In-Situ Metabolic Profiling of Different Kinds of Rheum palmatum L. by Laser Desorption-Dielectric Barrier Discharge Ionization Mass Spectrometry Imaging.

With its high resolving power and sensitivity, mass spectrometry is considered the most informative technique for metabolite qualitation and quantification in the plant sciences. However, the spatial location information, which is crucial for the exploration of plant physiological mechanisms, is lost. Mass spectrometry imaging (MSI) is able to visualize the spatial distribution of a large number of metabolites from the complex sample surface in a single experiment. In this paper, a flexible and low-cost laser desorption-dielectric barrier discharge ionization-MSI (LD-DBDI-MSI) platform was constructed by combining an LD system with an in-line DBDI source, a high-precision sample translation stage, and an ambient mass spectrometer. It can be operated at a spatial resolution of 20 µm in an atmospheric environment and requires minimal sample preparation. This study presents images of in-situ metabolic profiling of two kinds of plants from different origins, a wild and a farmed Rheum palmatum L. From the screen of these two root sections, the wild one presented five more endogenous molecules than the farmed one, which provides information about the differences in metabolomics.

A nodal EBV-positive T cell lymphoma with a T follicular helper cell phenotype.

AIMS: Nodal T follicular helper (TFH) cell lymphoma (nTFHL) is a rare type of clinically aggressive T cell lymphoma. With this lymphoma type, Epstein-Barr virus (EBV) infection is frequently detected in non-neoplastic B lymphocytes, but not yet identified in neoplastic T cells. We report two cases of nTFHL showing a classic morphology and immunoprofile, with EBV-encoded small RNAs (EBER) in-situ hybridisation positivity in neoplastic TFH cells. METHODS AND RESULTS: Clonal T cell receptor (TR) gene rearrangement was detected in both cases. Whole exome sequencing identified TET2, RHOA p. G17V, as well as gene mutations unique to each case. Microdissection analysis showed EBER positivity in tumour cells and in background non-neoplastic T lymphocytes. CONCLUSION: These two immunocompetent cases of nTFHL with EBV-positive tumour cells exhibit the featured gene mutation profile and poor prognosis of this disease. This novel finding of EBV positivity in our cases expands the currently recognised spectrum of EBV-positive nodal T cell lymphomas to include rare cases of nTFHL.

Systematic analysis on the mechanism of Zhizi-Bopi decoction against hepatitis B via network pharmacology and molecular docking.

PURPOSE: Zhizi-Bopi decoction (ZZBPD) is a classic herbal formula with wide clinical applications in treating liver diseases including hepatitis B. However, the mechanism needs to be elucidated. METHODS: Chemical components of ZZBPD were identified by ultra-high-performance liquid chromatography coupled with time-of-flight mass spectrometry (UHPLC-TOF-MS). Then we used network pharmacology to identify their potential targets. Network construction, coupled with protein-protein interaction and enrichment analysis was used to identify representative components and core targets. Finally, molecular docking simulation was conducted to further refine the drug-target interaction. RESULTS: One hundred and forty-eight active compounds were identified in ZZBPD, targeting 779 genes/proteins, among which 174 were related to hepatitis B. ZZBPD mainly influences the progression of hepatitis B through the hepatitis B pathway (hsa05161) via core anti-HBV targets (AKT1, PIK3CA, PIK3R1, SRC, TNF, MAPK1, and MAPK3). Enrichment analysis indicated that ZZBPD can also potentially regulate lipid metabolism and enhance cell survival. Molecular docking suggested that the representative active compounds can bind to the core anti-HBV targets with high affinity. CONCLUSION: The potential molecular mechanisms of ZZBPD in hepatitis B treatment were identified using network pharmacology and molecular docking approaches. The results serve as an important basis for the modernization of ZZBPD.

Direct Quantitative Analysis of Fluorine in Solid Samples by Cryogenic Laser Ablation and Ionization Time-of-Flight Mass Spectrometry.

The determination of fluorine, the lightest element in halogens, suffers from high ionization potential and spectral interference from water molecules in mass spectrometry. Herein, we introduced a liquid nitrogen cooling unit into the laser ablation and ionization source for the first time to construct a cryogenic laser ablation and ionization time-of-flight mass spectrometry (Cryo-LAI-TOFMS) system. With this system, the interference of water-related species at m/z 19 was effectively eliminated, and fluorine atomization and ionization efficiency could reach 6.3%. A direct quantitative analysis method was developed to determine fluorine contents in phosphate rock, copper ore, industrial byproduct gypsum, stream sediment, and soil. Considering the simplicity, high sensitivity, and low spectral interference of this technique, it can be extended to the determination of fluorine content as low as µg/g in complex solid samples.

Molecular Characterization Analysis of Prevalent Infectious Bronchitis Virus and Pathogenicity Assessment of Recombination Strain in China.

Avian coronavirus infectious bronchitis virus (IBV) is a respiratory pathogen of chickens, resulting in severe economic losses in the poultry industry. This study aimed to monitor and isolate the molecular identity of IBV in broiler flocks with respiratory symptoms in eight provinces of China. In total, 910 samples (oropharyngeal and cloacal mixed swabs) from broiler flocks showed IBV positive rates of 17.6% (160/910) using PCR assay. Phylogenetic analysis of the complete S1 genes of 160 IBV isolates was performed and revealed that QX-type (GI-19), TW-type (GI-7), 4/91-type (GI-13), HN08-type (GI-22),TC07-2-type (GVI-1), and LDT3-type (GI-28) exhibited IBV positive rates of 58.15, 25, 8.12, 1.86, 5.62, and 1.25%. In addition, recombination analyses revealed that the four newly IBV isolates presented different recombination patterns. The CK/CH/JS/YC10-3 isolate likely originated from recombination events between strain YX10 (QX-type) and strain TW2575-98 (TW-type), the pathogenicity of which was assessed, comparing it with strain GZ14 (TW-type) and strain CK/CH/GD/JR07-7 (QX-type). The complete S1 gene data from these isolates indicate that IBV has consistently evolved through genetic recombination or mutation, more likely changing the viral pathogenicity and leading to larger outbreaks in chick populations, in China.

Pathogenicity and molecular characterization of infectious bursal disease virus in China.

Infectious bursal disease virus (IBDV) caused an acute and highly contagious infectious disease, resulting in considerable economic losses in the world poultry industry. Although this disease was well-controlled under the widely use of commercial vaccines, the novel variant IBDV strain emerged due to the highly immunized-selection pressure in the field, posting new threats to poultry industry. Here, we reported the epidemic and pathogenicity of IBDV in Hubei Province from May to August 2020. We isolated 12 IBDV strains from the broiler flocks, including 9 novel variants, 2 very virulent strains and 1 medium virulent strain. Interestingly, we identified a series of changes of amino acid sites in the VP2. Further analysis indicated that the novel variant IBDV strains caused damage to bursa of fabricius and spleen, leading to immunosuppression. Our findings underscore the importance of IBDV surveillance, and provide evidence for understanding the evolution of IBDV.

High-Spatial Resolution Atmospheric Pressure Mass Spectrometry Imaging Using Fiber Probe Laser Ablation-Dielectric Barrier Discharge Ionization.

Atmospheric pressure mass spectrometry imaging (AP-MSI) is a powerful tool in many fields; however, there are still some difficulties to achieve high spatial resolution for AP-MSI, one of them being the need for a small ablation crater. Here, a fiber probe laser ablation (FPLA) system is introduced that uses an etched optical fiber with a sharp tip (o.d. 200 nm) to deliver ablation laser pulses to a sample surface to ablate materials with high spatial resolution. The tip-to-sample distance was adjusted to ∼10 µm using a micro-actuator having a stepping motor with submicron accuracy. The laser-ablated neutrals were post-ionized using a home-built in-line dielectric barrier discharge source, which can be interfaced to any mass spectrometer with an AP interface. Using MSI on a standard sample with a striped pattern and sections of fingernails treated with the drug methyl green zinc chloride salt, a FPLA-DBDI-MSI spatial resolution of ≈5 µm was demonstrated.

Distribution and molecular characterization of avian infectious bronchitis virus in southern China.

Avian infectious bronchitis virus (IBV) is causing considerable economic losses in the world poultry industry. The main difficulty of prevention and control of IB disease is the numerous genotypes and serotypes. The genetic analysis of IBV was mainly based on the S1 gene which played an important role in infectivity. In the study, One hundred and thirty-nine strains of avian infectious bronchitis virus were isolated from chickens showing signs of disease in southern China during the period from April 2019 to March 2020. The nucleotide and amino acid sequences from the isolated field strains were compared to 22 published references. Nucleotide homologies ranged from 64.5% to 100% and amino acid homologies ranging from 70% to 99.8%. Six genotype IBV strains were co-circulating in southern China. QX-type was still the most dominant genotype. Alignment of nucleotide and amino acid sequences of S1 gene revealed that the substitutions, insertions and deletions are widely among isolated strains. Recombination analysis showed that there is a large number of recombinant strains amongst these isolates, forming new sub branches, subtypes and variants. Therefore, long-term continuing surveillance is necessary for IBV prevention and control.

Atmospheric Pressure Mass Spectrometry Imaging Using Laser Ablation, Followed by Dielectric Barrier Discharge Ionization.

Mass spectrometry imaging (MSI) has become a powerful tool in diverse fields, for example, life science, biomaterials, and catalysis, for its ability of in situ and real-time visualization of the location of chemical compounds in samples. Although laser ablation (LA) achieves high spatial resolution in MSI, the ion yield can be very low. We therefore combined an LA system with an ambient ion source for post-ionization and an atmospheric pressure (AP) inlet mass spectrometer to construct a novel AP-MSI platform. A dielectric barrier discharge ionization (DBDI) source is operated in the "active sampling capillary" configuration, can be coupled to any mass spectrometer with an AP interface, and possesses high ion transmission efficiency. This study presents some application examples based on LA-DBDI, a low-cost and flexible strategy for AP-MSI, which does not require any sample pretreatment, and we show MS imaging of endogenous species in a traditional Chinese herbal medicine and of a drug molecule in zebra fish tissue, with a lateral resolution of ≈20 µm.

Xp11.2 translocation/TFE3 gene fusion renal cell carcinoma with a micropapillary pattern: cases report and literature review.

Xp11.2 translocation/transcription factor E3 (TFE3) gene fusion renal cell carcinoma (Xp11.2 translocation RCC) was first classified as a distinct type of renal tumor by the World Health Organization in 2004. However, its morphology and clinical manifestations often overlap with those of conventional RCCs. Moreover, a micropapillary pattern (MPP) comprising small papillary cell clusters surrounded by lacunar spaces has never been described in RCC. We compared the clinicopathological and prognostic characteristics of one patient with Xp11.2 translocation RCC exhibiting an MPP (TFE3-M) to those of four patients with conventional Xp11.2 translocation RCC (TFE3-N); all five tumors resembled conventional RCCs on gross pathology. All patients exhibited similar histologies, clinical manifestations, and prognoses, and all underwent radical nephrectomy. However, their characteristics differed significantly from those of other MPP-comprising neoplasms. Both tumor types were positive for TFE3 and vimentin; however, TFE3-M tumor cells expressed epithelial membrane antigen and human melanoma black-45 but not cluster of differentiation 10 (CD10), whereas the TFE3-N cells expressed P504S, CD10, and vimentin but not cytokeratin 7. Our RT-PCR analysis result showed that TFE3-N and TFE3-M tumor cells were identified expressing ASPSCR1-TFE3 and PRCC-TFE3 fusion genes, respectively. These findings suggest that TFE3-M should be classified as a histological subtype of Xp11.2 translocation RCC, although its relationship with other MPP-exhibiting neoplasms remains unclear. The histological characteristics of Xp11.2 translocation RCCs depend on MiT family transcription factors and their gene fusion partners. Xp11.2 translocation RCC should be considered for malignancies presenting with a particular pattern; such malignancies can be identified reliably by their morphological and immunohistochemical profiles.

Genome-Wide Association Analysis Reveals Key Genes Responsible for Egg Production of Lion Head Goose.

The lion head goose is one of the most important agricultural resources in China; however, its breeding process is relatively slow. In the present study, a genome-wide association study was performed for the genetic selection of egg production characters in lion head geese. We detected 30 single-nucleotide polymorphisms located in or near 30 genes that might be associated with egg production character, and quantitative real-time polymerase chain reaction was used to verify their expression level in lion head geese. The results showed that the expression levels of CRTC1 (encoding CREB-regulated transcription coactivator 1), FAAH2 (encoding fatty acid amide hydrolase 2), GPC3 (encoding glypican 3), and SERPINC1 (encoding serpin family C member 1) in high egg production population were significantly lower than those in the low egg production populations (*P < 0.05). The expression levels of CLPB (encoding caseinolytic peptidase B protein homolog), GNA12 (encoding guanine nucleotide-binding protein subunit alpha-12), and ZMAT5 (encoding zinc finger, matrin type 5) in the high egg production population were significantly higher than those in the low egg production populations (*P < 0.05). The expression of BMP4 (encoding bone morphogenetic protein 4), FRMPD3 (encoding FERM and PDZ domain containing 3), LIF (encoding leukemia inhibitory factor), and NFYC (encoding nuclear transcription factor Y subunit gamma) in the high egg production population were very significantly lower than those in the low egg production population (**P < 0.01). Our findings provide an insight into the economic traits of lion head goose. These candidate genes might be valuable for future breeding improvement.

Expressions of KAI1 and E-cadherin in nonsmall cell lung cancer and their correlation with vasculogenic mimicry.

BACKGROUND: Metastasis and recurrence are the most common reasons for treatment failure of nonsmall cell lung cancer (NSCLC). Vasculogenic mimicry (VM, new blood supply formation in malignant tumors), E-Cadherin (a calcium-dependent transmembrane glycoprotein that mediates intercellular adhesion), KAI1 (a suppressor gene of tumor metastasis) are all valuable factors for metastasis and prognosis in diverse common human cancers. However, the correlation of VM, E-Cadherin, and KAI1 in NSCLC is still unclear. In this study, we analyzed the correlations among these factors as well as their respective correlations with clinicopathological parameters and survival in NSCLC. METHODS: The level of VM, E-Cadherin, and KAI1 in 163 tissue samples of NSCLC was examined by immunhistochemistry. Clinical data were also collected. RESULTS: Levels of VM was significantly higher, and levels of KAI1 and E-Cadherin significantly lower in NSCLC tissues than in normal lung tissues. Levels of VM were positively associated with lymph node metastasis (LNM), size, grade, and tumor node metastasis (TNM) stages, and negatively associated with patients' overall survival (OS). Levels of KAI1 and E-Cadherin were negatively correlated with LNM, size, grade, and TNM stage, and positively associated with patients' OS. In multivariate analysis, high levels of VM, E-Cadherin, and KAI1, as well as TNM stages were independently correlated with lower OS in patients with NSCLC. CONCLUSION: VM and the expression of E-Cadherin and KAI1 may represent promising metastatic and prognostic biomarkers, as well as potential therapeutic targets for NSCLC.

Approaching Standardless Quantitative Elemental Analysis of Solids: Microsecond Pulsed Glow Discharge and Buffer-Gas-Assisted Laser Ionization Time-of-Flight Mass Spectrometry.

Among various ionization sources for mass spectrometry, microsecond pulsed glow discharge (MP-GD) and buffer-gas-assisted laser ionization (BGA-LI) sources have the potential for direct quantitative elemental analysis of solids without the requirement of standard reference materials. The analytical potential of these two ionization sources has been evaluated by coupling them to orthogonal time-of-flight mass spectrometry (MS). A straightforward method was proposed to achieve the quantitative result: if a spectrum contains little interference and elemental peak currents are proportional to their concentrations, then the molar concentration of each element is equal to its ion current proportion in the total ion current. Two series of metal standards were applied for the evaluation. Explicit spectra with little interference can be acquired by both techniques. The interferences contribute only a very small portion to the total ion current for MP-GD-MS and BGA-LI-MS; therefore, their influence on the quantitative result can be ignored. All metal elements can be determined quite accurately by the proposed quantitation method, while gaps exist for nonmetal elements due to the high ionization potentials or gas species interference. Between the two techniques, BGA-LI-MS offers a more accurate quantitative result, primarily due to its higher plasma temperature.

Avian Leukosis Virus Subgroup J Attenuates Type I Interferon Production Through Blocking IκB Phosphorylation.

Avian leukosis virus subgroup J (ALV-J) is an oncogenic retrovirus that causes immunosuppression and enhances susceptibility to secondary infection, resulting in great economic losses. Although ALV-J-induced immunosuppression has been well established, the underlying molecular mechanism for such induction is still unclear. Here, we report that the inhibitory effect of ALV-J infection on type I interferon expression is associated with the down-regulation of transcriptional regulator NF-κB in host cells. We found that ALV-J possess the inhibitory effect on type I interferon production in HD11 cells and that ALV-J causes the up-regulation of IκBα and down-regulation of NF-κB p65, and that ALV-J blocks the phosphorylation of IκBα on Ser32/36 amino acid residues. Collectively, our findings provide insights into the pathogenesis of ALV-J.

Vasculogenic mimicry and expression of slug and vimentin correlate with metastasis and prognosis in non-small cell lung cancer.

Background: Non-small cell lung cancer (NSCLC) has been the leading cause of cancer death in recent years, its morbidity and mortality were increasing yearly. The presence of vasculogenic mimicry (VM) is associated with a high tumor grade, short survival, invasion, and metastasis. Slug is a key regulating factor in the process of EMT. Vimentin is one of the cytoskeleton proteins that plays an important role in EMT. However, associations among VM, Slug and vimentin and their clinicopathologic significance in NSCLC are unclear. In this study, we analyzed associations among VM, Slug and vimentin in NSCLC, and their respective associations with clinicopathologic characteristics and survival in NSCLC. Methods: Positive expression of VM, Slug and vimentin in 198 whole NSCLC tissue samples were detected by immunohistochemical staining. Patients' clinical data were also collected. Results: Levels of VM, Slug and vimentin were significantly higher in NSCLC tissues than in normal lung tissues. Levels of VM, Slug and vimentin were positively associated with tumor grade, distant metastasis (DM), lymph node metastasis (LNM), and tumor-node metastasis (TNM) stage, and inversely with patients overall survival time (OST). In multivariate analysis, high expression of VM, Slug, vimentin, and tumor grade, DM, LNM, TNM stage, were potential to be independent prognostic factors for OST in patients with NSCLC. Conclusion: VM, Slug and vimentin affect NSCLC evolution; and the combined detection of VM, Slug and vimentin are valuable factors for metastasis and prognosis in NSCLC patients.

Expression of vimentin and Oct-4 in gallbladder adenocarcinoma and their relationship with vasculogenic mimicry and their clinical significance.

Vimentin (a marker of epithelial-mesenchymal transition), and Oct-4 (a marker of cancer stem cells) are predicative biomarkers for identifying malignant cell invasion and metastasis. Vasculogenic mimicry (VM), a newly discovered tumor characteristic that is common in highly invasive malignancies, is considered to be an important factor in evaluating the prognosis and metastasis of many malignancies. The following paper analyzes the correlation between vimentin, Oct-4, and VM in gallbladder adenocarcinoma (GBAC) specimens using immunohistochemistry in an attempt to elucidate the survival and clinicopathological parameters of changes in vimentin, Oct-4, and VM. Briefly, significantly higher positive expression rates of vimentin, Oct-4, and VM were observed in GBAC tissues than in the corresponding para-carcinoma tissues. In addition, the levels of vimentin, Oct-4, and VM were positively correlated with tumor grade, lymph node metastasis (LNM), infiltration of the surrounding tissues (STI), and tumor-node-metastasis (TNM) stage, as well as inversely with a patient's overall survival (OS) time. Moreover, the analysis of multiple factors shows that high vimentin, Oct-4, and VM levels, STI, and LNM as well as TNM stage were potential and significant factors for OS time in patients with GBAC. To sum up, the positive expression of vimentin, Oct-4, and VM may be undesirable factors for metastasis, invasion and prognosis, as well as effective therapeutic targets for GBAC.

Ollier disease: two case reports and a review of the literature.

Ollier disease is a rare tumor with unclear clinicopathological features and pathogenesis. We herein report two cases of Ollier disease in a 15-year-old boy and a 66-year-old man. We analyzed the clinicopathological, radiographical, and histochemical characteristics of Ollier disease in these two cases. Furthermore, we reviewed the literature to better understand the clinicopathological features of this disease. The boy had multiple enchondromas in the metaphysis and upper region of the left femur, and his left leg is short naturally. The 66-year-old man had multiple enchondromas in his left ribs and lower segment of the left femur. He was sent to the hospital because of pathological fracture of the ribs. In addition, he was diagnosed with gastric cancer 4 years before visiting an orthopedic clinic. Ollier disease is a rare bone disease that often renders a typical asymmetrical distribution and is confined to the appendicular skeleton. It is known as a benign bone tumor and has a high risk of malignant transformation into a chondrosarcoma (5%-50%). Correct diagnosis requires radiographic, histochemical, and morphological analyses. Better understanding of the clinical manifestations and pathological features can improve the diagnosis and prevent malignant transformation and deformity, especially in adolescent patient.

Microtrace Analysis of Rare Earth Element Residues in Femtogram Quantities by Laser Desorption and Laser Postionization Mass Spectrometry.

A newly developed laser desorption and laser postionization time-of-flight mass spectrometer (LD-LPI-TOFMS) for the direct microtrace determination of rare earth elements (REEs) in residues has been presented. Benefiting from spatially and temporally separated processes between desorption and ionization, LD-LPI-TOFMS plays a dual role in alleviating the barriers of deteriorating spectral resolution at high irradiance, serious matrix effects and elemental fractionation effects at low irradiance. Compared with the conventional laser desorption/ionization (LDI) method, this technique offers unambiguous full-elemental determination of 15 REEs with more uniform relative sensitivity coefficients (RSCs) ranging from 0.5 to 2.5 for all REEs investigated, satisfying the semiquantitative analysis criteria. More importantly, a highly sensitive analysis of REEs with very little consumption was achieved by getting the utmost out of desorbed neutral atoms instead of increasing the amount of the sample, resulting in outstanding relative and absolute limits of detection (LODs and ALODs) of ∼ng/mL and ∼femtogram. The results presented here indicate that LD-LPI-TOFMS offers great potential in microtrace determination for elements in solution samples with minor sample preparation.

Weighted next reaction method and parameter selection for efficient simulation of rare events in biochemical reaction systems.

The weighted stochastic simulation algorithm (wSSA) recently developed by Kuwahara and Mura and the refined wSSA proposed by Gillespie et al. based on the importance sampling technique open the door for efficient estimation of the probability of rare events in biochemical reaction systems. In this paper, we first apply the importance sampling technique to the next reaction method (NRM) of the stochastic simulation algorithm and develop a weighted NRM (wNRM). We then develop a systematic method for selecting the values of importance sampling parameters, which can be applied to both the wSSA and the wNRM. Numerical results demonstrate that our parameter selection method can substantially improve the performance of the wSSA and the wNRM in terms of simulation efficiency and accuracy.

Stochastic simulation of delay-induced circadian rhythms in Drosophila.

Circadian rhythms are ubiquitous in all eukaryotes and some prokaryotes. Several computational models with or without time delays have been developed for circadian rhythms. Exact stochastic simulations have been carried out for several models without time delays, but no exact stochastic simulation has been done for models with delays. In this paper, we proposed a detailed and a reduced stochastic model with delays for circadian rhythms in Drosophila based on two deterministic models of Smolen et al. and employed exact stochastic simulation to simulate circadian oscillations. Our simulations showed that both models can produce sustained oscillations and that the oscillation is robust to noise in the sense that there is very little variability in oscillation period although there are significant random fluctuations in oscillation peaks. Moreover, although average time delays are essential to simulation of oscillation, random changes in time delays within certain range around fixed average time delay cause little variability in the oscillation period. Our simulation results also showed that both models are robust to parameter variations and that oscillation can be entrained by light/dark circles. Our simulations further demonstrated that within a reasonable range around the experimental result, the rates that dclock and per promoters switch back and forth between activated and repressed sites have little impact on oscillation period.