bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sizing up DNA nanostructure assembly with native mass spectrometry and ion mobility
Authors: van Dyck Jeroen F. , Burns Jonathan R. , Le Huray Kyle I. P. , Konijnenberg Albert , Howorka Stefan , Sobott Frank 
Published: June 2022

AbstractRecent interest in biological and synthetic DNA nanostructures has highlighted the need for methods to comprehensively characterize intermediates and end products of multimeric DNA assembly. Here we use native mass spectrometry in combination with ion mobility to determine the mass, charge state and collision cross section of noncovalent DNA assemblies, and thereby elucidate their structural composition, oligomeric state, overall size and shape. We showcase the approach with a prototypical six-subunit DNA nanostructure to reveal how its assembly is governed by the ionic strength of the buffer, as well as how the mass and mobility of heterogeneous species can be well resolved by careful tuning of instrumental parameters. We find that the assembly of the hexameric, barrel-shaped complex is guided by positive cooperativity, while previously undetected higher-order 12- and 18-mer assemblies are assigned to defined larger-diameter geometric structures. Guided by our insight, ion mobility-mass spectrometry is poised to make significant contributions to understanding the formation and structural diversity of natural and synthetic oligonucleotide assemblies relevant in science and technology.
Insights into the mechanism of action of the arbitrium communication system in SPbeta phages
Authors: Gallego del Sol Francisca , Quiles-Puchalt Nuria , Brady Aisling , Penadés José R. , Marina Alberto 
Published: June 2022

AbstractThe arbitrium system is employed by phages of the SPbeta family to communicate with their progeny during infection to decide either to follow the lytic or the lysogenic cycle. The system is controlled by a peptide, AimP, that binds to the regulator AimR, inhibiting its DNA-binding activity and expression of aimX. Although the structure of AimR has been elucidated for phages SPβ and phi3T, there is still controversy regarding the molecular mechanism of AimR function, with two different proposed models for SPβ. In this study, we deepen our understanding of the system by solving the structure of an additional AimR that shows chimerical characteristics with the SPβ receptor. The crystal structures of this AimR (apo, AimP-bound and DNA-bound) together with in vitro and in vivo analyses confirm a mechanism of action by AimP-induced conformational restriction, shedding light on peptide specificity and cross regulation with relevant biological implications.
Cell surface glycan engineering reveals that matriglycan alone can recapitulate dystroglycan binding and function
Authors: Sheikh M. Osman , Capicciotti Chantelle J. , Liu Lin , Praissman Jeremy , Ding Dahai , Mead Daniel G. , Brindley Melinda A. , Willer Tobias , Campbell Kevin P. , Moremen Kelley W. , Wells Lance , Boons Geert-Jan 
Published: June 2022

Abstractα-Dystroglycan (α-DG) is uniquely modified on O-mannose sites by a repeating disaccharide (-Xylα1,3-GlcAβ1,3-)n termed matriglycan, which is a receptor for laminin-G domain-containing proteins and employed by old-world arenaviruses for infection. Using chemoenzymatically synthesized matriglycans printed as a microarray, we demonstrate length-dependent binding to Laminin, Lassa virus GP1, and the clinically-important antibody IIH6. Utilizing an enzymatic engineering approach, an N-linked glycoprotein was converted into a IIH6-positive Laminin-binding glycoprotein. Engineering of the surface of cells deficient for either α-DG or O-mannosylation with matriglycans of sufficient length recovers infection with a Lassa-pseudovirus. Finally, free matriglycan in a dose and length dependent manner inhibits viral infection of wildtype cells. These results indicate that matriglycan alone is necessary and sufficient for IIH6 staining, Laminin and LASV GP1 binding, and Lassa-pseudovirus infection and support a model in which it is a tunable receptor for which increasing chain length enhances ligand-binding capacity.
Bipolar membrane electrolyzers enable high single-pass CO2 electroreduction to multicarbon products
Authors: Xie Ke , Miao Rui Kai , Ozden Adnan , Liu Shijie , Chen Zhu , Dinh Cao-Thang , Huang Jianan Erick , Xu Qiucheng , Gabardo Christine M. , Lee Geonhui , Edwards Jonathan P. , O’Brien Colin P. , Boettcher Shannon W. , Sinton David , Sargent Edward H. 
Published: June 2022

AbstractIn alkaline and neutral MEA CO2 electrolyzers, CO2 rapidly converts to (bi)carbonate, imposing a significant energy penalty arising from separating CO2 from the anode gas outlets. Here we report a CO2 electrolyzer uses a bipolar membrane (BPM) to convert (bi)carbonate back to CO2, preventing crossover; and that surpasses the single-pass utilization (SPU) limit (25% for multi-carbon products, C2+) suffered by previous neutral-media electrolyzers. We employ a stationary unbuffered catholyte layer between BPM and cathode to promote C2+ products while ensuring that (bi)carbonate is converted back, in situ, to CO2 near the cathode. We develop a model that enables the design of the catholyte layer, finding that limiting the diffusion path length of reverted CO2 to ~10 μm balances the CO2 diffusion flux with the regeneration rate. We report a single-pass CO2 utilization of 78%, which lowers the energy associated with downstream separation of CO2 by 10× compared with past systems.
Construction of a synthetic Saccharomyces cerevisiae pan-genome neo-chromosome
Authors: Kutyna Dariusz R. , Onetto Cristobal A. , Williams Thomas C. , Goold Hugh D. , Paulsen Ian T. , Pretorius Isak S. , Johnson Daniel L. , Borneman Anthony R. 
Published: June 2022

AbstractThe Synthetic Yeast Genome Project (Sc2.0) represents the first foray into eukaryotic genome engineering and a framework for designing and building the next generation of industrial microbes. However, the laboratory strain S288c used lacks many of the genes that provide phenotypic diversity to industrial and environmental isolates. To address this shortcoming, we have designed and constructed a neo-chromosome that contains many of these diverse pan-genomic elements and which is compatible with the Sc2.0 design and test framework. The presence of this neo-chromosome provides phenotypic plasticity to the Sc2.0 parent strain, including expanding the range of utilizable carbon sources. We also demonstrate that the induction of programmable structural variation (SCRaMbLE) provides genetic diversity on which further adaptive gains could be selected. The presence of this neo-chromosome within the Sc2.0 backbone may therefore provide the means to adapt synthetic strains to a wider variety of environments, a process which will be vital to transitioning Sc2.0 from the laboratory into industrial applications.
A microfluidic optimal experimental design platform for forward design of cell-free genetic networks
Authors: van Sluijs Bob , Maas Roel J. M. , van der Linden Ardjan J. , de Greef Tom F. A. , Huck Wilhelm T. S. 
Published: June 2022

AbstractCell-free protein synthesis has been widely used as a “breadboard” for design of synthetic genetic networks. However, due to a severe lack of modularity, forward engineering of genetic networks remains challenging. Here, we demonstrate how a combination of optimal experimental design and microfluidics allows us to devise dynamic cell-free gene expression experiments providing maximum information content for subsequent non-linear model identification. Importantly, we reveal that applying this methodology to a library of genetic circuits, that share common elements, further increases the information content of the data resulting in higher accuracy of model parameters. To show modularity of model parameters, we design a pulse decoder and bistable switch, and predict their behaviour both qualitatively and quantitatively. Finally, we update the parameter database and indicate that network topology affects parameter estimation accuracy. Utilizing our methodology provides us with more accurate model parameters, a necessity for forward engineering of complex genetic networks.
A glycine-rich PE_PGRS protein governs mycobacterial actin-based motility
Authors: Hill Norbert S. , Welch Matthew D. 
Published: June 2022

AbstractMany key insights into actin regulation have been derived through examining how microbial pathogens intercept the actin cytoskeleton during infection.Mycobacterium marinum, a close relative of the human pathogenMycobacterium tuberculosis, polymerizes host actin at the bacterial surface to drive intracellular movement and cell-to-cell spread during infection. However, the mycobacterial factor that commandeers actin polymerization has remained elusive. Here, we report the identification and characterization of theM. marinumactin-based motility factor designated mycobacterial intracellular rockets A (MirA), which is a member of the glycine-rich PE_PGRS protein family. MirA contains an amphipathic helix to anchor into the mycobacterial outer membrane and, surprisingly, also the surface of host lipid droplet organelles. MirA directly binds to and activates the host protein N-WASP to stimulate actin polymerization through the Arp2/3 complex, directing both bacterial and lipid droplet actin-based motility. MirA is dissimilar to known N-WASP activating ligands and may represent a new class of microbial and host actin regulator. Additionally, the MirA-N-WASP interaction represents a model to understand how the enigmatic PE_PGRS proteins contribute to mycobacterial pathogenesis.
Visible light-controlled living cationic polymerization of methoxystyrene
Authors: Wang Lei , Xu Yupo , Zuo Quan , Dai Haojie , Huang Lei , Zhang Meng , Zheng Yongli , Yu Chunyang , Zhang Shaodong , Zhou Yongfeng 
Published: June 2022

AbstractPhoto-controlled living polymerization has received great attention in recent years. However, despite the great success therein, the report on photo-controlled living cationic polymerization has been greatly limited. We demonstrate here a novel decolorable, metal-free and visible light-controlled living cationic polymerization system by using tris(2,4-dimethoxyphenyl)methylium tetrafluoroborate as the photocatalyst and phosphate as the chain transfer agent (CTA) for polymerization of 4-methoxystyrene. This polymerization reaction under green LED light irradiation shows clear living characteristics including predictable molar mass, low molar-mass dispersity (Đ = 1.25), and sequential polymerization capability. In addition, the photocatalytic system exits excellent “on-off” photo switchability and shows the longest “off period” of 36 h up to now for photo-controlled cationic polymerization. Furthermore, the residual photo-catalyst is easily deactivated and decolored with addition of a base after the polymerization. The present study has extended the photo-controlled living cationic polymerization systems with new organic photocatalysts, phosphate CTA and polymerizable monomer as well as the new properties of excellent photostability and in-situ decolored capacity.
A review on pathology, mechanism, and therapy for cerebellum and tremor in Parkinson’s disease
Authors: Zhong Yuke , Liu Hang , Liu Guohui , Zhao Lili , Dai Chengcheng , Liang Yi , Du Juncong , Zhou Xuan , Mo Lijuan , Tan Changhong , Tan Xinjie , Deng Fen , Liu Xi , Chen Lifen 
Published: June 2022

AbstractTremor is one of the core symptoms of Parkinson’s disease (PD), but its mechanism is poorly understood. The cerebellum is a growing focus in PD-related researches and is reported to play an important role in tremor in PD. The cerebellum may participate in the modulation of tremor amplitude via cerebello-thalamo-cortical circuits. The cerebellar excitatory projections to the ventral intermediate nucleus of the thalamus may be enhanced due to PD-related changes, including dopaminergic/non-dopaminergic system abnormality, white matter damage, and deep nuclei impairment, which may contribute to dysregulation and resistance to levodopa of tremor. This review summarized the pathological, structural, and functional changes of the cerebellum in PD and discussed the role of the cerebellum in PD-related tremor, aiming to provide an overview of the cerebellum-related mechanism of tremor in PD.
FoxO3 restricts liver regeneration by suppressing the proliferation of hepatocytes
Authors: Liang Chi-Qian , Zhou Deng-Cheng , Peng Wen-Tao , Chen Wu-Yun , Wu Hai-Yan , Zhou Yi-Min , Gu Wei-Li , Park Kyu-Sang , Zhao Hui , Pi Long-Quan , Zheng Li , Feng Shan-Shan , Cai Dong-Qing , Qi Xu-Feng 
Published: June 2022

AbstractUpon injury, the liver is capable of substantial regeneration from the original tissue until an appropriate functional size. The underlying mechanisms controlling the liver regeneration processes are not well elucidated. Previous studies have proposed that the transcription factor FoxO3 is involved in various liver diseases, but its exact role in the regulation of liver regeneration remains largely unclear. To directly test the detailed role of FoxO3 in liver regeneration, both a constitutive Albumin-Cre driver line and adeno-associated virus serotype 8 (AAV8)-Tbg-Cre (AAV-Cre)-injected adult FoxO3fl/fl mice were subjected to 70% partial hepatectomy (PH). Our data demonstrate that FoxO3 deletion accelerates liver regeneration primarily by limiting polyploidization and promoting the proliferation of hepatocytes during liver regeneration. RNA-seq analysis indicates that FoxO3 deficiency greatly alters the expression of gene sets associated with cell proliferation and apoptosis during liver regeneration. Chromatin immunoprecipitation-PCR (ChIP-PCR) and luciferase reporter assays reveal that FoxO3 promotes the expression of Nox4 but suppresses the expression of Nr4a1 in hepatocytes. AAV8 virus-mediated overexpression of Nox4 and knockdown of Nr4a1 significantly suppressed hepatocyte proliferation and liver regeneration in FoxO3-deficient mice. We demonstrate that FoxO3 negatively controls hepatocyte proliferation through Nox4 upregulation and Nr4a1 downregulation, thereby ensuring appropriate functional regeneration of the liver. Our findings provide novel mechanistic insight into the therapeutic mechanisms of FoxO3 in liver damage and repair.
Proteoglycan 4 (PRG4) treatment enhances wound closure and tissue regeneration
Authors: Krawetz Roman J. , Abubacker Saleem , Leonard Catherine , Masson Anand O. , Shah Sophia , Narendran Nadia , Tailor Pankaj , Regmi Suresh C. , Labit Elodie , Ninkovic Nicoletta , Corpuz Jessica May , Ito Kenichi , Underhill T. Michael , Salo Paul T. , Schmidt Tannin A. , Biernaskie Jeff A. 
Published: June 2022

AbstractThe wound healing response is one of most primitive and conserved physiological responses in the animal kingdom, as restoring tissue integrity/homeostasis can be the difference between life and death. Wound healing in mammals is mediated by immune cells and inflammatory signaling molecules that regulate tissue resident cells, including local progenitor cells, to mediate closure of the wound through formation of a scar. Proteoglycan 4 (PRG4), a protein found throughout the animal kingdom from fish to elephants, is best known as a glycoprotein that reduces friction between articulating surfaces (e.g. cartilage). Previously, PRG4 was also shown to regulate the inflammatory and fibrotic response. Based on this, we asked whether PRG4 plays a role in the wound healing response. Using an ear wound model, topical application of exogenous recombinant human (rh)PRG4 hastened wound closure and enhanced tissue regeneration. Our results also suggest that rhPRG4 may impact the fibrotic response, angiogenesis/blood flow to the injury site, macrophage inflammatory dynamics, recruitment of immune and increased proliferation of adult mesenchymal progenitor cells (MPCs) and promoting chondrogenic differentiation of MPCs to form the auricular cartilage scaffold of the injured ear. These results suggest that PRG4 has the potential to suppress scar formation while enhancing connective tissue regeneration post-injury by modulating aspects of each wound healing stage (blood clotting, inflammation, tissue generation and tissue remodeling). Therefore, we propose that rhPRG4 may represent a potential therapy to mitigate scar and improve wound healing.
Discrete typing units of Trypanosoma cruzi: Geographical and biological distribution in the Americas
Authors: Velásquez-Ortiz Natalia , Herrera Giovanny , Hernández Carolina , Muñoz Marina , Ramírez Juan David 
Published: June 2022

AbstractChagas disease caused by Trypanosoma cruzi is a public health issue in Latin America. This highly diverse parasite is divided into at least seven discrete typing units (DTUs) TcI-TcVI and Tcbat. Some DTUs have been associated with geographical distribution in epidemiological scenarios and clinical manifestations, but these aspects remain poorly understood. Many studies have focused on studying the parasite and its vectors/hosts, using a wide variety of genetic markers and methods. Here, we performed a systematic review of the literature for the last 20 years to present an update of DTUs distribution in the Americas, collecting ecoepidemiological information. We found that the DTUs are widespread across the continent and that there is a whole gamma of genetic markers used for the identification and genotyping of the parasite. The data obtained in this descriptor could improve the molecular epidemiology studies of Chagas disease in endemic regions.
Kolmogorov compression complexity may differentiate different schools of Orthodox iconography
Authors: Peptenatu Daniel , Andronache Ion , Ahammer Helmut , Taylor Richard , Liritzis Ioannis , Radulovic Marko , Ciobanu Bogdan , Burcea Marin , Perc Matjaz , Pham Tuan D. , Tomić Bojan M. , Cîrstea Cosmin Iulian , Lemeni Adrian Nicolae , Gruia Andreea Karina , Grecu Alexandra , Marin Marian , Jelinek Herbert Franz 
Published: June 2022

AbstractThe complexity in the styles of 1200 Byzantine icons painted between 13th and 16th from Greece, Russia and Romania was investigated through the Kolmogorov algorithmic information theory. The aim was to identify specific quantitative patterns which define the key characteristics of the three different painting schools. Our novel approach using the artificial surface images generated with Inverse FFT and the Midpoint Displacement (MD) algorithms, was validated by comparison of results with eight fractal and non-fractal indices. From the analyzes performed, normalized Kolmogorov compression complexity (KC) proved to be the best solution because it had the best complexity pattern differentiations, is not sensitive to the image size and the least affected by noise. We conclude that normalized KC methodology does offer capability to differentiate the icons within a School and amongst the three Schools.
African mitochondrial haplogroup L7: a 100,000-year-old maternal human lineage discovered through reassessment and new sequencing
Authors: Maier Paul A. , Runfeldt Göran , Estes Roberta J. , Vilar Miguel G. 
Published: June 2022

AbstractArchaeological and genomic evidence suggest that modernHomo sapienshave roamed the planet for some 300–500 thousand years. In contrast, global human mitochondrial (mtDNA) diversity coalesces to one African female ancestor (“Mitochondrial Eve”) some 145 thousand years ago, owing to the ¼ gene pool size of our matrilineally inherited haploid genome. Therefore, most of human prehistory was spent in Africa where early ancestors of Southern African Khoisan and Central African rainforest hunter-gatherers (RFHGs) segregated into smaller groups. Their subdivisions followed climatic oscillations, new modes of subsistence, local adaptations, and cultural-linguistic differences, all prior to their exodus out of Africa. Seven African mtDNA haplogroups (L0–L6) traditionally captured this ancient structure—these L haplogroups have formed the backbone of the mtDNA tree for nearly two decades. Here we describe L7, an eighth haplogroup that we estimate to be ~ 100 thousand years old and which has been previously misclassified in the literature. In addition, L7 has a phylogenetic sublineage L7a*, the oldest singleton branch in the human mtDNA tree (~ 80 thousand years). We found that L7 and its sister group L5 are both low-frequency relics centered around East Africa, but in different populations (L7: Sandawe; L5: Mbuti). Although three small subclades of African foragers hint at the population origins of L5'7, the majority of subclades are divided into Afro-Asiatic and eastern Bantu groups, indicative of more recent admixture. A regular re-estimation of the entire mtDNA haplotype tree is needed to ensure correct cladistic placement of new samples in the future.
Fabrication of stainless-steel microfibers with amorphous-nanosized microstructure with enhanced mechanical properties
Authors: Sharifikolouei Elham , Sarac Baran , Zheng Yonghui , Bala Piotr , Eckert Jürgen 
Published: June 2022

AbstractMetallic glasses (MG) have attracted much attention due to their superior hardness and good corrosion resistance. However, designing new MG compositions is still a big challenge, and their integration into different systems is limited when they are in the shape of bulk materials. Here, we present a new method for the fabrication of MG in the form of microfibers which could greatly help them to be integrated within different systems. The newly proposed technique has the ability to form MG structure from commercially available alloy compositions thanks to its significantly improved quenching rate(~ 108 K.s−1). In this technique, individual melt droplets are ejected on a rotating wheel forming a thin film which are ruptured upon solidification leading to the formation of MG microfibers. In this regard, we have fabricated microfibers from a commercial DIN 1.4401 stainless-steel which could form a completely amorphous structure confirmed by DSC, XRD, and HRTEM. The fabricated MG microfibers show an increased hardness for more than two-fold from 3.5 ± 0.17 GPa for the as-received stainless-steel to 7.77 ± 0.60 GPa for the amorphous microfibers. Subsequent heat-treatment of the microfibers resulted in a nanocrystalline structure with the presence of amorphous regions when the hardness increases even further to 13.5 ± 2.0 GPa. We propose that confinement of both shear transformation zones and dislocations in the heat-treated MG microfibers plays a major role in enhancing strength.
A pupillometric study of developmental and individual differences in cognitive effort in visual word recognition
Authors: Shechter Adi , Hershman Ronen , Share David L. 
Published: June 2022

AbstractThroughout the history of modern psychology, the neural basis of cognitive performance, and particularly its efficiency, has been assumed to be an essential determinant of developmental and individual differences in a wide range of human behaviors. Here, we examine one aspect of cognitive efficiency—cognitive effort, using pupillometry to examine differences in word reading among adults (N = 34) and children (N = 34). The developmental analyses confirmed that children invested more effort in reading than adults, as indicated by larger and sustained pupillary responses. The within-age (individual difference) analyses comparing faster (N = 10) and slower (N = 10) performers revealed that in both age groups, the faster readers demonstrated accelerated pupillary responses compared to slower readers, although both groups invested a similar overall degree of cognitive effort. These findings have the potential to open up new avenues of research in the study of skill growth in word recognition and many other domains of skill learning.