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1.  Draft Genome Sequence of Bacillus subtilis Strain S1-4, Which Degrades Feathers Efficiently 
Genome Announcements  2013;1(5):e00766-13.
Bacillus subtilis strain S1-4, with the capacity to efficiently degrade feathers, was isolated from chicken feathers. Sequencing showed that the genome of strain S1-4 differs from that of other B. subtilis strains, with limited insertions and deletions. The genome encodes multiple extracellular proteases and keratinases.
doi:10.1128/genomeA.00766-13
PMCID: PMC3784786  PMID: 24072866
2.  Draft Genome Sequence of Bacillus pumilus BA06, a Producer of Alkaline Serine Protease with Leather-Dehairing Function 
Journal of Bacteriology  2012;194(23):6668-6669.
Bacillus pumilus BA06 was isolated from the proteinaceous soil and produced an extracellular alkaline protease with leather-dehairing function. The genome of BA06 was sequenced. The comparative genome analysis indicated that strain BA06 is different in genome from the other B. pumilus strains, with limited insertions, deletions, and rearrangements.
doi:10.1128/JB.01694-12
PMCID: PMC3497469  PMID: 23144411
3.  Draft Genome Sequence of Enterobacter cloacae subsp. cloacae Strain 08XA1, a Fecal Bacterium of Giant Pandas 
Journal of Bacteriology  2012;194(24):6928-6929.
Enterobacter cloacae, a common pathogenic bacterium, is a Gram-negative bacillus. We analyzed the draft genome of Enterobacter cloacae subsp. cloacae strain 08XA1 from the feces of a giant panda in China. Genes encoding a β-lactamase and efflux pumps, as well as other factors, have been found in the genome.
doi:10.1128/JB.01790-12
PMCID: PMC3510591  PMID: 23209197
4.  Expression and prognostic value of VEGFR-2, PDGFR-β, and c-Met in advanced hepatocellular carcinoma 
Background
We explore the clinical and prognostic significance of expression of vascular endothelial growth factor receptor (VEGFR)-2, platelet-derived growth factor receptor (PDGFR)-β, and c-Met in patients with hepatocellular carcinoma (HCC).
Methods
The expression of VEGFR-2, PDGFR-β, and c-Met were determined by immunohistochemical examination of the tissues of 93 HCC patients. The relationships of these markers with clinicopathological factors and prognosis were then analyzed.
Results
High expression of VEGFR-2, PDGFR-β, and c-Met was found in 86%, 19.4%, and 80.6% of patients, respectively. Expression of VEGFR-2 correlated with gender (P = 0.044), hepatitis B surface antigen positivity (P = 0.024), degree of tumor differentiation (P = 0.023), and hepatic cirrhosis (P = 0.026). Expression of PDGFR-β correlated with alpha-fetoprotein level (P = 0.029), tumor size (P = 0.033), and hepatic cirrhosis (P = 0.023). No significant correlations were identified between expression of c-Met and clinicopathological factors. Expression of PDGFR-β correlated with overall survival (P = 0.046) and expression of c-Met correlated with progression-free survival (P = 0.01).
Conclusions
We found that in patients with HCC, high expression of VEGFR-2 correlates with chronic hepatitis B virus infection and hepatic cirrhosis. High expression of PDGFR-β is a predictor of poor prognosis. High expression of C-Met may predict therapeutic effectiveness of sorafenib in HCC patients.
doi:10.1186/1756-9966-32-16
PMCID: PMC3623756  PMID: 23552472
Hepatocellular carcinoma; VEGFR-2; PDGFR-β; c-Met; Survival analysis; Sorafenib
5.  Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.] 
PLoS ONE  2012;7(4):e36234.
Background
Sweet potato (Ipomoea batatas L. [Lam.]) ranks among the top six most important food crops in the world. It is widely grown throughout the world with high and stable yield, strong adaptability, rich nutrient content, and multiple uses. However, little is known about the molecular biology of this important non-model organism due to lack of genomic resources. Hence, studies based on high-throughput sequencing technologies are needed to get a comprehensive and integrated genomic resource and better understanding of gene expression patterns in different tissues and at various developmental stages.
Methodology/Principal Findings
Illumina paired-end (PE) RNA-Sequencing was performed, and generated 48.7 million of 75 bp PE reads. These reads were de novo assembled into 128,052 transcripts (≥100 bp), which correspond to 41.1 million base pairs, by using a combined assembly strategy. Transcripts were annotated by Blast2GO and 51,763 transcripts got BLASTX hits, in which 39,677 transcripts have GO terms and 14,117 have ECs that are associated with 147 KEGG pathways. Furthermore, transcriptome differences of seven tissues were analyzed by using Illumina digital gene expression (DGE) tag profiling and numerous differentially and specifically expressed transcripts were identified. Moreover, the expression characteristics of genes involved in viral genomes, starch metabolism and potential stress tolerance and insect resistance were also identified.
Conclusions/Significance
The combined de novo transcriptome assembly strategy can be applied to other organisms whose reference genomes are not available. The data provided here represent the most comprehensive and integrated genomic resources for cloning and identifying genes of interest in sweet potato. Characterization of sweet potato transcriptome provides an effective tool for better understanding the molecular mechanisms of cellular processes including development of leaves and storage roots, tissue-specific gene expression, potential biotic and abiotic stress response in sweet potato.
doi:10.1371/journal.pone.0036234
PMCID: PMC3338685  PMID: 22558397
6.  Cotyledon damage affects seed number through final plant size in the annual grassland species Medicago lupulina 
Annals of Botany  2010;107(3):437-442.
Background and Aims
The effects of cotyledon damage on seedling growth and survival are relatively well established, but little is known about the effects on aspects of plant fitness such as seed number and size. Here the direct and indirect mechanisms linking cotyledon damage and plant fitness in the annual species Medicago lupulina are examined.
Methods
Growth and reproductive traits, including mature plant size, time to first flowering, flower number, seed number and individual seed mass were monitored in M. lupulina plants when zero, one or two cotyledons were removed at 7 d old. Structural equation modelling (SEM) was used to examine the mechanisms linking cotyledon damage to seed number and seed mass.
Key Results
Cotyledon damage reduced seed number but not individual seed mass. The primary mechanism was a reduction in plant biomass with cotyledon damage that in turn reduced seed number primarily through a reduction in flower numbers. Although cotyledon damage delayed flower initiation, it had little effect on seed number. Individual seed mass was not affected by cotyledon removal, but there was a trade-off between seed number and seed mass.
Conclusions
It is shown how a network of indirect mechanisms link damage to cotyledons and fitness in M. lupulina. Cotyledon damage had strong direct effects on both plant size and flowering phenology, but an analysis of the causal relationships among plant traits and fitness components showed that a reduction in plant size associated with cotyledon damage was an important mechanism influencing fitness.
doi:10.1093/aob/mcq259
PMCID: PMC3043934  PMID: 21196450
Cotyledon damage; herbivory; fitness; Medicago lupulina L.; alpine grassland; structural equation modelling (SEM); plant growth; flowering phenology
7.  Inhibition airway remodeling and transforming growth factor-β1/Smad signaling pathway by astragalus extract in asthmatic mice 
Airway remodeling is characterized by airway wall thickening, subepithelial fibrosis, increased smooth muscle mass, angiogenesis and increased mucous glands, which can lead to a chronic and obstinate asthma with pulmonary function depression. In the present study, we investigated whether the astragalus extract inhibits airway remodeling in a mouse asthma model and observed the effects of astragalus extract on the transforming growth factor-β1 (TGF-β1)/Smad signaling pathway in ovalbumin-sensitized mice. Mice were sensitized and challenged by ovalbumin to establish a model of asthma. Treatments included the astragalus extract and budesonide. Lung tissues were obtained for hematoxylin and eosin staining and Periodic acid-Schiff staining after the final ovalbumin challenge. Levels of TGF-β1 were assessed by immunohistology and ELISA, levels of TGF-β1 mRNA were measured by RT-PCR, and levels of P-Smad2/3 and T-Smad2/3 were assessed by western blotting. Astragalus extract and budesonide reduced allergen-induced increases in the thickness of bronchial airway and mucous gland hypertrophy, goblet cell hyperplasia and collagen deposition. Levels of lung TGF-β1, TGF-β1 mRNA and P-Smad2/3 were significantly reduced in mice treated with astragalus extract and budesonide. Astragalus extract improved asthma airway remodeling by inhibiting the expression of the TGF-β1/Smad signaling pathway, and may be a potential drug for the treatment of patients with a severe asthma airway.
doi:10.3892/ijmm.2011.868
PMCID: PMC3577142  PMID: 22200784
astragalus plant; airway remodeling; asthma; trans-forming growth factor-β1/Smad signaling pathway
8.  Enhanced Integration of Newborn Neurons after Neonatal Insults 
The production and integration of adult-generated neurons in the dentate gyrus is dramatically perturbed by a variety of pathological insults, including repetitive seizures and hypoxia/ischemia. Less is known about how insults affect early postnatal neurogenesis, during the developmental period when the majority of dentate neurons are produced. Here we tested how single episodes of hypoxia or chemically induced seizure activity in postnatal day 10 mice alter granule cell production and integration. Although neither insult was sufficient to alter the number of newborn neurons nor the population of proliferating cells, both treatments increased the dendritic complexity of newborn granule cells that were born around the time of the insult. Surprisingly, only the dendritic enhancement caused by hypoxia was associated with increased synaptic integration. These results suggest that alterations in dendritic integration can be dissociated from altered neural production and that integration appears to have a lower threshold for perturbation. Furthermore, newborn neurons in adult mice that experienced neonatal hypoxia had reduced dendritic length while having no alterations in number. Together these results suggest that single insults during the neonatal period can have both long- and short-term consequences for neuronal maturation.
doi:10.3389/fnins.2011.00045
PMCID: PMC3070953  PMID: 21490706
kainate; hypoxia; postnatal neurogenesis; dentate gyrus; synaptic; seizure; granule cell; neonate
9.  Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.) 
BMC Plant Biology  2010;10:3.
Background
MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy.
Results
In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts.
Conclusions
This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.
doi:10.1186/1471-2229-10-3
PMCID: PMC2826338  PMID: 20047695
10.  A system for screening agonists targeting β2-adrenoceptor from Chinese medicinal herbs*  
In order to develop a model for screening the agonists of human β2-adrenoceptor from Chinese medicinal herbs extracts, we used a cell-based functional assay based on a common G protein-coupled receptor (GPCR) regulation mechanism and destabilized enhanced green fluorescent protein (d2EGFP) reporter gene technique. The positive cell clone was confirmed by real-time polymerase chain reaction (PCR) and imaging analysis. To assess the value of this model, we screened over 2000 high performance liquid chromatography (HPLC)-fractionated samples from the ethanol extracts of Chinese medicinal herbs. Six fractions (isolated from Panax japonicus, Veratrum nigrum, Phellodendron amurense, Fructus Aurantii Immaturus, Chaenomeles speciosa, and Dictamnus dasycarpus) showed significant effects on active reporter gene expression, three of which (isolated from Phellodendron amurense, Fructus Aurantii Immaturus, and Chaenomeles speciosa) were selected for further concentration response analysis and the half maximal effective concentration (EC1/2 max) values were 4.2, 2.7, and 4.8 µg/ml, respectively. Therefore, this reporter gene assay was suitable for screening β2-adrenoceptor agonists. The results suggest that the six herbal extracts are the possible agonists of β2-adrenoceptor.
doi:10.1631/jzus.B0820340
PMCID: PMC2666200  PMID: 19353741
β2-adrenoceptor; Enhanced green fluorescent protein (EGFP); Chinese medicinal herbs; Screening
11.  1,5-Bis(4-bromo­phen­yl)-3-phenyl­pentane-1,5-dione 
The asymmetric unit of the title compound, C23H18Br2O2, contains two independent mol­ecules with slightly different conformations. In the absence of classical inter­molecular inter­actions, the crystal packing is stabilized by van der Waals forces.
doi:10.1107/S1600536808023970
PMCID: PMC2960541  PMID: 21201658
12.  Phase II trial of sequential gefitinib after minor response or partial response to chemotherapy in Chinese patients with advanced non-small-cell lung cancer 
BMC Cancer  2006;6:288.
Background
Basic research of gefitinib (Iressa, ZD1839) has demonstrated the combination effects of gefitinib and chemotherapy were sequence-dependent. To evaluate the efficacy of sequential administration of gefitinib following a minor response or partial response to two to three cycles of chemotherapy, a phase II clinical trial was done in Chinese patients with advanced non-small-cell lung cancer (NSCLC).
Methods
Thirty-three consecutive patients with advanced NSCLC that had been pretreated with at least one chemotherapeutic regimen and were responding to chemotherapy following 2 to 3 cycles of treatment, entered the trial from May 2004 to February 2006. Patients received gefitinib at an oral dose of 250 mg once daily for 4 weeks.
Results
Thirty-three patients were evaluable for response and toxicity. The objective response rate was 24.2% (8 of 33)(95% CI, 11% to 42%). The symptom improvement rate was 54.5% (18 of 33) (95% CI, 41% to 69%). The median duration of response was 7 months (95%CI, 4.0 to 13.2 months). The median time to disease progression (TTP) was 6.5 months (95%CI, 0.7 to 16.6 months). The median overall survival time (OS) was 9.8 months (range, 2.1 to 18.0 months), and the actuarial 1-year survival was 36.4%. Toxicity was relatively mild and included only one patient (3.0%) with grade 4 diarrhea, 1 (3.0%) with grade 3 rash, 1 (3.0%) with grade 3 nausea, and 1 with grade 3 vomiting (3.0%).
Conclusion
Preliminary results suggest that sequential administration of gefitinib following a response to chemotherapy may be beneficial for Chinese patients with advanced NSCLC. Further randomized clinical trials are needed.
doi:10.1186/1471-2407-6-288
PMCID: PMC1764758  PMID: 17173694

Results 1-12 (12)