bluuebunny/crossref_metadata_2025_split huggingface dataset:
Repurposing tRNA isodecoders for non-canonical functions via tRNA cleavage
Authors: Bhatter Nupur , Advani Vivek M. , Takenaka Yoshika , Lyons Shawn M. , Akiyama Yasutoshi , Anderson Paul J. , Ivanov Pavel 
Published: September 2024

AbstractTransfer RNAs (tRNAs) are the key adaptor molecules aiding protein synthesis. Hundreds of tRNA genes are found in the human genome but the biological significance of this genetic excess is still enigmatic. The tRNA repertoires are variable between tissues and cells as well as during development. Such variations can only be partially explained by the correlation to the physiological needs in protein production, e.g. by changes in the expression of tRNA isoacceptor sets (tRNAs charged with the same amino acid but bearing different anticodons). However, changes in the expression levels of individual isodecoders (tRNAs with the same anticodon) are less understood. Besides canonical functions in mRNA translation, tRNAs are implicated in non-canonical functions unrelated to protein synthesis. tRNAs are rich source of small non-protein coding RNAs called tRNA-derived RNAs (tDRs), which include tRNA-derived stress-induced RNAs (tiRNAs) formed in response to stress. Here, we show that tiRNAs derived from isodecoders different in a single nucleotide can also differ in their activities. Specifically, we show that isodecoder sets for tRNAHis-GTG, tRNAGly-GCCand tRNACys-GCAare cleaved by ribonucleases to yield 5’-tiRNAs showing differential activity towards mRNA reporter translation. Our data propose a model where cleavage repurposes specific tRNA isodecoders for non-canonical functions.Significance StatementThe human genome encodes hundreds of transfer RNA (tRNA) genes to decode 61 codons. The basis for such genetic redundancy is unclear but the increase in the number of tRNA genes goes in concert with the complexity of an organism. While changes in the expression of isoacceptor tRNA pools can reflect adaptation to demanding protein synthesis needs and/or codon usage, the variations in the expression of the individual tRNA isodecoders are documented but poorly understood. Such expression variations are hypothesized to contribute to non-canonical tRNA functions, yet physiological relevance remains ambiguous. We report here that specific tRNA isodecoders can be functionally repurposed through cleavage that produces tRNA-derived RNAs (tDRs). The repurposing employs nucleotide variations in isodecoders leading to the production of distinct sets of tDRs with variable bioactivities.
Two functional forms of the Meckel-Gruber syndrome protein TMEM67 generated by proteolytic cleavage by ADAMTS9 mediate Wnt signaling and ciliogenesis
Authors: Ahmed Manu , Fischer Sydney , Robert Karyn L. , Lange Karen I. , Stuck Michael W. , Best Sunayna , Johnson Colin A. , Pazour Gregory J. , Blacque Oliver E. , Nandadasa Sumeda 
Published: September 2024

ABSTRACTTMEM67mutations are the major cause of Meckel-Gruber syndrome. TMEM67 is involved in both ciliary transition zone assembly, and non-canonical Wnt signaling mediated by its extracellular domain. How TMEM67 performs these two separate functions is not known. We identify a novel cleavage motif in the extracellular domain of TMEM67 cleaved by the extracellular matrix metalloproteinase ADAMTS9. This cleavage regulates the abundance of two functional forms: A C-terminal portion which localizes to the ciliary transition zone regulating ciliogenesis, and a non- cleaved form which regulates Wnt signaling. By characterizing threeTMEM67ciliopathy patient variants within the cleavage motif utilizing mammalian cell culture andC. elegans,we show the cleavage motif is essential for cilia structure and function, highlighting its clinical significance. We generated a novel non-cleavable TMEM67 mouse model which develop severe ciliopathies phenocopyingTmem67-/-mice, but in contrast, undergo normal Wnt signaling, substantiating the existence of two functional forms of TMEM67.
Genome-Wide Mapping of RNA-Protein Associations via Sequencing
Authors: Qi Zhijie , Xue Shuanghong , Chen Junchen , Zhao Wenxin , Johnson Kara , Wen Xingzhao , Richard John Lalith Charles , Zhong Sheng 
Published: September 2024

AbstractRNA-protein interactions are crucial for regulating gene expression and cellular functions, with their dysregulation potentially impacting disease progression. Systematically mapping these interactions is resource-intensive due to the vast number of potential RNA and protein interactions. Here, we introduce PRIM-seq (Protein-RNA InteractionMapping by sequencing), a method for the concurrentde novoidentification of RNA-binding proteins (RBPs) and the elucidation of their associated RNAs. PRIM-seq works by converting each RNA-protein pair into a unique chimeric DNA sequence, which is then decoded through DNA sequencing. Applied to two human cell types, PRIM-seq generated a comprehensive human RNA-protein association network (HuRPA), consisting of more than 350,000 RNA-proteins pairs involving approximately 7,000 RNAs and 11,000 proteins. The data revealed an enrichment of previously reported RBPs and RNA-protein interactions within HuRPA. We also identified LINC00339 as a protein-associating non-coding RNA and PHGDH as an RNA-associating protein. Notably, PHGDH interacts with BECN1 and ATF4 mRNAs, suppressing their protein expression and consequently inhibiting autophagy, apoptosis, and neurite outgrowth while promoting cell proliferation. PRIM-seq offers a powerful tool for discovering RBPs and RNA-protein associations, contributing to more comprehensive functional genome annotations.
RCC1 depletion drives protein transport defects and rupture in micronuclei
Authors: Zych Molly G , Contreras Maya , Vashisth Manasvita , Mammel Anna E , Ha Gavin , Hatch Emily M 
Published: September 2024

AbstractMicronuclei (MN) are a commonly used marker of chromosome instability that form when missegregated chromatin recruits its own nuclear envelope (NE) after mitosis. MN frequently rupture, which results in genome instability, upregulation of metastatic genes, and increased immune signaling. MN rupture is linked to NE defects, but the cause of these defects is poorly understood. Previous work from our lab found that chromosome identity correlates with rupture timing for small MN,i.e.MN containing a short chromosome, with more euchromatic chromosomes forming more stable MN with fewer nuclear lamina gaps. Here we demonstrate that histone methylation promotes rupture and nuclear lamina defects in small MN. This correlates with increased MN size, and we go on to find that all MN have a constitutive nuclear export defect that drives MN growth and nuclear lamina gap expansion, making the MN susceptible to rupture. We demonstrate that these export defects arise from decreased RCC1 levels in MN and that additional loss of RCC1 caused by low histone methylation in small euchromatic MN results in additional import defects that suppress nuclear lamina gaps and MN rupture. Through analysis of mutational signatures associated with early and late rupturing chromosomes in the Pan-Cancer Analysis of Whole Genomes (PCAWG) dataset, we identify an enrichment of APOBEC and DNA polymerase E hypermutation signatures in chromothripsis events on early and mid rupturing chromosomes, respectively, suggesting that MN rupture timing could determine the landscape of structural variation in chromothripsis. Our study defines a new model of MN rupture where increased MN growth, caused by defects in protein export, drives gaps in nuclear lamina organization that make the MN susceptible to membrane rupture with long-lasting effects on genome architecture.
Observation of the protein-inorganic interface of ferritin by cryo-electron microscopy
Authors: Sen Sagnik , Thaker Amar , Williams Dewight , Chiu Po-Lin , Nannenga Brent L. 
Published: September 2024

AbstractVisualizing the structure of the protein-inorganic interface is critically important for our more complete understanding of biomineralization. Unfortunately, there are limited approaches for the direct and detailed study of biomolecules that interact with inorganic materials. Here we use single particle cryo-EM to study the protein-nanoparticle interactions of human light chain ferritin and visualize the high-resolution details of the protein-inorganic interface. In this work, we determined the 2.85 Å structure of human light chain ferritin bound to its native iron oxide nanoparticle substrate. The resulting cryo-EM maps confirmed and enhanced previously proposed interactions of the protein with the material along the B-helix, and revealed new interaction at the C-terminus of light chain ferritin. This work sheds new light on the mechanisms of ferritin biomineralization and further demonstrates the application of cryo-EM for the study of protein-inorganic systems.
Psoriasis-like inflammation induces mitochondrial function and structure changes in human keratinocytes and fibroblasts
Authors: Kulkovienė Gabrielė , Uldukytė Martyna , Haluts Sofiya , Kairytė Milda , Šoliūnas Jonas , Šalčiūtė Viktorija , Morkūnienė Ramunė , Jekabsone Aistė 
Published: September 2024

AbstractMitochondrial structural and functional changes accompany psoriasis; however, the mitochondrial response to psoriatic inflammation in keratinocytes and fibroblasts has not been studied. Here, we investigate the effect of psoriasis-like inflammation (PLI) induced by cytokine cocktail (IL-17, IL-22, TNF-α) on mitochondrial network morphology and function in living cultured keratinocytes (HaCaT) and fibroblasts (BJ-5ta). In both skin cell types, PLI triggered expression of psoriasis-related SKALP/Elafin and high amounts of cytokines (IL-1, IL-6), interferons (IFN-α, IFN-β, IFN-γ), and chemokines (CCL5, CXCL8), accompanied by mitochondrial ROS production, network fragmentation, swelling, and cristae disassembly. STED nanoscopy revealed that the mitochondrial cristae are disappearing in response to PLI, with the process starting faster and being more pronounced in keratinocytes than in fibroblasts. Moreover, in keratinocytes, PLI leads to mitochondrial respiration suppression and elimination of the organelles. These findings of cell-specific mitochondrial responses may guide future investigations into new pharmacological targets for managing psoriasis.Abstract Figure
Dynamics of recombination, X inactivation and centromere proteins during stick insect spermatogenesis
Authors: Dumas Zoé , Toubiana William , Delattre Marie , Schwander Tanja 
Published: September 2024

ABSTRACTIn eukaryotes, the cellular processes contributing to gamete formation form the building blocks of genetic inheritance across generations. While traditionally viewed as conserved across model organisms, emerging studies reveal significant variation among eukaryotes in meiotic and post-meiotic processes. Extending our knowledge to non-model organisms is therefore critical to improve our understanding of the evolutionary origin, significance and subsequent modifications associated with gamete formation. We describe the mechanisms underlying recombination, chromosome segregation and meiotic sex chromosome inactivation in the stick insect groupTimema. Our results reveal that in males, 1) recombination initiates before synapsis, 2) the mechanisms of X inactivation are variable among species and the X remains silenced despite two waves of transcriptional activation in autosomes during spermatogenesis, 3) chromosome segregation is preceded by the recruitment of centromere proteins that either bind locally or longitudinally along the chromosomes. Together, our observations help understand the evolutionary significance of key cellular processes related to spermatogenesis and shed light on the diversity of their underlying mechanisms among species, includingTimemastick insects.
Commercialisation of artificial intelligence: a research on entrepreneurial companies with challenges and opportunities
Authors: Güner Gültekin Duygu , Pinarbasi Fatih , Yazici Merve , Adiguzel Zafer 
Published: September 2024

PurposeThe research paper’s purpose is to contribute to the literature by analysing the essential resources and processes required for successful commercialisation, the contemporary challenges and opportunities of artificial intelligence initiatives in Türkiye, and the diverse models and methods employed by these initiatives.Design/methodology/approachWithin the scope of the research, interviews were conducted with 10 entrepreneurs who established artificial intelligence-oriented enterprises in technoparks in Istanbul and Antalya. All 10 interviews were analysed using the MAXQDA20 software tool. Structured qualitative content analysis was used for the data analysis procedure.FindingsBased on the research, external factors have a significant impact on the future growth opportunities of the market. Expanding the client base, gaining international recognition, and securing financing are crucial for success. However, the findings reveal challenges in the relatively young local ecosystem. One major criticism is the lack of support in marketing and sales activities for refined products. To address this, providing financial incentives and knowledge transfer to those in need is vital.Research limitations/implicationsSince the research was conducted only with entrepreneurs who established and successfully commercialised artificial intelligence-oriented enterprises, it is recommended that future studies be performed with a widespread sample group, considering this limited situation. Furthermore, to overcome survivorship bias, it is recommended that posterior studies include failed commercialisation attempts in AI ventures.Practical implicationsIt can be argued that there is no deliberate approach or model for commercialization. Entrepreneurs often draw from their own prior experiences or observe industry trends. Given the limited financial resources available in the domestic market and the challenge of attracting foreign investors to Turkish brands, entrepreneurs tend to rely on internal approaches for commercialisation.Originality/valueThis research delves into the commercialisation prospects and obstacles encountered by AI start-ups in Türkiye. It comprises qualitative insights into business models, commercialisation approaches, opportunities, and challenges. The data were obtained from interviews with entrepreneurs operating in the industry.
The thermal-mechanical deformations of CO2 mixture gases dry gas seal based on two-way thermal-fluid-solid coupling model
Authors: Chen Wei , Xu Hengjie , Mao Wenyuan , Liu Meihong , Sun Xuejian , Deng Qiangguo 
Published: September 2024

Purpose
This study aims to investigate the influence mechanism of thermal-mechanical deformations on the CO2 mixture gases dry gas seal (DGS) flow field and compare the deformation characteristics and sealing performance between two-way and one-way thermal-fluid-solid coupling models.

Design/methodology/approach
The authors established a two-way thermal-fluid-solid coupling model by using gas film thickness as the transfer parameter between the fluid and solid domain, and the model was solved using the finite difference method and finite element method. The thermal-mechanical deformations of the sealing rings, the influence of face deformation on the flow field and sealing performance were obtained.

Findings
Thermal-mechanical deformations cause a convergent gap between the two sealing end faces, resulting in an increase in the gas film thickness, but a decrease in the gas film temperature and sealing ring temperature. The axial relative deformations of rotating and stationary ring end faces caused by mechanical and thermal loads in the two-way coupling model are less than those in the one-way coupling (OWC) model, and the gas film thickness and leakage rate are larger than those in the OWC model, whereas the gas film stiffness is the opposite.

Originality/value
This paper provides a theoretical support and reference for the operational stability and structural optimization design of CO2 mixture gases DGS under high-pressure and high-speed operation conditions.
Network power and firm innovation: the moderating roles of power distance and procedural justice
Authors: Yang Naiding , Zhu Xianglin , Zhang Mingzhen , Wang Yu 
Published: September 2024

Purpose
This study aims to investigate the influence of network power on exploratory and exploitative innovation and examines the moderating effects of power distance and procedural justice on these untested relationships.

Design/methodology/approach
This study uses survey data collected from firms in China and explores the influential mechanisms of network power, power distance and procedural justice in firm innovation.

Findings
This study empirically shows that network power has an inverted U-shaped effect on exploratory and exploitative innovation. Power distance weakens the effect of network power on exploratory and exploitative innovation, and procedural justice enhances the effect of network power on exploratory and exploitative innovation.

Research limitations/implications
This study extends resource dependence theory and contributes to the literature on innovation management. Future studies should use different collection channels or research methods to provide more evidence for model promotion. In addition, the dynamic power game among network members and the roles of other mediators or moderators warrant further consideration.

Practical implications
Managers should exercise power strategies properly and ensure that their innovation income exceeds expenditures. Managers need to pay serious attention to power distance and procedural justice in the network and formulate suitable cooperation strategies based on actual conditions.

Originality/value
This study applies the resource dependence theory to investigate the influence of network power on exploratory and exploitative innovation. In addition, the moderating roles of power distance and procedural justice in the above relationships, which have rarely been discussed in previous studies, were tested.
Contemporaneous and lagged R2 decomposed connectedness technique to explore interlinkages between green logistics, environmental issues and green and dirty energy consumption in Vietnam
Authors: Ha Le Thanh 
Published: September 2024

Purpose
This study aims to empirically connect green logistics performance, renewable energy, non-renewable energy, CO2 emissions and gross domestic product in Vietnam from 2000 to 2022.

Design/methodology/approach
Within this study, the author uses innovative tools, specifically a R2 decomposed linkage method, to scrutinize the connections between green logistics, environmental issues and the use of green and dirty energy.

Findings
The results highlight the two-way relationship between green logistics and energy security in Vietnam. Green logistics plays various roles in diverse periods, from a net shock transmitter to a net shock receiver in the designed system. Using a dynamic and contemporaneous dynamic linkage method, this study emphasizes the change in the role and the dominance of green logistics and renewable energy consumption. Notably, the unexpected shocks also lead to changes in these variables’ roles.

Originality/value
This paper presents two significant contributions to the existing body of literature. Firstly, as previously emphasized, this research marks a pioneering effort to examine the connection between green logistics, environmental issues and the use of green and dirty energy when it comes to developing nations such as Vietnam. Secondly, this research introduces a novel approach to investigating the interconnectedness of volatility across diverse markets, offering a more suitable method for such analyses. Within this study, the author uses innovative tools, specifically an R2 decomposed linkage method, to scrutinize the connections between green logistics, environmental issues and the use of green and dirty energy. In this analysis, the author examined data from 2000 through 2022. A thorough analysis is presented using the data, exploring the connections between the volatilities resulting from various problems in Vietnam.
Trauma and adversity in forensic patients with an intellectual disability: a review of risk assessment reports
Authors: Ierna Adrian , Tolland Heather , McGinley Abi , Mathieson Laura 
Published: September 2024

Purpose
People with intellectual disabilities are at a significantly higher risk than the general population for experiencing a wide range of adverse and potentially traumatic events. This paper aims to explore the incidence of experiences of lifetime trauma across this population in one Forensic Intellectual Disability Service. Risk management recommendations and psychological risk formulations were also examined for their consideration of traumatic experiences.

Design/methodology/approach
Risk assessment reports (n = 39) were reviewed for evidence of traumatic experiences and the consideration of trauma in patient risk formulations and risk management treatment recommendations.

Findings
Trauma was rated as present or partially present in 84.6% (n = 33) of risk assessment reports reviewed. None of the patients had received a post-traumatic stress disorder (PTSD) diagnosis. Recommendations regarding trauma were identified in 39.4% (n = 13) of the risk assessment reports where trauma was rated either “present” or “partially present”.

Practical implications
Findings suggest a need for diagnostic tools to be used to measure trauma symptoms and potential cases of PTSD to best support needs of patients. Trauma-focused interventions should also be considered. Further investigation is needed to clarify the disparity between the consideration of trauma in formulations and treatment recommendations.

Originality/value
This study highlights the different traumatic experiences that forensic patients across three settings have been exposed to during their lifetimes.
Leading whole school spaces of agency for climate change and sustainability education. A case study of four schools from England
Authors: Rushton Elizabeth , Walshe Nicola , Kitson Alison , Sharp Sarah 
Published: September 2024

PurposeIn England, climate change and sustainability education (CCSE) is predominantly taught with a focus on knowledge in school geography and science. However, whole-school approaches to CCSE exist which encompasses curriculum, campus, community and culture. Drawing on conceptualisations of the ecological approach to teacher agency we explored the ways in which the leadership of a whole-school approach to CCSE was implemented across four case study schools.Design/methodology/approachFour case study schools were identified as having implemented CCSE across the areas of classroom, culture, campus and community, with opportunities to share good practice. During visits to each school, we completed a series of 15 interviews with teachers who had roles leading geography (n = 4) and science (n = 4) curricular; school leaders (n = 4) and sustainability coordinators (n = 3). We engaged with a range of school curricula and policy materials and toured each site.FindingsAt the heart of an effective approach to whole-school CCSE are leaders who create the conditions for teachers to achieve agency and enact curriculum making as a social practice. School leaders themselves are critical in ensuring the culture, professional norms and expectations are established and nurtured. Over time, teachers are able to identify and create spaces of agency in relation to CCSE which reach beyond their immediate communities.Originality/valueThis research brings together teacher agency, curriculum making and leadership practices to better understand why some schools achieve agentic cultures as part of whole-school CCSE.