Growth inhibition and altered gene transcript levels in earthworms (Eisenia fetida) exposed to 2,2',4,4'-tetrabromodiphenyl ether.

The toxic effects of the ubiquitous pollutant 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) on the earthworm Eisenia fetida were assessed by determining growth-inhibition and gene transcript levels of superoxide dismutase (SOD), catalase (CAT), glutathione transferase (GST), and transcriptional changes of the stress-response gene (heat-shock protein 70 [Hsp70]). Somatic growth and growth-inhibition rates in all BDE-47-treated groups were significantly different from those of the controls. The SOD gene transcripts were upregulated at all exposure doses and reached the maximum at the concentration of 400 mg/kg dry weight (dw) (3.84-fold, P < 0.01), which protected earthworms from oxidative stresses. However, downregulation of CAT and Hsp70 was present in all exposure doses and reached to the minimum at concentrations of 400 mg/kg dw (0.07-fold, P < 0.01 and 0.06-fold, P < 0.01, respectively). Upregulation of GST gene transcript level presented significant changes at concentrations of 10 (2.69-fold, P < 0.05) and 100 mg/kg dw (2.55-fold, P < 0.05). SOD maintained a dynamic balance to upregulate SOD expression to eliminate superoxide radicals in all dosage treatments, but downregulation of CAT decreased the ability to eliminate hydrogen peroxide. These changes could result in biochemical and physiological disturbances in earthworms.

Breakdown of food waste by anaerobic fermentation and non-oxygen producing photosynthesis using a photosynthetic bacterium.

Large volumes of food waste are produced by restaurants, hotels, etc generating problems in its collection, processing and disposal. Disposal as garbage increases the organic matter in landfills and leachates. The photosynthetic bacterium Rhodopseudomonas palustris (CGA 009) easily broke down food waste. R. palustris produces H2 under anaerobic conditions and digests a very wide range of organic compounds. R. palustris reduced BOD by ≈70% and COD by ≈33%, starch, ammonia, nitrate, was removed but had little effect on reducing sugar or the total phosphorus, lipid, protein, total solid in a 7-day incubation. R. palustris produced a maximum of 80ml H2/g COD/day. A two-stage anaerobic digestion using yeast as the first stage, followed by a R. palustris digestion was tested but production of H2 was low.

Biobased plastics in a bioeconomy.

Bioeconomy plans include a biobased industries sector in which some oil-derived plastics and chemicals are replaced by new or equivalent products derived, at least partially, from biomass. Some of these biobased products are here today, but to fulfil their societal potential, greater attention is required to promote awareness, and to improve their market share while making valuable contributions to climate change mitigation.

Comparative virulence of Infectious salmon anaemia virus isolates in Atlantic salmon, Salmo salar L.

Infectious salmon anaemia virus (ISAV) surveillance in the Bay of Fundy has identified the existence of a large number of genetically distinct ISAV isolates which appear to be of variable virulence. Genetically distinct isolates are currently being designated based on sequencing of the hyper polymorphic region (HPR) of genomic segment 6, which encodes the haemagglutinin-esterase protein, but it has been difficult to elucidate a clear association between these molecular variations and variations in virulence. This has hampered the establishment of proactive management decisions regarding infected fish, and ISAV infections, regardless of type, must be treated as one. Field data of ISAV infections is difficult to collect and to compare between infections because of a wide range of confounding factors including time of year, fish stock, cage site location, mitigating factors and stressors. An important tool in determining the relationship between molecular differences and virulence comes from analysis of quarantine studies. The goal of this study was to compare the virulence, by co-habitation and intraperitoneal injection, of four regionally common and recent ISAV isolates in a controlled environment. We found significant differences in mortality between ISAV molecular isolates, and present data showing that survival of ISAV infection confers significant resistance to re-infection with a different ISAV isolate. These findings, if borne out in field studies, will significantly alter the way ISAV infections are managed in the Bay of Fundy and elsewhere.

Identification and characterization of segments 3 and 4 of the ISAV genome.

Infectious Salmon Anaemia is a serious disease of farmed Atlantic Salmon on three continents. The disease causes severe anaemia and haemorrphagic liver necrosis, and carries major economic consequences for affected areas. Nevertheless, the causative agent, a novel orthomyxo-like Virus (Infectious Salmon Anaemia Virus - ISAV), is only partially characterized at the molecular level. We report the isolation and characterization of two novel ISAV segments at the genomic and proteomic levels. These segments are the third and fourth largest of the (ISAV) genome and may code for a nucleocapsid protein (NP) and a polymerase (PA). Western blot analysis using an ISAV polyclonal antibody identified one of these novel proteins as being the major tissue antigen. We discuss the implications of our findings for vaccine development and surveillance of Infectious Salmon Anaemia.

Identification of infectious salmon anaemia virus in Atlantic salmon from Nova Scotia (Canada): evidence for functional strain differences.

Infectious salmon anaemia (ISA) is a serious disease responsible for high morbidity in farmed Atlantic salmon Salmo salar in Norway, Scotland and New Brunswick, Canada. Recent attempts to identify different strains of ISA virus (ISAV) based on nucleotide sequence variation have shown that the Norwegian and Scottish samples are similar to one another but markedly different from New Brunswick samples. These data may suggest the presence of different strains on each side of the Atlantic but no functional difference has been found with either strain. We describe the first identification and characterisation of ISAV in Atlantic salmon from Nova Scotia, Canada. Further, salmon infected with the Nova Scotia ISAV do not show typical ISAV pathology or mortality. Sequencing of this new strain showed it to possess greater similarity to ISAV from Norway and Scotland than to ISAV from New Brunswick. These findings are discussed in terms of a possible origin of the Nova Scotia ISAV strain and the existence of an avirulent ISAV strain. The impact of current strain variation studies on our knowledge of ISAV is also discussed.

A large polymorphic repeat in the pericentromeric region of human chromosome 15q contains three partial gene duplications.

We report the identification of a partial duplication of GABRA5 , a gene within the imprinted 15q11-q13 region. The duplicated locus maps to the pericentromeric region of 15q, proximal to the large deletions associated with Angelman and Prader-Willi syndromes. We also observed variation in the number of copies of this locus in different individuals, indicating that the duplication is part of a variable repeat. Investigation of the duplication in individuals with a normal karyotype revealed between one and four copies of the repeat on each chromosome 15, whereas from eight to 20 copies were found in individuals possessing a cytogenetically detectable elongation of the 15q region. The variable region is roughly 1 Mb in size and contains two other non-processed duplications, the immunoglobulin heavy chain (IgH) D segment gene and the neurofibromatosis type 1 (NF1) gene. One unit of the pericentromeric repeat is thus composed of duplications of genes from different chromosomal regions. Moreover, we have found replication asynchrony across the GABRA5 duplication, suggesting for the first time that the imprinted part of chromosome 15q extends proximal of the region commonly deleted in Angelman and Prader-Willi syndromes.

Clonal heterogeneity at allelic methylation sites diagnostic for Prader-Willi and Angelman syndromes.

Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are developmental disorders resulting from the absence of the paternal or maternal contribution to the 15q11-13 region, respectively. Allele-specific methylation at D15S63 (PW71) has routinely been used as a diagnostic indicator of PWS and AS in DNA samples derived from peripheral blood. Extensive variation in allele-specific methylation patterns, however, has been observed at this site in different tissues, but the frequency or mechanism of this variation has remained uncharacterized. Herein, we have investigated the cellular basis of variation in methylation patterns at four sites of allelic methylation near SNRPN by using DNA samples derived from a panel of primary T lymphocyte clones. Interclonal variability was observed at three of these sites, including the diagnostic PW71 site. Changes in allele-specific methylation patterns occurred at a frequency of about one change in 50% of the cells every 22-25 doublings. In contrast, stable allele-specific methylation was observed in these clonal populations at exon 1 of SNRPN and the androgen receptor locus on the inactive X chromosome, suggesting that methylation at some CpG sites is more faithfully maintained than others. Clonal heterogeneity at PW71 was not an artifact of cell culture because the absence of allelic methylation was also observed in about 20% of the alleles in unstimulated peripheral blood. These results demonstrate that variation in allele-specific methylation at PW71 and other sites in the PWS/AS region appear to depend on the clonal complexity of the particular tissue and on the lack of strict maintenance of methylation within clones.

Population genetics of the FRAXE and FRAXF GCC repeats, and a novel CGG repeat, in Xq28.

Most of the rare folate sensitive fragile sites cloned to date arise from expansion of a CGG:CCG trinucleotide repeat array. Analysis of the CAG repeat at the Huntington Disease (HD) locus showed a positively skewed repeat distribution leading to the proposal that microsatellites are subject to a mutational bias toward expansion. Such a mutational bias predicts an increase in mean repeat size at all microsatellite loci. We present an analysis of repeats at two fragile site loci, FRAXE and FRAXF, and a novel CGG repeat in Xq28, in five different human populations, which suggests that these loci may also be subject to the same mutation process. The novel repeat array may represent the first evidence for the existence of a fourth fragile site in Xq27.3-28.

Driving Forces for Bicarbonate Transport in the Cyanobacterium Synechococcus R-2 (PCC 7942).

Air-grown Synechococcus R-2 (PCC 7942) cultures grown in BG-11 medium are very alkaline (outside pH is 10.0) and use HCO3- as their inorganic carbon source. The cells showed a dependence on Na+ for photosynthesis, but low Na+ conditions (1 mol m-3) were sufficient to support saturating photosynthesis. The intracellular dissolved inorganic carbon in the light was greater than 20 mol m-3 in both low-Na+ conditions and in BG-11 medium containing the usual [Na+] (24 mol m-3, designated high-Na+ conditions). The electrochemical potential for HCO3- in the light was in excess of 25 kJ mol-1, even in high-Na+ conditions. The Na+-motive force was greater than -12 kJ mol-1 under both Na+ conditions. On thermodynamic grounds, an Na+-driven co-port process would need to have a stoichiometry of 2 or greater ([greater than or equal to]2Na+ in/HCO3-1 in), but we show that Na+ or K+ fluxes cannot be linked to HCO3- transport. Na+ and K+ fluxes were unaffected by the presence or absence of dissolved inorganic carbon. In low-Na+ conditions, Na+ fluxes are too low to support the observed net 14C-carbon fixation rate. Active transport of HCO3- hyperpolarizes (not depolarizes) the membrane potential.

A study of FRAXE in mentally retarded individuals referred for fragile X syndrome (FRAXA) testing in the United Kingdom.

The folate-sensitive fragile site FRAXE is located in proximal Xq28 of the human X chromosome and lies approximately 600 kb distal to the fragile X syndrome (FRAXA) fragile site at Xq27.3. The cytogenetic expression of FRAXE is thought to be associated with mental handicap, but this is usually mild compared to that of the more common fragile X syndrome that is associated with the expression of the FRAXA fragile site. The exact incidence of FRAXE mental retardation is uncertain. We describe here the results of a U.K. survey designed to assess the frequency of FRAXE in a population of individuals referred for fragile X syndrome testing and found to be negative for expansion events at the FRAXA locus. No FRAXE expansion events were found in 362 cytogenetically negative males studied, and one expansion event was identified in a sample of 534 males for whom cytogenetic analyses were either unrecorded or not performed. Further FRAXE expansion events were detected in two related females known to be cytogenetically positive for a fragile site in Xq27.3-28. To gain insight into the FRAXE phenotype, the clinical details of the identified FRAXE male plus three other FRAXE individuals identified through previous referrals for fragile X syndrome testing are presented. For the population studied, we conclude that FRAXE mental retardation is a relatively rare but significant form of mental retardation for which genetic diagnosis would be appropriate.

The cloning of FRAXF: trinucleotide repeat expansion and methylation at a third fragile site in distal Xqter.

Three fragile sites, FRAXA, FRAXE and FRAXF lie in the Xq27-28 region of the human X chromosome. The expression of FRAXA is associated with the fragile X syndrome, the most prevalent form of inherited mental retardation whilst the expression of FRAXE is associated with a rarer and comparatively milder form of mental handicap. Both the FRAXA and FRAXE sites have been cloned and the fragile site expression found to be due to the expansion of analogous CGG/GCC trinucleotide repeat arrays. We describe here the cloning of the third fragile site, FRAXF, and demonstrate that it involves the expansion of a (GCCGTC)n(GCC)n compound array. PCR analyses across the repeat of normal individuals show that the number of triplets in the array ranges from 12-26 and the most common allele consists of 14 triplet units. Sequencing analyses show that 95% of normal individuals have three copies of the GCCGTC motif and in these individuals, the size variation observed by PCR is due to copy number alterations in the GCC array. In a cytogenetically positive male with developmental delay, the array is expanded by > 900 triplets and the adjacent CpG-rich region is methylated. The array is also expanded in cytogenetically positive carrier females from the family originally used to define the FRAXF site. We conclude that the expanded array corresponds to the FRAXF fragile site.

Insulin gene region-encoded susceptibility to type 1 diabetes is not restricted to HLA-DR4-positive individuals.

Type 1 or insulin-dependent diabetes mellitus (IDDM) is an autoimmune disease of the insulin-producing pancreatic beta-cells which is determined by both genetic and environmental factors. The major histocompatibility complex and the insulin gene region (INS) on human chromosomes 6p and 11p, respectively, contain susceptibility genes. Using a mostly French data set, evidence for linkage of INS to IDDM was recently obtained but only in male meioses (suggesting involvement of maternal imprinting) and only in HLA-DR4-positive diabetics. In contrast, we find evidence for linkage in both male and female meioses and that the effect of the susceptibility gene(s) in the INS region is not dependent on the presence of HLA-DR4.

Permeability of ammonia and amines in Rhodobacter sphaeroides and Bacillus firmus.

Permeabilities of uncharged ammonia (NH3), methylamine (CH3NH2), and ethylamine (CH3CH2NH2) in the gram-negative phototrophic bacterium Rhodobacter sphaeroides were measured directly in cells grown heterotrophically under aerobic conditions. The permeability of NH3 was 2.55 +/- 0.73 microns s-1 (n = 20), but the permeabilities of CH3NH2 (MA) and CH3CH2NH2 (EA) were higher, PMA = 17.8 +/- 2.8 microns s-1 (n = 50), PEA = 24.7 +/- 3.9 microns s-1 (n = 44). The relative permeabilities of amines were also determined from their effect on the pH gradient across the cell membrane at alkaline external pH. In aerobically grown R. sphaeroides, both techniques indicated that the permeability of CH3CH2NH2 was about 30% greater than that of CH3NH2 but that the permeability of NH3 was only about 1/5 that of CH3NH2. The relative permeabilities of NH3 (A) and CH3NH2 were different in R. sphaeroides cells grown under three different physiological conditions: (a) cells grown aerobically with ammonium sulfate (PA/PMA about 0.20), (b) cells grown anaerobically with ammonium sulfate as their nitrogen source (PA/PMA about 0.29), and (c) diazotrophic cells (PA/PMA about 0.38). NH3 was also found to be only about 1/3 as permeable as CH3NH2 in the alkalophilic gram-positive bacterium Bacillus firmus. The findings that permeability properties of NH3 and CH3NH2 are very different in different bacteria and vary according to the conditions under which the organism is grown need to be taken into account in the interpretation of experiments where [14C]methylamine is used as an ammonia analog.