Patients with chromosomal diseases or microdeletion/microduplication syndromes were diagnosed using a high-resolution genome-wide method. Our study revealed the potential of NGS to facilitate genetic diagnoses that were not evident in the prenatal and postnatal groups.Genet Med 18 9, 940-948.

Emerging studies suggest that low-pass genome sequencing (GS) provides additional diagnostic yield of clinically significant copy-number variants (CNVs) compared with chromosomal microarray analysis (CMA). However, a prospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of low-pass GS compared with CMA is warranted. Methods: A total of 1,023 women undergoing prenatal diagnosis were enrolled. Each sample was subjected to low-pass GS and CMA for CNV analysis in parallel. CNVs were classified according to guidelines of the American College of Medical Genetics and Genomics. Results: Low-pass GS not only identified all 124 numerical disorders or pathogenic or likely pathogenic (P/LP) CNVs detected by CMA in 121 cases (11.8%, 121/1,023), but also defined 17 additional and clinically relevant P/LP CNVs in 17 cases (1.7%, 17/1,023). In addition, low-pass GS significantly reduced the technical repeat rate from 4.6% (47/1,023) for CMA to 0.5% (5/1,023) and required less DNA (50 ng) as input. Conclusion: In the context of prenatal diagnosis, low-pass GS identified additional and clinically significant information with enhanced resolution and increased sensitivity of detecting mosaicism as compared with the CMA platform used. This study provides strong evidence for applying low-pass GS as an alternative prenatal diagnostic test.

Introduction: Cerebral ischemia-reperfusion (CI/R) injury is caused by blood flow recovery after ischemic stroke. Chlorogenic acid (CGA, 5-O-caffeoylquinic acid) is a major polyphenol component of Coffea canephora, Coffea arabica L. and Mate (Ilex paraguariensis A. StHil.). Previous studies have shown that CGA has a significant neuroprotective effect and can improve global CI/R injury. However, the underlying molecular mechanism of CGA in CI/R injury has not been fully revealed. Materials: In this study, CI/R rat model was constructed. The rats were randomly divided into nine groups with ten in each group: Control, CGA (500 mg•kg-1), CI/R, CI/R + CGA (20 mg•kg-1), CI/R + CGA (100 mg•kg-1), CI/R + CGA (500 mg•kg-1), ML385 (30 mg•kg-1), CI/R + ML385 (30 mg•kg-1), CI/R + CGA + ML385. Cerebral infarction volume was detected by TTC staining. Brain pathological damage was detected by H&E staining. Apoptosis of cortical cells was detected by TUNEL staining. The expression of related proteins was detected by RT-qPCR and Western blotting. Results: Step-down test and Y maze test showed that CGA dose-dependently mitigated CI/ R-induced brain damage and enhanced learning and spatial memory. Besides, CGA promoted the expression of BDNF and NGF in a dose-dependent manner and alleviated CI/R-induced nerve injury. Moreover, CGA increased the activity of SOD and the level of GSH, as well as decreased production of ROS and LDH and the accumulation of MDA. Notably, CGA attenuated oxidative stress-induced brain injury and apoptosis and inhibited the expression of apoptosis-related proteins (cleaved caspase 3 and caspase 9). Additionally, CGA reversed CI/R induced inactivation of Nrf2 pathway and promoted Nrf2, NQO-1 and HO-1 expression. Nrf2 pathway inhibitor ML385 destroyed this promotion. Discussion: All the data indicated that CGA had a neuroprotective effect on the CI/R rats by regulating oxidative stress-related Nrf2 pathway.

A fluorescent probe based on fluorescein displays excellent selectivity and sensitivity for cysteine and its application for bio-imaging is described.

Protein phosphorylation is a major form of post-translational modification (PTM) that regulates diverse cellular processes. In silico methods for phosphorylation site prediction can provide a useful and complementary strategy for complete phosphoproteome annotation. Here, we present a novel bioinformatics tool, PhosphoPredict, that combines protein sequence and functional features to predict kinase-specific substrates and their associated phosphorylation sites for 12 human kinases and kinase families, including ATM, CDKs, GSK-3, MAPKs, PKA, PKB, PKC, and SRC. To elucidate critical determinants, we identified feature subsets that were most informative and relevant for predicting substrate specificity for each individual kinase family. Extensive benchmarking experiments based on both five-fold cross-validation and independent tests indicated that the performance of PhosphoPredict is competitive with that of several other popular prediction tools, including KinasePhos, PPSP, GPS, and Musite. We found that combining protein functional and sequence features significantly improves phosphorylation site prediction performance across all kinases. Application of PhosphoPredict to the entire human proteome identified 150 to 800 potential phosphorylation substrates for each of the 12 kinases or kinase families. PhosphoPredict significantly extends the bioinformatics portfolio for kinase function analysis and will facilitate high-throughput identification of kinase-specific phosphorylation sites, thereby contributing to both basic and translational research programs.

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Gravitational lithosphere removal in continental interior has been inferred from various observations, including anomalous surface deflections and magmatism. We use numerical models and a simplified theoretical analysis to investigate how lithosphere removal can be recognized in the magmatic record. One style of removal is a Rayleigh‐Taylor‐type instability, where removal occurs through dripping. The associated magmatism depends on the lithosphere thermal structure. Four types of magmatism are predicted: (1) For relatively hot lithosphere (e.g., back arcs), the lithosphere can be conductively heated and melted during removal, while the asthenosphere upwells and undergoes decompression melting. If removal causes significant lithospheric thinning, the deep crust may be heated and melted. (2) For moderately warm lithosphere (e.g., average Phanerozoic lithosphere) in which the lithosphere root has a low density, only the lithosphere may melt. (3) If the lithosphere root has a high density in moderately warm lithosphere, only asthenosphere melt is predicted. (4) For cold lithosphere (e.g., cratons), no magmatism is induced. An alternate style of removal is delamination, where dense lithosphere peels along Moho. In most cases, the lithosphere sinks too rapidly to melt. However, asthenosphere can upwell to the base of the crust, resulting in asthenospheric and crustal melts. In delamination, magmatism migrates laterally with the detachment point; in contrast, magmatism in Rayleigh‐Taylor‐type instability has a symmetric shape and converges toward the drip center. The models may explain the diversity of magmatism observed in areas with inferred lithosphere removal, including the Puna Plateau and the southern Sierra Nevada.

Background: Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT. Methods: We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available. Results: Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site. Conclusions: Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.