@article{TangSullivanHongetal.2019, author = {Tang, Alan T. and Sullivan, Katie Rose and Hong, Courtney C. and Goddard, Lauren M. and Mahadevan, Aparna and Ren, Aileen and Pardo, Heidy and Peiper, Amy and Griffin, Erin and Tanes, Ceylan and Mattei, Lisa M. and Yang, Jisheng and Li, Li and Mericko-Ishizuka, Patricia and Shen, Le and Hobson, Nicholas and Girard, Romuald and Lightle, Rhonda and Moore, Thomas and Shenkar, Robert and Polster, Sean P. and Roedel, Claudia Jasmin and Li, Ning and Zhu, Qin and Whitehead, Kevin J. and Zheng, Xiangjian and Akers, Amy and Morrison, Leslie and Kim, Helen and Bittinger, Kyle and Lengner, Christopher J. and Schwaninger, Markus and Velcich, Anna and Augenlicht, Leonard and Abdelilah-Seyfried, Salim and Min, Wang and Marchuk, Douglas A. and Awad, Issam A. and Kahn, Mark L.}, title = {Distinct cellular roles for PDCD10 define a gut-brain axis in cerebral cavernous malformation}, series = {Science Translational Medicine}, volume = {11}, journal = {Science Translational Medicine}, number = {520}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {1946-6234}, doi = {10.1126/scitranslmed.aaw3521}, pages = {14}, year = {2019}, abstract = {Cerebral cavernous malformation (CCM) is a genetic, cerebrovascular disease. Familial CCM is caused by genetic mutations in KRIT1, CCM2, or PDCD10. Disease onset is earlier and more severe in individuals with PDCD10 mutations. Recent studies have shown that lesions arise from excess mitogen-activated protein kinase kinase kinase 3 (MEKK3) signaling downstream of Toll-like receptor 4 (TLR4) stimulation by lipopolysaccharide derived from the gut microbiome. These findings suggest a gut-brain CCM disease axis but fail to define it or explain the poor prognosis of patients with PDCD10 mutations. Here, we demonstrate that the gut barrier is a primary determinant of CCM disease course, independent of microbiome configuration, that explains the increased severity of CCM disease associated with PDCD10 deficiency. Chemical disruption of the gut barrier with dextran sulfate sodium augments CCM formation in a mouse model, as does genetic loss of Pdcd10, but not Krit1, in gut epithelial cells. Loss of gut epithelial Pdcd10 results in disruption of the colonic mucosal barrier. Accordingly, loss of Mucin-2 or exposure to dietary emulsifiers that reduce the mucus barrier increases CCM burden analogous to loss of Pdcd10 in the gut epithelium. Last, we show that treatment with dexamethasone potently inhibits CCM formation in mice because of the combined effect of action at both brain endothelial cells and gut epithelial cells. These studies define a gut-brain disease axis in an experimental model of CCM in which a single gene is required for two critical components: gut epithelial function and brain endothelial signaling.}, language = {en} } @article{YangZhuWolfetal.2018, author = {Yang, Jie and Zhu, Xiaolei and Wolf, Thomas J. A. and Li, Zheng and Nunes, Jo{\~a}o Pedro Figueira and Coffee, Ryan and Cryan, James P. and G{\"u}hr, Markus and Hegazy, Kareem and Heinz, Tony F. and Jobe, Keith and Li, Renkai and Shen, Xiaozhe and Veccione, Theodore and Weathersby, Stephen and Wilkin, Kyle J. and Yoneda, Charles and Zheng, Qiang and Martinez, Todd J. and Centurion, Martin and Wang, Xijie}, title = {Imaging CF3I conical intersection and photodissociation dynamics with ultrafast electron diffraction}, series = {Science}, volume = {361}, journal = {Science}, number = {6397}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.aat0049}, pages = {64 -- 67}, year = {2018}, abstract = {Conical intersections play a critical role in excited-state dynamics of polyatomic molecules because they govern the reaction pathways of many nonadiabatic processes. However, ultrafast probes have lacked sufficient spatial resolution to image wave-packet trajectories through these intersections directly. Here, we present the simultaneous experimental characterization of one-photon and two-photon excitation channels in isolated CF3I molecules using ultrafast gas-phase electron diffraction. In the two-photon channel, we have mapped out the real-space trajectories of a coherent nuclear wave packet, which bifurcates onto two potential energy surfaces when passing through a conical intersection. In the one-photon channel, we have resolved excitation of both the umbrella and the breathing vibrational modes in the CF3 fragment in multiple nuclear dimensions. These findings benchmark and validate ab initio nonadiabatic dynamics calculations.}, language = {en} } @article{BanksNishiyamaHasebeetal.2011, author = {Banks, Jo Ann and Nishiyama, Tomoaki and Hasebe, Mitsuyasu and Bowman, John L. and Gribskov, Michael and dePamphilis, Claude and Albert, Victor A. and Aono, Naoki and Aoyama, Tsuyoshi and Ambrose, Barbara A. and Ashton, Neil W. and Axtell, Michael J. and Barker, Elizabeth and Barker, Michael S. and Bennetzen, Jeffrey L. and Bonawitz, Nicholas D. and Chapple, Clint and Cheng, Chaoyang and Correa, Luiz Gustavo Guedes and Dacre, Michael and DeBarry, Jeremy and Dreyer, Ingo and Elias, Marek and Engstrom, Eric M. and Estelle, Mark and Feng, Liang and Finet, Cedric and Floyd, Sandra K. and Frommer, Wolf B. and Fujita, Tomomichi and Gramzow, Lydia and Gutensohn, Michael and Harholt, Jesper and Hattori, Mitsuru and Heyl, Alexander and Hirai, Tadayoshi and Hiwatashi, Yuji and Ishikawa, Masaki and Iwata, Mineko and Karol, Kenneth G. and Koehler, Barbara and Kolukisaoglu, Uener and Kubo, Minoru and Kurata, Tetsuya and Lalonde, Sylvie and Li, Kejie and Li, Ying and Litt, Amy and Lyons, Eric and Manning, Gerard and Maruyama, Takeshi and Michael, Todd P. and Mikami, Koji and Miyazaki, Saori and Morinaga, Shin-ichi and Murata, Takashi and M{\"u}ller-R{\"o}ber, Bernd and Nelson, David R. and Obara, Mari and Oguri, Yasuko and Olmstead, Richard G. and Onodera, Naoko and Petersen, Bent Larsen and Pils, Birgit and Prigge, Michael and Rensing, Stefan A. and Mauricio Riano-Pachon, Diego and Roberts, Alison W. and Sato, Yoshikatsu and Scheller, Henrik Vibe and Schulz, Burkhard and Schulz, Christian and Shakirov, Eugene V. and Shibagaki, Nakako and Shinohara, Naoki and Shippen, Dorothy E. and Sorensen, Iben and Sotooka, Ryo and Sugimoto, Nagisa and Sugita, Mamoru and Sumikawa, Naomi and Tanurdzic, Milos and Theissen, Guenter and Ulvskov, Peter and Wakazuki, Sachiko and Weng, Jing-Ke and Willats, William W. G. T. and Wipf, Daniel and Wolf, Paul G. and Yang, Lixing and Zimmer, Andreas D. and Zhu, Qihui and Mitros, Therese and Hellsten, Uffe and Loque, Dominique and Otillar, Robert and Salamov, Asaf and Schmutz, Jeremy and Shapiro, Harris and Lindquist, Erika and Lucas, Susan and Rokhsar, Daniel and Grigoriev, Igor V.}, title = {The selaginella genome identifies genetic changes associated with the evolution of vascular plants}, series = {Science}, volume = {332}, journal = {Science}, number = {6032}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1203810}, pages = {960 -- 963}, year = {2011}, abstract = {Vascular plants appeared similar to 410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.}, language = {en} } @misc{ShanGuanHubaceketal.2018, author = {Shan, Yuli and Guan, Dabo and Hubacek, Klaus and Zheng, Bo and Davis, Steven J. and Jia, Lichao and Liu, Jianghua and Liu, Zhu and Fromer, Neil and Mi, Zhifu and Meng, Jing and Deng, Xiangzheng and Li, Yuan and Lin, Jintai and Schroeder, Heike and Weisz, Helga and Schellnhuber, Hans Joachim}, title = {City-level climate change mitigation in China}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1096}, issn = {1866-8372}, doi = {10.25932/publishup-47154}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-471541}, pages = {18}, year = {2018}, abstract = {As national efforts to reduce CO2 emissions intensify, policy-makers need increasingly specific, subnational information about the sources of CO2 and the potential reductions and economic implications of different possible policies. This is particularly true in China, a large and economically diverse country that has rapidly industrialized and urbanized and that has pledged under the Paris Agreement that its emissions will peak by 2030. We present new, city level estimates of CO2 emissions for 182 Chinese cities, decomposed into 17 different fossil fuels, 46 socioeconomic sectors, and 7 industrial processes. We find that more affluent cities have systematically lower emissions per unit of gross domestic product (GDP), supported by imports from less affluent, industrial cities located nearby. In turn, clusters of industrial cities are supported by nearby centers of coal or oil extraction. Whereas policies directly targeting manufacturing and electric power infrastructure would drastically undermine the GDP of industrial cities, consumption based policies might allow emission reductions to be subsidized by those with greater ability to pay. In particular, sector based analysis of each city suggests that technological improvements could be a practical and effective means of reducing emissions while maintaining growth and the current economic structure and energy system. We explore city-level emission reductions under three scenarios of technological progress to show that substantial reductions (up to 31\%) are possible by updating a disproportionately small fraction of existing infrastructure.}, language = {en} } @article{ChengvandenBerghZengetal.2013, author = {Cheng, Shifeng and van den Bergh, Erik and Zeng, Peng and Zhong, Xiao and Xu, Jiajia and Liu, Xin and Hofberger, Johannes and de Bruijn, Suzanne and Bhide, Amey S. and Kuelahoglu, Canan and Bian, Chao and Chen, Jing and Fan, Guangyi and Kaufmann, Kerstin and Hall, Jocelyn C. and Becker, Annette and Br{\"a}utigam, Andrea and Weber, Andreas P. M. and Shi, Chengcheng and Zheng, Zhijun and Li, Wujiao and Lv, Mingju and Tao, Yimin and Wang, Junyi and Zou, Hongfeng and Quan, Zhiwu and Hibberd, Julian M. and Zhang, Gengyun and Zhu, Xin-Guang and Xu, Xun and Schranz, M. Eric}, title = {The Tarenaya hassleriana Genome Provides insight Into Reproductive Trait and Genome Evolution of Crucifers}, series = {The plant cell}, volume = {25}, journal = {The plant cell}, number = {8}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.113.113480}, pages = {2813 -- 2830}, year = {2013}, abstract = {The Brassicaceae, including Arabidopsis thaliana and Brassica crops, is unmatched among plants in its wealth of genomic and functional molecular data and has long served as a model for understanding gene, genome, and trait evolution. However, genome information from a phylogenetic outgroup that is essential for inferring directionality of evolutionary change has been lacking. We therefore sequenced the genome of the spider flower (Tarenaya hassleriana) from the Brassicaceae sister family, the Cleomaceae. By comparative analysis of the two lineages, we show that genome evolution following ancient polyploidy and gene duplication events affect reproductively important traits. We found an ancient genome triplication in Tarenaya (Th-alpha) that is independent of the Brassicaceae-specific duplication (At-alpha) and nested Brassica (Br-a) triplication. To showcase the potential of sister lineage genome analysis, we investigated the state of floral developmental genes and show Brassica retains twice as many floral MADS (for MINICHROMOSOME MAINTENANCE1, AGAMOUS, DEFICIENS and SERUM RESPONSE FACTOR) genes as Tarenaya that likely contribute to morphological diversity in Brassica. We also performed synteny analysis of gene families that confer self-incompatibility in Brassicaceae and found that the critical SERINE RECEPTOR KINASE receptor gene is derived from a lineage-specific tandem duplication. The T. hassleriana genome will facilitate future research toward elucidating the evolutionary history of Brassicaceae genomes.}, language = {en} } @article{LiangHuangLietal.2014, author = {Liang, Xu-Jing and Huang, Si-Min and Li, Jian-Ping and Zhu, Xian-Nv and Lu, Yong-Ping and Hocher, Berthold and Chen, You-Peng}, title = {Hepatic impairment induced by scrub typhus is associated with new onset of renal dysfunction}, series = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, volume = {60}, journal = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, number = {1}, publisher = {Clin Lab Publ., Verl. Klinisches Labor}, address = {Heidelberg}, issn = {1433-6510}, doi = {10.7754/Clin.Lab.2013.121203}, pages = {63 -- 68}, year = {2014}, abstract = {Background: Scrub typhus is a potentially fatal infectious disease caused by Orientia tsutsugamushi. There is little attention given to hepatic impairment in the adults with scrub typhus. This study investigated the incidence and the prognostic implications of hepatic impairment in patients with scrub typhus. Methods: We retrospectively reviewed a total of 143 adult patients with scrub typhus who were admitted between January 1999 and December 2010 in Guangdong province, China. The patients were divided into three groups, e.g., normal, mild, and moderate to severe groups based on the elevated serum ALT and/or total bilirubin levels. Furthermore, clinical characteristics and prognosis of the patient groups were compared. Results: 109 patients (76.2\%) had abnormal liver function. Among the patients with hepatic impairment 45 cases (31.4\%), 54 cases (37.8\%), and 10 cases (7.0\%) had mild, moderate, and severe hepatic damage, respectively. The moderate to severe hepatic impairment group had higher levels of serum creatinine compared with that of normal hepatic function. The incidence of new onset of renal dysfunction - defined as peak serum creatinine >= 176 mu mol/L during hospital stay with no evidence of renal disease prior hospitalization - was 0\% in the mild hepatic impairment group, 8.9\% in the moderate hepatic impairment group, and 21.9\% in the severe hepatic impairment group, (p = 0.005 for trend). Additionally, the patients with hepatic impairment (n = 109) had higher incidences of episodes of thrombocytopenia (45.9\% vs. 8.82\%, p < 0.001), hypoalbuminemia (50.5\% vs. 11.8\%, p < 0.001), new onset of renal dysfunction (16.5\% vs. 0.0\%, p = 0.011), and electrocardiogram abnormality (28.4\% vs. 8.82\%, p = 0.019) than the patients without hepatic impairment. Conclusions: The degree of hepatic impairment induced by scrub typhus is associated with new onset of renal dysfunction.}, language = {en} } @article{SunHuangMengetal.2012, author = {Sun, Sheng-Yun and Huang, Jin and Meng, Min-Jie and Lu, Jia-Hai and Hocher, Berthold and Liu, Kang-Li and Yang, Qin-He and Zhu, Xiao-Feng}, title = {Improvement of lipid profile and reduction of body weight by Shan He Jian Fei Granules in high fat diet-induced obese rats}, series = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, volume = {58}, journal = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, number = {1-2}, publisher = {Clin Lab Publ., Verl. Klinisches Labor}, address = {Heidelberg}, issn = {1433-6510}, pages = {81 -- 87}, year = {2012}, abstract = {Background: The goal was to study lipid profiles (TG, TC, LDL, HDL), effects on serum leptin, and fat tissue adiponectin, and resistin as well as body weight effects of Shan He Jian Fei Granules (SHJFG) in rats on a high fat diet. Methods: Rats were randomly divided into five groups: normal control group fed with normal fat diet, rats on high fat diet receiving low dosage, middle dosage, high dosage of Shan He Jian Fei Granules (SHJFG) as well as a high fat diet group receiving placebo. Rats were treated for 8 weeks. Body weight and naso-anal length of each rat were recorded and Lee's index was calculated. Serum TG, TC, LDL, HDL and leptin concentrations were analyzed. The gene expressions of adiponectin and resistin in adipose tissues were tested by RT-PCR. Results: Compared to the high-fat diet group, body weights, Lee's indexes, weight of fat tissues and serum TG, TC, LDL and leptin of SHJFG groups significantly decreased (p<0.05), whereas mRNA expressions of adiponectin and resistin of SHJFG groups significantly increased (p<0.05). Conclusions: SHJFG could significantly lower body weight and serum TG, TC, and LDL of obese rats. The effects of SHJFG in lowering leptin synthesis and raising mRNA expression of adiponectin and resistin in fat tissues may act as part of the mechanisms in lowering body weight of obese rats. Further studies are needed to demonstrate whether SHJFG may also reduce overall cardiovascular morbidity and mortality like other lipid lowering drugs.}, language = {en} } @article{PengZhuDongetal.2015, author = {Peng, Tao and Zhu, Ganghua and Dong, Yunpeng and Zeng, Junjie and Li, Wei and Guo, Weiwei and Chen, Yong and Duan, Maoli and Hocher, Berthold and Xie, Dinghua}, title = {BMP4: a possible key factor in differentiation of auditory neuron-like cells from bone-derived mesenchymal stromal cells}, series = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, volume = {61}, journal = {Clinical laboratory : the peer reviewed journal for clinical laboratories and laboratories related to blood transfusion}, number = {9}, publisher = {Clin Lab Publ., Verl. Klinisches Labor}, address = {Heidelberg}, issn = {1433-6510}, doi = {10.7754/Clin.Lab.2015.150217}, pages = {1171 -- 1178}, year = {2015}, abstract = {Background: Previous studies have shown that BMP4 may play an important part in the development of auditory neurons (ANs), which are degenerated in sensorineural hearing loss. However, whether BMP4 can promote sensory fate specification from mesenchymal stromal cells (MSCs) is unknown so far. Methods: MSCs isolated from Sprague-Dawley (SD) rats were confirmed by expression of MSC markers using flow cytometry and adipogenesis/osteogenesis using differentiation assays. MSCs treated with a complex of neurotrophic factors (BMP4 group and non-BMP4 group) were induced into auditory neuron-like cells, then the differences between the two groups were analyzed in morphological observation, cell growth curve, qRT-PCR, and immunofluorescence. Results: Flow cytometric analysis showed that the isolated cells expressed typical MSC surface markers. After adipogenic and osteogenic induction, the cells were stained by oil red O and Alizarin Red. The neuronal induced cells were in the growth plateau and had special forms of neurons. In the presence of BMP4, the inner ear genes NF-M, Neurog1, GluR4, NeuroD, Calretinin, NeuN, Tau, and GATA3 were up-regulated in MSCs. Conclusions: MSCs have the capacity to differentiate into auditory neuron-like cells in vitro. As an effective inducer, BMP4 may play a key role in transdifferentiation.}, language = {en} } @article{StefancuNanZhuetal.2022, author = {Stefancu, Andrei and Nan, Lin and Zhu, Li and Chis, Vasile and Bald, Ilko and Liu, Min and Leopold, Nicolae and Maier, Stefan A. and Cortes, Emiliano}, title = {Controlling plasmonic chemistry pathways through specific ion effects}, series = {Advanced optical materials}, volume = {10}, journal = {Advanced optical materials}, number = {14}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {2195-1071}, doi = {10.1002/adom.202200397}, pages = {10}, year = {2022}, abstract = {Plasmon-driven dehalogenation of brominated purines has been recently explored as a model system to understand fundamental aspects of plasmon-assisted chemical reactions. Here, it is shown that divalent Ca2+ ions strongly bridge the adsorption of bromoadenine (Br-Ade) to Ag surfaces. Such ion-mediated binding increases the molecule's adsorption energy leading to an overlap of the metal energy states and the molecular states, enabling the chemical interface damping (CID) of the plasmon modes of the Ag nanostructures (i.e., direct electron transfer from the metal to Br-Ade). Consequently, the conversion of Br-Ade to adenine almost doubles following the addition of Ca2+. These experimental results, supported by theoretical calculations of the local density of states of the Ag/Br-Ade complex, indicate a change of the charge transfer pathway driving the dehalogenation reaction, from Landau damping (in the lack of Ca2+ ions) to CID (after the addition of Ca2+). The results show that the surface dynamics of chemical species (including water molecules) play an essential role in charge transfer at plasmonic interfaces and cannot be ignored. It is envisioned that these results will help in designing more efficient nanoreactors, harnessing the full potential of plasmon-assisted chemistry.}, language = {en} } @article{CookLiCaietal.2019, author = {Cook, Katherine V. and Li, Chuang and Cai, Haiyuan and Krumholz, Lee R. and Hambright, K. David and Paerl, Hans W. and Steffen, Morgan M. and Wilson, Alan E. and Burford, Michele A. and Grossart, Hans-Peter and Hamilton, David P. and Jiang, Helong and Sukenik, Assaf and Latour, Delphine and Meyer, Elisabeth I. and Padisak, Judit and Qin, Boqiang and Zamor, Richard M. and Zhu, Guangwei}, title = {The global Microcystis interactome}, series = {Limnology and oceanography}, volume = {65}, journal = {Limnology and oceanography}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.11361}, pages = {S194 -- S207}, year = {2019}, abstract = {Bacteria play key roles in the function and diversity of aquatic systems, but aside from study of specific bloom systems, little is known about the diversity or biogeography of bacteria associated with harmful cyanobacterial blooms (cyanoHABs). CyanoHAB species are known to shape bacterial community composition and to rely on functions provided by the associated bacteria, leading to the hypothesized cyanoHAB interactome, a coevolved community of synergistic and interacting bacteria species, each necessary for the success of the others. Here, we surveyed the microbiome associated with Microcystis aeruginosa during blooms in 12 lakes spanning four continents as an initial test of the hypothesized Microcystis interactome. We predicted that microbiome composition and functional potential would be similar across blooms globally. Our results, as revealed by 16S rRNA sequence similarity, indicate that M. aeruginosa is cosmopolitan in lakes across a 280 degrees longitudinal and 90 degrees latitudinal gradient. The microbiome communities were represented by a wide range of operational taxonomic units and relative abundances. Highly abundant taxa were more related and shared across most sites and did not vary with geographic distance, thus, like Microcystis, revealing no evidence for dispersal limitation. High phylogenetic relatedness, both within and across lakes, indicates that microbiome bacteria with similar functional potential were associated with all blooms. While Microcystis and the microbiome bacteria shared many genes, whole-community metagenomic analysis revealed a suite of biochemical pathways that could be considered complementary. Our results demonstrate a high degree of similarity across global Microcystis blooms, thereby providing initial support for the hypothesized Microcystis interactome.}, language = {en} }