Miracle-dz/UniFAR-FTUs huggingface dataset:
Highly Divergent Genetic Variants of Soricid-Borne Altai Virus (Hantaviridae) in Eurasia Suggest Ancient Host-Switching Events

With the recent discovery of genetically distinct hantaviruses (family Hantaviridae) in shrews (order Eulipotyphla, family Soricidae), the once-conventional view that rodents (order Rodentia) served as the primordial reservoir hosts now appears improbable. The newly identified soricid-borne hantaviruses generally demonstrate well-resolved lineages organized according to host taxa and geographic origin. However, beginning in 2007, we detected sequences that did not conform to the prototypic hantaviruses associated with their soricid host species and/or geographic locations. That is, Eurasian common shrews (Sorex araneus), captured in Hungary and Russia, were found to harbor hantaviruses belonging to two separate and highly divergent lineages. We have since accumulated additional examples of these highly distinctive hantavirus sequences in the Laxmann’s shrew (Sorex caecutiens), flat-skulled shrew (Sorex roboratus) and Eurasian least shrew (Sorex minutissimus), captured at the same time and in the same location in the Sakha Republic in Far Eastern Russia. Pair-wise alignment and phylogenetic analysis of partial and full-length S-, M- and/or L-segment sequences indicate that a distinct hantavirus species related to Altai virus (ALTV), first reported in a Eurasian common shrew from Western Siberia, was being maintained in these closely related syntopic soricine shrew species. These findings suggest that genetic variants of ALTV might have resulted from ancient host-switching events with subsequent diversification within the Soricini tribe in Eurasia.
Mechanisms and Antitumor Activity of a Binary EGFR/DNA–Targeting Strategy Overcomes Resistance of Glioblastoma Stem Cells to Temozolomide

Purpose: Glioblastoma (GBM) is a fatal primary malignant brain tumor. GBM stem cells (GSC) contribute to resistance to the DNA-damaging chemotherapy, temozolomide. The epidermal growth factor receptor (EGFR) displays genomic alterations enabling DNA repair mechanisms in half of GBMs. We aimed to investigate EGFR/DNA combi-targeting in GBM. Experimental Design: ZR2002 is a “combi-molecule” designed to inflict DNA damage through its chlorethyl moiety and induce irreversible EGFR tyrosine kinase inhibition. We assessed its in vitro efficacy in temozolomide-resistant patient-derived GSCs, mesenchymal temozolomide-sensitive and resistant in vivo–derived GSC sublines, and U87/EGFR isogenic cell lines stably expressing EGFR/wild-type or variant III (EGFRvIII). We evaluated its antitumor activity in mice harboring orthotopic EGFRvIII or mesenchymal TMZ-resistant GSC tumors. Results: ZR2002 induced submicromolar antiproliferative effects and inhibited neurosphere formation of all GSCs with marginal effects on normal human astrocytes. ZR2002 inhibited EGF-induced autophosphorylation of EGFR, downstream Erk1/2 phosphorylation, increased DNA strand breaks, and induced activation of wild-type p53; the latter was required for its cytotoxicity through p53-dependent mechanism. ZR2002 induced similar effects on U87/EGFR cell lines and its oral administration significantly increased survival in an orthotopic EGFRvIII mouse model. ZR2002 improved survival of mice harboring intracranial mesenchymal temozolomide-resistant GSC line, decreased EGFR, Erk1/2, and AKT phosphorylation and was detected in tumor brain tissue by MALDI imaging mass spectrometry. Conclusions: These findings provide the molecular basis of binary EGFR/DNA targeting and uncover the oral bioavailability, blood–brain barrier permeability, and antitumor activity of ZR2002 supporting potential evaluation of this first-in-class drug in recurrent GBM.
Comparative landscape genetics reveals the evolution of viviparity reduces genetic connectivity in fire salamanders

Evolutionary changes in reproductive mode may affect co‐evolving traits, such as dispersal, although this subject remains largely underexplored. The shift from aquatic oviparous or larviparous reproduction to terrestrial viviparous reproduction in some amphibians entails skipping the aquatic larval stage and, thus, greater independence from water. Accordingly, amphibians exhibiting terrestrial viviparous reproduction may potentially disperse across a wider variety of suboptimal habitats and increase population connectivity in fragmented landscapes compared to aquatic‐breeding species. We investigated this hypothesis in the fire salamander (Salamandra salamandra), which exhibits both aquatic‐ (larviparity) and terrestrial‐breeding (viviparity) strategies. We genotyped 426 larviparous and 360 viviparous adult salamanders for 13 microsatellite loci and sequenced a mitochondrial marker for 133 larviparous and 119 viviparous individuals to compare population connectivity and landscape resistance to gene flow within a landscape genetics framework. Contrary to our predictions, viviparous populations exhibited greater differentiation and reduced genetic connectivity compared to larviparous populations. Landscape genetic analyses indicate viviparity may be partially responsible for this pattern, as water courses comprised a significant barrier only in viviparous salamanders, probably due to their fully terrestrial life cycle. Agricultural areas and, to a lesser extent, topography also decreased genetic connectivity in both larviparous and viviparous populations. This study is one of very few to explicitly demonstrate the evolution of a derived reproductive mode affects patterns of genetic connectivity. Our findings open avenues for future research to better understand the eco‐evolutionary implications underlying the emergence of terrestrial reproduction in amphibians.
Transcriptomic analysis and High dimensional phenotypic mapping of mononuclear phagocytes in mesenteric lymph nodes reveal differences between ulcerative colitis and Crohn's disease.

BACKGROUND & AIM Crohn's disease (CD) and ulcerative colitis (UC) are distinct forms of inflammatory bowel diseases. Heterogeneity of HLA-DR+SIRPα+ mononuclear phagocytes (MNPs), including macrophages (MΦ), monocyte-derived cells and dendritic cells (DCs), was reported in gut tissue but not yet investigated in mesenteric lymph nodes (MLNs) of IBD patients. We here compared the phenotype, function and molecular profile of HLA-DR+SIRPα+ MNPs in CD and UC MLNs. METHODS Cell distribution, morphology, immune function, transcriptomic (bulk RNAseq) and high dimensional protein expression profiles (CyTOF) of HLA-DR+SIRPα+ MNPs were examined in MLNs of UC (n=14), CD (n=35) and non-IBD (n=12) patients. RESULTS Elevated frequencies of CD14+CD64+CD163+ (Mono/MΦ-like) MNPs displaying monocytes/MΦ morphology and phagocytic function was a distinct feature of UC MLNs. In CD, the proportion of CD14-CD64-CD163- (DC-like) cells augmented relative to Mono/MΦ-like cells; DC-like cells drove naive T cell proliferation, Th1 polarization and Th17 TCM plasticity. Gene expression profile corroborated the nature of DC-like cells, best represented by BTLA, SERPINF, IGJ and, of Mono/MΦ-like cells, defined by CD163, MARCO, MAFB, CD300E, S100A9 expression. CyTOF analysis showed that CD123+ plasmacytoid cells predominated over conventional DCs in DC-like cells. Four CD163+ clusters were revealed in Mono/MΦ-like cells, two of which were enriched in MARCO-CD68dimHLA-DRdim monocyte-like cells and MARCOhiCD68hiHLA-DRhi Mɸ, whose proportion increased in UC relative to CD. CONCLUSIONS Defining the landscape of MNPs in MLNs provided evidence for expansion of CD163+ Mono/MΦ-like cells in UC only, highlighting a distinction between UC and CD, and thus the potential contribution of monocyte-like cells in driving colitis.
EpABC Genes in the Adaptive Responses of Exophiala pisciphila to Metal Stress: Functional Importance and Relation to Metal Tolerance

Many ABC transporters and their functions have been identified in animals and plants. However, little is known about ABC genes in filamentous fungi, especially DSEs, which tend to dominantly colonize the roots of plants growing in stressed environments. Our results deepen the understanding of the function of the ABC genes of a super-metal-tolerant DSE (E. pisciphila) in enhancing its heavy metal resistance and detoxification. Furthermore, the genetic resources of DSEs, e.g., numerous EpABC genes, especially from super-metal-tolerant strains in heavy metal-polluted environments, can be directly used for transgenic applications to improve tolerance and phytoextraction potential. ABSTRACT Exophiala pisciphila is one of the dominant dark septate endophytes (DSEs) colonizing metal-polluted slag heaps in southwest China. It shows numerous super-metal-tolerant characteristics, but the molecular mechanisms involved remain largely unknown. In the present study, the functional roles of a speciﬁc set of ATP-binding cassette (ABC) transporters in E. pisciphila were characterized. In total, 26 EpABC genes belonging to 6 subfamilies (ABCA to ABCG) were annotated in previous transcriptome sequencing libraries, and all were regulated by metal ions (Pb, Zn, and Cd), which was dependent on the metal species and/or concentrations tested. The results from the heterologous expression of 3 representative EpABC genes confirmed that the expression of EpABC2.1, EpABC3.1, or EpABC4.1 restored the growth of metal-sensitive mutant Saccharomyces cerevisiae strains and significantly improved the tolerance of Arabidopsis thaliana to Pb, Zn, and Cd. Interestingly, the expression of the 3 EpABC genes further altered metal (Pb, Zn, and Cd) uptake and accumulation and promoted growth by alleviating the inhibitory activity in yeast and thale cress caused by toxic ions. These functions along with their vacuolar location suggest that the 3 EpABC transporters may enhance the detoxification of vacuolar compartmentation via transport activities across their membranes. In conclusion, the 26 annotated EpABC transporters may play a major role in maintaining the homeostasis of various metal ions in different cellular compartments, conferring an extreme adaptative advantage to E. pisciphila in metal-polluted slag heaps. IMPORTANCE Many ABC transporters and their functions have been identified in animals and plants. However, little is known about ABC genes in filamentous fungi, especially DSEs, which tend to dominantly colonize the roots of plants growing in stressed environments. Our results deepen the understanding of the function of the ABC genes of a super-metal-tolerant DSE (E. pisciphila) in enhancing its heavy metal resistance and detoxification. Furthermore, the genetic resources of DSEs, e.g., numerous EpABC genes, especially from super-metal-tolerant strains in heavy metal-polluted environments, can be directly used for transgenic applications to improve tolerance and phytoextraction potential.
Why do G-quadruplexes dimerize through the 5’-ends? Driving forces for G4 DNA dimerization examined in atomic detail

G-quadruplexes (G4) are secondary structures formed by guanine-rich nucleic acid sequences and shown to exist in living cells where they participate in regulation of gene expression and chromosome maintenance. G-quadruplexes with solvent-exposed guanine tetrads show the tendency to associate together through cofacial stacking, which may be important for packaging of G4-forming sequences and allows for the design of higher-order G4 DNA structures. To understand the molecular driving forces for G4 association, here, we study the binding interaction between two parallel-stranded G-quadruplexes using all-atom molecular dynamics simulations. The predicted dimerization free energies show that direct binding through the 5’-G-tetrads is the most preferred of all possible end-to-end stacking orientations, consistently with all available experimental data. Decomposition of dimerization enthalpies in combination with simulations at varying ionic strength further indicate that the observed orientational preferences arise from a fine balance between the electrostatic repulsion of the sugar-phosphate backbones and favorable counterion binding at the dimeric interface. We also demonstrate how these molecular-scale findings can be used to devise means of controlling G4 dimerization equilibrium, e.g., by altering salt concentration and using G4-targeted ligands.
Revisiting the reduction of stochastic models of genetic feedback loops with fast promoter switching

Propensity functions of the Hill-type are commonly used to model transcriptional regulation in stochastic models of gene expression. This leads to an effective reduced master equation for the mRNA and protein dynamics only. Based on deterministic considerations, it is often stated or tacitly assumed that such models are valid in the limit of rapid promoter switching. Here, starting from the chemical master equation describing promoter-protein interactions, mRNA transcription, protein translation and decay, we prove that in the limit of fast promoter switching, the distribution of protein numbers is different than that given by standard stochastic models with Hill-type propensities. We show the differences are pronounced whenever the protein-DNA binding rate is much larger than the unbinding rate, a special case of fast promoter switching. Furthermore we show using both theory and simulations that use of the standard stochastic models leads to drastically incorrect predictions for the switching properties of positive feedback loops and that these differences decrease with increasing mean protein burst size. Our results confirm that commonly used stochastic models of gene regulatory networks are only accurate in a subset of the parameter space consistent with rapid promoter switching. Statement of Significance A large number of models of gene regulatory networks in the literature assume that since promoter switching is fast then transcriptional regulation can be effectively modeled using Hill functions. While this approach can be rigorously justified for deterministic models, it is presently unclear if it is also the case for stochastic models. In this article we prove that this is not the case, i.e. stochastic models of gene regulatory systems, namely those with feedback loops, describing transcriptional regulation using Hill functions are only valid in a subset of parameter conditions consistent with fast promoter switching. We identify parameter regimes where these models are correct and where their predictions cannot be trusted.
Linc‐ROR regulates apoptosis in esophageal squamous cell carcinoma via modulation of p53 ubiquitination by targeting miR‐204‐5p/MDM2

The long intergenic noncoding RNA, regulator of reprogramming (linc‐ROR) has been reported to participate in tumorigenesis, while its functions and fundamental mechanisms in esophageal squamous cell carcinoma (ESCC) remain unclear. In this study, gain‐of‐function assays showed that linc‐ROR upregulation enhanced cell viability, promoted cell proliferation, and inhibited apoptosis. Mechanistically, the regulatory network of linc‐ROR/miR‐204‐5p/MDM2 was established with bioinformatics analysis and online databases, then validated via dual‐luciferase reporter assays, RNA immunoprecipitation assays in ESCC cells. Linc‐ROR positively regulates the expression of MDM2 as a molecular sponge of miR‐204‐5p. Moreover, results of western blot and coimmunoprecipitation indicated that linc‐ROR overexpression enhanced the ubiquitination level of p53, and its downstream apoptosis‐related genes have showed higher bcl‐2 expression, lower bax, and cleaved caspase‐3 expressions, while miR‐204‐5p could counteract with this effect. Finally, small interfering RNAs tailored to linc‐ROR were established to further evaluate its effects on ESCC comprehensively. In summary, this study revealed that linc‐ROR modulated cell apoptosis and regulated p53 ubiquitination via targeting miR‐204‐5p/MDM2 axis, which provides a novel therapeutic insight into treatments for ESCC.
Melatonin safeguards against fatty liver by antagonizing TRAFs‐mediated ASK1 deubiquitination and stabilization in a β‐arrestin‐1 dependent manner

Melatonin has been previously shown to prevent nonalcoholic fatty liver disease (NAFLD), yet the underlying mechanisms are poorly understood. Here, we identified a previously unknown regulatory action of melatonin on apoptosis signal‐regulating kinase 1 (ASK1) signaling pathway in the pathogenesis and development of NAFLD. Although melatonin administration did not alter food intake, it significantly alleviated fatty liver phenotypes, including the body weight gain, insulin resistance, hepatic lipid accumulation, steatohepatitis, and fibrosis in a high‐fat diet (HFD)‐induced NAFLD mouse model (in vivo). The protection of melatonin against NAFLD was not affected by inactivation of Kupffer cell in this model. In NAFLD mice liver, ASK1 signal cascade was substantially activated, evidence by the enhancement of total ASK1, phospho‐ASK1, phospho‐MKK3/6, phospho‐p38, phospho‐MKK4/7, and phospho‐JNK. Melatonin treatment significantly suppressed the ASK1 upregulation and the phosphorylation of ASK1, MKK3/6, MKK4/7, p38, and JNK. Mechanistically, we found that lipid stress triggered the interaction between ASK1 and TNF receptor‐associated factors (TRAFs), including TRAF1, TRAF2, and TRAF6, which resulted in ASK1 deubiquitination and thereby increased ASK1 protein stability. Melatonin did not alter ASK1 mRNA level; however, it activated a scaffold protein β‐arrestin‐1 and enabled it to bind to ASK1, which antagonized the TRAFs‐mediated ASK1 deubiquitination, and thus reduced ASK1 protein stability. Consistent with these findings, knockout of β‐arrestin‐1 in mice partly abolished the protection of melatonin against NAFLD. Taken together, our results for the first time demonstrate that melatonin safeguards against NAFLD by eliminating ASK1 activation via inhibiting TRAFs‐mediated ASK1 deubiquitination and stabilization in a β‐arrestin‐1 dependent manner.
Adult MTM1-related myopathy carriers

Objective To better characterize adult myotubularin 1 (MTM1)–related myopathy carriers and recommend a phenotypic classification. Methods This cohort study was performed at the NIH Clinical Center. Participants were required to carry a confirmed MTM1 mutation and were recruited via the Congenital Muscle Disease International Registry (n = 8), a traveling local clinic of the Neuromuscular and Neurogenetic Disorders of Childhood Section, National Institute of Neurological Disorders and Stroke, NIH and Cure CMD (n = 1), and direct physician referral (n = 1). Neuromuscular examinations, muscle MRI, dynamic breathing MRI, cardiac MRI, pulmonary function tests (PFTs), physical therapy assessments including the Motor Function Measure 32 (MFM-32) scale, and X chromosome inactivation (XCI) studies were performed. Results Phenotypic categories were proposed based on ambulatory status and muscle weakness. Carriers were categorized as severe (nonambulatory; n = 1), moderate (minimal independent ambulation/assisted ambulation; n = 3), mild (independent ambulation but with evidence of muscle weakness; n = 4), and nonmanifesting (no evidence of muscle weakness; n = 2). Carriers with more severe muscle weakness exhibited greater degrees of respiratory insufficiency and abnormal signal on muscle imaging. Skeletal asymmetries were evident in both manifesting and nonmanifesting carriers. Skewed XCI did not explain phenotypic severity. Conclusion This work illustrates the phenotypic range of MTM1-related myopathy carriers in adulthood and recommends a phenotypic classification. This classification, defined by ambulatory status and muscle weakness, is supported by muscle MRI, PFT, and MFM-32 scale composite score findings, which may serve as markers of disease progression and outcome measures in future gene therapy or other clinical trials.
Two-center comparison of 10 fully-automated commercial procalcitonin (PCT) immunoassays

Abstract Background This two-center study was designed to verify comparability of procalcitonin (PCT) values among 10 different commercial immunoassays. Methods A total number of 176 routine lithium-heparin plasma samples were divided in identical aliquots and simultaneously analyzed with 10 different PCT immunoassays, including Kryptor BRAHMS PCT sensitive, Abbott Architect BRAHMS PCT, Beckman Coulter Access PCT (on Access and DXI), BioMérieux Vidas BRAHMS PCT, Diasorin Liaison BRAHMS PCT, Fujirebio Lumipulse G BRAHMS PCT, Roche BRAHMS PCT (on Cobas E801), Diazyme PCT (on Roche Cobas C702) and SNIBE Maglumi PCT. Results Highly significant correlation was always found across multiple comparisons, with correlation coefficients comprised between 0.918 and 0.997 (all p < 0.001). Bland and Altman plots analysis revealed highly variable bias among immunoassays, ranging between ±0.2% and ±38.6%. Diazyme PCT on Roche Cobas C702 and SNIBE Maglumi PCT displayed the larger overestimation, whilst PCT values were underestimated by Cobas BRAHAMS PCT. The agreement was always >80% (all p < 0.001), but varied largely across multiple comparisons, ranging between 90%–99% at 0.1 μg/L, 81%–99% at 0.25 μg/L, 83%–100% at 0.5 μg/L, 94%–100% at 2.0 μg/L and 90%–99% at 10 μg/L, respectively. The larger disagreement was observed comparing Diazyme PCT and Maglumi PCT with the other methods. Conclusions Although we found acceptable correlation among 10 commercial PCT immunoassays, the limited agreement at clinical decision thresholds remains a major issue, especially at lower end of PCT concentration, thus potentially contributing to jeopardize the clinical value of this biomarker.
Practical Guidance for Interventions in Adults with Metabolic Syndrome: Diet and Exercise vs. Changes in Body Composition

(1) Objective: to establish practical guidance for the design of future clinical trials in MS (metabolic syndrome) patients aged 18 and older, based on a systematic review of randomized clinical trials connecting diet, physical exercise and changes in body composition. (2) Method: this systematic review of randomized clinical trials (RCT) is based on the guidelines recommended by PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analyses). Criteria of selection: ≥18 years of age; patients diagnosed with MS; intervention programs including diet, physical exercise and/or modifications in the style of life as treatment, as well as the magnitude of changes in body composition (BC); randomized clinical trial published between 2004 and 2018. (3) Results: the multidisciplinary interventions describe major changes in BC, and the recurring pattern in these clinical trials is an energy reduction and control in the percentage of intake of macronutrients along with the performance of regularly structured exercise; the most analyzed parameter was waist circumference (88.9% of the trials), followed by body weight (85.2%), BMI (77.8%) and body fat (55.6%). (4) Conclusions: The analysis of the information here reported sheds light for the design of future clinical trials in adults with MS. The best anthropometric parameters and units of measurement to monitor the interventions are related to dietary and physical exercise interventions. A list of practical advice that is easy to implement in daily practice in consultation is here proposed in order to guarantee the best results in changes of body composition.