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Xiong W, Shen G, Bryant DA. Synechocystis sp. PCC 6803 CruA (sll0147) encodes lycopene cyclase and requires bound chlorophyll a for activity. PHOTOSYNTHESIS RESEARCH 2017; 131:267-280. [PMID: 27743323 DOI: 10.1007/s11120-016-0316-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 10/06/2016] [Indexed: 05/15/2023]
Abstract
The genome of the model cyanobacterium, Synechococcus sp. PCC 7002, encodes two paralogs of CruA-type lycopene cyclases, SynPCC7002_A2153 and SynPCC7002_A0043, which are denoted cruA and cruP, respectively. Unlike the wild-type strain, a cruA deletion mutant is light-sensitive, grows slowly, and accumulates lycopene, γ-carotene, and 1-OH-lycopene; however, this strain still produces β-carotene and other carotenoids derived from it. Expression of cruA from Synechocystis sp. PCC 6803 (cruA 6803) in Escherichia coli strains that synthesize either lycopene or γ-carotene did not lead to the synthesis of either γ-carotene or β-carotene, respectively. However, expression of this orthologous cruA 6803 gene (sll0147) in the Synechococcus sp. PCC 7002 cruA deletion mutant produced strains with phenotypic properties identical to the wild type. CruA6803 was purified from Synechococcus sp. PCC 7002 by affinity chromatography, and the purified protein was pale yellow-green due to the presence of bound chlorophyll (Chl) a and β-carotene. Native polyacrylamide gel electrophoresis of the partly purified protein in the presence of lithium dodecylsulfate at 4 °C confirmed that the protein was yellow-green in color. When purified CruA6803 was assayed in vitro with either lycopene or γ-carotene as substrate, β-carotene was synthesized. These data establish that CruA6803 is a lycopene cyclase and that it requires a bound Chl a molecule for activity. Possible binding sites for Chl a and the potential regulatory role of the Chl a in coordination of Chl and carotenoid biosynthesis are discussed.
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Ho MY, Gan F, Shen G, Zhao C, Bryant DA. Far-red light photoacclimation (FaRLiP) in Synechococcus sp. PCC 7335: I. Regulation of FaRLiP gene expression. PHOTOSYNTHESIS RESEARCH 2017; 131:173-186. [PMID: 27638320 DOI: 10.1007/s11120-016-0309-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/09/2016] [Indexed: 06/06/2023]
Abstract
Far-red light photoacclimation (FaRLiP) is a mechanism that allows some cyanobacteria to utilize far-red light (FRL) for oxygenic photosynthesis. During FaRLiP, cyanobacteria remodel photosystem (PS) I, PS II, and phycobilisomes while synthesizing Chl d, Chl f, and far-red-absorbing phycobiliproteins, and these changes enable these organisms to use FRL for growth. In this study, a conjugation-based genetic system was developed for Synechococcus sp. PCC 7335. Three antibiotic cassettes were successfully used to generate knockout mutations in genes in Synechococcus sp. PCC 7335, which should allow up to three gene loci to be modified in one strain. This system was used to delete the rfpA, rfpB, and rfpC genes individually, and characterization of the mutants demonstrated that these genes control the expression of the FaRLiP gene cluster in Synechococcus sp. PCC 7335. The mutant strains exhibited some surprising differences from similar mutants in other FaRLiP strains. Notably, mutations in any of the three master transcription regulatory genes led to enhanced synthesis of phycocyanin and PS II. A time-course study showed that acclimation of the photosynthetic apparatus from that produced in white light to that produced in FRL occurs very slowly over a period 12-14 days in this strain and that it is associated with a substantial reduction (~34 %) in the chlorophyll a content of the cells. This study shows that there are differences in the detailed responses of cyanobacteria to growth in FRL in spite of the obvious similarities in the organization and regulation of the FaRLiP gene cluster.
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Ho MY, Gan F, Shen G, Bryant DA. Far-red light photoacclimation (FaRLiP) in Synechococcus sp. PCC 7335. II.Characterization of phycobiliproteins produced during acclimation to far-red light. PHOTOSYNTHESIS RESEARCH 2017; 131:187-202. [PMID: 27623780 DOI: 10.1007/s11120-016-0303-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 08/30/2016] [Indexed: 06/06/2023]
Abstract
Phycobilisomes (PBS) are antenna complexes that harvest light for photosystem (PS) I and PS II in cyanobacteria and some algae. A process known as far-red light photoacclimation (FaRLiP) occurs when some cyanobacteria are grown in far-red light (FRL). They synthesize chlorophylls d and f and remodel PS I, PS II, and PBS using subunits paralogous to those produced in white light. The FaRLiP strain, Leptolyngbya sp. JSC-1, replaces hemidiscoidal PBS with pentacylindrical cores, which are produced when cells are grown in red or white light, with PBS with bicylindrical cores when cells are grown in FRL. This study shows that the PBS of another FaRLiP strain, Synechococcus sp. PCC 7335, are not remodeled in cells grown in FRL. Instead, cells grown in FRL produce bicylindrical cores that uniquely contain the paralogous allophycocyanin subunits encoded in the FaRLiP cluster, and these bicylindrical cores coexist with red-light-type PBS with tricylindrical cores. The bicylindrical cores have absorption maxima at 650 and 711 nm and a low-temperature fluorescence emission maximum at 730 nm. They contain ApcE2:ApcF:ApcD3:ApcD2:ApcD5:ApcB2 in the approximate ratio 2:2:4:6:12:22, and a structural model is proposed. Time course experiments showed that bicylindrical cores were detectable about 48 h after cells were transferred from RL to FRL and that synthesis of red-light-type PBS continued throughout a 21-day growth period. When considered in comparison with results for other FaRLiP cyanobacteria, the results here show that acclimation responses to FRL can differ considerably among FaRLiP cyanobacteria.
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Chen Y, Du W, Shen G, Zhuo S, Zhu X, Shen H, Huang Y, Su S, Lin N, Pei L, Zheng X, Wu J, Duan Y, Wang X, Liu W, Wong M, Tao S. Household air pollution and personal exposure to nitrated and oxygenated polycyclic aromatics (PAHs) in rural households: Influence of household cooking energies. INDOOR AIR 2017; 27:169-178. [PMID: 27008622 DOI: 10.1111/ina.12300] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Accepted: 03/15/2016] [Indexed: 05/22/2023]
Abstract
Residential solid fuels are widely consumed in rural China, contributing to severe household air pollution for many products of incomplete combustion, such as polycyclic aromatic hydrocarbons (PAHs) and their polar derivatives. In this study, concentrations of nitrated and oxygenated PAH derivatives (nPAHs and oPAHs) for household and personal air were measured and analyzed for influencing factors like smoking and cooking energy type. Concentrations of nPAHs and oPAHs in kitchens were higher than those in living rooms and in outdoor air. Exposure levels measured by personal samplers were lower than levels in indoor air, but higher than outdoor air levels. With increasing molecular weight, individual compounds tended to be more commonly partitioned to particulate matter (PM); moreover, higher molecular weight nPAHs and oPAHs were preferentially found in finer particles, suggesting a potential for increased health risks. Smoking behavior raised the concentrations of nPAHs and oPAHs in personal air significantly. People who cooked food also had higher personal exposures. Cooking and smoking have a significant interaction effect on personal exposure. Concentrations in kitchens and personal exposure to nPAHs and oPAHs for households using wood and peat were significantly higher than for those using electricity and liquid petroleum gas (LPG).
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55
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Shen G, Darendeliler MA. The Adaptive Remodeling of Condylar Cartilage— A Transition from Chondrogenesis to Osteogenesis. J Dent Res 2016; 84:691-9. [PMID: 16040724 DOI: 10.1177/154405910508400802] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Mandibular condylar cartilage is categorized as articular cartilage but markedly distinguishes itself in many biological aspects, such as its embryonic origin, ontogenetic development, post-natal growth mode, and histological structures. The most marked uniqueness of condylar cartilage lies in its capability of adaptive remodeling in response to external stimuli during or after natural growth. The adaptation of condylar cartilage to mandibular forward positioning constitutes the fundamental rationale for orthodontic functional therapy, which partially contributes to the correction of jaw discrepancies by achieving mandibular growth modification. The adaptive remodeling of condylar cartilage proceeds with the biomolecular pathway initiating from chondrogenesis and finalizing with osteogenesis. During condylar adaptation, chondrogenesis is activated when the external stimuli, e.g., condylar repositioning, generate the differentiation of mesenchymal cells in the articular layer of cartilage into chondrocytes, which proliferate and then progressively mature into hypertrophic cells. The expression of regulatory growth factors, which govern and control phenotypic conversions of chondrocytes during chondrogenesis, increases during adaptive remodeling to enhance the transition from chondrogenesis into osteogenesis, a process in which hypertrophic chondrocytes and matrices degrade and are replaced by bone. The transition is also sustained by increased neovascularization, which brings in osteoblasts that finally result in new bone formation beneath the degraded cartilage.
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56
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Shi L, Zhang J, Shen G, Xu Z, Xu Q, He L. Collaborative contribution of six cytochrome P450 monooxygenase genes to fenpropathrin resistance in Tetranychus cinnabarinus (Boisduval). INSECT MOLECULAR BIOLOGY 2016; 25:653-665. [PMID: 27351452 DOI: 10.1111/imb.12251] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Cytochrome P450 monooxygenases (P450s), as an important family of detoxification enzymes, participate in the metabolism of agrochemicals in almost all agricultural pests and play important roles in the development of insecticide resistance. Two P450 genes (CYP389B1 and CYP392A26) were identified and their expression patterns were investigated in our previous study. In this study, four more P450 gene sequences (CYP391A1, CYP384A1, CYP392D11 and CYP392A28) from the Clan 2, Clan 3 and Clan 4 families were identified and characterized. Quantitative PCR analysis showed that these four P450 genes were highly expressed in a fenpropathrin-resistant (FeR) strain of Tetranychus cinnabarinus. In addition, their expressions were much more sensitive to fenpropathrin induction in the FeR strain than the susceptible strain. Gene-silencing experiments via double-stranded RNA feeding were carried out. The results showed that mRNA levels of these six P450 genes were reduced in the FeR strain and the activities of P450s were decreased. Consequently mite susceptibilities to fenpropathrin were increased. Interestingly, silencing all six P450 genes simultaneously had an even greater effect on resistance than silencing them individually. This study increases our understanding of the molecular mechanisms of insecticide detoxification, suggesting that the overexpression of these six P450 genes might play important roles in fenpropathrin resistance in T. cinnabarinus collaboratively.
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Qiang W, Zhu YY, Shen G, Zou J. Identification of a novel HLA-B*44 allele, HLA-B*44:237N, in a Chinese individual. HLA 2016; 88:126-7. [PMID: 27522952 DOI: 10.1111/tan.12862] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 07/23/2016] [Accepted: 07/26/2016] [Indexed: 11/30/2022]
Abstract
B*44:237N differs from B*44:03:01 by nucleotides deletion at nucleotide 286 and 287 in exon 2.
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58
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Ho MY, Shen G, Canniffe DP, Zhao C, Bryant DA. Light-dependent chlorophyll f synthase is a highly divergent paralog of PsbA of photosystem II. Science 2016; 353:science.aaf9178. [PMID: 27386923 DOI: 10.1126/science.aaf9178] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 06/22/2016] [Indexed: 12/22/2022]
Abstract
Chlorophyll f (Chl f) permits some cyanobacteria to expand the spectral range for photosynthesis by absorbing far-red light. We used reverse genetics and heterologous expression to identify the enzyme for Chl f synthesis. Null mutants of "super-rogue" psbA4 genes, divergent paralogs of psbA genes encoding the D1 core subunit of photosystem II, abolished Chl f synthesis in two cyanobacteria that grow in far-red light. Heterologous expression of the psbA4 gene, which we rename chlF, enables Chl f biosynthesis in Synechococcus sp. PCC 7002. Because the reaction requires light, Chl f synthase is probably a photo-oxidoreductase that employs catalytically useful Chl a molecules, tyrosine YZ, and plastoquinone (as does photosystem II) but lacks a Mn4Ca1O5 cluster. Introduction of Chl f biosynthesis into crop plants could expand their ability to use solar energy.
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59
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Shen G, Gan F, Bryant DA. The siderophilic cyanobacterium Leptolyngbya sp. strain JSC-1 acclimates to iron starvation by expressing multiple isiA-family genes. PHOTOSYNTHESIS RESEARCH 2016; 128:325-340. [PMID: 27071628 DOI: 10.1007/s11120-016-0257-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 03/24/2016] [Indexed: 06/05/2023]
Abstract
In the evolution of different cyanobacteria performing oxygenic photosynthesis, the core complexes of the two photosystems were highly conserved. However, cyanobacteria exhibit significant diversification in their light-harvesting complexes and have flexible regulatory mechanisms to acclimate to changes in their growth environments. In the siderophilic, filamentous cyanobacterium, Leptolyngbya sp. strain JSC-1, five different isiA-family genes occur in two gene clusters. During acclimation to Fe limitation, relative transcript levels for more than 600 genes increased more than twofold. Relative transcript levels were ~250 to 300 times higher for the isiA1 gene cluster (isiA1-isiB-isiC), and ~440- to 540-fold for the isiA2-isiA3-isiA4-cpcG2-isiA5 gene cluster after 48 h of iron starvation. Chl-protein complexes were isolated and further purified from cells grown under Fe-replete and Fe-depleted conditions. A single class of particles, trimeric PSI, was identified by image analysis of electron micrographs of negatively stained PSI complexes from Fe-replete cells. However, three major classes of particles were observed for the Chl-protein supercomplexes from cells grown under iron starvation conditions. Based on LC-MS-MS analyses, the five IsiA-family proteins were found in the largest supercomplexes together with core components of the two photosystems; however, IsiA5 was not present in complexes in which only the core subunits of PSI were detected. IsiA5 belongs to the same clade as PcbC proteins in a phylogenetic classification, and it is proposed that IsiA5 is most likely involved in supercomplexes containing PSII dimers. IsiA4, which is a fusion of an IsiA domain and a C-terminal PsaL domain, was found together with IsiA1, IsiA2, and IsiA3 in complexes with monomeric PSI. The data indicate that horizontal gene transfer, gene duplication, and divergence have played important roles in the adaptive evolution of this cyanobacterium to iron starvation conditions.
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Hsiao J, Yuan TY, Tsai MS, Lu CY, Lin YC, Lee ML, Lin SW, Chang FC, Liu Pimentel H, Olive C, Coito C, Shen G, Young M, Thorne T, Lawrence M, Magistri M, Faghihi MA, Khorkova O, Wahlestedt C. Upregulation of Haploinsufficient Gene Expression in the Brain by Targeting a Long Non-coding RNA Improves Seizure Phenotype in a Model of Dravet Syndrome. EBioMedicine 2016; 9:257-277. [PMID: 27333023 PMCID: PMC4972487 DOI: 10.1016/j.ebiom.2016.05.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 02/07/2023] Open
Abstract
Dravet syndrome is a devastating genetic brain disorder caused by heterozygous loss-of-function mutation in the voltage-gated sodium channel gene SCN1A. There are currently no treatments, but the upregulation of SCN1A healthy allele represents an appealing therapeutic strategy. In this study we identified a novel, evolutionary conserved mechanism controlling the expression of SCN1A that is mediated by an antisense non-coding RNA (SCN1ANAT). Using oligonucleotide-based compounds (AntagoNATs) targeting SCN1ANAT we were able to induce specific upregulation of SCN1A both in vitro and in vivo, in the brain of Dravet knock-in mouse model and a non-human primate. AntagoNAT-mediated upregulation of Scn1a in postnatal Dravet mice led to significant improvements in seizure phenotype and excitability of hippocampal interneurons. These results further elucidate the pathophysiology of Dravet syndrome and outline a possible new approach for the treatment of this and other genetic disorders with similar etiology.
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61
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Zhu YY, Qiang W, Shen G, Zou J, Jiang YZ. A novel HLA-B allele, HLA-B*40:01:47. HLA 2016; 87:461-2. [PMID: 27140171 DOI: 10.1111/tan.12806] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 11/27/2022]
Abstract
HLA-B*40:01:47 differs from HLA-B*40:01:01 by one nucleotide exchange at position 420 in exon 3.
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62
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Chen Y, Shen G, Huang Y, Zhang Y, Han Y, Wang R, Shen H, Su S, Lin N, Zhu D, Pei L, Zheng X, Wu J, Wang X, Liu W, Wong M, Tao S. Household air pollution and personal exposure risk of polycyclic aromatic hydrocarbons among rural residents in Shanxi, China. INDOOR AIR 2016; 26:246-258. [PMID: 25808453 DOI: 10.1111/ina.12204] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/16/2015] [Indexed: 06/04/2023]
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are a group of pollutants of widespread concerns. Gaseous and size-segregated particulate-phase PAHs were collected in indoor and outdoor air in rural households. Personal exposure was measured and compared to the ingestion exposure. The average concentrations of 28 parent PAHs and benzo(a)pyrene (BaP) were 9000 ± 8390 and 131 ± 236 ng/m(3) for kitchen, 2590 ± 2270 and 43 ± 95 ng/m(3) for living room, and 2800 ± 3890 and 1.6 ± 0.7 ng/m(3) for outdoor air, respectively. The mass percent of high molecular weight (HMW) compounds with 5-6 rings contributed 1.3% to total 28 parent PAHs. Relatively higher fractions of HMW PAHs were found in indoor air compared to outdoor air. Majorities of particle-bound PAHs were found in the finest PM0.25 , and the highest levels of fine PM0.25 -bound PAHs were in the kitchen using peat and wood as energy sources. The 24-h personal PAH exposure concentration was 2100 ± 1300 ng/m(3) . Considering energies, exposures to those using wood were the highest. The PAH inhalation exposure comprised up to about 30% in total PAH exposure through food ingestion and inhalation, and the population attributable fraction (PAF) for lung cancer in the region was 0.85%. The risks for inhaled and ingested intakes of PAHs were 1.0 × 10(-5) and 1.1 × 10(-5) , respectively.
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63
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Zhu YY, Qiang W, Shen G, Zou J, Liu GJ. HLA-A*24:02:96, a novel variant of HLA-A*24:02:01:01, identified in a Chinese individual by sequence-based typing. HLA 2016; 87:171-2. [PMID: 26918921 DOI: 10.1111/tan.12758] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/26/2016] [Accepted: 01/31/2016] [Indexed: 11/30/2022]
Abstract
HLA-A*24:02:96 shows one nucleotide difference from HLA-A*24:02:01:01 at position 318 in exon 2 from C to T.
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64
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Qiang W, Shen G, Zhu YY, Zou J. A novel allele, HLA-B*55:77, identified by sequence-based typing in a Chinese individual. HLA 2016; 87:185-6. [PMID: 26916975 DOI: 10.1111/tan.12748] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 01/13/2016] [Accepted: 01/20/2016] [Indexed: 11/27/2022]
Abstract
HLA-B*55:77 differs from B*55:02:01:01 by a single nucleotide at position 164 in exon 2.
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65
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Zou J, Qiang W, Shen G, Zhu YY, Li WX, Liu GJ. Identification of a novel HLA-B*40 allele, HLA-B*40:324, by sequence-based typing, in a Chinese individual. HLA 2016; 87:110-1. [PMID: 26889906 DOI: 10.1111/tan.12746] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 01/13/2016] [Accepted: 01/20/2016] [Indexed: 11/29/2022]
Abstract
The new allele, HLA-B*40:324 differs from B*40:63 by two nucleotide changes in exon 3.
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66
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Li WX, Xia JA, Mao Y, Li G, Shen G. Identification of a new HLA-B allele, HLA-B*15:300, in a Chinese individual. HLA 2016; 87:175-6. [PMID: 26864906 DOI: 10.1111/tan.12747] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/12/2016] [Accepted: 01/20/2016] [Indexed: 11/28/2022]
Abstract
HLA-B*15:300 differs from B*15:01:01:01 by one nucleotide exchange at position 540(G > C) with an amino exchange.
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67
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Zhao C, Gan F, Shen G, Bryant DA. RfpA, RfpB, and RfpC are the Master Control Elements of Far-Red Light Photoacclimation (FaRLiP). Front Microbiol 2015; 6:1303. [PMID: 26635768 PMCID: PMC4658448 DOI: 10.3389/fmicb.2015.01303] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/06/2015] [Indexed: 11/24/2022] Open
Abstract
Terrestrial cyanobacteria often occur in niches that are strongly enriched in far-red light (FRL; λ > 700 nm). Some cyanobacteria exhibit a complex and extensive photoacclimation response, known as FRL photoacclimation (FaRLiP). During the FaRLiP response, specialized paralogous proteins replace 17 core subunits of the three major photosynthetic complexes: Photosystem (PS) I, PS II, and the phycobilisome. Additionally, the cells synthesize both chlorophyll (Chl) f and Chl d. Using biparental mating from Escherichia coli, we constructed null mutants of three genes, rfpA, rfpB, and rfpC, in the cyanobacteria Chlorogloeopsis fritschii PCC 9212 and Chroococcidiopsis thermalis PCC 7203. The resulting mutants were no longer able to modify their photosynthetic apparatus to absorb FRL, were no longer able to synthesize Chl f, inappropriately synthesized Chl d in white light, and were unable to transcribe genes of the FaRLiP gene cluster. We conclude that RfpA, RfpB, and RfpC constitute a FRL-activated signal transduction cascade that is the master control switch for the FaRLiP response. FRL is proposed to activate (or inactivate) the histidine kinase activity of RfpA, which leads to formation of the active state of RfpB, the key response regulator and transcription activator. RfpC may act as a phosphate shuttle between RfpA and RfpB. Our results show that reverse genetics via conjugation will be a powerful approach in detailed studies of the FaRLiP response.
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Shen G, Qiang W, Zhu YY, Zou J, Liu GJ, Yao L, Yin JP. A novel alleleHLA-A*11:152was identified by sequence-based typing in a Chinese individual. HLA 2015; 87:41-2. [DOI: 10.1111/tan.12707] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 10/12/2015] [Accepted: 10/25/2015] [Indexed: 11/30/2022]
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69
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Yu D, Nie P, Xing G, Shen G. Multi-dimension aesthetic evaluation of the patients with CLP wearing DDRD: a 5-year retrospective study. Int J Oral Maxillofac Surg 2015. [DOI: 10.1016/j.ijom.2015.08.399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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70
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Popov D, Park C, Kenney-Benson C, Shen G. High pressure Laue diffraction and its application to study microstructural changes during the α → β phase transition in Si. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:072204. [PMID: 26233344 DOI: 10.1063/1.4926894] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/10/2015] [Indexed: 06/04/2023]
Abstract
An approach using polychromatic x-ray Laue diffraction is described for studying pressure induced microstructural changes of materials under pressure. The advantages of this approach with respect to application of monochromatic x-ray diffraction and other techniques are discussed. Experiments to demonstrate the applications of the method have been performed on the α → β phase transition in Si at high pressures using a diamond anvil cell. We present the characterization of microstructures across the α-β phase transition, such as morphology of both the parent and product phases, relative orientation of single-crystals, and deviatoric strains. Subtle inhomogeneous strain of the single-crystal sample caused by lattice rotations becomes detectable with the approach.
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Nowack S, Olsen MT, Schaible GA, Becraft ED, Shen G, Klapper I, Bryant DA, Ward DM. The molecular dimension of microbial species: 2. Synechococcus strains representative of putative ecotypes inhabiting different depths in the Mushroom Spring microbial mat exhibit different adaptive and acclimative responses to light. Front Microbiol 2015; 6:626. [PMID: 26175719 PMCID: PMC4484337 DOI: 10.3389/fmicb.2015.00626] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/08/2015] [Indexed: 11/13/2022] Open
Abstract
Closely related strains of thermophilic Synechococcus were cultivated from the microbial mats found in the effluent channels of Mushroom Spring, Yellowstone National Park (YNP). These strains have identical or nearly identical 16S rRNA sequences but are representative of separate, predicted putative ecotype (PE) populations, which were identified by using the more highly resolving psaA locus and which predominate at different vertical positions within the 1-mm-thick upper-green layer of the mat. Pyrosequencing confirmed that each strain contained a single, predominant psaA genotype. Strains differed in growth rate as a function of irradiance. A strain with a psaA genotype corresponding to a predicted PE that predominates near the mat surface grew fastest at high irradiances, whereas strains with psaA genotypes representative of predominant subsurface populations grew faster at low irradiance and exhibited greater sensitivity to abrupt shifts to high light. The high-light-adapted and low-light-adapted strains also exhibited differences in pigment content and the composition of the photosynthetic apparatus (photosystem ratio) when grown under different light intensities. Cells representative of the different strains had similar morphologies under low-light conditions, but under high-light conditions, cells of low-light-adapted strains became elongated and formed short chains of cells. Collectively, the results presented here are consistent with the hypothesis that closely related, but distinct, ecological species of Synechococcus occupy different light niches in the Mushroom Spring microbial mat and acclimate differently to changing light environments.
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Shen G, Zhou H, Jia Z, Deng H. Diagnostic performance of diffusion-weighted MRI for detection of pelvic metastatic lymph nodes in patients with cervical cancer: a systematic review and meta-analysis. Br J Radiol 2015; 88:20150063. [PMID: 26111112 DOI: 10.1259/bjr.20150063] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
In recent years, diffusion-weighted (DW) MRI has emerged as a new technique for detecting the pelvic lymph metastases in patients with cervical cancer. The aim of this meta-analysis was to assess the diagnostic value of DW imaging (DWI) for benign/malignant discrimination of pelvic lymph nodes (LNs). Studies about DWI for the detection of metastatic LNs were searched in the PubMed, EMBASE, Web of Science, EBSCO, the Cochrane Library and three Chinese databases. Based on the extracted data, we determined pooled sensitivities, specificities and diagnostic odds ratios (DORs) across studies, calculated positive and negative likelihood ratios (LRs) and constructed summary receiver operating characteristic curves with area under the curve (AUC) and Q* obtained. We also analysed the heterogeneity between studies based on subgroup analysis, threshold effect and publication bias. In total, 15 studies involving 1021 patients met the inclusion criteria. The pooled sensitivity, specificity and DOR of DWI were 0.86 [95% confidence interval (CI), 0.84-0.89], 0.84 (95% CI, 0.83-0.86) and 47.21 (95% CI, 25.67-86.81), respectively. LR syntheses yielded overall positive LR of 6.55 (95% CI, 4.77-9.01) and negative LR of 0.17 (95% CI, 0.12-0.23). The AUC and Q* index were 0.9384 and 0.8754, respectively. The heterogeneity was relatively high between studies; however, there was no evidence for threshold effect and publication bias. DWI is beneficial in the pelvic nodal assessment in patients with cervical cancer. Large-scale, high-quality trials with standard protocols are required to evaluate its clinical value for discrimination of metastatic from non-metastatic pelvic LNs in patients with cervical cancer. Advances in knowledge include providing evidence to assess the role of DWI in nodal staging of cervical cancer.
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Li L, Li T, Zhang Y, Pan Z, Wu B, Huang X, Zhang Y, Mei Y, Ge L, Shen G, Ge RS, Zhu D, Lou Y. Peroxisome proliferator-activated receptorβ/δ activation is essential for modulating p-Foxo1/Foxo1 status in functional insulin-positive cell differentiation. Cell Death Dis 2015; 6:e1715. [PMID: 25855963 PMCID: PMC4650555 DOI: 10.1038/cddis.2015.88] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 11/25/2022]
Abstract
Peroxisome proliferator-activated receptors (PPARs) participate in energy homeostasis and play essential roles in diabetes therapy through their effects on non-pancreas tissues. Pathological microenvironment may influence the metabolic requirements for the maintenance of stem cell differentiation. Accordingly, understanding the mechanisms of PPARs on pancreatic β-cell differentiation may be helpful to find the underlying targets of disrupted energy homeostasis under the pancreatic disease condition. PPARs are involved in stem cell differentiation via mitochondrial oxidative phosphorylation, but the subtype member activation and the downstream regulation in functional insulin-positive (INS+) cell differentiation remain unclear. Here, we show a novel role of PPARβ/δ activation in determining INS+ cell differentiation and functional maturation. We found PPARβ/δ expression selectively upregulated in mouse embryonic pancreases or stem cells-derived INS+ cells at the pancreatic mature stage in vivo and in vitro. Strikingly, given the inefficiency of generating INS+ cells in vitro, PPARβ/δ activation displayed increasing mouse and human ES cell-derived INS+ cell numbers and insulin secretion. This phenomenon was closely associated with the forkhead box protein O1 (Foxo1) nuclear shuttling, which was dependent on PPARβ/δ downstream PI3K/Akt signaling transduction. The present study reveals the essential role of PPARβ/δ activation on p-Foxo1/Foxo1 status, and in turn, determining INS+ cell generation and insulin secretion via affecting pancreatic and duodenal homeobox-1 expression. The results demonstrate the underlying mechanism by which PPARβ/δ activation promotes functional INS+ cell differentiation. It also provides potential targets for anti-diabetes drug discovery and hopeful clinical applications in human cell therapy.
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Ruan ZS, Li T, Ren RR, Zhao Y, Li K, Mao YF, Shen G, Jiang L. Monitoring tissue blood oxygen saturation in the internal jugular venous area using near infrared spectroscopy. GENETICS AND MOLECULAR RESEARCH 2015; 14:2920-8. [PMID: 25867442 DOI: 10.4238/2015.march.31.23] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Central venous blood oxygen saturation (ScvO2) is an important monitoring index of fluid resuscitation. However, monitoring of ScvO2 is not continuous and invasive. Near infrared spectroscopy (NIRS) is an optical technology for the noninvasive detection of hemodynamic changes, with advantages of being real-time, continuous, low-cost, and portable. The present study aimed to determine whether a correlation exists between the tissue blood oxygen saturation in the internal jugular venous area (StO2) data obtained with NIRS and the ScvO2 and whether these two quantities are equivalent. Data were collected from 13 patients. We used ultrasound to locate the placement site for the NIRS light source outside the internal jugular vein. Meanwhile, a sample for blood gas analysis was obtained through the central venous catheter. A correlation analysis between the StO2 and ScvO2 of 13 samples was performed (Pearson correlation coefficient), suggesting a high correlation between them (r = 0.906, StO2 =1.0018 ScvO2 +2.8524). Bland-Altman analysis was also performed between the StO2 and ScvO2. Results were as follows: 100% of monitored points fell within the range of the mean ± 1.96 SD of the difference between the StO2 and ScvO2; range of the mean ± 1.96 SD of the difference between the StO2 and ScvO2 was 3 ± 10.2; confidence interval of the difference between the StO2 and ScvO2 was -7.2 to 13.2%. The StO2 monitored with NIRS correlated highly with the ScvO2 measured in the internal jugular vein. Therefore, the StO2 can be used for directing clinical treatment with further research.
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Marín AG, Núñez CG, Rodríguez P, Shen G, Kim SM, Kung P, Piqueras J, Pau JL. Continuous-flow system and monitoring tools for the dielectrophoretic integration of nanowires in light sensor arrays. NANOTECHNOLOGY 2015; 26:115502. [PMID: 25721912 DOI: 10.1088/0957-4484/26/11/115502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Although nanowires (NWs) may improve the performance of many optoelectronic devices such as light emitters and photodetectors, the mass commercialization of these devices is limited by the difficult task of finding reliable and reproducible methods to integrate the NWs on foreign substrates. This work shows the fabrication of zinc oxide NWs photodetectors on conventional glass using transparent conductive electrodes to effectively integrate the NWs at specific locations by dielectrophoresis (DEP). The paper describes the careful preparation of NW dispersions by sedimentation and the dielectrophoretic alignment of NWs in a home-made system. This system includes an impedance technique for the assessment of the alignment quality in real time. Following this procedure, ultraviolet photodetectors based on the electrical contacts formed by the DEP process on the transparent electrodes are fabricated. This cost-effective mean of contacting NWs enables front-and back-illumination operation modes, the latter eliminating shadowing effects caused by the deposition of metals. The electro-optical characterization of the devices shows uniform responsivities in the order of 106 A W(-1) below 390 nm under both modes, as well as, time responses of a few seconds.
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