Microplate fluorescence assay for the quantification of double stranded DNA using SYBR Green I dye

Characterization of the Fusarium circinatum biofilm environmental response role

The capacity to form biofilms is a common trait among many microorganisms present on Earth. In this study, we demonstrate for the first time that the fatal pine pitch canker agent, Fusarium circinatum, can lead a biofilm-like lifestyle with aggregated hyphal bundles wrapped in extracellular matrix (ECM). Our research shows F. circinatum's ability to adapt to environmental changes by assuming a biofilm-like lifestyle. This was demonstrated by varying metabolic activities exhibited by the biofilms in response to factors like temperature and pH. Further analysis revealed that while planktonic cells produced small amounts of ECM per unit of the biomass, heat- and azole-exposed biofilms produced significantly more ECM than nonexposed biofilms, further demonstrating the adaptability of F. circinatum to changing environments. The increased synthesis of ECM triggered by these abiotic factors highlights the link between ECM production in biofilm and resistance to abiotic stress. This suggests that ECM-mediated response may be one of the key survival strategies of F. circinatum biofilms in response to changing environments. Interestingly, azole exposure also led to biofilms that were resistant to DNase, which typically uncouples biofilms by penetrating the biofilm and degrading its extracellular DNA; we propose that DNases were likely hindered from reaching target cells by the ECM barricade. The interplay between antifungal treatment and DNase enzyme suggests a complex relationship between eDNA, ECM, and antifungal agents in F. circinatum biofilms. Therefore, our results show how a phytopathogen's sessile (biofilm) lifestyle could influence its response to the surrounding environment.

Deciphering the genomes of motility-deficient mutants of Vibrio alginolyticus 138-2

The motility of Vibrio species plays a pivotal role in their survival and adaptation to diverse environments and is intricately associated with pathogenicity in both humans and aquatic animals. Numerous mutant strains of Vibrio alginolyticus have been generated using UV or EMS mutagenesis to probe flagellar motility using molecular genetic approaches. Identifying these mutations promises to yield valuable insights into motility at the protein structural physiology level. In this study, we determined the complete genomic structure of 4 reference specimens of laboratory V. alginolyticus strains: a precursor strain, V. alginolyticus 138-2, two strains showing defects in the lateral flagellum (VIO5 and YM4), and one strain showing defects in the polar flagellum (YM19). Subsequently, we meticulously ascertained the specific mutation sites within the 18 motility-deficient strains related to the polar flagellum (they fall into three categories: flagellar-deficient, multi-flagellar, and chemotaxis-deficient strains) by whole genome sequencing and mapping to the complete genome of parental strains VIO5 or YM4. The mutant strains had an average of 20.6 (±12.7) mutations, most of which were randomly distributed throughout the genome. However, at least two or more different mutations in six flagellar-related genes were detected in 18 mutants specifically selected as chemotaxis-deficient mutants. Genomic analysis using a large number of mutant strains is a very effective tool to comprehensively identify genes associated with specific phenotypes using forward genetics.

Identification of plb1 mutation that extends longevity via activating Sty1 MAPK in Schizosaccharomyces pombe

To understand the lifespan of higher organisms, including humans, it is important to understand lifespan at the cellular level as a prerequisite. So, fission yeast is a good model organism for the study of lifespan. To identify the novel factors involved in longevity, we are conducting a large-scale screening of long-lived mutant strains that extend chronological lifespan (cell survival in the stationary phase) using fission yeast. One of the newly acquired long-lived mutant strains (No.98 mutant) was selected for analysis and found that the long-lived phenotype was due to a missense mutation (92Phe → Ile) in the plb1+ gene. plb1+ gene in fission yeast is a nonessential gene encoding a homolog of phospholipase B, but its functions under normal growth conditions, as well as phospholipase B activity, remain unresolved. Our analysis of the No.98 mutant revealed that the plb1 mutation reduces the integrity of the cellular membrane and cell wall and activates Sty1 via phosphorylation.

Probing the reduction of adhesion forces between biofilms and anti-biofouling filtration membrane surfaces using FluidFM technology

Biofouling is a persistent problem in many sectors (healthcare, medicine, marine, and membrane filtration processes). To control the biofouling of surfaces, it is essential to overcome or reduce the adhesion forces between biofilms and surfaces. To access and understand the molecular basis of these interactions, atomic force microscopy (AFM) is a well-suited technology that can measure adhesion forces at the piconewton level. However, AFM-based existing methods only probe interactions between individual cells and surfaces, which is not representative of realistic conditions given that bacteria mainly exist in biofilms. We develop here an original method using FluidFM, a combination of AFM and microfluidics, to probe the adhesion forces between biofilms and filtration membranes modified with an anti-biofouling agent, vanillin. This strategy involves i) growing bacterial biofilms on micrometer-sized polystyrene beads, ii) aspirating these biofilm beads at the aperture of microfluidic cantilevers and iii) using them as probes in force spectroscopy experiments. The results obtained first showed that COOH-functionalized polystyrene beads are more suitable for bacterial growth, and that biofilms obtained after 3 h of incubation could be used with FluidFM. Then, biofilm-scale force spectroscopy experiments showed a significant decrease in adhesion forces, adhesion work, and adhesion events after membrane modification, demonstrating the potential of vanillin-coated membranes to reduce biofouling. In addition, the comparison between results at the individual cell and biofilm scales highlighted the complexity of polymeric matrix unbinding and/or unfolding in the biofilm, showing that individual cells behave differently from biofilms. Overall, this method could have implications in the fields of materials science, chemical engineering, health, and the environment.

Increased Activity of β-Lactam Antibiotics in Combination with Carvacrol against MRSA Bacteremia and Catheter-Associated Biofilm Infections

β-Lactam antibiotics are the mainstay for the treatment of staphylococcal infections, but their utility is greatly limited by the emergence and rapid dissemination of methicillin-resistant Staphylococcus aureus (MRSA). Herein, we evaluated the ability of the plant-derived monoterpene carvacrol to act as an antibiotic adjuvant, revitalizing the anti-MRSA activity of β-lactam antibiotics. Increased susceptibility of MRSA to β-lactam antibiotics and significant synergistic activities were observed with carvacrol-based combinations. Carvacrol significantly inhibited MRSA biofilms and reduced the production of exopolysaccharide, polysaccharide intercellular adhesin, and extracellular DNA and showed synergistic biofilm inhibition in combination with β-lactams. Transcriptome analysis revealed profound downregulation in the expression of genes involved in two-component systems and S. aureus infection. Mechanistic studies indicate that carvacrol inhibits the expression of staphylococcal accessory regulator sarA and interferes with SarA-mecA promoter binding that decreases mecA-mediated β-lactam resistance. Consistently, the in vivo experiment also supported that carvacrol restored MRSA sensitivity to β-lactam antibiotic treatments in both murine models of bacteremia and biofilm-associated infection. Our results indicated that carvacrol has a potential role as a combinatorial partner with β-lactam antibiotics to address MRSA infections.

Point-of-Care DNA Amplification for Disease Diagnosis and Management

Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.

Preparation of bioplastic consisting of salmon milt DNA

The microplastic that pollutes the ocean is a serious problem around the world. The bioplastic consisting of biopolymers which is degraded in nature, is one of the strategies to solve this problem. Although the bioplastics consisting of protein, polysaccharide, polylactic acid, etc., have been reported, which consist of DNA, one of the most important materials in the genetic process, have not been reported to the best of our knowledge. In addition, a large amount of DNA-containing materials, such as salmon milts, is discarded as industrial waste around the world. Therefore, we demonstrated the preparation of a bioplastic consisting of salmon milt DNA. The DNA plastic was prepared by the immersion of a DNA pellet in a formaldehyde (HCHO) solution and heating. As a result, the water-stable DNA plastics were obtained at the HCHO concentration of 20% or more. Particularly, the DNA plastic with a 25% HCHO treatment showed water-insoluble, thermally stable, and highly mechanical properties. These are due to the formation of a three-dimensional network via the crosslinking reaction between the DNA chains. In addition, since DNA in plastic possesses the double-stranded structure, these plastics effectively accumulated the DNA intercalator, such as ethidium bromide. Furthermore, the DNA plastics indicated a biodegradable property in a nuclease-containing aqueous solution and the biodegradable stability was able to be controlled by the HCHO concentration. Therefore, salmon milt DNA has shown the potential to be a biodegradable plastic.

The Chondrogenic Potential of First-Trimester and Term Placental Mesenchymal Stem/Stromal Cells

OBJECTIVES

Mesenchymal stem/stromal cells (MSCs) are a well-established cell source for cartilage engineering, but challenges remain as differentiation often results in chondrocyte hypertrophy. Chondrogenic potential also varies with MSC source and donor age. We assessed the chondrogenic potential of first-trimester and term placental MSCs and compared their response to commonly used bone marrow MSCs (BM-MSCs).

DESIGN

MSCs were isolated from first-trimester and term placentae. BM-MSCs were commercially obtained. Chondrogenesis was induced by micromass culture in commercial chondrogenic media for 7, 14, or 21 days. Pellets were assessed for glycosaminoglycan (GAG) content, and types I, II, and X collagen. Gene expression was profiled using Qiagen RT2 human MSC arrays.

RESULTS

At day 0, first-trimester and term MSCs expression levels of many chondrogenic genes to BM-MSC after 21 days of culture. Only first trimester MSCs showed significant changes in chondrogenic gene expression during induction compared to day 0 undifferentiated MSCs (greater BMP4, KAT2B, and reduced GDF6 expression). Additionally, first-trimester MSCs showed significantly greater expression of ABCB1 (at days 14 and 21) and BMP4 (at days 7, 14, 21) compared with term MSCs. Both first-trimester and term pellets showed increased GAG content over time and term MSCs had significantly GAG greater compared with BM-MSCs at days 7 and 14. Type II collagen was present in all pellets but unlike BM-MSCs, type I collagen was not observed in first-trimester or term MSC pellets.

CONCLUSIONS

These data highlight differences in BM-MSC and placental MSC chondrogenesis and demonstrate that placental MSCs may be an alternative cell source.

The transcriptional landscape of Arabidopsis thaliana pattern-triggered immunity

Plants tailor their metabolism to environmental conditions, in part through the recognition of a wide array of self and non-self molecules. In particular, the perception of microbial or plant-derived molecular patterns by cell-surface-localized pattern recognition receptors (PRRs) induces pattern-triggered immunity, which includes massive transcriptional reprogramming1. An increasing number of plant PRRs and corresponding ligands are known, but whether plants tune their immune outputs to patterns of different biological origins or of different biochemical natures remains mostly unclear. Here, we performed a detailed transcriptomic analysis in an early time series focused to study rapid-signalling transcriptional outputs induced by well-characterized patterns in the model plant Arabidopsis thaliana. This revealed that the transcriptional responses to diverse patterns (independent of their origin, biochemical nature or type of PRR) are remarkably congruent. Moreover, many of the genes most rapidly and commonly upregulated by patterns are also induced by abiotic stresses, suggesting that the early transcriptional response to patterns is part of the plant general stress response (GSR). As such, plant cells' response is in the first instance mostly to danger. Notably, the genetic impairment of the GSR reduces pattern-induced antibacterial immunity, confirming the biological relevance of this initial danger response. Importantly, the definition of a small subset of 'core immunity response' genes common and specific to pattern response revealed the function of previously uncharacterized GLUTAMATE RECEPTOR-LIKE (GLR) calcium-permeable channels in immunity. This study thus illustrates general and unique properties of early immune transcriptional reprogramming and uncovers important components of plant immunity.

Low-cost and High-throughput RNA-seq Library Preparation for Illumina Sequencing from Plant Tissue

Transcriptome analysis can provide clues to biological processes affected in different genetic backgrounds or/and under various conditions. The price of RNA sequencing (RNA-seq) has decreased enough so that medium- to large-scale transcriptome analyses in a range of conditions are feasible. However, the price and variety of options for library preparation of RNA-seq can still be daunting to those who would like to use RNA-seq for their first time or for a single experiment. Among the criteria for selecting a library preparation protocol are the method of RNA isolation, nucleotide fragmentation to obtain desired size range, and library indexing to pool sequencing samples for multiplexing. Here, we present a high-quality and a high-throughput option for preparing libraries from polyadenylated mRNA for transcriptome analysis. Both high-quality and high-throughput protocol options include steps of mRNA enrichment through magnetic bead-enabled precipitation of the poly-A tail, cDNA synthesis, and then fragmentation and adapter addition simultaneously through Tn5-mediated 'tagmentation'. All steps of the protocols have been validated with Arabidopsis thaliana leaf and seedling tissues and streamlined to work together, with minimal cost in money and time, thus intended to provide a beginner-friendly start-to-finish RNA-seq library preparation for transcriptome analysis.

Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.

How to Cope With Heavy Metal Ions: Cellular and Proteome-Level Stress Response to Divalent Copper and Nickel in Halobacterium salinarum R1 Planktonic and Biofilm Cells

Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and forming biofilms, allowing it to adjust to a range of growth conditions. We have recently shown that living in biofilms facilitates its survival under Cu²⁺ and Ni²⁺ stress, with specific rearrangements of the biofilm architecture observed following exposition. In this study, quantitative analyses were performed by SWATH mass spectrometry to determine the respective proteomes of planktonic and biofilm cells after exposition to Cu²⁺ and Ni²⁺.Quantitative data for 1180 proteins were obtained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 of 1180 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred in Cu²⁺ and Ni²⁺ treated samples. In biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms. Deletion strains were generated to assess the potential role of selected target genes. Strongest effects were observed for ΔOE5245F and ΔOE2816F strains which exhibited increased and decreased biofilm mass after Ni²⁺ exposure, respectively. Moreover, EPS obviously plays a crucial role in H. salinarum metal ion resistance. Further efforts are required to elucidate the molecular basis and interplay of additional resistance mechanisms.

Linezolid and Rifampicin Combination to Combat cfr-Positive Multidrug-Resistant MRSA in Murine Models of Bacteremia and Skin and Skin Structure Infection

Linezolid resistance mediated by the cfr gene in MRSA represents a global concern. We investigated relevant phenotype differences between cfr-positive and -negative MRSA that contribute to pathogenesis, and the efficacy of linezolid-based combination therapies in murine models of bacteremia and skin and skin structure infection (SSSI). As a group, cfr-positive MRSA exhibited significantly reduced susceptibilities to the host defense peptides tPMPs, human neutrophil peptide-1 (hNP-1), and cathelicidin LL-37 (P < 0.01). In addition, increased binding to fibronectin (FN) and endothelial cells paralleled robust biofilm formation in cfr-positive vs. -negative MRSA. In vitro phenotypes of cfr-positive MRSA translated into poor outcomes of linezolid monotherapy in vivo in murine bacteremia and SSSI models. Importantly, rifampicin showed synergistic activity as a combinatorial partner with linezolid, and the EC₅₀ of linezolid decreased 6-fold in the presence of rifampicin. Furthermore, this combination therapy displayed efficacy against cfr-positive MRSA at clinically relevant doses. Altogether, these data suggest that the use of linezolid in combination with rifampicin poses a viable therapeutic alternative for bacteremia and SSSI caused by cfr-positive multidrug resistant MRSA.

Differential responses of myoblasts and myotubes to photobiomodulation are associated with mitochondrial number

OBJECTIVE

Photobiomodulation (PBM) is the application of light to promote tissue healing. Current indications suggest PBM induces its beneficial effects in vivo through upregulation of mitochondrial activity. However, how mitochondrial content influences such PBM responses have yet to be evaluated. Hence, the current study assessed the biological response of cells to PBM with varying mitochondrial contents.

METHODS

DNA was isolated from myoblasts and myotubes (differentiated myoblasts), and mitochondrial DNA (mtDNA) was amplified and quantified using a microplate assay. Cells were seeded in 96-wellplates, incubated overnight and subsequently irradiated using a light-emitting diode array (400, 450, 525, 660, 740, 810, 830 and white light, 24 mW/cm2 , 30-240 seconds, 0.72-5.76J/cm2 ). The effects of PBM on markers of mitochondrial activity including reactive-oxygen-species and real-time mitochondrial respiration (Seahorse XFe96) assays were assessed 8 hours post-irradiation. Datasets were analysed using general linear model followed by one-way analysis of variance (and post hoc-Tukey tests); P = 0.05).

RESULTS

Myotubes exhibited mtDNA levels 86% greater than myoblasts (P < 0.001). Irradiation of myotubes at 400, 450 or 810 nm induced 53%, 29% and 47% increases (relative to non-irradiated control) in maximal respiratory rates, respectively (P < 0.001). Conversely, irradiation of myoblasts at 400 or 450 nm had no significant effect on maximal respiratory rates.

CONCLUSION

This study suggests that mitochondrial content may influence cellular responses to PBM and as such explain the variability of PBM responses seen in the literature.

Comparing methods to normalize insulin secretion shows the process may not be needed

Glucose-stimulated insulin secretion (GSIS) is a well-accepted method to investigate the physiological and pathophysiological function of islets. However, there is little consensus about which method is best for normalizing and presenting GSIS data. In this study, we evaluated the sufficiency of islet area, total protein, total DNA, and total insulin content as parameters to normalize GSIS data. First, we tested if there is a linear correlation between each parameter and the number of islets (10, 20, 30, and 40 islets). Islet area, total protein, and insulin content produced excellent linear correlations with islet number (R2 >0.9 for each) from the same islet material. Insulin secretion in 11mM glucose also correlated reasonably well for islet area (R2=0.69), protein (R2=0.49), and insulin content (R2=0.58). DNA content was difficult to reliably measure and was excluded from additional comparisons. We next measured GSIS for 18 replicates of 20 islets each, measuring 3mM and 11mM glucose to calculate the stimulation index and to compare each normalization parameter. Using these similar islet masses for each replicate, none of the parameters produced linear correlations with GSIS (R2<0.05), suggesting that inherent differences in GSIS dominate small differences in islet mass. We conclude that when comparing GSIS for islets of reasonably similar size (<50% variance), normalization does not improve the representation of GSIS data. Normalization may be beneficial when substantial differences in islet mass are involved. In such situations, we suggest that using islet cross-sectional area is superior to other commonly used techniques for normalizing GSIS data.

Streptococcus mutans extracellular DNA levels depend on the number of bacteria in a biofilm

Streptococcus mutans is a component of oral plaque biofilm that accumulates on the surface of teeth. The biofilm consists of extracellular components including extracellular DNA (eDNA). This study was conducted to investigate the factors that may affect the eDNA levels of S. mutans in biofilms. For the study, S. mutans UA159 biofilms were formed for 52 h on hydroxyapatite (HA) discs in 0% (w/v) sucrose +0% glucose, 0.5% sucrose, 1% sucrose, 0.5% glucose, 1% glucose, or 0.5% sucrose +0.5% glucose. Acidogenicity of S. mutans in the biofilms was measured after biofilm formation (22 h) up to 52 h. eDNA was collected after 52 h biofilm formation and measured using DNA binding fluorescent dye, SYBR Green I. Biofilms cultured in 0.5% sucrose or glucose had more eDNA and colony forming units (CFUs) and less exopolysaccharides (EPSs) than the biofilms cultured in 1% sucrose or glucose at 52 h, respectively. The biofilms formed in 0% sucrose +0% glucose maintained pH around 7, while the biofilms grown in 0.5% sucrose had more acidogenicity than those grown in 1% sucrose, and the same pattern was shown in glucose. In conclusion, the results of this study show that the number of S. mutans in biofilms affects the concentrations of eDNA as well as the acidogenicity of S. mutans in the biofilms. In addition, the thickness of EPS is irrelevant to eDNA aggregation within biofilms.

Faecal microbiota of healthy adults in south India: Comparison of a tribal & a rural population

BACKGROUND & OBJECTIVES

The relevance of the gut microbiota to human health is increasingly appreciated. The objective of this study was to compare the gut microbiota of a group of adult tribals with that of healthy adult villagers in Tamil Nadu, India.

METHODS

Faeces were collected from 10 healthy tribal adults (TAs) in the Jawadhi hills and from 10 healthy villagers [rural adults (RAs)] in Vellore district, Tamil Nadu. DNA was extracted, and 456 bp segments comprising hypervariable regions 3 and 4 of the 16S rRNA gene were amplified, barcoded and 454 sequenced.

RESULTS

Totally 227,710 good-quality reads were analyzed. TAs consumed a millets-based diet, ate pork every day, and did not consume milk or milk products. RAs consumed a rice-based diet with meat intake once a week. In both groups, Firmicutes was the most abundant phylum, followed by Proteobacteria, Bacteroidetes and Actinobacteria. The median Firmicutes-to-Bacteroidetes ratio was 34.0 in TA and 92.9 in RA groups. Actinobacteria were significantly low in TA, possibly due to non-consumption of milk. Clostridium constituted the most abundant genus in both groups, but was significantly more abundant in TAs than RAs, while Streptococcus was significantly more abundant in RA (P<0.05). Analyses of genetic distance revealed that the microbiota were distinctly different between TA and RA, and principal component analysis using 550 distinct taxonomically identifiable sequences revealed a clear separation of microbiota composition in the two groups. Phylogenetic analysis of major microbiota indicated clustering of microbial groups at different major branch points for TAs and RAs.

INTERPRETATION & CONCLUSIONS

Phylum Firmicutes and genus Clostridium constituted the bulk of the faecal microbiota, while significant differences in composition between the groups were probably due to differences in diet and lifestyle.

NADPH oxidase-2 does not contribute to β-cell glucotoxicity in cultured pancreatic islets from C57BL/6J mice

High glucose-induced oxidative stress and increased NADPH oxidase-2 (NOX2) activity may contribute to the progressive decline of the functional β-cell mass in type 2 diabetes. To test that hypothesis, we characterized, in islets from male NOX2 knockout (NOX2-KO) and wild-type (WT) C57BL/6J mice cultured for up to 3 weeks at 10 or 30 mmol/l glucose (G10 or G30), the in vitro effects of glucose on cytosolic oxidative stress using probes sensing glutathione oxidation (GRX1-roGFP2), thiol oxidation (roGFP1) or H₂O₂ (roGFP2-Orp1), on β-cell stimulus-secretion coupling events and on β-cell apoptosis. After 1-2 days of culture in G10, the glucose stimulation of insulin secretion (GSIS) was ∼1.7-fold higher in NOX2-KO vs. WT islets at 20-30 mmol/l glucose despite similar rises in NAD(P)H and intracellular calcium concentration ([Ca²⁺]_i) and no differences in cytosolic GRX1-roGFP2 oxidation. After long-term culture at G10, roGFP1 and roGFP2-Orp1 oxidation and β-cell apoptosis remained low, and the glucose-induced rises in NAD(P)H, [Ca²⁺]_i and GSIS were similarly preserved in both islet types. After prolonged culture at G30, roGFP1 and roGFP2-Orp1 oxidation increased in parallel with β-cell apoptosis, the glucose sensitivity of the NADPH, [Ca²⁺]_i and insulin secretion responses increased, the maximal [Ca²⁺]_i response decreased, but maximal GSIS was preserved. These responses were almost identical in both islet types. In conclusion, NOX2 is a negative regulator of maximal GSIS in C57BL/6J mouse islets, but it does not detectably contribute to the in vitro glucotoxic induction of cytosolic oxidative stress and alterations of β-cell survival and function.

Biofilms and Antifungal Susceptibility Testing

Yeasts and filamentous fungi both exist as single cells and hyphal forms, two morphologies used by most fungal organisms to create a complex multilayered biofilm structure. In this chapter we describe the most widely used assays for the determination of biofilm production and assessment of susceptibility of biofilms to antifungal agents or host phagocytes as various methods, the most frequent of which are staining, confocal laser scanning microscopy, quantification of extracellular DNA and protein associated with extracellular matrix and XTT metabolic reduction assay. Pathway-focused biofilm gene expression profiling is assessed by real-time reverse transcriptase polymerase chain reaction.

Glucokinase activation is beneficial or toxic to cultured rat pancreatic islets depending on the prevailing glucose concentration

In rat pancreatic islets, β-cell gene expression, survival, and subsequent acute glucose stimulation of insulin secretion (GSIS) are optimally preserved by prolonged culture at 10 mM glucose (G10) and markedly altered by culture at G5 or G30. Here, we tested whether pharmacological glucokinase (GK) activation prevents these alterations during culture or improves GSIS after culture. Rat pancreatic islets were cultured 1-7 days at G5, G10, or G30 with or without 3 μM of the GK activator Ro 28-0450 (Ro). After culture, β-cell apoptosis and islet gene mRNA levels were measured, and the acute glucose-induced increase in NAD(P)H autofluorescence, intracellular calcium concentration, and insulin secretion were tested in the absence or presence of Ro. Prolonged culture of rat islets at G5 or G30 instead of G10 triggered β-cell apoptosis and reduced their glucose responsiveness. Addition of Ro during culture differently affected β-cell survival and glucose responsiveness depending on the glucose concentration during culture: it was beneficial to β-cell survival and function at G5, detrimental at G10, and ineffective at G30. In contrast, acute GK activation with Ro increased the glucose sensitivity of islets cultured at G10 but failed at restoring β-cell glucose responsiveness after culture at G5 or G30. We conclude that pharmacological GK activation prevents the alteration of β-cell survival and function by long-term culture at G5 but mimics glucotoxicity when added to G10. The complex effects of glucose on the β-cell phenotype result from changes in glucose metabolism and not from an effect of glucose per se.

Pyrosequencing analysis of bacterial diversity in dental unit waterlines

Some infections cases due to exposure to output water from dental unit waterlines (DUWL) have been reported in the literature. However, this type of healthcare-associated risk has remained unclear and up until now the overall bacterial composition of DUWL has been poorly documented. In this study, 454 high-throughput pyrosequencing was used to investigate the bacterial community in seven dental offices (N = 7) and to identify potential bacterial pathogenic sequences. Dental unit waters (DUW) were collected from the tap water supplying units (Incoming Water; IW) to the output exposure point of the turbine handpiece (Output water; OW) following a stagnation period (OWS), and immediately after the last patient of the sampling day (OWA). A high bacterial diversity was revealed in DUW with 394 operational taxonomic units detected at the genus level. In addition to the inter-unit variability observed, results showed increased total bacterial cell concentration and shifts in bacterial community composition and abundance at the genus level, mainly within the Gamma- and Alpha-Proteobacteria class, as water circulated in the dental unit (DU). Results showed that 96.7%, 96.8% and 97.4% of the total sequences from IW, OWS and OWA respectively were common to the 3 defined water groups, thereby highlighting a common core microbiome. Results also suggested that stagnation and DU maintenance practices were critical to composition of the bacterial community. The presence of potentially pathogenic genera was detected, including Pseudomonas and Legionella spp. Emerging and opportunistic pathogenic genera such as Mycobacterium, Propionibacterium and Stenotrophomonas were likewise recovered in DUW. For the first time, an exhaustive evaluation of the bacterial communities present in DUW was performed taking into account the circulation of water within the DU. This study highlights an ignored diversity of the DUWL bacterial community. Our findings also contribute to a better appreciation of the potential infectious risk associated with dental care and suggest the importance of better managing microbial quality in DUW.

Tilling by sequencing

TILLING is a method to find mutations in a gene of interest by scanning amplicons from a mutagenized population for sequence changes, commonly a single nucleotide. In the past 5 years, mutation detection by sequencing has become increasingly popular. This chapter details the experimental flow for TILLING-by-Sequencing, highlighting the critical steps involved in tridimensional pooling of genomic DNA templates, preparation of libraries for high-throughput sequencing, and bioinformatic processing of the sequence data.

Same-species phenotypic comparison of notochordal and mature nucleus pulposus cells

PURPOSE

The ratio of notochordal (NC) cells to mature nucleus pulposus (MNP) cells in the nucleus pulposus varies with species, age and health. Studies suggest that loss of NC cells is a key component of intervertebral disc degeneration. However, few studies have examined the phenotypes of these two cell populations. Therefore, this study aimed to isolate NC and MNP cells from the same intervertebral disc and study phenotypic differences in extracellular matrix production and cell morphology in 3D culture over 7 days.

METHODS

Sequential mechanical dissociation and enzymatic digestion were used to isolate NC cell clusters and single MNP cells from bovine caudal discs. Cells were cultured in alginate beads and subsequently analysed for viability, cytokeratin-8 expression, GAG production and extracellular matrix gene expression.

RESULTS

Mechanical dissociation allowed NC cells to be extracted as intact cell clusters. NC cells represented 8% of the NP cell population and expressed both cytokeratin-8 and vimentin. MNP cells expressed vimentin, only. Both cells types were viable for 7 days. In addition to morphological differences, NC cells produced up to 30 times more total proteoglycan than MNP cells. NC cells had significantly higher aggrecan and brachyury expression.

CONCLUSIONS

NC and MNP cells can be isolated from the same bovine disc and maintain their distinct phenotypes in 3D culture.

Extracellular DNA release confers heterogeneity in Candida albicans biofilm formation

Background

Biofilm formation by Candida albicans has shown to be highly variable and is directly associated with pathogenicity and poor clinical outcomes in patients at risk. The aim of this study was to test the hypotheses that the extracellular DNA release by C. albicans is strain dependent and is associated with biofilm heterogeneity.

Results

Initially, biofilm formed by C. albicans high biofilm formers (HBF) or low biofilm formers (LBF) were treated with DNase to find whether eDNA play a role in their biofilm formation. Digestion of biofilm eDNA significantly reduced the HBF biofilm biomass by five fold compared to untreated controls. In addition, quantification of eDNA over the period of biofilm formation by SYBR green assay demonstrate a significantly higher level of 2 to 6 fold in HBF compared to LBF. Biochemical and transcriptional analyses showed that chitinase activity and mRNA levels of chitinase genes, a marker of autolysis, were upregulated in 24 h biofilm formation by HBF compared to LBF, indicating autolysis pathway possibly involved in causing variation. The biofilm biomass and eDNA release by single (∆cht2, ∆cht3) and double knockout (∆cht2/∆cht3) chitinase mutants were significantly less compared to their parental strain CA14, confirming the role of chitinases in eDNA release and biofilm formation. Correlation analysis found a positive correlation between chitinases and HWP1, suggesting eDNA may release during the hyphal growth. Finally, we showed a combinational treatment of biofilms with DNase or chitinase inhibitor (acetazolamide) plus amphotericin B significantly improved antifungal susceptibility by 2 to 8 fold.

Conclusions

Collectively, these data show that eDNA release by C. albicans clinical isolates is variable and is associated with differential biofilm formation. Digestion of biofilm eDNA by DNase may provide a novel therapeutic strategies to destabilise biofilm growth and improves antifungal sensitivity.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-014-0303-6) contains supplementary material, which is available to authorized users.

Strain prioritization for natural product discovery by a high-throughput real-time PCR method

Natural products offer unmatched chemical and structural diversity compared to other small-molecule libraries, but traditional natural product discovery programs are not sustainable, demanding too much time, effort, and resources. Here we report a strain prioritization method for natural product discovery. Central to the method is the application of real-time PCR, targeting genes characteristic to the biosynthetic machinery of natural products with distinct scaffolds in a high-throughput format. The practicality and effectiveness of the method were showcased by prioritizing 1911 actinomycete strains for diterpenoid discovery. A total of 488 potential diterpenoid producers were identified, among which six were confirmed as platensimycin and platencin dual producers and one as a viguiepinol and oxaloterpin producer. While the method as described is most appropriate to prioritize strains for discovering specific natural products, variations of this method should be applicable to the discovery of other classes of natural products. Applications of genome sequencing and genome mining to the high-priority strains could essentially eliminate the chance elements from traditional discovery programs and fundamentally change how natural products are discovered.

Characterization of two novel cold-inducible K3 dehydrin genes from alfalfa (Medicago sativa spp. sativa L.)

Dehydrin defines a complex family of intrinsically disordered proteins with potential adaptive value with regard to freeze-induced cell dehydration. Search within an expressed sequence tags library from cDNAs of cold-acclimated crowns of alfalfa (Medicago sativa spp. sativa L.) identified transcripts putatively encoding K(3)-type dehydrins. Analysis of full-length coding sequences unveiled two highly homologous sequence variants, K(3)-A and K(3)-B. An increase in the frequency of genotypes yielding positive genomic amplification of the K(3)-dehydrin variants in response to selection for superior tolerance to freezing and the induction of their expression at low temperature strongly support a link with cold adaptation. The presence of multiple allelic forms within single genotypes and independent segregation indicate that the two K(3) dehydrin variants are encoded by distinct genes located at unlinked loci. The co-inheritance of the K(3)-A dehydrin with a Y(2)K(4) dehydrin restriction fragment length polymorphism with a demonstrated impact on freezing tolerance suggests the presence of a genome domain where these functionally related genes are located. These results provide additional evidence that dehydrin play important roles with regard to tolerance to subfreezing temperatures. They also underscore the value of recurrent selection to help identify variants within a large multigene family in allopolyploid species like alfalfa.

Extracellular DNA release acts as an antifungal resistance mechanism in mature Aspergillus fumigatus biofilms

Aspergillus fumigatus has been shown to form biofilms that are associated with adaptive antifungal resistance mechanisms. These include multidrug efflux pumps, heat shock proteins, and extracellular matrix (ECM). ECM is a key structural and protective component of microbial biofilms and in bacteria has been shown to contain extracellular DNA (eDNA). We therefore hypothesized that A. fumigatus biofilms also possess eDNA as part of the ECM, conferring a functional role. Fluorescence microscopy and quantitative PCR analyses demonstrated the presence of eDNA, which was released phase dependently (8 < 12 < 24 < 48 h). Random amplification of polymorphic DNA (RAPD) PCR showed that eDNA was identical to genomic DNA. Biofilm architectural integrity was destabilized by DNase treatment. Biochemical and transcriptional analyses showed that chitinase activity and mRNA levels of chitinase, a marker of autolysis, were significantly upregulated as the biofilm matured and that inhibition of chitinases affected biofilm growth and stability, indicating mechanistically that autolysis was possibly involved. Finally, using checkerboard assays, it was shown that combinational treatment of biofilms with DNase plus amphotericin B and caspofungin significantly improved antifungal susceptibility. Collectively, these data show that eDNA is an important structural component of A. fumigatus ECM that is released through autolysis, which is important for protection from environmental stresses, including antifungal therapy.

Protective antioxidant and antiapoptotic effects of ZnCl2 in rat pancreatic islets cultured in low and high glucose concentrations

Aim/Hypothesis

Rat pancreatic islet cell apoptosis is minimal after prolonged culture in 10 mmol/l glucose (G10), largely increased in 5 mmol/l glucose (G5) and moderately increased in 30 mmol/l glucose (G30). This glucose-dependent asymmetric V-shaped profile is preceded by parallel changes in the mRNA levels of oxidative stress-response genes like Metallothionein 1a (Mt1a). In this study, we tested the effect of ZnCl₂, a potent inducer of Mt1a, on apoptosis, mitochondrial oxidative stress and alterations of glucose-induced insulin secretion (GSIS) induced by prolonged exposure to low and high vs. intermediate glucose concentrations.

Methods

Male Wistar rat islets were cultured in RPMI medium. Islet gene mRNA levels were measured by RTq-PCR. Apoptosis was quantified by measuring islet cytosolic histone-associated DNA fragments and the percentage of TUNEL-positive β-cells. Mitochondrial thiol oxidation was measured in rat islet cell clusters expressing “redox sensitive GFP” targeted to the mitochondria (mt-roGFP1). Insulin secretion was measured by RIA.

Results

As observed for Mt1a mRNA levels, β-cell apoptosis and loss of GSIS, culture in either G5 or G30 vs. G10 significantly increased mt-roGFP1 oxidation. While TPEN decreased Mt1a/2a mRNA induction by G5, addition of 50–100 µM ZnCl₂ to the culture medium strongly increased Mt1a/2a mRNA and protein levels, reduced early mt-roGFP oxidation and significantly decreased late β-cell apoptosis after prolonged culture in G5 or G30 vs. G10. It did not, however, prevent the loss of GSIS under these culture conditions.

Conclusion

ZnCl₂ reduces mitochondrial oxidative stress and improves rat β-cell survival during culture in the presence of low and high vs. intermediate glucose concentrations without improving their acute GSIS.

Mitochondrial oxidative stress contributes differently to rat pancreatic islet cell apoptosis and insulin secretory defects after prolonged culture in a low non-stimulating glucose concentration

AIMS/HYPOTHESIS

Pancreatic beta cells chronically exposed to low glucose concentrations show signs of oxidative stress, loss of glucose-stimulated insulin secretion (GSIS) and increased apoptosis. Our aim was to confirm the role of mitochondrial oxidative stress in rat islet cell apoptosis under these culture conditions and to evaluate whether its reduction similarly improves survival and GSIS.

METHODS

Apoptosis, oxidative stress-response gene mRNA expression and glucose-induced stimulation of mitochondrial metabolism, intracellular Ca(2+) concentration and insulin secretion were measured in male Wistar rat islets cultured for 1 week in RPMI medium containing 5-10 mmol/l glucose with or without manganese(III)tetrakis(4-benzoic acid)porphyrin (MnTBAP) or N-acetyl-L-: cysteine (NAC). Oxidative stress was measured in islet cell clusters cultured under similar conditions using cytosolic and mitochondrial redox-sensitive green fluorescent protein (roGFP1/mt-roGFP1).

RESULTS

Prolonged culture in 5 vs 10 mmol/l glucose increased mt-roGFP1 (but not roGFP1) oxidation followed by beta cell apoptosis and loss of GSIS resulting from reduced insulin content, mitochondrial metabolism, Ca(2+) influx and Ca(2+)-induced secretion. Tolbutamide-induced, but not high K(+)-induced, Ca(2+) influx was also suppressed. Under these conditions, MnTBAP, but not NAC, triggered parallel ~50-70% reductions in mt-roGFP1 oxidation and beta cell apoptosis, but failed to protect against the loss of GSIS despite significant improvement in glucose-induced and tolbutamide-induced Ca(2+) influx.

CONCLUSIONS/INTERPRETATION

Mitochondrial oxidative stress contributes differently to rat pancreatic islet cell apoptosis and insulin secretory defects during culture in a low glucose concentration. Thus, targeting beta cell survival may not be sufficient to restore insulin secretion when beta cells suffer from prolonged mitochondrial oxidative stress, e.g. in the context of reduced glucose metabolism.

Oligonucleotide-based luminescent detection of metal ions

Metal ions are prevalent in biological systems and are critically involved in essential life processes. However, excess concentrations of metals can pose a serious danger to living organisms. Oligonucleotides represent a versatile sensing platform for the detection of various molecular entities including metal ions. This review summarizes the recent advances in the development of oligonucleotide-based luminescent detection methods for metal ions.

Flow cytometric analysis using SYBR Green I for genome size estimation in coffee

Plant genome size has been measured by flow cytometry using propidium iodide as a dye for nuclear DNA staining. However, some authors have reported the occurrence of genome size estimation errors, especially in plants rich in secondary metabolites, such as the coffee tree. In this context, we tested an alternative cytometric protocol using the SYBR Green I as a fluorochrome for stoichiometrically staining nuclear double-stranded DNA in Coffea canephora (2x) and Coffea arabica (4x). The results showed that the respective mean genome size measured from nuclei stained with SYBR Green I and propidium iodide was statistically identical. However, the G(0)/G(1) peaks of nuclei stained with SYBR Green I exhibited lower coefficient variations (1.57-2.85%) compared to those stained with propidium iodide (2.75-4.80%). Coefficient variation statistical data suggest that SYBR Green I is adequate for stoichiometric nuclei staining using this methodology. Our results provide evidence that SYBR Green I can be used in flow cytometry measurements of plants, with the advantages of minimizing errors in nuclear DNA content quantification, staining relatively quicker, with high affinity, and being less mutagenic than propidium iodide.

Effects of fructosamine-3-kinase deficiency on function and survival of mouse pancreatic islets after prolonged culture in high glucose or ribose concentrations

Due to their high glucose permeability, insulin-secreting pancreatic beta-cells likely undergo strong intracellular protein glycation at high glucose concentrations. They may, however, be partly protected from the glucotoxic alterations of their survival and function by fructosamine-3-kinase (FN3K), a ubiquitous enzyme that initiates deglycation of intracellular proteins. To test that hypothesis, we cultured pancreatic islets from Fn3k-knockout (Fn3k(-/-)) mice and their wild-type (WT) littermates for 1-3 wk in the presence of 10 or 30 mmol/l glucose (G10 or G30, respectively) and measured protein glycation, apoptosis, preproinsulin gene expression, and Ca(2+) and insulin secretory responses to acute glucose stimulation. The more potent glycating agent d-ribose (25 mmol/l) was used as positive control for protein glycation. In WT islets, a 1-wk culture in G30 significantly increased the amount of soluble intracellular protein-bound fructose-epsilon-lysines and the glucose sensitivity of beta-cells for changes in Ca(2+) and insulin secretion, whereas it decreased the islet insulin content. After 3 wk, culture in G30 also strongly decreased beta-cell glucose responsiveness and preproinsulin mRNA levels, whereas it increased islet cell apoptosis. Although protein-bound fructose-epsilon-lysines were more abundant in Fn3k(-/-) vs. WT islets, islet cell survival and function and their glucotoxic alterations were almost identical in both types of islets, except for a lower level of apoptosis in Fn3k(-/-) islets cultured for 3 wk in G30. In comparison, d-ribose (1 wk) similarly decreased preproinsulin expression and beta-cell glucose responsiveness in both types of islets, whereas it increased apoptosis to a larger extent in Fn3k(-/-) vs. WT islets. We conclude that, despite its ability to reduce the glycation of intracellular islet proteins, FN3K is neither required for the maintenance of beta-cell survival and function under control conditions nor involved in protection against beta-cell glucotoxicity. The latter, therefore, occurs independently from the associated increase in the level of intracellular fructose-epsilon-lysines.

Detection of prohibited animal products in livestock feeds by single-strand conformation polymorphism analysis

Single-strand conformation polymorphism (SSCP) analysis of amplicons produced from a mitochondrial DNA region between the tRNA(Lys) and ATPase8 genes was applied for the detection of animal product within livestock feeds. Identification of prohibited animal (cattle, elk, sheep, deer, and goat) and nonprohibited animal (pig and horse) products from North America was possible based on the differential display of the single-stranded DNA fragments for the different animal species on SSCP gels. This method allowed specific detection and identification of mixed genomic DNA from different animal species. Trace amounts of cattle-derived materials were also detected in pig meat and bone meal and in grain-based feeds fortified with 10, 5, 1, or 0% porcine meat and bone meal. This study demonstrates the applicability of SSCP analyses to successfully identify the origin of animal species derived materials potentially present in animal feeds.

Dissolved oxygen alteration of the spectrophotometric analysis and quantification of nucleic acid solutions

Nucleic acids are routinely and readily analysed using the A(260)/A(280) ratio, although this method is known to be prone to erroneous results owing to contaminants in solution that absorb at similar wavelengths. The aim of the present review, while highlighting the problems and alternatives of using UV spectrophotometry for nucleic acid measurements, is to bring forth an observational result from our recent studies, namely that DO (dissolved oxygen) and nitrogen can alter the A(260) of aqueous DNA solutions. Our finding is of importance because DO is highly variable between protocols and storage conditions of DNA preparations. The physicochemical nature of the oxygen-DNA interactions is briefly discussed.

Real-time PCR to determine transgene copy number and to quantitate the biolocalization of adoptively transferred cells from EGFP-transgenic mice

Quantitative real-time PCR (qPCR) is a sensitive technique for the detection and quantitation of specific DNA sequences. Here we describe a Taqman qPCR assay for quantification of tissue-localized, adoptively transferred enhanced green fluorescent protein (EGFP)-transgenic cells. A standard curve constructed from serial dilutions of a plasmid containing the EGFP transgene was (i) highly reproducible, (ii) detected as few as two copies, and (iii) was included in each qPCR assay. qPCR analysis of genomic DNA was used to determine transgene copy number in several mouse strains. Fluorescent microscopy of tissue sections showed that adoptively transferred vascular endothelial cells (VEC) from EGFP-transgenic mice specifically localized to tissue with metastatic tumors in syngeneic recipients. VEC microscopic enumeration of liver metastases strongly correlated with qPCR analysis of identical sections (Pearson correlation 0.81). EGFP was undetectable in tissue from control mice by qPCR. In another study using intra-tumor EGFP-VEC delivery to subcutaneous tumors, manual cell count and qPCR analysis of alternating sections also strongly correlated (Pearson correlation 0.82). Confocal microscopy of the subcutaneous tumor sections determined that visual fluorescent signals were frequently tissue artifacts. This qPCR methodology offers specific, objective, and rapid quantitation, uncomplicated by tissue autofluorescence, and should be readily transferable to other in vivo models to quantitate the biolocalization of transplanted cells.

Rapid discrimination of Salmonella isolates by single-strand conformation polymorphism analysis

A molecular typing technique was developed for the differentiation of Salmonella isolates based on single-strand conformation polymorphism (SSCP) analysis of amplicons generated by PCR. Amplicons from parts of the fimA (both the 5' and 3' ends), mdh, invA, and atpD genes were generated separately from a panel of Salmonella strains representing Salmonella bongori, and four subspecies and 17 serovars of Salmonella enterica. These amplicons were subjected to SSCP analysis for differentiation of the salmonellae on the basis of different conformational forms arising due to nucleotide sequence variations in the target genes. Several distinct SSCP banding patterns (a maximum of 14 each for atpD and fimA 3' end) were observed with this panel of Salmonella strains for amplicons generated from each target gene. The best discrimination of Salmonella subspecies and serovar was achieved from the SSCP analysis of a combination of at least three gene targets: atpD, invA, and either mdh or fimA 3' end. This demonstrates the applicability of SSCP analysis as an important additional method to classical typing approaches for the differentiation of foodborne Salmonella isolates. SSCP is simple to perform and should be readily transferable to food microbiology laboratories with basic PCR capability.

Mammalian cis-reporting plasmid may alter activities due to the derivation of host Escherichia coli strains

Methylation status of CpG dinucleotides in the promoter/regulatory region contributes to regulation of transcriptional activities of downstream genes. Nearly all plasmid vectors used in mammalian cells are generated from transformed Escherichia coli. However, these E. coli hosts may have different DNA methylation activities. For instance E. coli JM109 and DH5alpha contain Dam and Dcm methylases, which are absent in E. coli JM110 and GM2163. It has not been determined whether plasmids propagated from E. coli of different methylation activities result in altered expression in mammalian cells when transient transfection is conducted. In this report, cis-reporting plasmids were tested. When promoter/enhancer of tested plasmids contained several Dam/Dcm sites, the cis-reporting activity was 2 to 3 fold lower for those plasmids isolated from JM109 than from JM110. In contrast, the E. coli-derived methylation had little effect on transcription when the sites of methylation resided in the coding region. These findings suggest that cis-reporting plasmids used in comparative or successive experiments are required to be derived from the E. coli strain of the same methylation status. The plasmid for promoter-transcription factor studies should be Dam/Dcm negative E. coli strain.

Protocol for high-sensitivity/long linear-range spectrofluorimetric DNA quantification using ethidium bromide

Ethidium bromide (EtBr) is the most widely used fluorescent dye in nucleic acid gel electrophoresis since decades. However, it has been essentially forgotten in DNA quantification by spectrofluorimetry. While investigating sensitivity and dynamic range of available fluorochromes, we found that EtBr permits much more sensitive fluorimetric measurements than previously thought. We report here a revised, accurate, and easy-to-use protocol for EtBr-based DNA quantification in solution, which usefully complements the widely used indirect quantification on agarose gels.