ARGNet: using deep neural networks for robust identification and classification of antibiotic resistance genes from sequences.

BACKGROUND: Emergence of antibiotic resistance in bacteria is an important threat to global health. Antibiotic resistance genes (ARGs) are some of the key components to define bacterial resistance and their spread in different environments. Identification of ARGs, particularly from high-throughput sequencing data of the specimens, is the state-of-the-art method for comprehensively monitoring their spread and evolution. Current computational methods to identify ARGs mainly rely on alignment-based sequence similarities with known ARGs. Such approaches are limited by choice of reference databases and may potentially miss novel ARGs. The similarity thresholds are usually simple and could not accommodate variations across different gene families and regions. It is also difficult to scale up when sequence data are increasing. RESULTS: In this study, we developed ARGNet, a deep neural network that incorporates an unsupervised learning autoencoder model to identify ARGs and a multiclass classification convolutional neural network to classify ARGs that do not depend on sequence alignment. This approach enables a more efficient discovery of both known and novel ARGs. ARGNet accepts both amino acid and nucleotide sequences of variable lengths, from partial (30-50 aa; 100-150 nt) sequences to full-length protein or genes, allowing its application in both target sequencing and metagenomic sequencing. Our performance evaluation showed that ARGNet outperformed other deep learning models including DeepARG and HMD-ARG in most of the application scenarios especially quasi-negative test and the analysis of prediction consistency with phylogenetic tree. ARGNet has a reduced inference runtime by up to 57% relative to DeepARG. CONCLUSIONS: ARGNet is flexible, efficient, and accurate at predicting a broad range of ARGs from the sequencing data. ARGNet is freely available at https://github.com/id-bioinfo/ARGNet , with an online service provided at https://ARGNet.hku.hk . Video Abstract.

Eco-climate drivers shape virome diversity in a globally invasive tick species.

Spillovers of viruses into human occur more frequently under warmer conditions, particularly arboviruses. The invasive tick species Haemaphysalis longicornis poses a significant public health threat due to its global expansion and its potential to carry a wide range of pathogens. We analyzed meta-transcriptomic data from 3595 adult H. longicornis ticks collected between 2016 and 2019 in 22 provinces across China, encompassing diverse ecological conditions. Generalized additive modelling revealed that climate factors exerted a stronger influence on the virome of H. longicornis compared to other ecological factors, such as ecotypes, distance to coastline, animal host, tick gender, and anti-viral immunity. We investigated the mechanistic understanding of how climate changes drive the tick virome using causality inference and emphasized its significance for public health. Our findings demonstrated that higher temperatures and lower relative humidity/precipitation contribute to variations in animal host diversity, leading to an increased diversity of tick virome, particularly the evenness of vertebrate associated viruses. This finding may explain the evolution of tick-borne viruses into generalists across multiple hosts, thereby increasing the probability of spillover events involving tick-borne pathogens. Deep learning projections indicate that the diversity of H. longicornis virome is expected to increase in 81.9% of regions under the SSP8.5 scenario from 2019-2030. Extension of surveillance should be implemented to avert the spread of tick-borne diseases.

Robust expansion of phylogeny for fast-growing genome sequence data.

Massive sequencing of SARS-CoV-2 genomes has urged novel methods that employ existing phylogenies to add new samples efficiently instead of de novo inference. 'TIPars' was developed for such challenge integrating parsimony analysis with pre-computed ancestral sequences. It took about 21 seconds to insert 100 SARS-CoV-2 genomes into a 100k-taxa reference tree using 1.4 gigabytes. Benchmarking on four datasets, TIPars achieved the highest accuracy for phylogenies of moderately similar sequences. For highly similar and divergent scenarios, fully parsimony-based and likelihood-based phylogenetic placement methods performed the best respectively while TIPars was the second best. TIPars accomplished efficient and accurate expansion of phylogenies of both similar and divergent sequences, which would have broad biological applications beyond SARS-CoV-2. TIPars is accessible from https://tipars.hku.hk/ and source codes are available at https://github.com/id-bioinfo/TIPars.

Supramolecular gels - a panorama of low-molecular-weight gelators from ancient origins to next-generation technologies.

Supramolecular gels, self-assembled from low-molecular-weight gelators (LMWGs), have a long history and a bright future. This review provides an overview of these materials, from their use in lubrication and personal care in the ancient world, through to next-generation technologies. In academic terms, colloid scientists in the 19th and early 20th centuries first understood such gels as being physically assembled as a result of weak interactions, combining a solid-like network having a degree of crystalline order with a highly mobile liquid-like phase. During the 20th century, industrial scientists began using these materials in new applications in the polymer, oil and food industries. The advent of supramolecular chemistry in the late 20th century, with its focus on non-covalent interactions and controlled self-assembly, saw the horizons for these materials shifted significantly beyond their historic rheological applications, expanding their potential. The ability to tune the LMWG chemical structure, manipulate hierarchical assembly, develop multi-component systems, and introduce new types of responsive and interactive behaviour, has been transformative. Furthermore, the dynamics of these materials are increasingly understood, creating metastable gels and transiently-fueled systems. New approaches to shaping and patterning gels are providing a unique opportunity for more sophisticated uses. These supramolecular advances are increasingly underpinning and informing next-generation applications - from drug delivery and regenerative medicine to environmental remediation and sustainable energy. In summary, this article presents a panorama over the field of supramolecular gels, emphasising how both academic and industrial scientists are building on the past, and engaging new fundamental insights and innovative concepts to open up exciting horizons for their future use.

Fabricating Shaped and Patterned Supramolecular Multigelator Objects via Diffusion-Adhesion Gel Assembly.

We report the use of acid-diffusion to assemble core-shell supramolecular gel beads with different low-molecular-weight gelators (LMWGs) in the core and shell. These gel beads grow a shell of dibenzylidenesorbitol-based DBS-COOH onto a core comprising DBS-CONHNH2 and agarose that has been loaded with acetic acid. Diffusion of the acid from the core triggers shell assembly. The presence of DBS-CONHNH2 enables the gel core to be loaded with metal nanoparticles (NPs) as acyl hydrazide reduces metal salts in situ. The pH-responsiveness of DBS-COOH allows responsive assembly of the shell with both temporal and spatial control. By fixing multiple gel beads in a Petri dish, the cores become linked to one another by the assembled DBS-COOH gel shell─a process we describe as diffusion-adhesion assembly. By controlling the geometry of the beads with respect to one another, it is possible to pattern the structures, and using a layer-by-layer approach, 3D objects can be fabricated. If some of the beads are loaded with basic DBS-carboxylate instead of CH3COOH, they act as a "sink" for diffusing protons, preventing DBS-COOH shell assembly in the close proximity. Those beads do not adhere to the remainder of the growing gel object and can be simply removed once diffusion-assembly is complete, acting as templates, and enabling the fabrication of 3D "imprinted" multigel architectures. Preloading the gel beads with AuNPs or AgNPs suspends these functional units within the cores at precisely defined locations within a wider gel object. In summary, this approach enables the dynamic fabrication of shaped and patterned gels with embedded metal NPs─such objects have potential next-generation applications in areas including soft nanoelectronics and regenerative medicine.

Characterization of an Emergent Chicken H3N8 Influenza Virus in Southern China: a Potential Threat to Public Health.

Although influenza A viruses of several subtypes have occasionally infected humans, to date only those of the H1, H2, and H3 subtypes have led to pandemics and become established in humans. The detection of two human infections by avian H3N8 viruses in April and May of 2022 raised pandemic concerns. Recent studies have shown the H3N8 viruses were introduced into humans from poultry, although their genesis, prevalence, and transmissibility in mammals have not been fully elucidated. Findings generated from our systematic influenza surveillance showed that this H3N8 influenza virus was first detected in chickens in July 2021 and then disseminated and became established in chickens over wider regions of China. Phylogenetic analyses revealed that the H3 HA and N8 NA were derived from avian viruses prevalent in domestic ducks in the Guangxi-Guangdong region, while all internal genes were from enzootic poultry H9N2 viruses. The novel H3N8 viruses form independent lineages in the glycoprotein gene trees, but their internal genes are mixed with those of H9N2 viruses, indicating continuous gene exchange among these viruses. Experimental infection of ferrets with three chicken H3N8 viruses showed transmission through direct contact and inefficient transmission by airborne exposure. Examination of contemporary human sera detected only very limited antibody cross-reaction to these viruses. The continuing evolution of these viruses in poultry could pose an ongoing pandemic threat. IMPORTANCE A novel H3N8 virus with demonstrated zoonotic potential has emerged and disseminated in chickens in China. It was generated by reassortment between avian H3 and N8 virus(es) and long-term enzootic H9N2 viruses present in southern China. This H3N8 virus has maintained independent H3 and N8 gene lineages but continues to exchange internal genes with other H9N2 viruses to form novel variants. Our experimental studies showed that these H3N8 viruses were transmissible in ferrets, and serological data suggest that the human population lacks effective immunological protection against it. With its wide geographical distribution and continuing evolution in chickens, other spillovers to humans can be expected and might lead to more efficient transmission in humans.

Probing the Gelation Synergies and Anti-Escherichia coli Activity of Fmoc-Phenylalanine/Graphene Oxide Hybrid Hydrogel.

The N-fluorenyl-9-methyloxycarbonyl (Fmoc)-protected amino acids have shown high antimicrobial application potential, among which the phenylalanine derivative (Fmoc-F) is the most well-known representative. However, the activity spectrum of Fmoc-F is restricted to Gram-positive bacteria only. The demand for efficient antimicrobial materials expanded research into graphene and its derivatives, although the reported results are somewhat controversial. Herein, we combined graphene oxide (GO) flakes with Fmoc-F amino acid to form Fmoc-F/GO hybrid hydrogel for the first time. We studied the synergistic effect of each component on gelation and assessed the material's bactericidal activity on Gram-negative Escherichia coli (E. coli). GO flakes do not affect Fmoc-F self-assembly per se but modulate the elasticity of the gel and speed up its formation. The hybrid hydrogel affects E. coli survival, initially causing abrupt bacterial death followed by the recovery of the surviving ones due to the inoculum effect (IE). The combination of graphene with amino acids is a step forward in developing antimicrobial gels due to their easy preparation, chemical modification, graphene functionalization, cost-effectiveness, and physicochemical/biological synergy of each component.

Reconstruction of soft noncontractile tissue in the derived therizinosaur Nothronychus: The interplay of soft tissue and stress on hindlimb ossification and posture.

Nothronychus graffami was a large therizinosaur from the Upper Cretaceous of North America. Much of the skeleton is well-preserved and relatively undistorted. The synovial capsule, extracapsular, and intracapsular tendons are reconstructed in N. graffami using existing scars and comparison with the hips of extant theropods and models of extinct theropods. The iliofemoral, pubofemoral, and ischiofemoral ligaments are all modeled. Soft tissue, especially the ischiofemoral and pubofemoral ligaments reduced possible protraction/retraction of the femur at the hip while stabilizing the joint. Therefore, most hindlimb movements took place at the knee. Weight-bearing function in Nothronychus was transferred from the supra-acetabular crest to the pubic peduncle and associated labrum at rest. The femur possessed an intermediately angled neck, convergent with titanosaurs. Therefore, some lateral abduction is proposed, requiring a well-developed meniscus at the knee. Such a posture would result in considerable mediolateral stress along the femoral shaft, resulting in increased transverse ossification. The femur is considered somewhat abducted from the midline, especially when maximally pronated, as the preacetabular ala is more extensive than the post-acetabular ala. This trait would probably result in a laterally divergent femur, as in many birds, resulting in a broad-gauge trackway with wider separation between left and right footprints than observed in many theropod trackways. Limb ratios and ossification patterns suggest a slow, waddling gait. A standard digitiform pose is reconstructed as is common for theropods, but a plantigrade stance cannot be firmly rejected.

Mechanically Robust Hybrid Gel Beads Loaded with "Naked" Palladium Nanoparticles as Efficient, Reusable, and Sustainable Catalysts for the Suzuki-Miyaura Reaction.

The increase in demand for Pd and its low abundance pose a significant threat to its future availability, rendering research into more sustainable Pd-based technologies essential. Herein, we report Pd scavenging mechanically robust hybrid gel beads composed of agarose, a polymer gelator (PG), and an active low-molecular-weight gelator (LMWG) based on 1,3:2,4-dibenzylidenesorbitol (DBS), DBS-CONHNH 2 . The robustness of the PG and the ability of the LMWG to reduce Pd(II) in situ to generate naked Pd(0) nanoparticles (PdNPs) combine within these gel beads to give them potential as practical catalysts for Suzuki-Miyaura cross-coupling reactions. The optimized gel beads demonstrate good reusability, green metrics, and most importantly the ability to sustain stirring, improving reaction times and energy consumption compared to previous examples. In contrast to previous reports, the leaching of palladium from these next-generation beads is almost completely eliminated. Additionally, for the first time, a detailed investigation of these Pd-loaded gel beads explains precisely how the nanoparticles are formed in situ without a stabilizing ligand. Further, detailed catalytic investigations demonstrate that catalysis occurs within the gel beads. Hence, these beads can essentially be considered as robust "nonligated" heterogeneous PdNP catalysts. Given the challenges in developing ligand-free, naked Pd nanoparticles as stable catalysts, these gel beads may have future potential for the development of easily used systems to perform chemical reactions in "kit" form.

Organogel delivery vehicles for the stabilization of organolithium reagents.

Organolithium reagents are a vital tool in modern organic chemistry, enabling the synthesis of carbon-carbon bonds. However, due to their high reactivity, low temperatures, inert atmospheres and strictly dried solvents are usually necessary for their use. Here we report an encapsulating method for the stabilization of sensitive organolithium reagents-PhLi, n-BuLi and s-BuLi-in a low-cost hexatriacontane (C36H74) organogel. The use of this technology is showcased in nucleophilic addition reactions under ambient conditions, low-temperature bromine-lithium exchange, ortho-lithiation and C-H functionalization. The gel substantially enhances organolithium stability, allows simple storage, handling and delivery, and enables reproducible reagent portioning. The use of gels as easily divided delivery vehicles for hazardous organometallics has the potential to transform this area of synthetic chemistry, making these powerful reactions safer and more accessible to non-specialist researchers, and enabling the more widespread use of these common synthetic methods.

Wet-spinning multi-component low-molecular-weight gelators to print synergistic soft materials.

Two different low-molecular-weight gelators (LMWGs) have been 3D-printed as filaments by wet-spininng. When the two LMWGs are simultaneously wet-spun, the co-assembled hybrid gel filaments combine the individual properties of the two gelators (dynamic pH response and in-situ metal nanoparticle formation) in synergistic ways, creating gel objects with new properties.

Shaping and Patterning Supramolecular Materials─Stem Cell-Compatible Dual-Network Hybrid Gels Loaded with Silver Nanoparticles.

Hydrogels with spatio-temporally controlled properties are appealing materials for biological and pharmaceutical applications. We make use of mild acidification protocols to fabricate hybrid gels using calcium alginate in the presence of a preformed thermally triggered gel based on a low-molecular-weight gelator (LMWG) 1,3:2:4-di(4-acylhydrazide)-benzylidene sorbitol (DBS-CONHNH2). Nonwater-soluble calcium carbonate slowly releases calcium ions over time when exposed to an acidic pH, triggering the assembly of the calcium alginate gel network. We combined the gelators in different ways: (i) the LMWG was used as a template to spatially control slow calcium alginate gelation within preformed gel beads, using glucono-δ-lactone (GdL) to lower the pH; (ii) the LMWG was used as a template to spatially control slow calcium alginate gelation within preformed gel trays, using diphenyliodonium nitrate (DPIN) as a photoacid to lower the pH, and spatial resolution was achieved by masking. The dual-network hybrid gels display highly tunable properties, and the beads are compatible with stem cell growth. Furthermore, they preserve the LMWG function of inducing in situ silver nanoparticle (AgNP) formation, which provides the gels with antibacterial activity. These gels have potential for eventual regenerative medicine applications in (e.g.) bone tissue engineering.

Self-assembled gel tubes, filaments and 3D-printing with in situ metal nanoparticle formation and enhanced stem cell growth.

This paper reports simple strategies to fabricate self-assembled artificial tubular and filamentous systems from a low molecular weight gelator (LMWG). In the first strategy, tubular 'core-shell' gel structures based on the dibenzylidenesorbitol-based LMWG DBS-CONHNH2 were made in combination with the polymer gelator (PG) calcium alginate. In the second approach, gel filaments based on DBS-CONHNH2 alone were prepared by wet spinning at elevated concentrations using a 'solvent-switch' approach. The higher concentrations used in wet-spinning prevent the need for a supporting PG. Furthermore, this can be extended into a 3D-printing method, with the printed LMWG objects showing excellent stability for at least a week in water. The LMWG retains its unique ability for in situ precious metal reduction, yielding Au nanoparticles (AuNPs) within the tubes and filaments when they are exposed to AuCl3 solutions. Since the gel filaments have a higher loading of DBS-CONHNH2, they can be loaded with significantly more AuNPs. Cytotoxicity and viability studies on human mesenchymal stem cells show that the DBS-CONHNH2 and DBS-CONHNH2/alginate hybrid gels loaded with AuNPs are biocompatible, with the presence of AuNPs enhancing stem cell metabolism. Taken together, these results indicate that DBS-CONHNH2 can be shaped and 3D-printed, and has considerable potential for use in tissue engineering applications.

Chirality-directed hydrogel assembly and interactions with enantiomers of an active pharmaceutical ingredient.

Enantiomers of the low-molecular-weight gelator (LMWG) DBS-CONHNH2, based on D- or L- 1,3 : 2,4-dibenzylidenesorbitol (DBS), were synthesised. Enantiomeric gels are equivalent, but when mixtures of enantiomers are used, although gels still form, they are weaker than homochiral gels. Nanoscale chirality is lost on adding even a small proportion of the opposite enantiomer - homochiral assembly underpins effective gelation. Enantiomeric gels encapsulate the two enantiomers of anti-inflammatory drug naproxen, with thermal & mechanical differences between diastereomeric systems. We hence demonstrate the importance of chirality in DBS assembly and its interactions with chiral additives.

Double diffusion for the programmable spatiotemporal patterning of multi-domain supramolecular gels.

To achieve spatial resolution of a multi-component gel, a double diffusion approach is used which enables the precise programming of self-assembled patterned domains with well-defined shapes and sizes. The low-molecular-weight gelators (LMWGs) used in this study are pH-responsive DBS-CO2H and thermally-responsive DBS-CONHNH2 (both based on 1,3:2,4-dibenzylidenesorbitol, DBS). A DBS-CONHNH2 gel was initially assembled in a tray, and then loaded at carefully-selected positions with either basified DBS-CO2H (i.e. DBS-carboxylate) or an acid. These soluble components subsequently diffuse through the pre-formed gel matrix, and in the domains when/where they mix, protonation of the DBS-carboxylate induces self-assembly of the DBS-CO2H network, leading to a patterned gel-in-gel object with well-defined shape and dimensions. Using a strong acid achieves fast gelation kinetics, creating smaller, better-defined macroscale objects but with less nanoscale order. Using a weak acid source with slow kinetics, gives slightly larger objects, but on the nanoscale the DBS-CO2H network formation is better controlled, giving more homogeneous nanoscale structures and stiffer objects. The patterned objects can be further reinforced by the presence of agarose polymer gelator. The shape of the patterning is programmed by both the shape of the central reservoir and the starting geometry in which the reservoirs are organised, with the balance between factors depending on assembly kinetics, as dictated by the choice of acid. This simple methodology therefore enables programming of patterned gels with spatiotemporal control and emergent patterning characteristics.

Triggering a transient organo-gelation system in a chemically active solvent.

A transient organo-gelation system with spatiotemporal dynamic properties is described. Here, the solvent actively controls a complex set of equilibria that underpin the dynamic assembly event. The observed metastability is due to the in situ formation of a secondary solvent, acting as an antagonist against the primary solvent of the organogel.

Hybrid Self-Assembled Gel Beads for Tuneable pH-Controlled Rosuvastatin Delivery.

This article describes the fabrication of new pH-responsive hybrid gel beads combining the polymer gelator calcium alginate with two different low-molecular-weight gelators (LMWGs) based on 1,3 : 2,4-dibenzylidene-d-sorbitol: pH-responsive DBS-COOH and thermally responsive DBS-CONHNH2 , thus clearly demonstrating that different classes of LMWG can be fabricated into gel beads by using this approach. We also demonstrate that self-assembled multicomponent gel beads can be formed by using different combinations of these gelators. The different gel bead formulations exhibit different responsiveness - the DBS-COOH network can disassemble within those beads in which it is present upon raising the pH. To exemplify preliminary data for a potential application for these hybrid gel beads, we explored aspects of the delivery of the lipid-lowering active pharmaceutical ingredient (API) rosuvastatin. The release profile of this statin from the hybrid gel beads is pH-dependent, with greater release at pH 7.4 than at pH 4.0 - primary control of this process results from the pKa of the API. The extent of pH-mediated API release is also significantly further modified according to gel bead composition. The DBS-COOH/alginate beads show rapid, highly effective drug release at pH 7.4, whereas the three-component DBS-COOH/DBS-CONHNH2 /alginate system shows controlled slow release of the API under the same conditions. These initial results indicate that such gel beads constitute a promising, versatile and easily tuned platform suitable for further development for controlled drug-delivery applications.