MicroRNAs of Bombyx mori identified by Solexa sequencing

<p>Abstract</p> <p>Background</p> <p>MicroRNA (miRNA) and other small regulatory RNAs contribute to the modulation of a large number of cellular processes. We sequenced three small RNA libraries prepared from the whole body, and the anterior-middle and posterior silk glands of <it>Bombyx mori</it>, with a view to expanding the repertoire of silkworm miRNAs and exploring transcriptional differences in miRNAs between segments of the silk gland.</p> <p>Results</p> <p>With the aid of large-scale Solexa sequencing technology, we validated 257 unique miRNA genes, including 202 novel and 55 previously reported genes, corresponding to 324 loci in the silkworm genome. Over 30 known silkworm miRNAs were further corrected in their sequence constitutes and length. A number of reads originated from the loop regions of the precursors of two previously reported miRNAs (bmo-miR-1920 and miR-1921). Interestingly, the majority of the newly identified miRNAs were silkworm-specific, 23 unique miRNAs were widely conserved from invertebrates to vertebrates, 13 unique miRNAs were limited to invertebrates, and 32 were confined to insects. We identified 24 closely positioned clusters and 45 paralogs of miRNAs in the silkworm genome. However, sequence tags showed that paralogs or clusters were not prerequisites for coordinated transcription and accumulation. The majority of silkworm-specific miRNAs were located in transposable elements, and displayed significant differences in abundance between the anterior-middle and posterior silk gland.</p> <p>Conclusions</p> <p>Conservative analysis revealed that miRNAs can serve as phylogenetic markers and function in evolutionary signaling. The newly identified miRNAs greatly enrich the repertoire of insect miRNAs, and provide insights into miRNA evolution, biogenesis, and expression in insects. The differential expression of miRNAs in the anterior-middle and posterior silk glands supports their involvement as new levels in the regulation of the silkworm silk gland.</p

Calibration of DFT-based Models with Experimental Data

JAS thanks David Ponting and co‐workers at Lhasa Limited for useful suggestions and discussions. This work was also supported by the National Natural Science Foundation of China [Grant number 21875061, 21975066] and the program for Science & Technology Innovation Team in Universities of Henan Province [Grant number 19IRTSTHN029]. Publisher Copyright: © 2022 The Authors. Molecular Informatics published by Wiley-VCH GmbH.Random Forest (RF) QSPR models were developed with a data set of homolytic bond dissociation energies (BDE) previously calculated by B3LYP/6-311++G(d,p)//DFTB for 2263 sp3C−H covalent bonds. The best set of attributes consisted in 114 descriptors of the carbon atom (counts of atom types in 5 spheres around the kernel atom and ring descriptors). The optimized model predicted the DFT-calculated BDE of an independent test set of 224 bonds with MAE=2.86 kcal/mol. A new data set of 409 bonds from the iBonD database (http://ibond.nankai.edu.cn) was predicted by the RF with a modest MAE (5.36 kcal/mol) but a relatively high R2 (0.75) against experimental energies. A prediction scheme was explored that corrects the RF prediction with the average deviation observed for the k nearest neighbours (KNN) in an additional memory of experimental data. The corrected predictions achieved MAE=2.22 kcal/mol for an independent test set of 145 bonds and the corresponding experimental bond energies.publishersversionpublishe

Improvement of a low pH antigen-antibody dissociation procedure for ELISA measurement of circulating anti-Aβ antibodies

BACKGROUND: Prior work from our group found that acid dissociation (pH 2.5 incubation) of serum from APP transgenic mice vaccinated against Aβ increased the apparent anti-Aβ titers, suggesting antibody masking by antigen in the ELISA assay. Subsequently, we found that pH 2.5 incubation of serum from unvaccinated non-transgenic mice showed antibody binding to Aβ1–42, but no increase when other proteins, including shorter Aβ peptides, coated the ELISA plate. To investigate further the effects of low pH incubation on apparent anti-Aβ1–42 signals, we examined normal sera from nonTg unvaccinated mice, nonTg mice vaccinated with Aβ peptide (to produce authentic anti-Aβ antibodies) or a monoclonal antibody against Aβ (6E10) using competitive-inhibition ELISA and Aβ epitope mapping assays. In addition, we examined use of a less stringent low pH procedure at pH 3.5, to ascertain if it had the same effects as the pH 2.5 procedure. RESULTS: We believe there are three distinct effects of pH 2.5 incubation.; A) an artifactual increase in binding to full length Aβ by mouse immunoglobulin which has low affinity for Aβ, B) an inactivation of anti-Aβ antibodies that is time dependent and C) unmasking of high affinity anti-Aβ antibodies when high levels of circulating Aβ is present in APP transgenic mice. All three reactions can interact to produce the final ELISA signal. Incubation of sera from unvaccinated nonTg mice at pH 2.5 enhanced ELISA signals by process A. Conversely, pH 2.5 incubation of sera from vaccinated nonTg mice with caused a time dependent reduction of antibody signal by process B (overcoming the increase caused by A). The artifactual anti-Aβ ELISA signal enhanced by pH 2.5 incubation of normal mouse sera could not be effectively competed by low to moderate concentrations of Aβ, nor bind to shorter Aβ peptides in a manner similar to authentic anti-Aβ antibodies. Incubation of mouse sera at pH 3.5 caused neither an apparent increase in anti-Aβ ELISA signal, nor an inactivation of the ELISA signals resulting from either vaccination or monoclonal antibodies. However, incubation at pH 3.5 was able to completely reverse the reduction in ELISA signal caused by Aβ complexing with antibodies in sera from vaccinated mice or monoclonal anti-Aβ antibodies. CONCLUSION: Incubation at pH 3.5 is sufficient to dissociate Aβ bound to anti-Aβ antibodies without producing artifactual increases in the signal, or inactivating authentic antibody binding. Thus, use of pH 3.5 is a considerable improvement over pH 2.5 incubation for unmasking anti-Aβ antibodies in ELISA assays to measure antibodies in APP transgenic mouse sera

Secure Split Learning against Property Inference, Data Reconstruction, and Feature Space Hijacking Attacks

Split learning of deep neural networks (SplitNN) has provided a promising solution to learning jointly for the mutual interest of a guest and a host, which may come from different backgrounds, holding features partitioned vertically. However, SplitNN creates a new attack surface for the adversarial participant, holding back its practical use in the real world. By investigating the adversarial effects of highly threatening attacks, including property inference, data reconstruction, and feature hijacking attacks, we identify the underlying vulnerability of SplitNN and propose a countermeasure. To prevent potential threats and ensure the learning guarantees of SplitNN, we design a privacy-preserving tunnel for information exchange between the guest and the host. The intuition is to perturb the propagation of knowledge in each direction with a controllable unified solution. To this end, we propose a new activation function named R3eLU, transferring private smashed data and partial loss into randomized responses in forward and backward propagations, respectively. We give the first attempt to secure split learning against three threatening attacks and present a fine-grained privacy budget allocation scheme. The analysis proves that our privacy-preserving SplitNN solution provides a tight privacy budget, while the experimental results show that our solution performs better than existing solutions in most cases and achieves a good tradeoff between defense and model usability.Comment: 23 page

MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori)

<p>Abstract</p> <p>Background</p> <p>MicroRNAs (miRNAs) are expressed by a wide range of eukaryotic organisms, and function in diverse biological processes. Numerous miRNAs have been identified in <it>Bombyx mori</it>, but the temporal expression profiles of miRNAs corresponding to each stage transition over the entire life cycle of the silkworm remain to be established. To obtain a comprehensive overview of the correlation between miRNA expression and stage transitions, we performed a whole-life test and subsequent stage-by-stage examinations on nearly one hundred miRNAs in the silkworm.</p> <p>Results</p> <p>Our results show that miRNAs display a wide variety of expression profiles over the whole life of the silkworm, including continuous expression from embryo to adult (miR-184), up-regulation over the entire life cycle (let-7 and miR-100), down-regulation over the entire life cycle (miR-124), expression associated with embryogenesis (miR-29 and miR-92), up-regulation from early 3^rdinstar to pupa (miR-275), and complementary pulses in expression between miR-34b and miR-275. Stage-by-stage examinations revealed further expression patterns, such as emergence at specific time-points during embryogenesis and up-regulation of miRNA groups in late embryos (miR-1 and bantam), expression associated with stage transition between instar and molt larval stages (miR-34b), expression associated with silk gland growth and spinning activity (miR-274), continuous high expression from the spinning larval to pupal and adult stages (miR-252 and miR-31a), a coordinate expression trough in day 3 pupae of both sexes (miR-10b and miR-281), up-regulation in pupal metamorphosis of both sexes (miR-29b), and down-regulation in pupal metamorphosis of both sexes (miR-275).</p> <p>Conclusion</p> <p>We present the full-scale expression profiles of miRNAs throughout the life cycle of <it>Bombyx mori</it>. The whole-life expression profile was further investigated via stage-by-stage analysis. Our data provide an important resource for more detailed functional analysis of miRNAs in this animal.</p

Genome-wide annotation and comparative analysis of cuticular protein genes in the noctuid pest \u3cem\u3eSpodoptera litura\u3c/em\u3e

Insect cuticle is considered an adaptable and versatile building material with roles in the construction and function of exoskeleton. Its physical properties are varied, as the biological requirements differ among diverse structures and change during the life cycle of the insect. Although the bulk of cuticle consists basically of cuticular proteins (CPs) associated with chitin, the degree of cuticular sclerotization is an important factor in determining its physical properties. Spodoptera litura, the tobacco cutworm, is an important agricultural pest in Asia. Compared to the domestic silkworm, Bombyx mori, another lepidopteran whose CP genes have been well annotated, S. litura has a shorter life cycle, hides in soil during daytime beginning in the 5th instar and is exposed to soil in the pupal stage without the protection of a cocoon. In order to understand how the CP genes may have been adapted to support the characteristic life style of S. litura, we searched its genome and found 287 putative cuticular proteins that can be classified into 9 CP families (CPR with three groups (RR-1, RR-2, RR-3), CPAP1, CPAP3, CPF, CPFL, CPT, CPG, CPCFC and CPLCA), and a collection of unclassified CPs named CPH. There were also 112 cuticular proteins enriched in Histidine residues with content varying from 6% to 30%, comprising many more His-rich cuticular proteins than B. mori. A phylogenetic analysis between S. litura, M. sexta and B. mori uncovered large expansions of RR-1 and RR-2 CPs, forming large gene clusters in different regions of S. liturachromosome 9. We used RNA-seq analysis to document the expression profiles of CPs in different developmental stages and tissues of S. litura. The comparative genomic analysis of CPs between S. litura and B. moriintegrated with the unique behavior and life cycle of the two species offers new insights into their contrasting ecological adaptations

Plasma Homocysteine Level in Children With Postural Tachycardia Syndrome

The study was designed to evaluate the changes of plasma homocysteine (Hcy) level in children with postural tachycardia syndrome (POTS) and explore its significance. A total of 65 subjects were recruited in our study, of whom 35 children were in the POTS group and 30 healthy children were in the control group. Plasma Hcy levels were determined in all subjects. The relationship between the plasma Hcy level and the symptom score was analyzed in the 35 POTS patients. The relationship between the plasma Hcy level and the change in heart rate from the supine to upright position (ΔHR) and between the plasma Hcy level and the rate of increase in heart rate from the supine to upright position (ΔHR/sHR × 100%) were analyzed in all subjects. The plasma Hcy levels were significantly higher in the children with POTS than those in the control group (9.78 [7.68, 15.31] μmol/L vs. 7.79 [7.46, 9.63] μmol/L, P &lt; 0.05). The plasma Hcy levels were positively correlated with symptom scores in the POTS patients (n = 35, r = 0.522, P &lt; 0.01). The plasma Hcy levels were also positively correlated with ΔHR (n = 65, r = 0.332, P &lt; 0.01) and ΔHR/sHR × 100% (n = 65, r = 0.341, P &lt; 0.01) in all the subjects. In conclusion, the plasma Hcy levels were elevated in the children with POTS positively correlated with the severity of POTS, suggesting that Hcy might be involved in the pathogenesis of POTS