An Intensity-Demodulated Fiber-Optic Magnetometer Based on Nanostructured Magnetic Fluid-Filled Fluidic Photonic Crystal Fibers.

An intensity-demodulated fiber-optic magnetometer is proposed and experimentally investigated, which is fabricated via fusion splicing a segment of photonic crystal fiber (PCF) between single-mode fibers (SMFs), with the cladding air holes of PCF filled with magnetic fluid. Using the magneto-optical properties of the magnetic fluid, the transmission spectrum is changed with an external magnetic field. Based on the intensity variations in the transmission spectrum, the magnetic field is detected, and a sensitivity of 0.238 dB/mT is obtained at 1550.03 nm with the length of PCF 5.5 cm. By converting light signals into electrical signals, a sensitivity of 0.003 V/mT is achieved. The fiber-optic magnetometer possesses the advantages of simple fabrication, compact/robust structure, and low cost.

2D-Vector Magnetic Sensing Based on Ring-Shaped Fiber-Optic Structure Coated with Magnetic Fluid.

In this work, a novel fiber-optic sensor for 2D magnetic sensing is explored based on nanostructured magnetic fluid. The fiber-optic sensor comprises a ring-shaped fiber structure that is coated with magnetic fluid. The unique magneto-optical characteristic of the nanostructured magnetic fluid enables the fiber-optic structure to detect magnetic fields. By utilizing the 3D Monte Carlo method, the magneto-optical characteristic induced by the nanostructure changes in the magnetic fluid was analyzed. The sensor can realize 2D vector magnetic sensing by intensity demodulation and achieves a sensitivity of 2.402 dB/mT. The proposed fiber optic sensor helps in developing a high-sensitivity 2D vector magnetic field sensor, which has potential applications in the fields of navigation, electrical power systems, and biological detection.

Efficient fluorescence coupling microlens integrated fiber magnetometer probe based on nitrogen vacancy centers.

The nitrogen vacancy (NV) centers in diamonds have gathered increasing interest as an emerging quantum sensing platform with high sensitivity and spatial resolution. Integration of micro-sized diamond and fiber is an essential method to build an NV center endoscope probe and enable NV center sensors for practical application. However, the low fluorescence collection efficiency of fibers due to their small numerical aperture (NA) has limited the sensitivity of the sensors. In this paper, a cone-shape microlens was fabricated using the photopolymerization process at the end of a multimode fiber to boost the laser excitation and fluorescence collection efficiency of NV centers. Experiments demonstrated that over 21 times fluorescence intensity enhancement and 12 times sensitivity improvement were achieved. This fiber-microlens magnetometer probe exhibited a 2.1-nT/Hz1/2 sensitivity over a bandwidth of 100 Hz with ∼80-µm diameter diamond. This research presented a robust and large NA diamond integrated fiber-microlens magnetometer probe, which can also be expanded to magnetic field scan and real-time monitoring.

Construction of a one-step multiplex real-time PCR assay for the detection of serogroups A, B, and E of Pasteurella multocida associated with bovine pasteurellosis.

Bovine pasteurellosis, caused by serogroups A, B, and E of Pasteurella multocida (Pm), is mainly manifested as bovine respiratory disease (BRD) and hemorrhagic septicemia (HS). The disease has caused a great economic loss for the cattle industry globally. Therefore, identifying the Pm serogroups is critical for optimal diagnosis and subsequent clinical treatment and even epidemiological studies. In this study, a one-step multiplex real-time PCR assay was established. Three pairs of specific primers were prepared to detect the highly conserved genomic regions of serogroups A (HyaD), B (bcbD), and E (ecbJ) of Pm, respectively. The results depicted that the method had no cross-reaction with other bovine pathogens (Mannheimia hemolytica, Escherichia coli, Listeria monocytogenes, Staphylococcus aureus, Salmonella Dublin, Mycobacterium paratuberculosis, infectious bovine rhinotracheitis virus, and Mycoplasma bovis). The linear range (107 to 102 copies/µL) showed the R2 values for serogroups A, B, and E of Pm as 0.9975, 0.9964, and 0.996, respectively. The multiplex real-time PCR efficiency was 90.30%, 90.72%, and 90.57% for CartA, CartB, and CartE, respectively. The sensitivity result showed that the serogroups A, B, and E of Pm could be detected to be as low as 10 copies/µL. The repeatability result clarified that an intra-assay and an inter-assay coefficient of variation of serogroups A, B, and E of Pm was < 2%. For the clinical samples, the detection rate was higher than the OIE-recommended ordinary PCR. Overall, the established one-step multiplex real-time PCR assay may be a valuable tool for the rapid and early detection of the serogroups A, B, and E of Pm with high specificity and sensitivity.

All Fiber Vector Magnetometer Based on Nitrogen-Vacancy Center.

Magnetometers based on nitrogen-vacancy (NV) centers in diamonds have promising applications in fields of living systems biology, condensed matter physics, and industry. This paper proposes a portable and flexible all-fiber NV center vector magnetometer by using fibers to substitute all conventional spatial optical elements, realizing laser excitation and fluorescence collection of micro-diamond with multi-mode fibers simultaneously and efficiently. An optical model is established to investigate multi-mode fiber interrogation of micro-diamond to estimate the optical performance of NV center system. A new analysis method is proposed to extract the magnitude and direction of the magnetic field, combining the morphology of the micro-diamond, thus realizing µm-scale vector magnetic field detection at the tip of the fiber probe. Experimental testing shows our fabricated magnetometer has a sensitivity of 0.73 nT/Hz1/2, demonstrating its feasibility and performance in comparison with conventional confocal NV center magnetometers. This research presents a robust and compact magnetic endoscopy and remote-magnetic measurement approach, which will substantially promote the practical application of magnetometers based on NV centers.

The Pseudogene BMEA_B0173 Deficiency in Brucella melitensis Contributes to M-epitope Formation and Potentiates Virulence in a Mice Infection Model.

It is widely acknowledged that pseudogenes play important roles in bacterial diversification and evolution and participate in gene regulation and RNA interference (RNAi). However, the function of most pseudogenes in Brucella spp remains poorly understood, warranting further studies.To comprehensively analyze the function of the pseudogenes BMEA_B0173 in Brucella melitensis strain 63/9, a BMEA_B0173 in-frame deleted mutant strain was constructed. Then, the phenotypes of the mutant strain, such as growth characteristics and bacterial virulence, were assessed in mice infection models. Finally, iTRAQ analysis was performed to investigate the gene expression profile affected by the pseudogenes BMEA_B0173. In this study, we found that BMEA_B0173 deletion exhibited increased agglutination with M monospecific sera. In a mouse model of chronic infection, the BMEA_B0173 deletion strain displayed increased colonization in the spleen compared to the wild-type pathogen. The iTRAQ assay revealed that 252 proteins were differentially expressed between the BMEA_B0173 deletion and the wild-type strains. In addition, deletion of BMEA_B0173 significantly increased the expression of proteins involved in the denitrification pathway, iron metabolism, and several transcriptional regulators, which might cause increased virulence of the mutant strain. In conclusion, this study preliminary uncovered the function of the pseudogene BMEA_B0173 in Brucella melitensis 63/9 and provided novel insights for studying the pathogenesis of Brucella strains.

Simultaneous Measurement of Temperature and Refractive Index Using Michelson Interferometer Based on Waist-Enlarged Fiber Bitaper.

An all-fiber temperature and refractive dual-parameter-sensing Michelson interferometer is designed based on the waist-enlarged bitaper. At 5 mm from the fiber end, the waist-enlarged bitaper is manually spliced and the probe is formed. Since the input light encounters the waist-enlarged bitaper, it will excite high-order modes to transmit in the fiber cladding, and there will be an optical path difference between the basic mode and the higher-order mode. The light transmitted in the core and cladding is reflected upon encountering the fiber end face and the interference occurs due to the optical path difference between basic mode and higher-order mode. Changes in temperature and refractive index at the fiber probe can be detected by monitoring the interference fringes. The refractive response sensitivity is -191.06 dBm/RIU from 1.351 RIU to 1.4027 RIU, and the temperature response sensitivity is 0.12 nm/°C from 11 °C to 98 °C. Through the sensitivity matrix equation, the superimposed refractive index and temperature signals can be effectively demodulated. The sensor has the advantages of multi-parameter measurement, compact structure, low cost, easy fabrication and high reliability.

Research on the High Temperature and High Pressure Gold-Plated Fiber Grating Dual-Parameter Sensing Measurement System.

In electrohydrostatic drive actuators, there is a demand for temperature and pressure monitoring in complex environments. Fiber Bragg grating (FBG) has become a promising sensor for measuring temperature and pressure. However, there is a cross-sensitivity between temperature and pressure. A gold-plated FBG is proposed and manufactured, and an FBG is used as a reference grating to form a parallel all-fiber sensing system, which can realize the simultaneous measurement of pressure and temperature. Based on the simulation software, the mechanical distribution of the pressure diaphragm is analyzed, and the fixation scheme of the sensor is determined. Using the demodulator to monitor the changes in the reflectance spectrum in real-time, the pressure and ambient temperature applied to the sensor are measured. The experimental results show that the temperature sensitivity of gold-plated FBG is 3 times that of quartz FBG, which can effectively distinguish the temperature changes. The pressure response sensitivity of gold-plated FBG is 0.3 nm/MPa, which is same as the quartz FBG. Through the sensitivity matrix equation, the temperature and pressure dual-parameter sensing measurement is realized. The accuracy of the temperature and pressure measurement is 97.7% and 99.0%, and the corresponding response rates are 2.7 ms/°C and 2 ms/MPa, respectively. The sensor has a simple structure and high sensitivity, and it is promising to be applied in health monitoring in complex environments with a high temperature and high pressure.

Deletion of the Transcriptional Regulator MucR in Brucella canis Affects Stress Responses and Bacterial Virulence.

The transcriptional regulator MucR is related to normal growth, stress responses and Brucella virulence, and affects the expression of various virulence-related genes in smooth-type Brucella strains. However, the function of MucR in the rough-type Brucella canis remains unknown. In this study, we discovered that MucR protein was involved in resistance to heat stress, iron-limitation, and various antibiotics in B. canis. In addition, the expression level of various bacterial flagellum-related genes was altered in mucR mutant strain. Deletion of this transcriptional regulator in B. canis significantly affected Brucella virulence in RAW264.7 macrophage and mice infection model. To gain insight into the genetic basis for distinctive phenotypic properties exhibited by mucR mutant strain, RNA-seq was performed and the result showed that various genes involved in translation, ribosomal structure and biogenesis, signal transduction mechanisms, energy production, and conversion were significantly differently expressed in ΔmucR strain. Overall, these studies have not only discovered the phenotype of mucR mutant strain but also preliminarily uncovered the molecular mechanism between the transcriptional regulator MucR, stress response and bacterial virulence in B. canis.

Safety and Transcriptome Analysis of Live Attenuated Brucella Vaccine Strain S2 on Non-pregnant Cynomolgus Monkeys Without Abortive Effect on Pregnant Cynomolgus Monkeys.

Brucellosis, caused by Brucella spp., is an important zoonotic disease leading to enormous economic losses in livestock, posing a great threat to public health worldwide. The live attenuated Brucella suis (B. suis) strain S2, a safe and effective vaccine, is widely used in animals in China. However, S2 vaccination in animals may raise debates and concerns in terms of safety to primates, particularly humans. In this study, we used cynomolgus monkey as an animal model to evaluate the safety of the S2 vaccine strain on primates. In addition, we performed transcriptome analysis to determine gene expression profiling on cynomolgus monkeys immunized with the S2 vaccine. Our results suggested that the S2 vaccine was safe for cynomolgus monkeys. The transcriptome analysis identified 663 differentially expressed genes (DEGs), of which 348 were significantly upregulated and 315 were remarkably downregulated. The Gene Ontology (GO) classification and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these DEGs were involved in various biological processes (BPs), including the chemokine signaling pathway, actin cytoskeleton regulation, the defense response, immune system processing, and the type-I interferon signaling pathway. The molecular functions of the DEGs were mainly comprised of 2'-5'-oligoadenylate synthetase activity, double-stranded RNA binding, and actin-binding. Moreover, the cellular components of these DEGs included integrin complex, myosin II complex, and blood microparticle. Our findings alleviate the concerns over the safety of the S2 vaccine on primates and provide a genetic basis for the response from a mammalian host following vaccination with the S2 vaccine.

A Novel Micro-Displacement Sensor Based on Double Optical Fiber Probes Made through Photopolymer Materials.

In this paper, a novel micro-displacement sensor with double optical fiber probes is proposed and designed, which can realize the highly sensitive sensing of longitudinal or lateral micro-displacements. The optical fiber probes are made through photopolymer formulation, and the effects of reaction time and optical power on the growth length of the probe are illustrated. The relationship between light intensity and longitudinal micro-displacement is a power function in the range of 0-100 µm at room temperature with a correlation coefficient of 98.92%. For lateral micro-displacement, the sensitivity is -2.9697 dBm/µm in the range of 0-6 µm with a linear fit of 99.61%. In addition, the linear correlation coefficient decreases as the initial longitudinal distance increases, and the function of these correlation coefficients is also linear with a linearity of 96.14%. This sensor has a simple manufacturing process, low cost, high sensitivity, and fast response speed. It is suitable for harsh environments such as strong electromagnetic interference and corrosivity, and has a broad application prospect in the field of micro-displacement sensing.

Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens.

Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C. perfringens isolates with isolation time spanning an 80-year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of C. perfringens dates back to ~80 000 years ago. We showed that the pangenome of the 173 C. perfringens strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that C. perfringens had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of C. perfringens genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in C. perfringens isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that C. perfringens shared its 11 ARGs with 55 different bacterial species, and a high frequency of ARG transfer may have occurred between C. perfringens and species in the genera Streptococcus and Staphylococcus. Correlation analysis showed that the ARG number in C. perfringens strains increased with time, while the virulence gene number was relative stable. Our results, taken together with previous studies, revealed the high genome openness and genetic diversity of C. perfringens and provide a comprehensive view of the phylogeny, genomic features, virulence gene and ARG profiles of worldwide strains.

First identification of a Brucella abortus biovar 4 strain from yak in Tibet, China.

Brucellosis is one of the major zoonotic diseases in the world. In China, understanding on its causative agent Brucella is still limited. Recently, we isolated a Brucella strain XZ19-1 from yak in Lhasa, Tibet. Phenotypical characterization proved that it belongs to B. abortus biovar 4, a biotype that has never been reported in China. MLVA-16 genotyping revealed a novel profile (4-5-3-12-2-2-3-3-8-32-8-5-4-3-3-3) in this strain, while MLST sequence typing demonstrated that it belongs to ST 71. Furthermore, the whole genome of XZ19-1 strain was sequenced. Subsequent phylogenetic analysis demonstrated that XZ19-1was genetically more closely related to B. abortus strains originated from European countries rather than to those collected from China previously. Isolation and identification of XZ19-1 strain may thus indicate a unique Brucella lineage existing in Qing-Tibet plateau. These findings will help to improve the diagnosis and epidemiological studies of brucellosis in animals and human in this part of China.

Potential Diagnostic Value of the Peripheral Blood Mononuclear Cell Transcriptome From Cattle With Bovine Tuberculosis.

Bovine tuberculosis (bTB) is a chronic disease of cattle caused by Mycobacterium bovis. During early-stage infection, M. bovis-infected cattle shed mycobacteria through nasal secretions, which can be detected via nested-polymerase chain reaction (PCR) experiments. Little research has focused on immune responses in nested PCR-positive (bTB PCR-P) or nested PCR-negative (bTB PCR-N) M. bovis-infected cattle. Here, we investigated the transcriptomes of peripheral blood mononuclear cells (PBMCs), with or without stimulation by purified protein derivative of bovine tuberculin (PPD-B), among bTB PCR-P, bTB PCR-N, and healthy cattle using RNA-Seq. We also explored the potential value of PBMC transcripts as novel biomarkers for diagnosing bTB. Numerous differentially expressed genes were identified following pair-wise comparison of different groups, with or without PPD-B stimulation (adjusted p < 0.05). Compared with healthy cattle, bTB PCR-P, and bTB PCR-N cattle shared 5 significantly dysregulated biological pathways, including Cytokine-cytokine receptor interaction, NF-kappa B signaling pathway, Hematopoietic cell lineage, Osteoclast differentiation and HTLV-I infection. Notably, dysregulated biological pathways of bTB PCR-P and bTB PCR-N cattle were associated with cell death and phagocytosis, respectively. Lymphotoxin alpha and interleukin-8 could potentially differentiate M. bovis-infected and healthy cattle upon stimulation with PPD-B, with area-under-the-curve (AUC) values of 0.9991 and 0.9343, respectively. B cell lymphoma 2 and chitinase 3-like 1 might enable differentiation between bTB PCR-P and bTB PCR-N upon stimulation with PPD-B, with AUC values of 0.9100 and 0.8893, respectively. Thus, the PBMC transcriptome revealed the immune responses in M. bovis-infected cattle (bTB PCR-P and bTB PCR-N) and may provide a novel sight in bTB diagnosis.

Complete Genome Sequence of Mycoplasma bovis Strain XBY01, Isolated from Henan Province, China.

We report the complete genome sequence of Mycoplasma bovis strain XBY01, which was isolated from a severely diseased young calf in Henan Province, China, in 2019. The genome of XBY01 contains a single circular chromosome of 986,067 bp, with a GC content of 29.30%.

Mutations in PB2 and HA enhanced pathogenicity of H4N6 avian influenza virus in mice.

The H4 subtype avian influenza virus (AIV) continues to circulate in both wild birds and poultry, and occasionally infects mammals (e.g. pigs). H4-specific antibodies have also been detected in poultry farm workers, which suggests that H4 AIV poses a potential threat to public health. However, the molecular mechanism by which H4 AIVs could gain adaptation to mammals and whether this has occurred remain largely unknown. To better understand this mechanism, an avirulent H4N6 strain (A/mallard/Beijing/21/2011, BJ21) was serially passaged in mice and mutations were characterized after passaging. A virulent mouse-adapted strain was generated after 12 passages, which was tentatively designated BJ21-MA. The BJ21-MA strain replicated more efficiently than the parental BJ21, both in vivo and in vitro. Molecular analysis of BJ21-MA identified four mutations, located in proteins PB2 (E158K and E627K) and HA (L331I and G453R, H3 numbering). Further studies showed that the introduction of E158K and/or E627K substitutions into PB2 significantly increased polymerase activity, which led to the enhanced replication and virulence of BJ21-MA. Although individual L331I or G453R substitutions in HA did not change the pathogenicity of BJ21 in mice, both mutations significantly enhanced virulence. In conclusion, our data presented in this study demonstrate that avian H4 virus can adapt to mammals by point mutations in PB2 or HA, which consequently poses a potential threat to public health.

Complete Genome Sequence of Genotype Psittacine Beak and Feather Disease Virus, a Strain Identified from Budgerigars in China.

Psittacine beak and feather disease virus (PBFDV) has been reported in many countries, such as Australia, Poland, the United States, South Africa, etc. In this study, the complete genome of a PBFDV isolate was determined and characterized from budgerigars in China.

Complete Genome Sequence of an Avian Polyomavirus Strain First Isolated from a Pigeon in China.

Avian polyomavirus can infect multiple bird species and cause inflammatory disease with high mortality in young psittacine birds. In this study, we sequenced and analyzed an avian polyomavirus isolated from a pigeon in China, strain APV-P, which is closely related to a polyomavirus in psittacine birds.

Complete Genome Sequence of Brucella canis GB1, a Strain Isolated from a Poodle in Beijing, China.

Brucella spp. are facultative intracellular pathogens and zoonotic agents which pose a great threat to human health. Twelve different Brucella species have been identified to date. Here, we report the complete genome sequence of a Brucella canis GB1 strain, which contains two circular chromosomes of 3,277,308 bp in total.

Transcriptome analysis of gene expression profiling of infected macrophages between Brucella suis 1330 and live attenuated vaccine strain S2 displays mechanistic implication for regulation of virulence.

Brucellosis is one of the most common zoonotic epidemics worldwide. Vaccination against brucellosis is an important control strategy to prevent the disease in many high-prevalence regions. At present, Brucella vaccine strain S2 is the most widely used vaccine in China. To uncover the mechanisms underlying virulence attenuation of S2, in this study we characterized the transcriptional profile of S2 and 1330 infected macrophages by transcriptome analysis. The results revealed that expressions of 440 genes were significantly different between macrophages infected by 1330 and S2. Data analysis showed that in the gene ontology term, the different expressed genes involved in innate immune response, phagoctyosis, recognition, and inflammatory response were significantly enriched. Pathway enrichment analysis indicated that the genes involved in transcriptional misregulation in cancer, staphylococcus aureus infection pathways and NF-kappa B signaling pathway were significantly affected. To reveal the molecular mechanisms related to different expression profiles of infected macrophages, the transcription levels of the different genes between the two bacterial genomes were detected. In total, the transcription of 29 different genes was significantly changed in either culture medium or infected microphages. The results of this study can be conducive to the promotion of better understanding of the related mechanisms underlying virulence attenuation of S2 and interactions between host cells and Brucella strains.