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This letter indicates that immunohistochemical analysis to detect succinic dehydrogenase subunit B (SDHB) protein can screen renal tumors for underlying SDHB germline mutations at a fraction of the time and cost of formal genetic testing. To the Editor: The genes for the succinate dehydrogenase subunits A, B, C, and D ( SDHA, SDHB, SDHC, and SDHD, respectively) encode proteins that form part of the mitochondrial complex II, which links the Krebs cycle and the electron-transport chain. Heterozygous germline mutations of SDHB, SDHC, and SDHD cause the well-characterized familial pheochromocytoma-paraganglioma syndromes known respectively as PGL4, PGL3, and PGL1. 1 SDHB, SDHC, and SDHD mutations have also been linked to gastrointestinal stromal tumor, and SDHB and SDHD have been linked to renal-cell carcinoma. These kindreds are rarely recognized when they present with gastrointestinal stromal tumor and they are . . .

Synonymous codon choice can have dramatic effects on ribosome speed and protein expression. Ribosome profiling experiments have underscored that ribosomes do not move uniformly along mRNAs. Here, we have modeled this variation in translation elongation by using a feed-forward neural network to predict the ribosome density at each codon as a function of its sequence neighborhood. Our approach revealed sequence features affecting translation elongation and characterized large technical biases in ribosome profiling. We applied our model to design synonymous variants of a fluorescent protein spanning the range of translation speeds predicted with our model. Levels of the fluorescent protein in budding yeast closely tracked the predicted translation speeds across their full range. We therefore demonstrate that our model captures information determining translation dynamics in vivo; that this information can be harnessed to design coding sequences; and that control of translation elongation alone is sufficient to produce large quantitative differences in protein output.

Background Multiple sclerosis (MS) is a central nervous system (CNS) autoimmune disease characterized by both inflammatory demyelination and impaired remyelination. Studies indicate that Toll-like receptor 2 (TLR2) signaling contributes to both the inflammatory component and the defective remyelination in MS. While most MS therapeutics target adaptive immunity, we recently reported that reducing TLR2 signaling in innate immune cells by inducing TLR2 tolerance attenuates adoptively transferred experimental autoimmune encephalomyelitis. Given that previous reports suggest TLR2 signaling also inhibits myelin repair, the objective of this study was to assess how reducing TLR2 signaling through TLR2 tolerance induction affects CNS myelin repair . Methods Chow containing 0.2% cuprizone was fed to male and female wild-type (WT) C57BL/6 mice or TLR2-deficient (TLR2 −/− ) mice for 5 weeks to induce demyelination. During a 2-week remyelination period following discontinuation of cuprizone, WT mice received either low dose TLR2 ligands to induce systemic TLR2 tolerance or vehicle control (VC). Remyelination was evaluated via electron microscopy and immunohistochemical analysis of microglia and oligodendrocytes in the corpus callosum. Statistical tests included 2-way ANOVA and Mann-Whitney U analyses. Results Inducing TLR2 tolerance in WT mice during remyelination significantly enhanced myelin recovery, restoring unmyelinated axon frequency and myelin thickness to baseline levels compared to VC-treated mice. Mechanistically, enhanced remyelination in TLR2 tolerized mice was associated with a shift in corpus callosum microglia from a pro-inflammatory iNOS + phenotype to a non-inflammatory/pro-repair Arg1 + phenotype. This result was confirmed in vitro by inducing TLR2 tolerance in WT microglia cultures. TLR2 −/− mice, without TLR2 tolerance induction, also significantly enhanced myelin recovery compared to WT mice, adding confirmation that reduced TLR2 signaling is associated with enhanced remyelination. Discussion Our results suggest that reducing TLR2 signaling in vivo by inducing TLR2 tolerance significantly enhances myelin repair. Furthermore, the enhanced remyelination resulting from TLR2 tolerance induction is associated with a shift in corpus callosum microglia from a pro-inflammatory iNOS + phenotype to a non-inflammatory/pro-repair Arg1 + phenotype. While deletion of TLR2 would be an impractical approach in vivo, reducing innate immune signaling through TLR2 tolerance induction may represent a novel, two-pronged approach for treating both inflammatory and myelin repair components of MS.

Heterostructures between 2D and 3D electron systems remain critically important in developing novel and efficient optoelectronic and electronic devices. In this study, a vertical heterojunction between monolayer MoS 2 and bulk InSe was developed. This heterojunction exhibits a type-I band alignment that facilitates rapid energy transfer from the wide bandgap MoS 2 to the narrow bandgap InSe resulting in quenching of the MoS 2 photoluminescence (PL) emission and enhancement of the A exciton emission in InSe. Temperature-dependent PL measurements of MoS 2 on SiO 2 , MoS 2 on InSe, and bare InSe revealed the critical role of defect trapping and electron-phonon coupling in the optical response of MoS 2 on InSe. These results demonstrate that heterostructures combining monolayer MoS 2 on bulk InSe, showing marked improvement relative to bare InSe, would be advantageous when incorporated into optoelectronic devices such as photodetectors, light emitters, and color converters and highlights the benefit of creating van der Waals (vdW) heterostructures with tailored properties.

A discussion of some of the challenges and promise of single-cell technology.

Background Circulating microRNAs (miRNAs) are emerging as novel biomarkers for detecting cardiovascular diseases. In this study, we aimed to investigate the usefulness of miRNAs as biomarkers in diagnosing and predicting children with congenital heart defects (CHD), particularly in the context of multiple subtypes of CHD. Methods We recruited 26 families, each having a child with CHD and parents who do not have any cardiovascular disorder. 27 families unaffected by cardiovascular disease were also included as controls. Firstly, we screened 84 circulating miRNAs relating to cardiovascular development in 6 children with atrial septal defects (ASD) and 5 healthy children. We validated the selected miRNAs with differential expression in a larger sample size (n = 27 for controls, n = 26 for cases), and evaluated their signal in different types of septal defects. Finally, we examined the identified miRNAs signatures in the parent population and assessed their diagnostic values for predicting CHD. Results The three miRNAs hsa-let-7a, hsa-let-7b and hsa-miR-486 were significantly upregulated in children with ASD. A further validation study showed that overexpression of hsa-let-7a and hsa-let-7b was specifically present in ASD children, but not in children with other subtypes of septal defects. A similar expression profile of hsa-let-7a and hsa-let-7b was discovered in mothers of ASD children. Receiver-operating characteristic curve analyses indicated that hsa-let-7a and hsa-let-7b had significant diagnostic values for detecting ASD and in maternal samples predicting the occurrence of ASD in offspring. Conclusions Circulating miRNAs are important markers not only for diagnosing CHD, but also for predicting CHD risk in offspring. The distinct miRNA signatures are likely to present in various subtypes of CHD, and the phenotypic heterogeneity of CHD should be considered to develop such miRNA-based assays.

Pregnancy induces drastic biological changes systemically, and has a beneficial effect on some autoimmune conditions such as rheumatoid arthritis (RA). However, specific systemic changes that occur as a result of pregnancy have not been thoroughly examined in healthy women or women with RA. The goal of this study was to identify genes with expression patterns associated with pregnancy, compared to pre-pregnancy as baseline and determine whether those associations are modified by presence of RA. In our RNA sequencing (RNA-seq) dataset from 5 healthy women and 20 women with RA, normalized expression levels of 4,710 genes were significantly associated with pregnancy status (pre-pregnancy, first, second and third trimesters) over time, irrespective of presence of RA (False Discovery Rate (FDR)-adjusted p value<0.05). These genes were enriched in pathways spanning multiple systems, as would be expected during pregnancy. A subset of these genes (n = 256) showed greater than two-fold change in expression during pregnancy compared to baseline levels, with distinct temporal trends through pregnancy. Another 98 genes involved in various biological processes including immune regulation exhibited expression patterns that were differentially associated with pregnancy in the presence or absence of RA. Our findings support the hypothesis that the maternal immune system plays an active role during pregnancy, and also provide insight into other systemic changes that occur in the maternal transcriptome during pregnancy compared to the pre-pregnancy state. Only a small proportion of genes modulated by pregnancy were influenced by presence of RA in our data.

We report a three generation family with Beckwith Wiedemann syndrome (BWS) in whom we have identified a 330 kb deletion within the KCNQ1 locus, encompassing the 11p15.5 Imprinting Centre II (IC2). The deletion arose on the paternal chromosome in the first generation and was only associated with BWS when transmitted maternally to subsequent generations. The deletion on the maternal chromosome was associated with a lower median level of CDKN1C expression in the peripheral blood of affected individuals when compared to a cohort of unaffected controls (p<0.05), however was not significantly different to the expression levels in BWS cases with loss of methylation (LOM) within IC2 (p<0.78). Moreover the individual with a deletion on the paternal chromosome did not show evidence of elevated CDKN1C expression or features of Russell Silver syndrome. These observations support a model invoking the deletion of enhancer elements required for CDKN1C expression lying within or close to the imprinting centre and importantly extend and validate a single observation from an earlier study. Analysis of 94 cases with IC2 loss of methylation revealed that KCNQ1 deletion is a rare cause of loss of maternal methylation, occurring in only 3% of cases, or in 1.5% of BWS overall.

The development of high-precision large-area optical coatings and devices comprising low-dimensional materials hinges on scalable solution-based manufacturability with control over exfoliation procedure-dependent effects. As such, it is critical to understand the influence of technique-induced transition metal dichalcogenide (TMDC) optical properties that impact the design, performance, and integration of advanced optical coatings and devices. Here, we examine the optical properties of semiconducting MoS 2 films from the exfoliation formulations of four prominent approaches: solvent-mediated exfoliation, chemical exfoliation with phase reconversion, redox exfoliation, and native redox exfoliation. The resulting MoS 2 films exhibit distinct refractive indices ( n ), extinction coefficients ( k ), dielectric functions (ε 1 and ε 2 ), and absorption coefficients (α). For example, a large index contrast of Δ n  ≈ 2.3 is observed. These exfoliation procedures and related chemistries produce different exfoliated flake dimensions, chemical impurities, carrier doping, and lattice strain that influence the resulting optical properties. First-principles calculations further confirm the impact of lattice defects and doping characteristics on MoS 2 optical properties. Overall, incomplete phase reconfiguration (from 1T to mixed crystalline 2H and amorphous phases), lattice vacancies, intraflake strain, and Mo oxidation largely contribute to the observed differences in the reported MoS 2 optical properties. These findings highlight the need for controlled technique-induced effects as well as the opportunity for continued development of, and improvement to, liquid phase exfoliation methodologies. Such chemical and processing-induced effects present compelling routes to engineer exfoliated TMDC optical properties toward the development of next-generation high-performance mirrors, narrow bandpass filters, and wavelength-tailored absorbers.

The diversity of virus populations within single infected hosts presents a major difficulty for the natural immune response as well as for vaccine design and antiviral drug therapy. Recently developed pyrophosphate-based sequencing technologies (pyrosequencing) can be used for quantifying this diversity by ultra-deep sequencing of virus samples. We present computational methods for the analysis of such sequence data and apply these techniques to pyrosequencing data obtained from HIV populations within patients harboring drug-resistant virus strains. Our main result is the estimation of the population structure of the sample from the pyrosequencing reads. This inference is based on a statistical approach to error correction, followed by a combinatorial algorithm for constructing a minimal set of haplotypes that explain the data. Using this set of explaining haplotypes, we apply a statistical model to infer the frequencies of the haplotypes in the population via an expectation-maximization (EM) algorithm. We demonstrate that pyrosequencing reads allow for effective population reconstruction by extensive simulations and by comparison to 165 sequences obtained directly from clonal sequencing of four independent, diverse HIV populations. Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies.