Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of Cell Death Induced by Acetic Acid in Yeasts

Acetic acid has long been considered a molecule of great interest in the yeast research field. It is mostly recognized as a by-product of alcoholic fermentation or as a product of the metabolism of acetic and lactic acid bacteria, as well as of lignocellulosic biomass pretreatment. High acetic acid levels are commonly associated with arrested fermentations or with utilization as vinegar in the food industry. Due to its obvious interest to industrial processes, research on the mechanisms underlying the impact of acetic acid in yeast cells has been increasing. In the past twenty years, a plethora of studies have addressed the intricate cascade of molecular events involved in cell death induced by acetic acid, which is now considered a model in the yeast regulated cell death field. As such, understanding how acetic acid modulates cellular functions brought about important knowledge on modulable targets not only in biotechnology but also in biomedicine. Here, we performed a comprehensive literature review to compile information from published studies performed with lethal concentrations of acetic acid, which shed light on regulated cell death mechanisms. We present an historical retrospective of research on this topic, first providing an overview of the cell death process induced by acetic acid, including functional and structural alterations, followed by an in-depth description of its pharmacological and genetic regulation. As the mechanistic understanding of regulated cell death is crucial both to design improved biomedical strategies and to develop more robust and resilient yeast strains for industrial applications, acetic acid-induced cell death remains a fruitful and open field of study.
Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets (Panicum miliaceum L.) Revealed by Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

Broomcorn millet (Panicum miliaceum L.) is one of the earliest domesticated crops in the world. Weedy broomcorn millet [Panicum ruderale (Kitag.) Chang or Panicum miliaceum subsp. ruderale (Kitag.) Tzvel] is thought to be the descendant of the wild ancestor or the feral type of this cereal. The genealogical relationships and genetic divergence among these taxa have not been clarified. In this study, the genetic diversity and population structure of weedy and cultivated broomcorn millets were investigated by using the high-throughput sequencing technology, i.e., the specific-locus amplified fragment sequencing (SLAF-seq). Our analyses consistently revealed both the wild and the feral genotypes in the weedy broomcorn millets. The single nucleotide polymorphisms (SNPs) at the genomic level provided useful evidence to distinguish the wild and the endoferal/exoferal types of weedy broomcorn millets. The genetic divergence revealed between the cultivated broomcorn millet from eastern Eurasia and those from central-western Eurasia was probably derived from either the genetic introgression from weedy broomcorn millets along the spread routes or the founder effect, while the limited gene flow of broomcorn millets from eastern and central-western Eurasia was probably due to the different uses of broomcorn millets and eating habits of the local people.
Come Rain, Come Shine: Peatland Carbon Dynamics Shift Under Extreme Precipitation

Precipitation patterns are becoming increasingly extreme, particularly at northern latitudes. Current climate models predict that this trend will continue in the future. While droughts have been repeatedly studied in many ecosystems over the last decades, the consequences of increasingly intense, but less frequent rainfall events, on carbon (C) cycling are not well understood. At northern latitudes, peatlands store one third of the terrestrial carbon and their functioning is highly dependent on water. Shifts in rainfall regimes could disrupt peatland C dynamics and speed-up the rates of C loss. How will these immense stocks of C be able to withstand and recover from extreme rainfall? We tested the resistance and resilience effects of extreme precipitation regimes on peatland carbon dioxide (CO2) and methane (CH4) fluxes, pore water dissolved organic carbon (DOC) and litter decomposition rates by exposing intact peat cores to extreme, spring-time rainfall patterns in a controlled mesocosm experiment. We find that more intense but less frequent rainfall destabilized water table dynamics, with cascading effects on peatland C fluxes. Decomposition and respiration rates increased with a deeper mean water table depth (WTD) and larger WTD fluctuations. We observed similar patterns for CO2 uptake, which were likely mediated by improved vascular plant performance. After a three-week recovery period, CO2 fluxes still displayed responses to the earlier WTD dynamics, suggesting lagged effects of precipitation regime shifts. Furthermore, we found that CH4 emissions decreased with deeper mean WTD, but this showed a high resilience once WTD dynamics stabilised. Not only do our results illustrate that shifting rainfall patterns translate in altered WTD dynamics and, consequentially, influence C fluxes, they also demonstrate that exposure to altered rainfall early in the growing season can have lasting effects on CO2 exchange. Even though the increased CO2 assimilation under extreme precipitation patterns signals peatland resistance under changing climatic conditions, it may instead mark the onset of vascular plant encroachment and the associated C loss.
Trash or Treasure? Considerations for Future Ecological Research to Inform Oil and Gas Decommissioning

Numerous oil and gas (O&G) installations worldwide will need to be decommissioned in the near future. Complete removal of subsea structures is often the default approach although some regions retain structures under rigs-to-reefs programs. Here, we reviewed the published literature to understand the status of global research on decommissioning, and specifically identify gaps in ecological knowledge. We estimated the frequency of different research categories (i.e., themes, and spatial/temporal scales), and tested the assumption that the number of papers across the categories of each research aspect was even in distribution. However, the frequency of studies focusing on biodiversity at a local (≤100 km2) scale (relative to regional and oceanic and pan-oceanic scales) were significantly higher; while other theme categories (e.g., eco-toxicology, connectivity, structural-integrity, restoration and other) were significantly lower than expected. Temporally, ≤1-year studies were more frequent than multi-year studies, but these frequencies did not significantly deviate from the assumed distribution of equal frequencies. We propose that further research be carried out to evaluate the benefits of both retention and removal of structures. Ecological research on decommissioning should extend its focus beyond biodiversity, to include eco-toxicology, structural-integrity, connectivity at larger spatial and temporal scales. This would provide a more holistic assessment of ecological impacts to inform sustainable and equitable development choices in multiple Blue Economy sectors, as we transition from offshore O&G to marine renewables.
NtrBC Selectively Regulates Host-Pathogen Interactions, Virulence, and Ciprofloxacin Susceptibility of Pseudomonas aeruginosa

Pseudomonas aeruginosa is a metabolically versatile opportunistic pathogen capable of infecting distinct niches of the human body, including skin wounds and the lungs of cystic fibrosis patients. Eradication of P. aeruginosa infection is becoming increasingly difficult due to the numerous resistance mechanisms it employs. Adaptive resistance is characterized by a transient state of decreased susceptibility to antibiotic therapy that is distinct from acquired or intrinsic resistance, can be triggered by various environmental stimuli and reverted by removal of the stimulus. Further, adaptive resistance is intrinsically linked to lifestyles such as swarming motility and biofilm formation, both of which are important in infections and lead to multi-drug adaptive resistance. Here, we demonstrated that NtrBC, the master of nitrogen control, had a selective role in host colonization and a substantial role in determining intrinsic resistance to ciprofloxacin. P. aeruginosa mutant strains (ΔntrB, ΔntrC and ΔntrBC) colonized the skin but not the respiratory tract of mice as well as WT and, unlike WT, could be reduced or eradicated from the skin by ciprofloxacin. We hypothesized that nutrient availability contributed to these phenomena and found that susceptibility to ciprofloxacin was impacted by nitrogen source in laboratory media. P. aeruginosa ΔntrB, ΔntrC and ΔntrBC also exhibited distinct host interactions, including modestly increased cytotoxicity toward human bronchial epithelial cells, reduced virulence factor production and 10-fold increased uptake by macrophages. These data might explain why NtrBC mutants were less adept at colonizing the upper respiratory tract of mice. Thus, NtrBC represents a link between nitrogen metabolism, adaptation and virulence of the pathogen P. aeruginosa, and could represent a target for eradication of recalcitrant infections in situ.
Human Metapneumovirus Induces IRF1 via TANK-Binding Kinase 1 and Type I IFN

The innate immune and host-protective responses to viruses, such as the airway pathogen human metapneumovirus (HMPV), depend on interferons (IFNs) that is induced through TANK-binding kinase 1 (TBK1) and IFN regulatory factors (IRFs). The transcription factor IRF1 is important for host resistance against several viruses and has a key role in induction of IFN-λ at mucosal surfaces. In most cell types IRF1 is expressed at very low levels, but its mRNA is rapidly induced when the demand for IRF1 activity arises. Despite general recognition of the importance of IRF1 to antiviral responses, the molecular mechanisms by which IRF1 is regulated during viral infections are not well understood. Here we identify the serine/threonine kinase TBK1 and IFN-β as critical regulators of IRF1 mRNA and protein levels in human monocyte-derived macrophages. We find that inhibition of TBK1 activity either by the semi-selective TBK1/IKKε inhibitor BX795 or by siRNA-mediated knockdown abrogates HMPV-induced expression of IRF1. Moreover, we show that canonical NF-κB signaling is involved in IRF1 induction and that the TBK1/IKKε inhibitor BX795, but not siTBK1 treatment, impairs HMPV-induced phosphorylation of the NF-κB subunit p65. At later time-points of the infection, IRF1 expression depended heavily on IFN-β-mediated signaling via the IFNAR-STAT1 pathway. Hence, our results suggest that TBK1 activation and TBK1/IKKε-mediated phosphorylation of the NF-κB subunit p65 control transcription of IRF1. Our study identifies a novel mechanism for IRF1 induction in response to viral infection of human macrophages that could be relevant not only to defense against HMPV, but also to other viral, bacterial and fungal pathogens.
A Continuous Battle for Host-Derived Glycans Between a Mucus Specialist and a Glycan Generalist in vitro and in vivo

The human gastrointestinal tract is colonized by a diverse microbial community, which plays a crucial role in human health. In the gut, a protective mucus layer that consists of glycan structures separates the bacteria from the host epithelial cells. These host-derived glycans are utilized by bacteria that have adapted to this specific compound in the gastrointestinal tract. Our study investigated the close interaction between two distinct gut microbiota members known to use mucus glycans, the generalist Bacteroides thetaiotaomicron and the specialist Akkermansia muciniphila in vitro and in vivo. The in vitro study, in which mucin was the only nutrient source, indicated that B. thetaiotaomicron significantly upregulated genes coding for Glycoside Hydrolases (GHs) and mucin degradation activity when cultured in the presence of A. muciniphila. Furthermore, B. thetaiotaomicron significantly upregulated the expression of a gene encoding for membrane attack complex/perforin (MACPF) domain in co-culture. The transcriptome analysis also indicated that A. muciniphila was less affected by the environmental changes and was able to sustain its abundance in the presence of B. thetaiotaomicron while increasing the expression of LPS core biosynthesis activity encoding genes (O-antigen ligase, Lipid A and Glycosyl transferases) as well as ABC transporters. Using germ-free mice colonized with B. thetaiotaomicron and/or A. muciniphila, we observed a more general glycan degrading profile in B. thetaiotaomicron while the expression profile of A. muciniphila was not significantly affected when colonizing together, indicating that two different nutritional niches were established in mice gut. Thus, our results indicate that a mucin degrading generalist adapts to its changing environment, depending on available carbohydrates while a mucin degrading specialist adapts by coping with competing microorganism through upregulation of defense related genes.
Detection of Antibodies Against Tick-Borne Encephalitis Virus and Other Flaviviruses in a Zoological Collection in Slovenia

Monitoring infectious diseases is one of the most important pillars of preventative veterinary medicine in zoological collections. The zoo environment offers a great variety of different animal species living in proximity and in contact with small wild animals and vectors (e.g., ticks and mosquitos). In this context, tick-borne encephalitis virus (TBEV), Usutu virus (USUV), and West Nile virus (WNV) causing vector-borne diseases are emerging pathogens that raise concern. The aim of the study was to detect antibodies to selected flaviviruses in various animal species in the Ljubljana Zoo, Slovenia. In total, 874 sera from 96 animal species were tested for antibodies to TBEV by enzyme-linked immunosorbent assays (ELISA); positive samples were confirmed by a virus neutralization test (VNT) using TBEV, WNV, and USUV antigens. Antibodies to TBEV were detected by ELISA in 3.9% (34/874) of zoo animals, with 4% (30/753) in mammals and 5% (4/86) in birds; the sera of reptiles (n = 34) and amphibians (n = 1) were negative. Antibodies to TBEV were confirmed by VNT in 11 mammals; one bird was positive for both WNV and USUV. The mixture of exotic animal species and their contact with wild animals and vectors such as ticks and mosquitos suggest that screening of infectious diseases in zoo animals might provide good insight into the epizootological situation of the area. This is the first survey of TBEV, WNV, and USUV in a zoological collection in Slovenia.
Antioxidant Therapy and Antioxidant-Related Bionanomaterials in Diabetic Wound Healing

Ulcers are a lower-extremity complication of diabetes with high recurrence rates. Oxidative stress has been identified as a key factor in impaired diabetic wound healing. Hyperglycemia induces an accumulation of intracellular reactive oxygen species (ROS) and advanced glycation end products, activation of intracellular metabolic pathways, such as the polyol pathway, and PKC signaling leading to suppression of antioxidant enzymes and compounds. Excessive and uncontrolled oxidative stress impairs the function of cells involved in the wound healing process, resulting in chronic non-healing wounds. Given the central role of oxidative stress in the pathology of diabetic ulcers, we performed a comprehensive review on the mechanism of oxidative stress in diabetic wound healing, focusing on the progress of antioxidant therapeutics. We summarize the antioxidant therapies proposed in the past 5 years for use in diabetic wound healing, including Nrf2- and NFκB-pathway-related antioxidant therapy, vitamins, enzymes, hormones, medicinal plants, and biological materials.
Enhanced Drug Delivery to Solid Tumors via Drug-Loaded Nanocarriers: An Image-Based Computational Framework

Objective Nano-sized drug delivery systems (NSDDSs) offer a promising therapeutic technology with sufficient biocompatibility, stability, and drug-loading rates towards efficient drug delivery to solid tumors. We aim to apply a multi-scale computational model for evaluating drug delivery to predict treatment efficacy. Methodology Three strategies for drug delivery, namely conventional chemotherapy (one-stage), as well as chemotherapy through two- and three-stage NSDDSs, were simulated and compared. A geometric model of the tumor and the capillary network was obtained by processing a real image. Subsequently, equations related to intravascular and interstitial flows as well as drug transport in tissue were solved by considering real conditions as well as details such as drug binding to cells and cellular uptake. Finally, the role of periodic treatments was investigated considering tumor recurrence between treatments. The impact of different parameters, nanoparticle (NP) size, binding affinity of drug, and the kinetics of release rate, were additionally investigated to determine their therapeutic efficacy. Results Using NPs considerably increases the fraction of killed cells (FKCs) inside the tumor compared to conventional chemotherapy. Tumoral FKCs for two-stage DDS with smaller NP size (20nm) is higher than that of larger NPs (100nm), in all investigate release rates. Slower and continuous release of the chemotherapeutic agents from NPs have better treatment outcomes in comparison with faster release rate. In three-stage DDS, for intermediate and higher binding affinities, it is desirable for the secondary particle to be released at a faster rate, and the drug with slower rate. In lower binding affinities, high release rates have better performance. Results also demonstrate that after 5 treatments with three-stage DDS, 99.6% of tumor cells (TCs) are killed, while two-stage DDS and conventional chemotherapy kill 95.6% and 88.5% of tumor cells in the same period, respectively. Conclusion The presented framework has the potential to enable decision making for new drugs via computational modeling of treatment responses and has the potential to aid oncologists with personalized treatment plans towards more optimal treatment outcomes.
Investigating the Association of Wallerian Degeneration and Diaschisis After Ischemic Stroke With BOLD Cerebrovascular Reactivity

Introduction Wallerian degeneration and diaschisis are considered separate remote entities following ischemic stroke. They may, however, share common neurophysiological denominators, since they are both related to disruption of fiber tracts and brain atrophy over time. Therefore, with advanced multimodal neuroimaging, we investigate Wallerian degeneration and its association with diaschisis. Methods In order to determine different characteristics of Wallerian degeneration, we conducted examinations on seventeen patients with chronic unilateral ischemic stroke and persisting large vessel occlusion, conducting high-resolution anatomical magnetic resonance imaging (MRI) and blood oxygenation-level dependent cerebrovascular reactivity (BOLD-CVR) tests, as well as Diamox 15(O)–H2O–PET hemodynamic examinations. Wallerian degeneration was determined using a cerebral peduncle asymmetry index (% difference of volume of ipsilateral and contralateral cerebral peduncle) of more than two standard deviations away from the average of age-matched, healthy subjects (Here a cerebral peduncle asymmetry index > 11%). Diaschisis was derived from BOLD-CVR to assess the presence of ipsilateral thalamus diaschisis and/or crossed cerebellar diaschisis. Results Wallerian degeneration, found in 8 (47%) subjects, had a strong association with ipsilateral thalamic volume reduction (r2 = 0.60) and corticospinal-tract involvement of stroke (p < 0.001). It was also associated with ipsilateral thalamic diaschisis (p = 0.021), No cerebral peduncular hemodynamic differences were found in patients with Wallerian degeneration. In particular, no CBF decrease or BOLD-CVR impairment was found. Conclusion We show a strong association between Wallerian degeneration and ipsilateral thalamic diaschisis, indicating a structural pathophysiological relationship.
Predicting Severe Radiation Esophagitis in Patients With Locally Advanced Esophageal Squamous Cell Carcinoma Receiving Definitive Chemoradiotherapy: Construction and Validation of a Model Based in the Clinical and Dosimetric Parameters as Well as Inflammatory Indexes

Objective Radiation esophagitis (RE) is common in patients treated with radiotherapy (RT) for locally advanced esophageal squamous cell carcinoma (ESCC). We aim to construct a nomogram predicting the severe RE (grade ≥2) in patients with ESCC receiving definitive chemoradiotherapy (dCRT). Materials and Methods Logistic regression was performed to evaluate the risk factors in predicting RE. Nomogram was built based on the multivariate analysis result. The model was validated using the area under the receiver operating curve (ROC) curve (AUC), calibration curves, and decision curve analyses (DCA). Spearman correlation analysis was used to evaluate the correlation between inflammation indexes. Results A total of 547 patients with stage II–IVA ESCC treated with dCRT from the retrospective study were included. Two hundred and thirty-two of 547 patients (42.4%) developed grade ≥2 RE. Univariate analysis indicated that gender (p = 0.090), RT dose (p < 0.001), targeted therapy (p = 0.047), tumor thickness (p = 0.013), lymphocyte-monocyte ratio (LMR, p = 0.016), neutrophil-lymphocyte ratio (NLR, p < 0.001), and platelet-lymphocyte ratio (PLR, p < 0.001) were the significant factors for a higher incidence of RE. In multivariate analysis, RT dose [p < 0.001; odds ratio (OR), 4.680; 95% confidence interval (CI), 2.841–6.709], NLR (p < 0.001; OR, 0.384; 95% CI, 0.239–0.619), and PLR (p < 0.001; OR, 3.539; 95% CI: 2.226–5.626) were independently associated grade ≥2 RE and were involved in the nomogram. ROC curves showed the AUC of the nomogram was 0.714 (95% CI, 0.670–0.757), which was greater than each factor alone (RT dose: 0.615; NLR: 0.596; PLR: 0.590). Calibration curves showed good consistency between the actual observation and the predicted RE. DCA showed satisfactory positive net benefits of the nomogram among most threshold probabilities. Conclusions The study demonstrated that RT dose, NLR, and PLR were independent risk factors for grade ≥2 RE in patients with locally advanced ESCC receiving dCRT. A predictive model including all these factors was built and performed better than it based on each separately. Further validation in large patient populations is still warranted.
Coronavirus Disease 2019 and the Thyroid - Progress and Perspectives

SARS-CoV-2 infection (COVID-19) is currently a tremendous global health problem. COVID-19 causes considerable damage to a wide range of vital organs most prominently the respiratory system. Recently, clinical evidence for thyroidal insults during and after COVID-19 has been accumulated. As of today, almost all non-neoplastic thyroid diseases, i.e., Graves’ disease, Hashimoto’s thyroiditis, subacute, painless and postpartum thyroiditis, have been reported as a complication of COVID-19, and causality by the virus has been strongly implicated in all of them. Similar thyroid problems have been reported in the past with the SARS-CoV outbreak in 2002. In this review, we briefly look back at the reported evidence of alteration in thyroid functionality and thyroid diseases associated with SARS-CoV and then proceed to examine the issue with COVID-19 in detail, which is then followed by an in-depth discussion regarding a pathogenetic link between Coronavirus infection and thyroid disease.