BINA

The adaptive branch of the immune system learns pathogenic patterns and remembers them for future encounters. It does so through dynamic and diverse repertoires of T- and B- cell receptors (TCR and BCRs, respectively). These huge immune repertoires in each individual present investigators with the challenge of extracting meaningful biological information from multi-dimensional data. The ability to embed these DNA and amino acid textual sequences in a vector-space is an important step towards developing effective analysis methods. Here we present Immune2vec, an adaptation of a natural language processing (NLP)-based embedding technique for BCR repertoire sequencing data. We validate Immune2vec on amino acid 3-gram sequences, continuing to longer BCR sequences, and finally to entire repertoires. Our work demonstrates Immune2vec to be a reliable low-dimensional representation that preserves relevant information of immune sequencing data, such as n-gram properties and IGHV gene family classification. Applying Immune2vec along with machine learning approaches to patient data exemplifies how distinct clinical conditions can be effectively stratified, indicating that the embedding space can be used for feature extraction and exploratory data analysis.

Nanoparticles having magnetic and fluorescent properties could be considered as a gift to materials scientists due to their unique magneto-optical qualities. Multiple component particles can overcome challenges related with a single component and unveil bifunctional/multifunctional features that can enlarge their applications in diagnostic imaging agents and therapeutic delivery vehicles. Bifunctional nanoparticles that have both luminescent and magnetic features are termed as magnetic nanolights. Herein, we present recent progress of magneto-fluorescent nanoparticles (quantum dots based magnetic nanoparticles, Janus particles, and heterocrystalline fluorescent magnetic materials), comprehensively describing fabrication strategies, types, and biomedical applications. In this review, our aim is not only to encompass the preparation strategies of these special types of magneto-fluorescent nanomaterials but …

Kaposi’s sarcoma-associated herpesvirus (KSHV) is a cancer-related herpesvirus. Like other herpesviruses, the KSHV icosahedral capsid includes a portal vertex, composed of 12 protein subunits encoded by open reading frame (ORF) 43, which enables packaging and release of the viral genome into the nucleus through the nuclear pore complex (NPC). Capsid vertex-specific component (CVSC) tegument proteins, which directly mediate docking at the NPCs, are organized on the capsid vertices and are enriched on the portal vertex. Whether and how the portal vertex is selected for docking at the NPC is unknown. Here, we investigated the docking of incoming ORF43-null KSHV capsids at the NPCs, and describe a significantly lower fraction of capsids attached to the nuclear envelope compared to wild-type (WT) capsids. Like WT capsids, nuclear envelope-associated ORF43-null capsids co-localized with different nucleoporins (Nups) and did not detach upon salt treatment. Inhibition of nuclear export did not alter WT capsid docking. As ORF43-null capsids exhibit lower extent of association with the NPCs, we conclude that although not essential, the portal has a role in mediating the interaction of the CVSC proteins with Nups, and suggest a model whereby WT capsids can dock at the nuclear envelope through a non-portal penton vertex, resulting in an infection ‘dead end’.

Pt-Ni nanoparticles (NPs) are used as electrocatalysts toward the oxygen reduction reaction due to their high mass activity. However, degradation processes at the high potential in the acidic conditions of the proton exchange membrane fuel cell delay its massive implementation. The model presented here facilitates understanding the corrosion by clearing variables related to the electrochemical measurement (non-equilibrium condition and complex system) and focusing on the gradual etching of Ni via two-phase Ni(II) transfer treatment promoted by chelating agents (CAs). We synthesized Pt-Ni/C octahedral NPs and then used six chemically different CAs as corrosion agents for Ni. The corrosion yielded concave octahedral and hexapod NPs. Amine-rich CAs treatment results in particle detachment from the carbon substrates, while carboxylic rich preserve the carbon-particle interface. We correlate the detachment …

Post-traumatic-stress-disorder (PTSD) is a stress-related condition that may develop after exposure to a severe trauma-event. One of the core brain areas that is considered to be a key regulatory region of PTSD is the amygdala. Specifically, the central amygdala (CeA) is involved in emotion processing and associative fear learning memory, two main circuits involved in PTSD. Long term dysregulation of trauma-related emotional processing may be caused by neuroadaptations that affect gene expression. The adenosine-(A) to-inosine (I) RNA editing machinery is a post-transcriptional process that converts a genomic encoded A to I and is critical for normal brain function and development. Such editing has the potential to increase the transcriptome diversity, and disruption of this process has been linked to various central nervous system disorders. Here, we employed a unique animal model to examine the possibility …

Aqueous salt batteries with high concentrations of salt or water in salt aqueous systems have received considerable attention with focus on improving working voltage range and energy density. Here, the effect of NaClO4 salt concentration on the electrochemical performance and stability of tunnel-type Na0. 44MnO2 (NMO) cathodes and organic polyimide (PI) derivative anodes was studied. High capacity retention and 100% coulombic efficiency were shown for NMO/PI full cell in saturated NaClO4 electrolyte. A high, stable capacity of 115 mAh/g was achieved for the PI anode material, and the full cell showed a stable capacity of 41 mAh/g at 2C rate for 430 cycles (calculated for the weight of NMO cathode). Even at a fast 5C rate, a discharge capacity of 33 mAh/g was maintained for 2,400 prolonged cycles with nearly 100% efficiency. The full cell device can achieve an average voltage of 1 V with energy density of …

The current work presents the fabrication of micrometer‐thick single‐side‐coated surface‐engineered polypropylene (PP) film for versatile flexible electronics applications. Herein, the authors report, for the first time, photopolymerized thin coating of graphene nanofibers (GNFs) and iron oxide nanoparticles (IONPs) onto non‐polar plastic via surface chemistry. The fabrication is achieved by adopting three consecutive steps; initially corona treated PP films are treated with silane for thin layer silica coating. Then, the silylated PP films are brushed up by pyrrole/GNFs/IONPs mixture, followed by UV exposure. The coated films show surface conductivity in the range of ≈20 S cm−1 at room temperature. Moreover, ≈15 microns of the coated film is tested against electromagnetic waves in the X‐band region (8.2–12.4 GHz) and its shielding behavior (≈24 dB) is confirmed. To demonstrate its wide range of versatility, the …

Carbon dots (CDs)-based logic gates are smart nanoprobes that can respond to various analytes such as metal cations, anions, amino acids, pesticides, antioxidants, etc. Most of these logic gates are based on fluorescence techniques because they are inexpensive, give an instant response, and highly sensitive. Computations based on molecular logic can lead to advancement in modern science. This review focuses on different logic functions based on the sensing abilities of CDs and their synthesis. We also discuss the sensing mechanism of these logic gates and bring different types of possible logic operations. This review envisions that CDs-based logic gates have a promising future in computing nanodevices. In addition, we cover the advancement in CDs-based logic gates with the focus of understanding the fundamentals of how CDs have the potential for performing various logic functions depending upon their different categories.

In this paper, we demonstrate a digital micromirror device (DMD) based optical microscopic apparatus for quantitative differential phase contrast (qDIC) imaging, coherent structured illumination microscopy (SIM), and dual-modality (scattering/fluorescent) imaging. For both the qDIC imaging and the coherent SIM, two sets of fringe patterns with orthogonal orientations and five phase-shifts for each orientation, are generated by a DMD and projected on a sample. A CCD camera records the generated images in a defocusing manner for qDIC and an in-focus manner for coherent SIM. Both quantitative phase images and super-resolved scattering/fluorescence images can be reconstructed from the recorded intensity images. Moreover, fluorescent imaging modality is integrated, providing specific biochemical structures of the sample once using fluorescent labeling. We believe such a simple and versatile apparatus will find wide applications in biomedical fields or life science.

A detailed investigation is presented for the solvent-free mechanochemical synthesis of zinc oxide nanoparticles from ε-Zn (OH) 2 crystals by high-energy ball milling. Only a few works have ever explored the dry synthetic route from ε-Zn (OH) 2 to ZnO. The milling process of ε-Zn (OH) 2 was done in ambient conditions with a 1: 100 powder/ball mass ratio, and it produced uniform ZnO nanoparticles with sizes of 10–30 nm, based on the milling duration. The process was carefully monitored and the effect of the milling duration on the powder composition, nanoparticle size and strain, optical properties, aggregate size, and material activity was examined using XRD, TEM, DLS, UV-Vis, and FTIR. The mechanism for the transformation of ε-Zn (OH) 2 to ZnO was studied by TGA and XPS analysis. The study gave proof for a reaction mechanism starting with a phase transition of crystalline ε-Zn (OH) 2 to amorphous Zn (OH …

Among various renewable energy sources, namely, biomass, solar, wind, hydrothermal and geothermal, biomass standout as an environmentally benign, sustainable and an immediate substitute to fossil based fuels. This is due to the abundance of the carbon source in the form of cellulose in the biomass. Cellulose is the major chemical constituent of terrestrial biomass (40-50 wt.%, percentage by weight) with the other constituents being hemicellulose and lignin. However, owing to the extensive inter and intramolecular hydrogen bonding network existing in the cellulose structure, depolymerization of cellulose to monomeric carbohydrate glucose is nearly two orders of magnitude difficult than the hydrolysis of starch to glucose. The extensive inter and intramolecular hydrogen bonding network that hinders the access of acidic proton of the catalyst to attack the reaction site of β-1, 4 glycosidic bonds of cellulose (the linear homopolymer of glucose) is shown pictorially in Figure 1. The hydrogen bonding network within a single chain of glycose polymer in the cellulose structure is called intramolecular hydrogen bonding while such bonding between two neighbouring linear chains of glucose polymers is called as intermolecular hydrogen bonding. The bond energy of such hydrogen bonding is 2 eV which is nearly 3-6 orders of magnitude higher than microwave energy (1.24 x 10-6–1.24 10-3 eV)[1]. Yet, with the application of unconventional and novel methods of activation like microwave irradiation, the acid catalyzed hydrolysis of biomass (cellulose) to monosaccharides is accelerated by facilitating the access of the acidic proton of the chemical …

Hydrodynamic electron flow is a unique signature of strong electron interactions in a material. This effect has been observed in 2D materials, but observations in bulk materials are intriguing as high-carrier density should screen the interactions. In this work, we study hydrodynamic flow in the semimetal WTe2 to gain insight into the microscopic origin of its electron interactions. We image the spatial profile of the electric current by using a nitrogen-vacancy scanning tip. Using coherent quantum sensing, we obtain magnetic field resolution of~ 10nT and spatial resolution of~ 100nm. The current pattern we observe differs substantially from the flat profile of a normal metal, and indicates correlated flow through the semimetal. The pattern also shows non-monotonic temperature dependence, with hydrodynamic effects peaking at~ 20 K. We compare our results to a model which combines ab initio electron scattering rates …

Alu elements are repetitive short interspersed elements prevalent in the primate genome. These repeats account for over 10% of the genome with more than a million highly similar copies. A direct outcome of this is an enrichment in long structures of stable dsRNA, which are the target of adenosine deaminases acting on RNAs (ADARs), the enzymes catalyzing A-to-I RNA editing. Indeed, A-to-I editing by ADARs is extremely abundant in primates: over a hundred million editing sites exist in their genomes. However, despite the radical increase in ADAR targets brought on by the introduction of Alu elements, the few evolutionary conserved editing sites manage to retain their editing levels. Here, we review and discuss the cost of having an unusual amount of dsRNA and editing in the transcriptome, as well as the opportunities it presents, which possibly contributed to accelerating primate evolution.

Although liquid mercury (Hg) has been known since antiquity, the formation of stable solid nano forms of Hg at room temperature has not been reported so far. Here, for the first time, we report a simple sonochemical route to obtain solid mercury nanoparticles, stabilized by reduced graphene oxide at ambient conditions. The as-formed solid Hg nanoparticles were found to exhibit remarkable rhombohedral morphology and crystallinity at room temperature. Extensive characterization using various physicochemical techniques revealed the unique properties of the solid nanoparticles of Hg compared to its bulk liquid metal phase. Furthermore, the solid nature of the Hg nanoparticles was studied electrochemically, revealing distinctive properties. We believe that solid Hg nanoparticles have the potential for important applications in the fields of electroanalytical chemistry and electrocatalysis.

Exosomes are promising vectors for anti-tumor therapy, due to their biocompatibility, low immunogenicity, and innate ability to interact with target cells. However, promoting clinical application of exosome-based therapeutics requires elucidation of key issues, including exosome biodistribution, tumor targeting and accumulation, and the ability to overcome tumor barriers that limit the penetration of various nano-carriers and drugs. Here, we examined these parameters in exosomes derived from mesenchymal stem cells (MSC-exo) and from the A431 squamous cell carcinoma line (A431-exo), which both have potential use in cancer therapy. Using our novel technique combining gold nanoparticle (GNP) labeling of exosomes and non-invasive computed tomography imaging (CT), we longitudinally and quantitatively tracked the two intravenously-injected exosome types in A431 tumor-bearing mice. CT imaging up to 48 …

DTG Group Daniel Gryko's Group METHODOLOGY → DYES → APPLICATIONS Gryko's Group Home News DTG Members Publications (current) Teaching Vacancies 2021 M. Krzeszewski, M. Tasior, M. Grzybowski, DT Gryko Synthesis of Tetraaryl-, Pentaaryl-, and Hexaaryl-1,4-dihydropyrrolo[3,2-b]pyrroles Org. Synth., 2021, 98, 242-262 KV Vygranenko, YM Poronik, A. Wrzosek, A. Szewczyk, DT Gryko Red emissive sulfone-rhodols as mitochondrial imaging agents Chem. Commun., 2021, 57, 7782-7785 Ł. Kielesiński, OW Morawski, CA Barboza, DT Gryko Polarized Helical Coumarins: [1,5] Sigmatropic Rearrangement and Excited-State Intramolecular Proton Transfer J. Org. Chem., 2021, 86, 6148-6159 M. Jacquet, M. Izzo, S. Osella, S. Kozdra, PP Michałowski, D. Gołowicz, K. Kazimierczuk, MT Gorzkowski, A. Lewera, M. Teodorczyk, B. Trzaskowski, R. Jurczakowski, DT Gryko, J. Kargul Development of a universal …

Following nervous system injuries, such as peripheral or spinal cord injuries, severed nerves must regenerate to reinnervate tissues and restore lost-functionality. In many peripheral nerve injuries surgical intervention is required to bridge the gaps created and facilitate regrowth. The gold standard for peripheral nerve repair remains end-to-end suturing and nerve grafting, yet, these still present unmet challenges and limitation including misalignment of regenerating axons. Following spinal cord injuries currently there are no therapies capable of complete nerve restoration. Tissue engineering strategies include the design of structured tissue-like platforms to support growth and facilitate reconstructions of damaged tissues for both the peripheral and the central nervous systems. In the last two decades efforts to increase accuracy of regeneration through engineering growth-and-alignment promoting platforms …