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  • 1
    Publication Date: 2010-11-26
    Description: In bacteria, the rate of cell proliferation and the level of gene expression are intimately intertwined. Elucidating these relations is important both for understanding the physiological functions of endogenous genetic circuits and for designing robust synthetic systems. We describe a phenomenological study that reveals intrinsic constraints governing the allocation of resources toward protein synthesis and other aspects of cell growth. A theory incorporating these constraints can accurately predict how cell proliferation and gene expression affect one another, quantitatively accounting for the effect of translation-inhibiting antibiotics on gene expression and the effect of gratuitous protein expression on cell growth. The use of such empirical relations, analogous to phenomenological laws, may facilitate our understanding and manipulation of complex biological systems before underlying regulatory circuits are elucidated.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Scott, Matthew -- Gunderson, Carl W -- Mateescu, Eduard M -- Zhang, Zhongge -- Hwa, Terence -- R01GM77298/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Nov 19;330(6007):1099-102. doi: 10.1126/science.1192588.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Theoretical Biological Physics, Department of Physics, University of California, San Diego, La Jolla, CA 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21097934" target="_blank"〉PubMed〈/a〉
    Keywords: *Cell Proliferation ; Escherichia coli K12/*genetics/*growth & development ; Escherichia coli Proteins/genetics ; Gene Expression/*physiology ; Models, Biological ; Protein Biosynthesis ; RNA, Bacterial/genetics
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  • 2
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2011-10-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Zhiheng -- Feldman, L C -- Tolk, N H -- Zhang, Zhenyu -- Cohen, P I -- New York, N.Y. -- Science. 2011 Sep 30;333(6051):1824. doi: 10.1126/science.333.6051.1824-a.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21960607" target="_blank"〉PubMed〈/a〉
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  • 3
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" 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/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
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  • 4
    Publication Date: 2012-05-26
    Description: Crystal structure analyses for biological macromolecules without known structural relatives entail solving the crystallographic phase problem. Typical de novo phase evaluations depend on incorporating heavier atoms than those found natively; most commonly, multi- or single-wavelength anomalous diffraction (MAD or SAD) experiments exploit selenomethionyl proteins. Here, we realize routine structure determination using intrinsic anomalous scattering from native macromolecules. We devised robust procedures for enhancing the signal-to-noise ratio in the slight anomalous scattering from generic native structures by combining data measured from multiple crystals at lower-than-usual x-ray energy. Using this multicrystal SAD method (5 to 13 equivalent crystals), we determined structures at modest resolution (2.8 to 2.3 angstroms) for native proteins varying in size (127 to 1148 unique residues) and number of sulfur sites (3 to 28). With no requirement for heavy-atom incorporation, such experiments provide an attractive alternative to selenomethionyl SAD experiments.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3769101/" 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/PMC3769101/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Qun -- Dahmane, Tassadite -- Zhang, Zhen -- Assur, Zahra -- Brasch, Julia -- Shapiro, Lawrence -- Mancia, Filippo -- Hendrickson, Wayne A -- GM034102/GM/NIGMS NIH HHS/ -- GM062270/GM/NIGMS NIH HHS/ -- GM095315/GM/NIGMS NIH HHS/ -- R01 GM034102/GM/NIGMS NIH HHS/ -- R01 GM062270/GM/NIGMS NIH HHS/ -- U54 GM075026/GM/NIGMS NIH HHS/ -- U54 GM095315/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2012 May 25;336(6084):1033-7. doi: 10.1126/science.1218753.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉New York Structural Biology Center, National Synchrotron Light Source (NSLS) X4, Brookhaven National Laboratory, Upton, NY 11973, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22628655" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/chemistry ; Crystallography, X-Ray/*methods ; Data Interpretation, Statistical ; GPI-Linked Proteins/chemistry ; Models, Molecular ; Nerve Tissue Proteins/chemistry ; *Protein Conformation ; Protein Kinases/chemistry ; Protein Structure, Tertiary ; Proteins/*chemistry ; Selenomethionine/chemistry ; Signal-To-Noise Ratio ; Sulfur/chemistry ; X-Ray Diffraction
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  • 5
    Publication Date: 2013-03-16
    Description: The quantized version of the anomalous Hall effect has been predicted to occur in magnetic topological insulators, but the experimental realization has been challenging. Here, we report the observation of the quantum anomalous Hall (QAH) effect in thin films of chromium-doped (Bi,Sb)2Te3, a magnetic topological insulator. At zero magnetic field, the gate-tuned anomalous Hall resistance reaches the predicted quantized value of h/e(2), accompanied by a considerable drop in the longitudinal resistance. Under a strong magnetic field, the longitudinal resistance vanishes, whereas the Hall resistance remains at the quantized value. The realization of the QAH effect may lead to the development of low-power-consumption electronics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chang, Cui-Zu -- Zhang, Jinsong -- Feng, Xiao -- Shen, Jie -- Zhang, Zuocheng -- Guo, Minghua -- Li, Kang -- Ou, Yunbo -- Wei, Pang -- Wang, Li-Li -- Ji, Zhong-Qing -- Feng, Yang -- Ji, Shuaihua -- Chen, Xi -- Jia, Jinfeng -- Dai, Xi -- Fang, Zhong -- Zhang, Shou-Cheng -- He, Ke -- Wang, Yayu -- Lu, Li -- Ma, Xu-Cun -- Xue, Qi-Kun -- New York, N.Y. -- Science. 2013 Apr 12;340(6129):167-70. doi: 10.1126/science.1234414. Epub 2013 Mar 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Low-Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23493424" target="_blank"〉PubMed〈/a〉
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  • 6
    Publication Date: 2013-10-05
    Description: Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096153/" 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/PMC4096153/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiberg, Arne -- Wang, Ming -- Lin, Feng-Mao -- Zhao, Hongwei -- Zhang, Zhihong -- Kaloshian, Isgouhi -- Huang, Hsien-Da -- Jin, Hailing -- R01 GM093008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):118-23. doi: 10.1126/science.1239705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092744" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics ; Argonaute Proteins/genetics ; Botrytis/genetics/*pathogenicity ; Gene Expression Regulation, Plant ; Host-Pathogen Interactions/genetics/*immunology ; Lycopersicon esculentum/genetics/immunology/microbiology ; Mutation ; Plant Diseases/genetics/immunology/*microbiology ; *RNA Interference ; RNA, Fungal/*genetics ; RNA, Small Interfering/*genetics ; Virulence/genetics
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  • 7
    Publication Date: 2013-03-30
    Description: The breaking of time reversal symmetry in topological insulators may create previously unknown quantum effects. We observed a magnetic quantum phase transition in Cr-doped Bi2(SexTe1-x)3 topological insulator films grown by means of molecular beam epitaxy. Across the critical point, a topological quantum phase transition is revealed through both angle-resolved photoemission measurements and density functional theory calculations. We present strong evidence that the bulk band topology is the fundamental driving force for the magnetic quantum phase transition. The tunable topological and magnetic properties in this system are well suited for realizing the exotic topological quantum phenomena in magnetic topological insulators.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Jinsong -- Chang, Cui-Zu -- Tang, Peizhe -- Zhang, Zuocheng -- Feng, Xiao -- Li, Kang -- Wang, Li-Li -- Chen, Xi -- Liu, Chaoxing -- Duan, Wenhui -- He, Ke -- Xue, Qi-Kun -- Ma, Xucun -- Wang, Yayu -- New York, N.Y. -- Science. 2013 Mar 29;339(6127):1582-6. doi: 10.1126/science.1230905.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉State Key Laboratory of Low Dimensional Quantum Physics, Department of Physics, Tsinghua University, Beijing, P R China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23539598" target="_blank"〉PubMed〈/a〉
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  • 8
    Publication Date: 2014-11-15
    Description: Activators of innate immunity may have the potential to combat a broad range of infectious agents. We report that treatment with bacterial flagellin prevented rotavirus (RV) infection in mice and cured chronically RV-infected mice. Protection was independent of adaptive immunity and interferon (IFN, type I and II) and required flagellin receptors Toll-like receptor 5 (TLR5) and NOD-like receptor C4 (NLRC4). Flagellin-induced activation of TLR5 on dendritic cells elicited production of the cytokine interleukin-22 (IL-22), which induced a protective gene expression program in intestinal epithelial cells. Flagellin also induced NLRC4-dependent production of IL-18 and immediate elimination of RV-infected cells. Administration of IL-22 and IL-18 to mice fully recapitulated the capacity of flagellin to prevent or eliminate RV infection and thus holds promise as a broad-spectrum antiviral agent.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Benyue -- Chassaing, Benoit -- Shi, Zhenda -- Uchiyama, Robin -- Zhang, Zhan -- Denning, Timothy L -- Crawford, Sue E -- Pruijssers, Andrea J -- Iskarpatyoti, Jason A -- Estes, Mary K -- Dermody, Terence S -- Ouyang, Wenjun -- Williams, Ifor R -- Vijay-Kumar, Matam -- Gewirtz, Andrew T -- AI038296/AI/NIAID NIH HHS/ -- AI080656/AI/NIAID NIH HHS/ -- AI107943/AI/NIAID NIH HHS/ -- DK061417/DK/NIDDK NIH HHS/ -- DK064730/DK/NIDDK NIH HHS/ -- DK56338/DK/NIDDK NIH HHS/ -- R01 AI038296/AI/NIAID NIH HHS/ -- R37 AI038296/AI/NIAID NIH HHS/ -- New York, N.Y. -- Science. 2014 Nov 14;346(6211):861-5. doi: 10.1126/science.1256999.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA. ; Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA. Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. ; Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA. ; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, TN, USA. ; Elizabeth B. Lamb Center for Pediatric Research, Vanderbilt University School of Medicine, Nashville, TN, USA. Departments of Pediatrics, Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN, USA. ; Department of Immunology, Genentech, South San Francisco, CA, USA. ; Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. ; Department of Nutritional Sciences and Medicine, Pennsylvania State University, University Park, PA 16802, USA. ; Center for Inflammation, Immunity and Infection, Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA. Department of Pathology, Emory University School of Medicine, Atlanta, GA, USA. agewirtz@gsu.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25395539" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Diarrhea/immunology/therapy/virology ; Disease Models, Animal ; Feces/virology ; Flagellin/*administration & dosage/immunology ; Homeodomain Proteins/genetics ; *Immunity, Innate ; Interleukin-18/administration & dosage/genetics/*immunology ; Interleukins/administration & dosage/genetics/*immunology ; Mice ; Mice, Inbred C57BL ; Mice, Mutant Strains ; Mutation ; Rotavirus Infections/immunology/*prevention & control/therapy ; Toll-Like Receptor 5/genetics/*physiology ; Virus Shedding
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2014-07-19
    Description: Oceanic transports of heat, salt, fresh water, dissolved CO2, and other tracers regulate global climate change and the distribution of natural marine resources. The time-mean ocean circulation transports fluid as a conveyor belt, but fluid parcels can also be trapped and transported discretely by migrating mesoscale eddies. By combining available satellite altimetry and Argo profiling float data, we showed that the eddy-induced zonal mass transport can reach a total meridionally integrated value of up to 30 to 40 sverdrups (Sv) (1 Sv = 10(6) cubic meters per second), and it occurs mainly in subtropical regions, where the background flows are weak. This transport is comparable in magnitude to that of the large-scale wind- and thermohaline-driven circulation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Zhengguang -- Wang, Wei -- Qiu, Bo -- New York, N.Y. -- Science. 2014 Jul 18;345(6194):322-4. doi: 10.1126/science.1252418. Epub 2014 Jun 26.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Physical Oceanography Lab, Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of China, Qingdao, People's Republic of China. ; Physical Oceanography Lab, Qingdao Collaborative Innovation Center of Marine Science and Technology, Ocean University of China, Qingdao, People's Republic of China. wei@ouc.edu.cn. ; Department of Oceanography, University of Hawaii at Manoa, Honolulu, HI, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25035491" target="_blank"〉PubMed〈/a〉
    Keywords: *Climate Change ; *Hot Temperature ; Oceans and Seas ; *Water Cycle ; *Water Movements
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  • 10
    Publication Date: 2011-05-21
    Description: Near the 5' end of most eukaryotic genes, nucleosomes form highly regular arrays that begin at canonical distances from the transcriptional start site. Determinants of this and other aspects of genomic nucleosome organization have been ascribed to statistical positioning, intrinsically DNA-encoded positioning, or some aspect of transcription initiation. Here, we provide evidence for a different explanation. Biochemical reconstitution of proper nucleosome positioning, spacing, and occupancy levels was achieved across the 5' ends of most yeast genes by adenosine triphosphate-dependent trans-acting factors. These transcription-independent activities override DNA-intrinsic positioning and maintain uniform spacing at the 5' ends of genes even at low nucleosome densities. Thus, an active, nonstatistical nucleosome packing mechanism creates chromatin organizing centers at the 5' ends of genes where important regulatory elements reside.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhang, Zhenhai -- Wippo, Christian J -- Wal, Megha -- Ward, Elissa -- Korber, Philipp -- Pugh, B Franklin -- HG004160/HG/NHGRI NIH HHS/ -- New York, N.Y. -- Science. 2011 May 20;332(6032):977-80. doi: 10.1126/science.1200508.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21596991" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/*metabolism ; Base Sequence ; Chromatin Assembly and Disassembly ; Computational Biology ; DNA, Fungal/chemistry/genetics ; *Genes, Fungal ; *Genome, Fungal ; Histones/metabolism ; Nucleosomes/*genetics/*metabolism ; Poly dA-dT/analysis ; Saccharomyces cerevisiae/genetics ; Trans-Activators/genetics/metabolism ; Transcription Initiation Site ; Transcription, Genetic
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