bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into deuterostome evolution from the biphasic transcriptional programme of hemichordates
Authors: Perez-Posada Alberto , Lin Che-Yi , Fan Tzu-Pei , Lin Ching-Yi , Chen Yi-Chih , Gómez Skarmeta José Luis , Yu Jr-Kai , Su Yi-Hsien , Tena Juan J. 
Published: June 2022

AbstractEvolutionary history of deuterostomes remains unsolved and is intimately related to the origin of chordates. Among deuterostomes, hemichordates and echinoderms (collectively called Ambulacraria) are sister groups of chordates. Comparative studies involving these three groups provide valuable insights into deuterostome evolution. Indirect developing hemichordates produce planktonic larvae that bear resemblance to echinoderm larvae before undergoing metamorphosis into an adult body plan with anteroposterior polarity homologous to that of chordates. Therefore, understanding the developmental processes of indirect-developing hemichordates can help understand the evolution of deuterostomes and the origins of chordates. In this study, we analysed the transcriptomes and chromatin accessibility of multiple developmental stages of the indirect-developing hemichordatePtychodera flavaand discovered that it exhibits a biphasic developmental program controlled by distinct sets of transcription factors and their corresponding regulatory elements. Comparative analyses of transcriptomes and network analyses revealed that the gastrula transcriptome is relatively ancient, and the TFs orchestrating its gene expression are highly interconnected in networks of cis-regulatory interactions. Comparing the developmental transcriptomes of hemichordates, echinoderms, and amphioxus, revealed high conservation of gene expression during gastrulation that extends to the neurula stages of amphioxus, along with remarkable similarity in larval transcriptomes across the three species. Additionally, we show thatP. flavapossesses conserved interactions of transcription factors necessary for the development of echinoderm endomesoderm and chordate axial mesoderm, including conserved cis-regulatory elements of the FoxA transcription factor that is central to the two networks. These findings suggest the existence of a deuterostome phylotypic stage during gastrulation governed by gene regulatory networks with conserved cis-regulatory interactions. Conversely, integration of gene expression data with synteny data revealed that gene expression recapitulates the independent evolutionary history of the Ancestral Linkage Groups that underwent rearrangements in each deuterostome lineage, suggesting a potential role of genome rearrangement during the evolution of larval strategies in hemichordates and deuterostome body plans.
Hybrid immunity shifts the Fc-effector quality of SARS-CoV-2 mRNA vaccine-induced immunity
Authors: Bowman Kathryn A. , Stein Daniel , Shin Sally , Ferbas Kathie G. , Tobin Nicole H , Mann Colin , Fischinger Stephanie , Ollmann Saphire Erica , Lauffenburger Douglas , Rimoin Anne W. , Aldrovandi Grace , Alter Galit 
Published: June 2022

ABSTRACTDespite the robust immunogenicity of SARS-CoV-2 mRNA vaccines, emerging data reveal enhanced neutralizing antibody and T cell cross-reactivity among individuals that previously experienced COVID-19, pointing to a hybrid immune advantage with infection-associated immune priming. Beyond neutralizing antibodies and T cell immunity, mounting data point to a potential role for additional antibody effector functions, including opsinophagocytic activity, in the resolution of symptomatic COVID-19. Whether hybrid immunity modifies the Fc-effector profile of the mRNA vaccine-induced immune response remains incompletely understood. Thus, here we profiled the SARS-CoV-2 specific humoral immune response in a group of individuals with and without prior COVID-19. As expected, hybrid Spike-specific antibody titers were enhanced following the primary dose of the mRNA vaccine, but were similar to those achieved by naïve vaccinees after the second mRNA vaccine dose. Conversely, Spike-specific vaccine-induced Fc-receptor binding antibody levels were higher after the primary immunization in individuals with prior COVID-19, and remained higher following the second dose compared to naïve individuals, suggestive of a selective improvement in the quality, rather than the quantity, of the hybrid humoral immune response. Thus, while the magnitude of antibody titers alone may suggest that any two antigen exposures – either hybrid immunity or two doses of vaccine alone - represent a comparable prime/boost immunologic education, we find that hybrid immunity offers a qualitatively improved antibody response able to better leverage Fc effector functions against conserved regions of the virus.
Hydrodynamics shapes self-recruitment in anemonefishes
Authors: Sato Masaaki , Honda Kentaro , Nakamura Yohei , Bernardo Lawrence Patrick C. , Bolisay Klenthon O. , Yamamoto Takahiro , Herrera Eugene C. , Nakajima Yuichi , Lian Chunlan , Uy Wilfredo H. , Fortes Miguel D. , Nadaoka Kazuo , Nakaoka Masahiro 
Published: June 2022

AbstractMany marine species have a pelagic larval phase that undergo dispersal among habitats. Studies on marine larval dispersal have revealed a large variation in the spatial scale of dispersal, and accumulated evidence has shown that seascape patchiness is the major determinant for variation in self-recruitment. However, few studies have investigated the influence of geographic settings on marine larval dispersal. Bays or lagoons generally enhance the retention of larvae, while larvae are more likely to be flushed by strong currents in open coasts. To examine associations between larval dispersal, geographic setting, and hydrodynamics, we compared fin-scale dispersal patterns, self-recruitment, and local retention of two anemonefishes (Amphiprion frenatus and A. perideraion) between a semi-enclosed bay and an open coast in the Philippines combining genetic parentage analysis and biophysical dispersal modelling. Contrary to our expectations, parentage analysis revealed lower estimates of self-recruitment in the semi-closed bay (0–2%) than in the open coast (14–15%). The result was consistent with dispersal simulations predicting lower local retention and self-recruitment in the former (0.4% and 19%) than in the latter (2.9% and 38%). Dispersal modelling also showed that cross-shore currents toward offshore were much stronger around the semi-closed bay and were negatively correlated with local retention and self-recruitment. These results suggest that stronger cross-shore currents around the semi-closed bay transport anemonefish larvae to the offshore and mainly contributed to the lower self-recruitment. Our results highlight difficulty in predicting self-recruitment from geographic setting alone and importance of hydrodynamics on it.
Biofunctional nanodot arrays in living cells uncover synergistic co-condensation of Wnt signalodroplets
Authors: Philippi Michael , Richter Christian P. , Kappen Marie , Watrinet Isabelle , Miao Yi , Runge Mercedes , Jorde Lara , Korneev Sergej , Holtmannspötter Michael , Kurre Rainer , Holthuis Joost C. M. , Garcia K. Christopher , Plückthun Andreas , Steinhart Martin , Piehler Jacob , You Changjiang 
Published: June 2022

AbstractQualitative and quantitative analysis of transient signaling platforms in the plasma membrane has remained a key experimental challenge. Here, we have developed biofunctional nanodot arrays (bNDAs) to spatially control dimerization and clustering of cell surface receptors at nanoscale. High-contrast bNDAs with spot diameters of ∼300 nm were obtained by capillary nanostamping of BSA bioconjugates, which were subsequently biofunctionalized by reaction with tandem anti- GFP clamp fusions. We achieved spatially controlled assembly of active Wnt signalosomes at the nanoscale in the plasma membrane of live cells by capturing the co-receptor Lrp6 into bNDAs via an extracellular GFP tag. Strikingly, we observed co-recruitment of co-receptor Frizzled-8 as well as the cytosolic scaffold proteins Axin-1 and Disheveled-2 into Lrp6 nanodots in the absence of ligand. Density variation and the high dynamics of effector proteins uncover highly cooperative liquid-liquid phase separation (LLPS)-driven assembly of Wnt “signalodroplets” at the plasma membrane, pinpointing the synergistic effects of LLPS for Wnt signaling amplification. These insights highlight the potential of bNDAs for systematically interrogating nanoscale signaling platforms and condensation at the plasma membrane of live cells.
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice (Oryza sativa)
Authors: Zhou Yong , Yu Zhichao , Chebotarov Dmytro , Chougule Kapeel , Lu Zhenyuan , Rivera Luis F. , Kathiresan Nagarajan , Al-Bader Noor , Mohammed Nahed , Alsantely Aseel , Mussurova Saule , Santos João , Thimma Manjula , Troukhan Maxim , Fornasiero Alice , Green Carl D. , Copetti Dario , Kudrna Dave , Llaca Victor , Lorieux Mathias , Zuccolo Andrea , Ware Doreen , McNally Kenneth , Zhang Jianwei , Wing Rod A. 
Published: June 2022

AbstractUnderstanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Utilizing 16 high-quality genomes that represent the subpopulation structure of Asian rice (O. sativa), plus the genomes of two close relatives (O. rufipogonandO. punctata), we built a pan-genome inversion index of 1,054 non-redundant inversions that span an average of ∼ 14% of theO. sativacv. Nipponbare reference genome sequence. Using this index we estimated an inversion rate of 1,100 inversions per million years in Asian rice, which is 37 to 73 times higher than previously estimated for plants. Detailed analyses of these inversions showed evidence of their effects on gene regulation, recombination rate, linkage disequilibrium and agronomic trait performance. Our study uncovers the prevalence and scale of large inversions (≥ 100 kb) across the pan-genome of Asian rice, and hints at their largely unexplored role in functional biology and crop performance.
Hydrological dynamics drive the transition of antibiotic resistance genes between particle-attached and free-living lifestyles in a deep freshwater reservoir
Authors: Adyari Bob , Hou Liyuan , Zhang Lanping , Chen Nengwang , Ju Feng , Zhu Longji , Yu Chang-Ping , Hu Anyi 
Published: June 2022

AbstractDespite the growing awareness of antibiotic resistance genes (ARGs) spreading in the environment, there is a knowledge gap on the fate and transport of ARGs in particle-attached (PA) and free-living (FL) lifestyles in deep freshwater ecosystems experiencing seasonal hydrological changes. Here, we examined the ARG profiles using high-throughput quantitative PCR in PA and FL lifestyles at four seasons representing two hydrological seasons (i.e., vertical mixing and thermal stratification) in the Shuikou Reservoir (SR), Southern China. The results indicated that seasonal hydrological dynamics were critical for influencing ARGs in PA and FL fractions, and the transition of ARGs between the two lifestyles. Although both PA and FL ARG profiles were likely to be shaped by horizontal gene transfer, PA and FL ARGs had different responses to the changes in physico-chemicals (e.g., nutrients and dissolved oxygen) caused by seasonal hydrological dynamics. The particle-associated niche (PAN) index revealed that there were 94 non-conservative ARGs (i.e., no preferences for PA and FL), 23 conservative ARGs that preferred PA lifestyle, and 16 conservative ARGs for FL lifestyle. A sharp decline in the number of conservative ARGs in stratified seasons suggests a hydrological dynamics-dependent transition of ARGs between two lifestyles. Remarkably, the conservative ARGs (in PA or FL lifestyle) were more closely related to bacterial OTUs in their preferred lifestyle compared to their counterpart lifestyle, suggesting a lifestyle-dependent ARG enrichment. Altogether, these findings enhance our understanding of the role of seasonal hydrological changes in the dissemination of ARGs in different size fractions in deep aquatic ecosystems.
Filling gaps on the diversity and biogeography of Chilean millipedes (Myriapoda: Diplopoda)
Authors: Parra-Gómez Antonio , Fernández Leonardo D. 
Published: June 2022

AbstractResearch on the diversity and biogeography of Chilean millipedes (Diplopoda) represents a severe gap in knowledge. To reduce this gap we conducted a study to: (1) investigate the state of knowledge of millipede diversity, and (2) assess the pattern and causes underlying the latitudinal diversity gradient in Chilean millipedes. After combining the number of described species with those that have not yet been formally described, we concluded that there are 95 native millipede species in Chile. A diversity estimate suggested that in the future this number could increase to 125 or 197 species. However, this estimate is based on limited data. Therefore, the number of millipede species inhabiting Chile probably exceeds our estimate. Consistently, rarefaction-extrapolation curves revealed that we have not yet recorded a substantial fraction of millipede diversity and that increased sampling effort will reveal the presence of a greater number of millipede species in Chile. Most millipede species exhibited narrow geographic ranges in Chile. The north-south distribution of their species richness followed a bell-shaped latitudinal gradient of diversity, i.e. diversity peaked at the temperate climate of central Chile and then decreases towards the arid and polar climates of northern and southern Chile, respectively. The causes underlying this biogeographical pattern were water availability, ambient energy input and climate stability. This finding provided support for two of the five biogeographic hypotheses we tested: water-energy balance and climate stability. Thus, Chilean millipedes were more diverse at sites that exhibit warm and humid (temperate) climates for much of the year.
Clostridium scindens colonization of gnotobiotic mice promotes a chronic unresolving infection with Clostridioides difficile
Authors: Graham M , DiBenedetto N , Delaney ML , Lavin R , Pavao A , Yeliseyev V , Bry L 
Published: June 2022

AbstractThe commensal Clostridium scindens has been regarded as a promising bacteriotherapeutic against Clostridioides difficile infection due to its ability to consume host factors that can promote C. difficile growth, and its production of the antimicrobial compound 1-acetyl-β-carboline. We investigated C. scindens’ protective effects against C. difficile using defined colonization studies in gnotobiotic mice. Mice infected with C. difficile develop lethal infection within 48 hours. In contrast, 88% of mice pre-colonized with C. scindens survived acute infection with delayed C. difficile colonization, lower biomass, and toxin B levels at 24 hours after infection. However, two weeks post-challenge, surviving mice showed comparable levels of cecal C. difficile vegetative and spore biomass and toxin B, as seen during acute infection. After two weeks, co-colonized mice exhibited mucosal colonic hyperplasia with focal pseudomembranes, modeling a chronic and recurrent infection state. Our findings illustrate how the commensal microbiota can modulate host and pathogen interactions leading to chonic C. difficile carriage and infection.
Cell Wall Dynamics in a Filamentous Fungus
Authors: Chevalier Louis , Sala Mario Pinar , Le Borgne Rémi , Durieu Catherine , Peñalva Miguel , Boudaoud Arezki , Minc Nicolas 
Published: June 2022

ABSTRACTHyphal tip growth allows filamentous fungi to colonize space, reproduce or infect. It features remarkable morphogenetic plasticity including unusually fast elongation rates, tip turning, branching or bulging. These shape changes are all driven from the expansion of a protective cell wall (CW) secreted from apical pools of exocytic vesicles. How CW secretion, remodeling and deformation are modulated in concert to support rapid tip growth and morphogenesis while ensuring surface integrity remains poorly understood. We implemented sub-resolution imaging to map the dynamics of CW thickness and secretory vesicles in Aspergillus nidulans. We found that tip growth is associated with balanced rates of CW secretion and expansion, which limit temporal fluctuations in CW thickness, elongation speed and vesicle amount, to less than 10-15%. Affecting this balance through modulations of growth or trafficking yield to near-immediate changes in CW thickness, mechanics and shape. We developed a model with mechanical feedback which accounts for steady states of hyphal growth as well as rapid adaptation of CW mechanics and vesicle recruitment to different perturbations. These data provide unprecedented details on how CW dynamics emerges from material secretion and expansion, to stabilize fungal tip growth as well as promote its morphogenetic plasticity.
Fungi with history: Unveiling the mycobiota of historic documents of Costa Rica
Authors: Escudero-Leyva Efraín , Vieto Sofía , Avendaño Roberto , Rojas-Gätjens Diego , Agüero Paola , Pacheco Carlos , Montero Mavis L. , Chaverri Priscila , Chavarría Max 
Published: June 2022

AbstractThrough nondestructive techniques, we studied the physicochemical characteristics and mycobiota of five key historic documents from Costa Rica, including the Independence Act of Costa Rica from 1821. We determined that for documents dated between 1500 and 1900 (i.e., the Cloudy Days Act, the Independence Act, and two documents from the Guatemalan Series from 1539 and 1549), the paper composition was cotton, whereas the 1991 replicate of the Political Constitution from 1949 was made of wood cellulose with an increased lignin content. We also determined that the ink employed in 1821 documents is ferrogallic, i.e., formed by iron sulfate salts in combination with gallic and tannic acids. In total, 22 fungal isolates were obtained: 15 from the wood-cellulose-based Political Constitution and seven from the other three cotton-based documents. These results suggest that cotton-based paper is the most resistant to microbial colonization. Molecular identifications using three DNA markers (i.e., ITS nrDNA, beta-tubulin, and translation elongation factor 1-alpha) classified the isolates in eight orders and ten genera. The most frequent genera were Cladosporium, Penicillium, and Purpureocillium. Of the isolates, 95% presented cellulolytic activity correlated to their ability to cause deterioration of the paper. This work increases the knowledge of the fungal diversity that inhabits historic documents and its relationship with paper composition and provides valuable information to develop strategies to conserve and restore these invaluable documents.
The 2′-deoxyribofuranoside of 3-phenyltetrahydropyrimido[4,5-c]pyridazin-7-one: a bicyclic nucleoside with sugar residues in N and S conformations, and its molecular recognition
Authors: Mei Hui , Budow-Busse Simone , Kondhare Dasharath , Eickmeier Henning , Reuter Hans , Seela Frank 
Published: June 2022

The title compound 3-phenyltetrahydropyrimido[4,5-c]pyridazine 2′-deoxyribonucleoside [systematic name: 6-(2-deoxy-β-D-erythro-pentofuranosyl)-5,6,7,8-tetrahydro-3-phenylpyrimido[4,5-c]pyridazin-7-one monohydrate, C17H18N4O4·H2O, 1] shows two conformations in the crystalline state and the two conformers (1a and 1b) adopt different sugar puckers. The sugar residue of 1a shows a C2′-endo S-type conformation, while 1b displays a C3′-endo N-type sugar pucker. Both conformers adopt similar anti conformations around the N-glycosylic bonds, with χ = −97.5 (3)° for conformer 1a and χ = −103.8 (3)° for conformer 1b. The extended crystalline network is stabilized by several intermolecular hydrogen bonds involving nucleoside and water molecules. The nucleobases and phenyl substituents of the two conformers (1a and 1b) are stacked and display a reverse alignment. A Hirshfeld surface analysis supports the hydrogen-bonding pattern, while curvedness surfaces visualize the stacking interactions of neighbouring molecules. The recognition face of nucleoside 1 for base-pair formation mimics that of 2′-deoxythymidine. Nucleoside 1 shows two pK
a values: 1.8 for protonation and 11.2 for deprotonation. DNA oligonucleotides containing nucleoside 1 were synthesized and hybridized with complementary DNA strands. Nucleoside 1 forms a stable base pair with dA which is as stable as the canonical dA–dT pair. The bidentate 1–dA base pair is strengthened by a third hydrogen bond provided by the dA analogue 3-bromopyrazolo[3,4-d]pyrimidine-4,6-diamine 2′-deoxyribofuranoside (4). By this, duplex stability is increased and the suggested base-pairing patterns are supported.
Assessing the impacts of government environmental policies on the small and medium-sized firm's performances in Korea and China
Authors: Joo Hye-Young , Min Hokey 
Published: June 2022

PurposeThis paper aims to examine which role governments can play in facilitating the small and medium-sized enterprises (SMEs)' environmental capabilities in a global marketplace. It also investigates whether the extent of the impact of government intervention on firm performance varies depending on country-specific policies.Design/methodology/approachThe authors develop a series of hypotheses that are predicated on the ecological modernization theory and the institutional theory. To test those hypotheses, the authors collected cross-national data reflecting both Korean and Chinese SME practices and then used the structural equation model. In addition, the authors utilized cross-validation techniques for methodological rigor.FindingsA series of hypotheses test results revealed that government intervention had a positive impact on the MNF's environmental innovation capabilities and technological innovation capabilities. In addition, the authors discovered that SMEs' reaction to government intervention had a mediating effect between government intervention and the SME's performance. This discovery verifies the ecological modernization and institutional theories.Originality/valueThis is one of the few studies that conducted cross-cultural analyses of two different nations with contrasting government structures (i.e. capitalistic versus socialistic).