Automated artemia length measurement using U-shaped fully convolutional networks and second-order anisotropic Gaussian kernels

The brine shrimp Artemia, a small crustacean zooplankton organism, is universally used as live prey for larval fish and shrimps in aquaculture. In Artemia studies, it would be highly desired to have access to automated techniques to obtain the length information from Anemia images. However, this problem has so far not been addressed in literature. Moreover, conventional image-based length measurement approaches cannot be readily transferred to measure the Artemia length, due to the distortion of non-rigid bodies, the variation over growth stages and the interference from the antennae and other appendages. To address this problem, we compile a dataset containing 250 images as well as the corresponding label maps of length measuring lines. We propose an automated Anemia length measurement method using U-shaped fully convolutional networks (UNet) and second-order anisotropic Gaussian kernels. For a given Artemia image, the designed UNet model is used to extract a length measuring line structure, and, subsequently, the second-order Gaussian kernels are employed to transform the length measuring line structure into a thin measuring line. For comparison, we also follow conventional fish length measurement approaches and develop a non-learning-based method using mathematical morphology and polynomial curve fitting. We evaluate the proposed method and the competing methods on 100 test images taken from the dataset compiled. Experimental results show that the proposed method can accurately measure the length of Artemia objects in images, obtaining a mean absolute percentage error of 1.16%

The impact of one-decade ecological disturbance on genetic changes : a study on the brine shrimp Artemia urmiana from Urmia Lake, Iran

Urmia Lake, the largest natural habitat of the brine shrimp Artemia urmiana, has progressively desiccated over the last two decades, resulting in a loss of 80% of its surface area and producing thousands of hectares of arid salty land. This ecological crisis has seriously affected the lake's native biodiversity. Artemia urmiana has lost more than 90% of its population during the decade from 1994 (rainy period) to 2004 (drought period) due to salinity increasing to saturation levels (similar to 300 g/l). We studied the influence of this ecological crisis on the genetic diversity of A. urmiana in Urmia Lake, based on one cyst collections in 1994 and 2004. AMOVA analysis on ISSR data demonstrated a 21% genetic variation and there was a 5.5% reduction of polymorphic loci between samples. PCoA showed that 77.42% and 68.75% of specimens clustered separately in 1994 and 2004, respectively. Our analyses of four marker genes revealed different genetic diversity patterns with a decrease of diversity at ITS1 and an increase for Na+/K+ ATPase. There was no notable difference in genetic variation detected for CO/ and 16S genes between the two periods. However, they represented distinctly different haplotypes. ITS1 and COI followed a population expansion model, whereas Na+/K+ ATPase and 16S were under demographic equilibrium without selective pressure in the 1994 samples. Neutrality tests confirmed the excess of rare historical and recent mutations present in COI and ITS1 in both samples. It is evident that a short-term ecological disturbance has impacted the genetic diversity and structure of A. urmiana

Hatching and nutritional quality of Artemia cysts progressively deteriorates as a function of increased exposure to hydration/dehydration cycles

Nauplii hatching from Artemia cysts are crucial in larviculture nutrition. Artemia cysts may be exposed to repeated hydration/dehydration (H/D) cycles pre-harvesting or during processing and storage. To observe the effect of these cycles on cyst quality, Artemia franciscana cysts were exposed to a comprehensive set of various H/D treatments, differing in the number of cycles (1, 2, or 3) and the duration of the freshwater hydration period (2 or 4 h). Cyst quality was assessed using the criteria of immediate relevance for aquaculture use, such as hatching percentage directly after H/D treatment and after -18 A degrees C storage up to 1 month, longevity of axenically hatched starved nauplii, cyst and naupliar energy content, and (for the most extreme H/D treatment) cyst and naupliar fatty acid and vitamin C content. Repeated H/D cycles resulted in significantly (P < 0.05) decreased cyst hatching, reduced starved naupliar longevity and individual energy content, loss in vitamin C and fatty acid content, and moreover a close correlation between these parameters as a function of progressive H/D treatments. This is of immediate relevance for aquaculture nutrition, as commercial Artemia cysts may have gone through an unknown sequence of H/D cycles in nature or in the processing line, which affects the nutritional quality of the nauplii used in larviculture operations

Genetic differentiation of Artemia franciscana (Kellogg, 1906) in Kenyan coastal saltworks

The nature of genetic divergence between the Artemia population native to San Francisco Bay, (SFB) USA and those from the introductions of SFB material in the Kenyan coast two decades ago were investigated using the mitochondrial DNA (mtDNA) and heat shock protein 70 (Hsp70) gene molecular markers. The DNA was extracted from 80 single Artemia cysts using the Chelex protocol. The 1,500 bp fragment of the 12S - 16S region of the mtDNA and a 1,935 bp fragment of the Hsp70 gene were amplified through Polymerase Chain Reaction (PCR) followed by Restriction Fragment Length Polymorphism (RFLP) digestion using appropriate endonucleases. The mtDNA analysis indicated higher haplotype diversity (0.76 ± 0.07) in Artemia from Fundisha saltworks while the rest of the samples were monomorphic. A private haplotype (AAABBA) in Fundisha samples confirmed a molecular evidence of a systematic genetic differentiation albeit in an insignificant manner (P > 0.05). There was molecular evidence of coexistence of SFB and GSL Artemia strains in Fundisha saltworks. The monomorphic DNA fingerprint in Kensalt Artemia cysts was probably caused by non-sequential Artemia culture system and limited mtDNA fragment size analysed. The Hsp70 gene RFLP fingerprint did not show any unique gene signatures in the Kenyan Artemia samples suggesting that other factors other than Hsp70 were involved in their superior thermotolerance. Further genetical studies based on the larger mtDNA fragment using robust genetic markers are recommended. Ecological studies of the heat shock protein family and the stress response would be more relevant than the qualitative RFLP technique

Phylogenetic analysis of birne shrimp (Aretemia) in China using DNA barcoding

DNA barcoding is a powerful approach for characterizing species of organisms, especially those with almost identical morphological features, thereby helping to to establish phylogenetic relationships and reveal evolutionary histories. In this study, we chose a 648-bp segment of the mitochondrial gene, cytochrome c oxidase subunit 1 (COI), as a standard barcode region to establish phylogenetic relationships among brine shrimp (Artemia) species from major habitats around the world and further focused on the biodiversity of Artemia species in China, especially in the Tibetan Plateau. Samples from five major salt lakes of the Tibetan Plateau located at altitudes over 4,000m showed clear differences from other Artemia populations in China. We also observed two consistent amino acid changes, 153A/V and 183L/F, in the COI gene between the high and low altitude species in China. Moreover, indels in the COI sequence were identified in cyst and adult samples unique to the Co Qen population from the Tibetan Plateau, demonstrating the need for additional investigations of the mitochondrial genome among Tibetan Artemia populations

Ontogenetic development of the gastrointestinal tract of African lungfish larvae Protopterus aethiopicus (Heckel 1851) : a light microscopy study

The organogenesis of the digestive system was described in the African lungfish (Protopterus aethiopicus) from 6 days post-hatching (6 DPH) to 17 days post-hatching (17 DPH) reared at 27 degrees C. To elucidate the position of the gastrointestinal tract in relation to the neural tube, notochord and yolk sac at 6 DPH, and to the vertebral column, lungs and kidneys at 17 DPH, larvae were mapped by means of computer-assisted 3D reconstructions starting from histological serial sections. The larvae showed a simple digestive tract, which appeared as a straight undifferentiated and closed tube at 6 DPH. Microscopical observation showed that yolk reserves were not completely depleted by 17 DPH. During the endogenous feeding period at least up to 17 DPH, the larval digestive system experienced a fast transformation with almost complete development of most digestive organs (pharyngeal teeth, intestinal vestibule, intestine and liver). Our findings suggest that, by 17 DPH, African lungfish larvae are ready to start exogenous feeding

Microbial community management in aquaculture

Microbial community management in aquaculture creates benefits at the nutritional as well as at health level for cultured species. In addition, in case of biofloc application, it allows to link species at different trophic levels, making bioflocs the potential link in integrated multispecies aquaculture

Sequence and expression analysis of HSP70 family genes in Artemia franciscana

Thus far, only one gene from the heat shock protein 70 (HSP70) family has been identified in Artemia franciscana. Here, we used the draft Artemia transcriptome database to search for other genes in the HSP70 family. Four novel HSP70 genes were identified and designated heat shock cognate 70 (HSC70), heat shock 70 kDa cognate 5 (HSC70-5), lmmunoglobulin heavy-chain binding protein (BIP), and hypoxia up-regulated protein I (HYOUI). For each of these genes, we obtained nucleotide and deduced amino acid sequences, and reconstructed a phylogenetic tree. Expression analysis revealed that in the juvenile state, the transcription of HSP70 and HSC70 was significantly (P 0.05) induction. Gene expression analysis demonstrated that not all members of the HSP70 family are involved in the response to heat stress and selection and that especially altered expression of HSC70 plays a role in a population selected for increased thermotolerance

The chloride channel cystic fibrosis transmembrane conductance regulator (CFTR) controls cellular quiescence by hyperpolarizing the cell membrane during diapause in the crustacean Artemia

Cellular quiescence, a reversible state in which growth, proliferation, and other cellular activities are arrested, is important for self-renewal, differentiation, development, regeneration, and stress resistance. However, the physiological mechanisms underlying cellular quiescence remain largely unknown. In the present study, we used embryos of the crustacean Artemia in the diapause stage, in which these embryos remain quiescent for prolonged periods, as a model to explore the relationship between cell-membrane potential (V-mem) and quiescence. We found that V-mem is hyperpolarized and that the intracellular chloride concentration is high in diapause embryos, whereas V-mem is depolarized and intracellular chloride concentration is reduced in postdiapause embryos and during further embryonic development. We identified and characterized the chloride ion channel protein cystic fibrosis transmembrane conductance regulator (CFTR) of Artemia (Ar-CFTR) and found that its expression is silenced in quiescent cells of Artemia diapause embryos but remains constant in all other embryonic stages. Ar-CFTR knockdown and GlyH-101-mediated chemical inhibition of Ar-CFTR produced diapause embryos having a high V-mem and intracellular chloride concentration, whereas control Artemia embryos released free-swimming nauplius larvae. Transcriptome analysis of embryos at different developmental stages revealed that proliferation, differentiation, and metabolism are suppressed in diapause embryos and restored in postdiapause embryos. Combined with RNA sequencing (RNA-Seq) of GlyH-101-treated MCF-7 breast cancer cells, these analyses revealed that CFTR inhibition down-regulates the Wnt and Aurora Kinase A (AURKA) signaling pathways and up-regulates the p53 signaling pathway. Our findings provide insight into CFTR-mediated regulation of cellular quiescence and V-mem in the Artemia model

The complete mitochondrial genome of Artemia sinica Cai, 1989 (Crustacea : Anostraca) using next-generation sequencing

The complete mitochondrial genome of Artemia sinica was obtained using the next-generation sequencing (NGS) method. The mitochondrial genome is a circular molecule of 15,689 bp in length, with the typical structure of 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs) and 2 ribosomal RNA genes, and a non-coding control region (CR). The base composition is 31.53% A, 18.99% C, 16.50% G, and 32.98% T, with an A + T content of 64.51%. All tRNAs have a cloverleaf structure excepting tRNA-Ser(1), that represents the D-loop structure