Polymorphisms in the TNF gene cluster and MHC serotypes in the West of Scotland

 We examined the distribution of polymorphic elements within the tumor necrosis factor (TNF) gene cluster in 105 unrelated individuals and determined their relationship to class I and class II major histocompatibility complex (MHC) antigens, and to the highly polymorphic microsatellites TNFa and TNFb. The data demonstrate the contribution of elements within the TNF cluster to two extended haplotypes which are recognized to straddle the MHC. The A1.B8.DR3 haplotype appears to contain the TNF alleles TNFa2, TNFb3, LT.Nco-1.B ^* 1, and TNF-308.2, while the A3.B7.DR2 haplotype is associated with the TNF alleles TNFa11, TNFb6, TNFc1, LT.Nco-1.B ^* 2, LT.AspH1.1, TNF-308.1, and TNFe1. The presence of other extended associations which covered smaller parts of the MHC was also suggested. In most cases, the associations described here were in keeping with previously described extended haplotypes which dominate the structure of the MHC, but these did not always match completely. Taken together, these data suggest that the structure of the TNF locus is well integrated into the rest of the MHC but that important ethnic differences may exist. Received: 12 June 1996 / Revised: 27 September 1996     

Molecular phylogeny in the Lardizabalaceae

Eleven species belonging to seven genera in the Lardizabalaceae were analyzed in terms of restriction fragment length polymorphism (RFLP) of chloroplast DNA and the sequence of the chloroplast gene,rbcL, of Lardizabalaceae and its related families. Phylogenetic trees inferred from parsimony, neighbor joining and maximum likelihood methods based on RFLP data showed that two South American genera,Boquila andLardizabala, and three East Asian genera,Akebia, Holboellia andStauntonia are closely related to each other, respectively. On the other hand, the parsimony, neighbor joining and maximum likelihood trees constructed using sequence data of therbcL gene showed thatAkebia, Stauntonia, Boquila andLardizabala clustered as(((Akebia, Stauntonia), Boquila), Lardizabala). This difference may be attributable to fewer informative sites inrbcL genes than in RFLP in this family.Decaisnea diverges at the very base of the Lardizabalaceae.     

Patterns in the distribution of myctophid fish in the northern Scotia Sea ecosystem

The mesopelagic fish community of the northern Scotia Sea was investigated during the austral autumn using multi-frequency acoustics, opening and closing nets and pelagic trawls fished from the surface to 1,000 m. The Family Myctophidae (15 species in 5 genera) dominated the ichthyofauna, with larval notothenids caught over the South Georgia shelf and bathylagids and stomiids abundant in deeper hauls. The biomass of myctophids was estimated to be 2.93 g wet weight 1,000 m⁻³, with Electrona carlsbergi, E. antarctica, Protomyctophum bolini, P. choriodon, Gymnoscopelus braueri, G. fraseri, G. nicholsi and Krefftichthys anderssoni, being the most abundant species. Analysis of community structure indicated a high level of depth stratification within the myctophids, with evidence of diurnal vertical migration in some, but not all, species. Length-frequencies of G. braueri, G. nicholsi, E. antarctica and K. anderssoni were multimodal, suggesting that all life stages may be present in the northern Scotia Sea. In contrast, P. choriodon, P. bolini, G. fraseri and E. carlsbergi had unimodal distributions despite having multi-year lifecycles, indicating that they probably migrate into the region from warmer areas to the north.     

Genetic duplication in the white-split interval of the X chromosome in Drosophila melanogaster

A detailed cytogenetic study of male-viable and lethal deficiencies affecting the w-spl interval in Drosophila melanogaster has revealed the existence of genetic duplication such that, for example, the consequences of the loss of salivary chromosome band 3C3 are essentially compensated for by the presence of band 3C5-6, and vice versa. Although each of the duplicate elements possesses rst ⁺ and vt ⁺ activity, rst and vt phenotypes appear in males when 3C3 and part, but not all, of 3C5-6 are deleted. The degree of rst and vt expression can be correlated with the amount of material lost from 3C5-6. Deletions removing the entire 3C3-6 interval are male lethal. Despite the duplicate elements, at least one EMS-induced, presumptive point mutation expressing only rst is known; two others express both rst and vt. No loci other than rst and vt occur between W and spl. Band 3C2 appears to be associated with the w locus, which probably extends into the interband space between 3C1 and 3C2. The w locus is not involved in the rst-vt duplication in the 3C3-6 region. — The cytogenetic characteristics of the 3C region—a high coefficient of crossing over, frequent induced chromosome breakage, ectopic pairing, constriction, and an extended replication period—can be correlated with the fact that in 3C a relatively long stretch of DNA, nearly 2% of the entire X chromosome, is highly compacted into but few adjacent bands. These characteristics do not necessarily represent special properties of intercalary heterochromatin; they can be interpreted as reflecting the properties of any similarly organized euchromatic region.This investigation was aided by research grants from the U. S. Public Health Service (GM 13631) to G. Lefevre, Jr. and the National Science Foundation (GB 27599) to M. M. Green.     

Phragmoplastins,the Trentepohliales,and the Evolution of the Cytokinesis in Green Plants

Representatives of the monophyletic Trentepohliales are widely distributed in the tropics, subtropics, and temperate regions worldwide. They grow in soil, or are epilithic, epiphytic or endophytic. The family comprises approximately 70 species placed in at least four genera (Trentepohlia, Cephaleuros, Phycopeltis and Stomatochroon), with Trentepohlia sensu lato (including Printzina and Physolinum) accounting for half of the species in this family. PCR amplification and sequencing of the 18 SSU rDNA of 18 isolates of the Trentepohliaceae were used to assess the monophyly of the genus Cephaleuros and to determine the phylogenetic relationships among species of Trentepohlia sensu lato. Distance, Parsimony, and Maximum Likelihood analyses indicate that Trentepohlia sensu lato is basal and includes two species recently transferred to Phycopeltis (P. umbrina) and Printzina (P. lagenifera). In contrast, Cephaleuros is a derived monophyletic clade. Analysis of isolates of C. virescens, from the USA, Taiwan, and South Africa indicate that this taxon may consist of different species sharing a convergent morphology. The results of this study have implications for the taxonomy of the genera.     

Weak-acid transport in the small intestine: Discrimination in the lamina propria

Summary Studies on the intestinal transport of weak acids suggest that the subepithelial tissues exhibit a modest, but significant, ability to discriminate between the ionized and nonionized forms. This suggestion has been tested directly in experiments using anin vitro preparation of rat small intestine from which the epithelial cells were removed, but in which the structural and functional integrity of the subepithelial tissues was maintained. Studies on the effects of potential difference on the fluxes of weak acids in this preparation showed that the ratio of permeabilities for the ionized and nonionized species (P ⁱ /P ⁿⁱ ) was indeed less than one, and of a magnitude comparable to the value suggested by analysis of transport in the intact tissue. (P ⁱ /P ⁿⁱ ) for the subepithelial tissue decreased as pH was increased, and the discriminatory properties of the tissue were abolished [(P ⁱ /P ⁿⁱ )=1] on treatment with the cationic macromolecule polyethyleneimine (PEI). These observations suggested that the discriminatory properties of the subepithelial tissues were determined by fixed anionic sites, and morphological studies with PEI indicated that such sites were concentrated in the region of the basement membrane.     

Phylogeny of Itaquasconinae in the light of the evolution of the flexible pharyngeal tube in Tardigrada

The family Hypsibiidae comprises four subfamilies, among which Itaquasconinae are the most abundant in genera. Although being morphologically diverse and cosmopolitan, itaquasconins are scarcely reported and their taxonomy is entangled. Here, we present a phylogeny based on three DNA markers and morphological clues obtained from a detailed scanning electron microscopy analysis of bucco-pharyngeal apparatuses of 25 species representing seven genera. Our study revealed that (a) the polyphyletic Adropion consists of at least three evolutionary lineages, with Guidettion gen. nov. being the sister group of all remaining itaquasconins; (b) stylet supports were independently lost in Astatumen and Insulobius gen. nov.; (c) pharyngeal tube annulation can be divided into two general types, simple and complex, and is stable at the genus level, but being homoplasious (similarly to the apophyses for the insertion of stylet muscles and the shape of the claw bases), it is not useful in inferring phyletic relationships within the subfamily; and (d) Astatumen and Platicrista contain numerous similar species, challenging the current taxonomic classification; moreover, (e) three new taxa are proposed to accommodate the newly recognised lineages: Guidettion gen. nov. (the former Adropion prorsirostre group), Insulobius gen. nov. (for a new Malayan species with a mixture of Astatumen and Itaquascon traits), and Raribius gen. nov. (former Itaquascon spp. with an elongated and narrowed pharyngeal tube terminating with a spherical pharynx). The simple type of annulation is synapomorphic to Hypsibiidae, with single reversals to the uniform buccal tube in Parascon (Itaquasconinae) and in Hypsibiinae. The pharyngeal tube evolved convergently several times, and is of different character in classes Heterotardigrada and Eutardigrada.     

Distribution of the Transposable Element Minos in the Genus Drosophila

We analyzed 28 species of the genus Drosophilafor the presence of the Tc1-like transposable element Minosusing Southern blot hybridization under high stringency conditions. The Minostransposon was found in members of both the Drosophilaand the Sophophorasubgenus showing a distribution that is wider if compared to other well-studied Drosophilatransposons such as the Pelement, hoboand mariner. The presence of Minos-hybridizing sequences was discontinuous in the Sophophorasubgenus, especially in the melanogasterspecies group. Using the Polymerase Chain Reaction we amplified a portion corresponding to the putative Minostransposase from different Drosophilaspecies. Cloning and sequence analysis of randomly selected Minoscopies from D. mojavensisis, D. saltansand D. willistonisupports the idea that event(s) of horizontal transfer may have contributed to the spreading of this transposon in the Drosophilagenus. This revised version was published online in July 2006 with corrections to the Cover Date.     

Biology of the small pelagic fishes in the new Volta Lake in Ghana

Summary A number of small pelagic fish species were found in the new Volta Lake in Ghana. Three, the clupeids Cynothrissa mento and Pellonula afzeliusi, and the schilbeid Physailia pellucida, rapidly became dominant, and these together with another schilbeid Siluranodon auritus and the clupeid-like cyprinid Barilius niloticus are here considered. Pellonula and Physailia eat chiefly invertebrates; the former especially at the surface, the latter in mid-depths or at the bottom. Zooplankton is important to all sizes of Physailia, but only to juveniles of Pellonula. Barilius feeds almost entirely on adventitous forms taken at the surface and Siluranodon on algae and rotifers. Cynothrissa, the largest fish studied, feeds mainly on fish. The food range taken is thus wide, and differences in diet are discussed in terms of the probable future of each species in the new lake as it matures.This paper is taken from a thesis accepted for the M. Sc. Degree of the University of Dublin.     

Aminoacid profiles in the study of phylogenetic relationships in the genusOryza

Summary The amino acid profiles in seeds of thirteen different species ofOryza, including two cultivated rices,O. glaberrima andO. sativa and the two major geographical racesindica andjaponica were studied using an automatic amino acid analyser to assess differences in the profiles of cultivated species and their wild progenitors. The polygon graphic method was employed to envision the species relationship. Essential amino acid profiles in different species were also compared with those of the Food and Agriculture Organization (FAO) standards. The results suggest a wide range of variability amongOryza species for lysine (up to 4.4% as against 3.5% in cultivated rices) and other essential amino acids. This will be of considerable interest to rice breeders, when after overcoming genetic barriers, the possible utilization of these species in rice breeding becomes feasible.     

Seasonality affects the parasitism levels in two fish species in the eastern Amazon region

Fish parasite communities have strong interactions with the environment, the host fish, and the aquatic invertebrate communities. Thus, factors directly involving their different life cycles, such as different host populations and environments, as well as seasonal fluctuations in water levels can cause different responses. The main factors structuring parasite communities may be the hydrodynamic variations, together with seasonal variations in the availability of infectious stages of parasites in the environment. The purpose of this study was therefore to investigate the influence of the rainy and dry seasons on parasite infracommunities in fish species in the Amazon River System of Brazil. Between October 2009 and April 2011, specimens of Colossoma macropomum and Colossoma macropomum × Piaractus brachypomus hybrids (tambatinga) were examined for the presence of parasites. The parasite communities were similar in these two species that both showed aggregate dispersion, although the hybrid specimens were less parasitized. For both hosts, the Brillouin diversity, species richness, evenness and Berger‐Parker dominance indices were similar in the rainy season and dry season, except that the Berger‐Parker dominance index for the C. macropomum × P. brachypomus hybrid was higher during the dry season. Ichthyophthirius multifiliis was the dominant parasite, followed by Piscinoodinium pillulare, in both hosts. However, C. macropomum had a higher prevalence and abundance in the dry season, while in the C. macropomum × P. brachypomus hybrid, only the I. multifiliis prevalence increased. The abundance of monogenean species (Anacanthorus spathulatus, Linguadactyloides brinkmanni, Mymarothecium and Notozothecium janauachensis) was higher during the dry season in the gills of C. macropomum. Despite overdispersion of the lernaeid Perulernaea gamitanae, a seasonal pattern was seen only in the C. macropomum × P. brachypomus hybrid, with higher prevalence in the rainy season. The low prevalence and abundance of the ectoparasites Tetrahymena sp., Trichodina sp. and Braga patagonica, as well as of the endoparasites Procamallalus (Spirocamallanus) inopinatus and Neoechinorhynchus buttnerae, were not affected by seasonality. This information is applicable in farming practice for these economically important fish, as it indicates the best time for prophylactic management and treatment against parasites, in order to prevent economic losses in fish farms.     

Role of the immune-response region of the B complex in the control of the graft-vs-host reaction in chickens

The relative importance of the B and IR regions of the chicken B complex were compared as to their role in the graft-versus-host (GVH) reaction. Spleen enlargement (splenomegaly) on 19-day-old embryos, inoculated 5 days earlier with immune competent leukocytes, served as the test for the GVH reaction. The B blood group locus was the marker of the B region, and the Ir-GAT gene was the marker of the immune response (Ir) region of the B complex, the major histocompatibility system (MHS) of chickens. The test stocks consisted of B¹B¹ GAT-Low (1-Low) and B¹⁹B¹⁹ Gat-High (19-High) birds of our S1 Leghorn line plus the recombinant genotypes B¹B¹ Gat-High (1-High) and B¹⁹B¹⁹ GAT-low (19-Low). A dosage of 0.1 ml of donor white blood cells was injected into each of 191 recipient embryos on day 14, and the spleens were removed and weighed on day 19. Of 16 combinations of (donor blood)-(host embryos), arranged with respect to the four genotypes listed above, four were compatible, e. g., (1-Low)-(1-Low). There were four incompatible combinations at the B locus, four at the GAT locus, and four at both the B and GAT loci. All 16 combinations were replicated. Results were expressed as a splenomegaly index (SI), that is, the ratio of incompatible to compatible spleen weights corrected for differences in embryo weight. If (SI-1) is greater than 0, the GVH reaction is considered positive within sampling errors. The mean (SI-1) indexes obtained were: incompatible at GAT-0.5±0.07; incompatible at B-1.34±0.10. Thus, both GAT and B contributed to the GVH reaction, but the B region was much stronger than the IR region. The results were strongly asymmetrical: maximal stimulation occurred when the host embryo was B¹⁹B¹⁹ GAT-high and donor leukocytes were B¹B¹ GAT-Low. The parental donor-host paired combinations gave stronger GVH reactions than did the recombinant pairs. Effects of incompatibilities at the two regions proved additive when compared with two-locus differences of parental genotypes. In general, the results proved that the IR region, as specifically defined by recombinants obtained in our S1 line of Leghorns, plays a significant, but minor, role in the GVH reaction compared with the region of the B complex identified with the B blood-group locus.     

Identification of Mutations in the Pigment Cell-Specific Gene Located at the Brown Locus in Mouse

The pigment cell-specific gene, located at the brown (b)-locus in mouse, encodes the protein that determines the type of melanin synthesized. This protein is known as tyrosinase-related protein, but here we tentatively term it b-locus protein to avoid confusions with the related sequence cross-hybridizing to the tyrosinase gene. In order to identify the mutation at the b-locus, we have cloned and characterized the b-locus protein gene of BALB/c mouse (b/b, c/c). The gene is about 18 kb long and organized into 8 exons and 7 introns. Sequence analysis of the b-locus protein gene reveals four base changes within the protein-coding regions: two missense mutations and two silent mutations. Two missense mutations result in the Cys to Tyr substitution at position 86 (codon 110) and the Arg to His substitution at position 302 (codon 326) of a b-locus protein molecule. Using allele-specific amplification, we confirmed that these missense mutations are actually present in the genomic DNA of two b-mutant strains examined, BALB/c and DBA/2 (b/b, C/C) mice, suggesting that these mutations are specific for the mutant mice at the b-locus. Moreover, we are able to show that the b-locus protein containing Tyr 86 is not reactive with the anti-b-locus protein monoclonal antibody, TMH-1, in transient expression assays.     

Deoxyribonucleic acid reassociation in the taxonomy of the genus Chlorella

DNA hybridization techniques showed Chlorella fusca var. vacuolata and C. kessleri to be homogeneous species with DNA homologies of 90–100% C. fusca var. fusca and var. rubescens, however, have only about 15% DNA homology with C. fusca var. vacuolata and should no longer be regarded as varieties. A good correlation was found so far between biochemical and physiological characters used in the taxonomy of Chlorella and DNA relatedness. Mutant strains of Chlorella were tested for DNA homologies to prove the reliability of the taxonomical interpretation.     

Involvement of the narJ and mob gene products in distinct steps in the biosynthesis of the molybdoenzyme nitrate reductase in Escherichia coli

The Escherichia coli mob locus is required for synthesis of active molybdenum cofactor, molybdopterin guanine dinucleotide. The mobB gene is not essential for molybdenum cofactor biosynthesis because a deletion of both mob genes can be fully complemented by just mobA. Inactive nitrate reductase, purified from a mob strain, can be activated in vitro by incubation with protein FA (the mobA gene product), GTP, MgCl₂, and a further protein fraction, factor X. Factor X activity is present in strains that lack MobB, indicating that it is not an essential component of factor X, but over-expression of MobB increases the level of factor X. MobB, therefore, can participate in nitrate reductase activation. The narJ protein is not a component of mature nitrate reductase but narJ mutants cannot express active nitrate reductase A. Extracts from narJ strains are unable to support the in vitro activation of purified mob nitrate reductase: they lack factor X activity. Although the mob gene products are necessary for the biosynthesis of all E. coli molybdoenzymes as a result of their requirement for molybdopterin guanine dinucleotide, NarJ action is specific for nitrate reductase A. The inactive nitrate reductase A derivative in a narJ strain can be activated in vitro following incubation with cell extracts containing the narJ protein. NarJ acts to activate nitrate reductase after molybdenum cofactor biosynthesis is complete.     

Deciphering the role of the chitin synthase families 1 and 2 in the in vivo and in vitro growth of Aspergillus fumigatus by multiple gene targeting deletion

Although chitin is an essential component of the fungal cell wall (CW), its biosynthesis and role in virulence is poorly understood. In Aspergillus fumigatus, there are eight chitin synthase (CHS) genes belonging to two families CHSA‐C, CHSG in family 1 and CHSF, CHSD, CSMA, CSMB in family 2). To understand the function of these CHS genes, their single and multiple deletions were performed using β‐rec/six system to be able to delete all genes within each family (up to a quadruple ΔchsA/C/B/G mutant in family 1 and a quadruple ΔcsmA/csmB/F/D mutant in family 2). Radial growth, conidiation, mycelial/conidial morphology, CW polysaccharide content, Chs‐activity, susceptibility to antifungal molecules and pathogenicity in experimental animal aspergillosis were analysed for all the mutants. Among the family 1 CHS, ΔchsA, ΔchsB and ΔchsC mutants showed limited impact on chitin synthesis. In contrast, there was reduced conidiation, altered mycelial morphotype and reduced growth and Chs‐activity in the ΔchsG and ΔchsA/C/B/G mutants. In spite of this altered phenotype, these two mutants were as virulent as the parental strain in the experimental aspergillosis models. Among family 2 CHS, phenotypic defects mainly resulted from the CSMA deletion. Despite significant morphological mycelial and conidial growth phenotypes in the quadruple ΔcsmA/csmB/F/D mutant, the chitin content was poorly affected by gene deletions in this family. However, the entire mycelial cell wall structure was disorganized in the family 2 mutants that may be related to the reduced pathogenicity of the quadruple ΔcsmA/csmB/F/D mutant strain compared to the parental strain, in vivo. Deletion of the genes encompassing the two families (ΔcsmA/csmB/F/G) showed that in spite of being originated from an ancient divergence of fungi, these two families work cooperatively to synthesize chitin in A. fumigatus and demonstrate the essentiality of chitin biosynthesis for vegetative growth, resistance to antifungal drugs, and virulence of this filamentous fungus.     

Variants in the CNR1 and the FAAH Genes and Adiposity Traits in the Community

Pharmacologic blockade of the endocannabinoid receptor 1 leads to weight loss and an improved metabolic risk profile in overweight and obese individuals. We hypothesize that common genetic variants in the CNR1 (encoding endocannabinoid receptor 1) and FAAH genes (encoding fatty acid amide hydrolase, a key enzyme hydrolyzing endocannabinoids) are associated with adiposity traits. We genotyped 18 single‐nucleotide polymorphisms (SNPs) in the CNR1 gene and 9 SNPs in the FAAH gene in 2,415 Framingham Offspring Study participants (mean age 61 ± 10 years; 52.6% women; mean BMI 28.2 ± 5.4 kg/m²; 30.3% obese) and studied them for association with cross‐sectional and longitudinal measures of adiposity (BMI, waist circumference, change over time in BMI and waist circumference, visceral and subcutaneous adipose tissue) using linear mixed‐effect models. The selected SNPs captured 85% (r² = 0.8) of the common variation (minor allele frequency >5%) at the CNR1 locus and 96% (r² = 0.8) of the common variation at the FAAH locus (defined as the genomic segment containing the gene +20 kb upstream and +10 kb downstream). After correction for multiple testing, none of the SNPs in the CNR1 gene or in the FAAH gene displayed statistical evidence for association with BMI, waist circumference, and visceral adipose tissue or subcutaneous adipose tissue (all P > 0.18). Despite comprehensive SNP mapping across the genes and their regulatory regions in a large unselected sample, we failed to find evidence for an association of common variants in the CNR1 and FAAH genes with measures of adiposity in our community‐based sample.     

Analysis of the DDE Motif in the Mutator Superfamily

The eukaryotic Mutator family of transposable elements is widespread in plants. Active or potentially active copies are also found in fungi and protozoans, and sequences related to this family have been detected in metazoans as well. Members of this family are called Mutator-like elements (MULE s). They encode transposases, which contain a region conserved with transposases of the IS256 prokaryotic family, known to harbor a DDE catalytic domain. Different DDE or D34E motifs have been proposed in some groups of eukaryotic MULEs based on primary sequence conservation. On a large number of protein sequences related to, and representative of, all MULE families, we analyzed global conservation, the close environment of different acidic residues and the secondary structure. This allowed us to identify a potential DDE motif that is likely to be homologous to the one in IS256-like transposases. The characteristics of this motif are depicted in each known family of MULEs. Different hypotheses about the evolution of this triad are discussed. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.