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Human immunoglobulin heavy-chain minilocus recombination in transgenic mice: gene-segment use in mu and gamma transcripts.

We (N.L. and L.D.T.) have introduced a human heavy-chain minilocus into mice transgenically. Constructs contain 2 heavy-chain variable (VH; psi VH3-105 and VH5-251), 10 diversity (D), 6 heavy-chain joining (JH), and either constant (C)mu or C mu and C gamma gene segments. Several founder lines were established and studied before immunization. Seventy heavy-chain transcripts were cloned and sequenced from murine splenic B lymphocytes, and gene-segment use was assessed before and after class-switching. In general, the repertoire was "fetal" in appearance with little evidence of somatic mutation in any gene segment. The two VH gene segments were found rearranged to mu- and gamma-chain C segments, with a preference of VH5-251. We observed a preponderance of the most-J-proximal D gene (DHQ52) segments among the mu transcripts (44%). The JH gene-segment use mimics most patterns seen in human antibodies. Diversification in CDR3 was extensive and included clear examples of D inversions and D-D fusions. These data suggest that a human immunoglobulin minilocus can undergo recombinatorial processes in a manner analogous to that seen in the human fetal/preimmune repertoire. This model, in addition to providing a potential source of human monoclonal antibodies, is ideal for the study of further questions concerning immunoglobulin gene-segment recombination.

Amino Acid Sequence↗

Soft tissue segmentation of the body and fractionation of the upper and lower limbs.

The aim of this cadaver analyses study was to provide regression models for the prediction of major tissue components of the human body. Altogether 182 anthropometric measurements were taken bilaterally on six cadavers (3 male, 3 female). The cadavers were segmented by severance through soft tissue only and gross segments weighted in both air and water. Each limb segment was then fractionated into four components--skin, adipose tissue, muscle and bone--and each component was also weighed in both air and water. Regression equations were developed for the prediction of total segment masses from anthropometry and the prediction of intra-segmental tissue component masses from anthropometry. Weight, volume, density and percentage of body weight are given for 14 body segments and are compared with 19th and 20th century cadaver data. Ten regression equations were generated for the prediction of segmental masses and per segment the major issue components generated a total of 24 regressions.

Adolescent↗

Limb Segment Recruitment as Function of Movement Direction, Amplitude, and Speed.

Coordination of limb segments in graphic motor behavior has been studied primarily in cyclic tasks. In the present study, limb segment recruitment patterns were investigated in a discrete line-drawing task. Subjects (N = 11) performed pointing movements varying in direction, amplitude, and speed. The contributions of index finger, hand, and arm to the movement were analyzed by evaluating the angular displacements in 7 joint dimensions. The results showed that amplitude and direction affected limb segment involvement in the same way they have been reported to affect it in cyclic movements. Upward left- (up-left) directed movements were primarily achieved by fingers and arm, whereas upward right- (up-right) directed movements were accomplished with the hand and the arm. Large amplitudes elicited not only an increase of proximal but also a decrease of distal limb segment involvement, especially in the up-left direction. In the present discrete pointing task, effects of speed on limb segment involvement were different from speed effects that were observed earlier in cyclic tasks: Larger limb segments became more involved in fast than in slow discrete movements. With respect to the timing of limb segment recruitment, all joints tended to move simultaneously, but small deviations from synchronous joint movement onset and offset were present. The results are discussed in the context of recent theories of limb segment coordination.

Journal Article↗

Functional segments in tongue movement.

The tongue is a deformable object, and moves by compressing or expanding local functional segments. For any single phoneme, these functional tongue segments may move in similar or opposite directions, and may reach target maximum synchronously or not. This paper will discuss the independence of five proposed segments in the production of speech. Three studies used ultrasound and tagged Cine-MRI to explore the independence of the tongue segments. High correlations between tongue segments would suggest passive biomechanical constraints and low correlations would suggest active independent control. Both physiological and higher level linguistic constraints were seen in the correlation patterns. Physiological constraints were supported by high correlations between adjacent segments (positive) and distant segments (negative). Linguistic constraints were supported by segmental correlations that changed with the phonemic content of the task.

Adult↗

Adult aging and listening patterns for spoken prose: spontaneous segmentation versus self-paced listening.

Young and older adults were allowed to control the delivery rate of spoken prose for later recall using two methods. In one method (spontaneous segmentation), participants were allowed to interrupt speech passages whenever they wished. In the other method (self-paced listening), speech passages were presented in segments, with participants allowed to initiate presentation of subsequent segments via a key-press. Older adults' segment sizes in the spontaneous segmentation condition were unchanged when the passages were presented for a second time. By contrast, pause latencies to initiating subsequent segments in the self-paced listening condition were affected by experience with the passage. Results suggested that the segment sizes selected in the spontaneous segmentation condition were driven by the linguistic structure and prosody of the speech, rather than reflecting ineffective metamemory on the part of the older adults.

Adolescent↗

Correlation between a mid-ventricular volume segment and global left ventricular volume measured by the conductance catheter.

OBJECTIVES: To investigate whether acute volume changes in single volume segments of the left ventricle can be correlated with global volume changes. If so, changes in global volume might be predicted from changes in segmental volumes. DESIGN: Volume changes were recorded in six pigs in five intraventricular segments, from apex to heart base, using the conductance catheter (at baseline, after 60 min of apical ischaemia, during preload reduction and afterload increase). A computer algorithm was created to calculate the instantaneous absolute difference between the curve shape of global and normalized segmental volume as a percentage of global stroke volume. RESULTS: For a mid-cardiac volume segment constituting 34 (14-39)% [median (range)] of global stroke volume, the mean difference over a cardiac cycle was 4 (1-8)% at baseline. Apical ischaemia resulted in apical dyskinesia, but did not influence the mid-cardiac segment. CONCLUSIONS: The volume curve from a segment at mid-cardiac level seems to be a good estimator of the global volume curve, thus giving a foundation for estimation of global volume changes from such a segment.

Animals↗

Expression of Dictyostelium myosin tail segments in Escherichia coli: domains required for assembly and phosphorylation.

The assembly of myosins into filaments is a property common to all conventional myosins. The ability of myosins to form filaments is conferred by the tail of the large asymmetric molecule. We are studying cloned portions of the Dictyostelium myosin gene expressed in Escherichia coli to investigate functional properties of defined segments of the myosin tail. We have focused on five segments derived from the 68-kD carboxyl-terminus of the myosin tail. These have been expressed and purified to homogeneity from E. coli, and thus the boundaries of each segment within the myosin gene and protein sequence are known. We identified an internal 34-kD segment of the tail, N-LMM-34, which is required and sufficient for assembly. This 287-amino acid domain represents the smallest tail segment purified from any myosin that is capable of forming highly ordered paracrystals characteristic of myosin. Because the assembly of Dictyostelium myosin can be regulated by phosphorylation of the heavy chain, we have studied the in vitro phosphorylation of the expressed tail segments. We have determined which segments are phosphorylated to a high level by a Dictyostelium myosin heavy chain kinase purified from developed cells. While LMM-68, the 68-kD carboxyl terminus of Dictyostelium myosin, or LMM-58, which lacks the 10-kD carboxyl terminus of LMM-68, are phosphorylated to the same extent as purified myosin, subdomains of these segments do not serve as efficient substrates for the kinase. Thus LMM-58 is one minimal substrate for efficient phosphorylation by the myosin heavy chain kinase purified from developed cells. Taken together these results identify two functional domains in Dictyostelium myosin: a 34-kD assembly domain bounded by amino acids 1533-1819 within the myosin sequence and a larger 58-kD phosphorylation domain bounded by amino acids 1533-2034 within the myosin sequence.

Cloning, Molecular↗

Modulation of cell-adhesive activity of fibronectin by the alternatively spliced EDA segment.

Fibronectin (FN) has a complex pattern of alternative splicing at the mRNA level. One of the alternatively spliced segments, EDA, is prominently expressed during biological processes involving substantial cell migration and proliferation, such as embryonic development, malignant transformation, and wound healing. To examine the function of the EDA segment, we overexpressed recombinant FN isoforms with or without EDA in CHO cells and compared their cell-adhesive activities using purified proteins. EDA+ FN was significantly more potent than EDA- FN in promoting cell spreading and cell migration, irrespective of the presence or absence of a second alternatively spliced segment, EDB. The cell spreading activity of EDA+ FN was not affected by antibodies recognizing the EDA segment but was abolished by antibodies against integrin alpha5 and beta1 subunits and by Gly-Arg-Gly-Asp-Ser-Pro peptide, indicating that the EDA segment enhanced the cell-adhesive activity of FN by potentiating the interaction of FN with integrin alpha5beta1. In support of this conclusion, purified integrin alpha5beta1 bound more avidly to EDA+ FN than to EDA- FN. Augmentation of integrin binding by the EDA segment was, however, observed only in the context of the intact FN molecule, since the difference in integrin-binding activity between EDA+ FN and EDA- FN was abolished after limited proteolysis with thermolysin. Consistent with this observation, binding of integrin alpha5beta1 to a recombinant FN fragment, consisting of the central cell-binding domain and the adjacent heparin-binding domain Hep2, was not affected by insertion of the EDA segment. Since the insertion of an extra type III module such as EDA into an array of repeated type III modules is expected to rotate the polypeptide up to 180 degrees at the position of the insertion, the conformation of the FN molecule may be globally altered upon insertion of the EDA segment, resulting in an increased exposure of the RGD motif in III10 module and/or local unfolding of the module. Our results suggest that alternative splicing at the EDA exon is a novel mechanism for up-regulating integrin-binding affinity of FN operating when enhanced migration and proliferation of cells are required.

Alternative Splicing↗

Ankyrin-G coordinates assembly of the spectrin-based membrane skeleton, voltage-gated sodium channels, and L1 CAMs at Purkinje neuron initial segments.

The axon initial segment is an excitable membrane highly enriched in voltage-gated sodium channels that integrates neuronal inputs and initiates action potentials. This study identifies Nav1.6 as the voltage-gated sodium channel isoform at mature Purkinje neuron initial segments and reports an essential role for ankyrin-G in coordinating the physiological assembly of Nav1.6, betaIV spectrin, and the L1 cell adhesion molecules (L1 CAMs) neurofascin and NrCAM at initial segments of cerebellar Purkinje neurons. Ankyrin-G and betaIV spectrin appear at axon initial segments by postnatal day 2, whereas L1 CAMs and Nav1.6 are not fully assembled at continuous high density along axon initial segments until postnatal day 9. L1 CAMs and Nav1.6 therefore do not initiate protein assembly at initial segments. betaIV spectrin, Nav1.6, and L1 CAMs are not clustered in adult Purkinje neuron initial segments of mice lacking cerebellar ankyrin-G. These results support the conclusion that ankyrin-G coordinates the physiological assembly of a protein complex containing transmembrane adhesion molecules, voltage-gated sodium channels, and the spectrin membrane skeleton at axon initial segments.

Animals↗

Analysis of the structural correlates for antibody polyreactivity by multiple reassortments of chimeric human immunoglobulin heavy and light chain V segments.

Polyreactive antibodies (Abs) constitute a major proportion of the early Ab repertoire and are an important component of the natural defense mechanisms against infections. They are primarily immunoglobulin M (IgM) and bind a variety of structurally dissimilar self and exogenous antigens (Ags) with moderate affinity. We analyzed the contribution of Ig polyvalency and of heavy (H) and light (L) chain variable (V) regions to polyreactivity in recombinatorial experiments involving the VH-diversity(D)-JH and V kappa-J kappa gene segments of a human polyreactive IgM, monoclonal antibody 55 (mAb55), and those of a human monoreactive anti-insulin IgG, mAb13, in an in vitro C gamma l and C kappa human expression system. These mAbs are virtually identical in their VH and V kappa gene segment sequences. First, we expressed the VH-D-JH and V kappa-J kappa genes of the IgM mAb55 as V segments of an IgG molecule. The bivalent recombinant IgG Ab bound multiple Ags with an efficiency only slightly lower than that of the original decavalent IgM mAb55, suggesting that class switch to IgG does not affect the Ig polyreactivity. Second, we coexpressed the mAb55-derived H or kappa chain with the mAb13-derived kappa or H chain, respectively. The hybrid IgG Ab bearing the mAb55-derived H chain V segment paired with the mAb13-derived kappa V segment, but not that bearing the mAb13-derived H chain V segment paired with the mAb55-derived kappa V segment, bound multiple Ags, suggesting that the Ig H chain plays a major role in the Ig polyreactivity. Third, we shuffled the framework 1 (FR1)-FR3 and complementarity determining region 3 (CDR3) regions of the H and kappa chain V segments of the mAB55-derived IgG molecule with the corresponding regions of the monoreactive IgG mAb13. The mAb55-derived IgG molecule lost polyreactivity when the H chain CDR3, but not the FR1-FR3 region, was replaced by the corresponding region of mAb13, suggesting that within the H chain, the CDR3 provides the major structural correlate for multiple Ag-binding. This was formally proved by the multiple Ag-binding of the originally monoreactive mAb13-derived IgG molecule grafted with the mAb55-derived H chain CDR3. The polyreactivity of this chimeric IgG was maximized by grafting of the mAb55-derived kappa chain FR1-FR3, but not that of the kappa chain CDR3.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

Regulation of TCR delta and alpha repertoires by local and long-distance control of variable gene segment chromatin structure.

Murine Tcrd and Tcra gene segments reside in a single genetic locus and undergo recombination in CD4- CD8- (double negative [DN]) and CD4+ CD8+ (double positive [DP]) thymocytes, respectively. TcraTcrd locus variable gene segments are subject to complex regulation. Only a small subset of approximately 100 variable gene segments contributes substantially to the adult TCRdelta repertoire. Moreover, although most contribute to the TCRalpha repertoire, variable gene segments that are Jalpha proximal are preferentially used during primary Tcra recombination. We investigate the role of local chromatin accessibility in determining the developmental pattern of TcraTcrd locus variable gene segment recombination. We find variable gene segments to be heterogeneous with respect to acetylation of histones H3 and H4. Those that dominate the adult TCRdelta repertoire are hyperacetylated in DN thymocytes, independent of their position in the locus. Moreover, proximal variable gene segments show dramatic increases in histone acetylation and germline transcription in DP thymocytes, a result of super long-distance regulation by the Tcra enhancer. Our results imply that differences in chromatin accessibility contribute to biases in TcraTcrd locus variable gene segment recombination in DN and DP thymocytes and extend the distance over which the Tcra enhancer can regulate chromatin structure to a remarkable 525 kb.

Acetylation↗

Exploring developmental modes in a fossil arthropod: growth and trunk segmentation of the trilobite Aulacopleura konincki.

Trilobites offer the opportunity to explore postembryonic development within the fossil record of arthropod evolution. In contrast to most trilobites, the Silurian proetid Aulacopleura konincki from the Czech Republic exhibits marked variation in the mature number of thoracic segments, with five morphs with 18-22 thoracic segments. The combination of abundant articulated specimens available from a narrow stratigraphic interval and segmental intraspecific variation makes this trilobite singularly useful for studying postembryonic growth and segmentation. Trunk segmentation followed a hemianamorphic pattern, as seen in other arthropods and as characteristic of the Trilobita; during a first anamorphic phase, segments were accreted, while in the subsequent epimorphic phase, segmentation did not proceed further despite continued growth. Size increment during the anamorphic phase was targeted and followed Dyar's rule, a geometric progression typical of many arthropods. We consider alternative hypotheses for the control of the switch from anamorphic to epimorphic phases of development. Our analysis favors a scenario in which the mature number of thoracic segments was determined quite early in development rather than at a late stage in association with a critical size threshold. This study demonstrates that hypotheses concerning developmental pattern and control can be tested in organisms belonging to an extinct clade.

Animals↗

Segmentation of MR images for computer-assisted surgery of the lumbar spine.

This paper describes a segmentation algorithm designed to separate bone from soft tissue in magnetic resonance (MR) images developed for computer-assisted surgery of the spine. The algorithm was applied to MR images of the spine of healthy volunteers. Registration experiments were carried out on a physical model of a spine generated from computed tomography (CT) data of a surgical patient. Segmented CT, manually segmented MR and MR images segmented using the developed algorithm were compared. The algorithm performed well at segmenting bone from soft tissue on images taken of healthy volunteers. Registration experiments showed similar results between the CT and MR data. The MR data, which were manually segmented, performed worse on visual verification experiments than both the CT and semi-automatic segmented data. The algorithm developed performs well at segmenting bone from soft tissue in MR images of the spine as measured using registration experiments.

Algorithms↗

Segmenting eukaryotic genomes with the Generalized Gibbs Sampler.

Eukaryotic genomes display segmental patterns of variation in various properties, including GC content and degree of evolutionary conservation. DNA segmentation algorithms are aimed at identifying statistically significant boundaries between such segments. Such algorithms may provide a means of discovering new classes of functional elements in eukaryotic genomes. This paper presents a model and an algorithm for Bayesian DNA segmentation and considers the feasibility of using it to segment whole eukaryotic genomes. The algorithm is tested on a range of simulated and real DNA sequences, and the following conclusions are drawn. Firstly, the algorithm correctly identifies non-segmented sequence, and can thus be used to reject the null hypothesis of uniformity in the property of interest. Secondly, estimates of the number and locations of change-points produced by the algorithm are robust to variations in algorithm parameters and initial starting conditions and correspond to real features in the data. Thirdly, the algorithm is successfully used to segment human chromosome 1 according to GC content, thus demonstrating the feasibility of Bayesian segmentation of eukaryotic genomes. The software described in this paper is available from the author's website (www.uq.edu.au/ approximately uqjkeith/) or upon request to the author.

Algorithms↗

First prize: ureteral segmental replacement revisited.

BACKGROUND AND PURPOSE: Long strictures of the proximal ureter are difficult to manage, and circumferential replacement with various natural and synthetic materials has been unsuccessful. We sought to use cultured autologous cells seeded onto graft material for proximal-ureteral replacement. Additionally, we wished to determine if urothelial cell-seeded de-epithelialized small bowel would generate adequate ureteral replacement. MATERIALS AND METHODS: Three sets of experiments were performed. First, autologous pig-bladder smooth-muscle and urothelial cells were expanded in culture on large sheets of multilayer small-intestinal submucosa (SIS). These sheets were then tubularized and used to replace a 5-cm segment of proximal ureter in pigs. Second, autologous cells harvested from the bladders of Beagle dogs were cultured and seeded on porcine ureteral acellular matrix, which was used to replace a 3-cm segment of ureter in dogs. Segments were wrapped in omentum to enhance vascularity. Third, a de-epithelialized small-bowel segment seeded with autologous bladder-epithelial cells was transversally retubularized (Monti) into a 4-cm ureteral replacement. Follow-up studies consisted of retrograde pyelography, serum chemistry assays, hematoxylin/eosin studies, and immunohistopathologic examination using antibodies against alpha-smooth-muscle actin and pancytokeratin AE1-AE3. RESULTS: Coculture of urinary-tract cells on large segments of SIS failed to create adequate ureteral replacement. All grafts were contracted and stenotic, with complete obstruction of the ipsilateral renal unit. Similar results were seen in the Beagles. Despite clinical obstruction and gross contraction of the graft, a circumferential muscular ureteral wall lined with multilayer transitional epithelium was present. Urotheliumseeded de-epithelialized Monti bowel segments resulted in patent ureteral replacement without hydroureteronephrosis and with normal renal function, serum electrolytes, and acid-base balance. However, bowel mucosa fully regenerated, with multilayer transitional epithelium growing adluminally in continuity with the proximal and distal anastomotic sites. CONCLUSIONS: Seeding of ureteral grafts with autologous bladder cells does not promote success in two largeanimal models using different xenogenic acellular matrices. However, muscle and urothelium regeneration occurs with ureteral acellular matrix in the dog. Urothelium-seeded de-epithelialized Monti bowel segments may be an acceptable substitute for long proximal ureteral segments. Further technical refinements are required to replace the bowel mucosa completely with normal urothelium.

Animals↗

Cerebellar Purkinje neurons with altered terminal dendritic segments are present in all lobules of the cerebellar vermis of ageing, ethanol-treated F344 rats.

Previous studies from this Laboratory have shown that cerebellar Purkinje neurons (PN) in ageing, ethanol-fed Fischer 344 rats may have terminal dendritic segments that are longer than in control rats. They also showed that the longer terminal segments represented a toxic effect of ethanol on PN, because their increase in length resulted from an ethanol-induced deletion of other terminal dendritic segments and not from dendritic growth. The purpose of the present study was to determine whether this effect of ethanol was localized to specific lobules or was widely distributed within all lobules of the cerebellar vermis. Twelve-month-old male Fischer 344 rats were treated with a liquid ethanol diet for 48 weeks. Age- and weight-matched controls were pair-fed with an isocaloric control diet. Terminal dendritic segments in Golgi-Cox-stained PN in four groups of lobules in the cerebellar vermis of control and ethanol-fed rats were measured for treatment-related changes in length. Results from these measurements showed that ethanol-exposed PN with significantly longer terminal segments were present in all groups of lobules, i.e. they were widely distributed and not confined to specific lobules. Results from these measurements also confirmed in a large sample of neurons (40 neurons per rat) that the topologically distinct unpaired terminal segments were characteristically longer than the paired terminal segments in PN of control and ethanol-fed rats and that both types of terminal segments were longer in the ethanol-fed rats than in the controls.

Animals↗

Predicting alpha-helix and beta-strand segments of globular proteins.

All current methods of protein secondary structure prediction are based on evaluation of a single residue state. Although the accuracy of the best of them is approximately 60-70%, for reliable prediction of tertiary structure it is more useful to predict an approximate location of alpha-helix and beta-strand segments, especially prolonged ones. We have developed a simple method for protein secondary structure prediction which is oriented on the location of secondary structure segments. The method uses linear discriminant analysis to assign segments of a given amino acid sequence a particular type of secondary structure, by taking into account the amino acid composition of internal parts of segments as well as their terminal and adjacent regions. Four linear discriminant functions were constructed for recognition of short and long alpha-helix and beta-strand segments respectively. These functions combine three characteristics: hydrophobic moment, segment singlet, and pair preferences to an alpha-helix or beta-strand. The last two characteristics are calculated by summing the preference parameters of single residues and pairs of residues located in a segment and its adjacent regions. The final program SSP predicts all possible potential alpha-helices and beta-strands and resolves some possible overlap between them. Overall three-state (alpha, beta, c) prediction gives approximately 65.1% correctly predicted residues on 126 non-homologous proteins using the jackknife test procedure. Analysis of the prediction results shows a high prediction accuracy of long secondary structure segments (approximately 89% of alpha-helices of length > 8 and approximately 71% of beta-strands of length > 6 are correctly located with probability of correct prediction 0.82 and 0.78 respectively.(ABSTRACT TRUNCATED AT 250 WORDS)

Algorithms↗

Spontaneous rhythmic contractile behaviour of aortic ring segments isolated from pressure loaded regions of the vasculature.

STUDY OBJECTIVE: The aim was to study contractile responses of segments of rat arteries taken from pressure loaded and pressure protected regions and to examine the role of endothelial derived factors on the spontaneous activity of pressure loaded ring segments. DESIGN: Rats were subjected to complete aortic coarctation between the origins of the renal arteries and allowed to recover for 8 d. After 8 d arterial pressures were measured in awake animals from the pressure loaded and pressure protected regions simultaneously. Ring segments (2-3 mm) were taken from the two regions and mounted in a tissue bath for isometric force measurements. Similar studies were conducted in sham animals and in animals in which the kidney distal to the coarctation had been removed. EXPERIMENTAL MATERIAL: Female Sprague-Dawley rats, weight 200-250 g, were used. MEASUREMENTS AND MAIN RESULTS: Eight days after coarctation mean aortic pressure proximal to the occlusion was 168(SEM 1.29) mm Hg (n = 104) while distally it was 38(2.42) (n = 40). Of the rings tested 96% showed spontaneous rhythmic activity, having a mean frequency of 3.94(0.17) cycles.min-1. Spontaneous activity was not present in the pressure protected segments taken from the same animals. Rats with the distal kidney removed (n = 25) failed to become hypertensive and similarly prepared ring segments failed to show spontaneous rhythmic activity. Prior removal of the endothelial layer had no effect on the spontaneous contractile responses in pressure loaded segments. Histological examination showed that the media to lumen ratio was increased in coarcted rats in both pressure loaded and pressure protected regions compared to similar regions in sham operated animals. CONCLUSIONS: Pressure loaded arterial segments show spontaneous contractile activity when compared to sham segments by mechanisms not dependent on endothelial derived factors. The increase in pressure proximal to the occlusion is dependent on the renin-angiotensin system, since pressure was not increased when the distal kidney was removed. We hypothesise that the chronic pressure load induces fundamental changes in membrane permeability which leads to spontaneous contractile activity.

Acetylcholine↗