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Long-duration spaceflight imposes significant physiological stress on astronauts, including profound alterations in immune function. This study investigated epigenetic changes in immune cells following prolonged orbital spaceflight by analysing histone modifications in CD4+ and CD8+ T-cells from astronauts before, immediately after, and during recovery from spaceflight. Using Cleavage Under Targets and Tagmentation (Cut&Tag) to assess H3K27ac modifications, we identified significant alterations in chromatin accessibility, predominantly involving immune response pathways, gene regulation, and cellular adaptation mechanisms. While some epigenetic changes were transient, others persisted beyond 50 days post-return, suggesting long-term effects. These findings enhance our understanding of immune adaptation to spaceflight and have implications for mitigating spaceflight-associated health risks. Furthermore, they provide valuable insights into immune system regulation under high-stress conditions, potentially informing research on immunodeficiency disorders, cancer epigenetics, and aging-related immune decline on Earth. This study underscores the critical role of epigenetics in long-term space missions and terrestrial health applications.

The process by which visual information is incorporated into the brain’s spatial framework to represent landmarks is poorly understood. Studies in humans and rodents suggest that retrosplenial cortex (RSC) plays a key role in these computations. We developed an RSC-dependent behavioral task in which head-fixed mice learned the spatial relationship between visual landmark cues and hidden reward locations. Two-photon imaging revealed that these cues served as dominant reference points for most task-active neurons and anchored the spatial code in RSC. This encoding was more robust after task acquisition. Decoupling the virtual environment from mouse behavior degraded spatial representations and provided evidence that supralinear integration of visual and motor inputs contributes to landmark encoding. V1 axons recorded in RSC were less modulated by task engagement but showed surprisingly similar spatial tuning. Our data indicate that landmark representations in RSC are the result of local integration of visual, motor, and spatial information. When moving through a city, people often use notable or familiar landmarks to help them navigate. Landmarks provide us with information about where we are and where we need to go next. But despite the ease with which we – and most other animals – use landmarks to find our way around, it remains unclear exactly how the brain makes this possible. One area that seems to have a key role is the retrosplenial cortex, which is located deep within the back of the brain in humans. This area becomes more active when animals use visual landmarks to navigate. It is also one of the first brain regions to be affected in Alzheimer's disease, which may help to explain why patients with this condition can become lost and disoriented, even in places they have been many times before. To find out how the retrosplenial cortex supports navigation, Fischer et al. measured its activity in mice exploring a virtual reality world. The mice ran through simulated corridors in which visual landmarks indicated where hidden rewards could be found. The activity of most neurons in the retrosplenial cortex was most strongly influenced by the mouse’s position relative to the landmark; for example, some neurons were always active 10 centimeters after the landmark. In other experiments, when the landmarks were present but no longer indicated the location of a reward, the same neurons were much less active. Fischer et al. also measured the activity of the neurons when the mice were running with nothing shown on the virtual reality, and when they saw a landmark but did not run. Notably, the activity seen when the mice were using the landmarks to find rewards was greater than the sum of that recorded when the mice were just running or just seeing the landmark without a reward, making the “landmark response” an example of so-called supralinear processing. Fischer et al. showed that visual centers of the brain send information about landmarks to retrosplenial cortex. But only the latter adjusts its activity depending on whether the mouse is using that landmark to navigate. These findings provide the first evidence for a “landmark code” at the level of neurons and lay the foundations for studying impaired navigation in patients with Alzheimer's disease. By showing that retrosplenial cortex neurons combine different types of input in a supralinear fashion, the results also point to general principles for how neurons in the brain perform complex calculations.

Key messageWe extended the applicability of the BY-2 cell line as a model by introducing two new selection systems. Our protocol provides guidelines for optimising Basta selection in other recalcitrant models.Tobacco BY-2 cell line is the most commonly used cytological model in plant research. It is uniform, can be simply treated by chemicals, synchronised and easily transformed. However, only a few selection systems are available that complicate advanced studies using multiple stacked transgenes and extensive gene editing. In our work, we adopted for BY-2 cell line two other selection systems: sulfadiazine and phosphinothricin (PPT, an active ingredient of Basta herbicide). We show that sulfadiazine can be used in a wide range of concentrations. It is suitable for co-transformation and subsequent double selection with kanamycin or hygromycin, which are standardly used for BY-2 transformation. We also have domesticated the sulfadiazine resistance for the user-friendly GoldenBraid cloning system. Compared to sulfadiazine, establishing selection on phosphinothricin was considerably more challenging. It did not work in any concentration of PPT with standardly cultured cells. Since the selection is based on blocking glutamine synthetase and consequent ammonium toxicity and deficiency of assimilated nitrogen, we tried to manipulate nitrogen availability. We found that the PPT selection reliably works only with nitrogen-starved cells with reduced nitrate reserves that are selected on a medium without ammonium nitrate. Both these adjustments prevent the release of large amounts of ammonium, which can toxify the entire culture in the case of standardly cultured cells. Since high nitrogen reserves can be a common feature of in vitro cultures grown on MS media, nitrogen starvation could be a key step in establishing phosphinothricin resistance in other plant models.

RNA-directed DNA methylation (RdDM) is driven by small RNAs (sRNAs) complementary to the nascent transcript of RNA polymerase V (Pol V). sRNAs associated with ARGONAUTE (AGO) proteins are tethered to Pol V mainly by the AGO-hook domain of its subunit NRPE1. We found, by in silico analyses, that Pol V strongly colocalizes on chromatin with another AGO-hook protein, SPT6-like (SPT6L), which is a known essential transcription elongation factor of Pol II. Our phylogenetic analysis revealed that SPT6L acquired its AGO-binding capacity already in the most basal streptophyte algae, even before the emergence of Pol V, suggesting that SPT6L might be a driving force behind the RdDM evolution. Since its emergence, SPT6L with the AGO-hook represents the only conserved SPT6 homolog in Viridiplantae , implying that the same protein is involved in both Pol II and Pol V complexes. To better understand the role of SPT6L in the Pol V complex, we characterized genomic loci where these two colocalize and uncovered that DNA methylation there is more dynamic, driven by higher levels of sRNAs often from non-canonical RdDM pathways and more dependent on chromatin modifying and remodeling proteins like MORC. Pol V loci with SPT6L are highly depleted in helitrons but enriched in gene promoters for which locally and temporally precise methylation is necessary. In view of these results, we discuss potential roles of multiple AGO-hook domains present in the Pol V complex and speculate that SPT6L mediates de novo methylation of naïve loci by interconnecting Pol II and Pol V activities.

Swept Source Optical coherence tomography angiography (SS-OCTA) is a novel technique to visualize perfusion and vascular changes like ischemia in patients with diabetic retinopathy. The aim of this study was to compare non-perfusion areas on conventional fluorescein angiography (FA) with those on SS-OCTA using detailed manual annotation in patients with diabetic macular edema (DME) and to evaluate possible artifacts caused by DME on SS-OCTA. 27 eyes of 21 patients with DME were analyzed in this prospective, cross-sectional study; on all, standard ophthalmological examination, SS-OCTA and FA imaging were performed. Early-phase FA and SS-OCTA images were analyzed for capillary dropout and foveal avascular zone (FAZ) was measured on both modalities. Artifacts in SS-OCTA imaging caused by DME were marked and analyzed. The mean age of the patients was 62.6 ± 11.5 years. On FA the mean size of the annotated non-perfusion areas was 0.14 ± 0.31 mm2 whereas the mean size in SS-OCTA was 0.04 ± 0.13 mm2; areas marked on FA were statistically significantly larger than on SS-OCTA (p<0.01). Mean size of FAZs was similar between FA and OCTA images. (p = 0.91). Seven eyes (25.9 percent) showed imaging artifacts due to DME in SS-OCTA. SS-OCTA is a valid tool to analyze capillary perfusion status of patients with DME, although areas of non-perfusion were measured smaller than in conventional FA. More non-perfusion areas were found on SS-OCTA images. FAZ measurements were similar using the two modalities. However, SS-OCTA is prone to artifacts and therefore requires reviewing of imaging results: up to 25 percent of the analyzed eyes showed artifacts on OCTA, which occurred in the areas of diabetic macular edema and did not correspond to capillary drop out.

Background Plant transformation via Agrobacterium tumefaciens is characterized by integration of commonly low number of T-DNAs at random positions in the genome. When integrated into an active gene region, promoterless reporter genes placed near the T-DNA border sequence are frequently transcribed and even translated to reporter proteins, which is the principle of promoter- and gene-trap lines. Results Here we show that even internal promotorless regions of T-DNAs are often transcribed. Such spontaneous transcription was observed in the majority of independently transformed tobacco BY-2 lines (over 65%) and it could effectively induce silencing if an inverted repeat was present within the T-DNA . We documented that the transcription often occurred in both directions. It was not directly connected with any regulatory elements present within the T-DNAs and at least some of the transcripts were initiated outside of the T-DNA . The likeliness of this read-through transcription seemed to increase in lines with higher T-DNA copy number. Splicing and presence of a polyA tail in the transcripts indicated involvement of Pol II, but surprisingly, the transcription was able to run across two transcription terminators present within the T-DNA . Such pervasive transcription was observed with three different T-DNAs in BY-2 cells and with lower frequency was also detected in Arabidopsis thaliana . Conclusions Our results demonstrate unexpected pervasive read-through transcription of T-DNAs . We hypothesize that it was connected with a specific chromatin state of newly integrated DNA, possibly affected by the adjacent genomic region. Although this phenomenon can be easily overlooked, it can have significant consequences when working with highly sensitive systems like RNAi induction using an inverted repeat construct, so it should be generally considered when interpreting results obtained with the transgenic technology.

Cortical neural dynamics mediate information processing for the cerebral cortex, which is implicated in fundamental biological processes such as vision and olfaction, in addition to neurological and psychiatric diseases. Spontaneous pain is a key feature of human neuropathic pain. Whether spontaneous pain pushes the cortical network into an aberrant state and, if so, whether it can be brought back to a \"normal\" operating range to ameliorate pain are unknown. Using a clinically relevant mouse model of neuropathic pain with spontaneous pain-like behavior, we report that orofacial spontaneous pain activated a specific area within the primary somatosensory cortex (S1), displaying synchronized neural dynamics revealed by intravital two-photon calcium imaging. This synchronization was underpinned by local GABAergic interneuron hypoactivity. Pain-induced cortical synchronization could be attenuated by manipulating local S1 networks or clinically effective pain therapies. Specifically, both chemogenetic inhibition of pain-related c-Fos-expressing neurons and selective activation of GABAergic interneurons significantly attenuated S1 synchronization. Clinically effective pain therapies including carbamazepine and nerve root decompression could also dampen S1 synchronization. More important, restoring a \"normal\" range of neural dynamics through attenuation of pain-induced S1 synchronization alleviated pain-like behavior. These results suggest that spontaneous pain pushed the S1 regional network into a synchronized state, whereas reversal of this synchronization alleviated pain.

In the last decade, industry’s demand for deep learning (DL) has increased due to its high performance in complex scenarios. Due to the DL method’s complexity, experts and non-experts rely on blackbox software packages such as Tensorflow and Pytorch. The frameworks are constantly improving, and new versions are released frequently. As a natural process in software development, the released versions contain improvements/changes in the methods and their implementation. Moreover, versions may be bug-polluted, leading to the model performance decreasing or stopping the model from working. The aforementioned changes in implementation can lead to variance in obtained results. This work investigates the effect of implementation changes in different major releases of these frameworks on the model performance. We perform our study using a variety of standard datasets. Our study shows that users should consider that changing the framework version can affect the model performance. Moreover, they should consider the possibility of a bug-polluted version before starting to debug source code that had an excellent performance before a version change. This also shows the importance of using virtual environments, such as Docker, when delivering a software product to clients.

The main challenges are discussed together with the lessons learned from past and ongoing research along the development cycle of machine learning systems. This will be done by taking into account intrinsic conditions of nowadays deep learning models, data and software quality issues and human-centered artificial intelligence (AI) postulates, including confidentiality and ethical aspects. The analysis outlines a fundamental theory-practice gap which superimposes the challenges of AI system engineering at the level of data quality assurance, model building, software engineering and deployment. The aim of this paper is to pinpoint research topics to explore approaches to address these challenges.

In Graeco-Roman times in the Lower-Egyptian Fayoum region, a painted portrait was traditionally placed over the face of a deceased individual. These mummy portraits show considerable inter-individual diversity. This suggests that those portraits were created separately for each individual. In the present study, we investigated a completely wrapped young infant mummy with a typical mummy portrait by whole body CT analysis. This was used to obtain physical information on the infant and provided the basis for a virtual face reconstruction in order to compare it to the mummy portrait. We identified the mummy as a 3-4 years old male infant that had been prepared according to the typical ancient Egyptian mummification rites. It most probably suffered from a right-sided pulmonary infection which may also be the cause of death. The reconstructed face showed considerable similarities to the portrait, confirming the portrait's specificity to this individual. However, there are some differences between portrait and face. The portrait seems to show a slightly older individual which may be due to artistic conventions of that period.