Annotation and analysis of expressed sequence tags (ESTs) from Chinese sturgeon (Acipenser sinensis) pituitary cDNA library

Chinese sturgeon Acipenser sinensis belongs to the family Acipenseridae, an ancient species of actinopterygian fishes. In order to advance molecular research on its reproduction, ontogenetic development, we were seeking for genomic information in the NCBI expressed sequence tag (EST database). We found 3384 indentified cDNA sequences which were assembled into 861 unigenes. Blast analysis revealed 301 unigenes shared high similarity with genes in the public databases, and these were classified into three groups: 202 known genes, 81 putative genes and 8 unknown genes. The remainder (560 genes) had no significant match to any protein sequence. Further, 255 unigenes and 333 unmatched unigenes were annotated with Gene Ontology (GO), which could be classified into cellular component, molecular function, and biological process. Among the known genes, the hormone genes pomc A (proopiomelanocortin), pomc B, GtH alpha I subunit (gonadotropin hormone), GtH alpha II subunit and GH (growth hormone) were present in this library. Comparison of the Chinese sturgeon proteins (GH, GtH alpha subunit and POMC) to proteins of other species showed higher levels of homology among sturgeon species. We performed five hormone related genes including GnRHRI (gonadotropin-releasing hormone receptor I), cpH (carboxypeptidase H), ppiB (peptidylprolyl isomerase B), stmn3 (stathmin-like 3), 7B2 (neuroendocrine protein 7B2), and four novel genes (contig 192, 177, 170 and 168) a semi-quantitative RT-PCR on different tissues from Chinese sturgeon.     

Mitochondrial DNA variation, effective female population size and population history of the endangered Chinese sturgeon, Acipenser sinensis

The anadromous Chinese sturgeon (Acipenser sinensis), mainly endemic to the Yangtze River in China, is an endangered fish species. The natural population has declined since the Gezhouba Dam blocked its migratory route to the spawning grounds in 1981. In the near future, the completion of the Three Gorges Dam, the world's largest hydroelectric project, may further impact this species by altering the water flow of the Yangtze River. Little is currently known about the population genetic structure of the Chinese sturgeon. In this study, DNA sequence data were determined from the control region (D-loop) of the mitochondrial genome of adult sturgeons (n = 106) that were collected between 1995–2000. The molecular data were used to investigate genetic variation, effective female population size and population history of the Chinese sturgeon in the Yangtze River. Our results indicate that the reduction in abundance did not change genetic variation of the Chinese sturgeon, and that the population underwent an expansion in the past. AMOVA analysis indicated that 98.7% of the genetic variability occurred within each year's spawning populations, the year of collection had little influence on the diversity of annual temporary samples. The relative large effective female population size (N _ef) indicates that good potential exists for the recovery of this species in the future. Strikingly, the ratio of N _ef to the census female population size (N _f) is unusually high (0.77–0.93). This may be the result of a current bottleneck in the population of the Chinese sturgeon that is likely caused by human intervention. This revised version was published online in July 2006 with corrections to the Cover Date.     

长江口中华鲟自然保护区底层鱼类的群落结构特征

根据2004年8月、11月和2005年2月(Ⅰ年度)、2005年8月、11月和2006年2月、5月(Ⅱ年度)、2007年8月、11月和2008年2月和5月(Ⅲ年度)对长江口中华鲟自然保护区15个站位点的底拖网调查数据,对该水域的底层鱼类群落结构特征及时间和空间变化规律进行了分析。结果表明,调查中捕获底层鱼类42种,隶属于13目24科39属。底层鱼类的种类组成和群落结构进行聚类分析,15个站位聚合成两大类群,类群A位于南支北港和北港北沙近东滩水域,共出现20种底层鱼类,主要以淡水性和河口性鱼类为主;类群B位于北支和北港北沙近外海水域,共出现鱼类39种,主要以河口性和海洋性鱼类为主。ANOSIM和SIMPER分析表明底层鱼类群落结构不同季节间差异显著,造成这种趋势的主要原因可能是与棘头梅童鱼(Collichthys lucidus)和凤鲚(Coilia mystus)的繁殖和索饵洄游有关。     

Thermal maxima for juvenile shortnose sturgeon acclimated to different temperatures

Many populations of shortnose sturgeon, Acipenser brevirostrum, in the southeastern United States continue to suffer from poor juvenile recruitment. High summer water temperatures, which may be exacerbated by anthropogenic activities, are thought to affect recruitment by limiting available summer habitat. However, information regarding temperature thresholds of shortnose sturgeon is limited. In this study, the thermal maximum method and a heating rate of 0.1°C min⁻¹ was used to determine critical and lethal thermal maxima for young-of-the-year (YOY) shortnose sturgeon acclimated to temperatures of 19.5 and 24.1°C. Fish used in the experiment were 0.6 to 35.0 g in weight and 64 to 140 days post hatch (dph) in age. Critical thermal maxima were 33.7°C (±0.3) and 35.1°C (±0.2) for fish acclimated to 19.5 and 24.1°C, respectively. Critical thermal maxima significantly increased with an increase in acclimation temperature (p < 0.0001). Lethal thermal maxima were 34.8°C (±0.1) and 36.1°C (±0.1) for fish acclimated to 19.5 and 24.1°C, respectively. Lethal thermal maxima were significantly affected by acclimation temperature, the log₁₀ (fish weight), and the interaction between log₁₀(fish weight) and acclimation temperature (p < 0.0001). Thermal maxima were used to estimate upper limits of safe temperature, thermal preferences, and optimal growth temperatures of YOY shortnose sturgeon. Upper limits of safe temperature were similar to previous temperature tolerance information and indicate that summer temperatures in southeastern rivers may be lethal to YOY shortnose sturgeon if suitable thermal refuge cannot be found.     

Cell culture and karyotype of Sakhalin sturgeon Acipenser mikadoi

A cell culture of rare and threatened species of Sakhalin sturgeon Acipenser mikadoi was established from a fragment of the pectoral fin and neighboring tissues. Initially, the culture consisted of different cell types including typical fibroblasts as well as cells of epithelial origin, myofibroblasts, etc. After approximately five passages, the culture largely consisted of cells with fibroblast morphology. Under normal culture conditions, these cells grew for more than one year at a constant rate and passed about 80 population doublings. In the absence of serum, cells entered the state of proliferative quiescence (G₀-state). When cultured without medium replacement for a long period of time, cells fused to form myofibers of about 1 cm in length. These myofibers could branch and acquired cross striation with time. About forty days after myofibers emerged, they degenerated, lost their shape, detached from the substrate, and finally died. The induction of adipogenic differentiation arrested cell proliferation and introduced lipophilic inclusions formed in a minor fraction of cells. The number of these inclusions was low, and cells with inclusions demonstrated various morphology distinct from typical adipocytes. The induction of osteogenic differentiation gave rise to cells that produce mineralized extracellular matrix and bone nodules. Chromosome analysis revealed a set of chromosomes typical for “high chromosome” sturgeon species. The variation in the chromosome number was very high (mean, 247 ± 33; modal value, 248). The analysis involving AT- and GC-specific fluorochromes has demonstrated that the telomeric and centromeric regions of all chromosomes are enriched in GC content. The distribution of AT- and GC-rich sequences along the chromosomes was heterogeneous. Long chromosomes were preferentially stained by the AT-specific dye, whereas small chromosomes demonstrated brighter fluorescence after 7-amino-actinomycin D staining; in particular, several small chromosomes fluoresced extremely brightly. This work is the first report of cell culture and karyotype analysis of Sakhalin sturgeon.     

Habitat use of juvenile white sturgeon in the Kootenai River, Idaho and British Columbia

Ultrasonic telemetry was used to assess habitat features utilized by 36 endangered juvenile white sturgeon, Acipenser transmontanus, in the lower 120 km of the Kootenai River of Idaho, USA and British Columbia, Canada during the summer and early fall of 1999 and 2000. All 36 fish were initially captured in pools using gillnets and released there, but most of the subsequent telemetry contacts were in glides, indicating these fish moved freely between the two macro-habitats. The low electivity indices indicated little preference between glides and pools. Most contacts were in glides, in the outside bend of the river channel (50), and in or near a visually defined thalweg. Contacts were most often associated with sand substrates and no cover. Physical habitat characteristics (nose [bottom] water velocity, depth, substrate, and cover) were recorded at 168 contact locations. The combination of significantly greater velocities and depths at contact sites vs. non-contact sites (p < 0.01) indicated these fish actively found and used areas of higher velocity and greater depth within the Kootenai River. There was little cover found for fish in the river other than large sand dunes and depth. The combination of depth and nose velocity data supported the idea that large sand dunes are providing refugia in the form of velocity breaks.     

葛洲坝下游中华鲟（Acipenser sinensis）产卵场地形分析

根据1981年葛洲坝截流至1998年对葛洲坝坝下河床研究的历史资料,结合1999～2006年间获得的中华鲟产卵场所在江段河床的5次地形数据,采用ArcGIS 9.0软件,对中华鲟产卵场河床的高程、坡度、坡向等地形因子进行了详细分析。结果表明：葛洲坝至磨基山江段中华鲟产卵场与历史产卵场相比具有极其相似的特征,临江溪至虎牙滩江段中华鲟自然繁殖频率不高可能主要是因为地形不符合要求,从而造成相关的水文因子也不能满足需要。中华鲟自然繁殖前期的迁徙分布和产卵后受精卵的散播与河床地形都有一定的关系,葛洲坝水利枢纽下游河势调整工程较大地改变了葛洲坝至庙咀江段河床的地形,地形复杂度的增加可能对中华鲟自然繁殖前期的栖息有利,而河床坡度、底质的改变则可能会对中华鲟受精卵的散播和发育产生不利影响。有必要结合中华鲟历史产卵场精确的地形数据,对“中华鲟产卵场功能分区模型假说”进行验证,并针对产卵场地形对中华鲟自然繁殖的影响,做出进一步探讨。     

Karyotype of North American shortnose sturgeon Acipenser brevirostrum with the highest chromosome number in the Acipenseriformes

The shortnose sturgeon Acipenser brevirostrum was revealed to have a larger number of chromosomes than previously reported for other sturgeon species. Its chromosome number ranged from 362 to 372 (of ten specimens examined), showing intraindividual variation. The karyotype of metaphase with the highest chromosome number (372) consisted of 89 pairs of macrochromosomes and 97 pairs of microchromosomes (fundamental number; NF=550). Although the microchromosomes were relatively shorter than the macrochromosomes, most of them had discernible arms and centromeres. Silver-stained nucleolar organizer regions (Ag-NORs) were localized on the telomeric regions of 5 pairs of chromosomes (Ag-NORs=10): 4 were made up of small meta/submetacentrics and 1 of acrocentrics. Polyploidy of A. brevirostrum should be hexaploid based on the karyotype, numerous chromosomes, Ag-NORs, and previously reported large genome size (ca. 13pg DNA/cell).Supplementary material to this paper is available in electronic format at http://dx.doi.org/10.1007/s10228-004-0257-z     

Isolation of microsatellite loci from the endemic and endangered Adriatic sturgeon (<Emphasis Type="Italic">Acipenser naccarii</Emphasis>)

With the aim of elaborating a breeding plan on a captive stock of the highly endangered Adriatic sturgeon (Acipenser naccarii), a total of 10 polymorphic microsatellite loci were isolated from an enriched library. The results of cross amplification of additional 8 loci previously isolated from A. oxyrinchus, A. fulvescens and Scaphyrinchus platorhynchus are also reported. Given the tetraploid condition of the species the genetic variability was estimated basing on the number of alleles per individuals and the average band sharing.     

Male size effects on fertilization success: lack of evidence in chinook salmon spawning under experimental conditions

Synopsis Anadromous salmonid females exhibit indicators of mate choice based on male size. Direct benefits to females of mating with larger males have not been identified for semelparous Pacific salmon, Oncorhynchus spp. We tested the null hypothesis that females forced to spawn naturally in a stream channel and artificially (gametes removed manually) with males about half their body mass would experience egg fertilization rates similar to that of females forced to spawn with males of about equal mass. Fertilization rates did not differ significantly between large- and small-male pairs. The fertilization rates were also very similar for eggs deposited naturally and those that we fertilized artificially. Therefore, fertilization success does not appear to be the mechanism responsible for female mate choice based on male size. Benefits of females mating with larger males probably have only indirect (i.e., genetic) benefits to a females offspring, as suggested by previous authors.     

Effect of starvation and refeeding on digestive enzyme activities in sturgeon (Acipenser naccarii) and trout (Oncorhynchus mykiss)

The digestive enzyme activities were determined in Adriatic sturgeon and rainbow trout during starvation and refeeding period. Overall, the digestive enzyme activities are affected in the same sense in both species. The protease and lipase activities were decreased later than amylase activity. Even after 1 month of starvation, both species would be prepared to digest protein and lipids in an effective way. After 72 days of starvation, the digestive machinery of the sturgeon and of the trout shows an altered capacity to digest macronutrients. The capacity to digest proteins and lipids, after 60 days of refeeding, begins to become re-established in sturgeon and trout. In contrast, in this period, the capacity to digest carbohydrates remains depressed in both species.     

Morphology,mechanics, and locomotion: the relation between the notochord and swimming motions in sturgeon

Synopsis To examine the relation between morphology and performance, notochordal morphology was correlated with notochordal mechanics and with steady swimming motions in white sturgeon, Acipenser transmontanus. In a still-water tank, motions of four sturgeon varied with changes in swimming speed and axial position along the body. For a 1..34 m sturgeon, slow and fast swimming modes were distinguished, with speeds at the fast mode more than two times those at the slow mode without changes in tailbeat frequency. This increase in speed is correlated with an increase in the body's maximal midline curvature (m^–1), suggesting a role for curvature-related mechanical properties of the notochord. Maximal midline curvature also varied with axial position, and surprisingly was uncorrelated with axial changes in the notochord's cross-sectional shape - as measured by height, width, inner diameter, and lateral thickness of the sheaths. On the other hand, maximal midline curvature was negatively correlated with the axial changes in the notochord's angular stiffness (N m rad^–1) and change in internal pressure (% change from baseline of 58.6 kPa), both of which were measured during in vitro bending tests. In vivo curvature and in vitro angular stiffness were then used to estimate the bending moments (Nm) in the notochord during swimming. In the precaudal notochord, the axial pattern of maximal stiffness moments was congruent with the pattern of maximal notochordal curvature in the precaudal region, but in the caudal notochord maximal angular stiffness was located craniad to maximal curvature. One interpretation of this pattern is that the precaudal notochord resists bending moments generated by the muscles and that the caudal notochord resists bending moments generated by hydrodynamic forces acting on the tail.     

A hypothesis on the role of Aphanizomenon in translocating phosphorus

A mechanism for the upward translocation of phosphorus by flake-forming Aphanizomenon is hypothesized. Aphanizomenon germinates on oxic sediments and rises into the water column, then the flakes diurnally migrate. Observations from Spring Lake, Minnesota, U.S.A., indicate that Aphanizomenon translocates phosphorus to the summertime epilimnion. However, the observations cannot discriminate between which of two mechanisms related to Aphanizomenon flakes, upon germination or with subsequent diurnal migrations, is more important.     

A microsampling method for genotyping coral symbionts

Genotypic characterization of Symbiodinium symbionts in hard corals has routinely involved coring, or the removal of branches or a piece of the coral colony. These methods can potentially underestimate the complexity of the Symbiodinium community structure and may produce lesions. This study demonstrates that microscale sampling of individual coral polyps provided sufficient DNA for identifying zooxanthellae clades by RFLP analyses, and subclades through the use of PCR amplification of the ITS-2 region of rDNA and denaturing-gradient gel electrophoresis. Using this technique it was possible to detect distinct ITS-2 types of Symbiodinium from two or three adjacent coral polyps. These methods can be used to intensely sample coral-symbiont population/communities while causing minimal damage. The effectiveness and fine scale capabilities of these methods were demonstrated by sampling and identifying phylotypes of Symbiodinium clades A, B, and C that co-reside within a single Montastraea faveolata colony.     

Development of new microsatellite primers for green and white sturgeon

Sixty-eight primer sets for microsatellite loci were developed from microsatellite motif enriched genomic libraries of pooled DNA from the polyploid green and white sturgeon (Acipenser medirostris and A. transmontanus). Four individuals from each species were screened for polymorphism at these loci. Forty-eight loci amplified in both species, and some exhibited species-specific amplification for white or green sturgeon (8 and 12 loci, respectively). The number of alleles per locus ranged from one to 12. At least 68% of the green and 65% of the white sturgeon loci we developed are polysomic.     

Gonad morphology,oocyte development and spawning cycle of the calanoid copepod <Emphasis Type="Italic">Acartia clausi</Emphasis>

Information on gonad morphology and its relation to basic reproductive parameters such as clutch size and spawning frequency is lacking for Acartia clausi, a dominant calanoid copepod of the North Sea. To fill this gap, females of this species were sampled at Helgoland Roads from mid March to late May 2001. Gonad structure and oogenesis were studied using a combination of histology and whole-body-analysis. In addition, clutch size and spawning frequency were determined in incubation experiments, during which individual females were monitored at short intervals for 8 and 12 h, respectively. The histological analysis revealed that the ovary of A. clausi is w-shaped with two distinct tips pointing posteriorly. It is slightly different from that of other Acartia species and of other copepod taxa. From the ovary, two anterior diverticula extend into the head region, and two posterior diverticula extend to the genital opening in the abdomen. Developing oocytes change in shape and size, and in the appearance of the nucleus and the ooplasm. Based on these morphological characteristics, different oocyte development stages (OS) were identified. Mitotically dividing oogonia and young oocytes (OS 0) were restricted to the ovary, whereas vitellogenic oocytes (OS 1–4) were present in the diverticula. The development stage of the oocytes increased with distance to the ovary in both, anterior and posterior diverticula. Most advanced oocytes were situated ventrally, and their number varied between 1 and 18, at a median of 4. All oocyte development stages co-occur indicating that oogenesis in A. clausi is a continuous process. These morphological features reflect the reproductive traits of this species. In accordance with the low numbers of mature oocytes in the gonads, females usually produced small clutches of one to five eggs. Clutches were released throughout the entire observation period at intervals of 90 min (median) resulting in mean egg production rates of 18–28 eggs female⁻¹ day⁻¹.     

A hypothesis for thein vivo antioxidant action of salicyclic acid

This paper presents a new hypothesis for the physiological antioxidant action of salicylate. Current theories have focused on the radical scavenging nature of salicylate. This explanation may have limitations because it is unlikely that salicylate reaches the necessary concentrations to effectively prevent damage to cell components. We propose that salicylic acid decreases the flux of hydroxyl radicals through chelation, which causes a redox deactivation mechanism of iron Fenton reaction centers. This is due to voltammetric results which indicate that the iron-salicylate complex does not have the thermodynamic driving force to act as an effective Fenton reagent necessary for the production of damaging oxygen-containing radicals. Furthermore, despite the more facile thermodynamics associated with Fenton-type processes at acidic pH values, the complex maintains Fenton inactivity due to a pH-sensitive redox potential shift that follows asE _Fe[Sal] = 0.793 - (0.059 pH). This is important since inflammation sites are acidic relative to healthy tissue. This redox potential shift is unique to salicylates when compared with other common iron chelation agents such as EDTA. Further evidence for the lack of Fenton-type reactivity of the iron-salicylate complex is offered in the form of oxidation studies of calf thymus (CT) DNA by hydrogen peroxide. Salicylate prevents the iron-catalyzed oxidation of CT-DNA strands as indicated by the detection of the constituent bases by HPLC. However, salicylates were not able to prevent the copper-catalyzed oxidation of CT-DNA. These results are predicted by the cyclic voltammetry of copper-salicylate, which confirms that it is an effective Fenton-type catalyst, further adding to the proof that salicylate acts by redox deactivation of iron, not by hydroxyl radical scavenging. Finally, the iron-salicylate e.m.f. suggests that it may also act as a superoxide dismutase, which indicates another possible important antioxidant feature.     

A hypothesis on the biological role of ABH,lewis and P blood group determinant structures in glycosphingolipids and glycoproteins

A hypothesis is presented that glycosphingolipids of circulating erythrocytes are membrane-packing substances providing for an energetically cheap carbohydrate protective coat at the cell surface. The glycosphingolipids should cover the membrane surface not occupied by functional glycoproteins. This role is envisaged for the globo series of glycosphingolipids which are P^k and P antigens of human blood. Glycosphingolipids of the neolacto series terminated with non-informative A, B, H. Lewis, P₁ antigenic structures as well as with sialic acid residues should serve the same purpose. These carbohydrate structures may be also used for conferring biological inertness on otherwise functionally active carbohydrate structures and provide protection for circulatory and membrane glycoproteins from proteolysis, denaturation and recognition of potentially antigenic sites of protein moieties by the immunosurveillance system of the body. At the external body surface the same carbohydrate structures may protect cells from the action of pathogenic microorganisms and other environmental factors. The roles of the above mentioned carbohydrate sequences on glycosphingolipids and glycoproteins in the development, tumorigenesis and evolution of blood group polymorphism are discussed.Abbreviations GP glycoprotein - GSL glycosphingolipid - GC glycoconjugate     

Evaluation of Epicoccum nigrum for growth, morphology and production of natural colorants in liquid media and on a solid rice medium

Four nonpathogenic and nontoxigenic Epicoccum nigrum strains were evaluated for their growth, morphology and pigment producing ability in three complex and one defined liquid media. Epicoccum nigrum IBT 41028 produced pigments in all the four media tested with a maximum pigment of 3.68 AU at 410 nm in M1 medium (unoptimized) containing 5 g/l yeast autolysate. The color hue of the crude pigment extracts ranged from 74 to 102 exhibiting dark orange to green-yellow color. Pelleted morphology was shown to have a positive influence on the pigment production by E. nigrum strain IBT 41028 in the liquid media, and the use of Bis-tris buffer was found to diminish or reduce the pellet formation. Since Monascus is a well known pigment producer on rice. Pigment producing ability of E. nigrum IBT 41028 was tested on rice and compared to liquid media with Monascus ruber IBT 7904 as control. Though, both genera preferred rice but E. nigrum produced 4.6 folds higher pigment in the liquid unoptimized fermentation medium compared to M. ruber. Solid phase extraction and subsequently HPLC-DAD analysis of the crude pigment extracts showed qualitative as well as quantitative variation in the pigment composition under solid and liquid cultivations.