The yeast Gdt1 protein mediates the exchange of H+ for Ca2+ and Mn2+ influencing the Golgi pH

The GDT1 family is broadly spread and highly conserved among living organisms. GDT1 members have functions in key processes like glycosylation in humans and yeasts, and photosynthesis in plants. These functions are mediated by their ability to transport ions. While transport of Ca²⁺ or Mn²⁺ is well established for several GDT1 members, their transport mechanism is poorly understood. Here, we demonstrate that H⁺ ions are transported in exchange for Ca²⁺ and Mn²⁺ cations by the Golgi-localized yeast Gdt1 protein. We performed direct transport measurement across a biological membrane by expressing Gdt1p in Lactococcus lactis bacterial cells and by recording either the extracellular pH or the intracellular pH during the application of Ca²⁺, Mn²⁺ or H⁺ gradients. Besides, in vivo cytosolic and Golgi pH measurements were performed in Saccharomyces cerevisiae with genetically encoded pH probes targeted to those subcellular compartments. These data point out that the flow of H⁺ ions carried by Gdt1p could be reversed according to the physiological conditions. Together, our experiments unravel the influence of the relative concentration gradients for Gdt1p-mediated H⁺ transport and pave the way to decipher the regulatory mechanisms driving the activity of GDT1 orthologs in various biological contexts.

Citizen seismology helps decipher the 2021 Haiti earthquake

The August 14, Mw7.2, Nippes earthquake in Haiti occurred within the same fault zone as its devastating, Mw7.0, 2010 predecessor but struck the country when field access was limited by insecurity and conventional seismometers from the national network were inoperative. A network of citizen seismometers installed in 2019 provided near-field data critical to rapidly understand the mechanism of the mainshock and monitor its aftershock sequence. Their real-time data define two aftershock clusters that coincide with two areas of coseismic slip derived from inversions of conventional seismological and geodetic data. Machine learning applied to data from the citizen seismometer closest to the mainshock allows us to forecast aftershocks as accurately as with the network-derived catalog. This shows the utility of citizen science contributing to the understanding of a major earthquake.

The human Golgi protein TMEM165 transports calcium and manganese in yeast and bacterial cells

Cases of congenital disorders of glycosylation (CDG) have been associated with specific mutations within the gene encoding the human Golgi TMEM165 (transmembrane protein 165), belonging to UPF0016 (uncharacterized protein family 0016), a family of secondary ion transporters. To date, members of this family have been reported to be involved in calcium, manganese, and pH homeostases. Although it has been suggested that TMEM165 has cation transport activity, direct evidence for its Ca²⁺- and Mn²⁺-transporting activities is still lacking. Here, we functionally characterized human TMEM165 by heterologously expressing it in budding yeast (Saccharomyces cerevisiae) and in the bacterium Lactococcus lactis Protein production in these two microbial hosts was enhanced by codon optimization and truncation of the putatively autoregulatory N terminus of TMEM165. We show that TMEM165 expression in a yeast strain devoid of Golgi Ca²⁺ and Mn²⁺ transporters abrogates Ca²⁺- and Mn²⁺-induced growth defects, excessive Mn²⁺ accumulation in the cell, and glycosylation defects. Using bacterial cells loaded with the fluorescent Fura-2 probe, we further obtained direct biochemical evidence that TMEM165 mediates Ca²⁺ and Mn²⁺ influxes. We also used the yeast and bacterial systems to evaluate the impact of four disease-causing missense mutations identified in individuals with TMEM165-associated CDG. We found that a mutation leading to a E108G substitution within the conserved UPF0016 family motif significantly reduces TMEM165 activity. These results indicate that TMEM165 can transport Ca²⁺ and Mn²⁺, which are both required for proper protein glycosylation in cells. Our work also provides tools to better understand the pathogenicity of CDG-associated TMEM165 mutations.

The cosmic ray shadow of the Moon observed with the ANTARES neutrino telescope

One of the main objectives of the ANTARES telescope is the search for point-like neutrino sources. Both the pointing accuracy and the angular resolution of the detector are important in this context and a reliable way to evaluate this performance is needed. In order to measure the pointing accuracy of the detector, one possibility is to study the shadow of the Moon, i.e. the deficit of the atmospheric muon flux from the direction of the Moon induced by the absorption of cosmic rays. Analysing the data taken between 2007 and 2016, the Moon shadow is observed with 3.5 σ statistical significance. The detector angular resolution for downward-going muons is 0 . 73 ∘ ± 0 . 14 ∘ . The resulting pointing performance is consistent with the expectations. An independent check of the telescope pointing accuracy is realised with the data collected by a shower array detector onboard of a ship temporarily moving around the ANTARES location.

Insight into the Self-Assembling Properties of Peptergents: A Molecular Dynamics Simulation Study

By manipulating the various physicochemical properties of amino acids, the design of peptides with specific self-assembling properties has been emerging for more than a decade. In this context, short peptides possessing detergent properties (so-called "peptergents") have been developed to self-assemble into well-ordered nanostructures that can stabilize membrane proteins for crystallization. In this study, the peptide with "peptergency" properties, called ADA8 and extensively described by Tao et al., is studied by molecular dynamic simulations for its self-assembling properties in different conditions. In water, it spontaneously forms beta sheets with a β barrel-like structure. We next simulated the interaction of this peptide with a membrane protein, the bacteriorhodopsin, in the presence or absence of a micelle of dodecylphosphocholine. According to the literature, the peptergent ADA8 is thought to generate a belt of β structures around the hydrophobic helical domain that could help stabilize purified membrane proteins. Molecular dynamic simulations are here used to image this mechanism and provide further molecular details for the replacement of detergent molecules around the protein. In addition, we generalized this behavior by designing an amphipathic peptide with beta propensity, which was called ABZ12. Both peptides are able to surround the membrane protein and displace surfactant molecules. To our best knowledge, this is the first molecular mechanism proposed for "peptergency".

The yeast protein Gdt1p transports Mn2+ ions and thereby regulates manganese homeostasis in the Golgi

The uncharacterized protein family 0016 (UPF0016) is a family of secondary ion transporters implicated in calcium homeostasis and some diseases. More precisely, genetic variants of the human UPF0016 ortholog transmembrane protein 165 (TMEM165) have been linked to congenital disorders of glycosylation (CDG). The Saccharomyces cerevisiae ortholog Gdt1p has been shown to be involved in calcium homeostasis and protein glycosylation. Moreover, plant and bacterial UPF0016 members appear to have putative roles in Mn²⁺ homeostasis. Here, we produced the yeast UPF0016 member Gdt1p in the bacterial host Lactococcus lactis Using Mn²⁺-induced quenching of Fura-2-emitted fluorescence, we observed that Gdt1p mediates Mn²⁺ influx, in addition to its previously reported regulation of Ca²⁺ influx. The estimated K_m values of Gdt1p of 15.6 ± 2.6 μm for Ca²⁺ and 83.2 ± 9.8 μm for Mn²⁺ indicated that Gdt1p has a higher affinity for Ca²⁺ than for Mn²⁺ In yeast cells, we found that Gdt1p is involved in the resistance to high Mn²⁺ concentration and controls total Mn²⁺ stores. Lastly, we demonstrated that GDT1 deletion affects the activity of the yeast Mn²⁺-dependent Sod2p superoxide dismutase, most likely by modulating cytosolic Mn²⁺ concentrations. Taken together, we obtained first evidence that Gdt1p from yeast directly transports manganese, which strongly reinforces the suggested link between the UPF0016 family and Mn²⁺ homeostasis and provides new insights into the molecular causes of human TMEM165-associated CDGs. Our results also shed light on how yeast cells may regulate Golgi intraluminal concentrations of manganese, a key cofactor of many enzymes involved in protein glycosylation.

A combined characterization of clusters in naturally aged Al–Cu–(Li, Mg) alloys using small-angle neutron and X-ray scattering and atom probe tomography

A new methodology for the characterization of solute clusters leading to compositional fluctuations is presented and discussed. The methodology makes use of contrast variation arising from a combination of small-angle scattering using neutrons and X-rays, and adapts a model for solute correlation to extract the chemistry and length scale of clustered states after quench and after natural ageing. In three subsets of the Al–Cu system, Cu-rich clusters are reported for all cases. The presence of Mg strongly enhances Cu clustering in the naturally aged state and results in more than double the number of clusters in the complex Al–Cu–Li–Mg system. The results are compared with those obtained using atom probe tomography.

An algorithm for the reconstruction of high-energy neutrino-induced particle showers and its application to the ANTARES neutrino telescope

A novel algorithm to reconstruct neutrino-induced particle showers within the ANTARES neutrino telescope is presented. The method achieves a median angular resolution of [Formula: see text] for shower energies below 100 TeV. Applying this algorithm to 6 years of data taken with the ANTARES detector, 8 events with reconstructed shower energies above 10 TeV are observed. This is consistent with the expectation of about 5 events from atmospheric backgrounds, but also compatible with diffuse astrophysical flux measurements by the IceCube collaboration, from which 2-4 additional events are expected. A [Formula: see text] C.L. upper limit on the diffuse astrophysical neutrino flux with a value per neutrino flavour of [Formula: see text] is set, applicable to the energy range from 23 TeV to 7.8 PeV, assuming an unbroken [Formula: see text] spectrum and neutrino flavour equipartition at Earth.

Sperm whale long-range echolocation sounds revealed by ANTARES, a deep-sea neutrino telescope

Despite dedicated research has been carried out to adequately map the distribution of the sperm whale in the Mediterranean Sea, unlike other regions of the world, the species population status is still presently uncertain. The analysis of two years of continuous acoustic data provided by the ANTARES neutrino telescope revealed the year-round presence of sperm whales in the Ligurian Sea, probably associated with the availability of cephalopods in the region. The presence of the Ligurian Sea sperm whales was demonstrated through the real-time analysis of audio data streamed from a cabled-to-shore deep-sea observatory that allowed the hourly tracking of their long-range echolocation behaviour on the Internet. Interestingly, the same acoustic analysis indicated that the occurrence of surface shipping noise would apparently not condition the foraging behaviour of the sperm whale in the area, since shipping noise was almost always present when sperm whales were acoustically detected. The continuous presence of the sperm whale in the region confirms the ecological value of the Ligurian sea and the importance of ANTARES to help monitoring its ecosystems.

Single-blind, placebo controlled randomised clinical study of chitosan for body weight reduction

Background

Chitosan is a dietary fibre which acts by reducing fat absorption and thus used as a means for controlling weight. Weight loss clinical trial outcomes, however, have contradictory results regarding its efficacy. The primary objective of the present study was to evaluate the efficacy and safety of a chitosan from fungal origin in treatment of excess weight in the absence of dietary restrictions.

Methods

A phase IV, randomised, multicentre, single-blind, placebo-controlled, clinical study was conducted by administering chitosan capsules (500 mg, five/day) and indistinguishable placebo capsules as daily supplements to 96 overweight and obese subjects for 90 days. The study participants were divided in 2:1 ratio to receive either chitosan (n = 64) or placebo (n = 32). Efficacy was assessed by measuring body weight, body composition parameters, anthropometric measurements, HbA1C level and lipid profile at day 45 and day 90. Also, short form-36 quality of life (QoL) questionnaire was assessed to evaluate improvement in life-style and dietary habits were recorded for calorie intake. Safety was assessed by evaluating safety parameters and monitoring adverse events.

Results

The mean changes in body weight were -1.78 ± 1.37 kg and -3.10 ± 1.95 kg at day 45 and day 90 respectively in chitosan group which were significantly different (p < 0.0001) as compared to placebo. BMI was decreased by10.91 fold compared to placebo after 90 day administration. In concert with this, there was also reduction in body composition and anthropometric parameters together with improvement in QoL score. Chitosan was also able to reduce HbA1C levels (below 6 %) in subjects who had initial higher values. The mean caloric intake shows that there was no change in dietary habits of subjects in both groups. Lipid levels were unaffected and all adverse events were mild in nature and unrelated to study treatment.

Conclusion

Chitosan from fungal origin was able to reduce the mean body weight up to 3 kg during the 90 day study period. Together with this, there was also improvement in body composition, anthropometric parameters and HbA1C, reflecting overall benefits for the overweight individuals. Additionally, there was also improvement in QoL score. It was safe and well tolerated by all subjects.

Trial registration

CTRI/2014/08/004901.

Molecular evolution of a novel family of putative calcium transporters

The UPF0016 family is a group of uncharacterized membrane proteins, well conserved through evolution and defined by the presence of one or two copies of an E-Φ-G-D-(KR)-(ST) consensus motif. Our previous results have shown that two members of this family, the human TMEM165 and the budding yeast Gdt1p, are functionally related and might form a new group of cation/Ca2+ exchangers. Most members of the family are made of two homologous clusters of three transmembrane spans, separated by a central loop and assembled with an opposite orientation in the membrane. However, some bacterial members of the family have only one cluster of transmembrane domains. Among these 'single-domain membrane proteins' some cyanobacterial members were found as pairs of adjacent genes within the genome, but each gene was slightly different. We performed a bioinformatic analysis to propose the molecular evolution of the UPF0016 family and the emergence of the antiparallel topology. Our hypotheses were confirmed experimentally using functional complementation in yeast. This suggests an important and conserved function for UPF0016 proteins in a fundamental cellular process. We also show that members of the UPF0016 family share striking similarities, but no primary sequence homology, with members of the cation/Ca2+ exchangers (CaCA) superfamily. Such similarities could be an example of convergent evolution, supporting the previous hypothesis that members of the UPF0016 family are cation/Ca2+ exchangers.

A small-angle neutron scattering study of fine-scale NbC precipitation kinetics in the α-Fe–Nb–C system

The fine-scale precipitation of NbC in ferrite has been quantitatively characterized in the temperature range 873–1073 K for two alloy compositions, containing respectively 800 p.p.m. Nb and 400 p.p.m. Nb (by weight). Transmission electron microscopy (TEM) has revealed that the precipitates are located on dislocations, and have a plate-like morphology with an average aspect ratio between 2 and 3. Small-angle neutron scattering (SANS) has been systematically used to determine the precipitation kinetics. The validity of the quantitative SANS measurements of size and volume fraction has been assessed by TEM image analysis and chemical dissolution experiments. The precipitation kinetics is observed to depend strongly on temperature but to be similar for the two alloy compositions. From the measurements, it is inferred that precipitate nucleation is extremely rapid, in relation to the nature of the nucleation sites. A time–temperature transformation diagram is built from the kinetic data, showing a maximum reaction rate between 973 and 1073 K.

[Factors associated with hyperhomocysteinemia in Crohn's disease]

AIMS

The incidence of thromboembolic disease is increased in patients with inflammatory bowel disease. Hyperhomocysteinemia is one of the risk factors for thrombosis. The aims were: 1) to assess the prevalence of hyperhomocysteinemia in a large series of patients with Crohn's disease; 2) to search for clinical and biological factors associated with hyperhomocysteinemia.

PATIENTS AND METHODS

One hundred seventy-one patients with Crohn's disease (64 males, 107 females), median age 31 years (range: 16-82), were studied. The median duration of the disease was 7 years. The concentrations of homocysteine, folate, cobalamin and C-reactive protein were measured in serum from blood sample of each patient.

RESULTS

The mean concentration of seric homocysteine was 14.8 micromol/L (N: 4.4 - 12.4 micromol/L). Hyperhomocysteinemia was observed in 89 patients (52%). It was significantly associated with age, sex, smoking habit, serum cobalamin level and history of ileal surgical resection (P<0.05). In the group of operated patients, there was a statistically significant association between hyperhomocysteinemia and the length of small bowel resected. In multivariate analysis, sex and smoking were associated with hyperhomocysteinemia.

CONCLUSION

More than half of the patients with Crohn's disease have hyperhomocysteinemia. This result stresses the need for preventing reversible factors associated with hyperhomocysteinemia, such as smoking and cobalamin deficiency, in order to lower the thrombotic risk of patients with Crohn's disease.

Antimicrobial edible packaging based on cellulosic ethers, fatty acids, and nisin incorporation to inhibit Listeria innocua and Staphylococcus aureus

Edible cellulosic films made with hydroxypropylmethylcellulose (HPMC) have proven to be inadequate moisture barriers. To improve its water vapor barrier properties, different hydrophobic compounds were incorporated into the HPMC matrix. Some fatty acids and derivatives were included into the film-forming solution prior to film formation. Stearic acid was chosen because of its high capacity to reduce significantly the water vapor transmission rate. Antimicrobial activity of edible HPMC film was obtained by the incorporation of nisin into the film-forming solution. Nisin is an antimicrobial peptide effective against gram-positive bacteria. The inhibitory activity of this bacteriocin was tested for inhibition of Listeria innocua and Staphylococcus aureus. The use of stearic acid was observed to reduce the inhibitory activity of active HPMC film against both selected strains. This phenomenon may be explained by electrostatic interactions between the cationic nisin and the anionic stearic acid. Further studies showed that antimicrobial activity of film varied with the nature of the hydrophobic compound incorporated, in decreasing order: film without lipid, methylstearate film, and stearic acid film. This corroborated the idea of electrostatic interactions.

Acid and bile tolerance of spore-forming lactic acid bacteria

Criteria for screening probiotics such as bile tolerance and resistance to acids were studied with 13 spore-forming lactic acid producing bacteria. Different strains of Sporolactobacillus, Bacillus laevolacticus, Bacillus racemilacticus and Bacillus coagulans grown in MRS broth were subjected to low pH conditions (2, 2.5 and 3) and increasing bile concentrations. Among these microorganisms, Bacillus laevolacticus DSM 6475 and all Sporolactobacillus strains tested except Sporolactobacillus racemicus IAM 12395, were resistant to pH 3. Only Bacillus racemilacticus and Bacillus coagulans strains were tolerant to bile concentrations over 0.3% (w/v).

Abnormal IgG cardiolipin antibody titers in patients with Raynaud's phenomenon and/or related disorders: prevalence and clinical significance

BACKGROUND

The prevalence of antibodies to cardiolipin (a-CL) in patients with Raynaud's phenomenon (RP) and/or related disorders (rD) is not known.

OBJECTIVE

The purpose of this study was to determine the prevalence of these antibodies.

METHODS

We assayed IgG a-CL in 230 consecutive patients with RP/rD and compared the results with those in a series of 230 control blood donors.

RESULTS

Sixteen percent of patients were a-CL positive versus 7.8% of the control donors (p = 0.014). The prevalence of a-CL positivity was 8.7% for primary RP, 10.5% for secondary RP, 8% for chilblains, 25% for essential acrocyanosis, 20% for connective tissue diseases, and 17% for undifferentiated connective tissue diseases. Among patients with digital necrosis, 24% were a-CL positive.

CONCLUSION

The prevalence of abnormal a-CL titers is higher in patients with RP/rD than in control donors, especially in patients with a connective tissue disease.

Simultaneous administration of antithrombin III and protein C concentrates for the treatment of a devastating coagulopathy in a child

Severe disseminated intravascular coagulation (DIC) is a rare event in childhood. We report here a young body with a devastating DIC unresponsive to heparin, fresh frozen plasma and platelet support. This prompted the use of antithrombin III and protein C concentrates and the effects of this combination were temporarily spectacular. We suggest that the simultaneous administration of two inhibitors of blood coagulation could be of interest and should be evaluated in appropriate trials for the treatment of a devastating coagulopathy.

DNA probe and PCR-specific reaction for Lactobacillus plantarum

A 300 bp DNA fragment of Lactobacillus plantarum isolated by randomly amplified polymorphic DNA (RAPD) analysis was cloned and sequenced. This fragment was tested using a dot-blot DNA hybridization to technique for its ability to identify Lact. plantarum strains. This probe hybridized with all Lact. plantarum strains tested and with some strains of Lact. pentosus, albeit more weakly. Two internal primers of this probe were selected (LbP11 and LbP12) and polymerase chain reaction (PCR) was carried out. All Lact. plantarum strains tested amplified a 250 bp fragment contrary to the other LAB species tested. This specific PCR for Lact. plantarum was also performed from colonies grown on MRS medium with similar results. These methods enabled the rapid and specific detection and identification of Lact. plantarum.

Autoantibodies to phospholipids and to the coagulation proteins in AIDS

In HIV-1 infection, an increased prevalence of anticardiolipin autoantibodies (aCL) and lupus anticoagulant (LA) has been described. In order to see if these antibodies are isolated or, like in autoimmune diseases, associated with hematological disorders and with antibodies to other phospholipids and to proteins of coagulation, we investigated 3 groups of patients: 1. 342 HIV-1 infected patients, 2. 145 control patients including 61 systemic lupus erythematosus (SLE) patients, 58 patients with a connective tissue disease, 15 patients with stroke, 11 patients with syphilis and 3. 100 blood donors. In HIV-1 infection antiprothrombin (aPrT) antibodies were present in 2% of patients, the prevalence of antiphosphatidylcholine antibodies (aPC) (50%) was almost as high as aCL (64%), and 39% had both antibodies. Absorption on liposomes of the latter revealed an heterogeneous mixture of aCL and aPC or cross-reacting antibodies. In contrast with SLE, anti-beta 2-glycoprotein I (4%), LA (1%), biological false positive test for syphilis (0.3%), thrombosis (p < 0.001) were uncommon. In HIV-1 infection, antiphospholipid antibodies do not associated with features linked to them in SLE or syphilis.

Nailfold capillary microscopy in patients with anticardiolipin antibodies: a case-control study

BACKGROUND AND DESIGN

This case-control study was undertaken to determine whether anticardiolipin antibodies (ACA) are responsible for particular abnormalities in nailfold capillary microscopy (NCM). Cases comprised 33 consecutive patients positive for ACA (24 women and 7 men). Controls comprised the same number of ACA-negative patients, with the same sex ratio, the same diagnosis and the most similar duration of disease possible. Clinical data, serum samples and NCM recordings were obtained from all patients and controls.

RESULTS

In each group, 22 patients had connective-tissue-related disorders and 11 various other diseases. In ACA-positive patients, the mean IgG ACA titre was 39 +/- 58 IgG phospholipid units. Cases and controls displayed various cutaneous manifestations. In ACA-positive patients, there were Raynaud's phenomenon (54%), cutaneous vasculitis (24%), scleroderma changes (18%), photosensitivity (9%), a history of digital gangrene (6%), malar rash (6%), acrocyanosis (6%), chilblains (3%), livedo reticularis (3%) and purpura (3%). Cases and controls exhibited numerous NCM abnormalities. In ACA-positive patients, they included haemorrhages (54%), oedema (24%), bushy capillaries (21%), disordered capillaries (18%), capillary bed disorganization (12%), capillary rarefaction (9%), giant capillaries (6%) and 'desert areas' (3%). There were no correlations between the ACA titres on the one hand and the number of cutaneous manifestations or NCM abnormalities on the other.

CONCLUSIONS

ACA-positive patients frequently exhibit clinical skin lesions and abnormal NCM. In this study, these lesions and NCM abnormalities resembled those of the matched ACA-negative controls.

PCR methods for identification and specific detection of probiotic lactic acid bacteria

Probiotics are defined as "microbes improving animal feed." Three lactic acid bacteria, previously selected as probiotic for pig feeding, were identified by sequencing the variable V1 region of the 16S rDNA after PCR amplification primed in the flanking constant region. A VR region showing strong nucleotide differences between the three probiotic and the reference strains was delimited. Oligonucleotides specific for each strain were designed. A specific assay for probiotic detection was developed, based on a PCR reaction with three primers.