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.      

The ability of an environmental isolate of Pseudomonas fluorescens to utilize chrysene and other four-ring polynuclear aromatic hydrocarbons

A Pseudomonas fluorescens strain isolated from exhausted-oil-polluted soil was selected for its ability to grow on and degrade chrysene as a sole carbon source. The same strain was able to grow on and degrade benz[a]anthracene, benzo[b]naphthothiophene, but not benz[a]acridine. After 2 days of incubation on a mineral medium supplemented with chrysene at 1 g/ml, reached by adding the Polynuclear aromatic hydrocarbon dissolved in a water-miscible solvent to the medium, the cell number had increased by 10²–10³. The biodegradation rate followed first-order kinetics and at its maximum value was independent of substrate concentration, as happens when the substrates are solubilized.     

Changes in pyridine and adenine nucleotide levels in Friend erythroleukaemia cells during growth and differentiation.

Pyridine and adenine nucleotide levels were measured in Friend erythroleukaemia cells (FELC) stimulated to growth and induced to differentiate by hexamethylene bisacetamide (HMBA) and N'-methylnicotinamide (N'-MNAM). A three- to fourfold increase in the NADP(H) was found to parallel cell growth stimulation in both the presence and absence of differentiation inducers. NAD(H) increased about twofold in control and to a minor extent in HMBA-treated FELC but did not vary significantly in N'-MNAM-treated cells. ATP was significantly higher in control cells stimulated to growth than in resting ones, but it did not vary in inducer-treated cells. These data confirm the relationship between high NADP(H) levels and cell resumption to growth; moreover they show that NAD(H) pool reduction and NAD/NADH ratio rise are associated with the process of FELC differentiation. The activities of NAD pyrophosphorylase and NAD kinase are much more enhanced in growth-stimulated FELC than in resting ones. On the other hand transition from the quiescent to the proliferative state was accompanied by a decrease in the activity of poly(ADP-ribose) polymerase. A decrease in poly(ADP-ribose) polymerase activity was also found in differentiated cells in contrast to controls.     

Observations on the female internal reproductive organs of the brown howler monkey (Alouatta guariba clamitans)

Alouatta guariba clamitans (brown howler monkey) is an endemic primate from the southeastern Brazil tropical forests, classified as near threatened by the IUCN Red List 2007. The genus Alouatta is one of the most difficult New World monkeys to breed and rear in captivity. In this study we examined the macroscopic and histological aspects of the female genital tract of wild brown howler monkeys to provide baseline information for future reproduction research. The anatomical relationship between the vagina, uterus, broad ligament, oviducts and ovaries are those of a typical primate reproductive tract. The fundic portion of the uterus is globoid, the cervix is well developed, which confers to the uterus an elongated shape, and the vagina is a long flattened channel. Histological analysis conducted in females in the follicular phase revealed large quantities of interstitial luteinized tissue in the ovaries, a stratified nonkeratinized vaginal epithelium, lack of glands in the vaginal mucosa and simple tubular endometrial glands. The observed anatomical features should be considered in the adaptation and application of assisted reproductive techniques aimed at improving captive reproduction for species conservation. Am. J. Primatol. 71:145–152, 2009. © 2008 Wiley‐Liss, Inc.     

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.