Posttranscriptional regulation of FAN1 by miR-124-3p at rs3512 underlies onset-delaying genetic modification in Huntington's disease.

Many Mendelian disorders, such as Huntington's disease (HD) and spinocerebellar ataxias, arise from expansions of CAG trinucleotide repeats. Despite the clear genetic causes, additional genetic factors may influence the rate of those monogenic disorders. Notably, genome-wide association studies discovered somewhat expected modifiers, particularly mismatch repair genes involved in the CAG repeat instability, impacting age at onset of HD. Strikingly, FAN1, previously unrelated to repeat instability, produced the strongest HD modification signals. Diverse FAN1 haplotypes independently modify HD, with rare genetic variants diminishing DNA binding or nuclease activity of the FAN1 protein, hastening HD onset. However, the mechanism behind the frequent and the most significant onset-delaying FAN1 haplotype lacking missense variations has remained elusive. Here, we illustrated that a microRNA acting on 3'-UTR (untranslated region) SNP rs3512, rather than transcriptional regulation, is responsible for the significant FAN1 expression quantitative trait loci signal and allelic imbalance in FAN1 messenger ribonucleic acid (mRNA), accounting for the most significant and frequent onset-delaying modifier haplotype in HD. Specifically, miR-124-3p selectively targets the reference allele at rs3512, diminishing the stability of FAN1 mRNA harboring that allele and consequently reducing its levels. Subsequent validation analyses, including the use of antagomir and 3'-UTR reporter vectors with swapped alleles, confirmed the specificity of miR-124-3p at rs3512. Together, these findings indicate that the alternative allele at rs3512 renders the FAN1 mRNA less susceptible to miR-124-3p-mediated posttranscriptional regulation, resulting in increased FAN1 levels and a subsequent delay in HD onset by mitigating CAG repeat instability.

Genetic modifiers of Huntington disease differentially influence motor and cognitive domains.

Genome-wide association studies (GWASs) of Huntington disease (HD) have identified six DNA maintenance gene loci (among others) as modifiers and implicated a two step-mechanism of pathogenesis: somatic instability of the causative HTT CAG repeat with subsequent triggering of neuronal damage. The largest studies have been limited to HD individuals with a rater-estimated age at motor onset. To capitalize on the wealth of phenotypic data in several large HD natural history studies, we have performed algorithmic prediction by using common motor and cognitive measures to predict age at other disease landmarks as additional phenotypes for GWASs. Combined with imputation with the Trans-Omics for Precision Medicine reference panel, predictions using integrated measures provided objective landmark phenotypes with greater power to detect most modifier loci. Importantly, substantial differences in the relative modifier signal across loci, highlighted by comparing common modifiers at MSH3 and FAN1, revealed that individual modifier effects can act preferentially in the motor or cognitive domains. Individual components of the DNA maintenance modifier mechanisms may therefore act differentially on the neuronal circuits underlying the corresponding clinical measures. In addition, we identified additional modifier effects at the PMS1 and PMS2 loci and implicated a potential second locus on chromosome 7. These findings indicate that broadened discovery and characterization of HD genetic modifiers based on additional quantitative or qualitative phenotypes offers not only the promise of in-human validated therapeutic targets but also a route to dissecting the mechanisms and cell types involved in both the somatic instability and toxicity components of HD pathogenesis.

Nucleation and Crystallization of Ferrous Phosphate Hydrate via an Amorphous Intermediate.

The fundamental processes of nucleation and crystallization are widely observed in systems relevant to material synthesis and biomineralization; yet most often, their mechanism remains unclear. In this study, we unravel the discrete stages of nucleation and crystallization of Fe3(PO4)2·8H2O (vivianite). We experimentally monitored the formation and transformation from ions to solid products by employing correlated, time-resolved in situ and ex situ approaches. We show that vivianite crystallization occurs in distinct stages via a transient amorphous precursor phase. The metastable amorphous ferrous phosphate (AFEP) intermediate could be isolated and stabilized. We resolved the differences in bonding environments, structure, and symmetric changes of the Fe site during the transformation of AFEP to crystalline vivianite through synchrotron X-ray absorption spectroscopy at the Fe K-edge. This intermediate AFEP phase has a lower water content and less distorted local symmetry, compared to the crystalline end product vivianite. Our combined results indicate that a nonclassical, hydration-induced nucleation and transformation driven by the incorporation and rearrangement of water molecules and ions (Fe2+ and PO43-) within the AFEP is the dominating mechanism of vivianite formation at moderately high to low vivianite supersaturations (saturation index ≤ 10.19). We offer fundamental insights into the aqueous, amorphous-to-crystalline transformations in the Fe2+-PO4 system and highlight the different attributes of the AFEP, compared to its crystalline counterpart.

Imaging Protein Aggregates in Parkinson's Disease Serum Using Aptamer-Assisted Single-Molecule Pull-Down.

The formation of soluble α-synuclein (α-syn) and amyloid-ß (Aß) aggregates is associated with the development of Parkinson's disease (PD). Current methods mainly focus on the measurement of the aggregate concentration and are unable to determine their heterogeneous size and shape, which potentially also change during the development of PD due to increased protein aggregation. In this work, we introduce aptamer-assisted single-molecule pull-down (APSiMPull) combined with super-resolution fluorescence imaging of α-syn and Aß aggregates in human serum from early PD patients and age-matched controls. Our diffraction-limited imaging results indicate that the proportion of α-syn aggregates (α-syn/(α-syn+Aß)) can be used to distinguish PD and control groups with an area under the curve (AUC) of 0.85. Further, super resolution fluorescence imaging reveals that PD serums have a higher portion of larger and rounder α-syn aggregates than controls. Little difference was observed for Aß aggregates. Combining these two metrics, we constructed a new biomarker and achieved an AUC of 0.90. The combination of the aggregate number and morphology provides a new approach to early PD diagnosis.

Evolution of Structures and Optical Properties in a Series of Infrared Nonlinear Optical Crystals LixAg1-xInSe2 (0 ≤ x ≤ 1).

In this work, a number of new infrared nonlinear optical (NLO) crystals of LixAg1-xInSe2, in which the ratio x of Li/Ag varies in a wide range from 0 to 1, are investigated. Structural analysis reveals that the space group of LixAg1-xInSe2 evolved from I4̅2d in AgInSe2 to Pna21 in LiInSe2 as x increases from low values (0, 0.2, 0.37) to large values (0.55, 0.78, 0.81, 1). Compared to other Li/Ag coexisting chalcogenides such as LixAg1-xGaS2 and LixAg1-xGaSe2, the structural distortions in LixAg1-xInSe2 are much more prominent. This may explain the limited crystallization region in the phase graph of the tetragonal structure LixAg1-xInSe2. The fundamental optical absorption edges in these LixAg1-xInSe2 compounds are determined from the direct electronic transitions and the band gaps Eg gradually increase as the lithium content increases, consistent with the first-principles calculations. The composition x = 0.78 is calculated to have a good set of optical properties with a large NLO coefficient (dpowder = 28.8 pm/V) and moderate birefringence (Δn ∼ 0.04). Accordingly, the Li0.78Ag0.22InSe2 crystal is grown by the modified Bridgman-Stockbarger method, and it exhibits a wide transparency range from 0.546 to 14.3 µm at the 2% transmittance level.

Electronic, Structural, and Mechanical Properties of SiO_{2} Glass at High Pressure Inferred from its Refractive Index.

We report the first direct measurements of the refractive index of silica glass up to 145 GPa that allowed quantifying its density, bulk modulus, Lorenz-Lorentz polarizability, and band gap. These properties show two major anomalies at ∼10 and ∼40 GPa. The anomaly at ∼10 GPa signals the onset of the increase in Si coordination, and the anomaly at ∼40 GPa corresponds to a nearly complete vanishing of fourfold Si. More generally, we show that the compressibility and density of noncrystalline solids can be accurately measured in simple optical experiments up to at least 110 GPa.

Ethane and methane at high pressures: Structure and stability.

We have performed a combined experimental and theoretical study of ethane and methane at high pressures of up to 120 GPa at 300 K using x-ray diffraction and Raman spectroscopies and the USPEX ab initio evolutionary structural search algorithm, respectively. For ethane, we have determined the crystallization point, for room temperature, at 2.7 GPa and also the low pressure crystal structure (phase A). This crystal structure is orientationally disordered (plastic phase) and deviates from the known crystal structures for ethane at low temperatures. Moreover, a pressure induced phase transition has been identified, for the first time, at 13.6 GPa to a monoclinic phase B, the structure of which is solved based on good agreement with the experimental results and theoretical predictions. For methane, our x-ray diffraction measurements are in agreement with the previously reported high-pressure structures and equation of state (EOS). We have determined the EOSs of ethane and methane, which provides a solid basis for the discussion of their relative stability at high pressures.

Synthesis of Xenon and Iron-Nickel Intermetallic Compounds at Earth's Core Thermodynamic Conditions.

Using in situ synchrotron x-ray diffraction and Raman spectroscopy in concert with first principles calculations we demonstrate the synthesis of stable Xe(Fe,Fe/Ni)_{3} and XeNi_{3} compounds at thermodynamic conditions representative of Earth's core. Surprisingly, in the case of both the Xe-Fe and Xe-Ni systems Fe and Ni become highly electronegative and can act as oxidants. The results indicate the changing chemical properties of elements under extreme conditions by documenting that electropositive at ambient pressure elements could gain electrons and form anions.

Iodine in Metal-Organic Frameworks at High Pressure.

Capture of highly volatile radioactive iodine is a promising application of metal-organic frameworks (MOFs), thanks to their high porosity with flexible chemical architecture. Specifically, strong charge-transfer binding of iodine to the framework enables efficient and selective iodine uptake as well as its long-term storage. As such, precise knowledge of the electronic structure of iodine is essential for a detailed modeling of the iodine sorption process, which will allow for rational design of iodophilic MOFs in the future. Here we probe the electronic structure of iodine in MOFs at variable iodine···framework interaction by Raman and optical absorption spectroscopy at high pressure ( P). The electronic structure of iodine in the straight channels of SBMOF-1 (Ca- sdb, sdb = 4,4'-sulfonyldibenzoate) is modified irreversibly at P > 3.4 GPa by charge transfer, marking a polymerization of iodine molecules into a 1D polyiodide chain. In contrast, iodine in the sinusoidal channels of SBMOF-3 (Cd- sdb) retains its molecular (I2) character up to at least 8.4 GPa. Such divergent high-pressure behavior of iodine in the MOFs with similar port size and chemistry illustrates adaptations of the electronic structure of iodine to channel topology and strength of the iodine···framework interaction, which can be used to tailor iodine-immobilizing MOFs.

Polarization control of quantum dot emission by chiral photonic crystal slabs.

We investigate theoretically the polarization properties of the quantum dot's (QDs) optical emission from chiral photonic crystal structures made of achiral materials in the absence of external magnetic field at room temperature. The mirror symmetry of the local electromagnetic field is broken in this system due to the decreased symmetry of the chiral modulated layer. As a result, the radiation of randomly polarized QDs normal to the structure becomes partially circularly polarized. The sign and degree of circular polarization are determined by the geometry of the chiral modulated structure and depend on the radiation frequency. A degree of circular polarization up to 99% can be achieved for randomly distributed QDs, and can be close to 100% for some single QDs.

Backbone NxH compounds at high pressures.

Optical and synchrotron x-ray diffraction diamond anvil cell experiments have been combined with first-principles theoretical structure predictions to investigate mixtures of N2 and H2 up to 55 GPa. Our experiments show the formation of structurally complex van der Waals compounds [see also D. K. Spaulding et al., Nat. Commun. 5, 5739 (2014)] above 10 GPa. However, we found that these NxH (0.5 < x < 1.5) compounds transform abruptly to new oligomeric materials through barochemistry above 47 GPa and photochemistry at pressures as low as 10 GPa. These oligomeric compounds can be recovered to ambient pressure at T < 130 K, whereas at room temperature, they can be metastable on pressure release down to 3.5 GPa. Extensive theoretical calculations show that such oligomeric materials become thermodynamically more stable in comparison to mixtures of N2, H2, and NH3 above approximately 40 GPa. Our results suggest new pathways for synthesis of environmentally benign high energy-density materials. These materials could also exist as alternative planetary ices.

Recovery of phosphorus from dairy manure: a pilot-scale study.

Phosphorus was recovered from dairy manure via a microwave-enhanced advanced oxidation process (MW/H2O2-AOP) followed by struvite crystallization in a pilot-scale continuous flow operation. Soluble phosphorus in dairy manure increased by over 50% after the MW/H2O2-AOP, and the settleability of suspended solids was greatly improved. More than 50% of clear supernatant was obtained after microwave treatment, and the maximum volume of supernatant was obtained at a hydrogen peroxide dosage of 0.3% and pH 3.5. By adding oxalic acid into the supernatant, about 90% of calcium was removed, while more than 90% of magnesium was retained. As a result, the resulting solution was well suited for struvite crystallization. Nearly 95% of phosphorus in the treated supernatant was removed and recovered as struvite.

Pressure-induced metallization of molybdenum disulfide.

X-ray diffraction, Raman spectroscopy, and electrical conductivity measurements of molybdenum disulfide MoS(2) are performed at pressures up to 81 GPa in diamond anvil cells. Above 20 GPa, we find discontinuous changes in Raman spectra and x-ray diffraction patterns which provide evidence for isostructural phase transition from 2H(c) to 2H(a) modification through layer sliding previously predicted theoretically. This first-order transition, which is completed around 40 GPa, is characterized by a collapse in the c-lattice parameter and volume and also by changes in interlayer bonding. After the phase transition completion, MoS(2) becomes metallic. The reversibility of the phase transition is identified from all these techniques.

Modification of Huntington's disease by short tandem repeats.

Expansions of glutamine-coding CAG trinucleotide repeats cause a number of neurodegenerative diseases, including Huntington's disease and several of spinocerebellar ataxias. In general, age-at-onset of the polyglutamine diseases is inversely correlated with the size of the respective inherited expanded CAG repeat. Expanded CAG repeats are also somatically unstable in certain tissues, and age-at-onset of Huntington's disease corrected for individual HTT CAG repeat length (i.e. residual age-at-onset), is modified by repeat instability-related DNA maintenance/repair genes as demonstrated by recent genome-wide association studies. Modification of one polyglutamine disease (e.g. Huntington's disease) by the repeat length of another (e.g. ATXN3, CAG expansions in which cause spinocerebellar ataxia 3) has also been hypothesized. Consequently, we determined whether age-at-onset in Huntington's disease is modified by the CAG repeats of other polyglutamine disease genes. We found that the CAG measured repeat sizes of other polyglutamine disease genes that were polymorphic in Huntington's disease participants but did not influence Huntington's disease age-at-onset. Additional analysis focusing specifically on ATXN3 in a larger sample set (n = 1388) confirmed the lack of association between Huntington's disease residual age-at-onset and ATXN3 CAG repeat length. Additionally, neither our Huntington's disease onset modifier genome-wide association studies single nucleotide polymorphism data nor imputed short tandem repeat data supported the involvement of other polyglutamine disease genes in modifying Huntington's disease. By contrast, our genome-wide association studies based on imputed short tandem repeats revealed significant modification signals for other genomic regions. Together, our short tandem repeat genome-wide association studies show that modification of Huntington's disease is associated with short tandem repeats that do not involve other polyglutamine disease-causing genes, refining the landscape of Huntington's disease modification and highlighting the importance of rigorous data analysis, especially in genetic studies testing candidate modifiers.

Huntington's disease age at motor onset is modified by the tandem hexamer repeat in TCERG1.

Huntington's disease is caused by an expanded CAG tract in HTT. The length of the CAG tract accounts for over half the variance in age at onset of disease, and is influenced by other genetic factors, mostly implicating the DNA maintenance machinery. We examined a single nucleotide variant, rs79727797, on chromosome 5 in the TCERG1 gene, previously reported to be associated with Huntington's disease and a quasi-tandem repeat (QTR) hexamer in exon 4 of TCERG1 with a central pure repeat. We developed a method for calling perfect and imperfect repeats from exome-sequencing data, and tested association between the QTR in TCERG1 and residual age at motor onset (after correcting for the effects of CAG length in the HTT gene) in 610 individuals with Huntington's disease via regression analysis. We found a significant association between age at onset and the sum of the repeat lengths from both alleles of the QTR (p = 2.1 × 10-9), with each added repeat hexamer reducing age at onset by one year (95% confidence interval [0.7, 1.4]). This association explained that previously observed with rs79727797. The association with age at onset in the genome-wide association study is due to a QTR hexamer in TCERG1, translated to a glutamine/alanine tract in the protein. We could not distinguish whether this was due to cis-effects of the hexamer repeat on gene expression or of the encoded glutamine/alanine tract in the protein. These results motivate further study of the mechanisms by which TCERG1 modifies onset of HD.

Exome sequencing of individuals with Huntington's disease implicates FAN1 nuclease activity in slowing CAG expansion and disease onset.

The age at onset of motor symptoms in Huntington's disease (HD) is driven by HTT CAG repeat length but modified by other genes. In this study, we used exome sequencing of 683 patients with HD with extremes of onset or phenotype relative to CAG length to identify rare variants associated with clinical effect. We discovered damaging coding variants in candidate modifier genes identified in previous genome-wide association studies associated with altered HD onset or severity. Variants in FAN1 clustered in its DNA-binding and nuclease domains and were associated predominantly with earlier-onset HD. Nuclease activities of purified variants in vitro correlated with residual age at motor onset of HD. Mutating endogenous FAN1 to a nuclease-inactive form in an induced pluripotent stem cell model of HD led to rates of CAG expansion similar to those observed with complete FAN1 knockout. Together, these data implicate FAN1 nuclease activity in slowing somatic repeat expansion and hence onset of HD.

Association Analysis of Chromosome X to Identify Genetic Modifiers of Huntington's Disease.

BACKGROUND: Huntington's disease (HD) is caused by an expanded (>35) CAG trinucleotide repeat in huntingtin (HTT). Age-at-onset of motor symptoms is inversely correlated with the size of the inherited CAG repeat, which expands further in brain regions due to somatic repeat instability. Our recent genetic investigation focusing on autosomal SNPs revealed that age-at-onset is also influenced by genetic variation at many loci, the majority of which encode genes involved in DNA maintenance/repair processes and repeat instability. OBJECTIVE: We performed a complementary association analysis to determine whether variants in the X chromosome modify HD. METHODS: We imputed SNPs on chromosome X for ∼9,000 HD subjects of European ancestry and performed an X chromosome-wide association study (XWAS) to test for association with age-at-onset corrected for inherited CAG repeat length. RESULTS: In a mixed effects model XWAS analysis of all subjects (males and females), assuming random X-inactivation in females, no genome-wide significant onset modification signal was found. However, suggestive significant association signals were detected at Xq12 (top SNP, rs59098970; p-value, 1.4E-6), near moesin (MSN), in a region devoid of DNA maintenance genes. Additional suggestive signals not involving DNA repair genes were observed in male- and female-only analyses at other locations. CONCLUSION: Although not genome-wide significant, potentially due to small effect size compared to the power of the current study, our data leave open the possibility of modification of HD by a non-DNA repair process. Our XWAS results are publicly available at the updated GEM EURO 9K website hosted at https://www.hdinhd.org/ for browsing, pathway analysis, and data download.

Gated detection of supercontinuum pulses enables optical probing of solid and molten silicates at extreme pressure-temperature conditions.

Optical studies of materials at high pressure-temperature (P-T) conditions provide insights into their physical properties that may be inaccessible to direct determination at extreme conditions. Incandescent light sources, however, are insufficiently bright to optically probe samples with radiative temperatures above ∼1000 K. Here we report on a system to perform optical absorption experiments in a laser-heated diamond anvil cell at T up to at least 4000 K. This setup is based on a pulsed supercontinuum (broadband) light probe and a gated CCD detector. Precise and tight synchronization of the detector gates (3 ns) to the bright probe pulses (1 ns) diminishes the recorded thermal background and preserves an excellent probe signal at high temperature. We demonstrate the efficiency of this spectroscopic setup by measuring the optical absorbance of solid and molten (Mg,Fe)SiO3, an important constituent of planetary mantles, at P ∼30 GPa and T ∼1200 K to 4150 K. Optical absorbance of the hot solid (Mg,Fe)SiO3 is moderately sensitive to temperature but increases abruptly upon melting and acquires a strong temperature dependence. Our results enable quantitative estimates of the opacity of planetary mantles with implications to their thermal and electrical conductivities, all of which have never been constrained at representative P-T conditions, and call for an optical detection of melting in silicate-bearing systems to resolve the extant ambiguity in their high-pressure melting curves.

Low thermal conductivity of iron-silicon alloys at Earth's core conditions with implications for the geodynamo.

Earth's core is composed of iron (Fe) alloyed with light elements, e.g., silicon (Si). Its thermal conductivity critically affects Earth's thermal structure, evolution, and dynamics, as it controls the magnitude of thermal and compositional sources required to sustain a geodynamo over Earth's history. Here we directly measured thermal conductivities of solid Fe and Fe-Si alloys up to 144 GPa and 3300 K. 15 at% Si alloyed in Fe substantially reduces its conductivity by about 2 folds at 132 GPa and 3000 K. An outer core with 15 at% Si would have a conductivity of about 20 W m-1 K-1, lower than pure Fe at similar pressure-temperature conditions. This suggests a lower minimum heat flow, around 3 TW, across the core-mantle boundary than previously expected, and thus less thermal energy needed to operate the geodynamo. Our results provide key constraints on inner core age that could be older than two billion-years.