Adaptive Evolution of Conserved Noncoding Elements in Mammals

Conserved noncoding elements (CNCs) are an abundant feature of vertebrate genomes. Some CNCs have been shown to act as cis-regulatory modules, but the function of most CNCs remains unclear. To study the evolution of CNCs, we have developed a statistical method called the “shared rates test” to identify CNCs that show significant variation in substitution rates across branches of a phylogenetic tree. We report an application of this method to alignments of 98,910 CNCs from the human, chimpanzee, dog, mouse, and rat genomes. We find that ∼68% of CNCs evolve according to a null model where, for each CNC, a single parameter models the level of constraint acting throughout the phylogeny linking these five species. The remaining ∼32% of CNCs show departures from the basic model including speed-ups and slow-downs on particular branches and occasionally multiple rate changes on different branches. We find that a subset of the significant CNCs have evolved significantly faster than the local neutral rate on a particular branch, providing strong evidence for adaptive evolution in these CNCs. The distribution of these signals on the phylogeny suggests that adaptive evolution of CNCs occurs in occasional short bursts of evolution. Our analyses suggest a large set of promising targets for future functional studies of adaptation.</p

Rice sHsp genes: genomic organization and expression profiling under stress and development

<p>Abstract</p> <p>Background</p> <p>Heat shock proteins (Hsps) constitute an important component in the heat shock response of all living systems. Among the various plant Hsps (i.e. Hsp100, Hsp90, Hsp70 and Hsp20), Hsp20 or small Hsps (sHsps) are expressed in maximal amounts under high temperature stress. The characteristic feature of the sHsps is the presence of α-crystallin domain (ACD) at the C-terminus. sHsps cooperate with Hsp100/Hsp70 and co-chaperones in ATP-dependent manner in preventing aggregation of cellular proteins and in their subsequent refolding. Database search was performed to investigate the sHsp gene family across rice genome sequence followed by comprehensive expression analysis of these genes.</p> <p>Results</p> <p>We identified 40 α-crystallin domain containing genes in rice. Phylogenetic analysis showed that 23 out of these 40 genes constitute sHsps. The additional 17 genes containing ACD clustered with Acd proteins of <it>Arabidopsis</it>. Detailed scrutiny of 23 sHsp sequences enabled us to categorize these proteins in a revised scheme of classification constituting of 16 cytoplasmic/nuclear, 2 ER, 3 mitochondrial, 1 plastid and 1 peroxisomal genes. In the new classification proposed herein nucleo-cytoplasmic class of sHsps with 9 subfamilies is more complex in rice than in <it>Arabidopsis</it>. Strikingly, 17 of 23 rice sHsp genes were noted to be intronless. Expression analysis based on microarray and RT-PCR showed that 19 sHsp genes were upregulated by high temperature stress. Besides heat stress, expression of sHsp genes was up or downregulated by other abiotic and biotic stresses. In addition to stress regulation, various sHsp genes were differentially upregulated at different developmental stages of the rice plant. Majority of sHsp genes were expressed in seed.</p> <p>Conclusion</p> <p>We identified twenty three sHsp genes and seventeen Acd genes in rice. Three nucleocytoplasmic sHsp genes were found only in monocots. Analysis of expression profiling of sHsp genes revealed that these genes are differentially expressed under stress and at different stages in the life cycle of rice plant.</p

Charge Transfer Induced Molecular Hole Doping into Thin Film of Metal-Organic-Frameworks

Despite the highly porous nature with significantly large surface area, metal organic frameworks (MOFs) can be hardly used in electronic, and optoelectronic devices due to their extremely poor electrical conductivity. Therefore, the study of MOF thin films that require electron transport or conductivity in combination with the everlasting porosity is highly desirable. In the present work, thin films of Co3(NDC)3DMF4 MOFs with improved electronic conductivity are synthesized using layer-by-layer and doctor blade coating techniques followed by iodine doping. The as-prepared and doped films are characterized using FE-SEM, EDX, UV/Visible spectroscopy, XPS, current-voltage measurement, photoluminescence spectroscopy, cyclic voltammetry, and incident photon to current efficiency measurements. In addition, the electronic and semiconductor property of the MOF films are characterized using Hall Effect measurement, which reveals that in contrast to the insulator behavior of the as-prepared MOFs, the iodine doped MOFs behave as a p-type semiconductor. This is caused by charge transfer induced hole doping into the frameworks. The observed charge transfer induced hole doping phenomenon is also confirmed by calculating the densities of states of the as-prepared and iodine doped MOFs based on density functional theory. Photoluminescence spectroscopy demonstrate an efficient interfacial charge transfer between TiO2 and iodine doped MOFs, which can be applied to harvest solar radiations.Comment: Main paper (19 pages, 6 figures) and supplementary information (15 pages, 10 figures), accepted in ACS Appl. Materials & Interface

Data Watch: Research Data from Transition Economies

http://deepblue.lib.umich.edu/bitstream/2027.42/39800/3/wp416.pd

LYVE1 Marks the Divergence of Yolk Sac Definitive Hemogenic Endothelium from the Primitive Erythroid Lineage.

The contribution of the different waves and sites of&nbsp;developmental hematopoiesis to fetal and adult blood production remains unclear. Here, we identify lymphatic vessel endothelial hyaluronan receptor-1 (LYVE1) as a marker of yolk sac (YS) endothelium and definitive hematopoietic stem and progenitor cells (HSPCs). Endothelium in mid-gestation YS and&nbsp;vitelline vessels, but not the dorsal aorta and placenta, were labeled by Lyve1-Cre. Most YS HSPCs and erythro-myeloid progenitors were Lyve1-Cre lineage traced, but primitive erythroid cells were not, suggesting that they represent distinct lineages. Fetal liver (FL) and adult HSPCs showed 35%-40% Lyve1-Cre marking. Analysis of circulation-deficient Ncx1-/- concepti identified the YS as a major source of Lyve1-Cre labeled HSPCs. FL proerythroblast marking was extensive at embryonic day (E) 11.5-13.5, but decreased to hematopoietic stem cell (HSC) levels by E16.5, suggesting that HSCs from multiple sources became responsible for erythropoiesis. Lyve1-Cre thus marks the divergence between YS primitive and definitive hematopoiesis and provides a tool for targeting YS definitive hematopoiesis and FL colonization

Anatomical evaluation of CT-MRI combined femoral model

<p>Abstract</p> <p>Background</p> <p>Both CT and MRI are complementary to each other in that CT can produce a distinct contour of bones, and MRI can show the shape of both ligaments and bones. It will be ideal to build a CT-MRI combined model to take advantage of complementary information of each modality. This study evaluated the accuracy of the combined femoral model in terms of anatomical inspection.</p> <p>Methods</p> <p>Six normal porcine femora (180 ± 10 days, 3 lefts and 3 rights) with ball markers were scanned by CT and MRI. The 3D/3D registration was performed by two methods, i.e. the landmark-based 3 points-to-3 points and the surface matching using the iterative closest point (ICP) algorithm. The matching accuracy of the combined model was evaluated with statistical global deviation and locally measure anatomical contour-based deviation. Statistical analysis to assess any significant difference between accuracies of those two methods was performed using univariate repeated measures ANOVA with the Turkey post hoc test.</p> <p>Results</p> <p>This study revealed that the local 2D contour-based measurement of matching deviation was 0.5 ± 0.3 mm in the femoral condyle, and in the middle femoral shaft. The global 3D contour matching deviation of the landmark-based matching was 1.1 ± 0.3 mm, but local 2D contour deviation through anatomical inspection was much larger as much as 3.0 ± 1.8 mm.</p> <p>Conclusion</p> <p>Even with human-factor derived errors accumulated from segmentation of MRI images, and limited image quality, the matching accuracy of CT-&-MRI combined 3D models was 0.5 ± 0.3 mm in terms of local anatomical inspection.</p