Localization of Narrowband Single Photon Emitters in Nanodiamonds

Diamond nanocrystals that host room temperature narrowband single photon emitters are highly sought after for applications in nanophotonics and bioimaging. However, current understanding of the origin of these emitters is extremely limited. In this work, we demonstrate that the narrowband emitters are point defects localized at extended morphological defects in individual nanodiamonds. In particular, we show that nanocrystals with defects such as twin boundaries and secondary nucleation sites exhibit narrowband emission that is absent from pristine individual nanocrystals grown under the same conditions. Critically, we prove that the narrowband emission lines vanish when extended defects are removed deterministically using highly localized electron beam induced etching. Our results enhance the current understanding of single photon emitters in diamond and are directly relevant to fabrication of novel quantum optics devices and sensors.

Deep resequencing of CFTR in 762 F508del homozygotes reveals clusters of non-coding variants associated with cystic fibrosis disease traits

The basal transcription of CFTR is primarily driven by binding of factors at the 5′ promoter element.31 However, recent studies have shown that additional cis regulatory elements are required for tissue specificity, abundance and temporal expression.32,33 These cis regulatory elements have been shown to interact with the CFTR promoter, likely through a chromatin looping mechanism in part facilitated by CTCF binding.34 Multiple chromatin interaction studies have now shown that these regulatory loci are encompassed within a TAD,13,22,35 which is defined by boundary elements at −80 and +49 kb from CFTR. While much progress has been made regarding the chromatin structure in this region, resolving the function of each of these regulatory elements continues to be an active area of research. The results presented here posit that a burden of both rare and common variants at these key loci may modulate the CF phenotype by alteration in the level and/or timing of expression of CFTR bearing F508del. Our findings may inform future functional studies of the cis-regulatory elements identified in chromatin studies. The shared burden of rare and common variants associating with both CF traits at the −80 kb regulatory motif is possibly the most striking finding we report. We hypothesize that variants here may affect CTCF binding, or increase inherent enhancer activity. This could lead to altered expression of the F508del transcript, which has some residual processing and function.36,37,38,39,40,41 Presence of even small amounts of partially functional CFTR over the lifetime of an individual might be sufficient to moderate CF traits such as sweat chloride concentration and lung function.38 The concept that natural variation in the expression level of mutated genes may underlie differences in the severity of inherited diseases is supported by recent studies of loss-of-function C. elegans phenotypes.42 Additionally, we posit that the intragenic and extragenic variation present in the F508del population may confer increased or decreased response to Orkambi or future CFTR-specific drugs. The most 5′ regions of interest (Regions B and E, Figures 1 and 2) were located within the introns of WNT2 and ASZ1. The region in WNT2 is located in an adjacent TAD to CFTR. In a recent study, there was no report of this region interacting with the CFTR locus.22 However, previous studies in epididymis cells indicate there are weak long-range chromatin interactions with this region that may be cell type specific.13 It is possible that some of the rare variants associating with sweat chloride in this region modify overall chromatin organization in certain cell types, such as the sweat gland. Another distant region of interest was found within ASZ1, and is located just outside of the proposed CFTR TAD.22 These regions are often enriched for TAD-TAD interactions. Variants here could alter CTCF binding, TAD architecture or inter-TAD interactions. Assaying both of these possible inter-TAD interactions could lead to additional insight into distant regulatory elements in ASZ1 and WNT2. Of note, the 5′ TAD boundary proposed by Smith and Dekker22 closely follows the recombination event in intron 10 of ASZ1 in this study, suggesting a possible link between recombination events and chromatin structure in this region. Interestingly, adjacent regions within intron 3 of CFTR were found to associate with both sweat chloride levels and lung function (albeit, there is no distinct overlap given the coordinates identified here). To our knowledge, this region has not previously been shown to have regulatory function. While the intron 3 signal for sweat chloride was primarily composed of rare variation, common variation in the length of a poly T tract resulted in the lung function association. Interestingly, while not achieving significance, the 18T and 16T alleles at this locus trended toward association with sweat chloride levels as well (P=0.06, beta=−3.58 mM Cl− and P=0.08, β=+3.49 mM Cl−, respectively). We do note that this poly T tract still modulates lung function when the cohorts are considered independently (18T allele: P=0.051, β=+0.18, n=486 and P=0.12, β=+0.19, n=276). Given the lack of functional elements and low conservation in this region, it is challenging to imagine a mechanism by which this alteration could modulate CF traits. However, poly T tracts may regulate gene expression by acting as matrix attachment regions,43 or may participate in RNA triplex formation.44 A recurring theme throughout the variation observed in this study was variable lengths of repetitive elements associating with disease severity. These INDELs may represent a mode of phenotype modification that is not well characterized,45 but has been previously observed to modify the phenotype of other CF-causing alleles (i.e., R117H and polyT tract).46 This type of variation is observed in five of the seven regions of interest. A limitation of the current study is that insertion/deletion variants may be inadequately characterized because of limitations of current sequencing methods. However, all INDELs reported here were of both high mapping and variant call qualities, and variant frequencies did not deviate from Hardy-Weinberg equilibrium. It is possible that these small variants may be partially marking larger repetitive sequences that could not be typed in this study due to read length (or high homology). Additional studies of common and rare INDELs at these loci could reveal a mechanism of phenotype modification. Finally, we recognize that some of the associations employed here have limited power, especially at low minor allele frequencies given the cohort size (which ranges from 276 to 762, depending on the region). Power is additionally limited when assaying sweat chloride associations in the phase 2 cohort, as this cohort was selected for extremes of lung function, and thus contains intermediate sweat chloride values. Given these limitations, the study presented here likely contains false negatives, which could only be resolved using larger cohorts. Some sequencing studies fail to consider regions of known homology with the region of interest. In this study, we opted to allow for a higher frequency of false positives in regions of the capture with high homology to pseudogenes (specifically intron 9 and exon 10 of CFTR, Supplementary Table 2).20 This was to allow for more consistent tiling of baits, better detection of large structural variants and a more complete capture overall. Clinical labs should be aware of these regions when designing assays in order to minimize erroneous calls. For example, the nonsynonymous mutation A455E is a high-frequency CF-causing allele in exon 10. This variant is also present in a pseudogene present on chromosome 20. While this variant can be correctly typed using a longer read length, short amplifications cannot distinguish between these two forms.47 The variants reported in Supplementary Table 2 could be assigned to either the chromosome 9 or chromosome 20 pseudogenes due to their reoccurrence in a small subset of samples (n=5); however, alternative methods would be required in a clinical setting. Using the rich dataset produced by sequencing the entire CFTR locus, we were able to resolve the genetic architecture surrounding the common CF-causing variant to an unprecedented level of detail. We have now made available a detailed map of common variation and population-based haplotypes for the F508del locus (Supplementary Table 7). Specifically, we describe 13 haplotype-tagging SNPs that represent the vast majority of the genetic variation surrounding F508del. These SNPs could be used to parse F508del homozygotes into subpopulations to test whether variation at the CFTR locus underlies differences in responses to molecular-targeted treatments. Furthermore, they could be used to infer F508del carrier status in non-CF genome-wide association studies. Overall variation was rare within the LD block containing F508del, consistent with a single ancestral origin of this allele in the population. When considering only common SNPs, the majority of F508del chromosomes (~55%) are completely identical. These results indicate the F508del homozygous population is highly homogenous, with the majority of variation being private or due to a low-frequency recombination event within intron 15. Because this event is not observed on non-F508del chromosomes, it likely occurred after F508del arose. Previously, a recombination event was reported to have occurred within intron 22.25 However, this recombination event was based on population-level data provided by the HapMap project, which used wild-type CFTR and had significantly reduced marker density compared to this study.48 Newer HapMap releases suggest two possible primary recombination events in the general population: intron 11 and intron 15-intron 16. A recombination event at intron 15-intron 16 event appears to have occurred more than once, both in F508del-containing and in wild-type chromosomes. The previously reported intron 22 event may have some limited evidence in Mexican and Italian Hapmap cohorts. In summary, this study has methodically characterized variation in cis with the F508del allele and the genetic architecture of this locus in great depth. Collectively, our findings suggest a combination of rare and common variation within suspect and known regulatory regions at the CFTR locus may contribute to the phenotypic heterogeneity observed in F508del homozygous CF patients. The identified variation may modify CFTR expression levels and/or timing of expression, and should inform future regulatory studies of this locus. References Abstract • Introduction • Materials and methods • Results • Discussion • References • Acknowledgements • Author information • Supplementary information Gadsby DC, Vergani P, Csanady L. The ABC protein turned chloride channel whose failure causes cystic fibrosis. Nature 2006; 440: 477–483. ISI CAS PubMed Article Kerem E, Corey M, Kerem B-S, Rommens J, Markiewicz D, Levison H et al. The relation between genotype and phenotype in cystic fibrosis--analysis of the most common mutation (deltaF508). N Engl J Med 1990; 323: 1517–1522. ISI CAS PubMed Article Bobadilla JL, Macek M, Fine JP, Farrell PM. 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The presence of extra chromosomes leads to genomic instability

Aneuploidy is a hallmark of cancer and underlies genetic disorders characterized by severe developmental defects, yet the molecular mechanisms explaining its effects on cellular physiology remain elusive. Here we show, using a series of human cells with defined aneuploid karyotypes, that gain of a single chromosome increases genomic instability. Next-generation sequencing and SNP-array analysis reveal accumulation of chromosomal rearrangements in aneuploids, with break point junction patterns suggestive of replication defects. Trisomic and tetrasomic cells also show increased DNA damage and sensitivity to replication stress. Strikingly, we find that aneuploidy-induced genomic instability can be explained by the reduced expression of the replicative helicase MCM2-7. Accordingly, restoring near-wild-type levels of chromatin-bound MCM helicase partly rescues the genomic instability phenotypes. Thus, gain of chromosomes triggers replication stress, thereby promoting genomic instability and possibly contributing to tumorigenesis.

Spin Funneling for Enhanced Spin Injection into Ferromagnets

It is well-established that high spin-orbit coupling (SOC) materials convert a charge current density into a spin current density which can be used to switch a magnet efficiently and there is increasing interest in identifying materials with large spin Hall angle for lower switching current. Using experimentally benchmarked models, we show that composite structures can be designed using existing spin Hall materials such that the effective spin Hall angle is larger by an order of magnitude. The basic idea is to funnel spins from a large area of spin Hall material into a small area of ferromagnet using a normal metal with large spin diffusion length and low resistivity like Cu or Al. We show that this approach is increasingly effective as magnets get smaller. We avoid unwanted charge current shunting by the low resistive NM layer utilizing the newly discovered phenomenon of pure spin conduction in ferromagnetic insulators via magnon diffusion. We provide a spin circuit model for magnon diffusion in FMI that is benchmarked against recent experiments and theory.

Inhibition of cytochrome P450 3A by acetoxylated analogues of resveratrol in in vitro and in silico models

Many dietary compounds, including resveratrol, are potent inhibitors of CYP3A4. Here we examined the potential to predict inhibition capacity of dietary polyphenolics using an in silico and in vitro approaches and synthetic model compounds. Mono, di, and tri-acetoxy resveratrol were synthesized, a cell line of human intestine origin and microsomes from rat liver served to determine their in vitro inhibition of CYP3A4, and compared to that of resveratrol. Docking simulation served to predict the affinity of the synthetic model compounds to the enzyme. Modelling of the enzyme’s binding site revealed three types of interaction: hydrophobic, electrostatic and H-bonding. The simulation revealed that each of the examined acetylations of resveratrol led to the loss of important interactions of all types. Tri-acetoxy resveratrol was the weakest inhibitor in vitro despite being the more lipophilic and having the highest affinity for the binding site. The simulation demonstrated exclusion of all interactions between tri-acetoxy resveratrol and the heme due to distal binding, highlighting the complexity of the CYP3A4 binding site, which may allow simultaneous accommodation of two molecules. Finally, the use of computational modelling may serve as a quick predictive tool to identify potential harmful interactions between dietary compounds and prescribed drugs.

Multidimensional differentiation in foraging resource use during breeding of two sympatric top predators

Ecologically-similar species were found to develop specific strategies to partition their resources, leading to niche differentiation and divergence, in order to avoid interspecific competition. Our study determines multi-dimensional differentiation of two sympatric top-predators, long-legged buzzards (LLB) and short-toed eagles (STE), which recently became sympatric during their breeding season in the Judean Foothills, Israel. By combining information from comprehensive diet and movement analyses we found four dimensions of differentiation: (1) Geographic foraging area: LLB tended to forage relatively close to their nests (2.35 ± 0.62 km), while STE forage far from their nest (13.03 ± 2.20 km); (2) Foraging-habitat type: LLBs forage at low natural vegetation, avoiding cultivated fields, whereas STEs forage in cultivated fields, avoiding low natural vegetation; (3) Diurnal dynamics of foraging: LLBs are uniformly active during daytime, whereas STEs activity peaks in the early afternoon; and (4) Food-niche: while both species largely rely on reptiles (47.8% and 76.3% for LLB and STE, respectively), LLB had a more diverse diet and consumed significantly higher percentages of lizards, while STE consumed significantly higher percentages of snakes. Our results suggest that this multidimensional differentiation allows the spatial coexistence of these two dense populations in the study area.

Sulfur-tolerant BaO/ZrO2/TiO2/Al2O3 quaternary mixed oxides for deNOX catalysis

Phenotype-based variation as a biomarker of sensitivity to molecularly targeted therapy in melanoma

Transcriptomic phenotypes defined for melanoma have been reported to correlate with sensitivity to various drugs. In this study, we aimed to define a minimal signature that could be used to distinguish melanoma sub-types in vitro , and to determine suitable drugs by which these sub-types can be targeted. By using primary melanoma cell lines, as well as commercially available melanoma cell lines, we find that the evaluation of MLANA and INHBA expression is as capable as one based on a combined analysis performed with genes for stemness, EMT and invasion/proliferation, in identifying melanoma subtypes that differ in their sensitivity to molecularly targeted drugs. Using this approach, we find that 75% of melanoma cell lines can be treated with either the MEK inhibitor AZD6244 or the HSP90 inhibitor 17AAG.

Oxidatively degradable poly(thioketal urethane)/ceramic composite bone cements with bone-like strength

Synthetic bone cements are commonly used in orthopaedic procedures to aid in bone regeneration following trauma or disease. Polymeric cements like PMMA provide the mechanical strength necessary for orthopaedic applications, but they are not resorbable and do not integrate with host bone. Ceramic cements have a chemical composition similar to that of bone, but their brittle mechanical properties limit their use in weight-bearing applications. In this study, we designed oxidatively degradable, polymeric bone cements with mechanical properties suitable for bone tissue engineering applications. We synthesized a novel thioketal (TK) diol, which was crosslinked with a lysine triisocyanate (LTI) prepolymer to create hydrolytically stable poly(thioketal urethane)s (PTKUR) that degrade in the oxidative environment associated with bone defects. PTKUR films were hydrolytically stable for up to 6 months, but degraded rapidly (<1 week) under simulated oxidative conditions in vitro. When combined with ceramic micro- or nanoparticles, PTKUR cements exhibited working times comparable to calcium phosphate cements and strengths exceeding those of trabecular bone. PTKUR/ceramic composite cements supported appositional bone growth and integrated with host bone near the bone-cement interface at 6 and 12 weeks post-implantation in rabbit femoral condyle plug defects. Histological evidence of osteoclast-mediated resorption of the cements was observed at 6 and 12 weeks. These findings demonstrate that a PTKUR bone cement with bone-like strength can be selectively resorbed by cells involved in bone remodeling, and thus represent an important initial step toward the development of resorbable bone cements for weight-bearing applications.

Improved zero‐correlation linear cryptanalysis of reduced‐round Camellia under weak keys

Camellia is one of the widely used block ciphers, which has been included in the NESSIE block cipher portfolio and selected as a standard by ISO/IEC. In this study, the authors observe that there exist some interesting properties of the FL / FL −1 functions in Camellia. With this observation they derive some weak keys for the cipher, based on which they present the first known 8‐round zero‐correlation linear distinguisher of Camellia with FL / FL −1 layers. This result shows that the FL / FL −1 layers inserted in Camellia cannot resist zero‐correlation linear cryptanalysis effectively for some weak keys since the currently best zero‐correlation linear distinguisher for Camellia without FL / FL −1 layers also covers eight rounds. Moreover, by using the novel distinguisher, they launch key recovery attacks on 13‐round Camellia‐192 and 14‐round Camellia‐256. To their knowledge, these results are the best for Camellia‐192 and Camellia‐256 with FL / FL −1 and whitening layers.