bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome profiling of human colonic cells exposed to the gut pathobiontStreptococcus gallolyticussubsp.gallolyticus
Authors: Ewa Pasquereau-Kotula , du Merle Laurence , Sismeiro Odile , Pietrosemoli Natalia , Varet Hugo , Legendre Rachel , Trieu-Cuot Patrick , Dramsi Shaynoor 
Published: May 2023

AbstractStreptococcus gallolyticus sp. gallolyticus (SGG)is a gut pathobiont involved in the development of colorectal cancer (CRC). To decipher the contribution ofSGGin tumor initiation and/or acceleration respectively, a global transcriptome was performed in normal colonic cells (FHC) and in tumoral colonic cells (HT29). To identifySGG-specific alterations, we chose the phylogenetically closest relative,Streptococcus gallolyticussubsp.macedonicus(SGM)as the control bacterium. We show thatSGM,a bacterium generally considered as safe, did not induce any transcriptional changes on the two human colonic cells. The transcriptional reprogramming induced bySGGwas significantly different in FHC and HT29 cells, with most of the up- and down-regulated genes associated with cancer disease. Top up-regulated genes related to cancer were: (i)IL-20, CLK1, SORBS2, ERG1, PIM1, SNORD3Afor normal FHC cells and (ii)TSLP, BHLHA15, LAMP3, ZNF27B, KRT17, ATF3for cancerous HT29 cells.SGGinduces much stronger transcriptional changes in cancerous than in normal colonic cells (2,090vs128 genes being affected, respectively). Gene set enrichment analysis reveals thatSGG-induced strong ER- (endoplasmic reticulum) stress and UPR- (unfolded protein response) activation in colonic epithelial cells. Our results suggest thatSGGinduces a pro-tumoral shift in human colonic cells, particularly in transformed cells potentially accelerating tumor development in the colon.
TheToxoplasmaOxygen Sensing Protein, TgPhyA, Is Required for Resistance to Interferon-gamma Mediated Nutritional Immunity
Authors: Cordonnier Charlotte , Mandalasi Msano , Gigley Jason , Wohlfert Elizabeth A. , West Christopher M. , Blader Ira J 
Published: May 2023

AbstractAsToxoplasma gondiidisseminates through its host, the parasite must sense and adapt to its environment and scavenge nutrients. Oxygen (O2) is one such environmental factor and cytoplasmic prolyl 4-hydroxylases (PHDs) are evolutionarily conserved O2cellular sensing proteins that regulate responses to changes in O2availability.Toxoplasmaexpresses two PHDs. One of them, TgPHYa hydroxylates SKP1, a subunit of the SCF-E3 ubiquitin ligase complex.In vitro,TgPHYa is important for growth at low O2levels. However, studies have yet to examine the role that TgPHYa or any other pathogen encoded PHD plays in virulence and disease. Using a type II ME49ToxoplasmaTgPHYa knockout, we report that TgPHYa is important for Toxoplasma virulence and brain cyst formation in mice. We further find that while TgPHYa mutant parasites can establish an infection in the gut they are unable to efficiently disseminate to peripheral tissues because the mutant parasites are unable to survive within recruited immune cells. Since this phenotype abrogated in IFNγ knockout mice, we studied how TgPHYa mediates survival in IFNγ-treated cells. We find that TgPHYa is not required for release of parasite-encoded effectors into host cells that neutralize anti-parasitic processes induced by IFNγ. In contrast, we find that TgPHYa is required for the parasite to scavenge tryptophan, which is an amino acid whose levels are decreased after IFNγ upregulates the tryptophan-catabolizing enzyme, indoleamine dioxygenase (IDO). We further find that relative to wild-type mice that IDO knockout mice display increased morbidity when infected with TgPHYa knockout parasites. Together, these data identify the first parasite mechanism for evading IFNγ-induced nutritional immunity and highlight a novel role that oxygen sensing proteins play in pathogen growth and virulence.
Neurog1 and Olig2 integrate patterning and neurogenesis signals in development of zebrafish dopaminergic and glutamatergic dual transmitter neurons
Authors: Altbürger Christian , Rath Meta , Driever Wolfgang 
Published: May 2023

AbstractDopaminergic neurons develop in distinct neural domains by integrating local patterning and neurogenesis signals. While the proneural proteins Neurog1 and Olig2 have been previously linked to development of dopaminergic neurons, their dependence on local prepatterning and specific contributions to dopaminergic neurogenesis are not well understood. Here, we show that both transcription factors are differentially required for the development of defined dopaminergic glutamatergic subpopulations in the zebrafish posterior tuberculum, which are homologous to A11 dopaminergic neurons in mammals. Both Olig2 and Neurog1 are expressed inotpaexpressing progenitor cells and appear to act upstream of Otpa during dopaminergic neurogenesis. Our epistasis analysis confirmed that Neurog1 acts downstream of Notch signaling, while Olig2 acts downstream of Shh, but upstream and/or in parallel to Notch signaling. Furthermore, we identified Olig2 to be an upstream regulator ofneurog1in dopaminergic neurogenesis. This regulation occurs through Olig2-dependent repression of the proneural repressor and Notch target geneher2. Our study reveals how Neurog1 and Olig2 integrate local patterning signals, including Shh, with Notch neurogenic selection signaling, to specify the progenitor population and initiate neurogenesis and differentiation of A11-type dopaminergic neurons.
Exonuclease assisted mapping of protein-RNA interactions (ePRINT)
Authors: Hawkins Sophie , Mondaini Alexandre , Namboori Seema C. , Javed Asif , Bhinge Akshay 
Published: May 2023

AbstractRNA processing is a fundamental mode of gene regulation that is perturbed in a variety of diseases including cancer and neurodegenerative disorders. RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. We have developed a new method (ePRINT) to map RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT allows precise mapping of the 5’ end of the RBP binding site, and can uncover direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, for instance, as neural progenitors differentiate into neurons. Given its versatility, ePRINT has vast application potential as an investigative tool for RNA regulation in development, health and disease.
Impact of inter-species interactions between flower microbiota commensals and a floral pathogen on disease incidence and pathogen activity
Authors: Hassani M. Amine , Cui Zhouqi , LaReau Jacquelyn , B. Huntley Regan , Steven Blaire , Zeng Quan 
Published: May 2023

AbstractFlowers are colonized by a diverse community of microorganisms that alter plant health and interact with floral pathogens.Erwinia amylovorais a flower-inhabiting bacterium and a pathogen that infects different plant species, includingMalus × domestica(apple). Previously, we showed that the co-inoculation of two bacterial strains,PseudomonasandPantoeanatural inhabitants of apple flowers, reduced disease incidence caused by this floral pathogen. Here, we decipher the ecological interactions between these two flower-associated bacteria andE. amylovorain field experimentation andin vitroco-cultures. The two flower microbiota strains did not competitively excludeE. amylovorafrom the stigma habitat, as both commensal bacteria and the pathogen co-existed on the apple flowers, proscribing microbial antibiosis or niche exclusion as predominant mechanisms of host protection. Inspection of the total and the active microbiota populations on flowers revealed that strain co-inoculations altered microbiota activity. Using synthetic stigma exudation medium, tripartite co-culture of the bacterial strains strongly acidified the growth milieu and led to a substantial alteration of gene expression in both the pathogen and the two microbiota members. Our study emphasizes the critical role of emergent properties mediated by inter-species interactions within the plant holobiont and their impact on plant health and pathogen behavior.ImportanceFire blight, caused byErwinia amylovora, is one of the most important plant diseases of pome fruits. Plant-associated microbiota can influence plant disease occurrence through inter-species interactions. Previous studies have shown that plant microbiota commensals could suppress disease mainly by antagonizing of the pathogen growth, however, whether plant-associated microbiota could alter pathogen activity and behavior have not been well studied. Here, we show that the co-inoculation of two bacterial strains that naturally colonize the apple flowers reduce disease pressure. We further demonstrate that the interactions between these two microbiota commensals and the floral pathogen lead to a strong alteration of the pH and to the emergence of new gene expression patterns that may alter the pathogen behavior. Our findings emphasize the critical role of emergent properties mediated by inter-species interactions between plant microbiota and plant pathogens and their impact on plant health.
Automated model building and protein identification in cryo-EM maps
Authors: Jamali Kiarash , Käll Lukas , Zhang Rui , Brown Alan , Kimanius Dari , Scheres Sjors H.W. 
Published: May 2023

AbstractInterpreting electron cryo-microscopy (cryo-EM) maps with atomic models requires high levels of expertise and labour-intensive manual intervention. We present ModelAngelo, a machine-learning approach for automated atomic model building in cryo-EM maps. By combining information from the cryo-EM map with information from protein sequence and structure in a single graph neural network, ModelAngelo builds atomic models for proteins that are of similar quality as those generated by human experts. For nucleotides, ModelAngelo builds backbones with similar accuracy as humans. By using its predicted amino acid probabilities for each residue in hidden Markov model sequence searches, ModelAngelo outperforms human experts in the identification of proteins with unknown sequences. ModelAngelo will thus remove bottlenecks and increase objectivity in cryo-EM structure determination.
The curious case of cyanobacteria: a tale of light and darkness
Authors: Lee Victoria , Zheng Sally , Meza-Padilla Isaac , Nissimov Jozef I. 
Published: May 2023

ABSTRACTToxic algal bloom-forming cyanobacteria are a persistent problem globally for many aquatic environments. Their occurrence is attributed to eutrophication and rising temperatures due to climate change. The result of these blooms is often loss in biodiversity, economic impacts on tourism and fisheries, and risks to human and animal health. Of particular concern is the poorly understood interplay between viruses and toxic species that form blooms because viruses may exacerbate their harmful effects. Concurrently, cyanobacteria are also a source of bioactive compounds other than toxins, which makes them good candidates for drug discovery. We show that virus infection of the cyanobacteriumMicrocystis aeruginosa, results in as high as a 40-fold increase in the toxin microcystin two days post virus infection (dpi), and predict that microcystin levels may remain high in a body of water up to 7 dpi, long after water discoloration and cell lysis. This implicates viruses as major contributors to toxin release from cyanobacteria and emphasizes the importance of taking them into account in predictive models and in the assessment of water safety. We also show that bioactive compounds ofM. aeruginosainhibit and delay infection of single stranded DNA and single stranded RNA viruses. This highlights the potential of cyanobacteria as an excellent source for the discovery of novel antiviral compounds, and the ease with which screening for cyanobacterial antivirals can be achieved.
Native-state proteomics of Parvalbumin interneurons identifies novel molecular signatures and metabolic vulnerabilities to early Alzheimer’s disease pathology
Authors: Kumar Prateek , Goettemoeller Annie M , Espinosa-Garcia Claudia , Tobin Brendan R. , Tfaily Ali , Nelson Ruth S. , Natu Aditya , Dammer Eric B. , Santiago Juliet V. , Malepati Sneha , Cheng Lihong , Xiao Hailian , Duong Duc , Seyfried Nicholas T. , Wood Levi B. , Rowan Matthew JM , Rangaraju Srikant 
Published: May 2023

SUMMARYOne of the earliest pathophysiological perturbations in Alzheimer’s Disease (AD) may arise from dysfunction of fast-spiking parvalbumin (PV) interneurons (PV-INs). Defining early protein-level (proteomic) alterations in PV-INs can provide key biological and translationally relevant insights. Here, we use cell-type-specific in vivo biotinylation of proteins (CIBOP) coupled with mass spectrometry to obtain native-state proteomes of PV interneurons. PV-INs exhibited proteomic signatures of high metabolic, mitochondrial, and translational activity, with over-representation of causally linked AD genetic risk factors. Analyses of bulk brain proteomes indicated strong correlations between PV-IN proteins with cognitive decline in humans, and with progressive neuropathology in humans and mouse models of Aβ pathology. Furthermore, PV-IN-specific proteomes revealed unique signatures of increased mitochondrial and metabolic proteins, but decreased synaptic and mTOR signaling proteins in response to early Aβ pathology. PV-specific changes were not apparent in whole-brain proteomes. These findings showcase the first native state PV-IN proteomes in mammalian brain, revealing a molecular basis for their unique vulnerabilities in AD.
Cruise ship safety measures and their influence on passenger sense of security and purchase intention
Authors: Bahattab Shadi , Chen McCain Shiang-Lih , Lolli Jeffrey 
Published: May 2023

Purpose
The purpose of this study is to investigate whether customers perceive current cruise ship safety measures provided as meeting a sense of security and their influence on purchase intention. Three types of potential risks associated with cruise lines evaluated were external/internal attacks, malfunctions/accidents and onboard medical/health issues.

Design/methodology/approach
A survey used 12 safety measures questions to examine how cruise ships handle the above three risks, three questions to measure a sense of security and three questions to measure purchase intention. A seven-point Likert scale was applied. Convenience sampling was used. There were 163 valid responses collected.

Findings
All three safety measures evaluated in this study had a direct and positive effect on passengers' Sense of Security. Also, Safety Measure (SM) 2 and Sense of Security had direct and positive effects on purchase intention. Finally, SM1 and SM3 have only indirect impacts on Purchase Intentions via Sense of Security.

Research limitations/implications
Because of the small sample size and the convenience sampling method, the results of this study may lack generalizability.

Practical implications
Cruise managers should be aware that merely providing safety measures that are regulated by guidelines is not sufficient, and passengers must personally see and experience safety measures.

Originality/value
This study evaluated not only customers’ perceptions of safety measures on a cruise ship but also their impact on a sense of security and how that played a moderating role in purchase intention.
Connecting international and domestic dots: how conflict entanglement informs resolution and escalation
Authors: Melin Molly M. , Grigorescu Alexandru V. 
Published: May 2023

Purpose
This paper aims to seek to and understand how civil conflict and international claims inform one another. Does the existence of ongoing civil and international conflicts affect how a government addresses an international claim? The paper builds on existing literature that link international and domestic conflict. However, it suggests that the logic behind civil conflicts may be different from that for international ones as states decide how to deal with any one claim.

Design/methodology/approach
The paper posits that states faced with domestic conflicts and additional international claims are more likely to seek to resolve an international claim than those without similar conflicts. It develops a series of hypotheses about the likelihood of claim escalation and peaceful settlement attempts and proceed to test them quantitatively using the Issue Correlates of War data combined with the uppsala conflict data program/peace research institute oslo Armed Conflict Data.

Findings
On the one hand, the paper finds support for the argument regarding the difficulty states are faced with when seeking to resolve multiple international claims. On the other hand, it finds that the presence of civil conflicts incentivizes states to resolve international claims either by force or peacefully, suggesting internal violence can both lead to diversionary behavior and attempts at conflict resolution.

Research limitations/implications
The findings have important implications for work considering the complexity of domestic and international conflict linkages.

Originality/value
While many studies of claim militarization and peaceful attempts focus on dyadic and international characteristics, this paper creates a more nuanced understanding of the complexities of this foreign policy decision process.
Students with emotional and behavioural difficulties in Irish post-primary schools: a role for occupational therapy
Authors: O’Donnell Shóna , O’Reilly Aishling , Robinson Katie , Ní Riain Eimer , Pettigrew Judith 
Published: May 2023

Purpose
Higher levels of participation in school are linked to greater academic performance, better health and well-being and positive long-term outcomes for young people. Evidence shows that for students with emotional and behavioural difficulties (EBD), participation in school-based occupations is often restricted in comparison to their peers. Given the recent advancements towards introducing a new model of school-based occupational therapy in Ireland, this paper aims to discuss how occupational therapy can support students with EBD to increase their participation within the post-primary school context. The opinions in this paper are derived from the authors’ experience in the development of this practice in the Republic of Ireland.

Design/methodology/approach
The authors reviewed current literature and reflected on current practice to describe the unique role of occupational therapy in supporting students with EBD in the school environment.

Findings
Occupational therapists have potential to play a key role in school-based support for students with EBD. The authors describe how occupational therapists can promote whole school understanding of EBD and enable skill development, self-regulation, participation and school belonging, among youths with EBD. There is a significant lack of literature guiding practice in this area. Further research is required to explore professional issues and identify best practice.

Originality/value
This paper aims to provoke consideration of how school-based occupational therapists can play a crucial role in supporting students with EBD who are otherwise at risk of occupational injustice.
The quality of the Argentinean Malbec and the weather in the Mendoza region
Authors: Charlin Ventura , Cifuentes Arturo 
Published: May 2023

PurposeThe climate in Mendoza is significantly different from the climate in most global wine-making regions. This paper aims to explore the relationship between the quality of the Malbec wine from the Mendoza region and its weather.Design/methodology/approachThis study uses a multivariate regression model with fixed effects to assess how weather variations relate to wine quality. The Wine Spectator ratings are used as a measure of wine quality and to build a longitudinal data set of Malbec wine ratings from 1995 to 2020. The weather is described with several variables based on temperature, rainfall, humidity and cloudiness data from the Mendoza region. The model controls for wineries which are treated as fixed effects.FindingsThe results of this study indicate that the weather has a modest explanatory power when it comes to the quality of Mendoza’s Malbec. Additionally, the analyses show that the wineries are more important than the weather to explain quality differences in the wines. These findings are in agreement with previous studies carried out in regions with stable weather such as California and Australia.Practical implicationsThe quality of Mendoza’s Malbec depends more on the winery of origin than the year-to-year weather variations. Therefore, consumers should focus more on the winery and less on the vintage when making purchasing decisions. Additionally, given the relevance of the winery in relation to quality, the findings of this study indicate that future research efforts should focus on directly linking the wine ratings to quality-drivers behind the winery effects.Originality/valueTo the best of the authors’ knowledge, this is the first study that explores the relationship between wine quality assessed through wine ratings and the weather in the Mendoza (Argentina) region. Most such studies have been done in connection with northern hemisphere wines.
No big deal: how leader self-deprecating humor influences subordinate learning from failure
Authors: Wang Xi , Yang Fu , Liu Songbo , Feng Wen 
Published: May 2023

Purpose
Based on social information processing theory, this paper aims to explore how and when leader self-deprecating humor may spark subordinate learning from failure. The authors cast perspective taking as a novel explanatory mechanism for this indirect effect, and further consider leader–member exchange as a boundary condition of the relationship.

Design/methodology/approach
The authors tested the hypotheses by conducting a multiwave and multisource survey of 604 members from 152 teams in a Chinese high-technology company.

Findings
Results of multilevel path analyses demonstrate that leader self-deprecating humor positively influences subordinate learning from failure via perspective taking. Further, this mediation effect is stronger at higher levels of leader–member exchange.

Research limitations/implications
This study contributes to the theoretical understanding of the relationship between leader self-deprecating humor and subordinate learning from failure. However, the research design was not longitudinal or experimental, and thus the authors were unable to make strong inferences about absolute causality.

Practical implications
The work yields useful insights for practitioners aiming to encourage subordinates to learn from failure.

Originality/value
This study provides evidence that leader self-deprecating humor can stimulate subordinate learning from failure via perspective taking, and the indirect effect is further strengthened by leader–member exchange. The findings offer new directions for research on leader self-deprecating humor and learning from failure.