Role of duodenal iron transporters and hepcidin in patients with alcoholic liver disease

Patients with alcoholic liver disease (ALD) often display disturbed iron indices. Hepcidin, a key regulator of iron metabolism, has been shown to be down‐regulated by alcohol in cell lines and animal models. This down‐regulation led to increased duodenal iron transport and absorption in animals. In this study, we investigated gene expression of duodenal iron transport molecules and hepcidin in three groups of patients with ALD (with anaemia, with iron overload and without iron overload) and controls. Expression of DMT1, FPN1, DCYTB, HEPH, HFE and TFR1 was measured in duodenal biopsies by using real‐time PCR and Western blot. Serum hepcidin levels were measured by using ELISA. Serum hepcidin was decreased in patients with ALD. At the mRNA level, expressions of DMT1, FPN1 and TFR1 genes were significantly increased in ALD. This pattern was even more pronounced in the subgroups of patients without iron overload and with anaemia. Protein expression of FPN1 paralleled the increase at the mRNA level in the group of patients with ALD. Serum ferritin was negatively correlated with DMT1 mRNA. The down‐regulation of hepcidin expression leading to up‐regulation of iron transporters expression in the duodenum seems to explain iron metabolism disturbances in ALD. Alcohol consumption very probably causes suppression of hepcidin expression in patients with ALD.     

When the Body Hides the Ancestry: Phylogeny of Morphologically Modified Epizoic Earwigs Based on Molecular Evidence

Here, we present a study regarding the phylogenetic positions of two enigmatic earwig lineages whose unique phenotypic traits evolved in connection with ectoparasitic relationships with mammals. Extant earwigs (Dermaptera) have traditionally been divided into three suborders: the Hemimerina, Arixeniina, and Forficulina. While the Forficulina are typical, well-known, free-living earwigs, the Hemimerina and Arixeniina are unusual epizoic groups living on molossid bats (Arixeniina) or murid rodents (Hemimerina). The monophyly of both epizoic lineages is well established, but their relationship to the remainder of the Dermaptera is controversial because of their extremely modified morphology with paedomorphic features. We present phylogenetic analyses that include molecular data (18S and 28S ribosomal DNA and histone-3) for both Arixeniina and Hemimerina for the first time. This data set enabled us to apply a rigorous cladistics approach and to test competing hypotheses that were previously scattered in the literature. Our results demonstrate that Arixeniidae and Hemimeridae belong in the dermapteran suborder Neodermaptera, infraorder Epidermaptera, and superfamily Forficuloidea. The results support the sister group relationships of Arixeniidae+Chelisochidae and Hemimeridae+Forficulidae. This study demonstrates the potential for rapid and substantial macroevolutionary changes at the morphological level as related to adaptive evolution, in this case linked to the utilization of a novel trophic niche based on an epizoic life strategy. Our results also indicate that the evolutionary consequences of the transition to an ectoparazitic mode of living, which is extremely rare in earwigs, have biased previous morphology-based hypotheses regarding the phylogeny of this insect group.     

RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP

Various helicases and single-stranded DNA (ssDNA) binding proteins are known to destabilize G-quadruplex (GQ) structures, which otherwise result in genomic instability. Bulk biochemical studies have shown that Bloom helicase (BLM) unfolds both intermolecular and intramolecular GQ in the presence of ATP. Using single molecule FRET, we show that binding of RecQ-core of BLM (will be referred to as BLM) to ssDNA in the vicinity of an intramolecular GQ leads to destabilization and unfolding of the GQ in the absence of ATP. We show that the efficiency of BLM-mediated GQ unfolding correlates with the binding stability of BLM to ssDNA overhang, as modulated by the nucleotide state, ionic conditions, overhang length and overhang directionality. In particular, we observed enhanced GQ unfolding by BLM in the presence of non-hydrolysable ATP analogs, which has implications for the underlying mechanism. We also show that increasing GQ stability, via shorter loops or higher ionic strength, reduces BLM-mediated GQ unfolding. Finally, we show that while WRN has similar activity as BLM, RecQ and RECQ5 helicases do not unfold GQ in the absence of ATP at physiological ionic strength. In summary, our study points to a novel and potentially very common mechanism of GQ destabilization mediated by proteins binding to the vicinity of these structures.     

Tuberosphere and bulk soil microbial communities in fields differing in common scab severity are distinguished by soil chemistry and interactions with pathogens

Plant and Soil - Common scab of potatoes (CS) is influenced by plant-microbe-soil interactions, which are locally specific. The study aims to identify any common trends in such interactions across...     

Estimating a Logistic Discrimination Functions When One of the Training Samples Is Subject to Misclassification: A Maximum Likelihood Approach

The problem of discrimination and classification is central to much of epidemiology. Here we consider the estimation of a logistic regression/discrimination function from training samples, when one of the training samples is subject to misclassification or mislabeling, e.g. diseased individuals are incorrectly classified/labeled as healthy controls. We show that this leads to zero-inflated binomial model with a defective logistic regression or discrimination function, whose parameters can be estimated using standard statistical methods such as maximum likelihood. These parameters can be used to estimate the probability of true group membership among those, possibly erroneously, classified as controls. Two examples are analyzed and discussed. A simulation study explores properties of the maximum likelihood parameter estimates and the estimates of the number of mislabeled observations.     

Structural basis of RNA recognition by the SARS-CoV-2 nucleocapsid phosphoprotein

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19). SARS-CoV-2 is a single-stranded positive-sense RNA virus. Like other coronaviruses, SARS-CoV-2 has an unusually large genome that encodes four structural proteins and sixteen nonstructural proteins. The structural nucleocapsid phosphoprotein N is essential for linking the viral genome to the viral membrane. Both N-terminal RNA binding (N-NTD) and C-terminal dimerization domains are involved in capturing the RNA genome and, the intrinsically disordered region between these domains anchors the ribonucleoprotein complex to the viral membrane. Here, we characterized the structure of the N-NTD and its interaction with RNA using NMR spectroscopy. We observed a positively charged canyon on the surface of the N-NTD that might serve as a putative RNA binding site similarly to other coronaviruses. The subsequent NMR titrations using single-stranded and double-stranded RNA revealed a much more extensive U-shaped RNA-binding cleft lined with regularly distributed arginines and lysines. The NMR data supported by mutational analysis allowed us to construct hybrid atomic models of the N-NTD/RNA complex that provided detailed insight into RNA recognition.     

Characterization of the Drosophila adenosine receptor: the effect of adenosine analogs on cAMP signaling in Drosophila cells and their utility for in vivo experiments

Adenosine receptors (AR) belonging to the G protein-coupled receptor family influence a wide range of physiological processes. Recent elucidation of the structure of human A2AR revealed the conserved amino acids necessary for contact with the Ado moiety. However, the selectivity of Ado analogs for AR subtypes is still not well understood. We have shown previously that the Drosophila adenosine receptor (DmAdoR) evokes an increase in cAMP and calcium concentration in heterologous cells. In this study, we have characterized the second-messenger stimulation by endogenous DmAdoR in a Drosophila neuroblast cell line and examined a number of Ado analogs for their ability to interact with DmAdoR. We show that Ado can stimulate cAMP but not calcium levels in Drosophila cells. We found one full and four partial DmAdoR agonists, as well as four antagonists. The employment of the full agonist, 2-chloroadenosine, in flies mimicked in vivo the phenotype of DmAdoR over-expression, whereas the antagonist, SCH58261, rescued the flies from the lethality caused by DmAdoR over-expression. Differences in pharmacological effect of the tested analogs between DmAdoR and human A2AR can be partially explained by the dissimilarity of specific key amino acid residues disclosed by the alignment of these receptors.     

SCIMP, a transmembrane adaptor protein involved in major histocompatibility complex class II signaling

Formation of the immunological synapse between an antigen-presenting cell (APC) and a T cell leads to signal generation in both cells involved. In T cells, the lipid raft-associated transmembrane adaptor protein LAT plays a central role. Its phosphorylation is a crucial step in signal propagation, including the calcium response and mitogen-activated protein kinase activation, and largely depends on its association with the SLP76 adaptor protein. Here we report the discovery of a new palmitoylated transmembrane adaptor protein, termed SCIMP. SCIMP is expressed in B cells and other professional APCs and is localized in the immunological synapse due to its association with tetraspanin-enriched microdomains. In B cells, it is constitutively associated with Lyn kinase and becomes tyrosine phosphorylated after major histocompatibility complex type II (MHC-II) stimulation. When phosphorylated, SCIMP binds to the SLP65 adaptor protein and also to the inhibitory kinase Csk. While the association with SLP65 initiates the downstream signaling cascades, Csk binding functions as a negative regulatory loop. The results suggest that SCIMP is involved in signal transduction after MHC-II stimulation and therefore serves as a regulator of antigen presentation and other APC functions.     

Interaction of late apoptotic and necrotic cells with vitronectin

Background

Vitronectin is an abundant plasma glycoprotein identified also as a part of extracellular matrix. Vitronectin is substantially enriched at sites of injured, fibrosing, inflamed, and tumor tissues where it is believed to be involved in wound healing and tissue remodeling. Little is known about the mechanism of vitronectin localization into the damaged tissues.

Methodology/Principal Findings

2E12 antibody has been described to bind a subset of late apoptotic cells. Using immunoisolation followed by mass spectrometry, we identified the antigen recognized by 2E12 antibody as vitronectin. Based on flow cytometry, we described that vitronectin binds to the late apoptotic and necrotic cells in cell cultures in vitro as well as in murine thymus and spleen in vivo. Confocal microscopy revealed that vitronectin binds to an intracellular cytoplasmic structure after the membrane rupture.

Conclusions/Significance

We propose that vitronectin could serve as a marker of membrane disruption in necrosis and apoptosis for flow cytometry analysis. Moreover, we suggest that vitronectin binding to dead cells may represent one of the mechanisms of vitronectin incorporation into the injured tissues.