Optimized MLPA workflow for spinal muscular atrophy diagnosis: identification of a novel variant, NC_000005.10:g.(70919941_70927324)del in isolated exon 1 of SMN1 gene through long-range PCR.

BACKGROUND: Spinal muscular atrophy (SMA) is a rare autosomal recessive hereditary neuromuscular disease caused by survival motor neuron 1 (SMN1) gene deletion or mutation. Homozygous deletions of exon 7 in SMN1 result in 95% of SMA cases, while the remaining 5% are caused by other pathogenic variants of SMN1. METHODS: We analyzed two SMA-suspected cases that were collected, with no SMN1 gene deletion and point mutation in whole-exome sequencing. Exon 1 deletion of the SMN gene was detected using Multiplex ligation-dependent probe amplification (MLPA) P021. We used long-range polymerase chain reaction (PCR) to isolate the SMN1 template, optimized-MLPA P021 for copy number variation (CNV) analysis within SMN1 only, and validated the findings via third-generation sequencing. RESULTS: Two unrelated families shared a genotype with one copy of exon 7 and a novel variant, g.70919941_70927324del, in isolated exon 1 of the SMN1 gene. Case F1-II.1 demonstrated no exon 1 but retained other exons, whereas F2-II.1 had an exon 1 deletion in a single SMN1 gene. The read coverage in the third-generation sequencing results of both F1-II.1 and F2-II.1 revealed a deletion of approximately 7.3 kb in the 5' region of SMN1. The first nucleotide in the sequence data aligned to the 7385 bp of NG_008691.1. CONCLUSION: Remarkably, two proband families demonstrated identical SMN1 exon 1 breakpoint sites, hinting at a potential novel mutation hotspot in Chinese SMA, expanding the variation spectrum of the SMN1 gene and corroborating the specificity of isolated exon 1 deletion in SMA pathogenesis. The optimized-MLPA P021 determined a novel variant (g.70919941_70927324del) in isolated exon 1 of the SMN1 gene based on long-range PCR, enabling efficient and affordable detection of SMN gene variations in patients with SMA, providing new insight into SMA diagnosis to SMN1 deficiency and an optimized workflow for single exon CNV testing of the SMN gene.

Microphone array analysis of the first non-axisymmetric mode for the detection of pipe conditions.

This paper reports on the use of a circular microphone array to analyze the reflections from a pipe defect with enhanced resolution. A Bayesian maximum a posteriori algorithm is combined with the mode decomposition approach to localize pipe defects with six or fewer microphones. Unlike all previous acoustic reflectometry techniques, which only estimate the location of a pipe defect along the pipe, the proposed method uses the phase information about the wave propagated in the form of the first non-axisymmetric mode to estimate its circumferential position as well as axial location. The method is validated against data obtained from a laboratory measurement in a 150 mm diameter polyvinyl chloride pipe with a 20% in-pipe blockage and 100 mm lateral connection. The accuracy of localization of the lateral connection and blockage attained in this measurement was better than 2% of the axial sensing distance and 9° error in terms of the circumferential position. The practical significance of this approach is that it can be implemented remotely on an autonomous inspection robot so that accurate axial location and circumferential position of lateral connections and small blockages can be estimated with a computationally efficient algorithm.

Opportunities and challenges for ribosome-inactivating proteins in traditional Chinese medicine plants.

Ribosome-inactivating proteins (RIPs) are a class of cytotoxic rRNA N-glycosylase, which widely exist in higher plants in different taxonomy, including many traditional Chinese medicinal materials and vegetables and fruits. In this paper, the traditional Chinese medicinal plants containing RIPs protein were sorted out, and their pharmacological effects and clinical applications were analyzed. Since many RIPs in traditional Chinese medicine plants exhibit antiviral and antitumor activities and show great clinical application potential, people's interest in these proteins is on the rise. This paper summarizes the possible mechanism of RIPs's anti-virus and anti-tumor effects, and discusses its potential problems and risks, laying a foundation for subsequent research on how to exert its anti-virus and anti-tumor effects.

Microphone array analysis for simultaneous condition detection, localization, and classification in a pipe.

An acoustic method for simultaneous condition detection, localization, and classification in air-filled pipes is proposed. The contribution of this work is threefold: (1) a microphone array is used to extend the usable acoustic frequency range to estimate the reflection coefficient from blockages and lateral connections; (2) a robust regularization method of sparse representation based on a wavelet basis function is adapted to reduce the background noise in acoustical data; and (3) the wavelet components are used to localize and classify the condition of the pipe. The microphone array and sparse representation method enhance the acoustical signal reflected from blockages and lateral connections and suppress unwanted higher-order modes. Based on the sparse representation results, higher-level wavelet functions representing the impulse response are used to localize the position of the sensor corresponding to a blockage or lateral connection with higher spatial resolution. It is shown that the wavelet components can be used to train and to test a support vector machine (SVM) classifier for the condition identification more accurately than with a time domain SVM classifier. This work paves the way for the development of simultaneous condition classification and localization methods to be deployed on autonomous robots working in buried pipes.

Immobilization of EreB on Acid-Modified Palygorskite for Highly Efficient Degradation of Erythromycin.

Erythromycin is one of the most commonly used macrolide antibiotics. However, its pollution of the ecosystem is a significant risk to human health worldwide. Currently, there are no effective and environmentally friendly methods to resolve this issue. Although erythromycin esterase B (EreB) specifically degrades erythromycin, its non-recyclability and fragility limit the large-scale application of this enzyme. In this work, palygorskite was selected as a carrier for enzyme immobilization. The enzyme was attached to palygorskite via a crosslinking reaction to construct an effective erythromycin-degradation material (i.e., EreB@modified palygorskite), which was characterized using FT-IR, SEM, XRD, and Brunauer-Emmett-Teller techniques. The results suggested the successful modification of the material and the loading of the enzyme. The immobilized enzyme had a higher stability over varying temperatures (25-65 °C) and pH values (6.5-10.0) than the free enzyme, and the maximum rate of reaction (Vmax) and the turnover number (kcat) of the enzyme increased to 0.01 mM min-1 and 169 min-1, respectively, according to the enzyme-kinetics measurements. The EreB@modified palygorskite maintained about 45% of its activity after 10 cycles, and degraded erythromycin in polluted water to 20 mg L-1 within 300 min. These results indicate that EreB could serve as an effective immobilizing carrier for erythromycin degradation at the industrial scale.

Comparative Transcriptome Profiling Reveals the Genes Involved in Storage Root Expansion in Sweetpotato (Ipomoea batatas (L.) Lam.).

Sweetpotato (Ipomoea batatas (L.) Lam.) is recognized as one of the most important root crops in the world by the Food and Agriculture Organization of the United Nations. The yield of sweetpotato is closely correlated with the rate of storage root (SR) formation and expansion. At present, most of the studies on sweetpotato SR expansion are focused on the physiological mechanism. To explore the SR expansion mechanism of sweetpotato, we performed transcriptome sequencing of SR harvested at 60, 90, 120, and 150 days after planting (DAP) to analyze two sweetpotato lines, Xuzishu 8 and its crossing progenies named Xu 18-192, which were selected from an F1 segregation population of Xuzishu 8 and Meiguohong, in which SR expansion was delayed significantly. A total of 57,043 genes were produced using transcriptome sequencing, of which 1312 were differentially expressed genes (DEGs) in four SR growth periods of the sweetpotato lines. The combination of the KEGG and trend analysis revealed several key candidate genes involved in SR expansion. The SBEI gene involved in starch metabolism, and transcription factors ARF6, NF-YB3 and NF-YB10 were all significantly up-regulated during SR expansion. The data from this study provide insights into the complex mechanisms of SR formation and expansion in sweetpotato and identify new candidate genes for increasing the yield of sweetpotato.

Calcium-Mobilizing Properties of Salvia miltiorrhiza-Derived Carbon Dots Confer Enhanced Environmental Adaptability in Plants.

Biomass-derived carbon dots (CDs) are promising nanotools for agricultural applications and function as a reactive oxygen species (ROS) scavenger to alleviate plant oxidative stress under adverse environments. Nevertheless, plants need ROS burst to fully activate Ca2+-regulated defensive signaling pathway. The underlying mechanism of CDs to improve plant environmental adaptability without ROS is largely unknown. Here, Salvia miltiorrhiza-derived CDs triggered ROS-independent Ca2+ mobilization in plant roots. Mechanistic investigation attributed this function mainly to the hydroxyl and carboxyl groups on CDs. CDs-triggered Ca2+ mobilization was found to be dependent on the production of cyclic nucleotides and cyclic nucleotide-gated ion channels. Lectin receptor kinases were verified as essential for this Ca2+ mobilization. CDs hydroponic application promoted Ca2+ signaling and plant environmental adaptability under salinity and nutrient-deficient conditions. All these findings uncover that CDs have a Ca2+-mobilizing property and thus can be used as a simultaneous Ca2+ signaling amplifier and ROS scavenger for crop improvement.

Targeting of SPCSV-RNase3 via CRISPR-Cas13 confers resistance against sweet potato virus disease.

Sweet potato (Ipomoea batatas) is one of the most important crops in the world, and its production rate is mainly decreased by the sweet potato virus disease (SPVD) caused by the co-infection of sweet potato chlorotic stunt virus (SPCSV) and sweet potato feathery mottle virus. However, methods for improving SPVD resistance have not been established. Thus, this study aimed to enhance SPVD resistance by targeting one of its important pathogenesis-related factors (i.e., SPCSV-RNase3) by using the CRISPR-Cas13 technique. First, the RNA targeting activity of four CRISPR-Cas13 variants were compared using a transient expression system in Nicotiana benthamiana. LwaCas13a and RfxCas13d had more efficient RNA and RNA virus targeting activity than PspCas13b and LshCas13a. Driven by the pCmYLCV promoter for the expression of gRNAs, RfxCas13d exhibited higher RNA targeting activity than that driven by the pAtU6 promoter. Furthermore, the targeting of SPCSV-RNase3 using the LwaCas13a system inhibited its RNA silencing suppressor activity and recovered the RNA silencing activity in N. benthamiana leaf cells. Compared with the wild type, transgenic N. benthamiana plants carrying an RNase3-targeted LwaCas13a system exhibited enhanced resistance against turnip mosaic virus TuMV-GFP and cucumber mosaic virus CMV-RNase3 co-infection. Moreover, transgenic sweet potato plants carrying an RNase3-targeted RfxCas13d system exhibited substantially improved SPVD resistance. This method may contribute to the development of SPVD immune germplasm and the enhancement of sweet potato production in SPVD-prevalent regions.

Overexpression of phosphatidylserine synthase IbPSS1 affords cellular Na+ homeostasis and salt tolerance by activating plasma membrane Na+/H+ antiport activity in sweet potato roots.

Phosphatidylserine synthase (PSS)-mediated phosphatidylserine (PS) synthesis is crucial for plant development. However, little is known about the contribution of PSS to Na+ homeostasis regulation and salt tolerance in plants. Here, we cloned the IbPSS1 gene, which encodes an ortholog of Arabidopsis AtPSS1, from sweet potato (Ipomoea batatas (L.) Lam.). The transient expression of IbPSS1 in Nicotiana benthamiana leaves increased PS abundance. We then established an efficient Agrobacterium rhizogenes-mediated in vivo root transgenic system for sweet potato. Overexpression of IbPSS1 through this system markedly decreased cellular Na+ accumulation in salinized transgenic roots (TRs) compared with adventitious roots. The overexpression of IbPSS1 enhanced salt-induced Na+/H+ antiport activity and increased plasma membrane (PM) Ca2+-permeable channel sensitivity to NaCl and H2O2 in the TRs. We confirmed the important role of IbPSS1 in improving salt tolerance in transgenic sweet potato lines obtained from an Agrobacterium tumefaciens-mediated transformation system. Similarly, compared with the wild-type (WT) plants, the transgenic lines presented decreased Na+ accumulation, enhanced Na+ exclusion, and increased PM Ca2+-permeable channel sensitivity to NaCl and H2O2 in the roots. Exogenous application of lysophosphatidylserine triggered similar shifts in Na+ accumulation and Na+ and Ca2+ fluxes in the salinized roots of WT. Overall, this study provides an efficient and reliable transgenic method for functional genomic studies of sweet potato. Our results revealed that IbPSS1 contributes to the salt tolerance of sweet potato by enabling Na+ homeostasis and Na+ exclusion in the roots, and the latter process is possibly controlled by PS reinforcing Ca2+ signaling in the roots.

Genome-wide analysis of expression quantitative trait loci (eQTLs) reveals the regulatory architecture of gene expression variation in the storage roots of sweet potato.

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato.

Involvement of Phosphatidylserine and Triacylglycerol in the Response of Sweet Potato Leaves to Salt Stress.

Lipid remodeling plays an important role in the adaptation of plants to environmental factors, but the mechanism by which lipid remodeling mediates salt stress response remains unclear. In this study, we compared the root and leaf lipidome profiles of salt-tolerant and salt-sensitive sweet potato cultivars (Xu 22 and Xu 32, respectively) under salinity stress. After salt treatment, the leaf lipidome showed more significant remodeling than the root lipidome in both cultivars. Compared with Xu 32 leaves, Xu 22 leaves generally maintained higher abundance of phospholipids, glycolipids, sphingolipids, sterol derivatives, and diacylglycerol under salinity conditions. Interestingly, salinity stress significantly increased phosphatidylserine (PS) abundance in Xu 22 leaves by predominantly triggering the increase of PS (20:5/22:6). Furthermore, Xu 32 leaves accumulated higher triacylglycerol (TG) level than Xu 22 leaves under salinity conditions. The exogenous application of PS delayed salt-induced leaf senescence in Xu 32 by reducing salt-induced K+ efflux and upregulating plasma membrane H+-ATPase activity. However, the inhibition of TG mobilization in salinized-Xu 22 leaves disturbed energy and K+/Na+ homeostasis, as well as plasma membrane H+-ATPase activity. These results demonstrate alterations in the leaf lipidome of sweet potato under salinity condition, underscoring the importance of PS and TG in mediating salt-defensive responses in sweet potato leaves.

Multifunctional supramolecular self-assembly system for colorimetric detection of Hg2+, Fe3+, Cu2+ and continuous sensing of volatile acids and organic amine gases.

A novel multifunctional gelator (1) based on an azobenzene derivative was designed and characterized. This compound could gelate some solvents including hexane, petroleum ether, DMSO, acetonitrile and ethanol through a heating-cooling procedure. The self-assembly process in different solvents was studied by means of UV-vis absorption and Fourier transform infrared (FTIR) spectra, field emission scanning electron microscopy (FESEM), rheological measurements, X-ray powder diffraction and water contact angle experiments. Interestingly, compound 1 had a high-contrast colorimetric detection ability towards Hg2+, Cu2+, Fe3+ and volatile acids and further organic amine gases in solution through its color change. At the same time, organogel 1 in acetonitrile also exhibited detection performance through a color or gel state change. In the response process, the self-assembly structures were changed from a nanofiber into a microsphere under induction by analytes. More significantly, film 1 could continuously detect volatile acids and organic amine gases. The number of cycles of film 1 for the detection of volatile acids and organic amine gases was at least seven times. The limit of detection (LOD) of film 1 towards TFA was calculated to be 0.0848 ppb. The sensing mechanisms were studied using 1HNMR, FESEM, UV-vis absorption spectra and HRMS. The intramolecular cyclization occurred on molecule 1 and a H2S molecule was lost during the detection process of Hg2+. It was proposed that the -N[double bond, length as m-dash]N- bonding could be coordinated by Fe3+ and Cu2+ and this further induced the absorption spectra and color change. For a volatile acid, it was possible that the volatile acid was combined with the N,N-dimethyl amine group of molecule 1. This research opens up a novel pathway to the fabrication of supramolecular self-assembly gels to detect polymetallic ions and trace volatile acids in the environment.

Root-zone-specific sensitivity of K+-and Ca2+-permeable channels to H2O2 determines ion homeostasis in salinized diploid and hexaploid Ipomoea trifida.

Polyploids generally possess superior K+/Na+ homeostasis under saline conditions compared with their diploid progenitors. In this study, we identified the physiological mechanisms involved in the ploidy-related mediation of K+/Na+ homeostasis in the roots of diploid (2x) and hexaploid (6x; autohexaploid) Ipomoea trifida, which is the closest relative of cultivated sweet potato. Results showed that 6x I. trifida retained more K+ and accumulated less Na+ in the root and leaf tissues under salt stress than 2x I. trifida. Compared with its 2x ancestor, 6x I. trifida efficiently prevents K+ efflux from the meristem root zone under salt stress through its plasma membrane (PM) K+-permeable channels, which have low sensitivity to H2O2. Moreover, 6x I. trifida efficiently excludes Na+ from the elongation and mature root zones under salt stress because of the high sensitivity of PM Ca2+-permeable channels to H2O2. Our results suggest the root-zone-specific sensitivity to H2O2 of PM K+- and Ca2+-permeable channels in the co-ordinated control of K+/Na+ homeostasis in salinized 2x and 6x I. trifida. This work provides new insights into the improved maintenance of K+/Na+ homeostasis of polyploids under salt stress.

Melatonin-Stimulated Triacylglycerol Breakdown and Energy Turnover under Salinity Stress Contributes to the Maintenance of Plasma Membrane H+-ATPase Activity and K+/Na+ Homeostasis in Sweet Potato.

Melatonin (MT) is a multifunctional molecule in animals and plants and is involved in defense against salinity stress in various plant species. In this study, MT pretreatment was simultaneously applied to the roots and leaves of sweet potato seedlings [Ipomoea batatas (L.) Lam.], which is an important food and industry crop worldwide, followed by treatment of 150 mM NaCl. The roles of MT in mediating K+/Na+ homeostasis and lipid metabolism in salinized sweet potato were investigated. Exogenous MT enhanced the resistance to NaCl and improved K+/Na+ homeostasis in sweet potato seedlings as indicated by the low reduced K+ content in tissues and low accumulation of Na+ content in the shoot. Electrophysiological experiments revealed that exogenous MT significantly suppressed NaCl-induced K+ efflux in sweet potato roots and mesophyll tissues. Further experiments showed that MT enhanced the plasma membrane (PM) H+-ATPase activity and intracellular adenosine triphosphate (ATP) level in the roots and leaves of salinized sweet potato. Lipidomic profiling revealed that exogenous MT completely prevented salt-induced triacylglycerol (TAG) accumulation in the leaves. In addition, MT upregulated the expression of genes related to TAG breakdown, fatty acid (FA) ß-oxidation, and energy turnover. Chemical inhibition of the ß-oxidation pathway led to drastic accumulation of lipid droplets in the vegetative tissues of NaCl-stressed sweet potato and simultaneously disrupted the MT-stimulated energy state, PM H+-ATPase activity, and K+/Na+ homeostasis. Results revealed that exogenous MT stimulated TAG breakdown, FA ß-oxidation, and energy turnover under salinity conditions, thereby contributing to the maintenance of PM H+-ATPase activity and K+/Na+ homeostasis in sweet potato.

NaCl-elicited, vacuolar Ca(2+) release facilitates prolonged cytosolic Ca(2+) signaling in the salt response of Populus euphratica cells.

High environmental salt elicits an increase in cytosolic Ca(2+) ([Ca(2+)]cyt) in plants, which is generated by extracellular Ca(2+) influx and Ca(2+) release from intracellular stores, such as vacuole and endoplasmic reticulum. This study aimed to determine the physiological mechanisms underlying Ca(2+) release from vacuoles and its role in ionic homeostasis in Populus euphratica. In vivo Ca(2+) imaging showed that NaCl treatment induced a rapid elevation in [Ca(2+)]cyt, which was accompanied by a subsequent release of vacuolar Ca(2+). In cell cultures, NaCl-altered intracellular Ca(2+) mobilization was abolished by antagonists of inositol (1, 4, 5) trisphosphate (IP3) and cyclic adenosine diphosphate ribose (cADPR) signaling pathways, but not by slow vacuolar (SV) channel blockers. Furthermore, the NaCl-induced vacuolar Ca(2+) release was dependent on extracellular ATP, extracellular Ca(2+) influx, H2O2, and NO. In vitro Ca(2+) flux recordings confirmed that IP3, cADPR, and Ca(2+) induced substantial Ca(2+) efflux from intact vacuoles, but this vacuolar Ca(2+) flux did not directly respond to ATP, H2O2, or NO. Moreover, the IP3/cADPR-mediated vacuolar Ca(2+) release enhanced the expression of salt-responsive genes that regulated a wide range of cellular processes required for ion homeostasis, including cytosolic K(+) maintenance, Na(+) and Cl(-) exclusion across the plasma membrane, and Na(+)/H(+) and Cl(-)/H(+) exchanges across the vacuolar membrane.

Hydrogen sulfide alleviates cadmium toxicity through regulations of cadmium transport across the plasma and vacuolar membranes in Populus euphratica cells.

Hydrogen sulfide (H2S) is emerging as a novel signalling molecule involved in plant growth and responses against abiotic stresses. However, little information is known about its role in cadmium (Cd) detoxification. In the present study, the effects of H2S on Cd toxicity were investigated in Populus euphratica cells using fluorescence imaging technique and a non-invasive vibrating ion-selective microelectrode. Pretreatment with a H2S donor, sodium hydrosulfide (NaHS), significantly mitigated the Cd-induced programmed cell death in P. euphratica cells. The alleviation effect of NaHS was more pronounced at 50-100 µM as compared to low (25 µM) and high doses (200 µM). Under Cd stress, total activities of antioxidant enzymes, such as ascorbate peroxidase, catalase and glutathione reductase, were significantly enhanced in NaHS-treated cells, leading to a decline of H2O2 accumulation and lipid peroxidation. Moreover, NaHS reduced Cd accumulation in the cytoplasm but increased the fraction of Cd in the vacuole. Cd flux profiles revealed that H2S inhibited the Cd influx through the plasma membrane (PM) calcium channels that activated by H2O2. NaHS enhanced Cd influx into the vacuole, and the Cd influx was dependent on the pH gradients across the tonoplast. Taken together, these results suggest that H2S alleviates Cd toxicity via the improvement of antioxidant system and cellular Cd homeostasis. The up-regulation of antioxidant enzymes by H2S reduced the accumulation of H2O2, and thus decreased Cd influx through the H2O2-activated PM calcium channels. The H2S-simulated vacuolar Cd sequestration was presumably due to the activation of tonoplast Cd(2+)/H(+) antiporters.