Miracle-dz/UniFAR-FTUs huggingface dataset:
Compound Heterozygous KCNQ1 Mutations Causing Recessive Romano–Ward Syndrome: Functional Characterization by Mutant Co-expression

Next Generation Sequencing has identified many KCNQ1 genetic variants associated with type 1 long QT or Romano-Ward syndrome, most frequently inherited in an autosomal dominant fashion, although recessive forms have been reported. Particularly in the case of missense variants, functional studies of mutants are of aid to establish variant pathogenicity and to understand the mechanistic basis of disease. Two compound heterozygous KCNQ1 mutations (p.A300T and p.P535T) were previously found in a child who suffered sudden death. To provide further insight into the clinical significance and basis for pathogenicity of these variants, different combinations of wildtype, A300T and P535T alleles were co-expressed with the accessory β-subunit minK in HEK293 cells, to analyze colocalization with the plasma membrane and some biophysical phenotypes of homo and heterotetrameric channels using the patch-clamp technique. A300T homotetrameric channels showed left-shifted activation V1/2 as previously observed in Xenopus oocytes, decreased maximum conductance density, slow rise-time300ms, and a characteristic use-dependent response. A300T slow rise-time300ms and use-dependent response behaved as dominant biophysical traits for all allele combinations. The P535T variant significantly decreased maximum conductance density and Kv7.1-minK-plasma membrane colocalization. P535T/A300T heterotetrameric channels showed decreased colocalization with plasma membrane, slow rise-time300ms and the A300T characteristic use-dependent response. While A300T left shifted activation voltage dependence behaved as a recessive trait when co-expressed with WT alleles, it was dominant when co-expressed with P535T alleles. Conclusions: The combination of P535T/A300T channel biophysical properties is compatible with recessive Romano Ward syndrome. Further analysis of other biophysical traits may identify other mechanisms involved in the pathophysiology of this disease.
Periodic Polymerization and the Generation of Polymer Giant Vesicles Autonomously Driven by pH Oscillatory Chemistry

Using the radicals generated during pH oscillations, a semibatch pH oscillator is used as the chemical fuel and engine to drive polymerization induced self-assembly (PISA) for the one-pot autonomous synthesis of functional giant vesicles. Vesicles with diameters ranging from sub-micron to ∼5 µm are generated. Radical formation is found to be switched ON/OFF and be autonomously controlled by the pH oscillator itself, inducing a periodic polymerization process. The mechanism underlying these complex processes is studied and compared to conventional (non-oscillatory) initiation by the same redox pair. The pH oscillations along with the continuous increase in salt concentration in the semibatch reactor make the self-assembled objects undergo morphological evolution. This process provides a self-regulated means for the synthesis of soft giant polymersomes and opens the door for new applications of pH oscillators in a variety of contexts, from the exploration of new geochemical scenarios for the origin of life and the autonomous emergence of the necessary free-energy and proton gradients, to the creation of active functional microreactors and programmable release of cargo molecules for pH-responsive materials.
Targeting Mitochondrial Metabolism in Clear Cell Carcinoma of the Ovaries

Ovarian clear cell carcinoma (OCCC) is a rare but chemorefractory tumor. About 50% of all OCCC patients have inactivating mutations of ARID1A a member of the SWI/SNF chromatin remodeling complex. Members of the SWI/SNF remodeling have emerged as regulators of the energetic metabolism of mammalian cells, however the role of ARID1A as a modulator of the mitochondrial metabolism in OCCCs is yet to be defined. Here we show that ARID1A-loss results in increased mitochondrial metabolism and renders ARID1A-mutated cells increasingly and selectively dependent on it. The increase in mitochondrial activity following ARID1A loss is associated to increase of C-myc and to increased mitochondrial number and reduction of their size consistent with a higher mitochondrial cristae/outer membrane ratio. Significantly, preclinical testing of the complex I mitochondrial inhibitor IACS-010759 extends overall survival in a preclinical model of ARID1A-mutated OCCC. These findings provide the for targeting mitochondrial activity in ARID1A-mutanted OCCCs.
Functional basis for calmodulation of the TRPV5 calcium channel

Within the transient receptor potential (TRP) superfamily of ion channels, TRPV5 is a highly Ca2+‐selective channel important for active reabsorption of Ca2+ in the kidney. Its channel activity is controlled by a negative feedback mechanism involving calmodulin (CaM) binding. Combining advanced microscopy techniques and biochemical assays, this study characterized the dynamic lobe‐specific CaM regulation. We demonstrate for the first time that functional (full‐length) TRPV5 interacts with CaM in the absence of Ca2+, and this interaction is intensified at increasing Ca2+ concentrations sensed by the CaM C‐lobe that achieves channel pore blocking. Channel inactivation occurs without requiring CaM N‐lobe calcification. Moreover, we show a Ca2+‐dependent binding stoichiometry at the single channel level. In conclusion, our study proposes a new model for CaM‐dependent regulation – calmodulation – of this uniquely Ca2+‐selective TRP channel TRPV5 that involves apoCaM interaction and lobe‐specific actions, which may be of significant physiological relevance given its role as gatekeeper of Ca2+ transport in the kidney.
Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer

Phylogenetic placement of query samples on an existing phylogeny is increasingly used in molecular ecology, including sample identification and microbiome environmental sampling. As the size of available reference trees used in these analyses continues to grow, there is a growing need for methods that place sequences on ultra-large trees with high accuracy. Distance-based placement methods have recently emerged as a path to provide such scalability while allowing flexibility to analyze both assembled and unassembled environmental samples. In this paper, we introduce a distance-based phylogenetic placement method, APPLES-2, that is more accurate and scalable than existing distance-based methods and even some of the leading maximum likelihood methods. This scalability is owed to a divide-and-conquer technique that limits distance calculation and phylogenetic placement to parts of the tree most relevant to each query. The increased scalability and accuracy enables us to study the effectiveness of APPLES-2 for placing microbial genomes on a data set of 10,575 microbial species using subsets of 381 marker genes. APPLES-2 has very high accuracy in this setting, placing 97% of query genomes within three branches of the optimal position in the species tree using 50 marker genes. Our proof of concept results show that APPLES-2 can quickly place metagenomic scaffolds on ultra-large backbone trees with high accuracy as long as a scaffold includes tens of marker genes. These results pave the path for a more scalable and widespread use of distance-based placement in various areas of molecular ecology.
TGR5 Regulates Macrophage Inflammation in Nonalcoholic Steatohepatitis by Modulating NLRP3 Inflammasome Activation

Nonalcoholic steatohepatitis (NASH) is a chronic liver disease associated with dysregulation of liver metabolism and inflammation. G-protein coupled bile acid receptor 1 (TGR5) is a cell surface receptor that is involved in multiple metabolic pathways. However, the functions of TGR5 in regulating macrophage innate immune activation in NASH remain unclear. Here, we found that TGR5 expression was decreased in liver tissues from humans and mice with NASH. Compared to wild type (WT) mice, TGR5-knockout (TGR5−/−) mice exhibited exacerbated liver damage, increased levels of proinflammatory factors, and enhanced M1 macrophage polarization. Moreover, TGR5 deficiency facilitated M1 macrophage polarization by promoting NLRP3 inflammasome activation and caspase-1 cleavage. Taken together, our findings revealed that TGR5 signaling attenuated liver steatosis and inflammation and inhibited NLRP3-mediated M1 macrophage polarization in NASH.
Eukaryotic translation initiation factor 2A protects pancreatic beta cells during endoplasmic reticulum stress while rescuing translation inhibition

The endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) helps decide β cell survival in diabetes. The alternative eukaryotic initiation factor 2A (EIF2A) has been proposed to mediate EIF2S1-independent translation during cellular stress and viral infection, but its role in β cells is unknown. EIF2A abundance is high in human and mouse islets relative to other tissues, and both thapsigargin and palmitate significantly increased EIF2A mRNA and EIF2A protein levels in MIN6 cells, mouse islets and human islets. Knockdowns of EIF2A, the related factor EIF2D, or both EIF2A and EIF2D, were not sufficient to cause apoptosis. On the other hand, transient or stable EIF2A over-expression protected MIN6 cells, primary mouse islets, and human islets from ER stress-induced, caspase-3-dependent apoptosis. Mechanistically, EIF2A overexpression decreased ERN1 (also known as IRE1α) expression in thapsigargin-treated MIN6 cells or human islets. In vivo, β cell specific EIF2A viral overexpression reduced ER stress, improved insulin secretion, and abrogated hyperglycemia in Ins2Akita/WT mice. EIF2A overexpression significantly increased expression of genes involved in protein translation and reduced expression of pro-apoptotic genes (e.g. ALDH1A3). Remarkably, the decrease in global protein synthesis during UPR was prevented by EIF2A, despite ER stress-induced EIF2S1 phosphorylation. The protective effects of EIF2A were additive to those of ISRIB, a drug that counteracts the effects of EIF2S1 phosphorylation. Cells overexpressing EIF2A showed higher expression of translation factor EIF2B5, which may contribute to the lack of translational inhibition in these cells. We conclude that EIF2A is a novel target for β cell protection and the circumvention of EIF2S1-mediated translational repression.
Accuracy of the pneumatic method for estimating xylem vulnerability to embolism in temperate diffuse-porous tree species

The increasing frequency of global change-type droughts has created a need for fast, accurate and widely applicable techniques for estimating xylem embolism resistance to improve forecasts of future forest changes. We used data from 12 diffuse-porous temperate tree species covering a wide range of xylem safety to compare the pneumatic and flow-centrifuge method for constructing xylem vulnerability curves. We evaluated the agreement between parameters estimated with both methods and the sensitivity of pneumatic measurements to the measurement duration. The agreement between xylem water potentials at 50% air discharged (PAD) estimated with the Pneumatron and 50% loss of hydraulic conductivity (PLC) estimated with the flow-centrifuge method was high (mean signed deviation: 0.12 MPa, Pearson correlation: 0.96 after 15 sec of gas extraction). However, the relation between the estimated slopes was more variable, resulting in lower agreement in xylem water potential at 12% and 88% PAD/PLC. All parameters were sensitive to the duration of the pneumatic measurement, with highest overall agreement between methods after 16 sec. We conclude that, if applied correctly, the pneumatic method enables fast and inexpensive estimations of embolism resistance for a wide range of temperate, diffuse-porous species, which makes it attractive for predicting plant performance under climate change.
A Two-Gene Signature for Tuberculosis Diagnosis in Persons With Advanced HIV

Background: Transcriptomic signatures for tuberculosis (TB) have been proposed and represent a promising diagnostic tool. Data remain limited in persons with advanced HIV. Methods: We enrolled 30 patients with advanced HIV (CD4 <100 cells/mm3) in India; 16 with active TB and 14 without. Whole-blood RNA sequencing was performed; these data were merged with a publicly available dataset from Uganda (n = 33; 18 with TB and 15 without). Transcriptomic profiling and machine learning algorithms identified an optimal gene signature for TB classification. Receiver operating characteristic analysis was used to assess performance. Results: Among 565 differentially expressed genes identified for TB, 40 were shared across India and Uganda cohorts. Common upregulated pathways reflect Toll-like receptor cascades and neutrophil degranulation. The machine-learning decision-tree algorithm selected gene expression values from RAB20 and INSL3 as most informative for TB classification. The signature accurately classified TB in discovery cohorts (India AUC 0.95 and Uganda AUC 1.0; p < 0.001); accuracy was fair in external validation cohorts. Conclusions: Expression values of RAB20 and INSL3 genes in peripheral blood compose a biosignature that accurately classified TB status among patients with advanced HIV in two geographically distinct cohorts. The functional analysis suggests pathways previously reported in TB pathogenesis.
Using EEG Alpha States to Understand Learning During Alpha Neurofeedback Training for Chronic Pain

Objective Alpha-neurofeedback (α-NFB) is a novel therapy which trains individuals to volitionally increase their alpha power to improve pain. Learning during NFB is commonly measured using static parameters such as mean alpha power. Considering the biphasic nature of alpha rhythm (high and low alpha), dynamic parameters describing the time spent by individuals in high alpha state and the pattern of transitioning between states might be more useful. Here, we quantify the changes during α-NFB for chronic pain in terms of dynamic changes in alpha states. Methods Four chronic pain and four healthy participants received five NFB sessions designed to increase frontal alpha power. Changes in pain resilience were measured using visual analogue scale (VAS) during repeated cold-pressor tests (CPT). Changes in alpha state static and dynamic parameters such as fractional occupancy (time in high alpha state), dwell time (length of high alpha state) and transition probability (probability of moving from low to high alpha state) were analyzed using Friedman’s Test and correlated with changes in pain scores using Pearson’s correlation. Results There was no significant change in mean frontal alpha power during NFB. There was a trend of an increase in fractional occupancy, mean dwell duration and transition probability of high alpha state over the five sessions in chronic pain patients only. Significant correlations were observed between change in pain scores and fractional occupancy (r = −0.45, p = 0.03), mean dwell time (r = -0.48, p = 0.04) and transition probability from a low to high state (r = -0.47, p = 0.03) in chronic pain patients but not in healthy participants. Conclusion There is a differential effect between patients and healthy participants in terms of correlation between change in pain scores and alpha state parameters. Parameters providing a more precise description of the alpha power dynamics than the mean may help understand the therapeutic effect of neurofeedback on chronic pain.
Tenascin-W Is a Novel Stromal Marker in Biliary Tract Cancers

Extrahepatic cancers of the biliary system are typically asymptomatic until after metastasis, which contributes to their poor prognosis. Here we examined intrahepatic cholangiocarcinomas (n = 8), carcinomas of perihilar bile ducts (n = 7), carcinomas of the gallbladder (n = 11) and hepatic metastasis from carcinomas of the gallbladder (n = 4) for the expression of the extracellular matrix glycoproteins tenascin-C and tenascin-W. Anti-tenascin-C and anti-tenascin-W immunoreactivity was found in all biliary tract tumors examined. Unlike tenascin-C, tenascin-W was not detected in normal hepatobiliary tissue. Tenascin-W was also expressed by the cholangiocarcinoma-derived cell line Huh-28. However, co-culture of Huh-28 cells with immortalized bone marrow-derived stromal cells was necessary for the formation and organization of tenascin-W fibrils in vitro. Our results indicate that tenascin-W may be a novel marker of hepatobiliary tumor stroma, and its absence from many normal tissues suggests that it may be a potential target for biotherapies.
Anterior eye development in the brown anole, Anolis sagrei

Background Anterior eye development has been explored in different vertebrate species ranging from fish to mammals. However, missing from this diverse group is a representative of reptiles. A promising candidate to fill this void is the brown anole, Anolis sagrei, which is easily raised in the laboratory and for which genome editing techniques exist. Here we provide a detailed histological analysis of the development of the anterior structures of the eye in A. sagrei, which include the cornea, iris, ciliary body, lens, trabecular meshwork, and sclera ossicles. Results Development of the anterior segment in Anoles proceeds as for other vertebrates with the lens forming first followed by the cornea, then the iris, ciliary body, trabecular meshwork, and sclera ossicles. The onset of these latter structures occurs first temporally than nasally. Unlike the eyes of mammals and birds, anoles possess a remarkably thin cornea, flat ciliary body, and a trabecular meshwork that lacks an obvious Schlemm’s canal. Conclusions This study highlights several features present in anoles and represents an important step towards understanding reptile eye development. Key Findings The anole cornea epithelium is thin, composed mainly of a single basal cell layer. The ciliary body lacks a ciliary process. Iris and ciliary body formation occur in a spatiotemporal fashion, developing first temporally then nasally. The anole trabecular meshwork is composed of a spongiform tissue and lacks a Schlemm’s canal.
The Role of Dectin-1 Signaling in Altering Tumor Immune Microenvironment in the Context of Aging

An increased accumulation of immune-dysfunction-associated CD4+Foxp3+ regulatory T cells (Tregs) is observed in aging oral mucosa during infection. Here we studied the function of Tregs during oral cancer development in aging mucosa. First, we found heightened proportions of Tregs and Myeloid-derived suppressor cells (MDSC) accumulating in mouse and human oral squamous cell carcinoma (OSCC) tissues. Using mouse 4-Nitroquinoline 1-oxide(4-NQO) oral carcinogenesis model, we found aged mice displayed increased propensity to epithelial cell dysplasia, hyperplasia, and accelerated OSCC development, which coincided with a significantly increased abundance of IL-1β, Tregs, and MDSC in tongues. Partial depletion of Tregs reduced tumor burden. Moreover, fungal abundance and Dectin-1 signaling were elevated in aged mice suggesting a potential role for Dectin-1 in modulating immune environment and tumor development. Corroborating to this tenet, Dectin-1 deficient mice showed diminished IL-1β, reduced infiltration of Tregs and MDSC in the tongue, as well as slower progression and reduced severity in tumor burden, revealing that Dectin-1 signaling plays a critical role in promoting tumor incidence and cancer progression. Taken together, these data identify an important role of enhanced Dectin-1 signaling in establishing the intra-tumoral immunosuppressive milieu and promoting OSCC tumorigenesis in the context of aging.
Editorial: New Hypervalent Iodine Reagents for Oxidative Coupling

In theory, oxidative coupling is a straightforward method for reducing the number of synthetic steps, avoiding the preparation of pre-activated substrates and less waste co-product generation by using metal salts. However, attempts at oxidative cross-coupling are challenging due to its limited synthetic applications and chemoselective issues. In recent years new oxidative coupling methods have emerged, using the C–H bond of the two substrates, and enabling the selective formation of cross-coupling products (Stuart and Fagnou, 2007). One of the innovative research fronts in this area to have emerged in the past decade is the advance of oxidative coupling chemistry that uses hypervalent iodine reagents (Kita and Dohi, 2015; Yoshimura and Zhdankin, 2016), especially catalytic utilizations (Dohi and Kita, 2009; Dohi et al., 2013; Ito et al., 2013). This Research Topic discusses recent advancements of oxidative couplings and related reactions using hypervalent iodine compounds, highlighting the versatility of these reagents and their continuous development. Contributing to the recent advances in this area, the Research Topic includes contributions by experts exploring designs, preparations, reactions, mechanistic studies of hypervalent iodine compounds, and cooperative reaction systems with transition metals and photoredox catalysts, outlining how these synthetic applications can obtain useful organic molecules, such as pharmaceutical compounds. In recent years there have been a number of successes in the participation of hypervalent iodine compounds in transitionmetal chemistry, which serve as strong electrophiles and powerful oxidizing agents, especially for the palladium-catalyzed couplings. The review by Shetgaonkar and Singh narrates recent advancements in this area, summarizing extensive work in the field of Pd-catalyzed C–H functionalizations, arylations, and other miscellaneous transformations with hypervalent iodine reagents and diaryliodonium(III) salts. The synergistic combination of photoredox catalysis with hypervalent iodine reagents is one of many useful areas of organic synthesis. Chen et al. describe recent synthetic applications with visiblelight-induced photoredox catalysis, focusing on the photochemical roles of hypervalent iodine reagents. However, a wide range of hypervalent iodine compounds still need to be explored under these conditions to bring out more synthetically useful transformations. We anticipate an expansion of this hot research area in the next few years. In 2009, a novel cross-coupling method of heteroaromatic compounds was developed by exploiting the unique reactivities of diaryliodonium(III) salts (Kita et al., 2009). Since then, the chemistry of heteroaryliodonium(III) salts has undergone significant developments. They have Edited and reviewed by: Iwao Ojima, Stony Brook University, United States