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1.
J Phys Condens Matter ; 35(11)2023 Jan 09.
Artigo em Inglês | MEDLINE | ID: mdl-36580683

RESUMO

We develop a fully quantum theoretical approach which describes the dynamics of Frenkel excitons and bi-excitons induced by few photon quantum light in a quantum well or wire (atomic chain) of finite lateral size. The excitation process is found to consist in the Rabi-like oscillations between the collective symmetric states characterized by discrete energy levels. At the same time, the enhanced excitation of high-lying free exciton states being in resonance with these 'dressed' polariton eigenstates is revealed. This found new effect is referred to as the formation of Rabi-shifted resonances and appears to be the most important and new feature established for the excitation of 1D and 2D nanostructures with final lateral size. The found new physics changes dramatically the conventional concepts of exciton formation and play an important role for the development of nanoelectronics and quantum information protocols involving manifold excitations in nanosystems.

2.
Sci Rep ; 12(1): 21639, 2022 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-36517588

RESUMO

Exogenous bioactive peptides are considered promising for the wound healing therapy in humans. In this regard, parasitic trematodes proteins may potentially become a new perspective agents. Foodborne trematode Opisthorchis felineus is widespread in Europe and has the ability to stimulate proliferation of bile duct epithelium. In this study, we investigated skin wound healing potential of O. felineus proteins in mouse model. C57Bl/6 mice were inflicted with superficial wounds with 8 mm diameter. Experimental groups included several non-specific controls and specific treatment groups (excretory-secretory product and lysate). After 10 days of the experiment, the percentage of wound healing in the specific treatment groups significantly exceeded the control values. We also found that wound treatment with excretory-secretory product and worm lysate resulted in: (i) inflammation reducing, (ii) vascular response modulating, (iii) type 1 collagen deposition promoting dermal ECM remodeling. An additional proteomic analysis of excretory-secretory product and worm lysate samples was revealed 111 common proteins. The obtained data indicate a high wound-healing potential of liver fluke proteins and open prospects for further research as new therapeutic approaches.


Assuntos
Fasciola hepatica , Fasciolíase , Opisthorchis , Humanos , Animais , Camundongos , Proteômica , Cicatrização
3.
Int J Mol Sci ; 23(17)2022 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-36077272

RESUMO

CD133 is an extensively studied marker of the most malignant tumor cell population, designated as cancer stem cells (CSCs). However, the function of this glycoprotein and its involvement in cell regulatory cascades are still poorly understood. Here we show a positive correlation between the level of CD133 plasma membrane expression and the proliferative activity of cells of the Caco-2, HT-29, and HUH7 cancer cell lines. Despite a substantial difference in the proliferative activities of cell populations with different levels of CD133 expression, transcriptomic and proteomic profiling revealed only minor distinctions between them. Nonetheless, a further in silico assessment of the differentially expressed transcripts and proteins revealed 16 proteins that could be involved in the regulation of CD133 expression; these were assigned ranks reflecting the apparent extent of their involvement. Among them, the TRIM28 transcription factor had the highest rank. The prominent role of TRIM28 in CD133 expression modulation was confirmed experimentally in the Caco2 cell line clones: the knockout, though not the knockdown, of the TRIM28 gene downregulated CD133. These results for the first time highlight an important role of the TRIM28 transcription factor in the regulation of CD133-associated cancer cell heterogeneity.


Assuntos
Antígeno AC133/genética , Células-Tronco Neoplásicas/citologia , Proteína 28 com Motivo Tripartido/metabolismo , Antígeno AC133/metabolismo , Células CACO-2 , Linhagem Celular Tumoral , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias/metabolismo , Células-Tronco Neoplásicas/metabolismo , Fenótipo , Proteômica , Fatores de Transcrição/metabolismo
4.
Data Brief ; 42: 108274, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35647242

RESUMO

The HaCaT line of immortalized non-tumor cells is a popular model of keratinocytes used for dermatological studies, in the practice of toxicological tests, and in the study of skin allergic reactions. These cells maintain a stable keratinocyte phenotype, do not require specific growth factors during cultivation, and respond to keratinocyte differentiation stimuli. HaCaT cells bear two mutant p53 alleles - R282Q and H179Y. At least two mechanisms of GOF (gain-of-function) of mutant p53 are known: it affects functions of p63/p73 by inhibiting their binding to DNA; or it binds to new DNA sites by interacting with other transcription factors (NF-Y, E2F1, NF-KB, VDR, p63). Proteins of the P53 family play an important role in the regulation of proliferation and differentiation processes of human keratinocytes. Proteomic study of HaCaT cells with TP53 gene knockdown provides new data for understanding the limitations of HaCaT cells when using them as an experimental model of normal human keratinocytes. In this article we present datasets obtained through the high-throughput shotgun proteomics analysis of human immortalized HaCaT keratinocytes and p53 knockdown HaCaT keratinocytes. As a protocol for proteomic profiling of cells, we used the approach of obtaining LC-MS/MS measurements followed by their processing with MaxQuant software (version 1.6.3.4). The "RAW" files were deposited to the ProteomeXchange with identifier PXD033538.

5.
Data Brief ; 42: 108055, 2022 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-35345844

RESUMO

The data was acquired from 3 normal human liver tissues by LC-MS methods. The tissue liver samples from male subjects post mortem were obtained from ILSBio LLC (https://bioivt.com/). Liver tissue was frozen in liquid nitrogen, transported and shipped on dry ice. The proteins were extracted and purified followed up by trypsin hydrolysis. The peptide mixture was aliquoted and analyzed by different LC-MS approaches: one-dimensional shotgun LC-MS, two-dimensional LC-MS, two-dimensional SRM SIS (Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards). The Shotgun assay resulted in a qualitative in-depth human liver proteome, and a semi-quantitative iBAQ (intensity-based absolute quantification) value was calculated to show the relative protein content of the sample. Absolute quantitative concentrations of proteins encoded by human chromosome 18 using SRM SIS were obtained.

6.
Biomolecules ; 12(1)2022 01 14.
Artigo em Inglês | MEDLINE | ID: mdl-35053280

RESUMO

The effect of He-Ne laser irradiation on fishery parameters as well as on biochemical state, including the lipids and fatty acids, the activity of energy metabolism enzymes and the proteome in the blastula stage and in underyearlings of wild Atlantic salmon after irradiation at the cleavage stage/early blastula (considered as the stages when the cell has a high potential for differentiation) was studied. Low mortality rates of eggs were determined during embryogenesis, as well as increased weight gain and lower morality rates of underyearlings in the experimental group. This is confirmed by changes in a number of interrelated indicators of lipid metabolism: a decrease in total lipids content, including diacylglycerols, triacylglycerols, cholesterol esters, and the phospholipids content remained unchanged. The embryos in the blastula stage (experimental group) had higher aerobic capacity and an increase in pentose phosphate pathway activity. The proteome profiles of eggs in the blastula stage were 131 proteins, of which 48 were significantly identified. The major protein was found to be phosvitin. The proteomes of underyearlings were represented by 2018 proteins, of which 49 were unique for the control and 39 for the experimental group. He-Ne laser irradiation had a strong effect on the contents of histone proteins.


Assuntos
Ácidos Graxos , Salmo salar , Animais , Blástula , Hélio , Lasers , Neônio , Proteoma
7.
Data Brief ; 40: 107796, 2022 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-35036493

RESUMO

The data were obtained by a label-free quantification approach from a shotgun proteomics experiment, using STrap sample processing technique for protein digestion and high-performance liquid chromatography with tandem mass spectrometry (HPLC-MS/MS) for peptide analysis. MaxQuant data processing was used to obtain proteomics data. The dataset reflects changes in the liver protein profile of Japanese medaka exposed to 0, 5, 40 and 80 mg/L nominal concentrations of Sigma-Aldrich humic acid for 96 h. Actual concentrations of humic acid were measured using the potassium dichromate photometric method and reported in mg organic carbon/L. These proteomics data are relevant for further insights into fish stress responses to humic substances-related challenge.

8.
J Phys Condens Matter ; 34(6)2021 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-34724654

RESUMO

In this paper the excitations of collective electronic modes and currents induced in nanostructured semiconductor systems by two-mode quantum light with non-zero orbital angular momenta are investigated. Transfer of photon correlations to the excitations and currents induced in the semiconductor system is demonstrated. Birth of correlated electrons arising in the conduction band of the nanostructure due to the interaction with correlated photons of quantum light is found. Azimuthal and radial spatial distributions of the entangled electrons are established. The obtained results make possible to register the correlated electrons experimentally and to implement quantum information and nanoelectronics circuits in nanosystems using the found azimuthal and radial electron entanglement.

9.
Molecules ; 26(20)2021 Oct 12.
Artigo em Inglês | MEDLINE | ID: mdl-34684727

RESUMO

The proteins of extracellular vesicles (EVs) that originate from tumors reflect the producer cells' proteomes and can be detected in biological fluids. Thus, EVs provide proteomic signatures that are of great interest for screening and predictive cancer diagnostics. By applying targeted mass spectrometry with stable isotope-labeled peptide standards, we assessed the levels of 28 EV-associated proteins, including the conventional exosome markers CD9, CD63, CD81, CD82, and HSPA8, in vesicles derived from the lung cancer cell lines NCI-H23 and A549. Furthermore, we evaluated the detectability of these proteins and their abundance in plasma samples from 34 lung cancer patients and 23 healthy volunteers. The abundance of TLN1, TUBA4A, HSPA8, ITGB3, TSG101, and PACSIN2 in the plasma of lung cancer patients was measured using targeted mass spectrometry and compared to that in plasma from healthy volunteers. The most diagnostically potent markers were TLN1 (AUC, 0.95), TUBA4A (AUC, 0.91), and HSPA8 (AUC, 0.88). The obtained EV proteomic signature allowed us to distinguish between the lung adenocarcinoma and squamous cell carcinoma histological types. The proteomic cargo of the extracellular vesicles represents a promising source of potential biomarkers.


Assuntos
Vesículas Extracelulares/metabolismo , Neoplasias Pulmonares/metabolismo , Idoso , Biomarcadores Tumorais/sangue , Linhagem Celular Tumoral , Exossomos/metabolismo , Vesículas Extracelulares/fisiologia , Feminino , Humanos , Masculino , Espectrometria de Massas/métodos , Pessoa de Meia-Idade , Plasma/química , Proteoma/metabolismo , Proteômica/métodos
10.
Int J Mol Sci ; 22(12)2021 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-34204832

RESUMO

In vitro models are often used for studying macrophage functions, including the process of phagocytosis. The application of primary macrophages has limitations associated with the individual characteristics of animals, which can lead to insufficient standardization and higher variability of the obtained results. Immortalized cell lines do not have these disadvantages, but their responses to various signals can differ from those of the living organism. In the present study, a comparative proteomic analysis of immortalized PMJ2-R cell line and primary peritoneal macrophages isolated from C57BL/6 mice was performed. A total of 4005 proteins were identified, of which 797 were quantified. Obtained results indicate significant differences in the abundances of many proteins, including essential proteins associated with the process of phagocytosis, such as Elmo1, Gsn, Hspa8, Itgb1, Ncf2, Rac2, Rack1, Sirpa, Sod1, C3, and Msr1. These findings indicate that outcomes of studies utilizing PMJ2-R cells as a model of peritoneal macrophages should be carefully validated. All MS data are deposited in ProteomeXchange with the identifier PXD022133.


Assuntos
Macrófagos Peritoneais/metabolismo , Proteoma/metabolismo , Proteômica , Animais , Células Cultivadas , Regulação para Baixo , Ontologia Genética , Masculino , Camundongos Endogâmicos C57BL , Fagocitose , Mapas de Interação de Proteínas , Regulação para Cima
11.
Antioxidants (Basel) ; 10(7)2021 Jun 30.
Artigo em Inglês | MEDLINE | ID: mdl-34208791

RESUMO

A biologically active extract from the darkling beetle Ulomoides dermestoides was obtained using the electro-pulse plasma dynamic extraction method. The beetle water extract contained a complex of antioxidant substances such as antioxidant enzymes and nonprotein antioxidants, as well as a complex of heat shock antistress proteins. This determines the rather high antioxidant activity of the aqueous extract of the beetle, i.e., 1 mg of dry matter/mL of the extract has an equivalent antioxidant activity to 0.2 mM Trolox (a water-soluble analog of vitamin E). It was shown that the beetle extract can lead to a 25-30% increase in the average lifespan of nematode Caenorhabditiselegans, under normal conditions, and a 12-17% increase under conditions of oxidative stress (with paraquat), and significantly inhibits the fructosylation reaction of serum albumin. Therefore, the beetle aqueous extract shows promise as a biologically active complex exhibiting antioxidant activity.

12.
Opt Express ; 29(1): 330-341, 2021 Jan 04.
Artigo em Inglês | MEDLINE | ID: mdl-33362117

RESUMO

We show how novel photonic devices such as broadband quantum memory and efficient quantum frequency transduction can be implemented using three-wave mixing processes in a 1D array of nonlinear waveguides evanescently coupled to nearest neighbors. We do this using an analogy of an atom interacting with an external optical field using both classical and quantum models of the optical fields and adapting well-known coherent processes from atomic optics, such as electromagnetically induced transparency and stimulated Raman adiabatic passage to design. This approach allows the implementation of devices that are very difficult or impossible to implement by conventional techniques.

13.
J Proteome Res ; 19(12): 4901-4906, 2020 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-33202127

RESUMO

One of the main goals of the Chromosome-Centric Human Proteome Project (C-HPP) is detection of "missing proteins" (PE2-PE4). Using the UPS2 (Universal proteomics standard 2) set as a model to simulate the range of protein concentrations in the cell, we have previously shown that 2D fractionation enables the detection of more than 95% of UPS2 proteins in a complex biological mixture. In this study, we propose a novel experimental workflow for protein detection during the analysis of biological samples. This approach is extremely important in the context of the C-HPP and the neXt-MP50 Challenge, which can be solved by increasing the sensitivity and the coverage of the proteome encoded by a particular human chromosome. In this study, we used 2D fractionation for in-depth analysis of the proteins encoded by human chromosome 18 (Chr 18) in the HepG2 cell line. Use of 2D fractionation increased the sensitivity of the SRM SIS method by 1.3-fold (68 and 88 proteins were identified by 1D fractionation and 2D fractionation, respectively) and the shotgun MS/MS method by 2.5-fold (21 and 53 proteins encoded by Chr 18 were detected by 1D fractionation and 2D fractionation, respectively). The results of all experiments indicate that 111 proteins encoded by human Chr 18 have been identified; this list includes 42% of the Chr 18 protein-coding genes and 67% of the Chr 18 transcriptome species (Illumina RNaseq) in the HepG2 cell line obtained using a single sample. Corresponding mRNAs were not registered for 13 of the detected proteins. The combination of 2D fractionation technology with SRM SIS and shotgun mass spectrometric analysis did not achieve full coverage, i.e., identification of at least one protein product for each of the 265 protein-coding genes of the selected chromosome. To further increase the sensitivity of the method, we plan to use 5-10 crude synthetic peptides for each protein to identify the proteins and select one of the peptides based on the obtained mass spectra for the synthesis of an isotopically labeled standard for subsequent quantitative analysis. Data are available via ProteomeXchange with the identifier PXD019263.


Assuntos
Proteômica , Espectrometria de Massas em Tandem , Cromossomos Humanos , Humanos , Proteoma/genética , Transcriptoma
14.
FEBS J ; 287(24): 5394-5410, 2020 12.
Artigo em Inglês | MEDLINE | ID: mdl-32250538

RESUMO

We explore the principles of pressure tolerance in enzymes of deep-sea fishes using lactate dehydrogenases (LDH) as a case study. We compared the effects of pressure on the activities of LDH from hadal snailfishes Notoliparis kermadecensis and Pseudoliparis swirei with those from a shallow-adapted Liparis florae and an abyssal grenadier Coryphaenoides armatus. We then quantified the LDH content in muscle homogenates using mass-spectrometric determination of the LDH-specific conserved peptide LNLVQR. Existing theory suggests that adaptation to high pressure requires a decrease in volume changes in enzymatic catalysis. Accordingly, evolved pressure tolerance must be accompanied with an important reduction in the volume change associated with pressure-promoted alteration of enzymatic activity ( ΔVPP∘ ). Our results suggest an important revision to this paradigm. Here, we describe an opposite effect of pressure adaptation-a substantial increase in the absolute value of ΔVPP∘ in deep-living species compared to shallow-water counterparts. With this change, the enzyme activities in abyssal and hadal species do not substantially decrease their activity with pressure increasing up to 1-2 kbar, well beyond full-ocean depth pressures. In contrast, the activity of the enzyme from the tidepool snailfish, L. florae, decreases nearly linearly from 1 to 2500 bar. The increased tolerance of LDH activity to pressure comes at the expense of decreased catalytic efficiency, which is compensated with increased enzyme contents in high-pressure-adapted species. The newly discovered strategy is presumably used when the enzyme mechanism involves the formation of potentially unstable excited transient states associated with substantial changes in enzyme-solvent interactions.


Assuntos
Adaptação Fisiológica , Proteínas de Peixes/metabolismo , Peixes/fisiologia , Lactato Desidrogenases/metabolismo , Proteínas Musculares/metabolismo , Músculos/enzimologia , Pressão , Sequência de Aminoácidos , Animais , Peixes/classificação , Homologia de Sequência
15.
Beilstein J Nanotechnol ; 10: 1548-1558, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31467819

RESUMO

A theoretical approach to the consistent full quantum description of the ultrafast population transfer and magnetization reversal in superconducting meta-atoms induced by picosecond unipolar pulses of a magnetic field is developed. A promising scheme based on the regime of stimulated Raman Λ-type transitions between qubit states via upper-lying levels is suggested in order to provide ultrafast quantum operations on the picosecond time scale. The experimental realization of a circuit-on-chip for the discussed ultrafast control is presented.

16.
J Proteome Res ; 18(1): 120-129, 2019 01 04.
Artigo em Inglês | MEDLINE | ID: mdl-30480452

RESUMO

This work continues the series of the quantitative measurements of the proteins encoded by different chromosomes in the blood plasma of a healthy person. Selected Reaction Monitoring with Stable Isotope-labeled peptide Standards (SRM SIS) and a gene-centric approach, which is the basis for the implementation of the international Chromosome-centric Human Proteome Project (C-HPP), were applied for the quantitative measurement of proteins in human blood plasma. Analyses were carried out in the frame of C-HPP for each protein-coding gene of the four human chromosomes: 18, 13, Y, and mitochondrial. Concentrations of proteins encoded by 667 genes were measured in 54 blood plasma samples of the volunteers, whose health conditions were consistent with requirements for astronauts. The gene list included 276, 329, 47, and 15 genes of chromosomes 18, 13, Y, and the mitochondrial chromosome, respectively. This paper does not make claims about the detection of missing proteins. Only 205 proteins (30.7%) were detected in the samples. Of them, 84, 106, 10, and 5 belonged to chromosomes 18, 13, and Y and the mitochondrial chromosome, respectively. Each detected protein was found in at least one of the samples analyzed. The SRM SIS raw data are available in the ProteomeXchange repository (PXD004374, PASS01192).


Assuntos
Cromossomos Humanos/química , Plasma/química , Proteoma , Cromossomos Humanos/genética , Cromossomos Humanos Par 13/química , Cromossomos Humanos Par 18/química , Cromossomos Humanos Y/química , Bases de Dados de Proteínas , Voluntários Saudáveis , Humanos , Mitocôndrias/ultraestrutura , Proteoma/genética
17.
J Proteome Res ; 17(12): 4258-4266, 2018 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-30354151

RESUMO

Currently, great interest is paid to the identification of "missing" proteins that have not been detected in any biological material at the protein level (PE1). In this paper, using the Universal Proteomic Standard sets 1 and 2 (UPS1 and UPS2, respectively) as an example, we characterized mass spectrometric approaches from the point of view of sensitivity (Sn), specificity (Sp), and accuracy (Ac). The aim of the paper was to show the utility of a mass spectra approach for protein detection. This sets consists of 48 high-purity human proteins without single aminoacid polymorphism (SAP) or post translational modification (PTM). The UPS1 set consists of the same 48 proteins at 5 pmols each, and in UPS2, proteins were grouped into 5 groups in accordance with their molar concentration, ranging from 10-11 to 10-6 M. Single peptides from the 92% and 96% of all sets of proteins could be detected in a pure solution of UPS2 and UPS1, respectively, by selected reaction monitoring with stable isotope-labeled standards (SRM-SIS). We also found that, in the presence of a biological matrix such as Escherichia coli extract or human blood plasma (HBP), SRM-SIS makes it possible to detect from 63% to 79% of proteins in the UPS2 set (sensitivity) with the highest specificity (∼100%) and an accuracy of 80% by increasing the sensitivity of shotgun and selected reaction monitoring combined with a stable-isotope-labeled peptide standard (SRM-SIS technology) by fractionating samples using reverse-phase liquid chromatography under alkaline conditions (2D-LC_alk). It is shown that this technique of sample fractionation allows the SRM-SIS to detect 98% of the single peptides from the proteins present in the pure solution of UPS2 (47 out of 48 proteins). When the extracts of E. coli or Pichia pastoris are added as biological matrixes to the UPS2, 46, and 45 out of 48 proteins (∼95%) can be detected, respectively, using the SRM-SIS combined with 2D-LC_alk. The combination of the 2D-LC_alk SRM-SIS and shotgun technologies allows us to increase the sensitivity up to 100% in the case of the proteins of the UPS2 set. The usage of that technology can be a solution for identifying the so-called "missing" proteins and, eventually, creating the deep proteome of a particular chromosome of tissue or organs. Experimental data have been deposited in the PeptideAtlas SRM Experiment Library with the dataset identifier PASS01192 and the PRIDE repository with the dataset identifier PXD007643.


Assuntos
Cromatografia Líquida/métodos , Espectrometria de Massas/normas , Proteogenômica/métodos , Proteoma/análise , Cromatografia de Fase Reversa/métodos , Cromossomos Humanos/genética , Humanos , Proteínas/análise , Reprodutibilidade dos Testes , Sensibilidade e Especificidade
18.
Eur J Mass Spectrom (Chichester) ; 23(4): 202-208, 2017 08.
Artigo em Inglês | MEDLINE | ID: mdl-29028392

RESUMO

Targeted mass spectrometry represents a powerful tool for investigation of biological processes. The convenient approach of selected reaction monitoring using stable isotope-labeled peptide standard (SIS) is widely applied for protein quantification. Along with this method, high-resolution parallel reaction monitoring has been increasingly used for protein targeted analysis. Here we applied two targeted approaches (selected reaction monitoring with SIS and label-free parallel reaction monitoring) to investigate expression of 11 proteins during all-trans retinoic acid-induced differentiation of HL-60 cells. In our experiments, we have determined the proteins expression ratio at 3, 24, 48, and 96 h after all-trans retinoic acid treatment in comparison with 0 h, respectively. Expression profiles of four proteins (VAV1, PRAM1, LYN, and CEBPB) were highly correlated ( r > 0.75) and FGR expression was detected on proteome level starting from 24 h by both techniques. For prominent differences (fold change ≥ 2) label-free parallel reaction monitoring is not inferior to selected reaction monitoring with isotopically labeled peptide standards. Differentially expressed proteins, that have been determined in our study, can be considered as potential drug targets for acute myeloid leukemia (AML) treatment.


Assuntos
Diferenciação Celular/fisiologia , Células HL-60/citologia , Células HL-60/metabolismo , Espectrometria de Massas/métodos , Diferenciação Celular/efeitos dos fármacos , Humanos , Proteoma/análise , Proteoma/metabolismo , Proteômica , Tretinoína/farmacologia
19.
Phys Rev Lett ; 117(18): 183601, 2016 Oct 28.
Artigo em Inglês | MEDLINE | ID: mdl-27834994

RESUMO

Bright squeezed vacuum, a promising tool for quantum information, can be generated by high-gain parametric down-conversion. However, its frequency and angular spectra are typically quite broad, which is undesirable for applications requiring single-mode radiation. We tailor the frequency spectrum of high-gain parametric down-conversion using an SU(1,1) interferometer consisting of two nonlinear crystals with a dispersive medium separating them. The dispersive medium allows us to select a narrow band of the frequency spectrum to be exponentially amplified by high-gain parametric amplification. The frequency spectrum is thereby narrowed from (56.5±0.1) to (1.22±0.02) THz and, in doing so, the number of frequency modes is reduced from approximately 50 to 1.82±0.02. Moreover, this method provides control and flexibility over the spectrum of the generated light through the timing of the pump.

20.
J Proteome Res ; 15(11): 4030-4038, 2016 11 04.
Artigo em Inglês | MEDLINE | ID: mdl-27527821

RESUMO

A gene-centric approach was applied for a large-scale study of expression products of a single chromosome. Transcriptome profiling of liver tissue and HepG2 cell line was independently performed using two RNA-Seq platforms (SOLiD and Illumina) and also by Droplet Digital PCR (ddPCR) and quantitative RT-PCR. Proteome profiling was performed using shotgun LC-MS/MS as well as selected reaction monitoring with stable isotope-labeled standards (SRM/SIS) for liver tissue and HepG2 cells. On the basis of SRM/SIS measurements, protein copy numbers were estimated for the Chromosome 18 (Chr 18) encoded proteins in the selected types of biological material. These values were compared with expression levels of corresponding mRNA. As a result, we obtained information about 158 and 142 transcripts for HepG2 cell line and liver tissue, respectively. SRM/SIS measurements and shotgun LC-MS/MS allowed us to detect 91 Chr 18-encoded proteins in total, while an intersection between the HepG2 cell line and liver tissue proteomes was ∼66%. In total, there were 16 proteins specifically observed in HepG2 cell line, while 15 proteins were found solely in the liver tissue. Comparison between proteome and transcriptome revealed a poor correlation (R2 ≈ 0.1) between corresponding mRNA and protein expression levels. The SRM and shotgun data sets (obtained during 2015-2016) are available in PASSEL (PASS00697) and ProteomeExchange/PRIDE (PXD004407). All measurements were also uploaded into the in-house Chr 18 Knowledgebase at http://kb18.ru/protein/matrix/416126 .


Assuntos
Cromossomos Humanos Par 18 , Perfilação da Expressão Gênica , Proteoma/análise , Bases de Dados de Proteínas , Perfilação da Expressão Gênica/métodos , Células Hep G2 , Humanos , Fígado/química , Proteínas/análise , Proteoma/genética , Proteômica/métodos , RNA Mensageiro/análise
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