Species Detection and Identification in Sexual Organisms Using Population Genetic Theory and DNA Sequences

Phylogenetic trees of DNA sequences of a group of specimens may include clades of two kinds: those produced by stochastic processes (random genetic drift) within a species, and clades that represent different species. The ratio of the mean pairwise sequence difference between a pair of clades (K) to the mean pairwise sequence difference within a clade (θ) can be used to determine whether the clades are samples from different species (K/θ≥4) or the same species (K/θ<4) with probability ≥0.95. Previously I applied this criterion to delimit species of asexual organisms. Here I use data from the literature to show how it can also be applied to delimit sexual species using four groups of sexual organisms as examples: ravens, spotted leopards, sea butterflies, and liverworts. Mitochondrial or chloroplast genes are used because these segregate earlier during speciation than most nuclear genes and hence detect earlier stages of speciation. In several cases the K/θ ratio was greater than 4, confirming the original authors'' intuition that the clades were sufficiently different to be assigned to different species. But the K/θ ratio split each of two liverwort species into two evolutionary species, and showed that support for the distinction between the common and Chihuahuan raven species is weak. I also discuss some possible sources of error in using the K/θ ratio; the most significant one would be cases where males migrate between different populations but females do not, making the use of maternally inherited organelle genes problematic. The K/θ ratio must be used with some caution, like all other methods for species delimitation. Nevertheless, it is a simple theory-based quantitative method for using DNA sequences to make rigorous decisions about species delimitation in sexual as well as asexual eukaryotes.     

Associations between White Matter Hyperintensities and β Amyloid on Integrity of Projection,Association, and Limbic Fiber Tracts Measured with Diffusion Tensor MRI

The goal of this study was to assess the relationship between Aβ deposition and white matter pathology (i.e., white matter hyperintensities, WMH) on microstructural integrity of the white matter. Fifty-seven participants (mean age: 78±7 years) from an ongoing multi-site research program who spanned the spectrum of normal to mild cognitive impairment (Clinical dementia rating 0–0.5) and low to high risk factors for arteriosclerosis and WMH pathology (defined as WMH volume >0.5% total intracranial volume) were assessed with positron emission tomography (PET) with Pittsburg compound B (PiB) and magnetic resonance and diffusion tensor imaging (DTI). Multivariate analysis of covariance were used to investigate the relationship between Aβ deposition and WMH pathology on fractional anisotropy (FA) from 9 tracts of interest (i.e., corona radiata, internal capsule, cingulum, parahippocampal white matter, corpus callosum, superior longitudinal, superior and inferior front-occipital fasciculi, and fornix). WMH pathology was associated with reduced FA in projection (i.e., internal capsule and corona radiate) and association (i.e., superior longitudinal, superior and inferior fronto-occipital fasciculi) fiber tracts. Aβ deposition (i.e., PiB positivity) was associated with reduced FA in the fornix and splenium of the corpus callosum. There were interactions between PiB and WMH pathology in the internal capsule and parahippocampal white matter, where Aβ deposition reduced FA more among subjects with WMH pathology than those without. However, accounting for apoE ε4 genotype rendered these interactions insignificant. Although this finding suggests that apoE4 may increase amyloid deposition, both in the parenchyma (resulting in PiB positivity) and in blood vessels (resulting in amyloid angiopathy and WMH pathology), and that these two factors together may be associated with compromised white matter microstructural integrity in multiple brain regions, additional studies with a longitudinal design will be necessary to resolve this issue.     

A Positive GATA Element and a Negative Vitamin D Receptor-Like Element Control Atrial Chamber-Specific Expression of a Slow Myosin Heavy-Chain Gene during Cardiac Morphogenesis

We have used the slow myosin heavy chain (MyHC) 3 gene to study the molecular mechanisms that control atrial chamber-specific gene expression. Initially, slow MyHC 3 is uniformly expressed throughout the tubular heart of the quail embryo. As cardiac development proceeds, an anterior-posterior gradient of slow MyHC 3 expression develops, culminating in atrial chamber-restricted expression of this gene following chamberization. Two cis elements within the slow MyHC 3 gene promoter, a GATA-binding motif and a vitamin D receptor (VDR)-like binding motif, control chamber-specific expression. The GATA element of the slow MyHC 3 is sufficient for expression of a heterologous reporter gene in both atrial and ventricular cardiomyocytes, and expression of GATA-4, but not Nkx2-5 or myocyte enhancer factor 2C, activates reporter gene expression in fibroblasts. Equivalent levels of GATA-binding activity were found in extracts of atrial and ventricular cardiomyocytes from embryonic chamberized hearts. These observations suggest that GATA factors positively regulate slow MyHC 3 gene expression throughout the tubular heart and subsequently in the atria. In contrast, an inhibitory activity, operating through the VDR-like element, increased in ventricular cardiomyocytes during the transition of the heart from a tubular to a chambered structure. Overexpression of the VDR, acting via the VDR-like element, duplicates the inhibitory activity in ventricular but not in atrial cardiomyocytes. These data suggest that atrial chamber-specific expression of the slow MyHC 3 gene is achieved through the VDR-like inhibitory element in ventricular cardiomyocytes at the time distinct atrial and ventricular chambers form.     

Stereotypes Possess Heterogeneous Directionality: A Theoretical and Empirical Exploration of Stereotype Structure and Content

We advance a theory-driven approach to stereotype structure, informed by connectionist theories of cognition. Whereas traditional models define or tacitly assume that stereotypes possess inherently Group → Attribute activation directionality (e.g., Black activates criminal), our model predicts heterogeneous stereotype directionality. Alongside the classically studied Group → Attribute stereotypes, some stereotypes should be bidirectional (i.e., Group ⇄ Attribute) and others should have Attribute → Group unidirectionality (e.g., fashionable activates gay). We tested this prediction in several large-scale studies with human participants (N_Combined = 4,817), assessing stereotypic inferences among various groups and attributes. Supporting predictions, we found heterogeneous directionality both among the stereotype links related to a given social group and also between the links of different social groups. These efforts yield rich datasets that map the networks of stereotype links related to several social groups. We make these datasets publicly available, enabling other researchers to explore a number of questions related to stereotypes and stereotyping. Stereotype directionality is an understudied feature of stereotypes and stereotyping with widespread implications for the development, measurement, maintenance, expression, and change of stereotypes, stereotyping, prejudice, and discrimination.     

Effect of Light Quality (Red:Far-red Ratio) at the Apical Bud of the Main Stolon on Morphogenesis of Trifolium repens L.

A controlled environment experiment investigated whether thered:far-red (R:FR) ratio of light at the apical bud of the mainstolon could alter plant morphogenesis in clonal cuttings ofwhite clover (Trifolium repens L.) The apical bud included theapical meristem, five to six developing leaf primordia withassociated axillary bud primordia and stipules and the firstemerged folded leaf until development was greater than 0·3on the Carlson scale. Three light regimes were imposed on theapical bud by collimating light from R or FR light-emittingdiodes so that the R:FR ratio of light incident at the apicalbud was set at 0·25, 1·6 or 2·1, withoutsignificantly altering photosynthetically active radiation.The effect of these light regimes on white clover seedling growthwas also tested. At a low R:FR ratio seedling hypocotyl and cotyledon lengthswere significantly longer. However, with the cuttings, the lighttreatments did not alter node appearance rate or internode lengthof the main stolon, petiole length, area of leaves or totalshoot dry matter. There was one significant photomorphogeneticresponse in the cuttings, a delay of 0·5 of a phyllochronin the appearance of branches from axillary buds in the lowR:FR ratio treatment relative to the other treatments. Wherebranch appearance was delayed plants had fewer branches. Thisdifference could be ascribed solely to a delay in branch appearanceas there were no significant treatment effects on either theinitiation of axillary bud primordia within the apical bud,the probability of branching or on the rate of growth of branchesafter appearance. Because treatment of the apical bud inducedonly one of the many previously observed responses of whiteclover to a decrease in the R:FR ratio of light, we concludethat other plant organs must also sense the quality of incidentlight.Copyright 1994, 1999 Academic Press White clover, Trifolium repens, apical bud, light quality, red:far-red ratio, light-emitting diode, branching, axillary buds, photomorphogenesis     

Cutting edge: precursor frequency affects the helper dependence of cytotoxic T cells.

Generation of CTL immunity often depends on the availability of CD4 T cell help. In this report, we show that CTL responses induced by cross-priming can be converted from CD4-dependent to CD4-independent by increasing the frequency of CTL precursors. In the absence of CD4 T cells, high numbers of CTL precursors were able to expand in number and become effector CTL. The ability of high frequencies of CD8 T cells to override help was not due to their ability to signal CD40 via expression of CD154. These findings suggest that when precursor frequencies are high, priming of CD8 T cell responses may not require CD4 T cell help.     

Altered morphogenesis of the immature hamster uterus following neonatal exposure to diethylstilbestrol

Abstract. In previous studies, we found that a single neonatal exposure to diethylstilbestrol (DES) resulted in severe hyperplasia and a high incidence of endometrial adenocarcinoma in the uterus of adult hamsters. These observations prompted us to investigate the consequences of DES exposure on earlier stages of uterine morphogenesis. After neonates were treated within 6 h of birth (day 1) with 100 μg of DES or oil vehicle, uterine tissue morphometry plus cell labelling indices following in vivo pulse labeling with [³H]thymidine were determined on days 3–21 of life. The sequential findings were: (1) a precocious (day 3) burst of cellular proliferation throughout the uterus, (2) an early period (days 3–9) of hypertrophy and increased cell density in the luminal epithelium, (3) an extreme acceleration of uterine growth resulting in a persistent increase in total uterine mass (threefold enhancement on days 5–21), (4) precocious development of endometrial glands (day 9) that were sites of intense but transient proliferative activity, (5) a middle period (days 9–15) when the percentage of stromal cells engaged in proliferative activity was reduced, (6) a second wave (days 15–21) of enhanced proliferative activity in the luminal epithelium, and (7) later development (day 21) of reduced cell density in the uterine stroma, apparently due to increased intercellular collagen accumulation. These results support our working hypothesis that the acute uterotropic response to neonatal DES treatment initiates a change in the developing hamster uterus, and later estrogenic stimulation promotes neoplastic progression in the DES-altered adult organ, perhaps due to disruption of stromal-epithelial interactions.