1
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Sonnert ND, Rosen CE, Ghazi AR, Franzosa EA, Duncan-Lowey B, González-Hernández JA, Huck JD, Yang Y, Dai Y, Rice TA, Nguyen MT, Song D, Cao Y, Martin AL, Bielecka AA, Fischer S, Guan C, Oh J, Huttenhower C, Ring AM, Palm NW. A host-microbiota interactome reveals extensive transkingdom connectivity. Nature 2024; 628:171-179. [PMID: 38509360 DOI: 10.1038/s41586-024-07162-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 02/05/2024] [Indexed: 03/22/2024]
Abstract
The myriad microorganisms that live in close association with humans have diverse effects on physiology, yet the molecular bases for these impacts remain mostly unknown1-3. Classical pathogens often invade host tissues and modulate immune responses through interactions with human extracellular and secreted proteins (the 'exoproteome'). Commensal microorganisms may also facilitate niche colonization and shape host biology by engaging host exoproteins; however, direct exoproteome-microbiota interactions remain largely unexplored. Here we developed and validated a novel technology, BASEHIT, that enables proteome-scale assessment of human exoproteome-microbiome interactions. Using BASEHIT, we interrogated more than 1.7 million potential interactions between 519 human-associated bacterial strains from diverse phylogenies and tissues of origin and 3,324 human exoproteins. The resulting interactome revealed an extensive network of transkingdom connectivity consisting of thousands of previously undescribed host-microorganism interactions involving 383 strains and 651 host proteins. Specific binding patterns within this network implied underlying biological logic; for example, conspecific strains exhibited shared exoprotein-binding patterns, and individual tissue isolates uniquely bound tissue-specific exoproteins. Furthermore, we observed dozens of unique and often strain-specific interactions with potential roles in niche colonization, tissue remodelling and immunomodulation, and found that strains with differing host interaction profiles had divergent interactions with host cells in vitro and effects on the host immune system in vivo. Overall, these studies expose a previously unexplored landscape of molecular-level host-microbiota interactions that may underlie causal effects of indigenous microorganisms on human health and disease.
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Affiliation(s)
- Nicole D Sonnert
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA
| | - Connor E Rosen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Andrew R Ghazi
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Eric A Franzosa
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | | | | | - John D Huck
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yi Yang
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yile Dai
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Tyler A Rice
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Mytien T Nguyen
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Deguang Song
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Yiyun Cao
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Anjelica L Martin
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Agata A Bielecka
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Suzanne Fischer
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Ring
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
- Department of Pharmacology, Yale School of Medicine, New Haven, CT, USA.
| | - Noah W Palm
- Department of Immunobiology, Yale School of Medicine, New Haven, CT, USA.
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2
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Pulferer HS, Guan C, Muller-Putz GR. Continuous Erroneous Feedback Processing during Deviation from the Road within a 2D Steering Task . Annu Int Conf IEEE Eng Med Biol Soc 2023; 2023:1-4. [PMID: 38082976 DOI: 10.1109/embc40787.2023.10340764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Recent research of our group indicated that erroneous feedback processing can not only be detected via established correlates in the electroencephalogram (EEG) for discrete stimuli, but also arises as modulations of the brain signals when faced with a continuous and periodic error signal. However, limitations in our previous paradigm prevented a definitive statement on the error signal as the exclusive source of the modulations, as well as on the connection between the observed error-related negativity (ERN)-like and error positivity (Pe)-like continuous correlates. Within a new paradigm involving EEG recordings of 10 participants, we disentangled modulation sources, substantiating our hypothesis that the observed periodicity arises primarily due to feedback processing. Further, we provide evidence that the continuous ERN- and Pe-like potentials are locked to separate phases in the error signal, rather than time-locked to a shared event, indicating that both potentials arise independently of one another.
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3
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Spoto M, Riera Puma JP, Fleming E, Guan C, Ondouah Nzutchi Y, Kim D, Oh J. Large-Scale CRISPRi and Transcriptomics of Staphylococcus epidermidis Identify Genetic Factors Implicated in Lifestyle Versatility. mBio 2022; 13:e0263222. [PMID: 36409086 PMCID: PMC9765180 DOI: 10.1128/mbio.02632-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 10/27/2022] [Indexed: 11/23/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous human commensal skin bacterium that is also one of the most prevalent nosocomial pathogens. The genetic factors underlying this remarkable lifestyle plasticity are incompletely understood, mainly due to the difficulties of genetic manipulation, precluding high-throughput functional profiling of this species. To probe the versatility of S. epidermidis to survive across a diversity of environmental conditions, we developed a large-scale CRISPR interference (CRISPRi) screen complemented by transcriptional profiling (RNA sequencing) across 24 diverse conditions and piloted a droplet-based CRISPRi approach to enhance throughput and sensitivity. We identified putative essential genes, importantly revealing amino acid metabolism as crucial to survival across diverse environments, and demonstrated the importance of trace metal uptake for survival under multiple stress conditions. We identified pathways significantly enriched and repressed across our range of stress and nutrient-limited conditions, demonstrating the considerable plasticity of S. epidermidis in responding to environmental stressors. Additionally, we postulate a mechanism by which nitrogen metabolism is linked to lifestyle versatility in response to hyperosmotic challenges, such as those encountered on human skin. Finally, we examined the survival of S. epidermidis under acid stress and hypothesize a role for cell wall modification as a vital component of the survival response under acidic conditions. Taken together, this study integrates large-scale CRISPRi and transcriptomics data across multiple environments to provide insights into a keystone member of the human skin microbiome. Our results additionally provide a valuable benchmarking analysis for CRISPRi screens and are a rich resource for other staphylococcal researchers. IMPORTANCE Staphylococcus epidermidis is a bacteria that broadly inhabits healthy human skin, yet it is also a common cause of skin infections and bloodstream infections associated with implanted medical devices. Because human skin has many different types of S. epidermidis, each containing different genes, our goal is to determine how these different genes allow S. epidermidis to switch from healthy growth in the skin to being an infectious pathogen. Understanding this switch is critical to developing new strategies to prevent and treat S. epidermidis infections.
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Affiliation(s)
- Michelle Spoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
- The University of Connecticut Health Center, Farmington, Connecticut, USA
| | | | - Elizabeth Fleming
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | | | - Dean Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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4
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Hussain S, Li X, Bukhari SM, Zhou M, Ahmad S, Ahmad S, Javid A, Guan C, Hussain A, Ali W, Khalid N, Ahmad U, Tian L, Hou Z. Cross-genera amplification and identification of Colpodella sp. with Cryptosporidium primers in fecal samples of zoo felids from northeast China. BRAZ J BIOL 2021; 83:e247181. [PMID: 34495161 DOI: 10.1590/1519-6984.247181] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 02/18/2021] [Indexed: 11/22/2022] Open
Abstract
The protozoans include many intracellular human pathogens. Accurate detection of these pathogens is necessary to treat the diseases. In clinical epidemiology, molecular identification of protozoan is considered a more reliable and rapid method for identification than microscopy. Among these protozoans, Cryptosporidium considered being one of the important water-borne zoonotic pathogens and a major cause of a diarrheal disease named cryptosporidiosis in humans, domestic animals, and wild animals. This study was aimed to identify Cryptosporidium in zoo felids (N= 56) belonging to different zoo of China, but accidentlly Colpodella was encountered in the zoo felids sample and phylogenetic data confirmed this unexpected amplification from fecal samples using two-step nested-PCR. Phylogenetic analysis revealed the fact about the specific primers used previously by many researchers and cross-genera amplification. We came to know that genetically sequenced amplicon gives more accurate identification of species. This study suggests more investigation on Colpodella which has been neglected previously but gains the attention of researchers after identified from humans and animals and has been known to correlate with neurological symptoms in patients.
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Affiliation(s)
- S Hussain
- Northeast Forestry University, College of Wildlife and Protected Area, Harbin, China
| | - X Li
- Harbin Northern Forest Zoo, Harbin, China
| | - S M Bukhari
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - M Zhou
- Northeast Forestry University, College of Wildlife and Protected Area, Harbin, China
| | - S Ahmad
- Department of Entomology, University of the Punjab, Lahore, Pakistan
| | - S Ahmad
- Department of Entomology, University of the Punjab, Lahore, Pakistan
| | - A Javid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - C Guan
- Harbin Northern Forest Zoo, Harbin, China
| | - A Hussain
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - W Ali
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - N Khalid
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - U Ahmad
- University of Veterinary and Animal Sciences, Department of Wildlife and Ecology, Lahore, Pakistan
| | - L Tian
- Northeast Forestry University, College of Wildlife and Protected Area, Harbin, China
| | - Z Hou
- Northeast Forestry University, College of Wildlife and Protected Area, Harbin, China.,China State Forestry Administration, Key Laboratory of Wildlife Conservation, Harbin, China
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5
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Su S, Tang X, Che H, Zhen J, Liu L, Zhao N, Liu J, Guan C, Fu S, Wang L, Li H, Zhang D, Wang Q, Zhen D. [Correlation of baseline serum 25-hydroxyvitamin D level with the risk of type 2 diabetes mellitus: a prospective cohort study]. Nan Fang Yi Ke Da Xue Xue Bao 2021; 41:811-819. [PMID: 34238732 DOI: 10.12122/j.issn.1673-4254.2021.06.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To investigate the correlation of baseline serum 25(OH) D level with the risk of type 2 diabetes mellitus (T2DM) and blood glucose control in diabetic patients among the middle-aged and elderly individuals in Chengguan District of Lanzhou, Gansu Province. OBJECTIVE Residents aged 40 to 75 years in Lanzhou were selected from the "REACTION" study conducted in 2011 and had been followed up since 2014. A total of 5044 subjects with complete data from the two surveys were analyzed. Participants were divided into Q1, Q2, Q3, and Q4 subgroups based on quartiles of serum 25(OH)D level for comparison of the incidence of T2DM and blood glucose control. OBJECTIVE Baseline 25(OH)D level was not found to correlate with FPG, 2h-PG or HbA1c levels among the residents (P>0.05). The participants were followed up for a mean of 3.4±0.6 years, and compared with those in Q1 group, the participants in Q2, Q3 and Q4 groups did not show significantly lowered risk of prediabetes or diabetes regardless of glucose tolerance status. Among the patients with T2DM, the compliance rate of glycemic control after the follow-up was significantly higher than that before the follow-up (63.4% vs 60.6%), and the levels of HbA1c, FPG, and 2h-PG decreased obviously after the follow-up. But compared with Q1 group, Q2, Q3 and Q4 groups showed no significant changes in glycemic control compliance rate or levels of HbA1c, FPG and 2h-PG after the follow-up (P>0.05). OBJECTIVE There is no evidence that baseline 25(OH)D levels are associated with the risk of diabetes and blood glucose control in patients with T2DM.
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Affiliation(s)
- S Su
- First Clinical Medical College First Hospital of Lanzhou University, Lanzhou 730000 China.,Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - X Tang
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - H Che
- Department of Endocrinology, Gansu Provincial Third People's Hospital, Lanzhou 730000, China
| | - J Zhen
- Department of Gynecology, Gansu Provincial People's Hospital, Lanzhou 730000, China
| | - L Liu
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - N Zhao
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - J Liu
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - C Guan
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - S Fu
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - L Wang
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - H Li
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - D Zhang
- First Clinical Medical College First Hospital of Lanzhou University, Lanzhou 730000 China.,Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
| | - Q Wang
- First Clinical Medical College First Hospital of Lanzhou University, Lanzhou 730000 China.,Department of Endocrinology, Gansu Provincial Third People's Hospital, Lanzhou 730000, China
| | - D Zhen
- Department of Endocrinology, First Hospital of Lanzhou University, Lanzhou 730000 China
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6
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Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. Publisher Correction: Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun 2021; 12:4318. [PMID: 34238936 PMCID: PMC8266848 DOI: 10.1038/s41467-021-24441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Bahar Behsaz
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA.,Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA.,Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Edna Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florian Grundmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deepa Acharya
- Tiny Earth Chemistry Hub, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Annabell Linck
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Changhui Guan
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA.,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany. .,Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt & Senckenberg Research Institute, Frankfurt am Main, Germany. .,Max-Planck-Institute for Terrestrial Microbiology, Department for Natural Products in Organismic Interactions, Marburg, Germany.
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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7
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Yu R, Wang G, Yu X, Li L, Li C, Song Y, Xu Z, Zhang J, Guan C. Assessing alfalfa (Medicago sativa L.) tolerance to salinity at seedling stage and screening of the salinity tolerance traits. Plant Biol (Stuttg) 2021; 23:664-674. [PMID: 33884732 DOI: 10.1111/plb.13271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/11/2021] [Indexed: 06/12/2023]
Abstract
Salt is among the most harmful agents that negatively influences crop yield. Alfalfa is an important perennial forage crop that exhibits wide cultivar variations in salt tolerance. Developing salt-tolerant alfalfa plants is a promising way to utilize salinized land. A comprehensive method was developed to achieve reliable and effective evaluation of alfalfa salt resistance. This included principal components, membership functions and cluster and stepwise regression analyses. These were used to analyse the salt tolerance coefficients of 14 traits and to evaluate 20 diverse alfalfa cultivars at the seedling stage. The various morphological root parameters of six alfalfa cultivars with contrasting salt tolerance were also tested by a scanning apparatus. According to the comprehensive evaluation value (D value), one highly salt-tolerant, two salt-tolerant, four moderately salt-tolerant and 13 salt-sensitive alfalfa cultivars were screened. A mathematical equation for the evaluation of alfalfa salt tolerance was established: D' = -0.126 + 0.667SFW + 0.377SDW + 1.089K+ /Na+ + 0.172SFW/RFW (R2 = 0.988; average forecast accuracy of 96.95%), where four indices were closely related to the salt tolerance: shoot fresh weight, ratio of shoot fresh weight to root fresh weight, shoot dry weight and ratio of K+ to Na+ in the shoot. We also found that SSA correlated strongly with SFW, SDW, K+ /Na+ , D values, while SRV correlated obviously with SFW, SFW/RFW and D values after 150 mm NaCl treatment. In conclusion, the SFW, K+ /Na+ , SDW, SFW/RFW, SSA and SRV could be used as indicators of salt tolerance in alfalfa seedlings grown under 150 mm NaCl treatment.
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Affiliation(s)
- R Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - G Wang
- Shandong Institute of Agricultural Sustainable Development, Jinan, Shandong, China
| | - X Yu
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - L Li
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - C Li
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - Y Song
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
| | - Z Xu
- College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, China
- Purple pasture Co., Ltd, Wuhe, Bengbu, Anhui, China
| | - J Zhang
- Shandong Institute of Agricultural Sustainable Development, Jinan, Shandong, China
| | - C Guan
- Shandong Institute of Agricultural Sustainable Development, Jinan, Shandong, China
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8
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Behsaz B, Bode E, Gurevich A, Shi YN, Grundmann F, Acharya D, Caraballo-Rodríguez AM, Bouslimani A, Panitchpakdi M, Linck A, Guan C, Oh J, Dorrestein PC, Bode HB, Pevzner PA, Mohimani H. Integrating genomics and metabolomics for scalable non-ribosomal peptide discovery. Nat Commun 2021; 12:3225. [PMID: 34050176 PMCID: PMC8163882 DOI: 10.1038/s41467-021-23502-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Non-Ribosomal Peptides (NRPs) represent a biomedically important class of natural products that include a multitude of antibiotics and other clinically used drugs. NRPs are not directly encoded in the genome but are instead produced by metabolic pathways encoded by biosynthetic gene clusters (BGCs). Since the existing genome mining tools predict many putative NRPs synthesized by a given BGC, it remains unclear which of these putative NRPs are correct and how to identify post-assembly modifications of amino acids in these NRPs in a blind mode, without knowing which modifications exist in the sample. To address this challenge, here we report NRPminer, a modification-tolerant tool for NRP discovery from large (meta)genomic and mass spectrometry datasets. We show that NRPminer is able to identify many NRPs from different environments, including four previously unreported NRP families from soil-associated microbes and NRPs from human microbiota. Furthermore, in this work we demonstrate the anti-parasitic activities and the structure of two of these NRP families using direct bioactivity screening and nuclear magnetic resonance spectrometry, illustrating the power of NRPminer for discovering bioactive NRPs.
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Affiliation(s)
- Bahar Behsaz
- Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Edna Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alexey Gurevich
- Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, St. Petersburg State University, St Petersburg, Russia
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Florian Grundmann
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Deepa Acharya
- Tiny Earth Chemistry Hub, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrés Mauricio Caraballo-Rodríguez
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Morgan Panitchpakdi
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Annabell Linck
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Changhui Guan
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Julia Oh
- The Jackson Laboratory of Medical Genomics, Farmington, CT, USA
| | - Pieter C Dorrestein
- Center for Microbiome Innovation, University of California at San Diego, La Jolla, CA, USA
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Helge B Bode
- Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Buchmann Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt & Senckenberg Research Institute, Frankfurt am Main, Germany.
- Max-Planck-Institute for Terrestrial Microbiology, Department for Natural Products in Organismic Interactions, Marburg, Germany.
| | - Pavel A Pevzner
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
| | - Hosein Mohimani
- Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
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9
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Wang Y, Wang QY, Guan C, Zhang X, Guo YF. [Association between lipoprotein (a) level and chronic cardio-renal syndrome in elderly patients]. Zhonghua Xin Xue Guan Bing Za Zhi 2020; 48:1047-1052. [PMID: 33355749 DOI: 10.3760/cma.j.cn112148-20200331-00270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the relationship between lipoprotein(a) [Lp(a)] and chronic cardio-renal syndrome (CRS) in elderly patients. Methods: Chronic heart failure (CHF) patients age ≥ 65 years old, who hospitalized in the department of Cardiology of Hebei General Hospital from December 2017 to October 2019, were included in this study. According to the estimate glomerular filtration rate (eGFR) level, patients were divided into CRS group (eGFR<60 ml·min-1·1.73 m-2) and CHF group (eGFR ≥60 ml·min-1·1.73 m-2). The blood index and basic disease information were collected and compared. Left ventricular ejection fraction (LVEF) were measured by echocardiography. The correlation between clinical indicators and cardio-renal function (LVEF and eGFR) was assessed. The multivariate logistic regression analysis was used to evaluate the related risk factors of CRS in elderly patients; subgroup logistic regression analysis was performed according to the basic disease of patients to assess the relationship between Lp(a) and CRS. Results: A total of 172 elderly patients (85 males (49.4%), aged 79 (71, 84) years) were finally enrolled. Among them, 88 cases (51.2%) were in CRS group and 84 cases (48.8%) were in CHF group. Age (80 (74, 84) years old vs. 74 (70, 82) years old) and LP (a) levels (222.0 (112.0, 445.3) mg/L vs. 155.0 (97.0, 348.7) mg/L) were significantly higher in the CRS group than in the CHF group (P<0.05). Lp(a) levels were negatively correlated with LVEF (r=-0.155, P=0.043) and eGFR (r=-0.220, P=0.004) in total cohort. In the subgroup analysis of patients with 2 high-incidence basic diseases (coronary heart disease and hypertension), Lp(a) was negatively correlated with LVEF (r=-0.250, P=0.007) in the coronary heart disease group, and negatively correlated with eGFR (r=-0.233, P=0.013) in the hypertension group. Multivariate logistic regression analysis showed that age (OR = 1.069, 95%CI: 1.017-1.124, P= 0.009) and Lp(a) (OR = 3.719, 95%CI: 1.339-10.326, P = 0.012) were independent correlates of CRS. The results of logistic regression analysis showed that Lp(a) was an independent correlative factor of CRS in the subgroups of coronary heart disease (OR=3.207, 95%CI: 1.129-9.108, P=0.029) and hypertension (OR=3.054, 95%CI: 1.086-8.587, P=0.034). Conclusion: Serum Lp(a) level is independently related with CRS in elderly patients.
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Affiliation(s)
- Y Wang
- Department of Geriatric Cardiology, Hebei General Hospital, Shijiazhuang 050051, China
| | - Q Y Wang
- Department of Geriatric Cardiology, Hebei General Hospital, Shijiazhuang 050051, China
| | - C Guan
- Department of Cardiovascular Medicine, Hebei Medical University, Shijiazhuang 050000, China
| | - X Zhang
- Department of Geriatric Medicine, Northern College, Zhangjiakou 075000, China
| | - Y F Guo
- Department of Geriatric Cardiology, Hebei General Hospital, Shijiazhuang 050051, China
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10
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Abstract
The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful-focusing on CRISPRi as a potential application-as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species.IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.
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Affiliation(s)
- Michelle Spoto
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Changhui Guan
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Elizabeth Fleming
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
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11
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Zhou W, Spoto M, Hardy R, Guan C, Fleming E, Larson PJ, Brown JS, Oh J. Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin. Cell 2020; 180:454-470.e18. [PMID: 32004459 PMCID: PMC7192218 DOI: 10.1016/j.cell.2020.01.006] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 01/06/2020] [Indexed: 12/22/2022]
Abstract
Metagenomic inferences of bacterial strain diversity and infectious disease transmission studies largely assume a dominant, within-individual haplotype. We hypothesize that within-individual bacterial population diversity is critical for homeostasis of a healthy microbiome and infection risk. We characterized the evolutionary trajectory and functional distribution of Staphylococcus epidermidis-a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer. Transmission events, natural selection, and pervasive horizontal gene transfer result in population admixture within skin sites and dissemination of antibiotic resistance genes within-individual. We provide experimental evidence for how admixture can modulate virulence and metabolism. Leveraging data on the contextual microbiome, we assess how interspecies interactions can shape genetic diversity and mobile gene elements. Our study provides insights into how within-individual evolution of human skin microbes shapes their functional diversification.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory, Farmington, CT, USA
| | | | | | | | | | | | | | - Julia Oh
- The Jackson Laboratory, Farmington, CT, USA.
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12
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Sivakumar R, Ranjani J, Vishnu US, Jayashree S, Lozano GL, Miles J, Broderick NA, Guan C, Gunasekaran P, Handelsman J, Rajendhran J. Evaluation of INSeq To Identify Genes Essential for Pseudomonas aeruginosa PGPR2 Corn Root Colonization. G3 (Bethesda) 2019; 9:651-661. [PMID: 30705119 PMCID: PMC6404608 DOI: 10.1534/g3.118.200928] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 01/19/2019] [Indexed: 01/19/2023]
Abstract
The reciprocal interaction between rhizosphere bacteria and their plant hosts results in a complex battery of genetic and physiological responses. In this study, we used insertion sequencing (INSeq) to reveal the genetic determinants responsible for the fitness of Pseudomonas aeruginosa PGPR2 during root colonization. We generated a random transposon mutant library of Pseudomonas aeruginosa PGPR2 comprising 39,500 unique insertions and identified genes required for growth in culture and on corn roots. A total of 108 genes were identified as contributing to the fitness of strain PGPR2 on roots. The importance in root colonization of four genes identified in the INSeq screen was verified by constructing deletion mutants in the genes and testing them for the ability to colonize corn roots singly or in competition with the wild type. All four mutants were affected in corn root colonization, displaying 5- to 100-fold reductions in populations in single inoculations, and all were outcompeted by the wild type by almost 100-fold after seven days on corn roots in mixed inoculations of the wild type and mutant. The genes identified in the screen had homology to genes involved in amino acid catabolism, stress adaptation, detoxification, signal transduction, and transport. INSeq technology proved a successful tool to identify fitness factors in Paeruginosa PGPR2 for root colonization.
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Affiliation(s)
- Ramamoorthy Sivakumar
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jothi Ranjani
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Udayakumar S Vishnu
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | | | - Gabriel L Lozano
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
| | - Jessica Miles
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT
| | - Nichole A Broderick
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT
| | | | | | - Jo Handelsman
- Wisconsin Institute for Discovery and Department of Plant Pathology, University of Wisconsin, Madison, WI 53715
| | - Jeyaprakash Rajendhran
- Department of Genetics, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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13
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Xu X, Gao X, Guan C, Hu J. Psychology of cross cultural communication: an impact on the health care system. J BIOL REG HOMEOS AG 2018; 32:1211-1214. [PMID: 30165732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Cross culture communication has become an integral part of today's world, especially in developed countries with a large population of immigrants. The health care system is one of the important areas in which health care practitioners and patients may be of different cultures, therefore there is a need of effective communication between culturally different patients and health practitioners. However, cross-culture communication is affected by psychological factors related to cultures and mind-set. Acculturation orientation is one of the important factors, and people with different orientations interact differently with people of different cultures. Cultural orientation is another important factor is which different domains define the characteristic features of different cultures. Moreover, the inclination to use native or non-native language with culturally different patients is a key factor for establishing a good relationship between patients and health care practitioners.
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Affiliation(s)
- X Xu
- College of Foreign Studies, Hubei Normal University, Huangshi, Hubei, China
| | - X Gao
- College of Foreign Studies, Hubei Normal University, Huangshi, Hubei, China
| | - C Guan
- College of Foreign Studies, Hubei Normal University, Huangshi, Hubei, China
| | - J Hu
- College of Foreign Studies, Hubei Normal University, Huangshi, Hubei, China
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14
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Lin S, Zheng Z, Zhang H, Rao C, Yan H, Wu Y, Tang Y, Dou K, Guan C, Sun Z, Xu L, Xia R, Xu B. P1647Real-time SYNTAX score feedback during coronary angiography to improve appropriateness of coronary revascularization for patients with stable coronary artery disease. Eur Heart J 2018. [DOI: 10.1093/eurheartj/ehy565.p1647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S Lin
- Fu Wai Hospital, Beijing, China People's Republic of
| | - Z Zheng
- Fu Wai Hospital, Beijing, China People's Republic of
| | - H Zhang
- Fu Wai Hospital, Beijing, China People's Republic of
| | - C Rao
- Fu Wai Hospital, Beijing, China People's Republic of
| | - H Yan
- Fu Wai Hospital, Beijing, China People's Republic of
| | - Y Wu
- Fu Wai Hospital, Beijing, China People's Republic of
| | - Y Tang
- Fu Wai Hospital, Beijing, China People's Republic of
| | - K Dou
- Fu Wai Hospital, Beijing, China People's Republic of
| | - C Guan
- Fu Wai Hospital, Beijing, China People's Republic of
| | - Z Sun
- Fu Wai Hospital, Beijing, China People's Republic of
| | - L Xu
- Fu Wai Hospital, Beijing, China People's Republic of
| | - R Xia
- Fu Wai Hospital, Beijing, China People's Republic of
| | - B Xu
- Fu Wai Hospital, Beijing, China People's Republic of
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Tang N, Guan C, Ang K, Phua K, Chew E. Motor imagery-assisted brain-computer interface for gait retraining in neurorehabilitation in chronic stroke. Ann Phys Rehabil Med 2018. [DOI: 10.1016/j.rehab.2018.05.431] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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16
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Lin S, Zheng Z, Rao C, Xu B, Yan H, Wu Y, Dou K, Tang Y, Wu F, Guan C. P877The accuracy of subjective SYNTAX score category assessment and its influence on appropriateness of coronary revascularization in patients with stable coronary artery diseases. Eur Heart J 2017. [DOI: 10.1093/eurheartj/ehx501.p877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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17
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Wang W, Guan C, Zhou C, Peng Y, Pratt LM, Chen X, Chen L, Chen Z, Yuan X, Xiao S. Integrated carbon, sulfur, and nitrogen isotope chemostratigraphy of the Ediacaran Lantian Formation in South China: Spatial gradient, ocean redox oscillation, and fossil distribution. Geobiology 2017; 15:552-571. [PMID: 28063179 DOI: 10.1111/gbi.12226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 12/07/2016] [Indexed: 06/06/2023]
Abstract
The Ediacaran Doushantuo Formation in South China is a prime target for geobiological investigation because it offers opportunities to integrate chemostratigraphic and paleobiological data. Previous studies were mostly focused on successions in shallow-water shelf facies, but data from deep-water successions are needed to fully understand basinal redox structures. Here, we report δ13 Ccarb , δ13 Corg , δ34 Spyr , δ34 SCAS , and δ15 Nsed data from a drill core of the fossiliferous Lantian Formation, which is a deep-water equivalent of the Doushantuo Formation. Our data confirm a large (>10‰) spatial gradient in δ13 Ccarb in the lower Doushantuo/Lantian formations, but this gradient is probably due to the greater sensitivity of carbonate-poor deep-water sediments to isotopic mixing with 13 C-depleted carbonate cements. A pronounced negative δ13 Ccarb excursion (EN3) in the upper Doushantuo/Lantian formations, however, is spatially consistent and may be an equivalent of the Shuram excursion. δ34 Spyr is more negative in deeper-water facies than in shallow-water facies, particularly in the lower Doushantuo/Lantian formations, and this spatial pattern is interpreted as evidence for ocean redox stratification: Pyrite precipitated in euxinic deep waters has lower δ34 Spyr than that formed within shallow-water sediments. The Lantian Formation was probably deposited in oscillating oxic and euxinic conditions. Euxinic black shales have higher TOC and TN contents, but lower δ34 Spyr and δ15 Nsed values. In euxinic environments, pyrite was predominantly formed in the water column and organic nitrogen was predominantly derived from nitrogen fixation or NH4+ assimilation because of quantitative denitrification, resulting in lower δ34 Spyr and δ15 Nsed values. Benthic macroalgae and putative animals occur exclusively in euxinic black shales. If preserved in situ, these organisms must have lived in brief oxic episodes punctuating largely euxinic intervals, only to be decimated and preserved when the local environment switched back to euxinia again. Thus, taphonomy and ecology were the primary factors controlling the stratigraphic distribution of macrofossils in the Lantian Formation.
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Affiliation(s)
- W Wang
- Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
| | - C Guan
- Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - C Zhou
- Key Laboratory of Economic Stratigraphy and Palaeogeography, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - Y Peng
- Department of Geology and Geophysics, Louisiana State University, Baton Rouge, LA, USA
| | - L M Pratt
- Department of Geological Sciences, Indiana University, Bloomington, IN, USA
| | - X Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - L Chen
- College of Earth Science and Engineering, Shandong University of Science and Technology, Qingdao, Shandong, China
| | - Z Chen
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - X Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing, China
| | - S Xiao
- Department of Geosciences, Virginia Tech, Blacksburg, VA, USA
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He H, Yang Q, Zuo Y, Peng Y, Zhong H, Qian C, Guan C, Xu Z. 491P MicroRNA-494-3p promotes cell growth, migration and invasion of nasopharyngeal carcinoma by targeting SOX7. Ann Oncol 2015. [DOI: 10.1093/annonc/mdv533.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Zhan TLT, Guan C, Xie HJ, Chen YM. Vertical migration of leachate pollutants in clayey soils beneath an uncontrolled landfill at Huainan, China: a field and theoretical investigation. Sci Total Environ 2014; 470-471:290-298. [PMID: 24144934 DOI: 10.1016/j.scitotenv.2013.09.081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Revised: 08/25/2013] [Accepted: 09/27/2013] [Indexed: 06/02/2023]
Abstract
To assess the extent of leachate migration, continuous samples of clayey soils (about 9m) were obtained beneath a 17-year old uncontrolled landfill in southeastern China. The soil samples were sub sectioned and analyzed to determine the concentrations of chloride, sodium and COD in the pore water. Total nitrogen and soil organic matter content of the soil samples were also determined. Leachate-derived chloride was detected in the clayey soil to a maximum depth of 9m. Sodium and COD were found to migrate into the soils to depths of 3-4m due to the attenuation of solutes by the soil organic matter and clay minerals at the shallow soils. The estimated migration depths for the chloride are 3m in the case of pure diffusion. Advection and mechanical dispersion were found to be more important than molecular diffusion for this site with an 8m high leachate mound. By comparing the results obtained by the mathematical modeling for layered advection-dispersion problem with the measured concentration profiles, the ranges of the effective diffusion coefficient, retardation factor and dispersivity of the soils were estimated. Better fits are obtained by employing an artificial effective interface about 1m above the observed interface. The clayey soils showed a relatively high attenuation capacity for COD with the estimated retardation factor of 5.
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Affiliation(s)
- T L T Zhan
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou 310058, China
| | - C Guan
- Institute of Hydrology and Water Resources Engineering, Zhejiang University, Hangzhou 310058, China
| | - H J Xie
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou 310058, China; Institute of Hydrology and Water Resources Engineering, Zhejiang University, Hangzhou 310058, China.
| | - Y M Chen
- MOE Key Laboratory of Soft Soils and Geoenvironmental Engineering, Zhejiang University, Hangzhou 310058, China
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20
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Guan C, Xie HJ, Wang YZ, Chen YM, Jiang YS, Tang XW. An analytical model for solute transport through a GCL-based two-layered liner considering biodegradation. Sci Total Environ 2014; 466-467:221-231. [PMID: 23906856 DOI: 10.1016/j.scitotenv.2013.07.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 07/03/2013] [Accepted: 07/06/2013] [Indexed: 06/02/2023]
Abstract
An analytical model for solute advection and dispersion in a two-layered liner consisting of a geosynthetic clay liner (GCL) and a soil liner (SL) considering the effect of biodegradation was proposed. The analytical solution was derived by Laplace transformation and was validated over a range of parameters using the finite-layer method based software Pollute v7.0. Results show that if the half-life of the solute in GCL is larger than 1 year, the degradation in GCL can be neglected for solute transport in GCL/SL. When the half-life of GCL is less than 1 year, neglecting the effect of degradation in GCL on solute migration will result in a large difference of relative base concentration of GCL/SL (e.g., 32% for the case with half-life of 0.01 year). The 100-year solute base concentration can be reduced by a factor of 2.2 when the hydraulic conductivity of the SL was reduced by an order of magnitude. The 100-year base concentration was reduced by a factor of 155 when the half life of the contaminant in the SL was reduced by an order of magnitude. The effect of degradation is more important in approving the groundwater protection level than the hydraulic conductivity. The analytical solution can be used for experimental data fitting, verification of complicated numerical models and preliminary design of landfill liner systems.
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Affiliation(s)
- C Guan
- Institute of Hydrology and Water Resources Engineering, Zhejiang University, Hangzhou 310058, China
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He BJ, Nolte G, Nagata K, Takano D, Yamazaki T, Fujimaki Y, Maeda T, Satoh Y, Heckers S, George MS, Lopes da Silva F, de Munck JC, Van Houdt PJ, Verdaasdonk RM, Ossenblok P, Mullinger K, Bowtell R, Bagshaw AP, Keeser D, Karch S, Segmiller F, Hantschk I, Berman A, Padberg F, Pogarell O, Scharnowski F, Karch S, Hümmer S, Keeser D, Paolini M, Kirsch V, Koller G, Rauchmann B, Kupka M, Blautzik J, Pogarell O, Razavi N, Jann K, Koenig T, Kottlow M, Hauf M, Strik W, Dierks T, Gotman J, Vulliemoz S, Lu Y, Zhang H, Yang L, Worrell G, He B, Gruber O, Piguet C, Hubl D, Homan P, Kindler J, Dierks T, Kim K, Steinhoff U, Wakai R, Koenig T, Kottlow M, Melie-García L, Mucci A, Volpe U, Prinster A, Salvatore M, Galderisi S, Linden DEJ, Brandeis D, Schroeder CE, Kayser C, Panzeri S, Kleinschmidt A, Ritter P, Walther S, Haueisen J, Lau S, Flemming L, Sonntag H, Maess B, Knösche TR, Lanfer B, Dannhauer M, Wolters CH, Stenroos M, Haueisen J, Wolters C, Aydin U, Lanfer B, Lew S, Lucka F, Ruthotto L, Vorwerk J, Wagner S, Ramon C, Guan C, Ang KK, Chua SG, Kuah WK, Phua KS, Chew E, Zhou H, Chuang KH, Ang BT, Wang C, Zhang H, Yang H, Chin ZY, Yu H, Pan Y, Collins L, Mainsah B, Colwell K, Morton K, Ryan D, Sellers E, Caves K, Throckmorton S, Kübler A, Holz EM, Zickler C, Sellers E, Ryan D, Brown K, Colwell K, Mainsah B, Caves K, Throckmorton S, Collins L, Wennberg R, Ahlfors SP, Grova C, Chowdhury R, Hedrich T, Heers M, Zelmann R, Hall JA, Lina JM, Kobayashi E, Oostendorp T, van Dam P, Oosterhof P, Linnenbank A, Coronel R, van Dessel P, de Bakker J, Rossion B, Jacques C, Witthoft N, Weiner KS, Foster BL, Miller KJ, Hermes D, Parvizi J, Grill-Spector K, Recanzone GH, Murray MM, Haynes JD, Richiardi J, Greicius M, De Lucia M, Müller KR, Formisano E, Smieskova R, Schmidt A, Bendfeldt K, Walter A, Riecher-Rössler A, Borgwardt S, Fusar-Poli P, Eliez S, Schmidt A, Sekihara K, Nagarajan SS, Schoffelen JM, Guggisberg AG, Nolte G, Balazs S, Kermanshahi K, Kiesenhofer W, Binder H, Rattay F, Antal A, Chaieb L, Paulus W, Bodis-Wollner I, Maurer K, Fein G, Camchong J, Johnstone J, Cardenas-Nicolson V, Fiederer LDJ, Lucka F, Yang S, Vorwerk J, Dümpelmann M, Cosandier-Rimélé D, Schulze-Bonhage A, Aertsen A, Speck O, Wolters CH, Ball T, Fuchs M, Wagner M, Kastner J, Tech R, Dinh C, Haueisen J, Baumgarten D, Hämäläinen MS, Lau S, Vogrin SJ, D'Souza W, Haueisen J, Cook MJ, Custo A, Van De Ville D, Vulliemoz S, Grouiller F, Michel CM, Malmivuo J, Aydin U, Vorwerk J, Küpper P, Heers M, Kugel H, Wellmer J, Kellinghaus C, Scherg M, Rampp S, Wolters C, Storti SF, Boscolo Galazzo I, Del Felice A, Pizzini FB, Arcaro C, Formaggio E, Mai R, Manganotti P, Koessler L, Vignal J, Cecchin T, Colnat-Coulbois S, Vespignani H, Ramantani G, Maillard L, Rektor I, Kuba R, Brázdil M, Chrastina J, Rektorova I, van Mierlo P, Carrette E, Strobbe G, Montes-Restrepo V, Vonck K, Vandenberghe S, Ahmed B, Brodely C, Carlson C, Kuzniecky R, Devinsky O, French J, Thesen T, Bénis D, David O, Lachaux JP, Seigneuret E, Krack P, Fraix V, Chabardès S, Bastin J, Jann K, Gee D, Kilroy E, Cannon T, Wang DJ, Hale JR, Mayhew SD, Przezdzik I, Arvanitis TN, Bagshaw AP, Plomp G, Quairiaux C, Astolfi L, Michel CM, Mayhew SD, Mullinger KJ, Bagshaw AP, Bowtell R, Francis ST, Schouten AC, Campfens SF, van der Kooij H, Koles Z, Lind J, Flor-Henry P, Wirth M, Haase CM, Villeneuve S, Vogel J, Jagust WJ, Kambeitz-Ilankovic L, Simon-Vermot L, Gesierich B, Duering M, Ewers M, Rektorova I, Krajcovicova L, Marecek R, Mikl M, Bracht T, Horn H, Strik W, Federspiel A, Schnell S, Höfle O, Stegmayer K, Wiest R, Dierks T, Müller TJ, Walther S, Surmeli T, Ertem A, Eralp E, Kos IH, Skrandies W, Flüggen S, Klein A, Britz J, Díaz Hernàndez L, Ro T, Michel CM, Lenartowicz A, Lau E, Rodriguez C, Cohen MS, Loo SK, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Giannoudas I, La Porta P, Verardo AR, Niolu C, Fernandez I, Siracusano A, Flor-Henry P, Lind J, Koles Z, Bollmann S, Ghisleni C, O'Gorman R, Poil SS, Klaver P, Michels L, Martin E, Ball J, Eich-Höchli D, Brandeis D, Salisbury DF, Murphy TK, Butera CD, Mathalon DH, Fryer SL, Kiehl KA, Calhoun VC, Pearlson GD, Roach BJ, Ford JM, McGlashan TH, Woods SW, Volpe U, Merlotti E, Vignapiano A, Montefusco V, Plescia GM, Gallo O, Romano P, Mucci A, Galderisi S, Mingoia G, Langbein K, Dietzek M, Wagner G, Smesny, Scherpiet S, Maitra R, Gaser C, Sauer H, Nenadic I, Gonzalez Andino S, Grave de Peralta Menendez R, Grave de Peralta Menendez R, Sanchez Vives M, Rebollo B, Gonzalez Andino S, Frølich L, Andersen TS, Mørup M, Belfiore P, Gargiulo P, Ramon C, Vanhatalo S, Cho JH, Vorwerk J, Wolters CH, Knösche TR, Watanabe T, Kawabata Y, Ukegawa D, Kawabata S, Adachi Y, Sekihara K, Sekihara K, Nagarajan SS, Wagner S, Aydin U, Vorwerk J, Herrmann C, Burger M, Wolters C, Lucka F, Aydin U, Vorwerk J, Burger M, Wolters C, Bauer M, Trahms L, Sander T, Faber PL, Lehmann D, Gianotti LRR, Pascual-Marqui RD, Milz P, Kochi K, Kaneko S, Yamashita S, Yana K, Kalogianni K, Vardy AN, Schouten AC, van der Helm FCT, Sorrentino A, Luria G, Aramini R, Hunold A, Funke M, Eichardt R, Haueisen J, Gómez-Aguilar F, Vázquez-Olvera S, Cordova-Fraga T, Castro-López J, Hernández-Gonzalez MA, Solorio-Meza S, Sosa-Aquino M, Bernal-Alvarado JJ, Vargas-Luna M, Vorwerk J, Magyari L, Ludewig J, Oostenveld R, Wolters CH, Vorwerk J, Engwer C, Ludewig J, Wolters C, Sato K, Nishibe T, Furuya M, Yamashiro K, Yana K, Ono T, Puthanmadam Subramaniyam N, Hyttinen J, Lau S, Güllmar D, Flemming L, Haueisen J, Sonntag H, Vorwerk J, Wolters CH, Grasedyck L, Haueisen J, Maeß B, Freitag S, Graichen U, Fiedler P, Strohmeier D, Haueisen J, Stenroos M, Hauk O, Grigutsch M, Felber M, Maess B, Herrmann B, Strobbe G, van Mierlo P, Vandenberghe S, Strobbe G, Cárdenas-Peña D, Montes-Restrepo V, van Mierlo P, Castellanos-Dominguez G, Vandenberghe S, Lanfer B, Paul-Jordanov I, Scherg M, Wolters CH, Ito Y, Sato D, Kamada K, Kobayashi T, Dalal SS, Rampp S, Willomitzer F, Arold O, Fouladi-Movahed S, Häusler G, Stefan H, Ettl S, Zhang S, Zhang Y, Li H, Kong X, Montes-Restrepo V, Strobbe G, van Mierlo P, Vandenberghe S, Wong DDE, Bidet-Caulet A, Knight RT, Crone NE, Dalal SS, Birot G, Spinelli L, Vulliémoz S, Seeck M, Michel CM, Emory H, Wells C, Mizrahi N, Vogrin SJ, Lau S, Cook MJ, Karahanoglu FI, Grouiller F, Caballero-Gaudes C, Seeck M, Vulliemoz S, Van De Ville D, Spinelli L, Megevand P, Genetti M, Schaller K, Michel C, Vulliemoz S, Seeck M, Genetti M, Tyrand R, Grouiller F, Vulliemoz S, Spinelli L, Seeck M, Schaller K, Michel CM, Grouiller F, Heinzer S, Delattre B, Lazeyras F, Spinelli L, Pittau F, Seeck M, Ratib O, Vargas M, Garibotto V, Vulliemoz S, Vogrin SJ, Bailey CA, Kean M, Warren AE, Davidson A, Seal M, Harvey AS, Archer JS, Papadopoulou M, Leite M, van Mierlo P, Vonck K, Boon P, Friston K, Marinazzo D, Ramon C, Holmes M, Koessler L, Rikir E, Gavaret M, Bartolomei F, Vignal JP, Vespignani H, Maillard L, Centeno M, Perani S, Pier K, Lemieux L, Clayden J, Clark C, Pressler R, Cross H, Carmichael DW, Spring A, Bessemer R, Pittman D, Aghakhani Y, Federico P, Pittau F, Grouiller F, Vulliémoz S, Gotman J, Badier JM, Bénar CG, Bartolomei F, Cruto C, Chauvel P, Gavaret M, Brodbeck V, van Leeuwen T, Tagliazzuchi E, Melloni L, Laufs H, Griskova-Bulanova I, Dapsys K, Klein C, Hänggi J, Jäncke L, Ehinger BV, Fischer P, Gert AL, Kaufhold L, Weber F, Marchante Fernandez M, Pipa G, König P, Sekihara K, Hiyama E, Koga R, Iannilli E, Michel CM, Bartmuss AL, Gupta N, Hummel T, Boecker R, Holz N, Buchmann AF, Blomeyer D, Plichta MM, Wolf I, Baumeister S, Meyer-Lindenberg A, Banaschewski T, Brandeis D, Laucht M, Natahara S, Ueno M, Kobayashi T, Kottlow M, Bänninger A, Koenig T, Schwab S, Koenig T, Federspiel A, Dierks T, Jann K, Natsukawa H, Kobayashi T, Tüshaus L, Koenig T, Kottlow M, Achermann P, Wilson RS, Mayhew SD, Assecondi S, Arvanitis TN, Bagshaw AP, Darque A, Rihs TA, Grouiller F, Lazeyras F, Ha-Vinh Leuchter R, Caballero C, Michel CM, Hüppi PS, Hauser TU, Hunt LT, Iannaccone R, Stämpfli P, Brandeis D, Dolan RJ, Walitza S, Brem S, Graichen U, Eichardt R, Fiedler P, Strohmeier D, Freitag S, Zanow F, Haueisen J, Lordier L, Grouiller F, Van de Ville D, Sancho Rossignol A, Cordero I, Lazeyras F, Ansermet F, Hüppi P, Schläpfer A, Rubia K, Brandeis D, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Giannoudas I, Verardo AR, La Porta P, Niolu C, Fernandez I, Siracusano A, Tamura K, Karube C, Mizuba T, Matsufuji M, Takashima S, Iramina K, Assecondi S, Ostwald D, Bagshaw AP, Marecek R, Brazdil M, Lamos M, Slavícek T, Marecek R, Jan J, Meier NM, Perrig W, Koenig T, Minami T, Noritake Y, Nakauchi S, Azuma K, Minami T, Nakauchi S, Rodriguez C, Lenartowicz A, Cohen MS, Rodriguez C, Lenartowicz A, Cohen MS, Iramina K, Kinoshita H, Tamura K, Karube C, Kaneko M, Ide J, Noguchi Y, Cohen MS, Douglas PK, Rodriguez CM, Xia HJ, Zimmerman EM, Konopka CJ, Epstein PS, Konopka LM, Giezendanner S, Fisler M, Soravia L, Andreotti J, Wiest R, Dierks T, Federspiel A, Razavi N, Federspiel A, Dierks T, Hauf M, Jann K, Kamada K, Sato D, Ito Y, Okano K, Mizutani N, Kobayashi T, Thelen A, Murray M, Pastena L, Formaggio E, Storti SF, Faralli F, Melucci M, Gagliardi R, Ricciardi L, Ruffino G, Coito A, Macku P, Tyrand R, Astolfi L, He B, Wiest R, Seeck M, Michel C, Plomp G, Vulliemoz S, Fischmeister FPS, Glaser J, Schöpf V, Bauer H, Beisteiner R, Deligianni F, Centeno M, Carmichael DW, Clayden J, Mingoia G, Langbein K, Dietzek M, Wagner G, Smesny S, Scherpiet S, Maitra R, Gaser C, Sauer H, Nenadic I, Dürschmid S, Zaehle T, Pannek H, Chang HF, Voges J, Rieger J, Knight RT, Heinze HJ, Hinrichs H, Tsatsishvili V, Cong F, Puoliväli T, Alluri V, Toiviainen P, Nandi AK, Brattico E, Ristaniemi T, Grieder M, Crinelli RM, Jann K, Federspiel A, Wirth M, Koenig T, Stein M, Wahlund LO, Dierks T, Atsumori H, Yamaguchi R, Okano Y, Sato H, Funane T, Sakamoto K, Kiguchi M, Tränkner A, Schindler S, Schmidt F, Strauß M, Trampel R, Hegerl U, Turner R, Geyer S, Schönknecht P, Kebets V, van Assche M, Goldstein R, van der Meulen M, Vuilleumier P, Richiardi J, Van De Ville D, Assal F, Wozniak-Kwasniewska A, Szekely D, Harquel S, Bougerol T, David O, Bracht T, Jones DK, Horn H, Müller TJ, Walther S, Sos P, Klirova M, Novak T, Brunovsky M, Horacek J, Bares M, Hoschl C C, Fellhauer I, Zöllner FG, Schröder J, Kong L, Essig M, Schad LR, Arrubla J, Neuner I, Hahn D, Boers F, Shah NJ, Neuner I, Arrubla J, Hahn D, Boers F, Jon Shah N, Suriya Prakash M, Sharma R, Kawaguchi H, Kobayashi T, Fiedler P, Griebel S, Biller S, Fonseca C, Vaz F, Zentner L, Zanow F, Haueisen J, Rochas V, Rihs T, Thut G, Rosenberg N, Landis T, Michel C, Moliadze V, Schmanke T, Lyzhko E, Bassüner S, Freitag C, Siniatchkin M, Thézé R, Guggisberg AG, Nahum L, Schnider A, Meier L, Friedrich H, Jann K, Landis B, Wiest R, Federspiel A, Strik W, Dierks T, Witte M, Kober SE, Neuper C, Wood G, König R, Matysiak A, Kordecki W, Sieluzycki C, Zacharias N, Heil P, Wyss C, Boers F, Arrubla J, Dammers J, Kawohl W, Neuner I, Shah NJ, Braboszcz C, Cahn RB, Levy J, Fernandez M, Delorme A, Rosas-Martinez L, Milne E, Zheng Y, Urakami Y, Kawamura K, Washizawa Y, Hiyoshi K, Cichocki A, Giroud N, Dellwo V, Meyer M, Rufener KS, Liem F, Dellwo V, Meyer M, Jones-Rounds JD, Raizada R, Staljanssens W, Strobbe G, van Mierlo P, Van Holen R, Vandenberghe S, Pefkou M, Becker R, Michel C, Hervais-Adelman A, He W, Brock J, Johnson B, Ohla K, Hitz K, Heekeren K, Obermann C, Huber T, Juckel G, Kawohl W, Gabriel D, Comte A, Henriques J, Magnin E, Grigoryeva L, Ortega JP, Haffen E, Moulin T, Pazart L, Aubry R, Kukleta M, Baris Turak B, Louvel J, Crespo-Garcia M, Cantero JL, Atienza M, Connell S, Kilborn K, Damborská A, Brázdil M, Rektor I, Kukleta M, Koberda JL, Bienkiewicz A, Koberda I, Koberda P, Moses A, Tomescu M, Rihs T, Britz J, Custo A, Grouiller F, Schneider M, Debbané M, Eliez S, Michel C, Wang GY, Kydd R, Wouldes TA, Jensen M, Russell BR, Dissanayaka N, Au T, Angwin A, O'Sullivan J, Byrne G, Silburn P, Marsh R, Mellic G, Copland D, Bänninger A, Kottlow M, Díaz Hernàndez L, Koenig T, Díaz Hernàndez L, Bänninger A, Koenig T, Hauser TU, Iannaccone R, Mathys C, Ball J, Drechsler R, Brandeis D, Walitza S, Brem S, Boeijinga PH, Pang EW, Valica T, Macdonald MJ, Oh A, Lerch JP, Anagnostou E, Di Lorenzo G, Pagani M, Monaco L, Daverio A, Verardo AR, Giannoudas I, La Porta P, Niolu C, Fernandez I, Siracusano A, Shimada T, Matsuda Y, Monkawa A, Monkawa T, Hashimoto R, Watanabe K, Kawasaki Y, Matsuda Y, Shimada T, Monkawa T, Monkawa A, Watanabe K, Kawasaki Y, Stegmayer K, Horn H, Federspiel A, Razavi N, Bracht T, Laimböck K, Strik W, Dierks T, Wiest R, Müller TJ, Walther S, Koorenhof LJ, Swithenby SJ, Martins-Mourao A, Rihs TA, Tomescu M, Song KW, Custo A, Knebel JF, Murray M, Eliez S, Michel CM, Volpe U, Merlotti E, Vignapiano A, Montefusco V, Plescia GM, Gallo O, Romano P, Mucci A, Galderisi S, Laimboeck K, Jann K, Walther S, Federspiel A, Wiest R, Strik W, Horn H. Abstracts of Presentations at the International Conference on Basic and Clinical Multimodal Imaging (BaCI), a Joint Conference of the International Society for Neuroimaging in Psychiatry (ISNIP), the International Society for Functional Source Imaging (ISFSI), the International Society for Bioelectromagnetism (ISBEM), the International Society for Brain Electromagnetic Topography (ISBET), and the EEG and Clinical Neuroscience Society (ECNS), in Geneva, Switzerland, September 5-8, 2013. Clin EEG Neurosci 2013; 44:1550059413507209. [PMID: 24368763 DOI: 10.1177/1550059413507209] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- B J He
- National Institutes of Health, Bethesda, MD, USA
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Bi B, Xiao X, Zhang H, Gao J, Tao M, Niu H, Wang Y, Wang Q, Chen C, Sun N, Li K, Fu J, Gan Z, Sang W, Zhang G, Yang L, Tian T, Li Q, Yang Q, Sun L, Li Y, Rong H, Guan C, Zhao X, Ye D, Zhang Y, Ma Z, Li H, He K, Chen J, Cai Y, Zhou C, Luo Y, Wang S, Gao S, Liu J, Guo L, Guan J, Kang Z, Di D, Li Y, Shi S, Li Y, Chen Y, Flint J, Kendler K, Liu Y. A comparison of the clinical characteristics of women with recurrent major depression with and without suicidal symptomatology. Psychol Med 2012; 42:2591-2598. [PMID: 22716960 PMCID: PMC3488812 DOI: 10.1017/s003329171200058x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2011] [Revised: 03/02/2012] [Accepted: 03/06/2012] [Indexed: 11/22/2022]
Abstract
BACKGROUND The relationship between recurrent major depression (MD) in women and suicidality is complex. We investigated the extent to which patients who suffered with various forms of suicidal symptomatology can be distinguished from those subjects without such symptoms. METHOD We examined the clinical features of the worst episode in 1970 Han Chinese women with recurrent DSM-IV MD between the ages of 30 and 60 years from across China. Student's t tests, and logistic and multiple logistic regression models were used to determine the association between suicidality and other clinical features of MD. RESULTS Suicidal symptomatology is significantly associated with a more severe form of MD, as indexed by both the number of episodes and number of MD symptoms. Patients reporting suicidal thoughts, plans or attempts experienced a significantly greater number of stressful life events. The depressive symptom most strongly associated with lifetime suicide attempt was feelings of worthlessness (odds ratio 4.25, 95% confidence interval 2.9-6.3). Excessive guilt, diminished concentration and impaired decision-making were also significantly associated with a suicide attempt. CONCLUSIONS This study contributes to the existing literature on risk factors for suicidal symptomatology in depressed women. Identifying specific depressive symptoms and co-morbid psychiatric disorders may help improve the clinical assessment of suicide risk in depressed patients. These findings could be helpful in identifying those who need more intense treatment strategies in order to prevent suicide.
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Affiliation(s)
- B. Bi
- The First Hospital of China Medical University, Shenyang, People's Republic of China (PRC)
| | - X. Xiao
- The First Hospital of China Medical University, Shenyang, People's Republic of China (PRC)
| | - H. Zhang
- The First Hospital of China Medical University, Shenyang, People's Republic of China (PRC)
| | - J. Gao
- ZheJiang Traditional Chinese Medical Hospital, Hangzhou, PRC
| | - M. Tao
- Second Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, PRC
| | - H. Niu
- No. 1 Hospital of Zhengzhou University, Zhengzhou, PRC
| | - Y. Wang
- Shandong Mental Health Center, Shan Dong, PRC
| | - Q. Wang
- Beijing Anding Hospital, Capital Medical University, Beijing, PRC
| | - C. Chen
- No. 1 Hospital of Medical College of Xian Jiaotong University, Xian, Shaan Xi, PRC
| | - N. Sun
- No. 1 Hospital of Shanxi Medical University, Shanxi, PRC
| | - K. Li
- Mental Hospital of Jiangxi Province, Jiangxi, PRC
| | - J. Fu
- ShengJing Hospital of China Medical University, Liaoning, PRC
| | - Z. Gan
- No. 3 Affiliated Hospital of Zhongshan University, Guangdong, PRC
| | - W. Sang
- Hebei Mental Health Center, Hebei, PRC
| | - G. Zhang
- No. 4 Affiliated Hospital of Jiangsu University, Jiang Su, PRC
| | - L. Yang
- Jilin Brain Hospital, Jilin, PRC
| | - T. Tian
- Tianjin Anding Hospital, Tianjin, PRC
| | - Q. Li
- No. 1 Mental Health Center Affiliated Harbin Medical University, Heilongjiang, PRC
| | - Q. Yang
- Chongqing Mental Health Center, Chongqing, PRC
| | - L. Sun
- Psychiatric Hospital of Henan Province, Henan, PRC
| | - Ying Li
- Dalian No. 7 People's Hospital and Dalian Mental Health Center, Dalian, PRC
| | - H. Rong
- Shenzhen Kangning Hospital, Shenzhen, PRC
| | - C. Guan
- Nanjing Brain Hospital, Jiang Su, PRC
| | - X. Zhao
- The First Hospital of Hebei Medical University, Shijiazhuang, PRC
| | - D. Ye
- Sichuan Mental Health Center, Sichuan, PRC
| | - Y. Zhang
- Lanzhou University Second Hospital, Second Clinical Medical College of Lanzhou University, Gansu Province, PRC
| | - Z. Ma
- No. 1 Hospital of Chongqing Medical University, Chongqing, PRC
| | - H. Li
- Mental Health Center of West China Hospital of Sichuan University, Si Chuan, PRC
| | - K. He
- Shanghai Tongji University Affiliated Tongji Hospital, Shanghai, PRC
| | - J. Chen
- Shanghai Jiao Tong University School of Medicine Affiliated Shanghai Mental Health Center, Shanghai, PRC
| | - Y. Cai
- Fudan University Affiliated Huashan Hospital, Shanghai, PRC
| | - C. Zhou
- Wuhan Mental Health Center, Hubei, PRC
| | - Y. Luo
- No. 3 Hospital of Heilongjiang Province, Heilongjiang, PRC
| | - S. Wang
- The First Affiliated Hospital of Jinan University, Guangzhou, PRC
| | - S. Gao
- Ningbo Kangning Hospital, Zhejiang, PRC
| | - J. Liu
- Suzhou Guangji Hospital, Jiangsu, PRC
| | - L. Guo
- The Fourth Military Medical University Affiliated Xijing Hospital, Shaanxi, PRC
| | - J. Guan
- Guangzhou Brain Hospital/Guangzhou Psychiatric Hospital, Guangzhou, PRC
| | - Z. Kang
- No. 4 People's Hospital of Liaocheng, Shandong, PRC
| | - D. Di
- Mental Health Institute of Jining Medical College, Shandong, PRC
| | - Yajuan Li
- Xian Mental Health Center, Xian, Shanxi, PRC
| | - S. Shi
- Fudan University Affiliated Huashan Hospital, Shanghai, PRC
| | - Yihan Li
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - Y. Chen
- Clinical Trial Service Unit, Richard Doll Building, Oxford, UK
| | - J. Flint
- Wellcome Trust Centre for Human Genetics, Oxford, UK
| | - K. Kendler
- Virginia Commonwealth University (VCU), Department of Psychiatry, Virginia Institute for Psychiatric and Behavioral Genetics, Richmond, VA, USA
| | - Y. Liu
- The First Hospital of China Medical University, Shenyang, People's Republic of China (PRC)
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McMahon MD, Guan C, Handelsman J, Thomas MG. Metagenomic analysis of Streptomyces lividans reveals host-dependent functional expression. Appl Environ Microbiol 2012; 78:3622-9. [PMID: 22427497 PMCID: PMC3346366 DOI: 10.1128/aem.00044-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 03/07/2012] [Indexed: 11/20/2022] Open
Abstract
Most functional metagenomic studies have been limited by the poor expression of many genes derived from metagenomic DNA in Escherichia coli, which has been the predominant surrogate host to date. To expand the range of expressed genes, we developed tools for construction and functional screening of metagenomic libraries in Streptomyces lividans. We expanded on previously published protocols by constructing a system that enables retrieval and characterization of the metagenomic DNA from biologically active clones. To test the functionality of these methods, we constructed and screened two metagenomic libraries in S. lividans. One was constructed with pooled DNA from 14 bacterial isolates cultured from Alaskan soil and the second with DNA directly extracted from the same soil. Functional screening of these libraries identified numerous clones with hemolytic activity, one clone that produces melanin by a previously unknown mechanism, and one that induces the overproduction of a secondary metabolite native to S. lividans. All bioactive clones were functional in S. lividans but not in E. coli, demonstrating the advantages of screening metagenomic libraries in more than one host.
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Affiliation(s)
- Matthew D. McMahon
- Department of Bacteriology
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Changhui Guan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Jo Handelsman
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA
| | - Michael G. Thomas
- Department of Bacteriology
- Microbiology Doctoral Training Program, University of Wisconsin—Madison, Madison, Wisconsin, USA
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Yu B, Ma Z, Guan C, Liu G, Ding H, Yin Y, Han W. Clinical introtumoral chemoimmunotherapy for late stages of lung cancer. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.e21001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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25
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Xiao B, Kuper H, Guan C, Bailey K, Limburg H. Rapid assessment of avoidable blindness in three counties, Jiangxi Province, China. Br J Ophthalmol 2010; 94:1437-42. [DOI: 10.1136/bjo.2009.165308] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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26
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Allen HK, Cloud-Hansen KA, Wolinski JM, Guan C, Greene S, Lu S, Boeyink M, Broderick NA, Raffa KF, Handelsman J. Resident microbiota of the gypsy moth midgut harbors antibiotic resistance determinants. DNA Cell Biol 2010; 28:109-17. [PMID: 19206998 DOI: 10.1089/dna.2008.0812] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Little is known about the significance of insects as environmental reservoirs of antibiotic-resistant bacteria. We characterized the antibiotic resistome of the microbial community in gypsy moth larval midguts by applying functional metagenomics to cultured isolates. The minimum inhibitory concentrations of 12 antibiotics were determined for 44 cultured isolates, and antibiotic resistance genes were selected from metagenomic libraries derived from DNA extracted from a pool of the isolates. Six unique clones were identified. Two were highly resistant to penicillin-type beta-lactams, two were moderately resistant to erythromycin, and two were moderately resistant to a range of antibiotics, including erythromycin, carbenicillin, and chloramphenicol. Sequence analysis predicted that the active genes encoded efflux pumps, a transcriptional activator of efflux pump protein expression, and an extended-spectrum class A beta-lactamase. Insect guts are a reservoir of antibiotic resistance genes with the potential for dissemination.
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Affiliation(s)
- Heather K Allen
- Departments of Bacteriology and Plant Pathology, University of Wisconsin, Madison, Wisconsin, USA
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27
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Abstract
OBJECTIVES Human X-linked hypophosphatemia (XLH) and its murine homologue, Hyp are caused by inactivating mutations in PHEX gene. The protein encoded by PHEX gene is an endopeptidase whose physiological substrate(s) has not been identified. Dentin matrix protein 1 (DMP1) and dentin sialophosphoprotein (DSPP), two members of the Small Integrin-Binding LIgand, N-linked Glycoprotein (SIBLING) family are proteolytically processed. It has been speculated that PHEX endopeptidase may be responsible for the proteolytic cleavage of DMP1 and DSPP. To test this hypothesis and to analyse the distribution of SIBLING proteins in the predentin/dentin complex and mandible of Hyp mice, we compared the expression of four SIBLING proteins, DMP1, DSPP, bone sialoprotein (BSP) and osteopontin (OPN) between Hyp and wild-type mice. METHODS These SIBLING proteins were analysed by protein chemistry and immunohistochemistry. RESULTS (1) Dentin matrix protein 1 and DSPP fragments are present in the extracts of Hyp predentin/dentin and bone; (2) the level of DMP1 proteoglycan form, BSP and OPN is elevated in the Hyp bone. CONCLUSIONS The PHEX protein is not the enzyme responsible for the proteolytic processing of DMP1 and DSPP. The altered distribution of SIBLING proteins may be involved in the pathogenesis of bone and dentin defects in Hyp and XLH.
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Affiliation(s)
- B Zhang
- Department of Oral and Maxillofacial Surgery, 2nd Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China.
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29
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Pawlowski K, Jacobsen KR, Alloisio N, Ford Denison R, Klein M, Tjepkema JD, Winzer T, Sirrenberg A, Guan C, Berry AM. Truncated hemoglobins in actinorhizal nodules of Datisca glomerata. Plant Biol (Stuttg) 2007; 9:776-85. [PMID: 17682965 DOI: 10.1055/s-2007-965258] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Three types of hemoglobins exist in higher plants, symbiotic, non-symbiotic, and truncated hemoglobins. Symbiotic (class II) hemoglobins play a role in oxygen supply to intracellular nitrogen-fixing symbionts in legume root nodules, and in one case ( Parasponia Sp.), a non-symbiotic (class I) hemoglobin has been recruited for this function. Here we report the induction of a host gene, dgtrHB1, encoding a truncated hemoglobin in Frankia-induced nodules of the actinorhizal plant Datisca glomerata. Induction takes place specifically in cells infected by the microsymbiont, prior to the onset of bacterial nitrogen fixation. A bacterial gene (Frankia trHBO) encoding a truncated hemoglobin with O (2)-binding kinetics suitable for the facilitation of O (2) diffusion ( ) is also expressed in symbiosis. Nodule oximetry confirms the presence of a molecule that binds oxygen reversibly in D. glomerata nodules, but indicates a low overall hemoglobin concentration suggesting a local function. Frankia trHbO is likely to be responsible for this activity. The function of the D. glomerata truncated hemoglobin is unknown; a possible role in nitric oxide detoxification is suggested.
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Affiliation(s)
- K Pawlowski
- Department of Plant Biochemistry, Göttingen University, 37077 Göttingen, Germany.
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30
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Guan C, Ju J, Borlee BR, Williamson LL, Shen B, Raffa KF, Handelsman J. Signal mimics derived from a metagenomic analysis of the gypsy moth gut microbiota. Appl Environ Microbiol 2007; 73:3669-76. [PMID: 17435000 PMCID: PMC1932686 DOI: 10.1128/aem.02617-06] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bacterial signaling is an important part of community life, but little is known about the signal transduction pathways of the as-yet-uncultured members of microbial communities. To address this gap, we aimed to identify genes directing the synthesis of signals in uncultured bacteria associated with the midguts of gypsy moth larvae. We constructed a metagenomic library consisting of DNA extracted directly from the midgut microbiota and analyzed it using an intracellular screen designated METREX, which detects inducers of quorum sensing. In this screen, the metagenomic DNA and a biosensor reside in the same cell. The biosensor consists of a quorum-sensing promoter, which requires an acylhomoserine lactone or other small molecule ligand for activation, driving the expression of the reporter gene gfp. We identified an active metagenomic clone encoding a monooxygenase homologue that mediates a pathway of indole oxidation that leads to the production of a quorum-sensing inducing compound. The signal from this clone induces the activities of LuxR from Vibrio fischeri and CviR from Chromobacterium violaceum. This study is the first to identify a new structural class of quorum-sensing inducer from uncultured bacteria.
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Affiliation(s)
- Changhui Guan
- Department of Plant Pathology, University of Wisconsin-Madison, WI 53706, USA
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31
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Thulasidas M, Guan C, Ranganatha S, Wu JK, Zhu X, Xu W. Effect of ocular artifact removal in brain computer interface accuracy. Conf Proc IEEE Eng Med Biol Soc 2007; 2004:4385-8. [PMID: 17271277 DOI: 10.1109/iembs.2004.1404220] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report the effect of removing ocular artifacts on the performance of a word-processing application based on the event related potential P300. Various methods of removing artifacts have been reported. The efficiency of these algorithms are usually done by subjective visual comparisons. Noting that there is a direct correlation of artifact rectifying algorithms to the accuracy in a brain computer interface system's accuracy, we present this work as a means to compare different algorithms.
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Affiliation(s)
- M Thulasidas
- NeuroInformatics, Institute for Infocomm Research, Singapore
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32
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Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl Environ Microbiol 2005; 71:6335-44. [PMID: 16204555 PMCID: PMC1265936 DOI: 10.1128/aem.71.10.6335-6344.2005] [Citation(s) in RCA: 164] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The goal of this study was to design and evaluate a rapid screen to identify metagenomic clones that produce biologically active small molecules. We built metagenomic libraries with DNA from soil on the floodplain of the Tanana River in Alaska. We extracted DNA directly from the soil and cloned it into fosmid and bacterial artificial chromosome vectors, constructing eight metagenomic libraries that contain 53,000 clones with inserts ranging from 1 to 190 kb. To identify clones of interest, we designed a high throughput "intracellular" screen, designated METREX, in which metagenomic DNA is in a host cell containing a biosensor for compounds that induce bacterial quorum sensing. If the metagenomic clone produces a quorum-sensing inducer, the cell produces green fluorescent protein (GFP) and can be identified by fluorescence microscopy or captured by fluorescence-activated cell sorting. Our initial screen identified 11 clones that induce and two that inhibit expression of GFP. The intracellular screen detected quorum-sensing inducers among metagenomic clones that a traditional overlay screen would not. One inducing clone carries a LuxI homologue that directs the synthesis of an N-acyl homoserine lactone quorum-sensing signal molecule. The LuxI homologue has 62% amino acid sequence identity to its closest match in GenBank, AmfI from Pseudomonas fluorescens, and is on a 78-kb insert that contains 67 open reading frames. Another inducing clone carries a gene with homology to homocitrate synthase. Our results demonstrate the power of an intracellular screen to identify functionally active clones and biologically active small molecules in metagenomic libraries.
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Affiliation(s)
- Lynn L Williamson
- Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison, WI 53706, USA
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33
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Jeong J, Suh S, Guan C, Tsay YF, Moran N, Oh CJ, An CS, Demchenko KN, Pawlowski K, Lee Y. A nodule-specific dicarboxylate transporter from alder is a member of the peptide transporter family. Plant Physiol 2004; 134:969-78. [PMID: 15001700 PMCID: PMC389920 DOI: 10.1104/pp.103.032102] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2003] [Revised: 10/12/2003] [Accepted: 12/23/2003] [Indexed: 05/17/2023]
Abstract
Alder (Alnus glutinosa) and more than 200 angiosperms that encompass 24 genera are collectively called actinorhizal plants. These plants form a symbiotic relationship with the nitrogen-fixing actinomycete Frankia strain HFPArI3. The plants provide the bacteria with carbon sources in exchange for fixed nitrogen, but this metabolite exchange in actinorhizal nodules has not been well defined. We isolated an alder cDNA from a nodule cDNA library by differential screening with nodule versus root cDNA and found that it encoded a transporter of the PTR (peptide transporter) family, AgDCAT1. AgDCAT1 mRNA was detected only in the nodules and not in other plant organs. Immunolocalization analysis showed that AgDCAT1 protein is localized at the symbiotic interface. The AgDCAT1 substrate was determined by its heterologous expression in two systems. Xenopus laevis oocytes injected with AgDCAT1 cRNA showed an outward current when perfused with malate or succinate, and AgDCAT1 was able to complement a dicarboxylate uptake-deficient Escherichia coli mutant. Using the E. coli system, AgDCAT1 was shown to be a dicarboxylate transporter with a K(m) of 70 microm for malate. It also transported succinate, fumarate, and oxaloacetate. To our knowledge, AgDCAT1 is the first dicarboxylate transporter to be isolated from the nodules of symbiotic plants, and we suggest that it may supply the intracellular bacteria with dicarboxylates as carbon sources.
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Affiliation(s)
- Jeeyon Jeong
- Department of Life Science, Pohang University of Science and Technology, Hyoja-dong, san 31, Pohang 790-784, Korea
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Guan C, Rosen ES, Boonsirichai K, Poff KL, Masson PH. The ARG1-LIKE2 gene of Arabidopsis functions in a gravity signal transduction pathway that is genetically distinct from the PGM pathway. Plant Physiol 2003; 133:100-12. [PMID: 12970478 PMCID: PMC196584 DOI: 10.1104/pp.103.023358] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2003] [Revised: 04/08/2003] [Accepted: 05/22/2003] [Indexed: 05/18/2023]
Abstract
The arl2 mutants of Arabidopsis display altered root and hypocotyl gravitropism, whereas their inflorescence stems are fully gravitropic. Interestingly, mutant roots respond like the wild type to phytohormones and an inhibitor of polar auxin transport. Also, their cap columella cells accumulate starch similarly to wild-type cells, and mutant hypocotyls display strong phototropic responses to lateral light stimulation. The ARL2 gene encodes a DnaJ-like protein similar to ARG1, another protein previously implicated in gravity signal transduction in Arabidopsis seedlings. ARL2 is expressed at low levels in all organs of seedlings and plants. arl2-1 arg1-2 double mutant roots display kinetics of gravitropism similar to those of single mutants. However, double mutants carrying both arl2-1 and pgm-1 (a mutation in the starch-biosynthetic gene PHOSPHOGLUCOMUTASE) at the homozygous state display a more pronounced root gravitropic defect than the single mutants. On the other hand, seedlings with a null mutation in ARL1, a paralog of ARG1 and ARL2, behave similarly to the wild type in gravitropism and other related assays. Taken together, the results suggest that ARG1 and ARL2 function in the same gravity signal transduction pathway in the hypocotyl and root of Arabidopsis seedlings, distinct from the pathway involving PGM.
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Affiliation(s)
- Changhui Guan
- Laboratory of Genetics, University of Wisconsin, 445 Henry Mall, Madison, WI 53706, USA
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35
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Pawlowski K, Swensen S, Guan C, Hadri AE, Berry AM, Bisseling T. Distinct patterns of symbiosis-related gene expression in actinorhizal nodules from different plant families. Mol Plant Microbe Interact 2003; 16:796-807. [PMID: 12971603 DOI: 10.1094/mpmi.2003.16.9.796] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Phylogenetic analyses suggest that, among the members of the Eurosid I clade, nitrogen-fixing root nodule symbioses developed multiple times independently, four times with rhizobia and four times with the genus Frankia. In order to understand the degree of similarity between symbiotic systems of different phylogenetic subgroups, gene expression patterns were analyzed in root nodules of Datisca glomerata and compared with those in nodules of another actinorhizal plant, Alnus glutinosa, and with the expression patterns of homologous genes in legumes. In parallel, the phylogeny of actinorhizal plants was examined more closely. The results suggest that, although relationships between major groups are difficult to resolve using molecular phylogenetic analysis, the comparison of gene expression patterns can be used to inform evolutionary relationships. In this case, stronger similarities were found between legumes and intracellularly infected actinorhizal plants (Alnus) than between actinorhizal plants of two different phylogenetic subgroups (Alnus/Datisca).
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Affiliation(s)
- Katharina Pawlowski
- Department of Molecular Biology, Agricultural University, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands.
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Abstract
Based on recent discoveries, we introduce a method to project a single structured pattern onto an object and then reconstruct the three-dimensional range from the distortions in the reflected and captured image. Traditional structured light methods require several different patterns to recover the depth, without ambiguity or albedo sensitivity, and are corrupted by object movement during the projection/ capture process. Our method efficiently combines multiple patterns into a single composite pattern projection allowing for real-time implementations. Because structured light techniques require standard image capture and projection technology, unlike time of arrival techniques, they are relatively low cost.
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Qin X, Sun X, Luo Z, Guan C, Zhang C. [Affection of epidermal growth factor on VIP secretion and VIPR expression in airway epithelial cells]. Hunan Yi Ke Da Xue Xue Bao 2002; 24:99-102. [PMID: 11938800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
In order to confirm the essential role of vasoactive intestinal peptide(VIP) on protection of local airway epithelium and investigate the modulation of the protective effect of VIP, secretion of VIP and expression of VIP receptor(VIPR) were studied in bronchial epithelial cells(BEC), and alveolar macrophages (AM). The radioimmunoassay was used for determining VIP secretion and the radio-ligand affinity analysis for VIPR expression. The effect of epidermal growth factor(EGF) was observed. The results showed that: 1. Both BEC and AM secreted VIP basically without remarkable stimulus, and some vesicles with electron-dense core which usually exist specifically in neuropeptide secreting cells were found in plasma of BEC; 2. In a dose-dependent manner, EGF promoted BEC to secrete VIP(r = 0.84, P < 0.05), and it was found that VIP secretion from AM was also elevated in EGF pretreated group(P < 0.05); 3. EGF exhibited a dose-dependent up-regulatory effect on the expression of VIPR in BEC(r = 0.95, P < 0.01). These results indicate that VIP may play an essential role in the protection at local airway by autocrine or paracrine, and the protective effect can be modulated by growth factors.
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Affiliation(s)
- X Qin
- Department of Physiology, Hunan Medical University, Changsha 410078
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Abstract
Gravitropism allows plant organs to guide their growth in relation to the gravity vector. For most roots, this response to gravity allows downward growth into soil where water and nutrients are available for plant growth and development. The primary site for gravity sensing in roots includes the root cap and appears to involve the sedimentation of amyloplasts within the columella cells. This process triggers a signal transduction pathway that promotes both an acidification of the wall around the columella cells, an alkalinization of the columella cytoplasm, and the development of a lateral polarity across the root cap that allows for the establishment of a lateral auxin gradient. This gradient is then transmitted to the elongation zones where it triggers a differential cellular elongation on opposite flanks of the central elongation zone, responsible for part of the gravitropic curvature. Recent findings also suggest the involvement of a secondary site/mechanism of gravity sensing for gravitropism in roots, and the possibility that the early phases of graviresponse, which involve differential elongation on opposite flanks of the distal elongation zone, might be independent of this auxin gradient. This review discusses our current understanding of the molecular and physiological mechanisms underlying these various phases of the gravitropic response in roots.
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Affiliation(s)
- Rujin Chen
- Laboratory of Genetics, University of Wisconsin-Madison, 53706, USA
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Boonsirichai K, Guan C, Chen R, Masson PH. Root gravitropism: an experimental tool to investigate basic cellular and molecular processes underlying mechanosensing and signal transmission in plants. Annu Rev Plant Biol 2002; 53:421-47. [PMID: 12221983 DOI: 10.1146/annurev.arplant.53.100301.135158] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The ability of plant organs to use gravity as a guide for growth, named gravitropism, has been recognized for over two centuries. This growth response to the environment contributes significantly to the upward growth of shoots and the downward growth of roots commonly observed throughout the plant kingdom. Root gravitropism has received a great deal of attention because there is a physical separation between the primary site for gravity sensing, located in the root cap, and the site of differential growth response, located in the elongation zones (EZs). Hence, this system allows identification and characterization of different phases of gravitropism, including gravity perception, signal transduction, signal transmission, and curvature response. Recent studies support some aspects of an old model for gravity sensing, which postulates that root-cap columellar amyloplasts constitute the susceptors for gravity perception. Such studies have also allowed the identification of several molecules that appear to function as second messengers in gravity signal transduction and of potential signal transducers. Auxin has been implicated as a probable component of the signal that carries the gravitropic information between the gravity-sensing cap and the gravity-responding EZs. This has allowed the identification and characterization of important molecular processes underlying auxin transport and response in plants. New molecular models can be elaborated to explain how the gravity signal transduction pathway might regulate the polarity of auxin transport in roots. Further studies are required to test these models, as well as to study the molecular mechanisms underlying a poorly characterized phase of gravitropism that is independent of an auxin gradient.
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Affiliation(s)
- K Boonsirichai
- Laboratory of Genetics, University of Wisconsin-Madison, 445 Henry Mall, Madison, Wisconsin 53706, USA
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Masson PH, Tasaka M, Morita MT, Guan C, Chen R, Boonsirichai K. Arabidopsis thaliana: A Model for the Study of Root and Shoot Gravitropism. Arabidopsis Book 2002; 1:e0043. [PMID: 22303208 PMCID: PMC3243349 DOI: 10.1199/tab.0043] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
UNLABELLED For most plants, shoots grow upward and roots grow downward. These growth patterns illustrate the ability for plant organs to guide their growth at a specified angle from the gravity vector (gravitropism). They allow shoots to grow upward toward light, where they can photosynthesize, and roots to grow downward into the soil, where they can anchor the plant as well as take up water and mineral ions.Gravitropism involves several steps organized in a specific response pathway. These include the perception of a gravistimulus (reorientation within the gravity field), the transduction of this mechanical stimulus into a physiological signal, the transmission of this signal from the site of sensing to the site of response, and a curvature-response which allows the organ tip to resume growth at a predefined set angle from the gravity vector.The primary sites for gravity sensing are located in the cap for roots, and in the endodermis for shoots. The curvature response occurs in the elongation zones for each organ. Upon gravistimulation, a gradient of auxin appears to be generated across the stimulated organ, and be transmitted to the site of response where it promotes a differential growth response. Therefore, while the gravity-induced auxin gradient has to be transmitted from the cap to the elongation zones in roots, there is no need for a longitudinal transport in shoots, as sites for gravity sensing and response overlap in this organ.A combination of molecular genetics, physiology, biochemistry and cell biology, coupled with the utilization of Arabidopsis thaliana as a model system, have recently allowed the identification of a number of molecules involved in the regulation of each phase of gravitropism in shoots and roots of higher plants. In this review, we attempt to summarize the results of these experiments, and we conclude by comparing the molecular and physiological mechanisms that underlie gravitropism in these organs. ABBREVIATIONS GSPA: gravitational set point angle; IAA: indole-3-acetic acid; NAA: 1-naphthalene acetic acid; NPA: 1-N-naphthylphthalamic acid; 2,4-D: 2,4-dichlorphenoxy acetic acid; TIBA: 2,3,5-triiodobenzoic acid.
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Yuan L, He S, Guan C, Pang Q. [The preparation and study on hepatic targeting tendency of galactosyl-anti-CD3-McAb in mice]. Hua Xi Yi Ke Da Xue Xue Bao 2001; 32:424-6. [PMID: 12536583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
OBJECTIVE This study sought to reduce the recurrence rate of primary liver cacer (PLC) after hepatectomy by increasing the concentration of infiltrating lymphocytes(TILs) at the target organ. METHODS It has been reported that galactosyl-anti-CD3-McAb has an obvious hepatic targeting tendency in vitro. On the basis of that work, the present authors conducted a study in mice. Galactosyl-anti-CD3-McAb was prepared and its carbohydrate density was measured with the phenol-sulphyric acid method, and then anti-CD3-McAb (labeled with 125I) and galactosyl-anti-CD3-McAb (labeled with 131I) were infused respectively via the peripheral vein and the radioactivity in each organ was measured. RESULTS The carbohydrate density of galactosyl-anti-CD3-McAb in this experiment was 58.12, which effectively guaranteed the specific binding between galactosyl-anti-CD3-McAb and hepatic binding protein(HBP). It was also noticed that anti-CD3-McAb tended to aggregate in the lungs while being infused via the peripheral vein, and that galactosyl-anti-CD3-McAb had an obvious hepatic targeting tendency in vivo and it stayed in liver for quite a long period. CONCLUSIONS Galactosyl-anti-CD3-McAb has an obvious hepatic targeting tendency in vivo while being infused through peripheral vein; this may be due to the specific binding between galactose and HBP.
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Affiliation(s)
- L Yuan
- Department of Surgery, First Affiliated Hospital, WCUMS, Chengdu 610041, China
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Du Q, Ji W, Yu J, Guan C. [The clinical and pathological research of supraglottic carcinoma with bilateral cervical nodal metastasis]. Lin Chuang Er Bi Yan Hou Ke Za Zhi 2001; 15:387-8, 390. [PMID: 12541882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
OBJECTIVE To evaluate clinical and pathological characteristics in patients with supraglottic carcinoma and bilateral cervical nodal metastasis. METHOD 60 patients with supraglottic carcinoma treated in this hospital from 1985 to 1994 were retrospectively reviewed, including 30 cases with bilateral metastasis (experiment group) and 30 cases with unilateral metastasis (control group). The two groups were contrasted according to site of tumor, tumor diameter, surface morphology, clinical staging, the degree of invading the contralateral semilarynx, Border's grading, growth mode of tumor edge, the degree of invading preepiglottic space. RESULT In stage T4 cases with low grading of cell differentiation made up 63.6% (7/11) in the bilateral metastasis group, while 10% in the ipsilateral metastasis group (P < 0.05). Significant differences lied between N0 group and N2 group (P < 0.05). Moderate and severe invasion of contralateral semilarynx in the bilateral group made up 87.5% (14/16), significantly higher than that in ipsilateral group 53.3% (16/30). CONCLUSION Bilateral neck dissection should be used in T4 cases with low grading of cell differentiation in which the contralateral semilarynx was invaded. Bilateral neck dissection should be taken for the treatment of supraglottic carcinoma with N2.3 diseases. Bilateral neck dissection is recommended for the patients with moderate and severe invasion of the contralateral semilarynx.
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Affiliation(s)
- Q Du
- Department of Otolaryngology, First Affiliated Hospital of China Medical University, Shenyang 110001
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Cai Q, Guan C, Ren Z. [Detection mucin gene in cervical lymph nodes in supraglottic cancer by reverse transcription polymerase chain reaction]. Zhonghua Er Bi Yan Hou Ke Za Zhi 2001; 36:247-9. [PMID: 12761987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
OBJECTIVE To investigate the efficacy of discovery of cervical lymph nodes micrometastasis of supraglottic carcinomas by detection of mucin (MUC1) gene. METHODS Twenty-five supraglottic carcinoma patients with clinically negative lymph nodes were performed neck dissection. MUC1 gene mRNA in these resected lymph nodes was detected by reverse transcription polymerase chain reaction (RT-PCR) and histopathological examination to find the potential micrometastasis. RESULTS Of all 93 cervical lymph nodes, micrometastasis were found in 23 nodes of 6 case by histopathological examination and RT-PCR. Four of 19 cases with negative lymph nodes pathologically showed MUC1 gene expression and were identified to have metastasis by clinical recurrence and serial-sectioning. Therefore, the rate of detection of micrometastasis by this way was 16% (4/25), higher than that of regular pathologic methods. CONCLUSION Detection of lymph nodes micrometastasis with RT-PCR method was more sensitive than that of regular pathologic methods. It is a valuable method to detect early lymph nodes metastasis.
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Affiliation(s)
- Q Cai
- Department of Otorhinolaryngology, First Clinic College, China Medical University, Shenyang 110001, China
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Abstract
OBJECTIVE To determine the pharmacokinetics of testosterone following its administration using transdermal gel or buccal lozenges. DESIGN Pilot study. SETTING University-based hospital. PATIENT(S) Ten bilaterally oophorectomized women. INTERVENTION(S) Daily micronized testosterone gel (1 mg) and testosterone propionate lozenge (1 mg). MAIN OUTCOME MEASURE(S) Total testosterone, androstenedione, dihydrotestosterone, 3alpha-androstanediol glucuronide, and sex hormone-binding globulin were measured in serum by specific radioimmunoassays; free testosterone levels were also calculated. RESULT(S) Before treatment, serum testosterone levels in the groups using the lozenge and gel were 16 +/- 4.0 and 20 +/- 6.0 ng/dL, respectively. Mean maximum testosterone levels obtained with the lozenge occurred 1 hour after administration on days 1 (692 +/- 236 ng/dL) and 14 (836 +/- 309 ng/dL) of treatment and fell precipitously thereafter. In contrast, testosterone levels obtained with the gel showed a prolonged rise reaching maximal levels of 97 +/- 78 and 100 +/- 60 ng/dL after 18 hours. The serum level patterns of free testosterone, dihydrotestosterone, and 3alpha-androstanediol glucuronide were similar to the corresponding total testosterone levels. CONCLUSION(S) Administration of testosterone lozenge by buccal absorption produced a rapid and brief elevation of testosterone levels, with levels reaching upper limits of the male range. In contrast, transdermal testosterone gel absorption resulted in a prolonged elevation of testosterone levels, which were in the hyperandrogenic female range but resembled steady state pharmacokinetics.
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Affiliation(s)
- C C Slater
- Department of Obstetrics and Gynecology, University of Southern California, Keck School of Medicine, Los Angeles, California, USA.
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Abstract
Current contents of persistent organic contaminants, polychlorinated biphenyls (PCBs), polycyclic aromatic hydrocarbons (PAHs) and the congeners (naphthalene, fluorene, phenanthrene, anthracene, fluoranthene, pyrene, chrysene, benzo(a)anthracene, benzo(a)pyrene and benzo(e)pyrene), DDTs and metabolites in the intertidal sediments of the Bohai Sea and the Yellow Sea were studied. The mean levels of DDTs, PAHs and PCBs were 177.52, 877.2 and 3.4 ng g-1 dry weight, respectively. The spatial trends of the contaminant residue levels were analysed too.
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Affiliation(s)
- M Ma
- Institute of Marine Environmental Protection, State Oceanic Administration (SOA), 42 Linghe Street, Shahekon District, Dalian, People's Republic of China
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Ji W, Yu J, Guan C. Pathologic features of occult lymphatic metastasis in supraglottic carcinoma. Chin Med J (Engl) 2001; 114:88-9. [PMID: 11779445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023] Open
Abstract
OBJECTIVE To study the pathologic features of occult lymphatic metastasis in supraglottic carcinoma. METHODS Serial sections of 153 neck dissection specimens in 100 patients with supraglottic carcinoma were evaluated under the microscope. RESULTS In 100 patients, 38 had occult metastatic lymph nodes. 51 metastatic lymph nodes were found in pathology, and their sizes ranged from 0.5 cm to 2.6 cm (average 1.1 cm). The distribution of 51 lymph nodes was 1 in level I (2%), 37 in level II (73%), 12 in level III (24%), and 1 in level IV (2%). Among the 51 nodes, 21 (41%) were early stage, 18 (35%) were growth stage, 7 (14%) were tull stage, and 5 (10%) were extracapsular stage. The differentiation degree and appearance of supraglottic carcinoma was not directly related with occult metastasis. CONCLUSION The occult metastatic rate of supraglottic carcinoma is high, and selective neck dissection may be necessary.
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Affiliation(s)
- W Ji
- Department of Otorhinolaryngology, First Affiliated Hospital, China Medical University, Shenyang 110001, China
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Li Y, Guan C. [Pharmacologic stress myocardial perfusion imaging]. Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 2000; 17:457-60. [PMID: 11211840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
This paper expounds the imaging methods, mechanism of action, hemodynamic responses, efficacy and side effects of three pharmacologic stressors (dipyridamole, adenosine and dobutamine) for clinical use in experiment of diagnosis, thus providing vital reference materials for clinical pharmacologic stress myocardial perfusion imaging.
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Affiliation(s)
- Y Li
- Department of Nuclear Medicine, First University Hospital, West China University of Medical Sciences, Chengdu 610041
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Li F, Song L, Guan C, Ge D, Liu Z. [Coupling effect of water and fertilizers on spring wheat yield in semi-arid area of western Liaoning Province]. Ying Yong Sheng Tai Xue Bao 2000; 11:535-9. [PMID: 11767672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
With optimum saturation design, a field experiment was conducted to study the coupling effect of water and fertilizers on spring wheat yield in semiarid area of western Liaoning Province. Regression model shows that water was the most important factor affecting spring wheat yield. Under natural raining and when the upper and the lower limit of irrigation was 360 mm and 45 mm, respectively, N was the most sensitive factor, water was the second, and P was the third. The effects of N, P and water on yield were statistically significant, and met the law of diminishing return. The most economic matching pattern of N, P and water was N 186 kg.hm-2, P 63 kg.hm-2, and water 300 mm. Properly increasing phosphorus fertilizer at the lack of water could strengthen the drought-resistance of spring wheat.
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Affiliation(s)
- F Li
- College of Environmental and Life Sciences, Liaoning University, Shenyang 110036
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Pan M, Tan T, Guan C. [Evaluation of side-effects after 131I-therapy for differentiated thyroid carcinoma]. Hua Xi Yi Ke Da Xue Xue Bao 2000; 31:197-9. [PMID: 12515135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
The purpose of this study was to evaluate the side-effects of differentiated thyroid carcinoma after treatment with 3.7-7.4 GBq of 131I. A total of 342 patients were treated with 131I from May, 1989 to January, 1999. The acute side-effects, the short-term and long-term side-effects were analyzed. The follow-up lasted 1-10 years with an average of 5.4 years. The results showed that thyroiditis occurred predominantly in the patients with a rate of 131I uptake > 30%, whereas sialoadenitis occurred more prevalently in the patients with a rate of 131I uptake < 30% (P < 0.001). The rates of nausea, vomiting, diarrhea and gastralgia were 12.2%, 5.2%, 3.5% and 2.7% respectively. There were no significant changes in the hemogram after treatment, compared against that before treatment. The overall rates of transient platelet abnormalities and leukopenia were 10.4% and 4.0% respectively, but the rates of the abnormalities in the patients with cumulative doses of 131I > 18.5 GBq were significantly higher than those in patients with cumulative doses of 131 I < 18.5 GBq. The lower rate of acute and short-term side-effects and the absence of long-term side-effects in this study indicate that 131I can be safely used to treat differentiated thyroid carcinoma.
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Affiliation(s)
- M Pan
- Department of Nuclear Medicine, First Affiliated Hospital, WCUMS, Chengdu 610041
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Slater C, Zhang C, Guan C, Huang R, Paulson R, Roy S, Stanczyk F. Dihydrotestosterone (dht) accumulation as a consequence of long-term dhea supplementation in postmenopausal women. Fertil Steril 2000. [DOI: 10.1016/s0015-0282(00)00434-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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