Quantum control of a cat qubit with bit-flip times exceeding ten seconds

Quantum bits (qubits) are prone to several types of error as the result of uncontrolled interactions with their environment. Common strategies to correct these errors are based on architectures of qubits involving daunting hardware overheads1. One possible solution is to build qubits that are inherently protected against certain types of error, so the overhead required to correct the remaining errors is greatly reduced2-7. However, this strategy relies on one condition: any quantum manipulations of the qubit must not break the protection that has been so carefully engineered5,8. A type of qubit known as a cat qubit is encoded in the manifold of metastable states of a quantum dynamical system, and thereby acquires continuous and autonomous protection against bit-flips. Here, in a superconducting-circuit experiment, we implemented a cat qubit with bit-flip times exceeding 10 s. This is an improvement of four orders of magnitude over previously published cat-qubit implementations. We prepared and imaged quantum superposition states, and measured phase-flip times greater than 490 ns. Most importantly, we controlled the phase of these quantum superpositions without breaking the bit-flip protection. This experiment demonstrates the compatibility of quantum control and inherent bit-flip protection at an unprecedented level, showing the viability of these dynamical qubits for future quantum technologies.

NMR metabolite quantification of a synthetic urine sample: an inter-laboratory comparison of processing workflows

INTRODUCTION

Absolute quantification of individual metabolites in complex biological samples is crucial in targeted metabolomic profiling.

OBJECTIVES

An inter-laboratory test was performed to evaluate the impact of the NMR software, peak-area determination method (integration vs. deconvolution) and operator on quantification trueness and precision.

METHODS

A synthetic urine containing 32 compounds was prepared. One site prepared the urine and calibration samples, and performed NMR acquisition. NMR spectra were acquired with two pulse sequences including water suppression used in routine analyses. The pre-processed spectra were sent to the other sites where each operator quantified the metabolites using internal referencing or external calibration, and his/her favourite in-house, open-access or commercial NMR tool.

RESULTS

For 1D NMR measurements with solvent presaturation during the recovery delay (zgpr), 20 metabolites were successfully quantified by all processing strategies. Some metabolites could not be quantified by some methods. For internal referencing with TSP, only one half of the metabolites were quantified with a trueness below 5%. With peak integration and external calibration, about 90% of the metabolites were quantified with a trueness below 5%. The NMRProcFlow integration module allowed the quantification of several additional metabolites. The number of quantified metabolites and quantification trueness improved for some metabolites with deconvolution tools. Trueness and precision were not significantly different between zgpr- and NOESYpr-based spectra for about 70% of the variables.

CONCLUSION

External calibration performed better than TSP internal referencing. Inter-laboratory tests are useful when choosing to better rationalize the choice of quantification tools for NMR-based metabolomic profiling and confirm the value of spectra deconvolution tools.

Gestational exposure to bisphenol A induces region-specific changes in brain metabolomic fingerprints in sheep

Fetal brain development depends on maternofetal thyroid function. In rodents and sheep, perinatal BPA exposure is associated with maternal and/or fetal thyroid disruption and alterations in central nervous system development as demonstrated by metabolic modulations in the encephala of mice. We hypothesized that a gestational exposure to a low dose of BPA affects maternofetal thyroid function and fetal brain development in a region-specific manner. Pregnant ewes, a relevant model for human thyroid and brain development, were exposed to BPA (5 µg/kg bw/d, sc). The thyroid status of ewes during gestation and term fetuses at delivery was monitored. Fetal brain development was assessed by metabolic fingerprints at birth in 10 areas followed by metabolic network-based analysis. BPA treatment was associated with a significant time-dependent decrease in maternal TT4 serum concentrations. For 8 fetal brain regions, statistical models allowed discriminating BPA-treated from control lambs. Metabolic network computational analysis revealed that prenatal exposure to BPA modulated several metabolic pathways, in particular excitatory and inhibitory amino-acid, cholinergic, energy and lipid homeostasis pathways. These pathways might contribute to BPA-related neurobehavioral and cognitive disorders. Discrimination was particularly clear for the dorsal hippocampus, the cerebellar vermis, the dorsal hypothalamus, the caudate nucleus and the lateral part of the frontal cortex. Compared with previous results in rodents, the use of a larger animal model allowed to examine specific brain areas, and generate evidence of the distinct region-specific effects of fetal BPA exposure on the brain metabolome. These modifications occur concomitantly to subtle maternal thyroid function alteration. The functional link between such moderate thyroid changes and fetal brain metabolomic fingerprints remains to be determined as well as the potential implication of other modes of action triggered by BPA such as estrogenic ones. Our results pave the ways for new scientific strategies aiming at linking environmental endocrine disruption and altered neurodevelopment.

Transgenerational metabolomic fingerprints in mice ancestrally exposed to the obesogen TBT

BACKGROUND

Endocrine disrupting chemicals (EDCs) contribute to the etiology of metabolic disorders such as obesity, insulin resistance and hepatic dysfunction. Concern is growing about the consequences of perinatal EDC exposure on disease predisposition later in life. Metabolomics are promising approaches for studying long-term consequences of early life EDC exposure. These approaches allow for the identification and characterization of biomarkers of direct or ancestral exposures that could be diagnostic for individual susceptibility to disease and help to understand mechanisms through which EDCs act.

OBJECTIVES

We sought to identify metabolomic fingerprints in mice ancestrally exposed to the model obesogen tributyltin (TBT), to assess whether metabolomics could discriminate potential trans-generational susceptibility to obesity and recognize metabolic pathways modulated by ancestral TBT exposure.

METHODS

We used non-targeted ¹H NMR metabolomic analyses of plasma and liver samples collected from male and female mice ancestrally exposed to TBT in two independent transgenerational experiments in which F3 and F4 males became obese when challenged with increased dietary fat.

RESULTS

Metabolomics confirmed transgenerational obesogenic effects of environmentally relevant doses of TBT in F3 and F4 males, in two independent studies. Although females never became obese, their specific metabolomic fingerprint evidenced distinct transgenerational effects of TBT in female mice consistent with impaired capacity for liver biotransformation.

DISCUSSION

This study is the first application of metabolomics to unveil the transgenerational effects of EDC exposure. Very early, significant changes in the plasma metabolome were observed in animals ancestrally exposed to TBT. These changes preceded the onset of obesogenic effects elicited by increased dietary fat in the TBT groups, and which ultimately resulted in significant changes in the liver metabolome. Development of metabolomic fingerprints could facilitate the identification of individuals carrying the signature of ancestral obesogen exposure that might increase their susceptibility to other risk factor such as increased dietary fat.

Tailoring Multiloop Atom Interferometers with Adjustable Momentum Transfer

Multiloop matter-wave interferometers are essential in quantum sensing to measure the derivatives of physical quantities in time or space. Because multiloop interferometers require multiple reflections, imperfections of the matter-wave mirrors create spurious paths that scramble the signal of interest. Here, we demonstrate a method of adjustable momentum transfer that prevents the recombination of the spurious paths in a double-loop atom interferometer aimed at measuring rotation rates. We experimentally study the recombination condition of the spurious matter waves, which is quantitatively supported by a model accounting for the coherence properties of the atomic source. We finally demonstrate the effectiveness of the method in building a cold-atom gyroscope with a single-shot acceleration sensitivity suppressed by a factor of at least 50. Our study will impact the design of multiloop atom interferometers that measure a single inertial quantity.

Gut microbiota derived metabolites contribute to intestinal barrier maturation at the suckling-to-weaning transition

In suckling mammals, the onset of solid food ingestion is coincident with the maturation of the gut barrier. This ontogenic process is driven by the colonization of the intestine by the microbiota. However, the mechanisms underlying the microbial regulation of the intestinal development in early life are not fully understood. Here, we studied the co-maturation of the microbiota (composition and metabolic activity) and of the gut barrier at the suckling-to-weaning transition by using a combination of experiments in vivo (suckling rabbit model), ex vivo (Ussing chambers) and in vitro (epithelial cell lines and organoids). The microbiota composition, its metabolic activity, para-cellular epithelial permeability and the gene expression of key components of the gut barrier shifted sharply at the onset of solid food ingestion in vivo, despite milk was still predominant in the diet at that time. We found that cecal content sterile supernatant (i.e. containing a mixture of metabolites) obtained after the onset of solid food ingestion accelerated the formation of the epithelial barrier in Caco-2 cells in vitro and our results suggested that these effects were driven by the bacterial metabolite butyrate. Moreover, the treatment of organoids with cecal content sterile supernatant partially replicated in vitro the effects of solid food ingestion on the epithelial barrier in vivo. Altogether, our results show that the metabolites produced by the microbiota at the onset of solid food ingestion contribute to the maturation of the gut barrier at the suckling-to-weaning transition. Targeting the gut microbiota metabolic activity during this key developmental window might therefore be a promising strategy to promote intestinal homeostasis.

Proton NMR Enables the Absolute Quantification of Aqueous Metabolites and Lipid Classes in Unique Mouse Liver Samples

Hepatic metabolites provide valuable information on the physiological state of an organism, and thus, they are monitored in many clinical situations. Typically, monitoring requires several analyses for each class of targeted metabolite, which is time consuming. The present study aimed to evaluate a proton nuclear magnetic resonance (¹H-NMR) method for obtaining quantitative measurements of aqueous and lipidic metabolites. We optimized the extraction protocol, the standard samples, and the organic solvents for the absolute quantification of lipid species. To validate the method, we analyzed metabolic profiles in livers of mice fed three different diets. We compared our results with values obtained with conventional methods and found strong correlations. The ¹H-NMR protocol enabled the absolute quantification of 29 aqueous metabolites and eight lipid classes. Results showed that mice fed a diet enriched in saturated fatty acids had higher levels of triglycerides, cholesterol ester, monounsaturated fatty acids, lactate, 3-hydroxy-butyrate, and alanine and lower levels of glucose, compared to mice fed a control diet. In conclusion, proton NMR provided a rapid overview of the main lipid classes (triglycerides, cholesterol, phospholipids, fatty acids) and the most abundant aqueous metabolites in liver.

Metabolome disruption of pregnant rats and their offspring resulting from repeated exposure to a pesticide mixture representative of environmental contamination in Brittany

The use of pesticides exposes humans to numerous harmful molecules. Exposure in early-life may be responsible for adverse effects in later life. This study aimed to assess the metabolic modifications induced in pregnant rats and their offspring by a pesticide mixture representative of human exposure. Ten pregnant rats were exposed to a mixture of eight pesticides: acetochlor (246 μg/kg bw/d) + bromoxynil (12 μg/kg bw/d) + carbofuran (22.5 μg/kg bw/d) + chlormequat (35 μg/kg bw/d) + ethephon (22.5 μg/kg bw/d) + fenpropimorph (15.5 μg/kg bw/d) + glyphosate (12 μg/kg bw/d) + imidacloprid (12.5 μg/kg bw/d) representing the main environmental pesticide exposure in Brittany (France) in 2004. Another group of 10 pregnant rats served as controls. Females were fed ad libitum from early pregnancy, which is from gestational day (GD) 4 to GD 21. Urine samples were collected at GD 15. At the end of the exposure, mothers and pups were euthanized and blood, liver, and brain samples collected. 1H NMR-based metabolomics and GC-FID analyses were performed and PCA and PLS-DA used to discriminate between control and exposed groups. Metabolites for which the levels were significantly modified were then identified using the Kruskal-Wallis test, and p-values were adjusted for multiple testing correction using the False Discovery Rate. The metabolomics analysis revealed many differences between dams of the two groups, especially in the plasma, liver and brain. The modified metabolites are involved in TCA cycle, energy production and storage, lipid and carbohydrate metabolism, and amino-acid metabolism. These modifications suggest that the pesticide mixture may induce oxidative stress associated with mitochondrial dysfunction and the impairment of glucose and lipid metabolism. These observations may reflect liver dysfunction with increased relative liver weight and total lipid content. Similar findings were observed for glucose and energy metabolism in the liver of the offspring, and oxidative stress was also suggested in the brains of male offspring.

Cranial cruciate ligament rupture in large and giant dogs

Forty-two dogs weighing between 30 and 87 kg (mean body weight of 49 kg) with cranial cruciate ligament ruptures (CCLR) were treated with a modified lateral extra-capsular stabilization using braided polyester prosthetic ligament-suture anchor technique. Clinical and radiographic outcomes of 48 stifles were retrospectively evaluated with a mean follow-up of 18 months. Ten dogs had pulled out their bone anchors with no clinical relevance. Draining tracts did not appear. Despite mild radiographic progression of osteoarthritis, all of the dogs regained acceptable function of the operated limb.

Adaptive response under multiple stress exposure in fish: From the molecular to individual level

Aquatic systems are subjected to various sources of stress due to global changes, such as increasing temperature and pollution. A major challenge for the next decade will be to evaluate the combined effects of these multiple stressors on organisms and ecosystems. For organisms submitted to chemical, biological or physical stressors, the capacity to set up an efficient adaptive response is a fundamental prerequisite for their long-term survival and performance. In this study, goldfish (Carassius auratus) were subjected to individual and combined pesticide mixtures and increased temperatures to evaluate their adaptive response in multistress conditions from the molecular to the individual level. Fish were exposed for 16 days to a mixture of pesticides at environmental relevant concentrations (S-metolachlor, isoproturon, linuron, atrazine-desethyl, aclonifen, pendimethalin and tebuconazole) and at two temperatures (22 °C and 32 °C). Three major physiological traits of the stress response were measured: the hormonal response (i.e. plasma cortisol), the metabolic balance from molecular to individuals' levels (metabolomics, cellular energy allocation, energy reserves and global condition indexes), and the cellular defense system induction (SOD, CAT and GST). Results show that (1) environmentally relevant concentrations of pesticides lead to significant responses in fish at all biological levels; (2) the metabolic response depends on the nature of stress (thermal vs. chemical); and (3) fish may be unable to set up an efficient adaptive response when chemical and thermal stresses were combined, with adverse outcomes at the individuals' level.

Dynamic Metabolic Disruption in Rats Perinatally Exposed to Low Doses of Bisphenol-A

Along with the well-established effects on fertility and fecundity, perinatal exposure to endocrine disrupting chemicals, and notably to xeno-estrogens, is strongly suspected of modulating general metabolism. The metabolism of a perinatally exposed individual may be durably altered leading to a higher susceptibility of developing metabolic disorders such as obesity and diabetes; however, experimental designs involving the long term study of these dynamic changes in the metabolome raise novel challenges. ¹H-NMR-based metabolomics was applied to study the effects of bisphenol-A (BPA, 0; 0.25; 2.5, 25 and 250 μg/kg BW/day) in rats exposed perinatally. Serum and liver samples of exposed animals were analyzed on days 21, 50, 90, 140 and 200 in order to explore whether maternal exposure to BPA alters metabolism. Partial Least Squares-Discriminant Analysis (PLS-DA) was independently applied to each time point, demonstrating a significant pair-wise discrimination for liver as well as serum samples at all time-points, and highlighting unequivocal metabolic shifts in rats perinatally exposed to BPA, including those exposed to lower doses. In BPA exposed animals, metabolism of glucose, lactate and fatty acids was modified over time. To further explore dynamic variation, ANOVA-Simultaneous Component Analysis (A-SCA) was used to separate data into blocks corresponding to the different sources of variation (Time, Dose and Time*Dose interaction). A-SCA enabled the demonstration of a dynamic, time/age dependent shift of serum metabolome throughout the rats’ lifetimes. Variables responsible for the discrimination between groups clearly indicate that BPA modulates energy metabolism, and suggest alterations of neurotransmitter signaling, the latter finding being compatible with the neurodevelopmental effect of this xenoestrogen. In conclusion, long lasting metabolic effects of BPA could be characterized over 200 days, despite physiological (and thus metabolic) changes connected with sexual maturation and aging.

Combined theoretical and time-resolved photoluminescence investigations of [Mo6Bri8Bra6]2− metal cluster units: evidence of dual emission

Distinct emissive species have been identified in [Mo₆Brⁱ₈Br^a₆]²⁻ containing systems. Strong geometrical relaxations of the triplet excited states are responsible for the huge energy shift leading to intense red-NIR emission.

Influence of the cation size on the second harmonic generation response of chiral A(VO2)2(PO4)·3H2O (A = K+, NH4+ and Rb+)

Second harmonic generation responses of new chiral vanadium phosphate materials were shown to strongly increase upon contraction of the structure.

Effects of low doses of bisphenol A on the metabolome of perinatally exposed CD-1 mice

BACKGROUND

Bisphenol A (BPA) is a well-known endocrine disruptor used to manufacture polycarbonate plastics and epoxy resins. Exposure of pregnant rodents to low doses of BPA results in pleiotropic effects in their offspring.

OBJECTIVE

We used metabolomics--a method for determining metabolic changes in response to nutritional, pharmacological, or toxic stimuli--to examine metabolic shifts induced in vivo by perinatal exposure to low doses of BPA in CD-1 mice.

METHODS

Male offspring born to pregnant CD-1 mice that were exposed to vehicle or to 0.025, 0.25, or 25 µg BPA/kg body weight/day, from gestation day 8 through day 16 of lactation, were examined on postnatal day (PND) 2 or PND21. Aqueous extracts of newborns (PND2, whole animal) and of livers, brains, and serum samples from PND21 pups were submitted to (1)H nuclear magnetic resonance spectroscopy. Data were analyzed using partial least squares discriminant analysis.

RESULTS

Examination of endogenous metabolic fingerprints revealed remarkable discrimination in whole extracts of the four PND2 newborn treatment groups, strongly suggesting changes in the global metabolism. Furthermore, statistical analyses of liver, serum, and brain samples collected on PND21 successfully discriminated among treatment groups. Variations in glucose, pyruvate, some amino acids, and neurotransmitters (γ-aminobutyric acid and glutamate) were identified.

CONCLUSIONS

Low doses of BPA disrupt global metabolism, including energy metabolism and brain function, in perinatally exposed CD-1 mouse pups. Metabolomics can be used to highlight the effects of low doses of endocrine disruptors by linking perinatal exposure to changes in global metabolism.

NMR study of the LiMnPO(4)·OH and MPO(4)·H(2)O (M = Mn, V) homeotypic phases and DFT calculations

Following our previous work on the tavorite-like LiFePO(4)·OH and FePO(4)·H(2)O phases, we report here the magnetic and NMR characterizations of analogous LiMnPO(4)·OH, MnPO(4)·H(2)O and VPO(4)·H(2)O phases together with the DFT calculations of the NMR shifts. The first two compounds exhibit Curie-Weiss type magnetic behavior with Curie constants close to the theoretical ones for HS Mn(3+), while the vanadium compound is very close to a pure Curie-type behavior. (7)Li, (31)P and (1)H MAS NMR spectra are reported for the three compounds, and show strong Fermi-contact shifts for the first two nuclei, while the sign and magnitude of the (1)H shifts are very different for the three phases. DFT calculations (FLAPW in GGA+U approximation) using the WIEN2k code and the experimental susceptibilities are shown to reproduce closely the experimental data. This situation is compared to the case of the homologous and isostructural Fe compounds, which exhibit much more complex magnetic behaviors.

Electric field gradient calculations in paramagnetic compounds using the PAW approach. Application to ²³Na NMR in layered vanadium phosphates

This article presents ab initio calculations of electric field gradient (EFG) parameters as a tool for the structural characterization of paramagnetic crystalline compounds. Previously reported ²³Na NMR parameters of vanadium + IV containing vanado-phosphate compounds were computed within density functional theory using both cluster and fully periodic approaches. Quadrupolar parameter values measured by ²³Na NMR experiments were reproduced with a level of accuracy comparable to that achievable in diamagnetic compounds and allowed the assignment of observed ²³Na NMR signals. This work demonstrates the utility of the periodic planewave pseudopotential + PAW approach for the calculation of EFG parameters in paramagnetic compounds.

Ag(2.54)Tl(2)Mo(12)Se(15): a new structure type containing Mo(6) and Mo(9) clusters

The novel structure-type Ag(2.54)Tl(2)Mo(12)Se(15) (silver thallium molybdenum selenide) is built up of Mo(6)Se(i)(8)Se(a)(6) and Mo(9)Se(i)(11)Se(a)(6) cluster units in a 1:2 ratio, which are three-dimensionally connected to form the Mo-Se network. The Ag and Tl cations are distributed in several voids within the cluster network. Three of the seven independent Se atoms and one Tl atom lie on sites with 3.. symmetry (Wyckoff sites 2c or 2d).

Synthesis, crystal and electronic structures, and physical properties of the novel compounds LaR4Mo36O52 (R = Dy, Er, Yb, and Y) containing infinite chains of trans-edge-shared Mo6 octahedra and Mo2 pairs and rectangular Mo4 clusters with triple Mo-Mo bonds

The novel quaternary reduced molybdenum oxides LaR(4)Mo(36)O(52) (R = Dy, Er, Yb, and Y) have been synthesized with solid-state reactions at 1400 degrees C for 48 h in sealed molybdenum crucibles. The crystal structure was determined on a single crystal of LaEr(4)Mo(36)O(52) by X-ray diffraction. LaEr(4)Mo(36)O(52) crystallizes in the tetragonal space group I4 with two formula units per cell and the following lattice parameters: a = 19.8348(2) and c = 5.6594(1) A. The Mo network is dominated by infinite chains of trans-edge-shared Mo(6) octahedra, which coexist with Mo(2) pairs and rectangular Mo(4) clusters. The Mo-Mo distances within the infinite chains range from 2.5967(7) to 2.8529(8) A and from 2.239(3) to 2.667(2) A in the Mo(2) pairs and rectangular Mo(4) clusters, respectively. The Mo-O distances are comprised between 1.993(7) and 2.149(7) A, as usually observed in these types of compound. The La(3+) and Er(3+) ions are in a square-prismatic [LaO(8)] and a tricapped trigonal-prismatic [ErO(9)] environment of oxygen atoms, respectively. The La-O distances range from 2.555(6) to 2.719(6) A and the Er-O ones from 2.260(6) to 2.469(5) A. Theoretical calculations allow the determination of the optimal electron count of both motifs in the title compound. Weak interactions occur between neighboring dimetallic and tetrametallic clusters and between trans-edge-sharing infinite chains and dimers and tetramers. The presence of rectangular clusters is favored on the basis of theoretical considerations. Single-crystal resistivity measurements show that LaEr(4)Mo(36)O(52) is metallic between 4.2 and 300 K, in agreement with the band structure calculations. Magnetic susceptibility measurements indicate that the oxidation state of the magnetic rare earths is +3, and there is an absence of localized moments on the Mo network.

Polyarthrite associée à une leishmaniose chez un jeune chien

Un chien de race Cane corso, mâle, âgé de deux ans, est examiné en consultation pour abattement et dysorexie. Il présente également une boiterie d’appui persistante du membre postérieur gauche depuis plusieurs semaines. À l’examen clinique, le chien est en hyperthermie (39,3 °C) ; il a des saignements spontanés des babines, une polyadénomégalie périphérique, notamment des nœuds lymphatiques poplités, ainsi qu’une splénomégalie. Par ailleurs, l’examen orthopédique montre que les tarses sont gonflés et chauds. Cela laisse suspecter une synovite bilatérale. L’examen cytologique des nœuds lymphatiques et du liquide synovial permet de diagnostiquer avec certitude une leishmaniose. En effet, de très nombreuses formes amastigotes sont visualisées dans les macrophages. Une analyse par PCR sur sang, liquide synovial, suc ganglionnaire et ponction de moelle osseuse écarte l’ehrlichiose et la borréliose. Une PCR leishmaniose sur sang est également effectuée pour suivre la réponse au traitement. Malgré une forte infestation, une anémie non régénérative, une leucopénie, des signes de néphropathie et l’apparition d’une épistaxis, le chien est traité avec succès principalement à l’aide d’antimoniate de méglumine, d’allopurinol, de corticostéroïdes, associés à des antibiotiques.

Cranial cruciate ligament rupture in large and giant dogs. A retrospective evaluation of a modified lateral extracapsular stabilization

Forty-two dogs weighing between 30 and 87 kg (mean body weight of 49 kg) with cranial cruciate ligament ruptures (CCLR) were treated with a modified lateral extra-capsular stabilization using braided polyester prosthetic ligament-suture anchor technique. Clinical and radiographic outcomes of 48 stifles were retrospectively evaluated with a mean follow-up of 18 months. Ten dogs had pulled out their bone anchors with no clinical relevance. Draining tracts did not appear. Despite mild radiographic progression of osteoarthritis, all of the dogs regained acceptable function of the operated limb.

SABBAC: online Structural Alphabet-based protein BackBone reconstruction from Alpha-Carbon trace

SABBAC is an on-line service devoted to protein backbone reconstruction from alpha-carbon trace. It is based on the assembly of fragments taken from a library of reduced size, selected from the encoding of the protein trace in a hidden Markov model-derived structural alphabet. The assembly of the fragments is achieved by a greedy algorithm, using an energy-based scoring. Alpha-carbon coordinates remain unaffected. SABBAC simply positions the missing backbone atoms, no further refinement is performed. From our tests, SABBAC performs equal or better than other similar on-line approach and is robust to deviations on the alpha-carbon coordinates. It can be accessed at http://bioserv.rpbs.jussieu.fr/SABBAC.html.

SCit: web tools for protein side chain conformation analysis

SCit is a web server providing services for protein side chain conformation analysis and side chain positioning. Specific services use the dependence of the side chain conformations on the local backbone conformation, which is described using a structural alphabet that describes the conformation of fragments of four-residue length in a limited library of structural prototypes. Based on this concept, SCit uses sets of rotameric conformations dependent on the local backbone conformation of each protein for side chain positioning and the identification of side chains with unlikely conformations. The SCit web server is accessible at http://bioserv.rpbs.jussieu.fr/SCit.

A hidden markov model derived structural alphabet for proteins

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

Critical assessment of side-chain conformational space sampling procedures designed for quantifying the effect of side-chain environment

We introduce a family of procedures designed to sample side-chain conformational space at particular locations in protein structures. These procedures (CRSP) use intensive cycles of random assignment of side-chain conformations followed by minimization to determine all the conformations that a group of side-chains can adopt simultaneously. First, we consider a procedure evolving in the dihedral space (dCRSP). Our results suggest that it can accurately map low-energy conformations adopted by clusters of side-chains of a protein. dCRSP is relatively insensitive to various important parameters, and it is sufficiently accurate to capture efficiently the constraint induced by the environment on the conformations a particular side-chain can adopt. Our results show that dCRSP, compared with molecular dynamics (MD), can overcome the problem of the limited set of conformations reached in a reasonable amount of simulations. Next, we introduce procedures (vCRSP) in which valence angles are relaxed, and we assess how efficiently they quantify the conformational entropy of side-chains in the protein native state. For simple peptides, entropies obtained with vCRSP are fully compatible with those obtained with a Monte Carlo procedure. For side-chains in a protein environment, however, vCRSP appears of limited use. Finally, we consider a two-step procedure that combines dCRSP and vCRSP. Our tests suggest that it is able to overcome the limitations of vCRSP. We also note that dCRSP provides a reasonable initial approximation. This family of procedures offers promise in quantifying the contribution of conformational entropy to the energetics of protein structures.

Structural trends and the electronic structure of the rare-earth oxomolybdates RMo(5)O(8) (R = La, Ce, Pr, Nd, Sm, Eu and Gd) containing chains of bioctahedral Mo(10) clusters

The crystal structures of the rare-earth members of the series RMo(5)O(8) (R = Ce to Eu) have been investigated and compared with those of the La and Gd members previously published in order to understand the influences of the size and the charge of the cation on the different Mo-Mo bonds. The RMo(5)O(8) compounds crystallize in the monoclinic space group P2(1)/c. Their crystal structure is characterized by bioctahedral Mo(10) clusters forming extended chains. The results of our single-crystal studies show that the modification of charge predominantly affects the Mo-Mo bonds between the Mo(10) clusters and, to a lesser extent, the intra-cluster distances, while the cationic size induces only small variations. Theoretical investigations confirm this statement and allow the understanding of the bonding mode in these compounds.

New mercury vanadium phosphate hydrate Hg(4)(-)(x)()O(1-)(y)()((VO)(PO(4))(2).H(2)O with unprecedented tetrahedral oxo-cluster [Hg( approximately )(4)O( approximately )(5)]

The new mercury vanadium phosphate hydrate Hg(4)(-)(x)()O(1)(-)(y)()(VO)(PO(4))(2).H(2)O has been synthesized under hydrothermal conditions. X-ray investigations led to orthorhombic symmetry, space group P2(1)2(1)2(1) (No. 19), a = 6.3632(2) A, b = 12.4155(5) A, c = 14.2292(6) A, Z = 4. The crystal structure was solved and refined from single-crystal diffractometer data to residuals R[F(2) > 2sigmaF(2)] = 0.039, R(w)(F(2)) = 0.055. The VPO framework consists of infinite one-dimensional [VO(PO(4))(2)]( infinity ) chains with corner-connected VO(6) octahedra and PO(4) tetrahedra. The chains run along the [100] direction and are held together by the unprecedented tetrahedral cationic units [Hg(4)(-)(x)()O(1)(-)(y)()](4+). Presence of Hg-Hg bonding contacts is proved from theoretical calculations.

Synthesis, structural trends, and physical and electronic properties of the reduced molybdenum oxides R(4)Mo(4)O(11) (R = Nd-Tm and Y) containing infinite chains of trans-edge-shared octahedral clusters

The new compounds R(4)Mo(4)O(11) (R = Y, Nd, Sm-Tm) have been synthesized as crystalline powders by solid-state reaction in a sealed molybdenum crucible at 1400 degrees C. Single crystals suitable for X-ray structure determinations and resistivity measurements were also prepared. The R(4)Mo(4)O(11) compounds crystallize in the orthorhombic space group Pbam with four formulas per unit cell. The crystal structure of these compounds is based on infinite chains of trans-edge-shared molybdenum octahedra, which are widely separated by the rare-earth cations that are in monocapped trigonal prismatic coordination of oxygen atoms. Consequently, adjacent metallic chains do not share oxygen atoms and the shortest interchain Mo-Mo distance is greater than 7 A. Within the infinite chains, a strong pairing between the apical Mo atoms occurs, leading to a pattern of alternating short and long distances between these atoms. Resistivity measurements on single crystals show that the R(4)Mo(4)O(11) compounds are small band gap semiconductors, and magnetic susceptibility studies are in agreement with the presence of R(3+) ions. In addition, antiferromagnetic orderings have also been observed for the R(4)Mo(4)O(11) compounds with R = Gd-Tm below 5 K. Theoretical calculations confirm the stabilization of the structure by the distortion and agree with the resistivity and magnetic measurements.

MTi(0.7)Mo(0.3)Mo(5)O(10) (M = SR, Eu), first evidence of mono- and bicapped bioctahedral Mo(11) and Mo(12) clusters: synthesis, crystal structures, and physical properties

The novel quaternary reduced molybdenum oxides MTi(0.7)Mo(0.3)Mo(5)O(10) (M = Sr, Eu) have been synthesized by solid-state reaction at 1400 degrees C for 48 h in sealed molybdenum crucibles. Their crystal structures were determined on single crystals by X-ray diffraction. Both compounds crystallize in the orthorhombic space group Pbca with 8 formula units per cell and the following lattice parameters: a(Sr) = 9.1085 (7), b(Sr) = 11.418 (1), and c(Sr) = 15.092 (3) A; a(Eu) = 9.1069 (7), b(Eu) = 11.421 (2), and c(Eu) = 15.075 (1) A. The Mo network is dominated by bioctahedral Mo(10) clusters, which coexist randomly with Mo(11) and Mo(12) clusters (monocapped and bicapped Mo(10) clusters). The Mo-Mo distances within the clusters range from 2.62 to 2.92 A and the Mo-O distances from 1.99 to 2.17 A as usually observed in the reduced molybdenum oxides. The Sr(2+) and Eu(2+) ions occupy large cavities, which result from the fusion of two cubooctahedra and thus are surrounded by 11 oxygen atoms. The M-O distances range from 2.50 to 3.23 A for the Sr compound and from 2.49 to 3.24 A for the Eu analogue. Single-crystal resistivity measurements indicate that both materials are poor metals with transitions to semiconducting states below 50 and 40 K and room temperature resistivity values of 9 x 10(-3) and 5 x 10(-3) Omega.cm for the Sr and Eu compounds, respectively. The magnetic susceptibility data indicate paramagnetic behavior due to the Eu(2+) moment at high temperatures for the Eu compound and do not reveal the existence of localized moments on the Mo and Ti sublattice in the Sr compound. An XPS study clearly suggests that the isolated Ti ions are tetravalent. Theoretical considerations preclude the existence of heterometallic Mo-Ti clusters.

Gaussian process: an efficient technique to solve quantitative structure-property relationship problems

We introduce the Gaussian process (GP) model for the empirical modelling of the log P values of 44 1,2-dithiole-3-one molecules. A brief theoretical description of the method is given. Descriptive and predictive abilities of GP are evaluated and compared to multilinear regression results. Special attention is devoted to the automatic relevance determination (ARD) to reduce input variable numbers, which avoid the use of principal component analysis. The present approach was found to be an efficient method and a good alternative to more complicated using artificial neural network systems.

Tracing the progeny of the aortic hemangioblast in the avian embryo

A population of hematopoietic progenitors becomes committed within the embryo proper in the floor of the aorta (P-Sp/AGM in the mouse). In birds, this first aspect of intraembryonic hematopoiesis is prominent during embryonic day 3 (E3) as endothelium-associated "intra-aortic clusters." Between E6 and E8, diffuse hematopoiesis then occurs as "para-aortic foci" located in the dorsal mesentery ventral to the aorta. These foci are not associated with endothelium. Whether these two hematopoietic cell populations arise from distinct or common progenitors is not known. We could recently trace back the origin of intra-aortic clusters in the avian embryo by labeling aortic endothelial cells (EC) in vivo with acetylated low-density lipoproteins. This approach established the derivation of early intraembryonic hemopoietic cells from the endothelium, but did not indicate how long during ontogeny such a relationship may exist, since the progeny of EC labeled at E2 could be traced for 1-2 days at most. Here we report that, when E2 aortic ECs were infected prior to the formation of intra-aortic clusters with a nonreplicative LacZ-bearing retroviral vector, numerous cells were labeled in the para-aortic foci at E6. In contrast, when the retroviral vector was inoculated at E4 rather than E2, that is, after the disappearance of intra-aortic clusters, no cells in the para-aortic foci were labeled. Taken together, our results demonstrate that ECs from the aortic floor seed the two aspects of aorta-associated hemopoiesis and that these ECs with hemangioblastic potential are present only transiently in the aorta.

Avian reticuloendotheliosis virus strain A and spleen necrosis virus do not infect human cells

Spleen necrosis virus (SNV) and Reticuloendotheliosis virus strain A (REV-A) belong to the family of reticuloendotheliosis viruses and are 90% sequence related. SNV-derived retroviral vectors produced by the REV-A-based D17.2G packaging cell line were shown to infect human cells (H.-M. Koo, A. M. C. Brown, Y. Ron, and J. P. Dougherty, J. Virol. 65:4769-4776, 1991), while similar vectors produced by another SNV-based packaging cell line, DSH134G, are not infectious in human cells (reviewed by R. Dornburg, Gene Ther. 2:301-310, 1995). Here we describe a careful reevaluation of the infectivity of vectors produced from the most commonly used REV-A- or SNV-based packaging cells obtained from various sources with, among them, one batch of D17.2G packaging cells obtained from the American Type Culture Collection. None of these packaging cells produced vectors able to infect human cells. Thus, contrary to previously published data, we conclude that REV-based vectors are not infectious in human cells.

[Affiliation between endothelial and intra-embryonic hematopoietic stem cells]

We have investigated the developmental relationship of the hemopoietic and endothelial lineages in the floor of the chicken aorta, a site of hemopoietic progenitor emergence in the embryo proper. We show that, prior to the onset of hemopoiesis, the aortic endothelium uniformly expresses the endothelium-specific membrane receptor VEGF-R2. The onset of hemopoiesis can be precisely determined by detecting the common leukocyte antigen CD45. VEGF-R2 and CD45 are expressed in complementary fashion, namely the hemopoietic clusters in the floor of the aorta are CD45+/VEGF-R2-, while the rest of the aortic endothelium is CD45-/VEGF-R2+. To determine if the hemopoietic clusters are derived from EC, we tagged the E2 endothelial tree with a non-replicative retroviral vector and low density lipoproteins. Twenty four-48 hours later, labelled cells in the vascular tree were found to be either endothelial or hemopoietic but exceptionally both. Another 1-2 days later, groups of labelled cells appear in the dorsal mesentery within the hemopoietic "paraortic foci". Since no CD45+ cells were inserted among endothelial cells at the time of vascular labelling, hemopoietic clusters and foci must be concluded to derive from precursors with an endothelial phenotype.

Intraaortic hemopoietic cells are derived from endothelial cells during ontogeny

We have investigated the developmental relationship of the hemopoietic and endothelial lineages in the floor of the chicken aorta, a site of hemopoietic progenitor emergence in the embryo proper. We show that, prior to the onset of hemopoiesis, the aortic endothelium uniformly expresses the endothelium-specific membrane receptor VEGF-R2. The onset of hemopoiesis can be determined by detecting the common leukocyte antigen CD45. VEGF-R2 and CD45 are expressed in complementary fashion, namely the hemopoietic cluster-bearing floor of the aorta is CD45(+)/VEGF-R2(−), while the rest of the aortic endothelium is CD45(−)/VEGF-R2(+). To determine if the hemopoietic clusters are derived from endothelial cells, we tagged the E2 endothelial tree from the inside with low-density lipoproteins (LDL) coupled to DiI. 24 hours later, hemopoietic clusters were labelled by LDL. Since no CD45(+) cells were inserted among endothelial cells at the time of vascular labelling, hemopoietic clusters must be concluded to derive from precursors with an endothelial phenotype.

Blood-borne seeding by hematopoietic and endothelial precursors from the allantois

Until now the allantois has not been considered as a hematopoietic organ. Here we report experimental evidence demonstrating the in situ emergence of both hematopoietic and endothelial precursors in the avian allantoic bud. When the prevascularized allantoic bud from a quail embryo was grafted in the coelom of a chicken host, hematopoietic and endothelial cells later were found in the bone marrow of the host. Because the graft was located at a distance from the limb bud, these cells could reach the bone marrow only by the circulatory pathway. This blood-borne seeding may be accomplished by distinct hematopoietic and endothelial precursors, or by hemangioblasts, the postulated common precursors of these two lineages; we consider the latter interpretation more likely. We also show by reverse transcription-PCR that the allantois region expresses very early the GATA genes involved in hematopoiesis and some beta-globin chain genes.

Generation of small fusion genes carrying phleomycin resistance and Drosophila alcohol dehydrogenase reporter properties: their application in retroviral vectors

We have used the Drosophila ADH cDNA to engineer new fusion genes carrying both reporter activity and bleomycin/phleomycin resistance (Sh ble). Cassettes of ADH::Sh ble, Sh ble::ADH, or ADH::Sh ble::ADH with or without polyadenylation signals were constructed. Placed under the control of the strong CMV promoter, these constructs induced intense ADH substrate staining and phleomycin resistance, whatever the position of the ADH gene, in avian or mammalian cell lines. SW-based nonreplicative retroviral vectors were constructed and introduced into the appropriate packaging cell line. Titers up to 10(6) ADH forming units/ml of viral supernatant were obtained except for the ADH::Sh ble::ADH construct, which reached 10(5) ADH forming units. These retroviral vectors were inoculated to the E3 chick embryo via the coelom. Three days later, cells from different organs were put in culture for 24 h and stained to detect ADH activity. A large number of positive cells were found in cultures from all organs. The new fusion genes described here are, to our knowledge, the smallest (1.1 kb) published to date that carry both reporter and drug resistance properties. These genes represent the basis of a new retroviral vector model with three distinct properties in two genetic units; their advantage is to reduce the size and increase the efficiency of the vector.

Avian myeloblastic cell lines transformed by two nuclear oncoproteins, P135gag-myb-ets and p61/63myc: a model of retinoic acid-induced differentiation not abrogated by v-erbA

We previously demonstrated that the retroviral construct MHE226 transducing both the P135gag-myb-ets and p61/63myc nuclear proteins induces solid hemopoietic tumors in early chicken embryos. In the present paper, we report the characterization of two MHE226-transformed cell lines established from such hemopoietic tumors retrieved from the heart of a 13-day embryo. Cytological analysis indicated a myeloblastic phenotype. These MHE226 cell lines were positive for the MEP17 monoclonal antibody but were negative for the myeloblast-specific 51/2 monoclonal antibody. MHE226 cell lines displayed a doubling time of about 20-24 h and were maintained for at least 1 year. Contrary to E26 myeloblastic cell lines, MHE226 cell lines were independent of chicken myelomonocytic growth factor and could be maintained in serum-free medium. MHE226 cell lines could be induced to differentiate toward the monocytic lineage by retinoic acid. Retinoic acid inhibited proliferation of MHE226 cell lines as early as day 1. After 3 days, MHE226 cells displayed cytological, enzymatic (alpha-naphthyl acetate esterase and chloroacetate esterase), and functional (phagocytosis) characteristics of monocytic cells. The retinoic acid-induced differentiation of MHE226 cells could not be inhibited by v-erbA. Thus, MHE226-transformed cell lines represent a novel model of cell transformation by two nuclear oncoproteins. Furthermore, they provide a model to study molecular mechanisms implicated in the monocytic differentiation program.

Patterns of integration and expression of retroviral, non-replicative vectors in avian embryos: embryo developmental stage and virus subgroup envelope modulate tissue-tropism

We previously demonstrated that Avian Leukemia Viruses (ALV) carrying the v-myc gene specifically induce two types of tumors, cardiomyocytic tumors when the virus is injected before embryonic day 3 (E3), skin tumors when the virus is injected at E3 or E5. Aiming to elucidate the mechanisms which determine this time-dependent change in target, we infected chick and quail embryos at E3 and E5 with replication-deficient, lacZ gene-carrying, ALV-based viruses produced by a packaging cell line. Three constructs driven by 3 different Long Terminal Repeats (LTRs) were tested and yielded similar results. When the constructs were inoculated at E3 and the lacZ gene product revealed 5 days later, around 70% of the embryos carried lacZ+ clones in the heart, around 50% had positive clones in the skin anywhere on the body, while a few embryos displayed clones in internal organs (liver, stomach, lungs). Immunocytological identification of the heart cell type(s) expressing the virus revealed that the only cells infected were cardiomyocytes. When the constructs were inoculated at E5, no lacZ+ clones appeared in the heart but all were located in the cephalic skin. In order to examine the relationship between viral integration and expression, DNA of different organs or tissues from lacZ stained embryos was analyzed by PCR. A tight correlation between integration and expression in the heart and in the skin was revealed in most cases. In contrast, a significant PCR signal was often detected in the liver or the stomach despite weak or absent expression as revealed by lacZ+ clones. We then investigated the influence of envelope glycoprotein subgroups on the tropism of these constructs. The lacZ vector driven by RAV-2 LTRs was packaged as subgroups A, B or E viral particles. The A subgroup, used in the part of the study described above, infects both chick and quail while the B and E subgroups are specific for chick or quail respectively. These B and E subgroups induced lacZ+ clones in the heart (after E3 injection) while no clones or only a few were detected in the skin either after E3 or E5 injection. The following conclusions can be drawn: 1) cardiomyocytes are at E3 the major target for integration and expression of ALV-derived viruses in vivo; 2) targets change rapidly with embryonic age; and 3) tissue-specific infections depend on the envelope subgroup, thus presumably on the presence of the cognate receptor.(ABSTRACT TRUNCATED AT 400 WORDS)

Oncofetal mucin M1 epitope family: characterization and expression during colonic carcinogenesis

The gastric mucin M1 antigens, markers associated with colonic carcinogenesis, have been characterized by new antimucin monoclonal antibodies (MAbs). These MAbs, obtained against mucins isolated from a human ovarian mucinous cyst (MAbs 19M1, 21M1 and 45M1) and from a pancreatic adenocarcinoma (MAb 96RA), were compared with 5 other anti-M1 mucin MAbs described previously, which characterized the a, b, c, d and e mucin M1 epitopes. Using immunoperoxidase, these new MAbs exclusively stained the surface gastric epithelium of normal human gastro-intestinal tract and reacted with fetal, precancerous and cancerous colonic mucosa, but not with normal colon. Immunoradiofixation studies showed that these new MAbs are directed against 3 epitopes (f, g and h) which are different from the a, b, c, d and e mucin M1 epitopes, though present on the same a immunoreactive high-molecular-weight components (greater than 1,000 kDa) with a density of 1.4 by CsCl-density-gradient ultracentrifugation. M1 antigenicity is characterized by a family of 8 different M1 epitopes which were destroyed with beta-mercaptoethanol (except for the f epitope), sensitive to a 5 hr trypsin treatment and resistant to 5 mM periodate (except for the h epitope). Some epitopes (b, c and d) showed increasing immunoreactivity after 20 mM periodate treatment, suggesting cryptic location. In rat-colon adenocarcinomas, M1 mucin epitopes were masked but could be decrypted using high periodate treatment, similar to normal rat gastric mucosa, thus suggesting the absence of drastic changes in the saccharide coat of the peptide mucin portion bearing M1 epitopes. Cryptic location, periodate resistance, sensitivity to protease and conformational behavior strongly suggest that the peptidic core of gastric (or fetal colonic) mucin plays a role in M1 immunoreactivity. Indeed, the resurgence of M1 antigens during colonic carcinogenesis is due to re-expression of the peptide core of gastric (or fetal colonic) mucins.

Evidence of mucin M1 antigens in seminal plasma and normal cells of human prostatic urethra in relation to embryonic development and tumors

By employing immunoperoxidase methodology, using monoclonal antibodies against the peptide core of gastric mucins (M1 antigens), we demonstrate the presence of M1 mucin-producing cells that are associated with the prostatic urethral epithelium and located mainly in the veru montanum area near the prostatic ductal and utriculus junctions. The significance of these M1 cells is not yet clear. Using an immunoradiometric assay, these M1 mucins were found predominantly in the prostatic fraction obtained from seminal plasma. By chromatography on Sepharose 6B and 2B and cesium chloride gradient centrifugation, we demonstrate that high-molecular-weight components (greater than 10(7) Da) show a density of 1.45 g/ml, similar to mucins, and are immunochemically related to peptidic gastric M1 mucins. The particular location of these M1 antigens in prostatic adult urethra and their fetal expression in cloacal structures suggest that, in males, the prostatic urethral epithelium includes some remnant cells from the enteric cloaca. Finally, the presence of mucin-containing cells in the prostatic urethra could possibly explain the histogenesis of the rare benign villous tumors and primary mucinous adenocarcinomas arising from the prostatic urethral epithelium.