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PubMed2026

Genomic and Transcriptomic Correlates of Deep PSA Response in Patients with Metastatic Androgen Pathway Modulation-Sensitive Prostate Cancer.

BACKGROUND: Despite advances in metastatic androgen pathway modulation-sensitive prostate cancer (mAPMS) treatment, outcomes remain heterogeneous. Achieving a post-treatment undetectable prostate specific antigen (PSA) is a strong prognostic marker. We aimed to identify genomic and transcriptomic determinants of PSA response in a real-world clinical-genomic cohort. PATIENTS AND METHODS: Patients with mAPMS who underwent DNA (Tempus xT) and, in a subset, RNA (Tempus xR) sequencing were identified from the Tempus Lens database. Inclusion required stage IV disease within 90 days of sample collection and samples obtained within 12 months before or 3 months after treatment initiation. Patients with PSA at 6 months (n = 525) were classified as PSA-low (<0.1 ng/mL, n = 240) or PSA-high (≥0.1 ng/mL, n = 285). Overall survival (OS) was assessed by 6-month landmark analysis with delayed-entry adjustment. Logistic and Cox models were adjusted for clinical variables. Sensitivity analyses used a relative definition of > 95% PSA decline from baseline. RESULTS: Baseline PSA was lower in PSA-low versus PSA-high patients (24 vs 36 ng/mL, p = 0.01). SPOP (17% vs 11%) and ZFHX3 (2.5% vs 6%) alterations differed between groups, but neither persisted after adjustment. Using the relative definition, ZMYM3 and JAK1 alterations were independently associated with failure to achieve a deep PSA response. Expression of PSMA, TROP2, B7-H3, and STEAP1 did not differ between groups. PSA-low status was independently associated with improved OS, as was deep relative response. CONCLUSION: Deep PSA response at 6 months correlates with improved OS in mAPMS. Integrating molecular markers with PSA response may inform treatment intensification or de-escalation strategies.

Biomarkers↗

PubMed2001

A phylogeny of the land snails (Gastropoda: Pulmonata).

We have undertaken the first large-scale molecular phylogenetic analysis of the Stylommatophora. Sequences of the ribosomal RNA gene-cluster were examined in 104 species of snails and slugs from 50 families, encompassing all the currently recognized major groups. It allows an independent test of the present classification based on morphology. At the level of families our molecular phylogeny closely supports the current taxonomy, but the deep branches within the tree do not. Surprisingly, a single assemblage including the families Achatinidae, Subulinidae and Streptaxidae lies near the base of the tree, forming a sister group to all remaining stylommatophorans. This primary division into 'achatinoid' and 'non-achatinoid' taxa is unexpected, and demands a radical reinterpretation of early stylommatophoran evolution. In particular, the Orthurethra appear to be relatively advanced within the 'non-achatinoid clade', and broadly equivalent to other super-familial clusters. This indicates that supposedly primitive features such as the orthurethran kidney are derived. The molecular tree also suggests that the origin of the Stylommatophora is much earlier than the main period of their diversification.

Animals↗

PubMed1997

Quantitative analyses of myosin heavy-chain mRNA and protein isoforms in single fibers reveal a pronounced fiber heterogeneity in normal rabbit muscles.

A highly sensitive method of reverse-transcriptase polymerase chain reaction (RT-PCR) was established to study myosin heavy-chain (MHC) mRNA isoform expression in single fibers of rabbit limb muscles. In combination with myofibrillar adenosine triphosphatase histochemistry and electrophoretic separation of MHC protein isoforms in fragments of the same fibers, the direct RT-PCR method identified the pMHC20-40 and pMHC24-79 cDNA sequences as being specific to MHCIIb and MHCIId/x isoforms, respectively. In addition, a direct RT-PCR was established for determining relative amounts of MHC mRNA isoforms by using a sequence specific to alpha-skeletal actin as an endogenous reference. Analyses of large amounts of single fibers revealed an unexpected heterogeneity of the fast fiber population with regard to numerous fibers coexpressing MHCIIb and MHCIId/x. Based on quantitative RT-PCR, the percentages of MHCIIb/MHCIId hybrid fibers amounted to approximately 55% in the deep portion of gastrocnemius, to 43% in the adductor magnus, and to 12% in psoas muscle. Moreover, the two MHC mRNA isoforms were nonuniformly distributed along the fiber length. Qualitative RT-PCR detected even higher amounts of hybrid fibers in the three muscles. The percentages of hybrid fibers identified at the protein level were smaller in adductor magnus muscle (25%) and psoas muscle (5%), but equaled that of the mRNA analysis in gastrocnemius muscle (61%). The detection of high amounts of IIBD and IIDB fibers suggested that hybrid fibers represent functional elements within the fiber spectrum of normal muscles. Our observations on hybrid fibers reveal a heterogeneity within the fiber population of normal muscles that has not been realized to date.

Animals↗

PubMed1997

The T1/35kDa family of poxvirus-secreted proteins bind chemokines and modulate leukocyte influx into virus-infected tissues.

Immunomodulatory proteins encoded by the larger DNA viruses interact with a wide spectrum of immune effector molecules that regulate the antiviral response in the infected host. Here we show that certain poxviruses, including myxoma virus. Shope fibroma virus, rabbitpox virus, vaccinia virus (strain Lister), cowpox virus, and raccoonpox virus, express a new family of secreted proteins which interact with members of both the CC and CXC superfamilies of chemokines. However, swinepox virus and vaccinia virus (strain WR) do not express this activity Using a recombinant poxviruses, the myxoma M-T1 and rabbitpox virus 35kDa secreted proteins were identified as prototypic members of this family of chemokine binding proteins. Members of this T1/35kDa family of poxvirus-secreted proteins share multiple stretches of identical sequence motifs, including eight conserved cysteine residues, but are otherwise unrelated to any cellular genes in the database. The affinity of the CC chemokine RANTES interaction with M-T1 was assessed by Scatchard analysis and yielded a Kd of approximately 73 nM. In rabbits infected with a mutant rabbitpox virus, in which the 35kDa gene is deleted, there was an increased number of extravasating leukocytes in the deep dermis during the early phases of infection. These observations suggest that members of the T1/35kDa class of secreted viral proteins bind multiple members of the chemokine superfamily in vitro and modulate the influx of inflammatory cells into virus-infected tissues in vivo.

Amino Acid Sequence↗

PubMed2005

Population differentiation decreases with depth in deep-sea bivalves.

The deep sea is the largest ecosystem on Earth. Recent exploration has revealed that it supports a highly diverse and endemic benthic invertebrate fauna, yet the evolutionary processes that generate this remarkable species richness are virtually unknown. Environmental heterogeneity, topographic complexity, and morphological divergence all tend to decrease with depth, suggesting that the potential for population differentiation may decrease with depth. To test this hypothesis, we use mitochondrial DNA (16S rRNA gene) to examine patterns of population differentiation in four species of protobranch bivalves (Nuculoma similis, Deminucula atacellana, Malletia abyssorum, and Ledella ultima) distributed along a depth gradient in the western North Atlantic. We sequenced 268 individuals from formalin-fixed samples and found 45 haplotypes. The level of sequence divergence among haplotypes within species was similar, but shifted from between populations at bathyal depths to within populations at abyssal depths. Levels of population structure as measured by phiST were considerably greater in the upper bathyal species (N. similis = 0.755 and D. atacellana = 0.931; 530-3834 m) than in the lower bathyal/abyssal species (M. abyssorum = 0.071 and L. ultima = 0.045; 2864-4970 m). Pairwise genetic distances among the samples within each species also decreased with depth. Population trees (UPGMA) based on modified coancestry coefficients and nested clade analysis both indicated strong population-level divergence in the two upper bathyal species but little for the deeper species. The population genetic structure in these protobranch bivalves parallels depth-related morphological divergence observed in deep-sea gastropods. The higher level of genetic and morphological divergence, coupled with the strong biotic and abiotic heterogeneity at bathyal depths, suggests this region may be an active area of species formation. We suggest that the steep, topographically complex, and dynamic bathyal zone, which stretches as a narrow band along continental margins, plays a more important role in the evolutionary radiation of the deep-sea fauna than the much more extensive abyss.

Analysis of Variance↗

PubMed2003

[MR imaging of ano-perineal suppurations].

A good digital examination is usually sufficient for the diagnosis and the treatment planning of anal fistulae. Cross-sectional imaging techniques, however, can accurately identify deep abscesses and characterize complex fistulae. MRI is well suited for this examination, with almost no motion artifact, excellent contrast between muscles and fatty spaces, and multiplanar acquisition. A fistula starts from an internal opening in the digestive tube and can end in an abscess cavity or open at the skin at an external opening. The cryptoglandular anal fistulae (fistula-in-ano) are non-specific in origin and are usually simple, whereas specific fistulae are due to many diseases such as Crohn's disease, tuberculosis, trauma, radiation, colloid carcinoma, hidradenitis suppurative, actinomycosis or lymphoma and are often complex. MRI appears useful in the cases with recurrent fistulae, Crohn's disease, when the secondary orifice is atypically placed, during a multistep treatment for complex fistulae, or when an anal stenosis forbids a clinical or ultrasound examination. A good knowledge of the perineum anatomy is required for analysing the fistula tracts. The muscle planes separate fatty spaces which have an important role in the spread of the disease: sub-mucosal space, marginal space, intersphincteric space, postanal space of Courtney, supralevator space, and the two ischioanal spaces on both sides of the anal canal. The anal canal is surrounded by the ring-like internal sphincter, which continues the internal muscularis propria of the rectum, and the external sphincter, which is intermingled with the puborectalis muscle. We perform our MRI examination with an external phased array coil, and we place a cannula to identify the anal canal. The T2W sequences give the more interesting information, but the sequences with fat-suppression and gadolinium chelate injection are also very useful. The MRI examination allows the analysis of: 1) the location of the fistula tracts according to Park's classification, 2) the location of the internal opening, 3) the locations of the external opening(s), 4) the location of deep abscesses, 5) the long distance extensions, 6) the state of the ano-rectal wall and the perirectal spaces, 6) the damages of the anal sphincter.

Abscess↗

PubMed2003

Kinematics of the patella in deep flexion. Analysis with magnetic resonance imaging.

BACKGROUND: Little information is available on the kinematics of the normal knee in deep flexion. The purpose of this study was to use magnetic resonance imaging to analyze the patellofemoral articulation in deep flexion. METHODS: Axial scans were made of the patellofemoral joint of twenty healthy Japanese volunteers with the knee in approximately 90 degrees of flexion, in maximum active flexion (mean [and standard deviation], 140 degrees +/- 10 degrees ), and in maximum passive flexion (mean, 156 degrees +/- 5 degrees ). A fat-suppressed, three-dimensional, fast low-angle shot sequence was used to visualize the articular cartilage. The patellofemoral contact area was determined on sequential images and was reconstructed three-dimensionally. RESULTS: At 90 degrees of flexion, the contact area on the patella was continuous over the medial and lateral facets in fourteen knees and was located in the proximal half of the articular surface. At maximum active and passive flexion, the odd facet engaged in fifteen and eighteen knees, respectively. At maximum passive flexion, the contact area of the lateral facet moved distally and decreased significantly (p = 0.0002). From 90 degrees of flexion to maximum active flexion, the mean total contact area remained constant (3.43 +/- 0.70 and 3.62 +/- 0.72 cm (2), respectively); it then decreased significantly in maximum passive flexion (2.96 +/- 0.78 cm (2), p = 0.04). CONCLUSIONS: The contact area on the patella was divided into two parts (the odd and lateral facets) and moved distally in deep knee flexion. The size of the contact area on the lateral facet significantly decreased in maximum passive flexion.

Activities of Daily Living↗

PubMed2001

Identification of polymorphisms in the 5'-untranslated region of the TAFI gene: relationship with plasma TAFI levels and risk of venous thrombosis.

BACKGROUND AND OBJECTIVES: Thrombin activatable fibrinolysis inhibitor (TAFI) plays an important role in hemostasis, functioning as a potent fibrinolysis inhibitor. TAFI gene variations may contribute to plasma TAFI levels and thrombotic risk. DESIGN AND METHODS: We sequenced a 2083-bp region of the 5'-regulatory region of the TAFI gene in 127 healthy subjects searching for variations, and correlated identified polymorphisms with plasma TAFI levels. TAFI polymorphisms were examined as risk factors for venous thrombosis by determining their prevalence in 388 patients with deep venous thrombosis (DVT) and in 388 controls. RESULTS: Seven novel polymorphisms were identified: -152 A/G, -438 A/G, -530 C/T, -1053 T/C, -1102 T/G, -1690 G/A, and -1925 T/C. -152 A/G, -530 C/T and -1925 T/C were found to be in strong linkage disequilibrium, as were the -438 A/G, -1053 T/C, -1102 T/G and -1690 G/A. Plasma TAFI levels were higher in -438GG/-1053CC/-1102GG/-1690AA homozygotes than in -438AG/-1053TC/-1102TG/-1690GA heterozygotes, and -438AA/-1053TT/-1102TT/-1690GG homozygotes had the lowest TAFI levels (p=0.0003). TAFI concentrations in -152AA/-530CC/-1925TT homozygotes were somewhat higher but not significantly different from levels observed for -152AG/-530CT/-1925TC heterozygotes. Taken in combination, -438AG/-1053TC/-1102TG/-1690GA and -438AA/-1053TT/-1102TT/-1690GG yielded an OR for DVT of 0.8 (95%CI: 0.6-1). In subjects aged <35 years the OR was 0.7 (95%CI: 0.5-1.1). The OR for -152AG/-530CT/-1925TC was 1 (95%CI: 0.5-2.2) in the whole group of patients and controls, whereas in subjects aged <35 years the OR was 0.1 (95%CI: 0.02-0.9). INTERPRETATION AND CONCLUSIONS: Polymorphisms in the TAFI promoter determine plasma antigen levels and may influence the risk of venous thrombophilia.

5' Untranslated Regions↗

PubMed1972

The covalent and three-dimensional structure of concanavalin A.

The tentative amino-acid sequence and three-dimensional structure of the lectin concanavalin A have been determined. The amino-acid sequence, which was determined chemically, contains 238 residues. The sequences of three short stretches were assigned on the basis of x-ray crystallographic data. Interpretation of an electron density map at 2-A resolution indicates that the predominant structural element is extended polypeptide chain arranged in two anti-parallel pleated sheets or beta-structures. Residues not included in the beta-structures are arranged in regions of random coil. One of the pleated sheets contributes extensively to the interactions among the monomers to form both dimers and tetramers. The positions at which Mn(2+), Ca(2+), and saccharide are bound to the protein, and the point of cleavage for the formation of the naturally occurring fragments A(1) and A(2), have been tentatively assigned. Both metal-binding sites are at least 20-A removed from the position at which saccharides are bound. The saccharide-binding site is a deep pocket of approximately 6A x 7.5A x 18A, the inner portion of which is occupied by hydrophobic residues.

Amino Acid Sequence↗

PubMed1997

Crystal structure of tyrosine hydroxylase at 2.3 A and its implications for inherited neurodegenerative diseases.

Tyrosine hydroxylase (TyrOH) catalyzes the conversion of tyrosine to L-DOPA, the rate-limiting step in the biosynthesis of the catecholamines dopamine, adrenaline, and noradrenaline. TyrOH is highly homologous in terms of both protein sequence and catalytic mechanism to phenylalanine hydroxylase (PheOH) and tryptophan hydroxylase (TrpOH). The crystal structure of the catalytic and tetramerization domains of TyrOH reveals a novel alpha-helical basket holding the catalytic iron and a 40 A long anti-parallel coiled coil which forms the core of the tetramer. The catalytic iron is located 10 A below the enzyme surface in a 17 A deep active site pocket and is coordinated by the conserved residues His 331, His 336 and Glu 376. The structure provides a rationale for the effect of point mutations in TyrOH that cause L-DOPA responsive parkinsonism and Segawa's syndrome. The location of 112 different point mutations in PheOH that lead to phenylketonuria (PKU) are predicted based on the TyrOH structure.

Amino Acid Sequence↗

PubMed2005

Colonization, dispersal, and hybridization influence phylogeography of North Atlantic sea urchins (Strongylocentrotus droebachiensis).

We used frequency-based and coalescent-based phylogeographic analysis of sea urchin (Strongylocentrotus droebachiensis) mitochondrial DNA (mtDNA) sequences and previously published microsatellite data to understand the relative influence of colonization and gene flow from older (north Pacific) and younger (northeast Atlantic) sea urchin populations on genetic variation in the northwest Atlantic. We found strong evidence of survival of northwestern Atlantic populations in local Pleistocene glacial refugia: most haplotypes were the same as or closely related to Pacific haplotypes, with deep gene genealogies that reflect divergence times within the northwestern Atlantic that are much older than the last glacial maximum. We detected gene flow across the North Atlantic in the form of haplotypes shared with or recently descended from European populations. We also found evidence of significant introgression of haplotypes from a closely related species (S. pallidus). The relative magnitude of gene flow estimated by coalescent methods (and the effective population size differences among oceanic regions) depended on the genetic marker used. In general, we found very small effective population size in the northeastern Atlantic and high trans-Arctic gene flow between the Pacific and northwestern Atlantic. Both analyses suggested significant back-migration to the Pacific. However, microsatellites more strongly reflected older Pacific migration (with similar effective population sizes across the Arctic), whereas mtDNA sequences appeared to be more sensitive to recent trans- Atlantic dispersal (with larger differences in effective population size). These differences across marker types might have several biological or methodological causes, and they suggest caution in interpretation of the results from a single locus or class of markers.

Animals↗

PubMed2006

Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA.

MPSS (massively parallel signature sequencing) is a sequencing-based technology that uses a unique method to quantify gene expression level, generating millions of short sequence tags per library. We have created a series of databases for four species (Arabidopsis, rice, grape and Magnaporthe grisea, the rice blast fungus). Our MPSS databases measure the expression level of most genes under defined conditions and provide information about potentially novel transcripts (antisense transcripts, alternative splice isoforms and regulatory intergenic transcripts). A modified version of MPSS has been used to perform deep profiling of small RNAs from Arabidopsis, and we have recently adapted our database to display these data. Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu.

Arabidopsis↗

PubMed2005

A phylogeny of bacterial RNA nucleotidyltransferases: Bacillus halodurans contains two tRNA nucleotidyltransferases.

We have analyzed the distribution of RNA nucleotidyltransferases from the family that includes poly(A) polymerases (PAP) and tRNA nucleotidyltransferases (TNT) in 43 bacterial species. Genes of several bacterial species encode only one member of the nucleotidyltransferase superfamily (NTSF), and if that protein functions as a TNT, those organisms may not contain a poly(A) polymerase I like that of Escherichia coli. The genomes of several of the species examined encode more than one member of the nucleotidyltransferase superfamily. The function of some of those proteins is known, but in most cases no biochemical activity has been assigned to the NTSF. The NTSF protein sequences were used to construct an unrooted phylogenetic tree. To learn more about the function of the NTSFs in species whose genomes encode more than one, we have examined Bacillus halodurans. We have demonstrated that B. halodurans adds poly(A) tails to the 3' ends of RNAs in vivo. We have shown that the genes for both of the NTSFs encoded by the B. halodurans genome are transcribed in vivo. We have cloned, overexpressed, and purified the two NTSFs and have shown that neither functions as poly(A) polymerase in vitro. Rather, the two proteins function as tRNA nucleotidyltransferases, and our data suggest that, like some of the deep branching bacterial species previously studied by others, B. halodurans possesses separate CC- and A-adding tRNA nucleotidyltransferases. These observations raise the interesting question of the identity of the enzyme responsible for RNA polyadenylation in Bacillus.

Amino Acid Sequence↗

PubMed2003

Kinetic and phylogenetic characterization of an anaerobic dechlorinating microbial community.

The reductive dechlorination (RD) of tetrachloroethene (PCE) to vinyl chloride (VC) and, to a lesser extent, to ethene (ETH) by an anaerobic microbial community has been investigated by studying the processes and kinetics of the main physiological components of the consortium. Molecular hydrogen, produced by methanol-utilizing acetogens, was the electron donor for the PCE RD to VC and ETH without forming any appreciable amount of other chlorinated intermediates and in the near absence of methanogenic activity. The microbial community structure of the consortium was investigated by preparing a 16S rDNA clone library and by fluorescence in situ hybridization (FISH). The PCR primers used in the clone library allowed the harvest of 16S rDNA from both bacterial and archaeal members in the community. A total of 616 clones were screened by RFLP analysis of the clone inserts followed by the sequencing of RFLP group representatives and phylogenetic analysis. The clone library contained sequences mostly from hitherto undescribed bacteria. No sequences similar to those of the known RD bacteria like 'Dehalococcoides ethenogenes' or Dehalobacter restrictus were found in the clone library, and none of these bacteria was present in the RD consortium according to FISH. Almost all clones fell into six previously described phyla of the bacterial domain, with the majority (56.6 %) being deep-branching members of the Spirochaetes phylum. Other clones were in the Firmicutes phylum (18.5 %), the Chloroflexi phylum (16.4 %), the Bacteroidetes phylum (6.3 %), the Synergistes genus (1.1 %) and a lineage that could not be affiliated with existing phyla (1.1 %). No archaeal clones were found in the clone library. Owing to the phylogenetic novelty of the microbial community with regard to previously cultured micro-organisms, no specific microbial component(s) could be hypothetically affiliated with the RD phenotype. The predominance of Spirochaetes in the microbial consortium, the main group revealed by clone library analysis, was confirmed by FISH using a purposely developed probe.

Acetic Acid↗

PubMed2004

The first evidence of anaerobic CO oxidation coupled with H2 production by a hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent.

From 24 samples of hydrothermal venting structures collected at the East Pacific Rise (13 degrees N), 13 enrichments of coccoid cells were obtained which grew on CO, producing H2 and CO2 at 80 degrees C. A hyperthermophilic archaeon capable of lithotrophic growth on CO coupled with equimolar production of H2 was isolated. Based on its 16S rRNA sequence analysis, this organism was affiliated with the genus Thermococcus. Other strains of Thermococcales species ( Pyrococcus furiosus, Thermococcus peptonophilus, T. profundus, T. chitonophagus, T. stetteri, T. gorgonarius, T. litoralis, and T. pacificus) were shown to be unable to grow on CO. Searches in sequence databases failed to reveal deposited sequences of genes related to CO metabolism in Thermococcales. Our work provides the first evidence of anaerobic CO oxidation coupled with H2 production performed by an archaeon as well as the first documented case of lithotrophic growth of a Thermococcales representative.

Anaerobiosis↗

PubMed2000

Alfalfa (Medicago sativa) carbamoylphosphate synthetase gene structure records the deep lineage of plants.

Given the central role of carbamoylphosphate synthetases in pyrimidine and arginine metabolism in all living organisms, the absence of fundamental information regarding plant CPSase genes is a striking omission [Lawson et al., Mol. Biol. Evol. 13 (1996) 970-977; van den Hoff et al., J. Mol. Evol. 41 (1995) 813-832]. Whereas CPSase gene architecture and aa sequence have proven to be useful characters in establishing ancient and modern genetic affinities, phylogenetic analysis cannot be completed without the inclusion of plant CPSases. We describe the first isolation by molecular cloning of a plant CPSase gene (CPAII) derived from alfalfa (Medicago sativa). DNA sequence analysis reveals a proteobacterial architecture, namely closely linked carA and carB coding domains separated by a short intergenic region, and transcribed as a polycistronic mRNA. CPAII encodes the amino acid residues that typify a CPSase type II enzyme. In addition, an ancient internal duplication has been retained in the plant carB sequence. Partial nucleotide sequencing of additional clones reveals that the alfalfa genome contains multiple CPSase II gene copies which may be tissue-specific in their expression. It appears that with respect to CPSase genes, CPAII resembles the carAB gene of bacteria, and may have preserved much of this ancient gene structure in the alfalfa genome.

Amino Acid Sequence↗

PubMed2001

Rhodotorula lamellibrachii sp. nov., a new yeast species from a tubeworm collected at the deep-sea floor in Sagami bay and its phylogenetic analysis.

A new species of the genus Rhodotorula was isolated from a tubeworm (Lamellibrachia sp.) collected at a depth of 1156 m in Sagami Bay, Japan. Strain SY-89 had physiological properties quite similar to R. aurantiaca. Two phylogenetic trees, one based on internal transcribed spacer (ITS) regions and 5.8S rDNA sequences and the other based on the D1/D2 region of the large subunit (26S) rDNA sequences, united strain SY-89 to the type strain of Sakaguchia dacryoides through a considerable evolutionary distance. Strain SY-89 was differentiated from S. dacryoides by the G+C content of the nuclear DNA and differences in the ability to utilize specific carbon and nitrogen compounds. The low complementarity of strain SY-89 DNA to that of the type strain of S. dacryoides confirmed that this strain was genetically unrelated to previously known species. The tubeworm isolates are described as R. lamellibrachii sp. nov. The type strain of R. lamellibrachii is strain SY-89 (= JCM 10907). R. lamellibrachii formed a cluster with Erythrobasidium hasegawianum, R. lactosa, S. dacryoides and Sporobolomyces elongatus on the ITS and 5.8S rDNA phylogenetic tree. These five species shared a signature sequence in 26S rDNA, although this relationship was not supported by phylogeny based on the D1/D2 region of 26S rDNA.

Animals↗

PubMed1992

Cell motility driving mediolateral intercalation in explants of Xenopus laevis.

In Xenopus, convergence and extension are produced by active intercalation of the deep mesodermal cells between one another along the mediolateral axis (mediolateral cell intercalation), to form a narrower, longer array. The cell motility driving this intercalation is poorly understood. A companion paper shows that the endodermal epithelium organizes the outermost mesodermal cells immediately beneath it to undergo convergence and extension, and other evidence suggests that these deep cells are the most active participants in mediolateral intercalation (Shih, J. and Keller, R. (1992) Development 116, 887-899). In this paper, we shave off the deeper layers of mesodermal cells, which allows us to observe the protrusive activity of the mesodermal cells next to the organizing epithelium with high resolution video microscopy. These mesodermal cells divide in the early gastrula and show rapid, randomly directed protrusive activity. At the early midgastrula stage, they begin to express a characteristic sequence of behaviors, called mediolateral intercalation behavior (MIB): (1) large, stable, filiform and lamelliform protrusions form in the lateral and medial directions, thus making the cells bipolar; (2) these protrusions are applied directly to adjacent cell surfaces and exert traction on them, without contact inhibition; (3) as a result, the cells elongate and align parallel to the mediolateral axis and perpendicular to the axis of extension; (4) the elongate, aligned cells intercalate between one another along the mediolateral axis, thus producing a longer, narrower array. Explants of essentially a single layer of deep mesodermal cells, made at stage 10.5, converge and extend by mediolateral intercalation. Thus by stage 10.5 (early midgastrula), expression of MIB among deep mesodermal cells is physiologically and mechanically independent of the organizing influence of the endodermal epithelium, described previously (Shih, J. and Keller, R. (1992) Development 116 887-899), and is the fundamental cell motility underlying mediolateral intercalation and convergence and extension of the body axis.

Animals↗