Genome survey and microsatellite motif identification of Pogonophryne albipinna

The genus Pogonophryne is a speciose group that includes 28 species inhabiting the coastal or deep waters of the Antarctic Southern Ocean. The genus has been divided into five species groups, among which the P. albipinna group is the most deep-living group and is characterized by a lack of spots on the top of the head. Here, we carried out genome survey sequencing of P. albipinna using the Illumina HiSeq platform to estimate the genomic characteristics and identify genome-wide microsatellite motifs. The genome size was predicted to be ∼883.8 Mb by K-mer analysis (K = 25), and the heterozygosity and repeat ratio were 0.289 and 39.03%, respectively. The genome sequences were assembled into 571624 contigs, covering a total length of ∼819.3 Mb with an N50 of 2867 bp. A total of 2217422 simple sequence repeat (SSR) motifs were identified from the assembly data, and the number of repeats decreased as the length and number of repeats increased. These data will provide a useful foundation for the development of new molecular markers for the P. albipinna group as well as for further whole-genome sequencing of P. albipinna.     

Morphometric characterization of thalassohaline Artemia franciscana populations from the Colombian Caribbean

Aim To establish possible interpopulation relationships among Colombian Artemia franciscana (Crustacea, Anostraca) populations. Location Colombian Caribbean coast (Manaure, Galerazamba, Salina Cero and Tayrona) and a similar thalassohaline reference population from San Francisco Bay (SFB‐USA). Methods Morphometric characters of male and female cultured individuals of A. franciscana were measured. The populations were grouped according to: (1) population type (populations grouped according to two broad regions of origin: North America and the Caribbean coast), and (2) specific geographical origin (populations selected according to five specific local origins: Manaure, Galerazamba, Salina Cero, Tayrona and SFB) and evaluated using forward stepwise discriminant analysis (SPSS, Ver. 10). Results Optimal discriminant variables for males grouped by the type of population were left setae and antenna length, and for females they were abdominal length and antenna length. However, for males grouped by their specific geographical origin, the optimal variables were furca length, left setae, antenna length, eye separation, abdominal width and abdominal length, and for the females, they were furca length, abdominal length, left setae and eye separation. Male and female Colombian Caribbean populations were separated from the North American populations. However, our results show that the classification based on male characters provides better group membership than females. Main conclusions Male morphometric characters separated the type of population groups more clearly than the female characters, because all Colombian populations were correctly positioned in the Caribbean coast region and the SFB population in the North American region, with no overlapping between the two types, as was the case for the female individuals. Likewise, male individuals correctly position the Salina Cero population to its neighbouring Galerazamba population and to the other Colombian populations. In contrast, female individuals from Salina Cero did not cluster with the other Colombian coast populations (Galerazamba, Tayrona and Manaure) or with the SFB population.     

Long-term Lethal Toxicity Test with the Crustacean Artemia franciscana

Our research activities target the use of biological methods for the evaluation of environmental quality, with particular reference to saltwater/brackish water and sediment. The choice of biological indicators must be based on reliable scientific knowledge and, possibly, on the availability of standardized procedures. In this article, we present a standardized protocol that used the marine crustacean Artemia to evaluate the toxicity of chemicals and/or of marine environmental matrices. Scientists propose that the brine shrimp (Artemia) is a suitable candidate for the development of a standard bioassay for worldwide utilization. A number of papers have been published on the toxic effects of various chemicals and toxicants on brine shrimp (Artemia). The major advantage of this crustacean for toxicity studies is the overall availability of the dry cysts; these can be immediately used in testing and difficult cultivation is not demanded^1,2. Cyst-based toxicity assays are cheap, continuously available, simple and reliable and are thus an important answer to routine needs of toxicity screening, for industrial monitoring requirements or for regulatory purposes³. The proposed method involves the mortality as an endpoint. The numbers of survivors were counted and percentage of deaths were calculated. Larvae were considered dead if they did not exhibit any internal or external movement during several seconds of observation⁴. This procedure was standardized testing a reference substance (Sodium Dodecyl Sulfate); some results are reported in this work. This article accompanies a video that describes the performance of procedural toxicity testing, showing all the steps related to the protocol.     

Ontogeny of low molecular weight stress protein p26 during early development of the brine shrimp, Artemia franciscana

Embryogenesis in the brine shrimp, Artemia sp., occurs by one of two pathways: (i) the direct, uninterrupted development of nauplius larvae within the female or (ii) the production of embryos that arrest development at the gastrula stage and enter diapause. Diapause embryos are released from females into the aqueous environment where they remain in diapause until activated by appropriate environmental cues and resume development. These encysted embryos possess at least one low molecular weight stress protein, which we refer to as p26 and which has been implicated previously in the stress response of activated embryos. We investigated the appearance of p26 in developing diapause embryos in utero and looked for its presence in embryos developing directly into nauplii. We found p26 to be specific to diapause-destined embryos; it was not detected in direct-developing embryos. We conclude that p26 is not required for the basic developmental program that produces the nauplius. In diapause-destined embryos, p26 was first detectable after 3 days of development, at which time the embryos were late gastrulae. This protein continues to increase in amount until the encysted embryos are released, approximately 5 days after fertilization. At the time of release almost all p26 is located in the low speed supernatant fraction, but as released embryos continue diapause, p26 transfers to the pelleted nuclear fraction in increasing amounts. Our working hypothesis views p26 as a molecular chaperone preventing protein denaturation and aggregation under conditions associated with metabolic arrest and other stressful states, which these encysted embryos encounter.     

Characterization of polymorphic microsatellite markers in the brine shrimp Artemia (Branchiopoda, Anostraca)

The brine shrimp Artemia is a complex genus containing sexual species and parthenogenetic lineages. Artemia franciscana is native to America and its cysts (diapausing eggs) are used worldwide as a food source in aquaculture. As a consequence, this anostracan has become an invasive species in many hypersaline aquatic ecosystems of other continents. Parthenogenetic Artemia lineages occur only in the Old World. Ten and five microsatellite markers were developed to characterize two populations for A. franciscana and two populations for diploid parthenogenetic Artemia, respectively. For A. franciscana the number of alleles ranged from 11 to 58 per locus, while for parthenogens the number of alleles ranged from three to 10. The levels of heterozygosity in A. franciscana and in parthenogens ranged from 0.115 to 0.976 and from 0.000 to 0.971, respectively. These microsatellite loci showed a high population assignment power, which will be useful for future studies of population genetics and invasive processes in Artemia.     

Effect of Temperature and Salinity on the Biochemical Composition of Artemia franciscana KELLOGG 1906, from Araya (Venezuela) and San José (México)

The effect of different temperature and salinity combinations on the biochemical composition of Artemia franciscana from Venezuela and Mexico, is analyzed. Temperatures were 22 ± 0.5 °C, 26 ± 0.5 °C and 30 ± 0.5°C; salinities were 30‰, 60‰, and 120‰. Chaetoceros sp. was used as food. According to Tukey's Multiple Range Analysis for the A. franciscana population from Araya and San José, there were differences in the biochemical parameters and survival percentages among treatments and between populations. A positive correlation is observed among proximate composition values and survival, total length and growth rates. The observed variations reflect a genetic component resulting from the life history of the populations, and a non-genetic component produced by the experimental conditions.     

Further evidence and characterization of Artemia franciscana (Kellogg, 1906) populations in Argentina

Aim This paper reports the presence of Artemia franciscana ( Kellogg, 1906 ) in Mar Chiquita (CHI) salt lake and in Las Tunas (TUN) lagoon, as well as at a shallow lake in Salinas Grandes (Province of Córdoba) in Argentina. To date, this species has been considered absent from Argentina. This study also provides further data on the characterization of the A. franciscana populations from this area. Location Province of Córdoba (Argentina). Methods The cyst samples collected at the three hypersaline environments were measured to assess its mean diameter with a dissecting microscope. The length of the nauplii hatched from the cysts was also determined with the microscope. The adults raised from these nauplii under strictly controlled conditions were analysed for 12 morphological parameters and compared through multivariate discriminant analysis with other American populations. Fatty acids from the total lipids were analysed by gas chromatography. Reproductive compatibility was evaluated from single‐pair intraspecific and interspecific crosses of adult specimens. Results The results endorse the morphometric assimilation of the Artemia populations of this area to other American populations of the A. franciscana‘super‐species’, together with its morphometric differentiation from the species A. persimilis ( Piccinelli & Prosdocimi, 1968 ). The more conspicuous population from CHI shows cross‐fertility with A. franciscana original from San Francisco Bay (California, USA). Both populations from CHI and TUN show cross‐fertility between them and reproductive isolation with A. persimilis from Hidalgo (Province of La Pampa), which to date is considered to be endemic or exclusive of hypersaline ecosystems in Argentina. The reproductive characteristics displayed by the population from TUN lagoon suggest the existence of an occasional hybridization between A. franciscana and A. persimilis ( Papeschi et al., 2000 ). Artemia cysts from CHI and TUN show a fatty acid profile rich in eicosapentaenoic acid differing markedly from the fatty acid profiles found in A. persimilis cysts. Main conclusions: Artemia franciscana is present in Argentina at 36° S and north of this latitude. Artemia persimilis is confined to the south of latitude 37°10′ S. There are different pieces of evidence that point to a certain level of hybridization of the two species taking place in the land belt between these parallels.     

The heat shock response of adult Artemia franciscana

1. We studied responses of adult brine shrimp, Artemia franciscana, to high temperature, including LT₅₀ determination, induced thermotolerance (ITT), the Hsp-70 family of stress proteins and protein synthesis before and after heat shock.

2. Adults were grown in laboratory cultures from encysted embryos (cysts) obtained from San Francisco Bay (SF) and much warmer culture ponds in Vietnam (V).

3. Adults from V cysts were more tolerant of high temperatures than those from SF cysts, but this difference essentially disappeared in the second generation of adults.

4. Levels of constitutive Hsc-70 were very low in adults of both groups, but were strongly upregulated by a sublethal heat shock (37°C, 30 min), with V adults showing the greater degree of upregulation. Heat shock also induced Hsp-67, to a greater extent in V compared to SF adults

5. Incorporation of ¹⁴C-leucine into protein did not result in the “classic” heat shock response, possibly due to increased permeability of heat-shocked animals to the tracer.

Spatial organization and isotubulin composition of microtubules in epidermal tendon cells of Artemia franciscana

Epidermally derived tendon cells attach the exoskeleton (cuticle) of the Branchiopod crustacean, Artemia franciscana, to underlying muscle in the hindgut, while the structurally similar transalar tendon (epithelial) cells, which also arise from the epidermis and are polarized, connect dorsal and ventral exopodite surfaces. To establish these latter attachments the transalar tendon cells interact with cuticles on opposite sides of the exopodite by way of their apical surfaces and with one another via basal regions, or the cuticle attachments may be mediated through linkages with phagocytic storage cells found in the hemolymph. In some cases, phyllopod tendon cells attach directly to muscle cells. Tendon cells in the hindgut of Artemia possess microtubule bundles, as do the transalar cells, and they extend from the basal myotendinal junction to the apical domain located near the cuticle. The bundled microtubules intermingle with thin filaments reminiscent of microfilaments, but intermediate filament-like structures are absent. Microtubule bundles converging at apical cell surfaces contact structures termed apical invaginations, composed of cytoplasmic membrane infoldings associated with electron-dense material. Intracuticular rods protrude from apical invaginations, either into the cuticle during intermolt or the molting fluid in premolt. Confocal microscopy of immunofluorescently stained samples revealed tyrosinated, detyrosinated, and acetylated tubulins, the first time posttranslationally modified isoforms of this protein have been demonstrated in crustacean tendon cells. Microfilaments, as shown by staining with phalloidin, coincided spatially with microtubule bundles. Artemia tendon cells clearly represent an interesting system for study of cytoskeleton organization within the context of cytoplasmic polarity and the results in this article indicate functional cooperation of microtubules and microfilaments. These cytoskeletal elements, either acting independently or in concert, may transmit tension from muscle to cuticle in the hindgut and resist compression when connecting exopodite cuticular surfaces.     

The complete mitochondrial DNA sequence of the crustacean Artemia franciscana

The complete mitochondrial DNA (mtDNA) sequence of the brine shrimp Artemia franciscana has been determined. It extends the present knowledge of mitochondrial genomes to the crustacean class and supplies molecular markers for future comparative studies in this large branch of the arthropod phylum. Artemia mtDNA is 15,822 nucleotides long, and when compared with its Drosophila counterpart, it shows very few gene rearrangements, merely affecting two tRNAs placed 3 downstream of the ND 2 gene. In this position a stem-loop secondary structure with characteristics similar to the vertebrate mtDNA L-strand origin of replication is found. This suggests that, associated with tRNA changes, the diversification of the mitochondrial genome from an ancestor common to crustacea and insects could be explained by errors in the mtDNA replication process. Although the gene content is the same as in most animal mtDNAs, the sizes of the protein coding genes are in some cases considerably smaller. Artemia mtDNA uses the same genetic code as found in insects, ATN and GTG are used as initiation codons, and several genes end in incomplete T or TA codons.Correspondence to: R. Garesse     

尕海孤雌生殖卤虫基因组的特异DNA片段

Artemia is not only valuable for aquaculture but also exhibits unique biological characters. In this study, based on the silkworm Bmdsx gene, a pair of primers was designed. After amplification with these primers, a DNA fragment Apdsx900 from parthenogenesis Artemia genomic DNA was obtained. The following Southern blotting and FISH analysis also proved the fragment was specific for Gahai parthenogenesis Artemia genome. To our knowledge, this is the first report of parthenogenesis genome specific DNA fragments. Apdsxg00 shares little similarity with the silkworm Bmdsx gene. [Acta Zoologica Sinica 50 (3): 470-474, 2004].     

Acid exposure in euryhaline environments: ion regulation and acid tolerance in larval and adult Artemia franciscana

Mortality, and whole-body levels of [Na], [Cl] and [K]were measured in adult and naupliar stages of Brine Shrimp, Artemia franciscana, after 24h exposure to a waters of a range of acid (H₂SO₄)concentrations (pH 8.3 to 4.5). Acid effects were tested in both dilute (20%) and full strength artificial seawater (ASW). All stages showed high sensitivity to acid stress whether tested in 20% or100% ASW. Nauplii were more sensitive than adults in either medium. Mortality in each case was correlated with dramatic changes in whole body [Na] and [Cll but animals in 20% ASW lost [Na] and [Cl] to the environment while animals in 100% ASW gained them from the environment. Clearly animals which ion-regulate in euryhaline media are more sensitive than expected to acid stress which may thus pose a serious threat to sensitive euryhaline habitats. This revised version was published online in August 2006 with corrections to the Cover Date.     

东方粘虫(Pseudaletia separata(Walker))微卫星富集文库的构建与分析

根据生物素与链亲和素的强亲和性原理,用包被链亲和素的磁珠亲和捕捉与生物素标记的微卫星寡核苷酸探针(CA)15、(GA)15、(GTT)12、(GAT)12、(TAGA)8 和 (GTGA)8退火结合的含接头和微卫星序列的单链粘虫基因组DNA限制性酶切片段,获得单链目的片段.经PCR扩增形成双链后连接到pGEM-T 载体上,再转化到DH5α热感受态细胞中,首次成功构建粘虫基因组微卫星富集文库.随机抽样(16次抽样,每库共12～114个克隆)测序发现,6个文库总的微卫星阳性克隆率30.07%,CA/GAT/GTT 等3个文库的阳性克隆率达到40%以上.单次抽样最高阳性克隆率达到56%.粘虫微卫星富集文库的建立和高多态性微卫星单拷贝位点的筛选将为粘虫的生态遗传学研究、连锁图谱构建、分子进化和系统发育研究等提供大量遗传标记,对昆虫迁飞的分子生态研究也有重大意义.     

新疆沙冬青基因组调查测序与基因组大小预测

新疆沙冬青是中国荒漠地区代表性常绿阔叶植物,属于第三纪孑遗植物。其极强的逆境耐受性受到了研究者的广泛关注,但由于缺乏基因组序列,分子生物学研究水平进展缓慢。本研究对新疆沙冬青进行了基因组调查测序,共得到65 Gb大小的双端测序数据。结合基于K-mer分析和流式细胞分析的方法,预测基因组大小、杂合率和GC含量等特征,估计基因组大小为770~787 Mb。测序数据拼接构建得到contigs的N50为684 bp,总读长为0.538 Gb;进一步组装后scaffolds的N50为12.09 kb,总读长为0.602 Gb。对拼接数据进行SSR分子标记预测,共得到151858个SSR,其中二核苷酸重复单元比例最高为56.39%,在二核苷酸重复单元中,AT/TA组成形式占多数。本研究首次报道了荒漠植物新疆沙冬青的基因组特征,为后续基因组学研究提供参考。     

Respiration of Artemia franciscana embryos after continuous anoxia over 1-year period

Encysted embryos of the brine shrimp, Artemia franciscana, exhibit extraordinary longevity when exposed to continuous anoxia. To explore the metabolic basis of this ability, the post-anoxic respiration of embryos exposed to anoxia for periods exceeding 1 year was measured. Since anoxic metabolism might result in the accumulation of metabolic end products, an O₂ debt would be expected. Contrary to that expectation, post-anoxic embryos exhibited a marked depression in respiration rate whether embryos were hydrated under anoxic conditions or were exposed to a previous aerobic incubation and then placed under anoxia. These results, and those of previous studies, suggest that extended anoxia may bring the metabolism of these embryos to a reversible standstill.     

Potential role in development of the major cysteine protease in larvae of the brine shrimp Artemia franciscana

Encysted embryos and larvae of the brine shrimp Artemia franciscana contain a cysteine protease which represents over 90% of the protease activity in these organisms. We have used immunocytochemical methods to determine the localization and potential role of the cysteine protease in development of young larvae. In prenauplius larvae, there is intense staining for the protease on the basal side of the epidermal layer in the posterior region and diffuse staining for the protease throughout the embryo. In first instar larvae, cysteine-protease staining becomes intense in the midgut-forming area where a reticulum-like pattern emerges in cells with an abundance of yolk platelets. Cysteine-protease staining in second instar larvae becomes intense in the apical side of epidermal cells and in the basal and apical zones of midgut cells. Subcellular localization of the protease in the epidermis and midgut of young larvae using immunogold electron microscopy suggests that most is located in the cytosol and extracellular matrix adiacent to these cells. Addition of cysteine-protease inhibitors to the growth medium, especially the fluoromethyl ketone Z-Phe-Ala-CH₂F, inhibits growth and segmentation of the thorax. Collectively, these observations suggest that the major cysteine protease in embryos and larvae functions in yolk utilization, as a hatching enzyme, in apolysis during the molt cycle, and as a digestive enzyme when the swimming larvae begin to feed.     

Estimate of the effects of ultraviolet radiation on the mortality of Artemia franciscana in naupliar and adult stages

The impact of different doses of artificial ultraviolet (UV) radiation on the growth stages of a marine zooplankton was investigated using laboratory microcosms. Mortality percentages of naupliar and adult samples of Artemia franciscana were recorded in relation to different UV doses (single exposure: 75, 150, 300, 600, 1,200, 2,400, 3,900, 7,800 J m^–2) at specific observation times after exposure (24, 48, 72, 96 and 120 h). The relationship between mortality percentage and UV dose showed significant differences in relation to the zooplankton growth stage. The elevated susceptibility of the naupliar samples to UV radiation is described through a mortality model based on a logistic equation. The data analysis shows that the slope of mortality versus dose remains the same for the two growth stages while the lethal dose in the naupliar stage was 3.3 smaller than that determined for the adult stage. The slope of the UV mortality rate versus post-incubation time was found to be significantly different (P<0.05) at low UV doses for the two life stages examined, i.e. naupliar and adult. The lower value of LD₅₀ in naupliar stages compared to that for adults confirms that in the early growth stage this marine zooplankton is more susceptible to UV radiation.     

单细胞自由生物基因组全序列的测定和比较基因组研究

近几年来五种单细胞生物的基因组计划得以完成。本文介绍了从五种生物的全基因组序列获得的一些成果,包括全基因组鸟枪法测序、基因组分析和新比较基因组等三个方面,并对生物基因组计划的研究方法作一些探讨。     

Ecological similarities and differences among littoral species of Ceriodaphnia

In Artemia franciscana, enriched for 24 h with emulsified lipids, thefatty acid DHA (22:63) is unstable. In rotifers the level of DHA canbe stabilised by adding algae rich in DHA to the fish tanks. To test thismethod for A. franciscana, enriched A. franciscana was incubated with thealga Isochrysis galbana, which is rich in lipids and DHA, at sixconcentrations ranging from 1 to 20 mg C l^–1 at 13–14°C. After lipid enrichment, A. franciscana contained15% lipids of which 79% (116 mg g DW^–1) werefatty acids. Of the fatty acids, 17% was DHA (19.8 mg gDW^–1). After 72 hours incubation with I. galbana, the level ofDHA decreased to 1.6–3.2 mg g DW^–1, which was areduction by 84–92%. This was independent of the algalconcentration. The amount of total fatty acids decreased to 53–73 mg gDW^–1, a reduction by 37–54%, independent of thealgal concentration. The rates of loss of the fatty acids, and especiallyDHA, was greater during the first 24 h at the highest algal concentrations(8, 10 and 20 mg C l^–1). Enriched A. franciscana shouldtherefore not be incubated with high algal concentrations (>6 mg Cl^–1) during first feeding of marine fish larvae.