Limit and screen sequences with high degree of secondary structures in DNA storage by deep learning method.

BACKGROUND: In single-stranded DNAs/RNAs, secondary structures are very common especially in long sequences. It has been recognized that the high degree of secondary structures in DNA sequences could interfere with the correct writing and reading of information in DNA storage. However, how to circumvent its side-effect is seldom studied. METHOD: As the degree of secondary structures of DNA sequences is closely related to the magnitude of the free energy released in the complicated folding process, we first investigate the free-energy distribution at different encoding lengths based on randomly generated DNA sequences. Then, we construct a bidirectional long short-term (BiLSTM)-attention deep learning model to predict the free energy of sequences. RESULTS: Our simulation results indicate that the free energy of DNA sequences at a specific length follows a right skewed distribution and the mean increases as the length increases. Given a tolerable free energy threshold of 20 kcal/mol, we could control the ratio of serious secondary structures in the encoding sequences to within 1% of the significant level through selecting a feasible encoding length of 100 nt. Compared with traditional deep learning models, the proposed model could achieve a better prediction performance both in the mean relative error (MRE) and the coefficient of determination (R2). It achieved MRE = 0.109 and R2 = 0.918 respectively in the simulation experiment. The combination of the BiLSTM and attention module can handle the long-term dependencies and capture the feature of base pairing. Further, the prediction has a linear time complexity which is suitable for detecting sequences with severe secondary structures in future large-scale applications. Finally, 70 of 94 predicted free energy can be screened out on a real dataset. It demonstrates that the proposed model could screen out some highly suspicious sequences which are prone to produce more errors and low sequencing copies.

Ultra-Robust Deep-UV Photovoltaic Detector Based on Graphene/(AlGa)2O3/GaN with High-Performance in Temperature Fluctuations.

A strategy of adopting Ga2O3 alloyed with Al element to reduce the oxygen vacancy defect density and enhance the interface barrier height of Ga2O3 heterojunction is proposed to fabricate deep-UV photovoltaic detectors with high thermal stability, high photoresponsivity, and fast response speed. Here, a graphene/(AlGa)2O3/GaN device with a photoresponsivity of ∼20 mA/W, a rise time of ∼2 µs, and a decay time of ∼10 ms is presented at 0 V bias. At the working temperature of 453 K, the device still exhibits a photo-to-dark current ratio (PDCR) of ∼1.8 × 103, which is 1-2 orders of magnitude higher than that of the reported high-temperature deep-UV film detectors. By comparing the formation energy of oxygen vacancy defects and the interface barrier height of the heterojunction at different temperatures in graphene/Ga2O3/GaN and graphene/(AlGa)2O3/GaN systems, the strategy of synthesizing (AlGa)2O3 ternary composite alloy is proved to be reliable for fabricating high-performance deep-UV photovoltaic detectors. The method proposed in this paper can provide reference for the preparation of deep-UV photovoltaic detectors with high photoresponsivity and thermal stability in the future.

Expression pattern and splicing function of mouse ZNF265.

ZNF265 is a newly identified arginine/serine-rich (SR) protein and has two transcript isoforms (ZNF265-1 and ZNF265-2) that autoregulate between each other. Previous studies have shown that ZNF265 regulates the Tra2 beta isoform splicing. Here, we demonstrate that two ZNF-265 transcript isoforms are expressed in various mouse tissues and that ZNF265-1 is a major isoform. The ZNF265-1 protein level in the cerebral cortex is significantly lower in relative to other tissues. The recombinant proteins of both isoforms are nuclear, in consistent with its functions as pre-mRNA splicing regulators. Splicing analysis with GluR-B and SMN2 minigenes demonstrates that ZNF265-1 inhibits the Flop exon and exon 7 usages in the splicing of two minigenes, respectively. The regulation of GluR-B and SMN2 pre-mRNA splicing by ZNF265 implies this newly identified SR protein may play important roles in maintaining normal neuronal function and SMA pathogenesis.

Establishment and application of minigene models for studying pre-mRNA alternative splicing.

The objective of the present study is to establish a minigene model for studying pre-mRNA alternative splicing. To prepare the minigene DNA constructs, with human or mouse genomic DNA as templates, GluR-B, FGF-2R and Zis "minigene" fragments were amplified using PCR and cloned to the eukaryotic expression vectors. The three constructed minigenes and the expression vectors of Tra2beta1 and Zis2 were co-transfected in Hela cells. RT-PCR analysis was performed to semi-quantitatively determine the spliced products from the minigenes. The results demonstrated that the constructed minigenes are useful in studying the pre-mRNA alternative splicing in cultured cells. With the established Zis minigene, we for the first time found that Zis2 isoform regulates the alternative splicing of Zis minigene.

NSSR1 promotes neuronal differentiation of mouse embryonic carcinoma P19 cells.

We generated the small interference RNAs to specifically silence the expression of neural salient serine/arginine rich protein 1 (NSSR1) and showed that the inhibition of NSSR1 expression in mouse embryonic carcinoma cells (P19) reduces neuronal differentiation. By contrast, its over-expression promotes the differentiation. Neither inhibition nor over-expression shows distinct effect on cell proliferation. The over-expression increases the inclusion of NCAM L1 exon2 while the inhibition reduces the inclusion. The splicing of kinase insert free isoform of TrkC (TrkC-K1) is increased by the over-expression. The results demonstrate that NSSR1 promotes neuronal differentiation and the splicing of NCAML1 exon2 and TrkC-K1.

Expression of Tra2beta isoforms is developmentally regulated in a tissue- and temporal-specific pattern.

The contribution of Tra2-regulated alternative splicing to mammalian development is unknown. To address the question, we initiated studies by systemically characterizing the gene expression profile of Tra2beta isoforms in human fetal tissue at two different stages (11 and 16 weeks). Tra2beta has at least five isoforms of transcripts (Tra2beta1 approximately 5). Tra2beta1 encodes full-length Tra2beta proteins, whilst Tra2beta3, 4 and 5 encode the truncated proteins. The results show that Tra2beta1 transcript levels are developmentally regulated in a tissue- and temporal-specific pattern, although expression is ubiquitous. Compared to Tra2beta5, the expression of Tra2beta3 and 4 transcripts is significantly restricted and more vigorously regulated in a tissue- and temporal-specific pattern. Western blot analysis shows that Tra2beta1 proteins are ubiquitously expressed, but at a relatively higher level in neural tissues than non-neural tissues. However, there is no direct correlation between the transcript and protein levels for Tra2beta1, suggesting that multiple mechanisms are involved in the regulation of Tra2beta during development. This study indicates that Tra2beta-regulated splicing may contribute to the regulation of mammalian development in a tissue- and temporal-specific pattern.

[Tissue-specific expression of Na+ -H+ exchanger isoforms at two developmental stages of human fetus].

Na(+)-H(+) exchangers (NHE) are major membrane proteins that have been identified as signal transduction mediators in the regulation of cell differentiation and important membrane ion transporters in the regulation of the intercellular pH and the cell volume. NHE are composed of at least six isoforms and activated in growth factor-regulated cell differentiation. However, little is known about the differential regulation of NHE expression in the development. In the present study, we studied developmental regulation of the expression of NHE isoforms in human fetal tissues by comparing the expression of various isoforms between two developmental stages, i.e., week 11 (11 W) and week 16 (16 W). The results demonstrated that NHE1 transcripts were expressed ubiquitously. In comparison to the expression at 16 W, the level of NHE1 transcripts was low and varied significantly in a tissue-specific pattern at 11 W, suggesting that the house-keeping function of MHE1 occurs at 11 W or earlier and becomes well established at least as early as at 16 W. The tissue-specifically restricted expression of NHE2 and NHE3 was regulated at 11 W and 16 W in an opposite tendency, supporting the overlapping relationship between NHE2 and NHE3 in the tissue distribution as reported in adults. NHE5 expression was relatively ubiquitous at 11 W and became restricted in the cerebellum at 16 W, suggesting that the restrictive expression of NHE5 in the brain occurs later than that of other isoforms. The present study demonstrates a space time-dependent regulation of the tissue-specific expression pattern of NHE isoforms during human development between 11 W and 16 W. The results also suggest that at 16 W or earlier the expression pattern of developing tissues becomes similar to that of adult tissues. The observed developmental regulation of NHE expression provides a molecular basis for further study of the function and regulation of NHE gene during development.