OIST Institutional Repository
Not a member yet
2744 research outputs found
Sort by
New variants of AADC deficiency expand the knowledge of enzymatic phenotypes
Get PDFAADC deficiency is a rare genetic disease caused by mutations in the gene of aromatic amino acid decarboxylase, the pyridoxal 5'-phosphate dependent enzyme responsible for the synthesis of dopamine and serotonin. Here, following a biochemical approach together with an in silico bioinformatic analysis, we present a structural and functional characterization of 13 new variants of AADC. The amino acid substitutions are spread over the entire protein from the N-terminal (V60A), to its loop1 (H70Y and F77L), to the large domain (G96R) and its various motifs, i.e. loop2 (A110E), or a core beta-barrel either on the surface (P210L, F251S and E283A) or in a more hydrophobic milieu (L222P, F237S and W267R) or loop3 (L353P), and to the C-terminal domain (R453C). Results show that the beta-barrel variants exhibit a low solubility and those belonging to the surface tend to aggregate in their apo form, leading to the identification of a new enzymatic phenotype for AADC deficiency. Moreover, five variants of residues belonging to the large interface of AADC (V60A, G96R, A110E, L353P and R453C) are characterized by a decreased catalytic efficiency. The remaining ones (H70Y and F77L) present features typical of apo-to-holo impaired transition. Thus, defects in catalysis or in the acquirement of the correct holo structure are due not only to specific local domain effects but also to long-range effects at either the protein surface or the subunit interface. Altogether, the new characterized enzymatic phenotypes represent a further step in the elucidation of the molecular basis for the disease.journal articl
The Neandertal Progesterone Receptor
Get PDFThe hormone progesterone is important for preparing the uterine lining for egg implantation and for maintaining the early stages of pregnancy. The gene encoding the progesterone receptor (PGR) carries introgressed Neandertal haplotypes with two missense substitutions and a mobile Alu element. These Neandertal gene variants have reached nearly 20% frequency in non-Africans and have been associated with preterm birth. Here, we show that one of the missense substitutions appears fixed in Neandertals, while the other substitution as well as the Alu insertion were polymorphic among Neandertals. We show that two Neandertal haplotypes carrying the PGR gene entered the modern human population and that present-day carriers of the Neandertal haplotypes express higher levels of the receptor. In a cohort of present-day Britons, these carriers have more siblings, fewer miscarriages, and less bleeding during early pregnancy suggesting that the Neandertal progesterone receptor alleles promote fertility. This may explain their high frequency in modern human populations.journal articl
Feshbach engine in the Thomas-Fermi regime
Get PDFBose-Einstein condensates can be used to produce work by tuning the strength of the interparticle interactions with the help of Feshbach resonances. In inhomogeneous potentials, these interaction ramps change the volume of the trapped gas, allowing one to create a thermodynamic cycle known as the Feshbach engine. However, in order to obtain a large power output, the engine strokes must be performed on a short timescale, which is in contrast to the fact that the efficiency of the engine is reduced by irreversible work if the strokes are done in a nonadiabatic fashion. Here we investigate how such an engine can be run in the Thomas-Fermi regime and present a shortcut to adiabaticity that minimizes the irreversible work and allows for efficient engine operation.journal articl
Increased Mutation Rate Is Linked to Genome Reduction in Prokaryotes
Get PDFThe evolutionary processes that drive variation in genome size across the tree of life remain unresolved. Effective population size (Ne) is thought to play an important role in shaping genome size [1, 2, 3]—a key example being the reduced genomes of insect endosymbionts, which undergo population bottlenecks during transmission [4]. However, the existence of reduced genomes in marine and terrestrial prokaryote species with large Ne indicate that genome reduction is influenced by multiple processes [3]. One candidate process is enhanced mutation rate, which can increase adaptive capacity but can also promote gene loss. To investigate evolutionary forces associated with prokaryotic genome reduction, we performed molecular evolutionary and phylogenomic analyses of nine lineages from five bacterial and archaeal phyla. We found that gene-loss rate strongly correlated with synonymous substitution rate (a proxy for mutation rate) in seven of the nine lineages. However, gene-loss rate showed weak or no correlation with the ratio of nonsynonymous/synonymous substitution rate (dN/dS). These results indicate that genome reduction is largely associated with increased mutation rate, while the association between gene loss and changes in Ne is less well defined. Lineages with relatively high dS and dN, as well as smaller genomes, lacked multiple DNA repair genes, providing a proximate cause for increased mutation rates. Our findings suggest that similar mechanisms drive genome reduction in both intracellular and free-living prokaryotes, with implications for developing a comprehensive theory of prokaryote genome size evolution.journal articl
Using Modern Conservation Tools for Innovative Management of Coral Reefs: The MANACO Consortium
Get PDFCoral reefs are under threat and innovative management strategies are urgently required. However, discoveries from innovative fields of coral reef research are rarely transposed in practical conservation actions. This is mainly due to the difficulties in knowledge exchange between scientists and conservation stakeholders. The ManaCo consortium (http://manaco.ird.nc/) is an international network federating conservation stakeholders and researchers in a common effort to preserve the coral reefs. The focus is on using modern tools to build a bridge between indigenous knowledge and scientific innovation. ManaCo aims to orientate research toward relevant conservation needs and to facilitate the transposition of research into concrete management strategies. This will allow to coordinate a collaborative response against coral reef decline. We invite anyone sharing the same interests in joining us.journal articl
Graphene Nanoribbons: On‐Surface Synthesis and Integration into Electronic Devices
Get PDFGraphene nanoribbons (GNRs) are quasi-1D graphene strips, which have attracted attention as a novel class of semiconducting materials for various applications in electronics and optoelectronics. GNRs exhibit unique electronic and optical properties, which sensitively depend on their chemical structures, especially the width and edge configuration. Therefore, precision synthesis of GNRs with chemically defined structures is crucial for their fundamental studies as well as device applications. In contrast to top-down methods, bottom-up chemical synthesis using tailor-made molecular precursors can achieve atomically precise GNRs. Here, the synthesis of GNRs on metal surfaces under ultrahigh vacuum (UHV) and chemical vapor deposition (CVD) conditions is the main focus, and the recent progress in the field is summarized. The UHV method leads to successful unambiguous visualization of atomically precise structures of various GNRs with different edge configurations. The CVD protocol, in contrast, achieves simpler and industry-viable fabrication of GNRs, allowing for the scale up and efficient integration of the as-grown GNRs into devices. The recent updates in device studies are also addressed using GNRs synthesized by both the UHV method and CVD, mainly for transistor applications. Furthermore, views on the next steps and challenges in the field of on-surface synthesized GNRs are provided.journal articl
Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus
Get PDFSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently emerged to cause widespread infections in humans. SARS-CoV-2 infections have been reported in the Kingdom of Saudi Arabia, where Middle East respiratory syndrome coronavirus (MERS-CoV) causes seasonal outbreaks with a case fatality rate of ~37 %. Here we show that there exists a theoretical possibility of future recombination events between SARS-CoV-2 and MERS-CoV RNA. Through computational analyses, we have identified homologous genomic regions within the ORF1ab and S genes that could facilitate recombination, and have analysed co-expression patterns of the cellular receptors for SARS-CoV-2 and MERS-CoV, ACE2 and DPP4, respectively, to identify human anatomical sites that could facilitate co-infection. Furthermore, we have investigated the likely susceptibility of various animal species to MERS-CoV and SARS-CoV-2 infection by comparing known virus spike protein–receptor interacting residues. In conclusion, we suggest that a recombination between SARS-CoV-2 and MERS-CoV RNA is possible and urge public health laboratories in high-risk areas to develop diagnostic capability for the detection of recombined coronaviruses in patient samples.journal articl
Influence of Regional Oceanography and Hydrothermal Activity on Protist Diversity and Community Structure in the Okinawa Trough
Get PDFMicrobial eukaryotes (protists) contribute substantially to ecological functioning in marine ecosystems, but the relative importance of factors shaping protist diversity, such as environmental selection and dispersal, remains difficult to parse. Water masses of a back-arc basin with hydrothermal activity provide a unique opportunity for studying the effects of dispersal and environmental selection on protist communities. In this study, we used metabarcoding to characterize protist communities in the Okinawa Trough, a back-arc spreading basin containing at least twenty-five active hydrothermal vent fields. Water was sampled from four depths at fourteen stations spanning the length of the Okinawa Trough, including three sites influenced by nearby hydrothermal vent sites. While significant differences in community structure reflecting water depth were present, protist communities were mostly homogeneous horizontally. Protist communities in the bottom waters affected by hydrothermal activity were significantly different from communities in other bottom waters, suggesting that environmental factors can be especially important in shaping community composition under specific conditions. Amplicon sequence variants that were enriched in hydrothermally influenced bottom waters largely derived from cosmopolitan protists that were present, but rare, in other near-bottom samples, thus highlighting the importance of the rare biosphere.journal articl
Spin selection in single-frequency two-photon excitation of alkali-metal atoms
Get PDFWe develop a theoretical framework for spin selection in single-frequency two-photon excitation of alkali-metal atoms as a function of polarization of the excitation light. We verify the theory by experimentally probing the [Formula: see text] transition rate in ⁸⁷Rb in two configurations: paraxial light excitation of warm vapor and nonparaxial excitation of laser-cooled atoms. The transition rate follows a quadratic dependence on the helicity parameter linked to the excitation light's polarization. For paraxial excitation, the transition rate scales as the squared degree of linear polarization, being zero for circularly polarized light. In contrast, for nonparaxial excitation via an optical nanofiber, the two-photon transition is not completely extinguished by varying the light polarization. Our findings lead to a deeper and more universal understanding of the physics of multiphoton processes in atoms.journal articl
Magnetization plateau observed by ultrahigh-field Faraday rotation in the kagome antiferromagnet herbertsmithite
Get PDFTo capture the high-field magnetization process of herbertsmithite [ZnCu₃(OH)₆Cl₂], Faraday rotation (FR) measurements were carried out on a single crystal in magnetic fields of up to 190 T. The magnetization data evaluated from the FR angle exhibited a saturation behavior above 150 T at low temperatures, which was attributed to the 1/3 magnetization plateau. The overall behavior of the magnetization process was reproduced by theoretical models based on the nearest-neighbor Heisenberg model. This suggests that herbertsmithite is a proximate kagome antiferromagnet hosting an ideal quantum spin liquid in the ground state. A distinguishing feature is the superlinear magnetization increase, which is in contrast to the Brillouin function-type increase observed by conventional magnetization measurements and indicates a reduced contribution from free spins located at the Zn sites to the FR signal.journal articl