Supramolecular Nanofibers Ameliorate Bleomycin-Induced Pulmonary Fibrosis by Restoring Autophagy.

Idiopathic pulmonary fibrosis (IPF) is a progressive and ultimately fatal interstitial lung disease, with limited therapeutic options available. Impaired autophagy resulting from aberrant TRB3/p62 protein-protein interactions (PPIs) contributes to the progression of IPF. Restoration of autophagy by modulating the TRB3/p62 PPIs has rarely been reported for the treatment of IPF. Herein, peptide nanofibers are developed that specifically bind to TRB3 protein and explored their potential as a therapeutic approach for IPF. By conjugating with the self-assembling fragment (Ac-GFFY), a TRB3-binding peptide motif A2 allows for the formation of nanofibers with a stable α-helix secondary structure. The resulting peptide (Ac-GFFY-A2) nanofibers exhibit specific high-affinity binding to TRB3 protein in saline buffer and better capacity of cellular uptake to A2 peptide. Furthermore, the TRB3-targeting peptide nanofibers efficiently interfere with the aberrant TRB3/p62 PPIs in activated fibroblasts and fibrotic lung tissue of mice, thereby restoring autophagy dysfunction. The TRB3-targeting peptide nanofibers inhibit myofibroblast differentiation, collagen production, and fibroblast migration in vitro is demonstrated, as well as bleomycin-induced pulmonary fibrosis in vivo. This study provides a supramolecular method to modulate PPIs and highlights a promising strategy for treating IPF diseases by restoring autophagy.

Population coding of time-varying sounds in the nonlemniscal inferior colliculus.

The inferior colliculus (IC) of the midbrain is important for complex sound processing, such as discriminating conspecific vocalizations and human speech. The IC's nonlemniscal, dorsal "shell" region is likely important for this process, as neurons in these layers project to higher-order thalamic nuclei that subsequently funnel acoustic signals to the amygdala and nonprimary auditory cortices, forebrain circuits important for vocalization coding in a variety of mammals, including humans. However, the extent to which shell IC neurons transmit acoustic features necessary to discern vocalizations is less clear, owing to the technical difficulty of recording from neurons in the IC's superficial layers via traditional approaches. Here, we use two-photon Ca2+ imaging in mice of either sex to test how shell IC neuron populations encode the rate and depth of amplitude modulation, important sound cues for speech perception. Most shell IC neurons were broadly tuned, with a low neurometric discrimination of amplitude modulation rate; only a subset was highly selective to specific modulation rates. Nevertheless, neural network classifier trained on fluorescence data from shell IC neuron populations accurately classified amplitude modulation rate, and decoding accuracy was only marginally reduced when highly tuned neurons were omitted from training data. Rather, classifier accuracy increased monotonically with the modulation depth of the training data, such that classifiers trained on full-depth modulated sounds had median decoding errors of ∼0.2 octaves. Thus, shell IC neurons may transmit time-varying signals via a population code, with perhaps limited reliance on the discriminative capacity of any individual neuron.NEW & NOTEWORTHY The IC's shell layers originate a "nonlemniscal" pathway important for perceiving vocalization sounds. However, prior studies suggest that individual shell IC neurons are broadly tuned and have high response thresholds, implying a limited reliability of efferent signals. Using Ca2+ imaging, we show that amplitude modulation is accurately represented in the population activity of shell IC neurons. Thus, downstream targets can read out sounds' temporal envelopes from distributed rate codes transmitted by populations of broadly tuned neurons.

Assessment of visual function in blind mice and monkeys with subretinally implanted nanowire arrays as artificial photoreceptors.

Retinal prostheses could restore image-forming vision in conditions of photoreceptor degeneration. However, contrast sensitivity and visual acuity are often insufficient. Here we report the performance, in mice and monkeys with induced photoreceptor degeneration, of subretinally implanted gold-nanoparticle-coated titania nanowire arrays providing a spatial resolution of 77.5 µm and a temporal resolution of 3.92 Hz in ex vivo retinas (as determined by patch-clamp recording of retinal ganglion cells). In blind mice, the arrays allowed for the detection of drifting gratings and flashing objects at light-intensity thresholds of 15.70-18.09 µW mm-2, and offered visual acuities of 0.3-0.4 cycles per degree, as determined by recordings of visually evoked potentials and optomotor-response tests. In monkeys, the arrays were stable for 54 weeks, allowed for the detection of a 10-µW mm-2 beam of light (0.5° in beam angle) in visually guided saccade experiments, and induced plastic changes in the primary visual cortex, as indicated by long-term in vivo calcium imaging. Nanomaterials as artificial photoreceptors may ameliorate visual deficits in patients with photoreceptor degeneration.

Population coding of time-varying sounds in the non-lemniscal Inferior Colliculus.

The inferior colliculus (IC) of the midbrain is important for complex sound processing, such as discriminating conspecific vocalizations and human speech. The IC's non-lemniscal, dorsal "shell" region is likely important for this process, as neurons in these layers project to higher-order thalamic nuclei that subsequently funnel acoustic signals to the amygdala and non-primary auditory cortices; forebrain circuits important for vocalization coding in a variety of mammals, including humans. However, the extent to which shell IC neurons transmit acoustic features necessary to discern vocalizations is less clear, owing to the technical difficulty of recording from neurons in the IC's superficial layers via traditional approaches. Here we use 2-photon Ca2+ imaging in mice of either sex to test how shell IC neuron populations encode the rate and depth of amplitude modulation, important sound cues for speech perception. Most shell IC neurons were broadly tuned, with a low neurometric discrimination of amplitude modulation rate; only a subset were highly selective to specific modulation rates. Nevertheless, neural network classifier trained on fluorescence data from shell IC neuron populations accurately classified amplitude modulation rate, and decoding accuracy was only marginally reduced when highly tuned neurons were omitted from training data. Rather, classifier accuracy increased monotonically with the modulation depth of the training data, such that classifiers trained on full-depth modulated sounds had median decoding errors of ~0.2 octaves. Thus, shell IC neurons may transmit time-varying signals via a population code, with perhaps limited reliance on the discriminative capacity of any individual neuron.

Cholecystokinin neurons in mouse suprachiasmatic nucleus regulate the robustness of circadian clock.

The suprachiasmatic nucleus (SCN) can generate robust circadian behaviors in mammals under different environments, but the underlying neural mechanisms remained unclear. Here, we showed that the activities of cholecystokinin (CCK) neurons in the mouse SCN preceded the onset of behavioral activities under different photoperiods. CCK-neuron-deficient mice displayed shortened free-running periods, failed to compress their activities under a long photoperiod, and developed rapid splitting or became arrhythmic under constant light. Furthermore, unlike vasoactive intestinal polypeptide (VIP) neurons, CCK neurons are not directly light sensitive, but their activation can elicit phase advance and counter light-induced phase delay mediated by VIP neurons. Under long photoperiods, the impact of CCK neurons on SCN dominates over that of VIP neurons. Finally, we found that the slow-responding CCK neurons control the rate of recovery during jet lag. Together, our results demonstrated that SCN CCK neurons are crucial for the robustness and plasticity of the mammalian circadian clock.

Error Analysis of a PFEM Based on the Euler Semi-Implicit Scheme for the Unsteady MHD Equations.

In this article, we mainly consider a first order penalty finite element method (PFEM) for the 2D/3D unsteady incompressible magnetohydrodynamic (MHD) equations. The penalty method applies a penalty term to relax the constraint "∇·u=0", which allows us to transform the saddle point problem into two smaller problems to solve. The Euler semi-implicit scheme is based on a first order backward difference formula for time discretization and semi-implicit treatments for nonlinear terms. It is worth mentioning that the error estimates of the fully discrete PFEM are rigorously derived, which depend on the penalty parameter ϵ, the time-step size τ, and the mesh size h. Finally, two numerical tests show that our scheme is effective.

Gossypol ameliorates the IL-1ß-induced apoptosis and inflammation in chondrocytes by suppressing the activation of TLR4/MyD88/NF-κB pathway via downregulating CX43.

The effects of anti-inflammatory drug gossypol on osteoarthritis (OA) treatment were discussed in this paper. After identified using toluidine blue and immunofluorescence staining of type II collagen, chondrocytes from OA patients were treated with interleukin-1ß (IL-1ß), gossypol, and overexpressed connexin43 (CX43). In treated chondrocytes, according to MTT assay and flow cytometry, gossypol increased viability and reduced apoptosis of IL-1ß induced chondrocytes. Enzyme linked immunosorbent assay (ELISA) suggested that gossypol downregulated inflammatory tumor necrosis factor (TNF)-α level. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot confirmed that gossypol downregulated CX43, nuclear factor-kappa B (NF-κB) p65, TNF-α, toll like receptor 4 (TLR4), myeloid differentiation primary response gene 88 (MyD88) and interleukin-6 (IL-6) expressions. Besides, overexpressed CX43 reversed the effects of gossypol on viability, apoptosis, and expressions of factors related to TLR4/MyD88/NF-κB pathway of IL-1ß-induced chondrocytes. In conclusion, gossypol ameliorates IL-1ß-induced apoptosis and inflammation in chondrocytes by suppressing TLR4/MyD88/NF-κB pathway via downregulating CX43.

Genome-wide analysis of lncRNA stability in human.

Transcript stability is associated with many biological processes, and the factors affecting mRNA stability have been extensively studied. However, little is known about the features related to human long noncoding RNA (lncRNA) stability. By inhibiting transcription and collecting samples in 10 time points, genome-wide RNA-seq studies was performed in human lung adenocarcinoma cells (A549) and RNA half-life datasets were constructed. The following observations were obtained. First, the half-life distributions of both lncRNAs and messanger RNAs (mRNAs) with one exon (lnc-human1 and m-human1) were significantly different from those of both lncRNAs and mRNAs with more than one exon (lnc-human2 and m-human2). Furthermore, some factors such as full-length transcript secondary structures played a contrary role in lnc-human1 and m-human2. Second, through the half-life comparisons of nucleus- and cytoplasm-specific and common lncRNAs and mRNAs, lncRNAs (mRNAs) in the nucleus were found to be less stable than those in the cytoplasm, which was derived from transcripts themselves rather than cellular location. Third, kmers-based protein-RNA or RNA-RNA interactions promoted lncRNA stability from lnc-human1 and decreased mRNA stability from m-human2 with high probability. Finally, through applying deep learning-based regression, a non-linear relationship was found to exist between the half-lives of lncRNAs (mRNAs) and related factors. The present study established lncRNA and mRNA half-life regulation networks in the A549 cell line and shed new light on the degradation behaviors of both lncRNAs and mRNAs.

Deep learning methods improve linear B-cell epitope prediction.

BACKGROUND: B-cell epitopes play important roles in vaccine design, clinical diagnosis, and antibody production. Although some models have been developed to predict linear or conformational B-cell epitopes, their performance is still unsatisfactory. Hundreds of thousands of linear B-cell epitope data have accumulated in the Immune Epitope Database (IEDB). These data can be explored using the deep learning methods, in order to create better predictive models for linear B-cell epitopes. RESULTS: After data cleaning, we obtained 240,563 peptide samples with experimental evidence from the IEDB database, including 25,884 linear B-cell epitopes and 214,679 non-epitopes. Based on the peptide center, we adapted each peptide to the same length by trimming or extending. A random portion of the data, with the same amount of epitopes and non-epitopes, were set aside as test dataset. Then a same number of epitopes and non-epitopes were randomly selected from the remaining data to build a classifier with the feedforward deep neural network. We built eleven classifiers to form an ensemble prediction model. The model will report a peptide as an epitope if it was classified as epitope by all eleven classifiers. Then we used the test data set to evaluate the performance of the model using the area value under the receiver operating characteristic (ROC) curve (AUC) as an indicator. We established 40 models to predict linear B-cell epitopes of length from 11 to 50 separately, and found that the AUC value increased with the length and tended to be stable when the length was 38. Repeated results showed that the models constructed by this method were robust. Tested on our and two public test datasets, our models outperformed current major models available. CONCLUSIONS: We applied the feedforward deep neural network to the large amount of linear B-cell epitope data with experimental evidence in the IEDB database, and constructed ensemble prediction models with better performance than the current major models available. We named the models as DLBEpitope and provided web services using the models at http://ccb1.bmi.ac.cn:81/dlbepitope/.

Biodegradation of fenoxaprop-P-ethyl (FE) by Acinetobacter sp. strain DL-2 and cloning of FE hydrolase gene afeH.

Fenoxaprop-P-ethyl (FE) is widely used as a post-emergence aryloxyphenoxy propionate (AOPP) herbicide in agriculture. An efficient FE-degrading strain DL-2 was isolated from the enrichment culture and identified as Acinetobacter sp. and the metabolite fenoxaprop acid (FA) was identified by HPLC/MS analysis. The strain DL-2 could also degrade a wide range of other AOPP herbicides. A novel FE hydrolase esterase gene afeH was cloned from strain DL-2 and functionally expressed in Escherichia coli BL21(DE3). The specific activities of recombinant AfeH was 216.39 U mg(-1) for FE with Km and Vmax values of 0.82 µM and 7.94 µmol min(-1) mg(-1). AfeH could also hydrolyze various AOPP herbicides, p-nitrophenyl esters and triglycerides. The optimal pH and temperature for recombinant AfeH were 9.0 and 50°C, respectively; the enzyme was activated by Co(2+) and inhibited by Ca(2+), Zn(2+), Ba(2+). AfeH was inhibited strongly by phenylmethylsulfonyl and SDS and weakly by dimethyl sulfoxide.