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Most mercury exposure to humans comes from consumption of fish and shellfish; however, mercury concentrations are not known for all available seafood, particularly shrimp. Our objective was to estimate the concentration of mercury in a variety of store‐bought shrimp and then to compare total mercury concentrations to other information such as brand, harvest type, and total fat. We sampled a total of n = 159 shrimp from 10 different brands. Across 10 brands of shrimp, there was a significant effect of brand, with mean mercury concentrations among brands varying by up to an order of magnitude. We found no significant differences comparing shrimp between two capture types (wild‐caught and farm‐raised), which was perfectly collinear to whether shrimp were domestic or foreign. We did detect significant differences in mercury levels among different amounts of total fat in shrimp, with the lowest fat shrimp (1 g) having significantly more mercury than the highest fat shrimp (2 g). Although our results confirm that shrimp contains relatively low levels of mercury and is generally considered a good choice for consumers, this study is the first to report significant differences in mercury among both brands of shrimp and total fat content in shrimp., This study presents mercury concentrations in store‐bough (frozen) shrimp, which were all found to be low, but variable. No effect of harvest type or location was found, although total fat was related to mercury concentrations in shrimp.

Fishing of the brown shrimp Penaeus aztecus is an important socioeconomic activity, generating income and different jobs for the fishing sector; however, this species is exposed to contaminants such as toxic metals. The objective of this research was to determine the concentrations of Cd, Pb, Cr, and Ni in brown shrimp P. aztecus from the northwestern Gulf of Mexico, and to analyse morphometric measurements in this species. The determination of toxic metals in shrimp was carried out according to the method proposed by the USEPA. Sexual identification was carried out by examining the first pleopods of P. aztecus specimens; the stages of maturity and proportion of sexes were also determined, finding specimens at maturity stages I and II. Specimens collected in the Veracruz area presented higher morphometric values, with an average TL of 136.15 mm. It was identified in the same area that the batches were formed by a higher proportion of males at 72.2%. Ni was the metal with the highest concentration in the Veracruz area at 15.5 µg g−1, while Pb had a maximum concentration of 8.3 µg g−1. The concentrations obtained for the toxic metals in the shrimp exceeded the values of the international permissible limits established for Pb and Cd.

The kuruma shrimp Marsupenaeus japonicus (order Decapoda, family Penaeidae) is an economically important crustacean that occurs in shallow, warm seas across the Indo-Pacific. Here, using a combination of Illumina and Oxford Nanopore Technologies platforms, we produced a draft genome assembly of M. japonicus (1.70 Gbp; 18,210 scaffolds; scaffold N50 = 234.9 kbp; 34.38% GC, 93.4% BUSCO completeness) and a complete mitochondrial genome sequence (15,969 bp). As with other penaeid shrimp genomes, the M. japonicus genome is extremely rich in simple repeats, which occupies 27.4% of the assembly. A total of 26,381 protein-coding gene models (94.7% BUSCO completeness) were predicted, of which 18,005 genes (68.2%) were assigned functional description by at least one method. We also produced an Illumina-based transcriptome shotgun assembly (40,991 entries; 93.0% BUSCO completeness) and a PacBio Iso-Seq transcriptome assembly (25,415 entries; 67.5% BUSCO completeness). We envision that the M. japonicus genome and transcriptome assemblies will serve as useful resources for the basic research, fisheries management, and breeding programs of M. japonicus.

Shrimp aquaculture is an essential economic venture globally, but the industry faces numerous challenges, especially pathogenic infections. As invertebrates, shrimp rely mainly on their innate immune system for protection. An increasing number of studies have shown that ubiquitination plays a vital role in the innate immune response to microbial pathogens. As an important form of posttranslational modification (PTM), both hosts and pathogens have exploited ubiquitination and the ubiquitin system as an immune response strategy to outwit the other. This short review brings together recent findings on ubiquitination and how this PTM plays a critical role in immune modulation in penaeid shrimps. Key findings inferred from other species would help guide further studies on ubiquitination as an immune response strategy in shrimp-pathogen interactions.

Penaeid shrimp (family Penaeidae) represents one of the most economically and ecologically important groups of crustaceans. However, their genome sequencing and assembly have encountered extreme difficulties during the last 20 years. In this study, based on our previous genomic data, we investigated the genomic characteristics of four penaeid shrimp species and identified potential factors that result in their poor genome assembly, including heterozygosity, polyploidization, and repeats. Genome sequencing and comparison of somatic cells (diploid) of the four shrimp species and a single sperm cell (haploid) of Litopenaeus vannamei identified a common bimodal distribution of K-mer depths, suggesting either high heterozygosity or abundant homo-duplicated sequences present in their genomes. However, penaeids have not undergone whole-genome duplication as indicated by a series of approaches. Besides, the remarkable expansion of simple sequence repeats was another outstanding character of penaeid genomes, which also made the genome assembly highly fragmented. Due to this situation, we tried to assemble the genome of penaeid shrimp using various genome sequencing and assembly strategies and compared the quality. Therefore, this study provides new insights about the genomic characteristics of penaeid shrimps while improving their genome assemblies.

International audience; Stylicins are anionic antimicrobial host defense peptides (AAMPs) composed of a proline-rich Nterminal region and a C-terminal portion containing 13 conserved cysteine residues. Here, we have increased our knowledge about these unexplored crustacean AAMPs by the characterization of novel stylicin members in the most cultivated penaeid shrimp, Litopenaeus vannamei. We showed that the L. vannamei stylicin family is composed of two members (Lvan-Stylicin1 and Lvan-Stylicin2) encoded by different loci which vary in gene copy number. Unlike the other three gene-encoded antimicrobial peptide families from penaeid shrimp, the expression of Lvan-Stylicins is not restricted to hemocytes. Indeed, they are also produced by the columnar epithelial cells lining the midgut and its anterior caecum. Interestingly, Lvan-Stylicins are simultaneously transcribed at different transcriptional levels in a single shrimp and are differentially modulated in hemocytes after infections. While the expression of both genes showed to be responsive to damage-associated molecular patterns, only Lvan-Stylicin2 was induced after a Vibrio infection. Besides, Lvan-Stylicins also showed a distinct pattern of gene expression in the three portions of the midgut (anterior, middle and posterior) and during shrimp development. We provide here the first evidence of the diversity of the stylicin antimicrobial peptide family in terms of sequence and gene expression distribution and regulation.

The widespread use of systemic neonicotinoid insecticides in agriculture has resulted in the unintended contamination of aquatic environments at concentrations that could impact aquaculture stock. The high toxicity of neonicotinoids to non-target aquatic insects and crustaceans has been documented; however, the effects on commercial shrimp species are unclear. This thesis aimed to examine the impacts of sublethal neonicotinoid exposure on black tiger shrimp (Penaeus monodon) and assess the implications for shrimp aquaculture and consumer safety. A series of well-replicated controlled experiments compared the effects of aqueous and dietary exposure on survivorship, growth, behaviour, and biochemical stress indicators. Neonicotinoid residues were extracted from tissue and water by QuEChERS and solid-phase extraction, respectively, then analysed by liquid chromatography-mass spectrometry. Sublethal impacts on flesh biomarkers examined AChE, CAT and GST enzyme activity, as well as lipid and protein profiles. Acute toxicity tests showed that clothianidin (190 μg L-1), thiamethoxam (390 μg L-1), and imidacloprid (408 μg L-1) were acutely toxic to juvenile P. monodon, while acetamiprid was non-toxic to shrimp up to 500 μg L-1. Thiamethoxam, clothianidin, and imidacloprid residues accumulated rapidly in shrimp from either dietary or aqueous exposure, with accumulated residues exceeding maximum residue thresholds for seafood. A four-day depuration reduced accumulated residues, although a more extended depuration period is necessary for clothianidin exposed shrimp. Positive correlations existed between neonicotinoid tissue concentration and biomarker activity for aqueous and dietary exposure routes. Elevated AChE impacted neurotransmission affecting movement, while elevated CAT and GST confirmed an oxidative stress response. Routine monitoring of AChE, CAT, and GST biomarkers could provide an early warning of shrimp stress, with an elevated response in all three biomarkers indicating that investigating potential contamination by neonicotinoid insecticides would be worthwhile., Neonicotinoids reduced feed consumption affecting shrimp nutritional status, altering fatty acid composition, carbohydrate metabolism, amino acid biosynthesis, and calcium signalling. Exposure increased mortality and inter-moult interval and reduced weight gain and growth rate, thus posing a risk to aquaculture productivity. A reduced abundance of eicosanoid precursors and pathogen detection proteins suggest pathogen defences may be compromised. Allergenic protein abundance increased and may affect food safety. Overall, this study confirmed that shrimp are vulnerable to neonicotinoids from aqueous or dietary sources and that exposure could significantly impact food safety and aquaculture productivity. The threat of increased neonicotinoid use and the increased risk to shrimp aquaculture requires effective monitoring and regulation in shrimp producing areas.

The sesquiterpenoid methyl farnesoate (MF), a juvenile hormone (JH) analog, plays important roles in many physiological processes of crustaceans, such as morphogenesis, molting and reproduction. Juvenile hormone esterase-like (JHE-like) carboxylesterase (CXE) is a key enzyme in MF degradation, playing a significant role in regulating MF titer. However, its function is barely known in shrimp. In this study, a total of 21 JHE-like CXEs (LvCXEs) were characterized in Pacific white shrimp Litopenaeus vannamei, based on the full genome and multi-transcriptomic data. LvCXE has a conserved triplet catalytic site (Ser-Glu-His) and a characteristic GxSxG motif. Most LvCXEs were highly expressed in the hepatopancreas, which was the main site for MF degradation. LvCXEs containing a GESAG motif showed a specific expansion in the L. vannamei genome. Those GESAG-containing LvCXEs presented differential expressions at different larvae stages and different molting stages of L. vannamei, which suggested their potential functions in development and molting. Additionally, when the transcription level of CXEs was inhibited, it could lead to failed molt and death of L. vannamei. When we further detected the expression levels of the key ecdysone responsive transcription factors including LvE75, LvBr-C, LvHr3 and LvFtz-f1 after the CXE inhibitor was injected into L. vannamei, they all showed apparent down-regulation. These results suggested that the expansion of LvCXEs in the L. vannamei genome should contribute to the regulation of metamorphosis at larvae stages and frequent molting during the growth of L. vannamei.

The ingestion of microplastics by diverse marine organisms induces behavioral disorders, physiological changes, and immune and stress responses. The negative effects of microplastic exposure in penaeid shrimps are still unclear despite the annual increase in the consumption of these food sources by humans and in marine aquaculture. Therefore, this study aimed to investigate the potential negative effects of microplastic exposure and gain a deeper understanding of its impacts on culturing penaeid shrimp. We generated RNA sequencing data from the whiteleg shrimp (Penaeus vannamei) artificially exposed to microplastics and analyzed the differentially expressed genes. Based on transcriptional comparisons, exposure to microplastics induces cardiac muscle dysfunction and promotes stress and immune responses in whiteleg shrimp. Thus, we confirmed the negative impact of microplastic exposure in whiteleg shrimp. These results provide a foundation for studies on the biological effects of microplastic ingestion on aquaculture species and their potential impact on humans through their consumption of these important marine resources.

Acute hepatopancreatic necrosis disease (AHPND) is a major bacterial disease in the Pacific white shrimp Litopenaeus vannamei (L. vannamei) farming, which is caused by Vibrio parahaemolyticus (V. parahaemolyticus). It has led to a significant reduction of shrimp output since its outbreak. Selective breeding for disease resistance broodstocks is regarded as a key strategy for solving the disease problem. Understanding the relationship between genetic variance and AHPND resistance is the basis for marker-assisted selection (MAS) in shrimp. The purpose of this study is to identify the single nucleotide polymorphisms (SNPs) associated with the resistance against AHPND in L. vannamei. In this work, two independent populations were used for V. parahaemolyticus challenge and the resistant or susceptible shrimp were evaluated according to the survival time after Vibrio infection. The above two populations were genotyped separately by a SNP panel designed based on the target sequencing platform using a pooling strategy. The SNP panel contained 508 amplicons from DNA fragments distributed evenly along the genome and some immune related genes of L. vannamei. Through analyzing the allele frequency in the resistant and susceptible groups, 30 SNPs were found to be significantly associated with the resistance of the shrimp against V. parahaemolyticus infection (FDR corrected at P< 0.05). Three SNPs were further validated by individual genotyping in all samples of population 1. Our study illustrated that target sequencing and pooling sequencing were effective for identifying the markers associated with economic traits, and the SNPs identified in this study could be used as molecular markers for breeding disease resistance shrimp.

Improvements of growth traits are always the focus in selective breeding programs for the Pacific white shrimp Litopenaeus vannamei (L. vannamei). Identification of growth-related genes or markers can contribute to the application of modern breeding technologies, and thus accelerate the genetic improvement of growth traits. The aim of this study was to identify the genes and molecular markers associated with the growth traits of L. vannamei. A population of 200 individuals was genotyped using 2b-RAD techniques for genome-wide linkage disequilibrium (LD) analysis and genome-wide association study (GWAS). The results showed that the LD decayed fast in the studied population, which suggest that it is feasible to fine map the growth-related genes with GWAS in L. vannamei. One gene designated as LvSRC, encoding the class C scavenger receptor (SRC), was identified as a growth-related candidate gene by GWAS. Further targeted sequencing of the candidate gene in another population of 322 shrimps revealed that several non-synonymous mutations within LvSRC were significantly associated with the body weight (P < 0.01), and the most significant marker (SRC_24) located in the candidate gene could explain 13% of phenotypic variance. The current results provide not only molecular markers for genetic improvement in L. vannamei, but also new insights for understanding the growth regulation mechanism in penaeid shrimp.

Skewed family distributions are common in aquaculture species that are highly fecund, communally (mass) spawned, and/or communally reared. The magnitude of skews pose challenges for maintaining family-specific genetic diversity, as increased resources are required to detect individuals from underrepresented families, or reliably determine relative survival as a measure of family performance. There is limited understanding of family skews or changes in family proportion of communally reared shrimp under commercial rearing conditions and particularly how this may affect genotyping strategies to recover family performance data in breeding programs. In this study, three separate batches of shrimp, Penaeus monodon, were communally spawned and reared, and then sampled as larvae when ponds were stocked at 30 days of culture (DOC) and as juveniles from commercial ponds during harvest at 150 DOC. A total of 199 broodstock contributed to the 5,734 progeny that were genotyped with a custom multiplex single nucleotide polymorphism (SNP) panel, and family assignments were cross-referenced using two parentage assignment methods, CERVUS and COLONY. A total of 121 families were detected, with some families contributing up to 11% of progeny at 30 DOC and up to 18% of progeny at harvest. Significant changes were detected for 20% of families from 30 to 150 DOC, with up to a 9% change in relative contribution. Family skew data was applied in several models to determine the optimal sample size to detect families, along with the ability to detect changes in relative family contribution over time. Results showed that an order of magnitude increase in sampling was required to capture the lowest represented 25% of families, as well as significantly improve the accuracy to determine changes in family proportion from 30 to 150 DOC. Practical measures may be implemented at the hatchery to reduce family skews; a cost-effective measure may be to address the initial magnitude differences in viable progeny produced among families, by pooling equal quantities of hatched larvae from each family. This study demonstrates the relationships between skews in families under commercial conditions, the ability to accurately detect families, and the balance of sampling effort and genotyping cost in highly fecund species such as shrimp.

As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp.

The sesquiterpenoid methyl farnesoate (MF), a juvenile hormone (JH) analog, plays important roles in many physiological processes of crustaceans, such as morphogenesis, molting and reproduction. Juvenile hormone esterase-like (JHE-like) carboxylesterase (CXE) is a key enzyme in MF degradation, playing a significant role in regulating MF titer. However, its function is barely known in shrimp. In this study, a total of 21 JHE-like CXEs (LvCXEs) were characterized in Pacific white shrimp Litopenaeus vannamei, based on the full genome and multi-transcriptomic data. LvCXE has a conserved triplet catalytic site (Ser-Glu-His) and a characteristic GxSxG motif. Most LvCXEs were highly expressed in the hepatopancreas, which was the main site for MF degradation. LvCXEs containing a GESAG motif showed a specific expansion in the L. vannamei genome. Those GESAG-containing LvCXEs presented differential expressions at different larvae stages and different molting stages of L. vannamei, which suggested their potential functions in development and molting. Additionally, when the transcription level of CXEs was inhibited, it could lead to failed molt and death of L. vannamei. When we further detected the expression levels of the key ecdysone responsive transcription factors including LvE75, LvBr-C, LvHr3 and LvFtz-f1 after the CXE inhibitor was injected into L. vannamei, they all showed apparent down-regulation. These results suggested that the expansion of LvCXEs in the L. vannamei genome should contribute to the regulation of metamorphosis at larvae stages and frequent molting during the growth of L. vannamei.

This chapter contains sections titled: Introduction EST Collection as an Approach to Gene Discovery in Shrimp Medium- to High-Throughput Studies of Differential Expression and Gene Discovery RNAi-Based Applications in Shrimp Aquaculture: From Reverse Genetics to Control of Diseases Markers, Genetic Maps, and Large Insert Genomic Libraries in Shrimp Analytical Challenges in Genomics and Genetics of Shrimp Concluding Remarks Acknowledgments References

Penaeid shrimp aquaculture is an important industry in the Americas, and the industry is based almost entirely on the culture of the Pacific White Shrimp, Litopenaeus vannamei. Western Hemisphere shrimp farmers in 14 countries in 2004 produced more than 200,000 metric tons of shrimp, generated more than $2 billion in revenue, and employed more than 500,000 people. Disease has had a major impact on shrimp aquaculture in the Americas since it became a significant commercial entity in the 1970s. Diseases due to viruses, rickettsial-like bacteria, true bacteria, protozoa, and fungi have emerged as major diseases of farmed shrimp in the region. Many of the bacterial, fungal and protozoan caused diseases are managed using improved culture practices, routine sanitation, and the use of chemotherapeutics. However, the virus diseases have been far more problematic to manage and they have been responsible for the most costly epizootics. Examples include the Taura syndrome pandemic that began in 1991-1992 when the disease emerged in Ecuador, and the subsequent White Spot Disease pandemic that followed its introduction to Central America from Asia in 1999. Because of their socioeconomic significance to shrimp farming, seven of the nine crustacean diseases listed by the World Animal Organization (OIE) are virus diseases of shrimp. Of the seven virus diseases of penaeid shrimp, five are native to the Americas or have become enzootic following their introduction. The shrimp virus diseases in the Americas are increasingly being managed by exclusion using a combination of biosecurity and the practice of culturing domesticated specific pathogen-free (SPF) stocks or specific pathogen-resistant (SPR) stocks. Despite the significant challenges posed by disease, the shrimp farming industry of the Americas has responded to the challenges posed by disease and it has developed methods to manage its diseases and mature into a sustainable industry.

8 páginas, 4 figuras, 5 tablas, In this study, we infer the phylogenetic relationships within commercial shrimp using sequence data from a novel mitochondrial marker consisting of an approximately 530-bp region of the 16S ribosomal RNA (rRNA)/transfer RNA (tRNA)Val genes compared with two other mitochondrial genes: 16S rRNA and cytochrome c oxidase I (COI). All three mitochondrial markers were considerably AT rich, exhibiting values up to 78.2% for the species Penaeus monodon in the 16S rRNA/tRNAVal genes, notably higher than the average among other Malacostracan mitochondrial genomes. Unlike the 16S rRNA and COI genes, the 16S rRNA/tRNAVal marker evidenced that Parapenaeus is more closely related to Metapenaeus than to Solenocera, a result that seems to be more in agreement with the taxonomic status of these genera. To our knowledge, our study using the 16S rRNA/tRNAVal gene as a marker for phylogenetic analysis offers the first genetic evidence to confirm that Pleoticus muelleri and Solenocera agassizi constitute a separate group and that they are more related to each other than to genera belonging to the family Penaeidae. The 16S rRNA/tRNAVal region was also found to contain more variable sites (56%) than the other two regions studied (33.4% for the 16S rRNA region and 42.7% for the COI region). The presence of more variable sites in the 16S rRNA/tRNAVal marker allowed the interspecific differentiation of all 19 species examined. This is especially useful at the commercial level for the identification of a large number of shrimp species, particularly when the lack of morphological characteristics prevents their differentiation., The authors acknowledge the financial support from the National Food Program of the INIA (Spanish Ministry for Education, project CAL-03-030-C2-1) and from the PGIDIT Research Program in Marine Resources (project PGIDIT04RMA261004PR) of the Xunta de Galicia (Galician Council for Industry Commerce and Innovation).

The blue shrimp Litopenaeus stylirostris was exposed to pond sediment for 48 h and its physiological response was studied in relation to molt stage. Shrimp were maintained in cages within a semi-intensive pond after 4 months of rearing. Hypo-osmoregulatory capacity (hypo-OC), magnesium ions (Mg ions), glucose, total proteins and oxyhaemocyanin were assayed in haemolymph. An increase of 370% to 500% in Mg ions concentration and 200% to 266% in glucose concentration, and a decrease in hypo-OC in shrimp maintained close to the centre of the pond indicated a short-term stress response in all molt stages. Indicators of water and sediment pore water quality were within normal operating limits, however this area was characterized by high water content and relatively high total ammonia nitrogen in pore water of sediment. To a lesser extent, shrimp maintained in two other stations also presented a stress response. Physiological response of shrimp in molt stage D1 compared to C/D0 and D2 seems to indicate that shrimp were more sensitive to environment at this stage. The use and choice of physiological parameters to detect shrimp stress in a pond are discussed.

Litopenaeus vannamei were reared in close cycle over seven generations and tested for their capacity to digest starch and to metabolise glucose at different stages of the moulting cycle. After acclimation with 42.3% of carbohydrates (HCBH) or 2.3% carbohydrates (LCBH) diets and at high salinity (40 g kg(-1)) or low salinity (15 g kg(-1)), shrimp were sampled and hepatopancreas (HP) were stored. Total soluble protein in HP was affected by the interaction between salinity and moult stages (p0.05). Specific activity of alpha-amylase ranged from 44 to 241 U mg protein(-1) and a significant interaction between salinity and moult stages was observed (p0.05), resulting in highest values at stage C for low salinity (mean value 196.4 U mg protein(-1)), and at D0 in high salinity (mean value 175.7 U mg protein(-1)). Specific activity of alpha-glucosidase ranged between 0.09 and 0.63 U mg protein(-1), an interaction between dietary CBH and salinity was observed for the alpha-glucosidase (p0.05) and highest mean value was found in low salinity-LCBH diet treatment (0.329 U mg protein(-1)). Hexokinase specific activity (range 9-113 mU mg protein(-1)) showed no significant differences when measured at 5 mM glucose (p0.05). Total hexokinase specific activity (range 17-215 mU mg protein(-1)) showed a significant interaction between dietary CBH and salinity (p0.05) with highest value (mean value 78.5 mU mg protein(-1)) found in HCBH-high salinity treatment, whereas in the other treatments the activity was not significantly different (mean value 35.93 mU mg protein(-1)). A synergistic effect of dietary CBH, salinity and moult stages over hexokinase IV-like specific activity was also observed (p0.05). As result of this interaction, the highest value (135.5+/-81 mU mg protein(-1)) was observed in HCBH, high salinity at D0 moult stage. Digestive enzymes activity is enhanced in the presence of high starch diet (HCBH) and hexokinase can be induced at certain moulting stages under the influence of blood glucose level. Perspectives are opened to add more carbohydrates in a growing diet, exemplifying the potential approach for less-polluting feed.

Penyakit vibriosis pada budidaya udang dapat menyebabkan penurunan produksi yang cukup besar. Metode deteksi cepat akan sangat membantu dalam penanganan dan pencegahan awal untuk mengurangi kematian udang. Upaya untuk deteksi cepat adalah dengan menggunakan penanda molekular yang spesifik. Tujuan dari penelitian ini adalah untuk mengukur sensitivitas metode deteksi vibriosis pada udang penaeid (windu dan vaname) menggunakan penanda molekuler spesifik haemolysin (IAVh). Pengujian dilakukan untuk sampel udang yang diinfeksi buatan melalui injeksi maupun pada sampel yang dikoleksi dari tambak udang. Sampel organ udang hasil infeksi buatan ditanam pada media TCBSA untuk melihat koloni bakteri yang tumbuh. Selanjutnya koloni bakteri tersebut diuji secara biokimia dan molekuler. Deteksi vibriosis untuk sampel dari tambak budidaya hanya dilakukan secara molekuler menggunakan primer spesifik IAVh. Lokasi pengambilan sampel udang dari Provinsi Sulawesi Selatan (Kabupaten Takalar, Kabupaten Maros, Kabupaten Pangkep, Kabupaten Bulukumba, Kabupaten Barru, dan Kabupaten Pinrang), Provinsi Lampung (Desa Bakauheni dan Kalianda), Provinsi Jawa Timur (Kabupaten Situbondo) dan Provinsi Jawa Barat (Kabupaten Karawang). Hasil uji biokimia untuk sampel dengan infeksi buatan dapat menentukan spesies bakteri, namun waktu yang diperlukan relatif lama. Hasil uji menggunakan penanda molekuler haemolysin IAVh dapat secara spesifik mendeteksi vibrio patogen pada kepadatan bakteri 102–103 CFU/mL dari organ udang, baik pada sampel hasil infeksi buatan maupun pada sampel dari tambak.Vibriosis disease may cause a significant production losses in shrimp culture. The rapid detection method will be be very effective as earlier preventive measures to avoid mass mortality of shrimp. Effort for the rapid detection was done by specific molecular marker. The aim of this research was to evaluate the sensitivity of the specific molecular marker of haemolysin (IAVh) for vibriosis detection. Vibriosis detection was carried-out for both naturally infected shrimp and artificially infected through injection. Several organs of artificially-infected shrimp grown on TCBS media to find identify colonies of bacteria. After this, colonies of bacteria were tested biochemically and molecularly. Penaeid shrimp samples were collected from the shrimp brackishwater ponds in the South Sulawesi Province (Takalar Regency, Maros Regency, Pangkep Regency, Bulukumba Regency, Barru Regency, and Pinrang Regency). Lampung Province (Bakauheni and Kalianda District), East Java Province (Situbondo Regency) and West Java Province (Karawang Regency). The results of biochemical assay for artificially-infected shrimp could determine the species of vibrioses, but it took a relatively long time. The further results showed that specific molecular marker of haemolysin (IAVh) could detect Vibriosis directly from the shrimp organs in at density of 102-103CFU/mL on both natural and artificial infected vibrioses shrimp.

Although captured and cultivated marine shrimp constitute highly important seafood in terms of both economic value and production quantity, biologists have little knowledge of the shrimp genome and this partly hinders their ability to improve shrimp aquaculture. To help improve this situation, the Shrimp Gene and Protein Annotation Tool (ShrimpGPAT) was conceived as a community-based annotation platform for the acquisition and updating of full-length complementary DNAs (cDNAs), Expressed Sequence Tags (ESTs), transcript contigs and protein sequences of penaeid shrimp and their decapod relatives and for in-silico functional annotation and sequence analysis. ShrimpGPAT currently holds quality-filtered, molecular sequences of 14 decapod species (~500,000 records for six penaeid shrimp and eight other decapods). The database predominantly comprises transcript sequences derived by both traditional EST Sanger sequencing and more recently by massive-parallel sequencing technologies. The analysis pipeline provides putative functions in terms of sequence homologs, gene ontologies and protein-protein interactions. Data retrieval can be conducted easily either by a keyword text search or by a sequence query via BLAST, and users can save records of interest for later investigation using tools such as multiple sequence alignment and BLAST searches against pre-defined databases. In addition, ShrimpGPAT provides space for community insights by allowing functional annotation with tags and comments on sequences. Community-contributed information will allow for continuous database enrichment, for improvement of functions and for other aspects of sequence analysis. ShrimpGPAT is a new, free and easily accessed service for the shrimp research community that provides a comprehensive and up-to-date database of quality-filtered decapod gene and protein sequences together with putative functional prediction and sequence analysis tools. An important feature is its community-based functional annotation capability that allows the research community to contribute knowledge and insights about the properties of molecular sequences for better, shared, functional characterization of shrimp genes. Regularly updated and expanded with data on more decapods, ShrimpGPAT is publicly available at http://shrimpgpat.sc.mahidol.ac.th/ .

The ssRNA genome extracted from purified Taura Syndrome Virus (TSV) was transcribed into double-stranded, blunt-ended cDNA and was used to construct cDNA libraries either in pUC 18 or in pBluescript II KS-vectors. Twelve recombinant plasmids chosen after screening of the libraries were subjected to restriction enzyme digestions for determination of size inserts and restriction maps. Two of them, pP15 and pQ1, were selected for probe construction. The inserts, 1500 and 1300 base pairs (bp) respectively, were DIG-11dUTP-labelled and the corresponding probes were named P15 and Q1. On northern blots and dot blots, using different denaturation methods, the 2 probes hybridized specifically with extracted RNA-TSV genome, TSV and infected TS shrimp homogenates. No positive hybridization was obtained with other shrimp viruses tested [Infectious Hypodermal and Hematopoietic Necrosis Virus (IHHNV) and Hepatopancreatic Parvovirus (HPV)]. The specificity of the 2 probes was confirmed by in situ hybridization on histological sections of TS diseased shrimps.

A multiplex RT-nested PCR has been developed to detect and differentiate the closely related prawn viruses, gill-associated virus (GAV) from Australia and yellow head virus (YHV) from Thailand. RT-PCR using primers to conserved sequences in the ORF1b gene amplified a 794 bp region of either GAV or YHV. Nested PCR using a conserved sense primer and either a GAV- or YHV-specific antisense primer to a divergent sequence differentially amplified a 277 bp region of the primary PCR amplicon. Multiplexing the YHV antisense primer with a GAV antisense primer to another divergent sequence allowed the viruses to be distinguished in a single nested PCR. Nested PCR enhanced detection sensitivity between 100- and 1000-fold and GAV or YHV RNA was detectable in approximately 10 fg lymphoid organ total RNA. The multiplex RT-nested PCR was also able to co-detect GAV and YHV RNA mixed over a wide range of concentrations to simulate potential dual-infection states. The robustness of the test was examined using RNA samples from Penaeus monodon prawns infected either chronically or acutely with GAV or YHV and collected at different locations in Eastern Australia and Thailand between 1994 and 1998. GAV- (406 bp) or YHV-specific (277 bp) amplicons were differentially generated in all cases, including five YHV RNA samples in which no primary RT-PCR amplicon was detected. Sequence analysis of GAV and YHV PCR amplicons identified minor variations in the regions targeted by the virus-specific antisense primers. However, none occurred at positions that critically affected the PCR.

A truncated version of the white spot syndrome virus (WSSV) 27.5 kDa envelope protein was expressed as a histidine tag fusion protein in Escherichia coli. The bacterial expression system allowed the production of up to 10 mg of purified recombinant protein per liter of bacterial culture. Antiserum from a rabbit immunized with the recombinant protein recognized the 27.5 kDa viral envelope protein of WSSV isolated from different geographic regions. The antiserum did not recognize any of the other known WSSV structural proteins. A sensitive immunodot assay for WSSV was developed using the specific rabbit polyclonal antiserum.

Penaeidins are members of a new family of antimicrobial peptides isolated from a crustacean, which present both Gram-positive antibacterial and antifungal activities. We have studied the localization of synthesis and storage of penaeidins in the shrimp Penaeus vannamei. The distribution of penaeidin transcripts and peptides in various tissues reveals that penaeidins are constitutively synthesized and stored in the shrimp haemocytes. It was shown by immunocytochemistry, at both optical and ultrastructural levels, that the peptides are localized in granulocyte cytoplasmic granules. The expression and localization of penaeidins were further analysed in shrimp subjected to microbial challenge. We found that (1) penaeidin mRNA levels decrease in circulating haemocytes in the first 3 hours following stimulation and (2) an increase in plasma penaeidin concentration occurs after microbial challenge, together with (3) a penaeidin immunoreactivity in cuticular tissue, which can be related to the chitin-binding activity we demonstrate here for penaeidins.

"We contend there are currently two competing scenarios for the sustainable development of shrimp aquaculture in coastal areas of Southeast Asia. First, a landscape approach, where farming techniques for small-scale producers are integrated into intertidal areas in a way that the ecological functions of mangroves are maintained and shrimp farming diseases are controlled. Second, a closed system approach, where problems of disease and effluent are eliminated in closed recirculation ponds behind the intertidal zone controlled by industrial-scale producers. We use these scenarios as two ends of a spectrum of possible interactions at a range of scales between the ecological, social, and political dynamics that underlie the threat to the resilience of mangrove forested coastal ecosystems. We discuss how the analytical concepts of resilience, uncertainty, risk, and the organizing heuristic of scale can assist us to understand decision making over shrimp production, and in doing so, explore their use in the empirical research areas of coastal ecology, shrimp health management and epidemiology, livelihoods, and governance in response to the two scenarios. Our conclusion focuses on a series of questions that map out a new interdisciplinary research agenda for sustainable shrimp aquaculture in coastal areas."