Potential of a laser pointer contact lens to improve the reliability of video-based eye-trackers in indoor and outdoor conditions.

Many video-based eye trackers rely on detecting and tracking ocular features, a task that can be negatively affected by a number of individual or environmental factors. In this context, the aim of this study was to practically evaluate how the use of a scleral contact lens with two integrated nearinfrared lasers (denoted CLP) could improve the tracking robustness in difficult lighting conditions, particularly outdoor ones. We assessed the ability of the CLP (on a model eye) to detect the lasers and to deduce a gaze position with an accuracy better than 1° under four lighting conditions (1 lx, 250 lx, 50 klux and alternating 1lx /250 lx) on an artificial eye. These results were compared to the ability of a commercial eye tracker (Pupil Core) to detect the pupil on human eyes with a confidence score equal to or greater than 0.9. CLP provided good results in all conditions (tracking accuracy and detection rates). In comparison, the Pupil Core performed well in all indoor conditions (99% detection) but failed in outdoor conditions (9.85% detection). In conclusion, the CLP presents strong potential to improve the reliability of video-based eyetrackers in outdoor conditions by providing easy trackable feature.

Yeast zinc cluster transcription factors involved in the switch from fermentation to respiration show interdependency for DNA binding revealing a novel type of DNA recognition.

In budding yeast, fermentation is the most important pathway for energy production. Under low-glucose conditions, ethanol is used for synthesis of this sugar requiring a shift to respiration. This process is controlled by the transcriptional regulators Cat8, Sip4, Rds2 and Ert1. We characterized Gsm1 (glucose starvation modulator 1), a paralog of Rds2 and Ert1. Genome-wide analysis showed that Gsm1 has a DNA binding profile highly similar to Rds2. Binding of Gsm1 and Rds2 is interdependent at the gluconeogenic gene FBP1. However, Rds2 is required for Gsm1 to bind at other promoters but not the reverse. Gsm1 and Rds2 also bind to DNA independently of each other. Western blot analysis revealed that Rds2 controls expression of Gsm1. In addition, we showed that the DNA binding domains of Gsm1 and Rds2 bind cooperatively in vitro to the FBP1 promoter. In contrast, at the HAP4 gene, Ert1 cooperates with Rds2 for DNA binding. Mutational analysis suggests that Gsm1/Rds2 and Ert1/Rds2 bind to short common DNA stretches, revealing a novel mode of binding for this class of factors. Two-point mutations in a HAP4 site convert it to a Gsm1 binding site. Thus, Rds2 controls binding of Gsm1 at many promoters by two different mechanisms: regulation of Gsm1 levels and increased DNA binding by formation of heterodimers.

Transcription-coupled nucleosome assembly.

Eukaryotic transcription occurs on chromatin, where RNA polymerase II encounters nucleosomes during elongation. These nucleosomes must unravel for the DNA to enter the active site. However, in most transcribed genes, nucleosomes remain intact due to transcription-coupled chromatin assembly mechanisms. These mechanisms primarily involve the local reassembly of displaced nucleosomes to prevent (epi)genomic instability and the emergence of cryptic transcription. As a fail-safe mechanism, cells can assemble nucleosomes de novo, particularly in highly transcribed genes, but this may result in the loss of epigenetic information. This review examines transcription-coupled chromatin assembly, with an emphasis on studies in yeast and recent structural studies. These studies shed light on how elongation factors and histone chaperones coordinate to enable nucleosome recycling during transcription.

Uncoupling the TFIIH Core and Kinase Modules Leads To Unregulated RNA Polymerase II CTD Serine 5 Phosphorylation.

TFIIH is an essential transcription initiation factor for RNA polymerase II (RNApII). This multi-subunit complex comprises two modules that are physically linked by the subunit Tfb3 (MAT1 in metazoans). The TFIIH Core Module, with two DNA-dependent ATPases and several additional subunits, promotes DNA unwinding. The TFIIH Kinase Module phosphorylates Serine 5 of the C-terminal domain (CTD) of RNApII subunit Rpb1, a modification that coordinates exchange of initiation and early elongation factors. While it is not obvious why these two disparate activities are bundled into one factor, the connection may provide temporal coordination during early initiation. Here we show that Tfb3 can be split into two parts to uncouple the TFIIH modules. The resulting cells grow slower than normal, but are viable. Chromatin immunoprecipitation of the split TFIIH shows that the Core Module, but not the Kinase, is properly recruited to promoters. Instead of the normal promoter-proximal peak, high CTD Serine 5 phosphorylation is seen throughout transcribed regions. Therefore, coupling the TFIIH modules is necessary to localize and limit CTD kinase activity to early stages of transcription. These results are consistent with the idea that the two TFIIH modules began as independent functional entities that became connected by Tfb3 during early eukaryotic evolution.

When the +1 nucleosome gets in the way, TFIIH fails but does not fall.

In this issue of Molecular Cell, Abril-Garrido et al.1 used cryo-EM to uncover that the +1 nucleosome inhibits transcription by interfering with the function of the TFIIH translocase via mechanisms that depend on its position relative to the transcription start site.

Contact lens embedded holographic pointer.

In this paper we present an infrared laser pointer, consisting of a vertical-cavity surface-emitting laser (VCSEL) and a diffractive optical element (DOE), encapsulated into a scleral contact lens (SCL). The VCSEL is powered remotely by inductive coupling from a primary antenna embedded into an eyewear frame. The DOE is used either to collimate the laser beam or to project a pattern image at a chosen distance in front of the eye. We detail the different SCL constitutive blocks, how they are manufactured and assembled. We particularly emphasize the various technological challenges related to their encapsulation in the reduced volume of the SCL, while keeping the pupil free. Finally, we describe how the laser pointer operates, what are its performances (e.g. collimation, image formation) and how it can be used efficiently in various application fields such as visual assistance and augmented reality.

Adaptive partitioning of a gene locus to the nuclear envelope in Saccharomyces cerevisiae is driven by polymer-polymer phase separation.

Partitioning of active gene loci to the nuclear envelope (NE) is a mechanism by which organisms increase the speed of adaptation and metabolic robustness to fluctuating resources in the environment. In the yeast Saccharomyces cerevisiae, adaptation to nutrient depletion or other stresses, manifests as relocalization of active gene loci from nucleoplasm to the NE, resulting in more efficient transport and translation of mRNA. The mechanism by which this partitioning occurs remains a mystery. Here, we demonstrate that the yeast inositol depletion-responsive gene locus INO1 partitions to the nuclear envelope, driven by local histone acetylation-induced polymer-polymer phase separation from the nucleoplasmic phase. This demixing is consistent with recent evidence for chromatin phase separation by acetylation-mediated dissolution of multivalent histone association and fits a physical model where increased bending stiffness of acetylated chromatin polymer causes its phase separation from de-acetylated chromatin. Increased chromatin spring stiffness could explain nucleation of transcriptional machinery at active gene loci.

The Histone Variant H2A.Z C-Terminal Domain Has Locus-Specific Differential Effects on H2A.Z Occupancy and Nucleosome Localization.

The incorporation of histone variant H2A.Z into nucleosomes creates specialized chromatin domains that regulate DNA-templated processes, such as gene transcription. In Saccharomyces cerevisiae, the diverging H2A.Z C terminus is thought to provide the H2A.Z exclusive functions. To elucidate the roles of this H2A.Z C terminus genome-wide, we used derivatives in which the C terminus was replaced with the corresponding region of H2A (ZA protein), or the H2A region plus a transcriptional activating peptide (ZA-rII'), with the intent of regenerating the H2A.Z-dependent regulation globally. The distribution of these H2A.Z derivatives indicates that the H2A.Z C-terminal region is crucial for both maintaining the occupation level of H2A.Z and the proper positioning of targeted nucleosomes. Interestingly, the specific contribution on incorporation efficiency versus nucleosome positioning varies enormously depending on the locus analyzed. Specifically, the role of H2A.Z in global transcription regulation relies on its C-terminal region. Remarkably, however, this mostly involves genes without a H2A.Z nucleosome in the promoter. Lastly, we demonstrate that the main chaperone complex which deposits H2A.Z to gene regulatory region (SWR1-C) is necessary to localize all H2A.Z derivatives at their specific loci, indicating that the differential association of these derivatives is not due to impaired interaction with SWR1-C. IMPORTANCE We provide evidence that the Saccharomyces cerevisiae C-terminal region of histone variant H2A.Z can mediate its special function in performing gene regulation by interacting with effector proteins and chaperones. These functional interactions allow H2A.Z not only to incorporate to very specific gene regulatory regions, but also to facilitate the gene expression process. To achieve this, we used a chimeric protein which lacks the native H2A.Z C-terminal region but contains an acidic activating region, a module that is known to interact with components of chromatin-remodeling entities and/or transcription modulators. We reasoned that because this activating region can fulfill the role of the H2A.Z C-terminal region, at least in part, the role of the latter would be to interact with these activating region targets.

From structure to molecular condensates: emerging mechanisms for Mediator function.

Mediator is a large modular protein assembly whose function as a coactivator of transcription is conserved in all eukaryotes. The Mediator complex can integrate and relay signals from gene-specific activators bound at enhancers to activate the general transcription machinery located at promoters. It has thus been described as a bridge between these elements during initiation of transcription. Here, we review recent studies on Mediator relating to its structure, gene specificity and general requirement, roles in chromatin architecture as well as novel concepts involving phase separation and transcriptional bursting. We revisit the mechanism of action of Mediator and ultimately put forward models for its mode of action in gene activation.

In situ study of the evolution of NiFe nanocatalysts in reductive and oxidative environments upon thermal treatments.

The conversion of biomass as a sustainable path to access valuable chemicals and fuels is very attractive for the chemical industry, but catalytic conversions still often rely on the use of noble metals. Sustainability constraints require developing alternative catalysts from abundant and low-cost metals. In this context, NiFe nanoparticles are interesting candidates. In their reduced and supported form, they have been reported to be more active and selective than monometallic Ni in the hydrogenation of the polar functions of organic molecules, and the two metals are very abundant. However, unlike noble metals, Ni and Fe are easily oxidized in ambient conditions, and understanding their transformation in both oxidative and reductive atmospheres is an important though seldom investigated issue to be addressed before their application in catalysis. Three types of NiFe nanoparticles were prepared by an organometallic approach to ensure the formation of ultrasmall nanoparticles (<3.5 nm) with a narrow size distribution, controlled composition and chemical order, while working in mild conditions: Ni2Fe1 and Ni1Fe1, both with a Ni rich core and Fe rich surface, and an alloy with a Ni1Fe9 composition. Supported systems were obtained by the impregnation of silica with a colloidal solution of the preformed nanoparticles. Using advanced characterization techniques, such as wide-angle X-ray scattering (WAXS) and X-ray absorption spectroscopy (XAS) in in situ conditions, this study reports on the evolution of the chemical order and of the oxidation state of the metals upon exposure to air, hydrogen, and/or increasing temperature, all factors that may affect their degree of reduction and subsequent performance in catalysis. We show that if oxidation readily occurs upon exposure to air, the metals can revert to their initial state upon heating in the presence of H2 but with a change in structure and chemical ordering.

Synthesis of NiFeOx nanocatalysts from metal-organic precursors for the oxygen evolution reaction.

Production of hydrogen from a renewable source that is water requires the development of sustainable catalytic processes. This implies, among others, developing efficient catalytic materials from abundant and low-cost resources and investigating their performance, especially in the oxidation of water as this half-reaction is the bottleneck of the water splitting process. For this purpose, NiFe-based nanoparticles with sizes ca. 3-4 nm have been synthesized by an organometallic approach and characterized by complementary techniques (WAXS, TEM, STEM-HAADF, EDX, XPS, and ATR-FTIR). They display a Ni core and a mixed Ni-Fe oxide shell. Once deposited onto FTO electrodes, they have been assessed in the electrocatalytic oxygen evolution reaction under alkaline conditions. Three different Ni/Fe ratios (2/1, 1/1 and 1/9) have been studied in comparison with their monometallic counterparts. The Ni2Fe1 nanocatalyst displayed the lowest overpotential (320 mV at j = 10 mA cm-2) as well as excellent stability over 16 h.

VCSEL pair used as optical pointers in a contact lens for gaze tracking and visual target designation.

We present a new eye-tracking and target designation device based on a contact lens incorporating a pair of vertical-cavity surface-emitting lasers (VCSELs). We describe the operating principle, the manufacturing process and characterize the impact of the VCSELs encapsulation on their optical properties. We then describe how such device can be incorporated into an eye-wear or a visual augmented system. We compare two different detection set-ups, the first using a camera and the second a position sensitive device, both illustrating different laser beam detection modes. We analyze their performances in terms of angular accuracy, speed, compactness, manufacturability, compared to current conventional eye-tracking systems. We emphasize how the use of two VCSELs and the control of their orientation during the encapsulation can simplify their integration in host systems and improve the gaze detection performance. Finally, we describe various embodiments and discuss potential improvements that can be expected in future systems.

The histone chaperone FACT: a guardian of chromatin structure integrity.

The identification of FACT as a histone chaperone enabling transcription through chromatin in vitro has strongly shaped how its roles are envisioned. However, FACT has been implicated in essentially all aspects of chromatin biology, from transcription to DNA replication, DNA repair, and chromosome segregation. In this review, we focus on recent literature describing the role and mechanisms of FACT during transcription. We highlight the prime importance of FACT in preserving chromatin integrity during transcription and challenge its role as an elongation factor. We also review evidence for FACT's role as a cell-type/gene-specific regulator of gene expression and briefly summarize current efforts at using FACT inhibition as an anti-cancer strategy.

Oxygen and magnesium mass-independent isotopic fractionation induced by chemical reactions in plasma.

Enrichment or depletion ranging from -40 to +100% in the major isotopes 16O and 24Mg were observed experimentally in solids condensed from carbonaceous plasma composed of CO2/MgCl2/Pentanol or N2O/Pentanol for O and MgCl2/Pentanol for Mg. In NanoSims imaging, isotope effects appear as micrometer-size hotspots embedded in a carbonaceous matrix showing no isotope fractionation. For Mg, these hotspots are localized in carbonaceous grains, which show positive and negative isotopic effects so that the whole grain has a standard isotope composition. For O, no specific structure was observed at hotspot locations. These results suggest that MIF (mass-independent fractionation) effects can be induced by chemical reactions taking place in plasma. The close agreement between the slopes of the linear correlations observed between δ25Mg versus δ26Mg and between δ17O versus δ18O and the slopes calculated using the empirical MIF factor η discovered in ozone [M. H. Thiemens, J. E. Heidenreich, III. Science 219, 1073-1075; C. Janssen, J. Guenther, K. Mauersberger, D. Krankowsky. Phys. Chem. Chem. Phys 3, 4718-4721] attests to the ubiquity of this process. Although the chemical reactants used in the present experiments cannot be directly transposed to the protosolar nebula, a similar MIF mechanism is proposed for oxygen isotopes: at high temperature, at the surface of grains, a mass-independent isotope exchange could have taken place between condensing oxides and oxygen atoms originated form the dissociation of CO or H2O gas.

FACT is recruited to the +1 nucleosome of transcribed genes and spreads in a Chd1-dependent manner.

The histone chaperone FACT occupies transcribed regions where it plays prominent roles in maintaining chromatin integrity and preserving epigenetic information. How it is targeted to transcribed regions, however, remains unclear. Proposed models include docking on the RNA polymerase II (RNAPII) C-terminal domain (CTD), recruitment by elongation factors, recognition of modified histone tails, and binding partially disassembled nucleosomes. Here, we systematically test these and other scenarios in Saccharomyces cerevisiae and find that FACT binds transcribed chromatin, not RNAPII. Through a combination of high-resolution genome-wide mapping, single-molecule tracking, and mathematical modeling, we propose that FACT recognizes the +1 nucleosome, as it is partially unwrapped by the engaging RNAPII, and spreads to downstream nucleosomes aided by the chromatin remodeler Chd1. Our work clarifies how FACT interacts with genes, suggests a processive mechanism for FACT function, and provides a framework to further dissect the molecular mechanisms of transcription-coupled histone chaperoning.

Connection of core and tail Mediator modules restrains transcription from TFIID-dependent promoters.

The Mediator coactivator complex is divided into four modules: head, middle, tail, and kinase. Deletion of the architectural subunit Med16 separates core Mediator (cMed), comprising the head, middle, and scaffold (Med14), from the tail. However, the direct global effects of tail/cMed disconnection are unclear. We find that rapid depletion of Med16 downregulates genes that require the SAGA complex for full expression, consistent with their reported tail dependence, but also moderately overactivates TFIID-dependent genes in a manner partly dependent on the separated tail, which remains associated with upstream activating sequences. Suppression of TBP dynamics via removal of the Mot1 ATPase partially restores normal transcriptional activity to Med16-depleted cells, suggesting that cMed/tail separation results in an imbalance in the levels of PIC formation at SAGA-requiring and TFIID-dependent genes. We propose that the preferential regulation of SAGA-requiring genes by tailed Mediator helps maintain a proper balance of transcription between these genes and those more dependent on TFIID.

Correlation between surface chemistry and magnetism in iron nanoparticles.

To shed light on the factors governing the stability and surface properties of iron nanoparticles, a series of iron nanoparticles has been produced by hydrogenation of two different iron amido complexes: the bis[bis(trimethylsilyl)amido] Fe(ii), [Fe(N(SiMe3)2)2]2, and the bis(diphenylamido) Fe(ii), [Fe(NPh2)2]. Nanostructured materials of bcc structure, or nanoparticles displaying average sizes below 3 nm and a polytetrahedral structure, have been obtained. Depending on the synthesis conditions, the magnetization of the nanoparticles was either significantly lower than that of bulk iron, or much higher as for clusters elaborated under high vacuum conditions. Unexpectedly, hydrogenation of aromatic groups of the ligands of the [Fe(NPh2)2] precursor has been observed in some cases. Confrontation of the experimental results with DFT calculations made on polytetrahedral Fe91 model clusters bearing hydrides, amido and/or amine ligands at their surface, has shown that amido ligands can play a key role in the stabilisation of the nanoparticles in solution while the hydride surface coverage governs their surface magnetic properties. This study indicates that magnetic measurements give valuable indicators of the surface properties of iron nanoparticles in this size range, and beyond, of their potential reactivity.

The deubiquitylase Ubp15 couples transcription to mRNA export.

Nuclear export of messenger RNAs (mRNAs) is intimately coupled to their synthesis. pre-mRNAs assemble into dynamic ribonucleoparticles as they are being transcribed, processed, and exported. The role of ubiquitylation in this process is increasingly recognized but, while a few E3 ligases have been shown to regulate nuclear export, evidence for deubiquitylases is currently lacking. Here we identified deubiquitylase Ubp15 as a regulator of nuclear export in Saccharomyces cerevisiae. Ubp15 interacts with both RNA polymerase II and the nuclear pore complex, and its deletion reverts the nuclear export defect of E3 ligase Rsp5 mutants. The deletion of UBP15 leads to hyper-ubiquitylation of the main nuclear export receptor Mex67 and affects its association with THO, a complex coupling transcription to mRNA processing and involved in the recruitment of mRNA export factors to nascent transcripts. Collectively, our data support a role for Ubp15 in coupling transcription to mRNA export.