DeepPLM_mCNN: An approach for enhancing ion channel and ion transporter recognition by multi-window CNN based on features from pre-trained language models.

Accurate classification of membrane proteins like ion channels and transporters is critical for elucidating cellular processes and drug development. We present DeepPLM_mCNN, a novel framework combining Pretrained Language Models (PLMs) and multi-window convolutional neural networks (mCNNs) for effective classification of membrane proteins into ion channels and ion transporters. Our approach extracts informative features from protein sequences by utilizing various PLMs, including TAPE, ProtT5_XL_U50, ESM-1b, ESM-2_480, and ESM-2_1280. These PLM-derived features are then input into a mCNN architecture to learn conserved motifs important for classification. When evaluated on ion transporters, our best performing model utilizing ProtT5 achieved 90% sensitivity, 95.8% specificity, and 95.4% overall accuracy. For ion channels, we obtained 88.3% sensitivity, 95.7% specificity, and 95.2% overall accuracy using ESM-1b features. Our proposed DeepPLM_mCNN framework demonstrates significant improvements over previous methods on unseen test data. This study illustrates the potential of combining PLMs and deep learning for accurate computational identification of membrane proteins from sequence data alone. Our findings have important implications for membrane protein research and drug development targeting ion channels and transporters. The data and source codes in this study are publicly available at the following link: https://github.com/s1129108/DeepPLM_mCNN.

Ultrasensitive thin film infrared sensors enabled by hybrid nanomaterials.

IR sensing is an important technology with applications in renewable energy, environmental science and medical engineering. Herein environment-friendly IR sensors based on the single-walled carbon nanotube-copper sulfide nanoparticle (SWNT-CuS NP) hybrid nanomaterials are reported. The IR response in the photocurrent of a SWNT-CuS NP hybrid thin-film sensor is significantly enhanced when the IR light illuminates the thin-film device asymmetrically. We show that the change of photocurrent is up to 300%, which is 10× to 100× larger than those of other reported nanomaterial-based IR sensors. The detection limit can be as low as 48 µW mm(-2), among the lowest of the previously reported IR nanosensors. The dramatically enhanced sensitivity and detection limit are due to the temperature difference between the two junctions formed by the nanohybrid thin film and Cu-wire electrodes under asymmetric IR illumination, and the difference between the effective Seebeck coefficient of the nanohybrid thin film and that of the Cu wire. The IR sensor embedded in polydimethylsiloxane (PDMS) layers has been fabricated and tested, indicating its potential application as a flexible IR sensor.

Complete genomic profiles of 1496 Taiwanese reveal curated medical insights.

INTRODUCTION: The population of Taiwan has a long history of ethno-cultural evolution. The Taiwanese population was isolated from other large populations such as the European, Han Chinese, and Japanese population. The Taiwan Biobank (TWB) project has built a nationwide database, particularly for personal whole-genome sequence (WGS) to facilitate basic and clinical collaboration nationally and internationally, making it one of the most valuable public datasets of the East Asian population. OBJECTIVES: This study provides comprehensive medical genomic findings from TWB WGS data, for better characterization of disease susceptibility and the choice of ideal treatment regimens in Taiwanese population. METHODS: We reanalyzed 1496 WGS using a PrecisionFDA Truth challenge winner method Sentieon DNAscope. Single nucleotide variants (SNV) and small insertions/deletions (INDEL) were benchmarked. We also analyzed pharmacogenomic (PGx) drug-associated alleles, and copy number variants (CNV). Multiple practicing clinicians reviewed and curated the clinically significant variants. Variant annotations can be browsed at TaiwanGenomes (https://genomes.tw). RESULTS: We found that each participant had an average of 6,870.7 globally novel variants and 75.3% (831/1103) of the participants harbored at least one PharmGKB-selected high evidence level human leukocyte antigen (HLA) risk allele. 54 PharmGKB-reported high-level instances of evidence of Cytochrome P450 variant-drug pairs, with a population frequency of over 13.2%. We also identified 23 variants in the ACMG secondary finding V3 gene list from 25 participants, suggesting that 1.67% (25/1496) of the population is harboring at least one medical actionable variant. Our carrier status analyses suggest that one in 25 couples (3.94%) would risk having offspring with at least one pathogenic variant, which is in line with rates found in Japan and Singapore. For pathogenic CNV, we detected 6.88% and 2.02% carrier rates for alpha thalassemia and spinal muscular atrophy, respectively. CONCLUSION: Our study highlights the overall medical insights of a complete Taiwanese genomic profile.

Contribution of Phe-7 to Tat-dependent export of ß-lactamase in Xanthomonas campestris.

Strains of Xanthomonas campestris pv. campestris isolated in Taiwan are commonly resistant to ampicillin owing to the constitutive expression of a chromosomally encoded ß-lactamase that is secreted into the periplasm. In this study, we found that levels of ß-lactamase vary among X. campestris pv. campestris strains, a difference that can be attributed to amino acid substitutions at least at positions 7 and 206, with the former having the major impact. Bioinformatic and PCR analyses indicated that X. campestris pv. campestris possesses tatABC genes and that the signal peptide of X. campestris pv. campestris pre-Bla contains the typical twin-arginine motif (N-R-R-Q-F-L at amino acid residues 3 to 8 in strain X. campestris pv. campestris strain 11), suggesting that Bla is secreted via the Tat pathway. To assess the importance of Phe(7) in the efficient export of X. campestris pv. campestris Bla, we prepared mutant constructs containing amino acid substitutions and monitored their expression by measuring enzyme activity and detecting Bla protein by Western blotting. The results indicate that replacement of Phe(7) with Leu severely inhibited Bla export whereas replacement with Pro almost abolished it. Although a change to Arg caused moderate inhibition of export, replacement with Tyr had no effect. These results suggest that for efficient export of Bla by X. campestris pv. campestris, the aromatic-aromatic interactions and stability of protein structure around the twin-arginine motif are important, since only proteins that can attain a folded state in the cytoplasm are competent for export via the Tat pathway.

Optical and thermal response of single-walled carbon nanotube-copper sulfide nanoparticle hybrid nanomaterials.

This paper reports the optical and thermal response of a single-walled carbon nanotube-copper sulfide nanoparticle (SWNT-CuS NP) hybrid nanomaterial and its application as a thermoelectric generator. The hybrid nanomaterial was synthesized using oleylamine molecules as the linker molecules between SWNTs and CuS NPs. Measurements found that the hybrid nanomaterial has significantly increased light absorption (up to 80%) compared to the pure SWNT. Measurements also found that the hybrid nanomaterial thin-film devices exhibit a clear optical and thermal switching effect, which can be further enhanced up to 10 ×  by asymmetric illumination of light and thermal radiation on the thin-film devices instead of symmetric illumination. A simple prototype thermoelectric generator enabled by the hybrid nanomaterials is demonstrated, indicating a new route for achieving thermoelectricity.

A micromachined carbon nanotube film cantilever-based energy cell.

This paper reports a new type of energy cell based on micromachined carbon nanotube film (CNF)-lead zirconate titanate cantilevers that is fabricated on silicon substrates. Measurements found that this type of micro-energy cell generates both AC voltages due to the self-reciprocation of the microcantilevers and DC voltages due to the thermoelectric effect upon exposure to light and thermal radiation, resulting from the unique optical and thermal properties of the CNF. Typically the measured power density of the micro-energy cell can be from 4 to 300 µW cm(-2) when it is exposed to sunlight under different operational conditions. It is anticipated that hundreds of integrated micro-energy cells can generate power in the range of milliwatts, paving the way for the construction of self-powered micro- or nanosystems.

Studies of self-reciprocating characteristic of carbon nanotube film-based cantilevers under light and thermal radiation.

Self-reciprocating characteristic of carbon nanotube film (CNF)-Cu cantilevers upon exposure to light and thermal radiation was observed. This unique characteristic offers an attractive technical platform for harvesting solar and thermal energies on a single chip, which has been demonstrated recently. This paper reports the detailed experimental studies of this phenomenon. It reveals that the low-frequency self-reciprocation, sensitive to the thicknesses of CNF and Cu and the intensity of the light and thermal radiation, is mainly attributed to the electrostatic interaction among randomly connected carbon nanotubes (CNTs) in CNF. This is due to the fact that electrical currents in CNF induced by light and thermal radiation also exhibit an oscillating characteristic, similar to the self-reciprocating characteristic of the CNF-Cu cantilevers. The mechanism for this observed phenomenon is also discussed by relating the optical, thermal, electrical, elastic and mechanical properties of the CNF.

Spider web and silk performance landscapes across nutrient space.

Predators have been shown to alter their foraging as a regulatory response to recent feeding history, but it remains unknown whether trap building predators modulate their traps similarly as a regulatory strategy. Here we fed the orb web spider Nephila pilipes either live crickets, dead crickets with webs stimulated by flies, or dead crickets without web stimulation, over 21 days to enforce spiders to differentially extract nutrients from a single prey source. In addition to the nutrients extracted we measured web architectures, silk tensile properties, silk amino acid compositions, and web tension after each feeding round. We then plotted web and silk "performance landscapes" across nutrient space. The landscapes had multiple peaks and troughs for each web and silk performance parameter. The findings suggest that N. pilipes plastically adjusts the chemical and physical properties of their web and silk in accordance with its nutritional history. Our study expands the application of the geometric framework foraging model to include a type of predatory trap. Whether it can be applied to other predatory traps requires further testing.

Can differential nutrient extraction explain property variations in a predatory trap?

Predators exhibit flexible foraging to facilitate taking prey that offer important nutrients. Because trap-building predators have limited control over the prey they encounter, differential nutrient extraction and trap architectural flexibility may be used as a means of prey selection. Here, we tested whether differential nutrient extraction induces flexibility in architecture and stickiness of a spider's web by feeding Nephila pilipes live crickets (CC), live flies (FF), dead crickets with the web stimulated by flies (CD) or dead flies with the web stimulated by crickets (FD). Spiders in the CD group consumed less protein per mass of lipid or carbohydrate, and spiders in the FF group consumed less carbohydrates per mass of protein. Spiders from the CD group built stickier webs that used less silk, whereas spiders in the FF group built webs with more radii, greater catching areas and more silk, compared with other treatments. Our results suggest that differential nutrient extraction is a likely explanation for prey-induced spider web architecture and stickiness variations.

Magnetically Targeted Nanocapsules for PAA-Cisplatin-Conjugated Cores in PVA/SPIO Shells via Surfactant-Free Emulsion for Reduced Nephrotoxicity and Enhanced Lung Cancer Therapy.

Cis-diamminedichloroplatinum (II) (cisplatin, CDDP) is one of the most potent chemotherapy agents, but its side effects toward normal tissues, particularly toxicity in the kidney and nonspecific biodistribution, limit its ability to have significant clinical activity against a variety of solid tumors. A magnetic CDDP-encapsulated nanocapsule (CDDP-PAA-NC) with CDDP-polyacrylic acid (PAA) core in amphiphilic polyvinyl alcohol/superparamagnetic iron oxide nanoparticles shell is synthesized through a double emulsion to provide both high loading efficiency and controlled drug release. The CDDP-PAA-NCs significantly increase the blood circulation time of CDDP in vivo, with nearly 100-fold higher concentration, and drastically reduce side effects, including nephrotoxicity and hepatotoxicity, compared with the delivery of free CDDP. Furthermore, with a magnetic targeting effect, the CDDP-PAA-NCs show ninefold higher level accumulation in tumor tissue than the free CDDP treatment when administered at the equivalent dose, and mice treated with the CDDP-PAA-NCs display approximately 3.5-fold lower tumor volume than those of the control group on day 24. This result demonstrates that the magnetic CDDP-PAA-NCs, which are synthesized using a facile emulsion process, can significantly reduce toxicity and exhibit anticancer activity in A549-tumor bearing mice with negligible side effects.

Constitutive expression of a chromosomal class A (BJM group 2) beta-lactamase in Xanthomonas campestris.

Sequencing of the upstream region of the beta-lactamase gene from Xanthomonas campestris pv. campestris 11 (bla(XCC-1)) revealed the cognate ampR1 gene (289 amino acids, 31 kDa). It runs divergently from bla(XCC-1) with a 100-bp intergenic region (IG) containing partially overlapped promoters with structural features typical of the bla-ampR IG. The deduced AmpR1 protein shows significant identity in amino acid sequence and conserved motifs with AmpR proteins of other species, e.g., of Pseudomonas aeruginosa (58.2% amino acid identity). Results of insertional mutation, complementation tests, and beta-lactamase assays suggested that expression of bla(XCC-1) was constitutive and dependent on AmpR1. Four bla genes and two ampR genes are present in the fully sequenced X. campestris pv. campestris ATCC 33913 genome, with XCC3039 and XCC3040 considered the analogues of bla(XCC-1) and ampR1, respectively. An ampR1 homologue was detected by Southern hybridization in the ampicillin-resistant Xanthomonas strains, which appear to express beta-lactamase constitutively. Although the significance remains to be studied, constitutive expression of beta-lactamase by a widespread bacterial genus raises environmental concerns regarding the dissemination of resistance genes.