Miracle-dz/UniFAR-FTUs huggingface dataset:
TDP 2 modulates the expression of estrogen-responsive oncogenes

With its ligand estrogen, the estrogen receptor (ER) stimulates tumor cell growth by activating a global transcriptional program. This activation involves topoisomerase 2 (TOP2), which resolves topological problems by transiently creating and re-ligating DNA double-strand breaks (DSBs). Recent studies have uncovered the involvement of DNA repair proteins in the repair of TOP2-induced DSBs. These noncanonical repair pathways may serve as backup processes when TOP2 is halted and fails to re-ligate DSBs, but their impact on transcription remains elusive. In this study, we investigated the role of tyrosyl-DNA phosphodiesterase 2 (TDP2), an enzyme that acts for the removal of halted TOP2 from the 5’-end of the DNA, in the estrogen-induced transcriptome. Using TDP2-deficient ER-positive cells and mice, we showed that TDP2 regulates the expression of oncogene MYC. MYC induction by estrogen was a very early event (1 hour) and TOP2-dependent. In TDP2-deficient cells, the induction of MYC by estrogen became prolonged and volatile. Bulk and single-cell RNA-seq identified the oncogenes MYC and CCND1 as genes whose estrogen response was regulated by TDP2. These results suggest that TDP2 may play a role in the repair of TOP2-induced DSBs in specific genomic loci and tightly regulates the expression of oncogenes.
Finding rearrangements in nanopore DNA reads with last and dnarrange

Long-read DNA sequencing techniques such as nanopore are especially useful for characterizing complex sequence rearrangements, which occur in some genetic diseases and also during evolution. Analyzing the sequence data to understand such rearrangements is not trivial, due to sequencing error, rearrangement intricacy, and abundance of repeated similar sequences in genomes. The last and dnarrange software packages can resolve complex relationships between DNA sequences, and characterize changes such as gene conversion, processed pseudogene insertion, and chromosome shattering. They can filter out numerous rearrangements shared by controls, e.g. healthy humans versus a patient, to focus on rearrangements unique to the patient. One useful ingredient is last-train, which learns the rates (probabilities) of deletions, insertions, and each kind of base match and mismatch. These probabilities are then used to find the most likely sequence relationships/alignments, which is especially useful for DNA with unusual rates, such as DNA from Plasmodium falciparum (malaria) with ∼ 80% a+t. This is also useful for less-studied species that lack reference genomes, so the DNA reads are compared to a different species’ genome. We also point out that a reference genome with ancestral alleles would be ideal.
The tacit design process in architectural design education.

The purpose of the architectural design studio is that students learn to think and act like designers. However, communication between teachers and students seems to be problematic. Teachers barely seem to explain how designers work, which may be confusing for students. To learn professional reasoning processes and strategies, different teaching activities are involved, such as modelling, coaching, scaffolding, reflection, exploration and articulation. In the design studio it seems tradition that teachers only ask questions, while not articulating the design process. This paper focuses on the research question of whether teachers in architectural design education articulate the main ‘designerly’ actions and skills, performed by expert designers, and if so, to what extent and in which manner? To answer these questions video-recordings of 13 tutorial sessions are analysed with the help of an educational framework of five generic elements. The framework consists of the basic design process actions and skills, and is specifically developed as a vocabulary for making the design process explicit and to train students in the design process elements. The main conclusion is that teachers refer to the design product in an implicit way. They leave it to the students to discover the structure and components of the design process more or less by themselves.
A Chloroplast Protein Atlas Reveals Novel Structures and Spatial Organization of Biosynthetic Pathways

Chloroplasts are eukaryotic photosynthetic organelles that drive the global carbon cycle. Despite their importance, our understanding of their protein composition, function, and spatial organization remains limited. Here, we determined the localizations of 1,032 candidate chloroplast proteins by using fluorescent protein tagging in the model alga Chlamydomonas reinhardtii. The localizations provide insights into the functions of hundreds of poorly-characterized proteins, including identifying novel components of nucleoids, plastoglobules, and the pyrenoid. We discovered and further characterized novel organizational features, including eleven chloroplast punctate structures, cytosolic crescent structures, and diverse unexpected spatial distributions of enzymes within the chloroplast. We observed widespread protein targeting to multiple organelles, identifying proteins that likely function in multiple compartments. We also used machine learning to predict the localizations of all Chlamydomonas proteins. The strains and localization atlas developed here will serve as a resource to enable studies of chloroplast architecture and functions. Graphical Abstract Highlights 1,032 candidate chloroplast proteins localized by fluorescent tagging. This protein atlas reveals novel chloroplast structures, functional regions, and components. Prevalent dual-organelle localization suggests extensive cross-compartment coordination. Atlas-trained machine learning predicts localizations of all C. reinhardtii proteins.
Combined small molecule treatment accelerates timing of maturation in human pluripotent stem cell-derived neurons

The maturation of human pluripotent stem cell (hPSC)-derived neurons mimics the protracted timing of human brain development, extending over months and years to reach adult-like function. Prolonged in vitro maturation presents a major challenge to stem cell-based applications in modeling and treating neurological disease. We designed a high-content imaging assay based on morphological and functional readouts in hPSC-derived cortical neurons to reveal underlying pathways and to identify chemicals capable of accelerating neuronal maturation. Probing a library of 2688 bioactive drugs, we identified multiple compounds that drive neuronal maturation including inhibitors of LSD1 and DOT1L and activators of calcium-dependent transcription. A cocktail of 4 factors GSK-2879552, EPZ-5676, NMDA and Bay K 8644, which we collectively termed GENtoniK, triggered maturation across all assays tested including measures of synaptic density, electrophysiology and transcriptomics. Remarkably, GENtoniK was similarly effective in enhancing neuronal maturation in 3D cortical organoids and in spinal motoneurons, and improved aspects of cell maturation in non-neural lineages such as melanocytes and pancreatic beta cells. These results demonstrate that the maturation of multiple hPSC-derived cell types can be enhanced by simple pharmacological intervention and suggests that some of the mechanisms controlling the timing of human maturation are shared across lineages.
Of problems and opportunities—How to treat and how to not treat crystallographic fragment screening data

In their recent commentary in Protein Science, Jaskolski et al. analyze three randomly picked diffraction data sets from fragment-screening group depositions from the PDB and, based on that, claim that such data are principally problematic. We demonstrate here that if such data are treated properly, none of the proclaimed criticisms persist.
A Self-aware Resource Management Framework for Heterogeneous Multicore SoCs with Diverse QoS Targets

In modern heterogeneous MPSoCs, the management of shared memory resources is crucial in delivering end-to-end QoS. Previous frameworks have either focused on singular QoS targets or the allocation of partitionable resources among CPU applications at relatively slow timescales. However, heterogeneous MPSoCs typically require instant response from the memory system where most resources cannot be partitioned. Moreover, the health of different cores in a heterogeneous MPSoC is often measured by diverse performance objectives. In this work, we propose the Self-Aware Resource Allocation framework for heterogeneous MPSoCs. Priority-based adaptation allows cores to use different target performance and self-monitor their own intrinsic health. In response, the system allocates non-partitionable resources based on priorities. The proposed framework meets a diverse range of QoS demands from heterogeneous cores. Moreover, we present a runtime scheme to configure priority-based adaptation so that distinct sensitivities of heterogeneous QoS targets with respect to memory allocation can be accommodated. In addition, the priority of best-effort cores can also be regulated.
Intracellular level of S. cerevisiae Rad51 is regulated via proteolysis in a SUMO- and ubiquitin-dependent manner

Among various DNA lesions, the DNA double-strand breaks are particularly deleterious; especially, when an error-free repair pathway is unavailable, and the cell takes the risk of using the error-prone recombination pathways to repair the DNA breaks, resume the cell cycle, and continue growth. The latter comes at the expense of decreased well-being of the cells due to genome rearrangements. One of the major players involved in recombinational repair of DNA damage is Rad51 recombinase, a protein responsible for presynaptic complex formation. We previously noticed that the level of this protein is strongly increased when illegitimate recombination is engaged in repair. The regulation of Rad51 protein turnover is not known; therefore, we decided to look closer at this issue because we expect that an excessively high level of Rad51 may lead to genome instability. Here we show that the level of Rad51 is regulated via the ubiquitin-dependent proteolytic pathway. The ubiquitination of Rad51 depends on multiple E3 enzymes, including SUMO-targeted ubiquitin ligases. We also demonstrate that Rad51 can be modified by both ubiquitin and SUMO. Moreover, these modifications may lead to opposite effects. Ubiquitin-dependent degradation depends on Rad6, Rad18, Slx8, Dia2 and the anaphase-promoting complex. Rsp5-dependent ubiquitination leads to Rad51 stabilization.
The complexity of keratocyte migration in salmon explant cultures: initial results and future prospects

Intact skin is of uttermost importance for fish welfare. The fish skin provides an environmental barrier and protects against invading pathogens. However, both pathogens and physical insults cause skin wounds that are of major concern in modern fish farming. The behavior and interactions between keratocyte cells and sheets of cells are not well understood. The collective migration of keratocytes (skin epithelial cells) is of central importance for wound healing in fish. In this study, we aimed to elucidate the complex wound healing process in fish skin by studying in vitro cultures of these highly motile cells. Using explant cultures from farmed Atlantic salmon (Salmo salar) and differential interference contrast microscopy (DIC), we have captured the dynamics of sheets of cells from harvested fish scales and of individual cells interacting in the cell sheet vicinity. In addition to direct contact, the cells were observed to interact through long membrane tubes, turn, rotate, merge, and/or detach. Additionally, stationary cells and cells moving on top of the cell sheets were observed. Cell sheets approaching one another from different scales did not merge but dispersed.
A unique single nucleotide polymorphism in Agouti Signalling Protein (ASIP) gene changes coat colour of Sri Lankan leopard (Panthera pardus kotiya) to dark black

The Sri Lankan Leopard (Panthera pardus kotiya) is an endangered subspecies restricted to isolated and fragmented populations in Sri Lanka. Among them, the melanistic leopards have been recorded on rare occasions. The existing literature suggests that melanism evolved several times in the Felidae family, with three separate species revealing distinct mutations. Nevertheless, the mutations in the remaining species, including Sri Lankan black leopard, are unknown. We used reference-based assembled the nuclear genomes of Sri Lankan normal and black leopard and de novo assembled mitogenomes of the same to investigate the genetic basis, adaptive significance, and evolutionary history of the Sri Lankan black leopard. Our data suggested coalescence time of Sri Lankan regular and black leopards at ∼0.5 Million years, sisters to Panthera pardus lineage. Interestingly, in the black leopard, a single nucleotide polymorphism in exon-4 possibly completely ablates Agouti Signaling Protein (ASIP) function. Existing genomic data suggest new a species-specific mutation of the ASIP gene in the Felidae family, contributing to naturally occurring colouration polymorphism. As such, the Sri Lankan black leopard and normal leopard probably evolved from the same ancestor, while the mutation in the ASIP gene resulted in black coat colour. This rare mutation could be adaptable to the environment that back leopards reported, camouflage, with a likelihood of recurrence and transmission to future generations. However, protecting this sensitive environment is critical for the conservation of the existing populations and providing breeding grounds.
Stable and ancient endocytic structures navigate the complex pellicle of apicomplexan parasites

Apicomplexan parasites have an immense impact on humanity, but their basic cellular processes are often poorly understood. The sites of endocytosis, the conservation of this process with other eukaryotes, and its functions across Apicomplexa are major unanswered questions. Yet endocytosis in Plasmodium is implicated in antimalarial drug failure. Using the apicomplexan model Toxoplasma, we identified the molecular composition and behavior of unusual, fixed endocytic structures. Here, stable complexes of endocytic proteins differ markedly from the dynamic assembly/disassembly of these machineries in other eukaryotes. Moreover, conserved molecular adaptation of this structure is seen in Apicomplexa, including the kelch-domain protein K13 central to malarial drug-resistance. We determine that an essential function of endocytosis in Toxoplasma is plasma membrane homeostasis, rather than parasite nutrition, and that these specialized endocytic structures originated early in infrakingdom Alveolata, likely in response to the complex cell pellicle that defines this medically and ecologically important ancient eukaryotic lineage.
A framework for agile design of personalized gamification services

The interest in the application of gamification techniques under different contexts has increased during the last years, becoming a promising trend in many areas such as Human-Computer interaction (HCI) or educational technologies. Unfortunately, many instances of the use of these techniques do not meet their objectives of motivation, primarily due to poor design or a completely ``ad-hoc'' approach. Findings reveal that a formal design strategy is the key to success. This thesis presents the development and validation of a framework for the design of personalized gamification services. This framework, called FRAGGLE (FRamework for AGile Gamification of personalized Learning Experiences) is based on the use of the Agile methodologies in order to obtain a fast design ready for testing and iterated. It is aimed to the application of different techniques all the way down to the lowest levels of abstraction through a guided step-by-step process, including a design validation process of intrinsic motivation (SPARC). This approach was tested and assessed in two courses at an e-learning based Bachelor in Computer Science, its goals being the encouragement of learners in solving non-graded formative activities and increasing their sense of kinship as well the interest to the class group. The first case revealed a moderate positive assessment of the designed experience and student engagement in a ``one-size-fits-all'' proposal, meanwhile the second case of study allowed to assess which design elements had a greater impact in student engagement. Results in a further case of study also revealed that personalization worked better regarding students' behavioral and emotional engagement than previous generic approaches.Finally, the framework was also applied in a healthcare real environment through Preventive Neuro Health, a gamified crowdsourcing-inspired tool developed for cognitive impairment prevention of healthy older adults. It enabled a high degree of personalization both from clinical and engagement perspectives with the purpose of motivating its regular use among them.
A multifaceted architectural framework of the mouse claustrum complex

Accurate anatomical characterizations are necessary to investigate neural circuitry on a fine scale, but for the rodent claustrum complex (CC) this has yet to be fully accomplished. The CC is generally considered to comprise two major subdivisions, the claustrum (CL) and the dorsal endopiriform nucleus (DEn), but regional boundaries to these areas are highly debated. To address this, we conducted a multifaceted analysis of fiber- and cyto-architecture, genetic marker expression, and connectivity using mice of both sexes, to create a comprehensive guide for identifying and delineating borders to the CC. We identified four distinct subregions within the CC, subdividing both the CL and the DEn into two. Additionally, we conducted brain-wide tracing of inputs to the entire CC using a transgenic mouse line. Immunohistochemical staining against myelin basic protein (MBP), parvalbumin (PV), and calbindin (CB) revealed intricate fiber-architectural patterns enabling precise delineations of the CC and its subregions. Myelinated fibers were abundant in dorsal parts of the CL but absent in ventral parts, while parvalbumin labelled fibers occupied the entire CL. Calbindin staining revealed a central gap within the CL, which was also visible at levels anterior to the striatum. Furthermore, cells in the CL projecting to the retrosplenial-cortex were located within the myelin sparse area. By combining our own experimental data with digitally available datasets of gene expression and input connectivity, we could demonstrate that the proposed delineation scheme allows anchoring of datasets from different origins to a common reference framework. Significance statement Mice are a highly tractable model for studying the claustrum complex (CC). However, without a consensus on how to delineate the CC in rodents, comparing results between studies is challenging. It is therefore important to expand our anatomical knowledge of the CC, to match the level of detail needed to study its functional properties. Using multiple strategies for identifying claustral borders, we created a comprehensive guide to delineate the CC and its subregions. This anatomical framework will allow researchers to anchor future experimental data into a common reference space. We demonstrated the power of this new structural framework by combining our own experimental data with digitally available data on gene expression and input connectivity of the CC.
Genomic characterization of the recent monkeypox outbreak

The Monkeypox virus is the etiological cause of a recent multi-country outbreak, with nearly one hundred distinct cases detected outside the endemic areas of Africa in May 2022. In this article, we analyze the sequences of two full genomes of Monkeypox virus from Portugal and Belgium, and compare them with all available Monkeypox sequences, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Monkeypox, with >99% sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We also analyze specific mutations occurring in viral proteins A42R (for which a crystal structure is available) and H3L (an important epitope in host immune recognition), highlighting specific amino acids varying between the current outbreak, previous Monkeypox and Cowpox sequences and the historical Variola virus.
Can Membrane Composition Traffic Toxins? Mycolactone and Preferential Membrane Interactions

Mycolactone is a cytotoxic and immunosuppressive macrolide produced by Mycobacterium ulcerans and the sole causative agent of the neglected tropical skin disease Buruli ulcer. The toxin acts by invading host cells and interacting with intracellular targets to disrupt multiple fundamental cellular processes. Mycolactone’s amphiphilic nature enables strong interactions with lipophilic environments, including cellular membranes; however, the specificity of these interactions and the role of membranes in the toxin’s pathogenicity remain unknown. It is likely that preferential interactions with lipophilic carriers play a key role in the toxin’s distribution in the host, which, if understood, could provide insights to aid in the development of needed diagnostics for Buruli ulcer disease. In this work, molecular dynamics simulations were combined with enhanced free energy sampling to characterize mycolactone’s association with and permeation through models of the mammalian endoplasmic reticulum (ER) and plasma membranes (PM). We find that increased order in the PM not only leads to a different permeation mechanism compared to that in the ER membrane, but also an energetic driving force for ER localization. Increased hydration, membrane deformation, and preferential interactions with unsaturated lipid tails stabilize the toxin in the ER membrane, while disruption of lipid packing is a destabilizing force in the PM. STATEMENT OF SIGNIFICANCE Mycolactone is sole the causative agent of Buruli ulcer, a neglected tropical disease involving large necrotic lesions that can cause permanent disfigurement if left untreated. Due to its amphiphilic nature, the toxin hides from traditional diagnostic detection and the host immune system by associating with lipophilic carriers, including cellular membranes. Our work uses extensive all-atom simulations to query if the toxin has preferential interactions with different types of membranes. We find a clear preference for more disordered membranes, like the endoplasmic reticulum’s, via interactions with unsaturated lipid tails and membrane deformation. The revealed insights can be used to predict host cell distribution between different types of lipophilic carriers and to aid in the design of Buruli ulcer diagnostics.
Lagrangian Floer theory on compact toric manifolds II: bulk deformations

This is a continuation of part I in the series of the papers on Lagrangian Floer theory on toric manifolds. Using the deformations of Floer cohomology by the ambient cycles, which we call bulk deformations, we find a continuum of non-displaceable Lagrangian fibers on some compact toric manifolds. We also provide a method of finding all fibers with non-vanishing Floer cohomology with bulk deformations in arbitrary compact toric manifolds, which we call bulk-balanced Lagrangian fibers.