screening against combined Al and Zn (2.5 mM each) stress. This was followed with their co-inoculation in the Al- and Zn-stressed Glycine max L. plants, showing significantly higher plant growth attributes (shoot/root length, fresh/dry weight, and chlorophyll content) than the plants solely inoculated with LHL10 or LK11 and the non-inoculated (control) plants under metal stresses. Interestingly, under metal stress, the consortia exhibited lower metal uptake and inhibited metal transport in roots. Metal-induced oxidative stresses were modulated in co-inoculated plants through reduced hydrogen peroxide, lipid peroxidation, and antioxidant enzymes (catalase and superoxide dismutase) in comparison to the non-inoculated plants. In addition, endophytic co-inoculation enhanced plant macronutrient uptake (P, K, S, and N) and modulated soil enzymatic activities under stress conditions. It significantly downregulated the expression of heavy metal ATPase genes GmHMA13, GmHMA18, GmHMA19, and GmPHA1 and upregulated the expression of an ariadne-like ubiquitin ligase gene GmARI1 under heavy metals stress. Furthermore, the endogenous phytohormonal contents of co-inoculated plants revealed significantly enhanced gibberellins and reduced abscisic acid and jasmonic acid contents, suggesting that this endophytic interaction mitigated the adverse effect of metal stresses in host plants. In conclusion, the co-inoculation of the endophytic fungus LHL10 and bacteria LK11 actively contributed to the tripartite mutualistic symbiosis in G. max under heavy metal stresses; this could be used an excellent strategy for sustainable agriculture in the heavy metal-contaminated fields.
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| 9. |
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| 10. |
- Hussain, Adil, et al.
(författare)
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Nitric oxide mediated transcriptome profiling reveals activation of multiple regulatory pathways in Arabidopsis thaliana
- 2016
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Imbalance between the accumulation and removal of nitric oxide and its derivatives is a challenge faced by all plants at the cellular level, and is especially important under stress conditions. Exposure of plants to various biotic and abiotic stresses causes rapid changes in cellular redox tone potentiated by the rise in reactive nitrogen species that serve as signaling molecules in mediating defensive responses. To understand mechanisms mediated by these signaling molecules, we performed a large-scale analysis of the Arabidopsis transcriptome induced by nitrosative stress. We generated an average of 84 and 91 million reads from three replicates each of control and 1 mM S-nitrosocysteine (CysNO)-infiltrated Arabidopsis leaf samples, respectively. After alignment, more than 95% of all reads successfully mapped to the reference and 32,535 genes and 55,682 transcripts were obtained. CysNO infiltration caused differential expression of 6436 genes (3448 up-regulated and 2988 down-regulated) and 6214 transcripts (3335 up-regulated and 2879 down-regulated) 6 h post-infiltration. These differentially expressed genes were found to be involved in key physiological processes, including plant defense against various biotic and abiotic stresses, hormone signaling, and other developmental processes. After quantile normalization of the FPKM values followed by student's T-test (P < 0.05) we identified 1165 DEGs (463 up-regulated and 702 down-regulated) with at least 2-folds change in expression after CysNO treatment. Expression patterns of selected genes involved in various biological pathways were verified using quantitative real-time PCR. This study provides comprehensive information about plant responses to nitrosative stress at transcript level and would prove helpful in understanding and incorporating mechanisms associated with nitrosative stress responses in plants.
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| 11. |
- Imran, Qari Muhammad, et al.
(författare)
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Nitric oxide responsive heavy metal-associated gene AtHMAD1 contributes to development and disease resistance in Arabidopsis thaliana
- 2016
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Ingår i: Frontiers in Plant Science. - : Frontiers Media S.A.. - 1664-462X. ; 7
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Tidskriftsartikel (refereegranskat)abstract
- Exposure of plants to different biotic and abiotic stress condition instigates significant change in the cellular redox status; resulting in the elevation of reactive nitrogen species that play signaling role in mediating defense responses. Heavy metal associated (HMA) domain containing genes are required for spatio-temporal transportation of metal ions that bind with various enzymes and co-factors within the cell. To uncover the underlying mechanisms mediated by AtHMA genes, we identified 14 Arabidopsis HMA genes that were differentially expressed in response to nitrosative stress through RNA-seq analysis. Of those 14 genes, the expression of eight HMA genes was significantly increased, whereas that of six genes was significantly reduced. We further validated the RNA-seq results through quantitative real-time PCR analysis. Gene ontology analysis revealed the involvement of these genes in biological processes such as hemostasis and transport. The majority of these nitric oxide (NO)-responsive AtHMA gene products are carrier/transport proteins. AtHMAD1 (At1g51090) showed the highest fold change to S-nitrosocystein. We therefore, further investigated its role in oxidative and nitrosative mediated stress conditions and found that AtHMAD1 has antagonistic role in shoot and root growth. Characterization of AtHMAD1 through functional genomics showed that the knock out mutant athmad1 plants were resistant to virulent Pseudomonas syringae (DC3000) and showed early induction and high transcript accumulation of pathogenesis related gene. Furthermore, inoculation of athamd1 with avirulent strain of the same bacteria showed negative regulation of R-gene mediated resistance. These results were supported by hypersensitive cell death response and cell death induced electrolyte leakage. AtHMAD1 was also observed to negatively regulate systemic acquired resistance SAR as the KO mutant showed induction of SAR marker genes. Overall, these results imply that NO-responsive AtHMA domain containing genes may play an important role in plant development and immunity.
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| 12. |
- Imran, Qari Muhammad, et al.
(författare)
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Transcriptome profile of NO-induced Arabidopsis transcription factor genes suggests their putative regulatory role in multiple biological processes
- 2018
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- TFs are important proteins regulating plant responses during environmental stresses. These insults typically induce changes in cellular redox tone driven in part by promoting the production of reactive nitrogen species (RNS). The main source of these RNS is nitric oxide (NO), which serves as a signalling molecule, eliciting defence and resistance responses. To understand how these signalling molecules regulate key biological processes, we performed a large scale S-nitrosocysteine (CySNO)-mediated RNA-seq analysis. The DEGs were analysed to identify potential regulatory TFs. We found a total of 673 (up- and down-regulated) TFs representing a broad range of TF families. GO-enrichment and MapMan analysis suggests that more than 98% of TFs were mapped to the Arabidopsis thaliana genome and classified into pathways like hormone signalling, protein degradation, development, biotic and abiotic stress, etc. A functional analysis of three randomly selected TFs, DDF1, RAP2.6, and AtMYB48 identified a regulatory role in plant growth and immunity. Loss-of-function mutations within DDF1 and RAP2.6 showed compromised basal defence and effector triggered immunity, suggesting their positive role in two major plant defence systems. Together, these results imply an important data representing NO-responsive TFs that will help in exploring the core mechanisms involved in biological processes in plants.
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| 13. |
- Khan, Abdul Latif, et al.
(författare)
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Regulation of endogenous phytohormones and essential metabolites in frankincense-producing Boswellia sacra under wounding stress
- 2018
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Ingår i: Acta Physiologiae Plantarum. - : Springer. - 0137-5881 .- 1861-1664. ; 40:6
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Tidskriftsartikel (refereegranskat)abstract
- Boswellia sacra is an economically and ecologically important frankincense-producing tree, which is wounded to extract the aromatic resin. However, the underlying physiological mechanisms following this wounding stress are unknown. Our current goal was to elucidate the regulation of key physio-molecular determinants of wounded and preserved B. sacra populations. Wounding caused a twofold increase in calcium/magnesium content and a reduction in essential macronutrient (nitrogen) levels. Total amino acids were also reduced 1.74-fold; however, the levels of γ-amino butyric acid, hydroxyl-proline, and β-alanine were significantly higher (1- to 2.2-fold). In contrast, the fatty acids (linolenic, palmitic, stearic, and linoleic acids) were significantly higher in the preserved trees. Endogenous jasmonic acid (JA) was also significantly higher (67%) in the wounded trees, as was the expression of the JA-related genes allene oxide synthase and allene oxide cyclase. A similar twofold increase in stress-responsive abscisic acid was observed in the wounded trees. However, salicylic acid was down-regulated, and the pathogenesis-related genes PR1 and PR3 exhibited varying responses in the wounded plants. The presence of physiologically active (GA1, GA4, and GA3) and inactive (GA12, GA19, and GA20) gibberellins in both the wounded and control trees revealed similarity with the known GA biosynthesis in B. sacra. Both GA4 and GA3 were each significantly synthesized, which were buoyed by the increased expressions of ent-copalyl diphosphate synthase, cytochrome P450 monooxygenases, and gibberellin 20 oxidases under wounding stress. In conclusion, B. sacra responds to extraction of resin by regulating essential endogenous hormones and related transcripts, which in return retard tree growth and development.
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| 14. |
- Lee, Sang Wook, et al.
(författare)
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A Highly Sensitive Porous Silicon (P-Si)-Based Human Kallikrein 2 (hK2) Immunoassay Platform toward Accurate Diagnosis of Prostate Cancer.
- 2015
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Ingår i: Sensors. - : MDPI AG. - 1424-8220. ; 15:5, s. 11972-11987
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Tidskriftsartikel (refereegranskat)abstract
- Levels of total human kallikrein 2 (hK2), a protein involved the pathology of prostate cancer (PCa), could be used as a biomarker to aid in the diagnosis of this disease. In this study, we report on a porous silicon antibody immunoassay platform for the detection of serum levels of total hK2. The surface of porous silicon has a 3-dimensional macro- and nanoporous structure, which offers a large binding capacity for capturing probe molecules. The tailored pore size of the porous silicon also allows efficient immobilization of antibodies by surface adsorption, and does not require chemical immobilization. Monoclonal hK2 capture antibody (6B7) was dispensed onto P-Si chip using a piezoelectric dispenser. In total 13 × 13 arrays (169 spots) were spotted on the chip with its single spot volume of 300 pL. For an optimization of capture antibody condition, we firstly performed an immunoassay of the P-Si microarray under a titration series of hK2 in pure buffer (PBS) at three different antibody densities (75, 100 and 145 µg/mL). The best performance of the microarray platform was seen at 100 µg/mL of the capture antibody concentration (LOD was 100 fg/mL). The platform then was subsequently evaluated for a titration series of serum-spiked hK2 samples. The developed platform utilizes only 15 µL of serum per test and the total assay time is about 3 h, including immobilization of the capture antibody. The detection limit of the hK2 assay was 100 fg/mL in PBS buffer and 1 pg/mL in serum with a dynamic range of 106 (10-4 to 102 ng/mL).
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| 15. |
- Lee, Sang Wook, et al.
(författare)
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Development of a Sol-gel-assisted Reverse-phase Microarray Platform for Simple and Rapid Detection of Prostate-specific Antigen from Serum
- 2018
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Ingår i: Biochip Journal. - : Springer Science and Business Media LLC. - 1976-0280 .- 2092-7843. ; 12:1, s. 69-74
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Tidskriftsartikel (refereegranskat)abstract
- A sol-gel-based reverse-phase microarray was developed with improved sensitivity for prostatespecific antigen (PSA) from serum. The pore-sizecontrolled 3D sol-gel matrix was created with a large surface area to capture target molecules densely. Using the optically active sol-gel nanocomposites, human female serum was spiked with PSA and assessed using the reverse-phase protein microarray. The reverse-phase assay exhibited a limit of detection of 1 pg/mL for PSA and a dynamic range of 103 orders of magnitude. Notably, the platform matched the demand of the immunoassay in a simple and feasible manner. Moreover, the platform shortened the total assay time with an increased accuracy of diagnosis.
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| 16. |
- Lee, Sang Wook, et al.
(författare)
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Porous silicon microarray for simultaneous fluorometric immunoassay of the biomarkers prostate-specific antigen and human glandular kallikrein 2
- 2016
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Ingår i: Microchimica Acta. - : Springer Science and Business Media LLC. - 0026-3672 .- 1436-5073. ; 183:12, s. 3321-3327
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Tidskriftsartikel (refereegranskat)abstract
- The authors have developed a porous silicon (P-Si) based duplex antibody microarray platform for simultaneous quantitation of the biomarkers prostate-specific antigen (PSA) and human glandular kallikrein 2 (hK2) in serum. Pore size-controlled P-Si surfaces have an extremely enlarged surface area that enables high-density immobilization of fluorescently labeled antibodies by physical adsorption. Automated microarraying of the antibodies provides a fast and reproducible duplex format of antibody arrays on the P-Si chips placed in the wells of a microtiter plate. The assay platform showed a 100 fg·mL−1 limit of detection for both PSA and hK2, and a dynamic range that extends over five orders of magnitude. After optimization of the density of both capture antibodies, neither the PSA nor the hK2 array showed cross-sensitivity to non-target proteins or other plasma proteins. The microarray was evaluated by titration of PSA and hK2, respectively, in the same serum samples. In our perception, this highly sensitive and selective platform holds promise for improved detection of tumor markers in an early diagnostic stage, but also to monitor the recurrence of prostate cancer. [Figure not available: see fulltext.]
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| 17. |
- Mun, Bong-Gyu, et al.
(författare)
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Profile and time-scale dynamics of differentially expressed genes in transcriptome of Populus davidiana under drought stress
- 2017
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Ingår i: Plant Molecular Biology Reporter. - : Springer. - 0735-9640 .- 1572-9818. ; 35:6, s. 647-660
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Tidskriftsartikel (refereegranskat)abstract
- The genus Populus contains 25–35 species of deciduous flowering plants in the family Salicaceae. It has evolved to overcome various environmental stresses including drought stress through changes in physiological processes such a stomatal movement, photosynthesis, stress signaling, defense responses, and overall growth rate. In this study, we performed RNA-seq-based transcriptome profiling of Populus davidiana in response to drought stress induced by 10% PEG at two time points (6 and 12 h). We generated over 527 million reads by applying Populus trichocarpa as reference genome. Assembly of the reads yielded 32,650 genes and 75,820 transcripts; of these, after quantile normalization, a total of 997 genes were identified with dynamic expression over time, classifying them into nine different clusters. Among them, 550 genes responded significantly to drought stress treatment after 6 h (108 genes up-regulated and 201 genes down-regulated) and 12 h (161 up-regulated and 80 down-regulated) respectively, with at least twofold change in their expression. Based on analysis of these genes, we found several differentially expressed genes (DEGs) involved in cellular transport, transcriptional regulation, protein modification, regulation of cellular redox state, and those involved in response to other stresses. We also validated RNA-seq-mediated transcriptome data by RT-qPCR analysis of eight randomly selected DEGs. It showed significantly high correlation coefficient (0.95) suggesting high reliability of RNA-seq analysis. This study presents the first RNA-seq mediated transcriptome profile of P. davidiana in response to drought stress, providing critical information necessary for understanding the mechanisms underpinning drought stress tolerance in forest trees and other plant species.
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| 18. |
- Park, Jee Woong, et al.
(författare)
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Acoustofluidic harvesting of microalgae on a single chip
- 2016
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Ingår i: Biomicrofluidics. - : AIP Publishing. - 1932-1058. ; 10:3
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Tidskriftsartikel (refereegranskat)abstract
- We present an on-chip acoustofluidic platform for harvesting a target microalgal species from a heterogeneous population of cells and particles based on their size, density, and compressibility in a rapid, non-invasive, energy-efficient, continuously running, and automated manner. For our proof-of-principle demonstration, we use Euglena gracilis as a target species. Specifically, we show the simultaneous separation and enrichment of E. gracilis from a mixed population of E. gracilis in pond water (consisting of other microalgae and various kinds of particles as contaminants) on a single acoustofluidic chip with a recovery ratio of 92.6%, a target separation ratio of 90.1%, a concentration factor of 3.43, an enrichment factor of 12.76, and a cell viability rate of 98.3% at a high volume rate of 500 μl/min. Our results indicate that the on-chip acoustofluidic platform is an effective tool for harvesting target microalgae from mixed populations of microalgae and other contaminants.
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| 19. |
- Shahid, Muhammad, et al.
(författare)
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Comprehensive Analyses of Nitric Oxide-Induced Plant Stem Cell-Related Genes in Arabidopsis thaliana
- 2019
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Ingår i: Genes. - : MDPI. - 2073-4425. ; 10:3
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Tidskriftsartikel (refereegranskat)abstract
- Plant stem cells are pluripotent cells that have diverse applications in regenerative biology and medicine. However, their roles in plant growth and disease resistance are often overlooked. Using high-throughput RNA-seq data, we identified approximately 20 stem cell-related differentially expressed genes (DEGs) that were responsive to the nitric oxide (NO) donor S-nitrosocysteine (CySNO) after six hours of infiltration. Among these DEGs, the highest number of positive correlations (R ≥ 0.8) was observed for CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) 12. Gene ontology (GO) terms for molecular function showed DEGs associated with signal transduction and receptor activity. A promoter study of these DEGs showed the presence of cis-acting elements that are involved in growth as well as the regulation of abiotic and biotic stress. Phylogenetic analysis of the Arabidopsis stem cell-related genes and their common orthologs in rice, soybean, poplar, and tomato suggested that most soybean stem cell-related genes were grouped with the Arabidopsis CLE type of stem cell genes, while the rice stem cell-related genes were grouped with the Arabidopsis receptor-like proteins. The functional genomic-based characterization of the role of stem cell DEGs showed that under control conditions, the clv1 mutant showed a similar phenotype to that of the wild-type (WT) plants; however, under CySNO-mediated nitrosative stress, clv1 showed increased shoot and root length compared to WT. Furthermore, the inoculation of clv1 with virulent Pst DC3000 showed a resistant phenotype with fewer pathogens growing at early time points. The qRT-PCR validation and correlation with the RNA-seq data showed a Pearson correlation coefficient of >0.8, indicating the significantly high reliability of the RNA-seq analysis.
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