Rhomboid domain containing 2 (RHBDD2): A novel cancer-related gene over-expressed in breast cancer

In the course of breast cancer global gene expression studies, we identified an uncharacterized gene known as RHBDD2 (Rhomboid domain containing 2) to be markedly over-expressed in primary tumors from patients with recurrent disease. In this study, we identified RHBDD2 mRNA and protein expression significantly elevated in breast carcinomas compared with normal breast samples as analyzed by SAGE (n = 46) and immunohistochemistry (n = 213). Interestingly, specimens displaying RHBDD2 over-expression were predominantly advanced stage III breast carcinomas (p = 0.001). Western-blot, RT-PCR and cDNA sequencing analyses allowed us to identify two RHBDD2 alternatively spliced mRNA isoforms expressed in breast cancer cell lines. We further investigated the occurrence and frequency of gene amplification and over-expression affecting RHBDD2 in 131 breast samples. RHBDD2 gene amplification was detected in 21% of 98 invasive breast carcinomas analyzed. However, no RHBDD2 amplification was detected in normal breast tissues (n = 17) or breast benign lesions (n = 16) (p = 0.014). Interestingly, siRNA-mediated silencing of RHBDD2 expression results in a decrease of MCF7 breast cancer cells proliferation compared with the corresponding controls (p = 0.001). In addition, analysis of publicly available gene expression data showed a strong association between high RHBDD2 expression and decreased overall survival (p = 0.0023), relapse-free survival (p = 0.0013), and metastasis-free interval (p = 0.006) in patients with primary ER-negative breast carcinomas. In conclusion, our findings suggest that RHBDD2 over-expression behaves as an indicator of poor prognosis and may play a role facilitating breast cancer progression.     

Population structure in the catfish Trichogenes longipinnis: drift offset by asymmetrical migration in a tiny geographic range

Based on population genetic theory and empirical studies of small populations, we expect that species with very small ranges (narrow endemics) will exhibit reduced genetic diversity, increasing their susceptibility to the negative effects of genetic homogeneity. Although this pattern of reduced diversity applies to most narrow endemics, conservation biologists have yet to identify a general pattern for the degree of spatial population genetic structure expected in species with very small ranges. In part, this is because the degree of population structure within narrow endemics will be highly variable depending on the equilibrium between the homogenizing effects of dispersal and the diversifying effects of drift and local selection in small populations, thus precluding general predictions about the relative importance of small range, small population sizes, and habitat patchiness for maintaining genetic diversity in narrowly-distributed species. We document a striking example of high population structure in the tiny geographic range of a stream-dwelling catfish, Trichogenes longipinnis , endemic to the Atlantic Forest of Brazil. The maintenance of this diversity results from a combination of asymmetrical and limited dispersal, and drift in small populations. Our results highlight the need to understand population structure, and not only overall genetic diversity, of narrowly-distributed species for their conservation planning.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 97 , 259–274.     

Movement of Endogenous Calcium in the Elongating Zone of Graviresponding Roots of Zea mays

Endogenous calcium (Ca) accumulates along the lower side ofthe elongating zone of horizontally oriented roots of Zea mayscv. Yellow Dent. This accumulation of Ca correlates positivelywith the onset of gravicurvature, and occurs in the cytoplasm,cell walls and mucilage of epidermal cells. Corresponding changesin endogenous Ca do not occur in cortical cells of the elongatingzone of intact roots. These results indicate that the calciumasymmetries associated with root gravicurvature occur in theoutermost layers of the root Calcium, corn, gravitropism (root), Zea mays     

YMXM motifs and signaling by an insulin receptor substrate 1 molecule without tyrosine phosphorylation sites.

Tyrosine phosphorylation of insulin receptor substrate 1 (IRS-1) by the activated receptors for insulin, IGF-1, and various cytokines creates binding sites for signaling proteins with Src homology 2 domains (SH2 proteins). Determining the role of specific SH2 proteins during insulin signaling has been difficult because IRS-1 possesses as many as 18 potential tyrosine phosphorylation sites, several of which contain redundant motifs. Using 32D cells, which contain no endogenous IRS proteins, we compared the signaling ability of an IRS-1 molecule in which 18 potential tyrosine phosphorylation sites were replaced by phenylalanine (IRS-1(F18)) with two derivative molecules which retained three YMXM motifs (IRS-1(3YMXM)) or the two COOH-terminal SHP2-Fyn binding sites (IRS-1(YCT)). During insulin stimulation, IRS-1(F18) failed to undergo tyrosine phosphorylation or mediate activation of the phosphotidylinositol (PI) 3'-kinase or p70(s6k); IRS-1(YCT) was tyrosine phosphorylated but also failed to mediate these signaling events. Neither IRS-1(3YMXM) nor IRS-1(YCT) mediated activation of mitogen-activated protein kinases. IRS-1(F18) and IRS-1(YCT) partially mediated similar levels of insulin-stimulated mitogenesis at high insulin concentrations, however, suggesting that IRS-1 contains phosphotyrosine-independent elements which effect mitogenic signals, and that the sites in IRS-l(YCT) do not augment this signal. IRS-1(3YMXM) mediated the maximal mitogenic response to insulin, although the response to insulin was more sensitive with wild-type IRS-1. By contrast, the association of IRS-1(3YMXM) with PI 3'-kinase was more sensitive to insulin than the association with IRS-1. Thus, the binding of SH2 proteins (such as PI 3'-kinase) by YMXM motifs in IRS-1 is an important element in the mitogenic response, but other elements are essential for full mitogenic sensitivity.     

Seasonal hysteresis of net ecosystem exchange in response to temperature change: patterns and causes

Understanding how net ecosystem exchange (NEE) changes with temperature is central to the debate on climate change‐carbon cycle feedbacks, but still remains unclear. Here, we used eddy covariance measurements of NEE from 20 FLUXNET sites (203 site‐years of data) in mid‐ and high‐latitude forests to investigate the temperature response of NEE. Years were divided into two half thermal years (increasing temperature in spring and decreasing temperature in autumn) using the maximum daily mean temperature. We observed a parabolic‐like pattern of NEE in response to temperature change in both the spring and autumn half thermal years. However, at similar temperatures, NEE was considerably depressed during the decreasing temperature season as compared with the increasing temperature season, inducing a counter‐clockwise hysteresis pattern in the NEE–temperature relation at most sites. The magnitude of this hysteresis was attributable mostly (68%) to gross primary production (GPP) differences but little (8%) to ecosystem respiration (ER) differences between the two half thermal years. The main environmental factors contributing to the hysteresis responses of NEE and GPP were daily accumulated radiation. Soil water content (SWC) also contributed to the hysteresis response of GPP but only at some sites. Shorter day length, lower light intensity, lower SWC and reduced photosynthetic capacity may all have contributed to the depressed GPP and net carbon uptake during the decreasing temperature seasons. The resultant hysteresis loop is an important indicator of the existence of limiting factors. As such, the role of radiation, LAI and SWC should be considered when modeling the dynamics of carbon cycling in response to temperature change.     

An experimental study of the influence of periphytic algae on invertebrate abundance in a Hong Kong stream

1. Small cages (294cm²) containing unglazed clay quarry tiles were used to investigate the influence of periphytic algae on macroinvertebrate abundance in a Hong Kong stream. Algal biomass was manipulated by shading cages with plastic sheets. Individual cages were assigned to one of three treatment groups: unshaded, shaded and deeply shaded. Invertebrate densities and algal biomass within cages were monitored after 23, 37 and 65 days. 2. Multiple-regression analysis revealed that algal biomass, invertebrate morphospecies richness and total abundance declined with greater shading intensity. The responses of individual invertebrate taxa varied: some (especially Trichoptera) were unaffected by shading, whereas grazers (Baetidae, Psephenidae and Elmidae) declined as shading increased. 3. Significant regressions of the densities of individual taxa upon algal and detrital standing stocks in cages had positive slopes, but algal biomass increased during the study while detrital standing stocks declined. Abundance of invertebrates declined or remained rather stable over time. Density increases resulting from a positive association with algae were apparently offset by declines in abundance correlated with reductions in detritus. 4. Declines in algal biomass were associated with greater shading to which animals may respond directly. To uncouple the link between scarcity of algae and reduction of light intensity, the plastic covers on two groups of cages (deeply shaded and unshaded) which had been placed in the stream for 28 days were reversed so that cages which had been shaded became unshaded and vice versa. The cages were recovered on day 33, Only Coleoptera demonstrated a positive association with atgae inside cages; no relationship between population densities and algal biomass or light intensity was apparent for other taxa. However, the design may have been confounded by deposition of sediment in the cages (due to declining stream discharge) which reduced population densities of colonizers. 5. This study documents changes in invertebrate abundance and morphospecies richness in response periphyton and detritus standing stocks within patches. Summation of such responses may account for observed variations in benthic communities among Hong Kong streams which differ in the extent of shading by riparian vegetation.     

Ecological and evolutionary factors in the morphological diversification of South American spiny rats

Understanding the processes underlying morphological diversification is a central goal in ecology and evolutionary biology and requires the integration of information about phylogenetic divergence and ecological niche diversity. In the present study, we use geometric morphometrics and comparative methods to investigate morphological diversification in Neotropical spiny rats of the family Echimyidae. Morphological diversification is studied as shape variation in the skull, comprising a structure composed of four distinct units: vault, base, orognathofacial complex, and mandible. We demonstrate association among patterns of variation in shape in different cranial units, levels of phylogenetic divergence, and ecological niche diversification. At the lower level of phylogenetic divergence, there is significant and positive concordance between patterns of phylogenetic divergence and cranial shape variation in all cranial units. This concordance may be attributable to the phylogenetic and shape distances being calculated between species that occupy the same niche. At higher phylogenetic levels of divergence and with ecological niche diversity, there is significant concordance between shape variation in all four cranial units and the ecological niches. In particular, the orognathofacial complex revealed the most significant association between shape variation and ecological niche diversity. This association may be explained by the great functional importance of the orognathofacial complex.  © 2009 The Linnean Society of London, Biological Journal of the Linnean Society , 2009, 98 , 646–660.     

Hair-Trap Efficacy for Detecting Mammalian Carnivores in the Tropics

Abstract: Direct studies of mammalian carnivores are challenging due to the animals' secretive nature and the high costs associated with their capture and handling. Use of noninvasive hair sampling to survey these reclusive species has great potential as an alternative, with wide applicability in ecology and conservation. Hair-trapping has been extensively used for focal studies of temperate mammals, but its use and applicability as a means to survey mammals in tropical environs has never been addressed. We evaluated the effectiveness of 2 hair-trap types and 2 scents along an elevational gradient within El Cielo Biosphere Reserve (ECBR, Mexico) to detect presence of carnivores. Hair-traps that used roofing nails as a hair-collecting surface collected more hairs and detected a greater number of species than did hair-traps that used velcro strips. Different scent treatments (commercial fragrance and catnip oil) did not differ for these same variables. Of successful nail hair-traps, 60% collected ≥20 hairs (max. = 439), providing enough material for DNA analyses. Hair-trap surveys detected 74% of the potential target mammal species at ECBR with only 19 days of field effort. Developing countries have limited budgets for biodiversity monitoring and hair-traps compare favorably with other methods with a high cost-benefit ratio. Hair-traps are inexpensive, portable, can be made with over-the-counter materials, and can be successfully used to collect data applicable to population and genetic studies of tropical carnivores.     

Belowground infections of the invasive Phytophthora plurivora pathogen enhance the suitability of red oak leaves to the generalist herbivore Lymantria dispar

1. Globally, vast areas of forest are currently threatened by Lymantria dispar L. and Phytophthora species, which cause widespread declines and cascading ecological impacts. One important aim of evolutionary and ecological studies is to understand their interactions. 2. The present study tests whether Quercus rubra L. trees naturally infected with P. plurivora T. Jung & T.I. Burgess or free of infection are more suitable for L. dispar herbivory, and if relationships between L. dispar performance and herbivory may vary depending on whether trees are infected or free of infection. 3. In choice tests, the consumed area of leaves from trees infected by P. plurivora was four times larger than that from non‐infected trees, probably because the increased values of N, soluble protein, and water content observed in the leaves of infected trees enhanced acceptability. Although larval performance was better in Phytophthora‐infected trees, relationships between larval performance and defoliation did not significantly interact with the health status of trees. 4. The present results suggest that the impact of P. plurivora on natural and managed ecosystems may generate a positive feedback loop for oak decline. The link between the behavioural and physiological responses of L. dispar to infected trees and the population growth in nature deserves further investigation.     

Soil water repellency and its implications for organic matter decomposition – is there a link to extreme climatic events?

Earth system models associate the ongoing global warming with increasing frequency and intensity of extreme events such as droughts and heat waves. The carbon balance of soils may be more sensitive to the impact of such extremes than to homogeneously distributed changes in soil temperature (T_s) or soil water content (θ_s). One parameter influenced by more pronounced drying/rewetting cycles or increases in T_s is the wettability of soils. Results from laboratory and field studies showed that low θ_s, particularly in combination with high T_s can increase soil water repellency (SWR). Recent studies have provided evidence that the stability of soil organic matter (SOM) against microbial decomposition is substantially enhanced in water repellent soils. This review hypothesizes that SWR is an important SOM stabilization mechanism that could become more important because of the increase in extreme events. We discuss wettability‐induced changes in soil moisture distribution and in soil aggregate turnover as the main mechanisms explaining the reduced mineralization of SOM with increasing SWR. The creation of preferential flow paths and subsequent uneven penetration of rainwater may cause a long‐term reduction of soil water availability, affecting both microorganisms and plants. We conclude that climate change‐induced SWR may intensify the effects of climatic drought and thus affects ecosystem processes such as SOM decomposition and plant productivity, as well as changes in vegetation and microbial community structure. Future research on biosphere–climate interactions should consider the effects of increasing SWR on soil moisture and subsequently on both microbial activity and plant productivity, which ultimately determine the overall carbon balance.