bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and biochemical characterization of bifunctional XynA
Authors: Xie Wei , Yu Qi , Liu Yun , Cao Ruoting , Zhang Ruiqing , Wang Sidi , Zhan Ruoting , Liu Zhongqiu , Wang Kui , Wang Caiyan 
Published: October 2020

AbstractXylan and cellulose are the two major constituents in numerous types of lignocellulosic biomass, representing a promising resource for biofuels and other biobased industries. The efficient degradation of lignocellulose requires the synergistic actions of cellulase and xylanase. Thus, bifunctional enzyme incorporated xylanase/cellulase activity has attracted considerable attention since it has great cost savings potential. Recently, a novel GH10 family enzyme XynA identified fromBacillussp. is found to degrade both cellulose and xylan. To understand its molecular catalytic mechanism, here we first solve the crystal structure of XynA at 2.3 Å. XynA is characterized with a classic (α/β)8 TIM-barrel fold (GH10 domain) flanked by the flexible N-terminal domain and C-terminal domain. Circular dichroism, protein thermal shift and enzyme activity assays reveal that conserved residues Glu182 and Glu280 are both important for catalytic activities of XynA, which is verified by the crystal structure of XynA with E182A/E280A double mutant. Molecular docking studies of XynA with xylohexaose and cellohexaose as well as site-directed mutagenesis and enzyme activity assay demonstrat that Gln250 and His252 are indispensible to cellulase and bifunctional activity, separately. These results elucidate the structural and biochemical features of XynA, providing clues for further modification of XynA for industrial application.
Higher Variability in Fungi Compared to Bacteria in the Foraging Honey Bee Gut
Authors: Decker Leslie E. , San Juan Priscilla A. , Warren Magdalena L. , Duckworth Cory E. , Gao Cheng , Fukami Tadashi 
Published: October 2020

AbstractMicrobial communities in the honey bee gut have emerged as a model system to understand the effects of host-associated microbes on animals and plants. The specific distribution patterns of bacterial associates among honey bee gut regions remains a key finding within the field. The mid- and hindgut of foraging bees house a deterministic set of core species that affect host health. In contrast, the crop, or honey stomach, contains a more diverse set of bacteria that is highly variable in composition among individual bees. Whether this contrast between the two gut regions also applies to fungi, another major group of gut-associated microbes, remains unclear despite their potential influence on host health. In honey bees caught foraging at four sites across the San Francisco Peninsula, we found that fungi were much less distinct in species composition between the crop and the mid- and hindgut than bacteria. Unlike bacteria, fungi were highly variable in composition throughout the gut, and much of this variation was attributable to bee collection site. These patterns suggest that the fungi may be passengers rather than functionally significant gut symbionts. However, many of the fungi we found in the bees have been recognized as plant pathogens. Assuming that some fungi remain viable after passage through the gut, the distribution patterns we report here point to the potential importance of honey bees as vectors of fungal pathogens and suggest a more prominent role of honey bees in plant pathogen transmission than generally thought.Importance (Nontechnical explanation of why the work was undertaken)Along with bacteria, fungi make up a significant portion of animal- and plant-associated microbial communities. However, we have only begun to describe these fungi, much less examine their effects on most animals and plants. The honey bee,Apis mellifera, has emerged as a model system for studying host-associated microbes. Honey bees contain well-characterized bacteria specialized to inhabit different regions of the gut. Fungi also exist in the honey bee gut, but their composition and function remain largely undescribed. Here we show that, unlike bacteria, fungi vary substantially in species composition throughout the honey bee gut, contingent on where the bees are sampled. This observation suggests that fungi may be transient passengers and therefore unimportant as gut symbionts. However, our findings also indicate that honey bees could be major vectors of infectious plant diseases as many of the fungi we found in the honey bee gut are recognized as plant pathogens.
Stability of the Retinoid X Receptor-alpha Homodimer in the Presence and Absence of Rexinoid and Coactivator Peptide
Authors: Yang Zhengrong , Muccio Donald D. , Melo Nathalia , Atigadda Venkatram R. , Renfrow Matthew B. 
Published: October 2020

ABSTRACTDifferential scanning calorimetry and differential scanning fluorimetry were used to measure the thermal stability of human retinoid X receptor-alpha ligand binding domain (RXRα LBD) homodimer in the absence or presence of rexinoid and coactivator peptide, GRIP-1. Theapo-RXRα LBD homodimer displayed a single thermal unfolding transition with aTmof 58.7 °C and an unfolding enthalpy (ΔH) of 673 kJ/mol (12.5 J/g), much lower than average value (35 J/g) of small globular proteins. Using a heat capacity change (ΔCp) of 15 kJ/(mol·K) determined by measurements at different pH values, the free energy of unfolding (ΔG) of the native state was 33 kJ/mol at 37 °C. Rexinoid binding to theapo-homodimer increasedTmby 5 to 9 °C, and increased the ΔGof the native homodimer by 12 to 20 kJ/mol at 37 °C, consistent with the nanomolar dissociation constant (Kd) of the rexinoids. The increase in ΔGwas the result of a more favorable entropic change due to interactions between the rexinoid and hydrophobic residues in the binding pocket, with the larger increases caused by rexinoids containing larger hydrophobic end groups. GRIP-1 binding toholo-homodimers containing rexinoid resulted in additional increases in ΔGof 14 kJ/mol, a value same for all three rexinoids. Binding of rexinoid and GRIP-1 resulted in a combined 50% increase in unfolding enthalpy, consistent with reduced structural fluidity and more compact folding observed in other published structural studies. Thermodynamic analysis thus provided a quantitative evaluation of the interactions between RXR and its agonist and coactivator.
×Pseudorhiza nieschalkii(Senghas) P.F.Hunt nothosubsp.siculorumH.Kertész & N.Anghelescu, 2020 AN INTERGENERIC ORCHID HYBRID NEW TO SCIENCE FOUND IN TERRA SICULORUM, ROMANIA
Authors: Anghelescu Nora Eugenia D. G. , Kertész Hajnalka , Constantin Nicoleta , Simon-Gruiţa Alexandra , Duţă Cornescu Georgiana , Pojoga Maria D. , Georgescu Mihaela I. , Petra Sorina A. , Toma Florin 
Published: October 2020

AbstractWe describe the first reported intergeneric hybrid to naturally occur between two subspecies belonging to different genera,Dactylorhiza fuchsiisubsp.sooana(genusDactylorhiza) andPseudorchis albidasubsp.tricuspis(genusPseudorchis), as× Pseudorhiza nieschalkii(Senghas) P.F.Hunt nothosubsp.siculorumH.Kertész & N.Anghelescu, 2020. The hybrid was found and digitally photographed for the first time by Hajnalka Kertész in June, 2020, within Terra Siculorum, in one of the Natura 2000 protected areas, known as Harghita Mădăraş, ROSCI00090. Following detailed morphometric analysis using 67 characters and molecular karyological analyses, we identified this unique specimen as an intergeneric hybrid, new to science. The hybrid, an F1generation plant, most likely representing a single intergeneric pollination event, is phenotypically intermediate between its parental species in most of the characters scored, but it significantly closely resemblesPseudorchis albidasubsp.tricuspisparent. Since the parental species occurred in near proximity (1-10 meters distance), we suggest that the production of this hybrid required a minimum travel distance of ca 1-10 meters, by the pollinators and frequent exchange of pollen between the parental species was very likely. The parental species and the hybrid, which display a considerable synchronicity in their flowering time, overlap in pollinator community, sharing various species of Hymenopterans and Dipterans, very abundant in the heathland. This Terra Siculorum hybrid is thus best described as a rarely occurring intergeneric hybrid that shows strongPseudorchis albidasubsp.tricuspisparental dominance in inheritance patterns.
Human motor units in microfluidic devices are impaired by FUS mutations and improved by HDAC6 inhibition
Authors: Dittlau Katarina Stoklund , Krasnow Emily N. , Fumagalli Laura , Vandoorne Tijs , Baatsen Pieter , Kerstens Axelle , Giacomazzi Giorgia , Pavie Benjamin , Sampaolesi Maurilio , Van Damme Philip , Van Den Bosch Ludo 
Published: October 2020

AbstractNeuromuscular junctions (NMJs) ensure proper communication between motor neurons and muscle through the release of neurotransmitters. In motor neuron disorders, such as amyotrophic lateral sclerosis (ALS), NMJs degenerate resulting in muscle atrophy, paralysis and respiratory failure. The aim of this study was to establish a versatile and reproduciblein vitromodel of a human motor unit to study the effect of ALS-causing mutations. Therefore, we generated a co-culture of human induced pluripotent stem cell-derived motor neurons and human primary mesoangioblast-derived myotubes in microfluidic devices. A chemotactic and volumetric gradient facilitated the growth of motor neuron neurites through microgrooves resulting in the interaction with myotubes and the formation of NMJs. We observed that ALS-causingFUSmutations resulted in a reduced neurite outgrowth and in a decreased NMJ number. Interestingly, the selective HDAC6 inhibitor, Tubastatin A, improved the neurite outgrowth and the NMJ morphology ofFUS-ALS co-cultures, further prompting HDAC6 inhibition as a potential therapeutic strategy for ALS.
Structural basis for the inhibition of the SARS-CoV-2 RNA-dependent RNA polymerase by favipiravir-RTP
Authors: Naydenova Katerina , Muir Kyle W. , Wu Long-Fei , Zhang Ziguo , Coscia Francesca , Peet Mathew J. , Castro-Hartmann Pablo , Qian Pu , Sader Kasim , Dent Kyle , Kimanius Dari , Sutherland John D. , Löwe Jan , Barford David , Russo Christopher J. 
Published: October 2020

AbstractThe RNA polymerase inhibitor, favipiravir, is currently in clinical trials as a treatment for infection with SARS-CoV-2, despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, non-productive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.
Limb-clasping, cognitive deficit and increased vulnerability to kainic acid - induced seizures in neuronal GPI anchor deficiency mouse models
Authors: Kandasamy Lenin C. , Tsukamoto Mina , Banov Vitaliy , Tsetsegee Sambuu , Nagasawa Yutaro , Kato Mitsuhiro , Matsumoto Naomichi , Takeda Junji , Itohara Shigeyoshi , Ogawa Sonoko , Young Larry J. , Zhang Qi 
Published: October 2020

AbstractPost-translational modification of a protein with glycosylphosphatidylinositol (GPI) is a conserved mechanism exists in all eukaryotes. Thus far, more than 150 human GPI anchored proteins have been discovered and about 30 enzymes have been reported to be involved in the biosynthesis and maturation of mammalian GPI. Phosphatidylinositol glycan biosynthesis class A protein (PIGA) catalyzes the very first step of GPI anchor biosynthesis. Patients carrying a mutation of thePIGAgene usually suffer from intractable epilepsy and intellectual developmental disorder. We generated three mouse models with PIGA deficits specifically in telencephalon excitatory neurons (Ex-M-cko), inhibitory neurons (In-M-cko), or thalamic neurons (Th-H-cko), respectively. Both Ex-M-cko and In-M-cko mice showed impaired long-term fear memory and were more susceptible to kainic acid (KA)-induced seizures. In addition, In-M-cko demonstrated a severe limb-clasping phenotype. Hippocampal synapse changes were observed in Ex-M-cko mice. OurPigaconditional knockout mouse models provide powerful tools to understand the cell-type specific mechanisms underlying inherited GPI deficiency and to test different therapeutic modalities.
Insect wing extract: A novel source for green synthesis of nanoparticles of antioxidant and antimicrobial potential
Authors: Jakinala Parameshwar , Lingampally Nageshwar , Hameeda Bee , Sayyed R. Z. , Khan M Yahya , Elsayed Elsayed Ahmed , El Enshasy Hesham 
Published: October 2020

AbstractSilver nanoparticles (AgNPs) are among the most widely synthesized and used nanoparticles (NPs). AgNPs have been traditionally synthesized from plant extracts, cobwebs, microorganisms, etc. However, their synthesis from wing extracts of common insect;Mang maowhich is abundantly available in most of the Asian countries has not been explored yet. We report the synthesis of AgNPs fromM. maowings extract and its antioxidant and antimicrobial activity. The synthesized AgNPs were spherical, 40–60 nm in size and revealed strong absorption plasmon band around at 430 nm. Highly crystalline nature of these particles as determined by Energy-dispersive X-ray analysis and X-ray diffraction further confirmed the presence of AgNPs. Hydrodynamic size and zeta potential of AgNPs were observed to be 43.9 nm and −7.12 mV, respectively. Fourier-transform infrared spectroscopy analysis revealed the presence of characteristic amide proteins and aromatic functional groups. Thin-layer chromatography (TLC) and Gas chromatography-mass spectroscopy (GC-MS) analysis revealed the presence of fatty acids in the wings extract that may be responsible for biosynthesis and stabilization of AgNPs. Further, SDS-PAGE of the insect wing extract protein showed the molecular weight of 49 kDa.M. maosilver nanoparticles (MMAgNPs) exhibit strong antioxidant, broad-range antibacterial and antifungal activities, which signifies their biomedical and agricultural potential.
Asymmetry in Histone Rotation in Forced Unwrapping and Force Quench Rewrapping in a Nucleosome
Authors: Reddy Govardhan , Thirumalai D. 
Published: October 2020

AbstractNucleosomes, the building blocks of chromosomes, are also transcription regulators. Single molecule pulling experiments have shown that nucleosomes unwrap in two major stages, releasing nearly equal length of DNA in each stage. The first stage, attributed to the rupture of the outer turn is reversible, occurs at low forces (≈ (3 - 5) pNs) whereas in the second stage the inner turn ruptures irreversibly at high forces (between ≈ (9 - 15) or higher) pNs. We show that Brownian dynamics simulations using the Self-Organized Polymer model of the nucleosome capture the experimental findings, thus permitting us to discern the molecular details of the structural changes not only in DNA but also in the Histone Protein Core (HPC). Upon unwrapping of the outer turn, which is independent of the pulling direction, there is a transition from 1.6 turns to 1.0 turn DNA wound around the HPC. In contrast, the rupture of the inner turn, leading to less than 0.5 turn DNA around the HPC, depends on the pulling direction, and is controlled by energetic and kinetic barriers. The latter arises because the mechanical force has to produce sufficient torque to rotate (in an almost directed manner) the HPC by 180°. In contrast, during the rewrapping process, HPC rotation is stochastic, with the quenched force fQ playing no role. Interestingly, if fQ = 0 the HPC rotation is not required for rewrapping because the DNA ends are unconstrained. The assembly of the outer wrap upon force quench, as assessed by the decrease in the end-to-end distance (Ree) of the DNA, nearly coincides with the increase in Ree as force is increased, confirming the reversible nature of the 1.6 turns to 1.0 turn transition. The asymmetry in HPC rotation during unwrapping and rewrapping accounts for the observed hysteresis in the stretch-release cycles in single molecule pulling experiments. Experiments that could validate the prediction that HPC rotation, which gives rise to the kinetic barrier in the unwrapping process, are proposed.
The polymicrogyria-associatedGPR56promoter preferentially drives gene expression in developing GABAergic neurons in common marmosets
Authors: Murayama Ayako Y , Kuwako Ken-ichiro , Okahara Junko , Bae Byoung-Il , Okuno Misako , Mashiko Hiromi , Shimogori Tomomi , Walsh Christopher A , Sasaki Erika , Okano Hideyuki 
Published: October 2020

ABSTRACTGPR56, a member of the adhesion G protein-coupled receptor family, is abundantly expressed in cells of the developing cerebral cortex, including neural progenitor cells and developing neurons. The humanGPR56gene has multiple presumptive promoters that drive the expression of the GPR56 protein in distinct patterns. Similar to coding mutations of the humanGPR56gene that may cause GPR56 dysfunction, a 15-bp homozygous deletion in the cis-regulatory element upstream of the noncoding exon 1 ofGPR56(e1m) leads to the cerebral cortex malformation and epilepsy. To clarify the expression profile of thee1mpromoter-driven GPR56 in primate brain, we generated a transgenic marmoset line in which EGFP is expressed under the control of the human minimale1mpromoter. In contrast to the endogenous GPR56 protein, which is highly enriched in the ventricular zone of the cerebral cortex, EGFP is mostly expressed in developing neurons in the transgenic fetal brain. Furthermore, EGFP is predominantly expressed in GABAergic neurons, whereas the total GPR56 protein is evenly expressed in both GABAergic and glutamatergic neurons, suggesting the GABAergic neuron-preferential activity of the minimale1mpromoter. These results indicate a possible pathogenic role for GABAergic neuron in the cerebral cortex of patients withGPR56mutations.
Muc2 mucin limitsListeria monocytogenesdissemination and modulates its population dynamics
Authors: Zhang Ting , Sasabe Jumpei , Sit Brandon , Waldor Matthew K. 
Published: October 2020

AbstractThe mucin Muc2 is a major constituent of the mucus layer that covers the intestinal epithelium and creates a barrier between epithelial cells and luminal commensal or pathogenic microorganisms. The Gram-positive food-borne pathogenListeria monocytogenescan cause enteritis and also disseminate from the intestine to give rise to systemic disease.L. monocytogenescan bind to intestinal Muc2, but the influence of the Muc2 mucin barrier onL. monocytogenesintestinal colonization and systemic dissemination has not been explored. Here, we used an orogastricL. monocytogenesinfection model to investigate the role of Muc2 in host defense againstL. monocytogenes. Compared to wild-type mice, we found that Muc2-/-mice exhibited heightened susceptibility to orogastric challenge withL. monocytogenes, with higher mortality, elevated colonic pathology, and increased pathogen burdens in both the intestinal tract and distal organs. In contrast,L. monocytogenesburdens were equivalent in wild-type and Muc2-/-animals when the pathogen was administered intraperitoneally, suggesting that systemic immune defects do not explain the heightened pathogen dissemination observed with oral infection route. Using a barcodedL. monocytogeneslibrary to measure intra-host pathogen population dynamics, we found that Muc2-/-animals had larger pathogen founding population sizes in the intestine and distal sites than observed in wild-type animals. Comparisons of barcode frequencies revealed that, in the absence of Muc2, the colon becomes the major source for seeding the internal organs. Together, our findings reveal that Muc2 limitsL. monocytogenesdissemination from the intestinal tract and modulates its population dynamics during infection.
Executive function supports single-shot endowment of value to arbitrary transient goals
Authors: McDougle Samuel D. , Ballard Ian C. , Baribault Beth , Bishop Sonia J. , Collins Anne G.E. 
Published: October 2020

ABSTRACTPeople often learn from the outcomes of their actions, even when these outcomes do not involve material rewards or punishments. How does our brain provide this flexibility? We combined behavior, computational modeling, and functional neuroimaging to probe whether learning from transient goals harnesses the same circuitry that supports learning from secondary reinforcers. Behavior and neuroimaging revealed that “one-shot” transient goals (abstract fractal images seen once) can act as a substitute for rewards during instrumental learning, and produce reliable reward-like signals in dopaminergic reward circuits. Moreover, we found evidence that prefrontal correlates of executive control may play a role in shaping these responses in reward circuits. These results suggest that learning from abstract goal outcomes is supported by an interplay between high-level representations in prefrontal cortex and low-level responses in subcortical reward circuits. This interaction may allow humans to perform reinforcement learning over flexible, arbitrarily abstract reward functions.
Antisense oligonucleotides targeting alpha-synuclein reduce pre-formed fibril-induced Lewy pathology and improve some domains of cognitive and motor performance
Authors: Boutros Sydney Weber , Raber Jacob , Unni Vivek K. 
Published: October 2020

AbstractAlpha-synuclein (αsyn) is a small protein involved in neurodegenerative diseases known as synucleinopathies. The phosphorylated form (psyn) is the primary component of protein aggregates known as Lewy bodies (LBs), which are the hallmark of diseases such as Parkinson’s disease (PD) and Dementia with Lewy bodies (DLB). Synucleinopathies might spread in a prion-like fashion, leading to a progressive emergence of symptoms over time. αsyn pre-formed fibrils (PFFs) induce LB-like pathology in wild-type (WT) mice, but there are remaining questions about the progressive “spreading” of pathology and the cognitive and behavioral effects. Here, we induced LB-like pathology in the bilateral motor cortex of WT mice and assessed behavioral and cognitive performance. As there are no long-term effective treatments for synucleinopathies, and no therapies slow or reduce the spreading of LBs, we also assessed the effects of a mouse αsyn-targeted antisense oligonucleotides (ASOs) on pathology and behavioral and cognitive performance starting 5 weeks after ASO treatment. At 3 months post-PFF injection (mpi), mice injected with PFFs showed cognitive impairments and mild motor impairments. At 6 mpi, PFF-injected mice showed further cognitive and motor impairments that were partially ameliorated by the ASO. ASO treatment also reduced LB-like pathology, and pathology was significantly correlated with cognitive measures. However, the particular mouse ASO used in these assays was also associated with some possible off-target effects, defined as effects not involving lowering of αsyn, such as a decline in body weight. These results add to what is known about the progressive nature of the PFF model of synucleinopathies. These data also support the therapeutic potential of ASOs to improve Lewy pathology and associated behavioral and cognitive phenotypes.