PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.

Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.

HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.

MOTIVATION: As prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts' evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which it can replicate and thrive. Understanding host ranges of plasmids sheds light on studying the roles of plasmids in bacterial evolution and adaptation. Metagenomic sequencing has become a major means to obtain new plasmids and derive their hosts. However, host prediction for assembled plasmid contigs still needs to tackle several challenges: different sequence compositions and copy numbers between plasmids and the hosts, high diversity in plasmids, and limited plasmid annotations. Existing tools have not yet achieved an ideal tradeoff between sensitivity and precision on metagenomic assembled contigs. RESULTS: In this work, we construct a hierarchical classification tool named HOTSPOT, whose backbone is a phylogenetic tree of the bacterial hosts from phylum to species. By incorporating the state-of-the-art language model, Transformer, in each node's taxon classifier, the top-down tree search achieves an accurate host taxonomy prediction for the input plasmid contigs. We rigorously tested HOTSPOT on multiple datasets, including RefSeq complete plasmids, artificial contigs, simulated metagenomic data, mock metagenomic data, the Hi-C dataset, and the CAMI2 marine dataset. All experiments show that HOTSPOT outperforms other popular methods. AVAILABILITY AND IMPLEMENTATION: The source code of HOTSPOT is available via: https://github.com/Orin-beep/HOTSPOT.

Tri-primer-enhanced strand exchange amplification combined with rapid lateral flow fluorescence immunoassay to detect SARS-CoV-2.

The novel coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been surging rapidly around the world, which has exposed humanity to unprecedented economic, social and health impacts. To achieve efficient and accurate detection of SARS-CoV-2 on site, we developed and verified a rapid and sensitive fluorescence lateral flow immunoassay based on the innovative enhanced strand exchange amplification (ESEA-LFIA) in this study. With good amplification efficiency for short-sequence targets, ESEA is an ideal choice for the point-of-care testing of SARS-CoV-2 with a high mutation rate. ESEA reaction can be completed in one step and verified by restriction enzyme digestion. The design consisting of three working primers greatly improved the amplification efficiency. Amplification of the target sequences of the RdRP and N genes can be accomplished under the same reaction conditions, and does not require expensive instruments. The sensitivity of the ESEA-LFIA assay targeting the RdRP and N genes was 90 copies per µL and 70 copies per µL, respectively. Specificity tests showed that the novel assay can specifically detect SARS-CoV-2, and had no cross-reactivity with 9 closely-related human pathogenic coronaviruses and other common respiratory pathogens with similar clinical manifestations. The cutoff values of the RdRP and N gene assays are 11 and 12, respectively, and the assays can be completed within 1 h. The novel strategy proposed in this study is a sensitive and specific method for the rapid detection of SARS-CoV-2, and is suitable as an effective potential bioanalytical tool to respond to future regional or global outbreaks of emerging infectious pathogens with high mutation rates.

Lateral flow fluorescent immunoassay based on isothermal amplification for rapid quantitative detection of Salmonella spp.

Salmonella spp. are zoonotic pathogens of substantial public health concern. To enable detection in the field or under instrument-free conditions, we developed a rapid and robust lateral flow fluorescent immunoassay based on strand exchange amplification (SEA-LFIA) for the quantitative detection of Salmonella spp. As far as we know, this work is the first report regarding the use of Bst DNA polymerase-assisted SEA for fluorescence sensing to detect Salmonella spp. The SEA method was further confirmed by enzymatic digestion and Sanger dideoxy sequencing. The specificity of SEA-LFIA assay was verified by 89 Salmonella strains (18 Salmonella reference strains and 71 clinical isolates) and 15 non-Salmonella reference strains (different genera). The sensitivity of SEA-LFIA assay was 6 × 100 CFU mL-1 of Salmonella pure culture or 3 × 104 CFU 25 g-1 of artificially spiked raw chicken meat. Using this assay, it was found that 37 (16%) of the 236 samples collected were positive, which was consistent with the results of conventional PCR. The cutoff value is 15 and SEA-LFIA assay only takes ∼30 min without high equipment and reagent cost. In addition, the proposed strategy can be easily extended by redesigning the corresponding amplification primers to detect target analytes. In conclusion, the optimized SEA-LFIA assay is an efficient and specific method for the detection of Salmonella spp., and can potentially serve as a new on-site diagnostic tool in life sciences.

Antibody-Oriented Strategy and Mechanism for the Preparation of Fluorescent Nanoprobes for Fast and Sensitive Immunodetection.

Nanoprobes have been widely used in biomedical engineering. However, antibodies are generally conjugated onto nanoparticles disorderly, which reduces their antigen recognition ability. The existing antibody orientation approaches are usually complex. Here, we developed and demonstrated a simple antibody-oriented strategy for the lateral flow immunoassay of cardiac troponin I by conjugating antibodies onto polystyrene nanospheres at the optimal pH. The binding amount and orientation of antibodies as well as the detection sensitivity were significantly improved. Although pH regulation is commonly used to optimize antibody conjugation, this paper illustrates the mechanism of its antibody orientation enhancement ability for the first time and reveals the important influences of the density, the charge distribution and hydrophilicity of the antibody, the control of the velocities of physical adsorption and chemical coupling, and other factors on antibody orientation. It is of great significance to understand and regulate antibody conjugation on the surface of micro- or nanospheres to construct high-performance probes for in vitro diagnosis applications.

Polymerase chain reaction combined with fluorescent lateral flow immunoassay based on magnetic purification for rapid detection of canine parvovirus 2.

BACKGROUND: Canine parvovirus 2 (CPV-2) is one of the most common etiological agents that cause severe gastroenteritis in puppies. Early accurate diagnosis is important for infected dogs. In recent years, magnetic separation has become an efficient and useful tool for bioassays. In this study, polymerase chain reaction (PCR) combined with fluorescent lateral flow immunoassay (LFIA) based on magnetic purification assay was developed for the quantitative detection of CPV-2. RESULTS: The optimum working reaction volume and reaction time for LFIA was 100 µL and 2 min, respectively. The PCR-LFIA assay only detected CPV-2, and did not show cross-detection of non-CPV strains. Experiments showed analytical sensitivity of 3 × 101 copies/µL and demonstrated the PCR-LFIA has a diagnostic agreement of 100% with conventional PCR on detection of clinical samples (22.6% positive, 14/62). Cutoff value is 146. The results were further verified by sequencing and BLAST software. The entire process from PCR step only takes ~ 80 min. CONCLUSIONS: This approach provides an attractive platform for rapid and quantitative detection of CPV-2, indicating great promise as a convenient molecular detection tool to facilitate disease outbreak investigations and response timely.

Adaptive response in mouse bone-marrow stromal cells exposed to 900-MHz radiofrequency fields: Gamma-radiation-induced DNA strand breaks and repair.

The aim of this study was to examine whether radiofrequency field (RF) preexposure induced adaptive responses (AR) in mouse bone-marrow stromal cells (BMSC) and the mechanisms underlying the observed findings. Cells were preexposed to 900-MHz radiofrequency fields (RF) at 120 µW/cm(2) power intensity for 4 h/d for 5 d. Some cells were subjected to 1.5 Gy γ-radiation (GR) 4 h following the last RF exposure. The intensity of strand breaks in the DNA was assessed immediately at 4 h. Subsequently, some BMSC were examined at 30, 60, 90, or 120 min utilizing the alkaline comet assay and γ-H2AX foci technique. Data showed no significant differences in number and intensity of strand breaks in DNA between RF-exposed and control cells. A significant increase in number and intensity of DNA strand breaks was noted in cells exposed to GR exposure alone. RF followed by GR exposure significantly decreased number of strand breaks and resulted in faster kinetics of repair of DNA strand breaks compared to GR alone. Thus, data suggest that RF preexposure protected cells from damage induced by GR. Evidence indicates that in RF-mediated AR more rapid repair kinetics occurs under conditions of GR-induced damage, which may be attributed to diminished DNA strand breakage.

Induction of adaptive response in mice exposed to 900MHz radiofrequency fields: application of micronucleus assay.

Adult male ICR mice were pre-exposed to non-ionizing radiofrequency fields (RF), 900MHz at 120µW/cm(2) power density for 4h/day for 7 days (adaptation dose, AD) and then subjected to an acute whole body dose of 3Gy γ-radiation (challenge dose, CD). The classical micronucleus (MN) assay was used to determine the extent of genotoxicity in immature erythrocytes in peripheral blood and bone marrow. The data obtained in mice exposed to AD+CD were compared with those exposed to CD alone. The results indicated that in both tissues, the MN indices were similar in un-exposed controls and those exposed to AD alone while a significantly increased MN frequency was observed in mice exposed to CD alone. Exposure of mice to AD+CD resulted in a significant decrease in MN indices compared to those exposed to CD alone. Thus, the data suggested that pre-exposure of mice to non-ionizing RF is capable of 'protecting' the erythrocytes in the blood and bone marrow from genotoxic effects of subsequent γ-radiation. Such protective phenomenon is generally described as 'adaptive response' (AR) and is well documented in human and animal cells which were pre-exposed to very low doses of ionizing radiation. It is interesting to observe AR being induced by non-ionizing RF.

High-resolution strain-level microbiome composition analysis from short reads.

BACKGROUND: Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities. Metagenomic sequencing has become the major means for probing the microbial composition in host-associated or environmental samples. Although there are a plethora of composition analysis tools, they are not optimized to address the challenges in strain-level analysis: highly similar strain genomes and the presence of multiple strains under one species in a sample. Thus, this work aims to provide a high-resolution and more accurate strain-level analysis tool for short reads. RESULTS: In this work, we present a new strain-level composition analysis tool named StrainScan that employs a novel tree-based k-mers indexing structure to strike a balance between the strain identification accuracy and the computational complexity. We tested StrainScan extensively on a large number of simulated and real sequencing data and benchmarked StrainScan with popular strain-level analysis tools including Krakenuniq, StrainSeeker, Pathoscope2, Sigma, StrainGE, and StrainEst. The results show that StrainScan has higher accuracy and resolution than the state-of-the-art tools on strain-level composition analysis. It improves the F1 score by 20% in identifying multiple strains at the strain level. CONCLUSIONS: By using a novel k-mer indexing structure, StrainScan is able to provide strain-level analysis with higher resolution than existing tools, enabling it to return more informative strain composition analysis in one sample or across multiple samples. StrainScan takes short reads and a set of reference strains as input and its source codes are freely available at https://github.com/liaoherui/StrainScan . Video Abstract.

Rapid quantitative detection of Klebsiella pneumoniae in infants with severe infection disease by point-of-care immunochromatographic technique based on nanofluorescent microspheres.

Background: Klebsiella pneumoniae (KP, K. pneumoniae) is one of the most important nosocomial pathogens that cause severe respiratory infections. As evolutionary high-toxic strains with drug resistance genes increase year by year, the infections caused by it are often accompanied by high mortality, which may be fatal to infants and can cause invasive infections in healthy adults. At present, the traditional clinical methods for detecting K. pneumoniae are cumbersome and time-consuming, and the accuracy and sensitivity are not high. In this study, nanofluorescent microsphere (nFM)-based immunochromatographic test strip (ICTS) quantitative testing platform were developed for point-of-care testing (POCT) method of K. pneumoniae. Methods: 19 clinical samples of infants were collected, the genus-specific gene of mdh was screened from K. pneumoniae. Polymerase chain reaction (PCR) combined with nFM-ICTS based on magnetic purification assay (PCR-ICTS) and strand exchange amplification (SEA) combined with nFM-ICTS based on magnetic purification assay (SEA-ICTS) were developed for the quantitative detection of K. pneumoniae. The sensitivity and specificity of SEA-ICTS and PCR-ICTS were demonstrated by the existing used classical microbiological methods, the real-time fluorescent quantitative PCR (RTFQ-PCR) and PCR assay based on agarose gel electrophoresis (PCR-GE). Results: Under optimum working conditions, the detection limits of PCR-GE, RTFQ-PCR, PCR-ICTS and SEA-ICTS are 7.7 × 10-3, 2.5 × 10-6, 7.7 × 10-6, 2.82 × 10-7 ng/µL, respectively. The SEA-ICTS and PCR-ICTS assays can quickly identify K. pneumoniae, and could specifically distinguish K. pneumoniae samples from non-K. pneumoniae samples. Experiments have shown a diagnostic agreement of 100% between immunochromatographic test strip methods and the traditional clinical methods on the detection of clinical samples. During the purification process, the Silicon coated magnetic nanoparticles (Si-MNPs) were used to removed false positive results effectively from the products, which showed of great screening ability. The SEA-ICTS method was developed based on PCR-ICTS, which is a more rapid (20 min), low-costed method compared with PCR-ICTS assay for the detection of K. pneumoniae in infants. Only need a cheap thermostatic water bath and takes a short detection time, this new method can potentially serve as an efficient point-of-care testing method for on-site detection of pathogens and disease outbreaks without fluorescent polymerase chain reaction instruments and professional technicians operation.

Solving the Water Hypersensitive Challenge of Sulfated Solid Superacid in Acid-Catalyzed Reactions.

In the past decades, water tolerance has always been the long-pending key issue of sulfated solid superacids (SO42-/M xO y) toward industrial applications. Herein, we report a strategy for the facile coating of a thick tunable hydrophobic layer over SO42-/M xO y, which can significantly improve water tolerance, with negligible inhibition on the catalytic performance of SO42-/M xO y. Even after being directly immersed in water, the hydrophobic SO42-/M xO y can still maintain above 90% of original catalytic activity, whereas pristine SO42-/M xO y and control samples are almost completely deactivated. This strategy opens a new route to enhance the water tolerance of sulfated solid superacids.

Adaptive response in mice exposed to 900 MHZ radiofrequency fields: bleomycin-induced DNA and oxidative damage/repair.

PURPOSE: To determine whether mice exposed to radiofrequency fields (RF) and then injected with a radiomimetic drug, bleomycin (BLM), exhibit adaptive response and provide some mechanistic evidence for such response. MATERIALS AND METHODS: Adult mice were exposed to 900 MHz RF at 120 µW/cm(2) power density for 4 hours/day for 7 days. Immediately after the last exposure, some mice were sacrificed while the others were injected with BLM 4 h later. In each animal: (i) The primary DNA damage and BLM-induced damage as well as its repair kinetics were determined in blood leukocytes; and (ii) the oxidative damage was determined from malondialdehyde (MDA) levels and the antioxidant status was assessed from superoxide dismutase (SOD) levels in plasma, liver and lung tissues. RESULTS: There were no indications for increased DNA and oxidative damages in mice exposed to RF alone in contrast to those treated with BLM alone. Mice exposed to RF+ BLM showed significantly: (a) reduced BLM-induced DNA damage and that remained after each 30, 60, 90, 120 and 150 min repair time, and (b) decreased levels of MDA in plasma and liver, and increased SOD level in the lung. CONCLUSIONS: The overall data suggested that RF exposure was capable of inducing adaptive response and mitigated BLM- induced DNA and oxidative damages by activating certain cellular processes.