Three exonic variants in the PHEX gene cause aberrant splicing in a minigene assay.

Background: X-linked hypophosphatemia (XLH, OMIM 307800) is a rare phosphorus metabolism disorder caused by PHEX gene variants. Many variants simply classified as missense or nonsense variants were only analyzed at the DNA level. However, growing evidence indicates that some of these variants may alter pre-mRNA splicing, causing diseases. Therefore, this study aimed to use bioinformatics tools and a minigene assay to ascertain the effects of PHEX variations on pre-mRNA splicing. Methods: We analyzed 174 variants in the PHEX gene described as missense or nonsense variants. Finally, we selected eight candidate variants using bioinformatics tools to evaluate their effects on pre-mRNA splicing using a minigene assay system. The complementary DNA (cDNA) sequence for the PHEX gene (RefSeq NM_000444.6) serves as the basis for DNA variant numbering. Results: Of the eight candidate variants, three were found to cause abnormal splicing. Variants c.617T>G p.(Leu206Trp) and c.621T>A p.(Tyr207*) in exon 5 altered the splicing of pre-mRNA, owing to the activation of a cryptic splice site in exon 5, which produced an aberrant transcript lacking a part of exon 5, whereas variant c.1700G>C p.(Arg567Pro) in exon 16 led to the activation of a cryptic splice site in intron 16, resulting in a partial inclusion of intron 16. Conclusion: Our study employed a minigene system, which has a great degree of flexibility to assess abnormal splicing patterns under the circumstances of patient mRNA samples that are not available, to explore the impact of the exonic variants on pre-mRNA splicing. Based on the aforementioned experimental findings, we demonstrated the importance of analyzing exonic variants at the mRNA level.

Identification of seven variants in the col4a1 gene that alter RNA splicing by minigene assay.

Type IV collagen is an integral component of basement membranes. Mutations in COL4A1, one of the key genes encoding Type IV collagen, can result in a variety of diseases. It is clear that a significant proportion of mutations that affect splicing can cause disease directly or contribute to the susceptibility or severity of disease. Here, we analyzed exonic mutations and intronic mutations described in the COL4A1 gene using bioinformatics programs and identified candidate mutations that may alter the normal splicing pattern through a minigene system. We identified seven variants that induce splicing alterations by disrupting normal splice sites, creating new ones, or altering splice regulatory elements. These mutations are predicted to impact protein function. Our results help in the correct molecular characterization of variants in COL4A1 and may help develop more personalized treatment options.

A novel heterozygous variant of the SALL1 gene with atypical Townes-Brocks syndrome phenotypes in Chinese family.

Townes-Brocks syndrome (TBS) is an autosomal dominant disorder characterised by the triad of anorectal, thumb, and ear malformations. It may also be accompanied by defects in kidney, heart, eyes, hearing, and feet. TBS has been demonstrated to result from heterozygous variants in the SALL1 gene, which encodes zinc finger protein believed to function as a transcriptional repressor. The clinical characteristics of an atypical TBS phenotype patient from a Chinese family are described, with predominant manifestations including external ear dysplasia, unilateral renal hypoplasia with mild renal dysfunction, and hearing impairment. A novel heterozygous variant c.3060T>A (p.Tyr1020*) in exon 2 of the SALL1 gene was identified in this proband. Pyrosequencing of the complementary DNA of the proband revealed that the variant transcript accounted for 48% of the total transcripts in peripheral leukocytes, indicating that this variant transcript has not undergone nonsense-mediated mRNA decay. This variant c.3060T > A is located at the terminal end of exon 2, proximal to the 3' end of the SALL1 gene, and exerts a relatively minor impact on protein function. We suggest that the atypical TBS phenotype observed in the proband may be attributed to the truncated protein retaining partial SALL1 function.

Disentangling influences of driving forces on intra-annual variability in sediment discharge in karst watersheds.

The intra-annual variability in sediment discharge was considerably influenced by the climate variability and vegetation dynamics. Because of the coupled or relationships between climatic and vegetation variables, it is still challenging to decouple the direct and indirect effects of climate variability and vegetation dynamics on hydrological and sediment transport processes. The purpose of this study is to decouple influences of individual driving force on intra-annual distribution of sediment discharge during 2003-2017 using the partial least squares structural equation model (PLS-SEM) method in four typical karst watersheds of Southwest China. The coefficient of variation (Cv), Completely regulation coefficient (Cr), Lorenz asymmetry coefficient and Gini coefficient were used to represent the intra-annual sediment discharge variability. Results showed that the monthly sediment discharge (190 % < Cv < 353 %) exhibited greater variability than its potential affecting factors (18 % < Cv < 101 %). From the PLS-SEM analysis, the water discharge, climate, and vegetation together explain 57 %-75 %, 64 %-79 %, and 53 %-80 % of the total variance in Cv, Cr, and Gini coefficient, respectively. Specifically, water discharge exerts the largest influence on sediment discharge variability (0.65 ≤ direct effect ≤0.97, P < 0.05), while vegetation dynamic mainly indirectly affects sediment discharge variability (-0.88 ≤ indirect effect ≤ -0.01) through influencing water discharge. The climate factors also principally indirectly affect the sediment discharge variability (-0.47 ≤ indirect effect ≤0.19) by affecting water discharge and vegetation. The PLS-SEM can effectively reveal the driving force and influencing mechanism of intra-annual sediment discharge changes, and provide an important reference for regional soil and water resources management in karst watersheds. Future studies can decouple the influences of the extreme climate, unique lithology, discontinuous soil, heterogeneous landscape, and special geomorphology on spatial variability in sediment discharge across different karst watersheds.

Three exonic variants in the COL4A5 gene alter RNA splicing in a minigene assay.

BACKGROUND: X-linked Alport syndrome (XLAS) is an inherited renal disease caused by rare variants of COL4A5 on chromosome Xq22. Many studies have indicated that single nucleotide variants (SNVs) in exons can disrupt normal splicing process of the pre-mRNA by altering various splicing regulatory signals. The male patients with XLAS have a strong genotype-phenotype correlation. Confirming the effect of variants on splicing can help to predict kidney prognosis. This study aimed to investigate whether single nucleotide substitutions, located within three bases at the 5' end of the exons or internal position of the exons in COL4A5 gene, cause aberrant splicing process. METHODS: We analyzed 401 SNVs previously presumed missense and nonsense variants in COL4A5 gene by bioinformatics programs and identified candidate variants that may affect the splicing of pre-mRNA via minigene assays. RESULTS: Our study indicated three of eight candidate variants induced complete or partial exon skipping. Variants c.2678G>C and c.2918G>A probably disturb classic splice sites leading to corresponding exon skipping. Variant c.3700C>T may disrupt splicing enhancer motifs accompanying with generation of splicing silencer sequences resulting in the skipping of exon 41. CONCLUSION: Our study revealed that two missense variants positioned the first nucleotides of the 5' end of COL4A5 exons and one internal exonic nonsense variant caused aberrant splicing. Importantly, this study emphasized the necessity of assessing the effects of SNVs at the mRNA level.

Functional analysis of the CTNS gene exonic variants predicted to affect splicing.

Cystinosis is a severe, monogenic systemic disease caused by variants in CTNS gene. Currently, there is growing evidence that exonic variants in many diseases can affect pre-mRNA splicing. The impact of CTNS gene exonic variants on splicing regulation may be underestimated due to the lack of routine studies at the RNA level. Here, we analyzed 59 exonic variants in the CTNS gene using bioinformatics tools and identified candidate variants that may induce splicing alterations by minigene assays. We identified six exonic variants that induce splicing alterations by disrupting the ratio of exonic splicing enhancers/exonic splicing silencers (ESEs/ESSs) or by interfering with the recognition of classical splice sites, or both. Our results help in the correct molecular characterization of variants in cystinosis and inform emerging therapies. Furthermore, our work suggests that the combination of in silico and in vitro assays facilitates to assess the effects of DNA variants driving rare genetic diseases on splicing regulation and will enhance the clinical utility of variant functional annotation.

Identified eleven exon variants in PKD1 and PKD2 genes that altered RNA splicing by minigene assay.

BACKGROUND: Autosomal dominant polycystic kidney disease (ADPKD) is a common monogenic multisystem disease caused primarily by mutations in the PKD1 gene or PKD2 gene. There is increasing evidence that some of these variants, which are described as missense, synonymous or nonsense mutations in the literature or databases, may be deleterious by affecting the pre-mRNA splicing process. RESULTS: This study aimed to determine the effect of these PKD1 and PKD2 variants on exon splicing combined with predictive bioinformatics tools and minigene assay. As a result, among the 19 candidate single nucleotide alterations, 11 variants distributed in PKD1 (c.7866C > A, c.7960A > G, c.7979A > T, c.7987C > T, c.11248C > G, c.11251C > T, c.11257C > G, c.11257C > T, c.11346C > T, and c.11393C > G) and PKD2 (c.1480G > T) were identified to result in exon skipping. CONCLUSIONS: We confirmed that 11 variants in the gene of PKD1 and PKD2 affect normal splicing by interfering the recognition of classical splicing sites or by disrupting exon splicing enhancers and generating exon splicing silencers. This is the most comprehensive study to date on pre-mRNA splicing of exonic variants in ADPKD-associated disease-causing genes in consideration of the increasing number of identified variants in PKD1 and PKD2 gene in recent years. These results emphasize the significance of assessing the effect of exon single nucleotide variants in ADPKD at the mRNA level.

Idealizing Tauc Plot for Accurate Bandgap Determination of Semiconductor with Ultraviolet-Visible Spectroscopy: A Case Study for Cubic Boron Arsenide.

The Tauc plot is widely used to determine the bandgap of semiconductors, but the actual plot often exhibits significant baseline absorption below the expected bandgap, leading to bandgap discrepancies from two different extrapolations. In this work, we first discuss the origin of baseline absorption and show that both extrapolation methods can produce significant errors by simulating Tauc plots with varying levels of baseline absorption. We then propose and experimentally verify a new method that idealizes the absorption spectrum by removing its baseline before constructing the Tauc plot. Finally, we apply this new method to cubic boron arsenide (c-BAs), resolve its bandgap discrepancies, and obtain a converging bandgap of 1.835 eV based on both previous and new transmission spectra. The method is applicable to both indirect and direct bandgap semiconductors with absorption spectrum measured via transmission or diffuse reflectance, which will become essential to obtain accurate values of their bandgaps.

Carbon hollow fiber membranes for a molecular sieve with precise-cutoff ultramicropores for superior hydrogen separation.

Carbon molecular sieve (CMS) membranes with rigid and uniform pore structures are ideal candidates for high temperature- and pressure-demanded separations, such as hydrogen purification from the steam methane reforming process. Here, we report a facile and scalable method for the fabrication of cellulose-based asymmetric carbon hollow fiber membranes (CHFMs) with ultramicropores of 3-4 Å for superior H2 separation. The membrane fabrication process does not require complex pretreatments to avoid pore collapse before the carbonization of cellulose precursors. A H2/CO2 selectivity of 83.9 at 130 °C (H2/N2 selectivity of >800, H2/CH4 selectivity of >5700) demonstrates that the membrane provides a precise cutoff to discriminate between small gas molecules (H2) and larger gas molecules. In addition, the membrane exhibits superior mixed gas separation performances combined with water vapor- and high pressure-resistant stability. The present approach for the fabrication of high-performance CMS membranes derived from cellulose precursors opens a new avenue for H2-related separations.

Air/water interfacial assembled rubbery semiconducting nanofilm for fully rubbery integrated electronics.

A rubber-like stretchable semiconductor with high carrier mobility is the most important yet challenging material for constructing rubbery electronics and circuits with mechanical softness and stretchability at both microscopic (material) and macroscopic (structural) levels for many emerging applications. However, the development of such a rubbery semiconductor is still nascent. Here, we report the scalable manufacturing of high-performance stretchable semiconducting nanofilms and the development of fully rubbery transistors, integrated electronics, and functional devices. The rubbery semiconductor is assembled into a freestanding binary-phased composite nanofilm based on the air/water interfacial assembly method. Fully rubbery transistors and integrated electronics, including logic gates and an active matrix, were developed, and their electrical performances were retained even when stretched by 50%. An elastic smart skin for multiplexed spatiotemporal mapping of physical pressing and a medical robotic hand equipped with rubbery multifunctional electronic skin was developed to show the applications of fully rubbery-integrated functional devices.

Ultra-conformal drawn-on-skin electronics for multifunctional motion artifact-free sensing and point-of-care treatment.

An accurate extraction of physiological and physical signals from human skin is crucial for health monitoring, disease prevention, and treatment. Recent advances in wearable bioelectronics directly embedded to the epidermal surface are a promising solution for future epidermal sensing. However, the existing wearable bioelectronics are susceptible to motion artifacts as they lack proper adhesion and conformal interfacing with the skin during motion. Here, we present ultra-conformal, customizable, and deformable drawn-on-skin electronics, which is robust to motion due to strong adhesion and ultra-conformality of the electronic inks drawn directly on skin. Electronic inks, including conductors, semiconductors, and dielectrics, are drawn on-demand in a freeform manner to develop devices, such as transistors, strain sensors, temperature sensors, heaters, skin hydration sensors, and electrophysiological sensors. Electrophysiological signal monitoring during motion shows drawn-on-skin electronics' immunity to motion artifacts. Additionally, electrical stimulation based on drawn-on-skin electronics demonstrates accelerated healing of skin wounds.