The role of dyadic interactions in the mixed-mating strategies of the mangrove rivulus Kryptolebias marmoratus

The mangrove rivulus Kryptolebias marmoratus a small cyprinodont fish native to tropical and subtropical waters from Florida to Brazil, is one of two known self-fertilizing, hermaphroditic vertebrates of which K. marmoratus displays androdioecy, a complex system of reproduction in which hermaphrodites and males are present. This study describes the behavioral repertoires observed during dyadic interactions in the laboratory. Kryptolebias marmoratus exhibited 23 distinctive acts or behaviors. Acts were divided into four categories: aggressive, submissive, neutral, and reproductive. Leading and following behaviors played important roles in the behavioral repertoires of these fish. In hermaphrodite-male dyads, males exclusively initiated the reproductive process and actively pursued hermaphrodites. When hermaphrodites were paired, there was no evidence that they behaved like other simultaneous hermaphrodites that alternate sexual roles (e.g. serranids). Hermaphrodites were extremely aggressive towards one another, and the aggressor established dominance rapidly. Male-male dyads were divided into two subdivisions based on the presence or absence of the caudal ocellus on one fish. A caudal ocellus on one male appeared to signal the possibility of a potential mating partner to males lacking it. Pairings of males without an ocellus were similar to hermaphrodite-hermaphrodite dyads in that both members of the pair were aggressive towards one another. These observations may be indicative of interactions taking place in natural communities or assemblages of fish in which both males and hermaphrodites occur and provide evidence on the role of dyadic interactions in the mixed-mating strategies [Current Zoology 56 (1): 6-17, 2010].     

A fish out of water: gill and skin remodeling promotes osmo- and ionoregulation in the mangrove killifish Kryptolebias marmoratus

The euryhaline, amphibious mangrove killifish Kryptolebias marmoratus is known to survive weeks out of water in moist environments. We tested the hypothesis that the skin is a site of osmo- and ionoregulation in K. marmoratus. We predicted that under terrestrial conditions, gill and skin remodeling would result in an enhanced role for skin and a diminished role for the gills in osmo- and ionoregulation. Fish were exposed to water-either freshwater (FW, 1‰) or hypersaline water (saltwater [SW], 45‰)-or air over a moist surface of FW or SW for 9 d and then recovered in water. When fish were emersed for 9 d, (22)Na and (3)H-H(2)O were exchanged across the cutaneous surface. Homeostasis of whole-body Cl(-) and water levels but not of Na(+) levels was maintained over 9 d in air. In air-exposed fish, there was a significant increase in the size of skin ionocytes (in SW), a decrease in the number of skin mucous cells (in SW), and an increase in the gill interlamellar cell mass relative to those of fish in water. Gill ionocytes were mostly embedded away from the external surface in air-exposed fish, but the number and size of ionocytes increased (in FW). Interestingly, skin ionocytes formed distinct clusters of 20-30 cells. The estimated number of ionocytes over the whole skin surface was comparable to that in the gills. Overall, the findings support the hypothesis that the skin is a site of osmo- and ionoregulation in K. marmoratus in aquatic and terrestrial environments. Reversible cellular and morphological changes to the skin and gills during air exposure probably enhanced the cutaneous contribution to ion and water balance.     

鱼类实验动物遗传检测方法研究进展

随着生命科学和环境科学的迅猛发展,鱼类实验动物作为科学研究的重要手段和材料,其开发和研究日益活跃,备受国内外研究工作者的关注。本文就鱼类实验动物遗传检测的必要性、遗传检测方法的分类、研究现状和应用前景进行了综述。     

Asymmetrical Resource Ownership Increases Owners’ and Reduces Non‐Owners’ Motivation to Fight in the Mangrove Rivulus,Kryptolebias marmoratus

Resource ownership often increases an individual's aggressiveness and its probability of defeating a competitor. Individuals contesting resource owners could therefore incur higher costs, making individuals reluctant to compete with owners. We tested the hypothesis that animals use asymmetry in resource ownership as a cue for contest costs and adjust contest decisions accordingly. Using a mangrove rivulus fish (Kryptolebias marmoratus), we staged (1) contests with a randomly assigned asymmetry in resource ownership (one fish was provided with a shelter) and (2) contests in which neither fish had a shelter. Owners that were in their shelters at the contest start showed a greater tendency to fight and won more contests than their intruder opponents; those outside the shelter at the start did not. Compared with fish in contests with no shelters at stake, shelter owners had a higher tendency to fight whether or not they were in their shelters at the start; intruders, however, had a lower tendency to fight only against owners that were inside the shelter at the start. These results demonstrate (1) that ownership status influences both owners’ and intruders’ contest decisions (and in opposite directions), producing a detectable ownership advantage and (2) that intruders required confirmation of their opponents’ ownership status before retreating without challenging them. Ownership status per se is therefore important to the fish's contest decisions.     

Association behaviour of the self-fertilizing Kryptolebias marmoratus (Poey): the influence of microhabitat use on the potential for a complex mating system

Preliminary observations were conducted to identify conspicuous body postures and movements of males and hermaphrodites in the mangrove killifish Kryptolebias marmoratus . These behaviours were used quantitatively to examine the social interactions for experimental pairings of K. marmoratus of different sexual states ( i.e. simultaneous hermaphrodite and male) in an aquarium with an open-water area and simulated crab burrows. This allowed observation of behaviours that could not be observed in the field. Kryptolebias marmoratus , regardless of sexual state and experimental treatment, spent 40% of the time in the burrow. Hermaphrodites exhibited a preference for associating with males rather than other hermaphrodites. The observed complexity of displayed behaviours and interactions between paired conspecifics indicate that K. marmoratus has a rich repertoire of social behaviour not predicted for a strictly selfing species. Also, land crab burrows play an important role in their social interactions.     

FMiR: A Curated Resource of Mitochondrial DNA Information for Fish

Mitochondrial genome sequences have been widely used for evolutionary and phylogenetic studies. Among vertebrates, fish are an important, diverse group, and their mitogenome sequences are growing rapidly in public repositories. To facilitate mitochondrial genome analysis and to explore the valuable genetic information, we developed the Fish Mitogenome Resource (FMiR) database to provide a workbench for mitogenome annotation, species identification and microsatellite marker mining. The microsatellites are also known as simple sequence repeats (SSRs) and used as molecular markers in studies on population genetics, gene duplication and marker assisted selection. Here, easy-to-use tools have been implemented for mining SSRs and for designing primers to identify species/habitat specific markers. In addition, FMiR can analyze complete or partial mitochondrial genome sequence to identify species and to deduce relational distances among sequences across species. The database presently contains curated mitochondrial genomes from 1302 fish species belonging to 297 families and 47 orders reported from saltwater and freshwater ecosystems. In addition, the database covers information on fish species such as conservation status, ecosystem, family, distribution and occurrence downloaded from the FishBase and IUCN Red List databases. Those fish information have been used to browse mitogenome information for the species belonging to a particular category. The database is scalable in terms of content and inclusion of other analytical modules. The FMiR is running under Linux operating platform on high performance server accessible at URL http://mail.nbfgr.res.in/fmir.     

InterStoreDB:A Generic Integration Resource for Genetic and Genomic Data

Associating phenotypic traits and quantitative trait loci (QTL) to causative regions of the underlying genome is a key goal in agricultural research.InterStoreDB is a suite of integrated databases designed to assist in this process.The individual databases are species independent and generic in design,providing access to curated datasets relating to plant populations,phenotypic traits,genetic maps,marker loci and QTL,with links to functional gene annotation and genomic sequence data.Each component database provides access to associated metadata,including data provenance and parameters used in analyses,thus providing users with information to evaluate the relative worth of any associations identified.The databases include CropStoreDB,for management of population,genetic map,QTL and trait measurement data,SeqStoreDB for sequence-related data and AlignStoreDB,which stores sequence alignment information,and allows navigation between genetic and genomic datasets.Genetic maps are visualized and compared using the CMAP tool,and functional annotation from sequenced genomes is provided via an EnsEMBL-based genome browser.This framework facilitates navigation of the multiple biological domains involved in genetics and genomics research in a transparent manner within a single portal.We demonstrate the value of InterStoreDB as a tool for Brassica research.InterStoreDB is available from:http://www.interstoredb.org     

A Method for Fixation of Fish Larvae for Morphological and Genetic Studies

Journal of Ichthyology - Three aqueous buffer solutions that make it possible to stabilize DNA and also preserve the initial body shape and morphological structures are tested for fixation and...     

Trypanosoma vivax: Adaptation of Two East African Stocks to Laboratory Rodents1

Two Trypanosoma vivax stocks from East Africa have been adapted to rats and mice. Adaptation was induced by rapid passage at two- to four-day intervals in sublethally irradiated rats. After 200 such passages, the two stocks gave rise to parasitemias of 10⁹–10¹⁰ trypanosomes/ml in peripheral blood, and the infection was fatal in 90% of the rats. By passaging the rat-adapted T. vivax into normal mice at two- to three-day intervals for over 200 passages, the two stocks also became pathogenic to mice. One of the stocks was also capable of maintenance in non-irradiated rats. The two stocks displayed a marked degree of pleomorphism in irradiated and non-irradiated rats and mice. In the early rising parasitemia, the organisms were predominantly short, with a well formed undulating membrane, a pointed posterior end, and a large terminal kinetoplast. As parasitemia approached its peak, the organisms transformed into long, slender forms with an inconspicuous undulating membrane, an elongated posterior end, and a sub-terminal kinetoplast. The short forms associated with the early, rising parasitemia were more infective for mice than the long forms encountered at peak parasitemia. Although the two rodent-adapted stocks retained their pathogenicity for goats, neither the original stocks nor their corresponding rodent-adapted stocks could be cyclically transmitted by tsetse flies. The availability of these stocks will greatly facilitate investigations on East African T. vivax which would otherwise be difficult to carry out in experimental rodents.     

High Islands Versus Low Islands: A Comparison of Fish Faunal Composition of the Palau Islands

High islands, with potentially greater habitat diversity, are expected to have greater species richness and diversity compared to low islands, typically atolls and coral islands of lower habitat diversity, within the same geographical area. Patterns of species similarity, richness, and diversity were compared among coral reef fishes between the low island of the Southwest Palau Islands (SWPI), and the low and high islands of the Main Palauan Archipelago (MPA). Data from diurnal visual transects accounted for approximately 64% and 69% of the shorefish faunas known from the SWPI and MPA, respectively. Two distinct fish faunas were representative of low and high islands. The first was confined to the coral islands of the SWPI. The second was partitioned into both low and high islands of the MPA, and Helen Reef, a large atoll in the SWPI. The second type was clustered into atolls, low islands with atoll-like barrier reef systems, a coral island, and three high island systems, one with an extensive barrier reef system. Contrary to the prediction that high islands, with relatively greater habitat diversity, would have greater species richness and diversity, species richness and diversity were greatest at Kossol, a large atoll-like low island locality at the northern end of a high island in the MPA, followed by two atolls, Kayangel (MPA, north of Kossol) and Helen Reef. In contrast, species richness and diversity were lower at high island localities and lowest at small coral islands. These results suggest that habitat diversity for reef fishes increases as a function of increasing area regardless of whether the locality is a high or low island.     

Germ Cell Transplantation Using Sexually Competent Fish: An Approach for Rapid Propagation of Endangered and Valuable Germlines

The transplantation of germ cells into adult recipient gonads is a tool with wide applications in animal breeding and conservation of valuable and/or endangered species; it also provides a means for basic studies involving germ cell (GC) proliferation and differentiation. Here we describe the establishment of a working model for xenogeneic germ cell transplantation (GCT) in sexually competent fish. Spermatogonial cells isolated from juveniles of one species, the pejerrey Odontesthes bonariensis (Atherinopsidae), were surgically transplanted into the gonads of sexually mature Patagonian pejerrey O. hatcheri, which have been partially depleted of endogenous GCs by a combination of Busulfan (40 mg/kg) and high water temperature (25°C) treatments. The observation of the donor cells'' behavior showed that transplanted spermatogonial cells were able to recolonize the recipients'' gonads and resume spermatogenesis within 6 months from the GCT. The presence of donor-derived gametes was confirmed by PCR in 20% of the surrogate O. hatcheri fathers at 6 months and crosses with O. bonariensis mothers produced hybrids and pure O. bonariensis, with donor-derived germline transmission rates of 1.2–13.3%. These findings indicate that transplantation of spermatogonial cells into sexually competent fish can shorten considerably the production time of donor-derived gametes and offspring and could play a vital role in germline conservation and propagation of valued and/or endangered fish species.     

The Current Status of Demersal and Pelagic Fish Stocks in the Olyutorsky-Navarin Shelf Area

Russian Journal of Marine Biology - Stocks of demersal and pelagic fish species in the near-bottom layer over the outer shelf and upper part of the continental slope between Cape Olyutorsky and...     

Development of Genetic Techniques for the Psychrotrophic Fish Pathogen Flavobacterium psychrophilum

Flavobacterium psychrophilum, a member of the Cytophaga-Flavobacterium-Bacteroides group, is an important pathogen of salmonid fish. Previous attempts to develop genetic techniques for this fastidious, psychrotrophic bacterium have met with failure. Here we describe the development of techniques for the genetic manipulation of F. psychrophilum and the identification of plasmids, selectable markers, a reporter system, and a transposon that function in several isolates of this fish pathogen. The antibiotic resistance genes ermF, cfxA, and tetQ function in F. psychrophilum. Cloning vectors based on the F. psychrophilum cryptic plasmid pCP1 which carried these selectable markers were introduced by conjugation from E. coli, resulting in antibiotic-resistant colonies of F. psychrophilum. Conjugative transfer of DNA into F. psychrophilum was strain dependent. Efficient transfer was observed for two of the seven strains tested (THC02-90 and THC04-90). E. coli lacZY functioned in F. psychrophilum when expressed from a pCP1 promoter, allowing its development as a reporter for studies of gene expression. Plasmids isolated from F. psychrophilum were efficiently introduced into F. psychrophilum by electroporation, but plasmids isolated from E. coli were not suitable for transfer by this route, suggesting the presence of a restriction barrier. DNA isolated from F. psychrophilum was resistant to digestion by Sau3AI and BamHI, indicating that a Sau3AI-like restriction modification system may constitute part of this barrier. Tn4351 was introduced into F. psychrophilum from E. coli and transposed with apparent randomness, resulting in erythromycin-resistant colonies. The techniques developed in this study allow for genetic manipulation and analysis of this important fish pathogen.     

The Prevalence of Species and Strains in the Human Microbiome: A Resource for Experimental Efforts

Experimental efforts to characterize the human microbiota often use bacterial strains that were chosen for historical rather than biological reasons. Here, we report an analysis of 380 whole-genome shotgun samples from 100 subjects from the NIH Human Microbiome Project. By mapping their reads to 1,751 reference genome sequences and analyzing the resulting relative strain abundance in each sample we present metrics and visualizations that can help identify strains of interest for experimentalists. We also show that approximately 14 strains of 10 species account for 80% of the mapped reads from a typical stool sample, indicating that the function of a community may not be irreducibly complex. Some of these strains account for >20% of the sequence reads in a subset of samples but are absent in others, a dichotomy that could underlie biological differences among subjects. These data should serve as an important strain selection resource for the community of researchers who take experimental approaches to studying the human microbiota.     

SysPTM: A Systematic Resource for Proteomic Research on Post-translational Modifications

With the rapid expansion of protein post-translational modification (PTM) research based on large-scale proteomic work, there is an increasing demand for a suitable repository to analyze PTM data. Here we present a curated, web-accessible PTM data base, SysPTM. SysPTM provides a systematic and sophisticated platform for proteomic PTM research equipped not only with a knowledge base of manually curated multi-type modification data but also with four fully developed, in-depth data mining tools. Currently, SysPTM contains data detailing 117,349 experimentally determined PTM sites on 33,421 proteins involving nearly 50 PTM types, curated from public resources including five data bases and four web servers and more than one hundred peer-reviewed mass spectrometry papers. Protein annotations including Pfam domains, KEGG pathways, GO functional classification, and ortholog groups are integrated into the data base. Four online tools have been developed and incorporated, including PTMBlast, to compare a user''s PTM dataset with PTM data in SysPTM; PTMPathway, to map PTM proteins to KEGG pathways; PTMPhylog, to discover potentially conserved PTM sites; and PTMCluster, to find clusters of multi-site modifications. The workflow of SysPTM was demonstrated by analyzing an in-house phosphorylation dataset identified by MS/MS. It is shown that in SysPTM, the role of single-type and multi-type modifications can be systematically investigated in a full biological context. SysPTM could be an important contribution to modificomics research. SysPTM is freely available online at www.sysbio.ac.cn/SysPTM.Post-translational modifications (PTMs)¹ are various processing events that change the maturity, activity, and/or turnover of proteins. More than 200 different types of PTMs have been found, with new ones still being reported (1). PTMs not only change the physicochemical properties of proteins (2) but also dynamically regulate various biological events such as protein degradation, subcellular localization, conformational change, protein-protein interaction, and signal transduction (3–5). Previous studies have revealed the central roles of PTMs in human health and disease. For example, phosphorylation of pRB1 has been associated with tumorigenesis through controlling cell division (6); S-nitrosylation of parkin regulates its E3 ligase activity, resulting in protein accumulation in sporadic Parkinson disease (7); and defects in protein glycosylation have been related to several forms of congenital muscular dystrophy (8). Given this important role in health and disease, PTMs have been regarded as potential disease biomarkers or therapeutic targets. For example, Erlotinib (Tarceva), an inhibitor of epidermal growth factor receptor tyrosine kinase, has been approved by the Food and Drug Administration to treat non-small cell lung cancer (9); and histone deacetylase inhibitors have been demonstrated to have a potential therapeutic role in Huntington disease (10). The broad range of important roles played by PTMs in physiological and pathological processes has made PTM research an active field in recent years. Yet we remain limited in our knowledge of the full scope of PTM distribution on proteins and the precise location of PTM sites.There are two major kinds of experimental methods to identify PTMs: 1) traditional biological experiments such as radiolabeling PTM proteins (11), Western analysis with antibodies against specific modifications (12), and site-directed mutagenesis of potential modification sites (13); and 2) large-scale proteomic experiments, especially multiple-dimensional liquid chromatography tandem mass spectrometry. Traditional experiments are laborious and time-consuming, resulting in slow data accumulation. By contrast, more recent MS/MS experiments have led to the discovery of thousands of new phosphorylation (14), glycosylation (15), acetylation (16), sumoylation (17), S-nitrosylation (18), and other modification sites. For example, based on MS/MS data, more than 6,000 phosphopeptides have been reported in HeLa cells (14), and 159 candidate sumoylated proteins have been found in yeast (17). Although advanced technologies have allowed PTM data to accumulate rapidly, it is impossible to identify all PTM sites for a set of proteins in one experiment, due to biased modification enrichment related to experimental protocol, limited sensitivity of mass spectrometer instrumentation, and failures in spectrum matching. Data bases are needed to amass PTM data from various experiments for comprehensive understanding of PTMs.Most data bases for storing PTM information have fallen into two general classes. One class focuses on a single modification type, such as Phospho.ELM (19) for phosphorylation or O-GLYCBASE (20) for glycosylation. Although these data bases have been widely used, they are limited in utility due to recording only a single modification type. The other class of PTM data base is the primary protein data base; these data bases collect PTM information with multiple modification types but are more broadly focused on providing diverse information about proteins, rather than PTM information specifically. Swiss-Prot (21) and HPRD (22) are examples of such data bases. As compared with either of the above two types of data base, integrated PTM data bases are more desirable. One example is dbPTM (23), which integrated experimentally determined PTM information from four external data bases. PhosphoSite started the harvesting of phosphorylation sites from published literature with a focus on in vivo mammalian phosphorylation data (24), but recently it has expanded to integrate nine other modification types. Even integrated data bases, however, have not taken into full consideration the aforementioned quickly accumulating PTM data from MS/MS experiments. These data, many of which are reported in the published literature but not collected in any data base, continue to increase rapidly due to new experiments. Such a wealth of information should be incorporated more comprehensively into the current PTM knowledge domain.At the same time, the high-throughput nature and complexity of MS/MS data pose computational challenges for proteome-scale PTM analyses in a biological context. A pure data repository is insufficient for such tasks. Powerful computational tools must accompany data repositories to allow knowledge extraction.To address these needs, we developed a systematic resource for PTM research, SysPTM, consisting of a PTM data base and four analysis tools. The SysPTM data base incorporates the existing features of numerous previous data bases, with an emphasis on collecting modification datasets from MS/MS experiments reported in the literature. The current release of SysPTM (v1.1) contains data detailing 117,349 PTM sites on 33,421 proteins involving nearly 50 modification types. The four analysis tools are PTMBlast, PTMPathway, PTMPhylog, and PTMCluster, which, respectively, can compare user PTM datasets with PTM data stored in SysPTM, map PTM proteins to KEGG pathways, discover potentially conserved PTM sites, and find significant clusters of multi-site modifications.In this work, an in-house MS/MS phosphorylation dataset from mouse embryonic stem cells was analyzed to demonstrate the SysPTM workflow. SysPTM can be accessed online.     

GWYRE: A Resource for Mapping Variants onto Experimental and Modeled Structures of Human Protein Complexes

Rapid progress in structural modeling of proteins and their interactions is powered by advances in knowledge-based methodologies along with better understanding of physical principles of protein structure and function. The pool of structural data for modeling of proteins and protein–protein complexes is constantly increasing due to the rapid growth of protein interaction databases and Protein Data Bank. The GWYRE (Genome Wide PhYRE) project capitalizes on these developments by advancing and applying new powerful modeling methodologies to structural modeling of protein–protein interactions and genetic variation. The methods integrate knowledge-based tertiary structure prediction using Phyre2 and quaternary structure prediction using template-based docking by a full-structure alignment protocol to generate models for binary complexes. The predictions are incorporated in a comprehensive public resource for structural characterization of the human interactome and the location of human genetic variants. The GWYRE resource facilitates better understanding of principles of protein interaction and structure/function relationships. The resource is available at http://www.gwyre.org.