bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional and morpho-physiological responses of Marchantia polymorpha upon phosphate starvation
Authors: Rico-Reséndiz Felix , Cervantes-Pérez Sergio Alan , Espinal-Centeno Annie , Dipp-Álvarez Melissa , Oropeza-Aburto Araceli , Hurtado-Bautista Enrique , Cruz-Hernández Andres , Bowman John L. , Ishizaki Kimitsune , Arteaga-Vázquez Mario A. , Herrera-Estrella Luis , Cruz-Ramírez Alfredo 
Published: September 2020

AbstractPhosphate (Pi) is a pivotal nutrient that constraints plant development and productivity in natural ecosystems. Land colonization by plants, more than 470 million years ago, evolved adaptive mechanisms to conquer Pi-scarce environments. However, little is known about the molecular basis underlying such adaptations at early branches of plant phylogeny. To shed light on how early divergent plants respond to Pi limitation, we analyzed the morpho-physiological and transcriptional dynamics of Marchantia polymorpha upon Pi starvation. Our phylogenomic analysis highlights some gene networks present since the Chlorophytes and others established in the Streptophytes (eg. PHR1-SPX1 and STOP1-ALMT1, respectively). At the morpho-physiological level, the response is characterized by the induction of phosphatase activity, media acidification, accumulation of auronidins, reduction of internal Pi concentration and developmental modifications of rhizoids. The transcriptional response involves the induction of MpPHR1, Pi transporters, lipid turnover enzymes and MpMYB14, an essential transcription factor for auronidins biosynthesis. MpSTOP2 up-regulation correlates with expression changes in genes related to organic acid biosynthesis and transport, suggesting preference for citrate exudation. Analysis of MpPHR1 binding sequences (P1BS) shows enrichment of this cis regulatory element in differentially expressed genes. Our study unravels the strategies, at diverse levels of organization, exerted by M. polymorpha to cope with low Pi availability.Significance StatementThis study unravels the transcriptional and morphophysiological mechanisms executed by the non-vascular, and rootless, plant Marchantia polymorpha upon phosphate starvation conditions. The findings in this study shed light on the mechanisms that early land plants may have developed for the conquest of substrates poor in available phosphate, some of which are still conserved by current-day plants. Moreover, our results open several working hypotheses and novel perspectives for the study of Pi-starvation responses along plant evolution.
Slipped strand mispairing in the gene encoding sialidase NanH3 inGardnerellaspp
Authors: Kurukulasuriya Shakya P. , Patterson Mo H. , Hill Janet E. 
Published: September 2020

AbstractCell wall proteins with sialidase activity are involved in carbohydrate assimilation, adhesion to mucosal surfaces, and biofilm formation.Gardnerellaspp. inhabit the human vaginal microbiome and encode up to three sialidase enzymes, two of which are suspected to be cell wall associated. Here we demonstrate that the gene encoding extracellular sialidase NanH3 is found almost exclusively inG. piotiiand closely relatedGardnerellagenome sp. 3, and its presence correlates with sialidase positive phenotype in a collection of 112Gardnerellaisolates. ThenanH3gene sequence includes a homopolymeric repeat of cytosines that varies in length within cell populations, indicating that this gene is subject to slipped-strand mispairing, a mechanisms of phase variation in bacteria. Variation in the length of the homopolymer sequence results in encoding of either the full length sialidase protein or truncated peptides lacking the sialidase domain due to introduction of reading-frame shifts and premature stop codons. Phase variation in NanH3 may be involved in immune evasion or modulation of adhesion to host epithelial cells, and formation of biofilms characteristic of the vaginal dysbiosis known as bacterial vaginosis.
Modulation of fungal virulence through CRZ1 regulated F-BAR-dependent actin remodeling and endocytosis in chickpea infecting phytopathogenAscochyta rabiei
Authors: Sinha Manisha , Shree Ankita , Singh Kunal , Kumar Kamal , Kumar Vimlesh , Verma Praveen Kumar 
Published: September 2020

AbstractPolarized hyphal growth of filamentous pathogenic fungi is an essential event for host penetration and colonization. The long-range early endosomal trafficking during the hyphal growth is crucial for nutrient uptake, sensing of host-specific cues, and regulation of effector production. Bin1/Amphiphysin/Rvs167 (BAR) domain-containing proteins mediate fundamental cellular processes, including membrane remodeling and endocytosis. Here, we identified an F-BAR domain protein (ArF-BAR) in the necrotrophic fungusAscochyta rabieiand demonstrate its involvement in endosome-dependent fungal virulence on the host plant,Cicer arietinum. We show that ArF-BAR regulates endocytosis at the hyphal tip, localizes to the early endosomes, and is involved in actin dynamics. Functional studies involving gene knockout and complementation experiments reveal that ArF-BAR is essential for virulence. The loss-of-function of ArF-BAR results in delayed formation of first septa from the hyphal tip, crucial for host penetration and proliferation. ArF-BAR was induced in response to oxidative stress and infection and localized to endocytic vesicles within the fungal hyphae. We also show that ArF-BAR is able to tubulate synthetic liposomes, suggesting the functional role of F-BAR domain in membrane tubule formationin vivo. Further, our studies identified a stress-induced transcription factor, ArCRZ1 (Calcineurin-responsive zinc finger 1) as key regulator for transcriptional reprogramming of ArF-BAR. We propose a model in which ArCRZ1 functions upstream of ArF-BAR to regulate fungal pathogenesis through a mechanism that involves membrane remodeling and actin cytoskeleton regulation.Author summaryBAR-domain superfamily is known to mold amorphous lipid bilayer into defined tubular shapes and critical for endosome formation and trafficking. Although these processes are studied earlier in the context of their structural and biochemical properties, there is limited evidence on the direct role of F-BAR domain proteins in the pathophysiological development of other economically important fungi. Our study assumes functional significance for plant infection as we identified an F-BAR domain-containing protein that is regulated by a distinct transcriptional network. We characterized F-BAR in a necrotrophic fungal pathogen,Ascochyta rabieithat causes the Ascochyta blight (AB) disease in chickpea plants. Additionally, we have also identified a calcium-regulated CRZ1 transcription factor that regulates the transcription ofArF-BAR. Our study will help to understand the complex interplay underlying the endosome formation required for fungal virulence.
Fixed single-cell RNA sequencing for understanding virus infection and host response
Authors: Van Phan Hoang , van Gent Michiel , Drayman Nir , Basu Anindita , Gack Michaela U. , Tay Savaş 
Published: September 2020

ABSTRACTSingle-cell transcriptomic studies that require intracellular protein staining, rare cell sorting, or inactivation of infectious pathogens are severely limited because current high-throughput RNA sequencing methods are incompatible with paraformaldehyde treatment, a common tissue and cell fixation and preservation technique. Here we present FD-seq, a high-throughput method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single-cells. We show that FD-seq preserves the mRNA integrity and relative abundances during fixation and subsequent cell retrieval. Furthermore, FD-seq detects a higher number of genes and transcripts than methanol fixation. We applied FD-seq to investigate two important questions in Virology. First, by analyzing a rare population of cells supporting lytic reactivation of the human tumor virus KSHV, we identifiedTMEM119as a host factor that mediates viral reactivation. Second, we found that upon infection with the betacoronavirus OC43, which causes the common cold and is a close relative of SARS-CoV-2, pro-inflammatory pathways are primarily upregulated in lowly-infected cells that are exposed to the virus but fail to express high levels of viral genes. FD-seq thus enables integrating phenotypic with transcriptomic information in rare cell populations, and preserving and inactivating pathogenic samples that cannot be handled under regular biosafety measures.
Chemical Stabilization of the HIV-1 Capsid Results in Efficient HIV-1 Reverse Transcriptionin vitro
Authors: Jennings Jordan , Shi Jiong , Varadarajan Janani , Jamieson Parker J. , Aiken Christopher 
Published: September 2020

ABSTRACTA defining activity of retroviruses is reverse transcription, the process during which the viral genomic RNA is converted into the double strand DNA required for virus replication. Reverse transcriptase (RT), the viral enzyme responsible for this process, was identified in 1970 by assaying permeabilized retrovirus particles for DNA synthesisin vitro. Such reactions are inefficient with only a small fraction of viral genomes being converted to full-length double strand DNA molecules, possibly owing to disruption of the structure of the viral core. Here we show that reverse transcription in purified HIV-1 cores is enhanced by the addition of the capsid-binding host cell metabolite inositol hexakisphosphate (IP6). IP6 potently enhanced full-length minus strand synthesis, as did hexacarboxybenzene (HCB) which also stabilizes the HIV-1 capsid. Both IP6 and HCB stabilized the association of the viral CA and RT proteins with HIV-1 cores. In contrast to the wild type, cores isolated from mutant HIV-1 particles containing intrinsically hyperstable capsids exhibited efficient reverse transcription in the absence of IP6, further indicating that the compound promotes reverse transcription by stabilizing the viral capsid. Our results show that stabilization of the HIV-1 capsid permits efficient reverse transcription in HIV-1 cores, providing a sensitive experimental system for analyzing the functions of viral and host cell molecules and the role of capsid disassembly (uncoating) in the process.IMPORTANCEHIV-1 infection requires reverse transcription of the viral genome. While much is known about the biochemistry of reverse transcription from simplified biochemical reactions, reverse transcription during infection takes place within a viral core. However, endogenous reverse transcription reactions using permeabilized virions or purified viral cores have been inefficient. Using viral cores purified from infectious HIV-1 particles, we show that efficient reverse transcription is achievedin vitroby addition of the capsid-stabilizing metabolite inositol hexakisphosphate. Enhancement of reverse transcription was linked to the capsid-stabilizing effect of the compound, consistent with the known requirement for an intact or semi-intact viral capsid for HIV-1 infection. Our results establish a biologically relevant system for dissecting the function of the viral capsid and its disassembly during reverse transcription. The system may also prove useful for mechanistic studies of emerging capsid-targeting antiviral drugs.
Topography, spike dynamics and nanomechanics of individual native SARS-CoV-2 virions
Authors: Kiss Bálint , Kis Zoltán , Pályi Bernadett , Kellermayer Miklós S.Z. 
Published: September 2020

SUMMARYSARS-CoV-2, the virus responsible for the current COVID-19 pandemic, displays a corona-shaped layer of spikes which play fundamental role in the infection process. Recent structural data suggest that the spikes possess orientational freedom and the ribonucleoproteins segregate into basketlike structures. How these structural features regulate the dynamic and mechanical behavior of the native virion, however, remain unknown. By imaging and mechanically manipulating individual, native SARS-CoV-2 virions with atomic force microscopy, here we show that their surface displays a dynamic brush owing to the flexibility and rapid motion of the spikes. The virions are highly compliant and able to recover from drastic mechanical perturbations. Their global structure is remarkably temperature resistant, but the virion surface becomes progressively denuded of spikes upon thermal exposure. Thus, both the infectivity and thermal sensitivity of SARS-CoV-2 rely on the dynamics and the mechanics of the virus.One sentence summaryThe native coronavirus 2 displays a dynamic surface layer of spikes, a large mechanical compliance and unique self-healing capacity.
Insight into glycosphingolipid crypticity: Crystal structure of the anti-tumor antibody 14F7 and recognition of NeuGc GM3 ganglioside
Authors: Bjerregaard-Andersen Kaare , Johannesen Hedda , Abraha Fana , Šakanović Aleksandra , Groβer Daniel , Coskun Ünal , Anderluh Gregor , Oscarson Stefan , Moreno Ernesto , Grzybek Michal , Krengel Ute 
Published: September 2020

AbstractTumor-associated glycolipids such as NeuGc GM3 are auspicious molecular targets in antineoplastic therapies and vaccine strategies. 14F7 is an anti-tumor antibody with high clinical potential, which has extraordinary specificity for NeuGc GM3, but does not recognize the very similar, ubiquitous NeuAc GM3. Here we present the 2.3 Å crystal structure of the 14F7 binding domain (14F7 scFv) in complex with the NeuGc GM3 trisaccharide. Intriguingly, a water molecule appears to shape the specificity of 14F7. Using model membrane systems, we show that 14F7 recognizes NeuGc GM3 only above lipid concentrations that are likely to form glycolipid-rich domains. This “all-or-nothing” effect was exacerbated in giant unilamellar vesicles and multilamellar vesicles, whereas no binding was observed to 100 nm liposomes, emphasizing that the 14F7–NeuGc GM3 interaction is additionally modulated by membrane curvature. Unexpectedly, adding NeuAc GM3 strongly increased binding affinity to NeuGc GM3-containing liposomes. This effect may be important for tumor recognition, where the ubiquitous NeuAc GM3 may enhance 14F7 binding to NeuGc GM3-expressing cancer cells.
Detecting adaptive introgression in human evolution using convolutional neural networks
Authors: Gower Graham , Picazo Pablo Iáñez , Fumagalli Matteo , Racimo Fernando 
Published: September 2020

AbstractStudies in a variety of species have shown evidence for positively selected variants introduced into one population via introgression from another, distantly related population—a process known as adaptive introgression. However, there are few explicit frameworks for jointly modelling introgression and positive selection, in order to detect these variants using genomic sequence data. Here, we develop an approach based on convolutional neural networks (CNNs). CNNs do not require the specification of an analytical model of allele frequency dynamics, and have outperformed alternative methods for classification and parameter estimation tasks in various areas of population genetics. Thus, they are potentially well suited to the identification of adaptive introgression. Using simulations, we trained CNNs on genotype matrices derived from genomes sampled from the donor population, the recipient population and a related non-introgressed population, in order to distinguish regions of the genome evolving under adaptive introgression from those evolving neutrally or experiencing selective sweeps. Our CNN architecture exhibits 95% accuracy on simulated data, even when the genomes are unphased, and accuracy decreases only moderately in the presence of heterosis. As a proof of concept, we applied our trained CNNs to human genomic datasets—both phased and unphased—to detect candidates for adaptive introgression that shaped our evolutionary history.
A risk-adjusted decoupled-net-present-value model to determine the optimal concession period of BOT projects
Authors: Nguyen Nhat , Almarri Khalid , Boussabaine Halim 
Published: September 2020

PurposeThe net-present-value (NPV) method is well-known for its drawbacks. To overcome some of these NPV weaknesses this paper aims to provide a methodology to determine an optimal concession period that treats risk and time separately. The purpose of this paper is to apply the notion of risk-adjusted decoupled net present value (risk-adjusted DNPV) to determine a conception period taken into consideration synthetic insurance premiums as compensation for risks.Design/methodology/approachThis paper conducts theoretical and empirical analysis and provides an integrated model for deriving concession periods of any PPP projects. The model is able to capture several contractual issues such risks costing and other contractual scenarios. Methodologically, the paper addressees both the issues of risk-based cost–benefit analysis and cash flow analysis bearing an emphasis of risk-adjusted DNPV to compute an optimum concession period.FindingsThe results show that using DNPV will produce a shorter concession period comparatively to NPV. The consequence of this is that the public sector will gain financially from an earlier transfer of the concession.Research limitations/implicationsThis paper contributes to the PPP literature by combing DNPV and risk to determine the PPP concession period for the mutual benefits both the private and public sectors. The decoupling of risk from traditional NPV computation will allow for risk pricing and tradability through insurance and allocation.Originality/valueThe attempt to decouple time and risk in the computation of NPV is the added value to the body of knowledge.
Supply chain workforce training: addressing the digital skills gap
Authors: Foroughi Abbas 
Published: September 2020

PurposeThe purpose of this research was to address the critical need for supply chain workforce training to empower employees to use new digital technologies and to identify and evaluate current sources of supply chain training.Design/methodology/approachAn online search was performed to locate training that is available for supply chain employees. Training providers who met the online delivery criterion were identified and evaluated on: (1) amount of supply chain content and/or digital technology content, (2) flexibility, (3) customizable and (4) credentials offered.FindingsSeveral sources of supply chain training were identified—supply chain professional organizations, consultants, MOOC courses and MicroMasters programs at colleges and universities.Research limitations/implicationsThe results of this study are limited by the fact that the number of supply chain training providers identified is not exhaustive and because the study examined training opportunities available at a particular point in time. Course offerings will change over time; certification requirements will be updated, and new providers will appear.Practical implicationsBy identifying sources of supply chain training that are currently available to help bridge this serious skill shortage, the results can serve as a guide to enterprises moving toward supply chain digitalization.Social implicationsTo succeed in the current environment of digital transformation, employees need opportunities to build digital skills that are demanded by corporations around the world. This is especially important at a time when unemployment is at an alarming rate.Originality/valueAn earlier version of the paper was presented at the 2019 Meeting of the Decision Sciences Institute, November 23–25, 2019, in New Orleans, LA.
Auditing in times of social distancing: the effect of COVID-19 on auditing quality
Authors: Albitar Khaldoon , Gerged Ali Meftah , Kikhia Hassan , Hussainey Khaled 
Published: September 2020

Purpose
This paper aims to discuss the theoretical impact of COVID-19 social distancing outbreak on audit quality.

Design/methodology/approach
This paper uses a desk study method to explore the possible impact of COVID-19 crisis on five key considerations for audit quality during the pandemic. These include audit fees, going concern assessment, auditor human capital, audit procedures and audit personnel salaries.

Findings
As many believe that the COVID-19 outbreak is as yet not a financial crisis, the authors, on the contrary, believe that the effects of the COVID-19 pandemic would be the toughest challenge for auditors and their clients since the 2007–2008 global financial crisis. Specifically, the authors believe that the COVID-19 social distancing can largely affect audit fees, going concern assessment, audit human capital, audit procedures, audit personnel salaries and audit effort, which ultimately can pose a severe impact on audit quality.

Practical implications
Due to the implementations of work-from-home strategy, audit firms are highly recommended to invest more in digital programs, including artificial intelligence, blockchain, network security and data function development. This can help them to be more adaptable to working from home experience, which is ultimately expected to enhance the effectiveness and the flexibility of communication between auditors and their clients. Also, the authors recommend stock markets and other governmental bodies to provide temporary relaxations in compliance requirements to corporations. This procedure is expected to help firms that apply work-from-home strategy to report better earnings figures, which is appeared to be positively associated with audit quality.

Originality/value
To date, to the best of the authors’ knowledge, there is no academic study that explores the potential impact of the COVID-19 outbreak on audit quality. This paper, therefore, fills an important research gap in the auditing literature. In addition, this paper can be used as a base to construct a research instrument (e.g. questionnaire or interviews) to provide empirical evidence on the potential impact of COVID-19 on audit quality.
The neoliberal reality of higher education in Australia: how accountingisation is corporatising knowledge
Authors: Martin-Sardesai Ann , Guthrie AM James , Parker Lee 
Published: September 2020

Purpose
As accounting academics, the authors know that performance measurement is well-trodden ground in the literature. Yet rarely have they turned their gaze inwards to examine the performance controls which they are subject to in the own everyday working life. Over the past 40 years, the rise of the New Public Management paradigm and neoliberalism has intensified changes in the way universities, disciplines and individual academics justify the quality of their work. This paper aims to explore the impact of accountingisation on the field and the Australian public sector higher education sector.

Design/methodology/approach
The perceptions of accounting academics in Australia’s 37 business faculties and schools were collected via an online survey. Additionally, a document analysis of annual reports, internal reports, strategy documents and other confidential material were also used.

Findings
The changes have included the use of corporate and individual research metrics aimed at increasing institutional status, brand reputation and revenue generation. These changes have transformed business schools and universities into commercial enterprises and commoditised education. What this analysis demonstrates is the apparent relationship between various government agendas, the commercialisation of universities and the distortion of the research activities by individual academics. For increased profits and efficiencies, individual scholars have paid the highest price.

Practical implications
If the accounting discipline is to be sustainable in the long term, business schools in Australia must reconfigure their performance measurement systems.

Originality/value
To date, research on “accountingisation” has previously been primarily conducted in the health and social services sectors. This research raises rarely heard voices to expose the actual social and human costs of accountingisation in Australia’s higher education sector.