Catalog of triply periodic minimal surfaces, equation-based lattice structures, and their homogenized property data.

The use of lattice structure in the Design for Additive Manufacturing (DfAM) engineering practice offers the ability to tailor the properties (and therefore the response) of an engineered component independent of the material and overall geometry. The selection of a lattice topology is critical in maximizing the value of the lattice structure and its unique properties for the intended application. To support this, we have compiled a catalog of lattice structures from the literature that includes all Triply Periodic Minimal Surfaces (TPMS) for which a low-order Fourier series fit is known (so that they can be modeled and manufactured). We also include equations that do not directly correspond to known TPMS but do produce a triply periodic structure without sharp corners that would give rise to stress concentrations. This catalog includes images, elastic mechanical property data, and CAD models useful for the visualization, selection, and implementation of these lattice structures for any engineered structure.

A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins.

Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.

CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy.

The mammalian cryptochrome isoforms, CRY1 and CRY2, are core circadian clock regulators that work redundantly. Recent studies revealed distinct roles of these closely related homologs in clock output pathways. Isoform-selective control of CRY1 and CRY2 is critical for further understanding their redundant and distinct roles. KL001 was the first identified small-molecule CRY modulator that activates both CRY1 and CRY2. SHP656 is an orally available KL001 derivative and has shown efficacy in blood glucose control and inhibition of glioblastoma stem cell (GSC) growth in animal models. However, CRY isoform selectivity of SHP656 was uncharacterized, limiting understanding of the roles of CRY1 and CRY2. Here, we report the elucidation of CRY2 selectivity of SHP656. SHP656 lengthened cellular circadian period in a CRY2-dependent manner and selectively interacted with CRY2. By determining the X-ray crystal structure of CRY2 in complex with SHP656 and performing molecular dynamics simulations, we elucidated compound interaction mechanisms. SHP656 binding was compatible with the intrinsic CRY2 gatekeeper W417 "in" orientation and also a close "further in" conformation. Perturbation of W417 interaction with the lid loop resulted in a reduced effect of SHP656 on CRY2, supporting an important role of gatekeeper orientation in isoform selectivity. We also identified the R form of SHP656 (called SHP1703) as the active isomer. Treatment with SHP1703 effectively reduced GSC viability. Our results suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.

Molecular Tension Probe for In Vitro Bioassays.

Cell-free bioassays (CFBs) provide their own distinctive merits over cell-based bioassays (CBBs) including (i) rapid and on-site applicability, (ii) long-term utility, and (iii) bioanalytical versatility. The authors previously introduced a unique bioluminescent imaging probe for illuminating molecular tension appended by protein-protein interactions (PPIs) of interest. In this chapter, we exemplify that a full-length artificial luciferase is sandwiched between FRB (FKBP-rapamycin-binding domain of FKBP12-rapamycin-associated protein) and FKBP (FK506-binding protein) via minimal flexible linkers, named FRB-A23-FKBP. The rapamycin-activated PPIs between FRB and FKBP append molecular tension to the sandwiched luciferase, enhancing the enzymatic activity in a quantitative manner. The fusion protein, FRB-A23-FKBP, is three-step column-purified and the bioanalytical utility is characterized in various CFB conditions. This chapter guides the detailed protocols from the purification to the practical bioassays of FRB-A23-FKBP.

Structural and Chemical Biology Approaches Reveal Isoform-Selective Mechanisms of Ligand Interactions in Mammalian Cryptochromes.

Cryptochromes (CRYs) are core components of the circadian feedback loop in mammals, which regulates circadian rhythmicity in a variety of physiological processes including sleep-wake cycles and metabolism. Dysfunction of CRY1 and CRY2 isoforms has been associated with a host of diseases, such as sleep phase disorder and metabolic diseases. Accumulating evidence for distinct roles of CRY1 and CRY2 has highlighted the need for CRY isoform-selective regulation; however, highly conserved sequences in CRY ligand-binding sites have hindered the design of isoform-selective compounds. Chemical biology approaches have been identifying small-molecule modulators of CRY proteins, which act in isoform-non-selective and also isoform-selective manners. In this review, we describe advances in our understanding of CRY isoform selectivity by comparing X-ray crystal structures of mammalian CRY isoforms in apo form and in complexes with compounds. We discuss how intrinsic conformational differences in identical residues of CRY1 and CRY2 contribute to unique interactions with different compound moieties for isoform selectivity.

Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation.

The circadian clock is a biological timekeeper that operates through transcription-translation feedback loops in mammals. Cryptochrome 1 (CRY1) and Cryptochrome 2 (CRY2) are highly conserved core clock components having redundant and distinct functions. We recently identified the CRY1- and CRY2-selective compounds KL101 and TH301, respectively, which provide useful tools for the exploration of isoform-selective CRY regulation. However, intrinsic differences in the compound-binding FAD (flavin adenine dinucleotide) pockets between CRY1 and CRY2 are not well understood, partly because of nonoptimal properties of previously reported apo form structures in this particular region constituted by almost identical sequences. Here, we show unliganded CRY1 and CRY2 crystal structures with well-defined electron densities that are largely free of crystal contacts at the FAD pocket and nearby lid loop. We revealed conformational isomerism in key residues. In particular, CRY1 W399 and corresponding CRY2 W417 in the FAD pocket had distinct conformations ("out" for CRY1 and "in" for CRY2) by interacting with the lid loop residues CRY1 Q407 and CRY2 F424, respectively, resulting in different overall lid loop structures. Molecular dynamics simulations supported that these conformations were energetically favorable to each isoform. Isoform-selective compounds KL101 and TH301 preferred intrinsic "out" and "in" conformations of the tryptophan residue in CRY1 and CRY2, respectively, while the nonselective compound KL001 fit to both conformations. Mutations of lid loop residues designed to perturb their isoform-specific interaction with the tryptophan resulted in reversed responses of CRY1 and CRY2 to KL101 and TH301. We propose that these intrinsic structural differences of CRY1 and CRY2 can be targeted for isoform-selective regulation.

Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock.

CRY1 and CRY2 proteins are highly conserved components of the circadian clock that controls daily physiological rhythms. Disruption of CRY functions are related to many diseases, including circadian sleep phase disorder. Development of isoform-selective and spatiotemporally controllable tools will facilitate the understanding of shared and distinct functions of CRY1 and CRY2. Here, we developed CRY1-selective compounds that enable light-dependent manipulation of the circadian clock. From phenotypic chemical screening in human cells, we identified benzophenone derivatives that lengthened the circadian period. These compounds selectively interacted with the CRY1 photolyase homology region, resulting in activation of CRY1 but not CRY2. The benzophenone moiety rearranged a CRY1 region called the "lid loop" located outside of the compound-binding pocket and formed a unique interaction with Phe409 in the lid loop. Manipulation of this key interaction was achieved by rationally designed replacement of the benzophenone with a switchable azobenzene moiety whose cis-trans isomerization can be controlled by light. The metastable cis form exhibited sufficiently high half-life in aqueous solutions and structurally mimicked the benzophenone unit, enabling reversible period regulation over days by cellular irradiation with visible light. This study revealed an unprecedented role of the lid loop in CRY-compound interaction and paves the way for spatiotemporal regulation of CRY1 activity by photopharmacology for molecular understanding of CRY1-dependent functions in health and disease.

An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals.

Cryptochrome 1 (CRY1) and CRY2 are core regulators of the circadian clock, and the development of isoform-selective modulators is important for the elucidation of their redundant and distinct functions. Here, we report the identification and functional characterization of a small-molecule modulator of the mammalian circadian clock that selectively controls CRY1. Cell-based circadian chemical screening identified a thienopyrimidine derivative KL201 that lengthened the period of circadian rhythms in cells and tissues. Functional assays revealed stabilization of CRY1 but not CRY2 by KL201. A structure-activity relationship study of KL201 derivatives in combination with X-ray crystallography of the CRY1-KL201 complex uncovered critical sites and interactions required for CRY1 regulation. KL201 bound to CRY1 in overlap with FBXL3, a subunit of ubiquitin ligase complex, and the effect of KL201 was blunted by knockdown of FBXL3. KL201 will facilitate isoform-selective regulation of CRY1 to accelerate chronobiology research and therapeutics against clock-related diseases.

Isoform-selective regulation of mammalian cryptochromes.

CRY1 and CRY2 are essential components of the circadian clock controlling daily physiological rhythms. Accumulating evidences indicate distinct roles of these highly homologous proteins, in addition to redundant functions. Therefore, the development of isoform-selective compounds represents an effective approach towards understanding the similarities and differences of CRY1 and CRY2 by controlling each isoform individually. We conducted phenotypic screenings of circadian clock modulators, and identified KL101 and TH301 that selectively stabilize CRY1 and CRY2, respectively. Crystal structures of CRY-compound complexes revealed conservation of compound-binding sites between CRY1 and CRY2. We further discovered a unique mechanism underlying compound selectivity in which the disordered C-terminal region outside the pocket was required for the differential effects of KL101 and TH301 against CRY isoforms. By using these compounds, we found a new role of CRY1 and CRY2 as enhancers of brown adipocyte differentiation, providing the basis of CRY-mediated regulation of energy expenditure.

Pharmacological Interventions to Circadian Clocks and Their Molecular Bases.

Daily physiological rhythms are regulated by the body's internal timekeeper known as the circadian clock. Expression, post-translational modification, and degradation of clock proteins constituting the circadian clock are precisely controlled in a rhythmic manner. Perturbation of these processes by nature and nurture results in physiological dysfunction and diseases. Small-molecule modulators of clock or clock-related proteins can adjust clock functions, and thus represent a promising method of therapeutic treatment for a range of clock-related diseases. In this review, we will introduce the identification and development of small-molecule compounds that target clock proteins, as well as X-ray crystal structures of protein-compound complexes that facilitate the understanding of clock protein regulation and drug derivatization. Furthermore, we describe the effects of these compounds in a diseased setting and discuss the therapeutic potential of clock modulators.

The Scottish Orthodontic Peer Review project: the outcome of treatment and standard of record keeping by orthodontic specialist practitioners in Scotland.

OBJECTIVES: Assess occlusal outcomes of treatment and clinical record keeping in specialist practice in Scotland. DESIGN: A retrospective cohort study. SETTING: Specialist practices in Scotland. PARTICIPANTS: Specialist orthodontists in Scotland. METHODS: Every specialist practitioner in Scotland (51) was invited to take part in the peer review project with 38 (76%) enrolled. Scotland was split into four geographical areas, and each practitioner matched with a colleague from the same area. Practitioners took one day to visit their colleague and score 30 consecutively treated NHS cases using the Peer Assessment Rating (PAR) index. They also assessed the quality of the records taken. Practitioners then swapped roles and assessed their partner's occlusal outcomes and records. RESULTS: The mean pretreatment PAR score was 28.6 (SD 3.5). Mean posttreatment PAR score was 3.5 (SD 1.2). Mean reduction in PAR score was 25.1 (SD 3.8). Mean percentage PAR score reduction was 87.7% (SD 3.7%). Overall record keeping scores were written records 100%, study models 99.5%, Orthopantomogram radiograph 99.2%, photographs 86.3%, medical history 75% and consent 40.8%. CONCLUSIONS: Occlusal outcomes achieved by specialist practitioners in Scotland were of a high standard. They maintained a good standard of clinical record collection in most areas examined.

Getting to the Heart of the Matter: What is the Landscape of Exercise Rehabilitation for People With Heart Failure in Australia?

BACKGROUND: The benefits of exercise rehabilitation for people with heart failure (HF) are well established. In Australia, little is known about how the guidelines around exercise rehabilitation for people with HF are being implemented in clinical practice. Furthermore, it is unknown what organisational barriers are faced in providing exercise rehabilitation programs for this population. The aim of this study is to provide an updated review of exercise rehabilitation services for people with HF in Australia and to identify perceived organisational barriers to providing these services. METHODS: A cross-sectional survey of cardiac rehabilitation centres in Australia, investigating the number and characteristics of services providing exercise rehabilitation for people with HF. RESULTS: A total of 334 of 457 identified services responded to the survey. Of these, 251 reported providing a supervised group-based exercise rehabilitation program for people with HF. These services were mapped, showing their distribution across Australia. Services which were unable to provide group-based exercise training for HF patients reported organisational barriers including insufficient funding (60%), staffing (56%) and clinical resources (53%). Of the 78 services that reported patients in their local area were unable to access appropriate exercise guidance, 81% were located in regional or remote areas. We found that reported exercise practices align with current best-practice guidelines with 99% of group based exercise programs reportedly including endurance training and 89% including resistance training. CONCLUSIONS: In Australia, exercise practices for people with HF align with current best-practice guidelines for this condition. Limited resources, funding and geographic isolation are reported as the major organisational barriers to providing these programs. Future endeavours should include the development of alternative and flexible delivery models such as telerehabilitation and other home-based therapies to improve access for these individuals to such services.

A Bioluminescence Assay System for Imaging Metal Cationic Activities in Urban Aerosols.

A bioluminescence-based assay system was fabricated for an efficient determination of the activities of air pollutants. The following four components were integrated into this assay system: (1) an 8-channel assay platform uniquely designed for simultaneously sensing multiple optical samples, (2) single-chain probes illuminating toxic chemicals or heavy metal cations from air pollutants, (3) a microfluidic system for circulating medium mimicking the human body, and (4) the software manimulating the above system. In the protocol, we briefly introduce how to integrate the components into the system and the application to the illumination of the metal cationic activities in air pollutants.

COMPASS II: extended coverage for polymer and drug-like molecule databases.

The COMPASS II force field has been developed by extending the coverage of the COMPASS force field (J Phys Chem B 102(38):7338-7364, 1998) to polymer and drug-like molecules found in popular databases. Using a fragmentation method to systematically construct small molecules that exhibit key functional groups found in these databases, parameters applicable to database compounds were efficiently obtained. Based on the same parameterization paradigm as used in the development of the COMPASS force field, new parameters were derived by a combination of fits to quantum mechanical data for valence parameters and experimental liquid and crystal data for nonbond parameters. To preserve the quality of the original COMPASS parameters, a quality assurance suite was used and updated to ensure that additional atom-types and parameters do not interfere with the existing ones. Validation against molecular properties, liquid and crystal densities, and enthalpies, demonstrates that the quality of COMPASS is preserved and the same quality of prediction is achieved for the additional coverage.

Cation-driven Optical Properties of Artificial Luciferases.

The present study demonstrates cation-driven optical properties of artificial luciferases (ALucs) from copepod luciferases, as an optical readout for bioanalysis. An assignment of the supersecondary structure code (SSC) of ALucs revealed that ALucs carry a helix-loop-helix structure, which appears at the same sites of the EF-hands of typical Ca(2+)-binding proteins. A mutagenesis study shows that the EF-hand-like structure is a pivotal site for enzymatic activity. The effects of 20 kinds of mono- and multivalent cations on ALuc activities were estimated with column-purified ALuc16. High pH values boost the ALuc activities with both the native coelenterazine and an analog called 6-pi-OH-CTZ. Multivalent cations, Ca(II), Mg(II), and Cr(VI), elevate and prolong the ALuc activities, whereas Co(II), Cu(II) and Pb(II) greatly hamper the ALuc activities. Ca(II) greatly prolongs the optical intensities, suggesting a contribution to the structural robustness of ALucs. The inhibitory effect of multivalent cations on the ALuc activities was utilized for creating dose-response curves. The intrinsic cation-driven selectivity and optical intensity of ALucs enable researchers to constitute de novo biosensors for multivalent cations.

Gliotoxin suppresses NF-κB activation by selectively inhibiting linear ubiquitin chain assembly complex (LUBAC).

A linear ubiquitin chain, which consists of ubiquitin molecules linked via their N- and C-termini, is formed by a linear ubiquitin chain assembly complex (LUBAC) composed of HOIP, HOIL-1L, and SHARPIN, and conjugation of a linear ubiquitin chain on the NF-κB essential modulator (NEMO) is deeply involved in NF-κB activation induced by various signals. Since abnormal activation of NF-κB is associated with inflammatory disease and malignancy, we searched for an inhibitor of LUBAC by high-throughput screening (HTS) with a Tb(3+)-fluorescein FRET system. As a result, we found that the fungal metabolite gliotoxin inhibits LUBAC selectively by binding to the RING-IBR-RING domain of HOIP, the catalytic center of LUBAC. Gliotoxin has been well-known as an inhibitor of NF-κB activation, though its action mechanism has remained elusive. Here, we show that gliotoxin inhibits signal-induced NF-κB activation by selectively inhibiting LUBAC-mediated linear ubiquitin chain formation.

Dysphagia in Duchenne muscular dystrophy assessed by validated questionnaire.

BACKGROUND: Duchenne muscular dystrophy (DMD) leads to progressive muscular weakness and death, most typically from respiratory complications. Dysphagia is common in DMD; however, the most appropriate swallowing assessments have not been universally agreed and the symptoms of dysphagia remain under-reported. AIMS: To investigate symptoms of dysphagia in DMD and to determine the potential of the validated Sydney Swallow Questionnaire (SSQ) to diagnose dysphagia in this patient group. METHODS & PROCEDURES: Three participant groups completed the SSQ and the results were compared: nine DMD participants with dysphagia, six DMD participants without dysphagia and 12 healthy controls. OUTCOMES & RESULTS: The questionnaire scores for dysphagic DMD participants were significantly higher than for non-dysphagic DMD participants (p = 0.039) and for healthy controls (p ≤ 0.001). The diagnostic ability of the questionnaire was good for detecting dysphagia in participants with DMD (receiver operating characteristic (ROC) area under the curve = 0.89, p = 0.013), with a cut-off score of 224.5 (13.2%) giving a sensitivity of 0.78 and a specificity of 0.83 for determining dysphagia. Dysphagic participants rated time to eat a meal, swallowing hard food, swallowing thick liquids and needing to cough up or spit during meals with the highest severity of all questionnaire items. Results of the questionnaire by item are presented to inform the clinician of the symptoms of dysphagia in DMD. CONCLUSIONS & IMPLICATIONS: DMD leads to pervasive symptoms of dysphagia. The simple SSQ is a clinically informative assessment tool for patients with DMD.

Dysphagia in Duchenne muscular dystrophy assessed objectively by surface electromyography.

Objective swallowing assessment is indicated in the management of patients with Duchenne muscular dystrophy (DMD). Surface electromyography (sEMG) provides a non-invasive, objective method of quantifying muscle activity. It was hypothesised that the measurement of sEMG activity during swallowing would distinguish between preserved and disordered swallow function in DMD. This comparative study investigated the peak, duration, and relative timing of muscle activity during swallowing of four muscle groups: orbicularis oris, masseter, submental, and infrahyoid. The study included three groups of participants: Nine DMD patients with dysphagia (mean age = 21.7 ± 4.2 years), six DMD patients with preserved swallow function (21.0 ± 3.0 years), and 12 healthy controls (24.8 ± 3.1 years). Dysphagic DMD participants produced significantly higher normalised peak amplitude measurements than the healthy control group for masseter (61.77 vs. 5.07; p ≤ 0.01) and orbicularis oris muscles (71.87 vs. 26.22; p ≤ 0.05). Intrasubject variability for masseter peak amplitude was significantly greater for dysphagic DMD participants than the other groups (16.01 vs. 5.86 vs. 2.18; p ≤ 0.05). There were no differences in timing measurements between groups. Different characteristic sEMG waveforms were observed for the three groups. sEMG provides useful physiological information for the evaluation of swallowing in DMD patients, justifying further study.