Protein phase separation and determinants of in cell crystallization.

Liquid-liquid phase separation (LLPS) in cells is known as a complex physicochemical process causing the formation of membrane-less organelles (MLOs). Cells have well-defined different membrane-surrounded organelles like mitochondria, endoplasmic reticulum, lysosomes, peroxisomes, etc., however, on demand they can create MLOs as stress granules, nucleoli and P bodies to cover vital functions and regulatory activities. However, the mechanism of intracellular molecule assembly into functional compartments within a living cell remains till now not fully understood. in vitro and in vivo investigations unveiled that MLOs emerge after preceding liquid-liquid, liquid-gel, liquid-semi-crystalline, or liquid-crystalline phase separations. Liquid-liquid and liquid-gel MLOs form the majority of cellular phase separation events, while the occurrence of micro-sized crystals in cells was only rarely observed, however can be considered as a result of a preceding protein phase separation event. In vivo, also known and termed as in cellulo crystals, are reported since 1853. In some cases, they have been linked to vital cellular functions, such as storage and detoxification. However, the occurrence of in cellulo crystals is also associated to diseases like cataract, hemoglobin C diseases, etc. Therefore, better knowledge about the involved molecular processes will support drug discovery investigations to cure diseases related to in cellulo crystallization. We summarize physical and chemical determinants known today required for phase separation initiation and formation and in cellulo crystal growth. In recent years it has been demonstrated that LLPS plays a crucial role in cell compartmentalization and formation of MLOs. Here we discuss potential mechanisms and potential crowding agents involved in protein phase separation and in cellulo crystallization.

The landscape of transcriptional profiles in human oocytes with different chromatin configurations.

With increasingly used assisted reproductive technology (ART), the acquisition of high-quality oocytes and early embryos has become the focus of much attention. Studies in mice have found that the transition of chromatin conformation from non-surrounded nucleolus (NSN) to surrounded nucleolus (SN) is essential for oocyte maturation and early embryo development, and similar chromatin transition also exists in human oocytes. In this study, we collected human NSN and SN oocytes and investigated their transcriptome. The analysis of differentially expressed genes showed that epigenetic functions, cyclin-dependent kinases and transposable elements may play important roles in chromatin transition during human oocyte maturation. Our findings provide new insights into the molecular mechanism of NSN-to-SN transition of human oocyte and obtained new clues for improvement of oocyte in vitro maturation technique.

Viability variation of T-cells under ultrasound exposure according to adhesion condition with bubbles.

PURPOSE: Although cellular immunotherapy is expected as a new cancer treatment, its therapeutic efficiency is limited in solid tumors, because most cells return to the bloodstream rather than adhere to the target site. Therefore, we are motivated to develop a technique to concentrate the cells in the blood flow using active control of bubble-surrounded cells under ultrasound exposure considering both aspects of cell controllability and viability. METHODS: We prepared a lipid bubble conjugating ligand to adhere to the surface of the T-cells. First, we evaluated the cell controllability by retaining the cells on a wall of an artificial blood vessel through continuous ultrasound exposure. Next, we investigated the cell viability under ultrasound exposure in a suspension with various bubble concentrations. RESULTS: We estimated the concentration of bubbles when the adhesion to the cell surface was saturated. Then, we evaluated the cell viability with various conditions of ultrasound exposure and bubble concentrations. However, it was confirmed that cell damage occurred under conditions that achieved proper control of the cells. Therefore, we exposed the cells to burst waves to reduce the applied ultrasound intensity. Consequently, the significant increase in cell viability was confirmed to be inversely proportional to the duty ratio. CONCLUSION: To retain cells on a vessel wall, determining the appropriate ultrasound condition including sound pressure and waveform is important to maintain cell viability.

Development of n-Type Small-Molecule Acceptors for Low Dark Current Density and Fast Response Organic Photodetectors.

Suppressing the dark current density (Jd) while maintaining sufficient charge transport is important for improving the specific detectivity (D*) and dynamic characteristics of organic photodetectors (OPDs). In this study, we synthesized three novel small-molecule acceptors (SMAs) densely surrounded by insulating alkyl side chains to minimize the Jd in OPDs. Introducing trialkylated N-annulated perylene diimide as a terminal moiety to the alkylated π-conjugated core structure was highly efficient in suppressing Jd in the devices, resulting in an extremely low Jd of 4.60 × 10-11 A cm-2 and 10-100 times improved D* values in the devices. In addition, SMAs with a geometrically aligned backbone structure exhibited better intermolecular ordering in the blended films, resulting in 3-10 times as high responsivity (R) values in the OPDs. Outstanding OPD performances with a D* of 8.09 × 1012 Jones, -3 dB cutoff frequency of 205.2 kHz, and rising response time of 16 µs were achieved under a 530 nm illumination in photoconductive mode. Geometrically aligned core-terminal SMAs densely surrounded by insulating alkyl side chains are promising for improving the static and dynamic properties of OPDs.

On-Chip Electromembrane Surrounded Solid Phase Microextraction for Determination of Tricyclic Antidepressants from Biological Fluids Using Poly(3,4-ethylenedioxythiophene)-Graphene Oxide Nanocomposite as a Fiber Coating.

In the present study, on-chip electromembrane surrounded solid phase microextraction (EM-SPME) was employed in the determination of tricyclic antidepressants (TCAs), including amitriptyline, nortriptyline, imipramine, desipramine, maprotiline, and sertraline, from various biological fluids. In this regard, poly(3,4-ethylenedioxythiophene)-graphene oxide (PEDOT-GO) was electrodeposited on an SPME fiber as a conductive coating, then the fiber played the acceptor-electrode role during the extraction. Thus, the immigration of the analytes under the influence of an electric field and their absorption onto the fiber coating were accomplished simultaneously. Under the optimized conditions, the limits of detection for the target analytes were acquired in the range of 0.005-0.025 µg L-1 using gas chromatography-mass spectrometry. The linearity of the method was 0.010-500 µg L-1 for the imipramine and sertraline, 0.025-500 µg L-1 for the amitriptyline, nortriptyline, and desipramine, and 1.000-250 µg L-1 for the maprotiline (R2 ≥ 0.9984). Moreover, this method provided suitable precision and fiber-to-fiber reproducibility, with RSDs ≤ 8.4%. The applicability of the proposed setup was eventually investigated for extraction of the drugs from human bone marrow aspirate, urine, plasma, and well water samples, in which satisfactory relative recoveries, from 93-105%, were obtained.

SERS Immunosensor of Array Units Surrounded by Particles: A Platform for Auxiliary Diagnosis of Hepatocellular Carcinoma.

Hepatocellular carcinoma (HCC) is one of the diseases with high mortality worldwide, so its early diagnosis and treatment have attracted much attention. Due to the advantages of the high sensitivity of surface-enhanced Raman scattering (SERS) detection, SERS has excellent application value in the diagnosis of HCC. In this paper, silver nanoparticles (AgNPs) are modified by magnetron sputtering on the surface of polystyrene (PS) templates with spheres of two different diameters. The array of units surrounded by particles is successfully prepared and the SERS performance is characterized. The effect of the gap between AgNPs on plasmon coupling and hot spot distribution is discussed. Finite-difference time domain (FDTD) simulation is used to verify the electric fields and hot spot distribution of the array. The differences in the concentrations of HCC markers are analyzed by using the change of SERS signal intensity of the array. The whole process proves that the preparation of structures with a strong local electric field to provide highly sensitive SERS signals is a key link in the detection of HCC markers, which is conducive to the diagnosis of HCC and has potential application value in clinical diagnosis.

An approach to generate DNA polyhedral links of one/two strands.

Scientists can change programmed DNA strands to adjust edge length and vertex junction to control the 3D structures with precision space signatures. The number of strands plays an important role in sequence design, synthesis and constitutive property. However, the majority of DNA branched polyhedra comprise a number of single strands. Therefore, it is crucial to make the number of strands to be calculated as less as possible. DNA polyhedral links are regarded as ideal templates of DNA polyhedra. In this research, we introduce odd-half turn edges and pseudo-surrounded vertexes to build DNA polyhedral links and reduce the strands number of them to one or two. Compare to the known strategies, our strategy is well established to generate the DNA polyhedral links of one/two DNA strands easier and faster. All Platonic, pyramid and prism polyhedral links may provide candidates for DNA polyhedra synthesis.

The DFT study on neutral molecules with planar tetracoordinate oxygen surrounded by four carbon-based groups.

Oxygen usually forms two single bonds with other atoms. In contrast, here we reported the neutral molecules with the planar O(C)4-type tetracoordinate oxygen substructures. The molecules with planar tetracoordinate oxygen, as desirable targets for studying the nonclassical structures and unusual bonding features, remain an important challenge in only carbon-based groups as ligands. In this work, several neutral molecules with planar tetracoordinate oxygen atom surrounded by four carbon-based groups in the pagodane-like derivatives, have been designed out by using the "charge-compensation" and "mechanical" strategies, and studied at the B3LYP/6-311++G(3df,3pd) level of theory. The computational results show that they are all minima on the potential energy surfaces without any imaginary vibrational frequency, and unlike ptC delocalization of the oxygen 2pz lone pair in ptO(C)4 is no longer the principal reason for stabilizing a ptO substructure.

A novel retina-based human identification algorithm based on geometrical shape features using a hierarchical matching structure.

BACKGROUND AND OBJECTIVES: Retinal image is one of the most secure biometrics which is widely used in human identification application. This paper represents a rotation and translation-invariant human identification algorithm based on a new definition of geometrical shape features of the retinal image using a hierarchical matching structure. METHODS: In this algorithm, the retinal images are represented by regions which are surrounded by blood vessels that are named Surrounded Regions (SRs). A perfect set of region-based and boundary-based features are defined on the SRs. In the boundary-based features, by defining corner points of the SR, novel features such as angle of SR corner, centroid distance and weighted corner angle are defined which they can describe well the variation rate of boundary and geometry of the SR. To match the SR of a query with enrolled SR in database, the extracted features in a hierarchical structure from simpler features through more complex features are applied to filter the enrolled SRs in the database for search space reduction. At last, the matched candidate SRs with the query SRs determine the identification or rejection of query image by proposed decision making scenario. In this scenario, the identification is carried out when at least two SRs of the query are matched with two SRs of an individual in the database. RESULTS: The proposed algorithm is evaluated on STARE and DRIVE retinal image databases in six different experiments and is achieved an accuracy rate of 100% and an average processing time of 3.216sec and 3.225sec, respectively. The reported results demonstrate the efficiency of our proposed algorithm in the eye-movement condition. CONCLUSION: In our work, by defining the SR-based features and employing a hierarchical matching structure, the computational complexity of matching step is reduced and also the identification performance is improved. Moreover, the proposed algorithm overcomes the problem of natural movements of the head and eye during the capturing process.

Removal of oxyfluorfen from spiked soils using electrokinetic soil flushing with the surrounding arrangements of electrodes.

This work reports the results of a study in which the remediation of soil that undergoes an accidental discharge of oxyfluorfen is carried out by using electrokinetic soil flushing (EKSF). Two different electrode configurations were tested, consisting of several electrodes surrounding an electrode of different polarity (so-called 1A6C, one anode surrounded by six cathodes, and 1C6A, one cathode surrounded by six cathodes). A pilot plant scale was used (with a soil volume of 175dm(3)) to perform the studies. During the tests, different parameters were measured daily (flowrates, pH, electrical conductivity and herbicide concentration in different sampling positions). Furthermore, at the end of the test, a complete post-mortem analysis was carried out to obtain a 3-D map of the pollution, pH and electrical conductivity in the soil. The results demonstrate that electrode arrangement is a key factor for effective pollutant removal. In fact, the 1A6C configuration improves the removal rate by 41.3% versus the 27.0% obtained by the 1C6A configuration after a period of 35days. Finally, a bench mark comparison of this study of soil remediation polluted with 2,4-D allows for significant conclusions about the scale-up and full-scale application of this technology.

Application of a new nanocarbonaceous sorbent in electromembrane surrounded solid phase microextraction for analysis of amphetamine and methamphetamine in human urine and whole blood.

Application of a new carbon-based sorbent was studied for the first time for extraction and quantification of amphetamine and methamphetamine as model analytes by means of electromembrane surrounded solid phase microextraction (EM-SPME). Since the basis of this microextraction method is adsorption of target analytes on the sorbent surface (after transferring across a supported liquid membrane) in an electrical field, the sorbent, which also performs the electrical potential, should have a conductive nature. On the other hand, using a synthesized fiber is a suitable solution to eliminate the interfering compounds existing in the fiber. To extract the model analytes from acidic sample solution through a thin layer of organic phase and into the aqueous acceptor phase and their final adsorption, 150V electrical potential was applied for 15min. Regardless of the high sample cleanup ability of the proposed method, which makes the analysis of complicated biological fluids possible, admissible extraction recoveries (9.0-18.8%) and suitable detection limits (less than 2.0ngmL(-1)) were obtained. Repeatability and reproducibility of the method were studied and intra- and inter-assay precisions were in the ranges of 2.0-7.3% and 7.5-12.5%, respectively. Coefficients of determination larger than 0.9964 were achieved by scrutinizing of the linearity up to 500ngmL(-1) and calibration curves were utilized for quantification of analytes of interest in human urine and whole blood samples.

Electromembrane Surrounded Solid Phase Microextraction Followed by Injection Port Derivatization and Gas Chromatography-Flame Ionization Detector Analysis for Determination of Acidic Herbicides in Plant Tissue.

Electromembrane surrounded solid phase microextraction (EM-SPME) of acidic herbicides was studied for the first time. In order to investigate the capability of this new microextraction technique to analyze acidic targets, chlorophenoxy acid (CPA) herbicides were quantified in plant tissue. 1-Octanol, was sustained in the pores of the wall of a hollow fiber and served as supported liquid membrane (SLM). Other EM-SPME related parameters, including extraction time, applied voltage, and pHs of the sample solution and the acceptor phase, were optimized using experimental design. A 20 min time frame was needed to reach the highest extraction efficiency of the analytes from a 24 mL alkaline sample solution across the organic liquid membrane and into the aqueous acceptor phase through a 50 V electrical field, and to their final adsorption on a carbonaceous anode. In addition to high sample cleanup, which made the proposed method appropriate for analysis of acidic compounds in a complicated media (plant tissue), 4.8% of 2-methyl-4-chlorophenoxyacetic acid (MCPA) and 0.6% of 2,4-dichlorophenoxyacetic acid (2,4-D) were adsorbed on the anode, resulting in suitable detection limits (less than 5 ng mL-1), and admissible repeatability and reproducibility (intra- and interassay precision were in the ranges of 5.2-8.5% and 8.8-12.0%, respectively). Linearity of the method was scrutinized within the ranges of 1.0-500.0 and 10.0-500.0 ng mL-1 for MCPA and 2,4-D, respectively, and coefficients of determination greater than 0.9958 were obtained. Optimal conditions of EM-SPME of the herbicides were employed for analysis of CPAs in whole wheat tissue.