Identification and characterization of the reptilian GnRH-II gene in the leopard gecko, Eublepharis macularius, and its evolutionary considerations.

PubMed

Ikemoto, Tadahiro; Park, Min Kyun

2003-10-16

To elucidate the molecular phylogeny and evolution of a particular peptide, one must analyze not the limited primary amino acid sequences of the low molecular weight mature polypeptide, but rather the sequences of the corresponding precursors from various species. Of all the structural variants of gonadotropin-releasing hormone (GnRH), GnRH-II (chicken GnRH-II, or cGnRH-II) is remarkably conserved without any sequence substitutions among vertebrates, but its precursor sequences vary considerably. We have identified and characterized the full-length complementary DNA (cDNA) encoding the GnRH-II precursor and determined its genomic structure, consisting of four exons and three introns, in a reptilian species, the leopard gecko Eublepharis macularius. This is the first report about the GnRH-II precursor cDNA/gene from reptiles. The deduced leopard gecko prepro-GnRH-II polypeptide had the highest identities with the corresponding polypeptides of amphibians. The GnRH-II precursor mRNA was detected in more than half of the tissues and organs examined. This widespread expression is consistent with the previous findings in several species, though the roles of GnRH outside the hypothalamus-pituitary-gonadal axis remain largely unknown. Molecular phylogenetic analysis combined with sequence comparison showed that the leopard gecko is more similar to fishes and amphibians than to eutherian mammals with respect to the GnRH-II precursor sequence. These results strongly suggest that the divergence of the GnRH-II precursor sequences seen in eutherian mammals may have occurred along with amniote evolution.

Modeling the evolution of protein domain architectures using maximum parsimony.

PubMed

Fong, Jessica H; Geer, Lewis Y; Panchenko, Anna R; Bryant, Stephen H

2007-02-09

Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture "neighbors" identified in this way may lead to new insights about the evolution of protein function.

Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony

PubMed Central

Fong, Jessica H.; Geer, Lewis Y.; Panchenko, Anna R.; Bryant, Stephen H.

2007-01-01

Domains are basic evolutionary units of proteins and most proteins have more than one domain. Advances in domain modeling and collection are making it possible to annotate a large fraction of known protein sequences by a linear ordering of their domains, yielding their architecture. Protein domain architectures link evolutionarily related proteins and underscore their shared functions. Here, we attempt to better understand this association by identifying the evolutionary pathways by which extant architectures may have evolved. We propose a model of evolution in which architectures arise through rearrangements of inferred precursor architectures and acquisition of new domains. These pathways are ranked using a parsimony principle, whereby scenarios requiring the fewest number of independent recombination events, namely fission and fusion operations, are assumed to be more likely. Using a data set of domain architectures present in 159 proteomes that represent all three major branches of the tree of life allows us to estimate the history of over 85% of all architectures in the sequence database. We find that the distribution of rearrangement classes is robust with respect to alternative parsimony rules for inferring the presence of precursor architectures in ancestral species. Analyzing the most parsimonious pathways, we find 87% of architectures to gain complexity over time through simple changes, among which fusion events account for 5.6 times as many architectures as fission. Our results may be used to compute domain architecture similarities, for example, based on the number of historical recombination events separating them. Domain architecture “neighbors” identified in this way may lead to new insights about the evolution of protein function. PMID:17166515

Law, Policy and Nonproliferation Project Events and Workshops: Key Themes, Results and Related Materials 2008 - 2009

DTIC Science & Technology

2010-04-01

biological precursors are obtained legally from legitimate corporations, these suppliers should incorporate some sort of chemical or genetic “barcode...traditionally come under the rubric of limited engagement, especially as such policy evolved during the Cold War between the US and USSR. With the end...information that may enable access to dual-use technology. A “bar-coding” procedure, by which a genetic sequence or chemical signature is used to

A novel chlorophyll a/b binding (Cab) protein gene from petunia which encodes the lower molecular weight Cab precursor protein.

PubMed

Stayton, M M; Black, M; Bedbrook, J; Dunsmuir, P

1986-12-22

The 16 petunia Cab genes which have been characterized are all closely related at the nucleotide sequence level and they encode Cab precursor polypeptides which are similar in sequence and length. Here we describe a novel petunia Cab gene which encodes a unique Cab precursor protein. This protein is a member of the smallest class of Cab precursor proteins for which no gene has previously been assigned in petunia or any other species. The features of this Cab precursor protein are that it is shorter by 2-3 amino acids than the formerly characterized Cab precursors, its transit peptide sequence is unrelated, and the mature polypeptide is significantly diverged at the functionally important N terminus from other petunia Cab proteins. Gene structure also discriminates this gene which is the only intron containing Cab gene in petunia genomic DNA.

Identification of Regulatory Elements That Control PPARγ Expression in Adipocyte Progenitors

PubMed Central

Chou, Wen-Ling; Galmozzi, Andrea; Partida, David; Kwan, Kevin; Yeung, Hui; Su, Andrew I.; Saez, Enrique

2013-01-01

Adipose tissue renewal and obesity-driven expansion of fat cell number are dependent on proliferation and differentiation of adipose progenitors that reside in the vasculature that develops in coordination with adipose depots. The transcriptional events that regulate commitment of progenitors to the adipose lineage are poorly understood. Because expression of the nuclear receptor PPARγ defines the adipose lineage, isolation of elements that control PPARγ expression in adipose precursors may lead to discovery of transcriptional regulators of early adipocyte determination. Here, we describe the identification and validation in transgenic mice of 5 highly conserved non-coding sequences from the PPARγ locus that can drive expression of a reporter gene in a manner that recapitulates the tissue-specific pattern of PPARγ expression. Surprisingly, these 5 elements appear to control PPARγ expression in adipocyte precursors that are associated with the vasculature of adipose depots, but not in mature adipocytes. Characterization of these five PPARγ regulatory sequences may enable isolation of the transcription factors that bind these cis elements and provide insight into the molecular regulation of adipose tissue expansion in normal and pathological states. PMID:24009687

Identification of a precursor genomic segment that provided a sequence unique to glycophorin B and E genes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Onda, M.; Kudo, S.; Fukuda, M.

Human glycophorin A, B, and E (GPA, GPB, and GPE) genes belong to a gene family located at the long arm of chromosome 4. These three genes are homologous from the 5'-flanking sequence to the Alu sequence, which is 1 kb downstream from the exon encoding the transmembrane domain. Analysis of the Alu sequence and flanking direct repeat sequences suggested that the GPA gene most closely resembles the ancestral gene, whereas the GPB and GPE gene arose by homologous recombination within the Alu sequence, acquiring 3' sequences from an unrelated precursor genomic segment. Here the authors describe the identification ofmore » this putative precursor genomic segment. A human genomic library was screened by using the sequence of the 3' region of the GPB gene as a probe. The genomic clones isolated were found to contain an Alu sequence that appeared to be involved in the recombination. Downstream from the Alu sequence, the nucleotide sequence of the precursor genomic segment is almost identical to that of the GPB or GPE gene. In contrast, the upstream sequence of the genomic segment differs entirely from that of the GPA, GPB, and GPE genes. Conservation of the direct repeats flanking the Alu sequence of the genomic segment strongly suggests that the sequence of this genomic segment has been maintained during evolution. This identified genomic segment was found to reside downstream from the GPA gene by both gene mapping and in situ chromosomal localization. The precursor genomic segment was also identified in the orangutan genome, which is known to lack GPB and GPE genes. These results indicate that one of the duplicated ancestral glycophorin genes acquired a unique 3' sequence by unequal crossing-over through its Alu sequence and the further downstream Alu sequence present in the duplicated gene. Further duplication and divergence of this gene yielded the GPB and GPE genes. 37 refs., 5 figs.« less

Immunological and biochemical characterization of processing products from the neurotensin/neuromedin N precursor in the rat medullary thyroid carcinoma 6-23 cell line.

PubMed Central

Bidard, J N; de Nadai, F; Rovere, C; Moinier, D; Laur, J; Martinez, J; Cuber, J C; Kitabgi, P

1993-01-01

Neurotensin (NT) and neuromedin N (NN) are two related biologically active peptides that are encoded in the same precursor molecule. In the rat, the precursor consists of a 169-residue polypeptide starting with an N-terminal signal peptide and containing in its C-terminal region one copy each of NT and NN. NN precedes NT and is separated from it by a Lys-Arg sequence. Two other Lys-Arg sequences flank the N-terminus of NN and the C-terminus of NT. A fourth Lys-Arg sequence occurs near the middle of the precursor and is followed by an NN-like sequence. Finally, an Arg-Arg pair is present within the NT moiety. The four Lys-Arg doublets represent putative processing sites in the precursor molecule. The present study was designed to investigate the post-translational processing of the NT/NN precursor in the rat medullary thyroid carcinoma (rMTC) 6-23 cell line, which synthesizes large amounts of NT upon dexamethasone treatment. Five region-specific antisera recognizing the free N- or C-termini of sequences adjacent to the basic doublets were produced, characterized and used for immunoblotting and radioimmunoassay studies in combination with gel filtration, reverse-phase h.p.l.c. and trypsin digestion of rMTC 6-23 cell extracts. Because two of the antigenic sequences, i.e. NN and the NN-like sequence, start with a lysine residue that is essential for recognition by their respective antisera, a micromethod by which trypsin specifically cleaves at arginine residues was developed. The results show that dexamethasone-treated rMTC 6-23 cells produced comparable amounts of NT, NN and a peptide corresponding to a large N-terminal precursor fragment lacking the NN and NT moieties. This large fragment was purified. N-Terminal sequencing revealed that it started at residue Ser23 of the prepro-NT/NN sequence, and thus established the Cys22-Ser23 bond as the cleavage site of the signal peptide. Two other large N-terminal fragments bearing respectively the NN and NT sequences at their C-termini were present in lower amounts. The NN-like sequence was internal to all the large fragments. There was no evidence for the presence of peptides with the NN-like sequence at their N-termini. This shows that, in rMTC 6-23 cells, the precursor is readily processed at the three Lys-Arg doublets that flank and separate the NT and NN sequences. In contrast, the Lys-Arg doublet that precedes the NN-like sequence is not processed in this system.(ABSTRACT TRUNCATED AT 400 WORDS) Images Figure 3 PMID:8471039

The construction and partial characterization of plasmids containing complementary DNA sequences to human calcitonin precursor polyprotein.

PubMed Central

Allison, J; Hall, L; MacIntyre, I; Craig, R K

1981-01-01

(1) Total poly(A)-containing RNA isolated from human thyroid medullary carcinoma tissue was shown to direct the synthesis in the wheat germ cell-free system of a major (Mr 21000) and several minor forms of human calcitonin precursor polyproteins. Evidence for processing of these precursor(s) by the wheat germ cell-free system is also presented. (2) A small complementary DNA (cDNA) plasmid library has been constructed in the PstI site of the plasmid pAT153, using total human thyroid medullary carcinoma poly(A)-containing RNA as the starting material. (3) Plasmids containing abundant cDNA sequences were selected by hybridization in situ, and two of these (ph T-B3 and phT-B6) were characterized by hybridization--translation and restriction analysis. Each was shown to contain human calcitonin precursor polyprotein cDNA sequences. (4) RNA blotting techniques demonstrate that the human calcitonin precursor polyprotein is encoded within a mRNA containing 1000 bases. (5) The results demonstrate that human calcitonin is synthesized as a precursor polyprotein. Images Fig. 1. Fig. 2. Fig. 3. PMID:6896146

Mainshock-aftershock clustering in volcanic regions

USGS Publications Warehouse

Giron, Ricardo Garza; Brodsky, Emily E.; Prejean, Stephanie

2018-01-01

swarms and mainshock-aftershock sequences. The former is commonly thought to dominate in volcanic and geothermal regions, but aftershock production, including within swarms, is not well studied in volcanic regions. Here we compare mainshock-aftershock clustering in active volcanic regions in Japan to nearby nonvolcanic regions. We find that aftershock production is similar in both areas by two separate metrics: (1) Both volcanic and nonvolcanic regions have similar proportions of areas that cluster into mainshock-aftershock sequences. (2) Volcanic areas with mainshock-aftershock sequences have aftershock productivity at least as high as nonvolcanic regions. We also find that volcano-tectonic events that are precursors to an eruption are more common at volcanoes without mainshock-aftershock clusters than at volcanoes with well-defined mainshock-aftershock clusters. This last finding hints at a strategy to identify volcanic systems where cataloged earthquakes are good predictors of behavior.

Phylogenetic Relationship of Necoclí Virus to Other South American Hantaviruses (Bunyaviridae: Hantavirus).

PubMed

Montoya-Ruiz, Carolina; Cajimat, Maria N B; Milazzo, Mary Louise; Diaz, Francisco J; Rodas, Juan David; Valbuena, Gustavo; Fulhorst, Charles F

2015-07-01

The results of a previous study suggested that Cherrie's cane rat (Zygodontomys cherriei) is the principal host of Necoclí virus (family Bunyaviridae, genus Hantavirus) in Colombia. Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences in this study confirmed that Necoclí virus is phylogenetically closely related to Maporal virus, which is principally associated with the delicate pygmy rice rat (Oligoryzomys delicatus) in western Venezuela. In pairwise comparisons, nonidentities between the complete amino acid sequence of the nucleocapsid protein of Necoclí virus and the complete amino acid sequences of the nucleocapsid proteins of other hantaviruses were ≥8.7%. Likewise, nonidentities between the complete amino acid sequence of the glycoprotein precursor of Necoclí virus and the complete amino acid sequences of the glycoprotein precursors of other hantaviruses were ≥11.7%. Collectively, the unique association of Necoclí virus with Z. cherriei in Colombia, results of the Bayesian analyses of complete nucleocapsid protein gene sequences and complete glycoprotein precursor gene sequences, and results of the pairwise comparisons of amino acid sequences strongly support the notion that Necoclí virus represents a novel species in the genus Hantavirus. Further work is needed to determine whether Calabazo virus (a hantavirus associated with Z. brevicauda cherriei in Panama) and Necoclí virus are conspecific.

Processing of the precursor of protamine P2 in mouse. Peptide mapping and N-terminal sequence analysis of intermediates.

PubMed Central

Carré-Eusèbe, D; Lederer, F; Lê, K H; Elsevier, S M

1991-01-01

Protamine P2, the major basic chromosomal protein of mouse spermatozoa, is synthesized as a precursor almost twice as long as the mature protein, its extra length arising from an N-terminal extension of 44 amino acid residues. This precursor is integrated into chromatin of spermatids, and the extension is processed during chromatin condensation in the haploid cells. We have studied processing in the mouse and have identified two intermediates generated by proteolytic cleavage of the precursor. H.p.l.c. separated protamine P2 from four other spermatid proteins, including the precursor and three proteins known to possess physiological characteristics expected of processing intermediates. Peptide mapping indicated that all of these proteins were structurally similar. Two major proteins were further purified by PAGE, transferred to poly(vinylidene difluoride) membranes and submitted to automated N-terminal sequence analysis. Both sequences were found within the deduced sequence of the precursor extension. The N-terminus of the larger intermediate, PP2C, was Gly-12, whereas the N-terminus of the smaller, PP2D, was His-21. Both processing sites involved a peptide bond in which the carbonyl function was contributed by an acidic amino acid. Images Fig. 1. Fig. 3. Fig. 4. PMID:1854346

The proteolytic processing site of the precursor of lysyl oxidase.

PubMed Central

Cronshaw, A D; Fothergill-Gilmore, L A; Hulmes, D J

1995-01-01

The precise cleavage site of the N-terminal propeptide region of the precursor of lysyl oxidase has not yet been established, due to N-terminal blocking of the mature protein. Using a combination of peptide fragmentation, amino acid sequencing, time-of-flight m.s. and partial chemical unblocking procedures, it is shown that the mature form of lysyl oxidase begins at residue Asp-169 of the precursor protein (numbered according to the human sequence). The cleavage site is 28 residues to the C-terminal side of the site previously suggested on the basis of apparant molecular mass by SDS/PAGE, with the consequence that the two putative, N-linked glycosylation sites and the position of the Arg/Gln sequence polymorphism are now all in the precursor region. PMID:7864821

Phylogenetic analysis reveals conservation and diversification of micro RNA166 genes among diverse plant species.

PubMed

Barik, Suvakanta; SarkarDas, Shabari; Singh, Archita; Gautam, Vibhav; Kumar, Pramod; Majee, Manoj; Sarkar, Ananda K

2014-01-01

Similar to the majority of the microRNAs, mature miR166s are derived from multiple members of MIR166 genes (precursors) and regulate various aspects of plant development by negatively regulating their target genes (Class III HD-ZIP). The evolutionary conservation or functional diversification of miRNA166 family members remains elusive. Here, we show the phylogenetic relationships among MIR166 precursor and mature sequences from three diverse model plant species. Despite strong conservation, some mature miR166 sequences, such as ppt-miR166m, have undergone sequence variation. Critical sequence variation in ppt-miR166m has led to functional diversification, as it targets non-HD-ZIPIII gene transcript (s). MIR166 precursor sequences have diverged in a lineage specific manner, and both precursors and mature osa-miR166i/j are highly conserved. Interestingly, polycistronic MIR166s were present in Physcomitrella and Oryza but not in Arabidopsis. The nature of cis-regulatory motifs on the upstream promoter sequences of MIR166 genes indicates their possible contribution to the functional variation observed among miR166 species. Copyright © 2013 Elsevier Inc. All rights reserved.

Ogden R. Lindsley and the historical development of precision teaching

PubMed Central

Potts, Lisa; Eshleman, John W.; Cooper, John O.

1993-01-01

This paper presents the historical developments of precision teaching, a technological offshoot of radical behaviorism and free-operant conditioning. The sequence progresses from the scientific precursors of precision teaching and the beginnings of precision teaching to principal developments since 1965. Information about the persons, events, and accomplishments presented in this chronology was compiled in several ways. Journals, books, and conference presentations provided the essential information. The most important source for this account was Ogden Lindsley himself, because Lindsley and his students established the basic practices that define precision teaching. PMID:22478145

Mainshock-Aftershock Clustering in Volcanic Regions

NASA Astrophysics Data System (ADS)

Garza-Giron, Ricardo; Brodsky, Emily E.; Prejean, Stephanie G.

2018-02-01

Earthquakes break their general Poissonean behavior through two types of seismic bursts: swarms and mainshock-aftershock sequences. The former is commonly thought to dominate in volcanic and geothermal regions, but aftershock production, including within swarms, is not well studied in volcanic regions. Here we compare mainshock-aftershock clustering in active volcanic regions in Japan to nearby nonvolcanic regions. We find that aftershock production is similar in both areas by two separate metrics: (1) Both volcanic and nonvolcanic regions have similar proportions of areas that cluster into mainshock-aftershock sequences. (2) Volcanic areas with mainshock-aftershock sequences have aftershock productivity at least as high as nonvolcanic regions. We also find that volcano-tectonic events that are precursors to an eruption are more common at volcanoes without mainshock-aftershock clusters than at volcanoes with well-defined mainshock-aftershock clusters. This last finding hints at a strategy to identify volcanic systems where cataloged earthquakes are good predictors of behavior.

Extreme and superextreme events in a loss-modulated CO2 laser: Nonlinear resonance route and precursors

NASA Astrophysics Data System (ADS)

Bonatto, Cristian; Endler, Antonio

2017-07-01

We investigate the occurrence of extreme and rare events, i.e., giant and rare light pulses, in a periodically modulated CO2 laser model. Due to nonlinear resonant processes, we show a scenario of interaction between chaotic bands of different orders, which may lead to the formation of extreme and rare events. We identify a crisis line in the modulation parameter space, and we show that, when the modulation amplitude increases, remaining in the vicinity of the crisis, some statistical properties of the laser pulses, such as the average and dispersion of amplitudes, do not change much, whereas the amplitude of extreme events grows enormously, giving rise to extreme events with much larger deviations than usually reported, with a significant probability of occurrence, i.e., with a long-tailed non-Gaussian distribution. We identify recurrent regular patterns, i.e., precursors, that anticipate the emergence of extreme and rare events, and we associate these regular patterns with unstable periodic orbits embedded in a chaotic attractor. We show that the precursors may or may not lead to the emergence of extreme events. Thus, we compute the probability of success or failure (false alarm) in the prediction of the extreme events, once a precursor is identified in the deterministic time series. We show that this probability depends on the accuracy with which the precursor is identified in the laser intensity time series.

Vesuvius: Earthquakes from 1600 up to the 1631 eruption

NASA Astrophysics Data System (ADS)

Guidoboni, Emanuela; Mariotti, Dante

2011-03-01

This study examines the seismicity of Vesuvius in the decades leading up to the great eruption of 16th December 1631. The period 1600-1631 is analyzed with the aims to point out any long-term seismic precursor of the eruption. The historical research has focused on contemporary Neapolitan memoirs and a large screening of diplomatic correspondence from the main Italian courts of the age (Florence, Mantua, Parma, Venice and the Vatican). Information was gathered on 18 earthquakes that were felt in Naples between 1601 and 1630. These data were listed with the sequence of 34 shocks that took place in November and December 1631, that preceded the beginning of the eruption. The 52 seismic events that have been highlighted overall are unknown in the parametric catalogues of Italian historical seismicity and 17 are unknown even in the scientific literature. The authors' view is that it makes little sense to talk of one single previous seismic precursor in this case, given the frequent seismic sequences and tremors noted by contemporaries from January 1616 onwards. The present state of knowledge suggests that seismic activity is a strong, early and persistent warning sign of an eruption of Vesuvius, of the same type as that of December 1631.

Changes in the Probability of Extreme Events: Where to Look for their Causes?

NASA Astrophysics Data System (ADS)

Groisman, P. Y.; Gulev, S. K.

2011-12-01

When wet or dry events are extraordinary and are associated with flooding, water shortages, severe vegetation stress, crop failures, property losses, and harm to human health, we name them extremes. Numerous observational studies show that in the past several decades precipitation has become more intense over most of the extra-tropics. At the same time, (and often in the same regions) precipitation events may occur more or less frequently or come in sequences of prolonged no-rain and wet periods. Each extreme event which manifests itself is a consequence of individual factors that are difficult to foresee. However, when these events occur more frequently, we must admit that there are changes in the probability of their occurrence and try to estimate why this happens. For example, in attempts to project prolonged extreme events (such as droughts) in a given season, climatologists used to look for their precursors in the Earth system "memory" that include anomalies in sea ice (SI) and snow cover extents (SCE), sea surface temperature (SST), and soil moisture and for their patterns (e.g., Southern Oscillation). However, the major "memory" component of the Earth system is the Earth Climate System itself. It began changing (IPCC 2007) and is not any longer a constant factor: SST, SI, and SCE anomalies of the past now became "climatology" and it is time to include this new reality in our analyses of the frequency and intensity of extreme events. Furthermore, land use, urban development, industrial development, and water management keep changing landscapes and, there are good reasons to believe that regional environmental changes feed back causing in some areas changes in the probability of extreme events. The central United States is among the regions where the strongest increase in intense rainfall in the 20th century has been documented. This raises the question of how precipitation patterns in the central US will evolve in the future: Will the recent trends toward increases in intense rainfall continue? We present and try to substantiate a hypothesis that the observed changes in characteristics of precipitation in the central US during the 20th century have been produced by interactions of local and regional land use change with global climate changes. We shall describe climatological and anthropogenic precursors of several extreme outbreaks over the northern extratropics. These precursors were waiting for their time and manifested themselves when the time became right. For example, in order to anticipate changes in the probability of the future heat outbreaks over Europe (including European Russia), the factors that control prolonged summer anticyclone conditions over the region should be thoroughly monitored and skillfully projected. Apparently, anomalies and/or trends in regional mean surface air temperature and precipitation are not the best among these precursors.

Circular RNA biogenesis can proceed through an exon-containing lariat precursor.

PubMed

Barrett, Steven P; Wang, Peter L; Salzman, Julia

2015-06-09

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical 'backsplicing' event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure.

The Apollo program and amino acids. [precursors significance in molecular evolution

NASA Technical Reports Server (NTRS)

Fox, S. W.

1973-01-01

Apollo lunar sample analyses designed to detect the presence of organic compounds are reviewed, and the results are discussed from the viewpoint of relevance to laboratory experiments on the synthesis of amino acids and to theoretical models of cosmochemical processes resulting in the formation of organic compounds. Glycine, alanine, glutamic acid, aspartic acid, serine, and threonine have been found repeatedly in the hydrolyzates of hot aqueous extracts of lunar dust. These compounds represent an early step in the sequence of events leading to the rise of living material and were probably deposited by the solar wind. The results of the Apollo program so far suggest that the pathway from cosmic organic matter to life as it evolved on earth could have been pursued on the moon to the stage of amino acid precursors and then may have been terminated for lack of sufficient water.

Mature clustered, regularly interspaced, short palindromic repeats RNA (crRNA) length is measured by a ruler mechanism anchored at the precursor processing site.

PubMed

Hatoum-Aslan, Asma; Maniv, Inbal; Marraffini, Luciano A

2011-12-27

Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in Staphylococcus epidermidis. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.

Long-term surveillance of H7 influenza viruses in American wild aquatic birds: are the H7N3 influenza viruses in wild birds the precursors of highly pathogenic strains in domestic poultry?

PubMed Central

Krauss, Scott; Stucker, Karla M; Schobel, Seth A; Danner, Angela; Friedman, Kimberly; Knowles, James P; Kayali, Ghazi; Niles, Lawrence J; Dey, Amanda D; Raven, Garnet; Pryor, Paul; Lin, Xudong; Das, Suman R; Stockwell, Timothy B; Wentworth, David E; Webster, Robert G

2015-01-01

The emergence of influenza A virus (IAV) in domestic avian species and associated transmissions to mammals is unpredictable. In the Americas, the H7 IAVs are of particular concern, and there have been four separate outbreaks of highly pathogenic (HP) H7N3 in domestic poultry in North and South America between 2002 and 2012, with occasional spillover into humans. Here, we use long-term IAV surveillance in North American shorebirds at Delaware Bay, USA, from 1985 to 2012 and in ducks in Alberta, Canada, from 1976 to 2012 to determine which hemagglutinin (HA)–neuraminidase (NA) combinations predominated in Anseriformes (ducks) and Charadriiformes (shorebirds) and whether there is concordance between peaks of H7 prevalence and transmission in wild aquatic birds and the emergence of H7 IAVs in poultry and humans. Whole-genome sequencing supported phylogenetic and genomic constellation analyses to determine whether HP IAVs emerge in the context of specific internal gene segment sequences. Phylogenetic analysis of whole-genome sequences of the H7N3 influenza viruses from wild birds and HP H7N3 outbreaks in the Americas indicate that each HP outbreak was an independent emergence event and that the low pathogenic (LP) avian influenza precursors were most likely from dabbling ducks. The different polybasic cleavage sites in the four HP outbreaks support independent origins. At the 95% nucleotide percent identity-level phylogenetic analysis showed that the wild duck HA, PB1, and M sequences clustered with the poultry and human outbreak sequences. The genomic constellation analysis strongly suggests that gene segments/virus flow from wild birds to domestic poultry. PMID:26954883

Transcriptional diversity during lineage commitment of human blood progenitors.

PubMed

Chen, Lu; Kostadima, Myrto; Martens, Joost H A; Canu, Giovanni; Garcia, Sara P; Turro, Ernest; Downes, Kate; Macaulay, Iain C; Bielczyk-Maczynska, Ewa; Coe, Sophia; Farrow, Samantha; Poudel, Pawan; Burden, Frances; Jansen, Sjoert B G; Astle, William J; Attwood, Antony; Bariana, Tadbir; de Bono, Bernard; Breschi, Alessandra; Chambers, John C; Consortium, Bridge; Choudry, Fizzah A; Clarke, Laura; Coupland, Paul; van der Ent, Martijn; Erber, Wendy N; Jansen, Joop H; Favier, Rémi; Fenech, Matthew E; Foad, Nicola; Freson, Kathleen; van Geet, Chris; Gomez, Keith; Guigo, Roderic; Hampshire, Daniel; Kelly, Anne M; Kerstens, Hindrik H D; Kooner, Jaspal S; Laffan, Michael; Lentaigne, Claire; Labalette, Charlotte; Martin, Tiphaine; Meacham, Stuart; Mumford, Andrew; Nürnberg, Sylvia; Palumbo, Emilio; van der Reijden, Bert A; Richardson, David; Sammut, Stephen J; Slodkowicz, Greg; Tamuri, Asif U; Vasquez, Louella; Voss, Katrin; Watt, Stephen; Westbury, Sarah; Flicek, Paul; Loos, Remco; Goldman, Nick; Bertone, Paul; Read, Randy J; Richardson, Sylvia; Cvejic, Ana; Soranzo, Nicole; Ouwehand, Willem H; Stunnenberg, Hendrik G; Frontini, Mattia; Rendon, Augusto

2014-09-26

Blood cells derive from hematopoietic stem cells through stepwise fating events. To characterize gene expression programs driving lineage choice, we sequenced RNA from eight primary human hematopoietic progenitor populations representing the major myeloid commitment stages and the main lymphoid stage. We identified extensive cell type-specific expression changes: 6711 genes and 10,724 transcripts, enriched in non-protein-coding elements at early stages of differentiation. In addition, we found 7881 novel splice junctions and 2301 differentially used alternative splicing events, enriched in genes involved in regulatory processes. We demonstrated experimentally cell-specific isoform usage, identifying nuclear factor I/B (NFIB) as a regulator of megakaryocyte maturation-the platelet precursor. Our data highlight the complexity of fating events in closely related progenitor populations, the understanding of which is essential for the advancement of transplantation and regenerative medicine. Copyright © 2014, American Association for the Advancement of Science.

Characterization of gonadotrophin-releasing hormone precursor cDNA in the Old World mole-rat Cryptomys hottentotus pretoriae: high degree of identity with the New World guinea pig sequence.

PubMed

Kalamatianos, T; du Toit, L; Hrabovszky, E; Kalló, I; Marsh, P J; Bennett, N C; Coen, C W

2005-05-01

Regulation of pituitary gonadotrophins by the decapeptide gonadotrophin-releasing hormone 1 (GnRH1) is crucial for the development and maintenance of reproductive functions. A common amino acid sequence for this decapeptide, designated as 'mammalian' GnRH, has been identified in all mammals thus far investigated with the exception of the guinea pig, in which there are two amino acid substitutions. Among hystricognath rodents, the members of the family Bathyergidae regulate reproduction in response to diverse cues. Thus, highveld mole-rats (Cryptomys hottentotus pretoriae) are social bathyergids in which breeding is restricted to a particular season in the dominant female, but continuously suppressed in subordinate colony members. Elucidation of reproductive control in these animals will be facilitated by characterization of their GnRH1 gene. A partial sequence of GnRH1 precursor cDNA was isolated and characterized. Comparative analysis revealed the highest degree of identity (86%) to guinea pig GnRH1 precursor mRNA. Nevertheless, the deduced amino acid sequence of the mole-rat decapeptide is identical to the 'mammalian' sequence rather than that of guinea pigs. Successful detection of GnRH1-synthesizing neurones using either a guinea pig GnRH1 riboprobe or an antibody against the 'mammalian' decapeptide is consistent with the guinea pig-like sequence for the precursor and the classic 'mammalian' form for the decapeptide. The high degree of identity in the GnRH1 precursor sequence between this Old World mole-rat and the New World guinea pig is consistent with the theory that caviomorphs and phiomorphs originated from a common ancestral line in the Palaeocene to mid Eocene, some 63-45 million years ago.

Characterization of a molt-inhibiting hormone (MIH) of the crayfish, Orconectes limosus, by cDNA cloning and mass spectrometric analysis.

PubMed

Bulau, Patrick; Okuno, Atsuro; Thome, Elke; Schmitz, Tina; Peter-Katalinic, Jasna; Keller, Rainer

2005-11-01

The structure of the precursor of a molt-inhibiting hormone (MIH) of the American crayfish, Orconectes limosus was determined by cloning of a cDNA based on RNA from the neurosecretory perikarya of the X-organ in the eyestalk ganglia. The open reading frame includes the complete precursor sequence, consisting of a signal peptide of 29, and the MIH sequence of 77 amino acids. In addition, the mature peptide was isolated by HPLC from the neurohemal sinus gland and analyzed by ESI-MS and MALDI-TOF-MS peptide mapping. This showed that the mature peptide (Mass 8664.29 Da) consists of only 75 amino acids, having Ala75-NH2 as C-terminus. Thus, C-terminal Arg77 of the precursor is removed during processing, and Gly76 serves as an amide donor. Sequence comparison confirms this peptide as a novel member of the large family, which includes crustacean hyperglycaemic hormone (CHH), MIH and gonad (vitellogenesis)-inhibiting hormone (GIH/VIH). The lack of a CPRP (CHH-precursor related peptide) in the hormone precursor, the size and specific sequence characteristics show that Orl MIH belongs to the MIH/GIH(VIH) subgroup of this larger family. Comparison with the MIH of Procambarus clarkii, the only other MIH that has thus far been identified in freshwater crayfish, shows extremely high sequence conservation. Both MIHs differ in only one amino acid residue ( approximately 99% identity), whereas the sequence identity to several other known MIHs is between 40 and 46%.

Molecular characterization of an ependymin precursor from goldfish brain.

PubMed

Königstorfer, A; Sterrer, S; Eckerskorn, C; Lottspeich, F; Schmidt, R; Hoffmann, W

1989-01-01

Ependymins are thought to be implicated in fundamental processes involved in plasticity of the goldfish CNS. Gas-phase sequencing of purified ependymins beta and gamma revealed that they share the same N-terminal sequence. Each sequence displays microheterogeneities at several positions. Based on the protein sequences obtained, we constructed synthetic oligonucleotides and used them as hybridization probes for screening cDNA libraries of goldfish brain. In this article we describe the full-length sequence of a mRNA encoding a precursor of ependymins. A cleavable signal sequence characteristic of secretory proteins is located at the N-terminal end, followed directly by the ependymin sequence. Also, two potential N-glycosylation sites were detected. A computer search revealed that ependymins form a novel family of unique proteins.

Discovery of novel representatives of bilaterian neuropeptide families and reconstruction of neuropeptide precursor evolution in ophiuroid echinoderms

PubMed Central

Abylkassimova, Nikara; Hugall, Andrew F.; O'Hara, Timothy D.; Elphick, Maurice R.

2017-01-01

Neuropeptides are a diverse class of intercellular signalling molecules that mediate neuronal regulation of many physiological and behavioural processes. Recent advances in genome/transcriptome sequencing are enabling identification of neuropeptide precursor proteins in species from a growing variety of animal taxa, providing new insights into the evolution of neuropeptide signalling. Here, detailed analysis of transcriptome sequence data from three brittle star species, Ophionotus victoriae, Amphiura filiformis and Ophiopsila aranea, has enabled the first comprehensive identification of neuropeptide precursors in the class Ophiuroidea of the phylum Echinodermata. Representatives of over 30 bilaterian neuropeptide precursor families were identified, some of which occur as paralogues. Furthermore, homologues of endothelin/CCHamide, eclosion hormone, neuropeptide-F/Y and nucleobinin/nesfatin were discovered here in a deuterostome/echinoderm for the first time. The majority of ophiuroid neuropeptide precursors contain a single copy of a neuropeptide, but several precursors comprise multiple copies of identical or non-identical, but structurally related, neuropeptides. Here, we performed an unprecedented investigation of the evolution of neuropeptide copy number over a period of approximately 270 Myr by analysing sequence data from over 50 ophiuroid species, with reference to a robust phylogeny. Our analysis indicates that the composition of neuropeptide ‘cocktails’ is functionally important, but with plasticity over long evolutionary time scales. PMID:28878039

Neuropeptides encoded by the genomes of the Akoya pearl oyster Pinctata fucata and Pacific oyster Crassostrea gigas: a bioinformatic and peptidomic survey.

PubMed

Stewart, Michael J; Favrel, Pascal; Rotgans, Bronwyn A; Wang, Tianfang; Zhao, Min; Sohail, Manzar; O'Connor, Wayne A; Elizur, Abigail; Henry, Joel; Cummins, Scott F

2014-10-02

Oysters impart significant socio-ecological benefits from primary production of food supply, to estuarine ecosystems via reduction of water column nutrients, plankton and seston biomass. Little though is known at the molecular level of what genes are responsible for how oysters reproduce, filter nutrients, survive stressful physiological events and form reef communities. Neuropeptides represent a diverse class of chemical messengers, instrumental in orchestrating these complex physiological events in other species. By a combination of in silico data mining and peptide analysis of ganglia, 74 putative neuropeptide genes were identified from genome and transcriptome databases of the Akoya pearl oyster, Pinctata fucata and the Pacific oyster, Crassostrea gigas, encoding precursors for over 300 predicted bioactive peptide products, including three newly identified neuropeptide precursors PFGx8amide, RxIamide and Wx3Yamide. Our findings also include a gene for the gonadotropin-releasing hormone (GnRH) and two egg-laying hormones (ELH) which were identified from both oysters. Multiple sequence alignments and phylogenetic analysis supports similar global organization of these mature peptides. Computer-based peptide modeling of the molecular tertiary structures of ELH highlights the structural homologies within ELH family, which may facilitate ELH activity leading to the release of gametes. Our analysis demonstrates that oysters possess conserved molluscan neuropeptide domains and overall precursor organization whilst highlighting many previously unrecognized bivalve idiosyncrasies. This genomic analysis provides a solid foundation from which further studies aimed at the functional characterization of these molluscan neuropeptides can be conducted to further stimulate advances in understanding the ecology and cultivation of oysters.

Low-Temperature Molecular Layer Deposition Using Monofunctional Aromatic Precursors and Ozone-Based Ring-Opening Reactions.

PubMed

Svärd, Laura; Putkonen, Matti; Kenttä, Eija; Sajavaara, Timo; Krahl, Fabian; Karppinen, Maarit; Van de Kerckhove, Kevin; Detavernier, Christophe; Simell, Pekka

2017-09-26

Molecular layer deposition (MLD) is an increasingly used deposition technique for producing thin coatings consisting of purely organic or hybrid inorganic-organic materials. When organic materials are prepared, low deposition temperatures are often required to avoid decomposition, thus causing problems with low vapor pressure precursors. Monofunctional compounds have higher vapor pressures than traditional bi- or trifunctional MLD precursors, but do not offer the required functional groups for continuing the MLD growth in subsequent deposition cycles. In this study, we have used high vapor pressure monofunctional aromatic precursors in combination with ozone-triggered ring-opening reactions to achieve sustained sequential growth. MLD depositions were carried out by using three different aromatic precursors in an ABC sequence, namely with TMA + phenol + O 3 , TMA + 3-(trifluoromethyl)phenol + O 3 , and TMA + 2-fluoro-4-(trifluoromethyl)benzaldehyde + O 3 . Furthermore, the effect of hydrogen peroxide as a fourth step was evaluated for all studied processes resulting in a four-precursor ABCD sequence. According to the characterization results by ellipsometry, infrared spectroscopy, and X-ray reflectivity, self-limiting MLD processes could be obtained between 75 and 150 °C with each of the three aromatic precursors. In all cases, the GPC (growth per cycle) decreased with increasing temperature. In situ infrared spectroscopy indicated that ring-opening reactions occurred in each ABC sequence. Compositional analysis using time-of-flight elastic recoil detection indicated that fluorine could be incorporated into the film when 3-(trifluoromethyl)phenol and 2-fluoro-4-(trifluoromethyl)benzaldehyde were used as precursors.

Sequence of a cDNA encoding pancreatic preprosomatostatin-22.

PubMed Central

Magazin, M; Minth, C D; Funckes, C L; Deschenes, R; Tavianini, M A; Dixon, J E

1982-01-01

We report the nucleotide sequence of a precursor to somatostatin that upon proteolytic processing may give rise to a hormone of 22 amino acids. The nucleotide sequence of a cDNA from the channel catfish (Ictalurus punctatus) encodes a precursor to somatostatin that is 105 amino acids (Mr, 11,500). The cDNA coding for somatostatin-22 consists of 36 nucleotides in the 5' untranslated region, 315 nucleotides that code for the precursor to somatostatin-22, 269 nucleotides at the 3' untranslated region, and a variable length of poly(A). The putative preprohormone contains a sequence of hydrophobic amino acids at the amino terminus that has the properties of a "signal" peptide. A connecting sequence of approximately 57 amino acids is followed by a single Arg-Arg sequence, which immediately precedes the hormone. Somatostatin-22 is homologous to somatostatin-14 in 7 of the 14 amino acids, including the Phe-Trp-Lys sequence. Hybridization selection of mRNA, followed by its translation in a wheat germ cell-free system, resulted in the synthesis of a single polypeptide having a molecular weight of approximately 10,000 as estimated on Na-DodSO4/polyacrylamide gels. Images PMID:6127673

Mutations altering the gammaretrovirus endoproteolytic motif affect glycosylation of the envelope glycoprotein and early events of the virus life cycle

DOE Office of Scientific and Technical Information (OSTI.GOV)

Argaw, Takele; Wilson, Carolyn A., E-mail: carolyn.wilson@fda.hhs.gov

Previously, we found that mutation of glutamine to proline in the endoproteolytic cleavage signal of the PERV-C envelope (RQKK to RPKK) resulted in non-infectious vectors. Here, we show that RPKK results in a non-infectious vector when placed in not only a PERV envelope, but also the envelope of a related gammaretrovirus, FeLV-B. The amino acid substitutions do not prevent envelope precursor cleavage, viral core and genome assembly, or receptor binding. Rather, the mutations result in the formation of hyperglycosylated glycoprotein and a reduction in the reverse transcribed minus strand synthesis and undetectable 2-LTR circular DNA in cells exposed to vectorsmore » with these mutated envelopes. Our findings suggest novel functions associated with the cleavage signal sequence that may affect trafficking through the glycosylation machinery of the cell. Further, the glycosylation status of the envelope appears to impact post-binding events of the viral life cycle, either membrane fusion, internalization, or reverse transcription. - Highlights: • Env cleavage signal impacts infectivity of gammaretroviruses. • Non-infectious mutants have hyper-glycosylated envelope that bind target cells. • Non-infectious mutants have defects in the formation of the double-stranded DNA. • Env cleavage motif has functions beyond cleavage of the env precursor.« less

The unconventional antimicrobial peptides of the classical propionibacteria.

PubMed

Faye, Therese; Holo, Helge; Langsrud, Thor; Nes, Ingolf F; Brede, Dag A

2011-02-01

The classical propionibacteria produce genetically unique antimicrobial peptides, whose biological activities are without equivalents, and to which there are no homologous sequences in public databases. In this review, we summarize the genetics, biochemistry, biosynthesis, and biological activities of three extensively studied antimicrobial peptides from propionibacteria. The propionicin T1 peptide constitutes a bona fide example of an unmodified general secretory pathway (sec)-dependent bacteriocin, which is bactericidal towards all tested species of propionibacteria except Propionibacterium freudenreichii. The PAMP antimicrobial peptide represents a novel concept within bacterial antagonism, where an inactive precursor protein is secreted in large amounts, and which activation appears to rely on subsequent processing by proteases in its resident milieu. Propionicin F is a negatively charged bacteriocin that displays an intraspecies bactericidal inhibition spectrum. The biosynthesis of propionicin F appears to proceed through a series of unusual events requiring both N- and C-terminal processing of a precursor protein, which probably requires the radical SAM superfamily enzyme PcfB.

Circular RNA biogenesis can proceed through an exon-containing lariat precursor

PubMed Central

Barrett, Steven P; Wang, Peter L; Salzman, Julia

2015-01-01

Pervasive expression of circular RNA is a recently discovered feature of eukaryotic gene expression programs, yet its function remains largely unknown. The presumed biogenesis of these RNAs involves a non-canonical ‘backsplicing’ event. Recent studies in mammalian cell culture posit that backsplicing is facilitated by inverted repeats flanking the circularized exon(s). Although such sequence elements are common in mammals, they are rare in lower eukaryotes, making current models insufficient to describe circularization. Through systematic splice site mutagenesis and the identification of splicing intermediates, we show that circular RNA in Schizosaccharomyces pombe is generated through an exon-containing lariat precursor. Furthermore, we have performed high-throughput and comprehensive mutagenesis of a circle-forming exon, which enabled us to discover a systematic effect of exon length on RNA circularization. Our results uncover a mechanism for circular RNA biogenesis that may account for circularization in genes that lack noticeable flanking intronic secondary structure. DOI: http://dx.doi.org/10.7554/eLife.07540.001 PMID:26057830

Multiple Mechanisms of Transient Heating Events in the Protoplanetary Disk: Evidence from Precursors of Chondrules and Igneous Ca,Al-Rich Inclusions

NASA Astrophysics Data System (ADS)

Krot, A. N.; Nagashima, K.; Libourel, G.; Miller, K. E.

2017-02-01

Here we review the mineralogy, petrography, O-isotope compositions, and trace element abundances of precursors of chondrules and igneous CAIs which provide important constraints on the mechanisms of transient heating events in the protoplanetary disk.

North Atlantic weather regimes: A synoptic study of phase space. M.S. Thesis

NASA Technical Reports Server (NTRS)

Orrhede, Anna Karin

1990-01-01

In the phase space of weather, low frequency variability (LFV) of the atmosphere can be captured in a large scale subspace, where a trajectory connects consecutive large scale weather maps, thus revealing flow changes and recurrences. Using this approach, Vautard applied the trajectory speed minimization method (Vautard and Legras) to atmospheric data. From 37 winters of 700 mb geopotential height anomalies over the North Atlantic and the adjacent land masses, four persistent and recurrent weather patterns, interpreted as weather regimes, were discernable: a blocking regime, a zonal regime, a Greenland anticyclone regime, and an Atlantic regime. These regimes are studied further in terms of maintenance and transitions. A regime survey unveils preferences regarding event durations and precursors for the onset or break of an event. The transition frequencies between regimes vary, and together with the transition times, suggest the existence of easier transition routes. These matters are more systematically studied using complete synoptic map sequences from a number of events.

Precursors of vertebrate peptide antibiotics dermaseptin b and adenoregulin have extensive sequence identities with precursors of opioid peptides dermorphin, dermenkephalin, and deltorphins.

PubMed

Amiche, M; Ducancel, F; Mor, A; Boulain, J C; Menez, A; Nicolas, P

1994-07-08

The dermaseptins are a family of broad spectrum antimicrobial peptides, 27-34 amino acids long, involved in the defense of the naked skin of frogs against microbial invasion. They are the first vertebrate peptides to show lethal effects against the filamentous fungi responsible for severe opportunistic infections accompanying immunodeficiency syndrome and the use of immunosuppressive agents. A cDNA library was constructed from skin poly(A+) RNA of the arboreal frog Phyllomedusa bicolor and screened with an oligonucleotide probe complementary to the COOH terminus of dermaseptin b. Several clones contained a full-length DNA copy of a 443-nucleotide mRNA that encoded a 78-residue dermaseptin b precursor protein. The deduced precursor contained a putative signal sequence at the NH2 terminus, a 20-residue spacer sequence extremely rich (60%) in glutamic and aspartic acids, and a single copy of a dermaseptin b progenitor sequence at the COOH terminus. One clone contained a complete copy of adenoregulin, a 33-residue peptide reported to enhance the binding of agonists to the A1 adenosine receptor. The mRNAs encoding adenoregulin and dermaseptin b were very similar: 70 and 75% nucleotide identities between the 5'- and 3'-untranslated regions, respectively; 91% amino acid identity between the signal peptides; 82% identity between the acidic spacer sequences; and 38% identity between adenoregulin and dermaseptin b. Because adenoregulin and dermaseptin b have similar precursor designs and antimicrobial spectra, adenoregulin should be considered as a new member of the dermaseptin family and alternatively named dermaseptin b II. Preprodermaseptin b and preproadenoregulin have considerable sequence identities to the precursors encoding the opioid heptapeptides dermorphin, dermenkephalin, and deltorphins. This similarity extended into the 5'-untranslated regions of the mRNAs. These findings suggest that the genes encoding the four preproproteins are all members of the same family despite the fact that they encode end products having very different biological activities. These genes might contain a homologous export exon comprising the 5'-untranslated region, the 22-residue signal peptide, the 20-24-residue acidic spacer, and the basic pair Lys-Arg.

Investigation of phase evolution of CaCu{sub 3}Ti{sub 4}O{sub 12} (CCTO) by in situ synchrotron high-temperature powder diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ouyang, Xin; Huang, Saifang; School of Materials Science and Technology, China University of Geosciences

2014-03-15

In situ synchrotron X-ray powder diffraction was used to study the high-temperature phase evolution of CaCu{sub 3}Ti{sub 4}O{sub 12} (CCTO) precursors prepared via solid-state and sol–gel methods. After the precursors are heated to 1225 °C, the CCTO phase is the main phase observed in the calcined powder, with the presence of some minor impurities. Comparing the two precursors, we found that the onset temperature for the CCTO phase formation is 800 °C in the sol–gel precursor, lower than that in the solid-state precursor (875 °C). Intermediate phases were only observed in the sol–gel precursor. Both precursors are able to bemore » calcined to sub-micrometric sized powders. Based on the synchrotron data along with differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA), the phase formation sequence and mechanism during calcination are proposed in this study. -- Graphical abstract: The in situ synchrotron HT-XRD patterns of CCTO sol–gel and solid-state precursor. Highlights: • Phase formation sequence/mechanism in two CCTO precursors has been established. • Formation temperature of CCTO via sol–gel method is lower than solid-state method. • Intermediate phases are only observed in the sol–gel precursor. • Both precursors are able to be calcined into sub-micrometric sized powders.« less

Cross-correlation analysis of 2012-2014 seismic events in Central-Northern Italy: insights from the geochemical monitoring network of Tuscany

NASA Astrophysics Data System (ADS)

Pierotti, Lisa; Facca, Gianluca; Gherardi, Fabrizio

2015-04-01

Since late 2002, a geochemical monitoring network is operating in Tuscany, Central Italy, to collect data and possibly identify geochemical anomalies that characteristically occur before regionally significant (i.e. with magnitude > 3) seismic events. The network currently consists of 6 stations located in areas already investigated in detail for their geological setting, hydrogeological and geochemical background and boundary conditions. All these stations are equipped for remote, continuous monitoring of selected physicochemical parameters (temperature, pH, redox potential, electrical conductivity), and dissolved concentrations of CO2 and CH4. Additional information are obtained through in situ discrete monitoring. Field surveys are periodically performed to guarantee maintenance and performance control of the sensors of the automatic stations, and to collect water samples for the determination of the chemical and stable isotope composition of all the springs investigated for seismic precursors. Geochemical continuous signals are numerically processed to remove outliers, monitoring errors and aseismic effects from seasonal and climatic fluctuations. The elaboration of smoothed, long-term time series (more than 200000 data available today for each station) allows for a relatively accurate definition of geochemical background values. Geochemical values out of the two-sigma relative standard deviation domain are inspected as possible indicators of physicochemical changes related to regional seismic activity. Starting on November 2011, four stations of the Tuscany network located in two separate mountainous areas of Northern Apennines separating Tuscany from Emilia-Romagna region (Equi Terme and Gallicano), and Tuscany from Emilia-Romagna and Umbria regions (Vicchio and Caprese Michelangelo), started to register anomalous values in pH and CO2 partial pressure (PCO2). Cross-correlation analysis indicates an apparent relationship between the most important seismic events (magnitude >3 up to 5.4) experienced in the Tuscany, Emilia-Romagna and Umbria regions during the period 2012-2014, and these geochemical anomalies. Changes in pH (decreasing) and PCO2 (increasing) are generally observed from a few months to a few weeks before the main shock. This trend has been recognized for the Parma quake of 27 January 2012 (M = 5.4), for the Pieve Fosciana quake of 13 January 2013 (M = 4.8), for the Garfagnana-Lunigiana seismic sequence started June 21, 2013 (Mmax = 5.2), for the Montefeltro seismic sequence started July 11, 2013 (Mmax = 3.9), for the Gubbio seismic sequences of July and December 2013 (Mmax = 3.9), for the Città di Castello seismic sequences of April 2013 and December 2013 (Mmax = 3.9), for the Casentino seismic sequence started October 17, 2014 (Mmax = 3.5), and for the Chianti seismic sequence started December 19, 2014 (Mmax = 4.1). These features suggest that the selected mineral springs can be considered as appropriate sites for the search of geochemical earthquake precursors. Further investigations focused on in-depth analysis of signals are currently in progress.

Characterization of Urtica dioica agglutinin isolectins and the encoding gene family.

PubMed

Does, M P; Ng, D K; Dekker, H L; Peumans, W J; Houterman, P M; Van Damme, E J; Cornelissen, B J

1999-01-01

Urtica dioica agglutinin (UDA) has previously been found in roots and rhizomes of stinging nettles as a mixture of UDA-isolectins. Protein and cDNA sequencing have shown that mature UDA is composed of two hevein domains and is processed from a precursor protein. The precursor contains a signal peptide, two in-tandem hevein domains, a hinge region and a carboxyl-terminal chitinase domain. Genomic fragments encoding precursors for UDA-isolectins have been amplified by five independent polymerase chain reactions on genomic DNA from stinging nettle ecotype Weerselo. One amplified gene was completely sequenced. As compared to the published cDNA sequence, the genomic sequence contains, besides two basepair substitutions, two introns located at the same positions as in other plant chitinases. By partial sequence analysis of 40 amplified genes, 16 different genes were identified which encode seven putative UDA-isolectins. The deduced amino acid sequences share 78.9-98.9% identity. In extracts of roots and rhizomes of stinging nettle ecotype Weerselo six out of these seven isolectins were detected by mass spectrometry. One of them is an acidic form, which has not been identified before. Our results demonstrate that UDA is encoded by a large gene family.

Discovery and Characterization of Novel Cyclotides Originated from Chimeric Precursors Consisting of Albumin-1 Chain a and Cyclotide Domains in the Fabaceae Family*

PubMed Central

Nguyen, Giang Kien Truc; Zhang, Sen; Nguyen, Ngan Thi Kim; Nguyen, Phuong Quoc Thuc; Chiu, Ming Sheau; Hardjojo, Antony; Tam, James P.

2011-01-01

The tropical plant Clitoria ternatea is a member of the Fabaceae family well known for its medicinal values. Heat extraction of C. ternatea revealed that the bioactive fractions contained heat-stable cysteine-rich peptides (CRPs). The CRP family of A1b (Albumin-1 chain b/leginsulins), which is a linear cystine knot CRP, has been shown to present abundantly in the Fabaceae. In contrast, the cyclotide family, which also belongs to the cystine knot CRPs but with a cyclic structure, is commonly found in the Rubiaceae, Violaceae, and Cucurbitaceae families. In this study, we report the discovery of a panel of 15 heat-stable CRPs, of which 12 sequences (cliotide T1–T12) are novel. We show unambiguously that the cliotides are cyclotides and not A1bs, as determined by their sequence homology, disulfide connectivity, and membrane active properties indicated by their antimicrobial activities against Escherichia coli and cytotoxicities to HeLa cells. We also show that cliotides are prevalent in C. ternatea and are found in every plant tissue examined, including flowers, seeds, and nodules. In addition, we demonstrate that their precursors are chimeras, half from cyclotide and the other half from Albumin-1, with the cyclotide domain displacing the A1b domain in the precursor. Their chimeric structures likely originate from either horizontal gene transfer or convergent evolution in plant nuclear genomes, which are exceedingly rare events. Such atypical genetic arrangement also implies a different mechanism of biosynthetic processing of cyclotides in the Fabaceae and provides new understanding of their evolution in plants. PMID:21596752

An Internal Signal Sequence Directs Intramembrane Proteolysis of a Cellular Immunoglobulin Domain Protein*S⃞

PubMed Central

Robakis, Thalia; Bak, Beata; Lin, Shu-huei; Bernard, Daniel J.; Scheiffele, Peter

2008-01-01

Precursor proteolysis is a crucial mechanism for regulating protein structure and function. Signal peptidase (SP) is an enzyme with a well defined role in cleaving N-terminal signal sequences but no demonstrated function in the proteolysis of cellular precursor proteins. We provide evidence that SP mediates intraprotein cleavage of IgSF1, a large cellular Ig domain protein that is processed into two separate Ig domain proteins. In addition, our results suggest the involvement of signal peptide peptidase (SPP), an intramembrane protease, which acts on substrates that have been previously cleaved by SP. We show that IgSF1 is processed through sequential proteolysis by SP and SPP. Cleavage is directed by an internal signal sequence and generates two separate Ig domain proteins from a polytopic precursor. Our findings suggest that SP and SPP function are not restricted to N-terminal signal sequence cleavage but also contribute to the processing of cellular transmembrane proteins. PMID:18981173

Human adenovirus serotype 12 virion precursors pMu and pVI are cleaved at amino-terminal and carboxy-terminal sites that conform to the adenovirus 2 endoproteinase cleavage consensus sequence.

PubMed

Freimuth, P; Anderson, C W

1993-03-01

The sequence of a 1158-base pair fragment of the human adenovirus serotype 12 (Ad12) genome was determined. This segment encodes the precursors for virion components Mu and VI. Both Ad12 precursors contain two sequences that conform to a consensus sequence motif for cleavage by the endoproteinase of adenovirus 2 (Ad2). Analysis of the amino terminus of VI and of the peptide fragments found in Ad12 virions demonstrated that these sites are cleaved during Ad12 maturation. This observation suggests that the recognition motif for adenovirus endoproteinases is highly conserved among human serotypes. The adenovirus 2 endoproteinase polypeptide requires additional co-factors for activity (C. W. Anderson, Protein Expression Purif., 1993, 4, 8-15). Synthetic Ad12 or Ad2 pVI carboxy-terminal peptides each permitted efficient cleavage of an artificial endoproteinase substrate by recombinant Ad2 endoproteinase polypeptide.

Unraveling the Stepwise Melting of an Ionic Liquid.

PubMed

Lima, Thamires A; Paschoal, Vitor H; Faria, Luiz F O; Ribeiro, Mauro C C

2017-05-04

Differential scanning calorimetry, X-ray diffraction, and Raman spectroscopy were used to reveal the premelting events precursors of melting of the ionic liquid triethylsulfonium bis(trifluoromethanesufonyl)imide, [S 222 ][NTf 2 ]. On heating the crystalline phase of [S 222 ][NTf 2 ], melting occurs along a sequence of at least three steps. First, the crystalline long-range order breaks down, but local order is retained. The second step is characterized by conformational freedom of the ethyl chains of cations related to premelting of nonpolar domains, and the complete melting finally occurs when anions acquire conformational freedom. This work provides a microscopic view on the mechanism of melting of [S 222 ][NTf 2 ] in line with the picture of melting taking place as a sequence of structural changes. The results of this work shed light on the understanding of the complex melting process of ionic liquids.

Multipurpose Dissociation Cell for Enhanced ETD of Intact Protein Species

PubMed Central

Rose, Christopher M.; Russell, Jason D.; Ledvina, Aaron R.; McAlister, Graeme C.; Westphall, Michael S.; Griep-Raming, Jens; Schwartz, Jae C.; Coon, Joshua J.; Syka, John E.P.

2013-01-01

We describe and characterize an improved implementation of ETD on a modified hybrid linear ion trap-Orbitrap instrument. Instead of performing ETD in the mass-analyzing quadrupole linear ion trap (A-QLT), the instrument collision cell was modified to enable ETD. We partitioned the collision cell into a multi-section RF ion storage and transfer device to enable injection and simultaneous separate storage of precursor and reagent ions. Application of a secondary (axial) confinement voltage to the cell end lens electrodes enables charge-sign independent trapping for ion-ion reactions. The approximately two-fold higher quadrupole field frequency of this cell relative to that of the A-QLT, enables higher reagent ion densities and correspondingly faster ETD reactions, and, with the collision cell’s longer axial dimensions, larger populations of precursor ions may be reacted. The higher ion capacity of the collision cell permits the accumulation and reaction of multiple full loads of precursor ions from the A-QLT followed by FT Orbitrap m/z analysis of the ETD product ions. This extends the intra-scan dynamic range by increasing the maximum number of product ions in a single MS/MS event. For analyses of large peptide/small protein precursor cations, this reduces or eliminates the need for spectral averaging to achieve acceptable ETD product ion signal-to-noise levels. Using larger ion populations, we demonstrate improvements in protein sequence coverage and aggregate protein identifications in LC-MS/MS analysis of intact protein species as compared to the standard ETD implementation. PMID:23609185

Peptidomic analysis of the extensive array of host-defense peptides in skin secretions of the dodecaploid frog Xenopus ruwenzoriensis (Pipidae).

PubMed

Coquet, Laurent; Kolodziejek, Jolanta; Jouenne, Thierry; Nowotny, Norbert; King, Jay D; Conlon, J Michael

2016-09-01

The Uganda clawed frog Xenopus ruwenzoriensis with a karyotype of 2n=108 is one of the very few vertebrates with dodecaploid status. Peptidomic analysis of norepinephrine-stimulated skin secretions from this species led to the isolation and structural characterization of 23 host-defense peptides belonging to the following families: magainin (3 peptides), peptide glycine-leucine-amide (PGLa; 6 peptides), xenopsin precursor fragment (XPF; 3 peptides), caerulein precursor fragment (CPF; 8 peptides), and caerulein precursor fragment-related peptide (CPF-RP; 3 peptides). In addition, the secretions contained caerulein, identical to the peptide from Xenopus laevis, and two peptides that were identified as members of the trefoil factor family (TFF). The data indicate that silencing of the host-defense peptide genes following polyploidization has been appreciable and non-uniform. Consistent with data derived from comparison of nucleotide sequences of mitochrondrial and nuclear genes, cladistic analyses based upon the primary structures of the host-defense peptides provide support for an evolutionary scenario in which X. ruwenzoriensis arose from an allopolyploidization event involving an octoploid ancestor of the present-day frogs belonging to the Xenopus amieti species group and a tetraploid ancestor of Xenopus pygmaeus. Copyright © 2016 Elsevier Inc. All rights reserved.

What’s bad in cancer is good in the embryo: Importance of EMT in neural crest development

PubMed Central

Kerosuo, Laura; Bronner-Fraser, Marianne

2012-01-01

Although the epithelial to mesenchymal transition (EMT) is famous for its role in cancer metastasis, it also is a normal developmental event in which epithelial cells are converted into migratory mesenchymal cells. A prime example of EMT during development occurs when neural crest (NC) cells emigrate from the neural tube thus providing an excellent model to study the principles of EMT in a nonmalignant environment. NC cells start life as neuroepithelial cells intermixed with precursors of the central nervous system. After EMT, they delaminate and begin migrating, often to distant sites in the embryo. While proliferating and maintaining multipotency and cell survival the transitioning neural crest cells lose apicobasal polarity and the basement membrane is broken down. This review discusses how these events are coordinated and regulated, by series of events involving signaling factors, gene regulatory interactions, as well as epigenetic and post-transcriptional modifications. Even though the series of events involved in NC EMT are well known, the sequence in which these steps take place remains a subject of debate, raising the intriguing possibility that, rather than being a single event, neural crest EMT may involve multiple parallel mechanisms. PMID:22430756

Molecular cloning of a cDNA encoding the precursor of adenoregulin from frog skin. Relationships with the vertebrate defensive peptides, dermaseptins.

PubMed

Amiche, M; Ducancel, F; Lajeunesse, E; Boulain, J C; Ménez, A; Nicolas, P

1993-03-31

Adenoregulin has recently been isolated from Phyllomedusa skin as a 33 amino acid residues peptide which enhanced binding of agonists to the A1 adenosine receptor. In order to study the structure of the precursor of adenoregulin we constructed a cDNA library from mRNAs extracted from the skin of Phyllomedusa bicolor. We detected the complete nucleotide sequence of a cDNA encoding the adenoregulin biosynthetic precursor. The deduced sequence of the precursor is 81 amino acids long, exhibits a putative signal sequence at the NH2 terminus and contains a single copy of the biologically active peptide at the COOH terminus. Structural and conformational homologies that are observed between adenoregulin and the dermaseptins, antimicrobial peptides exhibiting strong membranolytic activities against various pathogenic agents, suggest that adenoregulin is an additional member of the growing family of cytotropic antimicrobial peptides that allow vertebrate animals to defend themselves against microorganisms. As such, the adenosine receptor regulating activity of adenoregulin could be due to its ability to interact with and disrupt membranes lipid bilayers.

Amyloid-like aggregation of provasopressin in diabetes insipidus and secretory granule sorting.

PubMed

Beuret, Nicole; Hasler, Franziska; Prescianotto-Baschong, Cristina; Birk, Julia; Rutishauser, Jonas; Spiess, Martin

2017-01-26

Aggregation of peptide hormone precursors in the trans-Golgi network is an essential process in the biogenesis of secretory granules in endocrine cells. It has recently been proposed that this aggregation corresponds to the formation of functional amyloids. Our previous finding that dominant mutations in provasopressin, which cause cell degeneration and diabetes insipidus, prevent native folding and produce fibrillar aggregates in the endoplasmic reticulum (ER) might thus reflect mislocalized amyloid formation by sequences that evolved to mediate granule sorting. Here we identified two sequences responsible for fibrillar aggregation of mutant precursors in the ER: the N-terminal vasopressin nonapeptide and the C-terminal glycopeptide. To test their role in granule sorting, the glycopeptide was deleted and/or vasopressin mutated to inactivate ER aggregation while still permitting precursor folding and ER exit. These mutations strongly reduced sorting into granules and regulated secretion in endocrine AtT20 cells. The same sequences - vasopressin and the glycopeptide - mediate physiological aggregation of the wild-type hormone precursor into secretory granules and the pathological fibrillar aggregation of disease mutants in the ER. These findings support the amyloid hypothesis for secretory granule biogenesis.

Partial structure of the phylloxin gene from the giant monkey frog, Phyllomedusa bicolor: parallel cloning of precursor cDNA and genomic DNA from lyophilized skin secretion.

PubMed

Chen, Tianbao; Gagliardo, Ron; Walker, Brian; Zhou, Mei; Shaw, Chris

2005-12-01

Phylloxin is a novel prototype antimicrobial peptide from the skin of Phyllomedusa bicolor. Here, we describe parallel identification and sequencing of phylloxin precursor transcript (mRNA) and partial gene structure (genomic DNA) from the same sample of lyophilized skin secretion using our recently-described cloning technique. The open-reading frame of the phylloxin precursor was identical in nucleotide sequence to that previously reported and alignment with the nucleotide sequence derived from genomic DNA indicated the presence of a 175 bp intron located in a near identical position to that found in the dermaseptins. The highly-conserved structural organization of skin secretion peptide genes in P. bicolor can thus be extended to include that encoding phylloxin (plx). These data further reinforce our assertion that application of the described methodology can provide robust genomic/transcriptomic/peptidomic data without the need for specimen sacrifice.

MicroRNA: Biogenesis, Function and Role in Cancer

PubMed Central

MacFarlane, Leigh-Ann; Murphy, Paul R.

2010-01-01

MicroRNAs are small, highly conserved non-coding RNA molecules involved in the regulation of gene expression. MicroRNAs are transcribed by RNA polymerases II and III, generating precursors that undergo a series of cleavage events to form mature microRNA. The conventional biogenesis pathway consists of two cleavage events, one nuclear and one cytoplasmic. However, alternative biogenesis pathways exist that differ in the number of cleavage events and enzymes responsible. How microRNA precursors are sorted to the different pathways is unclear but appears to be determined by the site of origin of the microRNA, its sequence and thermodynamic stability. The regulatory functions of microRNAs are accomplished through the RNA-induced silencing complex (RISC). MicroRNA assembles into RISC, activating the complex to target messenger RNA (mRNA) specified by the microRNA. Various RISC assembly models have been proposed and research continues to explore the mechanism(s) of RISC loading and activation. The degree and nature of the complementarity between the microRNA and target determine the gene silencing mechanism, slicer-dependent mRNA degradation or slicer-independent translation inhibition. Recent evidence indicates that P-bodies are essential for microRNA-mediated gene silencing and that RISC assembly and silencing occurs primarily within P-bodies. The P-body model outlines microRNA sorting and shuttling between specialized P-body compartments that house enzymes required for slicer –dependent and –independent silencing, addressing the reversibility of these silencing mechanisms. Detailed knowledge of the microRNA pathways is essential for understanding their physiological role and the implications associated with dysfunction and dysregulation. PMID:21532838

Variation in a surface-exposed region of the Mycoplasma pneumoniae P40 protein as a consequence of homologous DNA recombination between RepMP5 elements.

PubMed

Spuesens, Emiel B M; van de Kreeke, Nick; Estevão, Silvia; Hoogenboezem, Theo; Sluijter, Marcel; Hartwig, Nico G; van Rossum, Annemarie M C; Vink, Cornelis

2011-02-01

Mycoplasma pneumoniae is a human pathogen that causes a range of respiratory tract infections. The first step in infection is adherence of the bacteria to the respiratory epithelium. This step is mediated by a specialized organelle, which contains several proteins (cytadhesins) that have an important function in adherence. Two of these cytadhesins, P40 and P90, represent the proteolytic products from a single 130 kDa protein precursor, which is encoded by the MPN142 gene. Interestingly, MPN142 contains a repetitive DNA element, termed RepMP5, of which homologues are found at seven other loci within the M. pneumoniae genome. It has been hypothesized that these RepMP5 elements, which are similar but not identical in sequence, recombine with their counterpart within MPN142 and thereby provide a source of sequence variation for this gene. As this variation may give rise to amino acid changes within P40 and P90, the recombination between RepMP5 elements may constitute the basis of antigenic variation and, possibly, immune evasion by M. pneumoniae. To investigate the sequence variation of MPN142 in relation to inter-RepMP5 recombination, we determined the sequences of all RepMP5 elements in a collection of 25 strains. The results indicate that: (i) inter-RepMP5 recombination events have occurred in seven of the strains, and (ii) putative RepMP5 recombination events involving MPN142 have induced amino acid changes in a surface-exposed part of the P40 protein in two of the strains. We conclude that recombination between RepMP5 elements is a common phenomenon that may lead to sequence variation of MPN142-encoded proteins.

Spectroscopic determination of thermal impulse in sub-second heating events using lanthanide-doped oxide precursors and phenomenological modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Benjamin R., E-mail: branderson@wsu.edu; Gunawidjaja, Ray; Price, Patrick

2016-08-28

Using a mixture of crystalline-Ho:ZrO{sub 2}, precursor-Dy:Y{sub 2}O{sub 3}, and precursor-Eu:ZrO{sub 2} nanoparticles we develop thermal impulse sensors capable of measuring equivalent isothermal temperatures and durations during a heating event, with response times of <100 ms, and a temperature range of at least 673 K to 1173 K. In order to determine the temperature and duration from the sensors after the heating event we measure the sensors' fluorescence spectrum, which is then compared with lab based calibration data. By using two precursor materials with different reaction kinetics we are able to extract both temperature and duration. Based on blind sample testing we findmore » that the sensors and calculation method are accurate for measuring temperature and duration, but currently suffer a lack of precision due to difficulties in producing homogeneously heated samples.« less

High-Throughput Sequencing of Arabidopsis microRNAs: Evidence for Frequent Birth and Death of MIRNA Genes

PubMed Central

Fahlgren, Noah; Howell, Miya D.; Kasschau, Kristin D.; Chapman, Elisabeth J.; Sullivan, Christopher M.; Cumbie, Jason S.; Givan, Scott A.; Law, Theresa F.; Grant, Sarah R.; Dangl, Jeffery L.; Carrington, James C.

2007-01-01

In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep sequencing and computational methods to identify, profile and analyze non-conserved MIRNA genes in Arabidopsis thaliana. 48 non-conserved MIRNA families, nearly all of which were represented by single genes, were identified. Sequence similarity analyses of miRNA precursor foldback arms revealed evidence for recent evolutionary origin of 16 MIRNA loci through inverted duplication events from protein-coding gene sequences. Interestingly, these recently evolved MIRNA genes have taken distinct paths. Whereas some non-conserved miRNAs interact with and regulate target transcripts from gene families that donated parental sequences, others have drifted to the point of non-interaction with parental gene family transcripts. Some young MIRNA loci clearly originated from one gene family but form miRNAs that target transcripts in another family. We suggest that MIRNA genes are undergoing relatively frequent birth and death, with only a subset being stabilized by integration into regulatory networks. PMID:17299599

RNAi Mediated curcin precursor gene silencing in Jatropha (Jatropha curcas L.).

PubMed

Patade, Vikas Yadav; Khatri, Deepti; Kumar, Kamal; Grover, Atul; Kumari, Maya; Gupta, Sanjay Mohan; Kumar, Devender; Nasim, Mohammed

2014-07-01

Curcin, a type I ribosomal inhibiting protein-RIP, encoded by curcin precursor gene, is a phytotoxin present in Jatropha (Jatropha curcas L.). Here, we report designing of RNAi construct for the curcin precursor gene and further its genetic transformation of Jatropha to reduce its transcript expression. Curcin precursor gene was first cloned from Jatropha strain DARL-2 and part of the gene sequence was cloned in sense and antisense orientation separated by an intron sequence in plant expression binary vector pRI101 AN. The construction of the RNAi vector was confirmed by double digestion and nucleotide sequencing. The vector was then mobilized into Agrobacterium tumefaciens strain GV 3101 and used for tissue culture independent in planta transformation protocol optimized for Jatropha. Germinating seeds were injured with a needle before infection with Agrobacterium and then transferred to sterilized sand medium. The seedlings were grown for 90 days and genomic DNA was isolated from leaves for transgenic confirmation based on real time PCR with NPT II specific dual labeled probe. Result of the transgenic confirmation analysis revealed presence of the gene silencing construct in ten out of 30 tested seedlings. Further, quantitative transcript expression analysis of the curcin precursor gene revealed reduction in the transcript abundance by more than 98% to undetectable level. The transgenic plants are being grown in containment for further studies on reduction in curcin protein content in Jatropha seeds.

CID-miRNA: A web server for prediction of novel miRNA precursors in human genome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tyagi, Sonika; Vaz, Candida; Gupta, Vipin

2008-08-08

microRNAs (miRNA) are a class of non-protein coding functional RNAs that are thought to regulate expression of target genes by direct interaction with mRNAs. miRNAs have been identified through both experimental and computational methods in a variety of eukaryotic organisms. Though these approaches have been partially successful, there is a need to develop more tools for detection of these RNAs as they are also thought to be present in abundance in many genomes. In this report we describe a tool and a web server, named CID-miRNA, for identification of miRNA precursors in a given DNA sequence, utilising secondary structure-based filteringmore » systems and an algorithm based on stochastic context free grammar trained on human miRNAs. CID-miRNA analyses a given sequence using a web interface, for presence of putative miRNA precursors and the generated output lists all the potential regions that can form miRNA-like structures. It can also scan large genomic sequences for the presence of potential miRNA precursors in its stand-alone form. The web server can be accessed at (http://mirna.jnu.ac.in/cidmirna/)« less

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences.

PubMed

Nasser, Waleed; Beres, Stephen B; Olsen, Randall J; Dean, Melissa A; Rice, Kelsey A; Long, S Wesley; Kristinsson, Karl G; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A; Steinbakk, Martin; Low, Donald E; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A; Hoffmann, Steen; Musser, James M

2014-04-29

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD(+)-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide.

Evolutionary pathway to increased virulence and epidemic group A Streptococcus disease derived from 3,615 genome sequences

PubMed Central

Nasser, Waleed; Beres, Stephen B.; Olsen, Randall J.; Dean, Melissa A.; Rice, Kelsey A.; Long, S. Wesley; Kristinsson, Karl G.; Gottfredsson, Magnus; Vuopio, Jaana; Raisanen, Kati; Caugant, Dominique A.; Steinbakk, Martin; Low, Donald E.; McGeer, Allison; Darenberg, Jessica; Henriques-Normark, Birgitta; Van Beneden, Chris A.; Hoffmann, Steen; Musser, James M.

2014-01-01

We sequenced the genomes of 3,615 strains of serotype Emm protein 1 (M1) group A Streptococcus to unravel the nature and timing of molecular events contributing to the emergence, dissemination, and genetic diversification of an unusually virulent clone that now causes epidemic human infections worldwide. We discovered that the contemporary epidemic clone emerged in stepwise fashion from a precursor cell that first contained the phage encoding an extracellular DNase virulence factor (streptococcal DNase D2, SdaD2) and subsequently acquired the phage encoding the SpeA1 variant of the streptococcal pyrogenic exotoxin A superantigen. The SpeA2 toxin variant evolved from SpeA1 by a single-nucleotide change in the M1 progenitor strain before acquisition by horizontal gene transfer of a large chromosomal region encoding secreted toxins NAD+-glycohydrolase and streptolysin O. Acquisition of this 36-kb region in the early 1980s into just one cell containing the phage-encoded sdaD2 and speA2 genes was the final major molecular event preceding the emergence and rapid intercontinental spread of the contemporary epidemic clone. Thus, we resolve a decades-old controversy about the type and sequence of genomic alterations that produced this explosive epidemic. Analysis of comprehensive, population-based contemporary invasive strains from seven countries identified strong patterns of temporal population structure. Compared with a preepidemic reference strain, the contemporary clone is significantly more virulent in nonhuman primate models of pharyngitis and necrotizing fasciitis. A key finding is that the molecular evolutionary events transpiring in just one bacterial cell ultimately have produced millions of human infections worldwide. PMID:24733896

Using Markov chains of nucleotide sequences as a possible precursor to predict functional roles of human genome: a case study on inactive chromatin regions.

PubMed

Lee, K-E; Lee, E-J; Park, H-S

2016-08-30

Recent advances in computational epigenetics have provided new opportunities to evaluate n-gram probabilistic language models. In this paper, we describe a systematic genome-wide approach for predicting functional roles in inactive chromatin regions by using a sequence-based Markovian chromatin map of the human genome. We demonstrate that Markov chains of sequences can be used as a precursor to predict functional roles in heterochromatin regions and provide an example comparing two publicly available chromatin annotations of large-scale epigenomics projects: ENCODE project consortium and Roadmap Epigenomics consortium.

Immunohistochemical localization of beta-amyloid precursor protein sequences in Alzheimer and normal brain tissue by light and electron microscopy.

PubMed

McGeer, P L; Akiyama, H; Kawamata, T; Yamada, T; Walker, D G; Ishii, T

1992-03-01

Immunohistochemical staining with antibodies directed against four segments of the amyloid precursor protein (APP) was studied by light and electron microscopy in normal and Alzheimer (AD) brain tissue. The segments according to the Kang et al. sequence were: 18-38 (T97); 527-540 (R36); 597-620 (1-24 of beta-amyloid protein [BAP], R17); and 681-695 (R37) (Kang et al. [1987]: Nature 325:733-736). The antibodies recognized full length APP in Western blots of extracts of APP transfected cells. They stained cytoplasmic granules in some pyramidal neurons in normal appearing tissue from control and AD cases. In AD affected tissue, the antibodies to amino terminal sections of APP stained tangled neurons and neuropil threads, and intensely stained dystrophic neurites in senile plaques. By electron microscopy, this staining was localized to abnormal filaments. The antibody to the carboxy terminal segment failed to stain neurofibrillary tangles or neuropil threads; it did stain some neurites with globular swellings. It also stained globular and elongated deposits in senile plaque areas. The antibody against the BAP intensely stained extracellular material in senile plaques and diffuse deposits. By electron microscopy, the antibodies all stained intramicroglial deposits. Some of the extracellular and intracellular BAP-positive deposits were fibrillary. Communication between intramicroglial and extracellular fibrils was detected in plaque areas. These data suggest the following sequence of events. APP is normally concentrated in intraneuronal granules. In AD, it accumulates in damaged neuronal fibers. The amino terminal portion binds to abnormal neurofilaments. Major fragments of APP are phagocytosed and processed by microglia with the BAP portion being preserved. The preserved BAP is then extruded and accumulates in extracellular tissue.

Uncoupling GP1 and GP2 Expression in the Lassa Virus Glycoprotein Complex: Implications for GP1 Ectodomain Shedding

DTIC Science & Technology

2008-12-23

glycoprotein precursor (GPC) signal peptide (SP) or human IgG signal sequences (s.s.). GP2 was secreted from cells only when (1) the transmembrane (TM) domain... peptide (SP) or human IgG signal sequences (s.s.). GP2 was secreted from cells only when (1) the transmembrane (TM) domain was deleted, the...terminal signal peptide (SP), which directs the precursor to the endoplasmic retic- ulum (ER) for further processing [11]. The SP, which has been

Creep and slip: Seismic precursors to the Nuugaatsiaq landslide (Greenland)

NASA Astrophysics Data System (ADS)

Poli, Piero

2017-09-01

Precursory signals to material's failure are predicted by numerical models and observed in laboratory experiments or using field data. These precursory signals are a marker of slip acceleration on weak regions, such as crustal faults. Observation of these precursory signals of catastrophic natural events, such as earthquakes and landslides, is necessary for improving our knowledge about the physics of the nucleation process. Furthermore, observing such precursory signals may help to forecast these catastrophic events or reduce their hazard. I report here the observation of seismic precursors to the Nuugaatsiaq landslide in Greenland. Time evolution of the detected precursors implies that an aseismic slip event is taking place for hours before the landslide, with an exponential increase of slip velocity. Furthermore, time evolution of the precursory signals' amplitude sheds light on the evolution of the fault physics during the nucleation process.

Sequence-based design of bioactive small molecules that target precursor microRNAs.

PubMed

Velagapudi, Sai Pradeep; Gallo, Steven M; Disney, Matthew D

2014-04-01

Oligonucleotides are designed to target RNA using base pairing rules, but they can be hampered by poor cellular delivery and nonspecific stimulation of the immune system. Small molecules are preferred as lead drugs or probes but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA hairpin precursors, and it identified bioactive small molecules that inhibit biogenesis by binding nuclease-processing sites (44% hit rate). Among 27 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Markedly, microRNA profiling shows that 1 only affects microRNA-96 biogenesis and is at least as selective as an oligonucleotide.

Sequence-based design of bioactive small molecules that target precursor microRNAs

PubMed Central

Velagapudi, Sai Pradeep; Gallo, Steven M.; Disney, Matthew D.

2014-01-01

Oligonucleotides are designed to target RNA using base pairing rules, however, they are hampered by poor cellular delivery and non-specific stimulation of the immune system. Small molecules are preferred as lead drugs or probes, but cannot be designed from sequence. Herein, we describe an approach termed Inforna that designs lead small molecules for RNA from solely sequence. Inforna was applied to all human microRNA precursors and identified bioactive small molecules that inhibit biogenesis by binding to nuclease processing sites (41% hit rate). Amongst 29 lead interactions, the most avid interaction is between a benzimidazole (1) and precursor microRNA-96. Compound 1 selectively inhibits biogenesis of microRNA-96, upregulating a protein target (FOXO1) and inducing apoptosis in cancer cells. Apoptosis is ablated when FOXO1 mRNA expression is knocked down by an siRNA, validating compound selectivity. Importantly, microRNA profiling shows that 1 only significantly effects microRNA-96 biogenesis and is more selective than an oligonucleotide. PMID:24509821

Proteolytic processing of the vitellogenin precursor in the boll weevil, Anthonomus grandis.

PubMed

Heilmann, L J; Trewitt, P M; Kumaran, A K

1993-01-01

The soluble proteins of the eggs of the coleopteran insect Anthonomus grandis Boheman, the cotton boll weevil, consist almost entirely of two vitellin types with M(r)s of 160,000 and 47,000. We sequenced their N-terminal ends and one internal cyanogen bromide fragment of the large vitellin and compared these sequences with the deduced amino acid sequence from the vitellogenin gene. The results suggest that both the boll weevil vitellin proteins are products of the proteolytic cleavage of a single precursor protein. The smaller 47,000 M(r) vitellin protein is derived from the N-terminal portion of the precursor adjacent to an 18 amino acid signal peptide. The cleavage site between the large and small vitellins at amino acid 362 is adjacent to a pentapeptide sequence containing two pairs of arginine residues. Comparison of the boll weevil sequences with limited known sequences from the single 180,000 M(r) honey bee protein show that the honey bee vitellin N-terminal exhibits sequence homology to the N-terminal of the 47,000 M(r) boll weevil vitellin. Treatment of the vitellins with an N-glycosidase results in a decrease in molecular weight of both proteins, from 47,000 to 39,000 and from 160,000 to 145,000, indicating that about 10-15% of the molecular weight of each vitellin consists of N-linked carbohydrate. The molecular weight of the deglycosylated large vitellin is smaller than that predicted from the gene sequence, indicating possible further proteolytic processing at the C-terminal of that protein.

Whole-Genome Sequencing for Optimized Patient Management

PubMed Central

Bainbridge, Matthew N.; Wiszniewski, Wojciech; Murdock, David R.; Friedman, Jennifer; Gonzaga-Jauregui, Claudia; Newsham, Irene; Reid, Jeffrey G.; Fink, John K.; Morgan, Margaret B.; Gingras, Marie-Claude; Muzny, Donna M.; Hoang, Linh D.; Yousaf, Shahed; Lupski, James R.; Gibbs, Richard A.

2012-01-01

Whole-genome sequencing of patient DNA can facilitate diagnosis of a disease, but its potential for guiding treatment has been under-realized. We interrogated the complete genome sequences of a 14-year-old fraternal twin pair diagnosed with dopa (3,4-dihydroxyphenylalanine)–responsive dystonia (DRD; Mendelian Inheritance in Man #128230). DRD is a genetically heterogeneous and clinically complex movement disorder that is usually treated with l-dopa, a precursor of the neurotransmitter dopamine. Whole-genome sequencing identified compound heterozygous mutations in the SPR gene encoding sepiapterin reductase. Disruption of SPR causes a decrease in tetrahydrobiopterin, a cofactor required for the hydroxylase enzymes that synthesize the neurotransmitters dopamine and serotonin. Supplementation of l-dopa therapy with 5-hydroxytryptophan, a serotonin precursor, resulted in clinical improvements in both twins. PMID:21677200

Real-time eruption forecasting using the material Failure Forecast Method with a Bayesian approach

NASA Astrophysics Data System (ADS)

Boué, A.; Lesage, P.; Cortés, G.; Valette, B.; Reyes-Dávila, G.

2015-04-01

Many attempts for deterministic forecasting of eruptions and landslides have been performed using the material Failure Forecast Method (FFM). This method consists in adjusting an empirical power law on precursory patterns of seismicity or deformation. Until now, most of the studies have presented hindsight forecasts based on complete time series of precursors and do not evaluate the ability of the method for carrying out real-time forecasting with partial precursory sequences. In this study, we present a rigorous approach of the FFM designed for real-time applications on volcano-seismic precursors. We use a Bayesian approach based on the FFM theory and an automatic classification of seismic events. The probability distributions of the data deduced from the performance of this classification are used as input. As output, it provides the probability of the forecast time at each observation time before the eruption. The spread of the a posteriori probability density function of the prediction time and its stability with respect to the observation time are used as criteria to evaluate the reliability of the forecast. We test the method on precursory accelerations of long-period seismicity prior to vulcanian explosions at Volcán de Colima (Mexico). For explosions preceded by a single phase of seismic acceleration, we obtain accurate and reliable forecasts using approximately 80% of the whole precursory sequence. It is, however, more difficult to apply the method to multiple acceleration patterns.

MicroRNA-like RNAs from the same miRNA precursors play a role in cassava chilling responses.

PubMed

Zeng, Changying; Xia, Jing; Chen, Xin; Zhou, Yufei; Peng, Ming; Zhang, Weixiong

2017-12-07

MicroRNAs (miRNAs) are known to play important roles in various cellular processes and stress responses. MiRNAs can be identified by analyzing reads from high-throughput deep sequencing. The reads realigned to miRNA precursors besides canonical miRNAs were initially considered as sequencing noise and ignored from further analysis. Here we reported a small-RNA species of phased and half-phased miRNA-like RNAs different from canonical miRNAs from cassava miRNA precursors detected under four distinct chilling conditions. They can form abundant multiple small RNAs arranged along precursors in a tandem and phased or half-phased fashion. Some of these miRNA-like RNAs were experimentally confirmed by re-amplification and re-sequencing, and have a similar qRT-PCR detection ratio as their cognate canonical miRNAs. The target genes of those phased and half-phased miRNA-like RNAs function in process of cell growth metabolism and play roles in protein kinase. Half-phased miR171d.3 was confirmed to have cleavage activities on its target gene P-glycoprotein 11, a broad substrate efflux pump across cellular membranes, which is thought to provide protection for tropical cassava during sharp temperature decease. Our results showed that the RNAs from miRNA precursors are miRNA-like small RNAs that are viable negative gene regulators and may have potential functions in cassava chilling responses.

A novel peptide from the ACEI/BPP-CNP precursor in the venom of Crotalus durissus collilineatus.

PubMed

Higuchi, Shigesada; Murayama, Nobuhiro; Saguchi, Ken-ichi; Ohi, Hiroaki; Fujita, Yoshiaki; da Silva, Nelson Jorge; de Siqueira, Rodrigo José Bezerra; Lahlou, Saad; Aird, Steven D

2006-10-01

In crotaline venoms, angiotensin-converting enzyme inhibitors [ACEIs, also known as bradykinin potentiating peptides (BPPs)], are products of a gene coding for an ACEI/BPP-C-type natriuretic peptide (CNP) precursor. In the genes from Bothrops jararaca and Gloydius blomhoffii, ACEI/BPP sequences are repeated. Sequencing of a cDNA clone from venom glands of Crotalus durissus collilineatus showed that two ACEIs/BPPs are located together at the N-terminus, but without repeats. An additional sequence for CNP was unexpectedly found at the C-terminus. Homologous genes for the ACEI/BPP-CNP precursor suggest that most crotaline venoms contain both ACEIs/BPPs and CNP. The sequence of ACEIs/BPPs is separated from the CNP sequence by a long spacer sequence. Previously, there was no evidence that this spacer actually coded any expressed peptides. Aird and Kaiser (1986, unpublished) previously isolated and sequenced a peptide of 11 residues (TPPAGPDVGPR) from Crotalus viridis viridis venom. In the present study, analysis of the cDNA clone from C. d. collilineatus revealed a nearly identical sequence in the ACEI/BPP-CNP spacer. Fractionation of the crude venom by reverse phase HPLC (C(18)), and analysis of the fractions by mass spectrometry (MS) indicated a component of 1020.5 Da. Amino acid sequencing by MS/MS confirmed that C. d. collilineatus venom contains the peptide TPPAGPDGGPR. Its high proline content and paired proline residues are typical of venom hypotensive peptides, although it lacks the usual N-terminal pyroglutamate. It has no demonstrable hypotensive activity when injected intravenously in rats; however, its occurrence in the venoms of dissimilar species suggests that its presence is not accidental. Evidence suggests that these novel toxins probably activate anaphylatoxin C3a receptors.

Accelerated Evolution of the Pituitary Adenylate Cyclase-Activating Polypeptide Precursor Gene During Human Origin

PubMed Central

Wang, Yin-qiu; Qian, Ya-ping; Yang, Su; Shi, Hong; Liao, Cheng-hong; Zheng, Hong-Kun; Wang, Jun; Lin, Alice A.; Cavalli-Sforza, L. Luca; Underhill, Peter A.; Chakraborty, Ranajit; Jin, Li; Su, Bing

2005-01-01

Pituitary adenylate cyclase-activating polypeptide (PACAP) is a neuropeptide abundantly expressed in the central nervous system and involved in regulating neurogenesis and neuronal signal transduction. The amino acid sequence of PACAP is extremely conserved across vertebrate species, indicating a strong functional constraint during the course of evolution. However, through comparative sequence analysis, we demonstrated that the PACAP precursor gene underwent an accelerated evolution in the human lineage since the divergence from chimpanzees, and the amino acid substitution rate in humans is at least seven times faster than that in other mammal species resulting from strong Darwinian positive selection. Eleven human-specific amino acid changes were identified in the PACAP precursors, which are conserved from murine to African apes. Protein structural analysis suggested that a putative novel neuropeptide might have originated during human evolution and functioned in the human brain. Our data suggested that the PACAP precursor gene underwent adaptive changes during human origin and may have contributed to the formation of human cognition. PMID:15834139

Complex Patterns of Altered MicroRNA Expression during the Adenoma-Adenocarcinoma Sequence for Microsatellite-Stable Colorectal Cancer

PubMed Central

Bartley, Angela N.; Yao, Hui; Barkoh, Bedia A.; Ivan, Cristina; Mishra, Bal M.; Rashid, Asif; Calin, George A.; Luthra, Rajyalakshmi; Hamilton, Stanley R.

2012-01-01

Purpose MicroRNAs are short noncoding RNAs that regulate gene expression and are over- or under-expressed in most tumors, including colorectal adenocarcinoma. MicroRNAs are potential biomarkers and therapeutic targets and agents, but limited information on microRNAome alterations during progression in the well-known adenoma-adenocarcinoma sequence is available to guide their usage. Experimental Design We profiled 866 human microRNAs by microarray analysis in 69 matched specimens of microsatellite-stable adenocarcinomas, adjoining precursor adenomas including areas of high- and low-grade dysplasia, and nonneoplastic mucosa. Results We found 230 microRNAs that were significantly differentially expressed during progression, including 19 not reported previously. Altered microRNAs clustered into two major patterns of early (type I) and late (type II) differential expression. The largest number (n = 108) was altered at the earliest step from mucosa to low-grade dysplasia (subtype IA) prior to major nuclear localization of β-catenin, including 36 microRNAs that had persistent differential expression throughout the entire sequence to adenocarcinoma. Twenty microRNAs were intermittently altered (subtype IB), and six were transiently altered (subtype IC). In contrast, 33 microRNAs were altered late in high-grade dysplasia and adenocarcinoma (subtype IIA), and 63 in adenocarcinoma only (subtype IIB). Predicted targets in 12 molecular pathways were identified for highly altered microRNAs, including the Wnt signaling pathway leading to low-grade dysplasia. β-catenin expression correlated with downregulated microRNAs. Conclusions Our findings suggest that numerous microRNAs play roles in the sequence of molecular events, especially early events, resulting in colorectal adenocarcinoma. The temporal patterns and complexity of microRNAome alterations during progression will influence the efficacy of microRNAs for clinical purposes. PMID:21948089

Material State Awareness for Composites Part I: Precursor Damage Analysis Using Ultrasonic Guided Coda Wave Interferometry (CWI).

PubMed

Patra, Subir; Banerjee, Sourav

2017-12-16

Detection of precursor damage followed by the quantification of the degraded material properties could lead to more accurate progressive failure models for composite materials. However, such information is not readily available. In composite materials, the precursor damages-for example matrix cracking, microcracks, voids, interlaminar pre-delamination crack joining matrix cracks, fiber micro-buckling, local fiber breakage, local debonding, etc.-are insensitive to the low-frequency ultrasonic guided-wave-based online nondestructive evaluation (NDE) or Structural Health Monitoring (SHM) (~100-~500 kHz) systems. Overcoming this barrier, in this article, an online ultrasonic technique is proposed using the coda part of the guided wave signal, which is often neglected. Although the first-arrival wave packets that contain the fundamental guided Lamb wave modes are unaltered, the coda wave packets however carry significant information about the precursor events with predictable phase shifts. The Taylor-series-based modified Coda Wave Interferometry (CWI) technique is proposed to quantify the stretch parameter to compensate the phase shifts in the coda wave as a result of precursor damage in composites. The CWI analysis was performed on five woven composite-fiber-reinforced-laminate specimens, and the precursor events were identified. Next, the precursor damage states were verified using high-frequency Scanning Acoustic Microscopy (SAM) and optical microscopy imaging.

Beta.-glucosidase coding sequences and protein from orpinomyces PC-2

DOEpatents

Li, Xin-Liang; Ljungdahl, Lars G.; Chen, Huizhong; Ximenes, Eduardo A.

2001-02-06

Provided is a novel .beta.-glucosidase from Orpinomyces sp. PC2, nucleotide sequences encoding the mature protein and the precursor protein, and methods for recombinant production of this .beta.-glucosidase.

Precursors of the Forbush Decrease on 2006 December 14 Observed with the Global Muon Detector Network (GMDN)

NASA Astrophysics Data System (ADS)

Fushishita, A.; Kuwabara, T.; Kato, C.; Yasue, S.; Bieber, J. W.; Evenson, P.; Da Silva, M. R.; Dal Lago, A.; Schuch, N. J.; Tokumaru, M.; Duldig, M. L.; Humble, J. E.; Sabbah, I.; Jassar, H. K. Al; Sharma, M. M.; Munakata, K.

2010-06-01

We analyze the precursor of a Forbush decrease (FD) observed with the Global Muon Detector Network on 2006 December 14. An intense geomagnetic storm is also recorded during this FD with the peak Kp index of 8+. By using the "two-dimensional map" of the cosmic ray intensity produced after removing the contribution from the diurnal anisotropy, we succeed in extracting clear signatures of the precursor. A striking feature of this event is that a weak loss-cone (LC) signature is first recorded more than a day prior to the storm sudden commencement (SSC) onset. This suggests that the LC precursor appeared only 7 hr after the coronal mass ejection eruption from the Sun, when the interplanetary (IP) shock driven by the interplanetary coronal mass ejection was located at 0.4 AU from the Sun. We find the precursor being successively observed with multiple detectors in the network according to the Earth's spin and confirmed that the precursor continuously exists in space. The long lead time (15.6 hr) of this precursor which is almost twice the typical value indicates that the interplanetary magnetic field (IMF) was more quiet in this event than a typical power spectrum assumed for the IMF turbulence. The amplitude (-6.45%) of the LC anisotropy at the SSC onset is more than twice the FD size, indicating that the maximum intensity depression behind the IP shock is much larger than the FD size recorded at the Earth in this event. We also find the excess intensity from the sunward IMF direction clearly observed during ~10 hr preceding the SSC onset. It is shown that this excess intensity is consistent with the measurement of the particles accelerated by the head-on collisions with the approaching shock. This is the first detailed observation of the precursor due to the shock reflected particles with muon detectors.

Nucleotide sequence of the gag gene and gag-pol junction of feline leukemia virus.

PubMed Central

Laprevotte, I; Hampe, A; Sherr, C J; Galibert, F

1984-01-01

The nucleotide sequence of the gag gene of feline leukemia virus and its flanking sequences were determined and compared with the corresponding sequences of two strains of feline sarcoma virus and with that of the Moloney strain of murine leukemia virus. A high degree of nucleotide sequence homology between the feline leukemia virus and murine leukemia virus gag genes was observed, suggesting that retroviruses of domestic cats and laboratory mice have a common, proximal evolutionary progenitor. The predicted structure of the complete feline leukemia virus gag gene precursor suggests that the translation of nonglycosylated and glycosylated gag gene polypeptides is initiated at two different AUG codons. These initiator codons fall in the same reading frame and are separated by a 222-base-pair segment which encodes an amino terminal signal peptide. The nucleotide sequence predicts the order of amino acids in each of the individual gag-coded proteins (p15, p12, p30, p10), all of which derive from the gag gene precursor. Stable stem-and-loop secondary structures are proposed for two regions of viral RNA. The first falls within sequences at the 5' end of the viral genome, together with adjacent palindromic sequences which may play a role in dimer linkage of RNA subunits. The second includes coding sequences at the gag-pol junction and is proposed to be involved in translation of the pol gene product. Sequence analysis of the latter region shows that the gag and pol genes are translated in different reading frames. Classical consensus splice donor and acceptor sequences could not be localized to regions which would permit synthesis of the expected gag-pol precursor protein. Alternatively, we suggest that the pol gene product (RNA-dependent DNA polymerase) could be translated by a frameshift suppressing mechanism which could involve cleavage modification of stems and loops in a manner similar to that observed in tRNA processing. PMID:6328019

Sequence analyses reveal that a TPR-DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR-DP domains and prokaryotic GerD proteins.

PubMed

Hernández Torres, Jorge; Papandreou, Nikolaos; Chomilier, Jacques

2009-05-01

The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR-DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR-DP domains.

Identification of nitrosamine precursors from urban drainage during storm events: A case study in southern China.

PubMed

Bei, Er; Liao, Xiaobin; Meng, Xiangting; Li, Shixiang; Wang, Jun; Sheng, Deyang; Chao, Meng; Chen, Zhuohua; Zhang, Xiaojian; Chen, Chao

2016-10-01

The drinking water sources of many cities in southern China are frequently contaminated by upstream urban drainage during storm events, which brings high concentrations of N-nitrosamine (NA) precursors and poses a threat to the safety of drinking water. We conducted two sampling campaigns during the heavy rain season in 2015 in one representative city in southern China. We detected that the concentration of N-nitrosodimethylamine formation potential (NDMA FP) in urban drainage during two storm events was 80-115 ng/L and the total formation potential concentration of nine nitrosamines (TNA9 FP) was 145-165 ng/L. To address the deteriorated water quality, 30 mg/L of powdered activated carbon (PAC) was fed into the water intake. PAC adsorption alone could remove 52% of NDMA FP and 52% of TNA FP, while the subsequent conventional process only removed 8% of TNA FP. We isolated six chemicals (N,N-benzyldimethylamine, 5-[(dimethylamino)methyl]-2-furanmethanol, N,N-dimethyl-3-aminophenol, N,N-dimethylethylamine, Ziram, and N,N-dimethylaniline) and confirmed them to be NA precursors. Among these NA precursors, Ziram was identified for the first time as a NA precursor that is formed via chloramination; its molar yield for NDMA was 6.73 ± 0.40%. Copyright © 2016 Elsevier Ltd. All rights reserved.

Possible mechanisms for four regimes associated with cold events over East Asia

NASA Astrophysics Data System (ADS)

Yang, Zifan; Huang, Wenyu; Wang, Bin; Chen, Ruyan; Wright, Jonathon S.; Ma, Wenqian

2017-09-01

Circulation patterns associated with cold events over East Asia during the winter months of 1948-2014 are classified into four regimes by applying a k-means clustering method based on the area-weighted pattern correlation. The earliest precursor signals for two regimes are anticyclonic anomalies, which evolve into Ural and central Siberian blocking-like circulation patterns. The earliest precursor signals for the other two regimes are cyclonic anomalies, both of which evolve to amplify the East Asian trough (EAT). Both the blocking-like circulation patterns and amplified EAT favor the initialization of cold events. On average, the blocking-related regimes tend to last longer. The lead time of the earliest precursor signal for the central Siberian blocking-related regime is only 4 days, while those for the other regimes range from 16 to 18 days. The North Atlantic Oscillation plays essential roles both in triggering the precursor for the Ural blocking-related regime and in amplifying the precursors for all regimes. All regimes preferentially occur during the positive phase of the Eurasian teleconnection pattern and the negative phase of the El Niño-Southern Oscillation. For three regimes, surface cooling is primarily due to reduced downward infrared radiation and enhanced cold advection. For the remaining regime, which is associated with the southernmost cooling center, sensible and latent heat release and horizontal cold advection dominate the East Asian cooling.

Post-translational modification of Rauscher leukemia virus precursor polyproteins encoded by the gag gene.

PubMed Central

Schultz, A M; Rabin, E H; Oroszlan, S

1979-01-01

Post-translational modifications of retrovirus gag gene-encoded polyproteins include proteolytic cleavage, phosphorylation, and glycosylation. To study the sequence of these events, we labeled JLS-V9 cells chronically infected with Rauscher murine leukemia virus in pulse-chase experiments with the radioactive precursors [35S]methionine, [14C]mannose, [3H]glucosamine, and [32P]phosphate. Newly synthesized gag polyproteins which incorporated label, and the modified products derived from them, were identified by immunoprecipitation of cell lysates with anti-p30 rabbit serum, followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. Pulse-chase experiments were carried out in the presence as well as in the absence of tunicamycin, an inhibitor of glycosylation. Among the three major polyproteins synthesized in the absence of tunicamycin, two were found to be glycosylated but not phosphorylated. These were designated gPr80gag and gP94gag. Both shared identical [35S]methionine peptides with Pr65gag and p30. Of the two nonglycosylated precursors, Pr65gag and Pr75gag, only Pr65gag was found to be detectably phosphorylated, and Pr75gag could be readily identified only when glycosylation was inhibited. On the basis of these results, a scheme for the post-translational modification of gag polyproteins is proposed. According to this scheme the gag gene-encoded polyproteins are processed from a common precursor, Pr75gag, by two divergent pathways: one leading through the intermediate Pr65gag to internal virion components via cleavage and phosphorylation and the other via tunicamycin-sensitive mannosylation to the intermediate gPr80gag, which is further glycosylated to yield cell surface polyprotein gP94gag. Images PMID:480454

Highly specific gene silencing in a monocot species by artificial microRNAs derived from chimeric miRNA precursors

DOE PAGES

Carbonell, Alberto; Fahlgren, Noah; Mitchell, Skyler; ...

2015-05-20

Artificial microRNAs (amiRNAs) are used for selective gene silencing in plants. However, current methods to produce amiRNA constructs for silencing transcripts in monocot species are not suitable for simple, cost-effective and large-scale synthesis. Here, a series of expression vectors based on Oryza sativa MIR390 (OsMIR390) precursor was developed for high-throughput cloning and high expression of amiRNAs in monocots. Four different amiRNA sequences designed to target specifically endogenous genes and expressed from OsMIR390-based vectors were validated in transgenic Brachypodium distachyon plants. Surprisingly, amiRNAs accumulated to higher levels and were processed more accurately when expressed from chimeric OsMIR390-based precursors that include distalmore » stem-loop sequences from Arabidopsis thaliana MIR390a (AtMIR390a). In all cases, transgenic plants displayed the predicted phenotypes induced by target gene repression, and accumulated high levels of amiRNAs and low levels of the corresponding target transcripts. Genome-wide transcriptome profiling combined with 5-RLM-RACE analysis in transgenic plants confirmed that amiRNAs were highly specific. Finally, significance Statement A series of amiRNA vectors based on Oryza sativa MIR390 (OsMIR390) precursor were developed for simple, cost-effective and large-scale synthesis of amiRNA constructs to silence genes in monocots. Unexpectedly, amiRNAs produced from chimeric OsMIR390-based precursors including Arabidopsis thaliana MIR390a distal stem-loop sequences accumulated elevated levels of highly effective and specific amiRNAs in transgenic Brachypodium distachyon plants.« less

Processing of intervening sequences: a new yeast mutant which fails to excise intervening sequences from precursor tRNAs.

PubMed

Hopper, A K; Schultz, L D; Shapiro, R A

1980-03-01

By using conditional loss of suppression an an assay, we have been successful in screening for a yeast mutant which is defective in tRNA processing. The los1-1 mutation causes an accumulation of a subset of precursor tRNAs at the nonpermissive temperature. These pre-tRNAs are like those which accumulate in the yeast mutant ts 136 (rna1) in that they have transcribed intervening sequences. The mutations at los1-1 and rna1 complement and segregate independently of each other. The los1-1 mutation affects the expression of all 8 tyrosine-inserting suppressor loci, but does not seem to affect rRNA or mRNA synthesis.

Detecting primary precursors of January surface air temperature anomalies in China

NASA Astrophysics Data System (ADS)

Tan, Guirong; Ren, Hong-Li; Chen, Haishan; You, Qinglong

2017-12-01

This study aims to detect the primary precursors and impact mechanisms for January surface temperature anomaly (JSTA) events in China against the background of global warming, by comparing the causes of two extreme JSTA events occurring in 2008 and 2011 with the common mechanisms inferred from all typical episodes during 1979-2008. The results show that these two extreme events exhibit atmospheric circulation patterns in the mid-high latitudes of Eurasia, with a positive anomaly center over the Ural Mountains and a negative one to the south of Lake Baikal (UMLB), which is a pattern quite similar to that for all the typical events. However, the Eurasian teleconnection patterns in the 2011 event, which are accompanied by a negative phase of the North Atlantic Oscillation, are different to those of the typical events and the 2008 event. We further find that a common anomalous signal appearing in early summer over the tropical Indian Ocean may be responsible for the following late-winter Eurasian teleconnections and the associated JSTA events in China. We show that sea surface temperature anomalies (SSTAs) in the preceding summer over the western Indian Ocean (WIO) are intimately related to the UMLB-like circulation pattern in the following January. Positive WIOSSTAs in early summer tend to induce strong UMLB-like circulation anomalies in January, which may result in anomalously or extremely cold events in China, which can also be successfully reproduced in model experiments. Our results suggest that the WIOSSTAs may be a useful precursor for predicting JSTA events in China.

SEARCH FOR PRECURSOR ERUPTIONS AMONG TYPE IIB SUPERNOVAE

DOE Office of Scientific and Technical Information (OSTI.GOV)

Strotjohann, Nora L.; Ofek, Eran O.; Gal-Yam, Avishay

2015-10-01

The progenitor stars of several Type IIb supernovae (SNe) show indications of extended hydrogen envelopes. These envelopes might be the outcome of luminous energetic pre-explosion events, so-called precursor eruptions. We use the Palomar Transient Factory (PTF) pre-explosion observations of a sample of 27 nearby SNe IIb to look for such precursors during the final years prior to the SN explosion. No precursors are found when combining the observations in 15-day bins, and we calculate the absolute-magnitude-dependent upper limit on the precursor rate. At the 90% confidence level, SNe IIb have on average <0.86 precursors as bright as an absolute R-bandmore » magnitude of −14 in the final 3.5 years before the explosion and <0.56 events over the final year. In contrast, precursors among SNe IIn have a ≳5 times higher rate. The kinetic energy required to unbind a low-mass stellar envelope is comparable to the radiated energy of a few-weeks-long precursor that would be detectable for the closest SNe in our sample. Therefore, mass ejections, if they are common in such SNe, are radiatively inefficient or have durations longer than months. Indeed, when using 60-day bins, a faint precursor candidate is detected prior to SN 2012cs (∼2% false-alarm probability). We also report the detection of the progenitor of SN 2011dh that does not show detectable variability over the final two years before the explosion. The suggested progenitor of SN 2012P is still present, and hence is likely a compact star cluster or an unrelated object.« less

Characterizing the Specificity and Co-operation of Aminopeptidases in the Cytosol and ER During MHC Class I antigen Presentation1

PubMed Central

Hearn, Arron; York, Ian A.; Bishop, Courtney; Rock, Kenneth L.

2010-01-01

Many MHC class I binding peptides are generated as N-extended precursors during protein degradation by the proteasome. These peptides can be subsequently trimmed by aminopeptidases in the cytosol and/or the ER to produce mature epitope. However, the contribution and specificity of each of these subcellular compartments in removing N-terminal amino acids for antigen presentation is not well defined. Here we investigate this issue for antigenic precursors that are expressed in the cytosol. By systematically varying the N-terminal flanking sequences of peptides we show that the amino acids upstream of an epitope precursor are a major determinant of the amount of antigen presentation. In many cases MHC class I binding peptides are produced through sequential trimming in both the cytosol and ER. Trimming of flanking residues in the cytosol contributes most to sequences that are poorly trimmed in the ER. Since N-terminal trimming has different specificity in the cytosol and ER, the cleavage of peptides in both of these compartments serves to broaden the repertoire of sequences that are presented. PMID:20351195

Statistical study of spatio-temporal distribution of precursor solar flares associated with major flares

NASA Astrophysics Data System (ADS)

Gyenge, N.; Ballai, I.; Baranyi, T.

2016-07-01

The aim of the present investigation is to study the spatio-temporal distribution of precursor flares during the 24 h interval preceding M- and X-class major flares and the evolution of follower flares. Information on associated (precursor and follower) flares is provided by Reuven Ramaty High Energy Solar Spectroscopic Imager (RHESSI). Flare list, while the major flares are observed by the Geostationary Operational Environmental Satellite (GOES) system satellites between 2002 and 2014. There are distinct evolutionary differences between the spatio-temporal distributions of associated flares in about one-day period depending on the type of the main flare. The spatial distribution was characterized by the normalized frequency distribution of the quantity δ (the distance between the major flare and its precursor flare normalized by the sunspot group diameter) in four 6 h time intervals before the major event. The precursors of X-class flares have a double-peaked spatial distribution for more than half a day prior to the major flare, but it changes to a lognormal-like distribution roughly 6 h prior to the event. The precursors of M-class flares show lognormal-like distribution in each 6 h subinterval. The most frequent sites of the precursors in the active region are within a distance of about 0.1 diameter of sunspot group from the site of the major flare in each case. Our investigation shows that the build-up of energy is more effective than the release of energy because of precursors.

The nucleotide sequence of the intergenic region between the 5.8S and 26S rRNA genes of the yeast ribosomal RNA operon. Possible implications for the interaction between 5.8S and 26S rRNA and the processing of the primary transcript.

PubMed Central

Veldman, G M; Klootwijk, J; van Heerikhuizen, H; Planta, R J

1981-01-01

We have determined the nucleotide sequence of part of a cloned yeast ribosomal RNA operon extending from the 5.8S RNA gene downstream into the 5' -terminal region of the 26S RNA gene. We mapped the pertinent processing sites, viz. the 5' end of 26S rRNA and the 3'ends of 5.8S rRNA and its immediate precursor, 7S RNA. At the 3' end of 7S RNA we find the sequence UCGUUU which is very similar to the type I consensus sequence UCAUUA/U present at the 3' ends of 17S, 5.8S and 26S rRNA as well as 18S precursor rRNA in yeast. At the 5' end of the 26S RNA gene we find a sequence of thirteen nucleotides which is homologous to the type II sequence present at the 5' termini of both the 17S and the 5.8S RNA gene. These findings further support the suggestion put forward earlier (G.M. Veldman et al. (1980) Nucl. Acids Res. 8, 2907-2920) that both consensus sequences are involved in the recognition of precursor rRNA by the processing nuclease(s). We discuss a model for the processing of yeast rRNA in which a processing enzyme sequentially recognizes several combinations of a type I and a type II consensus sequence. We also describe the existence of a significant base complementarity between sequences in the 5' -terminal region of 26S rRNA and the 3' -terminal region of 5.8S rRNA. We suggest that base pairing between these sequences contributes to the binding between 5.8S and 26S rRNA. Images PMID:7312619

Crypteins derived from the mouse neuropeptide FF (NPFF)A precursor display NPFF-like effects in nociceptive tests in mice.

PubMed

Kotlinska, Jolanta H; Gibula-Bruzda, Ewa; Suder, Piotr; Wasielak, Magdalena; Bray, Lauriane; Raoof, Hana; Bodzon-Kulakowska, Anna; Silberring, Jerzy

2012-07-01

NPFF precursor, pro-NPFF(A) contains three known bioactive sequences: NPFF (FLFQPQRF-NH(2)), neuropeptide AF (NPAF; AGEGLSSPFWSLAAPQRF-NH(2)) and neuropeptide SF (NPSF; SLAAPQRF-NH(2)). The key-feature of these fragments is their common PQRF-amidated sequence at their C termini. Here, we evaluated the biological activity of two other sequences derived from the mouse NPFF(A) precursor, that does not have PQRF-amidated C-terminus. One peptide was residing between positions 85 and 99 in the mice pro-NPFF(A). This peptide was referred to as neuropeptide SA (NPSA; SAWGSWSKEQLNPQA), assigned due to its flanking amino acids. Another sequence used in the experiments was N-terminal fragment of NPSA, here referred to as neuropeptide SS (NPSS; SAWGSWS). These two peptides, classified as crypteins, were synthesized and tested in the hot-plate and tail immersion tests in mice for their pharmacological activity in morphine-induced antinociception. The effects of both crypteins were compared to NPFF. Our experiments indicated that both crypteins inhibited morphine antinociception and their effects were reversed by RF9, an antagonist of NPFF receptors. These data show that NPSA and NPSS possess NPFF-like anti-opioid activity in these behavioral tests. Copyright © 2012 Elsevier Inc. All rights reserved.

Complete cDNA sequence of SAP-like pentraxin from Limulus polyphemus: implications for pentraxin evolution.

PubMed

Tharia, Hazel A; Shrive, Annette K; Mills, John D; Arme, Chris; Williams, Gwyn T; Greenhough, Trevor J

2002-02-22

The serum amyloid P component (SAP)-like pentraxin Limulus polyphemus SAP is a recently discovered, distinct pentraxin species, of known structure, which does not bind phosphocholine and whose N-terminal sequence has been shown to differ markedly from the highly conserved N terminus of all other known horseshoe crab pentraxins. The complete cDNA sequence of Limulus SAP, and the derived amino acid sequence, the first invertebrate SAP-like pentraxin sequence, have been determined. Two sequences were identified that differed only in the length of the 3' untranslated region. Limulus SAP is synthesised as a precursor protein of 234 amino acid residues, the first 17 residues encoding a signal peptide that is absent from the mature protein. Phylogenetic analysis clusters Limulus SAP pentraxin with the horseshoe crab C-reactive proteins (CRPs) rather than the mammalian SAPs, which are clustered with mammalian CRPs. The deduced amino acid sequence shares 22% identity with both human SAP and CRP, which are 51% identical, and 31-35% with horseshoe crab CRPs. These analyses indicate that gene duplication of CRP (or SAP), followed by sequence divergence and the evolution of CRP and/or SAP function, occurred independently along the chordate and arthropod evolutionary lines rather than in a common ancestor. They further indicate that the CRP/SAP gene duplication event in Limulus occurred before both the emergence of the Limulus CRP variants and the mammalian CRP/SAP gene duplication. Limulus SAP, which does not exhibit the CRP characteristic of calcium-dependent binding to phosphocholine, is established as a pentraxin species distinct from all other known horseshoe crab pentraxins that exist in many variant forms sharing a high level of sequence homology. Copyright 2002 Elsevier Science Ltd.

Influence of gene dosage and autoregulation of the regulatory genes INO2 and INO4 on inositol/choline-repressible gene transcription in the yeast Saccharomyces cerevisiae.

PubMed

Schwank, S; Hoffmann, B; Sch-uller, H J

1997-06-01

Expression of structural genes of phospholipid biosynthesis in yeast is mediated by the inositol/choline-responsive element (ICRE). ICRE-dependent gene activation, requiring the regulatory genes INO2 and INO4, is repressed in the presence of the phospholipid precursors inositol and choline. INO2 and, to a less extent, INO4 are positively autoregulated by functional ICRE sequences in the respective upstream regions. However, an INO2 allele devoid of its ICRE functionally complemented an ino2 mutation and completely restored inositol/choline regulation of Ino2p-dependent reporter genes. Low-level expression of INO2 and INO4 genes, each under control of the heterologous MET25 promoter, did not alter the regulatory pattern of target genes. Thus, upstream regions of INO2 and INO4 are not crucial for transcriptional control of ICRE-dependent genes by inositol and choline. Interestingly, over-expression of INO2, but not of INO4, counteracted repression by phospholipid precursors. Possibly, a functional antagonism between INO2 and a negative regulator is the key event responsible for repression or de-repression.

Adventures with Insulin in the Islets of Langerhans

PubMed Central

Steiner, Donald F.

2011-01-01

Insulin is a small but beautifully organized protein with a unique two-chain structure, the first protein to be sequenced. The mechanism of its biosynthesis invited much initial speculation but was finally clarified by the discovery of proinsulin, its single-chain precursor. The rich present-day field of protein precursor processing via post-translational proteolysis within the secretory pathway arose in the early 1970s as an offshoot of studies on insulin biosynthesis, which provided a novel paradigm for the generation of many other small neuroendocrine peptides. Before long, this mechanism was also found to play a role in the production of a much wider spectrum of proteins traversing the secretory pathway (receptors, growth factors, blood-clotting components, and even many viral envelope proteins) occurring in almost all eukaryotic cells. Indeed, yeast provided a key clue in the search for the proprotein convertases, the endoproteases that work along with carboxypeptidases and other modifying enzymes, such as the amidating enzyme complex (PAM), in converting inactive or less active precursor proteins into their fully active peptide products. In this “Reflections” article, I have tried to recount the people and events in my life that led to my involvement first in basic biochemical research and then on to insulin, proinsulin, and many relevant related areas that continue to fascinate and challenge my colleagues and me, as well as many other biomedical scientists today, as diabetes mellitus increasingly threatens human health throughout our contemporary world. PMID:21454641

BIOPEP database and other programs for processing bioactive peptide sequences.

PubMed

Minkiewicz, Piotr; Dziuba, Jerzy; Iwaniak, Anna; Dziuba, Marta; Darewicz, Małgorzata

2008-01-01

This review presents the potential for application of computational tools in peptide science based on a sample BIOPEP database and program as well as other programs and databases available via the World Wide Web. The BIOPEP application contains a database of biologically active peptide sequences and a program enabling construction of profiles of the potential biological activity of protein fragments, calculation of quantitative descriptors as measures of the value of proteins as potential precursors of bioactive peptides, and prediction of bonds susceptible to hydrolysis by endopeptidases in a protein chain. Other bioactive and allergenic peptide sequence databases are also presented. Programs enabling the construction of binary and multiple alignments between peptide sequences, the construction of sequence motifs attributed to a given type of bioactivity, searching for potential precursors of bioactive peptides, and the prediction of sites susceptible to proteolytic cleavage in protein chains are available via the Internet as are other approaches concerning secondary structure prediction and calculation of physicochemical features based on amino acid sequence. Programs for prediction of allergenic and toxic properties have also been developed. This review explores the possibilities of cooperation between various programs.

Functional characterization of an alpha-factor-like Sordaria macrospora peptide pheromone and analysis of its interaction with its cognate receptor in Saccharomyces cerevisiae.

PubMed

Mayrhofer, Severine; Pöggeler, Stefanie

2005-04-01

The homothallic filamentous ascomycete Sordaria macrospora possesses genes which are thought to encode two pheromone precursors and two seven-transmembrane pheromone receptors. The pheromone precursor genes are termed ppg1 and ppg2. The putative products derived from the gene sequence show structural similarity to the alpha-factor precursors and a-factor precursors of the yeast Saccharomyces cerevisiae. Likewise, sequence similarity has been found between the putative products of the pheromone receptor genes pre2 and pre1 and the S. cerevisiae Ste2p alpha-factor receptor and Ste3p a-factor receptor, respectively. To investigate whether the alpha-factor-like pheromone-receptor pair of S. macrospora is functional, a heterologous yeast assay was used. Our results show that the S. macrospora alpha-factor-like pheromone precursor PPG1 is processed into an active pheromone by yeast MATalpha cells. The S. macrospora PRE2 protein was demonstrated to be a peptide pheromone receptor. In yeast MATa cells lacking the endogenous Ste2p receptor, the S. macrospora PRE2 receptor facilitated all aspects of the pheromone response. Using a synthetic peptide, we can now predict the sequence of one active form of the S. macrospora peptide pheromone. We proved that S. macrospora wild-type strains secrete an active pheromone into the culture medium and that disruption of the ppg1 gene in S. macrospora prevents pheromone production. However, loss of the ppg1 gene does not affect vegetative growth or fertility. Finally, we established the yeast assay as an easy and useful system for analyzing pheromone production in developmental mutants of S. macrospora.

The Search for Precursor Redline Auroral Events

NASA Astrophysics Data System (ADS)

Sobel, E. I.; Kepko, L.; Angelopoulos, V.; Donovan, E.; Spanswick, E.

2013-12-01

A popular theory of geomagnetic substorms postulates that substorms begin in the downtail region of the magnetosphere and propagate Earthward. This should result in a visible auroral precursor; however, observations have not shown such formations. This poster presents the results of our project to examine the little-studied redline data in search of these early-cycle auroral phenomena. We reviewed daily ground-based redline auroral observations for relevant months of 2008-2013 using software developed in IDL and created an event database with the observation stations, onset timestamp, available satellites, and notes. After narrowing the initial list of nearly 350 events to the best 5, we analyzed the redline events alongside white light and green light observations from the same stations, as well as in situ measurements from THEMIS and geomagnetic readings from ground-based stations. Preliminary results from 36 suspected cases and 5 confirmed cases show some instances of clear redline formations that precede visual onsets. These phenomena form above the equatorward auroral arc, descend over several minutes, and then appear to trigger onset within minutes of reaching the arc boundary. We also found evidence that these precursors are created by earthward plasma flows. This research helps answer the long-standing question of why there has been no visible precursor, despite strong evidence of pre-onset earthward flows. It is one of the first ventures into the lower spectra of the aurora, opening the door for future work on the longer-lasting, lower-energy, and more sensitive red wavelengths.

Atmospheric new particle formation at the research station Melpitz, Germany: connection with gaseous precursors and meteorological parameters

NASA Astrophysics Data System (ADS)

Größ, Johannes; Hamed, Amar; Sonntag, André; Spindler, Gerald; Elina Manninen, Hanna; Nieminen, Tuomo; Kulmala, Markku; Hõrrak, Urmas; Plass-Dülmer, Christian; Wiedensohler, Alfred; Birmili, Wolfram

2018-02-01

This paper revisits the atmospheric new particle formation (NPF) process in the polluted Central European troposphere, focusing on the connection with gas-phase precursors and meteorological parameters. Observations were made at the research station Melpitz (former East Germany) between 2008 and 2011 involving a neutral cluster and air ion spectrometer (NAIS). Particle formation events were classified by a new automated method based on the convolution integral of particle number concentration in the diameter interval 2-20 nm. To study the relevance of gaseous sulfuric acid as a precursor for nucleation, a proxy was derived on the basis of direct measurements during a 1-month campaign in May 2008. As a major result, the number concentration of freshly produced particles correlated significantly with the concentration of sulfur dioxide as the main precursor of sulfuric acid. The condensation sink, a factor potentially inhibiting NPF events, played a subordinate role only. The same held for experimentally determined ammonia concentrations. The analysis of meteorological parameters confirmed the absolute need for solar radiation to induce NPF events and demonstrated the presence of significant turbulence during those events. Due to its tight correlation with solar radiation, however, an independent effect of turbulence for NPF could not be established. Based on the diurnal evolution of aerosol, gas-phase, and meteorological parameters near the ground, we further conclude that the particle formation process is likely to start in elevated parts of the boundary layer rather than near ground level.

Different processing of CAPA and pyrokinin precursors in the giant mealworm beetle Zophobas atratus (Tenebrionidae) and the boll weevil Anthonomus grandis grandis (Curculionidae).

PubMed

Neupert, Susanne; Marciniak, Pawel; Köhler, Rene; Nachman, Ronald J; Suh, Charles P-C; Predel, Reinhard

2018-03-01

Capa and pyrokinin (pk) genes in hexapods share a common evolutionary origin. Using transcriptomics and peptidomics, we analyzed products of these genes in two beetles, the giant mealworm beetle (Zophobas atratus; Tenebrionidae) and the boll weevil (Anthonomus grandis grandis; Curculionidae). Our data revealed that even within Coleoptera, which represents a very well-defined group of insects, highly different evolutionary developments occurred in the neuropeptidergic system. These differences, however, primarily affect the general structure of the precursors and differential processing of mature peptides and, to a lesser degree, the sequences of the active core motifs. With the differential processing of the CAPA-precursor in Z. atratus we found a perfect example of completely different products cleaved from a single neuropeptide precursor in different cells. The CAPA precursor in abdominal ganglia of this species yields primarily periviscerokinins (PVKs) whereas processing of the same precursor in neurosecretory cells of the subesophageal ganglion results in CAPA-tryptoPK and a novel CAPA-PK. Particularly important was the detection of that CAPA-PK which has never been observed in the CNS of insects before. The three different types of CAPA peptides (CAPA-tryptoPK, CAPA-PK, PVK) each represent potential ligands which activate different receptors. In contrast to the processing of the CAPA precursor from Z. atratus, no indications of a differential processing of the CAPA precursor were found in A. g. grandis. These data suggest that rapid evolutionary changes regarding the processing of CAPA precursors were still going on when the different beetle lineages diverged. The sequence of the single known PVK of A. g. grandis occupies a special position within the known PVKs of insects and might serve asa basis to develop lineage-specific peptidomimetics capable of disrupting physiological processes regulated by PVKs. Copyright © 2017 Elsevier Inc. All rights reserved.

On factors controlling precursor slip fronts in the laboratory and their relation to slow slip events in nature

NASA Astrophysics Data System (ADS)

Selvadurai, Paul A.; Glaser, Steven D.; Parker, Jessica M.

2017-03-01

Spatial variations in frictional properties on natural faults are believed to be a factor influencing the presence of slow slip events (SSEs). This effect was tested on a laboratory frictional interface between two polymethyl methacrylate (PMMA) bodies. We studied the evolution of slip and slip rates that varied systematically based on the application of both high and low normal stress (σ0=0.8 or 0.4 MPa) and the far-field loading rate (VLP). A spontaneous, frictional rupture expanded from the central, weaker, and more compliant section of the fault that had fewer asperities. Slow rupture propagated at speeds Vslow˜0.8 to 26 mm s-1 with slip rates from 0.01 to 0.2 μm s-1, resulting in stress drops around 100 kPa. During certain nucleation sequences, the fault experienced a partial stress drop, referred to as precursor detachment fronts in tribology. Only at the higher level of normal stress did these fronts exist, and the slip and slip rates mimicked the moment and moment release rates during the 2013-2014 Boso SSE in Japan. The laboratory detachment fronts showed rupture propagation speeds Vslow/VR∈ (5 to 172) × 10-7 and stress drops ˜ 100 kPa, which both scaled to the aforementioned SSE. Distributions of asperities, measured using a pressure sensitive film, increased in complexity with additional normal stress—an increase in normal stress caused added complexity by increasing both the mean size and standard deviation of asperity distributions, and this appeared to control the presence of the detachment front.

A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs.

PubMed

Joy, Nisha; Maimoonath Beevi, Y P; Soniya, E V

2018-05-09

The central tenet of 'genome content' has been that the 'non-coding' parts are highly enriched with 'microsatellites' or 'Simple Sequence Repeats' (SSRs). We presume that the presence and change in number of repeat unit (n) of SSRs in different genomic locations may or may not become beneficial, depending on the position of SSRs in a gene. Very few studies have looked into the existence of SSRs in the hair-pin precursors of miRNAs (pre-miRNAs). The interplay between SSRs and miRNAs is not yet clearly understood. Considering the potential significance of SSRs in pre-miRNAs, we analysed the miRNA hair-pin precursors of 171 organisms, which revealed a noticeable (29.8%) existence of SSRs in their pre-miRNAs. The maintenance of SSRs in pre-miRNAs even in the complex, highly evolved phyla like Chordata and Magnoliophyta shed light upon its diverse functions. Putative effects of SSRs in either regulating the biogenesis or function of miRNAs were more underlined based on computational and experimental analysis. A preliminary computational analysis to explore the relevance of such SSRs maintained in pre-miRNA sequences led to the detection of splicing regulatory elements (SREs) either in or near to the SSRs. The absence of SSRs correspondingly decreased the detection of SREs. The present study is the first implication for the possible involvement of SSRs in shaping the SREs to undergo Alternative Splicing events to produce miRNA isoforms in accordance with different stress environments. This part of work well demonstrates the importance of studying such consistently maintained SSRs residing in pre-miRNAs and can enhance more and more research towards deciphering the exact function of SSRs in the near future.

Concise review: preleukemic stem cells: molecular biology and clinical implications of the precursors to leukemia stem cells.

PubMed

Pandolfi, Ashley; Barreyro, Laura; Steidl, Ulrich

2013-02-01

Recent experimental evidence has shown that acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) arise from transformed immature hematopoietic cells following the accumulation of multiple stepwise genetic and epigenetic changes in hematopoietic stem cells and committed progenitors. The series of transforming events initially gives rise to preleukemic stem cells (pre-LSC), preceding the formation of fully transformed leukemia stem cells (LSC). Despite the established use of poly-chemotherapy, relapse continues to be the most common cause of death in AML and MDS. The therapeutic elimination of all LSC, as well as pre-LSC, which provide a silent reservoir for the re-formation of LSC, will be essential for achieving lasting cures. Conventional sequencing and next-generation genome sequencing have allowed us to describe many of the recurrent mutations in the bulk cell populations in AML and MDS, and recent work has also focused on identifying the initial molecular changes contributing to leukemogenesis. Here we review recent and ongoing advances in understanding the roles of pre-LSC, and the aberrations that lead to pre-LSC formation and subsequent LSC transformation.

Impact face influence on low velocity impact performance of interply laminated plates

NASA Astrophysics Data System (ADS)

Manikandan, Periyasamy; Chai, Gin Boay

2015-03-01

Fibre Metal Laminate (FML), a metal sandwiched hybrid composite material is well-known for its enhanced impact properties and better damage tolerance and it has been successfully implemented in diverse engineering applications in aviation industry. With heterogeneous constituents, the stacking sequence of FML is believe to play a critical role to govern its overall energy absorption capability by means of controlling delamination of metal composite interface and plastic deformation of metal layers. As a precursor, low velocity impact experiments were conducted on interply configured transparent plastic plates in order to extract the significance of stacking sequence and realize the characteristics of each layer through naked eye which is not possible in FML due to opacity of metal layer. The stack configuration constitute hard acrylic (brittle) and soft polycarbonate (ductile) plates analogous to composite (brittle) and metal (ductile) layers on FML laminate and the impact event is performed on either hard or soft facing sides separately. Hard side samples resemble more protective than soft side impact sample, with large peak resistant force and expose smaller damage growth in all experimented cases.

Molecular cloning of mevalonate pathway genes from Taraxacum brevicorniculatum and functional characterisation of the key enzyme 3-hydroxy-3-methylglutaryl-coenzyme A reductase.

PubMed

van Deenen, Nicole; Bachmann, Anne-Lena; Schmidt, Thomas; Schaller, Hubert; Sand, Jennifer; Prüfer, Dirk; Schulze Gronover, Christian

2012-04-01

Taraxacum brevicorniculatum is known to produce high quality rubber. The biosynthesis of rubber is dependent on isopentenyl pyrophosphate (IPP) precursors derived from the mevalonate (MVA) pathway. The cDNA sequences of seven MVA pathway genes from latex of T. brevicorniculatum were isolated, including three cDNA sequences encoding for 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductases (TbHMGR1-3). Expression analyses indicate an important role of TbHMGR1 as well as for the HMG-CoA synthase (TbHMGS), the diphosphomevalonate decarboxylase and the mevalonate kinase in the provision of precursors for rubber biosynthesis. The amino acid sequences of the TbHMGRs show the typical motifs described for plant HMGRs such as two transmembrane domains and a catalytic domain containing two HMG-CoA and two NADP(H) binding sites. The functionality of the HMGRs was demonstrated by complementation assay using an IPP auxotroph mutant of Escherichia coli. Furthermore, the transient expression of the catalytic domains of TbHMGR1 and TbHMGR2 in Nicotiana benthamiana resulted in a strong accumulation of sterol precursors, one of the major groups of pathway end-products.

Differential processing of pro-neurotensin/neuromedin N and relationship to pro-hormone convertases.

PubMed

Kitabgi, Patrick

2006-10-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six amino acid neurotensin-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by endoproteases that belong to the recently identified family of pro-protein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Pro-NT/NN processing gives rise mainly to NT and NN in the brain, to NT and a large peptide ending with the NN sequence at its C-terminus (large NN) in the gut and to NT, large NN and a large peptide ending with the NT sequence (large NT) in the adrenals. Recent evidence indicates that PC1, PC2 and PC5-A are the pro-hormone convertases responsible for the processing patterns observed in the gut, brain and adrenals, respectively. As NT, NN, large NT and large NN are all endowed with biological activity, the evidence reviewed here supports the idea that post-translational processing of pro-NT/NN in tissues may generate biological diversity.

Mars Exploration 2003 to 2013 - An Integrated Perspective: Time Sequencing the Missions

NASA Technical Reports Server (NTRS)

Briggs, G.; McKay, C.

2000-01-01

The science goals for the Mars exploration program, together with the HEDS precursor environmental and technology needs, serve as a solid starting point for re-planning the program in an orderly way. Most recently, the community has recognized the significance of subsurface sampling as a key component in "following the water". Accessing samples from hundreds and even thousands of meters beneath the surface is a challenge that will call for technology development and for one or more demonstration missions. Recent mission failures and concerns about the complexity of the previously planned MSR missions indicate that, before we are ready to undertake sample return and deep sampling, the Mars exploration program needs to include: 1) technology development missions; and 2) basic landing site assessment missions. These precursor missions should demonstrate the capability for reliable & accurate soft landing and in situ propellant production. The precursor missions will need to carry out close-up site observations, ground-penetrating radar mapping from orbit and conduct seismic surveys. Clearly the programs should be planned as a single, continuous exploration effort. A prudent minimum list of missions, including surface rovers with ranges of more than 10 km, can be derived from the numerous goals and requirements; they can be sequenced in an orderly way to ensure that time is available to feed forward the results of the precursor missions. One such sequence of missions is proposed for the decade beginning in 2003.

Tuning the morphology, luminescence and magnetic properties of hexagonal-phase NaGdF4: Yb, Er nanocrystals via altering the addition sequence of the precursors

NASA Astrophysics Data System (ADS)

Zhao, Shuwen; Xia, Donglin; Zhao, Ruimin; Zhu, Hao; Zhu, Yiru; Xiong, Yuda; Wang, Youfa

2017-01-01

Hexagonal-phase NaGdF4: Yb, Er upconversion nanocrystals (UCNCs) with tunable morphology and properties were successfully prepared via a thermal decomposition method. The influences of the adding sequence of the precursors on the morphology, chemical composition, luminescence and magnetic properties were investigated by transmission electron microscopy (TEM), inductively coupled plasma-atomic emission spectrometry (ICP-AES), upconversion (UC) spectroscopy, and a vibrating sample magnetometer (VSM). It was found that the resulting nanocrystals, with different sizes ranging from 24 to 224 nm, are in the shape of spheres, hexagonal plates and flakes; moreover, the composition percentage of Yb3+-Er3+ and Gd3+ ions was found to vary in a regular pattern with the adding sequence. Furthermore, the intensity ratios of emission colors (f g/r, f g/p), and the magnetic mass susceptibility of hexagonal-phase NaGdF4: Yb, Er nanocrystals change along with the composition of the nanocrystals. A positive correlation between the susceptibility and f g/r of NaGdF4: Yb, Er was proposed. The decomposition processes of the precursors were investigated by a thermogravimetric (TG) analyzer. The result indicated that the decomposition of the resolved lanthanide trifluoroacetate is greatly different from lanthanide trifluoroacetate powder. It is of tremendous help to recognize the decomposition process of the precursors and to understand the related reaction mechanism.

Investigation of phase evolution of CaCu3Ti4O12 (CCTO) by in situ synchrotron high-temperature powder diffraction

NASA Astrophysics Data System (ADS)

Ouyang, Xin; Huang, Saifang; Zhang, Weijun; Cao, Peng; Huang, Zhaohui; Gao, Wei

2014-03-01

In situ synchrotron X-ray powder diffraction was used to study the high-temperature phase evolution of CaCu3Ti4O12 (CCTO) precursors prepared via solid-state and sol-gel methods. After the precursors are heated to 1225 °C, the CCTO phase is the main phase observed in the calcined powder, with the presence of some minor impurities. Comparing the two precursors, we found that the onset temperature for the CCTO phase formation is 800 °C in the sol-gel precursor, lower than that in the solid-state precursor (875 °C). Intermediate phases were only observed in the sol-gel precursor. Both precursors are able to be calcined to sub-micrometric sized powders. Based on the synchrotron data along with differential scanning calorimetry (DSC) and thermal gravimetric analysis (TGA), the phase formation sequence and mechanism during calcination are proposed in this study.

A Gene Encoding a Hevein-Like Protein from Elderberry Fruits Is Homologous to PR-4 and Class V Chitinase Genes1

PubMed Central

Van Damme, Els J.M.; Charels, Diana; Roy, Soma; Tierens, Koenraad; Barre, Annick; Martins, José C.; Rougé, Pierre; Van Leuven, Fred; Does, Mirjam; Peumans, Willy J.

1999-01-01

We isolated SN-HLPf (Sambucus nigra hevein-like fruit protein), a hevein-like chitin-binding protein, from mature elderberry fruits. Cloning of the corresponding gene demonstrated that SN-HLPf is synthesized as a chimeric precursor consisting of an N-terminal chitin-binding domain corresponding to the mature elderberry protein and an unrelated C-terminal domain. Sequence comparisons indicated that the N-terminal domain of this precursor has high sequence similarity with the N-terminal domain of class I PR-4 (pathogenesis-related) proteins, whereas the C terminus is most closely related to that of class V chitinases. On the basis of these sequence homologies the gene encoding SN-HLPf can be considered a hybrid between a PR-4 and a class V chitinase gene. PMID:10198114

Using ADOPT Algorithm and Operational Data to Discover Precursors to Aviation Adverse Events

NASA Technical Reports Server (NTRS)

Janakiraman, Vijay; Matthews, Bryan; Oza, Nikunj

2018-01-01

The US National Airspace System (NAS) is making its transition to the NextGen system and assuring safety is one of the top priorities in NextGen. At present, safety is managed reactively (correct after occurrence of an unsafe event). While this strategy works for current operations, it may soon become ineffective for future airspace designs and high density operations. There is a need for proactive management of safety risks by identifying hidden and "unknown" risks and evaluating the impacts on future operations. To this end, NASA Ames has developed data mining algorithms that finds anomalies and precursors (high-risk states) to safety issues in the NAS. In this paper, we describe a recently developed algorithm called ADOPT that analyzes large volumes of data and automatically identifies precursors from real world data. Precursors help in detecting safety risks early so that the operator can mitigate the risk in time. In addition, precursors also help identify causal factors and help predict the safety incident. The ADOPT algorithm scales well to large data sets and to multidimensional time series, reduce analyst time significantly, quantify multiple safety risks giving a holistic view of safety among other benefits. This paper details the algorithm and includes several case studies to demonstrate its application to discover the "known" and "unknown" safety precursors in aviation operation.

Characterization of rat calcitonin mRNA.

PubMed Central

Amara, S G; David, D N; Rosenfeld, M G; Roos, B A; Evans, R M

1980-01-01

A chimeric plasmic containing cDNA complementary to rat calcitonin mRNA has been constructed. Partial sequence analysis shows that the insert contains a nucleotide sequence encoding the complete amino acid sequence of calcitonin. Two basic amino acids precede and three basic amino acids follow the hormone sequence, suggesting that calcitonin is generated by the proteolytic cleavage of a larger precursor in a manner analogous to that of other small polypeptide hormones. The COOH-terminal proline, known to be amidated in the secreted hormone, is followed by a glycine in the precursor. The cloned calcitonin DNA was used to characterize the expression of calcitonin mRNA. Cytoplasmic mRNAs from calcitonin-producing rat medullary thyroid carcinoma lines and from normal rat thyroid glands contain a single species, 1050 nucleotides long, whch hybridizes to the cloned calcitonin cDNA. The concentration of calcitonin mRNA sequences is greater in those tumors that produce larger amounts of immunoreactive calcitonin. RNAs from other endocrine tissues, including anterior and neurointermediate lobes of rat pituitary, contain no detectable calcitonin mRNA. Images PMID:6933496

EventThread: Visual Summarization and Stage Analysis of Event Sequence Data.

PubMed

Guo, Shunan; Xu, Ke; Zhao, Rongwen; Gotz, David; Zha, Hongyuan; Cao, Nan

2018-01-01

Event sequence data such as electronic health records, a person's academic records, or car service records, are ordered series of events which have occurred over a period of time. Analyzing collections of event sequences can reveal common or semantically important sequential patterns. For example, event sequence analysis might reveal frequently used care plans for treating a disease, typical publishing patterns of professors, and the patterns of service that result in a well-maintained car. It is challenging, however, to visually explore large numbers of event sequences, or sequences with large numbers of event types. Existing methods focus on extracting explicitly matching patterns of events using statistical analysis to create stages of event progression over time. However, these methods fail to capture latent clusters of similar but not identical evolutions of event sequences. In this paper, we introduce a novel visualization system named EventThread which clusters event sequences into threads based on tensor analysis and visualizes the latent stage categories and evolution patterns by interactively grouping the threads by similarity into time-specific clusters. We demonstrate the effectiveness of EventThread through usage scenarios in three different application domains and via interviews with an expert user.

Sequence analyses reveal that a TPR–DP module, surrounded by recombinable flanking introns, could be at the origin of eukaryotic Hop and Hip TPR–DP domains and prokaryotic GerD proteins

PubMed Central

Papandreou, Nikolaos; Chomilier, Jacques

2008-01-01

The co-chaperone Hop [heat shock protein (HSP) organising protein] is known to bind both Hsp70 and Hsp90. Hop comprises three repeats of a tetratricopeptide repeat (TPR) domain, each consisting of three TPR motifs. The first and last TPR domains are followed by a domain containing several dipeptide (DP) repeats called the DP domain. These analyses suggest that the hop genes result from successive recombination events of an ancestral TPR–DP module. From a hydrophobic cluster analysis of homologous Hop protein sequences derived from gene families, we can postulate that shifts in the open reading frames are at the origin of the present sequences. Moreover, these shifts can be related to the presence or absence of biological function. We propose to extend the family of Hop co-chaperons into the kingdom of bacteria, as several structurally related genes have been identified by hydrophobic cluster analysis. We also provide evidence of common structural characteristics between hop and hip genes, suggesting a shared precursor of ancestral TPR–DP domains. Electronic supplementary material The online version of this article (doi:10.1007/s12192-008-0083-8) contains supplementary material, which is available to authorized users. PMID:18987995

The complete general secretory pathway in gram-negative bacteria.

PubMed Central

Pugsley, A P

1993-01-01

The unifying feature of all proteins that are transported out of the cytoplasm of gram-negative bacteria by the general secretory pathway (GSP) is the presence of a long stretch of predominantly hydrophobic amino acids, the signal sequence. The interaction between signal sequence-bearing proteins and the cytoplasmic membrane may be a spontaneous event driven by the electrochemical energy potential across the cytoplasmic membrane, leading to membrane integration. The translocation of large, hydrophilic polypeptide segments to the periplasmic side of this membrane almost always requires at least six different proteins encoded by the sec genes and is dependent on both ATP hydrolysis and the electrochemical energy potential. Signal peptidases process precursors with a single, amino-terminal signal sequence, allowing them to be released into the periplasm, where they may remain or whence they may be inserted into the outer membrane. Selected proteins may also be transported across this membrane for assembly into cell surface appendages or for release into the extracellular medium. Many bacteria secrete a variety of structurally different proteins by a common pathway, referred to here as the main terminal branch of the GSP. This recently discovered branch pathway comprises at least 14 gene products. Other, simpler terminal branches of the GSP are also used by gram-negative bacteria to secrete a more limited range of extracellular proteins. PMID:8096622

Investigation of atmospheric anomalies associated with Kashmir and Awaran Earthquakes

NASA Astrophysics Data System (ADS)

Mahmood, Irfan; Iqbal, Muhammad Farooq; Shahzad, Muhammad Imran; Qaiser, Saddam

2017-02-01

The earthquake precursors' anomalies at diverse elevation ranges over the seismogenic region and prior to the seismic events are perceived using Satellite Remote Sensing (SRS) techniques and reanalysis datasets. In the current research, seismic precursors are obtained by analyzing anomalies in Outgoing Longwave Radiation (OLR), Air Temperature (AT), and Relative Humidity (RH) before the two strong Mw>7 earthquakes in Pakistan occurred on 8th October 2005 in Azad Jammu Kashmir with Mw 7.6, and 24th September 2013 in Awaran, Balochistan with Mw 7.7. Multi-parameter data were computed based on multi-year background data for anomalies computation. Results indicate significant transient variations in observed parameters before the main event. Detailed analysis suggests presence of pre-seismic activities one to three weeks prior to the main earthquake event that vanishes after the event. These anomalies are due to increase in temperature after release of gases and physical and chemical interactions on earth surface before the earthquake. The parameter variations behavior for both Kashmir and Awaran earthquake events are similar to other earthquakes in different regions of the world. This study suggests that energy release is not concentrated to a single fault but instead is released along the fault zone. The influence of earthquake events on lightning were also investigated and it was concluded that there is a significant atmospheric lightning activity after the earthquake suggesting a strong possibility for an earthquake induced thunderstorm. This study is valuable for identifying earthquake precursors especially in earthquake prone areas.

Expansion of ribosomally produced natural products: a nitrile hydratase- and Nif11-related precursor family

PubMed Central

2010-01-01

Background A new family of natural products has been described in which cysteine, serine and threonine from ribosomally-produced peptides are converted to thiazoles, oxazoles and methyloxazoles, respectively. These metabolites and their biosynthetic gene clusters are now referred to as thiazole/oxazole-modified microcins (TOMM). As exemplified by microcin B17 and streptolysin S, TOMM precursors contain an N-terminal leader sequence and C-terminal core peptide. The leader sequence contains binding sites for the posttranslational modifying enzymes which subsequently act upon the core peptide. TOMM peptides are small and highly variable, frequently missed by gene-finders and occasionally situated far from the thiazole/oxazole forming genes. Thus, locating a substrate for a particular TOMM pathway can be a challenging endeavor. Results Examination of candidate TOMM precursors has revealed a subclass with an uncharacteristically long leader sequence closely related to the enzyme nitrile hydratase. Members of this nitrile hydratase leader peptide (NHLP) family lack the metal-binding residues required for catalysis. Instead, NHLP sequences display the classic Gly-Gly cleavage motif and have C-terminal regions rich in heterocyclizable residues. The NHLP family exhibits a correlated species distribution and local clustering with an ABC transport system. This study also provides evidence that a separate family, annotated as Nif11 nitrogen-fixing proteins, can serve as natural product precursors (N11P), but not always of the TOMM variety. Indeed, a number of cyanobacterial genomes show extensive N11P paralogous expansion, such as Nostoc, Prochlorococcus and Cyanothece, which replace the TOMM cluster with lanthionine biosynthetic machinery. Conclusions This study has united numerous TOMM gene clusters with their cognate substrates. These results suggest that two large protein families, the nitrile hydratases and Nif11, have been retailored for secondary metabolism. Precursors for TOMMs and lanthionine-containing peptides derived from larger proteins to which other functions are attributed, may be widespread. The functions of these natural products have yet to be elucidated, but it is probable that some will display valuable industrial or medical activities. PMID:20500830

Peptide de novo sequencing of mixture tandem mass spectra

PubMed Central

Hotta, Stéphanie Yuki Kolbeck; Verano‐Braga, Thiago; Kjeldsen, Frank

2016-01-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co‐isolation and thus prone to false identifications. The deconvolution approach matched complementary b‐, y‐ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co‐isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20–35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. PMID:27329701

Discovering ligands for a microRNA precursor with peptoid microarrays

PubMed Central

Chirayil, Sara; Chirayil, Rachel; Luebke, Kevin J.

2009-01-01

We have screened peptoid microarrays to identify specific ligands for the RNA hairpin precursor of miR-21, a microRNA involved in cancer and heart disease. Microarrays were printed by spotting a library of 7680 N-substituted oligoglycines (peptoids) onto glass slides. Two compounds on the array specifically bind RNA having the sequence and predicted secondary structure of the miR-21 precursor hairpin and have specific affinity for the target in solution. Their binding induces a conformational change around the hairpin loop, and the most specific compound recognizes the loop sequence and a bulged uridine in the proximal duplex. Functional groups contributing affinity and specificity were identified, and by varying a critical methylpyridine group, a compound with a dissociation constant of 1.9 μM for the miR-21 precursor hairpin and a 20-fold discrimination against a closely-related hairpin was created. This work describes a systematic approach to discovery of ligands for specific pre-defined novel RNA structures. It demonstrates discovery of new ligands for an RNA for which no specific lead compounds were previously known by screening a microarray of small molecules. PMID:19561197

Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications.

PubMed

Cheng, Chia-Ying; Tsai, Chia-Feng; Chen, Yu-Ju; Sung, Ting-Yi; Hsu, Wen-Lian

2013-05-03

As spectral library searching has received increasing attention for peptide identification, constructing good decoy spectra from the target spectra is the key to correctly estimating the false discovery rate in searching against the concatenated target-decoy spectral library. Several methods have been proposed to construct decoy spectral libraries. Most of them construct decoy peptide sequences and then generate theoretical spectra accordingly. In this paper, we propose a method, called precursor-swap, which directly constructs decoy spectral libraries directly at the "spectrum level" without generating decoy peptide sequences by swapping the precursors of two spectra selected according to a very simple rule. Our spectrum-based method does not require additional efforts to deal with ion types (e.g., a, b or c ions), fragment mechanism (e.g., CID, or ETD), or unannotated peaks, but preserves many spectral properties. The precursor-swap method is evaluated on different spectral libraries and the results of obtained decoy ratios show that it is comparable to other methods. Notably, it is efficient in time and memory usage for constructing decoy libraries. A software tool called Precursor-Swap-Decoy-Generation (PSDG) is publicly available for download at http://ms.iis.sinica.edu.tw/PSDG/.

Evidence that a laminin-like insect protein mediates early events in the interaction of a Phytoparasite with its vector's salivary gland.

PubMed

de Almeida Dias, Felipe; Souza dos Santos, Andre Luis; Santos Lery, Letícia Miranda; Alves e Silva, Thiago Luiz; Oliveira, Mauricio Martins; Bisch, Paulo Mascarello; Saraiva, Elvira Maria; Souto-Padrón, Thaïs Cristina; Lopes, Angela Hampshire

2012-01-01

Phytomonas species are plant parasites of the family Trypanosomatidae, which are transmitted by phytophagous insects. Some Phytomonas species cause major agricultural damages. The hemipteran Oncopeltus fasciatus is natural and experimental host for several species of trypanosomatids, including Phytomonas spp. The invasion of the insect vectors' salivary glands is one of the most important events for the life cycle of Phytomonas species. In the present study, we show the binding of Phytomonas serpens at the external face of O. fasciatus salivary glands by means of scanning electron microscopy and the in vitro interaction of living parasites with total proteins from the salivary glands in ligand blotting assays. This binding occurs primarily through an interaction with a 130 kDa salivary gland protein. The mass spectrometry of the trypsin-digest of this protein matched 23% of human laminin-5 β3 chain precursor sequence by 16 digested peptides. A protein sequence search through the transcriptome of O. fasciatus embryo showed a partial sequence with 51% similarity to human laminin β3 subunit. Anti-human laminin-5 β3 chain polyclonal antibodies recognized the 130 kDa protein by immunoblotting. The association of parasites with the salivary glands was strongly inhibited by human laminin-5, by the purified 130 kDa insect protein, and by polyclonal antibodies raised against the human laminin-5 β3 chain. This is the first report demonstrating that a laminin-like molecule from the salivary gland of O. fasciatus acts as a receptor for Phytomonas binding. The results presented in this investigation are important findings that will support further studies that aim at developing new approaches to prevent the transmission of Phytomonas species from insects to plants and vice-versa.

Evidence That a Laminin-Like Insect Protein Mediates Early Events in the Interaction of a Phytoparasite with Its Vector's Salivary Gland

PubMed Central

Dias, Felipe de Almeida; dos Santos, Andre Luis Souza; Lery, Letícia Miranda Santos; Alves e Silva, Thiago Luiz; Oliveira, Mauricio Martins; Bisch, Paulo Mascarello; Saraiva, Elvira Maria; Souto-Padrón, Thaïs Cristina; Lopes, Angela Hampshire

2012-01-01

Phytomonas species are plant parasites of the family Trypanosomatidae, which are transmitted by phytophagous insects. Some Phytomonas species cause major agricultural damages. The hemipteran Oncopeltus fasciatus is natural and experimental host for several species of trypanosomatids, including Phytomonas spp. The invasion of the insect vectors' salivary glands is one of the most important events for the life cycle of Phytomonas species. In the present study, we show the binding of Phytomonas serpens at the external face of O. fasciatus salivary glands by means of scanning electron microscopy and the in vitro interaction of living parasites with total proteins from the salivary glands in ligand blotting assays. This binding occurs primarily through an interaction with a 130 kDa salivary gland protein. The mass spectrometry of the trypsin-digest of this protein matched 23% of human laminin-5 β3 chain precursor sequence by 16 digested peptides. A protein sequence search through the transcriptome of O. fasciatus embryo showed a partial sequence with 51% similarity to human laminin β3 subunit. Anti-human laminin-5 β3 chain polyclonal antibodies recognized the 130 kDa protein by immunoblotting. The association of parasites with the salivary glands was strongly inhibited by human laminin-5, by the purified 130 kDa insect protein, and by polyclonal antibodies raised against the human laminin-5 β3 chain. This is the first report demonstrating that a laminin-like molecule from the salivary gland of O. fasciatus acts as a receptor for Phytomonas binding. The results presented in this investigation are important findings that will support further studies that aim at developing new approaches to prevent the transmission of Phytomonas species from insects to plants and vice-versa. PMID:23118944

The imprint of geologic history on within-island diversification of woodlouse-hunter spiders (Araneae, Dysderidae) in the Canary Islands.

PubMed

Macías-Hernández, Nuria; Bidegaray-Batista, Leticia; Emerson, Brent C; Oromí, Pedro; Arnedo, Miquel

2013-01-01

Geological processes and ecological adaptation are major drivers of diversification on oceanic islands. Although diversification in these islands is often interpreted as resulting from dispersal or island hopping rather than vicariance, this may not be the case in islands with complex geological histories. The island of Tenerife, in the Canary Islands, emerged in the late Miocene as 3 precursor islands that were subsequently connected and reisolated by volcanic cycles. The spider Dysdera verneaui is endemic to the island of Tenerife, where it is widely distributed throughout most island habitats, providing an excellent model to investigate the role of physical barriers and ecological adaptation in shaping within-island diversity. Here, we present evidence that the phylogeographic patterns of this species trace back to the independent emergence of the protoislands. Molecular markers (mitochondrial genes cox1, 16S, and nad1 and the nuclear genes ITS-2 and 28S) analyzed from 100 specimens (including a thorough sampling of D. verneaui populations and additional outgroups) identify 2 distinct evolutionary lineages that correspond to 2 precursor islands, each with diagnostic genital characters indicative of separate species status. Episodic introgression events between these 2 main evolutionary lineages explain the observed incongruence between mitochondrial and nuclear markers, probably as a result of the homogenization of their ITS-2 sequence types. The most widespread lineage exhibits a complex population structure, which is compatible with either secondary contact, following connection of deeply divergent lineages, or alternatively, a back colonization from 1 precursor island to another.

Identification, by molecular cloning, of a novel type of I2-superfamily conotoxin precursor and two novel I2-conotoxins from the worm-hunter snail Conus spurius from the Gulf of México.

PubMed

Zamora-Bustillos, Roberto; Aguilar, Manuel B; Falcón, Andrés

2010-03-01

cDNA was prepared from the venom duct of a single Conus spurius specimen collected near the coast of Campeche, México. From it, PCR products were generated aiming to clone I-conotoxin precursors. Thirty clones were sequenced and predicted to encode ten distinct precursors: seven of I(2)-conotoxins and three of I(2)-like-conotoxins. These precursors contain three different, mature toxins, sr11a, sr11b and sr11c, of which two are novel and one (sr11a) has been previously purified and characterized from the venom of this species. The precursors include a 26- (I(2)) or 23- residue signal peptide (I(2)-like), a 31-residue "pro" region (I(2)-like), and a 32-residue mature toxin region (I(2) and I(2)-like). In addition, all the precursors have a 13-residue "post" region which contains a gamma-carboxylation recognition sequence that directs the gamma-carboxylation of Glu-9 and Glu-10 of toxin sr11a and, possibly, Glu-13 of toxin sr11b and Glu-9 of toxin sr11c. This is the first time that a "post" region has been found in precursors of I-conotoxins that also contain a "pro" region. The "post" peptide is enzymatically processed to yield the amidated mature toxin sr11a, which implies that gamma-carboxylation occurs before amidation. Phylogenetic analysis at the whole precursor level indicates that the I(2)-like-conotoxins of C. spurius are more related to I(2)-conotoxins than to I(1)- and I(3)-conotoxins from other species, and that they might represent a new subgroup of the I(2)-superfamily. The three I-conotoxins from C. spurius have charge differences at seven to nine positions, suggesting that they might have different molecular target types or subtypes. (c) 2009 Elsevier Inc. All rights reserved.

Observations of Electromagnetic Whistler Precursors at Supercritical Interplanetary Shocks

NASA Technical Reports Server (NTRS)

Wilson, L. B., III; Koval, A.; Szabo, Adam; Breneman, A.; Cattell, C. A.; Goetz, K.; Kellogg, P. J.; Kersten, K.; Kasper, J. C.; Maruca, B. A.;

De novo transcriptome sequencing reveals a considerable bias in the incidence of simple sequence repeats towards the downstream of 'Pre-miRNAs' of black pepper.

PubMed

Joy, Nisha; Asha, Srinivasan; Mallika, Vijayan; Soniya, Eppurathu Vasudevan

2013-01-01

Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L.), an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs) are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs). We used the array of transcripts generated, for the in silico prediction and detection of '43 pre-miRNA candidates bearing different types of SSR motifs'. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted 'pre-miRNA candidates bearing SSRs'. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted 'pre-miRNA candidates'. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of 'tandem repeats' in miRNAs.

De novo Transcriptome Sequencing Reveals a Considerable Bias in the Incidence of Simple Sequence Repeats towards the Downstream of ‘Pre-miRNAs’ of Black Pepper

PubMed Central

Joy, Nisha; Asha, Srinivasan; Mallika, Vijayan; Soniya, Eppurathu Vasudevan

2013-01-01

Next generation sequencing has an advantageon transformational development of species with limited available sequence data as it helps to decode the genome and transcriptome. We carried out the de novo sequencing using illuminaHiSeq™ 2000 to generate the first leaf transcriptome of black pepper (Piper nigrum L.), an important spice variety native to South India and also grown in other tropical regions. Despite the economic and biochemical importance of pepper, a scientifically rigorous study at the molecular level is far from complete due to lack of sufficient sequence information and cytological complexity of its genome. The 55 million raw reads obtained, when assembled using Trinity program generated 2,23,386 contigs and 1,28,157 unigenes. Reports suggest that the repeat-rich genomic regions give rise to small non-coding functional RNAs. MicroRNAs (miRNAs) are the most abundant type of non-coding regulatory RNAs. In spite of the widespread research on miRNAs, little is known about the hair-pin precursors of miRNAs bearing Simple Sequence Repeats (SSRs). We used the array of transcripts generated, for the in silico prediction and detection of ‘43 pre-miRNA candidates bearing different types of SSR motifs’. The analysis identified 3913 different types of SSR motifs with an average of one SSR per 3.04 MB of thetranscriptome. About 0.033% of the transcriptome constituted ‘pre-miRNA candidates bearing SSRs’. The abundance, type and distribution of SSR motifs studied across the hair-pin miRNA precursors, showed a significant bias in the position of SSRs towards the downstream of predicted ‘pre-miRNA candidates’. The catalogue of transcripts identified, together with the demonstration of reliable existence of SSRs in the miRNA precursors, permits future opportunities for understanding the genetic mechanism of black pepper and likely functions of ‘tandem repeats’ in miRNAs. PMID:23469176

Molecular cloning and expression of a gene for a factor which stabilizes formation of inhibitor-mitochondrial ATPase complex from Saccharomyces cerevisiae.

PubMed

Akashi, A; Yoshida, Y; Nakagoshi, H; Kuroki, K; Hashimoto, T; Tagawa, K; Imamoto, F

1988-10-01

Stabilizing factor, a 9 kDa protein, stabilizes and facilitates formation of the complex between mitochondrial ATP synthase and its intrinsic inhibitor protein. A clone containing the gene encoding the 9 kDa protein was selected from a yeast genomic library to determine the structure of its precursor protein. As deduced from the nucleotide sequence, the precursor of the yeast 9 kDa stabilizing factor contains 86 amino acid residues and has a molecular weight of 10,062. From the predicted sequence we infer that the stabilizing factor precursor contains a presequence of 23 amino acid residues at its amino terminus. We also used S1 mapping to determine the initiation site of transcription under glucose-repressed or derepressed conditions. These experiments suggest that transcription of this gene starts at three different sites and that only one of them is not affected by the presence of glucose.

Diversity among Tacaribe serocomplex viruses (family Arenaviridae) naturally associated with the Mexican woodrat (Neotoma mexicana)

PubMed Central

Cajimat, Maria N. B.; Milazzo, Mary Louise; Borchert, Jeff N.; Abbott, Ken D.; Bradley, Robert D.; Fulhorst, Charles F.

2008-01-01

The results of analyses of glycoprotein precursor and nucleocapsid protein gene sequences indicated that an arenavirus isolated from a Mexican woodrat (Neotoma mexicana) captured in Arizona is a strain of a novel species (proposed name Skinner Tank virus) and that arenaviruses isolated from Mexican woodrats captured in Colorado, New Mexico, and Utah are strains of Whitewater Arroyo virus or species phylogenetically closely related to Whitewater Arroyo virus. Pairwise comparisons of glycoprotein precursor sequences and nucleocapsid protein sequences revealed a high level of divergence among the viruses isolated from the Mexican woodrats captured in Colorado, New Mexico, and Utah and the Whitewater Arroyo virus prototype strain AV 9310135, which originally was isolated from a white-throated woodrat (Neotoma albigula) captured in New Mexico. Conceptually, the viruses from Colorado, New Mexico, and Utah and strain AV 9310135 could be grouped together in a species complex in the family Arenaviridae, genus Arenavirus. PMID:18304671

Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

PubMed Central

Zhu, Yanglong; Stribinskis, Vilius; Ramos, Kenneth S.; Li, Yong

2006-01-01

RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5′ termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution. PMID:16540690

Plant MicroRNA Prediction by Supervised Machine Learning Using C5.0 Decision Trees.

PubMed

Williams, Philip H; Eyles, Rod; Weiller, Georg

2012-01-01

MicroRNAs (miRNAs) are nonprotein coding RNAs between 20 and 22 nucleotides long that attenuate protein production. Different types of sequence data are being investigated for novel miRNAs, including genomic and transcriptomic sequences. A variety of machine learning methods have successfully predicted miRNA precursors, mature miRNAs, and other nonprotein coding sequences. MirTools, mirDeep2, and miRanalyzer require "read count" to be included with the input sequences, which restricts their use to deep-sequencing data. Our aim was to train a predictor using a cross-section of different species to accurately predict miRNAs outside the training set. We wanted a system that did not require read-count for prediction and could therefore be applied to short sequences extracted from genomic, EST, or RNA-seq sources. A miRNA-predictive decision-tree model has been developed by supervised machine learning. It only requires that the corresponding genome or transcriptome is available within a sequence window that includes the precursor candidate so that the required sequence features can be collected. Some of the most critical features for training the predictor are the miRNA:miRNA(∗) duplex energy and the number of mismatches in the duplex. We present a cross-species plant miRNA predictor with 84.08% sensitivity and 98.53% specificity based on rigorous testing by leave-one-out validation.

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics

NASA Astrophysics Data System (ADS)

Van Bael, Sven; Zels, Sven; Boonen, Kurt; Beets, Isabel; Schoofs, Liliane; Temmerman, Liesbet

2018-05-01

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. [Figure not available: see fulltext.

The evolution of neuropeptide signalling: insights from echinoderms.

PubMed

Semmens, Dean C; Elphick, Maurice R

2017-09-01

Neuropeptides are evolutionarily ancient mediators of neuronal signalling that regulate a wide range of physiological processes and behaviours in animals. Neuropeptide signalling has been investigated extensively in vertebrates and protostomian invertebrates, which include the ecdysozoans Drosophila melanogaster (Phylum Arthropoda) and Caenorhabditis elegans (Phylum Nematoda). However, until recently, an understanding of evolutionary relationships between neuropeptide signalling systems in vertebrates and protostomes has been impaired by a lack of genome/transcriptome sequence data from non-ecdysozoan invertebrates. The echinoderms-a deuterostomian phylum that includes sea urchins, sea cucumbers and starfish-have been particularly important in providing new insights into neuropeptide evolution. Sequencing of the genome of the sea urchin Strongylocentrotus purpuratus (Class Echinoidea) enabled discovery of (i) the first invertebrate thyrotropin-releasing hormone-type precursor, (ii) the first deuterostomian pedal peptide/orcokinin-type precursors and (iii) NG peptides-the 'missing link' between neuropeptide S in tetrapod vertebrates and crustacean cardioactive peptide in protostomes. More recently, sequencing of the neural transcriptome of the starfish Asterias rubens (Class Asteroidea) enabled identification of 40 neuropeptide precursors, including the first kisspeptin and melanin-concentrating hormone-type precursors to be identified outside of the chordates. Furthermore, the characterization of a corazonin-type neuropeptide signalling system in A. rubens has provided important new insights into the evolution of gonadotropin-releasing hormone-related neuropeptides. Looking forward, the discovery of multiple neuropeptide signalling systems in echinoderms provides opportunities to investigate how these systems are used to regulate physiological and behavioural processes in the unique context of a decentralized, pentaradial bauplan. © The Author 2017. Published by Oxford University Press.

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics

NASA Astrophysics Data System (ADS)

Van Bael, Sven; Zels, Sven; Boonen, Kurt; Beets, Isabel; Schoofs, Liliane; Temmerman, Liesbet

2018-01-01

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies.

A Caenorhabditis elegans Mass Spectrometric Resource for Neuropeptidomics.

PubMed

Van Bael, Sven; Zels, Sven; Boonen, Kurt; Beets, Isabel; Schoofs, Liliane; Temmerman, Liesbet

2018-05-01

Neuropeptides are important signaling molecules used by nervous systems to mediate and fine-tune neuronal communication. They can function as neurotransmitters or neuromodulators in neural circuits, or they can be released as neurohormones to target distant cells and tissues. Neuropeptides are typically cleaved from larger precursor proteins by the action of proteases and can be the subject of post-translational modifications. The short, mature neuropeptide sequences often entail the only evolutionarily reasonably conserved regions in these precursor proteins. Therefore, it is particularly challenging to predict all putative bioactive peptides through in silico mining of neuropeptide precursor sequences. Peptidomics is an approach that allows de novo characterization of peptides extracted from body fluids, cells, tissues, organs, or whole-body preparations. Mass spectrometry, often combined with on-line liquid chromatography, is a hallmark technique used in peptidomics research. Here, we used an acidified methanol extraction procedure and a quadrupole-Orbitrap LC-MS/MS pipeline to analyze the neuropeptidome of Caenorhabditis elegans. We identified an unprecedented number of 203 mature neuropeptides from C. elegans whole-body extracts, including 35 peptides from known, hypothetical, as well as from completely novel neuropeptide precursor proteins that have not been predicted in silico. This set of biochemically verified peptide sequences provides the most elaborate C. elegans reference neurpeptidome so far. To exploit this resource to the fullest, we make our in-house database of known and predicted neuropeptides available to the community as a valuable resource. We are providing these collective data to help the community progress, amongst others, by supporting future differential and/or functional studies. Graphical Abstract ᅟ.

Human proinsulin C-peptide from a precursor overexpressed in Pichia pastoris.

PubMed

Huang, Yang-Bin; Li, Jiang; Gao, Xin; Sun, Jiu-Ru; Lu, Yi; Feng, Tao; Fei, Jian; Cui, Da-Fu; Xia, Qi-Chang; Ren, Jun; Zhang, You-Shang

2006-08-01

In this article we report the production of human proinsulin C-peptide with 31 amino acid residues from a precursor overexpressed in Pichia pastoris. A C-peptide precursor expression plasmid containing nine C-peptide genes in tandem was constructed and used to transform P. pastoris. Transformants with a high copy number of the C-peptide precursor gene integrated into the chromosome of P. pastoris were selected. In high-density fermentation in a 300 liter fermentor using a simple culture medium composed mainly of salt and methanol, the C-peptide precursor was overexpressed to a level of 2.28 g per liter. A simple procedure was established to purify the expression product from the culture medium. The purified C-peptide precursor was converted into C-peptide by trypsin and carboxypeptidase B joint digestion. The yield of C-peptide with a purity of 96% was 730 mg per liter of culture. The purified C-peptide was characterized by mass spectrometry, N- and C-terminal amino acid sequencing, and sodium dodecylsulfate-polyacrylamide gel electrophoresis.

Analysis of recently digitized continuous seismic data recorded during the March-May, 1980, eruption sequence at Mount St. Helens

NASA Astrophysics Data System (ADS)

Moran, S. C.; Malone, S. D.

2013-12-01

The May 18, 1980, eruption of Mount St. Helens (MSH) was an historic event, both for society and for the field of volcanology. However, our knowledge of the eruption and the precursory period leading up it is limited by the fact that most of the data, particularly seismic recordings, were not kept due to severe limitations in the amount of digital data that could be handled and stored using 1980 computer technology. Because of these limitations, only about 900 digital event files have been available for seismic studies of the March-May seismic sequence out of a total of more than 4,000 events that were counted using paper records. Fortunately, data from a subset of stations were also recorded continuously on a series of 24 analog 14-track IRIG magnetic tapes. We have recently digitized these tapes and time-corrected and cataloged the resultant digital data streams, enabling more in-depth studies of the (almost) complete pre-eruption seismic sequence using modern digital processing techniques. Of the fifteen seismic stations operating near MSH for at least a part of the two months between March 20 and May 18, six stations have relatively complete analog recordings. These recordings have gaps of minutes to days because of radio noise, poor tape quality, or missing tapes. In addition, several other stations have partial records. All stations had short-period vertical-component sensors with very limited dynamic range and unknown response details. Nevertheless, because the stations were at a range of distances and were operated at a range of gains, a variety of earthquake sizes were recorded on scale by at least one station, and therefore a much more complete understanding of the evolution of event types, sizes and character should be achievable. In our preliminary analysis of this dataset we have found over 10,000 individual events as recorded on stations 35-40 km from MSH, spanning a recalculated coda-duration magnitude range of ~1.5 to 4.1, including many M < 3.0 events that are not part of the PNSN catalog. The closest stations (2-7 km from the summit) recorded several times as many events as the more remote stations during the times they were operational, although many signals are clipped. We see a range of event types including long-period events, tremor, and occasional volcano-tectonic earthquakes. The latter group includes small volcano-tectonic events that occurred at depths of > 7 km during the crypto-dome intrusion phase, which were recognized in 1980 but not fully described. In our analysis of the hours to days prior to the May 18 eruption, we find no obvious changes in seismicity that could have been interpreted as a short-term precursor to the May 18 eruption initiation. This new dataset is currently being formatted for permanent archiving in the IRIS Data Management Center, where it will be available for anyone to use.

Self-assembly of proglycinin and hybrid proglycinin synthesized in vitro from cDNA

PubMed Central

Dickinson, Craig D.; Floener, Liliane A.; Lilley, Glenn G.; Nielsen, Niels C.

1987-01-01

An in vitro system was developed that results in the self-assembly of subunit precursors into complexes that resemble those found naturally in the endoplasmic reticulum. Subunits of glycinin, the predominant seed protein of soybeans, were synthesized from modified cDNAs using a combination of the SP6 transcription and the rabbit reticulocyte translation systems. Subunits produced from plasmid constructions that encoded either Gy4 or Gy5 gene products, but modified such that their signal sequences were absent, self-assembled into trimers equivalent in size to those precursors found in the endoplasmic reticulum. In contrast, proteins synthesized in vitro from Gy4 constructs failed to self-assemble when the signal sequence was left intact (e.g., preproglycinin) or when the coding sequence was modified to remove 27 amino acids from an internal hydrophobic region, which is highly conserved among the glycinin subunits. Various hybrid subunits were also produced by trading portions of Gy4 and Gy5 cDNAs and all self-assembled in our system. The in vitro assembly system provides an opportunity to study the self-assembly of precursors and to probe for regions important for assembly. It will also be helpful in attempts to engineer beneficial nutritional changes into this important food protein. Images PMID:16593868

Adaptor protein 2–mediated endocytosis of the β-secretase BACE1 is dispensable for amyloid precursor protein processing

PubMed Central

Prabhu, Yogikala; Burgos, Patricia V.; Schindler, Christina; Farías, Ginny G.; Magadár, Javier G.; Bonifacino, Juan S.

2012-01-01

The β-site amyloid precursor protein (APP)–cleaving enzyme 1 (BACE1) is a transmembrane aspartyl protease that catalyzes the proteolytic processing of APP and other plasma membrane protein precursors. BACE1 cycles between the trans-Golgi network (TGN), the plasma membrane, and endosomes by virtue of signals contained within its cytosolic C-terminal domain. One of these signals is the DXXLL-motif sequence DISLL, which controls transport between the TGN and endosomes via interaction with GGA proteins. Here we show that the DISLL sequence is embedded within a longer [DE]XXXL[LI]-motif sequence, DDISLL, which mediates internalization from the plasma membrane by interaction with the clathrin-associated, heterotetrameric adaptor protein 2 (AP-2) complex. Mutation of this signal or knockdown of either AP-2 or clathrin decreases endosomal localization and increases plasma membrane localization of BACE1. Remarkably, internalization-defective BACE1 is able to cleave an APP mutant that itself cannot be delivered to endosomes. The drug brefeldin A reversibly prevents BACE1-catalyzed APP cleavage, ruling out that this reaction occurs in the endoplasmic reticulum (ER) or ER–Golgi intermediate compartment. Taken together, these observations support the notion that BACE1 is capable of cleaving APP in late compartments of the secretory pathway. PMID:22553349

A pilot study of the Earthquake Precursors in the Southwest Peloponnes, Greece

NASA Astrophysics Data System (ADS)

Velez, A. P.; Tsinganos, K.; Karastathis, V. K.; Kafatos, M.; Ouzounov, D.; Papadopoulos, G. A.; Tselentis, A.; Eleftheriou, G.; Mouzakiotis, E.; Gika, F.; Aspiotis, T.; Liakopoulos, S.; Voulgaris, N.

2016-12-01

A seismic array of the most contemporary technology has been recently installed in the area of Southwest Peloponnese, Greece, an area well known for its high seismic activity. The tectonic regime of the Hellenic arc was the reason for many lethal earthquakes with considerable damage to the broader area of East Mediterranean sea. The seismic array is based on nine 32-bit stations with broadband borehole seismometers. The seismogenic region, monitored by the array, is offshore. At this place the earthquake location suffers by poor azimuthal coverage and the stations of the national seismic network are very distant to this area. Therefore, the existing network cannot effectively monitor the microseismicity. The new array achieved a detailed monitoring of the small events dropping considerably the magnitude of completeness. The detectability of the microearthquakes has been drastically improved permitting so the statistical assessment of earthquake sequences in the area. In parallel the monitored seismicity is directly related with Radon measurement in the soil, taken at three stations in the area.. Radon measurements are performed indirectly by means γ-ray spectrometry of its radioactive progenies 214Pb and 214Bi (emitted at 351 keV and 609 keV, respectively). NaI(Tl) detectors have been installed at 1 m depth, at sites in vicinity of faults providing continuous real time data. Local meteorological records for atmospheric corrections are also continuously recorded. According to the Lithosphere-Atmosphere-Ionosphere Coupling (LAIC) model atmospheric thermal anomalies observed before strong events can be attributed to increased radon concentration. This is also supported by the statistical analysis of AVHRR/NOAA-18 satellite thermal infrared (TIR) daily records. A combined study of precursor's signals is expected to provide a reliable assessment of their ability on short-term forecasting.

Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response.

PubMed

Temko, Daniel; Van Gool, Inge C; Rayner, Emily; Glaire, Mark; Makino, Seiko; Brown, Matthew; Chegwidden, Laura; Palles, Claire; Depreeuw, Jeroen; Beggs, Andrew; Stathopoulou, Chaido; Mason, John; Baker, Ann-Marie; Williams, Marc; Cerundolo, Vincenzo; Rei, Margarida; Taylor, Jenny C; Schuh, Anna; Ahmed, Ahmed; Amant, Frédéric; Lambrechts, Diether; Smit, Vincent Thbm; Bosse, Tjalling; Graham, Trevor A; Church, David N; Tomlinson, Ian

2018-03-31

Genomic instability, which is a hallmark of cancer, is generally thought to occur in the middle to late stages of tumourigenesis, following the acquisition of permissive molecular aberrations such as TP53 mutation or whole genome doubling. Tumours with somatic POLE exonuclease domain mutations are notable for their extreme genomic instability (their mutation burden is among the highest in human cancer), distinct mutational signature, lymphocytic infiltrate, and excellent prognosis. To what extent these characteristics are determined by the timing of POLE mutations in oncogenesis is unknown. Here, we have shown that pathogenic POLE mutations are detectable in non-malignant precursors of endometrial and colorectal cancer. Using genome and exome sequencing, we found that multiple driver mutations in POLE-mutant cancers show the characteristic POLE mutational signature, including those in genes conventionally regarded as initiators of tumourigenesis. In POLE-mutant cancers, the proportion of monoclonal predicted neoantigens was similar to that in other cancers, but the absolute number was much greater. We also found that the prominent CD8 + T-cell infiltrate present in POLE-mutant cancers was evident in their precursor lesions. Collectively, these data indicate that somatic POLE mutations are early, quite possibly initiating, events in the endometrial and colorectal cancers in which they occur. The resulting early onset of genomic instability may account for the striking immune response and excellent prognosis of these tumours, as well as their early presentation. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.

Isolation of dermatoxin from frog skin, an antibacterial peptide encoded by a novel member of the dermaseptin genes family.

PubMed

Amiche, M; Seon, A A; Wroblewski, H; Nicolas, P

2000-07-01

A 32-residue peptide, named dermatoxin, has been extracted from the skin of a single specimen of the tree frog Phyllomedusa bicolor, and purified to homogeneity using a four-step protocol. Mass spectral analysis and sequencing of the purified peptide, as well as chemical synthesis and cDNA analysis were consistent with the structure: SLGSFLKGVGTTLASVGKVVSDQF GKLLQAGQ. This peptide proved to be bactericidal towards mollicutes (wall-less eubacteria) and Gram-positive eubacteria, and also, though to a lesser extent, towards Gram-negative eubacteria. Measurement of the bacterial membrane potential revealed that the plasma membrane is the primary target of dermatoxin. Observation of bacterial cells using reflected light fluorescence microscopy after DNA-staining was consistent with a mechanism of cell killing based upon the alteration of membrane permeability rather than membrane solubilization, very likely by forming ion-conducting channels through the plasma membrane. CD spectroscopy and secondary structure predictions indicated that dermatoxin assumes an amphipathic alpha-helical conformation in low polarity media which mimic the lipophilicity of the membrane of target microorganisms. PCR analysis coupled with cDNA cloning and sequencing revealed that dermatoxin is expressed in the skin, the intestine and the brain. Preprodermatoxin from the brain and the intestine have the same sequence as the skin preproform except for two amino-acid substitutions in the preproregion of the brain precursor. The dermatoxin precursor displayed the characteristic features of preprodermaseptins, a family of peptide precursors found in the skin of Phyllomedusa ssp. Precursors of this family have a common N-terminal preproregion followed by markedly different C-terminal domains that give rise to 19-34-residue peptide antibiotics named dermaseptins B and phylloxin, and to the D-amino-acid-containing opioid heptapeptides dermorphins and deltorphins. Because the structures and cidal mechanisms of dermatoxin, dermaseptins B and phylloxin are very different, dermatoxin extends the repertoire of structurally and functionally diverse peptides derived from the rapidly evolving C-terminal domains of precursors of the dermaseptins family.

Prototype foamy virus envelope glycoprotein leader peptide processing is mediated by a furin-like cellular protease, but cleavage is not essential for viral infectivity.

PubMed

Duda, Anja; Stange, Annett; Lüftenegger, Daniel; Stanke, Nicole; Westphal, Dana; Pietschmann, Thomas; Eastman, Scott W; Linial, Maxine L; Rethwilm, Axel; Lindemann, Dirk

2004-12-01

Analogous to cellular glycoproteins, viral envelope proteins contain N-terminal signal sequences responsible for targeting them to the secretory pathway. The prototype foamy virus (PFV) envelope (Env) shows a highly unusual biosynthesis. Its precursor protein has a type III membrane topology with both the N and C terminus located in the cytoplasm. Coexpression of FV glycoprotein and interaction of its leader peptide (LP) with the viral capsid is essential for viral particle budding and egress. Processing of PFV Env into the particle-associated LP, surface (SU), and transmembrane (TM) subunits occur posttranslationally during transport to the cell surface by yet-unidentified cellular proteases. Here we provide strong evidence that furin itself or a furin-like protease and not the signal peptidase complex is responsible for both processing events. N-terminal protein sequencing of the SU and TM subunits of purified PFV Env-immunoglobulin G immunoadhesin identified furin consensus sequences upstream of both cleavage sites. Mutagenesis analysis of two overlapping furin consensus sequences at the PFV LP/SU cleavage site in the wild-type protein confirmed the sequencing data and demonstrated utilization of only the first site. Fully processed SU was almost completely absent in viral particles of mutants having conserved arginine residues replaced by alanines in the first furin consensus sequence, but normal processing was observed upon mutation of the second motif. Although these mutants displayed a significant loss in infectivity as a result of reduced particle release, no correlation to processing inhibition was observed, since another mutant having normal LP/SU processing had a similar defect.

Helios 1 energetic particle observations of the solar gamma-ray/neutron flare events of 1982 June 3 and 1980 June 21

NASA Technical Reports Server (NTRS)

Mcdonald, F. B.; Van Hollebeke, M. A. I.

1985-01-01

The characteristics of the energetic particles associated with the solar gamma-ray/neutron flare events of June 3, 1982 and June 21, 1980 observed by the Goddard cosmic-ray experiment on Helios 1 (at heliocentric distances of 0.57 and 0.54 AU, respectively) differ in several important respects from typical sonar particle increases. In particular, the June 3, 1982 event has a proton energy spectrum which fits a remarkable flat power law in kinetic energy with a spectral index of 1.2, an electron/proton ratio of 1 at 4 MeV, and a small but well-defined precursor event that began some 3 hr before the impulsive flare increase. Similar energetic particle precursors were observed for the gamma-ray associated 1980 June 21 and June 7 flare events. At energies less than about 40 MeV, the particle onset time measured for the June 3, 1982 event is anomalous, suggesting that these lower energy particles may have been released at the sun about 1-2 minutes before the higher energy particles.

Lentiviral CRISPR/Cas9 vector mediated miR-21 gene editing inhibits the epithelial to mesenchymal transition in ovarian cancer cells.

PubMed

Huo, Wenying; Zhao, Guannan; Yin, Jinggang; Ouyang, Xuan; Wang, Yinan; Yang, Chuanhe; Wang, Baojing; Dong, Peixin; Wang, Zhixiang; Watari, Hidemichi; Chaum, Edward; Pfeffer, Lawrence M; Yue, Junming

2017-01-01

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats) mediated genome editing is a powerful approach for loss of function studies. Here we report that lentiviral CRISPR/Cas9 vectors are highly efficient in introducing mutations in the precursor miRNA sequence, thus leading to the loss of miRNA expression and function. We constructed four different lentiviral CRISPR/Cas9 vectors that target different regions of the precursor miR-21 sequence and found that these lentiviral CRISPR/Cas9 miR-21 gRNA vectors induced mutations in the precursor sequences as shown by DNA surveyor mutation assay and Sanger sequencing. Two miR-21 lentiviral CRISPR/Cas9 gRNA vectors were selected to probe miR-21 function in ovarian cancer SKOV3 and OVCAR3 cell lines. Our data demonstrate that disruption of pre-miR-21 sequences leads to reduced cell proliferation, migration and invasion. Moreover, CRISPR/Cas9-mediated miR-21 gene editing sensitizes both SKOV3 and OVCAR3 cells to chemotherapeutic drug treatment. Disruption of miR-21 leads to the inhibition of epithelial to mesenchymal transition (EMT) in both SKOV3 and OVCAR3 cells as evidenced by the upregulation of epithelial cell marker E-cadherin and downregulation of mesenchymal marker genes, vimentin and Snai2. The miR-21 target genes PDCD4 and SPRY2 were upregulated in cells transduced with miR-21gRNAs compared to controls. Our study indicates that lentiviral CRISPR/Cas9-mediated miRNA gene editing is an effective approach to address miRNA function, and disruption of miR-21 inhibits EMT in ovarian cancer cells.

Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) are endogenously encoded small RNAs that post-transcriptionally regulate gene expression. MiRNAs play essential roles in almost all plant biological processes. Currently, few miRNAs have been identified in the model food legume Phaseolus vulgaris (common bean). Recent advances in next generation sequencing technologies have allowed the identification of conserved and novel miRNAs in many plant species. Here, we used Illumina's sequencing by synthesis (SBS) technology to identify and characterize the miRNA population of Phaseolus vulgaris. Results Small RNA libraries were generated from roots, flowers, leaves, and seedlings of P. vulgaris. Based on similarity to previously reported plant miRNAs,114 miRNAs belonging to 33 conserved miRNA families were identified. Stem-loop precursors and target gene sequences for several conserved common bean miRNAs were determined from publicly available databases. Less conserved miRNA families and species-specific common bean miRNA isoforms were also characterized. Moreover, novel miRNAs based on the small RNAs were found and their potential precursors were predicted. In addition, new target candidates for novel and conserved miRNAs were proposed. Finally, we studied organ-specific miRNA family expression levels through miRNA read frequencies. Conclusions This work represents the first massive-scale RNA sequencing study performed in Phaseolus vulgaris to identify and characterize its miRNA population. It significantly increases the number of miRNAs, precursors, and targets identified in this agronomically important species. The miRNA expression analysis provides a foundation for understanding common bean miRNA organ-specific expression patterns. The present study offers an expanded picture of P. vulgaris miRNAs in relation to those of other legumes. PMID:22394504

Lentiviral CRISPR/Cas9 vector mediated miR-21 gene editing inhibits the epithelial to mesenchymal transition in ovarian cancer cells

PubMed Central

Huo, Wenying; Zhao, Guannan; Yin, Jinggang; Ouyang, Xuan; Wang, Yinan; Yang, Chuanhe; Wang, Baojing; Dong, Peixin; Wang, Zhixiang; Watari, Hidemichi; Chaum, Edward; Pfeffer, Lawrence M.; Yue, Junming

2017-01-01

CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats) mediated genome editing is a powerful approach for loss of function studies. Here we report that lentiviral CRISPR/Cas9 vectors are highly efficient in introducing mutations in the precursor miRNA sequence, thus leading to the loss of miRNA expression and function. We constructed four different lentiviral CRISPR/Cas9 vectors that target different regions of the precursor miR-21 sequence and found that these lentiviral CRISPR/Cas9 miR-21 gRNA vectors induced mutations in the precursor sequences as shown by DNA surveyor mutation assay and Sanger sequencing. Two miR-21 lentiviral CRISPR/Cas9 gRNA vectors were selected to probe miR-21 function in ovarian cancer SKOV3 and OVCAR3 cell lines. Our data demonstrate that disruption of pre-miR-21 sequences leads to reduced cell proliferation, migration and invasion. Moreover, CRISPR/Cas9-mediated miR-21 gene editing sensitizes both SKOV3 and OVCAR3 cells to chemotherapeutic drug treatment. Disruption of miR-21 leads to the inhibition of epithelial to mesenchymal transition (EMT) in both SKOV3 and OVCAR3 cells as evidenced by the upregulation of epithelial cell marker E-cadherin and downregulation of mesenchymal marker genes, vimentin and Snai2. The miR-21 target genes PDCD4 and SPRY2 were upregulated in cells transduced with miR-21gRNAs compared to controls. Our study indicates that lentiviral CRISPR/Cas9-mediated miRNA gene editing is an effective approach to address miRNA function, and disruption of miR-21 inhibits EMT in ovarian cancer cells. PMID:28123598

Peptide de novo sequencing of mixture tandem mass spectra.

PubMed

Gorshkov, Vladimir; Hotta, Stéphanie Yuki Kolbeck; Verano-Braga, Thiago; Kjeldsen, Frank

2016-09-01

The impact of mixture spectra deconvolution on the performance of four popular de novo sequencing programs was tested using artificially constructed mixture spectra as well as experimental proteomics data. Mixture fragmentation spectra are recognized as a limitation in proteomics because they decrease the identification performance using database search engines. De novo sequencing approaches are expected to be even more sensitive to the reduction in mass spectrum quality resulting from peptide precursor co-isolation and thus prone to false identifications. The deconvolution approach matched complementary b-, y-ions to each precursor peptide mass, which allowed the creation of virtual spectra containing sequence specific fragment ions of each co-isolated peptide. Deconvolution processing resulted in equally efficient identification rates but increased the absolute number of correctly sequenced peptides. The improvement was in the range of 20-35% additional peptide identifications for a HeLa lysate sample. Some correct sequences were identified only using unprocessed spectra; however, the number of these was lower than those where improvement was obtained by mass spectral deconvolution. Tight candidate peptide score distribution and high sensitivity to small changes in the mass spectrum introduced by the employed deconvolution method could explain some of the missing peptide identifications. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Seasonal and spatial variability of nitrosamines and their precursor sources at a large-scale urban drinking water system.

PubMed

Woods, Gwen C; Trenholm, Rebecca A; Hale, Bruce; Campbell, Zeke; Dickenson, Eric R V

2015-07-01

Nitrosamines are considered to pose greater health risks than currently regulated DBPs and are subsequently listed as a priority pollutant by the EPA, with potential for future regulation. Denver Water, as part of the EPA's Unregulated Contaminant Monitoring Rule 2 (UCMR2) monitoring campaign, found detectable levels of N-nitrosodimethylamine (NDMA) at all sites of maximum residency within the distribution system. To better understand the occurrence of nitrosamines and nitrosamine precursors, Denver Water undertook a comprehensive year-long monitoring campaign. Samples were taken every two weeks to monitor for NDMA in the distribution system, and quarterly sampling events further examined 9 nitrosamines and nitrosamine precursors throughout the treatment and distribution systems. NDMA levels within the distribution system were typically low (>1.3 to 7.2 ng/L) with a remote distribution site (frequently >200 h of residency) experiencing the highest concentrations found. Eight other nitrosamines (N-nitrosomethylethylamine, N-nitrosodiethylamine, N-nitroso-di-n-propylamine, N-nitroso-di-n-butylamine, N-nitroso-di-phenylamine, N-nitrosopyrrolidine, N-nitrosopiperidine, N-nitrosomorpholine) were also monitored but none of these 8, or precursors of these 8 [as estimated with formation potential (FP) tests], were detected anywhere in raw, partially-treated or distribution samples. Throughout the year, there was evidence that seasonality may impact NDMA formation, such that lower temperatures (~5-10°C) produced greater NDMA than during warmer months. The year of sampling further provided evidence that water quality and weather events may impact NDMA precursor loads. Precursor loading estimates demonstrated that NDMA precursors increased during treatment (potentially from cationic polymer coagulant aids). The precursor analysis also provided evidence that precursors may have increased further within the distribution system itself. This comprehensive study of a large-scale drinking water system provides insight into the variability of NDMA occurrence in a chloraminated system, which may be impacted by seasonality, water quality changes and/or the varied origins of NDMA precursors within a given system. Copyright © 2015 Elsevier B.V. All rights reserved.

Amino- and carboxyl-terminal amino acid sequences of proteins coded by gag gene of murine leukemia virus

PubMed Central

Oroszlan, Stephen; Henderson, Louis E.; Stephenson, John R.; Copeland, Terry D.; Long, Cedric W.; Ihle, James N.; Gilden, Raymond V.

1978-01-01

The amino- and carboxyl-terminal amino acid sequences of proteins (p10, p12, p15, and p30) coded by the gag gene of Rauscher and AKR murine leukemia viruses were determined. Among these proteins, p15 from both viruses appears to have a blocked amino end. Proline was found to be the common NH2 terminus of both p30s and both p12s, and alanine of both p10s. The amino-terminal sequences of p30s are identical, as are those of p10s, while the p12 sequences are clearly distinctive but also show substantial homology. The carboxyl-terminal amino acids of both viral p30s and p12s are leucine and phenylalanine, respectively. Rauscher leukemia virus p15 has tyrosine as the carboxyl terminus while AKR virus p15 has phenylalanine in this position. The compositional and sequence data provide definite chemical criteria for the identification of analogous gag gene products and for the comparison of viral proteins isolated in different laboratories. On the basis of amino acid sequences and the previously proposed H-p15-p12-p30-p10-COOH peptide sequence in the precursor polyprotein, a model for cleavage sites involved in the post-translational processing of the precursor coded for by the gag gene is proposed. PMID:206897

An Approach for Peptide Identification by De Novo Sequencing of Mixture Spectra.

PubMed

Liu, Yi; Ma, Bin; Zhang, Kaizhong; Lajoie, Gilles

2017-01-01

Mixture spectra occur quite frequently in a typical wet-lab mass spectrometry experiment, which result from the concurrent fragmentation of multiple precursors. The ability to efficiently and confidently identify mixture spectra is essential to alleviate the existent bottleneck of low mass spectra identification rate. However, most of the traditional computational methods are not suitable for interpreting mixture spectra, because they still take the assumption that the acquired spectra come from the fragmentation of a single precursor. In this manuscript, we formulate the mixture spectra de novo sequencing problem mathematically, and propose a dynamic programming algorithm for the problem. Additionally, we use both simulated and real mixture spectra data sets to verify the merits of the proposed algorithm.

Getting a cue before getting a clue: Event-related potentials to inference in visual narrative comprehension

PubMed Central

Cohn, Neil; Kutas, Marta

2015-01-01

Inference has long been emphasized in the comprehension of verbal and visual narratives. Here, we measured event-related brain potentials to visual sequences designed to elicit inferential processing. In Impoverished sequences, an expressionless “onlooker” watches an undepicted event (e.g., person throws a ball for a dog, then watches the dog chase it) just prior to a surprising finale (e.g., someone else returns the ball), which should lead to an inference (i.e., the different person retrieved the ball). Implied sequences alter this narrative structure by adding visual cues to the critical panel such as a surprised facial expression to the onlooker implying they saw an unexpected, albeit undepicted, event. In contrast, Expected sequences show a predictable, but then confounded, event (i.e., dog retrieves ball, then different person returns it), and Explicit sequences depict the unexpected event (i.e., different person retrieves then returns ball). At the critical penultimate panel, sequences representing depicted events (Explicit, Expected) elicited a larger posterior positivity (P600) than the relatively passive events of an onlooker (Impoverished, Implied), though Implied sequences were slightly more positive than Impoverished sequences. At the subsequent and final panel, a posterior positivity (P600) was greater to images in Impoverished sequences than those in Explicit and Implied sequences, which did not differ. In addition, both sequence types requiring inference (Implied, Impoverished) elicited a larger frontal negativity than those explicitly depicting events (Expected, Explicit). These results show that neural processing differs for visual narratives omitting events versus those depicting events, and that the presence of subtle visual cues can modulate such effects presumably by altering narrative structure. PMID:26320706

Intermediate-term earthquake prediction

USGS Publications Warehouse

Knopoff, L.

1990-01-01

The problems in predicting earthquakes have been attacked by phenomenological methods from pre-historic times to the present. The associations of presumed precursors with large earthquakes often have been remarked upon. the difficulty in identifying whether such correlations are due to some chance coincidence or are real precursors is that usually one notes the associations only in the relatively short time intervals before the large events. Only rarely, if ever, is notice taken of whether the presumed precursor is to be found in the rather long intervals that follow large earthquakes, or in fact is absent in these post-earthquake intervals. If there are enough examples, the presumed correlation fails as a precursor in the former case, while in the latter case the precursor would be verified. Unfortunately, the observer is usually not concerned with the 'uniteresting' intervals that have no large earthquakes. 

Observed impacts of duration and seasonality of atmospheric-river landfalls on soil moisture and runoff in coastal northern California

USGS Publications Warehouse

Ralph, F.M.; Coleman, T.; Neiman, P.J.; Zamora, R.J.; Dettinger, Mike

2013-01-01

This study is motivated by diverse needs for better forecasts of extreme precipitation and floods. It is enabled by unique hourly observations collected over six years near California’s Russian River and by recent advances in the science of atmospheric rivers (ARs). This study fills key gaps limiting the prediction of ARs and, especially, their impacts by quantifying the duration of AR conditions and the role of duration in modulating hydrometeorological impacts. Precursor soil moisture conditions and their relationship to streamflow are also shown. On the basis of 91 well-observed events during 2004-10, the study shows that the passage of ARs over a coastal site lasted 20 h on average and that 12% of the AR events exceeded 30 h. Differences in storm-total water vapor transport directed up the mountain slope contribute 74% of the variance in storm-total rainfall across the events and 61% of the variance in storm-total runoff volume. ARs with double the composite mean duration produced nearly 6 times greater peak streamflow and more than 7 times the storm-total runoff volume. When precursor soil moisture was less than 20%, even heavy rainfall did not lead to significant streamflow. Predicting which AR events are likely to produce extreme impacts on precipitation and runoff requires accurate prediction of AR duration at landfall and observations of precursor soil moisture conditions.

When Do Students Ask Why? Examining the Precursors and Outcomes of Causal Search among First-Year College Students

ERIC Educational Resources Information Center

Stupnisky, Robert H.; Stewart, Tara L.; Daniels, Lia M.; Perry, Raymond P.

2011-01-01

It has been theorized that students are most likely to ask why following unexpected, negative, and/or important events (Weiner, 1985); however, the unique contribution of these precursors to causal search and the resultant cognitions, emotions, and behaviors remain largely unclear. In the current study we examined causal search regarding test…

One precursor, three apolipoproteins: the relationship between two crustacean lipoproteins, the large discoidal lipoprotein and the high density lipoprotein/β-glucan binding protein.

PubMed

Stieb, Stefanie; Roth, Ziv; Dal Magro, Christina; Fischer, Sabine; Butz, Eric; Sagi, Amir; Khalaila, Isam; Lieb, Bernhard; Schenk, Sven; Hoeger, Ulrich

2014-12-01

The novel discoidal lipoprotein (dLp) recently detected in the crayfish, differs from other crustacean lipoproteins in its large size, apoprotein composition and high lipid binding capacity, We identified the dLp sequence by transcriptome analyses of the hepatopancreas and mass spectrometry. Further de novo assembly of the NGS data followed by BLAST searches using the sequence of the high density lipoprotein/1-glucan binding protein (HDL-BGBP) of Astacus leptodactylus as query revealed a putative precursor molecule with an open reading frame of 14.7 kb and a deduced primary structure of 4889 amino acids. The presence of an N-terminal lipid bind- ing domain and a DUF 1943 domain suggests the relationship with the large lipid transfer proteins. Two-putative dibasic furin cleavage sites were identified bordering the sequence of the HDL-BGBP. When subjected to mass spectroscopic analyses, tryptic peptides of the large apoprotein of dLp matched the N-terminal part of the precursor, while the peptides obtained for its small apoprotein matched the C-terminal part. Repeating the analysis in the prawn Macrobrachium rosenbergii revealed a similar protein with identical domain architecture suggesting that our findings do not represent an isolated instance. Our results indicate that the above three apolipoproteins (i.e HDL-BGBP and both the large and the small subunit of dLp) are translated as a large precursor. Cleavage at the furin type sites releases two subunits forming a heterodimeric dLP particle, while the remaining part forms an HDL-BGBP whose relationship with other lipoproteins as well as specific functions are yet to be elucidated.

Episodic strain accumulation in southern california.

PubMed

Thatcher, W

1976-11-12

Reexamination of horizontal geodetic data in the region of recently discovered aseismic uplift has demonstrated that equally unusual horizontal crustal deformation accompanied the development of the uplift. During this time interval compressive strains were oriented roughly normal to the San Andreas fault, suggesting that the uplift produced little shear strain accumulation across this fault. On the other hand, the orientation of the anomalous shear straining is consistent with strain accumulation across northdipping range-front thrusts like the San Fernando fault. Accordingly, the horizontal and vertical crustal deformation disclosed by geodetic observation is interpreted as a short epoch of rapid strain accumulation on these frontal faults. If this interpretation is correct, thrust-type earthquakes will eventually release the accumulated strains, but the geodetic data examined here cannot be used to estimate when these events might occur. However, observation of an unusual sequence of tilts prior to 1971 on a level line lying to the north of the magnitude 6.4 San Fernando earthquake offers some promise for precursor monitoring. The data are adequately explained by a simple model of up-dip aseismic slip propagation toward the 1971 epicentral region. These observations and the simple model that accounts for them suggest a conceptually straightforward monitoring scheme to search for similar uplift and tilt precursors within the uplifted region. Such premonitory effects could be detected by a combination of frequenlty repeated short (30 to 70 km in length) level line measurements, precise gravity traverses, and continuously recording gravimeters sited to the north of the active frontal thrust faults. Once identified, such precursors could be closely followed in space and time, and might then provide effective warnings of impending potentially destructive earth-quakes.

Origins of gonadotropin-releasing hormone (GnRH) in vertebrates: identification of a novel GnRH in a basal vertebrate, the sea lamprey.

PubMed

Kavanaugh, Scott I; Nozaki, Masumi; Sower, Stacia A

2008-08-01

We cloned a cDNA encoding a novel (GnRH), named lamprey GnRH-II, from the sea lamprey, a basal vertebrate. The deduced amino acid sequence of the newly identified lamprey GnRH-II is QHWSHGWFPG. The architecture of the precursor is similar to that reported for other GnRH precursors consisting of a signal peptide, decapeptide, a downstream processing site, and a GnRH-associated peptide; however, the gene for lamprey GnRH-II does not have introns in comparison with the gene organization for all other vertebrate GnRHs. Lamprey GnRH-II precursor transcript was widely expressed in a variety of tissues. In situ hybridization of the brain showed expression and localization of the transcript in the hypothalamus, medulla, and olfactory regions, whereas immunohistochemistry using a specific antiserum showed only GnRH-II cell bodies and processes in the preoptic nucleus/hypothalamus areas. Lamprey GnRH-II was shown to stimulate the hypothalamic-pituitary axis using in vivo and in vitro studies. Lamprey GnRH-II was also shown to activate the inositol phosphate signaling system in COS-7 cells transiently transfected with the lamprey GnRH receptor. These studies provide evidence for a novel lamprey GnRH that has a role as a third hypothalamic GnRH. In summary, the newly discovered lamprey GnRH-II offers a new paradigm of the origin of the vertebrate GnRH family. We hypothesize that due to a genome/gene duplication event, an ancestral gene gave rise to two lineages of GnRHs: the gnathostome GnRH and lamprey GnRH-II.

Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi.

PubMed

Dorrell, Richard G; Hinksman, George A; Howe, Christopher J

2016-02-01

Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.

Effects of hydromechanical loading history and antecedent soil mechanical damage on shallow landslide triggering

NASA Astrophysics Data System (ADS)

Fan, Linfeng; Lehmann, Peter; Or, Dani

2015-10-01

Evidence suggests that the sudden triggering of rainfall-induced shallow landslides is preceded by accumulation of local internal failures in the soil mantle before their abrupt coalescence into a landslide failure plane. The mechanical status of a hillslope at any given time reflects competition between local damage accumulated during antecedent rainfall events and rates of mechanical healing (e.g., rebonding of microcracks and root regrowth). This dynamic interplay between damage accumulation and healing rates determines the initial mechanical state for landslide modeling. We evaluated the roles of these dynamic processes on landslide characteristics and patterns using a hydromechanical landslide-triggering model for a sequence of rainfall scenarios. The progressive nature of soil failure was represented by the fiber bundle model formalism that considers threshold strength of mechanical bonds linking adjacent soil columns and bedrock. The antecedent damage induced by prior rainfall events was expressed by the fraction of broken fibers that gradually regain strength or mechanically heal at rates specific to soil and roots. Results indicate that antecedent damage accelerates landslide initiation relative to pristine (undamaged) hillslopes. The volumes of first triggered landslides increase with increasing antecedent damage; however, for heavily damaged hillslopes, landslide volumes tend to decrease. Elapsed time between rainfall events allows mechanical healing that reduces the effects of antecedent damage. This study proposed a quantitative framework for systematically incorporating hydromechanical loading history and information on precursor events (e.g., such as recorded by acoustic emissions) into shallow landslide hazard assessment.

Characteristics of aerosol pollution during heavy haze events in Suzhou, China

NASA Astrophysics Data System (ADS)

Tian, M.; Wang, H. B.; Chen, Y.; Yang, F. M.; Zhang, X. H.; Zou, Q.; Zhang, R. Q.; Ma, Y. L.; He, K. B.

2015-11-01

A comprehensive measurement was carried out to analyze the heavy haze events in Suzhou in January 2013 when extremely severe haze pollution occurred in many cities in China especially in the East. Hourly concentrations of PM2.5, chemical composition (including water-soluble inorganic ions, OC, and EC), and gas-phase precursors were obtained via on-line monitoring system. Based on these data, detailed aerosol composition, light extinction and gas-phase precursors were analyzed to understand the characteristics of the haze events, moreover, the formation mechanism of nitrate and sulfate in PM2.5 and the regional sources deduced from trajectory and PSCF were discussed to explore the origin of the heavy aerosol pollution. The results showed that frequent haze events were occurred on January 2013 and the concentrations of PM2.5 often exceeded 150 μg m-3 during the haze occurrence, with a maximum concentration of 324 μg m-3 on 14 January 2013. Unfavorable weather conditions (high RH, and low rainfall, wind speed and atmospheric pressure), high concentration of secondary aerosol species (including SO42-, NO3-, NH4+, and SOC) and precursors were observed during the haze events. Additionally, OM, (NH4)2SO4, NH4NO3 were demonstrated to be the major contributors to the visibility impairment but the share differed from haze events. This study also found that the high concentration of sulfate might be explained by the heterogeneous reactions in the aqueous surface layer of pre-existing particles or in cloud processes while nitrate might be mainly formed through homogeneous gas-phase reactions. The results of trajectory clustering and the PSCF method manifested that aerosol pollutions in the studied areas were mainly affected by local activities and surrounding sources transported from nearby cities.

In Silico Prediction of Neuropeptides/Peptide Hormone Transcripts in the Cheilostome Bryozoan Bugula neritina

PubMed Central

Zhang, Gen; He, Li-Sheng; Qian, Pei-Yuan

2016-01-01

The bryozoan Bugula neritina has a biphasic life cycle that consists of a planktonic larval stage and a sessile juvenile/adult stage. The transition between these two stages is crucial for the development and recruitment of B. neritina. Metamorphosis in B. neritina is mediated by both the nervous system and the release of developmental signals. However, no research has been conducted to investigate the expression of neuropeptides (NP)/peptide hormones in B. neritina larvae. Here, we report a comprehensive study of the NP/peptide hormones in the marine bryozoan B. neritina based on in silico identification methods. We recovered 22 transcripts encompassing 11 NP/peptide hormone precursor transcript sequences. The transcript sequences of the 11 isolated NP precursors were validated by cDNA cloning using gene-specific primers. We also examined the expression of three peptide hormone precursor transcripts (BnFDSIG, BnILP1, BnGPB) in the coronate larvae of B. neritina, demonstrating their distinct expression patterns in the larvae. Overall, our findings serve as an important foundation for subsequent investigations of the peptidergic control of bryozoan larval behavior and settlement. PMID:27537380

Generation of the heterodimeric precursor GP3 of the Chlamydomonas cell wall.

PubMed

Voigt, Jürgen; Kiess, Michael; Getzlaff, Rita; Wöstemeyer, Johannes; Frank, Ronald

2010-09-01

The cell wall of the unicellular green alga Chlamydomonas reinhardtii exclusively consists of hydroxyproline-containing glycoproteins. Protein chemical analysis of its polypeptide constituents was hindered by their cross-linking via peroxidase-catalysed intermolecular isodityrosine formation and transaminase-dependent processes. To overcome this problem, we have identified putative soluble precursors using polyclonal antibodies raised against deglycosylation products of the highly purified insoluble wall fraction and analysed their amino acid sequence. The occurrence of the corresponding polypeptide in the insoluble glycoprotein framework was finally probed by epitope mapping of the polyclonal antibodies using overlapping scan peptides which, together, cover the whole amino acid sequence of the putative precursor. As a control, peptide fragments released from the insoluble wall fraction by trypsin treatment were analysed by mass spectroscopy. By this approach, the heterodimeric, chaotrope-soluble glycoprotein GP3 proved to be a constituent of the insoluble extracellular matrix of Chlamydomonas reinhardtii. Furthermore, we have shown that the polypeptide backbones of both GP3 subunits are encoded by the same gene and differ by a C-terminal truncation in the case of GP3A. © 2010 Blackwell Publishing Ltd.

The cleavage specificity of the aspartic protease of cocoa beans involved in the generation of the cocoa-specific aroma precursors.

PubMed

Janek, Katharina; Niewienda, Agathe; Wöstemeyer, Johannes; Voigt, Jürgen

2016-11-15

Particular peptides generated from the vicilin-class(7S) globulin of the cocoa beans by acid-induced proteolysis during cocoa fermentation are essential precursors of the cocoa-specific aroma notes. As revealed by in vitro studies, the formation of the cocoa-specific aroma precursors depends on the particular cleavage specificity of the cocoa aspartic protease, which cannot be substituted by pepsin. Therefore, we have investigated the effects of aspartic protease inhibitors on both enzymes and comparatively studied their cleavage specificities using different protein substrates and MALDI-TOF mass spectrometric analyses of the generated oligopeptides. Three classes of cleavage sites have been identified and characterized: (I) sequences exclusively cleaved by the cocoa enzyme, (II) sequences cleaved by both pepsin and the cocoa enzyme, and (III) those cleaved exclusively by pepsin. In contrast to most aspartic proteases from other origins, basic amino acid residues, particularly lysine, were found to be abundant in the specific cleavage sites of the cocoa enzyme. Copyright © 2016 Elsevier Ltd. All rights reserved.

Studies on transcription termination and splicing of the rRNA precursor in vivo in the presence of proflavine.

PubMed Central

Nielsen, O F; Carin, M; Westergaard, O

1984-01-01

In isolated nucleoli from Tetrahymena thermophila, low concentrations of the intercalating agent proflavine inhibit both transcription termination and splicing of the rRNA precursor. Proflavine also exerts an in vivo effect on the process of transcription termination under conditions, where the growth rate is only slightly reduced. Thus, approximately 40% of the rRNA precursor molecules, accumulated in nucleoli during 60 min of treatment with the drug, are longer than the normal 35S rRNA precursor. R-Loop mapping of these longer precursor molecules isolated after 30 and 60 min of incubation demonstrates that the RNA polymerases have a 50 fold lower elongation rate in the spacer region than in the coding region. Proflavine in the given concentration is found to have no significant effect on the splicing of properly terminated precursor molecules. In contrast, none of the longer non-terminated molecules are found to be spliced. These results indicate that proflavine primarily affects the process of transcription termination and that the splicing event is inhibited due to the improper termination of the precursor molecule. Images PMID:6694912

Mitotic position and morphology of committed precursor cells in the zebrafish retina adapt to architectural changes upon tissue maturation.

PubMed

Weber, Isabell P; Ramos, Ana P; Strzyz, Paulina J; Leung, Louis C; Young, Stephen; Norden, Caren

2014-04-24

The development of complex neuronal tissues like the vertebrate retina requires the tight orchestration of cell proliferation and differentiation. Although the complexity of transcription factors and signaling pathways involved in retinogenesis has been studied extensively, the influence of tissue maturation itself has not yet been systematically explored. Here, we present a quantitative analysis of mitotic events during zebrafish retinogenesis that reveals three types of committed neuronal precursors in addition to the previously known apical progenitors. The identified precursor types present at distinct developmental stages and exhibit different mitotic location (apical versus nonapical), cleavage plane orientation, and morphology. Interestingly, the emergence of nonapically dividing committed bipolar cell precursors can be linked to an increase in apical crowding caused by the developing photoreceptor cell layer. Furthermore, genetic interference with neuronal subset specification induces ectopic divisions of committed precursors, underlining the finding that progressing morphogenesis can effect precursor division position. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Computer-based prediction of mitochondria-targeting peptides.

PubMed

Martelli, Pier Luigi; Savojardo, Castrense; Fariselli, Piero; Tasco, Gianluca; Casadio, Rita

2015-01-01

Computational methods are invaluable when protein sequences, directly derived from genomic data, need functional and structural annotation. Subcellular localization is a feature necessary for understanding the protein role and the compartment where the mature protein is active and very difficult to characterize experimentally. Mitochondrial proteins encoded on the cytosolic ribosomes carry specific patterns in the precursor sequence from where it is possible to recognize a peptide targeting the protein to its final destination. Here we discuss to which extent it is feasible to develop computational methods for detecting mitochondrial targeting peptides in the precursor sequences and benchmark our and other methods on the human mitochondrial proteins endowed with experimentally characterized targeting peptides. Furthermore, we illustrate our newly implemented web server and its usage on the whole human proteome in order to infer mitochondrial targeting peptides, their cleavage sites, and whether the targeting peptide regions contain or not arginine-rich recurrent motifs. By this, we add some other 2,800 human proteins to the 124 ones already experimentally annotated with a mitochondrial targeting peptide.

Evolution of E × B shear and coherent fluctuations prior to H-L transitions in DIII-D and control strategies for H-L transitions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eldon, David; Boivin, Rejean L.; Chrystal, Colin

While operating a magnetic fusion device in H-mode has many advantages, care must be taken to understand and control the release of energy during the H-L back transition, as the extra energy stored within the H-mode transport barrier will have the potential to cause damage to material components of a large future tokamak such as ITER. Examining a scenario where the H-L back transition sequence begins before the E × B shearing layer decays on its own, we identify a long-lived precursor mode that is tied to the events of the H-L sequence and we develop a robust control strategymore » for ensuring gradual release of energy during the transition sequence. Back transitions in this scenario commonly begin with a rapid relaxation of the pedestal, which was previously shown to be inconsistent with ideal peeling-ballooning instability as the trigger, despite being otherwise similar to a large type-I Edge Localized Mode (ELM). Here, this so-called transient occurs when the E × B shearing rate ω E×B is significantly larger than the turbulence decorrelation rate ωT, indicating that this is not the result of runaway turbulence recovery. The transient is always synchronous with amplitude and propagation velocity modulations of the precursor mode, which has been dubbed the Modulating Pedestal Mode (MPM).The MPM is a coherent density fluctuation, which, in our scenario at least, reliably appears in the steep gradient region with f ≈ 70 kHz, k θ ≈ 0.3 cm –1, and it exists for ≳100 ms before the onset of back transitions. The transient may be reliably eliminated by reducing toroidal rotation in the co-current direction by the application of torque from counter-injecting neutral beams. The transient in these “soft” H-L transitions is then replaced by a small type-III ELM, which is also always synchronous with the MPM, and MPM shows the same behavior in both hard and soft cases.« less

Evolution of E × B shear and coherent fluctuations prior to H-L transitions in DIII-D and control strategies for H-L transitions

DOE PAGES

Eldon, David; Boivin, Rejean L.; Chrystal, Colin; ...

2015-11-19

While operating a magnetic fusion device in H-mode has many advantages, care must be taken to understand and control the release of energy during the H-L back transition, as the extra energy stored within the H-mode transport barrier will have the potential to cause damage to material components of a large future tokamak such as ITER. Examining a scenario where the H-L back transition sequence begins before the E × B shearing layer decays on its own, we identify a long-lived precursor mode that is tied to the events of the H-L sequence and we develop a robust control strategymore » for ensuring gradual release of energy during the transition sequence. Back transitions in this scenario commonly begin with a rapid relaxation of the pedestal, which was previously shown to be inconsistent with ideal peeling-ballooning instability as the trigger, despite being otherwise similar to a large type-I Edge Localized Mode (ELM). Here, this so-called transient occurs when the E × B shearing rate ω E×B is significantly larger than the turbulence decorrelation rate ωT, indicating that this is not the result of runaway turbulence recovery. The transient is always synchronous with amplitude and propagation velocity modulations of the precursor mode, which has been dubbed the Modulating Pedestal Mode (MPM).The MPM is a coherent density fluctuation, which, in our scenario at least, reliably appears in the steep gradient region with f ≈ 70 kHz, k θ ≈ 0.3 cm –1, and it exists for ≳100 ms before the onset of back transitions. The transient may be reliably eliminated by reducing toroidal rotation in the co-current direction by the application of torque from counter-injecting neutral beams. The transient in these “soft” H-L transitions is then replaced by a small type-III ELM, which is also always synchronous with the MPM, and MPM shows the same behavior in both hard and soft cases.« less

RNA-Seq analyses reveal the order of tRNA processing events and the maturation of C/D box and CRISPR RNAs in the hyperthermophile Methanopyrus kandleri

PubMed Central

Su, Andreas A. H.; Tripp, Vanessa; Randau, Lennart

2013-01-01

The methanogenic archaeon Methanopyrus kandleri grows near the upper temperature limit for life. Genome analyses revealed strategies to adapt to these harsh conditions and elucidated a unique transfer RNA (tRNA) C-to-U editing mechanism at base 8 for 30 different tRNA species. Here, RNA-Seq deep sequencing methodology was combined with computational analyses to characterize the small RNome of this hyperthermophilic organism and to obtain insights into the RNA metabolism at extreme temperatures. A large number of 132 small RNAs were identified that guide RNA modifications, which are expected to stabilize structured RNA molecules. The C/D box guide RNAs were shown to exist as circular RNA molecules. In addition, clustered regularly interspaced short palindromic repeats RNA processing and potential regulatory RNAs were identified. Finally, the identification of tRNA precursors before and after the unique C8-to-U8 editing activity enabled the determination of the order of tRNA processing events with termini truncation preceding intron removal. This order of tRNA maturation follows the compartmentalized tRNA processing order found in Eukaryotes and suggests its conservation during evolution. PMID:23620296

A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb

PubMed Central

Meng, Yijun; Yu, Dongliang; Xue, Jie; Lu, Jiangjie; Feng, Shangguo; Shen, Chenjia; Wang, Huizhong

2016-01-01

Dendrobium officinale is an important traditional Chinese herb. Here, we did a transcriptome-wide, organ-specific study on this valuable plant by combining RNA, small RNA (sRNA) and degradome sequencing. RNA sequencing of four organs (flower, root, leaf and stem) of Dendrobium officinale enabled us to obtain 536,558 assembled transcripts, from which 2,645, 256, 42 and 54 were identified to be highly expressed in the four organs respectively. Based on sRNA sequencing, 2,038, 2, 21 and 24 sRNAs were identified to be specifically accumulated in the four organs respectively. A total of 1,047 mature microRNA (miRNA) candidates were detected. Based on secondary structure predictions and sequencing, tens of potential miRNA precursors were identified from the assembled transcripts. Interestingly, phase-distributed sRNAs with degradome-based processing evidences were discovered on the long-stem structures of two precursors. Target identification was performed for the 1,047 miRNA candidates, resulting in the discovery of 1,257 miRNA--target pairs. Finally, some biological meaningful subnetworks involving hormone signaling, development, secondary metabolism and Argonaute 1-related regulation were established. All of the sequencing data sets are available at NCBI Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra/). Summarily, our study provides a valuable resource for the in-depth molecular and functional studies on this important Chinese orchid herb. PMID:26732614

Neurotensin and neuromedin N are differentially processed from a common precursor by prohormone convertases in tissues and cell lines.

PubMed

Kitabgi, Patrick

2010-01-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six amino acid NT-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by specialized endoproteases that belong to the family of proprotein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Processing gives rise mainly to NT and NN in the brain, NT and a large peptide with a C-terminal NN moiety (large NN) in the gut, and NT, large NN, and a large peptide with a C-terminal NT moiety (large NT) in the adrenals. Recent evidence indicates that PC1, PC2, and PC5-A are the prohormone convertases responsible for the processing patterns observed in the gut, brain, and adrenals, respectively. As NT, NN, large NT, and large NN are all endowed with biological activity, the evidence reviewed here supports the idea that posttranslational processing of pro-NT/NN in tissues may generate biological diversity of pathophysiological relevance.

Cbp80 is needed for the expression of piRNA components and piRNAs

PubMed Central

Colombo, Martino; Hernandez, Greco; Beuchle, Dirk; Berger, Fabienne; Peischl, Stephan; Bruggmann, Rémy

2017-01-01

Cap binding protein 80 (Cbp80) is the larger subunit of the nuclear cap-binding complex (nCBC), which is known to play important roles in nuclear mRNA processing, export, stability and quality control events. Reducing Cbp80 mRNA levels in the female germline revealed that Cbp80 is also involved in defending the germline against transposable elements. Combining such knockdown experiments with large scale sequencing of small RNAs further showed that Cbp80 is involved in the initial biogenesis of piRNAs as well as in the secondary biogenesis pathway, the ping-pong amplification cycle. We further found that Cbp80 knockdown not only led to the upregulation of transposons, but also to delocalization of Piwi, Aub and Ago3, key factors in the piRNA biosynthesis pathway. Furthermore, compared to controls, levels of Piwi and Aub were also reduced upon knock down of Cbp80. On the other hand, with the same treatment we could not detect significant changes in levels or subcellular distribution (nuage localization) of piRNA precursor transcripts. This shows that Cbp80 plays an important role in the production and localization of the protein components of the piRNA pathway and it seems to be less important for the production and export of the piRNA precursor transcripts. PMID:28746365

Evaluating MJO Event Initiation and Decay in the Skeleton Model using an RMM-like Index

DTIC Science & Technology

2015-11-25

climatology and document 35 the occurrence of primary, continuing, and terminating MJO events in the skeleton model. The 36 overall amount of MJO...solutions in a framework consistent with observations including MJO event 104 climatology and the precursor conditions associated with the initiation and...the 112 7 model along with several applications that include a comparison to the observed MJO event 113 climatology and identification of

Sequence of the structural gene for granule-bound starch synthase of potato (Solanum tuberosum L.) and evidence for a single point deletion in the amf allele.

PubMed

van der Leij, F R; Visser, R G; Ponstein, A S; Jacobsen, E; Feenstra, W J

1991-08-01

The genomic sequence of the potato gene for starch granule-bound starch synthase (GBSS; "waxy protein") has been determined for the wild-type allele of a monoploid genotype from which an amylose-free (amf) mutant was derived, and for the mutant part of the amf allele. Comparison of the wild-type sequence with a cDNA sequence from the literature and a newly isolated cDNA revealed the presence of 13 introns, the first of which is located in the untranslated leader. The promoter contains a G-box-like sequence. The deduced amino acid sequence of the precursor of GBSS shows a high degree of identity with monocot waxy protein sequences in the region corresponding to the mature form of the enzyme. The transit peptide of 77 amino acids, required for routing of the precursor to the plastids, shows much less identity with the transit peptides of the other waxy preproteins, but resembles the hydropathic distributions of these peptides. Alignment of the amino acid sequences of the four mature starch synthases with the Escherichia coli glgA gene product revealed the presence of at least three conserved boxes; there is no homology with previously proposed starch-binding domains of other enzymes involved in starch metabolism. We report the use of chimeric constructs with wild-type and amf sequences to localize, via complementation experiments, the region of the amf allele in which the mutation resides. Direct sequencing of polymerase chain reaction products confirmed that the amf mutation is a deletion of a single AT basepair in the region coding for the transit peptide.(ABSTRACT TRUNCATED AT 250 WORDS)

When and where the aftershock activity was depressed: Contrasting decay patterns of the proximate large earthquakes in southern California

USGS Publications Warehouse

Ogata, Y.; Jones, L.M.; Toda, S.

2003-01-01

Seismic quiescence has attracted attention as a possible precursor to a large earthquake. However, sensitive detection of quiescence requires accurate modeling of normal aftershock activity. We apply the epidemic-type aftershock sequence (ETAS) model that is a natural extension of the modified Omori formula for aftershock decay, allowing further clusters (secondary aftershocks) within an aftershock sequence. The Hector Mine aftershock activity has been normal, relative to the decay predicted by the ETAS model during the 14 months of available data. In contrast, although the aftershock sequence of the 1992 Landers earthquake (M = 7.3), including the 1992 Big Bear earthquake (M = 6.4) and its aftershocks, fits very well to the ETAS up until about 6 months after the main shock, the activity showed clear lowering relative to the modeled rate (relative quiescence) and lasted nearly 7 years, leading up to the Hector Mine earthquake (M = 7.1) in 1999. Specifically, the relative quiescence occurred only in the shallow aftershock activity, down to depths of 5-6 km. The sequence of deeper events showed clear, normal aftershock activity well fitted to the ETAS throughout the whole period. We argue several physical explanations for these results. Among them, we strongly suspect aseismic slips within the Hector Mine rupture source that could inhibit the crustal relaxation process within "shadow zones" of the Coulomb's failure stress change. Furthermore, the aftershock activity of the 1992 Joshua Tree earthquake (M = 6.1) sharply lowered in the same day of the main shock, which can be explained by a similar scenario.

Partial amino-acid sequence of the precursor of an immunoglobulin light chain containing NH2-terminal pyroglutamic acid.

PubMed Central

Burstein, Y; Kantour, F; Schechter, I

1976-01-01

Analyses of amino-acid sequences of the total cell-free products programmed by the mRNA of MOPC-104E gamma light (L)-chain show that over 95% of the products have sequences of a distinct protein that correspond to the L-chain precursor. In this precursor an extra piece is coupled to the NH2-terminus of the mature L-chain. Analyses of products labeled with [3H]alanine, [3H]leucine, and [3H]proline demonstrate that the extra piece is composed of at least 18 residues. Analyses of [35S]methione-labeled product indicate that the extra piece may contain an additional NH2-terminal methionine, which is detected in about 10% of the molecules. Partial recovery of the NJ2-terminal methionine (alanine, leucine, and proline are recovered in yields close to theoretical, greater than 95%) suggests that it is the initiator methionine, which is known to be short lived in eukaryotes due to rapid hydrolysis. Thus, the extra piece seems to be 19 residues in length, and it contains one methionine at the NH2-terminus, three alanines at positions 2, 12, and 17, and five leucines at positions 6, 8, 10, 11, and 13. The close gathering of leucine residues, as well as their abundance (26%), suggest that the extra piece would be quite hydrophobic. Hydrophobicity seems to be a general property of the extra piece, since similar clusters of leucine were found in the precursors of 3 KL-chains (Burstein, Y. & Schechter, I. (1976) Biochem. J. 157, 145-151). The NH2-terminus of the mature MOPC-104E gamma L-chain is blocked by pyroglutamic acid. The fact that in the precursor a peptide segment precedes this NH2-terminus establishes that pyroglutamic acid is not the initiator residue for synthesis of the L-chain. Apparently, the pyroglutamic acid is formed by cyclization of glutamic acid or glutamine during cleavage of the extra piece to yield the mature L-chain. Images PMID:822420

Effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events

DOE PAGES

Quan, Jiannong; Liu, Yangang; Liu, Quan; ...

2015-09-30

In this study, the effect of heterogeneous aqueous reactions on the secondary formation of inorganic aerosols during haze events was investigated by analysis of comprehensive measurements of aerosol composition and concentrations [e.g., particular matters (PM 2.5), nitrate (NO 3), sulfate (SO 4), ammonium (NH 4)], gas-phase precursors [e.g., nitrogen oxides (NOx), sulfur dioxide (SO 2), and ozone (O 3)], and relevant meteorological parameters [e.g., visibility and relative humidity (RH)]. The measurements were conducted in Beijing, China from Sep. 07, 2012 to Jan. 16, 2013. The results show that the conversion ratios of N from NOx to nitrate (N ratio) andmore » S from SO 2 to sulfate (S ratio) both significantly increased in haze events, suggesting enhanced conversions from NOx and SO 2 to their corresponding particle phases in the late haze period. Further analysis shows that N ratio and S ratio increased with increasing RH, with N ratio and S ratio being only 0.04 and 0.03, respectively, when RH < 40%, and increasing up to 0.16 and 0.12 when RH reached 60–80%, respectively. The enhanced conversion ratios of N and S in the late haze period is likely due to heterogeneous aqueous reactions, because solar radiation and thus the photochemical capacity are reduced by the increases in aerosols and RH. This point was further affirmed by the relationships of N ratio and S ratio to O 3: the conversion ratios increase with decreasing O 3 concentration when O 3 concentration is lower than <15 ppb but increased with increasing O 3 when O 3 concentration is higher than 15 ppb. The results suggest that heterogeneous aqueous reactions likely changed aerosols and their precursors during the haze events: in the beginning of haze events, the precursor gases accumulated quickly due to high emission and low reaction rate; the occurrence of heterogeneous aqueous reactions in the late haze period, together with the accumulated high concentrations of precursor gases such as SO 2 and NOx, accelerated the formation of secondary inorganic aerosols, and led to rapid increase of the PM 2.5 concentration.« less

Genome-wide characterization of microRNA in foxtail millet (Setaria italica)

PubMed Central

2013-01-01

Background MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood. Results In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing. Conclusions We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally. PMID:24330712

Genome-wide characterization of microRNA in foxtail millet (Setaria italica).

PubMed

Yi, Fei; Xie, Shaojun; Liu, Yuwei; Qi, Xin; Yu, Jingjuan

2013-12-13

MicroRNAs (miRNAs) are a class of short non-coding, endogenous RNAs that play key roles in many biological processes in both animals and plants. Although many miRNAs have been identified in a large number of organisms, the miRNAs in foxtail millet (Setaria italica) have, until now, been poorly understood. In this study, two replicate small RNA libraries from foxtail millet shoots were sequenced, and 40 million reads representing over 10 million unique sequences were generated. We identified 43 known miRNAs, 172 novel miRNAs and 2 mirtron precursor candidates in foxtail millet. Some miRNA*s of the known and novel miRNAs were detected as well. Further, eight novel miRNAs were validated by stem-loop RT-PCR. Potential targets of the foxtail millet miRNAs were predicted based on our strict criteria. Of the predicted target genes, 79% (351) had functional annotations in InterPro and GO analyses, indicating the targets of the miRNAs were involved in a wide range of regulatory functions and some specific biological processes. A total of 69 pairs of syntenic miRNA precursors that were conserved between foxtail millet and sorghum were found. Additionally, stem-loop RT-PCR was conducted to confirm the tissue-specific expression of some miRNAs in the four tissues identified by deep-sequencing. We predicted, for the first time, 215 miRNAs and 447 miRNA targets in foxtail millet at a genome-wide level. The precursors, expression levels, miRNA* sequences, target functions, conservation, and evolution of miRNAs we identified were investigated. Some of the novel foxtail millet miRNAs and miRNA targets were validated experimentally.

PTF13efv—AN OUTBURST 500 DAYS PRIOR TO THE SNHUNT 275 EXPLOSION AND ITS RADIATIVE EFFICIENCY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ofek, E. O.; Strotjohann, N.-L.; Rubin, A.

The progenitors of some supernovae (SNe) exhibit outbursts with super-Eddington luminosities prior to their final explosions. This behavior is common among SNe IIn, but the driving mechanisms of these precursors are not yet well-understood. SNHunt 275 was announced as a possible new SN during 2015 May. Here we report on pre-explosion observations of the location of this event by the Palomar Transient Factory (PTF) and report the detection of a precursor about 500 days prior to the 2015 May activity (PTF 13efv). The observed velocities in the 2015 transient and its 2013 precursor absorption spectra are low (1000–2000 km s{supmore » −1}), so it is not clear yet if the recent activity indeed marks the final disruption of the progenitor. Regardless of the nature of this event, we use the PTF photometric and spectral observations, as well as Swift -UVOT observations, to constrain the efficiency of the radiated energy relative to the total kinetic energy of the precursor. We find that, using an order-of-magnitude estimate and under the assumption of spherical symmetry, the ratio of the radiated energy to the kinetic energy is in the range of 4 × 10{sup −2} to 3.4 × 10{sup 3}.« less

Swallow Event Sequencing: Comparing Healthy Older and Younger Adults.

PubMed

Herzberg, Erica G; Lazarus, Cathy L; Steele, Catriona M; Molfenter, Sonja M

2018-04-23

Previous research has established that a great deal of variation exists in the temporal sequence of swallowing events for healthy adults. Yet, the impact of aging on swallow event sequence is not well understood. Kendall et al. (Dysphagia 18(2):85-91, 2003) suggested there are 4 obligatory paired-event sequences in swallowing. We directly compared adherence to these sequences, as well as event latencies, and quantified the percentage of unique sequences in two samples of healthy adults: young (< 45) and old (> 65). The 8 swallowing events that contribute to the sequences were reliably identified from videofluoroscopy in a sample of 23 healthy seniors (10 male, mean age 74.7) and 20 healthy young adults (10 male, mean age 31.5) with no evidence of penetration-aspiration or post-swallow residue. Chi-square analyses compared the proportions of obligatory pairs and unique sequences by age group. Compared to the older subjects, younger subjects had significantly lower adherence to two obligatory sequences: Upper Esophageal Sphincter (UES) opening occurs before (or simultaneous with) the bolus arriving at the UES and UES maximum distention occurs before maximum pharyngeal constriction. The associated latencies were significantly different between age groups as well. Further, significantly fewer unique swallow sequences were observed in the older group (61%) compared with the young (82%) (χ 2  = 31.8; p < 0.001). Our findings suggest that paired swallow event sequences may not be robust across the age continuum and that variation in swallow sequences appears to decrease with aging. These findings provide normative references for comparisons to older individuals with dysphagia.

The 1998 earthquake sequence south of Long Valley Caldera, California: Hints of magmatic involvement

USGS Publications Warehouse

Hough, S.E.; Dollar, R.S.; Johnson, P.

2000-01-01

A significant episode of seismic and geodetic unrest took place at Long Valley Caldera, California, beginning in the summer of 1997. Activity through late May of 1998 was concentrated in and around the south moat and the south margin of the resurgent dome. The Sierran Nevada block (SNB) region to the south/southeast remained relatively quiet until a M 5.1 event occurred there on 9 June 1998 (UT). A second M 5.1 event followed on 15 July (UT); both events were followed by appreciable aftershock sequences. An additional, distinct burst of activity began on 1 August 1998. The number of events in the August sequence (over the first week or two) was similar to the aftershock sequence of the 15 July 1998 M 5.1 event, but the later sequence was not associated with any events larger than M 4.3. All of the summer 1998 SNB activity was considered tectonic rather than magmatic; in general the SNB is considered an unlikely location for future eruptions. However, the August sequence-an 'aftershock sequence without a mainshock'-is suggestive of a strain event larger than the cumulative seismotectonic strain release. Moreover, a careful examination of waveforms from the August sequence reveals a small handful of events whose spectral signature is strikingly harmonic. We investigate the waveforms of these events using spectral, autocorrelation, and empirical Green's function techniques and conclude that they were most likely associated with a fluid-controlled source. Our observations suggest that there may have been some degree of magma or magma-derived fluid involvement in the 1998 SNB sequence.

Cleavage of precursors by the mitochondrial processing peptidase requires a compatible mature protein or an intermediate octapeptide

PubMed Central

1991-01-01

Many precursors of mitochondrial proteins are processed in two successive steps by independent matrix peptidases (MPP and MIP), whereas others are cleaved in a single step by MPP alone. To explain this dichotomy, we have constructed deletions of all or part of the octapeptide characteristic of a twice cleaved precursor (human ornithine transcarbamylase [pOTC]), have exchanged leader peptide sequences between once-cleaved (human methylmalonyl-CoA mutase [pMUT]; yeast F1ATPase beta-subunit [pF1 beta]) and twice-cleaved (pOTC; rat malate dehydrogenase (pMDH); Neurospora ubiquinol-cytochrome c reductase iron-sulfur subunit [pFe/S]) precursors, and have incubated these proteins with purified MPP and MIP. When the octapeptide of pOTC was deleted, or when the entire leader peptide of a once-cleaved precursor (pMUT or pF1 beta) was joined to the mature amino terminus of a twice-cleaved precursor (pOTC or pFe/S), no cleavage was produced by either protease. Cleavage of these constructs by MPP was restored by re- inserting as few as two amino-terminal residues of the octapeptide or of the mature amino terminus of a once-cleaved precursor. We conclude that the mature amino terminus of a twice-cleaved precursor is structurally incompatible with cleavage by MPP; such proteins have evolved octapeptides cleaved by MIP to overcome this incompatibility. PMID:1672532

Endogenous peptide profile for elucidating biosynthetic processing of the ghrelin precursor.

PubMed

Tsuchiya, Takashi; Iwakura, Hiroshi; Minamino, Naoto; Kangawa, Kenji; Sasaki, Kazuki

2017-09-02

Ghrelin is an orexigenic peptide primarily produced by gastric endocrine cells. The biosynthetic cleavage site of ghrelin has been well documented, but how its downstream region undergoes proteolytic processing remains poorly explored. Here, we provide the first snapshot of endogenous peptides from the ghrelin precursor by profiling the secretopeptidome of cultured mouse ghrelin-producing cells during exocytosis. Mapping of MS/MS sequenced peptides to the precursor highlighted three atypical monobasic processing sites, including the established C-terminus of ghrelin and the N-terminal cleavage site for obestatin, a putative 23-amino-acid C-terminally amidated peptide. However, we found that mouse obestatin does not occur in the form originally reported, but that a different amidation site is used to generate a shorter peptide. These data can be extended to study and characterize the precursor-derived peptides located downstream of ghrelin in different biological contexts. Copyright © 2017 Elsevier Inc. All rights reserved.

Uncoupling GP1 and GP2 Expression in the Lassa Virus Glycoprotein Complex: Implications for GPI Ectodomain Shedding

DTIC Science & Technology

2008-12-23

glycoprotein precursor (GPC) signal peptide (SP) or human IgG signal sequences (s.s.). GP2 was secreted from cells only when (1) the transmembrane (TM) domain...consistent with viral TM fusion proteins [9,10]. GPC con- tains a 58 residue hydrophobic N-terminal signal peptide (SP), which directs the precursor to the...including GPC, GP1, and GP2. Various signal peptides , purification tags, and modifications to internal domains were employed for the generation and

High Class-Imbalance in pre-miRNA Prediction: A Novel Approach Based on deepSOM.

PubMed

Stegmayer, Georgina; Yones, Cristian; Kamenetzky, Laura; Milone, Diego H

2017-01-01

The computational prediction of novel microRNA within a full genome involves identifying sequences having the highest chance of being a miRNA precursor (pre-miRNA). These sequences are usually named candidates to miRNA. The well-known pre-miRNAs are usually only a few in comparison to the hundreds of thousands of potential candidates to miRNA that have to be analyzed, which makes this task a high class-imbalance classification problem. The classical way of approaching it has been training a binary classifier in a supervised manner, using well-known pre-miRNAs as positive class and artificially defining the negative class. However, although the selection of positive labeled examples is straightforward, it is very difficult to build a set of negative examples in order to obtain a good set of training samples for a supervised method. In this work, we propose a novel and effective way of approaching this problem using machine learning, without the definition of negative examples. The proposal is based on clustering unlabeled sequences of a genome together with well-known miRNA precursors for the organism under study, which allows for the quick identification of the best candidates to miRNA as those sequences clustered with known precursors. Furthermore, we propose a deep model to overcome the problem of having very few positive class labels. They are always maintained in the deep levels as positive class while less likely pre-miRNA sequences are filtered level after level. Our approach has been compared with other methods for pre-miRNAs prediction in several species, showing effective predictivity of novel miRNAs. Additionally, we will show that our approach has a lower training time and allows for a better graphical navegability and interpretation of the results. A web-demo interface to try deepSOM is available at http://fich.unl.edu.ar/sinc/web-demo/deepsom/.

Functional characterization of a second pedal peptide/orcokinin‐type neuropeptide signaling system in the starfish Asterias rubens

PubMed Central

Lin, Ming; Egertová, Michaela; Zampronio, Cleidiane G.; Jones, Alexandra M.

2017-01-01

Abstract Molluscan pedal peptides (PPs) and arthropod orcokinins (OKs) are prototypes of a family of neuropeptides that have been identified in several phyla. Recently, starfish myorelaxant peptide (SMP) was identified as a PP/OK‐type neuropeptide in the starfish Patiria pectinifera (phylum Echinodermata). Furthermore, analysis of transcriptome sequence data from the starfish Asterias rubens revealed two PP/OK‐type precursors: an SMP‐type precursor (A. rubens PP‐like neuropeptide precursor 1; ArPPLNP1) and a second precursor (ArPPLNP2). We reported previously a detailed analysis of ArPPLNP1 expression in A. rubens and here we report the first functional characterization ArPPLNP2‐derived neuropeptides. Sequencing of a cDNA encoding ArPPLNP2 revealed that it comprises eleven related neuropeptides (ArPPLN2a‐k), the structures of several of which were confirmed using mass spectrometry. Analysis of the expression of ArPPLNP2 and neuropeptides derived from this precursor using mRNA in situ hybridization and immunohistochemistry revealed a widespread distribution, including expression in radial nerve cords, circumoral nerve ring, digestive system, tube feet and innervation of interossicular muscles. In vitro pharmacology revealed that the ArPPLNP2‐derived neuropeptide ArPPLN2h has no effect on the contractility of tube feet or the body wall‐associated apical muscle, contrasting with the relaxing effect of ArPPLN1b (ArSMP) on these preparations. ArPPLN2h does, however, cause dose‐dependent relaxation of cardiac stomach preparations, with greater potency/efficacy than ArPPLN1b and with similar potency/efficacy to the SALMFamide neuropeptide S2. In conclusion, there are similarities in the expression patterns of ArPPLNP1 and ArPPLNP2 but our data also indicate specialization in the roles of neuropeptides derived from these two PP/OK‐type precursors in starfish. PMID:29218721

Functional characterization of a second pedal peptide/orcokinin-type neuropeptide signaling system in the starfish Asterias rubens.

PubMed

Lin, Ming; Egertová, Michaela; Zampronio, Cleidiane G; Jones, Alexandra M; Elphick, Maurice R

2018-04-01

Molluscan pedal peptides (PPs) and arthropod orcokinins (OKs) are prototypes of a family of neuropeptides that have been identified in several phyla. Recently, starfish myorelaxant peptide (SMP) was identified as a PP/OK-type neuropeptide in the starfish Patiria pectinifera (phylum Echinodermata). Furthermore, analysis of transcriptome sequence data from the starfish Asterias rubens revealed two PP/OK-type precursors: an SMP-type precursor (A. rubens PP-like neuropeptide precursor 1; ArPPLNP1) and a second precursor (ArPPLNP2). We reported previously a detailed analysis of ArPPLNP1 expression in A. rubens and here we report the first functional characterization ArPPLNP2-derived neuropeptides. Sequencing of a cDNA encoding ArPPLNP2 revealed that it comprises eleven related neuropeptides (ArPPLN2a-k), the structures of several of which were confirmed using mass spectrometry. Analysis of the expression of ArPPLNP2 and neuropeptides derived from this precursor using mRNA in situ hybridization and immunohistochemistry revealed a widespread distribution, including expression in radial nerve cords, circumoral nerve ring, digestive system, tube feet and innervation of interossicular muscles. In vitro pharmacology revealed that the ArPPLNP2-derived neuropeptide ArPPLN2h has no effect on the contractility of tube feet or the body wall-associated apical muscle, contrasting with the relaxing effect of ArPPLN1b (ArSMP) on these preparations. ArPPLN2h does, however, cause dose-dependent relaxation of cardiac stomach preparations, with greater potency/efficacy than ArPPLN1b and with similar potency/efficacy to the SALMFamide neuropeptide S2. In conclusion, there are similarities in the expression patterns of ArPPLNP1 and ArPPLNP2 but our data also indicate specialization in the roles of neuropeptides derived from these two PP/OK-type precursors in starfish. © 2017 The Authors The Journal of Comparative Neurology Published by Wiley Periodicals, Inc.

Two ways of legumin-precursor processing in conifers. Characterization and evolutionary relationships of Metasequoia cDNAs representing two divergent legumin gene subfamilies.

PubMed

Häger, K P; Wind, C

1997-06-15

Subunit monomers and oligomers of crystalloid-type legumins are major components of SDS-soluble fractions from Metasequoia glyptostroboides (Dawn redwood, Taxodiaceae) seed proteins. The subunits are made up of disulfide linked alpha-polypeptides and beta-polypeptides with molecular masses of 33 kDa and 23-25 kDa, respectively. Unusually for legumins, those from Metasequoia are glycosylated and the carbohydrate moieties are residing in the C-terminal region of the respective beta-polypeptides. A Metasequoia endosperm cDNA library has been constructed and legumin-encoding transcripts representing two divergent gene subfamilies have been characterized. Intersubfamily comparisons reveal 75% identity at the amino acid level and the values range from 53-35% when the legumin precursors deduced were compared with those from angiosperms. The predicted sequences together with data from amino acid sequencing prove that post-translational processing of Metasequoia prolegumins is directed to two different processing sites, each of them specific for one of the legumin subfamilies. The sites involved differ in their relative position and in the junction to be cleaved: Metasequoia legumin precursors MgLeg18 and MgLeg26 contain the conventional post-translational Asn-Gly processing site, which is generally regarded as highly conserved. In contrast, the MgLeg4 precursor is lacking this site and post-translational cleavage is directed to an unusual Asn-Thr processing site located in its hypervariable region, causing N-terminal extension of the beta-polypeptide relative to those hitherto known. Evidence is given that the unusual variant of processing also occurs in other conifers. Phylogenetic analysis reveals the precursors concerned as representatives of a distinct legumin subfamily, originating from duplication of an ancestral gene prior to or at the beginning of Taxodiaceae diversification.

Field-Analytical approach of land-sea records for elucidating the Younger Dryas Boundary syndrome

NASA Astrophysics Data System (ADS)

Ge, T.; Courty, M. M.; Guichard, F.

2009-12-01

Linking lonsdaleite crystals, carbon spherules and diamond polymorphs from the North American dark layers at 12.9 cal yr B.P. to a cosmic event has questioned the nature and timing of the related impact processes. A global signal should trace the invoked airshocks and/or surface impacts from a swarm of comets or carbonaceous chondrites. Here we report on the contextual analytical study of debris fall events from three reference sequences of the Younger Dyras period (11-13 ka cal BP) : (1) sand dune fields along the French Atlantic coast at the Audenge site; (2) A 10 m record of detrital/bioorganic accumulation in the southern basin of the Caspian Sea with regular sedimentation rate (0.1 to 3 mm per year) from 14 to 2-ka BP cal; (3) the Paijan sequence (Peruvian coastal desert) offering fossiliferous fluvial layers with the last large mammals and aquatic fauna at 13 ka BP sealed by abiotic sand dunes. The three sequences display one remarkable layer of exogenous air-transported microdebris that is part of a complex time series of recurrent fine dust/wildfire events. The sharp debris-rich microfacies and its association to ashes derived from calcination of the local vegetation suggest instantaneous deposition synchronous to a high intensity wildfire. The debris assemblage comprises microtektite-like glassy spherules, partly devitrified glass shards, unmelted to partly melted sedimentary and igneous clasts, terrestrial native metals, and carbonaceous components. The later occur as grape-clustered polymers, vitrified graphitic carbon, amorphous carbon spherules with a honeycomb pattern, and green carbon fibres with recrystallized quartz and metal blebs. Evidence for high temperature formation from a heterogeneous melt with solid debris and volatile components derived from carbonaceous precursors supports an impact origin from an ejecta plume. The association of debris deposition to total firing would trace a high energy airburst with surface effects of the fireball. In contrast, microfacies and debris composition of the recurrent fine dust/wildfire events would trace a series of a low energy airburst. Their record is expressed in the Audenge sequence by a series of water-laid laminae of charred pine residues formed of carbonaceous spherules wrapped by carbonaceous polymers that includes lonsdaleite crystals as detected by high resolution in situ micro-Raman analysis. This association suggests recurrent flash forest wildfires ignited by hot spray of carbon-rich debris, followed by heavy snow falls. The record from the Peruvian desert suggests a possible linkage between the repeated debris fall/wildfires during the Younger Dryas and the following irreversible aridity along the Peruvian cost. In contrast the Caspian record of the Younger Dryas period indicates more gradual changes, possibly buffered by the hydrological functioning of the Caspian sea in a complex region. The Audenge context offers the amplified signal needed to understand at local to global scales the spatio-temporal pattern of impact-airburst events.

The Role of Prototypes in the Mental Representation of Temporally Related Events

ERIC Educational Resources Information Center

Colcombe, Stanley J.; Wyer, Robert S., Jr.

2002-01-01

Four experiments investigated the conditions in which people use a prototypic event sequence to comprehend a situation-specific sequence of events. Results of Experiment 1 confirmed Trafimow and Wyer's (1993) findings that when participants use a prototype (e.g., a cultural script) to comprehend a new sequence of events concerning a hypothetical…

Discovery of an unusual biosynthetic origin for circular proteins in legumes

PubMed Central

Poth, Aaron G.; Colgrave, Michelle L.; Lyons, Russell E.; Daly, Norelle L.; Craik, David J.

2011-01-01

Cyclotides are plant-derived proteins that have a unique cyclic cystine knot topology and are remarkably stable. Their natural function is host defense, but they have a diverse range of pharmaceutically important activities, including uterotonic activity and anti-HIV activity, and have also attracted recent interest as templates in drug design. Here we report an unusual biosynthetic origin of a precursor protein of a cyclotide from the butterfly pea, Clitoria ternatea, a representative member of the Fabaceae plant family. Unlike all previously reported cyclotides, the domain corresponding to the mature cyclotide from this Fabaceae plant is embedded within an albumin precursor protein. We confirmed the expression and correct processing of the cyclotide encoded by the Cter M precursor gene transcript following extraction from C. ternatea leaf and sequencing by tandem mass spectrometry. The sequence was verified by direct chemical synthesis and the peptide was found to adopt a classic knotted cyclotide fold as determined by NMR spectroscopy. Seven additional cyclotide sequences were also identified from C. ternatea leaf and flower, five of which were unique. Cter M displayed insecticidal activity against the cotton budworm Helicoverpa armigera and bound to phospholipid membranes, suggesting its activity is modulated by membrane disruption. The Fabaceae is the third largest family of flowering plants and many Fabaceous plants are of huge significance for human nutrition. Knowledge of Fabaceae cyclotide gene transcripts should enable the production of modified cyclotides in crop plants for a variety of agricultural or pharmaceutical applications, including plant-produced designer peptide drugs. PMID:21593408

Characterization of a polyketide synthase in Aspergillus niger whose product is a precursor for both dihydroxynaphthalene (DHN) melanin and naphtho-γ-pyrone.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chiang, Yi Ming; Meyer, Kristen M; Praseuth, Michael

2010-12-06

The genome sequencing of the fungus Aspergillus niger, an industrial workhorse, uncovered a large cache of genes encoding enzymes thought to be involved in the production of secondary metabolites yet to be identified. Identification and structural characterization of many of these predicted secondary metabolites are hampered by their low concentration relative to the known A. niger metabolites such as the naphtho-γ-pyrone family of polyketides. We deleted a nonreducing PKS gene in A. niger strain ATCC 11414, a daughter strain of A. niger ATCC strain 1015 whose genome was sequenced by the DOE Joint Genome Institute. This PKS encoding gene ismore » a predicted ortholog of alb1 from Aspergillus fumigatus which is responsible for production of YWA1, a precursor of fungal DHN melanin. Our results show that the A. niger alb1 PKS is responsible for the production of the polyketide precursor for DHN melanin biosynthesis. Deletion of alb1 elimnates the production of major metabolites, naphtho-γ-pyrones. The generation of an A. niger strain devoid of naphtho-γ-pyrones will greatly facilitate the elucidation of cryptic biosynthetic pathways in this organism.« less

Combining wet etching and real-time damage event imaging to reveal the most dangerous laser damage initiator in fused silica.

PubMed

Hu, Guohang; Zhao, Yuanan; Liu, Xiaofeng; Li, Dawei; Xiao, Qiling; Yi, Kui; Shao, Jianda

2013-08-01

A reliable method, combining a wet etch process and real-time damage event imaging during a raster scan laser damage test, has been developed to directly determine the most dangerous precursor inducing low-density laser damage at 355 nm in fused silica. It is revealed that ~16% of laser damage sites were initiated at the place of the scratches, ~49% initiated at the digs, and ~35% initiated at invisible defects. The morphologies of dangerous scratches and digs were compared with those of moderate ones. It is found that local sharp variation at the edge, twist, or inside of a subsurface defect is the most dangerous laser damage precursor.

Nuclear localization of foamy virus Gag precursor protein.

PubMed Central

Schliephake, A W; Rethwilm, A

1994-01-01

All foamy viruses give rise to a strong nuclear staining when infected cells are reacted with sera from infected hosts. This nuclear fluorescence distinguishes foamy viruses from all other retroviruses. The experiments reported here indicate that the foamy virus Gag precursor protein is transiently located in the nuclei of infected cells and this is the likely reason for the typical foamy virus nuclear fluorescence. By using the vaccinia virus expression system, a conserved basic sequence motif in the nucleocapsid domain of foamy virus Gag proteins was identified to be responsible for the nuclear transport of the gag precursor molecule. This motif was also found to be able to direct a heterologous protein, the Gag protein of human immunodeficiency virus, into the nucleus. Images PMID:8035493

Development of a Novel Anti-HIV-1 Agent from within: Effect of Chimeric Vpr-Containing Protease Cleavage Site Residues on Virus Replication

NASA Astrophysics Data System (ADS)

Serio, D.; Rizvi, T. A.; Cartas, M.; Kalyanaraman, V. S.; Weber, I. T.; Koprowski, H.; Srinivasan, A.

1997-04-01

Effective antiviral agents will be of great value in controlling virus replication and delaying the onset of HIV-1-related disease symptoms. Current therapy involves the use of antiviral agents that target the enzymatic functions of the virus, resulting in the emergence of resistant viruses to these agents, thus lowering their effectiveness. To overcome this problem, we have considered the idea of developing novel agents from within HIV-1 as inhibitors of virus replication. The specificity of the Vpr protein for the HIV-1 virus particle makes it an attractive molecule for the development of antiviral agents targeting the events associated with virus maturation. We have generated chimeric Vpr proteins containing HIV-1-specific sequences added to the C terminus of Vpr. These sequences correspond to nine cleavage sites of the Gag and Gag-Pol precursors of HIV-1. The chimeric Vpr constructs were introduced into HIV-1 proviral DNA to assess their effect on virus infectivity using single- and multiple-round replication assays. The virus particles generated exhibited a variable replication pattern depending on the protease cleavage site used as a fusion partner. Interestingly, the chimeric Vpr containing the cleavage sequences from the junction of p24 and p2, 24/2, completely abolished virus infectivity. These results show that chimeric proteins generated from within HIV-1 have the ability to suppress HIV-1 replication and make ideal agents for gene therapy or intracellular immunization to treat HIV-1 infection.

CD200/BTLA deletions in pediatric precursor B-cell acute lymphoblastic leukemia treated according to the EORTC-CLG 58951 protocol

PubMed Central

Ghazavi, Farzaneh; Clappier, Emmanuelle; Lammens, Tim; Suciu, Stefan; Caye, Aurélie; Zegrari, Samira; Bakkus, Marleen; Grardel, Nathalie; Benoit, Yves; Bertrand, Yves; Minckes, Odile; Costa, Vitor; Ferster, Alina; Mazingue, Françoise; Plat, Geneviève; Plouvier, Emmanuel; Poirée, Marilyne; Uyttebroeck, Anne; van der Werff-ten Bosch, Jutte; Yakouben, Karima; Helsmoortel, Hetty; Meul, Magali; Van Roy, Nadine; Philippé, Jan; Speleman, Frank; Cavé, Hélène; Van Vlierberghe, Pieter; De Moerloose, Barbara

2015-01-01

DNA copy number analysis has been instrumental for the identification of genetic alterations in B-cell precursor acute lymphoblastic leukemia. Notably, some of these genetic defects have been associated with poor treatment outcome and might be relevant for future risk stratification. In this study, we characterized recurrent deletions of CD200 and BTLA genes, mediated by recombination-activating genes, and used breakpoint-specific polymerase chain reaction assay to screen a cohort of 1154 cases of B-cell precursor acute lymphoblastic leukemia uniformly treated according to the EORTC-CLG 58951 protocol. CD200/BTLA deletions were identified in 56 of the patients (4.8%) and were associated with an inferior 8-year event free survival in this treatment protocol [70.2% ± 1.2% for patients with deletions versus 83.5% ± 6.4% for non-deleted cases (hazard ratio 2.02; 95% confidence interval 1.23–3.32; P=0.005)]. Genetically, CD200/BTLA deletions were strongly associated with ETV6-RUNX1-positive leukemias (P<0.0001), but were also identified in patients who did not have any genetic abnormality that is currently used for risk stratification. Within the latter population of patients, the presence of CD200/BTLA deletions was associated with inferior event-free survival and overall survival. Moreover, the multivariate Cox model indicated that these deletions had independent prognostic impact on event-free survival when adjusting for conventional risk criteria. All together, these findings further underscore the rationale for copy number profiling as an important tool for risk stratification in human B-cell precursor acute lymphoblastic leukemia. This trial was registered at www.ClinicalTrials.gov as #NCT00003728. PMID:26137961

CD200/BTLA deletions in pediatric precursor B-cell acute lymphoblastic leukemia treated according to the EORTC-CLG 58951 protocol.

PubMed

Ghazavi, Farzaneh; Clappier, Emmanuelle; Lammens, Tim; Suciu, Stefan; Caye, Aurélie; Zegrari, Samira; Bakkus, Marleen; Grardel, Nathalie; Benoit, Yves; Bertrand, Yves; Minckes, Odile; Costa, Vitor; Ferster, Alina; Mazingue, Françoise; Plat, Geneviève; Plouvier, Emmanuel; Poirée, Marilyne; Uyttebroeck, Anne; van der Werff-Ten Bosch, Jutte; Yakouben, Karima; Helsmoortel, Hetty; Meul, Magali; Van Roy, Nadine; Philippé, Jan; Speleman, Frank; Cavé, Hélène; Van Vlierberghe, Pieter; De Moerloose, Barbara

2015-10-01

DNA copy number analysis has been instrumental for the identification of genetic alterations in B-cell precursor acute lymphoblastic leukemia. Notably, some of these genetic defects have been associated with poor treatment outcome and might be relevant for future risk stratification. In this study, we characterized recurrent deletions of CD200 and BTLA genes, mediated by recombination-activating genes, and used breakpoint-specific polymerase chain reaction assay to screen a cohort of 1154 cases of B-cell precursor acute lymphoblastic leukemia uniformly treated according to the EORTC-CLG 58951 protocol. CD200/BTLA deletions were identified in 56 of the patients (4.8%) and were associated with an inferior 8-year event free survival in this treatment protocol [70.2% ± 1.2% for patients with deletions versus 83.5% ± 6.4% for non-deleted cases (hazard ratio 2.02; 95% confidence interval 1.23-3.32; P=0.005)]. Genetically, CD200/BTLA deletions were strongly associated with ETV6-RUNX1-positive leukemias (P<0.0001), but were also identified in patients who did not have any genetic abnormality that is currently used for risk stratification. Within the latter population of patients, the presence of CD200/BTLA deletions was associated with inferior event-free survival and overall survival. Moreover, the multivariate Cox model indicated that these deletions had independent prognostic impact on event-free survival when adjusting for conventional risk criteria. All together, these findings further underscore the rationale for copy number profiling as an important tool for risk stratification in human B-cell precursor acute lymphoblastic leukemia. This trial was registered at www.ClinicalTrials.gov as #NCT00003728. Copyright© Ferrata Storti Foundation.

Partial purification and functional properties of an endoprotease from bovine neurosecretory granules cleaving proocytocin/neurophysin peptides at the basic amino acid doublet.

PubMed

Clamagirand, C; Creminon, C; Fahy, C; Boussetta, H; Cohen, P

1987-09-22

An enriched preparation of neurosecretory granules from bovine pituitary neural lobes was used as a source of processing enzymes possibly involved in the cleavage of the proocytocin/neurophysin precursor. A synthetic eicosapeptide reproducing the entire (1-20) sequence of the NH2-terminal domain of the bovine ocytocin/neurophysin precursor was used as a substrate to monitor an endoprotease activity cleaving at the Lys11-Arg12 doublet. The 58-kDa endoprotease detected in the lysate of neurohypophyseal granules produced a single cleavage, after the doublet, at the Arg12-Ala13 peptide bond. This endoprotease with pHi 6.9 and 7.2 exhibits maximal activity at pH around neutrality (7.0) and was strongly inhibited by divalent cation chelating agents [ethylenediaminetetraacetic acid and ethylene glycol bis(beta-aminoethyl ether)-N,N,N',-N'-tetraacetic acid] and to some extent by p-(chloromercuri)benzoate and p-(chloromercuri)benzenesulfonic acid, while phenylmethanesulfonyl fluoride and pepstatin were not active. This endoprotease action was sensitive to any modification of the substrate at either basic amino acid of the doublet since replacement of either L-Lys11 or L-Arg12 by D-Lys or D-Arg and by L-Nle abolished the cleavage reaction. In contrast, reversal of the polarity of the doublet in [Arg11,Lys12]proocytocin/neurophysin(1-20) had no effect on the mode of endoproteolytic cleavage as well as modifications of Gly10 (replaced by Ala10). It is concluded that the selectivity of this endoprotease, which may be involved in the primary event occurring in proocytocin/neurophysin processing, is strictly dependent upon the integrity of the basic doublet but that other parameters determined by the amino acid sequence around this doublet may play an important role.

Mutational spectrum of intraepithelial neoplasia in pancreatic heterotopia.

PubMed

Ma, Changqing; Gocke, Christopher D; Hruban, Ralph H; Belchis, Deborah A

2016-02-01

Heterotopic pancreatic parenchyma recapitulates the normal pancreas in extrapancreatic locations and, on rare occasions, can even give rise to pancreatic adenocarcinoma. The genetic signatures of pancreatic adenocarcinoma and its precursor lesions are well characterized. We explored the genetic alterations in precursor lesions (intraductal papillary mucinous neoplasms [IPMN], pancreatic intraepithelial neoplasia [PanIN]) in patients with pancreatic heterotopias but without concomitant pancreatic ductal adenocarcinomas. This allowed us to determine whether the stereotypical dysplasia--infiltrating carcinoma sequence also occurs in these extrapancreatic foci. Seven cases of heterotopic pancreas with ductal precursor lesions were identified. These included 2 IPMNs with focal high-grade dysplasia and 5 PanINs with low- to moderate-grade dysplasia (PanIN grades 1-2). Neoplastic epithelium was microdissected and genomic DNA was extracted. Sequencing of commonly mutated hotspots (KRAS, TP53, CDKN2A, SMAD4, BRAF, and GNAS) in pancreatic ductal adenocarcinoma and its precursor lesions was performed. Both IPMNs were found to have KRAS codon 12 mutations. The identification of KRAS mutations suggests a genetic pathway shared with IPMN of the pancreas. No mutations were identified in our heterotopic PanINs. One of the possible mechanisms for the development of dysplasia in these lesions is field effect. At the time of these resections, there was no clinical or pathologic evidence of a prior or concomitant pancreatic lesion. However, a clinically undetectable lesion is theoretically possible. Therefore, although a field effect cannot be excluded, there was no evidence for it in this study. Copyright © 2015 Elsevier Inc. All rights reserved.

Cyclotides Associate with Leaf Vasculature and Are the Products of a Novel Precursor in Petunia (Solanaceae)*

PubMed Central

Poth, Aaron G.; Mylne, Joshua S.; Grassl, Julia; Lyons, Russell E.; Millar, A. Harvey; Colgrave, Michelle L.; Craik, David J.

2012-01-01

Cyclotides are a large family of plant peptides that are structurally defined by their cyclic backbone and a trifecta of disulfide bonds, collectively known as the cyclic cystine knot (CCK) motif. Structurally similar cyclotides have been isolated from plants within the Rubiaceae, Violaceae, and Fabaceae families and share the CCK motif with trypsin-inhibitory knottins from a plant in the Cucurbitaceae family. Cyclotides have previously been reported to be encoded by dedicated genes or as a domain within a knottin-encoding PA1-albumin-like gene. Here we report the discovery of cyclotides and related non-cyclic peptides we called “acyclotides” from petunia of the agronomically important Solanaceae plant family. Transcripts for petunia cyclotides and acyclotides encode the shortest known cyclotide precursors. Despite having a different precursor structure, their sequences suggest that petunia cyclotides mature via the same biosynthetic route as other cyclotides. We assessed the spatial distribution of cyclotides within a petunia leaf section by MALDI imaging and observed that the major cyclotide component Phyb A was non-uniformly distributed. Dissected leaf midvein extracts contained significantly higher concentrations of this cyclotide compared with the lamina and outer margins of leaves. This is the third distinct type of cyclotide precursor, and Solanaceae is the fourth phylogenetically disparate plant family to produce these structurally conserved cyclopeptides, suggesting either convergent evolution upon the CCK structure or movement of cyclotide-encoding sequences within the plant kingdom. PMID:22700981

Membrane-associated precursor to poliovirus VPg identified by immunoprecipitation with antibodies directed against a synthetic heptapeptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Semelr, B.L.; Anderson, C.W.; Hanecak, R.

1982-02-01

A synthetic heptapeptide corresponding to the C-terminal sequence of the poliovirus genome protein (VPg) has been linked to bovine serum albumin and used to raise antibodies in rabbits. These antibodies precipitate not only VPg but also at least two more virus-specific polypeptides. The smaller polypeptide, denoted P3-9 (12,000 daltons), has been mapped by Edman degradation and by fragmentation with cyanogen bromide and determined to be the N-terminal cleavage product of polypeptide P3-1b, a precursor to the RNA polymerase. P3-9 contains the sequence of the basic protein VPg (22 amino acids) at its C terminus. As predicted by the known RNAmore » sequence of poliovirus, P3-9 also contains a hydrophobic region of 22 amino acids preceding VPg, an observation suggesting that P3-9 may be membrane-associated. This was confirmed by fractionation of infected cells in the presence or absence of detergent. We speculate that P3-9 may be the donor of VPg to RNA chains in the membrane-bound RNA replication complex.« less

Purification and characterisation of a new hypothalamic satiety peptide, cocaine and amphetamine regulated transcript (CART), produced in yeast.

PubMed

Thim, L; Nielsen, P F; Judge, M E; Andersen, A S; Diers, I; Egel-Mitani, M; Hastrup, S

1998-05-29

Cocaine and amphetamine regulated transcript (CART) is a newly discovered hypothalamic peptide with a potent appetite suppressing activity following intracerebroventricular administration. When the mature rat CART sequence encoding CART(1-102) was inserted in the yeast expression plasmid three CART peptides could be purified from the fermentation broth reflecting processing at dibasic sequences. None of these corresponded to the naturally occurring CART(55-102). In order to obtain CART(55-102) the precursor Glu-Glu-Ile-Asp-CART(55-102) has been produced and CART(55-102) was generated by digestion of the precursor with dipeptidylaminopeptidase-1. All four generated CART peptides have been characterised by N-terminal amino acid sequencing and mass spectrometry. The CART peptides contain six cysteine residues and using the yeast expressed CART(62-102) the disulphide bond configuration was found to be I-III, II-V and IV-VI. When the four CART peptides were intracerebroventricularly injected in fasted mice (0.1 to 2.0 microg) they all produced a dose dependent inhibition of food intake.

Truncated presequences of mitochondrial F1-ATPase beta subunit from Nicotiana plumbaginifolia transport CAT and GUS proteins into mitochondria of transgenic tobacco.

PubMed

Chaumont, F; Silva Filho, M de C; Thomas, D; Leterme, S; Boutry, M

1994-02-01

The mitochondrial F1-ATPase beta subunit (ATPase-beta) of Nicotiana plumbaginifolia is nucleus-encoded as a precursor containing an NH2-terminal extension. By sequencing the mature N. tabacum ATPase-beta, we determined the length of the presequence, viz. 54 residues. To define the essential regions of this presequence, we produced a series of 3' deletions in the sequence coding for the 90 NH2-terminal residues of ATPase-beta. The truncated sequences were fused with the chloramphenicol acetyl transferase (cat) and beta-glucuronidase (gus) genes and introduced into tobacco plants. From the observed distribution of CAT and GUS activity in the plant cells, we conclude that the first 23 amino-acid residues of ATPase-beta remain capable of specifically targeting reporter proteins into mitochondria. Immunodetection in transgenic plants and in vitro import experiments with various CAT fusion proteins show that the precursors are processed at the expected cleavage site but also at a cryptic site located in the linker region between the presequence and the first methionine of native CAT.

An Accident Precursor Analysis Process Tailored for NASA Space Systems

NASA Technical Reports Server (NTRS)

Groen, Frank; Stamatelatos, Michael; Dezfuli, Homayoon; Maggio, Gaspare

2010-01-01

Accident Precursor Analysis (APA) serves as the bridge between existing risk modeling activities, which are often based on historical or generic failure statistics, and system anomalies, which provide crucial information about the failure mechanisms that are actually operative in the system and which may differ in frequency or type from those in the various models. These discrepancies between the models (perceived risk) and the system (actual risk) provide the leading indication of an underappreciated risk. This paper presents an APA process developed specifically for NASA Earth-to-Orbit space systems. The purpose of the process is to identify and characterize potential sources of system risk as evidenced by anomalous events which, although not necessarily presenting an immediate safety impact, may indicate that an unknown or insufficiently understood risk-significant condition exists in the system. Such anomalous events are considered accident precursors because they signal the potential for severe consequences that may occur in the future, due to causes that are discernible from their occurrence today. Their early identification allows them to be integrated into the overall system risk model used to intbrm decisions relating to safety.

Nanoscale Ex-Situ Thermal Impulse Sensors for Structural Fire Forensics.

PubMed

Anderson, Benjamin R; Gese, Natalie; Gunawidjaja, Ray; Eilers, Hergen

2017-01-01

We develop nanoscale ex situ thermal impulse (i.e., the temperature and duration of a heating event) sensors for structural fire forensics using a mixture of two lanthanide-doped oxide precursors (precursor Eu:ZrO 2 and precursor Dy:Y 2 O 3 ) that undergo irreversible phase changes when heated. These changes are probed using photoluminescence (PL) spectroscopy with the PL spectra being dependent on the thermal impulse (TI) experienced by the sensors. By correlating the PL spectra to different in-lab TIs, we are able to produce a spectroscopic calibration for our sensors. This calibration allows us to determine an unknown TI of a heating event using only the PL spectrum of the heated TI sensors. In this study, we report on the calibration of these sensors for isothermal heating durations up to 600 s and isothermal temperatures up to 1273 K. Using this calibration, we also demonstrate their ability to determine an unknown TI and demonstrate their functionality when dispersed into paint, which is heated in the presence of drywall.

Bilateral wilms tumor with TP53-related anaplasia.

PubMed

Popov, Sergey D; Vujanic, Gordan M; Sebire, Neil J; Chagtai, Tasnim; Williams, Richard; Vaidya, Sucheta; Pritchard-Jones, Kathy

2013-01-01

Wilms tumor (WT) with diffuse anaplasia has an unfavorable prognosis and is often (>70%) associated with mutations in the TP53 gene. Although most WTs are unilateral, 5-10% are bilateral, and they are almost always present with nephrogenic rests. The latter are considered a precursor of WT. Two cases of bilateral WTs with nephroblastomatosis, in which anaplastic changes were detected over a period of time, were analyzed using clinical, radiological, histopathological, and molecular-genetic data. TP53 was analyzed by direct sequencing of its full coding sequence and intron-exon boundaries in 11 fragments. DNA was extracted from paraffin-embedded or frozen specimens. High-resolution genomic copy number profiling was carried out by UCL Genomics on the Affymetrix Human Mapping 250K Nsp or Genome-Wide Human SNP Array 6.0 platform. Both cases demonstrated a strong association between the appearance of anaplastic clones and TP53 mutations. Synchronous ganglioneuroma was diagnosed in one case. Our cases are unique as they represent a long disease history and demonstrate the difficulties in managing rare cases of bilateral WT with anaplasia. These cases also emphasize the practical importance of modern molecular-genetic techniques and their clinical application. Moreover, they highlight the issue of the adequate sampling needed in order to gather comprehensive, efficient, and sufficient information about genetic events in a single tumor.

Transspecies Transmission of Gammaretroviruses and the Origin of the Gibbon Ape Leukaemia Virus (GaLV) and the Koala Retrovirus (KoRV).

PubMed

Denner, Joachim

2016-12-20

Transspecies transmission of retroviruses is a frequent event, and the human immunodeficiency virus-1 (HIV-1) is a well-known example. The gibbon ape leukaemia virus (GaLV) and koala retrovirus (KoRV), two gammaretroviruses, are also the result of a transspecies transmission, however from a still unknown host. Related retroviruses have been found in Southeast Asian mice although the sequence similarity was limited. Viruses with a higher sequence homology were isolated from Melomys burtoni , the Australian and Indonesian grassland melomys. However, only the habitats of the koalas and the grassland melomys in Australia are overlapping, indicating that the melomys virus may not be the precursor of the GaLV. Viruses closely related to GaLV/KoRV were also detected in bats. Therefore, given the fact that the habitats of the gibbons in Thailand and the koalas in Australia are far away, and that bats are able to fly over long distances, the hypothesis that retroviruses of bats are the origin of GaLV and KoRV deserves consideration. Analysis of previous transspecies transmissions of retroviruses may help to evaluate the potential of transmission of related retroviruses in the future, e.g., that of porcine endogenous retroviruses (PERVs) during xenotransplantation using pig cells, tissues or organs.

Random and externally controlled occurrences of Dansgaard-Oeschger events

NASA Astrophysics Data System (ADS)

Lohmann, Johannes; Ditlevsen, Peter D.

2018-05-01

Dansgaard-Oeschger (DO) events constitute the most pronounced mode of centennial to millennial climate variability of the last glacial period. Since their discovery, many decades of research have been devoted to understand the origin and nature of these rapid climate shifts. In recent years, a number of studies have appeared that report emergence of DO-type variability in fully coupled general circulation models via different mechanisms. These mechanisms result in the occurrence of DO events at varying degrees of regularity, ranging from periodic to random. When examining the full sequence of DO events as captured in the North Greenland Ice Core Project (NGRIP) ice core record, one can observe high irregularity in the timing of individual events at any stage within the last glacial period. In addition to the prevailing irregularity, certain properties of the DO event sequence, such as the average event frequency or the relative distribution of cold versus warm periods, appear to be changing throughout the glacial. By using statistical hypothesis tests on simple event models, we investigate whether the observed event sequence may have been generated by stationary random processes or rather was strongly modulated by external factors. We find that the sequence of DO warming events is consistent with a stationary random process, whereas dividing the event sequence into warming and cooling events leads to inconsistency with two independent event processes. As we include external forcing, we find a particularly good fit to the observed DO sequence in a model where the average residence time in warm periods are controlled by global ice volume and cold periods by boreal summer insolation.

The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection

PubMed Central

Kong, Yimeng; Pan, Bohu; Chen, Longxian; Wang, Hongbing; Hao, Pei; Li, Xuan

2016-01-01

The hydrolytic deamination of adenosine to inosine (A-to-I editing) in precursor mRNA induces variable gene products at the post-transcription level. How and to what extent A-to-I RNA editing diversifies transcriptome is not fully characterized in the evolution, and very little is known about the selective constraints that drive the evolution of RNA editing events. Here we present a study on A-to-I RNA editing, by generating a global profile of A-to-I editing for a phylogeny of seven Drosophila species, a model system spanning an evolutionary timeframe of approximately 45 million years. Of totally 9281 editing events identified, 5150 (55.5%) are located in the coding sequences (CDS) of 2734 genes. Phylogenetic analysis places these genes into 1,526 homologous families, about 5% of total gene families in the fly lineages. Based on conservation of the editing sites, the editing events in CDS are categorized into three distinct types, representing events on singleton genes (type I), and events not conserved (type II) or conserved (type III) within multi-gene families. While both type I and II events are subject to purifying selection, notably type III events are positively selected, and highly enriched in the components and functions of the nervous system. The tissue profiles are documented for three editing types, and their critical roles are further implicated by their shifting patterns during holometabolous development and in post-mating response. In conclusion, three A-to-I RNA editing types are found to have distinct evolutionary dynamics. It appears that nervous system functions are mainly tested to determine if an A-to-I editing is beneficial for an organism. The coding plasticity enabled by A-to-I editing creates a new class of binary variations, which is a superior alternative to maintain heterozygosity of expressed genes in a diploid mating system. PMID:27467689

Characterization of GM events by insert knowledge adapted re-sequencing approaches

PubMed Central

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-01-01

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events. PMID:24088728

Characterization of GM events by insert knowledge adapted re-sequencing approaches.

PubMed

Yang, Litao; Wang, Congmao; Holst-Jensen, Arne; Morisset, Dany; Lin, Yongjun; Zhang, Dabing

2013-10-03

Detection methods and data from molecular characterization of genetically modified (GM) events are needed by stakeholders of public risk assessors and regulators. Generally, the molecular characteristics of GM events are incomprehensively revealed by current approaches and biased towards detecting transformation vector derived sequences. GM events are classified based on available knowledge of the sequences of vectors and inserts (insert knowledge). Herein we present three insert knowledge-adapted approaches for characterization GM events (TT51-1 and T1c-19 rice as examples) based on paired-end re-sequencing with the advantages of comprehensiveness, accuracy, and automation. The comprehensive molecular characteristics of two rice events were revealed with additional unintended insertions comparing with the results from PCR and Southern blotting. Comprehensive transgene characterization of TT51-1 and T1c-19 is shown to be independent of a priori knowledge of the insert and vector sequences employing the developed approaches. This provides an opportunity to identify and characterize also unknown GM events.

Rapidly rotating polytropes in general relativity

NASA Technical Reports Server (NTRS)

Cook, Gregory B.; Shapiro, Stuart L.; Teukolsky, Saul A.

1994-01-01

We construct an extensive set of equilibrium sequences of rotating polytropes in general relativity. We determine a number of important physical parameters of such stars, including maximum mass and maximum spin rate. The stability of the configurations against quasi-radial perturbations is diagnosed. Two classes of evolutionary sequences of fixed rest mass and entropy are explored: normal sequences which behave very much like Newtonian evolutionary sequences, and supramassive sequences which exist solely because of relativistic effects. Dissipation leading to loss of angular momentum causes a star to evolve in a quasi-stationary fashion along an evolutionary sequence. Supramassive sequences evolve towards eventual catastrophic collapse to a black hole. Prior to collapse, the star must spin up as it loses angular momentum, an effect which may provide an observational precursor to gravitational collapse to a black hole.

Statistical analysis of life history calendar data.

PubMed

Eerola, Mervi; Helske, Satu

2016-04-01

The life history calendar is a data-collection tool for obtaining reliable retrospective data about life events. To illustrate the analysis of such data, we compare the model-based probabilistic event history analysis and the model-free data mining method, sequence analysis. In event history analysis, we estimate instead of transition hazards the cumulative prediction probabilities of life events in the entire trajectory. In sequence analysis, we compare several dissimilarity metrics and contrast data-driven and user-defined substitution costs. As an example, we study young adults' transition to adulthood as a sequence of events in three life domains. The events define the multistate event history model and the parallel life domains in multidimensional sequence analysis. The relationship between life trajectories and excess depressive symptoms in middle age is further studied by their joint prediction in the multistate model and by regressing the symptom scores on individual-specific cluster indices. The two approaches complement each other in life course analysis; sequence analysis can effectively find typical and atypical life patterns while event history analysis is needed for causal inquiries. © The Author(s) 2012.

From non-random molecular structure to life and mind

NASA Technical Reports Server (NTRS)

Fox, S. W.

1989-01-01

The evolutionary hierarchy molecular structure-->macromolecular structure-->protobiological structure-->biological structure-->biological functions has been traced by experiments. The sequence always moves through protein. Extension of the experiments traces the formation of nucleic acids instructed by proteins. The proteins themselves were, in this picture, instructed by the self-sequencing of precursor amino acids. While the sequence indicated explains the thread of the emergence of life, protein in cellular membrane also provides the only known material basis for the emergence of mind in the context of emergence of life.

The Specificity of Trimming of MHC Class I-Presented Peptides in the Endoplasmic Reticulum1

PubMed Central

Hearn, Arron; York, Ian A.; Rock, Kenneth L.

2010-01-01

Aminopeptidases in the endoplasmic reticulum (ER) can cleave antigenic peptides and in so doing either create or destroy MHC class I-presented epitopes. However the specificity of this trimming process overall and of the major ER aminopeptidase ERAP1 in particular is not well understood. This issue is important because peptide trimming influences the magnitude and specificity of CD8 T cell responses. By systematically varying the N-terminal flanking sequences of peptides in a cell free biochemical system and in intact cells, we elucidated the specificity of ERAP1 and of ER trimming overall. ERAP1 can cleave after many amino acids on the N-terminus of epitope precursors but does so at markedly different rates. The specificity seen with purified ERAP1 is similar to that observed for trimming and presentation of epitopes in the ER of intact cells. We define N-terminal sequences that are favorable or unfavorable for antigen presentation in ways that are independent from the epitopes core sequence. When databases of known presented peptides were analyzed, the residues that were preferred for the trimming of model peptide precursors were found to be overrepresented in N-terminal flanking sequences of epitopes generally. These data define key determinants in the specificity of antigen processing. PMID:19828632

The Nucleotide Sequence and Spliced pol mRNA Levels of the Nonprimate Spumavirus Bovine Foamy Virus

PubMed Central

Holzschu, Donald L.; Delaney, Mari A.; Renshaw, Randall W.; Casey, James W.

1998-01-01

We have determined the complete nucleotide sequence of a replication-competent clone of bovine foamy virus (BFV) and have quantitated the amount of splice pol mRNA processed early in infection. The 544-amino-acid Gag protein precursor has little sequence similarity with its primate foamy virus homologs, but the putative nucleocapsid (NC) protein, like the primate NCs, contains the three glycine-arginine-rich regions that are postulated to bind genomic RNA during virion assembly. The BFV gag and pol open reading frames overlap, with pro and pol in the same translational frame. As with the human foamy virus (HFV) and feline foamy virus, we have detected a spliced pol mRNA by PCR. Quantitatively, this mRNA approximates the level of full-length genomic RNA early in infection. The integrase (IN) domain of reverse transcriptase does not contain the canonical HH-CC zinc finger motif present in all characterized retroviral INs, but it does contain a nearby histidine residue that could conceivably participate as a member of the zinc finger. The env gene encodes a protein that is over 40% identical in sequence to the HFV Env. By comparison, the Gag precursor of BFV is predicted to be only 28% identical to the HFV protein. PMID:9499074

Transcriptome and Small RNA Deep Sequencing Reveals Deregulation of miRNA Biogenesis in Human Glioma

PubMed Central

Moore, Lynette M.; Kivinen, Virpi; Liu, Yuexin; Annala, Matti; Cogdell, David; Liu, Xiuping; Liu, Chang-Gong; Sawaya, Raymond; Yli-Harja, Olli; Shmulevich, Ilya; Fuller, Gregory N.; Zhang, Wei; Nykter, Matti

2013-01-01

Altered expression of oncogenic and tumor-suppressing microRNAs (miRNAs) is widely associated with tumorigenesis. However, the regulatory mechanisms underlying these alterations are poorly understood. We sought to shed light on the deregulation of miRNA biogenesis promoting the aberrant miRNA expression profiles identified in these tumors. Using sequencing technology to perform both whole-transcriptome and small RNA sequencing of glioma patient samples, we examined precursor and mature miRNAs to directly evaluate the miRNA maturation process, and interrogated expression profiles for genes involved in the major steps of miRNA biogenesis. We found that ratios of mature to precursor forms of a large number of miRNAs increased with the progression from normal brain to low-grade and then to high-grade gliomas. The expression levels of genes involved in each of the three major steps of miRNA biogenesis (nuclear processing, nucleo-cytoplasmic transport, and cytoplasmic processing) were systematically altered in glioma tissues. Survival analysis of an independent data set demonstrated that the alteration of genes involved in miRNA maturation correlates with survival in glioma patients. Direct quantification of miRNA maturation with deep sequencing demonstrated that deregulation of the miRNA biogenesis pathway is a hallmark for glioma genesis and progression. PMID:23007860

Potential Vorticity Streamers as Precursors to Tropical Cyclone Genesis in the Western Pacific

DTIC Science & Technology

2012-03-01

study a developing system with an extratropical precursor (TCS-037) developing into Tropical Storm 16W (TS 16W)” (Schönenberger 2010). This subsection...tropopause maps), the TC genesis event is termed a tropical transition (TT) case. If no such extratropical feature 38 is present, the storm in... extratropical origin is deemed to play an important role in the dynamical evolution leading to tropical cyclogenesis. In contrast, non-TT storms

Early T-cell precursor acute lymphoblastic leukaemia in children treated in AIEOP centres with AIEOP-BFM protocols: a retrospective analysis.

PubMed

Conter, Valentino; Valsecchi, Maria Grazia; Buldini, Barbara; Parasole, Rosanna; Locatelli, Franco; Colombini, Antonella; Rizzari, Carmelo; Putti, Maria Caterina; Barisone, Elena; Lo Nigro, Luca; Santoro, Nicola; Ziino, Ottavio; Pession, Andrea; Testi, Anna Maria; Micalizzi, Concetta; Casale, Fiorina; Pierani, Paolo; Cesaro, Simone; Cellini, Monica; Silvestri, Daniela; Cazzaniga, Giovanni; Biondi, Andrea; Basso, Giuseppe

2016-02-01

Early T-cell precursor acute lymphoblastic leukaemia was recently recognised as a distinct leukaemia and reported as associated with poor outcomes. We aimed to assess the outcome of early T-cell precursor acute lymphoblastic leukaemia in patients from the Italian Association of Pediatric Hematology Oncology (AIEOP) centres treated with AIEOP-Berlin-Frankfurt-Münster (AIEOP-BFM) protocols. In this retrospective analysis, we included all children aged from 1 to less than 18 years with early T-cell precursor acute lymphoblastic leukaemia immunophenotype diagnosed between Jan 1, 2008, and Oct 31, 2014, from AIEOP centres. Early T-cell precursors were defined as being CD1a and CD8 negative, CD5 weak positive or negative, and positive for at least one of the following antigens: CD34, CD117, HLADR, CD13, CD33, CD11b, or CD65. Treatment was based on AIEOP-BFM acute lymphoblastic leukaemia 2000 (NCT00613457) or AIEOP-BFM acute lymphoblastic leukaemia 2009 protocols (European Clinical Trials Database 2007-004270-43). The main differences in treatment and stratification of T-cell acute lymphoblastic leukaemia between the two protocols were that in the 2009 protocol only, pegylated L-asparaginase was substituted for Escherichia coli L-asparaginase, patients with prednisone poor response received an additional dose of cyclophosphamide at day 10 of phase IA, and high minimal residual disease at day 15 assessed by flow cytometry was used as a high-risk criterion. Outcomes were assessed in terms of event-free survival, disease-free survival, and overall survival. Early T-cell precursor acute lymphoblastic leukaemia was diagnosed in 49 patients. Compared with overall T-cell acute lymphoblastic leukaemia, it was associated with absence of molecular markers for PCR detection of minimal residual disease in 25 (56%) of 45 patients; prednisone poor response in 27 (55%) of 49 patients; high minimal residual disease at day 15 after starting therapy in 25 (64%) of 39 patients (bone marrow blasts ≥ 10%, by flow cytometry); no complete remission after phase IA in 7 (15%) of 46 patients (bone marrow blasts ≥ 5%, morphologically); and high PCR minimal residual disease (≥ 5 × 10(-4)) at day 33 after starting therapy in 17 (85%) of 20 patients with markers available. Overall, 38 (78%) of 49 patients are in continuous complete remission, including 13 of 18 after haemopoietic stem cell transplantation, with three deaths in induction, five deaths after haemopoietic stem cell transplantation, and three relapses. Severe adverse events in the 2009 study were reported in 10 (30%) of 33 patients with early T-cell precursor acute lymphoblastic leukaemia versus 24 (15%) of 164 patients without early T-cell precursor acute lymphoblastic leukaemia and life-threatening events in induction phase IA occurred in 4 (12%) of 33 patients with early T-cell precursor acute lymphoblastic leukaemia versus 7 (4%) of 164 patients without early T-cell precursor acute lymphoblastic leukaemia. No difference was seen in the subsequent consolidation phase IB of protocol I. Early T-cell precursor acute lymphoblastic leukaemia is characterised by poor early response to conventional induction treatment. Consolidation phase IB, based on cyclophosphamide, 6-mercaptopurine, and ara-C at conventional (non-high) doses is effective in reducing minimal residual disease. Although the number of patients and observational time are limited, patients with early T-cell precursor acute lymphoblastic leukaemia treated with current BFM stratification and treatment strategy have a favourable outcome compared with earlier reports. The role of innovative therapies and haemopoietic stem cell therapy in early T-cell precursor acute lymphoblastic leukaemia needs to be assessed. None. Copyright © 2016 Elsevier Ltd. All rights reserved.

Correlation of Foreshock Occurrence with Mainshock Depth, Rake, and Magnitude from the High Precision Catalog for Northern California

NASA Astrophysics Data System (ADS)

Schaff, D. P.; Waldhauser, F.; Lerner-Lam, A.

2010-12-01

Foreshocks are perhaps the best-documented and most undisputed precursors to some large earthquakes. The question remains, however, if foreshocks have any more predictive power for future mainshocks than any other earthquake. Several researchers argue for a single unifying triggering law for foreshocks, mainshocks, and aftershocks. An alternate model is that foreshocks are the byproduct of an aseismic pre-slip phase that scales with mainshock magnitude. In this case foreshocks are different than other earthquakes and have predictive value for the mainshock location, origin time, and magnitude. We examine 612 mainshocks with M ≥ 4 from the cross-correlation double-difference catalog for northern California. 235 (44%) of these had foreshock sequences, providing us with a data set more than an order of magnitude larger than those used in previous studies. We are able to confirm with improved accuracy correlations of foreshock occurrence and characteristics with depth. The proportion of mainshocks with associated foreshocks, the number of foreshocks in the sequence, the foreshock duration, and the foreshock radius in map view all decrease with increasing depth, all with statistical significance above 95%. This supports models where increasing normal stress due to lithostatic load inhibits foreshock occurrence. Other M ≥ 4 events that were classified as aftershocks of larger events did not show the depth dependence. However, our analysis does not confirm a previous observation that increased normal stress due to tectonic loading appears to inhibit foreshock occurrence. We observe a negative correlation of foreshock magnitude with foreshock duration which is consistent with a model of mainshocks triggered by increased pore pressure. We observe a statistically significant relationship between foreshock magnitude and mainshock magnitude, lending support to the pre-slip model.

Multidecadally resolved Asian summer monsoon dynamics during MIS 5a-5d

NASA Astrophysics Data System (ADS)

Shen, C. C.; Jiang, X.; Hu, H. M.; Spoetl, C.

2016-12-01

A strong correlation between the Asian summer monsoon (ASM) and the North Atlantic climate on millennial and sub-millennial timescales during the last glacial period (MIS 4-2) and deglacial sequence has been demonstrated. However, our knowledge of this millennial- and sub-millennial-scale climatic link before MIS 4 is limited. Here, we present a new U-Th-dated absolute chronology of ASM variability from 113.5 to 86.6 kyr BP, covering marine isotope stages (MIS) 5a-5d. This integrated multidecadally resolved record, based on 1435 oxygen isotope data and 46 U-Th dates with 2-sigma errors as low as ±0.3 kyr from three stalagmites collected in Sanxing Cave, southwestern China, can be a reference for calibrating paleoclimate proxy sequences. The Sanxing oxygen isotope record follows the 23 kyr precessional cycle of insolation and is punctuated by prominent millennial-scale oscillations of the Chinese Interstadials (CIS) 25 to 22, corresponding to Greenland Interstadials (GIS) 25 to 22. A centennial-scale precursor event at 104.1 ± 0.3 kyr BP preceding CIS 23 is clearly registered. These events in the Sanxing record are synchronous with those identified in stalagmites from the European Alps (NALPS), except for the onset of GIS 25 and the end of GIS 22, and are up to 2.3 kyr older than the corresponding ones in Greenland ice core records. The high degree of similarity of the oxygen isotope records between Sanxing Cave and Greenland supports the northern hemisphere forcing of the ASM. The anti-phase relationship of oxygen isotope records between Sanxing stalagmites and Antarctic ice cores suggests an additional ASM linkage to the Southern Hemisphere.

Structure of genes for dermaseptins B, antimicrobial peptides from frog skin. Exon 1-encoded prepropeptide is conserved in genes for peptides of highly different structures and activities.

PubMed

Vouille, V; Amiche, M; Nicolas, P

1997-09-01

We cloned the genes of two members of the dermaseptin family, broad-spectrum antimicrobial peptides isolated from the skin of the arboreal frog Phyllomedusa bicolor. The dermaseptin gene Drg2 has a 2-exon coding structure interrupted by a small 137-bp intron, wherein exon 1 encoded a 22-residue hydrophobic signal peptide and the first three amino acids of the acidic propiece; exon 2 contained the 18 additional acidic residues of the propiece plus a typical prohormone processing signal Lys-Arg and a 32-residue dermaseptin progenitor sequence. The dermaseptin genes Drg2 and Drg1g2 have conserved sequences at both untranslated ends and in the first and second coding exons. In contrast, Drg1g2 comprises a third coding exon for a short version of the acidic propiece and a second dermaseptin progenitor sequence. Structural conservation between the two genes suggests that Drg1g2 arose recently from an ancestral Drg2-like gene through amplification of part of the second coding exon and 3'-untranslated region. Analysis of the cDNAs coding precursors for several frog skin peptides of highly different structures and activities demonstrates that the signal peptides and part of the acidic propieces are encoded by conserved nucleotides encompassed by the first coding exon of the dermaseptin genes. The organization of the genes that belong to this family, with the signal peptide and the progenitor sequence on separate exons, permits strikingly different peptides to be directed into the secretory pathway. The recruitment of such a homologous 'secretory' exon by otherwise non-homologous genes may have been an early event in the evolution of amphibian.

Binary Gene Expression Patterning of the Molt Cycle: The Case of Chitin Metabolism

PubMed Central

Abehsera, Shai; Glazer, Lilah; Tynyakov, Jenny; Plaschkes, Inbar; Chalifa-Caspi, Vered; Khalaila, Isam; Aflalo, Eliahu D.; Sagi, Amir

2015-01-01

In crustaceans, like all arthropods, growth is accompanied by a molting cycle. This cycle comprises major physiological events in which mineralized chitinous structures are built and degraded. These events are in turn governed by genes whose patterns of expression are presumably linked to the molting cycle. To study these genes we performed next generation sequencing and constructed a molt-related transcriptomic library from two exoskeletal-forming tissues of the crayfish Cherax quadricarinatus, namely the gastrolith and the mandible cuticle-forming epithelium. To simplify the study of such a complex process as molting, a novel approach, binary patterning of gene expression, was employed. This approach revealed that key genes involved in the synthesis and breakdown of chitin exhibit a molt-related pattern in the gastrolith-forming epithelium. On the other hand, the same genes in the mandible cuticle-forming epithelium showed a molt-independent pattern of expression. Genes related to the metabolism of glucosamine-6-phosphate, a chitin precursor synthesized from simple sugars, showed a molt-related pattern of expression in both tissues. The binary patterning approach unfolds typical patterns of gene expression during the molt cycle of a crustacean. The use of such a simplifying integrative tool for assessing gene patterning seems appropriate for the study of complex biological processes. PMID:25919476

Characterization of vitellogenin and its derived yolk proteins in cloudy catshark (Scyliorhinus torazame).

PubMed

Yamane, Kodai; Yagai, Tomoki; Nishimiya, Osamu; Sugawara, Rieko; Amano, Haruna; Fujita, Toshiaki; Hiramatsu, Naoshi; Todo, Takashi; Matsubara, Takahiro; Hara, Akihiko

2013-04-01

Elasmobranchs (sharks and rays) exhibit unique reproductive characteristics and, in contrast to the situation in teleosts, very little is known about the identity, structure and physical characteristics of their egg yolk proteins. The aims of this study were to (1) detect and purify the vitellogenin (Vtg; egg yolk precursor) and yolk proteins (YPs) of the cloudy catshark (Scyliorhinus torazame), (2) examine the relationships between Vtg and YPs and (3) characterize and classify the deduced primary structure of the Vtg transcript (vtg). The apparent molecular weights of purified Vtg and putative Vtg-related YPs (lipovitellin: Lv, phosvitin: Pv) were determined by gel filtration and were ~560, >669 and ~58 kDa, respectively. Following SDS-PAGE, these purified products (i.e., Vtg, Lv and Pv) appeared as bands of ~210, ~110 and ~22 kDa, respectively. On Western blots, antisera against purified Vtg, Lv and Pv recognized the ~210 kDa Vtg band. Catshark Pv, in contrast to teleost Pvs, had a very low serine content. The catshark Vtg cDNA sequence (vtg) appeared to contain an open-reading frame consisting of domains encoding Lv, Pv and β'-component (β'-c). A phylogenetic analysis, with a consideration of genome duplication events, placed catshark vtg into the 'vtgAB type.' It is concluded that at least a single major type of Vtg protein, which is transcribed and translated from catshark vtgAB gene, is the precursor of three egg yolk proteins (Lv, Pv and β'-c) in catshark.

Caspase-activated ROCK-1 allows erythroblast terminal maturation independently of cytokine-induced Rho signaling

PubMed Central

Gabet, A-S; Coulon, S; Fricot, A; Vandekerckhove, J; Chang, Y; Ribeil, J-A; Lordier, L; Zermati, Y; Asnafi, V; Belaid, Z; Debili, N; Vainchenker, W; Varet, B; Hermine, O; Courtois, G

2011-01-01

Stem cell factor (SCF) and erythropoietin are strictly required for preventing apoptosis and stimulating proliferation, allowing the differentiation of erythroid precursors from colony-forming unit-E to the polychromatophilic stage. In contrast, terminal maturation to generate reticulocytes occurs independently of cytokine signaling by a mechanism not fully understood. Terminal differentiation is characterized by a sequence of morphological changes including a progressive decrease in cell size, chromatin condensation in the nucleus and disappearance of organelles, which requires transient caspase activation. These events are followed by nucleus extrusion as a consequence of plasma membrane and cytoskeleton reorganization. Here, we show that in early step, SCF stimulates the Rho/ROCK pathway until the basophilic stage. Thereafter, ROCK-1 is activated independently of Rho signaling by caspase-3-mediated cleavage, allowing terminal maturation at least in part through phosphorylation of the light chain of myosin II. Therefore, in this differentiation system, final maturation occurs independently of SCF signaling through caspase-induced ROCK-1 kinase activation. PMID:21072057

Hutton to Horton: views of sequence, progression and equilibrium in geomorphology

NASA Astrophysics Data System (ADS)

Kennedy, Barbara A.

1992-08-01

The papers by Strahler (1952) and Chorley (1962) strongly advocated the adoption of a "dynamic" as opposed to an "historical" approach to geomorphology. The opinion of some later workers—notably Simpson (1963) and Mayr (1982) —is, however, that any advance in the historical natural sciences depends upon the combined appreciation of immanent and configurational elements (Simpson's terminology); and the view that events may have an essential historical or timebound component is now accepted even in "experimental" sciences such as chemistry (Prigogine, 1978). In the light of these contrasting approaches to earth science, an attempt is made to analyse the mjor lines of thought concerning change, progression and equilibrium in the work of six leading precursors of modern geomorphology: James Hutton, Charles Lyell, Charles Darwin, James Dwight Dana, Grove Karl Gilbert and Robert E. Horton. Despite their perceived general adherence to the Uniformitarian tradition, it is suggested that the work of the six reveals two contrasting attitudes to ideas of change and of equilibrium, It is argued that those authors — Lyell, Dana, Horton—who are primarily concerned to demonstrate that the present state of the earth is in some sense the normal or optimum, tend at the same time to accept the existence or desirability of some equilibrium state and, paradoxically, to overstate the role of "unusual", "cataclysmic" or "catastrophic" events in creating and sustaining this equilibrium. The views of Horton, in particular, lend themselves to the description "punctuated equilibrium". In contrast, it is contended that Hutton, Darwin and Gilbert have no ideological commitment to the present state of the earth as anything other than one moment in time. Their ideas are considered to focus upon the entire sequence of changes which may be inferred to create the phenomena viewed at any time or place. As a consequence, the concept of equilibrium has only a minor role in the works of these authors, who accept that earth history reveals a mix of events of all physically possible magnitudes and frequencies. In the light of this analysis, the distinction between "dynamic" and "historical" geomorphology advocated by Strahler and Chorley is felt to be unhelpful. A truly historical study of the sequence of phenomena — exemplified by Chapter IV in Gilbert's Geology of the Henry Mountains (1877) — necessarily requires consideration of all scales of dynamic processes.

Two pheromone precursor genes are transcriptionally expressed in the homothallic ascomycete Sordaria macrospora.

PubMed

Pöggeler, S

2000-06-01

In order to analyze the involvement of pheromones in cell recognition and mating in a homothallic fungus, two putative pheromone precursor genes, named ppg1 and ppg2, were isolated from a genomic library of Sordaria macrospora. The ppg1 gene is predicted to encode a precursor pheromone that is processed by a Kex2-like protease to yield a pheromone that is structurally similar to the alpha-factor of the yeast Saccharomyces cerevisiae. The ppg2 gene encodes a 24-amino-acid polypeptide that contains a putative farnesylated and carboxy methylated C-terminal cysteine residue. The sequences of the predicted pheromones display strong structural similarity to those encoded by putative pheromones of heterothallic filamentous ascomycetes. Both genes are expressed during the life cycle of S. macrospora. This is the first description of pheromone precursor genes encoded by a homothallic fungus. Southern-hybridization experiments indicated that ppg1 and ppg2 homologues are also present in other homothallic ascomycetes.

Tumor suppressors BTG1 and IKZF1 cooperate during mouse leukemia development and increase relapse risk in B-cell precursor acute lymphoblastic leukemia patients.

PubMed

Scheijen, Blanca; Boer, Judith M; Marke, René; Tijchon, Esther; van Ingen Schenau, Dorette; Waanders, Esmé; van Emst, Liesbeth; van der Meer, Laurens T; Pieters, Rob; Escherich, Gabriele; Horstmann, Martin A; Sonneveld, Edwin; Venn, Nicola; Sutton, Rosemary; Dalla-Pozza, Luciano; Kuiper, Roland P; Hoogerbrugge, Peter M; den Boer, Monique L; van Leeuwen, Frank N

2017-03-01

Deletions and mutations affecting lymphoid transcription factor IKZF1 (IKAROS) are associated with an increased relapse risk and poor outcome in B-cell precursor acute lymphoblastic leukemia. However, additional genetic events may either enhance or negate the effects of IKZF1 deletions on prognosis. In a large discovery cohort of 533 childhood B-cell precursor acute lymphoblastic leukemia patients, we observed that single-copy losses of BTG1 were significantly enriched in IKZF1 -deleted B-cell precursor acute lymphoblastic leukemia ( P =0.007). While BTG1 deletions alone had no impact on prognosis, the combined presence of BTG1 and IKZF1 deletions was associated with a significantly lower 5-year event-free survival ( P =0.0003) and a higher 5-year cumulative incidence of relapse ( P =0.005), when compared with IKZF1 -deleted cases without BTG1 aberrations. In contrast, other copy number losses commonly observed in B-cell precursor acute lymphoblastic leukemia, such as CDKN2A/B, PAX5, EBF1 or RB1 , did not affect the outcome of IKZF1 -deleted acute lymphoblastic leukemia patients. To establish whether the combined loss of IKZF1 and BTG1 function cooperate in leukemogenesis, Btg1 -deficient mice were crossed onto an Ikzf1 heterozygous background. We observed that loss of Btg1 increased the tumor incidence of Ikzf1 +/- mice in a dose-dependent manner. Moreover, murine B cells deficient for Btg1 and Ikzf1 +/- displayed increased resistance to glucocorticoids, but not to other chemotherapeutic drugs. Together, our results identify BTG1 as a tumor suppressor in leukemia that, when deleted, strongly enhances the risk of relapse in IKZF1 -deleted B-cell precursor acute lymphoblastic leukemia, and augments the glucocorticoid resistance phenotype mediated by the loss of IKZF1 function. Copyright© Ferrata Storti Foundation.

Event-related potentials in response to violations of content and temporal event knowledge.

PubMed

Drummer, Janna; van der Meer, Elke; Schaadt, Gesa

2016-01-08

Scripts that store knowledge of everyday events are fundamentally important for managing daily routines. Content event knowledge (i.e., knowledge about which events belong to a script) and temporal event knowledge (i.e., knowledge about the chronological order of events in a script) constitute qualitatively different forms of knowledge. However, there is limited information about each distinct process and the time course involved in accessing content and temporal event knowledge. Therefore, we analyzed event-related potentials (ERPs) in response to either correctly presented event sequences or event sequences that contained a content or temporal error. We found an N400, which was followed by a posteriorly distributed P600 in response to content errors in event sequences. By contrast, we did not find an N400 but an anteriorly distributed P600 in response to temporal errors in event sequences. Thus, the N400 seems to be elicited as a response to a general mismatch between an event and the established event model. We assume that the expectancy violation of content event knowledge, as indicated by the N400, induces the collapse of the established event model, a process indicated by the posterior P600. The expectancy violation of temporal event knowledge is assumed to induce an attempt to reorganize the event model in working memory, a process indicated by the frontal P600. Copyright © 2015 Elsevier Ltd. All rights reserved.

A case study to determine the geographical origin of unknown GM papaya in routine food sample analysis, followed by identification of papaya events 16-0-1 and 18-2-4.

PubMed

Prins, Theo W; Scholtens, Ingrid M J; Bak, Arno W; van Dijk, Jeroen P; Voorhuijzen, Marleen M; Laurensse, Emile J; Kok, Esther J

2016-12-15

During routine monitoring for GMOs in food in the Netherlands, papaya-containing food supplements were found positive for the genetically modified (GM) elements P-35S and T-nos. The goal of this study was to identify the unknown and EU unauthorised GM papaya event(s). A screening strategy was applied using additional GM screening elements including a newly developed PRSV coat protein PCR. The detected PRSV coat protein PCR product was sequenced and the nucleotide sequence showed identity to PRSV YK strains indigenous to China and Taiwan. The GM events 16-0-1 and 18-2-4 could be identified by amplifying and sequencing events-specific sequences. Further analyses showed that both papaya event 16-0-1 and event 18-2-4 were transformed with the same construct. For use in routine analysis, derived TaqMan qPCR methods for events 16-0-1 and 18-2-4 were developed. Event 16-0-1 was detected in all samples tested whereas event 18-2-4 was detected in one sample. This study presents a strategy for combining information from different sources (literature, patent databases) and novel sequence data to identify unknown GM papaya events. Copyright © 2016 Elsevier Ltd. All rights reserved.

Multivoxel pattern similarity suggests the integration of temporal duration in hippocampal event sequence representations.

PubMed

Thavabalasingam, Sathesan; O'Neil, Edward B; Lee, Andy C H

2018-05-22

Recent rodent work suggests the hippocampus may provide a temporal representation of event sequences, in which the order of events and the interval durations between them are encoded. There is, however, limited human evidence for the latter, in particular whether the hippocampus processes duration information pertaining to the passage of time rather than qualitative or quantitative changes in event content. We scanned participants while they made match-mismatch judgements on each trial between a study sequence of events and a subsequent test sequence. Participants explicitly remembered event order or interval duration information (Experiment 1), or monitored order only, with duration being manipulated implicitly (Experiment 2). Hippocampal study-test pattern similarity was significantly reduced by changes to order or duration in mismatch trials, even when duration was processed implicitly. Our findings suggest the human hippocampus processes short intervals within sequences and support the idea that duration information is integrated into hippocampal mnemonic representations. Copyright © 2018 Elsevier Inc. All rights reserved.

Visual attention distracter insertion for improved EEG rapid serial visual presentation (RSVP) target stimuli detection

NASA Astrophysics Data System (ADS)

Khosla, Deepak; Huber, David J.; Martin, Kevin

2017-05-01

This paper† describes a technique in which we improve upon the prior performance of the Rapid Serial Visual Presentation (RSVP) EEG paradigm for image classification though the insertion of visual attention distracters and overall sequence reordering based upon the expected ratio of rare to common "events" in the environment and operational context. Inserting distracter images maintains the ratio of common events to rare events at an ideal level, maximizing the rare event detection via P300 EEG response to the RSVP stimuli. The method has two steps: first, we compute the optimal number of distracters needed for an RSVP stimuli based on the desired sequence length and expected number of targets and insert the distracters into the RSVP sequence, and then we reorder the RSVP sequence to maximize P300 detection. We show that by reducing the ratio of target events to nontarget events using this method, we can allow RSVP sequences with more targets without sacrificing area under the ROC curve (azimuth).

Complete genome sequence of Streptomyces venezuelae ATCC 15439, a promising cell factory for production of secondary metabolites.

PubMed

Song, Ju Yeon; Yoo, Young Ji; Lim, Si-Kyu; Cha, Sun Ho; Kim, Ji-Eun; Roe, Jung-Hye; Kim, Jihyun F; Yoon, Yeo Joon

2016-02-10

Streptomyces venezuelae ATCC 15439, which produces 12- and 14-membered ring macrolide antibiotics, is a platform strain for heterologous expression of secondary metabolites. Its 9.05-Mb genome sequence revealed an abundance of genes involved in the biosynthesis of secondary metabolites and their precursors, which should be useful for the production of bioactive compounds. Copyright © 2015 Elsevier B.V. All rights reserved.

Brain-Derived Neurotrophic Factor Induces Cell Survival and the Migration of Murine Adult Hippocampal Precursor Cells During Differentiation In Vitro.

PubMed

Ortiz-López, Leonardo; Vega-Rivera, Nelly Maritza; Babu, Harish; Ramírez-Rodríguez, Gerardo Bernabé

2017-01-01

The generation of new neurons during adulthood involves local precursor cell migration and terminal differentiation in the dentate gyrus. These events are influenced by the hippocampal microenvironment. Brain-derived neurotrophic factor (BDNF) is relevant for hippocampal neuronal development and behavior. Interestingly, studies that have been performed in controlled in vitro systems that involve isolated precursor cells that were derived from the dentate gyrus (AHPCs) have shown that BDNF induces the activation of the TrkB receptor and, consequentially, might activate signaling pathways that favor survival and neuronal differentiation. Based on the fact that the cellular events of AHPCs that are induced by single factors can be studied in this controlled in vitro system, we investigated the ability of BDNF and the involvement of protein kinase C (PKC), as one of the TrkB-downstream activated signaling proteins, in the regulation of migration, here reflected by motility, of AHPCs. Precursor cells were cultured following a concentration-response curve (1-640 ng/ml) for 24 or 96 h. We found that BDNF favored cell survival without altering the viability under culture proliferative conditions of the AHPCs. Concomitantly, glial- and neuronal-differentiated precursor cells increased as a consequence of survival promoted by BDNF. Additionally, pharmacological approaches showed that BDNF (40 ng/ml)-induced migration of AHPCs was blocked with the compounds K252a and GF109203x, which prevent the activation of TrkB and PKC, respectively. The results indicate that in the in vitro migration of differentiated AHPCs it is involved the BDNF and TrkB cascade. Our results provide additional information about the mechanism by which BDNF impacts adult neurogenesis in the hippocampus.

LATERAL OFFSET OF THE CORONAL MASS EJECTIONS FROM THE X-FLARE OF 2006 DECEMBER 13 AND ITS TWO PRECURSOR ERUPTIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sterling, Alphonse C.; Moore, Ronald L.; Harra, Louise K., E-mail: alphonse.sterling@nasa.gov, E-mail: ron.moore@nasa.gov, E-mail: lkh@mssl.ucl.ac.uk

2011-12-10

Two GOES sub-C-class precursor eruptions occurred within {approx}10 hr prior to and from the same active region as the 2006 December 13 X4.3-class flare. Each eruption generated a coronal mass ejection (CME) with center laterally far offset ({approx}> 45 Degree-Sign ) from the co-produced bright flare. Explaining such CME-to-flare lateral offsets in terms of the standard model for solar eruptions has been controversial. Using Hinode/X-Ray Telescope (XRT) and EUV Imaging Spectrometer (EIS) data, and Solar and Heliospheric Observatory (SOHO)/Large Angle and Spectrometric Coronagraph (LASCO) and Michelson Doppler Imager (MDI) data, we find or infer the following. (1) The first precursormore » was a 'magnetic-arch-blowout' event, where an initial standard-model eruption of the active region's core field blew out a lobe on one side of the active region's field. (2) The second precursor began similarly, but the core-field eruption stalled in the side-lobe field, with the side-lobe field erupting {approx}1 hr later to make the CME either by finally being blown out or by destabilizing and undergoing a standard-model eruption. (3) The third eruption, the X-flare event, blew out side lobes on both sides of the active region and clearly displayed characteristics of the standard model. (4) The two precursors were offset due in part to the CME originating from a side-lobe coronal arcade that was offset from the active region's core. The main eruption (and to some extent probably the precursor eruptions) was offset primarily because it pushed against the field of the large sunspot as it escaped outward. (5) All three CMEs were plausibly produced by a suitable version of the standard model.« less

A missense mutation in the vasopressin-neurophysin precursor gene cosegregates with human autosomal dominant neurohypophyseal diabetes insipidus.

PubMed Central

Bahnsen, U; Oosting, P; Swaab, D F; Nahke, P; Richter, D; Schmale, H

1992-01-01

Familial neurohypophyseal diabetes insipidus in humans is a rare disease transmitted as an autosomal dominant trait. Affected individuals have very low or undetectable levels of circulating vasopressin and suffer from polydipsia and polyuria. An obvious candidate gene for the disease is the vasopressin-neurophysin (AVP-NP) precursor gene on human chromosome 20. The 2 kb gene with three exons encodes a composite precursor protein consisting of the neuropeptide vasopressin and two associated proteins, neurophysin and a glycopeptide. Cloning and nucleotide sequence analysis of both alleles of the AVP-NP gene present in a Dutch ADNDI family reveals a point mutation in one allele of the affected family members. Comparison of the nucleotide sequences shows a G----T transversion within the neurophysin-encoding exon B. This missense mutation converts a highly conserved glycine (Gly17 of neurophysin) to a valine residue. RFLP analysis of six related family members indicates cosegregation of the mutant allele with the DI phenotype. The mutation is not present in 96 chromosomes of an unrelated control group. These data suggest that a single amino acid exchange within a highly conserved domain of the human vasopressin-associated neurophysin is the primary cause of one form of ADNDI. Images PMID:1740104

The 2016 Mihoub (north-central Algeria) earthquake sequence: Seismological and tectonic aspects

NASA Astrophysics Data System (ADS)

Khelif, M. F.; Yelles-Chaouche, A.; Benaissa, Z.; Semmane, F.; Beldjoudi, H.; Haned, A.; Issaadi, A.; Chami, A.; Chimouni, R.; Harbi, A.; Maouche, S.; Dabbouz, G.; Aidi, C.; Kherroubi, A.

2018-06-01

On 28 May 2016 at 23:54 (UTC), an Mw5.4 earthquake occurred in Mihoub village, Algeria, 60 km southeast of Algiers. This earthquake was the largest event in a sequence recorded from 10 April to 15 July 2016. In addition to the permanent national network, a temporary network was installed in the epicentral region after this shock. Recorded event locations allow us to give a general overview of the sequence and reveal the existence of two main fault segments. The first segment, on which the first event in the sequence was located, is near-vertical and trends E-W. The second fault plane, on which the largest event of the sequence was located, dips to the southeast and strikes NE-SW. A total of 46 well-constrained focal mechanisms were calculated. The events located on the E-W-striking fault segment show mainly right-lateral strike-slip (strike N70°E, dip 77° to the SSE, rake 150°). The events located on the NE-SW-striking segment show mainly reverse faulting (strike N60°E, dip 70° to the SE, rake 130°). We calculated the static stress change caused by the first event (Md4.9) of the sequence; the result shows that the fault plane of the largest event in the sequence (Mw5.4) and most of the aftershocks occurred within an area of increased Coulomb stress. Moreover, using the focal mechanisms calculated in this work, we estimated the orientations of the main axes of the local stress tensor ellipsoid. The results confirm previous findings that the general stress field in this area shows orientations aligned NNW-SSE to NW-SE. The 2016 Mihoub earthquake sequence study thus improves our understanding of seismic hazard in north-central Algeria.

Isolation and characterisation of mRNA encoding the salmon- and chicken-II type gonadotrophin-releasing hormones in the teleost fish Rutilus rutilus (Cyprinidae).

PubMed

Penlington, M C; Williams, M A; Sumpter, J P; Rand-Weaver, M; Hoole, D; Arme, C

1997-12-01

The complementary DNAs (cDNA) encoding the [Trp7,Leu8]-gonadotrophin-releasing hormone (salmon-type GnRH; sGnRH:GeneBank accession no. u60667) and the [His5,Trp7,Tyr8]-GnRH (chicken-II-type GnRH; cGnRH-II: GeneBank accession no. u60668) precursor in the roach (Rutilus rutilus) were isolated and sequenced following reverse transcription and rapid amplification of cDNA ends (RACE). The sGnRH and cGnRH-II precursor cDNAs consisted of 439 and 628 bp, and included open reading frames of 282 and 255 bp respectively. The structures of the encoded peptides were the same as GnRHs previously identified in other vertebrates. The sGnRH and cGnRH-II precursor cDNAs, including the non-coding regions, had 88.6 and 79.9% identity respectively, to those identified in goldfish (Carassius auratus). However, significant similarity was not observed between the non-coding regions of the GnRH cDNAs of Cyprinidae and other fish. The presumed third exon, encoding partial sGnRH associated peptide (GAP) of roach, demonstrated significant nucleotide and amino acid similarity with the appropriate regions in the goldfish, but not with other species, and this may indicate functional differences of GAP between different families of fish. cGnRH-II precursor cDNAs from roach had relatively high nucleotide similarity across this GnRH variant. Cladistic analysis classified the sGnRH and cGnRH-II precursor cDNAs into three and two groups respectively. However, the divergence between nucleotide sequences within the sGnRH variant was greater than those encoding the cGnRH-II precursors. Consistent with the consensus developed from previous studies, Northern blot analysis demonstrated that expression of sGnRH and cGnRH-II was restricted to the olfactory bulbs and midbrain of roach respectively. This work forms the basis for further study on the mechanisms by which the tapeworm, Ligula intestinalis, interacts with the pituitary-gonadal axis of its fish host.

NGFFFamide and echinotocin: structurally unrelated myoactive neuropeptides derived from neurophysin-containing precursors in sea urchins.

PubMed

Elphick, Maurice R; Rowe, Matthew L

2009-04-01

The myoactive neuropeptide NGIWYamide was originally isolated from the holothurian (sea cucumber) Apostichopus japonicus but there is evidence that NGIWYamide-like peptides also occur in other echinoderms. Here we report the discovery of a gene in the sea urchin Strongylocentrotus purpuratus that encodes two copies of an NGIWYamide-like peptide: Asn-Gly-Phe-Phe-Phe-(NH(2)) or NGFFFamide. Interestingly, the C-terminal region of the NGFFFamide precursor shares sequence similarity with neurophysins, carrier proteins hitherto uniquely associated with precursors of vasopressin/oxytocin-like neuropeptides. Thus, the NGFFFamide precursor is the first neurophysin-containing neuropeptide precursor to be discovered that does not contain a vasopressin/oxytocin-like peptide. However, it remains to be determined whether neurophysin acts as a carrier protein for NGFFFamide. The S. purpuratus genome also contains a gene encoding a precursor comprising a neurophysin polypeptide and 'echinotocin' (CFISNCPKGamide) - the first vasopressin/oxytocin-like peptide to be identified in an echinoderm. Therefore, in S. purpuratus there are two genes encoding precursors that have a neurophysin domain but which encode neuropeptides that are structurally unrelated. Furthermore, both NGFFFamide and echinotocin cause contraction of tube foot and oesophagus preparations from the sea urchin Echinus esculentus, consistent with the myoactivity of NGIWYamide in sea cucumbers and the myoactivity of vasopressin/oxytocin-like peptides in other animal phyla. Presumably the NGFFFamide precursor acquired its neurophysin domain following partial or complete duplication of a gene encoding a vasopressin/oxytocin-like peptide, but it remains to be determined when in evolutionary history this occurred.

Growth and splitting of neural sequences in songbird vocal development

PubMed Central

Okubo, Tatsuo S.; Mackevicius, Emily L.; Payne, Hannah L.; Lynch, Galen F.; Fee, Michale S.

2015-01-01

Neural sequences are a fundamental feature of brain dynamics underlying diverse behaviors, but the mechanisms by which they develop during learning remain unknown. Songbirds learn vocalizations composed of syllables; in adult birds, each syllable is produced by a different sequence of action potential bursts in the premotor cortical area HVC. Here we carried out recordings of large populations of HVC neurons in singing juvenile birds throughout learning to examine the emergence of neural sequences. Early in vocal development, HVC neurons begin producing rhythmic bursts, temporally locked to a ‘prototype’ syllable. Different neurons are active at different latencies relative to syllable onset to form a continuous sequence. Through development, as new syllables emerge from the prototype syllable, initially highly overlapping burst sequences become increasingly distinct. We propose a mechanistic model in which multiple neural sequences can emerge from the growth and splitting of a common precursor sequence. PMID:26618871

Immunoreactivity of polyclonal antibodies generated against the carboxy terminus of the predicted amino acid sequence of the Huntington disease gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alkatib, G.; Graham, R.; Pelmear-Telenius, A.

1994-09-01

A cDNA fragment spanning the 3{prime}-end of the Huntington disease gene (from 8052 to 9252) was cloned into a prokaryotic expression vector containing the E. Coli lac promoter and a portion of the coding sequence for {beta}-galactosidase. The truncated {beta}-galactosidase gene was cleaved with BamHl and fused in frame to the BamHl fragment of the Huntington disease gene 3{prime}-end. Expression analysis of proteins made in E. Coli revealed that 20-30% of the total cellular proteins was represented by the {beta}-galactosidase-huntingtin fusion protein. The identity of the Huntington disease protein amino acid sequences was confirmed by protein sequence analysis. Affinity chromatographymore » was used to purify large quantities of the fusion protein from bacterial cell lysates. Affinity-purified proteins were used to immunize New Zealand white rabbits for antibody production. The generated polyclonal antibodies were used to immunoprecipitate the Huntington disease gene product expressed in a neuroblastoma cell line. In this cell line the antibodies precipitated two protein bands of apparent gel migrations of 200 and 150 kd which together, correspond to the calculated molecular weight of the Huntington disease gene product (350 kd). Immunoblotting experiments revealed the presence of a large precursor protein in the range of 350-750 kd which is in agreement with the predicted molecular weight of the protein without post-translational modifications. These results indicate that the huntingtin protein is cleaved into two subunits in this neuroblastoma cell line and implicate that cleavage of a large precursor protein may contribute to its biological activity. Experiments are ongoing to determine the precursor-product relationship and to examine the synthesis of the huntingtin protein in freshly isolated rat brains, and to determine cellular and subcellular distribution of the gene product.« less

Electromagnetic Whistler Precursors at Supercritical Interplanetary Shocks

NASA Technical Reports Server (NTRS)

Wilson, L. B., III

2012-01-01

We present observations of electromagnetic precursor waves, identified as whistler mode waves, at supercritical interplanetary shocks using the Wind search coil magnetometer. The precursors propagate obliquely with respect to the local magnetic field, shock normal vector, solar wind velocity, and they are not phase standing structures. All are right-hand polarized with respect to the magnetic field (spacecraft frame), and all but one are right-hand polarized with respect to the shock normal vector in the normal incidence frame. Particle distributions show signatures of specularly reflected gyrating ions, which may be a source of free energy for the observed modes. In one event, we simultaneously observe perpendicular ion heating and parallel electron acceleration, consistent with wave heating/acceleration due to these waves.

Discriminative Prediction of A-To-I RNA Editing Events from DNA Sequence

PubMed Central

Sun, Jiangming; Singh, Pratibha; Bagge, Annika; Valtat, Bérengère; Vikman, Petter; Spégel, Peter; Mulder, Hindrik

2016-01-01

RNA editing is a post-transcriptional alteration of RNA sequences that, via insertions, deletions or base substitutions, can affect protein structure as well as RNA and protein expression. Recently, it has been suggested that RNA editing may be more frequent than previously thought. A great impediment, however, to a deeper understanding of this process is the paramount sequencing effort that needs to be undertaken to identify RNA editing events. Here, we describe an in silico approach, based on machine learning, that ameliorates this problem. Using 41 nucleotide long DNA sequences, we show that novel A-to-I RNA editing events can be predicted from known A-to-I RNA editing events intra- and interspecies. The validity of the proposed method was verified in an independent experimental dataset. Using our approach, 203 202 putative A-to-I RNA editing events were predicted in the whole human genome. Out of these, 9% were previously reported. The remaining sites require further validation, e.g., by targeted deep sequencing. In conclusion, the approach described here is a useful tool to identify potential A-to-I RNA editing events without the requirement of extensive RNA sequencing. PMID:27764195

Cell size control and a cell-intrinsic maturation program in proliferating oligodendrocyte precursor cells.

PubMed

Gao, F B; Raff, M

1997-09-22

We have used clonal analysis and time-lapse video recording to study the proliferative behavior of purified oligodendrocyte precursor cells isolated from the perinatal rat optic nerve growing in serum-free cultures. First, we show that the cell cycle time of precursor cells decreases with increasing concentrations of PDGF, the main mitogen for these cells, suggesting that PDGF levels may regulate the cell cycle time during development. Second, we show that precursor cells isolated from embryonic day 18 (E18) nerves differ from precursor cells isolated from postnatal day 7 (P7) or P14 nerves in a number of ways: they have a simpler morphology, and they divide faster and longer before they stop dividing and differentiate into postmitotic oligodendrocytes. Third, we show that purified E18 precursor cells proliferating in culture progressively change their properties to resemble postnatal cells, suggesting that progressive maturation is an intrinsic property of the precursors. Finally, we show that precursor cells, especially mature ones, sometimes divide unequally, such that one daughter cell is larger than the other; in each of these cases the larger daughter cell divides well before the smaller one, suggesting that the precursor cells, just like single-celled eucaryotes, have to reach a threshold size before they can divide. These and other findings raise the possibility that such stochastic unequal divisions, rather than the stochastic events occurring in G1 proposed by "transition probability" models, may explain the random variability of cell cycle times seen within clonal cell lines in culture.

Cell Size Control and a Cell-intrinsic Maturation Program in Proliferating Oligodendrocyte Precursor Cells

PubMed Central

Gao, Fen-Biao; Raff, Martin

1997-01-01

We have used clonal analysis and time-lapse video recording to study the proliferative behavior of purified oligodendrocyte precursor cells isolated from the perinatal rat optic nerve growing in serum-free cultures. First, we show that the cell cycle time of precursor cells decreases with increasing concentrations of PDGF, the main mitogen for these cells, suggesting that PDGF levels may regulate the cell cycle time during development. Second, we show that precursor cells isolated from embryonic day 18 (E18) nerves differ from precursor cells isolated from postnatal day 7 (P7) or P14 nerves in a number of ways: they have a simpler morphology, and they divide faster and longer before they stop dividing and differentiate into postmitotic oligodendrocytes. Third, we show that purified E18 precursor cells proliferating in culture progressively change their properties to resemble postnatal cells, suggesting that progressive maturation is an intrinsic property of the precursors. Finally, we show that precursor cells, especially mature ones, sometimes divide unequally, such that one daughter cell is larger than the other; in each of these cases the larger daughter cell divides well before the smaller one, suggesting that the precursor cells, just like single-celled eucaryotes, have to reach a threshold size before they can divide. These and other findings raise the possibility that such stochastic unequal divisions, rather than the stochastic events occurring in G1 proposed by “transition probability” models, may explain the random variability of cell cycle times seen within clonal cell lines in culture. PMID:9298991

The analysis of rapidly developing fog at the Kennedy Space Center

NASA Technical Reports Server (NTRS)

Wheeler, Mark M.; Atchison, Michael K.; Schumann, Robin; Taylor, Greg E.; Yersavich, Ann; Warburton, John D.

1994-01-01

This report documents fog precursors and fog climatology at Kennedy Space Center (KSC) Florida from 1986 to 1990. The major emphasis of this report focuses on rapidly developing fog events that would affect the less than 7-statute mile visibility rule for End-Of-Mission (EOM) Shuttle landing at KSC (Rule 4-64(A)). The Applied Meteorology Unit's (AMU's) work is to: develop a data base for study of fog associated weather conditions relating to violations of this landing constraint; develop forecast techniques or rules-of-thumb to determine whether or not current conditions are likely to result in an acceptable condition at landing; validate the forecast techniques; and transition techniques to operational use. As part of the analysis the fog events were categorized as either advection, pre-frontal or radiation. As a result of these analyses, the AMU developed a fog climatological data base, identified fog precursors and developed forecaster tools and decision trees. The fog climatological analysis indicates that during the fog season (October to April) there is a higher risk for a visibility violation at KSC during the early morning hours (0700 to 1200 UTC), while 95 percent of all fog events have dissipated by 1600 UTC. A high number of fog events are characterized by a westerly component to the surface wind at KSC (92 percent) and 83 percent of the fog events had fog develop west of KSC first (up to 2 hours). The AMU developed fog decision trees and forecaster tools that would help the forecaster identify fog precursors up to 12 hours in advance. Using the decision trees as process tools ensures the important meteorological data are not overlooked in the forecast process. With these tools and a better understanding of fog formation in the local KSC area, the Shuttle weather support forecaster should be able to give the Launch and Flight Directors a better KSC fog forecast with more confidence.

Thyroglobulin Represents a Novel Molecular Architecture of Vertebrates.

PubMed

Holzer, Guillaume; Morishita, Yoshiaki; Fini, Jean-Baptiste; Lorin, Thibault; Gillet, Benjamin; Hughes, Sandrine; Tohmé, Marie; Deléage, Gilbert; Demeneix, Barbara; Arvan, Peter; Laudet, Vincent

2016-08-05

Thyroid hormones modulate not only multiple functions in vertebrates (energy metabolism, central nervous system function, seasonal changes in physiology, and behavior) but also in some non-vertebrates where they control critical post-embryonic developmental transitions such as metamorphosis. Despite their obvious biological importance, the thyroid hormone precursor protein, thyroglobulin (Tg), has been experimentally investigated only in mammals. This may bias our view of how thyroid hormones are produced in other organisms. In this study we searched genomic databases and found Tg orthologs in all vertebrates including the sea lamprey (Petromyzon marinus). We cloned a full-size Tg coding sequence from western clawed frog (Xenopus tropicalis) and zebrafish (Danio rerio). Comparisons between the representative mammal, amphibian, teleost fish, and basal vertebrate indicate that all of the different domains of Tg, as well as Tg regional structure, are conserved throughout the vertebrates. Indeed, in Xenopus, zebrafish, and lamprey Tgs, key residues, including the hormonogenic tyrosines and the disulfide bond-forming cysteines critical for Tg function, are well conserved despite overall divergence of amino acid sequences. We uncovered upstream sequences that include start codons of zebrafish and Xenopus Tgs and experimentally proved that these are full-length secreted proteins, which are specifically recognized by antibodies against rat Tg. By contrast, we have not been able to find any orthologs of Tg among non-vertebrate species. Thus, Tg appears to be a novel protein elaborated as a single event at the base of vertebrates and virtually unchanged thereafter. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Jam1a-Jam2a interactions regulate haematopoietic stem cell fate through Notch signalling.

PubMed

Kobayashi, Isao; Kobayashi-Sun, Jingjing; Kim, Albert D; Pouget, Claire; Fujita, Naonobu; Suda, Toshio; Traver, David

2014-08-21

Notch signalling plays a key role in the generation of haematopoietic stem cells (HSCs) during vertebrate development and requires intimate contact between signal-emitting and signal-receiving cells, although little is known regarding when, where and how these intercellular events occur. We previously reported that the somitic Notch ligands, Dlc and Dld, are essential for HSC specification. It has remained unclear, however, how these somitic requirements are connected to the later emergence of HSCs from the dorsal aorta. Here we show in zebrafish that Notch signalling establishes HSC fate as their shared vascular precursors migrate across the ventral face of the somite and that junctional adhesion molecules (JAMs) mediate this required Notch signal transduction. HSC precursors express jam1a (also known as f11r) and migrate axially across the ventral somite, where Jam2a and the Notch ligands Dlc and Dld are expressed. Despite no alteration in the expression of Notch ligand or receptor genes, loss of function of jam1a led to loss of Notch signalling and loss of HSCs. Enforced activation of Notch in shared vascular precursors rescued HSCs in jam1a or jam2a deficient embryos. Together, these results indicate that Jam1a-Jam2a interactions facilitate the transduction of requisite Notch signals from the somite to the precursors of HSCs, and that these events occur well before formation of the dorsal aorta.

Intraductal papillary-mucinous neoplasia of the pancreas: Histopathology and molecular biology.

PubMed

Verbeke, Caroline S

2010-10-27

Intraductal papillary-mucinous neoplasm (IPMN) of the pancreas is a clinically and morphologically distinctive precursor lesion of pancreatic cancer, characterized by gradual progression through a sequence of neoplastic changes. Based on the nature of the constituting neoplastic epithelium, degree of dysplasia and location within the pancreatic duct system, IPMNs are divided in several types which differ in their biological properties and clinical outcome. Molecular analysis and recent animal studies suggest that IPMNs develop in the context of a field-defect and reveal their possible relationship with other neoplastic precursor lesions of pancreatic cancer.

Genome Sequence of Lactobacillus saerimneri 30a (Formerly Lactobacillus sp. Strain 30a), a Reference Lactic Acid Bacterium Strain Producing Biogenic Amines

PubMed Central

Romano, Andrea; Trip, Hein; Campbell-Sills, Hugo; Bouchez, Olivier; Sherman, David; Lolkema, Juke S.

2013-01-01

Lactobacillus sp. strain 30a (Lactobacillus saerimneri) produces the biogenic amines histamine, putrescine, and cadaverine by decarboxylating their amino acid precursors. We report its draft genome sequence (1,634,278 bases, 42.6% G+C content) and the principal findings from its annotation, which might shed light onto the enzymatic machineries that are involved in its production of biogenic amines. PMID:23405290

Analysis and Prediction of Exon Skipping Events from RNA-Seq with Sequence Information Using Rotation Forest.

PubMed

Du, Xiuquan; Hu, Changlin; Yao, Yu; Sun, Shiwei; Zhang, Yanping

2017-12-12

In bioinformatics, exon skipping (ES) event prediction is an essential part of alternative splicing (AS) event analysis. Although many methods have been developed to predict ES events, a solution has yet to be found. In this study, given the limitations of machine learning algorithms with RNA-Seq data or genome sequences, a new feature, called RS (RNA-seq and sequence) features, was constructed. These features include RNA-Seq features derived from the RNA-Seq data and sequence features derived from genome sequences. We propose a novel Rotation Forest classifier to predict ES events with the RS features (RotaF-RSES). To validate the efficacy of RotaF-RSES, a dataset from two human tissues was used, and RotaF-RSES achieved an accuracy of 98.4%, a specificity of 99.2%, a sensitivity of 94.1%, and an area under the curve (AUC) of 98.6%. When compared to the other available methods, the results indicate that RotaF-RSES is efficient and can predict ES events with RS features.

A Python Analytical Pipeline to Identify Prohormone Precursors and Predict Prohormone Cleavage Sites

PubMed Central

Southey, Bruce R.; Sweedler, Jonathan V.; Rodriguez-Zas, Sandra L.

2008-01-01

Neuropeptides and hormones are signaling molecules that support cell–cell communication in the central nervous system. Experimentally characterizing neuropeptides requires significant efforts because of the complex and variable processing of prohormone precursor proteins into neuropeptides and hormones. We demonstrate the power and flexibility of the Python language to develop components of an bioinformatic analytical pipeline to identify precursors from genomic data and to predict cleavage as these precursors are en route to the final bioactive peptides. We identified 75 precursors in the rhesus genome, predicted cleavage sites using support vector machines and compared the rhesus predictions to putative assignments based on homology to human sequences. The correct classification rate of cleavage using the support vector machines was over 97% for both human and rhesus data sets. The functionality of Python has been important to develop and maintain NeuroPred (http://neuroproteomics.scs.uiuc.edu/neuropred.html), a user-centered web application for the neuroscience community that provides cleavage site prediction from a wide range of models, precision and accuracy statistics, post-translational modifications, and the molecular mass of potential peptides. The combined results illustrate the suitability of the Python language to implement an all-inclusive bioinformatics approach to predict neuropeptides that encompasses a large number of interdependent steps, from scanning genomes for precursor genes to identification of potential bioactive neuropeptides. PMID:19169350

Isolation of pheromone precursor genes of Magnaporthe grisea.

PubMed

Shen, W C; Bobrowicz, P; Ebbole, D J

1999-01-01

In heterothallic ascomycetes one mating partner serves as the source of female tissue and is fertilized with spermatia from a partner of the opposite mating type. The role of pheromone signaling in mating is thought to involve recognition of cells of the opposite mating type. We have isolated two putative pheromone precursor genes of Magnaporthe grisea. The genes are present in both mating types of the fungus but they are expressed in a mating type-specific manner. The MF1-1 gene, expressed in Mat1-1 strains, is predicted to encode a 26-amino-acid polypeptide that is processed to produce a lipopeptide pheromone. The MF2-1 gene, expressed in Mat1-2 strains, is predicted to encode a precursor polypeptide that is processed by a Kex2-like protease to yield a pheromone with striking similarity to the predicted pheromone sequence of a close relative, Cryphonectria parasitica. Expression of the M. grisea putative pheromone precursor genes was observed under defined nutritional conditions and in field isolates. This suggests that the requirement for complex media for mating and the poor fertility of field isolates may not be due to limitation of pheromone precursor gene expression. Detection of putative pheromone precursor gene mRNA in conidia suggests that pheromones may be important for the fertility of conidia acting as spermatia. Copyright 1999 Academic Press.

Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

Time Separation Between Events in a Sequence: a Regional Property?

NASA Astrophysics Data System (ADS)

Muirwood, R.; Fitzenz, D. D.

2013-12-01

Earthquake sequences are loosely defined as events occurring too closely in time and space to appear unrelated. Depending on the declustering method, several, all, or no event(s) after the first large event might be recognized as independent mainshocks. It can therefore be argued that a probabilistic seismic hazard assessment (PSHA, traditionally dealing with mainshocks only) might already include the ground shaking effects of such sequences. Alternatively all but the largest event could be classified as an ';aftershock' and removed from the earthquake catalog. While in PSHA the question is only whether to keep or remove the events from the catalog, for Risk Management purposes, the community response to the earthquakes, as well as insurance risk transfer mechanisms, can be profoundly affected by the actual timing of events in such a sequence. In particular the repetition of damaging earthquakes over a period of weeks to months can lead to businesses closing and families evacuating from the region (as happened in Christchurch, New Zealand in 2011). Buildings that are damaged in the first earthquake may go on to be damaged again, even while they are being repaired. Insurance also functions around a set of critical timeframes - including the definition of a single 'event loss' for reinsurance recoveries within the 192 hour ';hours clause', the 6-18 month pace at which insurance claims are settled, and the annual renewal of insurance and reinsurance contracts. We show how temporal aspects of earthquake sequences need to be taken into account within models for Risk Management, and what time separation between events are most sensitive, both in terms of the modeled disruptions to lifelines and business activity as well as in the losses to different parties (such as insureds, insurers and reinsurers). We also explore the time separation between all events and between loss causing events for a collection of sequences from across the world and we point to the need to understand the rate controlling processes that determine such sequences per tectonic region and fluid/heat flow provinces.

Sequencing Larger Intact Proteins (30-70 kDa) with Activated Ion Electron Transfer Dissociation

NASA Astrophysics Data System (ADS)

Riley, Nicholas M.; Westphall, Michael S.; Coon, Joshua J.

2018-01-01

The analysis of intact proteins via mass spectrometry can offer several benefits to proteome characterization, although the majority of top-down experiments focus on proteoforms in a relatively low mass range (<30 kDa). Recent studies have focused on improving the analysis of larger intact proteins (up to 75 kDa), but they have also highlighted several challenges to be addressed. One major hurdle is the efficient dissociation of larger protein ions, which often to do not yield extensive fragmentation via conventional tandem MS methods. Here we describe the first application of activated ion electron transfer dissociation (AI-ETD) to proteins in the 30-70 kDa range. AI-ETD leverages infrared photo-activation concurrent to ETD reactions to improve sequence-informative product ion generation. This method generates more product ions and greater sequence coverage than conventional ETD, higher-energy collisional dissociation (HCD), and ETD combined with supplemental HCD activation (EThcD). Importantly, AI-ETD provides the most thorough protein characterization for every precursor ion charge state investigated in this study, making it suitable as a universal fragmentation method in top-down experiments. Additionally, we highlight several acquisition strategies that can benefit characterization of larger proteins with AI-ETD, including combination of spectra from multiple ETD reaction times for a given precursor ion, multiple spectral acquisitions of the same precursor ion, and combination of spectra from two different dissociation methods (e.g., AI-ETD and HCD). In all, AI-ETD shows great promise as a method for dissociating larger intact protein ions as top-down proteomics continues to advance into larger mass ranges. [Figure not available: see fulltext.

Gamma-Ray Burst Precursor Activity as Observed with BATSE

NASA Technical Reports Server (NTRS)

Koshut, Thomas M.; Kouveliotou, Chryssa; Paciesas, William S.; vanParadijs, Jan; Pendleton, Geoffrey N.; Briggs, Michael S.; Fishman, Gerald J.; Meegan, Charles A.

1995-01-01

Gamma-ray burst time histories often consist of multiple episodes of emission with the count rate dropping to the background level between adjacent episodes. We define precursor activity as any case in which the first episode (referred to as the precursor episode) has a lower peak intensity than that of the remaining emission (referred to as the main episode) and is separated from the remaining burst emission by a background interval that is at least as long as the remaining emission. We find that approx. 3% of the bursts observed with the Burst and Transient Source Experiment (BATSE) on Compton Gamma Ray Observatory (CGRO) satisfy this definition. We present the results of a study of the properties of these events. The spatial distribution of these sources is consistent with that of the larger set of all BATSE gamma-ray bursts: inhomogeneous and isotropic. A correlation between the duration of the precursor emission and the duration of the main episode emission is observed at about the 3 sigma confidence level. We find no meaningful significant correlations between or among any of the other characteristics of the precursor or main episode emission. It appears that the characteristics of the main episode emission are independent of the existence of the precursor emission.

Seismic sequences in the Sombrero Seismic Zone

NASA Astrophysics Data System (ADS)

Pulliam, J.; Huerfano, V. A.; ten Brink, U.; von Hillebrandt, C.

2007-05-01

The northeastern Caribbean, in the vicinity of Puerto Rico and the Virgin Islands, has a long and well-documented history of devastating earthquakes and tsunamis, including major events in 1670, 1787, 1867, 1916, 1918, and 1943. Recently, seismicity has been concentrated to the north and west of the British Virgin Islands, in the region referred to as the Sombrero Seismic Zone by the Puerto Rico Seismic Network (PRSN). In the combined seismicity catalog maintained by the PRSN, several hundred small to moderate magnitude events can be found in this region prior to 2006. However, beginning in 2006 and continuing to the present, the rate of seismicity in the Sombrero suddenly increased, and a new locus of activity developed to the east of the previous location. Accurate estimates of seismic hazard, and the tsunamigenic potential of seismic events, depend on an accurate and comprehensive understanding of how strain is being accommodated in this corner region. Are faults locked and accumulating strain for release in a major event? Or is strain being released via slip over a diffuse system of faults? A careful analysis of seismicity patterns in the Sombrero region has the potential to both identify faults and modes of failure, provided the aggregation scheme is tuned to properly identify related events. To this end, we experimented with a scheme to identify seismic sequences based on physical and temporal proximity, under the assumptions that (a) events occur on related fault systems as stress is refocused by immediately previous events and (b) such 'stress waves' die out with time, so that two events that occur on the same system within a relatively short time window can be said to have a similar 'trigger' in ways that two nearby events that occurred years apart cannot. Patterns that emerge from the identification, temporal sequence, and refined locations of such sequences of events carry information about stress accommodation that is obscured by large clouds of unrelated events in plots of the general catalog. One characteristic of these sequences is that their magnitudes tend to be consistently small (1.0 - 3.5 mb, with only five events greater than 3.5 mb) and they typically do not include an event that could confidently be identified as a "main" shock. Nevertheless, the numbers of events, temporal and geographic distribution of shocks in each sequence suggests that these are aftershock sequences, yet none includes an event that could confidently be identified as a "main" shock. This observation suggests several questions. Do these sequences truly represent aftershocks? If so, where are the main events? Are they perhaps related to "silent" or "slow" earthquakes in the subduction zone? If so, could such slow earthquakes be related to the dropping away of the subducting slab beneath the deep Puerto Rico Trench? Or do the sequences indicate tearing of the NA lithosphere of the North America plate as it subducts beneath the Caribbean plate?

Complex alternative splicing of acetylcholinesterase transcripts in Torpedo electric organ; primary structure of the precursor of the glycolipid-anchored dimeric form.

PubMed Central

Sikorav, J L; Duval, N; Anselmet, A; Bon, S; Krejci, E; Legay, C; Osterlund, M; Reimund, B; Massoulié, J

1988-01-01

In this paper, we show the existence of alternative splicing in the 3' region of the coding sequence of Torpedo acetylcholinesterase (AChE). We describe two cDNA structures which both diverge from the previously described coding sequence of the catalytic subunit of asymmetric (A) forms (Schumacher et al., 1986; Sikorav et al., 1987). They both contain a coding sequence followed by a non-coding sequence and a poly(A) stretch. Both of these structures were shown to exist in poly(A)+ RNAs, by S1 mapping experiments. The divergent region encoded by the first sequence corresponds to the precursor of the globular dimeric form (G2a), since it contains the expected C-terminal amino acids, Ala-Cys. These amino acids are followed by a 29 amino acid extension which contains a hydrophobic segment and must be replaced by a glycolipid in the mature protein. Analyses of intact G2a AChE showed that the common domain of the protein contains intersubunit disulphide bonds. The divergent region of the second type of cDNA consists of an adjacent genomic sequence, which is removed as an intron in A and Ga mRNAs, but may encode a distinct, less abundant catalytic subunit. The structures of the cDNA clones indicate that they are derived from minor mRNAs, shorter than the three major transcripts which have been described previously (14.5, 10.5 and 5.5 kb). Oligonucleotide probes specific for the asymmetric and globular terminal regions hybridize with the three major transcripts, indicating that their size is determined by 3'-untranslated regions which are not related to the differential splicing leading to A and Ga forms. Images PMID:3181125

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

PubMed Central

Chen, Kenian; Sloan, Steven A.; Bennett, Mariko L.; Scholze, Anja R.; O'Keeffe, Sean; Phatnani, Hemali P.; Guarnieri, Paolo; Caneda, Christine; Ruderisch, Nadine; Deng, Shuyun; Liddelow, Shane A.; Zhang, Chaolin; Daneman, Richard; Maniatis, Tom; Barres, Ben A.

2014-01-01

The major cell classes of the brain differ in their developmental processes, metabolism, signaling, and function. To better understand the functions and interactions of the cell types that comprise these classes, we acutely purified representative populations of neurons, astrocytes, oligodendrocyte precursor cells, newly formed oligodendrocytes, myelinating oligodendrocytes, microglia, endothelial cells, and pericytes from mouse cerebral cortex. We generated a transcriptome database for these eight cell types by RNA sequencing and used a sensitive algorithm to detect alternative splicing events in each cell type. Bioinformatic analyses identified thousands of new cell type-enriched genes and splicing isoforms that will provide novel markers for cell identification, tools for genetic manipulation, and insights into the biology of the brain. For example, our data provide clues as to how neurons and astrocytes differ in their ability to dynamically regulate glycolytic flux and lactate generation attributable to unique splicing of PKM2, the gene encoding the glycolytic enzyme pyruvate kinase. This dataset will provide a powerful new resource for understanding the development and function of the brain. To ensure the widespread distribution of these datasets, we have created a user-friendly website (http://web.stanford.edu/group/barres_lab/brain_rnaseq.html) that provides a platform for analyzing and comparing transciption and alternative splicing profiles for various cell classes in the brain. PMID:25186741

Plasmodium vivax: a monoclonal antibody recognizes a circumsporozoite protein precursor on the sporozoite surface.

PubMed

Gonzalez-Ceron, L; Rodriguez, M H; Wirtz, R A; Sina, B J; Palomeque, O L; Nettel, J A; Tsutsumi, V

1998-11-01

The major surface circumsporozoite (CS) proteins are known to play a role in malaria sporozoite development and invasion of invertebrate and vertebrate host cells. Plasmodium vivax CS protein processing during mosquito midgut oocyst and salivary gland sporozoite development was studied using monoclonal antibodies which recognize different CS protein epitopes. Monoclonal antibodies which react with the CS amino acid repeat sequences by ELISA recognized a 50-kDa precursor protein in immature oocyst and additional 47- and 42-kDa proteins in older oocysts. A 42-kDa CS protein was detected after initial sporozoite invasion of mosquito salivary glands and an additional 50-kDa precursor CS protein observed later in infected salivary glands. These data confirm previous results with other Plasmodium species, in which more CS protein precursors were detected in oocysts than in salivary gland sporozoites. A monoclonal antibody (PvPCS) was characterized which reacts with an epitope found only in the 50-kDa precursor CS protein. PvPCS reacted with all P. vivax sporozoite strains tested by indirect immunofluorescent assay, homogeneously staining the sporozoite periphery with much lower intensity than that produced by anti-CS repeat antibodies. Immunoelectron microscopy using PvPCS showed that the CS protein precursor was associated with peripheral cytoplasmic vacuoles and membranes of sporoblast and budding sporozoites in development oocysts. In salivary gland sporozoites, the CS protein precursor was primarily associated with micronemes and sporozoite membranes. Our results suggest that the 50-kDa CS protein precursor is synthesized intracellularly and secreted on the membrane surface, where it is proteolytically processed to form the 42-kDa mature CS protein. These data indicate that differences in CS protein processing in oocyst and salivary gland sporozoites development may occur. Copyright 1998 Academic Press.

Cluster self-organization of TR-containing germanate systems: Suprapolyhedral precursors and self-assembly of the crystal structures of the LiNdGeO{sub 4} and CeGeO{sub 4} compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ilyushin, G. D., E-mail: ilyushin@nc.cryst.ras.ru; Dem'yanets, L. N.

2007-07-15

A combinatorial-topological analysis of the orthogermanates LiNdGeO{sub 4} (space group Pbcn) and CeGeO{sub 4} (space group I 4{sub 1}/a, the scheelite structure type), which have MT frameworks composed of polyhedral structural units in the form of M dodecahedra (NdO{sub 8} and CeO{sub 8}) and T tetrahedra (GeO{sub 4}), is performed using the method of coordination sequences with the TOPOS program package. It is established that the structures of both orthogermanates are characterized by equivalent crystal-forming nets 4444. The cluster precursors of the M{sub 2}T{sub 2} cyclic type are identified by the method of two-color decomposition. The local symmetry of four-polyhedralmore » clusters corresponds to the point group 2. In the precursor of the LiNdGeO{sub 4} orthogermanate, the Li atom is located above the M{sub 2}T{sub 2} ring. The number of Li-O bonds in this precursor is 4. The cluster precursors M{sub 2}T{sub 2} and LiM{sub 2}T{sub 2} are responsible for the formation of crystal-forming clusters of a higher level according to the mechanism of matrix self-assembly. The coordination numbers of the cluster precursors in two-dimensional nets for these structures are found to be equal to 4. The equivalent bilayer TR,Ge stacks that consist of eight cluster precursors are revealed in the structures under investigation. It is demonstrated that there exist three types of translational interlayer arrangements of cluster precursors upon the formation of macrostructures of the orthogermanates.« less

The 2012-2014 eruptive cycle of Copahue Volcano, Southern Andes. Magmatic-Hydrothermal system interaction and manifestations.

NASA Astrophysics Data System (ADS)

Morales, Sergio; Alarcón, Alex; Basualto, Daniel; Bengoa, Cintia; Bertín, Daniel; Cardona, Carlos; Córdova, Maria; Franco, Luis; Gil, Fernando; Hernandez, Erasmo; Lara, Luis; Lazo, Jonathan; Mardones, Cristian; Medina, Roxana; Peña, Paola; Quijada, Jonathan; San Martín, Juan; Valderrama, Oscar

2015-04-01

Copahue Volcano (COPV), in Southern Andes of Chile, is an andesitic-basaltic stratovolcano, which is located on the western margin of Caviahue Caldera. The COPV have a NE-trending fissure with 9 aligned vents, being El Agrio the main currently active vent, with ca. 400 m in diameter. The COPV is placed into an extensive hydrothermal system which has modulated its recent 2012-2014 eruptive activity, with small phreatic to phreatomagmatic eruptions and isolated weak strombolian episodes and formation of crater lakes inside the main crater. Since 2012, the Southern Andes Volcano Observatory (OVDAS) carried out the real-time monitoring with seismic broadband stations, GPS, infrasound sensors and webcams. In this work, we report pre, sin, and post-eruptive seismic activity of the last two main eruptions (Dec, 2012 and Oct, 2014) both with different seismic precursors and superficial activity, showing the second one a particularly appearance of seismic quiescence episodes preceding explosive activity, as an indicator of interaction between magmatic-hydrothermal systems. The first episode, in late 2012, was characterized by a low frequency (0.3-0.4 Hz and 1.0-1.5 Hz) continuous tremor which increased gradually from background noise level amplitude to values of reduced displacement (DR), close to 50 cm2 at the peak of the eruption, reaching an eruptive column of ~1.5 km height. After few months of recording low energy seismicity, a sequence of low frequency, repetitive and low energy seismic events arose, with a frequency of occurrence up to 300 events/hour. Also, the VLP earthquakes were added to the record probably associated with magma intrusion into a deep magmatic chamber during all stages of eruptive process, joined to the record of VT seismicity during the same period, which is located throughout the Caviahue Caldera area. Both kind of seismic patterns were again recorded in October 2014, being the precursor of the new eruptive cycle at this time as well as the deformation of the volcanic edifice detected by GPS network. In this new eruptive process, the record of tremor was followed by particular seismic quiescence, as precursors of explosive activity which evolved from low acoustic energy signals toward more energetic signals with impulsive first arrivals and strong attenuation, joined to night incandescence in the main vent without evident juvenile material ejected, which could be associated to the temporal depression of the hydrothermal system located in the volcano system. The recent eruptive episode at Copahue Volcano is a good example of the complex temporal evolution of the interaction between magmatic and hydrothermal systems.

Context and meter enhance long-range planning in music performance

PubMed Central

Mathias, Brian; Pfordresher, Peter Q.; Palmer, Caroline

2015-01-01

Neural responses demonstrate evidence of resonance, or oscillation, during the production of periodic auditory events. Music contains periodic auditory events that give rise to a sense of beat, which in turn generates a sense of meter on the basis of multiple periodicities. Metrical hierarchies may aid memory for music by facilitating similarity-based associations among sequence events at different periodic distances that unfold in longer contexts. A fundamental question is how metrical associations arising from a musical context influence memory during music performance. Longer contexts may facilitate metrical associations at higher hierarchical levels more than shorter contexts, a prediction of the range model, a formal model of planning processes in music performance (Palmer and Pfordresher, 2003; Pfordresher et al., 2007). Serial ordering errors, in which intended sequence events are produced in incorrect sequence positions, were measured as skilled pianists performed musical pieces that contained excerpts embedded in long or short musical contexts. Pitch errors arose from metrically similar positions and further sequential distances more often when the excerpt was embedded in long contexts compared to short contexts. Musicians’ keystroke intensities and error rates also revealed influences of metrical hierarchies, which differed for performances in long and short contexts. The range model accounted for contextual effects and provided better fits to empirical findings when metrical associations between sequence events were included. Longer sequence contexts may facilitate planning during sequence production by increasing conceptual similarity between hierarchically associated events. These findings are consistent with the notion that neural oscillations at multiple periodicities may strengthen metrical associations across sequence events during planning. PMID:25628550

Evolution of Phosphofructokinase

DTIC Science & Technology

1988-07-31

sequence data suggests that mammalian phosphofructokinase (PFK) has evolved from a procaryotic precursor by gene duplication, fusion, and mutation of...reacts with the 60 kDa polypeptide but not 68 kDa peptide. The data support the idea that the plant PPi-PFK has evolved from the same procaryotic

Novel in situ resistance measurement for the investigation of CIGS growth in a selenization process

NASA Astrophysics Data System (ADS)

Liu, Wei; Tian, Jian-Guo; Li, Zu-Bin; He, Qing; Li, Feng-Yan; Li, Chang-Jian; Sun, Yun

2009-03-01

During the selenization process of CIGS thin films, the relation between the element loss rate and the precursor depositions are analyzed. The growth of the CIGS thin films during the selenization process is investigated by the novel in situ resistance measurement, by which the formation of compound semiconductors can be observed directly and simultaneously. Their structures, phase evolutions and element losses are analyzed by XRD and XRF. Based on the experimental results, it can be concluded that the phase transforms have nothing to do with the deposition sequences of precursors, while the element loss rates are related to the deposition sequences in this process. In addition, element loss mechanisms of CIGS thin films prepared by the selenization process are analyzed by the phase evolutions and chemical combined path in the In, Ga-Se reaction processes. Moreover it is verified that the element losses are depressed by increasing the ramping-up rate finally. The results provide effective methods to fabricate high-quality CIGS thin films with low element losses.

A saposin-like domain influences the intracellular localization, stability, and catalytic activity of human acyloxyacyl hydrolase.

PubMed

Staab, J F; Ginkel, D L; Rosenberg, G B; Munford, R S

1994-09-23

Acyloxyacyl hydrolase, a leukocyte enzyme that acts on bacterial lipopolysaccharides (LPSs) and many glycerolipids, is synthesized as a precursor polypeptide that undergoes internal disulfide linkage before being proteolytically processed into two subunits. The larger subunit contains an amino acid sequence (Gly-X-Ser-X-Gly) that is found at the active sites of many lipases, while the smaller subunit has amino acid sequence similarity to saposins (sphingolipid activator proteins), cofactors for sphingolipid glycohydrolases. We show here that both acyloxyacyl hydrolase subunits are required for catalytic activity toward LPS and glycerophosphatidylcholine. In addition, mutations that truncate or delete the small subunit have profound effects on the intracellular localization, proteolytic processing, and stability of the enzyme in baby hamster kidney cells. Remarkably, proteolytic cleavage of the precursor protein increases the activity of the enzyme toward LPS by 10-20-fold without altering its activity toward glycerophosphatidylcholine. Proper orientation of the two subunits thus seems very important for the substrate specificity of this unusual enzyme.

Cyclotide isolation and characterization.

PubMed

Craik, David J; Henriques, Sonia Troeira; Mylne, Joshua S; Wang, Conan K

2012-01-01

Cyclotides are disulfide-rich cyclic peptides produced by plants with the presumed natural function of defense agents against insect pests. They are present in a wide range of plant tissues, being ribosomally synthesized via precursor proteins that are posttranslationally processed to produce mature peptides with a characteristic cyclic backbone and cystine knot motif associated with their six conserved cysteine residues. Their processing is not fully understood but involves asparaginyl endoproteinase activity. In addition to interest in their defense roles and their unique topologies, cyclotides have attracted attention as potential templates in peptide-based drug design applications. This chapter provides protocols for the isolation of cyclotides from plants, their detection and sequencing by mass spectrometry, and their structural analysis by NMR, as well as describing methods for the isolation of nucleic acid sequences that encode their precursor proteins. Assays to assess their membrane-binding interactions are also described. These protocols provide a "starter kit" for researchers entering the cyclotide field. Copyright © 2012 Elsevier Inc. All rights reserved.

Identification of an miRNA candidate reflects the possible significance of transcribed microsatellites in the hairpin precursors of black pepper.

PubMed

Joy, Nisha; Soniya, Eppurathu Vasudevan

2012-06-01

Plant miRNAs (18-24nt) are generated by the RNase III-type Dicer endonuclease from the endogenous hairpin precursors ('pre-miRNAs') with significant regulatory functions. The transcribed regions display a higher frequency of microsatellites, when compared to other regions of the genomic DNA. Simple sequence repeats (SSRs) resulting from replication slippage occurring in transcripts affect the expression of genes. The available experimental evidence for the incidence of SSRs in the miRNA precursors is limited. Considering the potential significance of SSRs in the miRNA genes, we carried out a preliminary analysis to verify the presence of SSRs in the pri-miRNAs of black pepper (Piper nigrum L.). We isolated a (CT) dinucleotide SSR bearing transcript using SMART strategy. The transcript was predicted to be a 'pri-miRNA candidate' with Dicer sites based on miRNA prediction tools and MFOLD structural predictions. The presence of this 'miRNA candidate' was confirmed by real-time TaqMan assays. The upstream sequence of the 'miRNA candidate' by genome walking when subjected to PlantCARE showed the presence of certain promoter elements, and the deduced amino acid showed significant similarity with NAP1 gene, which affects the transcription of many genes. Moreover the hairpin-like precursor overlapped the neighbouring NAP1 gene. In silico analysis revealed distinct putative functions for the 'miRNA candidate', of which majority were related to growth. Hence, we assume that this 'miRNA candidate' may get activated during transcription of NAP gene, thereby regulating the expression of many genes involved in developmental processes.

Purification of extensin from cell walls of tomato (hybrid of Lycopersicon esculentum and L. peruvianum) cells in suspension culture.

PubMed

Brownleader, M D; Dey, P M

1993-01-01

Extensin, a hydroxyproline-rich glycoprotein comprising substantial amounts of beta-L-arabinose-hydroxyproline glycosidic linkages is believed to be insolubilized in the cell wall during host-pathogen interaction by a peroxidase/hydroperoxide-mediated cross-linking process. Both extensin precursor and extensin peroxidase were ionically eluted from intact water-washed tomato (hybrid of Lycopersicon esculentum Mill. and L. peruvianum L. (Mill.) cells in suspension cultures and purified to homogeneity by a rapid and simple procedure under mild and non-destructive experimental conditions. The molecular weight of native extensin precursor was estimated to be greater than 240-300 kDa by Superose-12 gel-filtration chromatography. Extensin monomers have previously been designated a molecular weight of approximately 80 kDa. Our results indicate that salt-eluted extensin precursor is not monomeric. Agarose-gel electrophoresis, Superose-12-gel-filtration, extensin-peroxidase-catalysed cross-linking, Mono-S ion-exchange fast protein liquid chromatography (FPLC), and peptide-sequencing data confirmed the homogeneity of the extensin preparation. Evidence that the purified protein was extensin is attributed to the presence of the putative sequence motif--Ser (Hyp)4--within the N-terminal end of the protein. Treatment of extensin with trifluoroacetic acid demonstrated that arabinose was the principal carbohydrate. The amino-acid composition of the purified extensin was similar to those reported in the literature. The cross-linking of extensin in vitro upon incubation with extensin peroxidase and exogenous H2O2 was characteristic of other reported extensins. Furthermore, Mono-S ion-exchange FPLC of native extensin precursor resolved it into two isoforms, A (90%) and B (10%). The amino-acid compositions of extensin A and extensin B were found to be similar to each other and both extensins were cross-linked in vitro by extensin peroxidase.

Identification of snake bradykinin-potentiating peptides (BPPs)-simile sequences in rat brain--Potential BPP-like precursor protein?

PubMed

Campeiro, Joana D'Arc; Neshich, Izabella P; Sant'Anna, Osvaldo A; Lopes, Robson; Ianzer, Danielle; Assakura, Marina T; Neshich, Goran; Hayashi, Mirian A F

2015-08-01

Bradykinin-potentiating peptides (BPPs) from the South American pit viper snake venom were the first natural inhibitors of the human angiotensin I-converting enzyme (ACE) described. The pioneer characterization of the BPPs precursor from the snake venom glands by our group showed for the first time the presence of the C-type natriuretic peptide (CNP) in this same viper precursor protein. The confirmation of the BPP/CNP expression in snake brain regions correlated with neuroendocrine functions stimulated us to pursue the physiological correlates of these vasoactive peptides in mammals. Notably, several snake toxins were shown to have endogenous physiological correlates in mammals. In the present work, we expressed in bacteria the BPPs domain of the snake venom gland precursor protein, and this purified recombinant protein was used to raise specific polyclonal anti-BPPs antibodies. The correspondent single protein band immune-recognized in adult rat brain cytosol was isolated by 2D-SDS/PAGE and/or HPLC, before characterization by MS fingerprint analysis, which identified this protein as superoxide dismutase (SOD, EC 1.15.1.1), a classically known enzyme with antioxidant activity and important roles in the blood pressure modulation. In silico analysis showed the exposition of the BPP-like peptide sequences on the surface of the 3D structure of rat SOD. These peptides were chemically synthesized to show the BPP-like biological activities in ex vivo and in vivo pharmacological bioassays. Taken together, our data suggest that SOD protein have the potential to be a source for putative BPP-like bioactive peptides, which once released may contribute to the blood pressure control in mammals. Copyright © 2015 Elsevier Inc. All rights reserved.

Atomistic kinetic Monte Carlo study of atomic layer deposition derived from density functional theory.

PubMed

Shirazi, Mahdi; Elliott, Simon D

2014-01-30

To describe the atomic layer deposition (ALD) reactions of HfO2 from Hf(N(CH3)2)4 and H2O, a three-dimensional on-lattice kinetic Monte-Carlo model is developed. In this model, all atomistic reaction pathways in density functional theory (DFT) are implemented as reaction events on the lattice. This contains all steps, from the early stage of adsorption of each ALD precursor, kinetics of the surface protons, interaction between the remaining precursors (steric effect), influence of remaining fragments on adsorption sites (blocking), densification of each ALD precursor, migration of each ALD precursors, and cooperation between the remaining precursors to adsorb H2O (cooperative effect). The essential chemistry of the ALD reactions depends on the local environment at the surface. The coordination number and a neighbor list are used to implement the dependencies. The validity and necessity of the proposed reaction pathways are statistically established at the mesoscale. The formation of one monolayer of precursor fragments is shown at the end of the metal pulse. Adsorption and dissociation of the H2O precursor onto that layer is described, leading to the delivery of oxygen and protons to the surface during the H2O pulse. Through these processes, the remaining precursor fragments desorb from the surface, leaving the surface with bulk-like and OH-terminated HfO2, ready for the next cycle. The migration of the low coordinated remaining precursor fragments is also proposed. This process introduces a slow reordering motion (crawling) at the mesoscale, leading to the smooth and conformal thin film that is characteristic of ALD. Copyright © 2013 Wiley Periodicals, Inc.

Influence of atomic layer deposition valve temperature on ZrN plasma enhanced atomic layer deposition growth

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muneshwar, Triratna, E-mail: muneshwa@ualberta.ca; Cadien, Ken

2015-11-15

Atomic layer deposition (ALD) relies on a sequence of self-limiting surface reactions for thin film growth. The effect of non-ALD side reactions, from insufficient purging between pulses and from precursor self-decomposition, on film growth is well known. In this article, precursor condensation within an ALD valve is described, and the effect of the continuous precursor source from condensate evaporation on ALD growth is discussed. The influence of the ALD valve temperature on growth and electrical resistivity of ZrN plasma enhanced ALD (PEALD) films is reported. Increasing ALD valve temperature from 75 to 95 °C, with other process parameters being identical, decreasedmore » both the growth per cycle and electrical resistivity (ρ) of ZrN PEALD films from 0.10 to 0.07 nm/cycle and from 560 to 350 μΩ cm, respectively. Our results show that the non-ALD growth resulting from condensate accumulation is eliminated at valve temperatures close to the pressure corrected boiling point of precursor.« less

Protein secretion and surface display in Gram-positive bacteria

PubMed Central

Schneewind, Olaf; Missiakas, Dominique M.

2012-01-01

The cell wall peptidoglycan of Gram-positive bacteria functions as a surface organelle for the transport and assembly of proteins that interact with the environment, in particular, the tissues of an infected host. Signal peptide-bearing precursor proteins are secreted across the plasma membrane of Gram-positive bacteria. Some precursors carry C-terminal sorting signals with unique sequence motifs that are cleaved by sortase enzymes and linked to the cell wall peptidoglycan of vegetative forms or spores. The sorting signals of pilin precursors are cleaved by pilus-specific sortases, which generate covalent bonds between proteins leading to the assembly of fimbrial structures. Other precursors harbour surface (S)-layer homology domains (SLH), which fold into a three-pronged spindle structure and bind secondary cell wall polysaccharides, thereby associating with the surface of specific Gram-positive microbes. Type VII secretion is a non-canonical secretion pathway for WXG100 family proteins in mycobacteria. Gram-positive bacteria also secrete WXG100 proteins and carry unique genes that either contribute to discrete steps in secretion or represent distinctive substrates for protein transport reactions. PMID:22411983

Arabidopsis Chloroplast Mini-Ribonuclease III Participates in rRNA Maturation and Intron Recycling

PubMed Central

Hotto, Amber M.; Castandet, Benoît; Gilet, Laetitia; Higdon, Andrea; Condon, Ciarán; Stern, David B.

2015-01-01

RNase III proteins recognize double-stranded RNA structures and catalyze endoribonucleolytic cleavages that often regulate gene expression. Here, we characterize the functions of RNC3 and RNC4, two Arabidopsis thaliana chloroplast Mini-RNase III-like enzymes sharing 75% amino acid sequence identity. Whereas rnc3 and rnc4 null mutants have no visible phenotype, rnc3/rnc4 (rnc3/4) double mutants are slightly smaller and chlorotic compared with the wild type. In Bacillus subtilis, the RNase Mini-III is integral to 23S rRNA maturation. In Arabidopsis, we observed imprecise maturation of 23S rRNA in the rnc3/4 double mutant, suggesting that exoribonucleases generated staggered ends in the absence of specific Mini-III-catalyzed cleavages. A similar phenotype was found at the 3′ end of the 16S rRNA, and the primary 4.5S rRNA transcript contained 3′ extensions, suggesting that Mini-III catalyzes several processing events of the polycistronic rRNA precursor. The rnc3/4 mutant showed overaccumulation of a noncoding RNA complementary to the 4.5S-5S rRNA intergenic region, and its presence correlated with that of the extended 4.5S rRNA precursor. Finally, we found rnc3/4-specific intron degradation intermediates that are probable substrates for Mini-III and show that B. subtilis Mini-III is also involved in intron regulation. Overall, this study extends our knowledge of the key role of Mini-III in intron and noncoding RNA regulation and provides important insight into plastid rRNA maturation. PMID:25724636

Purification and characterization of glutamate N-acetyltransferase involved in citrulline accumulation in wild watermelon.

PubMed

Takahara, Kentaro; Akashi, Kinya; Yokota, Akiho

2005-10-01

Citrulline is an efficient hydroxyl radical scavenger that can accumulate at concentrations of up to 30 mm in the leaves of wild watermelon during drought in the presence of strong light; however, the mechanism of this accumulation remains unclear. In this study, we characterized wild watermelon glutamate N-acetyltransferase (CLGAT) that catalyses the transacetylation reaction between acetylornithine and glutamate to form acetylglutamate and ornithine, thereby functioning in the first and fifth steps in citrulline biosynthesis. CLGAT enzyme purified 7000-fold from leaves was composed of two subunits with different N-terminal amino acid sequences. Analysis of the corresponding cDNA revealed that these two subunits have molecular masses of 21.3 and 23.5 kDa and are derived from a single precursor polypeptide, suggesting that the CLGAT precursor is cleaved autocatalytically at the conserved ATML motif, as in other glutamate N-acetyltransferases of microorganisms. A green fluorescence protein assay revealed that the first 26-amino acid sequence at the N-terminus of the precursor functions as a chloroplast transit peptide. The CLGAT exhibited thermostability up to 70 degrees C, suggesting an increase in enzyme activity under high leaf temperature conditions during drought/strong-light stresses. Moreover, CLGAT was not inhibited by citrulline or arginine at physiologically relevant high concentrations. These findings suggest that CLGAT can effectively participate in the biosynthesis of citrulline in wild watermelon leaves during drought/strong-light stress.

Prohormone convertases differentially process pro-neurotensin/neuromedin N in tissues and cell lines.

PubMed

Kitabgi, Patrick

2006-08-01

Neurotensin (NT) is synthesized as part of a larger precursor that also contains neuromedin N (NN), a six-amino acid neurotensin-like peptide. NT and NN are located in the C-terminal region of the precursor (pro-NT/NN) where they are flanked and separated by three Lys-Arg sequences. A fourth dibasic sequence is present in the middle of the precursor. Dibasics are the consensus sites recognized and cleaved by specialized endoproteases that belong to the family of proprotein convertases (PCs). In tissues that express pro-NT/NN, the three C-terminal Lys-Arg sites are differentially processed, whereas the middle dibasic is poorly cleaved. Processing gives rise mainly to NT and NN in the brain, to NT and a large peptide with a C-terminal NN moiety (large NN) in the gut, and to NT, large NN, and a large peptide with a C-terminal NT moiety (large NT) in the adrenals. Recent evidence indicates that PC1, PC2, and PC5-A are the prohormone convertases responsible for the processing patterns observed in the gut, brain, and adrenals, respectively. As NT, NN, large NT, and large NN are all endowed with biological activity, the evidence reviewed in this paper supports the idea that posttranslational processing of pro-NT/NN in tissues may generate biological diversity of pathophysiological relevance.

Amplification and chromosomal dispersion of human endogenous retroviral sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Steele, P.E.; Martin, M.A.; Rabson, A.B.

1986-09-01

Endogenous retroviral sequences have undergone amplification events involving both viral and flanking cellular sequences. The authors cloned members of an amplified family of full-length endogenous retroviral sequences. Genomic blotting, employing a flanking cellular DNA probe derived from a member of this family, revealed a similar array of reactive bands in both humans and chimpanzees, indicating that an amplification event involving retroviral and associated cellular DNA sequences occurred before the evolutionary separation of these two primates. Southern analyses of restricted somatic cell hybrid DNA preparations suggested that endogenous retroviral segments are widely dispersed in the human genome and that amplification andmore » dispersion events may be linked.« less

Intramolecular amide bonds stabilize pili on the surface of bacilli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Budzik, Jonathan M.; Poor, Catherine B.; Faull, Kym F.

Gram-positive bacteria elaborate pili and do so without the participation of folding chaperones or disulfide bond catalysts. Sortases, enzymes that cut pilin precursors, form covalent bonds that link pilin subunits and assemble pili on the bacterial surface. We determined the x-ray structure of BcpA, the major pilin subunit of Bacillus cereus. The BcpA precursor encompasses 2 Ig folds (CNA{sub 2} and CNA{sub 3}) and one jelly-roll domain (XNA) each of which synthesizes a single intramolecular amide bond. A fourth amide bond, derived from the Ig fold of CNA{sub 1}, is formed only after pilin subunits have been incorporated into pili.more » We report that the domains of pilin precursors have evolved to synthesize a discrete sequence of intramolecular amide bonds, thereby conferring structural stability and protease resistance to pili.« less

cDNAs encoding [D-Ala2]deltorphin precursors from skin of Phyllomedusa bicolor also contain genetic information for three dermorphin-related opioid peptides.

PubMed

Richter, K; Egger, R; Negri, L; Corsi, R; Severini, C; Kreil, G

1990-06-01

We present the structure of four precursors for [D-Ala2]deltorphins I and II as deduced from cDNAs cloned from skin of the frog Phyllomedusa bicolor. These contain the genetic information for one copy of [D-Ala2]deltorphin II and zero, one, or three copies of [D-Ala2]deltorphin I. In each case, the D-alanine of the end product is encoded by a normal GCG codon for L-alanine. In addition, the existence of three peptides related to dermorphin was predicted from the amino acid sequence of the precursors. These peptides were synthesized with a D-alanine in position 2 and their pharmacological properties were tested. Two of them, [Lys7]dermorphin-OH and [Trp4,Asn7]dermorphin-OH, were found to have roughly the same affinity and selectivity for mu-type opioid receptors as dermorphin.

cDNAs encoding [D-Ala2]deltorphin precursors from skin of Phyllomedusa bicolor also contain genetic information for three dermorphin-related opioid peptides.

PubMed Central

Richter, K; Egger, R; Negri, L; Corsi, R; Severini, C; Kreil, G

1990-01-01

We present the structure of four precursors for [D-Ala2]deltorphins I and II as deduced from cDNAs cloned from skin of the frog Phyllomedusa bicolor. These contain the genetic information for one copy of [D-Ala2]deltorphin II and zero, one, or three copies of [D-Ala2]deltorphin I. In each case, the D-alanine of the end product is encoded by a normal GCG codon for L-alanine. In addition, the existence of three peptides related to dermorphin was predicted from the amino acid sequence of the precursors. These peptides were synthesized with a D-alanine in position 2 and their pharmacological properties were tested. Two of them, [Lys7]dermorphin-OH and [Trp4,Asn7]dermorphin-OH, were found to have roughly the same affinity and selectivity for mu-type opioid receptors as dermorphin. PMID:2352951

Lateral release of proteins from the TOM complex into the outer membrane of mitochondria.

PubMed

Harner, Max; Neupert, Walter; Deponte, Marcel

2011-07-15

The TOM complex of the outer membrane of mitochondria is the entry gate for the vast majority of precursor proteins that are imported into the mitochondria. It is made up by receptors and a protein conducting channel. Although precursor proteins of all subcompartments of mitochondria use the TOM complex, it is not known whether its channel can only mediate passage across the outer membrane or also lateral release into the outer membrane. To study this, we have generated fusion proteins of GFP and Tim23 which are inserted into the inner membrane and, at the same time, are spanning either the TOM complex or are integrated into the outer membrane. Our results demonstrate that the TOM complex, depending on sequence determinants in the precursors, can act both as a protein conducting pore and as an insertase mediating lateral release into the outer membrane.

Sequencing Events: Exploring Art and Art Jobs.

ERIC Educational Resources Information Center

Stephens, Pamela Geiger; Shaddix, Robin K.

2000-01-01

Presents an activity for upper-elementary students that correlates the actions of archaeologists, patrons, and artists with the sequencing of events in a logical order. Features ancient Egyptian art images. Discusses the preparation of materials, motivation, a pre-writing activity, and writing a story in sequence. (CMK)

Influence of time and length size feature selections for human activity sequences recognition.

PubMed

Fang, Hongqing; Chen, Long; Srinivasan, Raghavendiran

2014-01-01

In this paper, Viterbi algorithm based on a hidden Markov model is applied to recognize activity sequences from observed sensors events. Alternative features selections of time feature values of sensors events and activity length size feature values are tested, respectively, and then the results of activity sequences recognition performances of Viterbi algorithm are evaluated. The results show that the selection of larger time feature values of sensor events and/or smaller activity length size feature values will generate relatively better results on the activity sequences recognition performances. © 2013 ISA Published by ISA All rights reserved.

Biosynthesis of the Polycyclic Antimicrobial Peptides Lacticin 481, Haloduracin, and Cinnamycin

ERIC Educational Resources Information Center

Cooper, Lisa E.

2009-01-01

Lantibiotics are bacterial-derived polycyclic antimicrobial peptides. They are genetically encoded and ribosomally synthesized as precursor peptides containing a structural region that undergoes post-translational modification and a leader sequence that is not modified. Specific serine and threonine residues in the pre-lantibiotic structural…

Object-Oriented Query Language For Events Detection From Images Sequences

NASA Astrophysics Data System (ADS)

Ganea, Ion Eugen

2015-09-01

In this paper is presented a method to represent the events extracted from images sequences and the query language used for events detection. Using an object oriented model the spatial and temporal relationships between salient objects and also between events are stored and queried. This works aims to unify the storing and querying phases for video events processing. The object oriented language syntax used for events processing allow the instantiation of the indexes classes in order to improve the accuracy of the query results. The experiments were performed on images sequences provided from sport domain and it shows the reliability and the robustness of the proposed language. To extend the language will be added a specific syntax for constructing the templates for abnormal events and for detection of the incidents as the final goal of the research.

Accident Precursor Analysis and Management: Reducing Technological Risk Through Diligence

NASA Technical Reports Server (NTRS)

Phimister, James R. (Editor); Bier, Vicki M. (Editor); Kunreuther, Howard C. (Editor)

2004-01-01

Almost every year there is at least one technological disaster that highlights the challenge of managing technological risk. On February 1, 2003, the space shuttle Columbia and her crew were lost during reentry into the atmosphere. In the summer of 2003, there was a blackout that left millions of people in the northeast United States without electricity. Forensic analyses, congressional hearings, investigations by scientific boards and panels, and journalistic and academic research have yielded a wealth of information about the events that led up to each disaster, and questions have arisen. Why were the events that led to the accident not recognized as harbingers? Why were risk-reducing steps not taken? This line of questioning is based on the assumption that signals before an accident can and should be recognized. To examine the validity of this assumption, the National Academy of Engineering (NAE) undertook the Accident Precursors Project in February 2003. The project was overseen by a committee of experts from the safety and risk-sciences communities. Rather than examining a single accident or incident, the committee decided to investigate how different organizations anticipate and assess the likelihood of accidents from accident precursors. The project culminated in a workshop held in Washington, D.C., in July 2003. This report includes the papers presented at the workshop, as well as findings and recommendations based on the workshop results and committee discussions. The papers describe precursor strategies in aviation, the chemical industry, health care, nuclear power and security operations. In addition to current practices, they also address some areas for future research.

Deformation and seismic precursors to dome-collapse and fountain-collapse nuées ardentes at Merapi Volcano, Java, Indonesia, 1994-1998

USGS Publications Warehouse

Voight, B.; Young, K.D.; Hidayat, D.; ,; Purbawinata, M.A.; Ratdomopurbo, Antonius; ,; ,; Sayudi, D.S.; LaHusen, R.; Marso, J.; Murray, T.L.; Dejean, M.; Iguchi, M.; Ishihara, K.

2000-01-01

Following the eruption of January 1992, episodes of lava dome growth accompanied by generation of dome-collapse nuées ardentes occurred in 1994–1998. In addition, nuées ardentes were generated by fountain-collapse in January 1997, and the 1998 events also suggest an explosive component. Significant tilt and seismic precursors on varying time scales preceded these events. Deformation about the summit has been detected by electronic tiltmeters since November 1992, with inflation corresponding generally to lava dome growth, and deflation (or decreased inflation) corresponding to loss of dome mass. Strong short-term (days to weeks) accelerations in tilt rate and seismicity occurred prior to the major nuées ardentes episodes, apart from those of 22 November 1994 which were preceded by steadily increasing tilt for over 200 days but lacked short-term precursors. Because of the combination of populated hazardous areas and the lack of an issued warning, about 100 casualties occurred in 1994. In contrast, the strong precursors in 1997 and 1998 provided advance warning to observatory scientists, enabled the stepped raising of alert levels, and aided hazard management. As a result of these factors, but also the fortunate fact that the large nuées ardentes did not quite descend into populated areas, no casualties occurred. The nuée ardente episode of 1994 is interpreted as purely due to gravitational collapse, whereas those of 1997 and 1998 were influenced by gas-pressurization of the lava dome.

Representation of ocean-atmosphere processes associated with extended monsoon episodes over South Asia in CFSv2

NASA Astrophysics Data System (ADS)

Mohan, T. S.; Annamalai, H.; Marx, Larry; Huang, Bohua; Kinter, James

2018-02-01

In the present study, we analyze 30-years output from free run solutions of CFSv2 coupled model to assess the model’s representation of extended (>7 days) active and break monsoon episodes over south Asia. Process based diagnostics is applied to the individual and composite events to identify precursor signals in both ocean and atmospheric variables. Our examination suggests that CFSv2, like most coupled models, depict systematic biases in variables important for ocean-atmosphere interactions. Nevertheless, model solutions capture many aspects of monsoon extended break and active episodes realistically, encouraging us to apply process-based diagnostics. Diagnostics reveal that sea surface temperature (SST) variations over the northern Bay of Bengal where the climatological mixed-layer is thin, lead the in-situ precipitation anomalies by about 8 (10) days during extended active (break) episodes, and the precipitation anomalies over central India by 10-14 days. Mixed-layer heat budget analysis indicates for a close correspondence between SST tendency and net surface heat flux (Q_net). MSE budgets indicate that horizontal moisture advection to be a coherent precursor signal ( 10 days) during both extended break (dry advection) and active (moist advection) events. The lead timings in these precursor signals in CFSv2 solutions will be of potential use to monitor and predict extended monsoon episodes. Diagnostics, however, also indicate that for about 1/3 of the identified extended break and active episodes, inconsistencies in budget terms suggest precursor signals could lead to false alarms. Apart from false alarms, compared to observations, CFSv2 systematically simulates a greater number of extended monsoon active episodes.

[Clonal association of flat epithelial atypia and tubular breast cancer].

PubMed

Aulmann, S; Elsawaf, Z; Penzel, R; Schirmacher, P; Sinn, H P

2008-11-01

Flat epithelial atypia (FEA) of the breast has recently gained attention as a possible precursor lesion of highly differentiated breast cancer. Especially tubular carcinomas, with which FEA shares cytological features, often occur in close proximity to each other. To examine a possible clonal relationship, we analysed mutations of the highly variable region of the mitochondrial genome in a series of tubular carcinomas, associated FEA and normal glands. Multiple sequence alignment showed identical mtDNA mutations in approximately 50% of paired FEA and tumour samples, indicative of a clonal relationship. Our data indicate a possible precursor role of FEA in the development of tubular breast cancer.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rorsman, F.; Bywater, M.; Knott, T.J.

The human platelet-derived growth factor (PDGF) A-chain locus was characterized by restriction endonuclease analysis, and the nucleotide sequence of its exons was determined. Seven exons were identified, spanning approximately 22 kilobase pairs of genomic DNA. Alternative exon usage, identified by cDNA cloning, occurs in a human glioblastoma cell line and may give rise to two types of A-chain precursors with different C termini. The exon-intron arrangement was similar to that of the PDGF B-chain/sis locus and seemed to divide the precursor proteins into functional domains. Southern blot analysis of genomic DNA showed that a single PDGF A-chain gene was presentmore » in the human genome.« less

Apollo Mission Techniques Lunar Orbit Activities - Part 1a

NASA Technical Reports Server (NTRS)

Interbartolo, Michael A.

2009-01-01

This slide presentation reviews the planned sequence of events and the rationale for all lunar missions, and the flight experiences and lessons learned for the lunar orbit activities from a trajectory perspective. Shown are trajectories which include the moon's position at the various stages in the complete trip from launch, to the return and reentry. Included in the presentation are objectives and the sequence of events,for the Apollo 8, and Apollo 10. This is followed by a discussion of Apollo 11, including: the primary mission objective, the sequence of events, and the flight experience. The next mission discussed was Apollo 12. It reviews the objectives, the ground tracking, procedure changes, and the sequence of events. The aborted Apollo 13 mission is reviewed, including the objectives, and the sequence of events. Brief summaries of the flight experiences for Apollo 14-16 are reviewed. The flight sequence of events of Apollo 17 are discussed. In summary each mission consistently performing precision landings required that Apollo lunar orbit activities devote considerable attention to: (1) Improving fidelity of lunar gravity models, (2) Maximizing availability of ground tracking, (3) Minimizing perturbations on the trajectory, (4) Maximizing LM propellant reserves for hover time. Also the use of radial separation maneuvers (1) allows passive re-rendezvous after each rev, but ... (2) sensitive to small dispersions in initial sep direction

Increased Foxo3a Nuclear Translocation and Activity is an Early Neuronal Response to βγ-Secretase-Mediated Processing of the Amyloid-β Protein Precursor: Utility of an AβPP-GAL4 Reporter Assay.

PubMed

Law, Bernard M; Guest, Amy L; Pullen, Matthew W J; Perkinton, Michael S; Williams, Robert J

2018-01-01

Sequential cleavage of the amyloid-β protein precursor (AβPP) by BACE1 (β-secretase) followed by theγ-secretase complex, is strongly implicated in Alzheimer's disease (AD) but the initial cellular responses to these cleavage events are not fully defined. β-secretase-mediated AβPP processing yields an extracellular domain (sAβPPβ) and a C-terminal fragment of AβPP of 99 amino acids (C99). Subsequent cleavage by γ-secretase produces amyloid-β (Aβ) and an AβPP intracellular domain (AICD). A cellular screen based on the generation of AICD from an AβPP-Gal4 fusion protein was adapted by introducing familial AD (FAD) mutations into the AβPP sequence and linking the assay to Gal4-UAS driven luciferase and GFP expression, to identify responses immediately downstream of AβPP processing in neurons with a focus on the transcription factor Foxo3a which has been implicated in neurodegeneration. The K670N/M671L, E682K, E693G, and V717I FAD mutations and the A673T protective mutation, were introduced into the AβPP sequence by site directed mutagenesis. When expressed in mouse cortical neurons, AβPP-Gal4-UAS driven luciferase and GFP expression was substantially reduced by γ-secretase inhibitors, lowered by β-secretase inhibitors, and enhanced by α-secretase inhibitors suggesting that AICD is a product of the βγ-secretase pathway. AβPP-Gal4-UAS driven GFP expression was exploited to identify individual neurons undergoing amyloidogenic AβPP processing, revealing increased nuclear localization of Foxo3a and enhanced Foxo3a-mediated transcription downstream of AICD production. Foxo3a translocation was not driven by AICD directly but correlated with reduced Akt phosphorylation. Collectively this suggests that βγ-secretase-mediated AβPP processing couples to Foxo3a which could be an early neuronal signaling response in AD.

Implicit Learning of Predictive Relationships in Three-element Visual Sequences by Young and Old Adults

PubMed Central

Howard, James H.; Howard, Darlene V.; Dennis, Nancy A.; Kelly, Andrew J.

2008-01-01

Knowledge of sequential relationships enables future events to be anticipated and processed efficiently. Research with the serial reaction time task (SRTT) has shown that sequence learning often occurs implicitly without effort or awareness. Here we report four experiments that use a triplet-learning task (TLT) to investigate sequence learning in young and older adults. In the TLT people respond only to the last target event in a series of discrete, three-event sequences or triplets. Target predictability is manipulated by varying the triplet frequency (joint probability) and/or the statistical relationships (conditional probabilities) among events within the triplets. Results revealed that both groups learned, though older adults showed less learning of both joint and conditional probabilities. Young people used the statistical information in both cues, but older adults relied primarily on information in the second cue alone. We conclude that the TLT complements and extends the SRTT and other tasks by offering flexibility in the kinds of sequential statistical regularities that may be studied as well as by controlling event timing and eliminating motor response sequencing. PMID:18763897

Computational sequence analysis of predicted long dsRNA transcriptomes of major crops reveals sequence complementarity with human genes.

PubMed

Jensen, Peter D; Zhang, Yuanji; Wiggins, B Elizabeth; Petrick, Jay S; Zhu, Jin; Kerstetter, Randall A; Heck, Gregory R; Ivashuta, Sergey I

2013-01-01

Long double-stranded RNAs (long dsRNAs) are precursors for the effector molecules of sequence-specific RNA-based gene silencing in eukaryotes. Plant cells can contain numerous endogenous long dsRNAs. This study demonstrates that such endogenous long dsRNAs in plants have sequence complementarity to human genes. Many of these complementary long dsRNAs have perfect sequence complementarity of at least 21 nucleotides to human genes; enough complementarity to potentially trigger gene silencing in targeted human cells if delivered in functional form. However, the number and diversity of long dsRNA molecules in plant tissue from crops such as lettuce, tomato, corn, soy and rice with complementarity to human genes that have a long history of safe consumption supports a conclusion that long dsRNAs do not present a significant dietary risk.

Import of honeybee prepromelittin into the endoplasmic reticulum: structural basis for independence of SRP and docking protein.

PubMed Central

Müller, G; Zimmermann, R

1987-01-01

Honeybee prepromelittin is correctly processed and imported by dog pancreas microsomes. Insertion of prepromelittin into microsomal membranes, as assayed by signal sequence removal, does not depend on signal recognition particle (SRP) and docking protein. We addressed the question as to how prepromelittin bypasses the SRP/docking protein system. Hybrid proteins between prepromelittin, or carboxy-terminally truncated derivatives, and the cytoplasmic protein dihydrofolate reductase from mouse were constructed. These hybrid proteins were analysed for membrane insertion and sequestration into microsomes. The results suggest the following: (i) The signal sequence of prepromelittin is capable of interacting with the SRP/docking protein system, but this interaction is not mandatory for membrane insertion; this is related to the small size of prepromelittin. (ii) In prepromelittin a cluster of negatively charged amino acids must be balanced by a cluster of positively charged amino acids in order to allow membrane insertion. (iii) In general, a signal sequence can be sufficient to mediate membrane insertion independently of SRP and docking protein in the case of short precursor proteins; however, the presence and distribution of charged amino acids within the mature part of these precursors can play distinct roles. Images Fig. 3. Fig. 4. Fig. 5. Fig. 6. Fig. 7. Fig. 8. Fig. 9. PMID:2820722

a Simple Symmetric Algorithm Using a Likeness with Introns Behavior in RNA Sequences

NASA Astrophysics Data System (ADS)

Regoli, Massimo

2009-02-01

The RNA-Crypto System (shortly RCS) is a symmetric key algorithm to cipher data. The idea for this new algorithm starts from the observation of nature. In particular from the observation of RNA behavior and some of its properties. The RNA sequences has some sections called Introns. Introns, derived from the term "intragenic regions", are non-coding sections of precursor mRNA (pre-mRNA) or other RNAs, that are removed (spliced out of the RNA) before the mature RNA is formed. Once the introns have been spliced out of a pre-mRNA, the resulting mRNA sequence is ready to be translated into a protein. The corresponding parts of a gene are known as introns as well. The nature and the role of Introns in the pre-mRNA is not clear and it is under ponderous researches by Biologists but, in our case, we will use the presence of Introns in the RNA-Crypto System output as a strong method to add chaotic non coding information and an unnecessary behaviour in the access to the secret key to code the messages. In the RNA-Crypto System algoritnm the introns are sections of the ciphered message with non-coding information as well as in the precursor mRNA.

Vitellogenesis in Bufo arenarum: Identification, characterization and immunolocalization of high molecular mass lipovitellin during oogenesis

PubMed Central

O’Brien, Emma D.; Salicioni, Ana M.; Cabada, Marcelo O.; Arranz, Silvia E.

2009-01-01

Vitellogenin (Vtg), a large lipoglycophosphoprotein, is the most important precursor of the yolk proteins, and the major source of nutrients for the developing embryo in oviparous species. After its uptake by the oocytes, Vtg is converted into lipovitellins (high and light) and phosvitin, which are deposited into crystalline yolk platelets. We describe here the presence of two high molecular mass lipovitellins isoforms in Bufo arenarum mature oocytes with masses of 113 and 100 kDa, respectively. The amino acid sequence analysis of p113 and p100 peptides showed a high sequence homology between both polypeptides and the complete reported sequences of Xenopus laevis vitellogenin. Using specific antibodies, we determined that the Vtg uptake begins early during oogenesis, at the previtellogenic stage, and continues until oocytes have reached their mature status. In addition, we found that large endocytic vesicles mediate Vtg uptake in stage I oocytes, and that the size of the endocytic vesicles declines with oogenesis progression. In terms of the Vtg protein trafficking, we detected the Vtg precursor (190 kDa) in the liver of estradiol-injected females. Finally, we propose a subclassification of B. arenarum stage-II oocytes into three physiologically and morphologically distinct periods (early, mid and late). PMID:19932187

Vitellogenesis in Bufo arenarum: identification, characterization and immunolocalization of high molecular mass lipovitellin during oogenesis.

PubMed

O'Brien, Emma D; Salicioni, Ana M; Cabada, Marcelo O; Arranz, Silvia E

2010-03-01

Vitellogenin (Vtg), a large lipoglycophosphoprotein, is the most important precursor of the yolk proteins, and the major source of nutrients for the developing embryo in oviparous species. After its uptake by the oocytes, Vtg is converted into lipovitellins (high and light) and phosvitin, which are deposited into crystalline yolk platelets. We describe here the presence of two high molecular mass lipovitellin isoforms in Bufo arenarum mature oocytes with masses of 113 and 100 kDa, respectively. The amino acid sequence analysis of p113 and p100 peptides showed a high sequence homology between both polypeptides and the complete reported sequences of Xenopus laevis vitellogenin. Using specific antibodies, we determined that the Vtg uptake begins early during oogenesis, at the previtellogenic stage, and continues until oocytes have reached their mature status. In addition, we found that large endocytic vesicles mediate Vtg uptake in stage I oocytes, and that the size of the endocytic vesicles declines with oogenesis progression. In terms of the Vtg protein trafficking, we detected the Vtg precursor (190 kDa) in the liver of estradiol-injected females. Finally, we propose a subclassification of B. arenarum stage II oocytes into three physiologically and morphologically distinct periods (early, mid and late). 2009 Elsevier Inc. All rights reserved.

Expression, Identification and Purification of Dictyostelium Acetoacetyl-CoA Thiolase Expressed in Escherichia coli

PubMed Central

Tanaka, Takeshi; Shima, Yasuyuki; Ogawa, Naoki; Nagayama, Koki; Yoshida, Takashi; Ohmachi, Tetsuo

2011-01-01

Acetoacetyl-CoA thiolase (AT) is an enzyme that catalyses the CoA-dependent thiolytic cleavage of acetoacetyl-CoA to yield 2 molecules of acetyl-CoA, or the reverse condensation reaction. A full-length cDNA clone pBSGT-3, which has homology to known thiolases, was isolated from Dictyostelium cDNA library. Expression of the protein encoded in pBSGT-3 in Escherichia coli, its thiolase enzyme activity, and the amino acid sequence homology search revealed that pBSGT-3 encodes an AT. The recombinant AT (r-thiolase) was expressed in an active form in an E. coli expression system, and purified to homogeneity by selective ammonium sulfate fractionation and two steps of column chromatography. The purified enzyme exhibited a specific activity of 4.70 mU/mg protein. Its N-terminal sequence was (NH2)-Arg-Met-Tyr-Thr-Thr-Ala-Lys-Asn-Leu-Glu-, which corresponds to the sequence from positions 15 to 24 of the amino acid sequence deduced from pBSGT-3 clone. The r-thiolase in the inclusion body expressed highly in E. coli was the precursor form, which is slightly larger than the purified r-thiolase. When incubated with the cell-free extract of Dictyostelium cells, the precursor was converted to the same size to the purified r-thiolase, suggesting that the presequence at the N-terminus is removed by a Dictyostelium processing peptidase. PMID:21209787

Molecular characterization of cDNA encoding oxygen evolving enhancer protein 1 increased by salt treatment in the mangrove Bruguiera gymnorrhiza.

PubMed

Sugihara, K; Hanagata, N; Dubinsky, Z; Baba, S; Karube, I

2000-11-01

Young plants of the common Okinawa mangrove species Bruguiera gymnorrhiza were transferred from freshwater to a medium with seawater salt level (500 mM NaCl). Two-dimensional gel electrophoresis revealed in the leaf extract of the plant a 33 kDa protein with pI 5.2, whose quantity increased as a result of NaCl treatment. The N-terminal amino acids sequence of this protein had a significant homology with mature region of oxygen evolving enhancer protein 1 (OEE1) precursor. The cloning of OEE1 precursor cDNA fragment was carried out by means of reverse transcription-PCR (RT-PCR) using degenerated primers. Both 3'- and 5'-regions were isolated by rapid amplification of cDNA ends (RACE) method. The deduced amino acid sequence consisted of 322 amino acids and was 87% identical to that of Nicotiana tabacum. In B. gymnorrhiza, the predicted amino acid sequence of the mature protein starts at the residue number 85 of the open reading frame. The first 84-amino acid residues correspond to a typical transit sequence for the signal directing OEE1 to its appropriate compartment of chloroplast. The expression of OEE1 was analyzed together with other OEE subunits and D1 protein of photosystem II. The transcript levels of all the three OEEs were enhanced by NaCl treatment, but the significant increase of D1 protein was not observed.

Membrane fractions active in poliovirus RNA replication contain VPg precursor polypeptides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Takegami, T.; Semler, B.L.; Anderson, C.W.

1983-01-01

The poliovirus specific polypeptide P3-9 is of special interest for studies of viral RNA replication because it contains a hydrophobic region and, separated by only seven amino acids from that region, the amino acid sequence of the genome-linked protein VPg. Membraneous complexes of poliovirus-infected HeLa cells that contain poliovirus RNA replicating proteins have been analyzed for the presence of P3-9 by immunoprecipitation. Incubation of a membrane fraction rich in P3-9 with proteinase leaves the C-terminal 69 amino acids of P3-9 intact, an observation suggesting that this portion is protected by its association with the cellular membrane. These studies have alsomore » revealed two hitherto undescribed viral polypeptides consisting of amino acid sequences of the P2 andf P3 regions of the polyprotein. Sequence analysis by stepwise Edman degradation show that these proteins are 3b/9 (M/sub r/77,000) and X/9 (M/sub r/50,000). 3b/9 and X/9 are membrane bound and are turned over rapidly and may be direct precursors to proteins P2-X and P3-9 of the RNA replication complex. P2-X, a polypeptide void of hydrophobic amino acid sequences but also found associated with membranes, is rapidly degraded when the membraneous complex is treated with trypsin. It is speculated that P2-X is associated with membranes by its affinity to the N-terminus of P3-9.« less

SVM-Based Prediction of Propeptide Cleavage Sites in Spider Toxins Identifies Toxin Innovation in an Australian Tarantula

PubMed Central

Wong, Emily S. W.; Hardy, Margaret C.; Wood, David; Bailey, Timothy; King, Glenn F.

2013-01-01

Spider neurotoxins are commonly used as pharmacological tools and are a popular source of novel compounds with therapeutic and agrochemical potential. Since venom peptides are inherently toxic, the host spider must employ strategies to avoid adverse effects prior to venom use. It is partly for this reason that most spider toxins encode a protective proregion that upon enzymatic cleavage is excised from the mature peptide. In order to identify the mature toxin sequence directly from toxin transcripts, without resorting to protein sequencing, the propeptide cleavage site in the toxin precursor must be predicted bioinformatically. We evaluated different machine learning strategies (support vector machines, hidden Markov model and decision tree) and developed an algorithm (SpiderP) for prediction of propeptide cleavage sites in spider toxins. Our strategy uses a support vector machine (SVM) framework that combines both local and global sequence information. Our method is superior or comparable to current tools for prediction of propeptide sequences in spider toxins. Evaluation of the SVM method on an independent test set of known toxin sequences yielded 96% sensitivity and 100% specificity. Furthermore, we sequenced five novel peptides (not used to train the final predictor) from the venom of the Australian tarantula Selenotypus plumipes to test the accuracy of the predictor and found 80% sensitivity and 99.6% 8-mer specificity. Finally, we used the predictor together with homology information to predict and characterize seven groups of novel toxins from the deeply sequenced venom gland transcriptome of S. plumipes, which revealed structural complexity and innovations in the evolution of the toxins. The precursor prediction tool (SpiderP) is freely available on ArachnoServer (http://www.arachnoserver.org/spiderP.html), a web portal to a comprehensive relational database of spider toxins. All training data, test data, and scripts used are available from the SpiderP website. PMID:23894279

Temporal and Rate Coding for Discrete Event Sequences in the Hippocampus.

PubMed

Terada, Satoshi; Sakurai, Yoshio; Nakahara, Hiroyuki; Fujisawa, Shigeyoshi

2017-06-21

Although the hippocampus is critical to episodic memory, neuronal representations supporting this role, especially relating to nonspatial information, remain elusive. Here, we investigated rate and temporal coding of hippocampal CA1 neurons in rats performing a cue-combination task that requires the integration of sequentially provided sound and odor cues. The majority of CA1 neurons displayed sensory cue-, combination-, or choice-specific (simply, "event"-specific) elevated discharge activities, which were sustained throughout the event period. These event cells underwent transient theta phase precession at event onset, followed by sustained phase locking to the early theta phases. As a result of this unique single neuron behavior, the theta sequences of CA1 cell assemblies of the event sequences had discrete representations. These results help to update the conceptual framework for space encoding toward a more general model of episodic event representations in the hippocampus. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolution of a tissue-specific splicing network

PubMed Central

Taliaferro, J. Matthew; Alvarez, Nehemiah; Green, Richard E.; Blanchette, Marco; Rio, Donald C.

2011-01-01

Alternative splicing of precursor mRNA (pre-mRNA) is a strategy employed by most eukaryotes to increase transcript and proteomic diversity. Many metazoan splicing factors are members of multigene families, with each member having different functions. How these highly related proteins evolve unique properties has been unclear. Here we characterize the evolution and function of a new Drosophila splicing factor, termed LS2 (Large Subunit 2), that arose from a gene duplication event of dU2AF50, the large subunit of the highly conserved heterodimeric general splicing factor U2AF (U2-associated factor). The quickly evolving LS2 gene has diverged from the splicing-promoting, ubiquitously expressed dU2AF50 such that it binds a markedly different RNA sequence, acts as a splicing repressor, and is preferentially expressed in testes. Target transcripts of LS2 are also enriched for performing testes-related functions. We therefore propose a path for the evolution of a new splicing factor in Drosophila that regulates specific pre-mRNAs and contributes to transcript diversity in a tissue-specific manner. PMID:21406555

Altered growth pattern, not altered growth per se, is the hallmark of early lesions preceding cancer development.

PubMed

Doratiotto, S; Marongiu, F; Faedda, S; Pani, P; Laconi, E

2009-01-01

Many human solid cancers arise from focal proliferative lesions that long precede the overt clinical appearance of the disease. The available evidence supports the notion that cancer precursor lesions are clonal in origin, and this notion forms the basis for most of the current theories on the pathogenesis of neoplastic disease. In contrast, far less attention has been devoted to the analysis of the phenotypic property that serves to define these focal lesions, i.e. their altered growth pattern. In fact, the latter is often considered a mere morphological by-product of clonal growth, with no specific relevance in the process. In the following study, evidence will be presented to support the concept that focal growth pattern is an inherent property of altered cells, independent of clonal growth; furthermore, it will be discussed how such a property, far from being merely descriptive, might indeed play a fundamental role in the sequence of events leading to the development of cancer. Within this paradigm, the earliest steps of neoplasia should be considered and analysed as defects in the mechanisms of tissue pattern formation.

The tale of a modern animal plague: Tracing the evolutionary history and determining the time-scale for foot and mouth disease virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tully, Damien C.; Fares, Mario A.

2008-12-20

Despite significant advances made in the understanding of its epidemiology, foot and mouth disease virus (FMDV) is among the most unexpected agricultural devastating plagues. While the disease manifests itself as seven immunologically distinct strains their origin, population dynamics, migration patterns and divergence times remain unknown. Herein we have assembled a comprehensive data set of gene sequences representing the global diversity of the disease and inferred the time-scale and evolutionary history for FMDV. Serotype-specific rates of evolution and divergence times were estimated using a Bayesian coalescent framework. We report that an ancient precursor FMDV gave rise to two major diversification eventsmore » spanning a relatively short interval of time. This radiation event is estimated to have taken place towards the end of the 17th and the beginning of the 18th century giving us the present circulating Euro-Asiatic and South African viral strains. Furthermore our results hint that Europe acted as a possible hub for the disease from where it successfully dispersed elsewhere via exploration and trading routes.« less

How Incidental Sequence Learning Creates Reportable Knowledge: The Role of Unexpected Events

ERIC Educational Resources Information Center

Runger, Dennis; Frensch, Peter A.

2008-01-01

Research on incidental sequence learning typically is concerned with the characteristics of implicit or nonconscious learning. In this article, the authors aim to elucidate the cognitive mechanisms that contribute to the generation of explicit, reportable sequence knowledge. According to the unexpected-event hypothesis (P. A. Frensch, H. Haider,…

Visual Prediction in Infancy: What Is the Association with Later Vocabulary?

ERIC Educational Resources Information Center

Ellis, Erica M.; Gonzalez, Marybel Robledo; Deák, Gedeon O.

2014-01-01

Young infants can learn statistical regularities and patterns in sequences of events. Studies have demonstrated a relationship between early sequence learning skills and later development of cognitive and language skills. We investigated the relation between infants' visual response speed to novel event sequences, and their later receptive and…

Contribution to the assessment of the imminent seismic hazard: Geophysical, statistical (and more) challenges in the territory of Greece

NASA Astrophysics Data System (ADS)

Adamaki, Angeliki K.; Papadimitriou, Eleftheria E.; Karakostas, Vassilis G.; Tsaklidis, George M.

2013-04-01

The necessity of the imminent seismic hazard assessment stems from a strong social component which is the outcome of the need of people to inquire more in order to understand nature exhaustively and not partially, either to satisfy their inner curiosity or in favor of their self preservation instinct against the physical phenomena that the human kind cannot control. Choosing this path to follow, many seismologists have focused on forecasting the temporal and spatial distribution of earthquakes in short time scales. The possibility of knowing with a degree of certainty the way an earthquake sequence evolves proves to be an important object of research. Being more specific, the present work summarizes applications of seismicity and statistical models on seismic catalogues of areas that are specified by their tectonic structures and their past seismicity, providing information on the temporal and spatial evolution of local seismic activity, which can point out seismicity rate "irregularities" or changes as precursors of strong events, either in case of a main shock or a strong aftershock. In order to study these rate changes both preceding and following a strong earthquake, seismicity models are applied in order to estimate the Coulomb stress changes resulting from the occurrence of a strong earthquake and their results are combined with the application of a Restricted Epidemic Type Aftershock Sequence model. There are many active tectonic structures in the territory of Greece that are related with the occurrence of strong earthquakes, especially near populated areas, and the aim of this work is to contribute to the assessment of the imminent seismic hazard by applying the aforementioned models and techniques and studying the temporal evolution of several seismic sequences that occurred in the Aegean area in the near past.

Genetic diversity of STLV-2 and interspecies transmission of STLV-3 in wild-living bonobos.

PubMed

Ahuka-Mundeke, Steve; Lunguya-Metila, Octavie; Mbenzo-Abokome, Valentin; Butel, Christelle; Inogwabini, Bila-Isia; Omasombo, Valentin; Muyembe-Tamfum, Jean-Jacques; Georgiev, Alexander V; Muller, Martin N; Ndjango, Jean-Bosco N; Li, Yingying; Delaporte, Eric; Hahn, Beatrice H; Peeters, Martine; Ayouba, Ahidjo

2016-01-01

There are currently four known primate T-cell lymphotropic virus groups (PTLV1-4), each of which comprises closely related simian (STLV) and human (HTLV) viruses. For PTLV-1 and PTLV-3, simian and human viruses are interspersed, suggesting multiple cross-species transmission events; however, for PTLV-2 this is not so clear because HTLV-2 and STLV-2 strains from captive bonobos ( Pan paniscus ) form two distinct clades. To determine to what extent bonobos are naturally infected with STLV, we screened fecal samples (n = 633) from wild-living bonobos (n = 312) at six different sites in the Democratic Republic of Congo (DRC) for the presence of STLV nucleic acids. STLV infection was detected in 8 of 312 bonobos at four of six field sites, suggesting an overall prevalence of 2.6% (ranging from 0 to 8%). Six samples contained STLV-2, while the two others contained STLV-3, as determined by phylogenetic analysis of partial tax and Long Terminal Repeats (LTR) sequences. The new STLV-2 sequences were highly diverse, but grouped with previously identified STLV-2 strains as a sister clade to HTLV-2. In contrast, the new STLV-3 sequences did not cluster together, but were more closely related to STLVs from sympatric monkey species. These results show for the first time that fecal samples can be used to detect STLV infection in apes. These results also show that wild-living bonobos are endemically infected with STLV-2, but have acquired STLV-3 on at least two occasions most likely by cross-species transmission from monkey species on which they prey. Future studies of bonobos and other non-human primate species in Central Africa are needed to identify the simian precursor of HTLV-2 in humans.

Genetic diversity of STLV-2 and interspecies transmission of STLV-3 in wild-living bonobos

PubMed Central

Ahuka-Mundeke, Steve; Lunguya-Metila, Octavie; Mbenzo-Abokome, Valentin; Butel, Christelle; Inogwabini, Bila-Isia; Omasombo, Valentin; Muyembe-Tamfum, Jean-Jacques; Georgiev, Alexander V.; Muller, Martin N.; Ndjango, Jean-Bosco N.; Li, Yingying; Delaporte, Eric; Hahn, Beatrice H.; Peeters, Martine; Ayouba, Ahidjo

2016-01-01

There are currently four known primate T-cell lymphotropic virus groups (PTLV1-4), each of which comprises closely related simian (STLV) and human (HTLV) viruses. For PTLV-1 and PTLV-3, simian and human viruses are interspersed, suggesting multiple cross-species transmission events; however, for PTLV-2 this is not so clear because HTLV-2 and STLV-2 strains from captive bonobos (Pan paniscus) form two distinct clades. To determine to what extent bonobos are naturally infected with STLV, we screened fecal samples (n = 633) from wild-living bonobos (n = 312) at six different sites in the Democratic Republic of Congo (DRC) for the presence of STLV nucleic acids. STLV infection was detected in 8 of 312 bonobos at four of six field sites, suggesting an overall prevalence of 2.6% (ranging from 0 to 8%). Six samples contained STLV-2, while the two others contained STLV-3, as determined by phylogenetic analysis of partial tax and Long Terminal Repeats (LTR) sequences. The new STLV-2 sequences were highly diverse, but grouped with previously identified STLV-2 strains as a sister clade to HTLV-2. In contrast, the new STLV-3 sequences did not cluster together, but were more closely related to STLVs from sympatric monkey species. These results show for the first time that fecal samples can be used to detect STLV infection in apes. These results also show that wild-living bonobos are endemically infected with STLV-2, but have acquired STLV-3 on at least two occasions most likely by cross-species transmission from monkey species on which they prey. Future studies of bonobos and other non-human primate species in Central Africa are needed to identify the simian precursor of HTLV-2 in humans. PMID:27774304

Molecular characteristics of insect vitellogenins and vitellogenin receptors.

PubMed

Sappington, T W; Raikhel, A S

1998-01-01

The recent cloning and sequencing of several insect vitellogenins (Vg), the major yolk protein precursor of most oviparous animals, and the mosquito Vg receptor (VgR) has brought the study of insect vitellogenesis to a new plane. Insect Vgs are homologous to nematode and vertebrate Vgs. All but one of the insect Vgs for which we know the primary structure are cleaved into two subunits at a site [(R/K)X(R/K)R or RXXR with an adjacent beta-turn] recognized by subtilisin-like proprotein convertases. In four of the Vgs, the cleavage site is near the N-terminus, but in one insect species, it is near the C-terminus of the Vg precursor. Multiple alignments of these Vg sequences indicate that the variation in cleavage location has not arisen through exon shuffling, but through local modifications of the amino acid sequences. A wasp Vg precursor is not cleaved, apparently because the sequence at the presumed ancestral cleavage site has been mutated from RXRR to LYRR and is no longer recognized by convertases. Some insect Vgs contain polyserine domains which are reminiscent of, but not homologous to, the phosvitin domain in vertebrate Vgs. The sequence of the mosquito VgR revealed that it is a member of the low-density lipoprotein receptor (LDLR) family. Though resembling chicken and frog VgRs, which are also members of the LDLR family, it is twice as big, carrying two clusters of cysteine-rich complement-type (Class A) repeats (implicated in ligand-binding) instead of one like vertebrate VgRs and LDLRs. It is very similar in sequence and domain arrangement to the Drosophila yolk protein receptor (YPR), despite a non-vitellogenin ligand for the latter. Though vertebrate VgRs, insect VgR/YPRs, and LDLR-related proteins/megalins all accommodate one cluster of eight Class A repeats, fingerprint analysis of the repeats in these clusters indicate they are not directly homologous with one another, but have undergone differing histories of duplications, deletions, and exon shuffling so that their apparent similarity is superficial. The so-called epidermal growth factor precursor region contains two types of motifs (cysteine-rich Class B repeats and YWXD repeats) which occur independently of one another in diverse proteins, and are often involved in protein-protein interactions, suggesting that they potentially are involved in dimerization of VgRs and other LDLR-family proteins. Like the LDLR, but unlike vertebrate VgRs and the Drosophila YPR, the mosquito VgR contains a putative O-linked sugar region on the extra-cellular side of the transmembrane domain. Its function is unclear, but may protect the receptor from membrane-bound proteases. The cytoplasmic tail of insect VgR/YPRs contains a di-leucine (or leucine-isoleucine) internalization signal, unlike the tight-turn tyrosine motif of other LDLR-family proteins. The importance of understanding the details of yolk protein uptake by oocytes lies in its potential for exploitation in novel insect control strategies, and the molecular characterization of the proteins involved has made the development of such strategies a realistic possibility.

The spatial alignment of time: Differences in alignment of deictic and sequence time along the sagittal and lateral axes.

PubMed

Walker, Esther J; Bergen, Benjamin K; Núñez, Rafael

2017-04-01

People use space in a variety of ways to structure their thoughts about time. The present report focuses on the different ways that space is employed when reasoning about deictic (past/future relationships) and sequence (earlier/later relationships) time. In the first study, we show that deictic and sequence time are aligned along the lateral axis in a manner consistent with previous work, with past and earlier events associated with left space and future and later events associated with right space. However, the alignment of time with space is different along the sagittal axis. Participants associated future events and earlier events-not later events-with the space in front of their body and past and later events with the space behind, consistent with the sagittal spatial terms (e.g., ahead, in front of) that we use to talk about deictic and sequence time. In the second study, we show that these associations between sequence time and sagittal space are sensitive to person-perspective. This suggests that the particular space-time associations observed in English speakers are influenced by a variety of different spatial properties, including spatial location and perspective. Copyright © 2016. Published by Elsevier B.V.

Sequence Effects in Conjugated Donor-Acceptor Trimers and Polymers.

PubMed

Zhang, Shaopeng; Hutchison, Geoffrey R; Meyer, Tara Y

2016-06-01

To investigate the sequence effect on donor-acceptor conjugated oligomers and polymers, the trimeric isomers PBP and BPP, comprising dialkoxy phenylene vinylene (P), benzothiadiazole vinylene (B), and alkyl endgroups with terminal olefins, are synthesized. Sequence effects are evident in the optical/electrochemical properties and thermal properties. Absorption maxima for PBP and BPP differ by 41 nm and the electrochemical band gaps by 0.1 V. The molar emission intensity is five times greater in PBP than BPP. Both trimers are crystalline and the melting points differ by 17 °C. The PBP and BPP trimers are used as macromonomers in an acyclic diene metathesis polymerization to give PolyPBP and PolyBPP. The optical and electrochemical properties are similar to those of their trimer precursors-sequence effects are still evident. These results suggest that sequence is a tunable variable for electronic materials and that the polymerization of oligomeric sequences is a useful approach to introducing sequence into polymers. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Hierarchical Convolutional Neural Network for vesicle fusion event classification.

PubMed

Li, Haohan; Mao, Yunxiang; Yin, Zhaozheng; Xu, Yingke

2017-09-01

Quantitative analysis of vesicle exocytosis and classification of different modes of vesicle fusion from the fluorescence microscopy are of primary importance for biomedical researches. In this paper, we propose a novel Hierarchical Convolutional Neural Network (HCNN) method to automatically identify vesicle fusion events in time-lapse Total Internal Reflection Fluorescence Microscopy (TIRFM) image sequences. Firstly, a detection and tracking method is developed to extract image patch sequences containing potential fusion events. Then, a Gaussian Mixture Model (GMM) is applied on each image patch of the patch sequence with outliers rejected for robust Gaussian fitting. By utilizing the high-level time-series intensity change features introduced by GMM and the visual appearance features embedded in some key moments of the fusion process, the proposed HCNN architecture is able to classify each candidate patch sequence into three classes: full fusion event, partial fusion event and non-fusion event. Finally, we validate the performance of our method on 9 challenging datasets that have been annotated by cell biologists, and our method achieves better performances when comparing with three previous methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

MS/MS-Assisted Design of Sequence-Controlled Synthetic Polymers for Improved Reading of Encoded Information

NASA Astrophysics Data System (ADS)

Charles, Laurence; Cavallo, Gianni; Monnier, Valérie; Oswald, Laurence; Szweda, Roza; Lutz, Jean-François

2017-06-01

In order to improve their MS/MS sequencing, structure of sequence-controlled synthetic polymers can be optimized based on considerations regarding their fragmentation behavior in collision-induced dissociation conditions, as demonstrated here for two digitally encoded polymer families. In poly(triazole amide)s, the main dissociation route proceeded via cleavage of the amide bond in each monomer, hence allowing the chains to be safely sequenced. However, a competitive cleavage of an ether bond in a tri(ethylene glycol) spacer placed between each coding moiety complicated MS/MS spectra while not bringing new structural information. Changing the tri(ethylene glycol) spacer to an alkyl group of the same size allowed this unwanted fragmentation pathway to be avoided, hence greatly simplifying the MS/MS reading step for such undecyl-based poly(triazole amide)s. In poly(alkoxyamine phosphodiester)s, a single dissociation pathway was achieved with repeating units containing an alkoxyamine linkage, which, by very low dissociation energy, made any other chemical bonds MS/MS-silent. Structure of these polymers was further tailored to enhance the stability of those precursor ions with a negatively charged phosphate group per monomer in order to improve their MS/MS readability. Increasing the size of both the alkyl coding moiety and the nitroxide spacer allowed sufficient distance between phosphate groups for all of them to be deprotonated simultaneously. Because the charge state of product ions increased with their polymerization degree, MS/MS spectra typically exhibited groups of fragments at one or the other side of the precursor ion depending on the original α or ω end-group they contain, allowing sequence reconstruction in a straightforward manner. [Figure not available: see fulltext.

Discovery of precursor and mature microRNAs and their putative gene targets using high-throughput sequencing in pineapple (Ananas comosus var. comosus).

PubMed

Yusuf, Noor Hydayaty Md; Ong, Wen Dee; Redwan, Raimi Mohamed; Latip, Mariam Abd; Kumar, S Vijay

2015-10-15

MicroRNAs (miRNAs) are a class of small, endogenous non-coding RNAs that negatively regulate gene expression, resulting in the silencing of target mRNA transcripts through mRNA cleavage or translational inhibition. MiRNAs play significant roles in various biological and physiological processes in plants. However, the miRNA-mediated gene regulatory network in pineapple, the model tropical non-climacteric fruit, remains largely unexplored. Here, we report a complete list of pineapple mature miRNAs obtained from high-throughput small RNA sequencing and precursor miRNAs (pre-miRNAs) obtained from ESTs. Two small RNA libraries were constructed from pineapple fruits and leaves, respectively, using Illumina's Solexa technology. Sequence similarity analysis using miRBase revealed 579,179 reads homologous to 153 miRNAs from 41 miRNA families. In addition, a pineapple fruit transcriptome library consisting of approximately 30,000 EST contigs constructed using Solexa sequencing was used for the discovery of pre-miRNAs. In all, four pre-miRNAs were identified (MIR156, MIR399, MIR444 and MIR2673). Furthermore, the same pineapple transcriptome was used to dissect the function of the miRNAs in pineapple by predicting their putative targets in conjunction with their regulatory networks. In total, 23 metabolic pathways were found to be regulated by miRNAs in pineapple. The use of high-throughput sequencing in pineapples to unveil the presence of miRNAs and their regulatory pathways provides insight into the repertoire of miRNA regulation used exclusively in this non-climacteric model plant. Copyright © 2015 Elsevier B.V. All rights reserved.

Chronodes: Interactive Multifocus Exploration of Event Sequences

PubMed Central

POLACK, PETER J.; CHEN, SHANG-TSE; KAHNG, MINSUK; DE BARBARO, KAYA; BASOLE, RAHUL; SHARMIN, MOUSHUMI; CHAU, DUEN HORNG

2018-01-01

The advent of mobile health (mHealth) technologies challenges the capabilities of current visualizations, interactive tools, and algorithms. We present Chronodes, an interactive system that unifies data mining and human-centric visualization techniques to support explorative analysis of longitudinal mHealth data. Chronodes extracts and visualizes frequent event sequences that reveal chronological patterns across multiple participant timelines of mHealth data. It then combines novel interaction and visualization techniques to enable multifocus event sequence analysis, which allows health researchers to interactively define, explore, and compare groups of participant behaviors using event sequence combinations. Through summarizing insights gained from a pilot study with 20 behavioral and biomedical health experts, we discuss Chronodes’s efficacy and potential impact in the mHealth domain. Ultimately, we outline important open challenges in mHealth, and offer recommendations and design guidelines for future research. PMID:29515937

RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.

PubMed

Garcia-Martin, Juan Antonio; Bayegan, Amir H; Dotu, Ivan; Clote, Peter

2016-10-19

RNA inverse folding is the problem of finding one or more sequences that fold into a user-specified target structure s 0 , i.e. whose minimum free energy secondary structure is identical to the target s 0 . Here we consider the ensemble of all RNA sequences that have low free energy with respect to a given target s 0 . We introduce the program RNAdualPF, which computes the dual partition function Z ∗ , defined as the sum of Boltzmann factors exp(-E(a,s 0 )/RT) of all RNA nucleotide sequences a compatible with target structure s 0 . Using RNAdualPF, we efficiently sample RNA sequences that approximately fold into s 0 , where additionally the user can specify IUPAC sequence constraints at certain positions, and whether to include dangles (energy terms for stacked, single-stranded nucleotides). Moreover, since we also compute the dual partition function Z ∗ (k) over all sequences having GC-content k, the user can require that all sampled sequences have a precise, specified GC-content. Using Z ∗ , we compute the dual expected energy 〈E ∗ 〉, and use it to show that natural RNAs from the Rfam 12.0 database have higher minimum free energy than expected, thus suggesting that functional RNAs are under evolutionary pressure to be only marginally thermodynamically stable. We show that C. elegans precursor microRNA (pre-miRNA) is significantly non-robust with respect to mutations, by comparing the robustness of each wild type pre-miRNA sequence with 2000 [resp. 500] sequences of the same GC-content generated by RNAdualPF, which approximately [resp. exactly] fold into the wild type target structure. We confirm and strengthen earlier findings that precursor microRNAs and bacterial small noncoding RNAs display plasticity, a measure of structural diversity. We describe RNAdualPF, which rapidly computes the dual partition function Z ∗ and samples sequences having low energy with respect to a target structure, allowing sequence constraints and specified GC-content. Using different inverse folding software, another group had earlier shown that pre-miRNA is mutationally robust, even controlling for compositional bias. Our opposite conclusion suggests a cautionary note that computationally based insights into molecular evolution may heavily depend on the software used. C/C++-software for RNAdualPF is available at http://bioinformatics.bc.edu/clotelab/RNAdualPF .

Genesis of the NASA Space Radiation Laboratory.

PubMed

Schimmerling, Walter

2016-06-01

A personal recollection of events leading up to the construction and commissioning of NSRL, including reference to precursor facilities and the development of the NASA Space Radiation Program. Copyright © 2016 The Committee on Space Research (COSPAR). Published by Elsevier Ltd. All rights reserved.

Tic40, a membrane-anchored co-chaperone homolog in the chloroplast protein translocon

PubMed Central

Chou, Ming-Lun; Fitzpatrick, Lynda M.; Tu, Shuh-Long; Budziszewski, Gregory; Potter-Lewis, Sharon; Akita, Mitsuru; Levin, Joshua Z.; Keegstra, Kenneth; Li, Hsou-min

2003-01-01

The function of Tic40 during chloroplast protein import was investigated. Tic40 is an inner envelope membrane protein with a large hydrophilic domain located in the stroma. Arabidopsis null mutants of the atTic40 gene were very pale green and grew slowly but were not seedling lethal. Isolated mutant chloroplasts imported precursor proteins at a lower rate than wild-type chloroplasts. Mutant chloroplasts were normal in allowing binding of precursor proteins. However, during subsequent translocation across the inner membrane, fewer precursors were translocated and more precursors were released from the mutant chloroplasts. Cross-linking experiments demonstrated that Tic40 was part of the translocon complex and functioned at the same stage of import as Tic110 and Hsp93, a member of the Hsp100 family of molecular chaperones. Tertiary structure prediction and immunological studies indicated that the C-terminal portion of Tic40 contains a TPR domain followed by a domain with sequence similarity to co-chaperones Sti1p/Hop and Hip. We propose that Tic40 functions as a co-chaperone in the stromal chaperone complex that facilitates protein translocation across the inner membrane. PMID:12805212

Reduction of precursor decay anomaly in single crystal lithium fluoride

NASA Astrophysics Data System (ADS)

Sano, Yukio

2000-08-01

The purpose of this study is to reveal that the precursor decay anomaly in single crystal lithium fluoride is reduced by Sano's decay curve [Y. Sano, J. Appl. Phys. 85, 7616 (1999)], which is much smaller in slope than Asay's decay curve [J. R. Asay, G. R. Fowles, G. E. Duvall, M. H. Miles, and R. F. Tinder, J. Appl. Phys. 43, 2132 (1972)]. To this end, strain, particle, velocity, and stress in a precursor and near the leading edge of the follower changing with time along Sano's decay curve are first analyzed quantitatively. The analysis verified the existence of degenerate contraction waves I and II and a subrarefaction wave R', and the decay process [Y. Sano, J. Appl. Phys. 77, 3746 (1995)] caused in sequence by evolving followers C, I, II, R', Rb. Next, inequalities relating decay rates qualitatively to plastic strain rates at the leading edge of the follower, which are derived using the properties of the followers, are incorporated into the analysis. Calculation results showed that the plastic strain rates were reduced by low decay rates. This indicates that the precursor decay anomaly might be greatly reduced by Sano's decay curve.

A murine model of autosomal dominant neurohypophyseal diabetes insipidus reveals progressive loss of vasopressin-producing neurons

PubMed Central

Russell, Theron A.; Ito, Masafumi; Ito, Mika; Yu, Richard N.; Martinson, Fred A.; Weiss, Jeffrey; Jameson, J. Larry

2003-01-01

Familial neurohypophyseal diabetes insipidus (FNDI) is an autosomal dominant disorder caused by mutations in the arginine vasopressin (AVP) precursor. The pathogenesis of FNDI is proposed to involve mutant protein–induced loss of AVP-producing neurons. We established murine knock-in models of two different naturally occurring human mutations that cause FNDI. A mutation in the AVP signal sequence [A(–1)T] is associated with a relatively mild phenotype or delayed presentation in humans. This mutation caused no apparent phenotype in mice. In contrast, heterozygous mice expressing a mutation that truncates the AVP precursor (C67X) exhibited polyuria and polydipsia by 2 months of age and these features of DI progressively worsened with age. Studies of the paraventricular and supraoptic nuclei revealed induction of the chaperone protein BiP and progressive loss of AVP-producing neurons relative to oxytocin-producing neurons. In addition, Avp gene products were not detected in the neuronal projections, suggesting retention of WT and mutant AVP precursors within the cell bodies. In summary, this murine model of FNDI recapitulates many features of the human disorder and demonstrates that expression of the mutant AVP precursor leads to progressive neuronal cell loss. PMID:14660745

Electrochemical genoassays on gold-coated magnetic nanoparticles to quantify genetically modified organisms (GMOs) in food and feed as GMO percentage.

PubMed

Plácido, Alexandra; Pereira, Clara; Guedes, Alexandra; Barroso, M Fátima; Miranda-Castro, Rebeca; de-Los-Santos-Álvarez, Noemí; Delerue-Matos, Cristina

2018-07-01

The integration of nanomaterials in the field of (bio)sensors has allowed developing strategies with improved analytical performance. In this work, ultrasmall core-shell Fe 3 O 4 @Au magnetic nanoparticles (MNPs) were used as the platform for the immobilization of event-specific Roundup Ready (RR) soybean and taxon-specific DNA sequences. Firstly, monodisperse Fe 3 O 4 MNPs were synthesized by thermal decomposition and subsequently coated with a gold shell through reduction of Au(III) precursor on the surface of the MNPs in the presence of an organic capping agent. This nanosupport exhibited high colloidal stability, average particle size of 10.2 ± 1.3 nm, and spherical shape. The covalent immobilization of ssDNA probe onto the Au shell of the Fe 3 O 4 @Au MNPs was achieved through a self-assembled monolayer (SAM) created from mixtures of alkane thiols (6-mercapto-1-hexanol and mercaptohexanoic acid). The influence of the thiols ratio on the electrochemical performance of the resulting electrochemical genoassays was studied, and remarkably, the best analytical performance was achieved for a pure mercaptohexanoic acid SAM. Two quantification assays were designed; one targeting an RR sequence and a second targeting a reference soybean gene, both with a sandwich format for hybridization, signaling probes labelled with fluorescein isothiocyanate (FITC), enzymatic amplification and chronoamperometric detection at screen-printed carbon electrodes (SPCE). The magnetogenoassays exhibited linear ranges from 0.1 to 10.0 nM and from 0.1 to 5.0 nM with similar detection limits of 0.02 nM and 0.05 nM for the event-specific (RR) and the taxon-specific (lectin) targets, respectively. The usefulness of the approach was demonstrated by its application to detect genetically modified organisms (GMOs) in feed and food. Copyright © 2018 Elsevier B.V. All rights reserved.

Temporal and Spatial Predictability of an Irrelevant Event Differently Affect Detection and Memory of Items in a Visual Sequence

PubMed Central

Ohyama, Junji; Watanabe, Katsumi

2016-01-01

We examined how the temporal and spatial predictability of a task-irrelevant visual event affects the detection and memory of a visual item embedded in a continuously changing sequence. Participants observed 11 sequentially presented letters, during which a task-irrelevant visual event was either present or absent. Predictabilities of spatial location and temporal position of the event were controlled in 2 × 2 conditions. In the spatially predictable conditions, the event occurred at the same location within the stimulus sequence or at another location, while, in the spatially unpredictable conditions, it occurred at random locations. In the temporally predictable conditions, the event timing was fixed relative to the order of the letters, while in the temporally unpredictable condition; it could not be predicted from the letter order. Participants performed a working memory task and a target detection reaction time (RT) task. Memory accuracy was higher for a letter simultaneously presented at the same location as the event in the temporally unpredictable conditions, irrespective of the spatial predictability of the event. On the other hand, the detection RTs were only faster for a letter simultaneously presented at the same location as the event when the event was both temporally and spatially predictable. Thus, to facilitate ongoing detection processes, an event must be predictable both in space and time, while memory processes are enhanced by temporally unpredictable (i.e., surprising) events. Evidently, temporal predictability has differential effects on detection and memory of a visual item embedded in a sequence of images. PMID:26869966

Temporal and Spatial Predictability of an Irrelevant Event Differently Affect Detection and Memory of Items in a Visual Sequence.

PubMed

Ohyama, Junji; Watanabe, Katsumi

2016-01-01

We examined how the temporal and spatial predictability of a task-irrelevant visual event affects the detection and memory of a visual item embedded in a continuously changing sequence. Participants observed 11 sequentially presented letters, during which a task-irrelevant visual event was either present or absent. Predictabilities of spatial location and temporal position of the event were controlled in 2 × 2 conditions. In the spatially predictable conditions, the event occurred at the same location within the stimulus sequence or at another location, while, in the spatially unpredictable conditions, it occurred at random locations. In the temporally predictable conditions, the event timing was fixed relative to the order of the letters, while in the temporally unpredictable condition; it could not be predicted from the letter order. Participants performed a working memory task and a target detection reaction time (RT) task. Memory accuracy was higher for a letter simultaneously presented at the same location as the event in the temporally unpredictable conditions, irrespective of the spatial predictability of the event. On the other hand, the detection RTs were only faster for a letter simultaneously presented at the same location as the event when the event was both temporally and spatially predictable. Thus, to facilitate ongoing detection processes, an event must be predictable both in space and time, while memory processes are enhanced by temporally unpredictable (i.e., surprising) events. Evidently, temporal predictability has differential effects on detection and memory of a visual item embedded in a sequence of images.

Event Boundaries Trigger Rapid Memory Reinstatement of the Prior Events to Promote Their Representation in Long-Term Memory.

PubMed

Sols, Ignasi; DuBrow, Sarah; Davachi, Lila; Fuentemilla, Lluís

2017-11-20

Although everyday experiences unfold continuously over time, shifts in context, or event boundaries, can influence how those events come to be represented in memory [1-4]. Specifically, mnemonic binding across sequential representations is more challenging at context shifts, such that successful temporal associations are more likely to be formed within than across contexts [1, 2, 5-9]. However, in order to preserve a subjective sense of continuity, it is important that the memory system bridge temporally adjacent events, even if they occur in seemingly distinct contexts. Here, we used pattern similarity analysis to scalp electroencephalographic (EEG) recordings during a sequential learning task [2, 3] in humans and showed that the detection of event boundaries triggered a rapid memory reinstatement of the just-encoded sequence episode. Memory reactivation was detected rapidly (∼200-800 ms from the onset of the event boundary) and was specific to context shifts that were preceded by an event sequence with episodic content. Memory reinstatement was not observed during the sequential encoding of events within an episode, indicating that memory reactivation was induced specifically upon context shifts. Finally, the degree of neural similarity between neural responses elicited during sequence encoding and at event boundaries correlated positively with participants' ability to later link across sequences of events, suggesting a critical role in binding temporally adjacent events in long-term memory. Current results shed light onto the neural mechanisms that promote episodic encoding not only for information within the event, but also, importantly, in the ability to link across events to create a memory representation of continuous experience. Copyright © 2017 Elsevier Ltd. All rights reserved.

Design and application of a data-independent precursor and product ion repository.

PubMed

Thalassinos, Konstantinos; Vissers, Johannes P C; Tenzer, Stefan; Levin, Yishai; Thompson, J Will; Daniel, David; Mann, Darrin; DeLong, Mark R; Moseley, M Arthur; America, Antoine H; Ottens, Andrew K; Cavey, Greg S; Efstathiou, Georgios; Scrivens, James H; Langridge, James I; Geromanos, Scott J

2012-10-01

The functional design and application of a data-independent LC-MS precursor and product ion repository for protein identification, quantification, and validation is conceptually described. The ion repository was constructed from the sequence search results of a broad range of discovery experiments investigating various tissue types of two closely related mammalian species. The relative high degree of similarity in protein complement, ion detection, and peptide and protein identification allows for the analysis of normalized precursor and product ion intensity values, as well as standardized retention times, creating a multidimensional/orthogonal queryable, qualitative, and quantitative space. Peptide ion map selection for identification and quantification is primarily based on replication and limited variation. The information is stored in a relational database and is used to create peptide- and protein-specific fragment ion maps that can be queried in a targeted fashion against the raw or time aligned ion detections. These queries can be conducted either individually or as groups, where the latter affords pathway and molecular machinery analysis of the protein complement. The presented results also suggest that peptide ionization and fragmentation efficiencies are highly conserved between experiments and practically independent of the analyzed biological sample when using similar instrumentation. Moreover, the data illustrate only minor variation in ionization efficiency with amino acid sequence substitutions occurring between species. Finally, the data and the presented results illustrate how LC-MS performance metrics can be extracted and utilized to ensure optimal performance of the employed analytical workflows.

Transcriptional Analysis of the vanC Cluster from Enterococcus gallinarum Strains with Constitutive and Inducible Vancomycin Resistance

PubMed Central

Panesso, Diana; Abadía-Patiño, Lorena; Vanegas, Natasha; Reynolds, Peter E.; Courvalin, Patrice; Arias, Cesar A.

2005-01-01

The vanC glycopeptide resistance gene cluster encodes enzymes required for synthesis of peptidoglycan precursors ending in d-Ala-d-Ser. Enterococcus gallinarum BM4174 and SC1 are constitutively and inducibly resistant to vancomycin, respectively. Analysis of peptidoglycan precursors in both strains indicated that UDP-MurNAc-tetrapeptide and UDP-MurNAc-pentapeptide[d-Ser] were synthesized in E. gallinarum SC1 only in the presence of vancomycin (4 μg/ml), whereas the “resistance” precursors accumulated in the cytoplasm of BM4174 cells under both inducing and noninducing conditions. Northern hybridization and reverse transcription-PCR experiments revealed that all the genes from the cluster, vanC-1, vanXYC, vanT, vanRC, and vanSC, were transcribed from a single promoter. In the inducible SC1 isolate, transcriptional regulation appeared to be responsible for inducible expression of resistance. Promoter mapping in E. gallinarum BM4174 revealed that the transcriptional start site was located 30 nucleotides upstream from vanC-1 and that the −10 promoter consensus sequence had high identity with that of the vanA cluster. Comparison of the deduced sequence of the vanSC genes from isolates with constitutive and inducible resistance revealed several amino acid substitutions located in the X box (R200L) and in the region between the F and G2 boxes (D312N, D312A, and G320S) of the putative sensor kinase proteins from isolates with constitutive resistance. PMID:15728903

Re-Os Isotopic Characteristics of the Earth's Oldest Preserved Oceanic Crustal Fragments (Isua Supracrustals Belt, W Greenland); A Vastly Disturbed System.

NASA Astrophysics Data System (ADS)

Frei, R.; Frei, R.; Jensen, B. K.

2001-12-01

Variably preserved pillow lavas from the Isua Supracrustals Belt (ISB; Western Greenland) exhibit strongly supra-chondritic Re/Os (range from 2 to 45) and highly radiogenic 187Os/188Os isotopic compositions (range from 0.3 to 20.5). Re-Os model ages are geologically meaningless and reflect the disturbances invoked by post-formational metamorphic overprinting and by metasomatic events that were associated with the intrusion of various generations of the precursors of tonalitic gneisses into the ISB. Most prominently, a late Archean (c. 2.8 Ga) tectono-metamorphic event has locally reset the Re-Os clock in high strain domains of the ISB. Disturbance of the Re-Os system was initially caused by Re addition in connection with metasomatic fluid flow during the early Archean (3.65 to 3.81 Ga) emplacement of central dome gneiss precursors and tonalite sheets into the supracrustals sequences. The effects of open system behaviour of the Re-Os system are similarly recorded by the U-Pb and Sm-Nd systems of these meta-basalts, principally revealing the influx of U, Th, Re; LREE and alkaline-rich fluids from the gneisses into the oceanic crustal sequences preserved at Isua (Blichert-Toft and Frei, 2001; Frei et al., in press; Frei and Rosing, in press). Ultramafic lenses with komatiitic chemical affinities within the ISB are equally affected by early addition of Re, but the very much higher Os concentrations (more than an order of magnitude higher than those of the meta-basalts with values ranging from 30 to 150 ppt) did efficiently mask the disturbances in the Os isotope compositions, so that reasonable Re depletion ages (TRD) can still be deduced. The least altered of these ultramafic lenses revealed a TRD) of 3725 Ma and a mantle extraction (TMA) age of 3807 Ma, dates which are compatible with independent U-Pb zircon ages from intrusive tonaltic gneisses (Nutman et al., 1997) and Pb-Pb age constraints from metasomatic minerals of strongly altered meta-basalts (Frei and Rosing, in press). They can be regarded as minimum ages of deposition of the supracrustals. The complexity of post-formational overprinting however makes it difficult to investigate and explore the Earth's mantle geochemical evolution before this time. Blichert-Toft, J. and Frei, R. (2001) Geochim. Cosmochim. Acta, 65, 3177-3187. Frei, R., Rosing, M.T., Waight, T.E., and Ulfbeck, D.G. (in press) Geochim. Cosmochim. Acta Frei,R. and Rosing, M.T. (in press) Chem. Geol. Nutman, A.P., Bennett, V.C., Friend, C.R.L., and Rosing, M.T. (1997) Chem. Geol., 141, 271-287.

Electrostatic precursors to granular slip events

PubMed Central

Shinbrot, Troy; Kim, Nam H.; Thyagu, N. Nirmal

2012-01-01

It has been known for over a century that electrical signals are produced by material failure, for example during crack formation of crystals and glasses, or stick-slip motion of liquid mercury on glass. We describe here new experiments revealing that slip events in cohesive powders also produce electrical signals, and remarkably these signals can appear significantly in advance of slip events. We have confirmed this effect in two different experimental systems and using two common powdered materials, and in a third experiment we have demonstrated that similar voltage signals are produced by crack-like defects in several powdered materials. PMID:22689956

Local Deformation Precursors of Large Earthquakes Derived from GNSS Observation Data

NASA Astrophysics Data System (ADS)

Kaftan, Vladimir; Melnikov, Andrey

2017-12-01

Research on deformation precursors of earthquakes was of immediate interest from the middle to the end of the previous century. The repeated conventional geodetic measurements, such as precise levelling and linear-angular networks, were used for the study. Many examples of studies referenced to strong seismic events using conventional geodetic techniques are presented in [T. Rikitake, 1976]. One of the first case studies of geodetic earthquake precursors was done by Yu.A. Meshcheryakov [1968]. Rare repetitions, insufficient densities and locations of control geodetic networks made difficult predicting future places and times of earthquakes occurrences. Intensive development of Global Navigation Satellite Systems (GNSS) during the recent decades makes research more effective. The results of GNSS observations in areas of three large earthquakes (Napa M6.1, USA, 2014; El Mayor Cucapah M7.2, USA, 2010; and Parkfield M6.0, USA, 2004) are treated and presented in the paper. The characteristics of land surface deformation before, during, and after earthquakes have been obtained. The results prove the presence of anomalous deformations near their epicentres. The temporal character of dilatation and shear strain changes show existence of spatial heterogeneity of deformation of the Earth’s surface from months to years before the main shock close to it and at some distance from it. The revealed heterogeneities can be considered as deformation precursors of strong earthquakes. According to historical data and proper research values of critical deformations which are offered to be used for seismic danger scale creation based on continuous GNSS observations are received in a reference to the mentioned large earthquakes. It is shown that the approach has restrictions owing to uncertainty of the moment in the beginning of deformation accumulation and the place of expectation of another seismic event. Verification and clarification of the derived conclusions are proposed.

Identification of the "minimal triangle" and other common event-to-event transitions in conflict and containment incidents.

PubMed

Bowers, Len; James, Karen; Quirk, Alan; Wright, Steve; Williams, Hilary; Stewart, Duncan

2013-07-01

Although individual conflict and containment events among acute psychiatric inpatients have been studied in some detail, the relationship of these events to each other has not. In particular, little is known about the temporal order of events for individual patients. This study aimed to identify the most common pathways from event to event. A sample of 522 patients was recruited from 84 acute psychiatric wards in 31 hospital locations in London and the surrounding areas during 2009-2010. Data on the order of conflict and containment events were collected for the first two weeks of admission from patients' case notes. Event-to-event transitions were tabulated and depicted diagrammatically. Event types were tested for their most common temporal placing in sequences of events. Most conflict and containment occurs within and between events of the minimal triangle (verbal aggression, de-escalation, and PRN medication), and the majority of these event sequences conclude in no further events; a minority transition to other, more severe, events. Verbal abuse and medication refusal were more likely to start sequences of disturbed behaviour. Training in the prevention and management of violence needs to acknowledge that a gradual escalation of patient behaviour does not always occur. Verbal aggression is a critical initiator of conflict events, and requires more detailed and sustained research on optimal management and prevention strategies. Similar research is required into medication refusal by inpatients.

High-precision relocation for aftershocks of the 2016 ML 5.8 Gyeongju earthquake in South Korea: Stress partitioning controlled by complex fault systems

NASA Astrophysics Data System (ADS)

Woo, J. U.; Rhie, J.; Kang, T. S.; Kim, S.; Chai, G.; Cho, E.

2017-12-01

Complex inherent fault system is one of key factors controlling the main shock occurrence and the pattern of aftershock sequence. Many field studies have shown that the fault systems in the Korean Peninsula are complex because they formed by various tectonic events since Proterozoic. Apart from that the mainshock is the largest one (ML 5.8) ever recorded in South Korea, the Gyeongju earthquake sequence shows particularly interesting features: ML 5.1 event preceded ML 5.8 event by 50 min and they are located closely to each other ( 1 km). In addition, ML 4.5 event occurred 2 3 km away from the two events after a week of the mainshock. Considering reported focal mechanisms and hypocenters of the three major events, it is unlikely that the earthquake sequence occurs on a single fault plane. To depict the detailed fault geometry associated with the sequence, we precisely determine the relative locations of 1,400 aftershocks recorded by 27 broadband stations, which started to be deployed less than one hour after the mainshock. Double difference algorithm is applied using relative travel time measurements by a waveform cross-correlation method. Relocated hypocenters show that a major fault striking NE-SW and some minor faults get involved in the sequence. In particular, aftershocks immediately following ML 4.5 event seem to occur on a fault striking NW-SE, which is orthogonal to the strike of a major fault. We expect that the Gyeongju earthquake sequence resulted from the stress transfer controlled by the complex inherent fault system in this region.

Tropinone reductases, enzymes at the branch point of tropane alkaloid metabolism.

PubMed

Dräger, Birgit

2006-02-01

Two stereospecific oxidoreductases constitute a branch point in tropane alkaloid metabolism. Products of tropane metabolism are the alkaloids hyoscyamine, scopolamine, cocaine, and polyhydroxylated nortropane alkaloids, the calystegines. Both tropinone reductases reduce the precursor tropinone to yield either tropine or pseudotropine. In Solanaceae, tropine is incorporated into hyoscyamine and scopolamine; pseudotropine is the first specific metabolite on the way to the calystegines. Isolation, cloning and heterologous expression of both tropinone reductases enabled kinetic characterisation, protein crystallisation, and structure elucidation. Stereospecificity of reduction is achieved by binding tropinone in the respective enzyme active centre in opposite orientation. Immunolocalisation of both enzyme proteins in cultured roots revealed a tissue-specific protein accumulation. Metabolite flux through both arms of the tropane alkaloid pathway appears to be regulated by the activity of both enzymes and by their access to the precursor tropinone. Both tropinone reductases are NADPH-dependent short-chain dehydrogenases with amino acid sequence similarity of more than 50% suggesting their descent from a common ancestor. Putative tropinone reductase sequences annotated in plant genomes other that Solanaceae await functional characterisation.

KU HAPLOINSUFFIENCY CAUSES A LYMPHOPROLIFERATIVE DISORDER OF IMMATURE T-CELL PRECURSORS DUE TO IKAROS MALFUNCTION

PubMed Central

Ozer, Zahide; Qazi, Sanjive; Ishkhanian, Rita; Hasty, Paul; Ma, Hong; Uckun, Fatih M.

2013-01-01

Ikaros (IK) malfunction has been implicated in the pathogenesis of acute lymphoblastic leukemia (ALL), the most common form of childhood cancer. Therefore, a stringent regulation of IK activity is very important. Here we provide unique genetic and biochemical evidence that the Ku protein components Ku70 and Ku80 act as positive regulators of IK function via formation of IK-Ku70 and IK-Ku80 heterodimers with augmented sequence-specific DNA binding activity. siRNA-mediated depletion of Ku70 or Ku80 reduced the sequence-specific DNA binding activity of IK in EMSA as well as the RT-PCR measured IK target gene expression levels in human cells. The interaction of Ku components with IK likely contributes to the anti-leukemic effects of IK as a tumor suppressor, because Ku70 as well as Ku80 haploinsuffiency in mice caused development of a lymphoproliferative disorder (LPD) involving CD2+CD4+CD8+CD1+IL7R+ thymic T-cell precursors with functional IK deficiency. PMID:24478815

Mutant fatty acid desaturase

DOEpatents

Shanklin, John; Cahoon, Edgar B.

2004-02-03

The present invention relates to a method for producing mutants of a fatty acid desaturase having a substantially increased activity towards fatty acid substrates with chains containing fewer than 18 carbons relative to an unmutagenized precursor desaturase having an 18 carbon atom chain length substrate specificity. The method involves inducing one or more mutations in the nucleic acid sequence encoding the precursor desaturase, transforming the mutated sequence into an unsaturated fatty acid auxotroph cell such as MH13 E. coli, culturing the cells in the absence of supplemental unsaturated fatty acids, thereby selecting for recipient cells which have received and which express a mutant fatty acid desaturase with an elevated specificity for fatty acid substrates having chain lengths of less than 18 carbon atoms. A variety of mutants having 16 or fewer carbon atom chain length substrate specificities are produced by this method. Mutant desaturases produced by this method can be introduced via expression vectors into prokaryotic and eukaryotic cells and can also be used in the production of transgenic plants which may be used to produce specific fatty acid products.

Pharmacological evidences for DFK167-sensitive presenilin-independent gamma-secretase-like activity.

PubMed

Sevalle, Jean; Ayral, Erwan; Hernandez, Jean-François; Martinez, Jean; Checler, Frédéric

2009-07-01

Amyloid-beta (Abeta) peptides production is thought to be a key event in the neurodegenerative process ultimately leading to Alzheimer's disease (AD) pathology. A bulk of studies concur to propose that the C-terminal moiety of Abeta is released from its precursor beta-amyloid precursor protein by a high molecular weight enzymatic complex referred to as gamma-secretase, that is composed of at least, nicastrin (NCT), Aph-1, Pen-2, and presenilins (PS) 1 or 2. They are thought to harbor the gamma-secretase catalytic activity. However, several lines of evidence suggest that additional gamma-secretase-like activities could potentially contribute to Abeta production. By means of a quenched fluorimetric substrate (JMV2660) mimicking the beta-amyloid precursor protein sequence targeted by gamma-secretase, we first show that as expected, this probe allows monitoring of an activity detectable in several cell systems including the neuronal cell line telencephalon specific murine neurons (TSM1). This activity is reduced by DFK167, N-[N-(3,5-difluorophenacetyl)-L-alanyl]-S-phenylglycine t-butyl ester (DAPT), and LY68458, three inhibitors known to functionally interact with PS. Interestingly, JMV2660 but not the unrelated peptide JMV2692, inhibits Abeta production in an in vitrogamma-secretase assay as expected from a putative substrate competitor. This activity is enhanced by PS1 and PS2 mutations known to be responsible for familial forms of AD and reduced by aspartyl mutations inactivating PS or in cells devoid of PS or NCT. However, we clearly establish that residual JMV2660-hydrolysing activity could be recovered in PS- and NCT-deficient fibroblasts and that this activity remained inhibited by DFK167. Overall, our study describes the presence of a proteolytic activity displaying gamma-secretase-like properties but independent of PS and still blocked by DFK167, suggesting that the PS-dependent complex could not be the unique gamma-secretase activity responsible for Abeta production and delineates PS-independent gamma-secretase activity as a potential additional therapeutic target to fight AD pathology.

Learning predictive statistics from temporal sequences: Dynamics and strategies

PubMed Central

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E.; Kourtzi, Zoe

2017-01-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics—that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments. PMID:28973111

Learning predictive statistics from temporal sequences: Dynamics and strategies.

PubMed

Wang, Rui; Shen, Yuan; Tino, Peter; Welchman, Andrew E; Kourtzi, Zoe

2017-10-01

Human behavior is guided by our expectations about the future. Often, we make predictions by monitoring how event sequences unfold, even though such sequences may appear incomprehensible. Event structures in the natural environment typically vary in complexity, from simple repetition to complex probabilistic combinations. How do we learn these structures? Here we investigate the dynamics of structure learning by tracking human responses to temporal sequences that change in structure unbeknownst to the participants. Participants were asked to predict the upcoming item following a probabilistic sequence of symbols. Using a Markov process, we created a family of sequences, from simple frequency statistics (e.g., some symbols are more probable than others) to context-based statistics (e.g., symbol probability is contingent on preceding symbols). We demonstrate the dynamics with which individuals adapt to changes in the environment's statistics-that is, they extract the behaviorally relevant structures to make predictions about upcoming events. Further, we show that this structure learning relates to individual decision strategy; faster learning of complex structures relates to selection of the most probable outcome in a given context (maximizing) rather than matching of the exact sequence statistics. Our findings provide evidence for alternate routes to learning of behaviorally relevant statistics that facilitate our ability to predict future events in variable environments.

Amplitude of foreshocks as a possible seismic precursor to earthquakes

USGS Publications Warehouse

Lindh, A.G.

1978-01-01

In recent years, we have made significant progress in being able to recognize the long-range pattern of events that precede large earthquakes. For example, in a recent issue of the Earthquake Information Bulletin, we saw how the pioneering work of S.A. Fedotov of the U.S.S.R in the Kamchatka-Kurile Islands region has been applied worldwide to forecast where large, shallow earthquakes might occur in the next decades. Indeed, such a "seismic gap" off the coast of Alaska was filled by the 1972 Sitka earthquake. Promising results are slowly accumulating from other techniques that suggest that intermediate-term precursors might also be seen: among these are tilt and geomagnetic anomalies and anomalous land uplift. But the crucial point remains that short-term precursors (days to hours) will be needed in many cases if there is to be a significant saving of lives. 

Lightning NOx and Impacts on Air Quality

NASA Technical Reports Server (NTRS)

Murray, Lee T.

2016-01-01

Lightning generates relatively large but uncertain quantities of nitrogen oxides, critical precursors for ozone and hydroxyl radical (OH), the primary tropospheric oxidants. Lightning nitrogen oxide strongly influences background ozone and OH due to high ozone production efficiencies in the free troposphere, effecting small but non-negligible contributions to surface pollutant concentrations. Lightning globally contributes 3-4 ppbv of simulated annual-mean policy-relevant background (PRB) surface ozone, comprised of local, regional, and hemispheric components, and up to 18 ppbv during individual events. Feedbacks via methane may counter some of these effects on decadal time scales. Lightning contributes approximately 1 percent to annual-mean surface particulate matter, as a direct precursor and by promoting faster oxidation of other precursors. Lightning also ignites wildfires and contributes to nitrogen deposition. Urban pollution influences lightning itself, with implications for regional lightning-nitrogen oxide production and feedbacks on downwind surface pollution. How lightning emissions will change in a warming world remains uncertain.

Transgenerationally inherited piRNAs trigger piRNA biogenesis by changing the chromatin of piRNA clusters and inducing precursor processing

PubMed Central

Le Thomas, Adrien; Stuwe, Evelyn; Li, Sisi; Marinov, Georgi; Rozhkov, Nikolay; Chen, Yung-Chia Ariel; Luo, Yicheng; Sachidanandam, Ravi; Toth, Katalin Fejes; Patel, Dinshaw; Aravin, Alexei A.

2014-01-01

Small noncoding RNAs that associate with Piwi proteins, called piRNAs, serve as guides for repression of diverse transposable elements in germ cells of metazoa. In Drosophila, the genomic regions that give rise to piRNAs, the so-called piRNA clusters, are transcribed to generate long precursor molecules that are processed into mature piRNAs. How genomic regions that give rise to piRNA precursor transcripts are differentiated from the rest of the genome and how these transcripts are specifically channeled into the piRNA biogenesis pathway are not known. We found that transgenerationally inherited piRNAs provide the critical trigger for piRNA production from homologous genomic regions in the next generation by two different mechanisms. First, inherited piRNAs enhance processing of homologous transcripts into mature piRNAs by initiating the ping-pong cycle in the cytoplasm. Second, inherited piRNAs induce installment of the histone 3 Lys9 trimethylation (H3K9me3) mark on genomic piRNA cluster sequences. The heterochromatin protein 1 (HP1) homolog Rhino binds to the H3K9me3 mark through its chromodomain and is enriched over piRNA clusters. Rhino recruits the piRNA biogenesis factor Cutoff to piRNA clusters and is required for efficient transcription of piRNA precursors. We propose that transgenerationally inherited piRNAs act as an epigenetic memory for identification of substrates for piRNA biogenesis on two levels: by inducing a permissive chromatin environment for piRNA precursor synthesis and by enhancing processing of these precursors. PMID:25085419

Distinctive and Complementary MS2 Fragmentation Characteristics for Identification of Sulfated Sialylated N-Glycopeptides by nanoLC-MS/MS Workflow

NASA Astrophysics Data System (ADS)

Kuo, Chu-Wei; Guu, Shih-Yun; Khoo, Kay-Hooi

2018-04-01

High sensitivity identification of sulfated glycans carried on specific sites of glycoproteins is an important requisite for investigation of molecular recognition events involved in diverse biological processes. However, aiming for resolving site-specific glycosylation of sulfated glycopeptides by direct LC-MS2 sequencing is technically most challenging. Other than the usual limiting factors such as lower abundance and ionization efficiency compared to analysis of non-glycosylated peptides, confident identification of sulfated glycopeptides among the more abundant non-sulfated glycopeptides requires additional considerations in the selective enrichment and detection strategies. Metal oxide has been applied to enrich phosphopeptides and sialylated glycopeptides, but its use to capture sulfated glycopeptides has not been investigated. Likewise, various complementary MS2 fragmentation modes have yet to be tested against sialylated and non-sialylated sulfoglycopeptides due to limited appropriate sample availability. In this study, we have investigated the feasibility of sequencing tryptic sulfated N-glycopeptide and its MS2 fragmentation characteristics by first optimizing the enrichment methods to allow efficient LC-MS detection and MS2 analysis by a combination of CID, HCD, ETD, and EThcD on hybrid and tribrid Orbitrap instruments. Characteristic sulfated glyco-oxonium ions and direct loss of sulfite from precursors were detected as evidences of sulfate modification. It is anticipated that the technical advances demonstrated in this study would allow a feasible extension of our sulfoglycomic analysis to sulfoglycoproteomics. [Figure not available: see fulltext.

Geodynamic setting of mesothermal gold deposits: An association with accretionary tectonic regimes

NASA Astrophysics Data System (ADS)

Kerrich, Robert; Wyman, Derek

1990-09-01

Mesothermal gold provinces of Phanerozoic age are characteristically associated with regional structures along which allochthonous terranes have been accreted onto continental margins or arcs. A recurring sequence of transpressive deformation, uplift, late kinematic mineralization, and shoshonitic magmatism is consistent with thermal reequilibration of tectonically thickened crust. Mesothermal gold camps in the Superior province are spatially associated with large-scale structures that have been interpreted as zones of transpressive accretion of individual subprovinces or allochthonous terranes: these boundary structures are characterized by the sequence of significant horizontal shortening, uplift, late-kinematic mineralization, and shoshonitic lamprophyres and therefore may have the same geodynamic significance as Phanerozoic counterparts. In this model, thermal re-equilibration of underplated and subducted oceanic lithosphere and sediments in a transpressive regime, over time scales of 10 to 40 m.y., is a necessary precursor to gold mineralization. Hydrothermal fluids are released along boundary faults and their splays during uplift: the uniform temperature, low salinity and mole% CO2 signify uniform source conditions, whereas the variable O, C, Sr, and Pb isotopic compositions of fluids reflect lithological complexity of the source regions and conduits. Ou the basis of this model it is suggested that mesothermal lode gold deposits are the product of subduction-related crustal underplating and deep, late metamorphism, rather than magmatic or metamorphic events in the supracrustal rocks. Secular variations in the generation of Archean, Proterozoic, and Phanerozoic mesothermal Au provinces reflect the timing of collisional orogenies within terranes of these eras.

Processing of the mother-cell sigma factor, sigma K, may depend on events occurring in the forespore during Bacillus subtilis development.

PubMed Central

Lu, S; Halberg, R; Kroos, L

1990-01-01

During sporulation of the Gram-positive bacterium Bacillus subtilis, transcription of genes encoding spore coat proteins in the mother-cell compartment of the sporangium is controlled by RNA polymerase containing the sigma subunit called sigma K. Based on comparison of the N-terminal amino acid sequence of sigma K with the nucleotide sequence of the gene encoding sigma K (sigK), the primary product of sigK was inferred to be a pro-protein (pro-sigma K) with 20 extra amino acids at the N terminus. Using antibodies generated against pro-sigma K, we have detected pro-sigma K beginning at the third hour of sporulation and sigma K beginning about 1 hr later. Even when pro-sigma K is expressed artificially during growth and throughout sporulation, sigma K appears at the normal time and expression of a sigma K-controlled gene occurs normally. These results suggest that pro-sigma K is an inactive precursor that is proteolytically processed to active sigma K in a developmentally regulated fashion. Mutations that block forespore gene expression block accumulation of sigma K but not accumulation of pro-sigma K, suggesting that pro-sigma K processing is a regulatory device that couples the programs of gene expression in the two compartments of the sporangium. We propose that this regulatory device ensures completion of forespore morphogenesis prior to the synthesis in the mother-cell of spore coat proteins that will encase the forespore. Images PMID:2124700

Processing of an anglerfish somatostatin precursor to a hydroxylysine-containing somatostatin 28.

PubMed Central

Spiess, J; Noe, B D

1985-01-01

A novel 28-residue somatostatin (SS) has been isolated from anglerfish pancreatic islets and characterized by complete Edman degradation, peptide mapping, and amino acid analysis. The primary structure of this anglerfish SS-28 (aSS-28) containing hydroxylysine (Hyl) was established to be H-Ser-Val-Asp-Ser-Thr-Asn-Asn-Leu-Pro-Pro-Arg-Glu-Arg-Lys-Ala-Gly-Cys- Lys-Asn-Phe-Tyr-Trp-Hyl-Gly-Phe-Thr-Ser-Cys-OH. This sequence (with the exception of hydroxylysine-23, which is replaced by lysine) is identical to the sequence of the COOH-terminal 28 residues of prepro-SS II predicted on the basis of cDNA analysis [Hobart, P., Crawford, R., Shen, L., Pictet, R. & Rutter, W. J. (1980) Nature (London) 288, 137-141]. This is the first instance in which hydroxylysine (to date characteristically observed in collagen or collagen-like structures) has been found in a potential regulatory peptide. Chromatographic characterization of peptides, radiolabeled in islet culture, revealed that aSS-28 contained 10-12% of the radioactivity incorporated into the 8000- to 1000-dalton SS-like polypeptides, whereas 88-90% of this radioactivity was detected in anglerfish SS-14. It appears probable that aSS-28 represents the predominant primary cleavage product derived from prepro-SS II by cleavage at the COOH-terminal side of a single arginine. Based on knowledge of the collagen biosynthesis, it is speculated that hydroxylation may take place as an early post-translational event. Images PMID:2857489

Horizontal transfer of a large and highly toxic secondary metabolic gene cluster between fungi.

PubMed

Slot, Jason C; Rokas, Antonis

2011-01-25

Genes involved in intermediary and secondary metabolism in fungi are frequently physically linked or clustered. For example, in Aspergillus nidulans the entire pathway for the production of sterigmatocystin (ST), a highly toxic secondary metabolite and a precursor to the aflatoxins (AF), is located in a ∼54 kb, 23 gene cluster. We discovered that a complete ST gene cluster in Podospora anserina was horizontally transferred from Aspergillus. Phylogenetic analysis shows that most Podospora cluster genes are adjacent to or nested within Aspergillus cluster genes, although the two genera belong to different taxonomic classes. Furthermore, the Podospora cluster is highly conserved in content, sequence, and microsynteny with the Aspergillus ST/AF clusters and its intergenic regions contain 14 putative binding sites for AflR, the transcription factor required for activation of the ST/AF biosynthetic genes. Examination of ∼52,000 Podospora expressed sequence tags identified transcripts for 14 genes in the cluster, with several expressed at multiple life cycle stages. The presence of putative AflR-binding sites and the expression evidence for several cluster genes, coupled with the recent independent discovery of ST production in Podospora [1], suggest that this HGT event probably resulted in a functional cluster. Given the abundance of metabolic gene clusters in fungi, our finding that one of the largest known metabolic gene clusters moved intact between species suggests that such transfers might have significantly contributed to fungal metabolic diversity. PAPERFLICK: Copyright © 2011 Elsevier Ltd. All rights reserved.

A classification of event sequences in the influence network

NASA Astrophysics Data System (ADS)

Walsh, James Lyons; Knuth, Kevin H.

2017-06-01

We build on the classification in [1] of event sequences in the influence network as respecting collinearity or not, so as to determine in future work what phenomena arise in each case. Collinearity enables each observer to uniquely associate each particle event of influencing with one of the observer's own events, even in the case of events of influencing the other observer. We further classify events as to whether they are spacetime events that obey in the fine-grained case the coarse-grained conditions of [2], finding that Newton's First and Second Laws of motion are obeyed at spacetime events. A proof of Newton's Third Law under particular circumstances is also presented.

Using ProMED-Mail and MedWorm blogs for cross-domain pattern analysis in epidemic intelligence.

PubMed

Stewart, Avaré; Denecke, Kerstin

2010-01-01

In this work we motivate the use of medical blog user generated content for gathering facts about disease reporting events to support biosurveillance investigation. Given the characteristics of blogs, the extraction of such events is made more difficult due to noise and data abundance. We address the problem of automatically inferring disease reporting event extraction patterns in this more noisy setting. The sublanguage used in outbreak reports is exploited to align with the sequences of disease reporting sentences in blogs. Based our Cross Domain Pattern Analysis Framework, experimental results show that Phase-Level sequences tend to produce more overlap across the domains than Word-Level sequences. The cross domain alignment process is effective at filtering noisy sequences from blogs and extracting good candidate sequence patterns from an abundance of text.

Investigation of Endogenous Retrovirus Sequences in the Neighborhood of Genes Up-regulated in a Neuroblastoma Model after Treatment with Hypoxia-Mimetic Cobalt Chloride

PubMed Central

Brütting, Christine; Narasimhan, Harini; Hoffmann, Frank; Kornhuber, Malte E.; Staege, Martin S.; Emmer, Alexander

2018-01-01

Human endogenous retroviruses (ERVs) have been found to be associated with different diseases, e.g., multiple sclerosis (MS). Most human ERVs integrated in our genome are not competent to replicate and these sequences are presumably silent. However, transcription of human ERVs can be reactivated, e.g., by hypoxia. Interestingly, MS has been linked to hypoxia since decades. As some patterns of demyelination are similar to white matter ischemia, hypoxic damage is discussed. Therefore, we are interested in the association between hypoxia and ERVs. As a model, we used human SH-SY5Y neuroblastoma cells after treatment with the hypoxia-mimetic cobalt chloride and analyzed differences in the gene expression profiles in comparison to untreated cells. The vicinity of up-regulated genes was scanned for endogenous retrovirus-derived sequences. Five genes were found to be strongly up-regulated in SH-SY5Y cells after treatment with cobalt chloride: clusterin, glutathione peroxidase 3, insulin-like growth factor 2, solute carrier family 7 member 11, and neural precursor cell expressed developmentally down-regulated protein 9. In the vicinity of these genes we identified large (>1,000 bp) open reading frames (ORFs). Most of these ORFs showed only low similarities to proteins from retro-transcribing viruses. However, we found very high similarity between retrovirus envelope sequences and a sequence in the vicinity of neural precursor cell expressed developmentally down-regulated protein 9. This sequence encodes the human endogenous retrovirus group FRD member 1, the encoded protein product is called syncytin 2. Transfection of syncytin 2 into the well-characterized Ewing sarcoma cell line A673 was not able to modulate the low immunostimulatory activity of this cell line. Future research is needed to determine whether the identified genes and the human endogenous retrovirus group FRD member 1 might play a role in the etiology of MS. PMID:29515560

Investigation of Endogenous Retrovirus Sequences in the Neighborhood of Genes Up-regulated in a Neuroblastoma Model after Treatment with Hypoxia-Mimetic Cobalt Chloride.

PubMed

Brütting, Christine; Narasimhan, Harini; Hoffmann, Frank; Kornhuber, Malte E; Staege, Martin S; Emmer, Alexander

2018-01-01

Human endogenous retroviruses (ERVs) have been found to be associated with different diseases, e.g., multiple sclerosis (MS). Most human ERVs integrated in our genome are not competent to replicate and these sequences are presumably silent. However, transcription of human ERVs can be reactivated, e.g., by hypoxia. Interestingly, MS has been linked to hypoxia since decades. As some patterns of demyelination are similar to white matter ischemia, hypoxic damage is discussed. Therefore, we are interested in the association between hypoxia and ERVs. As a model, we used human SH-SY5Y neuroblastoma cells after treatment with the hypoxia-mimetic cobalt chloride and analyzed differences in the gene expression profiles in comparison to untreated cells. The vicinity of up-regulated genes was scanned for endogenous retrovirus-derived sequences. Five genes were found to be strongly up-regulated in SH-SY5Y cells after treatment with cobalt chloride: clusterin, glutathione peroxidase 3, insulin-like growth factor 2, solute carrier family 7 member 11, and neural precursor cell expressed developmentally down-regulated protein 9. In the vicinity of these genes we identified large (>1,000 bp) open reading frames (ORFs). Most of these ORFs showed only low similarities to proteins from retro-transcribing viruses. However, we found very high similarity between retrovirus envelope sequences and a sequence in the vicinity of neural precursor cell expressed developmentally down-regulated protein 9. This sequence encodes the human endogenous retrovirus group FRD member 1, the encoded protein product is called syncytin 2. Transfection of syncytin 2 into the well-characterized Ewing sarcoma cell line A673 was not able to modulate the low immunostimulatory activity of this cell line. Future research is needed to determine whether the identified genes and the human endogenous retrovirus group FRD member 1 might play a role in the etiology of MS.

Host-defense and trefoil factor family peptides in skin secretions of the Mawa clawed frog Xenopus boumbaensis (Pipidae).

PubMed

Conlon, J Michael; Mechkarska, Milena; Kolodziejek, Jolanta; Leprince, Jérôme; Coquet, Laurent; Jouenne, Thierry; Vaudry, Hubert; Nowotny, Norbert; King, Jay D

2015-10-01

Peptidomic analysis of norepinephrine-stimulated skin secretions from the octoploid Mawa clawed frog Xenopus boumbaensis Loumont, 1983 led to the identification and characterization of 15 host-defense peptides belonging to the magainin (two peptides), peptide glycine-leucine-amide (PGLa; three peptides), xenopsin precursor fragment (XPF; three peptides), caerulein precursor fragment (CPF; two peptides), and caerulein precursor fragment-related peptide (CPF-RP; five peptides) families. In addition, caerulein and three peptides with structural similarity to the trefoil factor family (TFF) peptides, xP2 and xP4 from Xenopus laevis were also present in the secretions. Consistent with data from comparisons of the nucleotides sequence of mitochondrial and nuclear genes, the primary structures of the peptides suggest a close phylogenetic relationship between X. boumbaensis and the octoploid frogs Xenopus amieti and Xenopus andrei. As the three species occupy disjunct ranges within Cameroon, it is suggested that they diverged from a common ancestor by allopatric speciation. Copyright © 2015 Elsevier Inc. All rights reserved.

PECAN: Library Free Peptide Detection for Data-Independent Acquisition Tandem Mass Spectrometry Data

PubMed Central

Ting, Ying S.; Egertson, Jarrett D.; Bollinger, James G.; Searle, Brian C.; Payne, Samuel H.; Noble, William Stafford; MacCoss, Michael J.

2017-01-01

In mass spectrometry-based shogun proteomics, data-independent acquisition (DIA) is an emerging technique for unbiased and reproducible measurement of protein mixtures. Without targeting a specific precursor ion, DIA MS/MS spectra are often highly multiplexed, containing product ions from multiple co-fragmenting precursors. Thus, detecting peptides directly from DIA data is challenging; most DIA data analyses require spectral libraries. Here we present a new library-free, peptide-centric tool PECAN that detects peptides directly from DIA data. PECAN reports evidence of detection based on product ion scoring, enabling detection of low abundance analytes with poor precursor ion signal. We benchmarked PECAN with chromatographic peak picking accuracy and peptide detection capability. We further validated PECAN detection with data-dependent acquisition and targeted analyses. Last, we used PECAN to build a library from DIA data and to query sequence variants. Together, these results show that PECAN detects peptides robustly and accurately from DIA data without using a library. PMID:28783153

Amyloid Precursor Protein Translation Is Regulated by a 3’UTR Guanine Quadruplex

PubMed Central

Sharoni, Michal; Olson, Kalee; Sebastian, Neeraj P.; Ansaloni, Sara; Schweitzer-Stenner, Reinhard; Akins, Michael R.; Bevilacqua, Philip C.; Saunders, Aleister J.

2015-01-01

A central event in Alzheimer’s disease is the accumulation of amyloid β (Aβ) peptides generated by the proteolytic cleavage of the amyloid precursor protein (APP). APP overexpression leads to increased Aβ generation and Alzheimer’s disease in humans and altered neuronal migration and increased long term depression in mice. Conversely, reduction of APP expression results in decreased Aβ levels in mice as well as impaired learning and memory and decreased numbers of dendritic spines. Together these findings indicate that therapeutic interventions that aim to restore APP and Aβ levels must do so within an ideal range. To better understand the effects of modulating APP levels, we explored the mechanisms regulating APP expression focusing on post-transcriptional regulation. Such regulation can be mediated by RNA regulatory elements such as guanine quadruplexes (G-quadruplexes), non-canonical structured RNA motifs that affect RNA stability and translation. Via a bioinformatics approach, we identified a candidate G-quadruplex within the APP mRNA in its 3’UTR (untranslated region) at residues 3008–3027 (NM_201414.2). This sequence exhibited characteristics of a parallel G-quadruplex structure as revealed by circular dichroism spectrophotometry. Further, as with other G-quadruplexes, the formation of this structure was dependent on the presence of potassium ions. This G-quadruplex has no apparent role in regulating transcription or mRNA stability as wild type and mutant constructs exhibited equivalent mRNA levels as determined by real time PCR. Instead, we demonstrate that this G-quadruplex negatively regulates APP protein expression using dual luciferase reporter and Western blot analysis. Taken together, our studies reveal post-transcriptional regulation by a 3’UTR G-quadruplex as a novel mechanism regulating APP expression. PMID:26618502

Genetic and mechanistic diversity of piRNA 3' end formation

PubMed Central

Handler, Dominik; Mohn, Fabio; Ameres, Stefan L.; Brennecke, Julius

2016-01-01

Small regulatory RNAs guide Argonaute (Ago) proteins in a sequence-specific manner to their targets and thereby play important roles in eukaryotic gene silencing1. Of the three small RNA classes, microRNAs and siRNAs are processed from double-stranded precursors into defined 21- to 23-mers by Dicer, an endoribonuclease with intrinsic ruler function. piRNAs—the 22-30 nt long guides for PIWI-clade Ago proteins that silence transposons in animal gonads—are generated Dicer-independently from single-stranded precursors2,3. piRNA 5' ends are defined either by Zucchini, a mitochondria-anchored endonuclease4,5, or by piRNA-guided target cleavage6,7. Formation of piRNA 3' ends is poorly understood. Here, we find that two genetically and mechanistically distinct pathways generate piRNA 3' ends in Drosophila. The initiating nucleases are either Zucchini or the PIWI-clade proteins Aubergine (Aub)/Ago3. While Zucchini-mediated cleavages directly define mature piRNA 3' ends8,9, Aub/Ago3-mediated cleavages liberate pre-piRNAs that require extensive resection by the 3'-to-5' exoribonuclease Nibbler/Mut-710–13. The relative activity of these two pathways dictates the extent to which piRNAs are fueled into cytoplasmic or nuclear PIWI-clade proteins and thereby sets the balance between post-transcriptional and transcriptional silencing. Strikingly, loss of both Zucchini and Nibbler reveals a minimal, Argonaute-driven small RNA biogenesis pathway where piRNA 5' and 3' ends are directly produced by closely spaced Aub/Ago3-mediated cleavage events. Our data establish a coherent blueprint for piRNA biogenesis, and set the stage for the mechanistic dissection of the processes that govern piRNA 3' end formation. PMID:27851737

Characterization of a nuclear localization signal in the foot-and-mouth disease virus polymerase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanchez-Aparicio, Maria Teresa; Rosas, Maria Flora; Sobrino, Francisco, E-mail: fsobrino@cbm.uam.es

2013-09-15

We have experimentally tested whether the MRKTKLAPT sequence in FMDV 3D protein (residues 16 to 24) can act as a nuclear localization signal (NLS). Mutants with substitutions in two basic residues within this sequence, K18E and K20E, were generated. A decreased nuclear localization was observed in transiently expressed 3D and its precursor 3CD, suggesting a role of K18 and K20 in nuclear targeting. Fusion of MRKTKLAPT to the green fluorescence protein (GFP) increased the nuclear localization of GFP, which was not observed when GFP was fused to the 3D mutated sequences. These results indicate that the sequence MRKTKLAPT can bemore » functionally considered as a NLS. When introduced in a FMDV full length RNA replacements K18E and K20E led to production of revertant viruses that replaced the acidic residues introduced (E) by K, suggesting that the presence of lysins at positions 18 and 20 of 3D is essential for virus multiplication. - Highlights: • The FMDV 3D polymerase contains a nuclear localization signal. • Replacements K18E and K20E decrease nuclear localization of 3D and its precursor 3CD. • Fusion of the MRKTKLAPT 3D motif to GFP increases the nuclear localization of GFP. • Replacements K18E and K20E abolish the ability of MRKTKLAPT to relocate GFP. • RNAs harboring replacements K18E and K20E lead to recovery of revertant FMDVs.« less

Cloning and sequence analysis of Hemonchus contortus HC58cDNA.

PubMed

Muleke, Charles I; Ruofeng, Yan; Lixin, Xu; Xinwen, Bo; Xiangrui, Li

2007-06-01

The complete coding sequence of Hemonchus contortus HC58cDNA was generated by rapid amplification of cDNA ends and polymerase chain reaction using primers based on the 5' and 3' ends of the parasite mRNA, accession no. AF305964. The HC58cDNA gene was 851 bp long, with open reading frame of 717 bp, precursors to 239 amino acids coding for approximately 27 kDa protein. Analysis of amino acid sequence revealed conserved residues of cysteine, histidine, asparagine, occluding loop pattern, hemoglobinase motif and glutamine of the oxyanion hole characteristic of cathepsin B like proteases (CBL). Comparison of the predicted amino acid sequences showed the protein shared 33.5-58.7% identity to cathepsin B homologues in the papain clan CA family (family C1). Phylogenetic analysis revealed close evolutionary proximity of the protein sequence to counterpart sequences in the CBL, suggesting that HC58cDNA was a member of the papain family.

Statistical inference of the generation probability of T-cell receptors from sequence repertoires.

PubMed

Murugan, Anand; Mora, Thierry; Walczak, Aleksandra M; Callan, Curtis G

2012-10-02

Stochastic rearrangement of germline V-, D-, and J-genes to create variable coding sequence for certain cell surface receptors is at the origin of immune system diversity. This process, known as "VDJ recombination", is implemented via a series of stochastic molecular events involving gene choices and random nucleotide insertions between, and deletions from, genes. We use large sequence repertoires of the variable CDR3 region of human CD4+ T-cell receptor beta chains to infer the statistical properties of these basic biochemical events. Because any given CDR3 sequence can be produced in multiple ways, the probability distribution of hidden recombination events cannot be inferred directly from the observed sequences; we therefore develop a maximum likelihood inference method to achieve this end. To separate the properties of the molecular rearrangement mechanism from the effects of selection, we focus on nonproductive CDR3 sequences in T-cell DNA. We infer the joint distribution of the various generative events that occur when a new T-cell receptor gene is created. We find a rich picture of correlation (and absence thereof), providing insight into the molecular mechanisms involved. The generative event statistics are consistent between individuals, suggesting a universal biochemical process. Our probabilistic model predicts the generation probability of any specific CDR3 sequence by the primitive recombination process, allowing us to quantify the potential diversity of the T-cell repertoire and to understand why some sequences are shared between individuals. We argue that the use of formal statistical inference methods, of the kind presented in this paper, will be essential for quantitative understanding of the generation and evolution of diversity in the adaptive immune system.

Memory effect in M ≥ 7 earthquakes of Taiwan

NASA Astrophysics Data System (ADS)

Wang, Jeen-Hwa

2014-07-01

The M ≥ 7 earthquakes that occurred in the Taiwan region during 1906-2006 are taken to study the possibility of memory effect existing in the sequence of those large earthquakes. Those events are all mainshocks. The fluctuation analysis technique is applied to analyze two sequences in terms of earthquake magnitude and inter-event time represented in the natural time domain. For both magnitude and inter-event time, the calculations are made for three data sets, i.e., the original order data, the reverse-order data, and that of the mean values. Calculated results show that the exponents of scaling law of fluctuation versus window length are less than 0.5 for the sequences of both magnitude and inter-event time data. In addition, the phase portraits of two sequent magnitudes and two sequent inter-event times are also applied to explore if large (or small) earthquakes are followed by large (or small) events. Results lead to a negative answer. Together with all types of information in study, we make a conclusion that the earthquake sequence in study is short-term corrected and thus the short-term memory effect would be operative.

Evolutionary Origins of a Bioactive Peptide Buried within Preproalbumin[C][W

PubMed Central

Elliott, Alysha G.; Delay, Christina; Liu, Huanle; Phua, Zaiyang; Rosengren, K. Johan; Benfield, Aurélie H.; Panero, Jose L.; Colgrave, Michelle L.; Jayasena, Achala S.; Dunse, Kerry M.; Anderson, Marilyn A.; Schilling, Edward E.; Ortiz-Barrientos, Daniel; Craik, David J.; Mylne, Joshua S.

2014-01-01

The de novo evolution of proteins is now considered a frequented route for biological innovation, but the genetic and biochemical processes that lead to each newly created protein are often poorly documented. The common sunflower (Helianthus annuus) contains the unusual gene PawS1 (Preproalbumin with SFTI-1) that encodes a precursor for seed storage albumin; however, in a region usually discarded during albumin maturation, its sequence is matured into SFTI-1, a protease-inhibiting cyclic peptide with a motif homologous to unrelated inhibitors from legumes, cereals, and frogs. To understand how PawS1 acquired this additional peptide with novel biochemical functionality, we cloned PawS1 genes and showed that this dual destiny is over 18 million years old. This new family of mostly backbone-cyclic peptides is structurally diverse, but the protease-inhibitory motif was restricted to peptides from sunflower and close relatives from its subtribe. We describe a widely distributed, potential evolutionary intermediate PawS-Like1 (PawL1), which is matured into storage albumin, but makes no stable peptide despite possessing residues essential for processing and cyclization from within PawS1. Using sequences we cloned, we retrodict the likely stepwise creation of PawS1’s additional destiny within a simple albumin precursor. We propose that relaxed selection enabled SFTI-1 to evolve its inhibitor function by converging upon a successful sequence and structure. PMID:24681618

The influence of sequence of precursor films on CZTSe thin films prepared by ion-beam sputtering deposition

NASA Astrophysics Data System (ADS)

Zhao, Jun; Liang, Guangxing; Zeng, Yang; Fan, Ping; Hu, Juguang; Luo, Jingting; Zhang, Dongping

2017-02-01

The CuZnSn (CZT) precursor thin films are grown by ion-beam sputtering Cu, Zn, Sn targets with different orders and then sputtering Se target to fabricate Cu2ZnSnSe4 (CZTSe) absorber thin films on molybdenum substrates. They are annealed in the same vacuum chamber at 400 °C. The characterization methods of CZTSe thin films include X-ray diffraction (XRD), energy dispersive spectroscopy (EDS), scanning electron microscopy (SEM), and X-ray photoelectron spectra (XPS) in order to study the crystallographic properties, composition, surface morphology, electrical properties and so on. The results display that the CZTSe thin films got the strongest diffraction peak intensity and were with good crystalline quality and its morphology appeared smooth and compact with a sequence of Cu/Zn/Sn/Se, which reveals that the expected states for CZTSe are Cu1+, Zn2+, Sn4+, Se2+. With the good crystalline quality and close to ideal stoichiometric ratio the resistivity of the CZTSe film with the sequence of Cu/Zn/Sn/Se is lower, whose optical band gap is about 1.50 eV. Project supported by the National Natural Science Foundation of China (No. 61404086), the Basical Research Program of Shenzhen (Nos. JCYJ20150324140036866, JCYJ20150324141711581), and the Natural Science Foundation of SZU (No. 2014017).

cDNA, deduced polypeptide structure and chromosomal assignment of human pulmonary surfactant proteolipid, SPL(pVal)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glasser, S.W.; Korfhagen, T.R.; Weaver, T.E.

1988-01-05

In hyaline membrane disease of premature infants, lack of surfactant leads to pulmonary atelectasis and respiratory distress. Hydrophobic surfactant proteins of M/sub r/ = 5000-14,000 have been isolated from mammalian surfactants which enhance the rate of spreading and the surface tension lowering properties of phospholipids during dynamic compression. The authors have characterized the amino-terminal amino acid sequence of pulmonary proteolipids from ether/ethanol extracts of bovine, canine, and human surfactant. Two distinct peptides were identified and termed SPL(pVal) and SPL(Phe). An oligonucleotide probe based on the valine-rich amino-terminal amino acid sequence of SPL(pVal) was utilized to isolate cDNA and genomic DNAmore » encoding the human protein, termed surfactant proteolipid SPL(pVal) on the basis of its unique polyvaline domain. The primary structure of a precursor protein of 20,870 daltons, containing the SPL(pVal) peptide, was deduced from the nucleotide sequence of the cDNAs. Hybrid-arrested translation and immunoprecipitation of labeled translation products of human mRNA demonstrated a precursor protein, the active hydrophobic peptide being produced by proteolytic processing. Two classes of cDNAs encoding SPL(pVal) were identified. Human SPL(pVal) mRNA was more abundant in the adult than in fetal lung. The SPL(pVal) gene locus was assigned to chromosome 8.« less

Cloning and Characterization of the Polyether Salinomycin Biosynthesis Gene Cluster of Streptomyces albus XM211

PubMed Central

Jiang, Chunyan; Wang, Hougen; Kang, Qianjin; Liu, Jing

2012-01-01

Salinomycin is widely used in animal husbandry as a food additive due to its antibacterial and anticoccidial activities. However, its biosynthesis had only been studied by feeding experiments with isotope-labeled precursors. A strategy with degenerate primers based on the polyether-specific epoxidase sequences was successfully developed to clone the salinomycin gene cluster. Using this strategy, a putative epoxidase gene, slnC, was cloned from the salinomycin producer Streptomyces albus XM211. The targeted replacement of slnC and subsequent trans-complementation proved its involvement in salinomycin biosynthesis. A 127-kb DNA region containing slnC was sequenced, including genes for polyketide assembly and release, oxidative cyclization, modification, export, and regulation. In order to gain insight into the salinomycin biosynthesis mechanism, 13 gene replacements and deletions were conducted. Including slnC, 7 genes were identified as essential for salinomycin biosynthesis and putatively responsible for polyketide chain release, oxidative cyclization, modification, and regulation. Moreover, 6 genes were found to be relevant to salinomycin biosynthesis and possibly involved in precursor supply, removal of aberrant extender units, and regulation. Sequence analysis and a series of gene replacements suggest a proposed pathway for the biosynthesis of salinomycin. The information presented here expands the understanding of polyether biosynthesis mechanisms and paves the way for targeted engineering of salinomycin activity and productivity. PMID:22156425

A new variant of antimetabolic protein, arcelin from an Indian bean, Lablab purpureus (Linn.) and its effect on the stored product pest, Callosobruchus maculatus.

PubMed

Janarthanan, Sundaram; Sakthivelkumar, Shanmugavel; Veeramani, Velayutham; Radhika, Dixit; Muthukrishanan, Subbaratnam

2012-12-15

The anti-metabolic or insecticidal gene, arcelin (Arl) was isolated, cloned and sequenced using sequence specific degenerate primers from the seeds of Lablab purpureus collected from the Western Ghats, Tamil Nadu, India. The L. purpureus arcelin nucleotide sequence was homologous to Arl-3 and Arl-4 alleles from Phaseolus spp. The protein it encodes has 70% amino acid identity with the amino acid sequences of Arl-3I, Arl-3III, Arl-4 precursor, Arl-4 and Arl-4I. The partially purified arcelin from the seeds of L. purpureus using an artificial diet confirmed the complete retardation of development of the stored product pest Callosobruchus maculatus at 0.2% w/w arcelin-incorporated artificial seeds. Copyright © 2012 Elsevier Ltd. All rights reserved.

Preparation of 13C/15N-labeled oligomers using the polymerase chain reaction

DOEpatents

Chen, Xian; Gupta, Goutam; Bradbury, E. Morton

2001-01-01

Preparation of .sup.13 C/.sup.15 N-labeled DNA oligomers using the polymerase chain reaction (PCR). A PCR based method for uniform (.sup.13 C/.sup.15 N)-labeling of DNA duplexes is described. Multiple copies of a blunt-ended duplex are cloned into a plasmid, each copy containing the sequence of interest and restriction Hinc II sequences at both the 5' and 3' ends. PCR using bi-directional primers and uniformly .sup.13 C/.sup.15 N-labeled dNTP precursors generates labeled DNA duplexes containing multiple copies of the sequence of interest. Twenty-four cycles of PCR, followed by restriction and purification, gave the uniformly .sup.13 C/.sup.15 N-labeled duplex sequence with a 30% yield. Such labeled duplexes find significant applications in multinuclear magnetic resonance spectroscopy.

Sequencing of Oligourea Foldamers by Tandem Mass Spectrometry

NASA Astrophysics Data System (ADS)

Bathany, Katell; Owens, Neil W.; Guichard, Gilles; Schmitter, Jean-Marie

2013-03-01

This study is focused on sequence analysis of peptidomimetic helical oligoureas by means of tandem mass spectrometry, to build a basis for de novo sequencing for future high-throughput combinatorial library screening of oligourea foldamers. After the evaluation of MS/MS spectra obtained for model compounds with either MALDI or ESI sources, we found that the MALDI-TOF-TOF instrument gave more satisfactory results. MS/MS spectra of oligoureas generated by decay of singly charged precursor ions show major ion series corresponding to fragmentation across both CO-NH and N'H-CO urea bonds. Oligourea backbones fragment to produce a pattern of a, x, b, and y type fragment ions. De novo decoding of spectral information is facilitated by the occurrence of low mass reporter ions, representative of constitutive monomers, in an analogous manner to the use of immonium ions for peptide sequencing.

An early thymic precursor phenotype predicts outcome exclusively in HOXA-overexpressing adult T-cell acute lymphoblastic leukemia: a Group for Research in Adult Acute Lymphoblastic Leukemia study.

PubMed

Bond, Jonathan; Marchand, Tony; Touzart, Aurore; Cieslak, Agata; Trinquand, Amélie; Sutton, Laurent; Radford-Weiss, Isabelle; Lhermitte, Ludovic; Spicuglia, Salvatore; Dombret, Hervé; Macintyre, Elizabeth; Ifrah, Norbert; Hamel, Jean-François; Asnafi, Vahid

2016-06-01

Gene expression studies have consistently identified a HOXA-overexpressing cluster of T-cell acute lymphoblastic leukemias, but it is unclear whether these constitute a homogeneous clinical entity, and the biological consequences of HOXA overexpression have not been systematically examined. We characterized the biology and outcome of 55 HOXA-positive cases among 209 patients with adult T-cell acute lymphoblastic leukemia uniformly treated during the Group for Research on Adult Acute Lymphoblastic Leukemia (GRAALL)-2003 and -2005 studies. HOXA-positive patients had markedly higher rates of an early thymic precursor-like immunophenotype (40.8% versus 14.5%, P=0.0004), chemoresistance (59.3% versus 40.8%, P=0.026) and positivity for minimal residual disease (48.5% versus 23.5%, P=0.01) than the HOXA-negative group. These differences were due to particularly high frequencies of chemoresistant early thymic precursor-like acute lymphoblastic leukemia in HOXA-positive cases harboring fusion oncoproteins that transactivate HOXA Strikingly, the presence of an early thymic precursor-like immunophenotype was associated with marked outcome differences within the HOXA-positive group (5-year overall survival 31.2% in HOXA-positive early thymic precursor versus 66.7% in HOXA-positive non-early thymic precursor, P=0.03), but not in HOXA-negative cases (5-year overall survival 74.2% in HOXA-negative early thymic precursor versus 57.2% in HOXA-negative non-early thymic precursor, P=0.44). Multivariate analysis further revealed that HOXA positivity independently affected event-free survival (P=0.053) and relapse risk (P=0.039) of chemoresistant T-cell acute lymphoblastic leukemia. These results show that the underlying mechanism of HOXA deregulation dictates the clinico-biological phenotype, and that the negative prognosis of early thymic precursor acute lymphoblastic leukemia is exclusive to HOXA-positive patients, suggesting that early treatment intensification is currently suboptimal for therapeutic rescue of HOXA-positive chemoresistant adult early thymic precursor acute lymphoblastic leukemia. The GRAALL-2003 and -2005 studies were registered at http://www.clinicaltrials.gov as #NCT00222027 and #NCT00327678, respectively. Copyright© Ferrata Storti Foundation.

Genomics and its role in Cancer Risk Assessment

EPA Science Inventory

The traditional risk assessment paradigm is based on exposure - dose - response. The individual is exposed to a chemical or other stressor at some dose and a response in the organism or tissue is elicited. Though precursor events such as taret cell proliferation may be used as ...

Observations of a hydrofracture induced earthquake sequence in Harrison County Ohio in 2014

NASA Astrophysics Data System (ADS)

Friberg, P. A.; Brudzinski, M. R.; Currie, B. S.; Skoumal, R.

2015-12-01

On October 7, 2014, a Mw 1.9 earthquake was detected and located using the IRIS Earthscope Transportable Array stations in Ohio. The earthquake was located at a depth of ~3 km near the interface of the Paleozoic sedimentary rocks with the crystalline Precambrian basement. The location is within a few kilometers laterally of a 2013 earthquake sequence that was linked to hydraulic fracturing (HF) operations on three wells in Harrison county (Friberg et al, 2014). Using the Mw 1.9 event as a template in a multi-component cross correlation detector on station O53A, over 1000 matching detections were revealed between September 26 - October 17, 2014. These detections were all coincident in time with HF operations on 3 nearby (< 1km away) horizontally drilled wells (Tarbert 1H, 3H, and 5H) in the Utica formation (~2.4 km depth). The HF operations at two of the wells (1H and 5H) were coincident with the majority of the detected events. The final well (3H) stimulated in the series, produced only about 20 identified events. In addition to the coincident timing with nearby HF operations, the time clustered nature of the detections were similar to the 2013 sequence and two other Ohio HF induced sequences in 2014 (Skoumal et al, 2015). All of the other HF induced earthquake sequences in Ohio were related to operations in the Utica formation. Interestingly, this sequence of earthquakes did not follow a simple Gutenberg-Richter magnitude frequency relationship and was deficient in positive magnitude events; the magnitude 1.9 was preceded by a magnitude 1.7, and only a ½ dozen events slightly above magnitude 0.0. The majority of the events detected were below magnitude 0.0, with some as low as magnitude -2.0. While the majority of detections are too small to locate, high similarity in waveform character indicate they are spatially near to the magnitude 1.9 event. Furthermore, gradual shifts in P phase arrival relative to S phases indicate events are moving away from the station with progressive HF stages. Given the orientation of the wells relative to the station, the migration of events away from the station with progressive stages is also supportive of this being an induced sequence.

Kickoff to Conflict: A Sequence Analysis of Intra-State Conflict-Preceding Event Structures

PubMed Central

D'Orazio, Vito; Yonamine, James E.

2015-01-01

While many studies have suggested or assumed that the periods preceding the onset of intra-state conflict are similar across time and space, few have empirically tested this proposition. Using the Integrated Crisis Early Warning System's domestic event data in Asia from 1998–2010, we subject this proposition to empirical analysis. We code the similarity of government-rebel interactions in sequences preceding the onset of intra-state conflict to those preceding further periods of peace using three different metrics: Euclidean, Levenshtein, and mutual information. These scores are then used as predictors in a bivariate logistic regression to forecast whether we are likely to observe conflict in neither, one, or both of the states. We find that our model accurately classifies cases where both sequences precede peace, but struggles to distinguish between cases in which one sequence escalates to conflict and where both sequences escalate to conflict. These findings empirically suggest that generalizable patterns exist between event sequences that precede peace. PMID:25951105

Launch mission summary and sequence of events Telesat-F(anik-D1)/Delta-164

NASA Technical Reports Server (NTRS)

1982-01-01

The launch vehicle, spacecraft, and mission are summarized. Launch window information, vehicle telemetry coverage, real time data flow, telemetry coverage by station, selected trajectory information, and a brief sequence of flight events are included.

Rupture directivity of microseismic events recorded during hydraulic fracture stimulations.

NASA Astrophysics Data System (ADS)

Urbancic, T.; Smith-Boughner, L.; Baig, A.; Viegas, G.

2016-12-01

We model the dynamics of a complex rupture sequence with four sub-events. These events were recorded during hydraulic fracture stimulations in a gas-bearing shale formation. With force-balance accelerometers, 4.5Hz and 15Hz instruments recording the failure history, we study the directivity of the entire rupture sequence and each sub-event. Two models are considered: unilateral and bi-lateral failures of penny shaped cracks. From the seismic moment tensors of these sub-events, we consider different potential failure planes and rupture directions. Using numerical wave-propagation codes, we generate synthetic rupture sequences with both unilateral and bi-lateral ruptures. These are compared to the four sub-events to determine the directionality of the observed failures and the sensitivity of our recording bandwidth and geometry to distinguishing between different rupture processes. The frequency of unilateral and bilateral rupture processes throughout the fracture stimulation is estimated by comparing the directivity characteristics of the modeled sub-events to other high-quality microseismic events recorded during the same stimulation program. Understanding the failure processes of these microseismic events can provide great insight into the changes in the rock mass responsible for these complex rupture processes.

Whole genome sequence analysis of unidentified genetically modified papaya for development of a specific detection method.

PubMed

Nakamura, Kosuke; Kondo, Kazunari; Akiyama, Hiroshi; Ishigaki, Takumi; Noguchi, Akio; Katsumata, Hiroshi; Takasaki, Kazuto; Futo, Satoshi; Sakata, Kozue; Fukuda, Nozomi; Mano, Junichi; Kitta, Kazumi; Tanaka, Hidenori; Akashi, Ryo; Nishimaki-Mogami, Tomoko

2016-08-15

Identification of transgenic sequences in an unknown genetically modified (GM) papaya (Carica papaya L.) by whole genome sequence analysis was demonstrated. Whole genome sequence data were generated for a GM-positive fresh papaya fruit commodity detected in monitoring using real-time polymerase chain reaction (PCR). The sequences obtained were mapped against an open database for papaya genome sequence. Transgenic construct- and event-specific sequences were identified as a GM papaya developed to resist infection from a Papaya ringspot virus. Based on the transgenic sequences, a specific real-time PCR detection method for GM papaya applicable to various food commodities was developed. Whole genome sequence analysis enabled identifying unknown transgenic construct- and event-specific sequences in GM papaya and development of a reliable method for detecting them in papaya food commodities. Copyright © 2016 Elsevier Ltd. All rights reserved.

Categorizing accident sequences in the external radiotherapy for risk analysis

PubMed Central

2013-01-01

Purpose This study identifies accident sequences from the past accidents in order to help the risk analysis application to the external radiotherapy. Materials and Methods This study reviews 59 accidental cases in two retrospective safety analyses that have collected the incidents in the external radiotherapy extensively. Two accident analysis reports that accumulated past incidents are investigated to identify accident sequences including initiating events, failure of safety measures, and consequences. This study classifies the accidents by the treatments stages and sources of errors for initiating events, types of failures in the safety measures, and types of undesirable consequences and the number of affected patients. Then, the accident sequences are grouped into several categories on the basis of similarity of progression. As a result, these cases can be categorized into 14 groups of accident sequence. Results The result indicates that risk analysis needs to pay attention to not only the planning stage, but also the calibration stage that is committed prior to the main treatment process. It also shows that human error is the largest contributor to initiating events as well as to the failure of safety measures. This study also illustrates an event tree analysis for an accident sequence initiated in the calibration. Conclusion This study is expected to provide sights into the accident sequences for the prospective risk analysis through the review of experiences. PMID:23865005

On the difficulties of detecting PP precursors

NASA Astrophysics Data System (ADS)

Lessing, Stephan; Thomas, Christine; Saki, Morvarid; Schmerr, Nicholas; Vanacore, Elizabeth

2015-06-01

The PP precursors are seismic waves that form from underside reflections of P waves off discontinuities in the upper mantle transition zone (MTZ). These seismic phases are used to map discontinuity topography, sharpness, and impedance contrasts; the resulting structural variations are then often interpreted as evidence for temperature and/or mineralogy variations within the mantle. The PP precursors as well as other seismic phases have been used to establish the global presence of seismic discontinuities at 410 and 660 km depth. Intriguingly, in more than 80 per cent of PP precursor observations the seismic wave amplitudes are significantly weaker than the amplitudes predicted by seismic reference models. Even more perplexing is the observation that 1-5 per cent of all earthquakes (which are 20-25 per cent of earthquakes with clear PP waveforms) do not show any evidence for the PP precursors from the discontinuities even in the presence of well-developed PP waveforms. Non-detections are found in six different data sets consisting of tens to hundreds of events. We use synthetic modelling to examine a suite of factors that could be responsible for the absence of the PP precursors. The take-off angles for PP and the precursors differ by only 1.2-1.5°; thus source-related complexity would affect PP and the precursors. A PP wave attenuated in the upper mantle would increase the relative amplitude of the PP precursors. Attenuation within the transition zone could reduce precursor amplitudes, but this would be a regional phenomenon restricted to particular source receiver geometries. We also find little evidence for deviations from the theoretical travel path of seismic rays expected for scattered arrivals. Factors that have a strong influence include the stacking procedures used in seismic array techniques in the presence of large, interfering phases, the presence of topography on the discontinuities on the order of tens of kilometres, and 3-D lateral heterogeneity in the velocity and density changes with depth across the transition zone. We also compare the observed precursors' amplitudes with seismic models from calculations of phase equilibria and find that a seismic velocity model derived from a pyrolite composition reproduces the data better than the currently available 1-D earth models. This largely owes to the pyrolite models producing a stronger minimum in the reflection coefficient across the epicentral distances where the reduction in amplitudes of the PP precursors is observed. To suppress the precursors entirely in a small subset of earthquakes, other effects, such as localized discontinuity topography and seismic signal processing effects are required in addition to the changed velocity model.

Recognition of maximum flooding events in mixed siliciclastic-carbonate systems: Key to global chronostratigraphic correlation

USGS Publications Warehouse

Mancini, E.A.; Tew, B.H.

1997-01-01

The maximum flooding event within a depositional sequence is an important datum for correlation because it represents a virtually synchronous horizon. This event is typically recognized by a distinctive physical surface and/or a significant change in microfossil assemblages (relative fossil abundance peaks) in siliciclastic deposits from shoreline to continental slope environments in a passive margin setting. Recognition of maximum flooding events in mixed siliciclastic-carbonate sediments is more complicated because the entire section usually represents deposition in continental shelf environments with varying rates of biologic and carbonate productivity versus siliciclastic influx. Hence, this event cannot be consistently identified simply by relative fossil abundance peaks. Factors such as siliciclastic input, carbonate productivity, sediment accumulation rates, and paleoenvironmental conditions dramatically affect the relative abundances of microfossils. Failure to recognize these complications can lead to a sequence stratigraphic interpretation that substantially overestimates the number of depositional sequences of 1 to 10 m.y. duration.

Data Prediction for Public Events in Professional Domains Based on Improved RNN- LSTM

NASA Astrophysics Data System (ADS)

Song, Bonan; Fan, Chunxiao; Wu, Yuexin; Sun, Juanjuan

2018-02-01

The traditional data services of prediction for emergency or non-periodic events usually cannot generate satisfying result or fulfill the correct prediction purpose. However, these events are influenced by external causes, which mean certain a priori information of these events generally can be collected through the Internet. This paper studied the above problems and proposed an improved model—LSTM (Long Short-term Memory) dynamic prediction and a priori information sequence generation model by combining RNN-LSTM and public events a priori information. In prediction tasks, the model is qualified for determining trends, and its accuracy also is validated. This model generates a better performance and prediction results than the previous one. Using a priori information can increase the accuracy of prediction; LSTM can better adapt to the changes of time sequence; LSTM can be widely applied to the same type of prediction tasks, and other prediction tasks related to time sequence.

Metabolism of Cryptic Peptides Derived from Neuropeptide FF Precursors: The Involvement of Insulin-Degrading Enzyme

PubMed Central

Grasso, Giuseppe; Mielczarek, Przemyslaw; Niedziolka, Magdalena; Silberring, Jerzy

2014-01-01

The term “cryptome” refers to the subset of cryptic peptides with bioactivities that are often unpredictable and very different from the parent protein. These cryptic peptides are generated by proteolytic cleavage of proteases, whose identification in vivo can be very challenging. In this work, we show that insulin-degrading enzyme (IDE) is able to degrade specific amino acid sequences present in the neuropeptide pro-NPFFA (NPFF precursor), generating some cryptic peptides that are also observed after incubation with rat brain cortex homogenate. The reported experimental findings support the increasingly accredited hypothesis, according to which, due to its wide substrate selectivity, IDE is involved in a wide variety of physiopathological processes. PMID:25247577

Development and Preliminary Evaluation of a Positive Health Scale

ERIC Educational Resources Information Center

Becker, Craig; Dolbier, Christyn L.; Durham, Thomas W.; Glascoff, Mary A.; Adams, Troy B.

2008-01-01

Background: Health educators have long advocated health promotion, yet their health measurement techniques have a pathogenic focus. Pathogenesis refers to the origin of a disease and the chain of events (precursors) leading to that disease. Traditional health measurement tools with this focus therefore measure health by assessing for the absence…

Psychosocial Precursors and Correlates of Migraine Headache.

ERIC Educational Resources Information Center

Levor, Robert M.; And Others

1986-01-01

Tested the interactions of migraine headache cycles and sufferers' daily experiences of stressful events, emotional arousal, and physical activity. Results support a model of migraine characterized by parallel physiological and psychosocial instability during a 4-day cycle and by an interaction of personality and behavioral (self-reported stress)…

Biallelic Mutations in DNAJC12 Cause Hyperphenylalaninemia, Dystonia, and Intellectual Disability.

PubMed

Anikster, Yair; Haack, Tobias B; Vilboux, Thierry; Pode-Shakked, Ben; Thöny, Beat; Shen, Nan; Guarani, Virginia; Meissner, Thomas; Mayatepek, Ertan; Trefz, Friedrich K; Marek-Yagel, Dina; Martinez, Aurora; Huttlin, Edward L; Paulo, Joao A; Berutti, Riccardo; Benoist, Jean-François; Imbard, Apolline; Dorboz, Imen; Heimer, Gali; Landau, Yuval; Ziv-Strasser, Limor; Malicdan, May Christine V; Gemperle-Britschgi, Corinne; Cremer, Kirsten; Engels, Hartmut; Meili, David; Keller, Irene; Bruggmann, Rémy; Strom, Tim M; Meitinger, Thomas; Mullikin, James C; Schwartz, Gerard; Ben-Zeev, Bruria; Gahl, William A; Harper, J Wade; Blau, Nenad; Hoffmann, Georg F; Prokisch, Holger; Opladen, Thomas; Schiff, Manuel

2017-02-02

Phenylketonuria (PKU, phenylalanine hydroxylase deficiency), an inborn error of metabolism, can be detected through newborn screening for hyperphenylalaninemia (HPA). Most individuals with HPA harbor mutations in the gene encoding phenylalanine hydroxylase (PAH), and a small proportion (2%) exhibit tetrahydrobiopterin (BH 4 ) deficiency with additional neurotransmitter (dopamine and serotonin) deficiency. Here we report six individuals from four unrelated families with HPA who exhibited progressive neurodevelopmental delay, dystonia, and a unique profile of neurotransmitter deficiencies without mutations in PAH or BH 4 metabolism disorder-related genes. In these six affected individuals, whole-exome sequencing (WES) identified biallelic mutations in DNAJC12, which encodes a heat shock co-chaperone family member that interacts with phenylalanine, tyrosine, and tryptophan hydroxylases catalyzing the BH 4 -activated conversion of phenylalanine into tyrosine, tyrosine into L-dopa (the precursor of dopamine), and tryptophan into 5-hydroxytryptophan (the precursor of serotonin), respectively. DNAJC12 was undetectable in fibroblasts from the individuals with null mutations. PAH enzyme activity was reduced in the presence of DNAJC12 mutations. Early treatment with BH 4 and/or neurotransmitter precursors had dramatic beneficial effects and resulted in the prevention of neurodevelopmental delay in the one individual treated before symptom onset. Thus, DNAJC12 deficiency is a preventable and treatable cause of intellectual disability that should be considered in the early differential diagnosis when screening results are positive for HPA. Sequencing of DNAJC12 may resolve any uncertainty and should be considered in all children with unresolved HPA. Copyright © 2017 American Society of Human Genetics. All rights reserved.

Molecular evolution of the neurohypophysial hormone precursors in mammals: Comparative genomics reveals novel mammalian oxytocin and vasopressin analogues.

PubMed

Wallis, Michael

2012-11-01

Among vertebrates the neurohypophysial hormones show considerable variation. However, in eutherian mammals they have been considered rather conserved, with arginine vasopressin (AVP) and oxytocin (OT) in all species except pig and some relatives, where lysine vasopressin replaces AVP. The availability of genomic data for a wide range of mammals makes it possible to assess whether these peptides and their precursors may be more variable in Eutheria than previously suspected. A survey of these data confirms that AVP and OT occur in most eutherians, but with exceptions. In a New-World monkey (marmoset, Callithrix jacchus) and in tree shrew (Tupaia belangeri), Pro(8)OT replaces OT, confirming a recent report for these species. In armadillo (Dasypus novemcinctus) Leu(3)OT replaces OT, while in tenrec (Echinops telfairi) Thr(4)AVP replaces AVP. In these two species there is also evidence for additional genes/pseudogenes, encoding much-modified forms of AVP, but in most other eutherian species there is no evidence for additional neurohypophysial hormone genes. Evolutionary analysis shows that sequences of eutherian neurohypophysial hormone precursors are generally strongly conserved, particularly those regions encoding active peptide and neurophysin. The close association between OT and VP genes has led to frequent gene conversion of sequences encoding neurophysins. A monotreme, platypus (Ornithorhynchus anatinus) has genes for OT and AVP, organized tail-to-tail as in eutherians, but in marsupials 3-4 genes are present for neurohypophysial hormones, organized tail-to-head as in lower vertebrates. Copyright © 2012 Elsevier Inc. All rights reserved.

An Arg-Gly-Asp peptide stimulates Ca2+ efflux from osteoclast precursors through a novel mechanism

NASA Technical Reports Server (NTRS)

Yamakawa, K.; Duncan, R.; Hruska, K. A.

1994-01-01

We examined the effect of a peptide containing the Arg-Gly-Asp (RGD) sequence on 45Ca2+ efflux from osteoclast precursors. 45Ca(2+)-loaded osteoclast precursors were treated with GRGDSP (170 microM) for 10 min after 30 min of basal perfusion with a bicarbonate-containing buffer. GRGDSP significantly increased fractional efflux of Ca2+ from treated cells compared with vehicle-treated cells (P < 0.01) or cells treated with up to 200 micrograms/ml of a control peptide containing GRGESP. The effect of RGD was sustained for 15 min after the peptide was removed from the perfusate, but control levels of Ca2+ efflux returned by 1 h. The Ca2+ efflux effect of GRGDSP was most likely due to activation of the plasma membrane Ca(2+)-adenosinetriphosphatase (Ca(2+)-ATPase) pump, as indicated by its inhibition with vanadate and a calmodulin antagonist, N-(4-aminobutyl)-5-chloro-2-naphthalenesulfonamide, and the absence of an effect of Na+/Ca2+ exchange inhibition. An inhibitor of cyclic nucleotide-dependent protein kinases, N-[2-(methylamino)ethyl]-5-isoquinoline-sulfonamide (0.1 mM), failed to inhibit GRGDSP-stimulated Ca2+ efflux. However, genistein and herbimycin A, inhibitors of protein-tyrosine kinases, blocked Ca2+ efflux stimulated by GRGDSP. The results indicate that RGD sequences of matrix proteins may stimulate Ca2+ efflux from osteoclasts through activation of protein-tyrosine kinases and suggest that GRGDSP-stimulated Ca2+ efflux is mediated via the plasma membrane Ca(2+)-ATPase.

Novel peptides from adrenomedullary chromaffin vesicles.

PubMed Central

Sigafoos, J; Chestnut, W G; Merrill, B M; Taylor, L C; Diliberto, E J; Viveros, O H

1993-01-01

The adrenal medulla chromaffin vesicle (CV) contains, on a weight basis, as much soluble protein and peptide as catecholamine. The bulk of the protein is accounted for by chromogranins (Cgr) A, B and C. Additionally, a large variety of neuropeptides and their precursor proteins have been found recently within these vesicles. Nevertheless, fractionation of CV lysates indicates the presence of many more peptides than previously reported. In the hope of finding novel bioactive peptides, we initiated a systematic isolation and characterisation of CV peptides. Bovine CV pellets were prepared by sucrose gradient centrifugation and immediately boiled in water to avoid degradation of native proteins and peptides. The water lysates were fractionated through a battery of reversed-phase and ion-exchange high-performance chromatographic steps. We fully or partially characterised a substantial number of novel peptides derived from CgrA and CgrB. A tetradecapeptide and a 13 kDa extended peptide were derived from the bovine homologue of rat secretogranin III. Peptides corresponding to C-terminal fragments of 7B2 and proteoglycan II were also found. Additionally, several sequences had no known precursors. Of the sequences derived from known precursors some corresponded to fragments bracketed by pairs of basic amino acids, but others were preceded or followed by single basic residues or by unusual putative cleavage sites. Some of these peptides were postranslationally modified (pyroglutamylation, glycosylation, phosphorylation, amidation). A significant degree of structural conservation of some of these peptides across species suggests that they may exert biological effects when cosecreted with catecholamines during splanchnic stimulation. PMID:8300415

Biosynthetic Investigations of Lactonamycin and Lactonamycin Z: Cloning of the Biosynthetic Gene Clusters and Discovery of an Unusual Starter Unit▿ †

PubMed Central

Zhang, Xiujun; Alemany, Lawrence B.; Fiedler, Hans-Peter; Goodfellow, Michael; Parry, Ronald J.

2008-01-01

The antibiotics lactonamycin and lactonamycin Z provide attractive leads for antibacterial drug development. Both antibiotics contain a novel aglycone core called lactonamycinone. To gain insight into lactonamycinone biosynthesis, cloning and precursor incorporation experiments were undertaken. The lactonamycin gene cluster was initially cloned from Streptomyces rishiriensis. Sequencing of ca. 61 kb of S. rishiriensis DNA revealed the presence of 57 open reading frames. These included genes coding for the biosynthesis of l-rhodinose, the sugar found in lactonamycin, and genes similar to those in the tetracenomycin biosynthetic gene cluster. Since lactonamycin production by S. rishiriensis could not be sustained, additional proof for the identity of the S. rishiriensis cluster was obtained by cloning the lactonamycin Z gene cluster from Streptomyces sanglieri. Partial sequencing of the S. sanglieri cluster revealed 15 genes that exhibited a very high degree of similarity to genes within the lactonamycin cluster, as well as an identical organization. Double-crossover disruption of one gene in the S. sanglieri cluster abolished lactonamycin Z production, and production was restored by complementation. These results confirm the identity of the genetic locus cloned from S. sanglieri and indicate that the highly similar locus in S. rishiriensis encodes lactonamycin biosynthetic genes. Precursor incorporation experiments with S. sanglieri revealed that lactonamycinone is biosynthesized in an unusual manner whereby glycine or a glycine derivative serves as a starter unit that is extended by nine acetate units. Analysis of the gene clusters and of the precursor incorporation data suggested a hypothetical scheme for lactonamycinone biosynthesis. PMID:18070976

A lower size limit exists for export of fragments of an outer membrane protein (OmpA) of Escherichia coli K-12.

PubMed

Freudl, R; Schwarz, H; Degen, M; Henning, U

1989-02-20

The ompA gene codes for a 346 residue precursor of a 325 residue protein of the outer membrane of Escherichia coli K-12. Internally and/or COOH-terminally deleted genes were constructed that encode 123, 116, 88, 72 or 68 residue precursors. The former three were processed and localized to the periplasmic space; the latter two were not processed and remained cytosolic. These data suggest that the signal sequence has to interact with a component of the export apparatus (the Sec pathway) before translation is finished. Comparison of these results with others obtained for prokaryotic and eukaryotic systems shows that: (1) a very similar lower size limit exists for membrane translocation of the 147 residue chicken prelysozyme or the 229 residue bovine preprolactin; (2) precursors smaller than those reported here can be translocated in both systems; (3) the latter translocation, in contrast to, for example, the ompA gene products, does not depend on the cellular export machinery but most likely requires folding of the precursors into an export-competent conformation. In general, at least two quite different, not necessarily mutually exclusive, mechanisms for translocation of a protein across or assembly into a membrane appear to exist.

A Functional Interplay between Human Immunodeficiency Virus Type 1 Protease Residues 77 and 93 Involved in Differential Regulation of Precursor Autoprocessing and Mature Protease Activity

PubMed Central

Counts, Christopher J.; Ho, P. Shing; Donlin, Maureen J.; Tavis, John E.; Chen, Chaoping

2015-01-01

HIV-1 protease (PR) is a viral enzyme vital to the production of infectious virions. It is initially synthesized as part of the Gag-Pol polyprotein precursor in the infected cell. The free mature PR is liberated as a result of precursor autoprocessing upon virion release. We previously described a model system to examine autoprocessing in transfected mammalian cells. Here, we report that a covariance analysis of miniprecursor (p6*-PR) sequences derived from drug naïve patients identified a series of amino acid pairs that vary together across independent viral isolates. These covariance pairs were used to build the first topology map of the miniprecursor that suggests high levels of interaction between the p6* peptide and the mature PR. Additionally, several PR-PR covariance pairs are located far from each other (>12 Å Cα to Cα) relative to their positions in the mature PR structure. Biochemical characterization of one such covariance pair (77–93) revealed that each residue shows distinct preference for one of three alkyl amino acids (V, I, and L) and that a polar or charged amino acid at either of these two positions abolishes precursor autoprocessing. The most commonly observed 77V is preferred by the most commonly observed 93I, but the 77I variant is preferred by other 93 variances (L, V, or M) in supporting precursor autoprocessing. Furthermore, the 77I93V covariant enhanced precursor autoprocessing and Gag polyprotein processing but decreased the mature PR activity. Therefore, both covariance and biochemical analyses support a functional association between residues 77 and 93, which are spatially distant from each other in the mature PR structure. Our data also suggests that these covariance pairs differentially regulate precursor autoprocessing and the mature protease activity. PMID:25893662

Complete genome sequence of a Watermelon silver mottle virus isolate from China.

PubMed

Rao, Xueqin; Wu, Zhuyan; Li, Yuan

2013-06-01

The complete genome of a Watermelon silver mottle virus (WSMoV) (genus Tospovirus, family Bunyaviridae) isolate (WSMoV-GZ) from Guangdong province, China was sequenced. The genomes of WSMoV-GZ contained 3,603, 4,909, and 8,914 nt of small (S), medium (M), and large (L) RNA segments, respectively, and had a genomic organization characteristic of members of the genus Tospovirus. The amino acid sequence of the nucleocapsid (N) protein, S RNA-encoded nonstructural (NSs) protein, M RNA-encoded nonstructural (NSm) protein, Gn/Gc glycoprotein precursor, and RNA-dependent RNA polymerase (RdRp) protein showed 94.3-97.5 % identity with those of other WSMoV isolates. Phylogenetic analysis showed that the N protein of WSMoV-GZ was clustered together with those of the WSMoV isolates. The full sequence of WSMoV-GZ provides a reference genome for comparison with other tospoviruses.

The Swiss-Army-Knife Approach to the Nearly Automatic Analysis for Microearthquake Sequences.

NASA Astrophysics Data System (ADS)

Kraft, T.; Simon, V.; Tormann, T.; Diehl, T.; Herrmann, M.

2017-12-01

Many Swiss earthquake sequence have been studied using relative location techniques, which often allowed to constrain the active fault planes and shed light on the tectonic processes that drove the seismicity. Yet, in the majority of cases the number of located earthquakes was too small to infer the details of the space-time evolution of the sequences, or their statistical properties. Therefore, it has mostly been impossible to resolve clear patterns in the seismicity of individual sequences, which are needed to improve our understanding of the mechanisms behind them. Here we present a nearly automatic workflow that combines well-established seismological analysis techniques and allows to significantly improve the completeness of detected and located earthquakes of a sequence. We start from the manually timed routine catalog of the Swiss Seismological Service (SED), which contains the larger events of a sequence. From these well-analyzed earthquakes we dynamically assemble a template set and perform a matched filter analysis on the station with: the best SNR for the sequence; and a recording history of at least 10-15 years, our typical analysis period. This usually allows us to detect events several orders of magnitude below the SED catalog detection threshold. The waveform similarity of the events is then further exploited to derive accurate and consistent magnitudes. The enhanced catalog is then analyzed statistically to derive high-resolution time-lines of the a- and b-value and consequently the occurrence probability of larger events. Many of the detected events are strong enough to be located using double-differences. No further manual interaction is needed; we simply time-shift the arrival-time pattern of the detecting template to the associated detection. Waveform similarity assures a good approximation of the expected arrival-times, which we use to calculate event-pair arrival-time differences by cross correlation. After a SNR and cycle-skipping quality check these are directly fed into hypoDD. Using this procedure we usually improve the number of well-relocated events by a factor 2-5. We demonstrate the successful application of the workflow at the example of natural sequences in Switzerland and present first results of the advanced analysis the was possible with the enhanced catalogs.

Amorphous surface layer versus transient amorphous precursor phase in bone - A case study investigated by solid-state NMR spectroscopy.

PubMed

Von Euw, Stanislas; Ajili, Widad; Chan-Chang, Tsou-Hsi-Camille; Delices, Annette; Laurent, Guillaume; Babonneau, Florence; Nassif, Nadine; Azaïs, Thierry

2017-09-01

The presence of an amorphous surface layer that coats a crystalline core has been proposed for many biominerals, including bone mineral. In parallel, transient amorphous precursor phases have been proposed in various biomineralization processes, including bone biomineralization. Here we propose a methodology to investigate the origin of these amorphous environments taking the bone tissue as a key example. This study relies on the investigation of a bone tissue sample and its comparison with synthetic calcium phosphate samples, including a stoichiometric apatite, an amorphous calcium phosphate sample, and two different biomimetic apatites. To reveal if the amorphous environments in bone originate from an amorphous surface layer or a transient amorphous precursor phase, a combined solid-state nuclear magnetic resonance (NMR) experiment has been used. The latter consists of a double cross polarization 1 H→ 31 P→ 1 H pulse sequence followed by a 1 H magnetization exchange pulse sequence. The presence of an amorphous surface layer has been investigated through the study of the biomimetic apatites; while the presence of a transient amorphous precursor phase in the form of amorphous calcium phosphate particles has been mimicked with the help of a physical mixture of stoichiometric apatite and amorphous calcium phosphate. The NMR results show that the amorphous and the crystalline environments detected in our bone tissue sample belong to the same particle. The presence of an amorphous surface layer that coats the apatitic core of bone apatite particles has been unambiguously confirmed, and it is certain that this amorphous surface layer has strong implication on bone tissue biogenesis and regeneration. Questions still persist on the structural organization of bone and biomimetic apatites. The existing model proposes a core/shell structure, with an amorphous surface layer coating a crystalline bulk. The accuracy of this model is still debated because amorphous calcium phosphate (ACP) environments could also arise from a transient amorphous precursor phase of apatite. Here, we provide an NMR spectroscopy methodology to reveal the origin of these ACP environments in bone mineral or in biomimetic apatite. The 1 H magnetization exchange between protons arising from amorphous and crystalline domains shows unambiguously that an ACP layer coats the apatitic crystalline core of bone et biomimetic apatite platelets. Copyright © 2017 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Sequence heterogeneity of cannabidiolic- and tetrahydrocannabinolic acid-synthase in Cannabis sativa L. and its relationship with chemical phenotype.

PubMed

Onofri, Chiara; de Meijer, Etienne P M; Mandolino, Giuseppe

2015-08-01

Sequence variants of THCA- and CBDA-synthases were isolated from different Cannabis sativa L. strains expressing various wild-type and mutant chemical phenotypes (chemotypes). Expressed and complete sequences were obtained from mature inflorescences. Each strain was shown to have a different specificity and/or ability to convert the precursor CBGA into CBDA and/or THCA type products. The comparison of the expressed sequences led to the identification of different mutations, all of them due to SNPs. These SNPs were found to relate to the cannabinoid composition of the inflorescence at maturity and are therefore proposed to have a functional significance. The amount of variation was found to be higher within the CBDAS sequence family than in the THCAS family, suggesting a more recent evolution of THCA-forming enzymes from the CBDAS group. We therefore consider CBDAS as the ancestral type of these synthases. Copyright © 2015 Elsevier Ltd. All rights reserved.

Computational Analysis of Mouse piRNA Sequence and Biogenesis

PubMed Central

Betel, Doron; Sheridan, Robert; Marks, Debora S; Sander, Chris

2007-01-01

The recent discovery of a new class of 30-nucleotide long RNAs in mammalian testes, called PIWI-interacting RNA (piRNA), with similarities to microRNAs and repeat-associated small interfering RNAs (rasiRNAs), has raised puzzling questions regarding their biogenesis and function. We report a comparative analysis of currently available piRNA sequence data from the pachytene stage of mouse spermatogenesis that sheds light on their sequence diversity and mechanism of biogenesis. We conclude that (i) there are at least four times as many piRNAs in mouse testes than currently known; (ii) piRNAs, which originate from long precursor transcripts, are generated by quasi-random enzymatic processing that is guided by a weak sequence signature at the piRNA 5′ends resulting in a large number of distinct sequences; and (iii) many of the piRNA clusters contain inverted repeats segments capable of forming double-strand RNA fold-back segments that may initiate piRNA processing analogous to transposon silencing. PMID:17997596

DNA microarray-based genome comparison of a pathogenic and a nonpathogenic strain of Xylella fastidiosa delineates genes important for bacterial virulence.

PubMed

Koide, Tie; Zaini, Paulo A; Moreira, Leandro M; Vêncio, Ricardo Z N; Matsukuma, Adriana Y; Durham, Alan M; Teixeira, Diva C; El-Dorry, Hamza; Monteiro, Patrícia B; da Silva, Ana Claudia R; Verjovski-Almeida, Sergio; da Silva, Aline M; Gomes, Suely L

2004-08-01

Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease.

DNA Microarray-Based Genome Comparison of a Pathogenic and a Nonpathogenic Strain of Xylella fastidiosa Delineates Genes Important for Bacterial Virulence†

PubMed Central

Koide, Tie; Zaini, Paulo A.; Moreira, Leandro M.; Vêncio, Ricardo Z. N.; Matsukuma, Adriana Y.; Durham, Alan M.; Teixeira, Diva C.; El-Dorry, Hamza; Monteiro, Patrícia B.; da Silva, Ana Claudia R.; Verjovski-Almeida, Sergio; da Silva, Aline M.; Gomes, Suely L.

2004-01-01

Xylella fastidiosa is a phytopathogenic bacterium that causes serious diseases in a wide range of economically important crops. Despite extensive comparative analyses of genome sequences of Xylella pathogenic strains from different plant hosts, nonpathogenic strains have not been studied. In this report, we show that X. fastidiosa strain J1a12, associated with citrus variegated chlorosis (CVC), is nonpathogenic when injected into citrus and tobacco plants. Furthermore, a DNA microarray-based comparison of J1a12 with 9a5c, a CVC strain that is highly pathogenic and had its genome completely sequenced, revealed that 14 coding sequences of strain 9a5c are absent or highly divergent in strain J1a12. Among them, we found an arginase and a fimbrial adhesin precursor of type III pilus, which were confirmed to be absent in the nonpathogenic strain by PCR and DNA sequencing. The absence of arginase can be correlated to the inability of J1a12 to multiply in host plants. This enzyme has been recently shown to act as a bacterial survival mechanism by down-regulating host nitric oxide production. The lack of the adhesin precursor gene is in accordance with the less aggregated phenotype observed for J1a12 cells growing in vitro. Thus, the absence of both genes can be associated with the failure of the J1a12 strain to establish and spread in citrus and tobacco plants. These results provide the first detailed comparison between a nonpathogenic strain and a pathogenic strain of X. fastidiosa, constituting an important step towards understanding the molecular basis of the disease. PMID:15292146

Bone remodelling: its local regulation and the emergence of bone fragility.

PubMed

Martin, T John; Seeman, Ego

2008-10-01

Bone modelling prevents the occurrence of damage by adapting bone structure - and hence bone strength - to its loading circumstances. Bone remodelling removes damage, when it inevitably occurs, in order to maintain bone strength. This cellular machinery is successful during growth, but fails during advancing age because of the development of a negative balance between the volumes of bone resorbed and formed during remodelling by the basic multicellular unit (BMU), high rates of remodelling during midlife in women and late in life in both sexes, and a decline in periosteal bone formation. together resulting in bone loss and structural decay each time a remodelling event occurs. The two steps in remodelling - resorption of a volume of bone by osteoclasts and formation of a comparable volume by osteoblasts - are sequential, but the regulatory events leading to these two fully differentiated functions are not. Reparative remodelling is initiated by damage producing osteocyte apoptosis, which signals the location of damage via the osteocyte canalicular system to endosteal lining cells which forms the canopy of a bone-remodelling compartment (BRC). Within the BRC, local recruitment of osteoblast precursors from the lining cells, the marrow and circulation, direct contact with osteoclast precursors, osteoclastogenesis and molecular cross-talk between precursors, mature cells, cells of the immune system, and products of the resorbed matrix, titrate the birth, work and lifespan of the cells of this multicellular remodelling machinery to either remove or form a net volume of bone appropriate to the mechanical requirements.

T-REX on-demand redox targeting in live cells.

PubMed

Parvez, Saba; Long, Marcus J C; Lin, Hong-Yu; Zhao, Yi; Haegele, Joseph A; Pham, Vanha N; Lee, Dustin K; Aye, Yimon

2016-12-01

This protocol describes targetable reactive electrophiles and oxidants (T-REX)-a live-cell-based tool designed to (i) interrogate the consequences of specific and time-resolved redox events, and (ii) screen for bona fide redox-sensor targets. A small-molecule toolset comprising photocaged precursors to specific reactive redox signals is constructed such that these inert precursors specifically and irreversibly tag any HaloTag-fused protein of interest (POI) in mammalian and Escherichia coli cells. Syntheses of the alkyne-functionalized endogenous reactive signal 4-hydroxynonenal (HNE(alkyne)) and the HaloTag-targetable photocaged precursor to HNE(alkyne) (also known as Ht-PreHNE or HtPHA) are described. Low-energy light prompts photo-uncaging (t 1/2 <1-2 min) and target-specific modification. The targeted modification of the POI enables precisely timed and spatially controlled redox events with no off-target modification. Two independent pathways are described, along with a simple setup to functionally validate known targets or discover novel sensors. T-REX sidesteps mixed responses caused by uncontrolled whole-cell swamping with reactive signals. Modification and downstream response can be analyzed by in-gel fluorescence, proteomics, qRT-PCR, immunofluorescence, fluorescence resonance energy transfer (FRET)-based and dual-luciferase reporters, or flow cytometry assays. T-REX targeting takes 4 h from initial probe treatment. Analysis of targeted redox responses takes an additional 4-24 h, depending on the nature of the pathway and the type of readouts used.

T-REX on-demand redox targeting in live cells

PubMed Central

Parvez, Saba; Long, Marcus J C; Lin, Hong-Yu; Zhao, Yi; Haegele, Joseph A; Pham, Vanha N; Lee, Dustin K; Aye, Yimon

2017-01-01

This protocol describes targetable reactive electrophiles and oxidants (T-REX)—a live-cell-based tool designed to (i) interrogate the consequences of specific and time-resolved redox events, and (ii) screen for bona fide redox-sensor targets. A small-molecule toolset comprising photocaged precursors to specific reactive redox signals is constructed such that these inert precursors specifically and irreversibly tag any HaloTag-fused protein of interest (POI) in mammalian and Escherichia coli cells. Syntheses of the alkyne-functionalized endogenous reactive signal 4-hydroxynonenal (HNE (alkyne)) and the HaloTag-targetable photocaged precursor to HNE (alkyne) (also known as Ht-PreHNE or HtPHA) are described. Low-energy light prompts photo-uncaging (t1/2 <1–2 min) and target-specific modification. The targeted modification of the POI enables precisely timed and spatially controlled redox events with no off-target modification. Two independent pathways are described, along with a simple setup to functionally validate known targets or discover novel sensors. T-REX sidesteps mixed responses caused by uncontrolled whole-cell swamping with reactive signals. Modification and downstream response can be analyzed by in-gel fluorescence, proteomics, qRT-PCR, immunofluorescence, fluorescence resonance energy transfer (FRET)-based and dual-luciferase reporters, or flow cytometry assays. T-REX targeting takes 4 h from initial probe treatment. Analysis of targeted redox responses takes an additional 4–24 h, depending on the nature of the pathway and the type of readouts used. PMID:27809314

Formation and specification of a Drosophila dopaminergic precursor cell.

PubMed

Watson, Joseph D; Crews, Stephen T

2012-09-01

Dopaminergic neurons play important roles in animal behavior, including motivation, reward and locomotion. The Drosophila dopaminergic H-cell interneuron is an attractive system for studying the genetics of neural development because analysis is focused on a single neuronal cell type. Here we provide a mechanistic understanding of how MP3, the precursor to the H-cell, forms and acquires its identity. We show that the gooseberry/gooseberry-neuro (gsb/gsb-n) transcription factor genes act to specify MP3 cell fate. It is proposed that single-minded commits neuroectodermal cells to a midline fate, followed by a series of signaling events that result in the formation of a single gsb(+)/gsb-n(+) MP3 cell per segment. The wingless signaling pathway establishes a midline anterior domain by activating expression of the forkhead transcription factors sloppy paired 1 and sloppy paired 2. This is followed by hedgehog signaling that activates gsb/gsb-n expression in a subgroup of anterior cells. Finally, Notch signaling results in the selection of a single MP3, with the remaining cells becoming midline glia. In MP3, gsb/gsb-n direct H-cell development, in large part by activating expression of the lethal of scute and tailup H-cell regulatory genes. Thus, a series of signaling and transcriptional events result in the specification of a unique dopaminergic precursor cell. Additional genetic experiments indicate that the molecular mechanisms that govern MP3/H-cell development might also direct the development of non-midline dopaminergic neurons.

Formation and specification of a Drosophila dopaminergic precursor cell

PubMed Central

Watson, Joseph D.; Crews, Stephen T.

2012-01-01

Dopaminergic neurons play important roles in animal behavior, including motivation, reward and locomotion. The Drosophila dopaminergic H-cell interneuron is an attractive system for studying the genetics of neural development because analysis is focused on a single neuronal cell type. Here we provide a mechanistic understanding of how MP3, the precursor to the H-cell, forms and acquires its identity. We show that the gooseberry/gooseberry-neuro (gsb/gsb-n) transcription factor genes act to specify MP3 cell fate. It is proposed that single-minded commits neuroectodermal cells to a midline fate, followed by a series of signaling events that result in the formation of a single gsb+/gsb-n+ MP3 cell per segment. The wingless signaling pathway establishes a midline anterior domain by activating expression of the forkhead transcription factors sloppy paired 1 and sloppy paired 2. This is followed by hedgehog signaling that activates gsb/gsb-n expression in a subgroup of anterior cells. Finally, Notch signaling results in the selection of a single MP3, with the remaining cells becoming midline glia. In MP3, gsb/gsb-n direct H-cell development, in large part by activating expression of the lethal of scute and tailup H-cell regulatory genes. Thus, a series of signaling and transcriptional events result in the specification of a unique dopaminergic precursor cell. Additional genetic experiments indicate that the molecular mechanisms that govern MP3/H-cell development might also direct the development of non-midline dopaminergic neurons. PMID:22874915

Determination of the Gene Sequence of Poliovirus with Pactamycin

PubMed Central

Summers, D. F.; Maizel, J. V.

1971-01-01

By examination of the virus-specific polypeptides formed after the addition of pactamycin, an inhibitor of protein chain initiation, to infected cells, it has been possible to tentatively locate the virus coat proteins at the amino terminus of the large, virus-specific protein precursor, and, therefore, to assign the coat protein cistron to the 5′ end of the RNA. PMID:4330946

Identification and localization of gonadotropin-inhibitory hormone (GnIH) orthologs in the hypothalamus of the red-eared slider turtle, Trachemys scripta elegans.

PubMed

Ukena, Kazuyoshi; Iwakoshi-Ukena, Eiko; Osugi, Tomohiro; Tsutsui, Kazuyoshi

2016-02-01

Gonadotropin-inhibitory hormone (GnIH) was discovered in 2000 as a novel hypothalamic neuropeptide that inhibited gonadotropin release in the Japanese quail. GnIH and its orthologs have a common C-terminal LPXRFamide (X=L or Q) motif, and have been identified in vertebrates from agnathans to humans, apart from reptiles. In the present study, we characterized a cDNA encoding GnIH orthologs in the brain of the red-eared slider turtle. The deduced precursor protein consisted of 205 amino-acid residues, encoding three putative peptide sequences that included the LPXRFamide motif at their C-termini. In addition, the precursor sequence was most similar to those of avian species. Immunoaffinity purification combined with mass spectrometry confirmed that three mature peptides were produced in the brain. In situ hybridization and immunohistochemistry showed that turtle GnIH-containing cells were restricted to the periventricular hypothalamic nucleus. Immunoreactive fibers were densely distributed in the median eminence. Thus, GnIH and related peptides may act on the pituitary to regulate pituitary hormone release in turtles as well as other vertebrates. Copyright © 2015 Elsevier Inc. All rights reserved.

Rhizomucor miehei triglyceride lipase is processed and secreted from transformed Aspergillus oryzae.

PubMed

Huge-Jensen, B; Andreasen, F; Christensen, T; Christensen, M; Thim, L; Boel, E

1989-09-01

The cDNA encoding the precursor of the Rhizomucor miehei triglyceride lipase was inserted in an Aspergillus oryzae expression vector. In this vector the expression of the lipase cDNA is under control of the Aspergillus oryzae alpha-amylase gene promoter and the Aspergillus niger glucoamylase gene terminator. The recombinant plasmid was introduced into Aspergillus oryzae, and transformed colonies were selected and screened for lipase expression. Lipase-positive transformants were grown in a small fermentor, and recombinant triglyceride lipase was purified from the culture broth. The purified enzymatically active recombinant lipase (rRML) secreted from A. oryzae was shown to have the same characteristics with respect to mobility on reducing SDS-gels and amino acid composition as the native enzyme. N-terminal amino acid sequencing indicated that approximately 70% of the secreted rRML had the same N-terminal sequence as the native Rhizomucor miehei enzyme, whereas 30% of the secreted rRML was one amino acid residue shorter in the N-terminal. The recombinant lipase precursor, which has a 70 amino acid propeptide, is thus processed in and secreted from Aspergillus oryzae. We have hereby demonstrated the utility of this organism as a host for the production of recombinant triglyceride lipases.

New particle formation and growth from methanesulfonic acid, trimethylamine and water.

PubMed

Chen, Haihan; Ezell, Michael J; Arquero, Kristine D; Varner, Mychel E; Dawson, Matthew L; Gerber, R Benny; Finlayson-Pitts, Barbara J

2015-05-28

New particle formation from gas-to-particle conversion represents a dominant source of atmospheric particles and affects radiative forcing, climate and human health. The species involved in new particle formation and the underlying mechanisms remain uncertain. Although sulfuric acid is commonly recognized as driving new particle formation, increasing evidence suggests the involvement of other species. Here we study particle formation and growth from methanesulfonic acid, trimethylamine and water at reaction times from 2.3 to 32 s where particles are 2-10 nm in diameter using a newly designed and tested flow system. The flow system has multiple inlets to facilitate changing the mixing sequence of gaseous precursors. The relative humidity and precursor concentrations, as well as the mixing sequence, are varied to explore their effects on particle formation and growth in order to provide insight into the important mechanistic steps. We show that water is involved in the formation of initial clusters, greatly enhancing their formation as well as growth into detectable size ranges. A kinetics box model is developed that quantitatively reproduces the experimental data under various conditions. Although the proposed scheme is not definitive, it suggests that incorporating such mechanisms into atmospheric models may be feasible in the near future.

PsRobot: a web-based plant small RNA meta-analysis toolbox.

PubMed

Wu, Hua-Jun; Ma, Ying-Ke; Chen, Tong; Wang, Meng; Wang, Xiu-Jie

2012-07-01

Small RNAs (smRNAs) in plants, mainly microRNAs and small interfering RNAs, play important roles in both transcriptional and post-transcriptional gene regulation. The broad application of high-throughput sequencing technology has made routinely generation of bulk smRNA sequences in laboratories possible, thus has significantly increased the need for batch analysis tools. PsRobot is a web-based easy-to-use tool dedicated to the identification of smRNAs with stem-loop shaped precursors (such as microRNAs and short hairpin RNAs) and their target genes/transcripts. It performs fast analysis to identify smRNAs with stem-loop shaped precursors among batch input data and predicts their targets using a modified Smith-Waterman algorithm. PsRobot integrates the expression data of smRNAs in major plant smRNA biogenesis gene mutants and smRNA-associated protein complexes to give clues to the smRNA generation and functional processes. Besides improved specificity, the reliability of smRNA target prediction results can also be evaluated by mRNA cleavage (degradome) data. The cross species conservation statuses and the multiplicity of smRNA target sites are also provided. PsRobot is freely accessible at http://omicslab.genetics.ac.cn/psRobot/.

Application of Tandem Two-Dimensional Mass Spectrometry for Top-Down Deep Sequencing of Calmodulin.

PubMed

Floris, Federico; Chiron, Lionel; Lynch, Alice M; Barrow, Mark P; Delsuc, Marc-André; O'Connor, Peter B

2018-06-04

Two-dimensional mass spectrometry (2DMS) involves simultaneous acquisition of the fragmentation patterns of all the analytes in a mixture by correlating their precursor and fragment ions by modulating precursor ions systematically through a fragmentation zone. Tandem two-dimensional mass spectrometry (MS/2DMS) unites the ultra-high accuracy of Fourier transform ion cyclotron resonance (FT-ICR) MS/MS and the simultaneous data-independent fragmentation of 2DMS to achieve extensive inter-residue fragmentation of entire proteins. 2DMS was recently developed for top-down proteomics (TDP), and applied to the analysis of calmodulin (CaM), reporting a cleavage coverage of about ~23% using infrared multiphoton dissociation (IRMPD) as fragmentation technique. The goal of this work is to expand the utility of top-down protein analysis using MS/2DMS in order to extend the cleavage coverage in top-down proteomics further into the interior regions of the protein. In this case, using MS/2DMS, the cleavage coverage of CaM increased from ~23% to ~42%. Graphical Abstract Two-dimensional mass spectrometry, when applied to primary fragment ions from the source, allows deep-sequencing of the protein calmodulin.

Cloning and characterization of cDNAs encoding human gastrin-releasing peptide.

PubMed Central

Spindel, E R; Chin, W W; Price, J; Rees, L H; Besser, G M; Habener, J F

1984-01-01

We have prepared and cloned cDNAs derived from poly(A)+ RNA from a human pulmonary carcinoid tumor rich in immunoreactivity to gastrin-releasing peptide, a peptide closely related in structure to amphibian bombesin. Mixtures of synthetic oligodeoxyribonucleotides corresponding to amphibian bombesin were used as hybridization probes to screen a cDNA library prepared from the tumor RNA. Sequencing of the recombinant plasmids shows that human gastrin-releasing peptide (hGRP) mRNA encodes a precursor of 148 amino acids containing a typical signal sequence, hGRP consisting of 27 or 28 amino acids, and a carboxyl-terminal extension peptide. hGRP is flanked at its carboxyl terminus by two basic amino acids, following a glycine used for amidation of the carboxyl-terminal methionine. RNA blot analyses of tumor RNA show a major mRNA of 900 bases and a minor mRNA of 850 bases. Blot hybridization analyses using human genomic DNA are consistent with a single hGRP-encoding gene. The presence of two mRNAs encoding the hGRP precursor protein in the face of a single hGRP gene raises the possibility of alternative processing of the single RNA transcript. Images PMID:6207529

Transcriptogenomics identification and characterization of RNA editing sites in human primary monocytes using high-depth next generation sequencing data.

PubMed

Leong, Wai-Mun; Ripen, Adiratna Mat; Mirsafian, Hoda; Mohamad, Saharuddin Bin; Merican, Amir Feisal

2018-06-07

High-depth next generation sequencing data provide valuable insights into the number and distribution of RNA editing events. Here, we report the RNA editing events at cellular level of human primary monocyte using high-depth whole genomic and transcriptomic sequencing data. We identified over a ten thousand putative RNA editing sites and 69% of the sites were A-to-I editing sites. The sites enriched in repetitive sequences and intronic regions. High-depth sequencing datasets revealed that 90% of the canonical sites were edited at lower frequencies (<0.7). Single and multiple human monocytes and brain tissues samples were analyzed through genome sequence independent approach. The later approach was observed to identify more editing sites. Monocytes was observed to contain more C-to-U editing sites compared to brain tissues. Our results establish comparable pipeline that can address current limitations as well as demonstrate the potential for highly sensitive detection of RNA editing events in single cell type. Copyright © 2018 Elsevier Inc. All rights reserved.

Detection of Chemical Precursors of Explosives

NASA Technical Reports Server (NTRS)

Li, Jing

2012-01-01

Certain selected chemicals associated with terrorist activities are too unstable to be prepared in final form. These chemicals are often prepared as precursor components, to be combined at a time immediately preceding the detonation. One example is a liquid explosive, which usually requires an oxidizer, an energy source, and a chemical or physical mechanism to combine the other components. Detection of the oxidizer (e.g. H2O2) or the energy source (e.g., nitromethane) is often possible, but must be performed in a short time interval (e.g., 5 15 seconds) and in an environment with a very small concentration (e.g.,1 100 ppm), because the target chemical(s) is carried in a sealed container. These needs are met by this invention, which provides a system and associated method for detecting one or more chemical precursors (components) of a multi-component explosive compound. Different carbon nanotubes (CNTs) are loaded (by doping, impregnation, coating, or other functionalization process) for detecting of different chemical substances that are the chemical precursors, respectively, if these precursors are present in a gas to which the CNTs are exposed. After exposure to the gas, a measured electrical parameter (e.g. voltage or current that correlate to impedance, conductivity, capacitance, inductance, etc.) changes with time and concentration in a predictable manner if a selected chemical precursor is present, and will approach an asymptotic value promptly after exposure to the precursor. The measured voltage or current are compared with one or more sequences of their reference values for one or more known target precursor molecules, and a most probable concentration value is estimated for each one, two, or more target molecules. An error value is computed, based on differences of voltage or current for the measured and reference values, using the most probable concentration values. Where the error value is less than a threshold, the system concludes that the target molecule is likely. Presence of one, two, or more target molecules in the gas can be sensed from a single set of measurements.

Mesosphere-Stratosphere Coupling: Implications for Climate Variability and Trends

NASA Technical Reports Server (NTRS)

Baldwin, Mark P.

2004-01-01

A key aspect of this project is the establishment of a causal link from circulation anomalies in the lower mesosphere and stratopause region downward through the stratosphere to the troposphere. The observational link for stratospheric sudden warmings and surface climate is fairly clear. However, our understanding of the dynamics is incomplete. We have been making significant progress in the area of dynamical mechanisms by which circulation anomalies in the stratosphere affect the troposphere. We are trying to understand the details and sequence of events that occur when a middle atmosphere (wind) anomaly propagates downward to near the tropopause. The wind anomaly could be caused by a warming or solar variations in the low-latitude stratopause region, or could have other causes. The observations show a picture that is consistent with a circulation anomaly that descends to the tropopause region, and can be detected as low as the mid-troposphere. Processes near the stratopause in the tropics appear to be important precursors to the wintertime development of the northern polar vortex. This may affect significantly our understanding of the process by which low-latitude wind anomalies in the low mesosphere and upper stratosphere evolve through the winter and affect the polar vortex.

Intramembranous ossification of scleral ossicles in Chelydra serpentina.

PubMed

Franz-Odendaal, Tamara A

2006-01-01

Scleral ossicles are present in many reptiles, including turtles and birds. In both groups the sclerotic ring situated in the eye is composed of a number of imbricating scleral ossicles or plates. Despite this gross morphological similarity, Andrews (1996. An endochondral rather than a dermal origin for scleral ossicles in Cryptodiran turtles. J. Herpetol. 30, 257-260) reported that the scleral ossicles of turtles develop endochondrally unlike those in birds, which develop intramembranously after a complex epithelial-mesenchymal inductive event. This study re-explores one of the species examined by Andrews in order to determine the mode of ossification of scleral ossicles in turtles. A growth series of Chelydra serpentina embryos, including the stages examined by Andrews, were examined by staining separately for cartilage and bone. Results clearly contradict Andrews (1996) and show that the scleral ossicles of Chelydra serpentina develop similarly to those in birds. That is, they develop intramembranously without a cartilage precursor and are likely induced by transient scleral papillae. The sequence of scleral papillae development is broadly similar, but the papillae themselves are not as distinct as those seen in chicken embryos. This study has important consequences for understanding the homology of scleral ossicles among tetrapods.

Three-dimensional analysis of nuclear heterochromatin distribution during early development in the rabbit.

PubMed

Bonnet-Garnier, Amélie; Kiêu, Kiên; Aguirre-Lavin, Tiphaine; Tar, Krisztina; Flores, Pierre; Liu, Zichuan; Peynot, Nathalie; Chebrout, Martine; Dinnyés, András; Duranthon, Véronique; Beaujean, Nathalie

2018-04-18

Changes to the spatial organization of specific chromatin domains such as constitutive heterochromatin have been studied extensively in somatic cells. During early embryonic development, drastic epigenetic reprogramming of both the maternal and paternal genomes, followed by chromatin remodeling at the time of embryonic genome activation (EGA), have been observed in the mouse. Very few studies have been performed in other mammalian species (human, bovine, or rabbit) and the data are far from complete. During this work, we studied the three-dimensional organization of pericentromeric regions during the preimplantation period in the rabbit using specific techniques (3D-FISH) and tools (semi-automated image analysis). We observed that the pericentromeric regions (identified with specific probes for Rsat I and Rsat II genomic sequences) changed their shapes (from pearl necklaces to clusters), their nuclear localizations (from central to peripheral), as from the 4-cell stage. This reorganization goes along with histone modification changes and reduced amount of interactions with nucleolar precursor body surface. Altogether, our results suggest that the 4-cell stage may be a crucial window for events necessary before major EGA, which occurs during the 8-cell stage in the rabbit.

Learning Orthographic Structure with Sequential Generative Neural Networks

ERIC Educational Resources Information Center

Testolin, Alberto; Stoianov, Ivilin; Sperduti, Alessandro; Zorzi, Marco

2016-01-01

Learning the structure of event sequences is a ubiquitous problem in cognition and particularly in language. One possible solution is to learn a probabilistic generative model of sequences that allows making predictions about upcoming events. Though appealing from a neurobiological standpoint, this approach is typically not pursued in…

Toxic plants: Effects on reproduction and fetal and embryonic development in livestock

USDA-ARS?s Scientific Manuscript database

Reproductive success is dependent on a large number of carefully orchestrated biological events that must occur in a specifically timed sequence. The interference with one of more of these sequences or events may result in total reproductive failure or a more subtle reduction in reproductive potent...

Sequence specificity of the human mRNA N6-adenosine methylase in vitro.

PubMed Central

Harper, J E; Miceli, S M; Roberts, R J; Manley, J L

1990-01-01

N6-adenosine methylation is a frequent modification of mRNAs and their precursors, but little is known about the mechanism of the reaction or the function of the modification. To explore these questions, we developed conditions to examine N6-adenosine methylase activity in HeLa cell nuclear extracts. Transfer of the methyl group from S-[3H methyl]-adenosylmethionine to unlabeled random copolymer RNA substrates of varying ribonucleotide composition revealed a substrate specificity consistent with a previously deduced consensus sequence, Pu[G greater than A]AC[A/C/U]. 32-P labeled RNA substrates of defined sequence were used to examine the minimum sequence requirements for methylation. Each RNA was 20 nucleotides long, and contained either the core consensus sequence GGACU, or some variation of this sequence. RNAs containing GGACU, either in single or multiple copies, were good substrates for methylation, whereas RNAs containing single base substitutions within the GGACU sequence gave dramatically reduced methylation. These results demonstrate that the N6-adenosine methylase has a strict sequence specificity, and that there is no requirement for extended sequences or secondary structures for methylation. Recognition of this sequence does not require an RNA component, as micrococcal nuclease pretreatment of nuclear extracts actually increased methylation efficiency. Images PMID:2216767

Self-Exciting Point Process Modeling of Conversation Event Sequences

NASA Astrophysics Data System (ADS)

Masuda, Naoki; Takaguchi, Taro; Sato, Nobuo; Yano, Kazuo

Self-exciting processes of Hawkes type have been used to model various phenomena including earthquakes, neural activities, and views of online videos. Studies of temporal networks have revealed that sequences of social interevent times for individuals are highly bursty. We examine some basic properties of event sequences generated by the Hawkes self-exciting process to show that it generates bursty interevent times for a wide parameter range. Then, we fit the model to the data of conversation sequences recorded in company offices in Japan. In this way, we can estimate relative magnitudes of the self excitement, its temporal decay, and the base event rate independent of the self excitation. These variables highly depend on individuals. We also point out that the Hawkes model has an important limitation that the correlation in the interevent times and the burstiness cannot be independently modulated.

Uncontrolled angiogenic precursor expansion causes coronary artery anomalies in mice lacking Pofut1.

PubMed

Wang, Yidong; Wu, Bingruo; Lu, Pengfei; Zhang, Donghong; Wu, Brian; Varshney, Shweta; Del Monte-Nieto, Gonzalo; Zhuang, Zhenwu; Charafeddine, Rabab; Kramer, Adam H; Sibinga, Nicolas E; Frangogiannis, Nikolaos G; Kitsis, Richard N; Adams, Ralf H; Alitalo, Kari; Sharp, David J; Harvey, Richard P; Stanley, Pamela; Zhou, Bin

2017-09-18

Coronary artery anomalies may cause life-threatening cardiac complications; however, developmental mechanisms underpinning coronary artery formation remain ill-defined. Here we identify an angiogenic cell population for coronary artery formation in mice. Regulated by a DLL4/NOTCH1/VEGFA/VEGFR2 signaling axis, these angiogenic cells generate mature coronary arteries. The NOTCH modulator POFUT1 critically regulates this signaling axis. POFUT1 inactivation disrupts signaling events and results in excessive angiogenic cell proliferation and plexus formation, leading to anomalous coronary arteries, myocardial infarction and heart failure. Simultaneous VEGFR2 inactivation fully rescues these defects. These findings show that dysregulated angiogenic precursors link coronary anomalies to ischemic heart disease.Though coronary arteries are crucial for heart function, the mechanisms guiding their formation are largely unknown. Here, Wang et al. identify a unique, endocardially-derived angiogenic precursor cell population for coronary artery formation in mice and show that a DLL4/NOTCH1/VEGFA/VEGFR2 signaling axis is key for coronary artery development.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

PubMed Central

Schadt, Eric E.; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H.; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A.; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types. PMID:23093720

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.

PubMed

Schadt, Eric E; Banerjee, Onureena; Fang, Gang; Feng, Zhixing; Wong, Wing H; Zhang, Xuegong; Kislyuk, Andrey; Clark, Tyson A; Luong, Khai; Keren-Paz, Alona; Chess, Andrew; Kumar, Vipin; Chen-Plotkin, Alice; Sondheimer, Neal; Korlach, Jonas; Kasarskis, Andrew

2013-01-01

Current generation DNA sequencing instruments are moving closer to seamlessly sequencing genomes of entire populations as a routine part of scientific investigation. However, while significant inroads have been made identifying small nucleotide variation and structural variations in DNA that impact phenotypes of interest, progress has not been as dramatic regarding epigenetic changes and base-level damage to DNA, largely due to technological limitations in assaying all known and unknown types of modifications at genome scale. Recently, single-molecule real time (SMRT) sequencing has been reported to identify kinetic variation (KV) events that have been demonstrated to reflect epigenetic changes of every known type, providing a path forward for detecting base modifications as a routine part of sequencing. However, to date no statistical framework has been proposed to enhance the power to detect these events while also controlling for false-positive events. By modeling enzyme kinetics in the neighborhood of an arbitrary location in a genomic region of interest as a conditional random field, we provide a statistical framework for incorporating kinetic information at a test position of interest as well as at neighboring sites that help enhance the power to detect KV events. The performance of this and related models is explored, with the best-performing model applied to plasmid DNA isolated from Escherichia coli and mitochondrial DNA isolated from human brain tissue. We highlight widespread kinetic variation events, some of which strongly associate with known modification events, while others represent putative chemically modified sites of unknown types.

Polymeric peptide pigments with sequence-encoded properties

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lampel, Ayala; McPhee, Scott A.; Park, Hang-Ah

Melanins are a family of heterogeneous polymeric pigments that provide ultraviolet (UV) light protection, structural support, coloration, and free radical scavenging. Formed by oxidative oligomerization of catecholic small molecules, the physical properties of melanins are influenced by covalent and noncovalent disorder. We report the use of tyrosine-containing tripeptides as tunable precursors for polymeric pigments. In these structures, phenols are presented in a (supra-)molecular context dictated by the positions of the amino acids in the peptide sequence. Oxidative polymerization can be tuned in a sequence-dependent manner, resulting in peptide sequence–encoded properties such as UV absorbance, morphology, coloration, and electrochemical properties overmore » a considerable range. Short peptides have low barriers to application and can be easily scaled, suggesting near-term applications in cosmetics and biomedicine.« less

Video Image Stabilization and Registration

NASA Technical Reports Server (NTRS)

Hathaway, David H. (Inventor); Meyer, Paul J. (Inventor)

2002-01-01

A method of stabilizing and registering a video image in multiple video fields of a video sequence provides accurate determination of the image change in magnification, rotation and translation between video fields, so that the video fields may be accurately corrected for these changes in the image in the video sequence. In a described embodiment, a key area of a key video field is selected which contains an image which it is desired to stabilize in a video sequence. The key area is subdivided into nested pixel blocks and the translation of each of the pixel blocks from the key video field to a new video field is determined as a precursor to determining change in magnification, rotation and translation of the image from the key video field to the new video field.

Video Image Stabilization and Registration

NASA Technical Reports Server (NTRS)

Hathaway, David H. (Inventor); Meyer, Paul J. (Inventor)

2003-01-01

A method of stabilizing and registering a video image in multiple video fields of a video sequence provides accurate determination of the image change in magnification, rotation and translation between video fields, so that the video fields may be accurately corrected for these changes in the image in the video sequence. In a described embodiment, a key area of a key video field is selected which contains an image which it is desired to stabilize in a video sequence. The key area is subdivided into nested pixel blocks and the translation of each of the pixel blocks from the key video field to a new video field is determined as a precursor to determining change in magnification, rotation and translation of the image from the key video field to the new video field.

Detection of isocitrate dehydrogenase 1 mutation R132H in myelodysplastic syndrome by mutation-specific antibody and direct sequencing.

PubMed

Andrulis, Mindaugas; Capper, David; Luft, Thomas; Hartmann, Christian; Zentgraf, Hanswalter; von Deimling, Andreas

2010-08-01

Sequencing of the acute myeloid leukemia genome revealed somatic mutations in isocitrate dehydrogenase-1. Acute myeloid leukemia frequently develops from myelodysplastic syndrome. In order to test whether myelodysplastic syndrome also carries isocitrate dehydrogenase-1 mutations, we stained a series of bone marrow samples from patients with myelodysplastic syndrome using an antibody specific for the R132H mutation. Three out of 71 patients exhibited antibody binding to myeloid precursor cells. The presence of the R132H mutation was confirmed by DNA sequencing. We demonstrated that isocitrate dehydrogenase-1 mutations occur in myelodysplasia preceding acute myeloid leukemia and that the R132H alteration can be detected by immunohistochemistry. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

miRNAs involved in the development and differentiation of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri.

PubMed

Li, Weixing; He, Zhichong; Zhang, Li; Lu, Zhaogeng; Xu, Jing; Cui, Jiawen; Wang, Li; Jin, Biao

2017-10-13

Sterile and fertile flowers are important evolutionary developmental phenotypes in angiosperm flowers. The development of floral organs, critical in angiosperm reproduction, is regulated by microRNAs (miRNAs). However, the mechanisms underpinning the miRNA regulation of the differentiation and development of sterile and fertile flowers remain unclear. Here, based on investigations of the morphological differences between fertile and sterile flowers, we used high-throughput sequencing to characterize the miRNAs in the differentiated floral organs of Viburnum macrocephalum f. keteleeri. We identified 49 known miRNAs and 67 novel miRNAs by small RNA (sRNA) sequencing and bioinformatics analysis, and 17 of these known and novel miRNA precursors were validated by polymerase chain reaction (PCR) and Sanger sequencing. Furthermore, by comparing the sequencing results of two sRNA libraries, we found that 30 known and 39 novel miRNA sequences were differentially expressed, and 35 were upregulated and 34 downregulated in sterile compared with fertile flowers. Combined with their predicted targets, the potential roles of miRNAs in V. macrocephalum f. keteleeri flowers include involvement in floral organogenesis, cell proliferation, hormonal pathways, and stress responses. miRNA precursors and targets were further validated by quantitative real-time PCR (qRT-PCR). Specifically, miR156a-5p, miR156g, and miR156j expression levels were significantly higher in fertile flowers than in sterile flowers, while SPL genes displayed the opposite expression pattern. Considering that the targets of miR156 are predicted to be SPL genes, we propose that miR156 may be involved in the regulation of stamen development in V. macrocephalum f. keteleeri. We identified miRNAs differentially expressed between fertile and sterile flowers in V. macrocephalum f. keteleeri and provided new insights into the important regulatory roles of miRNAs in the differentiation and development of fertile and sterile flowers.

Transcriptome-wide identification of Rauvolfia serpentina microRNAs and prediction of their potential targets.

PubMed

Prakash, Pravin; Rajakani, Raja; Gupta, Vikrant

2016-04-01

MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 19-24 nucleotides (nt) in length and considered as potent regulators of gene expression at transcriptional and post-transcriptional levels. Here we report the identification and characterization of 15 conserved miRNAs belonging to 13 families from Rauvolfia serpentina through in silico analysis of available nucleotide dataset. The identified mature R. serpentina miRNAs (rse-miRNAs) ranged between 20 and 22nt in length, and the average minimal folding free energy index (MFEI) value of rse-miRNA precursor sequences was found to be -0.815 kcal/mol. Using the identified rse-miRNAs as query, their potential targets were predicted in R. serpentina and other plant species. Gene Ontology (GO) annotation showed that predicted targets of rse-miRNAs include transcription factors as well as genes involved in diverse biological processes such as primary and secondary metabolism, stress response, disease resistance, growth, and development. Few rse-miRNAs were predicted to target genes of pharmaceutically important secondary metabolic pathways such as alkaloids and anthocyanin biosynthesis. Phylogenetic analysis showed the evolutionary relationship of rse-miRNAs and their precursor sequences to homologous pre-miRNA sequences from other plant species. The findings under present study besides giving first hand information about R. serpentina miRNAs and their targets, also contributes towards the better understanding of miRNA-mediated gene regulatory processes in plants. Copyright © 2015 Elsevier Ltd. All rights reserved.

Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA.

PubMed

Velagapudi, Sai Pradeep; Luo, Yiling; Tran, Tuan; Haniff, Hafeez S; Nakai, Yoshio; Fallahi, Mohammad; Martinez, Gustavo J; Childs-Disney, Jessica L; Disney, Matthew D

2017-03-22

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.

Defining RNA–Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA

PubMed Central

2017-01-01

RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif–small molecule interactions identified via selection. Named High Throughput Structure–Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif–small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule–RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs. PMID:28386598

Identification of gene-specific polymorphisms and association with capsaicin pathway metabolites in Capsicum annuum L. collections.

PubMed

Reddy, Umesh K; Almeida, Aldo; Abburi, Venkata L; Alaparthi, Suresh Babu; Unselt, Desiree; Hankins, Gerald; Park, Minkyu; Choi, Doil; Nimmakayala, Padma

2014-01-01

Pepper (Capsicum annuum L.) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse Capsicum annuum collection during two seasons. The genes Pun1, CCR, KAS and HCT were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed Pun1 as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of Pun1 were found associated with capsaicin in plants from both seasons. Our results support that CCR is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. KAS was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of Pun1 suggested that the accumulation of capsaicinoids depends on the expression of Pun1, as revealed by the most important associated SNPs found in the promoter region of Pun1.

Identification of Gene-Specific Polymorphisms and Association with Capsaicin Pathway Metabolites in Capsicum annuum L. Collections

PubMed Central

Abburi, Venkata L.; Alaparthi, Suresh Babu; Unselt, Desiree; Hankins, Gerald; Park, Minkyu; Choi, Doil

2014-01-01

Pepper (Capsicum annuum L.) is an economically important crop with added nutritional value. Production of capsaicin is an important quantitative trait with high environmental variance, so the development of markers regulating capsaicinoid accumulation is important for pepper breeding programs. In this study, we performed association mapping at the gene level to identify single nucleotide polymorphisms (SNPs) associated with capsaicin pathway metabolites in a diverse Capsicum annuum collection during two seasons. The genes Pun1, CCR, KAS and HCT were sequenced and matched with the whole-genome sequence draft of pepper to identify SNP locations and for further characterization. The identified SNPs for each gene underwent candidate gene association mapping. Association mapping results revealed Pun1 as a key regulator of major metabolites in the capsaicin pathway mainly affecting capsaicinoids and precursors for acyl moieties of capsaicinoids. Six different SNPs in the promoter sequence of Pun1 were found associated with capsaicin in plants from both seasons. Our results support that CCR is an important control point for the flux of p-coumaric acid to specific biosynthesis pathways. KAS was found to regulate the major precursors for acyl moieties of capsaicinoids and may play a key role in capsaicinoid production. Candidate gene association mapping of Pun1 suggested that the accumulation of capsaicinoids depends on the expression of Pun1, as revealed by the most important associated SNPs found in the promoter region of Pun1. PMID:24475113

Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors.

PubMed

Alberti-Servera, Llucia; von Muenchow, Lilly; Tsapogas, Panagiotis; Capoferri, Giuseppina; Eschbach, Katja; Beisel, Christian; Ceredig, Rhodri; Ivanek, Robert; Rolink, Antonius

2017-12-15

Single-cell RNA sequencing is a powerful technology for assessing heterogeneity within defined cell populations. Here, we describe the heterogeneity of a B220 + CD117 int CD19 - NK1.1 - uncommitted hematopoietic progenitor having combined lymphoid and myeloid potential. Phenotypic and functional assays revealed four subpopulations within the progenitor with distinct lineage developmental potentials. Among them, the Ly6D + SiglecH - CD11c - fraction was lymphoid-restricted exhibiting strong B-cell potential, whereas the Ly6D - SiglecH - CD11c - fraction showed mixed lympho-myeloid potential. Single-cell RNA sequencing of these subsets revealed that the latter population comprised a mixture of cells with distinct lymphoid and myeloid transcriptional signatures and identified a subgroup as the potential precursor of Ly6D + SiglecH - CD11c - Subsequent functional assays confirmed that B220 + CD117 int CD19 - NK1.1 - single cells are, with rare exceptions, not bipotent for lymphoid and myeloid lineages. A B-cell priming gradient was observed within the Ly6D + SiglecH - CD11c - subset and we propose a herein newly identified subgroup as the direct precursor of the first B-cell committed stage. Therefore, the apparent multipotency of B220 + CD117 int CD19 - NK1.1 - progenitors results from underlying heterogeneity at the single-cell level and highlights the validity of single-cell transcriptomics for resolving cellular heterogeneity and developmental relationships among hematopoietic progenitors. © 2017 The Authors.

Impact of synoptic weather patterns on 24 h-average PM2.5 concentrations in the North China Plain during 2013-2017.

PubMed

Zhang, Hao; Yuan, Haiou; Liu, Xiaohui; Yu, Junyi; Jiao, Yongli

2018-06-15

North China Plain area (NCP) is one of the most densely populated and heavily polluted regions in the world. In the last five years, frequently happened fine particulate matter (PM 2.5 ) serious pollution events were one of the top environmental concerns in China. As PM 2.5 concentrations are highly influenced by synoptic flow patterns and local meteorological conditions, a two-stage hierarchical clustering method based on dynamic principal component analysis (DPCA) and standard k-means clustering algorithm was employed to classify synoptic wind fields into 6 patterns over the NCP area using the data of 5 PM 2.5 seasons (Sept. 15th-Apr. 15th) from 2013 to 2017. Among the six identified synoptic patterns, pattern of uniform pressure field (U) and that of zonal high pressure (Z H ) accounted for 78.21%, 65.55%, 63.56%, 57.11%, 59.13% and 58.27% studied heavy smog pollution events in Beijing, Tianjin, Tangshan, Baoding, Shijiazhuang and Xingtai city. The two particular patterns were associated with uniform pressure field and sparsely latitudinal isobar in 850 hPa level, respectively. They were also characterized by high relative humidity, low temperature, low-speed northerly wind in Tianjin and Tangshan, and southerly wind in the other cities. Under the continuous control of pattern Z H , the values of 24 h-average PM 2.5 were found to increase at a rate of 31.78 μg/m 3 per day. To evaluate the contribution of meteorological factors and precursors to PM 2.5 levels, linear mixed-effects models (LMMs) were applied to establish relations among 24 h-average PM 2.5 concentrations, concentrations of main precursors, local meteorological factors and synoptic patterns. Results show that the variations of precursors, local meteorological factors and synoptic flow patterns can explain 51.67%, 19.15% and 14.01% changes of the 24 h-average PM 2.5 concentrations, respectively. This study illustrates that dense precursor emissions are still the main cause for heavy haze pollution events, although meteorological conditions play almost equal roles sometimes. Copyright © 2018 Elsevier B.V. All rights reserved.

Cataloging the 1811-1812 New Madrid, central U.S., earthquake sequence

USGS Publications Warehouse

Hough, S.E.

2009-01-01

The three principal New Madrid, central U.S., mainshocks of 1811-1812 were followed by extensive aftershock sequences that included numerous felt events. Although no instrumental data are available for the sequence, historical accounts provide information that can be used to estimate magnitudes and locations for the large aftershocks as well as the mainshocks. Several detailed eyewitness accounts of the sequence provide sufficient information to identify times and rough magnitude estimates for a number of aftershocks that have not been analyzed previously. I also use three extended compilations of felt events to explore the overall sequence productivity. Although one generally cannot estimate magnitudes or locations for individual events, the intensity distributions of recent, instrumentally recorded earthquakes in the region provide a basis for estimation of the magnitude distribution of 1811-1812 aftershocks. The distribution is consistent with a b-value distribution. I estimate Mw 6-6.3 for the three largest identifiable aftershocks, apart from the so-called dawn aftershock on 16 December 1811.

The RNase P RNA from cyanobacteria: short tandemly repeated repetitive (STRR) sequences are present within the RNase P RNA gene in heterocyst-forming cyanobacteria.

PubMed Central

Vioque, A

1997-01-01

The RNase P RNA gene (rnpB) from 10 cyanobacteria has been characterized. These new RNAs, together with the previously available ones, provide a comprehensive data set of RNase P RNA from diverse cyanobacterial lineages. All heterocystous cyanobacteria, but none of the non-heterocystous strains analyzed, contain short tandemly repeated repetitive (STRR) sequences that increase the length of helix P12. Site-directed mutagenesis experiments indicate that the STRR sequences are not required for catalytic activity in vitro. STRR sequences seem to have recently and independently invaded the RNase P RNA genes in heterocyst-forming cyanobacteria because closely related strains contain unrelated STRR sequences. Most cyanobacteria RNase P RNAs lack the sequence GGU in the loop connecting helices P15 and P16 that has been established to interact with the 3'-end CCA in precursor tRNA substrates in other bacteria. This character is shared with plastid RNase P RNA. Helix P6 is longer than usual in most cyanobacteria as well as in plastid RNase P RNA. PMID:9254706

Cloning and purification of alpha-neurotoxins from king cobra (Ophiophagus hannah).

PubMed

He, Ying-Ying; Lee, Wei-Hui; Zhang, Yun

2004-09-01

Thirteen complete and three partial cDNA sequences were cloned from the constructed king cobra (Ophiophagus hannah) venom gland cDNA library. Phylogenetic analysis of nucleotide sequences of king cobra with those from other snake venoms revealed that obtained cDNAs are highly homologous to snake venom alpha-neurotoxins. Alignment of deduced mature peptide sequences of the obtained clones with those of other reported alpha-neurotoxins from the king cobra venom indicates that our obtained 16 clones belong to long-chain neurotoxins (seven), short-chain neurotoxins (seven), weak toxin (one) and variant (one), respectively. Up to now, two out of 16 newly cloned king cobra alpha-neurotoxins have identical amino acid sequences with CM-11 and Oh-6A/6B, which have been characterized from the same venom. Furthermore, five long-chain alpha-neurotoxins and two short-chain alpha-neurotoxins were purified from crude venom and their N-terminal amino acid sequences were determined. The cDNAs encoding the putative precursors of the purified native peptide were also determined based on the N-terminal amino acid sequencing. The purified alpha-neurotoxins showed different lethal activities on mice.

NASA RapidScat Observes El Nino Blowing in the Winds

NASA Image and Video Library

2016-01-21

While El Niño events have a significant impact on the entire Earth System, they are most easily visible in measurements of sea surface temperature (SST), sea surface height (SSH) and ocean winds near the surface. In fact, the precursor and the main driver of El Niño events is manifested in the weakening of the normally westward blowing trade winds, or even their complete reversal to blow from west to east, in the Western and Central tropical Pacific. http://photojournal.jpl.nasa.gov/catalog/PIA20365

Large-scale transcriptome sequencing and gene analyses in the crab-eating macaque (Macaca fascicularis) for biomedical research

PubMed Central

2012-01-01

Background As a human replacement, the crab-eating macaque (Macaca fascicularis) is an invaluable non-human primate model for biomedical research, but the lack of genetic information on this primate has represented a significant obstacle for its broader use. Results Here, we sequenced the transcriptome of 16 tissues originated from two individuals of crab-eating macaque (male and female), and identified genes to resolve the main obstacles for understanding the biological response of the crab-eating macaque. From 4 million reads with 1.4 billion base sequences, 31,786 isotigs containing genes similar to those of humans, 12,672 novel isotigs, and 348,160 singletons were identified using the GS FLX sequencing method. Approximately 86% of human genes were represented among the genes sequenced in this study. Additionally, 175 tissue-specific transcripts were identified, 81 of which were experimentally validated. In total, 4,314 alternative splicing (AS) events were identified and analyzed. Intriguingly, 10.4% of AS events were associated with transposable element (TE) insertions. Finally, investigation of TE exonization events and evolutionary analysis were conducted, revealing interesting phenomena of human-specific amplified trends in TE exonization events. Conclusions This report represents the first large-scale transcriptome sequencing and genetic analyses of M. fascicularis and could contribute to its utility for biomedical research and basic biology. PMID:22554259

Effects of a Training Package to Improve the Accuracy of Descriptive Analysis Data Recording

ERIC Educational Resources Information Center

Mayer, Kimberly L.; DiGennaro Reed, Florence D.

2013-01-01

Functional behavior assessment is an important precursor to developing interventions to address a problem behavior. Descriptive analysis, a type of functional behavior assessment, is effective in informing intervention design only if the gathered data accurately capture relevant events and behaviors. We investigated a training procedure to improve…

Visualization of Sedentary Behavior Using an Event-Based Approach

ERIC Educational Resources Information Center

Loudon, David; Granat, Malcolm H.

2015-01-01

Visualization is commonly used in the interpretation of physical behavior (PB) data, either in conjunction with or as precursor to formal analysis. Effective representations of the data can enable the identification of patterns of behavior, and how they relate to the temporal context in a single day, or across multiple days. An understanding of…

Magma hybridization in the Western Tatra Mts. granitoid intrusion (S-Poland, Western Carpathians).

PubMed

Burda, Jolanta; Gawęda, Aleksandra; Klötzli, Urs

In the Variscan Western Tatra granites hybridization phenomena such as mixing and mingling can be observed at the contact of mafic precursors of dioritic composition and more felsic granitic host rocks. The textural evidence of hybridization include: plagioclase-K-feldspar-sphene ocelli, hornblende- and biotite-rimmed quartz ocelli, plagioclase with Ca-rich spike zonation, inversely zoned K-feldspar crystals, mafic clots, poikilitic plagioclase and quartz crystals, mixed apatite morphologies, zoned K-feldspar phenocrysts. The apparent pressure range of the magma hybridization event was calculated at 6.1 kbar to 4.6 kbar, while the temperature, calculated by independent methods, is in the range of 810°C-770°C. U-Pb age data of the hybrid rocks were obtained by in-situ LA-MC-ICP-MS analysis of zircon. The oscillatory zoned zircon crystals yield a concordia age of 368 ± 8 Ma (MSWD = 1.1), interpreted as the age of magma hybridization and timing of formation of the magmatic precursors. It is the oldest Variscan magmatic event in that part of the Tatra Mountains.

Anomalous low tropospheric column ozone over eastern India during the severe drought event of monsoon 2002: a case study.

PubMed

Ghude, Sachin D; Kulkarni, Santosh H; Kulkarni, Pavan S; Kanawade, Vijay P; Fadnavis, Suvarna; Pokhrel, Samir; Jena, Chinmay; Beig, G; Bortoli, D

2011-09-01

The present study is an attempt to examine some of the probable causes of the unusually low tropospheric column ozone observed over eastern India during the exceptional drought event in July 2002. We examined horizontal wind and omega (vertical velocity) anomalies over the Indian region to understand the large-scale dynamical processes which prevailed in July 2002. We also examined anomalies in tropospheric carbon monoxide (CO), an important ozone precursor, and observed low CO mixing ratio in the free troposphere in 2002 over eastern India. It was found that instead of a normal large-scale ascent, the air was descending in the middle and lower troposphere over a vast part of India. This configuration was apparently responsible for the less convective upwelling of precursors and likely caused less photochemical ozone formation in the free troposphere over eastern India in July 2002. The insight gained from this case study will hopefully provide a better understanding of the process controlling the distribution of the tropospheric ozone over the Indian region.

Basophile: Accurate Fragment Charge State Prediction Improves Peptide Identification Rates

DOE PAGES

Wang, Dong; Dasari, Surendra; Chambers, Matthew C.; ...

2013-03-07

In shotgun proteomics, database search algorithms rely on fragmentation models to predict fragment ions that should be observed for a given peptide sequence. The most widely used strategy (Naive model) is oversimplified, cleaving all peptide bonds with equal probability to produce fragments of all charges below that of the precursor ion. More accurate models, based on fragmentation simulation, are too computationally intensive for on-the-fly use in database search algorithms. We have created an ordinal-regression-based model called Basophile that takes fragment size and basic residue distribution into account when determining the charge retention during CID/higher-energy collision induced dissociation (HCD) of chargedmore » peptides. This model improves the accuracy of predictions by reducing the number of unnecessary fragments that are routinely predicted for highly-charged precursors. Basophile increased the identification rates by 26% (on average) over the Naive model, when analyzing triply-charged precursors from ion trap data. Basophile achieves simplicity and speed by solving the prediction problem with an ordinal regression equation, which can be incorporated into any database search software for shotgun proteomic identification.« less

Signaling Networks among Stem Cell Precursors, Transit-Amplifying Progenitors, and their Niche in Developing Hair Follicles.

PubMed

Rezza, Amélie; Wang, Zichen; Sennett, Rachel; Qiao, Wenlian; Wang, Dongmei; Heitman, Nicholas; Mok, Ka Wai; Clavel, Carlos; Yi, Rui; Zandstra, Peter; Ma'ayan, Avi; Rendl, Michael

2016-03-29

The hair follicle (HF) is a complex miniorgan that serves as an ideal model system to study stem cell (SC) interactions with the niche during growth and regeneration. Dermal papilla (DP) cells are required for SC activation during the adult hair cycle, but signal exchange between niche and SC precursors/transit-amplifying cell (TAC) progenitors that regulates HF morphogenetic growth is largely unknown. Here we use six transgenic reporters to isolate 14 major skin and HF cell populations. With next-generation RNA sequencing, we characterize their transcriptomes and define unique molecular signatures. SC precursors, TACs, and the DP niche express a plethora of ligands and receptors. Signaling interaction network analysis reveals a bird's-eye view of pathways implicated in epithelial-mesenchymal interactions. Using a systematic tissue-wide approach, this work provides a comprehensive platform, linked to an interactive online database, to identify and further explore the SC/TAC/niche crosstalk regulating HF growth. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

The organization of prospective thinking: evidence of event clusters in freely generated future thoughts.

PubMed

Demblon, Julie; D'Argembeau, Arnaud

2014-02-01

Recent research suggests that many imagined future events are not represented in isolation, but instead are embedded in broader event sequences-referred to as event clusters. It remains unclear, however, whether the production of event clusters reflects the underlying organizational structure of prospective thinking or whether it is an artifact of the event-cuing task in which participants are explicitly required to provide chains of associated future events. To address this issue, the present study examined whether the occurrence of event clusters in prospective thought is apparent when people are left to think freely about events that might happen in their personal future. The results showed that the succession of events participants spontaneously produced when envisioning their future frequently included event clusters. This finding provides more compelling evidence that prospective thinking involves higher-order autobiographical knowledge structures that organize imagined events in coherent themes and sequences. Copyright © 2014 Elsevier Inc. All rights reserved.

On the predictability of individual events in power-law systems

NASA Astrophysics Data System (ADS)

de, Rumi

2006-11-01

We consider a modified Burridge-Knopoff model with a view to understand results of acoustic emission (AE) relevant to earthquakes by adding a dissipative term which mimics bursts of acous- tic signals. Interestingly, we find a precursor effect in the cumulative energy dissipated which allows identification of a large slip event. Further, the AE activity for several large slip events follows a universal stretched exponential behavior with corrections in terms of time-to-failure. We find that many features of the statistics of AE signals such as their amplitudes, durations and the intervals between successive AE bursts obey power laws consistent with recent experimental results. Large magnitude events have different power law from that of the small ones, the latter being sensitive to the pulling speed.

Involuntary memory chaining versus event cueing: Which is a better indicator of autobiographical memory organisation?

PubMed

Mace, John H; Clevinger, Amanda M; Martin, Cody

2010-11-01

Involuntary memory chains are spontaneous recollections of the past that occur in a sequence. Much like semantic memory priming, this memory phenomenon has provided some insights into the nature of associations in autobiographical memory. The event-cueing procedure (a laboratory-based memory sequencing task) has also provided some insights into the nature of autobiographical memory organisation. However, while both of these memory-sequencing phenomena have exhibited the same types of memory associations (conceptual associations and general-event or temporal associations), both have also produced discrepant results with respect to the relative proportions of such associations. This study investigated the possibility that the results from event cueing are artefacts of various memory production responses. Using a number of different approaches we demonstrated that these memory production responses cause overestimates of general-event association. We conclude that for this reason, the data from involuntary memory chains provide a better picture of the organisation of autobiographical memory.

Querying Event Sequences by Exact Match or Similarity Search: Design and Empirical Evaluation

PubMed Central

Wongsuphasawat, Krist; Plaisant, Catherine; Taieb-Maimon, Meirav; Shneiderman, Ben

2012-01-01

Specifying event sequence queries is challenging even for skilled computer professionals familiar with SQL. Most graphical user interfaces for database search use an exact match approach, which is often effective, but near misses may also be of interest. We describe a new similarity search interface, in which users specify a query by simply placing events on a blank timeline and retrieve a similarity-ranked list of results. Behind this user interface is a new similarity measure for event sequences which the users can customize by four decision criteria, enabling them to adjust the impact of missing, extra, or swapped events or the impact of time shifts. We describe a use case with Electronic Health Records based on our ongoing collaboration with hospital physicians. A controlled experiment with 18 participants compared exact match and similarity search interfaces. We report on the advantages and disadvantages of each interface and suggest a hybrid interface combining the best of both. PMID:22379286

Margaret F. Washburn in The American Journal of Psychology: A Cognitive Precursor?

PubMed

Boyano, Jose T

2017-01-01

In the early 20th century, Margaret F. Washburn (1871-1939) produced numerous studies on perception, affective value of stimulus, memory, emotions, and consciousness. This experimental work was published in The American Journal of Psychology. The purpose of this article is to analyze the temporal evolution of these kinds of experiments and relate them to Washburn's theoretical production. Contrary to other views, Washburn's experimental evolution follows a logical sequence and has a strong inner coherence. Among other reasons, the lack of a scientific and social framework to the study of the mind has tended to overshadow large areas of Washburn's thought. However, both the work published in AJP and the methods used in experiments provide reasons to consider.Washburn one of the precursors of contemporary cognitive psychology.

The origin of free brain malonate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Riley, K.M.; Dickson, A.C.; Koeppen, A.H.

Rat brain contains substantial concentrations of free malonate (192 nmol/g wet weight) but origin and biological importance of the dicarboxylic acid are poorly understood. A dietary source has been excluded. A recently described malonyl-CoA decarboxylase deficiency is associated with malonic aciduria and clinical manifestations, including mental retardation. In an effort to study the metabolic origin of free malonate, several labeled acetyl-CoA precursors were administered by intracerebral injection. (2-14C)pyruvate or (1,5-14C)citrate produced radioactive glutamate but failed to label malonate. In contrast, (1-14C)acetate, (2-14C)acetate, and (1-14C)butyrate were converted to labeled glutamate and malonate after the same route of administration. The intracerebral injectionmore » of (1-14C)-beta-alanine as a precursor of malonic semialdehyde and possibly free malonate did not give rise to radioactivity in the dicarboxylate. The labeling pattern of malonic acid is compatible with the reaction sequence: acetyl-CoA----malonyl-CoA----malonate. The final step is thought to occur by transfer of the CoA-group from malonyl-CoA to succinate and/or acetoacetate. Labeling of malonate from acetate is most effective at the age of 7 days when the net concentration of the dicarboxylic acid in rat brain is still very low. At this age, butyrate was a better precursor of malonate than acetate. It is proposed that fatty acid oxidation provides the acetyl-CoA which functions as the precursor of free brain malonate. Compartmentation of malonate biosynthesis is likely because the acetyl-CoA precursors citrate and pyruvate are ineffective.« less

Plant polycistronic precursors containing non-homologous microRNAs target transcripts encoding functionally related proteins

PubMed Central

2009-01-01

Background MicroRNAs (miRNAs) are endogenous single-stranded small RNAs that regulate the expression of specific mRNAs involved in diverse biological processes. In plants, miRNAs are generally encoded as a single species in independent transcriptional units, referred to as MIRNA genes, in contrast to animal miRNAs, which are frequently clustered. Results We performed a comparative genomic analysis in three model plants (rice, poplar and Arabidopsis) and characterized miRNA clusters containing two to eight miRNA species. These clusters usually encode miRNAs of the same family and certain share a common evolutionary origin across monocot and dicot lineages. In addition, we identified miRNA clusters harboring miRNAs with unrelated sequences that are usually not evolutionarily conserved. Strikingly, non-homologous miRNAs from the same cluster were predicted to target transcripts encoding related proteins. At least four Arabidopsis non-homologous clusters were expressed as single transcriptional units. Overexpression of one of these polycistronic precursors, producing Ath-miR859 and Ath-miR774, led to the DCL1-dependent accumulation of both miRNAs and down-regulation of their different mRNA targets encoding F-box proteins. Conclusions In addition to polycistronic precursors carrying related miRNAs, plants also contain precursors allowing coordinated expression of non-homologous miRNAs to co-regulate functionally related target transcripts. This mechanism paves the way for using polycistronic MIRNA precursors as a new molecular tool for plant biologists to simultaneously control the expression of different genes. PMID:19951405

Using Groundwater physiochemical properties for assessing potential earthquake precursor

NASA Astrophysics Data System (ADS)

Inbar, Nimrod; Reuveni, Yuval; Anker, Yaakov; Guttman, Joseph

2017-04-01

Worldwide studies reports pre-seismic, co-seismic and post-seismic reaction of groundwater to earthquakes. The unique hydrological and geological situation in Israel resulted in relatively deep water wells which are located close to seismically active tectonic plate boundary. Moreover, the Israeli experience show that anomalies may occurs 60-90 minutes prior to the seismic event (Guttman et al., 2005; Anker et al., 2016). Here, we try to assess the possible connection between changes in physiochemical parameters of groundwater and earthquakes along the Dead Sea Transform (DST) region. A designated network of monitoring stations was installed in MEKOROT abandoned deep water wells, continuously measuring water table, conductivity and temperature at a sampling rate of 1 minute. Preliminary analysis compares changes in the measured parameters with rain events, tidal effects and earthquake occurrences of all measured magnitudes (>2.5Md) at monitoring area surroundings. The acquired data set over one year recorded simultaneous abrupt changes in several wells which seems disconnected from standard hydrological occurrences such as precipitation, abstraction or tidal effects. At this stage, our research aims to determine and rationalize a baseline for "normal response" of the measured parameters to external occurrences while isolating those cases in which "deviations" from that base line is recorded. We apply several analysis techniques both in time and frequency domain with the measured signal as well as statistical analysis of several measured earthquake parameters, which indicate potential correlations between earthquakes occurrences and the measured signal. We show that at least in one seismic event (5.1 Md) a potential precursor may have been recorded. Reference: Anker, Y., N. Inbar, A. Y. Dror, Y. Reuveni, J. Guttman, A. Flexer, (2016). Groundwater response to ground movements, as a tool for earthquakes monitoring and a possible precursor. 8th International Conference on Urban Planning and Transportation. Guttman, J., Flexer, A. & Yellin-Dror, A. (2005). Water level changes in wells - a predictor for earthquakes? IAHS Publ. Vol. 303, pp. 1-5.

Speed, Accuracy, and Serial Order in Sequence Production

ERIC Educational Resources Information Center

Pfordresher, Peter Q.; Palmer, Caroline; Jungers, Melissa K.

2007-01-01

The production of complex sequences like music or speech requires the rapid and temporally precise production of events (e.g., notes and chords), often at fast rates. Memory retrieval in these circumstances may rely on the simultaneous activation of both the current event and the surrounding context (Lashley, 1951). We describe an extension to a…

Coping with Volume and Variety in Temporal Event Sequences: Strategies for Sharpening Analytic Focus.

PubMed

Fan Du; Shneiderman, Ben; Plaisant, Catherine; Malik, Sana; Perer, Adam

2017-06-01

The growing volume and variety of data presents both opportunities and challenges for visual analytics. Addressing these challenges is needed for big data to provide valuable insights and novel solutions for business, security, social media, and healthcare. In the case of temporal event sequence analytics it is the number of events in the data and variety of temporal sequence patterns that challenges users of visual analytic tools. This paper describes 15 strategies for sharpening analytic focus that analysts can use to reduce the data volume and pattern variety. Four groups of strategies are proposed: (1) extraction strategies, (2) temporal folding, (3) pattern simplification strategies, and (4) iterative strategies. For each strategy, we provide examples of the use and impact of this strategy on volume and/or variety. Examples are selected from 20 case studies gathered from either our own work, the literature, or based on email interviews with individuals who conducted the analyses and developers who observed analysts using the tools. Finally, we discuss how these strategies might be combined and report on the feedback from 10 senior event sequence analysts.

gr-MRI: A software package for magnetic resonance imaging using software defined radios

NASA Astrophysics Data System (ADS)

Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

2016-09-01

The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

Simultaneous Characterization of Somatic Events and HPV-18 Integration in a Metastatic Cervical Carcinoma Patient Using DNA and RNA Sequencing

PubMed Central

Liang, Winnie S.; Aldrich, Jessica; Nasser, Sara; Kurdoglu, Ahmet; Phillips, Lori; Reiman, Rebecca; McDonald, Jacquelyn; Izatt, Tyler; Christoforides, Alexis; Baker, Angela; Craig, Christine; Egan, Jan B.; Chase, Dana M.; Farley, John H.; Bryce, Alan H.; Stewart, A. Keith; Borad, Mitesh J.; Carpten, John D.; Craig, David W.; Monk, Bradley J.

2014-01-01

Objective Integration of carcinogenic human papillomaviruses (HPVs) into the host genome is a significant tumorigenic factor in specific cancers including cervical carcinoma. Although major strides have been made with respect to HPV diagnosis and prevention, identification and development of efficacious treatments for cervical cancer patients remains a goal and thus requires additional detailed characterization of both somatic events and HPV integration. Given this need, the goal of this study was to use the next generation sequencing to simultaneously evaluate somatic alterations and expression changes in a patient’s cervical squamous carcinoma lesion metastatic to the lung and to detect and analyze HPV infection in the same sample. Materials and Methods We performed tumor and normal exome, tumor and normal shallow whole-genome sequencing, and RNA sequencing of the patient’s lung metastasis. Results We generated over 1.2 billion mapped reads and identified 130 somatic point mutations and indels, 21 genic translocations, 16 coding regions demonstrating copy number changes, and over 36 genes demonstrating altered expression in the tumor (corrected P < 0.05). Sequencing also revealed the HPV type 18 (HPV-18) integration in the metastasis. Using both DNA and RNA reads, we pinpointed 3 major events indicating HPV-18 integration into an intronic region of chromosome 6p25.1 in the patient’s tumor and validated these events with Sanger sequencing. This integration site has not been reported for HPV-18. Conclusions We demonstrate that DNA and RNA sequencing can be used to concurrently characterize somatic alterations and expression changes in a biopsy and delineate HPV integration at base resolution in cervical cancer. Further sequencing will allow us to better understand the molecular basis of cervical cancer pathogenesis. PMID:24418928

Thermal and chemical evolution in the early solar system as recorded by FUN CAIs: Part I - Petrology, mineral chemistry, and isotopic composition of Allende FUN CAI CMS-1

NASA Astrophysics Data System (ADS)

Williams, C. D.; Ushikubo, T.; Bullock, E. S.; Janney, P. E.; Hines, R. R.; Kita, N. T.; Hervig, R. L.; MacPherson, G. J.; Mendybaev, R. A.; Richter, F. M.; Wadhwa, M.

2017-03-01

Detailed petrologic, geochemical and isotopic analyses of a new FUN CAI from the Allende CV3 meteorite (designated CMS-1) indicate that it formed by extensive melting and evaporation of primitive precursor material(s). The precursor material(s) condensed in a 16O-rich region (δ17O and δ18O ∼ -49‰) of the inner solar nebula dominated by gas of solar composition at total pressures of ∼10-3-10-6 bar. Subsequent melting of the precursor material(s) was accompanied by evaporative loss of magnesium, silicon and oxygen resulting in large mass-dependent isotope fractionations in these elements (δ25Mg = 30.71-39.26‰, δ29Si = 14.98-16.65‰, and δ18O = -41.57 to -15.50‰). This evaporative loss resulted in a bulk composition similar to that of compact Type A and Type B CAIs, but very distinct from the composition of the original precursor condensate(s). Kinetic fractionation factors and the measured mass-dependent fractionation of silicon and magnesium in CMS-1 suggest that ∼80% of the silicon and ∼85% of the magnesium were lost from its precursor material(s) through evaporative processes. These results suggest that the precursor material(s) of normal and FUN CAIs condensed in similar environments, but subsequently evolved under vastly different conditions such as total gas pressure. The chemical and isotopic differences between normal and FUN CAIs could be explained by sorting of early solar system materials into distinct physical and chemical regimes, in conjunction with discrete heating events, within the protoplanetary disk.

Determining sources of dissolved organic carbon and disinfection byproduct precursors to the McKenzie River, Oregon

USGS Publications Warehouse

Kraus, Tamara E.C.; Anderson, Chauncey W.; Morgenstern, Karl; Downing, Bryan D.; Pellerin, Brian A.; Bergamaschi, Brian A.

2010-01-01

This study was conducted to determine the main sources of dissolved organic carbon (DOC) and disinfection byproduct (DBP) precursors to the McKenzie River, Oregon (USA). Water samples collected from the mainstem, tributaries, and reservoir outflows were analyzed for DOC concentration and DBP formation potentials (trihalomethanes [THMFPs] and haloacetic acids [HAAFPs]). In addition, optical properties (absorbance and fluorescence) of dissolved organic matter (DOM) were measured to provide insight into DOM composition and assess whether optical properties are useful proxies for DOC and DBP precursor concentrations. Optical properties indicative of composition suggest that DOM in the McKenzie River mainstem was primarily allochthonous - derived from soils and plant material in the upstream watershed. Downstream tributaries had higher DOC concentrations than mainstem sites (1.6 ?? 0.4 vs. 0.7 ?? 0.3 mg L-1) but comprised <5% of mainstem flows and had minimal effect on overall DBP precursor loads. Water exiting two large upstream reservoirs also had higher DOC concentrations than the mainstem site upstream of the reservoirs, but optical data did not support in situ algal production as a source of the added DOC during the study. Results suggest that the first major rain event in the fall contributes DOM with high DBP precursor content. Although there was interference in the absorbance spectra in downstream tributary samples, fluorescence data were strongly correlated to DOC concentration (R 2 = 0.98), THMFP (R2 = 0.98), and HAAFP (R2 = 0.96). These results highlight the value of using optical measurements for identifying the concentration and sources of DBP precursors in watersheds, which will help drinking water utilities improve source water monitoring and management programs. Copyright ?? 2010 by the American Society of Agronomy.

Flexible theta sequence compression mediated via phase precessing interneurons

PubMed Central

Chadwick, Angus; van Rossum, Mark CW; Nolan, Matthew F

2016-01-01

Encoding of behavioral episodes as spike sequences during hippocampal theta oscillations provides a neural substrate for computations on events extended across time and space. However, the mechanisms underlying the numerous and diverse experimentally observed properties of theta sequences remain poorly understood. Here we account for theta sequences using a novel model constrained by the septo-hippocampal circuitry. We show that when spontaneously active interneurons integrate spatial signals and theta frequency pacemaker inputs, they generate phase precessing action potentials that can coordinate theta sequences in place cell populations. We reveal novel constraints on sequence generation, predict cellular properties and neural dynamics that characterize sequence compression, identify circuit organization principles for high capacity sequential representation, and show that theta sequences can be used as substrates for association of conditioned stimuli with recent and upcoming events. Our results suggest mechanisms for flexible sequence compression that are suited to associative learning across an animal’s lifespan. DOI: http://dx.doi.org/10.7554/eLife.20349.001 PMID:27929374

SBLOCA outside containment at Browns Ferry Unit One: accident sequence analysis. [Small break

DOE Office of Scientific and Technical Information (OSTI.GOV)

Condon, W.A.; Harrington, R.M.; Greene, S.R.

1982-11-01

This study describes the predicted response of Unit 1 at the Browns Ferry Nuclear Plant to a postulated small-break loss-of-coolant accident outside of the primary containment. The break has been assumed to occur in the scram discharge volume piping immediately following a reactor scram that cannot be reset. The events before core uncovering are discussed for both the worst-case accident sequence without operator action and for the more likely sequences with operator action. Without operator action, the events after core uncovering would include core meltdown and subsequent containment failure, and this event sequence has been determined through use of themore » MARCH code. An estimate of the magnitude and timing of the concomitant release of the noble gas, cesium, and iodine-based fission products to the environment is provided in Volume 2 of this report.« less

Rapidly rotating neutron stars in general relativity: Realistic equations of state

NASA Technical Reports Server (NTRS)

Cook, Gregory B.; Shapiro, Stuart L.; Teukolsky, Saul A.

1994-01-01

We construct equilibrium sequences of rotating neutron stars in general relativity. We compare results for 14 nuclear matter equations of state. We determine a number of important physical parameters for such stars, including the maximum mass and maximum spin rate. The stability of the configurations to quasi-radial perturbations is assessed. We employ a numerical scheme particularly well suited to handle rapid rotation and large departures from spherical symmetry. We provide an extensive tabulation of models for future reference. Two classes of evolutionary sequences of fixed baryon rest mass and entropy are explored: normal sequences, which behave very much like Newtonian sequences, and supramassive sequences, which exist for neutron stars solely because of general relativistic effects. Adiabatic dissipation of energy and angular momentum causes a star to evolve in quasi-stationary fashion along an evolutionary sequence. Supramassive sequences have masses exceeding the maximum mass of a nonrotating neutron star. A supramassive star evolves toward eventual catastrophic collapse to a black hole. Prior to collapse, the star actually spins up as it loses angular momentum, an effect that may provide an observable precursor to gravitational collapse to a black hole.

Working Memory Replay Prioritizes Weakly Attended Events.

PubMed

Jafarpour, Anna; Penny, Will; Barnes, Gareth; Knight, Robert T; Duzel, Emrah

2017-01-01

One view of working memory posits that maintaining a series of events requires their sequential and equal mnemonic replay. Another view is that the content of working memory maintenance is prioritized by attention. We decoded the dynamics for retaining a sequence of items using magnetoencephalography, wherein participants encoded sequences of three stimuli depicting a face, a manufactured object, or a natural item and maintained them in working memory for 5000 ms. Memory for sequence position and stimulus details were probed at the end of the maintenance period. Decoding of brain activity revealed that one of the three stimuli dominated maintenance independent of its sequence position or category; and memory was enhanced for the selectively replayed stimulus. Analysis of event-related responses during the encoding of the sequence showed that the selectively replayed stimuli were determined by the degree of attention at encoding. The selectively replayed stimuli had the weakest initial encoding indexed by weaker visual attention signals at encoding. These findings do not rule out sequential mnemonic replay but reveal that attention influences the content of working memory maintenance by prioritizing replay of weakly encoded events. We propose that the prioritization of weakly encoded stimuli protects them from interference during the maintenance period, whereas the more strongly encoded stimuli can be retrieved from long-term memory at the end of the delay period.

Y2O3-MgO Nano-Composite Synthesized by Plasma Spraying and Thermal Decomposition of Solution Precursors

NASA Astrophysics Data System (ADS)

Muoto, Chigozie Kenechukwu

This research aims to identify the key feedstock characteristics and processing conditions to produce Y2O3-MgO composite coatings with high density and hardness using solution precursor plasma spray (SPPS) and suspension plasma spray (SPS) processes, and also, to explore the phenomena involved in the production of homogenized nano-composite powders of this material system by thermal decomposition of solution precursor mixtures. The material system would find potential application in the fabrication of components for optical applications such as transparent windows. It was shown that a lack of major endothermic events during precursor decomposition and the resultant formation of highly dense particles upon pyrolysis are critical precursor characteristics for the deposition of dense and hard Y2O3-MgO coatings by SPPS. Using these principles, a new Y2O3-MgO precursor solution was developed, which yielded a coating with Vickers hardness of 560 Hv. This was a considerable improvement over the hardness of the coatings obtained using conventional solution precursors, which was as low as 110 Hv. In the thermal decomposition synthesis process, binary solution precursor mixtures of: yttrium nitrate (Y[n]) or yttrium acetate (Y[a]), with magnesium nitrate (Mg[n]) or magnesium acetate (Mg[a]) were used in order to study the effects of precursor chemistry on the structural characteristics of the resultant Y2O3-MgO powders. The phase domains were coarse and distributed rather inhomogeneously in the materials obtained from the Y[n]Mg[n] and Y[a]Mg[a] mixtures; finer and more homogeneously-distributed phase domains were obtained for ceramics produced from the Y[a]Mg[n] and Y[n]Mg[a] mixtures. It was established that these phenomena were related to the thermal characteristics for the decomposition of the precursors and their effect on phase separation during oxide crystallization. Addition of ammonium acetate to the Y[n[Mg[n] mixture changed the endothermic process to exothermic and improved the dispersion of the component phases. Two suspension types, made with powders synthesized from the Y[n]Mg[n] and Y[n]Mg[a] precursor mixtures were sprayed by SPS. The densities and hardnesses of the coatings deposited using the two powder types were similar. However, the microstructure of coatings deposited using the Y[n]Mg[a]-synthesized powder exhibited some eutectic configuration which was not observed in the coatings deposited using the Y[n]Mg[n]-synthesized powder.

Memory for sequences of events impaired in typical aging.

PubMed

Allen, Timothy A; Morris, Andrea M; Stark, Shauna M; Fortin, Norbert J; Stark, Craig E L

2015-03-01

Typical aging is associated with diminished episodic memory performance. To improve our understanding of the fundamental mechanisms underlying this age-related memory deficit, we previously developed an integrated, cross-species approach to link converging evidence from human and animal research. This novel approach focuses on the ability to remember sequences of events, an important feature of episodic memory. Unlike existing paradigms, this task is nonspatial, nonverbal, and can be used to isolate different cognitive processes that may be differentially affected in aging. Here, we used this task to make a comprehensive comparison of sequence memory performance between younger (18-22 yr) and older adults (62-86 yr). Specifically, participants viewed repeated sequences of six colored, fractal images and indicated whether each item was presented "in sequence" or "out of sequence." Several out of sequence probe trials were used to provide a detailed assessment of sequence memory, including: (i) repeating an item from earlier in the sequence ("Repeats"; e.g., AB A: DEF), (ii) skipping ahead in the sequence ("Skips"; e.g., AB D: DEF), and (iii) inserting an item from a different sequence into the same ordinal position ("Ordinal Transfers"; e.g., AB 3: DEF). We found that older adults performed as well as younger controls when tested on well-known and predictable sequences, but were severely impaired when tested using novel sequences. Importantly, overall sequence memory performance in older adults steadily declined with age, a decline not detected with other measures (RAVLT or BPS-O). We further characterized this deficit by showing that performance of older adults was severely impaired on specific probe trials that required detailed knowledge of the sequence (Skips and Ordinal Transfers), and was associated with a shift in their underlying mnemonic representation of the sequences. Collectively, these findings provide unambiguous evidence that the capacity to remember sequences of events is fundamentally affected by typical aging. © 2015 Allen et al.; Published by Cold Spring Harbor Laboratory Press.

Functional hypervariability and gene diversity of cardioactive neuropeptides.

PubMed

Möller, Carolina; Melaun, Christian; Castillo, Cecilia; Díaz, Mary E; Renzelman, Chad M; Estrada, Omar; Kuch, Ulrich; Lokey, Scott; Marí, Frank

2010-12-24

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions.

Sulfonium Ion Derivatization, Isobaric Stable Isotope Labeling and Data Dependent CID- and ETD-MS/MS for Enhanced Phosphopeptide Quantitation, Identification and Phosphorylation Site Characterization

PubMed Central

Lu, Yali; Zhou, Xiao; Stemmer, Paul M.; Reid, Gavin E.

2014-01-01

An amine specific peptide derivatization strategy involving the use of novel isobaric stable isotope encoded ‘fixed charge’ sulfonium ion reagents, coupled with an analysis strategy employing capillary HPLC, ESI-MS, and automated data dependent ion trap CID-MS/MS, -MS3, and/or ETD-MS/MS, has been developed for the improved quantitative analysis of protein phosphorylation, and for identification and characterization of their site(s) of modification. Derivatization of 50 synthetic phosphopeptides with S,S′-dimethylthiobutanoylhydroxysuccinimide ester iodide (DMBNHS), followed by analysis using capillary HPLC-ESI-MS, yielded an average 2.5-fold increase in ionization efficiencies and a significant increase in the presence and/or abundance of higher charge state precursor ions compared to the non-derivatized phosphopeptides. Notably, 44% of the phosphopeptides (22 of 50) in their underivatized states yielded precursor ions whose maximum charge states corresponded to +2, while only 8% (4 of 50) remained at this maximum charge state following DMBNHS derivatization. Quantitative analysis was achieved by measuring the abundances of the diagnostic product ions corresponding to the neutral losses of ‘light’ (S(CH3)2) and ‘heavy’ (S(CD3)2) dimethylsulfide exclusively formed upon CID-MS/MS of isobaric stable isotope labeled forms of the DMBNHS derivatized phosphopeptides. Under these conditions, the phosphate group stayed intact. Access for a greater number of peptides to provide enhanced phosphopeptide sequence identification and phosphorylation site characterization was achieved via automated data-dependent CID-MS3 or ETD-MS/MS analysis due to the formation of the higher charge state precursor ions. Importantly, improved sequence coverage was observed using ETD-MS/MS following introduction of the sulfonium ion fixed charge, but with no detrimental effects on ETD fragmentation efficiency. PMID:21952753

60 YEARS OF POMC: From the prohormone theory to pro-opiomelanocortin and to proprotein convertases (PCSK1 to PCSK9).

PubMed

Chrétien, Michel; Mbikay, Majambu

2016-05-01

Pro-opiomelanocortin (POMC), is a polyprotein expressed in the pituitary and the brain where it is proteolytically processed into peptide hormones and neuropeptides with distinct biological activities. It is the prototype of multipotent prohormones. The prohormone theory was first suggested in 1967 when Chrétien and Li discovered γ-lipotropin and observed that (i) it was part of β-lipotropin (β-LPH), a larger polypeptide characterized 2 years earlier and (ii) its C-terminus was β-melanocyte-stimulating hormone (β-MSH). This discovery led them to propose that the lipotropins might be related biosynthetically to the biologically active β-MSH in a precursor to end product relationship. The theory was widely confirmed in subsequent years. As we celebrate the 50th anniversary of the sequencing of β-LPH, we reflect over the lessons learned from the sequencing of those proteins; we explain their extension to the larger POMC precursor; we examine how the theory of precursor endoproteolysis they inspired became relevant for vast fields in biology; and how it led, after a long and arduous search, to the novel proteolytic enzymes called proprotein convertases. This family of nine enzymes plays multifaceted functions in growth, development, metabolism, endocrine, and brain functions. Their genetics has provided many insights into health and disease. Their therapeutic targeting is foreseeable in the near future. Thus, what started five decades ago as a theory based on POMC fragments, has opened up novel and productive avenues of biological and medical research, including, for our own current interest, a highly intriguing hypocholesterolemic Gln152His PCSK9 mutation in French-Canadian families. © 2016 Society for Endocrinology.

piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism.

PubMed

Beyret, Ergin; Liu, Na; Lin, Haifan

2012-10-01

piRNAs, a class of small non-coding RNAs associated with PIWI proteins, have broad functions in germline development, transposon silencing, and epigenetic regulation. In diverse organisms, a subset of piRNAs derived from repeat sequences are produced via the interplay between two PIWI proteins. This mechanism, termed "ping-pong" cycle, operates among the PIWI proteins of the primordial mouse testis; however, its involvement in postnatal testes remains elusive. Here we show that adult testicular piRNAs are produced independent of the ping-pong mechanism. We identified and characterized large populations of piRNAs in the adult and postnatal developing testes associated with MILI and MIWI, the only PIWI proteins detectable in these testes. No interaction between MILI and MIWI or sequence feature for the ping-pong mechanism among their piRNAs was detected in the adult testis. The majority of MILI- and MIWI-associated piRNAs originate from the same DNA strands within the same loci. Both populations of piRNAs are biased for 5' Uracil but not for Adenine on the 10th nucleotide position, and display no complementarity. Furthermore, in Miwi mutants, MILI-associated piRNAs are not downregulated, but instead upregulated. These results indicate that the adult testicular piRNAs are predominantly, if not exclusively, produced by a primary processing mechanism instead of the ping-pong mechanism. In this primary pathway, biogenesis of MILI- and MIWI-associated piRNAs may compete for the same precursors; the types of piRNAs produced tend to be non-selectively dictated by the available precursors in the cell; and precursors with introns tend to be spliced before processed into piRNAs.

Preliminary Analysis of Aircraft Loss of Control Accidents: Worst Case Precursor Combinations and Temporal Sequencing

NASA Technical Reports Server (NTRS)

Belcastro, Christine M.; Groff, Loren; Newman, Richard L.; Foster, John V.; Crider, Dennis H.; Klyde, David H.; Huston, A. McCall

2014-01-01

Aircraft loss of control (LOC) is a leading cause of fatal accidents across all transport airplane and operational classes, and can result from a wide spectrum of hazards, often occurring in combination. Technologies developed for LOC prevention and recovery must therefore be effective under a wide variety of conditions and uncertainties, including multiple hazards, and their validation must provide a means of assessing system effectiveness and coverage of these hazards. This requires the definition of a comprehensive set of LOC test scenarios based on accident and incident data as well as future risks. This paper defines a comprehensive set of accidents and incidents over a recent 15 year period, and presents preliminary analysis results to identify worst-case combinations of causal and contributing factors (i.e., accident precursors) and how they sequence in time. Such analyses can provide insight in developing effective solutions for LOC, and form the basis for developing test scenarios that can be used in evaluating them. Preliminary findings based on the results of this paper indicate that system failures or malfunctions, crew actions or inactions, vehicle impairment conditions, and vehicle upsets contributed the most to accidents and fatalities, followed by inclement weather or atmospheric disturbances and poor visibility. Follow-on research will include finalizing the analysis through a team consensus process, defining future risks, and developing a comprehensive set of test scenarios with correlation to the accidents, incidents, and future risks. Since enhanced engineering simulations are required for batch and piloted evaluations under realistic LOC precursor conditions, these test scenarios can also serve as a high-level requirement for defining the engineering simulation enhancements needed for generating them.

The first trimeric Galanthus nivalis agglutinin-related lectin of Orchidaceae was found in Dendrobium pendulum: purification, characterization, and effects of stress factors.

PubMed

Siripipatthana, Patthraporn; Phaonakrop, Narumon; Roytrakul, Sittiruk; Senawong, Gulsiri; Mudalige-Jayawickrama, Rasika G; Sattayasai, Nison

2015-07-01

Trimeric Galanthus nivalis agglutinin-related lectin of Orchidaceae with two conformational forms was first studied in Dendrobium pendulum . It was highly expressed by stress factors. Using mannan-agarose column chromatography, a mannose-binding protein was purified from Dendrobium pendulum Roxb. pseudobulb. After heating in the presence of sodium dodecyl sulfate (SDS) with or without 2-mercaptoethanol, the protein showed one band with molecular mass of 14.0 kDa on SDS-polyacrylamide gel electrophoresis (PAGE). Without heating, three bands were found at positions of 14.0, 39.4, and 41.5 kDa, but a higher amount of 39.4 and 41.5 kDa protein bands were seen in the presence of 2-mercaptoethanol. Liquid chromatography-tandem mass spectrometry and database search indicated that the 14.0 kDa protein band contained three peptide fragments identical to parts of a lectin precursor from Dendrobiu m findleyanum Parish & Rchb.f. Native-PAGE and Ferguson plot showed that the purified protein had two native forms with molecular masses of 44.2 and 45.3 kDa, indicating three 14.0 kDa polypeptide subunits. The purified protein exhibited the agglutination activity with trypsinized chicken erythrocytes. It was then recognized as a Galanthus nivalis agglutinin-related lectin and named D. pendulum agglutinin (DPA). Using reverse transcription-polymerase chain reaction and DNA sequencing, the deduced amino acid sequence of DPA precursor showed the highest homology (96.4%) with a lectin precursor of D. findleyanum and contained three mannose-binding sites. Greater amounts of DPA were found when the pseudobulbs were treated with stress factors including ultraviolet light, abscisic acid, hydrogen peroxide, and acetylene gas.

Identification of Putative Precursor Genes for the Biosynthesis of Cannabinoid-Like Compound in Radula marginata

PubMed Central

Hussain, Tajammul; Plunkett, Blue; Ejaz, Mahwish; Espley, Richard V.; Kayser, Oliver

2018-01-01

The liverwort Radula marginata belongs to the bryophyte division of land plants and is a prospective alternate source of cannabinoid-like compounds. However, mechanistic insights into the molecular pathways directing the synthesis of these cannabinoid-like compounds have been hindered due to the lack of genetic information. This prompted us to do deep sequencing, de novo assembly and annotation of R. marginata transcriptome, which resulted in the identification and validation of the genes for cannabinoid biosynthetic pathway. In total, we have identified 11,421 putative genes encoding 1,554 enzymes from 145 biosynthetic pathways. Interestingly, we have identified all the upstream genes of the central precursor of cannabinoid biosynthesis, cannabigerolic acid (CBGA), including its two first intermediates, stilbene acid (SA) and geranyl diphosphate (GPP). Expression of all these genes was validated using quantitative real-time PCR. We have characterized the protein structure of stilbene synthase (STS), which is considered as a homolog of olivetolic acid in R. marginata. Moreover, the metabolomics approach enabled us to identify CBGA-analogous compounds using electrospray ionization mass spectrometry (ESI-MS/MS) and gas chromatography mass spectrometry (GC-MS). Transcriptomic analysis revealed 1085 transcription factors (TF) from 39 families. Comparative analysis showed that six TF families have been uniquely predicted in R. marginata. In addition, the bioinformatics analysis predicted a large number of simple sequence repeats (SSRs) and non-coding RNAs (ncRNAs). Our results collectively provide mechanistic insights into the putative precursor genes for the biosynthesis of cannabinoid-like compounds and a novel transcriptomic resource for R. marginata. The large-scale transcriptomic resource generated in this study would further serve as a reference transcriptome to explore the Radulaceae family.

Functional Hypervariability and Gene Diversity of Cardioactive Neuropeptides*

PubMed Central

Möller, Carolina; Melaun, Christian; Castillo, Cecilia; Díaz, Mary E.; Renzelman, Chad M.; Estrada, Omar; Kuch, Ulrich; Lokey, Scott; Marí, Frank

2010-01-01

Crustacean cardioactive peptide (CCAP) and related peptides are multifunctional regulatory neurohormones found in invertebrates. We isolated a CCAP-related peptide (conoCAP-a, for cone snail CardioActive Peptide) and cloned the cDNA of its precursor from venom of Conus villepinii. The precursor of conoCAP-a encodes for two additional CCAP-like peptides: conoCAP-b and conoCAP-c. This multi-peptide precursor organization is analogous to recently predicted molluscan CCAP-like preprohormones, and suggests a mechanism for the generation of biological diversification without gene amplification. While arthropod CCAP is a cardio-accelerator, we found that conoCAP-a decreases the heart frequency in Drosophila larvae, demonstrating that conoCAP-a and CCAP have opposite effects. Intravenous injection of conoCAP-a in rats caused decreased heart frequency and blood pressure in contrast to the injection of CCAP, which did not elicit any cardiac effect. Perfusion of rat ventricular cardiac myocytes with conoCAP-a decreased systolic calcium, indicating that conoCAP-a cardiac negative inotropic effects might be mediated via impairment of intracellular calcium trafficking. The contrasting cardiac effects of conoCAP-a and CCAP indicate that molluscan CCAP-like peptides have functions that differ from those of their arthropod counterparts. Molluscan CCAP-like peptides sequences, while homologous, differ between taxa and have unique sequences within a species. This relates to the functional hypervariability of these peptides as structure activity relationship studies demonstrate that single amino acids variations strongly affect cardiac activity. The discovery of conoCAPs in cone snail venom emphasizes the significance of their gene plasticity to have mutations as an adaptive evolution in terms of structure, cellular site of expression, and physiological functions. PMID:20923766

High-Throughput Sequencing and Characterization of the Small RNA Transcriptome Reveal Features of Novel and Conserved MicroRNAs in Panax ginseng

PubMed Central

Ma, Yimian; Yuan, Lichai; Lu, Shanfa

2012-01-01

microRNAs (miRNAs) play vital regulatory roles in many organisms through direct cleavage of transcripts, translational repression, or chromatin modification. Identification of miRNAs has been carried out in various plant species. However, no information is available for miRNAs from Panax ginseng, an economically significant medicinal plant species. Using the next generation high-throughput sequencing technology, we obtained 13,326,328 small RNA reads from the roots, stems, leaves and flowers of P. ginseng. Analysis of these small RNAs revealed the existence of a large, diverse and highly complicated small RNA population in P. ginseng. We identified 73 conserved miRNAs, which could be grouped into 33 families, and 28 non-conserved ones belonging to 9 families. Characterization of P. ginseng miRNA precursors revealed many features, such as production of two miRNAs from distinct regions of a precursor, clusters of two precursors in a transcript, and generation of miRNAs from both sense and antisense transcripts. It suggests the complexity of miRNA production in P. gingseng. Using a computational approach, we predicted for the conserved and non-conserved miRNA families 99 and 31 target genes, respectively, of which eight were experimentally validated. Among all predicted targets, only about 20% are conserved among various plant species, whereas the others appear to be non-conserved, indicating the diversity of miRNA functions. Consistently, many miRNAs exhibited tissue-specific expression patterns. Moreover, we identified five dehydration- and ten heat-responsive miRNAs and found the existence of a crosstalk among some of the stress-responsive miRNAs. Our results provide the first clue to the elucidation of miRNA functions in P. ginseng. PMID:22962612

Characterization of the beta amyloid precursor protein-like gene in the central nervous system of the crab Chasmagnathus. Expression during memory consolidation.

PubMed

Fustiñana, Maria Sol; Ariel, Pablo; Federman, Noel; Freudenthal, Ramiro; Romano, Arturo

2010-09-01

Human β-amyloid, the main component in the neuritic plaques found in patients with Alzheimer's disease, is generated by cleavage of the β-amyloid precursor protein. Beyond the role in pathology, members of this protein family are synaptic proteins and have been associated with synaptogenesis, neuronal plasticity and memory, both in vertebrates and in invertebrates. Consolidation is necessary to convert a short-term labile memory to a long-term and stable form. During consolidation, gene expression and de novo protein synthesis are regulated in order to produce key proteins for the maintenance of plastic changes produced during the acquisition of new information. Here we partially cloned and sequenced the beta-amyloid precursor protein like gene homologue in the crab Chasmagnathus (cappl), showing a 37% of identity with the fruit fly Drosophila melanogaster homologue and 23% with Homo sapiens but with much higher degree of sequence similarity in certain regions. We observed a wide distribution of cappl mRNA in the nervous system as well as in muscle and gills. The protein localized in all tissues analyzed with the exception of muscle. Immunofluorescence revealed localization of cAPPL in associative and sensory brain areas. We studied gene and protein expression during long-term memory consolidation using a well characterized memory model: the context-signal associative memory in this crab species. mRNA levels varied at different time points during long-term memory consolidation and correlated with cAPPL protein levels cAPPL mRNA and protein is widely distributed in the central nervous system of the crab and the time course of expression suggests a role of cAPPL during long-term memory formation.

Viral Infection Induces Expression of Novel Phased MicroRNAs from Conserved Cellular MicroRNA Precursors

PubMed Central

Zhang, Jiayao; Zhao, Shuqi; Zheng, Hong; Gao, Ge; Wei, Liping; Li, Yi

2011-01-01

RNA silencing, mediated by small RNAs including microRNAs (miRNAs) and small interfering RNAs (siRNAs), is a potent antiviral or antibacterial mechanism, besides regulating normal cellular gene expression critical for development and physiology. To gain insights into host small RNA metabolism under infections by different viruses, we used Solexa/Illumina deep sequencing to characterize the small RNA profiles of rice plants infected by two distinct viruses, Rice dwarf virus (RDV, dsRNA virus) and Rice stripe virus (RSV, a negative sense and ambisense RNA virus), respectively, as compared with those from non-infected plants. Our analyses showed that RSV infection enhanced the accumulation of some rice miRNA*s, but not their corresponding miRNAs, as well as accumulation of phased siRNAs from a particular precursor. Furthermore, RSV infection also induced the expression of novel miRNAs in a phased pattern from several conserved miRNA precursors. In comparison, no such changes in host small RNA expression was observed in RDV-infected rice plants. Significantly RSV infection elevated the expression levels of selective OsDCLs and OsAGOs, whereas RDV infection only affected the expression of certain OsRDRs. Our results provide a comparative analysis, via deep sequencing, of changes in the small RNA profiles and in the genes of RNA silencing machinery induced by different viruses in a natural and economically important crop host plant. They uncover new mechanisms and complexity of virus-host interactions that may have important implications for further studies on the evolution of cellular small RNA biogenesis that impact pathogen infection, pathogenesis, as well as organismal development. PMID:21901091

Sequencing: Targeting Insurgents and Drugs in Colombia

DTIC Science & Technology

2007-03-01

process . In Colombia, proponents for a purely counter-insurgency strategy state Colombia’s violence existed decades before the drug industry...8 Both the AUC and the ELN will only be mentioned briefly as the demobilization process with the paramilitaries and the...that extracted revenues at every phase of the illicit drug process —from the transportation of precursor chemical to the transportation of the final

Web-ware bioinformatical analysis and structure modelling of N-terminus of human multisynthetase complex auxiliary component protein p43.

PubMed

Deineko, Viktor

2006-01-01

Human multisynthetase complex auxiliary component, protein p43 is an endothelial monocyte-activating polypeptide II precursor. In this study, comprehensive sequence analysis of N-terminus has been performed to identify structural domains, motifs, sites of post-translation modification and other functionally important parameters. The spatial structure model of full-chain protein p43 is obtained.

Efficient synthesis of cysteine-rich cyclic peptides through intramolecular native chemical ligation of N-Hnb-Cys peptide crypto-thioesters.

PubMed

Terrier, Victor P; Delmas, Agnès F; Aucagne, Vincent

2017-01-04

We herein introduce a straightforward synthetic route to cysteine-containing cyclic peptides based on the intramolecular native chemical ligation of in situ generated thioesters. Key precursors are N-Hnb-Cys crypto-thioesters, easily synthesized by Fmoc-based SPPS. The strategy is applied to a representative range of naturally occurring cyclic disulfide-rich peptide sequences.

Microparticle Shedding from Neural Progenitor Cells and Vascular Compartment Cells Is Increased in Ischemic Stroke.

PubMed

Chiva-Blanch, Gemma; Suades, Rosa; Crespo, Javier; Peña, Esther; Padró, Teresa; Jiménez-Xarrié, Elena; Martí-Fàbregas, Joan; Badimon, Lina

2016-01-01

Ischemic stroke has shown to induce platelet and endothelial microparticle shedding, but whether stroke induces microparticle shedding from additional blood and vascular compartment cells is unclear. Neural precursor cells have been shown to replace dying neurons at sites of brain injury; however, if neural precursor cell activation is associated to microparticle shedding, and whether this activation is maintained at long term and associates to stroke type and severity remains unknown. We analyzed neural precursor cells and blood and vascular compartment cells microparticle shedding after an acute ischemic stroke. Forty-four patients were included in the study within the first 48h after the onset of stroke. The cerebral lesion size was evaluated at 3-7 days of the stroke. Circulating microparticles from neural precursor cells and blood and vascular compartment cells (platelets, endothelial cells, erythrocytes, leukocytes, lymphocytes, monocytes and smooth muscle cells) were analyzed by flow cytometry at the onset of stroke and at 7 and 90 days. Forty-four age-matched high cardiovascular risk subjects without documented vascular disease were used as controls. Compared to high cardiovascular risk controls, patients showed higher number of neural precursor cell- and all blood and vascular compartment cell-derived microparticles at the onset of stroke, and after 7 and 90 days. At 90 days, neural precursor cell-derived microparticles decreased and smooth muscle cell-derived microparticles increased compared to levels at the onset of stroke, but only in those patients with the highest stroke-induced cerebral lesions. Stroke increases blood and vascular compartment cell and neural precursor cell microparticle shedding, an effect that is chronically maintained up to 90 days after the ischemic event. These results show that stroke induces a generalized blood and vascular cell activation and the initiation of neuronal cell repair process after stroke. Larger cerebral lesions associate with deeper vessel injury affecting vascular smooth muscle cells.

Microparticle Shedding from Neural Progenitor Cells and Vascular Compartment Cells Is Increased in Ischemic Stroke

PubMed Central

Chiva-Blanch, Gemma; Suades, Rosa; Crespo, Javier; Peña, Esther; Padró, Teresa; Jiménez-Xarrié, Elena; Martí-Fàbregas, Joan; Badimon, Lina

2016-01-01

Purpose Ischemic stroke has shown to induce platelet and endothelial microparticle shedding, but whether stroke induces microparticle shedding from additional blood and vascular compartment cells is unclear. Neural precursor cells have been shown to replace dying neurons at sites of brain injury; however, if neural precursor cell activation is associated to microparticle shedding, and whether this activation is maintained at long term and associates to stroke type and severity remains unknown. We analyzed neural precursor cells and blood and vascular compartment cells microparticle shedding after an acute ischemic stroke. Methods Forty-four patients were included in the study within the first 48h after the onset of stroke. The cerebral lesion size was evaluated at 3–7 days of the stroke. Circulating microparticles from neural precursor cells and blood and vascular compartment cells (platelets, endothelial cells, erythrocytes, leukocytes, lymphocytes, monocytes and smooth muscle cells) were analyzed by flow cytometry at the onset of stroke and at 7 and 90 days. Forty-four age-matched high cardiovascular risk subjects without documented vascular disease were used as controls. Results Compared to high cardiovascular risk controls, patients showed higher number of neural precursor cell- and all blood and vascular compartment cell-derived microparticles at the onset of stroke, and after 7 and 90 days. At 90 days, neural precursor cell-derived microparticles decreased and smooth muscle cell-derived microparticles increased compared to levels at the onset of stroke, but only in those patients with the highest stroke-induced cerebral lesions. Conclusions Stroke increases blood and vascular compartment cell and neural precursor cell microparticle shedding, an effect that is chronically maintained up to 90 days after the ischemic event. These results show that stroke induces a generalized blood and vascular cell activation and the initiation of neuronal cell repair process after stroke. Larger cerebral lesions associate with deeper vessel injury affecting vascular smooth muscle cells. PMID:26815842

Earthquake stress via event ratio levels: Application to the 2011 and 2016 Oklahoma seismic sequences

DOE Office of Scientific and Technical Information (OSTI.GOV)

Walter, William R.; Yoo, Seung -Hoon; Mayeda, Kevin

Here, we develop a new methodology for determining earthquake stress drop and apparent stress values via spectral ratio asymptotic levels. With sufficient bandwidth, the stress ratio for a pair of events can be directly related to these low- and high-frequency levels. This avoids the need to assume a particular spectral model and derive stress drop from cubed corner frequency measures. The method can be applied to spectral ratios for any pair of closely related earthquakes and is particularly well suited for coda envelope methods that provide good azimuthally averaged, point-source measures. We apply the new method to the 2011 Praguemore » and 2016 Pawnee earthquake sequences in Oklahoma. The sequences show stress scaling with size and depth, with the largest events having apparent stress levels near 1 MPa and smaller and/or shallower events having systematically lower stress values.« less

Earthquake stress via event ratio levels: Application to the 2011 and 2016 Oklahoma seismic sequences

DOE PAGES

Walter, William R.; Yoo, Seung -Hoon; Mayeda, Kevin; ...

2017-04-03

Here, we develop a new methodology for determining earthquake stress drop and apparent stress values via spectral ratio asymptotic levels. With sufficient bandwidth, the stress ratio for a pair of events can be directly related to these low- and high-frequency levels. This avoids the need to assume a particular spectral model and derive stress drop from cubed corner frequency measures. The method can be applied to spectral ratios for any pair of closely related earthquakes and is particularly well suited for coda envelope methods that provide good azimuthally averaged, point-source measures. We apply the new method to the 2011 Praguemore » and 2016 Pawnee earthquake sequences in Oklahoma. The sequences show stress scaling with size and depth, with the largest events having apparent stress levels near 1 MPa and smaller and/or shallower events having systematically lower stress values.« less

Enzymes processing somatostatin precursors: an Arg-Lys esteropeptidase from the rat brain cortex converting somatostatin-28 into somatostatin-14.

PubMed Central

Gluschankof, P; Morel, A; Gomez, S; Nicolas, P; Fahy, C; Cohen, P

1984-01-01

The post-translational proteolytic conversion of somatostatin-14 precursors was studied to characterize the enzyme system responsible for the production of the tetradecapeptide either from its 15-kDa precursor protein or from its COOH-terminal fragment, somatostatin-28. A synthetic undecapeptide Pro-Arg-Glu-Arg-Lys-Ala-Gly-Ala-Lys-Asn-Tyr(NH2), homologous to the amino acid sequence of the octacosapeptide at the putative Arg-Lys cleavage locus, was used as substrate, after 125I labeling on the COOH-terminal tyrosine residue. A 90-kDa proteolytic activity was detected in rat brain cortex extracts after molecular sieve fractionation followed by ion exchange chromatography. The protease released the peptide 125I-Ala-Gly-Ala-Lys-Asn-Tyr(NH2) from the synthetic undecapeptide substrate and converted somatostatin-28 into somatostatin-14 under similar conditions (pH 7.0). Under these experimental conditions, the product tetradecapeptide was not further degraded by the enzyme. In contrast, the purified 15-kDa hypothalamic precursor remained unaffected when exposed to the proteolytic enzyme under identical conditions. It is concluded that this Arg-Lys esteropeptidase from the brain cortex may be involved in the in vivo processing of the somatostatin-28 fragment of prosomatostatin into somatostatin-14, the former species being an obligatory intermediate in a two-step proteolytic mechanism leading to somatostatin-14. PMID:6149550

Waveform classification and statistical analysis of seismic precursors to the July 2008 Vulcanian Eruption of Soufrière Hills Volcano, Montserrat

NASA Astrophysics Data System (ADS)

Rodgers, Mel; Smith, Patrick; Pyle, David; Mather, Tamsin

2016-04-01

Understanding the transition between quiescence and eruption at dome-forming volcanoes, such as Soufrière Hills Volcano (SHV), Montserrat, is important for monitoring volcanic activity during long-lived eruptions. Statistical analysis of seismic events (e.g. spectral analysis and identification of multiplets via cross-correlation) can be useful for characterising seismicity patterns and can be a powerful tool for analysing temporal changes in behaviour. Waveform classification is crucial for volcano monitoring, but consistent classification, both during real-time analysis and for retrospective analysis of previous volcanic activity, remains a challenge. Automated classification allows consistent re-classification of events. We present a machine learning (random forest) approach to rapidly classify waveforms that requires minimal training data. We analyse the seismic precursors to the July 2008 Vulcanian explosion at SHV and show systematic changes in frequency content and multiplet behaviour that had not previously been recognised. These precursory patterns of seismicity may be interpreted as changes in pressure conditions within the conduit during magma ascent and could be linked to magma flow rates. Frequency analysis of the different waveform classes supports the growing consensus that LP and Hybrid events should be considered end members of a continuum of low-frequency source processes. By using both supervised and unsupervised machine-learning methods we investigate the nature of waveform classification and assess current classification schemes.