Microstructural, Densitometric and Metabolic Variations in Bones from Rats with Normal or Altered Skeletal States

Background: High resolution μCT, and combined μPET/CT have emerged as non-invasive techniques to enhance or even replace dual energy X-ray absorptiometry (DXA) as the current preferred approach for fragility fracture risk assessment. The aim of this study was to assess the ability of µPET/CT imaging to differentiate changes in rat bone tissue density and microstructure induced by metabolic bone diseases more accurately than current available methods. Methods: Thirty three rats were divided into three groups of control, ovariectomy and vitamin-D deficiency. At the conclusion of the study, animals were subjected to glucose (18FDG) and sodium fluoride (Na18F) PET/CT scanning. Then, specimens were subjected to µCT imaging and tensile mechanical testing. Results: Compared to control, those allocated to ovariectomy and vitamin D deficiency groups showed 4% and 22% (significant) increase in 18FDG uptake values, respectively. DXA-based bone mineral density was higher in the vitamin D deficiency group when compared to the other groups (cortical bone), yet μCT-based apparent and mineral density results were not different between groups. DXA-based bone mineral density was lower in the ovariectomy group when compared to the other groups (cancellous bone); yet μCT-based mineral density results were not different between groups, and the μCT-based apparent density results were lower in the ovariectomy group compared to the other groups. Conclusion: PET and micro-CT provide an accurate three-dimensional measurement of the changes in bone tissue mineral density, as well as microstructure for cortical and cancellous bone and metabolic activity. As osteomalacia is characterized by impaired bone mineralization, the use of densitometric analyses may lead to misinterpretation of the condition as osteoporosis. In contrast, µCT alone and in combination with the PET component certainly provides an accurate three-dimensional measurement of the changes in both bone tissue mineral density, as well as microstructure for cortical and cancellous bone and metabolic activity

Origin of low thermal conductivity in In4Se3

In4Se3 is an attractive n-type thermoelectric material for mid-range waste heat recovery, owing to its low thermal conductivity (~ 0.9 W∙m- 1 K- 1 at 300 K). Here, we explore the relationship between the elastic properties, thermal conductivity and structure of In4Se3. The experimentally-determined average sound velocity (2010 m s-1), Young’s modulus (47 GPa), and Debye temperature (198 K) of In4Se3 are rather low, indicating considerable lattice softening. This behavior, which is consistent with low thermal conductivity, can be related to the complex bonding found in this material, in which strong covalent In-In and In-Se bonds coexist with weaker electrostatic interactions. Phonon dispersion calculations show that Einstein-like modes occur at ~ 30 cm-1. These Einstein-like modes can be ascribed to weakly bonded In+ cations located between strongly-bonded [(In3)5+(Se2-)3]- layers. The Grüneisen parameter for the soft-bonded In+ at the frequencies of the Einstein-like modes is large, indicating a high degree of bond anharmonicity and hence increased phonon scattering. The calculated thermal conductivity and elastic properties are in good agreement with experimental results

Identifying the controls on nitrate and metabolic state within the Red River delta (Vietnam) with the use of stable isotopes

In many places around the world, anthropogenic activities have resulted in nitrate (NO3−) pollution and changes in the metabolic state of aquatic ecosystems. Here we combined stable isotope and physico-chemical monitoring to assess the sources of NO3− and the overall metabolic state within the Red River delta, Vietnam. River water stable isotope compositions (δ18O-H2O) ranged between −11.2 and −2.7 ‰, δ18O-NO3− between −7.1 and + 29.7 ‰ and δ15N-NO3− between −3.9 and + 14.0 ‰. We identified the dominant NO3− sources as: 1) soil leachate, 2) domestic waste flushed from urban areas, and 3) NH4+ fertilizers washed from paddy fields. The relative impact of each source depends on geographical location within the delta and the time of year, due to dilution and concentration effects during wet and dry seasons. The primary NO3−source upstream is natural soil leachates, predominantly from tributaries connected to the Red River’s main stream. Within the middle-lower section of Red River delta, urban pollution from manure and septic waste reaches as high as 50 % of the total NO3− load during dry season. NO3− leached from fertilizers is also high at sites in the middle of the delta, related to agricultural activities. Dissolved oxygen isotope (δ18O-O2) values calculated from δ18O-H2O and δ18O-NO3− values indicate that the aquatic metabolism is net autotrophic (oxygen from primary production exceeds consumption by respiration), but high inputs of biodegradable organic matter from untreated domestic waste and high rates of sediment oxygen demand (SOD) and chemical oxygen demand (COD) have resulted in the whole river system becoming undersaturated in oxygen. High NO3− loads and low DO saturation are of critical concern and require mitigation practices to improve water quality for millions of people

Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence

The remarkable structural polymorphism of quadruplex-forming sequences has been a considerable impediment in the elucidation of quadruplex folds. Sequence modifications have commonly been used to perturb and purportedly select a particular form out of the ensemble of folds for nuclear magnetic resonance (NMR) or X-ray crystallographic analysis. Here we report a simple chromatographic technique that separates the individual folds without need for sequence modification. The sequence d(GGTGGTGGTGGTTGTGGTGGTGGTGG) forms a compact quadruplex according to a variety of common biophysical techniques. However, NMR and chromatography showed that this oligonucleotide produces at least eight monomeric quadruplex species that interconvert very slowly at room temperature. We have used a combination of spectroscopic, hydrodynamic and thermodynamic techniques to evaluate the physicochemical properties of the mixture and the individual species. These species have almost identical thermodynamic, hydrodynamic and electrophoretic properties, but significantly different NMR and circular dichroism (CD) spectra, as well as kinetic stability. These results demonstrate that simple standard low-resolution techniques cannot always be used for quadruplex fold determination or quality control purposes, and that simple thermodynamic analysis does not directly provide interpretable thermodynamic parameters

HD 219134 Revisited: Planet d Transit Upper Limit and Planet f Transit Nondetection with ASTERIA and TESS

HD 219134 is a K3V dwarf star with six reported radial-velocity discovered planets. The two innermost planets b and c show transits, raising the possibility of this system to be the nearest (6.53 pc), brightest (V = 5.57) example of a star with a compact multiple transiting planet system. Ground-based searches for transits of planets beyond b and c are not feasible because of the infrequent transits, long transit duration (~5 hr), shallow transit depths (<1%), and large transit time uncertainty (~half a day). We use the space-based telescopes the Arcsecond Space Telescope Enabling Research in Astrophysics (ASTERIA) and the Transiting Exoplanet Survey Satellite (TESS) to search for transits of planets f (P = 22.717 days and M sin i = 7.3 ± 0.04M_⊕) and d (P = 46.859 days and M sin i = 16.7 ± 0.64M_⊕). ASTERIA was a technology demonstration CubeSat with an opportunity for science in an extended program. ASTERIA observations of HD 219134 were designed to cover the 3σ transit windows for planets f and d via repeated visits over many months. While TESS has much higher sensitivity and more continuous time coverage than ASTERIA, only the HD 219134 f transit window fell within the TESS survey's observations. Our TESS photometric results definitively rule out planetary transits for HD 219134 f. We do not detect the Neptune-mass HD 219134 d transits and our ASTERIA data are sensitive to planets as small as 3.6 R_⊕. We provide TESS updated transit times and periods for HD 219134 b and c, which are designated TOI 1469.01 and 1469.02 respectively

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Genomic sequencing has driven precision-based oncology therapy; however, the genetic drivers of many malignancies remain unknown or non-targetable, so alternative approaches to the identification of therapeutic leads are necessary. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated on the basis of anatomical location (supratentorial region or posterior fossa) and further divided into distinct molecular subgroups that reflect differences in the age of onset, gender predominance and response to therapy1,2,3. The most common and aggressive subgroup, posterior fossa ependymoma group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations2. Conversely, posterior fossa ependymoma group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinical outcomes1,3. More than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NF-κB subunit gene RELA (ST-EPN-RELA), and a smaller number involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1)1,3,4. Subependymomas, a distinct histologic variant, can also be found within the supratetorial and posterior fossa compartments, and account for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE. Here we describe mapping of active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts, with the goal of identifying essential super-enhancer-associated genes on which tumour cells depend. Enhancer regions revealed putative oncogenes, molecular targets and pathways; inhibition of these targets with small molecule inhibitors or short hairpin RNA diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat.This work was supported by an Alex's Lemonade Stand Young Investigator Award (S.C.M.), The CIHR Banting Fellowship (S.C.M.), The Cancer Prevention Research Institute of Texas (S.C.M., RR170023), Sibylle Assmus Award for Neurooncology (K.W.P.), the DKFZ-MOST (Ministry of Science, Technology & Space, Israel) program in cancer research (H.W.), James S. McDonnell Foundation (J.N.R.) and NIH grants: CA154130 (J.N.R.), R01 CA169117 (J.N.R.), R01 CA171652 (J.N.R.), R01 NS087913 (J.N.R.) and R01 NS089272 (J.N.R.). R.C.G. is supported by NIH grants T32GM00725 and F30CA217065. M.D.T. is supported by The Garron Family Chair in Childhood Cancer Research, and grants from the Pediatric Brain Tumour Foundation, Grand Challenge Award from CureSearch for Children’s Cancer, the National Institutes of Health (R01CA148699, R01CA159859), The Terry Fox Research Institute and Brainchild. M.D.T. is also supported by a Stand Up To Cancer St. Baldrick’s Pediatric Dream Team Translational Research Grant (SU2C-AACR-DT1113)

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Therapeutic impact of cytoreductive surgery and irradiation of posterior fossa ependymoma in the molecular era: a retrospective multicohort analysis

PURPOSE: Posterior fossa ependymoma comprises two distinct molecular variants termed EPN_PFA and EPN_PFB that have a distinct biology and natural history. The therapeutic value of cytoreductive surgery and radiation therapy for posterior fossa ependymoma after accounting for molecular subgroup is not known. METHODS: Four independent nonoverlapping retrospective cohorts of posterior fossa ependymomas (n = 820) were profiled using genome-wide methylation arrays. Risk stratification models were designed based on known clinical and newly described molecular biomarkers identified by multivariable Cox proportional hazards analyses. RESULTS: Molecular subgroup is a powerful independent predictor of outcome even when accounting for age or treatment regimen. Incompletely resected EPN_PFA ependymomas have a dismal prognosis, with a 5-year progression-free survival ranging from 26.1% to 56.8% across all four cohorts. Although first-line (adjuvant) radiation is clearly beneficial for completely resected EPN_PFA, a substantial proportion of patients with EPN_PFB can be cured with surgery alone, and patients with relapsed EPN_PFB can often be treated successfully with delayed external-beam irradiation. CONCLUSION: The most impactful biomarker for posterior fossa ependymoma is molecular subgroup affiliation, independent of other demographic or treatment variables. However, both EPN_PFA and EPN_PFB still benefit from increased extent of resection, with the survival rates being particularly poor for subtotally resected EPN_PFA, even with adjuvant radiation therapy. Patients with EPN_PFB who undergo gross total resection are at lower risk for relapse and should be considered for inclusion in a randomized clinical trial of observation alone with radiation reserved for those who experience recurrence