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Li YJ, Li LY, Li JL, Zhang L, Gao F, Zhou GH. Effects of dietary supplementation with ferulic Acid or vitamin e individually or in combination on meat quality and antioxidant capacity of finishing pigs. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:374-81. [PMID: 25656211 PMCID: PMC4341082 DOI: 10.5713/ajas.14.0432] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 08/27/2014] [Accepted: 10/16/2014] [Indexed: 02/07/2023]
Abstract
This study aimed to evaluate the effects of vitamin E (VE), ferulic acid (FA) and their combination supplementation on meat quality and antioxidant capacities of finishing pigs. Sixty barrows were randomly allocated to four experimental diets using a 2×2 factorial arrangement with 2 VE supplemental levels (0 or 400 mg/kg) and 2 FA supplemental levels (0 or 100 mg/kg) in basal diets. After 28 days, six pigs per treatment were slaughtered. The results showed that VE supplementation increased loin eye area of pigs (p<0.05) and FA supplementation increased pH45min value (p<0.05). The interaction of FA×VE was observed in shear force of longissimus dorsi muscle (p<0.05). Moreover, supplementation with VE decreased hepatic and sarcous malondialdehyde (MDA) content, increased hepatic glutathione (GSH) content and sarcous glutathione peroxidase (GSH-Px) activity (p<0.05). Additionally, supplementation with FA increased hepatic GSH-Px activity and decreased sarcous MDA content (p<0.05). However, dietary treatment did not affect the expression of genes related to nuclear factor, erythroid 2-like 2 (NFE2L2) pathway. These results suggest that dietary FA and VE could partially improve meat quality and antioxidant capacity of finishing pigs, but not by activating NFE2L2 pathway under the normal conditions of farming.
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Feng JB, Liu SK, Wang RJ, Zhang JR, Wang XL, Kaltenboeck L, Li JL, Liu ZJ. Molecular characterization, phylogenetic analysis and expression profiling of myoglobin and cytoglobin genes in response to heat stress in channel catfish Ictalurus punctatus. JOURNAL OF FISH BIOLOGY 2015; 86:592-604. [PMID: 25604925 DOI: 10.1111/jfb.12584] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
To understand the function of myoglobin (Mb) and cytoglobin (Cygb) in channel catfish Ictalurus punctatus in response to heat stress, mb and cygb genes were identified and characterized in this study. These genes were widely expressed in all the tested tissues, but strong tissue preferences were observed, with the mb gene being expressed most highly in the heart, cygb1 most highly expressed in the intestine and cygb2 most highly expressed in the brain. After heat-stress challenge, mb and cygb genes were up-regulated in almost all tested tissues. In general, such up-regulation was more dramatic in the tolerant group than in the intolerant group, suggesting that higher expression of mb and cygb genes contributed to greater tolerance of I. punctatus to heat stress.
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Xiao J, Li JL, Liu P, Yang GW. A new phase transformation path from nanodiamond to new-diamond via an intermediate carbon onion. NANOSCALE 2014; 6:15098-15106. [PMID: 25369973 DOI: 10.1039/c4nr05246c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The investigation of carbon allotropes such as graphite, diamond, fullerenes, nanotubes and carbon onions and mechanisms that underlie their mutual phase transformation is a long-standing problem of great fundamental importance. New diamond (n-diamond) is a novel metastable phase of carbon with a face-centered cubic structure; it is called "new diamond" because many reflections in its electron diffraction pattern are similar to those of diamond. However, producing n-diamond from raw carbon materials has so far been challenging due to n-diamond's higher formation energy than that of diamond. Here, we, for the first time, demonstrate a new phase transformation path from nanodiamond to n-diamond via an intermediate carbon onion in the unique process of laser ablation in water, and establish that water plays a crucial role in the formation of n-diamond. When a laser irradiates colloidal suspensions of nanodiamonds at ambient pressure and room temperature, nanodiamonds are first transformed into carbon onions serving as an intermediate phase, and sequentially carbon onions are transformed into n-diamonds driven by the laser-induced high temperature and high pressure from the carbon onion as a nanoscaled temperature and pressure cell upon the process of laser irradiation in a liquid. This phase transformation not only provides new insight into the physical mechanism involved, but also offers one suitable opportunity for breaking controllable pathways between n-diamond and carbon allotropes such as diamond and carbon onions.
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Pandit NP, Shen YB, Chen Y, Wang WJ, Li JL. Molecular characterization, expression, and immunological response analysis of the TWEAK and APRIL genes in grass carp, Ctenopharyngodon idella. GENETICS AND MOLECULAR RESEARCH 2014; 13:10105-20. [PMID: 25501222 DOI: 10.4238/2014.december.4.5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
TWEAK and APRIL are important members of the TNF superfamily, which play a crucial role in several diseases. Here, we describe the identification of grass carp (Ctenopharyngodon idella) homologs of TWEAK and APRIL (designated gcTWEAK and gcAPRIL, respectively) and their response to Aeromonas hydrophila and Aquareovirus infection. The gcTWEAK cDNA sequence contains 2273 bases with an open reading frame of 753 bases encoding 250-amino acid residues. The gcTWEAK protein contains a predicted transmembrane domain, a putative furin protease cleavage site, 3 conserved cysteine residues, and a typical TNF homology domain. The gcAPRIL cDNA sequence contains 1408 bases with an open reading frame of 747 bases encoding 248-amino acid residues. The gcAPRIL protein contains a predicted transmembrane domain, a putative furin protease cleavage site, 2 conserved cysteine residues, and a typical TNF homology domain corresponding to other, known APRIL homologs. Reverse transcription-polymerase chain reaction analysis shows that both gcTWEAK and gcAPRIL transcripts are predominantly expressed in the skin, spleen, and head kidney, and they are significantly upregulated in most immune tissues by A. hydrophila and Aquareovirus infections. Our results demonstrate that liver is the most responsive tissue against bacterial infection, whereas gill is the most responsive tissue against viral infection. The association of increased gcTWEAK and gcAPRIL expression after bacterial and viral infections suggests that they play a potentially important role in the immune system of fish.
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Ren ZQ, Wu WJ, Liu WH, Zheng R, Li JL, Zuo B, Xu DQ, Li FE, Lei MG, Ni DB, Xiong YZ. Differential expression and effect of the porcine ANGPTL4 gene on intramuscular fat. GENETICS AND MOLECULAR RESEARCH 2014; 13:2949-58. [PMID: 24782129 DOI: 10.4238/2014.april.16.3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
In a previous study, we investigated differences in gene expression in backfat between Meishan and Large White pigs and their F1 hybrids, Large White x Meishan, and Meishan x Large White pigs. One potential differentially expressed sequence tag from the mRNA differential display was a homolog of the human angiopoietin-like 4 (ANGPTL4) gene, which encodes a protein that is secreted by both liver and white adipose tissues and can inhibit lipoprotein lipase activity and stimulate white adipose tissue lipolysis. Here, ANGPTL4 mRNA was found to be upregulated in the backfat of Large White compared with that in the Meishan pigs and the F1 hybrids, Meishan x Large White and Large White x Meishan, whereas expression was lowest both in the longissimus dorsi and the heart, as shown by the tissue distribution profile. Only one mutation, a G/A transition located in the third intron, was found. The ANGPTL4 G/A polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) showed a significant effect on intramuscular fat (IMF), water moisture of the longissimus dorsi, meat marbling of the longissimus dorsi, and pH of the longissimus dorsi (P < 0.05). This site seemed to be significantly (P < 0.05) additive in its actions on IMF, water moisture, and pH, whereas it showed significant dominance in its action on meat marbling (P < 0.05). This locus can be potentially considered as a marker for IMF improvement.
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Fu H, Tang XR, Li JL, Tan DW. An experimental technique of split Hopkinson pressure bar using fiber micro-displacement interferometer system for any reflector. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:045120. [PMID: 24784672 DOI: 10.1063/1.4871955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel non-contact measurement technique had been developed for the mechanical properties of materials in Split Hopkinson Pressure Bars (SHPB). Instead of the traditional strain gages mounted on the surfaces of bars, two shutters were mounted on the end of bars to directly measure interfacial velocity using Fiber Micro-Displacement Interferometer System for Any Reflector. Using the new technique, the integrated stress-strain responses could be determined. The experimental technique was validated by SHPB test simulation. The technique had been used to investigate the dynamic response of a brittle explosive material. The results showed that the new experimental technique could be applied to the dynamic behavior in SHPB test.
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Wang LF, Li JL, Ma WH, Li JY. Drug resistance analysis of bacterial strains isolated from burn patients. GENETICS AND MOLECULAR RESEARCH 2014; 13:9727-34. [PMID: 24535909 DOI: 10.4238/2014.january.22.10] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This study aimed to analyze the spectrum and drug resistance of bacteria isolated from burn patients to provide a reference for rational clinical use of antibiotics. Up to 1914 bacterial strain specimens isolated from burn patients admitted to hospital between 2001 and 2010 were subjected to resistance monitoring by using the K-B paper disk method. Retrospective analysis was performed on drug resistance analysis of burn patients. The top eight bacterium strains according to detection rate. A total of 1355 strains of Gram-negative (G(-)) bacteria and 559 strains of Gram-positive (G(+)) bacteria were detected. The top eight bacterium strains, according to detection rate, were Acinetobacter baumannii, Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae, Enterobacter cloacae, and Enterococcus. Drug resistance rates were higher than 90% in A. baumannii, P. aeruginosa, S. epidermidis, and S. aureus, which accounted for 52.2, 21.7, 27.8, and 33.3%, respectively, of the entire sample. Those with drug resistance rates lower than 30% accounted for 4.3, 30.4, 16.7, and 16.7%, respectively. Multidrug-resistant S. aureus (MRSA) and methicillin-resistant S. epidermidis (MRSE) accounted for 49.2 and 76.4% of the S. epidermis and S. aureus resistance, respectively. Antibacterial drugs that had drug resistance rates to MRSE and MRSA higher than 90% accounted for 38.9 and 72.2%, respectively, whereas those with lower than 30% drug resistance rates accounted for 11.1 and 16.7%, respectively. The burn patients enrolled in the study were mainly infected with G(-) bacteria. These results strongly suggest that clinicians should practice rational use of antibiotics based on drug susceptibility test results.
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Li JL, Li YJ, Zhang KJ, Lan L, Shi JG, Yang X, Zhang MJ, Zhang FC, Gao XC. No association between FGD1 gene polymorphisms and intellectual developmental disability in the Qinba mountain area. GENETICS AND MOLECULAR RESEARCH 2014; 13:127-33. [PMID: 24446295 DOI: 10.4238/2014.january.10.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
FGD1 encoding a guanine nucleotide exchange factor, specifically activates Rho GTPase cell division cycle 42 (Cdc42). Dysfunction of FGD1 causes Aarskog-Scott syndrome (MIM #305400), an X-linked disorder that may affect bone and intellectual development. However, the relationship between FGD1 and intellectual developmental disorders (IDD) remains unclear. The purpose of this study was to investigate the genetic association between the FGD1 polymorphism and IDD. Working with families from the Qinba mountain area where the occurrence of IDD is higher than the average in China, we analyzed 456 samples from 130 nuclear families, effectively controlling for stratification and environmental factors. Five SNP loci (rs2230265, rs7881608, rs2239809, rs6614244, and rs2284710) were selected that were well distributed within the FGD1 gene. Genotyping was performed through single-strand conformation polymorphism and restriction fragment length polymorphism. The data were analyzed with transmission disequilibrium tests. In the Qinba mountain area, no significant association was observed between IDD and allele or genotype frequencies, or the haplotype of the 5 SNP loci of the FGD1 gene. The results indicate that FGD1 may not be a monogenetic X-linked factor in IDD. Further studies are required to investigate its role in intellectual development based on its specific interactions with Cdc42 or other partner proteins contributing to IDD.
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Chang XZ, Li JL, Bai ZY, Li XL. Cloning and expression analysis of the 37-kDa laminin receptor precursor gene from Hyriopsis cumingii. GENETICS AND MOLECULAR RESEARCH 2013; 12:6130-9. [PMID: 24338406 DOI: 10.4238/2013.december.2.10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Hyriopsis cumingii is an economically important freshwater pearl mussel with high pearl quality that is endemic in China. Investigation of genes relevant to shell formation is important for increased pearl output. The substances that form mollusk shells are secreted by epithelial cells in the mantle, the proliferation of which influences secretion ability. This study focused on the proliferation-related 37-kDa laminin receptor precursor (37LRP) of H. cumingii. The full-length cDNA (1133 bp) encoding this 300-amino acid protein was cloned from the mantle. Quantitative fluorescence analysis showed that 37LRP expressed in eight tissues, with the highest expression observed in the liver, and its expression pattern in the mantle reflected shell repair. During repair, 37LRP expression was higher in the experimental shell repair group than that in the control group, exhibiting an initial increase followed by a decrease in expression, and returning to basal levels on completion of the repair. A similar trend was also observed with respect to immunity and cellular metabolism. Expression of the 37LRP protein in the experimental group was significantly higher than that in the control group at the first and second days after shell injury. After 4 days, 37LRP expression in the experimental group was lower than that in the control group. In situ hybridization revealed a strong positive signal corresponding to the 37LRP mRNA at the horny grooves of the mantle, evagination, and in epithelial cells of the velum, which implicated these areas in the repair and formation of the cuticle, prismatic layer, and nacre.
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Shen XB, Xu D, Li JL, Lu LQ. Molecular cloning and immune responsive expression of a ribonuclease III orthologue involved in RNA interference, dicer, in grass carp Ctenopharyngodon idella. JOURNAL OF FISH BIOLOGY 2013; 83:1234-1248. [PMID: 24580665 DOI: 10.1111/jfb.12219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 07/19/2013] [Indexed: 06/03/2023]
Abstract
In this study, the dicer gene (designated as cidicer) was identified and characterized from grass carp Ctenopharyngodon idella. The complementary DNA (cDNA) of cidicer contained an open reading frame (ORF) of 5646 nucleotides (nts) encoding a putative protein of 1881 amino acids (aa). The deduced Dicer protein contained all known functional domains identified in other organisms. Tissue tropism analysis indicated that cidicer is abundantly expressed in brain, gill, head kidney, liver, spleen, heart, muscle and intestine. In the C. idella kidney (CIK) cells, messenger RNA (mRNA) expression of cidicer was significantly up-regulated at 24 h (6·36-fold, P < 0·01) after grass carp reovirus (GCRV) infection, and its transcriptional expression level was also transiently induced to a high level (6·54-fold, P < 0·01) at 2 h post-stimulation of synthetic double-stranded polyinosinic-polycytidylic potassium salt [poly(I:C)]. In vivo analysis further showed that the expression of cidicer mRNA in the liver was induced to a significantly high level at 12 h (8·46-fold, P < 0·01), and then dropped to normal level at 72 h post-challenge with GCRV. The transcriptional expression pattern of cidicer in the spleen tissue was similar to that of liver tissue upon GCRV challenge. These results collectively implied that the identified cidicer was an inducible gene responding to viral infection both in vitro and in vivo, and the data would shed light on the interaction between RNA interference (RNAi) antiviral pathway and aquareovirus infection.
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Cen P, Ye L, Su QJ, Wang X, Li JL, Lin XQ, Liang H, Ho WZ. Methamphetamine inhibits Toll-like receptor 9-mediated anti-HIV activity in macrophages. AIDS Res Hum Retroviruses 2013; 29:1129-37. [PMID: 23751096 DOI: 10.1089/aid.2012.0264] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Toll-like receptor 9 (TLR9) is one of the key sensors that recognize viral infection/replication in the host cells. Studies have demonstrated that methamphetamine (METH) dysregulated host cell innate immunity and facilitated HIV infection of macrophages. In this study, we present new evidence that METH suppressed TLR9-mediated anti-HIV activity in macrophages. Activation of TLR9 by its agonist CpG-ODN 2216 inhibits HIV replication, which was demonstrated by increased expression of TLR9, interferon (IFN)-α, IFN regulatory factor-7 (IRF-7), myeloid differentiation factor 88 (MyD88), and myxovirus resistance gene A (MxA) in macrophages. However, METH treatment of macrophages greatly compromised the TLR9 signaling-mediated anti-HIV effect and inhibited the expression of TLR9 downstream signaling factors. Dopamine D1 receptor (D1R) antagonists (SCH23390) could block METH-mediated inhibition of anti-HIV activity of TLR9 signaling. Investigation of the underlying mechanisms of the METH action showed that METH treatment selectively down-regulated the expression of TLR9 on macrophages, whereas it had little effect on the expression of other TLRs. Collectively, our results provide further evidence that METH suppresses host cell innate immunity against HIV infection by down-regulating TLR9 expression and its signaling-mediated antiviral effect in macrophages.
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Wang GL, Li XL, Li JL. Significant association between SNPs in the superoxide dismutase 3, extracellular (SOD3) gene and resistance to Aeromonas hydrophila in the freshwater mussel Hyriopsis cumingii. Anim Genet 2013; 44:693-702. [PMID: 23659320 DOI: 10.1111/age.12059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2013] [Indexed: 11/28/2022]
Abstract
Extracellular superoxide dismutase (SOD3) is a major antioxidant enzyme that protects organs from damage by reactive oxygen species (ROS). In this study, the SOD3 gene was identified and characterized from the freshwater mussel Hyriopsis cumingii (Hc-SOD3). The cDNA sequence consists of 763 bp, encoding a protein of 208 amino acids. The amino acid sequence possesses two CuZnSOD signature sequences, and amino acids required for binding of Cu (His-93, -95, -110 and -169) and Zn (His-110, -118, -129 and Asp-132) were conserved in Hc-SOD3. The Hc-SOD3 genomic sequence was 9165 bp in length, containing four exons and three introns. Eighteen single nucleotide polymorphisms were detected in the Hc-SOD3 gene from resistant stock (RS) and susceptible stock (SS) of H. cumingii to Aeromonas hydrophila. The genotype and allele distribution were examined in resistant and susceptible stocks. Among them, a C/G substitution at the g.7994C>G locus and G/C substitution at the g.8087G>C locus were significantly associated with resistance/susceptibility of H. cumingii to A. hydrophila, both in genotype (P = 0.017, P = 0.004 respectively) and allele frequency (P = 0.021, P = 0.006 respectively). Linkage disequilibrium analysis revealed that g.7994C>G, g.8001A>G, g.8035G>A, g.8087G>C and g.8191T>A were in linkage disequilibrium. The results suggest that the two polymorphic loci, g.7994C>G and g.8087G>C, could be potential genetic markers for future molecular selection of strains that are resistant to diseases.
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Xu W, Debeb BG, Smith DL, Li JL, Ueno NT, Alvarez DLLC, Larson RA, Schwba LP, Seagroves TN, Woodward WA. Abstract P5-03-10: HIF-1alpha knockout radiosensitizes select Inflammatory Breast Cancer cells through reduction of stem-like cancer cells. Cancer Res 2012. [DOI: 10.1158/0008-5472.sabcs12-p5-03-10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Independent of the tumor stroma, HIF-1α regulates tumor cell metabolism, cell proliferation and DNA repair pathways, which may produce conflicting responses to radiation, promoting either radioresistance or radiosensitization. Recently, HIF-1α was shown to increase tumor initiating cells (TICs) activity in normoxic tumor cells derived from the MMTV-PyMT trasngenic mouse model of luminal-like breast cancer. While TICs have been reported to be relatively radio-resistant, the role of HIF-1α in mediating the radation response in breast cancer TICs remains unknown. Herein, we examined radiosenstitivity of TICs derived from either PyMT HIF-1α knock out (KO) tumor cells or human breast cancer cell lines transduced with a HIF-1α dominant negative (DN) construct. Consistent prior results that loss of HIF-1 activity reduces TIC frequency, down-regulation of HIF-1 activity through the HIF DN construct reduced mammosphere formation in SUM-159, SUM-149 and MCF-7 cells (by 5.0-, 2.0-, and 2.0-fold respectively). Moreover, β-catenin expression was down-regulated in SUM-149 and SUM-159 cells transfected with the HIF-1α DN construct. Moreover, SUM-149 cells expressing the HIF-1α DN construct exhibited delayed tumor growth in vivo (p = 0.05). Standard clonogenic assays demonstrated that PyMT HIF-1α KO cells and SUM-149 cells expressing the HIF-1α DN construct were more sensitive to radiation therapy (SF6 of PyMT, HIF-1α:Control, 0.016:0.087), but that the PyMT KO and SUM-149 mammospheres that persisted after radiation were completely radioresistant (SF6 of PyMT, HIF-1 α: Control, 0.48:0.44). In contrast, MCF-7 cells were not radiosensitized in either standard or mammosphere assays. Interestingly, in HIF-1α DN MCF-7 cells, molecular features of IBC were observed, such as the increased expression of E-Cadherin and loss of Wisp3. But, Notch1 protein expression was unchanged between HIF-1α DN MCF7 or SUM149 cells. Moreover, concurrent radiation in the presence of a gamma secretase inhibitor or with a p53-MDM2 inhibitor nutlin failed to radiosensitize HIF KO mammosphere clonogens. We conclude that downregulation of HIF-1 activity selectively radiosensitizes IBC clonogenic cells but fails to radiosensitize the residual mammospheres. These data suggest that the known HIF-1α mediated mechanisms that favor radiosensitivity, such as the promotion of glycolysis and proliferation under stress, may predominate in mammospheres, which ultimately leads to radioresistance in residual mammospheres after HIF inhibition.
Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P5-03-10.
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Li JL, Wang LF, Wang HY, Bai LY, Yuan ZM. High-accuracy splice site prediction based on sequence component and position features. GENETICS AND MOLECULAR RESEARCH 2012; 11:3432-51. [PMID: 23079837 DOI: 10.4238/2012.september.25.12] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Identification of splice sites plays a key role in the annotation of genes. Consequently, improvement of computational prediction of splice sites would be very useful. We examined the effect of the window size and the number and position of the consensus bases with a chi-square test, and then extracted the sequence multi-scale component features and the position and adjacent position relationship features of consensus sites. Then, we constructed a novel classification model using a support vector machine with the previously selected features and applied it to the Homo sapiens splice site dataset. This method greatly improved cross-validation accuracies for training sets with true and spurious splice sites of both equal and different proportions. This method was also applied to the NN269 dataset for further evaluation and independent testing. The results were superior to those obtained with previous methods, and demonstrate the stability and superiority of this method for prediction of splice sites.
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Cerri RLA, Thompson IM, Kim IH, Ealy AD, Hansen PJ, Staples CR, Li JL, Santos JEP, Thatcher WW. Effects of lactation and pregnancy on gene expression of endometrium of Holstein cows at day 17 of the estrous cycle or pregnancy. J Dairy Sci 2012; 95:5657-75. [PMID: 22884349 PMCID: PMC7094660 DOI: 10.3168/jds.2011-5114] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2011] [Accepted: 05/29/2012] [Indexed: 01/08/2023]
Abstract
Objectives were to determine effects of lactation and pregnancy on endometrial gene expression on d 17 of the estrous cycle and pregnancy. Heifers (n = 33) were assigned randomly after parturition to lactating (L, n = 17) or nonlactating (NL, n = 16) groups. Cows were subjected to an ovulation synchronization program for a timed artificial insemination (TAI); 10 cows in L and 12 in NL were inseminated. Slaughter occurred 17 d after the day equivalent to TAI, and intercaruncular endometrial tissues were collected. Gene expression was determined by DNA microarray analysis for pregnant (L, n = 8; NL, n = 6) and noninseminated cyclic (L, n = 7; NL, n = 4) cows. Differentially expressed genes were selected with a P-value <0.01 and absolute expression >40. In addition, a fold effect >1.5 was used as a criterion for genes affected by pregnancy. In total, 210 genes were differentially regulated by lactation (136 downregulated and 74 upregulated), and 702 genes were differentially regulated by pregnancy (407 downregulated and 295 upregulated). The interaction effect of pregnancy and lactation affected 61 genes. Genes up- and downregulated in pregnant cows were associated with several gene ontology terms, such as defense response and interferon regulatory factor, cell adhesion, and extracellular matrix. The gene ontology analyses of up- and downregulated genes of lactating cows revealed terms related to immunoglobulin-like fold, immune response, COMM domain, and non-membrane-bounded organelle. Several genes upregulated by lactation, such as IGHG1, IGLL1, IGK, and TRD, were related to immune function, particularly for B cells and γδ T cells. Developmental genes related to limb and neural development and glucose homeostasis (e.g., DKK1, RELN, PDK4) were downregulated by lactation, whereas an interaction was also detected for RELN. The stated genes associated with immune function and developmental genes expressed in the endometrium affected by lactational state are possible candidate genes for interventions to improve fertility of lactating dairy cows.
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Lv Y, Cao LH, Pang H, Lu LN, Li JL, Fu Y, Qi SL, Luo Y, Li-Ling J. Combined genetic and imaging diagnosis for two large Chinese families affected with Pelizaeus-Merzbacher disease. GENETICS AND MOLECULAR RESEARCH 2012; 11:2035-44. [PMID: 22911587 DOI: 10.4238/2012.august.6.7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Pelizaeus-Merzbacher disease (PMD) is a rare X-linked recessive disorder characterized by nystagmus, impaired motor development, ataxia, and progressive spasticity. Genetically defective or altered levels of proteolipid protein (PLP1) or gap-junction alpha protein 12 gene have been found to be a common cause. Here we report on two large Han Chinese families affected with this disease. The probands of both families had produced sons featuring cerebral palsy that had never been correctly diagnosed. PMD was suspected after careful analysis of family history and clinical features. Three rounds of molecular testing, including RT-PCR, genetics linkage and SRY sequence analyses, in combination with fetal ultrasound and magnetic resonance imaging, confirmed the diagnosis. In Family 1, in addition to two patients, three carriers were identified, including one who was not yet married. Genetic testing indicated that a fetus did not have the disease. A healthy girl was born later. In Family 2, two patients and two carriers were identified, while a fetus was genetically normal. A healthy girl was born later. We concluded that by combining genetic testing and imaging, awareness of the symptoms of PMD and understanding of its molecular biology, there is great benefit for families that are at risk for producing offspring affected with this severe disease.
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Liu MQ, Zhou DJ, Wang X, Zhou W, Ye L, Li JL, Wang YZ, Ho WZ. IFN-λ3 inhibits HIV infection of macrophages through the JAK-STAT pathway. PLoS One 2012; 7:e35902. [PMID: 22558263 PMCID: PMC3338759 DOI: 10.1371/journal.pone.0035902] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 03/23/2012] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Interferon lambda 3 (IFN-λ3) is a newly identified cytokine with antiviral activity, and its single nucleotide polymorphisms are strongly associated with the treatment effectiveness and development of chronic hepatitis C virus infection. We thus examined the potential of IFN-λ3 to inhibit HIV replication and the possible mechanisms of the anti-HIV action by IFN-λ3 in human macrophages. PRINCIPAL FINDINGS Under different conditions (before, during, and after HIV infection), IFN-λ3 significantly inhibited viral replication in macrophages, which was associated with the induction of multiple antiviral cellular factors (ISG56, MxA, OAS-1, A3G/F and tetherin) and IFN regulatory factors (IRF-1, 3, 5, 7 and 9). This anti-HIV action of IFN-λ3 could be compromised by the JAK-STAT inhibitor. In addition, IFN-λ3 treatment of macrophages induced the expression of toll-like receptor 3 (TLR3) and two key adaptors (MyD88 and TRIF) in type I IFN pathway activation. However, HIV infection compromised IFN-λ3-mediated induction of the key elements in JAK-STAT signaling pathway. CONCLUSIONS These data indicate that IFN-λ3 exerts its anti-HIV function by activating JAK-STAT pathway-mediated innate immunity in macrophages. Future in vivo studies are necessary in order to explore the potential for developing IFN-λ3-based therapy for HIV disease.
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MESH Headings
- Adaptor Proteins, Vesicular Transport/genetics
- Adaptor Proteins, Vesicular Transport/immunology
- Antigens, Differentiation, B-Lymphocyte/genetics
- Antigens, Differentiation, B-Lymphocyte/immunology
- Cells, Cultured
- Gene Expression Regulation/drug effects
- HIV-1/drug effects
- HIV-1/physiology
- Humans
- Immunity, Innate
- Interferon Regulatory Factors/genetics
- Interferon Regulatory Factors/immunology
- Interferons
- Interleukins/immunology
- Interleukins/pharmacology
- Janus Kinases/antagonists & inhibitors
- Janus Kinases/genetics
- Janus Kinases/immunology
- Macrophages/drug effects
- Macrophages/immunology
- Macrophages/virology
- Membrane Glycoproteins/genetics
- Membrane Glycoproteins/immunology
- Phosphorylation
- Protein Kinase Inhibitors/pharmacology
- Receptors, Interleukin-1/genetics
- Receptors, Interleukin-1/immunology
- STAT Transcription Factors/genetics
- STAT Transcription Factors/immunology
- Signal Transduction/drug effects
- Toll-Like Receptor 3/genetics
- Toll-Like Receptor 3/immunology
- Virus Replication/drug effects
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143
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He T, Li JL, Yang GW. Physical origin of general oscillation of structure, surface energy, and electronic property in rutile TiO2 nanoslab. ACS APPLIED MATERIALS & INTERFACES 2012; 4:2192-2198. [PMID: 22468756 DOI: 10.1021/am300193d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Titanium oxide (TiO(2)) nanostructures have been attracting consistent focus in the past few years because of their enhanced power in solar-energy conversion. Surface and interface play a crucial role in the determination of thermodynamic stability and electronic structure of TiO(2) nanostructures. The rutile (110) nanoslab (NS) has been used as a common subject to investigate the surface relaxation, defect characters, molecule adsorption, and chemically dynamic reaction of TiO(2) nanostructures. Up to date, a long-time standing issue in TiO(2) NS, i.e., the general oscillation of structure, surface energy and electronic property with changing of NS thickness, has not been clear. We have presented a comprehensive investigation on the relationship between surface and oscillation behavior in the TiO(2) (110) NS by the first-principles calculations accompanied with the wave function analysis. We clearly, for the first time, pointed out that the dipoles and surface states bonding induced by the surface-surface interactions are the physical origin of general oscillations in the TiO(2) (110) NS. Our findings not only have a new insight into the basic interactions between surfaces in TiO(2) nanostructures, but also provide useful information for tuning the photocatalytic and photovoltaic properties by surface design.
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144
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Li JL, He T, Yang GW. An all-purpose building block: B12N12 fullerene. NANOSCALE 2012; 4:1665-1670. [PMID: 22294038 DOI: 10.1039/c2nr11808d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have theoretically shown that the boron nitride fullerene cage B(12)N(12) is an all-purpose building block for fabricating multifarious BN nanotubes. Firstly, we investigated the stability and structural of the boron nitride fullerene cage B(12)N(12) and the polymerized derivatives obtained from it. Interestingly we found out that two B(12)N(12) cages can spontaneously form one BN nanotube with two closed ends through the structural transformation when one cage meets another. These results indicated that the fullerene B(12)N(12) can be polymerized to build various remarkable polymers through the spontaneous structural transformation when they are together, which all have planer or tridimensional shapes with a hollow tubular structure, even at the juncture of the coalesced B(12)N(12). Simultaneously, after the structure optimization, the quadrangles at the juncture of the coalesced B(12)N(12) disappear to form a perfect surface only composed of hexagons. Then, we calculated the energy of all the considered nanostructures. The polymerization of the fullerene B(12)N(12) is exothermic and thus can form very stable derivative polymers. These theoretical conclusions stimulate us to use the fullerene B(12)N(12) as an all-purpose building block to construct various BN nanostructures for purpose of fundamental research and potential applications.
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145
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Bi L, Tschiersch J, Meisenberg O, Wielunski M, Li JL, Shang B. Development of a new thoron progeny detector based on SSNTD and the collection by an electric field. RADIATION PROTECTION DOSIMETRY 2011; 145:288-294. [PMID: 21493610 DOI: 10.1093/rpd/ncr078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The importance of (220)Rn (thoron) progeny for human exposure has been widely recognised in the past decades. Since no stable equilibrium factor was found between indoor thoron and its progeny, and the concentration of thoron progeny varies with time, it is necessary to develop detectors for long-term measurement that directly sample and detect thoron progeny. However, power supply of this kind of detectors has always been a problem. In this study, a set of device that is suitable for long-term measurement is introduced. A high-voltage electric field was formed for the collection of charged aerosols attached by (222)Rn (radon) and thoron progenies on solid-state nuclear track detector. Impact from radon progeny could be eliminated with a shield of Al foil of appropriate thickness. Tests were made both in an experimental house and in a thoron chamber in Helmholtz Zentrum München to determine the parameters and to verify the universality under different conditions.
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146
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Zhao PD, Lu FY, Chen R, Lin YL, Li JL, Lu L, Sun GL. A technique for combined dynamic compression-shear test. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:035110. [PMID: 21456792 DOI: 10.1063/1.3557826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
It is critically important to study the dynamic response of materials under a combined compression-shear loading for developing constitutive laws more accurately and fully. We present a novel technique to achieve the combined compression and shear loadings at high strain rates. The main apparatus consists of a strike bar, an incident bar, and two transmission bars. The close-to-specimen end of the incident bar is wedge-shaped with 90°. In each experiment, there are two identical specimens, respectively, agglutinated between one side of the wedge and one of transmission bars. When a loading impulse travels to specimens along the incident bar, because of the special geometrical shape, the specimen-incident bar interface gets an axial and a transverse velocity. Specimens endure a combined compression-shear loading at high strain rates. The compression stress and strain of the specimens are deduced from signals recorded by strain gages mounted on the bars. The shear stress is measured by two piezoelectric transducers of quartz (Y-cut with rotation angle 17.7°) embedded at the close-to-specimen end of transmission bars; the shear strain is measured with a novel optical technique, which is based on the luminous flux method. An analytic model was proposed and validated by the numerical simulations. The simulation results yield good agreement with the analytic results. The proposed technique was then validated through experiments carried out on lead specimens, by comparing experimental results with that of the split Hopkinson pressure bar experiments.
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147
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Han SL, Li JL, Liu Z, Cheng J, Guo SC, Wu SL. Malignant rhabdoid tumor of rectum: report of a case. Tech Coloproctol 2010; 14:199-200. [PMID: 20390315 DOI: 10.1007/s10151-010-0575-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
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148
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Bi L, Li WB, Tschiersch J, Li JL. Age and sex dependent inhalation doses to members of the public from indoor thoron progeny. JOURNAL OF RADIOLOGICAL PROTECTION : OFFICIAL JOURNAL OF THE SOCIETY FOR RADIOLOGICAL PROTECTION 2010; 30:639-658. [PMID: 21149944 DOI: 10.1088/0952-4746/30/4/001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The increased indoor thoron level in Europe, North America and Asia has shown that the exposure to thoron and its decay products cannot be ignored in some environments. The contribution of thoron and its progeny can be a significant component of the total exposure from radon and thoron. In the present paper, radiation dose assessment of members of the public of different age and sex exposed to (220)Rn progeny under different daily life activities is performed through a dosimetric approach. Dose conversion coefficients under typical indoor conditions were estimated to be in the range of 107 nSv (Bq h m(-3))(-1) for infant to 81.7 nSv (Bq h m(-3))(-1) for adult. The results of this work emphasized that small children receive a radiation dose of 25% more than adults under the same conditions, and people performing exercise receive a radiation dose 100% more than when sleeping. The results of this work are appropriate to the risk assessment of thoron exposure to members of the public who live in areas with high radon and thoron concentrations.
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149
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Li ZQ, Li JL, Feng XY, Xie N, Feng JB, Yue GH. Sixteen polymorphic microsatellites for breeding of Chinese soft-shelled turtles (Pelodiscus sinensis). Anim Genet 2010; 41:446-7. [PMID: 20331610 DOI: 10.1111/j.1365-2052.2010.02029.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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150
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Wang JT, Li S, Li JL, Zhang JW, Xu SW. Effects of cold stress on the messenger ribonucleic acid levels of peroxisome proliferator-activated receptor-{gamma} in spleen, thymus, and bursa of Fabricius of chickens. Poult Sci 2010; 88:2549-54. [PMID: 19903953 DOI: 10.3382/ps.2009-00404] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
This study was to investigate the expression trait of the peroxisome proliferator-activated receptor-gamma (PPAR-gamma) gene and the effect of cold stress on the mRNA levels of PPAR-gamma in spleen, thymus, and bursa of Fabricius of chickens. Eighty-four 1-d-old male chickens were randomly allocated to 12 groups (7 chickens per group). There was 1 control group and 5 treatment groups for acute cold stress and 3 control groups and 3 treatment groups for chronic cold stress. Chickens were maintained in our animal facility, kept under a 16L:8D cycle and temperature (30 +/- 2 degrees C), and given free access to standard chow and water. The cold stress was initiated when the birds were 15 d of age, with the duration of the acute cold stress being 1, 3, 6, 12, and 24 h, and the chronic cold stress was 5, 10, and 20 d, respectively. Cold stress temperature was 12 +/- 1 degrees C. Spleen, thymus, and bursa of Fabricius were collected for the assessment of the mRNA levels by real-time PCR after stress termination. The results showed that the PPAR-gamma gene is expressed in spleen, thymus, and bursa of Fabricius, and its expression level is different in different tissues and at different ages. Acute cold stress significantly decreased (P < 0.05) the mRNA levels of the PPAR-gamma gene of spleen and thymus in all treatment groups and significantly increased (P < 0.05) the mRNA levels of the PPAR-gamma gene of bursa of Fabricius in all treatment groups. Compared with the corresponding control groups, chronic cold stress resulted in a significant increase (P < 0.05) of the mRNA levels of the PPAR-gamma gene in spleen and a significant decrease (P < 0.05) of the mRNA levels of the PPAR-gamma gene in thymus and bursa of Fabricius. The results indicate that the PPAR-gamma gene is expressed in all 3 immune organs and has different expression traits. The magnitude and direction of change in PPAR-gamma gene expression differs with the type of cold stress applied and also varies by tissue.
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