Larkin-Ovchinnikov-Fulde-Ferrell state in quasi-one-dimensional superconductors

The properties of a quasi-one-dimensional (quasi-1D) superconductor with {\it an open Fermi surface} are expected to be unusual in a magnetic field. On the one hand, the quasi-1D structure of the Fermi surface strongly favors the formation of a non-uniform state (Larkin-Ovchinnikov-Fulde-Ferrell (LOFF) state) in the presence of a magnetic field acting on the electron spins. On the other hand, a magnetic field acting on an open Fermi surface induces a dimensional crossover by confining the electronic wave-functions wave-functions along the chains of highest conductivity, which results in a divergence of the orbital critical field and in a stabilization at low temperature of a cascade of superconducting phases separated by first order transistions. In this paper, we study the phase diagram as a function of the anisotropy. We discuss in details the experimental situation in the quasi-1D organic conductors of the Bechgaard salts family and argue that they appear as good candidates for the observation of the LOFF state, provided that their anisotropy is large enough. Recent experiments on the organic quasi-1D superconductor (TMTSF)$_2$ClO$_4$ are in agreement with the results obtained in this paper and could be interpreted as a signature of a high-field superconducting phase. We also point out the possibility to observe a LOFF state in some quasi-2D organic superconductors.Comment: 24 pages+17 figures (upon request), RevTex, ORSAY-LPS-24109

Interactions of Pleckstrin Homology Domains with Membranes: Adding Back the Bilayer via High-Throughput Molecular Dynamics

A molecular simulation pipeline for determining the mode of interaction of pleckstrin homology (PH) domains with phosphatidylinositol phosphate (PIP)-containing lipid bilayers is presented. We evaluate our methodology for the GRP1 PH domain via comparison with structural and biophysical data. Coarse-grained simulations yield a 2D density landscape for PH/membrane interactions alongside residue contact profiles. Predictions of the membrane localization and interactions of 13 PH domains reveal canonical, non-canonical, and dual PIP-binding sites on the proteins. Thus, the PH domains associate with the PIP molecules in the membrane via a highly positively charged loop. Some PH domains exhibit modes of interaction with PIP-containing membranes additional to this canonical binding mode. All 13 PH domains cause a degree of local clustering of PIP molecules upon binding to the membrane. This provides a global picture of PH domain interactions with membranes. The high-throughput approach could be extended to other families of peripheral membrane proteins

Structure and lipid binding properties of the kindlin-3 pleckstrin homology domain

Kindlins co-activate integrins alongside talin. They possess, like talin, a FERM domain comprising F0-F3 subdomains, but with a pleckstrin homology (PH) domain inserted in the F2 subdomain that enables membrane association. We present the crystal structure of murine kindlin-3 PH domain determined at 2.23Å resolution and characterise its lipid binding using biophysical and computational approaches. Molecular dynamics (MD) simulations suggest flexibility in the PH domain loops connecting β-strands forming the putative phosphatidylinositol phosphate (PtdInsP) binding site. Simulations with PtdInsP-containing bilayers reveal that the PH domain associates with PtdInsP molecules mainly via the positively charged surface presented by the β1-β2 loop and that it binds with somewhat higher affinity to PtdIns(3,4,5)P3 compared to PtdIns(4,5)P2. Surface plasmon resonance (SPR) with lipid headgroups immobilised and the PH domain as analyte indicate affinities of 300 μM for PtdIns(3,4,5)P3 and 1mM for PtdIns(4,5)P2. In contrast, SPR studies with immobilised PH domain and lipid nanodiscs as analyte show affinities of 0.40 µM for PtdIns(3,4,5)P3 and no affinity for PtdIns(4,5)P2 when the inositol phosphate constitutes 5% of the total lipids (~5 molecules per nanodisc). Reducing the PtdIns(3,4,5)P3 composition to 1% abolishes nanodisc binding to the PH domain, as does site-directed mutagenesis of two lysines within the β1-β2 loop. Binding of PtdIns(3,4,5)P3 by a canonical PH domain, Grp1, is not similarly influenced by SPR experimental design. These data suggest a role for PtdIns(3,4,5)P3 clustering in the binding of some PH domains and not others, highlighting the importance lipid mobility and clustering for the biophysical assessment of protein-membrane interactions

Minimizing errors in RT-PCR detection and quantification of SARS-CoV-2 RNA for wastewater surveillance

Wastewater surveillance for pathogens using reverse transcription-polymerase chain reaction (RT-PCR) is an effective and resource-efficient tool for gathering community-level public health information, including the incidence of coronavirus disease-19 (COVID-19). Surveillance of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) in wastewater can potentially provide an early warning signal of COVID-19 infections in a community. The capacity of the world's environmental microbiology and virology laboratories for SARS-CoV-2 RNA characterization in wastewater is increasing rapidly. However, there are no standardized protocols or harmonized quality assurance and quality control (QA/QC) procedures for SARS-CoV-2 wastewater surveillance. This paper is a technical review of factors that can cause false-positive and false-negative errors in the surveillance of SARS-CoV-2 RNA in wastewater, culminating in recommended strategies that can be implemented to identify and mitigate some of these errors. Recommendations include stringent QA/QC measures, representative sampling approaches, effective virus concentration and efficient RNA extraction, PCR inhibition assessment, inclusion of sample processing controls, and considerations for RT-PCR assay selection and data interpretation. Clear data interpretation guidelines (e.g., determination of positive and negative samples) are critical, particularly when the incidence of SARS-CoV-2 in wastewater is low. Corrective and confirmatory actions must be in place for inconclusive results or results diverging from current trends (e.g., initial onset or reemergence of COVID-19 in a community). It is also prudent to perform interlaboratory comparisons to ensure results' reliability and interpretability for prospective and retrospective analyses. The strategies that are recommended in this review aim to improve SARS-CoV-2 characterization and detection for wastewater surveillance applications. A silver lining of the COVID-19 pandemic is that the efficacy of wastewater surveillance continues to be demonstrated during this global crisis. In the future, wastewater should also play an important role in the surveillance of a range of other communicable diseases

Potencial atrator de peixes ósseos em recife artificial no litoral norte do estado do Rio de Janeiro, Brasil Attractor potential of osteichthyes in artificial reef on the northern coast of Rio de Janeiro State, Brazil

<abstract language="eng">Artificial reefs have become an important and popular resource enhancement technique by concentrating fishes and by increasing natural production of biological resources. In order to increase the necto-benthic colonization potencial, an artificial reef was installed on the northern coast of Rio de Janeiro (21º27'S, 41ºOO'W), an area with typically low relief bottom. Measuring nearly 1500 m², the reef consisted of four sets of different materials randomly disposed: concrete pipes (N = 12); tires structures (N = 20); and cement tanks (N = 7) and pre-made blocks (N = 4). ln order to determine the artificial reef effects on the teleost community, trammel nets were used for monthly sampling the reef site (RA) and on a control area (AC) with sandy bottom. During the 23-month survey from April/96 to March/98, were recorded: a) Chaetodipterus faber (Broussonet, 1782) and Haemulon aurolieatum (Cuvier, 1829) as exclusive species of the RA; b) higher values of species richness and abundance on the RA, at least in 5 of 8 periods; c) increase on the fish abundance on summer months. Correlation analysis indicated that salinity and precipitation were the most significant environmental factors correlated with the temporal fish community variation. This results highlight the importance of rainfall periodicity and the influence of Paraíba do Sul River on the nekton assemblage distribution. It is suggested that the functional role of the artificial reef might be related to higher availability of local shelter and food resources