Publications by authors named "Lizhi Gao"

18 Publications

  • Page 1 of 1

Effects of proanthocyanidins on the pasting, rheological and retrogradation properties of potato starch.

J Sci Food Agric 2021 Aug 19;101(11):4760-4767. Epub 2021 Feb 19.

State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, China.

Background: Proanthocyanidins (PAS) were complexed with potato starch (PS) to prepare polyphenol-starch complexes. The pasting, rheological and retrogradation properties of the complexes were investigated.

Results: The addition of PAS markedly affected the pasting, rheological and retrogradation properties of PS, especially at a concentration of 5% (w/w). Rapid viscosity analysis indicated that PAS significantly changed the viscosity, breakdown and setback value of PS. The rheological results showed that PAS decreased the flow behavior index and consistency coefficient, but increased the viscoelasticity of PS. Differential scanning calorimetry and X-ray diffraction indicated that PAS delayed the retrogradation of PS. Furthermore, scanning electron microscopy indicated that the morphologies of retrograded PS gels were greatly altered to a less compact structure with the presence of PAS. Moreover, Fourier transform infrared spectroscopy elucidated that PAS interacted with PS via a noncovalent interaction, and inhibited the retrogradation of PS.

Conclusions: The findings suggested that supplementing PS with PAS might be an effective and convenient method for modifying the physicochemical properties of PS. © 2021 Society of Chemical Industry.
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http://dx.doi.org/10.1002/jsfa.11122DOI Listing
August 2021

Population Genetics of (Diptera: Tephritidae) in China Based on Gene Sequence.

Insects 2019 Aug 2;10(8). Epub 2019 Aug 2.

Chongqing Key Laboratory of Entomology and Pest Control Engineering, College of Plant Protection, Southwest University, Chongqing 400715, China.

(Enderlein) (Diptera: Tephritidae) is an important citrus pest in Asia with a non-uniform distribution. In some locations, it had been reported to occur but was either eradicated or disappeared itself. To understand species dispersal of , we collected and analyzed 359 individuals from 18 localities in China. One mitochondrial DNA gene fragment () was used to investigate the genetic diversity and population genetic structure of . The populations were divided by phylogenetic analyses and statistical parsimony haplotype networks into three branches: a Central China (CC) branch, a Western China (WC) branch, and a Southern China (SC) branch. A total of 93 variable sites (15.6% of the 595 bp alignment) and 91 unique haplotypes were observed in the 359 individuals scored from the gene of the 18 populations. This indicated that had a high level of genetic diversity. These populations also showed a discrete distribution in both the scatter plots of genetic versus geographical distance for pairwise population comparisons and the median-joining network of haplotypes, which revealed the strong genetic structure of .
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http://dx.doi.org/10.3390/insects10080236DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6723541PMC
August 2019

The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition.

Gigascience 2019 05;8(5)

State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, No. 666 Wusu St., Lin'an District, Hangzhou 311300, China.

Background: Pecan (Carya illinoinensis) and Chinese hickory (C. cathayensis) are important commercially cultivated nut trees in the genus Carya (Juglandaceae), with high nutritional value and substantial health benefits.

Results: We obtained >187.22 and 178.87 gigabases of sequence, and ∼288× and 248× genome coverage, to a pecan cultivar ("Pawnee") and a domesticated Chinese hickory landrace (ZAFU-1), respectively. The total assembly size is 651.31 megabases (Mb) for pecan and 706.43 Mb for Chinese hickory. Two genome duplication events before the divergence from walnut were found in these species. Gene family analysis highlighted key genes in biotic and abiotic tolerance, oil, polyphenols, essential amino acids, and B vitamins. Further analyses of reduced-coverage genome sequences of 16 Carya and 2 Juglans species provide additional phylogenetic perspective on crop wild relatives.

Conclusions: Cooperative characterization of these valuable resources provides a window to their evolutionary development and a valuable foundation for future crop improvement.
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http://dx.doi.org/10.1093/gigascience/giz036DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6497033PMC
May 2019

Metabolomics and Transcriptomics Analyses Reveal Nitrogen Influences on the Accumulation of Flavonoids and Amino Acids in Young Shoots of Tea Plant ( Camellia sinensis L.) Associated with Tea Flavor.

J Agric Food Chem 2018 Sep 10;66(37):9828-9838. Epub 2018 Sep 10.

Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwestern China , Kunming Institute of Botany, Chinese Academy of Sciences , Kunming 650204 , China.

Tea-specialized metabolites contribute to rich flavors and healthy function of tea. Their accumulation patterns and underlying regulatory mechanism are significantly different under different nitrogen (N) conditions during adaptation stage. Here, we find that flavonoids associated with tea flavor are dominated by different metabolic and transcriptional responses among the four N conditions (N-deficiency, nitrate, ammonia, and nitric oxide). Nitrogen-deficiency tea plants accumulate diverse flavonoids, corresponding with higher expression of hub genes including F3H, FNS, UFGT, bHLH35, and bHLH36. Compared with N-deficiency, N-supply tea plants significantly increase proline, glutamine, and theanine, which are also associated with tea flavor, especially under NH-supply. As NH-tolerant species, tea plant exploits the adaptive strategy by substantial accumulation of amino acids including theanine to adapt excess NH, which attributes to, at least in part, efficient N transport and assimilation, and active protein degradation. A distinct divergence of N reallocation in young shoots of tea plant under different N sources contributes to diverse tea flavor.
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http://dx.doi.org/10.1021/acs.jafc.8b01995DOI Listing
September 2018

Pathological cyclic strain promotes proliferation of vascular smooth muscle cells via the ACTH/ERK/STAT3 pathway.

J Cell Biochem 2018 11 26;119(10):8260-8270. Epub 2018 Jun 26.

Institute of Mechanobiology and Medical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.

Abnormal proliferation of vascular smooth muscle cells (VSMCs) is closely related to hyperplasia in hypertension. Our previous study suggested that adrenocorticotropic hormone (ACTH) is mechano-responsive and may regulate VSMC proliferation. However, the molecular mechanism of VSMC abnormal proliferation induced by conditions of high cyclic strain, especially the role of ACTH in this process, is unclear. Our results revealed that ACTH and its specific receptor melanocortin receptor type 2 (MC2R) were highly expressed in hypertensive rat models. Furthermore, it was demonstrated that the expression of ACTH and MC2R was up-regulated when exposed to high cyclic strain in vitro, accompanied by abnormal proliferation of VSMCs. Next, it was proved that ACTH-dependent cell proliferation was related to the phosphorylation of extracellular regulated protein kinases (ERK) and signal transducer and activator of transcription 3 (STAT3). The study also found that ACTH could promote dimerization and glycosylation of melanocortin 2 receptor accessory protein (MRAP), which had a significant effect on MC2R membrane localization and signal activation. When VSMCs were treated with PD98059, a mitogen-activated protein kinase (MAP kinase) cascade antagonist, it was determined that phosphorylation of STAT3 at Ser727 was dependent on ERK phosphorylation. In summary, these data demonstrated that the abnormal proliferation of VSMCs induced by conditions of high cyclic strain is in part attributed to ACTH and its receptor MC2R. Identifying the mechanism of ACTH-dependent proliferation of VSMCs may help to provide new therapeutic targets for hypertension.
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http://dx.doi.org/10.1002/jcb.26839DOI Listing
November 2018

The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.

PLoS Genet 2016 Dec 22;12(12):e1006433. Epub 2016 Dec 22.

College of Forestry, Northwest A&F University, Yangling, China.

Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.
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http://dx.doi.org/10.1371/journal.pgen.1006433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5179053PMC
December 2016

Dynamic evolution of rht-1 homologous regions in grass genomes.

PLoS One 2013 24;8(9):e75544. Epub 2013 Sep 24.

Key Laboratory of Crop Germplasm Resources and Utilization, Ministry of Agriculture, the National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, the Chinese Academy of Agricultural Sciences, Beijing, China.

Hexaploid bread wheat contains A, B, and D three subgenomes with its well-characterized ancestral genomes existed at diploid and tetraploid levels, making the wheat act as a good model species for studying evolutionary genomic dynamics. Here, we performed intra- and inter-species comparative analyses of wheat and related grass genomes to examine the dynamics of homologous regions surrounding Rht-1, a well-known "green revolution" gene. Our results showed that the divergence of the two A genomes in the Rht-1 region from the diploid and tetraploid species is greater than that from the tetraploid and hexaploid wheat. The divergence of D genome between diploid and hexaploid is lower than those of A genome, suggesting that D genome diverged latter than others. The divergence among the A, B and D subgenomes was larger than that among different ploidy levels for each subgenome which mainly resulted from genomic structural variation of insertions and, perhaps deletions, of the repetitive sequences. Meanwhile, the repetitive sequences caused genome expansion further after the divergence of the three subgenomes. However, several conserved non-coding sequences were identified to be shared among the three subgenomes of wheat, suggesting that they may have played an important role to maintain the homolog of three subgenomes. This is a pilot study on evolutionary dynamics across the wheat ploids, subgenomes and differently related grasses. Our results gained new insights into evolutionary dynamics of Rht-1 region at sequence level as well as the evolution of wheat during the plolyploidization process.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075544PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3782514PMC
July 2014

Heterotrimerization of the growth factor receptors erbB2, erbB3, and insulin-like growth factor-i receptor in breast cancer cells resistant to herceptin.

Cancer Res 2010 Feb 26;70(3):1204-14. Epub 2010 Jan 26.

Departments of Pathology and Obstetrics and Gynecology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA.

Primary and acquired resistance to the breast cancer drug trastuzumab (Herceptin) is a significant clinical problem. Here, we report enhanced activation of downstream signaling pathways emanating from the growth factor receptors erbB2, erbB3, and insulin-like growth factor-I receptor (IGF-IR) in trastuzumab-resistant breast cancer cells. Interactions between IGF-IR and erbB2 or erbB3 occur exclusively in trastuzumab-resistant cells, where enhanced erbB2-erbB3 interactions are also observed. Moreover, these three receptors form a heterotrimeric complex in resistant cells. erbB3 or IGF-IR knockdown by short hairpin RNA-mediated strategies upregulates p27(kip1), inactivates downstream receptor signaling, and resensitizes resistant cells to trastuzumab. Our findings reveal a heterotrimer complex with a key role in trastuzumab resistance. On the basis of our results, we propose that trastuzumab resistance in breast cancer might be overcome by therapeutic strategies that jointly target erbB3, erbB2, and IGF-IR.
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http://dx.doi.org/10.1158/0008-5472.CAN-09-3321DOI Listing
February 2010

HDAC inhibitor SNDX-275 induces apoptosis in erbB2-overexpressing breast cancer cells via down-regulation of erbB3 expression.

Cancer Res 2009 Nov 13;69(21):8403-11. Epub 2009 Oct 13.

Department of Pathology, University of Colorado Denver School of Medicine, Aurora, Colorado 80045, USA.

Breast cancer is a highly heterogeneous disease with distinct histologic subtypes. Targeted therapies such as endocrine therapy and growth factor receptor inhibitors have had a significant impact on the treatment of metastatic breast cancer patients. Unfortunately, resistance to these agents eventually occurs, and currently represents a significant clinical problem in the management of breast cancers. Inhibitors of histone deacetylases (HDACi) exhibit anticancer activity in a variety of tumor cell models and have been shown to target mechanisms of resistance to a number of targeted agents. It is unclear, however, if there are specific breast cancer subtypes for which an HDACi may be more or less effective. Here, we report that the class I isoform-selective HDACi entinostat (SNDX-275) preferentially inhibits cell proliferation/survival and inactivates downstream signaling in erbB2-overexpressing compared with basal breast cancer cells. SNDX-275 reduces the levels of both erbB2 and erbB3, as well as significantly decreases P-erbB2, P-erbB3, P-Akt, and P-MAPK in erbB2-overexpressing cells. Additionally, SNDX-275 promotes apoptosis and induces cell cycle arrest predominantly at G(1) phase in erbB2-overexpressing cells, whereas SNDX-275 mainly induces G(2)-M arrest in basal breast cancer cells. The cellular bias of SNDX-275 is shown to be related partly to the levels of erbB3 expression that directly impact the ability of SNDX-275 to inhibit proliferation/survival of the erbB2-overexpressing breast cancer cells. These findings show that SNDX-275 may be developed as a novel therapeutic agent to treat breast cancers with coexpression of both erbB2 and erbB3.
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http://dx.doi.org/10.1158/0008-5472.CAN-09-2146DOI Listing
November 2009

Readthrough of nonsense mutation W822X in the SCN5A gene can effectively restore expression of cardiac Na+ channels.

Cardiovasc Res 2009 Aug 17;83(3):473-80. Epub 2009 Apr 17.

Cardiovascular Institute and Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.

Aims: Nonsense mutations in the SCN5A gene result in truncated, non-functional derivatives of the cardiac Na+ channel and thus cause arrhythmias. Studies of other genes suggest that pathogenic phenotypes of nonsense mutations may be alleviated by enhancing readthrough, which enables ribosomes to ignore premature termination codons and produce full-length proteins. Thus, we studied the functional restoration of nonsense-mutated SCN5A.

Methods And Results: HEK293 cells were transfected with SCN5A cDNA or its mutant carrying W822X, a nonsense mutation associated with Brugada syndrome and sudden cardiac death. The effects of readthrough-enhancing reagents on Na+ channel expression and function were examined in the transfected cells. W822X robustly reduced Na+ current, decreasing maximal Na+ current to <3% of the wild-type level, and inhibited the expression of full-length Na+ channels. When readthrough was enhanced by either reducing translational fidelity with aminoglycosides or decreasing translation termination efficiency with small-interfering RNA against eukaryotic release factor eRF3a, Na+ current of the mutant was restored to approximately 30% of the wild-type level; western blot and immunochemical staining analyses showed the increased expression of full-length channels. When the wild-type and mutant cDNAs were co-transfected, readthrough-enhancing reagents increased Na+ current from 56% to 74% of the wild-type level. Analysis of Na+ channel kinetics showed that the channels expressed from the mutant cDNA under readthrough-enhancing conditions retained the functions of wild-type channels.

Conclusion: Readthrough-enhancing reagents can effectively suppress SCN5A nonsense mutations and may restore the expression of full-length Na+ channels with normal functions, which might prevent sudden cardiac death in mutation carriers.
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http://dx.doi.org/10.1093/cvr/cvp116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2709462PMC
August 2009

Molecular and clinical characterization of a novel SCN5A mutation associated with atrioventricular block and dilated cardiomyopathy.

Circ Arrhythm Electrophysiol 2008 Jun 30;1(2):83-92. Epub 2008 Apr 30.

Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai, China.

Background: Increased susceptibility to dilated cardiomyopathy has been observed in patients carrying mutations in the SCN5A gene, but the underlying mechanism remains unclear. In this study, we identified and characterized, both in vitro and clinically, an SCN5A mutation associated with familial progressive atrioventricular block of adult onset and dilated cardiomyopathy in a Chinese family.

Methods And Results: Among 32 family members, 5 were initially diagnosed with atrioventricular block after age 30; 4 were studied, 3 of whom later developed dilated cardiomyopathy. We found a heterozygous single-nucleotide mutation resulting in an amino acid substitution (A1180V) in all studied patients and in 6 other younger unaffected members but not in 200 control chromosomes. When expressed with the beta1 subunit, the mutated channels exhibited a -4.5-mV shift of inactivation with slower recovery leading to a rate-dependent Na(+) current reduction and a moderate increase in late Na(+) current. Clinical study revealed that although QRS duration decreased with increasing heart rate in noncarrier family members, this change was blunted in unaffected carriers whose ECG and heart function were normal. Resting corrected QT interval of unaffected carriers was significantly longer than that of noncarriers, even though it was still within the normal range.

Conclusions: A1180V expresses a mild Na(+) channel phenotype in vitro and a corresponding clinical phenotype in unaffected mutation carriers, implying that A1180V caused structural heart disease in affected carriers by disturbing Na(+) influx and, hence, cellular Na(+) homeostasis. The high penetrance of A1180V suggests this phenotype as a high risk factor for dilated cardiomyopathy with preceding atrioventricular block.
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http://dx.doi.org/10.1161/CIRCEP.107.750752DOI Listing
June 2008

Expressed sequence tags (ESTs) and phylogenetic analysis of floral genes from a paleoherb species, Asarum caudigerum.

Ann Bot 2006 Jul 4;98(1):157-63. Epub 2006 May 4.

Laboratory of Biodiversity and Plant Biogeography, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China.

Background And Aims: Asarum caudigerum (Aristolochiaceae) is an important species of paleoherb in relation to understanding the origin and evolution of angiosperm flowers, due to its basal position in the angiosperms. The aim of this study was to isolate floral-related genes from A. caudigerum, and to infer evolutionary relationships among florally expression-related genes, to further illustrate the origin and diversification of flowers in angiosperms.

Methods: A subtracted floral cDNA library was constructed from floral buds using suppression subtractive hybridization (SSH). The cDNA of floral buds and leaves at the seedling stage were used as a tester and a driver, respectively. To further identify the function of putative MADS-box transcription factors, phylogenetic trees were reconstructed in order to infer evolutionary relationships within the MADS-box gene family.

Key Results: In the forward-subtracted floral cDNA library, 1920 clones were randomly sequenced, from which 567 unique expressed sequence tags (ESTs) were obtained. Among them, 127 genes failed to show significant similarity to any published sequences in GenBank and thus are putatively novel genes.

Conclusions: Phylogenetic analysis indicated that a total of 29 MADS-box transcription factors were members of the APETALA3(AP3) subfamily, while nine others were putative MADS-box transcription factors that formed a cluster with MADS-box genes isolated from Amborella, the basal-most angiosperm, and those from the gymnosperms. This suggests that the origin of A. caudigerum is intermediate between the angiosperms and gymnosperms.
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http://dx.doi.org/10.1093/aob/mcl081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2803548PMC
July 2006

Activation-coupled inactivation in the bacterial potassium channel KcsA.

Proc Natl Acad Sci U S A 2005 Dec 21;102(49):17630-5. Epub 2005 Nov 21.

Department of Physiology, University of Tennessee Health Science Center, Memphis, TN 38163, USA.

X-ray structures of the bacterial K+ channel KcsA have led to unparalleled progress in our understanding of ion channel structures. The KcsA channel has therefore been a prototypic model used to study the structural basis of ion channel function, including the gating mechanism. This channel was previously found to close at near-neutral intracellular pH (pH(i)) and to open at acidic pH(i). Here, we report the presence of a previously unknown channel inactivation process that occurs after the KcsA channel is activated. In our experiments, mammalian cells transfected with a codon-optimized synthetic gene encoding the KcsA protein expressed K+-selective channels that activated in response to a decrease in pH(i). Using patch-clamp and rapid solution exchange techniques, we observed that the KcsA channels inactivated within hundreds of milliseconds after channel activation. At all tested pHs, inactivation always accompanied activation, and it was profoundly accelerated in the same pH range at which activation increased steeply. Recovery from inactivation was observed, and its extent depended on the pH(i) and the amount of time that the channel was inactive. KcsA channel inactivation can be described by a kinetic model in which pH(i) controls inactivation through pH-dependent activation. This heretofore-undocumented inactivation process increases the complexity of KcsA channel function, but it also offers a potential model for studying the structural correspondence of ion channel inactivation.
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http://dx.doi.org/10.1073/pnas.0505158102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1287484PMC
December 2005

Population structure and conservation genetics of wild rice Oryza rufipogon (Poaceae): a region-wide perspective from microsatellite variation.

Authors:
Lizhi Gao

Mol Ecol 2004 May;13(5):1009-24

Institute of Crop Germplasm Resources, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Oryza rufipogon Griff. is the most agriculturally important but seriously endangered wild rice species. To better estimate how genetic structure can be used to obtained a conservation perspective of the species, genetic variability at six polymorphic microsatellite DNA loci was examined. High levels of genetic variability were detected at six loci in 1245 individuals of 47 natural populations covering most of the species' range in China (overall RS = 3.0740, HO = 0.2290, HS = 0.6700). Partitioning of genetic variability (FST = 0.246) showed that most microsatellite variation was distributed within populations. Significant departures from Hardy-Weinberg expectations and very strong linkage disequilibrium indicate a high degree of inbreeding in the species and severe subdivision within populations. A mean Nm value of 0.7662 suggested a limited gene flow among the assayed populations. Our study suggests that conservation and restoration genetics should focus in particular on the maintenance of historically significant processes such as high levels of outbreeding and gene flow and large effective population size in the species.
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http://dx.doi.org/10.1111/j.1365-294X.2004.02108.xDOI Listing
May 2004

Evolutionary history of Oryza sativa LTR retrotransposons: a preliminary survey of the rice genome sequences.

BMC Genomics 2004 Mar 2;5(1):18. Epub 2004 Mar 2.

Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.

Background: LTR Retrotransposons transpose through reverse transcription of an RNA intermediate and are ubiquitous components of all eukaryotic genomes thus far examined. Plant genomes, in particular, have been found to be comprised of a remarkably high number of LTR retrotransposons. There is a significant body of direct and indirect evidence that LTR retrotransposons have contributed to gene and genome evolution in plants.

Results: To explore the evolutionary history of long terminal repeat (LTR) retrotransposons and their impact on the genome of Oryza sativa, we have extended an earlier computer-based survey to include all identifiable full-length, fragmented and solo LTR elements in the rice genome database as of April 2002. A total of 1,219 retroelement sequences were identified, including 217 full-length elements, 822 fragmented elements, and 180 solo LTRs. In order to gain insight into the chromosomal distribution of LTR-retrotransposons in the rice genome, a detailed examination of LTR-retrotransposon sequences on Chromosome 10 was carried out. An average of 22.3 LTR-retrotransposons per Mb were detected in Chromosome 10.

Conclusions: Gypsy-like elements were found to be >4 x more abundant than copia-like elements. Eleven of the thirty-eight investigated LTR-retrotransposon families displayed significant subfamily structure. We estimate that at least 46.5% of LTR-retrotransposons in the rice genome are older than the age of the species (< 680,000 years). LTR-retrotransposons present in the rice genome range in age from those just recently inserted up to nearly 10 million years old. Approximately 20% of LTR retrotransposon sequences lie within putative genes. The distribution of elements across chromosome 10 is non-random with the highest density (48 elements per Mb) being present in the pericentric region.
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http://dx.doi.org/10.1186/1471-2164-5-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373447PMC
March 2004

Why are some human disease-associated mutations fixed in mice?

Trends Genet 2003 Dec;19(12):678-81

Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA.

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http://dx.doi.org/10.1016/j.tig.2003.10.002DOI Listing
December 2003

Phosphatidic acid stimulates cardiac KATP channels like phosphatidylinositols, but with novel gating kinetics.

Am J Physiol Cell Physiol 2003 Jan 18;284(1):C94-102. Epub 2002 Sep 18.

Department of Physiology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA.

Membrane-bound anionic phospholipids such as phosphatidylinositols have the capacity to modulate ATP-sensitive potassium (K(ATP)) channels through a mechanism involving long-range electrostatic interaction between the lipid headgroup and channel. However, it has not yet been determined whether the multiple effects of phosphatidylinositols reported in the literature all result from this general electrostatic interaction or require a specific headgroup structure. The present study investigated whether phosphatidic acid (PA), an anionic phospholipid substantially different in structure from phosphatidylinositols, evokes effects similar to phosphatidylinositols on native K(ATP) channels of rat heart and heterogeneous Kir6.2/SUR2A channels. Channels treated with PA (0.2-1 mg/ml applied to the cytoplasmic side of the membrane) exhibited higher activity, lower sensitivity to ATP inhibition, less Mg(2+)-dependent nucleotide stimulation, and poor sulfonylurea inhibition. These effects match the spectrum of phosphatidylinositols' effects, but, in addition, PA also induced a novel pattern in gating kinetics, represented by a decreased mean open time (from 12.2 +/- 2.0 to 3.3 +/- 0.7 ms). This impact on gating kinetics clearly distinguishes PA's effects from those of phosphatidylinositols. Results indicate that multiple effects of anionic phospholipids on K(ATP) channels are related phenomena and can likely be attributed to a common mechanism, but additional specific effects due to other mechanisms may also coincide.
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http://dx.doi.org/10.1152/ajpcell.00255.2002DOI Listing
January 2003

Long terminal repeat retrotransposons of Oryza sativa.

Genome Biol 2002 Sep 13;3(10):RESEARCH0053. Epub 2002 Sep 13.

Department of Genetics, University of Georgia, Athens, GA 30602, USA.

Background: Long terminal repeat (LTR) retrotransposons constitute a major fraction of the genomes of higher plants. For example, retrotransposons comprise more than 50% of the maize genome and more than 90% of the wheat genome. LTR retrotransposons are believed to have contributed significantly to the evolution of genome structure and function. The genome sequencing of selected experimental and agriculturally important species is providing an unprecedented opportunity to view the patterns of variation existing among the entire complement of retrotransposons in complete genomes.

Results: Using a new data-mining program, LTR_STRUC, (LTR retrotransposon structure program), we have mined the GenBank rice (Oryza sativa) database as well as the more extensive (259 Mb) Monsanto rice dataset for LTR retrotransposons. Almost two-thirds (37) of the 59 families identified consist of copia-like elements, but gypsy-like elements outnumber copia-like elements by a ratio of approximately 2:1. At least 17% of the rice genome consists of LTR retrotransposons. In addition to the ubiquitous gypsy- and copia-like classes of LTR retrotransposons, the rice genome contains at least two novel families of unusually small, non-coding (non-autonomous) LTR retrotransposons.

Conclusions: Each of the major clades of rice LTR retrotransposons is more closely related to elements present in other species than to the other clades of rice elements, suggesting that horizontal transfer may have occurred over the evolutionary history of rice LTR retrotransposons. Like LTR retrotransposons in other species with relatively small genomes, many rice LTR retrotransposons are relatively young, indicating a high rate of turnover.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC134482PMC
http://dx.doi.org/10.1186/gb-2002-3-10-research0053DOI Listing
September 2002
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