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>

Distribution of stress state in the Nankai subduction zone, southwest Japan and a comparison with Japan Trench

Lin, W.,Byrne, T.B.,Kinoshita, M.,McNeill, L.C.,Chang, C.,Lewis, J.C.,Yamamoto, Y.,Saffer, D.M.,Casey Moore, J.,Wu, H.Y.,Tsuji, T.,Yamada, Y.,Conin, M.,Saito, S.,Ito, T.,Tobin, H.J.,Kimura, G.,Kanagaw Elsevier Scientific Publishing Co 2016 Tectonophysics Vol.692 No.2

<P>To better understand the distribution of three dimensional stress states in the Nankai subduction zone, southwest Japan, we review various stress-related investigations carried out in the first and second stage expeditions of the Nankai Trough Seismogenic Zone Experiment (NanTroSEIZE) by the Integrated Ocean Drilling Program (IODP) and compile the stress data. Overall, the maximum principal stress sigma(l) in the shallower levels (<similar to 1 km) is vertical from near the center of forearc basin to near the trench and; the maximum horizontal stress S-Hmax (interpreted to be the intermediate principal stress sigma(2)) is generally parallel to the plate convergence vector. The exception to this generalization occurs along the shelf edge of the Nankai margin where S-Hmax, is along strike rather than parallel to the plate convergence vector. Reorientation of the principal stresses at deeper levels (e.g., >similar to 1 km below seafloor or in underlying accretionary prism) with sigma(1) becoming horizontal is also suggested at all deeper drilling sites. We also make a comparison of the stress state in the hanging wall of the frontal plate-interface between Site C0066 in the Nankai and Site C0019 in the Japan Trench subduction zone drilled after the 2011 Mw 9.0 Tohoku-Oki earthquake. In the Japan Trench, a comparison between stress state before and after the 2011 mega-earthquake shows that the stress changed from compression before the earthquake to extension after the earthquake. As a result of the comparison between the Nankai Trough and Japan Trench, a similar current stress state with trench parallel extension was recognized at both C0006 and C0019 sites. Hypothetically, this may indicate that in Nankai Trough it is still in an early stage of the interseismic cycle of a great earthquake which occurs on the decollement and propagates to the toe (around site C0006). (C) 2015 Elsevier B.V. All rights reserved.</P>

Translatome analysis of CHO cells to identify key growth genes

Courtes, F.C.,Lin, J.,Lim, H.L.,Ng, S.W.,Wong, N.S.C.,Koh, G.,Vardy, L.,Yap, M.G.S.,Loo, B.,Lee, D.Y. Elsevier Science Publishers 2013 Journal of biotechnology Vol.167 No.3

We report the first investigation of translational efficiency on a global scale, also known as translatome, of a Chinese hamster ovary (CHO) DG44 cell line producing monoclonal antibodies (mAb). The translatome data was generated via combined use of high resolution and streamlined polysome profiling technology and proprietary Nimblegen microarrays probing for more than 13K annotated CHO-specific genes. The distribution of ribosome loading during the exponential growth phase revealed the translational activity corresponding to the maximal growth rate, thus allowing us to identify stably and highly translated genes encoding heterogeneous nuclear ribonucleoproteins (Hnrnpc and Hnrnpa2b1), protein regulator of cytokinesis 1 (Prc1), glucose-6-phosphate dehydrogenase (G6pdh), UTP6 small subunit processome (Utp6) and RuvB-like protein 1 (Ruvbl1) as potential key players for cellular growth. Moreover, correlation analysis between transcriptome and translatome data sets showed that transcript level and translation efficiency were uncoupled for 95% of investigated genes, suggesting the implication of translational control mechanisms such as the mTOR pathway. Thus, the current translatome analysis platform offers new insights into gene expression in CHO cell cultures by bridging the gap between transcriptome and proteome data, which will enable researchers of the bioprocessing field to prioritize in high-potential candidate genes and to devise optimal strategies for cell engineering toward improving culture performance.

Extrusion 가공처리 계분사료의 첨가수준이 재래산양의 육성능력, 영양소 소화율 및 체조성에 미치는 영향

김창혁,라창식,고병대,박재인,임광철,신종서 한국동물자원과학회 2002 한국축산학회지 Vol.44 No.6

본 시험은 계분의 가축 사료화의 일환으로 계분, 옥수수 및 타피오카를 50:30:20의 비율로 혼합하여 extrusion 가공한 계분사료(EPM)의 급여수준이 반추가축의 증체량, 사료요구율, 영양소 소화율 및 도체성적에 미치는 영향을 구명하기 위하여 평균체중이 10㎏ 내외의 한국재래산양 수컷 15두를 이용하여 EPM을 시험사료중에 각각 0, 10, 20, 30 및 40%씩 첨가 급여하여 6주간 사양시험을 실시하였다. Extrusion 가공처리 계분사료의 수분, 조지방 및 조섬유 함량는 extrusion 가공처리 전보다 각각 10.8, 0.2 및 0.5% 감소하였고, NFE는 1.7% 증가하였다. 사료섭취량은 대조구의 596.1g/day에 비해 EPM 20 및 30% 첨가구에서 각각 620.6 및 698.5g/day로 증가하는 경향을 보였으나, 40% 첨가구에서는 590.7g/day로 감소하였다. 일당 증체량은 대조구에서 119.8g으로 EPM 10, 20 및 30% 첨가구의 96.8, 98.3 및 108.2g/day와 거의 유사한 수준을 보였으나 EPM 40% 첨가구에서는 78.3g/day로 대조구에 비해 유의적으로 낮았다(p<0.05). 사료요구율은 대조구(5.01)에 비하여 EPM 첨가수준이 증가할수록 높아지는 경향을 보였으며, 특히 EPM 40% 첨가구에서는 대조구에 비해 현저하게 높았다(p<0.05). 건물 및 조단백질 소화율은 각 처리간에 큰 차이는 인정되지 않았으나, 조섬유 소화율은 대조구의 63.7%에 비해 EPM 10, 20, 30 및 40% 첨가구에서 각각 65.3, 67.5, 70.4 및 71.8%로 증가하는 경향을 보였다. 조지방 소화율은 EPM 40% 첨가구에서 68.5%로 대조구에 비해 유의적으로 낮았고(p<0.05). 다른 EMP 첨가구에서는 거의 유사한 수준을 나타내었다. 도체율은 대조구의 49.7%에 비해 EPM 10, 20, 30 및 40% 첨가구에서 각각 49.7, 48.3, 47.8 및 45.2로 감소하는 경향을 나타내었다. 산양고기중의 지방 함량은 대조구의 16.3%에 비해 EPM 첨가구 모두에서 유의적으로 감소하였다(p<0.05). This experiment was conducted to investigate the effects of supplementary level of extruded poultry manure, corn and tapioca mixture (EPM) on growth performance, nutrient digestibility and body composition in korean native goats. Total 15 heads of Korean native goats (10 ㎏ B.W.) were randomly assigned into five treatment groups (EPM 10, 20, 30, 40% and control.) and feeding trial was done for six weeks with ad libitum. Protein level of the extrudate with poultry manure was directly proportional to corn supplements rate. NFE and Ca content in EPM also were functional of the tapioca supplements levels. Daily body weight gain was significantly (p<0.05) reduced in EPM 40% group, but no significant differences were observed in other groups. Concentrate feed intake was high in EPM 10 to 30% groups, compared to the control. Feed conversion ratio also was relatively higher in EPM groups than in the control. As EPM level increased, dry matter digestibility was proportionally decreased, but that of crude protein was enhanced. Dressed carcass percentage was significantly (p<0.05) reduced with the increase of EPM level, showing control 49.7, EPM 10% 49.8, EPM 20% 48.3, EPM 30% 47.9 and EPM 40% 45.2, respectively.

알코올 발효사료 급여가 한우의 육성성적 및 혈액의 생리적 변화에 미치는 영향

임광철,김창혁,오상집,성경일,김현숙,김종복,홍병주,신종서 한국동물자원과학회 2001 한국축산학회지 Vol.43 No.6

본 실험은 알코올 발효사료(alcohol 함량; 3.0∼3.2%, lactate 함량; 3.0∼3.5%) 처리가 한우 반추위내 혈액성분 및 비육능력에 미치는 영향을 검토하기 위하여 한우에 비지박 알코올 발효사료(Alcohol-fermented soybean curd dreg : AFS) 및 맥주박 알코올 발효사료(alcohol fermented brewery grain's : AFB)를 급여하여 평균체중이 329㎏인 한우 거세우 13두와 평균체중이 337㎏인 한우 비거세우 20두를 공시하여 증체량, 사료섭취량, 혈액성분, 혈중 알코올 함량을 측정하여 다음과 같은 결과를 얻었다. 거세우에서 비육전기의 일당증체량 및 사료효율은 알코올 발효사료 급여구들이 대조구에 비해 개선되는 경향을 보였으며, 비육후기의 일당증체량은 처리에 따른 유의적인 차이를 나타내지 않았으며, 비육후기의 사료효율은 알코올 발효사료 급여구가 개선되는 경향을 보였다. 비거세우에서 일당증체량 및 사료효율은 알코올 발효사료 급여로 개선되는 경향을 보였으나 유의성은 나타나지 않았으며, 비육 후기에는 개선효과가 없는 것으로 나타났다. 혈중 알코올 농도는 알코올 발효사료 급여구가 시험사료 급여 2시간 후에 유의적으로 높게 나타났으나(p<0.05), 사료급여 4시간째에는 급여전의 수준으로 낮아졌다. BUN 농도는 거세우가 비거세우에 비해 높았으며(14.3 vs 10.97 ㎎/㎗, p<0.05), 혈중 creatinine 농도는 거세우가 비거세우보다 낮았다(1.39 vs 1.49㎎/㎗, p<0.05). 혈중 cholesterol 농도는 전체적으로 체중이 증가함에 따라 증가하는 것으로 나타났고, 혈중 glucose 농도는 알코올 발효사료 급여로 비거세우에서는 감소하는 경향을 보인 반면 거세우에서는 증가하는 것으로 나타났다. 혈중 IP 농도는 알코올 발효사료 급여로 거세우 및 비거세우 모두 증가되었다.(p<0.05). This study was conducted to know the feeding effects of alcohol-fermented feedstuffs (alcohol concentration: 3.0∼3.2 %, lactate: 3.0∼3.5%) on the blood metabolites and fattening ability. Alcohol-fermented soybean curd dreg (AFS) and alcohol fermented brewery grain (AFB) were fed to 13 Korean steers (average body weight, 329㎏) and 20 Korean bulls (average 337㎏ B.W), and body weight gain, feed conversion rate, blood metabolites and blood alcohol concentration were analyzed. The feed conversion rates of steers at both fattening and finishing period were improved by feeding alcohol-fermented feedstuffs. However, improvement of daily body weight gain was observed only at fattening period. In bulls, body weight gains and feed conversion rate were also improved at fattening period (but not at finishing period) by feeding of alcohol-fermented feedstuffs, although a statistical significance was not detected. Blood alcohol concentrations of AFS and AFB group were significantly increased (p<0.05) at 2 hours after feeding, but dropped to the initial level at 4 hours after feeding. Blood urea nitrogen(BUN) concentrations of steers were higher than those of bulls (14.3 vs 10.97 ㎎/㎗), but creatinine was lower in steers than in bulls (1.39 vs 1.49㎎/㎗). Blood cholesterol concentration was generally proportional to the increment of body weight. While the blood glucose content was decreased in bulls by feeding alcohol-feedstuffs, it was increased in steers. Blood inorganic phosphorus(IP) level was increased in both steers and bulls.

The beneficial effects of a p-type GaInN spacer layer on the efficiency of GaInN/GaN light-emitting diodes

Lin, G.B.,Zhang, X.,Lee, S.M.,Papasouliotis, G.,Kim, J.K.,Schubert, E.F.,Cho, J. Elsevier 2015 Current Applied Physics Vol.15 No.10

Light-emitting diodes (LEDs) with a Mg-doped p-type Ga<SUB>1-x</SUB>In<SUB>x</SUB>N (0 @? x @? 0.07) spacer layer located between an undoped GaN spacer layer and the electron blocking layer are investigated. The LEDs are found to have comparable peak efficiency but less efficiency droop when the crystal quality of the p-type Ga<SUB>1-x</SUB>In<SUB>x</SUB>N spacer layer is well-controlled by lowering the growth temperature and by using a suitable In composition and Mg doping concentration. All LED samples with the p-type spacer layer show a smaller efficiency droop compared to a reference LED having an undoped GaN spacer. Among the sample sets investigated, an optical power enhancement of 12% at 111 A/cm<SUP>2</SUP> is obtained when inserting a 5 nm-thick p-type Ga<SUB>0.97</SUB>In<SUB>0.03</SUB>N spacer layer. The results support that carrier transport is the key factor in the efficiency droop observed in GaN-based LEDs.

Changes in Serum Metabolites and Growth Characteristics of Korean Native Steers Fed Alcohol-fermented Feeds

Lin, G.Z.,Kim, B.W.,Kim, C.H.,Kim, H.S.,Sung, K.I.,Ohh, S.J.,Hong, B.J.,Shin, J.S. Asian Australasian Association of Animal Productio 2004 Animal Bioscience Vol.17 No.5

This study was carried out to assess whether feeding of alcohol-fermented feeds (AFF) affects the nutritional metabolism and growth characteristics of Korean native steers. Ten steers were randomly assigned to one of two treatment groups. The dietary treatments were AFF (50% commercial beef cattle feed+30% alcohol-fermented soybean curd dregs+20% rice straw) and control (80% commercial beef cattle feed+20% rice straw). The change of serum metabolites and growth characteristics were measured every two months during the whole twelve months experimental period and the relationships between serum metabolites and growth characteristics were simultaneously analyzed. Four hours after feeding AFF, serum alcohol concentration reached its peak with a significantly higher value than that after control feeding (11.9 and 4.9 mg/dl, respectively). Serum glucose and inorganic phosphorus (IP) concentrations (63.1 and 8.4 mg/dl, respectively) of steers fed AFF were higher than those (56.6 and 7.0 mg/dl) fed the control diet. In both treatments, the serum glucose concentration rapidly increased when body weight (BW) of the steer reached about 600kg, while IP concentrations were rapidly diminished at that BW. Lower concentrations of both blood urea nitrogen (BUN) and cholesterol were observed in steers fed AFF up to 450 kg of BW. The IP concentration was correlated with concentrations of BUN, cholesterol and glucose in AFF fed cattle but not in the cattle fed control diets. Average daily gain was higher in steers fed AFF than steers fed control, particularly during the growing stage of cattle. These findings indicated a capability of AFF to improve BW gain of Korean native steers by decreased protein degradation as well as increased fat synthesis.

Analytic model for the efficiency droop in semiconductors with asymmetric carrier-transport properties based on drift-induced reduction of injection efficiency (4 pages)

Lin, G.-B.,Meyaard, D.,Cho, J.,Schubert, E.F.,Shim, H.,Sone, C. AMERICAN INSTITUTE OF PHYSICS 2012 APPLIED PHYSICS LETTERS Vol.100 No.16

Nuclear Receptor-Induced Chromosomal Proximity and DNA Breaks Underlie Specific Translocations in Cancer

Lin, C.,Yang, L.,Tanasa, B.,Hutt, K.,Ju, B.g.,Ohgi, K.A.,Zhang, J.,Rose, D.W.,Fu, X.D.,Glass, C.K.,Rosenfeld, M.G. Cell Press ; MIT Press 2009 Cell Vol.139 No.6

Chromosomal translocations are a hallmark of leukemia/lymphoma and also appear in solid tumors, but the underlying mechanism remains elusive. By establishing a cellular model that mimics the relative frequency of authentic translocation events without proliferation selection, we report mechanisms of nuclear receptor-dependent tumor translocations. Intronic binding of liganded androgen receptor (AR) first juxtaposes translocation loci by triggering intra- and interchromosomal interactions. AR then promotes site-specific DNA double-stranded breaks (DSBs) at translocation loci by recruiting two types of enzymatic activities induced by genotoxic stress and liganded AR, including activation-induced cytidine deaminase and the LINE-1 repeat-encoded ORF2 endonuclease. These enzymes synergistically generate site-selective DSBs at juxtaposed translocation loci that are ligated by nonhomologous end joining pathway for specific translocations. Our data suggest that the confluence of two parallel pathways initiated by liganded nuclear receptor and genotoxic stress underlies nonrandom tumor translocations, which may function in many types of tumors and pathological processes.

Physical properties and electronic evolution ofSr2FeMo1−xNbxO6(0≤x≤1)

Park, B.-G.,Jeong, Y.-H.,Park, J.-H.,Song, J. H.,Kim, J.-Y.,Noh, H.-J.,Lin, H.-J.,Chen, C. T. American Physical Society 2009 Physical review. B, Condensed matter and materials Vol.79 No.3