Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpha Event-related Desynchronization During Reward Processing in Schizophrenia

Background Deficits in the way the brain processes rewards may contribute to negative symptoms in schizophrenia. Synchronization of alpha band neural oscillations is a dominant EEG signal when people are awake, but at rest. In contrast, alpha desynchronization to salient events is thought to direct allocation of information processing resources away from the internal state, to process salient stimuli in the external environment. Here, we hypothesize that alpha event-related desynchronization (ERD) during reward processing is altered in schizophrenia, leading to less difference in alpha ERD magnitude between winning and losing outcomes. Methods EEG was recorded while participants (patients with schizophrenia (SZ)=54; healthy controls (HC) = 54) completed a casino-style slot machine gambling task. Total power, a measure of neural oscillation magnitude was measured in the alpha frequency range (8-14 Hz), time-locked to reward delivery, extracted via principal components analysis, and then compared between groups and equiprobable win and near miss loss reward outcomes. Associations between alpha power and negative symptoms and trait rumination were examined. Results A significant Group X Reward Outcome interaction (p=.018) was explained by differences within the HC group, driven by significant posterior-occipital alpha desynchronization to wins, relative to near miss losses (p<.001). In contrast, SZ did not modulate alpha power to wins vs. near miss losses (p>.1), nor did alpha power relate to negative symptoms (p>.1). However, across all participants, less alpha ERD to reward outcomes was related to more trait rumination, for both wins (p=.005) and near-miss losses (p=.002), with no group differences observed in the slopes of these relationships. Conclusion These findings suggest that event-related modulation of alpha power is altered in schizophrenia during reward outcome processing, even when reward attainment places minimal demands on higher-order cognitive processes during slot machine play. In addition, high trait rumination is associated with less event-related desynchronization to reward feedback, suggesting that rumination covaries with less external attentional allocation to reward processing, regardless of reward outcome valence and group membership.
Evaluation of the growth performance, physiological traits, antioxidant indices, and heat shock protein 70 to dietary supplementation of stinging nettle (Urtica dioica) in broilers exposed to chronic heat stress

Heat stress is known as one of the most prevalent environmental stressors in poultry production, which is associated with oxidative stress. Stinging nettle is a medicinal herb with strong antioxidant properties. The present study was conducted to evaluate the effects of dietary stinging nettle at two different levels (2% and 4%) on growth performance and oxidative stress indices of broilers exposed to chronic heat stress. On day 14, a total of 240 broiler chickens were randomly assigned to 6 treatment groups as follows: 1) NC: negative control; 2) HS: heat-stressed broiler; 3) HS-SN2: heat-stressed broiler fed by 2% dietary stinging nettle; 4) HS-SN4: heat-stressed broilers fed by 4% stinging nettle; 5) SN2: no heat-stressed broilers fed by 2% dietary stinging nettle; 6) SN4: no heat-stressed broilers fed by 4% dietary stinging nettle. Diet supplementation with stinging nettle was performed from days 14 to 35 and a chronic heat stress was induced from days 22 to 29. The growth performance and oxidative indices were evaluated on days 14, 21, 29, and 35. Rectal temperature and panting frequency were assessed on days 22, 25, and 29. As a result, weight gain and food intake decreased in the HS compared to the NC, and these parameters increased in the HS-SN2 and HS-SN4 compared to the HS (P<0.05). The HS, HS-SN2, and HS-SN4 groups had a significantly higher rectal temperature and panting frequency. The HS had the higher circulating MDA and HSP70, and lower T-AOC, SOD, and GSH-Px compared to the treatments. The HS-SN4 had a significantly lower MDA and HSP70, and higher T-AOC, GSH-Px, and SOD compared to the HS and HS-SN2. In conclusion, the addition of 4% stinging nettle powder to the broilers’ diet improved the oxidative status in heat-stressed birds. Furthermore, this herb could be utilized as a feed additive in poultry diet to improve bird’s health and defense mechanisms under stressful conditions.
Microglia become hypofunctional and release metalloproteases and tau seeds when phagocytosing live neurons with P301S tau aggregates

The microtubule-associated protein tau aggregates in multiple neurodegenerative diseases, causing inflammation and changing the inflammatory signature of microglia by unknown mechanisms. We have shown that microglia phagocytose live neurons containing tau aggregates cultured from P301S tau transgenic mice due to neuronal tau aggregate-induced exposure of the ‘eat me’ signal phosphatidylserine. Here we show that after phagocytosis, microglia become hypophagocytic while releasing seed-competent insoluble tau aggregates. These microglia activate acidic β-galactosidase, and release senescence-associated cytokines and matrix remodeling enzymes alongside tau, indicating a senescent phenotype. In particular, the marked NFκB-induced activation of matrix metalloprotease 3 (MMP3/stromelysinl) was replicated in the brains of P301S mutant tau transgenic mice, and in human brains from tauopathy patients. These data show that microglia that have been activated to ingest live neurons with tau aggregates behave hormetically, becoming hypofunctional while acting as vectors of tau aggregate spreading.
The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes

The signaling network of the unfolded protein response (UPR) adjusts the protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined the in-situ structure of IRE1α foci by cryogenic correlated light and electron microscopy (cryo-CLEM), combined with electron cryo-tomography (cryo-ET) and complementary immuno-electron microscopy. IRE1α oligomers localize to a network of narrow anastomosing ER tubes (diameter ~28 nm) with complex branching. The lumen of the tubes contains protein filaments, likely composed of linear arrays of IRE1α lumenal domain dimers, arranged in two intertwined, left-handed helices. Our findings define a previously unrecognized ER subdomain and suggest positive feedback in IRE1 signaling.
Using optogenetics to link myosin patterns to contractile cell behaviors during convergent extension

Distinct spatiotemporal patterns of actomyosin contractility are often associated with particular epithelial tissue shape changes during development. For example, a planar polarized pattern of myosin II localization regulated by Rho1 signaling during Drosophila body axis elongation is thought to drive the cell behaviors that contribute to convergent extension. However, it is not well understood how specific aspects of a myosin localization pattern influence the multiple cell behaviors—including cell intercalation, cell shape changes, and apical cell area fluctuations—that simultaneously occur within a tissue during morphogenesis. Here, we use optogenetic activation (optoGEF) and deactivation (optoGAP) of Rho1 signaling to perturb the myosin pattern in the germband epithelium during Drosophila axis elongation and analyze the effects on contractile cell behaviors within the tissue. We find that uniform photoactivation of optoGEF or optoGAP is sufficient to rapidly override the endogenous myosin pattern, abolishing myosin planar polarity and reducing cell intercalation and convergent extension. However, these two perturbations have distinct effects on junctional and medial myosin localization, apical cell area fluctuations, and cell packings within the germband. Activation of Rho1 signaling in optoGEF embryos increases myosin accumulation in the medial-apical domain of germband cells, leading to increased amplitudes of apical cell area fluctuations. This enhanced contractility is translated into heterogeneous reductions in apical cell areas across the tissue, disrupting cellular packings within the germband. Conversely, inactivation of Rho1 signaling in optoGAP embryos decreases both medial and junctional myosin accumulation, leading to a dramatic reduction in cell area fluctuations. These results demonstrate that the level of Rho1 activity and the balance between junctional and medial myosin regulate apical cell area fluctuations and cellular packings in the germband, which have been proposed to influence the biophysics of cell rearrangements and tissue fluidity. STATEMENT OF SIGNIFICANCE Tissues are shaped by forces produced by dynamic patterns of actomyosin contractility. However, the mechanisms underlying these myosin patterns and their translation into cell behavior and tissue-level movements are not understood. Here, we show that optogenetic tools designed to control upstream regulators of myosin II can be used to rapidly manipulate myosin patterns and analyze the effects on cell behaviors during tissue morphogenesis. Combining optogenetics with live imaging in the developing fruit fly embryo, we show that acute perturbations to upstream myosin regulators are sufficient to rapidly perturb existing myosin patterns and alter cell movements and shapes during axis elongation, resulting in abnormalities in embryo shape. These results directly link myosin contractility patterns to cell behaviors that shape tissues, providing new insights into the mechanisms that generate functional tissues.
DENTIST – using long reads to close assembly gaps at high accuracy

Long sequencing reads allow increasing contiguity and completeness of fragmented, shortread based genome assemblies by closing assembly gaps, ideally at high accuracy. While several gap closing methods have been developed, these methods often close an assembly gap with sequence that does not accurately represent the true sequence. Here, we developed DENTIST, a sensitive, highly-accurate and automated pipeline method to close gaps in short read assemblies with long reads. DENTIST comprehensively determines repetitive assembly regions to identify reliable and unambiguous alignments of long reads to the right loci, integrates a consensus sequence computation step to obtain a high base accuracy for the inserted sequence, and validates the accuracy of closed gaps. Unlike previous benchmarks, we generated test assemblies that have gaps at the exact positions where real short-read assemblies have gaps. Generating such realistic benchmarks for Drosophila (134 Mb genome), Arabidopsis (119 Mb), hummingbird (1 Gb) and human (3 Gb) and using simulated or real PacBio reads, we show that DENTIST consistently achieves a substantially higher accuracy compared to previous methods, while having a similar sensitivity. As another distinguishing feature, DENTIST can accurately scaffold the given contigs with long reads in addition to closing gaps, extending its application range to contig-only assemblies. In summary, DENTIST provides an accurate approach to improve the contiguity and completeness of fragmented assemblies with long reads. DENTIST’s source code including a Snakemake workflow and Docker container is available at https://github.com/a-ludi/dentist. All test assemblies as a resource for future benchmarking are at https://bds.mpi-cbg.de/hillerlab/DENTIST/.
Engineered Orange Ectopically Expressing the Arabidopsis β-Caryophyllene Synthase Is Not Attractive to Diaphorina citri, the Vector of the Bacterial Pathogen Associated to Huanglongbing

Huanglongbing (HLB) is a destructive disease, associated with psyllid-transmitted phloem-restricted pathogenic bacteria, which is seriously endangering citriculture worldwide. It affects all citrus species and cultivars regardless of the rootstock used, and despite intensive research in the last decades, there is no effective cure to control either the bacterial species (Candidatus Liberibacter spp.) or their insect vectors (Diaphorina citri and Trioza erytreae). Currently, the best attempts to manage HLB are based on three approaches: (i) reducing the psyllid population by intensive insecticide treatments; (ii) reducing inoculum sources by removing infected trees, and (iii) using nursery-certified healthy plants for replanting. The economic losses caused by HLB (decreased fruit quality, reduced yield, and tree destruction) and the huge environmental costs of disease management seriously threaten the sustainability of the citrus industry in affected regions. Here, we have generated genetically modified sweet orange lines to constitutively emit (E)-β-caryophyllene, a sesquiterpene repellent to D. citri, the main HLB psyllid vector. We demonstrate that this alteration in volatile emission affects behavioral responses of the psyllid in olfactometric and no-choice assays, making them repellent/less attractant to the HLB vector, opening a new alternative for possible HLB control in the field.
Latent Anti-nutrients and Unintentional Breeding Consequences in Australian Sorghum bicolor Varieties

Modern feed quality sorghum grain has been bred to reduce anti-nutrients, most conspicuously condensed tannins, but its inclusion in the diets of monogastric animals can still result in variable performance that is only partially understood. Sorghum grain contains several negative intrinsic factors, including non-tannin phenolics and polyphenols, phytate, and kafirin protein, which may be responsible for these muted feed performances. To better understand the non-tannin phenolic and polyphenolic metabolites that may have negative effects on nutritional parameters, the chemical composition of sorghum grain polyphenol extracts from three commercial varieties (MR-Buster, Cracka, and Liberty) was determined through the use of an under-studied, alternative analytical approach involving Fourier-transform infrared (FT-IR) spectroscopy and direct ionization mass spectrometry. Supervised analyses and interrogation of the data contributing to variation resulted in the identification of a variety of metabolites, including established polyphenols, lignin-like anti-nutrients, and complex sugars, as well as high levels of fatty acids which could contribute to nutritional variation and underperformance in monogastrics. FT-IR and mass spectrometry could both discriminate among the different sorghum varieties indicating that FT-IR, rather than more sophisticated chromatographic and mass spectrometric methods, could be incorporated into quality control applications.
The Association Between Smartphone Addiction and Sleep: A UK Cross-Sectional Study of Young Adults

Background: In a large UK study we investigated the relationship between smartphone addiction and sleep quality in a young adult population. Methods: We undertook a large UK cross-sectional observational study of 1,043 participants aged 18 to 30 between January 21st and February 30th 2019. Participants completed the Smartphone Addiction Scale Short Version, an adapted Pittsburgh Sleep Quality Score Index and reported smartphone use reduction strategies using both in-person (n = 968) and online (n = 75) questionnaires. A crude and adjusted logistic regression was fitted to assess risk factors for smartphone addiction, and the association between smartphone addiction and poor sleep. Results: One thousand seventy one questionnaires were returned, of which 1,043 participants were included, with median age 21.1 [interquartile range (IQR) 19–22]. Seven hundred and sixty three (73.2%) were female, and 406 reported smartphone addiction (38.9%). A large proportion of participants disclosed poor sleep (61.6%), and in those with smartphone addiction, 68.7% had poor sleep quality, compared to 57.1% of those without. Smartphone addiction was associated with poor sleep (aOR = 1.41, 95%CI: 1.06–1.87, p = 0.018). Conclusions: Using a validated instrument, 39% young adults reported smartphone addiction. Smartphone addiction was associated with poor sleep, independent of duration of usage, indicating that length of time should not be used as a proxy for harmful usage.
MANF Produced by MRL Mouse-Derived Mesenchymal Stem Cells Is Pro-regenerative and Protects From Osteoarthritis

The super healer Murphy Roths Large (MRL) mouse represents the “holy grail” of mammalian regenerative model to decipher the key mechanisms that underlies regeneration in mammals. At a time when mesenchymal stem cell (MSC)-based therapy represents the most promising approach to treat degenerative diseases such as osteoarthritis (OA), identification of key factors responsible for the regenerative potential of MSC derived from MRL mouse would be a major step forward for regenerative medicine. In the present study, we assessed and compared MSC derived from MRL (MRL MSC) and C57BL/6 (BL6 MSC) mice. First, we compare the phenotype and the differentiation potential of MRL and BL6 MSC and did not observe any difference. Then, we evaluated the proliferation and migration potential of the cells and found that while MRL MSC proliferate at a slower rate than BL6 MSC, they migrate at a significantly higher rate. This higher migration potential is mediated, in part, by MRL MSC-secreted products since MRL MSC conditioned medium that contains a complex of released factors significantly increased the migration potential of BL6 MSC. A comparative analysis of the secretome by quantitative shotgun proteomics and Western blotting revealed that MRL MSC produce and release higher levels of mesencephalic astrocyte-derived neurotrophic factor (MANF) as compared to MSC derived from BL6, BALB/c, and DBA1 mice. MANF knockdown in MRL MSC using a specific small interfering RNA (siRNA) reduced both MRL MSC migration potential in scratch wound assay and their regenerative potential in the ear punch model in BL6 mice. Finally, injection of MRL MSC silenced for MANF did not protect mice from OA development. In conclusion, our results evidence that the enhanced regenerative potential and protection from OA of MRL mice might be, in part, attributed to their MSC, an effective reservoir of MANF.
Therapeutic Effects of Probiotic Minas Frescal Cheese on the Attenuation of Ulcerative Colitis in a Murine Model

Inflammatory bowel diseases (IBDs) constitute disturbances of gastrointestinal tract that cause irreversible changes in the structure and function of tissues. Ulcerative colitis (UC), the most frequent IBD in the population, is characterized by prominent inflammation of the human colon. Functional foods containing probiotic bacteria have been studied as adjuvants to the treatment or prevention of IBDs. The selected probiotic strain Lactococcus lactis NCDO 2118 (L. lactis NCDO 2118) exhibits immunomodulatory effects, with promising results in UC mouse model induced by dextran sodium sulfate (DSS). Additionally, cheese is a dairy food that presents high nutritional value, besides being a good delivery system that can be used to improve survival and enhance the therapeutic effects of probiotic bacteria in the host. Therefore, this work investigated the probiotic therapeutic effects of an experimental Minas Frescal cheese containing L. lactis NCDO 2118 in DSS-induced colitis in mice. During colitis induction, mice that consumed the probiotic cheese exhibited reduced in the severity of colitis, with attenuated weight loss, lower disease activity index, limited shortening of the colon length, and reduced histopathological score. Moreover, probiotic cheese administration increased gene expression of tight junctions’ proteins zo-1, zo-2, ocln, and cln-1 in the colon and increase IL-10 release in the spleen and lymph nodes. In this way, this work demonstrates that consumption of probiotic Minas Frescal cheese, containing L. lactis NCDO 2118, prevents the inflammatory process during DSS-induced colitis in mice, opening perspectives for the development of new probiotic functional foods for personalized nutrition in the context of IBD.
Using scRNA-seq to Identify Transcriptional Variation in the Malaria Parasite Ookinete Stage

The crossing of the mosquito midgut epithelium by the malaria parasite motile ookinete form represents the most extreme population bottleneck in the parasite life cycle and is a prime target for transmission blocking strategies. However, we have little understanding of the clonal variation that exists in a population of ookinetes in the vector, partially because the parasites are difficult to access and are found in low numbers. Within a vector, variation may result as a response to specific environmental cues or may exist independent of those cues as a potential bet-hedging strategy. Here we use single-cell RNA-seq to profile transcriptional variation in Plasmodium berghei ookinetes across different vector species, and between and within individual midguts. We then compare our results to low-input transcriptomes from individual Anopheles coluzzii midguts infected with the human malaria parasite Plasmodium falciparum. Although the vast majority of transcriptional changes in ookinetes are driven by development, we have identified candidate genes that may be responding to environmental cues or are clonally variant within a population. Our results illustrate the value of single-cell and low-input technologies in understanding clonal variation of parasite populations.
Deficiency in Neuroserpin Exacerbates CoCl2 Induced Hypoxic Injury in the Zebrafish Model by Increased Oxidative Stress

Protective strategy against hypoxic-ischemic (H/I) induced injury has been intensively discussed. Neuroserpin, an inhibitor for tissue plasminogen activator (tPA), has been proved a vital neuroprotective agent in cerebral ischemia mouse model and oxygen-glucose deprivation and reoxygenation (OGD/R) cell model. Neuroserpin is a promising therapeutic hint for neonatal hypoxic-ischemia injury. Here, we established a neuroserpin deficient zebrafish to study its role in CoCl2 chemically induced hypoxic injury. CoCl2 exposure was beginning at the embryonic stage. Development defects, neuronal loss, and vascular malformation was assessed by imaging microscopy. Neuroserpin deficient zebrafish showed more development defects, neuronal loss and vascular malformation compared to wide-type. Apoptosis and oxidative stress were evaluated to further identify the possible mechanisms. These findings indicate that neuroserpin could protective against CoCl2 induced hypoxic injury by alleviating oxidative stress.