Miracle-dz/UniFAR-FTUs huggingface dataset:
Cellulose–Callose Hydrogels: Computational Exploration of Their Nanostructure and Mechanical Properties

Polysaccharides play a crucial role in virtually all living systems. They also represent the biocompatible and fully sustainable component of a variety of nanoparticles, which are of increasing interest in biomedicine, food processing, cosmetics, and structural reinforcement of polymeric materials. The computational modeling of complex polysaccharide phases will assist in understanding the properties and behavior of all these systems. In this paper, structural, bonding, and mechanical properties of 10 wt % cellulose–callose hydrogels (β-glucans coexisting in plant cell walls) were investigated by atomistic simulations. Systems of this kind have recently been introduced in experiments revealing unexpected interactions between the polysaccharides. Starting from initial configurations inspired by X-ray diffraction data, atomistic models made of ∼1.6 × 106 atoms provide a qualitatively consistent view of these hydrogels, displaying stability, homogeneity, connectivity, and elastic properties beyond those of a liquid suspension. The simulation shows that the relatively homogeneous distribution of saccharide nanofibers and chains in water is not due to the solubility of cellulose and callose, but to the formation of a number of cross-links among the various sample components. The broad distribution of strength and elasticity among the links implies a degree of anharmonicity and irreversible deformation already evident at low external load. Besides the qualitative agreement with experimental observations, the simulation results display also quantitative disagreements in the estimation of elastic coefficients, such as the Young’s modulus, that require further investigation. Complementary simulations of dense cellulose–callose mixtures (no hydrogels) highlight the role of callose in smoothing the contact surface of different nanofibers forming larger bundles. Cellulose–callose structures in these systems displayed an enhanced water uptake and delayed dye release when compared to cellulose alone, highlighting potential new applications as drug delivery scaffolds. The simulation trajectories provide a tuning and testing ground for the development of coarse-grained models that are required for the large scale investigation of mechanical properties of cellulose and callose mixtures in a watery environment.
Crossing the Mediterranean Sea by boat. Mapping and documenting migratory journeys and experiences, final project report

This report provides a unique, in-depth analysis of the impact of EU policies in addressing the so-called European migration or refugee ‘crisis’ in 2015 and 2016. Crossing the Mediterranean Sea by Boat undertook 257 in-depth qualitative interviews with a total of 271 participants across seven sites in two phases: Kos, Malta and Sicily from September-November 2015, and Athens, Berlin, Istanbul and Rome from May-July 2016. Uniquely, the project focused directly on the impact of policies upon people on the move, drawing together policy analysis and observational fieldwork with in-depth analysis of qualitative interview data from people making – or contemplating making – the dangerous journey across the Mediterranean Sea. As such, the report provides previously-unconsidered insights into the effects of policy on the journeys, experiences, understandings, expectations, concerns and demands of people on the move. In addition to providing seven site-based case study analyses, the project also provides the first detailed assessment of policies associated with A European Agenda on Migration in terms of policy effects both across routes (eastern and central Mediterranean) and over time (2015 and 2016). The findings and analysis summarised in this report are presented with the aim of informing policy developments, moving forward.
Specific Gravity, Dry Matter Content, and Starch Content of Potato (Solanum tuberosum L.) Varieties Cultivated in Eastern Ethiopia

Abstract: Several farmers’ and improved potato varieties are cultivated by farmers in the eastern highlands of Ethiopia. However, sufficient information is not available on tuber quality characteristics of the potato varieties. Therefore, experiments were conducted at three locations in the region, namely, Haramaya, Hirna and Arbarakatte in eastern Ethiopia during the 2012 to 2014 main cropping season to elucidate the internal tuber quality characteristics of 17 potato varieties and prepare a specific gravity conversion chart. The treatments consisted of 17 potato varieties (Araarsaa, Badhasa, Belete, Batte, Bubu, Bulle, Chala, Chiro, Gabbisa, Gera, Gorebela, Gudanie, Guasa, Jalenie, Jarso, Mara Charre and Zemen). The experiment at location was laid out as a randomized complete block design and replicated three times per treatment. The results revealed that tuber specific gravity (SG), dry matter (DM) and starch contents (SC) were significantly influenced by variety, location and year, while the interaction of the three factors significantly influenced SG and SC. All improved cultivars produced tubers with >1.085, >21% and > 14% of SG, DM and SC, respectively, and were found to be suitable for making French fries, chips and flakes. However, tubers of the local varieties had <1.07 gcm 2 , < 20% and < 11% SG, DM and SC, respectively, and were found to be suitable for making whole boiled potatoes. The dendrogram constructed using Unweighted Pair-group Method with Arithmetic means separated the varieties into three clusters of which Cluster I with distinct Sub-group I consisted of eight improved varieties (Ararsa, Bule, Marachere, Badhasa, Challa, Jalanine, Gabisa and Zemen) and Sub-group II six improved cultivars (Bubu, Gera, Gorbella, Gudenine, Gusa and Chiro) , and Clusters II and III consisted of one improved variety (Belete) and two farmers’ varieties (Batte and Jarso), respectively. The varieties found to be suitable for making processed potato products (French fries, etc) were grouped in the Sub-group I as they produced tubers with SG, DM and SC contents of acceptable standard for making such products while cultivars in Sub-group II and Belete (Cluster II) produced tubers with high SG, DM and SC contents that may produce too hard, dry and brittle French fries and chips. The correlation of specific gravity with dry matter and starch contents being perfect or near to perfect (r=0.962 to 1) across locations and seasons with high coefficient of determination (R 2 =0.924 to 0.999). It could, thus, be concluded that it is appropriate to use specific gravity and the conversion chart produced from this tuber quality trait to estimate the other two traits (dry matter and starch contents) and determine the quality of tubers for processing. Keywords: Coefficient of determination; Conversion chart; Correlation; Internal tuber quality.
A converged ubiquitin-proteasome pathway for the degradation of TOC and TOM tail-anchored receptors

In plants, thousands of nucleus-encoded proteins translated in the cytosol are sorted to chloroplasts and mitochondria by binding to specific receptors of the TOC (translocon at the outer membranes of chloroplasts) and the TOM (translocon at the outer membranes of mitochondria) complexes for import into those organelles. The degradation pathways for these receptors are unclear. Here, we discovered a converged ubiquitin-proteasome pathway for the degradation of Arabidopsis thaliana TOC and TOM tail-anchored receptors. The receptors are ubiquitinated by E3 ligase(s) and pulled from the outer membranes by the AAA+ ATPase CDC48, after which a previously characterized cytosolic protein, TTOP, binds to the exposed transmembrane domains (TMDs) at the C termini of the receptors and CDC48, and delivers these complexes to the 26S proteasome.
Concurrent Ascaris infection modulates host immunity resulting in impaired control of Salmonella infection in pigs

Ascaris is one of the most widespread helminth infections of humans and pigs, leading to chronic morbidity in humans and considerable economic losses in pig farming. Additionally, pigs are an important reservoir for the zoonotic bacterial pathogen Salmonella, where pigs can serve as asymptomatic carriers. Here, we investigated the impact of an ongoing Ascaris infection on the immune response to Salmonella in pigs. We observed higher bacterial burdens in experimentally coinfected pigs compared to pigs infected with Salmonella alone. Ascaris-infected pigs exhibited numerous hallmarks of a type 2 immune response in organs impacted by larval migration, including increased Th2 cells, increased IL-4 production, eosinophilia, and increased expression of CD206, a marker for alternatively activated macrophages. While we observed only mild changes in frequencies of CD4+ Treg, Ascaris- infected pigs had increased frequencies of CD8α+ Treg. We show that type 2 immune signals enhance susceptibility of macrophages to Salmonella infection in vitro. Furthermore, Ascaris impaired Salmonella-induced monocytosis and TNF-α production by myeloid cells. Hence, our data demonstrate widespread immunomodulation during an acute Ascaris infection that facilitates the microbial spread into gut-associated lymphoid tissue in a Salmonella coinfection. Importance In experimentally infected pigs we show that an ongoing infection with the parasitic worm Ascaris suum modulates host immunity to render pigs more susceptible to invading Salmonella. Both infections are widespread in pig production and the prevalence of Salmonella is high in endemic regions of human Ascariasis, indicating that this is a clinically meaningful coinfection. We observed a type 2 immune response to be induced during an Ascaris infection correlating with an increased susceptibility of pigs to the concurrent bacterial infection.
Graphene microelectrode arrays, 4D structured illumination microscopy, and a machine learning-based spike sorting algorithm permit the analysis of ultrastructural neuronal changes during neuronal signalling in a model of Niemann-Pick disease type C

Simultaneously recording network activity and ultrastructural changes of the synapse is essential for advancing our understanding of the basis of neuronal functions. However, the rapid millisecond-scale fluctuations in neuronal activity and the subtle sub-diffraction resolution changes of synaptic morphology pose significant challenges to this endeavour. Here, we use graphene microelectrode arrays (G-MEAs) to address these challenges, as they are compatible with high spatial resolution imaging across various scales as well as high temporal resolution electrophysiological recordings. Furthermore, alongside G-MEAs, we deploy an easy-to-implement machine learning-based algorithm to efficiently process the large datasets collected from MEA recordings. We demonstrate that the combined use of G-MEAs, machine learning (ML)-based spike analysis, and four-dimensional (4D) structured illumination microscopy (SIM) enables the monitoring of the impact of disease progression on hippocampal neurons which have been treated with an intracellular cholesterol transport inhibitor mimicking Niemann-Pick disease type C (NPC) and show that synaptic boutons, compared to untreated controls, significantly increase in size, which leads to a loss in neuronal signalling capacity.
DEVELOPMENTALLY STABLE REPRESENTATIONS OF NATURALISTIC IMAGE STRUCTURE IN MACAQUE VISUAL CORTEX

We studied visual development in macaque monkeys using texture stimuli, matched in local spectral content but varying in “naturalistic” structure. In adult monkeys, naturalistic textures preferentially drive neurons in areas V2 and V4, but not V1. We paired behavioral measurements of naturalness sensitivity with separately-obtained population recordings from neurons in areas V1, V2, V4, and inferotemporal cortex (IT). We made behavioral measurements from 16 weeks of age and physiological measurements as early as 20 weeks, and continued through 56 weeks. We measured behavior with a reinforced looking paradigm based on oddity detection. Behavioral sensitivity reached half of maximum at roughly 25 weeks of age. Neural sensitivities remained stable from the earliest ages tested. As in adults, neural sensitivity to naturalistic structure increased from V1 to V2 to V4. While sensitivities in V2 and IT were similar, the dimensionality of the IT representation was more similar to V4’s than to V2’s.
The sea urchin intestinal microbiome responds dynamically to food intake and contains nitrogen-fixing symbionts

Kelp deforestation by sea urchin grazing is a widespread phenomenon globally, with vast consequences for coastal ecosystems. The ability of sea urchins to survive on a kelp diet of poor nutritional quality is not well understood and bacterial communities in the sea urchin intestine may play an important role in digestion. A no-choice feeding experiment was conducted with the sea urchin Strongylocentrotus droebachiensis, offering three different seaweeds as diet, including the kelp Saccharina latissima. Starved sea urchins served as experimental control. Amplicons of the 16S rRNA gene were analyzed from fecal pellets. One dominant symbiont (Psychromonas marina) accounted for 44 % of all sequence reads and was especially abundant in the sea urchins fed seaweed diets. The starved and field captured sea urchins consistently displayed higher diversity than the seaweed-fed sea urchins and displayed a higher predicted abundance of genes involved in nitrogen fixation. Cloning and sequencing of the NifH gene revealed diverse nitrogen fixers. We demonstrate that the sea urchin intestinal microbiome is dynamic, responds to diet and has the capacity for nitrogen fixation. The microbiome thereby reflects the dietary flexibility of these sea urchins, and could be a key component in understanding catastrophic kelp forest grazing events.
Large herbivores link plant phenology and abundance in arctic tundra

Plant phenology has been well studied in relation to abiotic conditions and climate change, but poorly studied in relation to herbivory. In contrast, plant abundance dynamics have been well studied in relation to abiotic conditions and herbivory, but poorly studied in relation to phenology. Consequently, the contribution of herbivory to plant phenological dynamics and therefrom to plant abundance dynamics remains obscure. We conducted a nine-year herbivore exclusion experiment to investigate whether herbivory might link plant phenological and abundance dynamics in arctic tundra. From 2009 - 2017 we monitored annual green-up timing and abundance of nine plant taxa, including deciduous shrubs, forbs, and graminoids, on plots that were either grazed or experimentally exclosed from herbivory by caribou (Rangifer tarandus) and muskoxen (Ovibos moschatus). In 62% of cases, green-up occurred earlier under herbivory, and in 75% of cases abundance was greater under herbivory, compared to green-up and abundance under herbivore exclusion. Moreover, taxa that responded to herbivory with earlier green-up also had comparatively greater abundance later in the growing season. Conversely, taxa that responded to herbivory with delayed green-up exhibited comparatively lower abundance later in the growing season. Hence, well-documented influences of large herbivores on plant abundance and community composition in arctic tundra may, at least to some extent, relate to influences of herbivory on plant phenology. We recommend that ongoing and future assessments of the contribution of herbivores to plant abundance and community responses to climate change, especially in the Arctic, should also consider impacts of herbivores on plant phenology.
Five-leaf generalizations of the D-statistic reveal the directionality of admixture

Over the past 15 years, the D-statistic, a four-taxon test for organismal admixture (hybridization, or introgression) that incorporates single nucleotide polymorphism data with allelic patterns ABBA and BABA, has seen considerable use. This statistic seeks to discern significant deviation from either a given species tree assumption, or from the balanced incomplete lineage sorting that could otherwise defy this species tree. However, while the D-statistic can successfully discriminate admixture from incomplete lineage sorting, it is not a simple matter to determine the directionality of admixture using only four-leaf tree models. As such, methods have been developed that use 5 leaves to evaluate admixture trajectories. Among these, the DFOIL method, which tests allelic patterns on the “symmetric” tree S = (((1, 2), (3, 4)), 5), succeeds in finding admixture direction for many five-taxon examples. However, DFOIL does not make full use of all symmetry, nor can DFOIL properly accommodate the use of singleton patterns (such as BAAAA and ABAAA) when ancient samples are included. The latter becomes problematic since “mutational time” elapsed since ancient organism death is unequal to that of modern samples, and because damaged DNA can bias results in unknown ways. Here, we take inspiration from DFOIL to develop a new and completely general family of five-leaf admixture tests, dubbed Δ-statistics, that can either incorporate or exclude the singleton allelic patterns depending on individual taxon and age sampling choices. We describe two new shapes that are also fully testable, namely the “asymmetric” tree A = ((((1, 2), 3), 4), 5) and the “quasisymmetric” tree Q = (((1, 2), 3), (4, 5)), that can considerably supplement the “symmetric” S = (((1, 2), (3, 4)), 5) model used by DFOIL. We demonstrate the consistency of Δ-statistics under various simulated scenarios, and provide empirical examples using data from black, brown and polar bears, the latter also including two ancient samples from previous studies. Recently DFOIL and one of these ancient samples was used to argue for a dominant polar bear → brown bear introgression direction. However, we find, using both this ancient polar bear and our own, that by far the strongest signal using both DFOIL and Δ-statistics on tree S is actually bidirectional gene flow of indistinguishable direction. Further experiments on trees A and Q instead highlight what were likely two phases of admixture: one with stronger brown bear → polar bear introgression in ancient times, and a recent phase with predominant polar bear → brown bear directionality. Code and documentation available at https://github.com/KalleLeppala/Delta-statistics.
Photoreceptor-induced LHL4 protects photosystem II in Chlamydomonas reinhardtii

Photosynthesis, the fundamental process using light energy to convert CO2 to organic matter, is vital for life on Earth. It relies on capturing light through light-harvesting complexes in evolutionarily well-conserved photosystems (PS) I and II and on the conversion of light energy into chemical energy. Composition and organization of both photosystem core complexes are well conserved across evolution. PSII is particularly sensitive to photodamage but benefits from a large diversity of photoprotective mechanisms, finely tuned for the specific light conditions. Light Harvesting Complex protein family members (LHC and LHC-like families) have acquired a dual function during evolution. Members of the LHC antenna complexes of photosystems capture light energy whereas others dissipate excess energy that cannot be harnessed for photosynthesis. This process mainly occurs through non photochemical quenching (NPQ). In this work, we focus on the LHL4 protein, which is a LHC-like protein induced by UV-B and blue light photoreceptor signaling pathways in the model green microalgae Chlamydomonas reinhardtii. We demonstrate that alongside established NPQ effectors, LHL4 plays a key role in photoprotection, preventing singlet oxygen accumulation in PSII and promoting cell survival upon light stress. LHL4 protective function is distinct from that of NPQ-related proteins, as it specifically and uniquely binds to the transient monomeric form of the core PSII complex, safeguarding its integrity. LHL4 characterization expands our understanding of the interplay between light harvesting and photoprotection mechanisms upon light stress in photosynthetic microalgae.
Simultaneous circulation and coinfection of Dengue clades and serotypes in Southern Brazil

Dengue is an arthropod-borne virus with worldwide urban transmission mediated by anthropophilic vectors of the genus Aedes. Currently, there is a substantial genotype diversity that belongs to at least four known serotypes. Tropical regions, where several serotypes cocirculate in the population, are hyperendemic, driving multiple outbreaks with variable disease manifestations. Notably, the Dengue virus burden is increasing in subtropical and temperate regions of the globe due to climatic changes associated with new outbreaks in naive and previously unaffected human populations. The introduction and endemic transmission of different clades and serotypes in these regions is highly concerning due to the known and still unknown consequences of Dengue infection on populations with diverse genetic backgrounds. Here, we characterized the coinfection of different Dengue clades and serotypes in Rio Grande do Sul, Brazil’s southernmost and subtropical state, by combining serotype-specific RT-PCR and deep sequencing. We found five coinfected patients in four municipalities where these clades and serotypes circulated simultaneously. Our data suggests that coinfection events account for a minority of total cases, but these findings may reflect the early transmission phases of some Dengue clades. Hence, close monitoring is warranted to evaluate coinfection rates and associated clinical consequences as clade prevalence changes.
Characterisation of mesenchymal stromal cells in the skin of Atlantic salmon

Background The skin serves as the first line of defence for an organism against the external environment. Despite the global significance of salmon in aquaculture, a critical component of this first line of defence, mesenchymal stromal cells, remains unexplored. These pluripotent cells can differentiate into various tissues, including bone, cartilage, tendon, ligament, adipocytes, dermis, muscle and connective tissue within the skin. These cells are pivotal for preserving the integrity of skin tissue throughout an organism’s lifespan and actively participate in wound healing processes. Results In this study, we characterise mesenchymal stromal cells in detail for the first time in healthy Atlantic salmon tissue and during the wound healing process. Single-nucleus sequencing and spatial transcriptomics revealed the transcriptional dynamics of these cells, elucidating the differentiation pathways leading to osteogenic and fibroblast lineages in the skin of Atlantic salmon. We charted their activity during an in vivo wound healing time course, showing clear evidence of their active role during this process, as they become transcriptionally more active during the remodelling stage of wound healing. Conclusions For the first time, we chart the activity of sub-clusters of differentiating stromal cells during the process of wound healing, revealing different spatial niches of the various MSC subclusters, and setting the stage for investigations into the manipulation of MSCs to improve fish health.