Genome-wide identification and phylogenetic analysis of Family-1 UDP glycosyltransferases in maize (Zea mays)

Family-1 UDP glycosyltransferases (UGTs) from plants transfer sugar moieties from activated sugar donors to a wide range of small molecules, and control many metabolic processes during plant growth and development. Here, we report a genome-wide analysis of maize that identified 147 Family-1 glycosyltransferases based on their conserved PSPG motifs. Phylogenetic analysis of these genes with 18 Arabidopsis UGTs and two rice UGTs clustered them into 17 groups (A–Q). The patterns of intron gain/loss events, as well as their positions within UGTs from the same group, further aided elucidation of their divergence and evolutionary relationships between UGTs. Expression analysis of the maize UGT genes using both online microarray data and quantitative real-time PCR verification indicates that UGT genes are widely expressed in various tissues and likely play important roles in plant growth and development. Our study provides useful information on the Family-1 UGTs in maize, and will facilitate their further characterization to better understand their functions.     

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigella sonnei are prevalent in developing and developed countries respectively. To begin to explain these distinctive epidemiological and pathological features at the genome level, we have carried out comparative genomics on four representative strains. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants. The Shigella chromosomes share most of their genes with that of E.coli K12 strain MG1655, but each has over 200 pseudogenes, 300 approximately 700 copies of insertion sequence (IS) elements, and numerous deletions, insertions, translocations and inversions. There is extensive diversity of putative virulence genes, mostly acquired via bacteriophage-mediated lateral gene transfer. Hence, via convergent evolution involving gain and loss of functions, through bacteriophage-mediated gene acquisition, IS-mediated DNA rearrangements and formation of pseudogenes, the Shigella spp. became highly specific human pathogens with variable epidemiological and pathological features.     

Dietary supplementation with <Emphasis Type="Italic">Astragalus</Emphasis> polysaccharide enhances ileal digestibilities and serum concentrations of amino acids in early weaned piglets

Two experiments were conducted to evaluate the effects of dietary supplementation with Astragalus polysaccharide (APS) on growth performance, apparent ileal digestibilities (AID) of amino acids (AA), and their serum concentrations in early weaned piglets. In Exp. 1, 60 pigs were weaned at 21 days of age (BW 7.35 ± 0.23 kg) and allocated to three treatments (20 pigs/treatment), representing supplementing 0.0% (control), 0.02% colistin (antibiotic), or 0.1% APS to a corn- and soybean meal-based diet. Average daily gain (ADG), average daily feed intake (ADFI), and feed/gain ratio (F/G) were measured weekly. Blood samples were obtained from five pigs selected randomly from each treatment for the measurement of serum free AA concentrations on days 7, 14, and 28. In Exp. 2, 12 pigs were weaned at 21 day of age (BW 7.64 ± 0.71 kg), assigned to three treatment groups as in Exp. 1, and surgically fitted with a simple T-cannula at the terminal ileum. Ileal digesta samples were obtained for the measurement of AID of AA on days 7, 14 and 28. Dietary APS did not affect ADFI, but enhanced (P < 0.05) ADG by 11 and 4.4%, and improved F/G by 5.6 and 8.4%, respectively, compared with the control and antibiotic groups. Addition of APS to the diet increased AID and serum concentrations of most nutritionally essential and non-essential AA (including arginine, proline, glutamate, lysine, methionine, tryptophan, and threonine) on days 14 and 28. Circulating levels of total AA were affected by the age of pigs and treatment × time interaction. Collectively, these findings indicate that APS may ameliorate the digestive and absorptive function and regulate AA metabolism to beneficially increase the entry of dietary AA into the systemic circulation, which provide a mechanism to explain the growth-promoting effect of APS in early weaned piglets.     

Non‐invasive imaging of allogeneic transplanted skin graft by 131I‐anti‐TLR5 mAb

Although ¹⁸F‐fluorodeoxyglucose (¹⁸F‐FDG) uptake can be used for the non‐invasive detection and monitoring of allograft rejection by activated leucocytes, this non‐specific accumulation is easily impaired by immunosuppressants. Our aim was to evaluate a ¹³¹I‐radiolabelled anti‐Toll‐like receptor 5 (TLR5) mAb for non‐invasive in vivo graft visualization and quantification in allogeneic transplantation mice model, compared with the non‐specific radiotracer ¹⁸F‐FDG under using of immunosuppressant. Labelling, binding, and stability studies were performed. BALB/c mice transplanted with C57BL/6 skin grafts, with or without rapamycin treatment (named as allo‐treated group or allo‐rejection group), were injected with ¹³¹I‐anti‐TLR5 mAb, ¹⁸F‐FDG, or mouse isotype ¹³¹I‐IgG, respectively. Whole‐body phosphor‐autoradiography and ex vivo biodistribution studies were obtained. Whole‐body phosphor‐autoradiography showed ¹³¹I‐anti‐TLR5 mAb uptake into organs that were well perfused with blood at 1 hr and showed clear graft images from 12 hrs onwards. The ¹³¹I‐anti‐TLR5 mAb had significantly higher graft uptake and target‐to‐non‐target ratio in the allo‐treated group, as determined by semi‐quantification of phosphor‐autoradiography images; these results were consistent with ex vivo biodistribution studies. However, high ¹⁸F‐FDG uptake was not observed in the allo‐treated group. The highest allograft‐skin‐to‐native‐skin ratio (A:N) of ¹³¹I‐anti‐TLR5 mAb uptake was significantly higher than the ratio for ¹⁸F‐FDG (7.68 versus 1.16, respectively). ¹³¹I‐anti‐TLR5 mAb uptake in the grafts significantly correlated with TLR5 expression in the allograft area. The accumulation of ¹³¹I‐IgG was comparable in both groups. We conclude that radiolabelled anti‐TLR5 mAb is capable of detecting allograft with high target specificity after treatment with the immunosuppressive drug rapamycin.     

Characterization of Androgen Receptor Structure and Nucleocytoplasmic Shuttling of the Rice Field Eel

Androgen receptor (AR) plays a critical role in prostate cancer and male sexual differentiation. We have identified AR from a primitive vertebrate with a sex reversal characteristic, the rice field eel. AR of this species (eAR) is distinct from human AR, especially in the ligand binding domain (LBD), and its expression in gonads shows an increasing tendency during gonadal transformation from ovary via ovotestis to testis. eAR has a restricted androgen-dependent transactivation function after a nuclear translocation upon dihydrotestosterone exposure. A functional nuclear localization signal was further identified in the DNA binding domain and hinge region. Although nuclear export is CRM1-independent, eAR has a novel nuclear export signal, which is negatively charged, indicating that a nuclear export pathway may be mediated by electrostatic interaction. Further, our studies have identified critical sequences for ligand binding in the C terminus. A structure of three α-helices in the LBD has been conserved from eels to humans during vertebrate evolution, despite a distinct amino acid sequence. Mutation analysis confirmed that the LBD is essential for dihydrotestosterone-induced nuclear import of eAR and following transactivation function in the nucleus. In addition, eAR interacts with both Sox9a1 and Sox9a2, and their interaction regulates transactivation of eAR. Our data suggest that the primitive species conserves and especially acquires key novel domains, the nuclear export signal and LBD, for the eAR function in spite of a rapid sequence evolution.     

水分胁迫对不同小麦品种光系统功能基因psbA、psbD及cab表达的影响

两种小麦品种绵农4号T r itic u m a e s ti v u m L.c v.M i a n n o n g N o.4和绵农5号T r itic u m a e s ti v u m L.c v.M i a n n o n g N o.5在渐进水分胁迫下相对含水量、质膜相对透性及光系统D C I P2,62二氯酚靛酚光化学还原活性变化的差异显示,绵农5号小麦比绵农4号小麦具有较高的水分胁迫耐受力.进而对比了水分胁迫对这两种耐旱性不同的小麦品种的光系统在基因转录及蛋白代谢等方面的影响.结果表明:渐进水分胁迫下,两种小麦的光系统主要基因p sb A、p sb D、c a b的转录本水平及其编码蛋白D1,D2、L H C的稳态含量分别下降20%及14%以上,而绵农5号c a b基因的转录水平下降程度39.5%与绵农4号61.8%相比明显缓慢,这可能是其具有较高耐旱性的一个重要原因.     

Single nucleotide polymorphisms,haplotypes and combined genotypes of lactoferrin gene and their associations with mastitis in Chinese Holstein cattle

Lactoferrin (Lf) is naturally produced by the mammary gland, having biological functions of antibacterial and anti-inflammatory activities. To investigate whether the Lf gene is associated with mastitis in dairy cattle, a DNA sequencing approach was used to identify single nucleotide polymorphisms (SNPs) in the gene. Three previously reported SNPs in the 5′ flanking region and one novel SNP in exon1 of Lf gene were identified. A total of 353 individuals from Holstein cattle populations were genotyped for their SNPs using Created Restriction Site PCR (CRS-PCR) and PCR-RFLP methods. Twenty-two and nineteen combinations of three SNPs (g.3440T>G, g.3879_3880insG, and g.4432T>C) and another three SNPs (g.3429G>A, g.3440T>G, g.3879_3880insG) were observed, respectively. The result of haplotype analysis of four SNPs showed that fourteen different haplotypes were identified. Two major haplotypes (GECB and GECA) occurred with a frequency of 22.5 and 18.5% in the study population, respectively. Statistical analyses revealed no significant association between one single SNP of Lf gene and SCS, whereas significant associations between their combined genotypes of three SNPs, haplotype and SCS. Combined genotype EFCDBB and GGEFDD with the lowest SCS were favorable for the mastitis resistance. They may be used as a possible candidate for marker-assisted selection in dairy cattle breeding program.     

Therapeutic Effect of Intravenous Infusion of Perfluorocarbon Emulsion on LPS-Induced Acute Lung Injury in Rats

Acute lung injury (ALI) and its more severe form, acute respiratory distress syndrome (ARDS) are the leading causes of death in critical care. Despite extensive efforts in research and clinical medicine, mortality remains high in these diseases. Perfluorocarbon (PFC), a chemical compound known as liquid ventilation medium, is capable of dissolving large amounts of physiologically important gases (mainly oxygen and carbon dioxide). In this study we aimed to investigate the effect of intravenous infusion of PFC emulsion on lipopolysaccharide (LPS) induced ALI in rats and elucidate its mechanism of action. Forty two Wistar rats were randomly divided into three groups: 6 rats were treated with saline solution by intratracheal instillation (control group), 18 rats were treated with LPS by intratracheal instillation (LPS group) and the other 18 rats received PFC through femoral vein prior to LPS instillation (LPS+PFC group). The rats in the control group were sacrificed 6 hours later after saline instillation. At 2, 4 and 6 hours of exposure to LPS, 6 rats in the LPS group and 6 rats in LPS+PFC group were sacrificed at each time point. By analyzing pulmonary pathology, partial pressure of oxygen in the blood (PaO2) and lung wet-dry weight ratio (W/D) of each rat, we found that intravenous infusion of PFC significantly alleviated acute lung injury induced by LPS. Moreover, we showed that the expression of pulmonary myeloperoxidase (MPO), intercellular adhesion molecule-1 (ICAM-1) of endothelial cells and CD11b of polymorphonuclear neutrophils (PMN) induced by LPS were significantly decreased by PFC treatment in vivo. Our results indicate that intravenous infusion of PFC inhibits the infiltration of PMNs into lung tissue, which has been shown as the core pathogenesis of ALI/ARDS. Thus, our study provides a theoretical foundation for using intravenous infusion of PFC to prevent and treat ALI/ARDS in clinical practice.     

RNA-dependent dynamic histone acetylation regulates MCL1 alternative splicing

Histone deacetylases (HDACs) and lysine acetyltransferases (KATs) catalyze dynamic histone acetylation at regulatory and coding regions of transcribed genes. Highly phosphorylated HDAC2 is recruited within corepressor complexes to regulatory regions, while the nonphosphorylated form is associated with the gene body. In this study, we characterized the nonphosphorylated HDAC2 complexes recruited to the transcribed gene body and explored the function of HDAC-complex-mediated dynamic histone acetylation. HDAC1 and 2 were coimmunoprecipitated with several splicing factors, including serine/arginine-rich splicing factor 1 (SRSF1) which has roles in alternative splicing. The co-chromatin immunoprecipitation of HDAC1/2 and SRSF1 to the gene body was RNA-dependent. Inhibition of HDAC activity and knockdown of HDAC1, HDAC2 or SRSF1 showed that these proteins were involved in alternative splicing of MCL1. HDAC1/2 and KAT2B were associated with nascent pre-mRNA in general and with MCL1 pre-mRNA specifically. Inhibition of HDAC activity increased the occupancy of KAT2B and acetylation of H3 and H4 of the H3K4 methylated alternative MCL1 exon 2 nucleosome. Thus, nonphosphorylated HDAC1/2 is recruited to pre-mRNA by splicing factors to act at the RNA level with KAT2B and other KATs to catalyze dynamic histone acetylation of the MCL1 alternative exon and alter the splicing of MCL1 pre-mRNA.     

Microarray-based method to evaluate the accuracy of restriction endonucleases HpaII and MspI

A double-strand DNA (ds DNA) microarray was fabricated to analyze the structural perturbations caused by methylation and the different base mismatches in the interaction of the restriction endonucleases HpaII and MspI with DNA. First, a series of synthesized oligonucleotides were arrayed on the aldehyde-coated glass slides. Second, these oligonucleotides were hybridized with target sequences to obtain ds DNA microarray, which includes several types of double strands with the fully methylated, semi-methylated, and unmethylated canonical recognition sequences, semi-methylated and unmethylated base mismatches within the recognition sequences. The cleavage experiments were carried out under normal buffer conditions. The results indicated that MspI could partially cleave methylated and semi-methylated canonical recognition sequences. In contrast, HpaII could not cleave methylated and semi-methylated canonical recognition sequences. HpaII and MspI could both cleave the unmethylated canonical recognition sequence. However, HpaII could partially cleave the sequence containing one GG mismatch and not cleave other base mismatches in the corresponding recognition site. In contrast, MspI could not recognize the base mismatches within the recognition sequence. A good reproducibility was observed in several parallel experiments. The experiment indicates that the microarray technology has great potentials in high-throughput identifying important interactions between protein and DNA.