Correlation of the total superoxide dismutase activity between joint fluid and synovium in end-stage knee osteoarthritis.

Recently, we found significantly reduced total superoxide dismutase (SOD) activity in the cartilage of patients with end-stage knee osteoarthritis (OA). In this study, we aimed to evaluate the SOD activity in serum, joint fluid, cartilage, and synovial membrane samples collected from 52 patients with end-stage knee OA who underwent total knee arthroplasty. The relationship between the total SOD activity in each tissue was evaluated using Spearman's rank correlation coefficient. The joint fluid total SOD activity was used as the objective variable, and its association with the serum, cartilage, and synovial total SOD activities was evaluated using multiple linear regression analysis. Univariate analysis revealed that joint fluid total SOD activity was positively correlated with synovial total SOD activity. Multiple linear regression analysis using joint fluid total SOD activity as the objective variable showed a positive association with synovial total SOD activity (ß = 0.493, adjusted R2 = 0.172, P < 0.01). In patients with end-stage knee OA, the state of the synovial total SOD activity is better reflected by the total SOD activity in the joint fluid than that in the cartilage. Joint fluid total SOD activity may serve as a biomarker for the treatment and prevention of synovitis.

Formation of charge-transfer complexes in ionic crystals composed of 1,3-bis(dicyanomethylidene)indan anion and viologens bearing alkyl chains.

The relationship between charge-transfer (CT) properties and the molecular arrangement formed from π-electronic ion pairs remains unclear because of the limited variety of π-electron anions. This study addressed this issue by synthesising a series of ion pair assemblies composed of viologen dications with diverse alkyl chains as π-electron cations and 1,3-bis(dicyanomethilidene)indan anion (CMI-) as a stable π-electron anion. We obtained seven ionic crystals and identified their assembled structures using single-crystal X-ray analysis. These structures are categorized into three types: "columnar", "slipped columnar" and "independent". The CT properties were characterised using UV-Vis absorption spectroscopy, which revealed that the CT absorption bands were dependent on the alkyl chain length. This intriguing variation in the CT transitions can be explained by the differences in the type of assembled structure.

Non-destructive high-throughput measurement of elastic-viscous properties of maize using a novel ultra-micro sensor array and numerical validation.

Maize is the world's most produced cereal crop, and the selection of maize cultivars with a high stem elastic modulus is an effective method to prevent cereal crop lodging. We developed an ultra-compact sensor array inspired by earthquake engineering and proposed a method for the high-throughput evaluation of the elastic modulus of maize cultivars. A natural vibration analysis based on the obtained Young's modulus using finite element analysis (FEA) was performed and compared with the experimental results, which showed that the estimated Young's modulus is representative of the individual Young's modulus. FEA also showed the hotspot where the stalk was most deformed when the corn was vibrated by wind. The six tested cultivars were divided into two phenotypic groups based on the position and number of hotspots. In this study, we proposed a non-destructive high-throughput phenotyping technique for estimating the modulus of elasticity of maize stalks and successfully visualized which parts of the stalks should be improved for specific cultivars to prevent lodging.

Convergence of Modality Invariance and Attention Selectivity in the Cortical Semantic Circuit.

The human linguistic system is characterized by modality invariance and attention selectivity. Previous studies have examined these properties independently and reported perisylvian region involvement for both; however, their relationship and the linguistic information they harbor remain unknown. Participants were assessed by functional magnetic resonance imaging, while spoken narratives (auditory) and written texts (visual) were presented, either separately or simultaneously. Participants were asked to attend to one stimulus when both were presented. We extracted phonemic and semantic features from these auditory and visual modalities, to train multiple, voxel-wise encoding models. Cross-modal examinations of the trained models revealed that perisylvian regions were associated with modality-invariant semantic representations. Attentional selectivity was quantified by examining the modeling performance for attended and unattended conditions. We have determined that perisylvian regions exhibited attention selectivity. Both modality invariance and attention selectivity are both prominent in models that use semantic but not phonemic features. Modality invariance was significantly correlated with attention selectivity in some brain regions; however, we also identified cortical regions associated with only modality invariance or only attention selectivity. Thus, paying selective attention to a specific sensory input modality may regulate the semantic information that is partly processed in brain networks that are shared across modalities.

A design principle for posttranslational chaotic oscillators.

Chaos behavior has been observed in various cellular and molecular processes. Here, we modeled reversible phosphorylation dynamics to elucidate a design principle for autonomous chaos generation that may arise from generic enzymatic reactions. A comprehensive parameter search demonstrated that the reaction system composed of a set of kinases and phosphatases and two substrates with two modification sites exhibits chaos behavior. All reactions are described according to the Michaelis-Menten reaction scheme without exotic functions being applied to enzymes and substrates. Clustering analysis of parameter sets that can generate chaos behavior revealed the existence of motif structures. These chaos motifs allow the two-substrate species to interact via enzyme availability and constrain the two substrates' dynamic changes in phosphorylation status so that they occur at different timescales. This chaos motif structure is found in several enzymatic reactions, suggesting that chaos behavior may underlie cellular autonomy in a variety of biochemical systems.

Segmental coupling effects during correction of three-dimensional lumbar deformity using lateral lumbar interbody fusion.

PURPOSE: Lateral lumbar interbody fusion (LLIF) has been performed to correct spinal deformity associated with lumbar degenerative disease. Although its usefulness has been studied, there are no reports of quantitative evaluation in three dimensions. Our purpose is to quantitate 3D deformity of the patients with lumbar degenerative disease and correction of the deformity by LLIF using patient-specific 3D CT models. METHODS: We measured the disc height and 3D alignment of the lumbar spine in 28 patients with degenerative disease undergoing LLIF using patient-specific 3D CT models created preoperatively and 3 months after surgery. The 3D alignment was calculated as wedge, lordosis and axial rotation angles at each motion segment. The disc height and the rotational angles were compared between before and after LLIF. RESULTS: A strong positive correlation was found between the wedge angle and the axial rotation angles (r = 0.718, P < 0.001) in the patients with lumbar degenerative disease preoperatively. The wedge and axial rotation angles decreased after surgery (P < 0.001 and P < 0.001, respectively). A positive correlation was found between the corrected wedge angle and the corrected axial rotation angle (r = 0.46, P < 0.001). CONCLUSION: The present study demonstrated positive correlations between the wedge deformity and the axial rotational deformity in the patients with lumbar degenerative disease. The axial rotational deformity was simultaneously corrected with LLIF only by leveling the intervertebral wedge deformity via cage insertion without additional correction procedure. These slides can be retrieved under Electronic Supplementary Material.

Intraoperative ultrasound visualization of paravertebral anatomy in the retroperitoneal space during lateral lumbar spine surgery.

OBJECTIVE: Lumbar surgery via a lateral approach is a minimally invasive and highly useful procedure. However, care must be taken to avoid its potentially fatal complications of intestinal and vascular injuries. The object of this study was to evaluate the usefulness of intraoperative ultrasound in improving the safety of lateral lumbar spine surgery. METHODS: A transvaginal ultrasound probe was inserted into the operative field, and the intestinal tract, kidney, psoas muscle, and vertebral body were identified using B-mode ultrasound. The aorta, vena cava, common iliac vessels, and lumbar arteries and their associated branches were identified using the color Doppler mode. RESULTS: The study cohort comprised 100 patients who underwent lateral lumbar spine surgery, 92 via a left-sided approach. The intestinal tract and kidney lateral to the psoas muscle on the anatomical approach pathway were visualized in 36 and 26 patients, respectively. A detachment maneuver displaced the intestinal tract and kidneys in an anteroinferior direction, enabling confirmation of the absence of organ tissues above the psoas. In all patients, the major vessels anterior to the vertebral bodies and the lumbar arteries and associated branches in the psoas on the approach path were clearly visualized in the Doppler mode, and their orientation, location, and positional relationship with regard to the vertebral bodies, intervertebral discs, and psoas were determined. CONCLUSIONS: When approaching the lateral side of the lumbar spine in the retroperitoneal space, intraoperative ultrasound allows real-time identification of the blood vessels surrounding the lumbar spine, intestinal tract, and kidney in the approach path and improves the safety of surgery without increasing invasiveness.

Superoxide dismutase activity is significantly lower in end-stage osteoarthritic cartilage than non-osteoarthritic cartilage.

Recent studies have shown that superoxide dismutase 1 (SOD1), SOD2, and SOD3 are significantly decreased in human osteoarthritic cartilage. SOD activity is a marker that can be used to comprehensively evaluate the enzymatic capacities of SOD1, SOD2, and SOD3; however, the trend of SOD activity in end-stage osteoarthritic tissues remains unknown. In the present study, we found that SOD activity in end-stage osteoarthritic synovium of the knee was significantly lower than that in control synovium without the influence of age. The SOD activity was significantly lower in the end-stage knee osteoarthritic cartilage than in the control, but a weak negative correlation was observed between aging and SOD activity. However, SOD activity in end-stage hip osteoarthritic cartilage was significantly lower than that in control cartilage without the influence of aging. The relationship between osteoarthritis and SOD activity was stronger than the relationship between aging and SOD activity. These results indicate that direct regulation of SOD activity in joint tissues may lead to suppression of osteoarthritis progression.

Characterization of influenza virus variants induced by treatment with the endonuclease inhibitor baloxavir marboxil.

Baloxavir acid (BXA), derived from the prodrug baloxavir marboxil (BXM), potently and selectively inhibits the cap-dependent endonuclease within the polymerase PA subunit of influenza A and B viruses. In clinical trials, single doses of BXM profoundly decrease viral titers as well as alleviating influenza symptoms. Here, we characterize the impact on BXA susceptibility and replicative capacity of variant viruses detected in the post-treatment monitoring of the clinical studies. We find that the PA I38T substitution is a major pathway for reduced susceptibility to BXA, with 30- to 50-fold and 7-fold EC50 changes in A and B viruses, respectively. The viruses harboring the I38T substitution show severely impaired replicative fitness in cells, and correspondingly reduced endonuclease activity in vitro. Co-crystal structures of wild-type and I38T influenza A and B endonucleases bound to BXA show that the mutation reduces van der Waals contacts with the inhibitor. A reduced affinity to the I38T mutant is supported by the lower stability of the BXA-bound endonuclease. These mechanistic insights provide markers for future surveillance of treated populations.

Ligand-driven conformational changes of MurD visualized by paramagnetic NMR.

Proteins, especially multi-domain proteins, often undergo drastic conformational changes upon binding to ligands or by post-translational modifications, which is a key step to regulate their function. However, the detailed mechanisms of such dynamic regulation of the functional processes are poorly understood because of the lack of an efficient tool. We here demonstrate detailed characterization of conformational changes of MurD, a 47 kDa protein enzyme consisting of three domains, by the use of solution NMR equipped with paramagnetic lanthanide probe. Quantitative analysis of pseudocontact shifts has identified a novel conformational state of MurD, named semi-closed conformation, which is found to be the key to understand how MurD regulates the binding of the ligands. The modulation of the affinity coupled with conformational changes accentuates the importance of conformational state to be evaluated in drug design.

Structural reorganization of the bacterial cell-division protein FtsZ from Staphylococcus aureus.

FtsZ is a key molecule in bacterial cell division. In the presence of GTP, it polymerizes into tubulin-like protofilaments by head-to-tail association. Protofilaments of FtsZ seem to adopt a straight or a curved conformation in relation to the bound nucleotide. However, although several bacterial and archaeal FtsZ structures have been determined, all of the structures reported previously are considered to have a curved conformation. In this study, structures of FtsZ from Staphylococcus aureus (SaFtsZ) were determined in apo, GDP-bound and inhibitor-complex forms and it was found that SaFtsZ undergoes marked conformational changes. The accumulated evidence suggests that the GDP-bound structure has the features of the straight form. The structural change between the curved and straight forms shows intriguing similarity to the eukaryotic cytoskeletal protein tubulin. Furthermore, the structure of the apo form showed an unexpectedly large conformational change in the core region. FtsZ has also been recognized as a novel target for antibacterial drugs. The structure of the complex with the inhibitor PC190723, which has potent and selective antistaphylococcal activity, indicated that the inhibitor binds at the cleft between the two subdomains.

Crystallization and preliminary X-ray crystallographic analysis of human phosphodiesterase 12.

Phosphodiesterase PDE12 is a medically important esterase-family member that hydrolyzes 2'-5'-linked oligoadenylates (2-5A), which are involved in the regulation of biological processes related to the antiviral and antitumour activity that can be induced by interferons. Here, cloning, purification and crystallization of the C-terminal endonuclease/exonuclease/phosphatase-homology domain of human PDE12 is reported. The crystals belonged to space group P3(1)21 or P3(2)21, with unit-cell parameters a = b = 111.3, c = 192.4 A, and diffracted to 2.5 A resolution. Assuming the presence of three molecules in the asymmetric unit, the solvent content was estimated to be about 44.0%.

Potent inhibitor scaffold against Trypanosoma cruzi trans-sialidase.

The protozoan Trypanosoma cruzi, the causative agent of Chagas' disease, can infect the heart, causing cardiac arrest frequently followed by death. To treat this disease, a potential molecular drug target is T. cruzi trans-sialidase (TcTS). However, inhibitors found to date are not strong enough to serve as a lead scaffold; most inhibitors reported thus far are derivatives of the substrate sialic acid or a transition state analogue known as 2,3-dehydro-3-deoxy-N-acetylneuraminic acid (DANA) with an IC(50) value of more than hundreds of micromolar. Since natural products are highly stereodiversified and often provide highly specific biological activity, we screened a natural product library for inhibitors of TcTS and identified promising flavonoid and anthraquinone derivatives. A structure-activity relationship (SAR) analysis of the flavonoids revealed that apigenin had the minimal and sufficient structure for inhibition. Intriguingly, the compound has been reported to possess trypanocidal activity. An SAR analysis of anthraquinones showed that 6-chloro-9,10-dihydro-4,5,7-trihydroxy-9,10-dioxo-2-anthracenecarboxylic acid had the strongest inhibitory activity ever found against TcTS. Moreover, its inhibitory activity appeared to be specific to TcTS. These compounds may serve as potent lead chemotherapeutic scaffolds against Chagas' disease.

Phosphorylated intrinsically disordered region of FACT masks its nucleosomal DNA binding elements.

FACT is a heterodimer of SPT16 and SSRP1, which each contain several conserved regions in the primary structure. The interaction of FACT with nucleosomes induces chromatin remodeling through the combinatorial action of its distinct functional protein regions. However, there is little mechanistic insight into how these regions cooperatively contribute to FACT functions, particularly regarding the recognition of nucleosomal DNA. Here, we report the identification of novel phosphorylation sites of Drosophila melanogaster FACT (dFACT) expressed in Sf9 cells. These sites are densely concentrated in the acidic intrinsically disordered (ID) region of the SSRP1 subunit and control nucleosomal DNA binding by dFACT. This region and the adjacent segment of the HMG domain form weak electrostatic intramolecular interactions, which is reinforced by the phosphorylation, thereby blocking DNA binding competitively. Importantly, this control mechanism appears to support rapid chromatin transactions during early embryogenesis through the dephosphorylation of some sites in the maternally transmitted dSSRP1.

Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y-27632.

Rho-kinase is a main player in the regulation of cytoskeletal events and a promising drug target in the treatment of both vascular and neurological disorders. Here we report the crystal structure of the Rho-kinase catalytic domain in complex with the specific inhibitor Y-27632. Comparison with the structure of PKA bound to this inhibitor revealed a potential induced-fit binding mode that can be accommodated by the phosphate binding loop. This binding mode resembles to that observed in the Rho-kinase-fasudil complex. A structural database search indicated that a pocket underneath the phosphate-binding loop is present that favors binding to a small aromatic ring. Introduction of such a ring group might spawn a new modification scheme of pre-existing protein kinase inhibitors for improved binding capability.

Molecular mechanism for the regulation of rho-kinase by dimerization and its inhibition by fasudil.

Rho-kinase is a key regulator of cytoskeletal events and a promising drug target in the treatment of vascular diseases and neurological disorders. Unlike other protein kinases, Rho-kinase requires both N- and C-terminal extension segments outside the kinase domain for activity, although the details of this requirement have been elusive. The crystal structure of an active Rho-kinase fragment containing the kinase domain and both the extensions revealed a head-to-head homodimer through the N-terminal extension forming a helix bundle that structurally integrates the C-terminal extension. This structural organization enables binding of the C-terminal hydrophobic motif to the N-terminal lobe, which defines the correct disposition of helix alphaC that is important for the catalytic activity. The bound inhibitor fasudil significantly alters the conformation and, consequently, the mode of interaction with the catalytic cleft that contains local structural changes. Thus, both kinase and drug conformational pliability and stability confer selectivity.

Channel function is dissociated from the intrinsic kinase activity and autophosphorylation of TRPM7/ChaK1.

TRPM7/ChaK1 is a unique channel/kinase that contains a TRPM channel domain with 6 transmembrane segments fused to a novel serine-threonine kinase domain at its C terminus. The goal of this study was to investigate a possible role of kinase activity and autophosphorylation in regulation of channel activity of TRPM7/ChaK1. Residues essential for kinase activity were identified by site-directed mutagenesis. Two major sites of autophosphorylation were identified in vitro by mass spectrometry at Ser(1511) and Ser(1567), and these sites were found to be phosphorylated in intact cells. TRPM7/ChaK1 is a cation-selective channel that exhibits strong outward rectification and inhibition by millimolar levels of internal [Mg(2+)]. Mutation of the two autophosphorylation sites or of a key catalytic site that abolished kinase activity did not alter channel activity measured by whole-cell recording or Ca(2+) influx. Inhibition by internal Mg(2+) was also unaffected in the autophosphorylation site or "kinase-dead" mutants. Moreover, kinase activity was enhanced by Mg(2+), was decreased by Zn(2+), and was unaffected by Ca(2+). In contrast, channel activity was inhibited by all three of these divalent cations. However, deletion of much of C-terminal kinase domain resulted in expression of an apparently inactive channel. We conclude that neither current activity nor regulation by internal Mg(2+) is affected by kinase activity or autophosphorylation but that the kinase domain may play a structural role in channel assembly or subcellular localization.

Crystal structures of the signal transducing protein GlnK from Thermus thermophilus HB8.

The Thermus thermophilus HB8 genome encodes a signal transducing PII protein, GlnK. The crystal structures of GlnK have been determined in two different space groups, P2(1)2(1)2(1) and P3(1)21. The PII protein has the T-loop, which is essential for interactions with receptor proteins. In both crystal forms, three GlnK molecules form a trimer in the asymmetric unit. In one P2(1)2(1)2(1) crystal form, the three T-loops in the trimer are disordered, while in another P2(1)2(1)2(1) crystal form, the T-loop from one molecule in the trimer is ordered. In the P3(1)21 crystal, one T-loop is ordered while the other two T-loops are disordered. The conformations of the ordered T-loops significantly differ between the two crystal forms; one makes the alpha-helix in the middle of the T-loop, while the other has an extension of the beta-hairpin. Two different conformations are captured by the crystal contacts. The observation of multiple T-loop conformations suggests that the T-loop could potentially exhibit "polysterism," which would be important for interactions with receptor proteins. The crystal structures of the nucleotide-bound forms, GlnK.ATP and GlnK.ADP, have also been determined. ATP/ADP binding within a cleft at the interface of two adjacent T. thermophilus GlnK monomers might affect the conformation of the T-loop.

Structural basis for recruitment of human flap endonuclease 1 to PCNA.

Flap endonuclease-1 (FEN1) is a key enzyme for maintaining genomic stability and replication. Proliferating cell nuclear antigen (PCNA) binds FEN1 and stimulates its endonuclease activity. The structural basis of the FEN1-PCNA interaction was revealed by the crystal structure of the complex between human FEN1 and PCNA. The main interface involves the C-terminal tail of FEN1, which forms two beta-strands connected by a short helix, the betaA-alphaA-betaB motif, participating in beta-beta and hydrophobic interactions with PCNA. These interactions are similar to those previously observed for the p21CIP1/WAF1 peptide. However, this structure involving the full-length enzyme has revealed additional interfaces that are involved in the core domain. The interactions at the interfaces maintain the enzyme in an inactive 'locked-down' orientation and might be utilized in rapid DNA-tracking by preserving the central hole of PCNA for sliding along the DNA. A hinge region present between the core domain and the C-terminal tail of FEN1 would play a role in switching the FEN1 orientation from an inactive to an active orientation.

Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.

Protein TT0402 from Thermus thermophilus HB8 exhibits about 30-35% sequence identity with proteins belonging to subgroup IV in the aminotransferase family of the fold-type I pyridoxal 5'-phosphate (PLP)-dependent enzymes. In this study, we determined the crystal structure of TT0402 at 2.3 A resolution (R(factor) = 19.9%, R(free) = 23.6%). The overall structure of TT0402 exhibits the fold conserved in aminotransferases, and is most similar to that of the Escherichia coli phosphoserine aminotransferase, which belongs to subgroup IV but shares as little as 13% sequence identity with TT0402. Kinetic assays confirmed that TT0402 has higher transamination activities with the amino group donor, L-glutamate, and somewhat lower activities with L-aspartate. These results indicate that TT0402 is a subgroup IV aminotransferase for the synthesis/degradation of either L-aspartate or a similar compound.