Spermatozoon ultrastructure of Xenoturbella bocki (Westblad 1949)

Obst, M., Nakano, H., Bourlat, S.J., Thorndyke, M.C., Telford, M.J., Nyengaard, J.R. and Funch, P. 2011. Spermatozoon ultrastructure of Xenoturbella bocki (Westblad 1949). —Acta Zoologica (Stockholm) 92 : 109–115. Here, we report on the sperm ultrastructure of Xenoturbella bocki (Westblad 1949), which we studied for the first time in detail using light, scanning and transmission electron microscopy. The mature spermatozoa are of the bilaterian primitive type, also called aquasperm and develop as uniflagellate sperm consisting of a round head with distinct mitochondria at the base and a 9+2 flagellum of approximately 42 μm in length. The acrosomal complex consists of a small, round electron translucent acrosomal vesicle and a subacrosomal base. There is no separate midpiece, and the mitochondria surround the proximal and distal centriole in the posterior part of the head. The primitive structure of the spermatozoa suggests that these fertilize the egg by free spawning, probably the ancestral mode of fertilization in early bilaterians. When compared to the spermatozoa of other metazoans, we find that the arrangement of organelles in the Xenoturbella sperm shows similarities to a wide range of protostome and deuterostome taxa and does not seem to indicate any particular phylogenetic relationship.     

Fine Structural Observations on the Extracellular Matrix (ECM) of Xenoturbella bocki Westblad, 1949

Fine structural observations on the extracellular matrix (ECM) and connective tissue system of the enigmatic vermiform animal Xenoturbella bocki have demonstrated a complex and interesting organization of the ECM. Most conspicuous is the subepidermal membrane complex (SMC), and the major part of the ECM is present in this structure, which consists of a limiting basal lamina on each side of a central thick filamentous layer, probably of a collagenous nature. Distinct anchoring filaments are found as part of the SMC. A basal lamina is also observed in connection with the gastrodermal cells. The mesoderm is represented by a loose, ill-defined parenchyma, without filaments. The SMC is discussed in relation to subepidermal basal matrices occurring in turbellarians and enteropneusts, the two groups to which a relationship to Xenoturbella previously has been suggested. Comparisons between the ECM in Xenoturbella and in turbellarians do not support the notion of a relationship between these groups. Conversely, the present study strengthens previous indications of distinct similarities between certain characteristics of the epidermis and the SMC present in both enteropneusts and in Xenoturbella.     

Genetic analysis of the capsule polysaccharide (K antigen) and exopolysaccharide genes in pandemic <Emphasis Type="Italic">Vibrio parahaemolyticus</Emphasis> O3:K6

Background  

Pandemic Vibrio parahaemolyticus has undergone rapid changes in both K- and O-antigens, making detection of outbreaks more difficult. In order to understand these rapid changes, the genetic regions encoding these antigens must be examined. In Vibrio cholerae and Vibrio vulnificus, both O-antigen and capsular polysaccharides are encoded in a single region on the large chromosome; a similar arrangement in pandemic V. parahaemolyticus would help explain the rapid serotype changes. However, previous reports on "capsule" genes are controversial. Therefore, we set out to clarify and characterize these regions in pandemic V. parahaemolyticus O3:K6 by gene deletion using a chitin based transformation strategy.     

Comparative phylogeography of two co‐distributed but ecologically distinct rainbowfishes of far‐northern Australia

Aim

To test the influence of historical and contemporary environment in shaping the genetic diversity of freshwater fauna we contrast genetic structure in two co‐distributed, but ecologically distinct, rainbowfish; a habitat generalist (Melanotaenia splendida) and a habitat specialist (M. trifasciata).

Location

Fishes were sampled from far northern Australia (Queensland and Northern Territory).

Methods

We used sequence data from one mitochondrial gene and one nuclear gene to investigate patterns of genetic diversity in M. splendida and M. trifasciata to determine how differences in habitat preference and historical changes in drainage boundaries affected patterns of connectivity.

Results

Melanotaenia splendida showed high levels of genetic diversity and little population structure across its range. In contrast, M. trifasciata showed high levels of population structure. Whereas phylogeographic patterns differed, both species showed a strong relationship between geographical distance and genetic differentiation between populations. Melanotaenia splendida showed a shallower relationship with geographical distance, and genetic differentiation was best explained by stream length and a lower scaled ocean distance (11.98 times coast length). For M. trifasciata, genetic differentiation was best explained by overwater distance between catchments and ocean distance scaled at 1.16 × 10⁶ times coast length.

Main conclusions

Connectivity of freshwater populations inhabiting regions periodically interconnected during glacial periods appears to have been affected by ecological differences between species. Species‐specific differences are epitomized here by the contrast between co‐distributed congeners with different habitat requirements: for the habitat generalist, M. splendida, there was evidence for greater historical genetic connectivity with oceans as a weaker barrier to gene exchange in contrast with the habitat specialist, M. trifasciata.     

Predicting genome-wide redundancy using machine learning

Background  

Gene duplication can lead to genetic redundancy, which masks the function of mutated genes in genetic analyses. Methods to increase sensitivity in identifying genetic redundancy can improve the efficiency of reverse genetics and lend insights into the evolutionary outcomes of gene duplication. Machine learning techniques are well suited to classifying gene family members into redundant and non-redundant gene pairs in model species where sufficient genetic and genomic data is available, such as Arabidopsis thaliana, the test case used here.     

Classification of microarray data using gene networks

Background  

Microarrays have become extremely useful for analysing genetic phenomena, but establishing a relation between microarray analysis results (typically a list of genes) and their biological significance is often difficult. Currently, the standard approach is to map a posteriori the results onto gene networks in order to elucidate the functions perturbed at the level of pathways. However, integrating a priori knowledge of the gene networks could help in the statistical analysis of gene expression data and in their biological interpretation.     

A statistical analysis of the three-fold evolution of genomic compression through frame overlaps in prokaryotes

Background  

Among microbial genomes, genetic information is frequently compressed, exploiting redundancies in the genetic code in order to store information in overlapping genes. We investigate the length, phase and orientation properties of overlap in 58 prokaryotic species evaluating neutral and selective mechanisms of evolution.     

Genome-wide target profiling of <Emphasis Type="Italic">piggyBac</Emphasis> and <Emphasis Type="Italic">Tol2</Emphasis>in HEK 293: pros and cons for gene discovery and gene therapy

Background  

DNA transposons have emerged as indispensible tools for manipulating vertebrate genomes with applications ranging from insertional mutagenesis and transgenesis to gene therapy. To fully explore the potential of two highly active DNA transposons, piggyBac and Tol2, as mammalian genetic tools, we have conducted a side-by-side comparison of the two transposon systems in the same setting to evaluate their advantages and disadvantages for use in gene therapy and gene discovery.     

Candidate genes associated with bud dormancy release in blackcurrant (<Emphasis Type="Italic">Ribes nigrum</Emphasis>L.)

Background  

The detrimental effects of mild winter temperatures on the consistency of cropping of blackcurrant (Ribes nigrum L.) in parts of Europe have led to increasing interest in the genetic control of dormancy release in this species. This study examined patterns of gene expression in leaf buds of blackcurrant to identify key differential changes in these profiles around the time of budbreak.     

Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach

Background  

Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the clustering of functionally related genes observed in the highly rearranged chloroplast genome of the unicellular green alga Chlamydomonas reinhardtii, relative to ancestral chloroplast genomes.     

The <Emphasis Type="Italic">Mycoplasma pneumoniae</Emphasis> MPN229 gene encodes a protein that selectively binds single-stranded DNA and stimulates Recombinase A-mediated DNA strand exchange

Background  

Mycoplasma pneumoniae has previously been characterized as a micro-organism that is genetically highly stable. In spite of this genetic stability, homologous DNA recombination has been hypothesized to lie at the basis of antigenic variation of the major surface protein, P1, of M. pneumoniae. In order to identify the proteins that may be involved in homologous DNA recombination in M. pneumoniae, we set out to characterize the MPN229 open reading frame (ORF), which bears sequence similarity to the gene encoding the single-stranded DNA-binding (SSB) protein of other micro-organisms.     

What's in a name; Genetic structure in Solanum section Petota studied using population-genetic tools

Background  

The taxonomy and systematic relationships among species of Solanum section Petota are complicated and the section seems overclassified. Many of the presumed (sub)species from South America are very similar and they are able to exchange genetic material. We applied a population genetic approach to evaluate support for subgroups within this material, using AFLP data. Our approach is based on the following assumptions: (i) accessions that may exchange genetic material can be analyzed as if they are part of one gene pool, and (ii) genetic differentiation among species is expected to be higher than within species.     

Characterisation of the genetic diversity of <Emphasis Type="Italic">Brucella</Emphasis> by multilocus sequencing

Background  

Brucella species include economically important zoonotic pathogens that can infect a wide range of animals. There are currently six classically recognised species of Brucella although, as yet unnamed, isolates from various marine mammal species have been reported. In order to investigate genetic relationships within the group and identify potential diagnostic markers we have sequenced multiple genetic loci from a large sample of Brucella isolates representing the known diversity of the genus.     

Island selection on mammalian life-histories: genetic differentiation in offspring size

Background  

Since Darwin's pioneering work, evolutionary changes in isolated island populations of vertebrates have continued to provide the strongest evidence for the theory of natural selection. Besides macro-evolutionary changes, micro-evolutionary changes and the relative importance of natural selection vs. genetic drift are under intense investigation. Our study focuses on the genetic differentiation in morphological and life-history traits in insular populations of a small mammal the bank vole Myodes glareolus.     

Sequence similarity is more relevant than species specificity in probabilistic backtranslation

Background  

Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes backtranslation potentially ambiguous since most amino acids are encoded by multiple codons. The common approach to overcome this difficulty is based on imitation of codon usage within the target species.