The drivers of tropical speciation

© 2014 Macmillan Publishers Limited. All rights reserved. Since the recognition that allopatric speciation can be induced by large-scale reconfigurations of the landscape that isolate formerly continuous populations, such as the separation of continents by plate tectonics, the uplift of mountains or the formation of large rivers, landscape change has been viewed as a primary driver of biological diversification. This process is referred to in biogeography as vicariance. In the most species-rich region of the world, the Neotropics, the sundering of populations associated with the Andean uplift is ascribed this principal role in speciation. An alternative model posits that rather than being directly linked to landscape change, allopatric speciation is initiated to a greater extent by dispersal events, with the principal drivers of speciation being organism-specific abilities to persist and disperse in the landscape. Landscape change is not a necessity for speciation in this model. Here we show that spatial and temporal patterns of genetic differentiation in Neotropical birds are highly discordant across lineages and are not reconcilable with a model linking speciation solely to landscape change. Instead, the strongest predictors of speciation are the amount of time a lineage has persisted in the landscape and the ability of birds to move through the landscape matrix. These results, augmented by the observation that most species-level diversity originated after episodes of major Andean uplift in the Neogene period, suggest that dispersal and differentiation on a matrix previously shaped by large-scale landscape events was a major driver of avian speciation in lowland Neotropical rainforests

Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing

MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species

Ablation of neurogenesis attenuates recovery of motor function after focal cerebral ischemia in middle-aged mice.

Depletion of neurogenesis worsens functional outcome in young-adult mice after focal cerebral ischemia, but whether a similar effect occurs in older mice is unknown. Using middle-aged (12-month-old) transgenic (DCX-TK((+))) mice that express herpes simplex virus thymidine kinase (HSV-TK) under control of the doublecortin (DCX) promoter, we conditionally depleted DCX-positive cells in the subventricular zone (SVZ) and hippocampus by treatment with ganciclovir (GCV) for 14 days. Focal cerebral ischemia was induced by permanent occlusion of the middle cerebral artery (MCAO) or occlusion of the distal segment of middle cerebral artery (dMCAO) on day 14 of vehicle or GCV treatment and mice were killed 24 hr or 12 weeks later. Increased infarct volume or brain atrophy was found in GCV- compared to vehicle-treated middle-aged DCX-TK((+)) mice, both 24 hr after MCAO and 12 weeks after dMCAO. More severe motor deficits were also observed in GCV-treated, middle-aged DCX-TK((+)) transgenic mice at both time points. Our results indicate that ischemia-induced newborn neurons contribute to anatomical and functional outcome after experimental stroke in middle-aged mice

Activation of thromboxane A2 receptors mediates endothelial dysfunction in diabetic mice

Background: Diabetes is one of high-risk factors for cardiovascular disease. Improvement of endothelial dysfunction in diabetes reduces vascular complications. However, the underlying mechanism needs to be uncovered. This study was conducted to elucidate whether and how thromboxane A2 receptor (TPr) activation contributes to endothelial dysfunction in diabetes. Methods and Results: Exposure of human umbilical vein endothelial cells (HUVECs) to either TPr agonists, two structurally related thromboxane A2 (TxA2) mimetics, significantly reduced phosphorylations of endothelial nitric oxide synthase (eNOS) at Ser1177 and Akt at Ser473. These effects were abolished by pharmacological or genetic inhibitors of TPr. TPr-induced suppression of eNOS and Akt phosphorylation was accompanied by upregulation of PTEN (phosphatase and tension homolog deleted on chromosome 10) and Ser380/Thr382/383 PTEN phosphorylation. PTEN-specific siRNA restored Akt–eNOS signaling in the face of TPr activation. The small GTPase, Rho, was also activated by TPr stimulation, and pretreatment of HUVECs with Y27632, a Rho-associated kinase (ROCK) inhibitor, rescued TPr-impaired Akt–eNOS signaling. In mice, streptozotocin-induced diabetes was associated with aortic PTEN upregulation, PTEN-Ser380/Thr382/383 phosphorylation, and dephosphorylation of Akt (at Ser473) and eNOS (at Ser1177). Importantly, administration of TPr antagonist blocked these changes. Conclusion: We conclude that TPr activation impairs endothelial function by selectively inactivating the ROCK–PTEN–Akt–eNOS pathway in diabetic mice

Effective Browsing of Web Image Search Results

The rapid development of web image search engines has enabled users to search hundred million of images available on the Web. However, due to the unsatisfactory performance of current search technologies, people still need to spend much time in navigating through the large number of result pages to find images of their interest. In this paper, we analyze the user information needs for web image search results browsing and propose to employ a similarity-based organization to present the search results. A user study is carried out to compare our approach with a ranking-based list interface and a cluster-based interface. Experimental results show that similarity-based presentation can help users to explore image search results more naturally and efficiently

Conditional depletion of neurogenesis inhibits long-term recovery after experimental stroke in mice.

We reported previously that ablation of doublecortin (DCX)-immunopositive newborn neurons in mice worsens anatomical and functional outcome measured 1 day after experimental stroke, but whether this effect persists is unknown. We generated transgenic mice that express herpes simplex virus thymidine kinase under control of the DCX promoter (DCX-TK transgenic mice). DCX-expressing and recently divided cells in the rostral subventricular zone (SVZ) and hippocampus of DCX-TK transgenic mice, but not wild-type mice, were specifically depleted after ganciclovir (GCV) treatment for 14 days. Focal cerebral ischemia was induced by permanent distal middle cerebral artery occlusion (MCAO) on day 14 of vehicle or GCV treatment, and mice were killed 12 weeks after MCAO. Infarct volume was significantly increased and neurologic deficits were more severe in GCV- compared to vehicle-treated DCX-TK transgenic mice at first 8 weeks, after depletion of DCX- and bromodeoxyuridine-immunoreactive cells in the SVZ and dentate gyrus following focal ischemia. Our results indicate that endogenous neurogenesis in a critical period following experimental stroke influences the course of long-term recovery

EBST, limb-placing and rotarod testing in middle-aged DCX-TK⁽⁻⁾ and DCX-TK⁽⁺⁾ mice after dMCAO.

<p>Middle-aged DCX-TK⁽⁻⁾ and DCX-TK⁽⁺⁾ mice underwent dMCAO after treated with vehicle or GCV for 14 days, then behavioral tests were conducted at intervals over the next 12 wks. (<b>A</b>) Scores of elevated body swing test (EBST; lower scores correspond to more severe deficits). (<b>B</b>) Scores of limb-placing test (lower scores represent more severe deficits). (<b>C</b>) Scores of rotarod test (lower scores represent more severe deficits). *<i>P</i><0.05.</p

Infarct volume or volume loss in middle-aged DCX-TK⁽⁻⁾ and DCX-TK⁽⁺⁾ transgenic mice after dMCAO.

<p>(<b>A</b>) Middle-aged DCX-TK⁽⁻⁾ and DCX-TK⁽⁺⁾ transgenic mice were treated with vehicle or GCV for 14 days, underwent MCAO, and were killed 24 hr later. Top panel: representative images of infarct area in H&E-stained coronal brain sections. Bottom panel: infarct volumes, expressed as percentage hemispheric volume. *<i>P</i><0.05. (<b>B</b>) Middle-aged DCX-TK⁽⁻⁾ and DCX-TK⁽⁺⁾ transgenic mice were treated with vehicle or GCV for 14 days, underwent dMCAO, and were killed 12 weeks later. Top panel: representative images of atrophy area in H&E-stained coronal brain sections. Bottom panel: volume loss, expressed as percentage hemispheric volume. *<i>P</i><0.05.</p