A minimal colloid model of solution crystallization nucleates crystals classically.

A fundamental assumption of the classical theories of crystal nucleation is that the individual molecules from the "old" phase associate to an emerging nucleus individually and sequentially. Numerous recent studies of crystal nucleation in solution have revealed nonclassical pathways, whereby crystal nuclei are hosted and fed by amorphous clusters pre-formed in the solution. A sizable knowledge gap has persisted, however, in the definition of the molecular-level parameters that direct a solute towards classical or nonclassical nucleation. Here we construct a suspension of colloid particles of hydrodynamic diameter 1.1 µm and monitor their individual motions towards a quasi-two-dimensional crystal by scanning confocal microscopy. We combine electrostatic repulsion and polymer-induced attraction to obtain a simple isotropic pair interaction potential with a single attractive minimum of tunable depth between 1.2kBT and 2.7kBT. We find that even the smallest aggregates that form in this system structure as hexagonal two-dimensional crystals and grow and maturate by the association and exchange of single particles from the solution, signature behaviors during classical nucleation. The particles in the suspension equilibrate with those in the clusters and the volume fractions of suspensions at equilibrium correspond to straightforward thermodynamic predictions based on depth of the interparticle attraction. These results demonstrate that classical nucleation is selected by particles interacting with a minimal potential and present a benchmark for future modifications of the molecular interactions that may induce nonclassical nucleation.

Matrix Dynamics and Their Crucial Role in Non-radiative Decay during Thermally Activated Delayed Fluorescence.

We investigated the interplay of matrix dynamics with the molecular dynamics of a thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, to identify factors that influence the photophysical processes leading to TADF. The matrix dynamics surrounding NAI-DMAC molecules were varied continuously from the liquid to the solid state by depositing toluene solutions containing poly(methyl methacrylate) (PMMA) and NAI-DMAC onto optical substrates. We monitored changes of the NAI-DMAC emission as the liquid films dried to form solid PMMA films using temperature- and time-resolved photoluminescence spectroscopy. We observed that, in low-viscosity solutions, the proportion of delayed fluorescence from NAI-DMAC was much smaller than that of prompt fluorescence, indicating that negligible TADF occurred in the low-viscosity environment. However, as the viscosity of the environment diverged at the final stages of dry-down to form solid PMMA films, the delayed fluorescence component of NAI-DMAC emission was extended to longer time scales and increased in amplitude relative to prompt emission as the temperature increased─signatures that TADF occurred in the solid state as expected. Our findings reveal the influence that matrix dynamics have on the competition between conformational motion needed to access emissive states and undergo TADF versus larger amplitude structural fluctuations that lead to non-radiative decay. Insights from these studies will inform ongoing work to understand and predict how host matrices used in organic light-emitting devices can be designed to maximize the radiative properties of TADF emitters by allowing molecular motion needed to undergo TADF while restricting larger amplitude motion leading to non-radiative decay.

Interplay of molecular dynamics and radiative decay of a TADF emitter in a glass-forming liquid.

We investigate the role of molecular dynamics in the luminescent properties of a prototypical thermally activated delayed fluorescence (TADF) emitter, NAI-DMAC, in solution using a combination of temperature dependent time-resolved photoluminescence and absorption spectroscopies. We use a glass forming liquid, 2-methylfuran, to introduce an abrupt change in the temperature dependent diffusion dynamics of the solvent and examine the influence this has on the emission intensity of NAI-DMAC molecules. Comparison of experiment with first principles molecular dynamics simulations reveals that the emission intensity of NAI-DMAC molecules follows the temperature-dependent self-diffusion dynamics of the solvent. A marked reduction of emission intensity is observed as the temperature decreases toward the glass transition because the rate at which NAI-DMAC molecules can access emissive molecular conformations is greatly reduced. Below the glass transition, the diffusion dynamics of the solvent changes more slowly with temperature, which causes the emission intensity to decrease more slowly as well. The combination of experiment and computation suggests a pathway by which TADF emitters may transiently access a distribution of conformational states and avoid the need for an average conformation that strikes a balance between lower singlet-triplet energy splittings versus higher emission probabilities.

Cocaine-related DNA methylation in caudate neurons alters 3D chromatin structure of the IRXA gene cluster.

Epigenetic mechanisms, like those involving DNA methylation, are thought to mediate the relationship between chronic cocaine dependence and molecular changes in addiction-related neurocircuitry, but have been understudied in human brain. We initially used reduced representation bisulfite sequencing (RRBS) to generate a methylome-wide profile of cocaine dependence in human post-mortem caudate tissue. We focused on the Iroquois Homeobox A (IRXA) gene cluster, where hypomethylation in exon 3 of IRX2 in neuronal nuclei was associated with cocaine dependence. We replicated this finding in an independent cohort and found similar results in the dorsal striatum from cocaine self-administering mice. Using epigenome editing and 3C assays, we demonstrated a causal relationship between methylation within the IRX2 gene body, CTCF protein binding, three-dimensional (3D) chromatin interaction, and gene expression. Together, these findings suggest that cocaine-related hypomethylation of IRX2 contributes to the development and maintenance of cocaine dependence through alterations in 3D chromatin structure in the caudate nucleus.

Octahedral spinel electrocatalysts for alkaline fuel cells.

Designing high-performance nonprecious electrocatalysts to replace Pt for the oxygen reduction reaction (ORR) has been a key challenge for advancing fuel cell technologies. Here, we report a systematic study of 15 different AB2O4/C spinel nanoparticles with well-controlled octahedral morphology. The 3 most active ORR electrocatalysts were MnCo2O4/C, CoMn2O4/C, and CoFe2O4/C. CoMn2O4/C exhibited a half-wave potential of 0.89 V in 1 M KOH, equal to the benchmark activity of Pt/C, which was ascribed to charge transfer between Co and Mn, as evidenced by X-ray absorption spectroscopy. Scanning transmission electron microscopy (STEM) provided atomic-scale, spatially resolved images, and high-energy-resolution electron-loss near-edge structure (ELNES) enabled fingerprinting the local chemical environment around the active sites. The most active MnCo2O4/C was shown to have a unique Co-Mn core-shell structure. ELNES spectra indicate that the Co in the core is predominantly Co2.7+ while in the shell, it is mainly Co2+ Broader Mn ELNES spectra indicate less-ordered nearest oxygen neighbors. Co in the shell occupies mainly tetrahedral sites, which are likely candidates as the active sites for the ORR. Such microscopic-level investigation probes the heterogeneous electronic structure at the single-nanoparticle level, and may provide a more rational basis for the design of electrocatalysts for alkaline fuel cells.

Integrative DNA Methylation and Gene Expression Analysis in the Prefrontal Cortex of Mexicans Who Died by Suicide.

BACKGROUND: Suicide represents a major health concern, especially in developing countries. While many demographic risk factors have been proposed, the underlying molecular pathology of suicide remains poorly understood. A body of evidence suggests that aberrant DNA methylation and expression is involved. In this study, we examined DNA methylation profiles and concordant gene expression changes in the prefrontal cortex of Mexicans who died by suicide. METHODS: In collaboration with the coroner's office in Mexico City, brain samples of males who died by suicide (n = 35) and age-matched sudden death controls (n = 13) were collected. DNA and RNA were extracted from prefrontal cortex tissue and analyzed with the Infinium Methylation480k and the HumanHT-12 v4 Expression Beadchips, respectively. RESULTS: We report evidence of altered DNA methylation profiles at 4430 genomic regions together with 622 genes characterized by differential expression in cases vs controls. Seventy genes were found to have concordant methylation and expression changes. Metacore-enriched analysis identified 10 genes with biological relevance to psychiatric phenotypes and suicide (ADCY9, CRH, NFATC4, ABCC8, HMGA1, KAT2A, EPHA2, TRRAP, CD22, and CBLN1) and highlighted the association that ADCY9 has with various pathways, including signal transduction regulated by the cAMP-responsive element modulator, neurophysiological process regulated by the corticotrophin-releasing hormone, and synaptic plasticity. We therefore went on to validate the observed hypomethylation of ADCY9 in cases vs control through targeted bisulfite sequencing. CONCLUSION: Our study represents the first, to our knowledge, analysis of DNA methylation and gene expression associated with suicide in a Mexican population using postmortem brain, providing novel insights for convergent molecular alterations associated with suicide.

Differential ESR1 Promoter Methylation in the Peripheral Blood-Findings from the Women 40+ Healthy Aging Study.

Background Estrogen receptor α (ERα) contributes to maintaining biological processes preserving health during aging. DNA methylation changes of ERα gene (ESR1) were established as playing a direct role in the regulation of ERα levels. In this study, we hypothesized decreased DNA methylation of ESR1 associated with postmenopause, lower estradiol (E2) levels, and increased age among healthy middle-aged and older women. Methods We assessed DNA methylation of ESR1 promoter region from dried blood spots (DBSs) and E2 from saliva samples in 130 healthy women aged 40-73 years. Results We found that postmenopause and lower E2 levels were associated with lower DNA methylation of a distal regulatory region, but not with DNA methylation of proximal promoters. Conclusion Our results indicate that decreased methylation of ESR1 cytosine-phosphate-guanine island (CpGI) shore may be associated with conditions of lower E2 in older healthy women.

E2F6 functions as a competing endogenous RNA, and transcriptional repressor, to promote ovarian cancer stemness.

Ovarian cancer is the most lethal cancer of the female reproductive system. In that regard, several epidemiological studies suggest that long-term exposure to estrogen could increase ovarian cancer risk, although its precise role remains controversial. To decipher a mechanism for this, we previously generated a mathematical model of how estrogen-mediated upregulation of the transcription factor, E2F6, upregulates the ovarian cancer stem/initiating cell marker, c-Kit, by epigenetic silencing the tumor suppressor miR-193a, and a competing endogenous (ceRNA) mechanism. In this study, we tested that previous mathematical model, showing that estrogen treatment of immortalized ovarian surface epithelial cells upregulated both E2F6 and c-KIT, but downregulated miR-193a. Luciferase assays further confirmed that microRNA-193a targets both E2F6 and c-Kit. Interestingly, ChIP-PCR and bisulphite pyrosequencing showed that E2F6 also epigenetically suppresses miR-193a, through recruitment of EZH2, and by a complex ceRNA mechanism in ovarian cancer cell lines. Importantly, cell line and animal experiments both confirmed that E2F6 promotes ovarian cancer stemness, whereas E2F6 or EZH2 depletion derepressed miR-193a, which opposes cancer stemness, by alleviating DNA methylation and repressive chromatin. Finally, 118 ovarian cancer patients with miR-193a promoter hypermethylation had poorer survival than those without hypermethylation. These results suggest that an estrogen-mediated E2F6 ceRNA network epigenetically and competitively inhibits microRNA-193a activity, promoting ovarian cancer stemness and tumorigenesis.

A new microdeletion syndrome involving TBC1D24, ATP6V0C, and PDPK1 causes epilepsy, microcephaly, and developmental delay.

PURPOSE: Contiguous gene deletions are known to cause several neurodevelopmental syndromes, many of which are caused by recurrent events on chromosome 16. However, chromosomal microarray studies (CMA) still yield copy-number variants (CNVs) of unknown clinical significance. We sought to characterize eight individuals with overlapping 205-kb to 504-kb 16p13.3 microdeletions that are distinct from previously published deletion syndromes. METHODS: Clinical information on the patients and bioinformatic scores for the deleted genes were analyzed. RESULTS: All individuals in our cohort displayed developmental delay, intellectual disability, and various forms of seizures. Six individuals were microcephalic and two had strabismus. The deletion was absent in all 13 parents who were available for testing. The area of overlap encompasses seven genes including TBC1D24, ATP6V0C, and PDPK1 (also known as PDK1). Bi-allelic TBC1D24 pathogenic variants are known to cause nonsyndromic deafness, epileptic disorders, or DOORS syndrome (deafness, onychodystrophy, osteodystrophy, mental retardation, seizures). Sanger sequencing of the nondeleted TBC1D24 allele did not yield any additional pathogenic variants. CONCLUSIONS: We propose that 16p13.3 microdeletions resulting in simultaneous haploinsufficiencies of TBC1D24, ATP6V0C, and PDPK1 cause a novel rare contiguous gene deletion syndrome of microcephaly, developmental delay, intellectual disability, and epilepsy.

Correction: A new microdeletion syndrome involving TBC1D24, ATP6V0C, and PDPK1 causes epilepsy, microcephaly, and developmental delay.

The original version of this Article contained an error in the spelling of the author Siddharth Banka, which was incorrectly given as Siddhart Banka. This has now been corrected in both the PDF and HTML versions of the Article.

Isotope-selective chemistry in the Be+(2S1/2) + HOD → BeOD+/BeOH+ + H/D reaction.

Low temperature reactions between laser-cooled Be+(2S1/2) ions and partially deuterated water (HOD) molecules have been investigated using an ion trap and interpreted with zero-point corrected quasi-classical trajectory calculations on a highly accurate global potential energy surface for the ground electronic state. Both product channels have been observed for the first time, and the branching to BeOD+ + H is found to be 0.58 ± 0.14. The experimental observation is reproduced by both quasi-classical trajectory and statistical calculations. Theoretical analyses reveal that the branching to the two product channels is largely due to the availability of open states in each channel.

Iterative hard thresholding for model selection in genome-wide association studies.

A genome-wide association study (GWAS) correlates marker and trait variation in a study sample. Each subject is genotyped at a multitude of SNPs (single nucleotide polymorphisms) spanning the genome. Here, we assume that subjects are randomly collected unrelateds and that trait values are normally distributed or can be transformed to normality. Over the past decade, geneticists have been remarkably successful in applying GWAS analysis to hundreds of traits. The massive amount of data produced in these studies present unique computational challenges. Penalized regression with the ℓ1 penalty (LASSO) or minimax concave penalty (MCP) penalties is capable of selecting a handful of associated SNPs from millions of potential SNPs. Unfortunately, model selection can be corrupted by false positives and false negatives, obscuring the genetic underpinning of a trait. Here, we compare LASSO and MCP penalized regression to iterative hard thresholding (IHT). On GWAS regression data, IHT is better at model selection and comparable in speed to both methods of penalized regression. This conclusion holds for both simulated and real GWAS data. IHT fosters parallelization and scales well in problems with large numbers of causal markers. Our parallel implementation of IHT accommodates SNP genotype compression and exploits multiple CPU cores and graphics processing units (GPUs). This allows statistical geneticists to leverage commodity desktop computers in GWAS analysis and to avoid supercomputing. AVAILABILITY: Source code is freely available at https://github.com/klkeys/IHT.jl.

Evidence of Reduced Agmatine Concentrations in the Cerebral Cortex of Suicides.

Background: The polyamines are a group of ubiquitous low-molecular-weight aliphatic molecules that play an essential role in various physiological functions of the mammalian CNS. Previous literature has indicated alterations in the expression of polyamine-related genes in the brains of individuals who died by suicide, including downregulation of spermidine/spermine N1-acetyltransferase, a key enzyme involved in polyamine catabolism. One such polyamine, agmatine, has been shown to act as an antidepressant in animal models of depressive-like behavior. However, agmatine concentrations have not been explored in postmortem human brain of individuals who died by suicide. Methods: To measure agmatine in postmortem human brain tissue, we employed our previously published high-resolution capillary gas chromatography in combination with mass spectrometry method. Using this method, we analyzed agmatine levels in a total of 120 tissue samples from Brodmann areas 4, 11, and 44 of 40 male subjects comprising controls (n=13), individuals who died by suicide and met criteria for major depressive disorder (n=14), and subjects who died by suicide and did not meet criteria for major depressive disorder (n=13). Results: Agmatine fell within the expected nanomolar range and was significantly reduced in the cortex of suicides, irrespective of meeting criteria for major depressive disorder compared with controls. Conclusions: This is the first gas chromatography-mass spectrometry study to analyze agmatine concentrations in human postmortem brain of individuals who died by suicide. These results add to our mechanistic understanding of the role that the polyamine stress response pathway may play in the neurobiology of major depression and/or suicide.

Medium throughput bisulfite sequencing for accurate detection of 5-methylcytosine and 5-hydroxymethylcytosine.

BACKGROUND: Epigenetic modifications of DNA, such as 5-methylcytosine and 5-hydroxymethycytosine, play important roles in development and disease. Here, we present a cost-effective and versatile methodology for the analysis of DNA methylation in targeted genomic regions, which comprises multiplexed, PCR-based preparation of bisulfite DNA libraries followed by customized MiSeq sequencing. RESULTS: Using bisulfite and oxidative bisulfite conversion of DNA, we have performed multiplexed targeted sequencing to analyse several kilobases of genomic DNA in up to 478 samples, and achieved high coverage data of 5-methylcytosine and 5-hydroxymethycytosine at single-base resolution. Our results demonstrate the ability of this methodology to detect all levels of cytosine modifications at greater than 100× coverage in large sample sets at low cost compared to other targeted methods. CONCLUSIONS: This approach can be applied to multiple settings, from candidate gene to clinical studies, and is especially useful for validation of differentially methylated or hydroxymethylated regions following whole-genome analyses.

Molecular convergence of neurodevelopmental disorders.

Neurodevelopmental disorders (NDDs) are caused by mutations in diverse genes involved in different cellular functions, although there can be crosstalk, or convergence, between molecular pathways affected by different NDDs. To assess molecular convergence, we generated human neural progenitor cell models of 9q34 deletion syndrome, caused by haploinsufficiency of EHMT1, and 18q21 deletion syndrome, caused by haploinsufficiency of TCF4. Using next-generation RNA sequencing, methylation sequencing, chromatin immunoprecipitation sequencing, and whole-genome miRNA analysis, we identified several levels of convergence. We found mRNA and miRNA expression patterns that were more characteristic of differentiating cells than of proliferating cells, and we identified CpG clusters that had similar methylation states in both models of reduced gene dosage. There was significant overlap of gene targets of TCF4 and EHMT1, whereby 8.3% of TCF4 gene targets and 4.2% of EHMT1 gene targets were identical. These data suggest that 18q21 and 9q34 deletion syndromes show significant molecular convergence but distinct expression and methylation profiles. Common intersection points might highlight the most salient features of disease and provide avenues for similar treatments for NDDs caused by different genetic mutations.

cit: hypothesis testing software for mediation analysis in genomic applications.

MOTIVATION: The challenges of successfully applying causal inference methods include: (i) satisfying underlying assumptions, (ii) limitations in data/models accommodated by the software and (iii) low power of common multiple testing approaches. RESULTS: The causal inference test (CIT) is based on hypothesis testing rather than estimation, allowing the testable assumptions to be evaluated in the determination of statistical significance. A user-friendly software package provides P-values and optionally permutation-based FDR estimates (q-values) for potential mediators. It can handle single and multiple binary and continuous instrumental variables, binary or continuous outcome variables and adjustment covariates. Also, the permutation-based FDR option provides a non-parametric implementation. CONCLUSION: Simulation studies demonstrate the validity of the cit package and show a substantial advantage of permutation-based FDR over other common multiple testing strategies. AVAILABILITY AND IMPLEMENTATION: The cit open-source R package is freely available from the CRAN website (https://cran.r-project.org/web/packages/cit/index.html) with embedded C ++ code that utilizes the GNU Scientific Library, also freely available (http://www.gnu.org/software/gsl/). CONTACT: joshua.millstein@usc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The landscape of recombination in African Americans.

Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value < 10(-245)). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.

The Safety of Percutaneous Trigger Digit Release Increased by Neurovascular Displacement with Local Hydraulic Dilatation: An Anatomical and Clinical Study.

BACKGROUND Although percutaneous trigger digit release is common, controversy exists regarding its safety. The purpose of this study was to evaluate the feasibility and safety of the neurovascular displacement by local hydraulic dilatation (LHD) during percutaneous trigger digit release. MATERIAL AND METHODS Ten cadaver hands with 50 digits were dissected in this anatomical study. The distance between bilateral neurovascular bundles in each digit was measured before LHD and after LHD. The difference between the measured data before LHD and those after LHD in the same digit was compared to assess the feasibility of the neurovascular displacement by LHD. A further 81 patients with 106 trigger digits were treated by percutaneous release with neurovascular displacement by LHD in our clinical series. All patients were followed for 12 months. During the follow-up period, the presence of any postoperative complication and patient satisfaction were recorded. RESULTS In our anatomical study, there was a statistically significant difference (p<0.05) comparing the average distance of bilateral neurovascular bundles before LHD with that after LHD. In the current series, no complications, such as digital neurovascular injury or recurrence of trigger, were encountered. On subjective assessment, 80/81 patients (98.8%) with 105/106 digits (99.1%) were graded as satisfactory with complete resolution of symptoms by percutaneous release under LHD. CONCLUSIONS Based on our study anatomical and clinical results, the neurovascular displacement by LHD may be a feasible adjunctive technique that may play a role in increasing the safety of percutaneous trigger digit release.

Deep targeted sequencing of 12 breast cancer susceptibility regions in 4611 women across four different ethnicities.

BACKGROUND: Although genome-wide association studies (GWASs) have identified thousands of disease susceptibility regions, the underlying causal mechanism in these regions is not fully known. It is likely that the GWAS signal originates from one or many as yet unidentified causal variants. METHODS: Using next-generation sequencing, we characterized 12 breast cancer susceptibility regions identified by GWASs in 2288 breast cancer cases and 2323 controls across four populations of African American, European, Japanese, and Hispanic ancestry. RESULTS: After genotype calling and quality control, we identified 137,530 single-nucleotide variants (SNVs); of those, 87.2 % had a minor allele frequency (MAF) <0.005. For SNVs with MAF >0.005, we calculated the smallest number of SNVs needed to obtain a posterior probability set (PPS) such that there is 90 % probability that the causal SNV is included. We found that the PPS for two regions, 2q35 and 11q13, contained less than 5 % of the original SNVs, dramatically decreasing the number of potentially causal SNVs. However, we did not find strong evidence supporting a causal role for any individual SNV. In addition, there were no significant gene-based rare SNV associations after correcting for multiple testing. CONCLUSIONS: This study illustrates some of the challenges faced in fine-mapping studies in the post-GWAS era, most importantly the large sample sizes needed to identify rare-variant associations or to distinguish the effects of strongly correlated common SNVs.

A comprehensive examination of breast cancer risk loci in African American women.

Genome-wide association studies have identified 73 breast cancer risk variants mainly in European populations. Given considerable differences in linkage disequilibrium structure between populations of European and African ancestry, the known risk variants may not be informative for risk in African ancestry populations. In a previous fine-mapping investigation of 19 breast cancer loci, we were able to identify SNPs in four regions that better captured risk associations in African American women. In this study of breast cancer in African American women (3016 cases, 2745 controls), we tested an additional 54 novel breast cancer risk variants. Thirty-eight variants (70%) were found to have an association with breast cancer in the same direction as previously reported, with eight (15%) replicating at P < 0.05. Through fine-mapping, in three regions (1q32, 3p24, 10q25), we identified variants that better captured associations with overall breast cancer or estrogen receptor positive disease. We also observed suggestive associations with variants (at P < 5 × 10(-6)) in three separate regions (6q25, 14q13, 22q12) that may represent novel risk variants. Directional consistency of association observed for ∼65-70% of currently known genetic variants for breast cancer in women of African ancestry implies a shared functional common variant at most loci. To validate and enhance the spectrum of alleles that define associations at the known breast cancer risk loci, as well as genome-wide, will require even larger collaborative efforts in women of African ancestry.