Bacterial persisters are a stochastically formed subpopulation of low-energy cells.

Persisters represent a small subpopulation of non- or slow-growing bacterial cells that are tolerant to killing by antibiotics. Despite their prominent role in the recalcitrance of chronic infections to antibiotic therapy, the mechanism of their formation has remained elusive. We show that sorted cells of Escherichia coli with low levels of energy-generating enzymes are better able to survive antibiotic killing. Using microfluidics time-lapse microscopy and a fluorescent reporter for in vivo ATP measurements, we find that a subpopulation of cells with a low level of ATP survives killing by ampicillin. We propose that these low ATP cells are formed stochastically as a result of fluctuations in the abundance of energy-generating components. These findings point to a general "low energy" mechanism of persister formation.

Anti-synthetase syndrome in a child with pneumomediastinum: a case report and literature review.

BACKGROUND: Anti-synthetase syndrome (ASS) is a group of rare clinical subtypes within inflammatory myopathies, predominantly affecting adult females. Instances of critical illness associated with ASS in children are even rarer. CASE PRESENTATION: We report the case of a 7-year-old boy finally diagnosed with ASS, combined with pneumomediastinum. He presented with intermittent fever persisting for 12 days, paroxysmal cough for 11 days, chest pain, and shortness of breath for 4 days, prompting admission to our hospital. Pre-admission chest CT revealed diffuse pneumomediastinum, subcutaneous pneumatosis in the neck and bilateral chest wall, consolidation, atelectasis, and reticular nodular shadowing in both lungs, as well as pericardial effusion and bilateral pleural effusions. Laboratory tests revealed a positive result for serum MP immunoglobulin M (MP-IgM) and MP immunoglobulin G (MP-IgG). The patient was initially diagnosed with mycoplasma pneumoniae (MP) infection, and following 3 days of antibiotic treatment, the patient's tachypnea worsened. Positive results in muscle enzyme antibody tests included anti-PL-12 antibody IgG, anti-Jo-1 antibody IgG, and anti-RO-52 antibody IgG. Ultrasonography detected moderate effusions in the right shoulder, bilateral elbow, and knee joints. Corticosteroids pulse therapy was initiated on the 27th day following disease onset, and continued for 3 days, followed by sequential therapy for an additional 12 days. The child was discharged on the 43rd day, and subsequent follow-up revealed a significant improvement in consolidation and interstitial lesions in both lungs. CONCLUSIONS: ASS in children may combine with rapidly progressive interstitial lung disease (RPILD) and pneumomediastinum. It is crucial to promptly identify concurrent immunologic abnormalities during the outbreak of MP, particularly when the disease exhibits rapid progression with ineffective conventional antibiotic therapy.

Genome-Wide Identification and Characterization of Gibberellic Acid-Stimulated Arabidopsis Gene Family in Pineapple (Ananas comosus).

The gibberellic acid-stimulated Arabidopsis (GASA) gene family plays a crucial role in growth, development, and stress response, and it is specific to plants. This gene family has been extensively studied in various plant species, and its functional role in pineapple has yet to be characterized. In this study, 15 AcGASA genes were identified in pineapple through a genome-wide scan and categorized into three major branches based on a phylogenetic tree. All AcGASA proteins share a common structural domain with 12 cysteine residues, but they exhibit slight variations in their physicochemical properties and motif composition. Predictions regarding subcellular localization suggest that AcGASA proteins are present in the cell membrane, Golgi apparatus, nucleus, and cell wall. An analysis of gene synteny indicated that both tandem and segmental repeats have a significant impact on the expansion of the AcGASA gene family. Our findings demonstrate the differing regulatory effects of these hormones (GA, NAA, IAA, MeJA, and ABA) on the AcGASA genes. We analyzed the expression profiles of GASA genes in different pineapple tissue parts, and the results indicated that AcGASA genes exhibit diverse expression patterns during the development of different plant tissues, particularly in the regulation of floral organ development. This study provides a comprehensive understanding of GASA family genes in pineapple. It serves as a valuable reference for future studies on the functional characterization of GASA genes in other perennial herbaceous plants.

Integrative Analysis of Metabolome and Transcriptome Provides Insights into the Mechanism of Flower Induction in Pineapple (Ananas comosus (L.) Merr.) by Ethephon.

Exogenous ethylene is commonly utilized to initiate flower induction in pineapple (Ananas comosus (L.) Merr.). However, the molecular mechanisms and metabolic changes involved are not well understood. In this study, we explored the genetic network and metabolic shifts in the 'Comte de Paris' pineapple variety during ethylene-induced flowering. This was achieved through an integrative analysis of metabolome and transcriptome profiles at vegetative shoot apexes (0 d after ethephon treatment named BL_0d), the stage of bract primordia (8 d after ethephon treatment named BL_8d), stage of flower primordia (18 d after ethephon treatment named BL_18d), and the stage of stopped floret differentiation (34 d after ethephon treatment named BL_34d). We isolated and identified 804 metabolites in the pineapple shoot apex and inflorescence, categorized into 24 classes. Notably, 29, 31, and 46 metabolites showed significant changes from BL_0d to BL_8d, BL_8d to BL_18d, and BL_18d to BL_34d, respectively. A marked decrease in indole was observed, suggesting its role as a characteristic metabolite during flower induction. Transcriptomic analysis revealed 956, 1768, and 4483 differentially expressed genes (DEGs) for BL_0d vs. BL_8d, BL_8d vs. BL_18d, and BL_18d vs. BL_34d, respectively. These DEGs were significantly enriched in carbohydrate metabolism and hormone signaling pathways, indicating their potential involvement in flower induction. Integrating metabolomic and transcriptomic data, we identified several candidate genes, such as Agamous-Like9 (AGL9), Ethylene Insensitive 3-like (ETIL3), Apetala2 (AP2), AP2-like ethylene-responsive transcription factor ANT (ANT), and Sucrose synthase 2 (SS2), that play potentially crucial roles in ethylene-induced flower induction in pineapple. We also established a regulatory network for pineapple flower induction, correlating metabolites and DEGs, based on the Arabidopsis thaliana pathway as a reference. Overall, our findings offer a deeper understanding of the metabolomic and molecular mechanisms driving pineapple flowering.

A novel variant in the ROR2 gene underlying brachydactyly type B: a case report.

BACKGROUND: Brachydactyly type B is an autosomal dominant disorder that is characterized by hypoplasia of the distal phalanges and nails and can be divided into brachydactyly type B1 (BDB1) and brachydactyly type B2 (BDB2). BDB1 is the most severe form of brachydactyly and is caused by truncating variants in the receptor tyrosine kinase-like orphan receptor 2 (ROR2) gene. CASE PRESENTATION: Here, we report a five-generation Chinese family with brachydactyly with or without syndactyly. The proband and her mother underwent digital separation in syndactyly, and the genetic analyses of the proband and her parents were provided. The novel heterozygous frameshift variant c.1320dupG, p.(Arg441Alafs*18) in the ROR2 gene was identified in the affected individuals by whole-exome sequencing and Sanger sequencing. The c.1320dupG variant in ROR2 is predicted to produce a truncated protein that lacks tyrosine kinase and serine/threonine- and proline-rich structures and remarkably alters the tertiary structures of the mutant ROR2 protein. CONCLUSION: The c.1320dupG, p.(Arg441Alafs*18) variant in the ROR2 gene has not been reported in any databases thus far and therefore is novel. Our study extends the gene variant spectrum of brachydactyly and may provide information for the genetic counselling of family members.

Genome-Wide Identification and Expression Patterns of AcSWEET Family in Pineapple and AcSWEET11 Mediated Sugar Accumulation.

Pineapple (Ananas comosus L.) is an important fruit crop in tropical regions, and it requires efficient sugar allocation during fruit development. Sugars Will Eventually be Exported Transporters (SWEETs) are a group of novel sugar transporters which play critical roles in seed and fruit development. However, the function of AcSWEETs remains unknown in the sugar accumulation. Herein, 17 AcSWEETs were isolated and unevenly located in 11 chromosomes. Analysis of a phylogenetic tree indicated that 17 genes were classified into four clades, and the majority of AcSWEETs in each clade shared similar conserved motifs and gene structures. Tissue-specific gene expression showed that expression profiles of AcSWEETs displayed differences in different tissues and five AcSWEETs were strongly expressed during fruit development. AcSWEET11 was highly expressed in the stage of mature fruits in 'Tainong16' and 'Comte de paris', which indicates that AcSWEET11 was important to fruit development. Subcellular localization analysis showed that AcSWEET11 was located in the cell membrane. Notably, overexpression of AcSWEET11 could improve sugar accumulation in pineapple callus and transgenic tomato, which suggests that AcSWEET11 might positively contribute to sugar accumulation in pineapple fruit development. These results may provide insights to enhance sugar accumulation in fruit, thus improving pineapple quality in the future.

Genetic diversity of Ziziphus mauritiana germplasm based on SSR markers and ploidy level estimation.

MAIN CONCLUSION: A set of reliable SSR markers were developed for Ziziphus mauritiana. The genetic relationship of Z. mauritiana germplasms was generally consistent with their geographical origin, and low diversity in the maternal lineage was revealed. Ziziphus mauritiana, known as Indian jujube, is an important fruit crop that is native to southern Asia and eastern Africa. There is a variety of germplasm resources, and particularly many new cultivars were selected and introduced into wide tropical regions in recent years. However, there are few practical molecular markers for cultivar authentication and genetic analysis. In this study, we developed 55 polymorphic nuclear SSR markers based on restriction-site associated DNA sequences and transcriptome sequencing. We selected 14 robust nSSR markers for further analysis of 117 Z. mauritiana accessions from four countries (45 from China, 39 from Vietnam, 25 from Pakistan and 8 from Myanmar). In total, 137 alleles were detected and DNA fingerprints for each accession were constructed. Cluster analysis based on the unweighted pair group method with arithmetic mean displayed that most accessions clustered consistently with their geographic origin. In addition, there was common and high degree polyploidization based on nSSR and flow cytometry analyses. Only two of the 50 SSR loci in noncoding regions from the chloroplast genome had polymorphisms, and 5 haplotypes in total were identified among the 117 accessions. Haplotype C with 89 accessions was the most dominant haplotype and presented in four countries. This indicates low diversity in the maternal lineage of tested Z. mauritiana germplasm. Our research provides reliable marker resources for cultivar authentication and new insights into the genetic diversity, polyploidization and domestication of Z. mauritiana.

Unique clustering genes in the bacterial chromosome affecting the type-III secretion of enterohaemorrhagic Escherichia coli.

Bioinformatics analysis was used to search for unknown genes that might influence the phenotypic presentations of enterohaemorrhagic Escherichia coli (EHEC). By so doing and using the known genomic data from EHEC O157 : H7 and K-12, it has been deduced that genes Z4863 to Z4866 of EHEC do not exist in K-12 strains. These four gene sequences have low degrees of homology (18-40 % amino acid identities) to a set of genes in K-12, which have been known to encode fatty acid biosynthesis enzymes. We referred these four consecutive genes as a fasyn cluster and found that deletion of fasyn from EHEC resulted in a defective type-III secretion (T3S). This deletion apparently did not decrease the amounts of the T3S proteins ectopically expressed from plasmids. Examination of the corresponding mRNAs by real-time PCR revealed that the mRNAs readily decreased in the fasyn-deleted mutant and this suppressive effect on the mRNA levels appeared to spread across all lee operons. Complementation with fasyn reverted the T3S-deficient phenotype. Furthermore, this reversion was also seen when the mutant was supplemented with locus of enterocyte effacement activators (Ler or GrlA). Thus, these unique clustering genes located apart from locus of enterocyte effacement on the bacterial chromosome also play a role in affecting T3S of EHEC.

Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.

Conjugative type 4 secretion systems (T4SSs) are the main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. To deliver the DNA substrate to recipient cells, it must cross the cell envelopes of both donor and recipient bacteria. In the T4SS from the enterococcal conjugative plasmid pCF10, PrgK is known to be the active cell wall degrading enzyme. It has three predicted extracellular hydrolase domains: metallo-peptidase (LytM), soluble lytic transglycosylase (SLT), and cysteine, histidine-dependent amidohydrolases/peptidases (CHAP). Here, we report the structure of the LytM domain and show that its active site is degenerate and lacks the active site metal. Furthermore, we show that only the predicted SLT domain is functional in vitro and that it unexpectedly has a muramidase instead of a lytic transglycosylase activity. While we did not observe any peptidoglycan hydrolytic activity for the LytM or CHAP domain, we found that these domains downregulated the SLT muramidase activity. The CHAP domain was also found to be involved in PrgK dimer formation. Furthermore, we show that PrgK interacts with PrgL, which likely targets PrgK to the rest of the T4SS. The presented data provides important information for understanding the function of Gram-positive T4SSs.IMPORTANCEAntibiotic resistance is a large threat to human health and is getting more prevalent. One of the major contributors to the spread of antibiotic resistance among different bacteria is type 4 secretion systems (T4SS). However, mainly T4SSs from Gram-negative bacteria have been studied in detail. T4SSs from Gram-positive bacteria, which stand for more than half of all hospital-acquired infections, are much less understood. The significance of our research is in identifying the function and regulation of a cell wall hydrolase, a key component of the pCF10 T4SS from Enterococcus faecalis. This system is one of the best-studied Gram-positive T4SSs, and this added knowledge aids in our understanding of horizontal gene transfer in E. faecalis as well as other medically relevant Gram-positive bacteria.

Pulp cellulose-based core-sheath structure based on hyperbranched grafting strategy for development of reinforced soybean adhesive.

Formaldehyde adhesive is the primary source of indoor formaldehyde pollution, posing a serious threat to human health. Soybean meal (SM), as an abundant biomacromolecule and co-product of soybean oil industry, emerges as a promising alternative to formaldehyde adhesive. However, the SM adhesive exhibits inferior water resistance and unsatisfactory bonding strength. In this study, a novel core-sheath structure with an inexpensive pulp cellulose core and a hyperbranched polymer sheath is synthesized and introduced into SM to develop a robust bio-based adhesive. Specifically, aldehyde-functionalized pulp cellulose is grafted with hyperbranched polyamide, which is terminated via epoxy groups, to synthesize a core-sheath hybrid (APC@HBPA-EP). The core-sheath APC@HBPA-EP serves as both a crosslinker and an enhancer. The results show that the wet shear strength of the modified SM adhesive exhibits a remarkable 520 % increase to 0.93 MPa, and its dry shear strength reaches 2.10 MPa, meeting the established indoor use standards. The Young's modulus of the modified SM adhesive shows a significant 282 % increase to 19.27 GPa. Additionally, the modified SM adhesive exhibited superior impact toughness (7.48 KJ/m2), which increased by 24 times compared with pure SM adhesive. This study provides a versatile strategy for developing robust protein adhesives, hydrogel patch, and composite coatings.

PrgE: an OB-fold protein from plasmid pCF10 with striking differences to prototypical bacterial SSBs.

A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the Enterococcus faecalis plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.

Prognostic Values of Core Genes in Pilocytic Astrocytom.

BACKGROUND: Pilocytic astrocytoma (PA) is the most common primary brain tumor in children and adolescents. Treatment strategy largely depends on its key genes and molecular mutations. This study aimed to identify potential biomarkers of PA closely related to its prognosis. METHODS: The gene expression profiles (series numbers GSE50161, GSE66354, and GSE86574) of PA and normal brain tissues were downloaded from the Gene Expression Omnibus database. The Gene Expression Omnibus2R was used to identify differentially expressed genes. The overlapping differentially expressed genes were subjected to Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses using the Database for Annotation, Visualization, and Integrated Discovery (DAVID) database. A protein-protein interaction network was constructed using Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape. The Gene Expression Profiling Interactive Analysis 2 (GEPIA2) tool analyzed the impact of hub genes on PA prognosis based on the Kaplan-Meier curves. RESULTS: Compared with normal brain tissues (n = 36), a total of 37 upregulated and 144 downregulated genes were identified in PA (n = 40). In the protein-protein interaction network construction and GEPIA2 survival analysis, 2 of the top 10 hub genes were significantly associated with decreased overall survival of PA patients, namely Gamma-aminobutyric acid A receptor alpha 2 (hazard ratio = 2.8, P < 0.01) and regulating synaptic membrane exocytosis protein 1) (hazard ratio = 3.2, P  <  0.01). CONCLUSIONS: This bioinformatics analysis reveals that low expression of Gamma-aminobutyric acid A receptor alpha 2 and regulating synaptic membrane exocytosis protein 1 is associated with a favorable prognosis for PA patients. These 2 hub genes could be novel biomarkers for prognosis assessment, furthermore a key element for treatment decisions in the future.

Structural foundation for the role of enterococcal PrgB in conjugation, biofilm formation, and virulence.

Type 4 Secretion Systems are a main driver for the spread of antibiotic resistance genes and virulence factors in bacteria. In Gram-positives, these secretion systems often rely on surface adhesins to enhance cellular aggregation and mating-pair formation. One of the best studied adhesins is PrgB from the conjugative plasmid pCF10 of Enterococcus faecalis, which has been shown to play major roles in conjugation, biofilm formation, and importantly also in bacterial virulence. Since prgB orthologs exist on a large number of conjugative plasmids in various different species, this makes PrgB a model protein for this widespread virulence factor. After characterizing the polymer adhesin domain of PrgB previously, we here report the structure for almost the entire remainder of PrgB, which reveals that PrgB contains four immunoglobulin (Ig)-like domains. Based on this new insight, we re-evaluate previously studied variants and present new in vivo data where specific domains or conserved residues have been removed. For the first time, we can show a decoupling of cellular aggregation from biofilm formation and conjugation in prgB mutant phenotypes. Based on the presented data, we propose a new functional model to explain how PrgB mediates its different functions. We hypothesize that the Ig-like domains act as a rigid stalk that presents the polymer adhesin domain at the right distance from the cell wall.

Activation Map Reveals Language Impairment in Children with Benign Epilepsy with Centrotemporal Spikes (BECTS).

Objective: Neuropsychological evidence revealed language impairment in children with benign epilepsy with centrotemporal spikes (BECTS). This study investigates language function using task-activated fMRI. Methods: We conducted a language task fMRI study on three groups on a 3.0T MRI scanner, including a new onset drug naïve group (NODN-BECTS, n=11, age=9.6±1.6), an established epilepsy with medication-treated group (Med-BECTS, n=17, age=10.7±2.2) and a healthy control group (HC, n=18, age=10.8±1.7). We use MATLAB14 and SPM12 to pre-process and analyze the data. A one-sample t-test was used to identify task-related brain activation changes in each group, based on the general linear model (GLM). And, then two sample t-test was performed to compare different activated regions between groups. In addition, scores on the most recent Mandarin school exams were acquired to examine and contrast extra-scanner language performance. Results: Statistical results show that some language-related brain regions (such as the left superior frontal gyrus and cerebellar vermis) were additionally activated in the NODN-BECTS group compared with the HC group. Compared with NODN-BECTS and HC groups, decreased activations were found in language-related regions in the Med-BECTS group, including the left insula, superior and middle frontal gyri, and bilateral middle occipital gyri. On the Mandarin school exams, the average score for HC was 87.3±8.2, NODN was 84.8±7.8, and Med was 78.2±13.2. There was a trend toward statistical significance between the Med and the HC (p = 0.074) as well as NODN (p = 0.092) groups. No statistically significant differences were found between the HC and the NODN-BECTS groups. Significance: Language task fMRI reveals additional areas of activation in new onset BECTS compared to healthy controls which may be compensatory in nature. Antiseizure medications (ASMs) and/or longer duration of BECTS additionally appears to affect language-related regions and reduce their functional ability.

Fabrication of Durable Hydrophobic/Superhydrophobic Wood Using an Alkyl Ketene Dimer by a Simple and Feasible Method.

To improve the hydrophobicity of precious hardwood, a facile sanding pretreatment and alkyl ketene dimer (AKD) modification were performed. After the AKD modification, the wood was highly hydrophobic, and the contact angle was 143°. The increased hydrophobicity could be attributed to the ester bond formed between the wood hydroxyl groups and AKD, which was confirmed by attenuated total reflectance-Fourier transform infrared spectroscopy. Sanding pretreatment could further greatly increase the wood hydrophobicity and render it superhydrophobic, not only in a cross-section but also in the tangential and radial sections. The changed wood surface roughness could be responsible for the increased hydrophobicity, which was confirmed by characterization with a scanning electron microscope (SEM) and a three-dimensional optical microscope. Apart from the improved hydrophobicity, the AKD-modified wood exhibited excellent water, acid, and toluene resistance. After a 12 h immersion, the contact angle did not change significantly, and the acid immersion contributed to an improvement in the hydrophobicity of the wood. Furthermore, the resultant AKD-modified wood exhibited an excellent self-cleaning effect.

Structure of the enterococcal T4SS protein PrgL reveals unique dimerization interface in the VirB8 protein family.

Multidrug-resistant bacteria pose serious problems in hospital-acquired infections (HAIs). Most antibiotic resistance genes are acquired via conjugative gene transfer, mediated by type 4 secretion systems (T4SS). Although most multidrug-resistant bacteria responsible for HAIs are of Gram-positive origin, with enterococci being major contributors, mostly Gram-negative T4SSs have been characterized. Here, we describe the structure and organization of PrgL, a core protein of the T4SS channel, encoded by the pCF10 plasmid from Enterococcus faecalis. The structure of PrgL displays similarity to VirB8 proteins of Gram-negative T4SSs. In vitro experiments show that the soluble domain alone is enough to drive both dimerization and dodecamerization, with a dimerization interface that differs from all other known VirB8-like proteins. In vivo experiments verify the importance of PrgL dimerization. Our findings provide insight into the molecular building blocks of Gram-positive T4SS, highlighting similarities but also unique features in PrgL compared to other VirB8-like proteins.

Whole-Body MRI Is an Effective Imaging Modality for Hematological Malignancy Treatment Response Assessment: A Systematic Review and Meta-Analysis.

OBJECTIVES: To evaluate the diagnostic accuracy of whole-body MRI (WB-MRI) for assessment of hematological malignancies' therapeutic response. METHODS: PubMed, Embase, and Web of Science were searched up to August 2021 to identify studies reporting the diagnostic performance of WB-MRI for the assessment of hematological malignancies' treatment response. A bivariate random-effects model was applied for the generation of the pooled diagnostic performance. RESULTS: Fourteen studies with 457 patients with lymphoma, multiple myeloma, and sarcoma (very small proportion) were analyzed. Overall pooled sensitivity and specificity of WB-MRI were 0.88 (95% CI: 0.73-0.95) and 0.86 (95% CI: 0.73-0.93), respectively. Studies using whole-body diffusion-weighted imaging (WB-DWI) showed higher sensitivity than those that did not (0.94 vs. 0.55, p = 0.02). The pooled concordance rate of WB-MRI to assess hematological malignancies' treatment response with reference standard was 0.78 (95% CI: 0.59-0.96). WB-MRI and PET/CT showed similar diagnostic performance (sensitivity [0.83 vs. 0.92, p = 0.11] and specificity [0.87 vs. 0.76, p = 0.73]). CONCLUSION: WB-MRI has high diagnostic performance for hematological malignancies' treatment response assessment. The adding of WB-DWI is strongly associated with increased sensitivity.

Functional characterization of Trip10 in cancer cell growth and survival.

BACKGROUND: The Cdc42-interacting protein-4, Trip10 (also known as CIP4), is a multi-domain adaptor protein involved in diverse cellular processes, which functions in a tissue-specific and cell lineage-specific manner. We previously found that Trip10 is highly expressed in estrogen receptor-expressing (ER+) breast cancer cells. Estrogen receptor depletion reduced Trip10 expression by progressively increasing DNA methylation. We hypothesized that Trip10 functions as a tumor suppressor and may be involved in the malignancy of ER-negative (ER-) breast cancer. To test this hypothesis and evaluate whether Trip10 is epigenetically regulated by DNA methylation in other cancers, we evaluated DNA methylation of Trip10 in liver cancer, brain tumor, ovarian cancer, and breast cancer. METHODS: We applied methylation-specific polymerase chain reaction and bisulfite sequencing to determine the DNA methylation of Trip10 in various cancer cell lines and tumor specimens. We also overexpressed Trip10 to observe its effect on colony formation and in vivo tumorigenesis. RESULTS: We found that Trip10 is hypermethylated in brain tumor and breast cancer, but hypomethylated in liver cancer. Overexpressed Trip10 was associated with endogenous Cdc42 and huntingtin in IMR-32 brain tumor cells and CP70 ovarian cancer cells. However, overexpression of Trip10 promoted colony formation in IMR-32 cells and tumorigenesis in mice inoculated with IMR-32 cells, whereas overexpressed Trip10 substantially suppressed colony formation in CP70 cells and tumorigenesis in mice inoculated with CP70 cells. CONCLUSIONS: Trip10 regulates cancer cell growth and death in a cancer type-specific manner. Differential DNA methylation of Trip10 can either promote cell survival or cell death in a cell type-dependent manner.

DNA methylation of the Trip10 promoter accelerates mesenchymal stem cell lineage determination.

Epigenetic regulation of gene expression by DNA methylation and histone modification controls cell fate during development and homeostasis in adulthood. Aberrant epigenetic modifications may lead to abnormal development, even diseases. We have found that Trip10 (thyroid hormone receptor interactor 10), an adaptor protein involved in diverse functions, is epigenetically regulated during lineage-specific induction of human bone marrow-derived mesenchymal stem cells (MSCs). To determine whether DNA methylation-induced gene silencing is sufficient to restrict cell fate changes, we applied an invitro method to specifically methylate the promoter of Trip10. Our hypothesis was that the methylation status of the Trip10 promoter in MSCs alters the differentiation preference of MSCs. Transfection of in vitro-methylated Trip10 promoter DNA into MSCs resulted in progressive accumulation of cytosine methylation at the endogenous Trip10 promoter, reduced Trip10 expression, and accelerated MSC-to-neuron and MSC-to-osteocyte differentiation. A two-component EGFP reporter gene system was established to confirm the level of transcriptional silencing and visualize the targeted DNA methylation. EGFP expression induced in the reporter system by targeted Trip10 methylation was reversed by adding 5-aza-2'-deoxycytidine, a DNA methyltransferase inhibitor, confirming that the suppressed Trip10 expression and disrupted MSC differentiation resulted from the in vitro-introduced methylations in the Trip10 promoter. With this targeted DNA methylation and reporter system, we are able to monitor the progression of locus-specific DNA methylation in vivo and correlate such changes with potential functional changes. Using this approach, we have established a new role for Trip10, showing that the level of Trip10 expression is associated with the maintenance and differentiation of MSCs.

A role of ygfZ in the Escherichia coli response to plumbagin challenge.

Plumbagin is found in many herbal plants and inhibits the growth of various bacteria. Escherichia coli strains are relatively resistant to this drug. The mechanism of resistance is not clear. Previous findings showed that plumbagin treatment triggered up-regulation of many genes in E. coli including ahpC, mdaB, nfnB, nfo, sodA, yggX and ygfZ. By analyzing minimal inhibition concentration and inhibition zones of plumbagin in various gene-disruption mutants, ygfZ and sodA were found critical for the bacteria to resist plumbagin toxicity. We also found that the roles of YgfZ and SodA in detoxifying plumbagin are independent of each other. This is because of the fact that ectopically expressed SodA reduced the superoxide stress but not restore the resistance of bacteria when encountering plumbagin at the absence of ygfZ. On the other hand, an ectopically expressed YgfZ was unable to complement and failed to rescue the plumbagin resistance when sodA was perturbed. Furthermore, mutagenesis analysis showed that residue Cys228 within YgfZ fingerprint region was critical for the resistance of E. coli to plumbagin. By solvent extraction and HPLC analysis to follow the fate of the chemical, it was found that plumbagin vanished apparently from the culture of YgfZ-expressing E. coli. A less toxic form, methylated plumbagin, which may represent one of the YgfZ-dependent metabolites, was found in the culture supernatant of the wild type E. coli but not in the ΔygfZ mutant. Our results showed that the presence of ygfZ is not only critical for the E coli resistance to plumbagin but also facilitates the plumbagin degradation.