Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq

Chen, Lihe,Lee, Jae Wook,Chou, Chung-Lin,Nair, Anil V.,Battistone, Maria A.,Pă,unescu, Teodor G.,Merkulova, Maria,Breton, Sylvie,Verlander, Jill W.,Wall, Susan M.,Brown, Dennis,Burg, Maurice B. National Academy of Sciences 2017 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.114 No.46

<P><B>Significance</B></P><P>A long-term goal in mammalian biology is to identify the genes expressed in every cell type of the body. In the kidney, the expressed genes (i.e., transcriptome) of all epithelial cell types have already been identified with the exception of the cells that make up the renal collecting duct, which is responsible for regulation of blood pressure and body fluid composition. Here, single-cell RNA-sequencing was used in mouse to identify transcriptomes for the major collecting duct cell types: type A intercalated cells, type B intercalated cells, and principal cells. The information was used to create a publicly accessible online resource. The data allowed identification of genes that are selectively expressed in each cell type, which is informative for cell-level understanding of physiology and pathophysiology.</P><P>Prior RNA sequencing (RNA-seq) studies have identified complete transcriptomes for most renal epithelial cell types. The exceptions are the cell types that make up the renal collecting duct, namely intercalated cells (ICs) and principal cells (PCs), which account for only a small fraction of the kidney mass, but play critical physiological roles in the regulation of blood pressure, extracellular fluid volume, and extracellular fluid composition. To enrich these cell types, we used FACS that employed well-established lectin cell surface markers for PCs and type B ICs, as well as a newly identified cell surface marker for type A ICs, c-Kit. Single-cell RNA-seq using the IC- and PC-enriched populations as input enabled identification of complete transcriptomes of A-ICs, B-ICs, and PCs. The data were used to create a freely accessible online gene-expression database for collecting duct cells. This database allowed identification of genes that are selectively expressed in each cell type, including cell-surface receptors, transcription factors, transporters, and secreted proteins. The analysis also identified a small fraction of hybrid cells expressing aquaporin-2 and anion exchanger 1 or pendrin transcripts. In many cases, mRNAs for receptors and their ligands were identified in different cells (e.g., <I>Notch2</I> chiefly in PCs vs. <I>Jag1</I> chiefly in ICs), suggesting signaling cross-talk among the three cell types. The identified patterns of gene expression among the three types of collecting duct cells provide a foundation for understanding physiological regulation and pathophysiology in the renal collecting duct.</P>

Two-Step Mechanism of Membrane Disruption by Aβ through Membrane Fragmentation and Pore Formation

Sciacca, Michele F.M.,Kotler, Samuel A.,Brender, Jeffrey R.,Chen, J.,Lee, D.k.,Ramamoorthy, A. Biophysical Society ; Published for the Biophysica 2012 Biophysical journal Vol.103 No.4

Disruption of cell membranes by Aβ is believed to be one of the key components of Aβ toxicity. However, the mechanism by which this occurs is not fully understood. Here, we demonstrate that membrane disruption by Aβ occurs by a two-step process, with the initial formation of ion-selective pores followed by nonspecific fragmentation of the lipid membrane during amyloid fiber formation. Immediately after the addition of freshly dissolved Aβ<SUB>1-40</SUB>, defects form on the membrane that share many of the properties of Aβ channels originally reported from single-channel electrical recording, such as cation selectivity and the ability to be blockaded by zinc. By contrast, subsequent amyloid fiber formation on the surface of the membrane fragments the membrane in a way that is not cation selective and cannot be stopped by zinc ions. Moreover, we observed that the presence of ganglioside enhances both the initial pore formation and the fiber-dependent membrane fragmentation process. Whereas pore formation by freshly dissolved Aβ<SUB>1-40</SUB> is weakly observed in the absence of gangliosides, fiber-dependent membrane fragmentation can only be observed in their presence. These results provide insights into the toxicity of Aβ and may aid in the design of specific compounds to alleviate the neurodegeneration of Alzheimer's disease.

Systematic characterization of A-to-I RNA editing hotspots in microRNAs across human cancers

Wang, Yumeng,Xu, Xiaoyan,Yu, Shuangxing,Jeong, Kang Jin,Zhou, Zhicheng,Han, Leng,Tsang, Yiu Huen,Li, Jun,Chen, Hu,Mangala, Lingegowda S.,Yuan, Yuan,Eterovic, A. Karina,Lu, Yiling,Sood, Anil K.,Scott, Cold Spring Harbor Laboratory Press 2017 Genome research Vol.27 No.7

<P>RNA editing, a widespread post-transcriptional mechanism, has emerged as a new player in cancer biology. Recent studies have reported key roles for individual miRNA editing events, but a comprehensive picture of miRNA editing in human cancers remains largely unexplored. Here, we systematically characterized the miRNA editing profiles of 8595 samples across 20 cancer types from miRNA sequencing data of The Cancer Genome Atlas and identified 19 adenosine-to-inosine (A-to-I) RNA editing hotspots. We independently validated 15 of them by perturbation experiments in several cancer cell lines. These miRNA editing events show extensive correlations with key clinical variables (e.g., tumor subtype, disease stage, and patient survival time) and other molecular drivers. Focusing on the RNA editing hotspot in miR-200b, a key tumor metastasis suppressor, we found that the miR-200b editing level correlates with patient prognosis opposite to the pattern observed for the wild-type miR-200b expression. We further experimentally showed that, in contrast to wild-type miRNA, the edited miR-200b can promote cell invasion and migration through its impaired ability to inhibit <I>ZEB1/ZEB2</I> and acquired concomitant ability to repress new targets, including <I>LIFR</I>, a well-characterized metastasis suppressor. Our study highlights the importance of miRNA editing in gene regulation and suggests its potential as a biomarker for cancer prognosis and therapy.</P>

Anomalous Pseudocapacitive Behavior of a Nanostructured, Mixed-Valent Manganese Oxide Film for Electrical Energy Storage

Song, Min-Kyu,Cheng, Shuang,Chen, Haiyan,Qin, Wentao,Nam, Kyung-Wan,Xu, Shucheng,Yang, Xiao-Qing,Bongiorno, Angelo,Lee, Jangsoo,Bai, Jianming,Tyson, Trevor A.,Cho, Jaephil,Liu, Meilin American Chemical Society 2012 Nano letters Vol.12 No.7

<P>While pseudocapacitors represent a promising option for electrical energy storage, the performance of the existing ones must be dramatically enhanced to meet today’s ever-increasing demands for many emerging applications. Here we report a nanostructured, mixed-valent manganese oxide film that exhibits anomalously high specific capacitance (∼2530 F/g of manganese oxide, measured at 0.61 A/g in a two-electrode configuration with loading of active materials ∼0.16 mg/cm<SUP>2</SUP>) while maintaining excellent power density and cycling life. The dramatic performance enhancement is attributed to its unique mixed-valence state with porous nanoarchitecture, which may facilitate rapid mass transport and enhance surface double-layer capacitance, while promoting facile redox reactions associated with charge storage by both Mn and O sites, as suggested by in situ X-ray absorption spectroscopy (XAS) and density functional theory calculations. The new charge storage mechanisms (in addition to redox reactions of cations) may offer critical insights to rational design of a new-generation energy storage devices.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/nalefd/2012/nalefd.2012.12.issue-7/nl300984y/production/images/medium/nl-2012-00984y_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/nl300984y'>ACS Electronic Supporting Info</A></P>

Investigation of PCR-RFLPs within Major Histocompatibility Complex B-G Genes Using Two Restriction Enzymes in Eight Breeds of Chinese Indigenous Chickens

R. F. Xu,K. Li,G. H. Chen,B. Y. Z. Qiang,D. L. Mo,B. Fan,C. C. Li,M. Yu,M. J. Zhu,T. A. Xiong,B. Liu 아세아·태평양축산학회 2005 Animal Bioscience Vol.18 No.7

New polymorphism of major histocompatibility complex B-G genes was investigated by amplification and digestion of a 401bp fragment including intron 1 and exon 2 using polymerase chain reaction-restriction fragment length polymorphism (PCRRFLP) technique with two restriction enzymes of Msp I and Tas I in eight breeds of Chinese indigenous chickens and one exotic breed. In the fragment region of the gene, three novel single nucleotide polymorphisms (SNPs) were detected at the two restriction sites. We found the transition of two nucleotides of A294G and T295C occurred at Tas I restriction site, and consequently led to a nonsynonymous substitution of asparagine into serine at position 54 within the deduced amino acid sequence of immunoglobulin variableregion- like domain encoded by the exon 2 of B-G gene. It was observed at rare frequency that a single mutation of A294G occurring at the site, also caused an identical substitution of amino acid, asparagine 54-to-serine, to that we described previously. And the transversion of G319C at Msp I site led to a non-synonymous substitution, glutamine 62-to-histidine. The new alleles and allele frequencies identified by the PCR-RFLP method with the two enzymes were characterized, of which the allele A and B frequencies at Msp I and Tas I loci were given disequilibrium distribution either in the eight Chinese local breeds or in the exotic breed. By comparison, allele A at Msp I locus tended to be dominant, while, the allele B at Tas I locus tended to be dominant in all of the breeds analyzed. In Tibetan chickens, the preliminary association analysis revealed that no significant difference was observed between the different genotypes identified at the Msp I and Tas I loci and the laying performance traits, respectively.

Protective immunity against H5N1 influenza virus by a single dose vaccination with virus-like particles

Song, J.M.,Hossain, J.,Yoo, D.G.,Lipatov, A.S.,Davis, C.T.,Quan, F.S.,Chen, L.M.,Hogan, R.J.,Donis, R.O.,Compans, R.W.,Kang, S.M. Academic Press 2010 Virology Vol.405 No.1

We generated influenza virus-like particles (VLPs) containing the wild type (WT) H5 hemagglutinin (HA) from A/Viet Nam/1203/04 virus or a mutant H5 HA with a deletion of the multibasic cleavage motif. VLPs containing mutant H5 HA were found to be as immunogenic as VLPs containing WT HA. A single intramuscular vaccination with either type of H5 VLPs provided complete protection against lethal challenge. In contrast, the recombinant H5 HA vaccine was less immunogenic and vaccination even with a 5 fold higher dose did not induce protective immunity. VLP vaccines were superior to the recombinant HA in inducing T helper type 1 immune responses, hemagglutination inhibition titers, and antibody secreting cells, which significantly contribute to inducing protective immunity after a single dose vaccination. This study provides insights into the potential mechanisms of improved immunogenicity by H5 VLP vaccines as an approach to improve the protective efficacy against potential pandemic viruses.

Direct observation of asymmetric domain wall motion in a ferroelectric capacitor

Lee, J.K.,Shin, G.Y.,Song, K.,Choi, W.S.,Shin, Y.A.,Park, S.Y.,Britson, J.,Cao, Y.,Chen, L.Q.,Lee, H.N.,Oh, S.H. Elsevier Science 2013 ACTA MATERIALIA Vol.61 No.18

We report in situ transmission electron microscopy observations of the 180<SUP>o</SUP> polarization switching process of a PbZr<SUB>0.2</SUB>Ti<SUB>0.8</SUB>O<SUB>3</SUB> (PZT) capacitor. The preferential, but asymmetric, nucleation and forward growth of switched c-domains were observed at the PZT/electrode interfaces, arising due to the built-in electric field induced at each interface. The subsequent sideways growth of the switched domains was inhibited by the depolarization field due to the imperfect charge compensation at the counter-electrode and also at the boundaries with preexisting a-domains, which contributed further to the asymmetric switching behavior. It was found that the preexisting a-domains split into fine a- and c-domains constituting a 90<SUP>o</SUP> stripe domain pattern during the 180<SUP>o</SUP> polarization switching process, revealing that these domains also actively participated in the out-of-plane polarization switching. The real-time observations uncovered the origin of the switching asymmetry and further clarified the importance of charged domain walls and the interfaces with electrodes in the ferroelectric switching processes.

Diversity of pollinators and their role in the pollination biology of chickpea, Cicer arietinum L. (Fabaceae)

Abdul Latif,Saeed Ahmad Malik,Shafqat Saeed,Naeem Iqbal,Qamar Saeed,Khalid Ali Khan,Chen Ting,Hamed A. Ghramh 한국응용곤충학회 2019 Journal of Asia-Pacific Entomology Vol.22 No.2

Chickpea (Cicer arietinum L.) is an important source of food for people worldwide. In the current study, we studied its pollination biology with special reference to floral visitors along with their visitation rate, frequency and pollen load during 2012 and 2013. We also explored the effect of floral visitors on the capsule weight, seed weight, seed numbers and seed germination. Results revealed three bees, two wasps, five flies, one moth and three butterfly species on the flowers of chickpea. Apis dorsata, A. florea, Amegilla sp. and Eristalinus aeneus were the major species with 434–474, 223–311, 69–74 and 81–136 individuals, respectively in both years. Floral visitors differed significantly in term of visitation frequency with A. florea as the most frequent visitor (9.13–9.86 visits/flower/5 min) followed by E. aeneus (5.43–5.58 visits/flower/5 min) and A. dorsata (1.72–2.31 visits/ flower/5 min) in both years. Similarly, A. florea had statistically highest visitation rate (16.85–19.99 flowers visited/min) followed by E. aeneus (9.73–10.68 flowers visited/min). A. dorsata had significantly higher pollen load on its body (84629–85,104 pollen grains) followed by A. florea (64940–65,135 pollen grains) and Amegilla sp. (64020–65,120 pollen grains). The open-pollinated flowers had significantly higher capsule weight (0.27 ± 0.01 g), seed weight (0.18 ± 0.01 g), seed numbers (1.67 ± 0.07 seeds) and seed germination (95 ± 1.38%) as compared to flowers deprived of pollinators in cages. The results suggested A. florea, A. dorsata and E. aeneus could be effective pollinators of chickpea. Hence these three species can be properly utilized on commercial scale to increase crop yield.

Extraction of bridge aeroelastic parameters by one reference-based stochastic subspace technique

F.Y. Xu,A.R. Chen,D.L. Wang,R.J. Ma 한국풍공학회 2011 Wind and Structures, An International Journal (WAS Vol.14 No.5

Without output covariance estimation, one reference-based Stochastic Subspace Technique (SST) for extracting modal parameters and flutter derivatives of bridge deck is developed and programmed. Compared with the covariance-driven SST and the oscillation signals incurred by oncoming or signature turbulence that adopted by previous investigators, the newly-presented identification scheme is less time-consuming in computation and a more desired accuracy should be contributed to high-quality free oscillated signals excited by specific initial displacement. The reliability and identification precision of this technique are confirmed by a numerical example. For the 3-DOF sectional models of Sutong Bridge deck (streamlined) and Suramadu Bridge deck (bluff) in wind tunnel tests, with different wind velocities, the lateral bending, vertical bending, torsional frequencies and damping ratios as well as 18 flutter derivatives are extracted by using SST. The flutter derivatives of two kinds of typical decks are compared with the pseudo-steady theoretical values, and the performance of H_1^*, H_3^*, A_1^*, A_3^*is very stable and well-matched with each other, respectively. The lateral direct flutter derivatives P_5^*, P_6^* are comparatively more accurate than other relevant lateral components. Experimental procedure seems to be more critical than identification technique for refining the estimation precision.

Geographic and Breed Distribution Patterns of an A/G Polymorphism resent in the Mx Gene Suggests Balanced Selection in Village Chickens

Ommeh, S.,Jin, L.N.,Eding, H.,Muchadeyi, F.C.,Sulandari, S.,Zein, M.S.A.,Danbaro, G.,Wani, C.E.,Zhao, S.G.,Nie, Q.H.,Zhang, X.Q.,Ndila, M.,Preisinger, R.,Chen, G.H.,Yousif, I.A.,Heo, K.-N.,Oh, S.J.,Ta Science Alert 2010 International journal of poultry science Vol.9 No.1