ALBERT

Description: We report an experimental study of the domain structure of ferroelectric YMnO 3 and YMn 0.9 Fe 0.1 O 3 using polycrystalline samples prepared by direct hydrothermal crystallisation at 240 °C, well below their structural phase transition temperatures. Powder X-ray diffraction shows the expected P 6 3 cm space group for both samples with an increase in a and a small decrease in c with Fe incorporation, consistent with an adjustment of MnO 5 tilting, while XANES spectra at the Mn and Fe K edges show the oxidation state of both metals are maintained at +3 in the doped sample. High resolution TEM shows that curved stripe, annular and vortex domains can all be observed in the YMnO 3 crystals, proving that the structural phase transition is not the only driving force for the occurrence of the annular and vortex domains. Furthermore, the absence of the annular and vortex domains in YMn 0.9 Fe 0.1 O 3 indicates that the tilting state of MnO 5 bipyramids plays an important role in the domain formation. Atomic resolution STEM images confirm that the ferroelectric domain walls correspond to structural antiphase boundaries similar to the crystals made via high temperature solid-state reactions.

Description: DNA methylation is an important epigenetic modification involved in many biological processes and diseases. Recent developments in whole genome bisulfite sequencing (WGBS) technology have enabled genome-wide measurements of DNA methylation at single base pair resolution. Many experiments have been conducted to compare DNA methylation profiles under different biological contexts, with the goal of identifying differentially methylated regions (DMRs). Due to the high cost of WGBS experiments, many studies are still conducted without biological replicates. Methods and tools available for analyzing such data are very limited. We develop a statistical method, DSS-single, for detecting DMRs from WGBS data without replicates. We characterize the count data using a rigorous model that accounts for the spatial correlation of methylation levels, sequence depth and biological variation. We demonstrate that using information from neighboring CG sites, biological variation can be estimated accurately even without replicates. DMR detection is then carried out via a Wald test procedure. Simulations demonstrate that DSS-single has greater sensitivity and accuracy than existing methods, and an analysis of H1 versus IMR90 cell lines suggests that it also yields the most biologically meaningful results. DSS-single is implemented in the Bioconductor package DSS.

Description: We developed two tree ring-width chronologies (Qilian juniper, Sabina przewalskii Kom.) for the inland Heihe River Basin in arid northwest China using a large number of tree-ring samples (217 samples/92 trees) with accurate information about pith offsets based on Regional Curve Standardization (RCS) and standard dendrochronological (STD) methodologies. Two 1422-year reconstructions of annual (August–July) streamflow for the upstream region of the Heihe River are presented. The STD and RCS reconstructions account for 53.4% and 57.2% of the actual streamflow variance during the period 1958–2006, respectively. Both reconstructions display considerable low frequency (multidecadal to multicentury) fluctuations, although the RCS based reconstruction is superior to the STD based reconstruction for retention of low-frequency trends. Low-flow years in ad 818–852, 1112–1196, 1453–1495 and 1680–1710, and high-flow periods in ad 868–1000, 1056–1094, 1228–1271, 1327–1440, 1510–1583 and 1877–2006 are detected in both reconstructions. Both the STD and the RCS reconstructions testify to the fact that the 20th century witnessed intensified pluvial conditions in the upstream region of the Heihe River in the context of the last 1500 years. The streamflow reconstructions are anticipated to be useful to water resource planning and management for the Heihe River Basin in arid northwestern China.

Description: Environmental Science & Technology DOI: 10.1021/es2041288

Description: Author(s): H. X. Yang, H. F. Tian, Y. J. Song, Y. B. Qin, Y. G. Zhao, C. Ma, and J. Q. Li The magnetoelectric coupling and polar nanodomains in the charge-ordered Fe_{2} OBO_{3} have been extensively studied from room temperature down to 100 K. In situ TEM investigations demonstrate that the charge-ordering transition characterized by an incommensurate modulation could evidently result... [Phys. Rev. Lett. 106, 016406] Published Fri Jan 07, 2011

Description: The molecular basis of the thermal sensitivity of temperature-sensitive channels appears to arise from a specific protein domain rather than integration of global thermal effects. Using systematic chimeric analysis, we show that the N-terminal region that connects ankyrin repeats to the first transmembrane segment is crucial for temperature sensing in heat-activated vanilloid receptor channels. Changing this region both transformed temperature-insensitive isoforms into temperature-sensitive channels and significantly perturbed temperature sensing in temperature-sensitive wild-type channels. Swapping other domains such as the transmembrane core, the C terminus, and the rest of the N terminus had little effect on the steepness of temperature dependence. Our results support that thermal transient receptor potential channels contain modular thermal sensors that confer the unprecedentedly strong temperature dependence to these channels.

Description: 〈p〉A functional HIV cure requires immune reconstitution for lasting viremia control. A major immune dysfunction persisting in HIV infection is the impairment of T helper cell migration and homing to lymphoid tissues such as GALTs (gut-associated lymphoid tissues). ART (antiretroviral therapy) does not fully restore T cell motility for tissue repopulation. The molecular mechanism dictating this persistent T cell dysfunction is not understood. Cofilin is an actin-depolymerizing factor that regulates actin dynamics for T cell migration. Here, we demonstrate that blood CD4 T cells from HIV-infected patients (〈i〉n〈/i〉 = 193), with or without ART, exhibit significantly lower levels of cofilin phosphorylation (hyperactivation) than those from healthy controls (〈i〉n〈/i〉 = 100; ratio, 1.1:2.3; 〈i〉P〈/i〉 4β〈sub〉7〈/sub〉 integrin antibody can trigger signal transduction and modulate the cofilin pathway, partially restoring T cell motility in vitro〈i〉.〈/i〉 However, we also observed that severe T cell motility defect caused by high degrees of cofilin hyperactivation was not repairable by the anti-integrin antibody, demonstrating a mechanistic hindrance to restore immune functions in vivo. Our study suggests that cofilin is a key molecule that may need to be therapeutically targeted early for T cell tissue repopulation, immune reconstitution, and immune control of viremia.〈/p〉

Description: Visualization of chromosomal dynamics is important for understanding many fundamental intra-nuclear processes. Efficient and reliable live-cell multicolor labeling of chromosomal loci can realize this goal. However, the current methods are constrained mainly by insufficient labeling throughput, efficiency, flexibility as well as photostability. Here we have developed a new approach to realize dual-color chromosomal loci imaging based on a modified single-guide RNA (sgRNA) of the CRISPR/Cas9 system. The modification of sgRNA was optimized by structure-guided engineering of the original sgRNA, consisting of RNA aptamer insertions that bind fluorescent protein-tagged effectors. By labeling and tracking telomeres, centromeres and genomic loci, we demonstrate that the new approach is easy to implement and enables robust dual-color imaging of genomic elements. Importantly, our data also indicate that the fast exchange rate of RNA aptamer binding effectors makes our sgRNA-based labeling method much more tolerant to photobleaching than the Cas9-based labeling method. This is crucial for continuous, long-term tracking of chromosomal dynamics. Lastly, as our method is complementary to other live-cell genomic labeling systems, it is therefore possible to combine them into a plentiful palette for the study of native chromatin organization and genome ultrastructure dynamics in living cells.

Description: Microbial transformation of n -alkanes in anaerobic ecosystems plays a pivotal role in biogeochemical carbon cycling and bioremediation, but the requisite genetic machinery is not well elucidated. Desulfatibacillum alkenivorans AK-01 utilizes n -alkanes (C 13 to C 18 ) and contains two genomic loci encoding alkylsuccinate synthase (ASS) gene clusters. ASS catalyzes alkane addition to fumarate to form methylalkylsuccinic acids. We hypothesized that the genes in the two clusters would be differentially expressed depending on the alkane substrate utilized for growth. RT-qPCR was used to investigate ass -gene expression across AK-01's known substrate range, and microarray-based transcriptomic analysis served to investigate whole-cell responses to growth on n -hexadecane versus hexadecanoate. RT-qPCR revealed induction of ass gene cluster 1 during growth on all tested alkane substrates, and the transcriptional start sites in cluster 1 were determined via 5'RACE. Induction of ass gene cluster 2 was not observed under the tested conditions. Transcriptomic analysis indicated that the upregulation of genes potentially involved in methylalkylsuccinate metabolism, including methylmalonyl-CoA mutase and a putative carboxyl transferase. These findings provide new directions for studying the transcriptional regulation of genes involved in alkane addition to fumarate, fumarate recycling and the processing of methylalkylsuccinates with regard to isolates, enrichment cultures and ecological datasets.

Description: Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Myr ago). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species. Medicago truncatula is a long-established model for the study of legume biology. Here we describe the draft sequence of the M. truncatula euchromatin based on a recently completed BAC assembly supplemented with Illumina shotgun sequence, together capturing approximately 94% of all M. truncatula genes. A whole-genome duplication (WGD) approximately 58 Myr ago had a major role in shaping the M. truncatula genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the M. truncatula genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max and Lotus japonicus. M. truncatula is a close relative of alfalfa (Medicago sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the M. truncatula genome sequence provides significant opportunities to expand alfalfa's genomic toolbox.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272368/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272368/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Young, Nevin D -- Debelle, Frederic -- Oldroyd, Giles E D -- Geurts, Rene -- Cannon, Steven B -- Udvardi, Michael K -- Benedito, Vagner A -- Mayer, Klaus F X -- Gouzy, Jerome -- Schoof, Heiko -- Van de Peer, Yves -- Proost, Sebastian -- Cook, Douglas R -- Meyers, Blake C -- Spannagl, Manuel -- Cheung, Foo -- De Mita, Stephane -- Krishnakumar, Vivek -- Gundlach, Heidrun -- Zhou, Shiguo -- Mudge, Joann -- Bharti, Arvind K -- Murray, Jeremy D -- Naoumkina, Marina A -- Rosen, Benjamin -- Silverstein, Kevin A T -- Tang, Haibao -- Rombauts, Stephane -- Zhao, Patrick X -- Zhou, Peng -- Barbe, Valerie -- Bardou, Philippe -- Bechner, Michael -- Bellec, Arnaud -- Berger, Anne -- Berges, Helene -- Bidwell, Shelby -- Bisseling, Ton -- Choisne, Nathalie -- Couloux, Arnaud -- Denny, Roxanne -- Deshpande, Shweta -- Dai, Xinbin -- Doyle, Jeff J -- Dudez, Anne-Marie -- Farmer, Andrew D -- Fouteau, Stephanie -- Franken, Carolien -- Gibelin, Chrystel -- Gish, John -- Goldstein, Steven -- Gonzalez, Alvaro J -- Green, Pamela J -- Hallab, Asis -- Hartog, Marijke -- Hua, Axin -- Humphray, Sean J -- Jeong, Dong-Hoon -- Jing, Yi -- Jocker, Anika -- Kenton, Steve M -- Kim, Dong-Jin -- Klee, Kathrin -- Lai, Hongshing -- Lang, Chunting -- Lin, Shaoping -- Macmil, Simone L -- Magdelenat, Ghislaine -- Matthews, Lucy -- McCorrison, Jamison -- Monaghan, Erin L -- Mun, Jeong-Hwan -- Najar, Fares Z -- Nicholson, Christine -- Noirot, Celine -- O'Bleness, Majesta -- Paule, Charles R -- Poulain, Julie -- Prion, Florent -- Qin, Baifang -- Qu, Chunmei -- Retzel, Ernest F -- Riddle, Claire -- Sallet, Erika -- Samain, Sylvie -- Samson, Nicolas -- Sanders, Iryna -- Saurat, Olivier -- Scarpelli, Claude -- Schiex, Thomas -- Segurens, Beatrice -- Severin, Andrew J -- Sherrier, D Janine -- Shi, Ruihua -- Sims, Sarah -- Singer, Susan R -- Sinharoy, Senjuti -- Sterck, Lieven -- Viollet, Agnes -- Wang, Bing-Bing -- Wang, Keqin -- Wang, Mingyi -- Wang, Xiaohong -- Warfsmann, Jens -- Weissenbach, Jean -- White, Doug D -- White, Jim D -- Wiley, Graham B -- Wincker, Patrick -- Xing, Yanbo -- Yang, Limei -- Yao, Ziyun -- Ying, Fu -- Zhai, Jixian -- Zhou, Liping -- Zuber, Antoine -- Denarie, Jean -- Dixon, Richard A -- May, Gregory D -- Schwartz, David C -- Rogers, Jane -- Quetier, Francis -- Town, Christopher D -- Roe, Bruce A -- BB/G023832/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BBS/B/11524/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2011 Nov 16;480(7378):520-4. doi: 10.1038/nature10625.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology, University of Minnesota, St Paul, Minnesota 55108, USA. neviny@umn.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22089132" target="_blank"〉PubMed〈/a〉