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The sequencing, assembly, and analysis of bacterial genomes is central to tracking and characterizing foodborne pathogens. The bulk of bacterial genome sequencing at the US Food and Drug Administration is performed using short-read Illumina MiSeq technology, resulting in highly accurate but fragmented genomic sequences. The MinION sequencer from Oxford Nanopore is an evolving technology that produces long-read sequencing data with low equipment cost. The goal of this study was to compare Campylobacter genome assemblies generated from MiSeq and MinION data independently, as well as hybrid genome assemblies combining both data types. Two reference strains and two field isolates of C. jejuni were sequenced using MiSeq and MinION, and the sequence data were assembled using the software programs SPAdes and Canu, respectively. Hybrid genome assembly was performed using the program Unicycler. Comparison of the C. jejuni 81-176 and RM1221 genome assemblies to the PacBio reference genomes revealed that the SPAdes assemblies had the most accurate nucleotide identity, while the hybrid assemblies were the most contiguous. Assemblies generated only from MinION data using Canu were the least accurate, containing many indels and substitutions that affected downstream analyses. The hybrid sequencing approach was the most useful for detecting plasmids, large genome rearrangements, and repetitive elements such as rRNA and tRNA genes. The full genomes of both C. jejuni field isolates were completed and circularized using hybrid sequencing, and a plasmid was detected in one isolate. Continued development of nanopore sequencing technologies will likely enhance the accuracy of hybrid genome assemblies and enable public health laboratories to routinely generate complete circularized bacterial genome sequences. [ABSTRACT FROM AUTHOR]

Editor's Note: this Article has been retracted; the Retraction Note is available at https://doi.org/10.1038/s41598-023-32033-5 [ABSTRACT FROM AUTHOR]

Type 2 C protein phosphatases (PP2Cs) represent the major group of protein phosphatases in plants and play important roles in various plant processes. In this study, 94 MtPP2C genes were identified from Medicago truncatula and further phylogenetically classified into 13 subfamilies, as supported by exon-intron organization and conserved motif composition. Collinearity analysis indicated that segmental duplication events played a crucial role in the expansion of MtPP2C gene families in M. truncatula. Furthermore, the expression profiles of MtPP2Cs under different abiotic treatments were analyzed using qRT-PCR. Results showed that these MtPP2Cs genes displayed different expression patterns in response to drought, cold and ABA stress conditions and some of the key stress responsive MtPP2Cs genes have been identified. Our study presents a comprehensive overview of the PP2C gene family in M. truncatula, which will be useful for further functional characterization of MtPP2Cs in plant drought and cold stress responses. [ABSTRACT FROM AUTHOR]

Soliton propagation direction can be engineered in optical fibers in the presence of high-order effects (HOEs). It is well known that Raman effects can decelerate the soliton. Here we investigate the manipulation of the deceleration or acceleration of soliton emitted from Airy pulse whose spectrum is imposed an initial quadratic phase modulation (QPM) in optical fibers in the absence of HOEs. We show that, under the action of the anomalous second-order dispersion (SOD) and Kerr nonlinearity, Airy pulse with QPM is able to emit soliton with acceleration or deceleration depending on whether the QPM is negative or positive, and at a rate that is determined by the magnitude of QPM. The reason is that the acceleration behaviors of incident Airy pulse is altered depending on whether SOD and QPM have the same or opposite signs. Our study shows the possibility of controlling and manipulating the soliton propagation and interaction in optical fibers without HOEs, by purposely choosing appropriate QPM parameter of an Airy pulse. [ABSTRACT FROM AUTHOR]

First discovered in rural areas of middle-eastern China in 2009, severe fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne zoonosis affecting hundreds of cases reported in China each year. Using the national surveillance data from 2010 to 2013, we conducted this retrospective epidemiological study and risk assessment of SFTS in China. We found that the incidence of SFTS and its epidemic areas are continuing to grow, but the case fatality rate (CFR) has steadily decreased. SFTS most commonly affected elderly farmers who acquired infection between May and July in middle-eastern China. However, other epidemiological characteristics such as incidence, sex ratio, CFR, and seasonality differ substantially across the affected provinces, which seem to be consistent with local agricultural activities and the seasonal abundance of ticks. Spatial scan statistics detected three hot spots of SFTS that accounted for 69.1% of SFTS cases in China. There was a strong association of SFTS incidence with temporal changes in the climate within the clusters. Multivariate modeling identified climate conditions, elevation, forest coverage, cattle density, and the presence of Haemaphysalis longicornis ticks as independent risk factors in the distribution of SFTS, based on which a predicted risk map of the disease was derived. [ABSTRACT FROM AUTHOR]

Au nanoparticles synthesized from colloidal techniques have the capability in many applications such as catalysis and sensing. Au nanoparticles function as both catalyst and highly sensitive SERS probe can be employed for sustainable and green catalytic process. However, capping ligands that are necessary to stabilize nanoparticles during synthesis are negative for catalytic activity. In this work, a simple effective mild thermal treatment to remove capping ligands meanwhile preserving the high SERS sensitivity of Au nanoparticles is reported. We show that under the optimal treatment conditions (250 °C for 2 h), 50 nm Au nanoparticles surfaces are free from any capping molecules. The catalytic activity of treated Au nanoparticles is studied through H2O2 decomposition, which proves that the treatment is favorable for catalytic performance improvement. A reaction intermediate during H2O2 decomposition is observed and identified. [ABSTRACT FROM AUTHOR]

3D optical vortex trapping upon a polystyrene nanoparticle (NP) by a 1D gold dimer array is studied theoretically. The optical force field shows that the trapping mode can be contact or non-contact. For the former, the NP is attracted toward a corresponding dimer. For the latter, it is trapped toward a stagnation point of zero force with a 3D spiral trajectory, revealing optical vortex. Additionally the optical torque causes the NP to transversely spin, even though the system is irradiated by a linearly polarized light. The transverse spin-orbit interaction is manifested from the opposite helicities of the spin and spiral orbit. Along with the growth and decline of optical vortices the trapped NP performs a step-like motion, as the array continuously moves. Our results, in agreement with the previous experiment, identify the role of optical vortex in the near-field trapping of plasmonic nanostructure. [ABSTRACT FROM AUTHOR]

A single slot cavity coupled with two waveguides has been researched in theory and simulation. The results comparison between theory and simulation shows they agree well. It is found that the lateral displacement S plays an important role in transmission properties. Moreover, increasing the width of the slot cavity results in the emergence of new resonant peaks. At the same time, the shift of the resonant peaks have been explained well. The slot cavity with Kerr nonlinear material can act as a dynamically tunable four channel switch and filter. The single slot cavity has the advantages of simple and compact structure, easy fabrication, and the excellent properties are helpful to control light in photonics circuits. [ABSTRACT FROM AUTHOR]

Gastric cancer (GC) is the fourth most common malignant neoplasm and the second leading cause of cancer death. Identification of key molecular signaling pathways involved in gastric carcinogenesis and progression facilitates early GC diagnosis and the development of targeted therapies for advanced GC patients. Emerging evidence has revealed a close correlation between forkhead box (FOX) proteins and cancer development. However, the prognostic significance of forkhead box S1 (FOXS1) in patients with GC and the function of FOXS1 in GC progression remain undefined. In this study, we found that upregulation of FOXS1 was frequently detected in GC tissues and strongly correlated with an aggressive phenotype and poor prognosis. Functional assays confirmed that FOXS1 knockdown suppressed cell proliferation and colony numbers, with induction of cell arrest in the G0/G1 phase of the cell cycle, whereas forced expression of FOXS1 had the opposite effect. Additionally, forced expression of FOXS1 accelerated tumor growth in vivo and increased cell migration and invasion through promoting epithelial–mesenchymal transition (EMT) both in vitro and in vivo. Mechanistically, the core promoter region of FOXS1 was identified at nucleotides −660~ +1, and NFKB1 indirectly bind the motif on FOXS1 promoters and inhibit FOXS1 expression. Gene set enrichment analysis revealed that the FOXS1 gene was most abundantly enriched in the hedgehog signaling pathway and that GLI1 expression was significantly correlated with FOXS1 expression in GC. GLI1 directly bound to the promoter motif of FOXS1 and significantly decreased FOXS1 expression. Finally, we found that miR-125a-5p repressed FOXS1 expression at the translational level by binding to the 3′ untranslated region (UTR) of FOXS1. Together, these results suggest that FOXS1 can promote GC development and could be exploited as a diagnostic and prognostic biomarker for GC. [ABSTRACT FROM AUTHOR]

Conbercept is a recombinant fusion protein with high affinity for all vascular endothelial growth factor isoforms and placental growth factor. The repeated intravitreal injection of conbercept may cause intraocular pressure (IOP) fluctuations and long-term suppression of neurotrophic cytokines, which could lead to retinal nerve fiber layer (RNFL) damage. This retrospective fellow-eye controlled study included 98 eyes of 49 patients. The changes in IOP and RNFL thickness as well as the correlation between RNFL changes and associated factors were evaluated. The IOP value between the baseline and the last follow-up visit in the injection group and the IOP value of the last follow-up visit between the injection and non-injection groups were not significantly different (p = 0.452 and 0.476, respectively). The global average thickness of the RNFL (μm) in the injection group decreased from 108.9 to 106.1; however, the change was not statistically significant (p = 0.118). No significant difference in the average RNFL thickness was observed at the last follow-up visit between the injection and non-injection groups (p = 0.821). The type of disease was the only factor associated with RNFL thickness changes. In conclusion, repeated intravitreal injections with 0.05 mL conbercept revealed an excellent safety profile for RNFL thickness, although short-term IOP changes were observed. [ABSTRACT FROM AUTHOR]

Aegilops tauschii is the D-genome progenitor of hexaploid wheat (Triticum aestivum). It is considered to be an important source of genetic variation for wheat breeding, and its genome is an invaluable reference for wheat genomics. We conducted a genome-wide association study using 7,185 single nucleotide polymorphism (SNP) markers across 322 diverse accessions of Ae. tauschii that were systematically phenotyped for 29 morphological traits in order to identify marker-trait associations and candidate genes, assess genetic diversity, and classify the accessions based on phenotypic data and genotypic comparison. Using the general linear model and mixed linear model, we identified a total of 18 SNPs significantly associated with 10 morphological traits. Systematic search of the flanking sequences of trait-associated SNPs in public databases identified several genes that may be linked to variations in phenotypes. Cluster analysis using phenotypic data grouped accessions into four clusters, while accessions in the same cluster were not from the same Ae. tauschii subspecies or from the same area of origin. This work establishes a fundamental research platform for association studies in Ae. tauschii and also provides useful information for understanding the genetic mechanism of agronomic traits in wheat. [ABSTRACT FROM AUTHOR]

The increasing production and utilization of copper oxide nanoparticles (CuO NPs) result in the releases into the environment. However, the influence of CuO NPs on bacterial denitrification, one of the most important pathways to transform nitrate to dinitrogen in environment, has seldom been studied. Here we reported that CuO NPs caused a significant alteration of key protein expressions of a model denitrifier, Paracoccus denitrificans, leading to severe inhibition to denitrification. Total nitrogen removal efficiency was decreased from 98.3% to 62.1% with the increase of CuO NPs from 0.05 to 0.25 mg/L. Cellular morphology and integrity studies indicated that nanoparticles entered the cells. The proteomic bioinformatics analysis showed that CuO NPs caused regulation of proteins involved in nitrogen metabolism, electron transfer and substance transport. The down-regulation of GtsB protein (responsible for glucose transport) decreased the production of NADH (electron donor for denitrification). Also, the expressions of key electron-transfer proteins (including NADH dehydrogenase and cytochrome) were suppressed by CuO NPs, which adversely affected electrons transfer for denitrification. Further investigation revealed that CuO NPs significantly inhibited the expressions and catalytic activities of nitrate reductase and nitrite reductase. These results provided a fundamental understanding of the negative influences of CuO NPs on bacterial denitrification. [ABSTRACT FROM AUTHOR]

A new approach was established for the regeneration of Trichosanthes kirilowii from root, stem, and leaf explants by somatic embryogenesis (SE), involving a previously unreported SE structure, rhizoid tubers (RTBs). During SE, special rhizoids were first induced from root, stem, and leaf explants with average rhizoid numbers of 62.33, 40.17, and 11.53 per explant, respectively, on Murashige and Skoog (MS) medium (pH 4.0) supplemented with 1.0 mg/L 1-naphthaleneacetic acid (NAA) under dark conditions. Further, one RTB was formed from each of the rhizoids on MS medium (pH 4.0) supplemented with 20 mg/L thidiazuron (TDZ) under light conditions. In the suitable range (pH 4.0-9.0), a lower pH value increased the induction of rhizoids and RTBs. Approximately 37.77, 33.47, and 31.07% of in vivo RTBs from root, stem, and leaf explants, respectively, spontaneously developed into multiple plantlets on the same MS medium (supplemented with 20 mg/L TDZ) for induction of RTBs, whereas >95.00% of in vitro RTBs from each kind of explant developed into multiple plantlets on MS medium supplemented with 5.0 mg/L 6-benzylaminopurine (BAP). Morphological and histological analyses revealed that RTB is a novel type of SE structure that develops from the cortex cells of rhizoids. [ABSTRACT FROM AUTHOR]