Characterization of SSEA-1 glycolipids from the brain of a patient with fucosidosis

Neutral glycolipids from the brain of a patient with Fucosidosis were analyzed and two complex glycolipids containing five and eight sugars were isolated from the cortical grey matter. These two glycolipids reacted with antibodies recognizing the SSEA-1 [Le^x(X)] carbohydrate determinant. SSEA-1 glycolipids are normally expressed in human embryonic brain but are found in only small amounts in postnatal human brain. The accumulation of the two SSEA-1 glycolipids in Fucosidosis brain thus represents a defect which affects the normal developmentally regulated decrease in postnatal, expression of these glycolipids, and may be a contributing factor in the abnormal brain development associated with the disease. Chemical characterization of the two isolated glycolipids by gas chromatographic and mass spectrometric analyses has identified the two glycolipids as lacto-N-fucopentaosylceramide (III) and difucosyl-neolactonorhexaosylceramide.Abbreviations DCl direct chemical ionization - FAB tastatiom bombardment - GC gas chromatography - GSLs glycosphingolipids - MS mass spectrometry - SSEA-1 stage specific embryonic antigen-1 - TLC thin layer chromatographys     

Genetic and molecular analysis of a three-component transposable-element system in maize

Summary Two different factors control the mutability of an unstable allele (c2-m8810581) of the C2 gene of maize. Both an autonomous En/Spm element and an unrelated independent factor, named Mediator, are coordinately required for the excision of the insert in c2-m881058Y. According to genetic analysis, Mediator does not have the suppressor (S) function or mutator (M) function of En/Spm. Mediator has no effect on the timing or frequency of excision of Enl, En-low, or various I/dSpm elements. Hence, Mediator only mediates a specific interaction between En and the insert at c2m881058Y. Molecular analysis of c2-m881058Y has revealed a 3.3 kb, complex, En-related receptor element inserted into the second exon of the C2 gene. The ends of this element are homologous to the ends of En/Spm, but an internal l.7 kb region shows no En/Spm homology. A great degree (11–14%) of nucleotide changes, relative to Enl, occur within and between the 12 bp TNPA binding motifs. Alterations of these critical cis-determinants may account for the need for a helper factor for excision. This element is named Irma, for Inhibitor that requires Mediator also, and represents a unique, low copy number class of receptor element.     

The trade-off between growth rate and yield in microbial communities and the consequences for under-snow soil respiration in a high elevation coniferous forest

Soil microbial respiration is a critical component of the global carbon cycle, but it is uncertain how properties of microbes affect this process. Previous studies have noted a thermodynamic trade-off between the rate and efficiency of growth in heterotrophic organisms. Growth rate and yield determine the biomass-specific respiration rate of growing microbial populations, but these traits have not previously been used to scale from microbial communities to ecosystems. Here we report seasonal variation in microbial growth kinetics and temperature responses (Q₁₀) in a coniferous forest soil, relate these properties to cultured and uncultured soil microbes, and model the effects of shifting growth kinetics on soil heterotrophic respiration (R_h). Soil microbial communities from under-snow had higher growth rates and lower growth yields than the summer and fall communities from exposed soils, causing higher biomass-specific respiration rates. Growth rate and yield were strongly negatively correlated. Based on experiments using specific growth inhibitors, bacteria had higher growth rates and lower yields than fungi, overall, suggesting a more important role for bacteria in determining R_h. The dominant bacteria from laboratory-incubated soil differed seasonally: faster-growing, cold-adapted Janthinobacterium species dominated in winter and slower-growing, mesophilic Burkholderia and Variovorax species dominated in summer. Modeled R_h was sensitive to microbial kinetics and Q₁₀: a sixfold lower annual R_h resulted from using kinetic parameters from summer versus winter communities. Under the most realistic scenario using seasonally changing communities, the model estimated R_h at 22.67 mol m⁻² year⁻¹, or 47.0% of annual total ecosystem respiration (R_e) for this forest.     

EFOLD,a New Program Complex for Molecular Modeling: The Use of a Flexible Weighting Coefficient Scheme and the Standard Valence Geometry in Modeling the Enzyme Active Sites

An algorithm was proposed for the representation of biopolymer structures in an internal coordinate system (so-called structure regularization) by minimizing the target function using a flexible weighting coefficient scheme with three components that determine the reliability of deviations of each atom. For the structure regularization, an algorithm for taking into account the temperature factor was suggested for the first time. It was shown by the example of the aspartyl protease rhizopuspepsin that the representation in the internal coordinate system may result in an accurate reproduction of the structural details of separate molecule fragments, such as the enzyme active site region. This algorithm was implemented as one of the modules of EFOLD.     

wiser tsl : a recessive X-linked temperature-sensitive lethal mutation that affects the wings and the eyes in Drosophila melanogaster

In this study, we characterize a recessive X-linked temperature-sensitive mutation of the gene CG32711. The mutation, named wiser ^tsl (wings scalloped-eyes rough), was isolated from a dysgenic cross and is due to a natural P element insertion within the 5′ regulatory region of the gene. Mutant (wiser ^tsl ) individuals exhibit wing notching, rough eyes, tarsal malformations and reduced life-span. At 29°C they die at larval and late pharate stages or during eclosion. The CG32711 (wiser) gene is mainly expressed in the ventral midline cells, the peripheral neural system, the hemocytes and the tracheal system of embryos. It is also expressed in nurse cells of adult female ovaries. Our results show that the wiser gene is alternatively spliced generating two mRNAs, which share the same open reading frame, while western analysis identified two protein isoforms. Their expression pattern depends on the stage of development and the culture temperature. wiser ^tsl and wild-type individuals display different expression patterns of the two isoforms and this difference most probably accounts for the mutant phenotype. Our results indicate that wiser is a vital gene for the development of Drosophila melanogaster which has no orthologs outside the Drosophilidae. Sequence data from this article have been deposited with the EMBL/GenBank Data Libraries under accession nos. bankit1003537 EU071463–bankit1003860 EU071464.     

Hydrogen peroxide-induced chlorophyll a bleaching in the cytochrome b 6 f complex: a simple and effective assay for stability of the complex in detergent solutions

The instability of cytochrome b ₆ f complex in detergent solutions is a well-known problem that has been studied extensively, but without finding a satisfactory solution. One of the important reasons can be short of the useful method to verify whether the complex suspended in different detergent is in an intact state or not. In this article, a simple and effective assay for stability of the complex was proposed based on the investigation on the different effects of the two detergents, n-octyl-β-d-glucopyranoside (OG) and dodecyl-β-d-maltoside (DDM), on the properties of the complex. DDM stabilizes the complex preparation more effectively whereas OG denatures the interactions of the heme groups and pigment molecules with the protein environment, leading to the bleaching of chlorophyll a induced by addition of hydrogen peroxide. The assay of the use of hydrogen peroxide to characterize the complex by studying the bleaching of chlorophyll induced by hydrogen peroxide and the peroxidase activity of the complex was discussed. This simple method will probably be useful to study the stability of the complex. Xiao-Bo Chen and Xiao-Hui Zhao contributed equally to this work.     

Distribution,community structure and production of fishes in the upper Speed River,Ontario: a preimpoundment study

Synopsis The upper Speed River, on which a dam was under construction, was surveyed through fourteen qualitative and six quantitative collections to determine the distribution of fishes in the river above Guelph, Ontario and in a tributary, Luteral Creek. At the quantitative localities the removal method was used to estimate density and standing crop of all species. At three of these localities age and growth of the dominant species were determined and total ecological production calculated. Two approaches to the estimation of production for the 0–1 age class were compared and found to result in differences of 33–39% in the estimates of total production, thus illustrating the extent to which methodology may affect such estimates The dominant species in the river were, Semotilus atromaculatus, Notropis cornutus, Pimephales notatus, Rhinichthys atratulus, Hypentelium nigricans, Catostomus commersoni, Ambloplites rupestris, Micropterus dolomieui and Etheostoma flabellare. Density ranged from 11126 to 74765 individuals per hectare and standing crop from 32.4 to 190.0 kg ha⁻¹. Production values at the three localities were 15, 19 and 54 kg ha⁻¹ yr⁻¹ , and are low compared with estimates for other fluvial systems. Comparison with a 1951 survey of the Speed River revealed considerable changes in the composition and distribution of fish species. The ranges of several cold-water species had contracted towards the headwaters, whereas several warm-water species had extended their ranges up the river     

Isoasparagine as a marker amino acid in the taxonomy of Characeae

Fourteen species of Characeae were analyzed for their free amino acids. This study, in combination with previous results (Sakanoet al., 1984) showed that all the species that belong to the generaChara (6 species),Lamprothamnium (1 species),Nitellopsis (1 species),Lychnothammus (1 species) and 5Nitella species of the members of the subsectionAnarthrodactylae contained a large amount of isoasparagine. In contrast, no isoasparagine was found in the species belonging toTolypella (3 species) and otherNitella (7 species). Presence of isoasparagine in some species of Characeae (N. flexillis andNitellopsis obtusa) was found to be independent of their localities (Japan, Canada and England). Species lacking isoasparagine (N. oligogyra and N. axilliformis) did not produce isoasparagine even under the condition that induced a great increase of this amino acid in the species that contained it (C. corallina andN. flexilis). These results indicate that isoasparagine is a distinct taxonomic marker and suggest that theNitella species of the subsectionAnarthrodactylae are the most primitive group inNitelleae in that they share synthesis and accumulation of isoasparagine withChareae and, hence, support the view (Kasaki, 1964) that the subsection may be treated as an independent genus.     

Isolation and characterization of free glycans of the oligomannoside type from the extracellular medium of a plant cell suspension

The oligosaccharides Man₅GlcNAc and Man₃(Xyl)GlcNAc(Fuc)GlcNAc presumed to originate fromN-glycosyl proteins have been purified from an extracellular medium (concentration: 2–5 mg/l of 14 day cultures) of white campion (Silene alba) suspension culture. Their primary structures have been determined by¹H-400-MHz NMR spectroscopy and FAB-MS spectrometry. They are probably the result of an autophagic process including protein catabolism due to sucrose starvation. Additional identification of digalactosylglycerol (galactolipid breakdown) argues for this hypothesis.Abbreviations Fuc l-fucose - Man d-mannose - Xyl d-xylose - GlcNAc N-acetyl-d-glucosamine - Gal d-galactose - Glc d-glucose - FAB-MS fast atom bombardment mass spectrometry - NMR nuclear magnetic resonance     

Sprouty1 and Sprouty2 limit both the size of the otic placode and hindbrain Wnt8a by antagonizing FGF signaling

Multiple signaling molecules, including Fibroblast Growth Factor (FGF) and Wnt, induce two patches of ectoderm on either side of the hindbrain to form the progenitor cell population for the inner ear, or otic placode. Here we report that in Spry1, Spry2 compound mutant embryos (Spry1^−/−; Spry2^−/− embryos), the otic placode is increased in size. We demonstrate that the otic placode is larger due to the recruitment of cells, normally destined to become cranial epidermis, into the otic domain. The enlargement of the otic placode observed in Spry1^−/−; Spry2^−/− embryos is preceded by an expansion of a Wnt8a expression domain in the adjacent hindbrain. We demonstrate that both the enlargement of the otic placode and the expansion of the Wnt8a expression domain can be rescued in Spry1^−/−; Spry2^−/− embryos by reducing the gene dosage of Fgf10. Our results define a FGF-responsive window during which cells can be continually recruited into the otic domain and uncover SPRY regulation of the size of a putative Wnt inductive center.     

Probing the archaeal diversity of a mixed thermophilic bioleaching culture by TGGE and FISH

The archaeal community present in a sample of Mixed Thermophilic Culture-B (MTC-B) from a laboratory-scale thermophilic bioleaching reactor was investigated by temperature gradient gel electrophoresis (TGGE) and fluorescence in situ hybridisation (FISH). Both techniques were specifically adapted for use on native state bioleaching samples, with a view to establishing convenient means for monitoring culture composition. Using the TGGE protocol developed, the relative species composition of the thermophilic bioleaching sample was analysed, and included four phylotypes belonging to the Sulfolobales, which were related to Stygiolobus azoricus, Metallosphaera sp. J1, Acidianus infernus and Sulfurisphaera ohwakuensis. However, the St. azoricus-like phylotype was difficult to resolve and some micro-heterogeneity was observed within this phylotype. Specific FISH probes were designed to qualitatively assess the presence of the phylotypes in MTC-B. The sample was dominated by Sf. ohwakuensis-like Archaea. In addition, the St. azoricus-like, Metallosphaera species-like and Acidianus species-like cells appeared in similar low abundance in the community. Most strikingly, FISH identified Sulfolobus shibatae-like cells present in low numbers in the sample even though these were not detected by PCR-dependent TGGE. These results highlight the importance of using more than one molecular technique when investigating the archaeal diversity of complex bioleaching reactor samples.     

Induction of toxin production in dinoflagellates: the grazer makes a difference

The dinoflagellate Alexandrium minutum has previously been shown to produce paralytic shellfish toxins (PST) in response to waterborne cues from the copepod Acartia tonsa. In order to investigate if grazer-induced toxin production is a general or grazer-specific response of A. minutum to calanoid copepods, we exposed two strains of A. minutum to waterborne cues from three other species of calanoid copepods, Acartia clausi, Centropages typicus and Pseudocalanus sp. Both A. minutum strains responded to waterborne cues from Centropages and Acartia with significantly increased cell-specific toxicity. Waterborne cues from Centropages caused the strongest response in the A. minutum cells, with 5 to >20 times higher toxin concentrations compared to controls. In contrast, neither of the A. minutum strains responded with significantly increased toxicity to waterborne cues from Pseudocalanus. The absolute increase in PST content was proportional to the intrinsic toxicity of the different A. minutum strains that were used. The results show that grazer-induced PST production is a grazer-specific response in A. minutum, and its potential ecological importance will thus depend on the composition of the zooplankton community, as well as the intrinsic toxin-producing properties of the A. minutum population.     

Floating vegetation mats on a floodplain billabong in the Northern Territory of Australia

The floristics and physical structure of a floating mat of vegetation in the Finniss River area of the Northern Territory are described. During the dry season floating mats contain green productive vegetation when the adjacent flood plains are dry and many of the plants are withered. At this time insects are more abundant on the mats than on the adjacent flood plain. Some flood plain vertebrates appear to concentrate their activity on floating mats during the dry season. During the period 1963 to 1978 the area of floating mat in the Finniss River study area was greatly reduced, probably as a result of high densities of feral water buffalo (Bubalis bubalus).(Present address: c/o 38 Hardy Terrace, East Ivanhoe, Victoria 3079).(Present address: c/o 38 Hardy Terrace, East Ivanhoe, Victoria 3079).     

Autotrophic denitrification and inhibitory effect caused by the injection of spent sulfidic caustic in a modified Ludzack-Ettinger process

As spent sulfidic caustic (SSC) from petroleum plants contains a high concentration of alkalinity and sulfur compounds, SSC can be applied in sewage treatment system as an electron donor for autotrophic denitrification. In our previous study, the reuse of SSC in the biological nitrogen process was successful, and some neutralization may be required for stable treatment performance. In this study, the pH of SSC was neutralized to 12.0 from 13.3, and the modified Ludzack-Ettinger process was conducted for 90 days with the municipal wastewater. Some toxic effects of SSC on microorganisms were tested via a specific oxygen uptake rate (SOUR) assay. According to the SOUR assay, as compared with no SSC injection condition, SOUR was reduced by approximately 5.4% when 4 mL SSC/L was injected and the effective concentration of a toxicant causing 50% inhibition of the microorganism’s activity (EC₅₀) was 22.6 mL/L. During the days of operation, the COD removal and nitrification efficiency were over 53.0 and 98.2%, respectively. The TN removal efficiency was 56.6% and the nitrogen removal rate (NRR) was 0.15 kg/m³·d when the hydraulic retention time (HRT) in the anoxic tank was 3 h. The ratio of nitrifying bacteria was unaffected by the HRT, and Nitrobacter spp. and Nitrospira genus existed at similar ratios. The ratio of T. denitrificans increased after the injection of SSC and was approximately 6.5%.     

Utilisation of a tropical bay as a nursery area by sharks of the families Carcharhinidae and Sphyrnidae

Synopsis At least eight species of sharks of the families Carcharhinidae and Sphyrnidae use Cleveland Bay in northern Australia as a communal nursery area.Carcharhinus dussumieri, C. fitzroyensis, C. limbatus andC. tilstoni use the bay as a seasonal primary nursery, with juveniles occurring in it for only a few months each year immediately after birth. Alternatively,Carcharhinus sorrah, Rhizoprionodon acutus andR. taylori use the bay as a year-round primary and secondary nursery, with juveniles remaining in it up to the size at maturity. AdultR. taylori also persist in the bay, a behavioural pattern possibly explained by their small maximum size. While present immediately after birth the type of utilisation pattern displayed bySphyrna lewini could not be clarified in this study. Although diets of these species in the bay are similar, there is probably little direct competition for food due to the highly productive habitats in the bay supporting an abundance of food resources. The highest numbers of juveniles occur when prey species are the most abundant, and when temporal separation of some seasonally-occurring species of sharks in effect.     

Eya1 and Six1 promote neurogenesis in the cranial placodes in a SoxB1-dependent fashion

Genes of the Eya family and of the Six1/2 subfamily are expressed throughout development of vertebrate cranial placodes and are required for their differentiation into ganglia and sense organs. How they regulate placodal neurogenesis, however, remains unclear. Through loss of function studies in Xenopus we show that Eya1 and Six1 are required for neuronal differentiation in all neurogenic placodes. The effects of overexpression of Eya1 or Six1 are dose dependent. At higher levels, Eya1 and Six1 expand the expression of SoxB1 genes (Sox2, Sox3), maintain cells in a proliferative state and block expression of neuronal determination and differentiation genes. At lower levels, Eya1 and Six1 promote neuronal differentiation, acting downstream of and/or parallel to Ngnr1. Our findings suggest that Eya1 and Six1 are required for both the regulation of placodal neuronal progenitor proliferation, through their effects on SoxB1 expression, and subsequent neuronal differentiation.     

Root turnover in a beech and a spruce stand of the Belgian Ardennes

The theoretical basis of fine root turnover estimation in forest soils is discussed, in relation to appropriate experimental techniques of measurement. After sequential coring, the correct expression is the sum of significant positive increments of live and dead roots of the various diameter categories, to which the transfer of dead roots to organic matter derived from roots, OMDR, has to be added. This should not be confounded with dead root mineralization. The transfer rates should first be estimated in root dimensions and not in weight of dry matter. The measurements were carried out in a 120 year old beech (Fagus sylvatica L.) stand and a 35 year old Norway spruce (Picea abies Karst) stand, in the Eastern Ardennes, Belgium. The turnover rate of fine roots (diam. <5 mm) was 4393 kg ha⁻¹ year⁻¹ (root dry weight), including 711.2 kg ha⁻¹ year⁻¹ for dead root transfer to OMDR, for beech. For spruce, turnover rate was 7011 kg ha⁻¹ year⁻¹ (root dry weight), including 1498 kg ha⁻¹ year⁻¹ for dead root transfer to OMDR. Under beech, there was a slight root density increase in spring. No seasonal fluctuations were observed under spruce, but a strong irreversible drop in live root growth was found in the later season 1980–1981, corresponding to a decrease of tree height growth and trunk radius increment. Turnover rates were further expressed in dry weight and in amounts of elements (kg ha⁻¹ year⁻¹) (Ca, Mg, K, Na, Al, N, P, S). Correlative relations between root dimensions and dry weight and element concentrations show that the derived values, and in particular root specific density (dry weight volume⁻¹) vary according to species, root category, and seasonal sampling. Various schemes of seasonal variations of root growth, described in Europe, show that the major dependance on general climate is obscured by environmental factors (soil, exposure, species). It is suggested that root density fluctuation approach the steady state on an annual basis under mild Atlantic conditions.