Absence of N-terminal acetyltransferase diversification during evolution of eukaryotic organisms

Protein N-terminal acetylation is an ancient and ubiquitous co-translational modification catalyzed by a highly conserved family of N-terminal acetyltransferases (NATs). Prokaryotes have at least 3 NATs, whereas humans have six distinct but highly conserved NATs, suggesting an increase in regulatory complexity of this modification during eukaryotic evolution. Despite this, and against our initial expectations, we determined that NAT diversification did not occur in the eukaryotes, as all six major human NATs were most likely present in the Last Eukaryotic Common Ancestor (LECA). Furthermore, we also observed that some NATs were actually secondarily lost during evolution of major eukaryotic lineages; therefore, the increased complexity of the higher eukaryotic proteome occurred without a concomitant diversification of NAT complexes

The landscape of molecular chaperones across human tissues reveals a layered architecture of core and variable chaperones

The sensitivity of the protein-folding environment to chaperone disruption can be highly tissue-specific. Yet, the organization of the chaperone system across physiological human tissues has received little attention. Through computational analyses of large-scale tissue transcriptomes, we unveil that the chaperone system is composed of core elements that are uniformly expressed across tissues, and variable elements that are differentially expressed to fit with tissue-specific requirements. We demonstrate via a proteomic analysis that the muscle-specific signature is functional and conserved. Core chaperones are significantly more abundant across tissues and more important for cell survival than variable chaperones. Together with variable chaperones, they form tissue-specific functional networks. Analysis of human organ development and aging brain transcriptomes reveals that these functional networks are established in development and decline with age. In this work, we expand the known functional organization of de novo versus stress-inducible eukaryotic chaperones into a layered core-variable architecture in multi-cellular organisms

Genes Associated with Honey Bee Behavioral Maturation Affect Clock-Dependent and -Independent Aspects of Daily Rhythmic Activity in Fruit Flies

BACKGROUND: In the honey bee, the age-related and socially regulated transition of workers from in-hive task performance (e.g., caring for young) to foraging (provisioning the hive) is associated with changes in many behaviors including the 24-hour pattern of rhythmic activity. We have previously shown that the hive-bee to forager transition is associated with extensive changes in brain gene expression. In this study, we test the possible function of a subset of these genes in daily rhythmic activity pattern using neural-targeted RNA interference (RNAi) of an orthologous gene set in Drosophila melanogaster. PRINCIPAL FINDINGS: Of 10 genes tested, knockdown of six affected some aspect of locomotor activity under a 12 h:h light:dark regime (LD). Inos affected anticipatory activity preceding lights-off, suggesting a possible clock-dependent function. BM-40-SPARC, U2af50 and fax affected peak activity at dawn without affecting anticipation or overall inactivity (proportion of 15-min intervals without activity), suggesting that these effects may depend on the day-night light cycle. CAH1 affected overall inactivity. The remaining gene, abl, affected peak activity levels but was not clearly time-of-day-specific. No gene tested affected length of period or strength of rhythmicity in constant dark (DD), suggesting that these genes do not act in the core clock. SIGNIFICANCE: Taking advantage of Drosophila molecular genetic tools, our study provides an important step in understanding the large set of gene expression changes that occur in the honey bee transition from hive bee to forager. We show that orthologs of many of these genes influence locomotor activity in Drosophila, possibly through both clock-dependent and -independent pathways. Our results support the importance of both circadian clock and direct environmental stimuli (apart from entrainment) in shaping the bee's 24-hour pattern of activity. Our study also outlines a new approach to dissecting complex behavior in a social animal

Higher education students’ perceptions of ChatGPT: A global study of early reactions

The paper presents the most comprehensive and large-scale global study to date on how higher education students perceived the use of ChatGPT in early 2024. With a sample of 23,218 students from 109 countries and territories, the study reveals that students primarily used ChatGPT for brainstorming, summarizing texts, and finding research articles, with a few using it for professional and creative writing. They found it useful for simplifying complex information and summarizing content, but less reliable for providing information and supporting classroom learning, though some considered its information clearer than that from peers and teachers. Moreover, students agreed on the need for AI regulations at all levels due to concerns about ChatGPT promoting cheating, plagiarism, and social isolation. However, they believed ChatGPT could potentially enhance their access to knowledge and improve their learning experience, study efficiency, and chances of achieving good grades. While ChatGPT was perceived as effective in potentially improving AI literacy, digital communication, and content creation skills, it was less useful for interpersonal communication, decision-making, numeracy, native language proficiency, and the development of critical thinking skills. Students also felt that ChatGPT would boost demand for AI-related skills and facilitate remote work without significantly impacting unemployment. Emotionally, students mostly felt positive using ChatGPT, with curiosity and calmness being the most common emotions. Further examinations reveal variations in students’ perceptions across different socio-demographic and geographic factors, with key factors influencing students’ use of ChatGPT also being identified. Higher education institutions’ managers and teachers may benefit from these findings while formulating the curricula and instructions/regulations for ChatGPT use, as well as when designing the teaching methods and assessment tools. Moreover, policymakers may also consider the findings when formulating strategies for secondary and higher education system development, especially in light of changing labor market needs and related digital skills development

Recommendations and guidelines from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 1 -- In vivo small-animal imaging

The value of in vivo preclinical diffusion MRI (dMRI) is substantial. Small-animal dMRI has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. Many of the influential works in this field were first performed in small animals or ex vivo samples. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the data. This work aims to serve as a reference, presenting selected recommendations and guidelines from the diffusion community, on best practices for preclinical dMRI of in vivo animals. In each section, we also highlight areas for which no guidelines exist (and why), and where future work should focus. We first describe the value that small animal imaging adds to the field of dMRI, followed by general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss how they are appropriate for different studies. We then give guidelines for in vivo acquisition protocols, including decisions on hardware, animal preparation, imaging sequences and data processing, including pre-processing, model-fitting, and tractography. Finally, we provide an online resource which lists publicly available preclinical dMRI datasets and software packages, to promote responsible and reproducible research. An overarching goal herein is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge.Comment: 69 pages, 6 figures, 1 tabl

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 1: In vivo small-animal imaging

Small-animal diffusion MRI (dMRI) has been used for methodological development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. The steps from animal setup and monitoring, to acquisition, analysis, and interpretation are complex, with many decisions that may ultimately affect what questions can be answered using the resultant data. This work aims to present selected considerations and recommendations from the diffusion community on best practices for preclinical dMRI of in vivo animals. We describe the general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in animal species and disease models and discuss why some may be more or less appropriate for different studies. We, then, give recommendations for in vivo acquisition protocols, including decisions on hardware, animal preparation, and imaging sequences, followed by advice for data processing including preprocessing, model-fitting, and tractography. Finally, we provide an online resource that lists publicly available preclinical dMRI datasets and software packages to promote responsible and reproducible research. In each section, we attempt to provide guides and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should focus. Although we mainly cover the central nervous system (on which most preclinical dMRI studies are focused), we also provide, where possible and applicable, recommendations for other organs of interest. An overarching goal is to enhance the rigor and reproducibility of small animal dMRI acquisitions and analyses, and thereby advance biomedical knowledge

Considerations and recommendations from the ISMRM diffusion study group for preclinical diffusion MRI: Part 2-Ex vivo imaging: Added value and acquisition

The value of preclinical diffusion MRI (dMRI) is substantial. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages including higher SNR and spatial resolution compared to in vivo studies, and enabling more advanced diffusion contrasts for improved microstructure and connectivity characterization. Another major advantage of ex vivo dMRI is the direct comparison with histological data, as a crucial methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work represents "Part 2" of a three-part series of recommendations and considerations for preclinical dMRI. We describe best practices for dMRI of ex vivo tissue, with a focus on the value that ex vivo imaging adds to the field of dMRI and considerations in ex vivo image acquisition. We first give general considerations and foundational knowledge that must be considered when designing experiments. We briefly describe differences in specimens and models and discuss why some may be more or less appropriate for different studies. We then give guidelines for ex vivo protocols, including tissue fixation, sample preparation, and MR scanning. In each section, we attempt to provide guidelines and recommendations, but also highlight areas for which no guidelines exist (and why), and where future work should lie. An overarching goal herein is to enhance the rigor and reproducibility of ex vivo dMRI acquisitions and analyses, and thereby advance biomedical knowledge

Considerations and recommendations from the ISMRM Diffusion Study Group for preclinical diffusion MRI: Part 3—Ex vivo imaging: Data processing, comparisons with microscopy, and tractography

Preclinical diffusion MRI (dMRI) has proven value in methods development and validation, characterizing the biological basis of diffusion phenomena, and comparative anatomy. While dMRI enables in vivo non-invasive characterization of tissue, ex vivo dMRI is increasingly being used to probe tissue microstructure and brain connectivity. Ex vivo dMRI has several experimental advantages that facilitate high spatial resolution and high SNR images, cutting-edge diffusion contrasts, and direct comparison with histological data as a methodological validation. However, there are a number of considerations that must be made when performing ex vivo experiments. The steps from tissue preparation, image acquisition and processing, and interpretation of results are complex, with many decisions that not only differ dramatically from in vivo imaging of small animals, but ultimately affect what questions can be answered using the data. This work concludes a three-part series of recommendations and considerations for preclinical dMRI. Herein, we describe best practices for dMRI of ex vivo tissue, with a focus on image pre-processing, data processing, and comparisons with microscopy. In each section, we attempt to provide guidelines and recommendations but also highlight areas for which no guidelines exist (and why), and where future work should lie. We end by providing guidelines on code sharing and data sharing and point toward open-source software and databases specific to small animal and ex vivo imaging

Higher education students’ perceptions of ChatGPT: A global study of early reactions

© 2025 Ravšelj et al.The paper presents the most comprehensive and large-scale global study to date on how higher education students perceived the use of ChatGPT in early 2024. With a sample of 23,218 students from 109 countries and territories, the study reveals that students primarily used ChatGPT for brainstorming, summarizing texts, and finding research articles, with a few using it for professional and creative writing. They found it useful for simplifying complex information and summarizing content, but less reliable for providing information and supporting classroom learning, though some considered its information clearer than that from peers and teachers. Moreover, students agreed on the need for AI regulations at all levels due to concerns about ChatGPT promoting cheating, plagiarism, and social isolation. However, they believed ChatGPT could potentially enhance their access to knowledge and improve their learning experience, study efficiency, and chances of achieving good grades. While ChatGPT was perceived as effective in potentially improving AI literacy, digital communication, and content creation skills, it was less useful for interpersonal communication, decision-making, numeracy, native language proficiency, and the development of critical thinking skills. Students also felt that ChatGPT would boost demand for AI-related skills and facilitate remote work without significantly impacting unemployment. Emotionally, students mostly felt positive using ChatGPT, with curiosity and calmness being the most common emotions. Further examinations reveal variations in students’ perceptions across different socio-demographic and geographic factors, with key factors influencing students’ use of ChatGPT also being identified. Higher education institutions’ managers and teachers may benefit from these findings while formulating the curricula and instructions/regulations for ChatGPT use, as well as when designing the teaching methods and assessment tools. Moreover, policymakers may also consider the findings when formulating strategies for secondary and higher education system development, especially in light of changing labor market needs and related digital skills development.The authors acknowledge the financial support from the Slovenian Research and Innovation Agency (research core funding No. P5-0093 and project No. Z5-4569)