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PubMed2000

An ecological approach to planning dysfunction: script execution.

Planning, which concerns many activities in everyday life, is a two-stage process. The first one predetermines a course of actions aimed at achieving some specific goals. It is founded on managerial knowledge or overlearned sequences of events and may be tested by script generation. The second stage entails monitoring and guiding the execution of the plan to a successful conclusion. It must take into account environmental contingencies and may be tested by script execution. If the frontal lobes intervene not only in managerial knowledge (Grafman, 1989) but also in binding the plan with contextual environment (Damasio, Tranel and Damasio, 1991; Shallice and Burgess, 1991), script execution would be more sensitive than script generation to planning deficits. To test this hypothesis, script execution and script generation were compared in 11 patients with a dysexecutive syndrome and 10 matched controls, using three scripts of daily life activities: (1) 'shopping for groceries'; (2) 'cooking'; (3) 'answering a letter and finding the way to post the reply'. Two way ANOVAs showed more errors in execution than in generation, more errors in patients than in controls, and a greater difference between execution and generation in patients than in controls. Furthermore, 'context neglect' and 'environmental adherence' were the two types of errors that best differentiated patients from controls. Finally, the total number of errors in execution correlated with the score on behavioral questionnaires answered by occupational therapists. These results confirm our hypothesis and suggest that script execution may be a valid ecological approach to estimate the severity of deficits in daily life activities.

Activities of Daily Living↗
PubMed2003

Cryptic species and morphological plasticity in long-lived bivalves (Unionoida: Hyriidae) from inland Australia.

Molecular (mitochondrial DNA, isozyme) and morphological diversity of freshwater mussels (Family Hyriidae) was examined at 21 sites encompassing four large river systems, across southwest Queensland, Australia. Evidence was found for two major morphological groups. One group, which occurred in every river system, closely matched a recognized species (Velesunio ambiguus) both morphologically and in a well-supported lineage within a mitochondrial phylogeny generated from partial cytochrome c oxidase subunit I (COI) sequences. The second group most closely matched Velesunio wilsonii in shell morphology but formed three deeply divergent mitochondrial DNA lineages. All four lineages occurred sympatrically in some areas and displayed corresponding fixed differences at nuclear allozyme loci, which suggests an absence of recent hybridization and the presence of separate species.

Animals↗
PubMed2000

Transmission of the human mitochondrial genome.

The segregation and transmission of mitochondrial genomes in humans are complicated processes, but are particularly important for understanding the inheritance and clinical abnormalities of mitochondrial disorders. This review describes three aspects of mitochondrial genetics. First, that the segregation and transmission of mitochondrial (mt)DNA molecules are likely to be determined by their physical association within the organelles and by the dynamics of mitochondrial structure and subcellular organization. Second, that the transmission of heteroplasmic mtDNA sequence changes from one generation to the next often involves rapid shifts in allele frequency. For >20 years, the standard explanation has been that there is a developmental bottleneck in which, at some stage of oogenesis, there is a reduction in the effective number of mitochondrial units of inheritance. The third aspect is that ongoing analyses of the segregation and transmission of pathogenic mtDNA mutations indicate the operation of multiple genetic processes. Thus, the segregation and transmission of mtDNA mutations occurs predominantly, but not exclusively, under conditions of random genetic drift. However, there is also evidence for bias due to incomplete ascertainment of pedigrees and for negative selection of pathogenic mutations in rapidly dividing somatic tissues such as the white blood cell population.

Chromosome Segregation↗
PubMed2003

Temporal and spatiotemporal coherence in simple-cell responses: a generative model of natural image sequences.

We present a two-layer dynamic generative model of the statistical structure of natural image sequences. The second layer of the model is a linear mapping from simple-cell outputs to pixel values, as in most work on natural image statistics. The first layer models the dependencies of the activity levels (amplitudes or variances) of the simple cells, using a multivariate autoregressive model. The second layer shows the emergence of basis vectors that are localized, oriented and have different scales, just like in previous work. But in our new model, the first layer learns connections between the simple cells that are similar to complex cell pooling: connections are strong among cells with similar preferred location, frequency and orientation. In contrast to previous work in which one of the layers needed to be fixed in advance, the dynamic model enables us to estimate both of the layers simultaneously from natural data.

Models, Neurological↗
PubMed1992

Association of Fyn with the activated platelet-derived growth factor receptor: requirements for binding and phosphorylation.

Three members of the Src family of tyrosine kinases [pp60c-src (Src), p59fyn (Fyn) and pp62c-yes (Yes)] are ubiquitously expressed, and are thus likely to have general roles in growth control. We have previously shown that, after addition of platelet-derived growth factor (PDGF) to quiescent cells, all three kinases become activated and associated with the PDGF receptor. We have now addressed the requirements for this association. First, we have used a baculovirus expression system to show that Fyn associates with the activated PDGF receptor in vitro in the absence of other proteins, demonstrating that the association between the two molecules is direct. Second, by generating cell lines expressing chimeric molecules consisting of Fyn sequences fused to a portion of beta-galactosidase, we found that the SH2 domain of Fyn is necessary for ligand-stimulated association with the PDGF receptor in vivo. Third, those fusion proteins that associated with the PDGF receptor also became phosphorylated in vivo following PDGF treatment, and in in vitro kinase assays, suggesting that the amino-terminal half of Fyn contains the sites of PDGF-stimulated phosphorylation. Partially purified, kinase-negative Fyn also became phosphorylated in the activated PDGF receptor complex in vitro, demonstrating that the PDGF receptor phosphorylates Fyn, rather than the novel phosphorylations occurring by autophosphorylation.

Base Sequence↗
PubMed1994

Structural features of the bradykinin receptor as determined by computer simulations, mutagenesis experiments, and conformationally constrained ligands: establishing the framework for the design of new antagonists.

1. In recent years, two classes of second generation bradykinin receptor antagonists have been reported. Both are of the general sequence D-Arg0-Arg1-Pro2-W3-Gly4-X5-Ser6-Y7-Z8+ ++-Arg9, where W is either Pro or Hyp, and X is an aromatic or aliphatic side chain-containing amino acid. Y and Z are unnatural amino acids, presumed to enforce a beta-turn structure. The de novo design of a non-peptide receptor antagonist (or the optimization of a lead discovered by random screening) will ultimately require knowledge about the receptor topology. In the absence of an experimentally determined structure of the bradykinin-bradykinin receptor complex, we have attempted to gain insights from other sources. 2. We have synthesized conformationally constrained ligands and completed extensive computer modeling on the bradykinin receptor. Moreover, using systematic synthetic modifications, we have explored the relative importances of selected amide bonds and side chains in second generation peptides and have made a series of C alpha- and/or N-methyl substitutions at positions four and five which led to the discovery of two new cyclic peptide antagonists. 3. Computational simulations led to a proposed model of bradykinin bound to its receptor which was found to be in good agreement with mutagenesis results. This model led ultimately to the design and synthesis of D-Arg0-Arg1-(12-aminododecanoyl)2-Ser3-D-Tic4-Oic5+ ++-Arg6. Consideration of this new lead compound, together with the extensive structure-activity relationship (SAR) which has been developed for peptide ligands and the receptor, represents a tangible framework for the design of more potent and longer-lasting antagonists of the bradykinin receptor.

Amino Acid Sequence↗
PubMed1980

Insertion element IS102 resides in plasmid pSC101.

In vivo recombination was found to occur between plasmid pHS1, a temperature-sensitive replication mutant of pSC101 carrying tetracycline resistance, and plasmid ColE1 after selection for tetracycline resistance at the restrictive temperature, 42 degrees C. Extensive analysis of the physical structures of three of these recombinant plasmids, using restriction endonucleases and the electron microscope heteroduplex method, revealed that the plasmid pHS1 was integrated into different sites on ColE1. The recombinant plasmids contained a duplication of a unique 1-kilobase (kb) sequence of pHS1 in a direct orientation at the junctions between the two parental plasmid sequences. This was confirmed by comparing the nucleotide sequence of the recombinants and their parental plasmids. Nucleotide sequence analysis further revealed that nine nucleotides at the site of recombination of ColE1 were duplicated at the junction of each of the 1-kb sequences. The formation of recombinants was independent of RecA function. Based on our previous finding that a plasmid containing a deoxyribonucleic acid insertion (IS) element can recombine with a second plasmid to generate a duplication of the IS element, we conclude that the 1-kb sequence is an insertion sequence, which we named IS102. For convenience, we have also denoted the IS102 sequence as eta theta to assign the orientation of the sequence. Eighteen nucleotides at one end (eta end) were found to be repeated in an inverted orientation at the other end (theta end) of IS102. The nucleotide sequence of the eta end of the sequence was found to be identical to the sequence at the ends of the transposon Tn903, which is responsible for transposition of the kanamycin resistance gene.

Base Sequence↗
PubMed1996

Cloning and sequence comparison of AvaI and BsoBI restriction-modification systems.

AvaI and BsoBI restriction endonucleases are isoschizomers which recognize the symmetric sequence 5'CYCGRG3' and cleave between the first C and second Y to generate a four-base 5' extension. The AvaI restriction endonuclease gene (avaIR) and methylase gene (avaIM) were cloned into Escherichia coli by the methylase selection method. The BsoBI restriction endonuclease gene (bsoBIR) and part of the BsoBI methylase gene (bsoBIM) were cloned by the "endo-blue" method (SOS induction assay), and the remainder of bsoBIM was cloned by inverse PCR. The nucleotide sequences of the two restriction-modification (RM) systems were determined. Comparisons of the predicted amino acid sequences indicated that AvaI and BsoBI endonucleases share 55% identity, whereas the two methylases share 41% identity. Although the two systems show similarity in protein sequence, their gene organization differs. The avaIM gene precedes avaIR in the AvaI RM system, while the bsoBI R gene is located upstream of bsoBI M in the BsoBI RM system. Both AvaI and BsoBI methylases contain motifs conserved among the N4 cytosine methylases.

Amino Acid Sequence↗
PubMed1994

Studies of the processing of the protease which initiates degradation of small, acid-soluble proteins during germination of spores of Bacillus species.

Three mutant forms of the protease (GPR) that initiates degradation of small, acid-soluble spore proteins (SASP) during germination of spores of Bacillus species have been generated. In one variant (GPR delta), the putative pro sequence removed in conversion of the GPR zymogen (termed P46) to the active enzyme (termed P41) was deleted. GPR delta was expressed in both Escherichia coli and Bacillus subtilis as a polypeptide of 41 kDa (P41) which was active both in vivo and in vitro. The other two variants had changes in the sequence around the site where the pro sequence is removed, making this sequence even more like that recognized and cleaved by GPR in its SASP substrates. One of these variants (GPRS) was synthesized as P46S in both B. subtilis and E. coli, but P46S was processed to P41S earlier in B. subtilis sporulation than was wild-type P46. The second variant (GPREI) was made as P46EI but underwent extremely rapid processing to P41EI in both E. coli and B. subtilis. Expression of elevated (> 100-fold) levels of GPR delta or GPREI blocked sporulation at the time of synthesis of glucose dehydrogenase. Expression of elevated levels of GPRS or low levels (< 20% of the wild-type level) of GPR delta or GPREI did not retard sporulation, but the SASP level in the resultant spores was greatly reduced. Prolonged incubation of P41 delta, P41EI, or wild-type P41, either in vivo or with purified proteins in vitro, resulted in a second self-cleavage event generating a 39-kDa polypeptide termed P39. The sequence in the P(41)-->P(39) cleavage site was also quite similar to that recognized and cleaved by GPR in SASP. Together, these results strongly support a model in which activation of GPR during sporulation by conversion of P(46) to P(41) is a self-processing event triggered by a change in the spore core environment (i.e., dehydration) which precludes attack of the active P(41) on its SASP substrates. However, in the first minutes of spore germination, rapid spore core hydration allows rapid attack of active GPR on SASP.

Amino Acid Sequence↗
PubMed2004

Design, synthesis, and conformational analysis of eight-membered cyclic peptidomimetics prepared using ring closing metathesis.

As part of a program to identify novel scaffolds that adopt defined secondary structure when incorporated into peptides, we have designed and prepared a library of constrained eight-membered ring lactams based upon 7-amino-8-oxo-1,2,3,6,7-pentahydroazocine-2-carboxylic acid. Ring closing metathesis (RCM) was employed as the key step, proceeding in high yields to afford the Z olefin. In this reaction sequence, the first generation benzylidene ruthenium RCM catalyst was superior to the second-generation imidazoline catalyst, which gave extensive oligomerization at higher concentrations. Conformational analysis of the 2S,7S and 2R,7S stereoisomers revealed that the 2R,7S isomer is a Type VIa beta-turn in the solid state (X-ray crystal structure) and in water (NMR analysis). The Type VIa beta-turn is relatively rare, typically bearing the cis amide bond found in proline-containing sequences. The 2S,7S diastereomer has an extended geometry of the pendent amide chains. The corresponding saturated derivatives (7-amino-8-oxoazocane-2-carboxylic acid) were also synthesized and investigated. The 2S,7S azocane bears an extended geometry and mimics the C(+) conformer of ox-[Cys-Cys], found in a variety of naturally occurring peptides. The scaffolds described here are useful for the design of constrained peptidomimics with defined secondary structure.

Crystallography, X-Ray↗
PubMed1994

Interference by complex structures of target DNA with specific PCR amplification.

It has been considered that target DNA is a forgiving component for PCR amplification. Herein we present evidence to demonstrate that secondary structure located at the end of a template may interfere with the specificity of amplification. Experiments indicate that nonspecific amplification results from a long stretch of stem and loop structures at the 3' end of prochymosin cDNA. Based on the sequence of mRNA coding for prochymosin, it is argued that the sequence responsible for the formation of the complex structure described here is most likely generated during synthesis of the second cDNA strand.

Base Sequence↗
PubMed2002

Relative contributions of NO and gap junctional communication to endothelium-dependent relaxations of rabbit resistance arteries vary with vessel size.

Two synthetic peptide inhibitors of gap junctional communication have been used to compare the contribution of direct cell-cell coupling to acetylcholine-induced relaxations of the rabbit central ear artery (G(0)) and its second branch generation (G(2)). These peptides, designated (43)Gap 26 and (37,43)Gap 27, possess sequence homology with specific domains of the first extracellular loop of connexin 43 (Cx43) and second extracellular loop of Cxs 37 and 43, respectively. Immunohistochemistry confirmed the presence of Cxs 37, 40, and 43 in the vascular endothelium, but of only Cx43 in the media of G(0). At concentrations of 300 microM, (43)Gap 26 and (37,43)Gap 27 each inhibited the maximum response to acetylcholine in G(2) by approximately 50%, but by only approximately 20% in G(0), whereas inhibition of NO synthesis by 300 microM N(G)-nitro-L-arginine methyl ester attenuated maximum relaxations to acetylcholine by approximately 30% in G(2), but by approximately 70% in G(0). Residual endothelium-derived hyperpolanizing factor-type responses in G(0) and G(2) were abolished by (43)Gap 26 and (37,43)Gap 27. In HeLa cells transfected to express a chimeric Cx43-green fluorescent protein that forms functional gap junctions, the peptides were equally effective inhibitors of Lucifer yellow dye transfer. We conclude that the contribution of gap junctions to endothelium-dependent relaxation is inversely related to vessel size and exhibits an apparently reciprocal relationship with NO-mediated mechanisms of vasorelaxation in the rabbit ear.

Acetylcholine↗
PubMed1997

Computer simulation of noise resulting from random synaptic activities.

Neuronal behavior is dependent on random inputs from a multitude of synaptic contacts on the soma and dendritic tree. Therefore, simulations of different types of noise are often required in the experimental and theoretical investigation of the properties of neurons and neuronal assemblies. The direct simulation of these noise sources by simple difference equations may therefore be quite useful and a general approach is presented in this paper. Initially, a first order model and its time-discretization are analyzed in detail, followed by a generalization to more complex models. The firing patterns of neurons are dependent on the random behaviors of their membrane potentials at the trigger zone. These depend on the propagation of the randomly occurring postsynaptic potentials from specific places on the dendritic tree or soma to the trigger zone. Different models may represent a variety of circumstances in which random membrane potentials arise at the trigger zone. Simulations of different types of noise are often required in the experimental and theoretical investigation of the properties of neurons and neuronal assemblies. The direct simulation of these noise sources by simple difference equations may therefore be quite useful and a general approach is presented in this paper. This paper presents a detailed analysis of the very useful first order model and its time discretization. The criterion used is that the autocovariance sequence of the discrete time model be a sample of the original autocovariance function. Several cases are presented which are of practical interest, including the case of constant output variance independent of the model's time constant. General models are time-discretized by the impulse response invariance method. Two applications are presented, one is related to the modeling of the synaptic currents by the alpha function instead of the delta function and the second deals with analog synaptic noise generation by D/A conversion of computer generated noise sequences.

Action Potentials↗
PubMed2002

Identification of two novel ACTH-responsive genes encoding manganese-dependent superoxide dismutase (SOD2) and the zinc finger protein TIS11b [tetradecanoyl phorbol acetate (TPA)-inducible sequence 11b].

ACTH is the major trophic factor regulating and maintaining adrenocortical function, affecting such diverse processes as steroidogenesis, cell proliferation, cell migration, and cell survival. We used differential display RT-PCR to identify genes that are rapidly induced by ACTH in the bovine adrenal cortex. Of 42 PCR products differentially amplified from primary cultures of bovine adrenocortical cells treated with 10 nM ACTH, six identified mRNAs that were confirmed by Northern blot analysis to be induced by ACTH. Four of these amplicons encoded noninformative repetitive sequences. Of the other two sequenced amplicons, one encoded a partial sequence for mitochondrial manganese-dependent superoxide dismutase (SOD2), an enzyme that is likely to protect adrenocortical cells from the cytotoxic effects of radical oxygen species generated during steroid biosynthesis. The second was identified as TIS11b (phorbol-12-myristate-13-acetate-inducible sequence 11b)/ERF-1/cMG, a member of the CCCH double-zinc finger protein family. SOD2 induction by ACTH was independent of extracellular steroid concentration or oxidative stress. SOD2 and TIS11b mRNA expressions were rapidly induced by ACTH, reaching a maximal level after 8 h and 3 h of treatment, respectively. These ACTH effects were mimicked by forskolin but appeared independent of cortisol secretion. Upon ACTH treatment, induction of TIS11b expression closely followed the previously characterized peak of vascular endothelial growth factor (VEGF) expression. Transfection of a TIS11b expression plasmid into 3T3 fibroblasts induced a decrease in the expression of a reporter gene placed upstream of the VEGF 3'-untranslated region, indicating that TIS11b may be an important regulator of VEGF expression through interaction with its 3'-untranslated region.

Adrenal Cortex↗
PubMed2025

Whole genome sequencing-based detection of extensively drug-resistant tuberculosis from Ethiopia.

BACKGROUND: Rapid and accurate detection of extensively drug-resistant tuberculosis is crucial for effective intervention. Next-generation sequencing technologies have been recommended to rapidly and accurately detect resistance to second-line anti-TB drugs. We deployed whole-genome sequencing to detect mutations associated with drug resistance in pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis strains in Ethiopia. METHODS: This report is part of the routine laboratory-based drug-resistance surveillance in Ethiopia. Among 15 pre-extensively drug-resistant tuberculosis and extensively drug-resistant tuberculosis isolates identified during the study period, eleven isolates were retrieved by Whole-genome sequencing. Illumina NextSeq 550 instruments were used to generate genomic data. Lineage and drug-resistance prediction were performed with Tuberculosis Profiler, while phylogeny was conducted by IQ-tree. RESULTS: Of the genotyped isolates, whole-genome sequencing identifies five extensively drug-resistant tuberculosis and four pre-extensively drug-resistant tuberculosis strains. It detects fluoroquinolone resistance mutations gyrA (Ala90Val, Asp94Tyr, Asp94Gly). Bedaquiline resistance mutations are found in atpE (Glu61Asp) and Rv0678 (139dupG, 141 and 142dupTC). Cross-resistance is identified between bedaquiline and clofazimine (n&#x2009;=&#x2009;4) and delamanid and pretomanid (n&#x2009;=&#x2009;1). Concordance result is observed between phenotypic drug-susceptibility testing and whole-genome sequencing for eight cases, while three cases are discordant (fluoroquinolones, delamanid, and pretomanid). Phylogenetic analysis reveals three major lineages: Lineage 4 (Euro-American, n&#x2009;=&#x2009;6 isolates), Lineage 3 (East African-Indian, n&#x2009;=&#x2009;3 isolates), and Lineage 1 (Indo-Oceanic, n&#x2009;=&#x2009;2 isolates). CONCLUSIONS: Whole-genome sequencing identifies dominant mutations in genes such as gyrA, atpE, and Rv067 that are associated with resistance to second-line anti-tuberculosis drugs. Significant cross-resistance is observed between key second-line drugs, bedaquiline and clofazimine, as well as delamanid and pretomanid. This finding highlights the need for routine genomic surveillance to detect drug resistance early, improve treatment outcomes, and prevent transmission.

Journal Article↗
PubMed1995

Second-generation octarellins: two new de novo (beta/alpha)8 polypeptides designed for investigating the influence of beta-residue packing on the alpha/beta-barrel structure stability.

The sequence of octarellin I, the first de novo (beta/alpha)8 polypeptide, was revised according to several criteria, among others the symmetry of the sequence, beta-residue volume and hydrophobicity, and charge distribution. These considerations and the overall conclusions drawn from the first design led to two new sequences, corresponding to octarellins II and III. Octarellin II retains perfect 8-fold symmetry. Octarellin III has the same sequence as octarellin II, except for the beta-strands which exhibit a 4-fold symmetry. The two proteins were produced in Escherichia coli. Infrared and CD spectral analyses of octarellins II and III reveal a high secondary structure content. Non-denaturing gel electrophoresis, molecular sieve chromatography and analytical ultracentrifugation suggest that both of these second-generation artificial polypeptides exist as a mixture of a monomer and a dimer form. Octarellins II and III are at least 10 times more soluble than octarellin I. Urea-induced unfolding followed by fluorescence emission suggests that the tryptophan residues, designed to be buried in the (beta/alpha)8, are indeed packed in the hydrophobic core of both proteins. However, octarellin III displays a higher stability towards urea denaturation, indicating that introducing 4-fold symmetry into the beta-barrel might be important for stability of the overall folding.

Amino Acid Sequence↗
PubMed1995

Complex sensory-motor sequence learning based on recurrent state representation and reinforcement learning.

A novel neural network model is presented that learns by trial-and-error to reproduce complex sensory-motor sequences. One subnetwork, corresponding to the prefrontal cortex (PFC), is responsible for generating unique patterns of activity that represent the continuous state of sequence execution. A second subnetwork, corresponding to the striatum, associates these state-encoding patterns with the correct response at each point in the sequence execution. From a neuroscience perspective, the model is based on the known cortical and subcortical anatomy of the primate oculomotor system. From a theoretical perspective, the architecture is similar to that of a finite automaton in which outputs and state transitions are generated as a function of inputs and the current state. Simulation results for complex sequence reproduction and sequence discrimination are presented.

Animals↗