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The demand for tree nuts has significantly grown in recent years as epidemiological studies and clinical intervention trials demonstrated an inverse relationship between tree nut consumption and chronic diseases. However, mycotoxins are one of the main hazards responsible for increased “Rapid Alert System for Food and Feed” (RASFF) notifications and border rejections on nuts and nut products exported to the E.U. countries in the past few years. Mycotoxins are secondary metabolites that present serious threats to human and animal health. The most prevalent, toxic, and carcinogenic mycotoxins observed in human food and animal feed are the aflatoxins (AFs). This work analyzed notifications from the RASFF on nuts and nut products contaminated with mycotoxins, for a 10-year period from 2011 to 2021. A total of 4752 mycotoxin notifications were published on RASFF for food products worldwide, 63% (n = 3000) were notified in “nuts, nut products and seeds”. It was observed that 95% (n = 2669) notifications were due to AFs. Over half of these notifications (52%, n = 1545) were reported for groundnuts, where 29% (n = 441) of the notifications were received for groundnuts from China alone. Border rejection was reported for 91% (n = 2560) of the nuts and nut products which received the notifications from the E.U. countries. This study proffers understanding into the major reasons for RASFF notifications on nuts and nut products exported to E.U. countries. Also, the implications of this issue with some recommendations that could reduce the incidents of notifications for tree nuts have been outlined.

To prevent loss from disease, immunostimulants have been used as dietary supplements to improve immunity and survival of shrimps. Among the various types of immunostimulants, there is increasing evidence that a diet enriched with bacterial lipopolysaccharide can reduce the mortality rate of shrimp under exposure to pathogens. Here, the immunostimulatory effects of bacterial lipopolysaccharide (LPS) from various bacterial sources were explored. Bacterial LPS was extracted from a shrimp pathogen, Vibrio harveyi and its effects were compared with the commercially available LPS from the non-shrimp pathogen, Escherichia coli. Our results revealed that the LPS from V. harveyi was different in molecular size but contained similar functional groups to that from E. coli. To understand their molecular mechanisms, bacterial LPS from the two sources were applied as a supplementary diet and fed to juvenile shrimp for 4-week feeding period before tissue samples were collected for transcriptomic analysis by next generation sequencing. Gene expression profiling revealed that major immune-related genes such as pattern recognition proteins (PRPs), proteinases and proteinase inhibitors, prophenoloxidase systems (proPO system), antimicrobial peptides (AMPs), signaling transduction pathways, heat shock proteins (HSPs), oxidative stress responses, and other immune-related molecules such as mucins and peritrophins were modulated in the groups of shrimp fed with bacterial LPS from both sources, but at different levels. The results suggest that bacterial LPS could modulate shrimp immune system, and different LPS sources led to different activation of immune pathways. Additionally, metabolic-related genes were affected by LPS, suggesting that energy was required for immune stimulation. In the V. harveyi pathogen challenge trial, all shrimp groups fed with diets containing LPS from both bacterial sources showed better survival than the control group without LPS. When comparing groups fed with LPS supplemented diets, the higher concentration of LPS (8 μg/body weight) from E. coli resulted in a better survival rate than a lower concentration (4 μg/body weight). Conversely, shrimp fed with a diet containing LPS from V. harveyi showed a lower survival rate when a higher dose of LPS (8 μg/body weight) was administered than the group fed with a lower concentration of LPS (4 μg/body weight). This could be due to overstimulation of shrimp immune responses, especially by LPS derived from shrimp pathogens, resulting in a reverse effect. These results confirm that immunity in shrimp upon administration of bacterial LPS depends on the origin and dose of the LPS administered.

Microbial colonization is an essential process in the early life of animal hosts—a crucial phase that could help influence and determine their health status at the later stages. The establishment of bacterial community in a host has been comprehensively studied in many animal models; however, knowledge on bacterial community associated with the early life stages of Penaeus monodon (the black tiger shrimp) is still limited. Here, we examined the bacterial community structures in four life stages (nauplius, zoea, mysis and postlarva) of two black tiger shrimp families using 16S rRNA amplicon sequencing by a next-generation sequencing. Although the bacterial profiles exhibited different patterns in each developmental stage, Bacteroidetes, Proteobacteria, Actinobacteria and Planctomycetes were identified as common bacterial phyla associated with shrimp. Interestingly, the bacterial diversity became relatively stable once shrimp developed to postlarvae (5-day-old and 15-day-old postlarval stages), suggesting an establishment of the bacterial community in matured shrimp. To our knowledge, this is the first report on bacteria establishment and assembly in early developmental stages of P. monodon. Our findings showed that the bacterial compositions could be shaped by different host developmental stages where the interplay of various host-associated factors, such as physiology, immune status and required diets, could have a strong influence.

To understand the host-gut microbial relationship, we used multidisciplinary platforms, metagenome, transcriptome, and metabolome analyses, to determine shrimp and intestinal microbial interactions upon 0, 6, 12, 24, and 48 h exposure to 107 CFU/mL of Vibrio harveyi, a shrimp pathogen. The bacterial communities in the intestine of shrimp were disrupted during exposure to V. harveyi. The abundance of Vibrio ASVs in the Harveyi and Vulnificus clades was significantly increased after exposure to the pathogen (6, 12, and 24 h) and decreased later after 48 h. Conversely, Pseudoalteromonas was found in lower abundance (6, 12, and 24 h) but significantly increased after 48 h of the bacterial challenge. Gene expression analysis revealed that genes belonging to several immune-related pathways, including the Toll pathway, the immune deficiency (IMD) pathway, and pattern recognition proteins (PRPs), were significantly upregulated. Early responses in the first 6 h after exposure were the genes involved in phagocytosis, pattern recognition proteins (PRPs), and signal transduction (spätzle and ankyrin). Late responses (12–48 h) were genes related to proteinases and proteinase inhibitors (PPIs), antimicrobial peptides (AMPs), and oxidative stress. Genes related to lipid metabolisms such as fatty acid metabolism and choline metabolism were also upregulated. Metabolomics analysis also showed an increase in phospholipids, including phosphocholine groups, in the intestine of shrimp exposed to the pathogen. Taken together, the gene expression and metabolomics analyses suggest the importance of lipid metabolism in the defense mechanism against bacterial invasion. Moreover, our metabolomic analysis showed a decrease in tryptophan and indole-3-acrylic acid, metabolites related to intestinal immune homeostasis, after bacterial infection. Our observations suggest that pathogenic Vibrio disrupted biological processes in the shrimp intestine, resulting in a decrease in indole-3-acrylic acid and its derivatives which in turn compromised intestinal immunity. In addition, shrimp responded to the bacterial invasion by activating metabolites related to eicosanoid and phospholipid biosynthesis. Our findings on the interactions between shrimp and intestinal microbiota will be an indispensable gateway to systems biology to better understand the function of shrimp gut microbiota and its influence on shrimp innate immunity.

The emergence of Vibrio diseases, including acute hepatopancreatic necrosis disease (AHPND) caused by Vibrio spp., had resulted in heavy losses in global shrimp production. Biofloc technology is a closed aquaculture system developed as one of the sustainable solutions to increase system resilience in the shrimp industry. In this study, biofloc was formed externally (ex situ biofloc) with probiotics Bacillus sp. strain BME and Bacillus sp. strain BCE, diatom microalgae Chaetoceros calcitrans, and a consortium of nitrifying bacteria, in the ratio of 1:1:6:6 as a starter. The study showed that the ex situ biofloc supplementation in Pacific whiteleg shrimp (L. vannamei) postlarvae culture can increase the shrimp culture performance (shrimp survival and growth), reduce Vibrio counts in the water and shrimp body, and provide stimulation of the shrimp immune response through humoral immune responses, such as pattern recognition protein (C-type lectin) and melanization process (proPO). Overall, the results indicate that the supplementation of ex situ biofloc provided protection to shrimp under Vibrio infection, regardless of the timing of addition (before, simultaneously, or after addition of Vibrio sp. strain VPA). This suggests that the ex situ biofloc can be effective as a preventive and a supportive treatment against potential AHPND infection in L. vannamei postlarvae culture. Taken together, the ability of the ex situ biofloc to modulate immune-related gene expression and resistance of L. vannamei against potentially AHPND-causing Vibrio sp. strain makes it an effective aquaculture technology for infectious disease control in shrimp production with high-density and minimal water exchange culture. KEY POINTS: • Supplementation of ex situ produced biofloc in shrimp postlarvae culture. • Ex situ biofloc reduces Vibrio counts in the water and shrimp body. • Ex situ biofloc stimulates shrimp humoral immune responses and survival.

With the advantages that long-read sequencing platforms such as Pacific Biosciences (Menlo Park, CA, USA) (PacBio) and Oxford Nanopore Technologies (Oxford, UK) (ONT) can offer, various research fields such as genomics and transcriptomics can exploit their benefits. Selecting an appropriate sequencing platform is undoubtedly crucial for the success of the research outcome, thus there is a need to compare these long-read sequencing platforms and evaluate them for specific research questions. This study aims to compare the performance of PacBio and ONT platforms for transcriptomic analysis by utilizing transcriptome data from three different tissues (hepatopancreas, intestine, and gonads) of the juvenile black tiger shrimp, Penaeus monodon. We compared three important features: (i) main characteristics of the sequencing libraries and their alignment with the reference genome, (ii) transcript assembly features and isoform identification, and (iii) correlation of the quantification of gene expression levels for both platforms. Our analyses suggest that read-length bias and differences in sequencing throughput are highly influential factors when using long reads in transcriptome studies. These comparisons can provide a guideline when designing a transcriptome study utilizing these two long-read sequencing technologies.

Rice traceability is one of major challenges to prevent illegal rice trading by adulterating with low quality rice and mislabeling low quality rice with the premium one. Current measures to protect illegal rice trading have been established, but more accurate and practical methods are still needed to detect rice traceability to assure quality and authenticity of rice. This review describes metabolomics approaches applicable for rice geographical origin classification and quality assessment over the past two decades. In addition, future aspects for miniaturization and portability of ambient mass spectrometry and vibrational Raman spectroscopy to be used for rice traceability are discussed for on-site testing and industrial applicability.

A DNA-based bead array method was successfully developed to simultaneously discriminate 11 pathogens namely Listeria grayi, L. innocua, L. ivanovii, L. monocytogenes, L. seeligeri, L. welshimeri, Escherichia coli, E. coli O157:H7, Staphylococcus aureus, methicillin-resistant S. aureus, and Salmonella spp. for multi purposes: food safety, hygiene indication, antibiotic resistance treatment. The bead array technology is based on fluorescent-barcoded paramagnetic beads with unique 24 oligonucleotide (anti-TAG) sequences which can capture biotinylated PCR product with complementary TAG sequence. R-phycoerythrin labeled streptavidin is used to report the presence of the biotinylated PCR products. After optimizing assay conditions, amplification and biotinylation steps can be performed in a single reaction without further purification before hybridization between the biotinylated TAG products and anti-TAG beads. To ensure that the developed method could provide accurate testing with the real food sample, a total of 311 bacterial isolates from 194 chicken meat samples were tested. The results were compared with those from the conventional ISO methods and revealed the relative accuracy, relative specificity, and relative sensitivity of 96%, 100%, and 95%, respectively. Therefore, the developed method was demonstrated to be useful to distinguish 11 bacteria species at the same time with high accuracy, specificity, and sensitivity.

Lipomannan (LM), a glycophospholipid found on the cell surface of mycobacteria, involves the virulence and survival in host cells. However, there is little to no information on how exactly mannan alignment, including the number of mannose units and the branched motif of LM, affects protein engagement during host-pathogen interactions. In this study, we synthesized the exact substructures of the LM glycans that consist of an α(1,6) mannan core, with and without the complete α(1,2) mannose branching, and comparatively studied their protein-carbohydrate interactions. The synthetic LM glycans were equipped with a thiol linker for immobilizations on the surfaces of microarrays. As per our findings, the presence of the branching α(1,2) mannose on the LM glycans increases their binding toward the dendritic cell-specific intercellular adhesion molecule-3 grabbing non-integrin receptor. An increase in the number of mannose units on the glycans also increases the binding with the mannose receptor. Thus, the set of synthetic glycans can serve as a useful tool to study the biological activities of LM and can provide a better understanding of host-pathogen interactions.

While lateral flow immunoassay (LFIA) is a simple technique that offers a rapid, robust, user friendly, and point-of-care test, its capacity for multiplex detection is rather limited. This study therefore combined the multiplexity of microarray technique and the simple and rapid characteristics of LFIA to enable simultaneous and quantitative detection of five mycotoxins, namely aflatoxin B1 (AFB1), deoxynivalenol (DON), fumonisin B1 (FUMB1), T-2 toxin (T-2), and zearalenone (ZON). In addition, we have synthesized a novel extra-large Stokes shift and strong fluorescence organic compound to be used as a reporter molecule which can be detected under UV light without light filter requirement. Many parameters including microarray spotting buffer, blocking buffer, and concentrations of mycotoxin antibodies were optimized for the microarray LFIA (μLFIA) construction. With the optimal conditions, the μLFIA could accurately and quantitatively detect multiple mycotoxins at the same time. The limits of detection of AFB1, DON, FUMB1, T-2, and ZON were 1.3, 0.5, 0.4, 0.4, and 0.9 ppb, respectively. The recoveries of these five mycotoxins were 70.7%–119.5% and 80.4%–124.8% for intra-assay and inter-assay, respectively. Combining the advantages of the novel reporter molecule and the multiplex capability of μLFIA test, this system could simultaneously detect multiple mycotoxins in one sample with high specificity and high sensitivity. Moreover, this system presents a promising affordable point-of-care platform to detect other analytes as well.

To mitigate disease outbreak, an alternative approach through enhancing shrimp immunity was explored. Mannan oligosaccharides (MOS) have been previously reported to enhance shrimp immune system. Here, coprameal samples were digested with mannanase to yield MOS, namely, mannanase-hydrolyzed coprameal (MCM) and feasibility of MCM as shrimp immunostimulant in grow-out ponds was determined. Pacific white shrimp (Litopenaeus vannamei) were fed with the commercial diet containing 1% MCM as the MCM-supplemented group and compared to the non-MCM control diet. There was no significant difference in survival rates between the MCM-supplemented and the control groups throughout the 4-month-period of the trial (p > 0.05). Gene expression analysis in shrimp intestines revealed that the transcript levels of antimicrobial peptides (anti-lipopolysaccharide factor isoform 1 (alf1), penaeidin (pen3a) and crustin (crus)) and lysozymes (lyz) were not significantly different in the MCM-supplemented group. Meanwhile, C-type lectin and toll-like receptor transcript levels, whose gene products play roles as pattern recognition proteins, were significantly higher in a group fed with MCM for 2- and 4-month periods than those of the control group (p < 0.05). The increased transcript levels of C-type lectin and toll-like receptor provide evidence for potential implementation of MCM as feed supplement to modulate shrimp immune system.

To salvage marine ecosystems from fishery overexploitation, sustainable and efficient aquaculture must be emphasized. The knowledge obtained from available genome sequence of marine organisms has accelerated marine aquaculture in many cases. The black tiger shrimp (Penaeus monodon) is one of the most prominent cultured penaeid shrimps (Crustacean) with an average annual global production of half a million tons in the last decade. However, its currently available genome assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high‐quality, high‐molecular weight DNA. Here, we report the first chromosome‐level whole‐genome assembly of P. monodon. The combination of long‐read Pacific Biosciences (PacBio) and long‐range Chicago and Hi‐C technologies enabled a successful assembly of this first high‐quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), the highest of the figures reported among crustacean species. The availability of this high‐quality genome assembly enabled the identification of genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow‐growing and fast‐growing shrimps. The results highlighted several growth‐associated genes. Our high‐quality genome assembly provides an invaluable resource for genetic improvement and breeding penaeid shrimp in aquaculture. The availability of P. monodon genome enables analyses of ecological impact, environment adaptation and evolution, as well as the role of the genome to protect the ecological resources by promoting sustainable shrimp farming.

Understanding the correlation between shrimp growth and their intestinal bacteria would be necessary to optimize animal’s growth performance. Here, we compared the bacterial profiles along with the shrimp’s gene expression responses and metabolites in the intestines between the Top and the Bottom weight groups. Black tiger shrimp (Penaeus monodon) were collected from the same population and rearing environments. The two weight groups, the Top-weight group with an average weight of 36.82 ± 0.41 g and the Bottom-weight group with an average weight of 17.80 ± 11.81 g, were selected. Intestines were aseptically collected and subjected to microbiota, transcriptomic and metabolomic profile analyses. The weighted-principal coordinates analysis (PCoA) based on UniFrac distances showed similar bacterial profiles between the two groups, suggesting similar relative composition of the overall bacterial community structures. This observed similarity was likely due to the fact that shrimp were from the same genetic background and reared under the same habitat and diets. On the other hand, the unweighted-distance matrix revealed that the bacterial profiles associated in intestines of the Top-weight group were clustered distinctly from those of the Bottom-weight shrimp, suggesting that some unique non-dominant bacterial genera were found associated with either group. The key bacterial members associated to the Top-weight shrimp were mostly from Firmicutes (Brevibacillus and Fusibacter) and Bacteroidetes (Spongiimonas), both of which were found in significantly higher abundance than those of the Bottom-weight shrimp. Transcriptomic profile of shrimp intestines found significant upregulation of genes mostly involved in nutrient metabolisms and energy storage in the Top-weight shrimp. In addition to significantly expressed metabolic-related genes, the Bottom-weight shrimp also showed significant upregulation of stress and immune-related genes, suggesting that these pathways might contribute to different degrees of shrimp growth performance. A non-targeted metabolome analysis from shrimp intestines revealed different metabolic responsive patterns, in which the Top-weight shrimp contained significantly higher levels of short chain fatty acids, lipids and organic compounds than the Bottom-weight shrimp. The identified metabolites included those that were known to be produced by intestinal bacteria such as butyric acid, 4-indolecarbaldehyde and L-3-phenyllactic acid as well as those produced by shrimp such as acyl-carnitines and lysophosphatidylcholine. The functions of these metabolites were related to nutrient absorption and metabolisms. Our findings provide the first report utilizing multi-omics integration approach to investigate microbiota, metabolic and transcriptomics profiles of the host shrimp and their potential roles and relationship to shrimp growth performance.

The black tiger shrimp (Penaeus monodon) is one of the most prominent farmed crustacean species with an average annual global production of 0.5 million tons in the last decade. To ensure sustainable and profitable production through genetic selective breeding programs, several research groups have attempted to generate a reference genome using short-read sequencing technology. However, the currently available assemblies lack the contiguity and completeness required for accurate genome annotation due to the highly repetitive nature of the genome and technical difficulty in extracting high-quality, high-molecular weight DNA in this species. Here, we report the first chromosome-level whole-genome assembly of P. monodon. The combination of long-read Pacific Biosciences (PacBio) and long-range Chicago and Hi-C technologies enabled a successful assembly of this first high-quality genome sequence. The final assembly covered 2.39 Gb (92.3% of the estimated genome size) and contained 44 pseudomolecules, corresponding to the haploid chromosome number. Repetitive elements occupied a substantial portion of the assembly (62.5%), highest of the figures reported among crustacean species. The availability of this high-quality genome assembly enabled the identification of novel genes associated with rapid growth in the black tiger shrimp through the comparison of hepatopancreas transcriptome of slow-growing and fast-growing shrimps. The results highlighted several gene groups involved in nutrient metabolism pathways and revealed 67 newly identified growth-associated genes. Our high-quality genome assembly provides an invaluable resource for accelerating the development of improved shrimp strain in breeding programs and future studies on gene regulations and comparative genomics.

Acidovorax citrulli, a seedborne bacterium and quarantine pest, causes the devastating bacterial fruit blotch disease in cucurbit plants. Immunological assays such as ELISA are widely used in routine field inspections for this bacterium. However, to the best of our knowledge, none of the currently available monoclonal antibodies (MAbs) can detect all common A. citrulli strains. We therefore aimed to produce a panel of MAbs and to develop an ELISA-based method capable of detecting all A. citrulli strains. We used a high-throughput bead array technique to screen and characterize A. citrulli-specific MAbs produced from hybridoma clones. The hybridoma library was simultaneously screened against five A. citrulli strains (PSA, KK9, SQA, SQB and P) and the closely related bacterium, Delftia acidovorans. Three MAbs exhibiting different binding patterns to A. citrulli were used to develop an ELISA-based method called "double antibody pairs sandwich ELISA" (DAPS-ELISA). DAPS-ELISA employing mixtures of MAbs was able to specifically detect all 16 A. citrulli strains tested without cross-reactivity with other bacteria. By contrast, our previously developed MAb capture-sandwich ELISA (MC-sELISA) and a commercial test kit detected only 15 and 14 of 16 strains, respectively. The sensitivity of the DAPS-ELISA ranged from 5×105 to 1×106 CFU/mL, while those of the MC-sELISA and the commercial test kit ranged from 5×104 to 1×107 CFU/mL and 5×104 to 5×105 CFU/mL, respectively. DAPS-ELISA thus represents an alternative method enabling rapid, accurate, and inexpensive detection of all A. citrulli strains. The method can be applied to seed testing prior to planting as well as to routine field inspections.

Unilateral eyestalk ablation in the female black tiger shrimp Penaeus monodon is commonly employed to induce ovarian maturation. However, the importance of complementing this practice with the provision of live feed supplement (such as polychaetes) has not been emphasized in previous studies. Indeed, it has been less emphasized that female broodstock must be fed with live feeds such as polychaetes for this practice to be effective. While the effects of eyestalk ablation have been thoroughly studied in various aspects, the synergistic effects of feeding with live feeds and the ablation have never been elucidated at a transcriptome-wide level. With recent advances in the next-generation sequencing platforms, it is now possible to investigate the effects of eyestalk ablation and live feeds at the transcriptomic levels. This study employed both short-read Illumina RNA sequencing and long-read Pacific Biosciences (PacBio) isoform sequencing (Iso-seq) to generate the first high-quality ovarian reference transcriptome in P. monodon. This novel assembly allowed us to dissect the effects of feeds and eyestalk ablation and reveal their synergistic effects at the transcriptomic level through the regulation of important genes involved in fatty acid regulation, energy production, and hormone-mediated oocyte maturation pathways. The synergistic effects between the polychaete feeding and the eyestalk ablation in the process of ovarian maturation in black tiger shrimp suggest that without having proper nutrients from the polychaetes, female broodstock might not be ready to develop its ovary. However, even with proper nutrients, the eyestalk ablation is still necessary to perhaps manipulate the female endocrine of the black tiger shrimp. These findings shed the light on molecular mechanisms and key molecular pathways that lead to successful ovarian maturation.

Understanding brown planthopper (BPH) resistance mechanism will expedite selective breeding of better BPH resistant lines of rice (Oryza sativa). Metabolic responses during BPH infestation derived from wound stress imposed by insect feeding, comparing with mechanical piercing will provide an insight into resistance mechanism in rice. Therefore, this study aimed to compare the metabolic responses of needle piercing treatment and BPH feeding treatment in BPH-susceptible (KD) and BPH-resistant (RH) varieties at four different time points (0, 6, 24 and 96 h) using liquid chromatography-high resolution mass spectrometry (LC-HRMS). Phenotypes of RH were not different among the treatments, whereas KD exhibited hopperburn symptom at 96 h post-BPH infestation. Principal component and cluster analyses revealed that metabolite profiles between KD and RH were different in response to both insect and mechanical stimuli. Metabolite profiles of RH under BPH and mechanical treatments at 24 and 96 h were different from the untreated, whereas metabolite profiles of KD after BPH infestation at 24 and 96 h were distinct from needle piercing and no treatment, suggesting that the resistant variety has an ability to adapt and defend both mechanical and insect stimuli. Metabolomics result showed that BPH infestation perturbed purine salvage biosynthesis (e.g., inosine, hypoxanthine) in both varieties, amino acid biosynthesis (e.g., phenylalanine, tryptophan) in KD, while the infestation perturbed lysine metabolism (pipecolic acid) and phenylpropanoid pathway (2-anisic acid) only in RH. BPH and mechanical stimuli perturbed phenylamide only in RH, but not in KD. These findings revealed that different rice varieties utilize different metabolites in response to insect and mechanical stimuli, resulting in different degrees of resistance.

Higher-order Guided Mode Resonance (GMR) in a symmetric two-dimensional embedded grating-waveguide structure is theoretically demonstrated in this paper through a phase matching mechanism of leaky modes along second-order diffraction planes. In addition to the fundamental-order, multiple resonances are introduced at normal incidence and they are polarization independent. A strong localization of the resonance modes exists in both orders. The device is proposed for multiple color surface enhanced fluorescence that is compatible to a conventional fluorescence reader. The enhancement scheme is by increasing light absorption via the excitation of a strong evanescent wave as an extension of a resonance mode. GMR device is designed to have resonances overlapping fluorophores’ absorption spectra. The concept is verified using numerical calculations, Rigorous Coupled Wave Analysis and Homogeneous Waveguide Approach. The device is fabricated and experimentally performed for fluorescence enhancement using a microarray of Cyanine 3-labeled goat antibody and Cyanine 5-labeled goat antibody. The fluorescence signal is characterized using a low-cost CMOS array. This implementation can be very useful in a multiplex detection, where the cost of the reader can be minimized.

Creation of a highly sensitive test strip that can provide simple, rapid, and high-throughput determination of Hg2+ levels in consumer goods and industrial waste is extremely challenging since the portability and convenience of the paper-based platform often come at the expense of inferior sensitivity. In this work, a fluorescent electrospun fibrous membrane that can report mercury contamination down to sub-ppb level in less than a minute is developed. The key success of this user-friendly device relies on the design of novel mercury-favored organic dye (NF06) that displays specific fluorescence enhancement – “Turn-On” positive results – through fluorescence resonance energy transfer (FRET) mechanism and exhibits extremely large Stokes shift of 248 nm. The surface chemistry of the cellulose acetate(CA)/polycaprolactone(PCL) electrospun fibers on which the NF06 sensor is immobilized has been found to efficiently facilitate the FRET operation of the sensor. As a result, the detection limit of this NF06 strip reaches 0.309 ppb (0.697 nM), approximately an order of magnitude lower than the maximum mercury level permitted in drinking water (2 ppb) recommended by the US Environment Protection Agency. Instrument-free visual readout of Hg2+ level-dependent fluorescence enhancement after dipping the strips in Hg2+-spiked drinking water and skin whitening serum demonstrates that these low-cost test strips could certainly be used by general consumers for safety evaluation as well as by regulatory agencies for large-scale screening of a variety of commercial products without the need for expensive and highly sensitive detectors.

To employ a microsphere immunoassay (MIA) to simultaneously detect multiple plant pathogens (potyviruses, Watermelon silver mottle virus, Melon yellow spot virus, and Acidovorax avenae subsp. citrulli) in actual plant samples, several factors need to be optimized and rigorously validated. Here, a simple extraction method using a single extraction buffer was successfully selected to detect the four pathogens in various cucurbit samples (cucumber, cantaloupe, melon, and watermelon). The extraction method and assay performance were validated with inoculated and field cucurbit samples. The MIA showed 98-99% relative accuracy, 97-100% relative specificity and 92-100% relative sensitivity when compared to commercial ELISA kits and reverse transcription PCR. In addition, the MIA was also able to accurately detect multiple-infected field samples. The results demonstrate that one common extraction method for all tested cucurbit samples could be applied to detect multiple pathogens; avoiding the need for multiple protocols to be employed. This multiplex method can therefore be instrumental for high-throughput screening of multiple plant pathogens with many advantages such as a shorter assay time (2.5h) with single assay format, a lower cost of detection ($5 vs $19.7 for 4 pathogens/sample) and less labor requirement. Its multiplex capacity can also be expanded to detect up to 50 different pathogens upon the availability of specific antibodies.

Summary Quantitative real-time PCR (RT-qPCR) is often used for gene expression analysis to reveal molecular mechanism of how stresses can enhance the secondary metabolites production. For RT-qPCR to be valid, robust reference genes are required. This study validated nine candidate genes as reference genes using BestKeeper, NormFinder and geNorm methods in RT-qPCR analysis of postharvest tomatoes subjected to electricity-induced stress. The most stable genes as indicated by each method were EF-1α by BestKeeper; CAC by NormFinder; and PP2Acs/TIP41 by geNorm. Due to the inconsistency in the ranking of the candidate genes by the three methods, the pairwise variation from geNorm analysis was used to calculate the minimum numbers of reference genes for an accurate normalisation and revealed that a combination of PP2Acs and TIP41 was an optimum. This reference gene combination was further validated for their stability in RT-qPCR analysis of four carotenoid-related genes, and more reliable expression levels were obtained.

Introduction: Brown planthopper (BPH) is a phloem feeding insect that causes annual disease outbreaks, called hopper burn in many countries throughout Asia, resulting in severe damage to rice production. Currently, mechanistic understanding of BPH resistance in rice plant is limited, which has caused slow progression on developing effective rice varieties as well as effective farming practices against BPH infestation. Objective: To reveal rice metabolic responses during 8 days of BPH attack, this study examined polar metabolome extracts of BPH-susceptible (KD) and its BPH-resistant isogenic line (IL308) rice leaves. Methods: Ultra high performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QToF-MS) was combined with multi-block PCA to analyze potential metabolites in response to BPH attack. Results: This multivariate statistical model revealed different metabolic response patterns between the BPH-susceptible and BPH-resistant varieties during BPH infestation. The metabolite responses of the resistant IL308 variety occurred on Day 1, which was significantly earlier than those of the susceptible KD variety which showed an induced response by Days 4 and 8. BPH infestation caused metabolic perturbations in purine, phenylpropanoid, flavonoid, and terpenoid pathways. While found in both susceptible and resistant rice varieties, schaftoside (1.8 fold), iso-schaftoside (1.7 fold), rhoifolin (3.4 fold) and apigenin 6-C-α-l-arabinoside-8-C-β-l-arabinoside levels (1.6 fold) were significantly increased in the resistant variety by Day 1 post-infestation. 20-hydroxyecdysone acetate (2.5 fold) and dicaffeoylquinic acid (4.7 fold) levels were considerably higher in the resistant rice variety than those in the susceptible variety, both before and after infestation, suggesting that these secondary metabolites play important roles in inducible and constitutive defenses against the BPH infestation. Conclusions: These potential secondary metabolites will be useful as metabolite markers and/or bioactive compounds for effective and durable approaches to address the BPH problem.

Shrimp is an important food source consumed worldwide. An intensive aquaculture system with overuse of feed in combination with detrimental effects from climate change are serious problems leading to mass mortality of cultured shrimp. Biofloc technology is an approach to managing water quality and controlling the disease to counter the negative side of intensive culture system, however, most of the biofloc applications are naturally formed, which could be inconsistent. In this study, we employed an established optimal ratio of microbial consortium called “ex-situ biofloc (BF)” to be used as a feed supplement in shrimp cultured in a zero-water discharged system at low salinity conditions. Three feeding groups (100%commercial pellet (C), 95%C+BF, 90%C+BF) of shrimp were cultured for six weeks. The effect of an ex-situ biofloc supplement with commercial pellet reduction showed that levels of ammonium, nitrite, nitrate and phosphate were significantly decreased in water culture. Shrimp fed with ex-situ biofloc supplement with commercial pellet reduction exhibited significantly increased shrimp weight and survival, and significantly expressed growth-related genes involving lipolysis and energy metabolism higher than those fed with 100% commercial pellet. Nutritional analysis indicated a significant increase of docosahexaenoic acid (DHA) and eicosenoic acid (C20:1) concentrations in the ex-situ biofloc supplemented shrimp. This finding revealed the potential of ex-situ biofloc to manage water quality, improve shrimp growth performance and enhance shrimp nutritional value under intensive culture at low salinity conditions. The beneficial effects of the ex-situ biofloc in shrimp culture system make it a promising alternative strategy to mitigate climate change effects leading to the sustainable production of high-quality shrimp in the future.

This study rigorously evaluated a previously developed immunobead array method to simultaneously detect three important foodborne pathogens, Campylobacter jejuni, Listeria monocytogenes, and Salmonella spp., for its actual application in routine food testing. Due to the limitation of the detection limit of the developed method, an enrichment step was included in this study by using Campylobacter Enrichment Broth for C. jejuni and Universal Pre-enrichment Broth for L. monocytogenes and Salmonella spp.. The findings showed that the immunobead array method was capable of detecting as low as 1CFU of the pathogens spiked in the culture media after being cultured for 24h for all three pathogens. The immunobead array method was further evaluated for its pathogen detection capabilities in ready-to-eat (RTE) and ready-to-cook (RTC) chicken samples and proven to be able to detect as low as 1CFU of the pathogens spiked in the food samples after being cultured for 24h in the case of Salmonella spp., and L. monocytogenes and 48 h in the case of C. jejuni. The method was subsequently validated with three types of chicken products (RTE, n=30; RTC, n=20; raw chicken, n=20) and was found to give the same results as the conventional plating method. Our findings demonstrated that the previously developed immunobead array method could be used for actual food testing with minimal enrichment period of only 52 h, whereas the conventional ISO protocols for the same pathogens take 90-144 h. The immunobead array was therefore an inexpensive, rapid and simple method for the food testing.

The intestinal microbiota play important roles in health of their host, contributing to maintaining the balance and resilience against pathogen. To investigate effects of pathogen to intestinal microbiota, the bacterial dynamics upon a shrimp pathogen, Vibrio harveyi, exposures were determined in two economically important shrimp species; the black tiger shrimp (BT) and the Pacific white shrimp (PW). Both shrimp species were reared under the same diet and environmental conditions. Shrimp survival rates after the V. harveyi exposure revealed that the PW shrimp had a higher resistance to the pathogen than the BT shrimp. The intestinal bacterial profiles were determined by denaturing gradient gel electrophoresis (DGGE) and barcoded pyrosequencing of the 16S rRNA sequences under no pathogen challenge control and under pathogenic V. harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control in BT and PW intestines. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. The barcoded pyrosequencing analysis showed the similar bacterial community structures in intestines of BT and PW shrimp under a normal condition. However, during the time course exposure to V. harveyi, the relative abundance of bacteria belong to Vibrio genus was higher in the BT intestines at 12h after the exposure, whereas relative abundance of vibrios was more stable in PW intestines. The principle coordinates analysis based on weighted-UniFrac analysis showed that intestinal bacterial population in the BT shrimp lost their ability to restore their bacterial balance during the 72-h period of exposure to the pathogen, while the PW shrimp were able to reestablish their bacterial population to resemble those seen in the unexposed control group. This observation of bacterial disruption might correlate to different mortality rates observed between the two shrimp species. Our findings provide evidence of intestinal bacterial population altered by a presence of the pathogen in shrimp intestines and intestinal bacterial stability might provide colonization resistance against the invading pathogen in the host shrimp. Hence, intestinal microbial ecology management may potentially contribute to disease prevention in aquaculture.

Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.

This article reports the detection of Salmonella spp. based on M13 bacteriophage in a capacitive flow injection system. Salmonella -specific M13 bacteriophage was immobilized on a polytyramine/gold surface using glutaraldehyde as a crosslinker. The M13 bacteriophage modified electrode can specifically bind to Salmonella spp. via the amino acid groups on the filamentous phage. An alkaline solution was used to break the binding between the sensing surface and the analyte to allow renewable use up to 40 times. This capacitive system provided good reproducibility with a relative standard deviation (RSD) of 1.1%. A 75 µL min -1 flow rate and a 300 µL sample volume provided a wide linear range, from 2.0 × 10 2 to 1.0 × 10 7 cfu mL -1 , with a detection limit of 200 cfu mL -1 . Bacteria concentration can be analyzed within 40 min after the sample injection. When applied to test real samples (raw chicken meat) it provided good recoveries (100–111%). An enrichment process was also explored to increase the bacteria concentration, enabling a quantitative detection of S almonella spp. This biosensor opens a new opportunity for the detection of pathogenic bacteria using bacteriophage.