Big flies, small repeats: the "Thr-Gly" region of the period gene in Diptera

The region of the clock gene period (per) that encodes a repetitive tract of threonine-glycine (Thr-Gly) pairs has been compared between Dipteran species both within and outside the Drosophilidae. All the non- Drosophilidae sequences in this region are short and present a remarkably stable picture compared to the Drosophilidae, in which the region is much larger and extremely variable, both in size and composition. The accelerated evolution in the repetitive region of the Drosophilidae appears to be mainly due to an expansion of two ancestral repeats, one encoding a Thr-Gly dipeptide and the other a pentapeptide rich in serine, glycine, and asparagine or threonine. In some drosophilids the expansion involves a duplication of the pentapeptide sequence, but in Drosophila pseudoobscura both the dipeptide and the pentapeptide repeats are present in larger numbers. In the nondrosophilids, however, the pentapeptide sequence is represented by one copy and the dipeptide by two copies. These observations fulfill some of the predictions of recent theoretical models that have simulated the evolution of repetitive sequences.      

Adaptations to in situ feeding: novel nutrient acquisition pathways in an ancient vertebrate

During feeding, hagfish may immerse themselves in the body cavities of decaying carcasses, encountering high levels of dissolved organic nutrients. We hypothesized that this feeding environment might promote nutrient acquisition by the branchial and epidermal epithelia. The potential for Pacific hagfish, Eptatretus stoutii, to absorb amino acids from the environment across the skin and gill was thus investigated. l-alanine and glycine were absorbed via specific transport pathways across both gill and skin surfaces, the first such documentation of direct organic nutrient acquisition in a vertebrate animal. Uptake occurred via distinct mechanisms with respect to concentration dependence, sodium dependence and effects of putative transport inhibitors across each epithelium. Significant differences in the absorbed amino acid distribution between the skin of juveniles and adults were noted. The ability to absorb dissolved organic matter across the skin and gill may be an adaptation to a scavenging lifestyle, allowing hagfish to maximize sporadic opportunities for organic nutrient acquisition. From an evolutionary perspective, hagfish represent a transitory state between the generalized nutrient absorption pathways of aquatic invertebrates and the more specialized digestive systems of aquatic vertebrates.     

Gastrointestinal processing of Na+, Cl-, and K+ during digestion: implications for homeostatic balance in freshwater rainbow trout

The role of the gastrointestinal tract in maintaining ionic homeostasis during digestion, as well as the relative contribution of the diet for providing electrolytes, has been generally overlooked in many aquatic species. An experimental diet that contained an inert reference marker (lead-glass beads) was used to quantify the net transport of Na(+), K(+), and Cl(-) during the digestion and absorption of a single meal (3% ration) by freshwater rainbow trout (Oncorhynchus mykiss). Secretion of Cl(-) into the stomach peaked at 8 and 12 h following feeding at a rate of 1.1 mmol.kg(-1).h(-1), corresponding to a theoretical pH of 0.6 in the secreted fluid (i.e., 240 mmol/l HCl). The majority ( approximately 90%) of dietary Na(+) and K(+) was absorbed in the stomach, whereas subsequent large fluxes of Na(+) and Cl(-) into the anterior intestine corresponded to a large flux of water previously observed. The estimated concentration of Na(+) in fluids secreted into the anterior intestine was approximately 155 mmol/l, equivalent to reported hepatic bile values, whereas the estimated concentration of Cl(-) ( approximately 285 mmol/l) suggested seepage of HCl acid from the stomach in advance of the chyme front. Net absorption of K(+) in the stomach occurred following the cessation of Cl(-) secretion, providing indirect evidence of K(+) involvement with HCl acid production. Overall, 80-90% of the K(+) and Cl(-) contents of the meal were absorbed on a net basis, whereas net Na(+) absorption was negligible. Chyme-to-plasma ion concentration gradients were often opposed to the direction of ion transport, especially for Na(+) and Cl(-).     

Dissection of a metastatic gene expression signature into distinct components

Background

Metastasis, the process whereby cancer cells spread, is in part caused by an incompletely understood interplay between cancer cells and the surrounding stroma. Gene expression studies typically analyze samples containing tumor cells and stroma. Samples with less than 50% tumor cells are generally excluded, thereby reducing the number of patients that can benefit from clinically relevant signatures.

Results

For a head-neck squamous cell carcinoma (HNSCC) primary tumor expression signature that predicts the presence of lymph node metastasis, we first show that reduced proportions of tumor cells results in decreased predictive accuracy. To determine the influence of stroma on the predictive signature and to investigate the interaction between tumor cells and the surrounding microenvironment, we used laser capture microdissection to divide the metastatic signature into six distinct components based on tumor versus stroma expression and on association with the metastatic phenotype. A strikingly skewed distribution of metastasis associated genes is revealed.

Conclusion

Dissection of predictive signatures into different components has implications for design of expression signatures and for our understanding of the metastatic process. Compared to primary tumors that have not formed metastases, primary HNSCC tumors that have metastasized are characterized by predominant down-regulation of tumor cell specific genes and exclusive up-regulation of stromal cell specific genes. The skewed distribution agrees with poor signature performance on samples that contain less than 50% tumor cells. Methods for reducing tumor composition bias that lead to greater predictive accuracy and an increase in the types of samples that can be included are presented.     

Characterisation of <Emphasis Type="SmallCaps">l</Emphasis>-alanine and glycine absorption across the gut of an ancient vertebrate

This study utilised an in vitro technique to characterise absorption of two amino acids across the intestinal epithelium of Pacific hagfish, Eptatretus stoutii. Uptake of l-alanine and glycine conformed to Michaelis–Menten kinetics. An uptake affinity (K _m; substrate concentration required to attain a 50% uptake saturation) of 7.0 mM and an uptake capacity (J _max) of 83 nmol cm⁻² h⁻¹ were described for l-alanine. The K _m and J _max for glycine were 2.2 mM and 11.9 nmol cm⁻² h⁻¹, respectively. Evidence suggested that the pathways of l-alanine and glycine absorption were shared, and sodium dependent. Further analysis indicated that glycine uptake was independent of luminal pH and proline, but a component of uptake was significantly impaired by 100-fold excesses of threonine or asparagine. The presence of a short-term (24 h) exposure to waterborne glycine, similar in nature to that which may be expected to occur when feeding inside an animal carcass, had no significant impact on gastrointestinal glycine uptake. This may indicate a lack of cross talk between absorptive epithelia. These results are the first published data to describe gastrointestinal uptake of an organic nutrient in the oldest extant vertebrate and may provide potential insight into the evolution of nutrient transport systems.