Analysis of multidrug-resistant determinants of clinically isolated Acinetobacter baumannii CYZ via whole genome sequencing.

Acinetobacter baumannii is a multidrug-resistant coccobacillus responsible for severe nosocomial infectious diseases. This study mainly focuses on investigating the antimicrobial resistance features of a clinically isolated strain (A. baumannii CYZ) using the PacBio Sequel II sequencing platform. The chromosomal size of A. baumannii CYZ is 3,960,760 bp, which contains a total of 3803 genes with a G + C content of 39.06%. Functional analysis performed using the Clusters of Orthologous Groups of Proteins (COGs), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, as well as the Comprehensive Antibiotic Resistance Database (CARD) revealed a complicated set of antimicrobial resistance determinants in the genome of A. baumannii CYZ, which were mainly classified into multidrug efflux pumps and transport systems, ß-lactamase relative and penicillin-binding proteins, aminoglycoside modification enzymes, alternation of antibiotic target sites, lipopolysaccharide relative, and other mechanisms. A total of 35 antibiotics were tested for the antimicrobial susceptibility of A. baumannii CYZ, and the organism exhibited a stronger antimicrobial resistance ability. The phylogenetic relationship indicated that A. baumannii CYZ has high homology with A. baumannii ATCC 17978; however, the former also exhibited its specific genome characteristics. Our research results give insight into the genetic antimicrobial-resistant features of A. baumannii CYZ as well as provide a genetic basis for the further study of the phenotype.

Ferrets: A powerful model of SARS-CoV-2.

The rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent years not only caused a global pandemic but resulted in enormous social, economic, and health burdens worldwide. Despite considerable efforts to combat coronavirus disease 2019 (COVID-19), various SARS-CoV-2 variants have emerged, and their underlying mechanisms of pathogenicity remain largely unknown. Furthermore, effective therapeutic drugs are still under development. Thus, an ideal animal model is crucial for studying the pathogenesis of COVID-19 and for the preclinical evaluation of vaccines and antivirals against SARS-CoV-2 and variant infections. Currently, several animal models, including mice, hamsters, ferrets, and non-human primates (NHPs), have been established to study COVID-19. Among them, ferrets are naturally susceptible to SARS-CoV-2 infection and are considered suitable for COVID-19 study. Here, we summarize recent developments and application of SARS-CoV-2 ferret models in studies on pathogenesis, therapeutic agents, and vaccines, and provide a perspective on the role of these models in preventing COVID-19 spread.

Exploring the Relationship between Ecosystem Services under Different Socio-Economic Driving Degrees.

The large-scale transformation of natural ecosystems to socio-economic development land types under human activities was a primary reason for the decline of regional ecosystem services. It is a key issue for regional ecosystem planning and management to reveal the relationship between ecosystem services of different land use types under different socio-economic driving degrees. However, the current related research was not in-depth. Based on the land use data of Wuhan City in 1980, 1990, 2000, 2010, and 2020, this study classified land use into three categories according to the different degrees of human activities on natural ecosystem development: the land use of a natural ecosystem (LUNE), the land use of a productive ecosystem (LUPE), and the land use of a socio-economic system (LUSE). The InVEST model was used to simulate five ecosystem services (grain yield, water yield, carbon storage, habitat quality, and water purification), and the spatio-temporal distribution and functional transformation of the three land use types were analyzed. Results showed that with the intensified urban expansion in Wuhan, the LUSE types increased to 2.7 times that of the original. However, the natural land types basically maintained a stable area, coupling with the large-scale transformation between the LUPE and LUSE types. Land use change resulted in significant spatial changes of five ecosystem services, especially carbon storage and habitat quality. The correlation analysis indicated that the five kinds of ecosystem services mainly showed a synergistic relationship, meanwhile the LUSE type denoted the most significant correlation with ecosystem services among these three category types. This study indicated that besides the protection of natural ecosystems, the LUSE type would become the key land use type in the planning and management of improving regional ecological function.

Monkeypox virus: a re-emergent threat to humans.

Human monkeypox (MPX) is a rare zoonotic infection characterized by smallpox-like signs and symptoms. It is caused by monkeypox virus (MPXV), a double stranded DNA virus belonging to the genus Orthopoxvirus. MPX was first identified in 1970 and mostly prevailed in the rural rainforests of Central and West Africa in the past. Outside Africa, MPX was reported in the United Kingdom, the USA, Israel, and Singapore. In 2022, the resurgence of MPX in Europe and elsewhere posed a potential threat to humans. MPXV was transmitted by the animals-human or human-human pathway, and the symptoms of MPXV infection are similar to that of smallpox, but in a milder form and with lower mortality (1%-10%). Although the smallpox vaccination has been shown to provide 85% protection against MPXV infection, and two anti-smallpox virus drugs have been approved to treat MPXV, there are still no specific vaccines and drugs against MPXV infection. Therefore it is urgent to take active measures including the adoption of novel anti-MPXV strategies to control the spread of MPXV and prevent MPX epidemic. In this review, we summarize the biological features, epidemiology, pathogenicity, laboratory diagnosis, and prevention and treatment strategies on MPXV. This review provides the basic knowledge for prevention and control of future outbreaks of this emerging infection.

Strong evidence for a weakly oxygenated ocean-atmosphere system during the Proterozoic.

Earth's surface has undergone a protracted oxygenation, which is commonly assumed to have profoundly affected the biosphere. However, basic aspects of this history are still debated-foremost oxygen (O2) levels in the oceans and atmosphere during the billion years leading up to the rise of algae and animals. Here we use isotope ratios of iron (Fe) in ironstones-Fe-rich sedimentary rocks deposited in nearshore marine settings-as a proxy for O2 levels in shallow seawater. We show that partial oxidation of dissolved Fe(II) was characteristic of Proterozoic shallow marine environments, whereas younger ironstones formed via complete oxidation of Fe(II). Regardless of the Fe(II) source, partial Fe(II) oxidation requires low O2 in the shallow oceans, settings crucial to eukaryotic evolution. Low O2 in surface waters can be linked to markedly low atmospheric O2-likely requiring less than 1% of modern levels. Based on our records, these conditions persisted (at least periodically) until a shift toward higher surface O2 levels between ca 900 and 750 Ma, coincident with an apparent rise in eukaryotic ecosystem complexity. This supports the case that a first-order shift in surface O2 levels during this interval may have selected for life modes adapted to more oxygenated habitats.

Hold Breath: Autonomic Neural Regulation of Innate Immunity to Defend Against SARS-CoV-2 Infection.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel member of the genus of betacoronavirus, which caused a pandemic of coronavirus disease 2019 (COVID-19) worldwide. The innate immune system plays a critical role in eliminating the virus, which induces inflammatory cytokine and chemokine secretion, produces different interferons, and activates the adaptive immune system. Interactions between the autonomic nervous system and innate immunity release neurotransmitters or neuropeptides to balance the excess secretion of inflammatory cytokines, control the inflammation, and restore the host homeostasis. However, more neuro-immune mechanisms to defend against viral infection should be elucidated. Here, we mainly review and provide our understanding and viewpoint on the interaction between respiratory viral proteins and host cell receptors, innate immune responses to respiratory viral infection, and the autonomic neural regulation of the innate immune system to control respiratory viruses caused by lungs and airways inflammation.

Characteristic antimicrobial resistance of clinically isolated Stenotrophomonas maltophilia CYZ via complete genome sequence.

OBJECTIVES: Stenotrophomonas maltophilia is an important multidrug-resistant pathogen that is associated with various serious nosocomial infections. In our study, we investigated the antimicrobial resistance traits of clinical S. maltophilia strain CYZ isolated from the sputum of an immunocompromised patient. METHODS: The whole genome sequence of S. maltophilia CYZ was investigated using a PacBio RS II system. The functions of all the predicted genes were annotated by the COG, GO and KEGG databases. Several types of antibiotics were selected to test the antimicrobial susceptibility, and a phylogenetic tree was constructed based on 16S rRNA gene sequence. RESULTS: The genome of S. maltophilia CYZ has a length of 4,517,685 bp and contains 4077 predicted genes, with an average G + C content of 66.65%. Functional genomic analysis via the annotations of the COG and GO databases revealed that the isolate exhibited specific means to resist antibiotics. The annotated genes involved in flagella, pili or fimbriae, biofilm formation, polysaccharide and cyclic di-GMP may contribute to promote the ability of antimicrobial resistance. This strain showed susceptibility to levofloxacin, trimethoprim/sulfamethoxazole and minocycline according to antimicrobial susceptibility testing. The phylogenetic relationship indicated that S. maltophilia CYZ was closely related to S. maltophilia strains isolated from the nosocomial environment. CONCLUSIONS: The current results give a better understanding of the genetic characteristics of antimicrobial resistance in S. maltophilia CYZ and provide a genetic basis for further study of the phenotype.

Selective fiber Bragg grating inscription in four-core fiber for two-dimension vector bending sensing.

The paper presents selective fiber Bragg grating (FBG) inscription in four-core fiber based on a phase mask scanning method. The inscription factors are systematically investigated, which involves fiber core position and focused laser beam size in fiber, etc. Several specific inscriptions (including individual, dual and all inscriptions) are demonstrated. Two orthogonally positioned cores are selectively inscribed and applied to two-dimension vector bending measurement. The measured bending sensitivities of two FBGs range from -54.3 pm/m-1 to 52.2 pm/m-1 and -53.7 pm/m-1 to 52.8 pm/m-1, respectively. More importantly, it has been revealed that their sensitivities versus bending direction follow regular cosinoidal and sinusoidal distribution. The direction and amplitude of the vector bending can be recovered using measured central wavelength shifts of those two FBGs.

Polarization dependent cladding modes coupling and spectral analyses of excessively tilted fiber grating.

We report on the detailed analyses of mode coupling from fiber core to cladding in excessively tilted fiber gratings (ETFGs). Cladding modes responsible for the typical dual peak pairs in the transmission spectrum of ETFGs are identified with phase matching condition, which suggests two set of dual peak pairs generated from coupling to cladding modes with even and odd azimuthal order. The polarization dependence of those dual peak pairs are also investigated by calculating the coupling coefficients of cladding modes for two orthogonal polarizations. With the calculated coupling coefficients, the measured polarization dependent spectra can be reproduced numerically.

Tandem-pumped, tunable thulium-doped fiber laser in 2.1 µm wavelength region.

We present a continuously tunable thulium(Tm)-doped fiber laser operating in the important 2.1 µm region, which is tandem-pumped by another Tm-doped fiber laser at 1908 nm. The advantages of pumping a Tm-doped fiber laser at the long-wavelength absorption tail (>1900 nm) of the fiber include a reduced quantum-defect, and efficient suppression of the amplified spontaneous noise (and potential parasitic lasing) at the short-wavelength region. This facilitates attainment of stable lasing operation in the long-wave emission tail of the Tm fiber at ~2.1 µm. By rotating a diffraction grating inside the Tm fiber laser cavity, we experimentally achieved a wavelength-tuning range of 2000-2172 nm. At central wavelengths of 2050 nm, 2150 nm, and 2172 nm, the slope efficiencies were 23%, 16%, and 9.9%, respectively. To the best of our knowledge, this is the first demonstration of long-wavelength operation of a Tm fiber laser system tandem-pumped at >1900 nm.

An ultra-sensitive aptasensor on optical fibre for the direct detection of bisphenol A.

We present a plasmonic biosensor capable of detecting the presence of bisphenol A in ultra-low concentrations, yielding a wavelength shift of 0.15 ±â€¯0.01 nm in response to a solution of 1 fM concentration with limit of detection of 330 ±â€¯70 aM The biosensing device consists of an array of gold nano-antennae with a total length of 2.3 cm that generate coupled localised surface plasmons (cLSPs) and is covalently modified with an aptamer specific for bisphenol A recognition. The array of nano-antennae is fabricated on a lapped section of standard telecommunication optical fibre, allowing for potential multiplexing and its use in remote sensing applications. These results have been achieved without the use of enhancement techniques and therefore the approach allows the direct detection of bisphenol A, a low molecular weight (228 Da) target usually detectable only by indirect detection strategies. Its detection at such levels is a significant step forward in measuring small molecules at ultra-low concentrations. Furthermore, this new sensing platform paves the way for the development of portable systems for in-situ agricultural measurements capable of retrieving data on a substance of very high concern at ultra-low concentrations.

Legionella feeleii: pneumonia or Pontiac fever? Bacterial virulence traits and host immune response.

Gram-negative bacterium Legionella is able to proliferate intracellularly in mammalian host cells and amoeba, which became known in 1976 since they caused a large outbreak of pneumonia. It had been reported that different strains of Legionella pneumophila, Legionella micdadei, Legionella longbeachae, and Legionella feeleii caused human respiratory diseases, which were known as Pontiac fever or Legionnaires' disease. However, the differences of the virulence traits among the strains of the single species and the pathogenesis of the two diseases that were due to the bacterial virulence factors had not been well elucidated. L. feeleii is an important pathogenic organism in Legionellae, which attracted attention due to cause an outbreak of Pontiac fever in 1981 in Canada. In published researches, it has been found that L. feeleii serogroup 2 (ATCC 35849, LfLD) possess mono-polar flagellum, and L. feeleii serogroup 1 (ATCC 35072, WRLf) could secrete some exopolysaccharide (EPS) materials to the surrounding. Although the virulence of the L. feeleii strain was evidenced that could be promoted, the EPS might be dispensable for the bacteria that caused Pontiac fever. Based on the current knowledge, we focused on bacterial infection in human and murine host cells, intracellular growth, cytopathogenicity, stimulatory capacity of cytokines secretion, and pathogenic effects of the EPS of L. feeleii in this review.

Simultaneous directional curvature and temperature sensor based on a tilted few-mode fiber Bragg grating.

We demonstrate a directional curvature sensor based on tilted few-mode fiber Bragg gratings (FM-FBGs) inscribed by a UV laser. The eigenmodes of LP01 and LP11 mode groups are simulated along with the fiber bending. The directional curvature sensor is based on the LP11 mode resonance in the tilted FM-FBG. For curvature from 4.883 to 7.625 m-1, the curvature sensitivities at direction of 0° and 90° are measured to be -2.67 and 0.128 dB/m-1, respectively. The temperature variation barely affects the resonance depth of LP11 mode. The proposed curvature sensor clearly demonstrates the potential to simultaneous directional curvature and temperature measurement with the resolutions of 9.15×10-4 m-1 and 0.952°C, respectively.

Temperature-calibrated high-precision refractometer using a tilted fiber Bragg grating.

We present a refractometer with main- and vernier-scale to measure the refractive index (RI) of liquids with high precision by using the fine spectrum structure of a tilted fiber Bragg grating (TFBG). The absolute RI values are determined by the accurate wavelength of cut-off mode resonances. The main- and vernier-scale are calibrated by measuring large groups of fine spectra at different cut-off mode resonances in a small RI range, and the use of vernier-scale certainly reduces the RI measurement uncertainty resulted from the discrete cladding mode resonances. The performance of the TFBG-based vernier refractometer is experimentally verified by exploring the temperature dependence of RI of anhydrous ethanol in a near infrared region, showing an enhanced accuracy to the order of 10-4, high repeatability and temperature self-calibration capability.

Multi-channel mode converter based on a modal interferometer in a two-mode fiber.

In this Letter, we propose a multi-channel mode converter with the concept of a modal interferometer in a two-mode fiber (TMF). Two lateral stress points in a TMF function as in-line fiber mode couplers to construct the modal interferometer, and both transmission spectra and near-field patterns confirm that the LP01 mode is successfully converted into an LP11 mode at the multiple channels. The measured mode conversion efficiency almost completely follows the theoretical tendency. Finally, the mode conversion is realized at 20 channels in the C+L wavelength band with conversion efficiency up to 99.5% and insertion loss as low as 0.6 dB. Furthermore, the channel spacing can be freely tailored by adjusting the distance between two stress points.

Small-period long-period fiber grating with improved refractive index sensitivity and dual-parameter sensing ability.

We UV inscribe and characterize a long-period fiber grating with a period of 25 µm. A series of polarization-dependent dual-peak pairs can be seen in the transmission spectrum, even though only the symmetrical refractive index modification is introduced. The fabricated grating exhibits a lower temperature sensitivity compared with standard long-period gratings and an enhanced refractive index sensitivity of ∼312.5 nm/RIU averaged from 1.315 to 1.395, which is more than four-fold higher than standard long-period gratings in this range. The full width at half-maximum of the fabricated grating is only about 0.6 nm, allowing for high-resolution sensing. Moreover, the grating period is so small that the attenuation dip corresponding to a high-order Bragg resonance can also be seen, which can act as a monitor of the unwanted perturbation to realize dual-parameter sensing.

Graphene-induced unique polarization tuning properties of excessively tilted fiber grating.

By exploiting the polarization-sensitive coupling effect of graphene with the optical mode, we investigate the polarization modulation properties of a hybrid waveguide of graphene-integrated excessively tilted fiber grating (Ex-TFG). The theoretical analysis and experimental results demonstrate that the real and imaginary parts of complex refractive index of few-layer graphene exhibit different effects on transverse electric (TE) and transverse magnetic (TM) cladding modes of the Ex-TFG, enabling stronger absorption in the TE mode and more wavelength shift in the TM mode. Furthermore, the surrounding refractive index can modulate the complex optical constant of graphene and then the polarization properties of the hybrid waveguide, such as resonant wavelength and peak intensity. Therefore, the unique polarization tuning property induced by the integration of the graphene layer with Ex-TFG may endow potential applications in all-in-one fiber modulators, fiber lasers, and biochemical sensors.

Theoretical and experimental analysis of excessively tilted fiber gratings.

We have theoretically and experimentally investigated the dual-peak feature of tilted fiber gratings with excessively tilted structure (named as Ex-TFGs). We have explained the dual-peak feature by solving eigenvalue equations for TM0m and TE0m of a circular waveguide, in which the TE (transverse electric) and TM (transverse magnetic) core modes are coupled into TE and TM cladding modes, respectively. Meanwhile, in the experiment, we have verified that one of the dual peaks at the shorter wavelength is due to the TM mode coupling whereas the other one at the longer wavelength arises from TE mode coupling when a linearly polarized light launched into the Ex-TFG. We have also investigated the peak separation of TE and TM cladding mode for different surrounding medium refractive indexes (SRI), revealed that the dual peaks separation is decreasing as increasing of SRI, which agrees very well with the theoretical analysis results.

Colony types and virulence traits of Legionella feeleii determined by exopolysaccharide materials.

Legionella feeleii is a Gram-negative pathogenic bacterium that causes Pontiac fever and pneumonia in humans. When L. feeleii serogroup 1 (ATCC 35072) was cultured on BCYE agar plates, two types of colonies were observed and exhibited differences in color, opacity and morphology. Since the two colony types are white rugose and brown translucent, they were termed as white rugose L. feeleii (WRLf) and brown translucent L. feeleii (BTLf), respectively. They exhibited different growth capacities in BYE broth in vitro, and it was found that WRLf could transform to BTLf. Under the electron microscope, it was observed that WRLf secreted materials which could be stained with ruthenium red, which was absent in BTLf. When U937 macrophages and HeLa cells were infected with the bacteria, WRLf manifested stronger internalization ability than BTLf. Intracellular growth in murine macrophages and Acanthamoeba cells was affected by the level of initial phagocytosis. WRLf was more resistant to human serum bactericidal action than BTLf. After being inoculated to guinea pigs, both organisms caused fever in the animals. These results suggest that ruthenium red-stained materials secreted in the surroundings may play a crucial role in determining L. feeleii colony morphology and virulence traits.

Comparative analysis of virulence traits between a Legionella feeleii strain implicated in Pontiac fever and a strain that caused Legionnaires' disease.

Legionella strains of the same species and serogroup are known to cause Legionnaires' disease (a potentially fatal atypical pneumonia) or Pontiac fever (a mild, flu-like disease), but the bacterial factors that define these dramatic differences in pathology have not been elucidated. To gain a better understanding of these factors, we compared the characteristics of Legionella feeleii strains that were isolated from either a sample of freshwater implicated in an outbreak of Pontiac fever (ATCC 35072, serogroup 1, LfPF), or a patient with Legionnaires' disease (ATCC 38549, serogroup 2, LfLD). Growth of LfPF and LfLD in BYE broth was slower than the positive control, Legionella pneumophila strain JR32. However, LfLD grew faster than LfPF at 42 °C. After in vitro infection to J774 murine or U937 human macrophage cell lines and A549 human lung epithelial cell line, LfLD showed a higher cell infection rate, stronger internalization by host cells, and greater cytotoxicity than that of LfPF. Large amounts of IL-6 and IL-8 were secreted by human host cells after infection with LfLD, but not with LfPF. LfLD possessed mono-polar flagellum while LfPF was unflagellated. When LfLD was cultured at 25, 30 and 37 °C, the bacteria had higher motility rate at lower temperatures. Based on our results, this is the first study that showed distinct characteristics between LfPF and LfLD, which may give important leads in elucidating differences in their virulence.