Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties

The nucleosome is a fundamental unit of chromatin in which about 150 base pairs of DNA are wrapped around a histone octamer. The overlapping di-nucleosome has been proposed as a product of chromatin remodeling around the transcription start site, and previously found as a chromatin unit, in which about 250 base pairs of DNA continuously bind to the histone core composed of a hexamer and an octamer. In the present study, our genome-wide analysis of human cells suggests another higher nucleosome stacking structure, the overlapping tri-nucleosome, which wraps about 300-350 base-pairs of DNA in the region downstream of certain transcription start sites of actively transcribed genes. We determine the cryo-electron microscopy (cryo-EM) structure of the overlapping tri-nucleosome, in which three subnucleosome moieties, hexasome, hexasome, and octasome, are associated by short connecting DNA segments. Small angle X-ray scattering and coarse-grained molecular dynamics simulation analyses reveal that the cryo-EM structure of the overlapping tri-nucleosome may reflect its structure in solution. Our findings suggest that nucleosome stacking structures composed of hexasome and octasome moieties may be formed by nucleosome remodeling factors around transcription start sites for gene regulation.

Real-world treatment patterns and outcomes of abemaciclib for the treatment of HR + , HER2- metastatic breast cancer patients in Japan

INTRODUCTION

This study described, in routine clinical practice in Japan, the patient characteristics, treatment patterns, and outcomes of female patients with HR + /HER2- metastatic breast cancer (MBC) who started abemaciclib treatment.

METHODS

Clinical charts were reviewed for patients starting abemaciclib in 12/2018-08/2021 with a minimum of 3 months follow-up data post-abemaciclib initiation regardless of abemaciclib discontinuation. Patient characteristics, treatment patterns, and tumor response were descriptively summarized. Kaplan-Meier curves estimated progression-free survival (PFS).

RESULTS

200 patients from 14 institutions were included. At abemaciclib initiation, median age was 59 years, and the Eastern Cooperative Oncology Group performance status score was 0/1/2 for 102/68/5 patients (58.3/38.9/2.9%), respectively. Most had an abemaciclib starting dose of 150 mg (92.5%). The percentage of patients receiving abemaciclib as 1st, 2nd, or 3rd line treatment was 31.5%, 25.8%, and 25.2%, respectively. The most frequent endocrine therapy drugs used with abemaciclib were fulvestrant (59%) and aromatase inhibitors (40%). Evaluation of tumor response was available for 171 patients, 30.4% of whom had complete/partial response. Median PFS was 13.0 months (95% CI 10.1-15.8 months).

CONCLUSIONS

In a routine clinical practice setting in Japan, patients with HR + , HER2- MBC appear to benefit from abemaciclib treatment in terms of treatment response and median PFS, with the results broadly reflecting the evidence demonstrated in clinical trials.

Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B

The canonical nucleosome, which represents the major packaging unit of eukaryotic chromatin, has an octameric core composed of two histone H2A-H2B and H3-H4 dimers with ∼147 base pairs (bp) of DNA wrapped around it. Non-nucleosomal particles with alternative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Using cryo-electron microscopy, we solved the structure of the H3-H4 octasome, a nucleosome-like particle with a di-tetrameric core consisting exclusively of the H3 and H4 histones. The core is wrapped by ∼120 bp of DNA in 1.5 negative superhelical turns, forming two stacked disks that are connected by a H4-H4' four-helix bundle. Three conformations corresponding to alternative interdisk angles were observed, indicating the flexibility of the H3-H4 octasome structure. In vivo crosslinking experiments detected histone-histone interactions consistent with the H3-H4 octasome model, suggesting that H3-H4 octasomes or related structural features exist in cells.

Structural basis for p53 binding to its nucleosomal target DNA sequence

The tumor suppressor p53 functions as a pioneer transcription factor that binds a nucleosomal target DNA sequence. However, the mechanism by which p53 binds to its target DNA in the nucleosome remains elusive. Here we report the cryo-electron microscopy structures of the p53 DNA-binding domain and the full-length p53 protein complexed with a nucleosome containing the 20 base-pair target DNA sequence of p53 (p53BS). In the p53-nucleosome structures, the p53 DNA-binding domain forms a tetramer and specifically binds to the p53BS DNA, located near the entry/exit region of the nucleosome. The nucleosomal position of the p53BS DNA is within the genomic p21 promoter region. The p53 binding peels the DNA from the histone surface, and drastically changes the DNA path around the p53BS on the nucleosome. The C-terminal domain of p53 also binds to the DNA around the center and linker DNA regions of the nucleosome, as revealed by hydroxyl radical footprinting. These results provide important structural information for understanding the mechanism by which p53 binds the nucleosome and changes the chromatin structure for gene activation.

Si1-xGex anode synthesis on plastic films for flexible rechargeable batteries

SiGe is a promising anode material for replacing graphite in next generation thin-film batteries owing to its high theoretical charge/discharge capacity. Metal-induced layer exchange (LE) is a unique technique used for the low-temperature synthesis of SiGe layers on arbitrary substrates. Here, we demonstrate the synthesis of Si_1-xGe_x (x = 0-1) layers on plastic films using Al-induced LE. The resulting SiGe layers exhibited high electrical conductivity (up to 1200 S cm^-1), reflecting the self-organized doping effect of LE. Moreover, the Si_1-xGe_x layer synthesized by the same process was adopted as the anode for the lithium-ion battery. All Si_1-xGe_x anodes showed clear charge/discharge operation and high coulombic efficiency (≥ 97%) after 100 cycles. While the discharge capacities almost reflected the theoretical values at each x at 0.1 C, the capacity degradation with increasing current rate strongly depended on x. Si-rich samples exhibited high initial capacity and low capacity retention, while Ge-rich samples showed contrasting characteristics. In particular, the Si_1-xGe_x layers with x ≥ 0.8 showed excellent current rate performance owing to their high electrical conductivity and low volume expansion, maintaining a high capacity (> 500 mAh g^-1) even at a high current rate (10 C). Thus, we revealed the relationship between SiGe composition and anode characteristics for the SiGe layers formed by LE at low temperatures. These results will pave the way for the next generation of flexible batteries based on SiGe anodes.

Linker DNA and histone contributions in nucleosome binding by p53

The tumour suppressor protein p53 regulates various genes involved in cell-cycle arrest, apoptosis and DNA repair in response to cellular stress, and apparently functions as a pioneer transcription factor. The pioneer transcription factors can bind nucleosomal DNA, where many transcription factors are largely restricted. However, the mechanisms by which p53 recognizes the nucleosomal DNA are poorly understood. In the present study, we found that p53 requires linker DNAs for the efficient formation of p53-nucleosome complexes. p53 forms an additional specific complex with the nucleosome, when the p53 binding sequence is located around the entry/exit region of the nucleosomal DNA. We also showed that p53 directly binds to the histone H3-H4 complex via its N-terminal 1–93 amino acid region. These results shed light on the mechanism of nucleosome recognition by p53.

FRI0179 A STUDY ON THE ACHIEVEMENT OF LUPUS LOW DISEASE ACTIVITY STATE AND QUALITY OF LIFE IN PATIENTS WITH SYSTEMIC LUPUS ERYTHEMATOSUS: FROM THE JUNTENDO UNIVERSITY SLE PROSPECTIVE REGISTRY STUDY

Background:

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease of unknown etiology that affects mostly young women. Multiorgan complications and prolonged treatment significantly cause physical and mental stress in patients. Improving patients’ quality of life (QOL) in SLE treatment is essential. We examined the treatment effects on disease activity and QOL of SLE patients.

Objectives:

In recent years, lupus low disease activity state (LLDAS) has been proposed as a treatment target for SLE. Patients who achieve LLDAS have a low recurrence rate for lupus and a low risk of serious complications (1). The aim of this study is to investigate whether achieving LLDAS reduces not only recurrence rate and complications of SLE but also improves patients’ QOL.

Methods:

A total of 104 SLE patients were enrolled in our prospective SLE registry study (Juntendo, Multi-center, Prospective cohort for investigation of clinical course and outcome in SLE: JUMP) conducted at our institution. SLE was diagnosed using the American College of Rheumatology (ACR) 1982 criteria (revised in 1997). QOL was evaluated using the standard version of the 36-item short form health survey version 2 (SF36v2). Participants were divided into the LLDAS achievement and non-achievement groups, and the characteristics of each group including results of SF36v2 were examined.

Results:

This study included 104 SLE patients, 94 female and 10 male, and the average age and disease duration were 46.4±13.8 and 14.5±11.3 years, respectively. The average corticosteroid dose was 8.0±17.4 mg/day in terms of prednisolone, and anti-dsDNA antibody titer was 16.8±38.5 IU/ml. Of the 104 patients, 57 achieved LLDAS. The subscale’s standard scoring using SF36v2 for role physical (RP) was 78.9±24.0 and 64.6±27.6 (P<0.01), general health (GH) was 50.0±17.0 and 42.0±19.3 (P<0.05), vitality (VT) was 55.8±15.8 and 38.0±24.1 (P<0.01), social functioning (SF) was 82.0±20.7 and 66.5±26.3 (P<0.01), role emotional (RE) was 89.0±16.1 and 73.4±28.1 (P<0.01), and mental health (MH) was 72.4±15.9 and 58.3±21.8 (P<0.01) in the LLDAS achievement and non-achievement groups, respectively. Furthermore, scoring based on the national standard value in the LLDAS achievement group showed that two categories were >50. However, in the LLDAS non-achievement group, all categories were <50. In particular, RP, GH, VT, SF, RE, and MH of the LLDAS achievement group had significantly higher scores than the LLDAS non-achievement group (RP and GH: p<0.05 and VT, SF, RE and MH: p<0.01).

Conclusion:

Results of examining the association between LLDAS and QOL using SF36v2 in SLE patients showed that patients who achieved LLDAS had significantly better standard statistical scores in many subscale categories. Thus, LLDAS achievement as a treatment target for SLE patients greatly contributes to improving patients’ QOL.

References:

[1]Franklyn K, et al. Definition and initial validation of a Lupus Low Disease Activity State (LLDAS).Ann Rheum Dis. 2016 Sep;75(9):1615-21.

Disclosure of Interests:

None declared

Nine genes abundantly expressed in the epididymis are not essential for male fecundity in mice

Background

Spermatozoa become competent for fertilization during transit through the epididymis. As spermatozoa from the proximal caudal epididymis can fertilize eggs, proteins from the caput and corpus epididymis are required for sperm maturation.

Objectives

Microarray analysis identified that more than 17,000 genes are expressed in the epididymis; however, few of these genes demonstrate expression restricted to the epididymis. To analyze epididymis‐enriched gene function in vivo, we generated knockout (KO) mutations in nine genes that are abundantly expressed in the caput and corpus region of the epididymis.

Materials and methods

KO mice were generated using the CRISPR/Cas9 system. The histology of the epididymis was observed with hematoxylin and eosin staining. KO males were caged with wild‐type females for 3–6 months to check fertility.

Results

We generated individual mutant mouse lines having indel mutations in Pate1, Pate2, or Pate3. We also deleted the coding regions of Clpsl2, Epp13, and Rnase13, independently. Finally, the 150 kb region encoding Gm1110, Glb1l2, and Glb1l3 was deleted to generate a triple KO mouse line. Histology of the epididymis and sperm morphology of all KO lines were comparable to control males. The females mated with these KO males delivered pups at comparable numbers as control males.

Discussion and conclusion

We revealed that nine genes abundantly expressed in the caput and corpus epididymis are dispensable for sperm function and male fecundity. CRISPR/Cas9‐mediated KO mice generation accelerates the screening of epididymis‐enriched genes for potential functions in reproduction.

Crystallographic analysis of the overlapping dinucleosome as a novel chromatin unit

Recent evidence has suggested that chromatin is not simply repeats of the canonical nucleosome, called the “octasome”, but may include diverse repertoires of basic structural units. During the transcription process, a nucleosome is repositioned by a chromatin remodeler and collides with a neighboring nucleosome, thus creating an unusual nucleosome substructure termed the “overlapping dinucleosome”. We previously developed a method for the large-scale preparation of the overlapping dinucleosome. This method enabled us to solve the crystal structure of the overlapping dinucleosome, which revealed an unexpected structure composed of an octameric histone core associated with a hexameric histone core lacking one H2A-H2B dimer.

Intermetallic: A Pseudoelement for Catalysis

A clear correlation between electronic structure and CO₂ selectivity for steam reforming of methanol (SRM) was obtained with PdZn, PtZn, NiZn, and PdCd intermetallics on the basis of experiments and calculations. In order to rule out the effects of oxide supports, the intermetallic powders were simply prepared by alloying in an arc furnace followed by crushing in a mortar. PdZn and PdCd exhibit valence electronic densities of states similar to that of Cu and significant chemical shifts (larger than 1 eV) of Pd 3d states with respect to pure Pd, as verified by high-resolution hard X-ray photoelectron spectroscopy (HXPS) measurements and density functional theory (DFT) calculations. Consequently, they show the similar high selectivity of CO₂ for the SRM reaction. However, this is not the case for PtZn and NiZn because of the slight differences in their valence electronic structures from that of PdZn. The interval between the Fermi level and the top of the d band is closely related to the selectivity of CO₂ for the SRM: the larger the interval is, the higher is the selectivity of CO₂. According to DFT calculations for bulk PdZn performed by Chen et al. ( Phys. Rev. B 2003 , 68 , 075417 ), the (111) and (100) surfaces exposing Zn and Pd in an equimolar ratio are more stable than the (001) or (110) surfaces terminated by alternative Zn or Pd layers. First-principles slab calculations for PdZn, PtZn, and NiZn show that bond breaking on the surface leads to a reduction in the d bandwidth but that the d band for stable (111) or (100) surfaces remains essentially unchanged from that of the bulk. It is intriguing that PdZn and PdCd do not contain Cu but show similar valence electronic structure and catalytic selectivity, and hence, a concept is proposed where PdZn and PdCd are regarded as pseudoelements of Cu. The basis of this concept is like electronic structure, like catalysis, which has been demonstrated by experiments and calculations. This is a logical way to enable us to look for new catalysts in which precious metals are partially or completely replaced by base metals. We do not expect that this concept can be applied to all catalytic reactions, but this approach is one of most promising ways to derive a better understanding of the origin of catalytic mechanisms and eventually allow us to design useful catalysts intentionally in the future. This Account reviews the authors' published works on this topic.

Core Mediator structure at 3.4 Å extends model of transcription initiation complex

Mediator is a multiprotein co-activator that binds the transcription pre-initiation complex (PIC) and regulates RNA polymerase (Pol) II. The Mediator head and middle modules form the essential core Mediator (cMed), whereas the tail and kinase modules play regulatory roles. The architecture of Mediator and its position on the PIC are known, but atomic details are limited to Mediator subcomplexes. Here we report the crystal structure of the 15-subunit cMed from Schizosaccharomyces pombe at 3.4 Å resolution. The structure shows an unaltered head module, and reveals the intricate middle module, which we show is globally required for transcription. Sites of known Mediator mutations cluster at the interface between the head and middle modules, and in terminal regions of the head subunits Med6 (ref. 16) and Med17 (ref. 17) that tether the middle module. The structure led to a model for Saccharomyces cerevisiae cMed that could be combined with the 3.6 Å cryo-electron microscopy structure of the core PIC (cPIC). The resulting atomic model of the cPIC-cMed complex informs on interactions of the submodules forming the middle module, called beam, knob, plank, connector, and hook. The hook is flexibly linked to Mediator by a conserved hinge and contacts the transcription initiation factor IIH (TFIIH) kinase that phosphorylates the carboxy (C)-terminal domain (CTD) of Pol II and was recently positioned on the PIC. The hook also contains residues that crosslink to the CTD and reside in a previously described cradle. These results provide a framework for understanding Mediator function, including its role in stimulating CTD phosphorylation by TFIIH.

Quiet T1-Weighted Pointwise Encoding Time Reduction with Radial Acquisition for Assessing Myelination in the Pediatric Brain

BACKGROUND AND PURPOSE

T1-weighted pointwise encoding time reduction with radial acquisition (PETRA) sequences require limited gradient activity and allow quiet scanning. We aimed to assess the usefulness of PETRA in pediatric brain imaging.

MATERIALS AND METHODS

We included consecutive pediatric patients who underwent both MPRAGE and PETRA. The contrast-to-noise and contrast ratios between WM and GM were compared in the cerebellar WM, internal capsule, and corpus callosum. The degree of myelination was rated by using 4-point scales at each of these locations plus the subcortical WM in the anterior frontal, anterior temporal, and posterior occipital lobes. Two radiologists made all assessments, and the intra- and interrater agreement was calculated by using intraclass correlation coefficients. Acoustic noise on MPRAGE and PETRA was measured.

RESULTS

We included 56 patients 5 days to 14 years of age (mean age, 36.6 months) who underwent both MPRAGE and PETRA. The contrast-to-noise and contrast ratios for PETRA were significantly higher than those for MPRAGE (P < .05), excluding the signal ratio for cerebellar WM. Excellent intra- and interrater agreement were obtained for myelination at all locations except the cerebellar WM. The acoustic noise on PETRA (58.2 dB[A]) was much lower than that on MPRAGE (87.4 dB[A]).

CONCLUSIONS

PETRA generally showed better objective imaging quality without a difference in subjective image-quality evaluation and produced much less acoustic noise compared with MPRAGE. We conclude that PETRA can substitute for MPRAGE in pediatric brain imaging.

Mediator Architecture and RNA Polymerase II Interaction

Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism.

Templated quasicrystalline ordering of single elements and molecules

We have used quasicrystals as templates for the exploration of new epitaxial phenomena. Several interesting results have been observed in the growth on surfaces of the common Al-based quasicrystals [1]. These include pseudomorphic monolayers, quasiperiodically modulated multilayer structures, and fivefold-twinned islands with magic heights influenced by quantum size effects [1]. Here we present our recent works on the growth of various elements and molecules on a new substrate, icosahedral (i) Ag-In-Yb quasicrystal, which have resulted in various epitaxial phenomena not observed previously. The growth of Pb on the five-fold surface of i-Ag-In-Yb yields a film which possesses quasicrystalline ordering in three-dimension [2]. Using scanning tunneling microscopy (STM) and DFT calculations of adsorption energies, we find that lead atoms occupy the positions of atoms in the rhombic triacontahedral (RTH) cluster, the building block of the substrate, and thus grow in layers with different heights and adsorption energies. The adlayer–adlayer interaction is crucial for stabilizing the epitaxial quasicrystalline structure. We will also present the first example of quasicrystalline molecular layers. Pentacene adsorbs at tenfold-symmetric sites of Yb atoms around surface-bisected RTH clusters, yielding quasicrystalline order [3]. Similarly, C-60 growth on the five-fold surface of i-Al-Cu-Fe at elevated temperature produces quasicrystalline layer, where the growth is mediated by Fe atoms on the substrate surface [3]. The finding of quasicrystalline thin films of single elements and molecules opens an avenue for further investigation of the impact of the aperiodic atomic order over periodic order on the physical and chemical properties of materials.

Antibody against chromatin assembly factor-1 is a novel autoantibody specifically recognized in systemic lupus erythematosus

Autoantibodies to proliferating cell nuclear antigen (PCNA) are specifically, if rarely, present in systemic lupus erythematosus (SLE) patient sera. Even SLE patients lacking PCNA reactivity often show reaction to PCNA-binding protein. Here, immunoreactivity to chromatin assembly factor-1 (CAF-1), an essential molecule for DNA replication and a PCNA-binding protein, was compared for the sera of SLE patients, normal healthy controls (NHCs) and other disease controls, and in autoimmune sera reactive to standard autoantigens, by enzyme-linked immunosorbent assay (ELISA), indirect immunofluorescence, and immunoblotting. CAF1 and IRF1 expression in SLE and NHC peripheral mononuclear cells were compared by quantitative real-time polymerase chain reaction. Serum interferon-γ-inducing protein-10 and anti-double-stranded (ds)DNA antibody levels were measured by ELISA. Increased CAF-1 autoimmune reactivity was recognized in SLE or serum anti-dsDNA antibody-positive patients. Significantly greater central nervous system (CNS) involvement (aseptic meningitis) and serum anti-dsDNA antibody titers were present more often in anti-CAF-1 antibody-positive than antibody-negative SLE patients. IFN-γ positively regulated CAF-1 expression in vitro and was associated with anti-CAF-1 antibody production in SLE. Thus, a novel anti-CAF-1 autoantibody is frequently found in patients with SLE and is a useful biomarker for diagnosis, especially in cases with CNS involvement. Aberrant IFN-γ regulation appears to play an important role in anti-CAF-1 antibody production in SLE.

Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm

In all eukaryotes, transcribed precursor tRNAs are maturated by processing and modification processes in nucleus and are transported to the cytoplasm. The cytoplasmic export protein (Cex1p) captures mature tRNAs from the nuclear export receptor (Los1p) on the cytoplasmic side of the nuclear pore complex, and it delivers them to eukaryotic elongation factor 1α. This conserved Cex1p function is essential for the quality control of mature tRNAs to ensure accurate translation. However, the structural basis of how Cex1p recognizes tRNAs and shuttles them to the translational apparatus remains unclear. Here, we solved the 2.2 Å resolution crystal structure of Saccharomyces cerevisiae Cex1p with C-terminal 197 disordered residues truncated. Cex1p adopts an elongated architecture, consisting of N-terminal kinase-like and a C-terminal α-helical HEAT repeat domains. Structure-based biochemical analyses suggested that Cex1p binds tRNAs on its inner side, using the positively charged HEAT repeat surface and the C-terminal disordered region. The N-terminal kinase-like domain acts as a scaffold to interact with the Ran-exportin (Los1p·Gsp1p) machinery. These results provide the structural basis of Los1p·Gsp1p·Cex1p·tRNA complex formation, thus clarifying the dynamic mechanism of tRNA shuttling from exportin to the translational apparatus.

Molecular phylogeography and genetic diversity of East Asian goats

The domestic goat is one of the most important livestock species, but its origins and genetic diversity still remain uncertain. Multiple highly divergent maternal lineages of goat have been reported in previous studies. Although one of the mitochondrial DNA lineages, lineage B, was detected only in eastern and southern Asia, the geographic distribution of these lineages was previously unclear. Here, we examine the genetic diversity and phylogeographic structure of Asian goats by mitochondrial DNA sequences and morphological characteristics. The analyses of a total of 1661 Asian goats from 12 countries revealed a high frequency of lineage B in Southeast Asia. The frequency of this lineage tended to be higher in mountain areas than in plain areas in Southeast Asian countries, and there was a significant correlation between its frequency and morphological traits. The results suggest an original predominance of lineage B in Southeast Asia and the recent infiltration of lineage A into Southeast Asian goats.

Possible role of the JAK/STAT pathways in the regulation of T cell-interferon related genes in systemic lupus erythematosus

Changes in gene expression in CD3+ T cells associated with disease progression in systemic lupus erythematosus (SLE) patients were determined. The genes related to SLE disease-related activities were identified and their gene regulatory networks were investigated. Analyses of gene expression were performed by both DNA microarray and real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). The expression of certain genes including interferon (IFN) regulatory factor (IRF)-related genes, such as IFN-regulated, -related, and -signature genes was increased in the active phase of SLE. Pathway network analyses suggested that these IRF-related genes are regulated through the Janus kinase/signal transducer and activator of transcription (JAK/STAT) pathway. JAK/STAT pathway-mediated regulation of IRF-related genes may have an important role in the disease activity of SLE. Inhibitors of JAK/STAT cascade may be useful as therapeutic agents.

Chemical Bonding and Pseudogap in Zn- and Cd-based Compounds with Complex Hexagonal Structures

Electronic structures of hexagonal Zn-Mg-Y and Cd58Y13 compounds are studied by first-principles calculations. Both of the systems show deep pseudogap in the electronic density of states near the Fermi level and considered to be stabilized electronically. To illustrate bonding nature of electronic wavefunctions, the crystal orbital Hamilton population (COHP) is calculated for neighboring pairs of atoms in the unit cell. It is found that the bonding nature is changed from bonding to anti-bonding almost exactly at the Fermi level for Zn-Zn and Cd-Cd bonds. On the contrary, for Zn/Cd-Y bonds, both of the states below and above the pseudogap behave as bonding ones. Possible effects of the p-d hybridization are discussed.

A case of fulminant amebic colitis with multiple large intestinal perforations

Amebic colitis normally causes mucous and bloody diarrhea stool as predominant symptoms, thus leading to a course of chronic colitis. However, though rare, there exists a fulminating type that causes intestinal perforations due to wide necrosis of the large intestine. We encountered a case of fulminant amebic colitis that lead to death due to multiple large intestinal perforations. The patient was a 72-year-old female. The patient was admitted to our hospital with symptoms of fever, abdominal pain, and diarrhea. She continued to have a fever of over 38 degrees C and increased left abdominal pain. An abdominal computed tomography scan revealed free gas on the abdominal side of the kidney. Therefore, gastrointestinal perforations were diagnosed and surgery was performed. In surgery, many perforated parts were observed from the appendix to the descending colon, and subtotal colectomy was performed. However, sepsis and disseminated intravascular coagulation occurred, and the patient died on the eighth postoperative day.

Interactive role of protein phosphatase 2A and protein kinase Calpha in the stretch-induced triphosphorylation of myosin light chain in canine cerebral artery

The interactive role of protein kinase C (PKC) isoforms and protein phosphatase 2A (PP2A) in the mechanisms underlying the gradual reduction in stretch-induced contraction through triphosphorylation of 20-kDa myosin light chain (MLC(20)) was investigated in the canine basilar artery. In the presence of 5 mM tetraethylammonium, stretching at a rate of 1 mm/s from the initial length (L(i)) to 1.5 L(i) produced a contraction. Maintaining the stretched state for 15 min (15-min stretch) produced triphosphorylation of MLC(20 )at Ser-19, Thr-18 and Thr-9, and a gradual reduction in the contraction, both of which were reversed by Gö6976 (1 microM), an inhibitor of conventional PKC. The 15-min stretch increased PKCalpha activity whereas it decreased PP2A activity, both of which were blocked by Y-27632, an inhibitor of rho kinase. Okadaic acid (OA; 1 microM), a PP2A inhibitor, also produced triphosphorylation of MLC(20) at the same amino acid residues and activated PKCalpha, which was inhibited by Gö6976. Stretching and OA increased phosphorylation of 17-kDa PKC-potentiated inhibitory phosphoprotein (CPI-17), and this phosphorylation was inhibited by Gö6976. The present results suggest that activation of PKCalpha mediated by an inhibitor of PP2A is involved in the stretch-induced triphosphorylation of MLC(20), and that this triphosphorylation counteracts the stretch-induced contraction.

Changes in the gene expression of peripheral blood mononuclear cells during the menstrual cycle of females is associated with a gender bias in the incidence of systemic lupus erythematosus

OBJECTIVE

The incidence of systemic lupus erythematosus (SLE) is far higher in females than in males and the onset and/or disease activity is influenced by pregnancy and the menstrual cycle. Sex hormones seem to influence the pathogenesis of SLE, therefore, changes in gene expression in peripheral blood mononuclear cells (PBMC) were examined during the menstrual cycle in females, under the comparison of gene expression of patients with SLE.

METHODS

The detection and a quantitative analysis of the gene expression was performed by DNA microarray or real-time quantitative polymerase chain reaction (RQ-PCR) method.

RESULTS

There were thirteen known genes which showed significant quantitative changes during the menstrual cycles of females, but not in males. Among these genes, statistical quantitative differences between normal controls and SLE patients were observed in six genes.

CONCLUSION

Based on these findings, certain genes (such as the tumor necrosis factor receptor superfamily, member 14; TNFRSF14, and signal regulatory protein, gamma; SIRPG) appear to contribute to gender difference of SLE.

Pyrrolysyl-tRNA synthetase-tRNA(Pyl) structure reveals the molecular basis of orthogonality

Pyrrolysine (Pyl), the 22^nd natural amino acid, is genetically encoded by UAG and inserted into proteins by the unique suppressor tRNA^Pyl1. The Methanosarcinaceae produce Pyl and express Pyl-containing methyltransferases that allow growth on methylamines2. Homologous methyltransferases and the Pyl biosynthetic and coding machinery are also found in two bacterial species1,3. Pyl coding is maintained by pyrrolysyl-tRNA synthetase (PylRS), which catalyzes the formation of Pyl-tRNA^Pyl4,5. Pyl is not a recent addition to the genetic code. PylRS was already present in the last universal common ancestor6; it then persisted in organisms that utilize methylamines as energy sources. Recent protein engineering efforts added non-canonical amino acids to the genetic code7,8. This technology relies on the directed evolution of an ‘orthogonal’ tRNA synthetase:tRNA pair in which an engineered aminoacyl-tRNA synthetase (aaRS) specifically and exclusively acylates the orthogonal tRNA with a non-canonical amino acid. For Pyl the natural evolutionary process developed such a system some 3 billion years ago. When transformed into Escherichia coli, Methanosarcina barkeri PylRS and tRNA^Pyl function as an orthogonal pair in vivo5,9. Here we demonstrate that Desulfitobacterium hafniense PylRS:tRNA^Pyl is an orthogonal pair in vitro and in vivo, and present the crystal structure of this orthogonal pair. The ancient emergence of PylRS:tRNA^Pyl allowed for the evolution of unique structural features in both the protein and the tRNA. These structural elements manifest an intricate, specialized aaRS:tRNA interaction surface highly distinct from those observed in any other known aaRS:tRNA complex; it is this general property that underlies the molecular basis of orthogonality.

Genetic diversity of longtail macaques (Macaca fascicularis) on the island of Mauritius: an assessment of nuclear and mitochondrial DNA polymorphisms

BACKGROUND

Individuals from an introduced population of longtail macaques on Mauritius have been extensively used in recent research. This population has low MHC gene diversity, and is thus regarded as a valuable resource for research.

METHODS

We investigated the genetic diversity of this population using multiple molecular markers located in mitochondrial DNA and microsatellite DNA loci on the autosomes and the Y chromosome. We tested samples from 82 individuals taken from seven study sites.

RESULTS AND CONCLUSIONS

We found this population to be panmictic, with a low degree of genetic variability. On the basis of an mtDNA phylogeny, we inferred that these macaques' ancestors originated from Java in Asia. Weak gametic disequilibrium was observed, suggesting decay of non-random associations between genomic genes at the time of founding. The results suggest that macaques bred in Mauritius are valuable as model animals for biomedical research because of their genetic homogeneity.

Role of pathogenic auto-antibody production by Toll-like receptor 9 of B cells in active systemic lupus erythematosus

OBJECTIVES

Toll-like receptor 9 (TLR9) is a pattern-associated receptor functioning in innate immunity that may be involved in the recognition of self-antigens and the production of pathogenic auto-antibodies. Therefore, we examined the expression of TLR9 in systemic lupus erythematosus (SLE) to determine whether TLR9 is involved in the production of pathogenic auto-antibodies.

METHODS

B cells were collected from patients with active SLE, and subjected to analysis of the TLR9 molecule using flow cytometry fluorescence activated cell sorting (FACS) and TLR9 mRNA by reverse-transcriptase polymerase chain reaction. SLE B cells were stimulated with CpG-ODN, and subsequent cytokine and anti-dsDNA antibody production was measured by enzyme-linked immunosorbent assay.

RESULTS

The expression and mRNA level of TLR9 on B cells was up-regulated in SLE patients, and SLE disease activity index (SLEDAI) and CH50 were correlated with TLR9 expression on CD20+ B cells. Moreover, TLR9-CpG interaction enhanced the production of anti-dsDNA antibody and IL-10.

CONCLUSIONS

The present study demonstrated that higher expression of TLR9 on peripheral blood B cells from patients with active SLE was significantly correlated with CH50 and SLEDAI to TLR9, and induced the production of anti-dsDNA antibody and IL-10 by TLR9-CpG ligation. These results suggest that an abnormality of innate immunity plays a crucial role in the pathology of SLE, and that blockade of CpG-TLR9 interaction may be a new therapeutic approach for SLE.