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At least 199 records · Page 11

Arabinogalactan Structures of Repetitive Serine-Hydroxyproline Glycomodule Expressed by Arabidopsis Cell Suspension Cultures

Arabinogalactan-proteins (AGPs) are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily. They are heavily glycosylated with arabinogalactans, which are usually composed of a β-1,3-linked galactan backbone with 6-O-linked galactosyl, oligo-1,6-galactosyl, or 1,6-galactan side chains that are further decorated with arabinosyl, glucuronosyl, rhamnosyl, and/or fucosyl residues. Here, our work with Hyp-O-polysaccharides isolated from (Ser-Hyp)32-EGFP (enhanced green fluorescent protein) fusion glycoproteins overexpressed in transgenic Arabidopsis suspension culture is consistent with the common structural features of AGPs isolated from tobacco. In addition, this work confirms the presence of β-1,6-linkage on the galactan backbone identified previously in AGP fusion glycoproteins expressed in tobacco suspension culture. Furthermore, the AGPs expressed in Arabidopsis suspension culture lack terminal-rhamnosyl residues and have a much lower level of glucuronosylation compared with those expressed in tobacco suspension culture. These differences not only suggest the presence of distinct glycosyl transferases for AGP glycosylation in the two systems, but also indicate the existence of minimum AG structures for type II AG functional features.

59 BASIC BIOLOGICAL SCIENCES↗

Multi-phase equation of state of ultrapure hafnium to 120 GPa

Hafnium (Hf) is an industrially important material due to its large neutron absorption cross-section and its high corrosion resistance. When subjected to high pressure, Hf phase transforms from its hexagonal close packed α-Hf phase to the hexagonal ω-Hf phase. Upon further compression, ω-Hf phase transforms to the body centered cubic β-Hf phase. In this study, the high pressure phase transformations of Hf are studied by compressing and decompressing a well-characterized Hf sample in diamond anvil cells up to 120 GPa while collecting x-ray diffraction data. The phase transformations of Hf were compared in both a He pressure transmitting medium (PTM) and no PTM over several experiments. It was found that the α-Hf to ω-Hf phase transition occurs at a higher pressure during compression and lower pressure during decompression with a helium (He) PTM compared to using no PTM. Finally, there was little difference in the ω-Hf to β-Hf phase transition pressure between the He PTM and no PTM. The equation of state was fit for all three phases of Hf and under both PTM and no-PTM.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Beta decay of the axially asymmetric ground state of 192 Re

The β decay of 192 75 Re 117 , which lies near the boundary between the regions of predicted prolate and oblate deformations, has been investigated using the KEK Isotope Separation System (KISS) in RIKEN Nishina Center. This is the first case in which a low-energy beam of rhenium isotope has been successfully extracted from an argon gas-stopping cell using a laser-ionization technique, following production via multi-nucleon transfer between heavy ions. The ground state of 192 Re has been assigned J π = (0⁻) based on the observed β feedings and deduced logft values towards the 0⁺ and 2⁺ states in 192 Os, which is known as a typical γ-soft nucleus. Furthermore, the shape transition from axial symmetry to axial asymmetry in the Re isotopes is discussed from the viewpoint of single-particle structure using the nuclear Skyrme-Hartree-Fock model.

192Re↗

Broad betacoronavirus neutralization by a stem helix–specific human antibody

Targeting a range of betacoranaviruses In the past 20 years, three highly pathogenic β-coronaviruses have crossed from animals to humans, including the most recent: severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). A spike protein that decorates these viruses has an S1 domain that binds host cell receptors and an S2 domain that fuses the viral and cell membranes to allow cell entry. The S1 domain is the target of many neutralizing antibodies but is more genetically variable than S2, and antibodies can exert selective pressure, leading to resistant variants. Pinto et al . identified five monoclonal antibodies that interact with a helix in the S2 domain. The most broadly neutralizing antibody inhibited all β-coronavirus subgenera and reduced viral burden in hamsters infected with SARS-CoV-2. —VV

59 BASIC BIOLOGICAL SCIENCES↗

Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation

Abstract Background Human induced pluripotent stem cells (iPSC) have opened new avenues for regenerative medicine. Consequently, iPSC-derived motor neurons have emerged as potentially viable therapies for spinal cord injuries and neurodegenerative disorders including Amyotrophic Lateral Sclerosis. However, direct clinical application of iPSC bears in itself the risk of tumorigenesis and other unforeseeable genetic or epigenetic abnormalities. Results Employing RNA-seq technology, we identified and characterized gene regulatory networks triggered by in vitro chemical reprogramming of iPSC into cells with the molecular features of motor neurons (MNs) whose function in vivo is to innervate effector organs. We present meta-transcriptome signatures of 5 cell types: iPSCs, neural stem cells, motor neuron progenitors, early motor neurons, and mature motor neurons. In strict response to the chemical stimuli, along the MN differentiation axis we observed temporal downregulation of tumor growth factor-β signaling pathway and consistent activation of sonic hedgehog, Wnt/β-catenin, and Notch signaling. Together with gene networks defining neuronal differentiation (neurogenin 2, microtubule-associated protein 2, Pax6, and neuropilin-1), we observed steady accumulation of motor neuron-specific regulatory genes, including Islet-1 and homeobox protein HB9. Interestingly, transcriptome profiling of the differentiation process showed that Ca 2+ signaling through cAMP and LPC was downregulated during the conversion of the iPSC to neural stem cells and key regulatory gene activity of the pathway remained inhibited until later stages of motor neuron formation. Pathways shaping the neuronal development and function were well-represented in the early motor neuron cells including, neuroactive ligand-receptor interactions, axon guidance, and the cholinergic synapse formation. A notable hallmark of our in vitro motor neuron maturation in monoculture was the activation of genes encoding G-coupled muscarinic acetylcholine receptors and downregulation of the ionotropic nicotinic acetylcholine receptors expression. We observed the formation of functional neuronal networks as spontaneous oscillations in the extracellular action potentials recorded on multi-electrode array chip after 20 days of differentiation. Conclusions Detailed transcriptome profile of each developmental step from iPSC to motor neuron driven by chemical induction provides the guidelines to novel therapeutic approaches in the re-construction efforts of muscle innervation.

59 BASIC BIOLOGICAL SCIENCES↗

Synergistic Improvement of Carbohydrate and Lignin Processability by Biomimicking Biomass Processing

The sustainability and economic feasibility of modern biorefinery depend on the efficient processing of both carbohydrate and lignin fractions for value-added products. By mimicking the biomass degradation process in white-rote fungi, a tailored two-step fractionation process was developed to maximize the sugar release from switchgrass biomass and to optimize the lignin processability for bioconversion. Biomimicking biomass processing using Formic Acid: Fenton: Organosolv (F 2 O) and achieved high processability for both carbohydrate and lignin. Specifically, switchgrass pretreated by the F 2 O process had 99.6% of the theoretical yield for glucose release. The fractionated lignin was also readily processable by fermentation via Rhodococcus opacus PD630 with a lipid yield of 1.16 g/L. Scanning electron microscope analysis confirmed the fragmentation of switchgrass fiber and the cell wall deconstruction by the F 2 O process. 2D-HSQC NMR further revealed the cleavage of aryl ether linkages (β-O-4) in lignin components. These results revealed the mechanisms for efficient sugar release and lignin bioconversion. The F 2 O process demonstrated effective mimicking of natural biomass utilization system and paved a new path for improving the lignin and carbohydrate processability in next generation lignocellulosic biorefinery.

09 BIOMASS FUELS↗

Lactiplantibacillus plantarum 0111 Protects Against Influenza Virus by Modulating Intestinal Microbial-Mediated Immune Responses

There are some limitations of traditional influenza vaccines concerning novel mutant strains. Therefore, it is particularly important to develop preventive means for antigen-unrelated types of influenza viruses. Recent studies have shown that probiotics can modulate the immune system and reduce the severity of viral infections. In this study, we investigated the potential of Lactiplantibacillus plantarum 0111 against influenza virus H9N2. Challenge experiments showed that L. plantarum 0111 pretreatments could effectively improve mice’s survival rate and weight loss and reduce the inflammatory cytokines IL-6 and TNF-α in the lungs and bronchoalveolar lavage fluid (BALF) along with the degree of lung and intestinal injury. FMT experiment demonstrates that the protective effect produced by L. plantarum 0111 is associated with gut microorganisms. In addition, 16S high-throughput sequencing of the mouse intestinal microbiota showed that L. plantarum 0111 remodeled the intestinal microbiota after H9N2 infection and maintained the gut microbiota balance. In a mouse model, the oral administration of L. plantarum 0111 increased IFN-β expression in the serum and BALF. At the same time, the transcript levels of IFN-β and related ISGs in the intestine and lungs of mice were also increased. In addition, the activation and polarization of T cells in mesenteric lymph nodes (MLNs) and the spleen were detected by flow cytometry, and the results showed that L. plantarum 0111 modulated cytokines in T cells and increased IgA expression in B cells in the MLNs and spleen. Thus, L. plantarum 0111 may improve gut microbiota-mediated immune responses and thus, resist infection by the influenza virus, and it could be used as an effective preventive measure against the influenza virus.

Xing, Jun-Hong↗

Spectroscopic Characterization of Highly Active Fe–N–C Oxygen Reduction Catalysts and Discovery of Strong Interaction with Nafion Ionomer

Scaling up clean-energy applications necessitates the development of platinum group metal (PGM)-free fuel cell electrocatalysts with high activity, stability, and low cost. Here, X-ray absorption (XAS) at the Fe K-edge and Fe K β X-ray emission (XES) spectroscopies were used to study the electronic structure of Fe centers in highly active Fe–N–C oxygen reduction catalysts with significant commercial potential. X-ray absorption near-edge structure (XANES) analysis has shown that the majority (>95%) of Fe centers are in the Fe 3+ oxidation state, while extended X-ray absorption fine structure (EXAFS) detected a mixture of single site Fe–N 4 centers (>95%) and centers with short (~2.5 Å) Fe–Fe interactions of Fe metal and/or Fe-carbide nanoparticles (<5%) featuring the Fe o oxidation state. Surprisingly, addition of Nafion, the most widely used ionomer, resulted in pronounced changes in the XAS spectra, consistent with a strong catalyst–ionomer interaction where long Fe–Fe interactions at ~3.1 Å were shown to be a feature of Fe 3+ ions bound with the Nafion. We conclude that exposure to Nafion during the device formulation has a different effect from the aggressive acid leaching typically used in the preparation of Fe–N–C catalysts. Furthermore, it was hypothesized that the polymer interacts with single sites’ Fe 3+ centers, as well as with graphene layers protecting the Fe o nanoparticles, and extracts some Fe ions into the Nafion matrix.

25 ENERGY STORAGE↗

Deconstruction of plant biomass by a Cellulomonas strain isolated from an ultra-basic (lignin-stripping) spring

Plant material falling into the ultra-basic (pH 11.5-11.9) springs within The Cedars, an actively serpentinizing site in Sonoma County, California, is subject to conditions that mimic the industrial pretreatment of lignocellulosic biomass for biofuel production. In this research, we sought to obtain hemicellulolytic/cellulolytic bacteria from The Cedars springs that are capable of withstanding the extreme alkaline conditions wherein calcium hydroxide-rich water removes lignin, making cell wall polysaccharides more accessible to microorganisms and their enzymes. We enriched for such bacteria by adding plant debris from the springs into a synthetic alkaline medium with ground tissue of the biofuel crop switchgrass (Panicum virgatum L.) as the sole source of carbon. From the enrichment culture we isolated the facultative anaerobic bacterium Cellulomonas sp. strain FA1 (NBRC 114238), which tolerates high pH and catabolizes the major plant cell wall-associated polysaccharides cellulose, pectin, and hemicellulose. Strain FA1 in monoculture colonized the plant material and degraded switchgrass at a faster rate than the community from which it was derived. Cells of strain FA1 could be acclimated through subculturing to grow at a maximal concentration of 13.4% ethanol. A strain FA1-encoded β-1, 4-endoxylanase expressed in E. coli was active at a broad pH range, displaying near maximal activity at pH 6-9. Discovery of this bacterium illustrates the value of extreme alkaline springs in the search for microorganisms with potential for consolidated bioprocessing of plant biomass to biofuels and other valuable bio-inspired products.

59 BASIC BIOLOGICAL SCIENCES↗

Statistics of pressure fluctuations in turbulent kinetic plasmas

ABSTRACT In this study, we explore the statistics of pressure fluctuations in kinetic collisionless turbulence. A 2.5D kinetic particle-in-cell simulation of decaying turbulence is used to investigate pressure balance via the evolution of thermal and magnetic pressure in a plasma with β of order unity. We also discuss the behaviour of thermal, magnetic, and total pressure structure functions and their corresponding wavenumber spectra. The total pressure spectrum exhibits a slope of −7/3 extending for about a decade in the ion-inertial range. In contrast, shallower −5/3 spectra are characteristic of the magnetic pressure and thermal pressure. The steeper total pressure spectrum is a consequence of cancellation caused by density-magnetic field magnitude anti-correlation. Further, we evaluate higher order total pressure structure functions in an effort to discuss intermittency and compare the power exponents with higher order structure functions of velocity and magnetic fluctuations. Finally, applications to astrophysical systems are also discussed.

Astronomy & Astrophysics↗

Structural basis for ATG9A recruitment to the ULK1 complex in mitophagy initiation

The assembly of the autophagy initiation machinery nucleates autophagosome biogenesis, including in the PINK1- and Parkin-dependent mitophagy pathway implicated in Parkinson’s disease. The structural interaction between the sole transmembrane autophagy protein, autophagy-related protein 9A (ATG9A), and components of the Unc-51–like autophagy activating kinase (ULK1) complex is one of the major missing links needed to complete a structural map of autophagy initiation. We determined the 2.4-Å x-ray crystallographic structure of the ternary structure of ATG9A carboxyl-terminal tail bound to the ATG13:ATG101 Hop1/Rev7/Mad2 (HORMA) dimer, which is part of the ULK1 complex. We term the interacting portion of the extreme carboxyl-terminal part of the ATG9A tail the “HORMA dimer–interacting region” (HDIR). This structure shows that the HDIR binds to the HORMA domain of ATG101 by β sheet complementation such that the ATG9A tail resides in a deep cleft at the ATG13:ATG101 interface. Disruption of this complex in cells impairs damage-induced PINK1/Parkin mitophagy mediated by the cargo receptor NDP52.

59 BASIC BIOLOGICAL SCIENCES↗

Accumulation of Succinyl Coenzyme A Perturbs the Methicillin-Resistant Staphylococcus aureus (MRSA) Succinylome and Is Associated with Increased Susceptibility to Beta-Lactam Antibiotics

mecA -dependent methicillin resistance in MRSA is subject to regulation by numerous accessory factors involved in cell wall biosynthesis, nucleotide signaling, and central metabolism. Here, we report that mutations in the TCA cycle gene, sucC , increased susceptibility to β-lactam antibiotics and was accompanied by significant accumulation of succinyl-CoA, which in turn perturbed lysine succinylation in the proteome.

59 BASIC BIOLOGICAL SCIENCES↗

Inhibition of Amyloid β-Induced Lipid Membrane Permeation and Amyloid β Aggregation by K162

Alzheimer's disease (AD) is characterized by progressive neurodegeneration associated with amyloid β (Aβ) peptide aggregation. The aggregation of Aβ monomers (AβMs) leads to the formation of Aβ oligomers (AβOs), the neurotoxic Aβ form, capable of permeating the cell membrane. Here, we investigated the effect of a fluorene-based active drug candidate, named K162, on both Aβ aggregation and AβO toxicity toward the bilayer lipid membrane (BLM). Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and molecular dynamics (MD) were employed to show that K162 inhibits AβOs-induced BLM permeation, thus preserving BLM integrity. In the presence of K162, only shallow defects on the BLM surface were formed. Apparently, K162 modifies Aβ aggregation by bypassing the formation of toxic AβOs, and only nontoxic AβMs, dimers (AβDs), and fibrils (AβFs) are produced. Unlike other Aβ toxicity inhibitors, K162 preserves neurologically beneficial AβMs. This unique K162 inhibition mechanism provides an alternative AD therapeutic strategy that could be explored in the future.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Cross talk between RNA N6‐methyladenosine methyltransferase‐like 3 and miR‐186 regulates hepatoblastoma progression through Wnt/β‐catenin signalling pathway

Abstract Objectives N6‐methyladenosine (m6A) is a ubiquitous epigenetic RNA modification that plays a pivotal role in tumour development and metastasis. In this study, we aimed to investigate the expression profiling, clinical significance, biological function and the regulation of m6A‐related genes in hepatoblastoma (HB). Materials and Methods The mRNA and protein expression levels of m6A‐related genes were analysed using Gene Expression Omnibus (GEO) and tissue microarray (TMA) cohort. Kaplan‐Meier analysis was performed to evaluate the prognostic value of m6A‐related genes in HB. Knockdown of m6A‐related genes was conducted to analyse its function on cell proliferation, migration and invasion. Furthermore, bioinformatics analysis and experimental verification were used to explore the potential molecular mechanism and signalling pathway. Results We found that most m6A‐related genes were significantly upregulated in HB tumour tissues. High levels of methyltransferase‐like 3 (METTL3, P = .013), YTHDF2 ( P = .037) and FTO ( P = .032) indicated poor clinical outcomes, and the upregulation of METTL3 was an independent prognostic factor in HB patients. Functional assays showed that knockdown of METTL3 could dramatically suppress the proliferation, migration and invasion of HB cells. In addition, METTL3 was identified to be a direct target of microRNA‐186 (miR‐186). Consistently, miR‐186 was low expressed in HB tumour tissues. Moreover, overexpression of miR‐186 significantly inhibited cell aggressive phenotype both in vitro and in vivo, while the inhibitory effect could be reversed by METTL3 overexpression. Mechanism study indicated that miR‐186/METTL3 axis contributed to the progression of HB via the Wnt/β‐catenin signalling pathway. Conclusions M6A‐related genes were frequently dysregulated in HB. miR‐186/METTL3/Wnt/β‐catenin axis might serve as novel therapeutic targets and prognostic biomarkers in HB.

Cui, Xichun↗

Egr1 is a 3D matrix–specific mediator of mechanosensitive stem cell lineage commitment

While extracellular matrix (ECM) mechanics strongly regulate stem cell commitment, the field’s mechanistic understanding of this phenomenon largely derives from simplified two-dimensional (2D) culture substrates. Here, we found a 3D matrix–specific mechanoresponsive mechanism for neural stem cell (NSC) differentiation. NSC lineage commitment in 3D is maximally stiffness sensitive in the range of 0.1 to 1.2 kPa, a narrower and more brain-mimetic range than we had previously identified in 2D (0.75 to 75 kPa). Transcriptomics revealed stiffness-dependent up-regulation of early growth response 1 (Egr1) in 3D but not in 2D. Egr1 knockdown enhanced neurogenesis in stiff ECMs by driving β-catenin nuclear localization and activity in 3D, but not in 2D. Mechanical modeling and experimental studies under osmotic pressure indicate that stiff 3D ECMs are likely to stimulate Egr1 via increases in confining stress during cell volumetric growth. To our knowledge, Egr1 represents the first 3D-specific stem cell mechanoregulatory factor.

59 BASIC BIOLOGICAL SCIENCES↗

Radiation Damage Studies on Titanium Alloys as High Intensity Proton Accelerator Beam Window Materials

A high-strength dual a+ß phase titanium alloy Ti–6Al–4V is utilized as a material for beam windows in several accelerator target facilities. However, relatively little is known about how material properties of this alloy are affected by high-intensity proton beam irradiation. With plans to upgrade neutrino facilities at J-PARC and Fermilab to over 1 MW beam power, the radiation damage in the window material will reach a few displacements per atom (dpa) per year, significantly above the ~0.3 dpa level of existing data. The international RaDIATE collaboration, Radiation Damage In Accelerator Target Environments, has conducted a high intensity proton beam irradiation of various target and window material specimens at Brookhaven Linac Isotope Producer (BLIP) facility, including a variety of titanium alloys. Post-Irradiation Examination (PIE) of the specimens in the 1st capsule, irradiated at up to 0.25 dpa, is in progress. Tensile tests in a hot cell at Pacific Northwest National Laboratory (PNNL) exhibited a clear signature of radiation hardening and loss of ductility for Ti–6Al–4V, while Ti–3Al–2.5V, with less ß phase, exhibited less severe hardening. Microstructural investigations will follow to study the cause of the difference in tensile behavior between these alloys. High-cycle fatigue (HCF) performance is critical to the lifetime estimation of beam windows exposed to a periodic thermal stress from a pulsed proton beam. The first HCF data on irradiated titanium alloys are to be obtained by a conventional bend fatigue test at Fermilab and by an ultrasonic mesoscale fatigue test at Culham Laboratory. Specimens in the 2nd capsule, irradiated at up to ~1 dpa, cover typical titanium alloy grades, including possible radiation-resistant candidates. These systematic studies on the effects of radiation damage of titanium alloy materials are intended to enable us not only to predict realistic lifetimes of current beam windows made of Ti–6Al–4V, but also to extend the lifetime by choosing a more radiation and thermal shock tolerant alloy with a preferable heat treatment, or even by developing new materials.

Titanium Alloy, Beam Window, Proton Beam, Radiatio↗

Cosolvent enhanced lignocellulosic fractionation tailoring lignin chemistry and enhancing lignin bioconversion

Cosolvent Enhanced Lignocellulosic Fractionation (CELF) is an emerging solvolysis pretreatment to fractionate lignocellulosic biomass. Herein, the bioconversion performance of CELF lignin was fully evaluated for the first time. Results showed that CELF lignin possessed higher content of carboxylic acid OH, lower molecular weight, and disappeared β-O-4 and β-5 linkages compared to other two technical lignins including a conventional ethanol organosolv lignin (EOL) and a kraft lignin (KL). Rhodococcus opacus PD630 cell count from CELF lignin fermentation reached the highest value of 3.9 10 7 CFU/mL, representing a 62.5% and 77.3% improvement over EOL and KL, respectively. Correspondingly, lipid yield reached 143 mg/L from CELF lignin, which was 36.2% and 26.5% higher than from EOL and KL, respectively. Principal component analysis (PCA) revealed that more carboxylic acid groups and lower molecular weight contributed to the enhanced bioconversion performance of CELF lignin. This study demonstrates that CELF lignin is a promising candidate for bioconversion.

09 BIOMASS FUELS↗

Intercalation And High-Pressure Effects On Structural Phase Transitions In Layered As x P 1-x Alloys

This project was aimed at understanding the role of composition, intercalation, and high pressure on the structural evolution of black phosphorous (BP) and layered arsenic phosphorous alloys, As y P 1-y . Under normal conditions, BP is the most stable phase of phosphorous, known as the α-phase, characterized by an orthorhombic honeycomb puckered crystal structure with the Cmca space group. On the other hand, the most stable phase of arsenic is its β-phase, known as gray arsenic (g-As), which has a rhombohedral buckled layered crystal structure with the R3m space group. In a wide range of compositions (y < 0.83), the arsenic phosphorous alloys form the α-phase, known as black arsenic phosphorous (b-As y P 1-y ) with a similar structure to BP. The project was aimed at the synthesis of BP and b-As y P 1-y with different compositions and at studying the structural evolution of these materials during intercalation with alkali metal (especially Li), and under high-pressure conditions. The main goals were to gain a better understanding of these processes and structural changes taking place under these conditions. In particular, the project was aimed at addressing whether such conditions could induce a structural transition between the α- and β-phases. For this, a series of systematic in-situ studies were conducted, including electrochemical lithium intercalation in an in-situ electrochemical cell, and high-pressure experiments in a diamond anvil cell (DAC). Overall, both types of experiments have shown that above a certain composition-dependent threshold level of intercalation or high pressure, the system undergoes phase segregation rather than phase transition. Specifically, the segregation of the excess arsenic was observed, and a single-phase system of b-As y P 1-y transformed into a two-phase system consisting of b-As y P 1-y and g-As, through the following process: 1∗(b-As y P 1-y ) → 1∗(b As y-δ P 1-y ) + δ∗(g-As). Also, the study showed that intercalation and high-pressure are two competing rather than synergistic processes causing at least a partial cancelation of these two factors

36 MATERIALS SCIENCE↗