Establishment of highly specific and quantitative immunoassay systems for staphylococcal enterotoxin A, B, and C using newly-developed monoclonal antibodies

Staphylococcal enterotoxin (SE) activities remain after boiling or treating with proteases. The main symptoms such as vomiting and diarrhea, are caused by the ingestion of SEs. Among SEs, SEA has been reported to be the major and most toxic protein. A highly specific and simple assay system is required to diagnose staphylococcal food poisoning. Therefore, the development of a suitable assay system is strongly anticipated. In this study, we have established a highly specific and sensitive avidin-biotin sandwich ELISA (ABS-ELISA) system for SEA, SEB, and SEC1 using newly-developed monoclonal antibodies. The linearity of these systems obtained was in the range of 0.78-25 ng/ml for each SE, and furthermore, the lower concentrations of SEs could also be detected. The recoveries of SEs from murine serum, skim milk solution, and raw milk were found to be over 90%, suggesting that our systems could detect SEs without any interventions, such as these from milk or serum proteins. We were also able to quantify SEs in 22 specimens of culture supernatants of S. aureus isolated in past occurrences. Our established system should be very useful not only in the clinical field but also in various fields of investigation because of its quantifi-cation and simplicity in detecting SEs.     

A single-stranded DNA aptamer that selectively binds to Staphylococcus aureus enterotoxin B

The bacterium Staphylococcus aureus is a common foodborne pathogen capable of secreting a cocktail of small, stable, and strain-specific, staphylococcal enterotoxins (SEs). Staphylococcal food poisoning (SFP) results when improperly handled food contaminated with SEs is consumed. Gastrointestinal symptoms of SFP include emesis, diarrhea and severe abdominal pain, which manifest within hours of ingesting contaminated food. Immuno-affinity based methods directly detect, identify, and quantify several SEs within a food or clinical sample. However, the success of these assays depends upon the availability of a monoclonal antibody, the development of which is non-trivial and costly. The current scope of the available immuno-affinity based methods is limited to the classical SEs and does not encompass all of the known or emergent SEs. In contrast to antibodies, aptamers are short nucleic acids that exhibit high affinity and specificity for their targets without the high-costs and ethical concerns of animal husbandry. Further, researchers may choose to freely distribute aptamers and develop assays without the proprietary issues that increase the per-sample cost of immuno-affinity assays. This study describes a novel aptamer, selected in vitro, with affinity to staphylococcal enterotoxin B (SEB) that may be used in lieu of antibodies in SE detection assays. The aptamer, designated APT(SEB1), successfully isolates SEB from a complex mixture of SEs with extremely high discrimination. This work sets the foundation for future aptamer and assay development towards the entire family of SEs. The rapid, robust, and low-cost identification and quantification of all of the SEs in S. aureus contaminated food is essential for food safety and epidemiological efforts. An in vitro generated library of SE aptamers could potentially allow for the comprehensive and cost-effective analysis of food samples that immuno-affinity assays currently cannot provide.     

Evaluation of a commercial enzyme immunoassay kit (RIDASCREEN) for detection of staphylococcal enterotoxins A, B, C, D, and E in foods.

The RIDASCREEN SET kit (R-Biopharm GmbH, Darmstadt, Germany), a commercial staphylococcal enterotoxin (SE) visual immunoassay kit, was evaluated for its efficacy. The kit utilizes monovalent capture antibodies against SE types A to E (SEA to SEE); therefore, it simultaneously detects and identifies the enterotoxin types. The major advantages of the kit are (i) a high degree of specificity (except for naturally occurring peroxidases, food compositions or ingredients and microbiological products due to growth of nonstaphylococcal microorganisms did not cause false-positive results; additionally, no cross-reactions among reagents of the kits were observed), (ii) excellent sensitivity (minimum detectable limits were 0.20 to 0.30 ng of SEs per ml of extracts of ham, salami, and mushroom and 0.30 to 0.35 ng of SEs per ml of cheese extracts, or 0.50 to 0.75 ng of SEs per g of foods such as noodles, ham, salami, cheese, and turkey), (iii) simplicity (the kit enabled direct assay of SEs in food extracts without the need for lengthy extraction or concentration procedures), (iv) rapidity (it took less than 3 h to complete the analysis of individual enterotoxin types SEA to SEE), and (v) its semiquantitative results (optical density values could be read against a standard curve to estimate the amount of SE in the extract). The RIDASCREEN kit is a convenient, rapid, and reliable tool for the detection and identification of SEs in foods.     

Ultrastructural features of well-preserved and injured sieve elements: Minute clamps keep the phloem transport conduits free for mass flow

Summary After chemical fixation following two different preparation procedures, the ultrastructure of mature sieve elements (SEs) was systematically compared in the transport phloem ofVicia faba leaves andLycopersicon esculentum internodes. The SEs in samples obtained by gentle preparation were well preserved, while those in conventionally prepared samples were generally injured. (1) In well-preserved SEs, parietal P-proteins were associated with cisternae of the SE endoplasmic reticulum (ER). Additionally, theV. faba SEs had crystalline P-proteins, and a homogeneous network of filamentous P-proteins occurred in the lumen of theL. esculentum SEs. In injured SEs, all P-proteins were dispersed. (2) In well-preserved SEs, stacked ER cisternae associated with P-proteins lay also on the sieve-plate walls, but passages were kept free in front of the sieve pores. Injured SEs lacked these orderly arranged deposits. Instead, irregular filamentous and membranous materials occluded the sieve pores. (3) In well-preserved SEs, the sieve-pore lumen was free of obstructions, apart from small, lateral coatings of P-proteins. Sieve pores in injured SEs were always occluded. (4) The SE organelles and, in tomato SEs, also the parietal ER located at the longitudinal walls were firmly attached in the SE periphery and stayed in place after injury. The stable parietal attachment is likely exerted by minute, clamplike structures which link the outer membranes of the SE components with one another or to the SE plasma membrane. Single, straight clamps with a length of about 7 nm anchored the SE components directly to the SE plasma membrane. The connections between adjacent SE organelles and/or parietal ER cisternae were mostly twice as long (about 15 nm) and often were branched. Presumably, the long, branched clamps were constituted by the interaction of opposite short clamps. The ultrastructural results are discussed with respect to SE functioning.     

The emetic activity of staphylococcal enterotoxins,SEK, SEL,SEM, SEN and SEO in a small emetic animal model,the house musk shrew

Staphylococcal enterotoxins (SEs) produced by Staphylococcus aureus are the most recognizable causative agents of emetic food poisoning in humans. New types of SEs and SE‐like (SEl) toxins have been reported. Several epidemiological investigations have shown that the SEs and SEl genes, particularly, SEK, SEL, SEM, SEN and SEO genes, are frequently detected in strains isolated from patients with food poisoning. The purpose of the present study was to evaluate the emetic activity of recently identified SEs using a small emetic animal model, the house musk shrew. The emetic activity of these SEs in house musk shrews was evaluated by intraperitoneal administration and emetic responses, including the number of shrews that vomited, emetic frequency and latency of vomiting were documented. It was found that SEs induce emetic responses in these animals. This is the first time to demonstrate that SEK, SEL, SEM, SEN and SEO possess emetic activity in the house musk shrew.     

Somatic embryogenesis and plant regeneration from immature zygotic embryo cultures of mountain ash (<Emphasis Type="Italic">Sorbus pohuashanensis</Emphasis>)

Plant regeneration through somatic embryogenesis was achieved using immature zygotic embryos (ZE) of Sorbus pohuashanensis as explants. Over 50% of immature ZEs from immature seed collected at 30 days after pollination produced direct somatic embryos (SEs) on Murashige and Skoog (MS) medium supplemented with 0–0.44 μM 6-benzyladenine (BA) in combination with 5.73 μM naphthaleneacetic acid (NAA) or with 0.91–2.26 μM 2,4-dichlorophenoxyacetic acid (2,4-D) alone. Fourteen to 23 SEs per explant were regenerated on MS medium supplemented with BA 0.44 μM in combination with NAA 5.73 μM. SE formation decreased when sucrose concentrations were higher than 40 g L⁻¹. Repetitive embryogenesis occurred following culture on solid MS medium containing 12 μM abscisic acid, 75 g L⁻¹ polyethylene glycol, and 20 g L⁻¹ sucrose at 25 ± 1°C under a 16-h photoperiod with a light intensity of 40 μmol m⁻² s⁻¹. Over 40% of the mature SEs germinated on solid MS medium under light condition described previously. Up to 40% of the regenerated plantlets were successfully acclimatized under greenhouse conditions. Plantlets derived from SEs grew vigorously with similar morphology as those germinated from ZEs. Histological studies of explants at various developmental stages of somatic embryogenesis revealed that SEs passed through globular, heart, torpedo, and mature stages. Similar to ZE suspensors, similar structures of SE degenerated in later stages of embryo development. ZE and SE are a effective means of regenerating tissue culture plantlets for S. pohuashanesis.     

Effects of carbon source,polyethylene glycol and abscisic acid on secondary embryo induction and maturation in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.) microspore-derived embryos

In this study, the effects of carbon sources, abscisic acid (ABA) either alone or in combination with polyethylene glycol (PEG) were evaluated on secondary embryo (SE) induction and maturation in rapeseed microspore-derived embryos (MDE) of cultivars Global, PF₇₀₄ and Option. Among various carbon sources tested (sucrose, glucose, fructose and sorbitol), the use of 0.3 M (300 mOsml⁻¹) glucose and 0.2 M (200 mOsml⁻¹) sorbitol in SE induction medium (for cultivars Global and PF₇₀₄) and sorbitol at 0.2 and 0.3 M (200 and 300 mOsml⁻¹, for cultivar Option), induced the highest secondary embryogenesis percentage (%SE). The highest number of SEs per each MDE (SE/MDE) was observed with 0.2 M (200 mOsml⁻¹) sorbitol in cultivar Global and with 0.3 M (300 mOsml⁻¹) glucose in cultivars PF₇₀₄ and Option. In another part of this study, the effect of different concentrations of ABA (0, 20, 40, 60, 80 and 100 μM) and of a combined use of ABA (0 and 40 μM) and PEG 4000 or PEG 6000 at 15 g l⁻¹ (3.75 and 2.5 mOsml⁻¹, respectively) was examined on induction and maturation of SEs. In the first experiment, the use of ABA in SE induction medium reduced the mean number of SE/MDE in the three studied cultivars, whereas use of 40–80 μM ABA in SE induction medium increased the percentage of mature SEs in each cultivar. The combined use of PEG with or without ABA also reduced the mean number of SE/MDE compared with control, but resulted in significant enhancement of the percentages of mature SEs for the three cultivars.     

Interaction of plant growth regulators and organic C and N components in the formation and maturation of Abies alba somatic embryos

To promote SE maturation, the influence of different media components on different developmental stages was quantitatively evaluated. Advanced maturation was achieved with a sequence of culture media (prematuration medium and maturation medium) that contained various carbohydrates, organic nitrogen compounds and plant growth regulators. Application of lactose, BA, L-glutamine and casein hydrolysate in the prematuration medium enhanced the total number of SEs and promoted advanced differentiation. The highest number of late torpedo stage SEs was observed on maturation medium supplemented with 200 mM lactose and 29 mM sucrose. Lactose and sorbitol favoured SE maturation up to the early cotyledonary stage. With application of PEG and high ABA concentrations (20–40 M), only early torpedo stages were formed. The number of late torpedo stage SEs was significantly higher on hormone free media or with lower ABA concentrations (0–5 M). Formation of early and late cotyledonary SEs was significantly enhanced by adding BA in the maturation medium: neither Zeatin nor 2iP were effective. In addition, low sucrose concentrations in the proliferation medium (29 mM compared to 58 mM) also favoured the formation of cotyledonary SE in the maturation medium.     

Uncertainty in source partitioning using stable isotopes

Stable isotope analyses are often used to quantify the contribution of multiple sources to a mixture, such as proportions of food sources in an animal's diet, or C₃ and C₄ plant inputs to soil organic carbon. Linear mixing models can be used to partition two sources with a single isotopic signature (e.g., '¹³C) or three sources with a second isotopic signature (e.g., '¹⁵N). Although variability of source and mixture signatures is often reported, confidence interval calculations for source proportions typically use only the mixture variability. We provide examples showing that omission of source variability can lead to underestimation of the variability of source proportion estimates. For both two- and three-source mixing models, we present formulas for calculating variances, standard errors (SE), and confidence intervals for source proportion estimates that account for the observed variability in the isotopic signatures for the sources as well as the mixture. We then performed sensitivity analyses to assess the relative importance of: (1) the isotopic signature difference between the sources, (2) isotopic signature standard deviations (SD) in the source and mixture populations, (3) sample size, (4) analytical SD, and (5) the evenness of the source proportions, for determining the variability (SE) of source proportion estimates. The proportion SEs varied inversely with the signature difference between sources, so doubling the source difference from 2‰ to 4‰ reduced the SEs by half. Source and mixture signature SDs had a substantial linear effect on source proportion SEs. However, the population variability of the sources and the mixture are fixed and the sampling error component can be changed only by increasing sample size. Source proportion SEs varied inversely with the square root of sample size, so an increase from 1 to 4 samples per population cut the SE in half. Analytical SD had little effect over the range examined since it was generally substantially smaller than the population SDs. Proportion SEs were minimized when sources were evenly divided, but increased only slightly as the proportions varied. The variance formulas provided will enable quantification of the precision of source proportion estimates. Graphs are provided to allow rapid assessment of possible combinations of source differences and source and mixture population SDs that will allow source proportion estimates with desired precision. In addition, an Excel spreadsheet to perform the calculations for the source proportions and their variances, SEs, and 95% confidence intervals for the two-source and three-source mixing models can be accessed at http://www.epa.gov/wed/pages/models.htm.     

High-frequency somatic embryogenesis from germinated zygotic embryos of <Emphasis Type="Italic">Schisandra chinensis</Emphasis> and evaluation of the effects of medium strength,sucrose, GA<Subscript>3</Subscript>, and BA on somatic embryo development

We developed a new protocol for highly efficient somatic embryogenesis and plantlet conversion of Schisandra chinensis. Friable embryogenic callus was induced from cotyledonary leaves and hypocotyls of germinated zygotic embryos on Murashige and Skoog (MS) agar medium containing 2,4-dichlorophenoxyacetic acid (2,4-D). Preculture of zygotic embryos on 2,4-D-containing medium increased embryogenic callus induction efficiency. The highest embryogenic callus induction frequency of 56.7% was obtained from shoot apical meristem-containing hypocotyl explants from 1-week-old germinated embryos on MS medium containing 4.0 mg l⁻¹ 2,4-D. Embryogenic callus proliferation, somatic embryo (SE) formation, and subsequent plantlet conversion occurred under optimal culture conditions. The effects of MS medium strength, sucrose, gibberellic acid (GA₃), and 6-benzyladenine (BA) on SE formation and plantlet conversion were evaluated. Low MS medium strength (1/4 to 1/2) was necessary for SE formation, and the optimal sucrose concentration was 2.0%. Supplementing medium with GA₃ negatively impacted SE formation and subsequent development. BA significantly increased the number of SEs and the plantlet conversion capacity. One-third-strength MS medium with 1.0% sucrose and 0.5 mg l⁻¹ BA produced the highest number of SEs (309 embryos from 9 mg embryogenic callus) and the highest frequency of plantlet conversion from germinated SEs (52.6%). When transplanted to soil, 90% of the regenerated plants developed into normal plants.     

Cryopreservation of somatic embryos from <Emphasis Type="Italic">Petiveria alliacea</Emphasis> L. by different techniques based on vitrification

Petiveria alliacea L. is a medicinal plant originating from the Amazon region. This study describes an efficient cryopreservation protocol for somatic embryos (SEs) produced from roots of P. alliacea based on the comparison of vitrification, encapsulation-dehydration, and D cryo-plate techniques. With the vitrification technique, SEs treated with PVS2 solution (0.4 M sucrose, 3.3 M glycerol, 2.4 M ethylene glycol, and 1.9 M DMSO) for 30 min displayed high viability (85%) and intermediate proliferation recovery (about 12 adventitious SEs produced from original SEs [SEs/SE] after 90 d of culture). With the encapsulation-dehydration technique, lower viability (70%) and very low proliferation recovery (about two SEs/SE) were achieved with cryopreserved SEs dehydrated for 10 min in a laminar air flow cabinet. The D cryo-plate technique led to high viability (85%) and proliferation recovery (19 SEs/SE) of cryopreserved SEs after 90 min dehydration. In the experimental conditions tested, the D cryo-plate method was the most efficient technique for cryopreservation of P. alliacea SEs.     

Molecular epidemiological characterization of Staphylococcus aureus isolates originating from food poisoning outbreaks that occurred in Tokyo,Japan

Staphylococcal food poisoning (SFP), one of the commonest food‐borne diseases, results from the ingestion of one or more staphylococcal enterotoxins (SEs) produced in foods by Staphylococcus aureus. In the present study, 203 S. aureus strains originating from 83 outbreaks that had occurred in Tokyo were examined for their coagulase type and genotype of SEs to analyze their molecular epidemiological characteristics. The representative subsets of the 83 S. aureus isolates were analyzed by multilocus sequence typing (MLST) and S. aureus pathogenicity island (SaPI) scanning. The isolates were integrated into eight specific clonal complexes (CC) s; CC81, CC8, CC6, CC5, CC508, CC59, CC20 and CC30. The profiles of the coagulase type, SE/SEl genotype and the suspected type of enterotoxin‐encoding mobile genetic element (MGE) indicated a correlation with each CC. SaPI scanning showed fixed regularity between the distributions of genomic islands, including SaPIs, and the phylogenetic lineage based on MLST. These results indicate that the S. aureus isolates, which classified into eight CCs, have distinguishable properties concerning specific coagulase type, enterotoxin genotype and MGE type. Strains of S. aureus harboring these particular elements possess the potential to cause SFP.     

Terminal reassortment drives the quantum evolution of type III effectors in bacterial pathogens

Many bacterial pathogens employ a type III secretion system to deliver type III secreted effectors (T3SEs) into host cells, where they interact directly with host substrates to modulate defense pathways and promote disease. This interaction creates intense selective pressures on these secreted effectors, necessitating rapid evolution to overcome host surveillance systems and defenses. Using computational and evolutionary approaches, we have identified numerous mosaic and truncated T3SEs among animal and plant pathogens. We propose that these secreted virulence genes have evolved through a shuffling process we have called "terminal reassortment." In terminal reassortment, existing T3SE termini are mobilized within the genome, creating random genetic fusions that result in chimeric genes. Up to 32% of T3SE families in species with relatively large and well-characterized T3SE repertoires show evidence of terminal reassortment, as compared to only 7% of non-T3SE families. Terminal reassortment may permit the near instantaneous evolution of new T3SEs and appears responsible for major modifications to effector activity and function. Because this process plays a more significant role in the evolution of T3SEs than non-effectors, it provides insight into the evolutionary origins of T3SEs and may also help explain the rapid emergence of new infectious agents.     

Maturation of somatic embryos in two embryogenic cultures of <Emphasis Type="Italic">Picea morrisonicola</Emphasis> Hayata as affected by alternation of endogenous IAA content

Embryogenic culture lines T4 and T2 were initiated from two mature zygotic embryos of Picea morrisonicola Hay. Mature somatic embryos (SEs) were produced in culture line T2 but not in line T4 after 8-week abscisic acid (ABA) treatment. High performance liquid chromatography (HPLC) analysis of the endogenous indole-3-acetic acid (IAA) content has shown 7.5 times higher IAA production in T4 line than in T2 line during the proliferation phase. However, after ABA incubation the line T4 produced much less IAA than line T2. The application of an anti-auxin, 2,3,5-triiodobenzoic acid (TIBA) or 2-(4-chlorophenoxy)-2-methylpropionic acid (PCIB) induced culture line T4 to produce mature SEs. Both 1 μM TIBA and 5 μM PCIB increased the production of stage 2 SEs in T4 culture line when cultures were treated during the proliferation stage for 8 weeks. Occasionally cotyledonary (stage 3) SEs were even produced from treated T4 culture line. Both chemicals have also been demonstrated to significantly decrease the amount of IAA in the treated T4 and T2 embryogenic lines. However the decrease of the IAA level was not beneficial for SE production in the T2 embryogenic line. These results indicated the importance of endogenous IAA level in manipulating the process of SE maturation in spruce embryogenic cultures.     

Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers

Super enhancers (SEs) are broad enhancer domains usually containing multiple constituent enhancers that hold elevated activities in gene regulation. Disruption in one or more constituent enhancers causes aberrant SE activities that lead to gene dysregulation in diseases. To quantify SE aberrations, differential analysis is performed to compare SE activities between cell conditions. The state-of-art strategy in estimating differential SEs relies on overall activities and neglect the changes in length and structure of SEs. Here, we propose a novel computational method to identify differential SEs by weighting the combinatorial effects of constituent-enhancer activities and locations (i.e. internal dynamics). In addition to overall activity changes, our method identified four novel classes of differential SEs with distinct enhancer structural alterations. We demonstrate that these structure alterations hold distinct regulatory impact, such as regulating different number of genes and modulating gene expression with different strengths, highlighting the differentiated regulatory roles of these unexplored SE features. When compared to the existing method, our method showed improved identification of differential SEs that were linked to better discernment of cell-type-specific SE activity and functional interpretation.     

Staphylococcus aureus and its food poisoning toxins: characterization and outbreak investigation

Staphylococcal food poisoning (SFP) is one of the most common food-borne diseases and results from the ingestion of staphylococcal enterotoxins (SEs) preformed in food by enterotoxigenic strains of Staphylococcus aureus. To date, more than 20 SEs have been described: SEA to SElV. All of them have superantigenic activity whereas half of them have been proved to be emetic, representing a potential hazard for consumers. This review, divided into four parts, will focus on the following: (1) the worldwide story of SFP outbreaks, (2) the characteristics and behaviour of S. aureus in food environment, (3) the toxinogenic conditions and characteristics of SEs, and (4) SFP outbreaks including symptomatology, occurrence in the European Union and currently available methods used to characterize staphylococcal outbreaks.     

WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning

Background: The type III secreted effectors (T3SEs) are one of the indispensable proteins in the growth and reproduction of Gram-negative bacteria. In particular, the pathogenesis of Gram-negative bacteria depends on the type III secreted effectors, and by injecting T3SEs into a host cell, the host cell’s immunity can be destroyed. The high diversity of T3SE sequences and the lack of defined secretion signals make it difficult to identify and predict. Moreover, the related study of the pathological system associated with T3SE remains a hot topic in bioinformatics. Some computational tools have been developed to meet the growing demand for the recognition of T3SEs and the studies of type III secretion systems (T3SS). Although these tools can help biological experiments in certain procedures, there is still room for improvement, even for the current best model, as the existing methods adopt hand-designed feature and traditional machine learning methods. Methods: In this study, we propose a powerful predictor based on deep learning methods, called WEDeepT3. Our work consists mainly of three key steps. First, we train word embedding vectors for protein sequences in a large-scale amino acid sequence database. Second, we combine the word vectors with traditional features extracted from protein sequences, like PSSM, to construct a more comprehensive feature representation. Finally, we construct a deep neural network model in the prediction of type III secreted effectors. Results: The feature representation of WEDeepT3 consists of both word embedding and position-specific features. Working together with convolutional neural networks, the new model achieves superior performance to the state-of-the-art methods, demonstrating the effectiveness of the new feature representation and the powerful learning ability of deep models. Conclusion: WEDeepT3 exploits both semantic information of k-mer fragments and evolutional information of protein sequences to accurately differentiate between T3SEs and non-T3SEs. WEDeepT3 is available at bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html.