DWARF AND LOW-TILLERING 2 functions in brassinosteroid signaling and controls plant architecture and grain size in rice.

Brassinosteroids (BRs) are a class of steroid phytohormones that control various aspects of plant growth and development. Several transcriptional factors (TFs) have been suggested to play roles in BR signaling. However, their possible relationship remains largely unknown. Here, we identified a rice mutant dwarf and low-tillering 2 (dlt2) with altered plant architecture, increased grain width, and reduced BR sensitivity. DLT2 encodes a GIBBERELLIN INSENSITIVE (GAI)-REPRESSOR OF GAI (RGA)-SCARECROW (GRAS) TF that is mainly localized in the nucleus and has weak transcriptional activity. Our further genetic and biochemical analyses indicate that DLT2 interacts with two BR-signaling-related TFs, DLT and BRASSINAZOLE-RESISTANT 1, and probably modulates their transcriptional activity. These findings imply that DLT2 is implicated in a potentially transcriptional complex that mediates BR signaling and rice development and suggests that DLT2 could be a potential target for improving rice architecture and grain morphology. This work also sheds light on the role of rice GRAS members in regulating numerous developmental processes.

DGW1, encoding an hnRNP-like RNA binding protein, positively regulates grain size and weight by interacting with GW6 mRNA.

Grain size and weight determine rice yield. Although numerous genes and pathways involved in regulating grain size have been identified, our knowledge of post-transcriptional control of grain size remains elusive. In this study, we characterize a rice mutant, decreased grain width and weight 1 (dgw1), which produces small grains. We show that DGW1 encodes a member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family protein and preferentially expresses in developing panicles, positively regulating grain size by promoting cell expansion in spikelet hulls. Overexpression of DGW1 increases grain weight and grain numbers, leading to a significant rise in rice grain yield. We further demonstrate that DGW1 functions in grain size regulation by directly binding to the mRNA of Grain Width 6 (GW6), a critical grain size regulator in rice. Overexpression of GW6 restored the grain size phenotype of DGW1-knockout plants. DGW1 interacts with two oligouridylate binding proteins (OsUBP1a and OsUBP1b), which also bind the GW6 mRNA. In addition, the second RRM domain of DGW1 is indispensable for its mediated protein-RNA and protein-protein interactions. In summary, our findings identify a new regulatory module of DGW1-GW6 that regulates rice grain size and weight, providing important insights into the function of hnRNP-like proteins in the regulation of grain size.

Erythrocytic α-Synuclein and the Gut Microbiome: Kindling of the Gut-Brain Axis in Parkinson's Disease.

BACKGROUND: Progressive spreading of α-synuclein via gut-brain axis has been hypothesized in the pathogenesis of Parkinson's disease (PD). However, the source of seeding-capable α-synuclein in the gastrointestinal tract (GIT) has not been fully investigated. Additionally, the mechanism by which the GIT microbiome contributes to PD pathogenesis remains to be characterized. OBJECTIVES: We aimed to investigate whether blood-derived α-synuclein might contribute to PD pathology via a gut-driven pathway and involve GIT microbiota. METHODS: The GIT expression of α-synuclein and the transmission of extracellular vesicles (EVs) derived from erythrocytes/red blood cells (RBCs), with their cargo α-synuclein, to the GIT were explored with various methods, including radioactive labeling of RBC-EVs and direct analysis of the transfer of α-synuclein protein. The potential role of microbiota on the EVs transmission was further investigated by administering butyrate, the short-chain fatty acids produced by gut microbiota and studying mice with different α-synuclein genotypes. RESULTS: This study demonstrated that RBC-EVs can effectively transport α-synuclein to the GIT in a region-dependent manner, along with variations closely associated with regional differences in the expression of gut-vascular barrier markers. The investigation further revealed that the infiltration of α-synuclein into the GIT was influenced significantly by butyrate and α-synuclein genotypes, which may also affect the GIT microbiome directly. CONCLUSION: By demonstrating the transportation of α-synuclein through RBC-EVs to the GIT, and its potential association with gut-vascular barrier markers and gut microbiome, this work highlights a potential mechanism by which RBC α-synuclein may impact PD initiation and/or progression. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.

High heterogeneity undermines generalization of differential expression results in RNA-Seq analysis.

BACKGROUND: RNA sequencing (RNA-Seq) has been widely applied in oncology for monitoring transcriptome changes. However, the emerging problem that high variation of gene expression levels caused by tumor heterogeneity may affect the reproducibility of differential expression (DE) results has rarely been studied. Here, we investigated the reproducibility of DE results for any given number of biological replicates between 3 and 24 and explored why a great many differentially expressed genes (DEGs) were not reproducible. RESULTS: Our findings demonstrate that poor reproducibility of DE results exists not only for small sample sizes, but also for relatively large sample sizes. Quite a few of the DEGs detected are specific to the samples in use, rather than genuinely differentially expressed under different conditions. Poor reproducibility of DE results is mainly caused by high variation of gene expression levels for the same gene in different samples. Even though biological variation may account for much of the high variation of gene expression levels, the effect of outlier count data also needs to be treated seriously, as outlier data severely interfere with DE analysis. CONCLUSIONS: High heterogeneity exists not only in tumor tissue samples of each cancer type studied, but also in normal samples. High heterogeneity leads to poor reproducibility of DEGs, undermining generalization of differential expression results. Therefore, it is necessary to use large sample sizes (at least 10 if possible) in RNA-Seq experimental designs to reduce the impact of biological variability and DE results should be interpreted cautiously unless soundly validated.

Increasing the amount of phosphoric acid enhances the suitability of Bradford assay for proteomic research.

The Bradford assay is one of the most commonly used methods for protein quantification. However, in proteomic research, the lysis buffer generally used for dissolving proteins can cause some interference to the assay. The dye reagent of classical Bradford assay contains 8.50% (w/v) phosphoric acid, which is an important factor relating to the color yield of the assay. In this study, the phosphoric acid content in dye reagent was increased to 9.35% (w/v), 10.20% (w/v), and 11.05% (w/v) to evaluate the changes of interference and the effects of lysis buffer on the interaction between proteins and dye reagent. Results show that lysis buffer not only causes background interference but also affects the protein-dye chromogenic process. Analysis of different components in the lysis buffer showed that carrier ampholyte is the main factor that introduces interference to the Bradford assay. Detergents are well-known interfering compounds in the Bradford assay, but CHAPS and octyl b-D-glucopyranoside only cause slight interference. When the amount of phosphoric acid was increased from 8.50%(w/v) to 10.20% (w/v), the sensitivity of the Bradford assay to proteins in lysis buffer was increased, and the interference delivered by lysis buffer was considerably reduced.

[Roles of macrophages in formation and progression of intracranial aneurysms].

Studies have shown that chronic inflammatory response plays a key role in intracranial aneurysms (IA) formation and progression, and macrophages regulate the formation and progression of IA through a variety of pathways. Bone marrow monocyte-derived macrophages and resident-tissue macrophages infiltrate the vessel wall, after infiltration macrophages are polarized into various polarization phenotypes dominated by M1-like and M2-like cells. Polarized phenotypes of macrophages can regulate the formation and progression of intracranial aneurysms by releasing cytokines and regulating the inflammatory response of other immune cells, as well as release different cytokines to regulate the process of extracellular matrix remodeling. Some important progresses have been made in the clinical detection and treatment in targeting macrophages. This review provides a summary on the pathogenesis of IA and potential drug targets to prevent the formation and rupture of intracranial aneurysms.

[Autophagy regulates the function of vascular smooth muscle cells in the formation and rupture of intracranial aneurysms].

Vascular smooth muscle cells (VSMC) are the main cellular component of vessel wall. The changes of VSMC functions including phenotypic transformation and apoptosis play a critical role in the pathogenesis of intracranial aneurysm (IA). Autophagy can participate in the regulation of vascular function by regulating cell function. In the initial stage of IA, the activation of autophagy can accelerate the phenotypic transformation of VSMC and inhibit VSMC apoptosis. With the progress of IA, the relationship between autophagy and apoptosis changes from antagonism to synergy or promotion, and a large number of apoptotic VSMC lead to the rupture of IA. In this review, we describe the role of autophagy regulating the function of VSMC in the occurrence, development and rupture of IA, for further understanding the pathogenesis of IA and finding molecular targets to prevent the formation and rupture of IA.

Identification of the soluble form of tyrosine kinase receptor Axl as a potential biomarker for intracranial aneurysm rupture.

BACKGROUND: Subarachnoid hemorrhage caused by a ruptured intracranial aneurysm (RIA) is a devastating condition with significant morbidity and mortality. Despite the fact that RIAs can be prevented by microsurgical clipping or endovascular coiling, there are no reliable means of effectively predicting IA patients at risk for rupture. The purpose of our study was to discover differentially-expressed glycoproteins in IAs with or without rupture as potential biomarkers to predict rupture. METHODS: Forty age/gender-matched patients with RIA, unruptured IA (UIA), healthy controls (HCs) and disease controls (DCs) (discovery cohort, n = 10 per group) were recruited and a multiplex quantitative proteomic method, iTRAQ (isobaric Tagging for Relative and Absolute protein Quantification), was used to quantify relative changes in the lectin-purified glycoproteins in CSF from RIAs and UIAs compared to HCs and DCs. Then we verified the proteomic results in an independent set of samples (validation cohort, n = 20 per group) by enzyme-linked immunosorbent assay. Finally, we evaluated the specificity and sensitivity of the candidate marker with receiver operating characteristic (ROC) curve methods. RESULTS: The proteomic findings identified 294 proteins, 40 of which displayed quantitative changes unique to RIA, 13 to UIA, and 20 to IA. One of these proteins, receptor tyrosine kinase Axl, was significantly increased in RIA, as confirmed in CSF from the discovery cohort as well as in CSF and plasma from the validation cohort (p <0.05). Spearman's correlation analysis revealed that the CSF and plasma Axl levels were strongly correlated (r = 0.93, p <0.0001). The ROC curve indicated an optimal CSF Axl threshold of 0.12 nM for discriminating RIA from UIA with corresponding sensitivity/specificity of 73.33%/90% and an area under the curve (AUC) of 0.89 (95% CI: 0.80-0.97, p < 0.0001). The optimal threshold for plasma Axl was 1.7 nM with corresponding sensitivity/specificity of 50%/80% and an AUC of 0.71 (95% CI: 0.54-0.87, p = 0.027). CONCLUSIONS: Both CSF and plasma Axl levels are significantly elevated in RIA patients. Axl might serve as a promising biomarker to predict the rupture of IA.

Significant enhancement of hPrx1 chaperone activity through lysine acetylation.

The reversible acetylation of proteins plays a key role in regulating biological processes, including chromatin remodeling, progression of the cell cycle, and actin nucleation. Human peroxiredoxin 1(hPrx1), one of the most abundant proteins in the cytoplasm, has been shown to be acetylated in human liver-carcinoma tissues. However, little is known about what function(s) the acetylation serves for hPrx1. Herein, using the method of genetic code expansion, we incorporated N(ε)-acetyllysine (AcK) site-specifically into hPrx1. Our data showed that acetylation the K(27) residue promotes oligomerization of hPrx1 at low concentrations. In addition, K(27)-acetylated hPrx1(hPrx1-AcK27) exhibited greatly enhanced chaperone activity (e.g. protecting the protein malate dehydrogenase (MDH) from thermally induced aggregation and assisting the refolding of denatured citrate synthase (CS)). These findings suggest that the site-specific acetylation of hPrx1 may change its biological role in response to environmental changes.

Dokdonella immobilis sp. nov., isolated from a batch reactor for the treatment of triphenylmethane dye effluent.

A Gram-staining-negative, non-endospore-forming, non-flagellated, non-motile and rod-shaped bacterium, designated strain LM2-5(T), was isolated from activated sludge in a sequencing batch reactor used for the treatment of triphenylmethane dye effluent. The taxonomy of strain LM2-5(T) was studied by phenotypic, chemotaxonomic and phylogenetic methods. Strain LM2-5(T) was aerobic, heterotrophic and positive for oxidase but negative for catalase activity. It grew at 16-37 °C (optimum 25 °C) and at pH 5.0-8.5 (optimum between pH 6.5 and pH 7.0). NaCl was not obligatory for growth but was tolerated at concentrations up to 2.0 % (w/v) NaCl. The novel strain formed yellow colonies on trypticase soy agar. Cells of strain LM2-5(T) were rods that measured 0.3-0.5 µm in width and 3.0-5.0 µm in length. The predominant respiratory quinone was Q-8. The major fatty acids were iso-C15 : 0 and iso-C17 : 1ω9c. The genomic DNA G+C content was 66.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, strain LM2-5(T) clustered with members of the genus Dokdonella and appeared most closely related to Dokdonella koreensis DS-123(T) (96.4 % sequence similarity), Dokdonella fugitiva A3(T) (96.1 %), Dokdonella soli KIS28-6(T) (95.7 %) and Dokdonella ginsengisoli Gsoil 191(T) (95.7 %). On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain LM2-5(T) was considered to represent a novel species of the genus Dokdonella, for which the name Dokdonella immobilis is proposed. The type strain is LM2-5(T) ( = CGMCC 1.7659(T)  = JCM 15763(T)).

Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter.

A novel pyrene-degrading, Gram-negative bacterium, designated strain P-4(T), was isolated from a polycyclic aromatic hydrocarbon-degrading enrichment of polluted soils from a coking chemical plant. Cells of strain P-4(T) were non-motile rods. Strain P-4(T) grew at 15-45 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8.5) and 0-4 % (w/v) NaCl. Analysis of the 16S rRNA gene sequence showed that strain P-4(T) was related phylogenetically to members of the genus Parapedobacter, with sequence similarity of 93.7-95.1 %. The cellular fatty acids of strain P-4(T) were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0), anteiso-C15 : 0, iso-C15 : 0 3-OH, C16 : 0, iso-C15 : 1 G, C16 : 0 3-OH and C17 : 0 2-OH. Cells contained menaquinone 7 as the major quinone. The polyamine of strain P-4(T) was homospermidine, and the main polar lipids were phosphatidylethanolamine and a sphingolipid. The G+C content of the DNA was 45.4 mol%. Strain P-4(T) showed a range of phenotypic characteristics that differentiated it from previously recognized Parapedobacter species, particularly its ability to use pyrene as a sole carbon source for growth and its alkaline optimal pH for growth (pH 8.5). On the basis of these results, it is concluded that strain P-4(T) represents a novel species of the genus Parapedobacter, for which the name Parapedobacter pyrenivorans (type strain P-4(T) = NBRC 109113(T) = CGMCC 1.12195(T)) is proposed. An emended description of the genus Parapedobacter is also provided.

Prevalence of osteoporosis in patients with nephrolithiasis and vice versa: a cumulative analysis.

Purpose: Nephrolithiasis is thought to be a risk factor for osteoporosis, but data assessing if osteoporosis predisposes to the risk of nephrolithiasis are lacking. The present study aims to investigate whether patients with nephrolithiasis have a prominently higher prevalence of osteoporosis than the controls and vice versa via a cumulative analysis. Methods: Four databases were used to detect the eligible studies. We calculated the relative risk (RR) with a 95% confidence interval (CI) to assess the combined effect. The methodologies for conducting this study followed the PRISMA guidelines and were registered in the PROSPERO (ID: CRD42023395875). Results: Nine case-control or cohort studies with a total of 454,464 participants were finally included. Combined results indicated that there was a significantly higher prevalence of osteoporosis in patients with nephrolithiasis as compared to the general population without nephrolithiasis (overall RR from six studies= 1.204, 95%CI: 1.133 to 1.28, P< 0.001; heterogeneity: I2 = 34.8%, P= 0.162). Conversely, osteoporosis was significantly correlated to an increased risk of nephrolithiasis as compared to the controls without osteoporosis (overall RR from four studies= 1.505, 95%CI: 1.309 to 1.731, P< 0.001; I2 = 89.8%, P< 0.001). Sensitivity analysis on the two categories validated the above findings. No significant publication bias was identified in this study. Conclusions: The present study highlighted a significantly high prevalence of osteoporosis in patients with nephrolithiasis and vice versa. This reciprocal association reminded the clinicians to conduct a regular follow-up assessment when managing patients with nephrolithiasis or osteoporosis, especially for the elderly. Systematic review registration: https://www.crd.york.ac.uk/PROSPERO/#searchadvanced, identifier CRD42023395875.

Gut-derived ß-amyloid: Likely a centerpiece of the gut-brain axis contributing to Alzheimer's pathogenesis.

Peripheral ß-amyloid (Aß), including those contained in the gut, may contribute to the formation of Aß plaques in the brain, and gut microbiota appears to exert an impact on Alzheimer's disease (AD) via the gut-brain axis, although detailed mechanisms are not clearly defined. The current study focused on uncovering the potential interactions among gut-derived Aß in aging, gut microbiota, and AD pathogenesis. To achieve this goal, the expression levels of Aß and several key proteins involved in Aß metabolism were initially assessed in mouse gut, with key results confirmed in human tissue. The results demonstrated that a high level of Aß was detected throughout the gut in both mice and human, and gut Aß42 increased with age in wild type and mutant amyloid precursor protein/presenilin 1 (APP/PS1) mice. Next, the gut microbiome of mice was characterized by 16S rRNA sequencing, and we found the gut microbiome altered significantly in aged APP/PS1 mice and fecal microbiota transplantation (FMT) of aged APP/PS1 mice increased gut BACE1 and Aß42 levels. Intra-intestinal injection of isotope or fluorescence labeled Aß combined with vagotomy was also performed to investigate the transmission of Aß from gut to brain. The data showed that, in aged mice, the gut Aß42 was transported to the brain mainly via blood rather than the vagal nerve. Furthermore, FMT of APP/PS1 mice induced neuroinflammation, a phenotype that mimics early AD pathology. Taken together, this study suggests that the gut is likely a critical source of Aß in the brain, and gut microbiota can further upregulate gut Aß production, thereby potentially contributing to AD pathogenesis.

[Role of microglial activation induced by α-synuclein in pathogenesis of Parkinson's disease].

Parkinson's disease (PD), a progressive neurodegenerative disorder, is pathologically characterized by the progressive loss of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the presence of deposits of aggregated α-synuclein in intracellular inclusions known as Lewy bodies (LB). A highly localized inflammatory response mediated by reactive microglia is prominent in PD brains, but the mechanisms underlying the microglial activation are poorly understood. Recently some lines of evidences have shown that monomeric, or aggregated α-synuclein can activate microglia, the toxic factors released from activated microglia may lead to the cell death of dopaminergic neurons. This review is to summarize the recent progress on the role of α-synuclein induced microglia activation on the PD pathogenesis and progression, and to discuss the possible mechanisms involved.

[Protective effect of nicotinamide in a mouse Parkinson's disease model].

OBJECTIVE: To examine the protective effect of nicotinamide on 1-methyl-4-phenyl-1, 2, 3, 6-tetrahydropyridine (MPTP)-induced Parkinson's disease (PD) in mouse model and its mechanisms. METHODS: Parkinson's disease was induced by injection of MPTP in adult male C57BL/6 mice, nicotinamide (500 mg/kg,i.p.) was given prior to subacute (30 mg/kg/d × 5 d,i.p.) MPTP administration. Locomotor activities, striatal dopamine levels, lactate dehydrogenase (LDH) and NO synthase (NOS) activities of whole brains and striatum were analyzed at d5 after last MPTP injections. RESULTS: Pretreatment with nicotinamide significantly improved the locomotor activity in the open-field test (P<0.01), but not in the swimming test and grip & climbing test. Nicotinamide administration resulted in sparing striatal dopamine levels from MPTP-induced dopamine depletion. There was no significant difference in LDH and NOS activities in the whole brains among the groups; but the activities in the striatum were drastically elevated after MPTP treatment. Nicotinamide pretreatment markedly inhibited MPTP-induced LDH and NOS activities (P<0.01) and showed no significant difference compared to controls (P>0.05). CONCLUSION: Nicotinamide protects dopaminergic neurons against MPTP-induced neurodegeneration,which suggests that the neuroprotective effects be associated with the inhibition of cell injuries and NOS activities.

[Population shift and degrading characteristics of a pyrene-degrading bacterial consortium during incubation process].

OBJECTIVE: The work aimed to obtain pyrene-degrading bacterial consortium and use it for bioremediation of polycyclic aromatic hydrocarbons-contaminated soil. METHODS: We enriched and incubated a bacterial consortium utilizing pyrene as the sole carbon source from the contaminated soil of Beijing Coking Chemical Plant. We analyzed the degrading ability and growth of the consortium by high performance liquid chromatography (HPLC) and spectrophotometer. We investigated the degradation activities of the consortium after several times transfer and freeze-drying deposit. We also investigated the shift of bacterial consortium composition after several times transfer by combining of culture-dependent and culture-independent methods. We constructed and analyzed the 16S rRNA gene clone libraries at different transfer times (3 times PYR-3, 6 times PYR-6 and 9 times PYR-9) for monitoring the bacterial population changes. RESULTS: The degradation rate of pyrene, phenanthrene and fluoranthene reached 89%, 86% and 49% respectively after incubation of the consortium for 12 days. The degradation activities of the consortium were stable after several times transfer and freeze-drying deposit. We isolated nine strains from the consortium, affiliated to genus of Achromobacter, Bacillus, Arthrobacter, Exiguobacterium and Parapedobacter. Phylogenetic analyses showed that Proteobacteria were the main group at contaminated soil sample (100%) and bacterial consortium incubated in pyrene (PYR-3, 83%). Bacterial community structure was shifted and biodiversity was increased during the transfer process, the proportions of gamma-Proteobacteria was decreased from 77% (PYR-3) to 33% (PYR-6) and 18% (PYR-9), while beta-Proteobacteria increased from 13% (PYR-3) to 36% (PYR-6) and 55% (PYR-9). CONCLUSION: The bacterial consortium could utilize pyrene as sole carbon and energy source for growth and the degradation ability for pyrene was stable.

Assessing rupture risk by hemodynamics, morphology and plasma concentrations of the soluble form of tyrosine kinase receptor Axl in unruptured intracranial aneurysms.

OBJECTIVE: This study investigated the relationship between morphology, hemodynamic parameters, and plasma concentrations of the soluble form of tyrosine kinase receptor Axl (sAxl) and their potential role in assessing the intracranial aneurysm rupture risk. METHODS: Thirty-nine patients were retrospectively recruited and these patients were divided into low and high rupture risk groups based on the PHASES score. Plasma levels of sAxl were measured using an enzyme-linked immunosorbent assay-based method. Computational fluid dynamics were used to calculate the morphological and hemodynamic parameters. Differences between clinical data, morphological-hemodynamic parameters and sAxl level were initially determined using univariate analysis. The variables (p ＜ 0.05) were included in a logistic regression model, and the specificity and sensitivity of the selected parameters were evaluated both graphically and statistically using receiver operating characteristic (ROC) curve methods. RESULTS: Aneurysm size ratio (p = 0.023), and normalized wall shear stress (WSS) (p = 0.02) showed significant differences between the two groups. Plasma concentrations of sAXL with a high rupture risk were significantly higher than the low rupture risk (8.47 ± 4.43 ng/ml vs. 5.37 ± 3.21 ng/ml; p = 0.016). Binary logistic regression analysis indicated that the concentration of sAxl was an independent determinant of high rupture risk (odds ratio=1.41, 95%CI=1.08-1.83, p = 0.011). The combination of sAxl + size ration (SR) + WSS achieved the highest area under the curve (0.849) for predicting rupture risk. CONCLUSIONS: Unruptured intracranial aneurysms with a higher rupture risk had a larger SR, lower WSS, and higher plasma sAxl concentration. Combining sAxl, SR, and WSS could help estimate the rupture risk of intracranial saccular aneurysm.

[Isolation and identification of a pyrene-degrading bacterial strain from contaminated soil].

OBJECTIVE: The aim of this study was to isolate high-molecular-weight polycyclic aromatic hydrocarbons (HMW-PAHs) degrading bacterial strains, and to study their degradation potential. METHODS: We used sublimation method to enrich and isolate the degrading bacteria from coking plant samples. Morphological properties, the sequence homology of 16S rRNA and gyrb genes were used to identify the isolated strains. GC-MS was used to analyze the degradation potential against some HMW-PAHs. RESULTS: An HMW-PAHs degrading bacterium,HBS1, was obtained. HBS1 could use several HMW-PAHs such as pyrene, benzoanthracene, benzopyrene, chyrsene, indeno[ 1,2,3-cd] pyrene, benzo[g,h,i]perylene and fluoranthene as sole carbon source for growth. HBS1 was identified as Gordonia sp., based on the high sequence similarities (more than 99%) of both 16S rRNA gene and gyrb gene to those of Gordonia amicalis. When the initial concentration of pyrene was 50 mg/L, HBS1 could consume 97% of the pyrene in 17 days. One fragment of the dioxygenase gene was obtained by PCR with size about 300 bp, which was closest to the counterpart from Mycobacterium sp. with 93.8% similarity. CONCLUSION: We isolated a strain HBS1 from seriously PAHs-polluted soils and identified as a Gordonia sp. The isolate had the degradation potential of high-molecular weight polycyclic aromatic hydrocarbons.

Identification and Validation of TREM2 in Intracranial Aneurysms.

Background: Intracranial aneurysm (IA) is a cerebrovascular disease that seriously endangers human heath and life. However, the pathogenesis of IA has not been clarified. Objective: In this study, we explored the role of the triggering receptor expressed on myeloid cells-2 (TREM2) gene to explore a novel mechanism underlying IA. Methods: First, we verified the role of the candidate gene, TREM2 in a modified mouse model of IA. Second, we verified elevated expression of TREM2 using the Gene Expression Omnibus (GEO) database (GSE54083 and GSE75436) and developed protein interaction (PPI) network analysis using the top one hundred DEGs from GSE75436 dataset. Finally, we predicted a likely mechanism by which TREM2 is involved in the pathology of IA using single-gene Gene Set Enrichment Analysis (GSEA). Results: The expression of TREM2 and inflammatory factors was significantly increased in the modified mouse IA model, and showed a positive correlation. Elevated expression of TREM2 was also found in IA patients tissues from the GSE54083 and GSE75436 data sets. PPI network analyses suggested that the DEGs were involved in a variety of inflammatory processes. The GSEA results suggest that TREM2 may participate in IA progression by regulating macrophage function. Conclusion: TREM2 is highly expressed in both human and mouse IA tissues, and may participate in IA progression by regulating macrophage function and inflammatory factor expression. The molecular mechanism of TREM2 involvement in the IA process can be further studied using our modified mouse IA model.

Quantitative proteomic analysis of oligodendrogliomas with and without 1p/19q deletion.

Approximately 50-80% of oligodendrogliomas demonstrate a combined loss of chromosome 1p and 19q. Chromosome 1p/19q deletion, appearing early in tumorigenesis, is associated with improved clinical outcomes, including response to chemotherapy and radiation. Although many hypotheses have been proposed, the molecular mechanisms underlying improved clinical outcomes with 1p/19q deletion in oligodendrogliomas have not been characterized fully. To investigate the molecular differences between oligodendrogliomas, we employed an unbiased proteomic approach using microcapillary liquid chromatography mass spectrometry, along with a quantitative technique called isotope-coded affinity tags, on patient samples of grade II oligodendrogliomas. Following conventional biochemical separation of pooled tumor tissue from five samples of undeleted and 1p/19q deleted grade II oligodendrogliomas into nuclei-, mitochondria-, and cytosol-enriched fractions, relative changes in protein abundance were quantified. Among the 442 total proteins identified, 163 nonredundant proteins displayed significant changes in relative abundance in at least one of the three fractions between oligodendroglioma with and without 1p/19q deletion. Bioinformatic analyses of differentially regulated proteins supported the potential importance of metabolism and invasion/migration to the codeleted phenotype. A subset of altered proteins, including the pro-invasive extracellular matrix protein BCAN, was further validated by Western blotting as candidate markers for the more aggressive undeleted phenotype. These studies demonstrate the utility of proteomic analysis to identify candidate biological motifs and molecular mechanisms that drive differential malignancy related to 1p19q phenotypes. Future analysis of larger patient samples are warranted to further refine biomarker panels to predict biological behavior and assist in the identification of deleted gene products that define the 1p/19q phenotype.