Murine MyaK, a member of a family of yeast YAK1-related genes, is highly expressed in hormonally modulated epithelia in the reproductive system and in the embryonic central nervous system

We have cloned a mouse homologue (designated Myak) of the yeast protein kinase YAK1. The 1210 aa open reading frame contains a putative protein kinase domain, nuclear localization sequences and PEST sequences. Myak appears to be a member of a growing family of YAK1-related genes that include Drosophila and human Minibrain as well as a recently identified rat gene ANPK that encode a steroid hormone receptor interacting protein. RNA blot analysis revealed that Myak is expressed at low levels ubiquitously but at high levels in reproductive tissues, including testis, epididymis, ovary, uterus, and mammary gland, as well as in brain and kidney. In situ hybridization analysis on selected tissues revealed that Myak is particularly abundant in the hormonally modulated epithelia of the epididymis, mammary gland, and uterus, in round spermatids in the testis, and in the corpora lutea in the ovary, Myak is also highly expressed in the aqueduct of the adult brain and in the brain and spinal cord of day 12.5 embryos, Mol. Reprod. Dev. 55:372-378, 2000. (C) 2000 Wiley-Liss, Inc.

Phylogenetic analysis of the family Thermaceae with an emphasis on signature position and secondary structure of 16S rRNA

The sequences of the 16S rRNA genes from 38 strains of the family Thermaceae were compared by alignment analysis. The genus-specific and species-specific base substitutions or base deletions (signature positions) were found in three hypervariable regions (in the helices 6, 10 and 17). The differentiation of secondary structures of the high variable regions in the 5' end (38-497) containing several signature positions further supported the concept. Based on the comparisons of the secondary structures in the segments of 16S rRNAs, a key to the species of the family Thermaceae was proposed. (C) 2003 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

Impacts of two biomanipulation fishes stocked in a large pen on the plankton abundance and water quality during a period of phytoplankton seasonal succession

Silver and bighead carp were stocked in a large pen to control the nuisance cyanobacterial blooms in Meiliang Bay of Lake Taihu. Plankton abundance and water quality were investigated about once a week from 9 May to 7 July in 2005. Biomass of both total crustacean zooplankton and cladocerans was significantly suppressed by the predation of pen-cultured fishes. There was a significant negative correlation between the N:P weight ratio and phytoplankton biomass. The size-selective predation by the two carps had no effect on the biomass of green alga Ulothrix sp. It may be attributed to the low fish stocking density (less than 40 g m(-3)) before June. When Microcystis dominated in the water of fish pen, the pen-cultured carps effectively suppressed the biomass of Microcystis, as indicated by the significant decline of chlorophyll a in the >38 mu m fractions of the fish pen. Based on the results of our experiment and previous other studies, we conclude that silver and bighead carp are two efficient biomanipulation tools to control cyanobacterial (Microcystis) blooms in the tropical/subtropical eutrophic waters. Moreover, we should maintain an enough stocking density for an effective control of phytoplankton biomass. (C) 2008 Elsevier B.V All rights reserved

Discovery of a male-biased mutant family and identification of a male-specific SCAR marker in gynogenetic gibel carp Carassius auratus gibelio

Gibel carp ( Carassius auratus gibelio) is a uniquely gynogenetic species with a minor ratio of males in natural habitats, but its male origin and sex determination mechanisms have been unknown. In this study, a male-biased mutant family was discovered from the gynogenetic gibel carp, and a male-specific SCAR marker was identified from the mutant family. Normal spermatogenesis was observed in the male testes by immuno. fluorescence histochemistry. Nearly identical AFLP profiles were observed between males and females, but a male-specific 86 bp AFLP fragment was screened by sex-pool bulked segregant analysis and individual screening. Based on the male-specific AFLP fragment, a total of 579 bp sequences were cloned by genome walking. Subsequently, a male-specific SCAR marker was designed, and the male-specific DNA fragment was confirmed to be steadily transmitted to the next generation and consistently detected only in males. (C) 2009 National Natural Science Foundation of China and Chinese Academy of Sciences. Published by Elsevier Limited and Science in China Press. All rights reserved.

Diatom community succession in the recent history of a eutrophic Yunnan Plateau lake, Lake Dianchi, in subtropical China

Fish introduction, eutrophication and disappearance of aquatic vegetation are important disturbances of aquatic ecosystems, especially in plateau lakes, which are generally considered to be very vulnerable. Fish were introduced to Lake Dianchi, a eutrophic plateau lake in southwest China, in the late 1950s and 1970s. After the introduction, invasive fish became the dominant species, and the total fish yield increased. Meanwhile, the trophic level of Lake Dianchi had a tendency to increase in the past decades because of the increases in human activities in the watershed area. In addition, the area of aquatic vegetation decreased from more than 90 to 1.8% of the lake area from the 1950s to 2000. This study investigated the effects of fish introduction, eutrophication and aquatic vegetation on the diatom community of Lake Dianchi by examining the changes of microfossil diatom assemblage and abundance. Results showed that the absolute abundance and diatom assemblages changed after fish were introduced. The endemic species, Cyclotella rohomboideo-elliptica, disappeared with the introduction of fish and increasing trophic levels after 1958. Fragilaria crotonensis entered into the lake with the introduction of fish and gradually thrived in the lake after 1958. Diatom species numbers also decreased gradually from 21 to 9 from the past to present. Epiphytic diatoms disappeared with the decrease of aquatic vegetation after 1985. Our study indicated that eutrophication was the most important process determining diatom abundance, and fish introduction was a secondary process determining diatom abundance, while aquatic vegetation had a more important role in structuring the diatom community in this eutrophic plateau lake.

Plankton Community Succession in Artificial Systems Subjected to Cyanobacterial Blooms Removal using Chitosan-Modified Soils

Using artificial systems to simulate natural lake environments with cyanobacterial blooms, we investigated plankton community succession by polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprinting and morphological method. With this approach, we explored potential ecological effects of a newly developed cyanobacterial blooms removal method using chitosan-modified soils. Results of PCR-DGGE and morphological identification showed that plankton communities in the four test systems were nearly identical at the beginning of the experiment. After applying the newly developed and standard removal methods, there was a shift in community composition, but neither chemical conditions nor plankton succession were significantly affected by the cyanobacteria removal process. The planted Vallisneria natans successfully recovered after cyanobacteria removal, whereas that in the box without removal process did not. Additionally, canonical correspondence analysis indicated that other than for zooplankton abundance, total phosphorus was the most important environmental predictor of planktonic composition. The present study and others suggest that dealing with cyanobacteria removal using chitosan-modified soils can play an important role in controlling cyanobacterial blooms in eutrophicated freshwater systems.

Origin and evolution of the RIG-I like RNA helicase gene family

Background: The DExD/H domain containing RNA helicases such as retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated gene 5 (MDA5) are key cytosolic pattern recognition receptors (PRRs) for detecting nucleotide pathogen associated molecular patterns (PAMPs) of invading viruses. The RIG-I and MDA5 proteins differentially recognise conserved PAMPs in double stranded or single stranded viral RNA molecules, leading to activation of the interferon system in vertebrates. They share three core protein domains including a RNA helicase domain near the C terminus (HELICc), one or more caspase activation and recruitment domains (CARDs) and an ATP dependent DExD/H domain. The RIG-I/MDA5 directed interferon response is negatively regulated by laboratory of genetics and physiology 2 (LGP2) and is believed to be controlled by the mitochondria antiviral signalling protein (MAVS), a CARD containing protein associated with mitochondria. Results: The DExD/H containing RNA helicases including RIG-I, MDA5 and LGP2 were analysed in silico in a wide spectrum of invertebrate and vertebrate genomes. The gene synteny of MDA5 and LGP2 is well conserved among vertebrates whilst conservation of the gene synteny of RIG-I is less apparent. Invertebrate homologues had a closer phylogenetic relationship with the vertebrate RIG-Is than the MDA5/LGP2 molecules, suggesting the RIG-I homologues may have emerged earlier in evolution, possibly prior to the appearance of vertebrates. Our data suggest that the RIG-I like helicases possibly originated from three distinct genes coding for the core domains including the HELICc, CARD and ATP dependent DExD/H domains through gene fusion and gene/domain duplication. Furthermore, presence of domains similar to a prokaryotic DNA restriction enzyme III domain (Res III), and a zinc finger domain of transcription factor (TF) IIS have been detected by bioinformatic analysis. Conclusion: The RIG-I/MDA5 viral surveillance system is conserved in vertebrates. The RIG-I like helicase family appears to have evolved from a common ancestor that originated from genes encoding different core functional domains. Diversification of core functional domains might be fundamental to their functional divergence in terms of recognition of different viral PAMPs.

Identification of an additional two-cysteine containing type I interferon in rainbow trout Oncorhynchus mykiss provides evidence of a major gene duplication event within this gene family in teleosts

Multiple type I interferons (IFNs) have recently been identified in salmonids, containing two or four conserved cysteines. In this work, a novel two-cysteine containing (2C) IFN gene was identified in rainbow trout. This novel trout IFN gene (termed IFN5) formed a phylogenetic group that is distinct from the other three salmonid IFN groups sequenced to date and had a close evolutionary relationship with IFNs from advanced fish species. Our data demonstrate that two subgroups are apparent within each of the 2C and 4C type I IFNs, an evolutionary outcome possibly due to two rounds of genome duplication events that have occurred within teleosts. We have examined gene expression of the trout 2C type I IFN in cultured cells following stimulation with lipopolysaccharide, phytohaemagglutinin, polyI:C or recombinant IFN, or after transfection with polyI:C. The kinetics of gene expression was also studied after viral infection. Analysis of the regulatory elements in the IFN promoter region predicted several binding sites for key transcription factors that potentially play an important role in mediating IFN5 gene expression.

Bead-probe complex capture a couple of SINE and LINE family from genomes of two closely related species of East Asian cyprinid directly using magnetic separation

Background: Short and long interspersed elements (SINEs and LINEs, respectively), two types of retroposons, are active in shaping the architecture of genomes and powerful tools for studies of phylogeny and population biology. Here we developed special protocol to apply biotin-streptavidin bead system into isolation of interspersed repeated sequences rapidly and efficiently, in which SINEs and LINEs were captured directly from digested genomic DNA by hybridization to bead-probe complex in solution instead of traditional strategy including genomic library construction and screening. Results: A new couple of SINEs and LINEs that shared an almost identical 3'tail was isolated and characterized in silver carp and bighead carp of two closely related species. These SINEs (34 members), designated HAmo SINE family, were little divergent in sequence and flanked by obvious TSD indicated that HAmo SINE was very young family. The copy numbers of this family was estimated to 2 x 10(5) and 1.7 x 10(5) per haploid genome by Real-Time qPCR, respectively. The LINEs, identified as the homologs of LINE2 in other fishes, had a conserved primary sequence and secondary structures of the 3'tail region that was almost identical to that of HAmo SINE. These evidences suggest that HAmo SINEs are active and amplified recently utilizing the enzymatic machinery for retroposition of HAmoL2 through the recognition of higher-order structures of the conserved 42-tail region. We analyzed the possible structures of HAmo SINE that lead to successful amplification in genome and then deduced that HAmo SINE, SmaI SINE and FokI SINE that were similar in sequence each other, were probably generated independently and created by LINE family within the same lineage of a LINE phylogeny in the genomes of different hosts. Conclusion: The presented results show the advantage of the novel method for retroposons isolation and a pair of young SINE family and its partner LINE family in two carp fishes, which strengthened the hypotheses containing the slippage model for initiation of reverse transcription, retropositional parasitism of SINEs on LINEs, the formation of the stem loop structure in 3'tail region of some SINEs and LINEs and the mechanism of template switching in generating new SINE family.

Molecular evidence for diphyly of the Asian catfish family Amblycipitidae (Teleostei: Siluriformes) and exclusion of the South American Aspredinidae from Sisoroidea

Amblycipitidae Day, 1873 is an Asian family of catfishes (Siluriformes) usually considered to contain 28 species placed in three genera: Amblyceps (14 spp.), Liobagrus (12 spp.) and Xiurenbagrus (2 spp.). Morphology-based systematics has supported the monophyly of this family, with some authors placing Amblycipitidae within a larger group including Akysidae, Sisoridae and Aspredinidae, termed the Sisoroidea. Here we investigate the phylogenetic relationships among four species of Amblyceps, six species of Liobagrus and the two species of Xiurenbagrus with respect to other sisoroid taxa as well as other catfish groups using 6100 aligned base pairs of DNA sequence data from the rag1 and rag2 genes of the nuclear genome and from three regions (cyt b, COL ND4 plus tRNA-His and tRNA-Ser) of the mitochondrial genome. Parsimony and Bayesian analyses of the data indicate strong support for a diphyletic Amblycipitidae in which the genus Amblyceps is the sister group to the Sisoridae and a clade formed by genera Liobagrus and Xiurenbagrus is the sister group to Akysidae. These taxa together form a well supported monophyletic group that assembles all Asian sisoroid taxa, but excludes the South American Aspredinidae. Results for aspredinids are consistent with previous molecular studies that indicate these catfishes are not sisoroids, but the sister group to the South American doradoid catfishes (Auchenipteridae + Doradidae). The redefined sisoroid clade plus Bagridae, Horabagridae and (Ailia + Laides) make up a larger monophyletic group informally termed "Big Asia." Likelihood-based SH tests and Bayes Factor comparisons of the rag and the mitochondrial data partitions considered separately and combined reject both the hypothesis of amblycipitid monophyly and the hypothesis of aspredinid inclusion within Sisoroidea. This result for amblycipitids conflicts with a number of well documented morphological synapomorphies that we briefly review. Possible nomenclatural changes for amblycipitid taxa are noted.

Identification of a C1q family member associated with cortical granules and follicular cell apoptosis in Carassius auratus gibelio

C1q family proteins with C1q domain have been reported in vertebrates, but their biological roles are currently unknown. In this study, a C1q-like factor, designated Carassius auratus gibelio ovary-specific C1q-like factor (CagOC1q-like), was identified as a cortical granules component. Immunofluorescence localization revealed that the C1q family member was specifically expressed in follicular epithelial cells, and associated with cortical granules in fully grown oocytes. Moreover, it was discharged to the perivitelline space and egg envelope upon fertilization. As it is the first identified C1q family member that is expressed in follicular cells that surround oocyte, CagOC1q-like was applied to detection of follicular cell apoptosis and deletion. The entire cytological process of follicular cell apoptosis and deletion was clearly seen from double visualizations of follicular cells with CagOC1q-like immunofluorescence and apoptotic follicular cells labeled by terminal deoxynucleotidyl transferase (TdT)-mediated dUTP nick end labeling (TUNEL) during oocyte maturation and ovulation. (C) 2008 Elsevier Ireland Ltd. All rights reserved.

Controlling factors of spring-summer phytoplankton succession in Lake Taihu (Meiliang Bay, China)

The spring-summer successions of phytoplankton and crustacean zooplankton were examined weekly in Meiliang Bay of the subtropical Lake Taihu in 2004 and 2005. During the study period, the ecosystem of Meiliang Bay was characterized by (i) clearly declined nitrogen compounds (nitrate, TN, and ammonium) and slowly increased phosphorus compounds (TP and SRP), (ii) increased total phytoplankton density and rapid replacement of chlorophyta (mainly Ulothrix) by cyanobacteria (mainly Microcystis), and (iii) rapid replacement of large-sized crustaceans (Daphnia and Moina) by small-sized ones (Bosmina, Limnoithona, and Ceriodaphnia). Results from the CCA and correlation analysis indicate that the spring-summer phytoplankton succession was primarily controlled by abiotic factors. Cyanobacteria were mainly promoted by increased temperature and decreased concentrations of nitrogen compounds. The pure contribution of crustacean was low for the variation of phytoplankton suggesting a weak top-down control by crustacean zooplankton in the subtropical Lake Taihu.