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PubMed2004

A new isoelectric focusing system for fast two-dimensional gel electrophoresis using a low-concentration polyacrylamide gel supported by a loose multifilament string.

A new isoelectric focusing (IEF) system for two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) has been proposed. In this system, a super-soft and tough IEF gel was achieved by casting polyacrylamide gel down to 2.0% T using a loose multifilament string (LMS) of nylon as a gel support. The IEF apparatus for the LMS-gel, fabricated from acrylic boards, had a cooling water chamber, and eliminated the need of electrode solutions by directly connecting the two ends of individual gels to platinum electrodes. The carrier ampholyte-generated pH gradients using the new IEF system was stable over a long duration of time and a wide range of voltages, and the IEF time became shorter using a 2.0% T gel than using a 4.0% T gel. Also, the LMS-gels prepared in different runs exhibited excellent reproducibility. The new IEF system was applied to 2-D PAGE of a chicken skeletal muscle extract, and it was found that the protein loading capacity, protein entry into the LMS-gels, and protein transfer efficiency from the first-dimensional to the second-dimensional gels were significantly improved by using a low-concentration (2.5% T) gel. Also, proteins of high molecular weight of more than 200 kDa were observed in the 2-D maps, and therefore the new IEF system has a very good potential to be applied for fast 2-D PAGE of high molecular-weight proteins.

Journal Article↗

PubMed2002

Grouping of coefficients for the calculation of inter-molecular similarity and dissimilarity using 2D fragment bit-strings.

This paper compares 22 different similarity coefficients when they are used for searching databases of 2D fragment bit-strings. Experiments with the National Cancer Institute s AIDS and IDAlert databases show that the coefficients fall into several well-marked clusters, in which the members of a cluster will produce comparable rankings of a set of molecules. These clusters provide a basis for selecting combinations of coefficients for use in data fusion experiments. The results of these experiments provide a simple way of increasing the effectiveness of fragment-based similarity searching systems.

Acquired Immunodeficiency Syndrome↗

PubMed2005

Preparation of cherry-picked combinatorial libraries by string synthesis.

String synthesis [1-3] is an efficient and cheap manual method for preparation of combinatorial libraries by using macroscopic solid support units. Sorting the units between two synthetic steps is an important operation of the procedure. The software developed to guide sorting can be used only when complete combinatorial libraries are prepared. Since very often only selected components of the full libraries are needed, new software was constructed that guides sorting in preparation of non-complete combinatorial libraries. Application of the software is described in details.

Combinatorial Chemistry Techniques↗

PubMed1987

Effect of practice, mapping, stimulus and size on string matching.

The same-different discrepancy on a matching task on which the subject had to determine the number of common elements (physically identical and appearing in the same position) between two strings of size 1 to 4 was investigated. Manipulated also were the type of presentation (fixed or varied sets), amount of practice (four blocks), and type of stimulus (letters, words). Reaction times for pure positive responses (all same at each level) were faster than negative responses (all different), confirming the usual discrepancy shown in previous studies. The discrepancy was smaller for well-learned sets (fixed sets) and for words, indicating the development of a comparison process based on global characteristics of the stimulus.

Adult↗

PubMed2004

Repetitive motion in perception of tactile sensation in the fingers of string players.

Little is known about the mechanisms that underlie the pathophysiology involved in the development of cumulative trauma disorders. Musicians, specifically string players, may be a useful model to examine the cumulative effects of repetitive motion given the highly attended movements of their left hands and the stereotypical grasp of their right hands. Musculoskeletal disorders related to playing are experienced by 39% to 87% of musicians, making musicians a potentially good model for the study of factors involved in development of cumulative trauma disorders. Sensory thresholds for two-point discrimination and light touch were measured in all phalanges of each digit, of each hand. Comparisons were made within and between a control group of 10 nonmusicians who did not engage in repetitive motion and 10 healthy musicians who did. There were 5 violinists, 2 violists, and 3 cellists. The Non-musician group perceived two-points and light touch at significantly lower thresholds in the proximal phalanges of the left hand than the right hand. Significant differences were not present between right and left hands for the means of distal, middle, and proximal phalanges of the Musician group. This lack of significant difference may be due to higher sensory thresholds associated with repetitive use of the left hand of the musicians.

Adult↗

PubMed2000

Contiguous strings of strongly binding short oligonucleotides as a useful tool for completing sequencing experiments.

Large-scale DNA sequencing is currently based mostly on the shotgun approach. Although widely used, it is not free of shortcomings: the total length of randomly sequenced subclones appear to be five to eight times more than the total DNA length; such a high statistical redundancy of random sequences cannot guarantee the absence of unsequenced gaps. We calculated that these problems could be alleviated if the average length of the subcloned random fragments were increased. In this paper we present the primer walking approach based on the use of contiguous modified hexamer strings strongly binding to complementary templates as segmented primers. The approach exhibits the following characteristic features: 1) Single-stranded templates appear to have advantage over double-stranded ones. 2) With single-stranded templates, an overall sequencing success rate is about 80%. 3) A relatively small library of 1400 hexanucleotides selected according to the most frequent occurrence in the human genome is sufficient for sequencing all clones. The approach allows one to reduce the number of templates necessary for the shotgun strategy and also to decrease the number of gaps between sequenced contigs. This should be kept in mind when considering the ways for enhancement of the present strategy of large-scale sequencing.

DNA↗

PubMed2003

Generating anagrams from multiple core strings employing user-defined vocabularies and orthographic parameters.

Anagrams are used widely in psychological research. However, generating a range of strings with the same letter content is an inherently difficult and time-consuming task for humans, and current computer-based anagram generators do not provide the controls necessary for psychological research. In this article, we present a computational algorithm that overcomes these problems. Specifically, the algorithm processes automatically each word in a user-defined source vocabulary and outputs, for each word, all possible anagrams that exist as words (or as nonwords, if required) as defined by the same source vocabulary. Moreover, we show how the output of the algorithm can be filtered to produce anagrams within specific user-defined orthographic parameters. For example, the anagrams produced can be filtered to produce words that share, with each other or with other words in the source vocabulary, letters in only certain positions. Finally, we provide free access to the complete Windows-based program and source code containing these facilities for anagram generation.

Algorithms↗

PubMed1990

Image rotation of misoriented letter strings: effects of orientation cuing and repetition.

Three experiments were designed to investigate whether the characteristic function relating response time to stimulus orientation reflects the observer imagining the rotation of the stimulus to upright (the "image rotation" hypothesis) or rotation of an internal reference frame in response to the misoriented stimulus (the "frame rotation" hypothesis). Identification times in response to misoriented words were measured in Experiment 1, whereas in Experiments 2 and 3, lexical decision times in response to misoriented letter strings were measured. Trials occurred in blocks; words within a block were presented at the same orientation. It was argued that this mode of presentation would facilitate the use of a frame rotation strategy by allowing for a gradual readjustment of an internal reference frame. The characteristic "mental rotation" function was observed in all three experiments. However, the data indicated that observers continued to imagine the rotation of the word to upright in each trial; there was no evidence of readjustment of an internal reference frame. An additional finding of interest occurred in Experiment 1, in which observers identified the same set of misoriented words across two sessions. The identification times were faster, and the slope of the mental rotation function was lower, in the second session. These results are discussed as in relation to the image rotation hypothesis of mental rotation and to "instance-based skill acquisition" (Masson, 1986) in word recognition.

Adult↗

PubMed2001

Defined flanking spacers and enhanced proteolysis is essential for eradication of established tumors by an epitope string DNA vaccine.

Loss of immunogenic epitopes by tumors has urged the development of vaccines against multiple epitopes. Recombinant DNA technologies have opened the possibility to develop multiepitope vaccines in a relatively rapid and efficient way. We have constructed four naked DNA-based multiepitope vaccines, containing CTL, Th cell, and B cell epitopes of the human papillomavirus type 16. Here we show that gene gun-mediated vaccination with an epitope-based DNA vaccine protects 100% of the vaccinated mice against a lethal tumor challenge. The addition of spacers between the epitopes was crucial for the epitope-induced tumor protection, as the same DNA construct without spacers was significantly less effective and only protected 50% of the mice. When tested for therapeutic potential, only the epitope construct with defined spacers significantly reduced the size of established tumors, but failed to induce tumor regression. Only after targeting the vaccine-encoded protein to the protein degradation pathway by linking it to ubiquitin, the vaccine-induced T cell-mediated eradication of 100% of 7-day established tumors in mice. The finding that defined flanking sequences around epitopes and protein targeting dramatically increased the efficacy of epitope string DNA vaccines against established tumors will be of importance for the further development of multiepitope DNA vaccines toward clinical application.

Adjuvants, Immunologic↗

PubMed1991

Effect of tank liquid acoustic velocity on Doppler string phantom measurements.

The quantitative effects of degassed water in string phantom tank Doppler measurements are derived theoretically. The Doppler parameter measurements considered are range gate registration, range gate profile, image flow angle measurements, and velocity calculation. The equipment velocity calculation is demonstrated to have an appreciable error which is due to the water acoustic velocity and the transducer acquisition geometry. A velocity calibration technique is proposed that only needs a simple multiplicative factor to compensate for the water in the tank.

Calibration↗

PubMed1999

[PCR-monitoring of gastric juice obtained with the capsuled string for the evaluation of H. pylori eradication].

We have developed a highly sensitive semi-nested PCR assay, URA-PCR, for the detection of H. pylori ureA gene in gastric juice. The primers were designed according to nucleotide sequence analyses of clinical isolates. The PCR assay has higher sensitivity than conventional methods such as culture. Characteristics of culture-negative but PCR-positive patients were similar to those of culture-positive ones. The PCR assay, using gastric juice samples obtained with capsuled strings, detected 97% cases of relapsed infection within eight weeks after antimicrobial therapy.

Breath Tests↗

PubMed1999

Overexpression of cysteine-string proteins in Drosophila reveals interactions with syntaxin.

Cysteine-string proteins (CSPs) are associated with secretory vesicles and critical for regulated neurotransmitter release and peptide exocytosis. At nerve terminals, CSPs have been implicated in the mediation of neurotransmitter exocytosis by modulating presynaptic calcium channels; however, studies of CSPs in peptidergic secretion suggest a direct role in exocytosis independent of calcium transmembrane fluxes. Here we show that the individual expression of various CSP isoforms in Drosophila similarly rescues the loss of evoked neurotransmitter release at csp null mutant motor nerve terminals, suggesting widely overlapping functions for each isoform. Thus, the structural difference of CSP variants may not explain the opposing putative functions of CSP in neurotransmitter and peptide exocytosis. Consistently, the individual overexpression of each CSP isoform in wild-type Drosophila shows similar effects such as impaired viability and interference with wing and eye development. The dominant effects caused by the overexpression of CSP are suppressed by the simultaneous overexpression of syntaxin-1A but not by the coexpression of SNAP-25. Although overexpression of CSP itself has no apparent effect on the synaptic physiology of larval motor nerve terminals, it fully suppresses the decrease of evoked release induced by the overexpression of syntaxin-1A. A direct protein-protein interaction of CSP with syntaxin is further supported by coimmunoprecipitations of syntaxin with CSP and by protein binding assays using recombinant fusion proteins. Together, the genetic and biochemical interactions of CSP and syntaxin-1A suggest that CSP may chaperone or modulate protein-protein interactions of syntaxin-1A with either calcium channels or other components of the regulatory machinery mediating depolarization-dependent neurotransmitter exocytosis.

Animals↗

PubMed2000

Comparison of cysteine string protein (Csp) and mutant alpha-SNAP overexpression reveals a role for csp in late steps of membrane fusion in dense-core granule exocytosis in adrenal chromaffin cells.

Assembly of the SNARE complex and its disassembly caused by the action of soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein (SNAP) and NSF is crucial for the maintenance of vesicular traffic, including fusion of regulated exocytotic vesicles. Various other proteins may also have important roles in the processes leading to membrane fusion via interaction with the SNARE proteins, including the secretory vesicle cysteine string protein (Csp). Here we have examined the effect of overexpression of a dominant negative alpha-SNAP mutant or Csp on exocytosis of dense-core granules in single chromaffin cells monitored using amperometry to detect released catecholamine. Exocytosis of trans-Golgi network (TGN)-derived dense-core granules was substantially inhibited by expression of alpha-SNAP(L294A). The amplitude and characteristics of the individual release events were unaffected by expression of alpha-SNAP(L294A), consistent with an essential role for alpha-SNAP in early steps of priming but not in the fusion process. In contrast, Csp overexpression, which also inhibited the extent of exocytosis, also modified the kinetics of the individual release events seen as an increase in the rise time and a broadening of the residual amperometric spikes in Csp-transfected cells. These results suggest that unlike alpha-SNAP, Csp plays a key role in the protein interactions close to the fusion process or fusion pore opening during Ca(2+)-regulated exocytosis.

Adrenal Medulla↗

PubMed2000

Cysteine-string protein increases the calcium sensitivity of neurotransmitter exocytosis in Drosophila.

Previous studies suggest that the vesicular cysteine-string protein (CSP) may modulate presynaptic Ca(2+) channel activity in fast neurotransmitter release. To test this hypothesis, we analyzed the dynamics of presynaptic Ca(2+) ion influx with the Ca(2+) indicator fluo-4 AM at csp mutant neuromuscular junctions of Drosophila. From 24 to 30 degrees C, stimulus-evoked, relative presynaptic Ca(2+) signals were increasingly larger in csp mutant boutons than in controls. Above 30 degrees C, Ca(2+) signals declined and were similar to controls at 34 degrees C. A prolonged decay of Ca(2+) signals in mutant boutons at high temperatures indicated abnormally slow Ca(2+) clearance. Cytosolic Ca(2+) at rest was determined with the ratiometric Ca(2+) indicator fura-2 AM and was similar in mutant and control boutons at 24 degrees C but higher in mutant boutons at 34 degrees C. Despite larger Ca(2+) signals in mutant boutons, evoked neurotransmitter release was always reduced in csp mutants and exhibited pronounced facilitation. Thus, a lack of Ca(2+) entry cannot explain the reduction of neurotransmitter release in csp mutants. At all temperatures tested, raising extracellular Ca(2+) increased transmitter release elicited by single stimuli in csp mutants. Collectively, these data suggest multiple functions for CSP at synaptic terminals. Increased Ca(2+) signals coupled with reduced release suggest a direct function of CSP in exocytosis downstream from Ca(2+) entry. Because the reduction of evoked release in csp mutants is counteracted by increased Ca(2+) levels, we suggest that CSP primarily increases the Ca(2+) sensitivity of the exocytotic machinery.

Animals↗

PubMed1975

["Pearl-string artery" with mesenteric localization].

Angiorgrams sometimes show regular and symetrical corrugations of the arterial outline. The shadows have been given various names: pearl string arter, bamboo pattern and so on. Involved arteries are mostly those of the extremities, especially the lower limbs. The authors have found a case involving the mesenteric artery. Usually, there is no pathological state of the arterial wall. Thus, surgical action is unnecessary.

Adult↗

PubMed2001

The philanthropic string: medical aspects of military strategy.

Since antiquity, medical care has played an important role in both military strategy and conflict resolution. Although this is usually a negative and an unintended event, medical care can be a positive and a rational alternative to present-day weapons of mass destruction. Yet, military and civilian planners have not traditionally accepted, recognized, and used a "philanthropic string." Nevertheless, medical care can be an important factor in resolving international conflict, either in support of military operations or as a separate function. Therefore, it is timely, and pragmatic, to include humanitarian medical care in strategic military planning.

Altruism↗

PubMed2000

[Establishment of facial nerve elongation model by string-type loading].

OBJECTIVE: To study the repairing method of facial nerve defect using nerve elongation, and the biomechanical properties of peripheral nerves. METHODS: A novel device for peripheral nerve elongation was designed and manufactured. With the device, facial nerves of rabbits were expanded acutely and chronically by string-type loading. The facial nerves were studied with histological and electrophysiological examinations before and after elongation. RESULTS: There were no considerable necrosis, degeneration, and infection in the facial nerves after elongation. The experimental animals took food normally and their body temperature were stable. Histological examinations showed dispersing Sunderland degree III injury and occasionally broken capillary blood vessels in the acute group, thicker nerve and fibroblasts hyperplasia between nerve bundles in the chronic group. The electromyogram(EMG) of buccal muscle and nerve conductive velocity(NCV) showed the maximal range was (18.7 +/- 2.4)% in the acute group, and (30.8 +/- 2.4)% in the chronic group. CONCLUSION: It suggests that the novel nerve elongation method is feasible, and it can be used to study the nerve elongation basically and clinically.

Animals↗

PubMed2001

[Phase-specific elements of the regulatory zone of the Drosophila melanogaster string gene].

The phases of the reporter gene expression controlled by different fragments of the string (stg) gene regulatory region were determined in Drosophila neuroblasts by detection of beta-galactosidase activity and radioautography. In the D10 and D22 lines carrying the constructs pstg beta-E4.9 and pstg beta-E5.3, respectively, the reporter gene activity was detected in the G1 phase of the cell cycle. In the D12 and D20 lines (pstg beta-E6.4 and pstg beta-E2.6), no periodic expression was observed. The regulatory regions of the stg from lines D10 and D22 and that of Drosophila gene cyclin D shared consensus aagaactttg, which was also expressed in the G1 phase. The phase-specific expression of the cell-cycle genes was compared in a model for the mitotic-wave cells of eye imaginal disk and neuroblasts of the nerve ganglia.

Animals↗