bluuebunny/crossref_metadata_2025_split huggingface dataset:
Public health interventions successfully mitigated multiple incursions of SARS-CoV-2 Delta variant in the Australian Capital Territory
Authors: Hall Robyn , Jones Ashley , Crean Emma , Marriott Victoria , Pingault Nevada , Marmor Alexandra , Sloan-Gardner Timothy , Kennedy Karina , Coleman Kerryn , Johnston Vanessa , Schwessinger Benjamin 
Published: August 2022

SummaryThe Australian Capital Territory rapidly responded to an incursion of the SARS-CoV-2 Delta (B.1.617.2) variant on 12 August 2021 with several public health interventions, including a territory-wide lockdown and genomic sequencing. Prior to this date, SARS-CoV-2 had been eliminated locally since July 7, 2020. Sequencing of >75% of cases identified at least 13 independent incursions with onwards spread in the community during the study period, between 12 August and 11 November 2021. Two incursions resulted in the majority of community transmission during this period, with persistent transmission in vulnerable sections of the community. Ultimately, both major incursions were successfully mitigated through public health interventions, including COVID-19 vaccines. In this study we explore the demographic factors that contributed to the spread of these incursions. The high rates of SARS-CoV-2 sequencing in the Australian Capital Territory and the relatively small population size facilitated detailed investigations of the patterns of virus transmission. Genomic sequencing was critical to disentangling complex transmission chains to target interventions appropriately.Despite a strict lockdown and interstate travel restrictions, the Australian Capital Territory experienced at least 13 incursions of SARS-CoV-2 Delta (B.1.617.2) with onwards spread in the community between 12 August and 11 November 2021.This level of detail was only accessible because of the high rate of SARS-CoV-2 sequencing, with sequencing attempted on 1438/1793 (80%) of cases.Transmission chains varied in size and duration, with two dominant incursions (ACT.19 and ACT.20) comprising 35% and 53% of all sequenced cases during the study period, respectively.The ACT.20 outbreak persisted longer, due to specific challenges with implementing public health interventions in the affected populations.Both major incursions were successfully curbed through stringent public health measures, including the widespread acceptance of COVID-19 vaccines (>95% of the eligible population by the end of the study period).
TheVibrioType III Secretion System 2 is not restricted to theVibrionaceaeand encodes differentially distributed repertoires of effector proteins
Authors: Jerez SA , Plaza N , Bravo V , Urrutia IM , Blondel CJ 
Published: August 2022

ABSTRACTVibrio parahaemolyticusis the leading cause of seafood-borne gastroenteritis worldwide. A distinctive feature of the O3:K6 pandemic clone, and its derivatives, is the presence of a second, phylogenetically distinct, Type III Secretion System (T3SS2) encoded within the genomic island VPaI-7. The T3SS2 allows the delivery of effector proteins directly into the cytosol of infected eukaryotic cells to subvert key host cell processes, critical forV. parahaemolyticusto colonize and cause disease. Furthermore, the T3SS2 also increases the environmental fitness ofV. parahaemolyticusin its interaction with bacterivorous protists; hence it has been proposed that it contributed to the global oceanic spread of the pandemic clone. Several reports have identified T3SS2-related genes inVibrioand non-Vibriospecies, suggesting that the T3SS2 gene cluster is not restricted to theVibrionaceaeand can mobilize through horizontal gene transfer events. In this work, we performed a large-scale genomic analysis to determine the phylogenetic distribution of the T3SS2 gene cluster and its repertoire of effector proteins. We identified putative T3SS2 gene clusters in 1130 bacterial genomes from 8 bacterial genera, 5 bacterial families and 47 bacterial species. A hierarchical clustering analysis allowed us to define 6 T3SS2 subgroups (I-VI) with different repertoires of effector proteins, redefining the concepts of T3SS2 core and accessory effector proteins. Finally, we identified a subset of T3SS2 gene clusters (subgroup VI) that lack most T3SS2 effector proteins described to date and provided a list of 10 novel effector candidates for this subgroup through bioinformatic analysis. Collectively, our findings indicate that the T3SS2 extends beyond theVibrionaceaefamily and suggest that different effector protein repertories could have a differential impact on the pathogenic potential and environmental fitness of each bacteria that have acquired theVibrioT3SS2 gene cluster.DATA SUMMARYAll genome sequences used in this study were downloaded from the National Center for Biotechnology Information (NCBI) RefSeq or GenBank databases (SeeTable S1for accession numbers).Files for the T3SS2 reconstructed phylogenetic tree (Newick tree and MSA fasta file), hierarchical clustering data analysis file from MORPHEUS,Table S1with genome accession numbers and all the data of the absence/presence of T3SS2-related components, andTable S2with the prediction of novel effector proteins are available as part of the online Supporting Dataset at the Zenodo data repository (https://doi.org/10.5281/zenodo.7016552). The T3SS2 phylogenetic tree can be interactively visualized inhttps://itol.embl.de/tree/19016190125374711626959067#
CasDinG is an ATP-dependent 5’-3’ DNA helicase with accessory domains essential for type IV CRISPR immunity
Authors: Domgaard Hannah , Cahoon Christian , Armbrust Matthew J. , Redman Olive , Thomas Aaron , Jackson Ryan N. 
Published: August 2022

ABSTRACTCRISPR-associated DinG protein (CasDinG) is essential to type IV-A CRISPR function. However, the enzymatic activities of CasDinG are unknown. Here we demonstrate that CasDinG from Pseudomonas aeruginosa strain 83 is an ATP- and metal-dependent 5’-3’ DNA helicase. The crystal structure of CasDinG reveals a helicase core of two RecA-like domains with three accessory domains (N-terminal, arch, and vestigial FeS). To examine the in vivo function of these CasDinG domains, we first identified the preferred PAM sequence (5’-GNAWN-3’ on the 5’-side of the target) with a plasmid library containing all combinations of the five nucleotides upstream of the target sequence. Plasmid clearance assays (using a 5’-GGAAA-3’ PAM) with CasDinG domain mutants demonstrated the vFeS and arch accessory domains are both essential for type IV immunity. These results provide a needed structural and biochemical framework for understanding the type IV-A CRISPR system.
Optimizing E. coli as a formatotrophic platform for bioproduction via the reductive glycine pathway
Authors: Kim Seohyoung , Giraldo Néstor David , Rainaldi Vittorio , Machens Fabian , Collas Florent , Kubis Armin , Kensy Frank , Bar-Even Arren , Lindner Steffen N. 
Published: August 2022

AbstractMicrobial C1 fixation has a vast potential to support a sustainable circular economy. Hence, several biotechnologically important microorganisms have been recently engineered for fixing C1 substrates. However, reports about C1-based bioproduction with these organisms are scarce. Here, we describe the optimization of a previously engineered formatotrophic Escherichia coli strain. Short-term adaptive laboratory evolution enhanced biomass yield and accelerated growth of formatotrophic E. coli to 3.3 g-CDW/mol-formate and 6 hours doubling time, respectively. Genome sequence analysis revealed that manipulation of acetate metabolism is the reason for better growth performance, verified by subsequent reverse engineering of the parental E. coli strain. Moreover, the improved strain is capable of growing to an OD600 of 22 in bioreactor fed-batch experiments, highlighting its potential use for industrial bioprocesses. Finally, demonstrating the strain’s potential to support a sustainable, formate-based bioeconomy, lactate production from formate and CO2 was engineered. The optimized strain generated 1.2 mM lactate—10 % of the theoretical maximum—providing the first proof-of-concept application of the reductive glycine pathway for bioproduction.
Landscape configurations determining the genetic structure of the Yellow-Spotted Amazon River Turtle (Podocnemis unifilis) in Brazilian Amazonia
Authors: Agostini Maria Augusta Paes , Machado Arielli Fabrício , Ritter Camila Duarte , das Neves da Silva Viana Maria , dos Santos Monjeló Luiz Alberto , Andrade Paulo César Machado , Pantoja-Lima Jackson , Pezzuti Juarez C. B. , Félix-Silva Daniely , de Oliveira Waldesse Piragé , Vogt Richard C. , Hrbek Tomas , Farias Izeni Pires 
Published: August 2022

AbstractContextWaterfalls and rapids of Amazon basin have been suggested as causing the speciation and genetic structure of many freshwater species, including turtles. The species behavior affects the way waterfalls and rapids limit gene flow. The Yellow-spotted River Turtle (Podocnemis unifilis), a widely distributed and endangered Amazonian turtle, does not show the habit to migrate long distances for breeding or eating, but has a complex geographic pattern of genetic variation.ObjectivesHere, we investigate isolation by distance and by resistance of P. unifilis. We analyzed if the species ecological niche and waterfalls explain the genetic distance in Brazilian Amazonia.MethodsWe evaluated the P. unifilis spatial distribution of genetic variability and diversity using the control region of mitochondrial DNA. We tested the hypotheses of isolation either by distance and resistance through an integrative approach using genetic, geographic, and ecological data. We created a resistance matrix using species niche modeling. We compared the explanation power of geographical distance (both linear and in-water distance) and resistance distance on genetic distance (ΦST fixation index) using multiple regressions and Mantel tests.ResultsWe found a high genetic diversity and pattern of genetic structure proved to be geographically complex. The population structure followed some watersheds but also showed structuring within different rivers. We found that landscape resistance better explains genetic distance than linear and in-water distance.ConclusionsThe resistance of the landscape influences the displacement of individuals by aquatic, vegetational, biological, and geomorphological variables, and efforts to species conservation need to be applied throughout its distribution considering landscape genetics.
MyD88-Dependent Signaling Drives Toll-Like Receptor-Induced Trained Immunity in Macrophages
Authors: Owen Allison M. , Luan Liming , Burelbach Katherine R. , McBride Margaret A. , Stothers Cody L. , Boykin Olivia A. , Sivanesam Kalkena , Schaedel Jessica F. , Patil Tazeen K , Wang Jingbin , Hernandez Antonio , Patil Naeem K. , Sherwood Edward R. , Bohannon Julia K. 
Published: August 2022

ABSTRACTImmunocompromised populations are highly vulnerable to developing life-threatening infections. Strategies to protect patients with weak immune responses are urgently needed. Employing trained immunity, whereby innate leukocytes undergo reprogramming upon exposure to a microbial product and respond more robustly to subsequent infection, is a promising approach. Previously, we demonstrated that the TLR4 agonist monophosphoryl lipid A (MPLA) induces trained immunity and confers broad resistance to infection. TLR4 signals through both MyD88- and TRIF-dependent cascades, but the relative contribution of each pathway to induction of trained immunity is unknown. Here, we show that MPLA-induced resistance toStaphylococcus aureusinfection is lost in MyD88-KO, but not TRIF-KO, mice. The MyD88-activating agonist CpG (TLR9 agonist), but not TRIF-activating Poly I:C (TLR3 agonist), protects against infection in a macrophage-dependent manner. MPLA- and CpG-induced augmentation of macrophage metabolism and antimicrobial functions is blunted in MyD88-, but not TRIF-KO, macrophages. Augmentation of antimicrobial functions occurs in parallel to metabolic reprogramming and is dependent, in part, on mTOR activation. Splenic macrophages from CpG-treated mice confirmed that TLR/MyD88-induced reprogramming occurs in vivo. TLR/MyD88-triggered metabolic and functional reprogramming was reproduced in human monocyte-derived macrophages. These data show that MyD88-dependent signaling is critical in TLR-mediated trained immunity.
Functional hierarchy among different Rab27 effectors involved in secretory granule exocytosis
Authors: Zhao Kunli , Matsunaga Kohichi , Mizuno Kouichi , Wang Hao , Okunishi Katsuhide , Izumi Tetsuro 
Published: August 2022

AbstractThe Rab27 effectors play versatile roles in regulated exocytosis. In pancreatic beta cells, exophilin-8 anchors granules in the peripheral actin cortex, whereas granuphilin and melanophilin mediate granule fusion with and without stable docking to the plasma membrane, respectively. However, it is unknown whether these coexisting effectors function in parallel or in sequence to support the whole insulin secretory process. Here, we investigate their functional relationship by comparing the exocytic phenotypes in beta cells simultaneously lacking two effectors with those lacking one of them. Analyses of prefusion profiles by total internal reflection fluorescence microscopy indicate that melanophilin exclusively functions downstream of exophilin-8 to mobilize granules for fusion from the actin network to the plasma membrane after stimulation. The two effectors are physically linked via the exocyst complex. Downregulation of the exocyst component affects granule exocytosis only in the presence of exophilin-8. Exophilin-8 also promotes fusion of granules stably docked to the plasma membrane mediated by granuphilin, although it is dispensable for granule residence beneath the plasma membrane. The current study presents the first diagram for multiple intracellular paths of granule exocytosis and for functional hierarchy among different Rab27 effectors in the same cell.
Oat chromosome and genome evolution defined by widespread terminal intergenomic translocations in polyploids
Authors: Tomaszewska Paulina , Schwarzacher Trude , Heslop-Harrison Pat (J.S) 
Published: August 2022

AbstractStructural chromosome rearrangements involving translocations, fusions and fissions lead to evolutionary variation between species and potentially reproductive isolation and variation in gene expression. While the wheats (Triticeae, Poaceae) and oats (Aveneae) all maintain a basic chromosome number of x=7, genomes of oats show frequent intergenomic translocations, in contrast to wheats where these translocations are relatively rare. We aimed to show genome structural diversity and genome relationships in tetraploid, hexaploid and octoploid Avena species and amphiploids, establishing patterns of intergenomic translocations across different oat taxa using fluorescence in situ hybridization (FISH) with four well-characterized repetitive DNA sequences: pAs120, AF226603, Ast-R171 and Ast-T116. In A. agadiriana (2n=4x=28), the selected probes hybridized to all chromosomes indicating that this species originated from one (autotetraploid) or closely related ancestors with the same genomes. Hexaploid amphiploids were confirmed as having the genomic composition AACCDD, while octoploid amphiploids showed three different genome compositions: AACCCCDD, AAAACCDD or AABBCCDD. The A, B, C, and D genomes of oats differ significantly in their involvement in non-centromeric, intercalary translocations. There was a predominance of distal intergenomic translocations from the C-into the D-genome chromosomes. Translocations from A- to C-, or D- to C-genome chromosomes were less frequent, proving that at least some of the translocations in oat polyploids are non-reciprocal. Rare translocations from A- to D-, D- to A- and C- to B-genome chromosomes were also visualized. The fundamental research has implications for exploiting genomic biodiversity in oat breeding to through introgression from wild species potentially with contrasting chromosomal structures and hence deleterious segmental duplications or large deletions in amphiploid parental lines.
Optimization of cryo-electron microscopy for quantitative analysis of lipid bilayers
Authors: Heberle Frederick A. , Welsch Doug , Scott Haden L. , Waxham M. Neal 
Published: August 2022

AbstractCryogenic electron microscopy (cryo-EM) is among the most powerful tools available for interrogating nanoscale structure of biological structures. We recently showed that cryo-EM can be used to measure the bilayer thickness of lipid vesicles and biological membranes with sub-angstrom precision, resulting in the direct visualization of nanoscopic domains of different thickness in multicomponent lipid mixtures and giant plasma membrane vesicles. Despite the great potential of cryo-EM for revealing the lateral organization of biomembranes, a large parameter space of experimental conditions remains to be optimized. Here, we systematically investigate the influence of instrument parameters and image post-processing steps on the ability to accurately measure bilayer thickness and discriminate regions of different thickness within unilamellar liposomes. We also demonstrate a spatial autocorrelation analysis to extract additional information about lateral heterogeneity.SignificanceRaft domains in unstimulated cells have proven difficult to directly visualize owing to their nanoscopic size and fleeting existence. The few techniques capable of nanoscopic spatial resolution typically rely on interpretation of indirect spectroscopic or scattering signals or require stabilizing the membrane on a solid support. In contrast, cryo-EM yields direct images of nanoscale domains in probe-free, unsupported membranes. Here, we systematically optimize key steps in the experimental and analysis workflow for this new and specialized application. Our findings represent an important step toward developing cryo-EM into a robust method for investigating phase behavior of membranes at length scales relevant to lipid rafts.
Prison break from financialization: the case of the PRI reporting and assessment framework
Authors: Arjaliès Diane-Laure , Laurel-Fois Daniela , Mottis Nicolas 
Published: August 2022

PurposeThis article seeks to unravel the mechanisms through which financial actors agreed upon a sustainability accounting standard without financializing social and environmental issues, i.e. assigning a monetary value to sustainability.Design/methodology/approachThe article examines the Reporting and Assessment Framework created by the United Nations Principles for Responsible Investment (UN-PRI), the leading reporting sustainability framework in the asset management industry. It relies on a longitudinal case study that draws upon interviews, participant observation, and archival data.FindingsThe article demonstrates that the conception of the framework was a funnelling process of sustainability valuation comprising two co-constituted mechanisms: a process of valorization – judging what is deemed of value – and a process of evaluation – agreeing on how to assess value. This valuation process was unfolded by creating the framework, thanks to two enabling conditions: the creation of non-prescriptive evaluative criteria that avoided financialization and the valuation support of an enabling organization.Originality/valueThe article helps understand how an industry can encompass the diversity of motives and practices associated with the adoption of sustainability by its economic actors while suggesting a common framework to report on and assess those practices. It uncovers alternatives to the financialization process of sustainability accounting standards. The article also offers insights into the advantages and inconveniences of such a framework. The article enriches the literature in the sociology of valuation, financialization, and sustainability accounting.
Consumer adoption of digital grocery shopping: what is the impact of consumer’s prior-to-use knowledge?
Authors: Zolfaghari Alireza , Thomas-Francois Kimberly , Somogyi Simon 
Published: August 2022

PurposeSmart retail technology adoption models are largely focused on consumer perceptions of the technology and the characteristics of digital technologies. However, the impact of the prior-to-use knowledge of consumers on the adoption of the technologies has been understudied. This research examined to what extent social acceptance and consumer learning can facilitate consumer adoption of digital grocery shopping (DGS).Design/methodology/approachThis paper builds on the innovation–decision model to develop a framework to examine the impact of social acceptance and consumer learning on DGS. The research tested a structural model based on data collected from 611 North American participants.FindingsThis study found that the social acceptance of DGS directly and consumer learning indirectly affects the appeal of grocery shopping to consumers and consequently increases their intention to adopt this new shopping method. Furthermore, the results indicated that both hypothesised directions are parallelly mediated by digital convenience, the consumer’s digital readiness and digital trust.Originality/valueThis study extends the understanding of consumer adoption of DGS by highlighting the influence of consumer knowledge about DGS on their behavioural intention. Several important theoretical and practical implications are provided to help retail managers to develop service strategies.
Blockchain in sustainable supply chain management: an application of the analytical hierarchical process (AHP) methodology
Authors: Fernandez-Vazquez Simon , Rosillo Rafael , de la Fuente David , Puente Javier 
Published: August 2022

Purpose The analytical hierarchical process (AHP)’s main purpose is to assess higher hierarchy levels based on the cooperation of its various levels. It results in a well-designed model-based method in which the weights for the selected attribute are calculated using dimensions, criteria, and indicators. This paper aims to highlight the benefits of blockchain in supply chain management with the help of a literature review along with opinions of experts from various sectors.Design/methodology/approachWith the goal of enhancing the use of blockchain technology in supply chain management, particularly when comparing within the same industry, the AHP methodology has been used. In order to develop the AHP model, a total of eight elements are examined in this study, which are decentralization, resiliency, security, smart contracts, sustainability, traceability, transparency and trust. A calculation of a Desirability Index for conventional supply chain and blockchain-enabled supply chains has been also developed.FindingsFindings where that in a blockchain-enabled supply chain, the global weights of individual benefit variables are considerably larger than in conventional supply chains. When the score of the Desirability Index for conventional supply chain and blockchain-enabled supply chain is compared, the blockchain-enabled supply chain significantly surpasses the conventional supply chain in terms of increasing sustainable development in today’s supply networks.Originality/valueThis study takes into account the AHP methodology applying it on blockchain. This has not been done before in the academic world, at least as far as the authors may be aware of. The originality of combining such process with a recent technology such as blockchain highlights the value of this research.