Precise editing of pathogenic nucleotide repeat expansions in iPSCs using paired prime editor

Nucleotide repeat expansion disorders, a group of genetic diseases characterized by the expansion of specific DNA sequences, pose significant challenges to treatment and therapy development. Here, we present a precise and programmable method called prime editor-mediated correction of nucleotide repeat expansion (PE-CORE) for correcting pathogenic nucleotide repeat expansion. PE-CORE leverages a prime editor and paired pegRNAs to achieve targeted correction of repeat sequences. We demonstrate the effectiveness of PE-CORE in HEK293T cells and patient-derived induced pluripotent stem cells (iPSCs). Specifically, we focus on spinal and bulbar muscular atrophy and spinocerebellar ataxia type, two diseases associated with nucleotide repeat expansion. Our results demonstrate the successful correction of pathogenic expansions in iPSCs and subsequent differentiation into motor neurons. Specifically, we detect distinct downshifts in the size of both the mRNA and protein, confirming the functional correction of the iPSC-derived motor neurons. These findings highlight PE-CORE as a precision tool for addressing the intricate challenges of nucleotide repeat expansion disorders, paving the way for targeted therapies and potential clinical applications.

DNA double-strand break-free CRISPR interference delays Huntington's disease progression in mice

Huntington's disease (HD) is caused by a CAG repeat expansion in the huntingtin (HTT) gene. CRISPR-Cas9 nuclease causes double-strand breaks (DSBs) in the targeted DNA that induces toxicity, whereas CRISPR interference (CRISPRi) using dead Cas9 (dCas9) suppresses the target gene expression without DSBs. Delivery of dCas9-sgRNA targeting CAG repeat region does not damage the targeted DNA in HEK293T cells containing CAG repeats. When this study investigates whether CRISPRi can suppress mutant HTT (mHTT), CRISPRi results in reduced expression of mHTT with relative preservation of the wild-type HTT in human HD fibroblasts. Although both dCas9 and Cas9 treatments reduce mHTT by sgRNA targeting the CAG repeat region, CRISPRi delays behavioral deterioration and protects striatal neurons against cell death in HD mice. Collectively, CRISPRi can delay disease progression by suppressing mHtt, suggesting DNA DSB-free CRISPRi is a potential therapy for HD that can compensate for the shortcoming of CRISPR-Cas9 nuclease.

Targeted genomic translocations and inversions generated using a paired prime editing strategy

A variety of cancers have been found to have chromosomal rearrangements, and the genomic abnormalities often induced expression of fusion oncogenes. To date, a pair of engineered nucleases including ZFNs, TALENs, and CRISPR-Cas9 nucleases have been used to generate chromosomal rearrangement in living cells and organisms for disease modeling. However, these methods induce unwanted indel mutations at the DNA break junctions, resulting in incomplete disease modeling. Here, we developed prime editor nuclease-mediated translocation and inversion (PETI), a method for programmable chromosomal translocation and inversion using prime editor 2 nuclease (PE2 nuclease) and paired pegRNA. Using PETI method, we successfully introduced DNA recombination in episomal fluorescence reporters as well as precise chromosomal translocations in human cells. We applied PETI to create cancer-associated translocations and inversions such as NPM1-ALK and EML4-ALK in human cells. Our findings show that PETI generated chromosomal translocation and inversion in a programmable manner with efficiencies comparable of Cas9. PETI methods, we believe, could be used to create disease models or for gene therapy.

Expanded targeting scope of LbCas12a variants allows editing of multiple oncogenic mutations

RNA-guided CRISPR-Cas12a endonucleases are promising tools for genome engineering. Here we demonstrate that LbCas12a variants derived from Lachnospiraceae bacterium show a broad PAM preference, recognizing certain non-canonical PAMs with high efficiency. Furthermore, we engineered LbABE8e to carry G532R and/or K595R mutations, altering its original PAM specificities; these variants exhibited superior base editing activity in human cells compared with wild-type LbABE8e at sites with non-canonical PAMs. Based on this finding, we utilized the most effective LbCas12a and LbABE8e variants to demonstrate multiplexed and mutant-allele-specific gene editing in oncogenes, made possible by the variant’s recognition of non-canonical PAMs. Importantly, LbCas12a-G532R/K595R and LbABE8e-G532R/K595R with optimized crRNA arrays targeted to triple oncogenic mutations inhibited colon cancer cell proliferation. Taken together, these results demonstrate the potential of engineered LbCas12a and LbABE8e as tools for targeting sites with alternative PAMs for genome engineering and therapeutic editing in cancer cells.

Standardization of 129I using the movable 4πβ(LS)-X(NaI(Tl)) system

The ¹²⁹I standardization, using the movable 4πβ(LS)-X(NaI(Tl)) coincidence system, was performed for two ¹²⁹I radioactive sources - one was dissolved in 0.1M NaOH solution and the other in 0.1M HNO₃ solution. The system incorporates three movable PM tubes for a β-counter placed on a plane and a X-ray detector that can be moved up to the bottom of the vial. The β-efficiency depending on the amount of radioactive solution was investigated with 14 liquid scintillation samples prepared by gravimetrically dispensing 4.4-145 mg of ¹²⁹I radioactive solution. The β-efficiencies above 90% were observed at less than 56 mg, but it was at most 70% at 145 mg. This occurred regardless of the activity of the sample or the type of chemical solution used to dissolve ¹²⁹I source. The activity concentration of each ¹²⁹I source was determined by efficiency-extrapolation method for samples with an activity range of 0.28-4.5 kBq. The β-efficiency points were derived over 10 intervals by moving 3-PM tubes in fine steps of about 1 mm from the sample. The highest value for β-efficiency was 95%. The combined uncertainty were 0.25% and 0.26%, respectively. The stated precision obtained using the system is better than that previously reported in the literature obtained by the triple to double coincidence ratio (TDCR) or the CIEMAT/NIST efficiency tracing method.

Development of a movable 4πβ(LS)-γ coincidence counting system for activity standardization of β-γ emitters

A new movable 3PM-γ coincidence system, based on 4πβ(LS)-γ coincidence counting, for activity measurement of β-γ emitters has been designed at the Korea Research Institute of Standards and Science (KRISS). The system incorporates 3 PM tubes on the plane and two detectors placed above and below the center of the plane. The 3 PM tubes for β-counters in the plane are movable up to 100 mm from a liquid scintillation vial, thus enabling the variation of β-detection efficiencies by a geometrical technique. A NaI(Tl) γ-counter was set above for the present work. The β-event is determined by counting the logical sum of three double coincidences. All the necessary electronics, i.e., logical sum, adjusting the duration of dead-time of each counting channel and coincidence resolving times, and analyzing coincidence relation, were specially designed to be fabricated in an integrated circuit. Details of the detectors, the electronics, the overall movable 3PM-γ coincidence system are presented, as well as the results of investigations to assess its operating characteristics. Validation measurements have been performed with ⁶⁰Co and ⁵⁷Co sources. The highest β-detection efficiency achieved with ⁶⁰Co and ⁵⁷Co was 97% and 95%, respectively. The activity concentration determined with a new system agreed with calibrated values within the uncertainty range. Further results from validation measurements and the corresponding uncertainty budgets are presented.

Publisher Correction: Electronic structure of the parent compound of superconducting infinite-layer nickelates

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Electronic structure of the parent compound of superconducting infinite-layer nickelates

The search continues for nickel oxide-based materials with electronic properties similar to cuprate high-temperature superconductors^1-10. The recent discovery of superconductivity in the doped infinite-layer nickelate NdNiO₂ (refs. ^11,12) has strengthened these efforts. Here, we use X-ray spectroscopy and density functional theory to show that the electronic structure of LaNiO₂ and NdNiO₂, while similar to the cuprates, includes significant distinctions. Unlike cuprates, the rare-earth spacer layer in the infinite-layer nickelate supports a weakly interacting three-dimensional 5d metallic state, which hybridizes with a quasi-two-dimensional, strongly correlated state with [Formula: see text] symmetry in the NiO₂ layers. Thus, the infinite-layer nickelate can be regarded as a sibling of the rare-earth intermetallics^13-15, which are well known for heavy fermion behaviour, where the NiO₂ correlated layers play an analogous role to the 4f states in rare-earth heavy fermion compounds. This Kondo- or Anderson-lattice-like 'oxide-intermetallic' replaces the Mott insulator as the reference state from which superconductivity emerges upon doping.

Photoinduced Demagnetization and Insulator-to-Metal Transition in Ferromagnetic Insulating BaFeO_{3} Thin Films

We studied the electronic and magnetic dynamics of ferromagnetic insulating BaFeO_{3} thin films by using pump-probe time-resolved resonant x-ray reflectivity at the Fe 2p edge. By changing the excitation density, we found two distinctly different types of demagnetization with a clear threshold behavior. We assigned the demagnetization change from slow (∼150  ps) to fast (<70  ps) to a transition into a metallic state induced by laser excitation. These results provide a novel approach for locally tuning magnetic dynamics. In analogy to heat-assisted magnetic recording, metallization can locally tune the susceptibility for magnetic manipulation, allowing one to spatially encode magnetic information.

Design of a RANK-Mimetic Peptide Inhibitor of Osteoclastogenesis with Enhanced RANKL-Binding Affinity

The receptor activator of nuclear factor κB (RANK) and its ligand RANKL are key regulators of osteoclastogenesis and well-recognized targets in developing treatments for bone disorders associated with excessive bone resorption, such as osteoporosis. Our previous work on the structure of the RANK-RANKL complex revealed that Loop3 of RANK, specifically the non-canonical disulfide bond at the tip, performs a crucial role in specific recognition of RANKL. It also demonstrated that peptide mimics of Loop3 were capable of interfering with the function of RANKL in osteoclastogenesis. Here, we reported the structure-based design of a smaller peptide with enhanced inhibitory efficiency. The kinetic analysis and osteoclast differentiation assay showed that in addition to the sharp turn induced by the disulfide bond, two consecutive arginine residues were also important for binding to RANKL and inhibiting osteoclastogenesis. Docking and molecular dynamics simulations proposed the binding mode of the peptide to the RANKL trimer, showing that the arginine residues provide electrostatic interactions with RANKL and contribute to stabilizing the complex. These findings provided useful information for the rational design of therapeutics for bone diseases associated with RANK/RANKL function.

Relationship between early postoperative C-reactive protein elevation and long-term postoperative major adverse cardiovascular and cerebral events in patients undergoing off-pump coronary artery bypass graft surgery: a retrospective study

BACKGROUND

Inflammation plays a key role in the pathogenesis of vascular occlusive diseases, such as myocardial infarction and stroke. Additionally, these conditions are predicted by C-reactive protein (CRP), a general inflammation marker. We hypothesized that the inflammation induced by surgery itself augments vascular occlusive disease. We retrospectively evaluated the relationship between postoperative CRP elevation and postoperative major adverse cardiovascular and cerebral events (MACCE) in patients undergoing off-pump coronary artery bypass surgery (OPCAB).

METHODS

The electronic medical records of 1046 patients who underwent OPCAB were reviewed retrospectively. The relationship between postoperative serum CRP and long-term postoperative MACCE (median follow-up 28 months) was investigated.

RESULTS

Patients were divided into quartiles according to maximum postoperative CRP levels (<18, 18-22, 22-27, ≥27 mg dl(-1)). The adjusted hazard ratios (HRs) were 2.15, 2.45, and 2.81, respectively (P=0.004), compared with the lowest quartile (<18 mg dl(-1)). In the multivariate analysis, the postoperative CRP quartile (HR 2.81; P=0.004), postoperative non-use of statins (HR 1.86; P=0.003), and postoperative maximum troponin I (HR 1.02; P<0.001) independently predicted postoperative MACCE, while preoperative CRP did not (P=0.203). Several parameters were correlated with postoperative maximum CRP level: body temperature (P=0.001) and heart rate (P<0.001) at the end of surgery; intraoperative last lactate (P<0.001) and base excess (P<0.001); and red blood cell transfusion (P=0.019).

CONCLUSIONS

Postoperative CRP elevation was associated with long-term postoperative MACCE in OPCAB patients. This was mitigated by postoperative statin medication. Furthermore, postoperative CRP elevation was associated with intraoperative parameters reflecting hypoperfusion and inflammation.

Structural and functional characterization of an Isd-type haem-degradation enzyme fromListeria monocytogenes. Corrigendum

The author list in Duonget al.[(2014).Acta Cryst.D70, 615–626] is corrected.

Distinct Z-DNA binding mode of a PKR-like protein kinase containing a Z-DNA binding domain (PKZ)

Double-stranded ribonucleic acid-activated protein kinase (PKR) downregulates translation as a defense mechanism against viral infection. In fish species, PKZ, a PKR-like protein kinase containing left-handed deoxyribonucleic acid (Z-DNA) binding domains, performs a similar role in the antiviral response. To understand the role of PKZ in Z-DNA recognition and innate immune response, we performed structural and functional studies of the Z-DNA binding domain (Zα) of PKZ from Carassius auratus (caZα_PKZ). The 1.7-Å resolution crystal structure of caZα_PKZ:Z-DNA revealed that caZα_PKZ shares the overall fold with other Zα, but has discrete structural features that differentiate its DNA binding mode from others. Functional analyses of caZα_PKZ and its mutants revealed that caZα_PKZ mediates the fastest B-to-Z transition of DNA among Zα, and the minimal interaction for Z-DNA recognition is mediated by three backbone phosphates and six residues of caZα_PKZ. Structure-based mutagenesis and B-to-Z transition assays confirmed that Lys56 located in the β-wing contributes to its fast B-to-Z transition kinetics. Investigation of the DNA binding kinetics of caZα_PKZ further revealed that the B-to-Z transition rate is positively correlated with the association rate constant. Taking these results together, we conclude that the positive charge in the β-wing largely affects fast B-to-Z transition activity by enhancing the DNA binding rate.

Structural and functional characterization of an Isd-type haem-degradation enzyme fromListeria monocytogenes

Bacterial pathogens have evolved diverse types of efficient machinery to acquire haem, the most abundant source of iron in the human body, and degrade it for the utilization of iron. Gram-positive bacteria commonly encode IsdG-family proteins as haem-degrading monooxygenases.Listeria monocytogenesis predicted to possess an IsdG-type protein (Lmo2213), but the residues involved in haem monooxygenase activity are not well conserved and there is an extra N-terminal domain in Lmo2213. Therefore, its function and mechanism of action cannot be predicted. In this study, the crystal structure of Lmo2213 was determined at 1.75 Å resolution and its haem-binding and haem-degradation activities were confirmed. Structure-based mutational and functional assays of this protein, designated as an Isd-typeL. monocytogeneshaem-degrading enzyme (Isd-LmHde), identified that Glu71, Tyr87 and Trp129 play important roles in haem degradation and that the N-terminal domain is also critical for its haem-degrading activity. The haem-degradation product of Isd-LmHde is verified to be biliverdin, which is also known to be the degradation product of other bacterial haem oxygenases. This study, the first structural and functional report of the haem-degradation system inL. monocytogenes, sheds light on the concealed haem-utilization system in this life-threatening human pathogen.

Structural insights into the molecular mechanism of Escherichia coli SdiA, a quorum-sensing receptor

Escherichia coli SdiA is a quorum-sensing (QS) receptor that responds to autoinducers produced by other bacterial species to control cell division and virulence. Crystal structures reveal that E. coli SdiA, which is composed of an N-terminal ligand-binding domain and a C-terminal DNA-binding domain (DBD), forms a symmetrical dimer. Although each domain shows structural similarity to other QS receptors, SdiA differs from them in the relative orientation of the two domains, suggesting that its ligand-binding and DNA-binding functions are independent. Consistently, in DNA gel-shift assays the binding affinity of SdiA for the ftsQP2 promoter appeared to be insensitive to the presence of autoinducers. These results suggest that autoinducers increase the functionality of SdiA by enhancing the protein stability rather than by directly affecting the DNA-binding affinity. Structural analyses of the ligand-binding pocket showed that SdiA cannot accommodate ligands with long acyl chains, which was corroborated by isothermal titration calorimetry and thermal stability analyses. The formation of an intersubunit disulfide bond that might be relevant to modulation of the DNA-binding activity was predicted from the proximal position of two Cys residues in the DBDs of dimeric SdiA. It was confirmed that the binding affinity of SdiA for the uvrY promoter was reduced under oxidizing conditions, which suggested the possibility of regulation of SdiA by multiple independent signals such as quorum-sensing inducers and the oxidation state of the cell.

Titanium dxy ferromagnetism at the LaAlO3/SrTiO3 interface

A number of recent transport and magnetization studies have shown signs of ferromagnetism in the LaAlO3/SrTiO3 heterostructure, an unexpected property with no bulk analogue in the constituent materials. However, no experiment thus far has provided direct information on the host of the magnetism. Here we report spectroscopic investigations of the magnetism using element-specific techniques, including X-ray magnetic circular dichroism and X-ray absorption spectroscopy, along with corresponding model calculations. We find direct evidence for in-plane ferromagnetic order at the interface, with Ti(3+) character in the dxy orbital of the anisotropic t2g band. These findings establish a striking example of emergent phenomena at oxide interfaces.

Strongly spin-orbit coupled two-dimensional electron gas emerging near the surface of polar semiconductors

We investigate the two-dimensional highly spin-polarized electron accumulation layers commonly appearing near the surface of n-type polar semiconductors BiTeX (X=I, Br, and Cl) by angular-resolved photoemission spectroscopy. Because of the polarity and the strong spin-orbit interaction built in the bulk atomic configurations, the quantized conduction-band subbands show giant Rashba-type spin splitting. The characteristic 2D confinement effect is clearly observed also in the valence bands down to the binding energy of 4 eV. The X-dependent Rashba spin-orbit coupling is directly estimated from the observed spin-split subbands, which roughly scales with the inverse of the band-gap size in BiTeX.

Intramyocardial transfer of hepatocyte growth factor as an adjunct to CABG: phase I clinical study

The purpose of this phase I clinical trial was to evaluate the safety, tolerability and potential efficacy of VM202, naked DNA expressing two isoforms of hepatocyte growth factor, as an adjunct therapy to coronary artery bypass grafting (CABG) in patients with ischemic heart disease (IHD). Nine patients were assigned to receive increasing doses (0.5 to 2.0 mg) of VM202 injected into the right coronary artery (RCA) territory following completion of CABG for the left coronary artery territory. Patients were evaluated for safety and tolerability, and changes in myocardial functions were monitored via echocardiography, cardiac magnetic resonance imaging and myocardial single photon emission computed tomography throughout 6-month follow-up period. No serious complication related to VM202 was observed throughout the 6-month follow-up period. Global myocardial functions (wall motion score index, P=0.0084; stress perfusion, P=0.0002) improved during the follow-up period. In the RCA region, there was an increase in the stress perfusion (baseline vs 3-month, P=0.024; baseline vs 6-month, P=0.024) and also in the wall thickness of the diastolic and systolic phases. Intramyocardial injection of VM202 can be safely used in IHD patients with the tolerable dose of 2.0 mg. In addition, VM202 might appear to have improved regional myocardial perfusion and wall thickness in the injected region.

Subband structure of a two-dimensional electron gas formed at the polar surface of the strong spin-orbit perovskite KTaO3

We demonstrate the formation of a two-dimensional electron gas (2DEG) at the (100) surface of the 5d transition-metal oxide KTaO3. From angle-resolved photoemission, we find that quantum confinement lifts the orbital degeneracy of the bulk band structure and leads to a 2DEG composed of ladders of subband states of both light and heavy carriers. Despite the strong spin-orbit coupling, our measurements provide a direct upper bound for the potential Rashba spin splitting of only Δk(parallel)}~0.02 Å(-1) at the Fermi level. The polar nature of the KTaO3(100) surface appears to help mediate the formation of the 2DEG as compared to nonpolar SrTiO3(100).

Emergent phenomena at oxide interfaces

Recent technical advances in the atomic-scale synthesis of oxide heterostructures have provided a fertile new ground for creating novel states at their interfaces. Different symmetry constraints can be used to design structures exhibiting phenomena not found in the bulk constituents. A characteristic feature is the reconstruction of the charge, spin and orbital states at interfaces on the nanometre scale. Examples such as interface superconductivity, magneto-electric coupling, and the quantum Hall effect in oxide heterostructures are representative of the scientific and technological opportunities in this rapidly emerging field.

Fermi surface and superconductivity in low-density high-mobility δ-doped SrTiO3

The electronic structure of low-density n-type SrTiO3 δ-doped heterostructures is investigated by angular dependent Shubnikov-de Haas oscillations. In addition to a controllable crossover from a three- to two-dimensional Fermi surface, clear beating patterns for decreasing dopant layer thicknesses are found. These indicate the lifting of the degeneracy of the conduction band due to subband quantization in the two-dimensional limit. Analysis of the temperature-dependent oscillations shows that similar effective masses are found for all components, associated with the splitting of the light electron pocket. The dimensionality crossover in the superconducting state is found to be distinct from the normal state, resulting in a rich phase diagram as a function of dopant layer thickness.

Common origin of the circular-dichroism pattern in angle-resolved photoemission spectroscopy of SrTiO3 and Cu(x)Bi2Se3

Circular dichroism in the angular distribution of photoelectrons from SrTiO(3):Nb and Cu(x)Bi(2)Se(3) is investigated by 7-eV laser angle-resolved photoemission spectroscopy. In addition to the well-known node that occurs in the circular dichroism pattern when the incidence plane matches the mirror plane of the crystal, we show that another type of node occurs when the mirror plane of the crystal is vertical to the incidence plane and the electronic state is two-dimensional. The flower-shaped circular dichroism patterns in the angular distribution occurring around the Fermi level of SrTiO(3):Nb and around the Dirac point of Cu(x)Bi(2)Se(3) are explained on equal footings. We point out that the penetration depth of the topological states of Cu(x)Bi(2)Se(3) depends on momentum.

Structural basis for the negative regulation of bacterial stress response by RseB

The sigmaE-dependent stress response in bacterial cells is initiated by the DegS- and RseP-regulated intramembrane proteolysis of a membrane-spanning antisigma factor, RseA. RseB binds to RseA and inhibits its sequential cleavage, thereby functioning as a negative modulator of this response. In the crystal structure of the periplasmic domain of RseA bound to RseB, the DegS cleavage site of RseA is unstructured, however, its P1 residue is buried in the hydrophobic pocket of RseB, which suggests that RseB binding blocks the access of DegS to the cleavage site.

Microscopic origins for stabilizing room-temperature ferromagnetism in ultrathin manganite layers

La(0.7)Sr(0.3)MnO(3) is a conducting ferromagnet at room temperature. Combined with thin SrTiO(3) layers, the resulting heterostructures could be used as highly spin-polarized magnetic-tunnel-junction memories. However, when shrunk to dimensions below an apparent critical thickness, the structures become insulating and ferromagnetic ordering is suppressed. Interface spin and charge modulations are thought to create an interfacial dead layer, thus fundamentally limiting the use of this material in atomic-scale devices. The thickness of this dead layer, and whether it is intrinsic, is still controversial. Here we use atomic-resolution electron spectroscopy to demonstrate that the degradation of the magnetic and transport properties of La(0.7)Sr(0.3)MnO(3)/SrTiO(3) multilayers correlates with atomic intermixing at the interfaces, and the presence of extended two-dimensional cation defects in the La(0.7)Sr(0.3)MnO(3) layers (in contrast to three-dimensional precipitates in thick films). When these extrinsic defects are eliminated, metallic ferromagnetism at room temperature can be stabilized in five-unit-cell-thick manganite layers in superlattices, placing the upper limit for any intrinsic dead layer at two unit cells per interface.

Structural basis for the reaction mechanism of UDP-glucose pyrophosphorylase

UDP-glucose pyrophosphorylases (UGPase; EC 2.7.7.9) catalyze the conversion of UTP and glucose-1-phosphate to UDP-glucose and pyrophosphate and vice versa. Prokaryotic UGPases are distinct from their eukaryotic counterparts and are considered appropriate targets for the development of novel antibacterial agents since their product, UDP-glucose, is indispensable for the biosynthesis of virulence factors such as lipopolysaccharides and capsular polysaccharides. In this study, the crystal structures of UGPase from Helicobacter pylori (HpUGPase) were determined in apo- and UDP-glucose/Mg(2+)-bound forms at 2.9 A and 2.3 A resolutions, respectively. HpUGPase is a homotetramer and its active site is located in a deep pocket of each subunit. Magnesium ion is coordinated by Asp130, two oxygen atoms of phosphoryl groups, and three water molecules with octahedral geometry. Isothermal titration calorimetry analyses demonstrated that Mg(2+) ion plays a key role in the enzymatic activity of UGPase by enhancing the binding of UGPase to UTP or UDP-glucose, suggesting that this reaction is catalyzed by an ordered sequential Bi Bi mechanism. Furthermore, the crystal structure explains the specificity for uracil bases. The current structural study combined with functional analyses provides essential information for understanding the reaction mechanism of bacterial UGPases, as well as a platform for the development of novel antibacterial agents.

Two-dimensional confinement of 3d{1} electrons in LaTiO_{3}/LaAlO{3} multilayers

We report spectroscopic ellipsometry measurements of the anisotropy of the interband transitions parallel and perpendicular to the planes of (LaTiO3)n(LaAlO3)5 multilayers with n=1-3. These provide direct information about the electronic structure of the two-dimensional (2D) 3d{1} state of the Ti ions. In combination with local density approximation, including a Hubbard U calculation, we suggest that 2D confinement in the TiO2 slabs lifts the degeneracy of the t{2g} states leaving only the planar d{xy} orbitals occupied. We outline that these multilayers can serve as a model system for the study of the t{2g} 2D Hubbard model.

Dominant mobility modulation by the electric field effect at the LaAlO3/SrTiO3 interface

Caviglia et al. [Nature (London) 456, 624 (2008)] have found that the superconducting LaAlO3/SrTiO3 interface can be gate modulated. A central issue is to determine the principal effect of the applied electric field. Using magnetotransport studies of a gated structure, we find that the mobility variation is almost 5 times that of the sheet carrier density. Furthermore, superconductivity can be suppressed at both positive and negative gate bias. These results indicate that the relative disorder strength strongly increases across the superconductor-insulator transition.

Spectroscopic evidence for competing reconstructions in polar multilayers LaAlO3/LaVO3/LaAlO3

We have studied the valence redistribution of V in LaAlO(3)/LaVO(3)/LaAlO(3) trilayers, which are composed of only polar layers grown on SrTiO3 (001) substrates, by core-level photoemission spectroscopy. We have found that the V valence is intermediate between V3+ and V4+ for thin LaAlO3 cap layers, decreases with increasing cap-layer thickness, and finally recovers the bulk value of V3+ at approximately 10 unit-cell thickness. In order to interpret these results, we propose that the atomic reconstruction of the polar LaAlO3 surface competes with the purely electronic V valence change so that the polar catastrophe is avoided at the cost of minimum energy.

Structural and functional characterization of soluble endoglin receptor

Endoglin, an accessory membrane receptor of transforming growth factor-beta (TGF-beta)1, modulates the cellular response to TGF-beta via its interaction with type I and II TGF-beta receptors. It has been considered a promising target for the development of therapeutics and cancer markers. We have established stable CHO cell lines that efficiently secrete soluble endoglin (s-endoglin) fused with human growth hormone. Two oligomeric forms were observed in a homogeneous preparation of s-endoglin, as a dimer and a tetramer. The dimeric s-endoglin enhanced TGF-beta responsiveness in U937 cells, thus proving its potential for therapeutic applications. Small angle X-ray scattering (SAXS) experiments revealed elongated conformations of both dimeric and tetrameric s-endoglins in solution, suggesting that s-endoglin might undergo conformational adaptations upon TGF-beta binding. The current results provide important references and material for high-resolution structural studies and for medical applications of s-endoglin.

The structures of non-CG-repeat Z-DNAs co-crystallized with the Z-DNA-binding domain, hZ alpha(ADAR1)

The Z-DNA conformation preferentially occurs at alternating purine-pyrimidine repeats, and is specifically recognized by Z alpha domains identified in several Z-DNA-binding proteins. The binding of Z alpha to foreign or chromosomal DNA in various sequence contexts is known to influence various biological functions, including the DNA-mediated innate immune response and transcriptional modulation of gene expression. For these reasons, understanding its binding mode and the conformational diversity of Z alpha bound Z-DNAs is of considerable importance. However, structural studies of Z alpha bound Z-DNA have been mostly limited to standard CG-repeat DNAs. Here, we have solved the crystal structures of three representative non-CG repeat DNAs, d(CACGTG)(2), d(CGTACG)(2) and d(CGGCCG)(2) complexed to hZ alpha(ADAR1) and compared those structures with that of hZ alpha(ADAR1)/d(CGCGCG)(2) and the Z alpha-free Z-DNAs. hZ alpha(ADAR1) bound to each of the three Z-DNAs showed a well conserved binding mode with very limited structural deviation irrespective of the DNA sequence, although varying numbers of residues were in contact with Z-DNA. Z-DNAs display less structural alterations in the Z alpha-bound state than in their free form, thereby suggesting that conformational diversities of Z-DNAs are restrained by the binding pocket of Z alpha. These data suggest that Z-DNAs are recognized by Z alpha through common conformational features regardless of the sequence and structural alterations.

Efficient Selection of Stable Chinese Hamster Ovary (CHO) Cell Lines for Expression of Recombinant Proteins by Using Human Interferon β SAR Element

We describe the development of an efficient expression system suitable for the stable expression of recombinant genes in Chinese hamster ovary (CHO) cells using the human interferon beta SAR element. The insertion of two copies of the human interferon beta SAR element at the 5' and 3' flanking regions of the beta-galactosidase reporter gene increased the frequency of beta-galactosidase positive colonies by up to 75% and enhanced beta-galactosidase expression by 15- to 20-fold after G418 selection or 30- to 40-fold at the initial stage of the MTX selection procedure. Deletion analysis showed that the whole DNA regions of the human interferon beta SAR element are required for beta-galactosidase expression enhancement. The developed expression system was also highly effective at enhancing the stable expression of two therapeutically important proteins, namely, erythropoietin (EPO) and hepatocyte growth factor (HGF). We isolated stable colonies with expression levels of 47 microg/10(6) cells/day for EPO and 13 microg/10(6) cells/day for HGF, suggesting that the developed expression system based on the human beta SAR element is suitable for expressing high levels of recombinant proteins in CHO cells.

Vanishing hall coefficient in the extreme quantum limit in photocarrier-doped SrTiO3

We explore the extreme quantum limit of photogenerated electrons in quantum paraelectric SrTiO3. This regime is distinct from conventional semiconductors, due to the large electron effective mass and large dielectric constant. At low temperature, the magnetoresistance and Hall resistivity saturate at a high magnetic field, deviating from conventional behavior. As a result, the Hall coefficient vanishes on the scale of the ratio of the Landau level splitting to the thermal energy, indicating the essential role of lowest Landau level occupancy, as limited by thermal broadening.

Polar discontinuity doping of the LaVO_{3}/SrTiO_{3} interface

We have investigated the transport properties of LaVO_{3}/SrTiO_{3} Mott-insulator-band-insulator heterointerfaces for various configurations. The (001)-oriented n-type VO_{2}/LaO/TiO_{2} polar discontinuity is conducting, exhibiting a LaVO3 thickness-dependent metal-insulator transition and low temperature anomalous Hall effect. The (001) p-type VO_{2}/SrO/TiO_{2} interface, formed by inserting a single layer of bulk metallic SrVO3 or SrO, drives the interface insulating. The (110) heterointerface is also insulating, indicating interface conduction arising from electronic reconstructions.

Nanometer scale electronic reconstruction at the interface between LaVO3 and LaVO4

Electrons at interfaces, driven to minimize their free energy, are distributed differently than in bulk. This can be dramatic at interfaces involving heterovalent compounds. Here we profile an abrupt interface between V 3d2 LaVO3 and V 3d0 LaVO4 using electron energy loss spectroscopy. Although no bulk phase of LaVOx with a V 3d1 configuration exists, we find a nanometer-wide region of V 3d1 at the LaVO3/LaVO4 interface, rather than a mixture of V 3d0 and V 3d2. The two-dimensional sheet of 3d1 electrons is a prototypical electronic reconstruction at an interface between competing ground states.

Biochemical characterization and preliminary X-ray crystallographic study of the domains of human ZBP1 bound to left-handed Z-DNA

ZBP1 is involved in host responses against cellular stresses, including tumorigenesis and viral infection. Structurally, it harbors two copies of the Zalpha domain containing the Zalpha motif, at its N terminus. Here, we attempted to characterize the Z-DNA binding activities of two Zalpha domains in the human ZBP1, hZalpha(ZBP1) and hZbeta(ZBP1), using circular dichroism (CD). Our results indicated that both hZalpha(ZBP1) and hZbeta(ZBP1) are viable Z-DNA binders, and their binding activities are comparable to those of previously-established Zalpha domains. Additionally, we crystallized hZbeta(ZBP1) in a complex with Z-DNA, d(TCGCGCG)2. The crystal diffracted to 1.45 angstroms, and belongs to the P2(1)2(1)2(1) space group, with the unit-cell parameters: a = 29.53 angstroms, b = 58.25 angstroms, and c = 88.61 angstroms. The delineation of this structure will provide insight into the manner in which diverse Zalpha motifs recognize Z-DNA.

Standardization of 125I and 238Pu

A simple distance-variable detection table on which two detectors can be mounted and moved back and forth facing each other centred on a sample source has been constructed for photon-photon and alpha-photon coincidence counting for 125I and 238Pu, respectively. Two NaI(Tl) detectors were used for the standardization of 125I. A Si detector and an NaI(Tl) detector were employed for the standardization of 238Pu. The NaI(Tl) detectors have a very thin aluminium window for measuring low-energy photons from 125I and 238Pu while the Si-detector is a usable-in-air ion-implanted detector for alpha particles from 238Pu. A thin collodion film was used for 238Pu samples, whereas a thick polyester film was used for 125I samples to prevent 125I from leaking from the sample. The key comparison result of 125I showed good agreement, and the result of 238Pu was also compared with that of liquid scintillation counting.

A high-mobility electron gas at the LaAlO3/SrTiO3 heterointerface

Polarity discontinuities at the interfaces between different crystalline materials (heterointerfaces) can lead to nontrivial local atomic and electronic structure, owing to the presence of dangling bonds and incomplete atomic coordinations. These discontinuities often arise in naturally layered oxide structures, such as the superconducting copper oxides and ferroelectric titanates, as well as in artificial thin film oxide heterostructures such as manganite tunnel junctions. If polarity discontinuities can be atomically controlled, unusual charge states that are inaccessible in bulk materials could be realized. Here we have examined a model interface between two insulating perovskite oxides--LaAlO3 and SrTiO3--in which we control the termination layer at the interface on an atomic scale. In the simple ionic limit, this interface presents an extra half electron or hole per two-dimensional unit cell, depending on the structure of the interface. The hole-doped interface is found to be insulating, whereas the electron-doped interface is conducting, with extremely high carrier mobility exceeding 10,000 cm2 V(-1) s(-1). At low temperature, dramatic magnetoresistance oscillations periodic with the inverse magnetic field are observed, indicating quantum transport. These results present a broad opportunity to tailor low-dimensional charge states by atomically engineered oxide heteroepitaxy.

Crystal structure of the protease domain of a heat-shock protein HtrA from Thermotoga maritima

HtrA (high temperature requirement A), a periplasmic heat-shock protein, functions as a molecular chaperone at low temperatures, and its proteolytic activity is turned on at elevated temperatures. To investigate the mechanism of functional switch to protease, we determined the crystal structure of the NH(2)-terminal protease domain (PD) of HtrA from Thermotoga maritima, which was shown to retain both proteolytic and chaperone-like activities. Three subunits of HtrA PD compose a trimer, and multimerization architecture is similar to that found in the crystal structures of intact HtrA hexamer from Escherichia coli and human HtrA2 trimer. HtrA PD shares the same fold with chymotrypsin-like serine proteases, but it contains an additional lid that blocks access the of substrates to the active site. A corresponding lid found in E. coli HtrA is a long loop that also blocks the active site of another subunit. These results suggest that the activation of the proteolytic function of HtrA at elevated temperatures might occur by a conformational change, which includes the opening of the helical lid to expose the active site and subsequent rearrangement of a catalytic triad and an oxyanion hole.

Portal vein aneurysm of the umbilical portion: imaging features and the relationship with portal vein anomalies

BACKGROUND

We evaluated the imaging features of portal vein aneurysm occurring at the umbilical portion and the relation between portal vein aneurysm of the umbilical portion and portal vein anomaly.

METHODS

Retrograde analysis was performed in 18 patients with portal vein aneurysm of the umbilical portion of the portal vein. We analyzed the size, shape, and imaging findings of portal vein aneurysm. In addition, we evaluated associated portal vein anomalies, specifically, the branching pattern of the intrahepatic portal vein and the position of the umbilical portion of the left portal vein.

RESULTS

The diameter of the portal vein aneurysm ranged from 1.5 to 2.2 cm and the shape of the portal vein aneurysm was saccular (n = 14) or fusiform (n = 4). Imaging findings of the portal vein aneurysm of the umbilical portion were typical for its vascular nature. Portal vein anomalies were seen in eight of 18 patients (44%): the right anterior segmental portal vein (n = 7) or the right anterior and posterior segmental portal veins (n = 1) originating from the umbilical portion of the left portal vein and a rightward deviation of the umbilical portion of the left portal vein (n = 4).

CONCLUSION

Due to its vascular nature, noninvasive diagnostic modalities can enable the detection of portal vein aneurysm of the umbilical portion, and there is a close relation between portal vein aneurysm of the umbilical portion and portal vein anomaly.

Artificial charge-modulationin atomic-scale perovskite titanate superlattices

The nature and length scales of charge screening in complex oxides are fundamental to a wide range of systems, spanning ceramic voltage-dependent resistors (varistors), oxide tunnel junctions and charge ordering in mixed-valence compounds. There are wide variations in the degree of charge disproportionation, length scale, and orientation in the mixed-valence compounds: these have been the subject of intense theoretical study, but little is known about the microscopic electronic structure. Here we have fabricated an idealized structure to examine these issues by growing atomically abrupt layers of LaTi(3+)O(3) embedded in SrTi(4+)O(3). Using an atomic-scale electron beam, we have observed the spatial distribution of the extra electron on the titanium sites. This distribution results in metallic conductivity, even though the superlattice structure is based on two insulators. Despite the chemical abruptness of the interfaces, we find that a minimum thickness of five LaTiO(3) layers is required for the centre titanium site to recover bulk-like electronic properties. This represents a framework within which the short-length-scale electronic response can be probed and incorporated in thin-film oxide heterostructures.

Hyperhomocysteinemia due to methionine synthase deficiency, cblG: structure of the MTR gene, genotype diversity, and recognition of a common mutation, P1173L

Mutations in the MTR gene, which encodes methionine synthase on human chromosome 1p43, result in the methylcobalamin deficiency G (cblG) disorder, which is characterized by homocystinuria, hyperhomocysteinemia, and hypomethioninemia. To investigate the molecular basis of the disorder, we have characterized the structure of the MTR gene, thereby identifying exon-intron boundaries. This enabled amplification of each of the 33 exons of the gene, from genomic DNA from a panel of 21 patients with cblG. Thirteen novel mutations were identified. These included five deletions (c.12-13delGC, c.381delA, c.2101delT, c.2669-2670delTG, and c.2796-2800delAAGTC) and two nonsense mutations (R585X and E1204X) that would result in synthesis of truncated proteins that lack portions critical for enzyme function. One mutation was identified that resulted in conversion of A to C of the invariant A of the 3' splice site of intron 9. Five missense mutations (A410P, S437Y, S450H, H595P, and I804T) were identified. The latter mutations, as well as the splice-site mutation, were not detected in a panel of 50 anonymous DNA samples, suggesting that these sequence changes are not polymorphisms present in the general population. In addition, a previously described missense mutation, P1173L, was detected in 16 patients in an expanded panel of 24 patients with cblG. Analysis of haplotypes constructed using sequence polymorphisms identified within the MTR gene demonstrated that this mutation, a C-->T transition in a CpG island, has occurred on at least two separate genetic backgrounds.