Cryo-EM analysis of V/A-ATPase intermediates reveals the transition of the ground-state structure to steady-state structures by sequential ATP binding

Vacuolar/archaeal-type ATPase (V/A-ATPase) is a rotary ATPase that shares a common rotary catalytic mechanism with F_oF₁ ATP synthase. Structural images of V/A-ATPase obtained by single-particle cryo-electron microscopy during ATP hydrolysis identified several intermediates, revealing the rotary mechanism under steady-state conditions. However, further characterization is needed to understand the transition from the ground state to the steady state. Here, we identified the cryo-electron microscopy structures of V/A-ATPase corresponding to short-lived initial intermediates during the activation of the ground state structure by time-resolving snapshot analysis. These intermediate structures provide insights into how the ground-state structure changes to the active, steady state through the sequential binding of ATP to its three catalytic sites. All the intermediate structures of V/A-ATPase adopt the same asymmetric structure, whereas the three catalytic dimers adopt different conformations. This is significantly different from the initial activation process of F_oF₁, where the overall structure of the F₁ domain changes during the transition from a pseudo-symmetric to a canonical asymmetric structure (PNAS NEXUS, pgac116, 2022). In conclusion, our findings provide dynamical information that will enhance the future prospects for studying the initial activation processes of the enzymes, which have unknown intermediate structures in their functional pathway.

Structures of Multisubunit Membrane Complexes With the CRYO ARM 200

Progress in structural membrane biology has been significantly accelerated by the ongoing ‘Resolution Revolution’ in cryo-electron microscopy (cryo-EM). In particular, structure determination by single-particle analysis has evolved into the most powerful method for atomic model building of multisubunit membrane protein complexes. This has created an ever-increasing demand in cryo-EM machine time, which to satisfy is in need of new and affordable cryo-electron microscopes. Here, we review our experience in using the JEOL CRYO ARM 200 prototype for the structure determination by single-particle analysis of three different multisubunit membrane complexes: the Thermus thermophilus V-type ATPase V_O complex, the Thermosynechococcus elongatus photosystem I monomer and the flagellar motor lipopolysaccharide peptidoglycan ring (LP ring) from Salmonella enterica.

Structural basis of unisite catalysis of bacterial F0F1-ATPase

Adenosine triphosphate (ATP) synthases (F₀F₁-ATPases) are crucial for all aerobic organisms. F₁, a water-soluble domain, can catalyze both the synthesis and hydrolysis of ATP with the rotation of the central γε rotor inside a cylinder made of α ₃ β ₃ in three different conformations (referred to as β _E, β _TP, and β _DP). In this study, we determined multiple cryo-electron microscopy structures of bacterial F₀F₁ exposed to different reaction conditions. The structures of nucleotide-depleted F₀F₁ indicate that the ε subunit directly forces β _TP to adopt a closed form independent of the nucleotide binding to β _TP. The structure of F₀F₁ under conditions that permit only a single catalytic β subunit per enzyme to bind ATP is referred to as unisite catalysis and reveals that ATP hydrolysis unexpectedly occurs on β _TP instead of β _DP, where ATP hydrolysis proceeds in the steady-state catalysis of F₀F₁. This indicates that the unisite catalysis of bacterial F₀F₁ significantly differs from the kinetics of steady-state turnover with continuous rotation of the shaft.

A Japanese Multicenter Study on PET and Other Biomarkers for Subjects with Potential Preclinical and Prodromal Alzheimer's Disease

BACKGROUND

PET (positron emission tomography) and CSF (cerebrospinal fluid) provide the "ATN" (Amyloid, Tau, Neurodegeneration) classification and play an essential role in early and differential diagnosis of Alzheimer's disease (AD).

OBJECTIVE

Biomarkers were evaluated in a Japanese multicenter study on cognitively unimpaired subjects (CU) and early (E) and late (L) mild cognitive impairment (MCI) patients.

MEASUREMENTS

A total of 38 (26 CU, 7 EMCI, 5 LMCI) subjects with the age of 65-84 were enrolled. Amyloid-PET and FDG-PET as well as structural MRI were acquired on all of them, with an additional tau-PET with 18F-flortaucipir on 15 and CSF measurement of Aβ1-42, P-tau, and T-tau on 18 subjects. Positivity of amyloid and tau was determined based on the positive result of either PET or CSF.

RESULTS

The amyloid positivity was 13/38, with discordance between PET and CSF in 6/18. Cortical tau deposition quantified with PET was significantly correlated with CSF P-tau, in spite of discordance in the binary positivity between visual PET interpretation and CSF P-tau in 5/8 (PET-/CSF+). Tau was positive in 7/9 amyloid positive and 8/16 amyloid negative subjects who underwent tau measurement, respectively. Overall, a large number of subjects presented quantitative measures and/or visual read that are close to the borderline of binary positivity, which caused, at least partly, the discordance between PET and CSF in amyloid and/or tau. Nine subjects presented either tau or FDG-PET positive while amyloid was negative, suggesting the possibility of non-AD disorders.

CONCLUSION

Positivity rate of amyloid and tau, together with their relationship, was consistent with previous reports. Multicenter study on subjects with very mild or no cognitive impairment may need refining the positivity criteria and cutoff level as well as strict quality control of the measurements.

Mechanical inhibition of isolated Vo from V/A-ATPase for proton conductance

V-ATPase is an energy converting enzyme, coupling ATP hydrolysis/synthesis in the hydrophilic V₁ domain, with proton flow through the V_o membrane domain, via rotation of the central rotor complex relative to the surrounding stator apparatus. Upon dissociation from the V₁ domain, the V_o domain of the eukaryotic V-ATPase can adopt a physiologically relevant auto-inhibited form in which proton conductance through the V_o domain is prevented, however the molecular mechanism of this inhibition is not fully understood. Using cryo-electron microscopy, we determined the structure of both the holo V/A-ATPase and isolated V_o at near-atomic resolution, respectively. These structures clarify how the isolated V_o domain adopts the auto-inhibited form and how the holo complex prevents formation of the inhibited V_o form.

Cryo-EM studies of the rotary H+-ATPase/synthase from Thermus thermophilus

Proton-translocating rotary ATPases couple proton influx across the membrane domain and ATP hydrolysis/synthesis in the soluble domain through rotation of the central rotor axis against the surrounding peripheral stator apparatus. It is a significant challenge to determine the structure of rotary ATPases due to their intrinsic conformational heterogeneity and instability. Recent progress of single particle analysis of protein complexes using cryogenic electron microscopy (cryo-EM) has enabled the determination of whole rotary ATPase structures and made it possible to classify different rotational states of the enzymes at a near atomic resolution. Three cryo-EM maps corresponding to different rotational states of the V/A type H⁺-rotary ATPase from a bacterium Thermus thermophilus provide insights into the rotation of the whole complex, which allow us to determine the movement of each subunit during rotation. In addition, this review describes methodological developments to determine higher resolution cryo-EM structures, such as specimen preparation, to improve the image contrast of membrane proteins.

Asymmetric alloy formation at the Fe-on-Ti and Ti-on-Fe interfaces

The Fe-on-Ti and Ti-on-Fe interfaces were studied experimentally by Mössbauer spectroscopy (MS), transmission electron microscopy (TEM) and x-ray reflectometry (XRR) on Ti/Fe/Ti trilayers grown on Si(1 1 1) substrates by vacuum evaporation. The nanoscale structure and composition were explored in cross sections using TEM, the layer structure and the interface widths by specular x-ray reflectometry. MS was applied to identify the interface alloy phases and to determine the pure and alloyed Fe layer fractions. The experimental results were compared with molecular dynamics (MD) simulations of layer growth on Fe or Ti underlayers of different orientations. The concentration distributions provided by MD simulations show an asymmetry at the interfaces in the layer growth direction. The transition is atomically sharp at the Ti-on-Fe interface for the (0 0 1) and (1 1 0) crystallographic orientations of the Fe underlayer, while it spreads over a few atomic layers for Fe(1 1 1) underlayer and for all studied Ti underlayer orientations at the Fe-on-Ti interface. MS and XRR data on Ti/Fe/Ti trilayers confirm the asymmetry between the bottom and top Fe interface, but the inferred interface widths considerable exceed those deduced from the MD simulations.

Implications of PI3K/AKT/PTEN Signaling on Superoxide Dismutases Expression and in the Pathogenesis of Alzheimer's Disease

Alzheimer’s disease is a neurodegenerative sickness, where the speed of personal disease progression differs prominently due to genetic and environmental factors such as life style. Alzheimer’s disease is described by the construction of neuronal plaques and neurofibrillary tangles composed of phosphorylated tau protein. Mitochondrial dysfunction may be a noticeable feature of Alzheimer’s disease and increased production of reactive oxygen species has long been described. Superoxide dismutases (SODs) protect from excess reactive oxygen species to form less reactive hydrogen peroxide. It is suggested that SODs can play a protective role in neurodegeneration. In addition, PI3K/AKT pathway has been shown to play a critical role on the neuroprotection and inhibiting apoptosis via the enhancing expression of the SODs. This pathway appears to be crucial in Alzheimer’s disease because it is related to the tau protein hyper-phosphorylation. Dietary supplementation of several ordinary compounds may provide a novel therapeutic approach to brain disorders by modulating the function of the PI3K/AKT pathway. Understanding these systems may offer a better efficacy of new therapeutic approaches. In this review, we summarize recent progresses on the involvement of the SODs and PI3K/AKT pathway in neuroprotective signaling against Alzheimer’s disease.

General anesthetics cause mitochondrial dysfunction and reduction of intracellular ATP levels

General anesthetics are indispensable for effective clinical care. Although, the mechanism of action of general anesthetics remains controversial, lipid bilayers and proteins have been discussed as their targets. In this study, we focused on the relationship between cellular ATP levels and general anesthetics. The ATP levels of nematodes and cultured mammalian cells were decreased by exposure to three general anesthetics: isoflurane, pentobarbital, and 1-phenoxy-2-propanol. Furthermore, these general anesthetics abolished mitochondrial membrane potential, resulting in the inhibition of mitochondrial ATP synthesis. These results suggest that the observed decrease of cellular ATP level is a common phenomenon of general anesthetics.

n-3 polyunsaturated fatty acids stimulate osteoclastogenesis through PPARγ-mediated enhancement of c-Fos expression, and suppress osteoclastogenesis through PPARγ-dependent inhibition of NFkB activation

n-3 polyunsaturated fatty acids (PUFAs), eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) have been reported to suppress osteoclastogenesis in vivo. In this study, the effect of PUFAs on receptor for activation of nuclear factor-κB ligand (RANKL)-induced osteoclastogenesis was examined using bone marrow-derived monocytes/macrophage precursor cells (BMMs) or bone marrow cells (BMCs) in vitro. EPA and DHA stimulated the osteoclastic differentiation of BMMs, but n-6 PUFAs, linoleic acid and arachidonic acid had no effect. The stimulation of osteoclastogenesis of BMMs by EPA and DHA was associated with enhancement of the gene expressions of c-Fos, tartrate-resistant acid phosphatase, cathepsin K and peroxisome proliferator-activated receptor-γ (PPARγ) and the protein levels of c-Fos, PPARγ and nuclear factor of activated T cells, cytoplasmic, calcineurin-dependent-1 (NFATc1). The PPARγ agonists, rosiglitazone and GW1929, also stimulated the osteoclastogenesis of BMMs. The PPARγ antagonists, T0070907 and GW9662, inhibited the stimulations of osteoclastogenesis and c-Fos expression by EPA or DHA. However, EPA and DHA inhibited the osteoclastogenesis in BMCs including BMMs and mesenchymal stem cells (MSCs). This inhibition was associated with suppression of the expression of RANKL and nuclear factor-κB (NFκB)-regulating genes, cyclooxygenase 2, TNFα and IL-6 in BMCs and MSCs. The agonists and antagonists of PPARγ showed that the inhibitions of NFκB transcriptional activity and osteoclastogenesis by EPA and DHA were PPARγ-dependent. These results suggest that EPA and DHA directly act on BMMs and stimulate osteoclastogenesis through enhancing c-Fos expression mediated by PPARγ but suppress osteoclastogenesis through the PPARγ-dependent inhibition of NFκB activation of MSCs in BMCs.

The ingenious structure of central rotor apparatus in VoV1; key for both complex disassembly and energy coupling between V1 and Vo

Vacuolar type rotary H⁺-ATPases (V_oV₁) couple ATP synthesis/hydrolysis by V₁ with proton translocation by V_o via rotation of a central rotor apparatus composed of the V₁-DF rotor shaft, a socket-like V_o-C (eukaryotic V_o-d) and the hydrophobic rotor ring. Reconstitution experiments using subcomplexes revealed a weak binding affinity of V₁-DF to V_o-C despite the fact that torque needs to be transmitted between V₁-DF and V_o-C for the tight energy coupling between V₁ and V_o. Mutation of a short helix at the tip of V₁-DF caused intramolecular uncoupling of V_oV₁, suggesting that proper fitting of the short helix of V₁-D into the socket of V_o-C is required for tight energy coupling between V₁ and V_o. To account for the apparently contradictory properties of the interaction between V₁-DF and V_o-C (weak binding affinity but strict requirement for torque transmission), we propose a model in which the relationship between V₁-DF and V_o-C corresponds to that between a slotted screwdriver and a head of slotted screw. This model is consistent with our previous result in which the central rotor apparatus is not the major factor for the association of V₁ with V_o (Kishikawa and Yokoyama, J Biol Chem. 2012 24597-24603).

Neuron membrane trafficking and protein kinases involved in autism and ADHD

A brain-enriched multi-domain scaffolding protein, neurobeachin has been identified as a candidate gene for autism patients. Mutations in the synaptic adhesion protein cell adhesion molecule 1 (CADM1) are also associated with autism spectrum disorder, a neurodevelopmental disorder of uncertain molecular origin. Potential roles of neurobeachin and CADM1 have been suggested to a function of vesicle transport in endosomal trafficking. It seems that protein kinase B (AKT) and cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) have key roles in the neuron membrane trafficking involved in the pathogenesis of autism. Attention deficit hyperactivity disorder (ADHD) is documented to dopaminergic insufficiencies, which is attributed to synaptic dysfunction of dopamine transporter (DAT). AKT is also essential for the DAT cell-surface redistribution. In the present paper, we summarize and discuss the importance of several protein kinases that regulate the membrane trafficking involved in autism and ADHD, suggesting new targets for therapeutic intervention.

BRCA1 and p53 tumor suppressor molecules in Alzheimer's disease

Tumor suppressor molecules play a pivotal role in regulating DNA repair, cell proliferation, and cell death, which are also important processes in the pathogenesis of Alzheimer’s disease. Alzheimer’s disease is the most common neurodegenerative disorder, however, the precise molecular events that control the death of neuronal cells are unclear. Recently, a fundamental role for tumor suppressor molecules in regulating neurons in Alzheimer’s disease was highlighted. Generally, onset of neurodegenerative diseases including Alzheimer’s disease may be delayed with use of dietary neuro-protective agents against oxidative stresses. Studies suggest that dietary antioxidants are also beneficial for brain health in reducing disease-risk and in slowing down disease-progression. We summarize research advances in dietary regulation for the treatment of Alzheimer’s disease with a focus on its modulatory roles in BRCA1 and p53 tumor suppressor expression, in support of further therapeutic research in this field.

Functions and characteristics of PINK1 and Parkin in cancer

Most of the Parkinson disease (PD) linked genes are also associated with cancers. In particular, phosphatase and tensin homologue-induced kinase 1 (PINK1) and Parkin, both of which are involved in recessively inherited familial forms of PD linked to mitochondrial dysfunction, appear to be abnormally expressed in cancers. Functional studies have revealed that PINK1 recruits Parkin to mitochondria to initiate mitophagy, an important autophagic quality control mechanism that rids the cell of damaged mitochondria. Although PD and cancer are obviously disparate human disorders, there is an evidence for low cancer rates in patients with PD. The relationship between cancer rates and PD might be related to the involvement of common pathways in both diseases. This paper provides a concise overview on the cellular functions of the PINK1 and Parkin.

Connection between Tumor Suppressor BRCA1 and PTEN in Damaged DNA Repair

Genomic instability finally induces cell death or apoptosis. The tumor suppressor, phosphatase and tensin homolog on chromosome 10 (PTEN), is a dual-specificity phosphatase, which has protein phosphatase activity and lipid phosphatase activity that antagonizes PI3K activity. Cells that lack PTEN have constitutively higher levels of PIP3 and activated downstream PI3K/AKT targets. BRCA1, a well-known breast cancer tumor suppressor, is to associate with breast cancer risk and genetic susceptibility. Many studies have demonstrated that PTEN, as well as BRCA1, plays a critical role in DNA damage responses. The BRCA1 functionally cooperates with PTEN and might be an essential blockage in the development of several tumors. Actually, the PTEN and BRCA1 genes are recognized as one of the most frequently deleted and/or mutated in many human cancers. The PI3K/AKT pathway is constitutively active in BRCA1-defective human cancer cells. Loss or decrease of these PTEN or BRCA1 function, by either mutation or reduced expression, has a role in various tumor developments. This review summarizes recent findings of the function of BRCA1 and PTEN involved in genomic stability and cancer cell signaling.

Local current density measurement using a Rogowski probe in Tokyo Spherical Tokamak-2

A Rogowski probe consisting of a small multi-layer Rogowski coil, five magnetic pick-up coils, and a Langmuir probe was developed to measure the local current density and its direction. It can be moved along the major radius and can be turned around its axis. This probe was used to measure the current density profile near the last closed flux surface of Ohmic plasmas in Tokyo Spherical Tokamak-2. The current density profile was measured successfully with a signal to noise ratio of greater than 20.

Demonstration of improvement in the signal-to-noise ratio of Thomson scattering signal obtained by using a multi-pass optical cavity on the Tokyo Spherical Tokamak-2

The multi-pass Thomson scattering (TS) scheme enables obtaining many photons by accumulating multiple TS signals. The signal-to-noise ratio (SNR) depends on the accumulation number. In this study, we performed multi-pass TS measurements for ohmically heated plasmas, and the relationship between SNR and the accumulation number was investigated. As a result, improvement of SNR in this experiment indicated similar tendency to that calculated for the background noise dominant situation.

Certain Diet and Lifestyle May Contribute to Islet β-cells Protection in Type-2 Diabetes via the Modulation of Cellular PI3K/AKT Pathway

PI3K/AKT pathway has been shown to play a pivotal role on islet β-cell protection, enhancing β-cell survival by stimulating cell proliferation and inhibiting cell apoptosis. Accordingly, this pathway appears to be crucial in type-2 diabetes. Understanding the regulations of this pathway may provide a better efficacy of new therapeutic approaches. In this review, we summarize advances on the involvement of the PI3K/AKT pathway in hypothetical intra-cellular signaling of islet β-cells. As recent findings may show the nutritional regulation of the survival pathway in the islet β-cells through activation of the PI3K/AKT pathway, we also review studies on the features of several diets, correlated lifestyle, and its signaling pathway involved in type-2 diabetes. The molecular mechanisms contributing to the disease are the subject of considerable investigation, as a better understanding of the pathogenesis will lead to novel therapies against a condition of the disease.

PI3K/AKT/PTEN pathway as a target for Crohn's disease therapy (Review)

The pathogenesis of inflammatory bowel disease (IBD), including Crohn's disease, is a subject of increasing interest. Loss-of-function mutations in nucleotide-binding oligomerization domain-containing protein 2 (NOD2) are strong genetic factors linked to Crohn's disease, which eventually leads to an excessive mucosal inflammatory response directed against components of normal gut microbiota. Reactive oxygen species (ROS) play an important role in inflammation processes, as well as in transduction of signals from receptors for several cytokines, such as tumor necrosis factor α (TNFα). ROS activate nuclear factor-κB (NF-κB) via IκB kinase (IKK) through the PI3K/AKT/PTEN pathway. Therefore, this pathway is recognized to play a key role in Crohn's disease. Loss of function has been demonstrated to occur as an early event in a wide variety of diseases. Given this prevalent involvement in a number of diseases, the molecular development that modulates this pathway has been the subject of several studies. In addition, it has been the focus of extensive research and drug discovery activities. A better understanding of the molecular assemblies may reveal novel targets for the therapeutic development against Crohn's disease.

Computational materials design of negative effective U system in hole-doped chalcopyrite CuFeS2

A general rule of negative effective U(U(eff)) system caused by (i) exchange correlation and (ii) charge excitation mechanisms is proposed. Based on the general rule, we perform ab initio electronic structure calculations by generalized gradient approximation (GGA) + U method for hole-doped chalcopyrite CuFeS2 [Cu(+)(d(10))Fe(3+)(d(5))S(2-)(s(2)p(6))2]. It is found from our calculations that the hole-doped CuFeS2 has the negative U(eff) = -0.44 eV, where U(eff) ≡ E(N + 1) + E(N - 1) - 2E(N) < 0 and E(N) is the total energy of the hole-doped CuFeS2. The negative U(eff) is caused by the charge-excitation in the hole-doped Cu(2+)(d(9)) and S(-)(s(2)p(5)), and also caused by the exchange-correlation in the hole-doped Fe(4+)(d(4)). The strong attractive electron-electron interaction (U(eff) = -0.44 eV ∼ -5000 K) originates from the purely electronic mechanism. The closed shell of the d(10) electronic configuration is more stable than the d(9) electronic configuration, since the first excited state with the d(9)s(1) electronic configuration and the ground state with the d(10) electronic configuration are very close, then these two states repel very strongly through the second order perturbation. Therefore, the spin-polarized total energy curve for the hole-doped CuFeS2 shows the strong upward convexity with N - 1, N and N + 1 electronic configurations leading to the negative U(eff). The hole-doped paramagnetic and metallic CuFeS2 with the negative U(eff) may cause a possible high-Tc superconductor (Tc ∼ 1000 K, if 2Δ/kBTc ≈ 10 by assuming a strong coupling regime) because of the strong attractive electron-electron interactions (superconducting gap Δ ≈ |U(eff|) ∼ 5000 K). Finally, we propose a new computational materials design methodology to design ultra high-Tc superconductors by using three steps starting from the atomic number only.

Atherosclerosis and tumor suppressor molecules (review)

Atherosclerosis, the major cause of heart attack and stroke, is a chronic inflammatory disease characterized by the formation of atherosclerotic plaque. Oxidized low-density lipoprotein through increased oxidative stress has been identified as one of the primary factors responsible for atherogenesis. Cell proliferation and death are key processes in the progression of atherosclerosis. The oxidative environment in areas of lipid accumulation is mainly created by the production of reactive oxygen species, which are assumed to mediate vascular tissue injury. Oxidative DNA damage and levels of DNA repair are reduced during dietary lipid lowering. The tumor suppressor molecules play a pivotal role in regulating cell proliferation, DNA repair and cell death, which are important processes in regulating the composition of atherosclerotic plaque. Accordingly, in this review, we discuss the fundamental role of tumor suppressor molecules in regulating atherogenesis. In particular, we discuss how tumor suppressor molecules are activated in the complex environment of atherosclerotic plaque, and regulate growth arrest, cell senescence and the apoptosis of vascular smooth muscle cells, which may protect against the progression of atherosclerosis. In addition, we discuss promising alternatives to the use of medications (such as statin) against atherosclerosis, namely diet, with the use of plant-derived supplements to modulate the expression and/or activity of tumor suppressor molecules. We also summarize the progress of research made on herbs with a focus on the modulatory roles of tumor suppressors, and on the molecular mechanisms underlying the prevention if atherosclerosis, supporting designs for further research in this field.

Dietary regulation of PI3K/AKT/GSK-3β pathway in Alzheimer's disease

Alzheimer’s disease (AD) is characterized by the formation of senile plaques and neurofibrillary tangles composed of phosphorylated Tau. Several findings suggest that correcting signal dysregulation for Tau phosphorylation in AD may offer a potential therapeutic approach. The PI3K/AKT/GSK-3β pathway has been shown to play a pivotal role in neuroprotection, enhancing cell survival by stimulating cell proliferation and inhibiting apoptosis. This pathway appears to be crucial in AD because it promotes protein hyper-phosphorylation in Tau. Understanding those regulations may provide a better efficacy of new therapeutic approaches. In this review, we summarize advances in the involvement of the PI3K/AKT/GSK-3β pathways in cell signaling of neuronal cells. We also review recent studies on the features of several diets and the signaling pathway involved in AD.

Link between PI3K/AKT/PTEN Pathway and NOX Proteinin Diseases

Accumulating evidence has revealed that thePI3K/AKT/PTENpathway acts as a pivotal determinant of cell fate regarding senescence and apoptosis, which is mediated by intracellular reactive oxygen species (ROS) generation. NADPH oxidase (NOX) family of enzymes generates the ROS. The regulation of NOX enzymes is complex, with many members of this family exhibiting complexity in terms of subunit composition, cellular location, and tissue-specific expression. Cells are continuously exposed to the ROS, which represent mutagens and are thought to be a major contributor to several diseases including cancer and aging process. Therefore, cellular ROS sensing and metabolism are firmly regulated by a variety of proteins involved in the redox mechanism. In this review, the roles of oxidative stress in PI3K/AKT/PTEN signaling are summarized with a focus on the links between the pathways and NOX protein in several diseases including cancer and aging.

Note: Multi-pass Thomson scattering measurement on the TST-2 spherical tokamak

In multi-pass Thomson scattering (TS) scheme, a laser pulse makes multiple round trips through the plasma, and the effective laser energy is enhanced, and we can increase the signal-to-noise ratio as a result. We have developed a coaxial optical cavity in which a laser pulse is confined, and we performed TS measurements using the coaxial cavity in tokamak plasmas for the first time. In the optical cavity, the laser energy attenuation was approximately 30% in each round trip, and we achieved a photon number gain of about 3 compared with that obtained in the first round trip. In addition, the temperature measurement accuracy was improved by accumulating the first three round trip waveforms.

Molecular basis of ADP inhibition of vacuolar (V)-type ATPase/synthase

Reduction of ATP hydrolysis activity of vacuolar-type ATPase/synthase (V0V1) as a result of ADP inhibition occurs as part of the normal mechanism of V0V1 of Thermus thermophilus but not V0V1 of Enterococcus hirae or eukaryotes. To investigate the molecular basis for this difference, domain-swapped chimeric V1 consisting of both T. thermophilus and E. hirae enzymes were generated, and their function was analyzed. The data showed that the interaction between the nucleotide binding and C-terminal domains of the catalytic A subunit from E. hirae V1 is central to increasing binding affinity of the chimeric V1 for phosphate, resulting in reduction of the ADP inhibition. These findings together with a comparison of the crystal structures of T. thermophilus V1 with E. hirae V1 strongly suggest that the A subunit adopts a conformation in T. thermophilus V1 different from that in E. hirae V1. This key difference results in ADP inhibition of T. thermophilus V1 by abolishing the binding affinity for phosphate during ATP hydrolysis.

Construction of chromosome markers from the Lake Victoria cichlid Paralabidochromis chilotes and their application to comparative mapping

Cichlid fishes in the African Great Lakes are known as a spectacular example of adaptive radiation in vertebrates. Four linkage maps have been constructed to identify the genes responsible for adaptation and speciation, and the genetic linkages of those genes are assumed to play an important role during adaptive evolution. However, it is difficult to analyze such linkages because the linkage groups of one species do not match well with those of the other species. Chromosome markers are a powerful tool for the direct identification of linkage homology between different species. We used information about the linkage map of the Lake Malawi cichlid (Labeotropheus fuelleborni/Metriaclima zebra) to isolate bacterial artificial chromosome (BAC) clones from the BAC library of Paralabidochromis chilotes, Lake Victoria. We identified 18 of 22 P. chilotes chromosomes by single- and multi-color BAC fluorescence in situ hybridization using 19 BAC clones. Comparative mapping with the chromosome markers of P. chilotes in Astatotilapia burtoni (2n = 40) from Lake Tanganyika revealed the chromosome rearrangements that have occurred in this lineage. These chromosome markers will be useful for delineating the process of genome and chromosome evolution in African species.

Roles of PI3K/AKT/PTEN Pathway as a Target for Pharmaceutical Therapy

Multiple enzymes participate in the phosphorylation of a group of phosphoinositide lipids. Because of their important role in signal transduction, the dysregulated metabolism of phosphoinositides represents a key step in many disease settings. Loss of their function has been demonstrated to occur as an early event a wide variety of carcinogenesis and has therefore been suggested as a biomarker for the premalignant disease. In addition, genetic alterations at multiple nodes in the pathway have been implicated in several other diseases. Accordingly, given this pervasive involvement in many diseases, the development of molecules that modulates this pathway has been initiated in studies. They have been the focus of extensive research and drug discovery activities. A better understanding of the molecular connections could uncover new targets for drug development.

Ethanol increases osteoclastogenesis associated with the increased expression of RANK, PU.1 and MITF in vitro and in vivo

Ethanol has been known to induce osteopenia. However, the cellular and molecular mechanisms responsible for its effect have not been well characterized. This study investigated the effects of ethanol on bone metabolism and osteoclastogenesis using rats fed an ethanol-containing liquid diet (35% of calories from ethanol) for 3 weeks. Ethanol increased the activities of bone tartrate-resistant acid phosphatase (TRAP) and cathepsin K, without affecting the levels of serum osteocalcin or bone alkaline phosphatase activity. Histological analysis showed an increased number of osteoclasts in the proximal tibia, but no significant change in the number of osteoblasts. The mRNA levels of receptor for activation of NF-κB (RANK), c-fos, c-jun, TRAP and cathepsin K were significantly increased, although those of macrophage colony-stimulating factor and c-fms were unaltered. The mRNA and protein levels of PU.1 and microphthalmia-associated trascription factor (MITF) also increased. Further, the osteoclastic differentiation of bone marrow-derived macrophage/monocyte precursor cells (BMMs) in vitro was stimulated by ethanol. The increased osteoclastogenesis of BMMs was associated with increased levels of RANK, PU.1 and MITF expression, activated extracellular signal-regulated kinase (ERK), and reactive oxygen species (ROS). Higher lipid peroxide levels and lower glutathione levels were also observed in the serum of the ethanol-fed rats. These results suggested that ethanol promoted osteoclastogenesis by increasing RANK expression through increases in the production of ROS, activation of ERK and expression of PU.1 and MITF.

White matter alteration of the cingulum in Parkinson disease with and without dementia: evaluation by diffusion tensor tract-specific analysis

BACKGROUND AND PURPOSE

In PD, the neurodegenerative process begins in the brain stem and extends to the limbic system and finally into the cerebral cortex. We used diffusion tensor tractography to investigate the FA of the cingulate fiber tracts in patients with PD with and without dementia.

MATERIALS AND METHODS

Fifteen patients with PD, 15 patients with PDD, and 15 age-matched healthy controls underwent diffusion tensor imaging with a 3T MR imager. Diffusion tensor tractography images of the anterior and posterior cingulate fiber tracts were generated. Mean diffusivity and FA were measured along the tractography of the anterior and posterior cingulate fiber tracts. One-way ANOVA with the Scheffé post hoc test was used to compare results among the groups.

RESULTS

FA was significantly lower in patients with PDD than in healthy controls in both the anterior and the posterior cingulate fiber tracts (P = .003, P = .015) and significantly lower in patients with PD than in healthy controls (P = .003) in the anterior cingulate fiber tract. There were no significant mean diffusivity differences among the groups. MMSE and FA values of the anterior cingulate fiber tracts in patients with PDD were significantly correlated (r = 0.633, P < .05).

CONCLUSIONS

The reduced FA in patients with PD and PDD might reflect neuropathologic changes such as Lewy body pathology in the cingulate fibers. This abnormality might contribute to the dementing process in PD.

Zinc deficiency decreases osteoblasts and osteoclasts associated with the reduced expression of Runx2 and RANK

The effects of Zinc(Zn)-deficiency on the function and differentiation of osteoblasts and osteoclasts were investigated in vivo using rats, which were fed a Zn-adequate (control) or Zn-free diet (ZD) or pair-fed a Zn-adequate diet (PF) for 3 weeks. Levels of Zn, insulin, insulin-like growth factor I (IGF-I), and osteoclacin in serum and the activities and numbers of osteoblasts and osteoclasts in bone decreased in ZD rats compared with the control and PF rats. The frequency analyses showed that the precursors of osteoblasts and osteoclasts decreased in bone marrow of ZD, but not PF, rats. The expression of receptor for activation of NF-κB (RANK) decreased with the Zn-deficiency, although RANK ligand, osteoprotegerin, macrophage colony-stimulating factor, and c-fms levels were unaltered. The protein level of a transcription factor MITF, but not PU.1, decreased. The expression of Runx2 decreased associated with the decrease in β-catenin protein and the suppression of glycogen synthase kinase 3β (GSK3β) inhibition and Akt activation. The gene expression of the insulin receptor, IGF-I and the IGF-I receptor was decreased with a reduced level of transcription factor SP-1. These results suggested that a deficiency of Zn decreased osteoclastogenesis associated with the reduced expression of RANK through a decrease in MITF protein, and osteoblastogenesis associated with the reduced expression of Runx2 through the inhibition of Wnt/β-catenin signaling via the suppression of GSK3β inhibition and Akt activation preceded by the reduced level of SP-1 protein.

A CRM1-mediated nuclear export signal governs cytoplasmic localization of BRCA2 and is essential for centrosomal localization of BRCA2

Germ-line mutations of the BRCA2 gene cause inherited susceptibility to breast and ovarian cancers. BRCA2 contains two nuclear localization signals, predominantly localizes in the nucleus and plays significant roles in DNA double-strand break repair. Recently, we reported that BRCA2 localizes to the centrosomes during the S and early M phases of the cell cycle. In this study, for the first time, we identified a functional nuclear export sequence (NES1; (1383)DLSDLTFLEVA(1393)) in BRCA2. The green fluorescent protein (GFP)-NES1 fusion protein was localized in the cytoplasm and could be blocked by the chromosomal region maintenance 1-specific export inhibitor leptomycin B. Mutation of a leucine residue in the NES1 motif to alanine (L1384A) resulted in both cytoplasmic and nuclear localization of the GFP-NES1 fusion protein and a nuclear accumulation of ectopic full-length BRCA2-FLAG. Moreover, treatment of cells with leptomycin B decreased centrosomal localization of BRCA2. Finally, by microinjection of an anti-BRCA2 antibody into the cytoplasm of HeLa S3 cells, we found that depletion of normal BRCA2 proteins in the cytoplasm leads to centrosome amplification and binucleated cells. Our results suggest that disruption of the NES function by genetic changes results in deregulation of BRCA2 export, which ultimately leads to centrosome disorder.

Frequent reduced expression of alpha-1B-adrenergic receptor caused by aberrant promoter methylation in gastric cancers

Recent studies have suggested that epigenetic inactivation of tumour-related genes by promoter methylation participates in the development of gastric cancer. We newly identified the frequently aberrant promoter methylation of alpha-1B-adrenergic receptor (ADRA1B) in colorectal cancer by methylation-sensitive representational difference analysis (MS-RDA) and examined the methylation status of the ADRA1B promoter in 34 paired samples of colorectal cancer and surrounding epithelial tissue, and 34 paired samples of gastric cancer and surrounding epithelial tissue. In colorectal cancers, only four of 34 (11.8%) tumours showed ADRA1B promoter methylation. In contrast, ADRA1B promoter methylation was detected in 24 of 34 (70.6%) gastric cancers and in 14 of 34 (41.2%) surrounding epithelial tissues. The frequency of ADRA1B promoter methylation was higher in gastric epithelial tissues with intestinal metaplasia (41.6%) than in those without intestinal metaplasia (25.0%). Reverse transcription–PCR detected reduced ADRA1B expression in 12 of 18 (66.7%) gastric cancers, and its promoter methylation was detected in 11 of these 12 (91.7%) gastric cancers with reduced ADRA1B expression. Thus, ADRA1B promoter is frequently methylated in gastric cancer. Our results suggest that the ADRA1B gene is an important tumour-related gene frequently involved in the development and progression of gastric cancer.

Interannual genetic heterogeneity of pollen pools accepted by Quercus salicina individuals

Since flowering often varies among years in wind-pollinated woody species, the genetic composition of pollen pools accepted by seed parents can differ between years. The interannual heterogeneity of pollen flow may be important for maintaining genetic diversity within populations because it can increase genetic variation within populations and the effective sizes of the populations. In this study we examined heterogeneity, using paternity analysis and analysis of molecular variance, in the genetic composition of pollen pools among different reproductive years for six Quercus salicina seed parents in an 11.56-ha plot in a temperate old-growth evergreen broadleaved forest. The genotypes at seven microsatellite loci were determined for 111 adult trees and 777 offspring of the six seed parents in 2-5 reproductive years. Genetic differentiation of pollen pools among different reproductive years for each seed parent was significant over all seed parents and for each of four seed parents that were analysed for more than 2 years, but not for either of the other two seed parents (analysed for 2 years). For both the pollen pools originating from inside the plot and those originating from outside it, genetic differentiation among different reproductive years for each seed parent was significant over all seed parents. However, among-year genetic differentiation in the pollen pools originating from within the plot was detected for all four of the seed parents that were analysed for more than 2 years, but for only one of the four in the pools originating from outside the plot. Genetic diversity (estimated as allelic richness and gene diversity) was higher for pollen pools over all reproductive years than for pollen pools in single years. These results indicate that the year-to-year genetic variation of pollen pools increases genetic diversity in offspring and is strongly affected by the variation in pollen parents within the plot because of their high pollination contributions. The high year-to-year variation in pollen parents within the plot and overall supports the hypothesis that the offspring produced across years represent a larger genetic neighbourhood.

Discrete change of spin-density-wave modulation in Cr(100)/Sn multilayers as a function of Cr layer thickness

Magnetic structures of epitaxial Cr(001)/Sn multilayers, where monatomic Sn layers are periodically embedded in a Cr(001) film, were studied using neutron diffraction and Mössbauer spectroscopy. It was found that spin-density-wave (SDW) antiferromagnetic structures with the modulation along the perpendicular direction to the film plane are stabilized at low temperatures. The wavelength of the SDW discretely changes as a function of the superlattice period. The enhanced magnetic moments of Cr at the Cr/Sn interfaces are thought to pin the antimode of the SDW modulation at the interface, resulting in the SDW with the modulation harmonic to the superlattice period.

Soil N fluxes in three contrasting dry tropical forests

A comparative study of N fluxes in soil among a dry dipterocarp forest (DDF), a dry evergreen forest (DEF), and a hill evergreen forest (HEF) in Thailand was done. N fluxes in soil were estimated using an ion exchange resin core method and a buried bag method. Soil C and N pools were 38 C Mg/ha/30 cm and 2.5 N Mg/ha/30 cm in DDF, 82 C Mg/ha/30 cm and 6.2 N Mg/ha/30 cm in DEF, and 167 C Mg/ha/30 cm and 9.3 N Mg/ha/30 cm in HEF. Low C concentration in the DDF and DEF sites was compensated by high fine soil content. In the highly weathered tropical soil, fine soil content seemed to be important for C accumulation. Temporal and vertical fluctuations of N fluxes were different among the sites. The highest N flux was exhibited at the onset of the wet season in DDF, whereas inorganic N production and estimated uptake of N were relatively stable during the wet season in DEF and HEF. It is suggested that N cycling in soil becomes stable in dry tropical forests to intermediate in temperate forests. N deposition may result in large changes of N cycling in the DDF and DEF due to low accumulations of C and N.