Identification of Significant RNA-Binding Proteins in the Process of CD44 Splicing Using the Boosted Beta Regression Algorithm.

The expression of RNA-binding proteins and their interaction with the spliced pre-mRNA are the key factors in determining the final isoform profile. Transmembrane protein CD44 is involved in differentiation, invasion, motility, growth and survival of tumor cells, and is also a commonly accepted marker of cancer stem cells and epithelial-mesenchymal transition. However, the functions of the isoforms of this protein differ significantly. In this paper, we developed a method based on the boosted beta regression algorithm for identification of the significant RNA-binding proteins in the splicing process by modeling the isoform ratio. The application of this method to the analysis of CD44 splicing in colorectal cancer cells revealed 20 significant RNA-binding proteins. Many of them were previously shown as EMT regulators, but for the first time presented as potential CD44 splicing factors.

The RNA-Binding Proteins OAS1, ZFP36L2, and DHX58 Are Involved in the Regulation of CD44 mRNA Splicing in Colorectal Cancer Cells.

Regulation of alternative splicing is carried out by RNA-binding proteins. Each alternative splicing event is controlled by several RNA-binding proteins, which in combination create the distribution of alternative splicing products in a given cell type. Transmembrane protein CD44 plays an important role at various stages of the metastatic cascade and is considered as a promising molecule for the therapy of tumor diseases and the construction of prognostic classifiers. However, the functions of specific isoforms of this protein may differ significantly. In this work, we performed a bioinformatic search of RNA-binding proteins that can determine the expression of clinically significant isoforms 3 and 4 of CD44 protein. The analysis revealed five RNA-binding proteins, three of which (OAS1, ZFP36L2, and DHX58) are shown for the first time as potential regulators of the studied process.

Expression of CD44 Isoforms in Tumor Samples and Cell Lines of Human Colorectal Cancer.

Detection of colorectal cancer biomarkers (CRC) remains an urgent task for the diagnosis and prediction of the disease course. A promising approach is the study of cancer stem cell markers. The cell surface glycoprotein CD44 is very important for CRC and its stem cells. Alternative splicing of 9 variable exons of CD44 mRNA leads to the formation of various isoforms of the protein with different roles in the progression of cancer. Studies of the functions of CD44 isoforms require adequate models considering the distribution of CD44 isoforms in real tumor samples. In the present study, the expression profile of CD44 isoforms in CRC was assessed based on the publicly available mRNA sequencing data of patient tumors from the TCGA-COAD database. It was shown that normal tissues predominantly expressed isoforms 3 and 4 at nearly equal levels, whereas tumors mainly expressed isoforms 2, 3, and 4; isoform 3 was expressed at the highest level. Further, the most relevant cell lines for studying the role of CD44 in CRC were identified based on the analysis of mRNA sequencing data of 55 CRC cell lines form CCLE database.

Differences in Presentation of SARS-CoV-2 Omicron Strain Variant BA.1-BA.5 Peptides by HLA Molecules.

In this work, we analyzed the binding affinities of mutated peptides of Omicron strain variants BA.1-BA.5 and the worldwide prevalent HLA alleles. Bioinformatics analysis was conducted with the use of T-CoV web portal. We showed that, for all five viral variants, mutations cause a significant reduction in the number of tightly binding peptides for HLA-B*07:02 and HLA-C*01:02 molecules. At the same time, there were novel potential mutant epitopes (binding affinity less than 50 nM) in case of HLA-A*32:01 allele. Interestingly, mutations caused multidirectional effect on the binding affinities of the viral peptides and HLA-DRB1*03:01. Specifically, Spike protein mutations in the BA.1 variant caused more than 100-fold decrease in PINLVRDLPQGFSAL binding affinity, 10-fold decrease in affinity in the case of BA.2, BA.4, and BA.5 variants, and 30% increase in affinity for the BA.3 variant.

Investigations into Spin- and Unpolarized Secondary Electron-Induced Reactions in Self-Assembled Monolayers of Cysteine.

Cysteine is the simplest thiolated, chiral amino acid and is often used as the anchor for studies of self-assembled monolayers (SAMs) of complex biomolecules such as peptides. Understanding the interaction of SAMs of cysteine with low-energy secondary electrons (SEs) produced by X-rays can further our understanding of radiation damage in biomolecules. In particular, if the electrons are polarized, chiral-selective chemistry could have bearing on the origin of homochirality in nature. In the present paper, we use synchrotron radiation-based X-ray photoelectron spectroscopy to determine the changes that occur in the bonding of self-assembled layers of cysteine on gold as a result of soft X-ray irradiation. To investigate the possibility of chiral selectivity resulting from the interaction of low-energy, spin-polarized SEs (SPSEs), measurements were conducted on cysteine adsorbed on a 3 nm-thick gold layer deposited on a CoPt thin-film multilayer with perpendicular magnetic anisotropy. Time-dependent measurements of the C 1s, N 1s, O 1s, S 2p, and Au 4f core levels are used to follow the changes in surface chemistry and determine reaction cross-sections as a function of SE exposure. Analysis of the data results in cross-sections in the range of 5-7 Mb and suggests possible reaction pathways. Changing the magnetization direction of the CoPt multilayer produces SPSEs with opposite polarity. Some evidence of spin-dependent reactions is indicated but is inconclusive. Possible reasons for the discrepancy are posited.

Ultrasensitive detection enabled by nonlinear magnetization of nanomagnetic labels.

Geometrically confined magnetic particles due to their unique response to external magnetic fields find a variety of applications, including magnetic guidance, heat and drug delivery, magneto-mechanical actuation, and contrast enhancement. Highly sensitive detection and imaging techniques based on the nonlinear properties of nanomagnets were recently proposed as innovative strong-translational potential methods applicable in complex, often opaque, biological systems. Here we report on the significant enhancement of the detection capability using optical-lithography-defined, ferromagnetic iron-nickel alloy disk-shaped particles. We show that an irreversible transition between strongly non-collinear (vortex) and single domain states, driven by an alternating magnetic field, translates into a nonlinear magnetic response that enables ultrasensitive detection of these particles. The record sensitivity of ∼3.5 × 10-9 emu, which is equivalent to ∼39 pg of magnetic material is demonstrated at room temperature for arrays of patterned disks. We also show that unbound disks suspended in the aqueous buffer can be successfully detected and quantified in real-time when administered into a live animal allowing for tracing of their biodistribution. The use of nanoscale ferromagnetic particles with engineered nonlinear properties opens prospects for further enhancing the sensitivity, scalability, and tunability of noise-free magnetic tag detection in high-background environments for various applications spanning from biosensing and medical imaging to anti-counterfeiting technologies.

Vortex dynamics and frequency splitting in vertically coupled nanomagnets.

We explored the dynamic response of a vortex core in a circular nanomagnet by manipulating its dipole-dipole interaction with another vortex core confined locally on top of the nanomagnet. A clear frequency splitting is observed corresponding to the gyrofrequencies of the two vortex cores. The peak positions of the two resonance frequencies can be engineered by controlling the magnitude and direction of the external magnetic field. Both experimental and micromagnetic simulations show that the frequency spectra for the combined system is significantly dependent on the chirality of the circular nanomagnet and is asymmetric with respect to the external bias field. We attribute this result to the strong dynamic dipole-dipole interaction between the two vortex cores, which varies with the distance between them. The possibility of having multiple states in a single nanomagnet with vertical coupling could be of interest for magnetoresistive memories.

Observation of superconducting vortex clusters in S/F hybrids.

While Abrikosov vortices repel each other and form a uniform vortex lattice in bulk type-II superconductors, strong confinement potential profoundly affects their spatial distribution eventually leading to vortex cluster formation. The confinement could be induced by the geometric boundaries in mesoscopic-size superconductors or by the spatial modulation of the magnetic field in superconductor/ferromagnet (S/F) hybrids. Here we study the vortex confinement in S/F thin film heterostructures and we observe that vortex clusters appear near magnetization inhomogeneities in the ferromagnet, called bifurcations. We use magnetic force microscopy to image magnetic bifurcations and superconducting vortices, while high resolution scanning tunneling microscopy is used to obtain detailed information of the local electronic density of states outside and inside the vortex cluster. We find an intervortex spacing at the bifurcation shorter than the one predicted for the same superconductor in a uniform magnetic field equal to the thermodynamical upper critical field Hc2. This result is due to a local enhanced stray field and a competition between vortex-vortex repulsion and Lorentz force. Our findings suggest that special magnetic topologies could result in S/F hybrids that support superconductivity even when locally the vortex density exceeds the thermodynamic critical threshold value beyond which the superconductivity is destroyed.

Large Spin-Wave Bullet in a Ferrimagnetic Insulator Driven by the Spin Hall Effect.

Because of its transverse nature, spin Hall effects (SHE) provide the possibility to excite and detect spin currents and magnetization dynamics even in magnetic insulators. Magnetic insulators are outstanding materials for the investigation of nonlinear phenomena and for novel low power spintronics applications because of their extremely low Gilbert damping. Here, we report on the direct imaging of electrically driven spin-torque ferromagnetic resonance (ST-FMR) in the ferrimagnetic insulator Y_{3}Fe_{5}O_{12} based on the excitation and detection by SHEs. The driven spin dynamics in Y_{3}Fe_{5}O_{12} is directly imaged by spatially resolved microfocused Brillouin light scattering spectroscopy. Previously, ST-FMR experiments assumed a uniform precession across the sample, which is not valid in our measurements. A strong spin-wave localization in the center of the sample is observed indicating the formation of a nonlinear, self-localized spin-wave "bullet".

Visualizing domain wall and reverse domain superconductivity.

In magnetically coupled, planar ferromagnet-superconductor (F/S) hybrid structures, magnetic domain walls can be used to spatially confine the superconductivity. In contrast to a superconductor in a uniform applied magnetic field, the nucleation of the superconducting order parameter in F/S structures is governed by the inhomogeneous magnetic field distribution. The interplay between the superconductivity localized at the domain walls and far from the walls leads to effects such as re-entrant superconductivity and reverse domain superconductivity with the critical temperature depending upon the location. Here we use scanning tunnelling spectroscopy to directly image the nucleation of superconductivity at the domain wall in F/S structures realized with Co-Pd multilayers and Pb thin films. Our results demonstrate that such F/S structures are attractive model systems that offer the possibility to control the strength and the location of the superconducting nucleus by applying an external magnetic field, potentially useful to guide vortices for computing application.

Detection of B-mode polarization in the cosmic microwave background with data from the South Pole Telescope.

Gravitational lensing of the cosmic microwave background generates a curl pattern in the observed polarization. This "B-mode" signal provides a measure of the projected mass distribution over the entire observable Universe and also acts as a contaminant for the measurement of primordial gravity-wave signals. In this Letter we present the first detection of gravitational lensing B modes, using first-season data from the polarization-sensitive receiver on the South Pole Telescope (SPTpol). We construct a template for the lensing B-mode signal by combining E-mode polarization measured by SPTpol with estimates of the lensing potential from a Herschel-SPIRE map of the cosmic infrared background. We compare this template to the B modes measured directly by SPTpol, finding a nonzero correlation at 7.7σ significance. The correlation has an amplitude and scale dependence consistent with theoretical expectations, is robust with respect to analysis choices, and constitutes the first measurement of a powerful cosmological observable.

From chaos to selective ordering of vortex cores in interacting mesomagnets.

A spin vortex consists of an in-plane curling magnetization and a small core region (~10 nm) with out-of-plane magnetization. An oscillating field or current induce gyrotropic precession of the spin vortex. Dipole-dipole and exchange coupling between the interacting vortices may lead to excitation of collective modes whose frequencies depend on the core polarities. Here we demonstrate an effective method for controlling the relative core polarities in a model system of overlapping Ni(80)Fe(20) dots. This is achieved by driving the system to a chaotic regime of continuous core reversals and subsequently relaxing the cores to steady-state motion. It is shown that any particular core polarity combination (and therefore the spectral response of the entire system) can be deterministically preselected by tuning the excitation frequency or external magnetic field. We anticipate that this work would benefit the future development of magnonic crystals, spin-torque oscillators, magnetic storage and logic elements.

Hyperthermia induces injury to the intestinal mucosa in the mouse: evidence for an oxidative stress mechanism.

Loss of the intestinal barrier is critical to the clinical course of heat illness, but the underlying mechanisms are still poorly understood. We tested the hypothesis that conditions characteristic of mild heatstroke in mice are associated with injury to the epithelial lining of the intestinal tract and comprise a critical component of barrier dysfunction. Anesthetized mice were gavaged with 4 kDa FITC-dextran (FD-4) and exposed to increasing core temperatures, briefly reaching 42.4°C, followed by 30 min recovery. Arterial samples were collected to measure FD-4 concentration in plasma (in vivo gastrointestinal permeability). The small intestines were then removed to measure histological evidence of injury. Hyperthermia resulted in a ≈2.5-fold elevation in plasma FD-4 and was always associated with significant histological evidence of injury to the epithelial lining compared with matched controls, particularly in the duodenum. When isolated intestinal segments from control animals were exposed to ≥41.5°C, marked increases in permeability were observed within 60 min. These changes were associated with release of lactate dehydrogenase, evidence of protein oxidation via carbonyl formation and histological damage. Coincubation with N-acetylcysteine protected in vitro permeability during hyperthermia and reduced histological damage and protein oxidation. Chelation of intracellular Ca(2+) to block tight junction opening during 41.5°C exposure failed to reduce the permeability of in vitro segments. The results demonstrate that hyperthermia exposure in mouse intestine, at temperatures at or below those necessary to induce mild heatstroke, cause rapid and substantial injury to the intestinal lining that may be attributed, in part, to oxidative stress.

MULTIFUNCTIONAL NANO-BIO MATERIALS WITHIN CELLULAR MACHINERY.

Functional nanoscale materials that possess specific physical or chemical properties can leverage energy transduction in vivo. Once these materials integrate with biomolecules they combine physical properties of inorganic material and the biorecognition capabilities of bio-organic moieties. Such nano-bio hybrids can be interfaced with living cells, the elementary functional units of life. These nano-bio systems are capable of bio-manipulation or actuation via altering intracellular biochemical pathways. Thus, nano-bio conjugates are appealing for a wide range of applications from the life sciences and nanomedicine to catalysis and clean energy production. Here we highlight recent progress in our efforts to develop smart nano-bio hybrid materials, and to study their performance within cellular machinery under application of external stimuli, such as light or magnetic fields.

Novel magnetic tips developed for the switching magnetization magnetic force microscopy.

Using micromagnetic calculations we search for optimal magnetic properties of novel magnetic tips to be used for a Switching Magnetization Magnetic Force Microscopy (SM-MFM), a novel technique based on two-pass scanning with reversed tip magnetization. Within the technique the sum of two scans images local atomic forces and their difference maps the local magnetic forces. The tip magnetization is switched during the scanning by a small magnetic field. The technology of novel low-coercitive magnetic tips is proposed. For best performance the tips must exhibit low magnetic moment, low switching field, and single-domain state at remanence. Such tips are equipped with Permalloy objects of a precise shape that are defined on their tilted sides. We calculate switching fields of such tips by solving the micromagnetic problem to find the optimum shape and dimensions of the Permalloy objects located on the tips. Among them, hexagon was found as the best shape for the tips.

A broadband imaging system for research applications.

We have developed a compact, computer-piloted, high sensitivity broadband imaging system for laboratory research that is compatible with various detectors. Mirror optics allow application from the visible to the far infrared spectral range. A prototype tested in conjunction with a mercury cadmium telluride detector exhibits a peak detectivity of 6.7x10(10) cm Hz(1/2)/W at a wavelength of 11.8 microm. Temperature and spatial resolutions of 0.06 K and 1.6 mrad, respectively, were demonstrated.

Probing arrays of circular magnetic microdots by ferromagnetic resonance.

X-band ferromagnetic resonance (FMR) was used to characterize in-plane magnetic anisotropies in rectangular and square arrays of circular nickel and Permalloy microdots. In the case of a rectangular lattice, as interdot distances in one direction decrease, the in-plane uniaxial anisotropy field increases, in good agreement with a simple theory of magnetostatically interacting uniformly magnetized dots. In the case of a square lattice a four-fold anisotropy of the in-plane FMR field H(r) was found when the interdot distance a gets comparable to the dot diameter D. This anisotropy, not expected in the case of uniformly magnetized dots, was explained by a non-uniform magnetization m(r) in a dot in response to dipolar forces in the patterned magnetic structure. It is well described by an iterative solution of a continuous variation procedure. In the case of perpendicular magnetization multiple sharp resonance peaks were observed below the main FMR peak in all the samples, and the relative positions of these peaks were independent of the interdot separations. Quantitative description of the observed multiresonance FMR spectra was given using the dipole-exchange spin wave dispersion equation for a perpendicularly magnetized film where in-plane wave vector is quantized due to the finite dot radius, and the inhomogenetiy of the intradot static demagnetization field in the nonellipsoidal dot is taken into account. It was demonstrated that ferromagnetic resonance force microscopy (FMRFM) can be used to determine both local and global properties of patterned submicron ferromagnetic samples. Local spectroscopy together with the possibility to vary the tip-sample spacing enables the separation of those two contributions to a FMRFM spectrum. The global FMR properties of circular submicron dots determined using magnetic resonance force microscopy are in a good agreement with results obtained using conventional FMR and with theoretical descriptions.

Driven dynamic mode splitting of the magnetic vortex translational resonance.

A magnetic vortex in a restricted geometry possesses a nondegenerate translational excitation that corresponds to circular motion of its core at a characteristic frequency. For 40-nm thick, micron-sized permalloy elements, we find that the translational-mode microwave absorption peak splits into two peaks that differ in frequency by up to 25% as the driving field is increased. An analysis of micromagnetic equations shows that for large driving fields two stable solutions emerge.

Imprinting vortices into antiferromagnets.

The effect of imprinting symmetric and displaced vortex structures into an antiferromagnetic material is investigated in micron-sized disks consisting of exchange coupled ferromagnetic-antiferromagnetic bilayers. The imprint of displaced vortices manifests itself by the occurrence of a new type of asymmetric hysteresis loops characterized by curved, reversible, central sections with nonzero remanent magnetization. Such an imprint is achieved by cooling the disks through the blocking temperature of the system in small fields. Micromagnetic simulations reveal that asymmetric vortexlike loops naturally result from the competition between the different energies involved in the system.

Dynamic origin of stripe domains.

We investigate stripe domain formation in nanometer sized Co bars. The magnetic equilibrium states and the magnetic spin wave frequencies are obtained from micromagnetic-like simulations. We find that the lowest frequency standing-wave mode has the same spatial structure as the stripe domains at remanence and it goes soft at the field where the stripe domains emerge. We show, therefore, that the final domain structure at remanence, which is not the configuration with lowest energy, is predicted from a high-field analysis of the frequencies of the standing spin waves.