ProQ-associated small RNAs control motility in Vibrio cholerae.

Gene regulation at the post-transcriptional level is prevalent in all domains of life. In bacteria, ProQ-like proteins have emerged as important RNA chaperones facilitating RNA stability and RNA duplex formation. In the major human pathogen Vibrio cholerae, post-transcriptional gene regulation is key for virulence, biofilm formation, and antibiotic resistance, yet the role of ProQ has not been studied.

ChimericFragments: computation, analysis and visualization of global RNA networks.

RNA-RNA interactions are a key feature of post-transcriptional gene regulation in all domains of life. While ever more experimental protocols are being developed to study RNA duplex formation on a genome-wide scale, computational methods for the analysis and interpretation of the underlying data are lagging behind. Here, we present ChimericFragments, an analysis framework for RNA-seq experiments that produce chimeric RNA molecules.

Small RNAs direct attack and defense mechanisms in a quorum sensing phage and its host.

Many, if not all, bacteria use quorum sensing (QS) to control collective behaviors, and more recently, QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or "listen in" on the host's communication processes, to switch between lytic and lysogenic modes of infection. Here, we study the interaction of Vibrio cholerae with the lysogenic phage VP882, which is activated by the QS molecule DPO.

The global RNA-RNA interactome of unveils a small RNA regulator of cell division.

The ubiquitous RNA chaperone Hfq is involved in the regulation of key biological processes in many species across the bacterial kingdom. In the opportunistic human pathogen , deletion of the gene affects the global transcriptome, virulence, and stress resistance; however, the ligands of the major RNA-binding protein in this species have remained elusive. In this study, we have combined transcriptomic, co-immunoprecipitation, and global RNA interactome analyses to compile an inventory of conserved and species-specific RNAs bound by Hfq and to monitor Hfq-mediated RNA-RNA interactions.

An RNA sponge controls quorum sensing dynamics and biofilm formation in Vibrio cholerae.

Small regulatory RNAs (sRNAs) acting in concert with the RNA chaperone Hfq are prevalent in many bacteria and typically act by base-pairing with multiple target transcripts. In the human pathogen Vibrio cholerae, sRNAs play roles in various processes including antibiotic tolerance, competence, and quorum sensing (QS). Here, we use RIL-seq (RNA-interaction-by-ligation-and-sequencing) to identify Hfq-interacting sRNAs and their targets in V.

Conserved hydrogen-bond motifs of membrane transporters and receptors.

Membrane transporters and receptors often rely on conserved hydrogen bonds to assemble transient paths for ion transfer or long-distance conformational couplings. For transporters and receptors that use proton binding and proton transfer for function, inter-helical hydrogen bonds of titratable protein sidechains that could change protonation are of central interest to formulate hypotheses about reaction mechanisms. Knowledge of hydrogen bonds common at sites of potential interest for proton binding could thus inform and guide studies on functional mechanisms of protonation-coupled membrane proteins.

Interactive Interface for Graph-Based Analyses of Dynamic H-Bond Networks: Application to Spike Protein S.

Dynamic hydrogen-bond networks are key determinants of protein conformational dynamics. In the case of macromolecular protein complexes, which can have a large number of hydrogen bonds giving rise to extensive hydrogen-bond networks, efficient algorithms are required to analyze interactions that could be important for the dynamics and biological function of the complex. We present here a highly efficient, standalone interface designed for analyses of dynamical hydrogen-bond networks of biomolecules and macromolecular complexes.

The Systemic Immune Response in COVID-19 Is Associated with a Shift to Formyl-Peptide Unresponsive Eosinophils.

A malfunction of the innate immune response in COVID-19 is associated with eosinopenia, particularly in more severe cases. This study tested the hypothesis that this eosinopenia is COVID-19 specific and is associated with systemic activation of eosinophils. Blood of 15 healthy controls and 75 adult patients with suspected COVID-19 at the ER were included before PCR testing and analyzed by point-of-care automated flow cytometry (CD10, CD11b, CD16, and CD62L) in the absence or presence of a formyl peptide (fNLF).

A graph-based approach identifies dynamic H-bond communication networks in spike protein S of SARS-CoV-2.

Corona virus spike protein S is a large homo-trimeric protein anchored in the membrane of the virion particle. Protein S binds to angiotensin-converting-enzyme 2, ACE2, of the host cell, followed by proteolysis of the spike protein, drastic protein conformational change with exposure of the fusion peptide of the virus, and entry of the virion into the host cell. The structural elements that govern conformational plasticity of the spike protein are largely unknown.

Mechanism of Inward Proton Transport in an Antarctic Microbial Rhodopsin.

Although the outward-directed proton transport across biological membranes is well studied and its importance for bioenergetics is clearly understood, inward-directed light-driven proton pumping by microbial rhodopsins has remained a mystery both physiologically and mechanistically. A new family of Antarctic rhodopsins, which is a subgroup within a novel class of schizorhodopsins reported recently, includes a member, denoted as AntR, which proved amenable to extensive characterization with experiments and computation. Phylogenetic analyses identify AntR as distinct from the well-studied microbial rhodopsins that function as outward-directed ion pumps, and bioinformatics sequence analyses reveal amino acid substitutions at conserved sites essential for outward proton pumping.

Bridge: A Graph-Based Algorithm to Analyze Dynamic H-Bond Networks in Membrane Proteins.

Membrane proteins that function as transporters or receptors must communicate with both sides of the lipid bilayer in which they sit. This long distance communication enables transporters to move protons or other ions and small molecules across the bilayer and receptors to transmit an external signal to the cell. Hydrogen bonds, hydrogen-bond networks, and lipid-protein interactions are essential for the motions and functioning of the membrane protein and, consequently, of outmost interest to structural biology and numerical simulations.

Dynamics of Long-Distance Hydrogen-Bond Networks in Photosystem II.

Photosystem II uses the energy of absorbed light to split water molecules, generating molecular oxygen, electrons, and protons. The four protons generated during each reaction cycle are released to the lumen via mechanisms that are poorly understood. Given the complexity of photosystem II, which consists of multiple protein subunits and cofactor molecules and hosts numerous waters, a fundamental issue is finding transient networks of hydrogen bonds that bridge potential proton donor and acceptor groups.

Normal life expectancy for paraganglioma patients: a 50-year-old cohort revisited.

The objective of this study was to assess the long-term survival of patients with a paraganglioma of the head and neck compared with the survival of the general Dutch population. This historic cohort study was conducted using nationwide historical data of paraganglioma patients. We retrieved a cohort of 86 patients diagnosed with a paraganglioma of the head and neck between 1945 and 1960 in the Netherlands.

Mutations in SDHD are the major determinants of the clinical characteristics of Dutch head and neck paraganglioma patients.

Objective: Head and neck paragangliomas (HNPGL) are associated with mutations in genes encoding subunits of succinate dehydrogenase (SDH). The aim of this study was to evaluate SDH mutations, family history and phenotypes of patients with HNPGL in the Netherlands.

Design: We evaluated the clinical data and the mutation status of 236 patients referred between 1950 and 2009 to Leiden University Medical Center.

The Dutch founder mutation SDHD.D92Y shows a reduced penetrance for the development of paragangliomas in a large multigenerational family.

Germline mutations in SDHD predispose to the development of head and neck paragangliomas, and phaeochromocytomas. The risk of developing a tumor depends on the sex of the parent who transmits the mutation: paragangliomas only arise upon paternal transmission. In this study, both the risk of paraganglioma and phaeochromocytoma formation, and the risk of developing associated symptoms were investigated in 243 family members with the SDHD.

Paediatric hypopharyngeal perforation: child abuse until proved otherwise?

A case of paediatric hypopharyngeal perforation in a 7-month-old infant is reported. The diagnosis was delayed because it was not considered. It later transpired that the injury had been inflicted by one of the child's parents.

Contributions of GABAergic and glutamatergic mechanisms to isoflurane-induced suppression of thalamic somatosensory information transfer.

Indications for a pivotal role of the thalamocortical network in producing the state of anesthesia have come from in vivo animal studies as well as imaging studies in humans. We studied possible synaptic mechanisms of anesthesia-induced suppression of touch perception in the rat's thalamus. Thalamocortical relay neurons (TCNs) receive ascending and descending glutamatergic excitatory inputs via NMDA and non-NMDA receptors (AMPAR) and are subjected to GABA(A)ergic inhibitory input which shapes the sensory information conveyed to the cortex.

Differential effects of isoflurane on excitatory and inhibitory synaptic inputs to thalamic neurones in vivo.

Background: Mechanosensory thalamocortical relay neurones (TCNs) receive glutamatergic excitatory input and are subjected to gamma-aminobutyric acid (GABA)Aergic inhibitory input. This study assessed the effects of an increase in concentration of isoflurane on thalamic excitatory and inhibitory mechanisms.

Methods: TCNs (n = 15) of the thalamic ventral posteromedial nucleus responding to mechanical stimulation of whiskers were investigated in rats anaesthetized with end-tidal concentrations of isoflurane of approximately 0.

Is a "vanishing tumor" always a lymphoma?

The authors report clinical and radiologic characteristics and ultimate diagnosis in 12 patients with a regressing cerebral mass lesion. Primary CNS lymphoma (PCNL) was found in only half of the patients with such a lesion. In patients showing a complete resolution of the enhancing lesion the probability of finding a PCNL is smaller and survival is longer.

Increased responsiveness of cortical neurons in contrast to thalamic neurons during isoflurane-induced EEG bursts in rats.

The neuronal mechanisms underlying the electroencephalographic (EEG) burst-suppression pattern are not yet understood, however, they are generally attributed to interactions within thalamocortical networks. In contrast, we report that the sensory cortex and the thalamus are disconnected, with thalamic sensory processing being unaffected by cortical EEG bursts. We studied the activity of single neurons of the somatosensory thalamocortical system in rats during burst-suppression EEG induced by the volatile anesthetic, isoflurane.

Local GABA(A) receptor blockade reverses isoflurane's suppressive effects on thalamic neurons in vivo.

Many in vitro effects of volatile anesthetics are known, but the mechanisms of action are still under debate. Because suppression of sensory perception is one of the major goals of general anesthesia, we studied the effects of isoflurane on the processing of somatosensory information in anesthetized rats. Local iontophoretic administration of the gamma-aminobutyric acid-A (GABA(A)) receptor antagonist bicuculline in the thalamic ventral posteromedial nucleus reversed suppressive effects of isoflurane on thalamocortical relay neurons (TCNs).

Isoflurane induces dose-dependent changes of thalamic somatosensory information transfer.

In spite of several reports about suppressive effects of volatile anesthetics on somatosensation, their neuronal mechanisms are largely unknown. The present study investigates somatosensory impulse transmission at the thalamic level in rats under varied concentrations of isoflurane by recordings of neuronal responses to mechanical stimulation of the body surface. Single-unit recordings of thalamo-cortical relay neurons (TCNs, third order neurons; n=28) and presumed trigemino-thalamic fibers (TTFs, second order neurons; n=7) were performed in the ventral posteromedial nucleus.

[Peripheral arteriography at an advanced age using a new contrast agent].

A new non-ionic contrast agent containing 300 mg iodine/ml ( Jopamidol ) was used in angiographic examination of over 200 patients with a median age of about 70 years. A total of 492 arterial injections was performed. There were no serious side-effects, especially, there were no cardio-vascular disturbances nor any renal dysfunctions.

[Tolerance and contrast density in intravenous cholangiography and cholecystography using a new contrast medium (author's transl)].

The tolerance and diagnostic usefulness of the new intravenous bile contrast medium Endomirabil were subjected to clinical radiological testing. Endomirabil is well tolerated. It is our impression that it has a lower side effect quota than the other contrast media used so far.