Miracle-dz/UniFAR-FTUs huggingface dataset:
Recent Advances in AIV Biosensors Composed of Nanobio Hybrid Material

Since the beginning of the 2000s, globalization has accelerated because of the development of transportation systems that allow for human and material exchanges throughout the world. However, this globalization has brought with it the rise of various pathogenic viral agents, such as Middle East respiratory syndrome coronavirus (MERS-CoV), severe acute respiratory syndrome coronavirus (SARS-CoV), Zika virus, and Dengue virus. In particular, avian influenza virus (AIV) is highly infectious and causes economic, health, ethnical, and social problems to human beings, which has necessitated the development of an ultrasensitive and selective rapid-detection system of AIV. To prevent the damage associated with the spread of AIV, early detection and adequate treatment of AIV is key. There are traditional techniques that have been used to detect AIV in chickens, ducks, humans, and other living organisms. However, the development of a technique that allows for the more rapid diagnosis of AIV is still necessary. To achieve this goal, the present article reviews the use of an AIV biosensor employing nanobio hybrid materials to enhance the sensitivity and selectivity of the technique while also reducing the detection time and high-throughput process time. This review mainly focused on four techniques: the electrochemical detection system, electrical detection method, optical detection methods based on localized surface plasmon resonance, and fluorescence.
Oviposition by Spodoptera exigua on Solanum dulcamara Alters the Plant’s Response to Herbivory and Impairs Larval Performance

Plant resistance traits against insect herbivores are extremely plastic. Plants respond not only to the herbivory itself, but also to oviposition by herbivorous insects. How prior oviposition affects plant responses to larval herbivory is largely unknown. Combining bioassays and defense protein activity assays with microarray analyses and metabolite profiling, we investigated the impact of preceding oviposition on the interaction of Solanum dulcamara with the generalist lepidopteran herbivore Spodoptera exigua at the levels of the plant’s resistance, transcriptome and metabolome. We found that oviposition increased plant resistance to the subsequent feeding larvae. While constitutive and feeding-induced levels of defensive protease inhibitor activity remained unaffected, pre-exposure to eggs altered S. dulcamara’s transcriptional and metabolic response to larval feeding in leaves local and systemic to oviposition. In particular, genes involved in phenylpropanoid metabolism were more strongly expressed in previously oviposited plants, which was reflected by reciprocal changes of primary metabolites upstream and within these pathways. Our data highlight that plants integrate signals from non-threatening life stages of their natural enemies to optimize their response when they become actually attacked. The observed transcriptional and metabolic reshaping of S. dulcamara’s response to S. exigua herbivory suggests a role of phenylpropanoids in oviposition-primed plant resistance.
Cetuximab‐radiotherapy combination in the management of locally advanced cutaneous squamous cell carcinoma

We report the outcomes of using a combination of cetuximab with radiation therapy (Cetux‐RT) to treat a selected group of patients with locally advanced (unresectable) cutaneous squamous cell carcinoma (LA‐cSCC). This study presents two‐year efficacy and safety data for 8 patients with LA‐cSCC treated within a single institution.
Astrocyte‐targeted IL‐10 production decreases proliferation and induces a downregulation of activated microglia/macrophages after PPT

When central nervous system (CNS) homeostasis is altered, microglial cells become rapidly activated, proliferate and release a broad range of molecules. Among the plethora of molecules involved in the regulation of microglial activation, cytokines are considered crucial. Although production of interleukin‐10 (IL‐10) has been demonstrated after different types of CNS injuries and associated with protective functions, the specific role played by IL‐10 modulating microglial cells remains unclear. Hence, the objective of this study was to evaluate the effects of transgenic astrocyte IL‐10 production on microglial activation associated with axonal anterograde degeneration. To address it, the hippocampal area subjected to perforant pathway transection (PPT) was analyzed by immunohistochemistry (IHC), flow cytometry and protein microarray in transgenic (GFAP‐IL10Tg) mice and their corresponding wild types (WT) littermates. Our results demonstrated increased microglial/macrophages density in nonlesioned and PPT‐lesioned GFAP‐IL10Tg animals when compared with nonlesioned and lesioned WT, respectively. This increase was not due to proliferation, as GFAP‐IL10Tg mice showed a reduced proliferation of microglial cells, but was related to an increased population of CD11b+/CD45high monocyte/macrophages. Despite this higher number, the microglia/macrophage population in transgenic animals displayed a downregulated phenotype characterized by lower MHCII, ICOSL, and CD11c. Moreover, a sustained T‐cell infiltration was found in transgenic animals. We strongly suggest these modifications must be associated with indirect effects derived from the influence of IL‐10 on astrocytes and/or neurons, which express IL‐10R. We finally suggested that TGF‐β produced by astrocytes, along with IL‐2 and CXCL10 might be crucial molecules mediating the effects of transgenic IL‐10.
The role of extrolites secreted by nonaflatoxigenic Aspergillus flavus in biocontrol efficacy

Field control of aflatoxin contamination is thought to occur through competitive exclusion of native aflatoxigenic fungi by introduced nonaflatoxigenic Aspergillus flavus biocontrol strains. In this study, we explored another possible mechanism that could increase the efficacy of biocontrol strains—the production of secreted compounds termed extrolites.
Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of Radiation Use Efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programs in an attempt to alleviate this, however their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE we applied genome-wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31traits over two years under optimal growing conditions and genotyped using the 35K Wheat Breeders array. Marker-trait-association identified 94 SNPs significantly associated with yield, agronomic and phenology related traits along with RUE and biomass at various growth stages that explained 7–17 % of phenotypic variation. Common SNP markers were identified for grain yield, final biomass and RUE on chromosomes 5A and 7A. Additionally we show that landrace and synthetic derivative lines showed higher thousand grain weight (TGW), biomass and RUE but lower grain number (GNO) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker assisted breeding to systematically increase biomass, RUE and TGW and avoid the TGW/GNO and BM/HI trade-off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.
Intakes of Zinc, Potassium, Calcium, and Magnesium of Individuals with Type 2 Diabetes Mellitus and the Relationship with Glycemic Control

The role of the concomitant intake of zinc, potassium, calcium, and magnesium in the glycemic control of individuals with type 2 diabetes mellitus (T2DM) has not been extensively discussed. We evaluated the relationship between the dietary intake of these micronutrients and glycemic markers in 95 individuals with T2DM (mean age 48.6 ± 8.4 years). Hierarchical grouping analysis was used to divide the individuals into two clusters according to their micronutrient intake, and differences between clusters were statistically assessed. Effects of individual and combination intake of micronutrients on glycated hemoglobin percentage (%HbA1c) were assessed using multiple linear regression and binary logistic regression analysis. We observed a high likelihood of inadequate intake of the four micronutrients. The group with lower micronutrient intake (cluster 1) displayed higher %HbA1c (p = 0.006) and triglyceride (p = 0.010) levels. High %HbA1c showed an association with cluster 1 (odds ratio (OR) = 3.041, 95% confidence interval (CI) = 1.131; 8.175) and time of T2DM diagnosis (OR = 1.155, 95% CI = 1.043; 1.278). Potassium (β = −0.001, p = 0.017) and magnesium (β = −0.007, p = 0.015) intakes were inversely associated with %HbA1c. Reduced concomitant intake of the four micronutrients studied proved to be associated with risk of increased %HbA1c in individuals with T2DM, which was particularly predicted by magnesium and potassium intakes.
Differential gene expression profile in monocytic myeloid‐derived suppressor cells at maternal–fetal interface in a mouse model of spontaneous abortion

Monocytic myeloid‐derived suppressor cells (MO‐MDSCs) play an important role in maintaining normal pregnancy. However, it is still not clear what kind of changes in MO‐MDSCs may lead to miscarriage, and which gene expression changes take place when MO‐MDSCs migrate to the uterus as bone marrow‐derived cells.
Risk stratification and medical therapy of pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) remains a severe clinical condition despite the availability over the past 15 years of multiple drugs interfering with the endothelin, nitric oxide and prostacyclin pathways. The recent progress observed in medical therapy of PAH is not, therefore, related to the discovery of new pathways, but to the development of new strategies for combination therapy and on escalation of treatments based on systematic assessment of clinical response. The current treatment strategy is based on the severity of the newly diagnosed PAH patient as assessed by a multiparametric risk stratification approach. Clinical, exercise, right ventricular function and haemodynamic parameters are combined to define a low-, intermediate- or high-risk status according to the expected 1-year mortality. The current treatment algorithm provides the most appropriate initial strategy, including monotherapy, or double or triple combination therapy. Further treatment escalation is required in case low-risk status is not achieved in planned follow-up assessments. Lung transplantation may be required in most advanced cases on maximal medical therapy. State of the art and research perspectives on medical therapy of pulmonary arterial hypertension, including treatment algorithm http://ow.ly/4UkJ30md5GS
Global Expression Profiling Identifies a Novel Hyaluronan Synthases 2 Gene in the Pathogenesis of Lower Extremity Varicose Veins

Lower extremities varicose veins (VV) are among the most easily recognized venous abnormalities. The genetic mechanism of VV is largely unknown. In this study, we sought to explore the global expressional change of VV and identify novel genes that might play a role in VV. We used next-generation ribonucleic acid (RNA) sequence (RNA seq) technology to study the global messenger RNA expressional change in the venous samples of five diseased and five control patients. We identified several differentially expressed genes, which were further confirmed by conventional reverse transcription polymerase chain reaction (RT-PCR). Using these significant genes we performed in silico pathway analyses and found distinct transcriptional networks, such as angiogenesis, cell adhesion, vascular injury, and carbohydrate metabolisms that might be involved in the mechanism of VV. Among these significant genes, we also found hyaluronan synthases 2 gene (HAS2) played a pivotal role and governed all these pathways. We further confirmed that HAS2 expression was decreased in the venous samples of patients with VV. Finally, we used a zebrafish model with fluorescence emitting vasculature and red blood cells to see the morphological changes of the venous system and blood flow. We found that HAS2 knockdown in zebrafish resulted in dilated venous structural with static venous flow. HAS2 may modulate the transcriptional networks of angiogenesis, cell adhesion, vascular injury, and carbohydrate metabolisms in venous tissues and downregulation of HAS2 may underlie the mechanism of VV.
Aging differentially modulates the Wnt pro‐survival signalling pathways in vascular smooth muscle cells

We previously reported pro‐survival effects of Wnt3a and Wnt5a proteins in vascular smooth muscle cells (VSMCs). Wnt5a achieved this through induction of Wnt1‐inducible signalling pathway protein‐1 (WISP‐1) consequent to β‐catenin/CREB‐dependent, TCF‐independent, signalling. However, we found that as atherosclerosis advances, although Wnt5a protein was increased, WISP‐1 was reduced. We hypothesized this disconnect could be due to aging. In this study, we elucidate the mechanism underlying Wnt3a pro‐survival signalling and demonstrate the differential effect of age on Wnt3a‐ and Wnt5a‐mediated survival. We show Wnt3a protein was expressed in human atherosclerotic coronary arteries and co‐located with macrophages and VSMCs. Meanwhile, Wnt3a stimulation of primary mouse VSMCs increased β‐catenin nuclear translocation and TCF, but not CREB, activation. Wnt3a increased mRNA expression of the pro‐survival factor WISP‐2 in a TCF‐dependent manner. Functionally, β‐catenin/TCF inhibition or WISP‐2 neutralization significantly impaired Wnt3a‐mediated VSMC survival. WISP‐2 was upregulated in human atherosclerosis and partly co‐localized with Wnt3a. The pro‐survival action of Wnt3a was effective in VSMCs from young (2 month) and old (18–20 month) mice, whereas Wnt5a‐mediated rescue was impaired with age. Further investigation revealed that although Wnt5a induced β‐catenin nuclear translocation in VSMCs from both ages, CREB phosphorylation and WISP‐1 upregulation did not occur in old VSMCs. Unlike Wnt5a, pro‐survival Wnt3a signalling involves β‐catenin/TCF and WISP‐2. While Wnt3a‐mediated survival was unchanged with age, Wnt5a‐mediated survival was lost due to impaired CREB activation and WISP‐1 regulation. Greater understanding of the effect of age on Wnt signalling may identify targets to promote VSMC survival in elderly patients with atherosclerosis.
BRAF and MEK inhibitors differentially affect nivolumab-induced T cell activation by modulating the TCR and AKT signaling pathways

ABSTRACT Immune checkpoint inhibitors (ICIs) such as the anti-PD-1 antibody Nivolumab, achieve remarkable clinical efficacy in patients with late stage cancers. However, only a small subset of patients benefit from this therapy. Numerous clinical trials are underway testing whether combining ICIs with other anti-cancer therapies can increase this response rate. For example, anti-PD-1/PD-L1 therapy combined with MAP kinase inhibition using BRAF inhibitors (BRAFi) and/or MEK inhibitors (MEKi) are in development for treatment of late stage melanomas. However, the benefits and underlying mechanisms of these combinatorial therapies remain unclear. In the current study, we assess the effects of MAPK inhibition on Nivolumab-induced T cell responses. Using an in vitro mixed lymphocyte reaction assay, we demonstrate that Nivolumab-induced T cell activation is highly heterogeneous. While BRAFi inhibits Nivolumab-induced cytokine production, T cell proliferation, activation markers (CD69, CD25), and Granzyme B in a substantial proportion of donor pairs, a small subset of donor pairs shows an additive effect. MEKi alone significantly inhibits Nivolumab-induced T cell activation; the addition of BRAFi significantly enhances this inhibitory effect. Mechanistically, the effects of BRAFi and/or MEKi on Nivolumab-induced T cell activation may be due to alteration of the activation of the AKT and T cell receptor (TCR) signaling pathways. Our results suggest that MAPK inhibition may not provide a clinical benefit for most melanoma patients being treated with anti-PD-1 therapy.
Therapeutic Vulnerabilities in FLT3-Mutant AML Unmasked by Palbociclib

While significant progress has been made in the treatment of acute myeloid leukemia (AML), not all patients can be cured. Mutated in about 1/3 of de novo AML, the FLT3 receptor tyrosine kinase is an attractive target for drug development, activating mutations of the FLT3 map to the juxtamembrane domain (internal tandem duplications, ITD) or the tyrosine kinase domain (TKD), most frequently at codon D835. While small molecule tyrosine kinase inhibitors (TKI) effectively target ITD mutant forms, those on the TKD are not responsive. Moreover, FLT3 inhibition fails to induce a persistent response in patients due to mutational resistance. More potent compounds with broader inhibitory effects on multiple FLT3 mutations are highly desirable. We describe a critical role of CDK6 in the survival of FLT3+ AML cells as palbociclib induced apoptosis not only in FLT3–ITD+ cells but also in FLT3–D835Y+ cells. Antineoplastic effects were also seen in primary patient-derived cells and in a xenograft model, where therapy effectively suppressed tumor formation in vivo at clinically relevant concentrations. In cells with FLT3–ITD or -TKD mutations, the CDK6 protein not only affects cell cycle progression but also transcriptionally regulates oncogenic kinases mediating intrinsic drug resistance, including AURORA and AKT—a feature not shared by its homolog CDK4. While AKT and AURORA kinase inhibitors have significant therapeutic potential in AML, single agent activity has not been proven overly effective. We describe synergistic combination effects when applying these drugs together with palbociclib which could be readily translated to patients with AML bearing FLT3–ITD or –TKD mutations. Targeting synergistically acting vulnerabilities, with CDK6 being the common denominator, may represent a promising strategy to improve AML patient responses and to reduce the incidence of selection of resistance-inducing mutations.
Silencing Heat Shock Protein 27 Inhibits the Progression and Metastasis of Colorectal Cancer (CRC) by Maintaining the Stability of Stromal Interaction Molecule 1 (STIM1) Proteins

The incidence of colorectal cancer (CRC) has significantly increased in recent decades, and this disease has become an important health issue worldwide. Currently, there is no useful prognostic or diagnostic biomarker for CRC. Heat shock protein 27 (HSP27) is a chaperone that interacts with many proteins. HSP27 has been shown to be overexpressed in many cancers, including colon cancer, and its overexpression is related to poor disease outcome. Although the importance of HSP27 as a biomarker cannot be underrated, its detailed mechanisms in colon cancer are still unclear. In vitro studies have indicated that silencing HSP27 reduces the proliferation, migration and invasion of colon cancer cells, and xenograft models have shown that silencing HSP27 decreases tumor progression. Tissue array results showed that colon cancer patients with high expression of HSP27 exhibited poor prognosis. In addition, we found a reduction of calcium influx through a decrease in STIM1 protein after HSP27 was abolished. The formation of puncta was decreased in HSP27 knockdown (HSP27KD) cells after thapsigargin (TG) treatment. Finally, we confirmed that the reduction of STIM1 after HSP27 silencing may be due to a loss of STIM1 stability instead of transcription. HSP27 may interact with STIM1 but not Orai1, as shown by immunoprecipitation assays. HSP27 and STIM1 were co-expressed in CRC specimens. Our study showed that HSP27 is a key mediator in the progression and metastasis of CRC by regulating the store-operated calcium entry. This novel pathway may provide a new direction for development of therapeutic strategies for CRC.
Cholesterol increases protein levels of the E3 ligase MARCH6 and thereby stimulates protein degradation

The E3 ligase membrane-associated ring-CH-type finger 6 (MARCH6) is a polytopic enzyme bound to the membranes of the endoplasmic reticulum. It controls levels of several known protein substrates, including a key enzyme in cholesterol synthesis, squalene monooxygenase. However, beyond its own autodegradation, little is known about how MARCH6 itself is regulated. Using CRISPR/Cas9 gene-editing, MARCH6 overexpression, and immunoblotting, we found here that cholesterol stabilizes MARCH6 protein endogenously and in HEK293 cells that stably express MARCH6. Conversely, MARCH6-deficient HEK293 and HeLa cells lost their ability to degrade squalene monooxygenase in a cholesterol-dependent manner. The ability of cholesterol to boost MARCH6 did not seem to involve a putative sterol-sensing domain in this E3 ligase, but was abolished when either membrane extraction by valosin-containing protein (VCP/p97) or proteasomal degradation was inhibited. Furthermore, cholesterol-mediated stabilization was absent in two MARCH6 mutants that are unable to degrade themselves, indicating that cholesterol stabilizes MARCH6 protein by preventing its autodegradation. Experiments with chemical chaperones suggested that this likely occurs through a conformational change in MARCH6 upon cholesterol addition. Moreover, cholesterol reduced the levels of at least three known MARCH6 substrates, indicating that cholesterol-mediated MARCH6 stabilization increases its activity. Our findings highlight an important new role for cholesterol in controlling levels of proteins, extending the known repertoire of cholesterol homeostasis players.
SumSec: Accurate Prediction of Sumoylation Sites Using Predicted Secondary Structure

Post Translational Modification (PTM) is defined as the modification of amino acids along the protein sequences after the translation process. These modifications significantly impact on the functioning of proteins. Therefore, having a comprehensive understanding of the underlying mechanism of PTMs turns out to be critical in studying the biological roles of proteins. Among a wide range of PTMs, sumoylation is one of the most important modifications due to its known cellular functions which include transcriptional regulation, protein stability, and protein subcellular localization. Despite its importance, determining sumoylation sites via experimental methods is time-consuming and costly. This has led to a great demand for the development of fast computational methods able to accurately determine sumoylation sites in proteins. In this study, we present a new machine learning-based method for predicting sumoylation sites called SumSec. To do this, we employed the predicted secondary structure of amino acids to extract two types of structural features from neighboring amino acids along the protein sequence which has never been used for this task. As a result, our proposed method is able to enhance the sumoylation site prediction task, outperforming previously proposed methods in the literature. SumSec demonstrated high sensitivity (0.91), accuracy (0.94) and MCC (0.88). The prediction accuracy achieved in this study is 21% better than those reported in previous studies. The script and extracted features are publicly available at: https://github.com/YosvanyLopez/SumSec.