Transposable element and host silencing activity in gigantic genomes.

Transposable elements (TEs) and the silencing machinery of their hosts are engaged in a germline arms-race dynamic that shapes TE accumulation and, therefore, genome size. In animal species with extremely large genomes (>10 Gb), TE accumulation has been pushed to the extreme, prompting the question of whether TE silencing also deviates from typical conditions. To address this question, we characterize TE silencing two pathways-the piRNA pathway and KRAB-ZFP transcriptional repression-in the male and female gonads of , a salamander species with a ∼21 Gb genome.

Genome size drives morphological evolution in organ-specific ways.

Morphogenesis is an emergent property of biochemical and cellular interactions during development. Genome size and the correlated trait of cell size can influence these interactions through effects on developmental rate and tissue geometry, ultimately driving the evolution of morphology. We tested whether variation in genome and body size is related to morphological variation in the heart and liver using nine species of the salamander genus Plethodon (genome sizes 29-67 gigabases).

Gigantic Genomes Provide Empirical Tests of Transposable Element Dynamics Models.

Transposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and changes to anatomy and physiology.

Forever young: Linking regeneration and genome size in salamanders.

Background: Salamanders stand out among vertebrate animals in two key characteristics: their ability to regenerate body parts, and their large and variable genome sizes.

Results: Here we show how to unite seemingly disparate facets of salamander biology, regeneration ability, and genome size variation, into one synthetic view. Large and variable genome sizes may be the key to understanding the prodigious ability of most salamanders to regenerate damaged or lost body parts.

Miniaturization, Genome Size, and Biological Size in a Diverse Clade of Salamanders.

AbstractGenome size (C-value) can affect organismal traits across levels of biological organization from tissue complexity to metabolism. Neotropical salamanders show wide variation in genome and body sizes, including several clades with miniature species. Because miniaturization imposes strong constraints on morphology and development and because genome size is strongly correlated with cell size, we hypothesize that body size has played an important role in the evolution of genome size in bolitoglossine salamanders.

Reflections on Bateson's rule: Solving an old riddle about why extra legs are mirror-symmetric.

William Bateson was an obsessive observer of animal oddities, and at some point in his herculean survey of museum collections leading up to his monumental 1894 monograph (Materials for the study of variation), he noticed a peculiar trend among the preserved specimens (mainly insects) that possessed extra legs: multiple legs that branched from the same socket tended to be mirror images of their adjacent neighbors. He did not know why. These symmetry relationships have come to be known as Bateson's rule, and they have defied a satisfactory explanation for 125 years.

Morphological Polymorphism Associated with Alternative Reproductive Tactics in a Plethodontid Salamander.

Understanding polymorphism is a central problem in evolution and ecology, and alternative reproductive tactics (ARTs) provide compelling examples for studying the origin and maintenance of behavioral and morphological variation. Much attention has been given to examples where "parasitic" individuals exploit the reproductive investment of "bourgeois" individuals, but some ARTs are instead maintained by environmental heterogeneity, with alternative tactics exhibiting differential fitness in discontinuous reproductive niches. We use genomic, behavioral, karyological, and field observational data to demonstrate one such example in plethodontid salamanders.

Genetic Modification of Grapevine Embryogenic Cultures.

Precision breeding is an approach to grapevine genetic improvement that transfers only specific traits among sexually compatible species via the relatively stable mitotic cell division pathway in order to avoid the significant disruption imposed upon conventional breeding by meiosis. Factors enabling precision breeding include the availability of the Vitis genome sequence combined with highly optimized gene insertion and plant regeneration protocols. A protocol for the production of grapevine embryogenic cultures and their genetic transformation is described.

Intercomparison of methods of coupling between convection and large-scale circulation: 2. Comparison over nonuniform surface conditions.

As part of an international intercomparison project, the weak temperature gradient (WTG) and damped gravity wave (DGW) methods are used to parameterize large-scale dynamics in a set of cloud-resolving models (CRMs) and single column models (SCMs). The WTG or DGW method is implemented using a configuration that couples a model to a reference state defined with profiles obtained from the same model in radiative-convective equilibrium. We investigated the sensitivity of each model to changes in SST, given a fixed reference state.

Intercomparison of methods of coupling between convection and large-scale circulation: 1. Comparison over uniform surface conditions.

As part of an international intercomparison project, a set of single-column models (SCMs) and cloud-resolving models (CRMs) are run under the weak-temperature gradient (WTG) method and the damped gravity wave (DGW) method. For each model, the implementation of the WTG or DGW method involves a simulated column which is coupled to a reference state defined with profiles obtained from the same model in radiative-convective equilibrium. The simulated column has the same surface conditions as the reference state and is initialized with profiles from the reference state.

Evidence for Sex Chromosome Turnover in Proteid Salamanders.

A major goal of genomic and reproductive biology is to understand the evolution of sex determination and sex chromosomes. Species of the 2 genera of the Salamander family Proteidae - Necturus of eastern North America, and Proteus of Southern Europe - have similar-looking karyotypes with the same chromosome number (2n = 38), which differentiates them from all other salamanders. However, Necturus possesses strongly heteromorphic X and Y sex chromosomes that Proteus lacks.

Does the early frog catch the worm? Disentangling potential drivers of a parasite age-intensity relationship in tadpoles.

The manner in which parasite intensity and aggregation varies with host age can provide insights into parasite dynamics and help identify potential means of controlling infections in humans and wildlife. A significant challenge is to distinguish among competing mechanistic hypotheses for the relationship between age and parasite intensity or aggregation. Because different mechanisms can generate similar relationships, testing among competing hypotheses can be difficult, particularly in wildlife hosts, and often requires a combination of experimental and model fitting approaches.

Explanations for deformed frogs: plenty of research left to do (a response to Skelly and Benard).

Our recent study (Ballengeé and Sessions, 2009. J Exp Zool (Mol Dev Evol) 312B:1-10) shows that deformed frogs with missing limbs can be explained by sublethal "selective predation" by predators that are too small, or have mouthparts that are too small, to consume whole tadpoles. Skelly and Benard do not agree with our conclusions and feel that they are not well founded.

Explanation for missing limbs in deformed amphibians.

We present evidence that the most commonly found deformities in wild-caught amphibians, those featuring missing limbs and missing limb segments, may be the result of selective predation. Here we report that predatory dragonfly nymphs can severely injure and even fully amputate developing hind limbs of anuran tadpoles. Developmental responses of the injured/amputated tadpole limbs range from complete regeneration to no regeneration, with intermediate conditions represented by various idiosyncratic limb deformities, depending mainly on the developmental stage of the tadpole at the time of injury/amputation.

The necessity of Darwin: this journal's tribute to the most influential scientist of all time.

Charles Darwin is considered by many to be one of the most influential scientists of all time. His theory of evolution via natural selection was astonishingly prescient in terms of what modern biology has revealed in the 150 years since the publication of The Origin of Species, especially since Darwin was unaware of even the most fundamental aspects of transmission genetics, not to mention molecular biology. Here we speculate what impact it would have had on Darwin's thinking if he had known what we now know about molecular biology and cytogenetics.

Functional evaluation of isolated zebrafish hearts.

Traditional working heart preparations, based on the original Langendorff setup, are widely used experimental models that have tremendously advanced the cardiovascular field. However, these systems can be deceivingly complex, requiring the maintenance of pH with CO(2), the delivery of oxygenated perfusate, and the need for extensive laboratory equipment. We have examined the feasibility of using isolated zebrafish (Danio rerio) hearts as an experimental model system, in which experimental procedures can be performed in the absence of the traditional requirements and sophisticated setup equipment.

Understanding the net effects of pesticides on amphibian trematode infections.

Anthropogenic factors can have simultaneous positive and negative effects on parasite transmission, and thus it is important to quantify their net effects on disease risk. Net effects will be a product of changes in the survival and traits (e.g.

Cytogenetic analysis of the Asian plethodontid salamander, Karsenia koreana: evidence for karyotypic conservation, chromosome repatterning, and genome size evolution.

A cytogenetic analysis, including the karyotype, C-bands, silver-stained nucleolus organizer regions and genome size, was performed on the recently discovered species, Karsenia koreana, the first plethodontid salamander from Asia. The karyotype consists of 14 pairs of bi-armed chromosomes, with no evidence of heteromorphic sex chromosomes. C-banding reveals a concentration of heterochromatin at the centromeres as well as at interstitial locations.