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Systematic Analysis of Sequences and Expression Patterns of Drought-Responsive Members of the HD-Zip Gene Family in Maize  [PDF]
Yang Zhao, Yuqiong Zhou, Haiyang Jiang, Xiaoyu Li, Defang Gan, Xiaojian Peng, Suwen Zhu, Beijiu Cheng
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0028488
Abstract: Background Members of the homeodomain-leucine zipper (HD-Zip) gene family encode transcription factors that are unique to plants and have diverse functions in plant growth and development such as various stress responses, organ formation and vascular development. Although systematic characterization of this family has been carried out in Arabidopsis and rice, little is known about HD-Zip genes in maize (Zea mays L.). Methods and Findings In this study, we described the identification and structural characterization of HD-Zip genes in the maize genome. A complete set of 55 HD-Zip genes (Zmhdz1-55) were identified in the maize genome using Blast search tools and categorized into four classes (HD-Zip I-IV) based on phylogeny. Chromosomal location of these genes revealed that they are distributed unevenly across all 10 chromosomes. Segmental duplication contributed largely to the expansion of the maize HD-ZIP gene family, while tandem duplication was only responsible for the amplification of the HD-Zip II genes. Furthermore, most of the maize HD-Zip I genes were found to contain an overabundance of stress-related cis-elements in their promoter sequences. The expression levels of the 17 HD-Zip I genes under drought stress were also investigated by quantitative real-time PCR (qRT-PCR). All of the 17 maize HD-ZIP I genes were found to be regulated by drought stress, and the duplicated genes within a sister pair exhibited the similar expression patterns, suggesting their conserved functions during the process of evolution. Conclusions Our results reveal a comprehensive overview of the maize HD-Zip gene family and provide the first step towards the selection of Zmhdz genes for cloning and functional research to uncover their roles in maize growth and development.
Dumpy-30 family members as determinants of male fertility and interaction partners of metal-responsive transcription factor 1 (MTF-1) in Drosophila
Alla Vardanyan, Lilit Atanesyan, Dieter Egli, Sunil Raja, Monica Steinmann-Zwicky, Renate Renkawitz-Pohl, Oleg Georgiev, Walter Schaffner
BMC Developmental Biology , 2008, DOI: 10.1186/1471-213x-8-68
Abstract: Constitutive expression of the stronger interactor, Dpy-30L1 (CG6444), in transgenic flies inhibits MTF-1 activity and results in elevated sensitivity to Cd(II) and Zn(II), an effect that could be rescued by co-overexpression of dMTF-1. Electrophoretic mobility shift assays (EMSA) suggest that Dpy-30L1 interferes with the binding of MTF-1 to its cognate MRE binding site. Dpy-30L1 is expressed in the larval brain, gonads, imaginal discs, salivary glands and in the brain, testes, ovaries and salivary glands of adult flies. Expression of the second interactor, Dpy-30L2 (CG11591), is restricted to larval male gonads, and to the testes of adult males. Consistent with these findings, dpy-30-like transcripts are also prominently expressed in mouse testes. Targeted gene disruption by homologous recombination revealed that dpy-30L1 knockout flies are viable and show no overt disruption of metal homeostasis. In contrast, the knockout of the male-specific dpy-30L2 gene results in male sterility, as does the double knockout of dpy-30L1 and dpy-30L2. A closer inspection showed that Dpy-30L2 is expressed in elongated spermatids but not in early or mature sperm. Mutant sperm had impaired motility and failed to accumulate in sperm storage organs of females.Our studies help to elucidate the physiological roles of the Dumpy-30 proteins, which are conserved from yeast to humans and typically act in concert with other nuclear proteins to modify chromatin structure and gene expression. The results from these studies reveal an inhibitory effect of Dpy-30L1 on MTF-1 and an essential role for Dpy-30L2 in male fertility.Metal-responsive transcription factor 1 (MTF-1) can cooperate, in a positive or negative manner, with other transcription factors binding to their own DNA sites nearby (USF1, [1]; NFI, [2,3]; Sp1, [4]; NF-kB [5]), but no MTF-1-specific coactivators or corepressors were described so far. A general interaction analysis of Drosophila proteins by means of the yeast two-hybrid sy
Global Identification of Multiple OsGH9 Family Members and Their Involvement in Cellulose Crystallinity Modification in Rice  [PDF]
Guosheng Xie, Bo Yang, Zhengdan Xu, Fengcheng Li, Kai Guo, Mingliang Zhang, Lingqiang Wang, Weihua Zou, Yanting Wang, Liangcai Peng
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0050171
Abstract: Plant glycoside hydrolase family 9 (GH9) comprises typical endo-β-1,4-glucanase (EGases, EC3.2.1.4). Although GH9A (KORRIGAN) family genes have been reported to be involved in cellulose biosynthesis in plants, much remains unknown about other GH9 subclasses. In this study, we observed a global gene co-expression profiling and conducted a correlation analysis between OsGH9 and OsCESA among 66 tissues covering most periods of life cycles in 2 rice varieties. Our results showed that OsGH9A3 and B5 possessed an extremely high co-expression with OsCESA1, 3, and 8 typical for cellulose biosynthesis in rice. Using two distinct rice non-GH9 mutants and wild type, we performed integrative analysis of gene expression level by qRT-PCR, cellulase activities in situ and in vitro, and lignocellulose crystallinity index (CrI) in four internodes of stem tissues. For the first time, OsGH9B1, 3, and 16 were characterized with the potential role in lignocellulose crystallinity alteration in rice, whereas OsGH9A3 and B5 were suggested for cellulose biosynthesis. In addition, phylogenetic analysis and gene co-expression comparison revealed GH9 function similarity in Arabidopsis and rice. Hence, the data can provide insights into GH9 function in plants and offer the potential strategy for genetic manipulation of plant cell wall using the five aforementioned novel OsGH9 genes.
pH-Responsive Artemisinin Derivatives and Lipid Nanoparticle Formulations Inhibit Growth of Breast Cancer Cells In Vitro and Induce Down-Regulation of HER Family Members  [PDF]
Yitong J. Zhang, Byron Gallis, Michio Taya, Shusheng Wang, Rodney J. Y. Ho, Tomikazu Sasaki
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0059086
Abstract: Artemisinin (ART) dimers show potent anti-proliferative activities against breast cancer cells. To facilitate their clinical development, novel pH-responsive artemisinin dimers were synthesized for liposomal nanoparticle formulations. A new ART dimer was designed to become increasingly water-soluble as pH declines. The new artemisinin dimer piperazine derivatives (ADPs) remained tightly associated with liposomal nanoparticles (NPs) at neutral pH but were efficiently released at acidic pH's that are known to exist within solid tumors and organelles such as endosomes and lysosomes. ADPs incorporated into nanoparticles down regulated the anti-apoptotic protein, survivin, and cyclin D1 when incubated at low concentrations with breast cancer cell lines. We demonstrate for the first time, for any ART derivative, that ADP NPs can down regulate the oncogenic protein HER2, and its counterpart, HER3 in a HER2+ cell line. We also show that the wild type epidermal growth factor receptor (EGFR or HER1) declines in a triple negative breast cancer (TNBC) cell line in response to ADP NPs. The declines in these proteins are achieved at concentrations of NP109 at or below 1 μM. Furthermore, the new artemisinin derivatives showed improved cell-proliferation inhibition effects compared to known dimer derivatives.
Expression patterns of the rice class I metallothionein gene family in response to lead stress in rice seedlings and functional complementation of its members in lead-sensitive yeast cells
YuFeng Xu,GongKe Zhou,Lu Zhou,YiQin Li,JinYuan Liu
Chinese Science Bulletin , 2007, DOI: 10.1007/s11434-007-0335-5
Abstract: Metallothioneins (MTs) are a group of low molecular mass and cysteine-rich proteins that can chelate heavy-metal ions. In this paper, Northern blot analysis was used to investigate the influence of lead stress on the expression patterns of 10 rice class I MT genes (OsMT-Is) in rice seedlings. With the exception of OsMT-I-3b, the data demonstrate dynamic changes of 9 OsMT-I transcripts in response to Pb2+ treatment in rice seedling roots. Of these genes, transcription of OsMT-I-1a, OsMT-I-1b, OsMT-I-2c, OsMT-I-4a, OSMT-I-4b and OsMT-I-4c increased significantly, while transcription of OsMT-I-2a and OsMT-I-3a increased marginally. In contrast, the expression of OsMT-I-2b was inhibited. Pb2+ induced the expression of 6 OsMT-I genes in seedling shoots, but had no obvious effects on the expression of OsMT-I-1a, OsMT-I-1b, OsMT-I-4a and OsMT-I-4b. All the 10 OsMT-Is had enhanced lead tolerance when heterologously expressed in lead-sensitive yeast mutant cells. These results provide an expression profile of the rice MT gene family in response to Pb2+ stress in rice seedlings and demonstrate increased lead tolerance in sensitive yeast mutant cells expressing OsMT-Is. This study lays a foundation for further analysis of the role of the rice MT gene family in respond to Pb2+ stress.
SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure
Parida Swarup K,Mukerji Mitali,Singh Ashok K,Singh Nagendra K
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-426
Abstract: Background Single nucleotide polymorphism (SNP) validation and large-scale genotyping are required to maximize the use of DNA sequence variation and determine the functional relevance of candidate genes for complex stress tolerance traits through genetic association in rice. We used the bead array platform-based Illumina GoldenGate assay to validate and genotype SNPs in a select set of stress-responsive genes to understand their functional relevance and study the population structure in rice. Results Of the 384 putative SNPs assayed, we successfully validated and genotyped 362 (94.3%). Of these 325 (84.6%) showed polymorphism among the 91 rice genotypes examined. Physical distribution, degree of allele sharing, admixtures and introgression, and amino acid replacement of SNPs in 263 abiotic and 62 biotic stress-responsive genes provided clues for identification and targeted mapping of trait-associated genomic regions. We assessed the functional and adaptive significance of validated SNPs in a set of contrasting drought tolerant upland and sensitive lowland rice genotypes by correlating their allelic variation with amino acid sequence alterations in catalytic domains and three-dimensional secondary protein structure encoded by stress-responsive genes. We found a strong genetic association among SNPs in the nine stress-responsive genes with upland and lowland ecological adaptation. Higher nucleotide diversity was observed in indica accessions compared with other rice sub-populations based on different population genetic parameters. The inferred ancestry of 16% among rice genotypes was derived from admixed populations with the maximum between upland aus and wild Oryza species. Conclusions SNPs validated in biotic and abiotic stress-responsive rice genes can be used in association analyses to identify candidate genes and develop functional markers for stress tolerance in rice.
New members of Datura family  [PDF]
Alexey Rosaev,Eva Plavalova
Physics , 2015,
Abstract: The problem of origin and age of asteroid families is studied very intensively. Youngest families are most interesting due to possibility of the reconstruction collisional history. Here we report about three new members of Datura Family
Toothbrush contamination in family members
Contreras,Adolfo; Arce,Roger; Botero,Javier Enrique; Jaramillo,Adriana; Betancourt,Marisol;
Revista clínica de periodoncia, implantología y rehabilitación oral , 2010, DOI: 10.4067/S0719-01072010000100004
Abstract: objective: the purpose of this study was to determine the bacterial contamination of toothbrushes in family members. materials and methods: one hundred and two healthy subjects were included in this descriptive study. every individual was examined clinically and microbiologically using the cpitn index and collecting subgingival plaque samples. each participant received a toothbrush for home use and after one month they returned it to the investigators. all toothbrushes were cultured to determine the presence of periodontopathic bacteria and enteric rods. wilkoxon signed rank test and t student test (p d"0.05) were used to compare differences in the subgingival microbiota and toothbrush contamination and cpitn index among family members. results: a high proportion of toothbrushes resulted highly contaminated with enteric rods (p d"0.001) compared to the subgingival environment where periodontopathic bacteria were more prevalent. the most frequent microorganisms found in toothbrushes used by parents and children for one month were enterobacteriaceae, pseudomonadaceae species (>50%) and fusobacterium spp (30%). conclusions: high levels of enteric rods were commonly detected in toothbrushes used for 1 month among members of the families. these opportunistic organisms may have an important role in oral infections including gingivitis and periodontitis. monthly replacement or disinfection of the toothbrush can reduce the risk of bacterial transmission/translocation and thus diminish the incidence of biofilm associated oral diseases.
Toothbrush contamination in family members  [cached]
Adolfo Contreras,Roger Arce,Javier Enrique Botero,Adriana Jaramillo
Revista Clínica de Periodoncia, Implantología y Rehabilitación Oral , 2010,
Abstract: Objective: The purpose of this study was to determine the bacterial contamination of toothbrushes in family members. Materials and Methods: One hundred and two healthy subjects were included in this descriptive study. Every individual was examined clinically and microbiologically using the CPITN index and collecting subgingival plaque samples. Each participant received a toothbrush for home use and after one month they returned it to the investigators. All toothbrushes were cultured to determine the presence of periodontopathic bacteria and enteric rods. Wilkoxon signed rank test and t student test (P d"0.05) were used to compare differences in the subgingival microbiota and toothbrush contamination and CPITN index among family members. Results: A high proportion of toothbrushes resulted highly contaminated with enteric rods (P d"0.001) compared to the subgingival environment where periodontopathic bacteria were more prevalent. The most frequent microorganisms found in toothbrushes used by parents and children for one month were Enterobacteriaceae, Pseudomonadaceae species (>50%) and Fusobacterium spp (30%). Conclusions: High levels of enteric rods were commonly detected in toothbrushes used for 1 month among members of the families. These opportunistic organisms may have an important role in oral infections including gingivitis and periodontitis. Monthly replacement or disinfection of the toothbrush can reduce the risk of bacterial transmission/translocation and thus diminish the incidence of biofilm associated oral diseases.
Bioinformatic Analysis of Epigenetic and MicroRNA Mediated Regulation of Drought Responsive Genes in Rice  [PDF]
Rafi Shaik, Wusirika Ramakrishna
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049331
Abstract: Drought stress response is a complex trait regulated at multiple levels. Changes in the epigenetic and miRNA regulatory landscape can dramatically alter the outcome of a stress response. However, little is known about the scope and extent of these regulatory factors on drought related cellular processes and functions. To this end, we selected a list of 5468 drought responsive genes (DRGs) of rice identified in multiple microarray studies and mapped the DNA methylation regions found in a genome wide methylcytosine immunoprecipitation and sequencing (mCIP-Seq) study to their genic and promoter regions, identified the chromatin remodeling genes and the genes that are targets of miRNAs. We found statistically significant enrichment of DNA methylation reads and miRNA target sequences in DRGs compared to a random set of genes. About 75% of the DRGs annotated to be involved in chromatin remodeling were downregulated. We found one-third of the DRGs are targeted by two-thirds of all known/predicted miRNAs in rice which include many transcription factors targeted by more than five miRNAs. Clustering analysis of the DRGs with epigenetic and miRNA features revealed, upregulated cluster was enriched in drought tolerance mechanisms while the downregulated cluster was enriched in drought resistance mechanisms evident by their unique gene ontologies (GOs), protein-protein interactions (PPIs), specific transcription factors, protein domains and metabolic pathways. Further, we analyzed the proteome of two weeks old young rice plants treated with a global demethylating agent, 5-azacytidine (5-azaC), subjected to drought stress and identified 56 protein spots that are differentially expressed. Out of the 56 spots, 35 were differently expressed in the sample with both demethylation and drought stress treatments and 28 (50%) were part of DRGs considered in the bioinformatic analysis.
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