The inside scoop: Comparative genomics of two intranuclear bacteria, "Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae".

"Candidatus Berkiella cookevillensis" (strain CC99) and "Candidatus Berkiella aquae" (strain HT99), belonging to the Coxiellaceae family, are gram-negative bacteria isolated from amoebae in biofilms present in human-constructed water systems. Both bacteria are obligately intracellular, requiring host cells for growth and replication. The intracellular bacteria-containing vacuoles of both bacteria closely associate with or enter the nuclei of their host cells. In this study, we analyzed the genome sequences of CC99 and HT99 to better understand their biology and intracellular lifestyles. The CC99 genome has a size of 2.9Mb (37.9% GC) and contains 2,651 protein-encoding genes (PEGs) while the HT99 genome has a size of 3.6Mb (39.4% GC) and contains 3,238 PEGs. Both bacteria encode high proportions of hypothetical proteins (CC99: 46.5%; HT99: 51.3%). The central metabolic pathways of both bacteria appear largely intact. Genes for enzymes involved in the glycolytic pathway, the non-oxidative branch of the phosphate pathway, the tricarboxylic acid pathway, and the respiratory chain were present. Both bacteria, however, are missing genes for the synthesis of several amino acids, suggesting reliance on their host for amino acids and intermediates. Genes for type I and type IV (dot/icm) secretion systems as well as type IV pili were identified in both bacteria. Moreover, both bacteria contain genes encoding large numbers of putative effector proteins, including several with eukaryotic-like domains such as, ankyrin repeats, tetratricopeptide repeats, and leucine-rich repeats, characteristic of other intracellular bacteria.

Aurone-derived 1,2,3-triazoles as potential fluorescence molecules in vitro.

Aurones are a class of well-studied natural compounds primarily responsible for the yellow pigment in flowering plants and have been shown to have fluorescent properties as well as beneficial biological effects. Traditionally, aurones can be easily synthesized through a Knoevenagel condensation of benzofuranones with arylaldehydes. Recently, Kafle et al. unexpectedly synthesized a new aurone derivative containing a 1,2,3-triazole within its backbone. Since, 1,2,3-triazole containing structures have been shown to be useful as fluorophores with large Stokes shifts, we hypothesized that these new aurone-derived triazole compounds (ATs) could be utilized as potential fluorophores. Here we describe a newly-synthesized fluorescent compound which has potential for use as a live-cell probe, having a large Stokes shift of 118.3 ± 1.01 nm in phosphate-buffered saline with the benefit of increased fluorescence in protic environments, which is uncommon in aurone-derived fluorophores.

The SWI/SNF ATPase BRG1 facilitates multiple pro-tumorigenic gene expression programs in SMARCB1-deficient cancer cells.

Malignant rhabdoid tumor (MRT) is driven by the loss of the SNF5 subunit of the SWI/SNF chromatin remodeling complex and then thought to be maintained by residual SWI/SNF (rSWI/SNF) complexes that remain present in the absence of SNF5. rSWI/SNF subunits colocalize extensively on chromatin with the transcription factor MYC, an oncogene identified as a novel driver of MRT. Currently, the role of rSWI/SNF in modulating MYC activity has neither been delineated nor has a direct link between rSWI/SNF and other oncogenes been uncovered. Here, we expose the connection between rSWI/SNF and oncogenic processes using a well-characterized chemical degrader to deplete the SWI/SNF ATPase, BRG1. Using a combination of gene expression and chromatin accessibility assays we show that rSWI/SNF complexes facilitate MYC target gene expression. We also find that rSWI/SNF maintains open chromatin at sites associated with hallmark cancer genes linked to the AP-1 transcription factor, suggesting that AP-1 may drive oncogenesis in MRT. Interestingly, changes in MYC target gene expression are not overtly connected to the chromatin remodeling function of rSWI/SNF, revealing multiple mechanisms used by rSWI/SNF to control transcription. This work provides an understanding of how residual SWI/SNF complexes may converge on multiple oncogenic processes when normal SWI/SNF function is impaired.

Panax quinquefolius (North American Ginseng) Polysaccharides as Immunomodulators: Current Research Status and Future Directions.

Panax quinquefolius (North American ginseng, NAG) is a popular medicinal plant used widely in traditional medicine. NAG products are currently available in various forms such as roots, extracts, nutraceuticals, dietary supplements, energy drinks, etc. NAG polysaccharides are recognized as one of the major bioactive ingredients. However, most NAG reviews are focused on ginsenosides with little information on polysaccharides. NAG polysaccharides have demonstrated a therapeutic activity in numerous studies, in which many of the bioactivities involve regulation of the immune response. The purpose of this review is to summarize the structural features and the immunomodulatory properties of crude, partially purified, and pure polysaccharides isolated from NAG. Receptors of the innate immune system that potentially bind to NAG polysaccharides and the respective signal transduction pathways initiated by these compounds are discussed. Major challenges, recent innovations, and future directions in NAG polysaccharide research are also summarized.

An acidic polysaccharide (AGC3) isolated from North American ginseng (Panax quinquefolius) suspension culture as a potential immunomodulatory nutraceutical.

Polysaccharides isolated from Panax quinquefolius roots are widely used as nutraceuticals due to their immunomodulatory properties. Despite their popularity, several challenges exist in isolating ginseng root polysaccharides such as batch-to-batch structural inconsistencies and bacterial endotoxin contamination. A plant tissue culture-based platform offers a potential solution to isolate natural polysaccharide fractions with consistent chemical characteristics and reduced endotoxin content. In this study, an acidic polysaccharide fraction (AGC3) with immunomodulatory properties was isolated from Panax quinquefolius suspension cultures. The heterogeneous fraction (molecular weight: 4.81 and 32.14 kDa), purified by anion exchange chromatography, was predominantly composed of galactose (>60%) along with the presence of rhamnose, arabinose, glucose, glucuronic acid and galacturonic acid. The major glycosidic linkages were found to be t-Galp (47.7%), 4-Galp (15.6%), 2,4-Rhap (8.1%), 6-Galp (8.1%) and 4-GalAp (6.8%). Structural analyses indicated the presence of a pectic rhamnogalacturonan I polysaccharide in AGC3. AGC3 significantly (p < 0.05) stimulated RAW 264.7 murine macrophage cells and primary murine splenocytes by enhancing the production of several immunomodulatory mediators such as IL-6, TNF-α, GM-CSF and MCP-1. The results also indicated the putative roles of NF-κB (p65/RelA) and MAPK (p38) signaling pathways in the immunostimulatory response. Additionally, AGC3 induced murine splenocyte proliferation, another major indicator of immunostimulation. Overall, AGC3 has the potential to be used as an immunostimulatory nutraceutical.

Chemogenomic profiling to understand the antifungal action of a bioactive aurone compound.

Every year, more than 250,000 invasive candidiasis infections are reported with 50,000 deaths worldwide. The limited number of antifungal agents necessitates the need for alternative antifungals with potential novel targets. The 2-benzylidenebenzofuran-3-(2H)-ones have become an attractive scaffold for antifungal drug design. This study aimed to determine the antifungal activity of a synthetic aurone compound and characterize its mode of action. Using the broth microdilution method, aurone SH1009 exhibited inhibition against C. albicans, including resistant isolates, as well as C. glabrata, and C. tropicalis with IC50 values of 4-29 µM. Cytotoxicity assays using human THP-1, HepG2, and A549 human cell lines showed selective toxicity toward fungal cells. The mode of action for SH1009 was characterized using chemical-genetic interaction via haploinsufficiency (HIP) and homozygous (HOP) profiling of a uniquely barcoded Saccharomyces cerevisiae mutant collection. Approximately 5300 mutants were competitively treated with SH1009 followed by DNA extraction, amplification of unique barcodes, and quantification of each mutant using multiplexed next-generation sequencing. Barcode post-sequencing analysis revealed 238 sensitive and resistant mutants that significantly (FDR P values ≤ 0.05) responded to aurone SH1009. The enrichment analysis of KEGG pathways and gene ontology demonstrated the cell cycle pathway as the most significantly enriched pathway along with DNA replication, cell division, actin cytoskeleton organization, and endocytosis. Phenotypic studies of these significantly enriched responses were validated in C. albicans. Flow cytometric analysis of SH1009-treated C. albicans revealed a significant accumulation of cells in G1 phase, indicating cell cycle arrest. Fluorescence microscopy detected abnormally interrupted actin dynamics, resulting in enlarged, unbudded cells. RT-qPCR confirmed the effects of SH1009 in differentially expressed cell cycle, actin polymerization, and signal transduction genes. These findings indicate the target of SH1009 as a cell cycle-dependent organization of the actin cytoskeleton, suggesting a novel mode of action of the aurone compound as an antifungal inhibitor.

Panax quinquefolius (North American ginseng) cell suspension culture as a source of bioactive polysaccharides: Immunostimulatory activity and characterization of a neutral polysaccharide AGC1.

In this study, we propose the use of a plant tissue culture-based system for the production of polysaccharides with consistent chemical characteristics and reduced endotoxin content. Polysaccharides were isolated from suspension cultures of Panax quinquefolius (American ginseng), a widely used medicinal herb. A neutral fraction, AGC1, purified by anion exchange and size exclusion chromatography, displayed immunostimulatory activity in vitro and ex vivo. AGC1 (average molecular weight: 5.2kDa) was predominantly composed of galactose (>60%) along with the presence of several other neutral sugars such as arabinose, xylose, glucose, mannose and rhamnose in minor amounts. The major glycosidic linkages were found to be 3-Galp (48.5%), 3,6-Galp (10.2%), t-Galp (5.2%), 6-Galp (4.4%), 4-Glcp (5.7%), 4-Arap/5-Araf (4.0%) and t-Araf (4.5%). AGC1 significantly (p<0.05) stimulated the expression of a range of proinflammatory mediators in RAW 264.7 murine macrophages such as IL-6, TNF-α, MCP-1 and GM-CSF. Additionally, AGC1 treatment of RAW 264.7 cells stimulated NOS2 gene expression, leading to increased levels of iNOS and downstream NO. Consistent with this, AGC1 was able to act as an immunostimulant in primary murine splenocytes, enhancing cell proliferation, as well as NO and TNF-α production. Our results also indicate the partial role of NF-κB pathway in the immunostimulatory response.

Infection and nuclear interaction in mammalian cells by 'Candidatus Berkiella cookevillensis', a novel bacterium isolated from amoebae.

BACKGROUND: 'Candidatus Berkiella cookevillensis' and 'Ca. Berkiella aquae' have previously been described as intranuclear bacteria of amoebae. Both bacteria were isolated from amoebae and were described as appearing within the nuclei of Acanthamoeba polyphaga and ultimately lysing their host cells within 4 days. Both bacteria are Gammaproteobacteria in the order Legionellales with the greatest similarity to Coxiella burnetii. Neither bacterium grows axenically in artificial culture media. In this study, we further characterized 'Ca. B. cookevillensis' by demonstrating association with nuclei of human phagocytic and nonphagocytic cell lines. RESULTS: Transmission electron microscopy (TEM) and confocal microscopy were used to confirm nuclear co-localization of 'Ca. B. cookevillensis' in the amoeba host A. polyphaga with 100% of cells having bacteria co-localized with host nuclei by 48 h. TEM and confocal microscopy demonstrated that the bacterium was also observed to be closely associated with nuclei of human U937 and THP-1 differentiated macrophage cell lines and nonphagocytic HeLa human epithelial-like cells. Immunofluorescent staining revealed that the bacteria-containing vacuole invaginates the nuclear membranes and appears to cross from the cytoplasm into the nucleus as an intact vacuole. CONCLUSION: Results of this study indicate that a novel coccoid bacterium isolated from amoebae can infect human cell lines by associating with the host cell nuclei, either by crossing the nuclear membranes or by deeply invaginating the nuclear membranes. When associated with the nuclei, the bacteria appear to be bound within a vacuole and replicate to high numbers by 48 h. We believe this is the first report of such a process involving bacteria and human cell lines.

Isolation, structure elucidation, and immunostimulatory activity of polysaccharide fractions from Boswellia carterii frankincense resin.

Frankincense has a long history in religious, cultural, and medicinal use. In this study polysaccharides were extracted from frankincense from Boswellia carterii. The polysaccharides were purified by anion exchange chromatography on a DEAE-Sepharose Fast Flow 16/10 FPLC column. Six fractions were obtained and the three most active immunomodulatory fractions were further purified by size exclusion chromatography on a Superdex-200 column. The composition showed the monosaccharides present were predominantly galactose, arabinose, and glucuronic acid along with small amounts of rhamnose and glucose. The monosaccharide composition and glycosyl linkage analysis revealed the polysaccharides belong to the type II arabinogalactans. Fourier-transform infrared spectroscopy and bicinchoninic acid assay showed that the amount of protein in the samples was <1 wt%. One-dimensional 1H NMR were consistent with high molecular weight compounds. The monosaccharides were primarily in the ß conformation. The three fractions exhibited an immunostimulatory effect on RAW 264.7 murine macrophage cells. The most active immunostimulatory fraction FA2, stimulated a range of pro-inflammatory mediators including iNOS, NO, TNF-α, and IL-6 in RAW 264.7 cells. The fractions were effective in proliferating primary murine splenocytes. The results indicate that the polysaccharides isolated from frankincense have the potential to be used as an immunological stimulant or nutraceutical.

Draft Genome Sequence of Gardnerella vaginalis Strain ATCC 49145 Associated with Bacterial Vaginosis.

Gardnerella vaginalis is a Gram-variable bacterium associated with bacterial vaginosis, a common vaginal inflammation in women of reproductive age. This study reports the whole-genome sequencing for the clinical isolate strain ATCC 49145. The draft genome is composed of 21 contigs containing 1,325 protein-coding sequences, 45 tRNAs and a single tmRNA (SsrA).

Suppression of LPS-induced NF-κB activity in macrophages by the synthetic aurone, (Z)-2-((5-(hydroxymethyl) furan-2-yl) methylene) benzofuran-3(2H)-one.

Suppressing cytokine responses has frequently been shown to have promising therapeutic effects for many chronic inflammatory and autoimmune diseases. However, the severe side effects associated with the long-term use of current treatments, such as allergic reactions and increased risk of stroke, have focused attention towards the targeting of intracellular signaling mechanisms, such as NF-κB, that regulate inflammation. We synthesized a series of non-natural aurone derivatives and investigated their ability to suppress pro-inflammatory signaling in human monocyte (THP-1) and murine macrophage-like (RAW 267.4) cell lines. One of these derivatives, (Z)-2-((5-(hydroxymethyl) furan-2-yl) methylene) benzofuran-3(2H)-one (aurone 1), was found to inhibit LPS-induced secretion of the pro-inflammatory cytokines, tumor-necrosis factor α (TNFα), interleukin 1ß (IL-1ß), and IL-8 by THP-1 cells. To investigate the mechanism, we probed the effect of aurone 1 on LPS-induced MAPK and NF-κB signaling in both THP-1 and RAW264.7. While aurone 1 pre-treatment had no effect on the phosphorylation of ERK, JNK, or p38 MAPK, it strongly suppressed activation of IKK-ß, as indicated by attenuation of Ser176/180 phosphorylation, resulting in decreased phosphorylation of p65 (ser536) as well as phosphorylation (ser32) and degradation of IκBα. Consistent with this, aurone 1 significantly reduced LPS-stimulated nuclear translocation of p65-containing NF-κB transcription factors and expression of an mCherry reporter of TNFα gene transactivation in RAW264.7 cells. Inhibition of TNFα expression at the transcription level was also demonstrated in THP-1 by qRT-PCR. In addition to its effects on cytokine expression, aurone 1 pre-treatment decreased expression of iNOS, a bona fide NF-κB target gene and marker of macrophage M1 polarization, resulting in decreased NO production in RAW264.7 cells. Together, these data indicate that aurone 1 may have the potential to function as a pharmacological agent for the treatment of chronic inflammation disorders.

Cis- and Trans-gnetin H from Paeonia suffruticosa suppress inhibitor kappa B kinase phosphorylation in LPS-stimulated human THP-1 cells.

ETHNOPHARMACOLOGICAL RELEVANCE: The inflammatory response is an important mechanism in host defense; however, overstimulation and chronic inflammation are involved in many important human diseases. Currently, tumor necrosis factor-alpha blockers such as infliximab and adalimumab along with methotrexate are used in cases of severe and chronic disease. However, there are severe side effects and limitations associated with these treatments. Cis- and trans-gnetin H are compounds isolated from the seeds of Paeonia suffruticosa, a medicinal plant used in traditional Chinese medicine for the treatment of many conditions, including inflammatory diseases. In this study, we investigated possible anti-inflammatory mechanisms of cis- and trans-gnetin H against LPS-stimulated human THP-1 cells. MATERIAL AND METHODS: PMA-differentiated THP-1 cells were pretreated with increasing concentrations of cis- and trans-gnetin H with or without LPS. Following treatment, cytotoxicity and the TNF-α, IL-1ß, and IL-8 response were measured. We also characterized the nuclear translocation of NF-κB subunit p65 (RelA) by immunofluorescence and then investigated NF-κB activation by measuring the phosphorylation of NF-κB mediators, IKK-ß, IκB α, and p65 by western blotting. RESULTS: We found that cis- and trans-gnetin H significantly inhibited the cytokine response in a concentration-dependent manner without affecting cell viability. Cis- and trans-gnetin H effectively inhibited nuclear translocation of p65 and phosphorylation of IKK-ß, IκB α, and p65. While both compounds showed promising anti-inflammatory effects, trans-gnetin H was determined to be more effective in suppressing cytokine responses. CONCLUSION: We demonstrated that cis- and trans-gnetin H suppress cytokine response in LPS-stimulated THP-1 cells by preventing activation of key signaling molecules, IKK-ß, IκB α, and p65, involved in the NF-κB pathway and suggest the use of cis- and trans-gnetin H in potential therapies for conditions and diseases associated with chronic inflammation.

Draft Genome Sequences of Two Novel Amoeba-Resistant Intranuclear Bacteria, "Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae".

"Candidatus Berkiella cookevillensis" and "Candidatus Berkiella aquae" are obligate intranuclear endosymbionts of freshwater amoebae. Here, we present the draft genome sequences of these two bacteria, with total sizes of 2,990,361 bp and 3,626,027 bp, respectively.

Description of 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis', two intranuclear bacteria of freshwater amoebae.

Two novel bacteria of the phylum Proteobacteria were isolated during searches for amoeba-resistant micro-organisms in natural and constructed water systems. Strain HT99 was isolated from amoebae found in the biofilm of an outdoor hot tub in Cookeville, Tennessee, USA, and strain CC99 was isolated from amoebae in the biofilm of a cooling tower in the same city. Both bacteria were Gram-stain-negative cocci to coccobacilli, unculturable on conventional laboratory media, and were found to be intranuclear when maintained in Acanthamoeba polyphaga. The genomes of both isolates were completely sequenced. The genome of CC99 was found to be 3.0 Mbp with a 37.9 mol% DNA G+C content, while the genome of HT99 was 3.6 Mbp with a 39.5 mol% DNA G+C content. The 16S rRNA gene sequences of the two isolates were 94 % similar to each other. Phylogenetic comparisons of the 16S rRNA, mip and rpoB genes, the DNA G+C content and the fatty acid composition demonstrated that both bacteria are members of the order Legionellales, and are most closely related to Coxiella burnetii. The phenotypic and genetic evidence supports the proposal of novel taxa to accommodate these strains; however, because strains HT99 and CC99 cannot be cultured outside of the amoeba host, the respective names 'Candidatus Berkiella aquae' and 'Candidatus Berkiella cookevillensis' are proposed.

Gardnerella vaginalis triggers NLRP3 inflammasome recruitment in THP-1 monocytes.

Gardnerella vaginalis is a Gram-positive bacterium associated with bacterial vaginosis (BV), pelvic inflammatory disease, and preterm birth. BV is the most prevalent vaginal dysbiosis in women of childbearing age characterized by the absence of normal lactobacilli and an overgrowth of G. vaginalis and other bacteria. Although mucosal fluids from BV patients exhibit increases in proinflammatory cytokines and Toll-like receptor 2 and 4 mRNA, G. vaginalis has not been demonstrated to directly induce an inflammatory response. This study tested the hypothesis that G. vaginalis induces an inflammatory response in the human monocyte cell line, THP-1. The objectives of the study were to measure proinflammatory cytokine production, molecular mechanisms by which cytokines are produced, and whether G. vaginalis results in death of the monocytic cells. We found that G. vaginalis induced significant increases in the inflammasome-dependent cytokines IL-1ß, IL-18, as well as TNF-α in treated cells. G. vaginalis caused significant cell death by 24h post-treatment compared with untreated controls, but cells remained 66% viable. Caspase-1 cleavage in treated cells confirmed the inflammatory cell death, and NLRP3 knockdown confirmed its involvement through reduction of IL-1ß secretion. Using a stably expressing YFP-ASC THP-1 cell model with immunofluorescent staining, YFP-ASC colocalized with NLRP3 in G. vaginalis-treated cells and the addition of a caspase-1 inhibitor wholly ameliorated IL-1ß secretion. Our study provides new insight into the role of G. vaginalis in inflammatory conditions in the genital tract.

Bacterial enteropathogens associated with diarrhea in a rural population of Haiti.

PURPOSE: Diarrheal disease is one of the leading causes of morbidity in developing countries. To further understand the epidemiology of diarrheal disease among a rural population surrounding Robillard, Haiti, fecal swabs from patients with diarrhea were screened for the presence of enteropathogenic bacteria. PATIENTS AND METHODS: Fecal swabs were collected from 34 patients with signs and symptoms of diarrhea and stored in BBL™ Cary-Blair transport medium (Becton, Dickinson and Company, Sparks, MD) until transit to the USA. Swab material was inoculated on to different enrichment and selective agars for incubation. Fermenting and nonfermenting bacteria that grew on the enteric selection media were identified by the BBL™ Crystal™ Enteric/Nonferementing Identification system (Becton, Dickinson and Company). Organisms identified as Escherichia coli were further screened for the presence of virulence factors by polymerase chain reaction (PCR). RESULTS: Of 34 patients, no Campylobacter, Shigella, Salmonella, or Vibrio spp. were isolated from swabs transported to the USA for culture. Of 73 E. coli isolates cultured from the swabs, one enteropathogenic strain of E. coli was identified by multiplex PCR. Escherichia fergusonii and Cronobacter sakazakii, both potential gastrointestinal pathogens, were also isolated from patient stools. CONCLUSION: This study was undertaken to determine if bacterial enteropathogens could be detected in the stools of patients suffering from diarrhea or dysentery and, in the absence of sufficient facilities, rectal swabs could be transported to the USA for culture. Although several genera of overt enteropathogens were not detected, one enteropathogenic E. coli and other pathogenic enterobacteriaceae were successfully cultured and identified.

Reovirus strain-dependent inflammatory cytokine responses and replication patterns in a human monocyte cell line.

Mammalian Orthoreoviruses are important models for studies of viral pathogenesis. In the rat lung, Reovirus strain type 3 Dearing (T3D) induces substantially more inflammation than does strain type 1 Lang (T1L). To better understand mechanisms underlying differences in the host inflammatory response elicited by T1L and T3D, we characterized cytokine expression patterns induced by those strains after infection of THP-1 monocyte cells. THP-1 cells were adsorbed with either viable or ultraviolet- inactivated T1L and T3D and assayed for mRNA and protein production of growth-regulated oncogene-alpha (GRO-alpha), interleukin-8 (IL-8), or tumor necrosis factor-alpha (TNF-alpha). T3D stimulated mRNA and protein production of all three cytokines, whereas T1L stimulated mRNA and protein production of IL-8 and TNF-alpha but not GRO-alpha. In each case, T3D induced greater cytokine mRNA and protein expression than did T1L. Nonviable virus did not stimulate detectable cytokine secretion, suggesting a requirement for viral RNA synthesis in cytokine induction by THP-1 cells. A greater percentage of THP-1 cells was infected with T1L than T3D as assessed by infectious center assay, and T1L achieved higher yields of infectious progeny than did T3D in infected THP-1 cells as determined by plaque assay. These strain-dependent differences in cytokine responses and corresponding replication patterns in monocyte cells parallel findings made in studies of rat models of pneumonia and provide clues about how Reovirus interfaces with the host innate immune response to produce pulmonary disease.