Linkage disequilibrium in the neurofibromatosis 1 (NF1) region: implications for gene mapping.

To test the usefulness of linkage disequilibrium for gene mapping, we compared physical distances and linkage disequilibrium among eight RFLPs in the neurofibromatosis 1 (NF1) region. Seven of the polymorphisms span most of the NF1 gene, while the remaining polymorphism lies approximately 70 kb 3' to a stop codon in exon 49. By using Centre d'Etude du Polymorphisme Humain (CEPH) kindreds, 91-110 unrelated parents were genotyped. A high degree of disequilibrium is maintained among the seven intragenic polymorphisms (r > .82, P < 10(-7)), even though they are separated by as much as 340 kb. The 3' polymorphism is only 68 kb distal to the next polymorphism, but disequilibrium between the 3' polymorphism and all others is comparatively low (magnitude of 4 < .33, P values .27-.001). This result was replicated in three sets of unrelated kindreds: the Utah CEPH families, the non-Utah CEPH families, and an independent set of NF1 families. Trigenic, quadrigenic, three-locus, and four-locus disequilibrium measures were also estimated. There was little evidence of higher-order linkage disequilibrium. As expected for a disease with multiple mutations, no disequilibrium was observed between the disease gene and any of the RFLPs. The observed pattern of high disequilibrium within the gene and a loss of disequilibrium 3' to the stop codon could have implications for gene mapping studies. These are discussed, and guidelines for linkage disequilibrium studies are suggested.     

Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*

Intracellular membrane fusion requires the regulated assembly of SNARE (soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein receptor) proteins anchored in the apposed membranes. To exert the force required to drive fusion between lipid bilayers, juxtamembrane SNARE motifs zipper into four-helix bundles. Importantly, SNARE function is regulated by additional factors, none more extensively studied than the SM (Sec1/Munc18-like) proteins. SM proteins interact with both individual SNAREs and SNARE complexes, likely chaperoning SNARE complex formation and protecting assembly intermediates from premature disassembly by NSF. Four families of SM proteins have been identified, and representative members of two of these families (Sec1/Munc18 and Sly1) have been structurally characterized. We report here the 2.6 Å resolution crystal structure of an SM protein from the third family, Vps33. Although Vps33 shares with the first two families the same basic three-domain architecture, domain 1 is displaced by 15 Å, accompanied by a 40° rotation. A unique feature of the Vps33 family of SM proteins is that its members function as stable subunits within a multi-subunit tethering complex called HOPS (homotypic fusion and vacuolar protein sorting). Integration into the HOPS complex depends on the interaction between Vps33 and a second HOPS subunit, Vps16. The crystal structure of Vps33 bound to a C-terminal portion of Vps16, also at 2.6 Å resolution, reveals the structural basis for this interaction. Despite the extensive interface between the two HOPS subunits, the conformation of Vps33 is only subtly affected by binding to Vps16.     

Reproductive patterns within racemes in protandrous Aconitum gymnandrum (Ranunculaceae): potential mechanism and among-family variation

The adaptive significance and mechanism of patterns in floral sex allocation and female success within inflorescences has attracted attention recently, whereas few studies have examined genetic variation of intra-inflorescence pattern. The purpose of this study is to investigate patterns of reproduction within racemes in protandrous Aconitum gymnandrum Maxim., and illuminate potential mechanisms and genetic variation of such patterns. Data from pot experiment on 40 maternal families were collected in field. Anther number, pollen:ovule ratio and seed germination rate increased from bottom to top flowers within racemes, but other traits, such as gynoecium mass, carpel number, sepal galea height and seed production decreased significantly with flowering sequence. Variation in floral sex allocation within racemes in A. gymnandrum fitted entirely the prediction of protandry, which was not a result of architectural effect. Such selected pattern may result from a variety of factors influencing the mating environment, such as pollinator directionality, display size and flower longevity. Decline of female success within racemes in A. gymnandrum also resulted from male-biased allocation selected by variation in the mating environment, not resource competition or pollen limitation. Moreover, there was genetic variation for most reproductive traits and the position effect, as evinced by significant variation among families.     

Linkage analyses at the chromosome 1 loci 1q24-25 (HPC1), 1q42.2-43 (PCAP), and 1p36 (CAPB) in families with hereditary prostate cancer

Recent studies suggest that hereditary prostate cancer (PRCA) is a complex disease, involving multiple susceptibility genes and variable phenotypic expression. Through linkage analysis, potential prostate cancer susceptibility loci have been mapped to 3 regions on chromosome 1. To investigate the reported linkage to these regions, we conducted linkage studies on 144 PRCA families by using microsatellite markers in regions 1q24-25 (HPC1) and 1q42.2-43 (PCAP). We also examined the 1p36 (CAPB) region in 13 PRCA families with at least one case of brain cancer. No significant evidence of linkage to the HPC1 or PCAP region was found when the entire data set was analyzed. However, weak evidence for linkage to HPC1 was observed in the subset of families with male-to-male transmission (n=102; maximum multipoint nonparametric linkage [NPL] 1.99, P=.03). Weak evidence for linkage with heterogeneity within this subset was also observed (HLOD 1.21, P=.02), with approximately 20% of families linked. Although not statistically significant, suggestive evidence for linkage to PCAP was observed for the families (n=21) that met the three criteria of male-to-male transmission, average age of diagnosis <66 years, and >/=5 affected individuals (maximum multipoint NPL 1.45, P=.08). There was no evidence for linkage to CAPB in the brain cancer-prostate cancer subset. These results strengthen the argument that prostate cancer is a heterogeneous disease and that multiple genetic and environmental factors may be important for its etiology.     

Morphological diversity of wing structure in Rhinolophoid bats (Chiroptera,Rhinolophoidea)

The results of studies on the morphological diversity of wing structure in horseshoe bats (Rhinolophoidea) are considered in relation to ecological differentiation within the superfamily. Various skeletal elements of the wing are shown to form several groups of mutually correlated characters. The main groups comprise the characters that account for the size of the wing and play a role in the formation of its outer contours. The distribution of characters shows that they describe different aspects of variation and can provide a fairly complete picture of the morphological and ecological structure of the superfamily. The results obtained by means of multidimensional scaling and clustering methods primarily reflect ecological types of bats and only then characterize their taxonomic relationships. Analysis of variation in structural features of the wing within the superfamily Rhinolophoidea shows that the same wing form in different families may be accounted for by different ratios of digit elements, primarily the lengths of distal and proximal phalanges of digits III and IV.     

Short interspersed elements (SINEs) of squamate reptiles (Squam1 and Squam2): structure and phylogenetic significance

Short interspersed elements (SINEs) are important nuclear molecular markers of the evolution of many eukaryotes. However, the SINEs of squamate reptile genomes have been little studied. We first identified two families of SINEs, termed Squam1 and Squam2, in the DNA of meadow lizard Darevskia praticola (Lacertidae) by performing DNA hybridization and PCR. Later, the same families of retrotransposons were found using the same methods in members of another 25 lizard families (from Iguania, Scincomorpha, Gekkota, Varanoidea, and Diploglossa infraorders) and two snake families, but their abundances in these taxa varied greatly. Both SINEs were Squamata-specific and were absent from mammals, birds, crocodiles, turtles, amphibians, and fish. Squam1 possessed some characteristics common to tRNA-related SINEs from fish and mammals, while Squam2 belonged to the tRNA(Ala) group of SINEs and had a more unusual and divergent structure. Squam2-related sequences were found in several unannotated GenBank sequences of squamate reptiles. Squam1 abundance in the Polychrotidae, Agamidae, Leiolepididae, Chamaeleonidae, Scincidae, Lacertidae, Gekkonidae, Varanidae, Helodermatidae, and two snake families were 10(2) -10(4) times higher than those in other taxa (Corytophanidae, Iguanidae, Anguidae, Cordylidae, Gerrhosauridae, Pygopodidae, and Eublepharidae). A less dramatic degree of copy number variation was observed for Squam2 in different taxa. Several Squam1 copies from Lacertidae, Chamaeleonidae, Gekkonidae, Varanidae, and Colubridae were sequenced and found to have evident orthologous features, as well as taxa-specific autapomorphies. Squam1 from Lacertidae and Chamaeleonidae could be divided into several subgroups based on sequence differences. Possible applications of these SINEs as Squamata phylogeny markers are discussed.     

Exclusion of the phosphatidylinositol-specific phospholipase C β3 (PLC β3) gene as candidate for the multiple endocrine neoplasia type 1 (MEN 1) gene

Multiple endocrine neoplasia type 1 (MEN 1) is inherited as an autosomal dominant disorder, characterized by hyperplasia and neoplasia in several endocrine organs. The MEN 1 gene, which is most probably a tumor suppressor gene, has been localized to a 900-kb region on chromosome 11q13. The human phosphatidylinositol-specific phospholipase C β3 (PLC β3) gene, which is located within this region, was considered to be a good candidate for the MEN 1 gene. In this study, the structure and expression of the PLC β3 gene in MEN 1 patients were investigated in more detail, to determine its potential role in MEN 1 tumorigenesis. Southern blot analysis, using blood and tumor DNA from affected persons from seven different MEN 1 families, did not reveal structural abnormalities in the PLC β3 gene. To detect possible point mutations, or other small structural aberrations, direct sequencing of PLC β3 cDNAs from two affected persons from two different MEN 1 families was performed, but no MEN 1-specific abnormalities were revealed. Several common nucleotide sequence polymorphisms were detected in these cDNAs, proving that both alleles of the PLC β3 gene were expressed and analyzed. In conclusion, these results exclude the PLC β3 gene as a candidate gene for MEN 1. Received: 20 March 1996     

Ribosomal DNA variation and its phylogenetic implication in the genusBrachypodium (Poaceae)

The structure of ribosomal DNA ofBrachypodium and several other grass species was investigated using a heterologous rDNA probe from wheat. Several different rDNA families were present among perennial and annual species within the genus. In contrast to the annual species the perennial species exhibited a very low degree of repeat length variation. An extra Eco RI site and a Hin dIII site were observed in the IGS, which distinguishedBrachypodium from other grass genera. The restriction fragment length polymorphism and length variation of the repeat units have taxonomic value withinBrachypodium and are correlated with the classification ofBrachypodium derived from other data.     

A molecular phylogeny of the marine mussel genus Perna (Bivalvia: Mytilidae) based on nuclear (ITS1&2) and mitochondrial (COI) DNA sequences

A molecular phylogeny is presented for marine mussels of the genus Perna, based on nuclear (ITS1,ITS2) and mitochondrial (COI) DNA sequence data. The three generally recognised species (Perna viridis, Perna perna and Perna canaliculus) and one putative species (Perna picta) were each sampled from several locations within their known geographic distributions. A range of phylogenetic analyses was used to investigate the current taxonomic assignments, evolutionary relationships and the biogeographical history of the genus. The different analyses produced similar, well supported topologies and verified the monophyly of the genus with respect to five mytilid outgroup species. P. perna (Atlantic), P. viridis (Indo-West Pacific), and P. canaliculus (New Zealand) each formed distinct clades, confirming their specific status. Putative P. picta from North Africa clustered within the P. perna clade and is not regarded as a separate species. P. perna and P. canaliculus were the most closely related of the three species. Possible biogeographic explanations for the present species distributions are evaluated.     

THE SPERMATOZOA OF THE POLYCHAETA (ANNELIDA): AN ULTRASTRUCTURAL REVIEW

1. Polychaete sperm are divisible into ect-aquasperm, ent-aquasperm, and introsperm. 2. Ect-aquasperm are the commonest type of polychaete sperm and are considered plesiomorphic for the Polychaeta. Re-evolution of ect-aquasperm (as neo-aquasperm) is, nevertheless, tentatively hypothesized for some Sabellida. 3. In terms of ultrastructural studies of sperm in the investigated polychaete families, only ect-aquasperm have been demonstrated for 16 families; only ent-aquasperm for 3 families; ect- and ent-aquasperm for 3; ect- and intro-sperm for 2; ect-, ent- and intro-sperm for 1 family; and only introsperm for 11 families but investigations can only be regarded as preliminary. To date no family is known to have ent- and intro-sperm only. Sperm ultrastructure has yet to be examined in the orders Magelonida, Psammodrilida, Cossurida, Spintherida, Sternapsida, Flabelligerida and Fauvelopsida. 4. Much variation occurs in gross morphology, ultrastructure and configuration of the several components of ect-aquasperm: acrosome, nucleus, mitochondria, and centrioles and associated anchoring apparatus. A 9 + 2 axoneme is constant. 5. Group-specific sperm structure has been demonstrated for the Nereidae (chiefly ect-aquasperm), and for introsperm of the families Histriobdellidae, Questidae; Capitellidae, Spionidae and Protodrilidae. Species-specificity of all classes of spermatozoa is well established. 6. The very small size of ect-aquasperm is correlated with production of large numbers of sperm as an adaptation to broadcast spawning. Simplicity of structure may relate more to conservation of materials than to hydrodynamics. 7. Fertilization by ent-aquasperm requires fewer eggs than in external fertilization and is accompanied by a tendency to lecithotrophy. Elongation of the nucleus and development of asymmetry are seen in several of the few known examples of ent-aquasperm. Whether modifications are related to transfer or to other features, such as lecithotrophy, is uncertain. 8. Evident multiple origins of polychaete introsperm contraindicate their value in establishing relationship between families, in contrast with their utility in groups such as decapod crustacea. 9. At the intrafamilial level polychaete introsperm have taxonomic and phylogenetic value, as seen in the Spionidae, Capitellidae, and Histriobdellidae, and are distinctive of each of these and other families. 10. At higher taxonomic levels, the ultrastructure of the sperm of the oligochaetoid Questidae distinguishes this family from euclitellates, each class of which has its own distinctive subtype of the euclitellate introsperm. 11.(ABSTRACT TRUNCATED AT 400 WORDS)     

Segregation of the E1j gene for plasma cholinesterase in family studies

Four families are reported in which the E1j gene is segregating. Two E1jE1k and one E1jE1f genotypes have been recognised by genetic analysis. The biochemical characteristics of several E1j genotypes are presented.     

Selection on offspring size varies within and among families in relation to host nutritional quality

Life history theory often assumes a positive relationship between offspring size and fitness, although the strength and form of this relationship is expected to vary with environmental conditions. In arthropods, surprisingly few studies have examined the influence of larval environment on the offspring size–fitness relation. In phytophagous insects, the few studies that have examined variation in larval host plants have found a negative correlation between host plant nutritional quality and the strength of selection favoring larger offspring size, suggesting that this pattern might be general. I present experimental evidence for such a relationship in a population of the moth Rothschildia lebeau feeding on its three primary host plant species. Unlike previous studies, I consider the effect of offspring size on growth and survival at two levels, both among families and among siblings within families. Neonate caterpillar mass had a significant effect on growth and survival. The effect on growth, however, was weak, resulted primarily from variation among families, and did not differ among host plant diets. The effect on survival was stronger and varied among host plant diets, among families, and within families on different host plants in a manner that was generally consistent with the hypothesized negative correlation between host plant nutritional quality and the strength of selection favoring larger offspring size. Overall, results suggest that the consequences of variation in offspring size for survival within and among families are host plant-dependent in this system.     

Macrodasyida (Gastrotricha): a cladistic analysis of morphology

Abstract. A cladistic analysis based on 33 morphological characters was performed for the 31 genera currently assigned to the order Macrodasyida (Gastrotricha). Outgroup analysis indicated that the order is monophyletic and that it is defined by the structure of the pharynx and the complex distribution of duo-gland adhesive organs. Of the 6 currently recognized families in Macrodasyida, our analysis confirmed that 4 families are monophyletic: Dactylopodolidae, Macrodasyidae, Thaumastodermatidae and Turbanellidae. Dactylopodolidae was further confirmed as the most basal family within the order based on the retention of several plesiomorphies. The other three families have well-defined autapomorphies but will require further investigation to increase inter- and intrafamilial phylogenetic resolution. Planodasyidae appeared to be a paraphyletic taxon with no obvious autapomorphies; genera clustered among members of a polyphyletic family, Lepidodasyidae. We recommend that future research on macrodasyidan phylogeny focus on issues of comparative morphology and ultrastructure in lesser-known taxa such as the Dactylopodolidae, and on the taxa Lepidodasyidae and Planodasyidae.     

Identification of the microvillar 110-kDa calmodulin complex (myosin-1) in kidney.

The epithelial layer lining the proximal convoluted tubule of mammalian kidney contains a brush border of numerous microvilli. These microvilli appear in structure to be very similar to the microvilli on epithelial cells of the small intestine. Microvilli found in both the small intestine and the proximal convoluted tubules in kidney have a core bundle of actin filaments bundled by the accessory proteins villin and fimbrin. Along the length of intestinal microvilli, lateral links can be observed to connect the core bundle of actin filaments to the membrane. These cross-bridges are comprised of a 110-kDa calmodulin complex which belongs to a class of single-headed myosin molecules, collectively referred to as myosin-1. We now report that an analogous calmodulin-binding polypeptide of 105 kDa has been identified in rat kidney cortex. The 105-kDa polypeptide is preferentially found in purified kidney brush borders, can be extracted with ATP, and co-elutes with calmodulin on gel filtration and anion exchange chromatography. Fractions containing the 105-kDa polypeptide exhibit a modest ATPase activity in buffer containing CaCl2. The partially purified 105-kDa polypeptide will bind iodinated calmodulin and will sediment with F-actin in buffer containing ethylene glycol-bis-(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid (EGTA) or Ca2+. The addition of ATP partially reverses this association with F-actin. These results indicate that myosin-1, in addition to its presence in intestinal brush borders, is present in the brush border of kidney. We also provide preliminary evidence to indicate that the 105-kDa polypeptide is not restricted to tissues possessing a brush border.     

Evolution and phylogenetic information content of the ribosomal DNA repeat unit in the Blattodea (Insecta)

The organization, structure, and nucleotide variability of the ribosomal repeat unit was compared among families, genera, and species of cockroaches (Insecta:Blattodea). Sequence comparisons and molecular phylogenetic analyses were used to describe rDNA repeat unit variation at differing taxonomic levels. A reverse similar 1200 bp fragment of the 28S rDNA sequence was assessed for its potential utility in reconstructing higher-level phylogenetic relationships in cockroaches. Parsimony and maximum likelihood analyses of these data strongly support the expected pattern of relationships among cockroach groups. The examined 5' end of the 28S rDNA is shown to be an informative marker for larger studies of cockroach phylogeny. Comparative analysis of the nucleotide sequences of the rDNA internal transcribed spacers (ITS1 and ITS2) among closely related species of Blattella and Periplaneta reveals that ITS sequences can vary widely in primary sequence, length, and folding pattern. Secondary structure estimates for the ITS region of Blattella species indicate that variation in this spacer region can also influence the folding pattern of the 5.8S subunit. These results support the idea that ITS sequences play an important role in the stability and function of the rRNA cluster.     

Isozyme variation inFaidherbia albida (Leguminosae, Mimosoideae)

Genetic variation has been assessed in 30 populations (931 families) ofFaidherbia albida (Leguminosae, Mimosoideae) from across its entire African range, using six isozyme loci identified by five enzyme systems. Among the populations studied a null allele was proposed to explain the absence ofLap-1 activity in populations from southern and eastern Africa. The mean percentage of polymorphic loci per population, the mean number of alleles per locus and the mean genetic diversity within populations were 31.7%, 1.6 and 0.127 respectively. Genetic diversity was greatest in populations from West Africa and lowest in populations from eastern/southern Africa, with Ethiopian/Sudanese populations intermediate. The overall degree of genetic differentiation between populations (G_ST) indicated that approximately 56% of the enzyme variation resided within populations. Clustering of Nei's unbaised genetic distances calculated between all populations produced a dendrogram that generally followed the geographic distribution of the populations. Two major groups were identified that may be considered the eastern/southern African and the Ethiopian/West African clusters. Within the Ethiopian/West African cluster two subclusters could be recognised, one broadly corresponding to those populations from Ethiopia/Sudan and the other to those populations from West Africa. The implications of these results for theories regarding the origin ofF. albida in Africa are discussed.     

Comparative chemical and molecular variability of Cananga odorata (Lam.) Hook.f. & Thomson forma genuina (ylang-ylang) in the Western Indian Ocean Islands: implication for valorization

Cananga odorata (Lam.) Hook.f. & Thomson forma genuina (Annonaceae) is a tropical tree, grown for the production of ylang-ylang essential oil, which is extracted from its fresh and mature flowers. Despite its economic and social importance, very little information is available on its variability and the possible factors causing it. Therefore, the relationship between the genetic structure, revealed by amplified fragment length polymorphism (AFLP), and the essential oil chemical composition, determined by GC/MS analysis, of ylang-ylang grown in semi-managed systems in three Indian Ocean islands (Grande Comore, Mayotte, and Madagascar) was investigated. Our results revealed a low genetic variation within plantations and contrasted situations between islands. Variations of the chemical composition could be observed within plantations and between islands. The genetic differentiation pattern did not match the observed pattern of chemical variability. Hence, the chemical variation could not be attributed to a genetic control. As Grande Comore, Madagascar, and Mayotte present different environmental and agronomic conditions, it can be concluded that the influence of these conditions on the ylang-ylang essential oil composition is consistent with the patterns observed. Finally, several strategies were proposed to valorize the chemical composition variations.