Analysis of a set of RAPD markers by hybridization and sequencing in Brassica: a note of caution

A series of RAPD markers generated by a single 10-mer primer were analyzed by hybridization to amplified and genomic DNA and by sequencing in two Brassica species. Primer B18 produced different profiles of nine major bands each in both Brassica nigra (B genome) and B. napus (AC genomes). Cloning and sequencing of five B18 B. nigra amplification products revealed that they were all unrelated to each other. Only limited stretches of high similarity of up to 69 nucleotides were shared by some of these clones. Hybridization to genomic DNA indicated that only two corresponded to a highly repeated sequence, whereas the rest were low copy sequences. In spite of their lack of homology, when these clones were used as probes to amplified B. nigra DNA, they hybridized to multiple bands in the profile. Hybridization of B. nigra clones for bands of similar sizes in both species, failed to hybridize in B. napus, revealing lack of homology between the DNAs of the two species. Because of these inconsistencies, it is concluded that RAPD markers, although useful for genetical studies, should be used with caution specially when basing homology on cross-hybridization and fragment sizes.     

Low organotin contamination of harbour sediment in Svalbard

Arctic sea routes are opening up for maritime transport due to sea ice retreat leading to increasing human activities in the Arctic and concomitant pressures on the environment. Organotin compounds are used in antifouling paints of large seagoing vessels and are known to leach into the marine environment and accumulate in sediments and biota. As organotin levels in Svalbard sediments have not been documented in peer-reviewed literature before, this study describes the levels in sediment of harbours around Svalbard (Ny-Ålesund, Longyearbyen, Svea, Pyramiden and Barentsburg). Organotin levels in sediments of Svalbard harbours were low (below the detection limit up to 14 ng Sn/g dw sum-butyltin) compared to other Arctic regions with a longer history of shipping. Levels were below known no effect levels and in accordance, no imposex was found in marine whelks from Ny-Ålesund harbour. Of all other analysed compounds in sediments of Kongsfjorden (polycyclic aromatic hydrocarbon (PAHs), polychlorinated biphenyls, polybrominated diphenylethers and perfluorinated compounds) PAH levels were highest and in one sample above action levels. It is advised to continue monitoring contaminant levels, for which the current results form a good basis. If contaminant levels rise, mitigation measures can be taken in time.     

De Novo Occurrence of a Variant in ARL3 and Apparent Autosomal Dominant Transmission of Retinitis Pigmentosa

Background

Retinitis pigmentosa is a phenotype with diverse genetic causes. Due to this genetic heterogeneity, genome-wide identification and analysis of protein-altering DNA variants by exome sequencing is a powerful tool for novel variant and disease gene discovery. In this study, exome sequencing analysis was used to search for potentially causal DNA variants in a two-generation pedigree with apparent dominant retinitis pigmentosa.

Methods

Variant identification and analysis of three affected members (mother and two affected offspring) was performed via exome sequencing. Parental samples of the index case were used to establish inheritance. Follow-up testing of 94 additional retinitis pigmentosa pedigrees was performed via retrospective analysis or Sanger sequencing.

Results and Conclusions

A total of 136 high quality coding variants in 123 genes were identified which are consistent with autosomal dominant disease. Of these, one of the strongest genetic and functional candidates is a c.269A>G (p.Tyr90Cys) variant in ARL3. Follow-up testing established that this variant occurred de novo in the index case. No additional putative causal variants in ARL3 were identified in the follow-up cohort, suggesting that if ARL3 variants can cause adRP it is an extremely rare phenomenon.     

Paradoxical effects of cytokines in tumor immune surveillance and tumor immune escape

The role of cytokines in modulating the formation of new tumors is mediated by their ability to regulate antigen-specific anti-tumor responses and by the activation of non-specific mechanisms, including those involved in the processes of inflammation and innate resistance. Cytokines may influence the growth of tumors by acting directly on tumor cells as growth promoting or growth inhibiting factors or indirectly by attracting inflammatory cell types and affecting angiogenesis. Due to the potency and complexity of cytokine activity against tumor growth, the improvement of cloning techniques and the availability of recombinant forms of different cytokines, a great effort has been made in the recent years to exploit this anti-tumor potential for cancer therapy. This important goal has been difficult to achieve in most cases due to toxicity of most cytokines which could not be dissociated from their anti-tumoral functions. Nevertheless, if well designed, treatment protocols and/or modifications of the cytokine molecules may in some situations augment the anti-tumor effects while limiting the toxicity. One of these molecular approaches could be the design of peptides containing the functional domain of certain cytokines, exemplified by IT9302, a peptide homologous to the functional domain of IL-10, which has demonstrated to increase tumor NK cell sensitivity.     

Effect of nutrition and Enteromyxum leei infection on gilthead sea bream Sparus aurata intestinal carbohydrate distribution

The effect of a practical plant protein-based diet containing vegetable oils (VO) as the major lipid source on the mucosal carbohydrate pattern of the intestine was studied in gilthead sea bream Sparus aurata challenged with the myxosporean parasite Enteromyxum leei. Fish fed for 9 mo either a fish oil (FO) diet or a blend of VO at 66% of replacement (66VO diet) were exposed to parasite-contaminated water effluent. Samples of the anterior, middle and posterior intestine (AI, MI and PI, respectively) were obtained for parasite diagnosis and histochemistry. Fish were categorised as control (C, not exposed), early (E) or late (L) infected. Mucin and lectin histochemistry was applied to detect the different types of mucins and sialic acid in goblet cells (GC), the brush border and enterocytes. The number of GC stained with periodic acid Schiff (PAS), alcian blue (AB), aldehyde fuchsin-alcian blue (AF-AB), for the detection of neutral, acidic, sulphated and carboxylic mucins, and with the lectin Sambucus nigra agglutinin (SNA), were counted in digital images. The 66VO diet produced a significant decrease of GC with neutral and acidic mucins in the AI and MI, and also of those with carboxylic mucins and sialic acid in the MI. Sulphated mucins and sialic acid were less abundant in the AI than in the MI and PI in the C-66VO treatment. E. leei infection had a strong effect on the number of GC, as E and L infected fish had a significant decrease of GC positive for all the stains versus C fish in PI. Time and diet effects were also observed, since the lowest values were mostly registered in E-66VO fish in PI. In conclusion, though GC depletion was mainly induced by enteromyxosis, an effect of the diet was also observed. Thus, the diet can be a predisposing factor that worsens the disease course.     

Semiaerobic induction of a nitrate reductase activity in growing cultures of Rhodopseudomonas capsulata E1F1 containing NH 4 + ions as nitrogen source

Rhodopseudomonas capsulata E₁F₁ growing under chemo- or photoorganotrophic conditions shows nitrate reductase activity which:

1. Is not repressed by ammonium ions;
2. Is governed by the partial pressure of oxygen in the gas phase.

Upon induction of nitrate reductase activity under optimum conditions, and also in the presence of amonium ions, subsequent addition of nitrate does not result in nitrite production. The specific activity of the enzyme increases by a factor of 10, when the growth medium is supplemented by the addition of nitrate. The physiological role of this ammonium resistant activity is not known.     

Biogeochemistry and hydrography shape microbial community assembly and activity in the eastern tropical North Pacific Ocean oxygen minimum zone

Oceanic oxygen minimum zones (OMZs) play a pivotal role in biogeochemical cycles due to extensive microbial activity. How OMZ microbial communities assemble and respond to environmental variation is therefore essential to understanding OMZ functioning and ocean biogeochemistry. Sampling along depth profiles at five stations in the eastern tropical North Pacific Ocean (ETNP), we captured systematic variations in dissolved oxygen (DO) and associated variables (nitrite, chlorophyll, and ammonium) with depth and between stations. We quantitatively analysed relationships between oceanographic gradients and microbial community assembly and activity based on paired 16S rDNA and 16S rRNA sequencing. Overall microbial community composition and diversity were strongly related to regional variations in density, DO, and other variables (regression and redundancy analysis r² = 0.68–0.82), displaying predictable patterns with depth and between stations. Although similar factors influenced the active community, diversity was substantially lower within the OMZ. We also identified multiple active microbiological networks that tracked specific gradients or features – particularly subsurface ammonium and nitrite maxima. Our findings indicate that overall microbial community assembly is consistently shaped by hydrography and biogeochemistry, while active segments of the community form discrete networks inhabiting distinct portions of the water column, and that both are tightly tuned to environmental conditions in the ETNP.