Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitotic phosphorylation of the ULK complex regulates cell cycle progression

Autophagy is an intracellular degradation pathway targeting organelles and macromolecules, thereby regulating various cellular functions. Phosphorylation is a key posttranscriptional protein modification implicated in the regulation of biological function including autophagy. Under asynchronous conditions, autophagy activity is predominantly suppressed by mechanistic target of rapamycin (mTOR) kinase, but whether autophagy-related genes (ATG) proteins are phosphorylated differentially throughout the sequential phases of the cell cycle remains unclear. In this issue, Li and colleagues report that cyclin-dependent kinase 1 (CDK1) phosphorylates the ULK complex during mitosis. This phosphorylation induces autophagy and, surprisingly, is shown to drive cell cycle progression. This work reveals a yet-unappreciated role for autophagy in cell cycle progression and enhances our understanding of the specific phase-dependent autophagy regulation during cellular growth and proliferation.
Oncogenic Gene-Expression Programs in Leiomyosarcoma and Characterization of Conventional, Inflammatory, and Uterogenic Subtypes

Leiomyosarcoma (LMS) is a mesenchymal neoplasm with complex copy-number alterations and characteristic loss of tumor suppressor genes without known recurrent activating mutations. Clinical management of advanced LMS relies on chemotherapy and complementary palliative approaches, and research efforts to date have had limited success identifying clinically actionable biomarkers or targeted therapeutic vulnerabilities. To explore the biological underpinning of LMS, we evaluated gene-expression patterns of this disease in comparison with diverse sarcomas, nonmesenchymal neoplasms, and normal myogenic tissues. We identified a recurrent gene-expression program in LMS, with evidence of oncogenic evolution of an underlying smooth-muscle lineage-derived program characterized by activation of E2F1 and downstream effectors. Recurrently amplified or highly expressed genes in LMS were identified, including IGF1R and genes involved in retinoid signaling pathways. Though the majority of expressed transcripts were conserved across LMS samples, three separate subtypes were identified that were enriched for muscle-associated transcripts (conventional LMS), immune markers (inflammatory LMS), or a uterine-like gene-expression program (uterogenic LMS). Each of these subtypes expresses a unique subset of genes that may be useful in the management of LMS: IGF1R was enriched in conventional LMS, worse disease-specific survival was observed in inflammatory LMS, and prolactin was elaborated by uterogenic LMS. These results extend our understanding of LMS biology and identify several strategies and challenges for further translational investigation. Implications: LMS has a recurrent oncogenic transcriptional program and consists of molecular subtypes with biological and possible clinical implications.
Transforming growth factor β and tumor necrosis factor α inhibit both apoptosis and proliferation of activated rat hepatic stellate cells

Transforming growth factor β (TGF‐β) as well as tumor necrosis factor α (TNF‐α) gene expression are up‐regulated in chronically inflamed liver. These cytokines were investigated for their influence on apoptosis and proliferation of activated hepatic stellate cells (HSCs). Spontaneous apoptosis in activated HSC was significantly down‐regulated by 53% ± 8% (P < .01) under the influence of TGF‐β and by 28% ± 2% (P < .05) under the influence of TNF‐α. TGF‐β and TNF‐α significantly reduced expression of CD95L in activated HSCs, whereas CD95 expression remained unchanged. Furthermore, HSC apoptosis induced by CD95‐agonistic antibodies was reduced from 96% ± 2% to 51 ± 7% (P < .01) by TGF‐β, and from 96% ± 2% to 58 ± 2% (P < .01) by TNF‐α, suggesting that intracellular antiapoptotic mechanisms may also be activated by both cytokines. During activation, HSC cultures showed a reduced portion of cells in the G0/G1phase and a strong increment of G2‐phase cells. This increment was significantly inhibited (G1 arrest) by administration of TGF‐β and/or TNF‐α to activated cells. In liver sections of chronically damaged rat liver (CCl4 model), using desmin and CD95L as markers for activated HSC, most of these cells did not show apoptotic signs (TUNEL‐negative). Taken together, these findings indicate that TGF‐β and/or TNF‐α both inhibit proliferation and also apoptosis in activated HSC in vitro. Both processes seem to be linked to each other, and their inhibition could represent the mechanism responsible for prolonged survival of activated HSC in chronic liver damage in vivo.
Establishment and characterization of an in vitro 3D ovarian cancer model for drug screening assays

The acquired drug chemoresistance represents the main challenge of the ovarian cancer treatment. In addition, the absence of an adequate in vitro model able to reproduce the native tumor environment can contribute to the poor success rate of pre‐clinical studies of new compounds. Three‐dimensional (3D) culture models have been recently used for drug screening purposes due to their ability to reproduce the main characteristics of in vivo solid tumors. Here we describe the establishment and characterization of 3D ovarian cancer spheroids using different adenocarcinoma tumor cell lines (SKOV‐3 and OVCAR‐3 cells) in two different 3D scaffold‐free methods: forced‐floating in ultra‐low attachment (ULA) plates and hanging drop (HD). Spheroids were evaluated in both 3D cultures in order to establish the best condition to perform the drug response analysis with Paclitaxel, a common drug used to treat ovarian cancer. SKOV‐3 and OVCAR‐3 spheroids with the desired characteristics (roundness close to 1.0 and diameter in the 200–500 μm range) were obtained using both methods after addition of the methylcellulose (MC) in the culture medium (0.25% and 0.5%, w/v). We also observed the presence of microvilli on the surface of the spheroids, higher presence of apoptotic cells and higher drug resistance, when compared with 2D cultures. The 3D cultures obtained seem to provide more reliable results in terms of drug response than those provided by 2D monolayer culture. The forced floating method was considered more suitable and straightforward to generate ovarian cancer spheroids for drug screening/cytotoxicity assays.
Isolamento de Mycobacterium bovis em cão

This report describes the isolation of Mycobacterium bovis from a dog with a history of co-habitation with bufallos infected with Mycobacterium bovis. After necropsy, the microrganism was isolated from a mesenteric lymphatic node in Stonebrink media and bacterial identification was confirmed by biochemical tests.
Microbial translocation in type 2 diabetes: when bacterial invaders overcome host defence in human obesity

Metabolic endotoxemia, characterised by systemic influx of bacterial components, impairs lipid handling and glucoregulation.1 Early preclinical studies showed that high fat diet feeding facilitates bacterial translocation to metabolic tissues coinciding with dendritic cell (DC)-mediated inflammation.2 This process was aggravated in mice lacking either the canonical adaptor for inflammatory signalling pathways downstream of Toll-like receptor (TLR) families, MyD882 or the intracellular microbial pattern recognition receptor, NOD2.3 The first conceptual evidence for bacterial translocation in human type 2 diabetes (T2D) was reported in 2011 when Amar et al showed that 16S rDNA gene content in blood was associated with future T2D risk.4 These seminal papers pioneered the concept of bacterial translocation in metabolic diseases. Yet, it remains intensely debated whether bacterial translocation to extraintestinal tissues is a true phenomenon or a result of spurious data, as it is notoriously difficult to robustly distinguish biologically relevant bacterial DNA sequences in very low microbial biomass tissues from environmental contaminants.5 6 Indeed, low bacteria:host cell ratio obviously increases the risk of contamination during surgical procedures, biobanking and wet-laboratory processing of tissue samples. This has revivified the tenet that internal organs are sterile and casted doubt on emerging reports of tissue microbial signatures in a number of diseases, arguing that such findings may be confounded by sample contamination. In GUT, Massier et al challenge again the dogma of sterile internal organs …
Surprising low abundance of European wildcats in a Mediterranean protected area of southwestern Spain

Abstract The wildcat is a protected species in Europe but the lack of information on its status in many areas of its distribution range is an obstacle to conservation initiatives. To assess the status of the species over a 54,300 ha Mediterranean protected area in southwestern Spain (Doñana National Park, DNP), we carried out track censuses during the wet season of 2007–2008 and 2008–2009 in 2×2 km2 quadrants and set camera traps from June 2008 to October 2010 in quadrants or nearby quadrants where cat tracks were detected. We detected a total of 52 cat tracks for both study years and identified six different individuals from 28 photographs taken at 12 out of 166 trapping stations. We hypothesized that the causes of the a priori surprising low abundance of the species in the area might be multifold and might be explained by the historic competitive exclusion of the species by the Iberian lynx, the decrease of rabbit population in the DNP during the past decades, the isolation of DNP from the nearest natural areas that could have slowed the recovery of wildcat populations after a species declining and a potential increased mortality rate over time due to disease transmission from domestic cats.
Range-Wide Threats to a Foundation Tree Species from Disturbance Interactions

Abstract The geographic range of tanoak, Notholithocarpus densiflorus (Hook. & Arn.) Manos, Cannon & S. H. Oh (Fagaceae), encompasses tremendous physiographic variability, diverse plant communities, and complex disturbance regimes (e.g., development, timber harvest, and wildfire) that now also include serious threats posed by the invasive forest pathogen Phytophthora ramorum S. Werres, A.W. A.M. de Cock. Knowing where these disturbance factors interact is critical for developing comprehensive strategies for conserving the abundance, structure, and function of at-risk tanoak communities. In this study, we present a rule-based spatial model of the range-wide threat to tanoak populations from four disturbance factors that were parameterized to encode their additive effects and two-way interactions. Within a GIS, we mapped threats posed by silvicultural activities; disease caused by P. ramorum; human development; and altered fire regimes across the geographic range of tanoak, and we integrated spatially coinciding disturbances to quantify and map the additive and interacting threats to tanoak. We classified the majority of tanoak's range at low risk (3.7 million ha) from disturbance interactions, with smaller areas at intermediate (222,795 ha), and high (10,905 ha) risk. Elevated risk levels resulted from the interaction of disease and silviculture factors over small extents in northern California and southwest Oregon that included parts of Hoopa and Yurok tribal lands. Our results illustrate tanoak populations at risk from these interacting disturbances based on one set of hypothesized relationships. The model can be extended to other species affected by these factors, used as a guide for future research, and is a point of departure for developing a comprehensive understanding of threats to tanoak populations. Identifying the geographic location of disturbance interactions and risks to foundation species such as tanoak is critical for prioritizing and targeting conservation treatments with limited resources.
Induction of Autophagy by Vasicinone Protects Neural Cells from Mitochondrial Dysfunction and Attenuates Paraquat-Mediated Parkinson’s Disease Associated α-Synuclein Levels

Mitochondrial dysfunction and disturbed mitochondrial dynamics were found to be common phenomena in the pathogenesis of Parkinson’s disease (PD). Vasicinone is a quinazoline alkaloid from Adhatoda vasica. Here, we investigated the autophagy/mitophagy-enhancing effect of vasicinone and explored its neuroprotective mechanism in paraquat-mimic PD modal in SH-SY5Y cells. Vasicinone rescued the paraquat-induced loss of cell viability and mitochondrial membrane potential. Subsequently, the accumulation of mitochondrial reactive oxygen species (ROS) was balanced by an increase in the expression of antioxidant enzymes. Furthermore, vasicinone restored paraquat-impaired autophagy and mitophagy regulators DJ-1, PINK-1 and Parkin in SH-SY5Y cells. The vasicinone mediated autophagy pathways were abrogated by treatment with the autophagy inhibitor 3-MA, which lead to increases α-synuclein accumulation and decreased the expression of p-ULK and ATG proteins and the autophagy marker LC3-II compared to that observed without 3-MA treatment. These results demonstrated that vasicinone exerted neuroprotective effects by upregulating autophagy and PINK-1/Parkin mediated mitophagy in SH-SY5Y cells.
Incidence of Injury, Maltreatment, and Developmental Disorders Among Substance Exposed Infants

Recent changes to federal legislation created a requirement for states to address the needs of infants with prenatal substance exposure. Understanding clinical outcomes among substance exposed infants prior to these changes is important for establishing a baseline of risk and informing systems-level responses. Using North Carolina, Georgia, and Texas Medicaid data, we examined the incidence of inpatient and outpatient diagnoses for injury, maltreatment, and developmental disorders prior to age 12 months and compared types of diagnoses among substance exposed and unexposed infants. The cumulative incidence of maltreatment (1.2% vs. 0.2%) and developmental disorder (10.7% vs. 1.5%) diagnoses prior to age 12 months was significantly higher among substance exposed compared to unexposed infants. The incidence of injury diagnoses was similar (3.7% vs. 3.4%). We observed differences in types of maltreatment and injury diagnoses. For example, diagnoses for neglect were more common among substance exposed infants while diagnoses for physical abuse were more common among unexposed infants. Results provide insight for informing monitoring and intervention by medical and public health professionals.
The Construction and Immunoadjuvant Activities of the Oral Interleukin-17B Expressed by Lactobacillus plantarum NC8 Strain in the Infectious Bronchitis Virus Vaccination of Chickens

Interleukin-17B (IL-17B) is a protective cytokine of the IL-17 family and plays an essential role in the regulation of mucosal inflammation. However, little is known about the role of IL-17B in the control of viral infections. In this study, a recombinant Lactobacillus plantarum, designated as NC8-ChIL17B, was constructed to express the chicken IL-17B (ChIL-17B) gene. The recombinant ChIL17B (rChIL17B) protein was about 14 kDa and was anchored to the surface of NC8 cells. In vitro, it was found that the rChIL17B protein inhibited the proliferation of the infectious bronchitis virus (IBV) through activation of nuclear factor kappa B (NF-κB) and the JAK (Janus kinase)-STAT (signal transducers and activators of transcription) signaling. Moreover, to evaluate the immunoadjuvant activities of NC8-ChIL17B, 40 three-day-old specific pathogen-free (SPF) chickens were divided into four groups. Three groups were orally vaccinated with fresh NC8, NC8-ChIL17B, and phosphate buffered saline (PBS), along with the infectious bronchitis virus vaccine, and the other group was the PBS-negative control. The results of the IBV-specific antibody titer and the concentration of the cytokines IL-2, IL-4, IL-6, and interferon gamma (IFN-γ) in sera, as well as the concentration of secretory immunoglobulin A (sIgA) in the tracheal and small intestinal mucosa, the number of cluster of differentiation 4 positive (CD4+) and cluster of differentiation 8 positive (CD8+) T cells in the blood, and the expression of immune-related genes all indicated that NC8-ChIL17B efficiently enhanced the humoral and cellular immune responses to IBV vaccine. Moreover, the viral loads in the NC8-ChIL17B- and IBV-vaccinated group were significantly lower than in the control groups, suggesting a significant promotion of the immunoprotection of IBV vaccination against the virulent IBV strain. Therefore, ChIL-17B is a promising, effective adjuvant candidate for chicken virus vaccines.
NGT1 Is Essential for N-Acetylglucosamine-Mediated Filamentous Growth Inhibition and HXK1 Functions as a Positive Regulator of Filamentous Growth in Candida tropicalis

Candida tropicalis is a pathogenic fungus that can cause opportunistic infections in humans. The ability of Candida species to transition between yeast and filamentous growth forms is essential to their ability to undergo environmental adaptation and to maintain virulence. In other fungal species, such as Candida albicans, N-acetylglucosamine (GlcNAc) can induce filamentous growth, whereas it suppresses such growth in C. tropicalis. In the present study, we found that knocking out the GlcNA-specific transporter gene NGT1 was sufficient to enhance C. tropicalis filamentous growth on Lee’s plus GlcNAc medium. This suggests that GlcNAc uptake into C. tropicalis cells is essential to the disruption of mycelial growth. As such, we further studied how GlcNAc catabolism-related genes were able to influence C. tropicalis filamentation. We found that HXK1 overexpression drove filamentous growth on Lee’s media containing glucose and GlcNAc, whereas the deletion of the same gene disrupted this filamentous growth. Interestingly, the deletion of the DAC1 or NAG1 genes impaired C. tropicalis growth on Lee’s plus GlcNAc plates. Overall, these results indicate that HXK1 can serve as a positive regulator of filamentous growth, with excess GlcNAc-6-PO4 accumulation being toxic to C. tropicalis. These findings may highlight novel therapeutic targets worthy of future investigation.
Apical Dominance in Marchantia: Correlative Inhibition of Neighbor Lobe Growth

Growth factors may control the development of the typical fan-shaped appearance of Marchantia polymorpha in ways similar to the control of apical dominance in higher plants In Marchantia, apical dominance is characterized by the greater growth of one lobe compared with its neighboring lobe Two neighbor lobes develop from two apical notches or growing regions of a previously established lobe. The lobe which grows larger is invariably the one nearer the midrib of the growing thallus If the notches that will eventually give rise to separate unequal lobes are separated by a cut at an early stage of lobe growth, the smaller lobe is released from inhibition and grows to a size equal to the dominant lobe Indole-3-acetic acid (IAA), which is involved in maintaining apical dominance in higher plants, applied to the smaller lobe after cutting reestablishes the inhibition. It also increases the inhibition of the smaller lobe when applied to it on an intact plant. The growth of the dominant lobe is neither inhibited nor promoted by IAA We suggest that the type of neighbor lobe dominance in Marchantia resulting in its typical fan-shaped growth habit is maintained by auxin through a differential sensitivity of the two neighbors to auxin inhibition
Teaching Adequate Prehospital Use of Personal Protective Equipment During the COVID-19 Pandemic: Development of a Gamified e-Learning Module

Background The coronavirus disease (COVID-19) pandemic has led to increased use of personal protective equipment (PPE). Adequate use of this equipment is more critical than ever because the risk of shortages must be balanced against the need to effectively protect health care workers, including prehospital personnel. Specific training is therefore necessary; however, the need for social distancing has markedly disrupted the delivery of continuing education courses. Electronic learning (e-learning) may provide significant advantages because it requires neither the physical presence of learners nor the repetitive use of equipment for demonstration. Objective Inclusion of game mechanics, or “gamification,” has been shown to increase knowledge and skill acquisition. The objective of this research was to develop a gamified e-learning module to interactively deliver concepts and information regarding the correct choice and handling of PPE. Methods The SERES framework was used to define and describe the development process, including scientific and design foundations. After we defined the target audience and learning objectives by interviewing the stakeholders, we searched the scientific literature to establish relevant theoretical bases. The learning contents were validated by infection control and prehospital experts. Learning mechanics were then determined according to the learning objectives, and the content that could benefit from the inclusion of game mechanics was identified. Results The literature search resulted in the selection and inclusion of 12 articles. In addition to gamification, pretesting, feedback, avoiding content skipping, and demonstrations using embedded videos were used as learning mechanics. Gamification was used to enhance the interactivity of the PPE donning and doffing sequences, which presented the greatest learning challenges. The module was developed with Articulate Storyline 3 to ensure that it would be compatible with a wide array of devices, as this software generates HTML5-compatible output that can be accessed on smartphones, tablets, and regular computers as long as a recent browser is available. Conclusions A gamified e-learning module designed to promote better knowledge and understanding of PPE use among prehospital health care workers was created by following the SERES framework. The impact of this module should now be assessed by means of a randomized controlled trial.
Effect of hydrolysis time on the determination of the amino acid composition of diet, ileal digesta, and feces samples and on the determination of dietary amino acid digestibility coefficients

A study was undertaken to determine the effect of hydrolysis time during amino acid analysis on individual amino acid yields from samples of a mixed diet, pig ileal digesta, and feces. Representative feed, digesta, and feces samples were hydrolyzed in duplicate in 6 M HCl in sealed evacuated tubes for 16, 24, 48, and 72 h, respectively, and then analyzed for their yields of alanine, arginine, aspartate, glutamate, glycine, histidine, isoleucine, leucine, lysine, phenylalanine, proline, serine, threonine, tyrosine, and valine