Kit for detecting nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

2001-01-01

A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the

Hybridization and sequencing of nucleic acids using base pair mismatches

DOEpatents

Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

2001-01-01

Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

Mouse Vk gene classification by nucleic acid sequence similarity.

PubMed

Strohal, R; Helmberg, A; Kroemer, G; Kofler, R

1989-01-01

Analyses of immunoglobulin (Ig) variable (V) region gene usage in the immune response, estimates of V gene germline complexity, and other nucleic acid hybridization-based studies depend on the extent to which such genes are related (i.e., sequence similarity) and their organization in gene families. While mouse Igh heavy chain V region (VH) gene families are relatively well-established, a corresponding systematic classification of Igk light chain V region (Vk) genes has not been reported. The present analysis, in the course of which we reviewed the known extent of the Vk germline gene repertoire and Vk gene usage in a variety of responses to foreign and self antigens, provides a classification of mouse Vk genes in gene families composed of members with greater than 80% overall nucleic acid sequence similarity. This classification differed in several aspects from that of VH genes: only some Vk gene families were as clearly separated (by greater than 25% sequence dissimilarity) as typical VH gene families; most Vk gene families were closely related and, in several instances, members from different families were very similar (greater than 80%) over large sequence portions; frequently, classification by nucleic acid sequence similarity diverged from existing classifications based on amino-terminal protein sequence similarity. Our data have implications for Vk gene analyses by nucleic acid hybridization and describe potentially important differences in sequence organization between VH and Vk genes.

Biosynthesis of Lipoic Acid in Arabidopsis: Cloning and Characterization of the cDNA for Lipoic Acid Synthase1

PubMed Central

Yasuno, Rie; Wada, Hajime

1998-01-01

Lipoic acid is a coenzyme that is essential for the activity of enzyme complexes such as those of pyruvate dehydrogenase and glycine decarboxylase. We report here the isolation and characterization of LIP1 cDNA for lipoic acid synthase of Arabidopsis. The Arabidopsis LIP1 cDNA was isolated using an expressed sequence tag homologous to the lipoic acid synthase of Escherichia coli. This cDNA was shown to code for Arabidopsis lipoic acid synthase by its ability to complement a lipA mutant of E. coli defective in lipoic acid synthase. DNA-sequence analysis of the LIP1 cDNA revealed an open reading frame predicting a protein of 374 amino acids. Comparisons of the deduced amino acid sequence with those of E. coli and yeast lipoic acid synthase homologs showed a high degree of sequence similarity and the presence of a leader sequence presumably required for import into the mitochondria. Southern-hybridization analysis suggested that LIP1 is a single-copy gene in Arabidopsis. Western analysis with an antibody against lipoic acid synthase demonstrated that this enzyme is located in the mitochondrial compartment in Arabidopsis cells as a 43-kD polypeptide. PMID:9808738

The hydrophobic region of the DmsA twin-arginine leader peptide determines specificity with chaperone DmsD.

PubMed

Winstone, Tara M L; Tran, Vy A; Turner, Raymond J

2013-10-29

The system specific chaperone DmsD plays a role in the maturation of the catalytic subunit of dimethyl sulfoxide (DMSO) reductase, DmsA. Pre-DmsA contains a 45-amino acid twin-arginine leader peptide that is important for targeting and translocation of folded and cofactor-loaded DmsA by the twin-arginine translocase. DmsD has previously been shown to interact with the complete twin-arginine leader peptide of DmsA. In this study, isothermal titration calorimetry was used to investigate the thermodynamics of binding between synthetic peptides composed of different portions of the DmsA leader peptide and DmsD. Only those peptides that included the complete and contiguous hydrophobic region of the DmsA leader sequence were able to bind DmsD with a 1:1 stoichiometry. Each of the peptides that were able to bind DmsD also showed some α-helical structure as indicated by circular dichroism spectroscopy. Differential scanning calorimetry revealed that DmsD gained very little thermal stability upon binding any of the DmsA leader peptides tested. Together, these results suggest that a portion of the hydrophobic region of the DmsA leader peptide determines the specificity of binding and may produce helical properties upon binding to DmsD. Overall, this study demonstrates that the recognition of the DmsA twin-arginine leader sequence by the DmsD chaperone shows unexpected rules and confirms further that the biochemistry of the interaction of the chaperone with their leaders demonstrates differences in their molecular interactions.

Characteristics of lightning leader propagation and ground attachment

NASA Astrophysics Data System (ADS)

Jiang, Rubin; Qie, Xiushu; Wang, Zhichao; Zhang, Hongbo; Lu, Gaopeng; Sun, Zhuling; Liu, Mingyuan; Li, Xun

2015-12-01

The grounding process and the associated leader behavior were analyzed by using high-speed video record and time-correlated electric field change for 37 natural negative cloud-to-ground flashes. Weak luminous grounded channel was recognized below the downward leader tip in the frame preceding the return stroke, which is inferred as upward connecting leader considering the physical process of lightning attachment, though not directly confirmed by sequential frames. For stepped leader-first return strokes, the upward connecting leaders tend to be induced by those downward leader branches with brighter luminosity and lower channel tip above ground, and they may accomplish the attachment with great possibility. The upward connecting leaders for 2 out of 61 leader-subsequent stroke sequences were captured in the frame prior to the return stroke, exhibiting relatively long channel lengths of 340 m and 105 m, respectively. The inducing downward subsequent leaders were of the chaotic type characterized by irregular electric field pulse train with duration of 0.2-0.3 ms. The transient drop of the high potential difference between stepped leader system and ground when the attachment occurred would macroscopically terminate the propagation of those ungrounded branches while would not effectively prevent the development of the existing space stem systems in the low-conductivity streamer zone apart from the leader tip. When the ungrounded branches are of poor connection with the main stroke channel, their further propagation toward ground would be feasible. These two factors may contribute to the occurrence of multiple grounding within the same leader-return stroke sequence.

The amino acid sequence of Staphylococcus aureus penicillinase.

PubMed Central

Ambler, R P

1975-01-01

The amino acid sequence of the penicillinase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) from Staphylococcus aureus strain PC1 was determined. The protein consists of a single polypeptide chain of 257 residues, and the sequence was determined by characterization of tryptic, chymotryptic, peptic and CNBr peptides, with some additional evidence from thermolysin and S. aureus proteinase peptides. A mistake in the preliminary report of the sequence is corrected; residues 113-116 are now thought to be -Lys-Lys-Val-Lys- rather than -Lys-Val-Lys-Lys-. Detailed evidence for the amino acid sequence has been deposited as Supplementary Publication SUP 50056 (91 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1975) 145, 5. PMID:1218078

Detection and isolation of nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1997-01-01

A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided.

Detection and isolation of nucleic acid sequences using competitive hybridization probes

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1997-04-01

A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

Amino acid sequence of the human fibronectin receptor

PubMed Central

1987-01-01

The amino acid sequence deduced from cDNA of the human placental fibronectin receptor is reported. The receptor is composed of two subunits: an alpha subunit of 1,008 amino acids which is processed into two polypeptides disulfide bonded to one another, and a beta subunit of 778 amino acids. Each subunit has near its COOH terminus a hydrophobic segment. This and other sequence features suggest a structure for the receptor in which the hydrophobic segments serve as transmembrane domains anchoring each subunit to the membrane and dividing each into a large ectodomain and a short cytoplasmic domain. The alpha subunit ectodomain has five sequence elements homologous to consensus Ca2+- binding sites of several calcium-binding proteins, and the beta subunit contains a fourfold repeat strikingly rich in cysteine. The alpha subunit sequence is 46% homologous to the alpha subunit of the vitronectin receptor. The beta subunit is 44% homologous to the human platelet adhesion receptor subunit IIIa and 47% homologous to a leukocyte adhesion receptor beta subunit. The high degree of homology (85%) of the beta subunit with one of the polypeptides of a chicken adhesion receptor complex referred to as integrin complex strongly suggests that the latter polypeptide is the chicken homologue of the fibronectin receptor beta subunit. These receptor subunit homologies define a superfamily of adhesion receptors. The availability of the entire protein sequence for the fibronectin receptor will facilitate studies on the functions of these receptors. PMID:2958481

Phenolic acid esterases, coding sequences and methods

DOEpatents

Blum, David L.; Kataeva, Irina; Li, Xin-Liang; Ljungdahl, Lars G.

2002-01-01

Described herein are four phenolic acid esterases, three of which correspond to domains of previously unknown function within bacterial xylanases, from XynY and XynZ of Clostridium thermocellum and from a xylanase of Ruminococcus. The fourth specifically exemplified xylanase is a protein encoded within the genome of Orpinomyces PC-2. The amino acids of these polypeptides and nucleotide sequences encoding them are provided. Recombinant host cells, expression vectors and methods for the recombinant production of phenolic acid esterases are also provided.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

1998-01-01

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

DOEpatents

Lucas, J.N.; Straume, T.; Bogen, K.T.

1998-03-24

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification.

PubMed

Sinclair, Robert M; Ravantti, Janne J; Bamford, Dennis H

2017-04-15

Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids. Importantly

Nucleic and Amino Acid Sequences Support Structure-Based Viral Classification

PubMed Central

Sinclair, Robert M.; Ravantti, Janne J.

2017-01-01

ABSTRACT Viral capsids ensure viral genome integrity by protecting the enclosed nucleic acids. Interactions between the genome and capsid and between individual capsid proteins (i.e., capsid architecture) are intimate and are expected to be characterized by strong evolutionary conservation. For this reason, a capsid structure-based viral classification has been proposed as a way to bring order to the viral universe. The seeming lack of sufficient sequence similarity to reproduce this classification has made it difficult to reject structural convergence as the basis for the classification. We reinvestigate whether the structure-based classification for viral coat proteins making icosahedral virus capsids is in fact supported by previously undetected sequence similarity. Since codon choices can influence nascent protein folding cotranslationally, we searched for both amino acid and nucleotide sequence similarity. To demonstrate the sensitivity of the approach, we identify a candidate gene for the pandoravirus capsid protein. We show that the structure-based classification is strongly supported by amino acid and also nucleotide sequence similarities, suggesting that the similarities are due to common descent. The correspondence between structure-based and sequence-based analyses of the same proteins shown here allow them to be used in future analyses of the relationship between linear sequence information and macromolecular function, as well as between linear sequence and protein folds. IMPORTANCE Viral capsids protect nucleic acid genomes, which in turn encode capsid proteins. This tight coupling of protein shell and nucleic acids, together with strong functional constraints on capsid protein folding and architecture, leads to the hypothesis that capsid protein-coding nucleotide sequences may retain signatures of ancient viral evolution. We have been able to show that this is indeed the case, using the major capsid proteins of viruses forming icosahedral capsids

Structural Requirement in Clostridium perfringens Collagenase mRNA 5′ Leader Sequence for Translational Induction through Small RNA-mRNA Base Pairing

PubMed Central

Nomura, Nobuhiko; Nakamura, Kouji

2013-01-01

The Gram-positive anaerobic bacterium Clostridium perfringens is pathogenic to humans and animals, and the production of its toxins is strictly regulated during the exponential phase. We recently found that the 5′ leader sequence of the colA transcript encoding collagenase, which is a major toxin of this organism, is processed and stabilized in the presence of the small RNA VR-RNA. The primary colA 5′-untranslated region (5′UTR) forms a long stem-loop structure containing an internal bulge and masks its own ribosomal binding site. Here we found that VR-RNA directly regulates colA expression through base pairing with colA mRNA in vivo. However, when the internal bulge structure was closed by point mutations in colA mRNA, translation ceased despite the presence of VR-RNA. In addition, a mutation disrupting the colA stem-loop structure induced mRNA processing and ColA-FLAG translational activation in the absence of VR-RNA, indicating that the stem-loop and internal bulge structure of the colA 5′ leader sequence is important for regulation by VR-RNA. On the other hand, processing was required for maximal ColA expression but was not essential for VR-RNA-dependent colA regulation. Finally, colA processing and translational activation were induced at a high temperature without VR-RNA. These results suggest that inhibition of the colA 5′ leader structure through base pairing is the primary role of VR-RNA in colA regulation and that the colA 5′ leader structure is a possible thermosensor. PMID:23585542

[Comparative genomics and evolutionary analysis of CRISPR loci in acetic acid bacteria].

PubMed

Xia, Kai; Liang, Xin-le; Li, Yu-dong

2015-12-01

The clustered regularly interspaced short palindromic repeat (CRISPR) is a widespread adaptive immunity system that exists in most archaea and many bacteria against foreign DNA, such as phages, viruses and plasmids. In general, CRISPR system consists of direct repeat, leader, spacer and CRISPR-associated sequences. Acetic acid bacteria (AAB) play an important role in industrial fermentation of vinegar and bioelectrochemistry. To investigate the polymorphism and evolution pattern of CRISPR loci in acetic acid bacteria, bioinformatic analyses were performed on 48 species from three main genera (Acetobacter, Gluconacetobacter and Gluconobacter) with whole genome sequences available from the NCBI database. The results showed that the CRISPR system existed in 32 species of the 48 strains studied. Most of the CRISPR-Cas system in AAB belonged to type I CRISPR-Cas system (subtype E and C), but type II CRISPR-Cas system which contain cas9 gene was only found in the genus Acetobacter and Gluconacetobacter. The repeat sequences of some CRISPR were highly conserved among species from different genera, and the leader sequences of some CRISPR possessed conservative motif, which was associated with regulated promoters. Moreover, phylogenetic analysis of cas1 demonstrated that they were suitable for classification of species. The conservation of cas1 genes was associated with that of repeat sequences among different strains, suggesting they were subjected to similar functional constraints. Moreover, the number of spacer was positively correlated with the number of prophages and insertion sequences, indicating the acetic acid bacteria were continually invaded by new foreign DNA. The comparative analysis of CRISR loci in acetic acid bacteria provided the basis for investigating the molecular mechanism of different acetic acid tolerance and genome stability in acetic acid bacteria.

Complete amino acid sequence of bovine colostrum low-Mr cysteine proteinase inhibitor.

PubMed

Hirado, M; Tsunasawa, S; Sakiyama, F; Niinobe, M; Fujii, S

1985-07-01

The complete amino acid sequence of bovine colostrum cysteine proteinase inhibitor was determined by sequencing native inhibitor and peptides obtained by cyanogen bromide degradation, Achromobacter lysylendopeptidase digestion and partial acid hydrolysis of reduced and S-carboxymethylated protein. Achromobacter peptidase digestion was successfully used to isolate two disulfide-containing peptides. The inhibitor consists of 112 amino acids with an Mr of 12787. Two disulfide bonds were established between Cys 66 and Cys 77 and between Cys 90 and Cys 110. A high degree of homology in the sequence was found between the colostrum inhibitor and human gamma-trace, human salivary acidic protein and chicken egg-white cystatin.

Nucleic acid sequence detection using multiplexed oligonucleotide PCR

DOEpatents

Nolan, John P [Santa Fe, NM; White, P Scott [Los Alamos, NM

2006-12-26

Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion

PubMed Central

Thomsen, Martin Christen Frølund; Nielsen, Morten

2012-01-01

Seq2Logo is a web-based sequence logo generator. Sequence logos are a graphical representation of the information content stored in a multiple sequence alignment (MSA) and provide a compact and highly intuitive representation of the position-specific amino acid composition of binding motifs, active sites, etc. in biological sequences. Accurate generation of sequence logos is often compromised by sequence redundancy and low number of observations. Moreover, most methods available for sequence logo generation focus on displaying the position-specific enrichment of amino acids, discarding the equally valuable information related to amino acid depletion. Seq2logo aims at resolving these issues allowing the user to include sequence weighting to correct for data redundancy, pseudo counts to correct for low number of observations and different logotype representations each capturing different aspects related to amino acid enrichment and depletion. Besides allowing input in the format of peptides and MSA, Seq2Logo accepts input as Blast sequence profiles, providing easy access for non-expert end-users to characterize and identify functionally conserved/variable amino acids in any given protein of interest. The output from the server is a sequence logo and a PSSM. Seq2Logo is available at http://www.cbs.dtu.dk/biotools/Seq2Logo (14 May 2012, date last accessed). PMID:22638583

Presence of a Shared 5'-Leader Sequence in Ancestral Human and Mammalian Retroviruses and Its Transduction into Feline Leukemia Virus.

PubMed

Kawasaki, Junna; Kawamura, Maki; Ohsato, Yoshiharu; Ito, Jumpei; Nishigaki, Kazuo

2017-10-15

Recombination events induce significant genetic changes, and this process can result in virus genetic diversity or in the generation of novel pathogenicity. We discovered a new recombinant feline leukemia virus (FeLV) gag gene harboring an unrelated insertion, termed the X region, which was derived from Felis catus endogenous gammaretrovirus 4 (FcERV-gamma4). The identified FcERV-gamma4 proviruses have lost their coding capabilities, but some can express their viral RNA in feline tissues. Although the X-region-carrying recombinant FeLVs appeared to be replication-defective viruses, they were detected in 6.4% of tested FeLV-infected cats. All isolated recombinant FeLV clones commonly incorporated a middle part of the FcERV-gamma4 5'-leader region as an X region. Surprisingly, a sequence corresponding to the portion contained in all X regions is also present in at least 13 endogenous retroviruses (ERVs) observed in the cat, human, primate, and pig genomes. We termed this shared genetic feature the commonly shared (CS) sequence. Despite our phylogenetic analysis indicating that all CS-sequence-carrying ERVs are classified as gammaretroviruses, no obvious closeness was revealed among these ERVs. However, the Shannon entropy in the CS sequence was lower than that in other parts of the provirus genome. Notably, the CS sequence of human endogenous retrovirus T had 73.8% similarity with that of FcERV-gamma4, and specific signals were detected in the human genome by Southern blot analysis using a probe for the FcERV-gamma4 CS sequence. Our results provide an interesting evolutionary history for CS-sequence circulation among several distinct ancestral viruses and a novel recombined virus over a prolonged period. IMPORTANCE Recombination among ERVs or modern viral genomes causes a rapid evolution of retroviruses, and this phenomenon can result in the serious situation of viral disease reemergence. We identified a novel recombinant FeLV gag gene that contains an unrelated

WEB-server for search of a periodicity in amino acid and nucleotide sequences

NASA Astrophysics Data System (ADS)

E Frenkel, F.; Skryabin, K. G.; Korotkov, E. V.

2017-12-01

A new web server (http://victoria.biengi.ac.ru/splinter/login.php) was designed and developed to search for periodicity in nucleotide and amino acid sequences. The web server operation is based upon a new mathematical method of searching for multiple alignments, which is founded on the position weight matrices optimization, as well as on implementation of the two-dimensional dynamic programming. This approach allows the construction of multiple alignments of the indistinctly similar amino acid and nucleotide sequences that accumulated more than 1.5 substitutions per a single amino acid or a nucleotide without performing the sequences paired comparisons. The article examines the principles of the web server operation and two examples of studying amino acid and nucleotide sequences, as well as information that could be obtained using the web server.

Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe

DOEpatents

Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

2000-01-01

A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

Soil amino acid composition across a boreal forest successional sequence

Treesearch

Nancy R. Werdin-Pfisterer; Knut Kielland; Richard D. Boone

2009-01-01

Soil amino acids are important sources of organic nitrogen for plant nutrition, yet few studies have examined which amino acids are most prevalent in the soil. In this study, we examined the composition, concentration, and seasonal patterns of soil amino acids across a primary successional sequence encompassing a natural gradient of plant productivity and soil...

Preferential amino acid sequences in alumina-catalyzed peptide bond formation.

PubMed

Bujdák, J; Rode, B M

2002-05-21

The catalytic effect of activated alumina on amino acid condensation was investigated. The readiness of amino acids to form peptide sequences was estimated on the basis of the yield of dipeptides and was found to decrease in the order glycine (Gly), alanine (Ala), leucine (Leu), valine (Val), proline (Pro). For example, approximately 15% Gly was converted to the dipeptide (Gly(2)), 5% to cyclic anhydride (cyc(Gly(2))) and small amounts of tri- (Gly(3)) and tetrapeptide (Gly(4)) were formed after 28 days. On the other hand, only trace amounts of Pro(2) were formed from proline under the same conditions. Preferential formation of certain sequences was observed in the mixed reaction systems containing two amino acids. For example, almost ten times more Gly-Val than Val-Gly was formed in the Gly+Val reaction system. The preferred sequences can be explained on the basis of an inductive effect that side groups have on the nucleophilicity and electrophilicity, respectively, of the amino and carboxyl groups. A comparison with published data of amino acid reactions in other reaction systems revealed that the main trends of preferential sequence formation were the same as those described for the salt-induced peptide formation (SIPF) reaction. The results of this work and other previously published papers show that alumina and related mineral surfaces might have played a crucial role in the prebiotic formation of the first peptides on the primitive earth.

Conserved DNA motifs in the type II-A CRISPR leader region.

PubMed

Van Orden, Mason J; Klein, Peter; Babu, Kesavan; Najar, Fares Z; Rajan, Rakhi

2017-01-01

The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3' end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3' leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3' leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.

Conserved DNA motifs in the type II-A CRISPR leader region

PubMed Central

Babu, Kesavan; Najar, Fares Z.

2017-01-01

The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci. PMID:28392985

37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Nucleotide and/or amino acid... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences § 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications. (a) Nucleotide and...

37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01 false Nucleotide and/or amino acid... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences § 1.821 Nucleotide and/or amino acid sequence disclosures in patent applications. (a) Nucleotide and...

The cDNA sequence of a neutral horseradish peroxidase.

PubMed

Bartonek-Roxå, E; Eriksson, H; Mattiasson, B

1991-02-16

A cDNA clone encoding a horseradish (Armoracia rusticana) peroxidase has been isolated and characterized. The cDNA contains 1378 nucleotides excluding the poly(A) tail and the deduced protein contains 327 amino acids which includes a 28 amino acid leader sequence. The predicted amino acid sequence is nine amino acids shorter than the major isoenzyme belonging to the horseradish peroxidase C group (HRP-C) and the sequence shows 53.7% identity with this isoenzyme. The described clone encodes nine cysteines of which eight correspond well with the cysteines found in HRP-C. Five potential N-glycosylation sites with the general sequence Asn-X-Thr/Ser are present in the deduced sequence. Compared to the earlier described HRP-C this is three glycosylation sites less. The shorter sequence and fewer N-glycosylation sites give the native isoenzyme a molecular weight of several thousands less than the horseradish peroxidase C isoenzymes. Comparison with the net charge value of HRP-C indicates that the described cDNA clone encodes a peroxidase which has either the same or a slightly less basic pI value, depending on whether the encoded protein is N-terminally blocked or not. This excludes the possibility that HRP-n could belong to either the HRP-A, -D or -E groups. The low sequence identity (53.7%) with HRP-C indicates that the described clone does not belong to the HRP-C isoenzyme group and comparison of the total amino acid composition with the HRP-B group does not place the described clone within this isoenzyme group. Our conclusion is that the described cDNA clone encodes a neutral horseradish peroxidase which belongs to a new, not earlier described, horseradish peroxidase group.

The complete amino acid sequence of human skeletal-muscle fructose-bisphosphate aldolase.

PubMed Central

Freemont, P S; Dunbar, B; Fothergill-Gilmore, L A

1988-01-01

The complete amino acid sequence of human skeletal-muscle fructose-bisphosphate aldolase, comprising 363 residues, was determined. The sequence was deduced by automated sequencing of CNBr-cleavage, o-iodosobenzoic acid-cleavage, trypsin-digest and staphylococcal-proteinase-digest fragments. Comparison of the sequence with other class I aldolase sequences shows that the mammalian muscle isoenzyme is one of the most highly conserved enzymes known, with only about 2% of the residues changing per 100 million years. Non-mammalian aldolases appear to be evolving at the same rate as other glycolytic enzymes, with about 4% of the residues changing per 100 million years. Secondary-structure predictions are analysed in an accompanying paper [Sawyer, Fothergill-Gilmore & Freemont (1988) Biochem. J. 249, 789-793]. PMID:3355497

Sequences Of Amino Acids For Human Serum Albumin

NASA Technical Reports Server (NTRS)

Carter, Daniel C.

1992-01-01

Sequences of amino acids defined for use in making polypeptides one-third to one-sixth as large as parent human serum albumin molecule. Smaller, chemically stable peptides have diverse applications including service as artificial human serum and as active components of biosensors and chromatographic matrices. In applications involving production of artificial sera from new sequences, little or no concern about viral contaminants. Smaller genetically engineered polypeptides more easily expressed and produced in large quantities, making commercial isolation and production more feasible and profitable.

Comparative characterization of random-sequence proteins consisting of 5, 12, and 20 kinds of amino acids

PubMed Central

Tanaka, Junko; Doi, Nobuhide; Takashima, Hideaki; Yanagawa, Hiroshi

2010-01-01

Screening of functional proteins from a random-sequence library has been used to evolve novel proteins in the field of evolutionary protein engineering. However, random-sequence proteins consisting of the 20 natural amino acids tend to aggregate, and the occurrence rate of functional proteins in a random-sequence library is low. From the viewpoint of the origin of life, it has been proposed that primordial proteins consisted of a limited set of amino acids that could have been abundantly formed early during chemical evolution. We have previously found that members of a random-sequence protein library constructed with five primitive amino acids show high solubility (Doi et al., Protein Eng Des Sel 2005;18:279–284). Although such a library is expected to be appropriate for finding functional proteins, the functionality may be limited, because they have no positively charged amino acid. Here, we constructed three libraries of 120-amino acid, random-sequence proteins using alphabets of 5, 12, and 20 amino acids by preselection using mRNA display (to eliminate sequences containing stop codons and frameshifts) and characterized and compared the structural properties of random-sequence proteins arbitrarily chosen from these libraries. We found that random-sequence proteins constructed with the 12-member alphabet (including five primitive amino acids and positively charged amino acids) have higher solubility than those constructed with the 20-member alphabet, though other biophysical properties are very similar in the two libraries. Thus, a library of moderate complexity constructed from 12 amino acids may be a more appropriate resource for functional screening than one constructed from 20 amino acids. PMID:20162614

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2011 CFR

2011-07-01

... for nucleotide and/or amino acid sequence data. 1.822 Section 1.822 Patents, Trademarks, and... Amino Acid Sequences § 1.822 Symbols and format to be used for nucleotide and/or amino acid sequence data. (a) The symbols and format to be used for nucleotide and/or amino acid sequence data shall...

Negative effect of the 5'-untranslated leader sequence on Ac transposon promoter expression.

PubMed

Scortecci, K C; Raina, R; Fedoroff, N V; Van Sluys, M A

1999-08-01

Transposable elements are used in heterologous plant hosts to clone genes by insertional mutagenesis. The Activator (Ac) transposable element has been cloned from maize, and introduced into a variety of plants. However, differences in regulation and transposition frequency have been observed between different host plants. The cause of this variability is still unknown. To better understand the activity of the Ac element, we analyzed the Ac promoter region and its 5'-untranslated leader sequence (5' UTL). Transient assays in tobacco NT1 suspension cells showed that the Ac promoter is a weak promoter and its activity was localized by deletion analyses. The data presented here indicate that the core of the Ac promoter is contained within 153 bp fragment upstream to transcription start sites. An important inhibitory effect (80%) due to the presence of the 5' UTL was found on the expression of LUC reporter gene. Here we demonstrate that the presence of the 5' UTL in the constructs reduces the expression driven by either strong or weak promoters.

Amino acid sequence of a trypsin inhibitor from a Spirometra (Spirometra erinaceieuropaei).

PubMed

Sanda, A; Uchida, A; Itagaki, T; Kobayashi, H; Inokuchi, N; Koyama, T; Iwama, M; Ohgi, K; Irie, M

2001-12-01

A trypsin inhibitor that is highly homologous with bovine pancreatic trypsin inhibitor (BPTI) was co-purified along with RNase from Spirometra (Spirometra erinaceieuropaei). The amino acid sequence of this inhibitor (SETI) and the nucleotide sequence of the cDNA encoding this protein were determined by protein chemistry and gene technology. SETI contains 68 amino acid residues and has a molecular mass of 7,798 Da. SETI has 31 amino acid residues that are identical with BPTI's sequence, including 6 half-cystine and 5 aromatic amino acid residues. The active site Lys residue in BPTI is replaced by an Arg residue in SETI. SETI is an effective inhibitor of trypsin and moderately inhibits a-chymotrypsin, but less inhibits elastase or subtilisin. SETI was expressed by E. coli containing a PelB vector carrying the SETI encoding cDNA; an expression yield of 0.68 mg/l was obtained. The phylogenetic relationship of SETI and the other BPTI-like trypsin inhibitors was analyzed using most likelihood inference methods.

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2011 CFR

2011-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2013 CFR

2013-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2012 CFR

2012-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2010 CFR

2010-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

37 CFR 1.823 - Requirements for nucleotide and/or amino acid sequences as part of the application.

Code of Federal Regulations, 2014 CFR

2014-07-01

... and/or amino acid sequences as part of the application. 1.823 Section 1.823 Patents, Trademarks, and... Amino Acid Sequences § 1.823 Requirements for nucleotide and/or amino acid sequences as part of the... incorporation-by-reference of the Sequence Listing as required by § 1.52(e)(5). The presentation of the...

DNA sequence analysis of simian virus 40 mutants with deletions mapping in the leader region of the late viral mRNA's: mutants with deletions similar in size and position exhibit varied phenotypes.

PubMed

Barkan, A; Mertz, J E

1981-02-01

The nucleotide sequences of 10 viable yet partially defective deletion mutants of simian virus 40 were determined. The deletions mapped within, and, in many cases, 5' to, the predominant leader sequence of the late viral mRNA's. They ranged from 74 to 187 nucleotide pairs in length. Six of the mutants had lost the sequence that corresponds to the "cap" site (5' terminus) of the most abundant class of 16S mRNA's. One of these mutants had a deletion that extended 103 nucleotide pairs into the region preceding this primary cap site and, therefore, was missing many secondary cap sites as well. A seventh mutant lacked the entire major 16S leader sequence except for the first six nucleotides at its 5' end and the last nine at its 3' end. Although these mutants differed in the size and position of their deletions, we were unable to discover any simple correlations between their growth characteristics and their DNA sequences. This finding indicates that the secondary structures of the RNA transcripts may play a more important role than the exact nucleotide sequence of the RNAs in determining how they function within the cell.

Amino acid sequence of tyrosinase from Neurospora crassa.

PubMed Central

Lerch, K

1978-01-01

The amino-acid sequence of tyrosinase from Neurospora crassa (monophenol,dihydroxyphenylalanine:oxygen oxidoreductase, EC 1.14.18.1) is reported. This copper-containing oxidase consists of a single polypeptide chain of 407 amino acids. The primary structure was determined by automated and manual sequence analysis on fragments produced by cleavage with cyanogen bromide and on peptides obtained by digestion with trypsin, pepsin, thermolysin, or chymotrypsin. The amino terminus of the protein is acetylated and the single cysteinyl residue 96 is covalently linked via a thioether bridge to histidyl residue 94. The formation and the possible role of this unusual structure in Neurospora tyrosinase is discussed. Dye-sensitized photooxidation of apotyrosinase and active-site-directed inactivation of the native enzyme indicate the possible involvement of histidyl residues 188, 192, 289, and 305 or 306 as ligands to the active-site copper as well as in the catalytic mechanism of this monooxygenase. PMID:151279

Nanopores and nucleic acids: prospects for ultrarapid sequencing

NASA Technical Reports Server (NTRS)

Deamer, D. W.; Akeson, M.

2000-01-01

DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for directly reading information encoded in linear polymers. If single-nucleotide resolution can be achieved, it is possible that nucleic acid sequences can be determined at rates exceeding a thousand bases per second.

PubDNA Finder: a web database linking full-text articles to sequences of nucleic acids.

PubMed

García-Remesal, Miguel; Cuevas, Alejandro; Pérez-Rey, David; Martín, Luis; Anguita, Alberto; de la Iglesia, Diana; de la Calle, Guillermo; Crespo, José; Maojo, Víctor

2010-11-01

PubDNA Finder is an online repository that we have created to link PubMed Central manuscripts to the sequences of nucleic acids appearing in them. It extends the search capabilities provided by PubMed Central by enabling researchers to perform advanced searches involving sequences of nucleic acids. This includes, among other features (i) searching for papers mentioning one or more specific sequences of nucleic acids and (ii) retrieving the genetic sequences appearing in different articles. These additional query capabilities are provided by a searchable index that we created by using the full text of the 176 672 papers available at PubMed Central at the time of writing and the sequences of nucleic acids appearing in them. To automatically extract the genetic sequences occurring in each paper, we used an original method we have developed. The database is updated monthly by automatically connecting to the PubMed Central FTP site to retrieve and index new manuscripts. Users can query the database via the web interface provided. PubDNA Finder can be freely accessed at http://servet.dia.fi.upm.es:8080/pubdnafinder

Comparison of ZP3 protein sequences among vertebrate species: to obtain a consensus sequence for immunocontraception.

PubMed

Zhu, X; Naz, R K

1999-03-01

The deduced ZP3 amino acid (aa) sequences of 13 vertebrate species namely mouse, hamster, rabbit, pig, porcine, cow, dog, cat, human, bonnet, marmoset, carp, and frog were compared using the PILEUP and PRETTY alignment programs (GCG, Wisconsin, USA). The published aa sequences obtained from 13 vertebrate species indicated the overall evolutionarily conservation in the N-terminus, central region, and C-terminus of the ZP3 polypeptide. More variations of ZP3 polypeptide sequences were seen in the alignments of carp and frog from the 11 mammalian species making the leader sequence more prominent. The canonical furin proteolytic processing signal at the C-terminus was found in all the ZP3 polypeptide sequences except of carp and frog. In the central region, the ZP3 deduced aa sequences of all the 13 vertebrate species aligned well, and six relatively conserved sequences were found. There are 11 conserved cysteine residues in the central region across all species including carp and frog, indicating that these residues have longer evolutionary history. The ZP3 aa sequence similarities were examined using the GAP program (GCG). The highest aa similarities are observed between the members of the same order within the class mammalia, and also (95.4%) between pig (ungulata) and rabbit (lagomorpha). The deduced ZP3 aa sequences per se may not be enough to build a phylogenetic tree.

Complete complementary DNA-derived amino acid sequence of canine cardiac phospholamban.

PubMed Central

Fujii, J; Ueno, A; Kitano, K; Tanaka, S; Kadoma, M; Tada, M

1987-01-01

Complementary DNA (cDNA) clones specific for phospholamban of sarcoplasmic reticulum membranes have been isolated from a canine cardiac cDNA library. The amino acid sequence deduced from the cDNA sequence indicates that phospholamban consists of 52 amino acid residues and lacks an amino-terminal signal sequence. The protein has an inferred mol wt 6,080 that is in agreement with its apparent monomeric mol wt 6,000, estimated previously by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Phospholamban contains two distinct domains, a hydrophilic region at the amino terminus (domain I) and a hydrophobic region at the carboxy terminus (domain II). We propose that domain I is localized at the cytoplasmic surface and offers phosphorylatable sites whereas domain II is anchored into the sarcoplasmic reticulum membrane. PMID:3793929

The complete amino acid sequence of human erythrocyte diphosphoglycerate mutase.

PubMed Central

Haggarty, N W; Dunbar, B; Fothergill, L A

1983-01-01

The complete amino acid sequence of human erythrocyte diphosphoglycerate mutase, comprising 239 residues, was determined. The sequence was deduced from the four cyanogen bromide fragments, and from the peptides derived from these fragments after digestion with a number of proteolytic enzymes. Comparison of this sequence with that of the yeast glycolytic enzyme, phosphoglycerate mutase, shows that these enzymes are 47% identical. Most, but not all, of the residues implicated as being important for the activity of the glycolytic mutase are conserved in the erythrocyte diphosphoglycerate mutase. PMID:6313356

Quantum-Sequencing: Biophysics of quantum tunneling through nucleic acids

NASA Astrophysics Data System (ADS)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

Tunneling microscopy and spectroscopy has extensively been used in physical surface sciences to study quantum tunneling to measure electronic local density of states of nanomaterials and to characterize adsorbed species. Quantum-Sequencing (Q-Seq) is a new method based on tunneling microscopy for electronic sequencing of single molecule of nucleic acids. A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free single-molecule sequencing method. Here, we present the unique ``electronic fingerprints'' for all nucleotides on DNA and RNA using Q-Seq along their intrinsic biophysical parameters. We have analyzed tunneling spectra for the nucleotides at different pH conditions and analyzed the HOMO, LUMO and energy gap for all of them. In addition we show a number of biophysical parameters to further characterize all nucleobases (electron and hole transition voltage and energy barriers). These results highlight the robustness of Q-Seq as a technique for next-generation sequencing.

Amino acid sequence of the Amur tiger prion protein.

PubMed

Wu, Changde; Pang, Wanyong; Zhao, Deming

2006-10-01

Prion diseases are fatal neurodegenerative disorders in human and animal associated with conformational conversion of a cellular prion protein (PrP(C)) into the pathologic isoform (PrP(Sc)). Various data indicate that the polymorphisms within the open reading frame (ORF) of PrP are associated with the susceptibility and control the species barrier in prion diseases. In the present study, partial Prnp from 25 Amur tigers (tPrnp) were cloned and screened for polymorphisms. Four single nucleotide polymorphisms (T423C, A501G, C511A, A610G) were found; the C511A and A610G nucleotide substitutions resulted in the amino acid changes Lysine171Glutamine and Alanine204Threoine, respectively. The tPrnp amino acid sequence is similar to house cat (Felis catus ) and sheep, but differs significantly from other two cat Prnp sequences that were previously deposited in GenBank.

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F. William

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient.

Method for high-volume sequencing of nucleic acids: random and directed priming with libraries of oligonucleotides

DOEpatents

Studier, F.W.

1995-04-18

Random and directed priming methods for determining nucleotide sequences by enzymatic sequencing techniques, using libraries of primers of lengths 8, 9 or 10 bases, are disclosed. These methods permit direct sequencing of nucleic acids as large as 45,000 base pairs or larger without the necessity for subcloning. Individual primers are used repeatedly to prime sequence reactions in many different nucleic acid molecules. Libraries containing as few as 10,000 octamers, 14,200 nonamers, or 44,000 decamers would have the capacity to determine the sequence of almost any cosmid DNA. Random priming with a fixed set of primers from a smaller library can also be used to initiate the sequencing of individual nucleic acid molecules, with the sequence being completed by directed priming with primers from the library. In contrast to random cloning techniques, a combined random and directed priming strategy is far more efficient. 2 figs.

Nucleotide sequence analysis of the L gene of Newcastle disease virus: homologies with Sendai and vesicular stomatitis viruses.

PubMed Central

Yusoff, K; Millar, N S; Chambers, P; Emmerson, P T

1987-01-01

The nucleotide sequence of the L gene of the Beaudette C strain of Newcastle disease virus (NDV) has been determined. The L gene is 6704 nucleotides long and encodes a protein of 2204 amino acids with a calculated molecular weight of 248822. Mung bean nuclease mapping of the 5' terminus of the L gene mRNA indicates that the transcription of the L gene is initiated 11 nucleotides upstream of the translational start site. Comparison with the amino acid sequences of the L genes of Sendai virus and vesicular stomatitis virus (VSV) suggests that there are several regions of homology between the sequences. These data provide further evidence for an evolutionary relationship between the Paramyxoviridae and the Rhabdoviridae. A non-coding sequence of 46 nucleotides downstream of the presumed polyadenylation site of the L gene may be part of a negative strand leader RNA. Images PMID:3035486

Conservation of Shannon's redundancy for proteins. [information theory applied to amino acid sequences

NASA Technical Reports Server (NTRS)

Gatlin, L. L.

1974-01-01

Concepts of information theory are applied to examine various proteins in terms of their redundancy in natural originators such as animals and plants. The Monte Carlo method is used to derive information parameters for random protein sequences. Real protein sequence parameters are compared with the standard parameters of protein sequences having a specific length. The tendency of a chain to contain some amino acids more frequently than others and the tendency of a chain to contain certain amino acid pairs more frequently than other pairs are used as randomness measures of individual protein sequences. Non-periodic proteins are generally found to have random Shannon redundancies except in cases of constraints due to short chain length and genetic codes. Redundant characteristics of highly periodic proteins are discussed. A degree of periodicity parameter is derived.

Listening to Students and Faculty: The Value to Developmental Education Leaders

ERIC Educational Resources Information Center

Clifton, Connie J.

2013-01-01

Helping students complete developmental course sequences and graduate from college is one of the biggest challenges facing community college leaders and educators. The majority of entering students need one or more developmental courses yet most of these students never finish the developmental sequence. Colleges are continuously developing new…

Complete Amino Acid Sequence of a Copper/Zinc-Superoxide Dismutase from Ginger Rhizome.

PubMed

Nishiyama, Yuki; Fukamizo, Tamo; Yoneda, Kazunari; Araki, Tomohiro

2017-04-01

Superoxide dismutase (SOD) is an antioxidant enzyme protecting cells from oxidative stress. Ginger (Zingiber officinale) is known for its antioxidant properties, however, there are no data on SODs from ginger rhizomes. In this study, we purified SOD from the rhizome of Z. officinale (Zo-SOD) and determined its complete amino acid sequence using N terminal sequencing, amino acid analysis, and de novo sequencing by tandem mass spectrometry. Zo-SOD consists of 151 amino acids with two signature Cu/Zn-SOD motifs and has high similarity to other plant Cu/Zn-SODs. Multiple sequence alignment showed that Cu/Zn-binding residues and cysteines forming a disulfide bond, which are highly conserved in Cu/Zn-SODs, are also present in Zo-SOD. Phylogenetic analysis revealed that plant Cu/Zn-SODs clustered into distinct chloroplastic, cytoplasmic, and intermediate groups. Among them, only chloroplastic enzymes carried amino acid substitutions in the region functionally important for enzymatic activity, suggesting that chloroplastic SODs may have a function distinct from those of SODs localized in other subcellular compartments. The nucleotide sequence of the Zo-SOD coding region was obtained by reverse-translation, and the gene was synthesized, cloned, and expressed. The recombinant Zo-SOD demonstrated pH stability in the range of 5-10, which is similar to other reported Cu/Zn-SODs, and thermal stability in the range of 10-60 °C, which is higher than that for most plant Cu/Zn-SODs but lower compared to the enzyme from a Z. officinale relative Curcuma aromatica.

Protein location prediction using atomic composition and global features of the amino acid sequence

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

Cherian, Betsy Sheena, E-mail: betsy.skb@gmail.com; Nair, Achuthsankar S.

2010-01-22

Subcellular location of protein is constructive information in determining its function, screening for drug candidates, vaccine design, annotation of gene products and in selecting relevant proteins for further studies. Computational prediction of subcellular localization deals with predicting the location of a protein from its amino acid sequence. For a computational localization prediction method to be more accurate, it should exploit all possible relevant biological features that contribute to the subcellular localization. In this work, we extracted the biological features from the full length protein sequence to incorporate more biological information. A new biological feature, distribution of atomic composition is effectivelymore » used with, multiple physiochemical properties, amino acid composition, three part amino acid composition, and sequence similarity for predicting the subcellular location of the protein. Support Vector Machines are designed for four modules and prediction is made by a weighted voting system. Our system makes prediction with an accuracy of 100, 82.47, 88.81 for self-consistency test, jackknife test and independent data test respectively. Our results provide evidence that the prediction based on the biological features derived from the full length amino acid sequence gives better accuracy than those derived from N-terminal alone. Considering the features as a distribution within the entire sequence will bring out underlying property distribution to a greater detail to enhance the prediction accuracy.« less

Characteristics of negative lightning leaders to ground observed by TVLS

NASA Astrophysics Data System (ADS)

Qiu, Shi; Jiang, Zhidong; Shi, Lihua; Niu, Zhencong; Zhang, Peng

2015-12-01

The Thunder and VHF lightning Locating System (termed TVLS) is established and utilized to observe leader behaviors of negative cloud to ground (CG) flashes. This system takes advantages of VHF broadband interferometer and thunder imaging technique, which could provide the temporal and quasi-3D spatial evolution of lightning discharges. In conjunction with synchronized electric field changes (E-changes) and electric field derivatives (dE/dt) records, 10 leaders from two CG flashes are presented and analyzed. Based on the characteristic evolution of leader velocities, E-changes, dE/dt waveforms and VHF intervals, three stepped leaders, five dart leaders and two dart-stepped leaders are identified. The stepped leaders behave impulsive while approaching ground, with average speed (1.3∼3.9)×105 m/s. All normal dart leaders presented here exhibit irregular (or termed "chaotic") fluctuations in E-change and dE/dt waveforms, with the similar speeds ((1.0∼2.9)×107 m/s) and durations ((300∼700) μs) of the "chaotic" leaders observed by other investigators. The irregular fluctuations would be weak if the channels keep conductive until the leader enters the less conductive branches, coinciding with VHF radiations in time sequence. The dart-stepped leader could be divided into the dart stage and the stepped stage by a transition region, which usually lies around the branch junctions of previous active channel. The dart stage resembles the normal dart leader, and the stepped stage usually associates with regular pulse trains in E-change and dE/dt waveforms.

Human retroviruses and AIDS 1996. A compilation and analysis of nucleic acid and amino acid sequences

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

Myers, G.; Foley, B.; Korber, B.

1997-04-01

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (1) Nuclear Acid Alignments and Sequences; (2) Amino Acid Alignments; (3) Analysis; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated throughout the year on the Web site, http://hiv-web.lanl.gov. While this publication could take the form of a review or sequence monograph, it is not so conceived.more » Instead, the literature from which the database is derived has simply been summarized and some elementary computational analyses have been performed upon the data. Interpretation and commentary have been avoided insofar as possible so that the reader can form his or her own judgments concerning the complex information. In addition to the general descriptions of the parts of the compendium, the user should read the individual introductions for each part.« less

Streptococcal phosphoenolpyruvate-sugar phosphotransferase system: amino acid sequence and site of ATP-dependent phosphorylation of HPr

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

Deutscher, J.; Pevec, B.; Beyreuther, K.

1986-10-21

The amino acid sequence of histidine-containing protein (HPr) from Streptococcus faecalis has been determined by direct Edman degradation of intact HPr and by amino acid sequence analysis of tryptic peptides, V8 proteolyptic peptides, thermolytic peptides, and cyanogen bromide cleavage products. HPr from S. faecalis was found to contain 89 amino acid residues, corresponding to a molecular weight of 9438. The amino acid sequence of HPr from S. faecalis shows extended homology to the primary structure of HPr proteins from other bacteria. Besides the phosphoenolpyruvate-dependent phosphorylation of a histidyl residue in HPr, catalyzed by enzyme I of the bacterial phosphotransferase system,more » HPr was also found to be phosphorylated at a seryl residue in an ATP-dependent protein kinase catalyzed reaction. The site of ATP-dependent phosphorylation in HPr of S faecalis has now been determined. (/sup 32/P)P-Ser-HPr was digested with three different proteases, and in each case, a single labeled peptide was isolated. Following digestion with subtilisin, they obtained a peptide with the sequence -(P)Ser-Ile-Met-. Using chymotrypsin, they isolated a peptide with the sequence -Ser-Val-Asn-Leu-Lys-(P)Ser-Ile-Met-Gly-Val-Met-. The longest labeled peptide was obtained with V8 staphylococcal protease. According to amino acid analysis, this peptide contained 36 out of the 89 amino acid residues of HPr. The following sequence of 12 amino acid residues of the V8 peptide was determined: -Tyr-Lys-Gly-Lys-Ser-Val-Asn-Leu-Lys-(P)Ser-Ile-Met-. Thus, the site of ATP-dependent phosphorylation was determined to be Ser-46 within the primary structure of HPr.« less

Diagnostics based on nucleic acid sequence variant profiling: PCR, hybridization, and NGS approaches.

PubMed

Khodakov, Dmitriy; Wang, Chunyan; Zhang, David Yu

2016-10-01

Nucleic acid sequence variations have been implicated in many diseases, and reliable detection and quantitation of DNA/RNA biomarkers can inform effective therapeutic action, enabling precision medicine. Nucleic acid analysis technologies being translated into the clinic can broadly be classified into hybridization, PCR, and sequencing, as well as their combinations. Here we review the molecular mechanisms of popular commercial assays, and their progress in translation into in vitro diagnostics. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

"De-novo" amino acid sequence elucidation of protein G'e by combined "top-down" and "bottom-up" mass spectrometry.

PubMed

Yefremova, Yelena; Al-Majdoub, Mahmoud; Opuni, Kwabena F M; Koy, Cornelia; Cui, Weidong; Yan, Yuetian; Gross, Michael L; Glocker, Michael O

2015-03-01

Mass spectrometric de-novo sequencing was applied to review the amino acid sequence of a commercially available recombinant protein G´ with great scientific and economic importance. Substantial deviations to the published amino acid sequence (Uniprot Q54181) were found by the presence of 46 additional amino acids at the N-terminus, including a so-called "His-tag" as well as an N-terminal partial α-N-gluconoylation and α-N-phosphogluconoylation, respectively. The unexpected amino acid sequence of the commercial protein G' comprised 241 amino acids and resulted in a molecular mass of 25,998.9 ± 0.2 Da for the unmodified protein. Due to the higher mass that is caused by its extended amino acid sequence compared with the original protein G' (185 amino acids), we named this protein "protein G'e." By means of mass spectrometric peptide mapping, the suggested amino acid sequence, as well as the N-terminal partial α-N-gluconoylations, was confirmed with 100% sequence coverage. After the protein G'e sequence was determined, we were able to determine the expression vector pET-28b from Novagen with the Xho I restriction enzyme cleavage site as the best option that was used for cloning and expressing the recombinant protein G'e in E. coli. A dissociation constant (K(d)) value of 9.4 nM for protein G'e was determined thermophoretically, showing that the N-terminal flanking sequence extension did not cause significant changes in the binding affinity to immunoglobulins.

Correlation between fibroin amino acid sequence and physical silk properties.

PubMed

Fedic, Robert; Zurovec, Michal; Sehnal, Frantisek

2003-09-12

The fiber properties of lepidopteran silk depend on the amino acid repeats that interact during H-fibroin polymerization. The aim of our research was to relate repeat composition to insect biology and fiber strength. Representative regions of the H-fibroin genes were sequenced and analyzed in three pyralid species: wax moth (Galleria mellonella), European flour moth (Ephestia kuehniella), and Indian meal moth (Plodia interpunctella). The amino acid repeats are species-specific, evidently a diversification of an ancestral region of 43 residues, and include three types of regularly dispersed motifs: modifications of GSSAASAA sequence, stretches of tripeptides GXZ where X and Z represent bulky residues, and sequences similar to PVIVIEE. No concatenations of GX dipeptide or alanine, which are typical for Bombyx silkworms and Antheraea silk moths, respectively, were found. Despite different repeat structure, the silks of G. mellonella and E. kuehniella exhibit similar tensile strength as the Bombyx and Antheraea silks. We suggest that in these latter two species, variations in the repeat length obstruct repeat alignment, but sufficiently long stretches of iterated residues get superposed to interact. In the pyralid H-fibroins, interactions of the widely separated and diverse motifs depend on the precision of repeat matching; silk is strong in G. mellonella and E. kuehniella, with 2-3 types of long homogeneous repeats, and nearly 10 times weaker in P. interpunctella, with seven types of shorter erratic repeats. The high proportion of large amino acids in the H-fibroin of pyralids has probably evolved in connection with the spinning habit of caterpillars that live in protective silk tubes and spin continuously, enlarging the tubes on one end and partly devouring the other one. The silk serves as a depot of energetically rich and essential amino acids that may be scarce in the diet.

Characterization of shark complement factor I gene(s): genomic analysis of a novel shark-specific sequence.

PubMed

Shin, Dong-Ho; Webb, Barbara M; Nakao, Miki; Smith, Sylvia L

2009-07-01

Complement factor I is a crucial regulator of mammalian complement activity. Very little is known of complement regulators in non-mammalian species. We isolated and sequenced four highly similar complement factor I cDNAs from the liver of the nurse shark (Ginglymostoma cirratum), designated as GcIf-1, GcIf-2, GcIf-3 and GcIf-4 (previously referred to as nsFI-a, -b, -c and -d) which encode 689, 673, 673 and 657 amino acid residues, respectively. They share 95% (acid identities with each other, 35.4-39.6% and 62.8-65.9% with factor I of mammals and banded houndshark (Triakis scyllium), respectively. The modular structure of the GcIf is similar to that of mammals with one notable exception, the presence of a novel shark-specific sequence between the leader peptide (LP) and the factor I membrane attack complex (FIMAC) domain. The cDNA sequences differ only in the size and composition of the shark-specific region (SSR). Sequence analysis of each SSR has identified within the region two novel short sequences (SS1 and SS2) and three repeat sequences (RS1-3). Genomic analysis has revealed the existence of three introns between the leader peptide and the FIMAC domain, tentatively designated intron 1, intron 2, and intron 3 which span 4067, 2293 and 2082bp, respectively. Southern blot analysis suggests the presence of a single gene copy for each cDNA type. Phylogenetic analysis suggests that complement factor I of cartilaginous fish diverged prior to the emergence of mammals. All four GcIf cDNA species are expressed in four different tissues and the liver is the main tissue in which expression level of all four is high. This suggests that the expression of GcIf isotypes is tissue-dependent.

Characterization of shark complement factor I gene(s): genomic analysis of a novel shark-specific sequence

PubMed Central

Shin, Dong-Ho; Webb, Barbara M.; Nakao, Miki; Smith, Sylvia L.

2009-01-01

Complement factor I is a crucial regulator of mammalian complement activity. Very little is known of complement regulators in non-mammalian species. We isolated and sequenced four highly similar complement factor I cDNAs from the liver of the nurse shark (Ginglymostoma cirratum), designated as GcIf-1, GcIf-2, GcIf-3 and GcIf-4 (previously referred to as nsFI-a, -b, -c and –d) which encode 689, 673, 673 and 657 amino acid residues, respectively. They share 95% (≤) amino acid identities with each other, 35.4 ~ 39.6% and 62.8 ~ 65.9% with factor I of mammals and banded houndshark (Triakis scyllium), respectively. The modular structure of the GcIf is similar to that of mammals with one notable exception, the presence of a novel shark-specific sequence between the leader peptide (LP) and the factor I membrane attack complex (FIMAC) domain. The cDNA sequences differ only in the size and composition of the shark-specific region (SSR). Sequence analysis of each SSR has identified within the region two novel short sequences (SS1 and SS2) and three repeat sequences (RS1, 2 and 3). Genomic analysis has revealed the existence of three introns between the leader peptide and the FIMAC domain, tentatively designated intron 1, intron 2, and intron 3 which span 4067, 2293 and 2082 bp, respectively. Southern blot analysis suggests the presence of a single gene copy for each cDNA type. Phylogenetic analysis suggests that complement factor I of cartilaginous fish diverged prior to the emergence of mammals. All four GcIf cDNA species are expressed in four different tissues and the liver is the main tissue in which expression level of all four is high. This suggests that the expression of GcIf isotypes is tissue-dependent. PMID:19423168

Evaluation of leader peptides that affect the secretory ability of a multiple bacteriocin transporter, EnkT.

PubMed

Sushida, Hirotoshi; Ishibashi, Naoki; Zendo, Takeshi; Wilaipun, Pongtep; Leelawatcharamas, Vichien; Nakayama, Jiro; Sonomoto, Kenji

2018-02-13

EnkT is a novel ATP-binding cassette (ABC) transporter responsible for secretion of four bacteriocins, enterocins NKR-5-3A, C, D, and Z (Ent53A, C, D, and Z), produced by Enterococcus faecium NKR-5-3. It is generally recognized that the secretion of a bacteriocin requires a dedicated ABC transporter, although molecular mechanisms of this secretion are yet to be revealed. In order to characterize the unique ability of EnkT to secrete multiple bacteriocins, the role of N-terminal leader peptides of bacteriocin precursors was evaluated using Ent53C precursor as a model. The 18-amino acid leader peptide of Ent53C (Lc) was modified by site-directed mutagenesis to generate various point mutations, truncations, or extensions, and substitutions with other leader peptides. The impact of these Lc mutations on Ent53C secretion was evaluated using a quantitative antimicrobial activity assay. We observed that Ent53C production increased with Ala substitution of the highly conserved C-terminal double glycine residues that are recognized as the cleavage site. In contrast, Ent53C antimicrobial activity decreased, with decrease in the length of the putative α-helix-forming region of Lc. Furthermore, EnkT recognized and transported Ent53C of the transformants possessing heterologous leader peptides of enterocin A, pediocin PA-1, brochocins A and B, and lactococcins Qα and Qβ. These results indicated that EnkT shows significant tolerance towards the sequence and length of leader peptides, to secrete multiple bacteriocins. This further demonstrates the functional diversity of bacteriocin ABC transporters and the importance of leader peptides as their recognition motif. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

NMR studies of two spliced leader RNAs using isotope labeling

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

Lapham, J.; Crothers, D.M.

1994-12-01

Spliced leader RNAs are a class of RNA molecules (<200 nts) involved in the trans splicing of messenger RNA found in trypanosomes, nematodes, and other lower eukaryotes. The spliced leader RNA from the trypanosome Leptomonas Collosoma exists in two alternate structural forms with similar thermal stabilities. The 54 nucleotides on the 5{prime} end of the SL molecule is structurally independent from the 3{prime} half of the RNA, and displays the two structural forms. Furthermore, the favored of the two structures was shown to contain anomalous nuclease sensitivity and thermal stability features, which suggests that there may be tertiary interactions betweenmore » the splice site and other nucleotides in the 5{prime} end. Multidimensional NMR studies are underway to elucidate the structural elements present in the SL RNAs that give rise to their physical properties. Two spliced leader sequences have been studied. The first, the 54 nucleotides on the 5{prime} end of the L. Collosoma sequence, was selected because of earlier studies in our laboratory. The second sequence is the 5{prime} end of the trypanosome Crithidia Fasciculata, which was chosen because of its greater sequence homology to other SL sequences. Given the complexity of the NMR spectra for RNA molecules of this size, we have incorporated {sup 15}N/{sup 13}C-labeled nucleotides into the RNA. One of the techniques we have developed to simplify the spectra of these RNA molecules is isotope labeling of specific regions of the RNA. This has been especially helpful in assigning the secondary structure of molecules that may be able to adopt multiple conformations. Using this technique one can examine a part of the molecule without spectral interference from the unlabeled portion. We hope this approach will promote an avenue for studying the structure of larger RNAs in their native surroundings.« less

Synthetic oligonucleotide probes deduced from amino acid sequence data. Theoretical and practical considerations.

PubMed

Lathe, R

1985-05-05

Synthetic probes deduced from amino acid sequence data are widely used to detect cognate coding sequences in libraries of cloned DNA segments. The redundancy of the genetic code dictates that a choice must be made between (1) a mixture of probes reflecting all codon combinations, and (2) a single longer "optimal" probe. The second strategy is examined in detail. The frequency of sequences matching a given probe by chance alone can be determined and also the frequency of sequences closely resembling the probe and contributing to the hybridization background. Gene banks cannot be treated as random associations of the four nucleotides, and probe sequences deduced from amino acid sequence data occur more often than predicted by chance alone. Probe lengths must be increased to confer the necessary specificity. Examination of hybrids formed between unique homologous probes and their cognate targets reveals that short stretches of perfect homology occurring by chance make a significant contribution to the hybridization background. Statistical methods for improving homology are examined, taking human coding sequences as an example, and considerations of codon utilization and dinucleotide frequencies yield an overall homology of greater than 82%. Recommendations for probe design and hybridization are presented, and the choice between using multiple probes reflecting all codon possibilities and a unique optimal probe is discussed.

Complete cDNA sequence and amino acid analysis of a bovine ribonuclease K6 gene.

PubMed

Pietrowski, D; Förster, M

2000-01-01

The complete cDNA sequence of a ribonuclease k6 gene of Bos Taurus has been determined. It codes for a protein with 154 amino acids and contains the invariant cysteine, histidine and lysine residues as well as the characteristic motifs specific to ribonuclease active sites. The deduced protein sequence is 27 residues longer than other known ribonucleases k6 and shows amino acids exchanges which could reflect a strain specificity or polymorphism within the bovine genome. Based on sequence similarity we have termed the identified gene bovine ribonuclease k6 b (brk6b).

Concentric Tube Robots as Steerable Needles: Achieving Follow-the-Leader Deployment.

PubMed

Gilbert, Hunter B; Neimat, Joseph; Webster, Robert J

2015-04-01

Concentric tube robots can enable new clinical interventions if they are able to pass through soft tissue, deploy along desired paths through open cavities, or travel along winding lumens. These behaviors require the robot to deploy in such a way that the curved shape of its shaft remains unchanged as the tip progresses forward (i.e., "follow-the-leader" deployment). Follow-the-leader deployment is challenging for concentric tube robots due to elastic (and particularly torsional) coupling between the tubes that form the robot. However, as we show in this paper, follow-the-leader deployment is possible, provided that tube precurvatures and deployment sequences are appropriately selected. We begin by defining follow-the-leader deployment and providing conditions that must be satisfied for a concentric tube robot to achieve it. We then examine several useful special cases of follow-the-leader deployment, showing that both circular and helical precurvatures can be employed, and provide an experimental illustration of the helical case. We also explore approximate follow-the-leader behavior and provide a metric for the similarity of a general deployment to a follow-the-leader deployment. Finally, we consider access to the hippocampus in the brain to treat epilepsy, as a motivating clinical example for follow-the-leader deployment.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides

NASA Astrophysics Data System (ADS)

McMillen, Chelsea L.; Wright, Patience M.; Cassady, Carolyn J.

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

Negative Ion In-Source Decay Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry for Sequencing Acidic Peptides.

PubMed

McMillen, Chelsea L; Wright, Patience M; Cassady, Carolyn J

2016-05-01

Matrix-assisted laser desorption/ionization (MALDI) in-source decay was studied in the negative ion mode on deprotonated peptides to determine its usefulness for obtaining extensive sequence information for acidic peptides. Eight biological acidic peptides, ranging in size from 11 to 33 residues, were studied by negative ion mode ISD (nISD). The matrices 2,5-dihydroxybenzoic acid, 2-aminobenzoic acid, 2-aminobenzamide, 1,5-diaminonaphthalene, 5-amino-1-naphthol, 3-aminoquinoline, and 9-aminoacridine were used with each peptide. Optimal fragmentation was produced with 1,5-diaminonphthalene (DAN), and extensive sequence informative fragmentation was observed for every peptide except hirudin(54-65). Cleavage at the N-Cα bond of the peptide backbone, producing c' and z' ions, was dominant for all peptides. Cleavage of the N-Cα bond N-terminal to proline residues was not observed. The formation of c and z ions is also found in electron transfer dissociation (ETD), electron capture dissociation (ECD), and positive ion mode ISD, which are considered to be radical-driven techniques. Oxidized insulin chain A, which has four highly acidic oxidized cysteine residues, had less extensive fragmentation. This peptide also exhibited the only charged localized fragmentation, with more pronounced product ion formation adjacent to the highly acidic residues. In addition, spectra were obtained by positive ion mode ISD for each protonated peptide; more sequence informative fragmentation was observed via nISD for all peptides. Three of the peptides studied had no product ion formation in ISD, but extensive sequence informative fragmentation was found in their nISD spectra. The results of this study indicate that nISD can be used to readily obtain sequence information for acidic peptides.

37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

Code of Federal Regulations, 2014 CFR

2014-07-01

...” means those amino acids other than “Xaa” and those nucleotide bases other than “n”defined in accordance... 37 Patents, Trademarks, and Copyrights 1 2014-07-01 2014-07-01 false Nucleotide and/or amino acid... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences...

37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

Code of Federal Regulations, 2013 CFR

2013-07-01

...” means those amino acids other than “Xaa” and those nucleotide bases other than “n”defined in accordance... 37 Patents, Trademarks, and Copyrights 1 2013-07-01 2013-07-01 false Nucleotide and/or amino acid... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences...

37 CFR 1.821 - Nucleotide and/or amino acid sequence disclosures in patent applications.

Code of Federal Regulations, 2012 CFR

2012-07-01

...” means those amino acids other than “Xaa” and those nucleotide bases other than “n”defined in accordance... 37 Patents, Trademarks, and Copyrights 1 2012-07-01 2012-07-01 false Nucleotide and/or amino acid... Biotechnology Invention Disclosures Application Disclosures Containing Nucleotide And/or Amino Acid Sequences...

Full genome virus detection in fecal samples using sensitive nucleic acid preparation, deep sequencing, and a novel iterative sequence classification algorithm.

PubMed

Cotten, Matthew; Oude Munnink, Bas; Canuti, Marta; Deijs, Martin; Watson, Simon J; Kellam, Paul; van der Hoek, Lia

2014-01-01

We have developed a full genome virus detection process that combines sensitive nucleic acid preparation optimised for virus identification in fecal material with Illumina MiSeq sequencing and a novel post-sequencing virus identification algorithm. Enriched viral nucleic acid was converted to double-stranded DNA and subjected to Illumina MiSeq sequencing. The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. De novo assembly was then used to generate full viral genomes. The sensitivity of this process was demonstrated with a set of fecal samples from HIV-1 infected patients. A quantitative assessment of the mammalian, plant, and bacterial virus content of this compartment was generated and the deep sequencing data were sufficient to assembly 12 complete viral genomes from 6 virus families. The method detected high levels of enteropathic viruses that are normally controlled in healthy adults, but may be involved in the pathogenesis of HIV-1 infection and will provide a powerful tool for virus detection and for analyzing changes in the fecal virome associated with HIV-1 progression and pathogenesis.

Full Genome Virus Detection in Fecal Samples Using Sensitive Nucleic Acid Preparation, Deep Sequencing, and a Novel Iterative Sequence Classification Algorithm

PubMed Central

Cotten, Matthew; Oude Munnink, Bas; Canuti, Marta; Deijs, Martin; Watson, Simon J.; Kellam, Paul; van der Hoek, Lia

2014-01-01

We have developed a full genome virus detection process that combines sensitive nucleic acid preparation optimised for virus identification in fecal material with Illumina MiSeq sequencing and a novel post-sequencing virus identification algorithm. Enriched viral nucleic acid was converted to double-stranded DNA and subjected to Illumina MiSeq sequencing. The resulting short reads were processed with a novel iterative Python algorithm SLIM for the identification of sequences with homology to known viruses. De novo assembly was then used to generate full viral genomes. The sensitivity of this process was demonstrated with a set of fecal samples from HIV-1 infected patients. A quantitative assessment of the mammalian, plant, and bacterial virus content of this compartment was generated and the deep sequencing data were sufficient to assembly 12 complete viral genomes from 6 virus families. The method detected high levels of enteropathic viruses that are normally controlled in healthy adults, but may be involved in the pathogenesis of HIV-1 infection and will provide a powerful tool for virus detection and for analyzing changes in the fecal virome associated with HIV-1 progression and pathogenesis. PMID:24695106

NullSeq: A Tool for Generating Random Coding Sequences with Desired Amino Acid and GC Contents.

PubMed

Liu, Sophia S; Hockenberry, Adam J; Lancichinetti, Andrea; Jewett, Michael C; Amaral, Luís A N

2016-11-01

The existence of over- and under-represented sequence motifs in genomes provides evidence of selective evolutionary pressures on biological mechanisms such as transcription, translation, ligand-substrate binding, and host immunity. In order to accurately identify motifs and other genome-scale patterns of interest, it is essential to be able to generate accurate null models that are appropriate for the sequences under study. While many tools have been developed to create random nucleotide sequences, protein coding sequences are subject to a unique set of constraints that complicates the process of generating appropriate null models. There are currently no tools available that allow users to create random coding sequences with specified amino acid composition and GC content for the purpose of hypothesis testing. Using the principle of maximum entropy, we developed a method that generates unbiased random sequences with pre-specified amino acid and GC content, which we have developed into a python package. Our method is the simplest way to obtain maximally unbiased random sequences that are subject to GC usage and primary amino acid sequence constraints. Furthermore, this approach can easily be expanded to create unbiased random sequences that incorporate more complicated constraints such as individual nucleotide usage or even di-nucleotide frequencies. The ability to generate correctly specified null models will allow researchers to accurately identify sequence motifs which will lead to a better understanding of biological processes as well as more effective engineering of biological systems.

[Complete genome sequencing of polymalic acid-producing strain Aureobasidium pullulans CCTCC M2012223].

PubMed

Wang, Yongkang; Song, Xiaodan; Li, Xiaorong; Yang, Sang-tian; Zou, Xiang

2017-01-04

To explore the genome sequence of Aureobasidium pullulans CCTCC M2012223, analyze the key genes related to the biosynthesis of important metabolites, and provide genetic background for metabolic engineering. Complete genome of A. pullulans CCTCC M2012223 was sequenced by Illumina HiSeq high throughput sequencing platform. Then, fragment assembly, gene prediction, functional annotation, and GO/COG cluster were analyzed in comparison with those of other five A. pullulans varieties. The complete genome sequence of A. pullulans CCTCC M2012223 was 30756831 bp with an average GC content of 47.49%, and 9452 genes were successfully predicted. Genome-wide analysis showed that A. pullulans CCTCC M2012223 had the biggest genome assembly size. Protein sequences involved in the pullulan and polymalic acid pathway were highly conservative in all of six A. pullulans varieties. Although both A. pullulans CCTCC M2012223 and A. pullulans var. melanogenum have a close affinity, some point mutation and inserts were occurred in protein sequences involved in melanin biosynthesis. Genome information of A. pullulans CCTCC M2012223 was annotated and genes involved in melanin, pullulan and polymalic acid pathway were compared, which would provide a theoretical basis for genetic modification of metabolic pathway in A. pullulans.

Complete amino acid sequence of ananain and a comparison with stem bromelain and other plant cysteine proteases.

PubMed Central

Lee, K L; Albee, K L; Bernasconi, R J; Edmunds, T

1997-01-01

The amino acid sequences of ananain (EC3.4.22.31) and stem bromelain (3.4.22.32), two cysteine proteases from pineapple stem, are similar yet ananain and stem bromelain possess distinct specificities towards synthetic peptide substrates and different reactivities towards the cysteine protease inhibitors E-64 and chicken egg white cystatin. We present here the complete amino acid sequence of ananain and compare it with the reported sequences of pineapple stem bromelain, papain and chymopapain from papaya and actinidin from kiwifruit. Ananain is comprised of 216 residues with a theoretical mass of 23464 Da. This primary structure includes a sequence insert between residues 170 and 174 not present in stem bromelain or papain and a hydrophobic series of amino acids adjacent to His-157. It is possible that these sequence differences contribute to the different substrate and inhibitor specificities exhibited by ananain and stem bromelain. PMID:9355753

The tripartite leader sequence is required for ectopic expression of HAdV-B and HAdV-E E3 CR1 genes.

PubMed

Bair, Camden R; Kotha Lakshmi Narayan, Poornima; Kajon, Adriana E

2017-05-01

The unique repertoire of genes that characterizes the early region 3 (E3) of the different species of human adenovirus (HAdV) likely contributes to their distinct pathogenic traits. The function of many E3 CR1 proteins remains unknown possibly due to unidentified intrinsic properties that make them difficult to express ectopically. This study shows that the species HAdV-B- and HAdV-E-specific E3 CR1 genes can be expressed from vectors carrying the HAdV tripartite leader (TPL) sequence but not from traditional mammalian expression vectors. Insertion of the TPL sequence upstream of the HAdV-B and HAdV-E E3 CR1 open reading frames was sufficient to rescue protein expression from pCI-neo constructs in transfected 293T cells. The detection of higher levels of HAdV-B and HAdV-E E3 CR1 transcripts suggests that the TPL sequence may enhance gene expression at both the transcriptional and translational levels. Our findings will facilitate the characterization of additional AdV E3 proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Concentric Tube Robots as Steerable Needles: Achieving Follow-the-Leader Deployment

PubMed Central

Gilbert, Hunter B.; Neimat, Joseph; Webster, Robert J.

2015-01-01

Concentric tube robots can enable new clinical interventions if they are able to pass through soft tissue, deploy along desired paths through open cavities, or travel along winding lumens. These behaviors require the robot to deploy in such a way that the curved shape of its shaft remains unchanged as the tip progresses forward (i.e., “follow-the-leader” deployment). Follow-the-leader deployment is challenging for concentric tube robots due to elastic (and particularly torsional) coupling between the tubes that form the robot. However, as we show in this paper, follow-the-leader deployment is possible, provided that tube precurvatures and deployment sequences are appropriately selected. We begin by defining follow-the-leader deployment and providing conditions that must be satisfied for a concentric tube robot to achieve it. We then examine several useful special cases of follow-the-leader deployment, showing that both circular and helical precurvatures can be employed, and provide an experimental illustration of the helical case. We also explore approximate follow-the-leader behavior and provide a metric for the similarity of a general deployment to a follow-the-leader deployment. Finally, we consider access to the hippocampus in the brain to treat epilepsy, as a motivating clinical example for follow-the-leader deployment. PMID:26622208

A Signature in HIV-1 Envelope Leader Peptide Associated with Transition from Acute to Chronic Infection Impacts Envelope Processing and Infectivity

PubMed Central

Asmal, Mohammed; Hellmann, Ina; Liu, Weimin; Keele, Brandon F.; Perelson, Alan S.; Bhattacharya, Tanmoy; Gnanakaran, S.; Daniels, Marcus; Haynes, Barton F.; Korber, Bette T.; Hahn, Beatrice H.; Shaw, George M.; Letvin, Norman L.

2011-01-01

Mucosal transmission of the human immunodeficiency virus (HIV) results in a bottleneck in viral genetic diversity. Gnanakaran and colleagues used a computational strategy to identify signature amino acids at particular positions in Envelope that were associated either with transmitted sequences sampled very early in infection, or sequences sampled during chronic infection. Among the strongest signatures observed was an enrichment for the stable presence of histidine at position 12 at transmission and in early infection, and a recurrent loss of histidine at position 12 in chronic infection. This amino acid lies within the leader peptide of Envelope, a region of the protein that has been shown to influence envelope glycoprotein expression and virion infectivity. We show a strong association between a positively charged amino acid like histidine at position 12 in transmitted/founder viruses with more efficient trafficking of the nascent envelope polypeptide to the endoplasmic reticulum and higher steady-state glycoprotein expression compared to viruses that have a non-basic position 12 residue, a substitution that was enriched among viruses sampled from chronically infected individuals. When expressed in the context of other viral proteins, transmitted envelopes with a basic amino acid position 12 were incorporated at higher density into the virus and exhibited higher infectious titers than did non-signature envelopes. These results support the potential utility of using a computational approach to examine large viral sequence data sets for functional signatures and indicate the importance of Envelope expression levels for efficient HIV transmission. PMID:21876761

SNBRFinder: A Sequence-Based Hybrid Algorithm for Enhanced Prediction of Nucleic Acid-Binding Residues.

PubMed

Yang, Xiaoxia; Wang, Jia; Sun, Jun; Liu, Rong

2015-01-01

Protein-nucleic acid interactions are central to various fundamental biological processes. Automated methods capable of reliably identifying DNA- and RNA-binding residues in protein sequence are assuming ever-increasing importance. The majority of current algorithms rely on feature-based prediction, but their accuracy remains to be further improved. Here we propose a sequence-based hybrid algorithm SNBRFinder (Sequence-based Nucleic acid-Binding Residue Finder) by merging a feature predictor SNBRFinderF and a template predictor SNBRFinderT. SNBRFinderF was established using the support vector machine whose inputs include sequence profile and other complementary sequence descriptors, while SNBRFinderT was implemented with the sequence alignment algorithm based on profile hidden Markov models to capture the weakly homologous template of query sequence. Experimental results show that SNBRFinderF was clearly superior to the commonly used sequence profile-based predictor and SNBRFinderT can achieve comparable performance to the structure-based template methods. Leveraging the complementary relationship between these two predictors, SNBRFinder reasonably improved the performance of both DNA- and RNA-binding residue predictions. More importantly, the sequence-based hybrid prediction reached competitive performance relative to our previous structure-based counterpart. Our extensive and stringent comparisons show that SNBRFinder has obvious advantages over the existing sequence-based prediction algorithms. The value of our algorithm is highlighted by establishing an easy-to-use web server that is freely accessible at http://ibi.hzau.edu.cn/SNBRFinder.

CDSbank: taxonomy-aware extraction, selection, renaming and formatting of protein-coding DNA or amino acid sequences.

PubMed

Hazes, Bart

2014-02-28

Protein-coding DNA sequences and their corresponding amino acid sequences are routinely used to study relationships between sequence, structure, function, and evolution. The rapidly growing size of sequence databases increases the power of such comparative analyses but it makes it more challenging to prepare high quality sequence data sets with control over redundancy, quality, completeness, formatting, and labeling. Software tools for some individual steps in this process exist but manual intervention remains a common and time consuming necessity. CDSbank is a database that stores both the protein-coding DNA sequence (CDS) and amino acid sequence for each protein annotated in Genbank. CDSbank also stores Genbank feature annotation, a flag to indicate incomplete 5' and 3' ends, full taxonomic data, and a heuristic to rank the scientific interest of each species. This rich information allows fully automated data set preparation with a level of sophistication that aims to meet or exceed manual processing. Defaults ensure ease of use for typical scenarios while allowing great flexibility when needed. Access is via a free web server at http://hazeslab.med.ualberta.ca/CDSbank/. CDSbank presents a user-friendly web server to download, filter, format, and name large sequence data sets. Common usage scenarios can be accessed via pre-programmed default choices, while optional sections give full control over the processing pipeline. Particular strengths are: extract protein-coding DNA sequences just as easily as amino acid sequences, full access to taxonomy for labeling and filtering, awareness of incomplete sequences, and the ability to take one protein sequence and extract all synonymous CDS or identical protein sequences in other species. Finally, CDSbank can also create labeled property files to, for instance, annotate or re-label phylogenetic trees.

ANCAC: amino acid, nucleotide, and codon analysis of COGs--a tool for sequence bias analysis in microbial orthologs.

PubMed

Meiler, Arno; Klinger, Claudia; Kaufmann, Michael

2012-09-08

The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC's NUCOCOG dataset as the largest one available for that purpose thus far. Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills.

Translation of vph mRNA in Streptomyces lividans and Escherichia coli after removal of the 5' untranslated leader.

PubMed

Wu, C J; Janssen, G R

1996-10-01

The Streptomyces vinaceus viomycin phosphotransferase (vph) mRNA contains an untranslated leader with a conventional Shine-Dalgarno homology. The vph leader was removed by ligation of the vph coding sequence to the transcriptional start site of a Streptomyces or an Escherichia coli promoter, such that transcription would initiate at the first position of the vph start codon. Analysis of mRNA demonstrated that transcription initiated primarily at the A of the vph AUG translational start codon in both Streptomyces lividans and E. coli; cells expressing the unleadered vph mRNA were resistant to viomycin indicating that the Shine-Dalgarno sequence, or other features contained within the leader, was not necessary for vph translation. Addition of four nucleotides (5'-AUGC-3') onto the 5' end of the unleadered vph mRNA resulted in translation initiation from the vph start codon and the AUG triplet contained within the added sequence. Translational fusions of vph sequence to a Tn5 neo reporter gene indicated that the first 16 codons of vph coding sequence were sufficient to specify the translational start site and reading frame for expression of neomycin resistance in both E. coli and S. lividans.

Identification and Analysis of Novel Amino-Acid Sequence Repeats in Bacillus anthracis str. Ames Proteome Using Computational Tools

PubMed Central

Hemalatha, G. R.; Rao, D. Satyanarayana; Guruprasad, L.

2007-01-01

We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure. PMID:17538688

Trust in direct leaders and top leaders: A trickle-up model.

PubMed

Fulmer, C Ashley; Ostroff, Cheri

2017-04-01

Low levels of employee trust in top leaders pose challenges to organizations with respect to retention, performance, and profits. This research examines how trust in top leaders can be fostered through the relationships individuals have with their direct leaders. We propose a trickle-up model whereby trust in direct leaders exerts an upward influence on trust in top leaders. Drawing on the group value model, we predict that direct leaders' procedural justice serves as the key mechanism in facilitating the trickle-up process. Further, this process should be particularly strong for employees high on vertical collectivism, and the trickled-up trust in top leaders should exert a stronger impact on employees' overall performance in the organization than trust in direct leaders. Multiphase and multisource data from 336 individuals support these hypotheses. The findings advance our understanding of trust and leadership by highlighting that trust in leaders at different levels does not form independently and that trust in leaders trickles up across hierarchical levels. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Evidence of Divergent Amino Acid Usage in Comparative Analyses of R5- and X4-Associated HIV-1 Vpr Sequences

PubMed Central

Antell, Gregory C.; Zhong, Wen; Kercher, Katherine; Passic, Shendra; Williams, Jean; Liu, Yucheng; James, Tony; Jacobson, Jeffrey M.; Szep, Zsofia

2017-01-01

Vpr is an HIV-1 accessory protein that plays numerous roles during viral replication, and some of which are cell type dependent. To test the hypothesis that HIV-1 tropism extends beyond the envelope into the vpr gene, studies were performed to identify the associations between coreceptor usage and Vpr variation in HIV-1-infected patients. Colinear HIV-1 Env-V3 and Vpr amino acid sequences were obtained from the LANL HIV-1 sequence database and from well-suppressed patients in the Drexel/Temple Medicine CNS AIDS Research and Eradication Study (CARES) Cohort. Genotypic classification of Env-V3 sequences as X4 (CXCR4-utilizing) or R5 (CCR5-utilizing) was used to group colinear Vpr sequences. To reveal the sequences associated with a specific coreceptor usage genotype, Vpr amino acid sequences were assessed for amino acid diversity and Jensen-Shannon divergence between the two groups. Five amino acid alphabets were used to comprehensively examine the impact of amino acid substitutions involving side chains with similar physiochemical properties. Positions 36, 37, 41, 89, and 96 of Vpr were characterized by statistically significant divergence across multiple alphabets when X4 and R5 sequence groups were compared. In addition, consensus amino acid switches were found at positions 37 and 41 in comparisons of the R5 and X4 sequence populations. These results suggest an evolutionary link between Vpr and gp120 in HIV-1-infected patients. PMID:28620613

Human Retroviruses and AIDS. A compilation and analysis of nucleic acid and amino acid sequences: I--II; III--V

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

Myers, G.; Korber, B.; Wain-Hobson, S.

1993-12-31

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses. The scope of the compendium and database is best summarized by the five parts that it comprises: (I) HIV and SIV Nucleotide Sequences; (II) Amino Acid Sequences; (III) Analyses; (IV) Related Sequences; and (V) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.

GCPred: a web tool for guanylyl cyclase functional centre prediction from amino acid sequence.

PubMed

Xu, Nuo; Fu, Dongfang; Li, Shiang; Wang, Yuxuan; Wong, Aloysius

2018-06-15

GCPred is a webserver for the prediction of guanylyl cyclase (GC) functional centres from amino acid sequence. GCs are enzymes that generate the signalling molecule cyclic guanosine 3', 5'-monophosphate from guanosine-5'-triphosphate. A novel class of GC centres (GCCs) has been identified in complex plant proteins. Using currently available experimental data, GCPred is created to automate and facilitate the identification of similar GCCs. The server features GCC values that consider in its calculation, the physicochemical properties of amino acids constituting the GCC and the conserved amino acids within the centre. From user input amino acid sequence, the server returns a table of GCC values and graphs depicting deviations from mean values. The utility of this server is demonstrated using plant proteins and the human interleukin-1 receptor-associated kinase family of proteins as example. The GCPred server is available at http://gcpred.com. Supplementary data are available at Bioinformatics online.

Nucleotide sequence of the phosphoglycerate kinase gene from the extreme thermophile Thermus thermophilus. Comparison of the deduced amino acid sequence with that of the mesophilic yeast phosphoglycerate kinase.

PubMed Central

Bowen, D; Littlechild, J A; Fothergill, J E; Watson, H C; Hall, L

1988-01-01

Using oligonucleotide probes derived from amino acid sequencing information, the structural gene for phosphoglycerate kinase from the extreme thermophile, Thermus thermophilus, was cloned in Escherichia coli and its complete nucleotide sequence determined. The gene consists of an open reading frame corresponding to a protein of 390 amino acid residues (calculated Mr 41,791) with an extreme bias for G or C (93.1%) in the codon third base position. Comparison of the deduced amino acid sequence with that of the corresponding mesophilic yeast enzyme indicated a number of significant differences. These are discussed in terms of the unusual codon bias and their possible role in enhanced protein thermal stability. Images Fig. 1. PMID:3052437

Purification, characterization and sequence analysis of Omp50,a new porin isolated from Campylobacter jejuni.

PubMed Central

Bolla, J M; Dé, E; Dorez, A; Pagès, J M

2000-01-01

A novel pore-forming protein identified in Campylobacter was purified by ion-exchange chromatography and named Omp50 according to both its molecular mass and its outer membrane localization. We observed a pore-forming ability of Omp50 after re-incorporation into artificial membranes. The protein induced cation-selective channels with major conductance values of 50-60 pS in 1 M NaCl. N-terminal sequencing allowed us to identify the predicted coding sequence Cj1170c from the Campylobacter jejuni genome database as the corresponding gene in the NCTC 11168 genome sequence. The gene, designated omp50, consists of a 1425 bp open reading frame encoding a deduced 453-amino acid protein with a calculated pI of 5.81 and a molecular mass of 51169.2 Da. The protein possessed a 20-amino acid leader sequence. No significant similarity was found between Omp50 and porin protein sequences already determined. Moreover, the protein showed only weak sequence identity with the major outer-membrane protein (MOMP) of Campylobacter, correlating with the absence of antigenic cross-reactivity between these two proteins. Omp50 is expressed in C. jejuni and Campylobacter lari but not in Campylobacter coli. The gene, however, was detected in all three species by PCR. According to its conformation and functional properties, the protein would belong to the family of outer-membrane monomeric porins. PMID:11104668

The leader peptide of mutacin 1140 has distinct structural components compared to related class I lantibiotics

PubMed Central

Escano, Jerome; Stauffer, Byron; Brennan, Jacob; Bullock, Monica; Smith, Leif

2014-01-01

Lantibiotics are ribosomally synthesized peptide antibiotics composed of an N-terminal leader peptide that promotes the core peptide's interaction with the post translational modification (PTM) enzymes. Following PTMs, mutacin 1140 is transported out of the cell and the leader peptide is cleaved to yield the antibacterial peptide. Mutacin 1140 leader peptide is structurally unique compared to other class I lantibiotic leader peptides. Herein, we further our understanding of the structural differences of mutacin 1140 leader peptide with regard to other class I leader peptides. We have determined that the length of the leader peptide is important for the biosynthesis of mutacin 1140. We have also determined that mutacin 1140 leader peptide contains a novel four amino acid motif compared to related lantibiotics. PTM enzyme recognition of the leader peptide appears to be evolutionarily distinct from related class I lantibiotics. Our study on mutacin 1140 leader peptide provides a basis for future studies aimed at understanding its interaction with the PTM enzymes. PMID:25400246

Leader narcissism and follower outcomes: The counterbalancing effect of leader humility.

PubMed

Owens, Bradley P; Wallace, Angela S; Walker, Angela S; Waldman, David A

2015-07-01

[Correction Notice: An Erratum for this article was reported in Vol 100(4) of Journal of Applied Psychology (see record 2015-29666-001). The last name of the second author was misspelled in the Online First version of the article. All versions of this article have been corrected.] In response to recent calls to theorize and examine how multiple leader characteristics may work together in their effects, the current research examines how leader narcissism and humility interact to predict perceived leader effectiveness and follower (i.e., direct-report) job engagement and performance. Although an examination of leaders who are narcissistic yet humble may seem oxymoronic and even paradoxical, researchers have suggested that seemingly contradictory personal attributes may exist simultaneously and may actually work together to produce positive outcomes. Results from survey data from followers and leaders working for a large health insurance organization showed that the interaction of leader narcissism and leader humility is associated with perceptions of leader effectiveness, follower job engagement, and subjective and objective follower job performance. Together, these results suggest that narcissistic leaders can have positive effects on followers when their narcissism is tempered by humility. (c) 2015 APA, all rights reserved).

Trypanosomatidae: Phytomonas detection in plants and phytophagous insects by PCR amplification of a genus-specific sequence of the spliced leader gene.

PubMed

Serrano, M G; Nunes, L R; Campaner, M; Buck, G A; Camargo, E P; Teixeira, M M

1999-03-01

In this paper we describe a method for the detection of Phytomonas spp. from plants and phytophagous insects using the PCR technique by targeting a genus-specific sequence of the spliced leader (SL) gene. PCR amplification of DNA from 48 plant and insect isolates previously classified as Phytomonas by morphological, biochemical, and molecular criteria resulted in all cases in a 100-bp fragment that hybridized with the Phytomonas-specific spliced leader-derived probe SL3'. Moreover, this Phytomonas-specific PCR could also detect Phytomonas spp. in crude preparations of naturally infected plants and insects. This method shows no reaction with any other trypanosomatid genera or with plant and insect host DNA, revealing it to be able to detect Phytomonas spp. from fruit, latex, or phloem of various host plants as well as from salivary glands and digestive tubes of several species of insect hosts. Results demonstrated that SLPCR is a simple, fast, specific, and sensitive method that can be applied to the diagnosis of Phytomonas among cultured trypanosomatids and directly in plants and putative vector insects. Therefore, the method was shown to be a very specific and sensitive tool for diagnosis of Phytomonas without the need for isolation, culture, and DNA extraction of flagellates, a feature that is very convenient for practical and epidemiological purposes. Copyright 1999 Academic Press.

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2013 CFR

2013-07-01

... in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3. This incorporation by reference was... ST.25 (1998), Appendix 2, Tables 1 and 3, shall be listed in a given sequence as “n” or “Xaa... acids. (1) The amino acids in a protein or peptide sequence shall be listed using the three-letter...

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2010 CFR

2010-07-01

... in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3. This incorporation by reference was... ST.25 (1998), Appendix 2, Tables 1 and 3, shall be listed in a given sequence as “n” or “Xaa... acids. (1) The amino acids in a protein or peptide sequence shall be listed using the three-letter...

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2012 CFR

2012-07-01

... in WIPO Standard ST.25 (1998), Appendix 2, Tables 1 and 3. This incorporation by reference was... ST.25 (1998), Appendix 2, Tables 1 and 3, shall be listed in a given sequence as “n” or “Xaa... acids. (1) The amino acids in a protein or peptide sequence shall be listed using the three-letter...

Draft genome sequence of the docosahexaenoic acid producing thraustochytrid Aurantiochytrium sp. T66.

PubMed

Liu, Bin; Ertesvåg, Helga; Aasen, Inga Marie; Vadstein, Olav; Brautaset, Trygve; Heggeset, Tonje Marita Bjerkan

2016-06-01

Thraustochytrids are unicellular, marine protists, and there is a growing industrial interest in these organisms, particularly because some species, including strains belonging to the genus Aurantiochytrium, accumulate high levels of docosahexaenoic acid (DHA). Here, we report the draft genome sequence of Aurantiochytrium sp. T66 (ATCC PRA-276), with a size of 43 Mbp, and 11,683 predicted protein-coding sequences. The data has been deposited at DDBJ/EMBL/Genbank under the accession LNGJ00000000. The genome sequence will contribute new insight into DHA biosynthesis and regulation, providing a basis for metabolic engineering of thraustochytrids.

ANCAC: amino acid, nucleotide, and codon analysis of COGs – a tool for sequence bias analysis in microbial orthologs

PubMed Central

2012-01-01

Background The COG database is the most popular collection of orthologous proteins from many different completely sequenced microbial genomes. Per definition, a cluster of orthologous groups (COG) within this database exclusively contains proteins that most likely achieve the same cellular function. Recently, the COG database was extended by assigning to every protein both the corresponding amino acid and its encoding nucleotide sequence resulting in the NUCOCOG database. This extended version of the COG database is a valuable resource connecting sequence features with the functionality of the respective proteins. Results Here we present ANCAC, a web tool and MySQL database for the analysis of amino acid, nucleotide, and codon frequencies in COGs on the basis of freely definable phylogenetic patterns. We demonstrate the usefulness of ANCAC by analyzing amino acid frequencies, codon usage, and GC-content in a species- or function-specific context. With respect to amino acids we, at least in part, confirm the cognate bias hypothesis by using ANCAC’s NUCOCOG dataset as the largest one available for that purpose thus far. Conclusions Using the NUCOCOG datasets, ANCAC connects taxonomic, amino acid, and nucleotide sequence information with the functional classification via COGs and provides a GUI for flexible mining for sequence-bias. Thereby, to our knowledge, it is the only tool for the analysis of sequence composition in the light of physiological roles and phylogenetic context without requirement of substantial programming-skills. PMID:22958836

Amino acid selective unlabeling for sequence specific resonance assignments in proteins

PubMed Central

Krishnarjuna, B.; Jaipuria, Garima; Thakur, Anushikha

2010-01-01

Sequence specific resonance assignment constitutes an important step towards high-resolution structure determination of proteins by NMR and is aided by selective identification and assignment of amino acid types. The traditional approach to selective labeling yields only the chemical shifts of the particular amino acid being selected and does not help in establishing a link between adjacent residues along the polypeptide chain, which is important for sequential assignments. An alternative approach is the method of amino acid selective ‘unlabeling’ or reverse labeling, which involves selective unlabeling of specific amino acid types against a uniformly 13C/15N labeled background. Based on this method, we present a novel approach for sequential assignments in proteins. The method involves a new NMR experiment named, {12COi–15Ni+1}-filtered HSQC, which aids in linking the 1HN/15N resonances of the selectively unlabeled residue, i, and its C-terminal neighbor, i + 1, in HN-detected double and triple resonance spectra. This leads to the assignment of a tri-peptide segment from the knowledge of the amino acid types of residues: i − 1, i and i + 1, thereby speeding up the sequential assignment process. The method has the advantage of being relatively inexpensive, applicable to 2H labeled protein and can be coupled with cell-free synthesis and/or automated assignment approaches. A detailed survey involving unlabeling of different amino acid types individually or in pairs reveals that the proposed approach is also robust to misincorporation of 14N at undesired sites. Taken together, this study represents the first application of selective unlabeling for sequence specific resonance assignments and opens up new avenues to using this methodology in protein structural studies. Electronic supplementary material The online version of this article (doi:10.1007/s10858-010-9459-z) contains supplementary material, which is available to authorized users. PMID:21153044

The leader peptide of mutacin 1140 has distinct structural components compared to related class I lantibiotics.

PubMed

Escano, Jerome; Stauffer, Byron; Brennan, Jacob; Bullock, Monica; Smith, Leif

2014-12-01

Lantibiotics are ribosomally synthesized peptide antibiotics composed of an N-terminal leader peptide that promotes the core peptide's interaction with the post translational modification (PTM) enzymes. Following PTMs, mutacin 1140 is transported out of the cell and the leader peptide is cleaved to yield the antibacterial peptide. Mutacin 1140 leader peptide is structurally unique compared to other class I lantibiotic leader peptides. Herein, we further our understanding of the structural differences of mutacin 1140 leader peptide with regard to other class I leader peptides. We have determined that the length of the leader peptide is important for the biosynthesis of mutacin 1140. We have also determined that mutacin 1140 leader peptide contains a novel four amino acid motif compared to related lantibiotics. PTM enzyme recognition of the leader peptide appears to be evolutionarily distinct from related class I lantibiotics. Our study on mutacin 1140 leader peptide provides a basis for future studies aimed at understanding its interaction with the PTM enzymes. © 2014 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Dynamics of streamer-to-leader transition at reduced air densities and its implications for propagation of lightning leaders and gigantic jets

NASA Astrophysics Data System (ADS)

da Silva, Caitano L.; Pasko, Victor P.

2013-12-01

In this paper we present modeling studies of air heating by electrical discharges in a wide range of pressures. The developed model is capable of quantifying the different contributions for heating of air at the particle level and rigorously accounts for the vibration-dissociation-vibration coupling. The model is validated by calculating the breakdown times of short air gaps and comparing to available experimental data. Detailed discussion on the role of electron detachment in the development of the thermal-ionizational instability that triggers the spark development in short air gaps is presented. The dynamics of fast heating by quenching of excited electronic states is discussed and the scaling of its main channels with ambient air density is quantified. The developed model is employed to study the streamer-to-leader transition process and to obtain its scaling with ambient air density. Streamer-to-leader transition is the name given to a sequence of events occurring in a thin plasma channel through which a relatively strong current is forced through, culminating in heating of ambient gas and increase of the electrical conductivity of the channel. This process occurs during the inception of leaders (from sharp metallic structures, from hydrometeors inside the thundercloud, or in virgin air) and during their propagation (at the leader head or during the growth of a space leader). The development of a thermal-ionizational instability that culminates in the leader formation and propagation is characterized by a change in air ionization mechanism from electron impact to associative ionization and by contraction of the plasma channel. The introduced methodology for estimation of leader speeds shows that the propagation of a leader is limited by the air heating of every newly formed leader section. It is demonstrated that the streamer-to-leader transition time has an inverse-squared dependence on the ambient air density at near-ground pressures, in agreement with

Senior Leader Career Management: Implications for Senior Leaders and Organizations

ERIC Educational Resources Information Center

Larkin, Jean

2012-01-01

This qualitative research study across three large consumer products organizations explored career management of senior leaders to gain an understanding of what is important to senior leaders in their careers and what strategies they are using for career management. It also investigated senior leaders' expectations of organizations for career…

The good leader.

PubMed

Bottles, K

2001-01-01

What are the traits of successful leaders and can they be applied to those of us in health care? Leaders must deal with conflict to get a group of people to move in the same direction. Successful leaders learn to have difficult conversations that increase understanding and morale and creatively deal with the inevitable interpersonal conflicts present in every organization made up of people. Another useful trait for a leader during uncertain and chaotic times is the ability to see things as they really are, rather than as we wish or believe them to be. Successful leaders are also usually optimists who level with their co-workers.

37 CFR 1.824 - Form and format for nucleotide and/or amino acid sequence submissions in computer readable form.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Form and format for... And/or Amino Acid Sequences § 1.824 Form and format for nucleotide and/or amino acid sequence... Code for Information Interchange (ASCII) text. No other formats shall be allowed. (3) The computer...

Narcissistic leaders: An asset or a liability? Leader visibility, follower responses, and group-level absenteeism.

PubMed

Nevicka, Barbara; Van Vianen, Annelies E M; De Hoogh, Annebel H B; Voorn, Bart C M

2018-03-19

Although narcissists often emerge as leaders, research has thus far shown inconsistent results on the relationship between leader narcissism and effectiveness in the eyes of followers. Here we draw on leader distance theory (Shamir, 1995) and implicit leader theory (Lord & Maher, 1991) to propose that followers' assessment of a narcissistic leader and followers' overall job attitudes depend on the leader's visibility to the followers. The more opportunities followers have to observe narcissistic leaders the more they will experience these leaders' toxic behavior (e.g., exploitativeness) and the less they will perceive the leader as effective. To test our hypotheses we collected multisource, longitudinal data from 175 retail stores and obtained subjective (followers' perceptions of leader effectiveness and their overall job attitudes) as well as objective (leaders' organizational experience at time of hire, employee absenteeism trends) indices of leader functionality. Results showed that narcissistic leaders had less organizational experience at the time they were hired. Moreover, when followers had fewer opportunities to observe their leader, leader narcissism was positively related to perceived leadership effectiveness and job attitudes. However, when followers had more opportunity to observe their leader, the positive relationship disappeared. Finally, leader narcissism was neither positively nor negatively associated with absenteeism, whereas absenteeism declined over time under non-narcissistic leaders. These findings advance our knowledge of how followers respond to narcissistic leaders and how these leaders function in organizational settings where they have legitimate positions of power. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Sequencing, bioinformatic characterization and expression pattern of a putative amino acid transporter from the parasitic cestode Echinococcus granulosus.

PubMed

Camicia, Federico; Paredes, Rodolfo; Chalar, Cora; Galanti, Norbel; Kamenetzky, Laura; Gutierrez, Ariana; Rosenzvit, Mara C

2008-03-31

We have sequenced and partially characterized an Echinococcus granulosus cDNA, termed egat1, from a protoscolex signal sequence trap (SST) cDNA library. The isolated 1627 bp long cDNA contains an ORF of 489 amino acids and shows an amino acid identity of 30% with neutral and excitatory amino acid transporters members of the Dicarboxylate/Amino Acid Na+ and/or H+ Cation Symporter family (DAACS) (TC 2.A.23). Additional bioinformatics analysis of EgAT1, confirmed the results obtained by similarity searches and showed the presence of 9 to 10 transmembrane domains, consensus sequences for N-glycosylation between the third and fourth transmembrane domain, a highly similar hydropathy profile with ASCT1 (a known member of DAACS family), high score with SDF (Sodium Dicarboxilate Family) and similar motifs with EDTRANSPORT, a fingerprint of excitatory amino acid transporters. The localization of the putative amino acid transporter was analyzed by in situ hybridization and immunofluorescence in protoscoleces and associated germinal layer. The in situ hybridization labelling indicates the distribution of egat1 mRNA throughout the tegument. EgAT1 protein, which showed in Western blots a molecular mass of approximately 60 kD, is localized in the subtegumental region of the metacestode, particularly around suckers and rostellum of protoscoleces and layers from brood capsules. The sequence and expression analyses of EgAT1 pave the way for functional analysis of amino acids transporters of E. granulosus and its evaluation as new drug targets against cystic echinococcosis.

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

Implication of the cause of differences in 3D structures of proteins with high sequence identity based on analyses of amino acid sequences and 3D structures.

PubMed

Matsuoka, Masanari; Sugita, Masatake; Kikuchi, Takeshi

2014-09-18

Proteins that share a high sequence homology while exhibiting drastically different 3D structures are investigated in this study. Recently, artificial proteins related to the sequences of the GA and IgG binding GB domains of human serum albumin have been designed. These artificial proteins, referred to as GA and GB, share 98% amino acid sequence identity but exhibit different 3D structures, namely, a 3α bundle versus a 4β + α structure. Discriminating between their 3D structures based on their amino acid sequences is a very difficult problem. In the present work, in addition to using bioinformatics techniques, an analysis based on inter-residue average distance statistics is used to address this problem. It was hard to distinguish which structure a given sequence would take only with the results of ordinary analyses like BLAST and conservation analyses. However, in addition to these analyses, with the analysis based on the inter-residue average distance statistics and our sequence tendency analysis, we could infer which part would play an important role in its structural formation. The results suggest possible determinants of the different 3D structures for sequences with high sequence identity. The possibility of discriminating between the 3D structures based on the given sequences is also discussed.

Elementary Mathematics Leaders

ERIC Educational Resources Information Center

Fennell, Francis; Kobett, Beth McCord; Wray, Jonathan A.

2013-01-01

Elementary school mathematics leaders often come to the realization that their position, however titled and determined, although dedicated to addressing needs in math teaching and learning, also entails and directly involves leadership. Elementary school math specialists/instructional leaders (referenced here as elementary mathematics leaders, or…

Amino acid sequence of the smaller basic protein from rat brain myelin

PubMed Central

Dunkley, Peter R.; Carnegie, Patrick R.

1974-01-01

1. The complete amino acid sequence of the smaller basic protein from rat brain myelin was determined. This protein differs from myelin basic proteins of other species in having a deletion of a polypeptide of 40 amino acid residues from the centre of the molecule. 2. A detailed comparison is made of the constant and variable regions in a group of myelin basic proteins from six species. 3. An arginine residue in the rat protein was found to be partially methylated. The ratio of methylated to unmethylated arginine at this position differed from that found for the human basic protein. 4. Three tryptic peptides were isolated in more than one form. The differences between the two forms of each peptide are discussed in relation to the electrophoretic heterogeneity of myelin basic proteins, which is known to occur at alkaline pH values. 5. Detailed evidence for the amino acid sequence of the protein has been deposited as Supplementary Publication SUP 50029 at the British Library (Lending Division) (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1973) 131, 5. PMID:4141893

Homology analyses of the protein sequences of fatty acid synthases from chicken liver, rat mammary gland, and yeast

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

Chang, Soo-Ik; Hammes, G.G.

1989-11-01

Homology analyses of the protein sequences of chicken liver and rat mammary gland fatty acid synthases were carried out. The amino acid sequences of the chicken and rat enzymes are 67% identical. If conservative substitutions are allowed, 78% of the amino acids are matched. A region of low homologies exists between the functional domains, in particular around amino acid residues 1059-1264 of the chicken enzyme. Homologies between the active sites of chicken and rat and of chicken and yeast enzymes have been analyzed by an alignment method. A high degree of homology exists between the active sites of the chickenmore » and rat enzymes. However, the chicken and yeast enzymes show a lower degree of homology. The DADPH-binding dinucleotide folds of the {beta}-ketoacyl reductase and the enoyl reductase sites were identified by comparison with a known consensus sequence for the DADP- and FAD-binding dinucleotide folds. The active sites of all of the enzymes are primarily in hydrophobic regions of the protein. This study suggests that the genes for the functional domains of fatty acid synthase were originally separated, and these genes were connected to each other by using different connecting nucleotide sequences in different species. An alternative explanation for the differences in rat and chicken is a common ancestry and mutations in the joining regions during evolution.« less

Amino acid sequence analysis of the annexin super-gene family of proteins.

PubMed

Barton, G J; Newman, R H; Freemont, P S; Crumpton, M J

1991-06-15

The annexins are a widespread family of calcium-dependent membrane-binding proteins. No common function has been identified for the family and, until recently, no crystallographic data existed for an annexin. In this paper we draw together 22 available annexin sequences consisting of 88 similar repeat units, and apply the techniques of multiple sequence alignment, pattern matching, secondary structure prediction and conservation analysis to the characterisation of the molecules. The analysis clearly shows that the repeats cluster into four distinct families and that greatest variation occurs within the repeat 3 units. Multiple alignment of the 88 repeats shows amino acids with conserved physicochemical properties at 22 positions, with only Gly at position 23 being absolutely conserved in all repeats. Secondary structure prediction techniques identify five conserved helices in each repeat unit and patterns of conserved hydrophobic amino acids are consistent with one face of a helix packing against the protein core in predicted helices a, c, d, e. Helix b is generally hydrophobic in all repeats, but contains a striking pattern of repeat-specific residue conservation at position 31, with Arg in repeats 4 and Glu in repeats 2, but unconserved amino acids in repeats 1 and 3. This suggests repeats 2 and 4 may interact via a buried saltbridge. The loop between predicted helices a and b of repeat 3 shows features distinct from the equivalent loop in repeats 1, 2 and 4, suggesting an important structural and/or functional role for this region. No compelling evidence emerges from this study for uteroglobin and the annexins sharing similar tertiary structures, or for uteroglobin representing a derivative of a primordial one-repeat structure that underwent duplication to give the present day annexins. The analyses performed in this paper are re-evaluated in the Appendix, in the light of the recently published X-ray structure for human annexin V. The structure confirms most of

The Emotional Intelligence of Leaders as Antecedent to Leader-Member Exchanges: A Field Study

ERIC Educational Resources Information Center

Barbuto, John E., Jr.; Bugenhagen, Marilyn J.

2009-01-01

Eighty elected leaders and 388 followers were sampled to test the relationships between leaders' emotional intelligence and the quality of leader-member exchange. Results of the field study found a significant relationship between leaders' emotional intelligence (total) and leader-member exchange quality. Specific subscales of emotional…

Cloning and sequencing of a gene encoding the 69-kDa extracellular chitinase of Janthinobacterium lividum.

PubMed

Gleave, A P; Taylor, R K; Morris, B A; Greenwood, D R

1995-09-15

Janthinobacterium lividum secretes a major 56-kDa chitinase and a minor 69-kDa chitinase. A chitinase gene was defined on a 3-kb fragment of clone pRKT10, by virtue of fluorescent colonies in the presence of 4-methylumbelliferyl-beta-D-N,N',N"-chitotrioside. Nucleotide sequencing revealed an 1998-bp open reading frame with the potential to encode a 69,716-Da protein with amino acid sequences similar to those in other chitinases, suggesting it encodes the minor chitinase (Chi69). Chitinase activity of Escherichia coli (pRKT10) lysates was detected mainly in the periplasmic fraction and immunoblotting detected a 70-kDa protein in this fraction. Chi69 has an N-terminal secretory leader peptide preceding two probable chitin-binding domains and a catalytic domain. These functional domains are separated by linker regions of proline-threonine repeats. Amino acid sequencing of cyanogen bromide cleavage-derived peptides from the major 56-kDa chitinase suggested that Chi69 may be a precursor of Chi56. In addition, an N-terminally truncated version of Chi69 retained chitinase activity as expected if in vivo processing of Chi69 generates Chi56.

Solid phase sequencing of biopolymers

DOEpatents

Cantor, Charles; Koster, Hubert

2010-09-28

This invention relates to methods for detecting and sequencing target nucleic acid sequences, to mass modified nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probes comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include DNA or RNA in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated molecular weight analysis and identification of the target sequence.

N-Terminal Amino Acid Sequence Determination of Proteins by N-Terminal Dimethyl Labeling: Pitfalls and Advantages When Compared with Edman Degradation Sequence Analysis.

PubMed

Chang, Elizabeth; Pourmal, Sergei; Zhou, Chun; Kumar, Rupesh; Teplova, Marianna; Pavletich, Nikola P; Marians, Kenneth J; Erdjument-Bromage, Hediye

2016-07-01

In recent history, alternative approaches to Edman sequencing have been investigated, and to this end, the Association of Biomolecular Resource Facilities (ABRF) Protein Sequencing Research Group (PSRG) initiated studies in 2014 and 2015, looking into bottom-up and top-down N-terminal (Nt) dimethyl derivatization of standard quantities of intact proteins with the aim to determine Nt sequence information. We have expanded this initiative and used low picomole amounts of myoglobin to determine the efficiency of Nt-dimethylation. Application of this approach on protein domains, generated by limited proteolysis of overexpressed proteins, confirms that it is a universal labeling technique and is very sensitive when compared with Edman sequencing. Finally, we compared Edman sequencing and Nt-dimethylation of the same polypeptide fragments; results confirm that there is agreement in the identity of the Nt amino acid sequence between these 2 methods.

Extension of the COG and arCOG databases by amino acid and nucleotide sequences

PubMed Central

Meereis, Florian; Kaufmann, Michael

2008-01-01

Background The current versions of the COG and arCOG databases, both excellent frameworks for studies in comparative and functional genomics, do not contain the nucleotide sequences corresponding to their protein or protein domain entries. Results Using sequence information obtained from GenBank flat files covering the completely sequenced genomes of the COG and arCOG databases, we constructed NUCOCOG (nucleotide sequences containing COG databases) as an extended version including all nucleotide sequences and in addition the amino acid sequences originally utilized to construct the current COG and arCOG databases. We make available three comprehensive single XML files containing the complete databases including all sequence information. In addition, we provide a web interface as a utility suitable to browse the NUCOCOG database for sequence retrieval. The database is accessible at . Conclusion NUCOCOG offers the possibility to analyze any sequence related property in the context of the COG and arCOG framework simply by using script languages such as PERL applied to a large but single XML document. PMID:19014535

Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns

PubMed Central

2007-01-01

We have converted genome-encoded protein sequences into musical notes to reveal auditory patterns without compromising musicality. We derived a reduced range of 13 base notes by pairing similar amino acids and distinguishing them using variations of three-note chords and codon distribution to dictate rhythm. The conversion will help make genomic coding sequences more approachable for the general public, young children, and vision-impaired scientists. PMID:17477882

The amino acid motif L/IIxxFE defines a novel actin-binding sequence in PDZ-RhoGEF

PubMed Central

Banerjee, Jayashree; Fischer, Christopher C.; Wedegaertner, Philip B.

2009-01-01

PDZ-RhoGEF is a member of the regulator of G protein signaling (RGS) domain-containing RhoGEFs (RGS-RhoGEFs) that link activated heterotrimeric G protein α subunits of the G12 family to activation of the small GTPase RhoA. Unique among the RGS-RhoGEFs, PDZ-RhoGEF contains a short sequence that localizes the protein to the actin cytoskeleton. In this report, we demonstrate that the actin-binding domain, located between amino acids 561–585, directly binds to F-actin in vitro. Extensive mutagenesis identifies isoleucine 568, isoleucine 569, phenylalanine 572, and glutamic acid 573 as necessary for binding to actin and for co-localization with the actin cytoskeleton in cells. These results define a novel actin-binding sequence in PDZ-RhoGEF with a critical amino acid motif of IIxxFE. Moreover, sequence analysis identifies a similar actin-binding motif in the N-terminus of the RhoGEF frabin, and, as with PDZ-RhoGEF, mutagenesis and actin interaction experiments demonstrate a motif of LIxxFE, consisting of the key amino acids leucine 23, isoleucine 24, phenylalanine 27, and glutamic acid 28. Taken together, results with PDZ-RhoGEF and frabin identify a novel actin binding sequence. Lastly, inducible dimerization of the actin-binding region of PDZ-RhoGEF revealed a dimerization-dependent actin bundling activity in vitro. PDZ-RhoGEF exists in cells as a dimer, raising the possibility that PDZ-RhoGEF could influence actin structure independent of its ability to activate RhoA. PMID:19618964

alpha-Amylase gene of Streptomyces limosus: nucleotide sequence, expression motifs, and amino acid sequence homology to mammalian and invertebrate alpha-amylases.

PubMed Central

Long, C M; Virolle, M J; Chang, S Y; Chang, S; Bibb, M J

1987-01-01

The nucleotide sequence of the coding and regulatory regions of the alpha-amylase gene (aml) of Streptomyces limosus was determined. High-resolution S1 mapping was used to locate the 5' end of the transcript and demonstrated that the gene is transcribed from a unique promoter. The predicted amino acid sequence has considerable identity to mammalian and invertebrate alpha-amylases, but not to those of plant, fungal, or eubacterial origin. Consistent with this is the susceptibility of the enzyme to an inhibitor of mammalian alpha-amylases. The amino-terminal sequence of the extracellular enzyme was determined, revealing the presence of a typical signal peptide preceding the mature form of the alpha-amylase. Images PMID:3500166

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

ScienceCinema

Patel, Kamlesh D.

2018-01-22

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology (Seventh Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting 2012)

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

Patel, Kamlesh D.

2012-06-01

Kamlesh (Ken) Patel from Sandia National Laboratories (Livermore, California) presents "Preparation of Nucleic Acid Libraries for Personalized Sequencing Systems Using an Integrated Microfluidic Hub Technology " at the 7th Annual Sequencing, Finishing, Analysis in the Future (SFAF) Meeting held in June, 2012 in Santa Fe, NM.

The impact of previous leaders on the evaluation of new leaders: an alternative to prototype matching.

PubMed

Ritter, Barbara A; Lord, Robert G

2007-11-01

In 2 studies, this research demonstrated the existence of leader transference, a cognitive process whereby mental representations of previous leaders are activated and used for evaluation when new, similar leaders are encountered. The 1st study demonstrated that exposure to a new leader who was similar to a past leader led to erroneous generalization of leader characteristics and associated underlying attributions. The 2nd study showed that expectations of just treatment and abuse were also subject to transfer from old to new, similar leaders, although positive and negative affective responses were not. Results suggested that individuals exposed to a leader who was not reminiscent of an old leader were more likely to use a general leader prototype to form leader expectations, whereas individuals exposed to a leader who was similar to an old leader activated a significant other mental representation for use in making judgments. These results have implications for individual- and relational-level processes as characterized by implicit leadership theory and leader-member exchange theory as well as macro theories of leader succession and organizational culture change. (c) 2007 APA

Partial amino acid sequence of the branched chain amino acid aminotransferase (TmB) of E. coli JA199 pDU11

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

Feild, M.J.; Armstrong, F.B.

1987-05-01

E. coli JA199 pDU11 harbors a multicopy plasmid containing the ilv GEDAY gene cluster of S. typhimurium. TmB, gene product of ilv E, was purified, crystallized, and subjected to Edman degradation using a gas phase sequencer. The intact protein yielded an amino terminal 31 residue sequence. Both carboxymethylated apoenzyme and (/sup 3/H)-NaBH-reduced holoenzyme were then subjected to digestion by trypsin. The digests were fractionated using reversed phase HPLC, and the peptides isolated were sequenced. The borohydride-treated holoenzyme was used to isolate the cofactor-binding peptide. The peptide is 27 residues long and a comparison with known sequences of other aminotransferases revealedmore » limited homology. Peptides accounting for 211 of 288 predicted residues have been sequenced, including 9 residues of the carboxyl terminus. Comparison of peptides with the inferred amino acid sequence of the E. coli K-12 enzyme has helped determine the sequence of the amino terminal 59 residues; only two differences between the sequences are noted in this region.« less

Not even the past: The joint influence of former leader and new leader during leader succession in the midst of organizational change.

PubMed

Zhao, Helen H; Seibert, Scott E; Taylor, M Susan; Lee, Cynthia; Lam, Wing

2016-12-01

Leader succession often occurs during organizational change processes, but the implications of leader succession, in terms of reactions to the change, rarely have been investigated. Employee attitudes and behaviors during organizational change may be influenced jointly by a former leader who recently has transitioned out of the team and the new leader who recently has transitioned into it. We predict an interaction between former and new leaders' transformational leadership on employees' behavioral resistance to and support for change. On the basis of contrast effect theory, a highly transformational former leader constrains the potential effectiveness of the new leader, but a former leader low in transformational leadership enhances this potential effectiveness. We also propose conditional indirect effects transmitted through commitment to the changing organization. Our research was conducted in a large Chinese hospitality organization that was implementing radical organizational change, during which virtually all aspects of processes and products are changed. We collected a 2-wave multisource data from employees who had recently experienced a leader succession and their newly assigned leaders. On the basis of a final sample of 203 employees from 22 teams, we found empirical support for the proposed interaction effects. The conditional indirect effects were also consistent with our expectations, but the effect on behavioral resistance to change was stronger than the effect on behavioral support for change. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

37 CFR 1.822 - Symbols and format to be used for nucleotide and/or amino acid sequence data.

Code of Federal Regulations, 2014 CFR

2014-07-01

... base or modified or unusual amino acid may be presented in a given sequence as the corresponding unmodified base or amino acid if the modified base or modified or unusual amino acid is one of those listed... the Feature section. Otherwise, each occurrence of a base or amino acid not appearing in WIPO Standard...

Sustaining leaders of cancer support groups: the role, needs, and difficulties of leaders.

PubMed

Butow, Phyllis; Ussher, Jane; Kirsten, Laura; Hobbs, Kim; Smith, Katharine; Wain, Gerald; Sandoval, Mirjana; Stenlake, Annie

2005-01-01

Cancer support groups are an important source of support for cancer patients, yet little is known about the characteristics of, and barriers to, effective leadership, and the training needs of both professionally trained and untrained leaders. This study explored the views of 179 leaders of 184 cancer support groups in NSW, Australia, regarding these issues. Four hundred and sixteen members of 50 groups selected from the larger cohort completed questionnaires eliciting the importance of group processes, including leader qualities, and satisfaction with group leadership. Finally, members of nine groups participated in focus groups regarding effective group processes. The importance of the leader(s) was emphasized in all stages of the research. Fifty-nine percent of group leaders were currently experiencing a difficulty, primarily related to infrastructure or group process. Three characteristics of effective leaders were identified: educational qualities, facilitation skills, and personal qualities. There is clearly a need to develop and evaluate effective interventions to maintain leaders in these roles, if the proven benefits for cancer patients are to be protected.

Self-sequencing of amino acids and origins of polyfunctional protocells

NASA Technical Reports Server (NTRS)

Fox, S. W.

1984-01-01

The role of proteins in the origin of living things is discussed. It has been experimentally established that amino acids can sequence themselves under simulated geological conditions with highly nonrandom products which accordingly contain diverse information. Multiple copies of each type of macromolecule are formed, resulting in greater power for any protoenzymic molecule than would accrue from a single copy of each type. Thermal proteins are readily incorporated into laboratory protocells. The experimental evidence for original polyfunctional protocells is discussed.

Microwave-assisted acid and base hydrolysis of intact proteins containing disulfide bonds for protein sequence analysis by mass spectrometry.

PubMed

Reiz, Bela; Li, Liang

2010-09-01

Controlled hydrolysis of proteins to generate peptide ladders combined with mass spectrometric analysis of the resultant peptides can be used for protein sequencing. In this paper, two methods of improving the microwave-assisted protein hydrolysis process are described to enable rapid sequencing of proteins containing disulfide bonds and increase sequence coverage, respectively. It was demonstrated that proteins containing disulfide bonds could be sequenced by MS analysis by first performing hydrolysis for less than 2 min, followed by 1 h of reduction to release the peptides originally linked by disulfide bonds. It was shown that a strong base could be used as a catalyst for microwave-assisted protein hydrolysis, producing complementary sequence information to that generated by microwave-assisted acid hydrolysis. However, using either acid or base hydrolysis, amide bond breakages in small regions of the polypeptide chains of the model proteins (e.g., cytochrome c and lysozyme) were not detected. Dynamic light scattering measurement of the proteins solubilized in an acid or base indicated that protein-protein interaction or aggregation was not the cause of the failure to hydrolyze certain amide bonds. It was speculated that there were some unknown local structures that might play a role in preventing an acid or base from reacting with the peptide bonds therein. 2010 American Society for Mass Spectrometry. Published by Elsevier Inc. All rights reserved.

Cloning and sequence analysis of Galleria mellonella juvenile hormone binding protein--a search for ancestors and relatives.

PubMed

Rodriguez Parkitna, Jan M; Ozyhar, Andrzej; Wiśniewski, Jacek R; Kochman, Marian

2002-09-01

Juvenile hormone binding proteins (JHBPs) serve as specific carriers of juvenile hormone (JH) in insect hemolymph. As shown in this report, Galleria mellonella JHBP is encoded by a cDNA of 1063 nucleotides. The pre-protein consists of 245 amino acids with a 20 amino acid leader sequence. The concentration of the JHBP mRNA reaches a maximum on the third day of the last larval instar, and decreases five-fold towards pupation. Comparison of amino acid sequences of JHBPs from Bombyx mori, Heliothis virescens, Manduca sexta and G. mellonella shows that 57 positions out of 226 are occupied by identical amino acids. A phylogeny tree was constructed from 32 proteins, which function could be associated to JH. It has three major branches: (i) ligand binding domains of nuclear receptors, (ii) JHBPs and JH esterases (JHEs), and (iii) hypothetical proteins found in Drosophila melanogaster genome. Despite the close positioning of JHEs and JHBPs on the tree, which probably arises from the presence of a common JH binding motif, these proteins are unlikely to belong to the same family. Detailed analysis of the secondary structure modeling shows that JHBPs may contain a beta-barrel motif flanked by alpha-helices and thus be evolutionary related to the same superfamily as calycins.

Complete sequence of the genome of avian paramyxovirus type 2 (strain Yucaipa) and comparison with other paramyxoviruses

PubMed Central

Subbiah, Madhuri; Xiao, Sa; Collins, Peter L.; Samal, Siba K

2009-01-01

The complete RNA genome sequence of avian paramyxovirus (APMV) serotype 2, strain Yucaipa isolated from chicken has been determined. With genome size of 14,904 nucleotides (nt), strain Yucaipa is consistent with the “rule of six” and is the smallest virus reported to date among the members of subfamily Paramyxovirinae. The genome contains six non-overlapping genes in the order 3′-N-P/V-M-F-HN-L-5′. The genes are flanked on either side by highly-conserved transcription start and stop signals and have intergenic sequences varying in length from 3 to 23 nt. The genome contains a 55 nt leader sequence at 3′ end and a 154 nt trailer sequence at 5′ end. Alignment and phylogenetic analysis of the predicted amino acid sequences of strain Yucaipa proteins with the cognate proteins of viruses of all of the five genera of family Paramyxoviridae showed that APMV-2 strain Yucaipa is more closely related to APMV-6 than APMV-1. PMID:18603323

Positions of Trp Codons in the Leader Peptide-Coding Region of the at Operon Influence Anti-Trap Synthesis and trp Operon Expression in Bacillus licheniformis▿

PubMed Central

Levitin, Anastasia; Yanofsky, Charles

2010-01-01

Tryptophan, phenylalanine, tyrosine, and several other metabolites are all synthesized from a common precursor, chorismic acid. Since tryptophan is a product of an energetically expensive biosynthetic pathway, bacteria have developed sensing mechanisms to downregulate synthesis of the enzymes of tryptophan formation when synthesis of the amino acid is not needed. In Bacillus subtilis and some other Gram-positive bacteria, trp operon expression is regulated by two proteins, TRAP (the tryptophan-activated RNA binding protein) and AT (the anti-TRAP protein). TRAP is activated by bound tryptophan, and AT synthesis is increased upon accumulation of uncharged tRNATrp. Tryptophan-activated TRAP binds to trp operon leader RNA, generating a terminator structure that promotes transcription termination. AT binds to tryptophan-activated TRAP, inhibiting its RNA binding ability. In B. subtilis, AT synthesis is upregulated both transcriptionally and translationally in response to the accumulation of uncharged tRNATrp. In this paper, we focus on explaining the differences in organization and regulatory functions of the at operon's leader peptide-coding region, rtpLP, of B. subtilis and Bacillus licheniformis. Our objective was to correlate the greater growth sensitivity of B. licheniformis to tryptophan starvation with the spacing of the three Trp codons in its at operon leader peptide-coding region. Our findings suggest that the Trp codon location in rtpLP of B. licheniformis is designed to allow a mild charged-tRNATrp deficiency to expose the Shine-Dalgarno sequence and start codon for the AT protein, leading to increased AT synthesis. PMID:20061467

Statistical distribution of amino acid sequences: a proof of Darwinian evolution.

PubMed

Eitner, Krystian; Koch, Uwe; Gaweda, Tomasz; Marciniak, Jedrzej

2010-12-01

The article presents results of the listing of the quantity of amino acids, dipeptides and tripeptides for all proteins available in the UNIPROT-TREMBL database and the listing for selected species and enzymes. UNIPROT-TREMBL contains protein sequences associated with computationally generated annotations and large-scale functional characterization. Due to the distinct metabolic pathways of amino acid syntheses and their physicochemical properties, the quantities of subpeptides in proteins vary. We have proved that the distribution of amino acids, dipeptides and tripeptides is statistical which confirms that the evolutionary biodiversity development model is subject to the theory of independent events. It seems interesting that certain short peptide combinations occur relatively rarely or even not at all. First, it confirms the Darwinian theory of evolution and second, it opens up opportunities for designing pharmaceuticals among rarely represented short peptide combinations. Furthermore, an innovative approach to the mass analysis of bioinformatic data is presented. eitner@amu.edu.pl Supplementary data are available at Bioinformatics online.

Purification, characterization, gene cloning and nucleotide sequencing of D: -stereospecific amino acid amidase from soil bacterium: Delftia acidovorans.

PubMed

Hongpattarakere, Tipparat; Komeda, Hidenobu; Asano, Yasuhisa

2005-12-01

The D-amino acid amidase-producing bacterium was isolated from soil samples using an enrichment culture technique in medium broth containing D-phenylalanine amide as a sole source of nitrogen. The strain exhibiting the strongest activity was identified as Delftia acidovorans strain 16. This strain produced intracellular D-amino acid amidase constitutively. The enzyme was purified about 380-fold to homogeneity and its molecular mass was estimated to be about 50 kDa, on sodium dodecyl sulfate polyacrylamide gel electrophoresis. The enzyme was active preferentially toward D-amino acid amides rather than their L-counterparts. It exhibited strong amino acid amidase activity toward aromatic amino acid amides including D-phenylalanine amide, D-tryptophan amide and D-tyrosine amide, yet it was not specifically active toward low-molecular-weight D-amino acid amides such as D-alanine amide, L-alanine amide and L-serine amide. Moreover, it was not specifically active toward oligopeptides. The enzyme showed maximum activity at 40 degrees C and pH 8.5 and appeared to be very stable, with 92.5% remaining activity after the reaction was performed at 45 degrees C for 30 min. However, it was mostly inactivated in the presence of phenylmethanesulfonyl fluoride or Cd2+, Ag+, Zn2+, Hg2+ and As3+ . The NH2 terminal and internal amino acid sequences of the enzyme were determined; and the gene was cloned and sequenced. The enzyme gene damA encodes a 466-amino-acid protein (molecular mass 49,860.46 Da); and the deduced amino acid sequence exhibits homology to the D-amino acid amidase from Variovorax paradoxus (67.9% identity), the amidotransferase A subunit from Burkholderia fungorum (50% identity) and other enantioselective amidases.

A Novel Phytase with Sequence Similarity to Purple Acid Phosphatases Is Expressed in Cotyledons of Germinating Soybean Seedlings 1

PubMed Central

Hegeman, Carla E.; Grabau, Elizabeth A.

2001-01-01

Phytic acid (myo-inositol hexakisphosphate) is the major storage form of phosphorus in plant seeds. During germination, stored reserves are used as a source of nutrients by the plant seedling. Phytic acid is degraded by the activity of phytases to yield inositol and free phosphate. Due to the lack of phytases in the non-ruminant digestive tract, monogastric animals cannot utilize dietary phytic acid and it is excreted into manure. High phytic acid content in manure results in elevated phosphorus levels in soil and water and accompanying environmental concerns. The use of phytases to degrade seed phytic acid has potential for reducing the negative environmental impact of livestock production. A phytase was purified to electrophoretic homogeneity from cotyledons of germinated soybeans (Glycine max L. Merr.). Peptide sequence data generated from the purified enzyme facilitated the cloning of the phytase sequence (GmPhy) employing a polymerase chain reaction strategy. The introduction of GmPhy into soybean tissue culture resulted in increased phytase activity in transformed cells, which confirmed the identity of the phytase gene. It is surprising that the soybean phytase was unrelated to previously characterized microbial or maize (Zea mays) phytases, which were classified as histidine acid phosphatases. The soybean phytase sequence exhibited a high degree of similarity to purple acid phosphatases, a class of metallophosphoesterases. PMID:11500558

The isolation, purification and amino-acid sequence of insulin from the teleost fish Cottus scorpius (daddy sculpin).

PubMed

Cutfield, J F; Cutfield, S M; Carne, A; Emdin, S O; Falkmer, S

1986-07-01

Insulin from the principal islets of the teleost fish, Cottus scorpius (daddy sculpin), has been isolated and sequenced. Purification involved acid/alcohol extraction, gel filtration, and reverse-phase high-performance liquid chromatography to yield nearly 1 mg pure insulin/g wet weight islet tissue. Biological potency was estimated as 40% compared to porcine insulin. The sculpin insulin crystallised in the absence of zinc ions although zinc is known to be present in the islets in significant amounts. Two other hormones, glucagon and pancreatic polypeptide, were copurified with the insulin, and an N-terminal sequence for pancreatic polypeptide was determined. The primary structure of sculpin insulin shows a number of sequence changes unique so far amongst teleost fish. These changes occur at A14 (Arg), A15 (Val), and B2 (Asp). The B chain contains 29 amino acids and there is no N-terminal extension as seen with several other fish. Presumably as a result of the amino acid substitutions, sculpin insulin does not readily form crystals containing zinc-insulin hexamers, despite the presence of the coordinating B10 His.

Design of nucleic acid sequences for DNA computing based on a thermodynamic approach

PubMed Central

Tanaka, Fumiaki; Kameda, Atsushi; Yamamoto, Masahito; Ohuchi, Azuma

2005-01-01

We have developed an algorithm for designing multiple sequences of nucleic acids that have a uniform melting temperature between the sequence and its complement and that do not hybridize non-specifically with each other based on the minimum free energy (ΔGmin). Sequences that satisfy these constraints can be utilized in computations, various engineering applications such as microarrays, and nano-fabrications. Our algorithm is a random generate-and-test algorithm: it generates a candidate sequence randomly and tests whether the sequence satisfies the constraints. The novelty of our algorithm is that the filtering method uses a greedy search to calculate ΔGmin. This effectively excludes inappropriate sequences before ΔGmin is calculated, thereby reducing computation time drastically when compared with an algorithm without the filtering. Experimental results in silico showed the superiority of the greedy search over the traditional approach based on the hamming distance. In addition, experimental results in vitro demonstrated that the experimental free energy (ΔGexp) of 126 sequences correlated well with ΔGmin (|R| = 0.90) than with the hamming distance (|R| = 0.80). These results validate the rationality of a thermodynamic approach. We implemented our algorithm in a graphic user interface-based program written in Java. PMID:15701762

cis-β-Bromostyrene derivatives from cinnamic acids via a tandem substitutive bromination-decarboxylation sequence.

PubMed

Tang, Khanh G; Kent, Greggory T; Erden, Ihsan; Wu, Weiming

2017-10-04

cis -β-Bromostyrene derivatives were synthesized stereospecifically from cinnamic acids through β-lactone intermediates. The synthetic sequence did not require the purification of the β-lactone intermediates although they were found to be stable and readily purified in most cases.

Teaching Leaders to Lead Themselves: An Emerging Leader Exercise

ERIC Educational Resources Information Center

Chavez, Carolyn I.; Gomez, Claudia; Valenzuela, Marcus; Perera, Yasanthi B.

2017-01-01

This article describes an exercise that allows students to experience and understand the importance of perception in leader emergence. Based on implicit leadership theories, this exercise asks students to provide one another with anonymous feedback about what extent they exhibit various trait-based leader behaviors. This exercise, which can be…

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

DOEpatents

Weier, H.U.G.; Gray, J.W.

1995-06-27

A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

DOEpatents

Weier, Heinz-Ulrich G.; Gray, Joe W.

1995-01-01

A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

DNA Cloning of Plasmodium falciparum Circumsporozoite Gene: Amino Acid Sequence of Repetitive Epitope

NASA Astrophysics Data System (ADS)

Enea, Vincenzo; Ellis, Joan; Zavala, Fidel; Arnot, David E.; Asavanich, Achara; Masuda, Aoi; Quakyi, Isabella; Nussenzweig, Ruth S.

1984-08-01

A clone of complementary DNA encoding the circumsporozoite (CS) protein of the human malaria parasite Plasmodium falciparum has been isolated by screening an Escherichia coli complementary DNA library with a monoclonal antibody to the CS protein. The DNA sequence of the complementary DNA insert encodes a four-amino acid sequence: proline-asparagine-alanine-asparagine, tandemly repeated 23 times. The CS β -lactamase fusion protein specifically binds monoclonal antibodies to the CS protein and inhibits the binding of these antibodies to native Plasmodium falciparum CS protein. These findings provide a basis for the development of a vaccine against Plasmodium falciparum malaria.

Hydroquinone: O-glucosyltransferase from cultivated Rauvolfia cells: enrichment and partial amino acid sequences.

PubMed

Arend, J; Warzecha, H; Stöckigt, J

2000-01-01

Plant cell suspension cultures of Rauvolfia are able to produce a high amount of arbutin by glucosylation of exogenously added hydroquinone. A four step purification procedure using anion exchange, hydrophobic interaction, hydroxyapatite-chromatography and chromatofocusing delivered in a yield of 0.5%, an approximately 390 fold enrichment of the involved glucosyltransferase. SDS-PAGE showed a M(r) for the enzyme of 52 kDa. Proteolysis of the pure enzyme with endoproteinase LysC revealed six peptide fragments with 9-23 amino acids which were sequenced. Sequence alignment of the six peptides showed high homologies to glycosyltransferases from other higher plants.

Leader charisma and affective team climate: the moderating role of the leader's influence and interaction.

PubMed

Hernández Baeza, Ana; Araya Lao, Cristina; García Meneses, Juliana; González Romá, Vicente

2009-11-01

In this study, we evaluate the role of leader charisma in fostering positive affective team climate and preventing negative affective climate. The analysis of a longitudinal database of 137 bank branches by means of hierarchical moderated regression shows that leader charisma has a stronger effect on team optimism than on team tension. In addition, the leader's influence and the frequency of leader-team interaction moderate the relationship between charisma and affective climate. However, whereas the leader's influence enhances the relationship between leader charisma and positive affective climate, the frequency of interaction has counterproductive effects.

Online Leader Training Course: Nebraska Equine Extension Leader Certification

ERIC Educational Resources Information Center

Cottle, Lena; D'Angelo, Nicole

2015-01-01

The Nebraska Equine Advancement Level Leader Certification Program is an online learning tool that clarifies principles of the Nebraska 4-H Equine Advancement Programs. Through an online Moodle course through eXtension.org, 4-H leaders and Extension educators are able to fulfill the certification requirement from any location before allowing youth…

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

Evolution of sequence-defined highly functionalized nucleic acid polymers

NASA Astrophysics Data System (ADS)

Chen, Zhen; Lichtor, Phillip A.; Berliner, Adrian P.; Chen, Jonathan C.; Liu, David R.

2018-03-01

The evolution of sequence-defined synthetic polymers made of building blocks beyond those compatible with polymerase enzymes or the ribosome has the potential to generate new classes of receptors, catalysts and materials. Here we describe a ligase-mediated DNA-templated polymerization and in vitro selection system to evolve highly functionalized nucleic acid polymers (HFNAPs) made from 32 building blocks that contain eight chemically diverse side chains on a DNA backbone. Through iterated cycles of polymer translation, selection and reverse translation, we discovered HFNAPs that bind proprotein convertase subtilisin/kexin type 9 (PCSK9) and interleukin-6, two protein targets implicated in human diseases. Mutation and reselection of an active PCSK9-binding polymer yielded evolved polymers with high affinity (KD = 3 nM). This evolved polymer potently inhibited the binding between PCSK9 and the low-density lipoprotein receptor. Structure-activity relationship studies revealed that specific side chains at defined positions in the polymers are required for binding to their respective targets. Our findings expand the chemical space of evolvable polymers to include densely functionalized nucleic acids with diverse, researcher-defined chemical repertoires.

What about the leader? Crossover of emotional exhaustion and work engagement from followers to leaders.

PubMed

Wirtz, Nina; Rigotti, Thomas; Otto, Kathleen; Loeb, Carina

2017-01-01

Although a growing body of research links leadership behavior to follower health, comparatively little is known about the health effects of being in the lead. This longitudinal study of 315 team members and 67 leaders examined the crossover of emotional exhaustion and work engagement from followers to leaders. Leader emotional self-efficacy was tested as a moderator in the crossover process. Multiple regression analyses revealed that followers' work engagement was positively related to leaders' work engagement eight months later, controlling for followers' tenure with the leader, leader gender, autonomy, workload, and work engagement at Time 1. Leaders' emotional self-efficacy did not moderate the crossover of work engagement. Followers' emotional exhaustion was not directly related to leaders' emotional exhaustion over time. We did find a significant interaction effect for follower emotional exhaustion and leader emotional self-efficacy. This study is the first to show that crossover of emotional exhaustion and work engagement can unfold over time from team members to leaders. Main theoretical implications lie in the finding that-in line with job demands-resources theory-followers' psychological states can pose a demand or resource for leaders, and influence their well-being. For practitioners, our results offer valuable insights regarding the design of organizational health interventions as well as leadership development measures. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

An Alignment-Free Algorithm in Comparing the Similarity of Protein Sequences Based on Pseudo-Markov Transition Probabilities among Amino Acids

PubMed Central

Li, Yushuang; Yang, Jiasheng; Zhang, Yi

2016-01-01

In this paper, we have proposed a novel alignment-free method for comparing the similarity of protein sequences. We first encode a protein sequence into a 440 dimensional feature vector consisting of a 400 dimensional Pseudo-Markov transition probability vector among the 20 amino acids, a 20 dimensional content ratio vector, and a 20 dimensional position ratio vector of the amino acids in the sequence. By evaluating the Euclidean distances among the representing vectors, we compare the similarity of protein sequences. We then apply this method into the ND5 dataset consisting of the ND5 protein sequences of 9 species, and the F10 and G11 datasets representing two of the xylanases containing glycoside hydrolase families, i.e., families 10 and 11. As a result, our method achieves a correlation coefficient of 0.962 with the canonical protein sequence aligner ClustalW in the ND5 dataset, much higher than those of other 5 popular alignment-free methods. In addition, we successfully separate the xylanases sequences in the F10 family and the G11 family and illustrate that the F10 family is more heat stable than the G11 family, consistent with a few previous studies. Moreover, we prove mathematically an identity equation involving the Pseudo-Markov transition probability vector and the amino acids content ratio vector. PMID:27918587

Amino acid sequence of human cholinesterase. Annual report, 30 September 1984-30 September 1985

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

Lockridge, O.

1985-10-01

The active-site serine residue is located 198 amino acids from the N-terminal. The active-site peptide was isolated from three different genetic types of human serum cholinesterase: from usual, atypical, and atypical-silent genotypes. It was found that the amino acid sequence of the active-site peptide was identical in all three genotypes. Comparison of the complete sequences of cholinesterase from human serum and acetylcholinesterase from the electric organ of Torpedo californica shows an identity of 53%. Cholinesterase is of interest to the Department of Defense because cholinesterase protects against organophosphate poisons of the type used in chemical warfare. The structural results presentedmore » here will serve as the basis for cloning the gene for cholinesterase. The potential uses of large amounts of cholinesterase would be for cleaning up spills of organophosphates and possibly for detoxifying exposed personnel.« less

The sequence of sequencers: The history of sequencing DNA

PubMed Central

Heather, James M.; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

Two-level QSAR network (2L-QSAR) for peptide inhibitor design based on amino acid properties and sequence positions.

PubMed

Du, Q S; Ma, Y; Xie, N Z; Huang, R B

2014-01-01

In the design of peptide inhibitors the huge possible variety of the peptide sequences is of high concern. In collaboration with the fast accumulation of the peptide experimental data and database, a statistical method is suggested for peptide inhibitor design. In the two-level peptide prediction network (2L-QSAR) one level is the physicochemical properties of amino acids and the other level is the peptide sequence position. The activity contributions of amino acids are the functions of physicochemical properties and the sequence positions. In the prediction equation two weight coefficient sets {ak} and {bl} are assigned to the physicochemical properties and to the sequence positions, respectively. After the two coefficient sets are optimized based on the experimental data of known peptide inhibitors using the iterative double least square (IDLS) procedure, the coefficients are used to evaluate the bioactivities of new designed peptide inhibitors. The two-level prediction network can be applied to the peptide inhibitor design that may aim for different target proteins, or different positions of a protein. A notable advantage of the two-level statistical algorithm is that there is no need for host protein structural information. It may also provide useful insight into the amino acid properties and the roles of sequence positions.

Amino-acid sequence and predicted three-dimensional structure of pea seed (Pisum sativum) ferritin.

PubMed Central

Lobreaux, S; Yewdall, S J; Briat, J F; Harrison, P M

1992-01-01

The iron storage protein, ferritin, is widely distributed in the living kingdom. Here the complete cDNA and derived amino-acid sequence of pea seed ferritin are described, together with its predicted secondary structure, namely a four-helix-bundle fold similar to those of mammalian ferritins, with a fifth short helix at the C-terminus. An N-terminal extension of 71 residues contains a transit peptide (first 47 residues) responsible for plastid targetting as in other plant ferritins, and this is cleaved before assembly. The second part of the extension (24 residues) belongs to the mature subunit; it is cleaved during germination. The amino-acid sequence of pea seed ferritin is aligned with those of other ferritins (49% amino-acid identity with H-chains and 40% with L-chains of human liver ferritin in the aligned region). A three-dimensional model has been constructed by fitting the aligned sequence to the coordinates of human H-chains, with appropriate modifications. A folded conformation with an 11-residue helix is predicted for the N-terminal extension. As in mammalian ferritins, 24 subunits assemble into a hollow shell. In pea seed ferritin, its N-terminal extension is exposed on the outside surface of the shell. Within each pea subunit is a ferroxidase centre resembling those of human ferritin H-chains except for a replacement of Glu-62 by His. The channel at the 4-fold-symmetry axes defined by E-helices, is predicted to be hydrophilic in plant ferritins, whereas it is hydrophobic in mammalian ferritins. Images Fig. 3. Fig. 5. Fig. 6. PMID:1472006

Do lightning positive leaders really "step"?

NASA Astrophysics Data System (ADS)

Petersen, D.

2015-12-01

It has been known for some time that positive leaders exhibit impulsive charge motion and optical emissions as they extend. However, laboratory and field observations have not produced any evidence of a process analogous to the space leader mechanism of negative leader extension. Instead, observations have suggested that the positive leader tip undergoes a continuous to intermittent series of corona streamer bursts, each burst resulting in a small forward extension of the positive leader channel. Traditionally, it has been held that lightning positive leaders extend in a continuous or quasi-continuous fashion. Lately, however, many have become concerned that this position is incongruous with observations of impulsive activity during lightning positive leader extension. It is increasingly suggested that this impulsive activity is evidence that positive leaders also undergo "stepping". There are two issues that must be addressed. The first issue concerns whether or not the physical processes underlying impulsive extension in negative and positive leaders are distinct. We argue that these processes are in fact physically distinct, and offer new high-speed video evidence to support this position. The second issue regards the proper use of the term "step" as an identifier for the impulsive forward extension of a leader. Traditional use of this term has been applied only to negative leaders, due primarily to their stronger impulsive charge motions and photographic evidence of clearly discontinuous forward progression of the luminous channel. Recently, due to the increasing understanding of the distinct "space leader" process of negative leader extension, the term "step" has increasingly come to be associated with the space leader process itself. Should this emerging association, "step" = space leader attachment, be canonized? If not, then it seems reasonable to use the term "step" to describe impulsive positive leader extension. If, however, we do wish to associate the

The Importance of Volunteer Leaders: An Assessment of Volunteer Leader Competencies Following Volunteer Leader Identification and Training

ERIC Educational Resources Information Center

Morrison, Carley Calico

2017-01-01

Volunteer leaders are an underutilized resource in nonprofit organizations. However, as volunteer directors are stretched to their capacity, others in the organization must provide leadership to volunteers. One way for nonprofit organizations to increase their capacity is to develop the leadership skills of identified volunteer leaders. Because…

Exploring Leader Identity and Development.

PubMed

Priest, Kerry L; Middleton, Eric

2016-01-01

Taking on a leader identity can be a motivating force for pursuing leader development. This chapter explores the reciprocal and recursive nature of identity development and leader development, emphasizing how shifting views of self influence one's motivation to develop as a leader. © 2016 Wiley Periodicals, Inc., A Wiley Company.

Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions.

PubMed

Nishizawa, M; Nishizawa, K

2000-10-01

The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the 'between gene' GC content heterogeneity, which is linked to 'isochores', is a principal factor associated with the bias in substitution patterns in human, 'within gene' heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed.

Amino acid and nucleotide recurrence in aligned sequences: synonymous substitution patterns in association with global and local base compositions

PubMed Central

Nishizawa, Manami; Nishizawa, Kazuhisa

2000-01-01

The tendency for repetitiveness of nucleotides in DNA sequences has been reported for a variety of organisms. We show that the tendency for repetitive use of amino acids is widespread and is observed even for segments conserved between human and Drosophila melanogaster at the level of >50% amino acid identity. This indicates that repetitiveness influences not only the weakly constrained segments but also those sequence segments conserved among phyla. Not only glutamine (Q) but also many of the 20 amino acids show a comparable level of repetitiveness. Repetitiveness in bases at codon position 3 is stronger for human than for D.melanogaster, whereas local repetitiveness in intron sequences is similar between the two organisms. While genes for immune system-specific proteins, but not ancient human genes (i.e. human homologs of Escherichia coli genes), have repetitiveness at codon bases 1 and 2, repetitiveness at codon base 3 for these groups is similar, suggesting that the human genome has at least two mechanisms generating local repetitiveness. Neither amino acid nor nucleotide repetitiveness is observed beyond the exon boundary, denying the possibility that such repetitiveness could mainly stem from natural selection on mRNA or protein sequences. Analyses of mammalian sequence alignments show that while the ‘between gene’ GC content heterogeneity, which is linked to ‘isochores’, is a principal factor associated with the bias in substitution patterns in human, ‘within gene’ heterogeneity in nucleotide composition is also associated with such bias on a more local scale. The relationship amongst the various types of repetitiveness is discussed. PMID:11000273

Leaders who create change and those who manage it. How leaders limit success.

PubMed

Bruhn, John G

2004-01-01

There is no formula for either leading or managing change. Every organization and leader is unique. Leading change, however, is more art than science. Managing change is more science than art. Leading change is not simply a matter of a leader's style or personality; it is a leader's philosophy of how to generate and mobilize the total resources of an organization to enable it to be its best. Managing change, on the other hand, is focused on maintaining stability in an organization and containing the effects of unwanted and unexpected change. Leaders set the limits of success in their organizations by how they manage change. The different approaches of 2 leaders who have created change to correct problems in our health care delivery system are discussed.

Becoming a nursing faculty leader.

PubMed

Young, Patricia K; Pearsall, Catherine; Stiles, Kim A; Horton-Deutsch, Sara

2011-01-01

Academic leaders are one component of a well-prepared faculty that is required to achieve and sustain excellent educational programs. But what is it like to become an academic leader? How does one become a leader? These questions were addressed in an interpretive study in which nurse faculty leaders were interviewed about the experience of becoming a leader. Interview texts were analyzed hermeneutically by a research team to uncover three themes (common, shared experiences): Being Thrust into Leadership, Taking Risks, and Facing Challenges, which are explicated in this article. This study develops the evidence base for leadership preparation at a time when there is a strong need for nursing education leaders in academia.

Amino acid sequence of bovine muzzle epithelial desmocollin derived from cloned cDNA: a novel subtype of desmosomal cadherins.

PubMed

Koch, P J; Goldschmidt, M D; Walsh, M J; Zimbelmann, R; Schmelz, M; Franke, W W

1991-05-01

Desmosomes are cell-type-specific intercellular junctions found in epithelium, myocardium and certain other tissues. They consist of assemblies of molecules involved in the adhesion of specific cell types and in the anchorage of cell-type-specific cytoskeletal elements, the intermediate-size filaments, to the plasma membrane. To explore the individual desmosomal components and their functions we have isolated DNA clones encoding the desmosomal glycoprotein, desmocollin, using antibodies and a cDNA expression library from bovine muzzle epithelium. The cDNA-deduced amino-acid sequence of desmocollin (presently we cannot decide to which of the two desmocollins, DC I or DC II, this clone relates) defines a polypeptide with a calculated molecular weight of 85,000, with a single candidate sequence of 24 amino acids sufficiently long for a transmembrane arrangement, and an extracellular aminoterminal portion of 561 amino acid residues, compared to a cytoplasmic part of only 176 amino acids. Amino acid sequence comparisons have revealed that desmocollin is highly homologous to members of the cadherin family of cell adhesion molecules, including the previously sequenced desmoglein, another desmosome-specific cadherin. Using riboprobes derived from cDNAs for Northern-blot analyses, we have identified an mRNA of approximately 6 kb in stratified epithelia such as muzzle epithelium and tongue mucosa but not in two epithelial cell culture lines containing desmosomes and desmoplakins. The difference may indicate drastic differences in mRNA concentration or the existence of cell-type-specific desmocollin subforms. The molecular topology of desmocollin(s) is discussed in relation to possible functions of the individual molecular domains.

The amino acid sequence around the active-site cysteine and histidine residues of stem bromelain

PubMed Central

Husain, S. S.; Lowe, G.

1970-01-01

Stem bromelain that had been irreversibly inhibited with 1,3-dibromo[2-14C]-acetone was reduced with sodium borohydride and carboxymethylated with iodoacetic acid. After digestion with trypsin and α-chymotrypsin three radioactive peptides were isolated chromatographically. The amino acid sequences around the cross-linked cysteine and histidine residues were determined and showed a high degree of homology with those around the active-site cysteine and histidine residues of papain and ficin. PMID:5420046

Career anchors of dentist leaders.

PubMed

Tuononen, Tiina; Lammintakanen, Johanna; Suominen, Anna Liisa

2016-08-01

The work of a health care leader is demanding; in order to cope, leaders need motivation and support. The occurrence of intrinsic factors called career anchors (combination of one's competence, motives and values) could be a contributing factor in dentist leaders' career decisions. The aim of our study was to identify dentist leaders' career anchors and their association to dentist leaders' retention or turnover of the leadership position. Materials were gathered in 2014 via an electronic questionnaire from 156 current (Leaders) or former (Leavers) Finnish dentist leaders. Career anchor evaluation was conducted by the questionnaire and scoring-table taken from Edgar Schein's Career Anchors Self-Assessment. Both the most and the least important career anchors were detected by the highest and lowest scores and their occurrence reported as percentages. Associations between career anchor scores and tendency to stay were analyzed with logistic regression. 'Technical/Functional Competence' and 'Lifestyle' were most frequently reported as the most important and 'Entrepreneurial Creativity' and 'General Managerial Competence' as the least important career anchors. However, a higher level of 'General Managerial Competence' anchor was most significantly associated with staying in a leadership position. Instead, 'Pure Challenge' and 'Lifestyle' decreased the odds to stay. The knowledge of the important and essential career anchors of dentist leaders' and individuals' could perform crucial part in career choices and also in planning education, work opportunities and human resource policies promoting retention of dentist leaders and probably also other health care leaders.

Leader-Follower Output Synchronization of Linear Heterogeneous Systems With Active Leader Using Reinforcement Learning.

PubMed

Yang, Yongliang; Modares, Hamidreza; Wunsch, Donald C; Yin, Yixin

2018-06-01

This paper develops optimal control protocols for the distributed output synchronization problem of leader-follower multiagent systems with an active leader. Agents are assumed to be heterogeneous with different dynamics and dimensions. The desired trajectory is assumed to be preplanned and is generated by the leader. Other follower agents autonomously synchronize to the leader by interacting with each other using a communication network. The leader is assumed to be active in the sense that it has a nonzero control input so that it can act independently and update its control to keep the followers away from possible danger. A distributed observer is first designed to estimate the leader's state and generate the reference signal for each follower. Then, the output synchronization of leader-follower systems with an active leader is formulated as a distributed optimal tracking problem, and inhomogeneous algebraic Riccati equations (AREs) are derived to solve it. The resulting distributed optimal control protocols not only minimize the steady-state error but also optimize the transient response of the agents. An off-policy reinforcement learning algorithm is developed to solve the inhomogeneous AREs online in real time and without requiring any knowledge of the agents' dynamics. Finally, two simulation examples are conducted to illustrate the effectiveness of the proposed algorithm.

Predicted secondary structure similarity in the absence of primary amino acid sequence homology: hepatitis B virus open reading frames.

PubMed Central

Schaeffer, E; Sninsky, J J

1984-01-01

Proteins that are related evolutionarily may have diverged at the level of primary amino acid sequence while maintaining similar secondary structures. Computer analysis has been used to compare the open reading frames of the hepatitis B virus to those of the woodchuck hepatitis virus at the level of amino acid sequence, and to predict the relative hydrophilic character and the secondary structure of putative polypeptides. Similarity is seen at the levels of relative hydrophilicity and secondary structure, in the absence of sequence homology. These data reinforce the proposal that these open reading frames encode viral proteins. Computer analysis of this type can be more generally used to establish structural similarities between proteins that do not share obvious sequence homology as well as to assess whether an open reading frame is fortuitous or codes for a protein. PMID:6585835

The sequence of sequencers: The history of sequencing DNA.

PubMed

Heather, James M; Chain, Benjamin

2016-01-01

Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Establishing collaborative structures and relationships: Teacher leaders' experiences

NASA Astrophysics Data System (ADS)

Canizo, Thea Lynne

2002-04-01

The purpose of this study was to explore teacher leaders' experiences as they attempted to establish collaborative structures and relationships resulting in improved science instruction at their schools. Teacher leaders were middle school science facilitators, full-time classroom teachers who acted as liaisons between the science teachers at their schools and a change initiative funded by the National Science Foundation. This was a qualitative study, using interviews to create a case study. The researcher used a three-part interview design developed by Seidman (1991). Six research questions served as a framework for the data analysis. Participants identified the following as factors which contributed to their success: support from the principal, other science teachers, central staff personnel, and the district-wide group of science facilitators; professional development; and the successful completion of a scope and sequence for science instruction. Factors identified as hindering their success were: lack of support or conflict with the principal; resistance to change; time constraints; a district policy which limited meeting time; teacher and administrator turnover; tension between the middle school and junior high school models; and personal doubts. From descriptions of their understanding and exercising of leadership, the researcher concluded that teacher leaders had become empowered. The school culture was seen to have a great effect on teacher leaders. The contrasts between a school with a positive culture and another school in disarray were presented. Structures such as summer institutes and release time during the school day were identified as critical for giving teachers the time needed to establish more collaborative working relationships. Once greater trust and understanding were present, teachers were better able to examine their teaching practices more critically. Participants identified mentoring of new members, a continuing role for science

Nursing science leaders.

PubMed

Ortiz, Mario R

2015-04-01

This introduces the guest author's column on perspectives on the development of leaders in science. The need for leadership in science is discussed and a model for the development of science leaders in nursing is outlined. © The Author(s) 2015.

Influence of gag and RRE Sequences on HIV-1 RNA Packaging Signal Structure and Function.

PubMed

Kharytonchyk, Siarhei; Brown, Joshua D; Stilger, Krista; Yasin, Saif; Iyer, Aishwarya S; Collins, John; Summers, Michael F; Telesnitsky, Alice

2018-07-06

The packaging signal (Ψ) and Rev-responsive element (RRE) enable unspliced HIV-1 RNAs' export from the nucleus and packaging into virions. For some retroviruses, engrafting Ψ onto a heterologous RNA is sufficient to direct encapsidation. In contrast, HIV-1 RNA packaging requires 5' leader Ψ elements plus poorly defined additional features. We previously defined minimal 5' leader sequences competitive with intact Ψ for HIV-1 packaging, and here examined the potential roles of additional downstream elements. The findings confirmed that together, HIV-1 5' leader Ψ sequences plus a nuclear export element are sufficient to specify packaging. However, RNAs trafficked using a heterologous export element did not compete well with RNAs using HIV-1's RRE. Furthermore, some RNA additions to well-packaged minimal vectors rendered them packaging-defective. These defects were rescued by extending gag sequences in their native context. To understand these packaging defects' causes, in vitro dimerization properties of RNAs containing minimal packaging elements were compared to RNAs with sequence extensions that were or were not compatible with packaging. In vitro dimerization was found to correlate with packaging phenotypes, suggesting that HIV-1 evolved to prevent 5' leader residues' base pairing with downstream residues and misfolding of the packaging signal. Our findings explain why gag sequences have been implicated in packaging and show that RRE's packaging contributions appear more specific than nuclear export alone. Paired with recent work showing that sequences upstream of Ψ can dictate RNA folds, the current work explains how genetic context of minimal packaging elements contributes to HIV-1 RNA fate determination. Copyright © 2018 Elsevier Ltd. All rights reserved.

Who helps the leaders? Difficulties experienced by cancer support group leaders.

PubMed

Kirsten, Laura; Butow, Phyllis; Price, Melanie; Hobbs, Kim; Sunquist, Kendra

2006-07-01

Cancer support groups are an important source of support for cancer patients, yet little is known about the challenges and training needs of both professionally trained and untrained leaders. The aim of this study was to discover the difficulties experienced and training desired by cancer support group leaders. Twenty-seven leaders of 34 cancer support groups participated in focus groups or individual interviews. Groups were purposively selected as representative of 173 support groups identified in New South Wales which were for adults with cancer and/or their adult carers and were not therapeutic or education-only groups. Difficulties identified included dealing with people's different communication styles and needs; dealing with recurrence, metastases and death; practical issues, including resources, setting the programme and funding security; maintaining personal balance and preventing burn out; establishing group credibility; dealing with group cycles; and leading groups in rural areas. Leaders also identified benefits and rewards from group leadership such as contributing to others' well-being, self-development and insight into others' lives. Non-professionally trained leaders experienced more difficulties, particularly in dealing with group process and practical issues. Difficulties identified were related both to working with a cancer population specifically and to working with groups in general. While some issues were common to both health professionals and non-health professionals, non-health professionals reported greater supportive needs. Clear guidelines, targeted training and development of better methods of support to reduce the stress and burn out experienced by group leaders are needed.

Remembering the Leaders of China.

PubMed

Fu, Mingchen; Xue, Yan; DeSoto, K Andrew; Yuan, Ti-Fei

2016-01-01

In two studies, we examined Chinese students' memory for the names of the leaders of China. In Study 1, subjects were cued with the names of periods from China's history. Subjects listed as many leaders as possible from each period and put them in the correct ordinal position when they could (see Roediger and DeSoto, 2014). Results showed that within each period, a primacy effect and sometimes a recency effect emerged. Moreover, the average recall probability for leaders within a specific period was a function of the ordinal position of the period. In Study 2, we asked another group of subjects to identify the sources through which they were able to recall each leader. We found that most subjects remembered leaders due to class and coursework. We also found a relation between a leader's recall probability and the amount of information available on that leader on the Internet. Our findings further imply that the serial position function captures the form of collective memory.

From amino acid sequence to bioactivity: The biomedical potential of antitumor peptides.

PubMed

Blanco-Míguez, Aitor; Gutiérrez-Jácome, Alberto; Pérez-Pérez, Martín; Pérez-Rodríguez, Gael; Catalán-García, Sandra; Fdez-Riverola, Florentino; Lourenço, Anália; Sánchez, Borja

2016-06-01

Chemoprevention is the use of natural and/or synthetic substances to block, reverse, or retard the process of carcinogenesis. In this field, the use of antitumor peptides is of interest as, (i) these molecules are small in size, (ii) they show good cell diffusion and permeability, (iii) they affect one or more specific molecular pathways involved in carcinogenesis, and (iv) they are not usually genotoxic. We have checked the Web of Science Database (23/11/2015) in order to collect papers reporting on bioactive peptide (1691 registers), which was further filtered searching terms such as "antiproliferative," "antitumoral," or "apoptosis" among others. Works reporting the amino acid sequence of an antiproliferative peptide were kept (60 registers), and this was complemented with the peptides included in CancerPPD, an extensive resource for antiproliferative peptides and proteins. Peptides were grouped according to one of the following mechanism of action: inhibition of cell migration, inhibition of tumor angiogenesis, antioxidative mechanisms, inhibition of gene transcription/cell proliferation, induction of apoptosis, disorganization of tubulin structure, cytotoxicity, or unknown mechanisms. The main mechanisms of action of those antiproliferative peptides with known amino acid sequences are presented and finally, their potential clinical usefulness and future challenges on their application is discussed. © 2016 The Protein Society.

From amino acid sequence to bioactivity: The biomedical potential of antitumor peptides

PubMed Central

Blanco‐Míguez, Aitor; Gutiérrez‐Jácome, Alberto; Pérez‐Pérez, Martín; Pérez‐Rodríguez, Gael; Catalán‐García, Sandra; Fdez‐Riverola, Florentino; Lourenço, Anália

2016-01-01

Abstract Chemoprevention is the use of natural and/or synthetic substances to block, reverse, or retard the process of carcinogenesis. In this field, the use of antitumor peptides is of interest as, (i) these molecules are small in size, (ii) they show good cell diffusion and permeability, (iii) they affect one or more specific molecular pathways involved in carcinogenesis, and (iv) they are not usually genotoxic. We have checked the Web of Science Database (23/11/2015) in order to collect papers reporting on bioactive peptide (1691 registers), which was further filtered searching terms such as “antiproliferative,” “antitumoral,” or “apoptosis” among others. Works reporting the amino acid sequence of an antiproliferative peptide were kept (60 registers), and this was complemented with the peptides included in CancerPPD, an extensive resource for antiproliferative peptides and proteins. Peptides were grouped according to one of the following mechanism of action: inhibition of cell migration, inhibition of tumor angiogenesis, antioxidative mechanisms, inhibition of gene transcription/cell proliferation, induction of apoptosis, disorganization of tubulin structure, cytotoxicity, or unknown mechanisms. The main mechanisms of action of those antiproliferative peptides with known amino acid sequences are presented and finally, their potential clinical usefulness and future challenges on their application is discussed. PMID:27010507

Complete nucleotide and derived amino acid sequence of cDNA encoding the mitochondrial uncoupling protein of rat brown adipose tissue: lack of a mitochondrial targeting presequence.

PubMed Central

Ridley, R G; Patel, H V; Gerber, G E; Morton, R C; Freeman, K B

1986-01-01

A cDNA clone spanning the entire amino acid sequence of the nuclear-encoded uncoupling protein of rat brown adipose tissue mitochondria has been isolated and sequenced. With the exception of the N-terminal methionine the deduced N-terminus of the newly synthesized uncoupling protein is identical to the N-terminal 30 amino acids of the native uncoupling protein as determined by protein sequencing. This proves that the protein contains no N-terminal mitochondrial targeting prepiece and that a targeting region must reside within the amino acid sequence of the mature protein. Images PMID:3012461

Fatty Acid Profile and Unigene-Derived Simple Sequence Repeat Markers in Tung Tree (Vernicia fordii)

PubMed Central

Zhang, Lin; Jia, Baoguang; Tan, Xiaofeng; Thammina, Chandra S.; Long, Hongxu; Liu, Min; Wen, Shanna; Song, Xianliang; Cao, Heping

2014-01-01

Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Lack of fatty acid composition and molecular markers hinders biochemical, genetic and breeding research. The objectives of this study were to determine fatty acid profiles and develop unigene-derived simple sequence repeat (SSR) markers in tung tree. Fatty acid profiles of 41 accessions showed that the ratio of α-eleostearic acid was increasing continuously with a parallel trend to the amount of tung oil accumulation while the ratios of other fatty acids were decreasing in different stages of the seeds and that α-eleostearic acid (18∶3) consisted of 77% of the total fatty acids in tung oil. Transcriptome sequencing identified 81,805 unigenes from tung cDNA library constructed using seed mRNA and discovered 6,366 SSRs in 5,404 unigenes. The di- and tri-nucleotide microsatellites accounted for 92% of the SSRs with AG/CT and AAG/CTT being the most abundant SSR motifs. Fifteen polymorphic genic-SSR markers were developed from 98 unigene loci tested in 41 cultivated tung accessions by agarose gel and capillary electrophoresis. Genbank database search identified 10 of them putatively coding for functional proteins. Quantitative PCR demonstrated that all 15 polymorphic SSR-associated unigenes were expressed in tung seeds and some of them were highly correlated with oil composition in the seeds. Dendrogram revealed that most of the 41 accessions were clustered according to the geographic region. These new polymorphic genic-SSR markers will facilitate future studies on genetic diversity, molecular fingerprinting, comparative genomics and genetic mapping in tung tree. The lipid profiles in the seeds of 41 tung accessions will be valuable for biochemical and breeding studies. PMID:25167054

Genome Sequence of Lactobacillus rhamnosus Strain CASL, an Efficient l-Lactic Acid Producer from Cheap Substrate Cassava

PubMed Central

Yu, Bo; Su, Fei; Wang, Limin; Zhao, Bo; Qin, Jiayang; Ma, Cuiqing; Xu, Ping; Ma, Yanhe

2011-01-01

Lactobacillus rhamnosus is a type of probiotic bacteria with industrial potential for l-lactic acid production. We announce the draft genome sequence of L. rhamnosus CASL (2,855,156 bp with a G+C content of 46.6%), which is an efficient producer of l-lactic acid from cheap, nonfood substrate cassava with a high production titer. PMID:22123765

Fluorescence energy transfer as a probe for nucleic acid structures and sequences.

PubMed Central

Mergny, J L; Boutorine, A S; Garestier, T; Belloc, F; Rougée, M; Bulychev, N V; Koshkin, A A; Bourson, J; Lebedev, A V; Valeur, B

1994-01-01

The primary or secondary structure of single-stranded nucleic acids has been investigated with fluorescent oligonucleotides, i.e., oligonucleotides covalently linked to a fluorescent dye. Five different chromophores were used: 2-methoxy-6-chloro-9-amino-acridine, coumarin 500, fluorescein, rhodamine and ethidium. The chemical synthesis of derivatized oligonucleotides is described. Hybridization of two fluorescent oligonucleotides to adjacent nucleic acid sequences led to fluorescence excitation energy transfer between the donor and the acceptor dyes. This phenomenon was used to probe primary and secondary structures of DNA fragments and the orientation of oligodeoxynucleotides synthesized with the alpha-anomers of nucleoside units. Fluorescence energy transfer can be used to reveal the formation of hairpin structures and the translocation of genes between two chromosomes. PMID:8152922

On the Transition from Initial Leader to Stepped Leader in Negative Cloud-to-ground Lightning

NASA Astrophysics Data System (ADS)

Stolzenburg, M.; Marshall, T. C.; Karunarathne, S.; Orville, R. E.

2017-12-01

High-speed video and electric field change (E-change) data are used to describe the first 5 ms of a natural negative cloud-to-ground (CG) flash. These observations reveal differences in appearance of both the video luminosity and the E-change pulses before the leader transitions to propagating as a negative stepped leader (SL). During the initial breakdown (IB) stage, the initial leader advances intermittently forward in jumps of 78-175 m, at intervals of 100-280 μs, and in separate bursts that are bright for a few 20-μs video frames. The IB pulses accompanying these luminosity bursts have long duration, large amplitude, and a characteristic bipolar shape in nearby E-change observations. In the time between IB pulses, the initial leader is very dim or not visible during the earliest 1-2 ms of the IB stage. Over the next few milliseconds, the leader propagation transitions to an early SL phase, in which the leader tips advance 20-59 m forward at more regular intervals of 40-80 μs during relatively dim and brief steps. In the E-change data, the accompanying SL pulses have very short duration, small amplitude, and are typically unipolar. These data indicate that when the entire initial leader length behind the lower end begins to remain illuminated between bursts, the propagation mode changes from IB bursts to SL steps, and the IB stage ends. Additional differences in initial leader character are evident during the return stroke, as its luminosity speed decreases sharply upon reaching the topmost initial leader section of the channel, and that section of channel does not saturate the video intensity. Results of these analyses support a prior hypothesis that the early initial leader development occurs in the absence of a continuously hot channel, and consequently, the initial leader propagation is unlike the self-propagating advance of the later stepped leader.

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)

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification

PubMed Central

Schouten, Jan P.; McElgunn, Cathal J.; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-01-01

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down’s syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50–70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences. PMID:12060695

Relative quantification of 40 nucleic acid sequences by multiplex ligation-dependent probe amplification.

PubMed

Schouten, Jan P; McElgunn, Cathal J; Waaijer, Raymond; Zwijnenburg, Danny; Diepvens, Filip; Pals, Gerard

2002-06-15

We describe a new method for relative quantification of 40 different DNA sequences in an easy to perform reaction requiring only 20 ng of human DNA. Applications shown of this multiplex ligation-dependent probe amplification (MLPA) technique include the detection of exon deletions and duplications in the human BRCA1, MSH2 and MLH1 genes, detection of trisomies such as Down's syndrome, characterisation of chromosomal aberrations in cell lines and tumour samples and SNP/mutation detection. Relative quantification of mRNAs by MLPA will be described elsewhere. In MLPA, not sample nucleic acids but probes added to the samples are amplified and quantified. Amplification of probes by PCR depends on the presence of probe target sequences in the sample. Each probe consists of two oligonucleotides, one synthetic and one M13 derived, that hybridise to adjacent sites of the target sequence. Such hybridised probe oligonucleotides are ligated, permitting subsequent amplification. All ligated probes have identical end sequences, permitting simultaneous PCR amplification using only one primer pair. Each probe gives rise to an amplification product of unique size between 130 and 480 bp. Probe target sequences are small (50-70 nt). The prerequisite of a ligation reaction provides the opportunity to discriminate single nucleotide differences.

Biochemical and genetic characterization of enterocin A from Enterococcus faecium, a new antilisterial bacteriocin in the pediocin family of bacteriocins.

PubMed Central

Aymerich, T; Holo, H; Håvarstein, L S; Hugas, M; Garriga, M; Nes, I F

1996-01-01

A new bacteriocin has been isolated from an Enterococcus faecium strain. The bacteriocin, termed enterocin A, was purified to homogeneity as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, N-terminal amino acid sequencing, and mass spectrometry analysis. By combining the data obtained from amino acid and DNA sequencing, the primary structure of enterocin A was determined. It consists of 47 amino acid residues, and the molecular weight was calculated to be 4,829, assuming that the four cysteine residues form intramolecular disulfide bridges. This molecular weight was confirmed by mass spectrometry analysis. The amino acid sequence of enterocin A shared significant homology with a group of bacteriocins (now termed pediocin-like bacteriocins) isolated from a variety of lactic acid-producing bacteria, which include members of the genera Lactobacillus, Pediococcus, Leuconostoc, and Carnobacterium. Sequencing of the structural gene of enterocin A, which is located on the bacterial chromosome, revealed an N-terminal leader sequence of 18 amino acid residues, which was removed during the maturation process. The enterocin A leader belongs to the double-glycine leaders which are found among most other small nonlantibiotic bacteriocins, some lantibiotics, and colicin V. Downstream of the enterocin A gene was located a second open reading frame, encoding a putative protein of 103 amino acid residues. This gene may encode the immunity factor of enterocin A, and it shares 40% identity with a similar open reading frame in the operon of leucocin AUL 187, another pediocin-like bacteriocin. PMID:8633865

Army Leader Development Strategy: Developing Brigade Level Leaders through Balance, Emphasis, and Approach

DTIC Science & Technology

2014-06-13

accompanying assumption is that over a decade of 5 combat operations has created gaps in leader development visible at all levels of leadership. The third...future potential will steer leaders toward positions based on their aptitude rather than their previous experience and performance. This would...provides no metrics for determining how well leader development is understood from a pedagogical perspective. Lastly, responses indicate that a

Leaders and Leadership in Academe.

ERIC Educational Resources Information Center

Vroom, Victor H.

1983-01-01

Four contingency theories of leadership are explored and contrasted. Predictions of leader types and leader behaviors that would follow from each are counterposed. External functions of the leader and interactions with organizational members who are not subordinates are discussed. (Author/MLW)

Lessons from Leaders.

ERIC Educational Resources Information Center

Schuh, John H.

2002-01-01

A semistructured interview protocol was used to present perspectives on leadership from five national leaders in student affairs. Several major themes emerged. Issues were discussed about leaderships; how they manage difficulties; what work were they most proud of; and what was their advice for aspiring leaders. Reviews limitations and…

Evolutionary Distance of Amino Acid Sequence Orthologs across Macaque Subspecies: Identifying Candidate Genes for SIV Resistance in Chinese Rhesus Macaques

PubMed Central

Ross, Cody T.; Roodgar, Morteza; Smith, David Glenn

2015-01-01

We use the Reciprocal Smallest Distance (RSD) algorithm to identify amino acid sequence orthologs in the Chinese and Indian rhesus macaque draft sequences and estimate the evolutionary distance between such orthologs. We then use GOanna to map gene function annotations and human gene identifiers to the rhesus macaque amino acid sequences. We conclude methodologically by cross-tabulating a list of amino acid orthologs with large divergence scores with a list of genes known to be involved in SIV or HIV pathogenesis. We find that many of the amino acid sequences with large evolutionary divergence scores, as calculated by the RSD algorithm, have been shown to be related to HIV pathogenesis in previous laboratory studies. Four of the strongest candidate genes for SIVmac resistance in Chinese rhesus macaques identified in this study are CDK9, CXCL12, TRIM21, and TRIM32. Additionally, ANKRD30A, CTSZ, GORASP2, GTF2H1, IL13RA1, MUC16, NMDAR1, Notch1, NT5M, PDCD5, RAD50, and TM9SF2 were identified as possible candidates, among others. We failed to find many laboratory experiments contrasting the effects of Indian and Chinese orthologs at these sites on SIVmac pathogenesis, but future comparative studies might hold fertile ground for research into the biological mechanisms underlying innate resistance to SIVmac in Chinese rhesus macaques. PMID:25884674

Translation of the mRNA of the maize transcriptional activator Opaque-2 is inhibited by upstream open reading frames present in the leader sequence.

PubMed Central

Lohmer, S; Maddaloni, M; Motto, M; Salamini, F; Thompson, R D

1993-01-01

The protein encoded by the Opaque-2 (O2) gene is a transcription factor, translated from an mRNA that possesses an unusually long 5' leader sequence containing three upstream open reading frames (uORFs). The efficiency of translation of O2 mRNA has been tested in vivo by a transient assay in which the level of activation of the b32 promoter, a natural target of O2 protein, is measured. We show that uORF-less O2 alleles possess a higher transactivation value than the wild-type allele and that the reduction in transactivation due to the uORFs is a cis-dominant effect. The data presented indicate that both uORF1 and uORF2 are involved in the reducing effect and suggest that both are likely to be translated. PMID:8439744

The Inspirational Leader

ERIC Educational Resources Information Center

Benigni, Mark D.; Hughes, Mark A

2012-01-01

Amid the focus on improved standardized test scores, differentiated instruction, value-added initiatives and improved teacher evaluation, one must not ignore an education leader's need to inspire and be inspired. But how do education leaders inspire their students and teachers during some of the most difficult economic times the nation has ever…

Leadership behaviors of athletic training leaders compared with leaders in other fields.

PubMed

Laurent, Timothy G; Bradney, Debbie A

2007-01-01

Athletic trainers are in positions of leadership. To determine self-reported leadership practices of head athletic trainers (HATCs) and program directors (PDs). Cross-sectional study. Respondents' academic institutions. A total of 238 athletic training leaders completed the Leadership Practices Inventory. Of these, 50.4% (n = 120) were HATCs and 49.6% (n = 118) were PDs; 69.3% (n = 165) were men and 30.7% (n = 73) were women; almost all respondents (97.1%, n = 231) were white. Respondents typically reported having 11 to 15 years of experience as an athletic trainer (n = 57, 23.9%) and being between the ages of 30 and 39 years (n = 109, 45.8%). Categories of leadership behaviors (ie, Model, Inspire, Challenge, Encourage, and Enable) were scored from 1 (almost never) to 10 (almost always). Item scores were summed to compute mean category scores. We analyzed demographic information; used t ratios to compare the data from athletic training leaders (PDs and HATCs) with normative data; compared sex, age, position, ethnicity, and years of experience with leadership practices; and computed mean scores. Athletic training leaders reported using leadership behaviors similar to those of other leaders. The PDs reported using inspiring, challenging, enabling, and encouraging leadership behaviors more often than did the HATCs. No differences were found by ethnicity, age, years of experience, or leadership practices. Athletic training leaders are transformational leaders. Athletic training education program accreditation requirements likely account for the difference in leadership practices between PDs and HATCs.

Trauma team leaders' non-verbal communication: video registration during trauma team training.

PubMed

Härgestam, Maria; Hultin, Magnus; Brulin, Christine; Jacobsson, Maritha

2016-03-25

There is widespread consensus on the importance of safe and secure communication in healthcare, especially in trauma care where time is a limiting factor. Although non-verbal communication has an impact on communication between individuals, there is only limited knowledge of how trauma team leaders communicate. The purpose of this study was to investigate how trauma team members are positioned in the emergency room, and how leaders communicate in terms of gaze direction, vocal nuances, and gestures during trauma team training. Eighteen trauma teams were audio and video recorded during trauma team training in the emergency department of a hospital in northern Sweden. Quantitative content analysis was used to categorize the team members' positions and the leaders' non-verbal communication: gaze direction, vocal nuances, and gestures. The quantitative data were interpreted in relation to the specific context. Time sequences of the leaders' gaze direction, speech time, and gestures were identified separately and registered as time (seconds) and proportions (%) of the total training time. The team leaders who gained control over the most important area in the emergency room, the "inner circle", positioned themselves as heads over the team, using gaze direction, gestures, vocal nuances, and verbal commands that solidified their verbal message. Changes in position required both attention and collaboration. Leaders who spoke in a hesitant voice, or were silent, expressed ambiguity in their non-verbal communication: and other team members took over the leader's tasks. In teams where the leader had control over the inner circle, the members seemed to have an awareness of each other's roles and tasks, knowing when in time and where in space these tasks needed to be executed. Deviations in the leaders' communication increased the ambiguity in the communication, which had consequences for the teamwork. Communication cannot be taken for granted; it needs to be practiced

Identification of a novel bovine enterovirus possessing highly divergent amino acid sequences in capsid protein.

PubMed

Tsuchiaka, Shinobu; Rahpaya, Sayed Samim; Otomaru, Konosuke; Aoki, Hiroshi; Kishimoto, Mai; Naoi, Yuki; Omatsu, Tsutomu; Sano, Kaori; Okazaki-Terashima, Sachiko; Katayama, Yukie; Oba, Mami; Nagai, Makoto; Mizutani, Tetsuya

2017-01-17

Bovine enterovirus (BEV) belongs to the species Enterovirus E or F, genus Enterovirus and family Picornaviridae. Although numerous studies have identified BEVs in the feces of cattle with diarrhea, the pathogenicity of BEVs remains unclear. Previously, we reported the detection of novel kobu-like virus in calf feces, by metagenomics analysis. In the present study, we identified a novel BEV in diarrheal feces collected for that survey. Complete genome sequences were determined by deep sequencing in feces. Secondary RNA structure analysis of the 5' untranslated region (UTR), phylogenetic tree construction and pairwise identity analysis were conducted. The complete genome sequences of BEV were genetically distant from other EVs and the VP1 coding region contained novel and unique amino acid sequences. We named this strain as BEV AN12/Bos taurus/JPN/2014 (referred to as BEV-AN12). According to genome analysis, the genome length of this virus is 7414 nucleotides excluding the poly (A) tail and its genome consists of a 5'UTR, open reading frame encoding a single polyprotein, and 3'UTR. The results of secondary RNA structure analysis showed that in the 5'UTR, BEV-AN12 had an additional clover leaf structure and small stem loop structure, similarly to other BEVs. In pairwise identity analysis, BEV-AN12 showed high amino acid (aa) identities to Enterovirus F in the polyprotein, P2 and P3 regions (aa identity ≥82.4%). Therefore, BEV-AN12 is closely related to Enterovirus F. However, aa sequences in the capsid protein regions, particularly the VP1 encoding region, showed significantly low aa identity to other viruses in genus Enterovirus (VP1 aa identity ≤58.6%). In addition, BEV-AN12 branched separately from Enterovirus E and F in phylogenetic trees based on the aa sequences of P1 and VP1, although it clustered with Enterovirus F in trees based on sequences in the P2 and P3 genome region. We identified novel BEV possessing highly divergent aa sequences in the VP1 coding

Purification, amino acid sequence and characterisation of kangaroo IGF-I.

PubMed

Yandell, C A; Francis, G L; Wheldrake, J F; Upton, Z

1998-01-01

Insulin-like growth factor-I (IGF-I) and IGF-II have been purified to homogeneity from kangaroo (Macropus fuliginosus) serum, thus this represents the first report of the purification, sequencing and characterisation of marsupial IGFs. N-Terminal protein sequencing reveals that there are six amino acid differences between kangaroo and human IGF-I. Kangaroo IGF-II has been partially sequenced and no differences were found between human and kangaroo IGF-II in the 53 residues identified. Thus the IGFs appear to be remarkably structurally conserved during mammalian radiation. In addition, in vitro characterisation of kangaroo IGF-I demonstrated that the functional properties of human, kangaroo and chicken IGF-I are very similar. In an assay measuring the ability of the proteins to stimulate protein synthesis in rat L6 myoblasts, all IGF-I proteins were found to be equally potent. The ability of all three proteins to compete for binding with radiolabelled human IGF-I to type-1 IGF receptors in L6 myoblasts and in Sminthopsis crassicaudata transformed lung fibroblasts, a marsupial cell line, was comparable. Furthermore, kangaroo and human IGF-I react equally in a human IGF-I RIA using a human reference standard, radiolabelled human IGF-I and a polyclonal antibody raised against recombinant human IGF-I. This study indicates that not only is the primary structure of eutherian and metatherian IGF-I conserved, but also the proteins appear to be functionally similar.

What Is an Innovative Educational Leader?

ERIC Educational Resources Information Center

Marron, Joseph M.; Cunniff, Dan

2014-01-01

This paper outlined the traits of an innovative educational leader in our changing society. It discussed the difference in a manager and leader, as well as the specific dispositions that differentiate the innovative educational leader from what many consider the average leader. The authors used the acronym "HELPSS" to highlight the…

A peptide targeted against phosphoprotein and leader RNA interaction inhibits growth of Chandipura virus -- an emerging rhabdovirus.

PubMed

Roy, Arunava; Chakraborty, Prasenjit; Polley, Smarajit; Chattopadhyay, Dhrubajyoti; Roy, Siddhartha

2013-11-01

The fatal illness caused by Chandipura virus (CHPV), an emerging pathogen, presently lacks any therapeutic option. Previous research suggested that interaction between the virally encoded phosphoprotein (P) and the positive sense leader RNA (le-RNA) may play an important role in the viral lifecycle. In this report, we have identified a β-sheet/loop motif in the C-terminal domain of the CHPV P protein as essential for this interaction. A synthetic peptide encompassing this motif and spanning a continuous stretch of 36 amino acids (Pep208-243) was found to bind the le-RNA in vitro and inhibit CHPV growth in infected cells. Furthermore, a stretch of three amino acid residues at position 217-219 was identified as essential for this interaction, both in vitro and in infected cells. siRNA knockdown-rescue experiments demonstrated that these three amino acid residues are crucial for the leader RNA binding function of P protein in the CHPV life cycle. Mutations of these three amino acid residues render the peptide completely ineffective against CHPV. Effect of inhibition of phosphoprotein-leader RNA interaction on viral replication was assayed. Peptide Pep208-243 tagged with a cell penetrating peptide was found to inhibit CHPV replication as ascertained by real time RT-PCR. The specific inhibition of viral growth observed using this peptide suggests a new possibility for designing of anti-viral agents against Mononegavirale group of human viruses. Copyright © 2013. Published by Elsevier B.V.

Construction Strategy for an Internal Amplification Control for Real-Time Diagnostic Assays Using Nucleic Acid Sequence-Based Amplification: Development and Clinical Application

PubMed Central

Rodríguez-Lázaro, David; D'Agostino, Martin; Pla, Maria; Cook, Nigel

2004-01-01

An important analytical control in molecular amplification-based methods is an internal amplification control (IAC), which should be included in each reaction mixture. An IAC is a nontarget nucleic acid sequence which is coamplified simultaneously with the target sequence. With negative results for the target nucleic acid, the absence of an IAC signal indicates that amplification has failed. A general strategy for the construction of an IAC for inclusion in molecular beacon-based real-time nucleic acid sequence-based amplification (NASBA) assays is presented. Construction proceeds in two phases. In the first phase, a double-stranded DNA molecule that contains nontarget sequences flanked by target sequences complementary to the NASBA primers is produced. At the 5′ end of this DNA molecule is a T7 RNA polymerase binding sequence. In the second phase of construction, RNA transcripts are produced from the DNA by T7 RNA polymerase. This RNA is the IAC; it is amplified by the target NASBA primers and is detected by a molecular beacon probe complementary to the internal nontarget sequences. As a practical example, an IAC for use in an assay for the detection of Mycobacterium avium subsp. paratuberculosis is described, its incorporation and optimization within the assay are detailed, and its application to spiked and natural clinical samples is shown to illustrate the correct interpretation of the diagnostic results. PMID:15583319

Amino acid sequences of peptides from a chymotryptic digest of a urea-soluble protein fraction (U.S.3) from oxidized wool

PubMed Central

Corfield, M. C.; Fletcher, J. C.

1969-01-01

1. A chymotryptic digest of the protein fraction U.S.3. from oxidized wool was separated into 51 peptide fractions by chromatography on a column of cation-exchange resin. 2. The less acidic fractions were separated into their component peptides by a combination of cation-exchange-resin chromatography, paper chromatography and paper electrophoresis. 3. The amino acid sequences of 34 of these peptides were elucidated, and those of 14 others partially determined. 4. Overlaps between the tryptic and chymotryptic peptides from fraction U.S.3 have enabled ten extended amino acid sequences to be deduced, the longest containing 20 amino acid residues. 5. The relevance of the results to the structures of the helical and non-helical regions of wool is discussed. PMID:5395876

Responsible leader behavior in health sectors.

PubMed

Longest, Beaufort

2017-02-06

Purpose The purpose of this paper is to expand attention to responsible leader behavior in the world's health sectors by explaining how this concept applies to health sectors, considering why health sector leaders should behave responsibly, reviewing how they can do so, and asserting potential impact through an applied example. Design/methodology/approach This paper is a viewpoint, reflecting conceptualizations rooted in leadership literature which are then specifically applied to health sectors. A definition of responsible leader behavior is affirmed and applied specifically in health sectors. Conceptualizations and viewpoints about practice of responsible leader behavior in health sectors and potential consequences are then discussed and asserted. Findings Leadership failures and debacles found in health, but more so in other sectors, have led leadership researchers to offer insights, many of them empirical, into the challenges of leadership especially by more clearly delineating responsible leader behavior. Practical implications Much of what has been learned in the research about responsible leader behavior offers pathways for health sector leaders to more fully practice responsible leadership. Social implications This paper asserts and provides a supporting example that greater levels of responsible leader behavior in health sectors hold potentially important societal benefits. Originality/value This paper is the first to apply emerging conceptualizations and early empirical findings about responsible leader behavior specifically to leaders in health sectors.

Christian School Leaders and Spirituality

ERIC Educational Resources Information Center

Banke, Susan; Maldonado, Nancy; Lacey, Candace H.

2012-01-01

This phenomenological study examined the spiritual experiences of Christian school leaders who are the spiritual leaders of their schools. A purposeful, nominated sample of 12 Christian school leaders was selected. In-depth, open-ended interviews were conducted, audio taped, and then transcribed verbatim. Data analysis was based on Rudestam and…

SL2-like spliced leader RNAs in the basal nematode Prionchulus punctatus: New insight into the evolution of nematode SL2 RNAs.

PubMed

Harrison, Neale; Kalbfleisch, Andreas; Connolly, Bernadette; Pettitt, Jonathan; Müller, Berndt

2010-08-01

Spliced-leader (SL) trans-splicing has been found in all molecularly characterized nematode species to date, and it is likely to be a nematode synapomorphy. Most information regarding SL trans-splicing has come from the study of nematodes from a single monophyletic group, the Rhabditida, all of which employ SL RNAs that are identical to, or variants of, the SL1 RNA first characterized in Caenorhabditis elegans. In contrast, the more distantly related Trichinella spiralis, belonging to the subclass Dorylaimia, utilizes a distinct set of SL RNAs that display considerable sequence diversity. To investigate whether this is true of other members of the Dorylaimia, we have characterized SL RNAs from Prionchulus punctatus. Surprisingly, this revealed the presence of a set of SLs that show clear sequence similarity to the SL2 family of spliced leaders, which have previously only been found within the rhabditine group (which includes C. elegans). Expression of one of the P. punctatus SL RNAs in C. elegans reveals that it can compete specifically with the endogenous C. elegans SL2 spliced leaders, being spliced to the pre-mRNAs derived from downstream genes in operons, but does not compete with the SL1 spliced leaders. This discovery raises the possibility that SL2-like spliced leaders were present in the last common ancestor of the nematode phylum.

One member, two leaders: extending leader-member exchange theory to a dual leadership context.

PubMed

Vidyarthi, Prajya R; Erdogan, Berrin; Anand, Smriti; Liden, Robert C; Chaudhry, Anjali

2014-05-01

In this study, we develop and test a model that extends leader-member exchange (LMX) theory to a dual leadership context. Drawing upon relative deprivation theory, we assert that when employees work for 2 leaders, each relationship exists within the context of the other relationship. Thus, the level of alignment or misalignment between the 2 relationships has implications for employees' job satisfaction and voluntary turnover. Employing polynomial regression on time-lagged data gathered from 159 information technology consultants nested in 26 client projects, we found that employee outcomes are affected by the quality of the relationship with both agency and client leaders, such that the degree of alignment between the 2 LMXs explained variance in outcomes beyond that explained by both LMXs. Results also revealed that a lack of alignment in the 2 LMXs led to asymmetric effects on outcomes, such that the relationship with agency leader mattered more than the relationship with one's client leader. Finally, frequency of communication with the agency leader determined the degree to which agency LMX affected job satisfaction in the low client LMX condition. (c) 2014 APA, all rights reserved.

Control of a Salmonella virulence locus by an ATP-sensing leader messenger RNA.

PubMed

Lee, Eun-Jin; Groisman, Eduardo A

2012-06-13

The facultative intracellular pathogen Salmonella enterica resides within a membrane-bound compartment inside macrophages. This compartment must be acidified for Salmonella to survive within macrophages, possibly because acidic pH promotes expression of Salmonella virulence proteins. We reasoned that Salmonella might sense its surroundings have turned acidic not only upon protonation of the extracytoplasmic domain of a protein sensor but also by an increase in cytosolic ATP levels, because conditions that enhance the proton gradient across the bacterial inner membrane stimulate ATP synthesis. Here we report that an increase in cytosolic ATP promotes transcription of the coding region for the virulence gene mgtC, which is the most highly induced horizontally acquired gene when Salmonella is inside macrophages. This transcript is induced both upon media acidification and by physiological conditions that increase ATP levels independently of acidification. ATP is sensed by the coupling/uncoupling of transcription of the unusually long mgtC leader messenger RNA and translation of a short open reading frame located in this region. A mutation in the mgtC leader messenger RNA that eliminates the response to ATP hinders mgtC expression inside macrophages and attenuates Salmonella virulence in mice. Our results define a singular example of an ATP-sensing leader messenger RNA. Moreover, they indicate that pathogens can interpret extracellular cues by the impact they have on cellular metabolites.

Leadership Behaviors of Athletic Training Leaders Compared With Leaders in Other Fields

PubMed Central

Laurent, Timothy G; Bradney, Debbie A

2007-01-01

Context: Athletic trainers are in positions of leadership. Objective: To determine self-reported leadership practices of head athletic trainers (HATCs) and program directors (PDs). Design: Cross-sectional study. Setting: Respondents' academic institutions. Patients or Other Participants: A total of 238 athletic training leaders completed the Leadership Practices Inventory. Of these, 50.4% (n = 120) were HATCs and 49.6% (n = 118) were PDs; 69.3% (n = 165) were men and 30.7% (n = 73) were women; almost all respondents (97.1%, n = 231) were white. Respondents typically reported having 11 to 15 years of experience as an athletic trainer (n = 57, 23.9%) and being between the ages of 30 and 39 years (n = 109, 45.8%). Main Outcome Measure(s): Categories of leadership behaviors (ie, Model, Inspire, Challenge, Encourage, and Enable) were scored from 1 (almost never) to 10 (almost always). Item scores were summed to compute mean category scores. We analyzed demographic information; used t ratios to compare the data from athletic training leaders (PDs and HATCs) with normative data; compared sex, age, position, ethnicity, and years of experience with leadership practices; and computed mean scores. Results: Athletic training leaders reported using leadership behaviors similar to those of other leaders. The PDs reported using inspiring, challenging, enabling, and encouraging leadership behaviors more often than did the HATCs. No differences were found by ethnicity, age, years of experience, or leadership practices. Conclusions: Athletic training leaders are transformational leaders. Athletic training education program accreditation requirements likely account for the difference in leadership practices between PDs and HATCs. PMID:17597953

Leader emergence through interpersonal neural synchronization.

PubMed

Jiang, Jing; Chen, Chuansheng; Dai, Bohan; Shi, Guang; Ding, Guosheng; Liu, Li; Lu, Chunming

2015-04-07

The neural mechanism of leader emergence is not well understood. This study investigated (i) whether interpersonal neural synchronization (INS) plays an important role in leader emergence, and (ii) whether INS and leader emergence are associated with the frequency or the quality of communications. Eleven three-member groups were asked to perform a leaderless group discussion (LGD) task, and their brain activities were recorded via functional near infrared spectroscopy (fNIRS)-based hyperscanning. Video recordings of the discussions were coded for leadership and communication. Results showed that the INS for the leader-follower (LF) pairs was higher than that for the follower-follower (FF) pairs in the left temporo-parietal junction (TPJ), an area important for social mentalizing. Although communication frequency was higher for the LF pairs than for the FF pairs, the frequency of leader-initiated and follower-initiated communication did not differ significantly. Moreover, INS for the LF pairs was significantly higher during leader-initiated communication than during follower-initiated communications. In addition, INS for the LF pairs during leader-initiated communication was significantly correlated with the leaders' communication skills and competence, but not their communication frequency. Finally, leadership could be successfully predicted based on INS as well as communication frequency early during the LGD (before half a minute into the task). In sum, this study found that leader emergence was characterized by high-level neural synchronization between the leader and followers and that the quality, rather than the frequency, of communications was associated with synchronization. These results suggest that leaders emerge because they are able to say the right things at the right time.

fCCAC: functional canonical correlation analysis to evaluate covariance between nucleic acid sequencing datasets.

PubMed

Madrigal, Pedro

2017-03-01

Computational evaluation of variability across DNA or RNA sequencing datasets is a crucial step in genomic science, as it allows both to evaluate reproducibility of biological or technical replicates, and to compare different datasets to identify their potential correlations. Here we present fCCAC, an application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). We show how this method differs from other measures of correlation, and exemplify how it can reveal shared covariance between histone modifications and DNA binding proteins, such as the relationship between the H3K4me3 chromatin mark and its epigenetic writers and readers. An R/Bioconductor package is available at http://bioconductor.org/packages/fCCAC/ . pmb59@cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Prediction of beta-turns from amino acid sequences using the residue-coupled model.

PubMed

Guruprasad, K; Shukla, S

2003-04-01

We evaluated the prediction of beta-turns from amino acid sequences using the residue-coupled model with an enlarged representative protein data set selected from the Protein Data Bank. Our results show that the probability values derived from a data set comprising 425 protein chains yielded an overall beta-turn prediction accuracy 68.74%, compared with 94.7% reported earlier on a data set of 30 proteins using the same method. However, we noted that the overall beta-turn prediction accuracy using probability values derived from the 30-protein data set reduces to 40.74% when tested on the data set comprising 425 protein chains. In contrast, using probability values derived from the 425 data set used in this analysis, the overall beta-turn prediction accuracy yielded consistent results when tested on either the 30-protein data set (64.62%) used earlier or a more recent representative data set comprising 619 protein chains (64.66%) or on a jackknife data set comprising 476 representative protein chains (63.38%). We therefore recommend the use of probability values derived from the 425 representative protein chains data set reported here, which gives more realistic and consistent predictions of beta-turns from amino acid sequences.

The shikimate pathway: review of amino acid sequence, function and three-dimensional structures of the enzymes.

PubMed

Mir, Rafia; Jallu, Shais; Singh, T P

2015-06-01

The aromatic compounds such as aromatic amino acids, vitamin K and ubiquinone are important prerequisites for the metabolism of an organism. All organisms can synthesize these aromatic metabolites through shikimate pathway, except for mammals which are dependent on their diet for these compounds. The pathway converts phosphoenolpyruvate and erythrose 4-phosphate to chorismate through seven enzymatically catalyzed steps and chorismate serves as a precursor for the synthesis of variety of aromatic compounds. These enzymes have shown to play a vital role for the viability of microorganisms and thus are suggested to present attractive molecular targets for the design of novel antimicrobial drugs. This review focuses on the seven enzymes of the shikimate pathway, highlighting their primary sequences, functions and three-dimensional structures. The understanding of their active site amino acid maps, functions and three-dimensional structures will provide a framework on which the rational design of antimicrobial drugs would be based. Comparing the full length amino acid sequences and the X-ray crystal structures of these enzymes from bacteria, fungi and plant sources would contribute in designing a specific drug and/or in developing broad-spectrum compounds with efficacy against a variety of pathogens.

A mechanism for leader stepping

NASA Astrophysics Data System (ADS)

Ebert, U.; Carlson, B. E.; Koehn, C.

2013-12-01

The stepping of negative leaders is well observed, but not well understood. A major problem consists of the fact that the streamer corona is typically invisible within a thunderstorm, but determines the evolution of a leader. Motivated by recent observations of streamer and leader formation in the laboratory by T.M.P. Briels, S. Nijdam, P. Kochkin, A.P.J. van Deursen et al., by recent simulations of these processes by J. Teunissen, A. Sun et al., and by our theoretical understanding of the process, we suggest how laboratory phenomena can be extrapolated to lightning leaders to explain the stepping mechanism.

Ultra high-throughput nucleic acid sequencing as a tool for virus discovery in the turkey gut.

USDA-ARS?s Scientific Manuscript database

Recently, the use of the next generation of nucleic acid sequencing technology (i.e., 454 pyrosequencing, as developed by Roche/454 Life Sciences) has allowed an in-depth look at the uncultivated microorganisms present in complex environmental samples, including samples with agricultural importance....

A leader's framework for decision making. A leader's framework for decision making.

PubMed

Snowden, David J; Boone, Mary E

2007-11-01

Many executives are surprised when previously successful leadership approaches fail in new situations, but different contexts call for different kinds of responses. Before addressing a situation, leaders need to recognize which context governs it -and tailor their actions accordingly. Snowden and Boone have formed a new perspective on leadership and decision making that's based on complexity science. The result is the Cynefin framework, which helps executives sort issues into five contexts: Simple contexts are characterized by stability and cause-and-effect relationships that are clear to everyone. Often, the right answer is self-evident. In this realm of "known knowns," leaders must first assess the facts of a situation -that is, "sense" it -then categorize and respond to it. Complicated contexts may contain multiple right answers, and though there is a clear relationship between cause and effect, not everyone can see it. This is the realm of "known unknowns." Here, leaders must sense, analyze, and respond. In a complex context, right answers can't be ferreted out at all; rather, instructive patterns emerge if the leader conducts experiments that can safely fail. This is the realm of "unknown unknowns," where much of contemporary business operates. Leaders in this context need to probe first, then sense, and then respond. In a chaotic context, searching for right answers is pointless. The relationships between cause and effect are impossible to determine because they shift constantly and no manageable patterns exist. This is the realm of unknowables (the events of September 11, 2001, fall into this category). In this domain, a leader must first act to establish order, sense where stability is present, and then work to transform the situation from chaos to complexity. The fifth context, disorder, applies when it is unclear which of the other four contexts is predominant. The way out is to break the situation into its constituent parts and assign each to one of the

Fast computational methods for predicting protein structure from primary amino acid sequence

DOEpatents

Agarwal, Pratul Kumar [Knoxville, TN

2011-07-19

The present invention provides a method utilizing primary amino acid sequence of a protein, energy minimization, molecular dynamics and protein vibrational modes to predict three-dimensional structure of a protein. The present invention also determines possible intermediates in the protein folding pathway. The present invention has important applications to the design of novel drugs as well as protein engineering. The present invention predicts the three-dimensional structure of a protein independent of size of the protein, overcoming a significant limitation in the prior art.

A Comparison of Student Leader and Non Leader Attitudes Toward Legalizing Marihuana

ERIC Educational Resources Information Center

Bittner, John R.; Cash, William B.

1971-01-01

The data tends to imply that campus leaders have attitudes on the issue of marihuana legalization which conform to the norms of a major midwestern university sampling. Drug education programs might include student leaders with local credibility and who may possess attitudes very similar to their peers. (Author/BY)

Complete amino acid sequence of the myoglobin from the Pacific sei whale, Balaenoptera borealis.

PubMed

Jones, B N; Rothgeb, T M; England, R D; Gurd, F R

1979-04-25

The complete amino acid sequence of the major component myoglobin from Pacific sei whale, Balaenoptera borealis, was determined by specific cleavage of the protein to obtain large peptides which are readily degraded by the automatic sequencer. The acetimidated apomyoglobin was selectively cleaved at its two methionyl residues with cyanogen bromide and at its three arginyl residues by trypsin. From the sequence analysis of four of these peptides and the apomyoglobin, over 75% of the covalent structure of the protein was obtained. The remainder of the primary structure was determined by the sequence analysis of peptides that resulted from further digestion of the amino-terminal and central cyanogen bromide fragments. The amino-terminal fragment was specifically cleaved at its two tryptophanyl residues with N-chlorosuccinimide and the central cyanogen bromide fragment was cleaved at its glutamyl residues with staphylococcal protease and at its single tyrosyl residue with N-bromosuccinimide. The primary structure of this myoglobin proved identical with that from the gray whale but differs from that of the finback whale at four positions, from that of the minke whale at three positions and from the myoglobin of the humpback whale at one position. The above sequence identities and differences reflect the close taxonomic relationship of these five species of Cetacea.

On angry leaders and agreeable followers. How leaders' emotions and followers' personalities shape motivation and team performance.

PubMed

Van Kleef, Gerben A; Homan, Astrid C; Beersma, Bianca; van Knippenberg, Daan

2010-12-01

Do followers perform better when their leader expresses anger or when their leader expresses happiness? We propose that this depends on the follower's level of agreeableness. Anger is associated with hostility and conflict-states that are at odds with agreeable individuals' goals. Happiness facilitates affiliation and positive relations-states that are in line with agreeable individuals' goals. Accordingly, the two studies we conducted showed that agreeableness moderates the effects of a leader's emotional displays. In a scenario study, participants with lower levels of agreeableness responded more favorably to an angry leader, whereas participants with higher levels of agreeableness responded more favorably to a neutral leader. In an experiment involving four-person teams, teams composed of participants with lower average levels of agreeableness performed better when their leader expressed anger, whereas teams composed of participants with higher average levels of agreeableness performed better when their leader expressed happiness. Team performance was mediated by experienced workload, which was highest among agreeable followers with an angry leader. Besides having important practical implications, the findings shed new light on the fundamental question of how emotional expressions regulate social behavior.

Leader social accounts of subordinates' unethical behavior: Examining observer reactions to leader social accounts with moral disengagement language.

PubMed

Dang, Carolyn T; Umphress, Elizabeth E; Mitchell, Marie S

2017-10-01

When providing social accounts (Sitkin & Bies, 1993) for the unethical conduct of subordinates, leaders may use language consistent with cognitive strategies described by Bandura (1991, 1999) in his work on moral disengagement. That is, leader's social accounts may reframe or reconstrue subordinates' unethical conduct such that it appears less reprehensible. We predict observers will respond negatively to leaders when they use moral disengagement language within social accounts and, specifically, observers will ostracize these leaders. In addition, we predict that observer moral disengagement propensity moderates this effect, such that the relationship between leaders' use of moral disengagement language within a social account and ostracism is stronger when observer moral disengagement propensity is lower versus higher. Finally, we predict that the reason why observers ostracize the leader is because observers perceive the leader's social account with moral disengagement language as unethical. Thus, perceived leader social account ethicality is predicted to mediate the interaction effect of leader's use of moral disengagement language within social accounts and observer moral disengagement propensity on ostracism. Results from an experiment and field study support our predictions. Implications for theory and practice are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Predicting protein amidation sites by orchestrating amino acid sequence features

NASA Astrophysics Data System (ADS)

Zhao, Shuqiu; Yu, Hua; Gong, Xiujun

2017-08-01

Amidation is the fourth major category of post-translational modifications, which plays an important role in physiological and pathological processes. Identifying amidation sites can help us understanding the amidation and recognizing the original reason of many kinds of diseases. But the traditional experimental methods for predicting amidation sites are often time-consuming and expensive. In this study, we propose a computational method for predicting amidation sites by orchestrating amino acid sequence features. Three kinds of feature extraction methods are used to build a feature vector enabling to capture not only the physicochemical properties but also position related information of the amino acids. An extremely randomized trees algorithm is applied to choose the optimal features to remove redundancy and dependence among components of the feature vector by a supervised fashion. Finally the support vector machine classifier is used to label the amidation sites. When tested on an independent data set, it shows that the proposed method performs better than all the previous ones with the prediction accuracy of 0.962 at the Matthew's correlation coefficient of 0.89 and area under curve of 0.964.

Teacher Leader Administrators: Part 3 of a Symposium on Teachers as Leaders

ERIC Educational Resources Information Center

Smulyan, Lisa; Green, Jarrod; Lunstead, Jennifer; Norris, Becki

2017-01-01

In this latest continuation of our multipart symposium on teacher leadership, we examine what happens when self-defined teacher leaders become school administrators. Do teacher leaders who become administrators maintain a teacher identity? Can they remain committed to their vision of teacher leadership when they take on the normative requirements…

Complete sequence of the genome of avian paramyxovirus type 9 and comparison with other paramyxoviruses

PubMed Central

Samuel, Arthur S.; Kumar, Sachin; Madhuri, Subbiah; Collins, Peter L.; Samal, Siba K.

2009-01-01

The complete genome consensus sequence was determined for avian paramyxovirus (APMV) serotype 9 prototype strain PMV-9/domestic Duck/New York/22/78. The genome is 15,438 nucleotides (nt) long and encodes six non-overlapping genes in the order of 3′-N-P/V/W-M-F-HN-L-5′ with intergenic regions of 0–30 nt. The genome length follows the “rule of six” and contains a 55-nt leader sequence at the 3′ end and a 47-nt trailer sequence at the 5′ end. The cleavage site of the F protein is I-R-E-G-R-I↓F, which does not conform to the conventional cleavage site of the ubiquitous cellular protease furin. The virus required exogenous protease for in vitro replication and grew only in a few established cell lines, indicating a restricted host range. Alignment and phylogenetic analysis of the predicted amino acid sequences of APMV-9 proteins with the cognate proteins of viruses of all five genera of family Paramyxoviridae showed that APMV-9 is more closely related to APMV-1 than to other APMVs. The mean death time in embryonated chicken eggs was found to be more than 120 h, indicating APMV-9 to be avirulent for chickens. PMID:19185593

Differences in acid tolerance between Bifidobacterium breve BB8 and its acid-resistant derivative B. breve BB8dpH, revealed by RNA-sequencing and physiological analysis.

PubMed

Yang, Xu; Hang, Xiaomin; Tan, Jing; Yang, Hong

2015-06-01

Bifidobacteria are common inhabitants of the human gastrointestinal tract, and their application has increased dramatically in recent years due to their health-promoting effects. The ability of bifidobacteria to tolerate acidic environments is particularly important for their function as probiotics because they encounter such environments in food products and during passage through the gastrointestinal tract. In this study, we generated a derivative, Bifidobacterium breve BB8dpH, which displayed a stable, acid-resistant phenotype. To investigate the possible reasons for the higher acid tolerance of B. breve BB8dpH, as compared with its parental strain B. breve BB8, a combined transcriptome and physiological approach was used to characterize differences between the two strains. An analysis of the transcriptome by RNA-sequencing indicated that the expression of 121 genes was increased by more than 2-fold, while the expression of 146 genes was reduced more than 2-fold, in B. breve BB8dpH. Validation of the RNA-sequencing data using real-time quantitative PCR analysis demonstrated that the RNA-sequencing results were highly reliable. The comparison analysis, based on differentially expressed genes, suggested that the acid tolerance of B. breve BB8dpH was enhanced by regulating the expression of genes involved in carbohydrate transport and metabolism, energy production, synthesis of cell envelope components (peptidoglycan and exopolysaccharide), synthesis and transport of glutamate and glutamine, and histidine synthesis. Furthermore, an analysis of physiological data showed that B. breve BB8dpH displayed higher production of exopolysaccharide and lower H(+)-ATPase activity than B. breve BB8. The results presented here will improve our understanding of acid tolerance in bifidobacteria, and they will lead to the development of new strategies to enhance the acid tolerance of bifidobacterial strains. Copyright © 2015 Elsevier Ltd. All rights reserved.

Resilient Women Educational Leaders in Turbulent Times: Applying the Leader Resilience Profile® to Assess Women's Leadership Strengths

ERIC Educational Resources Information Center

Reed, Diane E.; Blaine, Bruce

2015-01-01

Women leaders across the world confront a common challenge: extremely turbulent times that challenge even the most skillful leaders. The paper begins with a brief overview of the meaning of leader resilience and describes the resilience cycle that all leaders experience when adversity strikes. Five phases of the resilience cycle discussed are:…

Creating tomorrow's leaders today: the Emerging Nurse Leaders Program of the Texas Nurses Association.

PubMed

Sportsman, Susan; Wieck, Lynn; Yoder-Wise, Patricia S; Light, Kathleen M; Jordan, Clair

2010-06-01

The Texas Nurses Association initiated an Emerging Nurse Leaders Program as an approach to engaging new nurses in the leadership of the professional association. This article explains the program's origin, the commitment of the Texas Nurses Association to this process, the implementation of the plan, and the discussions that launched a new way of connecting leaders across generations. Further, it is an approach that any professional organization can use to encourage the involvement of new leaders.

Synthesis and evaluations of an acid-cleavable, fluorescently labeled nucleotide as a reversible terminator for DNA sequencing.

PubMed

Tan, Lianjiang; Liu, Yazhi; Li, Xiaowei; Wu, Xin-Yan; Gong, Bing; Shen, Yu-Mei; Shao, Zhifeng

2016-02-11

An acid-cleavable linker based on a dimethylketal moiety was synthesized and used to connect a nucleotide with a fluorophore to produce a 3'-OH unblocked nucleotide analogue as an excellent reversible terminator for DNA sequencing by synthesis.

The double-edged sword of leader charisma: Understanding the curvilinear relationship between charismatic personality and leader effectiveness.

PubMed

Vergauwe, Jasmine; Wille, Bart; Hofmans, Joeri; Kaiser, Robert B; De Fruyt, Filip

2018-01-01

This study advanced knowledge on charisma by (a) introducing a new personality-based model to conceptualize and assess charisma and by (b) investigating curvilinear relationships between charismatic personality and leader effectiveness. Moreover, we delved deeper into this curvilinear association by (c) examining moderation by the leader's level of adjustment and by (d) testing a process model through which the effects of charismatic personality on effectiveness are explained with a consideration of specific leader behaviors. Study 1 validated HDS charisma (Hogan Development Survey) as a useful trait-based measure of charisma. In Study 2 a sample of leaders (N = 306) were assessed in the context of a 360-degree development center. In line with the too-much-of-a-good-thing effect, an inverted U-shaped relationship between charismatic personality and observer-rated leader effectiveness was found, indicating that moderate levels are better than low or high levels of charisma. Study 3 (N = 287) replicated this curvilinear relationship and further illustrated the moderating role of leader adjustment, in such a way that the inflection point after which the effects of charisma turn negative occurs at higher levels of charisma when adjustment is high. Nonlinear mediation modeling further confirmed that strategic and operational leader behaviors fully mediate the curvilinear relationship. Leaders low on charisma are less effective because they lack strategic behavior; highly charismatic leaders are less effective because they lack operational behavior. In sum, this work provides insight into the dispositional nature of charisma and uncovers the processes through which and conditions under which leader charisma translates into (in)effectiveness. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

Statistical potential-based amino acid similarity matrices for aligning distantly related protein sequences.

PubMed

Tan, Yen Hock; Huang, He; Kihara, Daisuke

2006-08-15

Aligning distantly related protein sequences is a long-standing problem in bioinformatics, and a key for successful protein structure prediction. Its importance is increasing recently in the context of structural genomics projects because more and more experimentally solved structures are available as templates for protein structure modeling. Toward this end, recent structure prediction methods employ profile-profile alignments, and various ways of aligning two profiles have been developed. More fundamentally, a better amino acid similarity matrix can improve a profile itself; thereby resulting in more accurate profile-profile alignments. Here we have developed novel amino acid similarity matrices from knowledge-based amino acid contact potentials. Contact potentials are used because the contact propensity to the other amino acids would be one of the most conserved features of each position of a protein structure. The derived amino acid similarity matrices are tested on benchmark alignments at three different levels, namely, the family, the superfamily, and the fold level. Compared to BLOSUM45 and the other existing matrices, the contact potential-based matrices perform comparably in the family level alignments, but clearly outperform in the fold level alignments. The contact potential-based matrices perform even better when suboptimal alignments are considered. Comparing the matrices themselves with each other revealed that the contact potential-based matrices are very different from BLOSUM45 and the other matrices, indicating that they are located in a different basin in the amino acid similarity matrix space.

Nucleotide and deduced amino acid sequence of the envelope gene of the Vasilchenko strain of TBE virus; comparison with other flaviviruses.

PubMed

Gritsun, T S; Frolova, T V; Pogodina, V V; Lashkevich, V A; Venugopal, K; Gould, E A

1993-02-01

A strain of tick-borne encephalitis virus known as Vasilchenko (Vs) exhibits relatively low virulence characteristics in monkeys, Syrian hamsters and humans. The gene encoding the envelope glycoprotein of this virus was cloned and sequenced. Alignment of the sequence with those of other known tick-borne flaviviruses and identification of the recognised amino acid genetic marker EHLPTA confirmed its identity as a member of the TBE complex. However, Vs virus was distinguishable from eastern and western tick-borne serotypes by the presence of the sequence AQQ at amino acid positions 232-234 and also by the presence of other specific amino acid substitutions which may be genetic markers for these viruses and could determine their pathogenetic characteristics. When compared with other tick-borne flaviviruses, Vs virus had 12 unique amino acid substitutions including an additional potential glycosylation site at position (315-317). The Vs virus strain shared closest nucleotide and amino acid homology (84.5% and 95.5% respectively) with western and far eastern strains of tick-borne encephalitis virus. Comparison with the far eastern serotype of tick-borne encephalitis virus, by cross-immunoelectrophoresis of Vs virions and PAGE analysis of the extracted virion proteins, revealed differences in surface charge and virus stability that may account for the different virulence characteristics of Vs virus. These results support and enlarge upon previous data obtained from molecular and serological analysis.

Portrait of a Leader.

ERIC Educational Resources Information Center

Mazzarella, Jo Ann; Grundy, Thomas

Chapter 1 of a revised volume on school leadership, this chapter examines several kinds of leader characteristics: inherited traits and those springing from early childhood experience; attitudes toward relationships with other people; and qualities differentiating effective from ineffective leaders. Modern researchers tend to stress nurture over…

How Can the Skills of Early Years Leaders Support Other Leaders in a Primary School Setting?

ERIC Educational Resources Information Center

Mistry, Malini; Sood, Krishan

2017-01-01

This study investigated the leadership skills Early Years leaders demonstrated through their daily practice of teaching, assessing and teamwork within their setting. It explored how revealing the potential of Early Years leaders could have a positive impact on the leadership practice of other leaders in the same setting to improve pupil outcomes.…

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor L.; Brow, Mary Ann D.; Dahlberg, James E.

2007-12-11

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow; Mary Ann D.; Dahlberg, James E.

2010-11-09

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2000-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Nucleic acid detection assays

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

2005-04-05

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Complete Genome Sequence of a thermotolerant sporogenic lactic acid bacterium, Bacillus coagulans strain 36D1

PubMed Central

Rhee, Mun Su; Moritz, Brélan E.; Xie, Gary; Glavina del Rio, T.; Dalin, E.; Tice, H.; Bruce, D.; Goodwin, L.; Chertkov, O.; Brettin, T.; Han, C.; Detter, C.; Pitluck, S.; Land, Miriam L.; Patel, Milind; Ou, Mark; Harbrucker, Roberta; Ingram, Lonnie O.; Shanmugam, K. T.

2011-01-01

Bacillus coagulans is a ubiquitous soil bacterium that grows at 50-55 °C and pH 5.0 and ferments various sugars that constitute plant biomass to L (+)-lactic acid. The ability of this sporogenic lactic acid bacterium to grow at 50-55 °C and pH 5.0 makes this organism an attractive microbial biocatalyst for production of optically pure lactic acid at industrial scale not only from glucose derived from cellulose but also from xylose, a major constituent of hemicellulose. This bacterium is also considered as a potential probiotic. Complete genome sequence of a representative strain, B. coagulans strain 36D1, is presented and discussed. PMID:22675583

Becoming a Professional Leader.

ERIC Educational Resources Information Center

Lemlech, Johanna K., Ed.

This book is about teacher-leaders who work in schools, universities, district and county offices, and other educational institutions and who serve as consultants, mentors, principals, project leaders, and teacher educators. The professional model of teaching emphasizes the role of teachers as informed, responsible decision makers, grounded in the…

Demands for School Leaders

ERIC Educational Resources Information Center

Bradley-Levine, Jill

2016-01-01

This article examines the ways that graduate courses in teacher leadership influenced the ways that teachers described the nature of leadership and their role as educational leaders. Using Foster's (1989) four demands for school leaders as a theoretical framework, participants' perceptions are examined to determine how teachers synthesized their…

Leader Effectiveness Index Manual.

ERIC Educational Resources Information Center

Moss, Jerome, Jr.; And Others

The "Leader Effectiveness Index (LEI) is a multirater instrument designed to assess the effectiveness of leadership performance of vocational educators. It consists of seven items. The first six items are statements of six broad tasks (or responsibilities) of a leader in vocational education: (1) inspires shared vision and establishes…

The hypervariable region 1 protein of hepatitis C virus broadly reactive with sera of patients with chronic hepatitis C has a similar amino acid sequence with the consensus sequence.

PubMed

Watanabe, K; Yoshioka, K; Ito, H; Ishigami, M; Takagi, K; Utsunomiya, S; Kobayashi, M; Kishimoto, H; Yano, M; Kakumu, S

1999-11-10

Hypervariable region 1 (HVR1) proteins of hepatitis C virus (HCV) have been reported to react broadly with sera of patients with HCV infection. However, the variability of the broad reactivity of individual HVR1 proteins has not been elucidated. We assessed the reactivity of 25 different HVR1 proteins (genotype 1b) with sera of 81 patients with HCV infection (genotype 1b) by Western blot. HVR1 proteins reacted with 2-60 sera. The number of sera reactive with each HVR1 protein significantly correlated with the number of amino acid residues identical to the consensus sequence defined by Puntoriero et al. (G. Puntoriero, A. Lahm, S. Zucchelli, B. B. Ercole, R. Tafi, M. Penzzanera, M. U. Mondelli, R. Cortese, A. Tramontano, G. Galfre', and A. Nicosia. 1998. EMBO J. 17, 3521-3533. ) (r = 0.561, P < 0.005). The most widely reactive HVR1 protein, 12-22, had a sequence similar to the consensus sequence. The peptide with C-terminal 13-amino-acids sequence of HVR1 protein 12-22 (NH2-CSFTSLFTPGPSQK) was injected into rabbits as an immunogen. The rabbit immune sera reacted with 9 of 25 HVR1 proteins of genotype 1b including HVR1 protein 12-22 and with 3 of 12 proteins of genotype 2a. These results indicate that the HVR1 protein broadly reactive with patients' sera has a sequence similar to the consensus sequence, can induce broadly reactive sera, and could be one of the candidate immunogens in a prophylactic vaccine against HCV. Copyright 1999 Academic Press.

Statements of IRAQI Communist Leaders.

DTIC Science & Technology

1960-07-19

Leader Abdul Karin Kassem J,.’l ; The Maintenance and Consolidation of Party Idfe Is a Deeply Sincere Policy of Cur Democratic Government STATEMENTS...OF IRAQI COMMUNIST LEADERS 1» Open Letter to His Excellency the Leader Abdul .Karflm Kassem /following is a ^translation of an article by the...they also exercised political influence and thus the fate of the feudalists was linked to the continued exploitation of our wealth, our natural

The academic story: introducing the clinical nurse leader role in a multifacility health care system.

PubMed

Moore, Penny

2013-01-01

Introducing the clinical nurse leader (CNL) role in a multifacility health care system is an exciting but obstacle-filled journey. This story includes facilitating factors, opportunities, and successes plus suggestions for other academic-practice partners considering implementing the CNL role. A sample course sequence with course descriptions is provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Conserved features of eukaryotic hsp70 genes revealed by comparison with the nucleotide sequence of human hsp70.

PubMed Central

Hunt, C; Morimoto, R I

1985-01-01

We have determined the nucleotide sequence of the human hsp70 gene and 5' flanking region. The hsp70 gene is transcribed as an uninterrupted primary transcript of 2440 nucleotides composed of a 5' noncoding leader sequence of 212 nucleotides, a 3' noncoding region of 242 nucleotides, and a continuous open reading frame of 1986 nucleotides that encodes a protein with predicted molecular mass of 69,800 daltons. Upstream of the 5' terminus are the canonical TATAAA box, the sequence ATTGG that corresponds in the inverted orientation to the CCAAT motif, and the dyad sequence CTGGAAT/ATTCCCG that shares homology in 12 of 14 positions with the consensus transcription regulatory sequence common to Drosophila heat shock genes. Comparison of the predicted amino acid sequences of human hsp70 with the published sequences of Drosophila hsp70 and Escherichia coli dnaK reveals that human hsp70 is 73% identical to Drosophila hsp70 and 47% identical to E. coli dnaK. Surprisingly, the nucleotide sequences of the human and Drosophila genes are 72% identical and human and E. coli genes are 50% identical, which is more highly conserved than necessary given the degeneracy of the genetic code. The lack of accumulated silent nucleotide substitutions leads us to propose that there may be additional information in the nucleotide sequence of the hsp70 gene or the corresponding mRNA that precludes the maximum divergence allowed in the silent codon positions. PMID:3931075

Impacts of opinion leaders on social contagions

NASA Astrophysics Data System (ADS)

Liu, Quan-Hui; Lü, Feng-Mao; Zhang, Qian; Tang, Ming; Zhou, Tao

2018-05-01

Opinion leaders are ubiquitous in both online and offline social networks, but the impacts of opinion leaders on social behavior contagions are still not fully understood, especially by using a mathematical model. Here, we generalize the classical Watts threshold model and address the influences of the opinion leaders, where an individual adopts a new behavior if one of his/her opinion leaders adopts the behavior. First, we choose the opinion leaders randomly from all individuals in the network and find that the impacts of opinion leaders make other individuals adopt the behavior more easily. Specifically, the existence of opinion leaders reduces the lowest mean degree of the network required for the global behavior adoption and increases the highest mean degree of the network that the global behavior adoption can occur. Besides, the introduction of opinion leaders accelerates the behavior adoption but does not change the adoption order of individuals. The developed theoretical predictions agree with the simulation results. Second, we randomly choose the opinion leaders from the top h % of the highest degree individuals and find an optimal h % for the network with the lowest mean degree that the global behavior adoption can occur. Meanwhile, the influences of opinion leaders on accelerating the adoption of behaviors become less significant and can even be ignored when reducing the value of h % .

Developing Local Community Leaders.

ERIC Educational Resources Information Center

Dyer, Delwyn A.; Williams, Oscar M.

The successful development of local leaders is the goal of leadership training and community development. Development involves defining and developing leadership. Although leader-centered leadership offers few chances of meeting the maintenance needs of the group as a whole, shared leadership allows the group to join in the decision-making…

Portrait of a Leader.

ERIC Educational Resources Information Center

Mazzarella, Jo Ann

Chapter 1 of a volume on school leadership, this chapter looks at research findings concerning the characteristics of leaders. The author begins by looking at those characteristics resulting from accidents of birth or early environmental influences and concludes that leaders are usually more intelligent than nonleaders, not firstborn, used to…

Homegrown Rural School Leaders

ERIC Educational Resources Information Center

Olsen, Dorian Dawn

2017-01-01

Background: Research on rural educational leadership is often overlooked in educational research, specifically within the context of homegrown leaders, or leaders who have been lifelong residents in the districts where they were students, teachers, and now lead as principal. Rural districts face many challenges that differ from urban districts.…

Position-dependent effects of locked nucleic acid (LNA) on DNA sequencing and PCR primers

PubMed Central

Levin, Joshua D.; Fiala, Dean; Samala, Meinrado F.; Kahn, Jason D.; Peterson, Raymond J.

2006-01-01

Genomes are becoming heavily annotated with important features. Analysis of these features often employs oligonucleotides that hybridize at defined locations. When the defined location lies in a poor sequence context, traditional design strategies may fail. Locked Nucleic Acid (LNA) can enhance oligonucleotide affinity and specificity. Though LNA has been used in many applications, formal design rules are still being defined. To further this effort we have investigated the effect of LNA on the performance of sequencing and PCR primers in AT-rich regions, where short primers yield poor sequencing reads or PCR yields. LNA was used in three positional patterns: near the 5′ end (LNA-5′), near the 3′ end (LNA-3′) and distributed throughout (LNA-Even). Quantitative measures of sequencing read length (Phred Q30 count) and real-time PCR signal (cycle threshold, CT) were characterized using two-way ANOVA. LNA-5′ increased the average Phred Q30 score by 60% and it was never observed to decrease performance. LNA-5′ generated cycle thresholds in quantitative PCR that were comparable to high-yielding conventional primers. In contrast, LNA-3′ and LNA-Even did not improve read lengths or CT. ANOVA demonstrated the statistical significance of these results and identified significant interaction between the positional design rule and primer sequence. PMID:17071964

Where Have All the Leaders Gone?

ERIC Educational Resources Information Center

Gmelch, Walter H.

This paper examines personal challenges that academic leaders face, attributes that institutional leaders should possess to succeed in transforming the university, how institutions of higher education can build the capacity for preparing new leaders, and how universities can respond to the leadership crisis in this time of transformation. Personal…

Leader emergence through interpersonal neural synchronization

PubMed Central

Jiang, Jing; Chen, Chuansheng; Dai, Bohan; Shi, Guang; Ding, Guosheng; Liu, Li; Lu, Chunming

2015-01-01

The neural mechanism of leader emergence is not well understood. This study investigated (i) whether interpersonal neural synchronization (INS) plays an important role in leader emergence, and (ii) whether INS and leader emergence are associated with the frequency or the quality of communications. Eleven three-member groups were asked to perform a leaderless group discussion (LGD) task, and their brain activities were recorded via functional near infrared spectroscopy (fNIRS)-based hyperscanning. Video recordings of the discussions were coded for leadership and communication. Results showed that the INS for the leader–follower (LF) pairs was higher than that for the follower–follower (FF) pairs in the left temporo-parietal junction (TPJ), an area important for social mentalizing. Although communication frequency was higher for the LF pairs than for the FF pairs, the frequency of leader-initiated and follower-initiated communication did not differ significantly. Moreover, INS for the LF pairs was significantly higher during leader-initiated communication than during follower-initiated communications. In addition, INS for the LF pairs during leader-initiated communication was significantly correlated with the leaders’ communication skills and competence, but not their communication frequency. Finally, leadership could be successfully predicted based on INS as well as communication frequency early during the LGD (before half a minute into the task). In sum, this study found that leader emergence was characterized by high-level neural synchronization between the leader and followers and that the quality, rather than the frequency, of communications was associated with synchronization. These results suggest that leaders emerge because they are able to say the right things at the right time. PMID:25831535

Comparison of the nucleotide and amino acid sequences of the RsrI and EcoRI restriction endonucleases.

PubMed

Stephenson, F H; Ballard, B T; Boyer, H W; Rosenberg, J M; Greene, P J

1989-12-21

The RsrI endonuclease, a type-II restriction endonuclease (ENase) found in Rhodobacter sphaeroides, is an isoschizomer of the EcoRI ENase. A clone containing an 11-kb BamHI fragment was isolated from an R. sphaeroides genomic DNA library by hybridization with synthetic oligodeoxyribonucleotide probes based on the N-terminal amino acid (aa) sequence of RsrI. Extracts of E. coli containing a subclone of the 11-kb fragment display RsrI activity. Nucleotide sequence analysis reveals an 831-bp open reading frame encoding a polypeptide of 277 aa. A 50% identity exists within a 266-aa overlap between the deduced aa sequences of RsrI and EcoRI. Regions of 75-100% aa sequence identity correspond to key structural and functional regions of EcoRI. The type-II ENases have many common properties, and a common origin might have been expected. Nevertheless, this is the first demonstration of aa sequence similarity between ENases produced by different organisms.

Leaders from Nursing's History.

ERIC Educational Resources Information Center

Fondiller, Shirley H.; And Others

1995-01-01

Looks at the lives and accomplishments of four leaders in professional nursing: (1) Loretta Ford, who championed the cause of nurse practitioners; (2) Mable Staupers, a pioneer in community health and nursing; (3) Janet Geister, a leader in private nursing; and (4) Isabel Stewart, who led the movement to standardize nursing education. (JOW)

Draft Genome Sequence of the Butyric Acid Producer Clostridium tyrobutyricum Strain CIP I-776 (IFP923).

PubMed

Wasels, François; Clément, Benjamin; Lopes Ferreira, Nicolas

2016-03-03

Here, we report the draft genome sequence of Clostridium tyrobutyricum CIP I-776 (IFP923), an efficient producer of butyric acid. The genome consists of a single chromosome of 3.19 Mb and provides useful data concerning the metabolic capacities of the strain. Copyright © 2016 Wasels et al.

Leadership and Leader Developmental Self-Efficacy: Their Role in Enhancing Leader Development Efforts.

PubMed

Murphy, Susan Elaine; Johnson, Stefanie K

2016-01-01

This chapter describes the role of two types of self-efficacy-leader self-efficacy and leader developmental efficacy-for enhancing leadership development. Practical implications for designing and developing leadership programs that take into account these two types of self-efficacy are discussed. © 2016 Wiley Periodicals, Inc., A Wiley Company.

The impact of stroke on world leaders.

PubMed

Brickfield, F X; Pyenson, L R

2001-03-01

Earlier studies by our unit documented frequent disability in world leaders resulting from stroke but did not quantify the incidence of cerebrovascular accidents. We sought to identify the frequency and impact of strokes in world leaders. Using various sources, we identified world leaders who had sustained strokes while in office from 1970 to 1999 and tabulated information on symptoms and subsequent ability to lead. Twenty leaders were identified who had sustained strokes during the study period, for an incidence of 0.444 strokes/100 leaders/year. Half of the affected leaders lost their political power within the year; most had persistent disabilities, which included motor, speech, cognitive, and emotional deficits. Strokes in world leaders may be slightly less common than expected based on studies of Western populations of similar age, but they are often devastating to a political career. Nonetheless, loss of political power is not inevitable.

Large-Scale Concatenation cDNA Sequencing

PubMed Central

Yu, Wei; Andersson, Björn; Worley, Kim C.; Muzny, Donna M.; Ding, Yan; Liu, Wen; Ricafrente, Jennifer Y.; Wentland, Meredith A.; Lennon, Greg; Gibbs, Richard A.

1997-01-01

A total of 100 kb of DNA derived from 69 individual human brain cDNA clones of 0.7–2.0 kb were sequenced by concatenated cDNA sequencing (CCS), whereby multiple individual DNA fragments are sequenced simultaneously in a single shotgun library. The method yielded accurate sequences and a similar efficiency compared with other shotgun libraries constructed from single DNA fragments (>20 kb). Computer analyses were carried out on 65 cDNA clone sequences and their corresponding end sequences to examine both nucleic acid and amino acid sequence similarities in the databases. Thirty-seven clones revealed no DNA database matches, 12 clones generated exact matches (≥98% identity), and 16 clones generated nonexact matches (57%–97% identity) to either known human or other species genes. Of those 28 matched clones, 8 had corresponding end sequences that failed to identify similarities. In a protein similarity search, 27 clone sequences displayed significant matches, whereas only 20 of the end sequences had matches to known protein sequences. Our data indicate that full-length cDNA insert sequences provide significantly more nucleic acid and protein sequence similarity matches than expressed sequence tags (ESTs) for database searching. [All 65 cDNA clone sequences described in this paper have been submitted to the GenBank data library under accession nos. U79240–U79304.] PMID:9110174

Fundamentals for New Leaders

DTIC Science & Technology

2015-06-12

in Initial Period) model is the author’s solution and a remedy for a new leader. The result of this research targets a particular audience―new...problem of being a first time leader is constant and present in all cultures. If it is a universal problem, there should be a solution on how to become

[Identification of community leaders].

PubMed

Chevalier, S; Dedobbeleer, N; Tremblay, M

1995-01-01

Although many methods of measuring leadership have been developed in sociological studies, there are few articles on the feasibility of these methods. The goal of this study was to verify the feasibility of the "modified positional-reputational approach" developed by Nix. The study was conducted in a small community located north of Montreal. Nix's questionnaire was translated, adapted and administered to 49 key informants. Two hundred and fourteen leaders were selected. Three types of leaders were identified: the legitimizers, the effectors and the activists. Through a sociometric analysis, we established links between the different leaders and we described the power structure of the community. Despite a few shortcomings, Nix's approach was found extremely useful.

The spliced leader trans-splicing mechanism in different organisms: molecular details and possible biological roles

PubMed Central

Bitar, Mainá; Boroni, Mariana; Macedo, Andréa M.; Machado, Carlos R.; Franco, Glória R.

2013-01-01

The spliced leader (SL) is a gene that generates a functional ncRNA that is composed of two regions: an intronic region of unknown function (SLi) and an exonic region (SLe), which is transferred to the 5′ end of independent transcripts yielding mature mRNAs, in a process known as spliced leader trans-splicing (SLTS). The best described function for SLTS is to solve polycistronic transcripts into monocistronic units, specifically in Trypanosomatids. In other metazoans, it is speculated that the SLe addition could lead to increased mRNA stability, differential recruitment of the translational machinery, modification of the 5′ region or a combination of these effects. Although important aspects of this mechanism have been revealed, several features remain to be elucidated. We have analyzed 157 SLe sequences from 148 species from seven phyla and found a high degree of conservation among the sequences of species from the same phylum, although no considerable similarity seems to exist between sequences of species from different phyla. When analyzing case studies, we found evidence that a given SLe will always be related to a given set of transcripts in different species from the same phylum, and therefore, different SLe sequences from the same species would regulate different sets of transcripts. In addition, we have observed distinct transcript categories to be preferential targets for the SLe addition in different phyla. This work sheds light into crucial and controversial aspects of the SLTS mechanism. It represents a comprehensive study concerning various species and different characteristics of this important post-transcriptional regulatory mechanism. PMID:24130571

Genome Sequence of Lactobacillus sakei LK-145 Isolated from a Japanese Sake Cellar as a High Producer of d-Amino Acids

PubMed Central

Kato, Shiro

2017-01-01

ABSTRACT This announcement reports the complete genome sequence of strain LK-145 of Lactobacillus sakei isolated from a Japanese sake cellar as a potent strain for the production of large amounts of d-amino acids. Three putative genes encoding an amino acid racemase were identified. PMID:28818888

Leader Responses to Collective Failure, and Maintenance of Group Integration, Task Motivation, Compliance, and Leader Endorsement

DTIC Science & Technology

1980-11-01

21 Table 2 - Analysis of Variance Summary Table: Leader Attributions . 21 Table 3 - Mean Leader Attributions to Four Factors under Success...been examined. Studies (Julian, Hollander, and Regula, 1969; !4ichener and Lawler, 1975) have indicated that leaders of groups which fail suffer signif ...the collective failure induction, one-way analyses of variance vere performed comparing the three performance evaluation conditions with the no

Leader Training Conference Report.

ERIC Educational Resources Information Center

Michigan-Ohio Regional Educational Lab., Inc., Detroit.

The purpose of this conference was to prepare key people in the field of education to function as inservice education leaders in their respective settings. It called for participants to learn what the MOREL inservice education program is and what it hopes to accomplish, to identify the role and functions of the inservice education leader, and to…

Developing Successful Global Leaders

ERIC Educational Resources Information Center

Training, 2011

2011-01-01

Everyone seems to agree the world desperately needs strong leaders who can manage a global workforce and all the inherent challenges that go with it. That's a big part of the raison d'etre for global leadership development programs. But are today's organizations fully utilizing these programs to develop global leaders, and, if so, are they…

In Search of the Congruent Leader.

ERIC Educational Resources Information Center

Kussrow, Paul G.; Purland, John

A lack of congruency on the part of many leaders results in diminished effectiveness, if not outright failure. The soundness of a person in authority is an essential characteristic for potency as a leader. Irrespective of what system of ethical thought is proposed, effectiveness for leaders only comes from a stream of thought that demonstrates a…

When the appeal of a dominant leader is greater than a prestige leader

PubMed Central

Sivanathan, Niro

2017-01-01

Across the globe we witness the rise of populist authoritarian leaders who are overbearing in their narrative, aggressive in behavior, and often exhibit questionable moral character. Drawing on evolutionary theory of leadership emergence, in which dominance and prestige are seen as dual routes to leadership, we provide a situational and psychological account for when and why dominant leaders are preferred over other respected and admired candidates. We test our hypothesis using three studies, encompassing more than 140,000 participants, across 69 countries and spanning the past two decades. We find robust support for our hypothesis that under a situational threat of economic uncertainty (as exemplified by the poverty rate, the housing vacancy rate, and the unemployment rate) people escalate their support for dominant leaders. Further, we find that this phenomenon is mediated by participants’ psychological sense of a lack of personal control. Together, these results provide large-scale, globally representative evidence for the structural and psychological antecedents that increase the preference for dominant leaders over their prestigious counterparts. PMID:28607061

The Humble Leader: Association of Discrepancies in Leader and Follower Ratings of Implementation Leadership With Organizational Climate in Mental Health.

PubMed

Aarons, Gregory A; Ehrhart, Mark G; Torres, Elisa M; Finn, Natalie K; Beidas, Rinad S

2017-02-01

Discrepancies, or perceptual distance, between leaders' self-ratings and followers' ratings of the leader are common but usually go unrecognized. Research on discrepancies is limited, but there is evidence that discrepancies are associated with organizational context. This study examined the association of leader-follower discrepancies in Implementation Leadership Scale (ILS) ratings of mental health clinic leaders and the association of those discrepancies with organizational climate for involvement and performance feedback. Both involvement and performance feedback are important for evidence-based practice (EBP) implementation in mental health. A total of 593 individuals-supervisors (leaders, N=80) and clinical service providers (followers, N=513)-completed surveys that included ratings of implementation leadership and organizational climate. Polynomial regression and response surface analyses were conducted to examine the associations of discrepancies in leader-follower ILS ratings with organizational involvement climate and performance feedback climate, aspects of climate likely to support EBP implementation. Both involvement climate and performance feedback climate were highest where leaders rated themselves low on the ILS and their followers rated those leaders high on the ILS ("humble leaders"). Teams with "humble leaders" showed more positive organizational climate for involvement and for performance feedback, contextual factors important during EBP implementation and sustainment. Discrepancy in leader and follower ratings of implementation leadership should be a consideration in understanding and improving leadership and organizational climate for mental health services and for EBP implementation and sustainment in mental health and other allied health settings.

Bearing-based localization for leader-follower formation control

PubMed Central

Han, Qing; Ren, Shan; Lang, Hao; Zhang, Changliang

2017-01-01

The observability of the leader robot system and the leader-follower formation control are studied. First, the nonlinear observability is studied for when the leader robot observes landmarks. Second, the system is shown to be completely observable when the leader robot observes two different landmarks. When the leader robot system is observable, multi-robots can rapidly form and maintain a formation based on the bearing-only information that the follower robots observe from the leader robot. Finally, simulations confirm the effectiveness of the proposed formation control. PMID:28426706

Genome sequence of the thermophilic strain Bacillus coagulans 2-6, an efficient producer of high-optical-purity L-lactic acid.

PubMed

Su, Fei; Yu, Bo; Sun, Jibin; Ou, Hong-Yu; Zhao, Bo; Wang, Limin; Qin, Jiayang; Tang, Hongzhi; Tao, Fei; Jarek, Michael; Scharfe, Maren; Ma, Cuiqing; Ma, Yanhe; Xu, Ping

2011-09-01

Bacillus coagulans 2-6 is an efficient producer of lactic acid. The genome of B. coagulans 2-6 has the smallest genome among the members of the genus Bacillus known to date. The frameshift mutation at the start of the d-lactate dehydrogenase sequence might be responsible for the production of high-optical-purity l-lactic acid.

Analyses of mitochondrial amino acid sequence datasets support the proposal that specimens of Hypodontus macropi from three species of macropodid hosts represent distinct species

PubMed Central

2013-01-01

Background Hypodontus macropi is a common intestinal nematode of a range of kangaroos and wallabies (macropodid marsupials). Based on previous multilocus enzyme electrophoresis (MEE) and nuclear ribosomal DNA sequence data sets, H. macropi has been proposed to be complex of species. To test this proposal using independent molecular data, we sequenced the whole mitochondrial (mt) genomes of individuals of H. macropi from three different species of hosts (Macropus robustus robustus, Thylogale billardierii and Macropus [Wallabia] bicolor) as well as that of Macropicola ocydromi (a related nematode), and undertook a comparative analysis of the amino acid sequence datasets derived from these genomes. Results The mt genomes sequenced by next-generation (454) technology from H. macropi from the three host species varied from 13,634 bp to 13,699 bp in size. Pairwise comparisons of the amino acid sequences predicted from these three mt genomes revealed differences of 5.8% to 18%. Phylogenetic analysis of the amino acid sequence data sets using Bayesian Inference (BI) showed that H. macropi from the three different host species formed distinct, well-supported clades. In addition, sliding window analysis of the mt genomes defined variable regions for future population genetic studies of H. macropi in different macropodid hosts and geographical regions around Australia. Conclusions The present analyses of inferred mt protein sequence datasets clearly supported the hypothesis that H. macropi from M. robustus robustus, M. bicolor and T. billardierii represent distinct species. PMID:24261823

Gender Bias in Leader Selection.

ERIC Educational Resources Information Center

Teaching of Psychology, 1995

1995-01-01

Describes a classroom exercise showing students how stereotypes can result in sex-biased leader selection. Finds that task-oriented competitive instructions produce a disproportionate number of selected male leaders. Includes procedures for replicating and evaluating the exercise. (CFR)

Taste, umami-enhance effect and amino acid sequence of peptides separated from silkworm pupa hydrolysate.

PubMed

Yu, Zilin; Jiang, Hongrui; Guo, Rongcan; Yang, Bo; You, Gang; Zhao, Mouming; Liu, Xiaoling

2018-06-01

Four umami peptides were separated and purified by ultrafiltration, gel filtration chromatography and identified by ultra-performance liquid chromatography tandem mass-spectrometry (UPLC-MS/MS), the amino acid sequences of four peptides are Val-Pro-Tyr (VPY), Thr-Ala-Tyr (TAY), Ala-Ala-Pro-Tyr (AAPY) and Gly-Phe-Pro (GFP). The result illustrates that the umami amino acids are not the content of umami peptides, but bitter amino acids are included. The threshold of VPY, TAY, AAPY and GFP were 1.65 mmol/L, 1.76 mmol/L, 2.97 mmol/L and 6.26 mmol/L, respectively. The peptide TAY, VPY and AAPY had an umami-enhancement effect on the monosodium glutamate (MSG) + sodium chloride (NaCl) solution, their concentrations were 2.5 g/L, 5 g/L and 5 g/L, respectively, while GFP has no significant umami-enhancement effect in solution. In addition, the peptides have better taste than its composing amino acids, which indicates that the taste of peptide does not depend on its composing amino acids. Copyright © 2018. Published by Elsevier Ltd.

The nucleotide sequence of HLA-B{sup *}2704 reveals a new amino acid substitution in exon 4 which is also present in HLA-B{sup *}2706

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

Rudwaleit, M.; Bowness, P.; Wordsworth, P.

1996-12-31

The HLA-B27 subtype HLA-B{sup *}2704 is virtually absent in Caucasians but common in Orientals, where it is associated with ankylosing spondylitis. The amino acid sequence of HLA-B{sup *}2704 has been established by peptide mapping and was shown to differ by two amino acids from HLA-B{sup *}2705, HLA-B{sup *}2704 is characterized by a serine for aspartic acid substitution at position 77 and glutamic acid for valine at position 152. To date, however, no nucleotide sequence confirming these changes at the DNA level has been published. 13 refs., 2 figs.

Nucleic acid arrays and methods of synthesis

DOEpatents

Sabanayagam, Chandran R.; Sano, Takeshi; Misasi, John; Hatch, Anson; Cantor, Charles

2001-01-01

The present invention generally relates to high density nucleic acid arrays and methods of synthesizing nucleic acid sequences on a solid surface. Specifically, the present invention contemplates the use of stabilized nucleic acid primer sequences immobilized on solid surfaces, and circular nucleic acid sequence templates combined with the use of isothermal rolling circle amplification to thereby increase nucleic acid sequence concentrations in a sample or on an array of nucleic acid sequences.

Nucleic Acid Amplification Testing and Sequencing Combined with Acid-Fast Staining in Needle Biopsy Lung Tissues for the Diagnosis of Smear-Negative Pulmonary Tuberculosis.

PubMed

Jiang, Faming; Huang, Weiwei; Wang, Ye; Tian, Panwen; Chen, Xuerong; Liang, Zongan

2016-01-01

Smear-negative pulmonary tuberculosis (PTB) is common and difficult to diagnose. In this study, we investigated the diagnostic value of nucleic acid amplification testing and sequencing combined with acid-fast bacteria (AFB) staining of needle biopsy lung tissues for patients with suspected smear-negative PTB. Patients with suspected smear-negative PTB who underwent percutaneous transthoracic needle biopsy between May 1, 2012, and June 30, 2015, were enrolled in this retrospective study. Patients with AFB in sputum smears were excluded. All lung biopsy specimens were fixed in formalin, embedded in paraffin, and subjected to acid-fast staining and tuberculous polymerase chain reaction (TB-PCR). For patients with positive AFB and negative TB-PCR results in lung tissues, probe assays and 16S rRNA sequencing were used for identification of nontuberculous mycobacteria (NTM). The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy of PCR and AFB staining were calculated separately and in combination. Among the 220 eligible patients, 133 were diagnosed with TB (men/women: 76/57; age range: 17-80 years, confirmed TB: 9, probable TB: 124). Forty-eight patients who were diagnosed with other specific diseases were assigned as negative controls, and 39 patients with indeterminate final diagnosis were excluded from statistical analysis. The sensitivity, specificity, PPV, NPV, and accuracy of histological AFB (HAFB) for the diagnosis of smear-negative were 61.7% (82/133), 100% (48/48), 100% (82/82), 48.5% (48/181), and 71.8% (130/181), respectively. The sensitivity, specificity, PPV, and NPV of histological PCR were 89.5% (119/133), 95.8% (46/48), 98.3% (119/121), and 76.7% (46/60), respectively, demonstrating that histological PCR had significantly higher accuracy (91.2% [165/181]) than histological acid-fast staining (71.8% [130/181]), P < 0.001. Parallel testing of histological AFB staining and PCR showed the

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

1999-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Invasive cleavage of nucleic acids

DOEpatents

Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann D.; Dahlberg, James E.

2002-01-01

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

Science Teacher Leaders: Exploring Practices and Potential

NASA Astrophysics Data System (ADS)

Stinson, John Kevin

It has become standard practice for teachers to step into the role of "teacher leaders" and perform a variety of curriculum, instruction and assessment tasks for schools and school districts. The literature regarding these Ohio K-12 teacher leaders, who may perform these tasks in addition to or in lieu of regular teaching assignments, rarely includes a disciplinary focus. In this exploratory, descriptive study the results of a web-based survey containing both closed and open-ended items were used in an inquiry into teacher leaders working with the discipline of science. Data from Ohio teachers responding to the survey were used first to create a standard profile for science teacher leaders. Descriptive statistics and correlations were then performed on quantitative survey data to explore science teacher leader tasks and factors that influence task performance. Analysis of data included descriptions of sense of purpose for their role held by these science teacher leaders. Results indicate that science teacher leaders appear to embrace their role as advocates for science and have great potential for implementing science education reform as well as other science-related school initiatives. Aligning performance, administrative oversight, impact on student achievement and teacher training concerning tasks science teacher leaders are expected to perform would enhance this potential. However, science teacher leaders face challenges to realizing that potential due to ambiguity of their leadership role, the breadth of tasks they tend to perform and lack of alignment between task and outcomes.

Leader to Leader: Enduring Insights on Leadership from the Drucker Foundation's Award-Winning Journal.

ERIC Educational Resources Information Center

Hesselbein, Frances, Ed.; Cohen, Paul M., Ed.

Amid unprecedented social, demographic, and economic changes, leaders must enhance performance and deliver desired results. The growing importance of managing the explosion in information requires attention to defining organizational missions and visions. The 37 chapters in this work are divided into 7 parts. Part 1, "On Leaders and…

Genome Sequence of Sphingomonas wittichii DP58, the First Reported Phenazine-1-Carboxylic Acid-Degrading Strain

PubMed Central

Ma, Zhiwei; Shen, Xuemei; Wang, Wei; Peng, Huasong; Xu, Ping; Zhang, Xuehong

2012-01-01

Sphingomonas wittichii DP58 (CCTCC M 2012027), the first reported phenazine-1-carboxylic acid (PCA)-degrading strain, was isolated from pimiento rhizosphere soils. Here we present a 5.6-Mb assembly of its genome. This sequence would contribute to the elucidation of the molecular mechanism of PCA degradation to improve the antifungal's effectiveness or remove superfluous PCA. PMID:22689229

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.; Wang, Chunwei; Jevons, Luis C.; Bernhart, Derek H.; Lipshutz, Robert J.

2004-05-11

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

1998-08-18

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

The Impact of Educational Change on School Leaders: Experiences of Pakistani School Leaders

ERIC Educational Resources Information Center

Razzaq, Jamila; Forde, Christine

2013-01-01

The Pakistani education system, like many other countries across the world, is going through a phase of concerted change in the first decade of the 21st century and school leaders are expected to play a crucial role in the management of this change programme. This article considers the impact of educational change on a group of school leaders who…

Completion of full length genome sequence of novel avian paramyxovirus strain APMV/Shimane67 isolated from migratory wild geese in Japan.

PubMed

Yamamoto, Eiji; Ito, Toshihiro; Ito, Hiroshi

2016-11-01

The nucleotide sequences of nucleocapsid protein (N); phosphoprotein (P); matrix protein (M); hemagglutinin-neuraminidase (HN); and large polymerase protein (L) genes, 3'-end leader, 5'-end trailer and intergenic regions of the avian paramyxovirus (APMV) strain goose/Shimane/67/2000 (APMV/Shimane67) were determined. Together with previously reported data on fusion protein (F) gene sequence [46], the determination of the genome sequence of APMV/Shimane67 has been completed in this study. The genome of APMV/Shimane67 comprised 16,146 nucleotides in length and contains six genes in the order of 3'-N-P-M-F-HN-L-5'. The features of the APMV/Shimane67 genome (e.g., nucleotide length of whole genome and each of the six genes, and predicted amino acid length of each of the six genes) were distinct from those of other APMV serotypes. Phylogenetic analysis indicated that although APMV/Shimane67 was grouped with APMV-1, -9 and -12, the evolutionary distance between APMV/Shimane67 and these viruses was longer than that observed between intra-serotype viruses. These results show that the genome sequence of APMV/Shimane67 contains specific characteristics and is distinguishable from other types of APMV.

Leaders produce leaders and managers produce followers

PubMed Central

Khoshhal, Khalid I.; Guraya, Salman Y.

2016-01-01

Objectives: To elaborate the desired qualities, traits, and styles of physician’s leadership with a deep insight into the recommended measures to inculcate leadership skills in physicians. Methods: The databases of MEDLINE, EMBASE, CINAHL, and the Cochrane Library were searched for the full-text English-language articles published during the period 2000-2015. Further search, including manual search of grey literature, was conducted from the bibliographic list of all included articles. Medical Subject Headings (MeSH) keywords “Leadership” AND “Leadership traits” AND “Leadership styles” AND “Physicians’ leadership” AND “Tomorrow’s doctors” were used for the literature search. This search followed a step-wise approach defined by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). The retrieved bibliographic list was analyzed and non-relevant material such as abstracts, conference proceedings, letters to editor, and short communications were excluded. Finally, 21 articles were selected for this review. Results: The literature search showed a number of leadership courses and formal training programs that can transform doctors to physician leaders. Leaders can inculcate confidence by integrating diverse views and listening; supporting skillful conversations through dialogue and helping others assess their influence and expertise. In addition to their clinical competence, physician leaders need to acquire the industry knowledge (clinical processes, health-care trends, budget), problem-solving skills, and emotional intelligence. Conclusion: This review emphasizes the need for embedding formal leadership courses in the medical curricula for fostering tomorrow doctors’ leadership and organizational skills. The in-house and off-campus training programs and workshops should be arranged for grooming the potential candidates for effective leadership. PMID:27652355

First draft genome sequencing of indole acetic acid producing and plant growth promoting fungus Preussia sp. BSL10.

PubMed

Khan, Abdul Latif; Asaf, Sajjad; Khan, Abdur Rahim; Al-Harrasi, Ahmed; Al-Rawahi, Ahmed; Lee, In-Jung

2016-05-10

Preussia sp. BSL10, family Sporormiaceae, was actively producing phytohormone (indole-3-acetic acid) and extra-cellular enzymes (phosphatases and glucosidases). The fungus was also promoting the growth of arid-land tree-Boswellia sacra. Looking at such prospects of this fungus, we sequenced its draft genome for the first time. The Illumina based sequence analysis reveals an approximate genome size of 31.4Mbp for Preussia sp. BSL10. Based on ab initio gene prediction, total 32,312 coding sequences were annotated consisting of 11,967 coding genes, pseudogenes, and 221 tRNA genes. Furthermore, 321 carbohydrate-active enzymes were predicted and classified into many functional families. Copyright © 2016 Elsevier B.V. All rights reserved.

Identifying opinion leaders to promote behavior change.

PubMed

Valente, Thomas W; Pumpuang, Patchareeya

2007-12-01

This article reviews 10 techniques used to identify opinion leaders to promote behavior change. Opinion leaders can act as gatekeepers for interventions, help change social norms, and accelerate behavior change. Few studies document the manner in which opinion leaders are identified, recruited, and trained to promote health. The authors categorize close to 200 studies that have studied or used opinion leaders to promote behavior change into 10 different methods. They present the advantages and disadvantages of the 10 opinion leader identification methods and provide sample instruments for each. Factors that might influence programs to select one or another method are then discussed, and the article closes with a discussion of combining and comparing methods.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, M.S.

1998-08-18

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments are improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device. 27 figs.

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

2003-08-19

A computer system for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area and sample sequences in another area on a display device.

Influence of the Amino Acid Sequence on Protein-Mineral Interactions in Soil

NASA Astrophysics Data System (ADS)

Chacon, S. S.; Reardon, P. N.; Purvine, S.; Lipton, M. S.; Washton, N.; Kleber, M.

2017-12-01

The intimate associations between protein and mineral surfaces have profound impacts on nutrient cycling in soil. Proteins are an important source of organic C and N, and a subset of proteins, extracellular enzymes (EE), can catalyze the depolymerization of soil organic matter (SOM). Our goal was to determine how variation in the amino acid sequence could influence a protein's susceptibility to become chemically altered by mineral surfaces to infer the fate of adsorbed EE function in soil. We hypothesized that (1) addition of charged amino acids would enhance the adsorption onto oppositely charged mineral surfaces (2) addition of aromatic amino acids would increase adsorption onto zero charged surfaces (3) Increase adsorption of modified proteins would enhance their susceptibility to alterations by redox active minerals. To test these hypotheses, we generated three engineered proxies of a model protein Gb1 (IEP 4.0, 6.2 kDA) by inserting either negatively charged, positively charged or aromatic amino acids in the second loop. These modified proteins were allowed to interact with functionally different mineral surfaces (goethite, montmorillonite, kaolinite and birnessite) at pH 5 and 7. We used LC-MS/MS and solution-state Heteronuclear Single Quantum Coherence Spectroscopy NMR to observe modifications on engineered proteins as a consequence to mineral interactions. Preliminary results indicate that addition of any amino acids to a protein increase its susceptibility to fragmentation and oxidation by redox active mineral surfaces, and alter adsorption to the other mineral surfaces. This suggest that not all mineral surfaces in soil may act as sorbents for EEs and chemical modification of their structure should also be considered as an explanation for decrease in EE activity. Fragmentation of proteins by minerals can bypass the need to produce proteases, but microbial acquisition of other nutrients that require enzymes such as cellulases, ligninases or phosphatases

Human leader and robot follower team: correcting leader's position from follower's heading

NASA Astrophysics Data System (ADS)

Borenstein, Johann; Thomas, David; Sights, Brandon; Ojeda, Lauro; Bankole, Peter; Fellars, Donald

2010-04-01

In multi-agent scenarios, there can be a disparity in the quality of position estimation amongst the various agents. Here, we consider the case of two agents - a leader and a follower - following the same path, in which the follower has a significantly better estimate of position and heading. This may be applicable to many situations, such as a robotic "mule" following a soldier. Another example is that of a convoy, in which only one vehicle (not necessarily the leading one) is instrumented with precision navigation instruments while all other vehicles use lower-precision instruments. We present an algorithm, called Follower-derived Heading Correction (FDHC), which substantially improves estimates of the leader's heading and, subsequently, position. Specifically, FHDC produces a very accurate estimate of heading errors caused by slow-changing errors (e.g., those caused by drift in gyros) of the leader's navigation system and corrects those errors.

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family.

PubMed

Kimura, M; Kimura, J; Hatakeyama, T

1988-11-21

The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).

Solving multi-leader-common-follower games.

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

Leyffer, S.; Munson, T.; Mathematics and Computer Science

Multi-leader-common-follower games arise when modelling two or more competitive firms, the leaders, that commit to their decisions prior to another group of competitive firms, the followers, that react to the decisions made by the leaders. These problems lead in a natural way to equilibrium problems with equilibrium constraints (EPECs). We develop a characterization of the solution sets for these problems and examine a variety of nonlinear optimization and nonlinear complementarity formulations of EPECs. We distinguish two broad cases: problems where the leaders can cost-differentiate and problems with price-consistent followers. We demonstrate the practical viability of our approach by solving amore » range of medium-sized test problems.« less

Today's Leader--"An Endangered Species"

ERIC Educational Resources Information Center

Tregoe, Ben

1976-01-01

Leadership behavior derives from the different ways in which leaders respond to different situations. Problems arise when only one type of behavior is utilized in a variety of different situations. A list of variables to be considered by leaders in making appropriate behavioral decisions is provided. (EC)

Encouraging Civility as a Community College Leader

ERIC Educational Resources Information Center

Elsner, Paul A., Ed.; Boggs, George R., Ed.

2006-01-01

The contributors relate examples of situations in which leaders encountered unexpected and sometimes unprecedented incivility in their role as community college leaders. The chapters present their experiences, observations, lessons, and recommendations for handling crises that may befall leaders in an academic setting. This book contains the…

Creative benefits from well-connected leaders: leader social network ties as facilitators of employee radical creativity.

PubMed

Venkataramani, Vijaya; Richter, Andreas W; Clarke, Ronald

2014-09-01

Employee radical creativity critically depends on substantive informational resources from others across the wider organization. We propose that the social network ties of employees' immediate leaders assume a central role in garnering these resources, thereby fostering their employees' radical creativity both independent of and interactively with employees' own network ties. Drawing on data from 214 employees working in 30 teams of a public technology and environmental services organization, we find that team leaders' betweenness centrality in the idea network within their teams as well as among their peer leaders provides creative benefits beyond employees' own internal and external ties. Further, employees' and leaders' ties within and external to the team interactively predict employee radical creativity. Implications for theory and practice are discussed. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Beyond the classroom: nurse leader preparation and practices.

PubMed

O'Connor, Mary

2011-01-01

Formal academic education and experience as a nurse are established preparation for the chief nurse executive (CNE) or upcoming nurse leaders. This article proposes that the nurse leader must build on these fundamentals through self-discipline, lifelong learning, and practice. Three critical ingredients are discussed to guide the nurse leader on a life/career for the CNE and the nurse leader at every level. These include fostering relationships, feeding intellectual curiosity, and engaging in self-care practices. These indispensable ingredients of the successful nurse leader serve as an augmentation to formal education and experience for the nurse aspiring to reach the CNE level and beyond as well as for the current CNE mentoring future leaders.

Supervisory Options for Instructional Leaders in Education

ERIC Educational Resources Information Center

Fritz, Carrie; Miller, Greg

2003-01-01

The principal purpose of this article was to identify supervisory approaches available to instructional leaders in education. Selected supervisory approaches served as the basis for creating the Supervisory Options for Instructional Leaders (SOIL) Model. Instructional leaders in a variety of educational settings could use this model. The SOIL…

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

1999-10-26

A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Computer-aided visualization and analysis system for sequence evaluation

DOEpatents

Chee, Mark S.

2001-06-05

A computer system (1) for analyzing nucleic acid sequences is provided. The computer system is used to perform multiple methods for determining unknown bases by analyzing the fluorescence intensities of hybridized nucleic acid probes. The results of individual experiments may be improved by processing nucleic acid sequences together. Comparative analysis of multiple experiments is also provided by displaying reference sequences in one area (814) and sample sequences in another area (816) on a display device (3).

Nucleic acid detection kits

DOEpatents

Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann; Kwiatkowski, Robert W.; Vavra, Stephanie H.

2005-03-29

The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of nucleic acid from various viruses in a sample.

Quantum-Sequencing: Fast electronic single DNA molecule sequencing

NASA Astrophysics Data System (ADS)

Casamada Ribot, Josep; Chatterjee, Anushree; Nagpal, Prashant

2014-03-01

A major goal of third-generation sequencing technologies is to develop a fast, reliable, enzyme-free, high-throughput and cost-effective, single-molecule sequencing method. Here, we present the first demonstration of unique ``electronic fingerprint'' of all nucleotides (A, G, T, C), with single-molecule DNA sequencing, using Quantum-tunneling Sequencing (Q-Seq) at room temperature. We show that the electronic state of the nucleobases shift depending on the pH, with most distinct states identified at acidic pH. We also demonstrate identification of single nucleotide modifications (methylation here). Using these unique electronic fingerprints (or tunneling data), we report a partial sequence of beta lactamase (bla) gene, which encodes resistance to beta-lactam antibiotics, with over 95% success rate. These results highlight the potential of Q-Seq as a robust technique for next-generation sequencing.

Comparative sequence analysis of acid sensitive/resistance proteins in Escherichia coli and Shigella flexneri

PubMed Central

Manikandan, Selvaraj; Balaji, Seetharaaman; Kumar, Anil; Kumar, Rita

2007-01-01

The molecular basis for the survival of bacteria under extreme conditions in which growth is inhibited is a question of great current interest. A preliminary study was carried out to determine residue pattern conservation among the antiporters of enteric bacteria, responsible for extreme acid sensitivity especially in Escherichia coli and Shigella flexneri. Here we found the molecular evidence that proved the relationship between E. coli and S. flexneri. Multiple sequence alignment of the gadC coded acid sensitive antiporter showed many conserved residue patterns at regular intervals at the N-terminal region. It was observed that as the alignment approaches towards the C-terminal, the number of conserved residues decreases, indicating that the N-terminal region of this protein has much active role when compared to the carboxyl terminal. The motif, FHLVFFLLLGG, is well conserved within the entire gadC coded protein at the amino terminal. The motif is also partially conserved among other antiporters (which are not coded by gadC) but involved in acid sensitive/resistance mechanism. Phylogenetic cluster analysis proves the relationship of Escherichia coli and Shigella flexneri. The gadC coded proteins are converged as a clade and diverged from other antiporters belongs to the amino acid-polyamine-organocation (APC) superfamily. PMID:21670792

Training College Outdoor Program Leaders.

ERIC Educational Resources Information Center

Curtis, Rick

This paper describes a training program for college outdoor program leaders developed by the Outdoor Action Program at Princeton University (New Jersey). The training program includes a leader training course, a safety management seminar, a wilderness first aid course, cardiopulmonary resuscitation, and group skills workshop. This paper describes…

Analysis multi-agent with precense of the leader

NASA Astrophysics Data System (ADS)

Achmadi, Sentot; Marjono, Miswanto

2017-12-01

The phenomenon of swarm is a natural phenomenon that is often done by a collection of living things in the form of motion from one place to another. By clustering, a group of animals can increase their effectiveness in food search and avoid predators. A group of geese also performs a swarm phenomenon when flying and forms an inverted V-formation with one of the geese acting as a leader. Each flying track of members of the geese group always follows the leader's path at a certain distance. This article discusses the mathematical modeling of the swarm phenomenon, which is the optimal tracking control for multi-agent model with the influence of the leader in the 2-dimensional space. The leader in this model is intended to track the specified path. Firstly, the leader's motion control is to follow the predetermined path using the Tracking Error Dynamic method. Then, the path from the leader is used to design the motion control of each agent to track the leader's path at a certain distance. The result of numerical simulation shows that the leader trajectory can track the specified path. Similarly, the motion of each agent can trace and follow the leader's path.

Psychological competence: the key to leader empowering behaviors.

PubMed

Havaei, Farinaz; Dahinten, V Susan; MacPhee, Maura

2014-05-01

The aim of this study was to examine the effects of specific cognitions or aspects of psychological empowerment on 5 major aspects of leader empowering behaviors. Leader empowering behaviors are linked to important employee outcomes such as work effectiveness. Psychologically empowered leaders are known to use more empowering behaviors in their practice. There is limited research examining what aspects of psychological empowerment are most associated with different aspects of leader empowering behaviors. Data from a sample of 103 frontline and midlevel nurse leaders were analyzed after they participated in a leadership development program. Psychological competence was the strongest predictor of the total score for leader empowering behaviors and 4 of 5 subscale scores, and meaning was the 2nd strongest predictor. Autonomy was not a significant predictor. Psychological empowerment, particularly in the form of psychological competence, is an important leader characteristic and should be a focus of leadership development strategies.

A Phenomenology of Outdoor Education Leader Experiences

ERIC Educational Resources Information Center

Field, Stephanie C.; Lauzon, Lara L.; Meldrum, John T.

2016-01-01

Limited qualitative research exists on the experiences of outdoor education leaders. The purpose of this phenomenological study was to explore the job-related experiences of outdoor education leaders within and outside the workplace. Five participants who had experience as outdoor education leaders completed in-depth, one-on-one interviews about…

Identifying Opinion Leaders to Promote Behavior Change

ERIC Educational Resources Information Center

Valente, Thomas W.; Pumpuang, Patchareeya

2007-01-01

This article reviews 10 techniques used to identify opinion leaders to promote behavior change. Opinion leaders can act as gatekeepers for interventions, help change social norms, and accelerate behavior change. Few studies document the manner in which opinion leaders are identified, recruited, and trained to promote health. The authors categorize…

Method of increasing conversion of a fatty acid to its corresponding dicarboxylic acid

DOEpatents

Craft, David L.; Wilson, C. Ron; Eirich, Dudley; Zhang, Yeyan

2004-09-14

A nucleic acid sequence including a CYP promoter operably linked to nucleic acid encoding a heterologous protein is provided to increase transcription of the nucleic acid. Expression vectors and host cells containing the nucleic acid sequence are also provided. The methods and compositions described herein are especially useful in the production of polycarboxylic acids by yeast cells.

Recognizing and defining clinical nurse leaders.

PubMed

Stanley, David

This article addresses the issue of clinical leadership and how it is defined. The concepts and definitions of clinical leadership are considered as well as the results of new research that suggests that clinical leaders can be seen as experts in their field, and because they are approachable and are effective communicators, are empowered to act as a role model, motivating others by matching their values and beliefs about nursing and care to their practice. This is supported by a new leadership theory, congruent leadership, proposed as the most appropriate leadership theory to support an understanding of clinical leadership. Congruent leaders (clinical nurse leaders) are followed because there is a match between the leader's values and beliefs and their actions.

Evaluating pharmacy leader development through the seven action logics.

PubMed

Philip, Achsah; Desai, Avani; Nguyen, Phouc Anne; Birney, Patrick; Colavecchia, Anthony; Karralli, Rusol; Smith, Lindsey; Lorimer, Dirk; Burgess, Gwen; Munch, Kyle; Daniel, Nelvin; Lionetti, Jason; Garey, Kevin W

2016-01-15

Pharmacy leader development over time was analyzed using the seven action logics. As part of an ongoing leadership seminar series, students were required to select a visionary pharmacy leader and conduct a structured interview to evaluate pharmacy leaders' action logics. A standardized questionnaire comprising 13 questions was created by the class. Questions addressed leadership qualities during the leaders' early years, education years, and work years. Transcripts were then coded by two separate trained investigators based on the leader's stage of life to provide a score for each action logic individually over time. Kappa coefficient was used to evaluate interrater agreement. A total of 14 leaders were interviewed. All leaders were currently employed and had won national awards for their contributions to pharmacy practice. Overall, there was 82% agreement between the two evaluators' scores for the various characteristics. Action logics changed based on the leaders' life stage. Using aggregate data from all leader interviews, a progression from lower-order action logics (opportunist, diplomat, expert) to higher-order action logics (strategist, alchemist) was found. Ten leaders (71%) were diplomats during their early years. Six leaders (43%) were experts during their education years, and 4 (29%) were strategists or alchemists. During the third life stage analyzed (the work years), 6 leaders (43%) were strategists, and 2 were alchemists. During their work years, all leaders had a percentage of their answers coded as alchemist (range, 5-22%). Throughout their professional careers, pharmacy leaders continually develop skills through formal education and mentorship that follow action logics. Copyright © 2016 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Future Leaders: The Way Forward?

ERIC Educational Resources Information Center

Earley, Peter; Weindling, Dick; Bubb, Sara; Glenn, Meli

2009-01-01

The recruitment and retention of senior school leaders is high on the UK Government's agenda with much attention currently being given to succession planning. Future Leaders and other fast track leadership development programmes are, in part, a response to this "crisis" brought about by demographic change--many headteachers are due to…

Stepped-to-dart Leaders in Cloud-to-ground Lightning

NASA Astrophysics Data System (ADS)

Stolzenburg, M.; Marshall, T. C.; Karunarathne, S.; Karunarathna, N.; Warner, T.; Orville, R. E.

2013-12-01

Using time-correlated high-speed video (50,000 frames per second) and fast electric field change (5 MegaSamples per second) data for lightning flashes in East-central Florida, we describe an apparently rare type of subsequent leader: a stepped leader that finds and follows a previously used channel. The observed 'stepped-to-dart leaders' occur in three natural negative ground flashes. Stepped-to-dart leader connection altitudes are 3.3, 1.6 and 0.7 km above ground in the three cases. Prior to the stepped-to-dart connection, the advancing leaders have properties typical of stepped leaders. After the connection, the behavior changes almost immediately (within 40-60 us) to dart or dart-stepped leader, with larger amplitude E-change pulses and faster average propagation speeds. In this presentation, we will also describe the upward luminosity after the connection in the prior return stroke channel and in the stepped leader path, along with properties of the return strokes and other leaders in the three flashes.

Complete genome sequences of avian paramyxovirus type 8 strains goose/Delaware/1053/76 and pintail/Wakuya/20/78

PubMed Central

Paldurai, Anandan; Subbiah, Madhuri; Kumar, Sachin; Collins, Peter L.; Samal, Siba K.

2009-01-01

Complete consensus genome sequences were determined for avian paramyxovirus type 8 (APMV-8) strains goose/Delaware/1053/76 (prototype strain) and pintail/Wakuya/20/78. The genome of each strain is 15,342 nucleotides (nt) long, which follows the “rule of six”. The genome consists of six genes in the order of 3′-N-P/V/W-M-F-HN-L-5′. The genes are flanked on either side by conserved transcription start and stop signals, and have intergenic regions ranging from 1 to 30 nt. The genome contains a 55 nt leader region at the 3′-end and a 171 nt trailer region at the 5′-end. Comparison of sequences of strains Delaware and Wakuya showed nucleotide identity of 96.8% at the genome level and amino acid identities of 99.3%, 96.5%, 98.6%, 99.4%, 98.6% and 99.1% for the predicted N, P, M, F, HN and L proteins, respectively. Both strains grew in embryonated chicken eggs and in primary chicken embryo kidney cells, and 293T cells. Both strains contained only a single basic residue at the cleavage activation site of the F protein and their efficiency of replication in vitro depended on and was augmented by, the presence of exogenous protease in most cell lines. Sequence alignment and phylogenic analysis of the predicted amino acid sequence of APMV-8 strain Delaware proteins with the cognate proteins of other available APMV serotypes showed that APMV-8 is more closely related to APMV-2 and -6 than to APMV-1, -3 and -4. PMID:19341613

Developing Military Health Care Leaders

PubMed Central

Kirby, Sheila Nataraj; Marsh, Julie A.; McCombs, Jennifer Sloan; Thie, Harry J.; Xia, Nailing; Sollinger, Jerry M.

2011-01-01

Abstract The U.S. Department of Defense has highlighted the importance of preparing health care leaders to succeed in joint, performance-based environments. The current wartime environment, rising health care costs, and an increased focus on joint operations have led to recommendations for Military Health System (MHS) transformation. Part of that transformation will involve improving the identification and development of potential MHS leaders. An examination of how candidates are identified for leadership positions, the training and education opportunities offered to them, and the competencies they are expected to achieve revealed both a range of approaches and several commonalities in the military, civilian, and government sectors. A conceptual framework guided a series of interviews with senior health care executives from a wide range of organizations and military health care leaders from the Army, Navy, and Air Force, as well as a case study of the leader development approaches used by the Veterans Health Administration. Several themes emerged in terms of how leaders are developed in each sector, including the importance of mentoring, career counseling, 360-degree feedback, self-development, and formal education and training programs. Lessons learned in the civilian and government sectors hold importance for transforming the way in which MHS identifies and develops health care officers with high leadership potential for senior executive positions. PMID:28083164

Leaders and followers: quantifying consistency in spatio-temporal propagation patterns

NASA Astrophysics Data System (ADS)

Kreuz, Thomas; Satuvuori, Eero; Pofahl, Martin; Mulansky, Mario

2017-04-01

Repetitive spatio-temporal propagation patterns are encountered in fields as wide-ranging as climatology, social communication and network science. In neuroscience, perfectly consistent repetitions of the same global propagation pattern are called a synfire pattern. For any recording of sequences of discrete events (in neuroscience terminology: sets of spike trains) the questions arise how closely it resembles such a synfire pattern and which are the spike trains that lead/follow. Here we address these questions and introduce an algorithm built on two new indicators, termed SPIKE-order and spike train order, that define the synfire indicator value, which allows to sort multiple spike trains from leader to follower and to quantify the consistency of the temporal leader-follower relationships for both the original and the optimized sorting. We demonstrate our new approach using artificially generated datasets before we apply it to analyze the consistency of propagation patterns in two real datasets from neuroscience (giant depolarized potentials in mice slices) and climatology (El Niño sea surface temperature recordings). The new algorithm is distinguished by conceptual and practical simplicity, low computational cost, as well as flexibility and universality.

Amino acid sequences of peptides from a tryptic digest of a urea-soluble protein fraction (U.S.3) from oxidized wool

PubMed Central

Corfield, M. C.; Fletcher, J. C.; Robson, A.

1967-01-01

1. A tryptic digest of the protein fraction U.S.3 from oxidized wool has been separated into 32 peptide fractions by cation-exchange resin chromatography. 2. Most of these fractions have been resolved into their component peptides by a combination of the techniques of cation-exchange resin chromatography, paper chromatography and paper electrophoresis. 3. The amino acid compositions of 58 of the peptides in the digest present in the largest amounts have been determined. 4. The amino acid sequences of 38 of these have been completely elucidated and those of six others partially derived. 5. These findings indicate that the parent protein in wool from which the protein fraction U.S.3 is derived has a minimum molecular weight of 74000. 6. The structures of wool proteins are discussed in the light of the peptide sequences determined, and, in particular, of those sequences in fraction U.S.3 that could not be elucidated. PMID:16742497

The IT Leader as Alchemist: Finding the True Gold

ERIC Educational Resources Information Center

Bleed, Ron

2006-01-01

The Information technology (IT) leader within higher education can be viewed from three scenarios: (1) the IT leader as plumber; (2) the IT leader as gardener; and (3) the IT leader as alchemist. In the first scenario, the college or university network consists of pipes, and the role of the IT leader resembles that of a plumber, who keeps the…

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

Kurilla, M.G.; Stone, H.O.; Keene, J.D.

The 3' end of the genomic RNA of Newcastle disease virus (NDV) has been sequenced and the leader RNA defined. Using hybridization to a 3'-end-labeled genome, leader RNA species from in vitro transcription reactions and from infected cell extracts were found to be 47 and 53 nucleotides long. In addition, the start site of the 3'-proximal mRNA was determined by sequence analysis of in vitro (beta-32P)GTP-labeled transcription products. The genomic sequence extending beyond the leader region demonstrated an open reading frame for at least 42 amino acids and probably represents the amino terminus of the nucleocapsid protein (NP). The terminalmore » 8 nucleotides of the NDV genome were identical to those of measles virus and Sendai virus while the sequence of the distal half of the leader region was more similar to that of vesicular stomatitis virus. These data argue for strong evolutionary relatedness between the paramyxovirus and rhabdovirus groups.« less

Leader's Guide: Facilitating Inquiry in the Classroom.

ERIC Educational Resources Information Center

Newton, Fred E.

This is the leader's guide and training materials for conducting workshops on an instructional system which utilizes the process of inquiry. The guide is designed for leaders of these workshops and lists the leader's activities. It is organized according to the 18 major workshop experiences, referred to as subset. Each subset guide is organized…

Isolation, sequencing and expression of RED, a novel human gene encoding an acidic-basic dipeptide repeat.

PubMed

Assier, E; Bouzinba-Segard, H; Stolzenberg, M C; Stephens, R; Bardos, J; Freemont, P; Charron, D; Trowsdale, J; Rich, T

1999-04-16

A novel human gene RED, and the murine homologue, MuRED, were cloned. These genes were named after the extensive stretch of alternating arginine (R) and glutamic acid (E) or aspartic acid (D) residues that they contain. We term this the 'RED' repeat. The genes of both species were expressed in a wide range of tissues and we have mapped the human gene to chromosome 5q22-24. MuRED and RED shared 98% sequence identity at the amino acid level. The open reading frame of both genes encodes a 557 amino acid protein. RED fused to a fluorescent tag was expressed in nuclei of transfected cells and localised to nuclear dots. Co-localisation studies showed that these nuclear dots did not contain either PML or Coilin, which are commonly found in the POD or coiled body nuclear compartments. Deletion of the amino terminal 265 amino acids resulted in a failure to sort efficiently to the nucleus, though nuclear dots were formed. Deletion of a further 50 amino acids from the amino terminus generates a protein that can sort to the nucleus but is unable to generate nuclear dots. Neither construct localised to the nucleolus. The characteristics of RED and its nuclear localisation implicate it as a regulatory protein, possibly involved in transcription.

It takes chutzpah: oncology nurse leaders.

PubMed

Green, E

1999-01-01

Chutzpah, according to the Oxford Dictionary of Current English (1996) is a slang term from the Yiddish language which means shameless audacity. Chutzpah has been used to identify people with courage who take on situations that others avoid and somehow achieve the impossible. Tim Porter-O'Grady (1997) recently wrote that management is dead, and has been replaced by process leadership. Health care organizations have made shifts from hierarchical structures to process or program models where people have dual/multiple reporting/communication relationship. In this new orientation, management functions of controlling, directing, organizing and disciplining are replaced by process leadership functions of coordinating, facilitating, linking and sustaining (Porter O'Grady, 1997). Herein lies the challenge for oncology nurse leaders: "what lies behind us and what lies before us are tiny matters compared to what lies within us" (Ralph Waldo Emerson). Leadership is not a function of job title. The evidence for this is clear in current practice.... There are no/few positions of nurse leaders. Titles have changed to eliminate the professional discipline, and reflect a non-descript orientation. The new titles are process leaders, program leaders, professional practice leaders. Nurse leaders need new points of reference to take in the challenges of influencing, facilitating and linking. Those points of reference are: principle-centered leadership, integrity and chutzpah. This presentation will focus on examining current thinking, defining key characteristics and attributes, and using scenarios to illustrate the impact of leadership. We, as leaders in oncology nursing, must use chutzpah to make positive change and long-term gains for patient care and the profession of nursing.

The School Leader Communication Model: An Emerging Method for Bridging School Leader Preparation and Practice

ERIC Educational Resources Information Center

Dotger, Benjamin H.

2011-01-01

School leaders make countless decisions but do not receive adequate preparation for communicating their decisions to parents, students, and teachers. Building on the need to prepare school leaders for a variety of complex professional situations, this article introduces the medical education pedagogy of standardized patients to the field of school…

Attractiveness and Leader Style: Evaluations of Male and Female Leaders by Male and Female Evaluators.

ERIC Educational Resources Information Center

Sopasakis, Maria; Snodgrass, Sara E.

Previous research has suggested that men are stereotypically believed to be better leaders than women; that more physically attractive people are evaluated more positively than less attractive people; and that men and women use different leadership styles. This study examined the interactions of sex, leader style, and physical attractiveness on…

Professional Ethics: Leader’s Business

DTIC Science & Technology

1990-02-20

not be uudued for apen publicatlon until it has bee clea by th appsopalt milituy mr or T IC PROFESSIONAL ETHICS: LEADER’S BUSINESS ELECTE JUN 20 1990...34Professional Ethics: Leader’s Business " Individual Study Project 6. PERFORMING ORG. REPORT NUMBER 7. AUTHOR(&) 8. CONTRACT OR GRANT NUMBER...ETHICS: LEADER’S BUSINESS AN INDIVIDUAL STUDY PROJECT ctWy by 0 Lieutenant Colonel Kevin P. Byrnes, FA Acce-ion For Colonel Robert B. TinsmanNT Project

The failure-tolerant leader.

PubMed

Farson, Richard; Keyes, Ralph

2002-08-01

"The fastest way to succeed," IBM's Thomas Watson, Sr., once said, "is to double your failure rate." In recent years, more and more executives have embraced Watson's point of view, coming to understand what innovators have always known: Failure is a prerequisite to invention. But while companies may grasp the value of making mistakes at the level of corporate practices, they have a harder time accepting the idea at the personal level. People are afraid to fail, and corporate culture reinforces that fear. In this article, psychologist and former Harvard Business School professor Richard Farson and coauthor Ralph Keyes discuss how companies can reduce the fear of miscues. What's crucial is the presence of failure-tolerant leaders--executives who, through their words and actions, help employees overcome their anxieties about making mistakes and, in the process, create a culture of intelligent risk-taking that leads to sustained innovation. Such leaders don't just accept productive failure, they promote it. Drawing from their research in business, politics, sports, and science, the authors identify common practices among failure-tolerant leaders. These leaders break down the social and bureaucratic barriers that separate them from their followers. They engage at a personal level with the people they lead. They avoid giving either praise or criticism, preferring to take a nonjudgmental, analytical posture as they interact with staff. They openly admit their own mistakes rather than trying to cover them up or shifting the blame. And they try to root out the destructive competitiveness built into most organizations. Above all else, failure-tolerant leaders push people to see beyond traditional definitions of success and failure. They know that as long as a person views failure as the opposite of success, rather than its complement, he or she will never be able to take the risks necessary for innovation.

The Key to Leadership Effectiveness--Leader Authenticity.

ERIC Educational Resources Information Center

Henderson, James E.

When an education leader develops and maintains policies that line up with the imperatives of ethical and authentic behavior, this defines the character of both the leader and the organization. Some of the questions surrounding this assertion are examined in this paper. It looks at what it means when a leader behaves in an authentic fashion, how…

Preparing nurse leaders for 2020.

PubMed

Huston, Carol

2008-11-01

This article highlights eight leadership competencies likely to be an essential part of the nurse leader's repertoire in 2020. Planning for the future is difficult, even when environments are relatively static. When environments are dynamic, the challenges multiply exponentially. Unfortunately, few environments have been more unpredictable in the 21st century than health care. The healthcare system is in chaos, as is much of the business world. It is critical then that contemporary nursing and healthcare leaders identify skill sets that will be needed by nurse leaders in 2020 and begin now to create the educational models and management development programs necessary to assure these skills are present. Essential nurse leader competencies for 2020 include: (i) A global perspective or mindset regarding healthcare and professional nursing issues. (ii) Technology skills which facilitate mobility and portability of relationships, interactions, and operational processes. (iii) Expert decision-making skills rooted in empirical science. (iv) The ability to create organization cultures that permeate quality healthcare and patient/worker safety. (v) Understanding and appropriately intervening in political processes. (vi) Highly developed collaborative and team building skills. (vii) The ability to balance authenticity and performance expectations. (viii) Being able to envision and proactively adapt to a healthcare system characterized by rapid change and chaos. Nursing education programmes and healthcare organizations must be begin now to prepare nurses to be effective leaders in 2020. This will require the formal education and training that are a part of most management development programmes as well as a development of appropriate attitudes through social learning. Proactive succession planning will also be key to having nurse leaders who can respond effectively to the new challenges and opportunities that will be presented to them in 2020.

The Servant as Religious Leader.

ERIC Educational Resources Information Center

Greenleaf, Robert K.

The importance of increasing the number of religious leaders and the roles of the seminary and church are considered. Religious leadership is needed to respond to widespread alienation in all sectors of society as well as to many institutions' inability or unwillingness to serve society. The leader needs three intellectual abilities: a sense for…

From the Field: Learning Leaders

ERIC Educational Resources Information Center

Weigel, Kathleen; Jones, Richard

2015-01-01

Leadership is essential to successful schools. One of the ways to support effective school leadership is to share ideas and best practices to address the common challenges faced by school leaders. This question and response format addresses common challenges and questions from practicing school leaders in the manner that a mentor might respond to…

Leader-team complementarity: Exploring the interactive effects of leader personality traits and team power distance values on team processes and performance.

PubMed

Hu, Jia; Judge, Timothy A

2017-06-01

Integrating the leader trait perspective with dominance complementarity theory, we propose team power distance as an important boundary condition for the indirect impact of leader extraversion, agreeableness, and conscientiousness on team performance through a team's potency beliefs and through relational identification with the leader. Using time-lagged, 3-source data from 71 teams, we found that leader extraversion had a positive indirect impact on team in-role and extrarole performance through relational identification, but only for high power distance teams; leader conscientiousness had a positive influence on team in-role performance through team potency, but only for high power distance teams; and leader agreeableness had a positive effect on team in-role and extrarole performance via relational identification and on team in-role performance via team potency, but only for low power distance teams. The findings address prior inconsistencies regarding the relationships between leader traits and team effectiveness, identify an important boundary condition and key team processes that bridge the links, and provide a deeper understanding of the role of leader traits in teams. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Isolation and amino acid sequences of squirrel monkey (Saimiri sciurea) insulin and glucagon

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

Yu, Jinghua; Eng, J.; Yalow, R.S.

1990-12-01

It was reported two decades ago that insulin was not detectable in the glucose-stimulated state in Saimiri sciurea, the New World squirrel monkey, by a radioimmunoassay system developed with guinea pig anti-pork insulin antibody and labeled park insulin. With the same system, reasonable levels were observed in rhesus monkeys and chimpanzees. This suggested that New World monkeys, like the New World hystricomorph rodents such as the guinea pig and the coypu, might have insulins whose sequences differ markedly from those of Old World mammals. In this report the authors describe the purification and amino acid sequences of squirrel monkey insulinmore » and glucagon. They demonstrate that the substitutions at B29, B27, A2, A4, and A17 of squirrel monkey insulin are identical with those previously found in another New World primate, the owl monkey (Aotus trivirgatus). The immunologic cross-reactivity of this insulin in their immunoassay system is only a few percent of that of human insulin. It appears that the peptides of the New World monkeys have diverged less from those of the Old World mammals than have those of the New World hystricomorph rodents. The striking improvements in peptide purification and sequencing have the potential for adding new information concerning the evolutionary divergence of species.« less

Leadership, Leaders, and Leading (Part One).

ERIC Educational Resources Information Center

Dean, Peter J.

2002-01-01

Presents an historical overview of the leadership literature. Highlights include "great man" theories; studies of leaders' traits; studies of leaders' behavioral style; studies of leadership functions; and studies of the situational aspects of leadership. (LRW)

The Malarial Host-Targeting Signal Is Conserved in the Irish Potato Famine Pathogen

PubMed Central

Liolios, Konstantinos; Win, Joe; Kanneganti, Thirumala-Devi; Young, Carolyn; Kamoun, Sophien; Haldar, Kasturi

2006-01-01

Animal and plant eukaryotic pathogens, such as the human malaria parasite Plasmodium falciparum and the potato late blight agent Phytophthora infestans, are widely divergent eukaryotic microbes. Yet they both produce secretory virulence and pathogenic proteins that alter host cell functions. In P. falciparum, export of parasite proteins to the host erythrocyte is mediated by leader sequences shown to contain a host-targeting (HT) motif centered on an RxLx (E, D, or Q) core: this motif appears to signify a major pathogenic export pathway with hundreds of putative effectors. Here we show that a secretory protein of P. infestans, which is perceived by plant disease resistance proteins and induces hypersensitive plant cell death, contains a leader sequence that is equivalent to the Plasmodium HT-leader in its ability to export fusion of green fluorescent protein (GFP) from the P. falciparum parasite to the host erythrocyte. This export is dependent on an RxLR sequence conserved in P. infestans leaders, as well as in leaders of all ten secretory oomycete proteins shown to function inside plant cells. The RxLR motif is also detected in hundreds of secretory proteins of P. infestans, Phytophthora sojae, and Phytophthora ramorum and has high value in predicting host-targeted leaders. A consensus motif further reveals E/D residues enriched within ~25 amino acids downstream of the RxLR, which are also needed for export. Together the data suggest that in these plant pathogenic oomycetes, a consensus HT motif may reside in an extended sequence of ~25–30 amino acids, rather than in a short linear sequence. Evidence is presented that although the consensus is much shorter in P. falciparum, information sufficient for vacuolar export is contained in a region of ~30 amino acids, which includes sequences flanking the HT core. Finally, positional conservation between Phytophthora RxLR and P. falciparum RxLx (E, D, Q) is consistent with the idea that the context of their

The Humble Leader: Association of Discrepancies in Leader and Follower Ratings of Implementation Leadership with Organizational Climate in Mental Health

PubMed Central

Aarons, Gregory A.; Ehrhart, Mark G.; Torres, Elisa M.; Finn, Natalie K.; Beidas, Rinad

2017-01-01

Objectives Discrepancies between leaders' self-ratings and follower ratings of the leader are common but usually go unrecognized. Research on discrepancies is limited but there is evidence that discrepancies are associated with organizational context. This study examined the association of leader-follower discrepancies in Implementation Leadership Scale (ILS) ratings of mental health clinic leaders, and the association of those discrepancies with organizational climate for involvement and performance feedback. Both involvement and performance feedback may be important for evidence-based practice implementation in mental health. Methods A total of 593 supervisors (i.e., leaders, n=80) and clinical service providers (i.e., followers, n=513) completed surveys including ratings of implementation leadership and organizational climate. Polynomial regression and response surface analyses were conducted to examine the associations of discrepancies in leader-follower ILS ratings with organizational involvement climate and performance feedback climate, aspects of climate likely to support EBP implementation. Results Both involvement climate and performance feedback climate were highest where leaders rated themselves low on the ILS and their followers rated those leaders high on the ILS (i.e., “humble leaders”). Conclusions Teams with “humble leaders” showed more positive organizational climate for involvement and for performance feedback, contextual factors important during EBP implementation and sustainment. Discrepancy in leader and follower ratings of implementation leadership should be a consideration in understanding and improving leadership and organizational climate for mental health services and for evidence-based practice implementation and sustainment in mental health and other allied health settings. PMID:27691380

Tainted visions: the effect of visionary leader behaviors and leader categorization tendencies on the financial performance of ethnically diverse teams.

PubMed

Greer, Lindred L; Homan, Astrid C; De Hoogh, Annebel H B; Den Hartog, Deanne N

2012-01-01

Despite the increasing prevalence of ethnic diversity, findings regarding its effects on team performance remain contradictory. We suggest that past inconsistencies can be reconciled by examining the joint impact of leader behavior and leader categorization tendencies in ethnically diverse teams. We propose that leaders who exhibit high levels of visionary leader behavior and also have the tendency to categorize their team members into in- and out-groups will facilitate a negative effect of ethnic diversity on team communication and financial performance, whereas leaders who exhibit visionary behaviors but do not tend to categorize will lead ethnically diverse teams to positive outcomes. We find support for these ideas in a study of 100 retail outlets.

Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition.

PubMed

Tamura, Takeyuki; Akutsu, Tatsuya

2007-11-30

Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino acid sequence of the protein is given as an input. This problem is becoming more important since information on subcellular location is helpful for annotation of proteins and genes and the number of complete genomes is rapidly increasing. Since existing predictors are based on various heuristics, it is important to develop a simple method with high prediction accuracies. In this paper, we propose a novel and general predicting method by combining techniques for sequence alignment and feature vectors based on amino acid composition. We implemented this method with support vector machines on plant data sets extracted from the TargetP database. Through fivefold cross validation tests, the obtained overall accuracies and average MCC were 0.9096 and 0.8655 respectively. We also applied our method to other datasets including that of WoLF PSORT. Although there is a predictor which uses the information of gene ontology and yields higher accuracy than ours, our accuracies are higher than existing predictors which use only sequence information. Since such information as gene ontology can be obtained only for known proteins, our predictor is considered to be useful for subcellular location prediction of newly-discovered proteins. Furthermore, the idea of combination of alignment and amino acid frequency is novel and general so that it may be applied to other problems in bioinformatics. Our method for plant is also implemented as a web-system and available on http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/slpfa.html.

Amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui.

PubMed

Hatakeyama, T; Hatakeyama, T

1990-07-06

The complete amino acid sequences of the ribosomal proteins HL30 and HmaL5 from the archaebacterium Halobacterium marismortui were determined. Protein HL30 was found to be acetylated at its N-terminal amino acid and shows homology to the eukaryotic ribosomal proteins YL34 from yeast and RL31 from rat. Protein HmaL5 was homologous to the protein L5 from Escherichia coli and Bacillus stearothermophilus as well as to YL16 from yeast. HmaL5 shows more similarities to its eukaryotic counterpart than to eubacterial ones.

Enhanced functional expression of aquaporin Z via fusion of in situ cleavable leader peptides in Escherichia coli cell-free system.

PubMed

Zhang, Xu; Lian, Jiazhang; Kai, Lei; Huang, Lei; Cen, Peilin; Xu, Zhinan

2014-02-05

Aquaporin Z (AqpZ) is a water channel protein from Escherichia coli and has attracted many attentions to develop the biomimetic water filtration technology. Cell-free protein synthesis (CFPS) system, one of the most complex multi-enzymatic systems, has the ability of producing the integral membrane protein in vitro. To enhance the synthesis of AqpZ in E. coli cell-free system, several natural leader peptides were respectively fused at the N-terminus and were verified to enhance the expression level significantly. Moreover, the supplementation of detergents or liposome could activate leader peptidase from the cell-free extract and provide hydrophobic environment for proper folding of AqpZ. Thus, the release of mature AqpZ via the in situ removal of leader peptide was achieved, with a specific water transport activity of (2.1 ± 0.1) × 10⁻¹⁴ cm³ s⁻¹ monomer⁻¹. Using this in situ removable leader peptide strategy, the transcription-translation, leader sequence cleavage and membrane protein folding were integrated into a simple process in the cell-free system, providing a convenient approach to enhance the expression of target proteins, especially those membrane proteins difficult to achieve. Copyright © 2013 Elsevier Inc. All rights reserved.

A putative carbohydrate-binding domain of the lactose-binding Cytisus sessilifolius anti-H(O) lectin has a similar amino acid sequence to that of the L-fucose-binding Ulex europaeus anti-H(O) lectin.

PubMed

Konami, Y; Yamamoto, K; Osawa, T; Irimura, T

1995-04-01

The complete amino acid sequence of a lactose-binding Cytisus sessilifolius anti-H(O) lectin II (CSA-II) was determined using a protein sequencer. After digestion of CSA-II with endoproteinase Lys-C or Asp-N, the resulting peptides were purified by reversed-phase high performance liquid chromatography (HPLC) and then subjected to sequence analysis. Comparison of the complete amino acid sequence of CSA-II with the sequences of other leguminous seed lectins revealed regions of extensive homology. The amino acid sequence of a putative carbohydrate-binding domain of CSA-II was found to be similar to those of several anti-H(O) leguminous lectins, especially to that of the L-fucose-binding Ulex europaeus lectin I (UEA-I).

Factors supporting dentist leaders' retention in leadership.

PubMed

Tuononen, T; Lammintakanen, J; Suominen, A L

2017-12-01

The aim was to study factors associated with staying in a dentist leadership position. We used an electronic questionnaire to gather data from 156 current or former Finnish dentist leaders in 2014. Principal component analysis categorized statements regarding time usage and opportunities in managerial work into five main components. Associations between these main component scores and the tendency to stay as a leader were analyzed with logistic regression. Out of the five main components, two were significantly associated with staying as a leader: 'career intentions', which represented intent to continue or to leave the leadership position; and 'work time control opportunities', which represented how leaders could control their own work time. Other factors that supported staying were leadership education, more work time available for leadership work, and lower age. The main component 'work pressure' decreased, although not significantly, the odds of continuing; it included lack of leadership work time, and pressure from superiors or subordinates. Leaders have important roles in health care, ensuring everyday operations as well as developing their organizations to meet future challenges. Knowledge of these supporting factors will enable dentist leaders and their organizations to improve working conditions in order to recruit and retain motivated and competent persons. In addition, well-designed education is important to inspire and encourage future leaders. Copyright© 2017 Dennis Barber Ltd.

Principals of Effective Schools Are Strong Instructional Leaders.

ERIC Educational Resources Information Center

Jordan, Ian

1986-01-01

Examines research on effective schools and on principals as instructional leaders. Research shows that principals of effective schools are strong instructional leaders. Mention is made of weaknesses found in the research on principals as instructional leaders. (MD)

A System Dynamic Model of Leader Emergence

DTIC Science & Technology

2008-03-01

Engineering and Management Air Force Institute of Technology Air University Air Education and Training Command In Partial Fulfillment of the...which in turn, have impacts on the success of the leader and the organization (Jung & Avolio, 1999). Group members can modify behaviors such as dissent...Contingency approaches to leadership suggest that environmental conditions combined with leader behavoirs, determine leader effectiveness (Judge

Conceptualizing clinical nurse leader practice: an interpretive synthesis.

PubMed

Bender, Miriam

2016-01-01

The Institute of Medicine's Future of Nursing report identifies the clinical nurse leader as an innovative new role for meeting higher health-care quality standards. However, specific clinical nurse leader practices influencing documented quality outcomes remain unclear. Lack of practice clarity limits the ability to articulate, implement and measure clinical nurse leader-specific practice and quality outcomes. Interpretive synthesis design and grounded theory analysis were used to develop a theoretical understanding of clinical nurse leader practice that can facilitate systematic and replicable implementation across health-care settings. The core phenomenon of clinical nurse leader practice is continuous clinical leadership, which involves four fundamental activities: facilitating effective ongoing communication; strengthening intra and interprofessional relationships; building and sustaining teams; and supporting staff engagement. Clinical nurse leaders continuously communicate and develop relationships within and across professions to promote and sustain information exchange, engagement, teamwork and effective care processes at the microsystem level. Clinical nurse leader-integrated care delivery systems highlight the benefits of nurse-led models of care for transforming health-care quality. Managers can use this study's findings to frame an implementation strategy that addresses theoretical domains of clinical nurse leader practice to help ensure practice success. © 2015 John Wiley & Sons Ltd.

Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase.

PubMed

Delong, Allison K; Wu, Mingham; Bennett, Diane; Parkin, Neil; Wu, Zhijin; Hogan, Joseph W; Kantor, Rami

2012-08-01

Access to antiretroviral therapy is increasing globally and drug resistance evolution is anticipated. Currently, protease (PR) and reverse transcriptase (RT) sequence generation is increasing, including the use of in-house sequencing assays, and quality assessment prior to sequence analysis is essential. We created a computational HIV PR/RT Sequence Quality Analysis Tool (SQUAT) that runs in the R statistical environment. Sequence quality thresholds are calculated from a large dataset (46,802 PR and 44,432 RT sequences) from the published literature ( http://hivdb.Stanford.edu ). Nucleic acid sequences are read into SQUAT, identified, aligned, and translated. Nucleic acid sequences are flagged if with >five 1-2-base insertions; >one 3-base insertion; >one deletion; >six PR or >18 RT ambiguous bases; >three consecutive PR or >four RT nucleic acid mutations; >zero stop codons; >three PR or >six RT ambiguous amino acids; >three consecutive PR or >four RT amino acid mutations; >zero unique amino acids; or <0.5% or >15% genetic distance from another submitted sequence. Thresholds are user modifiable. SQUAT output includes a summary report with detailed comments for troubleshooting of flagged sequences, histograms of pairwise genetic distances, neighbor joining phylogenetic trees, and aligned nucleic and amino acid sequences. SQUAT is a stand-alone, free, web-independent tool to ensure use of high-quality HIV PR/RT sequences in interpretation and reporting of drug resistance, while increasing awareness and expertise and facilitating troubleshooting of potentially problematic sequences.

Scouts in Contact: Tactical Vignettes for Cavalry Leaders

DTIC Science & Technology

2016-12-01

comprehension of those core fundamentals that must be mastered by all scout leaders and cavalry officers. These core fundamentals are intended to... listening post (LP) as an inferior force and maneuver the platoon to destroy the outpost with multiple forms of contact. If the platoon leader chooses a...leader now has to react to the contact. ○○○○ Cavalry leadership dilemma: The platoon leader must assess that this observation post (OP)/ listening

CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence.

PubMed

Petrie, Emma J; Clements, Craig S; Lin, Jie; Sullivan, Lucy C; Johnson, Darryl; Huyton, Trevor; Heroux, Annie; Hoare, Hilary L; Beddoe, Travis; Reid, Hugh H; Wilce, Matthew C J; Brooks, Andrew G; Rossjohn, Jamie

2008-03-17

The recognition of human leukocyte antigen (HLA)-E by the heterodimeric CD94-NKG2 natural killer (NK) receptor family is a central innate mechanism by which NK cells monitor the expression of other HLA molecules, yet the structural basis of this highly specific interaction is unclear. Here, we describe the crystal structure of CD94-NKG2A in complex with HLA-E bound to a peptide derived from the leader sequence of HLA-G. The CD94 subunit dominated the interaction with HLA-E, whereas the NKG2A subunit was more peripheral to the interface. Moreover, the invariant CD94 subunit dominated the peptide-mediated contacts, albeit with poor surface and chemical complementarity. This unusual binding mode was consistent with mutagenesis data at the CD94-NKG2A-HLA-E interface. There were few conformational changes in either CD94-NKG2A or HLA-E upon ligation, and such a "lock and key" interaction is typical of innate receptor-ligand interactions. Nevertheless, the structure also provided insight into how this interaction can be modulated by subtle changes in the peptide ligand or by the pairing of CD94 with other members of the NKG2 family. Differences in the docking strategies used by the NKG2D and CD94-NKG2A receptors provided a basis for understanding the promiscuous nature of ligand recognition by NKG2D compared with the fidelity of the CD94-NKG2 receptors.

Nurse leaders' perceptions of an approaching organizational change.

PubMed

Salmela, Susanne; Eriksson, Katie; Fagerström, Lisbeth

2013-05-01

The aim of the study was to achieve more profound understanding of nurse leaders' perceptions of an approaching organizational change. We used a three-dimensional hermeneutical method of interpretation to analyze text from 17 interviews. The results suggest that nurse leaders were positive toward and actively engaged in continual change to their units, even though they perceived themselves as mere spectators of the change process. The nurse leaders believed that change might benefit patients and patient care, yet their adaptation lacked deeper engagement. The approaching merger affected the nurse leaders' identities on a deeply personal level. They experienced uneasiness and anxiety with regard to being nurse leaders, the future of nursing care, and their mandate as patient advocates. Nurse leaders are in a critical position to influence the success of organizational change, but the organizations covered in this study were not incorporating their knowledge and experiences into the change.

Kansas nurse leader residency programme: advancing leader knowledge and skills.

PubMed

Shen, Qiuhua; Peltzer, Jill; Teel, Cynthia; Pierce, Janet

2018-03-01

To evaluate the effectiveness of the Kansas Nurse Leader Residency (KNLR) programme in improving nurses' leadership knowledge and skills and its acceptability, feasibility and fidelity. The Future of Nursing Report (Institute of Medicine, 2011) calls for nurses to lead change and advance health. The 6-month KNLR programme was developed by the Kansas Action Coalition to support nurses' leadership development. Nurses (n = 36) from four nursing specialties (acute care, long-term care, public health and school health) participated in the programme. The adapted Leader Knowledge and Skill Inventory was used to assess leadership knowledge and skills. Programme acceptability, feasibility and implementation fidelity also were evaluated. The programme completion rate was 67.7% (n = 24). Programme completers had significantly improved self-assessed and mentor-assessed leadership knowledge and skills (p < .05). These post-programme gains were maintained 3 months after programme completion. The KNLR programme effectively improved leadership knowledge and skills and was positively evaluated by participants. The implementation of the KNLR programme using a hybrid format of in-person sessions and online modules was feasible across four specialty areas in both rural and urban regions. The next steps include the development of an advanced programme. Residency programmes for new nurse leaders are critical for successful transition into management positions. © 2017 John Wiley & Sons Ltd.

Leaders' smiles reflect cultural differences in ideal affect.

PubMed

Tsai, Jeanne L; Ang, Jen Ying Zhen; Blevins, Elizabeth; Goernandt, Julia; Fung, Helene H; Jiang, Da; Elliott, Julian; Kölzer, Anna; Uchida, Yukiko; Lee, Yi-Chen; Lin, Yicheng; Zhang, Xiulan; Govindama, Yolande; Haddouk, Lise

2016-03-01

Cultures differ in the emotions they teach their members to value ("ideal affect"). We conducted 3 studies to examine whether leaders' smiles reflect these cultural differences in ideal affect. In Study 1, we compared the smiles of top-ranked American and Chinese government leaders, chief executive officers, and university presidents in their official photos. Consistent with findings that Americans value excitement and other high-arousal positive states more than Chinese, American top-ranked leaders (N = 98) showed more excited smiles than Chinese top-ranked leaders (N = 91) across occupations. In Study 2, we compared the smiles of winning versus losing political candidates and higher versus lower ranking chief executive officers and university presidents in the United States and Taiwan/China. American leaders (N = 223) showed more excited smiles than Taiwanese/Chinese leaders (N = 266), regardless of election outcome or ranking. In Study 3, we administered self-report measures of ideal affect in college student samples from 10 different nations (N = 1,267) and then 8 years later, coded the smiles that legislators from those nations showed in their official photos (N = 3,372). The more nations valued excitement and other high arousal positive states, the more their leaders showed excited smiles; similarly, the more nations valued calm and other low-arousal positive states, the more their leaders showed calm smiles. These results held after controlling for national differences in democratization, human development, and gross domestic product per capita. Together, these findings suggest that leaders' smiles reflect the affective states valued by their cultures. (c) 2016 APA, all rights reserved).

Leader-Member Exchange Theory in Higher and Distance Education

ERIC Educational Resources Information Center

Power, Robert Leo

2013-01-01

Unlike many other prominent leadership theories, leader-member exchange (LMX) theory does not focus on the specific characteristics of an effective organizational leader. Rather, LMX focuses on the nature and quality of the relationships between a leader and his or her individual subordinates. The ideal is for a leader to develop as many…

Dna Sequencing

DOEpatents

Tabor, Stanley; Richardson, Charles C.

1995-04-25

A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

Three Nightmare Traits in Leaders

PubMed Central

de Vries, Reinout E.

2018-01-01

This review offers an integration of dark leadership styles with dark personality traits. The core of dark leadership consists of Three Nightmare Traits (TNT)—leader dishonesty, leader disagreeableness, and leader carelessness—that are conceptualized as contextualized personality traits aligned with respectively (low) honesty-humility, (low) agreeableness, and (low) conscientiousness. It is argued that the TNT, when combined with high extraversion and low emotionality, can have serious (“explosive”) negative consequences for employees and their organizations. A Situation-Trait-Outcome Activation (STOA) model is presented in which a description is offered of situations that are attractive to TNT leaders (situation activation), situations that activate TNT traits (trait activation), and the kinds of outcomes that may result from TNT behaviors (outcome activation). Subsequently, the TNT and STOA models are combined to offer a description of the organizational actions that may strengthen or weaken the TNT during six career stages: attraction, selection, socialization, production, promotion, and attrition. Except for mainly negative consequences of the TNT, possible positive consequences of TNT leadership are also explored, and an outline of a research program is offered that may provide answers to the most pressing questions in dark leadership research. PMID:29915552

The hidden treasure in nursing leadership: informal leaders.

PubMed

Downey, Marty; Parslow, Susan; Smart, Marcia

2011-05-01

The goal of the present article was to generate awareness of characteristics of informal leaders in healthcare with the emphasis on nurses in acute care settings. There is limited research or literature regarding informal leaders in nursing and how they positively impact nursing management, the organization and, ultimately, patient care. Identification of nurses with leadership characteristics is important so that leadership development and mentoring can occur within the nursing profession. More than ever, nursing needs energetic, committed and dedicated leaders to meet the challenges of the healthcare climate and the nursing shortage. This requires nurse leaders to consider all avenues to ensure the ongoing profitability and viability of their healthcare facility. This paper discusses clinical nurses as informal leaders; characteristics of the informal nurse leader, the role they play, how they impact their unit and how they shape the organization.   Informal nurse leaders are an underutilized asset in health care. If identified early, these nurses can be developed and empowered to impact unit performance, efficiency and environmental culture in a positive manner. © 2011 The Authors. Journal compilation © 2011 Blackwell Publishing Ltd.

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

[Complete genome sequencing and analyses of rabies viruses isolated from wild animals (Chinese Ferret-Badger) in Zhejiang province].

PubMed

Lei, Yong-Liang; Wang, Xiao-Guang; Liu, Fu-Ming; Chen, Xiu-Ying; Ye, Bi-Feng; Mei, Jian-Hua; Lan, Jin-Quan; Tang, Qing

2009-08-01

Based on sequencing the full-length genomes of two Chinese Ferret-Badger, we analyzed the properties of rabies viruses genetic variation in molecular level to get information on prevalence and variation of rabies viruses in Zhejiang, and to enrich the genome database of rabies viruses street strains isolated from Chinese wildlife. Overlapped fragments were amplified by RT-PCR and full-length genomes were assembled to analyze the nucleotide and deduced protein similarities and phylogenetic analyses of the N genes from Chinese Ferret-Badger, sika deer, vole, dog. Vaccine strains were then determined. The two full-length genomes were completely sequenced to find out that they had the same genetic structure with 11 923 nts including 58 nts-Leader, 1353 nts-NP, 894 nts-PP, 609 nts-MP, 1575 nts-GP, 6386 nts-LP, and 2, 5, 5 nts- intergenic regions (IGRs), 423 nts-Pseudogene-like sequence (Psi), 70 nts-Trailer. The two full-length genomes were in accordance with the properties of Rhabdoviridae Lyssa virus by blast and multi-sequence alignment. The nucleotide and amino acid sequences among Chinese strains had the highest similarity, especially among animals of the same species. Of the two full-length genomes, the similarity in amino acid level was dramatically higher than that in nucleotide level, so that the nucleotide mutations happened in these two genomes were most probably as synonymous mutations. Compared to the referenced rabies viruses, the lengths of the five protein coding regions did not show any changes or recombination, but only with a few-point mutations. It was evident that the five proteins appeared to be stable. The variation sites and types of the two ferret badgers genomes were similar to the referenced vaccine or street strains. The two strains were genotype 1 according to the multi-sequence and phylogenetic analyses, which possessing the distinct geographyphic characteristics of China. All the evidence suggested a cue that these two ferret badgers

Transformation and Change Management for Strategic Leaders

DTIC Science & Technology

2002-04-09

TRANSFORMATION AND CHANGE MANAGEMENT FOR STRATEGIC LEADERS BY MR. KENNETH L. WRIGHT Department of the Army DISTRIBUTION STATEMENT A: Approved for Public...PROJECT TRANSFORMATION AND CHANGE MANAGEMENT FOR STRATEGIC LEADERS BY MR. KENNETH L. WRIGHT DEPARTMENT OF THE ARMY Dr. Robert M. Murphy Project Advisor The...STRATEGIC LEADERS FORMAT: Strategy Research Project DATE: 09 April 2002 PAGES: 33 CLASSIFICATION: Unclassified The objective of this work is to examine

Educators as Serving Leaders in the Classroom and on Campus

ERIC Educational Resources Information Center

Bowman, Richard

2014-01-01

Counterintuitively, the more one develops as a leader, the less of a leader one becomes. What do great leaders do? Great leaders are ambitious first and foremost for the cause, the mission, the work--not themselves. Educators as "serving leaders" sense that every action they take, together with every decision that they make, either…

RoboOligo: software for mass spectrometry data to support manual and de novo sequencing of post-transcriptionally modified ribonucleic acids

PubMed Central

Sample, Paul J.; Gaston, Kirk W.; Alfonzo, Juan D.; Limbach, Patrick A.

2015-01-01

Ribosomal ribonucleic acid (RNA), transfer RNA and other biological or synthetic RNA polymers can contain nucleotides that have been modified by the addition of chemical groups. Traditional Sanger sequencing methods cannot establish the chemical nature and sequence of these modified-nucleotide containing oligomers. Mass spectrometry (MS) has become the conventional approach for determining the nucleotide composition, modification status and sequence of modified RNAs. Modified RNAs are analyzed by MS using collision-induced dissociation tandem mass spectrometry (CID MS/MS), which produces a complex dataset of oligomeric fragments that must be interpreted to identify and place modified nucleosides within the RNA sequence. Here we report the development of RoboOligo, an interactive software program for the robust analysis of data generated by CID MS/MS of RNA oligomers. There are three main functions of RoboOligo: (i) automated de novo sequencing via the local search paradigm. (ii) Manual sequencing with real-time spectrum labeling and cumulative intensity scoring. (iii) A hybrid approach, coined ‘variable sequencing’, which combines the user intuition of manual sequencing with the high-throughput sampling of automated de novo sequencing. PMID:25820423

Facilitating social support: member-leader communication in a breast cancer support group.

PubMed

Beck, Stephenson J; Keyton, Joann

2014-01-01

Early detection and treatment have resulted in more women surviving breast cancer; increased survivorship has also increased the need for breast cancer support groups (BCSG). The ostensible goal of such groups is to provide support for the physical and emotional stressors that cancer survivors face, as well as provide information on coping and treatment options. Although scholars have examined the effects of support groups on their group members, the examination of group facilitator messages has been largely neglected. The goal of this study was to extend theory on group leader behavior, specifically investigating how member-leader messages create social support in support groups. The transcribed conversations of weekly meetings of a BCSG were examined using Interaction Process Analysis to discover how the member-leader facilitated the group's enactment and management of social support. Across the meetings, task talk dominated (primarily statements of orientation or information). Furthermore, analysis of interaction sequences between the support group facilitator and other members revealed 2 broad categories of task-oriented facilitation techniques (changing the focus, clarification) and 1 category of socioemotional facilitation techniques (showing support). Support group facilitators need the ability to facilitate both task and relational aspects of social support. Facilitator behaviors were highlighted as being instrumental to the creation of social support. The results from this study indicate that the ability to change the focus of interaction, to provide and require clarification on complex issues, and to show support through relational messages is needed in facilitator training.

TaALMT1 promoter sequence compositions, acid tolerance, and Al tolerance in wheat cultivars and landraces from Sichuan in China.

PubMed

Han, C; Dai, S F; Liu, D C; Pu, Z J; Wei, Y M; Zheng, Y L; Wen, D J; Zhao, L; Yan, Z H

2013-11-18

Previous genetic studies on wheat from various sources have indicated that aluminum (Al) tolerance may have originated independently in USA, Brazil, and China. Here, TaALMT1 promoter sequences of 92 landraces and cultivars from Sichuan, China, were sequenced. Five promoter types (I', II, III, IV, and V) were observed in 39 cultivars, and only three promoter types (I, II, and III) were observed in 53 landraces. Among the wheat collections worldwide, only the Chinese Spring (CS) landrace native to Sichuan, China, carried the TaALMT1 promoter type III. Besides CS, two other Sichuan-bred landraces and six cultivars with TaALMT1 promoter type III were identified in this study. In the phylogenetic tree constructed based on the TaALMT1 promoter sequences, type III formed a separate branch, which was supported by a high bootstrap value. It is likely that TaALMT1 promoter type III originated from Sichuan-bred wheat landraces of China. In addition, the landraces with promoter type I showed the lowest Al tolerance among all landraces and cultivars. Furthermore, the cultivars with promoter type IV showed better Al tolerance than landraces with promoter type II. A comparison of acid tolerance and Al tolerance between cultivars and landraces showed that the landraces had better acid tolerance than the cultivars, whereas the cultivars showed better Al tolerance than the landraces. Moreover, significant difference in Al tolerance was also observed between the cultivars raised by the National Ministry of Agriculture and by Sichuan Province. Among the landraces from different regions, those from the East showed better acid tolerance and Al tolerance than those from the South and West of Sichuan. Additional Al-tolerant and acid-tolerant wheat lines were also identified.

Complete amino acid sequences of the ribosomal proteins L25, L29 and L31 from the archaebacterium Halobacterium marismortui.

PubMed

Hatakeyama, T; Kimura, M

1988-03-15

Ribosomal proteins were extracted from 50S ribosomal subunits of the archaebacterium Halobacterium marismortui by decreasing the concentration of Mg2+ and K+, and the proteins were separated and purified by ion-exchange column chromatography on DEAE-cellulose. Ten proteins were purified to homogeneity and three of these proteins were subjected to sequence analysis. The complete amino acid sequences of the ribosomal proteins L25, L29 and L31 were established by analyses of the peptides obtained by enzymatic digestion with trypsin, Staphylococcus aureus protease, chymotrypsin and lysylendopeptidase. Proteins L25, L29 and L31 consist of 84, 115 and 95 amino acid residues with the molecular masses of 9472 Da, 12293 Da and 10418 Da respectively. A comparison of their sequences with those of other large-ribosomal-subunit proteins from other organisms revealed that protein L25 from H. marismortui is homologous to protein L23 from Escherichia coli (34.6%), Bacillus stearothermophilus (41.8%), and tobacco chloroplasts (16.3%) as well as to protein L25 from yeast (38.0%). Proteins L29 and L31 do not appear to be homologous to any other ribosomal proteins whose structures are so far known.

Healthcare Leaders' Intention to Serve as Organizational Teachers

ERIC Educational Resources Information Center

Aggarwal, Sushma Kumari

2014-01-01

Today's organizational leaders are expected to actively participate and facilitate learning. A highly engaged and knowledgeable workforce, inspired by leaders, may increase the quality of service, and aid in maintaining and attracting loyal employees and customers. These leaders are now being asked to serve as organizational teachers. However,…

Inspiring and Equipping Students to Be Ethical Leaders.

PubMed

Schwartz, Arthur J

2015-01-01

This chapter describes the behaviors of the ethical leader and explores the reasons why leaders do not always act ethically. The chapter also offers five recommendations to help educators integrate the practices of ethical leadership into their work with student leaders. © 2015 Wiley Periodicals, Inc., A Wiley Company.

School Leader Succession: A Description of Transitional Experiences

ERIC Educational Resources Information Center

Zimmerman, Judith A.

2007-01-01

This qualitative case study describes the transitional experiences (first 4 1/2 months) of four school leaders. The "life cycle" of leaders is often short, necessitating job changes with resulting transitions, when new leaders must simultaneously learn their positions and make changes to improve schools. Using previous leadership…

Health Professions Education Scholarship Unit Leaders as Institutional Entrepreneurs.

PubMed

Varpio, Lara; O'Brien, Bridget; J Durning, Steven; van der Vleuten, Cees; Gruppen, Larry; Ten Cate, Olle; Humphrey-Murto, Susan; Irby, David M; Hamstra, Stanley J; Hu, Wendy

2017-08-01

Health professions education scholarship units (HPESUs) are organizational structures within which a group is substantively engaged in health professions education scholarship. Little research investigates the strategies employed by HPESU administrative leaders to secure and maintain HPESU success. Using institutional entrepreneurship as a theoretical lens, this study asks: Do HPESU administrative leaders act as institutional entrepreneurs (IEs)? This study recontextualizes two preexisting qualitative datasets that comprised interviews with leaders in health professions education in Canada (2011-2012) and Australia and New Zealand (2013-1014). Two researchers iteratively analyzed the data using the institutional entrepreneurship construct until consensus was achieved. A third investigator independently reviewed and contributed to the recontextualized analyses. A summary of the analyses was shared with all authors, and their feedback was incorporated into the final interpretations. HPESU leaders act as IEs in three ways. First, HPESU leaders construct arguments and position statements about how the HPESU resolves an institution's problem(s). This theorization discourse justifies the existence and support of the HPESU. Second, the leaders strategically cultivate relationships with the leader of the institution within which the HPESU sits, the leaders of large academic groups with which the HPESU partners, and the clinician educators who want careers in health professions education. Third, the leaders work to increase the local visibility of the HPESU. Practical insights into how institutional leaders interested in launching an HPESU can harness these findings are discussed.

Role congruity theory of prejudice toward female leaders.

PubMed

Eagly, Alice H; Karau, Steven J

2002-07-01

A role congruity theory of prejudice toward female leaders proposes that perceived incongruity between the female gender role and leadership roles leads to 2 forms of prejudice: (a) perceiving women less favorably than men as potential occupants of leadership roles and (b) evaluating behavior that fulfills the prescriptions of a leader role less favorably when it is enacted by a woman. One consequence is that attitudes are less positive toward female than male leaders and potential leaders. Other consequences are that it is more difficult for women to become leaders and to achieve success in leadership roles. Evidence from varied research paradigms substantiates that these consequences occur, especially in situations that heighten perceptions of incongruity between the female gender role and leadership roles.

Structural positioning of nurse leaders and empowerment.

PubMed

Hughes, Kerri-Ann; Carryer, Jennifer Barbara; White, Jill

2015-08-01

To analyse the reporting structures of nursing leaders of publicly funded hospitals and seek both the views of nurse leaders and Chief Executive Officers/Chief Operating Officers on the structural positioning of nurse leaders in the organisation. Concern that the continuing restructuring within hospital structures and focus on economic outputs in health services is diminishing the value of nursing leadership. Qualitative surveys with Nursing leaders and Chief Executive Officers of public hospitals. Seventeen Directors of Nursing and 10 Chief Executive Officer/Chief Operating Officers' responses were received using two semi-structured questionnaires. Themes were developed from data coded and analysed by hand. Four broad themes emerged from analysis of the data: (1) variable positional reporting between Director of Nursing and Chief Executive Officers occurred; (2) variable levels of inclusion and influence at the executive decision-making level; (3) ambiguous financial responsibilities and accountabilities held by Director of Nursing; and (4) blurred lines existed between operational and professional reporting lines. Findings unique to the research indicate that the varying levels of visibility and inclusion impact on the structural positioning of nurse leaders which influences authority and empowerment. Responses from the data analysis indicate that the structural power of nurse leaders defined by the factors of opportunity, power and proportion were hindered by dual accountability reporting lines and a lack of financial control. The structural positioning of nurse leaders is vital to ensure that they are empowered and able to meet the adaptations required in a changing environment that supports the delivery of effective, quality healthcare. © 2015 John Wiley & Sons Ltd.

Christian School Leaders and Spirituality: A Phenomenological Study

ERIC Educational Resources Information Center

Banke, Susan; Maldonado, Nancy; Lacey, Candace H.

2011-01-01

This phenomenological study examined the spiritual experiences of Christian school leaders who are the spiritual leaders of their schools. A purposeful, nominated sample of 12 Christian school leaders was selected. In-depth, open-ended interviews were conducted, audio taped, and then transcribed verbatim. Data analysis was based on Rudestam and…

The Preparation of Inclusive Social Justice Education Leaders

ERIC Educational Resources Information Center

Celoria, Davide

2016-01-01

This article is intended to spark dialogue and debate related to the preparation of inclusive social justice education leaders in a time of colorblindness. Drawing attention to the reductionist construction of the professional standards for educational leaders when it comes to preparing educational leaders who are ready to address and eliminate…

Teacher Leadership: District and School Leader Readiness Tool

ERIC Educational Resources Information Center

American Institutes for Research, 2017

2017-01-01

As interest in teacher leadership has grown, many leading organizations have developed tools and guidance to support schools, districts, and teacher leaders themselves. For instance, the National Network of State Teachers of the Year developed resources on teacher leader career pathways and advocacy approaches, as well as teacher leader standards.…

Selection Practices of Group Leaders: A National Survey.

ERIC Educational Resources Information Center

Riva, Maria T.; Lippert, Laurel; Tackett, M. Jan

2000-01-01

Study surveys the selection practices of group leaders. Explores methods of selection, variables used to make selection decisions, and the types of selection errors that leaders have experienced. Results suggest that group leaders use clinical judgment to make selection decisions and endorse using some specific variables in selection. (Contains 22…

School Leaders' Problem Framing: A Sense-Making Approach to Problem-Solving Processes of Beginning School Leaders

ERIC Educational Resources Information Center

Sleegers, Peter; Wassink, Hartger; van Veen, Klaas; Imants, Jeroen

2009-01-01

In addition to cognitive research on school leaders' problem solving, this study focuses on the situated and personal nature of problem framing by combining insights from cognitive research on problem solving and sense-making theory. The study reports the results of a case study of two school leaders solving problems in their daily context by…

In praise of the incomplete leader.

PubMed

Ancona, Deborah; Malone, Thomas W; Orlikowski, Wanda J; Senge, Peter M

2007-02-01

Today's top executives are expected to do everything right, from coming up with solutions to unfathomably complex problems to having the charisma and prescience to rally stakeholders around a perfect vision of the future. But no one leader can be all things to all people. It's time to end the myth of the complete leader, say the authors. Those at the top must come to understand their weaknesses as well as their strengths. Only by embracing the ways in which they are incomplete can leaders fill in the gaps in their knowledge with others' skills. The incomplete leader has the confidence and humility to recognize unique talents and perspectives throughout the organization--and to let those qualities shine. The authors' work studying leadership over the past six years has led them to develop a framework of distributed leadership. Within that model, leadership consists of four capabilities: sensemaking, relating, "visioning," and inventing. Sensemaking involves understanding and mapping the context in which a company and its people operate. A leader skilled in this area can quickly identify the complexities of a given situation and explain them to others. The second capability, relating, means being able to build trusting relationships with others through inquiring (listening with intention), advocating (explaining one's own point of view), and connecting (establishing a network of allies who can help a leader accomplish his or her goals). Visioning, the third capability, means coming up with a compelling image of the future. It is a collaborative process that articulates what the members of an organization want to create. Finally, inventing involves developing new ways to bring that vision to life. Rarely will a single person be skilled in all four areas. That's why it's critical that leaders find others who can offset their limitations and complement their strengths. Those who don't will not only bear the burden of leadership alone but will find themselves at the helm

Assignment of fatty acid-beta-oxidizing syntrophic bacteria to Syntrophomonadaceae fam. nov. on the basis of 16S rRNA sequence analyses

NASA Technical Reports Server (NTRS)

Zhao, H.; Yang, D.; Woese, C. R.; Bryant, M. P.

1993-01-01

After enrichment from Chinese rural anaerobic digestor sludge, anaerobic, sporing and nonsporing, saturated fatty acid-beta-oxidizing syntrophic bacteria were isolated as cocultures with H2- and formate-utilizing Methanospirillum hungatei or Desulfovibrio sp. strain G-11. The syntrophs degraded C4 to C8 saturated fatty acids, including isobutyrate and 2-methylbutyrate. They were adapted to grow on crotonate and were isolated as pure cultures. The crotonate-grown pure cultures alone did not grow on butyrate in either the presence or the absence of some common electron acceptors. However, when they were reconstituted with M. hungatei, growth on butyrate again occurred. In contrast, crotonate-grown Clostridium kluyveri and Clostridium sticklandii, as well as Clostridium sporogenes, failed to grow on butyrate when these organisms were cocultured with M. hungatei. The crotonate-grown pure subcultures of the syntrophs described above were subjected to 16S rRNA sequence analysis. Several previously documented fatty acid-beta-oxidizing syntrophs grown in pure cultures with crotonate were also subjected to comparative sequence analyses. The sequence analyses revealed that the new sporing and nonsporing isolates and other syntrophs that we sequenced, which had either gram-negative or gram-positive cell wall ultrastructure, all belonged to the phylogenetically gram-positive phylum. They were not closely related to any of the previously known subdivisions in the gram-positive phylum with which they were compared, but were closely related to each other, forming a new subdivision in the phylum. We recommend that this group be designated Syntrophomonadaceae fam. nov.; a description is given.

Corona discharges and their effect on lightning attachment revisited: Upward leader initiation and downward leader interception

NASA Astrophysics Data System (ADS)

Becerra, Marley

2014-11-01

Previous studies have suggested the possibility of using glow corona discharges to control the frequency of lightning flashes to grounded objects. In order to revisit the theoretical basis of this proposal, the self-consistent leader inception and propagation model - SLIM - is used together with a two-dimensional glow corona drift model. The analysis is performed to quantify the effect of glow corona generated at the tip of ground-based objects on the initiation and propagation of upward positive connecting leaders under the influence of downward lightning leaders. It is found that the presence of glow corona does not influence the performance of Franklin lightning rods shorter than 15 m, while it slightly reduces the lateral distance of rods up to 60 m tall by a maximum of 10%. Furthermore, the results indicate that it is not possible to suppress the initiation of upward connecting leaders by means of glow corona. It is found instead that unconventional lightning protection systems based on the generation of glow corona attract downward lightning flashes in a similar way as a standard lightning rod with the same height.

Mitigating PTSD: Emotionally Intelligent Leaders

DTIC Science & Technology

2010-05-28

lower ranking, less educated members, those who had experienced childhood adversity, and who were single, separated or divorced .10 The number of...Pr og ra m R es ea rc h Pr oj ec t MITIGATING PTSD: EMOTIONALLY INTELLIGENT LEADERS BY COLONEL RAMONA M. FIOREY United States Army...COVERED (From - To) 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Mitigating PTSD: Emotionally Intelligent Leaders 5b. GRANT NUMBER

Exploring nurse leader fatigue: a mixed methods study.

PubMed

Steege, Linsey M; Pinekenstein, Barbara J; Arsenault Knudsen, Élise; Rainbow, Jessica G

2017-05-01

To describe hospital nurse leaders' experiences of fatigue. Fatigue is a critical challenge in nursing. Existing literature focuses on staff nurse fatigue, yet nurse leaders are exposed to high demands that may contribute to fatigue and associated risks to patient, nurse and organisational outcomes. A mixed method approach comprising semi-structured interviews and the Occupational Fatigue Exhaustion Recovery scale with 21 nurse administrators (10 nurse managers and 11 nurse executives) from hospitals in a Midwestern state. Most nurse leaders experience fatigue; nurse managers reported higher levels of chronic fatigue. Participants identified multiple sources of fatigue including 24 h accountability and intensity of role expectations, and used a combination of wellness, restorative, social support and boundary setting strategies to cope with fatigue. The consequences of nurse leader fatigue include an impact on decision-making, work-life balance and turnover intent. The high prevalence of nurse leader fatigue could impact the turnover intent of nurse administrators and quality of care. This study highlights the significance and consequences of nurse leader fatigue. As health care organisations continue to raise awareness and establish systems to reduce nurse fatigue, policies and programmes must be adapted to address nurse leader fatigue. © 2017 John Wiley & Sons Ltd.

An improved TCF sequence for biobleaching kenaf pulp: influence of the hexenuronic acid content and the use of xylanase.

PubMed

Andreu, Glòria; Vidal, Teresa

2014-01-01

Enzymatic delignification with laccase from Trametes villosa used in combination with chemical mediators (acetosyringone, acetovanillone and 1-hydroxybenzotriazole) to improve the totally chlorine-free (TCF) bleaching of kenaf pulp was studied. The best final pulp properties were obtained by using an LHBTQPo sequence developed by incorporating a laccase-mediator stage into an industrial bleaching sequence involving chelation and peroxide stages. The new sequence resulted in increased kenaf pulp delignification (90.4%) and brightness (77.2%ISO) relative to a conventional TCF chemical sequence (74.5% delignification and 74.5% brightness). Also, the sequence provided bleached kenaf fibers with high cellulose content (pulp viscosity of 890 g·mL(-1) vs 660 g·mL(-1)). Scanning electron micrographs revealed that xylanase altered fiber surfaces and facilitated reagent access as a result. However, the LHBTX (xylanase) stage removed 21% of hexenuronic acids in kenaf pulp. These recalcitrant compounds spent additional bleaching reagents and affected pulp properties after peroxide stage. Copyright © 2013 Elsevier Ltd. All rights reserved.

Vermont Guidelines for Teacher & Leader Effectiveness

ERIC Educational Resources Information Center

Vermont Department of Education, 2012

2012-01-01

In March 2011, the State of Vermont Department of Education charged the Vermont Task Force on Teacher & Leader Effectiveness to develop guidelines for teacher and leader evaluation. Knowing and respecting the fiercely independent nature of Vermonters, Task Force members were committed to developing these guidelines for creating and assessing…

Interprofessional Care and Role of Team Leaders.

PubMed

Kaini, B K

2015-01-01

Interprofessional care is an essential part of the health service delivery system. It helps to achieve improved care and to deliver the optimal and desired health outcomes by working together, sharing and learning skills. Health care organisation is a collective sum of many leaders and followers. Successful delivery of interprofessional care relies on the contribution of interprofessional care team leaders and health care professionals from all groups. The role of the interprofessional care team leader is vital to ensuring continuity and consistency of care and to mobilise and motivate health care professionals for the effective delivery of health services. Medical professionals usually lead interprofessional care teams. Interprofessional care leaders require various skills and competencies for the successful delivery of interprofessional care.

Developing Army Leaders for 21st Century Missions: Teaching Army Leaders Behavioral Science Theories to Educate and Prepare for Full Spectrum Operations

DTIC Science & Technology

2002-07-01

reckoned with and one that is likely to succeed. Leaders who effectively motivate their soldiers inspire , encourage, and guide them toward mission...Virginia 22134-5068 MASTER OF MILITARY STUDIES Developing Army Leaders for 21st Century Missions: Teaching Army Leaders Behavioral Science Theories to...REPORT TYPE Student research paper 3. DATES COVERED (FROM - TO) xx-xx-2001 to xx-xx-2002 4. TITLE AND SUBTITLE Developing Army Leaders for 21st Century

The role of leaders' working alliance in premarital education.

PubMed

Owen, Jesse J; Rhoades, Galena K; Stanley, Scott M; Markman, Howard J

2011-02-01

Premarital (and general relationship) education programs, as a prevention method, have been shown to have a positive effect on marital quality and can prevent divorce. However, it is unclear whether these positive effects are consistent across leaders who conduct premarital education programs. Examining the variability in relationship outcomes attributed to the leaders of premarital education programs, and the role of general therapeutic factors such as working alliance in explaining relationship outcomes, may help increase the effectiveness of these programs. Accordingly, this study examined 31 leaders who trained 118 couples (236 attendees) in a randomized clinical trial of the Prevention and Relationship Enhancement Program (PREP), a research-based and empirically supported premarital education program being compared with a treatment as usual track. The results demonstrated that couples' relationship outcomes from pre- to post-training varied on the basis of the leader who provided the premarital education training. Both training in PREP and aggregated leader working alliance quality (as rated by attendees) explained variability between leaders in change in attendees' observed negative and positive communication. Leaders' aggregated working alliance quality also explained change in relationship satisfaction. In addition, attendees' ratings of their leaders' working alliance predicted change in their relationship satisfaction and confidence, and attendees had higher positive communication when they reported better working alliance with their leader. PsycINFO Database Record (c) 2011 APA, all rights reserved.

Teaching Leaders

ERIC Educational Resources Information Center

DeAngelis, Lisa; Penney, Sherry

2015-01-01

In an age of instantaneous information sharing and increased interdependence, today's leaders must learn to work collaboratively, leveraging the strengths, skills, and experiences of those around them, in order to address the challenges they face. The Center for Collaborative Leadership is uniquely situated in the College of Management at the…

Ethical Practice: A Study of Chilean School Leaders

ERIC Educational Resources Information Center

Cuellar, Carolina; Giles, David L.

2012-01-01

Purpose: This article seeks to report on a research inquiry that explored the educational praxis of ethical school leaders in Chile. Behaving ethically is an imperative for school leaders. Being an ethical educational leader is something different. It is not only about behaving according to standards, but also rather involves an ethical way of…

[Sequencing and analysis of complete genome of rabies viruses isolated from Chinese Ferret-Badger and dog in Zhejiang province].

PubMed

Lei, Yong-Liang; Wang, Xiao-Guang; Tao, Xiao-Yan; Li, Hao; Meng, Sheng-Li; Chen, Xiu-Ying; Liu, Fu-Ming; Ye, Bi-Feng; Tang, Qing

2010-01-01

Based on sequencing the full-length genomes of four Chinese Ferret-Badger and dog, we analyze the properties of rabies viruses genetic variation in molecular level, get the information about rabies viruses prevalence and variation in Zhejiang, and enrich the genome database of rabies viruses street strains isolated from China. Rabies viruses in suckling mice were isolated, overlapped fragments were amplified by RT-PCR and full-length genomes were assembled to analyze the nucleotide and deduced protein similarities and phylogenetic analyses from Chinese Ferret-Badger, dog, sika deer, vole, used vaccine strain were determined. The four full-length genomes were sequenced completely and had the same genetic structure with the length of 11, 923 nts or 11, 925 nts including 58 nts-Leader, 1353 nts-NP, 894 nts-PP, 609 nts-MP, 1575 nts-GP, 6386 nts-LP, and 2, 5, 5 nts- intergenic regions(IGRs), 423 nts-Pseudogene-like sequence (psi), 70 nts-Trailer. The four full-length genomes were in accordance with the properties of Rhabdoviridae Lyssa virus by BLAST and multi-sequence alignment. The nucleotide and amino acid sequences among Chinese strains had the highest similarity, especially among animals of the same species. Of the four full-length genomes, the similarity in amino acid level was dramatically higher than that in nucleotide level, so the nucleotide mutations happened in these four genomes were most synonymous mutations. Compared with the reference rabies viruses, the lengths of the five protein coding regions had no change, no recombination, only with a few point mutations. It was evident that the five proteins appeared to be stable. The variation sites and types of the four genomes were similar to the reference vaccine or street strains. And the four strains were genotype 1 according to the multi-sequence and phylogenetic analyses, which possessed the distinct district characteristics of China. Therefore, these four rabies viruses are likely to be street viruses

Cross-cultural comparison of political leaders' operational codes.

PubMed

Dirilen-Gumus, Ozlem

2017-12-01

This study aims at comparing operational codes (namely, philosophical and instrumental beliefs about the political universe) of political leaders from different cultures. According to Schwartz (2004), cultures can be categorised into 3 dimensions: autonomy-embeddedness, egalitarianism-hierarchy and mastery-harmony. This study draws upon the 1st dimension (akin to the most popular cultural dimension of Hofstede: individualism-collectivism) and focuses on comparing the leaders of autonomous and embedded cultures based on how cooperative/conflictual they are. The main research hypothesis is as follows: the leaders of embedded cultures would be more cooperative than the leaders of autonomous cultures. For this purpose, 3 autonomous cultures (the UK, Canada and Australia) and embedded cultures (Singapore, South Africa and Malaysia) cultures were chosen randomly and the cooperativeness of the correspondent countries' leaders were compared after being profiled by Profiler Plus. The results indicated that the leaders of embedded cultures were significantly more cooperative than autonomous cultures after holding the control variables constant. The findings were discussed in the light of relevant literature. © 2016 International Union of Psychological Science.

Rise of an alternative majority against opinion leaders

NASA Astrophysics Data System (ADS)

Tucci, K.; González-Avella, J. C.; Cosenza, M. G.

2016-03-01

We investigate the role of opinion leaders or influentials in the collective behavior of a social system. Opinion leaders are characterized by their unidirectional influence on other agents. We employ a model based on Axelrod's dynamics for cultural interaction among social agents that allows for non-interacting states. We find three collective phases in the space of parameters of the system, given by the fraction of opinion leaders and a quantity representing the number of available states: one ordered phase having the state imposed by the leaders; another nontrivial ordered phase consisting of a majority group in a state orthogonal or alternative to that of the opinion leaders, and a disordered phase, where many small groups coexist. We show that the spontaneous rise of an alternative group in the presence of opinion leaders depends on the existence of a minimum number of long-range connections in the underlying network. This phenomenon challenges the common idea that influentials are fundamental to propagation processes in society, such as the formation of public opinion.

Educating Native Students: Inspiring Future Leaders.

ERIC Educational Resources Information Center

Lee, Tiffany

2003-01-01

A 7-week summer program for college-bound American Indian students prepares them for college and trains them to become leaders. Through role playing a fictitious Native tribe, students encounter realistic dilemmas similar to those facing tribal governments and realize that tribal leaders' decisions involve many social and political issues…

The Called, Chosen, and Faithful Leader

ERIC Educational Resources Information Center

Davis, Hartwell T. Paul

2009-01-01

Leaders are made, not born. Like so many other of life's complex issues, the question of nature vs. nurture in leadership is one that is analyzed, researched, and debated by educators, philosophers, social scientist, and even leaders themselves. Leadership has been dissected as to personality, character, and behavior. Researchers have developed…

Human somatostatin I: sequence of the cDNA.

PubMed Central

Shen, L P; Pictet, R L; Rutter, W J

1982-01-01

RNA has been isolated from a human pancreatic somatostatinoma and used to prepare a cDNA library. After prescreening, clones containing somatostatin I sequences were identified by hybridization with an anglerfish somatostatin I-cloned cDNA probe. From the nucleotide sequence of two of these clones, we have deduced an essentially full-length mRNA sequence, including the preprosomatostatin coding region, 105 nucleotides from the 5' untranslated region and the complete 150-nucleotide 3' untranslated region. The coding region predicts a 116-amino acid precursor protein (Mr, 12.727) that contains somatostatin-14 and -28 at its COOH terminus. The predicted amino acid sequence of human somatostatin-28 is identical to that of somatostatin-28 isolated from the porcine and ovine species. A comparison of the amino acid sequences of human and anglerfish preprosomatostatin I indicated that the COOH-terminal region encoding somatostatin-14 and the adjacent 6 amino acids are highly conserved, whereas the remainder of the molecule, including the signal peptide region, is more divergent. However, many of the amino acid differences found in the pro region of the human and anglerfish proteins are conservative changes. This suggests that the propeptides have a similar secondary structure, which in turn may imply a biological function for this region of the molecule. Images PMID:6126875

Commander’s Handbook for Unit Leader Development

DTIC Science & Technology

2007-07-02

Transforming Organizations: Growing Leaders for Tomorrow. Mahwah, NJ: Lawrence Erlbaum Associates. Kolb , D. (1984). Experiential learning : Experiences...development tools, job aides, or other on-the-job leader development interventions. Implicitly, the handbook employs adult learning theory to engage...most effective and efficient methods of leader development for a unit environment. Principles of adult learning theory were then applied to

A Single Electrochemical Probe Used for Analysis of Multiple Nucleic Acid Sequences

PubMed Central

Mills, Dawn M.; Calvo-Marzal, Percy; Pinzon, Jeffer M.; Armas, Stephanie; Kolpashchikov, Dmitry M.; Chumbimuni-Torres, Karin Y.

2017-01-01

Electrochemical hybridization sensors have been explored extensively for analysis of specific nucleic acids. However, commercialization of the platform is hindered by the need for attachment of separate oligonucleotide probes complementary to a RNA or DNA target to an electrode’s surface. Here we demonstrate that a single probe can be used to analyze several nucleic acid targets with high selectivity and low cost. The universal electrochemical four-way junction (4J)-forming (UE4J) sensor consists of a universal DNA stem-loop (USL) probe attached to the electrode’s surface and two adaptor strands (m and f) which hybridize to the USL probe and the analyte to form a 4J associate. The m adaptor strand was conjugated with a methylene blue redox marker for signal ON sensing and monitored using square wave voltammetry. We demonstrated that a single sensor can be used for detection of several different DNA/RNA sequences and can be regenerated in 30 seconds by a simple water rinse. The UE4J sensor enables a high selectivity by recognition of a single base substitution, even at room temperature. The UE4J sensor opens a venue for a re-useable universal platform that can be adopted at low cost for the analysis of DNA or RNA targets. PMID:29371782

Sowing Seeds to Cultivate Future Army Leaders

DTIC Science & Technology

2010-11-01

and can operate successfully in Sowing Seeds to Cultivate Future Army Leaders Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting...TITLE AND SUBTITLE Sowing Seeds to Cultivate Future Army Leaders 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) 5d...month will not de- velop the next Army Chief of Staff, it is imperative to plant the seeds of new ideas and concepts early into our ju- nior leaders

Leaders' mental health at work: Empirical, methodological, and policy directions.

PubMed

Barling, Julian; Cloutier, Anika

2017-07-01

While employees' mental health is the focus of considerable attention from researchers, the public, and policymakers, leaders' mental health has almost escaped attention. We start by considering several reasons for this, followed by discussions of the effects of leaders' mental health on their own leadership behaviors, the emotional toll of high-quality leadership, and interventions to enhance leaders' mental health. We offer 8 possible directions for future research on leaders' mental health. Finally, we discuss methodological obstacles encountered when investigating leaders' mental health, and policy dilemmas raised by leaders' mental health. (PsycINFO Database Record (c) 2017 APA, all rights reserved).