Pre-validation study of spectrophotometric direct peptide reactivity assay (Spectro-DPRA) as a modified in chemico skin sensitization test method

Skin sensitization is induced when certain chemicals bind to skin proteins. Direct peptide reactivity assay (DPRA) has been adopted by the OECD as an alternative method to evaluate skin sensitization by assessing a substance's reaction to two model peptides. A modified spectrophotometric method, Spectro-DPRA, can evaluate skin sensitization, in a high throughput fashion, to obviate some limitations of DPRA. Pre-validation studies for Spectro-DPRA were conducted to determine transferability and proficiency, within- and between-laboratory reproducibility, and predictive ability based on GLP principles at three laboratories (AP, KTR, and KCL). All laboratories confirmed high (> 90%) concordance for evaluating the sensitivity induced by ten chemical substances. The concordance among the three tests performed by each laboratory was 90% for AP, 100% for KTR, and 100% for KCL. The mean accuracy of the laboratories was 93.3% [compared to the standard operating procedure (SOP)]. The reproducibility among the three laboratories was as high as 86.7%; the accuracy was 86.7% for AP, 100% for KTR, and 86.7% for KCL (compared to the SOP). An additional 54 substances were assessed in 3 separate labs to verify the prediction rate. Based on the result, 29 out of 33 substances were classified as sensitizers, and 19 out of 21 identified as non-sensitizers; the corresponding sensitivity, specificity, and accuracy values were 87.9%, 90.5%, and 88.9%, respectively. These findings indicate that the Spectro-DPRA can address the molecular initiating event with improved predictability and reproducibility, while saving time and cost compared to DPRA or ADRA.

Geographical Relationships between Long-Tailed Goral (Naemorhedus caudatus) Populations Based on Gut Microbiome Analysis

The long-tailed goral (Naemorhedus caudatus) is an endangered species found in the mountains of eastern and northern Asia. Its populations have declined for various reasons, and this species has been designated as legally protected in South Korea. Although various ecological studies have been conducted on long-tailed gorals, none have investigated the gut microbiome until now. In the present study, we compared the diversity and composition of the gut microbiome of seven populations of Korean long-tailed gorals. By analyzing the gut microbiome composition for each regional population, it was found that four phyla-Firmicutes, Actinobacteriota, Bacteroidota, and Proteobacteria-were the most dominant in all regions on average. The alpha diversity of the gut microbiome of the goral population in the northern regions was high, while that in the southern regions was low. Through the analysis of beta diversity, the seven long-tailed goral populations have been divided into three groups: the Seoraksan population, the Samcheock population, and the Wangpicheon population. It was possible to confirm the regional migration of the animals using the gut microbiome based on the site-relational network analysis. It was found that the most stable population of long-tailed gorals in Korea was the Seoraksan population, and the closely related groups were the Samcheok and Wangpicheon populations, respectively. Wangpicheon appeared to be a major point of dispersal in the migration route of Korean long-tailed gorals.

Quorum Sensing System Affects the Plant Growth Promotion Traits of Serratia fonticola GS2

Quorum sensing (QS) enables bacteria to organize gene expression programs, thereby coordinating collective behaviors. It involves the production, release, and population-wide detection of extracellular signaling molecules. The cellular processes regulated by QS in bacteria are diverse and may be used in mutualistic coordination or in response to changing environmental conditions. Here, we focused on the influence of the QS-dependent genes of our model bacterial strain Serratia fonticola GS2 on potential plant growth promoting (PGP) activities including indole-3-acetic acid (IAA) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, and biofilm formation. Based on genomic and phenotypic experimental data we identified and investigated the function of QS genes in the genome of the model strain. Our gene deletion study confirmed the biological functionality of the QS auto-inducer (gloI) and receptor (gloR) on potential PGP activities of GS2. A transcriptomic approach was also undertaken to understand the role of QS genes in regulation of genes primarily involved in PGP activities (IAA, ACC deaminase activity, and biofilm formation). Both transcriptomic and phenotypic data revealed that the QS-deletion mutants had considerably less PGP activities, as compared to the wild type. In addition, in vivo plant experiments showed that plants treated with GS2 had significantly higher growth rates than plants treated with the QS-deletion mutants. Overall, our results showed how QS-dependent genes regulate the potential PGP activities of GS2. This information may be helpful in understanding the relationship between QS-dependent genes and the PGP activity of bacteria, which aid in the production of practical bio-fertilizers for plant growth promotion.

Irradiation-Induced Intestinal Damage Is Recovered by the Indigenous Gut Bacteria Lactobacillus acidophilus

The intestinal tract is one of the most sensitive organs following irradiation. The protective effect of specific indigenous microbiota on irradiation-induced damage to intestinal epithelial cells has not been reported. Mice were irradiated with a single dose of 6 Gy of gamma rays. The intestinal damage was analyzed by histopathology. Intestinal stemness and differentiation were determined by intestinal organoid culture. Microbiota community was observed by high-throughput 16S rRNA gene sequencing and oligotyping analysis. We showed that distal small intestine was damaged by sublethal dose of gamma irradiation. Intestinal organoids derived from the irradiated mice showed defects in budding and mucin expression, suggesting the detrimental effect of irradiation on the intestinal stemness and differentiation. In addition, irradiation reduced intestinal immunoglobulin A level, concomitant with decreased microbiota diversity based on our high-throughput 16S rRNA gene sequencing data. Especially, the relative abundance of Lactobacillus was reduced at early time point post-irradiation; however, it was recovered at late time point. Oligotyping analysis within the Lactobacillus genus indicated that Lactobacillus-related oligotype 1 (OT1) including Lactobacillus acidophilus might drive recovery after irradiation as it was associated with increased long-term numbers post-exposure. We showed that treatment with heat-killed L. acidophilus rescued the budding-impaired organoids and induced sufficient differentiation in epithelial cells, and particularly mucin-producing cells, in intestinal organoids. This study provides the first evidence that the indigenous gut bacteria L. acidophilus enhance intestinal epithelial function with respect to irradiation-induced intestinal damage by improving intestinal stem cell function and cell differentiation.

The first complete mitochondrial genome sequence of the korean endemic catfish Silurus microdorsalis (Actinopteri, Siluriformes, Siluridae)

The Silurus microdorsalis is known as Korean endemic slender catfish. Despite its value as a biological resource, there is no complete mitochondrial genome sequence. The complete mitochondrial genome consisted of 16,524 bp including 22 transfer RNA (tRNAs), 2 ribosomal RNA (rRNAs), 13 protein-coding genes (PCGs), and A + T rich region. The overall base composition of S. microdorsalis was A + T: 56.1%, C + G: 43.9%, apparently with slight AT bias. Phylogenetic relationship showed that S. microdorsalis was closely related to Silurus glanis.

Phenotypic and genotypic analyses of an attenuated porcine reproductive and respiratory syndrome virus strain after serial passages in cultured porcine alveolar macrophages

The porcine reproductive and respiratory syndrome virus (PRRSV) is a globally ubiquitous swine viral pathogen that causes major economic losses worldwide. We previously reported an over-attenuated phenotype of cell-adapted PRRSV strain CA-2-P100 in vivo. In the present study, CA-2-P100 was serially propagated in cultured porcine alveolar macrophage (PAM) cells for up to 20 passages to obtain the derivative strain CA-2-MP120. Animal inoculation studies revealed that both CA-2-P100 and CA-2-MP120 had decreased virulence, eliciting weight gains, body temperatures, and histopathologic lesions similar to those in the negative control group. However, compared to CA-2-P100 infection, CA-2-MP120 yielded consistently higher viremia kinetics and enhanced antibody responses in pigs. All pigs inoculated with CA-2-MP120 developed viremia and seroconverted to PRRSV. During 20 passages in PAM cells, CA-2-MP120 acquired 15 amino acid changes that were mostly distributed in nsp2 and minor structural protein-coding regions. Among these changes, 6 mutations represented reversions to the sequences of the reference CA-2 and parental CA-2-P20 strains. These genetic drifts may be hypothetical molecular markers associated with PRRSV macrophage tropism and virulence. Our results indicate that the PAM-passaged CA-2-MP120 strain is a potential candidate for developing a live, attenuated PRRSV vaccine.

The complete mitochondrial genome sequence of the intertidal crab Parasesarma Tripectinis (Arthropoda, Decapoda, Sesarmidae)

Parasesarma tripectinis is known as an intertidal crab and inhabits Asian region. This crab has larval release at semilunar rhythm. Here, we report the complete sequence of the mitochondrial genome (mitogenome), which is composed of 15,612 base pair (bp) encoding 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and an A + T rich region. The nucleotide composition of P. tripectinis was G + C: 25.8%, A + T: 74.2%, with a strong AT bias. Phylogenetic analysis using whole mitogenome figured out that P. tripectinis was closely related to Sesarma neglectum which belongs to the same family Sesarmidae.

Genome sequencing to develop Paenibacillus donghaensis strain JH8T (KCTC 13049T=LMG 23780T) as a microbial fertilizer and correlation to its plant growth-promoting phenotype

Paenibacillus donghaensis JH8^T (KCTC 13049^T=LMG 23780^T) is a Gram-positive, mesophilic, endospore-forming bacterium isolated from East Sea sediment at depth of 500m in Korea. The strain exhibited plant cell wall hydrolytic and plant growth promoting abilities. The complete genome of P. donghaensis strain JH8^T contains 7602 protein-coding sequences and an average GC content of 49.7% in its chromosome (8.54Mbp). Genes encoding proteins related to the degradation of plant cell wall, nitrogen-fixation, phosphate solubilization, and synthesis of siderophore were existed in the P. donghaensis strain JH8^T genome, indicating that this strain can be used as an eco-friendly microbial agent for increasing agricultural productivity.

The first complete mitochondrial genome sequence of the leucosiid crab Pyrhila pisum (Arthropoda, Decapoda, Leucosiidae)

Pyrhila pisum is known as leucosiid crab. So far, there is no study about whole mitochondrial genome in Leucosiidae family. Here, we report first the complete sequence of the mitochondrial genome from P. pisum, which is composed of 15,516 base pair encoding 13 protein-coding genes, 22 transfer RNAs, two ribosomal RNAs, and A + T-rich region. The nucleotide composition of P. pisum was G + C: 25.5%, A + T: 74.5%, with a strong AT bias. In phylogenetic analysis using whole mitogenome, it was figured out that P. pisum was closely related to Sesarma neglectum but their family is different.

The complete mitochondrial genome sequence of Liobagrus mediadiposalis (Teleostei, Siluriformes, Amblycipitidae)

The south torrent catfish Liobagrus mediadiposalis (Teleostei, Siluriformes, Amblycipitidae) is an endemic species of Korea. The complete mitochondrial genome sequence consisted of 16,534 base pairs (bp) encoding 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and two non-coding regions. The overall base composition of L. mediadiposalis was G + C: 44.8%, A + T: 55.2%, apparently with a slight AT bias. Phylogenetic analysis showed that L. mediadiposalis was closely related to Liobagrus reinii.

The complete mitochondrial genome sequence of the greater wax moth Galleria mellonella (Insecta, Lepidoptera, Pyralidae): sequence and phylogenetic analysis comparison based on whole mitogenome

The larva of Galleria mellonella is widely used as a model organism for in vivo toxicology and pathogenicity testing. Here, we report complete sequence of the mitochondrial genome (mitogenome) from G. mellonella, which is comprised of 15,320 base pairs encoding 13 protein-coding genes, two ribosomal RNAs, 22 transfer RNAs, and an A + T rich region. The overall base composition was G + C: 19.6%, A + T: 80.4%, with an apparent AT bias. Phylogenetic analysis using whole mitogenome revealed that G. mellonella was closely related to Corcyra cephalonica, which is in the same Pyralidae family.

Host plant growth promotion and cadmium detoxification in Solanum nigrum, mediated by endophytic fungi

Current investigation conducted to evaluate the associated fungal endophyte interactions of a Cd hyper-accumulator Solanum nigrum Korean ecotype under varying concentrations of Cd. Two indole-3-acetic acid (IAA) producing fungal strains, RSF-4L and RSF-6L, isolated from the leaves of S. nigrum, were initially screened for Cd tolerance and accumulation potential. In terms of dry biomass production, the strain RSF-6L showed higher tolerance and accumulation capacity for Cd toxicity in comparison to RSF-4L. Therefore, RSF-6L was applied in vivo to S. nigrum and grown for six weeks under Cd concentrations of 0, 10, and 30mgKg^-1 of dry sand. The effect of fungal inoculation assessed by plant physiological responses, endogenous biochemical regulations, and Cd profile in different tissues. Significant increase were observed in plant growth attributes such as shoot length, root length, dry biomass, leaf area, and chlorophyll contents in inoculated RSF-6L plants in comparison to non-inoculated plants with or without Cd contamination. RSF-6L inoculation decreased uptake of Cd in roots and above ground parts, as evidenced by a low bio-concentration factor (BCF) and improved tolerance index (TI). However, Cd concentration in the leaves remained the same for inoculated and non-inoculated plants under Cd spiking. Fungal inoculation protected the host plants, as evidenced by low peroxidase (POD) and polyphenol peroxidase (PPO) activities and high catalase (CAT) activity. Application of appropriate fungal inoculation that can improve tolerance mechanisms of hyper-accumulators and reduce Cd uptake can be recommended for phyto-stabilisation/immobilisation of heavy metals in crop fields.

The First Chloroplast Genome Sequence of Boswellia sacra, a Resin-Producing Plant in Oman

Boswellia sacra (Burseraceae), a keystone endemic species, is famous for the production of fragrant oleo-gum resin. However, the genetic make-up especially the genomic information about chloroplast is still unknown. Here, we described for the first time the chloroplast (cp) genome of B. sacra. The complete cp sequence revealed a circular genome of 160,543 bp size with 37.61% GC content. The cp genome is a typical quadripartite chloroplast structure with inverted repeats (IRs 26,763 bp) separated by small single copy (SSC; 18,962 bp) and large single copy (LSC; 88,055 bp) regions. De novo assembly and annotation showed the presence of 114 unique genes with 83 protein-coding regions. The phylogenetic analysis revealed that the B. sacra cp genome is closely related to the cp genome of Azadirachta indica and Citrus sinensis, while most of the syntenic differences were found in the non-coding regions. The pairwise distance among 76 shared genes of B. sacra and A. indica was highest for atpA, rpl2, rps12 and ycf1. The cp genome of B. sacra reveals a novel genome, which could be used for further studied to understand its diversity, taxonomy and phylogeny.

Genomic and phenotypic analyses of Serratia fonticola strain GS2: a rhizobacterium isolated from sesame rhizosphere that promotes plant growth and produces N-acyl homoserine lactone

The genus Serratia incorporates many agriculturally important species. Serratia fonticola strain GS2, isolated from a sesame rhizosphere, can produce N-acyl homoserine lactone quorum sensing signal molecules and indole-3-acetic acid (IAA). Here we report the complete genome sequence and phenotypic characteristics based on genomic information of this bacterium. The complete genome sequence of S. fonticola strain GS2 consists of a chromosome of 6.1 Mbp and two plasmids of 132 kbp and 94 kbp. The genome clusters for IAA and N-acyl homoserine lactone biosynthesis were identified in the genome. Subsequently, the Salkowski test and gas chromatography-mass spectrometry (GC-MS) analysis also revealed that the strain GS2 produces indolic compounds (27.1μgmL^-1) and IAA (6.7μgmL^-1) in its culture broth. HPLC analysis confirmed that the strain GS2 produced the quorum sensing signal molecules N-hexanoyl-_L-homoserine lactone and N-octanoyl-_L-homoserine lactone. This new information on the genome sequence and phenotype features will inform future ecological studies related to plant-microbe interactions.

Draft genome sequence of sulfur-reducing archaeon Thermococcus thioreducens DSM 14981T

Thermococcus thioreducens DSM 14981^T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981^T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications.

The whole chloroplast genome sequence of black nightshade plant (Solanum nigrum)

In this study, complete chloroplast genome of Solanum nigrum, a wild relative of potato and tomato being important for its medicinal features, was sequenced. The genome size is 154 671 bp in length, with 40% GC content. A pair of inverted repeats, IRa and IRSb, were separated by a large single-copy region and a small single-copy region of 82 315 bp and 33 411 bp, respectively. The genome harbored 73 protein-coding genes, 36 tRNA genes, and three rRNA genes. The evolutionary relationships in our phylogenetic analysis revealed that S. nigrum is closer to S. tuberosum when compared with those of known relatives' species belonging to Solanum genus.

The complete mitochondrial genome sequence of Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae)

The Kichulchoia multifasciata (Teleostei, Cypriniformes, Cobitidae) is one of the loaches and is endemic to Korea. The complete mitochondrial genome sequence consisted of 16 569 base pairs (bp) encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of K. multifasciata was G + C: 42.5% and A + T: 57.5%, apparently with a slight AT bias. Phylogenetic analysis showed that K. multifasciata was closely related to Koreocobitis rotundicaudata.

The complete mitochondrial genome sequence of Squalidus japonicus coreanus (Teleostei, Cypriniformes, Cyprinidae)

The short-barbel gudgeon Squalidus japonicus coreanus (Teleostei, Cypriniformes, Cyprinidae) is a subspecies of S. japonicus, and is endemic to Korea. The complete mitochondrial genome sequence consisted of 16 597 base pairs (bp) encoding 13 protein-coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs), and two non-coding regions. The overall base composition of S. japonicus coreanus was G + C: 47.4% and A + T: 52.6%, apparently with a slight AT bias. Phylogenetic analysis showed that S. japonicus coreanus was closely related to Pungtungia herzi.

Complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae)

In this study, we sequenced the complete mitochondrial genome of the Korean endemic species Microphysogobio yaluensis (Teleostei, Cypriniformes, Cyprinidae). The mitogenome, consisted of 16 601 base pairs (bp), encoding 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding regions. The overall base composition of M. yaluensis was G + C: 43.8%, A + T: 56.2%, apparently with a slight AT bias. Phylogenetic analysis showed that M. yaluensis was close to Hemibarbus mylodon.

Complete genome sequence of a keratin-degrading bacterium Chryseobacterium gallinarum strain DSM 27622(T) isolated from chicken

Chryseobacterium gallinarum strain DSM 27622(T) is a keratin-degrading bacterium belonging to the class Flavobacteriia, which was isolated from chicken. Here, we report the 4633,632bp complete genome sequence of the strain DSM 27622(T) with 4161 genes.

Complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae)

In this study, we sequenced the complete mitochondrial genome of the endemic species Korean aucha perch Coreoperca herzi (Teleostei, Centrarchiformes, Sinipercidae). The mitogenome, consisting of 16 495 base pairs (bp), encoded 13 protein-coding genes (PCGs), 2 ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and 2 non-coding region. The overall base composition of C. herzi is G + C: 46.3%, A + T: 53.7%, apparently with a slight AT bias. Phylogenetic analysis showed that the C. herzi was closed to Coreoperca kawamebari.

Complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae)

The complete mitochondrial genome of Cygnus olor (Aves, Anseriformes, Anatidae) was revealed in this study. Total 16 739 base pairs (bp) of this mitogenome encoded genes for 13 protein coding genes (PCGs), two ribosomal RNAs (rRNAs), 22 transfer RNAs (tRNAs) and a D-loop (control region). The 12S rRNA and 16S rRNA genes are located between tRNA-Phe and tRNA-Leu (UUR) and segmentalized by the tRNA-Val. D-loop is located between tRNA-Glu and tRNA-Phe. The overall base composition of C. olor is G + C: 47.8%, A + T: 52.2%, apparently with a slight AT bias. Following the phylogenetic analysis, the C. olor was closed to Anser cygnoides.

Soybean oil-degrading bacterial cultures as a potential for control of green peach aphids (Myzus persicae)

Microorganisms capable of degrading crude oil were isolated and grown in soybean oil as a sole carbon source. The microbial cultures were used to control green peach aphids in vitro. Approximately 60% mortality of aphids was observed when the cultures were applied alone onto aphids. To examine the cultures as a pesticide formulation mixture, the cultures were combined with a low dose of the insecticide imidacloprid (one-fourth dose of recommended field-application rate) and applied onto aphids. The cultures enhanced significantly the insecticidal effectiveness of imidacloprid, which was higher than imidacloprid alone applied at the low dose. The isolated microorganisms exhibited high emulsifying index values and decreased surface tension values after being grown in soybean oil media. GC/MS analyses showed that microorganisms degraded soybean oil to fatty acids. The cultures were suggested to play the roles of wetting, spreading, and sticking agents to improve the effectiveness of imidacloprid. This is the first report on the control of aphids by using oil-degrading microbial cultures.

Origin of lumbar spinal roots and their relationship to intervertebral discs: a cadaver and radiological study

Previous studies on the anatomy of the lumbar spine have not clarified the precise relationship of the origin of the lumbar roots to their corresponding discs or their angulation to the dural sac. We studied 33 cadavers (25 formalin-preserved and eight fresh-frozen) and their radiographs to determine these details. All cadavers showed a gradual decrease in the angle of the nerve root from L1 to S1. The origin of the root was found to be below the corresponding disc for the L1 to L4 roots. In the formalin-preserved cadavers 8% of the L5 roots originated above, 64% below and 28% at the L4/L5 disc. In the fresh cadavers the values were 12.5%, 62.5% and 25%, respectively. For the S1 root 76% originated above and 24% at the L5-S1 disc in the formalin-preserved cadavers and 75% and 25%, respectively, in the fresh cadavers.A herniated disc usually compresses the root before division of the root sleeve. Thus, compression of the thecal sac before the origin of the root sleeve is common for L1 to L5 whereas compression at the root sleeve is common for S1. Our findings are of value in understanding the pathophysiology of prolapse of the disc and in preventing complications during surgery.

Rapid increase of cytosolic content of acetyl-CoA carboxylase isoforms in H9c2 cells by short-term treatment with insulin and okadaic acid

Mammalian acetyl-CoA carboxylase (ACC) is present in two isoforms, alpha and beta, both of which catalyze formation of malonyl-CoA by fixing CO2 into acetyl-CoA. ACC-alpha is highly expressed in lipogenic tissues whereas ACC-beta is a predominant form in heart and skeletal muscle tissues. Even though the tissue-specific expression pattern of two ACC isoforms suggests that each form may have a distinct function, existence of two isoforms catalyzing the identical reaction in a same cell has been a puzzling question. As a first step to answer this question and to identify the possible role of ACC isoforms in myogenic differentiation, we have investigated in the present study whether the expression and the subcellular distribution of ACC isoforms in H9c2 cardiac myocyte change so that malonyl-CoA produced by each form may modulate fatty acid oxidation. We have observed that the expression levels of both ACC forms were correlated to the extent of myogenic differentiation and that they were present not only in cytoplasm but also in other subcellular compartment. Among the various tested compounds, short-term treatment of H9c2 myotubes with insulin or okadaic acid rapidly increased the cytosolic content of both ACC isoforms up to 2 folds without affecting the total cellular ACC content. Taken together, these observations suggest that both ACC isoforms may play a pivotal role in muscle differentiation and that they may translocate between cytoplasm and other subcellular compartment to achieve its specific goal under the various physiological conditions.

Primers determine the sensitivity of PCR-mediated hepatitis B virus DNA detection and pretreatment of PCR mixture with 8-methoxypsoralen eliminates false-positive results

Most methods for the diagnosis of hepatitis B virus (HBV) infection largely depend on viral DNA detection by polymerase chain reaction (PCR) or radioimmunological assay of viral antigens or antibodies. The quality assurance program recently established in Europe reported that PCR-mediated HBV DNA detection methods used in many laboratories produced a high rate of false-positive and false-negative results. Thus, we attempted to improve the conditions of current PCR methods for detection of HBV DNA. In the present study, we applied a recently developed method of releasing HBV DNA from virion by NaOH treatment of patient serum. Using four different primer sets specific to the HBV core region, we found that the sensitivity of first-round PCR can be improved by more than two orders of magnitude depending on the primers. The second round of PCR using nested primers was sensitive enough to detect up to 10(-6) pg of the HBV DNA, which is equivalent to approximately 3 copies of the HBV genome. Among the approximately 800 HBV-infected patient sera investigated in our laboratory, more than 60% of the tested samples gave positive results in the first-round PCR. The rate of positive results obtained using our experimental conditions is very high in comparison with other reports. The reamplification of the first-round PCR reaction mixture with the nested primers produced practically 100% positive results. For diagnosis of HBV infection, we routinely used 1 microliter of patient serum, which was found to be optimum in our laboratory. Surprisingly, from 20% of our positive results, even serum diluted to 1/100 (0.01 microliter) produced a stronger signal than 1 microliter. This observation suggests that direct PCR amplification of HBV DNA released from serum by NaOH treatment has to be compensated by other DNA detection methods for correct quantitation. In order to eliminate the false positive signal resulting from the carry-over due to massive screening of a large number of samples, PCR reaction mixture containing 8-methoxypsoralen was exposed to ultraviolet light prior to thermal cycle amplification. This exercise did not decrease the sensitivity of the detection method, but almost completely removed the false positive results caused by contaminated templates. We are in the process of improving PCR-mediated HBV DNA detection methods to attain more reliable and easily applicable methods.

Effect of urea treatment on recovery of staphylococcal enterotoxin A from heat-processed foods

The effects of urea treatment on the potential reactivation of heat-damaged antigenic components of staphylococcal enterotoxin A (SEA) were examined with cooked foods, including mushrooms, ham, bologna, salami, and turkey. The thermal stability of purified SEA spiked into foods and native SEA produced by Staphylococcus aureus in foods was also examined. Food samples containing either spiked or native SEA were thermally processed by autoclaving or retorting. This was followed sequentially by toxin extraction, urea treatment, dialysis, reconstitution, and SE assays with the reversed passive latex agglutination and/or enzyme immunoassay kit. The results indicate that (i) urea treatment did not result in any reactivation of heat-inactivated antigenic components of SEA in any of the foods tested, (ii) the serological components of purified SEA were destroyed (> or = 96%) by autoclaving at 121.1 degrees C for 5 to 15 min or by retorting at an F0 of 4 to 18, and (iii) the immunological property of the native SEA was approximately threefold-more heat resistant than that of the purified SEA. The study suggested that the current urea method is not suitable for the detection of heat-denatured SEA in the thermally processed foods.

A Collaborative Study on the Detection of Staphylococcal Enterotoxins in Foods with an Enzyme Immunoassay Kit (TECRA)

One of the commercially available enzyme immunoassay kits for the detection of staphylococcal enterotoxins (SEs) in foods, the TECRA screening kit (Bioenterprises Pty. Ltd., Roseville, New South Wales, Australia), has microtiter plates coated with a mixture of antibodies to all of the SEs. A collaborative study was conducted to ascertain whether specificity, sensitivity, repeatability, and reproducibility of the results obtained using this kit would meet food-safety criteria. Thirteen Canadian collaborators participated in this study to analyze both various foods to which 1.0 to 3.0 ng of SE/g of food had been added and negative control samples. In addition, the effect of animal serum in these analyses was examined. The results indicate that all collaborators (100%) were able to detect the minimum toxin levels of 1.0 ng of SEA/g of ham and 1.0 ng of SEB/g of salami and SE or SEs in other samples (chicken, turkey, and cheese) containing 2.0 to 3.0 ng/g, without any false-negative results. With regard to negative control samples, all collaborators obtained correct results except when analyzing two types of food: two collaborators (15%) showed weak false-positive results with salami and all analysts found strong false-positive results with mussels. The problem regarding specificity could be largely corrected by treating the sample with rabbit serum (0.1 volume in 1.0 volume food extract). The repeatability and reproducibility of results from the kit were acceptable.

A collaborative study on the detection of staphylococcal enterotoxins in foods by an enzyme immunoassay kit (RIDASCREEN)

The RIDASCREEN SET kit (R-Biopharm GmbH, Darmstadt, Germany), a commercial staphylococcal enterotoxin (SE) immunoassay kit, utilizes monovalent capture antibodies against SE types A to E (SEA to SEE); therefore, it simultaneously detects and identifies the enterotoxin types. A collaborative study was conducted to ascertain whether the specificity, sensitivity, repeatability and reproducibility of the kits would meet food safety criteria. Twelve Canadian laboratories participated in this study to analyze various foods to which 1.0 to 2.0 ng of SE/g had been added and negative control samples. The results indicate that the sensitivity and specificity of the kit were excellent; all collaborators were able to detect the minimum toxin levels of 1.0 ng SEA/g in ham and cheese, 1.0 ng SEB/g in salami and turkey, and 2.0 ng SED/g in other samples without any false-negative results. With regard to negative control samples, all analysts obtained correct results except for one analyst who recorded weak false-positive results with several foods detecting SEC or SEA. The overall rate of false-positive results was 0.7% for 600 triplicate assays. In addition, it was confirmed that the RIDASCREEN kit did not yield false-positive results with mussels in contrast to some other EIA kits. Overall repeatability and reproducibility of the kit were in the range of 11.69-42.57% and 17.25-68.05%, respectively.

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.

Simple solutions to false-positive staphylococcal enterotoxin assays with seafood tested with an enzyme-linked immunosorbent assay kit (TECRA)

The TECRA kit, a commercial staphylococcal enterotoxin visual immunoassay kit, is an enzyme-linked immunosorbent assay system which utilizes polyvalent antisera against staphylococcal enterotoxin types A to E. The test is simple and rapid to perform (4 h) and has therefore been widely used for screening purposes. In this study, the TECRA kit produced a number of false-positive reactions with seafood; 25% of 218 samples of seven types of seafood gave false-positive results, particularly shellfish such as mussels (85%), clams (32%), oysters (23%), winkles (20%), and squid (13%). Some nonshellfish samples also gave false-positive results with the TECRA kit (smelt [20%] and trout [10%]). The substance contributing to the false-positive results differed from true staphylococcal enterotoxins in that it was: (i) heat labile, being completely inactivated by heating for 3 min at 70 degrees C, compared with 5% inactivation of true staphylococcal enterotoxins by the same heat treatment, (ii) in a selective reaction with normal rabbit or calf serum (nonspecific reactions were completely abolished by these sera, whereas staphylococcal enterotoxins were not affected), and (iii) incapable of binding to a copper-chelate Sepharose gel (all of the substance remained in the unbound wash fraction, whereas staphylococcal enterotoxins were quantitatively bound to the gel). The false-positive reactions occurring with seafood were not associated with substances produced by microorganisms, since the bacterial isolates from the samples did not give positive results with the TECRA kit.(ABSTRACT TRUNCATED AT 250 WORDS)

Nonspecific reactions of a commercial enzyme-linked immunosorbent assay kit (TECRA) for detection of staphylococcal enterotoxins in foods

A staphylococcal enterotoxin visual immunoassay kit (TECRA) has recently become commercially available. Since the kit is an enzyme-linked immunosorbent assay system equipped with polyvalent antisera against staphylococcal enterotoxin types A to E (SEA to SEE) and the test is simple and rapid to perform (4 h), it has been widely used for screening purposes. In this study, the sensitivity of the kit for detection of SEA, SEB, and SEC in ham, cheese, and mushrooms was similar to those of kits based on an enzyme immunoassay and reversed passive latex agglutination: 0.75 to 1.0 ng of SEA per ml, 0.5 to 0.75 ng of SEB per ml, and 1.0 to 1.25 ng of SEC per ml. However, the TECRA kit showed nonspecific reactions with food samples contaminated by microorganisms other than Staphylococcus aureus, such as Enterobacter agglomerans, Enterobacter cloacae, Proteus mirabilis, Pseudomonas aeruginosa, and Serratia marcescens. The substance contributing to the false-positive results differed from true staphylococcal enterotoxins in that it was (i) heat labile (completely inactivated by heating for 2 min at 100 degrees C, whereas true staphylococcal enterotoxins were inactivated by about 10% with this treatment), (ii) lower in molecular weight than staphylococcal enterotoxins, and (iii) not bound to a copper chelate Sepharose gel (all of the substance remained in the unbound wash fraction, whereas staphylococcal enterotoxins were quantitatively bound to the gel). The problem of false-positive results with the TECRA kit could be resolved by heat treatment (2 min at 100 degrees C) or by cleanup procedures involving metal chelate affinity chromatography with copper chelate Sepharose for 4 h before use of the TECRA kit.

Occurrence of thermotolerant campylobacters in fresh vegetables sold at farmers' outdoor markets and supermarkets

A total of 1564 fresh samples of 10 vegetable types from two different retail levels (533 samples from farmers' outdoor markets and 1031 samples from supermarkets) were surveyed for the occurrence of thermotolerant campylobacters. In samples from the outdoor markets, campylobacters were detected on six types of vegetables; the detection rates were spinach, 3.3; lettuce, 3.1; radish, 2.7; green onions, 2.5; parsley, 2.4; and potatoes, 1.6%. Campylobacter jejuni was the predominant species (88%), with the remainder being C. lari (8%) and C. coli (4%). When the outdoor market samples were thoroughly washed with chlorinated water, all were negative for campylobacters. Of the samples from supermarkets, all were negative for campylobacters whether purchased in summer or winter. These results suggest that vegetables sold at farmers' outdoor markets are produced and (or) stored under less sanitary conditions than those sold at supermarkets, and they could constitute health hazards. Therefore, vegetables (e.g., potatoes and spinach) from farmers' markets must be decontaminated by washing with chlorinated water or cooked thoroughly before consumption.

Thermal inactivation of Campylobacter species, Yersinia enterocolitica, and hemorrhagic Escherichia coli O157:H7 in fluid milk

Heat treatment of raw milk in an HTST pasteurizer operated at 60.0 to 72.0 degrees C for a minimum holding time of 16.2 s rapidly inactivated mixtures of hemorrhagic Escherichia coli O157:H7, Yersinia enterocolitica and Campylobacter spp. (C. fetus, C. coli, and C. jejuni). Each of the three genera in the mixture was inoculated at a level of approximately 1.0 x 10(5) cfu/ml. At 60.0 degrees C, hemorrhagic E. coli showed a maximum 2 log10 reduction in counts and no viability at greater than or equal to 64.5 degrees C. Yersinia enterocolitica and Campylobacter spp. showed greater heat sensitivity with a 4 log10 reduction in counts at 60.0 degrees C and absence of viable cells at greater than or equal to 63.0 degrees C. These findings reiterate the need for stringent control of thermal processes in the manufacture of dairy products from raw or heat-treated (non-pasteurized) milk.

Evaluation of the reversed passive latex agglutination (RPLA) test kits for detection of staphylococcal enterotoxins A, B, C, and D in foods

Four lots of the SET-RPLA kit (Denka Seiken Co. Ltd., Tokyo), a commercial reverse passive latex agglutination test kit for the detection of staphylococcal enterotoxins A, B, C, and D in foods, have been evaluated for their efficacy. The kits showed high specificity and sensitivity with a detection limit of 0.75 ng enterotoxin/g of food. The test is simple, is completed within 24 h, and does not require complicated extraction or concentration procedures nor expensive equipment. In addition, the assay is semiquantitative. However, as in any other immunological system, routine verification of the specificity of the latex reagents against standard enterotoxins and toxin-free food extracts is necessary.

Effect of temperature, duration of incubation, and pH of enrichment culture on the recovery of Campylobacter jejuni from eviscerated market chickens

To establish an enrichment system of high efficiency for recovery of Campylobacter jejuni from market chickens, the effects of the temperature, duration of incubation, and pH of the enrichment culture on the isolation of the bacterium were evaluated. Whole chickens or chicken parts in plastic bags were individually rinsed, and the washings filtered through cheesecloth. The cells were separated from the washings by centrifugation, and the pellet was inoculated into 100 mL of enrichment broth. Isolation of C. jejuni from poultry samples was significantly increased by incubating these samples in an enrichment medium at 42 degrees C as opposed to 35 degrees C; for 48 h as opposed to 24 h or 72 h; and at pH 7.0 as opposed to pH 6.0, 6.5, 7.5, or 8.0.

Incidence of Campylobacter jejuni in fresh eviscerated whole market chickens

A total of 100 fresh eviscerated whole market chickens, purchased one per week over a 5-week period from each of 20 different food stores in the Ontario and Ohio regions, were examined for the presence of Campylobacter jejuni. The microorganism was recovered from 62 and 54% of the chickens in Ontario and Ohio, respectively.

Evidence of thermonuclease production by Bacillus spp. and enterococci in naturally contaminated cheese

Of 105 thermonuclease-positive (TNase-positive) cheese samples comprising 13 types, 92 (87.6%) contained coagulase-positive staphylococci, whereas 9 (8.6%) contained microorganisms other than staphylococci as the major contaminants. Of the latter group, six samples contained Bacillus spp. comprising three species (B. cereus, B. licheniformis, and B. subtilis), and three contained mainly enterococci (Streptococcus faecalis), which were proven to be TNase producers. The organisms responsible for TNase production in the other four samples (3.8%) are not known, because isolates from these samples failed to produce the enzyme. Unlike staphylococcal TNase, a greater part of nonstaphylococcal TNase remains in the cheese homogenate after extraction of the enzyme at pH 3.8 instead of pH 4.5.

A survey of microorganisms for thermonuclease production

A total of 1204 cultures comprising 16 genera were surveyed for production of thermonuclease (TNase) in milk. Cultures other than Staphylococcus capable of TNase production were restricted to two genera, Streptococcus and Bacillus. Nineteen percent of 338 group D streptococci comprising four species (85% of which were Streptococcus faecalis) and 17% of 60 streptococci belonging to other groups produced TNase. Nine percent of 130 Bacillus cultures comprising six species produced the enzyme. On the other hand, 99% of coagulase-positive staphylococci produced TNase and only 18% of the coagulase-negative staphylococci produced the enzyme. The amount of TNase produced by streptococci and bacilli was significantly lower than that produced by coagulase-positive staphylococci. The pH profile of the streptococci and Bacillus TNases was similar to that of the staphylococcal TNase; each enzyme exhibited a minor peak at pH 7.0 and a broad major peak ranging from pH 8.5 to 10. The nuclease produced by coagulase-positive Staphylococcus was more heat stable than the nucleases produced by Streptococcus and Bacillus; there was little loss in activity of the staphylococcal enzyme after 60 min at 100 degrees C, whereas 50% of the activity of the streptococcal and Bacillus nucleases was destroyed in 40-60 min and 60-80 min, respectively.

A modified pork plasma agar for the enumeration of Staphylococcus aureus in foods

The coagulase reaction of Staphylococcus aureus on the PPSA (pork plasma for S. aureus) agar of Devoyod et al. was found to be fibrinogen-deficient. By including bovine fibrinogen (BFG) in the medium, the fibrin halos around S. aureus colonies became more distinct, preparations of pork plasma previously unacceptable for inclusion in the original PPSA agar were performing well, and the amount of pork plasma required in PPSA agar could be reduced by nearly 90%. In the modified medium, designated PPF (pork plasma fibrinogen) agar, the agar base (Baird-Parker agar without egg yolk) was unchanged. After surface plating, the base was covered with 8 mL of a modified overpour agar: 2.5% pork plasma, 0.38% BFG, and 0.0015% soy trypsin inhibitor in 0.7% Bacto agar. Most S. aureus strains could be enumerated after 24 h of incubation at 35 degrees C; the others required 44 h. Without soy trypsin inhibitor, a number of strains showed considerable fibrinolysis between 24 and 44 h of growth; this activity was neutralized by the inhibitor. The S. aureus counts of 27 food samples on PPF agar were essentially the same as the confirmed S. aureus counts obtained by the Baird-Parker method.

Inhibitory effect of cocoa powder on the growth of a variety of bacteria in different media

The inhibitory effect of cocoa powder on 102 organisms belonging to 13 genera was determined. All organisms tested were inhibited by 5% cocoa. Shigella, Staphylococcus, Micrococcus, and Bacillus were the most sensitive. The degree of inhibition depended on the organism, temperature of incubation, and the medium in which the cocoa powder was suspended. Of six media tested, lactose broth and nutrient broth were the most inhibitory, while non-fat dry milk was the least inhibitory. Supplementing NB with tryptone or casein reduced the toxicity of cocoa.

Effect of non-fat dry milk on recovery of staphylococcal thermonuclease from foods

Modification of the method of Tatini et al. (1976) by addition of non-fat dry milk (NFDM) to food samples and subsequent acid precipitation at pH 3.8 enhanced the recovery of staphylococcal thermonuclease (TNase) from most of 37 foods tested. The modified TNase assay method allowed detection of 10 ng (0.002 units) of the enzyme per gram of each of the following foods: ground beef, boiled egg products, whey powder, fruit-containing yogurt, dressings and spreads, potato and egg salads, and pastas, all of which gave false-negative results without NFDM.

Evaluation of staphylococcal thermonuclease (TNase) assay as a means of screening foods for growth of staphylococci and possible enterotoxin production

Samples of food, naturally and artificially contaminated with Staphylococcus aureus, were analyzed for enterotoxin and thermonuclease (TNase). With the exception of egg, all naturally contaminated foods with detectable amounts of staphylococcal enterotoxin were positive for TNase. The enzyme was also present in the majority of foods with over 1 million S. aureus cells per gram. In artificially contaminated foods. TNase was detected in all samples except egg, acidic foods in which growth of S. aureus was suppressed, and some samples of raw ground beef. Recovery of TNase was influenced by the type of food.

Preenrichment procedure for detection of Salmonella in gelatin

Trypticase soy broth was superior to nutrient and lactose broths as a preenrichment medium for the detection of Salmonella in artificially and naturally contaiminated gelatin. The detection rate for Salmonella were further enhanced when homogenization of the gelatin-broth mixture was accomplished by the use of gelatinase rather than by heating of 45 degrees C. Detection rats were also increased by adjusting the pH of the gelatin-broth mixture of 7.0, optimum pH for gelatinase (EC 3.4.23.2) activity.