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Lockdowns due to the COVID-19 pandemic have forced universities to migrate entirely to eLearning to deliver classes. Students have found themselves using either synchronous, asynchronous, or mixed mode learning methods based on their universities' preferences. Many studies that investigated difficulties during the lockdown have been mainly concerned about technical difficulties. The reports lacked the investigation of differences among students' groups, with a few exceptions that highlighted differences among male and female students. Moreover, existing studies were found to focus on singular dimensions (TAM, IS success model, etc.). This study perceives that students, based on the various groups they belong to, can show different levels of perceptions towards determinants that influence the usage of eLearning. This study investigated differences among students in terms of determinants from TRI, TAM, and IS success model. A total of 915 participants from Malaysia and Saudi Arabia reported their perceptions. The findings reported in this study showed significant differences among participants, in particular, among groups of gender, age, country, and eLearning mode. It is noticeable that participants who used the asynchronous mode of eLearning gave more weight to information quality, system quality, service quality, perceived usefulness, perceived ease of use, innovation, optimism, satisfaction, and intention to use. Meanwhile, participants who used the synchronous mode experienced more discomfort. It could be said that the significant differences between the usage of synchronous and asynchronous modes should be considered for better quality of online learning.

The COVID-19 pandemic profoundly disrupted traditional education systems worldwide, prompting a rapid shift to online platforms and the emergence of innovative teaching strategies. This paper critically reviews the extensive body of research on post-COVID-19 education, focusing on the practical and feasible solutions proposed to maintain and enhance educational continuity. The review categorizes and examines studies on various approaches, including simulation-based training, project-based learning, and hybrid models, highlighting their effectiveness during and after the pandemic. Special attention is given to the role of information technology, the challenges faced by educators and students, and the importance of mental health support in the new educational landscape. The findings suggest that while digital tools such as virtual reality and 3D environments show promise, their implementation remains limited, particularly in resource-constrained settings. The study also identifies a significant gap in empirical research on these innovations in the post-pandemic era. Furthermore, the paper highlights the need for systemic changes in curriculum design, educator training, and policy development to address the long-term impacts of the pandemic on education. This review provides a comprehensive overview of the lessons learned from the COVID-19 pandemic, offering insights into how educational institutions can better prepare for future crises. [ABSTRACT FROM AUTHOR]

COVID-19 related lockdowns forced students of higher education to receive education entirely online as a replacement for physical attendance in classrooms. This new situation caused students to discover the advantages and disadvantages of e-learning and influenced their satisfaction in using it and intention to use it. Consequently, this study revisits the intention to use and satisfaction-related theories based on pre-COVID conditions. This revisit was necessary because the evidence suggests that students' new situation has changed some determinants related to their satisfaction and intention to use. This situation warranted the simultaneous consideration of many dimensions when measuring user satisfaction and intention to use during the lockdown. This cross-sectional study developed an integrated model to measure students' satisfaction and its impact on intention to use e-learning. Structural equation modeling was used to conduct the empirical analysis. Nine hundred respondents from Malaysia and Saudi Arabia participated in this study. Students from Malaysia and Saudi Arabia showed marginal differences in their perceptions of e-learning. The findings showed changes in students' perceptions toward satisfaction and intention to use e-learning, which might be due to using e-learning exclusively. [ABSTRACT FROM AUTHOR]

Globally, educational institutions have reported a dramatic shift to online learning in an effort to contain the COVID-19 pandemic. The fundamental concern has been the continuance of education. As a result, several novel solutions have been developed to address technical and pedagogical issues. However, these were not the only difficulties that students faced. The implemented solutions involved the operation of the educational process with less regard for students’ changing circumstances, which obliged them to study from home. Students should be asked to provide a full list of their concerns. As a result, student reflections, including those from Saudi Arabia, have been analysed to identify obstacles encountered during the COVID- 19 pandemic. However, most of the analyses relied on closed-ended questions, which limited student involvement. To delve into students’ responses, this study used open-ended questions, a qualitative method (content analysis), a quantitative method (topic modelling), and a sentimental analysis. This study also looked at students’ emotional states during and after the COVID-19 pandemic. In terms of determining trends in students’ input, the results showed that quantitative and qualitative methods produced similar outcomes. Students had unfavourable sentiments about studying during COVID-19 and positive sentiments about the face-to-face study. Furthermore, topic modelling has revealed that the majority of difficulties are more related to the environment (home) and social life. Students were less accepting of online learning. As a result, it is possible to conclude that face-to-face study still attracts students and provides benefits that online study cannot, such as social interaction and effective eye-to-eye communication. [ABSTRACT FROM AUTHOR]

In contrast to extensively studied prokaryotic 'small' transcriptomes (encompassing all small noncoding RNAs), small proteomes (here defined as including proteins ≤70 aa) are only now entering the limelight. The absence of a complete small protein catalogue in most prokaryotes precludes our understanding of how these molecules affect physiology. So far, archaeal genomes have not yet been analyzed broadly with a dedicated focus on small proteins. Here, we present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii. We demonstrate by MS and Ribo-seq that 67% of the 317 annotated small open reading frames (sORFs) are translated under standard growth conditions. Furthermore, annotation-independent analysis of Ribo-seq data showed ribosomal engagement for 47 novel sORFs in intergenic regions. A total of seven of these were also detected by proteomics, in addition to an eighth novel small protein solely identified by MS. We also provide independent experimental evidence in vivo for the translation of 12 sORFs (annotated and novel) using epitope tagging and western blotting, underlining the validity of our identification scheme. Several novel sORFs are conserved in Haloferax species and might have important functions. Based on our findings, we conclude that the small proteome of H. volcanii is larger than previously appreciated, and that combining MS with Ribo-seq is a powerful approach for the discovery of novel small protein coding genes in archaea. [ABSTRACT FROM AUTHOR]

Motivation CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to automatically define the cassette boundaries. In addition, we present a Cas-type predictive model used by the method to assign each gene located in the region defined by a cassette's boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules. Results We evaluate the predictive performance of our proposed method on data collected from the two most recent CRISPR classification studies. In our experiments, we obtain an average similarity of 0.86 between the predicted and expected cassettes. Besides, we achieve F -scores above 0.9 for the classification of cas genes of known types and 0.73 for the unknown ones. Finally, we conduct two additional study cases, where we investigate the occurrence of potentially new cas genes and the occurrence of module exchange between different genomes. Availability and implementation https://github.com/BackofenLab/Casboundary. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

The clustered regularly interspaced short palindromic repeat (CRISPR) system is a prokaryotic adaptive defense system against foreign nucleic acids. In the methanoarchaeon Methanosarcina mazei Gö1, two types of CRISPR-Cas systems are present (type I-B and type III-C). Both loci encode a Cas6 endonuclease, Cas6b-IB and Cas6b-IIIC, typically responsible for maturation of functional short CRISPR RNAs (crRNAs). To evaluate potential cross cleavage activity, we biochemically characterized both Cas6b proteins regarding their crRNA binding behavior and their ability to process pre-crRNA from the respective CRISPR array in vivo. Maturation of crRNA was studied in the respective single deletion mutants by northern blot and RNA-Seq analysis demonstrating that in vivo primarily Cas6b-IB is responsible for crRNA processing of both CRISPR arrays. Tentative protein level evidence for the translation of both Cas6b proteins under standard growth conditions was detected, arguing for different activities or a potential non-redundant role of Cas6b-IIIC within the cell. Conservation of both Cas6 endonucleases was observed in several other M. mazei isolates, though a wide variety was displayed. In general, repeat and leader sequence conservation revealed a close correlation in the M. mazei strains. The repeat sequences from both CRISPR arrays from M. mazei Gö1 contain the same sequence motif with differences only in two nucleotides. These data stand in contrast to all other analyzed M. mazei isolates, which have at least one additional CRISPR array with repeats belonging to another sequence motif. This conforms to the finding that Cas6b-IB is the crucial and functional endonuclease in M. mazei Gö1. Abbreviations: sRNA: small RNA; crRNA: CRISPR RNA; pre-crRNAs: Precursor CRISPR RNA; CRISPR: clustered regularly interspaced short palindromic repeats; Cas: CRISPR associated; nt: nucleotide; RNP: ribonucleoprotein; RBS: ribosome binding site [ABSTRACT FROM AUTHOR]

Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region. [ABSTRACT FROM AUTHOR]

Invading genetic elements pose a constant threat to prokaryotic survival, requiring an effective defence. Eleven years ago, the arsenal of known defence mechanisms was expanded by the discovery of the CRISPR-Cas system. Although CRISPR-Cas is present in the majority of archaea, research often focuses on bacterial models. Here, we provide a perspective based on insights gained studying CRISPR-Cas system I-B of the archaeon Haloferax volcanii. The system relies on more than 50 different crRNAs, whose stability and maintenance critically depend on the proteins Cas5 and Cas7, which bind the crRNA and form the Cascade complex. The interference machinery requires a seed sequence and can interact with multiple PAM sequences. H. volcanii stands out as the first example of an organism that can tolerate autoimmunity via the CRISPR-Cas system while maintaining a constitutively active system. In addition, the H. volcanii system was successfully developed into a tool for gene regulation. [ABSTRACT FROM AUTHOR]