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1.  Clinical application of the paraspinal erector approach for spinal canal decompression in upper lumber burst fractures 
Objective
Percutaneous pedicle screw fixation is commonly used for upper lumber burst fractures. The direct decompression remains challenging with this minimally invasive surgery. The objective was to evaluate a novel paraspinal erector approach for effective and direct decompression in patients with canal compromise and neurologic deficit.
Method
Patients (n = 21) with neurological deficiency and Denis B type upper lumbar burst fracture were enrolled in the study, including 14 cases in the L1 and 7 cases in the L2. The patients underwent removal of bone fragments from the spinal canal through intervertebral foramen followed by short-segment fixation. Evaluations included surgery-related, such as duration of surgery and blood loss, and 12-month follow-up, such as the kyphotic angle, the height ratio of the anterior edge of the vertebra, the ratio of sagittal canal compromise, visual analog scale (VAS), Oswestry Disability Index (ODI), and Frankel scores.
Results
All patients achieved direct spinal canal decompression using the paraspinal erector approach followed by percutaneous pedicle screw fixation. The mean operation time (SD) was 173 (23) min, and the mean (SD) blood loss was 301 (104) ml. Significant improvement was noted in the kyphotic angle, 26.2 ± 8.7 prior to operation versus 9.1 ± 4.7 at 12 months after operation (p <0.05); the height ratio of the anterior edge of the injured vertebra, 60 ± 16% versus 84 ± 9% (p <0.05); and the ratio of sagittal canal compromise, 46.5 ± 11.4% versus 4.3 ± 3.6% (p <0.05). Significant improvements in VAS (7.3 ± 1.2 vs. 1.9 ± 0.7, p <0.05), ODI (86.7 ± 5.8 vs. 16.7 ± 5.1, p <0.05), and Frankel scores were also noted.
Conclusions
The paraspinal erector approach was effective for direct spinal canal decompression with minimal injury in the paraspinal muscles or spine. Significant improvements in spinal function and prognostics were achieved after the percutaneous pedicle screw fixation.
doi:10.1186/s13018-014-0105-4
PMCID: PMC4240844  PMID: 25387608
Erector spinae; Direct spinal canal decompression; Minimally invasive spine surgery; Surgical approach; Upper lumber burst fractures
2.  Bcl-2 Family Proteins Are Involved in the Signal Crosstalk between Endoplasmic Reticulum Stress and Mitochondrial Dysfunction in Tumor Chemotherapy Resistance 
BioMed Research International  2014;2014:234370.
Tumor cells overexpress antiapoptotic proteins of the Bcl-2 (B-cell leukemia/lymphoma-2) family, which can lead to both escape from cell death and resistance to chemotherapeutic drugs. Recent studies suggest that the endoplasmic reticulum (ER) can produce proapoptotic signals, amplifying the apoptotic signaling cascade. The crosstalk between mitochondria and ER plays a decisive role in many cellular events but especially in cell death. Bcl-2 family proteins located in the ER and mitochondria can influence not only the function of the two organelles but also the interaction between them. Therefore, the Bcl-2 family of proteins may also be involved in the mechanism of tumor chemotherapy resistance by influencing crosstalk between the ER and mitochondria. In this review we will briefly discuss evidence to support this concept.
doi:10.1155/2014/234370
PMCID: PMC4142381  PMID: 25177684
3.  Ulcerative colitis as a polymicrobial infection characterized by sustained broken mucus barrier 
To reduce medication for patients with ulcerative colitis (UC), we need to establish the etiology of UC. The intestinal microbiota of patients with inflammatory bowel disease (IBD) has been shown to differ from that of healthy controls and abundant data indicate that it changes in both composition and localization. Small intestinal bacterial overgrowth is significantly higher in IBD patients compared with controls. Probiotics have been investigated for their capacity to reduce the severity of UC. The luminal surfaces of the gastrointestinal tract are covered by a mucus layer. This normally acts as a barrier that does not allow bacteria to reach the epithelial cells and thus limits the direct contact between the host and the bacteria. The mucus layer in the colon comprises an inner layer that is firmly adherent to the intestinal mucosa, and an outer layer that can be washed off with minimal rinsing. Some bacteria can dissolve the protective inner mucus layer. Defects in renewal and formation of the inner mucus layer allow bacteria to reach the epithelium and have implications for the causes of colitis. In this review, important elements of UC pathology are thought to be the intestinal bacteria, gut mucus, and the mucosa-associated immune system.
doi:10.3748/wjg.v20.i28.9468
PMCID: PMC4110578  PMID: 25071341
Ulcerative colitis; Mucus; Infection; Bacteria; Etiology
4.  Combination of symptoms, syndrome and disease: Treatment of refractory diabetic gastroparesis 
AIM: To assess effect of combination of symptoms, syndrome and disease on treatment of diabetic gastroparesis with severe nausea and vomiting.
METHODS: Professor Tong Xiaolin’s clinical electronic medical records of patients who were treated between January 1, 2006 and October 1, 2012 were used as a database. Patients who met the inclusion criteria were enrolled. General information (name, sex and age), symptoms and blood glucose levels were obtained from the clinic electronic medical record, which was supplemented by a telephone interview. The patient-rated Gastroparesis Cardinal Symptom Index (GCSI) was used to evaluate the severity of the symptoms of gastroparesis. The effects of the treatment were assessed by the change in the severity of the symptoms of gastroparesis and the change in blood glucose between the baseline levels and the post-treatment levels at 1, 2, 4, 8 and 12 wk.
RESULTS: Forty-five patients had a mean GCSI nausea and vomiting severity score of 4.21 ± 0.67 and a total GCSI score of 2.77 ± 0.63 before treatment. There was a significant improvement in the nausea and vomiting score at every return visit compared with the baseline score (1 wk: 3.02 ± 1.04 vs 4.18 ± 0.71, P < 0.001; 2 wk: 2.32 ± 1.25 vs 4.16 ± 0.73, P < 0.001; 4 wk: 2.12 ± 1.26 vs 4.12 ± 0.73, P < 0.001; 8 wk: 1.79 ± 1.09 vs 4.24 ± 0.77, P < 0.001; 12 wk: 0.69 ± 0.92 vs 4.25 ± 0.70, P < 0.001). Twenty-five of the 45 patients had complete resolution of vomiting during the observation period (mean time to resolution was 37.9 ± 27.3 d). The postprandial fullness and early satiety subscale, bloating subscale and total GCSI scores were also improved. Finally, the blood glucose levels improved after treatment, although the change was not significant.
CONCLUSION: Use of the combination of symptoms, syndrome and disease to treat diabetic gastroparesis with refractory nausea and vomiting may be a new treatment option.
doi:10.3748/wjg.v20.i26.8674
PMCID: PMC4093720  PMID: 25024625
Diabetic gastroparesis; Refractory nausea and vomiting; Traditional Chinese medicine; Treatment; Gastroparesis Cardinal Symptom Index
5.  Knockdown of OCT4 suppresses the growth and invasion of pancreatic cancer cells through inhibition of the AKT pathway 
Molecular Medicine Reports  2014;10(3):1335-1342.
Octamer-binding transcription factor 4 (OCT4) is one of the factors associated with self-renewal and differentiation in cancer stem cells, and is crucial for the progression of various types of human malignancy. However, the expression and function of OCT4 in human pancreatic cancer has not been fully elucidated. The purpose of the present study was to investigate the function and molecular mechanisms of OCT4 in pancreatic cancer cells. The clinical significance of OCT4 expression was assessed by an immunohistochemical assay using a tissue microarray procedure in pancreatic cancer tissues and cells with different degrees of differentiation. A loss-of-function approach was used to examine the effects of a lentivirus-mediated OCT4 small hairpin RNA vector on biological behaviors, including cell proliferative activity and invasive potential. The results demonstrated that the expression levels of OCT4 protein in cancer tissues were significantly elevated compared with those in adjacent non-cancerous tissues (65.0 vs. 42.5%; P=0.005), which was correlated with tumor differentiation (P=0.008). The knockdown of OCT4 inhibited the proliferation and invasion of pancreatic cancer cells (Panc-1) expressing high levels of OCT4, accompanied with decreased expression of AKT, proliferating cell nuclear antigen (PCNA) and matrix metalloproteinase-2 (MMP-2). In conclusion, the present study reveals that the increased expression of OCT4 is correlated with the differentiation of pancreatic cancer, while knockdown of OCT4 suppresses the growth and invasion of pancreatic cancer cells through inhibition of AKT pathway-mediated PCNA and MMP-2 expression, suggesting that OCT4 might serve as a potential therapeutic target for the treatment of pancreatic cancer.
doi:10.3892/mmr.2014.2367
PMCID: PMC4121418  PMID: 25017645
octamer-binding transcription factor 4; pancreatic cancer; AKT; growth; invasion
6.  Twinning-like lattice reorientation without a crystallographic twinning plane 
Nature Communications  2014;5:3297.
Twinning on the plane is a common mode of plastic deformation for hexagonal-close-packed metals. Here we report, by monitoring the deformation of submicron-sized single-crystal magnesium compressed normal to its prismatic plane with transmission electron microscopy, the reorientation of the parent lattice to a ‘twin’ lattice, producing an orientational relationship akin to that of the conventional twinning, but without a crystallographic mirror plane, and giving plastic strain that is not simple shear. Aberration-corrected transmission electron microscopy observations reveal that the boundary between the parent lattice and the ‘twin’ lattice is composed predominantly of semicoherent basal/prismatic interfaces instead of the twinning plane. The migration of this boundary is dominated by the movement of these interfaces undergoing basal/prismatic transformation via local rearrangements of atoms. This newly discovered deformation mode by boundary motion mimics conventional deformation twinning but is distinct from the latter and, as such, broadens the known mechanisms of plasticity.
Deformation twinning and dislocations are known to govern the plastic behaviour of metals at room temperature. Here the authors demonstrate a new deformation mechanism in single-crystal magnesium characterized by twin-like crystal reorientation and special interfaces.
doi:10.1038/ncomms4297
PMCID: PMC3929781  PMID: 24522756
7.  Genome characteristics reveal the impact of lichenization on lichen-forming fungus Endocarpon pusillum Hedwig (Verrucariales, Ascomycota) 
BMC Genomics  2014;15:34.
Background
Lichen is a classic mutualistic organism and the lichenization is one of the fungal symbioses. The lichen-forming fungus Endocarpon pusillum is living in symbiosis with the green alga Diplosphaera chodatii Bialsuknia as a lichen in the arid regions.
Results
454 and Illumina technologies were used to sequence the genome of E. pusillum. A total of 9,285 genes were annotated in the 37.5 Mb genome of E. pusillum. Analyses of the genes provided direct molecular evidence for certain natural characteristics, such as homothallic reproduction and drought-tolerance. Comparative genomics analysis indicated that the expansion and contraction of some protein families in the E. pusillum genome reflect the specific relationship with its photosynthetic partner (D. chodatii). Co-culture experiments using the lichen-forming fungus E. pusillum and its algal partner allowed the functional identification of genes involved in the nitrogen and carbon transfer between both symbionts, and three lectins without signal peptide domains were found to be essential for the symbiotic recognition in the lichen; interestingly, the ratio of the biomass of both lichen-forming fungus and its photosynthetic partner and their contact time were found to be important for the interaction between these two symbionts.
Conclusions
The present study lays a genomic analysis of the lichen-forming fungus E. pusillum for demonstrating its general biological features and the traits of the interaction between this fungus and its photosynthetic partner D. chodatii, and will provide research basis for investigating the nature of its drought resistance and symbiosis.
doi:10.1186/1471-2164-15-34
PMCID: PMC3897900  PMID: 24438332
Mycobiont; Phycobiont; Lichenization; Symbiosis; Symbiosis-related gene; Photosynthetic products
8.  Sleep Disorders in Parkinson’s Disease: Clinical Features, Iron Metabolism and Related Mechanism 
PLoS ONE  2013;8(12):e82924.
Objective
To investigate clinical features, iron metabolism and neuroinflammation in Parkinson’s disease (PD) patients with sleep disorders (SD).
Methods
211 PD patients were evaluated by Pittsburgh Sleep Quality Index (PSQI) and a body of scales for motor symptoms and non-motor symptoms. 94 blood and 38 cerebral spinal fluid (CSF) samples were collected and iron and its metabolism-relating proteins, neuroinflammatory factors were detected and analyzed.
Results
136 cases (64.5%) of PD patients were accompanied by SD. Factor with the highest score in PSQI was daytime dysfunction. Depression, restless leg syndrome, autonomic symptoms and fatigue contributed 68.6% of the variance of PSQI score. Transferrin level in serum and tumor necrosis factor–α level in CSF decreased, and the levels of iron, transferrin, lactoferrin and prostaglandin E2 in CSF increased in PD patients with SD compared with those without SD. In CSF, prostaglandin E2 level was positively correlated with the levels of transferrin and lactoferrin, and tumor necrosis factor–α level was negatively correlated with the levels of iron, transferrin and lactoferrin in CSF.
Conclusions
Depression, restless leg syndrome, autonomic disorders and fatigue are the important contributors for the poor sleep in PD patients. Abnormal iron metabolism may cause excessive iron deposition in brain and be related to SD in PD patients through dual potential mechanisms, including neuroinflammation by activating microglia and neurotoxicity by targeting neurons. Hence, inhibition of iron deposition-related neuroinflammation and neurotoxicity may cast a new light for drug development for SD in PD patients.
doi:10.1371/journal.pone.0082924
PMCID: PMC3871565  PMID: 24376607
9.  Human Infection with Eurasian Avian-like Influenza A(H1N1) Virus, China 
Emerging Infectious Diseases  2013;19(10):1709-1711.
doi:10.3201/eid1910.130420
PMCID: PMC3810748  PMID: 24050834
influenza; surveillance; serology; avian-like influenza A(H1N1); viruses
10.  Changes in Nitric Oxide, cGMP, and Nitrotyrosine Concentrations Over Skin Along the Meridians in Obese Subjects 
Obesity (Silver Spring, Md.)  2010;19(8):1560-1567.
The purposes of these studies were to quantify the concentrations of total nitrate and nitrite (NOx−) cyclic guanosine monophosphate (cGMP), and nitrotyrosine over skin surface in normal weight healthy volunteers (n = 64) compared to overweight/obese subjects (n = 54). A semicircular plastic tube was taped to the skin along acupuncture points (acupoints), meridian line without acupoint (MWOP), and nonmeridian control and filled with a 2-Phenyl-4,4,5,5-tetramethylimidazoline-3-oxide-1-oxyl solution for 20 min. The concentrations of NOx−, cGMP, and nitrotyrosine in the samples were quantified in a blinded fashion using chemiluminescence and enzyme-linked immunosorbent assay, respectively. In normal weight healthy volunteers, NOx− and cGMP concentrations were consistently increased over the pericardium meridian (PC) 4–7 compared with nonmeridian areas. NOx− concentration is enhanced over the bladder meridian (BL) 56–57, but cGMP level is similar between the regions. In overweight/obese subjects, NOx− contents were increased or tended to be elevated over PC and BL regions. cGMP is paradoxically decreased over PC acupoints and nonmeridian control on the forearm but the decreases were blunted along BL regions on the leg. Nitrotyrosine concentrations are markedly elevated (five- to sixfold) over both PC and BL in all areas of overweight/obese subjects. This is the first evidence showing that nitrotyrosine level is tremendously elevated over skin accompanied by paradoxical changes in nitric oxide (NO)-cGMP concentrations over PC skin region in overweight/obese subject. The results suggest that NO-related oxidant inflammation is systemically enhanced while cGMP generation is impaired over PC skin region but not over BL region in obesity.
doi:10.1038/oby.2010.294
PMCID: PMC3584154  PMID: 21151015
11.  Pretreatment of microcrystalline cellulose in organic electrolyte solutions for enzymatic hydrolysis 
Background
Previous studies have shown that the crystalline structure of cellulose is negatively correlated with enzymatic digestibility, therefore, pretreatment is required to break down the highly ordered crystalline structure in cellulose, and to increase the porosity of its surface. In the present study, an organic electrolyte solution (OES) composed of an ionic liquid (1-allyl-3-methylimidazolium chloride ([AMIM]Cl)) and an organic solvent (dimethyl sulfoxide; DMSO) was prepared, and used to pretreat microcrystalline cellulose for subsequent enzymatic hydrolysis; to our knowledge, this is the first time that this method has been used.
Results
Microcrystalline cellulose (5 wt%) rapidly dispersed and then completely dissolved in an OES with a molar fraction of [AMIM]Cl per OES (χ [AMIM]Cl) of greater than or equal to 0.2 at 110°C within 10 minutes. The cellulose was regenerated from the OES by precipitation with hot water, and enzymatically hydrolyzed. As the χ [AMIM]Cl of the OES increased from 0.1 to 0.9, both the hydrolysis yield and initial hydrolysis rate of the regenerated cellulose also increased gradually. After treatment using OES with χ [AMIM]Cl of 0.7, the glucose yield (54.1%) was 7.2 times that of untreated cellulose. This promotion of hydrolysis yield was mainly due to the decrease in the degree of crystallinity (that is, the crystallinity index of cellulose I).
Conclusions
An OES of [AMIM]Cl and DMSO with χ [AMIM]Cl of 0.7 was chosen for cellulose pretreatment because it dissolved cellulose rapidly to achieve a high glucose yield (54.1%), which was only slightly lower than the value (59.6%) obtained using pure [AMIM]Cl. OES pretreatment is a cost-effective and environmentally friendly technique for hydrolysis, because it 1) uses the less expensive OES instead of pure ionic liquids, 2) shortens dissolution time, 3) requires lower energy for stirring and transporting, and 4) is recyclable.
doi:10.1186/1754-6834-4-53
PMCID: PMC3305895  PMID: 22099703
12.  Interleukin-11-induced capillary leak syndrome in primary hepatic carcinoma patients with thrombocytopenia 
BMC Cancer  2011;11:204.
Background
Capillary leak syndrome (CLS) is a rare condition characterized by recurrent episodes of generalized edema and severe hypotension associated with hypoproteinemia. Interleukin-11 (IL-11) is a promising therapeutic agent for thrombocytopenia. A direct correlation between IL-11 and CLS has never been reported previously, particularly in patients with hepatic carcinoma.
Case presentation
We describe two cases of CLS after IL-11 administration in two males with thrombocytopenia. Case 1 was a 46-year-old man with recurrence of hepatic carcinoma who was treated with IL-11 (3 mg per day). After four days of therapy, hypotension and hypoproteinemia were detected. The chest X-ray and B ultrasound of the abdomen showed pleural effusion and ascites. IL-11 was then discontinued, fluid resuscitation was performed, and fresh frozen plasma and packed red blood cells were transfused into this patient. The patient had recovered after 19 days of treatment.
Case 2 was a 66-year-old man who had undergone radiofrequency ablation (RFA) for hepatic carcinoma. He was treated with IL-11 (3 mg per day) for thrombocytopenia. After two days of therapy, this patient complained of dyspnea with bilateral edema of the hands. Laboratory values showed hypoproteinemia. IL-11 was stopped and human albumin was transfused at a rate of 10 g per day. On the 4th day, fluid resuscitation was performed. The patient had recovered after treatment for two weeks.
Conclusions
The detection of IL-11-induced CLS supports the hypothesis that CLS could be a severe side effect of IL-11 treatment in some patients. These two case reports also demonstrate that patients with hepatic carcinoma who experience this rare form of CLS after treatment with IL-11 seem to respond to a therapeutic regimen that involves hydroxyethyl starch, albumin, and diuretic therapy. Liver cancer patients might be more susceptible to CLS because of poor liver function and hypersplenia. In addition, bleeding after RFA might be a further inducer of CLS.
doi:10.1186/1471-2407-11-204
PMCID: PMC3118946  PMID: 21619578
13.  Bis{tris­[3-(2-pyrid­yl)pyrazole]manganese(II)} dodeca­molybdosilicate hexa­hydrate 
The title compound, [Mn(C8H7N3)3]2[SiMo12O40]·6H2O, consists of an [SiMo12O40]4− heteropolyanion, lying on a centre of inversion, and a complex [Mn(C8H7N3)3]4+ cation. The MnII atom of the cation is hexa­coordinated in a distorted octa­hedral geometry by six N atoms from three chelating 3-(2-pyrid­yl)pyrazole ligands. In the heteropolyanion, the four O atoms of the tetra­hedral SiO4 group each half-occupy eight sites due to Si lying on the centre of inversion. N—H⋯O and O—H⋯O hydrogen bonding mediated by the water mol­ecules leads to a consolidation of the structure.
doi:10.1107/S1600536810001492
PMCID: PMC2979799  PMID: 21579665
14.  Bis(μ-biphenyl-2,2′-dicarboxyl­ato)bis­[aqua­(4,4′-dimethyl-2,2′-bipyridine-κ2 N,N′)copper(II)] 
The mol­ecule of the title binuclear copper(II) complex, [Cu2(C14H8O4)2(C12H12N2)2(H2O)2], is bis­ected by a crystallographic twofold axis. Each CuII atom is coordinated in a distorted octa­hedral geometry by three O atoms from two biphen­yl-2,2′-dicarboxyl­ate anions, one aqua O atom and two N atoms of a 4,4′-dimethyl-2,2′-bipyridine ligand. Intramolecular O—H⋯O hydrogen bonds between the coordinated water molecules and the carboxylate O atoms are also present.
doi:10.1107/S1600536809040628
PMCID: PMC2971185  PMID: 21578114
15.  Aqua­bis(benzoato-κO)(5,5′-dimethyl-2,2′-bipyridine-κ2 N,N′)copper(II) 
In the crystal structure of the title compound, [Cu(C7H5O2)2(C12H12N2)(H2O)], the CuII ion is penta­coordinated in a distorted square-pyramidal geometry by two O atoms of two benzoate anions and two N atoms of a 5,5′-dimethyl-2,2′-bipyridine ligand occupying the basal plane, and a water O atom located at the apical site. In the crystal structure, O—H⋯O hydrogen bonds link the mol­ecules into a supra­molecular structure. The crystal studied was a racemic twin, as suggested by the Flack parameter of 0.584 (14).
doi:10.1107/S1600536809039191
PMCID: PMC2971325  PMID: 21578058
16.  Serum leptin and soluble leptin receptor in non-alcoholic fatty liver disease 
AIM: To determine the role of leptin system in non-alcoholic fatty liver disease (NAFLD) development by delineating the changes in serum levels of leptin and soluble leptin receptor (sOB-R).
METHODS: Blood samples were collected from 30 consecutive patients with liver-biopsy-proven NAFLD and 30 patients with cholecystolithiasis (stationary phase) as controls. Serum leptin levels were determined by radioimmunoassay and concentration of sOB-R was measured by ELISA. Body mass index (BMI) was calculated for all subjects, and serum insulin, C-peptide, and lipoprotein levels were also detected.
RESULTS: Mean serum leptin level and BMI in the NAFLD group were significantly higher than in the controls (both P < 0.001), but mean sOB-R level was lower in the NAFLD group when compared to the controls. Both men and women in the NAFLD group had higher mean serum leptin levels and lower sOB-R levels than did the men and women in the control group (all P < 0.001). There was a significant negative correlation between serum leptin and sOB-R levels (r = -0.725, P < 0.001). Multivariate analysis showed that the percentage of hepatocyte steatosis, sex, BMI, and homeostasis model assessment of insulin resistance (HOMA IR) were independently related to serum leptin levels.
CONCLUSION: Elevated serum leptin seems to be a feature of steatosis, and serum leptin seems to increase as hepatocyte steatosis develops. An enhanced release of leptin is accompanied by an decrease in sOB-R concentration, which suggests higher resistance of peripheral tissues towards the action of leptin.
doi:10.3748/wjg.14.2888
PMCID: PMC2710733  PMID: 18473416
Leptin; Soluble leptin receptor; Non-alcoholic fatty liver disease
17.  The Genomes of Oryza sativa: A History of Duplications 
Yu, Jun | Wang, Jun | Lin, Wei | Li, Songgang | Li, Heng | Zhou, Jun | Ni, Peixiang | Dong, Wei | Hu, Songnian | Zeng, Changqing | Zhang, Jianguo | Zhang, Yong | Li, Ruiqiang | Xu, Zuyuan | Li, Shengting | Li, Xianran | Zheng, Hongkun | Cong, Lijuan | Lin, Liang | Yin, Jianning | Geng, Jianing | Li, Guangyuan | Shi, Jianping | Liu, Juan | Lv, Hong | Li, Jun | Wang, Jing | Deng, Yajun | Ran, Longhua | Shi, Xiaoli | Wang, Xiyin | Wu, Qingfa | Li, Changfeng | Ren, Xiaoyu | Wang, Jingqiang | Wang, Xiaoling | Li, Dawei | Liu, Dongyuan | Zhang, Xiaowei | Ji, Zhendong | Zhao, Wenming | Sun, Yongqiao | Zhang, Zhenpeng | Bao, Jingyue | Han, Yujun | Dong, Lingli | Ji, Jia | Chen, Peng | Wu, Shuming | Liu, Jinsong | Xiao, Ying | Bu, Dongbo | Tan, Jianlong | Yang, Li | Ye, Chen | Zhang, Jingfen | Xu, Jingyi | Zhou, Yan | Yu, Yingpu | Zhang, Bing | Zhuang, Shulin | Wei, Haibin | Liu, Bin | Lei, Meng | Yu, Hong | Li, Yuanzhe | Xu, Hao | Wei, Shulin | He, Ximiao | Fang, Lijun | Zhang, Zengjin | Zhang, Yunze | Huang, Xiangang | Su, Zhixi | Tong, Wei | Li, Jinhong | Tong, Zongzhong | Li, Shuangli | Ye, Jia | Wang, Lishun | Fang, Lin | Lei, Tingting | Chen, Chen | Chen, Huan | Xu, Zhao | Li, Haihong | Huang, Haiyan | Zhang, Feng | Xu, Huayong | Li, Na | Zhao, Caifeng | Li, Shuting | Dong, Lijun | Huang, Yanqing | Li, Long | Xi, Yan | Qi, Qiuhui | Li, Wenjie | Zhang, Bo | Hu, Wei | Zhang, Yanling | Tian, Xiangjun | Jiao, Yongzhi | Liang, Xiaohu | Jin, Jiao | Gao, Lei | Zheng, Weimou | Hao, Bailin | Liu, Siqi | Wang, Wen | Yuan, Longping | Cao, Mengliang | McDermott, Jason | Samudrala, Ram | Wang, Jian | Wong, Gane Ka-Shu | Yang, Huanming
PLoS Biology  2005;3(2):e38.
We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family.
Comparative genome sequencing of indica and japonica rice reveals that duplication of genes and genomic regions has played a major part in the evolution of grass genomes
doi:10.1371/journal.pbio.0030038
PMCID: PMC546038  PMID: 15685292

Results 1-17 (17)