Exploring the pH dependence of an improved PETase

Enzymatic recycling of plastic and especially of polyethylene terephthalate (PET) has shown great potential to reduce its negative impact on our society. PET hydrolases (PETases) have been optimized using rational design and machine learning, but the mechanistic details of the PET depolymerization process remain unclear. Belonging to the carboxylic-ester hydrolase family with a canonical Ser-His-Asp catalytic triad, their observed alkaline pH optimum is generally thought to be related to the protonation state of the catalytic His. Here, we explore this aspect in the context of LCCICCG, an optimized PETase, derived from the leaf-branch compost cutinase enzyme. We use NMR to identify the dominant tautomeric structure of the six histidines. Five show surprisingly low pKa values below 4.0, whereas the catalytic H242 in the active enzyme displays a pKa value that varies from 4.9 to 4.7 when temperatures increase from 30°C to 50°C. Whereas the hydrolytic activity of the enzyme toward a soluble substrate can be modeled by the corresponding protonation/deprotonation curve, an important discrepancy is found when the substrate is the solid plastic. This opens the way to further mechanistic understanding of the PETase activity and underscores the importance of studying the enzyme at the liquid-solid interface.

Atomic-Layer Controlled Transition from Inverse Rashba-Edelstein Effect to Inverse Spin Hall Effect in 2D PtSe2 Probed by THz Spintronic Emission

2D materials, such as transition metal dichalcogenides, are ideal platforms for spin-to-charge conversion (SCC) as they possess strong spin-orbit coupling (SOC), reduced dimensionality and crystal symmetries as well as tuneable band structure, compared to metallic structures. Moreover, SCC can be tuned with the number of layers, electric field, or strain. Here, SCC in epitaxially grown 2D PtSe2 by THz spintronic emission is studied since its 1T crystal symmetry and strong SOC favor SCC. High quality of as-grown PtSe2 layers is demonstrated, followed by in situ ferromagnet deposition by sputtering that leaves the PtSe2 unaffected, resulting in well-defined clean interfaces as evidenced with extensive characterization. Through this atomic growth control and using THz spintronic emission, the unique thickness-dependent electronic structure of PtSe2 allows the control of SCC. Indeed, the transition from the inverse Rashba-Edelstein effect (IREE) in 1-3 monolayers (ML) to the inverse spin Hall effect (ISHE) in multilayers (>3 ML) of PtSe2 enabling the extraction of the perpendicular spin diffusion length and relative strength of IREE and ISHE is demonstrated. This band structure flexibility makes PtSe2 an ideal candidate to explore the underlying mechanisms and engineering of the SCC as well as for the development of tuneable THz spintronic emitters.

Spin-Orbit Torques and Magnetization Switching in (Bi,Sb)2Te3/Fe3GeTe2 Heterostructures Grown by Molecular Beam Epitaxy

Topological insulators (TIs) hold promise for manipulating the magnetization of a ferromagnet (FM) through the spin-orbit torque (SOT) mechanism. However, integrating TIs with conventional FMs often leads to significant device-to-device variations and a broad distribution of SOT magnitudes. In this work, we present a scalable approach to grow a full van der Waals FM/TI heterostructure by molecular beam epitaxy, combining the charge-compensated TI (Bi,Sb)2Te3 with 2D FM Fe3GeTe2 (FGT). Harmonic magnetotransport measurements reveal that the SOT efficiency exhibits a non-monotonic temperature dependence and experiences a substantial enhancement with a reduction of the FGT thickness to 2 monolayers. Our study further demonstrates that the magnetization of ultrathin FGT films can be switched with a current density of Jc ∼ 1010 A/m2, with minimal device-to-device variations compared to previous investigations involving traditional FMs.

A maximum of two readily releasable vesicles per docking site at a cerebellar single active zone synapse

Recent research suggests that in central mammalian synapses, active zones contain several docking sites acting in parallel. Before release, one or several synaptic vesicles (SVs) are thought to bind to each docking site, forming the readily releasable pool (RRP). Determining the RRP size per docking site has important implications for short-term synaptic plasticity. Here, using mouse cerebellar slices, we take advantage of recently developed methods to count the number of released SVs at single glutamatergic synapses in response to trains of action potentials (APs). In each recording, the number of docking sites was determined by fitting with a binomial model the number of released SVs in response to individual APs. After normalization with respect to the number of docking sites, the summed number of released SVs following a train of APs was used to estimate of the RRP size per docking site. To improve this estimate, various steps were taken to maximize the release probability of docked SVs, the occupancy of docking sites, as well as the extent of synaptic depression. Under these conditions, the RRP size reached a maximum value close to two SVs per docking site. The results indicate that each docking site contains two distinct SV-binding sites that can simultaneously accommodate up to one SV each. They further suggest that under special experimental conditions, as both sites are close to full occupancy, a maximal RRP size of two SVs per docking site can be reached. More generally, the results validate a sequential two-step docking model previously proposed at this preparation.

Assessment of Four Engineered PET Degrading Enzymes Considering Large-Scale Industrial Applications

In recent years, enzymatic recycling of the widely used polyester polyethylene terephthalate (PET) has become a complementary solution to current thermomechanical recycling for colored, opaque, and mixed PET. A large set of promising hydrolases that depolymerize PET have been found and enhanced by worldwide initiatives using various methods of protein engineering. Despite the achievements made in these works, it remains difficult to compare enzymes' performance and their applicability to large-scale reactions due to a lack of homogeneity between the experimental protocols used. Here, we pave the way for a standardized enzymatic PET hydrolysis protocol using reaction conditions relevant for larger scale hydrolysis and apply these parameters to four recently reported PET hydrolases (LCCICCG, FAST-PETase, HotPETase, and PES-H1L92F/Q94Y). We show that FAST-PETase and HotPETase have intrinsic limitations that may not permit their application on larger reaction scales, mainly due to their relatively low depolymerization rates. With 80% PET depolymerization, PES-H1L92F/Q94Y may be a suitable candidate for industrial reaction scales upon further rounds of enzyme evolution. LCCICCG outperforms the other enzymes, converting 98% of PET into the monomeric products terephthalic acid (TPA) and ethylene glycol (EG) in 24 h. In addition, we optimized the reaction conditions of LCCICCG toward economic viability, reducing the required amount of enzyme by a factor of 3 and the temperature of the reaction from 72 to 68 °C. We anticipate our findings to advance enzymatic PET hydrolysis toward a coherent assessment of the enzymes and materialize feasibility at larger reaction scales.

Depolarization-induced bursts of miniature synaptic currents in individual synapses of developing cerebellum

In central synapses, spontaneous transmitter release observed in the absence of action potential firing is often considered as a random process lacking time or space specificity. However, when studying miniature glutamatergic currents at cerebellar synapses between parallel fibers and molecular layer interneurons, we found that these currents were sometimes organized in bursts of events occurring at high frequency (about 30 Hz). Bursts displayed homogeneous quantal size amplitudes. Furthermore, in the presence of the desensitization inhibitor cyclothiazide, successive events within a burst displayed quantal amplitude occlusion. Based on these findings, we conclude that bursts originate in individual synapses. Bursts were enhanced by increasing either the external potassium concentration or the external calcium concentration, and they were strongly inhibited when blocking voltage-gated calcium channels by cadmium. Bursts were prevalent in elevated potassium concentration during the formation of the molecular layer but were infrequent later in development. Since postsynaptic AMPA receptors are largely calcium permeant in developing parallel fiber-interneuron synapses, we propose that bursts involve presynaptic calcium transients implicating presynaptic voltage-gated calcium channels, together with postsynaptic calcium transients implicating postsynaptic AMPA receptors. These simultaneous pre- and postsynaptic calcium transients may contribute to the formation and/or stabilization of synaptic connections.

Energetic and Structural Characterizations of the PET-Water Interface as a Key Step in Understanding Its Depolymerization

We report molecular simulations of the interaction between poly(ethylene terephthalate) (PET) surfaces and water molecules with a short-term goal to better evaluate the different energy contributions governing the enzymatic degradation of amorphous PET. After checking that the glass transition temperature, density, entanglement mass, and mechanical properties of an amorphous PET are well reproduced by our molecular model, we extend the study to the extraction of a monomer from the bulk surface in different environments, i.e., water, vacuum, dodecane, and ethylene glycol. We complete this energetic characterization by the calculation of the work of adhesion of PET surfaces with water and dodecane molecules and by the determination of the contact angle of water droplets. These calculations are compared with experiments and should help us to better understand the enzymatic degradation of PET from both the thermodynamic and molecular viewpoints.

Enzymes' Power for Plastics Degradation

Plastics are everywhere in our modern way of living, and their production keeps increasing every year, causing major environmental concerns. Nowadays, the end-of-life management involves accumulation in landfills, incineration, and recycling to a lower extent. This ecological threat to the environment is inspiring alternative bio-based solutions for plastic waste treatment and recycling toward a circular economy. Over the past decade, considerable efforts have been made to degrade commodity plastics using biocatalytic approaches. Here, we provide a comprehensive review on the recent advances in enzyme-based biocatalysis and in the design of related biocatalytic processes to recycle or upcycle commodity plastics, including polyesters, polyamides, polyurethanes, and polyolefins. We also discuss scope and limitations, challenges, and opportunities of this field of research. An important message from this review is that polymer-assimilating enzymes are very likely part of the solution to reaching a circular plastic economy.

Prioritized docking of synaptic vesicles provided by a rapid recycling pathway

It is known that endocytosis of synaptic vesicles, and docking of these vesicles to their release sites, are regulated in a similar manner, but it has remained unclear whether the two processes are linked mechanistically. To address this issue, we studied vesicular release during repeated trains of presynaptic action potentials. Synaptic responses decreased when the inter-train interval was shortened, indicating a gradual exhaustion of the recycling pool of vesicles, with a resting size of 180 vesicles per active zone. This effect was counteracted by the activation of a rapid recycling pathway, which utilized vesicles ∼10 s after endocytosis and was able to generate 200 vesicles per active zone. Blocking the rapid recycling of vesicles revealed an enhanced probability of docking of recently endocytosed vesicles compared to those coming from the recycling pool. Thus, our results demonstrate a differential sorting of vesicles inside the readily releasable pool depending on their origin.

Visualizing Giant Ferroelectric Gating Effects in Large-Scale WSe2/BiFeO3 Heterostructures

Multilayers based on quantum materials (complex oxides, topological insulators, transition-metal dichalcogenides, etc.) have enabled the design of devices that could revolutionize microelectronics and optoelectronics. However, heterostructures incorporating quantum materials from different families remain scarce, while they would immensely broaden the range of possible applications. Here we demonstrate the large-scale integration of compounds from two highly multifunctional families: perovskite oxides and transition-metal dichalcogenides (TMDs). We couple BiFeO₃, a room-temperature multiferroic oxide, and WSe₂, a semiconducting two-dimensional material with potential for photovoltaics and photonics. WSe₂ is grown by molecular beam epitaxy and transferred on a centimeter-scale onto BiFeO₃ films. Using angle-resolved photoemission spectroscopy, we visualize the electronic structure of 1 to 3 monolayers of WSe₂ and evidence a giant energy shift as large as 0.75 eV induced by the ferroelectric polarization direction in the underlying BiFeO₃. Such a strong shift opens new perspectives in the efficient manipulation of TMD properties by proximity effects.

Evidence for highly p-type doping and type II band alignment in large scale monolayer WSe2/Se-terminated GaAs heterojunction grown by molecular beam epitaxy

Two-dimensional materials (2D) arranged in hybrid van der Waals (vdW) heterostructures provide a route toward the assembly of 2D and conventional III-V semiconductors. Here, we report the structural and electronic properties of single layer WSe₂ grown by molecular beam epitaxy on Se-terminated GaAs(111)B. Reflection high-energy electron diffraction images exhibit sharp streaky features indicative of a high-quality WSe₂ layer produced via vdW epitaxy. This is confirmed by in-plane X-ray diffraction. The single layer of WSe₂ and the absence of interdiffusion at the interface are confirmed by high resolution X-ray photoemission spectroscopy and high-resolution transmission microscopy. Angle-resolved photoemission investigation revealed a well-defined WSe₂ band dispersion and a high p-doping coming from the charge transfer between the WSe₂ monolayer and the Se-terminated GaAs substrate. By comparing our results with local and hybrid functionals theoretical calculation, we find that the top of the valence band of the experimental heterostructure is close to the calculations for free standing single layer WSe₂. Our experiments demonstrate that the proximity of the Se-terminated GaAs substrate can significantly tune the electronic properties of WSe₂. The valence band maximum (VBM, located at the K point of the Brillouin zone) presents an upshift of about 0.56 eV toward the Fermi level with respect to the VBM of the WSe₂ on graphene layer, which is indicative of high p-type doping and a key feature for applications in nanoelectronics and optoelectronics.

Calcium-dependent docking of synaptic vesicles

The concentration of calcium ions in presynaptic terminals regulates transmitter release, but underlying mechanisms have remained unclear. Here we review recent studies that shed new light on this issue. Fast-freezing electron microscopy and total internal reflection fluorescence microscopy studies reveal complex calcium-dependent vesicle movements including docking on a millisecond time scale. Recordings from so-called 'simple synapses' indicate that calcium not only triggers exocytosis, but also modifies synaptic strength by controlling a final, rapid vesicle maturation step before release. Molecular studies identify several calcium-sensitive domains on Munc13 and on synaptotagmin-1 that are likely involved in bringing the vesicular and plasma membranes closer together in response to calcium elevation. Together, these results suggest that calcium-dependent vesicle docking occurs in a wide range of time domains and plays a crucial role in several phenomena including synaptic facilitation, post-tetanic potentiation, and neuromodulator-induced potentiation.

Measurement of the Spin Absorption Anisotropy in Lateral Spin Valves

The spin absorption process in a ferromagnetic material depends on the spin orientation relative to the magnetization. Using a ferromagnet to absorb the pure spin current created within a lateral spin valve, we evidence and quantify a sizable orientation dependence of the spin absorption in Co, CoFe, and NiFe. These experiments allow us to determine the spin-mixing conductance, an elusive but fundamental parameter of the spin-dependent transport. We show that the obtained values cannot be understood within a model considering only the Larmor, transverse decoherence, and spin diffusion lengths, and rather suggest that the spin-mixing conductance is actually limited by the Sharvin conductance.

Engineering the Yeast Yarrowia lipolytica for Production of Polylactic Acid Homopolymer

Polylactic acid is a plastic polymer widely used in different applications from printing filaments for 3D printer to mulching films in agriculture, packaging materials, etc. Here, we report the production of poly-D-lactic acid (PDLA) in an engineered yeast strain of Yarrowia lipolytica. Firstly, the pathway for lactic acid consumption in this yeast was identified and interrupted. Then, the heterologous pathway for PDLA production, which contains a propionyl-CoA transferase (PCT) converting lactic acid into lactyl-CoA, and an evolved polyhydroxyalkanoic acid (PHA) synthase polymerizing lactyl-CoA, was introduced into the engineered strain. Among the different PCT proteins that were expressed in Y. lipolytica, the Clostridium propionicum PCT exhibited the highest efficiency in conversion of D-lactic acid to D-lactyl-CoA. We further evaluated the lactyl-CoA and PDLA productions by expressing this PCT and a variant of Pseudomonas aeruginosa PHA synthase at different subcellular localizations. The best PDLA production was obtained by expressing the PCT in the cytosol and the variant of PHA synthase in peroxisome. PDLA homopolymer accumulation in the cell reached 26 mg/g-DCW, and the molecular weights of the polymer (Mw = 50.5 × 103 g/mol and Mn = 12.5 × 103 g/mol) were among the highest reported for an in vivo production.

Differentially poised vesicles underlie fast and slow components of release at single synapses

In several types of central mammalian synapses, sustained presynaptic stimulation leads to a sequence of two components of synaptic vesicle release, reflecting the consecutive contributions of a fast-releasing pool (FRP) and of a slow-releasing pool (SRP). Previous work has shown that following common depletion by a strong stimulation, FRP and SRP recover with different kinetics. However, it has remained unclear whether any manipulation could lead to a selective enhancement of either FRP or SRP. To address this question, we have performed local presynaptic calcium uncaging in single presynaptic varicosities of cerebellar interneurons. These varicosities typically form "simple synapses" onto postsynaptic interneurons, involving several (one to six) docking/release sites within a single active zone. We find that strong uncaging laser pulses elicit two phases of release with time constants of ∼1 ms (FRP release) and ∼20 ms (SRP release). When uncaging was preceded by action potential-evoked vesicular release, the extent of SRP release was specifically enhanced. We interpret this effect as reflecting an increased likelihood of two-step release (docking then release) following the elimination of docked synaptic vesicles by action potential-evoked release. In contrast, a subthreshold laser-evoked calcium elevation in the presynaptic varicosity resulted in an enhancement of the FRP release. We interpret this latter effect as reflecting an increased probability of occupancy of docking sites following subthreshold calcium increase. In conclusion, both fast and slow components of release can be specifically enhanced by certain presynaptic manipulations. Our results have implications for the mechanism of docking site replenishment and the regulation of synaptic responses, in particular following activation of ionotropic presynaptic receptors.

New approach for the molecular beam epitaxy growth of scalable WSe2 monolayers

The search for high-quality transition metal dichalcogenides mono- and multi-layers grown on large areas is still a very active field of investigation. Here, we use molecular beam epitaxy to grow WSe₂ on 15 × 15 mm large mica in the van der Waals regime. By screening one-step growth conditions, we find that very high temperature (>900 °C) and very low deposition rate (<0.15 Å min^-1) are necessary to obtain high quality WSe₂ films. The domain size can be as large as 1 µm and the in-plane rotational misorientation of 1.25°. The WSe₂ monolayer is also robust against air exposure, can be easily transferred over 1 cm² on SiN/SiO₂ and exhibits strong photoluminescence signal. Moreover, by combining grazing incidence x-ray diffraction and transmission electron microscopy, we could detect the presence of few misoriented grains. A two-dimensional model based on atomic coincidences between the WSe₂ and mica crystals allows us to explain the formation of these misoriented grains and gives insight to achieve highly crystalline WSe₂.

Incomplete vesicular docking limits synaptic strength under high release probability conditions

Central mammalian synapses release synaptic vesicles in dedicated structures called docking/release sites. It has been assumed that when voltage-dependent calcium entry is sufficiently large, synaptic output attains a maximum value of one synaptic vesicle per action potential and per site. Here we use deconvolution to count synaptic vesicle output at single sites (mean site number per synapse: 3.6). When increasing calcium entry with tetraethylammonium in 1.5 mM external calcium concentration, we find that synaptic output saturates at 0.22 vesicle per site, not at 1 vesicle per site. Fitting the results with current models of calcium-dependent exocytosis indicates that the 0.22 vesicle limit reflects the probability of docking sites to be occupied by synaptic vesicles at rest, as only docked vesicles can be released. With 3 mM external calcium, the maximum output per site increases to 0.47, indicating an increase in docking site occupancy as a function of external calcium concentration.

Observation of Large Unidirectional Rashba Magnetoresistance in Ge(111)

Relating magnetotransport properties to specific spin textures at surfaces or interfaces is an intense field of research nowadays. Here, we investigate the variation of the electrical resistance of Ge(111) grown epitaxially on semi-insulating Si(111) under the application of an external magnetic field. We find a magnetoresistance term that is linear in current density j and magnetic field B, hence, odd in j and B, corresponding to a unidirectional magnetoresistance. At 15 K, for I=10  μA (or j=0.33  A m^{-1}) and B=1  T, it represents 0.5% of the zero field resistance, a much higher value compared to previous reports on unidirectional magnetoresistance (UMR). We ascribe the origin of this magnetoresistance to the interplay between the externally applied magnetic field and the pseudomagnetic field generated by the current applied in the spin-splitted subsurface states of Ge(111). This unidirectional magnetoresistance is independent of the current direction with respect to the Ge crystal axes. It progressively vanishes, either using a negative gate voltage due to carrier activation into the bulk (without spin-splitted bands), or by increasing the temperature due to the Rashba energy splitting of the subsurface states lower than ∼58k_{B}. We believe that UMR could be used as a powerful probe of the spin-orbit interaction in a wide range of materials.

Identification of a crucial amino acid implicated in the hydroxylation/desaturation ratio of CpFAH12 bifunctional hydroxylase

Claviceps purpurea bifunctional Δ12-hydroxylase/desaturase, CpFAH12, and monofunctional desaturase CpFAD2, share 86% of sequence identity. To identify the underlying determinants of the hydroxylation/desaturation specificity, chimeras of these two enzymes were tested for their fatty acid production in an engineered Yarrowia lipolytica strain. It reveals that transmembrane helices are not involved in the hydroxylation/desaturation specificity whereas all cytosolic domains have an impact on it. Especially, replacing the CpFAH12 cytosolic part near the second histidine-box by the corresponding CpFAD2 part annihilates all hydroxylation activity. Further mutagenesis experiments within this domain identified isoleucine 198 as the crucial element for the hydroxylation activity of CpFAH12. Monofunctional variants performing the only desaturation were obtained when this position was exchanged by the threonine of CpFAD2. Saturation mutagenesis at this position showed modulation in the hydroxylation/desaturation specificity in the different variants. The WT enzyme was demonstrated as the most efficient for ricinoleic acid production and some variants showed a better desaturation activity. A model based on the recently discovered membrane desaturase structures indicate that these changes in specificity are more likely due to modifications in the di-iron center geometry rather than changes in the substrate binding mode.

Production and characterization of two medium-chain-length polydroxyalkanoates by engineered strains of Yarrowia lipolytica

Background

The oleaginous yeast Yarrowia lipolytica is an organism of choice for the tailored production of various compounds such as biofuels or biopolymers. When properly engineered, it is capable of producing medium-chain-length polyhydroxyalkanoate (mcl-PHA), a biobased and biodegradable polymer that can be used as bioplastics or biopolymers for environmental and biomedical applications.

Results

This study describes the bioproduction and the main properties of two different mcl-PHA polymers. We generated by metabolic engineering, strains of Y. lipolytica capable of accumulating more than 25% (g/g) of mcl-PHA polymers. Depending of the strain genetic background and the culture conditions, we produced (i) a mcl-PHA homopolymer of 3-hydroxydodecanoic acids, with a mass-average molar mass (M_w) of 316,000 g/mol, showing soft thermoplastic properties with potential applications in packaging and (ii) a mcl-PHA copolymer made of 3-hydroxyoctanoic (3HO), decanoic (3HD), dodecanoic (3HDD) and tetradecanoic (3TD) acids with a M_w of 128,000 g/mol, behaving like a thermoplastic elastomer with potential applications in biomedical material.

Conclusion

The ability to engineer Y. lipolytica to produce tailored PHAs together with the range of possible applications regarding their biophysical and mechanical properties opens new perspectives in the field of PHA bioproduction.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1140-y) contains supplementary material, which is available to authorized users.

Impact of a van der Waals interface on intrinsic and extrinsic defects in an MoSe2 monolayer

In this work, we study growth and migration of atomic defects in MoSe₂ on graphene using multiple advanced transmission electron microscopy techniques to explore defect behavior in vdW heterostructures. A MoSe₂/graphene vdW heterostructure is prepared by a direct growth of both monolayers, thereby attaining an ideal vdW interface between the monolayers. We investigate the intrinsic defects (inversion domains and grain boundaries) in synthesized MoSe₂, their evolution amid growth processing steps, and their influence on the formation and movement of extrinsic defects. Electron diffraction identifies a preferential interlayer orientation of 2° between MoSe₂ and graphene, which is caused by the presence of intrinsic IBD defects. Extrinsic defects (point and line defects) are generated by in situ electron irradiation in the MoSe₂ layer. Our results shed light on how to independently modify the MoSe₂ atomic structure in vdW heterostructures for potential utilization in device processing.

Increasing medium chain fatty acids production in Yarrowia lipolytica by metabolic engineering

BACKGROUND

Oleaginous yeast Yarrowia lipolytica is an organism of choice for the development of biofuel and oleochemicals. It has become a chassis for metabolic engineering in order to produce targeted lipids. Understanding the function of key-enzymes involved in lipid metabolism is essential to design better routes for enhanced lipid production and for strains producing lipids of interest. Because medium chain fatty acids (MCFA) are valuable compounds for biokerosene production, we previously generated strains capable of producing MCFA up to 12% of total lipid content (Rigouin et al. in ACS Synth Biol 6:1870-1879, 2017). In order to improve accumulation and content of C14 fatty acid (FA), the elongation, degradation and accumulation of these MCFA in Yarrowia lipolytica were studied.

RESULTS

We brought evidence of the role of YALI0F0654 (YlELO1) protein in the elongation of exogenous or de novo synthesized C14 FA into C16 FA and C18 FA. YlELO1 deletion into a αFAS_I1220W expressing strain leads to the sole production of C14 FA. However, because this strain does not provide the FA essential for its growth, it requires being cultivated with essential fatty acids and C14 FA yield is limited. To promote MCFA accumulation in Y. lipolytica without compromising the growth, we overexpressed a plant diglyceride acyltransferase specific for MCFA and reached an accumulation of MCFA up to 45% of total lipid content.

CONCLUSION

We characterized the role of YlELO1 in Y. lipolytica by proving its involvement in Medium chain fatty acids elongation. We showed that MCFA content can be increased in Yarrowia lipolytica by promoting their accumulation into a stable storage form (triacylglycerides) to limit their elongation and their degradation.

A two-step docking site model predicting different short-term synaptic plasticity patterns

Established models of vesicular docking/release sites can account for synaptic depression. By incorporating a separate predocked state and by assuming that docking site occupancy is <1 at rest, Pulido and Marty extend previous models and explain facilitating and nonmonotonic synaptic responses.

The strength of synaptic transmission varies during trains of presynaptic action potentials, notably because of the depletion of synaptic vesicles available for release. It has remained unclear why some synapses display depression over time, whereas others facilitate or show a facilitation and depression sequence. Here we compare the predictions of various synaptic models assuming that several docking/release sites are acting in parallel. These models show variation of docking site occupancy during trains of action potentials due to vesicular release and site replenishment, which give rise to changes in synaptic strength. To conform with recent studies, we assume an initial docking site occupancy of <1, thus permitting site occupancy to increase during action potential trains and facilitation to occur. We consider both a standard one-step model and a more elaborate model that assumes a predocked state (two-step model). Whereas the one-step model predicts monotonic changes of synaptic strength during a train, the two-step model allows nonmonotonic changes, including the often-observed facilitation/depression sequence. Both models predict a partitioning of parameter space between initially depressing and facilitating synapses. Using data obtained from interneuron synapses in the cerebellum, we demonstrate an unusual form of depression/facilitation sequence for very high release probability after prolonged depolarization-induced transmitter release. These results indicate a depletion of predocked vesicles in the two-step model. By permitting docking site occupancy to be <1 at rest, and by incorporating a separate predocked state, we reveal that docking site models can be expanded to mimic the large variety of time-dependent changes of synaptic strength that have been observed during action potential trains. Furthermore, the two-step model provides an effective framework to identify the specific mechanisms responsible for short-term changes in synaptic strength.

Developing cellulolytic Yarrowia lipolytica as a platform for the production of valuable products in consolidated bioprocessing of cellulose

BACKGROUND

Both industrial biotechnology and the use of cellulosic biomass as feedstock for the manufacture of various commercial goods are prominent features of the bioeconomy. In previous work, with the aim of developing a consolidated bioprocess for cellulose bioconversion, we conferred cellulolytic activity of Yarrowia lipolytica, one of the most widely studied "nonconventional" oleaginous yeast species. However, further engineering this strain often leads to the loss of previously introduced heterologous genes due to the presence of multiple LoxP sites when using Cre-recombinase to remove previously employed selection markers.

RESULTS

In the present study, we first optimized the strategy of expression of multiple cellulases and rescued selection makers to obtain an auxotrophic cellulolytic Y. lipolytica strain. Then we pursued the quest, exemplifying how this cellulolytic Y. lipolytica strain can be used as a CBP platform for the production of target products. Our results reveal that overexpression of SCD1 gene, encoding stearoyl-CoA desaturase, and DGA1, encoding acyl-CoA:diacylglycerol acyltransferase, confers the obese phenotype to the cellulolytic Y. lipolytica. When grown in batch conditions and minimal medium, the resulting strain consumed 12 g/L cellulose and accumulated 14% (dry cell weight) lipids. Further enhancement of lipid production was achieved either by the addition of glucose or by enhancing cellulose consumption using a commercial cellulase cocktail. Regarding the latter option, although the addition of external cellulases is contrary to the concept of CBP, the amount of commercial cocktail used remained 50% lower than that used in a conventional process (i.e., without internalized production of cellulases). The introduction of the LIP2 gene into cellulolytic Y. lipolytica led to the production of a strain capable of producing lipase 2 while growing on cellulose. Remarkably, when the strain was grown on glucose, the expression of six cellulases did not alter the level of lipase production. When grown in batch conditions on cellulose, the engineered strain consumed 16 g/L cellulose and produced 9.0 U/mL lipase over a 96-h period. The lipase yield was 562 U lipase/g cellulose, which represents 60% of that obtained on glucose. Finally, expression of the hydroxylase from Claviceps purpurea (CpFAH12) in cellulolytic Y. lipolytica procured a strain that can produce ricinoleic acid (RA). Using this strain in batch cultures revealed that the consumption of 11 g/L cellulose sustained the production of 2.2 g/L RA in the decane phase, 69% of what was obtained on glucose.

CONCLUSIONS

In summary, this study has further demonstrated the potential of cellulolytic Y. lipolytica as a microbial platform for the bioconversion of cellulose into target products. Its ability to be used in consolidated process designs has been exemplified and clues revealing how cellulose consumption can be further enhanced using commercial cellulolytic cocktails are provided.

Beyond van der Waals Interaction: The Case of MoSe2 Epitaxially Grown on Few-Layer Graphene

Van der Waals heterojunctions composed of graphene and transition metal dichalcogenides have gain much attention because of the possibility to control and tailor band structure, promising applications in two-dimensional optoelectronics and electronics. In this report, we characterized the van der Waals heterojunction MoSe₂/few-layer graphene with a high-quality interface using cutting-edge surface techniques scaling from atomic to microscopic range. These surface analyses gave us a complete picture of the atomic structure and electronic properties of the heterojunction. In particular, we found two important results: the commensurability between the MoSe₂ and few-layer graphene lattices and a band-gap opening in the few-layer graphene. The band gap is as large as 250 meV, and we ascribed it to an interface charge transfer that results in an electronic depletion in the few-layer graphene. This conclusion is well supported by electron spectroscopy data and density functional theory calculations. The commensurability between the MoSe₂ and graphene lattices as well as the band-gap opening clearly show that the interlayer interaction goes beyond the simple van der Waals interaction. Hence, stacking two-dimensional materials in van der Waals heterojunctions enables us to tailor the atomic and electronic properties of individual layers. It also permits the introduction of a band gap in few-layer graphene by interface charge transfer.

Differential time to positivity of central and peripheral blood cultures is inaccurate for the diagnosis of Staphylococcus aureus long-term catheter-related sepsis

OBJECTIVES

Differential time to positivity of cultures of blood drawn simultaneously from central venous catheter and peripheral sites is widely used to diagnose catheter-related bloodstream infections without removing the catheter. However, the accuracy of this technique for some pathogens, such as Staphylococcus aureus, is debated in routine practice.

METHODS

In a 320-bed reference cancer centre, the charts of patients with at least one blood culture positive for S. aureus among paired blood cultures drawn over a six-year period were studied retrospectively. Microbiological data were extracted from the prospectively compiled database of the microbiology unit. Data concerning the 149 patients included were reviewed retrospectively by independent physicians blinded to the absolute and differential times to positivity, in order to establish or refute the diagnosis of catheter-related sepsis. Due to missing data, 48 charts were excluded, so 101 cases were actually analysed. The diagnosis was established in 62 cases, refuted in 15 cases and inconclusive in the remaining 24 cases.

RESULTS

For the 64 patients with both central and peripheral positive blood cultures, the differential positivity time was significantly greater for patients with catheter-related bloodstream infections due to S. aureus (P<0.02). However, because of the high number of false-negative cases, the classic cut-off limit of 120 min showed 100% specificity but only 42% sensitivity for the diagnosis of catheter-related bloodstream infection due to S. aureus.

CONCLUSIONS

These results strongly suggest that despite its high specificity, the differential time to positivity may not be reliable to rule out catheter-related bloodstream infection due to S. aureus.

Lipases: An Overview

Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century, and the associated research continuously increased due to the characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.

Production of Medium Chain Fatty Acids by Yarrowia lipolytica: Combining Molecular Design and TALEN to Engineer the Fatty Acid Synthase

Yarrowia lipolytica is a promising organism for the production of lipids of biotechnological interest and particularly for biofuel. In this study, we engineered the key enzyme involved in lipid biosynthesis, the giant multifunctional fatty acid synthase (FAS), to shorten chain length of the synthesized fatty acids. Taking as starting point that the ketoacyl synthase (KS) domain of Yarrowia lipolytica FAS is directly involved in chain length specificity, we used molecular modeling to investigate molecular recognition of palmitic acid (C16 fatty acid) by the KS. This enabled to point out the key role of an isoleucine residue, I1220, from the fatty acid binding site, which could be targeted by mutagenesis. To address this challenge, TALEN (transcription activator-like effector nucleases)-based genome editing technology was applied for the first time to Yarrowia lipolytica and proved to be very efficient for inducing targeted genome modifications. Among the generated FAS mutants, those having a bulky aromatic amino acid residue in place of the native isoleucine at position 1220 led to a significant increase of myristic acid (C14) production compared to parental wild-type KS. Particularly, the best performing mutant, I1220W, accumulates C14 at a level of 11.6% total fatty acids. Overall, this work illustrates how a combination of molecular modeling and genome-editing technology can offer novel opportunities to rationally engineer complex systems for synthetic biology.

Quantal Fluctuations in Central Mammalian Synapses: Functional Role of Vesicular Docking Sites

Quantal fluctuations are an integral part of synaptic signaling. At the frog neuromuscular junction, Bernard Katz proposed that quantal fluctuations originate at “reactive sites” where specific structures of the presynaptic membrane interact with synaptic vesicles. However, the physical nature of reactive sites has remained unclear, both at the frog neuromuscular junction and at central synapses. Many central synapses, called simple synapses, are small structures containing a single presynaptic active zone and a single postsynaptic density of receptors. Several lines of evidence indicate that simple synapses may release several synaptic vesicles in response to a single action potential. However, in some synapses at least, each release event activates a significant fraction of the postsynaptic receptors, giving rise to a sublinear relation between vesicular release and postsynaptic current. Partial receptor saturation as well as synaptic jitter gives to simple synapse signaling the appearance of a binary process. Recent investigations of simple synapses indicate that the number of released vesicles follows binomial statistics, with a maximum reflecting the number of docking sites present in the active zone. These results suggest that at central synapses, vesicular docking sites represent the reactive sites proposed by Katz. The macromolecular architecture and molecular composition of docking sites are presently investigated with novel combinations of techniques. It is proposed that variations in docking site numbers are central in defining intersynaptic variability and that docking site occupancy is a key parameter regulating short-term synaptic plasticity.

Conferring cellulose-degrading ability to Yarrowia lipolytica to facilitate a consolidated bioprocessing approach

BACKGROUND

Yarrowia lipolytica, one of the most widely studied "nonconventional" oleaginous yeast species, is unable to grow on cellulose. Recently, we identified and overexpressed two endogenous β-glucosidases in Y. lipolytica, thus enabling this yeast to use cello-oligosaccharides as a carbon source for growth. Using this engineered yeast platform, we have now gone further toward building a fully cellulolytic Y. lipolytica for use in consolidated bioprocessing of cellulose.

RESULTS

Initially, different essential enzyme components of a cellulase cocktail (i.e,. cellobiohydrolases and endoglucanases) were individually expressed in Y. lipolytica in order to ascertain the viability of the strategy. Accordingly, the Trichoderma reesei endoglucanase I (TrEG I) and II (TrEG II) were secreted as active proteins in Y. lipolytica, with the secretion yield of EG II being twice that of EG I. Characterization of the purified His-tagged recombinant EG proteins (rhTrEGs) revealed that rhTrEG I displayed higher specific activity than rhTrEG II on both cellotriose and insoluble cellulosic substrates, such as Avicel, β-1, 3 glucan, β-1, 4 glucan, and PASC. Similarly, cellobiohydrolases, such as T. reesei CBH I and II (TrCBH I and II), and the CBH I from Neurospora crassa (NcCBH I) were successfully expressed in Y. lipolytica. However, the yield of the expressed TrCBH I was low, so work on this was not pursued. Contrastingly, rhNcCBH I was not only well expressed, but also highly active on PASC and more active on Avicel (0.11 U/mg) than wild-type TrCBH I (0.065 U/mg). Therefore, work was pursued using a combination of NcCBH I and TrCBH II. The quantification of enzyme levels in culture supernatants revealed that the use of a hybrid promoter instead of the primarily used TEF promoter procured four and eight times more NcCBH I and TrCBH II expressions, respectively. Finally, the coexpression of the previously described Y. lipolytica β-glucosidases, the CBH II, and EG I and II from T. reesei, and the N. crassa CBH I procured an engineered Y. lipolytica strain that was able to grow both on model cellulose substrates, such as highly crystalline Avicel, and on industrial cellulose pulp, such as that obtained using an organosolv process.

CONCLUSIONS

A Y. lipolytica strain coexpressing six cellulolytic enzyme components has been successfully developed. In addition, the results presented show how the recombinant strain can be optimized, for example, using artificial promoters to tailor expression levels. Most significantly, this study has provided a demonstration of how the strain can grow on a sample of industrial cellulose as sole carbon source, thus revealing the feasibility of Yarrowia-based consolidated bioprocess for the production of fuel and chemical precursors. Further, enzyme and strain optimization, coupled to appropriate process design, will undoubtedly lead to much better performances in the future.

Expressing accessory proteins in cellulolytic Yarrowia lipolytica to improve the conversion yield of recalcitrant cellulose

BACKGROUND

A recently constructed cellulolytic Yarrowia lipolytica is able to grow efficiently on an industrial organosolv cellulose pulp, but shows limited ability to degrade crystalline cellulose. In this work, we have further engineered this strain, adding accessory proteins xylanase II (XYNII), lytic polysaccharide monooxygenase (LPMO), and swollenin (SWO) from Trichoderma reesei in order to enhance the degradation of recalcitrant substrate.

RESULTS

The production of EG I was enhanced using a promoter engineering strategy. This provided a new cellulolytic Y. lipolytica strain, which compared to the parent strain, exhibited higher hydrolytic activity on different cellulosic substrates. Furthermore, three accessory proteins, TrXYNII, TrLPMOA and TrSWO, were individually expressed in cellulolytic and non-cellulolytic Y. lipolytica. The amount of rhTrXYNII and rhTrLPMOA secreted by non-cellulolytic Y. lipolytica in YTD medium during batch cultivation in flasks was approximately 62 and 52 mg/L, respectively. The purified rhTrXYNII showed a specific activity of 532 U/mg-protein on beechwood xylan, while rhTrLPMOA exhibited a specific activity of 14.4 U/g-protein when using the Amplex Red/horseradish peroxidase assay. Characterization of rhTrLPMOA revealed that this protein displays broad specificity against β-(1,4)-linked glucans, but is inactive on xylan. Further studies showed that the presence of TrLPMOA synergistically enhanced enzymatic hydrolysis of cellulose by cellulases, while TrSWO1 boosted cellulose hydrolysis only when it was applied before the action of cellulases. The presence of rTrXYNII enhanced enzymatic hydrolysis of an industrial cellulose pulp and of wheat straw. Co-expressing TrXYNII and TrLPMOA in cellulolytic Y. lipolytica with enhanced EG I production procured a novel engineered Y. lipolytica strain that displayed enhanced ability to degrade both amorphous (CIMV-cellulose) and recalcitrant crystalline cellulose in complex biomass (wheat straw) by 16 and 90%, respectively.

CONCLUSIONS

This study has provided a potent cellulose-degrading Y. lipolytica strain that co-expresses a core set of cellulolytic enzymes and some accessory proteins. Results reveal that the tuning of cellulase production and the production of accessory proteins leads to optimized performance. Accordingly, the beneficial effect of accessory proteins for cellulase-mediated degradation of cellulose is underlined, especially when crystalline cellulose and complex biomass are used as substrates. Findings specifically underline the benefits and specific properties of swollenin. Although in our study swollenin clearly promoted cellulase action, its use requires process redesign to accommodate its specific mode of action.

Evidence for spin-to-charge conversion by Rashba coupling in metallic states at the Fe/Ge(111) interface

The spin-orbit coupling relating the electron spin and momentum allows for spin generation, detection and manipulation. It thus fulfils the three basic functions of the spin field-effect transistor. However, the spin Hall effect in bulk germanium is too weak to produce spin currents, whereas large Rashba effect at Ge(111) surfaces covered with heavy metals could generate spin-polarized currents. The Rashba spin splitting can actually be as large as hundreds of meV. Here we show a giant spin-to-charge conversion in metallic states at the Fe/Ge(111) interface due to the Rashba coupling. We generate very large charge currents by direct spin pumping into the interface states from 20 K to room temperature. The presence of these metallic states at the Fe/Ge(111) interface is demonstrated by first-principles electronic structure calculations. By this, we demonstrate how to take advantage of the spin-orbit coupling for the development of the spin field-effect transistor.

Ferromagnetic/Nonmagnetic Nanostructures for the Electrical Measurement of the Spin Hall Effect

Spin-orbitronics is based on the ability of spin-orbit interactions to achieve the conversion between charge currents and pure spin currents. As the precise evaluation of the conversion efficiency becomes a crucial issue, the need for straightforward ways to observe this conversion has emerged as one of the main challenges in spintronics. Here, we propose a simple device, akin to the ferromagnetic/nonmagnetic bilayers used in most spin-orbit torques experiments, and consisting of a spin Hall effect wire connected to two transverse ferromagnetic electrodes. We show that this system allows probing electrically the direct and inverse conversion in a spin Hall effect system and measuring both the spin Hall angle and the spin diffusion length. By applying this method to several spin Hall effect materials (Pt, Pd, Au, Ta, W), we show that it represents a promising tool for the metrology of spin-orbit materials.

Cloning, expression, and characterization of Aureobasidium melanogenum lipase in Pichia pastoris

cDNA of Aureobasidium melanogenum lipase comprises 1254 bp encoding 417 amino acids, whereas genomic DNA of lipase comprises 1311 bp with one intron (57 bp). The lipase gene contains a putative signal peptide encoding 26 amino acids. The A. melanogenum lipase gene was successfully expressed in Pichia pastoris. Recombinant lipase in an inducible expression system showed the highest lipase activity of 3.8 U/mL after six days of 2% v/v methanol induction. The molecular mass of purified recombinant lipase was estimated as 39 kDa using SDS-PAGE. Optimal lipase activity was observed at 35–37 °C and pH 7.0 using p-nitrophenyl laurate as the substrate. Lipase activity was enhanced by Mg2+, Mn2+, Li+, Ca2+, Ni2+, CHAPS, DTT, and EDTA and inhibited by Hg2+, Ag+, SDS, Tween 20, and Triton X-100. The addition of 10% v/v acetone, DMSO, p-xylene, and octanol increased lipase activity, whereas that of propanol and butanol strongly inhibited it.

Magneto-optical micromechanical systems for magnetic field mapping

A new method for magnetic field mapping based on the optical response of organized dense arrays of flexible magnetic cantilevers is explored. When subjected to the stray field of a magnetized material, the mobile parts of the cantilevers deviate from their initial positions, which locally changes the light reflectivity on the magneto-optical surface, thus allowing to visualize the field lines. While the final goal is to be able to map and quantify non-uniform fields, calibrating and testing the device can be done with uniform fields. Under a uniform field, the device can be assimilated to a magnetic-field-sensitive diffraction grating, and therefore, can be analyzed by coherent light diffraction. A theoretical model for the diffraction patterns, which accounts for both magnetic and mechanical interactions within each cantilever, is proposed and confronted to the experimental data.

Spin transport in p-type germanium

We report on the spin transport properties in p-doped germanium (Ge-p) using low temperature magnetoresistance measurements, electrical spin injection from a ferromagnetic metal and the spin pumping-inverse spin Hall effect method. Electrical spin injection is carried out using three-terminal measurements and the Hanle effect. In the 2-20 K temperature range, weak antilocalization and the Hanle effect provide the same spin lifetime in the germanium valence band (≈1 ps) in agreement with predicted values and previous optical measurements. These results, combined with dynamical spin injection by spin pumping and the inverse spin Hall effect, demonstrate successful spin accumulation in Ge. We also estimate the spin Hall angle θ(SHE) in Ge-p (6-7 x 10(-4) at room temperature, pointing out the essential role of ionized impurities in spin dependent scattering.

Spin to Charge Conversion at Room Temperature by Spin Pumping into a New Type of Topological Insulator: α-Sn Films

We present results on spin to charge current conversion in experiments of resonant spin pumping into the Dirac cone with helical spin polarization of the elemental topological insulator (TI) α-Sn. By angle-resolved photoelectron spectroscopy (ARPES), we first check that the Dirac cone (DC) at the α-Sn (0 0 1) surface subsists after covering Sn with Ag. Then we show that resonant spin pumping at room temperature from Fe through Ag into α-Sn layers induces a lateral charge current that can be ascribed to the inverse Edelstein effect by the DC states. Our observation of an inverse Edelstein effect length much longer than those generally found for Rashba interfaces demonstrates the potential of TIs for the conversion between spin and charge in spintronic devices. By comparing our results with data on the relaxation time of TI free surface states from time-resolved ARPES, we can anticipate the ultimate potential of the TI for spin to charge conversion and the conditions to reach it.

Comparison of the use of NiFe and CoFe as electrodes for metallic lateral spin valves

Spin injection and detection in Co60Fe40-based all-metallic lateral spin valves have been studied at both room and low temperatures. The obtained spin signals amplitudes have been compared to those of identical Ni80Fe20-based devices. The replacement of Ni80Fe20 by CoFe allows increasing the spin signal amplitude by up to one order of magnitude, thus reaching 50 mΩ at room temperature. The spin signal dependence with the distance between the ferromagnetic electrodes has been analyzed using both a 1D spin-transport model and finite element method simulations. The enhancement of the spin signal amplitude when using CoFe electrodes can be explained by a higher effective polarization.

Comprehensive Analysis of a Yeast Lipase Family in the Yarrowia Clade

Lipases are currently the subject of intensive studies due to their large range of industrial applications. The Lip2p lipase from the yeast Yarrowia lipolytica (YlLIP2) was recently shown to be a good candidate for different biotechnological applications. Using a combination of comparative genomics approaches based on sequence similarity, synteny conservation, and phylogeny, we constructed the evolutionary scenario of the lipase family for six species of the Yarrowia clade. RNA-seq based transcriptome analysis revealed the primary role of LIP2 homologues in the assimilation of different substrates. Once identified, these YlLIP2 homologues were expressed in Y. lipolytica. The lipase Lip2a from Candida phangngensis was shown to naturally present better activity and enantioselectivity than YlLip2. Enantioselectivity was further improved by site-directed mutagenesis targeted to the substrate binding site. The mono-substituted variant V232S displayed enantioselectivity greater than 200 and a 2.5 fold increase in velocity. A double-substituted variant 97A-V232F presented reversed enantioselectivity, with a total preference for the R-enantiomer.

An excitatory GABA loop operating in vivo

While it has been proposed that the conventional inhibitory neurotransmitter GABA can be excitatory in the mammalian brain, much remains to be learned concerning the circumstances and the cellular mechanisms governing potential excitatory GABA action. Using a combination of optogenetics and two-photon calcium imaging in vivo, we find that activation of chloride-permeable GABA_A receptors in parallel fibers (PFs) of the cerebellar molecular layer of adult mice causes parallel fiber excitation. Stimulation of PFs at submaximal stimulus intensities leads to GABA release from molecular layer interneurons (MLIs), thus creating a positive feedback loop that enhances excitation near the center of an activated PF bundle. Our results imply that elevated chloride concentration can occur in specific intracellular compartments of mature mammalian neurons and suggest an excitatory role for GABA_A receptors in the cerebellar cortex of adult mice.