bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogenic CD8 T cell responses are driven by neutrophil-mediated hypoxia in cutaneous leishmaniasis
Authors: Fowler Erin A. , Amorim Camila Farias , Mostacada Klauss , Yan Allison , Sacramento Laís Amorim , Stanco Rae A. , Hales Emily D. S. , Varkey Aditi , Zong Wenjing , Wu Gary D. , de Oliveira Camila I. , Collins Patrick L. , Novais Fernanda O. 
Published: October 2023

AbstractCutaneous leishmaniasis caused byLeishmaniaparasites exhibits a wide range of clinical manifestations. Although parasites influence disease severity, cytolytic CD8 T cell responses mediate disease. While these responses originate in the lymph node, we find that expression of the cytolytic effector molecule granzyme B is restricted to lesional CD8 T cells inLeishmania- infected mice, suggesting that local cues within inflamed skin induce cytolytic function. Expression of Blimp-1 (Prdm1), a transcription factor necessary for cytolytic CD8 T cell differentiation, is driven by hypoxia within the inflamed skin. Hypoxia is further enhanced by the recruitment of neutrophils that consume oxygen to produce reactive oxygen species, ultimately increasing granzyme B expression in CD8 T cells. Importantly, lesions from cutaneous leishmaniasis patients exhibit hypoxia transcription signatures that correlate with the presence of neutrophils. Thus, targeting hypoxia-driven signals that support local differentiation of cytolytic CD8 T cells may improve the prognosis for patients with cutaneous leishmaniasis, as well as other inflammatory skin diseases where cytolytic CD8 T cells contribute to pathogenesis.
AGAMOUS-like 6andMYB DOMAIN PROTEIN 80regulate the development of female and male cones inPinus densifloraS. et Z
Authors: Lee Dayoung , Kim Yang-Gil , Kang Kyu-Suk 
Published: October 2023

AbstractTo shorten the long breeding period of forest trees, it is necessary to explore biological factors and key genes involved in reproduction. We compared the transcriptomes of female and male cones and then identified major biological processes and hub genes associated with the development of female and male cones inPinus densiflora. The reproductive and vegetative tissues ofP. densiflorawere sampled from various developmental stages and a reference transcriptome was generated. Functional annotation and Gene Ontology enrichment analysis of differentially expressed genes were performed as well as gene co-expression network analysis for identifying the hub genes involved in the cone development. Lignin biosynthesis and cell wall loosening were activated in the early and late female cones, respectively. Metabolism of pollen wall components was predominant in the early male cones compared with the later stage. In addition, phytohormone-related genes were highly expressed in the early female cones in contrast to the early male cones. Finally, we found thatAGAMOUS-like 6andMYB DOMAIN PROTEIN 80were hub genes of the female and male cone development, respectively. This study suggests that various biological factors contribute to reproductive developmental processes. Furthermore, these data will provide the new insight into biotechnology and breeding methods for improving cone and seed production ofP. densiflora.
Functional specialization of cytochromeb5prior to the invention of syringyl lignin biosynthesis
Authors: Zhao Xianhai , Zhao Yunjun , Zeng Qing-yin , Liu Chang-Jun 
Published: October 2023

AbstractThe production of lignin represents a hallmark of vascular plant evolution. But syringyl-lignin production is lineage specific. Its emergence in angiosperms has been regarded as a recent evolution event, as is the appearance of syringyl monomer biosynthetic F5H (CYP84A1). Angiosperm F5H uniquely requires cytochromeb5protein CB5D as an obligatory redox partner. However, it remains unclear how CB5D functionally evolved and specialized and whether it co-evolved with F5H. Here we show that plant CB5 family expanded and functionally specialized at the early stage of plant terrestrialization. CB5D was absent in green algae but emerged in bryophytes and conserved in most embryophytes, particularly proliferating in angiosperms. The innovation of CB5D is attributed to the evolution and maintenance of acidic amino residues in the helix 5 of CB5 protein. Interestingly, the syringyl-lignin producing lycophyteSelaginellalacks the functionally specialized CB5D. TheSelaginellaF5H (CYP788A1) solely relies on cytochrome P450 reductase as a redox partner. These results suggest that CB5 functionally diversified and specialized prior to the divergence of land plant lineages but lost inSelaginella; and the recently evolved angiosperm F5H has co-opted the anciently invented CB5D to form a modern cytochrome P450 monooxygenase system enabling the re-emergence of syringyl-lignin biosynthesis in higher plants.One Sentence SummaryCytochromeb5D, an indispensable electron donor for F5H-catalyzed S-lignin biosynthesis, was invented prior to the divergence of land plant lineages, earlier than the emergence of vascular plant F5Hs.
Minimized dark cataplerosis of the Calvin cycle ensures prompt photosynthetic initiation in cyanobacteria
Authors: Tanaka Kenya , Kondo Akihiko , Hasunuma Tomohisa 
Published: October 2023

AbstractAs primary contributors to oxygenic photosynthesis, cyanobacteria intricately regulate their metabolic pathways during the diurnal cycle to ensure survival and growth. Under dark conditions, breakdown of stored energy reserves of glycogen replenishes the intermediates, especially the downstream glycolytic metabolites necessary for photosynthetic initiation upon light irradiation. The intracellular level of the intermediates is maintained throughout the dark period. However, it remains unclear how their accumulation is maintained in the dark despite the limited availability of glycogen. Here, we showed that the metabolite accumulation stability is ensured by the low activities of phosphoenolpyruvate (PEP) converting enzymes, namely PEP carboxylase and pyruvate kinase, during the dark period. Overexpression of these enzymes significantly decreased the accumulation of glycolytic intermediates after dark incubation. The oxygen evolution ability simultaneously decreased in the overexpressing strains, indicating that the dark limitation of the PEP-consuming pathway facilitates photosynthetic initiation through the maintenance of glycolytic intermediates. This finding shed light on the importance of controlling cataplerotic flux during the dark for maintaining stable operation of the Calvin cycle.
Fine needle aspiration of human lymph nodes reveals cell populations and soluble interactors pivotal to immunological priming
Authors: Provine Nicholas M. , Al-Diwani Adam , Agarwal Devika , Dooley Kyla , Heslington Amelia , Murchison Andrew G. , Garner Lucy C. , Sheerin Fintan , Klenerman Paul , Irani Sarosh R. 
Published: October 2023

ABSTRACTLymph node (LN) fine needle aspiration (LN FNA) represents a powerful technique for minimally invasive sampling of human lymph nodesin vivoand has been used to good effect to directly study aspects of the human germinal center response. However, systematic deep phenotyping of the cellular populations and cell-free proteins recovered by LN FNA has not been performed. Thus, we studied human cervical LN FNAs as a proof-of-concept and used single-cell RNA-sequencing and proteomic analysis to benchmark this compartment, define the purity of LN FNA material, and facilitate future studies into this immunologically pivotal environment. Our data provide evidence that LN FNAs containbone fideLN-resident innate immune populations, with minimal contamination of cells or proteins from blood. Examination of these populations reveals unique biology not predictable from equivalent blood-derived populations. LN FNA supernatants represent a specific source of lymph- and lymph node-derived proteins, and can, in combination with transcriptomic approaches, identify likely receptor-ligand interactions. This study provides the first description of the types and abundance of immune cell populations and cell-free proteins that can be efficiently studied by LN FNA. These findings are of broad utility for understanding LN physiology both in health and disease, including infectious or autoimmune perturbations, and in the case of cervical nodes, neuroscience.
Trophic Efficiency Facilitates Larval Shortbelly Rockfish (Sebastes jordani) Development
Authors: Kwan Garfield T. , Walsh Kamran A. , Thompson Andrew R. , Ben-Aderet Noah J. , Fennie H. William , Semmens Brice X. , Swalethorp Rasmus 
Published: October 2023

AbstractIdentifying the factors influencing fish recruitment is critical for fishery management, and failure to do so can have major ecological and economic consequences. Many hypotheses over the past century have been proposed, and the recently postulated Trophic Efficiency in Early Life (TEEL) hypothesis argues that a shorter food chain length can result in more efficient energy transfer from primary producers to young fishes, thereby increasing growth rate and larval condition, reducing early-life mortality and ultimately leading to a stronger recruitment cohort. To test this hypothesis, we analyzed the trophic position (TP) through compound-specific isotopic analysis of amino acids, as well as otolith microstructure and stomach content of larval shortbelly rockfish (Sebastes jordani). Results show larval rockfish that ate lower TP prey were both heavier and faster growing. This suggests the trophic characteristics of early life diet are critical to larval survival, and provide evidence in support of the TEEL hypothesis.
Conversion of aromatic compounds from fractionated industrial hydrolysis lignin byPseudomonas putidaand environmental microbial strains
Authors: Morehead Philip A. , Vider Henry , Mürk Christina , Viggor Signe , Jõesaar Merike , Bottoms Scott , Salmar Siim , Kivisaar Maia , Loog Mart 
Published: October 2023

AbstractBackgroundThe utilization ofPseudomonas putidawas explored in this study as a promising approach for lignin valorization. To this end, dry hydrolysis lignin was used as a feedstock for the first time. Hydrolysis lignin is a product of the enzymatic hydrolysis and separation of cellulose and hemicellulose from the lignin backbone in diverse lignocellulosic sources. Various fractionation techniques were applied to obtain lignin monomers and multimers in solution for use as a growth medium forP. putida, whose tolerance of inhibitory phenolic compounds distinguishes it from most bacteria.ResultsPhysiological evaluations revealed thatPseudomonas putidastrains KT2440 and PaW85 exhibited broad pH tolerance ranges, with robust growth observed at elevated pH levels. Batch fermentations using hydrolysis lignin (HL) solutions showed complete consumption of sugars within 24 hours, demonstrating the viability of fractionated HL as a substrate forP. putidacultivation. HPLC analysis of HL monomer concentrations during simulated fed-batch fermentation revealed rapid catabolism of catechol and increased CCMA concentration, followed by stabilization, indicating that CCMA is synthesized more quickly than degraded when the initial catechol concentration is high. Filtered alkaline HL fractionations yielded more than twice as much catechol as unfiltered fractionations. Screening of indigenous bacterial strains isolated from various soil and water samples (CELMS Collection, websitehttp://eemb.ut.ee) identified five new candidate strains for CCMA production, two for PCA production, and three for vanillic acid production.ConclusionsThe novel use of fractionated hydrolysis lignin as a growth medium shows potential for lignin valorization and chemical production. Filtered alkaline fractionation yields more catechol and is superior forcis,cis-muconic acid production; however, unfiltered fractionations may be more suitable for other compounds and upscaling. Further investigation of screened strains could reveal more efficient enzymes, which could be optimized and transformed intoP. putidain future research.
3DVascNet: an automated software for segmentation and quantification of vascular networks in 3D
Authors: Narotamo Hemaxi , Silveira Margarida , Franco Cláudio A. 
Published: October 2023

AbstractBackgroundAnalysis of vascular networks is an essential step to unravel the mechanisms regulating the physiological and pathological organization of blood vessels. So far, most of the analyses are performed using 2D projections of 3D networks, a strategy that has several obvious shortcomings. For instance, it does not capture the true geometry of the vasculature, and generates artifacts on vessel connectivity. These limitations are accepted in the field because manual analysis of 3D vascular networks is a laborious and complex process that is often prohibitive for large volumes.MethodsTo overcome these issues, we developed 3DVascNet, a deep learning (DL) based software for automated segmentation and quantification of 3D retinal vascular networks. 3DVascNet performs segmentation based on a DL model, and it quantifies vascular morphometric parameters such as the vessel density, branch length, vessel radius, and branching point density.ResultsWe tested 3DVascNet’s performance using a large dataset of 3D microscopy images of mouse retinal blood vessels. We demonstrated that 3DVascNet efficiently segments vascular networks in 3D, and that vascular morphometric parameters capture phenotypes detected by using manual segmentation and quantification in 2D. In addition, we showed that, despite being trained on retinal images, 3DVascNet has high generalization capability and successfully segments images originating from other datasets and organs. More-over, the source code of 3DVascNet is publicly available, thus it can be easily extended for the analysis of other 3D vascular networks by other users.ConclusionsOverall, we present 3DVascNet, a freely-available software that includes a user-friendly graphical interface for researchers with no program-ming experience, which will greatly facilitate the ability to study vascular networks in 3D in health and disease.
The function of CozE proteins is linked to lipoteichoic acid biosynthesis inStaphylococcus aureus
Authors: Barbuti Maria Disen , Lambert Elisabeth , Myrbråten Ine Storaker , Ducret Adrien , Stamsås Gro Anita , Wilhelm Linus , Liu Xue , Salehian Zhian , Veening Jan-Willem , Straume Daniel , Grangeasse Christophe , Perez Camilo , Kjos Morten 
Published: October 2023

AbstractTo maintain cell integrity and facilitate cell division inStaphylococcus aureus, a well-coordinated interplay between membrane biogenesis, peptidoglycan formation, and teichoic acid synthesis is crucial. However, the molecular mechanisms and regulatory pathways that underpin their coordination are still poorly understood. CozE constitute a conserved family of membrane proteins implicated in cell division via regulation of penicillin binding proteins. It has been shown that the two staphylococcalcozEgenes (cozEaandcozEb) constitute a synthetic lethal gene pair. Depletion of CozEa and CozEb simultaneously inS. aureusresulted in severely defective cell division phenotypes, reminiscent of cell lacking lipoteichoic acid (LTA). Indeed, we demonstrate that there is an intricate interplay between CozE, biosynthesis of LTA, and membrane homeostasis inS. aureus. By screening for potential genetic links, we establish that there is synthetic lethal relationship between CozE and UgtP, the enzyme synthesizing the LTA glycolipid anchor Glc2DAG. On the contrary, in cells lacking LtaA, the flippase of Glc2DAG, the essentiality of CozEa and CozEb was alleviated. Furthermore, by immunoblotting, we found that CozEb plays a unique role in controlling LTA polymer length and stability. Using reconstituted proteoliposomes, we also demonstrated that CozE proteins modulate the glycolipid flipping activity of LtaAin vitro. Together, the results demonstrate a new function of CozE proteins, facilitating proper membrane homeostasis and LTA biosynthesis inS. aureus.
Activation of innate immunity selectively compromises mitochondrial complex I, proline oxidation and flight activity in the major arbovirus vectorAedes aegypti
Authors: Gaviraghi Alessandro , Barletta Ana Beatriz F. , Alves E Silva Thiago Luiz , Oliveira Matheus P. , Sorgine Marcos H.F. , Oliveira Marcus F. 
Published: October 2023

AbstractAedes aegyptifemales are natural vectors of important arboviruses such as Dengue, Zika, and yellow fever. Mosquitoes activate innate immune response signaling pathways upon infection, as a resistance mechanism to fight pathogens and limit their propagation. Despite the beneficial effects of immune activation for insect vectors, phenotypic costs ultimately affect their fitness. However, the underlying mechanisms that mediate these fitness costs remain poorly understood. Given the high energy required to mount a proper immune response, we hypothesized that systemic activation of innate immunity would impair flight muscle mitochondrial function, compromising tissue energy demand and flight activity. Here, we investigated the dynamic effects of activation of innate immunity by intra-thoracic zymosan injection onA. aegyptiflight muscle mitochondrial metabolism. Zymosan injection significantly increased defensin expression in fat bodies in a time-dependent manner that compromised flight activity. Although oxidant levels in flight muscle were hardly altered, ATP-linked respiratory rates driven by mitochondrial pyruvate+proline oxidation were significantly reduced at 24h upon zymosan injection. Oxidative phosphorylation coupling was preserved regardless of innate immune response activation along 24h. Importantly, rotenone-sensitive respiration and complex I-III activity were specifically reduced 24h upon zymosan injection. Also, loss of complex I activity compromised ATP-linked and maximal respiratory rates mediated by mitochondrial proline oxidation. Finally, the magnitude of innate immune response activation negatively correlated with respiratory rates, regardless of the metabolic states. Collectively, we demonstrate that activation of innate immunity is strongly associated with reduced flight muscle complex I activity with direct consequences to mitochondrial proline oxidation and flight activity. Remarkably, our results indicate a trade-off between dispersal and immunity exists in an insect vector, underscoring the potential consequences of disrupted flight muscle mitochondrial energy metabolism to arbovirus transmission.
The design of retailers' online review systems – a systematic literature review and future research agenda
Authors: Pham Doan Thao Tram , Steinmann Sascha , Jensen Birger Boutrup 
Published: October 2023

PurposeIn this paper the authors aim to review the state-of-the-art literature on online review systems and their impacts on consumer behavior and retailers' performance with the aim of identifying research gaps related to different design features of review systems and developing future research agenda.Design/methodology/approachThe authors conducted a systematic review based on PRISMA 2020 protocol, focusing on studies published in the domains of retailing and marketing. This procedure resulted in 48 selected papers investigating the design features of retailer online review systems.FindingsThe authors identify eight design features that are controllable by retailers in an online review system. The design features have been researched independently in previous literature, with some features receiving more attention. Most selected studies focus on the design features adapted metrics and review presentations, while other features are generally neglected (e.g. rating dimensions). Previous literature argues that design features affect consumer behaviors and retailers' performance. However, the interactions among the features are still neglected in the literature, creating a relevant gap for future research.Originality/valueThis paper distinguishes between different types of retailer online review systems based on how they are implemented. The authors summarize the state-of-the-art of relevant literature on design features of online review systems and their effects on consumer- and retailer-related outcome variables. This systematic literature review distinguishes between online reviews provided on websites controlled by retailers (internal systems) and third-party websites (external systems).
How does leader career calling stimulate employee career growth? The role of career crafting and supervisor–subordinate guanxi
Authors: Ni Xudong , Zhu Xingkui , Bian Wenjun , Li Jiyu , Pan Chen , Pan Chengkai 
Published: October 2023

PurposeThis paper aims to explore how leader career calling stimulates employee career growth, with the supervisor–subordinate guanxi serving as a moderating factor.Design/methodology/approachStudy 1 demonstrated that high leader career calling served as a catalyst for employee career crafting. The experiment provided causal evidence for the relationship between these two constructs, exhibiting strong internal validity. However, due to the challenges in measuring supervisor–subordinate guanxi and career growth within the context of a scenario experiment, Study 2 was designed to test the entire model and enhance the external validity of the findings.FindingsLeader career calling significantly predicts employee career growth, while employee career crafting serves as a mediating mechanism in the relationship between leader career calling and employee career growth. Moreover, supervisor–subordinate guanxi positively moderates the relationship between leader career calling and employee career crafting. Furthermore, the mediating effect of employee career crafting in the relationship between leader career calling and employee career growth is contingent upon the quality of supervisor–subordinate guanxi. This study sheds light on the role of leader career calling in employee career growth and provides insights into the mechanisms facilitating employee career growth.Originality/valueFirstly, it explores leader-to-employee career calling transmission, extending the career calling study beyond individual impacts. It emphasizes how leaders' work attitudes shape employee career growth. Secondly, it reveals career crafting as a mediator between leader career calling and employee career growth, identifying a new influence mechanism and expanding upon the primarily job crafting-focused existing literature. Lastly, it identifies supervisor–subordinate guanxi quality as a moderator in the leader career calling-employee career crafting relationship. This perspective enriches career calling research, illustrating how specific conditions stimulate career crafting.
Perceived research productivity of women in higher education: An investigation of the impact of COVID‐19
Authors: Ermiş‐Mert Aslı 
Published: October 2023

AbstractThis study focuses on the predictors of women academics' perceived research productivity during the pandemic in Türkiye, by taking the changes in paid and unpaid workload alongside the felt pressure concerning productivity into consideration. Predicting the odds to report an above the mean level of decrease in perceived research productivity, unlike expected, increased housework time and administrative workload presented no statistically significant effect. On the other hand, extended care responsibilities (including but not limited to childcare) and felt pressure concerning research performance during the pandemic strongly predicted a high level of reported decrease in research productivity. Findings highlight that institutional care support mechanisms should be among the primary concerns since the pandemic has made the already existing gender inequalities in academia more visible in terms of the challenges women face in balancing paid and unpaid work. In addition, as excess pressure felt by women academics regarding research performance is linked to a decline in reported productivity, creating a compassionate environment in academia not only in unprecedented circumstances but at all times needs to be priority.