Novel TUBA4A variant causes congenital myopathy with focal myofibrillar disorganisation.

BACKGROUND: Congenital myopathies are a clinical, histopathological and genetic heterogeneous group of inherited muscle disorders that are defined on peculiar architectural abnormalities in the muscle fibres. Although there have been at least 33 different genetic causes of the disease, a significant percentage of congenital myopathies remain genetically unresolved. The present study aimed to report a novel TUBA4A variant in two unrelated Chinese patients with sporadic congenital myopathy. METHODS: A comprehensive strategy combining laser capture microdissection, proteomics and whole-exome sequencing was performed to identify the candidate genes. In addition, the available clinical data, myopathological changes, the findings of electrophysiological examinations and thigh muscle MRIs were also reviewed. A cellular model was established to assess the pathogenicity of the TUBA4A variant. RESULTS: We identified a recurrent novel heterozygous de novo c.679C>T (p.L227F) variant in the TUBA4A (NM_006000), encoding tubulin alpha-4A, in two unrelated patients with clinicopathologically diagnosed sporadic congenital myopathy. The prominent myopathological changes in both patients were muscle fibres with focal myofibrillar disorganisation and rimmed vacuoles. Immunofluorescence showed ubiquitin-positive TUBA4A protein aggregates in the muscle fibres with rimmed vacuoles. Overexpression of the L227F mutant TUBA4A resulted in cytoplasmic aggregates which colocalised with ubiquitin in cellular model. CONCLUSION: Our findings expanded the phenotypic and genetic manifestations of TUBA4A as well as tubulinopathies, and added a new type of congenital myopathy to be taken into consideration in the differential diagnosis.

A broadly applicable, stress-mediated bacterial death pathway regulated by the phosphotransferase system (PTS) and the cAMP-Crp cascade.

Recent work indicates that killing of bacteria by diverse antimicrobial classes can involve reactive oxygen species (ROS), as if a common, self-destructive response to antibiotics occurs. However, the ROS-bacterial death theory has been challenged. To better understand stress-mediated bacterial death, we enriched spontaneous antideath mutants of Escherichia coli that survive treatment by diverse bactericidal agents that include antibiotics, disinfectants, and environmental stressors, without a priori consideration of ROS. The mutants retained bacteriostatic susceptibility, thereby ruling out resistance. Surprisingly, pan-tolerance arose from carbohydrate metabolism deficiencies in ptsI (phosphotransferase) and cyaA (adenyl cyclase); these genes displayed the activity of upstream regulators of a widely shared, stress-mediated death pathway. The antideath effect was reversed by genetic complementation, exogenous cAMP, or a Crp variant that bypasses cAMP binding for activation. Downstream events comprised a metabolic shift from the TCA cycle to glycolysis and to the pentose phosphate pathway, suppression of stress-mediated ATP surges, and reduced accumulation of ROS. These observations reveal how upstream signals from diverse stress-mediated lesions stimulate shared, late-stage, ROS-mediated events. Cultures of these stable, pan-tolerant mutants grew normally and were therefore distinct from tolerance derived from growth defects described previously. Pan-tolerance raises the potential for unrestricted disinfectant use to contribute to antibiotic tolerance and resistance. It also weakens host defenses, because three agents (hypochlorite, hydrogen peroxide, and low pH) affected by pan-tolerance are used by the immune system to fight infections. Understanding and manipulating the PtsI-CyaA-Crp­mediated death process can help better control pathogens and maintain beneficial microbiota during antimicrobial treatment.

Transcriptome analysis reveals important regulatory factors for condensed tannins synthesis in acorn.

Condensed tannins are widely present in the fruits and seeds of plants and effectively prevent them from being eaten by animals before maturity due to their astringent taste. In addition, condensed tannins are a natural compound with strong antioxidant properties and significant antibacterial effects. Four samples of mature and near-mature Quercus fabri acorns, with the highest and lowest condensed tannin content, were used for genome-based transcriptome sequencing. The KEGG enrichment analysis revealed that the differentially expressed genes (DEGs) were highly enriched in phenylpropanoid biosynthesis and starch and sucrose metabolism. Given that the phenylpropanoid biosynthesis pathway is a crucial step in the synthesis of condensed tannins, we screened for significantly differentially expressed transcription factors and structural genes from the transcriptome data of this pathway and found that the expression levels of four MADS-box, PAL, and 4CL genes were significantly increased in acorns with high condensed tannin content. The quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) experiment further validated this result. In addition, yeast one-hybrid assay confirmed that three MADS-box transcription factors could bind the promoter of the 4CL gene, thereby regulating gene expression levels. This study utilized transcriptome sequencing to discover new important regulatory factors that can regulate the synthesis of acorn condensed tannins, providing new evidence for MADS-box transcription factors to regulate the synthesis of secondary metabolites in fruits.

An adaptive seamless 2-in-1 design with biomarker-driven subgroup enrichment.

Adaptive seamless phase 2/3 subgroup enrichment design plays a pivotal role in streamlining efficient drug development within a competitive landscape, while also enhancing patient access to promising treatments. This design approach identifies biomarker subgroups with the highest potential to benefit from investigational regimens. The seamless integration of Phase 2 and Phase 3 ensures a timely confirmation of clinical benefits. One significant challenge in adaptive enrichment decisions is determining the optimal timing and maturity of the primary endpoint. In this paper, we propose an adaptive seamless 2-in-1 biomarker-driven subgroup enrichment design that addresses this challenge by allowing subgroup selection using an early intermediate endpoint that predicts clinical benefits (i.e. a surrogate endpoint). The proposed design initiates with a Phase 2 stage involving all participants and can potentially expand into a Phase 3 study focused on the subgroup demonstrating the most favorable clinical outcomes. We will show that, under certain correlation assumptions, the overall type I error may not be inflated at the end of the study. In scenarios where the assumptions may not hold, we present a general framework to control the multiplicity. The flexibility and efficacy of the proposed design are highlighted through an extensive simulation study and illustrated in a case study in multiple myeloma.

Flexible seamless 2-in-1 design with sample size adaptation.

The 2-in-1 design is becoming popular in oncology drug development, with the flexibility in using different endpoints at different decision time. Based on the observed interim data, sponsors can choose to seamlessly advance a small phase 2 trial to a full-scale confirmatory phase 3 trial with a pre-determined maximum sample size or remain in a phase 2 trial. While this approach may increase efficiency in drug development, it is rigid and requires a pre-specified fixed sample size. In this paper, we propose a flexible 2-in-1 design with sample size adaptation, while retaining the advantage of allowing an intermediate endpoint for interim decision-making. The proposed design reflects the needs of the recent FDA's Project FrontRunner initiative, which encourages the use of an earlier surrogate endpoint to potentially support accelerated approval with conversion to standard approval with long-term endpoints from the same randomized study. Additionally, we identify the interim decision cut-off to allow a conventional test procedure at the final analysis. Extensive simulation studies showed that the proposed design requires much a smaller sample size and shorter timeline than the simple 2-in-1 design, while achieving similar power. We present a case study in multiple myeloma to demonstrate the benefits of the proposed design.

[Research progress on biomarkers for the monitoring of Spinal muscular atrophy].

Spinal muscular atrophy (SMA) is the most common neuromuscular disease in children, which seriously affects children's health. At present, gene and molecular modification therapy for SMA have become hot spots. However, there are many uncertainties about when people with SMA should start treatment, how well the drugs can treat, and the prognosis. Therefore, reliable biomarkers for monitoring and evaluation are urgently needed. This review will summarize the progress made in SMA biomarker research in recent years.

In Situ Spectroscopic Identification of the Electron-Transfer Intermediates of Photoelectrochemical Proton-Coupled Electron Transfer of Water Oxidation on Au.

Experimental elucidation of the decoupling of electron and proton transfer at a molecular level is essential for thoroughly understanding the kinetics of heterogeneous (photo)electrochemical proton-coupled electron transfer water oxidation. Here we illustrate the electron-transfer intermediates of positively charged surface oxygenated species on Au (Au-OH+) and their correlations with the rate of water oxidation by in situ microphotoelectrochemical surface-enhanced Raman spectroscopy (SERS) and ambient-pressure X-ray photoelectron spectroscopy. At the intermediate stage of water oxidation, a characteristic blue shift of the vibration of Au-OH species in laser-power-density-dependent measurements was assigned to the light-induced production of Au-OH+ in water oxidation. The photothermal effect was excluded according to the vibrational frequencies of Au-OH species as the temperature was increased in a variable-temperature SERS measurement. Density functional theory calculations evidenced that the frequency blue shift is from the positively charged Au-OH species. The photocurrent-dependent frequency blue shift indicated that Au-OH+ is the key electron-transfer intermediate in water oxidation by decoupled electron and proton transfer.

Adaptive randomization in a two-stage sequential multiple assignment randomized trial.

Sequential multiple assignment randomized trials (SMARTs) are systematic and efficient media for comparing dynamic treatment regimes (DTRs), where each patient is involved in multiple stages of treatment with the randomization at each stage depending on the patient's previous treatment history and interim outcomes. Generally, patients enrolled in SMARTs are randomized equally to ethically acceptable treatment options regardless of how effective those treatments were during the previous stages, which results in some undesirable consequences in practice, such as low recruitment, less retention, and lower treatment adherence. In this article, we propose a response-adaptive SMART (RA-SMART) design where the allocation probabilities are imbalanced in favor of more promising treatments based on the accumulated information on treatment efficacy from previous patients and stages. The operating characteristics of the RA-SMART design relative to SMART design, including the consistency and efficiency of estimated response rate under each DTR, the power of identifying the optimal DTR, and the number of patients treated with the optimal and the worst DTRs, are assessed through extensive simulation studies. Some practical suggestions are discussed in the conclusion.

Interim monitoring in sequential multiple assignment randomized trials.

A sequential multiple assignment randomized trial (SMART) facilitates the comparison of multiple adaptive treatment strategies (ATSs) simultaneously. Previous studies have established a framework to test the homogeneity of multiple ATSs by a global Wald test through inverse probability weighting. SMARTs are generally lengthier than classical clinical trials due to the sequential nature of treatment randomization in multiple stages. Thus, it would be beneficial to add interim analyses allowing for an early stop if overwhelming efficacy is observed. We introduce group sequential methods to SMARTs to facilitate interim monitoring based on the multivariate chi-square distribution. Simulation studies demonstrate that the proposed interim monitoring in SMART (IM-SMART) maintains the desired type I error and power with reduced expected sample size compared to the classical SMART. Finally, we illustrate our method by reanalyzing a SMART assessing the effects of cognitive behavioral and physical therapies in patients with knee osteoarthritis and comorbid subsyndromal depressive symptoms.

A spectroscopic study of the mechanism of Au(III) (hydro-)oxides in promoting plasmon-mediated photoelectrochemical water-oxidation.

To understand the roles of Au(III) (hydro-)oxides in promoting plasmon-mediated photoelectrochemical (PMPEC) water-oxidation, we employed in situ microphotoelectrochemical surface-enhanced Raman spectroscopy and ambient-pressure x-ray photoelectron spectroscopy to elucidate the correlations between the amount of surface Au(III) (hydro-)oxides and the photocurrent of PMPEC water-oxidation on Au. By applying preoxidation potentials, we made surface Au(III) (hydro-)oxides on a plasmonic Au photoanode. According to the charge of reductively stripping surface oxygenated species before and after PMPEC water-oxidation, we found that a negative shift of an onset potential, increase in photocurrent, and much less growth of surface (hydro-)oxides were correlated with each other as a result of the increase in the coverage of Au (III) (hydro-)oxides. These results suggest that the surface Au(III) (hydro-)oxides kinetically promoted water-oxidation by restricting the growth of surface (hydro-)oxides.

LcWRKY17, a WRKY Transcription Factor from Litsea cubeba, Effectively Promotes Monoterpene Synthesis.

The WRKY gene family is one of the most significant transcription factor (TF) families in higher plants and participates in many secondary metabolic processes in plants. Litsea cubeba (Lour.) Person is an important woody oil plant that is high in terpenoids. However, no studies have been conducted to investigate the WRKY TFs that regulate the synthesis of terpene in L. cubeba. This paper provides a comprehensive genomic analysis of the LcWRKYs. In the L. cubeba genome, 64 LcWRKY genes were discovered. According to a comparative phylogenetic study with Arabidopsis thaliana, these L. cubeba WRKYs were divided into three groups. Some LcWRKY genes may have arisen from gene duplication, but the majority of LcWRKY evolution has been driven by segmental duplication events. Based on transcriptome data, a consistent expression pattern of LcWRKY17 and terpene synthase LcTPS42 was found at different stages of L. cubeba fruit development. Furthermore, the function of LcWRKY17 was verified by subcellular localization and transient overexpression, and overexpression of LcWRKY17 promotes monoterpene synthesis. Meanwhile, dual-Luciferase and yeast one-hybrid (Y1H) experiments showed that the LcWRKY17 transcription factor binds to W-box motifs of LcTPS42 and enhances its transcription. In conclusion, this research provided a fundamental framework for future functional analysis of the WRKY gene families, as well as breeding improvement and the regulation of secondary metabolism in L. cubeba.

Distributional environmental justice of residential walking space: The lens of urban ecosystem services supply and demand.

Urban ecosystem services (UES), as an important concept in nature-based solutions, can effectively mitigate adverse environmental burdens and have great potential in addressing environmental justice issues. However, few studies linking UES with environmental justice have considered both supply and demand sides of UES, particularly at the spatial scale of residential walking space. Against this backdrop, we investigated the distributional justice of supply and demand for urban cooling, flood mitigation, air purification, and outdoor recreation in residential walking spaces in Shanghai among socially vulnerable groups (i.e., elderly residents, children, females, low-income residents, no-hukou residents, and ethnic minorities). We found that (1) the UES supply of residential walking space was much lower than that of non-residential walking space, while the UES demand was much higher than that of non-residential walking space. (2) Higher proportions of ethnic minorities, no-hukou residents, and females in Shanghai were positively correlated with several UES demands but were not positively correlated with ES supply, indicating a higher possibility of unsatisfied UES demand for these disadvantaged groups. Future urban blue-green space planning should pay more attention to the spatial allocation of blue-green space, especially placing more blue-green space around residential walking spaces with high UES demand and with a high proportion of socially disadvantaged groups.

A series of two-sample non-parametric tests for quantile residual life time.

Quantile residual lifetime (QRL) is of significant interest in many clinical studies as an easily interpretable quantity compared to other summary measures of survival distributions. In cancer or other chronic diseases, treatments are often compared based on the distributions or quantiles of the residual lifetime. Thus a common problem of interest is to test the equality of the QRL between two populations. In this paper, we propose two classes of tests to compare two QRLs; one class is based on the difference between two estimated QRLs, and the other is based on the estimating function of the QRL, where the estimated QRL from one sample is plugged into the QRL-estimating-function of the other sample. We outline the asymptotic properties of these test statistics. Simulation studies demonstrate that the proposed tests produced Type I errors closer to the nominal level and are superior to some existing tests based on both Type I error and power. Our proposed test statistics are also computationally less intensive and more straightforward compared to tests based on the confidence intervals. We applied the proposed methods to a randomized multicenter phase III trial for breast cancer patients.

[Genetic analysis of a child with early onset neurodevelopmental disorder with involuntary movement and a literature review].

OBJECTIVE: To explore the clinical phenotype and genetic basis of a child with early onset neurodevelopmental disorder with involuntary movement (NEDIM). METHODS: A child who presented at Department of Neurology of Hunan Children's Hospital on October 8, 2020 was selected as the study subject. Clinical data of the child were collected. Genomic DNA was extracted from peripheral blood samples of the child and his parents. Whole exome sequencing (WES) was carried out for the child. Candidate variant was verified by Sanger sequencing and bioinformatic analysis. Relevant literature was searched from the CNKI, PubMed and Google Scholar databases to summarize the clinical phenotypes and genetic variants of the patients. RESULTS: This child was a 3-year-and-3-month boy with involuntary trembling of limbs and motor and language delay. WES revealed that the child has harbored a c.626G>A (p.Arg209His) variant of the GNAO1 gene. Sanger sequencing confirmed that neither of his parents has carried the same variant. The variant had been reported in HGMD and ClinVar databases, but not in the dbSNP, ExAC and 1000 Genomes databases. Prediction with SIFT, PolyPhen-2, and Mutation Taster online software suggested that the variant may be deleterious to the protein function. By UniProt database analysis, the encode amino acid is highly conserved among various species. Prediction with Modeller and PyMOL software indicated that the variant may affect the function of GαO protein. Based on the guideline of the American College of Medical Genetics and Genomics (ACMG), the variant was rated as pathogenic. CONCLUSION: The GNAO1 gene c.626G>A (p.Arg209His) variant probably underlay the NEDIM in this child. Above finding has expanded the phenotypic spectrum of GNAO1 gene c.626G>A (p.Arg209His) variant and provided a reference for clinical diagnosis and genetic counseling.

[Analysis of clinical phenotype and genetic variants in a child with mitochondrial F-S disease due to variants of FDXR gene].

OBJECTIVE: To analyze the clinical phenotype and genetic variants of a child suspected for mitochondrial F-S disease. METHODS: A child with mitochondrial F-S disease who visited Department of Neurology, Hunan Provincial children's Hospital on November 5, 2020 was selected as research subject of this study. Clinical data of the child was collected. The child was subjected to whole exome sequencing (WES). Bioinformatics tools were used to analyze the pathogenic variants. Candidate variants were verified by Sanger sequencing of the child and her parents. RESULTS: WES revealed that the child has harbored compound heterozygous variants of the FDXR gene, namely c.310C>T (p.R104C) and c.235C>T (p.R79C), which were inherited from her father and mother, respectively. Neither variant has been reported in HGMD, PubMed, 1000 Genomes, and dbSNP databases. Both of the variants have been suggested as deleterious according to the prediction results from different bioinformatics analysis software. CONCLUSION: Mitochondrial diseases should be suspected for patients with multiple system involvement. The compound heterozygous variants of the FDXR gene probably underlay the disease in this child. Above finding has enriched the spectrum of FDXR gene mutations underlying mitochondrial F-S disease. WES can facilitate the diagnosis of mitochondrial F-S disease at the molecular level.

Finding a Sensitive Surface-Enhanced Raman Spectroscopic Thermometer at the Nanoscale by Examining the Functional Groups.

Temperature variation at the nanoscale is pivotal for the thermodynamics and kinetics of small entities. Surface-enhanced Raman spectroscopy (SERS) is a promising technique for monitoring temperature variations at the nanoscale. A key but ambiguous topic is methods to design a sensitive SERS thermometer. Here, we elucidate that the type of chemical bond of molecular probes and the surface chemical bonding effect are crucial for maximizing the sensitivity of the SERS thermometer, as illustrated by the variable-temperature SERS measurements and quantum chemistry calculations for the frequency-temperature functions of a series of molecules. The sensitivity of the frequency-temperature function follows the sequence of triple bond > double bond > single bond, which is available for both aliphatic and aromatic molecules. The surface chemical bonding effect between the SERS substrate and molecular probe substantially increases the sensitivity of the frequency-temperature function. These results provide universally available guidelines for the rational design of a sensitive SERS thermometer by examining the functional groups of molecular probes.

Genetic analysis of developmental and epileptic encephalopathy caused by novel biallelic SZT2 gene mutations in three Chinese Han infants: a case series and literature review.

BACKGROUND: Developmental and epileptic encephalopathy (DEE) exhibits phenotypic and genetic heterogeneity. Biallelic variants of the SZT2 gene can lead to DEE18, of which few cases have been reported. This study aimed to analyze the potential pathogenic factors in three cases of DEE18. METHODS: Trio-whole exome sequencing and crystal structure simulation analysis were performed, along with a literature review of DEE18 cases. RESULTS: All three patients had compound heterozygous variants in the SZT2 gene (patient 1, c.2887A > G/c.7970G > A; patient 2, c.3508A > G/c.7936C > T; and patient 3, c.2489G > T/c.8640_8641insC). The variants were predicted to have structural effects on the protein. Particularly, c.3508A > G/p.Ser1170Gly may lead to impaired binding of SZT2 to GATOR1, potentially resulting in the overactivation of the mTORC1 signaling pathway, causing seizures. Through the literature review, we observed that 27 patients with DEE had different degrees of intellectual and developmental disorders (DDs), and the variants leading to protein truncation cause severe DD and refractory epilepsy. Therefore, the phenotypic severity of patients may be related to the residual activity of variant SZT2 protein. CONCLUSION: We provide recently developed knowledge on the DEE18 genotype-phenotype spectrum and suggest that gene detection is of great value for the accurate diagnosis of patients with early-onset epilepsy. Further research is required for the development of individualized interventions for patients with DEE.

Clinical spectrum and genetic variations of LMNA-related muscular dystrophies in a large cohort of Chinese patients.

BACKGROUND: LMNA-related muscular dystrophy is caused by mutations in LMNA gene. We aimed to identify genetic variations and clinical features in a large cohort of Chinese patients with LMNA mutations in an attempt to establish genotype-phenotype correlation. METHODS: The clinical presentations of patients with LMNA-related muscular dystrophy were recorded using retrospective and prospective cohort study. LMNA mutation analysis was performed by Sanger sequencing or next-generation sequencing. Mosaicism was detected by personal genome machine amplicon deep sequencing for mosaicism. RESULTS: Eighty-four patients were identified to harbour LMNA mutations. Forty-one of those were diagnosed with LMNA-related congenital muscular dystrophy (L-CMD), 32 with Emery-Dreifuss muscular dystrophy (EDMD) and 11 with limb-girdle muscular dystrophy type 1B (LGMD1B). We identified 21 novel and 29 known LMNA mutations. Two frequent mutations were identified: c.745C>T and c.1357C>T. A correlation between the location of mutation and the clinical phenotype was observed: mutations affecting the head and coil 2A domains mainly occurred in L-CMD, while the coil 2B and Ig-like domains mainly related to EDMD and LGMD1B. We found somatic mosaicism in one parent of four probands. Muscle biopsies revealed 11 of 20 biopsied L-CMD exhibited inflammatory changes, and muscle cell ultrastructure showed abnormal nuclear morphology. CONCLUSIONS: Our detailed clinical and genetic analysis of 84 patients with LMNA-related muscular dystrophy expands clinical spectrum and broadens genetic variations caused by LMNA mutations. We identified 21 novel and 29 known LMNA mutations and found two frequent mutations. A correlation between the location of mutation and the clinical severity was observed. Preliminary data suggested that low-dose corticosteroid treatment may be effective.

Using surrogate information to improve confirmatory platform trial with sample size re-estimation.

Platform design which allows exploring multiple arms with a common control simultaneously is becoming essential for efficient drug development. However, one of the critical challenges for confirmatory platform trials is immature data for interim decisions, particularly for the treatment arm selection and sample size determination with limited data available. We use a modified conditional power (CP) for both treatment arm selection and sample size determination at interim analysis for the proposed platform trial. The modified CP uses the available data from both primary and surrogate endpoints. We also demonstrated the application in a case study of a lung cancer trial.

Change in intestinal flora after treatment in children with focal epilepsy. / å±€ç¶æ€§ç™«ç—«æ‚£å„¿æ²»ç–—å‰åŽè‚ é“èŒç¾¤çš„å˜åŒ–åŠæ„ä¹‰.

OBJECTIVES: To study the difference in intestinal flora between children with focal epilepsy and healthy children and the change in intestinal flora after treatment in children with epilepsy. METHODS: A total of 10 children with newly diagnosed focal epilepsy were recruited as the case group and were all treated with oxcarbazepine alone. Their clinical data were recorded. Fecal specimens before treatment and after 3 months of treatment were collected. Fourteen aged-matched healthy children were recruited as the control group. Total bacterial DNA was extracted from the fecal specimens for 16S rDNA sequencing and bioinformatics analysis. RESULTS: After 3 months of carbamazepine treatment, the seizure frequency was reduced by >50% in the case group. At the phylum level, the abundance of Actinobacteria in the case group before treatment was significantly higher than that in the control group (P<0.05), and it was reduced after treatment (P<0.05). At the genus level, the abundances of Escherichia/Shigella, Streptococcus, Collinsella, and Megamonas in the case group before treatment were significantly higher than those in the control group (P<0.05), and the abundances of these bacteria decreased significantly after treatment (P<0.05). CONCLUSIONS: There is a significant difference in intestinal flora between children with focal epilepsy and healthy children. Oxcarbazepine can significantly improve the symptoms and intestinal flora in children with epilepsy.