Fourfold Differential Photoelectron Circular Dichroism

We report on a joint experimental and theoretical study of photoelectron circular dichroism (PECD) in methyloxirane. By detecting O 1s photoelectrons in coincidence with fragment ions, we deduce the molecule's orientation and photoelectron emission direction in the laboratory frame. Thereby, we retrieve a fourfold differential PECD clearly beyond 50%. This strong chiral asymmetry is reproduced by ab initio electronic structure calculations. Providing such a pronounced contrast makes PECD of fixed-in-space chiral molecules an even more sensitive tool for chiral recognition in the gas phase.

Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

Time zero determination for FEL pump-probe studies based on ultrafast melting of bismuth

A common challenge for pump-probe studies of structural dynamics at X-ray free-electron lasers (XFELs) is the determination of time zero (T₀)-the time an optical pulse (e.g., an optical laser) arrives coincidently with the probe pulse (e.g., a XFEL pulse) at the sample position. In some cases, T₀ might be extracted from the structural dynamics of the sample's observed response itself, but generally, an independent robust method is required or would be superior to the inferred determination of T₀. In this paper, we present how the structural dynamics in ultrafast melting of bismuth can be exploited for a quickly performed, reliable and accurate determination of T₀ with a precision below 20 fs and an overall experimental accuracy of 50 fs to 150 fs (estimated). Our approach is potentially useful and applicable for fixed-target XFEL experiments, such as serial femtosecond crystallography, utilizing an optical pump pulse in the ultraviolet to near infrared spectral range and a pixelated 2D photon detector for recording crystallographic diffraction patterns in transmission geometry. In comparison to many other suitable approaches, our method is fairly independent of the pumping wavelength (UV-IR) as well as of the X-ray energy and offers a favorable signal contrast. The technique is exploitable not only for the determination of temporal characteristics of the experiment at the interaction point but also for investigating important conditions affecting experimental control such as spatial overlap and beam spot sizes.

Accurate prediction of X-ray pulse properties from a free-electron laser using machine learning

Free-electron lasers providing ultra-short high-brightness pulses of X-ray radiation have great potential for a wide impact on science, and are a critical element for unravelling the structural dynamics of matter. To fully harness this potential, we must accurately know the X-ray properties: intensity, spectrum and temporal profile. Owing to the inherent fluctuations in free-electron lasers, this mandates a full characterization of the properties for each and every pulse. While diagnostics of these properties exist, they are often invasive and many cannot operate at a high-repetition rate. Here, we present a technique for circumventing this limitation. Employing a machine learning strategy, we can accurately predict X-ray properties for every shot using only parameters that are easily recorded at high-repetition rate, by training a model on a small set of fully diagnosed pulses. This opens the door to fully realizing the promise of next-generation high-repetition rate X-ray lasers.

Charge transfer to ground-state ions produces free electrons

Inner-shell ionization of an isolated atom typically leads to Auger decay. In an environment, for example, a liquid or a van der Waals bonded system, this process will be modified, and becomes part of a complex cascade of relaxation steps. Understanding these steps is important, as they determine the production of slow electrons and singly charged radicals, the most abundant products in radiation chemistry. In this communication, we present experimental evidence for a so-far unobserved, but potentially very important step in such relaxation cascades: Multiply charged ionic states after Auger decay may partially be neutralized by electron transfer, simultaneously evoking the creation of a low-energy free electron (electron transfer-mediated decay). This process is effective even after Auger decay into the dicationic ground state. In our experiment, we observe the decay of Ne²⁺ produced after Ne 1s photoionization in Ne-Kr mixed clusters.

Time-Resolved Measurement of Interatomic Coulombic Decay Induced by Two-Photon Double Excitation of Ne_{2}

The hitherto unexplored two-photon doubly excited states [Ne^{*}(2p^{-1}3s)]_{2} were experimentally identified using the seeded, fully coherent, intense extreme ultraviolet free-electron laser FERMI. These states undergo ultrafast interatomic Coulombic decay (ICD), which predominantly produces singly ionized dimers. In order to obtain the rate of ICD, the resulting yield of Ne_{2}^{+} ions was recorded as a function of delay between the extreme ultraviolet pump and UV probe laser pulses. The extracted lifetimes of the long-lived doubly excited states, 390(-130/+450)  fs, and of the short-lived ones, less than 150 fs, are in good agreement with ab initio quantum mechanical calculations.

Slow Interatomic Coulombic Decay of Multiply Excited Neon Clusters

Ne clusters (∼5000  atoms) were resonantly excited (2p→3s) by intense free electron laser (FEL) radiation at FERMI. Such multiply excited clusters can decay nonradiatively via energy exchange between at least two neighboring excited atoms. Benefiting from the precise tunability and narrow bandwidth of seeded FEL radiation, specific sites of the Ne clusters were probed. We found that the relaxation of cluster surface atoms proceeds via a sequence of interatomic or intermolecular Coulombic decay (ICD) processes while ICD of bulk atoms is additionally affected by the surrounding excited medium via inelastic electron scattering. For both cases, cluster excitations relax to atomic states prior to ICD, showing that this kind of ICD is rather slow (picosecond range). Controlling the average number of excitations per cluster via the FEL intensity allows a coarse tuning of the ICD rate.

Interatomic Coulombic decay cascades in multiply excited neon clusters

In high-intensity laser light, matter can be ionized by direct multiphoton absorption even at photon energies below the ionization threshold. However on tuning the laser to the lowest resonant transition, the system becomes multiply excited, and more efficient, indirect ionization pathways become operative. These mechanisms are known as interatomic Coulombic decay (ICD), where one of the species de-excites to its ground state, transferring its energy to ionize another excited species. Here we show that on tuning to a higher resonant transition, a previously unknown type of interatomic Coulombic decay, intra-Rydberg ICD occurs. In it, de-excitation of an atom to a close-lying Rydberg state leads to electron emission from another neighbouring Rydberg atom. Moreover, systems multiply excited to higher Rydberg states will decay by a cascade of such processes, producing even more ions. The intra-Rydberg ICD and cascades are expected to be ubiquitous in weakly-bound systems exposed to high-intensity resonant radiation.

Interatomic Coulombic decay (ICD) is a relaxation of an atom in a weakly bound environment by the transfer of excess energy to ionize the neighbouring atom. Here the authors observe intra-Rydberg ICD in neon clusters, which is a decay that involves the ionization of Rydberg atoms in the cluster.

Femtosecond charge and molecular dynamics of I-containing organic molecules induced by intense X-ray free-electron laser pulses

We studied the electronic and nuclear dynamics of I-containing organic molecules induced by intense hard X-ray pulses at the XFEL facility SACLA in Japan. The interaction with the intense XFEL pulse causes absorption of multiple X-ray photons by the iodine atom, which results in the creation of many electronic vacancies (positive charges) via the sequential electronic relaxation in the iodine, followed by intramolecular charge redistribution. In a previous study we investigated the subsequent fragmentation by Coulomb explosion of the simplest I-substituted hydrocarbon, iodomethane (CH₃I). We carried out three-dimensional momentum correlation measurements of the atomic ions created via Coulomb explosion of the molecule and found that a classical Coulomb explosion model including charge evolution (CCE-CE model), which accounts for the concerted dynamics of nuclear motion and charge creation/charge redistribution, reproduces well the observed momentum correlation maps of fragment ions emitted after XFEL irradiation. Then we extended the study to 5-iodouracil (C₄H₃IN₂O₂, 5-IU), which is a more complex molecule of biological relevance, and confirmed that, in both CH₃I and 5-IU, the charge build-up takes about 10 fs, while the charge is redistributed among atoms within only a few fs. We also adopted a self-consistent charge density-functional based tight-binding (SCC-DFTB) method to treat the fragmentations of highly charged 5-IU ions created by XFEL pulses. Our SCC-DFTB modeling reproduces well the experimental and CCE-CE results. We have also investigated the influence of the nuclear dynamics on the charge redistribution (charge transfer) using nonadiabatic quantum-mechanical molecular dynamics (NAQMD) simulation. The time scale of the charge transfer from the iodine atomic site to the uracil ring induced by nuclear motion turned out to be only ∼5 fs, indicating that, besides the molecular Auger decay in which molecular orbitals delocalized over the iodine site and the uracil ring are involved, the nuclear dynamics also play a role for ultrafast charge redistribution. The present study illustrates that the CCE-CE model as well as the SCC-DFTB method can be used for reconstructing the positions of atoms in motion, in combination with the momentum correlation measurement of the atomic ions created via XFEL-induced Coulomb explosion of molecules.

Characterization of Carbonic Anhydrase Isozyme CA2, Which Is theCAH2Gene Product, inChlamydomonas reinhardtii

From high-CO2 (5% CO2) grown unicellular green alga, Chlamydomonas reinhardtii, carbonic anhydrase (CA) was isolated by affinity chromatography and characterized. Isolated CA was identified as an isozyme (CA2) which is the product from the second gene CAH2 by peptide sequencing. The CA2 was inactivated by dithiothreitol. This treatment caused dissociation of CA2 into the large (38 kDa) and small subunits (4243 Da). The molecular mass of the CA2 holoenzyme measured by low-angle laser light-scattering photometry and precision differential refractometry combined with gel-filtration HPLC was 87.9 kDa. These results and gene structure indicate that CA2 is a heterotetramer consisting of two large and two small subunits linked by disulfide bonds like CA1, which is the CAH1 gene product. The specific activity of CA2 purified by anion-exchange HPLC was 3300 units per mg protein, which was approximately 1.6 times higher than that of CA1. Therefore, it was concluded that two structurally related isozymes, CA1 and CA2, are present in the wild type cells of C. reinhardtii and differentially regulated by the atmospheric CO2 concentration.

Deep inner-shell multiphoton ionization by intense x-ray free-electron laser pulses

We have investigated multiphoton multiple ionization dynamics of xenon atoms using a new x-ray free-electron laser facility, SPring-8 Angstrom Compact free electron LAser (SACLA) in Japan, and identified that Xe(n+) with n up to 26 is produced at a photon energy of 5.5 keV. The observed high charge states (n≥24) are produced via five-photon absorption, evidencing the occurrence of multiphoton absorption involving deep inner shells. A newly developed theoretical model, which shows good agreement with the experiment, elucidates the complex pathways of sequential electronic decay cascades accessible in heavy atoms. The present study of heavy-atom ionization dynamics in high-intensity hard-x-ray pulses makes a step forward towards molecular structure determination with x-ray free-electron lasers.

Second-order autocorrelation of XUV FEL pulses via time resolved two-photon single ionization of He

Second-order autocorrelation spectra of XUV free-electron laser pulses from the Spring-8 Compact SASE Source (SCSS) have been recorded by time and momentum resolved detection of two-photon single ionization of He at 20.45 eV using a split-mirror delay-stage in combination with high-resolution recoil-ion momentum spectroscopy (COLTRIMS). From the autocorrelation trace we extract a coherence time of 8 ± 2 fs and a mean pulse duration of 28 ± 5 fs, much shorter than estimations based on electron bunch-length measurements. Simulations within the partial coherence model [Opt. Lett. 35, 3441 (2010)] are in agreement with experiment if a pulse-front tilt across the FEL beam diameter is taken into account that leads to a temporal shift of about 6 fs between both pulse replicas.

Three-electron interatomic Coulombic decay from the inner-valence double-vacancy states in NeAr

We have unambiguously identified interatomic Coulombic decay in NeAr from the inner-valence double-vacancy state Ne-Ar(2+)(3s(-2)) to outer-valence triple-vacancy states Ne(+)(2p(-1))-Ar(2+)(3p(-2)) by momentum-resolved electron-ion multicoincidence. This is the first observation of interatomic Coulombic decay where three electrons (3e) participate. The results suggest that this 3e interatomic Coulombic decay is significantly faster than other competing processes like fluorescence decay and charge transfer via curve crossing.

Electron-transfer-mediated decay and interatomic Coulombic decay from the triply ionized states in argon dimers

We report the first observation of electron-transfer-mediated decay (ETMD) and interatomic Coulombic decay (ICD) from the triply charged states with an inner-valence vacancy, using the Ar dimer as an example. These ETMD and ICD processes, which lead to fragmentation of Ar(3+)-Ar into Ar(2+)-Ar(2+) and Ar(3+)-Ar+, respectively, are unambiguously identified by electron-ion-ion coincidence spectroscopy in which the kinetic energy of the ETMD or ICD electron and the kinetic energy release between the two fragment ions are measured in coincidence.

Enhancement of magnetoresistance by hydrogen ion treatment for current-perpendicular-to-plane giant magnetoresistive films with a current-confined-path nano-oxide layer

We have enhanced magnetoresistance (MR) for current-perpendicular-to-plane giant-magnetoresistive (CPP-GMR) films with a current-confined-path nano-oxide layer (CCP-NOL). In order to realize higher purity in Cu for CCPs, hydrogen ion treatment (HIT) was applied as the CuO(x) reduction process. By applying the HIT process, an MR ratio was increased to 27.4% even in the case of using conventional FeCo magnetic layer, from 13.0% for a reference without the HIT process. Atom probe tomography data confirmed oxygen reduction by the HIT process in the CCP-NOL. The relationship between oxygen counts and MR ratio indicates that further oxygen reduction would realize an MR ratio greater than 50%.

Site-specific behavior in de-excitation spectra of F(3)SiCH(2)CH(2)Si(CH(3))(3) in the Si 1s excitation region

Excitation (total ion yield) and de-excitation (resonant photoemission) spectra have been measured in the Si 1s photoexcitation region of the F(3)SiCH(2)CH(2)Si(CH(3))(3) molecule using monochromatized undulator radiation. Theoretical calculations within the framework of density functional theory have reproduced the observed total ion yield spectrum very well. The first peak at the lowest photon energy, coming from Si 1s excitation at the trimethyl side into a vacant orbital, induces spectator Auger decays in which the excited electron remains in its valence orbital. The second peak produced through excitation of Si 1s electron at the trifluoride side generates resonant Auger decays in which the excited valence electron remains predominantly also in the valence orbital or is partly shaken up into higher Rydberg orbitals. The third peak generated through Si 1s excitation at the trifluoride side produces resonant Auger decays in which the excited Rydberg electron remains or is partly shaken down to a lower lying valence molecular orbital. These findings exhibit a clear distinction between resonant Auger decays following photoexcitation of Si 1s electrons under different chemical environments.

Photo- and auger-electron recoil induced dynamics of interatomic Coulombic decay

At photon energies near the Ne K edge it is shown that for 1s ionization the Auger electron, and for 2s ionization the fast photoelectron, launch vibrational wave packets in a Ne dimer. These wave packets then decay by emission of a slow electron via interatomic Coulombic decay (ICD). The measured and computed ICD electron spectra are shown to be significantly modified by the recoil induced nuclear motion.

Cold-target recoil-ion momentum spectroscopy for diagnostics of high harmonics of the extreme-ultraviolet free-electron laser light source at SPring-8

We have developed a cold-target recoil-ion momentum spectroscopy apparatus dedicated to the experiments using the extreme-ultraviolet light pulses at the free-electron laser facility, SPring-8 Compact SASE Source test accelerator, in Japan and used it to measure spatial distributions of fundamental, second, and third harmonics at the end station.

Molecular-frame angular distributions of resonant CO:C(1s) Auger electrons

The molecular-frame angular distributions of resonantly excited CO:C(1s) --> pi* Auger electrons were determined using angle-resolved electron-ion coincidence spectroscopy in combination with a novel transformation procedure. Our new methodology yields full three-dimensional electron angular distributions with high energy resolution from the measurement of electrons at only two angles. The experimentally determined distributions are well reproduced by calculations performed in a simple one-center approximation, allowing an unambiguous identification of several overlapping Auger lines.

Is CO carbon KVV Auger electron emission affected by the photoelectron?

Angular distributions (ADs) of O+ fragments from C 1s photoexcited CO detected in coincidence with carbon KVV Auger electrons emitted in the horizontal direction were measured at photon energies of 298, 305, 320, and 450 eV. At 450 eV, the ADs are polarization-independent and coincide with the molecular-frame Auger electron angular distribution. All measured ADs can be rationalized as a product of the same molecular-frame Auger electron angular distribution and the axial selectivity in the photoionization process. Thus the interaction between the photoelectron and the Auger electron for the normal Auger decay of CO can be neglected, and the two-step model is a good approximation.

Breakdown of the two-step model in K-shell photoemission and subsequent decay probed by the molecular-frame photoelectron angular distributions of CO2

We report results of measurements and of Hartree-Fock level calculations of molecular-frame photoelectron angular distributions (MFPADs) for C 1s photoemission from CO2. The agreement between the measured and calculated MFPADs is on average reasonable. The measured MFPADs display a weak but definite asymmetry with respect to the O+ and CO+ fragment ions at certain energies, providing evidence for an overlap of gerade and ungerade final ionic states giving rise to a partial breakdown of the two-step model of core-level photoionization and its subsequent Auger decay.

Internal inelastic scattering satellite probed by molecular-frame photoelectron angular distributions from CO2

The molecular-frame photoelectron angular distribution (MFPAD) of the satellite accompanying the C 1s photoline of the CO2 molecule has been measured at the C 1s(2sigmag)-->4sigmau* shape resonance, using electron-ion multicoincidence momentum spectroscopy. The observed MFPAD indicates that the conjugate satellite is excited by internal inelastic scattering. In this scenario, a photoelectron is ejected from the C 1s(2sigmag) orbital along the molecular axis and collides with an O lone-pair electron in the highest occupied molecular orbital 1pig. Then one of the colliding electrons is trapped to the lowest unoccupied molecular orbital 2piu*, while the other is emitted as a satellite photoelectron of sigmag symmetry, losing the information of the original photoelectron emission direction and parity.

Acclimation to low [CO(2)] by an inorganic carbon-concentrating mechanism in Cyanophora paradoxa

The glaucocystophyte Cyanophora paradoxa contains cyanelles, plastids with prokaroytic features such as a peptidoglycan wall and a central proteinaceous inclusion body. While this central body includes the majority of the enzyme ribulose 1,5-bisphosphate carboxylase/oxgenase Rubisco), the presence of a carbon-concentrating mechanism (CCM) in C. paradoxa has only been hypothesized. Here, we present physiological data in support of a CCM: CO(2) exchange activity as well as apparent affinity against inorganic carbon were found to increase under CO(2)-limiting stress. Further, expressed sequence tags (ESTs) of C. paradoxa were obtained from two cDNA libraries, one from cells grown in high [CO(2)] conditions and one from cells grown under low [CO(2)] conditions. A cDNA microarray platform assembled from 2378 cDNA sequences revealed that 142 genes significantly responded to a shift from high to low [CO(2)]. Trends in gene expression were comparable to those reported for Chlamydomonas reinhardtii and the cyanobacterium Synechocystis 6803, both possessing a CCM. Among genes regulated by [CO(2)], transcripts were identified encoding carbonic anhydrases (CAs), Rubisco activase and a putative bicarbonate transporter in C. paradoxa, likely functionally involved in the CCM. These results and the polyhedric appearance of the central body further support the hypothesis of a unique 'eukaryotic carboxysome' in Cyanophora.

Combining high mass resolution and velocity imaging in a time-of-flight ion spectrometer using pulsed fields and an electrostatic lens

We describe a momentum resolving time-of-flight ion mass spectrometer that combines a high mass resolution, a velocity focusing condition for improved momentum resolution, and field-free conditions in the source region for high resolution electron detection. It is used in electron-ion coincidence experiments to record multiple ionic fragments produced in breakup reactions of small to medium sized molecules, such as F(3)SiCH(2)CH(2)Si(CH(3))(3). These breakup reactions are caused by soft x rays or intense laser fields. The ion spectrometer uses pulsed extraction fields, an electrostatic lens, and a delay line detector to resolve the position. Additionally, we describe a simple analytical method for calculating the momentum from the measured hit position and the time of flight of the ions.

The transcriptional program of synchronous gametogenesis in Chlamydomonas reinhardtii

Cells of Chlamydomonas reinhardtii undergo gametogenesis to produce sexually competent gametes under nitrogen-starved conditions. By using a synchronized system for gametogenesis of early G1 cells, several previously identified marker genes and 18 novel nitrogen-starved gametogenesis (NSG) genes isolated by macroarray analysis were placed into at least three temporal classes of expression. Early genes are induced transiently in the first 2 h after transfer to nitrogen-free medium. Middle genes are strongly induced between 3 h and 4 h after nitrogen removal, a time corresponding to the acquisition of mating competency, suggesting their involvement in the gamete program. Late genes are induced between 5 h and 8 h after nitrogen removal, a time after the completion of gametic differentiation, suggesting that they are not directly involved in the formation of sexually competent gametes. All of the 18 NSG genes examined are induced in both mating-type plus and minus gametes and about two-thirds of the genes are also expressed in the mitotic cell cycle, especially at S/M phases.

Involvement of tumor necrosis factor alpha in intestinal epithelial cell proliferation following Paneth cell destruction

BACKGROUND

An intravenous injection of diphenylthiocarbazone (dithizone), a zinc chelator, induces selective killing of Paneth cells which have a large amount of zinc in their cytoplasmic granules. A transient wave of intestinal epithelial cell proliferation occurs at 12 h after the injection. Paneth cells have tumor necrosis factor (TNF)-alpha protein in their cytoplasmic granules, and TNF-alpha has a proliferative effect on intestinal epithelial cells in vitro. The aim of this study is to clarify the in vivo role of TNF-alpha in intestinal epithelial cell proliferation using a dithizone-treated rat model.

METHODS

Male Wistar rats received a dithizone (100 mg/kg of body weight) injection with or without TNF-alpha inhibitor, pentoxifylline (100 mg/kg), neutralizing anti-TNF-alpha antibody (2 mg/kg), or nuclear transcription factor kappaB (NF-kappaB) inhibitors: pyrrolidine dithiocarbamate (100 mg/kg) or N-acetyl-L-cystein (100 mg/kg). The activation of NF-kappaB was examined by the electrophoretic mobility shift assay, and cellular proliferation by BrdU labeling.

RESULTS

Without any inhibitors, dithizone treatment evoked NF-kappaB activation in the ileal mucosa with its peak level at 2 h after the injection. TNF-alpha inhibition reduced the NF-kappaB activation, and blocked a transient wave of epithelial cell proliferation 12 h after the injection. NF-kappaB inhibitors also reduced the NF-kappaB activation and epithelial cell proliferation.

CONCLUSIONS

TNF-alpha released from degenerated Paneth cells was, in part, responsible for the intestinal cell proliferation through the activation of NF-kappaB, suggesting its proliferative effect on intestinal epithelial cells.

Characteristics and sequence of phosphoglycolate phosphatase from a eukaryotic green alga Chlamydomonas reinhardtii

Phosphoglycolate phosphatase (PGPase), a key enzyme of photorespiration in photosynthetic organisms, was purified from Chlamydomonas reinhardtii. The enzyme was an approximately 65-kDa homodimer with a pI value of 5.1 composed of approximately 32-kDa subunits not connected by any S-S bridges. It was also highly specific for phosphoglycolate with a K(m) value of 140 microm and an optimal pH between 8 and 9. The activity was strongly inhibited by CaCl(2), and it recovered competitively following the addition of MgCl(2) or EGTA. A mobility shift was observed in SDS-polyacrylamide gel electrophoresis by the addition of CaCl(2), indicating that the enzyme binds to Ca(2+). The N-terminal region of amino acid sequence deduced from cDNA sequence that was not contained in the purified PGPase had similar characteristics to those of typical stroma-targeting transit peptides in C. reinhardtii. The following region of the deduced sequence containing 302 amino acid residues was similar to p-nitrophenylphosphatase-like proteins, although the purified PGPase did not hydrolyze p-nitrophenylphosphate. Genomic DNA fragments from wild type containing the sequence homologous to the cDNA for PGPase complemented the PGPase-deficient mutant pgp1. Possible regulatory mechanisms during adaptation to limiting CO(2) were discussed based on the characteristics of the purified PGPase and the deduced amino acid sequence.

Isolation of X and Y chromosome-specific DNA markers from a liverwort, Marchantia polymorpha, by representational difference analysis

The liverwort Marchantia polymorpha has X and Y chromosomes in the respective female and male haploids. Here we report the successful exploitation of representational difference analyses to isolate DNA markers for the sex chromosomes. Two female-specific and six male-specific DNA fragments were genetically confirmed to originate from the X and Y chromosomes, respectively.

Distinct constitutive and low-CO2-induced CO2 uptake systems in cyanobacteria: genes involved and their phylogenetic relationship with homologous genes in other organisms

Cyanobacteria possess a CO(2)-concentrating mechanism that involves active CO(2) uptake and HCO(3)(-) transport. For CO(2) uptake, we have identified two systems in the cyanobacterium Synechocystis sp. strain PCC 6803, one induced at low CO(2) and one constitutive. The low CO(2)-induced system showed higher maximal activity and higher affinity for CO(2) than the constitutive system. On the basis of speculation that separate NAD(P)H dehydrogenase complexes were essential for each of these systems, we reasoned that inactivation of one system would allow selection of mutants defective in the other. Thus, mutants unable to grow at pH 7.0 in air were recovered after transformation of a DeltandhD3 mutant with a transposon-bearing library. Four of them had tags within slr1302 (designated cupB), a homologue of sll1734 (cupA), which is cotranscribed with ndhF3 and ndhD3. The DeltacupB, DeltandhD4, and DeltandhF4 mutants showed CO(2)-uptake characteristics of the low CO(2)induced system observed in wild type. In contrast, mutants DeltacupA, DeltandhD3, and DeltandhF3 showed characteristics of the constitutive CO(2)-uptake system. Double mutants impaired in one component of each of the systems were unable to take up CO(2) and required high CO(2) for growth. Phylogenetic analysis indicated that the ndhD3/ndhD4-, ndhF3/ndhF4-, and cupA/cupB-type genes are present only in cyanobacteria. Most of the cyanobacterial strains studied possess the ndhD3/ndhD4-, ndhF3/ndhF4-, and cupA/cupB-type genes in pairs. Thus, the two types of NAD(P)H dehydrogenase complexes essential for low CO(2)-induced and constitutive CO(2)-uptake systems associated with the NdhD3/NdhF3/CupA-homologues and NdhD4/NdhF4/CupB-homologues, respectively, appear to be present in these cyanobacterial strains but not in other organisms.

Two tandemly-located matrix metalloprotease genes with different expression patterns in the chlamydomonas sexual cell cycle

Cloning of the gametolysin gene, mmp1, of Chlamydomonas reinhardtii revealed that the gene has six introns in its coding region and that a novel structurally related gene. mmp2, is located just upstream of the mmp1 gene. The mmp2 gene has ten introns and the deduced amino acid sequence has the hallmark motif characteristics of metzincin-type matrix metalloproteases. Southern analysis showed that mmp1 and mmp2 are single copy genes and that a RFLP is found between the mt+ and mt- strains employed. Northern analysis revealed that the two genes are expressed at different stages in the Chlamydomonas sexual cell cycle: steady-state levels of mmp1 mRNA increased during gametogenesis, while those of mmp2 mRNA increased in young zygotes. Transcription of mmp2 was insensitive to cycloheximide and did not occur when a non-fusing mutant, fus mt+, was mated with wild-type mt- gametes, suggesting that mmp2 is a member of the early zygote-specific genes, which are under the regulation of transcription factors pre-existing in gametes and activated by cytoplasmic fusion.

The Y chromosome in the liverwort Marchantia polymorpha has accumulated unique repeat sequences harboring a male-specific gene

The haploid liverwort Marchantia polymorpha has heteromorphic sex chromosomes, an X chromosome in the female and a Y chromosome in the male. We here report on the repetitive structure of the liverwort Y chromosome through the analysis of male-specific P1-derived artificial chromosome (PAC) clones, pMM4G7 and pMM23-130F12. Several chromosome-specific sequence elements of approximately 70 to 400 nt are combined into larger arrangements, which in turn are assembled into extensive Y chromosome-specific stretches. These repeat sequences contribute 2-3 Mb to the Y chromosome based on the observations of three different approaches: fluorescence in situ hybridization, dot blot hybridization, and the frequency of clones containing the repeat sequences in the genomic library. A novel Y chromosome-specific gene family was found embedded among these repeat sequences. This gene family encodes a putative protein with a RING finger motif and is expressed specifically in male sexual organs. To our knowledge, there have been no other reports for an active Y chromosome-specific gene in plants. The chromosome-specific repeat sequences possibly contribute to determining the identity of the Y chromosome in M. polymorpha as well as to maintaining genes required for male functions, as in mammals such as human.

Identification of xanthine dehydrogenase/xanthine oxidase as a rat Paneth cell zinc-binding protein

Paneth cells are zinc-containing cells localized in small intestinal crypts, but their function has not been fully elucidated. Previously, we showed that an intravenous injection of diphenylthiocarbazone (dithizone), a zinc chelator, induced selective killing of Paneth cells, and purified a zinc-binding protein in Paneth cells. In the present study, we further characterized one of these proteins, named zinc-binding protein of Paneth cells (ZBPP)-1. Partial amino acid sequences of ZBPP-1 showed identity with rat xanthine dehydrogenase (XD)/xanthine oxidase (XO). Anti-rat XD antibody (Ab) recognized ZBPP-1, and conversely anti ZBPP-1 Ab recognized 85 kDa fragment of rat XD in Western blotting. Messenger RNA and protein levels of XD were consistent with our previous data on the fluctuation of Paneth cell population after dithizone injection. Thus, ZBPP-1 is an 85 kDa fragment of XD/XO in Paneth cells. XD/XO in Paneth cells may play important roles in intestinal function.

Enhanced expression of transforming growth factor (TGF) -alpha precursor and TGF-beta1 during Paneth cell regeneration

An intravenous injection of diphenylthiocarbazone (dithizone), a zinc chelator, induces selective killing and rapid regeneration of Paneth cells, which have a large amount of zinc in their cytoplasmic granules. We examined the expression pattern of transforming growth factor (TGF) -alpha and TGF-beta1 in this regenerative process. Messenger RNA expression of TGF-alpha and TGF-beta1 reached their peaks at 12 and 24 hr after dithizone injection, respectively. Protein expression of TGF-alpha precursor and TGF-beta1 increased to a maximum at 24 and 72 hr, respectively. Their immunoreactivities were localized in the epithelial cells in the vicinity of Paneth cells, whereas they were prominent in the upper half of the crypts in control rats. In conclusion, destruction of Paneth cells induced TGF-alpha precursor expression, followed by an increase of TGF-beta1 especially in the crypt bases. This unique expression pattern of two growth factors may be involved in rapid regeneration of Paneth cells.

Ccm1, a regulatory gene controlling the induction of a carbon-concentrating mechanism in Chlamydomonas reinhardtii by sensing CO2 availability

Aquatic photosynthetic organisms, including the green alga Chlamydomonas reinhardtii, induce a set of genes for a carbon-concentrating mechanism (CCM) to acclimate to CO2-limiting conditions. This acclimation is modulated by some mechanisms in the cell to sense CO2 availability. Previously, a high-CO2-requiring mutant C16 defective in an induction of the CCM was isolated from C. reinhardtii by gene tagging. By using this pleiotropic mutant, we isolated a nuclear regulatory gene, Ccm1, encoding a 699-aa hydrophilic protein with a putative zinc-finger motif in its N-terminal region and a Gln repeat characteristic of transcriptional activators. Introduction of Ccm1 into this mutant restored an active carbon transport through the CCM, development of a pyrenoid structure in the chloroplast, and induction of a set of CCM-related genes. That a 5,128-base Ccm1 transcript and also the translation product of 76 kDa were detected in both high- and low-CO2 conditions suggests that CCM1 might be modified posttranslationally. These data indicate that Ccm1 is essential to control the induction of CCM by sensing CO2 availability in Chlamydomonas cells. In addition, complementation assay and identification of the mutation site of another pleiotropic mutant, cia5, revealed that His-54 within the putative zinc-finger motif of the CCM1 is crucial to its regulatory function.

Construction of male and female PAC genomic libraries suitable for identification of Y-chromosome-specific clones from the liverwort, Marchantia polymorpha

Unlike higher plants, the dioecious liverwort, Marchantia polymorpha, has uniquely small sex chromosomes, with X chromosomes present only in female gametophytes and Y chromosomes only in male gametophytes. We have constructed respective genomic libraries for male and female plantlets using a P1-derived artificial chromosome (pCYPAC2). With an average insert size of approximately 90 kb, each PAC library is estimated to cover the entire genome with a probability of more than 99.9%. Male-specific PAC clones were screened for by differential hybridization using male and female genomic DNAs as separate probes. Seventy male-specific PAC clones were identified. The male specificity of one of the clones, pMM4G7, was verified by Southern hybridization and PCR analysis. This clone was indeed located on the Y chromosome as verified by fluorescence in situ hybridization (FISH). This result shows that the Y chromosome contains unique sequences that are not present either on the X chromosome or any of the autosomes. Thus, the respective male and female libraries for M. polymorpha offer an opportunity to identify key genes involved in the process of sex differentiation and this unique system of sex determination.

Generation of expressed sequence tags from low-CO2 and high-CO2 adapted cells of Chlamydomonas reinhardtii

To characterize genes whose expression is induced in carbon-stress conditions, 12,969 and 13,450 5'-end expressed sequence tags (ESTs) were generated from cells grown in low-CO2 and high-CO2 conditions of the unicellular green alga, Chlamydomonas reinhardtii. These ESTs were clustered into 4436 and 3566 non-redundant EST groups, respectively. Comparison of their sequences with those of 3433 non-redundant ESTs previously generated from the cells under the standard growth condition indicated that 2665 and 1879 EST groups occurred only in the low-CO2 and high-CO2 populations, respectively. It was also noted that 96.2% and 96.0% of the cDNA species respectively obtained from the low-CO2 and high-CO2 conditions had no similar EST sequence deposited in the public databases. The EST species identified only in the low-CO2 treated cells included genes previously reported to be expressed specifically in low-CO2 acclimatized cells, suggesting that the ESTs generated in this study will be a useful source for analysis of genes related to carbon-stress acclimatization. The sequence information and search results of each clone will appear at the web site: http://www.kazusa.or.jp/en/plant/chlamy/EST/.

Comparison of expressed sequence tags from male and female sexual organs of Marchantia polymorpha

A total of 935 expressed sequence tags (ESTs) from male immature sexual organ were determined, of which 600 ESTs were assembled into 110 non-redundant groups, resulting in 445 unique EST sequences. Of these, 244 sequences shared significant similarities to known nucleotide or amino acid sequences in other organisms. The remaining 201 unique sequences showed no significant matches and thus are likely to be novel transcripts. ESTs from male and female immature sexual organs of a liverwort, Marchantia polymorpha, were compared to characterize gene expression patterns during sex differentiation. Ninety-nine male ESTs turned out to be common genes found also in the female library. Interestingly, one of the ESTs found only in male shows a significant similarity to the transformer-2 gene involved in sex determination in Drosophila. In female, several unique lectin ESTs were found that are not present in the male library.

Direct transformation and plant regeneration of the haploid liverwort Marchantia polymorpha L

Thalli of the haploid liverwort Marchantial polymorpha were successfully used for direct particle bombardment with plasmid pMT, which carries a hygromycin phosphotransferase gene (hpt) controlled by the CaMV 35S promoter and the NOS polyadenylation region. Hygromycin-resistant cell masses arose from the thallus surface and developed directly into hygromycin-resistant thalli. Southern blot analyses indicated that these thalli carried at least 1-4 copies of the hpt gene, which were stably transmitted to their asexual thallus progenies via gemma propagation for three generations. This transformation and direct plant regeneration protocol is expected to be a valuable tool for the molecular analysis of this lower land plant.

Bright light treatment for night-time insomnia and daytime sleepiness in elderly people: comparison with a short-acting hypnotic

Night-time bright light (BL) treatment and triazolam (0.125 mg/day) were given to three healthy elderly people in a cross-over design. They kept a daytime sleepiness test and a sleep log, and their wrist-activity was monitored simultaneously. Subjectively, BL increased daytime sleepiness and naps, and decreased night-time sleep. Triazolam decreased daytime sleepiness and naps, and increased night-time sleep. Actigraphic night-time sleep and naps on the first day were similar to these results. However, on the fourth day night-time insomnia induced by BL had recovered, and naps were shorter than the baseline. Triazolam increased actigraphic naps as the days passed.

Seasonal changes in human sleep-wake rhythm in Antarctica and Japan

The subjects were eight men of the Japanese Antarctic Research Expedition (average age 35.8 years), and 10 healthy people living around Kofu, Japan (28.9 years). They completed a sleep log for 12 to 18 months, and the sleep-wake state was scored in 10-min epochs. Q24 values calculated by chi2 periodgram were low in the Antarctic midwinter. This means that there was difficulty in synchronizing to a 24-h period in the Antarctic midwinter. In Antarctica, sleep onset and offset times were delayed mostly in the midwinter. In Japan, sleep offset time was delayed mostly around the winter solstice.

Identification of a novel alternative splicing of human FGF receptor 4: soluble-form splice variant expressed in human gastrointestinal epithelial cells

Among four closely related members of the FGF receptor family, FGFR 1, 2, and 3 have alternative splicing forms encoded by different exons for the C-terminal half of the third Ig-like domain, but FGFR 4 has no such alternative exon. Furthermore, FGFR 1, 2, and 3 have another splice variant of nontransmembrane type; however, such a variant has not been reported for FGFR 4. While searching for a novel receptor-type tyrosine kinase by RT-PCR, we identified a non-transmembrane-type receptor of FGFR 4 in human intestinal epithelial cell lines (Intestine 407 and Caco-2). Sequence analysis of this receptor revealed that exon 9 coding the single transmembrane domain was displaced by intron 9. Consequently, this variant form was 120 bp shorter than the normal form and had no transmembrane portion. Moreover, the signal sequence in exon 2 was maintained, suggesting that this splice variant is a soluble receptor. This soluble receptor was detected in human gastrointestinal epithelial cells and pancreas, and also in gastric, colon, and pancreatic cancer cell lines. Single cell RT-PCR showed that this soluble receptor was expressed simultaneously with the transmembrane-type receptor in the same cell. Western blot analysis revealed that this receptor was secreted from the transfected COS7 cells. Thus, a soluble-form splice variant of FGFR 4 was identified in human gastrointestinal epithelial cells and cancer cells. This is the first report of alternative splicing of FGFR 4.