bluuebunny/crossref_metadata_2025_split huggingface dataset:
An expanded genetic toolkit for inducible expression and targeted gene silencing inRickettsia parkeri
Authors: McGinn Jon , Wen Annie , Edwards Desmond L. , Brinkley David M. , Lamason Rebecca L. 
Published: March 2024

ABSTRACTPathogenic species within theRickettsiagenus are transmitted to humans through arthropod vectors and cause a spectrum of diseases ranging from mild to life-threatening. Despite rickettsiae posing an emerging global health risk, the genetic requirements of their infectious life cycles remain poorly understood. A major hurdle toward building this understanding has been the lack of efficient tools for genetic manipulation, owing to the technical difficulties associated with their obligate intracellular nature. To this end, we implemented the Tet-On system to enable conditional gene expression inRickettsia parkeri. Using Tet-On, we show inducible expression of antibiotic resistance and a fluorescent reporter. We further used this inducible promoter to screen the ability ofR. parkerito express four variants of the catalytically dead Cas9 (dCas9). We demonstrate that all four dCas9 variants can be expressed inR. parkeriand used for CRISPR interference (CRISPRi)-mediated targeted gene knockdown. We show targeted knockdown of an antibiotic resistance gene as well as the endogenous virulence factorsca2. Altogether, we have developed systems for inducible gene expression and CRISPRi-mediated gene knockdown for the first time in rickettsiae, laying the groundwork for more scalable, targeted mechanistic investigations into their infectious life cycles.IMPORTANCEThe spotted fever group ofRickettsiacontains vector-borne pathogenic bacteria that are neglected and emerging threats to public health. Due to the obligate intracellular nature of rickettsiae, the development of tools for genetic manipulation has been stunted, and the molecular and genetic underpinnings of their infectious lifecycle remain poorly understood. Here, we expand the genetic toolkit by introducing systems for conditional gene expression and CRISPRi-mediated gene knockdown. These systems allow for relatively easy manipulation of rickettsial gene expression. We demonstrate the effectiveness of these tools by disrupting the intracellular life cycle using CRISPRi to deplete thesca2virulence factor. These tools will be crucial for building a more comprehensive and detailed understanding of rickettsial biology and pathogenesis.
Phase separation of polyubiquitinated proteins in UBQLN2 condensates controls substrate fate
Authors: Valentino Isabella M. , Llivicota-Guaman Jeniffer G. , Dao Thuy P. , Mulvey Erin O. , Lehman Andrew M. , Galagedera Sarasi K. K. , Mallon Erica L. , Castañeda Carlos A. , Kraut Daniel A. 
Published: March 2024

AbstractUbiquitination is one of the most common post-translational modifications in eukaryotic cells. Depending on the architecture of polyubiquitin chains, substrate proteins can meet different cellular fates, but our understanding of how chain linkage controls protein fate remains limited. UBL-UBA shuttle proteins, such as UBQLN2, bind to ubiquitinated proteins and to the proteasome or other protein quality control machinery elements and play a role in substrate fate determination. Under physiological conditions, UBQLN2 forms biomolecular condensates through phase separation, a physicochemical phenomenon in which multivalent interactions drive the formation of a macromolecule-rich dense phase. Ubiquitin and polyubiquitin chains modulate UBQLN2’s phase separation in a linkage-dependent manner, suggesting a possible link to substrate fate determination, but polyubiquitinated substrates have not been examined directly. Using sedimentation assays and microscopy we show that polyubiquitinated substrates induce UBQLN2 phase separation and incorporate into the resulting condensates. This substrate effect is strongest with K63-linked substrates, intermediate with mixed-linkage substrates, and weakest with K48-linked substrates. Proteasomes can be recruited to these condensates, but proteasome activity towards K63-linked and mixed linkage substrates is inhibited in condensates. Substrates are also protected from deubiquitinases by UBQLN2-induced phase separation. Our results suggest that phase separation could regulate the fate of ubiquitinated substrates in a chain-linkage dependent manner, thus serving as an interpreter of the ubiquitin code.SignificanceCovalent attachment of polyubiquitin chains to eukaryotic proteins is a common protein quality control signal. Ubiquitination often marks proteins for degradation by the proteasome, but can also drive non-degradative outcomes. Proteins, including UBQLN2, that bind both polyubiquitin and the proteasome can either enhance or inhibit degradation. The ALS-related UBQLN2 is recruited to membraneless organelles, including stress granules, and undergoes phase separationin vitro, but the effects of phase separation on substrate fate are unknown. Herein we show that UBQLN2 phase separation is modulated by polyubiquitinated substrates in a linkage-dependent fashion. We show that two functional outcomes, degradation and deubiquitination, are differentially affected by phase separation. Our results suggest that phase separation of substrates and UBQLN2 could control protein fates.
Advancing microbial isolation: The impact of leaf mold extract agar on soil samples
Authors: Miyashita Atsushi , Mikami Kazuhiro , Ishii Masaki , Miyauchi Masanobu , Tabuchi Fumiaki 
Published: March 2024

AbstractIn this study, we developed a new agar medium using leaf mold extract and evaluated its microbial cultivation performance with soil samples. As a control for performance evaluation, the general-purpose nutrient medium YME agar was used. For YME agar, isolated microbes were confirmed to belong mainly to theBacillusgenus through 16S rRNA gene sequencing. In contrast, for the leaf mold agar, bacteria belonging to eitherStreptomycesorRhizobiumwere frequently isolated. Also, of the 51 sequenced isolates on the leaf mold agar medium, an unidentified species (i.e., not listed in databases) with 16S rRNA sequence identity below 98.7% was found. The unidentified species did not grow in standard nutrient media (YME, BHI, LB10, or TSB) but grew in 10% leaf mold extract. The findings of this study suggest that the use of leaf mold agar medium can effectively isolate soil microbes that are difficult to culture in general-purpose nutrient media such as YME. Moreover, this approach indicates a viable method for discovering unknown, previously-uncultured microbial species from soil samples.
Solvation Free Energy in Governing Equations for DNA Hybridization, Protein–Ligand Binding, and Protein Folding
Authors: Harmon Caroline , Bui Austin , Espejo Jasmin M. , Gancayco Marc , Le Jennifer M. , Rangel Juan , Eggers Daryl K. 
Published: March 2024

ABSTRACTThis work examines the thermodynamics of model biomolecular interactions using a governing equation that accounts for the participation of bulk water in the balanced reaction. In the first example, the binding affinities of two model DNA duplexes, one of nine and one of ten base pairs in length, are measured and characterized by isothermal titration calorimetry as a function of concentration. The results indicate that the change in solvation free energy that accompanies duplex formation (ΔGS) is large and unfavorable. When normalized to the number of base pairs, the duplex with the larger number of G:C pairings yields the largest change in solvation free energy, ΔGS= +460 kcal/mol/base pair at 25 °C. A modelling study demonstrates how the solvation free energy alters the output of a typical titration experiment. Hybridization measurements are completed at four different temperatures, however a van’t Hoff analysis of the data is complicated by the varying degree of intramolecular base stacking within each DNA strand as a function of temperature. The same thermodynamic framework is applied to a model protein– ligand interaction, the binding of ribonuclease A with the nucleotide inhibitor 3’-UMP, and to a conformational equilibrium, the change in tertiary structure of α-lactalbumin in molar guanidinium chloride solutions. The ribonuclease study yields a value of ΔGS= +160 kcal/mol, whereas the folding equilibrium yields ΔGS≈ 0, an apparent characteristic of hydrophobic interactions. These examples complement previous applications of the governing equation to the interaction of smaller molecules and demonstrate the importance of solvation energy in biothermodynamics.
Repatterning of mammalian backbone regionalization in cetaceans
Authors: Gillet Amandine , Jones Katrina E. , Pierce Stephanie E. 
Published: March 2024

AbstractThe reinvasion of the aquatic realm by cetaceans is one of the most iconic ecological transitions that led to drastic modifications of the mammalian body plan, especially the axial skeleton. Relative to the vertebral column of other mammals that is subdivided into numerous anatomical regions, regional boundaries of the cetacean backbone appear obscured. Whether the traditional mammalian regions are present in cetaceans but hard to detect due to anatomical homogenization or if regions have been entirely repatterned remains unresolved. Here we combine a segmented linear regression approach with spectral clustering to quantitatively investigate the number, position, and homology of vertebral regions across species from all major cetacean clades. We propose the new “Nested Regions” hypothesis under which the cetacean backbone is composed of six homologous modules subdivided into six to nine post-cervical regions, with the degree of regionalization dependent on vertebral count and ecology. Compared to terrestrial mammals, the cetacean backbone is less regionalized in the precaudal segment but more regionalized in the caudal segment, indicating repatterning of the vertebral column associated with the transition from limb-powered to axial-driven locomotion.
Biochemical analysis of the endoribonuclease activity of the human mitochondrial topoisomerase 1
Authors: Bader Cyrielle P. J. , Kasho Erika , Forslund Josefin M. E. , Wessels Malgorzata , Wanrooij Paulina H. 
Published: March 2024

AbstractThe incorporation of ribonucleotides (rNMPs) into the nuclear genome leads to severe genomic instability, including strand breaks and short 2-5 bp deletions at repetitive sequences. Curiously, the detrimental effects of rNMPs are not observed for the human mitochondrial genome (mtDNA) that typically contains several rNMPs per molecule. Given that the nuclear genome instability phenotype is dependent on the activity of the nuclear topoisomerase 1 enzyme (hTop1), and mammalian mitochondria contain a distinct topoisomerase 1 paralog (hTop1mt), we hypothesized that the differential effects of rNMPs on the two genomes may reflect differing properties of the two cellular topoisomerase 1 enzymes. Here, we characterized the endoribonuclease activity of hTop1mt and found it to be less efficient than that of its nuclear counterpart, a finding that was partly explained by its substrate binding properties. While hTop1 and yeast Top1 showed higher affinity for an rNMP-containing substrate and were able to cleave at an rNMP located outside of the consensus cleavage site, hTop1mt showed no preference for rNMPs. As a consequence, hTop1mt was inefficient at producing the short rNMP-dependent deletions that are characteristic of Top1-driven genome instability. These findings help explain the tolerance of rNMPs in the mitochondrial genome.
Consumer xenocentrism when domestic products are better
Authors: Thoumrungroje Amonrat , Diamantopoulos Adamantios , Scherer Nathalie Caroline 
Published: March 2024

PurposeDrawing on cue utilization theory and the theory of motivated reasoning, we investigate the impact of consumer xenocentrism on product preferences in a situation where domestic products objectively outperform their foreign counterparts.Design/methodology/approachWe develop and test a model linking xenocentrism to consumers’ preference towards domestic vs. foreign products by (1) examining the mediating role of consumers’ ability to identify the superior product and (2) assessing the role of product involvement in potentially moderating this relationship. An experimental design was employed, whereby respondents (Thai consumers, N = 579) were asked to compare two products in the same product category, one foreign and one domestic. In one condition, the foreign product outperformed the domestic one on a range of relevant product attributes, whereas in a second condition, the opposite was the case.FindingsOur findings provide clear evidence that xenocentric consumers often cannot recognize the superiority of domestic products and, even if they do, they still exhibit preferences toward (inferior) foreign products. Thus, for xenocentric consumers, it seems that the country of origin (COO) overrides other cues and often results in suboptimal product choices.Originality/valueOur study adds to our theoretical understanding of the functioning of the consumer xenocentrism construct and has important implications for foreign companies targeting xenocentric consumers as well as for local firms seeking to counteract xenocentric tendencies.
Real Estate Insights AI: real estate’s new roommate – the good, the bad and the algorithmic
Authors: Szumilo Nikodem , Wiegelmann Thomas 
Published: March 2024

PurposeThis paper aims to provide a comprehensive analysis of the transformative impact of Artificial Intelligence (AI) and Large Language Models (LLMs), such as GPT-4, on the real estate industry. It explores how these technologies are reshaping various aspects of the sector, from market analysis and valuation to customer interactions and evaluates the balance between technological efficiency and the preservation of human elements in business.Design/methodology/approachThe study is based on an analysis of the strengths and weaknesses of AI as a technology in applications for real estate. It uses this framework to assess the potential of this technology in different use cases. This is supplemented by an emerging literature on the topic, practical insights and industry expert opinions to provide a balanced perspective on the subject.FindingsThe paper reveals that AI and LLMs offer significant benefits in real estate, including enhanced data-driven decision-making, predictive analytics and operational efficiency. However, it also uncovers critical challenges, such as potential biases in AI algorithms and the risk of depersonalising customer interactions.Practical implicationsThe paper advocates for a balanced approach to adopting AI, emphasising the importance of understanding its strengths and limitations while ensuring ethical usage in the diverse and complex landscape of real estate.Originality/valueThis work stands out for its balanced examination of both the advantages and limitations of AI in real estate. It introduces the novel concept of the “jagged technological frontier” in real estate, providing a unique framework for understanding the interplay between AI and human expertise in the industry.
Conclusion: what should be the role of tourism education social structures to create and support collaborative learning environments and the tourism sector?
Authors: Guden Nafiya , Safaeimanesh Farzad 
Published: March 2024

PurposeThis theme issue sought to find answers to the question: What should be the role of tourism education social structures to create and support collaborative learning environments and the tourism sector?Design/methodology/approachA thematic analysis of the articles in this collection draws together the key outcomes related to the strategic question, with particular reference to the contribution to knowledge, important to generate ideas and conceptual researches that will support institutions teaching tourism and hospitality. Archive research results and recommendations to encourage the collaboration of different stakeholders involved in sustainable tourism development. Most importantly to raise awareness of the question of what educators are doing in tourism education for social, organizational structures in learning environments and the actual tourism sector.FindingsTwo key players, the educator and sector has been challenged to consider their roles in education as well as depicting the role of social and organizational structures that support the students, institutions and the tourism sector. The main findings have proven the important role education plays for a truly sustainable tourism model, suggesting that it is not possible to create awareness of the sustainable development goals without incorporating them in the tourism education system with the support of information computer technology.Originality/valueThis paper reflects on the strategic question discussed in this theme issue, and it contains valid reviews, research studies by practitioners who are experienced in the field of tourism education with an opportunity to research, reflect and develop new possibilities in learning, mitigate negative points and increase positive tourism education roles for sustainable tourism development, in the destination and industry.
Soil microbial gene abundance rather than diversity and network complexity predominantly determines soil multifunctionality in Tibetan alpine grasslands along a precipitation gradient
Authors: Pan Junxiao , Li Yang , Zhang Ruiyang , Tian Dashuan , Wang Peiyan , Song Lei , Quan Quan , Chen Chen , Niu Shuli , Zhang Xinyu , Wang Jinsong 
Published: March 2024

Abstract

The relationship between biodiversity and ecosystem functioning has mainly focused on plant communities, with comparably little known about soil microbial‐driven ecosystem functions. Climate change severely threatens soil microbial roles, but how soil microbial communities determine soil multifunctionality under climate change is poorly understood.

Here, we evaluated the effects of diverse bacterial and fungal properties, including microbial gene abundance, diversity and network complexity, on soil multifunctionality (nine soil functions) across a 3000 km transect along a natural precipitation gradient in Tibetan alpine grasslands. Variation partitioning analyses were performed to disentangle the relative importance of bacterial and fungal properties to the variation of soil multifunctionality. Moreover, structural equation modelling was adopted to explore the influencing pathways of precipitation‐induced changes in plant and edaphic factors to soil microbial properties and, consequently, soil multifunctionality.

Soil multifunctionality was positively associated with bacterial and fungal gene abundance, diversity and network complexity. Microbial gene abundance was the more important driver influencing soil multifunctionality than microbial diversity and network complexity. In addition, microbial gene abundance was mainly determined by precipitation‐induced changes in soil pH. Meanwhile, the effects of bacterial properties on soil multifunctionality were much larger than those of fungi. Soil multifunctionality was closely associated with different bacterial (cellulolysis, ligninolysis, nitrogen reduction, denitrification and nitrate fixation etc.) and fungal (soil saprotrophs, arbuscular mycorrhizal and plant pathogens etc.) functional guilds, which exert vital regulations on an array of soil biogeochemical cycling processes.

Our results provide the large‐scale evidence of the relative contribution of soil microbial gene abundance, diversity and network complexity to the variation of soil multifunctionality in alpine grasslands with changing precipitation, which is pivotal for understanding microbial roles in modulating and predicting soil multifunctionality under future precipitation changes.

Read the free Plain Language Summary for this article on the Journal blog.
How are the impacts of multiple anthropogenic drivers considered in marine ecosystem service research? A systematic literature review
Authors: Solé Figueras Liliana , Zandt Emma I. , Buschbaum Christian , Meunier Cédric Léo 
Published: March 2024

Abstract

In recent decades, great research efforts have been made to understand how specific anthropogenic drivers impact coastal marine ecosystems and their services. Nevertheless, we still lack a synthesis of the existing knowledge on single and multiple anthropogenic drivers impacts to coastal marine systems, which is necessary to guide future work.

The objective of this paper is to assess the current knowledge on the impacts of anthropogenic drivers and their interactions on coastal marine ecosystem services, with emphasis on abiotic drivers as dissolved nutrients (eutrophication or de‐eutrophication), temperature (warming), pH (acidification) and oxygen (hypoxia). We performed a systematic review of the literature consisting of 164 papers using the PRISMA method (Preferred Reporting Items for Systematic Reviews and Meta‐Analyses). We only include English‐written papers, we exclude non‐English papers to avoid potential errors in representing or interpreting scientific information due to language limitations among the authors.

The results show that coastal marine ecosystem service research has largely focused on single drivers, while multiple driver assessments are less common.

Assessments partially integrate multiple driver complexity, but they do not consider (1) relations and feedbacks between drivers; 2() social processes dynamics; and (3) temporal and spatial scales.

Synthesis and applications. We have reviewed the current scientific knowledge on how human drivers affect coastal marine ecosystem services. We found that understanding the combined effects of different drivers and considering various time and space scales is still a pending issue. Ignoring multiple drivers, their interactions and time and space scales limits our understanding of reality, and results in high levels of uncertainty. This affects policies and actions, as they rely on uncertain information. Thus, incomplete knowledge leads to poor management of coastal ecosystem services. To improve this, we propose research framework to better consider multiple drivers and time and space factors.