We herein report the case of a neonate with pulmonary atresia with intact ventricular septum, right ventricular hypoplasia and severe aortic stenosis. Repetitive aortic valve surgeries in early infancy resulted in early relapse of the aortic stenosis due to the small aortic annulus, bicuspid configuration and duct-dependent pulmonary circulation. The infant underwent a successful mini-Konno procedure using a 10 mm handmade valve and bidirectional Glenn shunt at 6 months of age.
Pulmonary atresia; Aortic valve stenosis; Right ventricle hypoplasia
The aim of this study is to clarify the association between teaching and support skills and the subjective effectiveness of nutritional guidance of registered dietitians working at hospitals.
We carried out a questionnaire survey of registered dietitians at hospitals in a Japanese prefecture. The utilization of nutritional teaching skills in nutritional guidance was investigated using a self-produced 36-item questionnaire that was designed to be mainly used for diabetic patients in 4 settings: first guidance, first assessment, contemplation stage, and preparation stage. The support skills were evaluated by Kikuchi’s Scale of Social Skills: 18 items. The subjective effectiveness of nutritional guidance was defined by the behavioral change of the patients after nutritional guidance as evaluated by a registered dietitian.
There were 75 respondents (response rate 46.6 %). Among the teaching skills, basic skills in an interview were often used, but some related to coaching skills were not in common use in nutritional guidance. Based on the results of principal component analysis, we created a scale for scoring the utilization of nutritional teaching skills in each setting. Multiple linear regression analysis illustrated that high subjective effectiveness of nutritional guidance was associated with high score of teaching skills in the preparation stage setting and high score of support skills.
These results show that, in addition to frequent use of nutritional teaching skills, improvement of support skills is also necessary to enhance the effectiveness of nutritional guidance.
Registered dietitian; Nutritional guidance; Effectiveness; Support skills; Multiple linear regression analysis
The structures of Pim1 kinase in complex with in silico screening hits and several subsequently optimized inhibitors, are reported.
The serine/threonine kinase Pim-1 is emerging as a promising target for cancer therapeutics. Much attention has recently been focused on identifying potential Pim-1 inhibitor candidates for the treatment of haematopoietic malignancies. The outcome of a rational drug-design project has recently been reported [Nakano et al. (2012 ▶), J. Med. Chem.
55, 5151–5156]. The report described the process of optimization of the structure–activity relationship and detailed from a medicinal chemistry perspective the development of a low-potency and nonselective compound initially identified from in silico screening into a potent, selective and metabolically stable Pim-1 inhibitor. Here, the structures of the initial in silico hits are reported and the noteworthy features of the Pim-1 complex structures are described. A particular focus was placed on the rearrangement of the glycine-rich P-loop region that was observed for one of the initial compounds, (Z)-7-(azepan-1-ylmethyl)-2-[(1H-indol-3-yl)methylidene]-6-hydroxy-1-benzofuran-3(2H)-one (compound 1), and was also found in all further derivatives. This novel P-loop conformation, which appears to be stabilized by an additional interaction with the β3 strand located above the binding site, is not usually observed in Pim-1 structures.
Pim-1; kinases; inhibitors
Ribosomal protein S6 kinase 1 (S6K1) is a serine/threonine protein kinase that plays an important role in the PIK3/mTOR signaling pathway, and is implicated in diseases including diabetes, obesity, and cancer. The crystal structures of the S6K1 kinase domain in complexes with staurosporine and the S6K1-specific inhibitor PF-4708671 have been reported. In the present study, five compounds (F108, F109, F176, F177, and F179) were newly identified by in silico screening of a chemical library and kinase assay. The crystal structures of the five inhibitors in complexes with the S6K1 kinase domain were determined at resolutions between 1.85 and 2.10 Å. All of the inhibitors bound to the ATP binding site, lying along the P-loop, while the activation loop stayed in the inactive form. Compound F179, with a carbonyl group in the middle of the molecule, altered the αC helix conformation by interacting with the invariant Lys123. Compounds F176 and F177 bound slightly distant from the hinge region, and their sulfoamide groups formed polar interactions with the protein. The structural features required for the specific binding of inhibitors are discussed.
Protein kinases; Inhibitors; p70 S6 kinase; S6K1
A total of 324 Japanese rice accessions, including landrace, improved, and weedy types were used to 1) investigate genetic variations in blast resistance to standard differential isolates, and 2) across the genome using polymorphism data on 64 SSR markers. From the polymorphism data, the accessions were classified into two clusters. Accessions from irrigated lowland areas were included mainly in cluster I, and upland and Indica types were mainly in cluster II. The accessions were classified into three resistance subgroups, A2, B1 and B2, based on the reaction patterns to blast isolates. The accessions in A2 were postulated to have at least two resistance genes Pish and Pik-s, whereas those in B1 had various combinations of the resistance genes Pish, Pia, Pii, Pi3, Pi5(t), and Pik alleles. The B2 accessions were resistant to almost all isolates, and many accessions of cluster II were included, and had Pish, Pia, Pii, Pi3, Pi5(t), certain Pik, Piz and Pita alleles, and unknown genes. The frequencies of accessions of B1 originating in Hokkaido, and those of B2 originating in the Kanto and Tohoku regions were remarkably higher than in the other regions.
blast (Pyricularia oryzae Cavara); differential system; genetic variation; resistance; rice (Oryza sativa L.)
We have previously demonstrated that an alkaline extract of shredded pinecones yields a polyphenylpropanoid polysaccharide complex (PPC) that functions as an orally active immune adjuvant. Specifically, oral PPC can boost the number of antigen-specific memory CD8+ T cells generated in response to a variety of vaccine types (DNA, protein, and dendritic cell) and bias the response towards one that is predominately a T helper 1 type.
An immune response was initiated by intraperitoneal injection of mice with Staphylococcus enterotoxin B (SEB). A group of mice received PPC by gavage three times per day on Days 0 and 1. The draining lymph nodes were analyzed 48–96 h post-injection for the numbers of reactive T cells, cytokine production, the generation of reactive oxygen species, and apoptotsis.
In this study we examined whether the ability of PPC to boost a T cell response is due to an effect on the proliferative or contraction phases, or both, of the primary response. We present data to demonstrate that oral PPC significantly enhances the primary T cell response by affecting the expansion of T cells (both CD4 and CD8) during the proliferative phase, while having no apparent effects on the activation-induced cell death associated with the contraction phase.
These findings suggest that PPC could potentially be utilized to enhance the T cell response generated by a variety of prophylactic and therapeutic vaccines designed to target a cellular response.
Polyphenylpropanoid polysaccharide complex; Primary T cell response; Pine cone extract
Cyanide-insensitive alternative oxidase from T. brucei brucei has been purified and crystallized for X-ray structure analysis.
Cyanide-insensitive alternative oxidase (AOX) is a mitochondrial membrane protein and a non-proton-pumping ubiquinol oxidase that catalyzes the four-electron reduction of dioxygen to water. In the African trypanosomes, trypanosome alternative oxidase (TAO) functions as a cytochrome-independent terminal oxidase that is essential for survival in the mammalian host; hence, the enzyme is considered to be a promising drug target for the treatment of trypanosomiasis. In the present study, recombinant TAO (rTAO) overexpressed in haem-deficient Escherichia coli was purified and crystallized at 293 K by the hanging-drop vapour-diffusion method using polyethylene glycol 400 as a precipitant. X-ray diffraction data were collected at 100 K and were processed to 2.9 Å resolution with 93.1% completeness and an overall R
merge of 9.5%. The TAO crystals belonged to the orthorhombic space group I222 or I212121, with unit-cell parameters a = 63.11, b = 136.44, c = 223.06 Å. Assuming the presence of two rTAO molecules in the asymmetric unit (2 × 38 kDa), the calculated Matthews coefficient (V
M) was 3.2 Å3 Da−1, which corresponds to a solvent content of 61.0%. This is the first report of a crystal of the membrane-bound diiron proteins, which include AOXs.
alternative oxidases; membrane proteins; Trypanosoma brucei brucei; ascofuranone
Glycerol kinase from human African trypanosomes has been purified and crystallized for X-ray structure analysis.
In the bloodstream forms of human trypanosomes, glycerol kinase (GK; EC 184.108.40.206) is one of the nine glycosomally compartmentalized enzymes that are essential for energy metabolism. In this study, a recombinant Trypanosoma brucei gambiense GK (rTbgGK) with an N-terminal cleavable His6 tag was overexpressed, purified to homogeneity and crystallized by the sitting-drop vapour-diffusion method using PEG 400 as a precipitant. A complete X-ray diffraction data set to 2.75 Å resolution indicated that the crystals belonged to the orthorhombic space group P212121, with unit-cell parameters a = 63.84, b = 121.50, c = 154.59 Å. The presence of two rTbgGK molecules in the asymmetric unit gives a Matthews coefficient (V
M) of 2.5 Å3 Da−1, corresponding to 50% solvent content.
human African trypanosomiasis; Trypanosoma brucei gambiense; drug design; glycerol kinases
Aspartate transcarbamoylase, the second enzyme of the de novo pyrimidine-biosynthetic pathway, from T. cruzi has been purified and crystallized for X-ray structure analysis.
Aspartate transcarbamoylase (ATCase), the second enzyme of the de novo pyrimidine-biosynthetic pathway, catalyzes the production of carbamoyl aspartate from carbamoyl phosphate and l-aspartate. In contrast to Escherichia coli ATCase and eukaryotic CAD multifunctional fusion enzymes, Trypanosoma cruzi ATCase lacks regulatory subunits and is not part of the multifunctional fusion enzyme. Recombinant T. cruzi ATCase expressed in E. coli was purified and crystallized in a ligand-free form and in a complex with carbamoyl phosphate at 277 K by the sitting-drop vapour-diffusion technique using polyethylene glycol 3350 as a precipitant. Ligand-free crystals (space group P1, unit-cell parameters a = 78.42, b = 79.28, c = 92.02 Å, α = 69.56, β = 82.90, γ = 63.25°) diffracted X-rays to 2.8 Å resolution, while those cocrystallized with carbamoyl phosphate (space group P21, unit-cell parameters a = 88.41, b = 158.38, c = 89.00 Å, β = 119.66°) diffracted to 1.6 Å resolution. The presence of two homotrimers in the asymmetric unit (38 kDa × 6) gives V
M values of 2.3 and 2.5 Å3 Da−1 for the P1 and P21 crystal forms, respectively.
aspartate transcarbamoylase; Trypanosoma cruzi; Chagas disease; drug targets
Human Transformer2-β (hTra2-β) is an important member of the serine/arginine-rich protein family, and contains one RNA recognition motif (RRM). It controls the alternative splicing of several pre-mRNAs, including those of the calcitonin/calcitonin gene-related peptide (CGRP), the survival motor neuron 1 (SMN1) protein and the tau protein. Accordingly, the RRM of hTra2-β specifically binds to two types of RNA sequences [the CAA and (GAA)2 sequences]. We determined the solution structure of the hTra2-β RRM (spanning residues Asn110–Thr201), which not only has a canonical RRM fold, but also an unusual alignment of the aromatic amino acids on the β-sheet surface. We then solved the complex structure of the hTra2-β RRM with the (GAA)2 sequence, and found that the AGAA tetra-nucleotide was specifically recognized through hydrogen-bond formation with several amino acids on the N- and C-terminal extensions, as well as stacking interactions mediated by the unusually aligned aromatic rings on the β-sheet surface. Further NMR experiments revealed that the hTra2-β RRM recognizes the CAA sequence when it is integrated in the stem-loop structure. This study indicates that the hTra2-β RRM recognizes two types of RNA sequences in different RNA binding modes.
For almost 2000 years it has been recognized that aqueous extracts from pine cones possess medicinal properties beneficial for the treatment of a broad variety of diseases and conditions. In this report, the ability of an orally administered poly phenylpropanoid-polysaccharide rich extract of pine cones (PPC) to suppress the generation of IgE and to significantly enhance antigen-specific cellular responses to a variety of vaccines was tested.
A variety of vaccine protocols were utilized to determine the affects of orally administered PPC on the Th1/Th2 cytokine balance, the production of IgE antibodies, and the generation of antigen-specific cytotoxic T cells. The effect of PPC on the Th1/Th2 balance in aged mice was also investigated.
Oral delivery of PPC was found to significantly suppress serum IgE levels in naïve mice and in mice sensitized to ovalbumin. PPC was also found to enhance the generation of antigen-specific CD8+ T cells in mice immunized with DNA, dendritic cell, and soluble protein vaccines. The suppression of IgE was associated with reduction of IL-4 secretion and the enhanced production of IL-12 and IFNγ by antigen-stimulated splenocytes from PPC treated mice. PPC also suppressed the Th2 response and enhanced the Th1 response of splenocytes from aged mice.
Oral delivery of PPC enhances the generation of an antigen-specific CD8+ T cell responses induced by soluble protein, DNA, and dendritic cell vaccines while at the same time suppressing the generation of a Th2 dominant IgE response. This effect on the Th1/Th2 balance was also observed in aged mice.
A truncated variant of human ribosomal protien L10 was prepared and crystallized. Diffraction data were collected to 2.5 Å resolution.
Eukaryotic ribosomal protein L10 is an essential component of the large ribosomal subunit, which organizes the architecture of the aminoacyl-tRNA binding site. The human L10 protein is also called the QM protein and consists of 214 amino-acid residues. For crystallization, the L10 core domain (L10CD, Phe34–Glu182) was recombinantly expressed in Escherichia coli and purified to homogeneity. A hexagonal crystal of L10CD was obtained by the sitting-drop vapour-diffusion method. The L10CD crystal diffracted to 2.5 Å resolution and belongs to space group P3121 or P3221.
ribsomal protein L10; core domain; QM protein; ribosome
The C-terminal bromodomain of human BRD2 was cloned, expressed, purified and crystallized. A complete diffraction data set has been collected to 1.80 Å resolution.
BRD2 is a bromodomain-containing BET-family protein that associates with acetylated histones throughout the cell cycle. Although the tertiary structures of the bromodomains involved in histone acetyl transfer are already known, the structures of the BET-type bromodomains, which are required for tight association with acetylated chromatin, are poorly understood. Here, the expression, purification and crystallization of the C-terminal bromodomain of human BRD2 are reported. The protein was crystallized by the sitting-drop vapour-diffusion method in the orthorhombic space group P21212, with unit-cell parameters a = 71.78, b = 52.60, c = 32.06 Å and one molecule per asymmetric unit. The crystal diffracted beyond 1.80 Å resolution using synchrotron radiation.
acetylation; cell cycle; chromatin; gene expression; histones; transcription
The CUG-binding protein 1 (CUG-BP1) is a member of the CUG-BP1 and ETR-like factors (CELF) family or the Bruno-like family and is involved in the control of splicing, translation and mRNA degradation. Several target RNA sequences of CUG-BP1 have been predicted, such as the CUG triplet repeat, the GU-rich sequences and the AU-rich element of nuclear pre-mRNAs and/or cytoplasmic mRNA. CUG-BP1 has three RNA-recognition motifs (RRMs), among which the third RRM (RRM3) can bind to the target RNAs on its own. In this study, we solved the solution structure of the CUG-BP1 RRM3 by hetero-nuclear NMR spectroscopy. The CUG-BP1 RRM3 exhibited a noncanonical RRM fold, with the four-stranded β-sheet surface tightly associated with the N-terminal extension. Furthermore, we determined the solution structure of the CUG-BP1 RRM3 in the complex with (UG)3 RNA, and discovered that the UGU trinucleotide is specifically recognized through extensive stacking interactions and hydrogen bonds within the pocket formed by the β-sheet surface and the N-terminal extension. This study revealed the unique mechanism that enables the CUG-BP1 RRM3 to discriminate the short RNA segment from other sequences, thus providing the molecular basis for the comprehension of the role of the RRM3s in the CELF/Bruno-like family.
The complex of the non-ATPase subunit Nas6 with the C-terminal domain of the ATPase subunit Rpt3 of the 26S proteasome from S. cerevisiae was co-expressed in E. coli and purified to homogeneity. The crystals obtained from the protein complex diffracted to a resolution of 2.2 Å.
The non-ATPase subunit Nas6, which is the human orthologue of gankyrin, was co-expressed with the C-terminal domain of the ATPase subunit Rpt3 of the yeast 26S proteasome in Escherichia coli, purified to near-homogeneity and crystallized using the hanging-drop vapour-diffusion method. The protein crystallized in space group P21, with unit-cell parameters a = 60.38, b = 100.22, c = 72.20 Å, β = 94.70° and with three Nas6–Rpt3C molecules per asymmetric unit. The crystal diffracted to beyond 2.2 Å resolution using synchrotron radiation.
Nas6; gankyrin; oncoproteins; Rpt3; proteasome; protein degradation; ubiquitin
Crystallization of the transcription termination factor NusA under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 Å, with similar unit-cell parameters.
The transcription termination factor NusA from Aeropyrum pernix was crystallized using a counter-diffusion technique in both terrestrial and microgravity environments. Crystallization under microgravity conditions significantly reduced the twinning content (1.0%) compared with terrestrially grown crystals (18.3%) and improved the maximum resolution from 3.0 to 2.29 Å, with similar unit-cell parameters. Based on a comparison of the crystal parameters, the effect of microgravity on protein crystallization is discussed.
counter-diffusion; gel-tube method; hemihedral twinning; microgravity; transcription factors
The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3′ specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m7GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m7GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic α-helical extension at its C-terminus, which covers the β-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N7-methyl guanosine (m7G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second β-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.
The histone chaperone cia1 from fission yeast has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
In fission yeast, cia1
+ is an essential gene that encodes a histone chaperone, a homologue of human CIA (CCG1-interacting factor A) and budding yeast Asf1p (anti-silencing function-1), which both facilitate nucleosome assembly by interacting with the core histones H3/H4. The conserved domain (residues 1–161) of the cia1
+-encoded protein was expressed in Escherichia coli, purified to near-homogeneity and crystallized by the sitting-drop vapour-diffusion method. The protein was crystallized in the monoclinic space group C2, with unit-cell parameters a = 79.16, b = 40.53, c = 69.79 Å, β = 115.93° and one molecule per asymmetric unit. The crystal diffracted to beyond 2.10 Å resolution using synchrotron radiation.
gene silencing; nucleosome assembly; transcription
Keap1-DC (Kelch/double-glycine repeat and C-terminal region) of mouse Keap1 has been overexpressed in E. coli, purified and crystallized using the vapour-diffusion method.
Keap1 (Kelch-like ECH-associating protein 1) is a negative regulator of the Nrf2 transcription factor in the cytoplasm. The Kelch/DGR (double-glycine repeat) domain of Keap1 associates with Nrf2 as well as with actin filaments. A recombinant protein containing both the Kelch/DGR domain and the C-terminal region of mouse Keap1 was expressed in Escherichia coli, purified to near-homogeneity and crystallized by the sitting-drop vapour-diffusion method. The crystal belongs to space group P61 or P65, with unit-cell parameters a = b = 102.95, c = 55.21 Å, and contains one molecule in the asymmetric unit. A complete diffraction data was collected to 2.25 Å resolution using an R-AXIS IV++ imaging plate mounted on an RA-Micro7 Cu Kα rotating-anode X-ray generator.
Nrf2; transcription factor; Keap1; actin binding; antioxidants
The polypeptide composition of Chlamydia was examined by acrylamide gel electrophoresis. When the polypeptide patterns of purified infectious elementary bodies (EB) of C. psittaci meningopneumonitis strain, 6BC strain, and C. trachomatis T'ang strain were compared, no significant differences were observed. The polypeptide patterns of whole EB and reticulate bodies (RB) appeared to overlap, but differences were found. In EB cell walls, nine main and several minor bands of polypeptides were observed in gels containing sodium lauryl sulfate, and the eighth main band from the top of the gel stained positive with periodic acid-Schiff reagent. On the other hand, the polypeptides in bands 3, 6, and 8 in EB cell walls were missing or minor in RB cell walls, and the ninth band was clearly stained by PAS. Band 8 was also stained slightly. Purified subunits, which occur as a lattice structure on the inside layer of EB cell walls but are largely missing in RB cell walls, contained bands 4, 6, and 8, and band 8 was PAS positive. These results indicate that significant polypeptide synthesis or reorganization in the cell walls occurs during the growth cycle.