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Sample records for abundant lea protein

  1. Late Embryogenesis Abundant (LEA) proteins in legumes

    PubMed Central

    Battaglia, Marina; Covarrubias, Alejandra A.

    2013-01-01

    Plants are exposed to different external conditions that affect growth, development, and productivity. Water deficit is one of these adverse conditions caused by drought, salinity, and extreme temperatures. Plants have developed different responses to prevent, ameliorate or repair the damage inflicted by these stressful environments. One of these responses is the activation of a set of genes encoding a group of hydrophilic proteins that typically accumulate to high levels during seed dehydration, at the last stage of embryogenesis, hence named Late Embryogenesis Abundant (LEA) proteins. LEA proteins also accumulate in response to water limitation in vegetative tissues, and have been classified in seven groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. These proteins are widely distributed in the plant kingdom, from ferns to angiosperms, suggesting a relevant role in the plant response to this unfavorable environmental condition. In this review, we analyzed the LEA proteins from those legumes whose complete genomes have been sequenced such as Phaseolus vulgaris, Glycine max, Medicago truncatula, Lotus japonicus, Cajanus cajan, and Cicer arietinum. Considering their distinctive motifs, LEA proteins from the different groups were identified, and their sequence analysis allowed the recognition of novel legume specific motifs. Moreover, we compile their transcript accumulation patterns based on publicly available data. In spite of the limited information on these proteins in legumes, the analysis and data compiled here confirm the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions. PMID:23805145

  2. Late Embryogenesis Abundant (LEA) proteins in legumes.

    PubMed

    Battaglia, Marina; Covarrubias, Alejandra A

    2013-01-01

    Plants are exposed to different external conditions that affect growth, development, and productivity. Water deficit is one of these adverse conditions caused by drought, salinity, and extreme temperatures. Plants have developed different responses to prevent, ameliorate or repair the damage inflicted by these stressful environments. One of these responses is the activation of a set of genes encoding a group of hydrophilic proteins that typically accumulate to high levels during seed dehydration, at the last stage of embryogenesis, hence named Late Embryogenesis Abundant (LEA) proteins. LEA proteins also accumulate in response to water limitation in vegetative tissues, and have been classified in seven groups based on their amino acid sequence similarity and on the presence of distinctive conserved motifs. These proteins are widely distributed in the plant kingdom, from ferns to angiosperms, suggesting a relevant role in the plant response to this unfavorable environmental condition. In this review, we analyzed the LEA proteins from those legumes whose complete genomes have been sequenced such as Phaseolus vulgaris, Glycine max, Medicago truncatula, Lotus japonicus, Cajanus cajan, and Cicer arietinum. Considering their distinctive motifs, LEA proteins from the different groups were identified, and their sequence analysis allowed the recognition of novel legume specific motifs. Moreover, we compile their transcript accumulation patterns based on publicly available data. In spite of the limited information on these proteins in legumes, the analysis and data compiled here confirm the high correlation between their accumulation and water deficit, reinforcing their functional relevance under this detrimental conditions. PMID:23805145

  3. LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance

    PubMed Central

    Hundertmark, Michaela; Buitink, Julia

    2013-01-01

    In contrast to orthodox seeds that acquire desiccation tolerance during maturation, recalcitrant seeds are unable to survive drying. These desiccation-sensitive seeds constitute an interesting model for comparative analysis with phylogenetically close species that are desiccation tolerant. Considering the importance of LEA (late embryogenesis abundant) proteins as protective molecules both in drought and in desiccation tolerance, the heat-stable proteome was characterized in cotyledons of the legume Castanospermum australe and it was compared with that of the orthodox model legume Medicago truncatula. RNA sequencing identified transcripts of 16 homologues out of 17 LEA genes for which polypeptides are detected in M. truncatula seeds. It is shown that for 12 LEA genes, polypeptides were either absent or strongly reduced in C. australe cotyledons compared with M. truncatula seeds. Instead, osmotically responsive, non-seed-specific dehydrins accumulated to high levels in the recalcitrant cotyledons compared with orthodox seeds. Next, M. truncatula mutants of the ABSCISIC ACID INSENSITIVE3 (ABI3) gene were characterized. Mature Mtabi3 seeds were found to be desiccation sensitive when dried below a critical water content of 0.4g H2O g DW–1. Characterization of the LEA proteome of the Mtabi3 seeds revealed a subset of LEA proteins with severely reduced abundance that were also found to be reduced or absent in C. australe cotyledons. Transcripts of these genes were indeed shown to be ABI3 responsive. The results highlight those LEA proteins that are critical to desiccation tolerance and suggest that comparable regulatory pathways responsible for their accumulation are missing in both desiccation-sensitive genotypes, revealing new insights into the mechanistic basis of the recalcitrant trait in seeds. PMID:24043848

  4. Biochemical and structural characterization of an endoplasmic reticulum-localized late embryogenesis abundant (LEA) protein from the liverwort Marchantia polymorpha.

    PubMed

    Hatanaka, Rie; Furuki, Takao; Shimizu, Tempei; Takezawa, Daisuke; Kikawada, Takahiro; Sakurai, Minoru; Sugawara, Yasutake

    2014-11-28

    Late embryogenesis abundant (LEA) proteins, which accumulate to high levels in seeds during late maturation, are associated with desiccation tolerance. A member of the LEA protein family was found in cultured cells of the liverwort Marchantia polymorpha; preculture treatment of these cells with 0.5M sucrose medium led to their acquisition of desiccation tolerance. We characterized this preculture-induced LEA protein, designated as MpLEA1. MpLEA1 is predominantly hydrophilic with a few hydrophobic residues that may represent its putative signal peptide. The protein also contains a putative endoplasmic reticulum (ER) retention sequence, HEEL, at the C-terminus. Microscopic observations indicated that GFP-fused MpLEA1 was mainly localized in the ER. The recombinant protein MpLEA1 is intrinsically disordered in solution. On drying, MpLEA1 shifted predominantly toward α-helices from random coils. Such changes in conformation are a typical feature of the group 3 LEA proteins. Recombinant MpLEA1 prevented the aggregation of α-casein during desiccation-rehydration events, suggesting that MpLEA1 exerts anti-aggregation activity against desiccation-sensitive proteins by functioning as a "molecular shield". Moreover, the anti-aggregation activity of MpLEA1 was ten times greater than that of BSA or insect LEA proteins, which are known to prevent aggregation on drying. Here, we show that an ER-localized LEA protein, MpLEA1, possesses biochemical and structural features specific to group 3 LEA proteins. PMID:25450698

  5. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli.

    PubMed

    Gao, Jie; Lan, Ting

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty-three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers. PMID:26781930

  6. Functional characterization of the late embryogenesis abundant (LEA) protein gene family from Pinus tabuliformis (Pinaceae) in Escherichia coli

    PubMed Central

    Gao, Jie; Lan, Ting

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a large and highly diverse gene family present in a wide range of plant species. LEAs are proposed to play a role in various stress tolerance responses. Our study represents the first-ever survey of LEA proteins and their encoding genes in a widely distributed pine (Pinus tabuliformis) in China. Twenty–three LEA genes were identified from the P. tabuliformis belonging to seven groups. Proteins with repeated motifs are an important feature specific to LEA groups. Ten of 23 pine LEA genes were selectively expressed in specific tissues, and showed expression divergence within each group. In addition, we selected 13 genes representing each group and introduced theses genes into Escherichia coli to assess the protective function of PtaLEA under heat and salt stresses. Compared with control cells, the E. coli cells expressing PtaLEA fusion protein exhibited enhanced salt and heat resistance and viability, indicating the protein may play a protective role in cells under stress conditions. Furthermore, among these enhanced tolerance genes, a certain extent of function divergence appeared within a gene group as well as between gene groups, suggesting potential functional diversity of this gene family in conifers. PMID:26781930

  7. Study of model systems to test the potential function of Artemia group 1 late embryogenesis abundant (LEA) proteins.

    PubMed

    Warner, Alden H; Guo, Zhi-hao; Moshi, Sandra; Hudson, John W; Kozarova, Anna

    2016-01-01

    Embryos of the brine shrimp, Artemia franciscana, are genetically programmed to develop either ovoviparously or oviparously depending on environmental conditions. Shortly upon their release from the female, oviparous embryos enter diapause during which time they undergo major metabolic rate depression while simultaneously synthesize proteins that permit them to tolerate a wide range of stressful environmental events including prolonged periods of desiccation, freezing, and anoxia. Among the known stress-related proteins that accumulate in embryos entering diapause are the late embryogenesis abundant (LEA) proteins. This large group of intrinsically disordered proteins has been proposed to act as molecular shields or chaperones of macromolecules which are otherwise intolerant to harsh conditions associated with diapause. In this research, we used two model systems to study the potential function of the group 1 LEA proteins from Artemia. Expression of the Artemia group 1 gene (AfrLEA-1) in Escherichia coli inhibited growth in proportion to the number of 20-mer amino acid motifs expressed. As well, clones of E. coli, transformed with the AfrLEA-1 gene, expressed multiple bands of LEA proteins, either intrinsically or upon induction with isopropyl-β-thiogalactoside (IPTG), in a vector-specific manner. Expression of AfrLEA-1 in E. coli did not overcome the inhibitory effects of high concentrations of NaCl and KCl but modulated growth inhibition resulting from high concentrations of sorbitol in the growth medium. In contrast, expression of the AfrLEA-1 gene in Saccharomyces cerevisiae did not alter the growth kinetics or permit yeast to tolerate high concentrations of NaCl, KCl, or sorbitol. However, expression of AfrLEA-1 in yeast improved its tolerance to drying (desiccation) and freezing. Under our experimental conditions, both E. coli and S. cerevisiae appear to be potentially suitable hosts to study the function of Artemia group 1 LEA proteins under environmentally

  8. CpLEA5, the Late Embryogenesis Abundant Protein Gene from Chimonanthus praecox, Possesses Low Temperature and Osmotic Resistances in Prokaryote and Eukaryotes.

    PubMed

    Liu, Yiling; Xie, Lixia; Liang, Xilong; Zhang, Shihong

    2015-01-01

    Plants synthesize and accumulate a series of stress-resistance proteins to protect normal physiological activities under adverse conditions. Chimonanthus praecox which blooms in freezing weather accumulates late embryogenesis abundant proteins (LEAs) in flowers, but C. praecox LEAs are little reported. Here, we report a group of five LEA genes of C. praecox (CpLEA5, KT727031). Prokaryotic-expressed CpLEA5 was employed in Escherichia coli to investigate bioactivities and membrane permeability at low-temperature. In comparison with the vacant strains, CpLEA5-containing strains survived in a 20% higher rate; and the degree of cell membrane damage in CpLEA5-containing strains was 55% of that of the vacant strains according to a conductivity test, revealing the low-temperature resistance of CpLEA5 in bacteria. CpLEA5 was also expressed in Pichia pastoris. Interestingly, besides low-temperature resistance, CpLEA5 conferred high resistance to salt and alkali in CpLEA5 overexpressing yeast. The CpLEA5 gene was transferred into Arabidopsis thaliana to also demonstrate CpLEA5 actions in plants. As expected, the transgenic lines were more resistant against low-temperature and drought while compared with the wild type. Taken together, CpLEA5-conferred resistances to several conditions in prokaryote and eukaryotes could have great value as a genetic technology to enhance osmotic stress and low-temperature tolerance. PMID:26569231

  9. CpLEA5, the Late Embryogenesis Abundant Protein Gene from Chimonanthus praecox, Possesses Low Temperature and Osmotic Resistances in Prokaryote and Eukaryotes

    PubMed Central

    Liu, Yiling; Xie, Lixia; Liang, Xilong; Zhang, Shihong

    2015-01-01

    Plants synthesize and accumulate a series of stress-resistance proteins to protect normal physiological activities under adverse conditions. Chimonanthus praecox which blooms in freezing weather accumulates late embryogenesis abundant proteins (LEAs) in flowers, but C. praecox LEAs are little reported. Here, we report a group of five LEA genes of C. praecox (CpLEA5, KT727031). Prokaryotic-expressed CpLEA5 was employed in Escherichia coli to investigate bioactivities and membrane permeability at low-temperature. In comparison with the vacant strains, CpLEA5-containing strains survived in a 20% higher rate; and the degree of cell membrane damage in CpLEA5-containing strains was 55% of that of the vacant strains according to a conductivity test, revealing the low-temperature resistance of CpLEA5 in bacteria. CpLEA5 was also expressed in Pichia pastoris. Interestingly, besides low-temperature resistance, CpLEA5 conferred high resistance to salt and alkali in CpLEA5 overexpressing yeast. The CpLEA5 gene was transferred into Arabidopsis thaliana to also demonstrate CpLEA5 actions in plants. As expected, the transgenic lines were more resistant against low-temperature and drought while compared with the wild type. Taken together, CpLEA5-conferred resistances to several conditions in prokaryote and eukaryotes could have great value as a genetic technology to enhance osmotic stress and low-temperature tolerance. PMID:26569231

  10. Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.)

    PubMed Central

    Pedrosa, Andresa Muniz; Martins, Cristina de Paula Santos; Gonçalves, Luana Pereira; Costa, Marcio Gilberto Cardoso

    2015-01-01

    Late Embryogenesis Abundant (LEA) proteins are an ubiquitous group of polypeptides that were first described to accumulate during plant seed dehydration, at the later stages of embryogenesis. Since then they have also been recorded in vegetative plant tissues experiencing water limitation and in anhydrobiotic bacteria and invertebrates and, thereby, correlated with the acquisition of desiccation tolerance. This study provides the first comprehensive study about the LEA gene family in sweet orange (Citrus sinensis L. Osb.), the most important and widely grown fruit crop around the world. A surprisingly high number (72) of genes encoding C. sinensis LEAs (CsLEAs) were identified and classified into seven groups (LEA_1, LEA_2, LEA_3 and LEA_4, LEA_5, DEHYDRIN and SMP) based on their predicted amino acid sequences and also on their phylogenetic relationships with the complete set of Arabidopsis thaliana LEA proteins (AtLEAs). Approximately 60% of the CsLEAs identified in this study belongs to the unusual LEA_2 group of more hydrophobic LEA proteins, while the other LEA groups contained a relatively small number of members typically hydrophilic. A correlation between gene structure and motif composition was observed within each LEA group. Investigation of their chromosomal localizations revealed that the CsLEAs were non-randomly distributed across all nine chromosomes and that 33% of all CsLEAs are segmentally or tandemly duplicated genes. Analysis of the upstream sequences required for transcription revealed the presence of various stress-responsive cis-acting regulatory elements in the promoter regions of CsLEAs, including ABRE, DRE/CRT, MYBS and LTRE. Expression analysis using both RNA-seq data and quantitative real-time RT-PCR (qPCR) revealed that the CsLEA genes are widely expressed in various tissues, and that many genes containing the ABRE promoter sequence are induced by drought, salt and PEG. These results provide a useful reference for further exploration of

  11. Late Embryogenesis Abundant (LEA) Constitutes a Large and Diverse Family of Proteins Involved in Development and Abiotic Stress Responses in Sweet Orange (Citrus sinensis L. Osb.).

    PubMed

    Pedrosa, Andresa Muniz; Martins, Cristina de Paula Santos; Gonçalves, Luana Pereira; Costa, Marcio Gilberto Cardoso

    2015-01-01

    Late Embryogenesis Abundant (LEA) proteins are an ubiquitous group of polypeptides that were first described to accumulate during plant seed dehydration, at the later stages of embryogenesis. Since then they have also been recorded in vegetative plant tissues experiencing water limitation and in anhydrobiotic bacteria and invertebrates and, thereby, correlated with the acquisition of desiccation tolerance. This study provides the first comprehensive study about the LEA gene family in sweet orange (Citrus sinensis L. Osb.), the most important and widely grown fruit crop around the world. A surprisingly high number (72) of genes encoding C. sinensis LEAs (CsLEAs) were identified and classified into seven groups (LEA_1, LEA_2, LEA_3 and LEA_4, LEA_5, DEHYDRIN and SMP) based on their predicted amino acid sequences and also on their phylogenetic relationships with the complete set of Arabidopsis thaliana LEA proteins (AtLEAs). Approximately 60% of the CsLEAs identified in this study belongs to the unusual LEA_2 group of more hydrophobic LEA proteins, while the other LEA groups contained a relatively small number of members typically hydrophilic. A correlation between gene structure and motif composition was observed within each LEA group. Investigation of their chromosomal localizations revealed that the CsLEAs were non-randomly distributed across all nine chromosomes and that 33% of all CsLEAs are segmentally or tandemly duplicated genes. Analysis of the upstream sequences required for transcription revealed the presence of various stress-responsive cis-acting regulatory elements in the promoter regions of CsLEAs, including ABRE, DRE/CRT, MYBS and LTRE. Expression analysis using both RNA-seq data and quantitative real-time RT-PCR (qPCR) revealed that the CsLEA genes are widely expressed in various tissues, and that many genes containing the ABRE promoter sequence are induced by drought, salt and PEG. These results provide a useful reference for further exploration of

  12. The pepper late embryogenesis abundant protein CaLEA1 acts in regulating abscisic acid signaling, drought and salt stress response.

    PubMed

    Lim, Chae Woo; Lim, Sohee; Baek, Woonhee; Lee, Sung Chul

    2015-08-01

    As sessile organisms, plants are constantly challenged by environmental stresses, including drought and high salinity. Among the various abiotic stresses, osmotic stress is one of the most important factors for growth and significantly reduces crop productivity in agriculture. Here, we report a function of the CaLEA1 protein in the defense responses of plants to osmotic stress. Our analyses showed that the CaLEA1 gene was strongly induced in pepper leaves exposed to drought and increased salinity. Furthermore, we determined that the CaLEA1 protein has a late embryogenesis abundant (LEA)_3 homolog domain highly conserved among other known group 5 LEA proteins and is localized in the processing body. We generated CaLEA1-silenced peppers and CaLEA1-overexpressing (OX) transgenic Arabidopsis plants to evaluate their responses to dehydration and high salinity. Virus-induced gene silencing of CaLEA1 in pepper plants conferred enhanced sensitivity to drought and salt stresses, which was accompanied by high levels of lipid peroxidation in dehydrated and NaCl-treated leaves. CaLEA1-OX plants exhibited enhanced sensitivity to abscisic acid (ABA) during seed germination and in the seedling stage; furthermore, these plants were more tolerant to drought and salt stress than the wild-type plants because of enhanced stomatal closure and increased expression of stress-responsive genes. Collectively, our data suggest that CaLEA1 positively regulates drought and salinity tolerance through ABA-mediated cell signaling. PMID:25302464

  13. RcLEA, a late embryogenesis abundant protein gene isolated from Rosa chinensis, confers tolerance to Escherichia coli and Arabidopsis thaliana and stabilizes enzyme activity under diverse stresses.

    PubMed

    Zhang, Xuan; Lu, Songchong; Jiang, Changhua; Wang, Yaofeng; Lv, Bo; Shen, Jiabin; Ming, Feng

    2014-07-01

    The late embryogenesis abundant (LEA) protein family is a large protein family that is closely associated with resistance to abiotic stresses in many organisms, such as plants, bacteria and animals. In this study, we isolated a LEA gene, RcLEA, which was cytoplasm-localized, from Rosa chinensis. RcLEA was found to be induced by high temperature through RT-PCR. Overexpression of RcLEA in Escherichia coli improved its growth performance compared with the control under high temperature, low temperature, NaCl and oxidative stress conditions. RcLEA was also overexpressed in Arabidopsis thaliana. The transgenic Arabidopsis showed better growth after high and low temperature treatment and exhibited less peroxide according to 3, 3-diaminobenzidine staining. However, RcLEA did not improve the tolerance to NaCl or osmotic stress in Arabidopsis. In vitro analysis showed that RcLEA was able to prevent the freeze-thaw-induced inactivation or heat-induced aggregation of various substrates, such as lactate dehydrogenase and citrate synthase. It also protected the proteome of E. coli from denaturation when the proteins were heat-shocked or subjected to acidic conditions. Furthermore, bimolecular fluorescence complementation assays suggested that RcLEA proteins function in a complex manner by making the form of homodimers. PMID:24760474

  14. KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses

    PubMed Central

    Tang, Xiaoli; Wang, Hongyan; Chu, Liye; Shao, Hongbo

    2016-01-01

    The LEA proteins are a kind of hydrophilic proteins, playing main functions in desiccation tolerance. However, their importance as a kind of stress proteins in abiotic stress is being clarified little by little. In this study we isolated, cloned, and identified the first KvLEA gene in Kosteletzkya virginica. Bioinformatic analysis showed that the protein encoded by this gene had common properties of LEA proteins and the multiple sequences alignment and phylogenetic analysis further showed that this protein had high homology with two Arabidopsis LEA proteins. Gene expression analysis revealed that this gene had a higher expression in root and it was induced obviously by salt stress. Moreover, the transcripts of KvLEA were also induced by other abiotic stresses including drought, high temperature, chilling, and ABA treatment. Among these abiotic stresses, ABA treatment brought about the biggest changes to this gene. Collectively, our research discovered a novel LEA gene and uncovered its involvement in multiabiotic stresses in K. virginica. This research not only enriched studies on LEA gene in plant but also would accelerate more studies on K. virginica in the future. PMID:27123459

  15. KvLEA, a New Isolated Late Embryogenesis Abundant Protein Gene from Kosteletzkya virginica Responding to Multiabiotic Stresses.

    PubMed

    Tang, Xiaoli; Wang, Hongyan; Chu, Liye; Shao, Hongbo

    2016-01-01

    The LEA proteins are a kind of hydrophilic proteins, playing main functions in desiccation tolerance. However, their importance as a kind of stress proteins in abiotic stress is being clarified little by little. In this study we isolated, cloned, and identified the first KvLEA gene in Kosteletzkya virginica. Bioinformatic analysis showed that the protein encoded by this gene had common properties of LEA proteins and the multiple sequences alignment and phylogenetic analysis further showed that this protein had high homology with two Arabidopsis LEA proteins. Gene expression analysis revealed that this gene had a higher expression in root and it was induced obviously by salt stress. Moreover, the transcripts of KvLEA were also induced by other abiotic stresses including drought, high temperature, chilling, and ABA treatment. Among these abiotic stresses, ABA treatment brought about the biggest changes to this gene. Collectively, our research discovered a novel LEA gene and uncovered its involvement in multiabiotic stresses in K. virginica. This research not only enriched studies on LEA gene in plant but also would accelerate more studies on K. virginica in the future. PMID:27123459

  16. Heterologous Expression of MeLEA3: A 10 kDa Late Embryogenesis Abundant Protein of Cassava, Confers Tolerance to Abiotic Stress in Escherichia coli with Recombinant Protein Showing In Vitro Chaperone Activity.

    PubMed

    Barros, Nicolle L F; da Silva, Diehgo T; Marques, Deyvid N; de Brito, Fabiano M; dos Reis, Savio P; de Souza, Claudia R B

    2015-01-01

    Late embryogenesis abundant (LEA) proteins are small molecular weight proteins involved in acquisition of tolerance to drought, salinity, high temperature, cold, and freezing stress in many plants. Previous studies revealed a cDNA sequence coding for a 10 kDa atypical LEA protein, named MeLEA3, predicted to be located into mitochondria with potential role in salt stress response of cassava (Manihot esculenta Crantz). Here we aimed to produce the recombinant MeLEA3 protein by heterologous expression in Escherichia coli and evaluate the tolerance of bacteria expressing this protein under abiotic stress. Our result revealed that the recombinant MeLEA3 protein conferred a protective function against heat and salt stress in bacterial cells. Also, the recombinant MeLEA3 protein showed in vitro chaperone activity by protection of NdeI restriction enzyme activity under heat stress. PMID:25990084

  17. LEA proteins prevent protein aggregation due to water stress

    PubMed Central

    Goyal, Kshamata; Walton, Laura J.; Tunnacliffe, Alan

    2005-01-01

    LEA (late embryogenesis abundant) proteins in both plants and animals are associated with tolerance to water stress resulting from desiccation and cold shock. However, although various functions of LEA proteins have been proposed, their precise role has not been defined. Recent bioinformatics studies suggest that LEA proteins might behave as molecular chaperones, and the current study was undertaken to test this hypothesis. Recombinant forms of AavLEA1, a group 3 LEA protein from the anhydrobiotic nematode Aphelenchus avenae, and Em, a group 1 LEA protein from wheat, have been subjected to functional analysis. Heat-stress experiments with citrate synthase, which is susceptible to aggregation at high temperatures, suggest that LEA proteins do not behave as classical molecular chaperones, but they do exhibit a protective, synergistic effect in the presence of the so-called chemical chaperone, trehalose. In contrast, both LEA proteins can independently protect citrate synthase from aggregation due to desiccation and freezing, in keeping with a role in water-stress tolerance; similar results were obtained with lactate dehydrogenase. This is the first evidence of anti-aggregation activity of LEA proteins due to water stress. Again, a synergistic effect of LEA and trehalose was observed, which is significant given that non-reducing disaccharides are known to accumulate during dehydration in plants and nematodes. A model is proposed whereby LEA proteins might act as a novel form of molecular chaperone, or ‘molecular shield’, to help prevent the formation of damaging protein aggregates during water stress. PMID:15631617

  18. The continuing conundrum of the LEA proteins

    NASA Astrophysics Data System (ADS)

    Tunnacliffe, Alan; Wise, Michael J.

    2007-10-01

    Research into late embryogenesis abundant (LEA) proteins has been ongoing for more than 20 years but, although there is a strong association of LEA proteins with abiotic stress tolerance particularly dehydration and cold stress, for most of that time, their function has been entirely obscure. After their initial discovery in plant seeds, three major groups (numbered 1, 2 and 3) of LEA proteins have been described in a range of different plants and plant tissues. Homologues of groups 1 and 3 proteins have also been found in bacteria and in certain invertebrates. In this review, we present some new data, survey the biochemistry, biophysics and bioinformatics of the LEA proteins and highlight several possible functions. These include roles as antioxidants and as membrane and protein stabilisers during water stress, either by direct interaction or by acting as molecular shields. Along with other hydrophilic proteins and compatible solutes, LEA proteins might also serve as “space fillers” to prevent cellular collapse at low water activities. This multifunctional capacity of the LEA proteins is probably attributable in part to their structural plasticity, as they are largely lacking in secondary structure in the fully hydrated state, but can become more folded during water stress and/or through association with membrane surfaces. The challenge now facing researchers investigating these enigmatic proteins is to make sense of the various in vitro defined functions in the living cell: Are the LEA proteins truly multi-talented, or are they still just misunderstood?

  19. The Unstructured N-terminal Region of Arabidopsis Group 4 Late Embryogenesis Abundant (LEA) Proteins Is Required for Folding and for Chaperone-like Activity under Water Deficit.

    PubMed

    Cuevas-Velazquez, Cesar L; Saab-Rincón, Gloria; Reyes, José Luis; Covarrubias, Alejandra A

    2016-05-13

    Late embryogenesis abundant (LEA) proteins are a conserved group of proteins widely distributed in the plant kingdom that participate in the tolerance to water deficit of different plant species. In silico analyses indicate that most LEA proteins are structurally disordered. The structural plasticity of these proteins opens the question of whether water deficit modulates their conformation and whether these possible changes are related to their function. In this work, we characterized the secondary structure of Arabidopsis group 4 LEA proteins. We found that they are disordered in aqueous solution, with high intrinsic potential to fold into α-helix. We demonstrate that complete dehydration is not required for these proteins to sample ordered structures because milder water deficit and macromolecular crowding induce high α-helix levels in vitro, suggesting that prevalent conditions under water deficit modulate their conformation. We also show that the N-terminal region, conserved across all group 4 LEA proteins, is necessary and sufficient for conformational transitions and that their protective function is confined to this region, suggesting that folding into α-helix is required for chaperone-like activity under water limitation. We propose that these proteins can exist as different conformers, favoring functional diversity, a moonlighting property arising from their structural dynamics. PMID:27006402

  20. Group 3 LEA Protein, ZmLEA3, Is Involved in Protection from Low Temperature Stress

    PubMed Central

    Liu, Yang; Liang, Jianan; Sun, Liping; Yang, Xinghong; Li, Dequan

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a family of small highly hydrophilic proteins that accumulate at the onset of seed desiccation and in response to adverse conditions such as drought, salinity, low temperature, or water deficit. In previous studies, we demonstrated that ZmLEA3 could enhance the transgenic tobacco tolerance to osmotic and oxidative stresses. Here, we demonstrated that the transcription of ZmLEA3 in the maize stems could be significantly induced by low temperature and osmotic stresses and by treatment with abscisic acid (ABA) and H2O2. Further study indicated that ZmLEA3 is a single copy gene in the maize genome. The ZmLEA3 protein could protect lactate dehydrogenase (LDH) activity at low temperatures. The overexpression of ZmLEA3 conferred tolerance to low-temperature stress to transgenic tobacco, yeast (GS115) and E. coli (BL21). PMID:27471509

  1. Group 3 LEA Protein, ZmLEA3, Is Involved in Protection from Low Temperature Stress.

    PubMed

    Liu, Yang; Liang, Jianan; Sun, Liping; Yang, Xinghong; Li, Dequan

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a family of small highly hydrophilic proteins that accumulate at the onset of seed desiccation and in response to adverse conditions such as drought, salinity, low temperature, or water deficit. In previous studies, we demonstrated that ZmLEA3 could enhance the transgenic tobacco tolerance to osmotic and oxidative stresses. Here, we demonstrated that the transcription of ZmLEA3 in the maize stems could be significantly induced by low temperature and osmotic stresses and by treatment with abscisic acid (ABA) and H2O2. Further study indicated that ZmLEA3 is a single copy gene in the maize genome. The ZmLEA3 protein could protect lactate dehydrogenase (LDH) activity at low temperatures. The overexpression of ZmLEA3 conferred tolerance to low-temperature stress to transgenic tobacco, yeast (GS115) and E. coli (BL21). PMID:27471509

  2. A stress-responsive late embryogenesis abundant protein 7 (CsLEA7) of tea [Camellia sinensis (L.) O. Kuntze] encodes for a chaperone that imparts tolerance to Escherichia coli against stresses.

    PubMed

    Paul, Asosii; Singh, Sewa; Sharma, Shweta; Kumar, Sanjay

    2014-11-01

    The present study characterized CsLEA7, a group 7 late embryogenesis abundant (LEA) gene, from tea [Camellia sinensis (L.) O. Kuntze]. The gene had an open reading frame of 462 base pairs encoding 153 amino acids with calculated molecular weight of 16.63 kDa and an isoelectric point (pI) of 4.93. Analysis revealed CsLEA7 to be an intrinsically ordered protein consisting of nine β-strands and two α-helices. CsLEA7 expressed ubiquitously in all the tissues analyzed with highest level of transcripts in mature leaf as compared to in flower bud, younger leaves, stem and fruit. Expression was the least in root tissue. CsLEA7 exhibited up-regulation in response to low temperature, polyethylene glycol-8000, sodium chloride and hydrogen peroxide in tea. Analysis of the promoter of CsLEA7 revealed a core promoter element and distinct cis-acting regulatory elements regulating gene expression under abiotic stresses. CsLEA7 exhibited chaperonic activity as evinced by protection to malate dehydrogenase against heat denaturation assay. Recombinant Escherichia coli cells producing CsLEA7 exhibited improved tolerance against diverse cues: polyethylene glycol-8000, sodium chloride, hydrogen peroxide and low temperature signifying its role in imparting stress tolerance. PMID:25052187

  3. Intracellular localization of group 3 LEA proteins in embryos of Artemia franciscana.

    PubMed

    Boswell, Leaf C; Hand, Steven C

    2014-12-01

    Late embryogenesis abundant (LEA) proteins are accumulated by anhydrobiotic organisms in response to desiccation and improve survivorship during water stress. In this study we provide the first direct evidence for the subcellular localizations of AfrLEA2 and AfrLEA3m (and its subforms) in anhydrobiotic embryos of Artemia franciscana. Immunohistochemistry shows AfrLEA2 to reside in the cytoplasm and nucleus, and the four AfrLEA3m proteins to be localized to the mitochondrion. Cellular locations are supported by Western blots of mitochondrial, nuclear and cytoplasmic fractions. The presence of LEA proteins in multiple subcellular compartments of A. franciscana embryos suggests the need to protect biological structures in many areas of a cell in order for an organism to survive desiccation stress, and may explain in part why a multitude of different LEA proteins are expressed by a single organism. PMID:25311474

  4. Late embryogenesis abundant proteins

    PubMed Central

    Olvera-Carrillo, Yadira; Reyes, José Luis

    2011-01-01

    Late Embryogenesis Abundant (LEA) proteins accumulate at the onset of seed desiccation and in response to water deficit in vegetative plant tissues. The typical LEA proteins are highly hydrophilic and intrinsically unstructured. They have been classified in different families, each one showing distinctive conserved motifs. In this manuscript we present and discuss some of the recent findings regarding their role in plant adaptation to water deficit, as well as those concerning to their possible function, and how it can be related to their intrinsic structural flexibility. PMID:21447997

  5. Group 5 LEA protein, ZmLEA5C, enhance tolerance to osmotic and low temperature stresses in transgenic tobacco and yeast.

    PubMed

    Liu, Yang; Wang, Li; Jiang, Shanshan; Pan, Jiaowen; Cai, Guohua; Li, Dequan

    2014-11-01

    Group 5 LEA (Late Embryogenesis Abundant) proteins contain a significantly higher proportion of hydrophobic residues but lack significant signature motifs or consensus sequences. This group is considered as an atypical group of LEA proteins. Up to now, there is little known about group 5C LEA proteins in maize. Here, we identified a novel group 5C LEA protein from maize. The accumulation of transcripts demonstrated that ZmLEA5C displayed similar induced characteristics in leaves and roots. Transcription of ZmLEA5C could be induced by low temperature, osmotic and oxidative stress and some signaling molecules, such as abscisic acid (ABA), salicylic acid (SA) and methyl jasmonate (MeJA). However, transcription of ZmLEA5C was significantly inhibited by high salinity. Further study indicated that the ZmLEA5C protein could be phosphorylated by the protein kinase CKII. ZmLEA5C could protect the activity of LDH under water deficit and low temperature stresses. Overexpression of ZmLEA5C conferred to transgenic tobacco (Nicotiana benthamiana) and yeast (GS115) tolerance to osmotic and low temperature stresses. PMID:25240107

  6. The Potential Roles of the G1LEA and G3LEA Proteins in Early Embryo Development and in Response to Low Temperature and High Salinity in Artemia sinica.

    PubMed

    Zhao, Wei; Yao, Feng; Zhang, Mengchen; Jing, Ting; Zhang, Shuang; Hou, Lin; Zou, Xiangyang

    2016-01-01

    Late embryogenesis abundant proteins (LEA) are stress resistance-related proteins that play crucial roles in protecting against desiccation, cold and high salinity in a variety of animals and plants. However, the expression pattern, distribution and functions of LEA proteins in the post-diapause period of Artemia sinica, and under high salinity and low temperature stresses, remain unknown. In this study, the complete cDNA sequences of the group 1 LEA (As-g1lea) and group 3 LEA (As-g3lea) genes from A. sinica were cloned. The expression patterns and location of As-G1LEA and As-G1LEA were investigated. The protein abundances of As-G1LEA, As-G3LEA and Trehalase were analyzed during different developmental stages of the embryo and under low temperature and high salinity stresses in A. sinica. The full-length cDNA of As-g1lea was 960 bp, encoding a 182 amino acid protein, and As-g3lea was 2089 bp, encoding a 364 amino acid protein. As-g1lea and As-g3lea showed their highest expressions at 0 h of embryonic development and both showed higher relative expression in embryonic, rather than adult, development stages. The abundances of As-G1LEA, As-G3LEA and trehalose were upregulated under low temperature and downregulated under high salinity stress. These two genes did not show any tissue or organ specific expression. Our results suggested that these LEA proteins might play a pivotal role in stress tolerance in A. sinica. PMID:27603306

  7. JcLEA, a novel LEA-like protein from Jatropha curcas, confers a high level of tolerance to dehydration and salinity in Arabidopsis thaliana.

    PubMed

    Liang, Jing; Zhou, Mingqi; Zhou, Xin; Jin, Yuanjie; Xu, Ming; Lin, Juan

    2013-01-01

    Jatropha curcas L. is a highly drought and salt tolerant plant species that is typically used as a traditional folk medicine and biofuel crop in many countries. Understanding the molecular mechanisms that underlie the response to various abiotic environmental stimuli, especially to drought and salt stresses, in J. curcas could be important to crop improvement efforts. In this study, we cloned and characterized the gene for a late embryogenesis abundant (LEA) protein from J. curcas that we designated JcLEA. Sequence analyses showed that the JcLEA protein belongs to group 5, a subgroup of the LEA protein family. In young seedlings, expression of JcLEA is significantly induced by abscisic acid (ABA), dehydration, and salt stress. Subcellular localization analysis shows that that JcLEA protein is distributed in both the nucleus and cytoplasm. Moreover, based on growth status and physiological indices, the overexpression of JcLEA in transgenic Arabidopsis plants conferred increased resistance to both drought and salt stresses compared to the WT. Our data suggests that the group 5 JcLEA protein contributes to drought and salt stress tolerance in plants. Thus, JcLEA is a potential candidate gene for plant genetic modification. PMID:24391737

  8. Liposomes with diverse compositions are protected during desiccation by LEA proteins from Artemia franciscana and trehalose.

    PubMed

    Moore, Daniel S; Hansen, Richard; Hand, Steven C

    2016-01-01

    Intracellular accumulation of Late Embryogenesis Abundant (LEA) proteins and the disaccharide trehalose is associated with cellular desiccation tolerance in a number of animal species. Two LEA proteins from anhydrobiotic embryos of the brine shrimp Artemia franciscana were tested for the ability to protect liposomes of various compositions against desiccation-induced damage in the presence and absence of trehalose. Damage was assessed by carboxyfluorescein leakage after drying and rehydration. Further, using a cytoplasmic-localized (AfrLEA2) and a mitochondrial-targeted (AfrLEA3m) LEA protein allowed us to evaluate whether each may preferentially stabilize membranes of a particular lipid composition based on the protein's subcellular location. Both LEA proteins were able to offset damage during drying of liposomes that mimicked the lipid compositions of the inner mitochondrial membrane (with cardiolipin), outer mitochondrial membrane, and the inner leaflet of the plasma membrane. Thus liposome stabilization by AfrLEA3m or AfrLEA2 was not dependent on lipid composition, provided physiological amounts of bilayer and non-bilayer-forming lipids were present (liposomes with a non-biological composition of 100% phosphatidylcholine were not protected by either protein). Additive protection by LEA proteins plus trehalose was dependent on the lipid composition of the target membrane. Minimal additional damage occurred to liposomes stored at room temperature in the dried state for one week compared to liposomes rehydrated after 24h. Consistent with the ability to stabilize lipid bilayers, molecular modeling of the secondary structures for AfrLEA2 and AfrLEA3m revealed bands of charged amino acids similar to other amphipathic proteins that interact directly with membranes. PMID:26518519

  9. Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus

    PubMed Central

    Liang, Yu; Xiong, Ziyi; Zheng, Jianxiao; Xu, Dongyang; Zhu, Zeyang; Xiang, Jun; Gan, Jianping; Raboanatahiry, Nadia; Yin, Yongtai; Li, Maoteng

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family. PMID:27072743

  10. Genome-wide identification, structural analysis and new insights into late embryogenesis abundant (LEA) gene family formation pattern in Brassica napus.

    PubMed

    Liang, Yu; Xiong, Ziyi; Zheng, Jianxiao; Xu, Dongyang; Zhu, Zeyang; Xiang, Jun; Gan, Jianping; Raboanatahiry, Nadia; Yin, Yongtai; Li, Maoteng

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a diverse and large group of polypeptides that play important roles in desiccation and freezing tolerance in plants. The LEA family has been systematically characterized in some plants but not Brassica napus. In this study, 108 BnLEA genes were identified in the B. napus genome and classified into eight families based on their conserved domains. Protein sequence alignments revealed an abundance of alanine, lysine and glutamic acid residues in BnLEA proteins. The BnLEA gene structure has few introns (<3), and they are distributed unevenly across all 19 chromosomes in B. napus, occurring as gene clusters in chromosomes A9, C2, C4 and C5. More than two-thirds of the BnLEA genes are associated with segmental duplication. Synteny analysis revealed that most LEA genes are conserved, although gene losses or gains were also identified. These results suggest that segmental duplication and whole-genome duplication played a major role in the expansion of the BnLEA gene family. Expression profiles analysis indicated that expression of most BnLEAs was increased in leaves and late stage seeds. This study presents a comprehensive overview of the LEA gene family in B. napus and provides new insights into the formation of this family. PMID:27072743

  11. Group 3 LEA protein model peptides protect enzymes against desiccation stress.

    PubMed

    Furuki, Takao; Sakurai, Minoru

    2016-09-01

    We tested whether model peptides for group 3 late embryogenesis abundant (G3LEA) proteins, which we developed previously, are capable of maintaining the catalytic activities of enzymes dried in their presence. Three different peptides were compared: 1) PvLEA-22, which consists of two tandem repeats of the 11-mer motif found in G3LEA proteins from an African sleeping chironomid; 2) PvLEA-44, which is made of four tandem repeats of the same 11-mer motif; and 3) a peptide whose amino acid composition is the same as that of PvLEA-22, but whose sequence is scrambled. We selected two enzymes, lactate dehydrogenase (LDH) and β-d-galactosidase (BDG), as targets because they have different isoelectric point (pI) values, in the alkaline and acidic range, respectively. While these enzymes were almost inactivated when dried alone, their catalytic activity was preserved at ≥70% of native levels in the presence of any of the above three peptides. This degree of protection is comparable to that conferred by several full-length G3LEA proteins, as reported previously for LDH. Interestingly, the protective activity of the peptides was enhanced slightly when they were mixed with trehalose, especially when the molar content of the peptides was low. On the basis of these results, the G3LEA model peptides show promise as protectants for the dry preservation of enzymes/proteins with a wide range of pI values. PMID:27131872

  12. Expression of the moss PpLEA4-20 gene in rice enhances membrane protection and client proteins stability.

    PubMed

    Li, Li; Deng, Dandan; Chen, Xi; Wu, Baomei; Hu, Ke; Qiu, Tianhang; Cui, Suxia; Huang, Fang

    2015-05-01

    Green vegetative tissues of the moss Physcomitrella patens possess a powerful ability to tolerate severe drought stress. Proteomics analysis have revealed that a large number of late embryogenesis abundant (LEA) proteins were key players in the drought tolerance of the photosynthetic tissues. PpLEA4-20, a member of the moss LEA protein family, was selected for further function study using an ectopic expression method in rice. Through molecular identification via PCR, southern blotting and TAIL-PCR, we demonstrated that the PpLEA4-20 gene was transformed and inserted into a non-encoded region in chromosome 4 of rice and expressed stably in transgenic rice. Unexpectedly, PpLEA4-20 protein emerged as two high-expressed spots on 2-D gels generated from transgenic rice, suggesting that PpLEA4-20 proteins are complete compatible and might be modified in rice. Both growth and physiological analysis showed that seedlings of transgenic PpLEA4-20 rice displayed altered phenotypes and tolerance to salt. In addition, electrolyte leakage was reduced in transgenic PpLEA4-20 compared to wild type under stress conditions. Anti-aggregation analysis found that the PpLEA4-20 protein expressed in rice remained soluble at high temperature and in addition to some native proteins from transgenic PpLEA4-20 rice. Based on Nano LC MS/MS analysis, we identified several proteins from transgenic PpLEA4-20 rice of increased heat-stability. Our results provide evidence for a role of PpLEA4-20 in salt tolerance and stabilization of client proteins. PMID:25791479

  13. FcLDP1, a Gene Encoding a Late Embryogenesis Abundant (LEA) Domain Protein, Responds to Brassinosteroids and Abscisic Acid during the Development of Fruits in Fragaria chiloensis.

    PubMed

    Espinoza, Analía; Contreras, Rodrigo; Zúñiga, Gustavo E; Herrera, Raúl; Moya-León, María Alejandra; Norambuena, Lorena; Handford, Michael

    2016-01-01

    White Chilean strawberries (Fragaria chiloensis) are non-climacteric fruits, with an exotic color and aroma. In order to discover genes involved in the development of these fruits, we identified a fragment of a gene encoding a late embryogenesis abundant domain protein, FcLDP1, that was expressed in early stages of fruit development, particularly in receptacles. Hormones play key roles in regulating the development of non-climacteric fruits. We show that the brassinosteroid content of the white strawberry varies during development. Additionally, FcLDP1 as well as the closest ortholog in the woodland strawberry, F. vesca (FvLDP1) possess multiple brassinosteroid, as well as abscisic acid (ABA) response motifs in the promoter region, consistent with the response of transiently expressed FcLDP1 promoter-GFP fusions to these hormones, and the rise in FcLDP1 transcript levels in white strawberry fruits treated with brassinosteroids or ABA. These findings suggest that both hormones regulate FcLDP1 expression during the development of white strawberries. PMID:27379111

  14. FcLDP1, a Gene Encoding a Late Embryogenesis Abundant (LEA) Domain Protein, Responds to Brassinosteroids and Abscisic Acid during the Development of Fruits in Fragaria chiloensis

    PubMed Central

    Espinoza, Analía; Contreras, Rodrigo; Zúñiga, Gustavo E.; Herrera, Raúl; Moya-León, María Alejandra; Norambuena, Lorena; Handford, Michael

    2016-01-01

    White Chilean strawberries (Fragaria chiloensis) are non-climacteric fruits, with an exotic color and aroma. In order to discover genes involved in the development of these fruits, we identified a fragment of a gene encoding a late embryogenesis abundant domain protein, FcLDP1, that was expressed in early stages of fruit development, particularly in receptacles. Hormones play key roles in regulating the development of non-climacteric fruits. We show that the brassinosteroid content of the white strawberry varies during development. Additionally, FcLDP1 as well as the closest ortholog in the woodland strawberry, F. vesca (FvLDP1) possess multiple brassinosteroid, as well as abscisic acid (ABA) response motifs in the promoter region, consistent with the response of transiently expressed FcLDP1 promoter-GFP fusions to these hormones, and the rise in FcLDP1 transcript levels in white strawberry fruits treated with brassinosteroids or ABA. These findings suggest that both hormones regulate FcLDP1 expression during the development of white strawberries. PMID:27379111

  15. Group 1 LEA proteins contribute to the desiccation and freeze tolerance of Artemia franciscana embryos during diapause.

    PubMed

    Toxopeus, Jantina; Warner, Alden H; MacRae, Thomas H

    2014-11-01

    Water loss either by desiccation or freezing causes multiple forms of cellular damage. The encysted embryos (cysts) of the crustacean Artemia franciscana have several molecular mechanisms to enable anhydrobiosis-life without water-during diapause. To better understand how cysts survive reduced hydration, group 1 late embryogenesis abundant (LEA) proteins, hydrophilic unstructured proteins that accumulate in the stress-tolerant cysts of A. franciscana, were knocked down using RNA interference (RNAi). Embryos lacking group 1 LEA proteins showed significantly lower survival than control embryos after desiccation and freezing, or freezing alone, demonstrating a role for group 1 LEA proteins in A. franciscana tolerance of low water conditions. In contrast, regardless of group 1 LEA protein presence, cysts responded similarly to hydrogen peroxide (H2O2) exposure, indicating little to no function for these proteins in diapause termination. This is the first in vivo study of group 1 LEA proteins in an animal and it contributes to the fundamental understanding of these proteins. Knowing how LEA proteins protect A. franciscana cysts from desiccation and freezing may have applied significance in aquaculture, where Artemia is an important feed source, and in the cryopreservation of cells for therapeutic applications. PMID:24846336

  16. Ectopic Expression of an Atypical Hydrophobic Group 5 LEA Protein from Wild Peanut, Arachis diogoi Confers Abiotic Stress Tolerance in Tobacco.

    PubMed

    Sharma, Akanksha; Kumar, Dilip; Kumar, Sumit; Rampuria, Sakshi; Reddy, Attipalli R; Kirti, Pulugurtha Bharadwaja

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a group of hydrophilic proteins, which accumulate in plants under varied stress conditions like drought, salinity, extreme temperatures and oxidative stress suggesting their role in the protection of plants against these stresses. A transcript derived fragment (TDF) corresponding to LEA gene, which got differentially expressed in wild peanut, Arachis diogoi against the late leaf spot pathogen, Phaeoisariopsis personata was used in this study. We have cloned its full length cDNA by RACE-PCR, which was designated as AdLEA. AdLEA belongs to the atypical Group 5C of LEA protein family as confirmed by sequence analysis. Group 5C LEA protein subfamily contains Pfam LEA_2 domain and is highly hydrophobic. In native conditions, expression of AdLEA was upregulated considerably upon hormonal and abiotic stress treatments emphasizing its role in abiotic stress tolerance. Subcellular localization studies showed that AdLEA protein is distributed in both nucleus and cytosol. Ectopic expression of AdLEA in tobacco resulted in enhanced tolerance of plants to dehydration, salinity and oxidative stress with the transgenic plants showing higher chlorophyll content and reduced lipid peroxidation as compared to wild type plants. Overexpressed AdLEA tobacco plants maintained better photosynthetic efficiency under drought conditions as demonstrated by chlorophyll fluorescence measurements. These plants showed enhanced transcript accumulation of some stress-responsive genes. Our study also elucidates that ROS levels were significantly reduced in leaves and stomatal guard cells of transgenic plants upon stress treatments. These results suggest that AdLEA confers multiple stress tolerance to plants, which make it a potential gene for genetic modification in plants. PMID:26938884

  17. Ectopic Expression of an Atypical Hydrophobic Group 5 LEA Protein from Wild Peanut, Arachis diogoi Confers Abiotic Stress Tolerance in Tobacco

    PubMed Central

    Sharma, Akanksha; Kumar, Dilip; Kumar, Sumit; Rampuria, Sakshi; Reddy, Attipalli R.; Kirti, Pulugurtha Bharadwaja

    2016-01-01

    Late embryogenesis abundant (LEA) proteins are a group of hydrophilic proteins, which accumulate in plants under varied stress conditions like drought, salinity, extreme temperatures and oxidative stress suggesting their role in the protection of plants against these stresses. A transcript derived fragment (TDF) corresponding to LEA gene, which got differentially expressed in wild peanut, Arachis diogoi against the late leaf spot pathogen, Phaeoisariopsis personata was used in this study. We have cloned its full length cDNA by RACE-PCR, which was designated as AdLEA. AdLEA belongs to the atypical Group 5C of LEA protein family as confirmed by sequence analysis. Group 5C LEA protein subfamily contains Pfam LEA_2 domain and is highly hydrophobic. In native conditions, expression of AdLEA was upregulated considerably upon hormonal and abiotic stress treatments emphasizing its role in abiotic stress tolerance. Subcellular localization studies showed that AdLEA protein is distributed in both nucleus and cytosol. Ectopic expression of AdLEA in tobacco resulted in enhanced tolerance of plants to dehydration, salinity and oxidative stress with the transgenic plants showing higher chlorophyll content and reduced lipid peroxidation as compared to wild type plants. Overexpressed AdLEA tobacco plants maintained better photosynthetic efficiency under drought conditions as demonstrated by chlorophyll fluorescence measurements. These plants showed enhanced transcript accumulation of some stress-responsive genes. Our study also elucidates that ROS levels were significantly reduced in leaves and stomatal guard cells of transgenic plants upon stress treatments. These results suggest that AdLEA confers multiple stress tolerance to plants, which make it a potential gene for genetic modification in plants. PMID:26938884

  18. Dehydration stress-induced oscillations in LEA protein transcripts involves abscisic acid in the moss, Physcomitrella patens.

    PubMed

    Shinde, Suhas; Nurul Islam, M; Ng, Carl K-Y

    2012-07-01

    • Physcomitrella patens is a bryophyte belonging to early diverging lineages of land plants following colonization of land in the Ordovician period. Mosses are typically found in refugial habitats and can experience rapidly fluctuating environmental conditions. The acquisition of dehydration tolerance by bryophytes is of fundamental importance as they lack water-conducting tissues and are generally one cell layer thick. • Here, we show that dehydration induced oscillations in the steady-state transcript abundances of two group 3 late embryogenesis abundant (LEA) protein genes in P. patens protonemata, and that the amplitudes of these oscillations are reflective of the severity of dehydration stress. • Dehydration stress also induced elevations in the concentrations of abscisic acid (ABA), and ABA alone can also induce dosage-dependent oscillatory increases in the steady-state abundance of LEA protein transcripts. Additionally, removal of ABA resulted in rapid attenuation of these oscillatory increases. • Our data demonstrate that dehydration stress-regulated expression of LEA protein genes is temporally dynamic and highlight the importance of oscillations as a robust mechanism for optimal responses. Our results suggest that dehydration stress-induced oscillations in the steady-state abundance of LEA protein transcripts may constitute an important cellular strategy for adaptation to life in a constantly changing environment. PMID:22591374

  19. A LEA 4 protein up-regulated by ABA is involved in drought response in maize roots.

    PubMed

    Zamora-Briseño, Jesús Alejandro; de Jiménez, Estela Sánchez

    2016-04-01

    Late embryogenesis abundant (LEA) proteins are hydrophilic proteins that accumulate to high concentrations during the late stages of seeds development, which are integral to desiccation tolerance. LEA proteins also play a protective role under other abiotic stresses. We analyzed in silico a maize protein predicted to be highly hydrophilic and intrinsically disordered. This prediction was experimentally corroborated by solubility assays under denaturing conditions. Based on its amino acid sequence, we propose that this protein belongs to group four of the LEA proteins. The accumulation pattern of this protein was similar to that of dehydrins during the desiccation process that takes place during seed development. This protein was induced by exogenous abscisic acid in immature embryos, but during imbibition was down-regulated by gibberellins. It was also induced in maize roots under osmotic stress. So far, this is the first member of the LEA proteins belonging to group four to be characterized in maize, and it plays a role in the response to osmotic stress. PMID:26922182

  20. Group 1 LEA proteins, an ancestral plant protein group, are also present in other eukaryotes, and in the archeae and bacteria domains.

    PubMed

    Campos, F; Cuevas-Velazquez, C; Fares, M A; Reyes, J L; Covarrubias, A A

    2013-10-01

    Water is an essential element for living organisms, such that various responses have evolved to withstand water deficit in all living species. The study of these responses in plants has had particular relevance given the negative impact of water scarcity on agriculture. Among the molecules highly associated with plant responses to water limitation are the so-called late embryogenesis abundant (LEA) proteins. These proteins are ubiquitous in the plant kingdom and accumulate during the late phase of embryogenesis and in vegetative tissues in response to water deficit. To know about the evolution of these proteins, we have studied the distribution of group 1 LEA proteins, a set that has also been found beyond the plant kingdom, in Bacillus subtilis and Artemia franciscana. Here, we report the presence of group 1 LEA proteins in green algae (Chlorophyita and Streptophyta), suggesting that these group of proteins emerged before plant land colonization. By sequence analysis of public genomic databases, we also show that 34 prokaryote genomes encode group 1 LEA-like proteins; two of them belong to Archaea domain and 32 to bacterial phyla. Most of these microbes live in soil-associated habitats suggesting horizontal transfer from plants to bacteria; however, our phylogenetic analysis points to convergent evolution. Furthermore, we present data showing that bacterial group 1 LEA proteins are able to prevent enzyme inactivation upon freeze-thaw treatments in vitro, suggesting that they have analogous functions to plant LEA proteins. Overall, data in this work indicate that LEA1 proteins' properties might be relevant to cope with water deficit in different organisms. PMID:23861025

  1. Structural transitions in the intrinsically disordered plant dehydration stress protein LEA7 upon drying are modulated by the presence of membranes.

    PubMed

    Popova, Antoaneta V; Hundertmark, Michaela; Seckler, Robert; Hincha, Dirk K

    2011-07-01

    Dehydration stress-related late embryogenesis abundant (LEA) proteins have been found in plants, invertebrates and bacteria. Most LEA proteins are unstructured in solution, but some fold into amphipathic α-helices during drying. The Pfam LEA_4 (Group 3) protein LEA7 from the higher plant Arabidopsis thaliana was predicted to be 87% α-helical, while CD spectroscopy showed it to be largely unstructured in solution and only 35% α-helical in the dry state. However, the dry protein contained 15% β-sheets. FTIR spectroscopy revealed the β-sheets to be largely due to aggregation. β-Sheet content was reduced and α-helix content increased when LEA7 was dried in the presence of liposomes with secondary structure apparently influenced by lipid composition. Secondary structure was also affected by the presence of membranes in the fully hydrated state. A temperature-induced increase in the flexibility of the dry protein was also only observed in the presence of membranes. Functional interactions of LEA7 with membranes in the dry state were indicated by its influence on the thermotropic phase transitions of the lipids and interactions with the lipid headgroup phosphates. PMID:21443857

  2. The intrinsically disordered protein LEA7 from Arabidopsis thaliana protects the isolated enzyme lactate dehydrogenase and enzymes in a soluble leaf proteome during freezing and drying.

    PubMed

    Popova, Antoaneta V; Rausch, Saskia; Hundertmark, Michaela; Gibon, Yves; Hincha, Dirk K

    2015-10-01

    The accumulation of Late Embryogenesis Abundant (LEA) proteins in plants is associated with tolerance against stresses such as freezing and desiccation. Two main functions have been attributed to LEA proteins: membrane stabilization and enzyme protection. We have hypothesized previously that LEA7 from Arabidopsis thaliana may stabilize membranes because it interacts with liposomes in the dry state. Here we show that LEA7, contrary to this expectation, did not stabilize liposomes during drying and rehydration. Instead, it partially preserved the activity of the enzyme lactate dehydrogenase (LDH) during drying and freezing. Fourier-transform infrared (FTIR) spectroscopy showed no evidence of aggregation of LDH in the dry or rehydrated state under conditions that lead to complete loss of activity. To approximate the complex influence of intracellular conditions on the protective effects of a LEA protein in a convenient in-vitro assay, we measured the activity of two Arabidopsis enzymes (glucose-6-P dehydrogenase and ADP-glucose pyrophosphorylase) in total soluble leaf protein extract (Arabidopsis soluble proteome, ASP) after drying and rehydration or freezing and thawing. LEA7 partially preserved the activity of both enzymes under these conditions, suggesting its role as an enzyme protectant in vivo. Further FTIR analyses indicated the partial reversibility of protein aggregation in the dry ASP during rehydration. Similarly, aggregation in the dry ASP was strongly reduced by LEA7. In addition, mixtures of LEA7 with sucrose or verbascose reduced aggregation more than the single additives, presumably through the effects of the protein on the H-bonding network of the sugar glasses. PMID:25988244

  3. Group 3 late embryogenesis abundant proteins from embryos of Artemia franciscana: structural properties and protective abilities during desiccation.

    PubMed

    Boswell, Leaf C; Menze, Michael A; Hand, Steven C

    2014-01-01

    Group 3 late embryogenesis abundant (LEA) proteins are highly hydrophilic, and their expression is associated with desiccation tolerance in both plants and animals. Here we show that two LEA proteins from embryos of Artemia franciscana, AfrLEA2 and AfrLEA3m, are intrinsically disordered in solution but upon desiccation gain secondary structure, as measured by circular dichroism. Trifluoroethanol and sodium dodecyl sulfate are both shown to induce α-helical structure in AfrLEA2 and AfrLEA3m. Bioinformatic predictions of secondary-structure content for both proteins correspond most closely to conformations measured in the dry state. Because some LEA proteins afford protection to desiccation-sensitive proteins during drying and subsequent rehydration, we tested for this capacity in AfrLEA2 and AfrLEA3m. The protective capacities vary, depending on the target enzyme. For the cytoplasmic enzyme lactate dehydrogenase, neither AfrLEA2 nor AfrLEA3m, with or without trehalose present, was able to afford protection better than that provided by bovine serum albumin (BSA) under the same conditions. However, for another cytoplasmic enzyme, phosphofructokinase, both AfrLEA2 and AfrLEA3m in the presence of trehalose were able to afford protection far greater than that provided by BSA with trehalose. Finally, for the mitochondrial enzyme citrate synthase, 400-μg/mL AfrLEA3m without trehalose provided significantly more protection than the same concentration of either AfrLEA2 or BSA. PMID:25244376

  4. Cellular Concentrations and Uniformity of Cell-Type Accumulation of Two Lea Proteins in Cotton Embryos.

    PubMed Central

    Roberts, JK; DeSimone, NA; Lingle, WL; Dure, L

    1993-01-01

    The levels and cell-type distribution of late embryogenesis abundant (Lea) proteins D-7 and D-113 have been determined in mature cotton embryos by immunochemical methods. The two proteins were expressed in and purified from Escherichia coli and utilized for antibody production in rabbits. The antiserum to each protein was found to interact with all members of each protein family in cotton extracts by protein gel blotting. Using these antibodies in quantitative "rocket" immunoelectrophoreses, D-7 proteins were found to accumulate to ~8 x 1015 molecules per embryo, which is equivalent to ~109 molecules per "average cell." D-113 proteins accumulate to ~1016 molecules per embryo, which equates to ~1.3 x 109 molecules per average cell. These values calculate to concentrations of about 226 and 283 [mu]M, respectively, in the cell aqueous phase immediately prior to seed desiccation. In immunocytochemical studies using the fluorophor rhodamine linked to the secondary antibody, both proteins appeared to be evenly present in the cytosol of all cell types present in the embryo, including both cotyledon and axis epidermal cells. Thus, their function does not appear related to unique functions of specific cell or tissue types. The very high molar concentrations of the two proteins, coupled with their unusual predicted structure and their cytosol location, would seem to reduce the number of their conceivable functions. PMID:12271086

  5. Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade

    PubMed Central

    Yamaguchi, Ayami; Tanaka, Sae; Yamaguchi, Shiho; Kuwahara, Hirokazu; Takamura, Chizuko; Imajoh-Ohmi, Shinobu; Horikawa, Daiki D.; Toyoda, Atsushi; Katayama, Toshiaki; Arakawa, Kazuharu; Fujiyama, Asao; Kubo, Takeo; Kunieda, Takekazu

    2012-01-01

    Tardigrades are able to tolerate almost complete dehydration by reversibly switching to an ametabolic state. This ability is called anhydrobiosis. In the anhydrobiotic state, tardigrades can withstand various extreme environments including space, but their molecular basis remains largely unknown. Late embryogenesis abundant (LEA) proteins are heat-soluble proteins and can prevent protein-aggregation in dehydrated conditions in other anhydrobiotic organisms, but their relevance to tardigrade anhydrobiosis is not clarified. In this study, we focused on the heat-soluble property characteristic of LEA proteins and conducted heat-soluble proteomics using an anhydrobiotic tardigrade. Our heat-soluble proteomics identified five abundant heat-soluble proteins. All of them showed no sequence similarity with LEA proteins and formed two novel protein families with distinct subcellular localizations. We named them Cytoplasmic Abundant Heat Soluble (CAHS) and Secretory Abundant Heat Soluble (SAHS) protein families, according to their localization. Both protein families were conserved among tardigrades, but not found in other phyla. Although CAHS protein was intrinsically unstructured and SAHS protein was rich in β-structure in the hydrated condition, proteins in both families changed their conformation to an α-helical structure in water-deficient conditions as LEA proteins do. Two conserved repeats of 19-mer motifs in CAHS proteins were capable to form amphiphilic stripes in α-helices, suggesting their roles as molecular shield in water-deficient condition, though charge distribution pattern in α-helices were different between CAHS and LEA proteins. Tardigrades might have evolved novel protein families with a heat-soluble property and this study revealed a novel repertoire of major heat-soluble proteins in these anhydrobiotic animals. PMID:22937162

  6. Molecular analysis of OsLEA4 and its contributions to improve E. coli viability.

    PubMed

    Hu, Tingzhang; Zeng, Hua; He, Shuai; Wu, Yingmei; Wang, Guixue; Huang, Xiaoyun

    2012-01-01

    OsLEA4, a late embryogenesis abundant (LEA) protein gene from rice (Oryza sativa L.), contains a 312-bp open reading frame encoding a putative polypeptide of 103 amino acids with a calculated molecular mass of 11.19 kDa and a theoretical pI of 10.04. OsLEA4 polypeptide is rich in Ala (22%), Lys (15%), Glu (9%), His (8%), Thr (8%), and Arg (7%) and lacking in Trp, Cys, Asn, and Phe residues. OsLEA4 protein contains a Pfam:LEA_1 domain architecture at positions 1-73 with three α-helical domains and without β-sheet domain. In silico predictions showed that OsLEA4 protein was strongly hydrophilic with the grand average of hydropathy value of -0.816 and instability index of 27.31. The hydrophilic regions were found in the conserved motif of OsLEA4. OsLEA4 gene was introduced into Escherichia coli, and a fusion protein (∼29.4 kDa) was expressed after isopropylthio-β-D: -galactoside inducting by sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. OsLEA4 protein enhanced the tolerance of E. coli recombinant to high salinity, heat, freezing, and UV radiation, which suggested that OsLEA4 protein may play a protective role under stressed conditions. This is the first successful use of E. coli as a prokaryotic system for LEA production from rice. PMID:22057936

  7. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress.

    PubMed

    Candat, Adrien; Paszkiewicz, Gaël; Neveu, Martine; Gautier, Romain; Logan, David C; Avelange-Macherel, Marie-Hélène; Macherel, David

    2014-07-01

    Late embryogenesis abundant (LEA) proteins are hydrophilic, mostly intrinsically disordered proteins, which play major roles in desiccation tolerance. In Arabidopsis thaliana, 51 genes encoding LEA proteins clustered into nine families have been inventoried. To increase our understanding of the yet enigmatic functions of these gene families, we report the subcellular location of each protein. Experimental data highlight the limits of in silico predictions for analysis of subcellular localization. Thirty-six LEA proteins localized to the cytosol, with most being able to diffuse into the nucleus. Three proteins were exclusively localized in plastids or mitochondria, while two others were found dually targeted to these organelles. Targeting cleavage sites could be determined for five of these proteins. Three proteins were found to be endoplasmic reticulum (ER) residents, two were vacuolar, and two were secreted. A single protein was identified in pexophagosomes. While most LEA protein families have a unique subcellular localization, members of the LEA_4 family are widely distributed (cytosol, mitochondria, plastid, ER, and pexophagosome) but share the presence of the class A α-helix motif. They are thus expected to establish interactions with various cellular membranes under stress conditions. The broad subcellular distribution of LEA proteins highlights the requirement for each cellular compartment to be provided with protective mechanisms to cope with desiccation or cold stress. PMID:25005920

  8. Expression profiles of 12 late embryogenesis abundant protein genes from Tamarix hispida in response to abiotic stress.

    PubMed

    Gao, Caiqiu; Liu, Yali; Wang, Chao; Zhang, Kaimin; Wang, Yucheng

    2014-01-01

    Twelve embryogenesis abundant protein (LEA) genes (named ThLEA-1 to -12) were cloned from Tamarix hispida. The expression profiles of these genes in response to NaCl, PEG, and abscisic acid (ABA) in roots, stems, and leaves of T. hispida were assessed using real-time reverse transcriptase-polymerase chain reaction (RT-PCR). These ThLEAs all showed tissue-specific expression patterns in roots, stems, and leaves under normal growth conditions. However, they shared a high similar expression patterns in the roots, stems, and leaves when exposed to NaCl and PEG stress. Furthermore, ThLEA-1, -2, -3, -4, and -11 were induced by NaCl and PEG, but ThLEA-5, -6, -8, -10, and -12 were downregulated by salt and drought stresses. Under ABA treatment, some ThLEA genes, such as ThLEA-1, -2, and -3, were only slightly differentially expressed in roots, stems, and leaves, indicating that they may be involved in the ABA-independent signaling pathway. These findings provide a basis for the elucidation of the function of LEA genes in future work. PMID:25133264

  9. Cold-regulated cereal chloroplast late embryogenesis abundant-like proteins. Molecular characterization and functional analyses.

    PubMed

    NDong, Christian; Danyluk, Jean; Wilson, Kenneth E; Pocock, Tessa; Huner, Norman P A; Sarhan, Fathey

    2002-07-01

    Cold acclimation and freezing tolerance are the result of complex interaction between low temperature, light, and photosystem II (PSII) excitation pressure. Previous results have shown that expression of the Wcs19 gene is correlated with PSII excitation pressure measured in vivo as the relative reduction state of PSII. Using cDNA library screening and data mining, we have identified three different groups of proteins, late embryogenesis abundant (LEA) 3-L1, LEA3-L2, and LEA3-L3, sharing identities with WCS19. These groups represent a new class of proteins in cereals related to group 3 LEA proteins. They share important characteristics such as a sorting signal that is predicted to target them to either the chloroplast or mitochondria and a C-terminal sequence that may be involved in oligomerization. The results of subcellular fractionation, immunolocalization by electron microscopy and the analyses of target sequences within the Wcs19 gene are consistent with the localization of WCS19 within the chloroplast stroma of wheat (Triticum aestivum) and rye (Secale cereale). Western analysis showed that the accumulation of chloroplastic LEA3-L2 proteins is correlated with the capacity of different wheat and rye cultivars to develop freezing tolerance. Arabidopsis was transformed with the Wcs19 gene and the transgenic plants showed a significant increase in their freezing tolerance. This increase was only evident in cold-acclimated plants. The putative function of this protein in the enhancement of freezing tolerance is discussed. PMID:12114590

  10. Cold-Regulated Cereal Chloroplast Late Embryogenesis Abundant-Like Proteins. Molecular Characterization and Functional Analyses

    PubMed Central

    NDong, Christian; Danyluk, Jean; Wilson, Kenneth E.; Pocock, Tessa; Huner, Norman P.A.; Sarhan, Fathey

    2002-01-01

    Cold acclimation and freezing tolerance are the result of complex interaction between low temperature, light, and photosystem II (PSII) excitation pressure. Previous results have shown that expression of the Wcs19 gene is correlated with PSII excitation pressure measured in vivo as the relative reduction state of PSII. Using cDNA library screening and data mining, we have identified three different groups of proteins, late embryogenesis abundant (LEA) 3-L1, LEA3-L2, and LEA3-L3, sharing identities with WCS19. These groups represent a new class of proteins in cereals related to group 3 LEA proteins. They share important characteristics such as a sorting signal that is predicted to target them to either the chloroplast or mitochondria and a C-terminal sequence that may be involved in oligomerization. The results of subcellular fractionation, immunolocalization by electron microscopy and the analyses of target sequences within the Wcs19 gene are consistent with the localization of WCS19 within the chloroplast stroma of wheat (Triticum aestivum) and rye (Secale cereale). Western analysis showed that the accumulation of chloroplastic LEA3-L2 proteins is correlated with the capacity of different wheat and rye cultivars to develop freezing tolerance. Arabidopsis was transformed with the Wcs19 gene and the transgenic plants showed a significant increase in their freezing tolerance. This increase was only evident in cold-acclimated plants. The putative function of this protein in the enhancement of freezing tolerance is discussed. PMID:12114590

  11. Three-dimensional structure and mimetic-membrane association of consensus 11-amino-acid motif from soybean LEA3 protein.

    PubMed

    Xue, Rong; Liu, Yun; Zheng, Yizhi; Wu, Yijie; Li, Xiaojing; Pei, Fengkui; Ni, Jiazuan

    2012-01-01

    The occurrence of a highly conserved 11-mer repeating motif in the primary sequence is a major characteristic of group 3 late embryogenesis abundant (LEA3) proteins, which are strongly associated with abiotic stress tolerance of the plants. In this study, the three-dimensional structure, mimetic membrane association, and salt effect for consensus 11-mer motif from soybean PM2 protein (LEA3) were investigated in sodium dodecyl sulfate (SDS) micelles by NMR techniques. It was shown that the 11-mer motif was disordered in aqueous solution, but adopted an α-helix in SDS micelles. NMR diffusion measurements demonstrated that the 11-mer motif was associated with SDS micelles. Paramagnetic quenching NMR experiments further revealed the orientation of the 11-mer motif with respect to the mimetic membrane: the ordered N-terminal segment was inserted into the mimetic membrane, and the disordered C-terminal segment was exposed to water. In addition, salt addition could not change the secondary structure of the 11-mer motif, but might slightly alter the relative spatial position of some N-terminal residue atoms. These results implied that the 11-mer motif would take an important role in structural plasticity and membrane stabilization for LEA3 proteins. PMID:23325560

  12. Improved tolerance to salt and water stress in Drosophila melanogaster cells conferred by late embryogenesis abundant protein.

    PubMed

    Marunde, Matthew R; Samarajeewa, Dilini A; Anderson, John; Li, Shumin; Hand, Steven C; Menze, Michael A

    2013-04-01

    Mechanisms that govern anhydrobiosis involve the accumulation of highly hydrophilic macromolecules, such as late embryogenesis abundant (LEA) proteins. Group 1 LEA proteins comprised of 181 (AfLEA1.1) and 197 (AfLEA1.3) amino acids were cloned from embryos of Artemia franciscana and expressed in Drosophila melanogaster cells (Kc167). Confocal microscopy revealed a construct composed of green fluorescent protein (GFP) and AfLEA1.3 accumulates in the mitochondria (AfLEA1.3-GFP), while AfLEA1.1-GFP was found in the cytoplasm. In the presence of mixed substrates, oxygen consumption was statistically identical for permeabilized Kc167 control and Kc167-AfLEA1.3 cells. Acute titrations of permeabilized cells with NaCl up to 500 mM led to successive drops in oxygen flux, which were significantly ameliorated by 18% in Kc167-AfLEA1.3 cells compared to Kc167 controls. Mitochondria were isolated from both cell types and resuspended in a sucrose-based buffer solution. The purified mitochondria from Kc167 control cells showed significantly larger reductions in respiratory capacities after one freeze-thaw cycle (-80°C) compared to mitochondria isolated from Kc167-AfLEA1.3 cells. When cultured in the presence of a non-permeant osmolyte (50-200 mM sucrose) cells expressing AfLEA1.3 showed significantly improved viability (10-15%) during this hyperosmotic challenge as compared to Kc167 controls. Furthermore, Kc167-AfLEA1.3 cells survived desiccation by convective air drying in presence of 200 mM extracellular trehalose to lower final moisture contents than did control Kc167 cells (0.36 g H2O/g DW vs.1.02 g H2O/g DW). Thus, AfLEA1.3 exerts a protective influence on mitochondrial function and increases viability of Kc167 cells during water stress. PMID:23376561

  13. Overexpression of SmLEA enhances salt and drought tolerance in Escherichia coli and Salvia miltiorrhiza.

    PubMed

    Wu, Yucui; Liu, Congling; Kuang, Jing; Ge, Qian; Zhang, Yuan; Wang, Zhezhi

    2014-09-01

    Salinity and drought are important abiotic stresses limiting plant growth and development. Late embryogenesis abundant (LEA) proteins are a group of proteins associated with tolerance to water-related stress. We previously cloned an LEA gene, SmLEA, from Salvia miltiorrhiza Bunge. Phylogenetic analysis indicated that SmLEA belongs to Group LEA14, which is involved in the dehydration response. To determine its function in detail, we have now overexpressed SmLEA in Escherichia coli and S. miltiorrhiza. The logarithmic increase in accumulations of SmLEA proteins in E. coli occurred earlier under salinity than under standard conditions. SmLEA-transformed S. miltiorrhiza plants also showed faster root elongation and a lower malondialdehyde concentration than the empty vector control plants did when cultured on MS media supplemented with 60 mM NaCl or 150 mM mannitol. Moreover, SmLEA-overexpressing transgenics experienced a less rapid rate of water loss. Under either salinity or drought, overexpressing plants had greater superoxide dismutase activity and a higher glutathione concentration. These results suggest that SmLEA may be useful in efforts to improve drought and salinity tolerance in S. miltiorrhiza. Our data also provide a good foundation for further studies into the stress resistance mechanism and molecular breeding of this valuable medicinal plant. PMID:24595620

  14. The LEA protein, ABR, is regulated by ABI5 and involved in dark-induced leaf senescence in Arabidopsis thaliana.

    PubMed

    Su, Mengying; Huang, Gan; Zhang, Qing; Wang, Xiao; Li, Chunxin; Tao, Yujin; Zhang, Shengchun; Lai, Jianbin; Yang, Chengwei; Wang, Yaqin

    2016-06-01

    The phytohormone abscisic acid (ABA) modulates plant growth and developmental processes such as leaf senescence. In this study, we investigated the role of the Arabidopsis late embryogenesis abundant (LEA) protein ABR (ABA-response protein) in delaying dark-induced leaf senescence. The ABR gene was up-regulated by treatment with ABA, NaCl and mannitol, as well as by light deprivation. In the dark, abr mutant plants displayed a premature leaf senescence phenotype, and various senescence-associated indicators, such as an increase in chlorophyll degradation and membrane leakiness, were enhanced, whereas 35S:ABR/abr transgenic lines showed a marked delay in dark-induced leaf senescence phenotypes. In vitro and in vivo assays showed that ABI5 bind to the ABR promoter, indicating that ABI5 directly regulates the expression of ABR. The disruption of ABI5 function in abr abi5-1 plants abolished the senescence-accelerating phenotype of the abr mutant, demonstrating that ABI5 is epistatic to ABR. In summary, these results highlight the important role that ABR, which is negatively regulated by ABI5, plays in delaying dark-induced leaf senescence. PMID:27095403

  15. Uses of Phage Display in Agriculture: Sequence Analysis and Comparative Modeling of Late Embryogenesis Abundant Client Proteins Suggest Protein-Nucleic Acid Binding Functionality

    PubMed Central

    Kushwaha, Rekha; Downie, A. Bruce; Payne, Christina M.

    2013-01-01

    A group of intrinsically disordered, hydrophilic proteins—Late Embryogenesis Abundant (LEA) proteins—has been linked to survival in plants and animals in periods of stress, putatively through safeguarding enzymatic function and prevention of aggregation in times of dehydration/heat. Yet despite decades of effort, the molecular-level mechanisms defining this protective function remain unknown. A recent effort to understand LEA functionality began with the unique application of phage display, wherein phage display and biopanning over recombinant Seed Maturation Protein homologs from Arabidopsis thaliana and Glycine max were used to retrieve client proteins at two different temperatures, with one intended to represent heat stress. From this previous study, we identified 21 client proteins for which clones were recovered, sometimes repeatedly. Here, we use sequence analysis and homology modeling of the client proteins to ascertain common sequence and structural properties that may contribute to binding affinity with the protective LEA protein. Our methods uncover what appears to be a predilection for protein-nucleic acid interactions among LEA client proteins, which is suggestive of subcellular residence. The results from this initial computational study will guide future efforts to uncover the protein protective mechanisms during heat stress, potentially leading to phage-display-directed evolution of synthetic LEA molecules. PMID:23956788

  16. Structure and function of a mitochondrial late embryogenesis abundant protein are revealed by desiccation.

    PubMed

    Tolleter, Dimitri; Jaquinod, Michel; Mangavel, Cécile; Passirani, Catherine; Saulnier, Patrick; Manon, Stephen; Teyssier, Emeline; Payet, Nicole; Avelange-Macherel, Marie-Hélène; Macherel, David

    2007-05-01

    Few organisms are able to withstand desiccation stress; however, desiccation tolerance is widespread among plant seeds. Survival without water relies on an array of mechanisms, including the accumulation of stress proteins such as the late embryogenesis abundant (LEA) proteins. These hydrophilic proteins are prominent in plant seeds but also found in desiccation-tolerant organisms. In spite of many theories and observations, LEA protein function remains unclear. Here, we show that LEAM, a mitochondrial LEA protein expressed in seeds, is a natively unfolded protein, which reversibly folds into alpha-helices upon desiccation. Structural modeling revealed an analogy with class A amphipathic helices of apolipoproteins that coat low-density lipoprotein particles in mammals. LEAM appears spontaneously modified by deamidation and oxidation of several residues that contribute to its structural features. LEAM interacts with membranes in the dry state and protects liposomes subjected to drying. The overall results provide strong evidence that LEAM protects the inner mitochondrial membrane during desiccation. According to sequence analyses of several homologous proteins from various desiccation-tolerant organisms, a similar protection mechanism likely acts with other types of cellular membranes. PMID:17526751

  17. A group 6 late embryogenesis abundant protein from common bean is a disordered protein with extended helical structure and oligomer-forming properties.

    PubMed

    Rivera-Najera, Lucero Y; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O; García-Hernández, Enrique; Solórzano, Rosa M; Reyes, José L; Covarrubias, Alejandra A

    2014-11-14

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  18. A Group 6 Late Embryogenesis Abundant Protein from Common Bean Is a Disordered Protein with Extended Helical Structure and Oligomer-forming Properties*

    PubMed Central

    Rivera-Najera, Lucero Y.; Saab-Rincón, Gloria; Battaglia, Marina; Amero, Carlos; Pulido, Nancy O.; García-Hernández, Enrique; Solórzano, Rosa M.; Reyes, José L.; Covarrubias, Alejandra A.

    2014-01-01

    Late embryogenesis-abundant proteins accumulate to high levels in dry seeds. Some of them also accumulate in response to water deficit in vegetative tissues, which leads to a remarkable association between their presence and low water availability conditions. A major sub-group of these proteins, also known as typical LEA proteins, shows high hydrophilicity and a high percentage of glycine and other small amino acid residues, distinctive physicochemical properties that predict a high content of structural disorder. Although all typical LEA proteins share these characteristics, seven groups can be distinguished by sequence similarity, indicating structural and functional diversity among them. Some of these groups have been extensively studied; however, others require a more detailed analysis to advance in their functional understanding. In this work, we report the structural characterization of a group 6 LEA protein from a common bean (Phaseolus vulgaris L.) (PvLEA6) by circular dichroism and nuclear magnetic resonance showing that it is a disordered protein in aqueous solution. Using the same techniques, we show that despite its unstructured nature, the addition of trifluoroethanol exhibited an intrinsic potential in this protein to gain helicity. This property was also promoted by high osmotic potentials or molecular crowding. Furthermore, we demonstrate that PvLEA6 protein is able to form soluble homo-oligomeric complexes that also show high levels of structural disorder. The association between PvLEA6 monomers to form dimers was shown to occur in plant cells by bimolecular fluorescence complementation, pointing to the in vivo functional relevance of this association. PMID:25271167

  19. Characterization of OsLEA1a and its inhibitory effect on the resistance of E. coli to diverse abiotic stresses.

    PubMed

    Hu, Tingzhang; Zhou, Nong; Fu, Meiling; Qin, Juan; Huang, Xiaoyun

    2016-10-01

    OsLEA1a is a late embryogenesis abundant (LEA) protein gene from Oryza sativa L, which contains an open reading frame of 282-bp that encodes a putative polypeptide of 93 amino acids. OsLEA1a protein contains abundant of Lys, Ala, Glu, Asp, Gly, Arg and Leu, but depleted in Cys, His, Phe, Trp and Tyr residues; and is strongly hydrophilic. OsLEA1a includes six helical domains and a β-sheet domain. Real-time PCR analysis showed that OsLEA1a was expressed in roots, leaves and panicles of rice, with no or only a few transcripts in stem tissues, and remained at a relatively higher level in leaves during the tillering period, the heading period, the filling period and the full ripe period. To make sense of OsLEA1a functions, TrxA-OsLEA1a fusion protein expression vector and OsLEA1a protein expression vector were transformed into Escherichia coli DL21 (DE3), respectively. The accumulation of the TrxA-OsLEA1a fusion protein or OsLEA1a protein interfered with the resistance of E. coli to high salinity, metal ions, hyperosmotic, oxidation, heat and freeze-thaw stresses. The purified TrxA-OsLEA1a fusion protein reduced stabilization of LDH and increased damage of diverse abiotic stresses to LDH. The findings suggested that the OsLEA1a may confor antibacterial activity under abiotic stresses. PMID:27339321

  20. Overexpression of OsEm1 encoding a group I LEA protein confers enhanced drought tolerance in rice.

    PubMed

    Yu, Jing; Lai, Yongmin; Wu, Xi; Wu, Gang; Guo, Changkui

    2016-09-16

    Drought is the greatest threat for crops, including rice. In an effort to identify rice genes responsible for drought tolerance, a drought-responsive gene OsEm1 encoding a group I LEA protein, was chosen for this study. OsEm1 was shown at vegetative stages to be responsive to various abiotic stresses, including drought, salt, cold and the hormone ABA. In this study, we generated OsEm1-overexpressing rice plants to explore the function of OsEm1 under drought conditions. Overexpression of OsEm1 increases ABA sensitivity and enhances osmotic tolerance in rice. Compared with wild type, the OsEm1-overexpressing rice plants showed enhanced plant survival ratio at the vegetative stage; moreover, over expression of OsEm1 in rice increased the expression of other LEA genes, including RAB16A, RAB16C, RAB21, and LEA3, likely protecting organ integrity against harsh environments. Interestingly, the elevated level of OsEm1 had no different phenotype compared with wild type under normal condition. Our findings suggest that OsEm1 is a positive regulator of drought tolerance and is potentially promising for engineering drought tolerance in rice. PMID:27524243

  1. Predicting the dynamics of protein abundance.

    PubMed

    Mehdi, Ahmed M; Patrick, Ralph; Bailey, Timothy L; Bodén, Mikael

    2014-05-01

    Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA-protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation efficiency

  2. Predicting the Dynamics of Protein Abundance

    PubMed Central

    Mehdi, Ahmed M.; Patrick, Ralph; Bailey, Timothy L.; Bodén, Mikael

    2014-01-01

    Protein synthesis is finely regulated across all organisms, from bacteria to humans, and its integrity underpins many important processes. Emerging evidence suggests that the dynamic range of protein abundance is greater than that observed at the transcript level. Technological breakthroughs now mean that sequencing-based measurement of mRNA levels is routine, but protocols for measuring protein abundance remain both complex and expensive. This paper introduces a Bayesian network that integrates transcriptomic and proteomic data to predict protein abundance and to model the effects of its determinants. We aim to use this model to follow a molecular response over time, from condition-specific data, in order to understand adaptation during processes such as the cell cycle. With microarray data now available for many conditions, the general utility of a protein abundance predictor is broad. Whereas most quantitative proteomics studies have focused on higher organisms, we developed a predictive model of protein abundance for both Saccharomyces cerevisiae and Schizosaccharomyces pombe to explore the latitude at the protein level. Our predictor primarily relies on mRNA level, mRNA–protein interaction, mRNA folding energy and half-life, and tRNA adaptation. The combination of key features, allowing for the low certainty and uneven coverage of experimental observations, gives comparatively minor but robust prediction accuracy. The model substantially improved the analysis of protein regulation during the cell cycle: predicted protein abundance identified twice as many cell-cycle-associated proteins as experimental mRNA levels. Predicted protein abundance was more dynamic than observed mRNA expression, agreeing with experimental protein abundance from a human cell line. We illustrate how the same model can be used to predict the folding energy of mRNA when protein abundance is available, lending credence to the emerging view that mRNA folding affects translation

  3. On protein abundance distributions in complex mixtures

    PubMed Central

    2013-01-01

    Mass spectrometry, an analytical technique that measures the mass-to-charge ratio of ionized atoms or molecules, dates back more than 100 years, and has both qualitative and quantitative uses for determining chemical and structural information. Quantitative proteomic mass spectrometry on biological samples focuses on identifying the proteins present in the samples, and establishing the relative abundances of those proteins. Such protein inventories create the opportunity to discover novel biomarkers and disease targets. We have previously introduced a normalized, label-free method for quantification of protein abundances under a shotgun proteomics platform (Griffin et al., 2010). The introduction of this method for quantifying and comparing protein levels leads naturally to the issue of modeling protein abundances in individual samples. We here report that protein abundance levels from two recent proteomics experiments conducted by the authors can be adequately represented by Sichel distributions. Mathematically, Sichel distributions are mixtures of Poisson distributions with a rather complex mixing distribution, and have been previously and successfully applied to linguistics and species abundance data. The Sichel model can provide a direct measure of the heterogeneity of protein abundances, and can reveal protein abundance differences that simpler models fail to show. PMID:23360617

  4. Proteomic analysis reveals differential accumulation of small heat shock proteins and late embryogenesis abundant proteins between ABA-deficient mutant vp5 seeds and wild-type Vp5 seeds in maize.

    PubMed

    Wu, Xiaolin; Gong, Fangping; Yang, Le; Hu, Xiuli; Tai, Fuju; Wang, Wei

    2014-01-01

    ABA is a major plant hormone that plays important roles during many phases of plant life cycle, including seed development, maturity and dormancy, and especially the acquisition of desiccation tolerance. Understanding of the molecular basis of ABA-mediated plant response to stress is of interest not only in basic research on plant adaptation but also in applied research on plant productivity. Maize mutant viviparous-5 (vp5), deficient in ABA biosynthesis in seeds, is a useful material for studying ABA-mediated response in maize. Due to carotenoid deficiency, vp5 endosperm is white, compared to yellow Vp5 endosperm. However, the background difference at proteome level between vp5 and Vp5 seeds is unclear. This study aimed to characterize proteome alterations of maize vp5 seeds and to identify ABA-dependent proteins during seed maturation. We compared the embryo and endosperm proteomes of vp5 and Vp5 seeds by gel-based proteomics. Up to 46 protein spots, most in embryos, were found to be differentially accumulated between vp5 and Vp5. The identified proteins included small heat shock proteins (sHSPs), late embryogenesis abundant (LEA) proteins, stress proteins, storage proteins and enzymes among others. However, EMB564, the most abundant LEA protein in maize embryo, accumulated in comparable levels between vp5 and Vp5 embryos, which contrasted to previously characterized, greatly lowered expression of emb564 mRNA in vp5 embryos. Moreover, LEA proteins and sHSPs displayed differential accumulations in vp5 embryos: six out of eight identified LEA proteins decreased while nine sHSPs increased in abundance. Finally, we discussed the possible causes of global proteome alterations, especially the observed differential accumulation of identified LEA proteins and sHSPs in vp5 embryos. The data derived from this study provides new insight into ABA-dependent proteins and ABA-mediated response during maize seed maturation. PMID:25653661

  5. Pvlea-18, a Member of a New Late-Embryogenesis-Abundant Protein Family That Accumulates during Water Stress and in the Growing Regions of Well-Irrigated Bean Seedlings1

    PubMed Central

    Colmenero-Flores, José M.; Moreno, Liz P.; Smith, Claudia E.; Covarrubias, Alejandra A.

    1999-01-01

    Pvlea-18 is a novel stress gene whose transcript is present in the dry embryo and the endosperm from bean (Phaseolus vulgaris) seeds. It accumulates in vegetative tissues in response to water deficit and abscisic acid application (J.M. Colmenero-Flores, F. Campos, A. Garciarrubio, A.A. Covarrubias [1997] Plant Mol Biol 35: 393–405). We show that the Pvlea-18 gene encodes a 14-kD protein that accumulates during late embryogenesis. Related proteins have been detected in both monocots and dicots, indicating that PvLEA-18 is a member of a new family of LEA (Late Embryogenesis Abundant) proteins. We also show that the PvLEA-18 transcript and protein accumulate not only in different organs of the bean seedlings during water stress but also in well-irrigated seedlings. This accumulation occurs in seedling regions with more negative values of water and osmotic potentials, such as the growing region of the hypocotyl. This phenomenon has not previously been described for LEA proteins. Immunohistochemical localization showed that the PvLEA-18 protein is present in the nucleus and cytoplasm of all cell types, with a higher accumulation in the epidermis and vascular cylinder tissues, particularly in protoxylem cells and root meristematic tissues. We found a similar localization but a higher abundance in water-stressed seedlings. PMID:10318687

  6. Overexpression of Late Embryogenesis Abundant 14 enhances Arabidopsis salt stress tolerance

    SciTech Connect

    Jia, Fengjuan Qi, Shengdong Li, Hui Liu, Pu Li, Pengcheng Wu, Changai Zheng, Chengchao Huang, Jinguang

    2014-11-28

    Highlights: • It is the first time to investigate the biological function of AtLEA14 in salt stress response. • AtLEA14 enhances the salt stress tolerance both in Arabidopsis and yeast. • AtLEA14 responses to salt stress by stabilizing AtPP2-B11, an E3 ligase, under normal or salt stress conditions. - Abstract: Late embryogenesis abundant (LEA) proteins are implicated in various abiotic stresses in higher plants. In this study, we identified a LEA protein from Arabidopsis thaliana, AtLEA14, which was ubiquitously expressed in different tissues and remarkably induced with increased duration of salt treatment. Subcellular distribution analysis demonstrated that AtLEA14 was mainly localized in the cytoplasm. Transgenic Arabidopsis and yeast overexpressing AtLEA14 all exhibited enhanced tolerance to high salinity. The transcripts of salt stress-responsive marker genes (COR15a, KIN1, RD29B and ERD10) were overactivated in AtLEA14 overexpressing lines compared with those in wild type plants under normal or salt stress conditions. In vivo and in vitro analysis showed that AtLEA14 could effectively stabilize AtPP2-B11, an important E3 ligase. These results suggested that AtLEA14 had important protective functions under salt stress conditions in Arabidopsis.

  7. Abiotic stress-induced oscillations in steady-state transcript levels of Group 3 LEA protein genes in the moss, Physcomitrella patens.

    PubMed

    Shinde, Suhas; Shinde, Rupali; Downey, Frances; Ng, Carl K-Y

    2013-01-01

    The moss, Physcomitrella patens is a non-seed land plant belonging to early diverging lineages of land plants following colonization of land in the Ordovician period in Earth's history. Evidence suggests that mosses can be highly tolerant of abiotic stress. We showed previously that dehydration stress and abscisic acid treatments induced oscillations in steady-state levels of LEA (Late Embryogenesis Abundant) protein transcripts, and that removal of ABA resulted in rapid attenuation of oscillatory increases in transcript levels. Here, we show that other abiotic stresses like salt and osmotic stresses also induced oscillations in steady-state transcript levels and that the amplitudes of the oscillatory increases in steady-state transcript levels are reflective of the severity of the abiotic stress treatment. Together, our results suggest that oscillatory increases in transcript levels in response to abiotic stresses may be a general phenomenon in P. patens and that temporally dynamic increases in steady-state transcript levels may be important for adaptation to life in constantly fluctuating environmental conditions. PMID:23221763

  8. DISTINCTIVE LOCALIZATION OF GROUP 3 LATE EMBRYOGENESIS ABUNDANT SYNTHESIZING CELLS DURING BRINE SHRIMP DEVELOPMENT.

    PubMed

    Kim, Bo Yong; Song, Hwa Young; Kim, Mi Young; Lee, Bong Hee; Kim, Kyung Joo; Jo, Kyung Jin; Kim, Suhng Wook; Lee, Seung Gwan; Lee, Boo Hyung

    2015-07-01

    Despite numerous studies on late embryogenesis abundant (LEA) proteins, their functions, roles, and localizations during developmental stages in arthropods remain unknown. LEA proteins protect crucial proteins against osmotic stress during the development and growth of various organisms. Thus, in this study, fluorescence in situ hybridization was used to determine the crucial regions protected against osmotic stress as well as the distinctive localization of group 3 (G3) LEA(+) cells during brine shrimp development. Several cell types were found to synthesize G3 LEA RNA, including neurons, muscular cells, APH-1(+) cells, and renal cells. The G3 LEA(+) neuronal cell bodies outside of the mushroom body projected their axonal bundles to the central body, but those inside the mushroom body projected their axonal bundles toward the deutocerebrum without innervating the central body. The cell bodies inside the mushroom body received axons of the G3 LEA(+) sensory cells at the medial ventral cup of the nauplius eye. Several glands were found to synthesize G3 LEA RNA during the nauplius stages of brine shrimp, including the sinus, antennal I and II, salt, and three ectodermal glands. This study provides the first demonstration of the formation of G3 LEA(+) sinus glands at the emergence stages of brine shrimp. These results suggest that G3 LEA protein is synthesized in several cell types. In particular, specific glands play crucial roles during the emergence and nauplius stages of brine shrimp. PMID:25781424

  9. Genome-wide identification and expression profiling of the late embryogenesis abundant genes in potato with emphasis on dehydrins.

    PubMed

    Charfeddine, Safa; Saïdi, Mohammed Najib; Charfeddine, Mariam; Gargouri-Bouzid, Radhia

    2015-07-01

    Late embryogenesis abundant (LEA) proteins were first described as accumulating late in plant seed development. They were also shown to be involved in plant responses to environmental stress and as well as in bacteria, yeast and invertebrates. They are known to play crucial roles in dehydration tolerance. This study describes a genome-wide analysis of LEA proteins and the corresponding genes in Solanum tuberosum. Twenty-nine LEA family members encoding genes in the Solanum genome were identified. Phylogenetic analyses allowed the classification of the potato LEA proteins into nine distinct groups. Some of them were identified as putative orthologs of Arabidopsis and rice LEA genes. In silico analyses confirmed the hydrophilicity of most of the StLEA proteins, whereas some of them can be folded. The in silico expression analyses showed that the identified genes displayed tissue-specific, stress and hormone-responsive expression profiles. Five StLEA classified as dehydrins were selected for expression analyses under salt and drought stresses. The data revealed that they were induced by both stresses. The analyses indicate that several factors such us developmental stages, hormones, and dehydration, can regulate the expression and activities of LEA protein. This report can be helpful for the further functional diversity studies and analyses of LEA proteins in potato. These genes can be overexpressed to improve potato abiotic stress response. PMID:25638043

  10. Transformation of radish (Raphanus sativus L.) via sonication and vacuum infiltration of germinated seeds with Agrobacterium harboring a group 3 LEA gene from B. napus.

    PubMed

    Park, Byong-Jin; Liu, Zaochang; Kanno, Akira; Kameya, Toshiaki

    2005-10-01

    A protocol for producing transgenic radish (Raphanus sativus) was obtained by using both ultrasonic and vacuum infiltration assisted, Agrobacterium-mediated transformation. The Agrobacterium strain LBA4404 contained the binary vector pBI121-LEA (late embyogenesis abundant), which carried a Group 3 LEA gene, from Brassica napus. Among six combinations, Agrobacterium-mediated transformation assisted by a combination of 5-min sonication with 5-min vacuum infiltration resulted in the highest transformation frequency. The existence, integration and expression of transferred LEA gene in transgenic T(1) plants were confirmed by PCR, genomic Southern and Western blot analysis. Transgenic radish demonstrated better growth performance than non-transformed control plants under osmotic and salt stress conditions. Accumulation of Group 3 LEA protein in the vegetative tissue of transgenic radish conferred increased tolerance to water deficit and salt stress. PMID:15843933

  11. Overexpression of Late Embryogenesis Abundant 14 enhances Arabidopsis salt stress tolerance.

    PubMed

    Jia, Fengjuan; Qi, Shengdong; Li, Hui; Liu, Pu; Li, Pengcheng; Wu, Changai; Zheng, Chengchao; Huang, Jinguang

    2014-11-28

    Late embryogenesis abundant (LEA) proteins are implicated in various abiotic stresses in higher plants. In this study, we identified a LEA protein from Arabidopsis thaliana, AtLEA14, which was ubiquitously expressed in different tissues and remarkably induced with increased duration of salt treatment. Subcellular distribution analysis demonstrated that AtLEA14 was mainly localized in the cytoplasm. Transgenic Arabidopsis and yeast overexpressing AtLEA14 all exhibited enhanced tolerance to high salinity. The transcripts of salt stress-responsive marker genes (COR15a, KIN1, RD29B and ERD10) were overactivated in AtLEA14 overexpressing lines compared with those in wild type plants under normal or salt stress conditions. In vivo and in vitro analysis showed that AtLEA14 could effectively stabilize AtPP2-B11, an important E3 ligase. These results suggested that AtLEA14 had important protective functions under salt stress conditions in Arabidopsis. PMID:25450686

  12. Enhanced water stress tolerance of transgenic maize plants over-expressing LEA Rab28 gene.

    PubMed

    Amara, Imen; Capellades, Montserrat; Ludevid, M Dolors; Pagès, Montserrat; Goday, Adela

    2013-06-15

    Late Embryogenesis Abundant (LEA) proteins participate in plant stress responses and contribute to the acquisition of desiccation tolerance. In this report Rab28 LEA gene has been over-expressed in maize plants under a constitutive maize promoter. The expression of Rab28 transcripts led to the accumulation and stability of Rab28 protein in the transgenic plants. Native Rab28 protein is localized to nucleoli in wild type maize embryo cells; here we find by whole-mount immunocytochemistry that in root cells of Rab28 transgenic and wild-type plants the protein is also associated to nucleolar structures. Transgenic plants were tested for stress tolerance and resulted in sustained growth under polyethyleneglycol (PEG)-mediated dehydration compared to wild-type controls. Under osmotic stress transgenic seedlings showed increased leaf and root areas, higher relative water content (RWC), reduced chlorophyll loss and lower Malondialdehyde (MDA) production in relation to wild-type plants. Moreover, transgenic seeds exhibited higher germination rates than wild-type seeds under water deficit. Overall, our results highlight the presence of transgenic Rab28 protein in nucleolar structures and point to the potential of group 5 LEA Rab28 gene as candidate to enhance stress tolerance in maize plants. PMID:23384757

  13. Influence of drying on the secondary structure of intrinsically disordered and globular proteins.

    PubMed

    Hundertmark, Michaela; Popova, Antoaneta V; Rausch, Saskia; Seckler, Robert; Hincha, Dirk K

    2012-01-01

    Circular dichroism (CD) spectroscopy of five Arabidopsis late embryogenesis abundant (LEA) proteins constituting the plant specific families LEA_5 and LEA_6 showed that they are intrinsically disordered in solution and partially fold during drying. Structural predictions were comparable to these results for hydrated LEA_6, but not for LEA_5 proteins. FTIR spectroscopy showed that verbascose, but not sucrose, strongly affected the structure of the dry proteins. The four investigated globular proteins were only mildly affected by drying in the absence, but strongly in the presence of sugars. These data highlight the larger structural flexibility of disordered compared to globular proteins and the impact of sugars on the structure of both disordered and globular proteins during drying. PMID:22155233

  14. SoyProLow: A protein database enriched in low abundant soybean proteins

    PubMed Central

    Tavakolan, Mona; Alkharouf, Nadim W; Matthews, Benjamin F; Natarajan, Savithiry S

    2014-01-01

    Soybeans are an important legume crop that contain 2 major storage proteins, β-conglycinin and glycinin, which account about 70- 80% of total seed proteins. These abundant proteins hinder the isolation and characterization of several low abundant proteins in soybean seeds. Several protein extraction methodologies were developed in our laboratory to decrease these abundant storage proteins in seed extracts and to also decrease the amount of ribulose-1, 5-bisphosphate carboxylase/oxygenase (RuBisCO), which is normally very abundant in leaf extracts. One of the extraction methodologies used 40% isopropanol and was more effective in depleting soybean storage proteins and enhancing low abundant seed proteins than similar methods using 10-80% isopropanol. Extractions performed with 40% isopropanol decreased the amount of storage proteins and revealed 107 low abundant proteins when using the combined approaches of two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and Mass Spectrometry (MS). The separation of proteins was achieved by iso-electric focusing (IEF) and 2D-PAGE. The proteins were analyzed with MS techniques to provide amino acid sequence. The proteins were identified by comparing their amino acid sequences with those in different databases including NCBI-non redundant, UniprotKB and MSDB databases. In this investigation, previously published results on low abundant soybean seed proteins were used to create an online database (SoyProLow) to provide a data repository that can be used as a reference to identify and characterize low abundance proteins. This database is freely accessible to individuals using similar techniques and can be for the subsequent genetic manipulation to produce value added soybean traits. An intuitive user interface based on dynamic HTML enables users to browse the network and the profiles of the low abundant proteins. Availability http://bioinformatics.towson.edu/Soybean_low_abundance_proteins_2D_Gel_DB/Gel1.aspx PMID:25352730

  15. Estimating relative abundances of proteins from shotgun proteomics data

    PubMed Central

    2012-01-01

    Background Spectral counting methods provide an easy means of identifying proteins with differing abundances between complex mixtures using shotgun proteomics data. The crux spectral-counts command, implemented as part of the Crux software toolkit, implements four previously reported spectral counting methods, the spectral index (SIN), the exponentially modified protein abundance index (emPAI), the normalized spectral abundance factor (NSAF), and the distributed normalized spectral abundance factor (dNSAF). Results We compared the reproducibility and the linearity relative to each protein’s abundance of the four spectral counting metrics. Our analysis suggests that NSAF yields the most reproducible counts across technical and biological replicates, and both SIN and NSAF achieve the best linearity. Conclusions With the crux spectral-counts command, Crux provides open-source modular methods to analyze mass spectrometry data for identifying and now quantifying peptides and proteins. The C++ source code, compiled binaries, spectra and sequence databases are available at http://noble.gs.washington.edu/proj/crux-spectral-counts. PMID:23164367

  16. Total protein or high-abundance protein: Which offers the best loading control for Western blotting?

    PubMed

    Thacker, Jonathan S; Yeung, Derrick H; Staines, W Richard; Mielke, John G

    2016-03-01

    Western blotting routinely involves a control for variability in the amount of protein across immunoblot lanes. Normalizing a target signal to one found for an abundantly expressed protein is widely regarded as a reliable loading control; however, this approach is being increasingly questioned. As a result, we compared blotting for two high-abundance proteins (actin and glyceraldehyde 3-phosphate dehydrogenase [GAPDH]) and two total protein membrane staining methods (Ponceau and Coomassie Brilliant Blue) to determine the best control for loading variability. We found that Ponceau staining optimally balanced accuracy and precision, and we suggest that this approach be considered as an alternative to normalizing with a high-abundance protein. PMID:26706797

  17. Antibody arrays for determination of relative protein abundances.

    PubMed

    Chaga, Grigoriy S

    2008-01-01

    As a large number of genome-sequencing projects reached completion, the attention of the scientific community is turning toward understanding the structure-functions of gene translation products-the proteins as well as the complete complement of proteins-the proteome. One goal of proteomics is to correlate changes in protein abundance with biological processes and disease states. To help accelerate this avenue of proteomics, a significant effort has been devoted to the development of multiplexed methods for protein analyses. We have developed an Antibody Microarray, a chip-based technology for multiparallel determination of relative abundance of hundreds of proteins. The Antibody Microarray is composed of hundreds of distinct monoclonal antibodies printed at high density on a glass slide. It utilizes a novel experimental setup and data analysis algorithm, which enables scientists to assay hundreds of cytosolic, nuclear, and membrane-bound proteins with a single experiment. Examples of biological samples that are analyzed on the Antibody Microarray include tissue samples, cell cultures, and body fluids. PMID:18370316

  18. 34 CFR 200.71 - LEA eligibility.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... (2) Greater than two percent of the LEA's total population ages 5 to 17 years, inclusive. (b...) 15 percent of the LEA's total population ages 5 to 17 years, inclusive. (c) Targeted grants. An LEA... least five percent of the LEA's total population ages 5 to 17 years, inclusive. (d) Education...

  19. Abundant protein phosphorylation potentially regulates Arabidopsis anther development

    PubMed Central

    Ye, Juanying; Zhang, Zaibao; You, Chenjiang; Zhang, Xumin; Lu, Jianan; Ma, Hong

    2016-01-01

    As the male reproductive organ of flowering plants, the stamen consists of the anther and filament. Previous studies on stamen development mainly focused on single gene functions by genetic methods or gene expression changes using comparative transcriptomic approaches, especially in model plants such as Arabidopsis thaliana. However, studies on Arabidopsis anther protein expression and post-translational modifications are still lacking. Here we report proteomic and phosphoproteomic studies on developing Arabidopsis anthers at stages 4–7 and 8–12. We identified 3908 high-confidence phosphorylation sites corresponding to 1637 phosphoproteins. Among the 1637 phosphoproteins, 493 were newly identified, with 952 phosphorylation sites. Phosphopeptide enrichment prior to LC-MS analysis facilitated the identification of low-abundance proteins and regulatory proteins, thereby increasing the coverage of proteomic analysis, and facilitated the analysis of more regulatory proteins. Thirty-nine serine and six threonine phosphorylation motifs were uncovered from the anther phosphoproteome and further analysis supports that phosphorylation of casein kinase II, mitogen-activated protein kinases, and 14-3-3 proteins is a key regulatory mechanism in anther development. Phosphorylated residues were preferentially located in variable protein regions among family members, but they were they were conserved across angiosperms in general. Moreover, phosphorylation might reduce activity of reactive oxygen species scavenging enzymes and hamper brassinosteroid signaling in early anther development. Most of the novel phosphoproteins showed tissue-specific expression in the anther according to previous microarray data. This study provides a community resource with information on the abundance and phosphorylation status of thousands of proteins in developing anthers, contributing to understanding post-translational regulatory mechanisms during anther development. PMID:27531888

  20. Abundant protein phosphorylation potentially regulates Arabidopsis anther development.

    PubMed

    Ye, Juanying; Zhang, Zaibao; You, Chenjiang; Zhang, Xumin; Lu, Jianan; Ma, Hong

    2016-09-01

    As the male reproductive organ of flowering plants, the stamen consists of the anther and filament. Previous studies on stamen development mainly focused on single gene functions by genetic methods or gene expression changes using comparative transcriptomic approaches, especially in model plants such as Arabidopsis thaliana However, studies on Arabidopsis anther protein expression and post-translational modifications are still lacking. Here we report proteomic and phosphoproteomic studies on developing Arabidopsis anthers at stages 4-7 and 8-12. We identified 3908 high-confidence phosphorylation sites corresponding to 1637 phosphoproteins. Among the 1637 phosphoproteins, 493 were newly identified, with 952 phosphorylation sites. Phosphopeptide enrichment prior to LC-MS analysis facilitated the identification of low-abundance proteins and regulatory proteins, thereby increasing the coverage of proteomic analysis, and facilitated the analysis of more regulatory proteins. Thirty-nine serine and six threonine phosphorylation motifs were uncovered from the anther phosphoproteome and further analysis supports that phosphorylation of casein kinase II, mitogen-activated protein kinases, and 14-3-3 proteins is a key regulatory mechanism in anther development. Phosphorylated residues were preferentially located in variable protein regions among family members, but they were they were conserved across angiosperms in general. Moreover, phosphorylation might reduce activity of reactive oxygen species scavenging enzymes and hamper brassinosteroid signaling in early anther development. Most of the novel phosphoproteins showed tissue-specific expression in the anther according to previous microarray data. This study provides a community resource with information on the abundance and phosphorylation status of thousands of proteins in developing anthers, contributing to understanding post-translational regulatory mechanisms during anther development. PMID:27531888

  1. Topology of Protein Interaction Network Shapes Protein Abundances and Strengths of Their Functional and Nonspecific Interactions

    SciTech Connect

    Maslov, S.; Heo, M.; Shakhnovich, E.

    2011-03-08

    How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous nonfunctional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are directly determined from its genome through biophysical properties of protein structures and binding interactions in a crowded cellular environment. The model cell includes three independent prototypical pathways, whose topologies of protein-protein interaction (PPI) subnetworks are different, but whose contributions to the cell fitness are equal. Model cells evolve through genotypic mutations and phenotypic protein copy number variations. We found a strong relationship between evolved physical-chemical properties of protein interactions and their abundances due to a 'frustration' effect: Strengthening of functional interactions brings about hydrophobic interfaces, which make proteins prone to promiscuous binding. The balancing act is achieved by lowering concentrations of hub proteins while raising solubilities and abundances of functional monomers. On the basis of these principles we generated and analyzed a possible realization of the proteome-wide PPI network in yeast. In this simulation we found that high-throughput affinity capture-mass spectroscopy experiments can detect functional interactions with high fidelity only for high-abundance proteins while missing most interactions for low-abundance proteins.

  2. Determination of optimal protein quantity required to identify abundant and less abundant soybean seed proteins by 2D-PAGE and MS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Optimizing the amounts of proteins required to separate and characterize both abundant and less abundant proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) is critical for conducting proteomic research. In this study, we tested five different levels of soybean seed proteins (7...

  3. Practical Immunoaffinity-Enrichment LC-MS for Measuring Protein Kinetics of Low-Abundance Proteins

    PubMed Central

    Lassman, Michael E.; McAvoy, Thomas; Lee, Anita Y.H.; Chappell, Derek; Wong, Oitak; Zhou, Haihong; Reyes-Soffer, Gissette; Ginsberg, Henry N.; Millar, John S.; Rader, Daniel J.; Gutstein, David E.; Laterza, Omar

    2016-01-01

    BACKGROUND For a more complete understanding of pharmacodynamic, metabolic, and pathophysiologic effects, protein kinetics, such as production rate and fractional catabolic rate, can offer substantially more information than protein concentration alone. Kinetic experiments with stable isotope tracers typically require laborious sample preparation and are most often used for studying abundant proteins. Here we describe a practical methodology for measuring isotope enrichment into low-abundance proteins that uses an automated procedure and immunoaffinity enrichment (IA) with LC-MS. Low-abundance plasma proteins cholesteryl ester transfer protein (CETP) and proprotein convertase subtilisin/kexin type 9 (PCSK9) were studied as examples. METHODS Human participants (n = 39) were infused with [2H3]leucine, and blood samples were collected at multiple time points. Sample preparation and analysis were automated and multiplexed to increase throughput. Proteins were concentrated from plasma by use of IA and digested with trypsin to yield proteotypic peptides that were analyzed by microflow chromatography-mass spectrometry to measure isotope enrichment. RESULTS The IA procedure was optimized to provide the greatest signal intensity. Use of a gel-free method increased throughput while increasing the signal. The intra- and interassay CVs were <15% at all isotope enrichment levels studied. More than 1400 samples were analyzed in <3 weeks without the need for instrument stoppages or user interventions. CONCLUSIONS The use of automated gel-free methods to multiplex the measurement of isotope enrichment was applied to the low-abundance proteins CETP and PCSK9. PMID:24751376

  4. 34 CFR 300.705 - Subgrants to LEAs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... reasonable period of time prior to the end of the carryover period in 34 CFR 76.709, whether the LEA has... under § 300.704 to LEAs (including public charter schools that operate as LEAs) in the State that have... LEAs, including public charter schools that operate as LEAs, even if the LEA is not serving...

  5. 34 CFR 300.705 - Subgrants to LEAs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... reasonable period of time prior to the end of the carryover period in 34 CFR 76.709, whether the LEA has... under § 300.704 to LEAs (including public charter schools that operate as LEAs) in the State that have... LEAs, including public charter schools that operate as LEAs, even if the LEA is not serving...

  6. 34 CFR 300.705 - Subgrants to LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... reasonable period of time prior to the end of the carryover period in 34 CFR 76.709, whether the LEA has... under § 300.704 to LEAs (including public charter schools that operate as LEAs) in the State that have... LEAs, including public charter schools that operate as LEAs, even if the LEA is not serving...

  7. 34 CFR 300.705 - Subgrants to LEAs.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... reasonable period of time prior to the end of the carryover period in 34 CFR 76.709, whether the LEA has... under § 300.704 to LEAs (including public charter schools that operate as LEAs) in the State that have... LEAs, including public charter schools that operate as LEAs, even if the LEA is not serving...

  8. 34 CFR 300.705 - Subgrants to LEAs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... reasonable period of time prior to the end of the carryover period in 34 CFR 76.709, whether the LEA has... under § 300.704 to LEAs (including public charter schools that operate as LEAs) in the State that have... LEAs, including public charter schools that operate as LEAs, even if the LEA is not serving...

  9. 34 CFR 200.52 - LEA improvement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., school staff, and others in developing or revising its improvement plan. (3) The LEA improvement plan... 1117 of the ESEA. (2) The purpose of the technical assistance is to better enable the LEA to—...

  10. Wheat and barley dehydrins under cold, drought, and salinity - what can LEA-II proteins tell us about plant stress response?

    PubMed

    Kosová, Klára; Vítámvás, Pavel; Prášil, Ilja T

    2014-01-01

    Dehydrins as a group of late embryogenesis abundant II proteins represent important dehydration-inducible proteins whose accumulation is induced by developmental processes (embryo maturation) as well as by several abiotic stress factors (low temperatures, drought, salinity). In the review, an overview of studies aimed at investigation of dehydrin accumulation patterns at transcript and protein levels as well as their possible functions in common wheat (Triticum aestivum), durum wheat (T. durum), and barley (Hordeum vulgare) plants exposed to various abiotic stress factors (cold, frost, drought, salinity) is provided. Possible roles of dehydrin proteins in an acquisition and maintenance of an enhanced frost tolerance are analyzed in the context of plant developmental processes (vernalization). Quantitative and qualitative differences as well as post-translational modifications in accumulated dehydrin proteins between barley cultivars revealing differential tolerance to drought and salinity are also discussed. Current knowledge on dehydrin role in wheat and barley response to major dehydrative stresses is summarized and the major challenges in dehydrin research are outlined. PMID:25071816

  11. Label-Free Protein Quantification for Plant Golgi Protein Localization and Abundance1[W

    PubMed Central

    Nikolovski, Nino; Shliaha, Pavel V.; Gatto, Laurent; Dupree, Paul; Lilley, Kathryn S.

    2014-01-01

    The proteomic composition of the Arabidopsis (Arabidopsis thaliana) Golgi apparatus is currently reasonably well documented; however, little is known about the relative abundances between different proteins within this compartment. Accurate quantitative information of Golgi resident proteins is of great importance: it facilitates a better understanding of the biochemical processes that take place within this organelle, especially those of different polysaccharide synthesis pathways. Golgi resident proteins are challenging to quantify because the abundance of this organelle is relatively low within the cell. In this study, an organelle fractionation approach targeting the Golgi apparatus was combined with a label-free quantitative mass spectrometry (data-independent acquisition method using ion mobility separation known as LC-IMS-MSE [or HDMSE]) to simultaneously localize proteins to the Golgi apparatus and assess their relative quantity. In total, 102 Golgi-localized proteins were quantified. These data show that organelle fractionation in conjunction with label-free quantitative mass spectrometry is a powerful and relatively simple tool to access protein organelle localization and their relative abundances. The findings presented open a unique view on the organization of the plant Golgi apparatus, leading toward unique hypotheses centered on the biochemical processes of this organelle. PMID:25122472

  12. Abundant storage protein depletion from tuber proteins using ethanol precipitation method: Suitability to proteomics study.

    PubMed

    Lee, Hye Min; Gupta, Ravi; Kim, Sun Hyung; Wang, Yiming; Rakwal, Randeep; Agrawal, Ganesh Kumar; Kim, Sun Tae

    2015-05-01

    High-abundance proteins (HAPs) hamper in-depth proteome study necessitating development of a HAPs depletion method. Here, we report a novel ethanol precipitation method (EPM) for HAPs depletion from total tuber proteins. Ethanol showed a dose-dependent effect on depletion of sporamin from sweet potato and patatin from potato tubers, respectively. The 50% ethanol was an optimal concentration. 2DE analysis of EPM-prepared sweet potato proteins also revealed enrichment of storage proteins (SPs) in ethanol supernatant (ES) resulting in detection of new low-abundance proteins in ethanol pellet (EP), compared to total fraction. The ES fraction showed even higher trypsin inhibitor activity than total proteins, further showing the efficacy of EPM in enrichment of sporamin in ES fraction. Application of this method was demonstrated for comparative proteomics of two sweet potato cultivars (Hwang-geum and Ho-bac) and purification of SP (sporamin) in its native form, as examples. Comparative proteomics identified many cultivar specific protein spots and selected spots were confidently assigned for their protein identity using MALDI-TOF-TOF analysis. Overall, the EPM is simple, reproducible, and economical for depletion of SPs and is suitable for downstream proteomics study. This study opens a door for its potential application to other tuber crops or fruits rich in carbohydrates. PMID:25689267

  13. An efficient extraction method to enhance analysis of low abundant proteins from soybean seed.

    PubMed

    Natarajan, Savithiry S; Krishnan, Hari B; Lakshman, Sukla; Garrett, Wesley M

    2009-11-15

    Large amounts of the major storage proteins, beta-conglycinin and glycinin, in soybean (Glycine max) seeds hinder the isolation and characterization of less abundant seed proteins. We investigated whether isopropanol extraction could facilitate resolution of the low abundant proteins, different from the main storage protein fractions, in one-dimensional polyacrylamide gel electrophoresis (1D-PAGE) and two-dimensional polyacrylamide gel electrophoresis (2D-PAGE). 1D-PAGE of proteins extracted by different concentrations (10%, 20%, 30%, 40%, 50%, 60%, 70% and 80%) of isopropanol showed that greater than 30% isopropanol was suitable for preferential enrichment of low abundant proteins. Analysis of 2D-PAGE showed that proteins which were less abundant or absent by the conventional extraction procedure were clearly seen in the 40% isopropanol extracts. Increasing isopropanol concentration above 40% resulted in a decrease in the number of less abundant protein spots. We have identified a total of 107 protein spots using matrix-assisted laser desorption/ionization time of flight mass spectrophotometry (MALDI-TOF-MS) and liquid chromatography-mass spectrometry (LC-MS/MS). Our results suggest that extraction of soybean seed powder with 40% isopropanol enriches lower abundance proteins and is a suitable method for 2D-PAGE separation and identification. This methodology could potentially allow the extraction and characterization of low abundant proteins of other legume seeds containing highly abundant storage proteins. PMID:19651100

  14. An efficient extraction method to enhance analysis of low abundant proteins from soybean seed

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Large amounts of the major seed storage proteins, such as ß-conglycinin and glycinin, in soybean (Glycine max) seeds hinder the isolation and characterization of less abundant seed proteins. We investigated whether isopropanol extraction could facilitate resolution of the less abundant proteins fro...

  15. Regular Patterns for Proteome-Wide Distribution of Protein Abundance across Species

    PubMed Central

    Jiang, Ying; Ying, Wantao; Wu, Songfeng; Zhu, Yunping; Liu, Siqi; Yang, Pengyuan; Qian, Xiaohong; He, Fuchu

    2012-01-01

    A proteome of the bio-entity, including cell, tissue, organ, and organism, consists of proteins of diverse abundance. The principle that determines the abundance of different proteins in a proteome is of fundamental significance for an understanding of the building blocks of the bio-entity. Here, we report three regular patterns in the proteome-wide distribution of protein abundance across species such as human, mouse, fly, worm, yeast, and bacteria: in most cases, protein abundance is positively correlated with the protein's origination time or sequence conservation during evolution; it is negatively correlated with the protein's domain number and positively correlated with domain coverage in protein structure, and the correlations became stronger during the course of evolution; protein abundance can be further stratified by the function of the protein, whereby proteins that act on material conversion and transportation (mass category) are more abundant than those that act on information modulation (information category). Thus, protein abundance is intrinsically related to the protein's inherent characters of evolution, structure, and function. PMID:22427835

  16. Proteomics-Based Identification of Differentially Abundant Proteins from Human Keratinocytes Exposed to Arsenic Trioxide

    PubMed Central

    Udensi, Udensi K; Tackett, Alan J; Byrum, Stephanie; Avaritt, Nathan L; Sengupta, Deepanwita; Moreland, Linley W; Tchounwou, Paul B; Isokpehi, Raphael D

    2014-01-01

    Introduction Arsenic is a widely distributed environmental toxicant that can cause multi-tissue pathologies. Proteomic assays allow for the identification of biological processes modulated by arsenic in diverse tissue types. Method The altered abundance of proteins from HaCaT human keratinocyte cell line exposed to arsenic was quantified using a label-free LC-MS/MS mass spectrometry workflow. Selected proteomics results were validated using western blot and RT-PCR. A functional annotation analytics strategy that included visual analytical integration of heterogeneous data sets was developed to elucidate functional categories. The annotations integrated were mainly tissue localization, biological process and gene family. Result The abundance of 173 proteins was altered in keratinocytes exposed to arsenic; in which 96 proteins had increased abundance while 77 proteins had decreased abundance. These proteins were also classified into 69 Gene Ontology biological process terms. The increased abundance of transferrin receptor protein (TFRC) was validated and also annotated to participate in response to hypoxia. A total of 33 proteins (11 increased abundance and 22 decreased abundance) were associated with 18 metabolic process terms. The Glutamate--cysteine ligase catalytic subunit (GCLC), the only protein annotated with the term sulfur amino acid metabolism process, had increased abundance while succinate dehydrogenase [ubiquinone] iron-sulfur subunit, mitochondrial precursor (SDHB), a tumor suppressor, had decreased abundance. Conclusion A list of 173 differentially abundant proteins in response to arsenic trioxide was grouped using three major functional annotations covering tissue localization, biological process and protein families. A possible explanation for hyperpigmentation pathologies observed in arsenic toxicity is that arsenic exposure leads to increased iron uptake in the normally hypoxic human skin. The proteins mapped to metabolic process terms and

  17. 34 CFR 300.815 - Subgrants to LEAs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... schools that operate as LEAs, even if the LEA is not serving any preschool children with disabilities... DISABILITIES Preschool Grants for Children with Disabilities § 300.815 Subgrants to LEAs. Each State...

  18. Impact of Protein Stability, Cellular Localization, and Abundance on Proteomic Detection of Tumor-Derived Proteins in Plasma

    PubMed Central

    Faca, Vitor M.; Zhang, Wenxuan; Zhang, Qing; Jain, Anjali; Hanash, Sam; Agus, David B.; McIntosh, Martin W.; Mallick, Parag

    2011-01-01

    Tumor-derived, circulating proteins are potentially useful as biomarkers for detection of cancer, for monitoring of disease progression, regression and recurrence, and for assessment of therapeutic response. Here we interrogated how a protein's stability, cellular localization, and abundance affect its observability in blood by mass-spectrometry-based proteomics techniques. We performed proteomic profiling on tumors and plasma from two different xenograft mouse models. A statistical analysis of this data revealed protein properties indicative of the detection level in plasma. Though 20% of the proteins identified in plasma were tumor-derived, only 5% of the proteins observed in the tumor tissue were found in plasma. Both intracellular and extracellular tumor proteins were observed in plasma; however, after normalizing for tumor abundance, extracellular proteins were seven times more likely to be detected. Although proteins that were more abundant in the tumor were also more likely to be observed in plasma, the relationship was nonlinear: Doubling the spectral count increased detection rate by only 50%. Many secreted proteins, even those with relatively low spectral count, were observed in plasma, but few low abundance intracellular proteins were observed. Proteins predicted to be stable by dipeptide composition were significantly more likely to be identified in plasma than less stable proteins. The number of tryptic peptides in a protein was not significantly related to the chance of a protein being observed in plasma. Quantitative comparison of large versus small tumors revealed that the abundance of proteins in plasma as measured by spectral count was associated with the tumor size, but the relationship was not one-to-one; a 3-fold decrease in tumor size resulted in a 16-fold decrease in protein abundance in plasma. This study provides quantitative support for a tumor-derived marker prioritization strategy that favors secreted and stable proteins over all but the

  19. Impact of protein stability, cellular localization, and abundance on proteomic detection of tumor-derived proteins in plasma.

    PubMed

    Fang, Qiaojun; Kani, Kian; Faca, Vitor M; Zhang, Wenxuan; Zhang, Qing; Jain, Anjali; Hanash, Sam; Agus, David B; McIntosh, Martin W; Mallick, Parag

    2011-01-01

    Tumor-derived, circulating proteins are potentially useful as biomarkers for detection of cancer, for monitoring of disease progression, regression and recurrence, and for assessment of therapeutic response. Here we interrogated how a protein's stability, cellular localization, and abundance affect its observability in blood by mass-spectrometry-based proteomics techniques. We performed proteomic profiling on tumors and plasma from two different xenograft mouse models. A statistical analysis of this data revealed protein properties indicative of the detection level in plasma. Though 20% of the proteins identified in plasma were tumor-derived, only 5% of the proteins observed in the tumor tissue were found in plasma. Both intracellular and extracellular tumor proteins were observed in plasma; however, after normalizing for tumor abundance, extracellular proteins were seven times more likely to be detected. Although proteins that were more abundant in the tumor were also more likely to be observed in plasma, the relationship was nonlinear: Doubling the spectral count increased detection rate by only 50%. Many secreted proteins, even those with relatively low spectral count, were observed in plasma, but few low abundance intracellular proteins were observed. Proteins predicted to be stable by dipeptide composition were significantly more likely to be identified in plasma than less stable proteins. The number of tryptic peptides in a protein was not significantly related to the chance of a protein being observed in plasma. Quantitative comparison of large versus small tumors revealed that the abundance of proteins in plasma as measured by spectral count was associated with the tumor size, but the relationship was not one-to-one; a 3-fold decrease in tumor size resulted in a 16-fold decrease in protein abundance in plasma. This study provides quantitative support for a tumor-derived marker prioritization strategy that favors secreted and stable proteins over all but the

  20. Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins.

    PubMed

    Cundiff, Judy K; McConnell, Elizabeth J; Lohe, Kimberly J; Maria, Sarah D; McMahon, Robert J; Zhang, Qiang

    2016-01-01

    Mass spectrometry (MS)-based proteomic approaches have largely facilitated our systemic understanding of cellular processes and biological functions. Cutoffs in protein expression fold changes (FCs) are often arbitrarily determined in MS-based quantification with no demonstrable determination of small magnitude changes in protein expression. Therefore, many biological insights may remain veiled due to high FC cutoffs. Herein, we employ the intestinal epithelial cell (IEC) line Caco-2 as a model system to demonstrate the dynamicity of tandem-mass-tag (TMT) labeling over a range of 5-40% changes in protein abundance, with the variance controls of ± 5% FC for around 95% of TMT ratios when sampling 9-12 biological replicates. We further applied this procedure to examine the temporal proteome of Caco-2 cells upon exposure to human whey proteins (WP). Pathway assessments predict subtle effects due to WP in moderating xenobiotic metabolism, promoting proliferation and various other cellular functions in differentiating enterocyte-like Caco-2 cells. This demonstration of a sensitive MS approach may open up new perspectives in the system-wide exploration of elusive or transient biological effects by facilitating scrutiny of narrow windows of proteome abundance changes. Furthermore, we anticipate this study will encourage more investigations of WP on infant gastrointestinal tract development. PMID:26586228

  1. Chloroplast isolation and affinity chromatography for enrichment of low-abundant proteins in complex proteomes.

    PubMed

    Bayer, Roman G; Stael, Simon; Teige, Markus

    2015-01-01

    Detailed knowledge of the proteome is crucial to advance the biological sciences. Low-abundant proteins are of particular interest to many biologists as they include, for example those proteins involved in signal transduction. Recent technological advances resulted in a tremendous increase in protein identification sensitivity by mass spectrometry (MS). However, the dynamic range in protein abundance still forms a fundamental problem that limits the detection of low-abundant proteins in complex proteomes. These proteins will typically escape detection in shotgun MS experiments due to the presence of other proteins at an abundance several-fold higher in order of magnitude. Therefore, specific enrichment strategies are required to overcome this technical limitation of MS-based protein discovery. We have searched for novel signal transduction proteins, more specifically kinases and calcium-binding proteins, and here we describe different approaches for enrichment of these low-abundant proteins from isolated chloroplasts from pea and Arabidopsis for subsequent proteomic analysis by MS. These approaches could be extended to include other signal transduction proteins and target different organelles. PMID:25820724

  2. Identification of Differentially Abundant Proteins of Edwardsiella ictaluri during Iron Restriction

    PubMed Central

    Dumpala, Pradeep R.; Peterson, Brian C.; Lawrence, Mark L.; Karsi, Attila

    2015-01-01

    Edwardsiella ictaluri is a Gram-negative facultative anaerobe intracellular bacterium that causes enteric septicemia in channel catfish. Iron is an essential inorganic nutrient of bacteria and is crucial for bacterial invasion. Reduced availability of iron by the host may cause significant stress for bacterial pathogens and is considered a signal that leads to significant alteration in virulence gene expression. However, the precise effect of iron-restriction on E. ictaluri protein abundance is unknown. The purpose of this study was to identify differentially abundant proteins of E. ictaluri during in vitro iron-restricted conditions. We applied two-dimensional difference in gel electrophoresis (2D-DIGE) for determining differentially abundant proteins and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF/TOF MS) for protein identification. Gene ontology and pathway-based functional modeling of differentially abundant proteins was also conducted. A total of 50 unique differentially abundant proteins at a minimum of 2-fold (p ≤ 0.05) difference in abundance due to iron-restriction were detected. The numbers of up- and down-regulated proteins were 37 and 13, respectively. We noted several proteins, including EsrB, LamB, MalM, MalE, FdaA, and TonB-dependent heme/hemoglobin receptor family proteins responded to iron restriction in E. ictaluri. PMID:26168192

  3. Natural variability in abundance of prevalent soybean proteins.

    PubMed

    Natarajan, Savithiry S

    2010-12-01

    Soybean is an inexpensive source of protein for humans and animals. Genetic modifications (GMO) to soybean have become inevitable on two fronts, both quality and yield will need to improve to meet increasing global demand. To ensure the safety of the crop for consumers it is important to determine the natural variation in seed protein constituents as well as any unintended changes that may occur in the GMO as a result of genetic modification. Understanding the natural variation of seed proteins in wild and cultivated soybeans that have been used in conventional soybean breeding programs is critical for determining unintended protein expression in GMO soybeans. In recent years, proteomic technologies have been used as an effective analytical tool for examining modifications of protein profiles. We have standardized and applied these technologies to determine and quantify the spectrum of proteins present in soybean seed. We used two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF-MS), and liquid chromatography mass spectrometry (LC-MS) for the separation, quantification, and identification of different classes of soybean seed proteins. We have observed significant variations in different classes of proteins, including storage, allergen and anti-nutritional protein profiles, between non-GMO cultivated and wild soybean varieties. This information is useful for scientists and regulatory agencies to determine whether the unintended expression of proteins found in transgenic soybean is within the range of natural variation. PMID:20709130

  4. The LEA Perspective on Competency Testing.

    ERIC Educational Resources Information Center

    Kean, Michael H.; Mattleman, Marciene S.

    1979-01-01

    The controversy over minimum competency testing (MCT) is multi-faceted and it is the Local Education Agency (LEA) which will bear the burden of the MCT movement. Among the concerns of the LEAs are the means of assessment, the content of tests, and the curricular implications of MCT. (RLV)

  5. Genomic analysis of membrane protein families: abundance and conserved motifs

    PubMed Central

    Liu, Yang; Engelman, Donald M; Gerstein, Mark

    2002-01-01

    Background Polytopic membrane proteins can be related to each other on the basis of the number of transmembrane helices and sequence similarities. Building on the Pfam classification of protein domain families, and using transmembrane-helix prediction and sequence-similarity searching, we identified a total of 526 well-characterized membrane protein families in 26 recently sequenced genomes. To this we added a clustering of a number of predicted but unclassified membrane proteins, resulting in a total of 637 membrane protein families. Results Analysis of the occurrence and composition of these families revealed several interesting trends. The number of assigned membrane protein domains has an approximately linear relationship to the total number of open reading frames (ORFs) in 26 genomes studied. Caenorhabditis elegans is an apparent outlier, because of its high representation of seven-span transmembrane (7-TM) chemoreceptor families. In all genomes, including that of C. elegans, the number of distinct membrane protein families has a logarithmic relation to the number of ORFs. Glycine, proline, and tyrosine locations tend to be conserved in transmembrane regions within families, whereas isoleucine, valine, and methionine locations are relatively mutable. Analysis of motifs in putative transmembrane helices reveals that GxxxG and GxxxxxxG (which can be written GG4 and GG7, respectively; see Materials and methods) are among the most prevalent. This was noted in earlier studies; we now find these motifs are particularly well conserved in families, however, especially those corresponding to transporters, symporters, and channels. Conclusions We carried out a genome-wide analysis on patterns of the classified polytopic membrane protein families and analyzed the distribution of conserved amino acids and motifs in the transmembrane helix regions in these families. PMID:12372142

  6. Transcriptional abundance is not the single force driving the evolution of bacterial proteins

    PubMed Central

    2013-01-01

    Background Despite rapid progress in understanding the mechanisms that shape the evolution of proteins, the relative importance of various factors remain to be elucidated. In this study, we have assessed the effects of 16 different biological features on the evolutionary rates (ERs) of protein-coding sequences in bacterial genomes. Results Our analysis of 18 bacterial species revealed new correlations between ERs and constraining factors. Previous studies have suggested that transcriptional abundance overwhelmingly constrains the evolution of yeast protein sequences. This transcriptional abundance leads to selection against misfolding or misinteractions. In this study we found that there was no single factor in determining the evolution of bacterial proteins. Not only transcriptional abundance (codon adaptation index and expression level), but also protein-protein associations (PPAs), essentiality (ESS), subcellular localization of cytoplasmic membrane (SLM), transmembrane helices (TMH) and hydropathicity score (HS) independently and significantly affected the ERs of bacterial proteins. In some species, PPA and ESS demonstrate higher correlations with ER than transcriptional abundance. Conclusions Different forces drive the evolution of protein sequences in yeast and bacteria. In bacteria, the constraints are involved in avoiding a build-up of toxic molecules caused by misfolding/misinteraction (transcriptional abundance), while retaining important functions (ESS, PPA) and maintaining the cell membrane (SLM, TMH and HS). Each of these independently contributes to the variation in protein evolution. PMID:23914835

  7. Depletion of cells and abundant proteins from biological samples by enhanced dielectrophoresis✩

    PubMed Central

    Gupta, C.; Provine, J.; Davis, R.W.; Howe, R.T.

    2016-01-01

    Platforms that are sensitive and specific enough to assay low-abundance protein biomarkers, in a high throughput multiplex format, within a complex biological fluid specimen, are necessary to enable protein biomarker based diagnostics for diseases such as cancer. The signal from an assay for a low-abundance protein biomarker in a biological fluid sample like blood is typically buried in a background that arises from the presence of blood cells and from high-abundance proteins that make up 90% of the assayed protein mass. We present an automated on-chip platform for the depletion of cells and highly abundant serum proteins in blood. Our platform consists of two components, the first of which is a microfluidic mixer that mixes beads containing antibodies against the highly abundant proteins in the whole blood. This complex mixture (consisting of beads, cells, and serum proteins) is then injected into the second component of our microfluidic platform, which comprises a filter trench to capture all the cells and the beads. The size-based trapping of the cells and beads into the filter trench is significantly enhanced by leveraging additional negative dielectrophoretic forces to push the micron sized particles (cells and beads which have captured the highly abundant proteins) down into the trench, allowing the serum proteins of lower abundance to flow through. In general, dielectrophoresis using bare electrodes is incapable of producing forces beyond the low piconewton range that tend to be insufficient for separation applications. However, by using electrodes passivated with atomic layer deposition, we demonstrate the application of enhanced negative DEP electrodes together with size-based flltration induced by the filter trench, to deplete 100% of the micron sized particles in the mixture. PMID:26924893

  8. 34 CFR 200.50 - SEA review of LEA progress.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 1 2012-07-01 2012-07-01 false SEA review of LEA progress. 200.50 Section 200.50... Basic Programs Operated by Local Educational Agencies Lea and School Improvement § 200.50 SEA review of LEA progress. (a) State review. (1) An SEA must annually review the progress of each LEA in its...

  9. 34 CFR 200.50 - SEA review of LEA progress.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false SEA review of LEA progress. 200.50 Section 200.50... Basic Programs Operated by Local Educational Agencies Lea and School Improvement § 200.50 SEA review of LEA progress. (a) State review. (1) An SEA must annually review the progress of each LEA in its...

  10. 34 CFR 200.50 - SEA review of LEA progress.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 1 2013-07-01 2013-07-01 false SEA review of LEA progress. 200.50 Section 200.50... Basic Programs Operated by Local Educational Agencies Lea and School Improvement § 200.50 SEA review of LEA progress. (a) State review. (1) An SEA must annually review the progress of each LEA in its...

  11. 34 CFR 200.50 - SEA review of LEA progress.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false SEA review of LEA progress. 200.50 Section 200.50... Basic Programs Operated by Local Educational Agencies Lea and School Improvement § 200.50 SEA review of LEA progress. (a) State review. (1) An SEA must annually review the progress of each LEA in its...

  12. Protein abundance changes of Zygosaccharomyces rouxii in different sugar concentrations.

    PubMed

    Guo, Hong; Niu, Chen; Liu, Bin; Wei, JianPing; Wang, HuXuan; Yuan, YaHong; Yue, TianLi

    2016-09-16

    Zygosaccharomyces rouxii is a yeast which can cause spoilage in the concentrated juice industries. It exhibits resistance to high sugar concentrations but genome- and proteome-wide studies on Z. rouxii in response to high sugar concentrations have been poorly investigated. Herein, by using a 2-D electrophoresis based workflow, the proteome of a wild strain of Z. rouxii under different sugar concentrations has been analyzed. Proteins were extracted, quantified, and subjected to 2-DE analysis in the pH range 4-7. Differences in growth (lag phase), protein content (13.97-19.23mg/g cell dry weight) and number of resolved spots (196-296) were found between sugar concentrations. ANOVA test showed that 168 spots were different, and 47 spots, corresponding to 40 unique gene products have been identified. These protein species are involved in carbohydrate and energy metabolism, amino acid metabolism, response to stimulus, protein transport and vesicle organization, cell morphogenesis regulation, transcription and translation, nucleotide metabolism, amino-sugar nucleotide-sugar pathways, oxidoreductases balancing, and ribosome biogenesis. The present study provides important information about how Z. rouxii acts to cope with high sugar concentration at molecular levels, which might enhance our global understanding of Z. rouxii's high sugar-tolerance trait. PMID:27322723

  13. Lea County 001, an H5 chondrite, and Lea County 002, an ungrouped type 3 chondrite

    SciTech Connect

    Zolensky, M.E.; Score, R.; Clayton, R.N.; Mayeda, T.K.; Schutt, J.W. Lockheed Engineering and Sciences Co., Houston, TX Chicago Univ., IL )

    1989-12-01

    A search of active deflation basins near Jal, Lea County, New Mexico resulted in the discovery of two meteorites, Lea County 001 and 002. Lea County 001 has mean olivine and low-Ca pyroxene compositions of Fa(19) and Fs(17), respectively. These and all other mineralogical and petrological data collected indicate a classification of H5 for this stone. Lea County 002 has mean olivine and low-Ca pyroxene compositions of Fa(2) and Fs(4), and is unequilibrated. Although it is mineralogically most similar to Kakangari and chondritic clasts within Cumberland Falls, the high modal amount of forsterite makes Lea County a unique type 3 chondrite. Oxygen isotope data for Lea County 002 fall on an 0-16-mixing line through those of the enstatite meteorites and IAB irons, a feature shared by Kakangari. 28 refs.

  14. Assessment of the natural variation of low abundant metabolic proteins in soybean seeds using proteomics

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Using two-dimensional polyacrylamide gel electrophoresis and mass spectrometry, we investigated the distribution of the low abundant proteins that are involved in soybean seed development in four wild and twelve cultivated soybean genotypes. We found proteomic variation of these proteins within and...

  15. Measurement of Cysteine Dioxygenase Activity and Protein Abundance

    PubMed Central

    Stipanuk, Martha H.; Dominy, John E.; Ueki, Iori; Hirschberger, Lawrence L.

    2009-01-01

    Cysteine dioxygenase is an iron (Fe2+)-dependent thiol dioxygenase that uses molecular oxygen to oxidize the sulfhydryl group of cysteine to generate 3-sulfinoalanine (commonly called cysteinesulfinic acid). Cysteine dioxygenase activity is routinely assayed by measuring cysteinesulfinate formation from substrate L-cysteine at pH 6.1 in the presence of ferrous ions to saturate the enzyme with metal cofactor, a copper chelator to diminish substrate oxidation, and hydroxylamine to inhibit pyridoxal 5′-phosphate-dependent degradation of product. The amount of cysteine dioxygenase may be measured by immunoblotting. Upon SDS-PAGE, cysteine dioxygenase can be separated into two major bands, with the upper band representing the 23-kDa protein and the lower band representing the mature enzyme that has undergone formation of an internal thioether cross link in the active site. Formation of this cross link is dependent upon the catalytic turnover of substrate and produces an enzyme with a higher catalytic efficiency and catalytic half-life. PMID:19885389

  16. The effect of colostrum intake on blood plasma proteome profile in newborn lambs: low abundance proteins

    PubMed Central

    2014-01-01

    Background Colostrum intake by newborn lambs plays a fundamental role in the perinatal period, ensuring lamb survival. In this study, blood plasma samples from two groups of newborn lambs (Colostrum group and Delayed Colostrum group) at 2 and 14 h after birth were treated to reduce the content of high abundance proteins and analyzed using Two-Dimensional Differential in Gel Electrophoresis and MALDI MS/MS for protein identification in order to investigate low abundance proteins with immune function in newborn lambs. Results The results showed that four proteins were increased in the blood plasma of lambs due to colostrum intake. These proteins have not been previously described as increased in blood plasma of newborn ruminants by colostrum intake. Moreover, these proteins have been described as having an immune function in other species, some of which were previously identified in colostrum and milk. Conclusions In conclusion, colostrum intake modified the low abundance proteome profile of blood plasma from newborn lambs, increasing the concentration of apolipoprotein A-IV, plasminogen, serum amyloid A and fibrinogen, demonstrating that colostrum is essential, not only for the provision of immunoglobulins, but also because of increases in several low abundance proteins with immune function. PMID:24708841

  17. Depletion of the highly abundant protein albumin from human plasma using the Gradiflow.

    PubMed

    Rothemund, Deborah L; Locke, Vicki L; Liew, Audrey; Thomas, Theresa M; Wasinger, Valerie; Rylatt, Dennis B

    2003-03-01

    Analysis of complex protein samples by two-dimensional electrophoresis (2-DE) is often more difficult in the presence of a few predominant proteins. In plasma, proteins such as albumin mask proteins of lower abundance, as well as significantly limiting the amount of protein that can be loaded onto the immobilized pH gradient strip. In this paper the Gradiflow, a preparative electrophoresis system, has been used to deplete human plasma of the highly abundant protein albumin under native and denatured conditions. A three step protocol incorporating a charge separation to collect proteins with an isoelectric point greater than albumin and two size separations to isolate proteins larger and smaller than albumin, was used. When the albumin depleted fractions were analysed on pH 3-10 2-DE gels, proteins that were masked by albumin were revealed and proteins not seen in the unfractionated plasma sample were visualised. Matrix-assisted laser desorption/ionisation-time of flight mass spectrometry analysis confirmed the identification of the protein that lies beneath albumin to be C4B-binding protein alpha chain. The liquid fractions from the Gradiflow separations were also analysed by liquid chromatography-tandem mass spectrometry to confirm the proteins were separated according to their size and charge mobility in an electric field. PMID:12627381

  18. Choice of dietary protein of vegetarians and omnivores is reflected in their hair protein 13C and 15N abundance.

    PubMed

    Petzke, Klaus J; Boeing, Heiner; Metges, Cornelia C

    2005-01-01

    Stable isotopic (15N, 13C) composition of tissues depends on isotopic pattern of food sources. We investigated whether the isotopic compositions of human hair protein and amino acids reflect the habitual dietary protein intake. Hair samples were analyzed from 100 omnivores (selected randomly out of the 1987-1988 German nutrition survey VERA), and from 15 ovo-lacto-vegetarians (OLV), and from 6 vegans recruited separately. Hair bulk and amino acid specific isotopic compositions were analyzed by isotope-ratio mass spectrometry (EA/IRMS and GC/C/IRMS, respectively) and the results were correlated with data of the 7 day dietary records. Hair bulk 15N and 13C abundances clearly reflect the particular eating habits. Vegans can be distinguished from OLV and both are significantly distinct from omnivores in both 15N and 13C abundances. 15N and 13C abundances rose with a higher proportion of animal to total protein intake (PAPI). Individual proportions of animal protein consumption (IPAP) were calculated using isotopic abundances and a linear regression model using animal protein consumption data of vegans (PAPI = 0) and omnivores (mean PAPI = 0.639). IPAP values positively correlated with the intake of protein, meat, meat products, and animal protein. Distinct patterns for hair amino acid specific 15N and 13C abundances were measured but with lower resolution between food preference groups compared with bulk values. In conclusion, hair 13C and 15N values both reflected the extent of animal protein consumption. Bulk isotopic abundance of hair can be tested for future use in the validation of dietary assessment methods. PMID:15880664

  19. Genetics of single-cell protein abundance variation in large yeast populations.

    PubMed

    Albert, Frank W; Treusch, Sebastian; Shockley, Arthur H; Bloom, Joshua S; Kruglyak, Leonid

    2014-02-27

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in 'hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  20. Genetics of single-cell protein abundance variation in large yeast populations

    NASA Astrophysics Data System (ADS)

    Albert, Frank W.; Treusch, Sebastian; Shockley, Arthur H.; Bloom, Joshua S.; Kruglyak, Leonid

    2014-02-01

    Variation among individuals arises in part from differences in DNA sequences, but the genetic basis for variation in most traits, including common diseases, remains only partly understood. Many DNA variants influence phenotypes by altering the expression level of one or several genes. The effects of such variants can be detected as expression quantitative trait loci (eQTL). Traditional eQTL mapping requires large-scale genotype and gene expression data for each individual in the study sample, which limits sample sizes to hundreds of individuals in both humans and model organisms and reduces statistical power. Consequently, many eQTL are probably missed, especially those with smaller effects. Furthermore, most studies use messenger RNA rather than protein abundance as the measure of gene expression. Studies that have used mass-spectrometry proteomics reported unexpected differences between eQTL and protein QTL (pQTL) for the same genes, but these studies have been even more limited in scope. Here we introduce a powerful method for identifying genetic loci that influence protein expression in the yeast Saccharomyces cerevisiae. We measure single-cell protein abundance through the use of green fluorescent protein tags in very large populations of genetically variable cells, and use pooled sequencing to compare allele frequencies across the genome in thousands of individuals with high versus low protein abundance. We applied this method to 160 genes and detected many more loci per gene than previous studies. We also observed closer correspondence between loci that influence protein abundance and loci that influence mRNA abundance of a given gene. Most loci that we detected were clustered in `hotspots' that influence multiple proteins, and some hotspots were found to influence more than half of the proteins that we examined. The variants that underlie these hotspots have profound effects on the gene regulatory network and provide insights into genetic variation in cell

  1. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    NASA Astrophysics Data System (ADS)

    He, Yi-Ming; Ma, Bin-Guang

    2016-05-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

  2. Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

    PubMed Central

    He, Yi-Ming; Ma, Bin-Guang

    2016-01-01

    Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

  3. Natural Genetic Variation Influences Protein Abundances in C. elegans Developmental Signalling Pathways

    PubMed Central

    Singh, Kapil Dev; Roschitzki, Bernd; Snoek, L. Basten; Grossmann, Jonas; Zheng, Xue; Elvin, Mark; Kamkina, Polina; Schrimpf, Sabine P.; Poulin, Gino B.; Kammenga, Jan E.; Hengartner, Michael O.

    2016-01-01

    Complex traits, including common disease-related traits, are affected by many different genes that function in multiple pathways and networks. The apoptosis, MAPK, Notch, and Wnt signalling pathways play important roles in development and disease progression. At the moment we have a poor understanding of how allelic variation affects gene expression in these pathways at the level of translation. Here we report the effect of natural genetic variation on transcript and protein abundance involved in developmental signalling pathways in Caenorhabditis elegans. We used selected reaction monitoring to analyse proteins from the abovementioned four pathways in a set of recombinant inbred lines (RILs) generated from the wild-type strains N2 (Bristol) and CB4856 (Hawaii) to enable quantitative trait locus (QTL) mapping. About half of the cases from the 44 genes tested showed a statistically significant change in protein abundance between various strains, most of these were however very weak (below 1.3-fold change). We detected a distant QTL on the left arm of chromosome II that affected protein abundance of the phosphatidylserine receptor protein PSR-1, and two separate QTLs that influenced embryonic and ionizing radiation-induced apoptosis on chromosome IV. Our results demonstrate that natural variation in C. elegans is sufficient to cause significant changes in signalling pathways both at the gene expression (transcript and protein abundance) and phenotypic levels. PMID:26985669

  4. Visualization and Dissemination of Multidimensional Proteomics Data Comparing Protein Abundance During Caenorhabditis elegans Development

    NASA Astrophysics Data System (ADS)

    Riffle, Michael; Merrihew, Gennifer E.; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N.; Noble, William S.; MacCoss, Michael J.

    2015-11-01

    Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/.

  5. Visualization and dissemination of multidimensional proteomics data comparing protein abundance during Caenorhabditis elegans development.

    PubMed

    Riffle, Michael; Merrihew, Gennifer E; Jaschob, Daniel; Sharma, Vagisha; Davis, Trisha N; Noble, William S; MacCoss, Michael J

    2015-11-01

    Regulation of protein abundance is a critical aspect of cellular function, organism development, and aging. Alternative splicing may give rise to multiple possible proteoforms of gene products where the abundance of each proteoform is independently regulated. Understanding how the abundances of these distinct gene products change is essential to understanding the underlying mechanisms of many biological processes. Bottom-up proteomics mass spectrometry techniques may be used to estimate protein abundance indirectly by sequencing and quantifying peptides that are later mapped to proteins based on sequence. However, quantifying the abundance of distinct gene products is routinely confounded by peptides that map to multiple possible proteoforms. In this work, we describe a technique that may be used to help mitigate the effects of confounding ambiguous peptides and multiple proteoforms when quantifying proteins. We have applied this technique to visualize the distribution of distinct gene products for the whole proteome across 11 developmental stages of the model organism Caenorhabditis elegans. The result is a large multidimensional dataset for which web-based tools were developed for visualizing how translated gene products change during development and identifying possible proteoforms. The underlying instrument raw files and tandem mass spectra may also be downloaded. The data resource is freely available on the web at http://www.yeastrc.org/wormpes/ . Graphical Abstract ᅟ. PMID:26133526

  6. Evaluation of two high-abundance protein depletion kits and optimization of downstream isoelectric focusing.

    PubMed

    Qiu, Fanghua; Hou, Tieying; Huang, Dehong; Xue, Zhifeng; Liang, Dongyan; Li, Qiuming; Lin, Weimiao

    2015-11-01

    Disease biomarkers for diagnostic and prognostic purposes are most likely within an extremely low concentration range and are thus masked by the presence of high‑abundance proteins. Therefore, removing high‑abundance proteins is the main challenge for identifying disease biomarkers. In addition, the solution obtained from high‑abundance protein depletion kits contains a rich array of compounds, which interfere with isoelectric focusing (IEF). In the present study, the effect of two commercial kits was evaluated and the downstream IEF protocol was optimized. High‑resolution results could be obtained according to the following conditions: The ProteoPrep Blue Albumin and IgG Depletion kit depleted albumin and IgG; immobilized pH gradient strips (typically 18 cm) were rehydrated with sample buffer containing 250 µg serum proteins at 30 v for 6 h, 60 v for 6 h, 200 v for 2 h, 500 v for 2 h, 1,000 v for 2 h, 5,000 v for 2 h, 10,000 v for 2 h and then focusing at 10,000 v up to 110 k vhs. In addition, the protein spots identified by matrix‑assisted laser desorption ionization time‑of‑flight mass spectrometry demonstrated that all proteins had a low abundance. The present study not only provides a definite and effective method for removing high‑abundance proteins, but also provides a proper protocol (protocol C) for downstream IEF. The present study includes a comprehensive investigation of serum proteomics, which paves the way for serum protein research. PMID:26460178

  7. Determination of relative protein abundance by internally normalized ratio algorithm with antibody arrays.

    PubMed

    Andersson, Oskar; Kozlowski, Mark; Garachtchenko, Tatiana; Nikoloff, Corina; Lew, Nancy; Litman, David J; Chaga, Grigoriy

    2005-01-01

    In this paper, we report an experimental setup and mathematical algorithm for determination of relative protein abundance from directly labeled native protein samples applied to an array of antibodies. The application of the proposed experimental system compensates internally at each array element for a number of deficiencies in array experiments such as differential labeling efficiency in dual color assay systems, differential solubility of protein molecules in dual color assay systems, and differential affinity of capture reagents toward proteins labeled with two different fluorescent dyes. This system offers full compensation for variable amounts of capture reagents on separate array structures, as well as limited compensation for nonspecific interactions between capture reagents and analytes. The proposed experimental strategy enables the use of a large number of capture reagents to develop a true multiplex analysis system that will yield complete relative protein abundance information in two biological systems. PMID:15952723

  8. Mapping protein abundance patterns in the brain using voxelation combined with liquid chromatography and mass spectrometry

    SciTech Connect

    Petyuk, Vladislav A.; Qian, Weijun; Smith, Richard D.; Smith, Desmond J.

    2010-02-01

    Voxelation creates expression atlases by high-throughput analysis of spatially registered cubes or voxels harvested from the brain. The modality independence of voxelation allows a variety of bioanalytical techniques to be used to map abundance. Protein expression patterns in the brain can be obtained using liquid chromatography (LC) combined with mass spectrometry (MS). Here we describe the methodology of voxelation as it pertains particularly to LC-MS proteomic analysis: sample preparation, instrumental set up and analysis, peptide identification and protein relative abundance quantitation. We also briefly describe some of the advantages, limitations and insights into the brain that can be obtained using combined proteomic and transcriptomic maps

  9. Conservation of protein abundance patterns reveals the regulatory architecture of the EGFR-MAPK pathway.

    PubMed

    Shi, Tujin; Niepel, Mario; McDermott, Jason E; Gao, Yuqian; Nicora, Carrie D; Chrisler, William B; Markillie, Lye M; Petyuk, Vladislav A; Smith, Richard D; Rodland, Karin D; Sorger, Peter K; Qian, Wei-Jun; Wiley, H Steven

    2016-01-01

    Various genetic mutations associated with cancer are known to alter cell signaling, but it is not clear whether they dysregulate signaling pathways by altering the abundance of pathway proteins. Using a combination of RNA sequencing and ultrasensitive targeted proteomics, we defined the primary components-16 core proteins and 10 feedback regulators-of the epidermal growth factor receptor (EGFR)-mitogen-activated protein kinase (MAPK) pathway in normal human mammary epithelial cells and then quantified their absolute abundance across a panel of normal and breast cancer cell lines as well as fibroblasts. We found that core pathway proteins were present at very similar concentrations across all cell types, with a variance similar to that of proteins previously shown to display conserved abundances across species. In contrast, EGFR and transcriptionally controlled feedback regulators were present at highly variable concentrations. The absolute abundance of most core proteins was between 50,000 and 70,000 copies per cell, but the adaptors SOS1, SOS2, and GAB1 were found at far lower amounts (2000 to 5000 copies per cell). MAPK signaling showed saturation in all cells between 3000 and 10,000 occupied EGFRs, consistent with the idea that adaptors limit signaling. Our results suggest that the relative stoichiometry of core MAPK pathway proteins is very similar across different cell types, with cell-specific differences mostly restricted to variable amounts of feedback regulators and receptors. The low abundance of adaptors relative to EGFR could be responsible for previous observations that only a fraction of total cell surface EGFR is capable of rapid endocytosis, high-affinity binding, and mitogenic signaling. PMID:27405981

  10. Improvements in proteomic metrics of low abundance proteins through proteome equalization using ProteoMiner prior to MudPIT

    PubMed Central

    Fonslow, Bryan R.; Carvalho, Paulo C.; Academia, Katrina; Freeby, Steve; Xu, Tao; Nakorchevsky, Aleksey; Paulus, Aran; Yates, John R.

    2011-01-01

    Ideally shotgun proteomics would facilitate the identification of an entire proteome with 100% protein sequence coverage. In reality, the large dynamic range and complexity of cellular proteomes results in oversampling of abundant proteins, while peptides from low abundance proteins are undersampled or remain undetected. We tested the proteome equalization technology, ProteoMiner, in conjunction with Multidimensional Protein Identification Technology (MudPIT) to determine how the equalization of protein dynamic range could improve shotgun proteomics methods for the analysis of cellular proteomes. Our results suggest low abundance protein identifications were improved by two mechanisms: (1) depletion of high abundance proteins freed ion trap sampling space usually occupied by high abundance peptides and (2) enrichment of low abundance proteins increased the probability of sampling their corresponding more abundant peptides. Both mechanisms also contributed to dramatic increases in the quantity of peptides identified and the quality of MS/MS spectra acquired due to increases in precursor intensity of peptides from low abundance proteins. From our large data set of identified proteins, we categorized the dominant physicochemical factors which facilitate proteome equalization with a hexapeptide library. These results illustrate that equalization of the dynamic range of the cellular proteome is a promising methodology to improve low abundance protein identification confidence, reproducibility, and sequence coverage in shotgun proteomics experiments, opening a new avenue of research for improving proteome coverage. PMID:21702434

  11. Mining the plasma proteome for disease applications across seven logs of protein abundance.

    PubMed

    Zhang, Q; Faca, V; Hanash, S

    2011-01-01

    The current state of proteomics technologies has sufficiently advanced to allow in-depth quantitative analysis of the plasma proteome and development of a related knowledge base. Here we review approaches that have been applied to increase depth of analysis by mass spectrometry given the substantial complexity of plasma and the vast dynamic range of protein abundance. Fractionation strategies resulting in reduced complexity of individual fractions followed by mass spectrometry analysis of digests from individual fractions has allowed well in excess of 1000 proteins to be identified and quantified with high confidence that span more than seven logs of protein abundance. Such depth of analysis has contributed to elucidation of plasma proteome variation in health and of protein changes associated with disease states. PMID:21062094

  12. Hsp90 is involved in the regulation of cytosolic precursor protein abundance in tomato.

    PubMed

    Tillmann, Bodo; Röth, Sascha; Bublak, Daniela; Sommer, Manuel; Stelzer, Ernst H K; Scharf, Klaus-Dieter; Schleiff, Enrico

    2015-02-01

    Cytosolic chaperones are involved in the regulation of cellular protein homeostasis in general. Members of the families of heat stress proteins 70 (Hsp70) and 90 (Hsp90) assist the transport of preproteins to organelles such as chloroplasts or mitochondria. In addition, Hsp70 was described to be involved in the degradation of chloroplast preproteins that accumulate in the cytosol. Because a similar function has not been established for Hsp90, we analyzed the influences of Hsp90 and Hsp70 on the protein abundance in the cellular context using an in vivo system based on mesophyll protoplasts. We observed a differential behavior of preproteins with respect to the cytosolic chaperone-dependent regulation. Some preproteins such as pOE33 show a high dependence on Hsp90, whereas the abundance of preproteins such as pSSU is more strongly dependent on Hsp70. The E3 ligase, C-terminus of Hsp70-interacting protein (Chip), appears to have a more general role in the control of cytosolic protein abundance. We discuss why the different reaction modes are comparable with the cytosolic unfolded protein response. PMID:25619681

  13. 34 CFR 300.816 - Allocations to LEAs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... DISABILITIES Preschool Grants for Children with Disabilities § 300.816 Allocations to LEAs. (a) Base payments... annual child count in which the LEA reports that it is serving any children with disabilities aged...

  14. PM2, a group 3 LEA protein from soybean, and its 22-mer repeating region confer salt tolerance in Escherichia coli

    SciTech Connect

    Yun Liu; Zheng Yizhi . E-mail: yzzheng@szu.edu.cn

    2005-05-27

    To have knowledge of the effect of soybean PM2 protein in protecting dehydrated cells and its functional region, PM2 cDNA was isolated from soybean immature seeds. The recombinants expressing full-length PM2, truncated polypeptides of PM2A (aa 1-262) or PM2B (aa 129-262, 22-mer repeating region), or artificial polypeptide PM2C (duplication of 22-mer repeating region) were constructed. By using SDS-PAGE and mass spectrometry approaches, these fusion polypeptides were identified and proved to be hydrophilic and heat-stable. Spot assays of BL/PM2 and BL/pET28 (as control) showed that protein PM2 increased salt tolerance (500 mM NaCl or 500 mM KCl) of Escherichia coli, rather than osmotic tolerance (1100 mM sorbitol). In addition, comparing the survival ratios of the transformants under 500 mM NaCl or 500 mM KCl stresses, the results showed that: (1) the survival ratios of BL/PM2 and BL/PM2B were quite similar, both showing much higher values than those of BL/pET28. (2) The survival ratios of BL/PM2C were much higher than those of BL/PM2, BL/PM2A, and BL/PM2B. This provides the first experimental evidence that PM2 polypeptide enhances salt tolerance of E. coli cells, and the 22-mer repeat region is an important functional region.

  15. LDL Receptor-related Protein 1 Regulates the Abundance of Diverse Cell-signaling Proteins in the Plasma Membrane Proteome

    PubMed Central

    Gaultier, Alban; Simon, Gabriel; Niessen, Sherry; Dix, Melissa; Takimoto, Shinako; Cravatt, Benjamin F.; Gonias, Steven L.

    2010-01-01

    LDL receptor-related protein 1 (LRP1) is an endocytic receptor, reported to regulate the abundance of other receptors in the plasma membrane, including uPAR and tissue factor. The goal of this study was to identify novel plasma membrane proteins, involved in cell-signaling, which are regulated by LRP1. Membrane protein ectodomains were prepared from RAW 264.7 cells in which LRP1 was silenced and control cells using protease K. Peptides were identified by LC-MS/MS. By analysis of spectral counts, 31 transmembrane and secreted proteins were regulated in abundance at least 2-fold when LRP1 was silenced. Validation studies confirmed that semaphorin4D (Sema4D), plexin domain-containing protein-1 (Plxdc1), and neuropilin-1 were more abundant in the membranes of LRP1 gene-silenced cells. Regulation of Plxdc1 by LRP1 was confirmed in CHO cells, as a second model system. Plxdc1 co-immunoprecipitated with LRP1 from extracts of RAW 264.7 cells and mouse liver. Although Sema4D did not co-immunoprecipitate with LRP1, the cell-surface level of Sema4D was increased by RAP, which binds to LRP1 and inhibits binding of other ligands. These studies identify Plxdc1, Sema4D, and neuropilin-1 as novel LRP1-regulated cell-signaling proteins. Overall, LRP1 emerges as a generalized regulator of the plasma membrane proteome. PMID:20919742

  16. Hsp90 is involved in the regulation of cytosolic precursor protein abundance in tomato.

    PubMed

    Tillmann, Bodo; Röth, Sascha; Bublak, Daniela; Sommer, Manuel; Stelzer, Ernst H K; Scharf, Klaus-Dieter; Schleiff, Enrico

    2014-10-20

    Cytosolic chaperones are involved in the regulation of cellular protein homeostasis in general. Members of the heat stress protein 70 and 90 (Hsp70 or Hsp90) families assist the transport of preproteins to organelles such as chloroplasts or mitochondria. In addition, Hsp70 was described to be involved in the degradation of chloroplast preproteins that accumulate in the cytosol. Because a similar function has not been established for Hsp90, we analyzed the influences of Hsp90 and Hsp70 on the protein abundance in the cellular context using an in vivo system based on mesophyll protoplasts. We observed a differential behavior of preproteins in respect to the cytosolic chaperone dependent regulation. Some preproteins like pOE33 show a high dependence on Hsp90, whereas the abundance of preproteins like pSSU is more strongly dependent on Hsp70. The E3 ligase Chip appears to have a more general role in the control of cytosolic protein abundance. We discuss why the different reaction modes are comparable to the cytosolic unfolded protein response. PMID:25336566

  17. Using antibody arrays to measure protein abundance and glycosylation: considerations for optimal performance.

    PubMed

    Haab, Brian B; Partyka, Katie; Cao, Zheng

    2013-01-01

    Antibody arrays provide a valuable method for obtaining multiple protein measurements from small volumes of biological samples. Antibody arrays can be designed to target not only core protein abundances (relative or absolute abundances, depending on the availability of standards for calibration), but also posttranslational modifications, provided antibodies or other affinity reagents are available to detect them. Glycosylation is a common modification that has important and diverse functions in both normal and disease biology. Significant progress has been made in developing methods for measuring glycan levels on multiple specific proteins using antibody arrays and glycan-binding reagents. This unit describes practical approaches for developing, optimizing, and using antibody array assays to determine both protein abundance and glycosylation state. Low-volume arrays can be used to reduce sample consumption, and a new way to improve the binding strength of particular glycan-binding reagents through multimerization is discussed. These methods can be useful for a wide range of biological studies in which glycosylation may change and/or affect protein function. PMID:24510592

  18. Identification of Proteins of Altered Abundance in Oil Palm Infected with Ganoderma boninense

    PubMed Central

    Al-Obaidi, Jameel R.; Mohd-Yusuf, Yusmin; Razali, Nurhanani; Jayapalan, Jaime Jacqueline; Tey, Chin-Chong; Md-Noh, Normahnani; Junit, Sarni Mat; Othman, Rofina Yasmin; Hashim, Onn Haji

    2014-01-01

    Basal stem rot is a common disease that affects oil palm, causing loss of yield and finally killing the trees. The disease, caused by fungus Ganoderma boninense, devastates thousands of hectares of oil palm plantings in Southeast Asia every year. In the present study, root proteins of healthy oil palm seedlings, and those infected with G. boninense, were analyzed by 2-dimensional gel electrophoresis (2-DE). When the 2-DE profiles were analyzed for proteins, which exhibit consistent significant change of abundance upon infection with G. boninense, 21 passed our screening criteria. Subsequent analyses by mass spectrometry and database search identified caffeoyl-CoA O-methyltransferase, caffeic acid O-methyltransferase, enolase, fructokinase, cysteine synthase, malate dehydrogenase, and ATP synthase as among proteins of which abundances were markedly altered. PMID:24663087

  19. Hydrogel nanoparticle harvesting of plasma or urine for detecting low abundance proteins.

    PubMed

    Magni, Ruben; Espina, Benjamin H; Liotta, Lance A; Luchini, Alessandra; Espina, Virginia

    2014-01-01

    Novel biomarker discovery plays a crucial role in providing more sensitive and specific disease detection. Unfortunately many low-abundance biomarkers that exist in biological fluids cannot be easily detected with mass spectrometry or immunoassays because they are present in very low concentration, are labile, and are often masked by high-abundance proteins such as albumin or immunoglobulin. Bait containing poly(N-isopropylacrylamide) (NIPAm) based nanoparticles are able to overcome these physiological barriers. In one step they are able to capture, concentrate and preserve biomarkers from body fluids. Low-molecular weight analytes enter the core of the nanoparticle and are captured by different organic chemical dyes, which act as high affinity protein baits. The nanoparticles are able to concentrate the proteins of interest by several orders of magnitude. This concentration factor is sufficient to increase the protein level such that the proteins are within the detection limit of current mass spectrometers, western blotting, and immunoassays. Nanoparticles can be incubated with a plethora of biological fluids and they are able to greatly enrich the concentration of low-molecular weight proteins and peptides while excluding albumin and other high-molecular weight proteins. Our data show that a 10,000 fold amplification in the concentration of a particular analyte can be achieved, enabling mass spectrometry and immunoassays to detect previously undetectable biomarkers. PMID:25145492

  20. PETROPHYSICAL INVESTIGATION OF THE SECONDARY RECOVERY POTENTIAL IN THE CHERRY CANYON FORMATION NE LEA FIELD LEA COUNTY, NEW MEXICO

    SciTech Connect

    T. Scott Hickman

    2002-06-01

    Read and Stevens has proposed the evaluation of the waterflood potential from the Cherry Canyon formation in the NE Lea Field in lea County, New Mexico. Much of the development in this area is approaching primary recovery limitations; additional recovery of remaining oil reserves by waterflood needs to be evaluated. The Cherry Canyon formation is composed of fine grained sandstone, containing clay material which results in high water saturation, and also has the tendency to swell and reduce reservoir permeability--the ability of fluid to flow through the rock pores and fractures. There are also abundant organic materials that interfere with obtaining reliable well logs. These complications have limited oil in place calculations and identification of net pay zones, presenting a challenge to the planned waterflood. Core analysis of the Cherry Canyon should improve the understanding of existing well logs and possibly indicate secondary recovery measures, such as waterflood, to enhance field recovery. Lacking truly representative core to provide accurate analyses, Read and Stevens will obtain and preserve fresh core. The consulting firm of T. Scott Hickman and Associates will then collaborate on special core analyses and obtain additional well logs for a more detailed analysis of reservoir properties. The log interpretation will be compared to the core analysis results, and the entire collected data set will be used to assess the potential and economic viability of successfully waterflooding the identified oil zones. Successful results from the project will improve accuracy of log interpretation and establish a methodology for evaluating secondary recovery by waterflood.

  1. Trans-splicing Into Highly Abundant Albumin Transcripts for Production of Therapeutic Proteins In Vivo

    PubMed Central

    Wang, Jun; Mansfield, S Gary; Cote, Colette A; Jiang, Ping Du; Weng, Ke; Amar, Marcelo JA; Brewer, Bryan H; Remaley, Alan T; McGarrity, Gerard J; Garcia-Blanco, Mariano A; Puttaraju, M

    2008-01-01

    Spliceosome-mediated RNA trans-splicing has emerged as an exciting mode of RNA therapy. Here we describe a novel trans-splicing strategy, which targets highly abundant pre-mRNAs, to produce therapeutic proteins in vivo. First, we used a pre-trans-splicing molecule (PTM) that mediated trans-splicing of human apolipoprotein A-I (hapoA-I) into the highly abundant mouse albumin exon 1. Hydrodynamic tail vein injection of the hapoA-I PTM plasmid in mice followed by analysis of the chimeric transcripts and protein, confirmed accurate and efficient trans-splicing into albumin pre-mRNA and production of hapoA-I protein. The versatility of this approach was demonstrated by producing functional human papillomavirus type-16 E7 (HPV16-E7) single-chain antibody in C57BL/6 mice and functional factor VIII (FVIII) and phenotypic correction in hemophilia A mice. Altogether, these studies demonstrate that trans-splicing to highly abundant albumin transcripts can be used as a general platform to produce therapeutic proteins in vivo. PMID:19066600

  2. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer.

    PubMed

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease. PMID:27453073

  3. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer

    PubMed Central

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease. PMID:27453073

  4. Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine

    PubMed Central

    Filip, Szymon; Vougas, Konstantinos; Zoidakis, Jerome; Latosinska, Agnieszka; Mullen, William; Spasovski, Goce; Mischak, Harald; Vlahou, Antonia; Jankowski, Joachim

    2015-01-01

    Proteome analysis of complex biological samples for biomarker identification remains challenging, among others due to the extended range of protein concentrations. High-abundance proteins like albumin or IgG of plasma and urine, may interfere with the detection of potential disease biomarkers. Currently, several options are available for the depletion of abundant proteins in plasma. However, the applicability of these methods in urine has not been thoroughly investigated. In this study, we compared different, commercially available immunodepletion and ion-exchange based approaches on urine samples from both healthy subjects and CKD patients, for their reproducibility and efficiency in protein depletion. A starting urine volume of 500 μL was used to simulate conditions of a multi-institutional biomarker discovery study. All depletion approaches showed satisfactory reproducibility (n=5) in protein identification as well as protein abundance. Comparison of the depletion efficiency between the unfractionated and fractionated samples and the different depletion strategies, showed efficient depletion in all cases, with the exception of the ion-exchange kit. The depletion efficiency was found slightly higher in normal than in CKD samples and normal samples yielded more protein identifications than CKD samples when using both initial as well as corresponding depleted fractions. Along these lines, decrease in the amount of albumin and other targets as applicable, following depletion, was observed. Nevertheless, these depletion strategies did not yield a higher number of identifications in neither the urine from normal nor CKD patients. Collectively, when analyzing urine in the context of CKD biomarker identification, no added value of depletion strategies can be observed and analysis of unfractionated starting urine appears to be preferable. PMID:26208298

  5. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells

    PubMed Central

    Barati, Michelle T.; Gould, James C.; Salyer, Sarah A.; Isaacs, Susan; Wilkey, Daniel W.; Merchant, Michael L.

    2016-01-01

    The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG⁎) conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1) proteins involved in cell survival/cell signaling and (2) proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB), supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase), suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis. PMID:26839892

  6. Influence of Acute High Glucose on Protein Abundance Changes in Murine Glomerular Mesangial Cells.

    PubMed

    Barati, Michelle T; Gould, James C; Salyer, Sarah A; Isaacs, Susan; Wilkey, Daniel W; Merchant, Michael L

    2016-01-01

    The effects of acute exposure to high glucose levels as experienced by glomerular mesangial cells in postprandial conditions and states such as in prediabetes were investigated using proteomic methods. Two-dimensional gel electrophoresis and matrix assisted laser desorption ionization time of flight mass spectrometry methods were used to identify protein expression patterns in immortalized rat mesangial cells altered by 2 h high glucose (HG) growth conditions as compared to isoosmotic/normal glucose control (NG(⁎)) conditions. Unique protein expression changes at 2 h HG treatment were measured for 51 protein spots. These proteins could be broadly grouped into two categories: (1) proteins involved in cell survival/cell signaling and (2) proteins involved in stress response. Immunoblot experiments for a protein belonging to both categories, prohibitin (PHB), supported a trend for increased total expression as well as significant increases in an acidic PHB isoform. Additional studies confirmed the regulation of proteasomal subunit alpha-type 2 and the endoplasmic reticulum chaperone and oxidoreductase PDI (protein disulfide isomerase), suggesting altered ER protein folding capacity and proteasomal function in response to acute HG. We conclude that short term high glucose induces subtle changes in protein abundances suggesting posttranslational modifications and regulation of pathways involved in proteostasis. PMID:26839892

  7. Mature adipocyte proteome reveals differentially altered protein abundances between lean, overweight and morbidly obese human subjects.

    PubMed

    Benabdelkamel, Hicham; Masood, Afshan; Almidani, Ghaith M; Alsadhan, Abdulmajeed A; Bassas, Abdulelah F; Duncan, Mark W; Alfadda, Assim A

    2015-02-01

    Overweight (OW) and obese individuals are considered to be graded parts of the scale having increasing weight as a common feature. They may not, however, be part of the same continuum and may differ metabolically. In this study we applied an untargeted proteomic approach to compare protein abundances in mature adipocytes derived from the subcutaneous adipose tissue of overweight and morbidly obese female subjects to those of lean age matched controls. Mature adipocytes were isolated from liposuction samples of abdominal subcutaneous adipose tissue collected from both lean (L; n = 7, 23.3 ± 0.4 kg/m(2); mean BMI ± SD), overweight (OW; n = 8, 27.9 ± 0.6 kg/m(2); mean BMI ± SD) and morbidly obese (MOB; n = 7, 44.8 ± 3.8 kg/m(2); mean BMI ± SD) individuals. Total protein extracts were then compared by two-dimensional difference in gel electrophoresis (2D DIGE). One hundred and ten differentially expressed protein spots (i.e., fitting the statistical criteria ANOVA test, p < 0.05; fold-change ≥1.5) were detected, and of these, 89 were identified by MALDI-TOF mass spectrometry. Of these, 66 protein spots were common to both groups whereas 23 were unique to the MOB group. Significant differences were evident in the abundances of key proteins involved in glucose and lipid metabolism, energy regulation, cytoskeletal structure and redox control signaling pathways. Differences in the abundance of some chaperones were also evident. The differentially abundant proteins were investigated using Ingenuity Pathway Analysis (IPA) to establish their associations with known biological functions. The network identified in the OW group with the highest score relates to-: cell-to-cell signaling and interaction; in contrast, in the MOB group the major interacting pathways are associated with lipid metabolism, small molecule biochemistry and cancer. The differences in abundance of the differentially regulated proteins were validated by

  8. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed.

    PubMed

    Rocca, Jennifer D; Hall, Edward K; Lennon, Jay T; Evans, Sarah E; Waldrop, Mark P; Cotner, James B; Nemergut, Diana R; Graham, Emily B; Wallenstein, Matthew D

    2015-08-01

    For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes. PMID:25535936

  9. Relationships between protein-encoding gene abundance and corresponding process are commonly assumed yet rarely observed

    PubMed Central

    Rocca, Jennifer D; Hall, Edward K; Lennon, Jay T; Evans, Sarah E; Waldrop, Mark P; Cotner, James B; Nemergut, Diana R; Graham, Emily B; Wallenstein, Matthew D

    2015-01-01

    For any enzyme-catalyzed reaction to occur, the corresponding protein-encoding genes and transcripts are necessary prerequisites. Thus, a positive relationship between the abundance of gene or transcripts and corresponding process rates is often assumed. To test this assumption, we conducted a meta-analysis of the relationships between gene and/or transcript abundances and corresponding process rates. We identified 415 studies that quantified the abundance of genes or transcripts for enzymes involved in carbon or nitrogen cycling. However, in only 59 of these manuscripts did the authors report both gene or transcript abundance and rates of the appropriate process. We found that within studies there was a significant but weak positive relationship between gene abundance and the corresponding process. Correlations were not strengthened by accounting for habitat type, differences among genes or reaction products versus reactants, suggesting that other ecological and methodological factors may affect the strength of this relationship. Our findings highlight the need for fundamental research on the factors that control transcription, translation and enzyme function in natural systems to better link genomic and transcriptomic data to ecosystem processes. PMID:25535936

  10. LEA Title VII Program Evaluations. Panel Presentations.

    ERIC Educational Resources Information Center

    Balu, Raj

    These panel presentations focus on LEA Title VII Program Evaluations. Raj Balu, an administrator of bilingual programs in Chicago presents information regarding the bilingual education program in the Chicago public schools, as well as information on Title VII programs and what kind of evaluation is being done. Jesus Salazar, who is currently…

  11. 34 CFR 200.71 - LEA eligibility.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false LEA eligibility. 200.71 Section 200.71 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT OF EDUCATION TITLE I-IMPROVING THE ACADEMIC ACHIEVEMENT OF THE DISADVANTAGED Improving...

  12. 34 CFR 200.52 - LEA improvement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... academic achievement standards; (iii) Address the professional development needs of the instructional staff serving the LEA by committing to spend for professional development not less than 10 percent of the funds... for improvement. These funds— (A) May include funds reserved by schools for professional...

  13. Depletion of abundant plant RuBisCO protein using the protamine sulfate precipitation method.

    PubMed

    Kim, Yu Ji; Lee, Hye Min; Wang, Yiming; Wu, Jingni; Kim, Sang Gon; Kang, Kyu Young; Park, Ki Hun; Kim, Yong Chul; Choi, In Soo; Agrawal, Ganesh Kumar; Rakwal, Randeep; Kim, Sun Tae

    2013-07-01

    Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is the most abundant plant leaf protein, hampering deep analysis of the leaf proteome. Here, we describe a novel protamine sulfate precipitation (PSP) method for the depletion of RuBisCO. For this purpose, soybean leaf total proteins were extracted using Tris-Mg/NP-40 extraction buffer. Obtained clear supernatant was subjected to the PSP method, followed by 13% SDS-PAGE analysis of total, PS-supernatant and -precipitation derived protein samples. In a dose-dependent experiment, 0.1% w/v PS was found to be sufficient for precipitating RuBisCO large and small subunits (LSU and SSU). Western blot analysis confirmed no detection of RuBisCO LSU in the PS-supernatant proteins. Application of this method to Arabidopsis, rice, and maize leaf proteins revealed results similar to soybean. Furthermore, 2DE analyses of PS-treated soybean leaf displayed enriched protein profile for the protein sample derived from the PS-supernatant than total proteins. Some enriched 2D spots were subjected to MALDI-TOF-TOF analysis and were successfully assigned for their protein identity. Hence, the PSP method is: (i) simple, fast, economical, and reproducible for RuBisCO precipitation from the plant leaf sample; (ii) applicable to both dicot and monocot plants; and (iii) suitable for downstream proteomics analysis. PMID:23576416

  14. Changes in protein abundance are observed in bacterial isolates from a natural host

    PubMed Central

    Rees, Megan A.; Stinear, Timothy P.; Goode, Robert J. A.; Coppel, Ross L.; Smith, Alexander I.; Kleifeld, Oded

    2015-01-01

    Bacterial proteomic studies frequently use strains cultured in synthetic liquid media over many generations. It is uncertain whether bacterial proteins expressed under these conditions will be the same as the repertoire found in natural environments, or when bacteria are infecting a host organism. Thus, genomic and proteomic characterization of bacteria derived from the host environment in comparison to reference strains grown in the lab, should aid understanding of pathogenesis. Isolates of Corynebacterium pseudotuberculosis were obtained from the lymph nodes of three naturally infected sheep and compared to a laboratory reference strain using bottom-up proteomics, after whole genome sequencing of each of the field isolates. These comparisons were performed following growth in liquid media that allowed us to reach the required protein amount for proteomic analysis. Over 1350 proteins were identified in the isolated strains, from which unique proteome features were revealed. Several of the identified proteins demonstrated a significant abundance difference in the field isolates compared to the reference strain even though there were no obvious differences in the DNA sequence of the corresponding gene or in nearby non-coding DNA. Higher abundance in the field isolates was observed for proteins related to hypoxia and nutrient deficiency responses as well as to thiopeptide biosynthesis. PMID:26528441

  15. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces.

    PubMed

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota. PMID:27042829

  16. Intake of Meat Proteins Substantially Increased the Relative Abundance of Genus Lactobacillus in Rat Feces

    PubMed Central

    Zhu, Yingying; Lin, Xisha; Li, He; Li, Yingqiu; Shi, Xuebin; Zhao, Fan; Xu, Xinglian; Li, Chunbao; Zhou, Guanghong

    2016-01-01

    Diet has been shown to have a critical influence on gut bacteria and host health, and high levels of red meat in diet have been shown to increase colonic DNA damage and thus be harmful to gut health. However, previous studies focused more on the effects of meat than of meat proteins. In order to investigate whether intake of meat proteins affects the composition and metabolic activities of gut microbiota, feces were collected from growing rats that were fed with either meat proteins (from beef, pork or fish) or non-meat proteins (casein or soy) for 14 days. The resulting composition of gut microbiota was profiled by sequencing the V4-V5 region of the 16S ribosomal RNA genes and the short chain fatty acids (SCFAs) were analyzed using gas chromatography. The composition of gut microbiota and SCFA levels were significantly different between the five diet groups. At a recommended dose of 20% protein in the diet, meat protein-fed rats had a higher relative abundance of the beneficial genus Lactobacillus, but lower levels of SCFAs and SCFA-producing bacteria including Fusobacterium, Bacteroides and Prevotella, compared with the soy protein-fed group. Further work is needed on the regulatory pathways linking dietary protein intake to gut microbiota. PMID:27042829

  17. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast.

    PubMed

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-08-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis. PMID:25971257

  18. A Systems Approach to Elucidate Heterosis of Protein Abundances in Yeast*

    PubMed Central

    Blein-Nicolas, Mélisande; Albertin, Warren; da Silva, Telma; Valot, Benoît; Balliau, Thierry; Masneuf-Pomarède, Isabelle; Bely, Marina; Marullo, Philippe; Sicard, Delphine; Dillmann, Christine; de Vienne, Dominique; Zivy, Michel

    2015-01-01

    Heterosis is a universal phenomenon that has major implications in evolution and is of tremendous agro-economic value. To study the molecular manifestations of heterosis and to find factors that maximize its strength, we implemented a large-scale proteomic experiment in yeast. We analyzed the inheritance of 1,396 proteins in 55 inter- and intraspecific hybrids obtained from Saccharomyces cerevisiae and S. uvarum that were grown in grape juice at two temperatures. We showed that the proportion of heterotic proteins was highly variable depending on the parental strain and on the temperature considered. For intraspecific hybrids, this proportion was higher at nonoptimal temperature. Unexpectedly, heterosis for protein abundance was strongly biased toward positive values in interspecific hybrids but not in intraspecific hybrids. Computer modeling showed that this observation could be accounted for by assuming concave relationships between protein abundances and their controlling factors, in line with the metabolic model of heterosis. These results point to nonlinear processes that could play a central role in heterosis. PMID:25971257

  19. Exoproteome analysis reveals higher abundance of proteins linked to alkaline stress in persistent Listeria monocytogenes strains.

    PubMed

    Rychli, Kathrin; Grunert, Tom; Ciolacu, Luminita; Zaiser, Andreas; Razzazi-Fazeli, Ebrahim; Schmitz-Esser, Stephan; Ehling-Schulz, Monika; Wagner, Martin

    2016-02-01

    The foodborne pathogen Listeria monocytogenes, responsible for listeriosis a rare but severe infection disease, can survive in the food processing environment for month or even years. So-called persistent L. monocytogenes strains greatly increase the risk of (re)contamination of food products, and are therefore a great challenge for food safety. However, our understanding of the mechanism underlying persistence is still fragmented. In this study we compared the exoproteome of three persistent strains with the reference strain EGDe under mild stress conditions using 2D differential gel electrophoresis. Principal component analysis including all differentially abundant protein spots showed that the exoproteome of strain EGDe (sequence type (ST) 35) is distinct from that of the persistent strain R479a (ST8) and the two closely related ST121 strains 4423 and 6179. Phylogenetic analyses based on multilocus ST genes showed similar grouping of the strains. Comparing the exoproteome of strain EGDe and the three persistent strains resulted in identification of 22 differentially expressed protein spots corresponding to 16 proteins. Six proteins were significantly increased in the persistent L. monocytogenes exoproteomes, among them proteins involved in alkaline stress response (e.g. the membrane anchored lipoprotein Lmo2637 and the NADPH dehydrogenase NamA). In parallel the persistent strains showed increased survival under alkaline stress, which is often provided during cleaning and disinfection in the food processing environments. In addition, gene expression of the proteins linked to stress response (Lmo2637, NamA, Fhs and QoxA) was higher in the persistent strain not only at 37 °C but also at 10 °C. Invasion efficiency of EGDe was higher in intestinal epithelial Caco2 and macrophage-like THP1 cells compared to the persistent strains. Concurrently we found higher expression of proteins involved in virulence in EGDe e.g. the actin-assembly-inducing protein ActA and the

  20. 34 CFR 76.799 - Do the requirements in this subpart apply to LEAs?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...? (a) Each LEA that is responsible for funding a charter school under a covered program must comply..., and 76.787) to LEAs, references to SEA (or State), charter school LEA, and LEA must be read as references to LEA, charter school, and public school, respectively. (Authority: 20 U.S.C. 8065a)...

  1. 34 CFR 76.799 - Do the requirements in this subpart apply to LEAs?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...? (a) Each LEA that is responsible for funding a charter school under a covered program must comply..., and 76.787) to LEAs, references to SEA (or State), charter school LEA, and LEA must be read as references to LEA, charter school, and public school, respectively. (Authority: 20 U.S.C. 8065a)...

  2. 34 CFR 76.799 - Do the requirements in this subpart apply to LEAs?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...? (a) Each LEA that is responsible for funding a charter school under a covered program must comply..., and 76.787) to LEAs, references to SEA (or State), charter school LEA, and LEA must be read as references to LEA, charter school, and public school, respectively. (Authority: 20 U.S.C. 8065a)...

  3. 34 CFR 76.799 - Do the requirements in this subpart apply to LEAs?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...? (a) Each LEA that is responsible for funding a charter school under a covered program must comply..., and 76.787) to LEAs, references to SEA (or State), charter school LEA, and LEA must be read as references to LEA, charter school, and public school, respectively. (Authority: 20 U.S.C. 8065a)...

  4. 34 CFR 76.799 - Do the requirements in this subpart apply to LEAs?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ...? (a) Each LEA that is responsible for funding a charter school under a covered program must comply..., and 76.787) to LEAs, references to SEA (or State), charter school LEA, and LEA must be read as references to LEA, charter school, and public school, respectively. (Authority: 20 U.S.C. 8065a)...

  5. Mass Spectrometry and Next-Generation Sequencing Reveal an Abundant and Rapidly Evolving Abalone Sperm Protein

    PubMed Central

    Palmer, Melody R.; McDowall, Margo H.; Stewart, Lia; Ouaddi, Aleena; MacCoss, Michael J.; Swanson, Willie J.

    2014-01-01

    SUMMARY Abalone, a broadcast spawning marine mollusk, is an important model for molecular interactions and positive selection in fertilization, but the focus has previously been on only two sperm proteins, lysin and sp18.We used genomic and proteomic techniques to bring new insights to this model by characterizing the testis transcriptome and sperm proteome of the Red abalone Haliotis rufescens. One pair of homologous, testis-specific proteins contains a secretion signal and is small, abundant, and associated with the acrosome. Comparative analysis revealed that homologs are extremely divergent between species, and show strong evidence for positive selection. The acrosomal localization and rapid evolution of these proteins indicates that they play an important role in fertilization, and could be involved in the species-specificity of sperm-egg interactions in abalone. Our genomic and proteomic characterization of abalone fertilization resulted in the identification of interesting, novel peptides that have eluded detection in this important model system for 20 years. PMID:23585193

  6. Changes in Relative Thylakoid Protein Abundance Induced by Fluctuating Light in the Diatom Thalassiosira pseudonana.

    PubMed

    Grouneva, Irina; Muth-Pawlak, Dorota; Battchikova, Natalia; Aro, Eva-Mari

    2016-05-01

    One of the hallmarks of marine diatom biology is their ability to cope with rapid changes in light availability due to mixing of the water column and the lens effect. We investigated how irradiance fluctuations influence the relative abundance of key photosynthetic proteins in the centric diatom Thalassiosira pseudonana by means of mass-spectrometry-based approaches for relative protein quantitation. Most notably, fluctuating-light conditions lead to a substantial overall up-regulation of light-harvesting complex proteins as well as several subunits of photosystems II and I. Despite an initial delay in growth under FL, there were no indications of FL-induced photosynthesis limitation, in contrast to other photosynthetic organisms. Our findings further strengthen the notion that diatoms use a qualitatively different mechanism of photosynthetic regulation in which chloroplast-mitochondria interaction has overtaken crucial regulatory processes of photosynthetic light reactions that are typical for the survival of land plants, green algae, and cyanobacteria. PMID:27025989

  7. Three abundant germ line-specific transcripts in Volvox carteri encode photosynthetic proteins.

    PubMed

    Choi, G; Przybylska, M; Straus, D

    1996-09-01

    Volvox carteri is a multicellular eukaryotic green alga composed of about 2000 cells of only two differentiated types: somatic and germ line. To understand how embryonic cells are assigned either to somatic or germ line fates, we are investigating the regulation of transcripts that are abundant in only one cell type. Here we report the identity of three transcripts that are coordinately expressed at high levels in germ line cells but not in somatic cells. Surprisingly, all three transcripts encode photosynthetic chloroplast proteins (light-harvesting complex protein, oxygen-evolving enhancer protein 3, and ferredoxin-NADP+ reductase) that are transcribed from nuclear genes. We discuss why these mRNAs might be required at high levels in germ line cells and present a hypothesis, suggested by our results, on the evolution of cell specialization in the Volvocales. PMID:8781179

  8. Protein Abundance Changes and Ubiquitylation Targets Identified after Inhibition of the Proteasome with Syringolin A*

    PubMed Central

    Svozil, Julia; Hirsch-Hoffmann, Matthias; Dudler, Robert; Gruissem, Wilhelm; Baerenfaller, Katja

    2014-01-01

    As proteins are the main effectors inside cells, their levels need to be tightly regulated. This is partly achieved by specific protein degradation via the Ubiquitin-26S proteasome system (UPS). In plants, an exceptionally high number of proteins are involved in Ubiquitin-26S proteasome system-mediated protein degradation and it is known to regulate most, if not all, important cellular processes. Here, we investigated the response to the inhibition of the proteasome at the protein level treating leaves with the specific inhibitor Syringolin A (SylA) in a daytime specific manner and found 109 accumulated and 140 decreased proteins. The patterns of protein level changes indicate that the accumulating proteins cause proteotoxic stress that triggers various responses. Comparing protein level changes in SylA treated with those in a transgenic line over-expressing a mutated ubiquitin unable to form polyubiquitylated proteins produced little overlap pointing to different response pathways. To distinguish between direct and indirect targets of the UPS we also enriched and identified ubiquitylated proteins after inhibition of the proteasome, revealing a total of 1791 ubiquitylated proteins in leaves and roots and 1209 that were uniquely identified in our study. The comparison of the ubiquitylated proteins with those changing in abundance after SylA-mediated inhibition of the proteasome confirmed the complexity of the response and revealed that some proteins are regulated both at transcriptional and post-transcriptional level. For the ubiquitylated proteins that accumulate in the cytoplasm but are targeted to the plastid or the mitochondrion, we often found peptides in their target sequences, demonstrating that the UPS is involved in controlling organellar protein levels. Attempts to identify the sites of ubiquitylation revealed that the specific properties of this post-translational modification can lead to incorrect peptide spectrum assignments in complex peptide mixtures

  9. Isolation and characterization of haemoporin, an abundant haemolymph protein from Aplysia californica.

    PubMed Central

    Jaenicke, Elmar; Walsh, Patrick J; Decker, Heinz

    2003-01-01

    In the present study, we show the isolation and characterization of the protein haemoporin, which constitutes the second most abundant protein fraction in the haemolymph of the marine gastropod Aplysia californica. Although Aplysia is commonly used to investigate the molecular basis of learning, not much is known about the proteins in its haemolymph, which is in contact with the neurons owing to the open circulatory system of molluscs. In the native state, haemoporin is a macromolecular complex forming a cylinder with a central solvent-filled pore. The native complex most probably is a homopentamer made up from 70 kDa subunits with a molecular mass of 360 kDa and a sedimentation coefficient of 11.7 S. Prediction of the secondary structure by CD spectroscopy revealed that haemoporin contains 36% alpha-helices and 19% beta-strands. An absorption band in the 300-400 nm region indicates that haemoporin probably contains a bound substance. Haemoporin also contains a below average amount of tryptophan as evident from absorption and fluorescence spectra. The specific absorption coefficient at 280 nm (a (280 nm, 1 mg/ml)) varies between 0.42 and 0.59 l x g(-1) x cm(-1) depending on the method. The function of the protein is not yet known, but there are structural parallels between haemoporin and a pore protein reported previously in the haemolymph of another marine gastropod Megathura crenulata. The alanine-rich N-terminal sequence (AAVPEAAAEATAEAAPVSEF) is unique among protein sequences and indicates an alpha-helical structure. Whereas one side of the helix is hydrophobic and faces the interior of the protein, the other side contains a glutamic cluster, which may form the channel of the pore in the quaternary structure. Thus both proteins might belong to a new class of haemolymph proteins present in the haemolymph of marine gastropods. PMID:12889987

  10. The highly abundant protein Ag-lbp55 from Ascaridia galli represents a novel type of lipid-binding proteins.

    PubMed

    Jordanova, Rositsa; Radoslavov, Georgi; Fischer, Peter; Torda, Andrew; Lottspeich, Friedrich; Boteva, Raina; Walter, Rolf D; Bankov, Ilia; Liebau, Eva

    2005-12-16

    Lipid-binding proteins exhibit important functions in lipid transport, cellular signaling, gene transcription, and cytoprotection. Their functional analogues in nematodes are nematode polyprotein allergens/antigens and fatty acid and retinoid-binding proteins. This work describes a novel 55-kDa protein, Ag-lbp55, purified from the parasitic nematode Ascaridia galli. By direct N-terminal sequencing, a partial amino acid sequence was obtained that allowed the design of oligonucleotide primers to obtain the full-length cDNA sequence. Sequence analysis revealed the presence of an N-terminal signal peptide of 25 amino acid residues and a FAR domain at the C terminus. Data base searches showed almost no significant homologies to other described proteins. The secondary structure of Ag-lbp55 was predominantly alpha-helical (65%) as shown by CD spectroscopy. It was found to bind with high affinity fatty acids (caprylic, oleic, and palmitic acid) and their fluorescent analogue dansylaminoundecanic acid. Immunolocalization showed that Ag-lbp55 is a highly abundant protein, mainly distributed in the inner hypodermis and extracellularly in the pseudocoelomatic fluid. A similar staining pattern was observed in other pathogenic nematodes, indicating the existence of similar proteins in these species. PMID:16210327

  11. Ultrasensitive Detection of Low-Abundance Protein Biomarkers by Mass Spectrometry Signal Amplification Assay.

    PubMed

    Du, Ruijun; Zhu, Lina; Gan, Jinrui; Wang, Yuning; Qiao, Liang; Liu, Baohong

    2016-07-01

    A mass spectrometry signal amplification method is developed for the ultrasensitive and selective detection of low-abundance protein biomarkers by utilizing tag molecules on gold nanoparticles (AuNPs). EpCAM and thrombin as model targets are captured by specific aptamers immobilized on the AuNPs. With laser desorption/ionization time-of-flight mass spectrometry (LDI-TOF MS), the mass tag molecules are detected to represent the protein biomarkers. Benefiting from the MS signal amplification, the assay can achieve a limit of detection of 100 aM. The method is further applied to detect thrombin in fetal bovine serum and EpCAM in cell lysates to demonstrate its selectivity and feasibility in complex biological samples. With the high sensitivity and specificity, the protocol shows great promise for providing a new route to single-cell analysis and early disease diagnosis. PMID:27253396

  12. Spatial Mapping of Protein Abundances in the Mouse Brain by Voxelation Integrated with High-Throughput Liquid Chromatography - Mass Spectrometry

    SciTech Connect

    Petyuk, Vladislav A; Qian, Weijun; Chin, Mark H; Wang, Haixing H; Livesay, Eric A; Monroe, Matthew E; Adkins, Joshua N; Jaitly, Navdeep; Anderson, David J; Camp, David G; Smith, Desmond J; Smith, Richard D

    2007-01-25

    Temporally and spatially resolved mapping of protein abundance patterns within the mammalian brain is of significant interest for understanding brain function and molecular etiologies of neurodegenerative diseases; however, such imaging efforts have been greatly challenged by complexity of the proteome, throughput and sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Here, we describe a methodology for comprehensive spatial proteome mapping that addresses these challenges by employing voxelation integrated with automated microscale sample processing, high-throughput LC system coupled with high resolution Fourier transform ion cyclotron mass spectrometer and a “universal” stable isotope labeled reference sample approach for robust quantitation. We applied this methodology as a proof-of-concept trial for the analysis of protein distribution within a single coronal slice of a C57BL/6J mouse brain. For relative quantitation of the protein abundances across the slice, an 18O-isotopically labeled reference sample, derived from a whole control coronal slice from another mouse, was spiked into each voxel sample and stable isotopic intensity ratios were used to obtain measures of relative protein abundances. In total, we generated maps of protein abundance patterns for 1,028 proteins. The significant agreement of the protein distributions with previously reported data supports the validity of this methodology, which opens new opportunities for studying the spatial brain proteome and its dynamics during the course of disease progression and other important biological and associated health aspects in a discovery-driven fashion.

  13. Identification and cDNA cloning of a protein abundantly expressed during apple fruit development.

    PubMed

    Yamada, K; Mori, H; Yamaki, S

    1999-02-01

    A 60 kDa protein (MF-60) abundantly appearing in matured apple fruit was detected by SDS-PAGE of the soluble protein. It was partially purified through Butyl-Toyopearl and DEAE-cellulose. Its partial amino acid sequences were determined to isolate a full-length cDNA. MF-60 cDNA (mf-60) consisting of 1,825 bp containing an open reading frame of 1,524 bp and encoding a 54.2 kDa polypeptide. The deduced polypeptide of mf-60 has 81.1% identity to turgor-responsive protein 26 g from wilted garden pea shoot. Northern blot and Western blot analyses showed that the levels of the protein and the transcript of MF-60 changed in parallel through the developmental season; they were very low in young fruit at 36 DAF and 60 DAF, started to increase at 85 DAF, and then remained at a higher level from 114 DAF to 176 DAF. These results suggested that MF-60 functions are connected with fruit development but not with the fruit ripening induced by ethylene. PMID:10202815

  14. Differential Gene Expression and Protein Abundance Evince Ontogenetic Bias toward Castes in a Primitively Eusocial Wasp

    PubMed Central

    Hunt, James H.; Wolschin, Florian; Henshaw, Michael T.; Newman, Thomas C.; Toth, Amy L.; Amdam, Gro V.

    2010-01-01

    Polistes paper wasps are models for understanding conditions that may have characterized the origin of worker and queen castes and, therefore, the origin of paper wasp sociality. Polistes is “primitively eusocial” by virtue of having context-dependent caste determination and no morphological differences between castes. Even so, Polistes colonies have a temporal pattern in which most female larvae reared by the foundress become workers, and most reared by workers become future-reproductive gynes. This pattern is hypothesized to reflect development onto two pathways, which may utilize mechanisms that regulate diapause in other insects. Using expressed sequence tags (ESTs) for Polistes metricus we selected candidate genes differentially expressed in other insects in three categories: 1) diapause vs. non-diapause phenotypes and/or worker vs. queen differentiation, 2) behavioral subcastes of worker honey bees, and 3) no a priori expectation of a role in worker/gyne development. We also used a non-targeted proteomics screen to test for peptide/protein abundance differences that could reflect larval developmental divergence. We found that foundress-reared larvae (putative worker-destined) and worker-reared larvae (putative gyne-destined) differed in quantitative expression of sixteen genes, twelve of which were associated with caste and/or diapause in other insects, and they also differed in abundance of nine peptides/proteins. Some differentially-expressed genes are involved in diapause regulation in other insects, and other differentially-expressed genes and proteins are involved in the insulin signaling pathway, nutrient metabolism, and caste determination in highly social bees. Differential expression of a gene and a peptide encoding hexameric storage proteins is especially noteworthy. Although not conclusive, our results support hypotheses of 1) larval developmental pathway divergence that can lead to caste bias in adults and 2) nutritional differences as the

  15. Continuing Professional Development for LEA Staff. FEU Bulletin No. 1.

    ERIC Educational Resources Information Center

    Further Education Unit, London (England).

    Objectives of the ongoing Continuing Professional Development for Local Education Authority (LEA) project in the United Kingdom are to enhance the skills of LEA staff by defining the future education curriculum, exploring definitions of quality, developing a program of continuing professional development (CPD) for curriculum managers at the LEA…

  16. Beginning to Read in English the LEA Way.

    ERIC Educational Resources Information Center

    Rigg, Pat

    The language experience approach (LEA) has been used successfully with students who are beginning to read in English as a second language. In an LEA lesson the teacher can elicit students' comments on a wordless picture book, transcribe students' sentences, read the resultant story aloud (or have the class read it), and have the story copied.…

  17. 34 CFR 300.817 - Reallocation of LEA funds.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... carryover period in 34 CFR 76.709, whether the LEA has obligated the funds. The SEA may reallocate any of... 34 Education 2 2010-07-01 2010-07-01 false Reallocation of LEA funds. 300.817 Section 300.817 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL...

  18. Not Just Location: LEAs and Inequalities among Schools

    ERIC Educational Resources Information Center

    Yair, Gad

    2005-01-01

    Purpose: With growing decentralization, local education authorities (LEAs) face new tasks and responsibilities in providing schools with administrative services and resources. This study aims to use a multilevel framework to assess the extent to which LEAs differentially affect the provision of resources and administrative services to schools, and…

  19. Proteome analysis of abundant proteins extracted from the leaf of Gynura procumbens (Lour.) Merr.

    PubMed

    Hew, Chaw-Sen; Gam, Lay-Harn

    2011-12-01

    Gynura procumbens (Lour.) Merr. is a traditionally used medicinal plant to decrease cholesterol level, reduce high blood pressure, control diabetics, and for treatment of cancer. In our present study, a proteomic approach was applied to study the proteome of the plant that had never analyzed before. We have identified 92 abundantly expressed proteins from the leaves of G. procumbens (Lour.) Merr. Amongst the identified proteins was miraculin, a taste-masking agent with high commercial value. Miraculin made up ∼0.1% of the total protein extracted; the finding of miraculin gave a great commercial value to G. procumbens (Lour.) Merr. as miraculin's natural source is limited while the production of recombinant miraculin faced challenges of not being able to exhibit the taste-masking effect as in the natural miraculin. We believe the discovery of miraculin in G. procumbens (Lour.) Merr., provides commercial feasibility of miraculin in view of the availability of G. procumbens (Lour.) Merr. that grow wildly and easily in tropical climate. PMID:21938418

  20. Increased abundance of proteins involved in phytosiderophore production in boron-tolerant barley.

    PubMed

    Patterson, John; Ford, Kris; Cassin, Andrew; Natera, Siria; Bacic, Antony

    2007-07-01

    Boron (B) phytotoxicity affects cereal-growing regions worldwide. Although B-tolerant barley (Hordeum vulgare) germplasm is available, molecules responsible for this tolerance mechanism have not been defined. We describe and use a new comparative proteomic technique, iTRAQ peptide tagging (iTRAQ), to compare the abundances of proteins from B-tolerant and -intolerant barley plants from a 'Clipper' x 'Sahara' doubled-haploid population selected on the basis of a presence or absence of two B-tolerance quantitative trait loci. iTRAQ was used to identify three enzymes involved in siderophore production (Iron Deficiency Sensitive2 [IDS2], IDS3, and a methylthio-ribose kinase) as being elevated in abundance in the B-tolerant plants. Following from this result, we report a potential link between iron, B, and the siderophore hydroxymugineic acid. We believe that this study highlights the potency of the iTRAQ approach to better understand mechanisms of abiotic stress tolerance in cereals, particularly when applied in conjunction with bulked segregant analysis. PMID:17478636

  1. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells.

    PubMed

    Tichon, Ailone; Gil, Noa; Lubelsky, Yoav; Havkin Solomon, Tal; Lemze, Doron; Itzkovitz, Shalev; Stern-Ginossar, Noam; Ulitsky, Igor

    2016-01-01

    Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionarily conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD-an abundant and highly conserved cytoplasmic lncRNA. Here we show that most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two mammalian Pumilio homologues. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA-binding proteins, an activity which positions them at key junctions of cellular signalling pathways. PMID:27406171

  2. A conserved abundant cytoplasmic long noncoding RNA modulates repression by Pumilio proteins in human cells

    PubMed Central

    Tichon, Ailone; Gil, Noa; Lubelsky, Yoav; Havkin Solomon, Tal; Lemze, Doron; Itzkovitz, Shalev; Stern-Ginossar, Noam; Ulitsky, Igor

    2016-01-01

    Thousands of long noncoding RNA (lncRNA) genes are encoded in the human genome, and hundreds of them are evolutionarily conserved, but their functions and modes of action remain largely obscure. Particularly enigmatic lncRNAs are those that are exported to the cytoplasm, including NORAD—an abundant and highly conserved cytoplasmic lncRNA. Here we show that most of the sequence of NORAD is comprised of repetitive units that together contain at least 17 functional binding sites for the two mammalian Pumilio homologues. Through binding to PUM1 and PUM2, NORAD modulates the mRNA levels of their targets, which are enriched for genes involved in chromosome segregation during cell division. Our results suggest that some cytoplasmic lncRNAs function by modulating the activities of RNA-binding proteins, an activity which positions them at key junctions of cellular signalling pathways. PMID:27406171

  3. Relative Abundance of Integral Plasma Membrane Proteins in Arabidopsis Leaf and Root Tissue Determined by Metabolic Labeling and Mass Spectrometry

    PubMed Central

    Bernfur, Katja; Larsson, Olaf; Larsson, Christer; Gustavsson, Niklas

    2013-01-01

    Metabolic labeling of proteins with a stable isotope (15N) in intact Arabidopsis plants was used for accurate determination by mass spectrometry of differences in protein abundance between plasma membranes isolated from leaves and roots. In total, 703 proteins were identified, of which 188 were predicted to be integral membrane proteins. Major classes were transporters, receptors, proteins involved in membrane trafficking and cell wall-related proteins. Forty-one of the integral proteins, including nine of the 13 isoforms of the PIP (plasma membrane intrinsic protein) aquaporin subfamily, could be identified by peptides unique to these proteins, which made it possible to determine their relative abundance in leaf and root tissue. In addition, peptides shared between isoforms gave information on the proportions of these isoforms. A comparison between our data for protein levels and corresponding data for mRNA levels in the widely used database Genevestigator showed an agreement for only about two thirds of the proteins. By contrast, localization data available in the literature for 21 of the 41 proteins show a much better agreement with our data, in particular data based on immunostaining of proteins and GUS-staining of promoter activity. Thus, although mRNA levels may provide a useful approximation for protein levels, detection and quantification of isoform-specific peptides by proteomics should generate the most reliable data for the proteome. PMID:23990937

  4. Ubiquitous Autofragmentation of Fluorescent Proteins Creates Abundant Defective Ribosomal Products (DRiPs) for Immunosurveillance.

    PubMed

    Wei, Jiajie; Gibbs, James S; Hickman, Heather D; Cush, Stephanie S; Bennink, Jack R; Yewdell, Jonathan W

    2015-06-26

    broadly, given the wide use of fluorescent proteins, their ubiquitous and abundant fragmentation must be considered when interpreting experiments using these extremely useful probes. PMID:25971973

  5. Ubiquitous Autofragmentation of Fluorescent Proteins Creates Abundant Defective Ribosomal Products (DRiPs) for Immunosurveillance*

    PubMed Central

    Wei, Jiajie; Gibbs, James S.; Hickman, Heather D.; Cush, Stephanie S.; Bennink, Jack R.; Yewdell, Jonathan W.

    2015-01-01

    broadly, given the wide use of fluorescent proteins, their ubiquitous and abundant fragmentation must be considered when interpreting experiments using these extremely useful probes. PMID:25971973

  6. Novel mitochondria-targeted heat-soluble proteins identified in the anhydrobiotic Tardigrade improve osmotic tolerance of human cells.

    PubMed

    Tanaka, Sae; Tanaka, Junko; Miwa, Yoshihiro; Horikawa, Daiki D; Katayama, Toshiaki; Arakawa, Kazuharu; Toyoda, Atsushi; Kubo, Takeo; Kunieda, Takekazu

    2015-01-01

    Tardigrades are able to tolerate almost complete dehydration through transition to a metabolically inactive state, called "anhydrobiosis". Late Embryogenesis Abundant (LEA) proteins are heat-soluble proteins involved in the desiccation tolerance of many anhydrobiotic organisms. Tardigrades, Ramazzottius varieornatus, however, express predominantly tardigrade-unique heat-soluble proteins: CAHS (Cytoplasmic Abundant Heat Soluble) and SAHS (Secretory Abundant Heat Soluble) proteins, which are secreted or localized in most intracellular compartments, except the mitochondria. Although mitochondrial integrity is crucial to ensure cellular survival, protective molecules for mitochondria have remained elusive. Here, we identified two novel mitochondrial heat-soluble proteins, RvLEAM and MAHS (Mitochondrial Abundant Heat Soluble), as potent mitochondrial protectants from Ramazzottius varieornatus. RvLEAM is a group3 LEA protein and immunohistochemistry confirmed its mitochondrial localization in tardigrade cells. MAHS-green fluorescent protein fusion protein localized in human mitochondria and was heat-soluble in vitro, though no sequence similarity with other known proteins was found, and one region was conserved among tardigrades. Furthermore, we demonstrated that RvLEAM protein as well as MAHS protein improved the hyperosmotic tolerance of human cells. The findings of the present study revealed that tardigrade mitochondria contain at least two types of heat-soluble proteins that might have protective roles in water-deficient environments. PMID:25675104

  7. Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells

    PubMed Central

    Tanaka, Sae; Tanaka, Junko; Miwa, Yoshihiro; Horikawa, Daiki D.; Katayama, Toshiaki; Arakawa, Kazuharu; Toyoda, Atsushi; Kubo, Takeo; Kunieda, Takekazu

    2015-01-01

    Tardigrades are able to tolerate almost complete dehydration through transition to a metabolically inactive state, called “anhydrobiosis”. Late Embryogenesis Abundant (LEA) proteins are heat-soluble proteins involved in the desiccation tolerance of many anhydrobiotic organisms. Tardigrades, Ramazzottius varieornatus, however, express predominantly tardigrade-unique heat-soluble proteins: CAHS (Cytoplasmic Abundant Heat Soluble) and SAHS (Secretory Abundant Heat Soluble) proteins, which are secreted or localized in most intracellular compartments, except the mitochondria. Although mitochondrial integrity is crucial to ensure cellular survival, protective molecules for mitochondria have remained elusive. Here, we identified two novel mitochondrial heat-soluble proteins, RvLEAM and MAHS (Mitochondrial Abundant Heat Soluble), as potent mitochondrial protectants from Ramazzottius varieornatus. RvLEAM is a group3 LEA protein and immunohistochemistry confirmed its mitochondrial localization in tardigrade cells. MAHS-green fluorescent protein fusion protein localized in human mitochondria and was heat-soluble in vitro, though no sequence similarity with other known proteins was found, and one region was conserved among tardigrades. Furthermore, we demonstrated that RvLEAM protein as well as MAHS protein improved the hyperosmotic tolerance of human cells. The findings of the present study revealed that tardigrade mitochondria contain at least two types of heat-soluble proteins that might have protective roles in water-deficient environments. PMID:25675104

  8. Mass spectrometry in cancer biomarker research: a case for immunodepletion of abundant blood-derived proteins from clinical tissue specimens

    PubMed Central

    Prieto, DaRue A; Johann, Donald J; Wei, Bih-Rong; Ye, Xiaoying; Chan, King C; Nissley, Dwight V; Simpson, R Mark; Citrin, Deborah E; Mackall, Crystal L; Linehan, W Marston; Blonder, Josip

    2014-01-01

    The discovery of clinically relevant cancer biomarkers using mass spectrometry (MS)-based proteomics has proven difficult, primarily because of the enormous dynamic range of blood-derived protein concentrations and the fact that the 22 most abundant blood-derived proteins constitute approximately 99% of the total plasma protein mass. Immunodepletion of clinical body fluid specimens (e.g., serum/plasma) for the removal of highly abundant proteins is a reasonable and reproducible solution. Often overlooked, clinical tissue specimens also contain a formidable amount of highly abundant blood-derived proteins present in tissue-embedded networks of blood/lymph capillaries and interstitial fluid. Hence, the dynamic range impediment to biomarker discovery remains a formidable obstacle, regardless of clinical sample type (solid tissue and/or body fluid). Thus, we optimized and applied simultaneous immunodepletion of blood-derived proteins from solid tissue and peripheral blood, using clear cell renal cell carcinoma as a model disease. Integrative analysis of data from this approach and genomic data obtained from the same type of tumor revealed concordant key pathways and protein targets germane to clear cell renal cell carcinoma. This includes the activation of the lipogenic pathway characterized by increased expression of adipophilin (PLIN2) along with 'cadherin switching', a phenomenon indicative of transcriptional reprogramming linked to renal epithelial dedifferentiation. We also applied immunodepletion of abundant blood-derived proteins to various tissue types (e.g., adipose tissue and breast tissue) showing unambiguously that the removal of abundant blood-derived proteins represents a powerful tool for the reproducible profiling of tissue proteomes. Herein, we show that the removal of abundant blood-derived proteins from solid tissue specimens is of equal importance to depletion of body fluids and recommend its routine use in the context of biological discovery and

  9. Brugia malayi abundant larval transcript 2 protein treatment attenuates experimentally-induced colitis in mice.

    PubMed

    Khatri, Vishal; Amdare, Nitin; Yadav, Ravi Shankar; Tarnekar, Aaditya; Goswami, Kalyan; Reddy, Maryada Venkata Rami

    2015-11-01

    Helminths are known to modulate host's immunity by suppressing host protective pro-inflammatory responses. Such immunomodulatory effects have been experimentally shown to have therapeutic implications in immune mediated disorders. In the present study, we have explored a filarial protein i.e. Brugia malayi recombinant abundant larval transcript 2 (rBmALT2) for its therapeutic effect in dextran sodium sulfate (DSS) induced colitis in mouse model. The immunomodulatory activity of rBmALT-2 was initially confirmed by demonstrating that it suppressed the lipopolysaccharide (LPS) induced nitric oxide synthesis and down-regulated the expression of pro-inflammatory cytokines in vitro by peritoneal exudate cells of mice. Treatment with rBmALT2 reduced severity of colitis associated with significant reduction in weight loss, disease activity, colon damage, mucosal edema and histopathological score including myeloperoxidase activity in colon tissues. rBmALT2 was comparatively more effective in attenuation of colitis when used in the preventive mode than when used for curative purpose. The therapeutic effect of rBmALT2 was found to be associated with downregulation of IFN-γ, IL-6, IL-17 and upregulation of IL-10 cytokines. These results provide strong experimental evidence that BmALT2 could be a potential alternative therapeutic agent in colitis. PMID:26669016

  10. Phylogenetic analysis of microalgae based on highly abundant proteins using mass spectrometry.

    PubMed

    Lee, Hae-Won; Roh, Seong Woon; Cho, Kichul; Kim, Kil-Nam; Cha, In-Tae; Yim, Kyung June; Song, Hye Seon; Nam, Young-Do; Oda, Tatsuya; Chung, Young-Ho; Kim, Soo Jung; Choi, Jong-Soon; Kim, Daekyung

    2015-01-01

    The blooms of toxic phototrophic microorganisms, such as microalgae and cyanobacteria, which are typically found in freshwater and marine environments, are becoming more frequent and problematic in aquatic systems. Due to accumulation of toxic algae, harmful algal blooms (HABs) exert negative effects on aquatic systems. Therefore, rapid detection of harmful microalgae is important for monitoring the occurrence of HABs. Mass spectrometry-based methods have become sensitive, specific techniques for the identification and characterization of microorganisms. Matrix-assisted laser desorption/ionization (MALDI) with time-of-flight (TOF) mass spectrometry (MS) allows us to measure a unique molecular fingerprint of highly abundant proteins in a microorganism and has been used for the rapid, accurate identification of bacteria and fungi in clinical microbiology. Here, we tested the specificity of MALDI-TOF MS using microalgal strains (Heterocapsa, Alexandrium, Nannochloropsis, Chaetoceros, Chlorella, and Dunaliella spp.). Our research suggested that this method was comparable in terms of the rapid identification of microalgea to conventional methods based on genetic information and morphology. Thus, this efficient mass spectrometry-based technique may have applications in the rapid identification of harmful microorganisms from aquatic environmental samples. PMID:25476355

  11. Combining subproteome enrichment and Rubisco depletion enables identification of low abundance proteins differentially regulated during plant defense.

    PubMed

    Widjaja, Ivy; Naumann, Kai; Roth, Udo; Wolf, Noreen; Mackey, David; Dangl, Jeffery L; Scheel, Dierk; Lee, Justin

    2009-01-01

    Transgenic Arabidopsis conditionally expressing the bacterial avrRpm1 type III effector under the control of a dexamethasone-responsive promoter were used for proteomics studies. This model system permits study of an individual effector without interference from additional bacterial components. Coupling of different prefractionation approaches to high resolution 2-DE facilitated the discovery of low abundance proteins - enabling the identification of proteins that have escaped detection in similar experiments. A total of 34 differentially regulated protein spots were identified. Four of these (a remorin, a protein phosphatase 2C (PP2C), an RNA-binding protein, and a C2-domain-containing protein) are potentially early signaling components in the interaction between AvrRpm1 and the cognate disease resistance gene product, resistance to Pseudomonas syringae pv. maculicola 1 (RPM1). For the remorin and RNA-binding protein, involvement of PTM and post-transcriptional regulation are implicated, respectively. PMID:19053141

  12. Molecular biology of Lea genes of higher plants

    SciTech Connect

    Not Available

    1991-07-01

    This report contains our progress to date in determining the function of the D-7 Lea proteins in cotton embryos. We have completely sequenced the D-7 gene and established {ital E. coli} transformants which synthesize reasonable amounts of the D-7 protein. Two-dimensional electrophoresis was required to assay fractions for D-7 protein during purification to homogeneity, since D-7 has no known enzymatic activity, contains no Trp, and little Phe or Tyr, and {ital E. coli} has several proteins of similar molecular weight to D-7. Purified D-7 was used to generate monospecific antibodies which are being used for determination of the cellular distribution of D-7, and also for exact quantitation of D-7 in late-stage cotton embryos. Computerized modelling of D-7 has shown similarities to proteins with a coiled-coil structure, but fitting D-7 to this structure resulted in a violation of the handedness rule. If the pitch of the helix is changed from 3.6 to 3.667, however, a three dimensional structure (not a coiled coil) is generated which has overall energetics of formation nearly as favorable as the traditional {alpha} helix. The driving force for the change in pitch is proposed to result from favorable energetics of dimerization. Preliminary evidence indicates that D-7 does indeed dimerize in solution. Future experiments will determine the exact 3D structure of D-7 and the related protein D-29, as well as test the hypothesis that D-7 and D-29 are involved in mitigating dehydration of embryos and plants through sequestering phosphate or other ions in sufficient quantity to prevent ion precipitation or crystallization. 13 refs., 3 figs. (MHB)

  13. CYCLoPs: A Comprehensive Database Constructed from Automated Analysis of Protein Abundance and Subcellular Localization Patterns in Saccharomyces cerevisiae

    PubMed Central

    Koh, Judice L. Y.; Chong, Yolanda T.; Friesen, Helena; Moses, Alan; Boone, Charles; Andrews, Brenda J.; Moffat, Jason

    2015-01-01

    Changes in protein subcellular localization and abundance are central to biological regulation in eukaryotic cells. Quantitative measures of protein dynamics in vivo are therefore highly useful for elucidating specific regulatory pathways. Using a combinatorial approach of yeast synthetic genetic array technology, high-content screening, and machine learning classifiers, we developed an automated platform to characterize protein localization and abundance patterns from images of log phase cells from the open-reading frame−green fluorescent protein collection in the budding yeast, Saccharomyces cerevisiae. For each protein, we produced quantitative profiles of localization scores for 16 subcellular compartments at single-cell resolution to trace proteome-wide relocalization in conditions over time. We generated a collection of ∼300,000 micrographs, comprising more than 20 million cells and ∼9 billion quantitative measurements. The images depict the localization and abundance dynamics of more than 4000 proteins under two chemical treatments and in a selected mutant background. Here, we describe CYCLoPs (Collection of Yeast Cells Localization Patterns), a web database resource that provides a central platform for housing and analyzing our yeast proteome dynamics datasets at the single cell level. CYCLoPs version 1.0 is available at http://cyclops.ccbr.utoronto.ca. CYCLoPs will provide a valuable resource for the yeast and eukaryotic cell biology communities and will be updated as new experiments become available. PMID:26048563

  14. A rapid method for depletion of Rubisco from soybean (Glycine max) leaf for proteomic analysis of lower abundance proteins.

    PubMed

    Krishnan, Hari B; Natarajan, Savithiry S

    2009-12-01

    2-DE analysis of complex plant proteomes has limited dynamic resolution because only abundant proteins can be detected. Proteomic assessment of the low abundance proteins within leaf tissue is difficult when it is comprised of 30-50% of the CO(2) fixation enzyme Rubisco. Resolution can be improved through depletion of Rubisco using fractionation techniques based upon different physiological or biochemical principles. We have developed a fast and simple fractionation technique using 10 mM Ca(2+) and 10 mM phytate to precipitate Rubisco from soybean leaf soluble protein extract. This method is not only rapid, but also inexpensive, and capable of removing 85% of the extremely abundant Rubisco enzyme from soybean leaf soluble protein extract. This method allowed for roughly 230 previously inconspicuous protein spots in soybean leaf to be more easily detectable (3-fold increase in vol%) using fluorescent detection and allowed 28 phosphorylated proteins previously undetected, to be isolated and identified by MALDI-TOF-MS. PMID:19766275

  15. e-LEA3D: a computational-aided drug design web server

    PubMed Central

    Douguet, Dominique

    2010-01-01

    e-LEA3D web server integrates three complementary tools to perform computer-aided drug design based on molecular fragments. In drug discovery projects, there is a considerable interest in identifying novel and diverse molecular scaffolds to enhance chances of success. The de novo drug design tool is used to invent new ligands to optimize a user-specified scoring function. The composite scoring function includes both structure- and ligand-based evaluations. The de novo approach is an alternative to a blind virtual screening of large compound collections. A heuristic based on a genetic algorithm rapidly finds which fragments or combination of fragments fit a QSAR model or the binding site of a protein. While the approach is ideally suited for scaffold-hopping, this module also allows a scan for possible substituents to a user-specified scaffold. The second tool offers a traditional virtual screening and filtering of an uploaded library of compounds. The third module addresses the combinatorial library design that is based on a user-drawn scaffold and reactants coming, for example, from a chemical supplier. The e-LEA3D server is available at: http://bioinfo.ipmc.cnrs.fr/lea.html. PMID:20444867

  16. 34 CFR 300.817 - Reallocation of LEA funds.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... carryover period in 34 CFR 76.709, whether the LEA has obligated the funds. The SEA may reallocate any of... CHILDREN WITH DISABILITIES Preschool Grants for Children with Disabilities § 300.817 Reallocation of...

  17. 34 CFR 300.815 - Subgrants to LEAs.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... the State does not reserve under § 300.812 to LEAs (including public charter schools that operate as... responsible for providing education to children aged three through five years, including public...

  18. 34 CFR 300.815 - Subgrants to LEAs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... the State does not reserve under § 300.812 to LEAs (including public charter schools that operate as... responsible for providing education to children aged three through five years, including public...

  19. 34 CFR 300.815 - Subgrants to LEAs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... the State does not reserve under § 300.812 to LEAs (including public charter schools that operate as... responsible for providing education to children aged three through five years, including public...

  20. Alteration in abundance of specific membrane proteins of Aggregatibacter actinomycetemcomitans is attributed to deletion of the inner membrane protein MorC

    PubMed Central

    Smith, Kenneth P.; Fields, Julia G.; Voogt, Richard D.; Deng, Bin; Lam, Ying-Wai; Mintz, Keith P.

    2015-01-01

    Aggregatibacter actinomycetemcomitans is an important pathogen in the etiology of human periodontal and systemic diseases. Inactivation of the gene coding for the inner membrane protein, morphogenesis protein C (MorC), results is pleotropic effects pertaining to the membrane structure and function of this bacterium. The role of this protein in membrane biogenesis is unknown. To begin to understand the role of this conserved protein, stable isotope dimethyl labeling in conjunction with mass spectrometry was used to quantitatively analyze differences in the membrane proteomes of the isogenic mutant and wild-type strain. A total of 613 proteins were quantified and 601 of these proteins were found to be equal in abundance between the two strains. The remaining 12 proteins were found in lesser (10) or greater (2) abundance in the membrane preparation of the mutant strain compared with the wild-type strain. The 12 proteins were ascribed functions associated with protein quality control systems, oxidative stress responses, and protein secretion. The potential relationship between these proteins and the phenotypes of the morC mutant strain is discussed. PMID:25684173

  1. Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    PubMed

    McKinney, Caleb; Perez, Cesar; Mohr, Ian

    2012-04-10

    By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting translation initiation factors. Curiously, inactivating the host translational repressor 4E-BP1 in HCMV-infected cells stimulates synthesis of the cellular poly(A) binding protein (PABP), significantly increasing PABP abundance. Here, we establish that new PABP synthesis is translationally controlled by the HCMV-encoded UL38 mammalian target of rapamycin complex 1-activator. The 5' UTR within the mRNA encoding PABP contains a terminal oligopyrimidine (TOP) element found in mRNAs, the translation of which is stimulated in response to mitogenic, growth, and nutritional stimuli, and proteins encoded by TOP-containing mRNAs accumulated in HCMV-infected cells. Furthermore, UL38 expression was necessary and sufficient to regulate expression of a PABP TOP-containing reporter. Remarkably, preventing the rise in PABP abundance by RNAi impaired eIF4E binding to eIF4G, thereby reducing assembly of the multisubunit initiation factor eIF4F, viral protein production, and replication. This finding demonstrates that viruses can increase host translation initiation factor concentration to foster their replication and defines a unique mechanism whereby control of PABP abundance regulates eIF4F assembly. PMID:22431630

  2. Assessment of 24-hours Aldosterone Administration on Protein Abundances in Fluorescence-Sorted Mouse Distal Renal Tubules by Mass Spectrometry

    PubMed Central

    Jensen, Thomas B; Pisitkun, Trairak; Hoffert, Jason D; Jensen, Uffe B; Fenton, Robert A; Praetorius, Helle A; Knepper, Mark A; Praetorius, Jeppe

    2013-01-01

    Background/Aims Aldosterone exerts multiple long-term effects in the distal renal tubules. The aim of this study was to establish a method for identifying proteins in these tubules that change in abundance by only 24-hours aldosterone administration. Methods Mice endogenously expressing green fluorescent protein (eGFP) in the connecting tubule and cortical collecting ducts were treated with a subcutaneous injection of 2.0 mg/kg aldosterone or vehicle (n=5), and sacrificed 24 hours later. Suspensions of single cells were obtained enzymatically, and eGFP positive cells were isolated by fluorescence activated cell sorting (FACS). Samples of 100 μg proteins were digested with trypsin and labeled with 8-plex iTRAQ reagents and processed for liquid chromatography tandem mass spectrometry (LC-MS/MS). Results FACS yielded 1.4 million cells per mouse. The LC-MS/MS spectra were matched to peptides by the SEQUEST search algorithm, which identified 3002 peptides corresponding to 506 unique proteins of which 20 significantly changed abundance 24-hours after aldosterone injection. Conclusion We find the method suitable and useful for studying hormonal effects on protein abundance in distal tubular segments. PMID:23428628

  3. Dexamethasone modulates rat renal brush border membrane phosphate transporter mRNA and protein abundance and glycosphingolipid composition.

    PubMed Central

    Levi, M; Shayman, J A; Abe, A; Gross, S K; McCluer, R H; Biber, J; Murer, H; Lötscher, M; Cronin, R E

    1995-01-01

    Glucocorticoids are important regulators of renal phosphate transport. This study investigates the role of alterations in renal brush border membrane (BBM) sodium gradient-dependent phosphate transport (Na-Pi cotransporter) mRNA and protein abundance in the dexamethasone induced inhibition of Na-Pi cotransport in the rat. Dexamethasone administration for 4 d caused a 1.5-fold increase in the Vmax of Na-Pi cotransport (1785 +/- 119 vs. 2759 +/- 375 pmol/5 s per mg BBM protein in control, P < 0.01), which was paralleled by a 2.5-fold decrease in the abundance of Na-Pi mRNA and Na-Pi protein. There was also a 1.7-fold increase in BBM glucosylceramide content (528 +/- 63 vs. 312 +/- 41 ng/mg BBM protein in control, P < 0.02). To determine whether the alteration in glucosylceramide content per se played a functional role in the decrease in Na-Pi cotransport, control rats were treated with the glucosylceramide synthase inhibitor, D-threo-1-phenyl-2-decanoyl-amino-3-morpholino-1-propanol (PDMP). The resultant 1.5-fold decrease in BBM glucosylceramide content (199 +/- 19 vs. 312 +/- 41 ng/mg BBM protein in control, P < 0.02) was associated with a 1.4-fold increase in Na-Pi cotransport activity (1422 +/- 73 vs. 1048 +/- 85 pmol/5 s per mg BBM protein in control, P < 0.01), and a 1.5-fold increase in BBM Na-Pi protein abundance. Thus, dexamethasone-induced inhibition of Na-Pi cotransport is associated with a decrease in BBM Na-Pi cotransporter abundance, and an increase in glucosylceramide. Since primary alteration in BBM glucosylceramide content per se directly and selectively modulates BBM Na-Pi cotransport activity and Na-Pi protein abundance, we propose that the increase in BBM glucosylceramide content plays an important role in mediating the inhibitory effect of dexamethasone on Na-Pi cotransport activity. Images PMID:7615789

  4. Region-Specific Protein Abundance Changes in the Brain of MPTP-induced Parkinson’s Disease Mouse Model

    SciTech Connect

    Zhang, Xu; Zhou, Jianying; Chin, Mark H; Schepmoes, Athena A; Petyuk, Vladislav A; Weitz, Karl K; Petritis, Brianne O; Monroe, Matthew E; Camp, David G; Wood, Stephen A; Melega, William P; Bigelow, Diana J; Smith, Desmond J; Qian, Weijun; Smith, Richard D

    2010-02-15

    Parkinson’s disease (PD) is characterized by dopaminergic neurodegeneration in the nigrostriatal region of the brain; however, the neurodegeneration extends well beyond dopaminergic neurons. To gain a better understanding of the molecular changes relevant to PD, we applied two-dimensional LC-MS/MS to comparatively analyze the proteome changes in four brain regions (striatum, cerebellum, cortex, and the rest of brain) using a MPTP-induced PD mouse model with the objective to identify nigrostriatal-specific and other region-specific protein abundance changes. The combined analyses resulted in the identification of 4,895 non-redundant proteins with at least two unique peptides per protein. The relative abundance changes in each analyzed brain region were estimated based on the spectral count information. A total of 518 proteins were observed with significant MPTP-induced changes across different brain regions. 270 of these proteins were observed with specific changes occurring either only in the striatum and/or in the rest of the brain region that contains substantia nigra, suggesting that these proteins are associated with the underlying nigrostriatal pathways. Many of the proteins that exhibit significant abundance changes were associated with dopamine signaling, mitochondrial dysfunction, the ubiquitin system, calcium signaling, the oxidative stress response, and apoptosis. A set of proteins with either consistent change across all brain regions or with changes specific to the cortex and cerebellum regions were also detected. One of the interesting proteins is ubiquitin specific protease (USP9X), a deubiquination enzyme involved in the protection of proteins from degradation and promotion of the TGF-β pathway, which exhibited altered abundances in all brain regions. Western blot validation showed similar spatial changes, suggesting that USP9X is potentially associated with neurodegeneration. Together, this study for the first time presents an overall picture of

  5. Abundant class III acidic chitinase homologue in tamarind (Tamarindus indica) seed serves as the major storage protein.

    PubMed

    Rao, Devavratha H; Gowda, Lalitha R

    2008-03-26

    The phyla Leguminosae contains protease inhibitors, lectins, chitinases, and glycohydrolases as major defense proteins in their seeds. Electrophoretic analysis of the seed proteins of tamarind ( Tamarindus indica L.), an agri-waste material, indicated the unusual presence of two major proteins comparable to overexpression of recombinant proteins. These proteins were identified by amino-terminal analysis to be (1) Kunitz-type trypsin inhibitor and (2) class III endochitinase (34000 Da). These two proteins were purified to apparent homogeneity by a single-step chitin bead affinity chromatography and characterized. The Kunitz inhibitor was specific toward inhibiting trypsin with a stoichiometry of 1:1. The 33000 +/- 1000 Da protein, accounting for >50% of the total seed protein, is an acidic glycoprotein exhibiting a very low endotype hydrolytic activity toward chitin derivatives. SDS-PAGE followed by densitometry of tamarind seed germination indicates the disappearance of the chitinase with the concomitant appearance of a cysteine endopeptidase. On the basis of its abundance, accumulation without any pathogenesis-related stimulus, temporal regulation, amino acid composition, and very low enzyme activity, this 34000 Da protein designated "tamarinin" physiologically serves as the major storage protein. PMID:18298067

  6. Lactate dehydrogenase A as a highly abundant eye lens protein in platypus (Ornithorhynchus anatinus): upsilon (upsilon)-crystallin.

    PubMed

    van Rheede, Teun; Amons, Reinout; Stewart, Niall; de Jong, Wilfried W

    2003-06-01

    Vertebrate eye lenses mostly contain two abundant types of proteins, the alpha-crystallins and the beta/gamma-crystallins. In addition, certain housekeeping enzymes are highly expressed as crystallins in various taxa. We now observed an unusual approximately 41-kd protein that makes up 16% to 18% of the total protein in the platypus eye lens. Its cDNA sequence was determined, which identified the protein as muscle-type lactate dehydrogenase A (LDH-A). It is the first observation of LDH-A as a crystallin, and we designate it upsilon (upsilon)-crystallin. Interestingly, the related heart-type LDH-B occurs as an abundant lens protein, known as epsilon-crystallin, in many birds and crocodiles. Thus, two members of the ldh gene family have independently been recruited as crystallins in different higher vertebrate lineages, suggesting that they are particularly suited for this purpose in terms of gene regulatory or protein structural properties. To establish whether platypus LDH-A/upsilon-crystallin has been under different selective constraints as compared with other vertebrate LDH-A sequences, we reconstructed the vertebrate ldh-a gene phylogeny. No conspicuous rate deviations or amino acid replacements were observed. PMID:12716980

  7. Pharmacological zinc and phytase supplementation enhance metallothionein mRNA abundance and protein concentration in newly weaned pigs.

    PubMed

    Martínez, Michelle M; Hill, Gretchen M; Link, Jane E; Raney, Nancy E; Tempelman, Robert J; Ernst, Catherine W

    2004-03-01

    The swine industry feeds pharmacological zinc (Zn) to newly weaned pigs to improve health. Because most swine diets are plant-based with a high phytic acid content, we hypothesized that adding phytase to diets could reduce the amount of Zn required to obtain beneficial responses. The role of metallothionein (MT) in Zn homeostasis could be important in this positive response. Thus, the goal of this study was to investigate the effect of dietary Zn and phytase on relative MT mRNA abundance and protein concentration in newly weaned pigs. Diets containing adequate (150 mg Zn/kg) or pharmacological concentrations of Zn (1000 or 2000 mg Zn/kg), as zinc oxide, with or without phytase [0, 500 phytase units (FTU)/kg, Natuphos, BASF] were fed in a 3 x 2 factorial design. Plasma and tissue minerals were measured in pigs killed after 14 d of dietary intervention. Hepatic and renal relative MT mRNA abundance and protein were greater (P < 0.05) in pigs fed 1000 mg Zn/kg with phytase, or 2000 mg Zn/kg with or without phytase vs. the remaining treatments. Intestinal mucosa MT mRNA abundance and protein were greater (P < 0.05) in pigs fed 2000 mg Zn/kg with phytase than in pigs fed 2000 mg Zn/kg alone or 1000 mg Zn/kg with phytase. Pigs fed 1000 mg Zn/kg plus phytase or 2000 mg Zn/kg with or without phytase had higher plasma, hepatic, and renal Zn than those fed the adequate Zn diets or 1000 mg Zn/kg. We conclude that feeding 1000 mg Zn/kg with phytase enhances MT mRNA abundance and protein and Zn absorption to the same degree as 2000 mg Zn/kg with and without phytase. PMID:14988443

  8. Proteomics reveals differences in protein abundance and highly similar antigenic profiles between Besnoitia besnoiti and Besnoitia tarandi.

    PubMed

    García-Lunar, P; Regidor-Cerrillo, J; Ortega-Mora, L M; Gutiérrez-Expósito, D; Alvarez-García, G

    2014-10-15

    Besnoitia besnoiti and Besnoitia tarandi are two cyst-forming apicomplexan parasites of the genus Besnoitia. B. besnoiti uses cattle as an intermediate host, in which it causes a disease that progresses in two sequential phases: the acute anasarca stage and the chronic scleroderma stage. Reindeer and caribou act as intermediate hosts for B. tarandi, which causes clinical signs similar to those caused by B. besnoiti. Previous studies demonstrated high molecular similarity, as determined by 18S and ITS-1 RNA sequences, between these Besnoitia spp., and strong serological cross-reactivity between these species has recently been demonstrated. Thus, a difference gel electrophoresis approach and mass spectrometry analysis were used to describe the proteomes and explore differences in protein abundance between B. besnoiti and B. tarandi in tachyzoite extracts. Immunoproteomes were also compared using 2-DE immunoblotting with polyclonal sera from experimentally infected rabbits. From approximately 1400 spots detected in DIGE-gels, 28 and 29 spots were differentially abundant in B. besnoiti and B. tarandi tachyzoites, respectively (± 1.5-fold, p<0.05). Four and 13 spots were exclusively detected in B. besnoiti and B. tarandi, respectively. Of the 32 differentially abundant spots analyzed by MALDI-TOF/MS, 6 up-regulated B. besnoiti proteins (LDH; HSP90; purine nucleoside phosphorylase and 3 hypothetical proteins) and 6 up-regulated B. tarandi proteins (G3PDH; LDH; PDI; mRNA decapping protein and 2 hypothetical proteins) were identified. Interestingly, no specific antigen spots were recognized by sera on any of the Besnoitia species studied and a similar antigen profile has been observed for B. tarandi and B. besnoiti sera when cross reactions were studied. This fact corroborates the difficulty in discerning Besnoitia infections using current serological assays. The present study underscores the importance of sequencing the B. besnoiti genome for species diversity studies of

  9. A cherry protein and its gene, abundantly expressed in ripening fruit, have been identified as thaumatin-like.

    PubMed Central

    Fils-Lycaon, B R; Wiersma, P A; Eastwell, K C; Sautiere, P

    1996-01-01

    A 29-kD polypeptide is the most abundant soluble protein in ripe cherry fruit (Prunus avium L); accumulation begins at the onset of ripening as the fruit turns from yellow to red. This protein was extracted from ripe cherries and purified by size-exclusion and ion-exchange chromatography. Antibodies to the purified protein were used to screen a cDNA library from ripe cherries. Numerous recombinant plaques reacted positively with the antibodies; the DNA sequence of representative clones encoded a polypeptide of 245 amino acid residues. A signal peptide was indicated, and the predicted mature protein corresponded to the purified protein in size (23.3 kD, by mass spectrometry) and isoelectric point (4.2). A search of known protein sequences revealed a strong similarity between this polypeptide and the thaumatin family of pathogenesis-related proteins. The cherry thaumatin-like protein does not have a sweet taste, and no antifungal activity was seen in preliminary assays. Expression of the protein appears to be regulated at the gene level, with mRNA levels at their highest in the ripe fruit. PMID:8685266

  10. Cellular expression of human centromere protein C demonstrates a cyclic behavior with highest abundance in the G1 phase.

    PubMed Central

    Knehr, M; Poppe, M; Schroeter, D; Eickelbaum, W; Finze, E M; Kiesewetter, U L; Enulescu, M; Arand, M; Paweletz, N

    1996-01-01

    Centromere proteins are localized within the centromere-kinetochore complex, which can be proven by means of immunofluorescence microscopy and immunoelectron microscopy. In consequence, their putative functions seem to be related exclusively to mitosis, namely to the interaction of the chromosomal kinetochores with spindle microtubules. However, electron microscopy using immune sera enriched with specific antibodies against human centromere protein C (CENP-C) showed that it occurs not only in mitosis but during the whole cell cycle. Therefore, we investigated the cell cycle-specific expression of CENP-C systematically on protein and mRNA levels applying HeLa cells synchronized in all cell cycle phases. Immunoblotting confirmed protein expression during the whole cell cycle and revealed an increase of CENP-C from the S phase through the G2 phase and mitosis to highest abundance in the G1 phase. Since this was rather surprising, we verified it by quantifying phase-specific mRNA levels of CENP-C, paralleled by the amplification of suitable internal standards, using the polymerase chain reaction. The results were in excellent agreement with abundant protein amounts and confirmed the cyclic behavior of CENP-C during the cell cycle. In consequence, we postulate that in addition to its role in mitosis, CENP-C has a further role in the G1 phase that may be related to cell cycle control. Images Fig. 1 Fig. 2 Fig. 4 PMID:8816782

  11. Size-related variation in protein abundance in the brain and abdominal tissue of bumble bee workers.

    PubMed

    Wolschin, F; Shpigler, H; Amdam, G V; Bloch, G

    2012-06-01

    Female bumble bee workers of the same species often show a profound body size variation that is linked to a division of labour. Large individuals are more likely to forage whereas small individuals are more likely to perform in-nest activities. A higher sensory sensitivity, stronger circadian rhythms as well as better learning and memory performances appear to better equip large individuals for outdoor activities compared to their smaller siblings. The molecular mechanisms underlying worker functional polymorphism remain unclear. Proteins are major determinants of an individual's morphology and behaviour. We hypothesized that the abundance of proteins such as metabolic enzymes as well as proteins involved in neuronal functions would differ with body size and provide insights into the mechanisms underlying size-dependent physiological specialization in bumble bee workers. We conducted protein quantification measurements based on liquid chromatography coupled with tandem mass spectrometry on tissue samples derived from small and large Bombus impatiens and Bombus terrestris workers. Proteins found to differ significantly in abundance between small and large workers belong to the categories of structure, energy metabolism and stress response. These findings provide the first proteomic insight into mechanisms associated with size-based division of labour in social insects. PMID:22568679

  12. An in vivo detection system for transient and low‐abundant protein interactions and their kinetics in budding yeast

    PubMed Central

    Brezovich, Andrea; Schuschnig, Martina; Ammerer, Gustav

    2015-01-01

    Abstract Methylation tracking (M‐Track) is a protein‐proximity assay in Saccharomyces cerevisiae, allowing the detection of transient protein–protein interactions in living cells. The bait protein is fused to a histone lysine methyl transferase and the prey protein to a methylation acceptor peptide derived from histone 3. Upon interaction, the histone 3 fragment is stably methylated on lysine 9 and can be detected by methylation‐specific antibodies. Since methylation marking is irreversible in budding yeast and only takes place in living cells, the occurrence of artifacts during cell lysate preparation is greatly reduced, leading to a more accurate representation of native interactions. So far, this method has been limited to highly abundant or overexpressed proteins. However, many proteins of interest are low‐abundant, and overexpression of proteins may interfere with their function, leading to an artificial situation. Here we report the generation of a toolbox including a novel cleavage‐enrichment system for the analysis of very low‐abundant proteins at their native expression levels. In addition, we developed a system for the parallel analysis of two prey proteins in a single cell, as well as an inducible methylation system. The inducible system allows precise control over the time during which the interaction is detected and can be used to determine interaction kinetics. Furthermore, we generated a set of constructs facilitating the cloning‐free genomic tagging of proteins at their endogenous locus by homologous recombination, and their expression from centromeric plasmids. GenBank submissions: pCK900; KM407502, pCK901; KM407503, pCK902; KM407504, pCK903; KM407505, pCK904; KM407506, pCK905; KM407507, pCK906; KM407508, pCK907; KM407509, pCK908; KM407510, pCK909; KM407511, pCK910; KM407512, pCK911; KM407513. © 2015 The Authors. Yeast published by John Wiley & Sons Ltd. PMID:25582094

  13. Application of an improved proteomics method for abundant protein cleanup: molecular and genomic mechanisms study in plant defense.

    PubMed

    Zhang, Yixiang; Gao, Peng; Xing, Zhuo; Jin, Shumei; Chen, Zhide; Liu, Lantao; Constantino, Nasie; Wang, Xinwang; Shi, Weibing; Yuan, Joshua S; Dai, Susie Y

    2013-11-01

    High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery. PMID:23943779

  14. Application of an Improved Proteomics Method for Abundant Protein Cleanup: Molecular and Genomic Mechanisms Study in Plant Defense*

    PubMed Central

    Zhang, Yixiang; Gao, Peng; Xing, Zhuo; Jin, Shumei; Chen, Zhide; Liu, Lantao; Constantino, Nasie; Wang, Xinwang; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

    2013-01-01

    High abundance proteins like ribulose-1,5-bisphosphate carboxylase oxygenase (Rubisco) impose a consistent challenge for the whole proteome characterization using shot-gun proteomics. To address this challenge, we developed and evaluated Polyethyleneimine Assisted Rubisco Cleanup (PARC) as a new method by combining both abundant protein removal and fractionation. The new approach was applied to a plant insect interaction study to validate the platform and investigate mechanisms for plant defense against herbivorous insects. Our results indicated that PARC can effectively remove Rubisco, improve the protein identification, and discover almost three times more differentially regulated proteins. The significantly enhanced shot-gun proteomics performance was translated into in-depth proteomic and molecular mechanisms for plant insect interaction, where carbon re-distribution was used to play an essential role. Moreover, the transcriptomic validation also confirmed the reliability of PARC analysis. Finally, functional studies were carried out for two differentially regulated genes as revealed by PARC analysis. Insect resistance was induced by over-expressing either jacalin-like or cupin-like genes in rice. The results further highlighted that PARC can serve as an effective strategy for proteomics analysis and gene discovery. PMID:23943779

  15. 34 CFR 76.788 - What are a charter school LEA's responsibilities under this subpart?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false What are a charter school LEA's responsibilities under...? Reponsibilities for Notice and Information § 76.788 What are a charter school LEA's responsibilities under this subpart? (a) Notice. At least 120 days before the date a charter school LEA is scheduled to open...

  16. 34 CFR 76.788 - What are a charter school LEA's responsibilities under this subpart?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 1 2013-07-01 2013-07-01 false What are a charter school LEA's responsibilities under...? Reponsibilities for Notice and Information § 76.788 What are a charter school LEA's responsibilities under this subpart? (a) Notice. At least 120 days before the date a charter school LEA is scheduled to open...

  17. 34 CFR 76.788 - What are a charter school LEA's responsibilities under this subpart?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 1 2012-07-01 2012-07-01 false What are a charter school LEA's responsibilities under...? Reponsibilities for Notice and Information § 76.788 What are a charter school LEA's responsibilities under this subpart? (a) Notice. At least 120 days before the date a charter school LEA is scheduled to open...

  18. 34 CFR 76.788 - What are a charter school LEA's responsibilities under this subpart?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false What are a charter school LEA's responsibilities under...? Reponsibilities for Notice and Information § 76.788 What are a charter school LEA's responsibilities under this subpart? (a) Notice. At least 120 days before the date a charter school LEA is scheduled to open...

  19. 34 CFR 76.788 - What are a charter school LEA's responsibilities under this subpart?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 1 2014-07-01 2014-07-01 false What are a charter school LEA's responsibilities under...? Reponsibilities for Notice and Information § 76.788 What are a charter school LEA's responsibilities under this subpart? (a) Notice. At least 120 days before the date a charter school LEA is scheduled to open...

  20. Comparison of Amino Acids Physico-Chemical Properties and Usage of Late Embryogenesis Abundant Proteins, Hydrophilins and WHy Domain

    PubMed Central

    Jaspard, Emmanuel; Hunault, Gilles

    2014-01-01

    Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance. PMID:25296175

  1. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR).

    PubMed

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J; Laclette, Juan P; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-01-01

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

  2. Comparison of amino acids physico-chemical properties and usage of late embryogenesis abundant proteins, hydrophilins and WHy domain.

    PubMed

    Jaspard, Emmanuel; Hunault, Gilles

    2014-01-01

    Late Embryogenesis Abundant proteins (LEAPs) comprise several diverse protein families and are mostly involved in stress tolerance. Most of LEAPs are intrinsically disordered and thus poorly functionally characterized. LEAPs have been classified and a large number of their physico-chemical properties have been statistically analyzed. LEAPs were previously proposed to be a subset of a very wide family of proteins called hydrophilins, while a domain called WHy (Water stress and Hypersensitive response) was found in LEAP class 8 (according to our previous classification). Since little is known about hydrophilins and WHy domain, the cross-analysis of their amino acids physico-chemical properties and amino acids usage together with those of LEAPs helps to describe some of their structural features and to make hypothesis about their function. Physico-chemical properties of hydrophilins and WHy domain strongly suggest their role in dehydration tolerance, probably by interacting with water and small polar molecules. The computational analysis reveals that LEAP class 8 and hydrophilins are distinct protein families and that not all LEAPs are a protein subset of hydrophilins family as proposed earlier. Hydrophilins seem related to LEAP class 2 (also called dehydrins) and to Heat Shock Proteins 12 (HSP12). Hydrophilins are likely unstructured proteins while WHy domain is structured. LEAP class 2, hydrophilins and WHy domain are thus proposed to share a common physiological role by interacting with water or other polar/charged small molecules, hence contributing to dehydration tolerance. PMID:25296175

  3. Genome analysis of Excretory/Secretory proteins in Taenia solium reveals their Abundance of Antigenic Regions (AAR)

    PubMed Central

    Gomez, Sandra; Adalid-Peralta, Laura; Palafox-Fonseca, Hector; Cantu-Robles, Vito Adrian; Soberón, Xavier; Sciutto, Edda; Fragoso, Gladis; Bobes, Raúl J.; Laclette, Juan P.; Yauner, Luis del Pozo; Ochoa-Leyva, Adrián

    2015-01-01

    Excretory/Secretory (ES) proteins play an important role in the host-parasite interactions. Experimental identification of ES proteins is time-consuming and expensive. Alternative bioinformatics approaches are cost-effective and can be used to prioritize the experimental analysis of therapeutic targets for parasitic diseases. Here we predicted and functionally annotated the ES proteins in T. solium genome using an integration of bioinformatics tools. Additionally, we developed a novel measurement to evaluate the potential antigenicity of T. solium secretome using sequence length and number of antigenic regions of ES proteins. This measurement was formalized as the Abundance of Antigenic Regions (AAR) value. AAR value for secretome showed a similar value to that obtained for a set of experimentally determined antigenic proteins and was different to the calculated value for the non-ES proteins of T. solium genome. Furthermore, we calculated the AAR values for known helminth secretomes and they were similar to that obtained for T. solium. The results reveal the utility of AAR value as a novel genomic measurement to evaluate the potential antigenicity of secretomes. This comprehensive analysis of T. solium secretome provides functional information for future experimental studies, including the identification of novel ES proteins of therapeutic, diagnosis and immunological interest. PMID:25989346

  4. Pro-inflammatory flagellin proteins of prevalent motile commensal bacteria are variably abundant in the intestinal microbiome of elderly humans.

    PubMed

    Neville, B Anne; Sheridan, Paul O; Harris, Hugh M B; Coughlan, Simone; Flint, Harry J; Duncan, Sylvia H; Jeffery, Ian B; Claesson, Marcus J; Ross, R Paul; Scott, Karen P; O'Toole, Paul W

    2013-01-01

    Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute "cell motility" category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ(28). The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13-4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved

  5. Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans

    PubMed Central

    Neville, B. Anne; Sheridan, Paul O.; Harris, Hugh M. B.; Coughlan, Simone; Flint, Harry J.; Duncan, Sylvia H.; Jeffery, Ian B.; Claesson, Marcus J.; Ross, R. Paul; Scott, Karen P.; O'Toole, Paul W.

    2013-01-01

    Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute “cell motility” category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ28. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13–4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved

  6. Effects of Tamarindus indica fruit pulp extract on abundance of HepG2 cell lysate proteins and their possible consequential impact on metabolism and inflammation.

    PubMed

    Chong, Ursula R W; Abdul-Rahman, Puteri S; Abdul-Aziz, Azlina; Hashim, Onn H; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism. PMID:24455694

  7. Effects of Tamarindus indica Fruit Pulp Extract on Abundance of HepG2 Cell Lysate Proteins and Their Possible Consequential Impact on Metabolism and Inflammation

    PubMed Central

    Chong, Ursula R. W.; Abdul-Rahman, Puteri S.; Abdul-Aziz, Azlina; Hashim, Onn H.; Mat-Junit, Sarni

    2013-01-01

    The fruit pulp extract of Tamarindus indica has been reported for its antioxidant and hypolipidemic properties. In this study, the methanol extract of T. indica fruit pulp was investigated for its effects on the abundance of HepG2 cell lysate proteins. Cell lysate was extracted from HepG2 cells grown in the absence and presence of the methanol extract of T. indica fruit pulp. Approximately 2500 spots were resolved using two-dimensional gel electrophoresis and the abundance of 20 cellular proteins was found to be significantly reduced. Among the proteins of reduced abundance, fourteen, including six proteins involved in metabolism (including ethanolamine phosphate cytidylyltransferase), four mitochondrial proteins (including prohibitin and respiratory chain proteins), and four proteins involved in translation and splicing, were positively identified by mass spectrometry and database search. The identified HepG2 altered abundance proteins, when taken together and analyzed by Ingenuity Pathways Analysis (IPA) software, are suggestive of the effects of T. indica fruit pulp extract on metabolism and inflammation, which are modulated by LXR/RXR. In conclusion, the methanol fruit pulp extract of T. indica was shown to cause reduced abundance of HepG2 mitochondrial, metabolic, and regulatory proteins involved in oxidative phosphorylation, protein synthesis, and cellular metabolism. PMID:24455694

  8. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics.

    PubMed

    Thomas, Funmilola Clara; Mullen, William; Tassi, Riccardo; Ramírez-Torres, Adela; Mudaliar, Manikhandan; McNeilly, Tom N; Zadoks, Ruth N; Burchmore, Richard; David Eckersall, P

    2016-08-16

    A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30-48 hours post challenge with peak concentrations of APPs at 72-96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection. PMID:27412456

  9. An odorant-binding protein is abundantly expressed in the nose and in the seminal fluid of the rabbit.

    PubMed

    Mastrogiacomo, Rosa; D'Ambrosio, Chiara; Niccolini, Alberto; Serra, Andrea; Gazzano, Angelo; Scaloni, Andrea; Pelosi, Paolo

    2014-01-01

    We have purified an abundant lipocalin from the seminal fluid of the rabbit, which shows significant similarity with the sub-class of pheromone carriers "urinary" and "salivary" and presents an N-terminal sequence identical with that of an odorant-binding protein (rabOBP3) expressed in the nasal tissue of the same species. This protein is synthesised in the prostate and found in the seminal fluid, but not in sperm cells. The same protein is also expressed in the nasal epithelium of both sexes, but is completely absent in female reproductive organs. It presents four cysteines, among which two are arranged to form a disulphide bridge, and is glycosylated. This is the first report of an OBP identified at the protein level in the seminal fluid of a vertebrate species. The protein purified from seminal fluid is bound to some organic chemicals whose structure is currently under investigation. We reasonably speculate that, like urinary and salivary proteins reported in other species of mammals, this lipocalin performs a dual role, as carrier of semiochemicals in the seminal fluid and as detector of chemical signals in the nose. PMID:25391153

  10. An Odorant-Binding Protein Is Abundantly Expressed in the Nose and in the Seminal Fluid of the Rabbit

    PubMed Central

    Niccolini, Alberto; Serra, Andrea; Gazzano, Angelo; Scaloni, Andrea; Pelosi, Paolo

    2014-01-01

    We have purified an abundant lipocalin from the seminal fluid of the rabbit, which shows significant similarity with the sub-class of pheromone carriers “urinary” and “salivary” and presents an N-terminal sequence identical with that of an odorant-binding protein (rabOBP3) expressed in the nasal tissue of the same species. This protein is synthesised in the prostate and found in the seminal fluid, but not in sperm cells. The same protein is also expressed in the nasal epithelium of both sexes, but is completely absent in female reproductive organs. It presents four cysteines, among which two are arranged to form a disulphide bridge, and is glycosylated. This is the first report of an OBP identified at the protein level in the seminal fluid of a vertebrate species. The protein purified from seminal fluid is bound to some organic chemicals whose structure is currently under investigation. We reasonably speculate that, like urinary and salivary proteins reported in other species of mammals, this lipocalin performs a dual role, as carrier of semiochemicals in the seminal fluid and as detector of chemical signals in the nose. PMID:25391153

  11. Thousand and one ways to quantify and compare protein abundances in label-free bottom-up proteomics.

    PubMed

    Blein-Nicolas, Mélisande; Zivy, Michel

    2016-08-01

    How to process and analyze MS data to quantify and statistically compare protein abundances in bottom-up proteomics has been an open debate for nearly fifteen years. Two main approaches are generally used: the first is based on spectral data generated during the process of identification (e.g. peptide counting, spectral counting), while the second makes use of extracted ion currents to quantify chromatographic peaks and infer protein abundances based on peptide quantification. These two approaches actually refer to multiple methods which have been developed during the last decade, but were submitted to deep evaluations only recently. In this paper, we compiled these different methods as exhaustively as possible. We also summarized the way they address the different problems raised by bottom-up protein quantification such as normalization, the presence of shared peptides, unequal peptide measurability and missing data. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock. PMID:26947242

  12. Cell Cycle-Regulated Protein Abundance Changes in Synchronously Proliferating HeLa Cells Include Regulation of Pre-mRNA Splicing Proteins

    PubMed Central

    Lane, Karen R.; Yu, Yanbao; Lackey, Patrick E.; Chen, Xian; Marzluff, William F.; Cook, Jeanette Gowen

    2013-01-01

    Cell proliferation involves dramatic changes in DNA metabolism and cell division, and control of DNA replication, mitosis, and cytokinesis have received the greatest attention in the cell cycle field. To catalogue a wider range of cell cycle-regulated processes, we employed quantitative proteomics of synchronized HeLa cells. We quantified changes in protein abundance as cells actively progress from G1 to S phase and from S to G2 phase. We also describe a cohort of proteins whose abundance changes in response to pharmacological inhibition of the proteasome. Our analysis reveals not only the expected changes in proteins required for DNA replication and mitosis but also cell cycle-associated changes in proteins required for biological processes not known to be cell-cycle regulated. For example, many pre-mRNA alternative splicing proteins are down-regulated in S phase. Comparison of this dataset to several other proteomic datasets sheds light on global mechanisms of cell cycle phase transitions and underscores the importance of both phosphorylation and ubiquitination in cell cycle changes. PMID:23520512

  13. 34 CFR 611.47 - What are a scholarship recipient's reporting responsibilities upon the close of the LEA's...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... responsibilities upon the close of the LEA's academic year? 611.47 Section 611.47 Education Regulations of the...'s reporting responsibilities upon the close of the LEA's academic year? (a) At the close of the LEA's academic year, a scholarship recipient whose LEA reports under § 611.46(a) that he or she...

  14. 34 CFR 611.47 - What are a scholarship recipient's reporting responsibilities upon the close of the LEA's...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... responsibilities upon the close of the LEA's academic year? 611.47 Section 611.47 Education Regulations of the...'s reporting responsibilities upon the close of the LEA's academic year? (a) At the close of the LEA's academic year, a scholarship recipient whose LEA reports under § 611.46(a) that he or she...

  15. Sodium-pump gene-expression, protein abundance and enzyme activity in isolated nephron segments of the aging rat kidney

    PubMed Central

    Scherzer, Pnina; Gal-Moscovici, Anca; Sheikh-Hamad, David; Popovtzer, Mordecai M

    2015-01-01

    Aging is associated with alteration in renal tubular functions, including sodium handling and concentrating ability. Na-K-ATPase plays a key role in driving tubular transport, and we hypothesized that decreased concentrating ability of the aging kidney is due in part to downregulation of Na-K-ATPase. In this study, we evaluated Na and K balance, aldosterone levels, and Na-K-ATPase gene expression, protein abundance, and activity in aging rat kidney. Na-K-ATPase activity (assayed microfluorometrically), mRNA (RT-PCR), and protein abundance (immunoblotting) were quantitated in the following isolated nephron segments: PCT, PST, MTAL, DCT, and CCD from 2, 8, 15, and 24 month-old-rats. In the course of aging, creatinine clearance decreased from 0.48 ± 0.02 mL/min/100 g BW to 0.28 ± 0.06 (P < 0.001) and aldosterone decreased from 23.6 ± 0.8 ng/dL to 13.2 ± 0.6 (P < 0.001). Serum Na+ and K+ increased by 4.0% and 22.5%, respectively. Na-K-ATPase activity, mRNA, and protein abundance of the α1 subunit displayed similar trends in all assayed segments; increasing in PCT and PST; decreasing in MTAL and DCT; increasing in CCD: in PCT they increased by 40%, 75%, and 250%, respectively; while in PST they increased by 80%, 50%, and 100%, respectively (P < 0.001). In MTAL they declined by 36%, 24%, and 34%, respectively, and in DCT by 38%, 59%, and 60%, respectively (P < 0.001). They were higher in CCD by 110%, 115%, and 246%, respectively (P < 0.001). Rats maintained Na/K balance; however with a steady state elevated serum K+. These results reveal quantitative changes in axial distribution of Na-K-ATPase at the level of gene expression, protein abundance, and activity in the nephrons of aging animals and may explain, in part, the pathophysiology of the senescent kidney. PMID:26056060

  16. A High-Content Imaging Screen for Cellular Regulators of β-Catenin Protein Abundance.

    PubMed

    Zeng, Xin; Montoute, Monica; Bee, Tiger W; Lin, Hong; Kallal, Lorena A; Liu, Yan; Agarwal, Pankaj; Wang, Dayuan; Lu, Quinn; Morrow, Dwight; Pope, Andrew J; Wu, Zining

    2016-03-01

    Abnormal accumulation of β-catenin protein, a key transcriptional activator required for Wnt signaling, is the hallmark of many tumor types, including colon cancer. In normal cells, β-catenin protein level is tightly controlled by a multiprotein complex through the proteosome pathway. Mutations in the components of the β-catenin degradation complex, such as adenomatous polyposis coli (APC) and Axin, lead to β-catenin stabilization and the constitutive activation of target genes. Since the signal transduction of Wnt/β-catenin is mainly mediated by protein-protein interactions, this pathway has been particularly refractory to conventional target-based small-molecule screening. Here we designed a cellular high-content imaging assay to detect β-catenin protein through immunofluorescent staining in the SW480 colon cancer cell line, which has elevated β-catenin endogenously. We demonstrate that the assay is robust and specific to screen a focused biologically diverse chemical library set against known targets that play diverse cellular functions. We identified a number of hits that reduce β-catenin levels without causing cell death. These hits may serve as tools to understand the dynamics of β-catenin degradation. This study demonstrates that detecting cell-based β-catenin protein stability is a viable approach to identifying novel mechanisms of β-catenin regulation as well as small molecules of therapeutic potential. PMID:26656867

  17. 34 CFR 200.50 - SEA review of LEA progress.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 1 2014-07-01 2014-07-01 false SEA review of LEA progress. 200.50 Section 200.50 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT OF EDUCATION TITLE I-IMPROVING THE ACADEMIC ACHIEVEMENT OF THE DISADVANTAGED Improving Basic Programs Operated by...

  18. Efficient hardware implementation of the lightweight block encryption algorithm LEA.

    PubMed

    Lee, Donggeon; Kim, Dong-Chan; Kwon, Daesung; Kim, Howon

    2014-01-01

    Recently, due to the advent of resource-constrained trends, such as smartphones and smart devices, the computing environment is changing. Because our daily life is deeply intertwined with ubiquitous networks, the importance of security is growing. A lightweight encryption algorithm is essential for secure communication between these kinds of resource-constrained devices, and many researchers have been investigating this field. Recently, a lightweight block cipher called LEA was proposed. LEA was originally targeted for efficient implementation on microprocessors, as it is fast when implemented in software and furthermore, it has a small memory footprint. To reflect on recent technology, all required calculations utilize 32-bit wide operations. In addition, the algorithm is comprised of not complex S-Box-like structures but simple Addition, Rotation, and XOR operations. To the best of our knowledge, this paper is the first report on a comprehensive hardware implementation of LEA. We present various hardware structures and their implementation results according to key sizes. Even though LEA was originally targeted at software efficiency, it also shows high efficiency when implemented as hardware. PMID:24406859

  19. 34 CFR 300.816 - Allocations to LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Allocations to LEAs. 300.816 Section 300.816 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION OF CHILDREN...

  20. 34 CFR 300.815 - Subgrants to LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 2 2010-07-01 2010-07-01 false Subgrants to LEAs. 300.815 Section 300.815 Education Regulations of the Offices of the Department of Education (Continued) OFFICE OF SPECIAL EDUCATION AND REHABILITATIVE SERVICES, DEPARTMENT OF EDUCATION ASSISTANCE TO STATES FOR THE EDUCATION OF CHILDREN...

  1. Efficient Hardware Implementation of the Lightweight Block Encryption Algorithm LEA

    PubMed Central

    Lee, Donggeon; Kim, Dong-Chan; Kwon, Daesung; Kim, Howon

    2014-01-01

    Recently, due to the advent of resource-constrained trends, such as smartphones and smart devices, the computing environment is changing. Because our daily life is deeply intertwined with ubiquitous networks, the importance of security is growing. A lightweight encryption algorithm is essential for secure communication between these kinds of resource-constrained devices, and many researchers have been investigating this field. Recently, a lightweight block cipher called LEA was proposed. LEA was originally targeted for efficient implementation on microprocessors, as it is fast when implemented in software and furthermore, it has a small memory footprint. To reflect on recent technology, all required calculations utilize 32-bit wide operations. In addition, the algorithm is comprised of not complex S-Box-like structures but simple Addition, Rotation, and XOR operations. To the best of our knowledge, this paper is the first report on a comprehensive hardware implementation of LEA. We present various hardware structures and their implementation results according to key sizes. Even though LEA was originally targeted at software efficiency, it also shows high efficiency when implemented as hardware. PMID:24406859

  2. Abundance of plasma antioxidant proteins confers tolerance to acute hypobaric hypoxia exposure.

    PubMed

    Padhy, Gayatri; Sethy, Niroj Kumar; Ganju, Lilly; Bhargava, Kalpana

    2013-09-01

    Systematic identification of molecular signatures for hypobaric hypoxia can aid in better understanding of human adaptation to high altitude. In an attempt to identify proteins promoting hypoxia tolerance during acute exposure to high altitude, we screened and identified hypoxia tolerant and susceptible rats based on hyperventilation time to a simulated altitude of 32,000 ft (9754 m). The hypoxia tolerance was further validated by estimating 8-isoprotane levels and protein carbonyls, which revealed that hypoxia tolerant rats possessed significant lower plasma levels as compared to susceptible rats. We used a comparative plasma proteome profiling approach using 2-dimensional gel electrophoresis (2-DGE) combined with MALDI TOF/TOF for both groups, along with an hypoxic control group. This resulted in the identification of 19 differentially expressed proteins. Seven proteins (TTR, GPx-3, PON1, Rab-3D, CLC11, CRP, and Hp) were upregulated in hypoxia tolerant rats, while apolipoprotein A-I (APOA1) was upregulated in hypoxia susceptible rats. We further confirmed the consistent higher expression levels of three antioxidant proteins (PON1, TTR, and GPx-3) in hypoxia-tolerant animals using ELISA and immunoblotting. Collectively, these proteomics-based results highlight the role of antioxidant enzymes in conferring hypoxia tolerance during acute hypobaric hypoxia. The expression of these antioxidant enzymes could be used as putative biomarkers for screening altitude adaptation as well as aiding in better management of altered oxygen pathophysiologies. PMID:24067188

  3. Direct Correlation between Motile Behavior and Protein Abundance in Single Cells.

    PubMed

    Dufour, Yann S; Gillet, Sébastien; Frankel, Nicholas W; Weibel, Douglas B; Emonet, Thierry

    2016-09-01

    Understanding how stochastic molecular fluctuations affect cell behavior requires the quantification of both behavior and protein numbers in the same cells. Here, we combine automated microscopy with in situ hydrogel polymerization to measure single-cell protein expression after tracking swimming behavior. We characterized the distribution of non-genetic phenotypic diversity in Escherichia coli motility, which affects single-cell exploration. By expressing fluorescently tagged chemotaxis proteins (CheR and CheB) at different levels, we quantitatively mapped motile phenotype (tumble bias) to protein numbers using thousands of single-cell measurements. Our results disagreed with established models until we incorporated the role of CheB in receptor deamidation and the slow fluctuations in receptor methylation. Beyond refining models, our central finding is that changes in numbers of CheR and CheB affect the population mean tumble bias and its variance independently. Therefore, it is possible to adjust the degree of phenotypic diversity of a population by adjusting the global level of expression of CheR and CheB while keeping their ratio constant, which, as shown in previous studies, confers functional robustness to the system. Since genetic control of protein expression is heritable, our results suggest that non-genetic diversity in motile behavior is selectable, supporting earlier hypotheses that such diversity confers a selective advantage. PMID:27599206

  4. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment

    PubMed Central

    Rashydov, Namik M.; Hajduch, Martin

    2015-01-01

    Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk. PMID:26217350

  5. Chernobyl seed project. Advances in the identification of differentially abundant proteins in a radio-contaminated environment.

    PubMed

    Rashydov, Namik M; Hajduch, Martin

    2015-01-01

    Plants have the ability to grow and successfully reproduce in radio-contaminated environments, which has been highlighted by nuclear accidents at Chernobyl (1986) and Fukushima (2011). The main aim of this article is to summarize the advances of the Chernobyl seed project which has the purpose to provide proteomic characterization of plants grown in the Chernobyl area. We present a summary of comparative proteomic studies on soybean and flax seeds harvested from radio-contaminated Chernobyl areas during two successive generations. Using experimental design developed for radio-contaminated areas, altered abundances of glycine betaine, seed storage proteins, and proteins associated with carbon assimilation into fatty acids were detected. Similar studies in Fukushima radio-contaminated areas might complement these data. The results from these Chernobyl experiments can be viewed in a user-friendly format at a dedicated web-based database freely available at http://www.chernobylproteomics.sav.sk. PMID:26217350

  6. New genetic regulators question relevance of abundant yolk protein production in C. elegans

    PubMed Central

    Rompay, Liesbeth Van; Borghgraef, Charline; Beets, Isabel; Caers, Jelle; Temmerman, Liesbet

    2015-01-01

    Vitellogenesis or maternal yolk formation is considered critical to the reproduction of egg-laying animals. In invertebrates, however, most of its regulatory genes are still unknown. Via a combined mapping and whole-genome sequencing strategy, we performed a forward genetic screen to isolate novel regulators of yolk production in the nematode model system Caenorhabditis elegans. In addition to isolating new alleles of rab-35, rab-10 and M04F3.2, we identified five mutant alleles corresponding to three novel regulatory genes potently suppressing the expression of a GFP-based yolk reporter. We confirmed that mutations in vrp-1, ceh-60 and lrp-2 disrupt endogenous yolk protein synthesis at the transcriptional and translational level. In contrast to current beliefs, our discovered set of mutants with strongly reduced yolk proteins did not show serious reproduction defects. This raises questions as to whether yolk proteins per se are needed for ultimate reproductive success. PMID:26553710

  7. Spatial mapping of protein abundances in the mouse brain by voxelation integrated with high-throughput liquid chromatography-mass spectrometry.

    PubMed

    Petyuk, Vladislav A; Qian, Wei-Jun; Chin, Mark H; Wang, Haixing; Livesay, Eric A; Monroe, Matthew E; Adkins, Joshua N; Jaitly, Navdeep; Anderson, David J; Camp, David G; Smith, Desmond J; Smith, Richard D

    2007-03-01

    Temporally and spatially resolved mapping of protein abundance patterns within the mammalian brain is of significant interest for understanding brain function and molecular etiologies of neurodegenerative diseases; however, such imaging efforts have been greatly challenged by complexity of the proteome, throughput and sensitivity of applied analytical methodologies, and accurate quantitation of protein abundances across the brain. Here, we describe a methodology for comprehensive spatial proteome mapping that addresses these challenges by employing voxelation integrated with automated microscale sample processing, high-throughput liquid chromatography (LC) system coupled with high-resolution Fourier transform ion cyclotron resonance (FTICR) mass spectrometer, and a "universal" stable isotope labeled reference sample approach for robust quantitation. We applied this methodology as a proof-of-concept trial for the analysis of protein distribution within a single coronal slice of a C57BL/6J mouse brain. For relative quantitation of the protein abundances across the slice, an 18O-isotopically labeled reference sample, derived from a whole control coronal slice from another mouse, was spiked into each voxel sample, and stable isotopic intensity ratios were used to obtain measures of relative protein abundances. In total, we generated maps of protein abundance patterns for 1028 proteins. The significant agreement of the protein distributions with previously reported data supports the validity of this methodology, which opens new opportunities for studying the spatial brain proteome and its dynamics during the course of disease progression and other important biological and associated health aspects in a discovery-driven fashion. PMID:17255552

  8. Discovery and initial verification of differentially abundant proteins between multiple sclerosis patients and controls using iTRAQ and SID-SRM.

    PubMed

    Kroksveen, Ann C; Aasebø, Elise; Vethe, Heidrun; Van Pesch, Vincent; Franciotta, Diego; Teunissen, Charlotte E; Ulvik, Rune J; Vedeler, Christian; Myhr, Kjell-Morten; Barsnes, Harald; Berven, Frode S

    2013-01-14

    In the present study, we aimed to discover cerebrospinal fluid (CSF) proteins with significant abundance difference between early multiple sclerosis patients and controls, and do an initial verification of these proteins using selected reaction monitoring (SRM). iTRAQ and Orbitrap MS were used to compare the CSF proteome of patients with clinically isolated syndrome (CIS) (n=5), patients with relapsing-remitting multiple sclerosis that had CIS at the time of lumbar puncture (n=5), and controls with other inflammatory neurological disease (n=5). Of more than 1200 identified proteins, five proteins were identified with significant abundance difference between the patients and controls. In the initial verification using SRM we analyzed a larger patient and control cohort (n=132) and also included proteins reported as differentially abundant in multiple sclerosis in the literature. We found significant abundance difference for 11 proteins after verification, of which the five proteins alpha-1-antichymotrypsin, contactin-1, apolipoprotein D, clusterin, and kallikrein-6 were significantly differentially abundant in several of the group comparisons. This initial study form the basis for further biomarker verification studies in even larger sample cohorts, to determine if these proteins have relevance as diagnostic or prognostic biomarkers for multiple sclerosis. PMID:23059536

  9. Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

    PubMed

    Wang, Chen; Uversky, Vladimir N; Kurgan, Lukasz

    2016-05-01

    Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. PMID:27037624

  10. Visualizing and Quantifying Intracellular Behavior and Abundance of the Core Circadian Clock Protein PERIOD2.

    PubMed

    Smyllie, Nicola J; Pilorz, Violetta; Boyd, James; Meng, Qing-Jun; Saer, Ben; Chesham, Johanna E; Maywood, Elizabeth S; Krogager, Toke P; Spiller, David G; Boot-Handford, Raymond; White, Michael R H; Hastings, Michael H; Loudon, Andrew S I

    2016-07-25

    Transcriptional-translational feedback loops (TTFLs) are a conserved molecular motif of circadian clocks. The principal clock in mammals is the suprachiasmatic nucleus (SCN) of the hypothalamus. In SCN neurons, auto-regulatory feedback on core clock genes Period (Per) and Cryptochrome (Cry) following nuclear entry of their protein products is the basis of circadian oscillation [1, 2]. In Drosophila clock neurons, the movement of dPer into the nucleus is subject to a circadian gate that generates a delay in the TTFL, and this delay is thought to be critical for oscillation [3, 4]. Analysis of the Drosophila clock has strongly influenced models of the mammalian clock, and such models typically infer complex spatiotemporal, intracellular behaviors of mammalian clock proteins. There are, however, no direct measures of the intracellular behavior of endogenous circadian proteins to support this: dynamic analyses have been limited and often have no circadian dimension [5-7]. We therefore generated a knockin mouse expressing a fluorescent fusion of native PER2 protein (PER2::VENUS) for live imaging. PER2::VENUS recapitulates the circadian functions of wild-type PER2 and, importantly, the behavior of PER2::VENUS runs counter to the Drosophila model: it does not exhibit circadian gating of nuclear entry. Using fluorescent imaging of PER2::VENUS, we acquired the first measures of mobility, molecular concentration, and localization of an endogenous circadian protein in individual mammalian cells, and we showed how the mobility and nuclear translocation of PER2 are regulated by casein kinase. These results provide new qualitative and quantitative insights into the cellular mechanism of the mammalian circadian clock. PMID:27374340

  11. Abundant and broad expression of transcription-induced chimeras and protein products in mammalian genomes.

    PubMed

    Lu, Guanting; Wu, Jin; Zhao, Gangbin; Wang, Zhiqiang; Chen, Weihua; Mu, Shijie

    2016-02-12

    The expression of transcription-induced chimeras (TICs) was underestimated due to strategic and logical reasons. In order to thoroughly examine TICs, systematic survey of TIC events was conducted in mammalian genomes using ESTs, followed by experimental validation using RT-PCR and real-time quantitative PCR (qPCR). The expression of ∼98% TIC events in at least one tissue or cell line from both mouse and human was verified. Besides, ∼40% TICs were broadly expressed, and ∼33% of TICs showed expression levels comparable to or higher than their upstream parental genes. We further identified putative chimeric proteins in public databases and validated two using Western blotting. GO analysis revealed that proteins resided in one multi-protein complex or functioning in metabolic or signaling pathway tended to produce fused products. Taken together, we have shown substantial evidence for the underestimated TIC events; and TICs could be a novel regulated way to further increases the proteome complexity in mammalian genomes. Possible regulation mechanisms and evolution of TICs were also discussed. PMID:26718406

  12. A novel bacterial Water Hypersensitivity-like protein shows in vivo protection against cold and freeze damage.

    PubMed

    Anderson, Dominique; Ferreras, Eloy; Trindade, Marla; Cowan, Don

    2015-08-01

    Metagenomic library screening, by functional or sequence analysis, has become an established method for the identification of novel genes and gene products, including genetic elements implicated in microbial stress response and adaptation. We have identified, using a sequence-based approach, a fosmid clone from an Antarctic desert soil metagenome library containing a novel gene which codes for a protein homologous to a Water Hypersensitivity domain (WHy). The WHy domain is typically found as a component of specific LEA (Late Embryogenesis Abundant) proteins, particularly the LEA-14 (LEA-8) variants, which occur widely in plants, nematodes, bacteria and archaea and which are typically induced by exposure to stress conditions. The novel WHy-like protein (165 amino acid, 18.6 kDa) exhibits a largely invariant NPN motif at the N-terminus and has high sequence identity to genes identified in Pseudomonas genomes. Expression of this protein in Escherichia coli significantly protected the recombinant host against cold and freeze stress. PMID:26187747

  13. Do Countywide LEAs Allocate Expenditures Differently from Community-Centric LEAs? Evidence from National Center for Education Statistics Common Core Data

    ERIC Educational Resources Information Center

    DeLuca, Thomas A.

    2015-01-01

    As K-12 (kindergarten through twelfth grade) local education agencies (LEAs) face continued fiscal pressure, noninstructional service consolidation advocates point to states like Florida, with its countywide school systems, as an example of LEAs exploiting scale economies to reduce per-pupil spending, especially in administration and other…

  14. Norvaline and Norleucine May Have Been More Abundant Protein Components during Early Stages of Cell Evolution

    NASA Astrophysics Data System (ADS)

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2013-10-01

    The absence of the hydrophobic norvaline and norleucine in the inventory of protein amino acids is readdressed. The well-documented intracellular accumulation of these two amino acids results from the low-substrate specificity of the branched-chain amino acid biosynthetic enzymes that act over a number of related α-ketoacids. The lack of absolute substrate specificity of leucyl-tRNA synthase leads to a mischarged norvalyl-tRNALeu that evades the translational proofreading activites and produces norvaline-containing proteins, (cf. Apostol et al. J Biol Chem 272:28980-28988, 1997). A similar situation explains the presence of minute but detectable amounts of norleucine in place of methionine. Since with few exceptions both leucine and methionine are rarely found in the catalytic sites of most enzymes, their substitution by norvaline and norleucine, respectively, would have not been strongly hindered in small structurally simple catalytic polypeptides during the early stages of biological evolution. The report that down-shifts of free oxygen lead to high levels of intracellular accumulation of pyruvate and the subsequent biosynthesis of norvaline (Soini et al. Microb Cell Factories 7:30, 2008) demonstrates the biochemical and metabolic consequences of the development of a highly oxidizing environment. The results discussed here also suggest that a broader definition of biomarkers in the search for extraterrestrial life may be required.

  15. Proteome profiling of the growth phases of Leishmania pifanoi promastigotes in axenic culture reveals differential abundance of immunostimulatory proteins.

    PubMed

    Alcolea, Pedro J; Alonso, Ana; García-Tabares, Francisco; Mena, María del Carmen; Ciordia, Sergio; Larraga, Vicente

    2016-06-01

    Leishmaniasis is a term that encompasses a compendium of neglected tropical diseases caused by dimorphic and digenetic protozoan parasites from the genus Leishmania (Kinetoplastida: Trypanosomatidae). The clinical manifestations of neotropical cutaneous leishmaniasis (NCL) caused by Leishmania pifanoi and other species of the "Leishmania mexicana complex" mainly correspond to anergic diffuse cutaneous leishmaniasis (ADCL), which is the origin of considerable morbidity. Despite the outstanding advances in the characterization of the trypanosomatid genomes and proteomes, the biology of this species has been scarcely explored. However, the close relation of L. pifanoi to the sequenced species L. mexicana and others included in the "L. mexicana complex" allowed us to perform a two-dimension electrophoresis (2DE) approach to the promastigote proteome at the differential expression level. Protein identifications were performed by matrix-assisted laser desorption-ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF). This insight has revealed similarities and differences between L. pifanoi and other species responsible for cutaneous and visceral leishmaniasis. Interestingly, certain proteins that were previously described as immunostimulatory (elongation factor 1β, trypanothione peroxidase, heat shock protein 70, enolase, GDP-forming succinyl-CoA and aldehyde dehydrogenase) are more abundant in the final growth stages of promastigotes (late-logarithmic and/or stationary phase) in the case of L. pifanoi. PMID:26992294

  16. Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk

    PubMed Central

    Zhao, Jianguo; Xu, Weijie; Ross, Jason W.; Walters, Eric M.; Butler, Stephen P.; Whyte, Jeff J.; Kelso, Lindsey; Fatemi, Mostafa; Vanderslice, Nicholas C.; Giroux, Keith; Spate, Lee D.; Samuel, Melissa S.; Murphy, Cliff N.; Wells, Kevin D.; Masiello, Nick C.; Prather, Randall S.; Velander, William H.

    2015-01-01

    Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to <20% of the world’s population. We used transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock. PMID:26387706

  17. Engineering protein processing of the mammary gland to produce abundant hemophilia B therapy in milk.

    PubMed

    Zhao, Jianguo; Xu, Weijie; Ross, Jason W; Walters, Eric M; Butler, Stephen P; Whyte, Jeff J; Kelso, Lindsey; Fatemi, Mostafa; Vanderslice, Nicholas C; Giroux, Keith; Spate, Lee D; Samuel, Melissa S; Murphy, Cliff N; Wells, Kevin D; Masiello, Nick C; Prather, Randall S; Velander, William H

    2015-01-01

    Both the low animal cell density of bioreactors and their ability to post-translationally process recombinant factor IX (rFIX) limit hemophilia B therapy to <20% of the world's population. We used transgenic pigs to make rFIX in milk at about 3,000-fold higher output than provided by industrial bioreactors. However, this resulted in incomplete γ-carboxylation and propeptide cleavage where both processes are transmembrane mediated. We then bioengineered the co-expression of truncated, soluble human furin (rFurin) with pro-rFIX at a favorable enzyme to substrate ratio. This resulted in the complete conversion of pro-rFIX to rFIX while yielding a normal lactation. Importantly, these high levels of propeptide processing by soluble rFurin did not preempt γ-carboxylation in the ER and therefore was compartmentalized to the Trans-Golgi Network (TGN) and also to milk. The Golgi specific engineering demonstrated here segues the ER targeted enhancement of γ-carboxylation needed to biomanufacture coagulation proteins like rFIX using transgenic livestock. PMID:26387706

  18. Myosin Gene Expression and Protein Abundance in Different Castes of the Formosan Subterranean Termite (Coptotermes formosanus).

    PubMed

    Tarver, Matthew R; Florane, Christopher B; Mattison, Christopher P; Holloway, Beth A; Lax, Alan

    2012-01-01

    The Formosan subterranean termite (Coptotermes formosanus) is an important worldwide pest, each year causing millions of dollars in structural damage and control costs. Termite colonies are composed of several phenotypically distinct castes. Termites utilize these multiple castes to efficiently perform unique roles within the colony. During the molting/caste differentiation process, multiple genes are believed to be involved in the massive reorganization of the body plan. The objective of this research was to analyze the muscle gene, myosin, to further understand the role it plays in C. formosanus development. We find that comparing worker vs. solider caste myosin gene expression is up-regulated in the soldier and a myosin antibody-reactive protein suggests changes in splicing. Comparison of body regions of mature soldier and worker castes indicates a greater level of myosin transcript in the heads. The differential expression of this important muscle-related gene is anticipated considering the large amount of body plan reorganization and muscle found in the soldier caste. These results have a direct impact on our understanding of the downstream genes in the caste differentiation process and may lead to new targets for termite control. PMID:26466734

  19. Integrated analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: Zero-Inflated Poisson regression models to predict abundance of undetected proteins

    SciTech Connect

    Nie, Lei; Wu, Gang; Brockman, Fred J.; Zhang, Weiwen

    2006-05-04

    Abstract Advances in DNA microarray and proteomics technologies have enabled high-throughput measurement of mRNA expression and protein abundance. Parallel profiling of mRNA and protein on a global scale and integrative analysis of these two data types could provide additional insight into the metabolic mechanisms underlying complex biological systems. However, because protein abundance and mRNA expression are affected by many cellular and physical processes, there have been conflicting results on the correlation of these two measurements. In addition, as current proteomic methods can detect only a small fraction of proteins present in cells, no correlation study of these two data types has been done thus far at the whole-genome level. In this study, we describe a novel data-driven statistical model to integrate whole-genome microarray and proteomic data collected from Desulfovibrio vulgaris grown under three different conditions. Based on the Poisson distribution pattern of proteomic data and the fact that a large number of proteins were undetected (excess zeros), Zero-inflated Poisson models were used to define the correlation pattern of mRNA and protein abundance. The models assumed that there is a probability mass at zero representing some of the undetected proteins because of technical limitations. The models thus use abundance measurements of transcripts and proteins experimentally detected as input to generate predictions of protein abundances as output for all genes in the genome. We demonstrated the statistical models by comparatively analyzing D. vulgaris grown on lactate-based versus formate-based media. The increased expressions of Ech hydrogenase and alcohol dehydrogenase (Adh)-periplasmic Fe-only hydrogenase (Hyd) pathway for ATP synthesis were predicted for D. vulgaris grown on formate.

  20. Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis

    PubMed Central

    Soy, Judit; Leivar, Pablo; González-Schain, Nahuel; Sentandreu, Maria; Prat, Salomé; Quail, Peter H.; Monte, Elena

    2012-01-01

    SUMMARY Arabidopsis seedlings display rhythmic growth when grown under diurnal conditions, with maximal elongation rates occurring at the end of the night under short-day photoperiods. Current evidence indicates that this behavior involves the action of the growth-promoting bHLH factors PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) at the end of the night, through a coincidence mechanism that combines their transcriptional regulation by the circadian clock with control of protein accumulation by light. To assess the possible role of PIF3 in this process, we have analyzed hypocotyl responses and marker gene expression in pif single- and higher-order mutants. The data show that PIF3 plays a prominent role as a promoter of seedling growth under diurnal light/dark conditions, in conjunction with PIF4 and PIF5. In addition, we provide evidence that PIF3 functions in this process through its intrinsic transcriptional regulatory activity, at least in part by directly targeting growth-related genes, and independently of its ability to regulate phytochrome B (phyB) levels. Furthermore, in sharp contrast to PIF4 and PIF5, our data show that the PIF3 gene is not subject to transcriptional regulation by the clock, but that PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period. Collectively, the data suggest that phyB-mediated, post-translational regulation allows PIF3 accumulation to peak just before dawn, at which time it accelerates hypocotyl growth, together with PIF4 and PIF5, by directly regulating the induction of growth-related genes. PMID:22409654

  1. Competition between Heterochromatic Loci Allows the Abundance of the Silencing Protein, Sir4, to Regulate de novo Assembly of Heterochromatin

    PubMed Central

    Larin, Michelle L.; Harding, Katherine; Williams, Elizabeth C.; Lianga, Noel; Doré, Carole; Pilon, Sophie; Langis, Éric; Yanofsky, Corey; Rudner, Adam D.

    2015-01-01

    Changes in the locations and boundaries of heterochromatin are critical during development, and de novo assembly of silent chromatin in budding yeast is a well-studied model for how new sites of heterochromatin assemble. De novo assembly cannot occur in the G1 phase of the cell cycle and one to two divisions are needed for complete silent chromatin assembly and transcriptional repression. Mutation of DOT1, the histone H3 lysine 79 (K79) methyltransferase, and SET1, the histone H3 lysine 4 (K4) methyltransferase, speed de novo assembly. These observations have led to the model that regulated demethylation of histones may be a mechanism for how cells control the establishment of heterochromatin. We find that the abundance of Sir4, a protein required for the assembly of silent chromatin, decreases dramatically during a G1 arrest and therefore tested if changing the levels of Sir4 would also alter the speed of de novo establishment. Halving the level of Sir4 slows heterochromatin establishment, while increasing Sir4 speeds establishment. yku70Δ and ubp10Δ cells also speed de novo assembly, and like dot1Δ cells have defects in subtelomeric silencing, suggesting that these mutants may indirectly speed de novo establishment by liberating Sir4 from telomeres. Deleting RIF1 and RIF2, which suppresses the subtelomeric silencing defects in these mutants, rescues the advanced de novo establishment in yku70Δ and ubp10Δ cells, but not in dot1Δ cells, suggesting that YKU70 and UBP10 regulate Sir4 availability by modulating subtelomeric silencing, while DOT1 functions directly to regulate establishment. Our data support a model whereby the demethylation of histone H3 K79 and changes in Sir4 abundance and availability define two rate-limiting steps that regulate de novo assembly of heterochromatin. PMID:26587833

  2. Integrated Proteomic and Glycoproteomic Analyses of Prostate Cancer Cells Reveal Glycoprotein Alteration in Protein Abundance and Glycosylation.

    PubMed

    Shah, Punit; Wang, Xiangchun; Yang, Weiming; Toghi Eshghi, Shadi; Sun, Shisheng; Hoti, Naseruddin; Chen, Lijun; Yang, Shuang; Pasay, Jered; Rubin, Abby; Zhang, Hui

    2015-10-01

    Prostate cancer is the most common cancer among men in the U.S. and worldwide, and androgen-deprivation therapy remains the principal treatment for patients. Although a majority of patients initially respond to androgen-deprivation therapy, most will eventually develop castration resistance. An increased understanding of the mechanisms that underline the pathogenesis of castration resistance is therefore needed to develop novel therapeutics. LNCaP and PC3 prostate cancer cell lines are models for androgen-dependence and androgen-independence, respectively. Herein, we report the comparative analysis of these two prostate cancer cell lines using integrated global proteomics and glycoproteomics. Global proteome profiling of the cell lines using isobaric tags for relative and absolute quantitation (iTRAQ) labeling and two- dimensional (2D) liquid chromatography-tandem MS (LC-MS/MS) led to the quantification of 8063 proteins. To analyze the glycoproteins, glycosite-containing peptides were isolated from the same iTRAQ-labeled peptides from the cell lines using solid phase extraction followed by LC-MS/MS analysis. Among the 1810 unique N-linked glycosite-containing peptides from 653 identified N-glycoproteins, 176 glycoproteins were observed to be different between the two cell lines. A majority of the altered glycoproteins were also observed with changes in their global protein expression levels. However, alterations in 21 differentially expressed glycoproteins showed no change at the protein abundance level, indicating that the glycosylation site occupancy was different between the two cell lines. To determine the glycosylation heterogeneity at specific glycosylation sites, we further identified and quantified 1145 N-linked glycopeptides with attached glycans in the same iTRAQ-labeled samples. These intact glycopeptides contained 67 glycan compositions and showed increased fucosylation in PC3 cells in several of the examined glycosylation sites. The increase in

  3. Simplified and efficient quantification of low-abundance proteins at very high multiplex via targeted mass spectrometry.

    PubMed

    Burgess, Michael W; Keshishian, Hasmik; Mani, D R; Gillette, Michael A; Carr, Steven A

    2014-04-01

    Liquid chromatography-multiple reaction monitoring mass spectrometry (LC-MRM-MS) of plasma that has been depleted of abundant proteins and fractionated at the peptide level into six to eight fractions is a proven method for quantifying proteins present at low nanogram-per-milliliter levels. A drawback of fraction-MRM is the increased analysis time due to the generation of multiple fractions per biological sample. We now report that the use of heated, long, fused silica columns (>30 cm) packed with 1.9 μm of packing material can reduce or eliminate the need for fractionation prior to LC-MRM-MS without a significant loss of sensitivity or precision relative to fraction-MRM. We empirically determined the optimal column length, temperature, gradient duration, and sample load for such assays and used these conditions to study detection sensitivity and assay precision. In addition to increased peak capacity, longer columns packed with smaller beads tolerated a 4- to 6-fold increase in analyte load without a loss of robustness or reproducibility. The longer columns also provided a 4-fold improvement in median limit-of-quantitation values with increased assay precision relative to the standard 12 cm columns packed with 3 μm material. Overall, the optimized chromatography provided an approximately 3-fold increase in analysis throughput with excellent robustness and less than a 2-fold reduction in quantitative sensitivity relative to fraction-MRM. The value of the system for increased multiplexing was demonstrated by the ability to configure an 800-plex MRM-MS assay, run in a single analysis, comprising 2400 transitions with retention time scheduling to monitor 400 unlabeled and heavy labeled peptide pairs. PMID:24522978

  4. Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

    PubMed Central

    Chen, Wei-Hua; van Noort, Vera; Lluch-Senar, Maria; Hennrich, Marco L.; H. Wodke, Judith A.; Yus, Eva; Alibés, Andreu; Roma, Guglielmo; Mende, Daniel R.; Pesavento, Christina; Typas, Athanasios; Gavin, Anne-Claude; Serrano, Luis; Bork, Peer

    2016-01-01

    We developed a comprehensive resource for the genome-reduced bacterium Mycoplasma pneumoniae comprising 1748 consistently generated ‘-omics’ data sets, and used it to quantify the power of antisense non-coding RNAs (ncRNAs), lysine acetylation, and protein phosphorylation in predicting protein abundance (11%, 24% and 8%, respectively). These factors taken together are four times more predictive of the proteome abundance than of mRNA abundance. In bacteria, post-translational modifications (PTMs) and ncRNA transcription were both found to increase with decreasing genomic GC-content and genome size. Thus, the evolutionary forces constraining genome size and GC-content modify the relative contributions of the different regulatory layers to proteome homeostasis, and impact more genomic and genetic features than previously appreciated. Indeed, these scaling principles will enable us to develop more informed approaches when engineering minimal synthetic genomes. PMID:26773059

  5. 34 CFR 200.77 - Reservation of funds by an LEA.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... § 200.48, unless the LEA meets these requirements with non-Title I funds; (d) Address the professional development needs of instructional staff, including— (1) Professional development requirements under § 200.52(a)(3)(iii) if the LEA has been identified for improvement or corrective action; and (2)...

  6. 34 CFR 200.77 - Reservation of funds by an LEA.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... § 200.48, unless the LEA meets these requirements with non-Title I funds; (d) Address the professional development needs of instructional staff, including— (1) Professional development requirements under § 200.52(a)(3)(iii) if the LEA has been identified for improvement or corrective action; and (2)...

  7. 34 CFR 200.77 - Reservation of funds by an LEA.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... § 200.48, unless the LEA meets these requirements with non-Title I funds; (d) Address the professional development needs of instructional staff, including— (1) Professional development requirements under § 200.52(a)(3)(iii) if the LEA has been identified for improvement or corrective action; and (2)...

  8. 45 CFR 86.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 1 2013-10-01 2013-10-01 false Access to schools operated by L.E.A.s. 86.35 Section 86.35 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION... operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of...

  9. 45 CFR 86.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 1 2011-10-01 2011-10-01 false Access to schools operated by L.E.A.s. 86.35 Section 86.35 Public Welfare DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL ADMINISTRATION... operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of...

  10. 7 CFR 15a.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 1 2011-01-01 2011-01-01 false Access to schools operated by L.E.A.s. 15a.35 Section 15a.35 Agriculture Office of the Secretary of Agriculture EDUCATION PROGRAMS OR ACTIVITIES RECEIVING... Programs and Activities Prohibited § 15a.35 Access to schools operated by L.E.A.s. A recipient which is...

  11. The LEA's Role in a Decentralized School System: The School Principals' View

    ERIC Educational Resources Information Center

    Addi-Raccah, Audrey; Gavish, Yakov

    2010-01-01

    Since the wave of school reform decentralization, schools now maintain a more dynamic and diverse relationship with their environment than they did in the past. School principals' relationships with the local educational authority (LEA) are a prominent example of this change in Israel. LEAs try to gain more pedagogic influence over schools while…

  12. 34 CFR 222.187 - Which year's data must an SEA or LEA provide?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Which year's data must an SEA or LEA provide? 222.187 Section 222.187 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY... data must an SEA or LEA provide? (a) Except as provided in paragraph (b) of this section, the...

  13. Managing the Performance of Staff in LEAs in Wales: Practice, Problems and Possibilities

    ERIC Educational Resources Information Center

    James, Chris; Colebourne, David

    2004-01-01

    Recent policy developments are changing the work of local education authorities (LEAs) in Wales requiring them to play a broader role in the community and a significant role in raising educational achievement. LEAs are obligated to set out their improvement targets in institutional plans and are called to account by external inspection, which…

  14. Interleukin (IL)-1 in rat parturition: IL-1 receptors 1 and 2 and accessory proteins abundance in pregnant rat uterus at term - regulation by progesterone.

    PubMed

    Ishiguro, Tomohito; Takeda, Jun; Fang, Xin; Bronson, Heather; Olson, David M

    2016-07-01

    The role of interleukin-1 (IL-1), a pro-inflammatory cytokine, in parturition is typically noted by changes in its concentrations. Studying the expression of its receptor family, IL-1 receptor (IL-1R) 1, IL-1R2, IL-1R accessory protein (IL-1RAcP), and its predominantly brain isoform, IL-1RAcPb, during late gestation in the uterus in the Long-Evans rat is another. We assessed changes in their mRNA and protein relative abundance in the uterus and compared IL-1RAcP and IL-1RAcPb mRNA abundance in uterus, cervix, ovaries, placenta, and whole blood of Long-Evans rats during late gestation or in RU486 and progesterone-treated dams using quantitative real-time PCR and western immunoblotting. IL-1R1, IL-1RAcP, and IL-1RAcPb mRNA abundance significantly increased in the uterus at delivery whereas IL-1R2 mRNA abundance significantly decreased. IL-1R1 protein increased at term and IL-1R2 protein decreased at term compared to nonpregnant uteri. IL1-RAcPb mRNA abundance was less than IL-1RAcP, but in the lower uterine segment it was the highest of all tissues examined. RU486 stimulated preterm delivery and an increase in IL-1R1 mRNA abundance whereas progesterone administration extended pregnancy and suppressed the increase in IL-1R1. These data suggest that changes in uterine sensitivity to IL-1 occur during late gestation and suggest another level of regulation for the control of delivery. The roles for IL-1RAcP and IL-1RAcPb need to be determined, but may relate to different intracellular signaling pathways. PMID:27440742

  15. 76 FR 71417 - Privacy Act of 1974, as Amended; Computer Matching Program (SSA/Law Enforcement Agencies (LEA...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-17

    ... ADMINISTRATION Privacy Act of 1974, as Amended; Computer Matching Program (SSA/ Law Enforcement Agencies (LEA... program that we are currently conducting with LEA. DATES: We will file a report of the subject matching... General Counsel. Notice of Computer Matching Program, SSA With the Law Enforcement Agency (LEA)...

  16. [Comparative sequence analysis of the LEA gene fragment in Pinus sibirica du tour and Pinus pumila (Pallas) regel].

    PubMed

    Mglinets, A V; Sokolov, V A; Petrova, E A; Goroshkevich, S N

    2014-02-01

    A comparative sequence analysis of the LEA (Late Embryogenesis Abundant (LEA)-like gene) intron fragment was performed in Pinus sibirica and P. pumila differing in geographic origin. It was demonstrated that in P. sibirica this fragment was represented by two types of PCR products, 224 and 202 bp in size. Similarly, in accessions of P. pumila, two PCR products of 224 and 159 bp in size were identified. Comparison of 224 bp fragments in P. sibirica and P. pumila showed that they differed in single nucleotide substitutions. Analysis of the intron fragment in a plant, which was characterized as an interspecific hybrid based on morphological characters, showed that it had fragments of 224 and 159 bp in size. The sequence of 224 bp fragment was similar to that of the corresponding fragment in P. sibirica. The structure of the short fragment was the same as the structure of the corresponding fragment in P. pumila. The data obtained are discussed in terms of the use of the sequences examined for species taxonomic classification and of an analysis of species hybridization. PMID:25711024

  17. SOLiD-SAGE of Endophyte-Infected Red Fescue Reveals Numerous Effects on Host Transcriptome and an Abundance of Highly Expressed Fungal Secreted Proteins

    PubMed Central

    Ambrose, Karen V.; Belanger, Faith C.

    2012-01-01

    One of the most important plant-fungal symbiotic relationships is that of cool season grasses with endophytic fungi of the genera Epichloë and Neotyphodium. These associations often confer benefits, such as resistance to herbivores and improved drought tolerance, to the hosts. One benefit that appears to be unique to fine fescue grasses is disease resistance. As a first step towards understanding the basis of the endophyte-mediated disease resistance in Festuca rubra we carried out a SOLiD-SAGE quantitative transcriptome comparison of endophyte-free and Epichloë festucae-infected F. rubra. Over 200 plant genes involved in a wide variety of physiological processes were statistically significantly differentially expressed between the two samples. Many of the endophyte expressed genes were surprisingly abundant, with the most abundant fungal tag representing over 10% of the fungal mapped tags. Many of the abundant fungal tags were for secreted proteins. The second most abundantly expressed fungal gene was for a secreted antifungal protein and is of particular interest regarding the endophyte-mediated disease resistance. Similar genes in Penicillium and Aspergillus spp. have been demonstrated to have antifungal activity. Of the 10 epichloae whole genome sequences available, only one isolate of E. festucae and Neotyphodium gansuense var inebrians have an antifungal protein gene. The uniqueness of this gene in E. festucae from F. rubra, its transcript abundance, and the secreted nature of the protein, all suggest it may be involved in the disease resistance conferred to the host, which is a unique feature of the fine fescue–endophyte symbiosis. PMID:23285269

  18. 34 CFR 76.791 - On what basis does an SEA determine whether a charter school LEA that opens or significantly...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... charter school LEA that opens or significantly expands its enrollment is eligible to receive funds under a covered program? (a) For purposes of this subpart, an SEA must determine whether a charter school LEA is... the charter school LEA on or after the date the charter school LEA opens or significantly expands...

  19. 34 CFR 76.791 - On what basis does an SEA determine whether a charter school LEA that opens or significantly...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... charter school LEA that opens or significantly expands its enrollment is eligible to receive funds under a covered program? (a) For purposes of this subpart, an SEA must determine whether a charter school LEA is... the charter school LEA on or after the date the charter school LEA opens or significantly expands...

  20. 34 CFR 76.791 - On what basis does an SEA determine whether a charter school LEA that opens or significantly...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... charter school LEA that opens or significantly expands its enrollment is eligible to receive funds under a covered program? (a) For purposes of this subpart, an SEA must determine whether a charter school LEA is... the charter school LEA on or after the date the charter school LEA opens or significantly expands...

  1. 34 CFR 76.791 - On what basis does an SEA determine whether a charter school LEA that opens or significantly...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... charter school LEA that opens or significantly expands its enrollment is eligible to receive funds under a covered program? (a) For purposes of this subpart, an SEA must determine whether a charter school LEA is... the charter school LEA on or after the date the charter school LEA opens or significantly expands...

  2. 34 CFR 76.791 - On what basis does an SEA determine whether a charter school LEA that opens or significantly...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... charter school LEA that opens or significantly expands its enrollment is eligible to receive funds under a covered program? (a) For purposes of this subpart, an SEA must determine whether a charter school LEA is... the charter school LEA on or after the date the charter school LEA opens or significantly expands...

  3. 34 CFR 76.796 - What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... fewer funds to a charter school LEA under a covered program than the amount for which the charter school LEA is eligible when the charter school LEA actually opens or significantly expands its enrollment? 76....796 What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

  4. 34 CFR 76.796 - What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... fewer funds to a charter school LEA under a covered program than the amount for which the charter school LEA is eligible when the charter school LEA actually opens or significantly expands its enrollment? 76....796 What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

  5. 34 CFR 76.796 - What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... fewer funds to a charter school LEA under a covered program than the amount for which the charter school LEA is eligible when the charter school LEA actually opens or significantly expands its enrollment? 76....796 What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

  6. 34 CFR 76.796 - What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... fewer funds to a charter school LEA under a covered program than the amount for which the charter school LEA is eligible when the charter school LEA actually opens or significantly expands its enrollment? 76....796 What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

  7. 34 CFR 76.796 - What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... fewer funds to a charter school LEA under a covered program than the amount for which the charter school LEA is eligible when the charter school LEA actually opens or significantly expands its enrollment? 76....796 What are the consequences of an SEA allocating more or fewer funds to a charter school LEA under...

  8. Selectivity of monolithic supports under overloading conditions and their use for separation of human plasma and isolation of low abundance proteins

    PubMed Central

    Brgles, Marija; Clifton, James; Walsh, Robert; Huang, Feilei; Rucevic, Marijana; Cao, Lulu; Hixson, Douglas; Müller, Egbert

    2011-01-01

    Human serum albumin (HSA) and immunoglobulin G (IgG) represent over 75% of all proteins present in human plasma. These two proteins frequently interfere with detection, determination and purification of low abundance proteins that can be potential biomarkers and biomarker candidates for various diseases. Some low abundance plasma proteins such as clotting factors and inhibitors are also important therapeutic agents. In this paper, the characterization of ion-exchange monolithic supports under overloading conditions was performed by use of sample displacement chromatography (SDC). If these supports were used for separation of human plasma, the composition of bound and eluted proteins in both anion- and cation-exchange mode is dependent on column loading. Under overloading conditions, the weakly bound proteins such as HSA in anion-exchange and IgG in cation-exchange mode are displaced by stronger binding proteins, and this phenomenon was not dependent on column size. Consequently, small monolithic columns with a column volume of 100 and 200 μL are ideal supports for high-throughput screening in order to develop new methods for separation of complex mixtures, and for sample preparation in proteomic technology. PMID:21186030

  9. The relative abundance of a salivary protein, bSP30, is correlated with susceptibility to bloat in cattle herds selected for high or low bloat susceptibility.

    PubMed

    Rajan, G H; Morris, C A; Carruthers, V R; Wilkins, R J; Wheeler, T T

    1996-12-01

    Pasture bloat is a serious economic and animal welfare problem in cattle grazed on legumes in New Zealand. Analysis of salivary proteins from dairy cattle in herds bred for either low or high susceptibility to bloat has resulted in the identification of a 30 kilodalton protein, which we term bSP30, whose relative abundance is negatively correlated with bloat score (r = -0.40 +/- 0.12). From 74 animals sampled, relative abundance of bSP30 was 66 +/- 15% higher in the low-susceptibility herd than in the high-susceptibility herd. Relative abundance of bSP30 also varied significantly within individuals, according to feeding or time of day, and from day to day. A sequence homology search of 38 amino acids derived from three tryptic fragments of the protein suggests that the amino acid sequence of bSP30 has not been described previously. Amino acid analysis indicates that bSP30 is not a member of the proline-rich family of salivary proteins. The function of bSP30 is unknown but it is conceivable that it plays a role in the aetiology of bloat. PMID:9022155

  10. Correlation of mRNA expression and protein abundance affected by multiple sequence features related to translational efficiency in Desulfovibrio vulgaris: A quantitative analysis

    SciTech Connect

    Nie, Lei; Wu, Gang; Zhang, Weiwen

    2006-12-01

    The modest correlation between mRNA expression and protein abundance in large scale datasets is explained in part by experimental challenges, such as technological limitations, and in part by fundamental biological factors in the transcription and translation processes. Among various factors affecting the mRNA-protein correlation, the roles of biological factors related to translation are poorly understood. In this study, using experimental mRNA expression and protein abundance data collected from Desulfovibrio vulgaris by DNA microarray and LC-MS/MS proteomic analysis, we quantitatively examined the effects of several translational-efficiency-related sequence features on mRNA-protein correlation. Three classes of sequence features were investigated according to different translational stages: (1) initiation: Shine-Dalgarno sequences, start codon identity and start codon context; (2) elongation: codon usage and amino acid usage; and (3) termination: stop codon identity and stop codon context. Surprisingly, although it is widely accepted that translation initiation is a rate-limiting step for translation, our results showed that the mRNA-protein correlation was affected the most by the features at elongation stages, codon usage and amino acid composition (7.4-12.6% and 5.3-9.3% of the total variation of mRNA-protein correlation, respectively), followed by stop codon context and the Shine-Dalgarno sequence (2.5-4.2% and 2.3%, respectively). Taken together, all sequence features contributed to 18.4-21.8% of the total variation of mRNA-protein correlation. As the first comprehensive quantitative analysis of the mRNA-protein correlation in bacterial D. vulgaris, our results suggest that the traditional view of the relative importance of various sequence features in prokaryotic protein translation might be questionable.

  11. Preovulatory Aging In Vivo and In Vitro Affects Maturation Rates, Abundance of Selected Proteins, Histone Methylation Pattern and Spindle Integrity in Murine Oocytes.

    PubMed

    Demond, Hannah; Trapphoff, Tom; Dankert, Deborah; Heiligentag, Martyna; Grümmer, Ruth; Horsthemke, Bernhard; Eichenlaub-Ritter, Ursula

    2016-01-01

    Delayed ovulation and delayed fertilization can lead to reduced developmental competence of the oocyte. In contrast to the consequences of postovulatory aging of the oocyte, hardly anything is known about the molecular processes occurring during oocyte maturation if ovulation is delayed (preovulatory aging). We investigated several aspects of oocyte maturation in two models of preovulatory aging: an in vitro follicle culture and an in vivo mouse model in which ovulation was postponed using the GnRH antagonist cetrorelix. Both models showed significantly reduced oocyte maturation rates after aging. Furthermore, in vitro preovulatory aging deregulated the protein abundance of the maternal effect genes Smarca4 and Nlrp5, decreased the levels of histone H3K9 trimethylation and caused major deterioration of chromosome alignment and spindle conformation. Protein abundance of YBX2, an important regulator of mRNA stability, storage and recruitment in the oocyte, was not affected by in vitro aging. In contrast, in vivo preovulatory aging led to reduction in Ybx2 transcript and YBX2 protein abundance. Taken together, preovulatory aging seems to affect various processes in the oocyte, which could explain the low maturation rates and the previously described failures in fertilization and embryonic development. PMID:27611906

  12. A combined blood based gene expression and plasma protein abundance signature for diagnosis of epithelial ovarian cancer - a study of the OVCAD consortium

    PubMed Central

    2013-01-01

    Background The immune system is a key player in fighting cancer. Thus, we sought to identify a molecular ‘immune response signature’ indicating the presence of epithelial ovarian cancer (EOC) and to combine this with a serum protein biomarker panel to increase the specificity and sensitivity for earlier detection of EOC. Methods Comparing the expression of 32,000 genes in a leukocytes fraction from 44 EOC patients and 19 controls, three uncorrelated shrunken centroid models were selected, comprised of 7, 14, and 6 genes. A second selection step using RT-qPCR data and significance analysis of microarrays yielded 13 genes (AP2A1, B4GALT1, C1orf63, CCR2, CFP, DIS3, NEAT1, NOXA1, OSM, PAPOLG, PRIC285, ZNF419, and BC037918) which were finally used in 343 samples (90 healthy, six cystadenoma, eight low malignant potential tumor, 19 FIGO I/II, and 220 FIGO III/IV EOC patients). Using new 65 controls and 224 EOC patients (thereof 14 FIGO I/II) the abundances of six plasma proteins (MIF, prolactin, CA125, leptin, osteopondin, and IGF2) was determined and used in combination with the expression values from the 13 genes for diagnosis of EOC. Results Combined diagnostic models using either each five gene expression and plasma protein abundance values or 13 gene expression and six plasma protein abundance values can discriminate controls from patients with EOC with Receiver Operator Characteristics Area Under the Curve values of 0.998 and bootstrap .632+ validated classification errors of 3.1% and 2.8%, respectively. The sensitivities were 97.8% and 95.6%, respectively, at a set specificity of 99.6%. Conclusions The combination of gene expression and plasma protein based blood derived biomarkers in one diagnostic model increases the sensitivity and the specificity significantly. Such a diagnostic test may allow earlier diagnosis of epithelial ovarian cancer. PMID:23551967

  13. 34 CFR 222.171 - What LEAs may be eligible for Discretionary Construction grants?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT OF EDUCATION IMPACT AID PROGRAMS Impact...) Generally, to be eligible for a modernization construction grant, an LEA must— (i) Be eligible for...

  14. 34 CFR 200.70 - Allocation of funds to LEAs in general.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... school attendance areas of the LEA (hereinafter referred to as the “Census list”). (b) In establishing... 17, inclusive (hereinafter referred to as “formula children”)— (1) From families below the...

  15. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function.

    PubMed

    Krey, Jocelyn F; Drummond, Meghan; Foster, Sarah; Porsov, Edward; Vijayakumar, Sarath; Choi, Dongseok; Friderici, Karen; Jones, Sherri M; Nuttall, Alfred L; Barr-Gillespie, Peter G

    2016-01-01

    The phospholipid- and Ca(2+)-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, the inner ear's sensory organelle. Using quantitative mass spectrometry, we estimated that ANXA5 accounts for ~15,000 copies per stereocilium, or ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were present at levels near ANXA5 in bundles and none were upregulated in stereocilia of Anxa5(-/-) mice. Annexins have been proposed to mediate Ca(2+)-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, mature Anxa5(-/-) mice not only have normal hearing and balance function, but following noise exposure, they are identical to wild-type mice in their temporary or permanent changes in hearing sensitivity. We suggest that despite the unusually high levels of ANXA5 in bundles, it does not play a role in the bundle's key function, mechanotransduction, at least until after two months of age in the cochlea and six months of age in the vestibular system. These results reinforce the lack of correlation between abundance of a protein in a specific compartment or cellular structure and its functional significance. PMID:27251877

  16. Correlated Changes in the Activity, Amount of Protein, and Abundance of Transcript of NADPH:Protochlorophyllide Oxidoreductase and Chlorophyll Accumulation during Greening of Cucumber Cotyledons.

    PubMed Central

    Yoshida, K.; Chen, R. M.; Tanaka, A.; Teramoto, H.; Tanaka, R.; Timko, M. P.; Tsuji, H.

    1995-01-01

    Changes in the activity and abundance of NADPH:protochlorophyllide oxidoreductase (NPR) and the abundance of mRNA encoding it were examined during the greening of 5-d-old etiolated cucumber cotyledons under continuous illumination. To measure NPR activity in the extracts from fully greened tissues, we have developed an improved method of assay. Upon exposure of etiolated cotyledons to light, NPR activity decreased rapidly within the first 2 h of exposure. Thereafter, enzymatic activity increased transiently, reaching a submaximum level at 12 h, and decreased slowly. The level of immunodetectable NPR protein followed the same pattern of changes during 96 h of greening as observed for NPR activity. The NPR mRNA in etiolated cotyledons disappeared quickly in the 1st h of irradiation. However, the level of mRNA increased thereafter to reach 3-fold or more of the dark level at 12 h and then decreased. The changes in the activity, protein level, and mRNA level after the first rapid decreases corresponded chronologically and nearly paralleled the increase in the rate of chlorophyll accumulation. These findings suggest that the greening of cucumber cotyledons is regulated basically by the level of NPR protein without activation or repression of enzymatic activity and that NPR mRNA increased by light maintains the level of enzyme protein necessary for greening. PMID:12228591

  17. Annexin A5 is the Most Abundant Membrane-Associated Protein in Stereocilia but is Dispensable for Hair-Bundle Development and Function

    PubMed Central

    Krey, Jocelyn F.; Drummond, Meghan; Foster, Sarah; Porsov, Edward; Vijayakumar, Sarath; Choi, Dongseok; Friderici, Karen; Jones, Sherri M.; Nuttall, Alfred L.; Barr-Gillespie, Peter G.

    2016-01-01

    The phospholipid- and Ca2+-binding protein annexin A5 (ANXA5) is the most abundant membrane-associated protein of ~P23 mouse vestibular hair bundles, the inner ear’s sensory organelle. Using quantitative mass spectrometry, we estimated that ANXA5 accounts for ~15,000 copies per stereocilium, or ~2% of the total protein there. Although seven other annexin genes are expressed in mouse utricles, mass spectrometry showed that none were present at levels near ANXA5 in bundles and none were upregulated in stereocilia of Anxa5−/− mice. Annexins have been proposed to mediate Ca2+-dependent repair of membrane lesions, which could be part of the repair mechanism in hair cells after noise damage. Nevertheless, mature Anxa5−/− mice not only have normal hearing and balance function, but following noise exposure, they are identical to wild-type mice in their temporary or permanent changes in hearing sensitivity. We suggest that despite the unusually high levels of ANXA5 in bundles, it does not play a role in the bundle’s key function, mechanotransduction, at least until after two months of age in the cochlea and six months of age in the vestibular system. These results reinforce the lack of correlation between abundance of a protein in a specific compartment or cellular structure and its functional significance. PMID:27251877

  18. Effect of ultrasonic stimulation on mRNA abundance of uncoupling protein (UCP) 2 and UCP 3 in gastrocnemius muscle of rats.

    PubMed

    Kogure, Akinori; Yoshida, Toshihide; Takakura, Yasuto; Umekawa, Tsunekazu; Hioki, Chizuko; Yoshioka, Keiji; Yoshimoto, Kanji; Yoshikawa, Toshikazu

    2005-01-01

    1. The hypothesis that ultrasonic stimulation upregulates uncoupling protein (UCP) 2 and UCP3 in gastrocnemius muscle by a different mechanism of exercise was investigated in Wister rats. 2. The ultrasnonic-stimulated group was given ultrasonic stimulation to the leg (1 MHz frequency, 1 W/cm2 intensity, 10 min continuously). 3. The exercise group was given exercise training by swimming for 10 min in plastic barrels filled with warm water. 4. After 3 h, rats were killed and the gastrocnemius muscle was removed rapidly, weighed and frozen in liquid nitrogen for real-time quantitative reverse transcription-polymerase chain reaction analysis. 5. In gastrocnenius muscles of ultrasonic-stimulated rats, UCP3 mRNA abundance was significantly increased 3.6-fold and UCP2 mRNA abundance was significantly increased 2.2-fold compared with control rats. 6. In gastrocnenius muscles of exercised rats, UCP3 mRNA abundance was significantly increased 3.5-fold compared with control rats, but no change in UCP2 mRNA abundance was observed. 7. Plasma free fatty acid (FFA) levels were also significantly increased in the ultrasonic stimulation group, as well as the exercise group, compared with the control group. 8. These findings show that ultrasonic stimulation lipolyses subcutaneous fat into FFA and glycerol and upregulates UCP2 and UCP3 mRNA by a mechanism different to that of exercise. PMID:15730441

  19. The pro-oxidant buthionine sulfoximine (BSO) reduces tumor growth of implanted Lewis lung carcinoma in mice associated with increased protein carbonyl, tubulin abundance, and aminopeptidase activity.

    PubMed

    Rodríguez-Gómez, Isabel; Carmona-Cortés, Javier; Wangensteen, Rosemary; Vargas-Tendero, Pablo; Banegas, Inmaculada; Quesada, Andrés; García-Lora, Angel M; Vargas, Félix

    2014-08-01

    This study evaluated the effects of the pro-oxidant buthionine sulfoximine (BSO) and of the interaction between BSO and TETRAC, an antagonist of αvß3 integrin, on tumor development and aminopeptidase (AP) activity in a murine model of implanted Lewis's carcinoma. Male CBA-C57 mice were untreated (controls) or treated with BSO (222 mg/100 mL in drinking water), TETRAC (10 mg/kg/day, i.p.), or BSO + TETRAC. BSO for 28 days and TETRAC were given for the last 20 days. Mice were subcutaneously inoculated with 1 × 10(6) Lewis carcinoma 3LL cells into the dorsum. Study variables were tumor weight (TW); Hb, as index of tumor-mediated angiogenesis; vascular endothelial growth factor (VEGF) protein abundance; protein carbonyl content; α-tubulin abundance; and GluAp, AlaAp, and AspAp activities. BSO produced a major decrease in TW (203 ± 18 mg) with respect to controls (365 ± 26) and a reduction in Hb content. The TETRAC group also showed marked reductions in TW (129 ± 15) and Hb concentration associated with a reduced VEGF content. The BSO + TETRAC group showed a major TW reduction (125 ± 13); although, the difference with the TETRAC group was not significant. BSO treatment increased protein carbonyl and tubulin abundance in comparison to controls. The activity of all APs was increased in the three experimental groups and was strongly and negatively correlated with TW. In conclusion, administration of BSO reduced the TW, which inversely correlated with protein carbonyl content, suggesting a loss of microtubule polymerization. The finding of a negative correlation between TW and AP activity opens up new perspectives for the study of APs as tumor growth modulators. PMID:24816945

  20. Bee bread increases honeybee haemolymph protein and promote better survival despite of causing higher Nosema ceranae abundance in honeybees.

    PubMed

    Basualdo, Marina; Barragán, Sergio; Antúnez, Karina

    2014-08-01

    Adequate protein nutrition supports healthy honeybees and reduces the susceptibility to disease. However little is known concerning the effect of the diet on Nosema ceranae development, an obligate intracellular parasite that disturbs the protein metabolism of honeybees (Apis mellifera). Here we tested the effect of natural (bee bread) and non-natural protein diets (substitute) on haemolymph proteins titers of honeybee and N. ceranae spore production. The natural diet induced higher levels of protein and parasite development, but the survival of bees was also higher than with non-natural diets. The data showed that the administration of an artificially high nutritious diet in terms of crude protein content is not sufficient to promote healthy bees; rather the protein ingested should be efficiently assimilated. The overall results support the idea that the physiological condition of the bees is linked to protein levels in the haemolymph, which affects the tolerance to parasite; consequently the negative impact of the parasite on host fitness is not associated only with the level of infection. PMID:24992539

  1. The reliability and validity of the Japanese version of the Levels of Emotional Awareness Scale (LEAS-J)

    PubMed Central

    2011-01-01

    Background The Levels of Emotional Awareness Scale (LEAS) was developed to assess five levels of emotional awareness: bodily sensations, action tendencies, single emotions, blends of emotion, and combinations of blends. It is a paper and pencil performance questionnaire that presents 20 emotion-evoking scenes. We developed a Japanese version of the LEAS (LEAS-J), and its reliability and validity were examined. Methods The LEAS-J level was independently assessed by two researchers who scored each response according to the LEAS scoring manual. High inter-rater reliability and internal consistency were obtained for the LEAS-J. Measures were socioeconomic status, LEAS-J, Toronto Alexithymia Scale-20 (TAS-20), Interpersonal Reactivity Index (IRI), and NEO Five-Factor Inventory (NEO-FFI). TAS-20, IRI and NEO-FFI were the measures used to explore the construct validity of LEAS-J, as it was predicted that higher scores on the LEAS-J would be related to fewer alexithymic features, greater empathetic ability, and a greater sense of cooperation with others. Questionnaires were completed by 344 university students. Results The criterion-referenced validity was determined: a significant negative relationship was found with the externally-oriented thinking scores of TAS-20, and positive relationships were found with fantasy, perspective taking, and empathic concern on IRI and with extraversion, openness to experience, and agreeableness on NEO-FFI. Conclusions Consistent with our expectations, the findings provide evidence that the LEAS-J has good reliability and validity. In addition, women had significantly higher scores than men on LEAS-J, showing that the gender difference identified in the original LEAS was cross-culturally consistent. PMID:21281491

  2. PHYSCOMITRELLA PATENS ARABINOGALACTAN PROTEINS CONTAIN ABUNDANT TERMINAL 3-O-METHYL-L-RHAMMOSYL RESIDUES NOT FOUND IN ANGIOSPERMS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A biochemical investigation of arabinogalactan proteins (AGPs) in Physcomitrella patens was undertaken with particular emphasis on the glycan chains. Following homogenization and differential centrifugation of moss gametophytes, AGPs were obtained by Arrive phenylglycoside-induced precipitation from...

  3. Correlation between mRNA and protein abundance in Desulfovibrio vulgaris: A multiple regression to identify sources of variations

    SciTech Connect

    Nie, Lei; Wu, G; Zhang, Weiwen

    2006-01-13

    Using whole-genome microarray and LC-MC/MS proteomic data collected from Desulfovibrio vulgaris grown under three different conditions, we systematically investigate the relationship between mRNA and protein abundunce by a multiple regression approach.

  4. Core-shell molecularly imprinted polymer nanoparticles with assistant recognition polymer chains for effective recognition and enrichment of natural low-abundance protein.

    PubMed

    Liu, Dejing; Yang, Qian; Jin, Susu; Song, Yingying; Gao, Junfei; Wang, Ying; Mi, Huaifeng

    2014-02-01

    Core-shell molecular imprinting of nanomaterials overcomes difficulties with template transfer and achieves higher binding capacities for macromolecular imprinting, which are more important to the imprinting of natural low-abundance proteins from cell extracts. In the present study, a novel strategy of preparing core-shell nanostructured molecularly imprinted polymers (MIPs) was developed that combined the core-shell approach with assistant recognition polymer chains (ARPCs). Vinyl-modified silica nanoparticles were used as support and ARPCs were used as additional functional monomers. Immunoglobulin heavy chain binding protein (BiP) from the endoplasmic reticulum (ER) was chosen as the model protein. The cloned template protein BiP was selectively assembled with ARPCs from their library, which contained numerous limited-length polymer chains with randomly distributed recognition and immobilization sites. The resulting complex was copolymerized onto the surface of vinyl-modified silica nanoparticles under low concentrations of the monomers. After template removal, core-shell-structured nanoparticles with a thin imprinted polymer layer were produced. The particles demonstrated considerably high adsorption capacity, fast adsorption kinetics and selective binding affinities toward the template BiP. Furthermore, the synthesized MIP nanoparticles successfully isolated cloned protein BiP from protein mixtures and highly enriched BiP from an ER extract containing thousands of kinds of proteins. The enrichment reached 115-fold and the binding capacity was 5.4 μg g(-1), which were higher than those achieved by using traditional MIP microspheres. The advantageous properties of MIP nanoparticles hold promise for further practical applications in biology, such as protein analysis and purification. PMID:24140608

  5. The highly abundant chlorophyll-protein complex of iron-deficient Synechococcus sp. PCC7942 (CP43') is encoded by the isiA gene.

    PubMed Central

    Burnap, R L; Troyan, T; Sherman, L A

    1993-01-01

    A chlorophyll (Chl)-protein complex designated CPVI-4 becomes the major pigment-protein complex in Synechococcus sp. PCC7942 cells grown under conditions of iron limitation. Work by Laudenbach et al. (J Bacteriol [1988] 170: 5018-5026) has identified an iron-repressible operon, designated isiAB, containing the flavodoxin gene and a gene predicted to encode a Chl-binding protein resembling CP43 of photosystem II. To test the hypothesis that the CP43-like protein is a component of the CPVI-4 complex, we have inactivated the isiAB operon in Synechococcus sp. PCC7942 using directed insertional mutagenesis. Mutant cells grown under conditions of iron limitation exhibit pronounced changes in their spectroscopic and photosynthetic properties relative to similarly grown wild-type cells. Notably, the strong 77 K fluorescence emission at 685 nm, which dominates the spectrum of iron-deficient wild-type cells, is dramatically reduced in the mutant. The loss of this emission appears to unmask the otherwise obscured photosystem II emissions at 685 and 695 nm. Most importantly, mildly denaturing gel electrophoresis shows that mutant cells no longer express the CPVI-4 complex, indicating that the isiA gene encodes a component of this abundant Chl-protein complex. PMID:8022940

  6. Identification of Putative Genes Involved in Bisphenol A Degradation Using Differential Protein Abundance Analysis of Sphingobium sp. BiD32.

    PubMed

    Zhou, Nicolette A; Kjeldal, Henrik; Gough, Heidi L; Nielsen, Jeppe L

    2015-10-20

    Discharge of the endocrine disrupting compound bisphenol A (BPA) with wastewater treatment plant (WWTP) effluents into surface waters results in deleterious effects on aquatic life. Sphingobium sp. BiD32 was previously isolated from activated sludge based on its ability to degrade BPA. This study investigated BPA metabolism by Sphingobium sp. BiD32 using label-free quantitative proteomics. The genome of Sphingobium sp. BiD32 was sequenced to provide a species-specific platform for optimal protein identification. The bacterial proteomes of Sphingobium sp. BiD32 in the presence and absence of BPA were identified and quantified. A total of 2155 proteins were identified; 1174 of these proteins were quantified, and 184 of these proteins had a statistically significant change in abundance in response to the presence/absence of BPA (p ≤ 0.05). Proteins encoded by genes previously identified to be responsible for protocatechuate degradation were upregulated in the presence of BPA. The analysis of the metabolites from BPA degradation by Sphingobium sp. BiD32 detected a hydroxylated metabolite. A novel p-hydroxybenzoate hydroxylase enzyme detected by proteomics was implicated in the metabolic pathway associated with the detected metabolite. This enzyme is hypothesized to be involved in BPA degradation by Sphingobium sp. BiD32, and may serve as a future genetic marker for BPA degradation. PMID:26390302

  7. Studies of individual carbon sites of proteins in solution by natural abundance carbon 13 nuclear magnetic resonance spectroscopy. Strategies for assignments.

    PubMed

    Oldfield, E; Norton, R S; Allerhand, A

    1975-08-25

    Natural abundance 13C Fourier transform NMR spectra (at 15.18 MHz, in 20-mm sample tubes) of aqueous native proteins yield numerous narrow single carbon resonances of nonprotonated aromatic carbons. Techniques for the assignment of these resonances are presented. Each technique is applied to one or more of the following proteins: ferricytochrome c from horse heart and Candida krusei, ferrocytochrome c and cyanoferricytochrome c from horse heart, lysozyme from hen egg white, cyanoferrimyoglobins from horse and sperm whale skeletal muscle, and carbon monoxide myoglobin from horse. In all of the protein spectra we have examined, methine aromatic carbons give rise to broad bands. Studies of the narrow resonances of nonprotonated aromatic carbons of proteins are facilitated by removal of these broad bands by means of the convolution-difference method, preferably from spectra recorded under conditions of noise-modulated off-resonance proton decoupling. We present a summary of the chemical shift ranges for the various types of nonprotonated aromatic carbons of amino acid residues and hemes of diamagnetic proteins, based on our results for hen egg white lysozyme, horse heart ferrocytochrome c, horse carbon monoxide myoglobin, and carbon monoxide hemoglobins from various species... PMID:169240

  8. Modification of expansin protein abundance in tomato fruit alters softening and cell wall polymer metabolism during ripening

    PubMed Central

    Brummell, DA; Harpster, MH; Civello, PM; Palys, JM; Bennett, AB; Dunsmuir, P

    1999-01-01

    The role of the ripening-specific expansin Exp1 protein in fruit softening and cell wall metabolism was investigated by suppression and overexpression of Exp1 in transgenic tomato plants. Fruit in which Exp1 protein accumulation was suppressed to 3% that of wild-type levels were firmer than controls throughout ripening. Suppression of Exp1 protein also substantially inhibited polyuronide depolymerization late in ripening but did not prevent the breakdown of structurally important hemicelluloses, a major contributor to softening. In contrast, fruit overexpressing high levels of recombinant Exp1 protein were much softer than controls, even in mature green fruit before ripening commenced. This softening was correlated with the precocious and extensive depolymerization of structural hemicelluloses, whereas polyuronide depolymerization was not altered. These data are consistent with there being at least three components to fruit softening and textural changes. One component is a relaxation of the wall directly mediated by Exp1, which indirectly limits part of a second component due to polyuronide depolymerization late in ripening, perhaps by controlling access of a pectinase to its substrate. The third component is caused by depolymerization of hemicelluloses, which occurs independently of or requires only very small amounts of Exp1 protein. PMID:10559444

  9. Dataset of liver proteins of eu- and hypothyroid rats affected in abundance by any of three factors: in vivo exposure to hexabromocyclododecane (HBCD), thyroid status, gender differences.

    PubMed

    Miller, I; Renaut, J; Cambier, S; Murk, A J; Gutleb, A C; Serchi, T

    2016-09-01

    Male Wistar rats with different thyroid status (eu-, hypothyroid) were exposed to 0, 3 or 30 mg/kg body weight of the flame retardant HBCD for 7 days and obtained data compared with a previous study in females, "Hexabromocyclododecane (HBCD) induced changes in the liver proteome of eu- and hypothyroid female rats" (Miller et al., 2016) [1]. Specifically, proteomic investigation of liver protein patterns obtained by 2D-DIGE was performed and differences between animals groups recorded, based on the factors exposure, thyroid status and gender. All proteins with significantly changed abundance in any of these comparisons were identified by mass spectrometry. General, hormone and proteomic data of both the present and the previous studies are discussed in Miller et al. (2016) [1] and in "Gender specific differences in the liver proteome of rats exposed to hexabromocyclododecane (HBCD)" Miller et al. (2016) [2]. PMID:27579339

  10. The abundant class III chitinase homolog in young developing banana fruits behaves as a transient vegetative storage protein and most probably serves as an important supply of amino acids for the synthesis of ripening-associated proteins.

    PubMed

    Peumans, Willy J; Proost, Paul; Swennen, Rony L; Van Damme, Els J M

    2002-10-01

    Analyses of the protein content and composition revealed dramatic changes in gene expression during in situ banana (Musa spp.) fruit formation/ripening. The total banana protein content rapidly increases during the first 60 to 70 d, but remains constant for the rest of fruit formation/ripening. During the phase of rapid protein accumulation, an inactive homolog of class III chitinases accounts for up to 40% (w/v) of the total protein. Concomitant with the arrest of net protein accumulation, the chitinase-related protein (CRP) progressively decreases and several novel proteins appear in the electropherograms. Hence, CRP behaves as a fruit-specific vegetative storage protein that accumulates during early fruit formation and serves as a source of amino acids for the synthesis of ripening-associated proteins. Analyses of individual proteins revealed that a thaumatin-like protein, a beta-1,3-glucanase, a class I chitinase, and a mannose-binding lectin are the most abundant ripening-associated proteins. Because during the ripening of prematurely harvested bananas, similar changes take place as in the in situ ripening bananas, CRP present in immature fruits is a sufficient source of amino acids for a quasi-normal synthesis of ripening-associated proteins. However, it is evident that the conversion of CRP in ripening-associated proteins takes place at an accelerated rate, especially when climacteric ripening is induced by ethylene. The present report also includes a discussion of the accumulation of the major banana allergens and the identification of suitable promoters for the production of vaccines in transgenic bananas. PMID:12376669

  11. LEA Detection and Tracking Method for Color-Independent Visual-MIMO

    PubMed Central

    Kim, Jai-Eun; Kim, Ji-Won; Kim, Ki-Doo

    2016-01-01

    Communication performance in the color-independent visual-multiple input multiple output (visual-MIMO) technique is deteriorated by light emitting array (LEA) detection and tracking errors in the received image because the image sensor included in the camera must be used as the receiver in the visual-MIMO system. In this paper, in order to improve detection reliability, we first set up the color-space-based region of interest (ROI) in which an LEA is likely to be placed, and then use the Harris corner detection method. Next, we use Kalman filtering for robust tracking by predicting the most probable location of the LEA when the relative position between the camera and the LEA varies. In the last step of our proposed method, the perspective projection is used to correct the distorted image, which can improve the symbol decision accuracy. Finally, through numerical simulation, we show the possibility of robust detection and tracking of the LEA, which results in a symbol error rate (SER) performance improvement. PMID:27384563

  12. LEA Detection and Tracking Method for Color-Independent Visual-MIMO.

    PubMed

    Kim, Jai-Eun; Kim, Ji-Won; Kim, Ki-Doo

    2016-01-01

    Communication performance in the color-independent visual-multiple input multiple output (visual-MIMO) technique is deteriorated by light emitting array (LEA) detection and tracking errors in the received image because the image sensor included in the camera must be used as the receiver in the visual-MIMO system. In this paper, in order to improve detection reliability, we first set up the color-space-based region of interest (ROI) in which an LEA is likely to be placed, and then use the Harris corner detection method. Next, we use Kalman filtering for robust tracking by predicting the most probable location of the LEA when the relative position between the camera and the LEA varies. In the last step of our proposed method, the perspective projection is used to correct the distorted image, which can improve the symbol decision accuracy. Finally, through numerical simulation, we show the possibility of robust detection and tracking of the LEA, which results in a symbol error rate (SER) performance improvement. PMID:27384563

  13. Overexpression of Drosophila juvenile hormone esterase binding protein results in anti-JH effects and reduced pheromone abundance

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The titer of juvenile hormone (JH), which has wide ranging physiological effects in insects, is regulated in part by JH esterase (JHE). We show that overexpression in Drosophila melanogaster of the JHE binding protein, DmP29 results in a series of apparent anti-JH effects. We hypothesize that DmP29 ...

  14. Identification of an abundant 56 kDa protein implicated in food allergy as granule-bound starch synthase

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Rice, the staple food of South and East Asian counties, is considered to be hypoallergenic. However, several clinical studies have documented rice-induced allergy in sensitive patients. Rice proteins with molecular weights of 14-16 kDa, 26 kDa, 33 kDa and 56 kDa have been identified as allergens. Re...

  15. Analysis of crude protein and allergen abundance in peanuts (Arachis hypogaea cv. Walter) from three growing regions in Australia.

    PubMed

    Walczyk, Nicole E; Smith, Penelope M C; Tovey, Euan; Wright, Graeme C; Fleischfresser, Dayle B; Roberts, Thomas H

    2013-04-17

    The effects of plant growth conditions on concentrations of proteins, including allergens, in peanut ( Arachis hypogaea L.) kernels are largely unknown. Peanuts (cv. Walter) were grown at five sites (Taabinga, Redvale, Childers, Bundaberg, and Kairi) covering three commercial growing regions in Queensland, Australia. Differences in temperature, rainfall, and solar radiation during the growing season were evaluated. Kernel yield varied from 2.3 t/ha (Kairi) to 3.9 t/ha (Childers), probably due to differences in solar radiation. Crude protein appeared to vary only between Kairi and Childers, whereas Ara h 1 and 2 concentrations were similar in all locations. 2D-DIGE revealed significant differences in spot volumes for only two minor protein spots from peanuts grown in the five locations. Western blotting using peanut-allergic serum revealed no qualitative differences in recognition of antigens. It was concluded that peanuts grown in different growing regions in Queensland, Australia, had similar protein compositions and therefore were unlikely to show differences in allergenicity. PMID:23495786

  16. The COG and COPI Complexes Interact to Control the Abundance of GEARs, a Subset of Golgi Integral Membrane ProteinsD⃞

    PubMed Central

    Oka, Toshihiko; Ungar, Daniel; Hughson, Frederick M.; Krieger, Monty

    2004-01-01

    The conserved oligomeric Golgi (COG) complex is a soluble hetero-octamer associated with the cytoplasmic surface of the Golgi. Mammalian somatic cell mutants lacking the Cog1 (ldlB) or Cog2 (ldlC) subunits exhibit pleiotropic defects in Golgi-associated glycoprotein and glycolipid processing that suggest COG is involved in the localization, transport, and/or function of multiple Golgi processing proteins. We have identified a set of COG-sensitive, integral membrane Golgi proteins called GEARs (mannosidase II, GOS-28, GS15, GPP130, CASP, giantin, and golgin-84) whose abundances were reduced in the mutant cells and, in some cases, increased in COG-overexpressing cells. In the mutants, some GEARs were abnormally localized in the endoplasmic reticulum and were degraded by proteasomes. The distributions of the GEARs were altered by small interfering RNA depletion of ε-COP in wild-type cells under conditions in which COG-insensitive proteins were unaffected. Furthermore, synthetic phenotypes arose in mutants deficient in both ε-COP and either Cog1 or Cog2. COG and COPI may work in concert to ensure the proper retention or retrieval of a subset of proteins in the Golgi, and COG helps prevent the endoplasmic reticulum accumulation and degradation of some GEARs. PMID:15004235

  17. 75 FR 20390 - La-Z-Boy Casegoods, Inc.-LEA Also Known as American Drew Wilkesboro, NC; Amended Certification...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-04-19

    ..., 2008 (73 FR 13017). In order to avoid an overlap in worker group coverage, the Department is amending... Employment and Training Administration La-Z-Boy Casegoods, Inc.--LEA Also Known as American Drew Wilkesboro..., 2010 applicable to workers of La-Z-Boy Casegoods, Inc.- LEA, also known as American Drew,...

  18. Ubiquitous LEA29Y Expression Blocks T Cell Co-Stimulation but Permits Sexual Reproduction in Genetically Modified Pigs

    PubMed Central

    Bähr, Andrea; Käser, Tobias; Kemter, Elisabeth; Gerner, Wilhelm; Kurome, Mayuko; Baars, Wiebke; Herbach, Nadja; Witter, Kirsti; Wünsch, Annegret; Talker, Stephanie C.; Kessler, Barbara; Nagashima, Hiroshi; Saalmüller, Armin; Schwinzer, Reinhard; Wolf, Eckhard; Klymiuk, Nikolai

    2016-01-01

    We have successfully established and characterized a genetically modified pig line with ubiquitous expression of LEA29Y, a human CTLA4-Ig derivate. LEA29Y binds human B7.1/CD80 and B7.2/CD86 with high affinity and is thus a potent inhibitor of T cell co-stimulation via this pathway. We have characterized the expression pattern and the biological function of the transgene as well as its impact on the porcine immune system and have evaluated the potential of these transgenic pigs to propagate via assisted breeding methods. The analysis of LEA29Y expression in serum and multiple organs of CAG-LEA transgenic pigs revealed that these animals produce a biologically active transgenic product at a considerable level. They present with an immune system affected by transgene expression, but can be maintained until sexual maturity and propagated by assisted reproduction techniques. Based on previous experience with pancreatic islets expressing LEA29Y, tissues from CAG-LEA29Y transgenic pigs should be protected against rejection by human T cells. Furthermore, their immune-compromised phenotype makes CAG-LEA29Y transgenic pigs an interesting large animal model for testing human cell therapies and will provide an important tool for further clarifying the LEA29Y mode of action. PMID:27175998

  19. Retinoic acid-induced differentiation of human neuroblastoma SH-SY5Y cells is associated with changes in the abundance of G proteins.

    PubMed

    Ammer, H; Schulz, R

    1994-04-01

    Western blot analysis, using subtype-specific anti-G protein antibodies, revealed the presence of the following G protein subunits in human neuroblastoma SH-SY5Y cells: Gs alpha, Gi alpha 1, Gi alpha 2, Go alpha, Gz alpha, and G beta. Differentiation of the cells by all-trans-retinoic acid (RA) treatment (10 mumol/L; 6 days) caused substantial alterations in the abundance of distinct G protein subunits. Concomitant with an enhanced expression of mu-opioid binding sites, the levels of the inhibitory G proteins Gi alpha 1 and Gi alpha 2 were found to be significantly increased. This coordinate up-regulation is accompanied by functional changes in mu-opioid receptor-stimulated low-Km GTPase, mu-receptor-mediated adenylate cyclase inhibition, and receptor-independent guanosine 5'-(beta gamma-imido)triphosphate [Gpp(NH)p; 10 nmol/L]-mediated attenuation of adenylate cyclase activity. In contrast, increased levels of inhibitory G proteins had no effect on muscarinic cholinergic receptor-mediated adenylate cyclase inhibition. With respect to stimulatory receptor systems, a reciprocal regulation was observed for prostaglandin E1 (PGE1) receptors and Gs alpha, the G protein subunit activating adenylate cyclase. RA treatment of SH-SY5Y cells increases both the number of PGE1 binding sites and PGE1-stimulated adenylate cyclase activity, but significantly reduced amounts of Gs alpha were found. This down-regulation is paralleled by a decrease in the stimulatory activity of Gs alpha as assessed in S49 cyc- reconstitution assays.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8133263

  20. The freshwater Amazonian stingray, Potamotrygon motoro, up-regulates glutamine synthetase activity and protein abundance, and accumulates glutamine when exposed to brackish (15 per thousand) water.

    PubMed

    Ip, Y K; Loong, A M; Ching, B; Tham, G H Y; Wong, W P; Chew, S F

    2009-12-01

    This study aimed to examine whether the stenohaline freshwater stingray, Potamotrygon motoro, which lacks a functional ornithine-urea cycle, would up-regulate glutamine synthetase (GS) activity and protein abundance, and accumulate glutamine during a progressive transfer from freshwater to brackish (15 per thousand) water with daily feeding. Our results revealed that, similar to other freshwater teleosts, P. motoro performed hyperosmotic regulation, with very low urea concentrations in plasma and tissues, in freshwater. In 15 per thousand water, it was non-ureotelic and non-ureoosmotic, acting mainly as an osmoconformer with its plasma osmolality, [Na+] and [Cl-] comparable to those of the external medium. There were significant increases in the content of several free amino acids (FAAs), including glutamate, glutamine and glycine, in muscle and liver, but not in plasma, indicating that FAAs could contribute in part to cell volume regulation. Furthermore, exposure of P. motoro to 15 per thousand water led to up-regulation of GS activity and protein abundance in both liver and muscle. Thus, our results indicate for the first time that, despite the inability to synthesize urea and the lack of functional carbamoyl phosphate synthetase III (CPS III) which uses glutamine as a substrate, P. motoro retained the capacity to up-regulate the activity and protein expression of GS in response to salinity stress. Potamotrygon motoro was not nitrogen (N) limited when exposed to 15 per thousand water with feeding, and there were no significant changes in the amination and deamination activities of hepatic glutamate dehydrogenase. In contrast, P. motoro became N limited when exposed to 10 per thousand water with fasting and could not survive well in 15 per thousand water without food. PMID:19915125

  1. Abundant Type III Lipid Transfer Proteins in Arabidopsis Tapetum Are Secreted to the Locule and Become a Constituent of the Pollen Exine1[W][OPEN

    PubMed Central

    Huang, Ming-Der; Chen, Tung-Ling L.; Huang, Anthony H.C.

    2013-01-01

    Lipid transfer proteins (LTPs) are small secretory proteins in plants with defined lipid-binding structures for possible lipid exocytosis. Special groups of LTPs unique to the anther tapetum are abundant, but their functions are unclear. We studied a special group of LTPs, type III LTPs, in Arabidopsis (Arabidopsis thaliana). Their transcripts were restricted to the anther tapetum, with levels peaking at the developmental stage of maximal pollen-wall exine synthesis. We constructed an LTP-Green Fluorescent Protein (LTP-GFP) plasmid, transformed it into wild-type plants, and monitored LTP-GFP in developing anthers with confocal laser scanning microscopy. LTP-GFP appeared in the tapetum and was secreted via the endoplasmic reticulum-trans-Golgi network machinery into the locule. It then moved to the microspore surface and remained as a component of exine. Immuno-transmission electron microscopy of native LTP in anthers confirmed the LTP-GFP observations. The in vivo association of LTP-GFP and exine in anthers was not observed with non-type III or structurally modified type III LTPs or in transformed exine-defective mutant plants. RNA interference knockdown of individual type III LTPs produced no observable mutant phenotypes. RNA interference knockdown of two type III LTPs produced microscopy-observable morphologic changes in the intine underneath the exine (presumably as a consequence of changes in the exine not observed by transmission electron microscopy) and pollen susceptible to dehydration damage. Overall, we reveal a novel transfer pathway of LTPs in which LTPs bound or nonbound to exine precursors are secreted from the tapetum to become microspore exine constituents; this pathway explains the need for plentiful LTPs to incorporate into the abundant exine. PMID:24096413

  2. DNA polymorphisms and transcript abundance of PRKAG2 and phosphorylated AMP-activated protein kinase in the rumen are associated with gain and feed intake in beef steers.

    PubMed

    Lindholm-Perry, A K; Kuehn, L A; Oliver, W T; Kern, R J; Cushman, R A; Miles, J R; McNeel, A K; Freetly, H C

    2014-08-01

    Beef steers with variation in feed efficiency phenotypes were evaluated previously on a high-density SNP panel. Ten markers from rs110125325-rs41652818 on bovine chromosome 4 were associated with average daily gain (ADG). To identify the gene(s) in this 1.2-Mb region responsible for variation in ADG, genotyping with 157 additional markers was performed. Several markers (n = 41) were nominally associated with ADG, and three of these, including the only marker to withstand Bonferroni correction, were located within the protein kinase, AMP-activated, gamma 2 non-catalytic subunit (PRKAG2) gene. An additional population of cross-bred steers (n = 406) was genotyped for validation. One marker located within the PRKAG2 loci approached a significant association with gain. To evaluate PRKAG2 for differences in transcript abundance, we measured expression in the liver, muscle, rumen and intestine from steers (n = 32) with extreme feed efficiency phenotypes collected over two seasons. No differences in PRKAG2 transcript abundance were detected in small intestine, liver or muscle. Correlation between gene expression level of PRKAG2 in rumen and average daily feed intake (ADFI) was detected in both seasons (P < 0.05); however, the direction differed by season. Lastly, we evaluated AMP-activated protein kinase (AMPK), of which PRKAG2 is a subunit, for differences among ADG and ADFI and found that the phosphorylated form of AMPK was associated with ADFI in the rumen. These data suggest that PRKAG2 and its mature protein, AMPK, are involved in feed efficiency traits in beef steers. This is the first evidence to suggest that rumen AMPK may be contributing to ADFI in cattle. PMID:24730749

  3. Abundant type III lipid transfer proteins in Arabidopsis tapetum are secreted to the locule and become a constituent of the pollen exine.

    PubMed

    Huang, Ming-Der; Chen, Tung-Ling L; Huang, Anthony H C

    2013-11-01

    Lipid transfer proteins (LTPs) are small secretory proteins in plants with defined lipid-binding structures for possible lipid exocytosis. Special groups of LTPs unique to the anther tapetum are abundant, but their functions are unclear. We studied a special group of LTPs, type III LTPs, in Arabidopsis (Arabidopsis thaliana). Their transcripts were restricted to the anther tapetum, with levels peaking at the developmental stage of maximal pollen-wall exine synthesis. We constructed an LTP-Green Fluorescent Protein (LTP-GFP) plasmid, transformed it into wild-type plants, and monitored LTP-GFP in developing anthers with confocal laser scanning microscopy. LTP-GFP appeared in the tapetum and was secreted via the endoplasmic reticulum-trans-Golgi network machinery into the locule. It then moved to the microspore surface and remained as a component of exine. Immuno-transmission electron microscopy of native LTP in anthers confirmed the LTP-GFP observations. The in vivo association of LTP-GFP and exine in anthers was not observed with non-type III or structurally modified type III LTPs or in transformed exine-defective mutant plants. RNA interference knockdown of individual type III LTPs produced no observable mutant phenotypes. RNA interference knockdown of two type III LTPs produced microscopy-observable morphologic changes in the intine underneath the exine (presumably as a consequence of changes in the exine not observed by transmission electron microscopy) and pollen susceptible to dehydration damage. Overall, we reveal a novel transfer pathway of LTPs in which LTPs bound or nonbound to exine precursors are secreted from the tapetum to become microspore exine constituents; this pathway explains the need for plentiful LTPs to incorporate into the abundant exine. PMID:24096413

  4. 34 CFR 76.794 - How does an SEA allocate funds to charter school LEAs under a covered program in which the SEA...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... charter school LEA in the State that is scheduled to open on or before the closing date of any competition... 34 Education 1 2010-07-01 2010-07-01 false How does an SEA allocate funds to charter school LEAs... Educational Agencies § 76.794 How does an SEA allocate funds to charter school LEAs under a covered program...

  5. 34 CFR 76.794 - How does an SEA allocate funds to charter school LEAs under a covered program in which the SEA...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... charter school LEA in the State that is scheduled to open on or before the closing date of any competition... 34 Education 1 2014-07-01 2014-07-01 false How does an SEA allocate funds to charter school LEAs... Educational Agencies § 76.794 How does an SEA allocate funds to charter school LEAs under a covered program...

  6. 34 CFR 76.794 - How does an SEA allocate funds to charter school LEAs under a covered program in which the SEA...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... charter school LEA in the State that is scheduled to open on or before the closing date of any competition... 34 Education 1 2012-07-01 2012-07-01 false How does an SEA allocate funds to charter school LEAs... Educational Agencies § 76.794 How does an SEA allocate funds to charter school LEAs under a covered program...

  7. 34 CFR 76.794 - How does an SEA allocate funds to charter school LEAs under a covered program in which the SEA...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... charter school LEA in the State that is scheduled to open on or before the closing date of any competition... 34 Education 1 2011-07-01 2011-07-01 false How does an SEA allocate funds to charter school LEAs... Educational Agencies § 76.794 How does an SEA allocate funds to charter school LEAs under a covered program...

  8. 34 CFR 76.794 - How does an SEA allocate funds to charter school LEAs under a covered program in which the SEA...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... charter school LEA in the State that is scheduled to open on or before the closing date of any competition... 34 Education 1 2013-07-01 2013-07-01 false How does an SEA allocate funds to charter school LEAs... Educational Agencies § 76.794 How does an SEA allocate funds to charter school LEAs under a covered program...

  9. 34 CFR 76.793 - When is an SEA required to allocate funds to a charter school LEA under this subpart?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... funds to a charter school LEA under this subpart? Except as provided in §§ 76.788(b) and 76.789(b)(3): (a) For each eligible charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must allocate funds to the charter school LEA within...

  10. 34 CFR 76.793 - When is an SEA required to allocate funds to a charter school LEA under this subpart?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... funds to a charter school LEA under this subpart? Except as provided in §§ 76.788(b) and 76.789(b)(3): (a) For each eligible charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must allocate funds to the charter school LEA within...

  11. 34 CFR 76.793 - When is an SEA required to allocate funds to a charter school LEA under this subpart?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... funds to a charter school LEA under this subpart? Except as provided in §§ 76.788(b) and 76.789(b)(3): (a) For each eligible charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must allocate funds to the charter school LEA within...

  12. 34 CFR 76.792 - How does an SEA allocate funds to eligible charter school LEAs under a covered program in which...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... State Educational Agencies § 76.792 How does an SEA allocate funds to eligible charter school LEAs under... charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must implement procedures that ensure that the charter school LEA receives...

  13. 34 CFR 76.792 - How does an SEA allocate funds to eligible charter school LEAs under a covered program in which...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... State Educational Agencies § 76.792 How does an SEA allocate funds to eligible charter school LEAs under... charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must implement procedures that ensure that the charter school LEA receives...

  14. 34 CFR 76.792 - How does an SEA allocate funds to eligible charter school LEAs under a covered program in which...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... State Educational Agencies § 76.792 How does an SEA allocate funds to eligible charter school LEAs under... charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must implement procedures that ensure that the charter school LEA receives...

  15. 34 CFR 76.792 - How does an SEA allocate funds to eligible charter school LEAs under a covered program in which...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... State Educational Agencies § 76.792 How does an SEA allocate funds to eligible charter school LEAs under... charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must implement procedures that ensure that the charter school LEA receives...

  16. 34 CFR 76.793 - When is an SEA required to allocate funds to a charter school LEA under this subpart?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... funds to a charter school LEA under this subpart? Except as provided in §§ 76.788(b) and 76.789(b)(3): (a) For each eligible charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must allocate funds to the charter school LEA within...

  17. 34 CFR 76.792 - How does an SEA allocate funds to eligible charter school LEAs under a covered program in which...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... State Educational Agencies § 76.792 How does an SEA allocate funds to eligible charter school LEAs under... charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must implement procedures that ensure that the charter school LEA receives...

  18. 34 CFR 76.793 - When is an SEA required to allocate funds to a charter school LEA under this subpart?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... funds to a charter school LEA under this subpart? Except as provided in §§ 76.788(b) and 76.789(b)(3): (a) For each eligible charter school LEA that opens or significantly expands its enrollment on or before November 1 of an academic year, the SEA must allocate funds to the charter school LEA within...

  19. Dimerization and DNA-binding of ASR1, a small hydrophilic protein abundant in plant tissues suffering from water loss

    SciTech Connect

    Maskin, Laura; Frankel, Nicolas; Gudesblat, Gustavo; Demergasso, Maria J.; Pietrasanta, Lia I.; Iusem, Norberto D. . E-mail: norbius@fbmc.fcen.uba.ar

    2007-01-26

    The Asr gene family is present in Spermatophyta. Its members are generally activated under water stress. We present evidence that tomato ASR1, one of the proteins of the family, accumulates in seed during late stages of embryogenesis, a physiological process characterized by water loss. In vitro, electrophoretic assays show a homo-dimeric structure for ASR1 and highlight strong non-covalent interactions between monomers prone to self-assemble. Direct visualization of single molecules by atomic force microscopy (AFM) confirms that ASR1 forms homodimers and that uncovers both monomers and dimers bind double stranded DNA.

  20. An abundantly expressed mucin-like protein from Toxocara canis infective larvae: the precursor of the larval surface coat glycoproteins.

    PubMed Central

    Gems, D; Maizels, R M

    1996-01-01

    Evasion of host immunity by Toxocara canis infective larvae is mediated by the nematode surface coat, which is shed in response to binding by host antibody molecules or effector cells. The major constituent of the coat is the TES-120 glycoprotein series. We have isolated a 730-bp cDNA from the gene encoding the apoprotein precursor of TES-120. The mRNA is absent from T. canis adults but hyperabundant in larvae, making up approximately 10% of total mRNA, and is trans-spliced with the nematode 5' leader sequence SL1. It encodes a 15.8-kDa protein (after signal peptide removal) containing a typical mucin domain: 86 amino acid residues, 72.1% of which are Ser or Thr, organized into an array of heptameric repeats, interspersed with proline residues. At the C-terminal end of the putative protein are two 36-amino acid repeats containing six Cys residues, in a motif that can also be identified in several genes in Caenorhabditis elegans. Although TES-120 displays size and charge heterogeneity, there is a single copy gene and a homogeneous size of mRNA. The association of overexpression of some membrane-associated mucins with immunosuppression and tumor metastasis suggests a possible model for the role of the surface coat in immune evasion by parasitic nematodes. Images Fig. 1 Fig. 4 PMID:8643687

  1. Protein covalent immobilization via its scarce thiol versus abundant amine groups: Effect on orientation, cell binding domain exposure and conformational lability.

    PubMed

    Ba, O M; Hindie, M; Marmey, P; Gallet, O; Anselme, K; Ponche, A; Duncan, A C

    2015-10-01

    Quantity, orientation, conformation and covalent linkage of naturally cell adhesive proteins adsorbed or covalently linked to a surface, are known to influence the preservation of their subsequent long term cell adhesion properties and bioactivity. In the present work, we explore two different strategies for the covalent linking of plasma fibronectin (pFN) - used as a cell adhesive model protein, onto a polystyrene (PS) surface. One is aimed at tethering the protein to the surface in a semi-oriented fashion (via one of the 4 free thiol reactive groups on the protein) with a heterofunctional coupling agent (SSMPB method). The other aims to immobilize the protein in a more random fashion by reaction between the abundant pendant primary amine bearing amino acids of the pFN and activated carboxylic surface functions obtained after glutaric anhydride surface treatment (GA method). The overall goal will be to verify the hypothesis of a correlation between covalent immobilization of a model cell adhesive protein to a PS surface in a semi-oriented configuration (versus randomly oriented) with promotion of enhanced exposure of the protein's cell binding domain. This in turn would lead to enhanced cell adhesion. Ideally the goal is to elaborate substrates exhibiting a long term stable protein monolayer with preserved cell adhesive properties and bioactivity for biomaterial and/or cell adhesion commercial plate applications. However, the initial restrictive objective of this paper is to first quantitatively and qualitatively investigate the reversibly (merely adsorbed) versus covalently irreversibly bound protein to the surface after the immobilization procedure. Although immobilized surface amounts were similar (close to the monolayer range) for all immobilization approaches, covalent grafting showed improved retention and stronger "tethering" of the pFN protein to the surface (roughly 40%) after SDS rinsing compared to that for mere adsorption (0%) suggesting an added value

  2. Regulation of mRNA Abundance by Polypyrimidine Tract-Binding Protein-Controlled Alternate 5′ Splice Site Choice

    PubMed Central

    Hamid, Fursham M.; Makeyev, Eugene V.

    2014-01-01

    Alternative splicing (AS) provides a potent mechanism for increasing protein diversity and modulating gene expression levels. How alternate splice sites are selected by the splicing machinery and how AS is integrated into gene regulation networks remain important questions of eukaryotic biology. Here we report that polypyrimidine tract-binding protein 1 (Ptbp1/PTB/hnRNP-I) controls alternate 5′ and 3′ splice site (5′ss and 3′ss) usage in a large set of mammalian transcripts. A top scoring event identified by our analysis was the choice between competing upstream and downstream 5′ss (u5′ss and d5′ss) in the exon 18 of the Hps1 gene. Hps1 is essential for proper biogenesis of lysosome-related organelles and loss of its function leads to a disease called type 1 Hermansky-Pudlak Syndrome (HPS). We show that Ptbp1 promotes preferential utilization of the u5′ss giving rise to stable mRNAs encoding a full-length Hps1 protein, whereas bias towards d5′ss triggered by Ptbp1 down-regulation generates transcripts susceptible to nonsense-mediated decay (NMD). We further demonstrate that Ptbp1 binds to pyrimidine-rich sequences between the u5′ss and d5′ss and activates the former site rather than repressing the latter. Consistent with this mechanism, u5′ss is intrinsically weaker than d5′ss, with a similar tendency observed for other genes with Ptbp1-induced u5′ss bias. Interestingly, the brain-enriched Ptbp1 paralog Ptbp2/nPTB/brPTB stimulated the u5′ss utilization but with a considerably lower efficiency than Ptbp1. This may account for the tight correlation between Hps1 with Ptbp1 expression levels observed across mammalian tissues. More generally, these data expand our understanding of AS regulation and uncover a post-transcriptional strategy ensuring co-expression of a subordinate gene with its master regulator through an AS-NMD tracking mechanism. PMID:25375251

  3. Disorder and function: a review of the dehydrin protein family.

    PubMed

    Graether, Steffen P; Boddington, Kelly F

    2014-01-01

    Dehydration proteins (dehydrins) are group 2 members of the late embryogenesis abundant (LEA) protein family. The protein architecture of dehydrins can be described by the presence of three types of conserved sequence motifs that have been named the K-, Y-, and S-segments. By definition, a dehydrin must contain at least one copy of the lysine-rich K-segment. Abiotic stresses such as drought, cold, and salinity cause the upregulation of dehydrin mRNA and protein levels. Despite the large body of genetic and protein evidence of the importance of these proteins in stress response, the in vivo protective mechanism is not fully known. In vitro experimental evidence from biochemical assays and localization experiments suggests multiple roles for dehydrins, including membrane protection, cryoprotection of enzymes, and protection from reactive oxygen species. Membrane binding by dehydrins is likely to be as a peripheral membrane protein, since the protein sequences are highly hydrophilic and contain many charged amino acids. Because of this, dehydrins in solution are intrinsically disordered proteins, that is, they have no well-defined secondary or tertiary structure. Despite their disorder, dehydrins have been shown to gain structure when bound to ligands such as membranes, and to possibly change their oligomeric state when bound to ions. We review what is currently known about dehydrin sequences and their structures, and examine the various ligands that have been shown to bind to this family of proteins. PMID:25400646

  4. Disorder and function: a review of the dehydrin protein family

    PubMed Central

    Graether, Steffen P.; Boddington, Kelly F.

    2014-01-01

    Dehydration proteins (dehydrins) are group 2 members of the late embryogenesis abundant (LEA) protein family. The protein architecture of dehydrins can be described by the presence of three types of conserved sequence motifs that have been named the K-, Y-, and S-segments. By definition, a dehydrin must contain at least one copy of the lysine-rich K-segment. Abiotic stresses such as drought, cold, and salinity cause the upregulation of dehydrin mRNA and protein levels. Despite the large body of genetic and protein evidence of the importance of these proteins in stress response, the in vivo protective mechanism is not fully known. In vitro experimental evidence from biochemical assays and localization experiments suggests multiple roles for dehydrins, including membrane protection, cryoprotection of enzymes, and protection from reactive oxygen species. Membrane binding by dehydrins is likely to be as a peripheral membrane protein, since the protein sequences are highly hydrophilic and contain many charged amino acids. Because of this, dehydrins in solution are intrinsically disordered proteins, that is, they have no well-defined secondary or tertiary structure. Despite their disorder, dehydrins have been shown to gain structure when bound to ligands such as membranes, and to possibly change their oligomeric state when bound to ions. We review what is currently known about dehydrin sequences and their structures, and examine the various ligands that have been shown to bind to this family of proteins. PMID:25400646

  5. The AP2 clathrin adaptor protein complex regulates the abundance of GLR-1 glutamate receptors in the ventral nerve cord of Caenorhabditis elegans

    PubMed Central

    Garafalo, Steven D.; Luth, Eric S.; Moss, Benjamin J.; Monteiro, Michael I.; Malkin, Emily; Juo, Peter

    2015-01-01

    Regulation of glutamate receptor (GluR) abundance at synapses by clathrin-mediated endocytosis can control synaptic strength and plasticity. We take advantage of viable, null mutations in subunits of the clathrin adaptor protein 2 (AP2) complex in Caenorhabditis elegans to characterize the in vivo role of AP2 in GluR trafficking. In contrast to our predictions for an endocytic adaptor, we found that levels of the GluR GLR-1 are decreased at synapses in the ventral nerve cord (VNC) of animals with mutations in the AP2 subunits APM-2/μ2, APA-2/α, or APS-2/σ2. Rescue experiments indicate that APM-2/μ2 functions in glr-1–expressing interneurons and the mature nervous system to promote GLR-1 levels in the VNC. Genetic analyses suggest that APM-2/μ2 acts upstream of GLR-1 endocytosis in the VNC. Consistent with this, GLR-1 accumulates in cell bodies of apm-2 mutants. However, GLR-1 does not appear to accumulate at the plasma membrane of the cell body as expected, but instead accumulates in intracellular compartments including Syntaxin-13– and RAB-14–labeled endosomes. This study reveals a novel role for the AP2 clathrin adaptor in promoting the abundance of GluRs at synapses in vivo, and implicates AP2 in the regulation of GluR trafficking at an early step in the secretory pathway. PMID:25788288

  6. Knockout of the abundant Trichomonas vaginalis hydrogenosomal membrane protein TvHMP23 increases hydrogenosome size but induces no compensatory up-regulation of paralogous copies.

    PubMed

    Brás, Xavier Pereira; Zimorski, Verena; Bolte, Kathrin; Maier, Uwe-G; Martin, William F; Gould, Sven B

    2013-05-01

    The Trichomonas vaginalis genome encodes up to 60000 genes, many of which stem from genome duplication events. Paralogous copies thus accompany most T. vaginalis genes, a phenomenon that limits genetic manipulation. We characterized one of the parasite's most abundant hydrogenosomal membrane proteins, TvHMP23, which is phylogenetically distinct from canonical metabolite carriers, and which localizes to the inner hydrogenosomal membrane as shown through sub-organellar fractionation and protease protection assays. Knockout of Tvhmp23 through insertion of the selectable neomycin marker led to a size increase of hydrogenosomes, the first knockout-induced phenotypes reported for Trichomonas, but no growth impairment. The transcriptional response of its four paralogous copies then analyzed revealed that they are not up-regulated, and hence do not compensate for the Tvhmp23 knockout. PMID:23499435

  7. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: Analysis of human plasma and cerebrospinal fluid

    SciTech Connect

    Hyung, Seok Won; Piehowski, Paul D.; Moore, Ronald J.; Orton, Daniel J.; Schepmoes, Athena A.; Clauss, Therese R.; Chu, Rosalie K.; Fillmore, Thomas L.; Brewer, Heather M.; Liu, Tao; Zhao, Rui; Smith, Richard D.

    2014-09-06

    Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 µL) due to low yields stemming from losses caused by nonspecific binding to the column matrix. Additionally, the cost of the depletion media can be prohibitive for larger scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large scale studies. We characterized the performance of a 346 µL column volume micro-scale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6 μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10 mL depletion column served as the control. Results showed depletion efficiency of the micro-scale column increased as flow rate decreased, and that our micro-depletion was reproducible. We found, in an initial application, a 600 µL sample of human cerebral spinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.

  8. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: Analysis of human plasma and cerebrospinal fluid

    DOE PAGESBeta

    Hyung, Seok Won; Piehowski, Paul D.; Moore, Ronald J.; Orton, Daniel J.; Schepmoes, Athena A.; Clauss, Therese R.; Chu, Rosalie K.; Fillmore, Thomas L.; Brewer, Heather M.; Liu, Tao; et al

    2014-09-06

    Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 µL) due to low yields stemming from losses caused by nonspecific binding to the column matrix. Additionally, the cost of the depletion media can be prohibitive for larger scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizingmore » sample recovery when samples are limited, as well as for reducing the expense of large scale studies. We characterized the performance of a 346 µL column volume micro-scale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6 μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10 mL depletion column served as the control. Results showed depletion efficiency of the micro-scale column increased as flow rate decreased, and that our micro-depletion was reproducible. We found, in an initial application, a 600 µL sample of human cerebral spinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.« less

  9. Microscale Depletion of High Abundance Proteins in Human Biofluids using IgY14 Immunoaffinity Resin. Analysis of Human Plasma and Cerebrospinal Fluid

    SciTech Connect

    Hyung, Seok Won; Piehowski, Paul D.; Moore, Ronald J.; Orton, Daniel J.; Schepmoes, Athena A.; Clauss, Therese RW; Chu, Rosalie K.; Fillmore, Thomas L.; Brewer, Heather M.; Liu, Tao; Zhao, Rui; Smith, Richard D.

    2014-09-06

    Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 µL) due to low yields stemming from losses caused by nonspecific binding to the column matrix. Additionally, the cost of the depletion media can be prohibitive for larger scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large scale studies. We characterized the performance of a 346 µL column volume micro-scale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6 μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10 mL depletion column served as the control. Results showed depletion efficiency of the micro-scale column increased as flow rate decreased, and that our micro-depletion was reproducible. In an initial application, a 600 µL sample of human cerebral spinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited.

  10. Microscale depletion of high abundance proteins in human biofluids using IgY14 immunoaffinity resin: analysis of human plasma and cerebrospinal fluid

    PubMed Central

    Hyung, Seok-Won; Piehowski, Paul D.; Moore, Ronald J.; Orton, Daniel J.; Schepmoes, Athena A.; Clauss, Therese R.; Chu, Rosalie K.; Fillmore, Thomas L.; Brewer, Heather; Liu, Tao; Zhao, Rui; Smith, Richard D.

    2014-01-01

    Removal of highly abundant proteins in plasma is often carried out using immunoaffinity depletion to extend the dynamic range of measurements to lower abundance species. While commercial depletion columns are available for this purpose, they generally are not applicable to limited sample quantities (<20 μL) due to low yields stemming from losses caused by nonspecific binding to the column matrix and concentration of large eluent volumes. Additionally, the cost of the depletion media can be prohibitive for larger-scale studies. Modern LC-MS instrumentation provides the sensitivity necessary to scale-down depletion methods with minimal sacrifice to proteome coverage, which makes smaller volume depletion columns desirable for maximizing sample recovery when samples are limited, as well as for reducing the expense of large-scale studies. We characterized the performance of a 346 μL column volume microscale depletion system, using four different flow rates to determine the most effective depletion conditions for ~6-μL injections of human plasma proteins and then evaluated depletion reproducibility at the optimum flow rate condition. Depletion of plasma using a commercial 10-mL depletion column served as the control. Results showed depletion efficiency of the microscale column increased as flow rate decreased, and that our microdepletion was reproducible. In an initial application, a 600-μL sample of human cerebrospinal fluid (CSF) pooled from multiple sclerosis patients was depleted and then analyzed using reversed phase liquid chromatography-mass spectrometry to demonstrate the utility of the system for this important biofluid where sample quantities are more commonly limited. PMID:25192788

  11. Ruminant Nutrition Symposium: The utility of lipid extracted algae as a protein source in forage or starch-based ruminant diets.

    PubMed

    Lodge-Ivey, S L; Tracey, L N; Salazar, A

    2014-04-01

    (P < 0.01). Microbial efficiency results for Chlorella were more variable for Nannochloropsis with 1 Chlorella spp. increasing microbial efficiency by 36% over SOY (P < 0.05) and the other Chlorella spp. decreasing microbial efficiency by approximately 42% compared with SOY (P < 0.01). Overall, the results from both experiments are promising for LEA as a protein feedstuff in ruminant diets. Further research is necessary to fully understand the interactions and consequences of upstream processes and what role algal strain plays in LEA quality. PMID:24243898

  12. Enhanced Colorimetric Immunoassay Accompanying with Enzyme Cascade Amplification Strategy for Ultrasensitive Detection of Low-Abundance Protein

    PubMed Central

    Gao, Zhuangqiang; Hou, Li; Xu, Mingdi; Tang, Dianping

    2014-01-01

    Methods based on enzyme labels have been developed for colorimetric immunoassays, but most involve poor sensitivity and are unsuitable for routine use. Herein, we design an enhanced colorimetric immunoassay for prostate-specific antigen (PSA) coupling with an enzyme-cascade-amplification strategy (ECAS-CIA). In the presence of target PSA, the labeled alkaline phosphatase on secondary antibody catalyzes the formation of palladium nanostructures, which catalyze 3,3′,5,5′-tetramethylbenzidine-H2O2 system to produce the colored products, thus resulting in the signal cascade amplification. Results indicated that the ECAS-CIA presents good responses toward PSA, and allows detection of PSA at a concentration as low as 0.05 ng mL−1. Intra- and inter-assay coefficients of variation are below 9.5% and 10.7%, respectively. Additionally, the methodology is validated for analysis of clinical serum specimens with consistent results obtained by PSA ELISA kit. Importantly, the ECAS-CIA opens a new horizon for protein diagnostics and biosecurity. PMID:24509941

  13. Influence of pregnancy in mid-to-late gestation on circulating metabolites, visceral organ mass, and abundance of proteins relating to energy metabolism in mature beef cows.

    PubMed

    Wood, K M; Awda, B J; Fitzsimmons, C; Miller, S P; McBride, B W; Swanson, K C

    2013-12-01

    In mid-to-late gestation, nutrient demand increases to meet the growth requirements of the conceptus and cows may alter metabolism in response to energy demands of pregnancy. By better understanding the metabolic role of pregnancy, there may be opportunities to better understand maintenance energy costs and improve overall feed efficiency. Eighteen mature Simmental/Angus crossbred cows, pregnant (PREG; n = 9) and nonpregnant (OPEN; n = 9), were used to investigate the effect of pregnancy on BW change, carcass traits, visceral organ mass, and circulating serum metabolites. Cows were blocked by day of expected parturition such that each block was slaughtered 4 to 5 wk before parturition. Cows were individually fed for ad libitum intake using Calan gates for 89 to 105 d. Cows were weighed, ultrasounded for rib (over the 12th and 13th rib) and rump fat, and a serum sample obtained at d 1, 56, and 3 to 5 d before slaughter. At slaughter, organs were removed, trimmed of fat, and weighed. Serum was analyzed for β-hydroxybutyrate (BHBA), NEFA, glucose, urea, total cholesterol, and triiodothyronine (T3). Tissue samples from liver, kidney, sternomandibularis muscle, ruminal papillae, pancreas, and small intestinal mucosa were collected at slaughter and snap frozen in liquid N. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen (PCNA), ATP synthase, ubiquitin, and Na(+)/K+ ATPase for all tissues; PPARγ, PPARγ coactivator 1α (PGC1-α), 5'-adenosine monophosphate-activated protein kinase (AMPK) and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase (PEPCK) for liver and kidney; and uncoupling protein 2 (UCP2) for liver. Data were analyzed using PROC MIXED in SAS as a replicated randomized complete block. Liver weights (actual, relative to BW, relative to HCW) were heavier (P ≤ 0.02) in OPEN. Rumen mass and kidney fat weight, both relative to BW, were also greater (P ≤ 0.04) in OPEN. On d 56

  14. How Can LEAs Help Schools to Use Research for School Improvement?

    ERIC Educational Resources Information Center

    Sharp, Caroline

    2004-01-01

    Few people would disagree with the principle of evidence-informed practice. Actually using evidence to improve teaching and learning is not so easy to achieve. The Local Government Agency recently asked the National Foundation for Educational Research (NFER) to find out how Local Education Authorities (LEAs) are helping schools to use research…

  15. 40 CFR 5.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 5.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  16. 43 CFR 41.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 41.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  17. 14 CFR 1253.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 1253.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  18. 28 CFR 54.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 54.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  19. Job Functions of an LEA Director and Application for Local Education Agencies Right to Read Services.

    ERIC Educational Resources Information Center

    California State Dept. of Education, Sacramento. Right to Read Unit.

    This document consists of three parts: (1) an application form for local education agencies (LEA) wishing to apply to participate in the California Right to Read Program; (2) evidence agencies must submit of a formal Board Resolution encompassing the following elements: commitment to reading as a curricular priority in the district; designation of…

  20. 36 CFR 1211.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Access to schools operated by... Prohibited § 1211.420 Access to schools operated by LEAs. A recipient that is a local educational agency... education operated by such recipient; or (b) Any other school or educational unit operated by such...

  1. 44 CFR 19.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Access to schools operated by... Activities Prohibited § 19.420 Access to schools operated by LEAs. A recipient that is a local educational... vocational education operated by such recipient; or (b) Any other school or educational unit operated by...

  2. 49 CFR 25.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 25.420 Access to schools operated by LEAs... from admission to: (a) Any institution of vocational education operated by such recipient; or (b)...

  3. 10 CFR 1042.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 1042.420 Access to schools operated by LEAs. A... admission to: (a) Any institution of vocational education operated by such recipient; or (b) Any...

  4. 43 CFR 41.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 41.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  5. 45 CFR 86.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 86.35 Access to schools operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of...

  6. 45 CFR 86.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 86.35 Access to schools operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of...

  7. 49 CFR 25.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 25.420 Transportation Office of the Secretary of Transportation NONDISCRIMINATION ON THE BASIS OF SEX... Basis of Sex in Education Programs or Activities Prohibited § 25.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex, exclude any...

  8. 45 CFR 86.35 - Access to schools operated by L.E.A.s.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... NONDISCRIMINATION ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 86.35 Access to schools operated by L.E.A.s. A recipient which is a local educational agency shall not, on the basis of...

  9. 28 CFR 54.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 54.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  10. 40 CFR 5.420 - Access to schools operated by LEAs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... ON THE BASIS OF SEX IN EDUCATION PROGRAMS OR ACTIVITIES RECEIVING FEDERAL FINANCIAL ASSISTANCE Discrimination on the Basis of Sex in Education Programs or Activities Prohibited § 5.420 Access to schools operated by LEAs. A recipient that is a local educational agency shall not, on the basis of sex,...

  11. 34 CFR 222.171 - What LEAs may be eligible for Discretionary Construction grants?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .... uniformed services; (ii) Have a school that enrolls a high proportion of one of these types of students....S. uniformed services; (iv) Have a school that enrolls a high proportion of one of these types of... such factors as an LEA's total assessed value of real property that may be taxed for school...

  12. 34 CFR 222.183 - How does an LEA apply for a grant?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... system, and asbestos in floor tiles. The LEA may submit a single application for all of these conditions... present varying degrees of urgency. (b) An application must— (1) Contain the information required in... application notice. (Approved by the Office of Management and Budget under control number...

  13. 34 CFR 200.77 - Reservation of funds by an LEA.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... EDUCATION, DEPARTMENT OF EDUCATION TITLE I-IMPROVING THE ACADEMIC ACHIEVEMENT OF THE DISADVANTAGED Improving... § 200.48, unless the LEA meets these requirements with non-Title I funds; (d) Address the professional development needs of instructional staff, including— (1) Professional development requirements under §...

  14. 34 CFR 200.70 - Allocation of funds to LEAs in general.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false Allocation of funds to LEAs in general. 200.70 Section 200.70 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT OF EDUCATION TITLE I-IMPROVING THE ACADEMIC ACHIEVEMENT OF THE...

  15. 34 CFR 222.171 - What LEAs may be eligible for Discretionary Construction grants?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    .... uniformed services; (ii) Have a school that enrolls a high proportion of one of these types of students....S. uniformed services; (iv) Have a school that enrolls a high proportion of one of these types of... 34 Education 1 2014-07-01 2014-07-01 false What LEAs may be eligible for...

  16. 34 CFR 222.171 - What LEAs may be eligible for Discretionary Construction grants?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    .... uniformed services; (ii) Have a school that enrolls a high proportion of one of these types of students....S. uniformed services; (iv) Have a school that enrolls a high proportion of one of these types of... 34 Education 1 2010-07-01 2010-07-01 false What LEAs may be eligible for...

  17. 34 CFR 222.171 - What LEAs may be eligible for Discretionary Construction grants?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .... uniformed services; (ii) Have a school that enrolls a high proportion of one of these types of students....S. uniformed services; (iv) Have a school that enrolls a high proportion of one of these types of... 34 Education 1 2012-07-01 2012-07-01 false What LEAs may be eligible for...

  18. A late embryogenesis abundant protein HVA1 regulated by an inducible promoter enhances root growth and abiotic stress tolerance in rice without yield penalty.

    PubMed

    Chen, Yi-Shih; Lo, Shuen-Fang; Sun, Peng-Kai; Lu, Chung-An; Ho, Tuan-Hua D; Yu, Su-May

    2015-01-01

    Regulation of root architecture is essential for maintaining plant growth under adverse environment. A synthetic abscisic acid (ABA)/stress-inducible promoter was designed to control the expression of a late embryogenesis abundant protein (HVA1) in transgenic rice. The background of HVA1 is low but highly inducible by ABA, salt, dehydration and cold. HVA1 was highly accumulated in root apical meristem (RAM) and lateral root primordia (LRP) after ABA/stress treatments, leading to enhanced root system expansion. Water-use efficiency (WUE) and biomass also increased in transgenic rice, likely due to the maintenance of normal cell functions and metabolic activities conferred by HVA1 which is capable of stabilizing proteins, under osmotic stress. HVA1 promotes lateral root (LR) initiation, elongation and emergence and primary root (PR) elongation via an auxin-dependent process, particularly by intensifying asymmetrical accumulation of auxin in LRP founder cells and RAM, even under ABA/stress-suppressive conditions. We demonstrate a successful application of an inducible promoter in regulating the spatial and temporal expression of HVA1 for improving root architecture and multiple stress tolerance without yield penalty. PMID:25200982

  19. High Throughput Screening for Compounds That Alter Muscle Cell Glycosylation Identifies New Role for N-Glycans in Regulating Sarcolemmal Protein Abundance and Laminin Binding*

    PubMed Central

    Cabrera, Paula V.; Pang, Mabel; Marshall, Jamie L.; Kung, Raymond; Nelson, Stanley F.; Stalnaker, Stephanie H.; Wells, Lance; Crosbie-Watson, Rachelle H.; Baum, Linda G.

    2012-01-01

    Duchenne muscular dystrophy is an X-linked disorder characterized by loss of dystrophin, a cytoskeletal protein that connects the actin cytoskeleton in skeletal muscle cells to extracellular matrix. Dystrophin binds to the cytoplasmic domain of the transmembrane glycoprotein β-dystroglycan (β-DG), which associates with cell surface α-dystroglycan (α-DG) that binds laminin in the extracellular matrix. β-DG can also associate with utrophin, and this differential association correlates with specific glycosylation changes on α-DG. Genetic modification of α-DG glycosylation can promote utrophin binding and rescue dystrophic phenotypes in mouse dystrophy models. We used high throughput screening with the plant lectin Wisteria floribunda agglutinin (WFA) to identify compounds that altered muscle cell surface glycosylation, with the goal of finding compounds that increase abundance of α-DG and associated sarcolemmal glycoproteins, increase utrophin usage, and increase laminin binding. We identified one compound, lobeline, from the Prestwick library of Food and Drug Administration-approved compounds that fulfilled these criteria, increasing WFA binding to C2C12 cells and to primary muscle cells from wild type and mdx mice. WFA binding and enhancement by lobeline required complex N-glycans but not O-mannose glycans that bind laminin. However, inhibiting complex N-glycan processing reduced laminin binding to muscle cell glycoproteins, although O-mannosylation was intact. Glycan analysis demonstrated a general increase in N-glycans on lobeline-treated cells rather than specific alterations in cell surface glycosylation, consistent with increased abundance of multiple sarcolemmal glycoproteins. This demonstrates the feasibility of high throughput screening with plant lectins to identify compounds that alter muscle cell glycosylation and identifies a novel role for N-glycans in regulating muscle cell function. PMID:22570487

  20. Co-transforming bar and CsLEA enhanced tolerance to drought and salt stress in transgenic alfalfa (Medicago sativa L.).

    PubMed

    Zhang, Jiyu; Duan, Zhen; Zhang, Daiyu; Zhang, Jianquan; Di, Hongyan; Wu, Fan; Wang, Yanrong

    2016-03-25

    Drought and high salinity are two major abiotic factors that restrict alfalfa productivity. A dehydrin protein, CsLEA, from the desert grass Cleistogenes songorica was transformed into alfalfa (Medicago sativa L.) via Agrobacterium-mediated transformation using the bar gene as a selectable marker, and the drought and salt stress tolerances of the transgenic plants were assessed. Thirty-nine of 119 transformants were positive, as screened by Basta, and further molecularly authenticated using PCR and RT-PCR. Phenotype observations revealed that the transgenic plants grew better than the wild-type (WT) plants after 15d of drought stress and 10d of salt stress: the leaves of WT alfalfa turned yellow, whereas the transgenic alfalfa leaves only wilted; after rewatering, the transgenic plants returned to a normal state, though the WT plants could not be restored. Evaluation of physiologic and biochemical indices during drought and salt stresses showed a relatively lower Na(+) content in the leaves of the transgenic plants, which would reduce toxic ion effects. In addition, the transgenic plants were able to maintain a higher relative water content (RWC), higher shoot biomass, fewer photosystem changes, decreased membrane injury, and a lower level of osmotic stress injury. These results demonstrate that overexpression of the CsLEA gene can enhance the drought and salt tolerance of transgenic alfalfa; in addition, carrying the bar gene in the genome may increase herbicide resistance. PMID:26906624

  1. Analysis of genetic diversity of the heat shock protein 70 gene on the basis of abundant sequence polymorphisms in chicken breeds.

    PubMed

    Gan, J K; Jiang, L Y; Kong, L N; Zhang, X Q; Luo, Q B

    2015-01-01

    This study was designed to detect the sequence variation of the chicken heat shock protein 70 (HSP70) gene. A total of 102 individuals from 8 native Chinese breeds together with Dwarf White Chicken and Red Junglefowl were used to detect sequence variations. The coding regions of the chicken HSP70 gene from 102 individuals were cloned and sequenced. Thirty-six variations were identified, which included 34 single nucleotide polymorphisms and 2 indel mutations. Fifty-seven haplotypes were observed, of which, 43 were breed-specific and 14 were shared. There were 7 Red Junglefowl-specific haplotypes, while Haidong and Silkie only had 2 specific haplotypes. Eleven and 3 haplotypes were shared between and within species, respectively. The variation in nucleotide diversity (Pi) and average number of nucleotide differences (K) among species were consistent. The total Pi of HSP70 was 0.0016, and the total K was 4.1998. The Pi value of Red Junglefowl was the highest (0.0018) and K was 4.8000, while the Pi of Silkie was the lowest (0.0010) and K was 2.5000. These results demonstrated that variation in chicken HSP70 was abundant between and within species. PMID:25867297

  2. THE LOCAL EXPRESSION AND ABUNDANCE OF INSULIN-LIKE GROWTH FACTOR (IGF) BINDING PROTEINS IN SKELETAL MUSCLE ARE REGULATED BY AGE AND GENDER BUT NOT LOCAL IGF-I "IN VIVO"

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We wished to determine whether sustained IGF-I production in skeletal muscle increases local IGF binding protein (IGFBP) abundance, thereby mitigating the long-term stimulation of muscle growth by IGF-I. Muscle growth of transgenic mice that overexpress IGF-I in muscle (SIS2) and of wild-type (Wt) m...

  3. Increased Reactive Oxygen Species Production and Lower Abundance of Complex I Subunits and Carnitine Palmitoyltransferase 1B Protein Despite Normal Mitochondrial Respiration in Insulin-Resistant Human Skeletal Muscle

    PubMed Central

    Lefort, Natalie; Glancy, Brian; Bowen, Benjamin; Willis, Wayne T.; Bailowitz, Zachary; De Filippis, Elena A.; Brophy, Colleen; Meyer, Christian; Højlund, Kurt; Yi, Zhengping; Mandarino, Lawrence J.

    2010-01-01

    OBJECTIVE The contribution of mitochondrial dysfunction to skeletal muscle insulin resistance remains elusive. Comparative proteomics are being applied to generate new hypotheses in human biology and were applied here to isolated mitochondria to identify novel changes in mitochondrial protein abundance present in insulin-resistant muscle. RESEARCH DESIGN AND METHODS Mitochondria were isolated from vastus lateralis muscle from lean and insulin-sensitive individuals and from obese and insulin-resistant individuals who were otherwise healthy. Respiration and reactive oxygen species (ROS) production rates were measured in vitro. Relative abundances of proteins detected by mass spectrometry were determined using a normalized spectral abundance factor method. RESULTS NADH- and FADH2-linked maximal respiration rates were similar between lean and obese individuals. Rates of pyruvate and palmitoyl-dl-carnitine (both including malate) ROS production were significantly higher in obesity. Mitochondria from obese individuals maintained higher (more negative) extramitochondrial ATP free energy at low metabolic flux, suggesting that stronger mitochondrial thermodynamic driving forces may underlie the higher ROS production. Tandem mass spectrometry identified protein abundance differences per mitochondrial mass in insulin resistance, including lower abundance of complex I subunits and enzymes involved in the oxidation of branched-chain amino acids (BCAA) and fatty acids (e.g., carnitine palmitoyltransferase 1B). CONCLUSIONS We provide data suggesting normal oxidative capacity of mitochondria in insulin-resistant skeletal muscle in parallel with high rates of ROS production. Furthermore, we show specific abundance differences in proteins involved in fat and BCAA oxidation that might contribute to the accumulation of lipid and BCAA frequently associated with the pathogenesis of insulin resistance. PMID:20682693

  4. Induction of ketosis in rats fed low-carbohydrate, high-fat diets depends on the relative abundance of dietary fat and protein.

    PubMed

    Bielohuby, Maximilian; Menhofer, Dominik; Kirchner, Henriette; Stoehr, Barbara J M; Müller, Timo D; Stock, Peggy; Hempel, Madlen; Stemmer, Kerstin; Pfluger, Paul T; Kienzle, Ellen; Christ, Bruno; Tschöp, Matthias H; Bidlingmaier, Martin

    2011-01-01

    Low-carbohydrate/high-fat diets (LC-HFDs) in rodent models have been implicated with both weight loss and as a therapeutic approach to treat neurological diseases. LC-HFDs are known to induce ketosis; however, systematic studies analyzing the impact of the macronutrient composition on ketosis induction and weight loss success are lacking. Male Wistar rats were pair-fed for 4 wk either a standard chow diet or one of three different LC-HFDs, which only differed in the relative abundance of fat and protein (percentages of fat/protein in dry matter: LC-75/10; LC-65/20; LC-55/30). We subsequently measured body composition by nuclear magnetic resonance (NMR), analyzed blood chemistry and urine acetone content, evaluated gene expression changes of key ketogenic and gluconeogenic genes, and measured energy expenditure (EE) and locomotor activity (LA) during the first 4 days and after 3 wk on the respective diets. Compared with chow, rats fed with LC-75/10, LC-65/20, and LC-55/30 gained significantly less body weight. Reductions in body weight were mainly due to lower lean body mass and paralleled by significantly increased fat mass. Levels of β-hydroxybutyate were significantly elevated feeding LC-75/10 and LC-65/20 but decreased in parallel to reductions in dietary fat. Acetone was about 16-fold higher with LC-75/10 only (P < 0.001). In contrast, rats fed with LC-55/30 were not ketotic. Serum fibroblast growth factor-21, hepatic mRNA expression of hydroxymethylglutaryl-CoA-lyase, peroxisome proliferator-activated receptor-γ coactivator-1α, and peroxisome proliferator-activated receptor-γ coactivator-1β were increased with LC-75/10 only. Expression of phosphoenolpyruvate carboxykinase and glucose-6-phosphatase was downregulated by 50-70% in LC-HF groups. Furthermore, EE and LA were significantly decreased in all groups fed with LC-HFDs after 3 wk on the diets. In rats, the absence of dietary carbohydrates per se does not induce ketosis. LC-HFDs must be high in fat

  5. Proteomics of stress responses in wheat and barley—search for potential protein markers of stress tolerance

    PubMed Central

    Kosová, Klára; Vítámvás, Pavel; Prášil, Ilja T.

    2014-01-01

    Wheat (Triticum aestivum; T. durum) and barley (Hordeum vulgare) agricultural production is severely limited by various abiotic and biotic stress factors. Proteins are directly involved in plant stress response so it is important to study proteome changes under various stress conditions. Generally, both abiotic and biotic stress factors induce profound alterations in protein network covering signaling, energy metabolism (glycolysis, Krebs cycle, ATP biosynthesis, photosynthesis), storage proteins, protein metabolism, several other biosynthetic pathways (e.g., S-adenosylmethionine metabolism, lignin metabolism), transport proteins, proteins involved in protein folding and chaperone activities, other protective proteins (LEA, PR proteins), ROS scavenging enzymes as well as proteins affecting regulation of plant growth and development. Proteins which have been reported to reveal significant differences in their relative abundance or posttranslational modifications between wheat, barley or related species genotypes under stress conditions are listed and their potential role in underlying the differential stress response is discussed. In conclusion, potential future roles of the results of proteomic studies in practical applications such as breeding for an enhanced stress tolerance and the possibilities to test and use protein markers in the breeding are suggested. PMID:25566285

  6. Development of the Levels of Emotional Awareness Scale for Children (LEAS-C)

    ERIC Educational Resources Information Center

    Bajgar, Jane; Ciarrochi, Joseph; Lane, Richard; Deane, Frank P.

    2005-01-01

    A performance-based assessment of the structure and complexity of emotional awareness was developed, the Levels of Emotional Awareness Scale for Children (LEAS-C). A pilot study (N=6, ages 9-12, M [subscript age]=10.2 years) was conducted to construct, trial, and select scenarios suitable for the scale. A larger validity study (N=51, ages 10-11, M…

  7. Red light-regulated growth. I. Changes in the abundance of indoleacetic acid and a 22-kilodalton auxin-binding protein in the maize mesocotyl

    NASA Technical Reports Server (NTRS)

    Jones, A. M.; Cochran, D. S.; Lamerson, P. M.; Evans, M. L.; Cohen, J. D.

    1991-01-01

    We examined the changes in the levels of indoleacetic acid (IAA), IAA esters, and a 22-kilodalton subunit auxin-binding protein (ABP1) in apical mesocotyl tissue of maize (Zea mays L.) during continuous red light (R) irradiation. These changes were compared with the kinetics of R-induced growth inhibition in the same tissue. Upon the onset of continuous irradiation, growth decreased in a continuous manner following a brief lag period. The decrease in growth continued for 5 hours, then remained constant at 25% of the dark rate. The abundance of ABP1 and the level of free IAA both decreased in the mesocotyl. Only the kinetics of the decrease in IAA within the apical mesocotyl correlated with the initial change in growth, although growth continued to decrease even after IAA content reached its final level, 50% of the dark control. This decrease in IAA within the mesocotyl probably occurs primarily by a change in its transport within the shoot since auxin applied as a pulse move basipetally in R-irradiated tissue at the same rate but with half the area as dark control tissue. In situ localization of auxin in etiolated maize shoots revealed that R-irradiated shoots contained less auxin in the epidermis than the dark controls. Irradiated mesocotyl grew 50% less than the dark controls even when incubated in an optimal level of auxin. However, irradiated and dark tissue contained essentially the same amount of radioactivity after incubation in [14C]IAA indicating that the light treatment does not affect the uptake into the tissue through the cut end, although it is possible that a small subset of cells within the mesocotyl is affected. These observations support the hypothesis that R causes a decrease in the level of auxin in epidermal cells of the mesocotyl, consequently constraining the growth of the entire mesocotyl.

  8. The local expression and abundance of insulin-like growth factor (IGF) binding proteins in skeletal muscle are regulated by age and gender but not local IGF-I in vivo.

    PubMed

    Oliver, William T; Rosenberger, Judy; Lopez, Rusmely; Gomez, Adam; Cummings, Kathleen K; Fiorotto, Marta L

    2005-12-01

    We wished to determine whether sustained IGF-I production in skeletal muscle increases local IGF binding protein (IGFBP) abundance, thereby mitigating the long-term stimulation of muscle growth by IGF-I. Muscle growth of transgenic mice that overexpress IGF-I in muscle (SIS2) and of wild-type (Wt) mice was compared. At 3, 5, 10, and 20 wk of age, hind-limb muscle weights and IGFBP-3, -4, -5, and -6 mRNA and protein abundances were quantified. Additional mice were injected with IGF-I or LR3-IGF-I, and phosphorylation of the type 1 IGF receptor (IGF-1R) was compared. Muscle mass was 20% greater in SIS2 compared with Wt mice by 10 wk of age (P < 0.01), and this difference was maintained to 20 wk. IGFBP mRNA and protein abundances were unaffected by genotype. IGFBP-4 and -5 protein abundances increased with age, whereas for IGFBP-3 and -6, there was a sexual dimorphic response (P < 0.01); after 5 wk of age, IGFBP-3 decreased in males but increased in females, whereas IGFBP-6 decreased in females and remained unchanged in males. These protein expression patterns resulted from differences at both the transcriptional and posttranscriptional levels. LR3-IGF-I stimulated IGF-1R phosphorylation to a greater extent than IGF-I at both 5 and 10 wk of age (P < 0.01), regardless of gender or genotype (P > 0.21). Thus, variations in local IGF-I levels do not appear to regulate muscle IGFBP expression. The age- and gender-specific differences in muscle IGFBP expression are not sufficient to alter the response of the muscle to the IGFs but may impact the IGF-independent effects of these IGFBPs. PMID:16166219

  9. Interaction of two intrinsically disordered plant stress proteins (COR15A and COR15B) with lipid membranes in the dry state.

    PubMed

    Thalhammer, Anja; Hundertmark, Michaela; Popova, Antoaneta V; Seckler, Robert; Hincha, Dirk K

    2010-09-01

    COR15A and COR15B form a tandem repeat of highly homologous genes in Arabidopsis thaliana. Both genes are highly cold induced and the encoded proteins belong to the Pfam LEA_4 group (group 3) of the late embryogenesis abundant (LEA) proteins. Both proteins were predicted to be intrinsically disordered in solution. Only COR15A has previously been characterized and it was shown to be localized in the soluble stroma fraction of chloroplasts. Ectopic expression of COR15A in Arabidopsis resulted in increased freezing tolerance of both chloroplasts after freezing and thawing of intact leaves and of isolated protoplasts frozen and thawed in vitro. In the present study we have generated recombinant mature COR15A and COR15B for a comparative study of their structure and possible function as membrane protectants. CD spectroscopy showed that both proteins are predominantly unstructured in solution and mainly alpha-helical after drying. Both proteins showed similar effects on the thermotropic phase behavior of dry liposomes. A decrease in the gel to liquid-crystalline phase transition temperature depended on both the unsaturation of the fatty acyl chains and lipid headgroup structure. FTIR spectroscopy indicated no strong interactions between the proteins and the lipid phosphate and carbonyl groups, but significant interactions with the galactose headgroup of the chloroplast lipid monogalactosyldiacylglycerol. These findings were rationalized by modeling the secondary structure of COR15A and COR15B. Helical wheel projection indicated the presence of amphipathic alpha-helices in both proteins. The helices lacked a clear separation of positive and negative charges on the hydrophilic face, but contained several hydroxylated amino acids. PMID:20510170

  10. Evaluation from an LEA Perspective: Proceedings from an AERA Symposium. Annual Meeting of the American Educational Research Association (66th, New York, New York, March 19-23, 1982).

    ERIC Educational Resources Information Center

    Thompson, Bruce; And Others

    The views of local education agency (LEA) evaluators tend to be underrepresented in the evaluation literature. This symposium was organized to fill this gap. The non-LEA symposium participants (Carol H. Weiss and Bruce Thompson) were asked to pose questions to the LEA participants (Steven Frankel, Montgomery County (MD) Public Schools; Freda…

  11. Improved method for identification of low abundance proteins using 2D-gel electrophoresis, MALDI-TOF and TOF/TOF

    EPA Science Inventory

    Introduction: Differential protein expression studies have been routinely performed in our laboratory to determine the health effects of environmentally-important chemicals. In this abstract, improvements in the in-gel protein digestion, MALDI plate spotting and data acquisition...

  12. Cohort Profile: The French Childhood Cancer Survivor Study For Leukaemia (LEA Cohort)

    PubMed Central

    Berbis, Julie; Michel, Gérard; Baruchel, André; Bertrand, Yves; Chastagner, Pascal; Demeocq, François; Kanold, Justyna; Leverger, Guy; Plantaz, Dominique; Poirée, Marilyne; Stephan, Jean-Louis; Auquier, Pascal; Contet, Audrey; Dalle, Jean-Hugues; Ducassou, Stéphane; Gandemer, Virginie; Lutz, Patrick; Sirvent, Nicolas; Tabone, Marie-Dominique; Thouvenin-Doulet, Sandrine

    2015-01-01

    The main aim of the Leucémies de l’Enfant et l’Adolescent (LEA) project (Childhood and Adolescent Leukaemia) is to study the determinants (medical, socioeconomic, behavioural and environmental) of medium- and long-term outcomes of patients treated for childhood acute leukaemia (AL). The LEA study began in 2004 and is based on a French multicentric prospective cohort. Included are children treated for AL since January 1980 (incident and prevalent cases), surviving at month 24 for myeloblastic AL and lymphoblastic AL grafted in first complete remission or at month 48 for lymphoblastic AL not grafted in first complete remission. Information is collected during specific medical visits and notably includes the following data: socioeconomic data, AL history, physical late effects (such as fertility, cardiac function and metabolic syndrome) and quality of life. Data are collected every 2 years until the patient is 20 years old and has had a 10-year follow-up duration from diagnosis or last relapse. Thereafter, assessments are planned every 4 years. In active centres in 2013, eligible patients number more than 3000. The cohort has already included 2385 survivors, with rate of exhaustiveness of almost 80%. Data access can be requested from principal coordinators and must be approved by the steering committee. PMID:24639445

  13. 34 CFR 611.47 - What are a scholarship recipient's reporting responsibilities upon the close of the LEA's...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 3 2013-07-01 2013-07-01 false What are a scholarship recipient's reporting... EDUCATION TEACHER QUALITY ENHANCEMENT GRANTS PROGRAM Scholarships § 611.47 What are a scholarship recipient...'s academic year, a scholarship recipient whose LEA reports under § 611.46(a) that he or she...

  14. 34 CFR 611.47 - What are a scholarship recipient's reporting responsibilities upon the close of the LEA's...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 3 2014-07-01 2014-07-01 false What are a scholarship recipient's reporting... EDUCATION TEACHER QUALITY ENHANCEMENT GRANTS PROGRAM Scholarships § 611.47 What are a scholarship recipient...'s academic year, a scholarship recipient whose LEA reports under § 611.46(a) that he or she...

  15. 34 CFR 611.47 - What are a scholarship recipient's reporting responsibilities upon the close of the LEA's...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 3 2012-07-01 2012-07-01 false What are a scholarship recipient's reporting... EDUCATION TEACHER QUALITY ENHANCEMENT GRANTS PROGRAM Scholarships § 611.47 What are a scholarship recipient...'s academic year, a scholarship recipient whose LEA reports under § 611.46(a) that he or she...

  16. 45 CFR 2516.420 - What must an LEA, local partnership, qualified organization or other eligible entity include in...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 4 2010-10-01 2010-10-01 false What must an LEA, local partnership, qualified organization or other eligible entity include in an application for a subgrant? 2516.420 Section 2516.420 Public Welfare Regulations Relating to Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE SCHOOL-BASED...

  17. 45 CFR 2516.420 - What must an LEA, local partnership, qualified organization or other eligible entity include in...

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 4 2011-10-01 2011-10-01 false What must an LEA, local partnership, qualified organization or other eligible entity include in an application for a subgrant? 2516.420 Section 2516.420 Public Welfare Regulations Relating to Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE SCHOOL-BASED...

  18. 34 CFR 222.16 - What information and documentation must an LEA submit for an eligible overpayment to be...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... for an eligible overpayment to be considered for forgiveness? 222.16 Section 222.16 Education... submit for an eligible overpayment to be considered for forgiveness? (a) Every LEA requesting forgiveness... documentation for the fiscal year immediately preceding the date of the forgiveness request (“preceding...

  19. 34 CFR 222.16 - What information and documentation must an LEA submit for an eligible overpayment to be...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... for an eligible overpayment to be considered for forgiveness? 222.16 Section 222.16 Education... submit for an eligible overpayment to be considered for forgiveness? (a) Every LEA requesting forgiveness... documentation for the fiscal year immediately preceding the date of the forgiveness request (“preceding...

  20. 34 CFR 222.16 - What information and documentation must an LEA submit for an eligible overpayment to be...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... for an eligible overpayment to be considered for forgiveness? 222.16 Section 222.16 Education... submit for an eligible overpayment to be considered for forgiveness? (a) Every LEA requesting forgiveness... documentation for the fiscal year immediately preceding the date of the forgiveness request (“preceding...

  1. 34 CFR 222.16 - What information and documentation must an LEA submit for an eligible overpayment to be...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... for an eligible overpayment to be considered for forgiveness? 222.16 Section 222.16 Education... submit for an eligible overpayment to be considered for forgiveness? (a) Every LEA requesting forgiveness... documentation for the fiscal year immediately preceding the date of the forgiveness request (“preceding...

  2. 34 CFR 222.16 - What information and documentation must an LEA submit for an eligible overpayment to be...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... for an eligible overpayment to be considered for forgiveness? 222.16 Section 222.16 Education... submit for an eligible overpayment to be considered for forgiveness? (a) Every LEA requesting forgiveness... documentation for the fiscal year immediately preceding the date of the forgiveness request (“preceding...

  3. 34 CFR 222.172 - What activities may an LEA conduct with funds received under this program?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Aid Discretionary Construction Grant Program Under Section 8007(b) of the Act General § 222.172 What... for free public education to ensure the health and safety of students and personnel, including providing accessibility for the disabled as part of a larger project. (b) An LEA may use modernization...

  4. 34 CFR 222.172 - What activities may an LEA conduct with funds received under this program?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Aid Discretionary Construction Grant Program Under Section 8007(b) of the Act General § 222.172 What... for free public education to ensure the health and safety of students and personnel, including providing accessibility for the disabled as part of a larger project. (b) An LEA may use modernization...

  5. 34 CFR 222.172 - What activities may an LEA conduct with funds received under this program?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Aid Discretionary Construction Grant Program Under Section 8007(b) of the Act General § 222.172 What... for free public education to ensure the health and safety of students and personnel, including providing accessibility for the disabled as part of a larger project. (b) An LEA may use modernization...

  6. 34 CFR 222.172 - What activities may an LEA conduct with funds received under this program?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Aid Discretionary Construction Grant Program Under Section 8007(b) of the Act General § 222.172 What... for free public education to ensure the health and safety of students and personnel, including providing accessibility for the disabled as part of a larger project. (b) An LEA may use modernization...

  7. 34 CFR 200.72 - Procedures for adjusting allocations determined by the Secretary to account for eligible LEAs not...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Procedures for adjusting allocations determined by the Secretary to account for eligible LEAs not on the Census list. 200.72 Section 200.72 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY...

  8. 34 CFR 222.181 - What eligibility requirements must an LEA meet to apply for a modernization grant under the...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false What eligibility requirements must an LEA meet to apply for a modernization grant under the fourth priority? 222.181 Section 222.181 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT...

  9. The soybean GmDi19-5 interacts with GmLEA3.1 and increases sensitivity of transgenic plants to abiotic stresses

    PubMed Central

    Feng, Zhi-Juan; Cui, Xiao-Yu; Cui, Xi-Yan; Chen, Ming; Yang, Guang-Xiao; Ma, You-Zhi; He, Guang-Yuan; Xu, Zhao-Shi

    2015-01-01

    Drought-induced (Di19) proteins played important roles in plant growth, development, and abiotic stress responses. In the present study, a total of seven Di19 genes were identified in soybean. Each soybean Di19 gene showed specific responses to salt, drought, oxidative, and ABA stresses based on expression profiles. With a relatively higher transcript level among Di19 members under four stress treatments, GmDi19-5 was selected for detailed analysis. Inhibitor assays revealed that ABA inhibitor (Fluridone) or H2O2 inhibitor (DMTU) was involved in the drought- or salt-induced transcription of GmDi19-5. The GUS activity driven by the GmDi19-5 promoter was induced by salt, PEG, ABA, and MV treatments and tended to be accumulated in the vascular bundles and young leaves. A subcellular localization assay showed that GmDi19-5 protein localized in the nucleus. Further investigation showed that GmDi19-5 protein was involved in the interaction with GmLEA3.1. Overexpression of GmDi19-5 increased sensitivity of transgenic Arabidopsis plants to salt, drought, oxidative, and ABA stresses and regulated expression of several ABA/stress-associated genes. This present investigation showed that GmDi19-5 functioned as a negative factor under abiotic stresses and was involved in ABA and SOS signaling pathway by altering transcription of stress-associated genes. PMID:25852726

  10. Meteorite search in the deflation basins in Lea County, New Mexico and Winkler County, Texas, USA: Discovery of Lea County 003 (H4)

    SciTech Connect

    Mikouchi, T; Buchanan, P C; Zolensky, M E; Welten, K C; Hutchison, R; Hutchison, M

    2000-01-14

    During the past few decades great numbers of meteorites have been recovered from the ice accumulation zones of Antarctica and from the vast Sahara. Although these two great deserts are the two most productive areas, the Southern High Plains in USA (New Mexico and Texas) and Nullarbor Plain, Western Australia have great potential for meteorite recovery. The number of meteorite finds from Roosevelt County, New Mexico alone exceeds 100 in only approximately 11 km{sup 2} area. Most meteorites from this area have been found on the floors of active deflation basins (blowouts) that have been excavated from a mantle of sand dunes. This area has no apparent fluvial or permafrost activity within the last 50,000 years, suggesting that only prevailing winds and natural aridity aid in the concentration and preservation of meteorites. The authors investigated these deflation surfaces in Lea County (the SE corner of New Mexico) and neighboring Winkler County, Texas following a prior search in this area which found two chondrites. They found a tiny H4 chondrite in this search and here they report its mineralogy and petrology along with preliminary data on its exposure history.

  11. Lea's Pies

    NASA Technical Reports Server (NTRS)

    1996-01-01

    The Technology Transfer Office at Stennis Space Center worked with a pie company owner to develop an inexpensive container that would protect pies and keep them in a near frozen condition for shipping in 48 hours. A NASA engineer made a thermal barrier envelope from a metalized mylar called 'space blanket material,' developed during the Apollo era. The envelope protects the pies from heat transfer. Pictured, a NASA engineer removes the temperature logger from a pecan pie shipped to him in a prototype envelope.

  12. Fibroblast Growth Factor (FGF) Signaling during Gastrulation Negatively Modulates the Abundance of MicroRNAs That Regulate Proteins Required for Cell Migration and Embryo Patterning*

    PubMed Central

    Bobbs, Alexander S.; Saarela, Aleksi V.; Yatskievych, Tatiana A.; Antin, Parker B.

    2012-01-01

    FGF signaling plays a pivotal role in regulating cell movements and lineage induction during gastrulation. Here we identify 44 microRNAs that are expressed in the primitive streak region of gastrula stage chicken embryos. We show that the primary effect of FGF signaling on microRNA abundance is to negatively regulate the levels of miR-let-7b, -9, -19b, -107, -130b, and -218. LIN28B inhibits microRNA processing and is positively regulated by FGF signaling. Gain- and loss-of-function experiments show that LIN28B negatively regulates the expression of miR-19b, -130b, and let-7b, whereas negative modulation of miR-9, -107, and -218 appears to be independent of LIN28B function. Predicted mRNA targets of the FGF-regulated microRNAs are over-represented in serine/threonine and tyrosine kinase receptors, including ACVR1, ACVR2B, PDGFRA, TGFBR1, and TGFBR3. Luciferase assays show that these and other candidates are targeted by FGF-regulated microRNAs. PDGFRA, a receptor whose activity is required for cell migration through the primitive streak, is a target of miR-130b and -218 in vivo. These results identify a novel mechanism by which FGF signaling regulates gene expression by negatively modulating microRNA abundance through both LIN28B-dependent and LIN28B-independent pathways. PMID:22995917

  13. The SLE variant Ala71Thr of BLK severely decreases protein abundance and binding to BANK1 through impairment of the SH3 domain function.

    PubMed

    Díaz-Barreiro, A; Bernal-Quirós, M; Georg, I; Marañón, C; Alarcón-Riquelme, M E; Castillejo-López, C

    2016-03-01

    The B-lymphocyte kinase (BLK) gene is associated genetically with several human autoimmune diseases including systemic lupus erythematosus. We recently described that the genetic risk is given by two haplotypes: one covering several strongly linked single-nucleotide polymorphisms within the promoter of the gene that correlated with low transcript levels, and a second haplotype that includes a rare nonsynonymous variant (Ala71Thr). Here we show that this variant, located within the BLK SH3 domain, is a major determinant of protein levels. In vitro analyses show that the 71Thr isoform is hyperphosphorylated and promotes kinase activation. As a consequence, BLK is ubiquitinated, its proteasomal degradation enhanced and the average life of the protein is reduced by half. Altogether, these findings suggest that an intrinsic autoregulatory mechanism previously unappreciated in BLK is disrupted by the 71Thr substitution. Because the SH3 domain is also involved in protein interactions, we sought for differences between the two isoforms in trafficking and binding to protein partners. We found that binding of the 71Thr variant to the adaptor protein BANK1 is severely reduced. Our study provides new insights on the intrinsic regulation of BLK activation and highlights the dominant role of its SH3 domain in BANK1 binding. PMID:26821283

  14. The absence of protein Y4yS affects negatively the abundance of T3SS Mesorhizobium loti secretin, RhcC2, in bacterial membranes

    PubMed Central

    Mercante, Virginia; Duarte, Cecilia M.; Sánchez, Cintia M.; Zalguizuri, Andrés; Caetano-Anollés, Gustavo; Lepek, Viviana C.

    2015-01-01

    Mesorhizobium loti MAFF303099 has a functional type III secretion system (T3SS) that is involved in the determination of nodulation competitiveness on Lotus. The M. loti T3SS cluster contains gene y4yS (mlr8765) that codes for a protein of unknown function (Y4yS). A mutation in the y4yS gene favors the M. loti symbiotic competitive ability on Lotus tenuis cv. Esmeralda and affects negatively the secretion of proteins through T3SS. Here we localize Y4yS in the bacterial membrane using a translational reporter peptide fusion. In silico analysis indicated that this protein presents a tetratricopeptide repeat (TPR) domain, a signal peptide and a canonical lipobox LGCC in the N-terminal sequence. These features that are shared with proteins required for the formation of the secretin complex in type IV secretion systems and in the Tad system, together with its localization, suggest that the y4yS-encoded protein is required for the formation of the M. loti T3SS secretin (RhcC2) complex. Remarkably, analysis of RhcC2 in the wild-type and M. loti y4yS mutant strains indicated that the absence of Y4yS affects negatively the accumulation of normal levels of RhcC2 in the membrane. PMID:25688250

  15. An evaluation of the CO/sub 2/ pilot, Maljamar Field, Lea County, New Mexico

    SciTech Connect

    Plumb, L.B.; Ferrell, H.H.

    1989-02-01

    This report reviews the performance of the miscible CO/sub 2/ pilot in the Maljamar Field, Lea County, New Mexico. The project was conducted by Conoco under the Tertiary Incentive Crude Oil Program. The project was initiated in 1981 and completed January 1, 1986. The project involved CO/sub 2/ floods in two separate reservoirs conducted simultaneously using dually completed wells in a 5-acre inverted 5-spot pattern. Control of fluid movement in the pilot was achieved by utilizing four confining injection wells outside the pattern, as well as two observation wells inside the pattern. The purpose of the pilot was to provide data for computer modelling of the reservoir and for facilities design and economic analysis of a full scale project. Conoco accomplished this purpose and has begun fieldwide expansion of CO/sub 2/ flooding in both Maljamar reservoirs based on the results of this pilot. 14 refs., 4 figs., 4 tabs.

  16. Apical Na(+)-D-glucose cotransporter 1 (SGLT1) activity and protein abundance are expressed along the jejunal crypt-villus axis in the neonatal pig

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Gut apical Na(+)-glucose cotransporter 1 (SGLT1) activity is high at the birth and during suckling, thus contributing substantially to neonatal glucose homeostasis. We hypothesize that neonates possess high SGLT1 maximal activity by expressing apical SGLT1 protein along the intestinal crypt-villus a...

  17. 34 CFR 200.74 - Use of an alternative method to distribute grants to LEAs with fewer than 20,000 total residents.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... poverty measure consistently for small LEAs across the State for all Title I, part A programs. (d) Based on the alternative poverty data selected, the SEA must— (1) Re-determine eligibility of its...

  18. 34 CFR 200.74 - Use of an alternative method to distribute grants to LEAs with fewer than 20,000 total residents.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... poverty measure consistently for small LEAs across the State for all Title I, part A programs. (d) Based on the alternative poverty data selected, the SEA must— (1) Re-determine eligibility of its...

  19. 34 CFR 200.74 - Use of an alternative method to distribute grants to LEAs with fewer than 20,000 total residents.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... poverty measure consistently for small LEAs across the State for all Title I, part A programs. (d) Based on the alternative poverty data selected, the SEA must— (1) Re-determine eligibility of its...

  20. An abundant and ubiquitous homo-oligomeric ring-shaped ATPase particle related to the putative vesicle fusion proteins Sec18p and NSF.

    PubMed Central

    Peters, J M; Walsh, M J; Franke, W W

    1990-01-01

    We have discovered a ring-shaped particle of 12.5 nm diameter, 14.5S and apparent molecular weight of approximately 570,000 that displays 6-fold radial symmetry and is composed of a single kind of an acidic (pI approximately 5.5) polypeptide of Mr 97,000 (p97). Using antibodies to this protein we have detected its occurrence in a wide range of cells and tissues of diverse species from frog to man, including highly specialized cells such as mammalian erythrocytes and spermatozoa. In Xenopus laevis oocytes, the particle is found in both isolated nuclei and in manually enucleated ooplasms, which corresponds to immunofluorescence staining dispersed over both nucleoplasm and cytoplasm. The particle has a N-ethylmaleimide (NEM)-inhibitable Mg2(+)-ATPase activity, and its amino acid sequence, as deduced from cDNA clones, displays considerable homology to the mammalian NEM-sensitive fusion protein (NSF) and yeast Sec18p believed to be essential for vesicle fusion in secretory processes, indicating that these three proteins belong to the same multigene family. Images Fig. 1. Fig. 2. Fig. 3. Fig. 4. Fig. 5. PMID:2140770

  1. A plant cell model of polyglutamine aggregation: Identification and characterisation of macromolecular and small-molecule anti-protein aggregation activity in vivo.

    PubMed

    Liu, Guobao; Hu, Yueming; Tunnacliffe, Alan; Zheng, Yizhi

    2015-08-10

    In vitro studies have shown that LEA proteins from plants and invertebrates protect and stabilise other proteins under conditions of water stress, suggesting a role in stress tolerance. However, there is little information on LEA protein function in whole plants or plant cells, particularly with respect to their anti-aggregation activity. To address this, we expressed in tobacco BY-2 suspension cells an aggregation-prone protein based on that responsible for Huntington's disease (HD). In HD, abnormally long stretches of polyglutamine (polyQ) in huntingtin (Htt) protein cause aggregation of Htt fragments within cells. We constructed stably transformed BY-2 cell lines expressing enhanced green fluorescent protein (EGFP)-HttQ23 or EGFP-HttQ52 fusion proteins (encoding 23 or 52 glutamine residues, pertaining to the normal and disease states, respectively), as well as an EGFP control. EGFP-HttQ52 protein aggregated in the cytoplasm of transformed tobacco cells, which showed slow growth kinetics; in contrast, EGFP-HttQ23 or EGFP did not form aggregates and cells expressing these constructs grew normally. To test the effect of LEA proteins on protein aggregation in plant cells, we constructed cell lines expressing both EGFP-HttQ52 and LEA proteins (PM1, PM18, ZLDE-2 or AavLEA1) or a sHSP (PM31). Of these, AavLEA1 and PM31 reduced intracellular EGFP-HttQ52 aggregation and alleviated the associated growth inhibition, while PM18 and ZLDE-2 partially restored growth rates. Treatment of EGFP-HttQ52-expressing BY2 cells with the polyphenol epigallocatechin-3-gallate (EGCG) also reduced EGFP-HttQ52 aggregation and improved cell growth rate. The EGFP-HttQ52 cell line therefore has potential for characterising both macromolecular and small molecule inhibitors of protein aggregation in plant cells. PMID:26003885

  2. Solar abundance of osmium

    PubMed Central

    Jacoby, George; Aller, Lawrence H.

    1976-01-01

    The abundance parameter, log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance (by numbers of atoms with respect to hydrogen), has been derived for three lines of osmium by a method of spectrum synthesis. An apparent discordance of the derived abundance with that found from the carbonaceous chondrites is probably to be attributed primarily to errors in the f-values, and blending with unknown contributors. PMID:16592314

  3. Perturbations of Amino Acid Metabolism Associated with Glyphosate-Dependent Inhibition of Shikimic Acid Metabolism Affect Cellular Redox Homeostasis and Alter the Abundance of Proteins Involved in Photosynthesis and Photorespiration1[W][OA

    PubMed Central

    Vivancos, Pedro Diaz; Driscoll, Simon P.; Bulman, Christopher A.; Ying, Liu; Emami, Kaveh; Treumann, Achim; Mauve, Caroline; Noctor, Graham; Foyer, Christine H.

    2011-01-01

    The herbicide glyphosate inhibits the shikimate pathway of the synthesis of amino acids such as phenylalanine, tyrosine, and tryptophan. However, much uncertainty remains concerning precisely how glyphosate kills plants or affects cellular redox homeostasis and related processes in glyphosate-sensitive and glyphosate-resistant crop plants. To address this issue, we performed an integrated study of photosynthesis, leaf proteomes, amino acid profiles, and redox profiles in the glyphosate-sensitive soybean (Glycine max) genotype PAN809 and glyphosate-resistant Roundup Ready Soybean (RRS). RRS leaves accumulated much more glyphosate than the sensitive line but showed relatively few changes in amino acid metabolism. Photosynthesis was unaffected by glyphosate in RRS leaves, but decreased abundance of photosynthesis/photorespiratory pathway proteins was observed together with oxidation of major redox pools. While treatment of a sensitive genotype with glyphosate rapidly inhibited photosynthesis and triggered the appearance of a nitrogen-rich amino acid profile, there was no evidence of oxidation of the redox pools. There was, however, an increase in starvation-associated and defense proteins. We conclude that glyphosate-dependent inhibition of soybean leaf metabolism leads to the induction of defense proteins without sustained oxidation. Conversely, the accumulation of high levels of glyphosate in RRS enhances cellular oxidation, possibly through mechanisms involving stimulation of the photorespiratory pathway. PMID:21757634

  4. Application of Natural Isotopic Abundance ¹H-¹³C- and ¹H-¹⁵N-Correlated Two-Dimensional NMR for Evaluation of the Structure of Protein Therapeutics.

    PubMed

    Arbogast, Luke W; Brinson, Robert G; Marino, John P

    2016-01-01

    Methods for characterizing the higher-order structure of protein therapeutics are in great demand for establishing consistency in drug manufacturing, for detecting drug product variations resulting from modifications in the manufacturing process, and for comparing a biosimilar to an innovator reference product. In principle, solution NMR can provide a robust approach for characterization of the conformation(s) of protein therapeutics in formulation at atomic resolution. However, molecular weight limitations and the perceived need for stable isotope labeling have to date limited its practical applications in the biopharmaceutical industry. Advances in NMR magnet and console technologies, cryogenically cooled probes, and new rapid acquisition methodologies, particularly selective optimized flip-angle short transient pulse schemes and nonuniform sampling, have greatly ameliorated these limitations. Here, we describe experimental methods for the collection and analysis of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra applied to protein drug products at natural isotopic abundance, including representatives from the rapidly growing class of monoclonal antibody (mAb) therapeutics. Practical aspects of experimental setup and data acquisition for both standard and rapid acquisition NMR techniques are described. Furthermore, strategies for the statistical comparison of 2D (1)H(N)-(15)N-amide- and (1)H-(13)C-methyl-correlated spectra are detailed. PMID:26791974

  5. Exploring the limit of metazoan thermal tolerance via comparative proteomics: thermally induced changes in protein abundance by two hydrothermal vent polychaetes

    PubMed Central

    Dilly, Geoffrey F.; Young, C. Robert; Lane, William S.; Pangilinan, Jasmyn; Girguis, Peter R.

    2012-01-01

    Temperatures around hydrothermal vents are highly variable, ranging from near freezing up to 300°C. Nevertheless, animals thrive around vents, some of which live near the known limits of animal thermotolerance. Paralvinella sulfincola, an extremely thermotolerant vent polychaete, and Paralvinella palmiformis, a cooler-adapted congener, are found along the Juan de Fuca Ridge in the northwestern Pacific. We conducted shipboard high-pressure thermotolerance experiments on both species to characterize the physiological adaptations underlying P. sulfincola's pronounced thermotolerance. Quantitative proteomics, expressed sequence tag (EST) libraries and glutathione assays revealed that P. sulfincola (i) exhibited an upregulation in the synthesis and recycling of glutathione with increasing temperature, (ii) downregulated nicotinamide adenine dinucleotide (NADH) and succinate dehydrogenases (key enzymes in oxidative phosphorylation) with increasing temperature, and (iii) maintained elevated levels of heat shock proteins (HSPs) across all treatments. In contrast, P. palmiformis exhibited more typical responses to increasing temperatures (e.g. increasing HSPs at higher temperatures). These data reveal differences in how a mesotolerant and extremely thermotolerant eukaryote respond to thermal stress, and suggest that P. sulfincola's capacity to mitigate oxidative stress via increased synthesis of antioxidants and decreased flux through the mitochondrial electron transport chain enable pronounced thermotolerance. Ultimately, oxidative stress may be the key factor in limiting all metazoan thermotolerance. PMID:22553092

  6. Enhanced Detection of Low-Abundance Host Cell Protein Impurities in High-Purity Monoclonal Antibodies Down to 1 ppm Using Ion Mobility Mass Spectrometry Coupled with Multidimensional Liquid Chromatography.

    PubMed

    Doneanu, Catalin E; Anderson, Malcolm; Williams, Brad J; Lauber, Matthew A; Chakraborty, Asish; Chen, Weibin

    2015-10-20

    The enormous dynamic range of proteinaceous species present in protein biotherapeutics poses a significant challenge for current mass spectrometry (MS)-based methods to detect low-abundance HCP impurities. Previously, an HCP assay based on two-dimensional chromatographic separation (high pH/low pH) coupled to high-resolution quadrupole time-of-flight (QTOF) mass spectrometry and developed in the author's laboratory has been shown to achieve a detection limit of about 50 ppm (parts per milion) for the identification and quantification of HCPs present in monoclonal antibodies following Protein A purification.1 To improve the HCP detection limit we have explored the utility of several new analytical techniques for HCP analysis and thereby developed an improved liquid chromatography-mass spectrometry (LC-MS) methodology for enhanced detection of HCPs. The new method includes (1) the use of a new charge-surface-modified (CSH) C18 stationary phase to mitigate the challenges of column saturation, peak tailing, and distortion that are commonly observed in the HCP analysis; (2) the incorporation of traveling-wave ion mobility (TWIM) separation of coeluting peptide precursors, and (3) the improvement of fragmentation efficiency of low-abundance HCP peptides by correlating the collision energy used for precursor fragmentation with their mobility drift time. As a result of these improvements, the detection limit of the new methodology was greatly improved, and HCPs present at a concentration as low as 1 ppm (1 ng HCP/mg mAb) were successfully identified and quantified. The newly developed method was applied to analyze two high-purity mAbs (NIST mAb and Infliximab) expressed in a murine cell line. For both samples, low-abundance HCPs (down to 1 ppm) were confidently identified, and the identities of the HCPs were further confirmed by targeted MS/MS experiments. In addition, the performance of the assay was evaluated by an interlaboratory study in which three independent

  7. Global transcriptome analysis of Human Bone Marrow Stromal Cells (BMSCs) reveals proliferative, mobile, and Interactive cells that produce abundant extracellular matrix proteins, some of which may affect BMSC Potency

    PubMed Central

    Ren, Jiaqiang; Jin, Ping; Sabatino, Marianna; Balakumaran, Arun; Feng, Ji; Kuznetsov, Sergei A.; Klein, Harvey G.; Robey, Pamela G.; Stroncek, David F.

    2012-01-01

    Background Bone marrow stromal cells (BMSCs) are being used for immune modulatory, anti-inflammatory and tissue engineering applications, but the properties responsible for these effects are not completely understood. Human BMSCs were characterized to identify factors that might be responsible for their clinical effects and biomarkers for assessing their quality. Methods Early passage BMSCs prepared from marrow aspirates of 4 healthy subjects were compared to 3 human embryonic stem cell (hESC) samples, CD34+ cells from 3 healthy subjects and 3 fibroblast cell lines. The cells were analyzed with oligonucleotide expression microarrays with more than 35,000 probes. Results BMSC gene expression signatures of BMSCs differed from those of hematopoietic stem cells (HSCs), hESCs and fibroblasts. Genes up-regulated in BMSCs were involved with cell movement, cell-to-cell signaling and interaction and proliferation. The up-regulated genes most likely belonged to pathways for integrin signaling, integrin linked kinase (ILK) signaling, NFR2-mediated oxidative stress response, regulation of actin-based motility by Rho, actin cytoskeletal signaling, caveolar-mediated endocytosis, clathrin-mediated endocytosis and Wnt/β catenin signaling. Among the most highly up-regulated genes were structural extracellular (ECM) proteins:α5 and β 5 integrin chains, fibronectin, collagen type IIIα1 and Vα1; and functional EMC proteins: connective tissue growth factor (CTGF), transforming growth factor beta induced protein (TGFBI) and ADAM12. Conclusions Global analysis of human BMSCs suggests that they are mobile, metabolically active, proliferative and interactive cells that make use of integrins and integrin signaling. They produce abundant ECM proteins that may contribute to their clinical immune modulatory and anti-inflammatory effects. PMID:21250865

  8. Salt deposits in Los Medanos area, Eddy and Lea counties, New Mexico

    USGS Publications Warehouse

    Jones, C.L.; with sections on Ground water hydrology, Cooley, Maurice E.; and Surficial Geology, Bachman, George Odell

    1973-01-01

    The salt deposits of Los Medanos area, in Eddy and Lea Counties, southeastern New Mexico, are being considered for possible use as a receptacle for radioactive wastes in a pilot-plant repository. The salt deposits of the area. are in three evaporite formations: the Castile, Salado, and Rustler Formations, in ascending order. The three formations are dominantly anhydrite and rock salt, but some gypsum, potassium ores, carbonate rock, and fine-grained clastic rocks are present. They have combined thicknesses of slightly more than 4,000 feet, of which roughly one-half belongs to the Salado. Both the Castile and the Rustler are-richer in anhydrite-and poorer in rock salt-than the Salado, and they provide this salt-rich formation with considerable Protection from any fluids which might be present in underlying or overlying rocks. The Salado Formation contains many thick seams of rock salt at moderate depths below the surface. The rock salt has a substantial cover of well-consolidated rocks, and it is very little deformed structurally. Certain geological details essential for Waste-storage purposes are unknown or poorly known, and additional study involving drilling is required to identify seams of rock salt suitable for storage purposes and to establish critical details of their chemistry, stratigraphy, and structure.

  9. OXYGEN ABUNDANCES IN CEPHEIDS

    SciTech Connect

    Luck, R. E.; Andrievsky, S. M.; Korotin, S. N.; Kovtyukh, V. V. E-mail: serkor@skyline.od.ua E-mail: scan@deneb1.odessa.ua

    2013-07-01

    Oxygen abundances in later-type stars, and intermediate-mass stars in particular, are usually determined from the [O I] line at 630.0 nm, and to a lesser extent, from the O I triplet at 615.7 nm. The near-IR triplets at 777.4 nm and 844.6 nm are strong in these stars and generally do not suffer from severe blending with other species. However, these latter two triplets suffer from strong non-local thermodynamic equilibrium (NLTE) effects and thus see limited use in abundance analyses. In this paper, we derive oxygen abundances in a large sample of Cepheids using the near-IR triplets from an NLTE analysis, and compare those abundances to values derived from a local thermodynamic equilibrium (LTE) analysis of the [O I] 630.0 nm line and the O I 615.7 nm triplet as well as LTE abundances for the 777.4 nm triplet. All of these lines suffer from line strength problems making them sensitive to either measurement complications (weak lines) or to line saturation difficulties (strong lines). Upon this realization, the LTE results for the [O I] lines and the O I 615.7 nm triplet are in adequate agreement with the abundance from the NLTE analysis of the near-IR triplets.

  10. Solar abundance of platinum

    PubMed Central

    Burger, Harry; Aller, Lawrence H.

    1975-01-01

    Three lines of neutral platinum, located at λ 2997.98 Å, λ 3064.71 Å, and λ 3301.86 Å have been used to determine the solar platinum abundance by the method of spectral synthesis. On the scale, log A(H) = 12.00, the thus-derived solar platinum abundance is 1.75 ± 0.10, in fair accord with Cameron's value of log A(Pt) = 1.69 derived by Mason from carbonaceous chondrites and calculated on the assumption that log A(Si) = 7.55 in the sun. PMID:16592278

  11. Stellar Oxygen Abundances

    NASA Astrophysics Data System (ADS)

    King, Jeremy

    1994-04-01

    This dissertation addresses several issues concerning stellar oxygen abundances. The 7774 {\\AA} O I triplet equivalent widths of Abia & Rebolo [1989, AJ, 347, 186] for metal-poor dwarfs are found to be systematically too high. I also argue that current effective temperatures used in halo star abundance studies may be ~150 K too low. New color-Teff relations are derived for metal-poor stars. Using the revised Teff values and improved equivalent widths for the 7774A O I triplet, the mean [O/Fe] ratio for a handful of halo stars is found to be +0.52 with no dependence on Teff or [Fe/H]. Possible cosmological implications of the hotter Teff scale are discussed along with additional evidence supporting the need for a higher temperature scale for metal-poor stars. Our Teff scale leads to a Spite Li plateau value of N(Li)=2.28 +/- 0.09. A conservative minimal primordial value of N(Li)=2.35 is inferred. If errors in the observations and models are considered, consistency with standard models of Big Bang nucleosynthesis is still achieved with this larger Li abundance. The revised Teff scale raises the observed B/Be ratio of HD 140283 from 10 to 12, making its value more comfortably consistent with the production of the observed B and Be by ordinary spallation. Our Teff values are found to be in good agreement with values predicted from both the Victoria and Yale isochrone color-Teff relations. Thus, it appears likely that no changes in globular cluster ages would result. Next, we examine the location of the break in the [O/Fe] versus [Fe/H] plane in a quantitative fashion. Analysis of a relatively homogeneous data set does not favor any unique break point in the range -1.7 /= -3), in agreement with the new results for halo dwarfs. We find that the gap in the observed [O/H] distribution, noted by Wheeler et al

  12. Abundances of light elements.

    PubMed Central

    Pagel, B E

    1993-01-01

    Recent developments in the study of abundances of light elements and their relevance to cosmological nucleosynthesis are briefly reviewed. The simplest model, based on standard cosmology and particle physics and assuming homogeneous baryon density at the relevant times, continues to stand up well. PMID:11607388

  13. The impaired intestinal mucosal immune system by valine deficiency for young grass carp (Ctenopharyngodon idella) is associated with decreasing immune status and regulating tight junction proteins transcript abundance in the intestine.

    PubMed

    Luo, Jian-Bo; Feng, Lin; Jiang, Wei-Dan; Liu, Yang; Wu, Pei; Jiang, Jun; Kuang, Sheng-Yao; Tang, Ling; Zhang, Yong-An; Zhou, Xiao-Qiu

    2014-09-01

    This study investigated the effects of dietary valine on the growth, intestinal immune response, tight junction proteins transcript abundance and gene expression of immune-related signaling molecules in the intestine of young grass carp (Ctenopharyngodon idella). Six iso-nitrogenous diets containing graded levels of valine (4.3-19.1 g kg(-)(1) diet) were fed to the fish for 8 weeks. The results showed that percentage weight gain (PWG), feed intake and feed efficiency of fish were the lowest in fish fed the valine-deficient diet (P < 0.05). In addition, valine deficiency decreased lysozyme, acid phosphatase activities and complement 3 content in the intestine (P < 0.05), down-regulated mRNA levels of interleukin 10, transforming growth factor β1, IκBα and target of rapamycin (TOR) (P < 0.05), and up-regulated tumor necrosis factor α, interleukin 8 and nuclear factor κB P65 (NF-κB P65) gene expression (P < 0.05). Additionally, valine deficiency significantly decreased transcript of Occludin, Claudin b, Claudin c, Claudin 3, and ZO-1 (P < 0.05), and improved Claudin 15 expression in the fish intestine (P < 0.05). However, valine did not have a significant effect on expression of Claudin 12 in the intestine of grass carp (P > 0.05). In conclusion, valine deficiency decreased fish growth and intestinal immune status, as well as regulated gene expression of tight junction proteins, NF-κB P65, IκBα and TOR in the fish intestine. Based on the quadratic regression analysis of lysozyme activity or PWG, the dietary valine requirement of young grass carp (268-679 g) were established to be 14.47 g kg(-1) diet (4.82 g 100 g(-1) CP) or 14.00 g kg(-1) diet (4.77 g 100 g(-1) CP), respectively. PMID:25014314

  14. Click chemistry: a new facile and efficient strategy for the preparation of Fe3O4 nanoparticles covalently functionalized with IDA-Cu and their application in the depletion of abundant protein in blood samples

    NASA Astrophysics Data System (ADS)

    Jian, Guiqin; Liu, Yuxing; He, Xiwen; Chen, Langxing; Zhang, Yukui

    2012-09-01

    In this study, we report a novel method to synthesize core-shell structured Fe3O4 nanoparticles (NPs) covalently functionalized with iminodiacetic acid (IDA) via click chemistry between the azide and alkyne groups and charged with Cu2+. Firstly, the Fe3O4@SiO2 NPs were obtained using tetraethoxysilane (TEOS) to form a silica shell on the surface of the Fe3O4 core. The azide group-modified Fe3O4@SiO2 NPs were obtained by a sol-gel process using 3-azidopropyltriethoxysilane (AzPTES) as the silane agent. Fe3O4@SiO2-N3 was directly reacted with N-propargyl iminodiacetic via click chemistry, in the presence of a Cu(I) catalyst, to acquire the IDA-modified Fe3O4 NPs. Finally, through the addition of Cu2+, the Fe3O4@SiO2-IDA-Cu NP product was obtained. The morphology, structure and composition of the NPs were characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The resulting NPs showed a strong magnetic response to an externally applied magnetic field, a high adsorption capacity and excellent specificity towards hemoglobin (Hb). In addition, the Fe3O4@SiO2-IDA-Cu NPs can be used for the selective removal of abundant Hb protein in bovine and human blood samples.

  15. Changing Transcriptional Initiation Sites and Alternative 5'- and 3'-Splice Site Selection of the First Intron Deploys the Arabidopsis Protein Isoaspartyl Methyltransferase2 Variants to Different Subcellular Compartments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Arabidopsis thaliana (L.) Heynh. possesses two PROTEIN-L-ISOASPARTATE METHYLTRANSFERASE (PIMT), genes encoding an enzyme (EC 2.1.1.77) capable of converting uncoded, L-isoaspartyl residues, arising spontaneously at L-asparaginyl and L-aspartyl sites in proteins, to L-aspartate. PIMT2 produces at lea...

  16. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma.

    PubMed

    Rafalko, Agnes; Dai, Shujia; Hancock, William S; Karger, Barry L; Hincapie, Marina

    2012-02-01

    Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an important tool for biomarker verification studies in highly complex biological samples. Analyte enrichment or sample fractionation is often necessary to reduce sample complexity and improve sensitivity of SRM for quantitation of clinically relevant biomarker candidates present at the low ng/mL range in blood. In this paper, we describe an alternative method for sample preparation for LC-SRM MS, which does not rely on availability of antibodies. This new platform is based on selective enrichment of proteotypic peptides from complex biological peptide mixtures via isoelectric focusing (IEF) on a digital ProteomeChip (dPC) for SRM quantitation using a triple quadrupole (QQQ) instrument with an LC-Chip (Chip/Chip/SRM). To demonstrate the value of this approach, the optimization of the Chip/Chip/SRM platform was performed using prostate specific antigen (PSA) added to female plasma as a model system. The combination of immunodepletion of albumin and IgG with peptide fractionation on the dPC, followed by SRM analysis, resulted in a limit of quantitation of PSA added to female plasma at the level of ∼1-2.5 ng/mL with a CV of ∼13%. The optimized platform was applied to measure levels of PSA in plasma of a small cohort of male patients with prostate cancer (PCa) and healthy matched controls with concentrations ranging from 1.5 to 25 ng/mL. A good correlation (r(2) = 0.9459) was observed between standard clinical ELISA tests and the SRM-based assay. Our data demonstrate that the combination of IEF on the dPC and SRM (Chip/Chip/SRM) can be successfully applied for verification of low abundance protein biomarkers in complex samples. PMID:22098410

  17. Development of a Chip/Chip/SRM platform using digital chip isoelectric focusing and LC-Chip mass spectrometry for enrichment and quantitation of low abundance protein biomarkers in human plasma

    PubMed Central

    Rafalko, Agnes; Dai, Shujia; Hancock, William S.; Karger, Barry L.; Hincapie, Marina

    2013-01-01

    Protein biomarkers are critical for diagnosis, prognosis, and treatment of disease. The transition from protein biomarker discovery to verification can be a rate limiting step in clinical development of new diagnostics. Liquid chromatography-selected reaction monitoring mass spectrometry (LC-SRM MS) is becoming an important tool for biomarker verification studies in highly complex biological samples. Analyte enrichment or sample fractionation is often necessary to reduce sample complexity and improve sensitivity of SRM for quantitation of clinically relevant biomarker candidates present at the low ng/mL range in blood. In this paper, we describe an alternative method for sample preparation for LC-SRM MS, which does not rely on availability of antibodies. This new platform is based on selective enrichment of proteotypic peptides from complex biological peptide mixtures via isoelectric focusing (IEF) on a digital ProteomeChip (dPC™) for SRM quantitation using a triple quadrupole (QQQ) instrument with an LC-Chip (Chip/Chip/SRM). To demonstrate the value of this approach, the optimization of the Chip/Chip/SRM platform was performed using prostate specific antigen (PSA) added to female plasma as a model system. The combination of immunodepletion of albumin and IgG with peptide fractionation on the dPC, followed by SRM analysis, resulted in a limit of quantitation of PSA added to female plasma at the level of ~1–2.5 ng/mL with a CV of ~13%. The optimized platform was applied to measure levels of PSA in plasma of a small cohort of male patients with prostate cancer (PCa) and healthy matched controls with concentrations ranging from 1.5 to 25 ng/mL. A good correlation (r2 = 0.9459) was observed between standard clinical ELISA tests and the SRM-based-assay. Our data demonstrate that the combination of IEF on the dPC and SRM (Chip/Chip/SRM) can be successfully applied for verification of low abundance protein biomarkers in complex samples. PMID:22098410

  18. Solar abundance of iridium

    PubMed Central

    Drake, Stephen; Aller, Lawrence H.

    1976-01-01

    By a method of spectrum synthesis, which yields log gfA, where g is the statistical weight of the lower level, f is the oscillator strength, and A is the abundance, an attempt is made to deduce the solar iridium abundance from one relatively unblended, but fairly weak IrI line, λ 3220.78 Å. If the Corliss-Bozman f-value for this line is adopted, we find log A(Ir) = 0.82 on the scale log A(H) = 12.00. The discordance with the value found from carbonaceous chondrites may arise from faulty f-values or from difficulties arising from line blending in this far ultraviolet domain of the solar spectrum. PMID:16578735

  19. Click chemistry: a new facile and efficient strategy for the preparation of Fe3O4 nanoparticles covalently functionalized with IDA-Cu and their application in the depletion of abundant protein in blood samples.

    PubMed

    Jian, Guiqin; Liu, Yuxing; He, Xiwen; Chen, Langxing; Zhang, Yukui

    2012-10-21

    In this study, we report a novel method to synthesize core-shell structured Fe(3)O(4) nanoparticles (NPs) covalently functionalized with iminodiacetic acid (IDA) via click chemistry between the azide and alkyne groups and charged with Cu(2+). Firstly, the Fe(3)O(4)@SiO(2) NPs were obtained using tetraethoxysilane (TEOS) to form a silica shell on the surface of the Fe(3)O(4) core. The azide group-modified Fe(3)O(4)@SiO(2) NPs were obtained by a sol-gel process using 3-azidopropyltriethoxysilane (AzPTES) as the silane agent. Fe(3)O(4)@SiO(2)-N(3) was directly reacted with N-propargyl iminodiacetic via click chemistry, in the presence of a Cu(I) catalyst, to acquire the IDA-modified Fe(3)O(4) NPs. Finally, through the addition of Cu(2+), the Fe(3)O(4)@SiO(2)-IDA-Cu NP product was obtained. The morphology, structure and composition of the NPs were characterized by transmission electron microscopy (TEM), X-ray powder diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron spectroscopy (XPS). The resulting NPs showed a strong magnetic response to an externally applied magnetic field, a high adsorption capacity and excellent specificity towards hemoglobin (Hb). In addition, the Fe(3)O(4)@SiO(2)-IDA-Cu NPs can be used for the selective removal of abundant Hb protein in bovine and human blood samples. PMID:22941423

  20. Distributing College Budgets: A Study of Local Education Authority (LEA) Planning and Formulae-Funding Mechanisms in England. AIR 1989 Annual Forum Paper.

    ERIC Educational Resources Information Center

    Birch, Derek W.; Spencer, Anne C.

    The Education Reform Act 1988 provides for the reform of the funding and governance of colleges of further education in England and Wales, comprising about 400 colleges (equivalent to community colleges and vocational schools) across 104 local education authorities (LEAs). The process and formula for budget-setting is described, and a number of…

  1. 34 CFR 222.178 - What eligibility requirements must an LEA meet to apply for an emergency grant under the second...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false What eligibility requirements must an LEA meet to apply for an emergency grant under the second priority? 222.178 Section 222.178 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT...

  2. 34 CFR 222.179 - Under what circumstances may an ineligible LEA apply on behalf of a school for an emergency grant...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Under what circumstances may an ineligible LEA apply on behalf of a school for an emergency grant under the second priority? 222.179 Section 222.179 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY...

  3. 34 CFR 222.182 - Under what circumstances may an ineligible LEA apply on behalf of a school for a modernization...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 34 Education 1 2010-07-01 2010-07-01 false Under what circumstances may an ineligible LEA apply on behalf of a school for a modernization grant under the fourth priority? 222.182 Section 222.182 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY...

  4. Dimeric Le(a) (Le(a)-on-Le(a)) status of beta-haptoglobin in sera of colon cancer, chronic inflammatory disease and normal subjects.

    PubMed

    Park, Seung-Yeol; Yoon, Seon-Joo; Hakomori, Sen-Itiroh; Kim, Jin-Man; Kim, Ji-Yeon; Bernert, Bradford; Ullman, Thomas; Itzkowitz, Steven H; Kim, Jung Hoe

    2010-05-01

    The glycosyl epitope dimeric Lea (Lea-on-Lea), defined by mouse monoclonal antibody NCC-ST-421, was identified previously as tumor-associated antigen, expressed highly in various human cancer tissues and cell lines derived therefrom, but with minimal expression in various normal tissues. In the present study, we observed clearly higher expression of this epitope, defined by ST421, in beta-haptoglobin (beta-Hap) from sera of patients with colorectal cancer, compared to normal, healthy subjects or patients with chronic inflammatory processes (Crohn's disease, ulcerative colitis). We focused, therefore, on biochemical characterization of glycosyl epitope status expressed in beta-Hap. We concluded that the dimeric Lea epitope is carried by O-linked but not by N-linked structure, based on the following observations: i) Treatment of beta-Hap with alpha-L-fucosidase reduced its reactivity with ST421, but did not affect its reactivity with anti-Hap antibody. In contrast, treatment of purified beta-Hap with PNGase F, which releases N-linked glycans, had no effect on reactivity with ST421, but changed molecular mass from 40 kDa to 30 kDa. ii) Strong reactivity of Colo205 supernatant with ST421 was reduced clearly by pre-incubation of cells with benzyl-alpha-GalNAc. PMID:20372805

  5. 34 CFR 222.180 - What eligibility requirements must an LEA meet to apply for a modernization grant under the third...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 1 2013-07-01 2013-07-01 false What eligibility requirements must an LEA meet to apply for a modernization grant under the third priority? 222.180 Section 222.180 Education Regulations of the Offices of the Department of Education OFFICE OF ELEMENTARY AND SECONDARY EDUCATION, DEPARTMENT OF EDUCATION IMPACT AID PROGRAMS Impact...

  6. 34 CFR 222.180 - What eligibility requirements must an LEA meet to apply for a modernization grant under the third...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... for a modernization grant under the third priority? 222.180 Section 222.180 Education Regulations of... the Act Eligibility § 222.180 What eligibility requirements must an LEA meet to apply for a... (c) Has facility needs resulting from the presence of the Federal Government, such as the...

  7. 34 CFR 200.74 - Use of an alternative method to distribute grants to LEAs with fewer than 20,000 total residents.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 1 2011-07-01 2011-07-01 false Use of an alternative method to distribute grants to... Local Educational Agencies Allocations to Leas § 200.74 Use of an alternative method to distribute... to the Secretary to use an alternative method to distribute basic grant, concentration...

  8. Ablation of the Stimulatory G Protein α-Subunit in Renal Proximal Tubules Leads to Parathyroid Hormone-Resistance With Increased Renal Cyp24a1 mRNA Abundance and Reduced Serum 1,25-Dihydroxyvitamin D.

    PubMed

    Zhu, Yan; He, Qing; Aydin, Cumhur; Rubera, Isabelle; Tauc, Michel; Chen, Min; Weinstein, Lee S; Marshansky, Vladimir; Jüppner, Harald; Bastepe, Murat

    2016-02-01

    PTH regulates serum calcium, phosphate, and 1,25-dihydroxyvitamin D (1,25(OH)2D) levels by acting on bone and kidney. In renal proximal tubules (PTs), PTH inhibits reabsorption of phosphate and stimulates the synthesis of 1,25(OH)2D. The PTH receptor couples to multiple G proteins. We here ablated the α-subunit of the stimulatory G protein (Gsα) in mouse PTs by using Cre recombinase driven by the promoter of type-2 sodium-glucose cotransporter (Gsα(Sglt2KO) mice). Gsα(Sglt2KO) mice were normophosphatemic but displayed, relative to controls, hypocalcemia (1.19 ±0.01 vs 1.23 ±0.01 mmol/L; P < .05), reduced serum 1,25(OH)2D (59.3 ±7.0 vs 102.5 ±12.2 pmol/L; P < .05), and elevated serum PTH (834 ±133 vs 438 ±59 pg/mL; P < .05). PTH-induced elevation in urinary cAMP excretion was blunted in Gsα(Sglt2KO) mice (2- vs 4-fold over baseline in controls; P < .05). Relative to baseline in controls, PTH-induced reduction in serum phosphate tended to be blunted in Gsα(Sglt2KO) mice (-0.39 ±0.33 vs -1.34 ±0.36 mg/dL; P = .07). Gsα(Sglt2KO) mice showed elevated renal vitamin D 24-hydroxylase and bone fibroblast growth factor-23 (FGF23) mRNA abundance (∼3.4- and ∼11-fold over controls, respectively; P < .05) and tended to have elevated serum FGF23 (829 ±76 vs 632 ±60 pg/mL in controls; P = .07). Heterozygous mice having constitutive ablation of the maternal Gsα allele (E1(m-/+)) (model of pseudohypoparathyroidism type-Ia), in which Gsα levels in PT are reduced, also exhibited elevated serum FGF23 (474 ±20 vs 374 ±27 pg/mL in controls; P < .05). Our findings indicate that Gsα is required in PTs for suppressing renal vitamin D 24-hydroxylase mRNA levels and for maintaining normal serum 1,25(OH)2D. PMID:26671181

  9. Abundance of field galaxies

    NASA Astrophysics Data System (ADS)

    Klypin, Anatoly; Karachentsev, Igor; Makarov, Dmitry; Nasonova, Olga

    2015-12-01

    We present new measurements of the abundance of galaxies with a given circular velocity in the Local Volume: a region centred on the Milky Way Galaxy and extending to distance ˜10 Mpc. The sample of ˜750 mostly dwarf galaxies provides a unique opportunity to study the abundance and properties of galaxies down to absolute magnitudes MB ≈ -10 and virial masses M_vir= 109{ M_{⊙}}. We find that the standard Λ cold dark matter (ΛCDM) model gives remarkably accurate estimates for the velocity function of galaxies with circular velocities V ≳ 70 kms-1 and corresponding virial masses M_vir≳ 5× 10^{10}{ M_{⊙}}, but it badly fails by overpredicting ˜5 times the abundance of large dwarfs with velocities V = 30-40 kms-1. The warm dark matter (WDM) models cannot explain the data either, regardless of mass of WDM particle. Just as in previous observational studies, we find a shallow asymptotic slope dN/dlog V ∝ Vα, α ≈ -1 of the velocity function, which is inconsistent with the standard ΛCDM model that predicts the slope α = -3. Though reminiscent to the known overabundance of satellite problem, the overabundance of field galaxies is a much more difficult problem. For the standard ΛCDM model to survive, in the 10 Mpc radius of the Milky Way there should be 1000 not yet detected galaxies with virial mass M_vir≈ 10^{10}{ M_{⊙}}, extremely low surface brightness and no detectable H I gas. So far none of this type of galaxies have been discovered.

  10. Flare Plasma Iron Abundance

    NASA Technical Reports Server (NTRS)

    Dennis, Brian R.; Dan, Chau; Jain, Rajmal; Schwartz, Richard A.; Tolbert, Anne K.

    2008-01-01

    The equivalent width of the iron-line complex at 6.7 keV seen in flare X-ray spectra suggests that the iron abundance of the hottest plasma at temperatures >approx.10 MK may sometimes be significantly lower than the nominal coronal abundance of four times the photospheric value that is commonly assumed. This conclusion is based on X-ray spectral observations of several flares seen in common with the Ramaty High Energy Solar Spectroscopic Imager (RHESSI) and the Solar X-ray Spectrometer (SOXS) on the second Indian geostationary satellite, GSAT-2. The implications of this will be discussed as it relates to the origin of the hot flare plasma - either plasma already in the corona that is directly heated during the flare energy release process or chromospheric plasma that is heated by flare-accelerated particles and driven up into the corona. Other possible explanations of lower-than-expected equivalent widths of the iron-line complex will also be discussed.

  11. A new rice zinc-finger protein binds to the O2S box of the alpha-amylase gene promoter.

    PubMed

    Peng, Rihe; Yao, Quanhong; Xiong, Aisheng; Fan, Huiqin; Li, Xian; Peng, Youliang; Cheng, Zong-Ming; Li, Yi

    2004-07-01

    A putative transcription factor, named RAMY, that binds to the 20-bp O2S sequences of the regulatory region of the Amy2 gene promoter has been identified using the yeast one-hybrid system from a rice library. The full length RAMY cDNA clone encodes a 218-amino acid protein and is homologous to the late embryogenesis-abundant protein (LEA5). In vitro mutagenesis and electrophoretic mobility shift assays confirmed that RAMY can bind with O2S specifically through an unusual zinc finger with a CXCX(4)CX(2)H consensus sequence. Low levels of RAMY mRNAs were detected in rice leaves and roots by Northern blot hybridization. The plant hormone gibberellin (GA) induces expression of both RAMY and Amy2 genes, as performed by Northern blot hybridization, but the increase in RAMY mRNA level occurs prior to that of the Amy2 mRNA level in the GA-treated aleurone tissues. These data suggest that RAMY may act as a trans-acting protein and is probably involved in the GA-induced expression of the rice alpha-amylase gene. PMID:15233790

  12. Variability within a pea core collection of LEAM and HSP22, two mitochondrial seed proteins involved in stress tolerance.

    PubMed

    Avelange-Macherel, Marie-Hélène; Payet, Nicole; Lalanne, David; Neveu, Martine; Tolleter, Dimitri; Burstin, Judith; Macherel, David

    2015-07-01

    LEAM, a late embryogenesis abundant protein, and HSP22, a small heat shock protein, were shown to accumulate in the mitochondria during pea (Pisum sativum L.) seed development, where they are expected to contribute to desiccation tolerance. Here, their expression was examined in seeds of 89 pea genotypes by Western blot analysis. All genotypes expressed LEAM and HSP22 in similar amounts. In contrast with HSP22, LEAM displayed different isoforms according to apparent molecular mass. Each of the 89 genotypes harboured a single LEAM isoform. Genomic and RT-PCR analysis revealed four LEAM genes differing by a small variable indel in the coding region. These variations were consistent with the apparent molecular mass of each isoform. Indels, which occurred in repeated domains, did not alter the main properties of LEAM. Structural modelling indicated that the class A α-helix structure, which allows interactions with the mitochondrial inner membrane in the dry state, was preserved in all isoforms, suggesting functionality is maintained. The overall results point out the essential character of LEAM and HSP22 in pea seeds. LEAM variability is discussed in terms of pea breeding history as well as LEA gene evolution mechanisms. PMID:25367071

  13. EVALUATION OF THE FLOOD POTENTIAL OF THE SOUTH HOUSE (BLINEBRY) FIELD, LEA COUNTY, NEW MEXICO

    SciTech Connect

    L. Stephen Melzer

    2000-12-01

    The Blinebry (Permian) formation of eastern Lea County, NM has a long history of exploitation for petroleum and continues even today to be a strong target horizon for new drilling in the Permian Basin. Because of this long-standing interest it should be classified of strategic interest to domestic oil production; however, the formation has gained a reputation as a primary production target with limited to no flooding potential. In late May of 1999, a project to examine the feasibility of waterflooding the Blinebry formation was proposed to the U.S. Department of Energy's National Petroleum Technology Office (Tulsa, OK). A new well was proposed in one region (the South House area) to examine the reputation by acquiring core and borehole logging data for the collection of formation property data in order to conduct the waterflood evaluation. Notice of the DOE award was received on August 19, 1999 and the preparations for drilling, coring and logging were immediately made for a drilling start on 9/9/99. The Blinebry formation at 6000 feet, foot depth was reached on 9/16/99 and the coring of two 60 foot intervals of the Blinebry was completed on 9/19/99 with more than 98% core recovery. The well was drilled to a total depth of 7800 feet and the Blinebry interval was logged with spectral gamma ray, photoelectric cross section, porosity, resistivity, and borehole image logs on 8/24/99. The well was determined to be likely productive from the Blinebry interval and five & 1/2 inch casing was cemented in the hole on 9/25/99. Detailed core descriptions including environment of deposition have been accomplished. Whole core (a 4-inch diameter) and plug (1.5 inch diameter) testing for formation properties has been completed and are reported. Acquisition and analysis of the borehole logging results have been completed and are reported. Perforation of the Blinebry intervals was accomplished on November 8, 1999. The intervals were acidized and hydrofraced on 11/9 and 11

  14. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  15. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  16. Oxygen abundance and convection

    NASA Astrophysics Data System (ADS)

    Van't Veer, C.; Cayrel, R.

    The triplet IR lines of O I near 777 nm are computed with the Kurucz's code, modified to accept several convection models. The program has been run with the MLT algorithm, with l/H = 1.25 and 0.5, and with the Canuto-Mazzitelli and Canuto-Goldman-Mazzitelli approaches, on a metal-poor turnoff-star model atmosphere with Teff=6200 K, log g = 4.3, [Fe/H]= -1.5. The results show that the differences in equivalent widths for the 4 cases do not exceed 2 per cent (0.3 mA). The convection treatment is therefore not an issue for the oxygen abundance derived from the permitted lines.

  17. Actinide abundances in ordinary chondrites

    NASA Technical Reports Server (NTRS)

    Hagee, B.; Bernatowicz, T. J.; Podosek, F. A.; Johnson, M. L.; Burnett, D. S.

    1990-01-01

    Measurements of actinide and light REE (LREE) abundances and of phosphate abundances in equilibrated ordinary chondrites were obtained and were used to define the Pu abundance in the solar system and to determine the degree of variation of actinide and LREE abundances. The results were also used to compare directly the Pu/U ratio with the earlier obtained ratio determined indirectly, as (Pu/Nd)x(Nd/U), assuming that Pu behaves chemically as a LREE. The data, combined with high-accuracy isotope-dilution data from the literature, show that the degree of gram-scale variability of the Th, U, and LREE abundances for equilibrated ordinary chondrites is a factor of 2-3 for absolute abundances and up to 50 percent for relative abundances. The observed variations are interpreted as reflecting the differences in the compositions and/or proportions of solar nebula components accreted to ordinary chondrite parent bodies.

  18. Protein inference: A protein quantification perspective.

    PubMed

    He, Zengyou; Huang, Ting; Liu, Xiaoqing; Zhu, Peijun; Teng, Ben; Deng, Shengchun

    2016-08-01

    In mass spectrometry-based shotgun proteomics, protein quantification and protein identification are two major computational problems. To quantify the protein abundance, a list of proteins must be firstly inferred from the raw data. Then the relative or absolute protein abundance is estimated with quantification methods, such as spectral counting. Until now, most researchers have been dealing with these two processes separately. In fact, the protein inference problem can be regarded as a special protein quantification problem in the sense that truly present proteins are those proteins whose abundance values are not zero. Some recent published papers have conceptually discussed this possibility. However, there is still a lack of rigorous experimental studies to test this hypothesis. In this paper, we investigate the feasibility of using protein quantification methods to solve the protein inference problem. Protein inference methods aim to determine whether each candidate protein is present in the sample or not. Protein quantification methods estimate the abundance value of each inferred protein. Naturally, the abundance value of an absent protein should be zero. Thus, we argue that the protein inference problem can be viewed as a special protein quantification problem in which one protein is considered to be present if its abundance is not zero. Based on this idea, our paper tries to use three simple protein quantification methods to solve the protein inference problem effectively. The experimental results on six data sets show that these three methods are competitive with previous protein inference algorithms. This demonstrates that it is plausible to model the protein inference problem as a special protein quantification task, which opens the door of devising more effective protein inference algorithms from a quantification perspective. The source codes of our methods are available at: http://code.google.com/p/protein-inference/. PMID:26935399

  19. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of EUVE spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous Advanced Satellite for Cosmology and Astrophysics (ASCA) data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated. With these new models applied to the ASCA spectrum, better fits were obtained. Findings are that: (1) ASCA and EUVE spectra are both dominated by a region at 6 x 10(exp 6) K. (2) The high energy cut-off of the ASCA spectrum is consistent with emission from the highest ionization stages of EUVE, namely Fe XXIV. (3) EUVE requires a continuous emission measure distribution with more than two temperatures. (4) The ASCA spectra are of such high statistical significance that systematic uncertainties dominate, including atomic physics issues and calibration issues. (5) While the ASCA spectral fits achieve lower Chi(exp 2 with two-temperature fits, the EUVE-derived emission measure distribution models are also consistent with the spectra. (6) The Fe/H ratio obtained from the ASCA fit is within 20 % of the Fe/H abundance obtained from the summed spectra of Capella over 5 EUVE pointings, as well as the 1996 EUVE data. This result confirms our claims that quasi-continua composed of weak emission lines in the short wavelength spectrometer of EUVE are not major contributors to the measured Capella continuum. Other abundance ratios are also determined from the ASCA data, using models derived with EUVE. Si, Si, and Mg appear to be close to solar photospheric values, while the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined

  20. Morphological features of different polyploids for adaptation and molecular characterization of CC-NBS-LRR and LEA gene families in Agave L.

    PubMed

    Tamayo-Ordóñez, M C; Rodriguez-Zapata, L C; Narváez-Zapata, J A; Tamayo-Ordóñez, Y J; Ayil-Gutiérrez, B A; Barredo-Pool, F; Sánchez-Teyer, L F

    2016-05-20

    Polyploidy has been widely described in many Agave L. species, but its influence on environmental response to stress is still unknown. With the objective of knowing the morphological adaptations and regulation responses of genes related to biotic (LEA) and abiotic (NBS-LRR) stress in species of Agave with different levels of ploidy, and how these factors contribute to major response of Agave against environmental stresses, we analyzed 16 morphological trials on five accessions of three species (Agave tequilana Weber, Agave angustifolia Haw. and Agave fourcroydes Lem.) with different ploidy levels (2n=2x=60 2n=3x=90, 2n=5x=150, 2n=6x=180) and evaluated the expression of NBS-LRR and LEA genes regulated by biotic and abiotic stress. It was possible to associate some morphological traits (spines, nuclei, and stomata) to ploidy level. The genetic characterization of stress-related genes NBS-LRR induced by pathogenic infection and LEA by heat or saline stresses indicated that amino acid sequence analysis in these genes showed more substitutions in higher ploidy level accessions of A. fourcroydes Lem. 'Sac Ki' (2n=5x=150) and A. angustifolia Haw. 'Chelem Ki' (2n=6x=180), and a higher LEA and NBS-LRR representativeness when compared to their diploid and triploid counterparts. In all studied Agave accessions expression of LEA and NBS-LRR genes was induced by saline or heat stresses or by infection with Erwinia carotovora, respectively. The transcriptional activation was also higher in A. angustifolia Haw. 'Chelem Ki' (2n=6x=180) and A. fourcroydes 'Sac Ki' (2n=5x=150) than in their diploid and triploid counterparts, which suggests higher adaptation to stress. Finally, the diploid accession A. tequilana Weber 'Azul' showed a differentiated genetic profile relative to other Agave accessions. The differences include similar or higher genetic representativeness and transcript accumulation of LEA and NBS-LRR genes than in polyploid (2n=5x=150 and 2n=6x=180) Agave accessions

  1. Ground-water investigations of the Project Gnome area, Eddy and Lea Counties, New Mexico

    USGS Publications Warehouse

    Cooper, J.B.

    1962-01-01

    The U.S. Atomic Energy Commission, through the Office of Test Operations, Albuquerque Operations Office, plans to detonate a nuclear device in a massive salt bed 1,200 feet beneath the land surface. The project, known as Project Gnome, is an element of the Plowshare program--a study of peacetime applications of nuclear fission. The location of the proposed underground shot is in a sparsely-populated area in southeastern Eddy County, N. Mex., east of the Pecos River and about 25 miles southeast of the city of Carlsbad. The area is arid to Semiarid and ground water is a vital factor in the economic utilization of the land, which is primarily used for stock raising. An investigation of the Project Gnome site and surrounding area for the purposes of evaluating the ground-water resources and the possible effect upon them from the detonation of the nuclear shot was desired by the Commission. This report describes work done by the U.S. Geological Survey on behalf of the Commission and presents results of the investigation of the ground-water resources and geology of the area. The most intensive investigations were made within a 15-mile radius of the site of Project Gnome and mainly on the east side of the Pecos River. The total area of study of over 1,200 square miles includes parts of Eddy and Lea Counties, N. Mex. The Project Gnome site is in the sedimentary Delaware Basin. It is underlain by about 18,000 feet of sedimentary rocks ranging in age from Ordovician to Recent. Upper Permian evaporitic rocks, which contain the principal source of potash available in the United States, are worked in nearby mines. The potash minerals are found in a massive salt bed about 1,400 feet thick in the Salado Formation of Permian age. The land surface of the area is covered mostly by a wind-blown sand and caliche; however, rocks of the Rustler Formation of Permian age and younger rocks of Permian, Triassic, Pleistocene(?) and Recent age crop out at several localities. Solution by

  2. Capella: Structure and Abundances

    NASA Technical Reports Server (NTRS)

    Brickhouse, Nancy S.

    1999-01-01

    This grant covers the analysis of ASCA spectra of the cool star binary system Capella. This project has also required the analysis of simultaneous EUVE data. The ASCA spectrum of Capella could not be fit with standard models; by imposing models based on strong lines observed with EUVE, a problem wavelength region was identified. Correcting the problem required calculations of atomic collision strengths of higher principal quantum number than had ever been calculated, resulting in a paper in process by Liedahl and Brickhouse. With these new models applied to the ASCA spectrum, better fits were obtained. While solar abundance ratios are generally consistent with the ASCA data, the ratio of Ne/Fe is three to four times lower than solar photospheric values. Whether there is a general First Ionization Potential (FIP) effect or a specific neon anomaly cannot be determined from these data. Detailed discussion has been provided to NASA in the most recent annual report (1997). Two poster presentations have been made regarding modeling requirements. A substantial paper is in the final revision form, following review by six co-authors. The results of this work have wide implications, since the newly calculated emission lines almost certainly contribute to other problems in fitting not only other stellar spectra, but also composite supernova remnants, galaxies, and cooling flow clusters of galaxies. Furthermore, Liedahl and Brickhouse have identified other species for which lines of a similar nature (high principal quantum number) will contribute significant flux. For moderate resolution X-ray spectra, lines left out of the models in relatively isolated bands, will be attributed to continuum flux by spectral fitting engines, causing errors in line-to-continuum ratios. Thus addressing the general theoretical problem is of crucial importance.

  3. Abundances in dwarf irregular galaxies

    NASA Technical Reports Server (NTRS)

    Dufour, Reginald J.

    1986-01-01

    The results of abundance studies of dwarf irregular galaxies and similar objects are reviewed with special attention to variations in the CNO element group. Observations of the forbidden N II and semiforbidden C III lines in the most metal-poor galaxy known, IZw 18, are presented for the first time and CNO abundances are derived via a photoionization model and discussed in the context of the abundances found in other metal-poor H II regions and galaxies.

  4. Abundance coefficients, a new method for measuring microorganism relative abundance

    USGS Publications Warehouse

    Forester, R.M.

    1977-01-01

    A new method of measuring the relative abundance of microorganisms by using a set of interrelated coefficients, termed 'abundance coefficients' or 'AC', is proposed. These coefficients provide a means of recording abundance for geometric density categories, and each density measurement represents an approximation of the Poisson parameter ??t. The AC is the natural logarithm of a 'characteristic value,' which is a particular number for each geometric density category. The 'characteristic values' are based upon a probabilistic error statement derived from the Poisson formula, and they present evidence for separation of the geometric category boundaries by e = 2.71828. The proposed AC provide a means for recording species abundance in a manner suitable for arithmetic manipulation, for population structure studies, and for the determination of practical limits for defining the presence or absence of a species. Further, these coefficients provide for both intrasample and intersample abundance comparisons. ?? 1977 Plenum Publishing Corporation.

  5. Descriptions and key to the larvae of the Tasmanian endemic genus Hoplogonus Parry (Coleoptera: Lucanidae), and comparison with the sympatric Lissotes rudis Lea.

    PubMed

    Richards, Karen; Spencer, Chris P

    2014-01-01

    The stag beetle (Coleoptera: Lucaindae) genus Hoplogonus Parry is endemic to northeastern Tasmania and contains three recognised species. Descriptions of the imagines have been published previously, but not the larvae. Descriptions of the larvae of the three Hoplogonus species and the sympatric Lissotes rudis Lea (also Lucanidae) are presented and discussed, and a key to aid identification of Hoplogonus larvae is included. The classification of Hoplogonus within the tribe Platycerini is proposed, alongside Lissotes. PMID:25543792

  6. Erratum: Interstellar Abundance Standards Revisited

    NASA Astrophysics Data System (ADS)

    Sofia, U. J.; Meyer, D. M.

    2001-09-01

    In the Letter ``Interstellar Abundance Standards Revisited'' by U. J. Sofia and D. M. Meyer (ApJ, 554, L221 [2001]), Table 2 and its footnotes contain several typographical errors. The corrected table is shown below. We note that the solar reference standard now implies a positive abundance of nitrogen in halo dust.

  7. Protein Analysis

    NASA Astrophysics Data System (ADS)

    Chang, Sam K. C.

    Proteins are an abundant component in all cells, and almost all except storage proteins are important for biological functions and cell structure. Food proteins are very complex. Many have been purified and characterized. Proteins vary in molecular mass, ranging from approximately 5000 to more than a million Daltons. They are composed of elements including hydrogen, carbon, nitrogen, oxygen, and sulfur. Twenty α-amino acids are the building blocks of proteins; the amino acid residues in a protein are linked by peptide bonds. Nitrogen is the most distinguishing element present in proteins. However, nitrogen content in various food proteins ranges from 13.4 to 19.1% (1) due to the variation in the specific amino acid composition of proteins. Generally, proteins rich in basic amino acids contain more nitrogen.

  8. The boron abundance of Procyon

    NASA Technical Reports Server (NTRS)

    Lemke, Michael; Lambert, David L.; Edvardsson, Bengt

    1993-01-01

    The B I 2496.8 A resonance line and HST/GHRS echelle spectra are used with model atmospheres and synthetic spectra to derive the B abundance of the F dwarfs Procyon (Alpha Canis Minoris), Theta Ursae Majoris, and Iota Pegasi. The B abundance of Theta UMa and Iota Peg is similar to that derived by Boesgaard and Heacox (1978) from the B II resonance line in spectra of A- and B-type stars. These two dwarfs show normal abundances of Li, Be, and B. Procyon, which is highly depleted in Li and Be, is depleted in B by a factor of at least 3. Comparison of the spectra of Procyon and the halo dwarf HD 140283 shows that the B abundance assigned by Duncan et al. (1992) to three halo dwarfs is not greatly overestimated as a result of contamination of the B I line by an unidentified line.

  9. Current (2004-07) Conditions and Changes in Ground-Water Levels from Predevelopment to 2007, Southern High Plains Aquifer, Southeast New Mexico-Lea County Underground Water Basin

    USGS Publications Warehouse

    Tillery, Anne

    2008-01-01

    The Southern High Plains aquifer is the principal aquifer and primary source of water in southeastern New Mexico. The Lea County portion of the aquifer covers approximately the northern two thirds of the 4,393-square-mile county. Successful water-supply planning for New Mexico's Southern High Plains requires knowledge of the current aquifer conditions and a context from which to estimate future trends given current aquifer-management policy. Maps representing water-level declines, current (2007) water levels, aquifer saturated thickness, and depth to water accompanied by hydrographs from representative wells for the Southern High Plains aquifer in the Lea County Underground Water Basin were prepared in cooperation with the New Mexico Office of the State Engineer. Results of this mapping effort show the water level has declined as much as 97 feet in the Lea County Underground Water Basin from predevelopment (1914-54) to 2007 with rates as high as 0.88 feet per year.

  10. Solar and stellar photospheric abundances

    NASA Astrophysics Data System (ADS)

    Allende Prieto, Carlos

    2016-07-01

    The determination of photospheric abundances in late-type stars from spectroscopic observations is a well-established field, built on solid theoretical foundations. Improving those foundations to refine the accuracy of the inferred abundances has proven challenging, but progress has been made. In parallel, developments on instrumentation, chiefly regarding multi-object spectroscopy, have been spectacular, and a number of projects are collecting large numbers of observations for stars across the Milky Way and nearby galaxies, promising important advances in our understanding of galaxy formation and evolution. After providing a brief description of the basic physics and input data involved in the analysis of stellar spectra, a review is made of the analysis steps, and the available tools to cope with large observational efforts. The paper closes with a quick overview of relevant ongoing and planned spectroscopic surveys, and highlights of recent research on photospheric abundances.

  11. Robust Abundance Estimation in Animal Abundance Surveys with Imperfect Detection

    EPA Science Inventory

    Surveys of animal abundance are central to the conservation and management of living natural resources. However, detection uncertainty complicates the sampling process of many species. One sampling method employed to deal with this problem is depletion (or removal) surveys in whi...

  12. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1995-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on the Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred during the period of 15 April 1994 to 15 April 1995.

  13. The solar abundance of beryllium

    NASA Technical Reports Server (NTRS)

    Ross, J. E.; Aller, L. H.

    1974-01-01

    The solar abundance of beryllium is deduced from high-resolution Kitt Peak observations of the 3130.43- and 3131.08-A lines of Be II interpreted by the method of spectrum synthesis. The results are in good agreement with those previously obtained by Grevesse (1968) and by Hauge and Engvold (1968) and indicate that in the photospheric layers, beryllium is depleted below the chondritic value by a factor of about two. It is found that the beryllium abundance is equal to logN(Be)/N(H) + 12 = 1.08 plus or minus 0.05.

  14. Chemical Abundances of Symbiotic Giants

    NASA Astrophysics Data System (ADS)

    Gałan, C.; Mikołajewska, J.; Hinkle, K. H.; Joyce, R. R.

    2015-12-01

    High resolution (R ˜ 50000), near-IR spectra were used to measure photospheric abundances of CNO and elements around the iron peak for 24 symbiotic giants. Spectrum synthesis was employed using local thermal equilibrium and hydrostatic model atmospheres. The metallicities are distributed in a wide range with maximum around [Fe/H] ˜-0.4 - - 0.3 dex. Enrichment in 14N indicates that all the sample giants have experienced the first dredge-up. The relative abundance of [Ti/Fe] is generally large in red symbiotic systems.

  15. Coronal Abundances and Their Variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1996-01-01

    This contract supported the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution soft X-ray spectra from the Flat Crystal Spectrometer on NASA's Solar Maximum Mission. The goals of the study were a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This is the Final Report, summarizing the data analysis and reporting activities which occurred during the period of performance, June 1993 - December 1996.

  16. SOLAR MODELS WITH REVISED ABUNDANCE

    SciTech Connect

    Bi, S. L.; Li, T. D.; Yang, W. M.; Li, L. H.

    2011-04-20

    We present new solar models in which we use the latest low abundances and further include the effects of rotation, magnetic fields, and extra-mixing processes. We assume that the extra-element mixing can be treated as a diffusion process, with the diffusion coefficient depending mainly on the solar internal configuration of rotation and magnetic fields. We find that such models can well reproduce the observed solar rotation profile in the radiative region. Furthermore, the proposed models can match the seismic constraints better than the standard solar models, also when these include the latest abundances, but neglect the effects of rotation and magnetic fields.

  17. THE SOLAR FLARE IRON ABUNDANCE

    SciTech Connect

    Phillips, K. J. H.; Dennis, B. R. E-mail: Brian.R.Dennis@nasa.gov

    2012-03-20

    The abundance of iron is measured from emission line complexes at 6.65 keV (Fe line) and 8 keV (Fe/Ni line) in RHESSI X-ray spectra during solar flares. Spectra during long-duration flares with steady declines were selected, with an isothermal assumption and improved data analysis methods over previous work. Two spectral fitting models give comparable results, viz., an iron abundance that is lower than previous coronal values but higher than photospheric values. In the preferred method, the estimated Fe abundance is A(Fe) = 7.91 {+-} 0.10 (on a logarithmic scale, with A(H) = 12) or 2.6 {+-} 0.6 times the photospheric Fe abundance. Our estimate is based on a detailed analysis of 1898 spectra taken during 20 flares. No variation from flare to flare is indicated. This argues for a fractionation mechanism similar to quiet-Sun plasma. The new value of A(Fe) has important implications for radiation loss curves, which are estimated.

  18. Actinide abundances in ordinary chondrites

    USGS Publications Warehouse

    Hagee, B.; Bernatowicz, T.J.; Podosek, F.A.; Johnson, M.L.; Burnett, D.S.; Tatsumoto, M.

    1990-01-01

    Measurements of 244Pu fission Xe, U, Th, and light REE (LREE) abundances, along with modal petrographic determinations of phosphate abundances, were carried out on equilibrated ordinary chondrites in order to define better the solar system Pu abundance and to determine the degree of variation of actinide and LREE abundances. Our data permit comparison of the directly measured Pu/ U ratio with that determined indirectly as (Pu/Nd) ?? (Nd/U) assuming that Pu behaves chemically as a LREE. Except for Guaren??a, and perhaps H chondrites in general, Pu concentrations are similar to that determined previously for St. Se??verin, although less precise because of higher trapped Xe contents. Trapped 130Xe 136Xe ratios appear to vary from meteorite to meteorite, but, relative to AVCC, all are similar in the sense of having less of the interstellar heavy Xe found in carbonaceous chondrite acid residues. The Pu/U and Pu/Nd ratios are consistent with previous data for St. Se??verin, but both tend to be slightly higher than those inferred from previous data on Angra dos Reis. Although significant variations exist, the distribution of our Th/U ratios, along with other precise isotope dilution data for ordinary chondrites, is rather symmetric about the CI chondrite value; however, actinide/(LREE) ratios are systematically lower than the CI value. Variations in actinide or LREE absolute and relative abundances are interpreted as reflecting differences in the proportions and/or compositions of more primitive components (chondrules and CAI materials?) incorporated into different regions of the ordinary chondrite parent bodies. The observed variations of Th/U, Nd/U, or Ce/U suggest that measurements of Pu/U on any single equilibrated ordinary chondrite specimen, such as St. Se??verin, should statistically be within ??20-30% of the average solar system value, although it is also clear that anomalous samples exist. ?? 1990.

  19. Coronal abundances and their variation

    NASA Technical Reports Server (NTRS)

    Saba, Julia L. R.

    1994-01-01

    This contract supports the investigation of elemental abundances in the solar corona, principally through analysis of high-resolution software X-ray spectra from the Flat Crystal Spectrometer on NASA's Solar Maximum Mission. The goals of the study are a characterization of the mean values of relative abundances of elements accessible in the FCS data, and information on the extent and circumstances of their variability. This report is a summation of the data analysis and reporting activities which occurred since the last report, submitted two months early, in April 1994, to facilitate evaluation of the first year's progress for contract renewal. Hence this report covers the period 15 April 1994 - 15 December 1994. A list of publications resulting from this research is included.

  20. The solar abundance of thulium

    NASA Technical Reports Server (NTRS)

    Ross, J. E.; Aller, L. H.

    1974-01-01

    Consideration of one relatively unblended line of the solar spectrum, namely, the 3131.258-A line of Tm II, which yields a thulium abundance of 0.80 plus or minus 0.10 with the Corliss and Bozman (1962) f-value. The uncertainty of this figure is discussed in conjunction with the contradictory findings of some other investigators. The need for further detailed study of the lanthanides by the method of spectrum synthesis is pointed out.

  1. Chlorine Abundances in Martian Meteorites

    NASA Technical Reports Server (NTRS)

    Bogard, D.D.; Garrison, D.H.; Park, J.

    2009-01-01

    Chlorine measurements made in martian surface rocks by robotic spacecraft typically give Chlorine (Cl) abundances of approximately 0.1-0.8%. In contrast, Cl abundances in martian meteorites appear lower, although data is limited, and martian nakhlites were also subjected to Cl contamination by Mars surface brines. Chlorine abundances reported by one lab for whole rock (WR) samples of Shergotty, ALH77005, and EET79001 range 108-14 ppm, whereas Cl in nakhlites range 73-1900 ppm. Measurements of Cl in various martian weathering phases of nakhlites varied 0.04-4.7% and reveal significant concentration of Cl by martian brines Martian meteorites contain much lower Chlorine than those measured in martian surface rocks and give further confirmation that Cl in these surface rocks was introduced by brines and weathering. It has been argued that Cl is twice as effective as water in lowering the melting point and promoting melting at shallower martian depths, and that significant Cl in the shergottite source region would negate any need for significant water. However, this conclusion was based on experiments that utilized Cl concentrations more analogous to martian surface rocks than to shergottite meteorites, and may not be applicable to shergottites.

  2. Surface abundances of OC supergiants

    NASA Astrophysics Data System (ADS)

    Martins, F.; Foschino, S.; Bouret, J.-C.; Barbá, R.; Howarth, I.

    2016-04-01

    Context. Some O and B stars show unusually strong or weak lines of carbon and/or nitrogen. These objects are classified as OBN or OBC stars. It has recently been shown that nitrogen enrichment and carbon depletion are the most likely explanations for the existence of the ON class. Aims: We investigate OC stars (all being supergiants) to check that surface abundances are responsible for the observed anomalous line strengths. Methods: We perform a spectroscopic analysis of three OC supergiants using atmosphere models. A fourth star was previously studied by us. Our sample thus comprises all OC stars known to date in the Galaxy. We determine the stellar parameters and He, C, N, and O surface abundances. Results: We show that all stars have effective temperatures and surface gravities fully consistent with morphologically normal O supergiants. However, OC stars show little, if any, nitrogen enrichment and carbon surface abundances consistent with the initial composition. OC supergiants are thus barely chemically evolved, unlike morphologically normal O supergiants. Based on observations obtained at the ESO/La Silla Observatory under programs 081.D-2008, 083.D-0589, 089.D-0975.

  3. The Abundance of Interstellar Fluorine

    NASA Technical Reports Server (NTRS)

    Lauroesch, James T.

    2005-01-01

    The primary objective of this program was to obtain FUSE observations of the interstellar absorption lines of F I at 951 and 954 Angstroms to derive the abundance of fluorine toward the star HD 164816. The nucleosynthetic source(s) of fluorine are still a matter of debate - the present day abundance of fluorine can potentially constrain models for pulsationally driven dredge-up in asymptotic giant branch stars. An accurate measure for the depletion behavior of fluorine will determine whether it may be detectable in QSO absorption line systems - an unambiguous detection of fluorine at suitably high redshifts would provide the best evidence to date for the neutrino process in massive stars. Furthermore, due to its extreme reactivity, measurement of the gas-phase interstellar fluorine abundance is important for models of grain chemistry. Despite the importance of measuring the interstellar fluorine abundance, at the time of our proposal only one previous detection has been made due to the low relative abundance of fluorine, the lack of lines outside the far-UV, and the blending of the available F I transitions with lines of Hz. The star HD 164816 is associated with the Lagoon nebula (M8), and at a distance of approximately 1.5 kpc probes both distant and local gas. Beginning April 8th, 2004 FUSE FP-Split observations of the star HD 164816 were obtained for this program. This data became available in the FUSE data archive May 21, 2004, and these observations were then downloaded and we began our analysis. Our analysis procedure has involved (1) fitting stellar models to the FUSE spectra, (2) using the multiple lines of Hz and N I at other wavelengths in the FUSE bandpass to derive column densities for the lines of H2 and N I which are blended with the F I features at 951 and 954 angstroms (3) the measurement of the column densities of F I and the species O I and C1 I which are important species for the dis-entangling of dust and nucleosynthetic effects. As discussed in

  4. Type-1 chain histo-blood group antigens (Le(a), monosialosyl-Le(a), disialosyl-Le(a), Le(b), and H) in normal and malignant human endometrium.

    PubMed

    Ravn, V; Mandel, U; Svenstrup, B; Dabelsteen, E

    1994-01-01

    Type-1 chain histo-blood group antigens such as the Lewis (Le)a, monosialosyl-Le(a), Le(b) and H antigens show an increased expression in endometrial carcinomas. However, the possibility that these antigens are expressed under genetic or hormonal influence in endometrial carcinomas has not been considered. In the present study, the expression of type-1 chain carbohydrate antigens in normal and malignant endometrium was evaluated by immunohistochemistry and related to both genetic and hormonal factors. The glands of normal, non-secretory endometria expressed, in contrast with surface epithelial cells, Le(a), Le(b), disialosyl-Le(a), and H determinants infrequently. Adenomatous hyperplasias and endometrial carcinomas showed an increased expression of type-1 chain carbohydrates that was qualitatively influenced by the erythrocyte Lewis phenotype and the secretor status. Whereas Le(a+b-) non-secretors mainly accumulated Le(a) antigen, and only limited amounts of Le(b) antigen, Le(a-b+) secretors expressed H, Le(b) and Le(a) antigens. The expression of type-1 chain antigens showed no association with the serum-oestrogen level or to the hormone-receptor status. Thus the Lewis secretor status has a qualitative influence on the increased expression of type-1 chain antigens, which, however, seem to be unrelated to hormonal factors. Our findings suggest an increased activity of the Se-gene-defined or a closely related fucosyl-transferase in neoplastic endometrial epithelial cells. PMID:8032530

  5. Origin of cosmic chemical abundances

    NASA Astrophysics Data System (ADS)

    Maio, Umberto; Tescari, Edoardo

    2015-11-01

    Cosmological N-body hydrodynamic computations following atomic and molecular chemistry (e-, H, H+, H-, He, He+, He++, D, D+, H2, H_2^+, HD, HeH+), gas cooling, star formation and production of heavy elements (C, N, O, Ne, Mg, Si, S, Ca, Fe, etc.) from stars covering a range of mass and metallicity are used to explore the origin of several chemical abundance patterns and to study both the metal and molecular content during simulated galaxy assembly. The resulting trends show a remarkable similarity to up-to-date observations of the most metal-poor damped Lyman α absorbers at redshift z ≳ 2. These exhibit a transient nature and represent collapsing gaseous structures captured while cooling is becoming effective in lowering the temperature below ˜ 104 K, before they are disrupted by episodes of star formation or tidal effects. Our theoretical results agree with the available data for typical elemental ratios, such as [C/O], [Si/Fe], [O/Fe], [Si/O], [Fe/H], [O/H] at redshifts z ˜ 2-7. Correlations between H I and H2 abundances show temporal and local variations and large spreads as a result of the increasing cosmic star formation activity from z ˜ 6 to 3. The scatter we find in the abundance ratios is compatible with the observational data and is explained by simultaneous enrichment by sources from different stellar phases or belonging to different stellar populations. Simulated synthetic spectra support the existence of metal-poor cold clumps with large optical depth at z ˜ 6 that could be potential Population III sites at low or intermediate redshift. The expected dust content is in line with recent determinations.

  6. Element abundances of classical novae

    NASA Astrophysics Data System (ADS)

    Andrea, J.; Drechsel, H.; Starrfield, S.

    1994-11-01

    Physical conditions and element abundances in the optically thin shells of 11 classical novae with outbursts between 1978 and 1989 were determined from an analysis of UV and optical spectra obtained during the nebular stage. Eight novae were studied on the basis of new optical and UV spectra. The accuracy of the element abundances depends on whether or not simultaneous UV spectra were available to determine individual ionization stage dependent gas temperatures. Generally, slightly higher than solar abundances of helium and pronounced overabundances of the heavier elements were found. QU Vul turned out to be an ONeMg nova, while the other objects belong to the class of CO novae. The nature of V2214 Oph could not be completely clarified. The novae V1668 Cyg (1978), V693 CrA (1981), and V1370 Aql (1982), for which published element abundances exist, were reanalyzed to check the consistency of our spectral analysis approach. Satisfactory agreement of the results was found. Photoionization calculations were carried out for PW Vul using the code of Aldrovandi, Pequignot, and Stasinska. A synthetic spectrum was generated for the parameters derived from the analysis of the UV and optical spectra, which is in very good agreement with the observations. The spectral analysis technique was then applied to the model spectrum and reproduced the model parameters well. Electron temperatures for the C(2+) and C(3+) ions between 7 500 and 12,000 K and for N(4+) betwen 12,000 and 16,000 K were derived. For PW Vul these temperatures remained relatively constant over several months. The decline in density of the ejected shells with time could be investigated for V842 Cen, QV Vul, V977 Sco, and V443 Sct, and was found to deviate from the relation Ne proportional to t-2 for free expansion of a shell in a different way for each object. A possible explanation may be the complex density structure of the shells. This suspicion is supported by high resolution spectra (ESO 3.6m telescope

  7. Abundance measurements in stellar environments

    NASA Astrophysics Data System (ADS)

    Leone, F.

    2014-05-01

    Most of what we know about stars, and systems of stars, is derived from the analysis of their electromagnetic radiation. This lesson is an attempt to describe to Physicists, without any Astrophysical background, the framework to understand the present status of abundance determination in stellar environments and its limit. These notes are dedicated to the recently passed, November 21, 2013, Prof. Dimitri Mihalas who spent his life confuting the 19th century positivist philosopher Auguste Comte who stated that we shall not at all be able to determine the chemical composition of stars.

  8. Abundance measurements in stellar environments

    SciTech Connect

    Leone, F.

    2014-05-09

    Most of what we know about stars, and systems of stars, is derived from the analysis of their electromagnetic radiation. This lesson is an attempt to describe to Physicists, without any Astrophysical background, the framework to understand the present status of abundance determination in stellar environments and its limit. These notes are dedicated to the recently passed, November 21, 2013, Prof. Dimitri Mihalas who spent his life confuting the 19th century positivist philosopher Auguste Comte who stated that we shall not at all be able to determine the chemical composition of stars.

  9. The solar abundance of Oxygen

    NASA Astrophysics Data System (ADS)

    Grevesse, N.

    2009-07-01

    With Martin Asplund (Max Planck Institute of Astrophysics, Garching) and Jacques Sauval (Observatoire Royal de Belgique, Brussels) I recently published detailed reviews on the solar chemical composition ({Asplund et al. 2005}, {Grevesse et al. 2007}). A new one, with Pat Scott (Stockholm University) as additional co-author, will appear in Annual Review of Astronomy and Astrophysics ({Asplund et al. 2009}). Here we briefly analyze recent works on the solar abundance of Oxygen and recommend a value of 8.70 in the usual astronomical scale.

  10. Elemental Abundances in NGC 3516

    NASA Technical Reports Server (NTRS)

    Turner, T. J.; Kraemer, S. B.; Mushotzky, R. F.; George, I. M.; Gabel, J. R.

    2003-01-01

    We present Reflection Grating Spectrometer data from an XMM-Newton observation of the Seyfert 1 galaxy NGC 3516, taken while the continuum source was in an extremely low flux state. This observation offers a rare opportunity for a detailed study of emission from a Seyfert 1 galaxy as these are usually dominated by high nuclear continuum levels and heavy absorption. The spectrum shows numerous narrow emission lines (FWHM approximately less than 1300 kilometers per second) in the 0.3 - 2 keV range, including the H-like lines of C, N, and O and the He-like lines of N, O and Ne. The emission-line ratios and the narrow width of the radiative recombination continuum of CVI indicate that the gas is photoionized and of fairly low temperature (kT approximately less than 0.01 keV). The availability of emission lines from different elements for two iso-electronic sequences allows us to constrain the element abundances. These data show that the N lines are far stronger than would be expected from gas of solar abundances. Based on our photoionization models we find that nitrogen is overabundant in the central regions of the galaxy, compared to carbon, oxygen and neon by at least a factor of 2.5. We suggest that this is the result of secondary production of nitrogen in intermediate mass stars, and indicative of the history of star formation in NGC 3516.

  11. Metaproteomics reveals abundant transposase expression in mutualistic endosymbionts

    SciTech Connect

    Kleiner, Manuel; Young, Jacque C; Shah, Manesh B; Verberkmoes, Nathan C; Dubilier, Nicole

    2013-01-01

    Transposases, enzymes that catalyze the movement of mobile genetic elements, are the most abundant genes in nature. While many bacteria encode an abundance of transposases in their genomes, the current paradigm is that transposase gene expression is tightly regulated and generally low due to its severe mutagenic effects. In the current study, we detected the highest number of transposase proteins ever reported in bacteria, in symbionts of the gutless marine worm Olavius algarvensis using metaproteomics. At least 26 different transposases from 12 different families were detected and genomic and proteomic analyses suggest many of these are active. This high expression of transposases indicates that the mechanisms for their tight regulation have been disabled or destroyed. Based on recent studies on other symbionts and pathogens that showed high transposase transcription, we speculate that abundant transposase expression might be common in symbionts and pathogens.

  12. The SEM and TEM study on the laminated structure of individual aragonitic nacre tablet in freshwater bivalve H. cumingii Lea shell.

    PubMed

    Xie, Lei; Wang, Xiao-Xiang; Li, Jian

    2010-01-01

    Nacre (mother-of-pearl), one of the natural composite materials, is renowned for its excellent mechanical properties and becomes a model for study on the biominerals. In the present study on bivalve H. cumingii Lea, the forming nacre tablet was observed with SEM to show laminated character on the lateral growing surfaces. Correspondingly, HRTEM showed dense crystal defects on (001) plane of the aragonite nacre tablet which might be caused by the adsorption of organic macromolecules on the plane. The correlation of the laminated growth mode and crystal defects on (001) plane was discussed. These findings could enhance our understanding to the formation mechanism of the nacre tablet as well as the superior mechanical properties of the nacre. PMID:19733246

  13. Abundance of Hepatic Transporters in Caucasians: A Meta-Analysis.

    PubMed

    Burt, Howard J; Riedmaier, Arian Emami; Harwood, Matthew D; Crewe, H Kim; Gill, Katherine L; Neuhoff, Sibylle

    2016-10-01

    This study aimed to derive quantitative abundance values for key hepatic transporters suitable for in vitro-in vivo extrapolation within a physiologically based pharmacokinetic modeling framework. A meta-analysis was performed whereby data on abundance measurements, sample preparation methods, and donor demography were collated from the literature. To define values for a healthy Caucasian population, a subdatabase was created whereby exclusion criteria were applied to remove samples from non-Caucasian individuals, those with underlying disease, or those with subcellular fractions other than crude membrane. Where a clinically relevant active genotype was known, only samples from individuals with an extensive transporter phenotype were included. Authors were contacted directly when additional information was required. After removing duplicated samples, the weighted mean, geometric mean, standard deviation, coefficient of variation, and between-study homogeneity of transporter abundances were determined. From the complete database containing 24 transporters, suitable abundance data were available for 11 hepatic transporters from nine studies after exclusion criteria were applied. Organic anion transporting polypeptides OATP1B1 and OATP1B3 showed the highest population abundance in healthy adult Caucasians. For several transporters, the variability in abundance was reduced significantly once the exclusion criteria were applied. The highest variability was observed for OATP1B3 > OATP1B1 > multidrug resistance protein 2 > multidrug resistance gene 1. No relationship was found between transporter expression and donor age. To our knowledge, this study provides the first in-depth analysis of current quantitative abundance data for a wide range of hepatic transporters, with the aim of using these data for in vitro-in vivo extrapolation, and highlights the significance of investigating the background of tissue(s) used in quantitative transporter proteomic studies. Similar

  14. Abundance patterns in planetary nebulae

    NASA Astrophysics Data System (ADS)

    Henry, Richard B. C.

    1990-06-01

    Abundances of He, N, O, and Ne have been uniformly calculated for 192 planetary nebulas residing in the Galactic disk and halo, the LMC, the SMC, and M31. Direct correlations appear to exist for type I as well as non-type I objects for the following pairs of parameters: N/O-He/H, N/O-N/H, and Ne/H-O/H. Separately, type I planetaries show a weak anticorrelation between N/O and O/H, while non-type I's exhibit direct correlations between N/H and O/H and between N/O and O/H. From these patterns, it is inferred that non-type I's synthesize N via the CN cycle. Type I planetaries, on the other hand, manufacture N at least partially via the ON cycle, destroying O in the process. Neither type appears to synthesize O or Ne.

  15. Quantitation of Vacuolar Sugar Transporter Abundance Changes Using QconCAT Synthtetic Peptides.

    PubMed

    Pertl-Obermeyer, Heidi; Trentmann, Oliver; Duscha, Kerstin; Neuhaus, H Ekkehard; Schulze, Waltraud X

    2016-01-01

    Measurements of protein abundance changes are important for biological conclusions on protein-related processes such as activity or complex formation. Proteomic analyses in general are almost routine tasks in many laboratories, but a precise and quantitative description of (absolute) protein abundance changes require careful experimental design and precise data quality. Today, a vast choice of metabolic labeling and label-free quantitation protocols are available, but the trade-off between quantitative precision and proteome coverage of quantified proteins including missing value problems remain. Here, we provide an example of a targeted proteomic approach using artificial standard proteins consisting of concatenated peptides of interest (QconCAT) to specifically quantify abiotic stress-induced abundance changes in low abundant vacuolar transporters. An advantage of this approach is the reliable quantitation of alimited set of low-abundant target proteins throughout different conditions. We show that vacuolar ATPase AVP1 and sugar transporters of the ERDL (early responsive to dehydration-like) family and TMT2 (tonoplast monosaccharide transporter 2) showed increased abundance upon salt stress. PMID:27148277

  16. Quantitation of Vacuolar Sugar Transporter Abundance Changes Using QconCAT Synthtetic Peptides

    PubMed Central

    Pertl-Obermeyer, Heidi; Trentmann, Oliver; Duscha, Kerstin; Neuhaus, H. Ekkehard; Schulze, Waltraud X.

    2016-01-01

    Measurements of protein abundance changes are important for biological conclusions on protein-related processes such as activity or complex formation. Proteomic analyses in general are almost routine tasks in many laboratories, but a precise and quantitative description of (absolute) protein abundance changes require careful experimental design and precise data quality. Today, a vast choice of metabolic labeling and label-free quantitation protocols are available, but the trade-off between quantitative precision and proteome coverage of quantified proteins including missing value problems remain. Here, we provide an example of a targeted proteomic approach using artificial standard proteins consisting of concatenated peptides of interest (QconCAT) to specifically quantify abiotic stress-induced abundance changes in low abundant vacuolar transporters. An advantage of this approach is the reliable quantitation of alimited set of low-abundant target proteins throughout different conditions. We show that vacuolar ATPase AVP1 and sugar transporters of the ERDL (early responsive to dehydration-like) family and TMT2 (tonoplast monosaccharide transporter 2) showed increased abundance upon salt stress. PMID:27148277

  17. Lithium Abundance in Planet Search Stars

    NASA Astrophysics Data System (ADS)

    Myles, Justin; Yale Exoplanets

    2016-01-01

    Since most lithium in the universe is primordial and is destroyed in stars, lithium abundance can be used as a stellar age indicator. Some research seems to show that planet formation may also affect lithium abundance in exoplanet host stars (EHS). However, small and heterogenous samples have made both of these phenomena unclear. Further study of lithium abundance in EHS is needed to better understand possible physical roles of lithium in planet formation theory. We use a large homogenous sample with accurate stellar parameters on which we will use equivalent width analysis to determine precise lithium abundances. From these abundance values we determine an age vs. abundance relation. Additionally, we aim to explore correlation between lithium abundance and planet formation.

  18. Surface abundances of ON stars

    NASA Astrophysics Data System (ADS)

    Martins, F.; Simón-Díaz, S.; Palacios, A.; Howarth, I.; Georgy, C.; Walborn, N. R.; Bouret, J.-C.; Barbá, R.

    2015-06-01

    Context. Massive stars burn hydrogen through the CNO cycle during most of their evolution. When mixing is efficient or when mass transfer in binary systems occurs, chemically processed material is observed at the surface of O and B stars. Aims: ON stars show stronger lines of nitrogen than morphologically normal counterparts. Whether this corresponds to the presence of material processed through the CNO cycle is not known. Our goal is to answer this question. Methods: We performed a spectroscopic analysis of a sample of ON stars with atmosphere models. We determined the fundamental parameters as well as the He, C, N, and O surface abundances. We also measured the projected rotational velocities. We compared the properties of the ON stars to those of normal O stars. Results: We show that ON stars are usually rich in helium. Their CNO surface abundances are fully consistent with predictions of nucleosynthesis. ON stars are more chemically evolved and rotate - on average - faster than normal O stars. Evolutionary models including rotation cannot account for the extreme enrichment observed among ON main sequence stars. Some ON stars are members of binary systems, but others are single stars as indicated by stable radial velocities. Mass transfer is therefore not a simple explanation for the observed chemical properties. Conclusions: We conclude that ON stars show extreme chemical enrichment at their surface, consistent with nucleosynthesis through the CNO cycle. Its origin is not clear at present. Based on observations obtained 1) at the Anglo-Australian Telescope; 2) at the Canada-France-Hawaii Telescope (CFHT), which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l'Univers of the Centre National de la Recherche Scientifique (CNRS) of France, and the University of Hawaii; 3) at the ESO/La Silla Observatory under programs 081.D-2008, 083.D-0589, 086.D-0997; 4) the Nordic Optical Telescope, operated on the island of La

  19. Significant biases affecting abundance determinations

    NASA Astrophysics Data System (ADS)

    Wesson, Roger

    2015-08-01

    I have developed two highly efficient codes to automate analyses of emission line nebulae. The tools place particular emphasis on the propagation of uncertainties. The first tool, ALFA, uses a genetic algorithm to rapidly optimise the parameters of gaussian fits to line profiles. It can fit emission line spectra of arbitrary resolution, wavelength range and depth, with no user input at all. It is well suited to highly multiplexed spectroscopy such as that now being carried out with instruments such as MUSE at the VLT. The second tool, NEAT, carries out a full analysis of emission line fluxes, robustly propagating uncertainties using a Monte Carlo technique.Using these tools, I have found that considerable biases can be introduced into abundance determinations if the uncertainty distribution of emission lines is not well characterised. For weak lines, normally distributed uncertainties are generally assumed, though it is incorrect to do so, and significant biases can result. I discuss observational evidence of these biases. The two new codes contain routines to correctly characterise the probability distributions, giving more reliable results in analyses of emission line nebulae.

  20. Cellulose synthase interacting protein

    PubMed Central

    Somerville, Chris

    2010-01-01

    Cellulose is the most abundant biopolymer on earth. The great abundance of cellulose places it at the forefront as a primary source of biomass for renewable biofuels. However, the knowledge of how plant cells make cellulose remains very rudimentary. Cellulose microfibrils are synthesized at the plasma membrane by hexameric protein complexes, also known as cellulose synthase complexes. The only known components of cellulose synthase complexes are cellulose synthase (CESA) proteins until the recent identification of a novel component. CSI1, which encodes CESA interacting protein 1 (CSI1) in Arabidopsis. CSI1, as the first non-CESA proteins associated with cellulose synthase complexes, opens up many opportunities. PMID:21150290