Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

Cannon, Barbara, and Jan Nedergaard. Brown Adipose Tissue: Function and Physiological Significance. Physiol Rev 84: 277–359, 2004; 10.1152/physrev.00015.2003.—The function of brown adipose tissue i...

Brown Adipose Tissue: Function and Physiological Significance

The evidentiary basis of the currently accepted classification of living amphibians is discussed and shown not to warrant the degree of authority conferred on it by use and tradition. A new taxonomy of living amphibians is proposed to correct the deficiencies of the old one. This new taxonomy is based on the largest phylogenetic analysis of living Amphibia so far accomplished. We combined the comparative anatomical character evidence of Haas (2003) with DNA sequences from the mitochondrial transcription unit H1 (12S and 16S ribosomal RNA and tRNAValine genes, ≈ 2,400 bp of mitochondrial sequences) and the nuclear genes histone H3, rhodopsin, tyrosinase, and seven in absentia, and the large ribosomal subunit 28S (≈ 2,300 bp of nuclear sequences; ca. 1.8 million base pairs; x = 3.7 kb/terminal). The dataset includes 532 terminals sampled from 522 species representative of the global diversity of amphibians as well as seven of the closest living relatives of amphibians for outgroup comparisons. The...

https://bioone.org/journals/Bulletin-of-the-American-Museum-of-Natural-History/volume-2006/issue-297/0003-0090(2006)297[0001:TATOL]2.0.CO;2/THE-AMPHIBIAN-TREE-OF-LIFE/10.1206/0003-0090(2006)297[0001:TATOL]2.0.CO;2.pdf

The amphibian tree of life

Polyploids — organisms that have multiple sets of chromosomes — are common in certain plant and animal taxa, and can be surprisingly stable. The evidence that has emerged from genome analyses also indicates that many other eukaryotic genomes have a polyploid ancestry, suggesting that both humans and most other eukaryotes have either benefited from or endured polyploidy. Studies of polyploids soon after their formation have revealed genetic and epigenetic interactions between redundant genes. These interactions can be related to the phenotypes and evolutionary fates of polyploids. Here, I consider the advantages and challenges of polyploidy, and its evolutionary potential.

/pdf/the-advantages-and-disadvantages-of-being-polyploid-3szbdyr9u1.pdf

The advantages and disadvantages of being polyploid

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

/pdf/automated-eukaryotic-gene-structure-annotation-using-3fo28wpira.pdf

Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

transcriptomic shock’ [Buggs et al., 2011], rapid and repeated gene loss in young allopolyploids [Buggs et al., 2012b] as well as changes in polyploid gene expression [Roulin et al., 2012]. Schartl et al. [2013] hypothesize that paralog retention after ancient genome duplication may have supported the high level of behavioral complexity in some teleosts. A role of small RNAs in allopolyploid and hybrid gene expression has been suggested [Ignacio et al., 2012], which generate morphological variation and hybrid vigor as well as transgressive phenotypes with potential for adaptive evolution [Ng et al., 2012]. Latest studies propose a role of cis and trans -regulatory elements and chromatin modifications on gene expression diversity in allotetraploids [Shi et al., 2012]. Technological advances will soon also allow testing newly proposed mechanisms for gene expression in relation to cellular volume and genome size [Marguerat and Bähler, 2012]. Polyploidy is currently further studied regarding modifications of the cell cycle, biological networks, metabolic phenotypes, and in context to tumor biology [Mayfield-Jones et al., 2013]. Latest applications of research on ploidy changes include the creation of haploid mammalian pluripotent cell lines from which live transgenic mice could be produced [Li et al., 2012]. Despite its path-making character, not all the scientific progress depends on technology. Especially interactions between organisms of different ploidy levels ‘ Major botanical advances often suffer the worst of fates – the scientific community ignores them until they are independently ‘discovered’ or confirmed by zoologists. For example, the principles of inheritance, initially worked out in the garden pea were not generally accepted until verified in animals (Bateson 1902) ’ Rieseberg and Burke [2001]

Why Comparing Polyploidy Research in Animals and Plants

Arapaima gigas is one of the largest freshwater fish species of high ecological and economic importance. Overfishing and habitat destruction are severe threats to the remaining wild populations. By incorporating a chromosomal Hi-C contact map, we improved the arapaima genome assembly to chromosome-level, revealing an unexpected high degree of chromosome rearrangements during evolution of the bonytongues (Osteoglossiformes). Combining this new assembly with pool-sequencing of male and female genomes, we identified id2bbY, a duplicated copy of the inhibitor of DNA binding 2b (id2b) gene on the Y chromosome as candidate male sex-determining gene. A PCR-test for id2bbY was developed, demonstrating that this gene is a reliable male-specific marker for genotyping. Expression analyses showed that this gene is expressed in juvenile male gonads. Its paralog, id2ba, exhibits a male-biased expression in immature gonads. Transcriptome analyses and protein structure predictions confirm id2bbY as a prime candidate for the master sex-determiner. Acting through the TGFβ signaling pathway, id2bbY from arapaima would provide the first evidence for a link of this family of transcriptional regulators to sex determination. Our study broadens our current understanding about the evolution of sex determination genetic networks and provide a tool for improving arapaima aquaculture for commercial and conservation purposes.

A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas).

Presenting rats with a 0.9 per cent sodium chloride solution to drink instead of water had little or no effect on body weight gain and food intake, but resting oxygen consumption and total energy expenditure (corrected for body size) were elevated, and thermogenic responses to both noradrenaline and a meal were enhanced. Brown adipose tissue (BAT) mass and protein content were significantly elevated in saline treated rats, but mitochondrial GDP-binding capacity was depressed. Basal Na+, K+-ATPase activity was slightly increased in BAT homogenates from rats given saline, but noradrenaline-stimulated enzyme activity was much greater than control values. In rats drinking 1.8 per cent saline, energy intake, body weight gain and the efficiency of gain (g gain/MJ eaten) were all markedly depressed. BAT mass, corrected for differences in body size, was slightly greater than controls and the protein content of BAT was increased by 45 per cent. Rats allowed 0.9 per cent saline to drink for 7 d, and then presented with a palatable cafeteria diet, showed a more rapid rise in metabolic rate than cafeteria-fed animals drinking water. This difference was apparent only over the first 3-4 d of cafeteria feeding, and energy balance over 14 d was similar for both groups. These data show that increasing sodium intake with isotonic saline has very little effect on food intake or resting metabolic rate, but causes a marked increase in thermogenic capacity and responses to food or noradrenaline, probably because of an increase in active BAT mass. Changes in plasma ion concentrations or osmolarity, therefore, could be involved in the thermogenic response to food.

Influence of sodium intake on thermogenesis and brown adipose tissue in the rat

Effects of tube-feeding iso-energetic amounts of various dietary lipids on energy balance in the rat.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/raq.12542

Matthias Stöck

Papers

Why Comparing Polyploidy Research in Animals and Plants

A duplicated copy of id2b is an unusual sex-determining candidate gene on the Y chromosome of arapaima (Arapaima gigas).

Influence of sodium intake on thermogenesis and brown adipose tissue in the rat

Effects of tube-feeding iso-energetic amounts of various dietary lipids on energy balance in the rat.

The immune system of sturgeons and paddlefish (Acipenseriformes): a review with new data from a chromosome‐scale sturgeon genome