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PubMed1997

Mesoderm is required for the formation of a segmented endodermal cell layer in the leech Helobdella.

The homeobox gene Lox3 is expressed in a segmentally iterated pattern within the endoderm of the leech Helobdella. We use that expression here to study endoderm differentiation following experimental ablations of mesoderm. Lox3 RNA was first detected by in situ hybridization at the stage when a definitive cellular endoderm is formed from its syncytial precursor and was never observed in derivatives of other germ layers. Expression is initially distributed throughout the endoderm, but rapidly disappears from specific regions of the nascent gut wall so as to produce a pattern of segmental stripes. The stripe pattern differs markedly between midgut organs, with thin stripes of Lox3 expression in the intercaecal constrictions of the crop and wide stripes of Lox3 expression marking the caecal bulges of the intestine. Lox3 expression in the rectum is not obviously segmental. Ablation of segmental mesoderm in the early Helobdella embryo prevents the formation of definitive endoderm and the expression of Lox3 RNA and leads to abnormalities in the morphogenesis of the gut tube. These endodermal deficits are precisely coextensive with the zone of mesodermal deficiency, suggesting that the mesoderm normally acts to promote the formation of the endodermal cell layer via local cell interactions. The segmental pattern of Lox3 expression is largely unaffected in portions of the endoderm surrounding such deficits, suggesting that endodermal segmentation is not established by lateral interactions within that tissue layer. Rather, we propose that the segmental organization of the endoderm is imprinted by vertical interactions with the segmental mesoderm.

Amino Acid Sequence↗

PubMed1999

Notch-mediated segmentation and growth control of the Drosophila leg.

The possession of segmented appendages is a defining characteristic of the arthropods. By analyzing both loss-of-function and ectopic expression experiments, we show that the Notch signaling pathway plays a fundamental role in the segmentation and growth of the Drosophila leg. Local activation of Notch is necessary and sufficient to promote the formation of joints between segments. This segmentation process requires the participation of the Notch ligands, Serrate and Delta, as well as Fringe. These three proteins are each expressed in the developing leg and antennal imaginal discs in a segmentally repeated pattern that is regulated downstream of the action of Wingless and Decapentaplegic. Our studies further show that Notch activation is both necessary and sufficient to promote leg growth. We also identify target genes regulated both positively and negatively downstream of Notch signaling that are required for normal leg development. Together, these observations outline a regulatory hierarchy for the segmentation and growth of the leg. The Notch pathway is also deployed for segmentation during vertebrate somitogenesis, which raises the possibility of a common origin for the segmentation of these distinct tissues.

Aging↗

PubMed2000

islet reveals segmentation in the Amphioxus hindbrain homolog.

The vertebrate embryonic hindbrain is segmented into rhombomeres. Gene expression studies suggest that amphioxus, the closest invertebrate relative of vertebrates, has a hindbrain homolog. However, this region is not overtly segmented in amphioxus, raising the question of how hindbrain segmentation arose in chordate evolution. Vertebrate hindbrain segmentation includes the patterning of cranial motor neurons, which can be identified by their expression of the LIM-homeodomain transcription factor islet1. To learn if the amphioxus hindbrain homolog is cryptically segmented, we cloned an amphioxus gene closely related to islet1, which we named simply islet. We report that amphioxus islet expression includes a domain of segmentally arranged cells in the ventral hindbrain homolog. We hypothesize that these cells are developing motor neurons and reveal a form of hindbrain segmentation in amphioxus. Hence, vertebrate rhombomeres may derive from a cryptically segmented brain present in the amphioxus/vertebrate ancestor. Other islet expression domains provide evidence for amphioxus homologs of the pineal gland, adenohypophysis, and endocrine pancreas. Surprisingly, homologs of vertebrate islet1-expressing spinal motor neurons and Rohon-Beard sensory neurons appear to be absent.

Amino Acid Sequence↗

PubMed1994

Organization of the V gene segments in mouse T-cell antigen receptor alpha/delta locus.

The mouse T-cell receptor (TCR) alpha/delta locus was mapped using 17 V alpha and 4 V beta subfamily-specific probes. Four complementary methods were used: (1) an estimate of the V gene repertoire by Southern blot analysis of genomic DNA with subfamily-specific probes; (2) an analysis of V gene segments deleted by TCR gene rearrangements from a panel of T-cell tumors and hybridomas; (3) an analysis of overlapping clusters of cosmid clones; and (4) an analysis of large DNA fragments separated by field-inversion gel electrophoresis. The alpha/delta locus spans about 1 Mb. The distance between the 3'-most V gene segment (V delta 1) and the delta constant gene (C delta) is no more than 150 kb. Sixty-six V gene segments have been mapped physically on cosmids. The members of individual V alpha gene segment subfamilies are dispersed throughout the locus. In contrast, the V delta gene segments V delta 1 to 5 are clustered at the 3' end of the V gene segment cluster. At least two DNA segment duplications, 45 to 80 kb in length, are present in the locus. These data provide information on the evolution of the alpha/delta locus and on organization features that might influence the expression of specific V gene segments in gamma delta cells.

Animals↗

PubMed1994

Recent translocation of variable and diversity segments of the human immunoglobulin heavy chain from chromosome 14 to chromosomes 15 and 16.

We studied the organization and origin of three orphon regions, VH-F, D5-a, and D5-b, of the human immunoglobulin heavy-chain gene using yeast artificial chromosomes. VH-F and two D5 regions were mapped to chromosome bands 16p11 and 15q11-q12, respectively, by using human/rodent somatic cell hybrids and fluorescence in situ hybridization. No D5 segments were found on chromosome 14, in contradiction to previous reports. The VH-F region consists of 7 VH segments and encompasses 160 kb of DNA. A cluster of VH segments homologous to the VH-F region orphons was found in the region 245-430 kb (V2-26 to V3-11) upstream of the JH cluster on chromosome 14. Comparison of VH sequences between the VH-F and the chromosome 14 loci indicates that the translocation of the VH-F region took place, at the earliest, 20 x 10(6) years ago. The D5-a and D5-b regions were obtained in two independent contigs. The former contains only D segments in 140 kb of DNA, while the latter carries 3 VH segments downstream of D segments in 110 kb of DNA. V54, one of these VH orphon segments, is about 95% homologous to V1-18, which is located within the putative ancestor of the VH-F region on chromosome 14. Furthermore, the region detected by two DNA probes flanking the V54 segment was found only in the proximity of V1-18 within the 0.8-Mb VH region on chromosome 14. These results suggest that the two orphon loci on chromosomes 15 and 16 may have been translocated simultaneously.

Animals↗

PubMed1996

Dimerisation of the glycophorin A transmembrane segment in membranes probed with the ToxR transcription activator.

Specific interactions between membrane spanning polypeptide segments are important for folding and oligomerisation of integral membrane proteins. Previously the dimerisation of glycophorin A has been shown to depend on interactions between its transmembrane segment by studying chimeric proteins in detergent solution. Here, we examined dimerisation of the glycophorin A transmembrane segment in a natural membrane employing the ToxR transcription activator from Vibrio cholerae. The ToxR protein is integral to the bacterial inner membrane and its activity requires a dimeric state. Therefore, the ToxR protein is suited to monitor quantitative homophilic interactions. We replaced the ToxR transmembrane segment with parts of the glycophorin A transmembrane segment containing the amino acid motif LIxxGVxxGVxxT previously shown to be sufficient for dimerisation in detergent solution. Expression of these chimeric proteins in an indicator strain resulted in strong transcription activation. This is indicative of efficient dimerisation mediated by the glycophorin transmembrane segment inserted into the inner membrane. Analysis of individual point mutants revealed that at least four residues out of this motif are critical for dimer formation in membranes. However, dimerisation of the glycophorin A transmembrane segment appears to be less sensitive to mutations when localised within a natural lipid bilayer compared to measurements in detergent solution. This may be related to a slightly altered structure of the dimer and/or to a higher local concentration and preorientation of the interacting molecules in a membrane. This makes the ToxR system well suited for probing low-affinity interactions between the transmembrane segments of other proteins.

Amino Acid Sequence↗

PubMed1998

Lambda repressor N-terminal DNA-binding domain as an assay for protein transmembrane segment interactions in vivo.

To understand the determinants of membrane protein interactions, we have developed an in vivo genetic assay system for detecting homodimerization of transmembrane (TM) segments from integral membrane proteins. Our approach is to generate gene fusions between potentially dimerizing TM segments and a cytoplasmic DNA-binding protein that lacks its intrinsic dimerization domain. This genetic approach allows us to screen and distinguish among known dimerizing domains and weakly dimerizing mutants, as well as non-dimerizing TM segments. We replaced the bacteriophage lambda cI repressor C-terminal dimerization domain with the human erythrocyte glycophorin A transmembrane segment (GpA TM). GpA TM forms SDS-resistant homodimers in vitro. Expression of this membrane-associated fusion in Escherichia coli conferred the same degree of immunity to lambda cI phages as the wild-type, intact lambda repressor. Single amino acid substitutions that disrupt the GpA TM dimer interface were introduced into the lambda-GpA TM fusion proteins. These mutations dramatically reduced immunity of E. coli to lambda cI, such that the efficiency of plating these phages increased by greater than 10,000-fold over that conferred by the wild-type lambda-GpA TM fusion. Introduction of the putatively non-dimerizing first TM from E. coli MalF into the lambda-TM fusion vector resulted in no immunity to lambda cI phages. Fusion of the homodimeric, periplasmically localized, mature alkaline phosphatase domain to the C terminus of the lambda-TM fusion proteins containing weakly to non-dimerizing TM segments restored immunity to lambda cI phages. Results from this in vivo genetic assay system demonstrate that (1) dimerization of the lambda cI DNA-binding domain can be promoted by dimerizing TM segments, (2) strongly, weakly, and non-dimerizing TM segments can be distinguished on the basis of their ability to confer immunity to lambda cI phages, and (3) introduction of a dimerizing periplasmic domain can provide functionality to lambda-TM fusions containing weakly to non-dimerizing TM segments.

Alkaline Phosphatase↗

PubMedDate not supplied

Three-dimensional membrane crystals in amphibian cone outer segments. 1. Light-dependent crystal formation in frog retinas.

When frog retinas are exposed to light, a series of three-dimensional crystals develop within the outer segment disk system of cones but not rods. The crystals involve components that span cytoplasmic, disk membrane, and intradisk domains of the outer segment. The crystalline membrane domains are directly continuous with adjacent, noncrystalline lamellar regions. In axial extent, the crystals may involve as few as 1 or 2 disks or as many as 30 disks. However, within each disk, only one crystalline domain typically is observed. Within a crystal, the membranes are more planar in shape and more uniform in axial spacing then adjacent, noncrystalline lamellar regions. Furthermore, as crystalline domains expand laterally, one observes increased axial spacing disorder in noncrystalline lamellar regions, along with an increase in the width of the intradisk compartment. Thus, crystals appear to grow laterally by depleting adjacent lamellar regions of components that influence the normal membrane pair separation and axial spacing of cone outer segment disks. In isolated retinas, the crystalline domains appear to be randomly distributed along the length of the outer segment and show no preference for association with either the closed or open margins of the disk. After 45 min in the light, the crystals occupy approximately 10% of the cone outer segment volume. On the basis of comparative structural, biochemical, and physiological data, cone outer segment crystals may represent a cocrystal between bleached, phosphorylated opsin (providing transmembrane and intradisk elements) and the cytoplasmic protein, arrestin (providing trans-cytoplasmic elements). Thus, crystal formation may provide one mechanism of light adaptation within the cone outer segment. The spontaneous, bleaching-induced formation of these crystals in situ offers the possibility that cocrystals of cone outer segment components can be prepared in vitro for higher resolution crystallographic analyses.

Animals↗

PubMed1995

Complete nucleotide sequences of 5'- and 3'-noncoding regions of both genome segments of different strains of infectious bursal disease virus.

The terminal sequences of both genomic dsRNA segments of different strains of infectious bursal disease virus were determined. Analysis of the linear sequences revealed in the 5'-noncoding region of both segments the presence of a 32-nucleotide sequence with motifs conserved between segments and serotypes. The 3'-noncoding regions showed a high degree of conservation within segment A or B, but differed between segments. Different inverted terminal repeats were detected in both segments. A sequence of 13 nucleotides found in the 5'-noncoding regions of both segments could function as a binding site for chicken 18 S rRNA. Secondary structure prediction of the different noncoding regions showed a high degree of similarity. Surprisingly, the predicted secondary structure of the 5'-noncoding region of segment A differed between serotypes. A possible influence of these different RNA structures on viral replication is discussed.

Animals↗

PubMed2005

Spectral clustering algorithms for ultrasound image segmentation.

Image segmentation algorithms derived from spectral clustering analysis rely on the eigenvectors of the Laplacian of a weighted graph obtained from the image. The NCut criterion was previously used for image segmentation in supervised manner. We derive a new strategy for unsupervised image segmentation. This article describes an initial investigation to determine the suitability of such segmentation techniques for ultrasound images. The extension of the NCut technique to the unsupervised clustering is first described. The novel segmentation algorithm is then performed on simulated ultrasound images. Tests are also performed on abdominal and fetal images with the segmentation results compared to manual segmentation. Comparisons with the classical NCut algorithm are also presented. Finally, segmentation results on other types of medical images are shown.

Algorithms↗

PubMed2003

Expectation maximization strategies for multi-atlas multi-label segmentation.

It is well-known in the pattern recognition community that the accuracy of classifications obtained by combining decisions made by independent classifiers can be substantially higher that the accuracy of the individual classifiers. In order to combine multiple segmentations we introduce two extensions to an expectation maximization (EM) algorithm for ground truth estimation based on multiple experts (Warfield et al., MICCAI 2002). The first method repeatedly applies the Warfield algorithm with a subsequent integration step. The second method is a multi-label extension of the Warfield algorithm. Both extensions integrate multiple segmentations into one that is closer to the unknown ground truth than the individual segmentations. In atlas-based image segmentation, multiple classifiers arise naturally by applying different registration methods to the same atlas, or the same registration method to different atlases, or both. We perform a validation study designed to quantify the success of classifier combination methods in atlas-based segmentation. By applying random deformations, a given ground truth atlas is transformed into multiple segmentations that could result from imperfect registrations of an image to multiple atlas images. We demonstrate that a segmentation produced by combining multiple individual registration-based segmentations is more accurate for the two EM methods we propose than for simple label averaging.

Algorithms↗

PubMed1998

Phylogenetic analysis of African horse sickness virus segment 10: sequence variation, virulence characteristics and cell exit.

African horse sickness virus (AHSV) genome segment 10 encodes the non-structural proteins NS3/NS3a, which is involved in release of virus from cells. Full length segment 10 cDNAs were amplified by reverse transcription-polymerase chain reaction, from isolates of AHSV serotypes 2, 3, 4, 5, 7, 8 and 9. These cDNAs were cloned, sequenced and their phylogenetic relationships analysed. High levels of sequence homology were detected in segment 10 from some isolates of different serotypes, confirming that they could be grouped on this basis (serotypes 4, 5, 6 and 9 (group alpha); serotypes 3 and 7 (group beta); serotypes 1, 2, and 8 (group gamma). However, data from bluetongue virus (the prototype orbivirus) indicate that the AHSV serotype is determined exclusively by the structural outer coat proteins VP2 and VP5, encoded by genome segments 2 and 5 respectively. Therefore, as a direct consequence of genome segment reassortment between AHSV strains from different serotypes, the differences observed in segment 10 do not give a reliable indication of virus serotype. Segment 10 of AHSV 3 (virulent) and AHSV 3att (attenuated) were also analysed. These strains, together with AHSV 8, have been used to study of the genetic basis of virulence using reassortment (O'Hara et al., this publication). Virus release studies, using Culicoides cell cultures, indicate that differences in segment 10 of AHSV 3att and 8 can influence the timing of virus release from the infected cell.

African Horse Sickness Virus↗

PubMed1991

The effect of heat shocks, which alter somite segmentation, on Rohon-Beard neurite outgrowth from the spinal cord of Xenopus embryos.

The vertebrate spinal cord shows a segmental pattern of dorsal and ventral nerve roots. It is believed that this peripheral neural segmentation depends on the segmentation of the somitic mesoderm into somites. I have studied the relationship between somite segmentation and the pattern of Rohon-Beard sensory neurite outgrowth from the spinal cord in Xenopus embryos. Most Rohon-Beard neurites grow out in fascicles from the spinal cord at the intersomite clefts, a smaller number of neurites growing out over the dorsal somite margins. Previous work on peripheral neural segmentation has relied on transplanting or destroying somitic mesoderm. Here a non-invasive technique has been used. The pattern of somite segmentation was disrupted by heat shocks, leading to regions of somite fusion where one or two intersomite clefts are absent. At the regions of somite fusion the number of sensory fascicles is then unchanged but their distribution is different. The segmental pattern of sensory fascicle outgrowth is replaced by a fairly even distribution of outgrowth fascicles. Two interpretations of the difference in fascicle outgrowth at fused and control somites are discussed. Firstly, that heat shocks have a direct affect on fascicle outgrowth. Secondly, that heat shocks affect fascicle outgrowth indirectly by disrupting somite segmentation.

Animals↗

PubMed1992

Sensory segmentation with coupled neural oscillators.

We present a model of sensory segmentation that is based on the generation and processing of temporal tags in the form of oscillations, as suggested by the Dynamic Link Architecture. The model forms the basis for a natural solution to the sensory segmentation problem. It can deal with multiple segments, can integrate different cues and has the potential for processing hierarchical structures. Temporally tagged segments can easily be utilized in neural systems and form a natural basis for object recognition and learning. The model consists of a "cortical" circuit, an array of units that act as local feature detectors. Units are formulated as neural oscillators. Knowledge relevant to segmentation is encoded by connections. In accord with simple Gestalt laws, our concrete model has intracolumnar connections, between all units with overlapping receptive fields, and intercolumnar connections, between units responding to the same quality in different positions. An inhibitory connection system prevents total correlation and controls the grain of the segmentation. In simulations with synthetic input data we show the performance of the circuit, which produces signal correlation within segments and anticorrelation between segments.

Animals↗

PubMed1989

Outer segment growth and periciliary vesicle turnover in developing photoreceptors of Xenopus laevis.

It has been proposed that periciliary vesicles in the photoreceptor inner segment represent newly synthesized membrane en route to the outer segment, and that membrane is delivered to the outer segment via fusion of these vesicles with the plasma membrane at the base of the connecting cilium and sclerad flow of the ciliary membrane. The present research was undertaken to test the periciliary vesicle hypothesis and clarify the dynamics of membrane flow in vertebrate photoreceptors. Light- and electron-microscopic measurements on developing photoreceptors in the retina of Xenopus laevis were used to determine the amount of membrane in outer segments and in periciliary vesicles. No significant diurnal variations were found in outer segment growth rate or size of the periciliary vesicle population. In all rods and in cones at the end of the experiment, the area of periciliary vesicle membrane was proportional to the rate at which membrane was added to the outer segment. Thus, the turnover time for the periciliary vesicle population was similar in rods and cones, supporting the periciliary vesicle hypothesis. Quantification of periciliary vesicle membrane in inner segments provides a method for determining the rate at which membrane is added to outer segments, heretofore not possible for cones.

Animals↗

PubMed1978

The outer segments of photoreceptive pinealocytes in the pineal organ of the funa, Carassius gibelio langsdorfi. A scanning electron microscopic study.

The form and size of the outer segments of photoreceptive pinealocytes in the pineal organ of the funa, Carassius gibelio langsdorfi, were observed with the scanning electron microscope. The height of the outer segments measures between 1 and 3 micrometer and the diameter varies widely from 1.5 to 8 micrometer. Various forms of outer segments, i.e. a slender type, a dome-like type, a cap-like type and a helical type, were demonstrated. The parallel-oriented filamentous processes of the inner segments have the same length as the outer segments and a diameter of approximately 100 nm; they are projections from the apical border of the inner segment and surround the cone-like outer segments. The processes make a right angle with the lamellar disks. The distance between two processes averages 100 nm. The lamellar disks of the outer segments are oriented at right angles to the modified cilium in the basal part, but the angle often changes in the peripheral part, where the lamellar disks are raised and become parallel to the cilium.

Animals↗

PubMed1990

Distal invaginations and the renewal of cone outer segments in anuran and monkey retinas.

Although it is now clear that the outer segments of mature vertebrate cones are regularly renewed, it is not known how a cone outer segment can maintain a tapered shape if its narrower tip is periodically lost by shedding. This problem was addressed by morphological examination of photoreceptors in retinas of anurans (Xenopus laevis) and monkeys (Macaca fascicularis). Light microscopy revealed a marked daily change in the shape of cone outer segments in X. laevis: at light offset they were long and conical, at light onset they had shed their narrow tips, were sharply truncated, and 40% shorter. Electron microscopy revealed previously undescribed fine-structural features in these mature cone outer segments, most notably the presence of many partial membrane infoldings within their distal lamellae. The growth of each of these "distal invaginations" apparently split 1 pre-existing distal lamella into 2 daughter lamellae of reduced width. The formation of distal invaginations at various heights within a cone outer segment would thus make it longer and narrower. Similar ultrastructural features were also found in cone outer segments of monkey retinas. These findings suggest that during outer segment renewal the tapered shape of mature cone outer segments is maintained via a remodelling process that accompanies the formation of distal invaginations.

Animals↗

PubMed1990

High endocytotic and lysosomal activities in segments of rat myotubes differentiated in vitro.

Endocytosis and the lysosome system have been studied in rat myotubes differentiated in vitro. Horseradish peroxidase was used as marker for endocytosis and was found to accumulate unevenly in the myotubes. Small segments of myotubes display very high endocytotic activity. Similar segments contained numerous lysosomes, as seen by the accumulation of neutral red or histochemical staining for acid phosphatase. The segments also contained accumulations of acetylcholine receptors as determined by binding of tetramethyl rhodamine-labelled alpha-bungarotoxin. Unstained segments in living cultures could be recognized by phase-contrast microscopy since they often appeared somewhat dilated and were not as well spread on the culture surface as the main parts of the myotubes. Ultrastructurally, the segments contained an intensely proliferating tubular system in communication with the extracellular space, which therefore probably represents the developing transverse tubular system. The segments also contained endocytosed marker within large phagosomes. Contractile filaments occurred in the segments but were frequently less well-organized than in other parts of the myotubes. The described characteristics of the segments in rat myotubes differentiated in vitro bear resemblance to some of the characteristics of the denervated endplate region of adult muscle.

Animals↗